diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000000.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000000.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf75e03739bd2ec80c475be72556b4ae05e161b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000000.fa
@@ -0,0 +1,307 @@
+>0_60
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGFTRLAYTEALEDERTVTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYT
+>0_1289
+MTHANAPLTPTGRLRMVQRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLASEGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRAHGRESEAGRASKRGAG
+RRVGYTYLHSAIDGFTRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNN
+YRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSERARREALQV
+WVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYI
+>0_1892
+MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLPSRPHRSPAQLDPVLV
+AQIHALRRERKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRLRDLTPAGEDLRQRPQ
+KITARGPGHMVHLDVKKIGKIPDGGGWRAHGRESEAGRASKRGAGRRVGYTYLHSAIDGY
+TRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVITDNGNNYRAVDFTAKVVSLGG
+RHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAVWVNHYNYHRPHTSCG
+DAPPASLAPARVNNVMPSYS
+>0_2007
+MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLPSRPHRSPAQLDPVLV
+AQIHALRRERKWSARRIHHHLVSEGHQVCLRTVGRWLHRAGISRLRDLTPAGEDLRRQPA
+RRITARGPGHMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRGPGRRVGYTYLHSAIDG
+FTRLAYTEALPDERAATTVSFFCRARAFFAAHGITVDRVITDNGNNYRAADFTAKVVSLG
+GRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSEQARREALAVWVNHYNYHRPHTSC
+GDAPPASLAPARVNNVMTSYI
+>0_2050
+MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLPSRPHRSPAQLDPEVV
+AQIQTLRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRLRDLTPAGEDLRQRPQ
+KITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPGRRVGYTYLHSAIDGF
+TRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIRIDRVITDNGNNYRAVDFTRKVVSLGG
+RHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAVWVNHYNYHRPHTSCG
+DAPPASLAPARVNNVMPSYI
+>0_2217
+MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLPSRPHRSPAQLDPEVV
+AQIQTLRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRLRDLTPAGEDLRQRPQ
+KITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPGRRVGYTYLHSAIDGF
+TRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIRIDRVITDNGNNYRAVDFTRKVVSLGG
+RHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAVWVNHYNYHRPHTSCG
+DAPPASLAPARVNNVMPSYN
+>1_10
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPEVVAQIQTLRRREKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYN
+>1_36
+MTHANAPLTPTGRLRMVHRHLNDGIPQSHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGRIPEGGGWRTHGRDSEAGRASKRGS
+GQRVGYTYLHSAIDGYTRLAYTEALEDERTVTTIGFYCRARAFFAAHGITVDRVVTDNGN
+NYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALQ
+VWVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYT
+>1_125
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLLDRP
+SRPRRSPAQLDPEVVAQIQTLRRREKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRAHGRESEAGRASKRGAG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYT
+>1_297
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRDSEAGRASKRGAG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVITDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSEQARREALQV
+WVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYT
+>1_336
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+SRPHHCPAQLDIAILAEIEALRRDQKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIPDGGGWRAHGRDCENARAAKRGPG
+RRVGYTYLHSAVDGFTRLAYTEALPDERAATTVSFFCRARAFFAAHGITVDRVITDNGAN
+YRAAEFTMKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVIYARPYTSEQARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYN
+>1_1079
+MVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGAGRRVGYTYLHSAIDGFTRLAYTEAL
+EDEKAVTTIGFFCRARAFFAEHGITVDRVITDNGNNYRAADFTAKVVSLGGRHHRIRPYT
+PRHNGKVERYNRLMVDEVLYARPYSSEQARREALQVWVNHYNYHRPHTSCGNAPPASLAP
+ARVNNVMPSYN
+>1_1117
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGAG
+RRVGYTYLHSAIDGFTRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNN
+YRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYS
+>1_1192
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRDSEAGRASKRGPG
+RRVGYTYLHSAIDGFTRLAYTEALEDERTVTTIGFFCRARAFFAAHGITVDRVITDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRPHTSCGDAPPTSLAPARVNNVMPSYN
+>1_1768
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPEVVAQIQTLRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIRIDRVITDNGNN
+YRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYI
+>1_1771
+MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLPSRPHRSPAQLDPVLV
+AQIHALRRERKWSARRIHHHLVSEGHQLCLRTVGRWLHRAGISRLRDLTPAGEDLRRQPA
+RRITARGPGHMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRGPGRRVGYTYLHSAIDG
+FTRLAYTEALPDERAATTVSFFCRARAFFAAHGIRIDRVITDNGNNYRAVDFTAKVVSLG
+GRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARREALAVWVNHYNYHRPHTSC
+GDAPPASLAPARVNNVMTSYT
+>1_1918
+MVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGPGRRVGYTYLHSAIDGFTRLAYTEAL
+EDERAATTVSFYCRARAFFAAHGITVDRVITDNGNNYRAADFTAKVVSLGGRHHRIRPYT
+PRHNGKVERYNRLMVDEVLYARPYTSEQARREALAVWVNHYNYHRPHTSCGDAPPTSLAP
+ARVNNVMPSYI
+>1_1921
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLLDRP
+SRPHRSPAQLDPEVVAQIQTLRRREKWSARRIHHYLVSEGHQLCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGAG
+RRVGYTYLHSAIDGFTRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNN
+YRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYS
+>1_2024
+MIHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLLDRP
+SRPRRSPAQLDPVLVAQIHALRRERKWSARRIHHHLASEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVITDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYS
+>2_37
+MVHLDVKKIGKIPDGGGWRAHGRDSQAGRASKRGAGRRVGYTYLHSAIDGFTRLAYTEAL
+EDERAVTTIGFFCRARAFFAAHGITLDRVITDNGNNYRAADFTAKVVSLGGRHHRIRPYT
+PRHNGKVERYNRLMVDEVLYARPYSSETARREAMQVWVNHYNYHRPHTSCGGAPPASLAP
+ARVNNVMPSYT
+>2_137
+MTTIGFFCRARAFFAAHGITVDRVVTDNGNNYRAADFTRKVVSLGGRHHRIRPYTPRHNG
+KVERYNRLMVDEVLYARPYTSEAARREALQVWVNHYNYHRPHTSCGDTPPASLAPVRVNN
+VMTSYT
+>2_217
+MTHANAPLTPTGRLRMVQRHLHEGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+CRPRRSPAQLDPALVTQILTLRRECKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAMTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARREALQV
+WVNHYNYHRPHTSCGNAPPASLAPARVNNVMPSYT
+>2_538
+MTHANAPLTPTGRLRMVQRHLIDGIPQSHVAAEFRVSRPTVATWVARYLAEGAAGLQDRS
+SRPHHCPDQLDAEVVTELETLRRDHKWSARRIHHHLLAQGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPAKKITARAPGHMVHLDVKKIGKIPDGGGWRAHGRDSQAGRASKRGA
+GRRVGYTYLHSAIDGFTRLAYTEALEDERAVTTIGFFCRARAFFAAHGITLDRVITDNGN
+NYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARREAMQ
+VWVNHYNYHRPHTSCGGAPPASLAPARVNNVMPSYS
+>2_674
+MTHANAPLTPTGRLRMVQRHLIDGIPQSHVAAEFRVSRPTVATWVARYLAEGAAGLQDRS
+SRPHHCPDQLDAEVVTELETLRRDHKWSARRIHHHLLAQGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPAKKITARAPGHMVHLDVKKIGKIPDGGGWRAHGRDSQAGRASKRGA
+GRRVGYTYLHSAIDGFTRLAYTEALEDERAVTTIGFFCRARAFFAAHGITLDRVITDNGN
+NYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARREAMQ
+VWVNHYNYHRPHTSCGGAPPASLAPARVNNVMPSYT
+>2_761
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLPSASRPGGSPRGAGAHGAPGREEDRKDPRGGGWRAHGRDSEAGRASKRGP
+GARVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFYCRARAFFAAHGITVDRVVTDNGN
+NYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARREALQ
+VWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT
+>2_1469
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGKIPEGGGWRAHGRDSEAGRASKRGP
+GARVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFYCRARAFFAAHGITVDRVVTDNGN
+NYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARREALQ
+VWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT
+>2_1475
+MVHLDVKKVGRIPDGGGWRIHGRNSDQARTAGRAKSAGAKRGYTYLHSAVDGFSRLSYTE
+PLTDEKGPTAAAFLARAKAWFAAHGISHIHRVITDNGACYRSADFARIVGNRTRHQKTRP
+YTPRHNGKVERYQRILAEELLYAREFESEEARDTAIGIWNIHYNYHRPHSGAGGHPPASR
+LRAGVTNVWPSYS
+>2_1706
+MTHANAPLTPTGRLRMVQRHLHEGIPQAHVAAEFRVSRPTVATWVARYRAEGEVGLQDRS
+CRPRRSPAQLDPALVTQILTLRRECKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARREALQV
+WVNHYNYHRPHTSCGNAPPASLAPARVNNVMPSYT
+>2_1737
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+CRVGYTYLHSAIDGYTRLAYTEALEDEKAMTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARREALQV
+WVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT
+>2_2285
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+CRVGYTYLHSAIDGYTRLAYTEALEDEKAMTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARREALQV
+WVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT
+>2_2288
+MAYTESLENEKATTAVAFLNRAREWFASHGITRIERVITDNGACYRSAAFTAALDGADHR
+RTRPYTPKHNGKVERYNRILAEEFLYARTWTSEEQREKALETWNLHYNYHRPHGVHDGKP
+PASATPSRVNNVLASYS
+>2_2418
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGKIPEGGGWRAHGRDSEAGRASKRGP
+GARVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFYCRARAFFAAHGITVDRVVTDNGN
+NYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARREALQ
+VWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT
+>2_2499
+MTHANAPLTPTGRLRMVQRHLHEGIPQAHVAAEFRVSRPTVATWVARYRAEGEVGLQDRS
+CRPRRSPAQLDPALVTQILTLRRECKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARREALQV
+WVNHYNYHRPHTSCGNAPPASLAPARVNNVMPSYT
+>2_2555
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGKIPEGGGWRAHGRDSEAGRASKRGP
+GARVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFYCRARAFFAAHGITVDRVVTDNGN
+NYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARREALQ
+VWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYN
+>2_2573
+MVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGAGRRVGYTYLHSAIDGFTRLAYTEAL
+EDERAATTVSFYCRARAFFAAHGIRIDRAVTDNGNNYRAAEFTRKVVSLGGRHHRIRPYT
+PRHNGKVERYNRLMVDEVLHARPYSSETARREALQVWVNHYNYHRPHTSCGNAPPASLAP
+ARVNNVMTSYT
+>2_2578
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+CRVGYTYLHSAIDGYTRLAYTEALEDEKAMTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARREALQV
+WVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYI
+>4_265
+MTHANAPLTPTGRLRMVQRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLASEGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVITDNGNN
+YRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYS
+>4_495
+MAQRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLPSRPHRSPAQLDPVLV
+AQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRLRDLTPAGEDLRQRPQ
+KITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGAGRRVGYTYLHSAIDGF
+TRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNNYRAADFTAKVVSLGG
+RHHRIRPYTPRHNGKVERYNRLMVDEVIYARPYSSEQARREALAVWVNHYNYHRPHTSCG
+DAPPTSLAPARVNNVMPSYN
+>4_770
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVTQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNN
+YRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRSHTSCGDAPPASLAPARVNNVMPSYT
+>4_845
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNN
+YRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYN
+>4_1128
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVTQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNN
+YRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRSHTSCGDAPPASLAPARVNNVMPSYI
+>4_1492
+MTHANAPLTPTGRLRMVQRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLASEGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVITDNGNN
+YRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYS
+>4_1516
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNN
+YRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALQV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYT
+>4_1937
+MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLPSRPHRSPAQLDPVLV
+AQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRLRDLTPAGEDLRQRPQ
+KITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGPGRRVGYTYLHSAIDGF
+TRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNNYRAADFTAKVVSLGG
+RHHRIRPYTPRHNGKVERYNRLMVDEVIYARPYTSEQARREALTVWVNHYNYHRPHTSCG
+DAPPTSLAPARVYNVMPSYS
+>4_2042
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+CRPRRSPAQLDPEVVAQIQTLRRREKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRPQKITARGPGRMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGFTRLAYTEALPDERAATTVSFFCRARAFFAAHGIRIDRVITDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYT
+>4_2046
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+CRPRRSPAQLDPEVVAQIQTLRRREKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRPQKITARGPGRMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGFTRLAYTEALPDERAATTVSFFCRARAFFAAHGIRIDRVITDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYNYLFGLLMVTRSPECALLGHGPDQRG
+WLLDTYLRGLRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000001.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000001.fa
new file mode 100644
index 0000000000000000000000000000000000000000..933eebe0c570f379dfc5af2c3a3b7418c41b6e3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000001.fa
@@ -0,0 +1,235 @@
+>0_166
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT
+>0_564
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT
+>0_577
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKLPVVAEHLDAARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAAGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVSNTGSEVNPDTAPALEFSA
+>0_578
+MTAPHILDPAGLLGEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPSSSRTAQR
+NGYRHRDLDTRVGTLDVAIPKLRSGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGVNALSKSQVSRMATELDEQVEAFRHRPLGVAGPFTFVAADALSMKVREGGRV
+VNAVVLLATGVNADGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHTGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAASVHAQFDRLLD
+YVSGKLPTVAEHLDAARADILAFTTFPKDVWTQVWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVTNTGDEVDPDTELTLGLSA
+>0_598
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVTDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDAVGIFPNR
+DAVIRLVGAVLAEQTDEWAEGRRYLGLELLARCSNQDPDTPSTTGASAEVMPTLA
+>0_687
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT
+>0_1025
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKLPVVAEHLDAARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAAGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVSNTGSEVNPDTAPALEFSA
+>0_1155
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKLPAVAEHLGDARADILAFTTFPKDVWTQVWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTPVEDTGSEVGTDTDTALELSA
+>0_1346
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQTLGITGLSKSQVSEMSKDLDAQVEAFRTRPLDAGPYRFVAADALVLKVREHGRVV
+KVAAMVATGINNDGYREILGLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLVE
+AAGAVFGTAQWQRCRTHYAANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMIDS
+LATHLPAAAEHLEGARDEVLTFTKFPKEVWKKIWSNNPNERLNKEIRRRTDVVGIFPSRV
+EVIRLLGAVLAEQHDEWTESRRYMSLELLTATDTMLAEAAAKAAAEQAALQVSDTMTDDP
+GHAALAA
+>0_1351
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT
+>0_1451
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVAGAWPGSGWSPLMPTPGSR
+TPSPRTCPVRCGNAAAPTTRRT
+>0_1452
+MGITPKSMWPAVKAMLHSGYDQPDAASVNAQFDRLLDYVSEKLPVVAEHLDAARADILAF
+TTFPKDVWTQIWSNNPAERLNREIRRRTDAAGIFPNRAAIVRLVGAVLAEQTDEGPRAVA
+TRALGATRACC
+>0_1969
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKLPAVAEHLGDARADILAFTTFPKDVWTQVWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTPVEDTGSEVGTDTDTALELSA
+>0_2003
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFSATGLWARPARSCSSPPTP
+>0_2004
+MFLAADALTMKVREGGRVVNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVA
+RGLAGVALVTSDSHRGLVEAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSV
+YDQPDGPAVHAQFERLLDYVQDRLPAVAAHLDAARQDILAFTSFPRDVWCQIWSNNPAER
+LNREIRRRTDAVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQE
+TVMSTEVMPTLQT
+>0_2165
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+INAVAMVATGVNADGRREVLGLRVATTETGAAWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT
+>0_2168
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGQASQSRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFERLLD
+YVQDRLPAVAAHLDAARQDILAFTSFPRDVWCQIWSNNPAERLNREIRRRTDAVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT
+>0_2170
+MVADCYLAGVSTRRMDKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFL
+AADALTMKVREGGRVVNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGL
+AGVALVTSDSHRGLVEAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQ
+PDGPAVHAQFERLLDYVQDRLPAVAAHLDAARQDILAFTSFPRDVWCQIWSNNPAERLNR
+EIRRRTDAVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVM
+STEVMPTLQT
+>0_2171
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPNGCSSAANGPSPH
+>0_2205
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFERLLD
+YVQDRLPAVAAHLDAARQDILAFTSFPRDVWCQIWSNNPAERLNREIRRRTDAVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT
+>0_2210
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKLPVVAEHLDAARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAAGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVSNTGSEVNPDTAPALEFSA
+>1_1087
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQTRHHGPVEIAGLRDE
+>1_1088
+MSKDLDAQVEAFRTRPLDAGPYRFVAADALVLKVREHGRVVKVAAMVATGINNDGYREIL
+GLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLVEAAGAVFGTAQWQRCRTHYA
+ANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMIDSLATHLPAAAEHLEGARDEV
+LTFTKFPKEVWKKIWSNNPNERLNKEIRRRTDVVGIFPSRVAVIRLLGAVLAEQHDEWTE
+SRRYMSLELLTATDTMLAEAAAKAAAEQAALQVSDTMTDDPGHAALAA
+>2_673
+MTAPHILDPAGLLREALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPGRATQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMATELDEHVESFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHTGLR
+EAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAQAVDAQFDRLLD
+YVSEKLPAVAEHLDAARADILAFTTFPKDVWTQVWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLHRCRLTPVSNTGDEVDTDTALELSA
+>2_703
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKLPVVAEHLDAARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVSNTGNEVNPDTAPALEFSA
+>2_876
+MTAPHILDPAGLLREALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPGRATQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMATELDEHVESFRHRPLGEALPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHTGLR
+EAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAQAVDAQFDRLLD
+YVSEKLLYGGRAPGRCPGGHPGLHDLPEGRVDAGLVEQSGRAAQPRDPPPHRRGGHLPQP
+GSHRQAGRCGAGRADR
+>2_2445
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKLPVVAEHLDAARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVSNTGNEVNPDTAPALEFSA
+>2_2612
+MTAPHILDPAGLLGEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPSSSRTAQR
+NGYRHRDLDTRVGTLDVAIPKLRSGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGVNALSKSQVSRMATELDEQVEAFRHRPLGVAGPFTFVAADALSMKVREGGPV
+VNAVVLLATGVNADGHREVLGLRVATSETGAAWNEFFADLVARGLAGLRLVTSDAHTGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAASVHAQFDRLLD
+YVSEKLPTVAEHLDAARADILAFTTFPKDVWTQVWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVTNTGDEVDPDTELTLGLSA
+>4_1295
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQTLGITGLSKSQVSEMSKDLDAPVEAFRTRPLDAGPYRFVAADALVLKVREHGRVV
+KVAAMVATGINNDGYREILGLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLVE
+AAGAVFGTAQWQRCRTHYAANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMIDS
+LATHLPAAAEHLEGARDEVLTFTKFPKEVWKKIWSNNPNERLNKEIRRRTDVVGIFPSRV
+AVIRLLGAVLAEQHDEWTESRRYMSLELLTATDTMLAEAAAKAAAEQAALQVSDTMTDDP
+GHAALAA
+>4_1936
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQTLGITGLSKSQVSEMSKDLDAQVEAFRTRPLDAGPYRFVAADALVLKVREHGRVV
+KVAAMVATGINNDGYREILGLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLVE
+AAGAVFGTAQWQRCRTHYAANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMIDS
+LATHLPAAAEHLEGARDEVLTFTKFPKEVWKKIWSNNPNERLNKEIRRRTDVVGIFPSRV
+AVIRLLGAVLAEQHDEWTESRRYMSLELLTATDTMLAEAAAKAAAEQAALQVSDTMTDDP
+GHAALAA
+>4_2137
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKLPAVAEHLGDARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTPVEDTGSEVGTDTDTALELSA
+>4_2154
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKLPAVAEHLGDARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTPVEDTGSEVGTDTDTALELSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000006.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000006.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f38adce59ef3ce24a9ae3cc12ae77bcf6e1dd0d0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000006.fa
@@ -0,0 +1,100 @@
+>0_149
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>0_993
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>0_1244
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>0_1336
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETGDSQNVRTE
+>0_2016
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>1_972
+MVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIK
+ICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWA
+GTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRH
+SSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>1_1065
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>1_1073
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>1_1075
+MSERIACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINRFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>1_1971
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMEIGDSQNVRTE
+>2_1189
+MACRLVGLSRSAYRRPLKGDTVADPDRALRQWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>4_563
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVASRGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>4_565
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVVDWAGTR
+TGLWADPVS
+>4_1201
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>4_1290
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTH
+>4_1826
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLGHV
+>4_2145
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVASRGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000008.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000008.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6251500c011077a0fc02953f18f1f2e5eabbd54d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000008.fa
@@ -0,0 +1,83 @@
+>0_685
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>0_1350
+MEGSLEGSHGDRVRLEDGRGHRGGLHHYPGLNSFTTWDPGASSIPAPTQQSLRTLEWLSR
+RENLVVCGPSGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARI
+LRADLIVIDDIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATAT
+VDRLLHHAHVCQTTGDSVRMTQAMAGKGVMPLN
+>0_1449
+MAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIGLLPVADDAAEGLYRIVDAA
+YEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQTTGDSVRMTQAMAGKGVMP
+LN
+>0_2164
+MLWKVRSKAPTVTASVSKMVVATGEGYTTIRDSTPKTLATATVDRLLHHAHVCQTTGDSV
+RMTQAMAGKGVMPLN
+>0_2166
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTVKSLEVV
+>1_80
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>1_327
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>1_974
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>1_1350
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>1_2226
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>4_581
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>4_971
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPIADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>4_1111
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPIADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>4_1300
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>4_2104
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000012.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000012.fa
new file mode 100644
index 0000000000000000000000000000000000000000..66c8c7320258b7877f3721c32af24bca8a425620
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000012.fa
@@ -0,0 +1,42 @@
+>0_148
+MKGAAQLDFIRRGQAVGLTLAQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQ
+LRTTIADLREDAAAGDPATCSPEDVCRYL
+>0_151
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLGPAVG
+>0_1030
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAVGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATC
+SPEDVCRYL
+>0_2002
+MRIGEVAAASGVTTKALRFYEERGLLPQADRATNGYRDYPEDTIVRLEFIRRSQVAGLTL
+AEILDILQIRDAGTAPCGHVRDQLAEHLTNLDRHIAELTALRETVAGLHGTAAAGDPAQC
+NAEVICSYL
+>1_282
+MRIGELAERAGTTAKTLRFYEEQGLLPPAERTPSGYRDYAPETAARIDFVHRGQAAGLTL
+AQIRQILDIRDDGAAPCEHVRDLLDARLAEIEQQIAQLAALRDTITELRRDAAQPDPDSC
+SADQVCRYL
+>1_322
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL
+>1_329
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL
+>1_758
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL
+>2_702
+MLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATCSPEDV
+CRYL
+>2_704
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGSSPMKWC
+SG
+>3_2171
+MRIGEVAAASGVTTKALRFYEERGLLPQADRATNGYRDYPEDTIVRLEFIRRSQVAGLTL
+AEILDILQIRDAGTAPCGHVRDQLAEHLTNLDRHIAELTALRETVAGLHGTAAAGDPAQC
+NAEVICSYL
+>4_979
+MLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATCSPEDV
+CRYL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000013.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000013.fa
new file mode 100644
index 0000000000000000000000000000000000000000..113fe8abe87ae199c75993706484f3a05d8e2ac9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000013.fa
@@ -0,0 +1,60 @@
+>1_325
+MKELAAVGIPVAVTCRVLKLSRQPYYRWLADPVTDAELAEAYRANALFDAHQDDPEFGYR
+FLVDEAKEAGEVMCERSAWRICRDNGWWSVFGKKRGKNGKKPGPPVHDDLVERDFTAGGS
+NQLWLTDVTEHRTAEGKLYMCAIKDVFSGRIVGYSIDSRMKARLAVQALQNAVARRGDVA
+GCIVHSDRGSQFRSRKFVHALNRHGLVGSMGKVGAAGDNAAMESFFALLQKNVLDRRSWT
+TRDELRIAIVTWTERTYHRRRRQARLGRLTPIEYETMMKPAVTLPA
+>1_1715
+MYPLVSELAADQIPVAVSLRVLKLARQPYYRWRDQPVAVSEVEQAYRANALHAAHLNDPE
+FGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCGFGAKRGKYGTRPGPPVHDDHVRRDFS
+AEAPNRLWLTDITEHPTSEGKLYLCAIKDLYAGRIVGYSMAGRMQASLAVNALEQAVARR
+GGTDAVAGCIVHSDRGSQFRSALFQDALTTHGLIGSMGQVGAAGDNAAMESFFALLQKNV
+LDRRDWDTRDELRAGIITWIERTYHRRRRQVRLGRLTPVEYELIMDHTPADAA
+>2_688
+MMYPHVKELATDGIPVVVSVRMLKLARQPYCRWLENPLTRTDLDQAYRANALHAAHQNEK
+ALAHRSAS
+>2_2226
+MYPLVSELAADGVPVAVSLRVLKLARQPYYRWREKPVAVSEVEQAHRANALHAAHLNDPE
+FGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCAFGAKRGKNGRRPGPPVHDDRVRRDFS
+AEAPNRLWLTDITEHPTGEGKLYLCAIKDVHAGRIVGYSMAGRMQASLAVNALEQAVARR
+GGTDAVAGCIVHSDRGSQFRSALFQDALTAHGVIGSMGQVGAAGDNAAMESFFALLQKNV
+LDRRDWDTRDELRAGIITWIERSYHRRRRQVRLGRLTPVEYELIMDHTPADPA
+>2_2440
+MHDDRVRRDFSAEAPNRLWLTDITEHPTGEGKLYLCAIKDVHAGRIVGYSMAGRMQASLA
+GNALEQAVARRGGTDAVAGCIVHSDRGSQFRSALFQDALTAHGLIGSMGQVGAAGDNAAM
+ESFFALLQKNVLDRRDWDTRDELRAGIITWIERTYHRRRRQVRLGRLTPVEYELIMDHTP
+ADPA
+>2_2441
+MYPLVSELAADGVPVAVSLRVLKLARQPYYRWRDQPVAVSEVEQAHRANALHAAHLNDPE
+FGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCAFGGQARQERALYLALPCMMTASAGTS
+LPKLRTGCG
+>2_2557
+MYPLVSELAADGVPVAVSLRVLKLARQPYYRWRDQPVAVSEVEQAHRANALHAAHLNDPE
+FGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCAFGAKRGKNGRRPGPPVHDDRVRRDFS
+AEAPNRLWLTDITEHPTGEGKLYLCAIKDVHAGRIVGYSMAGRMQASLAGNALEQAVARR
+GGTDAVAGCIVHSDRGSQFRSALFQDALTAHGLIGSMGQVGAAGDNAAMESFFALLQKNV
+LDRRDWDTRDELRAGIITWIERTYHRRRRQVRLGRLTPVEYELIMDHTPADPA
+>2_2577
+MEQAHRANALHAAHLNDPEFGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCAFGAKRGK
+NGRRPGPPVHDDRVRRDFSAEAPNRLWLTDITEHPTGEGKLYLCAIKDVHAGRIVGYSMA
+GRMQASLAVNALEQAVARRGGTDAVAGCIVHSDRGSQFRSALFQDALTAHGVIGSMGQVG
+AAGDNAAMESFFALLQKNVLDRRDWDTRDDLRAGIITWIERAYHRRRRQVRLGRLTPVEY
+ELIMDHTPADPA
+>3_1844
+MHPLVRELAVDGIPVAVTCRVLKIARQPYYRWLASPVTPAELDEAYRANALFDAHKDDPE
+FGYRFLADEAREAGESMAERTAWRICSDMGWWSAFGKKRGRNGKKPGSPVHDDLCAVTDE
+KGRIRHQFNADAVNELWIGDITEHRTGEDRLYLCAFKDVYSNRIVGYSIDSRMKSSLAVT
+ALNNAVARRGEVAGCVVHTDRGSQCRSRKFVHALNRHGMVGSMGRVGATGDNAAMASFFA
+LLQKNVLERRSWATREDLRIAIVTWIERTYHRRRRQVALGRLTPIEYEAIMTTPASQAA
+>4_864
+MYPLVRELAVDGIPVAVTCRVLKIARQPYYRWLASPVTPAELDETYRANALFDAHKDDPE
+FGYRFLADEAREAGELMAERTAWRICSDMGWWSAFGKKRGRNGKKPGSPVHDDLCAATDE
+KGRIWHQFNADAVNELWIGDITEHRTGEGRLYLCAFKDVYSNRIVGYSIDSRMKSSLAVT
+ALNNAVARRGEVAGCVVHTDRGSQFRSRKFVHALNRHGMVGSMGRVGAAGDNAAMESFFS
+LLQKNVLDRRSWATREDLRIAIVTSIERTYHRRRRQAALGRLTPIEYEAIMTTPASQAA
+>4_1490
+MTYPLVAELADAGILVTVSCRVLKLARQPYYRWRNAPVRDADMLRAYRINALHDAHHDDP
+TFGYRYLADEARRAGWRMSRRTAWKLCSQAGILSSAQRRRRGKGKKTGPPVFDDHVQRVF
+RADAPNRLWLTDITEHRTSEGKLYCCAIKDVFSNRIVGYSISDRMTAKLAVDAVRNAVAR
+RGEVAGCILHADRGSQFRSRAMARELRRHDMVGSMGRVGAAGDNAAMESFWSLLQTNVLN
+QQRWTTRQELRLVIVVWIERKYHRQRAQDILGGLTPIEFEAKLAEPHTLAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000014.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000014.fa
new file mode 100644
index 0000000000000000000000000000000000000000..78f1164f19ac4435a16a5db56cb3fe695b627dc7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000014.fa
@@ -0,0 +1,97 @@
+>0_152
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA
+>0_1029
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA
+>0_1999
+MNEAVPHFDLAIIGSGGGAFAAAIRATNLDKRVVMIERGTVGGTCVNTGCIPSKALLAAA
+EARHTAQDAGRFPGLTATAGPVDMEALIAGKRALVENVRSDKYVDLVADYGWELRHGNAV
+FTGTAADPALEVTAQDGTRETITAAHYLVATGSTPWAAPINGLDTVDYLTSTTAMELDEV
+PESLLVIGGGYVALEQAQLFARLGSKVTMLVRSRLASGEEPEASRALMSVFANEGIRVIR
+RSTVSSITQDTDGGIAAQADIAGGRETLRASKVLVATGRRPVTDGLNLAGVSVKTGDKGE
+VVVEDTLVSSNPRVWAAGDVTGHPEYVYVAASHGTLMVDNAFSDAGRAVDYSHLPRVTFT
+SPNLAVVGMTDKQARDAGIRCECRVVPLEYIPRAVVNRDTRGFIKMVADADTGRIVGITA
+VAKEAGDLAATGVYILQAGMTVDQVANLWSPYLTMAEGIKIVAQSFKTDVSKLSCCAA
+>1_283
+MPTKYDLAIIGSGGGAFAAAIRATTLGKSVVMIERGTLGGTCVNTGCVPSKALIAAADAR
+HSAADAADRFPGIATTAGPVDMPALIAGKQALVESLRGEKYADVADSYGWAVRRGDAAFA
+GTPDAPVLQVAGDDGSTETIEAGHFLVATGSRPWAPPIDGLDETGYLTSTTAMELTELPE
+SLLVLGGGYVALEQAQLFARLGSQVTVLVRSRLASKEEPEVSRTLEEVFADEGIRVVRRA
+LPTRVSRDAATGQAVVTADVAGGREEFRADQVLVALGRRPVTDGLGLDRVGVETGDLGEV
+VVSDRMQSSHPRIWAAGDVTGHPEFVYVAAHHGTLVAENAFADADRAVDYARLPRVTFTG
+PAIGAVGMTEKDVVAAGIRCDCRVLPLHHVPRALVNRDTRGFVKIVVDADTGKILGITAV
+AKDAGELAAAGVHVLGKTVAEVADAWAPYLTMAEGIRIAAKAFTTDPSLLSCCA
+>1_321
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTCGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA
+>1_330
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA
+>1_757
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPLPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTCGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA
+>2_705
+MTATANSRSYDLAMIGSGGAAFAAAIRATSLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPLPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA
+>3_2168
+MNEAVPHFDLAIIGSGGGAFAAAIRATNLDKRVVMIERGTVGGTCVNTGCIPSKALLAAA
+EARHTAQDAGRFPGLTATAGPVDMEALIAGERALVENVRSDKYVDLVADYGWELRHGNAV
+FTGTAADPALEVTAQDGTRETITAAHYLVATGSTPWAAPINGLDTVDYLTSTTAMDLDEV
+PESLLVIGGGYVALEHAQLFARLGSKVTMLVRSRLASGEEPEASRALMSVFANEGIRVIR
+RSTVSSITQDTDGGIAAQADIAGGRETLRASKVLIATGRRPVTDGLNLAGVSVKTGDKGE
+VVVEDTLVSSNPRVWAAGDVTGHPEYVYVAASHGTLMVDNAFSDAGRAVDYSHLPRVTFT
+SPNLAVVGMTDKQARDAGIRCECRVVPLEYIPRAVVNRDTRGFIKMVADADTGRIVGITA
+VAKEAGDLAATGVYILQAGMTVDQVANLWSPYLTMAEGIKIVAQSFKTDVSKLSCCAA
+>4_978
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPLPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDGHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000019.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000019.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f2d4fdf68ee88d48656da567ab86dd6f09ae246
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000019.fa
@@ -0,0 +1,27 @@
+>1_326
+MPAPYPQEFRDDVVRVARSREEGVTLAQIAKDFGTHEMTLSKWMRQADVEDGAKPGTTKA
+ESAENRELKKRIRLLEQENEVLRRAAAYLSQANLPGKGSTRS
+>1_1716
+MPAPYPKEFRDDVVRVAQNREPGTHLKDIAKDFGISESCLTNWIRQADIEAGNIPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK
+>2_2225
+MPAPYPQEFRDEVVRVAQNREPGTQLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK
+>2_2442
+MPAPYPQEFRDDVVRVAQNREPGTHLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK
+>2_2558
+MPAPYPQEFRDDVVRVAQNREPGTHLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK
+>2_2575
+MPAPYPQEFRDDVVRVAQNREPGTQLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK
+>3_1843
+MSKPYPKEFRDDVVRIARNREPGVELSQIAKDFGIHFTTLYAWMKKADIEDGDRPGTTEA
+QYAELREAKRRIRTLEQEVEVLRRAAAYLSQAHLPGK
+>4_865
+MSKPYPKEFRDDVVRVARNRGPGVELSQIAKDSGIHVTTLYAWMKKADIEDGDRPGTTEA
+QSAELREAKRRIRTLEQEVEVLRRAAAYLSQAHPPGK
+>4_1489
+MPGPCPREFREDVVAVARSRESGVTIKQIATDFGVSEATLQNWLRQADVEDGNRPGQTAA
+DAAEARELKKRIRLLEQENEVLRRAAAYLSQANLRLGGSPK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000020.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000020.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb1e51b61429e266be8af715edb0d0c4dc2c20d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000020.fa
@@ -0,0 +1,73 @@
+>0_501
+MTIVDFFRLLRANLLLLLAAALVGGLLGWGYSALQPRIYASESQGFLAARAADQSLITSN
+LPAESRAQAYVALINSEAVRERVAQDTGQDGDGSLSAVLVPESSMIKVTATSTDPETAAQ
+LANSALQATADVAADVDKNSPLEVVPLSDARVPSAPVSPDTRRNVLLGVVAGLGAGLAIA
+VLRRLLDVKVRSRADVKEITGAGVIGAVPENASLTRTGEEAVDLDPRAGEAIRALRTNLK
+FVSVDEPPRVVSFTSADPSEGKSTVASNLARALALAGERVLVVDADLRRPRQHDLFQVAG
+DVGLSEVLAGEVQPDDALAATGIPNLTLLPAGRTPPNPSELLGSKRMRALLKLASEDFFV
+IVDSPPLLPVTDGSLLATAVDGTVLVVRQGRTRKDHLEAAVENLAAVDAHLLGVVMNGVA
+RSQRGGGYSYGYGYESTYHKSHDKYLQGTGKGGKKSRRAARAKKG
+>1_231
+MTIVDFFRLLRANLLLLLAAALVGGLLGWGYSALQPRIYASESQGFLAARAADQSLITSN
+LPAESRAQAYVALINSEAVRERVAQDTGQDGDGSLSAVLVPESSMIKVTATSTDPETAAQ
+LANSALQATADVAADVDKNSPLEVVPLSDARVPSAPVSPDTRRNVLLGVVAGLGAGLAIA
+VLRRLLDVKVRSRADVKEITGAGVIGAVPENASLTRTGEEAVDLDPRAGEAIRALRTNLK
+FVSVDEPPRVVSFTSADPSEGKSTVASNLARALALAGERVLVVDADLRRPRQHELFQVAG
+DVGLSEVLAGEVQPDDALAATGIPNLTLLPAGRTPPNPSELLGSKRMRALLKLASEDFFV
+IVDSPPLLPVTDGSLLATAVDGTVLVVRQGRTRKDHLEAAVENLAAVDAHLLGVVMNGVA
+RSQRGGGYSYGYGYESTYHKSHDKYLSGVGSSAKKGRRSRRKARTRG
+>1_242
+MNIIDFLRVLRANRLVILGCAALGLALGLLYSLLQPTLYTATSTAFVTVEGEASISGTET
+AQTRAQSYIPLINSRTVRERIAAEGLDTAGATLSAALVPNSNLITVSAVAPDAQQAAALA
+NGALVATADVANELDPTSNVKVTAMEDALAPAAPSSPDRVRHLLYGLGAGLVLGLIVAFL
+RRLLDVNVRTTTDAQVAGGAGLLGAIPLDPSMKAERTAPMAPLSPRASEAVRQLRTNLRF
+AAVDDPPRTIAFTSSNPGEGKSTVIGNLALTVAAAGQPVILIDADLRRPRQALQFGVDGR
+VGLSEVLNGDVALQDVLIPVGEDGLLLLPAGRTPPNPSEQLGSERMRDLLTALAETHMVL
+VDAPPVLPVTDSTLLATAVDGTVLVIRHGKTRKEHLEVARDMLAGVNARVLGVVLNGTPA
+SGVGSDYYGGGYGADGGSYDAYYQAPRDAAEAAAGTAGDASRR
+>2_1186
+MDLQQYLQTFRKYWRSILTVLSVCVGAALVFTFLQTPKYSSTSSALIAVDTAATPGELSS
+GALYAERQVSSFVALADSALVLDPVINELGLNVTPQALRSRVSVSAPAGTSIVDVTVTDT
+NAGRAAEVANAITASLKNVTSDVVPTGPDGDEIVTVTVVEPAAASSRPVSPRPVVNIALG
+LIAGVVIGLGQALVRRLLDSRIRTRDDLVEITDAPVLASVVHHKGSDRPKDEAAPARGTA
+WASAESYRKLRTAVGFVALGGERRSSIVVTSSVQGEGKTETSTNLAKVLAETGARVLLVD
+ADLRRPQVGARLGLDDELGLSDVLTGRADLNDVLLSVDDLSVLTAGTVPPNPSELLGSEA
+MAELLALVEAHFEYVILDAPPLLPVTDAAILSHQAGGAIVVARSGVARQNQLAEALSILE
+AADASVYGVVLNDVPVSHIDGYSQYYR
+>2_2364
+MNIIDFLRVLRANRLVILGCAALGLVAGLVYSLLQPTLYTATSTGFVTVQGEATISGTET
+AQTRAQSYIPLINSRTVREKIAEGGLDTAGASLSAAVVPGSNLITVSAESEDPEQAAALA
+NSALVATAETANGLDPTSNVQVTAMEDALAPTSPTSPDYVRNMLYGLGAGLLLGLVIAVL
+RRILDVNVRTTTDAQVASGAGLLGAIPLDATLKAERDAPRGEPSPRAAEAVRQLRTNLRF
+AAVDDPPRTIAFTSANPGEGKSTVIGSLALAVAASGQPVILIDADLRRPRQALQFGVDGR
+VGLSEVLNGDVALQDVLVPVGDHGLLLLPAGRTPPNPSEQLGSARMRDLLTALAETHMVL
+VDAPPVLPVTDSTLLSTAVDGTVLVVRHGKARKEHVEVARDMLAGVNARVLGVVLNGTPA
+SGVGSDYYGGSYASKGDDYHAYYQASRDAESRPSDEAVPEGPAAQR
+>3_2245
+MNILDFLRVLRANRLVLLGGVVLGLLGGLVYSLLQPTLYTSTSTGFVTVAGEASISGTET
+ALTRAQSYVPLINSRTVREKVAESGVDVSGSTLSAQVVPNSNLITVTALAPDPQRAADLA
+NTALGATAEVANSLDPTSNVKVTAMEDALPPAGPSSPDHLRNALIGAGIGLLAALAVAFL
+RRVLDVNVRTTTDATEASGAGLLGAIPQDGTMKAERTAPLGVPSPRAAEALRQLRTNLRF
+AAVDDPPRVVMVTSSNPGEGKSTVIAGLAQAVAVSGQPVILVDADLRRPRQASQFGVDGR
+VGLSEVLSGDVLLEDAVQDLGDGLLLLPAGRTPPNPSEQLGSHRMQELLRVLAETHLVLV
+DAPPGAAGDGLHPAGGRRGRDRAGGAPRQDPEGPCGGGPGHAGQGQRPHAGRGAQRRARL
+RCGLGLLRRGLRRGRRQLRRLLPGAPGRRRRRGRDRGRHVATLIAPGGRARSSHRRRRPG
+DAEGPRL
+>4_501
+MTIVDFFRLLRANLLLLLAAALVGGLLGWGYSALQPRIYASESQGFLAARAADQSLITSN
+LPAESRAQAYVALINSEAVRERVAQDTGQDGDGSLSAVLVPESSMIKVTATSTDPETAAQ
+LANSALQATADVAADVDKNSPLEVVPLSDARVPSAPVSPDTRRNVLLGAVAGLGAGLAIA
+VLRRLLDVKVRSRADVKEITGAGVIGAVPENASLTRTGEEAVDLDPRAGEAIRALRTNLK
+FVSVDEPPRVVSFTSADPSEGKSTVASNLARALALAGERVLVVDADLRRPRQHDLFQVAG
+DVGLSEVLAGEVQPDDALAATGIPNLTLLPAGRTPPNPSELLGSKRMRALLKLASEDFFV
+IVDSPPLLPVTDGSLLATAVDGTVLVVRQGRTRKDHLEAAVENLAAVDAHLLGVVMNGVA
+RSQRGGGYSYGYGYESTYHKSHDKYLQGTGTAGKGGKKSRRAARAKKG
+>4_512
+MNIIDFLRVLRANRLVILGCAALGLAMGLVYSLLQPTLYTATSSAFVTVEGEASISGTET
+AQTRAQSYIPLINSRTVRERIASEGLDTAGATMSAALVPNSNLITVSAVAPDAQQAAALA
+NGALVATADVANELDPTSNVKVTAMEDALAPATPSSPDRVRHLLYGLGAGLVLGLIVALL
+RRLLDVNVRTTTDAQVAGGAGLLGAIPLDPSMKAERTAPMAPLSPRASEAVRQLRTNLRF
+AAVDDPPRTIAFTSSNPGEGKSTVIGNLALTVAAAGQPVILIDADLRRPRQAMQFGVDGR
+VGLSEVLNGDVALQDVLIPVGEDGLLLLPAGRTPPNPSEQLGSERMRDLLTALAETHMVL
+VDAPPVLPVTDSTLLATAVDGTVLVIRHGKTRKEHLEVARDMLAGVNARVLGVVLNGTPA
+SGVGSDYYGGGYGADGGSYDAYYQAPRDAPEAAAGTAGDTSRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000021.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000021.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d8f80ac866954cedb7bed9baea3ada31bb3cd808
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000021.fa
@@ -0,0 +1,48 @@
+>0_546
+MHAGWSLGAAAGAGLGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPVDSASAR
+GAADQSPAPSETSAPPAPAAQALPRRAAVAVLVPAVVIAMAGFGVEEFGNAWATLFLITE
+RGLDPAAAVLGASTLLGAQFVGRLAGDRTLAVLGRRGALTAGLGAVVVGLGLALAPLPGP
+VAVPAAFAGLALAGLGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGA
+LAGAVGLAPALTVFLGLAAVGTVLAARLPAAP
+>0_547
+MSEAPPHLPTADDGVARARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDPAAFGLL
+VIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAGAGHGAG
+TAAAWLLWVFAGLVLASGVLDAVVDTAQNAQGLQV
+>1_279
+MHAGWSLGAAAGAGLGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPVDSASAR
+GAADQSPAPSETSTPPAPAAQALPRRAAVAVLVPAVVIAMAGFGVEEFGNAWATLFLITE
+RGLDPAAAVLGASTLLGAQFVGRLAGDRTLAALGRRGALTAGLGAVVVGLGLALAPLPEP
+VAVPAAFAGLALAGLGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGA
+LAGAVGLAPALTVFLGLAAVGAVLAARLPAAP
+>1_280
+MSEAPPHLPTADDGVARARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDPAAFGLL
+VIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAGAGHGAG
+TAAAWPLWVFAGLVVASGVLDAVVDTAQNAQGLQV
+>2_2322
+MPSASPSSPAARRARAHPVARRDVVRARWAATLAFLTNGGMLGALIPHYPQAKAAFGLDA
+DAFGLLVVALAAGAAAAGSLPAPVLRRWGSRRVMLAGTVVMAVVVVAAGLVVDLSAPAQG
+RPWAGAVWLFAALLGVAGILDAVVDTAQNAQGLTVQTRLARPVLTSMHAGWSLGAGLGAG
+LGALAVGAGMPAGLHLGLNGAACVAVLVAAGRRFLPDDARPAPDADAPEGTAAPAPGPSP
+RRPARPPPPRPAPPPGWPCSP
+>2_2323
+MAGFGVEEFGNAWTALFLQSERGLDVAAAGLGASTLLLAQFVGRLVGDRVLHRLGRRRTL
+AGSLAVVVAALVLVLTAPAAPAVFAGLALAGLGCAVVVPTAYALGDEVPGLPPRTGLAVV
+SWLMRVAGIGLSPLVGLLATGLPLPAALAVFPALAVLGLVGTGVVGRRRRRP
+>3_2201
+MTSAPADTPRIDRRAATRSRWAATAAFFTNGALAAAMIPHYPQAKAAFGLDPAGFGLLVT
+VMTLGAACAGPAGAPILRRAGSRATVLWGSLAIAVVLTGAGLALDLGARSDAAGPWLGAY
+AAAVFASGLCDAVVDTAQNAQGLRAQHALGRPVLTSMHAGWSLGAAVGAALGAAAVGAGV
+PAGLHLGLNGAACVLLLALTLPRFLPDTPDHAPAPALLTADDPGPESEATPASHRHPWLL
+LAPIVVISMAGFSVEEFGNSWTSLFLQAERGLDPATAGLGASTLLGAQFLGRLTGDRVLA
+ALGRTRALTGGLAVVLAGLTVTLLVPTPAAMFTGLALAGLGSAVVVPTAFALADEVPGLP
+AQTGLAVVSWLMRLAGLGLSPLVGLLAGVLPLTAALGAFVVLAALGTVLALTLRAPRLAP
+DFR
+>4_548
+MSEAPPHLPTADDGFARARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDPAAFGLL
+VIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAGAGHGAG
+TAAAWPLWVFAGLVLASGVLDAVVDTAQNAQGLQVQTRLARPVLTTMHAGWSLGAAAGAG
+LGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPTDSASARDASDQSPAPSETST
+PPAPAAQALPRRAAVAALLPAVVIAMAGFGVEEFGNAWATLFLITERGLDPAAAVLGAST
+LLGAQFVGRLAGDRTLAALGRRGALTAGLGAVVVGLGLALAPLPGPVAVPAAFVGLALAG
+LGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGALAGAVGLAPALTVF
+LGLAAVGAVLAARLPAAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000027.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000027.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3e3eef2e4b26f937c05d0c64c7161229dae4f41f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000027.fa
@@ -0,0 +1,14 @@
+>0_153
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>0_1028
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>1_320
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>1_331
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>1_756
+MAAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>2_706
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>4_977
+MAAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000029.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000029.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3dac019c952bb94007ce4faf138b88c86faaf737
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000029.fa
@@ -0,0 +1,28 @@
+>0_155
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>0_1026
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>1_318
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>1_333
+MSVTLLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>1_754
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARVLYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>2_708
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLADPRRARVLYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>4_975
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARVLYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000031.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000031.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7cd65152173ab2670f6ebe34ae5b4a3ec311ebc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000031.fa
@@ -0,0 +1,48 @@
+>0_164
+MPGRLIGWPRKPTLLELLFGLAMWEHAVMQIISFFNHKGGVGKTTMLFNAAVEMGRLGKR
+ILMVDFDAQANLTAISIDDDMLSMIYAPDEDGKTVAHAFAPLVGGSGDVFAPEAIEVREG
+KVWLAAGDLRLSEFDAILPSAWTEALAGNERGFRVTSAPYRLICEIAEEIKADYVFVDLG
+PNVGALNRAVLLGSDYMIIPMAADLFSIRALPSVGNSVDTWVRQWNTARSVAPRLNFDIQ
+KGLPKVLGYVSQQFNIYRGEATLAFSHWIDEMPAQIQSGLLEPLAVHSDGKGATLADPAQ
+SKGPGVGDLKNFHSLVPHAQTLRKAIFELRADDVVRGGQVTRARQSEEQFKELCANIIAR
+AV
+>0_1359
+MGEDPDTPTTAAAARRGPRPGVQTTVEGAGAAVTSREPIPVMTIHGEPVLGPTGRPKHDF
+PEPAPLTSHGPARIISMVNQKGGVGKTTSTINLGAALAGYGRRVLMVDFDPQGALSAGLG
+ANPHELDTTVYNVLMERSVTAKDAILSTDFENMDLLPANIDLSAAEVQLVNEVAREQVLE
+RALRQVRDDYDVVLIDCQPSLGLLTVNALTASHGVIIPLTAEFFALRAVALLVETIEKVQ
+DRLNPDLEIDGVLATMFDQRTLHSKEVVGSLVAGFGDRVFETVIKRSIKFADATVAATPI
+TLFAENHDGAKAYRQLARELISRGGAP
+>1_1098
+MGEDPDTPTTAAAARRGPRPGVQTTVEGAGAAVTSREPIPVMTIHGEPVLGPTGRPKHDF
+PEPAPLTSHGPARIISMVNQKGGVGKTTSTINLGAALAGYGRRVLMVDFDPQGALSAGLG
+ANPHELDTTVYNVLMERSVTAKDAILSTDFENMDLLPANIDLSAAEVQLVNEVAREQVLE
+RALRQVRDDYDVVLIDCQPSLGLLTVNALTASHGVIIPLTAEFFALRAVALLVETIEKVQ
+DRLNPDLEIDGVLATMFDQRTLHSKEVVGSLVAGFGDRVFETVIKRSIKFADATVAATPI
+TLFAENHDGAKAYRQLARELICRGGAP
+>2_1459
+MQTSLEGAGAAVTSREPIPVMTIHGEPVLGPTGRPKHDFPEPAPLSSHGPARIISMVNQK
+GGVGKTTSTINLGAALAGYGRKVLMVDFDPQGALSAGLGANPHDLETTVYNVLMERSVTA
+RDAILPTPFEGMDLLPANIDLSAAEVQLVNEVAREQVLERALRQVRDDYDVVLIDCQPSL
+GLLTVNALTASHGVIIPLTAEFFALRAVALLVETIEKVQDRLNPDLEIDGVLATMFDQRT
+LHSKEVVGSLVAGFGDKVFETVIKRSIKFADATVAATPITLFAENHDGAKAYRQLARELI
+CRGGAP
+>3_1370
+MTPKEPIPVMTVHGEPVLGPTGRPKHEFPEPTPLAGHGPARIISMVNQKGGVGKTTSTIN
+LGAALAGYGRKVLMVDFDPQGALSAGLGADPYELDVTVYNVLMERKVTARDAILPTAFEN
+MDVLPANIDLSAAEVQLVNEVAREQVLDRALRQVKDDYDVVLIDCQPSLGLLTVNALTAS
+DGVIIPLTAEFFALRAVALLVETIEKVQDRLNPDLEIDGVLATMFDQRTLHSKEVVGSLV
+DGFGDRVFETVIKRSIKFADATVAATPITVFAENHDGAKAYRQLARELICRGGAP
+>3_2178
+MHTLMVYSEAGGVAKTTTAVSLAMSWAEQGRQVVLIDLDPRAAATKWVDVEPTEPGLHIG
+AVIGNPDPTGWVQDLAVPSGWHENLRVVPSDRSLSHQESDRADHAHLRLRMALSDLQADL
+VVIDCPNRQGGPLTQNAFTASDGVIYAARPTSDGCDGVHGARQSVAAFKQSMALLGAPDR
+LVEVGIVVSDYRDHITPKDQTVAVEELRETGLLLTPLVPARSIVPKARLACDWLGRYEKG
+EPVAAAYADLAGLIFERITA
+>4_1308
+MGEDPDTPTTAAAARRGPRPGVQTTVEGAGAAVTSREPIPVMTIHGEPVLGPTGRPKHDF
+PEPAPLTSHGPARIISMVNQKGGVGKTTSTINLGAALAGYGRRVLMVDFDPQGALSAGLG
+ANPHELDTTVYNVLMERSVTAKDAILSTDFENMDLLPANIDLSAAEVQLVNEVAREQVLE
+RALRQVRDDYDVVLIDCQPSLGLLTVNALTASHGVIIPLTAEFFALRAVALLVETIEKVQ
+DRLNPDLEIDGVLATMFDQRTLHSKEVVGSLVAGFGDRVFETVIKRSIKFADATVAATPI
+TLFAENHDGAKAYRQLARELICRGGAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000032.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000032.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2296a0f272b3232fec3f336edf8e7d07e724305
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000032.fa
@@ -0,0 +1,42 @@
+>0_236
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEALEVAATIASKSKPASWMAKEAVNAAFETTLAQGIAFERRVFHA
+AFATADQKEGMDAFTAKREAGWQHR
+>1_84
+MSTGLHIETVDRIGIIRLDRPAELNALTFATVEEIAAQVQRWEVDGETDGVVITGSGQKA
+FAAGADIRELQHKSVQEMTARGMQHAMTALRESSLISVAAVNGLALGGGFELALSCDIRL
+ATPQASFGLPELGLGIIPGAGGTQLLTRYTNASVASYHILTGQPISADRAHQLGLVSELH
+EAEDLMAAAMEVIGTIASKGPLARQLAKRAIHGAAHAGMDSGLEIELLAQAAIFGTQERE
+EGLNAFLERRTPSFIPRPRPRKD
+>1_88
+MTDRIRTSVEQGVCTITLNRPGALNALENTMIATIVAELERAGADPDVRAILLRGEGKAF
+CAGDDLVDMGTEEHPESPDLVERYSRGYPAIVERMLTLEKPIVASVRRYALGAGLEMALA
+ADLIVAEPQAKLGLPFVLRGIAAGTSLLPKRAPVQLVQRMLYLGEMITAEDAHRMGVVGH
+LAEDEDVDELALATARRLAVGATRAIGLMKTALRTSETLSARDALAVQVGATAASVLTED
+FTEGKVAFTQKRDPEFGGR
+>1_2199
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEALEVAATIASKSKPASWMAKEAVNAAFETTLAQGIAFERRVFHS
+AFATADQKEGMDAFTAKREAGWQHR
+>2_115
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEAQEVAAAIASKSKPAAWMAKETVNAAFETTLAQGIAFERRVFHS
+AFATTDQKEGMDAFANKREAGWQHR
+>3_84
+MNEQNRTEAAEAEQPVIVGRDGRVGRIQLNRPKALNALNAATMEAVVAAAVEMDADPEVG
+AILLLGSAKAFAAGADIKEMKDKDAADMYAADWFRRWEDLARLRTPIVACVQGYALGGGC
+ELAMMADVLVAGRSAKFGQPEITLGVLPGMGGSQRLTKSVGKAKAMDMVLTGRMVEAEEA
+ERMGLVSRLVEDEDAVATAEEVAATIAGFSKPVAQMNKEVVLNAFETPLTQGLVFERRVF
+HGVFSSEDQAEGMAAFAEKRSPVWKHR
+>4_236
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDLEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEAKEVAAAIASKSKPAAWMAKETVNAAFETTLAQGIAFERRVFHS
+AFATADQKEGMDAFTAKREAGWRHR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000035.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000035.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8fbd2016898774fb9f47e125b62bb14a7f11dff0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000035.fa
@@ -0,0 +1,21 @@
+>0_602
+MPAAYPREFRQDVVAIARKGQIPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>1_356
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>2_373
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGVTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLVQSPK
+>2_377
+MPAAYHREFRQDVIAIARKGQMPIAQVAKDFGIAESRLRRWLAQDDVEAGIRPGVTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLVQSPK
+>2_394
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGVTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>3_2137
+MPAAYPREFRQDVVAIARNGQMPIAQVAKDLGITASCLRRWLAQDDVEAGIRPGLTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>4_579
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000036.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000036.fa
new file mode 100644
index 0000000000000000000000000000000000000000..feead10c7e51ddd2de6864c1f8afb20144194d08
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000036.fa
@@ -0,0 +1,58 @@
+>0_606
+MTGRRRYQGLAARFFLAQLLVVGASVLAAVVVASLAGPPLFHEHLEQAGAGHDAAQMLHV
+EQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAM
+GAGTEVEELAGSFNTMAARLQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD
+EPTGELMGEQLARLTRLVEDINDVSRAEEGRIELDRSPQGVSGLLHAATEAHKEAYATKG
+VALTMDADPGLAVDVDRQRMGQVLGNLLTNALRHTPAGGRVTLEARQSPSGVTLSVTDTG
+EGISPEHLPHVFERFYRGDTARDRDHGGSGVGLAISRALIQTHGGTLSATSTTAGATFTI
+DLPTKQPPTSPPTGAPVYPP
+>2_387
+MTGRRRYQGLAARFFLAQLLVVGASVLAAVVVASLAGPPLFREHLEPAGAGHDAAQMLHV
+EQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAM
+GAGTEVEELAGSFNTMAARLQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD
+EPTGELMGEQLARLTRLVEDINDVSRAEEGRIELDRSPQGVSGLLHAATEAHKEAYATKG
+VALTMDADPGLAVDVDRQRMGQVLGNLLTNALRHTPAGGRVTLEARQSPSGVTLSVTDTG
+EGISPEHLPHVFERFYRGDTARDRDHGGSGVGLAISRALIQAHGGTLSATSTTAGATFTI
+DLPTKQPPDQPTYRRTRSSTVNTGAPPLA
+>2_1228
+MRTRLSTLLALVLVLSLAVSGITAYAVLRITVNDRIEASLQRAVEQVALLSETGVDPETG
+EPPDSAAAFIRLAMLRVLPHDNEGILGLAPDRAELAASDAVELRLEEDPELVAWALARVG
+DQEARAETVTTASATYRAVVVPVTGWGQDDAGALLLAVDVDAEVGRLDRTFLGFAGGALL
+TTVFALAVGVPLLRRVFAPLESLQEAVGEVTEHDLDRRVEVIGHDDVAALGHSFNAMLER
+LEDSFASQRRLLDDAGHELRTPVTIVQGHLEVMDPDDPADVRETTRLTLDELDRMSRLVD
+DLLVLAKAQHPDFLRPAPVDVAELTRGVLARASGFDGHVWELDGVAEATVSLDAQRITQA
+WLQLAANAVRYSEPGSVVRLGSAVEGDTLRLWVQDHGVGVRPEDRAQIFERFGRGAHGTR
+ADGSGLGLAIVSSIAAAHGGEVSLDSVPGLGSVFRIELPLSTPSRPAGSLTPGKDPA
+>2_1305
+MTRSKPTGRLSASGRARVVAWILGVSALGMVLMLVSIVLTLRWVERDAIETSLTQESDEV
+AVFAQNGRDPETGEPFATPERFVGHYLERQRVEPTELMFGGTAATPVIAQIHGDAAAPVE
+LLAPATRQAMEQPRSRGTLVDPTHGRISYANLTVTTPADTGHVVVAVFHERYEQRVMTQT
+LLLSALALAALAATAAAAWLVSSRILGHTVEFHRAVDASLKDRGLRRLPENGSEEYAGLA
+RRANDLVRRADRRLEEERRFAEDVTFALRTPLTVIEGGLRNPGGDEQERRTSYRHIGAEA
+TRVRGLLEDLVILSRLQQDDVVLERTPVDVGVLVATAAQAWRERHPDAADEPRLDVEAPA
+EGLTAVTDRARLVQVLEELLDNARHAVRFAPGSDLPRDLTAVTPLERTLSVRVREEERDG
+EPWAVVEVADRGRGIPEEDREEVFERLANASNDPYPGNGLGLPVAALLSTALDGELTLEP
+GPGAAGTVARLAVPLTADQDGEDA
+>3_434
+MSPTPALRGRPAPGPDAALVARAARRIGLRTALACAALVLGGAGVFFGYLWWQIAHPGVD
+PRDADATVTVQLDLVDLATAAILAGAAAVLITGFASLWFSRSAVQPLADALRRQREFVSN
+ASHELRTPLTVLSARTQVLQARVPAGDPLEPLADELRRDTDVMAGVVEDMLSTARLDSAP
+EGMCDAGEVAAAACADLSLVGAEERGVRLRADLPSLPVALPEAALRRMLAALLDNALGFA
+PPGTEVTVSGERVRGVVELRVADRGAGIQGVEPDHVFDRFARGRPAAVPGSGPGAVPRSS
+HGIGLALVRETAHRYRGEVRVESTGPEGTVMLLTLPAAQEAR
+>3_2146
+MTSRRRYQGLAARFFLAQLLVVGASVLAAVVVASLAGPPLFHEHLEQAGAGHDAAQMLHV
+EQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAM
+GAGTEVEELAGSFNTMAARLQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD
+EPTGELMGGQLARLTRLVEDINDVSRAEEGRIELDRSPQGVSGLLHAATEAHKEAYATKG
+VALTMDADPGLAVDVDRQRMGQVLDNLLTNALRHTPAGGRVTLEARQSPSGVTLSVTDTG
+EGISPEHLPHVFERFYRGDTARDRDHGGSGVGLAISRALIQTHGGTLSVTSTTAGATFTI
+DLPTKQPPDQPTYRRTRLSTVNTGAPPLE
+>4_575
+MTGRRRYQGLAARFFLAQLLVVGASVLAAVVVASLAGPPLFHEHLEQAGAGHDAAQMLHV
+EQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAM
+GAGTEVEELAGSFNTMAARLQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD
+EPTGELMGEQLARLTRLVEDINDVSRAEEGRIELDRSPQGVSGLLHAATEAHKEAYATKG
+VALTMDADPGLAVDVDRQRMGQVLGNLLTNALRHTPAGGRVTLEARQSPSGVTLSVTDTG
+EGISPEHLPHVFERFYRGDTARDRDHGGSGVGLAISRALIQTHGGTLSATSTTAGATFTI
+DLPTKQPPTSPPTGAPVYPP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000039.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000039.fa
new file mode 100644
index 0000000000000000000000000000000000000000..32e98b604a47abbe4a611be74b82aca86c921c35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000039.fa
@@ -0,0 +1,121 @@
+>0_851
+MNTHHPDRLTDAAGVRVLLYGDVDLNVIDGSATWLPSLAETLARTGASVDVQLKAVERRD
+LLTAPLRALTGVRVLTAEPAAGQGGMTPSRAADVLARRDEESRYDVVLVRGIHACLELAD
+RGAFPGRLWSYVTEYGYVEDGFPAGRVEELGRIAAASRLMLAQTPQARAVLEAMVPAAAG
+RTELLSPMVPDGLVPAERAEAPADGPVRLVYTGKFAHDWRTDLMPDVLTALHEAGVPATL
+TMVGDKVHPERDRPGWAAAMRSRLEAERPDFEWTGALSREESMARTAAADVSLGWRAPAL
+DLSLEISTKVLESCAVGVPPLLNRTVAHEELLGADYPLFVDGVRDSARDVAARIAAARHD
+LPALSRRVVEAAAPYRMAARARALTGVMDRLGLLDRRPARGGSRTRVVLAGHDLKFAGEL
+VDLLRDDPGVELRIDHWQGLHRHDEAASRRLVEWADVVVCEWAGPNAVWYARHKRPGQRL
+VVRLHMFELRGGWLSALETEAVDRLVTVSDLYRDLVREHLPIEPTRVTVIPNAVSVADLD
+RPGLPGRRFRLGLVGVVPLRKRLDRAVDLLEILRAHDERFTLHVRGRMPWEYPHEWRKPL
+QREGYLDLFARLGAGPLREAVAFEPFGADMGSWLTKIGWVLSPSTTESFHLAPAEGMVSG
+AVPLVWDRPGARGVFGDEFVLDDTDAAARRVLEAVADDARWDALSALARERVRAYDERVV
+AGLWREALGLD
+>0_861
+MNVAGARLRRWAGRARIVGERAAATAGDAGASALRAARGARGLATLPERTWRAADVHVPD
+ASAALPLPAAAVLRRALTGARVPSLDAFSPLGPRPAAAPAVLLLPVDEPAARGWSVEAAA
+ELAARRCADLEMPAGAPGLHTVLMSDPASRRALTAALRTAGGRLPGVLVVACPDPATAAG
+RARVLAALGLVDAVLAPEGTRLDPPLARAAARAGRAVIGPDRAAETWERLAAAGRAARLD
+ALTPAEAAGPPAAPAPRVRVTAEPRRVVVAGHDLKFAGALMDRLRADGHEVRVDAWRGHA
+RHDVERSRALAAWADVVHCEWSLGNLAWYSRHLDSPHRTTRLTSRLHLQEAGTAFPSRVR
+QDALDEWVFVAEHVRAQVLRDTRFPASRTSVVPNAVAVPPTLPDGDDDRRFVLGLVGVLP
+ERKGLHRALDLLAALRRVEPRYTLRIRGHHPEEVGWMAQRPAAAAYYRAQLRRIETDPVL
+AGAVTWDPHGPDMPAWYARVGVALSVSDFESFHFTLPDGAAHGCLPAALAWAGADLLYPA
+AWLSPDVATMAEALRRATADARAWRSAVAQARRDVAHTYAEEDVVPALVRRILGGAAA
+>1_582
+MNTHHPDRLTDAAGVRVLLYGDVDLNVIDGSATWLPSLAETLARTGASVDVQLKAVERRD
+LLTAPLRALTGVRVLPAEPAAGQGGMTPSRAADVLARRDEESRYDVVLVRGIHACLELAD
+RGAFPGRLWSYVTEYGYVEDGFPAGRVEELGRIAAASRLMLAQTPQARAVLEAMVPAAAG
+RTELLSPMVPDGLAPAERAEAPADGPVRLVYTGKFAHDWRTDLMPDVLTALHEAGVPATL
+TMVGDKVHPERDRPGWAAAMRSRLEADRPDFEWTGALSREESMARTAAADVSLGWRAPAL
+DLSLEISTKVLESCAVGVPPLLNRTVAHEELLGADYPLFVDGVRDSARDVAARIAAVRHD
+LPALSRRVVEAAAPYRVAARARALTGVMDRLGLLDRRPARGGSRTRVVLAGHDLKFAGEL
+VDLLRDDPGVELRIDHWQGLHRHDEAASRRLVEWADVVVCEWAGPNAVWYARHKRPGQRL
+VVRLHMFELRGGWLSALETDAVDRLVTVSDLYRDLVREHLPIDPARVSVIPNAVSVADLD
+RPGLPGRRFRLGLVGVVPLRKRLDRAVDLLEVLRAHDERFTLHVRGRMPWEYPHEWRKPL
+QREGYLDLFARLGAGPLREAVAFEPFGADMGSWLTKIGWVLSPSTTESFHLAPAEGMVSG
+AVPLVWDRPGARGVFGEEFVLDDTDAAARRVLEATADDARWDALSALARDRVRSYDERVV
+AGLWREALGLD
+>1_592
+MNVAGARLRRWAGRARVVGERAVVTAGDAGASALRAARGARGTATLPERTWRAADVHVPD
+AAAALPLPAAAALRRALTGVRDPSLDAFSPLGPRPAAAPAVLLLPVDDGPAARGWSVEAA
+AELAARRCADLQMPAGAPGLHTVLVTDPASRGALIAALRPAGARLPGVLVVACPDPATAA
+GRARALAALGLVDAVLAPEGTRLDPALPSVAARAGRAVIGPDRAAETWERLAAAGRAARL
+DSLTPAEATGPPAAPGPRVRVTAEPRRVVVAGHDLKFAGALMERLRADGHEVRVDAWLGH
+ARHDAERSRALAAWADVVHCEWSLGNLAWYSRHLDSPHRTTRLTSRLHLQEAGTAFPSRV
+RQDALDEWVFVAEHVRAQVLRDTRFPAARTSVVPNAVAVPPTLPDGDDDRRFVLGLVGVL
+PERKGLHRALDLLAVLRRTEPRFTLRIRGHHPEEVGWMAQRPAAAAYYRAQLRRIETDPM
+LAGAVAWDPHGPDMPAWYARVGVALSVSDFESFHFTLPDGAAHGCLPAALAWAGADLLYP
+AAWLSPDVATMADALRRATADARAWRSAVAQARRDVAHTYAEEDVVPALVCRILGGTAT
+>2_2002
+MGEADTPAPTPEGPLAGRSFRLVAVAERPDWEPGLIAQLRAAGAAVVSTTEVVRTSSAHV
+DVLLAVDVESAAALRAAGWDRFQVWTVVQTDPGTPLMPRGLSAAGVGRAVAESRRVVVFD
+EASRSAVESTLWNAAGKVVVMPRFTAEEVEAVSFGGNRVEGPHEPGEAILVLHAGLLGSE
+GAHVLREYSDAVRARRHVRKVLVVAPGDLRVAVRSEEGQRHLARIPGASLIDGGAELSRA
+AAGRRTVTVLPRWSTPQDSRAEDLLAWAAAVGAQVWAEPGAVPPQVSGRPVGQLPGDNLS
+AALDWADQHAGGTTFGAAPINRVAQAFAPHVPALSTVPAHPNAPLKVLFVGADYKFAGDL
+VEALILRPDAEVRVDQWKTNGDRPTPNSAELLAWADVVICEFASRNAVWASQHIREHQRL
+IVHLHGYELRNPLIHDIVMDRVHTVVFASEFYRADAVVTTGWRVEQTAVIPNSVQSAELR
+RPKTADARFHLGLAGYVPELKRMDRALDLLEELLRRDDRFVLHLRGRHPWNYPYVWRHPL
+RRDTYLANYERLRSNPRLRRAVVFDDFGPDMGNWFRNIGWMLSPSTRETFHLAPAEGMAS
+GAVPVVWRREGSDGIFPPESLVTDAASAADRIHRTAGDRDAYNSAARSAIEFATRYEAGA
+VVDHWLRLILHGERPGGPPSPEHLQRARPVATALAGRADWNRVGRLLRDGRVEQAAAVAQ
+EESRPAWEQPEDVRRLAAHVNGYSALAQRAHRLVPSAPCVPPLLPLAAGADSARSLTLTE
+GPAGTYVTRSGDIAVGRGDILDDVNAEFDRLVDQAFRIGAQNRATALTVIGDEMLALAGG
+AVAGWLGIPFVWDLTSQPAARDLLMRMRALPDAPTPQGRLALLAAASATRLIGAGPAERL
+PVPFETFIGMADLDRPRRVGVIGRSLGDLVGRSWGEPVNLSPGRWREQTVPRLDVALLDA
+QVLHPRNAWRASEGNTGPLGALITHVRRHATPLAIVDLGHEGLDSAGIAQARRVDAVVTA
+HPDDVQRLHDVRIVPSQVAVSTAPWGIRSGEEHVLRPGDRVRLAMRMLGVAETH
+>3_1900
+MRQIDEMALWTSRDVGVRVRYAGAEELIRGVRSRADATHDASDGGTDLEAADVAGPGTPE
+PSDHVAEVPWRLRVLNTGRVRQIRRWIYHARRAPAHAAAARVKRLLRTPGRWSETLRRPL
+ARTRAAAPAPERADAAVATPAPAAEPTGERTLAALRAALAERPSASALHALVAALYRDGQ
+LRAPAAALEEHPELVGQFTPAQAKLARNVREQARLLDHPPVVPARAVGTALRPEAGRILY
+CAHGVHPYQSNGYAIRTRGIVAGLRDAGHDVVVAARPGFPWDAKVTRAARKKQSYPELVD
+GIEHVYSFGPSLRNQALAAYLESAVDSYLQVIARNRPAHVHAASNHITALPALIAARLSG
+LPFTYEVRGFWEYGMEPGEEGLQERGELAGRLEDLVMVEADHVFVLTAEMRDELRGRGVD
+PDRMTVTPNGVDPEQFQPLPAVGELHRRLGLDPDRAVIGYLGSLVSYEGLEDLLEACLQL
+AEERDDFQLVVAGDGPVLPRLKEIAAERDTSLPVHLLGRIDADLIPALMSEVDVVACPRT
+ATRVTRLVSPLKPLEALAAGVPVVLSDLPVLRSLAEECGGAVVFPAGDRHGLAEAIAGLL
+DDPERRLDLGRSGRAWALRERRWDVLGAHLGSGILAAVPSTGAEGGSRPLSTVRLGVIAD
+TFTTSGLAEQVQTVPLQRAGQGWRRQLAEERLDAVFVESAWSGNDGAWTRGVGHYSDEES
+ADLRALLEDCRAAGVPTVFWNKEDPVHFNRFVENARLFDLVLTTDNRSIQGYQARVDRSR
+QTVGSMAFFAQPSLHHPVTDGPAVADRPVMYAGSYYGDRYRDRSEVLRGLLHVARPFGVT
+IYDRQADLPDSPYRFPEELQPFVEGGLPYSEMVKAYRRYPLHVNVNSVTASETMFSRRVM
+EISCAGGVVASGPSAGVNHMFRGLVPTIGRREVAERAMSTLLSDPGLRNVQGWNLRRLVR
+RSHTLSDRLLVLLRRLGLAVSPDPTPGTTVVLTGPADRADWDGLLAQTRPVDRVVADEMS
+ETVRERLSAAGIEVSAGSASLDPAHLAWEWDGARLDRVVHEDLANVLLDSGYSAAVLDTT
+PVTDLATPLAVVGGAPVPSGASLVLRWGGGDDGVVTVRRGLLESVEDLGAKQRPAAVALT
+PEALDRMERPLRVVVAGHDLKFAGELINRFRSDGHEVRLDQWASHQDHDDELSRELVDWA
+DVVLCEWGLGNAVWYSKHKREGQRLYVRVHSQELFRDNWSRMNLPAVDRFIFVAPHIRDS
+ARRYRGVAARPSEVIPNIVLPGAGLKRDPDSRFVLGLVGIVPRGKRFDRALDLLAMLRRE
+DPRYSLRVKGKQPEDYPWMAAREEEMAYYGTIRERIAQDPALQGAVHLDGFSTDRAELDR
+WYSSIGIGLSVSDFESFHFTSVDGAQNGAVPAVLAWPGADRIFPAEWLSPTLESMARRIL
+GLREPEVFRAAADTARRETSARFDGGRSLDRWSELVAGE
+>4_812
+MIQLFLRFSRRQQLVMGLFILLAVVGSVLAFLVDHAILIVALFWMLCAAVFVMIMYHRRL
+NAKINRTARAARMGSSAVAGRGGTRPATGRRISTQESLDSLQAAFARRRTVAAGLPLARK
+LIQERGDLSGAREVLDQLRGKSGLTDSEENFVRRVDSLNRLLEADYPLPARHRTCNYLPV
+RGRVLYAVGMSPVSVTNGYTSRTKGVAAGLVAQGLDVVVAPLPGKPWDKKSVVPGRRVPV
+KQRRDVSEIDGVRHVHNPGLPAWEGDLDVFFQVAADAYVREAMIEKPEFILAASNYLSAL
+PALIAARRLGVPFVYEMRGFWEVSAASVRPGWEQSDQYRLDRRYEDLVAREADRVVVITD
+EMREDLAARGIDADKVTVAPNCVDPEVFAPLGKDHALLRGLGFTDTEAPVVGFAGSVTDY
+EGLDLVTDALATLKAEGVRFNFLIIGGGAYLDTLKARIATRGLDPETRFVMNVPNADMPA
+YLSSIDVFPLARKSLPVTELVSPLKPLEAMAVGGAVVLSDVSPHKVFCGPDGDTAVSFQK
+DDLASLVERLRETLAAPDAARAMGVRARRWVKENRRWPVTGERIAASLMALAEEFRASLD
+DAERPLTDYTVAFIGDEFTTDTFVPELTALRVRPEDWRETFEDHRVDALFIESAWRGNDS
+AWTGIIGYYDDETHAPVVELIAHCRLHEIPVMFWNKEDPVHFNRFKRTAALCDYVFTTDA
+RTIVDYNALPDNQITTVASAPFAAQPLLHNPLPSTRAQDEAIAYGGTYYGDKYATRKQGL
+DFLFYESAPHGLAIYERVHNDPNSPYRLPDRFRRYARGSLSYPEMCQAYKAHPIHLNGNS
+VVDSPSMFSRRVVEITASGSTVLSSAGRGVDETLAGTVPTVTTPDEAAAYLEGWKSSEQR
+RHAGLWEAFRHVYETHTCAHRLVYMMRVAGFRVRSPQAAPIAVECAAADVPLFEAQTMRP
+ALYLVTDTTEGVDAASPVVLAAPPERAAKLQEAGIRNVVIHREGAPALDEHLVEDFSLAL
+HFGHWKAVGTRTVEWSPGDAHVRIAALTADIDEGTVLVDADVYAGSVLGERPALADDEVF
+AWQHVVEHVGKVTYTDSTAVPIDTAVVHEEADPLPPVASGEAGPPVGETQTVPLNVLVAG
+HDLKFLPQIMAQLEAAGHRVIVDQWDGHDIHDEERSLRLLAEADVIFCEWALGNVKWYSH
+HKQDDQRLVVRLHAQELRTRYLKDADLSAVDTFVFVSPVGMRRAQLLFGVPVDRSVVIGN
+TFDFERFAAPRNAPDPHALGLVGSVPHSKRLDLALDVTELLASHDPTYRLDVMGKEYHEY
+AWLMKRTAERSYFEAQYLRIESSAVLREAVRFGGHSYDIAEWYRAKPGIILSTSDHEGTH
+QAIAEGGAAGCVPVIFPWAGAEAVYDDRWVVEGVRDAADRIRRYSSDPALFLEESERAQA
+FMRERFSPEEIGAQILAVVEGRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000043.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000043.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ebd5101f4d107cc5b86bce00f321e1a59bf8229b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000043.fa
@@ -0,0 +1,21 @@
+>0_1349
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVNRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEAQRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>1_1091
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVNRVATQLGYGVESVRMWVK
+QADIDDGVTSDVSSAEAQRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>2_396
+MPKEQTAGKPTTRRYSPEEAAAVRMVRTMRAELGTEHGTVQRVATQLGYGVESVRMWVKQ
+ADIDDGVTSGVSSAEAQRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>3_311
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVQRVATQLGYGVESVRMWVK
+HADIDDGVTSGVSSAEAQRVRELEQEVRKLRRANEVLKRAASFFGAELDRHYRK
+>3_631
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRVELGTEHGTVQRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEARRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>3_2164
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRVELGTEHGTVQRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEARRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>4_1298
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVNRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEARRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000044.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000044.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ebe654df2d1724e8d301f12411ae5e7c7052740
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000044.fa
@@ -0,0 +1,40 @@
+>0_1353
+MAVSGSFPGHLWAAFHGRLHSVRDEELIPQLVELWETNYRVYGVRKLWKTARRAGIDIGR
+DQTGRLMRAAGIKGATRSKRVKTTRPDPTAARHPDLVKREFTAPAPNRLWVTDLAFVTTW
+AGVAYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFT
+SIRYGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAELVRGPARPGPWRTVEDLELAT
+LGWVSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLSESNSASLHQTQGASGPTLWSP
+TRSILDRAARPLRKF
+>1_1092
+MAPSSYYAAKTRAPSARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGRDQA
+ARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTWAGV
+AYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDPRCHSDAGSQFTSIR
+YGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAEHVRGPARPGPWRTVEDLELATLGW
+VSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK
+>2_397
+MAPSSYYAAKTRAPSARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGRDRA
+ARLMRAAGIEGARRSKRVKTTRPDPASARYPDLVKREFTAPAPNRLWATDLTFVPTWAGV
+AYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIAMARWSRGARHEDLRCHSDAGSQFTSIR
+YGERLAEIGATPSIGTVGDSYDNSLAETVNGYYKAELVRGPARPGPWRTVEDLELATLGW
+VSWHTTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIQ
+>3_312
+MAPSSYYAAKTRTPSARAARDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGRDQT
+ARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTWAGV
+AYVCFIIDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFTSIR
+YGERLAEIGATPSIGTVGDSYDNALAETVNGYDKAELIRGPARPGPWRTTDDVELATLGW
+VHWHNNQRLHGYLDDLPLTEFEERFYATQQGQYALVEIK
+>3_632
+MAPSSYYAAKTRAPSARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGRDQT
+ARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTWAGV
+AYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFTSIR
+YGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAELVRGPARPGPWRTVEDLELATLGW
+VSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK
+>3_2165
+MAPSSYYAAKTRAPSARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGRDQT
+ARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTWAGV
+AYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFTSIR
+YGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAELVRGPARPGPWRTVEDLELATLGW
+VSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK
+>4_1302
+MGSFSWPLTHSDAGSQFTSIRYGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAEHVR
+GPARPGPWRTVEDLELATLGWVSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000047.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000047.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a6ffd8a8645a9338e76432fbc42f38f99c481d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000047.fa
@@ -0,0 +1,78 @@
+>0_1747
+MSSKAARTRSEPVTLPRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAG
+PEIVDQWIEDNPVWGPVLDALQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQ
+PPARTPRNLTRLPASGVVVLEEGGPSPEEAVARAQAWLRKRRYRVERRLEAGGASVGAER
+GYLREIGNILFHVSLIGVLVFMAYGGMTKYGGQKIIVEGEGFANNLVAYDSFTPGTYFSA
+DDLQPFSLTLDSFDAVFDRESETHYGQPLDYTAVMDVREGSGGELQRQILKVNQPLDIDG
+VRVYLVGNGYAPVVTIRDGAGDVAFQGPVVTRVFDQNYGSQATIKVPDARPDQLGFVGFF
+LPSAVEDEEGAAFSADPELLNPELQLNSYYGDLGLDTGRPQNVYVLDTASLTELNSRTNE
+NGGIVLSPGQTYELPEGKGSISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLAISLFV
+RRRRVWVRARTDDDGRTRVEYALLARGEEFGLHEEHVALRAAMEKWWPIVAATETADDAA
+AGAAPQSTPTAPETPAGPADARSGD
+>1_1455
+MSSKAARTRSEPVTLPRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAG
+PEIVDQWIEDNPVWGPVLDALQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQ
+PPARTPRNLTRLPASGVVVLEDGGPGPEEAVARAQAWLRKRRYRVEHRPEAGGASVGAER
+GYLREIGNILFHVSLIGVLVFMAYGGMTKYGGQKIIVEGEGFANNLVAYDSFTPGTYFSA
+DDLQPFSLTLDSFDAVFERQSETTYGQPLDYTAVMDVREGTGGELQRQILKVNQPLDIDG
+VRVYLVGNGYAPVVTIRDGAGDVAFQGPVVTRVFDQNYGSQATIKVPDARPDQLGFVGFF
+LPSAVEDEEGAAFSADPELLNPELQLNSYYGDLGLDTGRPQNVYVLDTASLTELNSRTNE
+NGGIVLSPGQTYELPEGKGSISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLVISLFV
+RRRRVWVRARTDEAGRTRVEYALLARGEEFGLHEEHVALRSAMERWWPVAAPESEEEAVA
+SAAAVGHTGTTPETLAGPRTPRSGD
+>2_381
+MSRTEDQDPGRRPEVALPALGFWGTLRFAWTQLTSMRTALMLLLLLAVAAVPGSLFPQRP
+AGPGIVQDYIDDNPVLGEWLDRFQMFDVYSSVWFSAIYLLLFISLIGCVAPRAVKHAQAL
+RSAPPRTPRRLSRLPEYGRVVLEPGGPAPVEAVEQAARYLKRRGYRIEVRQEDAGGASVG
+AARGYLREVGNIVFHLSLIGVLVFMATGSLLSYRGQKILVEGEGFANTLVAYDAFTPGSA
+FSEEMLTPFSMTLKRVEYVYDRQSPTHYGQPLD
+>2_1047
+MGDAPVSSKAARTRSEPVTLPRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVP
+QRRAGPEIVDQWIEDNPVWGPVLDALQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHA
+KALRQPPARTPRNLTRLPASGVVVLEEGGPSPEEAVARAQAWLRKRRYRVEHRPEASGAS
+VGAERGYLREIGNILFHVSLIGVLVFMAYGGMTKYYGQKIIVEGEGFANNLVSYDSFTPG
+TYFSADDLQPFSLTLDSFDVVFDRESEALYGQPLDYTAVMQVQEGGGGEPREEILKVNHP
+LSMDGVRVYLVGNGYAPVLTVRDGEGDIAFQGPVVTRVQDVNFNSLVTLKVPDARPDQLG
+FVGQFMPAAVEDESGVAVSVDPELYNPQLILDSYYGDLGLDGGVPQNVYVLDTETLTELN
+SRKNENGGIVLSQGQTYELPEGKGSISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLA
+ISLFVRRRRVWVRARTDEAGRTRVEYALLARGEEFGLHEEHVALRAAMEKWWPVAAATAP
+ETTPETPCRPRRRPIRRLTVFNPTAPVNEQLALYSDLFMLIAAFVYAAAFVLFTIDMATS
+SATIRRLEEDLAAQRGPARLAPARETVGAGFGGSSLGGSSSVGSTGAGSSAGGPGVLPGE
+ARAAGLGDEPGLVDEDMDYTGGGRRPIANVAVAVLAVGWALHAFAVIARGLAASRVPWGN
+LYEFMTTGALVITTVYLLFLFRKDLRFVGTFVTGLVVAMMCAATMGFPTPVGHLQPPLQS
+PWLVIHVSIAVLATALFTLTAAMSMLQLIQDRAEKRAAATGERPWAFLRLVPSAQALENW
+SYRINAVGFVMWTFTLIAGAIWAEASWGRYWNWDTKEVWTFVIWVVYAAYLHARATRGWT
+GARAAWLSIVGFLCVVFNYTIVNTYFPGLHSYAGLPG
+>2_2582
+MSRPSDYDDGTGAGGTLRAESPELGFAGWLRWFWRQLTSMRVALILLLLLAVAAIPGSLV
+PQRGADPNGVVQYQKDHPDLFPILDAFPIQAFDVYGSVWFSAIYLLLFISLIGCVLPRIA
+HHWKAWRGRPPKTPARLQRMAGFSEIRLSNPDATPAEREAFAARAVDEAAAILKKLRYRV
+EVQRASRRGVDEVSVSAERGYLRETGNLLFHVSLLGVLVSVGLGGVFTFNGQKVLIEGET
+MVNQLIDYDTATSGRSFDSSSLEPFSLRLDTLDVTYNTPDDGNVQAIGLVKDYTANMTLI
+SPEGDESEHVIRVNHPLRVHGSPIYLIANGYAPKITIRNAEGTVVYSEAMPFIPQDNLNM
+TSLGVVKVPDGIVDESGEPVQLGLRGFFYPTKADLDTGAYTSNYPDLENPVLTLDVFVGD
+LGINDGIPKSVYALDTSDMEQVTGRAVDLDSIELRPGEQTELPNGFGTIEFESVPRYASF
+DVMQNPAQEWILVFAVLALGGLMWSLFVPRRRMWVKALPSEDGVVLQYAALARGDDPALE
+RAVEELRDRHRELL
+>3_983
+MGDAPVSSTSAPKDPAPRNRTRDDVTLPALGVGGTLRWAWTQLTSMRTALLLLLLLAVAA
+VPGSLVPQRRAGPEAVDQWIEDNPFWGPILDALQFFDVYTSVWFSAIYLLLFISLVGCVL
+PRALKHAKALRQPPARTPRNLGRLPESGVVVLEAGGPAPEEAVRQAQRWLKRKRYRVELR
+PEAGGASVGAERGYLREIGNILFHFSLIGVLAFMAYGGMTKYTGQKIIVEGEGFANNLVA
+YDSFTPGMYFDAASLQPFQLTLKSFDATFERQSQTHWGAPLDYTAVMEVRHGTGGDPEEQ
+VLKVNHPLEIDGAKVYLVGNGYAPVVTVRDGNGDIAFQGPVVTRVTDQNFNSLAVIKAPD
+ARPDQLGFVGQFMPAAADVGQGVEVSVDPEPLNPKLILNSYSGDLGLDAGVPQNVYVLDT
+STLTELNSRRSENGGITLSVGQTHVLPDGKGSISLDGVRRYVGLDIHYDAGKWGVGVFSV
+LALIGLAVSLFTRRRRVWVRARTGDDGRTRVEYALLARGEEFGLREEHVALREAFEKMWP
+VSAPEADTGETTPATPAPAAAPTPRSGD
+>4_1669
+MSSKAARTRSEPVTLPRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAG
+PEIVDQWIEDNPVWGPVLDALQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQ
+PPARTPRNLTRLPASGVVVLEEGGPSPEEAVARAQAWLRKRRYRVEHRPEAGGASVGAER
+GYLREIGNILFHVSLIGVLVFMAYGGMTKYGGQKIIVEGEGFANNLVAYDSFTPGTYFSA
+DDLQPFSLTLDSFDAVFDRESETHYGQPLDYTAVMDVREGSGGELQRQILKVNQPLDIDG
+VRVYLVGNGYAPVVTIRDGAGDVAFQGPVVTRVFDQNYGSQATIKVPDARPDQLGFVGFF
+LPSAVEDEEGAAFSADPELLNPELQLNSYYGDLGLDTGRPQNVYVLDTASLTELNSRTNE
+NGGIVLSPGQTYELPEGKGSISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLAISLFV
+RRRRVWVRARTDDDGRTRVEYALLARGEEFGLHEEHVALRAAMEKWWPIVAATETADDAA
+AGAAPQSTSTTPETPAGPADARSGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000048.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000048.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f2a867e40be1344793cfeb746641ee3dcbe9b35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000048.fa
@@ -0,0 +1,35 @@
+>0_1749
+MQTPRPSRRTVLTGLSLLGLAPVLAACSGDDSLTRQAGNADGKNYIAGDGSVLEIAPAER
+GAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVRFL
+GVNVRDTVTTAQAFERTFEIPYPSIEDARGEVLLNMTDYVPPQAVPSTLVLDVEGRVAAR
+VLGAVEESTLRALLTTVVDEAAA
+>1_1457
+MQTPRPSRRTVLTGLSLLGLAPVLAACSGDDSLTRQAGNADGKNYIAGDGSVLEIAPAER
+GAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVRFL
+GVNVRDTVTTAQAFERTFEIPYPSIEDARGEVLLNMTDYVPPQAVPSTLVLDVEGRVAAR
+VLGAVEESTLRALLTTVVDEAAA
+>2_382
+MPIPQPHREGHHRPPGLPPRPGRRQVLAGLAGVASLPLLAACSAEDPLAAQAGKADGKNY
+IAGDGSVLEIGPAERGEPVQFSSAMFSGEPIIAQDLAGDPAVLNFWYAACAPCRVEAPDL
+QALHEQFAPEGVRFLGINVRDTIATAQAFERKFGITYPSVEDRGGQVLLAMTDYVPPQAV
+PTTIVLDHQGRVSARILGIAERSTLRTLITTVLDEQA
+>2_1045
+MHTPPRPSRRTLLTGLALASLAPALAACSGGDDSLARQAGNADGKNYIAGDGSVLEIAPA
+ERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVR
+FLGVNVRDTVTTAQAFERTFEIPYPSIEDTRGDVLLNMADYVPPQAVPSTLVLDVEGRVA
+ARVLGAVEESTLRALLTTVVDEAAA
+>2_2584
+MNRRRTGAALALPIAALFALAGCSGGDGNLAAEWNEASGKGYVSGDGSSLSIAPDQRTEP
+VEFSGETEDGDIYGSDDTVGSVTVVNFWYAGCAPCRAEAPDLVEAYDEFSPQGVKFVGVN
+TRDQVAQARQFSVRFDIEYPSIMDNAGGRAVQRAFAGQVPLNAVPTTLVLDAEGRVAHRV
+LGQLAGASQLRTLIGETLAEAGGGAAADPASDPAPADEATEQ
+>3_981
+MPFPPRPSRRAALAGLSAAALAPLLAACSGTDDSLAQQAGNAGGKNYIAGDGSVVEYAAD
+QRGAPVEFSAAGFDGETVSGETLRGEPALLNFWYAACAPCRVEAPHLVKLHGEFEPKGVR
+FLGVNVRDTVTTAQAFERTFGIPYSSVDDTSGSVLLAMSDYVPPQAVPSTLVLDRQGRVA
+ARVLGAVEEGTLRALLDTVVAEA
+>4_1671
+MHTPPRPSRRTLLTGLALASLAPALAACSGGDDSLARQAGNADGKNYIAGDGSVLEIAPA
+ERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVR
+FLGVNVRDTVTTAQAFERTFEIPYPSIEDARGDVLLNMTDYVPPQAVPSTLVLDVEGRVA
+ARVLGAVEESTLRALLTTVVDEAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000049.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000049.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3509f1426a12f9a68b0616442aea3b7d2d5bb77
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000049.fa
@@ -0,0 +1,70 @@
+>0_1944
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRPHRLEIGQADGIQARSVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARPDYGWAFETLEDTNDGEHPVL
+VTLRRTVDAEENALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGVM
+DALADTDFPDIRTKCAIHSSSGSILLIPREGGHLSRMYVDLGEVPADDDHKVRQTPLEEI
+IRRAQQILRPYTLDVKEVAWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGLAPVELVPTYAEERKEIAKNLIDFDKEWSTLMATPTS
+ELGDPNEVAEFYTKTAEFPAGFMTEYQPSLLTTDATGQALAQGYPIGKRFKSALVERSCD
+TNVKHLGHLHRADGRWRVYVFADAASPRAEDSKVAAWAKAIEEDPRSFRNRHTPSDGPED
+ARFDIKVVYQQKQTEFAHPDVPSIFRPTTGSLGLHDLNNIFATCRPQHGEDIFEARGISR
+DGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN
+>1_1665
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRPHRLEIGQADGIQARSVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARPDYGWAFETLEDTNDGEHPVL
+VTLRRTVDAQGNALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGVM
+DALADTDFPDIRTKCAIHSSSGSILLIPREGGHLFRMYVDLGEVPADDNHKVRQTPLEEI
+IRRAQQILRPYTLDVKEVAWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGMAPVELVPTYSEERKEIAKNLIDFDKEWSTLMAKPTS
+ELGDPNEVAEFYTKTAEFPAGFMTEYQPSLLTTDATGQALAQGYPIGKRFKSGLVERSCD
+TNVKHLGHLHRADGRWRVYVFADTASPRAEDSKVAAWAKAIVEDPRSFRNRHTPSDGPED
+ARFDIKVVYQQKQTEFAHPDVPSIFRPTTGPLGLHDLNNIFATCQPKHGEDIFEARGISR
+DGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN
+>2_818
+MLFHHHGYVSTDPRVQPAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRSHRLEIGQADGIQARSVETFQAFGFASQIIDEAYDLTSMAFWNPSSEDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAAYMKNSPTRAEPDYGWSFESLEDSAEGEYPVL
+VTLRRTVDAQGEPLADPESGETRQVRAKYVVGADGAGSRVRKAIGHSLAGGASNHAWGVM
+DALAVSDFPDIRTKCAIHSSTGSILHIPREGGHLFRMYVDLGEVPADDNHKVRQTPIEEI
+IRRAQQIIRPYTLEVKDVAWHSVYEVGHRLTSGFDNRERVDHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGVAPAELVPTYSEERKEIAKNLIDFDKEWSTLMAKPTS
+ELGDPNEVADFYTKTAEFPAGFMTEYKPSILTTDATGQSLAAGFPIGKRFKSALVERSCD
+TNVKHLGHLHRADGRWRVYVFADAASPRSADSKVAAWAKAVEEDPRSFRNRHTPADGPQD
+ARFDVKVVYQQKQTEFAHPDVPAVFRPTSGDLRLLDLNNIFATCQPKHGEDIFEARGISR
+DGAVVVVRPDHYVSGVFGLDEVERLNEFFAGVLLDAS
+>3_756
+MLFHHHGYVSTDPRMKPAAGIGLDRPAELPDEMDVLIVGTGPAGMIAAAQLAMFPDVHTR
+IIERRGKRLEIGQADGIQARSVETFQAFGFASQIIDEAYDLTSMAFWNPSPEDEDAIVRT
+SLAEDDPHGVSEFPHLIVNQARILDWFAEFMKNSPTRATPDYGWEFVSLDDSDQDAERPV
+QVTLRRTVDAKGNPLAEGVAGEERVVRAKYVIGADGAGSRVRKAIGHSLSGDAANHAWGV
+MDVLADSNFPDIRTKCAIHSSSGSILHIPREGGHLFRMYVDLGEVPADDNHKVRQTPIEE
+VIRRAQQIIRPYTLDVKDVAWSSVYEVGHRLTSGFDNRERCTHPNVFLLGDACHTHSAKA
+GQGMNVSMQDGWNLAWKLGQVLSGIAPAELVPTYSEERKEIAKNLIDFDKEWSTLMAKPT
+SELGDPNEVAEFYTKTAEFPAGFMTEYRPSMLTTDAAGQELATGFPIGKRFKSAKVERSC
+DTNVKHLGHLHTADGRWRVYVFADAAAPHDADSKVAAWAEAVEEDPQSFRNRHTPAGAPQ
+DERFDLKVVYQQKQTEFAFPDVPAVFRPTTGPLGLHDLNNIFAVCRPEHAEDIFELRGVS
+RDGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN
+>4_165
+MFIAGDACHTHSAKAGQGMNVSMQDGWNLAWKLGQVLEGRSDASLLATYSEERQQIAENL
+IEFDKAWEGMMSKRPDELEDPQAVGRFYKDNAEFPNGFATQYPASSVTGEDTHQALAAGV
+PIGKRFESAAVRRVADTSPRQLGHLFEADGRWRLYAFADEDRTAVGELADWLADSPDSPV
+RRFTPESADLNSVFDAKVVYQQPYQEVELADVPALFLPKMGPYQLTDKEVVFAADLADDI
+FEARGIDRGGALIIQRPDMYVAHVLPLSAREEITAFFEQNMVSASV
+>4_166
+MRGAADPRRSLSTLPTTAVSEFPFLIVNQARVIDYFAEYAERGPQGQERTVRAKYVVGCD
+GSRSRVRDCTGIEVVRDPSAHAWSVMDVLLETDFPDNRQKCGIQSDKDGTILLIPREGGF
+LARFYVSLGSIDDAPRPRSGGGIRACSSPATPATPTPPRPARA
+>4_1883
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRPHRLEIGQADGIQARSVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARPDYGWAFETLEDTNDGEHPVL
+VTLRRTVDAQGNALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGVM
+DALADTDFPDIRTKCAIHSSSGSILLIPREGGHLFRMYVDLGEVPADDNHQVRQTPLEEI
+IRRAQQILRPYTLDVKEVAWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGMAPVELVPTYSEERKEIAKNLIDFDKEWSTLMAKPTS
+ELGDPNEVAEFYTKTAEFPAGFMTEYRPSLLTTDATGQALAQGYPIGKRFKSALVERSCD
+TNVKHLGHLHRADGRWRVYVFADAASPRAEDSKVAAWAKAIEEDPRSFRNRHTPSDGPED
+ARFDIKVVYQQKQTEFAHPDVPSVFRPTTGSLGLHDLNNIFATCRPTHGEDIFEARGISR
+DGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000050.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000050.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d9fde6577c5de84200766d1cdad291824c45b242
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000050.fa
@@ -0,0 +1,62 @@
+>0_2028
+MSTDPRRQTPAPRGSDTGTPPLPEGRARWLVASNALDAGGRSATDVALDVLAVLLLGVGA
+DGMGVLMTLSGLGFLLLGVPLGIVVDRHLSPRLLAATGLAKAAVLGSLVAAWALDALTFG
+HLAAVMTLLGVLTVLAETTQTALVPRVVPATAVARLTARLESADAALVLIVPAAAGVLVG
+SLGAGPVLGIATAFLFAAAIVALRVRLRPSAAADVPDDDGDPGVADVLSRWARFGKDAAE
+GWTVLRRTPVLWLLTMGSVAANVGMALFAPVEAVWILTDLRLGPEFLGIQITAGAVGALT
+ASSLAGRAIDRLGERRCILLGSVGCAVAVGLHLLAYADRAHAGPWLLAGAALWGFMVLLG
+NITQAAVTARACPEGTLGRVTAMRRTLTRGSVPLATLAGGALGATLGVGWALAGWQVLAV
+VSLAAVVPAARWVDAGRDDVD
+>1_1744
+MSTDPRRQTPAPRGSDTGTPPLPEGRARWLVASNALDAGGRSATDVALDVLAVLLLGVGA
+DGMGVLMTLSGLGFLLLGVPLGIVVDRHLSPRLLAATGLAKAAVLGSLVAAWALDALTFG
+HLAAVMTLLGVLTVLAETTQTALVPRVVPATAVARLTARLESADAALVLIVPAAAGVLVG
+SLGAGPVLGIATAFLFAAAIVALRVRLRPSAAADVPDDDGDPGVADVLSRWARFGKDAAE
+GWTVLRRTPVLWLLTMGSVAANVGMALFAPVEAVWILTDLRLGPEFLGIQITAGAVGALT
+ASSLAGRAIDRLGERRCILLGSVGCAVAVGLHLLAYADRAHAGPWLLAGAALWGFMVLLG
+NITQAAVTARACPEGTLGRVTAMRRTLTRGSVPLATLAGGALGATLGVGWALAGWQVLAV
+VSLAAVVPAARHLGPRTAER
+>2_676
+MSTDPRRQTPAPRVPDTGTRPPPEGRARWLVASNALDAGGRSATDVALDVLAVLLLGVGA
+DGMGVLMTLSGLGFLLLGVPIGIVVDRHLSPRLLAATGLAKAAVLGSLVVAWALDALTFG
+HLAAVMALLGVLTVLAETTQTALVPRVVPATAVARLTARLESADAALVLIVPAAAGVLVG
+SLGAGPVLGIATSFLFAAAIVALRVRLRPSAAVDIPDDDGDPGVADVLSRWARFGKDAAE
+GWTVLRRAPVLWLLTMGSVAANVGMALFAPVEAVWILTDLRLGPEFLGVQITAGAVGALA
+ASSLAGRAIDRLGERRCILLGSVGCAVAVGLHLLAYADRAHAGPWLLAGAALWGFMVLLG
+NITQAAVTARACPEGTLGRVTAMRRTLTRGSVPLATLAGGALGATLGVGWALAGWQVLAV
+VSLAAVVPATRHLGPRTAER
+>2_1283
+MVSSPLTDDTTAPENAAPAKRLGRARWLVASNALDAGGRSATDVAIDVLAVLALGVGAAQ
+MGVLMTLSGLGFLLLGVPIGILVDRHLSPRLLVATDLAKAALLGTLVLAWALDALTFAHL
+AAVMALLGVLTVLAETTQATLVPRVVAPDTVSRLAARLESADAALGLIVPAAAGLLVAAL
+GAGPVLGIAAAFLAAAALVALKVRMNPAPVTEDTRDEETPAAAVVLTRWSRFWSEAAHGW
+TTLRRTPVLWLLTLNSMAGNIGMALFAPIEAVWVLTDLQLGPEFVGFQLTAGALGALTVS
+ALAPRAIDTLGEKGCILAGSAGCAAAVALHLAAFFDRAHAGPLLLAGAALWGFMVVLGNI
+TSGAIFARSCPEGTLGRVTAMRRTLTRGSVPLATLAGGALGAAFGPGWVLAGWQAMALLS
+LAFAFAATRLARRPQ
+>3_645
+MTRVSAWRSRDFRRLWGASTASALGGEIGELAMPVLALVWLGASAEELSWVRVATFLPYL
+VLPLWLGVLVDRWRRRPLMITAETVSGITLLGIAGAALAGWLTVPALVAAAAVLGAMSVL
+HMLADFSFTPQVVSRAALPDANAKMTATYSAIGIGGSGVGGALVQWLTAPFAVAINGAGR
+LLSVVLLRRIQTHEPPAEAPDTSARQQAREGFLALLRHRVVRALAAEATIWNLGNEVFML
+ALTVLIVDARDDGPLVLGLIFMAGGLGAFLGAGISARLTERFGYGRSLITAMLVGNTAPL
+IGVLFSSDTSVTSLVVLAAAFFASGFGTGIANSQAVTVRQVTVPEELRGRVNASYRMLSW
+GALAIGALLGGWLISAVGGWLAAALGTAAMAASTLPVALSPVRQMRDLDDGAPPAAE
+>3_2185
+MSSPLTDDTTAPENAARAKRLGHARWLVASNALDAGGRSATDVAIDVLAVLALGVGAAQM
+GVLMTLSGLGFLLLGVPIGILVDRHLSPRLLVATDLAKAALLGTLVLAWALDALTFAHLA
+AVMALLGVLTVLAETTQATLVPRVVAPDTVSRLAARLESADAALGLIVPAAAGLLVAALG
+AGPVLGIAAAFLATAALVALKVRINPAPVTEDTQDEETPAAAVVLTRWSRFWSEAAHGWT
+TLRRTPVLWLLTLNSMAGNIGMALFAPIEAVWVLTDLQLGPEFVGFQLTAGALGALTVST
+LAPRAIDTLGEKGCILAGAAGCAAAVALHLAAFFDRAHAGPLLLAGAALWGFMVVLGNIT
+SGAIFARSCPEGTLGRVTAMRRTLTRGSVPLATLAGGALGAAFGPGWVLAGWQAMALLSL
+AFAIAATRLARRPH
+>4_1968
+MSTDPRRQTPAPRTPDTGTPPPPEGRARWLVASNALDAGGRSASDVALDVLAVLLLGVGA
+DGMGVLMALSGLGFLLLGVPIGIVVDRHLSPRLLAATGLAKAAVLGSLVVAWALDALTFG
+HLAAVMALLGVLTVLAETTQTALVPRVVPATAVARLTARLESADAALVLIVPAAAGVLVG
+SLGAGPVLGTATAFLFAAAIVALRVRLRPSAAADVPDDDGDPGVADVLSRWARFGKDAAE
+GWTVLRRTPVLWLLTMGSVAANVGMALFAPVEAVWILTDLRLGPEFLGIQITAGAVGALT
+ASSLAGRAIDRLGERRCILLGSVGCAVAVGLHLLAYADRAHAGPWLLAGAALWGFMVLLG
+NITQAAVTARACPEGTLGRVTAMRRTLTRGSVPLATLAGGALGATLGVGWALAGWQVLAV
+VSLAAVVPAARWVDAGRDDVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000052.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000052.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a3bb4ddecc1150cccb6107ccfb9530e9c584f968
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000052.fa
@@ -0,0 +1,35 @@
+>0_2099
+MSSEETVPVRVALVDDQALIRSGLAMLVDSQPDLTVVAEAGSGREAVASVSVAGADVVLM
+DVRMPEMDGIEATRALLRRPDAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAPPEELLA
+AIRTVHRGDAVIAPSTTRRLLTHMAPRLRSDQVRSAECEEQQAAVASLTPREHEVLVLMA
+QGAANLEIAAELVLSEATVKTHVGRVLAKLGARDRVQAVLIAHRAGLVQF
+>1_1823
+MSSEETVPVRVALVDDQALIRSGLAMLVDSQPDLTVVAEAGSGREAVASVSVAGADVVLM
+DVRMPEMDGIEATRALLRRPDAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAPPEELLA
+AIRTVHRGDAVIAPSTTRRLLTHMAPRLRSDQVRSAECEEQQAAVASLTPREHEVLVLMA
+QGAANLEIAAELVLSEATVKTHVGRVLAKLGARDRVQAVLIAHRAGLVQF
+>2_571
+MTTRVLLVDDQPLIRLGFAAILQSQDDIEVVGEAGDGAECLERAAALDPDVICMDVQMPR
+MDGIEATRALAEAGTRAAVLILTTFDRDDFLFETLEAGASGFLLKSAEAEHLIDAVRVLG
+RGDALLDPQVTRRVLRRMASAAPEGVDGPAGVGQPRDDDGAAPGQAEASDAVGKAGLTGR
+EAEILTLMARGLSNGEIAGQLFVGESTVKTHVSNVLMKLGARDRVHAVIWAFEHGVAG
+>2_580
+MSTDAENAPVRVALVDDQALIRSGLAMLVDSQPDLTVVAEAGSGREAVASVSVAGADVVL
+MDVRMPEMDGIEATRTLLQRPDAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAPPEELL
+AAIRTVHRGDAVIAPSTTRRLMAHMAPRLRSDHARTAECEHEQAAVESLTPREREVLVLM
+AQGSANLEIAGELVLSEATVKTHVGRVLAKLGARDRVQAVLIAHRAGLVQF
+>2_2524
+MVLPDAGVRGGVRVRTSRTGVVGDIRLVEGAVSGDLDSADLLLGGVNSLGETRQVARQGR
+DVPPFLLVAEATIVEELSGIDASGAAAVLAYPLDTVELASVAHGIAGSGPFLSPRLPQLS
+VEPLGEGLSAREAEVVVALGEGLSDAEIAQALCVSVKTVHTHVLNLRRKLGARNRAHAVS
+LARSVGPLGDACSEPGLVAAL
+>3_503
+MSPDDAQPTPIRVALVDDQALIRSGLAMLIDSQPDLTVVAQASDGREAAASVAVAGADVV
+LMDVRMPEMDGIEATRALLRRPDAPRVVVLTTFDLDEHVMDAIEAGASGFLLKDAPPEEL
+LAAIRTVHGGDAVIAPSTTRRLLAHMAPRLRQDAARSAECADEQAAVGSLTPREREVLVL
+MGQGAANPEIAAQLVLSEATVKTHVGRVLAKLSARDRVQAVLIAHRTGLVGF
+>4_2044
+MSSEETAPVRVALVDDQALIRSGLAMLVDSQPDLTVVAEAGSGREAVASVSVAGADVVLM
+DVRMPEMDGIEATRALLRRPDAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAPPEELLA
+AIRTVHRGDAVIAPSTTRRLLTHMAPRLRSDQVRSAECEEQQAAVASLTPREREVLVLMA
+QGAANLEIAAELVLSEATVKTHVGRVLAKLGARDRVQAVLIAHRAGLVQF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000056.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000056.fa
new file mode 100644
index 0000000000000000000000000000000000000000..605505c34944fbfd1d10c98e546ac4b035fbb15c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000056.fa
@@ -0,0 +1,35 @@
+>0_22
+MERGPVVGLLDNLERGLERAVRSAFSAGGPRAVKPVEIASALRQAMDDESIALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRGGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGATAPAPDRLVEDPPAAAPREPSPAPRVGP
+RPAPRRAAAPAAPAAPSHADQPTVVMGRPVTEPAGPALELDGRMLPLDGDDLILGRSAER
+ADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRDGDVVTVGQTE
+LLFFGGTGGRA
+>1_1991
+MERGPVVGLLDNLERGLERVVRSAFSAGGPRAVKPVEIASALRQAMDDESLALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRAGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGASAAAPDRLVEDLPAAAPREPSPAPRVGP
+RPAPRRAAAPAAPAAPAAPAAPAHADQPTVVMGRPVTGPAGPALELDGRMLPLDGDDLIL
+GRSAERADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRDGDVV
+TVGQTELLFFGGTGGRA
+>2_354
+MERGPVVGLLDNLERGLERAVRSAFSAGGPRAVKPVEIASALRQAMDDESFALSEGHTVA
+PNSYVVHFSPADFDRARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDTDVRAGD
+LRVVTGLDDGSLPAPAPHDDGASPATAHGPGATATAPDRLVEDLLGGRTP
+>2_355
+MGRPVTEPSGPALELDGRMLPLDGDDLILGRSAERADLVIPDSSVSREHLRLLTVGSTVT
+LLDLGSRNGVLVNGRRVDGSVTLRDGDVVTVGQTELLFFSGTGGRA
+>3_338
+MGLLDNLERGLEKAVRSAFSAGGARAVQPVEIASALRHAMDDESFALSEGHTVAPNDFTV
+HFAPADFDRARTWGSTLAGELCDEVIRHAQSQGYTLPGSVRVAFHEDAQVHAGQVEVDAR
+IDDGSSPVPSPPAATSAPAPAAARTADDRGPRPSRAPRHGATAAPAPRRDPSPAPRPAPT
+PARSESARRAPADEQATVVMPRRTSPAPAVPWLEADGVRHPLTHEDMVLGRSSERADVVV
+PDSSVSRQHARLVRVGRSVTLIDLGSRNGVTVNGRRVDGSTVLREGDRITVGQTDLVFHI
+DPADGRPRA
+>4_22
+MERGPVVGLLDNLERGLERVVRSAFSAGGPRAVKPVEIASALRQAMDDESFALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRAGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGASAAAPDRLVEDLPAAAPRKPSPAPRVGP
+RPAPRRAAAPTAPAAPAHADQPTVVMGRPVAEPAGPALELDGRMLPLDGDDLILGRSAER
+ADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRDGDVVTVGQTE
+LLFFGGTGGRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000058.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000058.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ddfd4a020bd8f01c28a4d52f5bc8dd89603ec457
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000058.fa
@@ -0,0 +1,44 @@
+>0_45
+MQRIHDPQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHFGEDA
+TVWPMFNGTGANVVGLQAMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDGKL
+TPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPDEVKAITDYAHEHGMRVYMDGAR
+IANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAADGLVYLRKNQMQL
+ASKMRFVSAQLLALFDGDLYLRSARHANAMAARLRAGIEAGVADGSLAGVEFTQATDANA
+VFAVLPEGVADRLRARFRFYDWDAARREVRWVCGFDTTEEDVDAFTAALRAELVPAA
+>1_2009
+MQRIHDPQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHFGEDA
+TVWPMFNGTGANVVGLQAMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDGKL
+TPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPEEVKAITDYAHEHGMRVYMDGAR
+IANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAADGLVYLRKNQMQL
+ASKMRFVSAQLLALFDGDLYLRSARHANAMAARLRAGIEAGVADGSLAGVEFTQATDANA
+VFAVLPEGVADRLRTRFRFYDWDAARREVRWVCGFDTTEEDVDAFTAALRAELVPAA
+>2_339
+MQQIHDPASRGFASDNYSGVHPEVLAAIAEANGGHQTAYGEDAYTGRLAEVVRGHFGEDA
+QVWPMFNGTGANVVALQSMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLTVPTPDGKL
+TPELIDVQAWGWGDEHRAQPLVVAITQSTELGTLYTPEEIRAITEHAHARGMTVFLDGAR
+LANAAAALDLPLRAFTTDVGVDVLSLGGTKNGALGAEAVVALNPAATTGMTYLRKSQMQL
+ASKMRFVSAQLLALFDGDLYLRTARHANAMAQRLQDAVAAGIADGSLPGVALTQRAQVNA
+VFATLPAGVADRLRRSFRFYDWDEANGEVRWVCSFDTAEEDVDAFVAALRAELAPAD
+>2_1578
+MSAGAPAAGLRAFASDNYAGVHPDVWAALADVDAHHAPAYGADPHTERLQEAVREAFDAP
+DAVALPVFNGTGANVVALQSMLPPWGAVVAADTSHIHHDEGGAPERMGRTKLFTVPTPDG
+RLTPELVDREAHGWGFVHRAQPAVVEIAQVTELGTVYTPEQVRALADHAHGHGMGLYMDG
+ARLFNAAAALELPLSAFTTHAGVHVVSLGGTKAGALGAEAVVVLRPEAVTLASLVPERDL
+PADAGPRERARLAVEYVRKSSMQLASKMRYVSAQLTALLKGDLGIRLAGHANAMARELAG
+RVAGIDGVEVTRTPEANAVFAVLDPQAADRARVRHPFYDWDAARHEVRWMTSWDTTAADV
+DSFAAALGEALSPGRRR
+>3_1473
+MSAARPAGLRAFASDNYAGVHPDVWAAMADADADHAVSYGEDPTSAALQEKVREVFGERA
+FAVPVFTGTAANVLALQALTPPWGSVVTAASSHLIHDEGGAPERLGRTPLVPVPTPDGRL
+TGELAAAHVRRDGFVHASQPAVVEIAQATELGTVYSAAQVREVADAAHAAGAALYMDGAR
+LSNAAAALDLPLRAFTTDAGVDVVSYGGTKNGGLGAEAVIVLNPEAVVAARMVGPADVPG
+GDAADARDRARAALGYLRKQDMQLASKHRYLAAQLLALLTDDLGIALAAQANRMARVLAD
+AVAGLDDVELARAPEANAVFARLDPDVAAEVRLRHPFYDWDAAAHEVRWMTSWDTTDADV
+ESFVDALAAALRARRPR
+>4_40
+MQRIHDPQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHFGKDA
+TAWPMFNGTGANVVGLQTMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDGKL
+TPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPDEVKAITDYAHEHGMRVYMDGAR
+IANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAADGLVYLRKNQMQL
+ASKMRFISAQLLALFDGDLYLRSARHANAMAARLRAGIEAGVADGSLAGVEFTQATDANA
+VFAVLPEGVADRLRARFRFYDWDAARREVRWVCGFDTTEEDVDAFTAALRAELVPAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000060.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000060.fa
new file mode 100644
index 0000000000000000000000000000000000000000..203fa7d32c355ca05ead9c1d205cbbdf27383923
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000060.fa
@@ -0,0 +1,47 @@
+>0_59
+MTPEWWMALAALVLLALLVVVVVVLAVRQVRLGVQHERTRLLVDALDARVGGVQRRLEEV
+PGIGTGRHEVALVLNPIKTHADRVRRELERLAEAEGLGEVLVLETQEDDPGTAMARQALD
+AGARLVIAAGGDGTVRTVAEQLAGTDVALGVVPLGTGNLLARNLDLPINDVEQCLRIAVG
+GRQRRIDTVDVRFTHEDGRVTRQTFTVIGGAGYDADIMGDTKDELKSLAGWLAYSEAGMR
+HLRGKRHEVTVALDGGQPRRFKVRTVMVANCGMLTGGVELLPQAKLDDGLLDVMVLSPRH
+ALDWARIAVKTVTRHRSSVPAMHTEQAQRVKVEFAEPMPSQLDGDATGVITALDARVQPD
+SLVVMLVAEDDASVRDDGVSAAAPVPEPAPHI
+>1_2023
+MTPEWWMALAALVLLALLVVVVVVLAARQVRLGVQHKRMRLRVDALDARVGGVQRRLEKV
+PGIGTGRHEVALVLNPIKTNAGQVRRELERLAEAEGLGEVLVLETQEDDPGTAMARQALG
+AGARLVIAAGGDGTVRTVAEQLAGTDVALGVVPLGTGNLLARNLDLPINDVEQCLRIAVG
+GRQRRIDTVDVRFTHEDGRVTRQTFTVIGGAGYDADIMGDTKDELKDLAGWLAYSEAGIR
+HLRGKRHEVTVALDGGQPRRFKVRTVMVANCGMLTGGVELLPQAKLDDGLLDVMVLSPRH
+ALDWARIAVKTVTRHRSSVPAMHTEQAQRVKVEFAEPMPSQLDGDATGVITALDARVRPD
+SLVVMLVAEDDASVRDDGVSAAAPVPEPAPHI
+>2_191
+MTPGSPDDDGAPAVRRRVLVLLNPHAGRRRSLARAQARLRTHPGLALDLVVPDPADHAAQ
+LAAGRTALADGVDAVVVRGGDGMVAAGVGLVGDHAEATGRRVPLGIVPAGTGNDLARAAG
+LHRRDPGAALEAVLRALEDPAAPVRRIDALRLTVTRAGAVVERRWAANSVNIGFDARVNA
+RANALGAVPGPLRYLAALGLEARAFAAVEMGLGLDDGPVRRERVALVSVQNGPTIGGGIP
+LAPGARLDDGRAEATVVGPLPTAGLALLFPLVYVRAHRLLRPLCTERARRVRVAVPDGVP
+VYADGDEVLPASHGGAAVEVEAVPGAVALLG
+>2_317
+MALVALVLGAVLAVAVIVLAVRHRGLAERHERTRGQLDAVEHRLDAAQRRLGELPGVDRP
+RQEIALVLNPVKARADEVRRTLEAMADREGLGSVLVLETEEDDPGTQMAKDALEAGVRLV
+IAAGGDGTVRTVAEQLTGTDVALGVVPLGTGNLLARNLDLPINDIEECLRIALTGRQRRI
+DTVDVRFTHEEGEVTRQTFTVIGGAGYDADIMADTKDELKDVAGWLAYSEAGMRHLRGKR
+HDVSISLDGGASRRFKVRTVMVANCGMLTGGVELLPEAKLDDGLLDVLVLSPRHALDWAR
+IAAKTVTRHGANIPVMHTEQAQRVKVEFADPMPSQLDGDATGHIVALDARVQPDSLVVML
+LDEKEASVHDDGRSEAAPVPEPAPHI
+>3_259
+MALAALVLAALFAVAVVVLGLRLRRLDGAHERTRGQLDAVEARLGDLRRRAGRAPGVDLP
+GPQVALVLNPVKARADEVRRAMEALAEKEGLGEVLVLETTEEDPGTAMTREALTAGVRLV
+VAAGGDGTVRTVAEQLAGTDVALGVMPLGTGNLLARNLDLPINDIEECLRIALTGRQRRI
+DTVDVRLTHEDGARTRQTFTVIGGAGYDADIMGDTKDELKDMAGWLAYSEAGMRHLRGRR
+HEVSITLDGGAVQRFKVRSVMVANCGMLTGGMELLPEAKLDDGLLDVLVLSPRHALDWVR
+IAAKTLTRHRASIPVMHTEQAQRVQVRFAEPMSSQLDGDATGDITALDARIQPDSLVVML
+GDEDDASVEDGGRSAEAPVPEPAPHI
+>4_54
+MALAALVLLAVLAVVVVVLAVRQVRLGVQHQRTRLLVDALDARVGGVQRRLEEVPGIGTG
+RHEVALVLNPIKTHADRVRRELERLAAAEGLGEVLVLETQEDDPGTAMARQALDAGARLV
+IAAGGDGTVRTVAEQLAGTDVALGVVPLGTGNLLARNLDLPINDVEQCLRIAVGGRQRRI
+DTVDVRFTHEDGRVTRQTFTVIGGAGYDADIMGDTKDELKDLAGWLAYSEAGIRHLRGKR
+HEVTVALDGGQPRRFKVRTVMVANCGMLTGGVELLPQAKLDDGLLDVMVLSPRHALDWAR
+IAVKTVTRSRSSIPVMHTEQAQRVKVEFAEPMPSQLDGDATGVITALDARVQPDSLVVML
+VAEDDASVRDDGVSAAAPVPQPAPRI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000061.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000061.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e51b48626feabfe4679fbc601ceccf5e2a61e1af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000061.fa
@@ -0,0 +1,29 @@
+>0_64
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+YLPGFDLVPGCVVEARPIGVFNMTDDGGGDAKLLCVPADKRYDHITELEHVEESLKQEIE
+HFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFDAEGEESPTDEPQGRAVDTEEAQ
+PATEEGEATDEPQGR
+>1_2028
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+YLPGFDLVPGCVVEARPVGVFNMTDDGGGDAKLLCVPADKRYDHITELEHVEESLKQEIE
+HFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFNAEGEESPTDEPQGRAVDTEEAQ
+PATEEGEATDEPQGR
+>2_311
+MPHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDAMV
+LLPGFDLVPGCVVEARPVGVFNMTDDGGGDAKLLCVPADKRFDHITELEHIEESLKQEIE
+HFFTRYKDLEPGKWVKAEGWQGRADAEAELEASIARFDAAGEHSPTDEPQGRDVETEDPS
+PATEEGEEKDVPQGR
+>3_252
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+FLPGFDLVPGCIVEARPVGVFNMTDDGGGDAKLLCVPADKRFDHIQELEDVEESLKQEIE
+HFFTRYKDLEPGKWVKADGWEGREAAEKELEASIERFAAEGEHSPSDEPQGRDVDTEEAA
+PAAEQEA
+>3_667
+MLFDVTIEIPRGSGNKYEVDHTTGRIRLDRAVFTSMVFPQDYGSIDNTLGDDGDPLDALV
+LLPRPTFPGVVITVRPVGMLRMVDENGGDDKILTVPAGDDRFAQLRDITDVPEHTLAEIE
+HFFAHYKEIEHGKHVTTNGWADRAAAEAVIRTAQNAHTRHP
+>4_58
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+YLPGFDLVPGCVVEARPIGVFNMTDDGGGDAKLLCVPADKRYDHITELEHVEESLKQEIE
+HFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFDAQGEESPTDEPQGRDVDTEEAQ
+PATEEGEPQGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000067.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000067.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8eee2c9a717c4716ba68583b06684b004185f7e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000067.fa
@@ -0,0 +1,53 @@
+>0_199
+MSTAENAGAGAPTRPDEHRAILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTHLAQ
+TLEKGLFDGLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVT
+AGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQMEHDERYEHADEY
+LDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAHEGRYFTVPGHAVTEPSVQRTPVI
+YQAGASTRGRAFAGKHAEAVFINSPTKELAAATVKKIRQALVDAGRDPYDVKIFAMQTIV
+TGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDVKSNAIQSAVETF
+QKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPG
+AFEDVVEFVVPALQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFALRRR
+>1_2143
+MSTAENAGAGAPTRPDEHRAILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTHLAQ
+TLEKGLFDGLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVT
+AGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQMEHDERYEHADEY
+LDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAHEGRYFTVPGHAVTEPSVQRTPVI
+YQAGASTRGRAFAGKHAEAVFINSPTKELAAATVKKIRQALVDAGRDPYDVKIFAMQTIV
+TGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDVKSNAIQSTVETF
+QKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPG
+TFEDIVEFVVPELQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFALRRR
+>2_174
+MAEHPAARPEQDATTSTSAATSTSPASRAGRELLFNAFDMNCVAHQSPGLWRHPEDRARD
+YNTLGYWTHLAQTLEKGLFDGLFIADVLGPYSVYGGTAEAAIRSGAQTPVNDPFLLVSAM
+AAVTGHLGFGVTAGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQM
+EHDERYEHADEYLDVVYKLLEGSWEDDAVRYDKETGVFADPAKVHDIGHEGRYFKVPGAA
+VTEPSPQRTPVIYQAGASTRGRAFAGKHAEAVFINSPTKELTAATVKKIRQALVDAGRDP
+YDVKIFAMQTIVTGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDV
+KSNAIQSAVEAFQKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDV
+DGYNLAYHITPGTFEDVVEFVVPELQKLGRYKTAYTDGTLRHKLFGRGDHLPEGHHGASF
+ALRRRG
+>3_120
+MSTAENAGAGAPTRPDEHREILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTRLAQ
+TLEKGLFDGLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVT
+AGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQMEHDERYEHADEY
+LDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAHEGTWFKVPGHAVTEPSVQRTPVI
+YQAGASTRGRAFAGKHAEAVFINSPTKELAAATVKKIRQALVDAGRDPYDVKIFAMQTIV
+TGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDVKSNAIQSAVETF
+QKASGTDEGWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPG
+TFEDIVEFVVPELQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFAFRNRRG
+>3_122
+MSTPTPTLGIALTTQTPADARGHWTRLSQALEETSLDWAVLTDPLGTAPQAGTHRIDAVL
+AACWTATRTHRIGLVPEVTTTHTEPFHVSIGLATLDHVSHGRAGWLATVSAAPEVSALFG
+RRRHPAERTPGLQASRVDLELWEELQDAVAAVRDLWESWEPDAEIRDIATGRFIDRERVH
+HVDVEAERFSVRGPSITPRPPQGRLPVLVEAAGPAGLEAARRTADVVLLPAAEVGRTDAA
+RLPDRRRRGATPAVPVEPTRIVADVTLEGDGARVADAVRHALQAGADGARLVPNPTADPF
+DALALAADVHDRLDDIRPPDTGTVPLRECLGLAPALSPWRHPEDPTARPTDEEATA
+>4_199
+MSTAENAGAGAPTRPDEHRAILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTHLAQ
+TLEKGLFDGLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVT
+AGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQMEHDERYEHADEY
+LDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAHEGRYFTVPGHAVTEPSVQRTPVI
+YQAGASTRGRAFAGKHAEAVFINSPTKELAAATVKKIRQALVDAGRDPYDVKIFAMQTIV
+TGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDVKSNAIQSAVETF
+QKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPG
+AFEDVVEFVVPALQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFALRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000068.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000068.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad5512ea98f0ac321faa72af0103deabea527009
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000068.fa
@@ -0,0 +1,17 @@
+>0_208
+MENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIEDLF
+TPDGNAG
+>1_2152
+MENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIEDLF
+TPDGNAG
+>2_157
+MENSLPAERARLGWSQQRLADELGVSRQTVISLEKGRHDPSLALAFRLAETFGTRIEDLF
+SPDPPA
+>2_2156
+MSIDRLAEAAAIHRRTIIQIEAGRTAPRVTTLYAIAEATGTPLRDLLAPLDEALERGTR
+>3_307
+MARLARAFKVHKANSGMTYDQLAEATGLARQTLLNLAAGRTYGDLRTWLILAKVWGVTLD
+DLTAAAWRGHAGG
+>4_208
+MENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIEDLF
+TPDGNAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000073.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000073.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a96398d738de3cb0f0f9a9983689aa71d7b45f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000073.fa
@@ -0,0 +1,31 @@
+>0_249
+MSEELRILIADDQPLMSGALRVLVDSAPGMTCVGVVANGVEAVEACAAIEPDVVLMDMQM
+PLMDGMEATRRIKDTHPAIRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQA
+VHRGESVLSPAVATKLLASIERDRPTVGPTSVQPGSPDGSDLTERELGVLRLLARGQSNP
+EIAANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD
+>1_2214
+MSEELRILIADDQPLMSGALRVLVASAPGMTCVGVVANGVEAVEACAAVEPDVVLMDMQM
+PLMDGVEATRRIKEAHPEVRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQA
+VHRGESVLSPAVATKLLASIERDRPTVGPTSVQPGSPDGSDLTERELGVLRLLARGQSNP
+EIAANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD
+>2_102
+MHDAGHTDYSAAHIARTADGTAASGAVSAGPGGRRPGPTTPADAGRSRGSRYADRVSEDL
+RILIADDQPLMSGALRVLVSSAPGMTCVGVVANGAEAVEACAAVEPDVVLMDMQMPLMDG
+VEATSRIKEAHPGIRILAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIHAVHRGE
+SVLSPAVASKLLASIERDHPVVGPAQARPGDPDGSDLTDRERDVLRLLARGQSNPEIAAN
+LHVSESTIKSNLTRIMDKLEVRDRVQVIIRAAQLGLVTLSLD
+>3_70
+MPDSPEDEIRVLIADDQPLMSGALRVLVDSAPGMRCVGLVADGVEAVEAVEATRVDVVLM
+DMQMPRMDGVEATRRITASRPGTRVLAVTTFSSEDYLVPALRAGAAGYLLKDAEPATVLG
+AVEAVRRGESVLSPAVAAKLIAAVERDHPVVGPAAAEPGDPDGSDLTEREHQVLTLLARG
+RSNPEIAAELQVSESTVKANVGRVIDKLEVRDRVQVVIRAAQLGLVTLSLD
+>3_509
+MDAITVLIVEDEPLLTQAYTMILEADPGIRVVGTASDGAAGVAEHERLRPDVVLMDLRMP
+VLDGVEATGRIMREHPEAKVLVVTSMTTEDYLSPALANGAAGYLTKDTDAEGLVRAVRAV
+EAGTMALGPSIAREVVDLLLRSGVAPRTDAPASPRDLPEALTPREQDVLELLAEGLTNQE
+MAARLYVSDSTVKSNLARVMHKLGANNRVQALVLGVRAGLVSIPG
+>4_248
+MSEELRILIADDQPLMSGALRVLVDSAPGMTCVGVVANGVEAVEACAAIEPDVVLMDMQM
+PLMDGVEATRRIKDTHPAIRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQA
+VHRGESVLSPAVATKLLASIERDRPTVGPTSVQPGSPDGSDLTERELGVLRLLARGQSNP
+EIAANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000075.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000075.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6fb827975ac604dd12a7f7400ee2313433a90d65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000075.fa
@@ -0,0 +1,30 @@
+>0_273
+MTGGDPAALMDALGAWFHPLTALLVALDAPIPPVPSEVVVIGSGALAAEGRVSPVAAVLA
+AWLGCWAGDVGLYALFRHGLADRLDRWAWWRRIHRGIRSLLVRVGPAGSLAGLSVLRFVS
+GGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSSSMVGLGWITGRATGLPWWASAMVGMVF
+GTLAGLMIAGIMAHRRRGRKG
+>1_2239
+MTGGDPAALMDALGAWFHPLTALLVALDAPIPPVPSEVVVIGSGALAAEGRVSPVAAVLA
+AWLGCWAGDVGLYALFRHGLADRLDRWAWWRRIHRGIRTLLVRVGPAGSLAGLSVLRFVS
+GGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSGSMVGLGWLTGRATGLPWWASAVVGMVF
+GTLAGLMIAGIMAHRRRGRKG
+>2_62
+MTVLTPAWFAASGGVPTMGAGAAAASGAGAWDPSALLDSLGAWFHPLTALLVALDAPIPP
+VPSEVFVIGSGALAAEGRVGLAAAVLTAWLGCWAGDVGLYALFRHGLADRLDRWAWWRRV
+HRGIRVLLVRVGPAGSLAGLSVLRFVSGGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSG
+WMVGLGWLTGRTTGLPWWASAVVGMVFGTLAGLIIAGVVARRRARKG
+>3_48
+MTDVTALLEGLGPWFHPLTFLLVALDAPVPPTPSEVLVIGSGSLAAAGRLGLATSVLTAW
+LGCWAGDVGLYALFRHRLTSVLDRWGWGRAVHAGIRRLMEKAGPASSLAGLFVLRFVSGG
+RTASMAAAGVAGVRWRPFLWLSGTGSLAWSVYMVGLGWITGSATGLPWWASAVVGVVLGT
+LLGAAVAAVIAWRRRGKEGA
+>3_433
+MPVLTNILDAASILHSLGPWTLGGIGSMVFIESGVLFPFLPGDSLLVTAAALHVELGIAL
+WAIILVAGLAAILGDQVGFYLGHRYGRRLFKDDARVLKTERLAQAEAFFERRGPLALVLG
+RFVPIVRTYVPVAAGTAGMPYRSFVGWNIGGAVAWVCSMVAVGALLGQIPGITKSIDGIM
+ILIIVISVAPIAIQALRARRKARRDAVMTEGQPVA
+>4_272
+MTGGDPAALMDALGVWFHPLTALLVALDAPIPPVPSEVVVIGSGALAAEGRVSPVAAVLA
+AWLGCWAGDVGLYALFRHGLADRLDRWAWWRRIHRGIRSLLVRVGPAGSLAGLSVLRFVS
+GGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSGSMVGLGWITGRATGLPWWASAVVGMVF
+GTLAGLMIAGIMAHRRRGRKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000078.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000078.fa
new file mode 100644
index 0000000000000000000000000000000000000000..94cc218094840a385aa519cf3ac2d1d45780917a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000078.fa
@@ -0,0 +1,43 @@
+>0_297
+MDVPAQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQREGRYPPP
+RGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCALLAGGGFAEYVAVPAGQLMAVP
+DGVGLVEAAALPEVACTVHSTLVGRAGVQAGDRVLVHGATGGIGSFAVQFLTAVGARVLG
+TAGGPEKVALGRGLGAEHMFDHRAAESGAFAPWVKEVTDGHGADVILDVVGAPYLAPNVS
+ALAPEGRIVTLAVQGGAVPEDFNIMKLVVKRGWLTGATLRSRSVTDKAGIVAAAERAVWP
+LVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLVTDPADARRPSGDRA
+>1_21
+MDVPAQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQREGRYPPP
+RGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCALLAGGGFAEYVAVPTGQLMAVP
+DGVGLVEAAALPEVACTVHSALVGRAGVQAGDRVLVHGATGGIGSFAVQFLAALGARVLG
+TAGGPEKVALGRRLGTEHMFDHRAAESGAFAPWVKEVTDGHGADVILDVVGAPYLAPNVS
+ALAPEGRIVTLAVQGGAVPEDFNIMKLVVKRGWLTGATLRSRSVVDKAGIVAAAERAVWP
+LVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLVTDPADARRPSGDRA
+>2_22
+MSETTRTPGTGRGTMRAVRFTGEGGAGSLAVGQEPIPTPGPGEVLVKVAAAGLNRADVMQ
+REGKYPPPPGASDVPGLEVSGVVVALGEEAGLPGEGRFAPGDEVCALLAGGGYAEHVVVP
+AGQLMAVPPGVDLVTAAALPEVACTVWSTMSERGGVRAGDVVLVHGGSGGIGTFAVQYLA
+AIGARVLATAGGPAKCERVRGLGAEDVFDHRSGEPGAFADWVLERTGGRGADVVLDVVGG
+PYLDANVRCLAEEGRIVVIAVQGGPKADGFNLMRLVSKRGWLTGATLRARSVVDKARIVA
+GTERAVAPLVAAGRIDLAVGARFPLDDAAAAHRRFEAEDRVGRVLLVTDPADALWPQEDR
+T
+>3_18
+MDTAPDMLAVRFAGAGGTDVIRVGREPVPEPGPGEVLVRVAAAGLNRADVVQREGHYPVP
+PGASEVPGLEVSGTVVALGPQAGVAGEGRFAVGDRVCALLAGGGYAEHVAVPAGQLMSVP
+DGLDLVSAAGLPEVACTVHSNLEGRAGVRPGEWALVHGATGGIGAFAVQYLSAVGVRVLA
+TAGGPAKVARALELGADAAFDHRAAAPGAFADWVREITGGHGADVVLDVVGGPYLAPNVK
+ALAMDGRIVVIAAQDGPVPEDFHLMRLAARRGWVTGSLLRPRPPDEKAGIVAAAERAVWP
+LVAAGRIDPGVTARFPLREAAAAHAHFEGAARMGKVLLVTDDADALLPGGAA
+>3_637
+MHPSLPRTMLAAIIPAPGGRPELRQCPVPEPGPGEVLVRVMASSVNPTDVMTWRRGMFVT
+GQTVPFVGGYDMSGIVVKLGRGVTALDVGDAVTGMPRFPAPAAAFAQYSAVPARHLARIP
+TGTEDLSAGAWGRWAGLPLAGLTAYQALVDTAHLQSGQTVLVHAASGGVGSLACQLAVNL
+GAQVTAVTSDRGRTLVEVLGTRHVVDRATVDWQRFAGCFDVVLDTVGGDTTPRSLAMASP
+DGVVVALHPYAHDDLAQRDPRLRRMLVEPDHHALELLIEQAARGRLTVQVGAGYPLSDLG
+DALLHVETNKTPGKTIIHIQGDNA
+>4_304
+MDVPAQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQREGRYPPP
+RGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCALLAGGGFAEYVAVPAGQLMAVP
+DGVGLVEAAALPEVACTVHSALVGRAGVQAGDRVLVHGATGGIGSFAVQFLAALGARVLG
+TAGGPEKVALGRRLGAEHMFDHRAAESGAFAPWVKEVTDGHGADVILDVVGAPYLAPNVS
+ALAPEGRIVTLAVQGGAVPEDFNIMKLVVKRGWLTGATLRSRSVVDKAGIVAAAERAVWP
+LVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLVTDPADARRPSGDRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000084.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000084.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85668a158293de60c4d3080027b5f286bc180f2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000084.fa
@@ -0,0 +1,54 @@
+>0_397
+MPESTLYWIIAAIIVVLLILIILSVIASRRRREAEAEAAETRLERRGTTADTADTAGEQA
+AAPAAPTRLSRLDEVAAEQDARPAAAVKPAGGPAASETAAAGRETDESVAGVAGGAGVTV
+DQQDAPRTDATAETSRPTAAPTTRGTLRPAAAAPSTAREADTVGLGAAGVAGGSGITLDE
+QTPAADVAAAPASPSPVTETPAPAAPAAEAPQHRSHLTPAPEHVHGTVPAEEVAAEHTPT
+KEFATDAIPVAQGEHLETNTVATTAHGSVTVVAAESDQTQQNDADGAERSAAGSLRIDGT
+PGVPGRVAEAGREPARTEDHRADAAQPAAVEPAAERPSLEAAAERPSLEATPATRRAEAP
+ETHAGTTPATPLGGAPELDPTAASSGRAEDATPATRREARAAQSAAAAGTAATAGTAGTA
+APTSSTPTTVAPDTSTSSAPTNEEPAEDDTEGAALPDLRADRDETRGSDAEGESKLAQAG
+AVAASAFETVRDKVAIPLRDNVAVPAKDKAVKVVKDKLAQAQERRWGKR
+>1_127
+MPQSTLYWIIAAIIVVLLILIIVSVIASRRRREAEAEAAETRLERRGVSADTAGEQAAAP
+AAPTRLSRLDEVAAEKDARPAPAVRPAGGLAAFDTAAADRETDESGAGVAGGAGVTVDQQ
+DAPSTEATAQTHRRDAAAPATRGTLRPAPAVPSTVREADTVGLGAAGVAGGSGVTLDEQT
+PAADVPATPASPSPVTETPAPAAPVAEAPQQRSHLTPAPEHVHGTVPADEVAAEHTPTKE
+FATDGIPVPQGEHLETHTVATTAHGSVTVVATESDQAQQTGVDGTERSAAGSLRIDGTPG
+VPGRVAEADREPARTDDHGADVAQPAAVEPAAERPPLEAAPATRRAEAPETHAGTTPATP
+LGGAPELDPTAASSGRAEDATPATRREARAAQSAAAAGTAGTAAPTSSTPTTVAPDTSTS
+SAPTDEEPAEDDTEGAALPDLRADRDETRASDAEGESKLAQAGAVAASAFETVRDKVAVP
+LRDNVAVPAKDKVVKVVKDKLSQAQERRWGKR
+>2_2485
+MPTDAEPAADDTEGAALPVQDATRADAVRPGTARTDASAGDSKLAQAGAAAGTVLETVRD
+KVAIPLRDNVAIPAKDKAVKVLKAKLAEAQERRRNKR
+>2_2486
+MGESTLYWIIGAIIVVLLILIILSVVASRRRRAAEAEAAEAQLERRRVTPTAAGVGASHE
+DALEETHDADARPHTVASTGGDVAPAAAAGAAAGTTRLSQLDDVAPVAAAAADADAESLP
+ADGVAAGSGVTVDQQDASDQSVRPAAPAAPAGADTRGPNASVKSAGAAAAAVGLGAAGVA
+GGRGVTVDQQDAAADVPSTPASPSPVAQTPAAPSSAGATTAQDDRADRTAQDAADAEPVK
+GTVPLSEDAHAVPPAADPPSGGDAVADDAHLEAHTVATTEHGSVVVVTAEQDEDDQATAA
+SRETETETDDSRGDDAGQDRDAERAVAEGVAGGTGVTVDQKAVAEAAATQGAPASAAGAA
+SAAGAAARRRDRGRRLDPACGGARLLQDRRHAGHARPRRLRGAGRGRGGDRPARPPRRRP
+GDARLHHPRDAPGRRAGAGPGRRRRGLPQGRGRDPAAPPRGRRPGAKPRRRPTSTRPRPR
+PPRRTAPAR
+>3_2354
+MPQSTLYWIIGIIIVVLVIILIVSSLRAKRGREEEAAAAGRHADSAPAPLAATAARGGTV
+GASTVPATGDAPADRTDGRAAGATALPSFDVDEVDRRAAEQREQDVVERRRATGAEAGAA
+GHAAVPGVTGGSGVSVDEAEGVAKDATGQDVTPVADAQRRNGSSAAPAATGAGLGLAAAG
+VAGGTGVTVDDAGTGADLPAPKGSPAGVVEVAETQAEAAQADAAPAEHTVVPGVAGGDAV
+TVDTADVQSSSAPQGAQAAAGRSDLTDAEARTYPVTGLPGVPSAVDPEQVAAARVQDAAE
+LKAAEGQGAEHERGASQPADPESVPGTVPLTGEEAVIEAPVHTHEMPEPVLGTPAYIQDS
+TTGQDPTEDLPEGQVYGTTPLSGEDAIVEPADQLPAEAAETEDRAASDAGTASAETAVVP
+VEETETAVVPVAETRSADAGPSEDSVALTGQGVETADRVEPAAPVAGTPARDEARTHDEH
+RSRLEIVKDAVAETAGTVATTAGTAAEKAAPVVRSAARTVGKAAGSAASTLKDKLAQAQE
+RRWGKR
+>4_400
+MPESTLYWIIAAIIVVLLILIILSVIASRRRREAEAEAAETRLERRGTTADTADTAGEQA
+AAPAAPTRLSRLDEVAAEQDARPAAAVKPAGGPAASETAAAGRETDESVAGVAGGAGVTV
+DQQDAPRTDATAETSRPTAAPTTRGTLRPAAAAPSTAREADTVGLGAAGVAGGSGITLDE
+QTPAADVAAAPASPSPVTETPAPAAPAAEAPQHRSHLTPAPEHVHGTVPAEEVAAEHTPT
+KEFATDAIPVAQGEHLETNTVATTAHGSVTVVAAESDQTRQNDADGAERSAAGSLRIDGT
+PGVPGRVAEAGREPARTEDHRADAAQPAAVEPAAERPSLEAAAERPSLEATPATRRAEAP
+ETHAGTTPATPLGGAPELDPTAASSGRAEDATPATRREARAAQSAAAAGTAATAGTAGTA
+APTSSTPTTVAPDTSTSSAPTNEEPAEDDTEGAALPDLRADRDETRGSDAEGESKLAQAG
+AVAASAFETVRDKVAIPLRDNVAVPAKDKAVKVVKDKLAQAQERRWGKR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000091.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000091.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21824ece44c6169e2e27e4268807ee17412ef8b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000091.fa
@@ -0,0 +1,32 @@
+>0_524
+MHPDDAPTPDLTWLDSAGSTQDELLARLDREGHRHGAAVATADQRAGRGRHSRVWSAAPG
+AALALSVYLRPESGGVPVSPAHLSWLSLVASATVAERLAARGVPTHVKWPNDVLATDGRK
+LCGVLATVALSSDGKGPGVVVGMGVNLDHRGAAPVDTATDLAEWIGADAVPAPRDLAVEL
+RDAVVAAVDRFAAGVAGQAAAVDGRHPAVAAVADRLSTLGRAVRAELPGGGVLEGTAVGL
+GPGGTLRVKRVTPDRGTIETEVSAGDVAHLRGDVHRGA
+>1_258
+MHPDDAPTPDLTWLDSAGSTQDELLARLDREGHRHGAAVATADQRAGRGRHSRVWSAAPG
+AALALSVYLRPESGGVPVSPAHLSWLSLVASATVAERLAARGVPTHVKWPNDVLATDGRK
+LCGVLATVALSSDGKGPGVVVGMGVNLDHRGAAPVDTATDLAEWIGADAVPAPRDLAVEL
+RDAVVAAVDRFAAGVAGQTAAVDGHHPAVAAVADRLSTLGRAVRAELPGGGVLEGTAVGL
+GPGGTLRMRHVTPDRGTIETEVSAGDVAHLRGDVHRGA
+>2_2346
+MGVNLDHRGAAPVATATDLAEQIGAEAVPAPRGLAAALRDAVVGAADRFAAAVAGEAEAV
+DGRHPAVAAVTQRLSTLGREVRAELPGGDVLEGTAVALGPGGALRVSHVTADRGRIETEV
+SAGDVAHLRGDVHRGA
+>2_2347
+MHAPHDPAAPGLVWLDSAGSTQDEVLARVGREGPRHGLAVATADQRAGRGRHSRVWSAAP
+GAALALSVHLRPAAGGTPLAPVHLSWLSLVASAAVVEHLAGLGAAAHLKWPNDVLAPDGR
+KLCGVLATVAPAADGGGPGWSWAWG
+>3_2230
+MGYTWGMGTLLWLDAADSTQDELLRRLAAADGAARPGHGDGVGTADQRAGRGRHGRAWQA
+PPGAALALSVHLRPTGPSGPLAPAHLSWLSLVASAAVARRLVGLGVPAHLKWPNDVLDAE
+GRKLCGVLATLAPAPVFPGADAGETPGVVVGMGVNVDLSSGRPVPTAAALTDHLPGAEVP
+APRDLAQALLRDVAAAADRLARDLDGVVEPVDGTHPALAEVAAVLSTPGRRIRAELPGGE
+VLEGVATGLGAGGVLAVRVVTGERETITREISAGDVVHLRGDVRRGG
+>4_527
+MHPDDAPTPDLTWLDSAGSTQDELLARLDREGHRHGAAVATADQRAGRGRHSRVWSAAPG
+AALALSVYLRPESGGVPVSPAHLSWLSLVASATVAERLAARGVLTHVKWPNDVLATDGRK
+LCGVLATVALSSDGKGPGVVVGMGVNLDHRGAAPVDTASDLAEWIGADAVPAPRDLAVEL
+RDAVVAAVDRFAAGVAGQTAAVDGRHPAVAAVADRLSTLGRAVRAELPGGGVLEGTAVGL
+GPGGTLRVKHVTPDRGTIETEVSAGDVAHLRGDVHRGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000095.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000095.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0fd6e069b3e083d61fcb29a135a92417d92614d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000095.fa
@@ -0,0 +1,42 @@
+>0_586
+MTSTDPTPAKAASAPNRQRRAKIIVWVVLAALVLAGVVAFFAARAPSTPEAAPAQAGQAA
+SSGTGQTAASEAAPVVRPDSRVLSQAPNEKAVLVEFLDFECEGCKAAHPVVEELRAEYAD
+TVTFVHRYFPLPGHPNSMTAAVAVEAAAQQGAYEAMYQKMFDTQEQWSHTGQDRSPVFRG
+YAEDLGLDMTAYDKAVADPATRARIEADVADGVALGVQGTPTFFLDGQVLTLNTLEQFRA
+EVDAAASN
+>1_311
+MSTPTRNPTPSDPSTPGTTSRKAKTIVWVVLAAVVLAGLIVGVVAASGPRDAAPQGSGQT
+ASSGTGQSAPSEATPVMRPDSRVLSKAPNEQAVLVEFLDFECEGCKAAYPVVEELRAEYA
+DTVTFVHRYFPLPGHPNSMTAAVAVEAAGQQGQYEAMYQQMFDTQEQWSHTTEDRSPVFR
+GYAEDLGLDMAAYDAAVADPATRDRIEADVADGTALGVQGTPTFFLDGQMLTLNTLEQFR
+AEVDAAATTD
+>1_1721
+MTSPDPTASTPSSPTPSRQRRAKIVVWVLLGLVVAAALIGYLVARGTATAQQQDPNQSTA
+QSTGQSTGSAGQLVRENSRVLSQAPNEKAVLVEFLDFECEACAAAYPFVEDLRAEYADTV
+TFVHRYFPLPGHPNSVTAAIAVEAAAQQGAYESMYQKMFETQTEWSHTTEDRSPVFRAYA
+EELGLDMAAYDAAVADPATRDRVELDVADGTALGVAGTPTFYLDGEPLTVNSLEEFTAAV
+EAATQD
+>2_2293
+MSTPTRNPTPANSSTSGTTSRKAKTIVWVVLAAVVVAGVIAGVVAVGAARNATPDAAATQ
+AGQSAAQGSGPTTAEEAGELVVRPNSRVLSKAPNEQAVLVEFLDFECEGCGAAYPVVEEL
+RAEYADTVTFVTRYFPLPGHRNAMPAAVAVEAAAQQGEYEAMYQRMFETQAQWGEATEDK
+SPVFRGYAEELGLDMAAYDKAVADPATRARVEADVADGIALGVQGTPTFFLDGEMLTLTS
+LEQFRAEVDAAASN
+>3_1166
+MSWRTIRTEAGSAVLLVVVTAVALLWANSPLSEAYFGLWDVEIGFDVGGFGLHMNLHHWI
+NDGLMMTFFLVVGLEVRQEFAHGTLRDASRARLALIAGVVGVALPAVFYILIVAAAGGEG
+LGGWGAVVGTDTAFLLGALALVGPKLSGQLRVFLLTLTVVDDFLAVSIIGIVYSDEIRLV
+PLLIAGACLVGLWLLGRSRQWSATPYVLIVIVLWFATVESGVHASLAGMVAGLLIPAYPT
+RRQQVVEARQLFRDFWQSPSAASARAVDRGLAQGISVNERMHEVLRMPTALVIVPIFALA
+NAGVDLRGGVLVDSFQSSVTWGVIVGLVLGKLLGIGLATFVAVKLGAGRLPEGVGMGSVF
+GGAALSGIGFTVSLLVIGLAFGSTSDLGRQATVGVLVAMVLATALGWLIFRVAAKRWGEE
+TADLPMVLTPPVDPEVDHIRGPEDAQLTLVEYIDFECAYCAHATGSWDDLRSRFGDDLRY
+VVRQLPHHPHGPLAARASEAASNQGMFWPWLDFVFTRQDALEREDLIRYAEELGLDVAQF
+TADLDSAAVGARVERDLESADASGAHATPTFFVDGRRLLGSYDARTLTSALEASRRGTRT
+QEVRS
+>4_1948
+MSTPTRNPTPSDPSTPGTTSRKAKTIVWVVLAAVVLAGLIVGVVAASGPRDAAPQGSGQT
+ASSGTGQSAPSEATPVMRPDSRVLSKAPNEQAVLVEFLDFECEGCKAAYPVVEELRAEYA
+DTVTFVHRYFPLPGHPNSMTAAVAVEAAGQQGQYEAMYQQMFDTQEQWSHTTEDRSPVFR
+GYAEDLGLDMAAYDAAVADPATRDRIEADVADGTALGVQGTPTFFLDGQMLTLNTLEQFR
+AEVDAAATTD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000104.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000104.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa735df2cc3262c11172a2c98510dc931ea3137c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000104.fa
@@ -0,0 +1,115 @@
+>0_705
+MAWSVRILGGAAPETWRVEHFPADADEQDRAVRERFPARSLHRCAAGPRSVTYAERVGSA
+PARGPELAVVTEHGPDAGRLVPLGEGGLSTGRGGARLLLDDPSAPSRPMRLRLAPTGLHV
+HDGPRDTGRLWDGRSPLPVGRTALGLVRGPGAALPRPVTPEPPAVDLGSPPARQSVVIPL
+VAALGPLVLGVALVLMMGNPVFLLFGVLSVTVALVMLAMQRRTRLRHARLLAARADALVR
+RRAQAALSPGAVARAVRSGATDRFGLTSGADEAVAVSWGSGVGALSLSRDDPDEAWVEAV
+TSRRTVMTTSPPESRVVVLGPPRDVAGACRWAVFQLLRHAVAADGAFVVEAGGVRRTWWS
+GGSGPRLLVSAPEDAALDPAWRAWRAAIGGDAGTTPTARADLPWTRYDFTGPSPAPGDAV
+VDLRGRTVVVPAEQQRFEDVTADGLADGTLVAWLTELADDVVDLGLLPADDGDGTLTPPG
+QVGARDAVDGLTVTLARSGDETGVVEMDLAADGPHLLIAGTTGSGKSDLLLSLLLGAAAH
+HPPAEVAFLLLDFKGGASFGPLGALPHTMSLETNHVGTASLRALSAIRAELHRREALFAE
+AGVSDYPGFRRRHPDAALPRLVVAIDELRVLVDDHPDAAAVLQRLAATGRSLGFHLILAT
+QRATGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAAARLDPRRPGSAILSTAGRPTVS
+FRASQWTVDGGTPVWRRLGEAAAAPAVAPWEAVVSVLVENYAAGDWPTPPPVVTPALPER
+WVPDRARRAEATALALLDDAAHGRHRPWRWPTGAEGRTAWIVEAAGGRAETLAAVVEVAL
+RSGRPVAVLDGTGEAAAAARSGTPVLTPDAEGAGEAALARLRELAAAGGTAVITGWNAWS
+GLRVGDTYRTVEEDVHDWLGRPTAAGLRLAVFGGRELATGRLLLHLPHRFFVPAGTNAEH
+RLIWPRLTEVEPLPGRAVHISPAVPEPGMPCQLASPAPA
+>1_445
+MAWSVRILGGAAPETWRVEHFPADADEQDRAVRERFPARSLHRCAAGRRSVTYAEGVGSA
+PARGPELAVVTEHGPDAGRIVPLGEGGLSVGRGGARLLLDDPSAPSRPMRLRLAPTGLHV
+HDGPRATGRLWDGRSPLPVGRTALGLVRGPGSALPRPITPEPPVVDLGSPPARQSVVIPL
+VAALGPLVLGVALVLMMGNPMFLLFGVLSVTVALVMLAMQRRTRLRHARLLAARADAVVR
+RRARVALSPGAVARAVRSGATDRFGLTAGADEAVAVSWGSGVGALSLSRDDPDEAWVEAV
+TSRRTVMTTSPPESRVVVLGPPRDVAGACRWAVFQLLRHAVAADGAFVVEAGGVRRIWWS
+GGSGPQLLVMAPEDAALDPAWRAWRAAIGDDAGTTPTARTDLPWTRYDFTGPPPAPGDAV
+VDLRGRTVVVPAEQQRFEDMAADGLADGTLVAWLTELADDVVDLGLLPTDDGDGTLTPPG
+QVGARDAVDGLTVALARSRDEAGVVEMDLAADGPHLLIAGTTGSGKSDLLLSLLLGAAAH
+HPPAEVAFLLLDFKGGASFGPLGALPHTMSLETNHVGAASLRALSAIRAELHRREALFAE
+AGVSDYPGFRRRHPDAALPRLVVAIDELRVLVDDHPDAAAVLQRLAATGRSLGFHLILAT
+QRATGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAAARLDPRRPGSAILSTAGRPTVS
+FRASQWTVDGGTPVWRRLGEAAAAPAVAPWEAVVSVLVENYAAGDWPTPPPVVTPALPER
+WVPDRARRAEATALALLDDAAHGRHRPWRWPTGAEGRTAWIVEAAGGRAETLAAVVEVAM
+RSGRPVAVLDGTGEAATAARSGTPVLTPDSEGAGEAVLARLRELAAAGGTAVITGWNAWS
+GLRVGDTYRTVEEDVHDWLGRPAAAGLRLAVFGGRELATGRLLLHLPHRFFVPAGTNAEH
+RLVWPRLTEVEPLPGRAVHISPAVPEPGMPCQLASPAPA
+>2_2172
+MGWTVRILGGRTPETWRVSPLPRDPTLRDRAVRERAPGRSLRAVASGPGSVTYAPWGGAE
+PAPGPELSVVTERGPDGGRLAPLTGGGVSVGRGRARLLLDDPAAPSRPTRLRLAAAGLHV
+EGAVEGAPRLWDGRRPHRIGRTTLGLVRGPQPPLPPPSLPAPPCVDLGSPPAGQSLAIPL
+LTAAAPLVIGVALVLVMRNPIFLLFGLLSVAVALTMLGLQRRARMRHAALLAERAAAVTA
+HRASAALSPGDVARAVRARTPDRFGLTGAAEGPATLSWGLGMGALGLSRDDPDQAWVAAV
+TARREALTVPSPAARTVVLGPPREAAGVCRWVVFQLLRHAVAAGACLVVESGGSRRCWWA
+GGTGGALLVTAPADAALEAAWTAWTAGIGGAPGERTGAQPARIDFTGADCAPGETVVDLR
+GGMLTDPGQEQRITGLEADGIAPATLPGWAAELADDVVDLGLLPADAGAGALFPPADVGT
+RDAVDALRVSLEAGSDGGPGALALDLAADGPHLLLAGTTGSGKSDLLLSLLLGVAAHHPP
+AEAAFLLLDFKGGASFGPLAALPHTMSLETNHVGAASLRALNAIRAELHRREALFAEAGV
+SDYPAFRRRHPEAALPRLVVAVDELRVLVDDHPDAAAVLQRLAATGRSLGFHLVLATQRA
+TGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAATRLDPRRPGSAILSTAGREPVPFRA
+SRWAVDGGAPVWRRLGEAAETPAAAPWKAVVAQLVERYAAGRWPTPPPVVTPALPERWVP
+DRTRRAGATALALLDDAAHGRHRPWRWAPGGGGRAAWIVEPAGGRAEALAAVLEVGVRGG
+APVVVLDGTGEAAAIAAPEGVRLLRPDEEGAGERAAACLRELAAAGGTAVLTGWTTWAGL
+RLGESYRTLEEDAQGWLGGREAAGLRVAAFGGRELATSRLLLHLPHRFFVPAGTSAEHRL
+VWPRLVEVEPLPGRAVHVSPDVPEPGLPCQLASPGAHRSGAADAASTL
+>3_328
+MTRRLVHRPGRTVPPARLLPEDVITGPQPVDPAMDQGSGPNLLMIVPMVAAAASMLTMMA
+FRQSPFAAVGALAMVVTLTAMLILYGSQAGKARRRRTTLRETYTRYLDRQRRRLIAEDEQ
+ARAIAASAAPPPGALLDVVRRPDRLWERRRTDEDFLQTRVGLGARPVRALRVAVQDNATQ
+VQDEFMLKQAESLATRFRTTDDMPVSLPLDSLGNLAVVGPREFGLTAARSLVLGACVQQA
+PEDLVVALLVPPERRADWPWFDRLPHARVADAASPTGNRLLVAADADDLMRMLRADLARR
+AGIAAETLRASTRDGRAATELSRLVIVVDSHGEPAAGLPLEGSHLPLVSRGITLITLVSD
+RLDEPSDVRLRLSATGGTDVTGAAEFQVDDARQDEGRPTVSHGRLDTFDAATALGVATDL
+QPLRLSADSLEHAEDDLSSTQTFLQMLGLSPELTLEELRRRWRPRGQDEFLRVPIGEDDR
+GDAVHLDLKEAAQLGMGPHGLCVGATGSGKSELLRALVFALLASHAPERMSLLLVDFKGG
+ATFAPFHGAPHVAGIITNLSDDLSLVERVYASLSGEILRRQEVLKAAGNLANITDYQVHR
+ERELAQGRSVEALPHLIVIIDEFGELLTARPDFIDLFLSIGRIGRSIGVHLLLSSQRIES
+GRLRGLETYLSYRLGLRTLSESESRTVLDTADAFHLPPLPGFGYLKVDTSVYTRFRSGYV
+SSPLEEEAAARAEQERVLTADDDVPPALPVPDYGLQLVLPTEGAEPQLSSGAGAAQVMEE
+PEDHRPTIMETLMDRLREVPSPVEPLWLPPLPEALTLDQAAGDVAVTDHGLRLPAGGDLE
+VPIGLIDDPEHQWQGLWMLDFASGSGHLIVQGGPRSGKSTLLQTIVTSLALTHSPQQVGV
+YCVDLLGSSLLPLQGLPHVGGVAIRTNREMVTRTLREVSAMLTLREKLFEAEGIDSMTTL
+RRRHADGSLPDLGSADVFLVLDGYGQVNEEFADLTPVLNGLISRGAAYGIHIITTVARQG
+EIRSTQQTFFTHRVELRLSTPSDSAIDRKAAEEVREDTPGRGLASTRLHGQVALPRVDGA
+ADPGTAAEGLAETVQRIAESARGEAMAVRVLPPTTERPPLEQLEDPGRLPVGLLEDDLSV
+RSLDIDGRERHVVALGDAQTGRSSMLRQFARHFMDTHADTEMMFVVFDPRGELKGVIPDA
+YMAGYAGNATVAVPLARALVSELEKRQSTDPKDAGPMRQARIVVLVDDYDVLTVAGDSPL
+APLLPYLPMARELKLHVFLTRRMKGASRGLYEKFLASLVSQDAVTLMFSGDRSEGVLFDG
+LRPKRLPPGRAVLIGASRRHETVQTFTGPPAPGRG
+>3_2047
+MTWRVRVLGLPVEQDWAVSELPLDVDGQDRVVAEHFAPLRVERARGGGTTLTYVAHPSGT
+PPVPAAGSGPELAVGTSAGPDAGRLVPLTAAGLTVGRGRSRMLLDDPQCPSRPVRLALGP
+SGVSVDDGRTRRTWDGLDGLPIGDSILRLVRGRQRPLPPALTPPPAQIDLGAAPAEQSLL
+VSLAMAVGPVLIGLVLAVTTRSPLFLLFGIVSLLGVGVLLGVQRRTRRRHADLLRERALD
+VVRRRVAAVSGPADVSAACRAKAEDRFGLVSARPGDGPALLWGRARGSVAFTRGDVADHW
+RSAACVDQPVLGVAAADRGTVLCGTGRPAQAAARWTLFQLLRHAVATGSSLVVRSPDGAR
+VWWPAVPGAPTIALELEDTAPLAGAWEVWTASLGAEMSETRRHGCADEVLVRCTGTPPAD
+LDADVVDLDARQATLPGQGLELTDLTPLGISADTLQWWLAELADDVAHLGLGGPPASAPP
+LRRPHDVGAHRAVRNLAVPLTSSSAGDAAPMVLDLAADGPHALIAGTTGSGKSDLLLSVL
+VGLAARHAPAEVSFVLLDFKGGASFGPLRRLPHTMSVETNHVGAASLRALQAIGAELRRR
+EALFAEARVADYPAFRAAHPDTALPRLVVAVDELRVLVDEHPDANAVLQRLAATGRSLGF
+HLLLATQRPGGAVSADVRSNLGTTIALRTATEQESWDLVGSAAASRIDPAAPGTALLARG
+TGAPVPFRASPWSAGPVRPRWTPWGVPVASAASGTDWPSVVEDLVQACRDRDLPIPEPVV
+SPPLPGSFAPDRSRRRSADVLALVDDAARARHVPWRWPLGAQGNGAWIVEPAGGRALVLA
+AVLEAAGRTSPAVLILDGSGECAAALPTVADALPDLADVTLLTPEAQPADVGEQVCGAVA
+DLAAVGGTLVITGWQSWAGVRVGETYRTLDEELHRLLGTQAARGLRVAAVGGRELVTARI
+APHLPHRFYVPAGTTPDHRLVWPPKLVEVEQLPGRAVHVHPGGPTVGVPAQLAFPAHSAA
+GAGTDSDDQQ
+>4_669
+MAWSVRILGGAAPETWRVEHFPADADEQDRAVRERFPARSLHRCAAGPRSVTYAERVGSA
+PARGPELAVVTEHGPDAGRLVPLGEGGLSTGRGGARLLLDDPSAPSRPMRLRLAPTGLHV
+HDGPRDTGRLWDGRSPLPVGRTALGLVRGPGAALPRPVTPEPPAVDLGSPPARQSVVIPL
+VAALGPLVLGVALVLMMGNPVFLLFGVLSVTVALVMLAMQRRTRLRHARLLAARADAVVR
+RRAQAALSPGAVARAVRSGATDRFGLTSGADEAVAVSWGSGVGALSLSRDDPDEAWVEAV
+TSRRTVMTTSPPESRVVVLGPPRDVAGACRWAVFQLLRHAVAADGAFVVEAGGVRRTWWS
+GGSGPRLLVSAPEDAALDPAWRAWRAAIGGDAGTTPTARADLPWTRHDFTGPSPAPGDAV
+VDLRGRTVVVPAEQQRFEDVTADGLADGTLVAWLTELADDVVDLGLLPTDDGDGTLTPPG
+QVGARDAVDGLTVTLARSGDETGVVEMDLAADGPHLLIAGTTGSGKSDLLLSLLLGAAAH
+HPPAEVAFLLLDFKGGASFGPLGALPHTMSLETNHVGTASLRALSAIRAELHRREALFAE
+AGVSDYPGFRRRHPDAALPRLVVAIDELRVLVDDHPDAAAVLQRLAATGRSLGFHLILAT
+QRATGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAAARLDPRRPGSAILSTAGRPTVS
+FRASQWTVDGGTPVWRRLGEAAAAPAVAPWEAVVSVLVEKYAAGDWPTPPPVVTPALPER
+WVPDRARRAEATALALLDDAAHGRHRPWRWPTGAEGRTAWIVEAAGGRAETLAAVVEVAL
+RSGRPVAVLDGTGEAAAAARSGTPVLTPDVEGAGEAALARLRELAAAGGTAVITGWNAWS
+GLRVGDTYRTVEEDVHDWLGRPTAAGLRLAVFGGRELATGRLLLHLPHRFFVPAGTNAEH
+RLIWPRLTEVEPLPGRAVHISPAVPEPGMPCQLASPAPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000105.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000105.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4d61716d132cb3492c6fe337da3608f60b95e8a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000105.fa
@@ -0,0 +1,22 @@
+>0_720
+MLSGFCLALGTWSTVAAEAADAALARRWGAAARLWTAHLGLGLVAVVVGWGAGLGLHAVL
+AG
+>0_721
+MSGAGYEVFALFQVALLACLAAGGVLGALARRRLTDRLGPRGLLTANTTAALLLGVTVGL
+AVPELVYASGG
+>1_460
+MSGAGYEVFALFQVALLACLAAGGALGALARGRLTDRLGPRGLLTANTTAALVLGATVGL
+AVPELVYASESWGDGQGLMLVAAVSAVVSGFCLALGTWSTVAAEAADAALARRWGAAARL
+WTAHLGLGLVAVVVGWGAGLGLHAVLAG
+>2_2133
+MSPALMGASPWEWVLGLAVLAAGGALGALLRLTLQEHLPRRGVLAANTLAAGVLGFSLAL
+ALPSLVYASGLAGDPLGVAGLLVASLTAGFCLALGTWSTVAGQAADAVLAGRWGAAGRIW
+AAHLGLGLLAAAAGWGLGLGARLLVA
+>3_2027
+MSAGTVLLTVLLAGLAAAVGAGLRHLADHRWGGRGVLLANVTASALAGALFAIGFGPGSA
+DPEGPAGAALALGAAGAFVLALGTWSTVAFQAAQEVLAGRTRRAVRVWLVHLASGTAAAV
+VGVLAVGFLVR
+>4_685
+MSGAGYEVFALLQVALLACLAAGGALGALVRRRLTDRLGPRGLLTANTTAALLLGVTVGL
+AVPELVYASGGGGDGQGLVLVAAVSAVVSGFCLALGTWSTVAAEAADAVLARRWGTAARL
+WAAHLGLGLVAVVVGWGAGLGLHAVLAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000106.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000106.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fbfdaec0e1603a7028183a78e79b6a8a3b2bb8c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000106.fa
@@ -0,0 +1,35 @@
+>0_735
+MNASFPAGAAAATPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT
+ALAGLSDPASGALEVLGEDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLGWFR
+RFRREDRDIVRAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPMTGL
+DIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMGGRVVASGSPRDVLTVENL
+DIAYGRGALHGPSTAVEDAADFLDDPAGGRRH
+>1_474
+MNASFPAGAAATPPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT
+ALAGLSDPASGALEVLGEDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLGWFR
+RFRREDRDIVRAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPMTGL
+DIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMGGRVVASGPPRDVLTVENL
+DIAYGRGALHGPSTAVEDAADFLDDPAGGRRH
+>2_2119
+MSRSAAVVPEAAPAPLAVAEHLELRHGDHLAVEASSFTLPAGCVVAVIGPNGSGKSTLLQ
+ALAGVLDPAAGRLEVRGESPSRHGRLTSFVMQSLQFPQGVPLTVRDVVTMGRYTTAGWFR
+RLGATDRAAVAAAMERVRVTDLADRHLDQLSGGQRQRVYVAQGLAQEHDVLMLDEPVTGL
+DIVSARTIDEIIHEQPERGVSVVYTTHDLDEAAAADHVVLMDGRVVASGPPAQVLTAANL
+DAVYGRGALHAPLLVHLDDPADCSPDRG
+>3_511
+MNPAAPAPAIRLADVSAAYDRRRPVFTGADLVIDGPGLVRVHGRNGGGKSTLIELVSGYL
+RPSDGQVRIGGLPAHDPRAHERRRVCRTEPALYPLMDVHDHVVFASRWAGADPAEGLARA
+ERYGLGPWMHAPAQTLSTGNRRRLWIVQCTVGAFDTVVLDEPFNGLDDESSAVLAAELAA
+WARTRCVVLICHLPPPGLAFDRVVRWPPGQAAADPAPPADPGVRP
+>3_2013
+MTRTVPTAPTPGAGVLAEARGLELRRAAHVAVAPSDLTLPAGVLVAVIGPNGSGKSTLLH
+ALAGTLEPAAGSLTVRGESPSRHARRTAFVMQTIPVPQGVPLTVRDVVRMGRYPRVGWFG
+RFGAADREAVDAAMERMSVTDLARRHLDELSGGQRQRVYVAQALAQEHDVLMLDEPLTGL
+DLVSARTIDRLLHEEPARGVSVVHTTHDLDEAAAADFVVLMSGRVVAAGTPRQVLTEANL
+EAAYGHGVLHGPRLPFLDDPVDGVR
+>4_699
+MNASFPAGAAAAPPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT
+ALAGLSDPASGALEVLGEDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLGWFR
+RFRREDRDIVGAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPMTGL
+DIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMSGRVVASGPPRDVLTVENL
+DIAYGRGALHGPSTAVEDAAEFLDDPAGGIRH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000115.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000115.fa
new file mode 100644
index 0000000000000000000000000000000000000000..922ba402b5d8c79ce3259858c502ead47ab26fab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000115.fa
@@ -0,0 +1,30 @@
+>0_989
+MIDRFQNLDWGYYGPELMTAVGDTLYMVGWSFILGGILGLLVGLVLYTTRPGGIFANRAV
+YLVTNFIVNLIRPIPFVILIAALQPLTIAVLGTGIGNTAVVFCMIWASTFGIARIVEQNL
+VSLDPGVIEAARAMGASRMRIVRAVVLPEALGPLILGFTFVIISLVDMSAMAGIIGGGGV
+GNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR
+>1_713
+MIDRFQNLDWGYYGPELMTAVGDTLYMVGWSFILGGILGLLVGLVLYTTRPGGIFANRAV
+YLVTNFIVNLIRPIPFVILIAALQPLTIAVLGTGIGNTAVVFCMIWASTFGIARIVEQNL
+VSLDPGVIEAARAMGASRMRIVRAVVLPEALGPLILGFTFVIISLVDMSAMAGIIGGGGV
+GNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR
+>2_176
+MSEALSRILQVWPEIVVALGQTLTMLAVTIPLAVLLGTPLGIWLFTHAPGGLSPSPRLHR
+VVDAAVSMLRSFPFLILLIAIIPVTRLIVGTTIGTAAVIVPLTVNAIPYFARFVEQNLAQ
+LGPGPVEAARAMGATRGQIVRDVLLVDARPALVGSLTIMSVSFISYSAMAGLVGGGGIGD
+FAIRYGYYRYETPLMVVAILLMIGLVALLQFAGTRLSQRLDHRRPRTARRPRRRALAPAG
+>2_1817
+MTWLETLTTNPAITDALPEALVETLLMVAISGVATVLIGGLLGIVLHVTRPGGLNPMPAL
+YTVLSTVIVNITRSVPYAILMVALIPLTKWLVGTAIGPIAATVSLTIGTAPFFARLVESA
+LREIPSGTVDAAQVMGSTRGQVIRKVLLPEAMPGLIAATTTTLVTLVGYSAMAGLIGGGG
+LGRLAYNYGYQRFQTEVMVVTIVVIVILVQLIQWIGDLLIRRVDHR
+>3_1705
+MIDRFQNLDWGYYGPELMTAVGDTLYMVGWAFILGGILGLLVGLVLYTTRPGGIFANRAV
+YLVTNFVVNLIRPIPFVILIAALQPLTIAVLGSGIGNTAVVFCMIWASTFGIARIVEQNL
+VSLDPGVIEAARAMGASRMRIVRTVVLPEALGPLILGFTFVIISLVDMSAMAGIIGGGGV
+GNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR
+>4_933
+MIDRFQNLDWGYYGPELMTAVGDTLYMVGWSFILGGILGLLVGLVLYTTRPGGIFANRAV
+YLVTNFIVNLIRPIPFVILIAALQPLTIAVLGTGIGNTAVVFCMIWASTFGIARIVEQNL
+VSLDPGVIEAARAMGASRMRIVRAVVLPEALGPLILGFTFVIISLVDMSAMAGIIGGGGV
+GNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000117.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000117.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1ec019d706eb068d04b91df0b3a04ce13d4c1e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000117.fa
@@ -0,0 +1,54 @@
+>0_1056
+MTPHTDAPEGPSLRRLADAAEDRLGEHGLALRDLGVLGPEDPAASHFAAAVERGFYETVP
+TGAALRQQLEAHAADGRRRLGVYAPGDDPAARRPAATFEDFVQPLTTSPGRTVDAWLITD
+VTVSPDARRRGVLRAMMLRSLADARDAGLCAAALTATEAAIYGRFGFGAATRWHAVRIDV
+SGAPAFTGAPAGGRVTVEEPREIPGLVDELYGRVLPATPGSVQRTSFSVPRWEDREASRN
+EGRGSGLYAAVHRDDDGRVQGVALYRFEGWEKEPPTITVTAFLAATADARRGLVHHLARL
+DLVERIEWGRAPEPGWLEALFVDERRVSRHRGSDDLYLRVLNLPAAMAARGWAGDGEVVV
+AVEDALGAIDGTWRLTVRQGRGAAERLGPAADAVGLDAGLRLDAARFSALWLGGHSRGAG
+AAVLAEAGVVAELRAGAAEAFDGLVRPSRPLHTLVGF
+>1_784
+MTPHTDTPEGPSLRRLADAAEARLGEHGLALRDLGVLGPEDPAASHFAAAVERGFYETVP
+TGAALRQQLEAHAADGRRRLGVYAPGEDPAARRPAATFEDFVQPLTTWPGRAVDAWLITD
+VTVSPDARRRGVLRAMMLRSLADARDAGLCAAALTATEAAIYGRFGFGAATRWHAVRIDV
+SGAPALTGAPAGGRVTVEEPREMPGLVDELYGRVLPATPGSVQRTSFSVPRWEDREASRN
+EGRGSGLYAAVHRDDDGRVQGVALYRFEGWEKEPPTITVTAFLAATADARRGLVHHLARL
+DLVERIEWGRAPEPGWLEALFVDERRVSRHRGSDDLYLRVLNLPAAMAARGWAGDGEVVV
+AVEDALGAIDGTWRLTVRQGRGAAERLGPAADAVRMGAGLRLDAARFSALWLGGHSRGAG
+AAVLAEAGVVAELRAGAAEAFDGLVRPSRPLHTLVGF
+>2_1761
+MSINPAAAAHAADATAAQDALARHGLVLRTLAPLSRGFDGADPARAEHPAHVRHTAAVEK
+GFYEEVPQGAAADQDLGVSADDAKVLRGVYLSADDPARREPVGTFVDWTSRLTTSPGAEL
+PVWMISNVTVSPGHRRRGILRAMMTASLEEAVAAGVPVAALTASESTIYGRFGFGAASTA
+RTVRVDVRGDVVLAADAAGRTDEDAGTVLREDPRELAGVVEALHDRVRRGTPGSVHRPTG
+HVIRWEDRSAAKNDGRGSGLFAAVHRDADGAVQGVALYRFDGWGKEPTTVSVEVFLAATD
+AAARQLWRYLTRLDLIERLRMTRCPDDGGLEQVLADRRRVRTKSVWDDLYLRVLDVPVCL
+GGRGYAPEVVGEVVLAVADAAGHAAGTWRLRVADGVGRAERLADDARADLALDVAHLSAV
+WLGGVRAGALVRAGVVDEREPGAAARLDALLAPAAAVHLLTGF
+>2_1762
+MTPRTDAPDAWLDPAPATAEALAAHGLELLRVPSPWETGDADPDAPFDHARRWADAPAVR
+RHTAVLQRNFHEVGDPDFALADRFIGVEQGDRRRLSGVYPQGADPAATDPVGTLVDFTKD
+LNVGDGRMLPAWCLTEVTVSPTHRRRGILRAMMTESLRRAHAARVPIALLTATEATLYRR
+FGFGVSTYHRSVWLDVTRGVQLRGRRPDGSFRFVEPTASGALIDGLWRRAFEAQAGSVER
+IRFHAARETDRDPRVGEGRPQGLRAVVYSAPDGEDLGVAVYRVTGSTAELVADDPVTATV
+VALWAATPEAHRALLEFLGNLDLVVRLRLPAVAADRLLEFLVLDESRIYTRGVHHHLWHR
+VLDVAACFEARPYLHEGAVTVTVEDDLGYAAGTWEIAAADGVGRVRPAPQDAAELTLDVA
+ELGSVLLGGVKAEMMREAGILLAHRPGAAADLDTLLRQARPPYSLTGF
+>3_1651
+MRPHTDLQPTATPRADAEVLAEQGLALVVAPGRAADPAFERHTTAVERGFYEQVPSGEAM
+AQLLEAGEADGRRMVDVLPLGADPATTRPVATFEDFRSELTVSPGVAVSAWLISGVTVDP
+GFRRRGLLRTMMTRSLADAVAAGVPVAALTASEAAIYGRFGFGAATRWRRARLDTRGDVR
+LRGAPSAGRVTREEPREVGALADELYQHVRRLTPGATQRPTMTAIGWEDRSRFKNDGKGS
+GLYAAVHRDAAGTAQGIALYRPQGWDVEPPTVTMELFLALTPDARRGLLTHLTSLDLIER
+IVWERAPEAGWPEALLEDERRLRTERDGDDLYLRILDVPAALGARADLGDGEVVVDVTDP
+LGHAAGAWRIRARDGVAEVTEAAEGEAELGLDVADLSAVWLGGHGSAGGVAARVATGLVR
+EVVPGAGARLDALLRPSVPVRSLVGF
+>4_1005
+MTPHTDAPEGPSLRRLADAAEDRLGEHGLALRDLGVLGPEDPAASHFAAAVERGFYETVP
+TGAALRQQLEAHAADGRRRLGVYAPGDDPAARRPAATFEDFVQPLTTWPGRTVDAWLITD
+VTVSPDARRRGVLRAMMLRSLADARDAGLCAAALTATEAAIYGRFGFGAATRWHAVRIDV
+SGAPAFTGAPAGGRVTVEEPREIPGLVDELYGRVLPATPGSVQRTSFSVPRWEDREASRN
+EGRGSGLYAAVHRDDDGRVQGVALYRFEGWEKEPPTITVTAFLAATADARRGLVHHLARL
+DLVERIEWGRAPEPGWLEALFVDERRVSRHRGSDDLYLRVLNLPAAMAARGWAGDGEVVV
+AVEDALGAIDGTWRLTVRQGRGAAERLGPAADAVRMGAGLRLDAARFSALWLGGHSRGAG
+AAVLAEAGVVAELRAGAAEAFDGLVRPSRPLHTLVGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000119.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000119.fa
new file mode 100644
index 0000000000000000000000000000000000000000..48be6a2c98c002fba5db2410fe3f93851d93c334
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000119.fa
@@ -0,0 +1,106 @@
+>0_1071
+MPKNSSTTVSSAVEAHPGGLASGSGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVF
+TGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKS
+TNRNPRSTVGTITEIYDYMRLLWARVGVPHCPQCGEPVSRQTPQQIVDQLEELPERTRFQ
+VLAPVVRGRKGEFVDLFKDLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRLAM
+KEGIRQRLTDSVETALKLADGLVVAEFVDVEPVAEKGRKNTAEFGGRDAEGNPRYRSFSE
+KLSCPNGHEQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVV
+PWSLGKSTSDYWLRVLGGLGKEMGFSLDTPWKDLTEAERDAVLHGKDFKVEVTFRNRFGR
+ERRYTTGFEGVIPYVMRKHGETESDGARERYESFMREIPCPACHGARLNPTVLNVLVGGL
+SIADATRLPMREAMEFFSGLRLTDRERQIADQVLKEILARLAFLLDVGLEYLNLERPAGT
+LSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEH
+DEDTIAEADWIVDIGPRAGEHGGEVVHSGSLADLKANTRSVTGDYLSGRRSIAVPERRRV
+PEKGRVLTVRGAQENNLKDVSVEVPLGVLTAVTGVSGSGKSTLINEILYKVLANRLNGAK
+LVPGRHRSVEGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDAIRKLFAETPEAKVRGYQ
+QGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTYKGKNIAE
+VLDMPIEEAADFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKR
+SNGRTIYVLDEPTTGLHFDDIRKLLHVLQSLVDKGNTVLTIEHNLDVIKSADHVIDLGPE
+GGSGGGTIVAAGTPEEVAHVAESHTGRFLAELLA
+>1_357
+MVESSSFVPPKLSVQPDVRVLGARENNLQDVDLTVPRDATVVFTGVSGSGKSSLAFGTLY
+AESQRRYLESVAPYARRLIDQAGVPDVDSITGMPPAVALQQQRGSGNARSTVGSITTLSS
+LVRMLYSRAGDYPEGQPMLYAEDFSANTVQGACSECHGIGRVYEVNEQQMVPDPSLTIRE
+RAIASWPTAWHGHQLRDVLVALGYDVDVPWRDLPKKDRDWILYTDETPFVPVHSRLTLSE
+SKAAIEAGVEPSYSGTFVGARRYILDTFANTKSASMKRRVAQFLTAAICPTCNGKRLKPE
+ALSVTFEGFDIAEFSQLPLRELATILSGVVAREEDHEAASSDVRPTASRTPEKRAAAVQL
+ASGVLQRLRPLVDLGLGYLSLSRTTPTLSGGELQRLRLATQLSSDLFGVVYVLDEPSAGL
+HPQDVAALLEILDGLKGRGNSLFIVEHSVAVMRHADWLVDIGPGAGEHGGRVLYSGPPDG
+LAGVTESVTRGYLFGGRGLPLRTPREARSWLRLENVTRNNLHDLTVDIPLGVFTAVTGVS
+GSGKSSLVSQALPSLLGDRLGLAARADDEPVSDESLLADAPEHLEGRVAGPVTGVQRLVV
+IDQRPIGRTPRSNVATYTGLFDHVRRRFADTPEARSRGYKPGRFSFNVAGGRCPTCEGEG
+SVMVELLFLPSVYTECPDCHGTRYKASTLEVTWRGRTIADVLSMSVEEANLFFVGDEEIT
+RSLAALSDVGLEYLRLGQPATELSGGEAQRVKLATELQRAQRGDTLYVLDEPTSGLHCAD
+TDRLVAHLQTLVDAGNTVVAAELDMRVVAVADHVIDLGPGAGDAGGTVVAAGTPAHVADQ
+GVGASAGYLAAALQAATNVTPS
+>1_799
+MPKNSSTTVSSAVEAHPGGLASGSGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVF
+TGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKS
+TNRNPRSTVGTITEIYDYMRLLWARVGVPHCPQCGEPVSRQTPQQIVDQLEELPERTRFQ
+VLAPVVRGRKGEFVDLFQDLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRLAM
+KEGIRQRLTDSVETALKLADGLVVAEFVDVEPVAEKGKKNTAEFGGRDAEGNPRYRSFSE
+KLSCPNGHEQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVV
+PWSLGKSTSDYWLRVLGGLGKEMGFSLDTPWKDLTEAERDAVLHGKDFKVEVTFRNRFGR
+ERRYTTGFEGVIPYVMRKHGETESDGARERYESFMREIPCPACHGARLNPTVLNVLVGGL
+SIADATRLPMREAMEFFSGLRLTDRERQIADQVLKEILARLAFLLDVGLEYLNLERPAGT
+LSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEH
+DEDTIAEADWIVDIGPRAGEHGGEVVHSGSLADLKANTRSVTGDYLSGRRSIAVPERRRV
+PEKGRVLTVRGAQENNLKDVSVEVPLGVLTAVTGVSGSGKSTLINEILYKVLANRLNGAK
+LVPGRHRSVEGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDAIRKLFAETPEAKVRGYQ
+QGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTYKGKNIAE
+VLDMPIEEAADFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKR
+SNGRTIYVLDEPTTGLHFDDIRKLLHVLQSLVDKGNTVLTIEHNLDVIKSADHVIDLGPE
+GGSGGGTIVATGTPEEVARAAESHTGRFLAELLA
+>2_1745
+MPKNSSTTVSSAVETHAGGLASGPGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVF
+TGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKS
+TNRNPRSTVGTITEVYDYLRLLWARVGVPHCPQCGEPVSRQTPQQIVDQLEELPERTRFQ
+VLAPVVRGRKGEFVDLFADLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRLAM
+KEGIRQRLTDSVETALKLADGLVVAEFVDVEVVAEKGKKNTAEFGGRDAEGNPRYRSFSE
+KLSCPNGHEQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVV
+PWSLGKSTSDYWLRVLGGLAKEMGFSLDTPWRELEPAQREAVLHGKDFKVEVTFRNRFGR
+ERRYTTGFEGVVPYVLRKHGETESDGARERYESFMREIPCPVCHGARLNPTVLNVLVGGL
+SIAEATRLPLREARDFLAGLELSARERQIADQVLKEILARLAFLLDVGLEYLNLERPAGT
+LSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEH
+DEDTIAEADWIVDIGPRAGEHGGEVVHSGSLEDLKANTASITGDYLAGRRAITAPQTRRA
+PQEGRTLTVRGARENNLKDVSVDIPLGVLTAVTGVSGSGKSTLINEILYKVLANRLNGAK
+LVPGRHRAVDGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDAIRKLFAETPEAKVRGYQ
+QGRFSFNIKGGRCEACSGDGTLKIEMNFLPDVYVPCEVCDGARYNRETLEVTYKGKNIAE
+VLDMPIEEAAQFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKR
+SNGRSVYVLDEPTTGLHFDDIRKLLQVLQSLVDKGNTVITIEHNLDVVKCADHVIDLGPE
+GGSGGGTIVATGTPEEVARVEASHTGRFLAELLA
+>3_1637
+MPKNSSSAAAPARPDAAARGGLASGPARGSAQHERIVVKGAREHNLKNVDVSIPRDSMVV
+FTGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQK
+STNRNPRSTVGTITEIYDYMRLLWARVGVAHCPVCGEVVSKQTPQQIVDQLEQLPERTRF
+QVLAPVVRGRKGEFVDLFSSLSTQGYARALVDGELIQLSDPPALKKQNKHTIAVVVDRLA
+VKEGIRQRLTDSVETALKLADGLVAVEFVDVDVVAQAGKKNQGDLAGEDAEGNPRFRTFS
+EKLSCPHGHPQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVPNDELSLNEGAI
+LPWSLGKSTSDYWLRVLGGLAKEMKFSLDTPFKDLTAQQRDAVLNGKDFKVEVSFRNRFG
+RERRYTTGFEGVLPYVMRKHGETESDNARERYESFMRQIPCPACHGARLNPTVLNVRVGG
+LSIADATRLPLRESLAFLDGLQLTERELAIADQVVREIRARLEFLLDVGLDYLNLERNAG
+TLSGGEAQRIRLATQIGAGLVGVLYVLDEPSIGLHQRDNRRLIDTLIRLRDLGNTLIVVE
+HDEDTIAEADWIVDIGPRAGEHGGEVVHSGSLDELKANTRSVTGDYLAGRRRIEVPAARR
+PVDPKRRLTVKGATENNLKDVTVDIPLGVFTAVTGVSGSGKSTLINEILYKVLADKLNGA
+KMVPGRHRSVAGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDQIRKLFAETPEAKVRGY
+QQGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTYKGKNIA
+EVLDMPIEEAAEFFGAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQK
+RSTGRTVYVLDEPTTGLHFEDIRKLLQVLQTLVDKGNTVLTIEHNLDVVKCADHVIDLGP
+EGGSGGGTVVATGTPEEVAAVPESHTGRFLAELLG
+>4_1021
+MPKNSSTTVSSAVEAHPGGLASGPGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVF
+TGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKS
+TNRNPRSTVGTITEIYDYMRLLWARVGVPHCPQCGEPVSRQTPQQIVDQLEELPERTRFQ
+VLAPVVRGRKGEFVDLFQDLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRLAM
+KEGIRQRLTDSVETALKLADGLVVAEFVDVEPVAEKGRKNTAEFGGRDAEGNPRYRSFSE
+KLSCPNGHEQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVV
+PWSLGKSTSDYWLRVLGGLGKEMGFSLDTPWKDLTEAERDAVLHGKDFKVEVTFRNRFGR
+ERRYTTGFEGVIPYVMRKHGETESDGARERYESFMREIPCPACHGARLNPTVLNVLVGGL
+SIADATRLPMREAMEFFSGLRLTDRERQIADQVLKEILARLAFLLDVGLEYLNLERPAGT
+LSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEH
+DEDTIAEADWIVDIGPRAGEHGGEVVHSGSLADLKANTRSVTGDYLSGRRSIAVPERRRV
+PEKGRVLTVRGAQENNLKDVSVEVPLGVLTAVTGVSGSGKSTLINEILYKVLANRLNGAK
+LVPGRHRSVEGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDAIRKLFAETPEAKVRGYQ
+QGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTYKGKNIAE
+VLDMPIEEAADFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKR
+SNGRTIYVLDEPTTGLHFDDIRKLLHVLQSLVDKGNTVLTIEHNLDVIKSADHVIDLGPE
+GGSGGGTIVAAGTPEEVAHVAESHTGRFLAELLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000125.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000125.fa
new file mode 100644
index 0000000000000000000000000000000000000000..945eaa685fd3cf3d122b8f5c39b0f2080aecdb4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000125.fa
@@ -0,0 +1,43 @@
+>0_1286
+MTEHTAPTPLPLSLLDLALVRDGAPMGEAFAESVEQARVAEAAGFRRVWYAEHHNMPSIA
+SSATAVLIAHVAAHTDSIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDLGLGRAPGT
+DQRTLQALRRDPSAAERFPQDVLELQGYLTGQSLIPGIDAYPGKGTNVPLYILGSSAFGA
+QLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHFIAAANVIAADTEEVAER
+EWQAAQRARIRMMLGRGRTLTDDEVEMLLHSPAGQQVLGMLECTAVGTGPTTAAWLHDFA
+ARVQADELIITTAAQDAGVRRRTLELLGEHVVRA
+>1_1016
+MTEHTAPTPLPLSLLDLALVRDGAPMGEAFAESVEQARVAEAAGFRRVWYAEHHNMPSIA
+SSATAVLIAHVAAHTDSIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDLGLGRAPGT
+DQRTLQALRRDPSAAERFPQDVLELQGYLTGQSLIPGIDAYPGKGTNVPLYILGSSAFGA
+QLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHFTAAANVIAADTEEVAER
+EWQAAQRARIRMMLGRGRTLTDDEVEMLLHSPAGQQVLGMLECTAVGTGPTTAAWLHDFA
+ARVQADELIITTAAQDAGVRRRTLELLGEHVVRA
+>2_1527
+MTEHTAPTPLPLSLLDLATVRDGASVAEAVAESVEQAQAAERAGFRRVWYAEHHNMPAIA
+SSATSVLIAHVAAHTESIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDLGLGRAPGT
+DQRTLQALRRDPSAAERFPQDVLELQGYLTGRTRIPGIEAYPGKGTDVPLYILGSSAFGA
+QLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHFIAAANVIAADTREEADR
+EWEAARRARIRMMLGRGRTLSDDEVEMLLHSPAGQQVLTMLECTAVGTGEETATWLRDFA
+AKVQADELIITTAAQDAGVRRRTLELLGEHVVRA
+>3_121
+MSIPLSVFDPVLLPAETDPREAIDDARTLAAAADALGYRRLWHGEHHLNPGVLGSNPALT
+LALVGPVTQHIRLGSAASLVGPRTPLVLAEDFGLLAAAFPGRIDLGLGRAAAPGGPPPGT
+RAETPTGDGGPAQDPQREPAGAGASSGQDPAAGPSEVDGVVIPAAPDLSAALGSPLRAAS
+RALLPTPSTPALDYGAQVDLLLGLLDGTAQHDGAALGQVVARPAVDVEPWVLGSGPGVSA
+EVAARRGLRFGANYHVSPAGTVAAVRRYRELFRPSPEVPCPVVSVSAEVLIADTAAEARR
+RASGYAAWVLSIRSGAGAVPYPSPAHPEPSRTPQEEALVADRLQTRFVGTAEQVAERLDA
+LARLTGADELLISASAHRVEHRVETLTRLAEIWRTA
+>3_1423
+MTADVRPVVPPETAPAGVPLSLLDLATVRGDQRIGEALGQSVELAQTAEAQGFTRVWYAE
+HHNMPGIASSATAVLLAHVAAHTERIRVGSGGVMLPNHSPLVVAEQFGTLAELHPGRVDL
+GLGRAPGTDQRTLQALRRSPEAADRFPQDVLELQGYLRGESRMPGIDAYPGRGTDVPLWI
+LGSSAFGANLAAQLGLGYAFASHFAPQMLEHAARLYREHFTPTDALDAPHFIAAANVVVA
+DTDEEAQRLWEATRRSRVRMFLGRGRHLTEDELDMLMDSPAGEQVLGMLRHTAVGTPDVV
+RAWLDDFAARVEADELIVTAAAVDHPARVRTLELLGEHVIRR
+>4_1241
+MTEHTAPTPLPLSLLDLALVRDGAPMGEAFAESVEQARVAEAAGFRRVWYAEHHNMPSIA
+SSATAVLIAHVAAHTDSIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDLGLGRAPGT
+DQRTLQALRRDPSAAERFPQDVLELQGYLTGQSLIPGIDAYPGKGTNVPLYILGSSAFGA
+QLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHFIAAANVIAADTEEVAER
+EWQAAQRARIRMMLGRGRTLTDDEVEMLLHSPAGQQVLGMLECTAVGTGPTTAAWLHDFA
+ARVQADELIITTAAQDAGVRRRTLELLGEHVVRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000126.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000126.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b4c1db2077a2cf7dde4aaab486c26d118435b09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000126.fa
@@ -0,0 +1,37 @@
+>0_1293
+MTTHTSTAQRSSKYPTTIGIDVGGTGMKGGLVRLGSGPKAGTLRGDRFRIPTPQTAMPEP
+VAATLAAITAELDGREKAPKPSAPLGVCFPSIVKDGVCLSANNIDHSWIGTDLRGTFEEH
+LRRPVTVVNDADAAGLAEARYGAGRGVRGLVHVITLGTGIGGAMIHDGMLVPNFEVGSLE
+LDGVMAESRASAKARERDQLSWAEYAERLQRFFSHVERIFSPDLFIVGGGISKRPDDYLP
+LLRLRTPIVPAQLQNNAGIVGAALAAHGSLADGN
+>1_1022
+MTTHTSTAQRSSKYPTTIGIDVGGTGMKGGLVRLGSGPKAGTLRGDRFRIPTPQPAMPEP
+VAATLAAITAELDGREKAPKPSAPLGVCFPSIVKDGVCLSANNIDHSWIGTDLRGRFEEH
+LRRPVTVVNDADAAGLAEARYGAGRGVRGLVHVITLGTGIGGAMIHDGVLVPNFEVGSLE
+LDGVMAESRASAKARERDQLSWAEYAERLQRFFSHVERIFSPDLFIVGGGISKRPDDYLP
+LLRLRTPIVPAQLQNNAGIVGAALAAHGSLADGN
+>2_1521
+MTTHTTTAQRSSKHPTTIGIDVGGTGMKGGLVRLGSGPKSGTLRGDRFRIPTPQPAMAEP
+VAATLAAITAELDARDKAPAPTAPLGVCFPSIVKDGVCLSANNIDPSWIGTDLKAAFEEH
+LRRPVRVVNDADAAGLAEARYGAGRGVSGLVLVITLGTGIGGAMVHDGVLVPNFEVGSLE
+LDGVMAETRASAKAREREDLSWAEYAQRLQRFFSHVEHVFSPDLFIVGGGISKRPDDYLP
+LLSLRTPIVPAQLRNNAGIVGAALAAHDSLADAR
+>3_1385
+MHRSRPAPPSPPAPSAYPRRLLGVDLGGTAAKAGVLELARDGRARILARSRAAHAGADPA
+SAVTRAAADALSRAGVRVPDGAGFACAAWLDPATGRARASPHLPSLVGIRPAALLTPVLE
+AAGAAGHGLVPVALNDADAAALAESRLGAARPAPGDLPGAPTLFVALGTGVGGAVIVDGA
+VLPGARGMHGEAGHICVDPDGPACPCGARGCWELYASASALARTLPGRPIADVLEAAVAG
+PGPERDAVLDAGEWLGRGLAPAVCLLDPVRVVVGGGLMAAGELLLPTARAALRRALPTAA
+ADRPPELVAAALGNDAGWIGAALADGARV
+>3_1417
+MSFPNTGVIPRLPPAPSKHPSVLGVDIGGTGMKGGIVRLGHGPKSGTLRGDRFRLDTPQP
+ASPATMARTLAQIVSELDHREKAPDADSRVGVCFPSIVQHGVCRSANNIDPSWIGVSLQD
+TFEEALQRPVTVVNDADAAGLAEARYGAGAGVPGLVMVITLGTGIGGAMINDGVLVPNFE
+VGSLELDGVMAESRASAKAREREGLDWPEYALRLQRFFSHLERIFSPDLFIVGGGISKRP
+HDYLPLLQLETPIVPAMLQNNAGIVGAALAAHADPADGLLR
+>4_1247
+MTTHTSTAQRSSKYPTTIGIDVGGTGMKGGLVRLGSGPKAGTLRGDRFRIPTPQPAMPEP
+VAATLAAITAELDGREKAPKPSAPLGVCFPSIVKDGVCLSANNIDHSWIGTDLRGRFEEH
+LRRPVTVVNDADAAGLAEARYGAGRGVRGLVHVITLGTGIGGAMIHDGVLVPNFEVGSLE
+LDGVMAESRASAKARERDQLSWAEYAERLQRFFSHVERIFSPDLFIVGGGISKRPDDYLP
+LLRLRTPIVPAQLQNNAGIVGAALAAHGSLADGN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000130.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000130.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b8359e33de7955b69fe537f48cbcd9583f20ec9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000130.fa
@@ -0,0 +1,79 @@
+>0_1485
+MTQNSEHTPASADLDPTVAAIAEDIVTEDAAPVAPEQTFADFGVHPAIVEALEAKGIVHP
+FPIQAMTLPVALGGHDIIGQAKTGTGKTLGFGIPALQRAIGPGEPGWDGLEAKGTAGAPQ
+ALIVAPTRELAVQVAGDLTAAAARRPLRIATIYGGRAYEPQIEELQRGVEIVVGTPGRLI
+DLMRQRHLRLDLVNTVVLDEADEMLDLGFLPDVETLLAAVPAVRQTMLFSATMPGPVVAM
+ARRYMTQPTHIRAADPEDEGLTKKDIRQLVYRAHHMDKDELVARALQAEGRGRTIIFTRT
+KRTAARVADELTARGFAAGALHGDLGQGAREQALRAFRNGKVDILVATDVAARGIDVDDV
+THVFNFQAPEDEKTYVHRVGRTGRAGNKGVAVTLVDWEDMPRWSLIDKALGLGQPEPVET
+YSSSPHLFSDLGIPKGTKGRLPQAKRVLEGLEGETLEDLGGPEAKQRDGGRGRGREGGRS
+RDGERGGREGGRGGRGGRGRGGRSGEGRDAARGGSRGERSERSGRGRGEAPAEQRAEGRG
+RGRGEGRKRTASRSETPAARTSEPVAGVELTEARRAERAEARAEARRRRGGRSRTRRRNG
+EVVDG
+>1_1205
+MTQNSEHTPAPADVDPTVAEIAEDIVTEDAAPVAPEQTFADFGVHPKIVEALEAKGIVHP
+FPIQAMTLPVALGGHDIIGQAKTGTGKTLGFGIPALQRAIGPGEPGWDGLEAKGTAGAPQ
+ALIVAPTRELAVQVAGDLTAAAARRPLRIATIYGGRAYEPQIEELQRGVEIVVGTPGRLI
+DLMRQRHLRLDLVNTVVLDEADEMLDLGFLPDVETLLAAVPAVRQTMLFSATMPGTVVAM
+ARRYMTQPTHIRAADPEDEGLTKKDIRQLVYRAHHMDKDELVARALQAEGRGRTIIFTRT
+KRTAARVADELTARGFAAGALHGDLGQGAREQALRAFRNGKVDILVATDVAARGIDVDDV
+THVFNFQAPEDEKTYVHRVGRTGRAGNKGVAVTLVDWEDMPRWSLIDKALGLGQPEPVET
+YSSSPHLFSDLDIPKGTKGRLPQAKRVLEGLEGETLEDLGGPEAKQRDGGRGRGREGGRS
+RDGERGGRGRGGRSGEGRDRARGGGRGERTERSPRGRDEARAEGRGRGEAPAEQRAEGRG
+RGRGEGRERTASRPETPAARTPEPVAGVELTEARRAERAEARAEARRRRGGRTRTRRSNG
+EVVDG
+>2_1361
+MNRAHGASGPSRPPCRRPNRNASRHDPELRAHPRPGRRRPPQVADIAEEIVTEEAVETAP
+EQTFADFGVHPAIVQALEAKGIVHPFPIQAMTLPVALGGHDIIGQAKTGTGKTLGFGIPA
+LQRAIGPGEPGWDKLEAQGSAGAPQALIVAPTRELAVQVAGDLTAAAAQRPLRIATIYGG
+RAYEPQIEELQRGVEVVVGTPGRLIDLMRQRHLRLDLVNTVVLDEADEMLDLGFLPDVET
+LLGAVPAVRQTMLFSATMPGPVVAMARRYMTQPTHIRAADPEDEGLTKKDIRQLVYRAHH
+MDKDELVARALQAEGRGRTIIFTRTKRTAARVADELTARGFAAGALHGDLGQGAREQALR
+AFRNGKVDILVATDVAARGIDVDDVTHVFNFQAPEDEKTYVHRVGRTGRAGNKGVAVTLV
+DWEDMPRWSLIDKALGLGQPEPQETYSSSPHLFADLGIPKGTKGRLPKEKRVLEGLEGEV
+LEDLGGPESAPRGRGGRSRDGERDGGRGGRGGRGERGGRGGRSRDDERGGREGGRGGRGE
+RAGREGGRGRDAEQSSARGEEAGESKGRGRGGERAGREGGRGESTGRGRGGRSGESRTRG
+ESRTEASEARAAQPVAGVERTEARMAERAEARAEARRRRGGRTRTRRRNGEVVDG
+>3_272
+MKSIDNVNVKLGDDLKAEITAGSKVRIAASAFSIYAFEALREELEGLEELQFIFTDPAFS
+ASSIDGTPRREHRRYFIPPLDIESSLTGTEFEVRLRNRLTQRAIARECADWVRRKVRFRS
+NTSGKGMQPIIGVGDDAAYLPVQDFSTSALGYEAGGALSNVVGKFEGPLEAAGLLTVFDQ
+VWNDPSALEDVTSTVLERIEQVYAENSPRHIYFLILNSIFSDFLADLSEDALPNDRTGYR
+ETKVWRALYDFQRDAAESIIQKLETYNGCILADSVGLGKTFTALAVIQYYEKRNKSVLVL
+CPKKLAENWTTYNNNYVTNPFVEDRFNYDVLAHTDLSRTRGESLGVRLDRINWGNYDLVV
+IDESHNFRNATYGEDRDTRYQRLMEKVIREGVRTKVLMLSATPVNNRFNDLKNQLQLAYE
+GEEENLSQHLNLSTTIDGVFRGAQAAFNEWSKLPAEERTPGRILGMLDFDFFELLDAVTI
+ARSRKQIQRFYDTAAIGAFPTRLPPLSLQEPLSEDKSVPSYNDIFEQLQALNLAVYTPLA
+FVHASRRYKYETGPGEENTDNFRSGRGQAGRETGLKRLMTVNLLKRLESSVHAFRKTLVS
+IESQVDALHRRLESEALGPLRVDAPAVEEDILREDDDVAEALFALPGDLELDLNDVDVLS
+WTSALWHDRETLRELIGEMDKITPERDLKLQRLRRLIRDKATSPLNEGNRKVLVFSAFAD
+TADYLYEQLSPALSAAGLETGIITGGSHSARSTLDGAVDFQTLMTLFSPVSKNRSALMPE
+ETREVDVLIGTDVISEGQNLQDCDFLVNYDIHWNPVRIVQRFGRIDRIGSTNERIQLVNF
+WPDMDLDAYIQLKDRVENRMVMVDVTGTADDNVLTPQQEQDAAYRTAQLKRMREEVVELE
+DTQAGVSITDLGLNEFRSALMAYVREHGDLTRAPRGLHAVVPADPDAGLPAGVIFALHNL
+QADPAMHRGNRLHPYYLVYVGEDGATVLEHTKAKPLLDLLRSAAEKQSVPLADAVRAFNT
+ATAEGTDMAAYSALLTRAIESMVEADEEQDVASLFTAGPTTALTSAIRGLEDFELIAFLA
+VVDTAGTDA
+>3_1253
+MTENTAAAEAVAPTAPEQTFADFGVQEPIVRALSEKGIVHPFPIQAMTLPVALGGHDIIG
+QAKTGTGKTLGFGIPALQRAVGPDEAGWDTRVAAGAAGAPQALVVAPTRELAVQVAGDLV
+AAAKHRPLRIATIYGGRAYEPQIEELQRGVEVVVGTPGRLIDLLRQKHLRLDAVNTVVLD
+EADEMLDLGFLPDVETLLAAVPEVRQTMLFSATMPGPVIAMARRYMTRPTHIRASDPEDE
+GLTKKDIRQLVYRAHHMDKDELVARALQAEGRGRTIIFTRTKRTAARVAEELTNRGFAAG
+PLHGDLGQGAREQALRAFRNGKVDILVATDVAARGIDVDDVTHVINFQAPEDAKTYVHRV
+GRTGRAGHKGTAVTLVDWEDMPRWSLIDKALGLNQPEPVETYSSSPHLFSDLGIPKGTKG
+RLPKEKRVLAGLDAERLEDLGGPEAKEKAARGGRDERSGSRSGGRGERSGGRGGRAGGGS
+RASREDRPPREDRTPRGERAPRPEKTVKAERAPRAERAPRAEKADRPAAAERSEGASGER
+RRRTRTRRRGGDVIDG
+>4_1412
+MTQNSEHTPASADLDPTVAAIAEDIVTEDAAPVAPEQTFADFGVHPAIVEALEAKGIVHP
+FPIQAMTLPVALGGHDIIGQAKTGTGKTLGFGIPALQRAIGPGEPGWDGLEAKGTAGAPQ
+ALIVAPTRELAVQVAGDLTAAAARRPLRIATIYGGRAYEPQIEELQRGVEIVVGTPGRLI
+DLMRQRHLRLDLVNTVVLDEADEMLDLGFLPDVETLLAAVPAVRQTMLFSATMPGPVVAM
+ARRYMTQPTHIRAADPEDEGLTKKDIRQLVYRAHHMDKDELVARALQAEGRGRTIIFTRT
+KRTAARVADELTARGFAAGALHGDLGQGAREQALRAFRNGKVDILVATDVAARGIDVDDV
+THVFNFQAPEDEKTYVHRVGRTGRAGNKGVAVTLVDWEDMPRWSLIDKALGLGQPEPVET
+YSSSPHLFSDLGIPKGTKGRLPQAKRVLEGLEGETLEDLGGPEAKQRDGGRGRGRDGGRS
+RDGERGGRGRGGRSGEGRDRARGGGRGERNRGGRSGEGRDDARGGGRGERSGRGRGEAPA
+EQRAEGRGRGRGEGRERTASRSETPAARTSEPVAGVELTEARRAERAEARAEARRRRGGR
+SRTRRRNGEVVDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000134.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000134.fa
new file mode 100644
index 0000000000000000000000000000000000000000..830ceb63bb76fd0a5122b08cbcbd9a18a557017a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000134.fa
@@ -0,0 +1,49 @@
+>0_1527
+MSTTLDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVACAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFALPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVSALR
+>1_1247
+MSTTLDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAVALLEDARARVARAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVAALR
+>2_1317
+MSAALYLDHAATAPVRRVALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVARAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGSDLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFAEAEAERAAAADAWSGLRDRFAARALDGVQELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHSTEPSPALLALGLSEDEARTALR
+CTFGPDADEAMLAAAADAIVDAVRTVSALR
+>3_1211
+MSTILDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVARAIG
+ARAGQIVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVTALR
+>3_1730
+MALDVAAVRQDFPILRSTLADGRPLVYLDSGATSQRPRQVIEAEVEFLTISNAAVKRGAH
+QLAEAATDRYESARETVAAFVGATDPRELVFTRNATEALNLVAYALGNGDDATPEHLRVR
+AGDEILVTEMEHHANLVPWQELARRTGATLRHIPLGEDFALDLVDLGSLVTERTKVVAFT
+HQSNVTGTVNPVATLGEAARAVGALTVLDACQSVPHMPVDVAALGVDFLAFSGHKMLGPT
+GIGALWGRYELLAELPPFLLGGSMIEVVHLDRSTYAEPPARFEAGTPPISQAVGLAAACD
+YLSALGMDAVAEHEHALTARALEHLAGMDRVRVIGAPAGPERSGAVSFAVEGIHPHDVGQ
+VLDSLGVQVRVGHHCAWPLHRRYGVPGTTRASFSVYSTLDEVDAFADGLAQTLAFFQGFG
+R
+>4_1454
+MSTTLDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVARAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVAALR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000135.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000135.fa
new file mode 100644
index 0000000000000000000000000000000000000000..23d796e992f1b9f461a7bcfe85bd5a60638b3305
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000135.fa
@@ -0,0 +1,48 @@
+>0_1528
+MSLACVPHPGPVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKVLRGRFARGLTLRSGWV
+DGATDHTAKILADTLPSDTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATKPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYADVPVIAQWDDHETTNNWWPGEVLED
+PRYTQVRDVDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDM
+RTHKGENTPGLETHETPILGEEQLQWLIRGLRASTATWKVIANDLPLGLVVPDGTGQESL
+SNGDDGAPLGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWE
+FVAGPINAGSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRL
+INAAGRTVYSRTLTAA
+>1_1248
+MRLACVPHPGPVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKVLRGRFARGLTLRSGWV
+DGATDHTAKILADTLPSDTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATKPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYADVPVIAQWDDHETTNNW
+>1_1249
+MDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDMRTHKGENT
+PGLETHETPILGEEQLQWLIRGLRASTATWKVIANDLPLGLVVPDGTGQESLSNGDDGAP
+LGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFESFWEFVAGPINA
+GSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRLINAVGRTV
+YSRTLTAA
+>2_1315
+MKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWEFVAGPINAGSFGPNTLDGTFGPRLDF
+EAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRLINAVGRTVYSRTLTAA
+>3_1210
+MSLACVPHPGSVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKVLRGRFARGLTLRSGWV
+DGATDHTAKILADTLPSGTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATQPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYADVPVIAQWDDHETTNNWWPGEVLED
+PRYTQVRDVDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDM
+RTHKGENTPGLETHETPILGEEQLQWLIHGLRASTATWKVIANDLPLGLVVPDGTGQESL
+SNGDDGAPLGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWE
+FVAGPINAGSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRL
+INANGRTVYARTLTAA
+>4_1455
+MSLACVPHPGPVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKALRGRFSRGLTLRSGWV
+DGATDHTAKILADTLPSGTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATQPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYTDVPVIAQWDDHETTNNWWPGEVLED
+PRYTQVRDVDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDM
+RTHKGENTPGLETHETPILGEEQLQWLIRGLRASTATWKVIANDLPLGLIVPDGTGQESL
+SNGDDGAPLGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWE
+FVAGPINAGSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEGGREFRVRL
+INAAGRTVYSRTLTAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000140.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000140.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b9e752d6a91f9df6dfe6ae1b4ce62390f2a6aa63
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000140.fa
@@ -0,0 +1,52 @@
+>0_1570
+MRDASAAAGPPVDCRTVALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVV
+NLPDERLPQLAEIFGSERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVV
+RAFDDGDVVHVDGKVDPASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEAL
+KAALAVLERGETIFAAKDKDKLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRD
+LVAPADAVFLDAKLESDLVELSEEEAAEMLEMAGQDESGLDQLARVGFSTLGLQTYLTAG
+PKETRAWTIPVGATAPEAAGVIHTDFQRGFIKAEIVSFDDLIAAGSMADAKAAGKVRMEG
+KDYVMKDGDVVEFRFNV
+>1_1286
+MRDASAAAGPPVDCRTVALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVV
+NLPDERLPQLAEIFGSERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVV
+RAFDDGDVVHVDGKVDPASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEAL
+QAALAVLERGETIFAAKDKDKLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRD
+LVAPADAVFLDAKLESDLVELSEEEAAEMLEMAGQDESGLDQLARVGFSTLGLQTYLTAG
+PKETRAWTIPVGATAPEAAGVIHTDFQRGFIKAEIVSFEDLIAAGSMADAKAAGKVRMEG
+KDYVMKDGDVVEFRFNV
+>2_1248
+MALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVVNLPDERLPQLAEIFGS
+ERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVVRAFDDGDVVHVDGKVD
+PASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEALKAALAVLERGETIFAA
+KDKDKLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRDLVAPADAVFLDAKLES
+DLVELSEEEAAEMLEMAGQNESGLDQLARVGFSTLGLQTYLTAGPKETRAWTIPVGATAP
+EAAGVIHTDFQRGFIKAEIVSFEDLIAAGSMADAKAAGKVRMEGKDYVMKDGDVVEFRFN
+V
+>3_763
+MSHAHHHGGGSSAAVLDSSLTRLGLVGSPNSGKSTLFNALTGLRVKTGNYPGVTVSRAEG
+VMVAEDGTRVVLEDLPGTYSLDPISPDEQVVADLLALDPADADHPQALLLVADATTLRRG
+LTMVAHALAVELPATLVLTFGDELALRGGSVDVTRLSRALGIPVLAATAGDARQREAVRA
+HLATDPAGWAVPPVAPPTDPAGIAAWIDSVLEAARYAVPRPDGRTRRIDDVLLHPVWGTL
+VFLVTMFAFFQVIFTVAAPLQALVEELFGWLGERAAALIPIEWLGRFVAEALIGGVGGVV
+VFLPQILLLFLMISLLESTGYMTRAAFLMDRVMSRFGLEGRSFVALLSSLACAVPGIMAT
+RSLPSARDRLATMMAAPSMTCSARLPVYVLLISLLVPSEVRWGPVGLQGLVMFALYLGGA
+TASMLTAAFWSRVVGRRQAAMPFYMEMPPYRLPKARTVVTSMWASAEGFLRKVTSIILVT
+TALLWVLLNVPVRSEEEMAGAGVAMDDPAAVAQYTIDHSAAAAVGKAVEPAFEPLGFDWR
+IDVGVLASLAAREVFVATLGQMAAAEDPEDPGDALASWTVTDDAGVERPLFTPDVVAALL
+VFFMLALQCMSTLAVMRRETGTWRWPLLAFGYYFTLAWLAAFAVRHVVLALT
+>3_1158
+MALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVVNLPDERLPQLAEIFGS
+ERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVVRAFDDGDVVHVDGKVD
+PASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEALKAALAVLERGETIFAA
+KDKDKLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRDLVAPADAVFLDAKLES
+DLVELSEEEAAEMLEMAGQDESGLDQLARVGFSTLGLQTYLTAGPKETRAWTIPVGATAP
+EAAGVIHTDFQRGFIKAEIVSFDDLIAAGSMNDAKAAGKVRMEGKDYVMKDGDVVEFRFN
+V
+>4_1497
+MGPPVDCRTVALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVVNLPDERL
+PRLAEIFGSERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVVRVFDDGD
+VVHVDGKVDPASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEALQAALAVL
+ERGETIFAAKDKDTLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRDLVAPADA
+VFLDAKLESDLVELSEEEAAEMLEMAGQDESGMDQLARVGFSTLGLQTYLTAGPKETRAW
+TIPVGATAPEAAGVIHTDFQRGFIKAEIVSFDDLIAAGSMNDAKAAGKVRMEGKDYVMKD
+GDVVEFRFNV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000152.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000152.fa
new file mode 100644
index 0000000000000000000000000000000000000000..240e2d061afcdfcd822f34858897f3754d5de591
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000152.fa
@@ -0,0 +1,59 @@
+>0_1879
+MEATVEQITAAITALNDKYWYVVMALLFVAGVWFTIRTVGVQVRMLPEMLRSVTAKSQTG
+FENDGVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWLLAIIGGATAFVESTL
+AQLYKQKGSDGYFGGPAYYIRDGLGAKWLAAVFAVAITVTYGFVFNAVQSNSISESVQAN
+WGASSTTAWIVGLGLAALTGLVIFGGVRRLSAVTNVLVPVMATFYIFLALIVMVVNITEV
+PGMIALIVGHAFGLREVAGAAVGMTMVMQGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQ
+GFVQSLGVYFDTLIVCSATAFVILLSNPAYGRGEAIGMQVTQGALQQAVGAWAGPALTVI
+IFFLAWSSVLGNTYYGEANIRYLAGRHAGPAITVFRVLVLVCVVGGALGSVALVWNLADT
+FAALMATINLVAIIPLGGLAVKLLRDYERKLKAGMNPGFHISDLPEARNVALWRDEPKTS
+PLQD
+>1_1586
+MEATVEQITAAVTAFNDKYWYVVMALLFVAGVWFTIRTVGVQVRMLPEMLRSVTAKSQTG
+FENDGVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWLLAIIGGATAFVESTL
+AQLYKQKGADGYFGGPAYYIRDGLGAKWLAAVFAVAITVTYGFVFNAVQSNSISESVQAN
+WGASSTTAWIVGLGLAALTGLVIFGGVRRLSAVTNVLVPVMATFYIFLALIVMVVNITEV
+PGMIALIVGHAFGLREVAGAAVGMTMVMQGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQ
+GFVQSLGVYFDTLIVCSATAFVILLSNPAYGRGEALGMQVTQGALQQAVGAWAGPALTVI
+IFFLAWSSVLGNTYYGEANIRYLAGRHAGRAITVFRVLVLVCVVGGALGSVALVWNLADT
+FAALMATINLVAIIPLGGLAVKLLRDYERKLKAGMDPGFHISDLPEARNVALWRDEPKTS
+PLQD
+>2_900
+MEAITAAVSAFNDKYWYVVMALLFTAGVWFTIRTVGVQVRMLPEMLRSVTAGSQKGFEND
+GVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWVLAIIGGATAFVESTLAQLY
+KQKGPDGFYGGPAYYIRDGLRSKWLAAVFAVAITVTYGFVFNAVQSNSISESVQANWGVS
+TTTAWIVGVALAVITGLVIFGGVRRLSAVTNVIVPVMAVFYLVLALIVMAVNITEIPGLI
+ALIVGHAFGLQEVTGAAVGMAMVMMGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQGFVQ
+SLGVYFDTLIVCSATAFIILLSNPSYGDGEALGMAVTQGALQQAVGAWAGPALTVIIFFL
+AWSSVLGNTYYGEANIRYLAGKRADAAITVFRVLVLLCVVGGALGSVALVWNLADTFAAL
+MATINLVAIIPLGGLAVKLLRDYERKLKAGEDPGFHVSDLPEARNVALWQDTPETAPLQK
+>3_835
+MGALADAISAFNSKYWYLVMALLAFAGVWFTVRTVGVQVRMLPEMIRSVAAKSPEGGADD
+GVSPFRAFTISAASRVGTGNVAGVAIAIVLGGPGAVFWMWVMAILGGATAFVESTLAQLY
+KRKDRDGFFGGPAYYIRDGLGLKWLAALFAVAITVTYGFVFNAVQSNSISESVQANWGAS
+TTTAWIVGVALAVITALVIFGGVQRLSSVTNVIVPVMAVAYVLLAVVVMVINITEIPAMF
+ALIVRHALGFEQVAGAAVGMAMVMQGVRRGMFSNEAGMGSAPNAAAAAAVSHPAKQGFVQ
+SLGVYFDTLLVCSATAFIILLSNPEYGNTDALGMVVTQNALQQAVGAWAGPFLTVVIFFL
+AWSSVLGNTYYGEANIRYLAGERAPQWITAFRVLVLLCVVGGALGTVSLVWNLADTFAAL
+MATINLVAIIPLGGLAVKLLQDYERKLKAGEDPHFRLADLPEAKNVPLWGDEDAELMRTE
+QGHGAGAREELHHADRPGRGHGGGSHSA
+>3_2083
+MDAFVTAATDGLGELSGIIWGPFVLIPLLFLTGLYLTIRLGFVQFLRLGAGLHLGLLRRK
+DDGDAEGEISQFQALTTALAATVGTGNIVGVATAIAVGGPGALFWMWVTGVLGMASKYSE
+AFLAVRFRTTDDAGEKSGGPQYYLQRGIKGGLGKGLALFFSVAALLACFGIGNMTQGNSI
+AVNVDSAFGVPTWITGAVLAVMTMVVLVGGIKSIGKVTAGFVPVMIVFYVLGALWILIVN
+ASAIPSAFATIFTEAFTGSAAVGGFTGSAMIVAVQYGMARGIFSNESGMGSAAIAAAAAQ
+TTHPVRQGLVSMTQTFIDTIIVVTCTGLVLITTGTWTEGKATAATMTSDAFATGLPGNWG
+HWIVTIGLVMFAYSTILGWSYYGERQVERLFGTRLIMPFRVLFSLVVFFGCTTELDLAWT
+FSDVMNGLMAIPNLLGLLILSGLIARETRLYLKHDPKLVATEAQIRDFMAEDPGYREWLA
+QEKQLDRAHAEHLHPHATGGSSVR
+>4_1799
+MEATVEQITAAITALNDKYWYVVMALLFVAGVWFTIRTVGVQVRMLPEMLRSVTAKSQTG
+FENDGVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWLLAIIGGATAFVESTL
+AQLYKQKGSDGYFGGPAYYIRDGLGAKWLAAVFAVAITVTYGFVFNAVQSNSISESVQAN
+WGASSTTAWIVGLGLAALTGLVIFGGVRRLSAVTNVLVPVMATFYIFLALIVMVVNITEV
+PGMIALIVGHAFGLREVAGAAVGMTMVMQGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQ
+GFVQSLGVYFDTLIVCSATAFVILLSNPAYGRGEAIGMQVTQGALQQAVGAWAGPALTVI
+IFFLAWSSVLGNTYYGEANIRYLAGRHAGPAITVFRVLVLVCVVGGALGSVALVWNLADT
+FAALMATINLVAIIPLGGLAVKLLRDYERKLKAGMNPGFHISDLPEARNVALWRDEPKTS
+PLQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000154.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000154.fa
new file mode 100644
index 0000000000000000000000000000000000000000..576bc2f0c7a7190531f8fe0b3690c0b4b6c2d7aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000154.fa
@@ -0,0 +1,24 @@
+>0_1922
+MTPALISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGVIAAGLAV
+AGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVVGLFLGFAVGLFASQWARTR
+DARAALSSSIGALTAMGVGMLVEFCCALGSLTAVGVGALVHGLTA
+>1_1627
+MTPALISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGVIAAGLAV
+AGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVVGLFLGFAVGLFASQWARTR
+DARAALSSSIGALTAMGMGMLVEFCCALGSLTAVGVGALVHGLTA
+>2_856
+MTLAIVVSVLAVLLLIVGVVGTVYPILPGSMLILVTAVAWAWILGSGASWTFGLLAAGLA
+VAGMSASAVLTGRRLLRERVTRGPIAAGVVGAIVGFFVIPVVGLFIGFAVGLFGSQWART
+KDARAALASSWGALKAMGLGMLVELGCAMLALVSVGVGILVHFVF
+>3_792
+MTPALISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGLIAAGLAV
+AGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVAGLFLGFAVGLFASQWARTR
+DARTALSSSIGALTAMGVGMLVEFCCALGSLTAVGVGALVHGVTA
+>3_805
+MTFAILVSLLAVLLLIVGLVGTVYPVLPGSVLNAVVSLAWAWVLGSVASWTFGLIACAFS
+IAGMSASAALTGRRLVKERIPRGPILTGVAAAVVGFFVIPVVGVFVGFAAGLFGAEWARR
+RDARAALTSSWGALKAMGLGMLVEFGCAMVALASVGAGALVHVLSL
+>4_1849
+MTPALISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGVIAAGLAV
+AGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVVGLFLGFAVGLFASQWARTR
+DARAALSSSIGALTAMGVGMLVEFCCALGSLTAVGVGALVHGLTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000155.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000155.fa
new file mode 100644
index 0000000000000000000000000000000000000000..336c26104fd9f0ad2f7111fd133eb914388c678a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000155.fa
@@ -0,0 +1,30 @@
+>0_1924
+MSPQKTVGVLALQGDVREHVHVLESLGARTRPVRRPADLEGLDGIVLPGGESSVMDRLAR
+IMGMRDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVDS
+FEEDLDIPAVAAEPVHAVFIRAPAVLQAGEGVEVLASVPASRLSVPAADPGLDGDARLPV
+AVRQGHLLATAFHPEVTGDWSFHRAFLAGL
+>1_1629
+MSPQKTVGVFALQGDVREHVHVLEALGARTRPVRRPADLEGLDGIVLPGGESSVMDRLAR
+IMGLKDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVDS
+FEEDLDIPAVAAEPVHAVFIRAPAVLQAGEGVEVLASVPTSRLSVPAADPGLDGDARLPV
+AVRQGHLLATAFHPEVTGDWSFHRAFLAGLRPPRAPRR
+>2_853
+MSALLVGVFALQGDVREHVRVLEGLGARTRPVRRAADLTGLDGIVLPGGESSVMDRLAGL
+MGLKEPLADAIGAGLPAYGTCAGIILLAREIQNPAPGQGSLGVLDVTVRRNAFGAQVDSF
+EADLEVPAVSAEPVHAVFIRAPAVLRAGGEVEVLASVPASRLSAAPPELGLDDAAQVPVA
+VRQGRVLATSFHPEVTGDHSFHREFLRGL
+>3_790
+MSPQKTVGVFALQGDVREHVHVLESLGARTRPVRRPADLEGLDGIVLPGGESSVMDRLAR
+IMGLKDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVDS
+FEEDLDVPAVAAEPVHAVFIRAPAVVQAGEGVEVLASVPASRLSLPAADPGLDGDARLPV
+AVRQGHLLATAFHPEVTGDWSFHRAFLAGL
+>3_800
+MRAVQKTVGVFALQGDVREHVHVLEALGARTRPVRRPADLAGLDGIVLPGEESSVMDRLA
+RIMGLRDPLAEAVRAGLPVYGTCAGMILLAAGIENPAPGQGSLGVLDVTVRRNAFGSQAD
+SLEADLQVPAVSADPMHAVLIRAPAVVRVGEGVEVLASVPAARAVAASSSTAETDDGAPA
+ADLPVAVRAGNVSATSFHPEVTGDWSFHRAFLAGL
+>4_1851
+MSPQKTVGVFALQGDVREHVHVLEALGARTRPVRRPADLEGLDGIVLPGGESSVMDRLAR
+IMGLKDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVDS
+FEEDLDVPAVAAEPVHAVFIRAPAVLQAGEGVEVLASVPASRLSVPAADPGLDGDARLPV
+AVRQGHLLATAFHPEVTGDWSFHRAFLAGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000156.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000156.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e189090c7a7bed5a0073bd09929b59fdb5bfc7a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000156.fa
@@ -0,0 +1,54 @@
+>0_1953
+MSHTVASPAAPVPARDRREERKVIAGTVVGTTIEWYDFFIFAQATALVFAALFFQPMGEN
+GSQIAAWVTLGISFLVRPLGAIVAGHLGDRFGRKLVLSLTLIGMGLATTLIGLLPTYAQI
+GVWAPILLVALRLLQGLSAGGEWGGAALLSVEHAPHGKRGLFGSAPQIGVPLGMILATGV
+LFIVRSTMSEEQFLTWGWRIPFLISVILIVVGYLIRKAVEESPVFKEMQQLKVDESAPLG
+ELFRHHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLVGGVGWFI
+FTLLGGWVSDKIGRKLTFVFGYGFLIVWAFPLFGLLNTASLPLFSLGLFVLTLGLGPSYG
+PQSAMYAEMFPARVRFSGVSIGYALGTIIGGAFAPLLADQLVKTGWENVAWYIIVISAIS
+LIAVLFVPKGIQDRELHDEQVVATRSNPVVPT
+>1_1674
+MSHTVASPAAPAPARDRREERKVIAGTVVGTTIEWYDFFIFAQATALVFAALFFQPMGES
+GSQIAAWATLGISFLIRPLGAIVAGHLGDRFGRKFVLSLTLIGMGLATTLIGLLPTYAQI
+GVWAPILLVALRLLQGLSAGGEWGGAALLSVEHAPHGKRGLFGSAPQIGVPLGMILATGV
+LFIVRSTMSEEQFLTWGWRIPFLISVVLIVVGYLIRKAVEESPVFKEMQQLKVDESAPLG
+ELFRHHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLVGGVGWFI
+FTLLGGWVSDKIGRKLTFILGYGFLIIWAFPLFGLLNTASLPLFSLGLFVLTLGLGPSYG
+PQSAMYAEMFPARVRFSGVSIGYALGTIIGGAFAPLLADQLVKTGWENVAWYIIVISAVS
+LIAVLFVPKGIQDRELHDEQVVATRSNPVVPA
+>2_120
+MAEFSAAPTAHPAESDTHVSPAQRRKAFVGAIAGHLIEWYDYGVYGFLAVYVAANFFKSE
+NPMVGILAAFAVFALSFFVRPLGGLFFGPLADKIGRRKTLMIVLGLMCGATAVIGMLPTY
+ATIGVFAPILLVLMRLVQGFSAGGEVSTISAFVAEYAVKGRRGFATSFLMVTAASGLLLG
+GVVANGLGAIIGTEAMAEWGWRLPFLLAGVLGVVAVFIRMKLEDSPEFRRLHSEGKTSKT
+PLRETLRYQRQLFLMGALITLLGSTFYLVLTYLTTYMRTILELTPGAIFWLVLLTGAAAA
+AFMPVGGAISDRMGDRRPMLAIGAVLVAGAVVWFFLTAPGTDGGLPLVPSLLALGITTGL
+YCGVPYATMTELMPAHVRSTGIALGYNVPVAVFGGSAPFIASWLINETGDVASPMYFFLL
+TAAIALVGVAMLRPTDLLGHEDVPVTGSIDAVGGKVTRTVAPRPKADAL
+>2_807
+MSHTTVAHGAEHPARTRDRAEERKVLAGTLVGTTIEWYDFFIYAQAAALVFAPLFFAPMG
+EQGAQIASWASLGISFLVRPLGAIVAGHMGDRFGRKLVLSLTLIGMGAATVLIGLLPTYA
+SIGIWAPILLVVFRLLQGFSAGGEWGGAALLSVEHAPRGKRGLFGSAPQIGVPLGMLLAT
+GVLFAVRASMTNEQFLAWGWRIPFLISVILIFIGYIIRKAVEESPVFKEMQQLKKDESAP
+LGELFRNHTKEVVLAALIFAANNAVGYLVIAWFSKYGQKNLGMAPNDTLIAALVGGFGWF
+IFTLFGGWISDKIGRKTAFVAGYALIIAWAFPMFQMMNTASLPMFAAALFILSIGLGPSY
+GPQSAMYAEMFPARVRFSGVSIGYAIGAIIGGAFAPLIADLLLNDGGWVPVAWYMIIISA
+VSLIAVLFVPKGIQDRNLHDEGVVVAETGTREPVA
+>3_747
+MSHTVASPAVAAARDPREERKVLAGTLVGTTIEWYDFFIFAQATALVFATLFFQPMGESG
+AQIAAWVTLGISFLVRPLGAIIAGHLGDKFGRKLVLSLTLIGMGAATTLIGLLPTYAQIG
+VWAPILLVLLRLLQGFSAGGEWGGAALLAVEHAPHGKRGLFGSAPQIGVPLGMILATGVL
+FLVRSTMSEEQFLTWGWRIPFLVSVLLIVVGYFIRKAVEESPVFKEMQQLKVDESAPLGE
+LFRHHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLVGGVGWFIF
+TLLGGWISDKIGRKTTFVIGYAILIAWAFPMFQLLNTASLLLFSLALFVLTMGLGPSYGP
+QSAMYAEMFPARVRFSGVSIGYAIGTIIGGAFAPLIADELVKSGWPSVAWYIIGISAISL
+IAVLFVPKGIQDRELHDEEVVATRSNPVVPA
+>4_1892
+MSHTVASPAAPVPARDRREERKVIAGTVVGTTIEWYDFFIFAQATALVFAALFFQPMGES
+GSQIAAWVTLGISFLVRPLGAIIAGHLGDRFGRKLVLSLTLIGMGLATTLIGLLPTYAQI
+GVWAPILLVALRLLQGLSAGGEWGGAALLSVEHAPHGKRGLFGSAPQIGVPLGMILATGV
+LFIVRSTMSEEQFLTWGWRIPFLISVALIVVGYLIRKAVEESPVFKEMQQLKVDESAPLG
+ELFRNHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLIGGVGWFI
+FTLLGGWISDKIGRKLTFVLGYGFLIVWAFPLFGLLNTASLPLFSLGLFVLTLGLGPSYG
+PQSAMYAEMFPARVRFSGVSIGYALGTIIGGAFAPLLADQLVKTGWENVAWYIIVISAIS
+LIAVLFVPKGIQDRELHDEQVVATRSNPVVPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000161.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000161.fa
new file mode 100644
index 0000000000000000000000000000000000000000..50a7f71a08ed64ca1ae2c2eac6d0528b329daff0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000161.fa
@@ -0,0 +1,42 @@
+>0_2018
+MPDIIEFPLPASSDDPHWRAYCRLGDEYNHELIGTTEWDETPTDALIQAAAETDHTQRRY
+LAYVDGEAVGYARVLINHVDDPDAAALNVYVLPRHRGRGHGRALAERLVQDTAGLTRFET
+WPLTPRPVAGQRTLTPPNGAGAVPAEHPGVRLAQSYGFALVQIERVSRYDFADPGIDPAV
+ALAEAERVSSDYELHAWEGAADASLQDDLAVLKARMATDVPSGERTVVEQVWDAARVRRM
+DEQILTTGRLFRAVARHRATGRIVALSELVAPRSRPDGLIDQWDTIVLPEHRGHRLGMRV
+KAANLIAVRDALPEARAIITWNAEENRHMLDVNEALGFRPVLVEASMEAPAPLRRR
+>1_1733
+MPDIIEFPLPASSDDPHWRAYCHLGDEYNHELIGTTEWDETPRDALIQAAAETDHTQRRY
+LAYVDGEAVGYARVLINHVDDPDAAALNVYIHPRHRGRGHGRALAERLVLDTAGLTRFET
+WPLTPRPVAGQRTLTPPNGAGAVPAEHPGVRLAQSYGFALVQTERVSRYDFADPGIDPAV
+ALAEAEGVSSDYELHAWEGAADASLQDDVAVLKARMATDVPSGERTVVEQVWDAARVRRM
+DEQILTTGRLFRAVARHRATGRIVALSELVAPRSRPDGLIDQWDTIVLPEHRGRRLGMRV
+KAANLIAVRDALPGARAIITWNAEENRHMLDVNEALGFRPVLVEASMEAPAPLRRR
+>2_687
+MPDIIEFPLPASSDDPHWRAYCQLGDEYNHELIGTTEWDETPTDALIQAAAETDHTLRRY
+LAYVDGEAVGYARVLINHVDDPDAASLTVYVHPRHRGRGHGRALAERLVLDTAGLTRFET
+WPLTPRPAVGQRALTPPNGAGMVPAGHPGVRLAQSYGFALVQIERVSRYDFADPGIDPAV
+AVAEAERVSSGYELHAWEGAADASLQDDLAVLKARMATDVPSGERTVVEQVWDAARVRRM
+DEQILTTGRLFRAVARHRATGRIVALSELVAPRSRPDGLIDQWDTIVLPEHRGHRLGMRV
+KAANLIAVRDALPEARAIITWNAEENRHMLDVNEALGFRPVLVEASMEAPAPLRRR
+>3_598
+MPDIIEFPLPASSDDPHWRAYCQLGDEYNHELIGTTEWDETPTDALIQAAAETDYTQRRY
+LAYVDGEAVGYARVLINHVDDPDAASLNVYVHPRHRGRGHGRALAERLVQDTAGLTRFET
+WPLTPRPVAGQRALTPPNGAGVVPAEHPGVRLAQSYGFALVQIERVSRYDFADPGIDPAV
+ALAEAERVSSDYELHAWEGAADAALQDDLAVLKARMATDVPSGERTVVEQVWDAARVRRM
+DEQILTTGRLFRAVARHRATGRIVALSELVAPRSRPDGLIDQWDTIVLPEHRGHRLGMRV
+KAANLIAVRDALPEARAIITWNAEENRHMLDVNEALGFRPVLVEASMEAPAPLRRR
+>3_602
+MPDILEFPLPATADEAHWQAYCRLNRDHNHELLGTTEWDESPDDALLDAAAESDYTLRRF
+LALDDGTPVGNGRILVNHVDEPDAASLSVFIHPDHRRRGHGRALAERIAREADGFTRFET
+WPMTPLPAEGERALRPSSGAGAVPADHPGVRLALSYGFALGQVERVSRYDVLTPAVDPAD
+ALAEAERPGADYEVLTWEGPADEAVRADLAVLKERMATDVPSGDLTVAEQTWDAGRVRRQ
+EEQILLTGRLFRAAVRHRDTGRIVGVNELVAPRSRTSGLVDQWDTIVSPEHRGHRLGMRV
+KAANLVALRRALTEARAIITWNAEENRPMLDVNEALGFQPILVEAEMQAHGPLRRVVP
+>4_1957
+MPDIIEFPLPVSSDDPHWRAYCQLGDEYNHELIGTTEWDETPTDALIQAAAETDHTLRRY
+LAYVDGEAVGYARVLINHVDDPDAAALNVYVHPRHRGRGHGRALAERLVLDTAGLTRFET
+WPLTPPPVAGQRALTPPNGAGAVPAEHPGVRLAQSYGFALAQIERVSRYDFADPGIDPAV
+ALAEAERVSSDYELHAWEGAADASLQDDLAVLKACMATDVPSGERTVVEQVWDAARVRRM
+DEQILTTGRLFRAVARHRATGRIVALSELVAPRSRPDGLIDQWDTIVLPEHRGHRLGMRV
+KAANLIAVRDALPEARAIITWNAEENRHMLDVNEALGFRPVLAEASMEAPAPLRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000162.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000162.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d481069454618c04ca7b67727dc8cc40145b32d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000162.fa
@@ -0,0 +1,22 @@
+>0_2032
+MTDTTTARPKRPAHRDDGPPVRGIGHLRHPAVSGGLIGVIGGGAFLFGGIAGLPAEHRAT
+LRGIAISLISFTLVVVLLRRRMLPTVPTPARGALRVYGIAVVAMLAFLPVTRLVALALDA
+PTAQIALVAAVVGGHFLPFARAFQAPVFWWIGGAMAALGLAGAALAALGDPVAGPAGAAA
+AGVAMLVIVAAQGLLASPRQD
+>1_1750
+MSHVMRGGTMTDTTTARPMRPAHFDDDPPVRGIGHLRHPVVWGGLIGVVGGGAFLFGGIA
+GLPAEHQGTLRGSAIALIGFTLVVVLLRRRVLPAVQAPARGASTGSPSSRCWRSSP
+>1_1751
+MLALLPVTRLVALALDAPTAQIALVAAVVGGHFLPFARAFQAPVFWWIGGAMAVLGLAGA
+VVAVLGDPVAGPAGAAEAGAAMLVIVAAQGLLASPRQD
+>2_667
+MSHVTRGGTMTDTTTARPMRPTHHDDDPPVRGIGHLRHPVVSGGLIDGAMAAQGLLASPR
+PD
+>3_538
+MERDSTHARGIAHPMHPAVLGAVVGMVGGSLFMLLSRPELPFPWPTVTLVAWIALLAAAA
+WAVFLAPRRLRDVGAPSRHAGPIYGLSVLGMVALIIASPHLVRALGIEAAQPAVVVMAVG
+LHFIPFASAFGARVFAWLGGSLTAIGLAGVIAAAVVGAPAGAVAAVLAGAAMLAFLAVDA
+RRGA
+>3_584
+MSHVMRGGTMTATTTARPMRPTHHDDDPPVRGVGHLRHPVVSGGLIDGAMAAQGLLASPR
+QD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000163.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000163.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6c6096a573786caedfab7537261066b15558207
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000163.fa
@@ -0,0 +1,123 @@
+>0_2037
+MATADSGDVLPHLRTEAIRAVVGPTSADRGFAVAASGAVGRLRYDAATGRLSASVQGTAP
+SPYRVQVQLQEAYDDAAEDGAGALMEPVGGRCTCPVGTDCKHVAAALYQVVRLDADQALD
+DARRKLAEMVTTADALPAPAGRGHDGGGPAGLDAPAADGAAPPPPAGLDWRRVMEPLAGL
+HGPRRVGTPPALAIGVELVAESSRNAFQQWGPATAGEEQVREGRPLYVTVRPLKRGAKGT
+WIKGGLTWKAFQFPRAEFAPAQERAMRLIWRQVQAEDSYPGDAWFGLHVFDSPRIWQLLA
+EAREVGVELVPLGLLTDVVLEAPVAVGLDVTAAPDGGLDVAPSLDPAPPGPGLSGVHAVG
+GIGFYRVELTDEEAVLHLIPAARPVPEAVQQLVLAGGPVRVPAADREEFLGRIYPRLRGA
+LPVTSGDASVELPEFEPPVLRLRADFRPGHELVLRWSWLYFDPPRELGLDAGGDPLRDTR
+HEDAVLRAVAELWPRAGRAEEQVLEGVGAARFSEQVLPLLQRADHVRVDVTGDRPDYREL
+KAAPRIEVGTKATQNDWFDLGVQVSVDGHVLPFVELFTALVQGRTTLILADGSYLGLDHP
+AFDRLRALLSEAATLQEWTPEHTPVSRHQVGFWEDLKELADEVDEDPEWTAAVGRLAAVE
+RLPEAPRPAGLKADLRPYQEEGLRWLAFLWEQDLGGILADDMGLGKTVQTLALFAHARQA
+RPEPPPFLVVAPSSVVSVWAAEAEKFTPDLDVRVLDTTTRKRGTAVADEVAGADVVVTSY
+TLLRIDAGQYGGLDWGGVVFDEAQFLKNRAAKVHTVARDLRAPFRLAITGTPMENSLSDL
+WALLDVVVPGLFPSHRRFRETYVTPIETGGDPERMAALRRRVRPFMLRRSKELVAKDLPS
+KQEQILQVELEPAHRKLYDRVLQRERRKVLGLLGDMDGNRFTIFTSLTLLRMLALAPQIV
+DDQYASVPSSKLERFLDDLTEVIGEGHRVIVFSQFTSFLRVIAEELDHLEIEHAYLDGST
+RGRADVIRGFREGEAPVFLISLKAGGFGLTLTEADYVFLMDPWWNPAAEAQAVDRAHRIG
+QERTVMVYRLVSEGTIEEKVLELQRRKAELFGALMDESDDSGAGAFTDSLTAEDIREMLG
+AEE
+>1_1755
+MATADSGDVLPHLRTEAIRAVVGPTSADRGFAVAASGAVGRLRYDAATGRLSASVQGTAP
+SPYRVQVQLQEAYDDAAEDGAGALMEPVGGRCTCPVGTDCKHVAAALYQVVRLDADQALD
+DARRKLAEMVTTADALPAPAGRGHDGGGPAGLDAPAADGAAPPPPAGLDWRRVMEPLAGL
+HGPRRVGTPPALAIGVELVAESSRNAFQQWGPATAGEEQVREGRPLYVTVRPLKRGAKGT
+WIKGGLTWKAFQFPRAEFAPAQERAMRLIWRQVQAEDSYPGDAWFGLHVFDSPRIWQLLA
+EAREVGVELVPLGLLTDVVLEAPVAVGLDVTAAPDGGLDVAPSLDPAPPGPGLSGVHAVG
+GIGFYRVELTDEEAVLHLIPAARPVPEAVQQLVLAGGPVRVPAADREEFLGRIYPRLRGA
+LPVTSGDASVELPEFEPPVLRLRADFRPGHELVLRWSWLYFDPPRELGLDAGGDPLRDTR
+HEDAVLRAVAELWPRAGRAEEQVLEGVGAARFSEQVLPLLQRADHVRVDVTGDRPDYREL
+KAAPRIEVGTKATQNDWFDLGVQVSVDGHVLPFVELFTALVQGRTTLILADGSYLGLDHP
+AFDRLRALLSEAATLQEWTPEHTPVSRHQVGFWEDLKELADEVDEDPEWTAAVGRLAAVE
+RLPEAPRPAGLKADLRPYQEEGLRWLAFLWEQDLGGILADDMGLGKTVQTLALFAHARQA
+RPEPPPFLVVAPSSVVSVWAAEAEKFTPDLDVRVLDTTTRKRGTAVADEVAGADVVVTSY
+TLLRIDAGQYGGLDWGGVVFDEAQFLKNRAAKVHTVARDLRAPFRLAITGTPMENSLSDL
+WALLDVVVPGLFPSHRRFRETYVTPIETGGDPERMAALRRRVRPFMLRRSKELVAKDLPS
+KQEQILQVELEPAHRKLYDRVLQRERRKVLGLLGDMDGNRFTIFTSLTLLRMLALAPQIV
+DDQYASVPSSKLERFLDDLTEVIGEGHRVIVFSQFTSFLRVIAEELDHLEIEHAYLDGST
+RGRADVIRGFREGEAPVFLISLKAGGFGLTLTEADYVFLMDPWWNPAAEAQAVDRAHRIG
+QERTVMVYRLVSEGTIEEKVLELQRRKAELFGALMDESDDSGAGAFTDSLTAEDIREMLG
+AEE
+>2_663
+MATADSGDVLPHLRTEAIRAVVGPTSADRGFAVAASGAVGRLRYDAATGRLSASVQGTAP
+SPYRVQVQLQEAYDDAAEAGAGALMEPVGGRCTCPVGTDCKHVAAALYQVVRLDAHQALD
+DARRKLAEMVTTADALPAPAGRGHDDAARPDAGPRGAAAGPDGESAAPEAPHSGLDWRRV
+MEPLAGLDAPRRLGAPPALAIGVELVAESSRNAFQQWGPAPAGEDQVREGRPLYVTLRPL
+KRGAKGTWIKGGLTWKNFQFGRAEFAPAQERAMRLIWRQLQAEDSYPTDAWFGLHSFDSP
+RIWQLLAEAREVGVELVPLGLLTDVVLEAPAAVGLDVARAPDGGLDVAPSLDPAPPGRGL
+AGVHAVGGIGFYRVELTDEEAVLHLIPAERPVPEAVQQLVLAGGPVRVPAVDREEFLGRI
+YPRLRGALPVTSGDASVELPEFEPPVLRLRADFRPDHELVLRWSWLYFDPPRELGLDAGG
+DPLRDTRHEDAVLRAVAELWPRAGRAEEQVLEGVAAARFSEQVLPLLQQAEHVRVDVTGH
+RPDYRELKSAPRIEVGTKATKNDWFDLGVQVSVDGHVLPFVELFTALVQGKTTLILADGS
+YLGLDHPAFDRLRALLSEAATLQEWTPENTAVSRHQVGFWEDLKELADEVEEDPEWTAAV
+GRLAAVERLPEAPEVPGLQADLRPYQEDGLRWLAFLWEQDLGGILADDMGLGKTVQTLAL
+SAHARQARPERPPFLVVAPSSVVSVWAAEAQTFTPDLDVRVLDTTVRKRGTDVAAEAAGA
+DVVVTSYTLLRIDAGQFGGIDWGGVVFDEAQFLKNRAAKVHTVARDLRAPFRLAITGTPM
+ENSLTDLWALLGVVVPGLFPSHRRFREAYVTPIETGEDPERMVALRRRVRPFMLRRSKEL
+VAKDLPPKQEQVLNVELEPAHRKLYDRVLQRERRKVLGLLGDMDGNRFTIFKSLTLLRML
+ALAPQIVDEQYASVPSSKLERFLDDLTEVIAEGHRVIVFSQFTSFLRVIAEELDHMEVAH
+AYLDGSTRGRADVIRGFREGQAPVFLISLKAGGFGLTLTEADYVFLMDPWWNPAAEAQAV
+DRAHRIGQERTVMVYRLVSEGTIEEKVLELQRRKAELFGALMDESDDSGAGAFTDSLTAE
+DIRELLGAED
+>2_1470
+MNLPLTDYQAKYYAHELQRSYANDHVGKLAGLLFDAQVEPKPHQIDAALFALQTPFLPGV
+ILADEVGLGKTIEAGIVISQYWAERRRSILIVAPSSLRQQWQQELYEKFLIPSAILDPKS
+KDSLLAAAGGRSAQVLICSYEFALRHETSLLKAWDLVVADEAHRLRNYWTGKTKAAEAVA
+HVVSGAHKTVLLTATPLQNKLEELYGLVSIFDPNYFYSLDAFRERYVKNRDLGGDDDLVE
+RVATVSKRTLRRDADKYIHFTKRLPLTVEFTPSPDEARLYDLVNDYLQRDELFAFAGSQR
+HLSALIIRKRLGSSTYAVASTLENIANRLAEEVAAGQRRDGRGGLVTADFTVDDEITSEE
+LEEAEEIEGAGPASRPSSSPLDESLLEAMRAEVAELRDYAALARSITENQKAVKLGEALD
+LGFERLRELGAPQKAIIFTDSTKTQEYIARSLREAGRGDGLVLFNGSNNGPEQTAIYQAW
+LKANQDGDLITGIAAVDRRKALVDYFRTEGTIMIATEAAAEGINLQFCSMLVNYDLPWNP
+QRVEQRIGRVHRFGQKHNVVVVNFSNKGNIAEQRILELLTNKFQLFSSVFGASDEVLGAI
+EDGLDFEKTISDILTRCRTADELDAAFRELEGQYASEISREMASAKAKVFDNLDPHVQDR
+LKAYDTQSGEVLNKFERLLLAVTRHELDRFATFEGDGRAFVLNESPVQDVPTGRYFFKSQ
+PLENAHQYRYASSLAQYVVDTSKGHETPARELTFSLGQSERVSSAIRALEGTSGELTVNL
+ATFRMKARDEDVSESYMLAGALTDDGQWLDEEYVADILDLACISVGEQPVAIDESRFTPH
+LDARRAELEKEVQGRNSRYYDQQEELLYRNQQDRKAEHEGKIREYRAKEKEARKLARQAD
+DPMEQLRLKKEARKWEQRAEEADEDFRDTRKKLRAEADKYLELIEQSLQGTQETEHLFTI
+RWRITT
+>3_578
+MAPGVSGDPLPHLRTEAIRALVGPTSADRGFDIAAEGGVLRVTYDASRLRLTSAVRGTAP
+QPYRQAVRLQPSGETGPDGEPLLEPTAGRCQCPVGEDCKHVAAALYEITRRHADAARHAA
+REELASRVTTADRLPSPERAGAAPARPDAPAPEAGLPWRGVLESLAGLDGGPRRLAPPPD
+LAIGVELVAESSRNAFAQWGPAPAGEEHLREARLLYVIVRPLKRGAKGTWIKGGLTWKAF
+QFPRAEYDPAQERALRLIWRQLQAEDSYPTEGWFGLHAFDSPRIWQLLAEAQEAGVELVP
+QGILADVVLDAPVEVGLDVASAPDGGLEVAPSLAPAGGAGEGAPADDAAARPDAERLRDT
+HAIGSIGFYRADEEEDGTWTLHLLPAVRRVPEPVQEMVLAGRPVHVPTADREEFLGRIYP
+RLRAALDVGSADASVELPEFEPPVLRLQADFRPGHRLVLRWSWLYFDPPRELGLGHDGLR
+DPRHEEAVLRAAAQVWPRVGRAEEQELEGVGAARFSESVLPQLQRLDHVRVDVTGERPDY
+RELKAAPRIEVSTKAAQNDWFDLGVQVSVDGHVLPFVELFTALVHGKTTLMLQDGTWLGL
+DHPAFDRLRALLSEAAALQEWTPEHTTLSRHQVGFWEDLKELADEAEEDPEWTAAVGRLA
+AVERLPEAPAVPGLKAELRPYQEDGLRWLRFLHDQDLGGILADDMGLGKTVQTLALMAYA
+RAEHPDRPPFLVVAPSSVLSVWASEAAKFTPGLDVRVLDTTTRKRGTSVTEAAEGADVVV
+TSYTLLRIDAAQHADASWAGIVLDEAQFLKNRASKVHQVARDLRAPFRLAITGTPMENSL
+SDLWALLEVVVPGLFPSHRRFRETYVTPIETGEHPERMASLRRRVRPFMLRRSKELVAKD
+LPPKQEQVLRVELDAAHRKVYDRVLARERRKVLGLLGDMDGNRFTIFKSLTLLRMLALAP
+QIVDREYAAVPSSKLERFLDDLEEVLAEGHRVIVFSQFTSFLRVVAEELDAMEVEHAYLD
+GSTRNRAEVIQDFREGDAPVFLISLKAGGFGLTLTEADYVFLMDPWWNPAAENQAVDRAH
+RIGQERTVMVYRMVSEGTIEEKVLELQQRKAELFGALMDESDDSGAGAFTDSLTADDIRE
+LLGAEE
+>4_1978
+MATADSGDVLPHLRTEAIRAVVGPTSADRGFAVAASGAVGRLRYDAATGRLSASVQGTAP
+SPYRVQVQLQEAYDDAAEDGAGALMEPVGGRCTCPVGTDCKHVAAALYQVVRLDADQALD
+DARRKLAEMVTTADALPAPAGRGHDGGGPAGLDAPAADGAAPPPPAGLDWRRVMEPLAGL
+HGPRRVGTPPALAIGVELVAESSRNAFQQWGPATAGEEQVREGRPLYVTVRPLKRGAKGT
+WIKGGLTWKAFQFPRAEFAPAQERAMRLIWRQVQAEDSYPGDAWFGLHVFDSPRIWQLLA
+EAREVGVELVPLGLLTDVVLEAPVAVGLDVTRAPDGGLDVAPSLDPAPPGLGLSGVHAVG
+GIGFYRVELTDEEAVLHLIPAARPVPEAVQQLVLAGGPVRVPAADREEFLGRIYPRLRGA
+LPVTSGDASVELPEFEPPVLRLRADFRPGHELVLRWSWLYFDPPRELGLDAGGDPLRDTR
+HEDAVLRAVAELWPRAGRAEEQVLEGVGAARFSEQVLPLLQRADHVRVDVTGDRPDYREL
+KAAPRIEVGTKATQNDWFDLGVQVSVDGHVLPFVELFTALVQGRTTLILADGSYLGLDHP
+AFDRLRALLSEAATLQEWTPEHTPVSRHQVGFWEDLKELADEVDEDPEWTAAVGRLAAVE
+RLPEAPRPAGLKADLRPYQEEGLRWLAFLWEQDLGGILADDMGLGKTVQTLALFAHARQA
+RPERPPFLVVAPSSVVSVWAAEAEKFTPDLDVRVLDTTTRKRGTAVADEVAGADVVVTSY
+TLLRIDAGQYGGLDWGGVVFDEAQFLKNRAAKVHTVARDLRAPFRLAITGTPMENSLSDL
+WALLGVVVPGLFPSHRRFRETYVTPIETGGDPERMAALRRRVRPFMLRRSKELVAKDLPS
+KQEQILQVELEPAHRKLYDRVLQRERRKVLGLLGDMDGNRFTIFTSLTLLRMLALAPQIV
+DDQYASVPSSKLERFLDDLTEVIGEGHRVIVFSQFTSFLRVIAEELDHLEIEHAYLDGST
+RGRADVIRGFREGEAPVFLISLKAGGFGLTLTEADYVFLMDPWWNPAAEAQAVDRAHRIG
+QERTVMVYRLVSEGTIEEKVLELQRRKAELFGALMDESDDSGAGAFTDSLTAEDIREMLG
+AEE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000168.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000168.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71904b4415df3a775ca09b047f20051c2b0cf88a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000168.fa
@@ -0,0 +1,42 @@
+>0_2191
+MTAQTPATPAIPETMKAVVMRAPGDVVVEEVDTPRVAQPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSQAQYMRVELADGSLVKVPGGEPSDPDRLADYLAASDVLGTGWYAAVAAQAGPGKT
+IAVVGDGAVGLCAVLGAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQVRE
+LTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFGRQIHLEGGP
+APVRRFLPELIERIQSGEIQPGRVFTARRPIDDAAEAYQAMDERREIKVLLEV
+>0_2215
+MTTETPTLAAPEIPATMKAVVMRAPGDVVVEEVDTPRVAQPTDVVLKLAAACVCGSDLWP
+YRGHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVN
+AGEYTGSQAQYMRVELADGSLVKVPGGEPSDPDRLTDYLAASDVLGTGWYAAVAAQAGPG
+KTIAVVGDGAVGLCAVLAAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQV
+RELTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFGREIHLEG
+GPAPVRRFLPELIERIQSGEIQPGRVFTARRPIDDAAEAYQAMDERREIKVLLEV
+>1_1901
+MTAQTLATPAIPETMKAVVMRAPGDVVVEEVDTPRVAQPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSRAQYMRVELADGSLVKVPGGEPSDPDRLADYLAASDVLGTGWYAAVAAQAGPGKT
+IAVVGDGAVGLCAVLAAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQVRE
+LTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFAREIHLEGGP
+APVRRFLPELIERIQSGEIQPGRVFTARMPLDDAAEAYRAMDERREIKVLLEV
+>2_471
+MTAQTPATPAVPETMKAVIMRAPGDVVVEEVDTPRVAKPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSQAQYMRVELADGSLVKVPGGEPADPDRLADYLAASDVLGTGWYAAVAANAGPGKT
+IAVVGDGAVGLCAVLAAKTLGAEQVIAFSRHEDRAALAREFGADVIIAERGEEGAAKVKE
+LTNGYGAHGVCEAVGTQESMDQALASVRPGGHVGFVGVSHDQTIDGSRLFGLEIHLEGGP
+APVRRFLPELIERIQAGEIQPGRVFTARMPIDDAAEAYKAMDERREIKVLLEV
+>3_418
+MTAQTPTTPAIPETMKAVVMRAPGDVVVEEVDTPRVVQPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSQAQYMRVELADGSLVKVPGGEPSDPDRLADYLAASDVLGTGWYAAVAAQAGPGKT
+IAVVGDGAVGLCAVLAAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQVRE
+LTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFGREIHLEGGP
+APVRRFLPELIERIQSGEIQPGRVFTARMPLDDAAEAYRAMDERREIKVLLEV
+>4_2123
+MTAQTLATPAIPETMKAVVMRAPGDVVVEEVDTPRVAQPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSQAQYMRVELADGSLVKVPGGEPSDPDRLADYLAASDVLGTGWYAAVAAQAGPGKT
+IAVVGDGAVGLCAVLAAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQVRE
+LTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFAREIHLEGGP
+APVRRFLPELIERIQSGEIQPGRVFTARMPLDDAAEAYQAMDERREIKVLLEV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000171.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000171.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d0d831b2b30bf7ec04a378c315b48524c29313c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000171.fa
@@ -0,0 +1,47 @@
+>0_2244
+MPTVKAPSKRATSATSSRKEPGDSSVESAATEGTVSADIAVLREIPVGDIHPNPRQPREV
+FDEDHMAELVTSIREVGILQPIVVREVDGPTPHELIMGERRWRATQKAGLDTIPAIVRQT
+PDQDLLRDALLENLHRSQLNPLEEAAAYQQLMEDFACTQEELSQRIGRSRPQISNTLRLL
+KLPPLVQRRVAAGTLSAGHARALLGLTDPSDMERLAQRIQSEGLSVRSTEEAVAQLQGGL
+RPGRTPRRSTDDARHERLDHYATALTSRLDTAVKITLGARKGRIAIDFTTVEDLNRIMDL
+IQGGQDGKGKGKKS
+>1_1948
+MPTVKAPSKRATSATSSRKEPGDSSVESAATEGTVSADIAVLREIPVGDIHPNPRQPREV
+FDEDHMAELVTSIREVGILQPIVVREVDGPTPHELIMGERRWRATQKAGLDTIPAIVRQT
+PDQDLLRDALLENLHRSQLNPLEEAAAYQQLMEDFACTQEELSQRIGRSRPQISNTLRLL
+KLPPLVQRRVAAGTLSAGHARALLGLTDPSDMERLAQRIQSEGLSVRSTEEAVAQLQGGL
+RPGRTPRRSTDDARHERLDHYATALTSRLDTAVKITLGARKGRIAIDFTTVEDLNRIMDL
+IQGGQDGKGKGKKS
+>2_414
+MKTSRRGGLGRGLGALIQSTAEPVDEAPQEADATAEDATAPTAAPAEKKAATSTARRLSK
+ETSEAKTPAPRAASASKSSGGAAKEAPADKKAGSAGRAPAAAKKATPTKKASSSAGEAKA
+NSAAAPAAARKTPDRAAQRPVDVFFSPDPEDAPAARRGTKARPAMPTVKAPTKREAASSS
+GEEAAAGASTAAEGTVSTDIAVLREIPVGDIHPNPRQPREVFDEEHMAELVTSIREVGIL
+QPIVVREVDGPTPYELIMGERRWRATQKAGLDAIPAIVRQTPDQDLLRDALLENLHRSQL
+NALEEAAAYQQLMEDFACTQEELAERIGRSRPQISNTLRLLKLPPLVQRRVAAGTLSAGH
+ARALLGLTDPSDMERLAQRIQAEGLSVRATEEAVAQLQGGLRPGRTPRRTADDARHERLD
+HYATALTSRLDTSVKITLGARKGRIAIDFTTVEDLNRIMDVIQGEKGGRGAAS
+>2_1906
+MVASVKTQGLLQPLVVAPNPTLEGDYTIIAGHRRLDALKRAGRDDAPVIVRTDLDTEEKQ
+VAAMLQENLHRQDLTAVEEADAFAQLSLFEGWDVKRIARETGVAQTRVRSRIKLTYLSEA
+TLASLHDGQVTLERAQALAEFAGSPEEELLEEHLTATATNWDFYLARAKQTRDRRKALSA
+EQKAHEEAGFEVVPMPESLYTPEREWDRQDFESPTAALEAGAVVAFDPDYDAPVYLVKHA
+EQELEKDAAAAERKAEAAERAARNEALERELATAQETVRLWLVDTVFPKAAAGDERILRV
+AARHLAATACEETHFRRAGLAAIFCPDLGAYAPELRTAVAEVLAGKSAQELAVIIAVATR
+WTSTARVHAWRDATREDSSPAVWLAMRQELGRELAAPEQVAFDAAKAGEL
+>3_367
+MSTRRGGLGRGLGALIQNTAEIEQPPTREDSSPSAASSNKTTAAPAKRSTRTARTAESSQ
+NGLPASDGATQQDHSSDRAEKTASSGTGSQKTSRSTGSKGAKTPEPTATRSAQEEVPRPA
+DIFFGGGEGTSDEPPESGRHRPTRSARPSMPTVKAPSKPAPKSETEQAAPVRKDEPEGTV
+SADIAVLRELPVGDIHPNPRQPREVFDEDHMAELVASITEVGVLQPIVVREVEGAATPYE
+LIMGERRWRATQRAGLATIPAIVRQTPDQDLLRDALLENLHRSQLNPLEEAAAYQQLMED
+FSCTQEELSQRIGRSRPQISNTLRLLKLPPLVQRRVAAGALTAGHARALLGLTDPAEMER
+LAQRIVSEGLSVRATEDAVAQLQGAVRPAPKSTRSREESTRHERLDYFATALTSRLDTQV
+KITLGARKGKIAIDFASVEDLNRIMDLIQGGGDSTPVKG
+>4_2186
+MPTVKAPSKRATSATSSRKEPGDSSVESAATEGTVSADIAVLREIPVGDIHPNPRQPREV
+FDEDHMAELVTSIREVGILQPIVVREVDGPTPYELIMGERRWRATQKAGLDTIPAIVRQT
+PDQDLLRDALLENLHRSQLNPLEEAAAYQQLMEDFACTQEELSQRIGRSRPQISNTLRLL
+KLPPLVQRRVAAGTLSAGHARALLGLTDPSDMERLAQRIQSEGLSVRSTEEAVAQLQGGL
+RPGRTPRRSTDDARHERLDHYATALTSRLDTAVKITLGARKGRIAIDFTTVEDLNRIMDL
+IQGGQDGKGKGKKS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000175.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000175.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8c22a064a7e4d547e480feff424d6ad00f5c478e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000175.fa
@@ -0,0 +1,39 @@
+>0_1
+MQLVKFTVERDILTDAVSWAARSLSPRPPVPVLSGLLITAEAGVVSIASFDYETSARLEI
+EADVETAGQVLVSGRLLNDIVRSLPQAQVTVELDGGKVLVTCRSSRFALATMPVGDYPAL
+PELPAPAGTVDGAAFAHAVAQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMK
+EIRWTPADPSLSTSLLIKARTLTEVAKSLGSGGDLEILLGQTADLVGFASGGRRTTSVLV
+DGEYPKIRSLFPESSPIQAVVDTAALVEASRRVALVAERNTALRMVFTDGQVTLDAGTGD
+DASANESVPCTLEGEDITVAFNPSYLSEGLAVVDQPQVRFAFTSAPKPALLTGVNQEDGV
+VSDYRYLVMPVRIA
+>1_1957
+MQLVKFTVERDILTDAVSWAARSLSPRPPVPVLSGLLITAEAGVVSIASFDYETSARLEI
+EADVETAGQVLVSGRLLNDIVRSLPQAQVTVELDGGKVLVTCRSSRFALATMPVGDYPAL
+PELPAPAGTVDGAAFAHAVAQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMK
+EIRWTPADPSLSTSLLIKARTLTEVAKSLGSGGDLEILLGQTADLVGFASGGRRTTSVLV
+DGEYPKIRSLFPESSPIQAVVDTAALVEASRRVALVAERNTALRMVFTDGQVTLDAGTGD
+DASANESVPCTLEGEDITVAFNPSYLSEGLAVVDQPQVRFAFTSAPKPALLTGVNQEDGV
+VSDYRYLVMPVRIA
+>2_404
+MPVLSGLLITAEAGVVSIASFDYETSARLEIEADVETDGQVLVSGRLLNDIVRALPHAQV
+TVELDGGKVVVTCRSSRFALATMPVGDYPALPELPTPAGTVDGAAFAHAVAQVTVAASKD
+DTLPILTAVKVEIEGDTMTFLATDRYRLAMKEIRWTPADPSISTSLLVKARTLTEVAKSL
+GAGGDLEILLGEGTDLVGFSSGGRRTTSVLVDGEYPKIRSLFPETSPIQAVVDTAALVEA
+SRRVALVAERNTALRMVFTDGQVTLDAGTGDDASANESVPCTLEGEDITVAFNPSYLSEG
+LAVVDQPQVRFAFTSAPKPALLTGVNQEDGVVSDYRYLVMPVRIA
+>3_358
+MKFTVARDILSDAVSWAARSLSPRPPVPVLSGLLVTAEAGLVSIASFDYETSARLQIEAD
+VEDEGQVLVSGRLLNDIVRALPNAPVTLELDGGKVLVTCRSSRFQLATMPVADYPALPEL
+PEPAGTVDGAAFAHAVNQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMTEIR
+WNPADPAISTSLLIKARTLTEVAKSLGGGGRLEIMFGSSHDLVGFSSGGRRTTSVLVDGE
+YPKIRSLFPETSPIQAAVDTEELIAASRRVALVAERNTALRMVFTDGQVTLDAGTGDDAT
+ANESVPCTLEGEEITVAFNPAYLSEGLAVVDQPQVRFSFTAAPKPALLTGVHEEDGTVSD
+HRYLVMPVRLT
+>4_1
+MQLVKFTVERDILTDAVSWAARSLSPRPPVPVLSGLLITAEAGVVSIASFDYETSARLEI
+EADVETAGQVLVSGRLLNDIVRSLPQAQVTVELDGGKVLVTCRSSRFALATMPVGDYPAL
+PELPAPAGTVDGAAFAHAVAQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMK
+EIRWTPADPSLSTSLLIKARTLTEVAKSLGSGGDLEILLGQTADLVGFASGGRRTTSVLV
+DGEYPKIRSLFPESSPIQAVVDTAALVEASRRVALVAERNTALRMVFTDGQVTLDAGTGD
+DASANESVPCTLEGEDITVAFNPSYLSEGLAVVDQPQVRFAFTSAPKPALLTGVNQEDGV
+VSDYRYLVMPVRIA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000176.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000176.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09e575d1bae897d32233732abc2d448089be8576
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000176.fa
@@ -0,0 +1,41 @@
+>0_2
+MYLSHLTVADFRSYRWADLELTPGSTVLLGANGVGKTNLVEAIGYLGAQQSHRVSSDAQL
+VRFGRDRARIAGRVHRGSRAVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLSLVTGEPGGRRRLLDQLMVQLRPALGEAAADYERVLRQRNALLKSSRGSRRWGPEEDA
+TLAVWDEHLCAAGARLLHGRLHVLRLLARPLQEMYAALTNGSKAAAYAYESTVPLARGTH
+AEVPAVADLAVDMRRTLETQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRMAAYDVLVADDPDPDARPVLILDDVFAELDAARRRRLAALVHRAEQVIVTAAALE
+DVPEELTAHRVLIRQDAEGSEAVAAAAPVEGDIREPRREGGADG
+>1_1958
+MYLSHLTVADFRSYRWADLELTPGSTVLLGANGVGKTNLVEAIGYLGAQQSHRVSSDAQL
+VRFGRDRARIAGRVHRGSRAVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLGLVTGEPGGRRRLLDQLMVQLRPALGEAAADYERVLRQRNALLKAGRGSRRWGPEEDA
+TLAVWDEHLCAAGARLLHGRLHVLRLLARPLQEMYAALTNGSKAAAYAYESTVPLARGTH
+AEVPAVADLAVDMRRTLETQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRMAAYDVLVADDPDPDARPVLILDDVFAELDAARRRRLAALVHRAEQVIVTAAALE
+DVPEELTAHRVLIRQDAEGSEAVAAAAPVEGDIREPRREGGADG
+>2_403
+MHLSHLTVADFRSYRWADLELGPGSTVLLGANGVGKTNLVEAVGYLGSHQSHRVSSDAQL
+VRFGQDRARIAGRVHRGSRTVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLNLVTGEPGGRRRLLDQLMVQLRPALGEAAADFERVLRQRNALLKSARKARRWGPEEEA
+TLEVWDEHLCAAGARLLHGRLHVLRLLAHPLREMYGALTNGSKAATYAYESTVPLARGTH
+AEVPPVAELAADMRRALVAQRDEEQARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRLAAYDVLVADDPDPDGRPVLILDDVFAELDAARRRRLAALVGRAEQVIVTAAALE
+DVPAELAGPRVLIRQDAEGSEAVPAAAPVEGDIRAPRGAGGTEGEAPGARRGRRRRRRHA
+PADPAEDDPDG
+>3_357
+MHLSHLTVQDFRSYRWADLELSPGSTVLLGANGVGKTNLVEAIGYLGSHQSHRVSQDAQL
+VRFGQDRARIAGRVHRGARSVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLGLVTQDPGGRRRFLDQLMVQLRPALGQAAADYERVLRQRNALLKSARKARRWGAEEDA
+TLAVWDEHLCAAGARLLHGRLHVLRLLAHPLQEDYAALTNGSKTATYSYESTVPAARGTH
+VQAPPVAELAASMHAALVEQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRLAAYDVLVADDSDPEGRPVLILDDVFAELDAARRERLAGLVGRAEQVIVTAAALA
+DIPASLAGHRVLIRQDAEGSEAVAAAEPVEGDIRAPRPGAAPGAAASEAEEPEDGDARA
+>4_2
+MYLSHLTVADFRSYRWADLELTPGSTVLLGANGVGKTNLVEAIGYLGAQQSHRVSSDAQL
+VRFGRDRARIAGRVHRGSRTVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLSLVTGEPGGRRRLLDQLMVQLRPALGEAAADYERVLRQRNALLKSSRGSRRWGPEEDA
+TLAVWDEHLCAAGARLLHGRLHVLRLLARPLQEMYAALTNGSKAAAYAYESTVPLARGTH
+AEVPAVADLAADMHRTLEAQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRMAAYDVLVADDPDPDARPVLILDDVFAELDAARRRRLAALVHRAEQVIVTAAALE
+DVPEELTAHRVLIRQDAEGSEAVAAAAPVEGDIREPRREGGADG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000179.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000179.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d7ae88a0a21c411c265402ba808121a98726174
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000179.fa
@@ -0,0 +1,82 @@
+>0_5
+MSDETTPQTPDEPVEGAPTPQPPQTGLDIEVEHYVLPEGAADKVEPVDLESEMKRSYLDY
+AMAVIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRAFNKSARVVGDVMGNYHPHGDTA
+IYDALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVD
+MQDNYDGKQQEPVVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEAT
+REELLEALLARVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVT
+ELPYMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLY
+KHTELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTAFRKRKAEERAHILR
+GLLKALDMLDEVIATIRRSASAEVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQ
+DEYDDLMAKIAEYNRILESPQRQREVISEELAEIVAKHGDDRRTEIMAGFDGDMSIEDLI
+PEEEMVVSITRGGYVKRTRIDQYRSQARGGKGVRGATLRGDDVVEHFLTVSTHHWLLFFT
+NFGRVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLVDYGRAPYLVLATRGGL
+VKKTPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISHKGQSLRFTATDEALR
+PMGRATSGVTGMKFRDDDSLLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRPQNRGGLGIK
+VAKLVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDR
+IVAVTLNNEQEMEAKADAEAEAGPDVPLDADIDPTDPVAAPEDALTQDAGEGADGGEQ
+>1_1961
+MSDETTPQTPDEPVEGAPTPQTGLDIEVEHYVLPEGAADKVEPVDLESEMKRSYLDYAMA
+VIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRAFNKSARVVGDVMGNYHPHGDTAIYD
+ALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVDMQD
+NYDGKQQEPVVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEATREE
+LLEALLARVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVTELP
+YMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLYKHT
+ELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTAFRKRKAEERAHILRGLL
+KALDMLDEVIATIRRSASADVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQDEY
+DDLMAKIAEYNRILESPQRQREVISEELAEIVAKHGDDRRTEIMAGFDGDMSIEDLIPEE
+EMVVSITRGGYVKRTRIDQYRSQARGGKGVRGATLRGDDVVEHFLTVSTHHWLLFFTNFG
+RVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLVDYGRAPYLVLATRGGLVKK
+TPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISRKGQSLRFTATDEALRPMG
+RATSGVTGMKFRDDDSLLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRLQNRGGLGIKVAK
+LVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDRIVA
+VTLNNEQEMEAKADAEAEAGPDVPLDADIDPTDPVAAPEDALTQDAGEGADGGEQ
+>2_400
+MSDETTPQTPDESAEVPETPETGQDVAVEQYVLPEGAADKVEPVDLESEMKRSYLDYAMA
+VIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRSFNKSARVVGDVMGNYHPHGDTAIYD
+ALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVDMQD
+NYDGKQQEPAVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEATREE
+LLEALLTRVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVTELP
+YMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLYKHT
+ELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTVFRKRKAEERAHILRGLL
+KALDMLDEVIATIRRSASADVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQDEY
+DELMARIAEYDRILESPQRQREVISEELGEIVAKHGDDRRTEIMAGYDGDMSMEDLIPEE
+EMVVSITRGGYVKRTRIDQYRSQGRGGKGVRGATLRGDDIVEHFLTVSTHHWLLFFTNFG
+RVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLTGYDRAPYLVLATRNGLVKK
+TPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISHKGQSLRFTATDEALRPMG
+RATSGVTGMKFRDDDALLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRLQNRGGLGIKVAK
+LVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDRIVA
+VTLNNEHEMEAQADAEAAEDPVSEGSAAAAGVLPEGEPEALVGAEATAGAAADADVRLDA
+DIDPTDPAAAPEGLFEEDADGEGADGGEQ
+>3_353
+MSDETTPGTAPGTPQDGHDADQTPQIGQDVAVEHYVLPEGAADKVEPVDLESEMKRSYLD
+YAMAVIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRSFNKSARVVGEVMGNYHPHGDT
+AIYDALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTV
+DMQENYDGKQLEPTVLPARFPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEA
+TREELLAALMQRIKGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVV
+TELPYMTNPDNLAAKIAEMVRDGKIAGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNL
+YKHTELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIEVIVRRTAFRKKKAEARAHIL
+QGLLKALDMLDEVIATIRRSASAEVAREALKTLLDIDDEQAQAILQMQLRQLAALESQKI
+QDEYDELMARIAEYTAILESPQRQREVVSDELGELVAKHGDERRTEIVAGFDGDMSIEDL
+IPEEEMVVTITRGGYVKRTRIDQYRSQARGGKGVRGAALRGDDVVEHFLTVSTHHWLLFF
+TNLGRVYRIKTYELQEAGRDAKGQHVANLLAFQPDERIAQIQPLAGYDGDAPYLVLATRN
+GLVKKTPLEDYDTNRQAGLIAIKLREGDELVSARVVSAQDDLLLISRQGQSVRFTATDEA
+LRPMGRATSGVTGMKFRGDDALLAMDVIRAGDEDSYVFTVTDGGFAKRTHVDEYRTQGRG
+GLGIKVARLVDDRGELAGGLVVGEDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVVFAKP
+DKRDRIVAVTLNNEDEIEATADERAAAEGAAPEAAGAADGAGVPLDAVNDQTDPAAAAEA
+EAAGEDADGGEQ
+>4_5
+MSDETTPQTPDEPVEGAPTPQTGLDIEVEHYVLPEGAADKVEPVDLESEMKRSYLDYAMA
+VIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRAFNKSARVVGDVMGNYHPHGDTAIYD
+ALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVDMQD
+NYDGKQQEPVVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEATREE
+LLEALLARVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVTELP
+YMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLYKHT
+ELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTAFRKRKAEERAHILRGLL
+KALDMLDEVIATIRRSASADVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQDEY
+DDLMAKIAEYNRILESPQRQREVISEELAEIVAKHGDDRRTEIMAGFDGDMSIEDLIPEE
+EMVVSITRGGYVKRTRIDQYRSQARGGKGVRGATLRGDDVVEHFLTVSTHHWLLFFTNFG
+RVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLVDYGRAPYLVLATRGGLVKK
+TPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISHKGQSLRFTATDEALRPMG
+RATSGVTGMKFRDDDSLLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRLQNRGGLGIKVAK
+LVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDRIVA
+VTLNNEQEMEAKADAEAEAGPDVPLDADIDPTDPVAAPEDALTQDAGEGADGGEQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000181.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000181.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3d7f1ee76ff320c65823b016e0d45a1d4b59c060
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000181.fa
@@ -0,0 +1,10 @@
+>0_7
+MGRLARVALVVSAAAAAYGARLWRENSARKDVWATATDDLPEDADGVEPAPED
+>1_1963
+MGRLARVALVVSAAAAAYGARLWRENSAGKDVWATATDDLPEDADGVEPAPED
+>2_398
+MGRLARVALVAGAAAAAYGARLWQQNREGKDIWATATDDLPEDAEGVEPAPED
+>3_351
+MRLARIATLVAGAAAAYGVRSWRQQREDKAVWASATDSLEPRKAPAEDGRGEDEETPQG
+>4_7
+MGRLARVALVVSAAAAAYGARLWRENSAGKDVWATATDDLPEDADGVEPAPED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000182.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000182.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa9ffda68dc5918329ba6374868e614e82226455
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000182.fa
@@ -0,0 +1,30 @@
+>0_8
+MNTTIDTPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYGPTVPVI
+SDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAALTYTVVS
+WTTPVEGFEVWDQALAPMLRITVAGVVAFLVGSLLNASIVVRLKERMKERHVAFRLILST
+VVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRALKRREPT
+YRAPGFEIHRDDDPALAPAASR
+>1_1977
+MNTTTHAPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYGPTVPVI
+SDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAALTYTVVS
+WTTPVEGFEVWDQALAPMLRITVAGFVAFLVGSLLNASIVVRLKERMKERHVAFRLILST
+VVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRALKRREPT
+YRAPGFEIHRDDDPALAPAASR
+>2_370
+MVLDGPVNTTIDTPSPDQPVSGQGTPAYARVPASYYDIFVGVFVALLILSGVTAAKLFYG
+PTVPVFSDVFYGGGPLIFDGGAFLFPFAYIIGDILAEVYGWRRARRAILLGFAMLVLAAL
+TYTVVSWTTPVEGFEVWDQALAPMLRITVAGFVAFLAGSLINATIVVRLKERMRERHVAF
+RLILSTIVGQFFDTLIFCTIAFAGTITLLELANYTFTGFLYKTLVEILIVPITLLVIRRV
+KASEPTYRPASSPARAAADAA
+>3_2129
+MNTTPASRSEPTSGQGAAASAAAPHSHYDIFVGVFVALLILSGVTAAKLFYGPTVPGVSD
+VFYGGGPLIFDGGAFLFPLSYVVGDILAEVYGLRRARRAIYIGFAMLVVAALTYRLVALT
+TPVEGFEAWDQALAPTLRITLAGLAGYIVGSLLNATVVARMKARMAERAVAWRLIASTLV
+GEFFDTLIFCLVAFAGTITLADLANYTVTGYVYKCLVEICIVPVTLLVIRWLKRHEPTYR
+AQPTPAPVSAPTA
+>4_8
+MNTTIDTPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYGPTVPVI
+SDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAALTYTVVS
+WTTPVEGFEVWDQALAPMLRITVAGFVAFLVGSLLNASIVVRLKERMRERHVAFRLILST
+VVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRALKRREPT
+YRAPGFEIHRDDDPALAPAASR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000184.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000184.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f30472710f5867be5d032835e64d0d0b7da5086
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000184.fa
@@ -0,0 +1,20 @@
+>0_12
+MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA
+>1_1981
+MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA
+>2_366
+MARMANATHIATIKTNQGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGVGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEESQQVVDRLNAVATDPRDRPLEDVVIESVEIAEA
+>3_348
+MTRMTNATQIATIHTNQGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDQLNSVATDPRDRPLEDVVIESVEISEA
+>4_12
+MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000185.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000185.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54ae4e506bfb10abc256d37b27d5436da03a8622
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000185.fa
@@ -0,0 +1,34 @@
+>0_13
+MSTTPSDPHGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS
+GVVAGPAPTVAPAGAAASVPARRRTGFTASPVTWILLAVTTVVYAAQWMTRDQASGVTEA
+LWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLALY
+VLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVFS
+FLLPGVAWQVHMGGLLTGAVVAVVFSLAGGLRPGRARVPSVGAQVAGLVVVAAALAALTV
+LGAARVTVAGLLG
+>1_1982
+MSTTPSDPYGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS
+GVVAGPAPTSPPAAGAAATVPARRRTGFAASPVTWILLAVTTVVYAAQWMTRDQASGVTE
+ALWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLAL
+YVLSAVGGAVFALWASDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVF
+SFLLPGVAWQVHVGGLLTGAVVAVVFSLAGGLRPGRARLPSVGAQVAGLVVVAAALAALT
+VLGAARVTVAGLLG
+>2_365
+MDCAAQGGAPAGTTTSPAAVGSPGPGGVGMAGAAGRGAPARRRTGLAAAPVTWTLIAVTV
+AAYVAQWATRDTVPGVTEALWYAGLYTSPFGLEPWRMATYALVHDLSGPTHLILNMLALW
+VIGRVLEPALGWWRFAALYVLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLVTRV
+RGGQVRSIAVLIGLNLVISFLLPGISWQVHVGGLITGAVVALVYSLAGGLRPGRASAPSA
+GAQAAGLVLVAAVLAVLTVLGADRIGLDAVLR
+>3_347
+MSTTPSDPHGPDVAEGTPPVCPRHPGRAAYVRCASCADPVCLDCQRPAAGGLTLCPDCAA
+RLAAGVPGPASGTTTSPAPASAGAGRGGVGAALRAAPVTWTLLAVTLLVYAGQWLTRGSR
+TGVTESLWYAGAYTSAIGMEPWRMLTYALVHDVSGPTHVALNMVALWVIGRVLELALGWW
+RFLALYLVSALGGAVFALWTADPLQPVVGASGAVYGLFAALFAVTRFRGGQVTSIAVLIG
+LNLVFSFLMPGISWQVHVGGLLTGAVAGALLVSAGGPPGRSAAADGTARRSSAGVHVAGL
+VLLAAVLAVLTLVGAARLSPAALLG
+>4_13
+MSTTPSDPHGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS
+GVVAGPAPTVAPAGAAASVPVRRRTGFAASPVTWILLAVTAVVYAAQWMTRDQASGVTEA
+LWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLALY
+VLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVFS
+FLLPGVAWQVHVGGLLTGAVVAVVFSLAGGLRPGRARVPSVGAQAAGLVVVAAALAALTV
+LGAARVTVAGLLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000186.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000186.fa
new file mode 100644
index 0000000000000000000000000000000000000000..47f08a470bb492c20a20b2192083e1b8db7e2fb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000186.fa
@@ -0,0 +1,15 @@
+>0_14
+MAAPAGKRKDSARRKREELEAARRSRSAVRTDLGDVDPGPKPLSPVYKAVMFGLLILGLL
+WIIVYYLTQGLLPIVQIGGWNILVGFGIALVGFLMMSRWSE
+>1_1983
+MAAPAGKRKDSARRKREELEAARRSRSAVRTDLGDVDPGPKPLSPVYKAVMFGLLILGLL
+WIIVYYLTQGLFPIVQIGGWNILVGFGLALVGFLMMSRWSE
+>2_364
+MAAPSGKRKDSARRKHEELEDARRGARRGSSAVTTDLGDVDPGPKPLSPVYKAVMFGLMI
+VGLLWIVVYYLTQGLFPIVAIGGWNILVGFGIALVGFLMMSRWSE
+>3_346
+MATTSGKRKDSARRKRRELEQARSRRGRTASVSTDLGDVDATPAPLPRWYKAVMFGLLIL
+GLLWIVVYYLSQGLFPIPDAGGWNILIGFGIALVGFLMMSRWSE
+>4_14
+MAAPAGKRKDSARRKREELEAARRSRSAVRTDLGDVDPGPKPLSPVYKAVMFGLLILGLL
+WIIVYYLTQGLFPIVQIGGWNILVGFGIALVGFLMMSRWSE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000189.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000189.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc2d137c2c41de1db4bcabb26a38dc4c9193e9e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000189.fa
@@ -0,0 +1,64 @@
+>0_17
+MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEKGSAYLVMELVPGQPLSSILEKEKVLSPERTLRIIAQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPPLPDTVPAPV
+RALIMCMLSKDPKERPSDATALSEAADALRRKDTRGAVEAVPGLAVFLEEQGVADPSGAE
+TAPLDYDGLRTTHPRTEGIRTDGSPATAALPVTAAQPRTDDAARGPGAAGAAAVGAAGAA
+ASASTRDHEIAAVRDQQTRPGDVVDPGPPAGGGSAPARRRRANPWPLWALLGLVVFALLG
+ALLWPLLTGGRGDGGSAPATSQEESSVNVDPEAYKGRPVSEVRAELEGLGLAVREEDRDA
+QSPQGTVEEINPVGALQRGETVTLAVSTGEGVIPEGLVGQPVDSAIQTLRDRGFTVDRVD
+DPSADGADGEVVRVVPGEGERHRYDTHVQLIVATGGSDAAPTREASQPASEPVPSASEEP
+SSEPSPSASDEPSPSPTAESPTATADPEPTQEPTEEPTTPTGDPTTESSGESTAPTGEPT
+TDPSADARGAEASSADATPSA
+>1_1986
+MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRNTAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEEGSAYLVMELVPGQPLSSILEKEKVLSPERTLGIIAQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPPLPDTVPAPV
+RALIMCMLSKDPKERPSDATALSEAADALRRKDTCGAVEAVPGLAVFLEEQGVADPSGAE
+TAPLDYDGMRTTHPRAEGTRADGSPATAALPVTAAQPRTDDAARGPGAAGAAAVGAAGAA
+GAAGAVASTRDHEIAAVRDQQTRPGDVVDPAPPAGGGSAPARRRRANRWPLWALLGLVVF
+ALLGALLWPLLTGGRGIGGSAPATSQDESSVRVDPEAYRGRPVSEVRTELEGLGLAVREE
+DRDAQSPQGTVEEINPVGALRRGETVTLAVSTGEGVIPEGLVGQPVESAIQTLRDRGFTV
+DRVDDPSADGADGEVVRVVPGEGERHRYDTHVQLIVATGGSDAAPTREASQPASEPEPSA
+SEEPSTEPSPSASDEPSPSPTAESPTATADPEPTPEPSEEPTTPTGDPTTESSGESTAPT
+GESTTDPSADARGAEASSADATPSA
+>2_360
+MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEKGSAYLVMELVPGQPLSAILEKEKVLSPERTLRIIAQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDAPPPLPSTVPAPV
+RALIMCMLSKDPKERPTDATAASEAADALRRKDTRAAVEAVPGLAAFLAAEGVADPSGAE
+TAPLDYDGMRTAHPRPEGTRADGTPATAALPVTAAQPRTDDGARGSAATAAGAAGAAGLA
+GAAAAGARPANEEIAAVRDPQTRPSDVVQEAPPAGQGSAPVKRRRANRWPVFALLGLVLF
+ALLGALLWPWITGDRTPGGSTPSGTSQASSVSVDPEAYKGRPAAEVRAELERLGLVVREE
+DRDARNPRGTVEEVNPVGSLQRGETVTLAVSTGEGVVPDGLVGQPVDSAIQLLRDRGFTV
+DRVDDPSADGAEGEVVRVVPGEGQRHRYDTHVQLIVAGGAGGDEPAPTPEPSEPAEPTAE
+PSDEPTTEPTSEPTEEPTTEPTAPSEEPTEEPTEEPTTEPTSDPTGEPTGEPTADPTDDA
+GGSASPTAEESPTA
+>3_343
+MRPTSGITLGGRYALTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEKGSAYLVMELVPGQPLSAILEKDRTLSTDRTLSIIRQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDIYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPALPDTISAPV
+RALIMCMLSKNPKDRPANATALSEAAEALRRKDVAGAVAAVPTLAAFLADQGVHSTGGPG
+DAETTALDAAPRTAPQPTVPLGTTTEPAAPATAALPVAAARPDVAATRSPRAAEPARSVP
+AAAPADPAPRTAKPRRRNRWPLFALLALVAFAVLGALLYPLLSGESGAGAGASSSTGTDA
+QVEVDAAAYRGRPADEVRAELEGRGLAVEEEQRDANDPQGTVVEVTPTGTLRRGDTVTLA
+VSTGQGTIPQDLVGQPADTVVGILRDRGFSVDRVDDPNADGATGQVVRVVPGEGQTHRFD
+TPVQVIVAGGTGSSPVTQSVVTAPTAAPASESPAEPAPASSSSGDPAPSSAQPTPSEAST
+EPSPESPAPTSESAAPSTEPSAGTPSTPDASGPSSQGSDAGSPSTDPAG
+>4_17
+MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEEGSAYLVMELVPGQPLSSILEKEKVLSPERTLGIIAQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPPLPDTVPAPV
+RALIMCMLSKDPKERPSDATALSEAAEALRRKDTCGAVEAVPCLAVFLEEQGVADPSGAE
+TAPLDYDGMRTTHPRAEGIRTDGSPATAALPVTAAQPRTADDARGPGAAGAAAVGAAGAA
+GAAASTRDHEIAAVRDQQTRPGDVVDPGPPAGGGSAPARRRRANRWPLWALLGLVVFALL
+GALLWPLLTGGRGVGGSAPATSQEESSVHVDPEAYRGRPVSEVRTELEGLGLAVREEDRD
+AQSPQGTVEEINPVGALRRGETVTLAVSTGEGVIPEGLVGQPVESAIQTLRDRGFTVDRV
+DDPSADGADGEVVRVVPGEGERHRYDTHVQLIVATGGSDAAPTREASQPASEPEPSASEE
+PSTGPSPSASDEPSPSPTAESPTATADPEPTPEPSEEPTTPTADPTTESSGESTAPTGEP
+TTDPSADARGAGASSADATPSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000193.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000193.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a3d528de4701fb8e54a55d91f52240ab71e40a48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000193.fa
@@ -0,0 +1,25 @@
+>0_21
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGA
+AGAGSSAVDRPAPASTPSPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRAVPVGPGTAIRIGKT
+VMELEA
+>1_1990
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGA
+AGAGSSAVDRPAPASTPSPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRALPVGPGTAIRIGKT
+VMELEA
+>2_356
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGV
+AGAGSSAVDRPAPASTPAPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRALPVGPGTAIRIGKT
+VMELEA
+>3_339
+MNELAVAVLRLGLLLALWILIISIVLSQGRDLVVGRRNKLRLEQARRDAGLVTAVPAAGA
+HAASADRPAPAATPAAERPAPVPPAPAPRLARTLRITEGPLAGQTVDLGGRPLLIGRAQD
+ADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTFVDGDPVTRTLPVGTSSTIRIGKTV
+MGLED
+>4_21
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGV
+AGAGSSAADRPAPASTPSPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRALPVGPGTAIRIGKT
+VMELEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000200.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000200.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c5f11f1551255132d1482de19f71fb0571313ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000200.fa
@@ -0,0 +1,45 @@
+>0_38
+MSPTPTRPSRGPGWRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA
+LTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAATTIGGTGAALGGILV
+TGLLLTVIGVIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPVTTFGTAL
+AVVLTAVAFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVREAAWIGLPPFHGPELRWDL
+LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSGAGGGVGTTTYA
+ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGMMG
+VRIWVQNRVDFSNTVNLMAAGAGLIIAIADPQLVVGGLVFGGITLGTVAALVVYHLMTAI
+ARARGTEPVPEDEEQFEASEAGRLG
+>1_2002
+MSPTPTRPSRGPGWRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA
+LTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAAAAIGGTGAALGGILV
+TGLLLTVIGAIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPVTTFGTAL
+AVVLTAVTFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVGEAAWIGLPPFHGPELRWDL
+LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSGAGGGVGTTTYA
+ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGMMG
+VRIWVQNRVDFSNTVNLMTAGAGLIIAIADPQLVVGGLVFGGITLGTVAALVVYHLMTAI
+ARARGTEPVPEDEEQFEASEAGRLG
+>2_343
+MSSSPSRPAPGFGWRLHGDGRTITSGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA
+LTGMPATTALLFSGVGTLLFLLLTGNRLPSYLGSSFAFIAPITAATTAGGVGAALGGVLV
+TGVLLAVIGLIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPLTTFGTAL
+AIVLTAVLFRGLLGRLSILVGIVVGYLLALAQGQVDFTAVGEAGWLGLPPFHAPELHWNL
+LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTTLSGLGGGVGTTTYA
+ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGVMG
+VRIWVQNRVDFSSTINLMTAGAGLIIAIADPQLVLGGLVFGGITLGTIAALVVYHLMTAI
+ARVRGTEPVSEDDEAYEASEAGRLG
+>3_286
+MSSSPTPSAPRAGHVPGPGPAVRSWRLHGDGRTITPGTVVAPDERLSWGRTVGIGVQHVM
+AMFGATVLVPAITGMPATTALLFSGLGTLLFLLITGNRLPSYLGSSFAFIAPLTAASASH
+GVGAALGGIAATGVLLMVIGVVVGWAGTGWIHALMPPAVMGTIVALIGLNLAGATTQAMQ
+EVPLTTFGTALAVVLTAVLFKGLLGRLSILVGIVVGYLLALAQGQVDFTAVGQAAWVGLP
+PFHTPELHWSLLPLFLPVVLVLIAENIGHVRTVGLMTKRDLDPLTGRALLADGLATTLSG
+LGGGVGTTTYAENIGVMASSKVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAG
+IILYGMIGVMGVRIWVQNRVDFSNTINLMTAGAGLIVAIANPELVVGGLVFGGITLGTLT
+ALVVYHLMTLVARVRGTEPVDEDTEDPASYRAAEAGRLG
+>4_33
+MSPTPTRPSRGPGWRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA
+LTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAAAAIGGTGAALGGILV
+TGLLLTVIGAIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPVTTFGTAL
+AVVLTAVTFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVGEAAWIGLPPFHGPELRWDL
+LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSGAGGGVGTTTYA
+ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGMMG
+VRIWVQNRVDFSNTVNLMTAGAGLIIAIADPQLVVGGLVFGGITLGTVAALVVYHLMTAI
+ARARGTEPVPEDEEEFEASEAGRLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000211.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000211.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dd2db47e1525133e3558e565cc4f19003c71a21e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000211.fa
@@ -0,0 +1,65 @@
+>0_54
+MVSFSHTDDGTSEAAWAEGGVGELPELRLPVWDAQTLLLVAVAHPDDETLAATGLIRSAL
+RDGARVHVLVATAGEASHPHSPTHTPEDLVRLRRDEMEHALDALAAGLPASAGPGSPARD
+RLTWASLALPDSGVAEHEDAVRDAVAAALDAHPGPAVLASHDPGDGHADHEAVGRAVGAV
+AGECDLPLYAFPIWFWHWADPADLPARRYRRLPLTDDDRAARRAALDAHASQVRPLSAAP
+GDEAILGPAVLAHHERPFEAHRVSGPDDADAHRAAAVFDRLYRAQEDPWRYLSSSYEARK
+RALTLAALPRPRYGTVVEAGASIGVLTADVAARADRVVGLEASSTAVERAAARLAGAPHA
+EVRRAVLPADWPADVAGADLVIASEIGYFLQPEELDALIDDADAALAPGGELLLCHWRHP
+IEGWPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVVVPAKDEQERLP
+AALAALAAALDRWEEHHAQGTAAVVVAADRCDDATVAAALEARAADPRIHVLELGEPTAG
+QAGVGRARLEGARRARALFPDVPAERLWLASTDADSRVPADWLLAQTVAAGHDEVLVLGT
+VDVHQGPLRQAWLRGYRHEEGHPHVHGANLGLPWSLYEAVGGFPPVAEHEDVGLAEAVRA
+LAGERDGGDGRRVRVIATDTTRVLTSSRLEGRTPGGFSGYLKAVGRPG
+>1_2018
+MVSFSHTDDGTSEAAWAEGGVGELPELRLPVWDAQTLLLVAVAHPDDETLAATGLIRSAL
+RGGARVHVLVATAGEASHPHSPTHTPADLVRLRRDEMEHALDALAAGLPASAGPGSPARD
+RLTWASLALPDSGVAEHEDAVRDAVAAALDAHPGPAVLASHDPGDGHADHEAVGRAVGAV
+AGECDLPLYAFPIWFWHWADPADLPARRYRRLPLTDDDRAARRAALDAHASQVRPLSAAP
+GDEAILGPAVLAHHERPFEAHRVSGPDDADAHRAAAVFDRLYRAQEDPWRYLSSSYEARK
+RALTLAALPRPRYGTVVEAGASIGVLTAAVAARAGRVVGLEASPTAVERAAARLAGAPHA
+EVRRAVLPADWPADVAGADLVIASEIGYFLQPEELDALIDDADAALAPGGELLLCHWRHP
+IEGWPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVVVPAKDEQERLP
+AALAALTAALDRWEEHHAQGTAAVVVAADRCDDATVAAALEARAADPRIHVLELGEPTAG
+QAGVGRARLEGARRARALFPDVPAERLWLASTDADSRVPADWLLAQTVAAGRDEALVLGT
+VDVRQGPLRQAWLRGYRHEEGHAHVHGANLGLPWSLYEAVGGFPPVAEHEDVGLAEAVRA
+LAGERDGGEGRRVRVIATDTTRVLTSSRLEGRTPGGFSGYLKAVGRPG
+>2_322
+MVSFSHTDAGTSEEAWAAAGVGALPVLESPAWDADTLLLVAVAHPDDETLGATGLIRSAL
+RGGARVHVLVATAGEASHPDSPTHAPEDLVRLRRAEMEHALDALAADLPGPGEDRRSALT
+WESLGLPDSGVAGREDAVRAAVVAALAAHPGPAVLASHDPGDGHADHEAVGRAVGELAGE
+RDLPLCAFPIWFWHWADPAELPARRYRRLALTDDDRAARRAALDAHASQVRPLSDAPGDE
+AVLGPQVLAHHDRPFEAHRLSGPDDADAHRAAAVFDRLYREHEDPWRYLSSPYEARKRAL
+TLAVLPRPRYGTVVEAGASIGVLTGEVAARADRVVGLEASPTAVERAAARLADTPHAEVR
+RAVLPGHWPDDVAGADLVIASEIGYFLQPEELDALVDDADAALAPGGELLLCHWRHPIEG
+WPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVIVPAKDEQERLPAAL
+AALGAALDRWEEHHAQGSAAVVVAADRCDDATVAAAVAARHADPRVHVLELGEPGPGEAG
+VGRARAEAARRARALFPDVPAQRLWLASTDADSRVPADWLLAQTTAAGPDGALVLGTVDV
+REGALRRAWVRDYRHEEGHPHVHGANLGLPWSLYEAAGGFPPVAEHEDVRLVEAVRALAE
+ARVRATDTTRVLTSSRLTGRTPGGFAGHLQEVGGEAVPRRGAQARP
+>3_263
+MVSFDHRDDGTAEAVWMAAGVGELPALPARAWTRADTLLVAVAHPDDETLGAAGLIRAAL
+RGGAAVHVAVATAGEASHPDSPTHTPADLVRLRRAEMDHALAALADGLGPDAGALTWESL
+ALPDGGLTDRPDEVRAALERVLAGRTPAEEGGGAVVLVSHDPDDGHGDHDAVGAAAAALA
+ADHDLELYAFPLWLWHWGAPEDLAPRRYRRLELAAGDDAARLAALDAHASQTRPLSAAPG
+DEAILPERMIAHFTRGFETYRRTAPDDADASRASAVFDRLYREHEDPWRYLTSPYEARKR
+ALTLAVLPRPRYGTVVEAGASIGVLTAALAERAERVVGLEASQVAVERAAAHLAEIPHAE
+VRRAVLPADWPADVGPAEEGAGAPADLVVASEIGYFLQPEELDALVDAADASLGAGGELL
+LCHWRQPITGWPLDGDAVHDRVAADPRWRLLSEHVEADLRLSVHARAAAATHAVAVVPAM
+DEAEHLPAGLDALSAALDLWEAQHTQGSAAVVTVVPADDAPTLEAAHAARARDPRIRVLE
+LAPGAGGVGRARAAAARHARGLFPDVPAEALWLASTDADTRVPADWLVGQPALAARRRAD
+GQVLVLGTVDLPAHADDDLAHRWRADYEHREDHPHVHGANLGLPWGLYERAGGFAEVAEH
+EDVRLAEAVRALGEDRVLATDRVRVHTSSRLEGRTPGGFAGFLRGLLEEGAAEG
+>4_49
+MVSFSHTDDGTSEAAWAEGGVGELPELRLPVWDAQTLLLVAVAHPDDETLAATGLIRSAL
+RGGARVHVLVATAGEASHPHSPTHTPEDLVRLRRDEMEHALDALAAGLPASAGPGSPARD
+RLTWASLALPDSGVAEHEDAVRDAVAAALDAHPGPAVLASHDPGDGHADHEAVGRAVGAV
+AGECDLPLYAFPIWFWHWADPADLPARRYRRLRLTDDDRAARRAALDAHASQVRPLSAAP
+GDEAILGPAVLAHHERPFEAHRVSGPDDADAHRAAAVFDRLYRAQEDPWRYLSSSYEARK
+RALTLAALPRPRYGTVVEAGASIGVLTADVAARADRVVGLEASPTAVERAAARLAGAPHA
+EVRRAVLPADWPADVAGADLVIASEIGYFLQPEELDALIDDADAALAPGGELLLCHWRHP
+IEGWPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVVVPAKDEQERLP
+AALAALTAALDRWEEHHAQGTAAVVVAADRCDDATVAAALEARAADPRIHVLELGEPTAG
+QAGVGRARLEGARRARALFPDVPAERLWLASTDADSRVPADWLLAQTVAAGRDEALVLGT
+VDVRQGPLRQAWLRGYRHEEGHAHVHGANLGLPWSLYEAVGGFPPVAEHEDVGLAEAVRA
+LAGERDGGDGRRVRVIATDTTRVLTSSRLEGRTPGGFSGYLKAVGRPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000213.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000213.fa
new file mode 100644
index 0000000000000000000000000000000000000000..484b2bda0f1c270a8b8a22797b8ded939ccc4b0c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000213.fa
@@ -0,0 +1,15 @@
+>0_57
+MSAFETVDVNEIPADAAILDVREDDEWALGRAAGAQHIPLGQLPDRLEELDPDTDYYLIC
+RTGGRSARAAEFMTGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK
+>1_2021
+MSAFETVDVNEIPADATILDVREDDEWALGRAAGAQHIPLGQLPDRLEELDPDTDYYLIC
+RTGGRSARAAEFMTGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK
+>2_319
+MSAFETVDVNEIPADAAILDVREDDEWALGRAAGAQHLPLGQLPDRLEELDPDTDYYVIC
+RTGGRSARAAEFMVGRGYTAINVAGGSGAWLEAGKPMEADGGAEPTVK
+>3_261
+MSHFETVTVDQIPADAAILDVREDDEWALGRAAGAQHLPLGQLPERIEELDPDTDYYVIC
+RTGGRSARAAEYMVGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK
+>4_52
+MSAFETVDVNEIPADAAILDVREDDEWALGRAAGAQHIPLGQLPDRLEELDPDTDYYLIC
+RTGGRSARAAEFMTGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000218.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000218.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e8693761a3d0ed417663ecc94171a6ddcda48dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000218.fa
@@ -0,0 +1,46 @@
+>0_65
+MGQVDTGRTGRRDRRTERPRSRSLHAVLLAALAAVLVACGPVTAPPAPSSAPASSTTAAP
+TSSSPSAGPTAAEVAAAVEPGLETSPGTASAEFRDLATGEVLYARDADEPVAPASSLKVL
+AAAAIVSALGPETTLQTTVVAQPTADDAATELVLVGGGDVLLGTGASDSTHVSGRAGLRT
+LAQRTVAGLVEDGVTGQVVVSTDLRLFTDRTALNPRWTSDIPESGNIAPVQPLATYGGRE
+APGTGEDRIEDPAQFAALTFQAALDDAVAASGADLEVGLRDTLPATEVPRATVLAAAPVA
+AVESASVGEQVAYLLAHSENQVVEALAHTAAPATDLPATHEGATRLLTATVEDLGVDTAG
+MALVDSSGLSPDNRVSAGQLAGVVAGVARTPALATVLEGLPRPGEDSTLGDRFPDAPARQ
+AVAAKTGTLDQTVSLTGTVTTTSGRVLAFSIICSDLQWKLEPARAAVDEAVSAVAGL
+>1_2029
+MGQVDTGRAGRRDRRTEHRRSRSLPAVLLAALAAVLVACGPVTAPTAPSSASASTSTAAP
+TSSSPSAGPTAAEVAAAVEPGLETSPGTVSAEFRDLATGEVLYARDADEPVAPASSLKVL
+AAAAIVSALGPETTLQTTVVAQPTADGAATELVLVGGGDVLLGTGASDSKAVSGRAGLRT
+LAERTVAGLVEDGVTGRVVVSTDLRLFADRTALNPRWTSDIPESGNIAPVQPLATYGGRE
+APGTGEDRIEDPAQFAALTFQAALDDAVAASGADLEVGLRDTFPATEVPRATVLAAAPVA
+AVESAPVGQQVAYLLAHSENQVVEALAHTAAPATDLPATHEGATQLLTATAEDLGVDTAG
+MALVDSSGLSPDNRVSAGQLAGVVAGVARTPALGTVLEGLPRPGEDSTLGDRFPDAPARQ
+AVAAKTGTLDQTVSLTGTVTTTSGRVLAFSIICSDLQWKLEPARAAVDEAVSAVAGL
+>2_308
+MTPGSPFASLLAALAAALLSAAPVLTPLAGPAALAPGNPVTAEAVAAPSPDARALASAVD
+AALDASPGRVAAQVRDAATGEVLHARDADFLAAPASSLKVLTAAAALRTLGPERTLRTRV
+VAVPAADDGATELVLVGGGDVLLGDGASDPDAVAGRAGLRTLAERTVAGLAEAGVSGDVV
+VSVDLRLFDGAAVNPAWTPDLLEDGHVSAVQPLATWGGREVPGVDEERIEDPAGHAALVF
+QRLLDEEIERTGADLDLGLRDSIPATTAVRDDVVAAEPTAQVESAPVAEVAAYMLAHSEN
+QVAEALGHLSAYAVGRPATHEGAADLLEDVAADLGADTAGMAVLDASGLAEGSLVSPAQL
+AAVVSAASRVPWLAPVLDGLPRPGEDSTLDERFRGTAAEGAVAAKTGTLDHTVSLTGTVT
+TQDGRVLAFSIVASDLDWRLDEAREAVDAAVTAMAGL
+>3_251
+MTPSNRAARVAAVTRVLLALAICALLGLLAHDVLLPRLPTPAAPAASAPSAPVPAASPSG
+GATAPSSTALASVAPVDPADVAAAVAPALAQAPGTASAEVRDAATGEVLYARSADQAVAP
+ASALKILTAVTAVDVLGADRALTTSVVALPGGGATELVLVGGGDALLGAGASDPGRVDGR
+AGLRTLARRTVAGLRERGVTGPVAVSTDLRLFTDASPLNPAWSAGLVESGNITAVQPLAT
+YGGRTAPGTGEDRIADPAAFAALAFQRELTAAVADSGADLSVRARDVVPATSAPRGDVLA
+TEPVARVESAPVGQQVAYLLAHSENQVAEVLARVAAAADGRPATHAAVPGLLRDRAAAHG
+VDTAGMRLVDASGLSPQNRVTAHQLAGLVEAVQADPALAPVRDGLPRPGEDSTLAERFPG
+SPAREAVAAKTGTLDQTVSLTGTVTTGSGRVLAFSIVCSGVDWRIAPARAAIDEAVSALA
+AL
+>4_59
+MGQVDTGRAGRRDRRTEHRRSRSLPAVLLAALAAVLVACGPVTAPPAPSSAPAASTTAAP
+TSTSPSAGPTAAEVAAAVEPGLATSPGTVSAEFRDLATGEVLYARDADEPVAPASSLKVL
+AAAAIVSALGPETTLQTTVVAQPTADGAATELVLVGGGDVLLGTGASDSTHVSGRAGLRT
+LAERTVAGLVEDGVTGQVVVSTDLRLFTDRTALNPRWTSDIPESGNIAPVQPLATYGGRE
+APGTGEDRIEAPAQFAALTFQAALDDAVAASGADLEVGLRDTLPATEVPRATVLAAAPVA
+AVESASVGEQVAYLLAHSENQVVEALAHTAAPATDLPATHEGATRLLTATAEDLGVDTAG
+MALVDSSGLSPDNRVSAGQLAGVVAGVARTPALATVLEGLPRPGEDSTLGDRFPDAPARQ
+AVAAKTGTLDQTVSLTGTVTATSGRVLAFSIICSDLQWKLEPARAAVDEAVSAVAGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000222.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000222.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27da5b90ff639232a4b763d45a1d0468d1ea543f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000222.fa
@@ -0,0 +1,65 @@
+>0_70
+MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQR
+VDLTLREPYKQDDRDLGKEVYFYFATARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGF
+MVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE
+IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVDAPDLEGRAKILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL
+AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVG
+GAAGGSSREYSEELAYLVDAEVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQE
+AIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRSRHDGGEQTPVGVEGTTVPVR
+PEGAPPSSLGGDAAGPGLPPHGGPSNTPGPGEGPTF
+>1_2034
+MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQR
+VDLTLREPYKQDDRDLGKEVYFYFATARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGF
+MVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE
+IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVDAPDLEGRAKILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL
+AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVG
+GAAGGSSREYSEELAYLVDAEVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQE
+AIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRSRHDGGQQTPVGVEGTTVPVR
+PEGAPPSSLGGDAAGPGLPPHGGPSNTPGPGEGPTF
+>2_304
+MKKLFNKPYIWILLGLLVLAVAIPLATSQTGRTMVDTNVGMAMLQDDKAAQARVVDGDQR
+VDLTLREPYSQDGRDLGKEVYFHFATARASDVVTAVDDSALDGYTDEPVRSNWLLSLLGF
+MIPFLLIALLFWFLLSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE
+IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVEAPDLEGRAKILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL
+AYALGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGNSEPFVG
+GGGGGSSREYSEELAYLVDAEVRGLLDGAHAEAHWVLTENRDVLDRLAYELLEKETLTQE
+AIAEIFRDVRKRPERDVWLASDERLPQDIPPVLSPSERRSRHEGGEQTPVGVEGTTVPVH
+PEGAPPSSLGGDAPTPGLPPHGGPSSSPGAGEGPTY
+>3_246
+MKKQFNKPYIWILLGLLVLGLVIPLTTAQSGRGMVDTNVGMALLRDDKVAQARVVDGEQR
+VDLTLREPLSQDGRDLGRDVYFQFSAARAQDVVRTVQDSSVDGYQDEPVRDSWLLSLLGL
+MIPFLLISLLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELHE
+IKEFLTEPERFHAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKANAPAIIFVDEIDAVGRSRGVGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVEAPDLDGRAKILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSRNNVIDNAALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPENDKYSVTRNELLDQL
+AYAMGGRVAEEVVFKDPSSGAANDIQKATETARKMVTDYGMSSKVGAVKLGSANTDPFLG
+GGGAASREYSEELAYLVDAEVRALLDGAHAEAHWVLTENRDVLDRLAAELLEKETLTQEQ
+IAEIFKDVRKRPERPLWLAADDRPPHDVPPVLTARERASRLEGEQPEAVGVEGTTVPDAP
+EGAPPTALGGAGGSAGGPGDLPGQHSPTPGPTY
+>4_64
+MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQR
+VDLTLREPYKQDDRDLGKEVYFYFASARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGF
+MVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE
+IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVDAPDLEGRARILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL
+AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVG
+GAPGGSSREYSEELAYLVDAEVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQE
+AIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRSRHDGGEQTPVGVEGTTVPVR
+PEGAPPSSLGGDAAGPGLPPHGGPSNTPGPGEGPTF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000224.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000224.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5a1095b27d5846a802573d1881ef89c0434569bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000224.fa
@@ -0,0 +1,20 @@
+>0_73
+MSARDRIRLAGLSAVGHHGVFDHERRDGQPFVTDVVLHLDAGPAAAGDDLARTANYAEVA
+DTVVRLVTGEPVDLIETLADRIARAVLAEQPVVTAVEVTVHKPQAPIPHDFADAAVTVHR
+TREDLA
+>1_2037
+MSARDRIRLAGLSAVGHHGVFDHERRDGQPFVTDVVLHLDAGPAAADDDLARTANYAEVA
+DTVVRLVTGEPVDLIETLADRIARAVLAEQPVVAAVEVTVHKPQAPIPHDFADAAVTVHR
+TREDLA
+>2_301
+MSARDRIRLTGLSAVGHHGVFDHERRDGQPFVTDVVLHLNAGPAAAGDDLARTANYAEVA
+DTVVRLVTGEPVDLIETLAERIARAVLAEQPVVEAVEVTVHKPQAPIPHDFADAAVTVHR
+TRRDAS
+>3_243
+MSDVIRLTGLTATGRHGVFEHERRDGQPFTTDVALTLDAGPAAARDDLARTANYAEVAET
+VVRLVTGEPFDLIETLAVRIAEAVLAEQPVVTAVEVTVHKPQAPIPHDFTDVSVTVARRR
+GA
+>4_67
+MSARDRIRLAGLSAVGHHGVFDHERRDGQPFVTDVVLHLDAGPAAAGDDLARTANYAEVA
+DTVVRLVTGEPVDLIETLADRIARTVLAEQPVVAAVEVTVHKPQAPIPHDFADAAVTVHR
+TREDLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000228.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000228.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35f43575fd0803a72bd9525c96b361a3754a0418
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000228.fa
@@ -0,0 +1,56 @@
+>0_77
+MSAAAPPPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGGGD
+GSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVD
+LQHPLVARLLGLATVKVEAADGGESALELSFLRRAEAEAVRREILDRASGMLGGAGADAS
+APERAAEPGLPDADAADAGELMLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLALVVAL
+LPEAVLDEGETLTGIGAAASLPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGLTETT
+HQTVPPGRVQGVTVSQPLFWRPFGWYRVNMAVAGYLQESDGARDVALPVGPWEDVLRVLT
+VVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWWFNWFAWRRTGFTT
+TRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRDLDED
+VAVDLYAREARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGVVGGA
+VVGEESGAHVPAVRGEEER
+>1_2041
+MSAAAPPPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGGGD
+GSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVD
+LQHPLVARLLGLATVKVEAADGGESALELSFLRRAEAEAVRREILDRASGVLGGAGADAS
+APERAAEPGLADADPDAVDADAGELLLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLAL
+VVALLPEAVLDEGETLTGIGAAASLPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGL
+TETTHQTVPPGRVQGVTVSQPLFWRPFGWYRVNMAVAGYLQESDGARDVALPVGPWEDVL
+RVLTVVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWWFNWFAWRRT
+GFTTTRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRD
+LDEDVAVDLYAREARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGV
+VGGAVVGEESGAHVPAVRGEEER
+>2_297
+MSAAAPVPATRPADDDGWARVHPASPWVRGWTFLLLILFFLGRNAVEDFAAGRFGAGAGG
+GSGEGEGSLLVAGGILLGVTLLVSLAFFFSWWFTRFRIGEDQIELRQGWLFRTRRQMKYD
+RIQAVDLQHPLVARLLGLAVVKVEAADGGESALELSFLPKARAEQVRREILDRASGVLVG
+PASAPRIAEGADAAAGVIPGVMPGVMPGAEAGPGVAPPGADADPTTPRADAPEGAAPSSS
+DPGLARRADDEGELMLRVPSGRLIGSVLLSGGVAGTVAVYLVVVLGTSLFFALAPGTWLE
+GEDTPLTGIVVAWGLPLAFAVVGQAWSGLNGGWGFQVRRSADGLRLRHGLTETTHQTVPP
+GRVQGVTVSQPLFWRPFGWHRVKVSVAGYGEDAAGKRSTALPVGPWEDVLRVLTVVAPDP
+GLDGDPREAEGLTPARLMHLGLHGSGTEGGFHHIPHRGRWWFNWFAWRRRGFTTTRALLV
+VRSGRWNRVLQTLQHERVQTAALDQGPVQRRLRLATVHVRTAGGRAVLPDLDEAVALELF
+AEEARHAAVSRRLADRDRWMRPEELARFEQRTREVAATEVGREELARAGVARPAAPAGGV
+AGTDPEPRTSHEERP
+>3_239
+MSAPAPRPEGLASGPSPEDGRIAPAPAADDAGWVRVHPASPWIRGWVMVATFLFFALRDV
+VERWIGGLFGADAGGGPGVDGRGLLIGGGIALGVLLLVGLAFFFSWWFTRFRIGAEEIEL
+KQGWLFRSRRQMHYDRLQAVDLQHPLPARLIGLAVVKVEAADGGGDSALELAYLPKAQAA
+AVRRQILDRASGAAAARPVPSAAPEAAGGPAAAGPVRGLLVDPEEQGPVLLRVPAGRLIG
+SVLLSSTVMGLLGAVVAVPAVLSLLLLLFPDANAGEEAGVWAVTLGSTFPLLFSLAGAVW
+SGLNKGWGFTVRDSSDGLRLRYGFTETVSQTVPPGRVQGVEISQPLFWRPFGWHRVKVSV
+AGYGGLEAEGRRRDVALPVGPWEDVLRVLQVVAPDPGLGGDARAAGELMRTAMTGSGEEG
+GFRHVPRRAAWWWHWLTWRRHGYALTPTLLVVRHGRLSRSVQTVQHERLQAVALTQGPVQ
+RRLRVATLRVHMAGGAARLRGLDEDVLAELFEVESRHAAVSRRLTDRNRWMLPEELERFE
+RRTAEVARTEVGRAEMAAAGVVPMETGPRPGDTPPVATTEHRGEETA
+>4_71
+MSAAAPPPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGGGD
+GSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVD
+LQHPLVARLLGLATVKVEAADGGESALELSFLRRAEAEAVRREILDRASGMLGGAGADAS
+APERAAEPGLPDADAADAGELMLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLALVVAL
+LPEAVLDEGETLTGIGAAAALPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGLTETT
+HQTVPPGRVQGVTVSQPLFWRPFGWYRVNMAVAGYLQESDGARDVALPVGPWEDVLRVLT
+VVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWWFNWFAWRRTGFTT
+TRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRDLDED
+VAVDLYAREARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGVVGGA
+VVGEESGAHVPAVRGEEER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000231.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000231.fa
new file mode 100644
index 0000000000000000000000000000000000000000..567ea2500ce012343076772faef40f005a5c1dcc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000231.fa
@@ -0,0 +1,41 @@
+>0_82
+MTSVRRHAARGLVALAAAVAVSAPLAAPAAAAPAAPTTPAAAQSVTGKPVVRPDVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRK
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER
+LSARYGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEYGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGAPYDSVAAGDGLRDYDFYETAAGMREVRAAGVDTLGPAFAQ
+IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDPNARGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDTWMQGKKEHPGRGVGKTAQRGLKVR
+>1_2046
+MTSVRRHAARGLVALAAAVAVSAPLAAPAVAAPAATETPAAAQSVTGKPVVRPDVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRR
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER
+LSARHGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGAPYDSVAAGDELRDYDFYETAAGMREIRAAGVDTLGPAFAQ
+IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDRNAQGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDVWMQGKKEHPGRGVGKTAQRGLQGR
+>2_290
+MISVRRHAARGLVALAAAVAVSAPLAAPAVAAPAAPTAPAAAQSATGKPVVRPEVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRK
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYNGRYQVPTFEEVLELRER
+LSDRYGRQIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGTPYDSVAAGDTVRDYDFYETAAGMREVRAAGVDTLGPAFAQ
+VITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSADSNAQGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDTWMQGKKEHPGRGVGKSAQRGLQVR
+>3_236
+MTALRTTARGLAALTAAVAVAAPLAVPASAAIPAKEPITQAERPDVVAHRGASAYRPEHT
+LAAYELAVAQGADVIEPDLVSTKDGVLVDRHENDITGTTDVSERPEFADRKTTKTVDGVE
+ITGWFTEDFTLAELKTLRAKERLPEARPGSAAYDGMYQVPTFEEDLKLREELSAKYGREI
+GIIPEIKHPSYFDGIGLSQEEEVIELLEEHGLNHADGRAVVQSFEFSNLAEMNTRLGLQA
+DTAYLLWYEGSGYDAVLSGDTARDYAYFSTPAGAAEAAFNGIDIYGPELRQVIALNQDGS
+LGAPTGLVEVAHDAGLTVVPYTFRAENQSLPLQFRSSENPVEHGDLAAYITEVLDAGVDG
+FFTDFPDVGVAARDAWLAEKPAEQPSEQPSDGSHAVPGKVQTGDAAAWLPAGLAAAAAGV
+LVALRRRLTAAR
+>4_77
+MTSVRRHAARGLVALAAAVAVSAPLAAPAVAAPAATETPAAAQSVTGKPVVRPDVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRR
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER
+LSARHGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGAPYDSVAAGDELRDYDFYETAAGMREIRAAGVDTLGPAFAQ
+IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDRNAQGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDVWMQGKKEHPGRGVGKTAQRGLKGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000232.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000232.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4e7ad06bc4bfda5b077918151c548a239061393
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000232.fa
@@ -0,0 +1,30 @@
+>0_83
+MTTNTPKNAHGSSAEGRDAKDQAKDKAQQAAGEAQGQAKAVAQDAKDKAQDLAATAKHEA
+GQVKDEAADQVQSLVGSAQEQVGAQVQTQQERFAGQVRSYTDDLHRVVSGEQPQTDLVRQ
+GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA
+VQPDSAASTSPRRHTTRPDAVHADVTPHHLDSQAPAYSSDSLSQADGRVADGAGPRRAAG
+VGDTPYGTQAPVQQGLTAERPFDQTRPGGDA
+>1_2047
+MTTNTPKNAHGSSAEGRDAKDQAKGKAQQAAGEAQGQAKAVAHDAKDKAQDLAATAKHEA
+GQVKDEAADQVQSLVGSAQEQVGAQVQTQQERLAGQVRSYTDDLHRVVSGEQPQTDLVRQ
+GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA
+AQPDSTASTSPRRHETRPDAVHADVTPHHLDSQAPAYSSDSLSQADGRVADGAGPRRAAG
+VGDVPYGTQAPVQQGLTAERPFDQTRPGGDA
+>2_289
+MTTNTPKNAHGSSAEGRDAKDQAKDKAQQAAGEAQGQAKAVANDAKDKVQDLAATAKHEA
+GQVKDEAADQVQSLVGSAQEEVGAQVQTQQERLAGQVRSYTDDLHRVVSGEQPQTDLVRQ
+GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA
+AQPDAAAPTAPRRRDTRPEAVHADVTPHHLDSQAPAYSSDSLSQADGRVASGAGPRRAAG
+VGDTPYGVEAPEQHGLTAERPFDRSQPGGRA
+>3_235
+MAKNHSARAADPQQSETRQKAEAAAGAAQDQAAGVAQDAKAHAQDLAQSAQQEAVAVKDE
+AVQHAKSLAGSLQDQAAQQASTQQGRLAEQSRGITDDLHRLLSGEQPQGDAVRQAVAAVA
+DRAETLTQRLETAQPMDLVDDVRRFAARRPGTFLAIALGAGVLAGRMTRGVRDASQDGPA
+SLSSAPRTPQHRRELEPQGVQADVTPHHLDSQIPAHTGDDAPRPVSDTAAGLPYGTEPLP
+TIDPLTGEPVAEDPYDQTRDGGRA
+>4_78
+MTTNTPKNAHGSSAEGRDAKDQAKGKAQQAAGEAQGQAKAVAHDAKDKAQDLAATAKHEA
+GQVKDEAADQVQSLVGSAQEQVGAQVQTQQERLAGQVRSYTDDLHRVVSGEQPQTDLVRQ
+GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA
+AQPDSTASTAPRRHETRPDAVHADVTPHHLDSQAPAYSSDSLSQADGRVADGAGPRRAAG
+VGDVPYGTQAPVQQGLTAERPFDQTRPGGDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000235.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000235.fa
new file mode 100644
index 0000000000000000000000000000000000000000..352fb2afc269a5576914d5cbe43df87fc155753d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000235.fa
@@ -0,0 +1,35 @@
+>0_86
+MTPLDRVPDQRPVPAGTGLTLEDALPAPVTAEADGVSARPRLARTVAEMRSALRELVAHA
+TDDGDAEPVTVGLIPTMGALHGGHAALVRRARAENDVVAVSIFVNPLQFGDPADLEHYPR
+TLDADLDLLAAAGADVVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGASRPGHFDGVAT
+VVAKLWNIVRPAVPALRSYFGQKDAQQLTVLRRLATDLDIDVDVRAVPIVRSPEGLALSS
+RNTRLDAAGLEHALVLSRALRSLADAAAAGEPVDVQAARRMVEDEPGVELDHLVVVDRDT
+FAELGPELLCQPLRREALALVAAHVPPVRLIDTMVLPVAGPLP
+>1_2050
+MTPLDRVPDQRPVPAGTGLTLEDALPAPVTAEADGVSARPRLARTVAEMRSALRELVAHA
+TDDGDAEPVTVGLIPTMGALHGGHAALVRRARAENDVVAVSIFVNPLQFGDPADLEHYPR
+TLDADLDLLAAAGADVVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGASRPGHFDGVAT
+VVAKLWNIVRPAVPALRSYFGQKDAQQLTVLRRLATDLDIDVDVRAVPIVRSPEGLALSS
+RNTRLDAAGLEHALVLSRALRSLADAAAAGEPVDVQAARRMVEDEPGVELDHLVVVDRDT
+FAELGPELLCQPLRREALALVAAHVPPVRLIDTMVLPVAGPLP
+>2_286
+MTPLDRVPDRTPVPPRTGLTLEDQVPEAGGTRPRLTTTKADFRAAVAELVGRAAAEDPGE
+EVSVGLVPTMGALHGGHAALARQARSENDVVAASIFVNPLQFGDRADLEHYPRTLEADLD
+LLGAVGVDVVFAPSVDEMYPGHPDAPIVSVSAGRMGEVLEGASRPGHFDGVCTVVAKLWN
+LSMPPAPAVLRSYFGQKDAQQLAVLRRLAHDLDVAVDVRAVPIVRSPEGLALSSRNTRLD
+EAGLHAALVLNRALTRLEEAAVAGRVLDVQAAREEVAAEPGVTLDHLVVVDRETLEELGA
+ELLCQPLRRDALALVAAHVPPVRLIDNRVLPAAGPLP
+>3_232
+MTPLDRTPDRRPVPAGTGLTLEDALPVADGARRPRLARTVAEARAALRELTAAAGQERGG
+APVVVGMVPTMGALHGGHAALIRQARAENDVVVASIFVNPLQFGDPADLENYPRTLEADL
+DLLGAAGADLVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGVSRPGHFDGVVTVVAKLW
+NIVRPAVPALRSYFGQKDAQQLAILRRLAHDLDVDVEVRAVPIVRSPEGLALSSRNTRLD
+ADGLEHALVLSRALRALVDAAEAGEPIDVRAARQMVSDEPGVTLDHLVVVDRETLEELGP
+ELLCQPLRREALALVAAHVPPVRLIDNMVLPAAGPLP
+>4_81
+MTPLDRVPDQRPVPAGTGLTLEDALPAPVTAEADGVSARPRLARTVAEMRSALRELVAHA
+TDDGDAEPVTVGLIPTMGALHGGHAALVRRARAENDVVAVSIFVNPLQFGDPADLEHYPR
+TLDADLDLLAAAGADVVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGASRPGHFDGVAT
+VVAKLWNIVRPAVPALRSYFGQKDAQQLTVLRRLATDLDIDVDVRAVPIVRSPEGLALSS
+RNTRLDAAGLEHALVLSRALRSLADAAAAGEPVDVQAARRMVEDEPGVELDHLVVVDRDT
+FAELGPELLCQPLRREALALVAAHVPPVRLIDTMVLPVAGPLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000239.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000239.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20ee7f050b257d88ebef4adb007e68e4e25545da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000239.fa
@@ -0,0 +1,21 @@
+>0_90
+MADGAPDPGGGGDDAGFEAAVQGLEQAFSRLVLQHRQVMVRYAAALSPALSVGAMKAFMM
+LANEGTMTPSAVAEGLLVDRAQVSRMVRDLEAAGLITREPDPRDRRSALLSASPEGLARL
+DAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAESE
+>1_2054
+MVDGAPDPGGGGDDAGFEAAVQGLEQAFSRLVLQHRQVMARYAEALSPTLSVGAMKAFMM
+LANEGTMTPSAVAEGMLVDRAQVSRMVRDLEAAGLITREPDPRDRRSALLSASPEGLARL
+DAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAESE
+>2_282
+MAERGHGDDRGLDGVGAERGDAGGEIDGFEAAVRGLEDAFARMVRQHRQVVTRQAAALKP
+GLSAGAMKAFITLCNAGTMTPSTLAEHLLLDRAQVSRMVRDLEDEGLITREPDPVDRRSA
+LLTATEEGRARLDAVRGGPAGEGLRADLAHWDRADIHTLVRLLGRLVEEQQARVDRTPDA
+G
+>3_228
+MADPADHGSDGRGTGADAFAPEAFDAAVRELEGSFNRLVRQYRATLARQAEAVHPGLPLG
+AMKAFVAICHRGPLTPSDLAEHLMLDRTQISRVLKDLEGDGLIHREPDPRDRRSALLTAT
+DEARARLDAVRQGPAGGGTRARLQRWDLEDVRALSALLRRFVDEREDPAADDACRP
+>4_85
+MADGAPDPGRGGDDAGFEAAVQGLEQAFSRLVLQHRQVMVRYAAALSPALSVGAMKAFMM
+LANEGTMTPSAVAEGLLVDRAQVSRMVRDLEAAGLITREPDPRDRRSALLSASPEGLARL
+DAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAESE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000240.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000240.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a61c4607a3ea0bc0e4fbdd39860893e634ca121c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000240.fa
@@ -0,0 +1,61 @@
+>0_91
+MTPTSPAPEAVAPAGAPSLERAAADAARHRSVLQALTGLLLGMFVSMIANTVVSTSMPVI
+IHDIGGDQTAYTWVITSALLATAIATPIWGKLADLVNRKVLFQVALAIFVAASAAAGFTH
+DPTFLIVCRTVQGLGGGGLVALSQVIMADIISPRERGRYMGLFGAVMAVATVGGPLAGGV
+ITDLWGWRWNFFVAVPFAVVALVMVQRTLHLPHRERQKVSIDYLGIVFLTAATALLLIWV
+TSAGRDFDWASTTSAWMLGGAAVATVLFVVTELRVAEPLIPLTLFRDRTFTLATIASIAT
+GLAMFGSSVYLAQYMQLARGATPTQAGLMTIPMILGLLVSSTVIGGLITRTGVWKRWLVI
+GAVLLIAGTALLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQMGVASS
+GVTFFRTLGGSIGVAVMGAVVSNVVPDRIEERRADLAAALRSLGPDAAEWSESLQSSTLP
+RVAEMPDSLRVIFEDVYAQGIALAFLVAVPLAIVALIAILFLPNLPLGRMTTSERLHATR
+ADLATHATAEAMQTLPATGPIPVVTAAQGQHPAEDPEESRSVSAERPATAVADRPVVPAA
+LAVAGTALLAAVVTALVRARRG
+>1_2055
+MTPTSPAPEAVAPAGAPSLERAAADAARHRSVLQALTGLLLGMFVSMIANTVVSTSMPVI
+IHDIGGDQTAYTWVITSALLATAIATPIWGKLADLVNRKVLFQVALAIFVAASAAAGFTH
+DPTFLIVCRTVQGLGGGGLVALSQVIMADIISPRERGRYMGLFGAVMAVATVGGPLAGGV
+ITDLWGWRWNFFVAVPFAVVALVMVQRTLHLPHRERQKVSIDYLGIVFLTAATALLLIWV
+TSAGRDFDWASTTTAWMLGGAAVATVLFVVTELRVAEPLIPLTLFRDRTFTLATIASIAT
+GLAMFGSSVYLAQYMQLARGATPTQAGLMTIPMILGLLVSSTVIGGLITRTGVWKRWLVI
+GAVLLIAGTALLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQMGVASS
+GVTFFRTLGGSIGVAVMGAVVSNVVPDRIEERRADLAAALRSLGPDAAEWSESLQSSTLP
+RVAEMPDGLRSIFEDVYATGISHAFLVGVPLAIVALIAILFLPNIPLGRMTTSERLHATR
+ADLATHATAEAMQTLPATGPIPVVTAAQGQHPAEDPEESRSVSAERPATAVADRPVVPAA
+LAVAGTALLAAVVTALVRARRG
+>2_281
+MIDHRQSLTAVNHSDDPAEGPHEPHLPAVAGTAPAGAPSLERAAADAARHRAVLQALTGL
+LLGMFVSMIANTVVSTSMPVIISDIGGNQNDYTWVITAALLATAVSTPVWGKLADLMDRK
+MLFQVALVIFVGASAAAGFTNDPTFLIVCRVVQGLGGGGLAALSQVIMADIISPRERGRY
+MGLFGAVMAVATVGGPLAGGVITDLWGWRWNFFVAVPFALVALVMVQRTLHLPAREPRKV
+SIDYLGIVLLGVATSLLLIWVTTAGQQFPWASWTTAWMVGGAVLAAALFVVVELKVTEPL
+IPLTLFRNRTFTLATIASIATGLAMFGAGVYLAQYMQLARGATPTQAGLMTIPMIAGLLI
+TSTVIGRVITRTGVWKRWLIVGAVLLTAGMALLATLHYDTPFVLVSLHMLLLGAGVGMTM
+QNLVLVVQNTTDPRQMGVASSGVTFFRSLGGSVGVAAMGAVVANVVPSRFEARGADLAAA
+LQSLGADGPVWAQRLQSGTLPRVAEMPEPLRVVVEDVYATGISQAFLVGVPLAVVAVVAI
+VFLPNIPLGRMTTSERLDASRADLATVTAPAAMQKVPATGEIPVVAPAAGGAGGTDDACT
+AEDADGTEGVPAAQGPTTAPAEPTAERAERPAVQPAAESVPARVVAPAAAAPSTAAASGR
+SGGARPGARAAAAVALLTAIAVLMRQARRG
+>3_227
+MSTTTAPPATAGPAAVGNSPAVPSLERAADDAARHRTVLRALTGLLLGMFVSMIANTVVS
+TSMPVIISDIGGDQTAYTWVITAALLATAIATPIWGKLADLVDRKVLFQVALVLFVAASA
+AAGFTTDPTFLIVCRVIQGLGGGGLAALSQVIMADIISPRERGRYAGLFGAVMAVATVGG
+PLAGGIITDLWGWRWNFFVSLPFALVALVMVQRTLHLPARESRKVSIDYLGIVLLSTATA
+LLLIWVTNAGHQFDWASATTAWMLGGAALAAVLFVVVELTVAEPLIPLTLFRDRTFTLGT
+IASIATGLAMFGASVYLSQYMQLARGATPTQAGLMTIPMIVGLLVSSTVIGGVITRTGVW
+KRWLVIGAVLLIAGAAMLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQ
+MGVASSGVTFFRSLGGTIGVAVMGAVVANVVPDQVEQRRTDIGAALASLGPAGAEWAQRL
+QSGSLPRVAEMPDALRVIFEDVYATGISQAFLVGVPLAVVALAAILFLPNIPLGHMTTTE
+RIDAERADLATVSVPQAMQTLPATGSTPVVAQAQVQEAAPASTTTTPAPAARALRVPAGL
+RERRIAPAGTGRSTAWRATASALAAGAAAAAFVPLLRRSRRG
+>4_86
+MTPTSPAPEAVAPAGAPSLERAAADAARHRSVLQALTGLLLGMFVSMIANTVVSTSMPVI
+IHDIGGDQTAYTWVITSALLATAIATPIWGKLADLVNRKVLFQVALAIFVAASAAAGFTH
+DPTFLIVCRTVQGLGGGGLVALSQVIMADIISPRERGRYMGLFGAVMAVATVGGPLAGGV
+ITDLWGWRWNFFVAVPFAVVALVMVQRTLHLPHRERQKVSIDYLGIVFLTAATALLLIWV
+TSAGRDFDWASTTTAWMLGGAAVATVLFVVTELRVAEPLIPLTLFRDRTFTLATIASIAT
+GLAMFGSSVYLAQYMQLARGATPTQAGLMTIPMILGLLVSSTVIGGLITRTGVWKRWLVI
+GAVLLIAGTALLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQMGVASS
+GVTFFRTLGGSIGVAVMGAVVSNVVPDRIEERRADLAAALRSLGPDAAEWSESLQSSTLP
+RVAEMPDGLRSIFEDVYATGISHAFLVGVPLAIVALIAILFLPNIPLGRMTTSERLHATR
+ADLATHATAEAMQTLPATGPIPVVTAAQGQHPAEDPEESRAVAAERPATASPVAGRPVAP
+AALAVAGTALLAAVVTALVRARRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000241.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000241.fa
new file mode 100644
index 0000000000000000000000000000000000000000..15b02d3a77dbc28715dd9861bd9e8ea30aac67ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000241.fa
@@ -0,0 +1,35 @@
+>0_92
+MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD
+VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE
+GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMEVVFAPRPPAH
+REVAAAELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDADVIAKMKDDAVLVN
+TARGPVVDEAALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA
+AMAELAARNAIAMATGAEAPALVNPEVRG
+>1_2056
+MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD
+VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE
+GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH
+REVAAEELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDAEVIAKMKDDAVLVN
+TARGPVVDEVALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA
+AMAELAARNAIAMATGAEVPALVNPEVRG
+>2_280
+MSPRFLLMTEIPEPGLGMLREAGEVTLGSEVGGNDALPALAASGDYDVVVCALAQKFDAD
+VLAQARLKGIANYAVGYNNVDVAAATEAGIAVGNTPDVLTDATADIALLLILGVSRRAHE
+GEAMMRAGEFTGWRADLLVGKDVKGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH
+REVAPEELGELAGRVEQVRWEELVERSDFLSLHVPLTADTEHLVDADVLARMKDDAVLIN
+TARGPVVDEAALVEALRAGRLFGAGLDVYEDEPAMAPGLAELDNVMLLPHLGSATRDTRA
+AMAELTARNAIAMATGGEVPALVNPDVRR
+>3_226
+MSPRFLLMADLPEPGLGMLREAGEVVRGGDVGGNAALADLCASGEYDVVVGALDQRYDAD
+LLARARVKGIANYAVGFDNVDVPAATEHGILVGNTPDVLTAATADIALLLILGVTRRAVE
+GERMMREGRFEGWRADMLVGKDVVGATLGLAGFGRIGRAVAERALAFGMEVVFAPRPPAH
+REVPAEELGDLAGRVRQVRWEELVETADVLSLHVPLTEDTRHLVDEDVIARMKDDAVLVN
+TARGPVVDEAALVTALREGRLFGAGFDVYEDEPAMAEGLAELPNVMLLPHLGSATRDARA
+AMAELTARNAIGMATDGEAPALVNPEARG
+>4_87
+MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD
+VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE
+GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH
+REVAAEELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDAEVIAKMKDDAVLVN
+TARGPVVDEVALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA
+AMAELAARNAIAMATGAEVPALVNPGVRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000243.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000243.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b2f21ddb5855ae46c05b317baca27fed27c75e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000243.fa
@@ -0,0 +1,15 @@
+>0_94
+MAAFWDYFSVLAPSIGLGLIFWLVMRSLLRSDTGERESQARRLSGADARAAREEAEAREW
+AARRRAEGGPGADPEDRAR
+>1_2058
+MADFWDYFSVLAPSIGLGLIFWLVMRSLLRSDTGERESQARRLSGADARAAREEAEAREW
+AARRRAEGGPGADPEDRAR
+>2_278
+MATFWEYFSVLAPSIGLGLIFWLVMRSLLRSDTAERESMGRRSTGEDARAAREEADAREW
+ARRRGGDDVPRRGDDSR
+>3_224
+MAAFWEYFSVLAPSVGIGLVFWLVMRSLLRSDTAEREARQRRGEDARAAREEAEAREWAA
+RRRGDAPAGPGGAERP
+>4_89
+MAAFWDYFSVLAPSIGLGLIFWLVMRSLLRSDTGERESQARRLSGADARAAREEAEAREW
+AARRRAEGGPGADPEDRAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000244.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000244.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98045a70e73ddc8b27f7ac85aa577974b70d8c7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000244.fa
@@ -0,0 +1,80 @@
+>0_96
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG
+DVPETLRDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVAEPSVEDAT
+EILRGLRDRYEAHHKVSITDGALKAAAGLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLGDERREKEQAWRTGADADV
+ATVDEDLIAEVLSKSTGIPVFKLTEEETDRLRNMEDELHRRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVEIVDLFVSRLGKRLAEQDLSIELTQSAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFAFSGGREALEGADLAELESG
+AGDPVDADRSV
+>1_2060
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG
+DVPETLRDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVAEPSVEDAT
+EILRGLRDRYEAHHKVSITDGALKAAAGLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLGDERREKEQAWRTGADADV
+ATVDEDLIAEVLSKSTGIPVFKLTEEETDRLRNMEDELHRRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVQIVDLFVSRLGKRLAEQDLSIELTQSAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDTTGEGEGAELTFAFSGGREALEGADLAELEPG
+AGDPVDADRSA
+>2_276
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVKLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG
+DVPETLKDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVPEPSVEDAT
+EILRGLRDRYEAHHRVSITDGALKAAATLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLEDERRQKEEAWRTGADSDV
+ATVDEELIAEVLSKSTGIPVFKLTAEETDRLRTMEDELHKRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVEIVDLFVSRLGKRLAEQDLSIELTQAAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFGFSGGREALEGAELPELEPG
+SGETVEAGRSA
+>3_223
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLAAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGSEGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAQEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIERG
+DVPETLKGKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVPEPSVEDAT
+QILRGLRDRYEAHHKVSITDGALSAAASLADRYISDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEVKAYEERIAEVKAQKEAAIDGQDFEGAARLRDQEKQLEEEREQKEQAWRAGQDAAV
+ATVDEDLIAEVLSLSTGIPVFKLTEEETDRLRNMEAELHQRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHADLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSSTDTSTGYERMKGKVREELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVEIVDLFVSRLAKRLAEQDLSIELTPAAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFAFAGGRAALEGDDAAEPAAL
+PAAADAPVEGREAPGADVPRGDDAGQDGPEAGGALGARLD
+>4_91
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG
+DVPETLRDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVAEPSVEDAT
+EILRGLRDRYEAHHKVSITDGALKAAAGLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLGDERREKEQAWRTGADADV
+ATVDEDLIAEVLSKSTGIPVFKLTEEETDRLRNMEDELHRRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVEIVDLFVSRLGKRLAEQDLSIELTQSAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFAFSGGREALEGADLAELEPG
+AGDPVDADRSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000247.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000247.fa
new file mode 100644
index 0000000000000000000000000000000000000000..80dae9e09ca41fff1d3138b58b89f54f9a983535
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000247.fa
@@ -0,0 +1,35 @@
+>0_99
+MPAPAPLVPPTVDVPHLHDAMLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL
+PRWREWLERWPTPADLAAAPTADVLTAWDRLGYPRRALRLQEAARAVVGRHDGRVPADPA
+ALRALPGIGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA
+LMPEDPARANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA
+GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGRLGSHRPDDAQWARCVAGLVSDGLLAR
+DDDGGLTFPA
+>1_2063
+MPAPAPLVPPTVDVPRLHDAVLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL
+PRWREWLERWPTPADLASAPTADVLTAWDRLGYPRRALRLQEAARAVVERHDGRVPADPA
+ALRALPGVGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA
+LMPEDPARANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA
+GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGRLGSHRPDDAQWARCVAGLVSDGLLAR
+DDDGGLTFPD
+>2_272
+MPAHETAVPPSVDVPRLHDAVLDWFAVHARDLPWRSPDCPPWGVLVSEIMLQQTPVARVL
+PRWHAWLERWPTAADLAAAPTADVLTAWDRLGYPRRALRLQEAARAIVERHSGEVPADPA
+ALRALPGIGEYTAAAVSSFAFGLPETVVDTNVRRVIARAVGGQALPGRSLTRAEMRRAHA
+LMPEDPDRAQAWNAGVMELGALVCTARSPACERCPLADACAWVAAGSPPPEQAPRGQAWA
+GTDRQVRGAVMAAVREHGRVAGDGLRAVVVAGGRLGAHRPGDAQWERCVAGLLADGLLAR
+DDDGALAFPS
+>3_219
+MPAHDDAAPRPDLTALQDEVLDWFAAHGRDLPWRDPDCPPWGVLVSEIMLQQTPVVRVLP
+RWRAWMERWPTPADLAAAPTADVLTAWDRLGYPRRALRLQEAARAIVERHGGEVPADPAA
+LRALPGIGEYTAAAVSSFAFGIPETVVDTNVRRVLARALRGEGLPGRTLTRAEMAAAHAA
+LPADEHRANRWNAAVMELGALVCTARSPACDRCPIRARCAWVAAGSPAPEVARRGQAWVG
+TDRQVRGAVMAAVREHGRVPRGGLREAVDGTGRLGAHTPDDAQWERAVAGLLGDGLLVAH
+DDGALAFPA
+>4_94
+MPAPAPLVPPTVDVPRLHDAVLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL
+PRWREWLERWPTPADLASAPTADVLTAWDRLGYPRRALRLQEAARAVVERHDGRVPADPA
+ALRALPGVGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA
+LMPEDPTRANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA
+GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGWLGSHRPEDAQWARCVAGLVSDGLLAR
+DADGGLTFPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000248.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000248.fa
new file mode 100644
index 0000000000000000000000000000000000000000..beb6bd3e03ae5f7273b12852e81f785a2c02afc9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000248.fa
@@ -0,0 +1,31 @@
+>0_100
+MPSRPTSPGSKPSPAVYRRRRLVAALLALVLLLLVGWAVVALVRAGIGAFSSEDADPSAA
+PTPVHSPSPAPATDAESSSASPTVALEDAAECQPSDLRIAASADRSEYQRGEEAELRLGI
+TNLSSTPCRTDVGTARQEFTIRTAEGDDVFSTRICQADPAEAQRVLYPHEELTAVYRWSG
+RASSQDCGRLGALAEPGPHLLTVSLGDVTSRPVALKILEELAPGAQDSSSSAAPSSATPS
+SATPSSSGSASPSGSASDPASASTTDPSPSSSR
+>1_2064
+MPSRPTSPGSKPSPAVYRRRRLVAALLALVLLLLVGWAVVSLVRAGIDAFSSEDADPSAA
+PTPVHSPSPAPATDAESGSASPTVALEDAAECQPSDLRIAASADRSEYQRGEEAELRLGI
+TNLSSTPCRKDVGTARQEFTIRTAEGDDVFSTRICQADPAEAPRVLYPHEELTAVYRWSG
+RASSQDCGRPGALAEPGPHLLTVSLGDVTSRPVALKILEELAPGAQDSSSSAAPSSATPS
+SATPSSSGSASPSGSASDPASASTTDPSPSSSR
+>2_271
+MPSRPSSPGPKPSAAVYRRRRLVAALLALILLLLVGWGLWSLIRLGMGALSGDDAEPSVS
+APPTPVHSPSPAPPSGATPGSAAPTVALEDAAECQPSDLRLVASADKAQYLRGEEAVLRL
+GVTNLSSSPCRADVGTARQEFTVRTAEGDDVFSTRVCQADPTSSERVLTPHEELTAVYRW
+SGHASNEDCGTPGALAAAGPHLLTVTLGEQTSRPVALRIQEEAAPGAWDGASSGAPASGS
+PAPSTPASPSASPSATGSAPAASSPAPASGSPAASTPATPSASPSR
+>3_218
+MPSASPAPRPRPSAAVLRRRRVVAGCLAAAFLLLVGWGIGALVNALLPSGRPDAEPSAAP
+TPVSSPTPAAARSLDAQAGQTQDPASVESCAPMDLRLVAAADRERYAPGEEAVLRLEVTN
+LSGRPCRTDVGTAQQEFRVTDASEQQVMSTRVCQADPTHEDVVLEPRDQKAAVYRWNGRA
+SSADCARLGPAVEPGEYRLTVTLGEVTSRPVALTVTDGTKSAAPASSPAASSAAPGPSAT
+TAPASAETSSASPSASSSSAQPSSPAPRASEPTSSAPTSSPAGSGRASSSPAAPSSSAAS
+PTR
+>4_95
+MPSRPTSPGSKPSPAVYRRRRLVAALLALVLLLLVGWAVVSLVRAGIDAFSSEDADPSAA
+PTPVHSPSPAPATDAESGSASPTVALEDAAECQPSDLRIAASADRSEYQRGEEAELRLGI
+TNLSSTPCRTDVGTARQEFTIRTAEGDDVFSTRICQADPAEAPRVLYPHEELTAVYRWSG
+RASSQDCGRLGALAEPGPHLLTVSLGDVTSRPVALKILEELAPGAQDGGSSATPSSATPS
+SSGSASPSASASAPASASASASASASASASPSAAPATTTDPSPSPSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000249.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000249.fa
new file mode 100644
index 0000000000000000000000000000000000000000..552d5ac5686eed83d2087d529336be9f83f043bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000249.fa
@@ -0,0 +1,40 @@
+>0_102
+MTDRFATATGTVPMVDPQTRGERLGRFLRRRARAGWSRVRSSVGQAALVAVCAVGAYWFA
+EAVLGHQQPLFASTALLIALGFQREPKLRKVAEVAVGCTVGILIGDLLMVGLGRGLWQAS
+VVLFVSVMVARFLDSGATFTMQMSLQSVLVVLLPTGTGGPFVRSQDAIVGGVLALLVTFL
+SPQDVRRPAVRQLGGLYDSIATVLRDLSRALRENDSRTAWMALVASRGTHTTLEALRKEL
+RVTHEQTVFNPLHRSSRSFVEDAVNAADRSDLAVRSLRIVARRVVSVLDEGVFDDDDRER
+LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASALDPHQLGGGSVHGEAL
+VMLLRPMMVDLIEATGAEHDEARGYLPRV
+>1_2066
+MTDRFATATGTVPMVDPQTRGERLGRFLRRRARAGWSRVRSSVGQAALVAVCAVGAYWFA
+ETVLGHQQPLFASTALLIALGFQREPKLRKVAEVAVGCTVGILIGDLLMVGLGRGLWQAS
+VVLFVSVMVARFLDSGATFTMQMSLQSVLVVLLPIGTGGPFVRSQDAIVGGVLALLVTFL
+SPQDVRRPAVRQLGGLYDSIATVLRDLSRALREDDSRTAWMALVASRGTHTTLEALRKEL
+RVTHEQTVFNPLHRSSRSFVEDAVNAADRSDLAVRSLRIVARRVVSALDEGVLDDDVRER
+LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASALDPHQLGGGSVHGEAL
+VMLLRPMMVDLIEATGAEHDEARAYLPRV
+>2_269
+MSDRFATATGTVPMVAPESRGARLRRFLRRRSRAGWSRVRSSVAHAALMAVCAVGAYWFA
+ETVLGHHQPLFSSTALLIALGFQREPTLRKVAEVAVGCTVGILIGDLLLAALGRGLWQAT
+VVVFVSVMVARFLDSGATFTMQMSLQSVLVVLLPAAQGGPFARSADALVGGLLALVVTFL
+SPQDVRRGTARHLEGLYDSMATVLRDLSRALRQEDSRTAWMALVACRGTQGTLESIRAEL
+KMAQEQATFNPLQRGSRSFVSDAANAADRSDLAVRSLRIVARRVVSVLDEGAFDDDHRER
+LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASRLDPRELGGGSLHGEAL
+VMLLRPMMVDLLEATGAPHDEARAYLPRV
+>3_211
+MTDRHATATGTLPAVPAAAGPSGVGRFLRRRARAGWSRLRSSVGHAALMAVCAVGAYWFA
+ETVLGHAQPLFAATALLIALGFQREPRVRKVAEVAFGCTLGILIGDLMMAALGRGLWQAV
+LVVFVSVLAARFLDSGATFTMQMSLQSVLVVLLPLNADGPFARSADALVGGLLALLVTLL
+SPRDPTRLPARQLRGLYESMASVLRELSAALRAEESRTAWMALVECRRTQSTLEDVRKEL
+KVTREQTVLNPLQRPARDAADVMAVAADRSDLAVRSLRIVARRVVSILDHGAVDGDHRER
+LAAWFDDAADAVEILHRSLAEPQAEGRHRSLDVARDALGASASWLDPHELAGGTVHGEAL
+VMLLRPMMVDLIEATGASHAEALTYLPRV
+>4_97
+MTDRFATATGTVPMVDPQTRGERLGRFLRRRARAGWSRVRSSVGQAALVAVCAVGAYWFA
+EAVLGHQQPLFASTALLIALGFQREPKLRKVAEVAVGCTVGILIGDLLMVGLGRGLWQAS
+VVLFVSVMVARFLDSGATFTMQMSLQSVLVVLLPTGTGGPFVRSQDAIVGGVLALLVTFL
+SPQDVRRPAVRQLGGLYDSIATVLRDLSRALRENDSRTAWMALVASRGTHTTLEALRKEL
+RVTHEQTVFNPLHRSSRSFVEDAVNAADRSDLAVRSLRIVARRVVSALDEGVLDDDVRER
+LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASALDPHQLGGGSVHGEAL
+VMLLRPMMVDLIEATGAEHDEARGYLPRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000251.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000251.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e19a267118ed42b8372b246ec82de8d62a27bb88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000251.fa
@@ -0,0 +1,35 @@
+>0_104
+MSSTTNEAAPKPSSLRGPRRGAAGDKLLSGGALAAAVLILLVLAFVAVFLLTEAWPALQP
+GAELVSADSFFQYVWPLMAGTVMVSIIALLIATPVAIGVALFISHYAPPRIAQSVGFVID
+LLAAIPSVVYGVWGWLTLAPLMVPIYGWLNENLGFIPFFGGSATTTGRTLLTSGVVLAVM
+VLPIITALCREIFTQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIISSIMLGLGRALG
+ETMAVTMVLSGGVFSWSLVESGRNQTIPSEIALNFPEAFNMRLHELIAAGLMLFIITLAV
+NMIARAIVNKHKEFSGAN
+>1_2068
+MSSTTNEAAPKPSSLRGPRRGAAGDKLLSGGALAAAVLILLVLAFVAVFLLTEAWPALQP
+GAELVSADSFFQYVWPLMAGTVMVSIIALLIATPVAIGVALFISHYAPPRIAQSVGFVID
+LLAAIPSVVYGVWGWLTLAPLMVPIYGWLNENLGFIPFFGGSATTTGRTLLTSGVVLAVM
+VLPIITALCREIFTQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIISSIMLGLGRALG
+ETMAVTMVLSGGVFSWSLVESGRNQTIPSEIALNFPEAFNMRLHELIAAGLMLFIITLAV
+NMIARAIVNKHKEFSGAN
+>2_267
+MTSPATEAPPRATTLKSSRGGAAGDKVFSGLSLAAGVLILLTLAFVAIFLVVRSLPALFP
+DAYGTQLKSADTFFQYVWPLMAGTIMAAVIALLLATPVAVGVALFISHYAPPKIAQPVGY
+VIDLLAAIPSVIYGIWGWLTLAPVMVPIYQWLNEYLGFIPFFGGPVTGTGRVIMTSGVVL
+AVMILPIITALCREIFRQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIVSSVMLGLGR
+ALGETMAVTLVLSAGGFSLSLIEEGRNATIPSEIALNFPEAYGIRLNELIAAGLMLFVIT
+LVVNMTARWIVNKHKEFSGAN
+>3_209
+MSHTATEAAPSSSALKSSRAGAAGDKVFSGLALAAGVLILLILAFVAIFLVSEAWPALFP
+AEGANLESGDSFWGYVWPLMAGTVMAAIIALLLATPVAVGVALFISHYAPPKIAQPVGYV
+IDLLAAIPSVVYGIWGWLTLAPLMVPIYEWLNEYLGWLPFFGGSVTSTGRVLMTSGIVLA
+VMVVPIITALCREIFSQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIVSSIMLGLGRA
+LGETMAVTMVLSPGKFSPSVIEEGRNATIPSEIALNFPEAYGIRLNELIAAGLMLFVITL
+VVNMVARWIVNKHKEFSGAN
+>4_99
+MSSTTNEAAPKPSSLRGPRRGAAGDKLLSGGALAAAVLILLVLAFVAVFLLTEAWPALQP
+GAELVSADSFFQYVWPLMAGTVMVSIIALLIATPVAIGVALFISHYAPPRIAQSVGFVID
+LLAAIPSVVYGVWGWLTLAPLMVPIYGWLNENLGFIPFFGGSATTTGRTLLTSGVVLAVM
+VLPIITALCREIFTQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIVSSIMLGLGRALG
+ETMAVTMVLSGGVFSWSLVESGRNQTIPSEIALNFPEAFNMRLHELIAAGLMLFIITLAV
+NMIARAIVNKHKEFSGAN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000255.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000255.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e121b3209a0f66c77e34c001c68c48a4478e986
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000255.fa
@@ -0,0 +1,25 @@
+>0_108
+MSPRMPWLVTRDTPALRHMADLAEALHRSVHLVAQVAGTRGPEADRAARELEELDSSSSA
+TLMAFLTALRSAYVTPLPRQDLYRLASGVHATTRRVVSAGVLIQRADLEELPTHALDVLE
+TVGRQAELLARGAAEMRDLDALEATWMQLLRASRRTERIMVEWLADLGMDLLQRDYNRQR
+EVAWALHAALEALSRVNMDLGMVLVRES
+>1_2072
+MSPRMPWLVTRDTPALRHMADLAEALHRSVHLVAQVAGTRGPEADRAARELEELDSSSSA
+TLMAFLTALRSAYVTPLPRQDLYRLASGVHATTRRVVSAGVLIQRADLEELPTHALDVLE
+TVGRQAELLARGAAEMRDLDALEATWMQLLRASRRTERIMVEWLADLGMDLLQRDYNRQR
+EVAWALHAALEALSRVNMDLGMVLVRES
+>2_263
+MSPRMPWPVTRDTPALRHIVDLAEALRRSVHLVAQVAGARGPEADRTARELEDLDAASTA
+SLMSFLTALRSAYVTPLPRQDLYRLAGGVHAATQRVVSAGVLIQRADLEHLPAHALDVLE
+TVGRQAELLGRSTTELRDLDALEATWMQLLRASRRTERIMVQWLADLGMDLLQRDFNRQR
+EVAWALQSALEALGRVNTDLGMVLVRES
+>3_205
+MTPRPAWLVTRDSPALGHLTDLCDTLGRAVRAVAQAVAADGSERDRVERDLSALDAAATA
+ALMAFLTALRSAYVTPVPRPDLYRLADGVKTAAHRVVGAGVLVHRADLDALPRNAVELLE
+TLGRQAELLAHGTRQLRDLDALEDTWMQLERGIRRMERLMVDWLAALGTDLLQRDYNRQR
+EIASALRDAVLALDRVNTDLGVVLVRES
+>4_103
+MSPRMPWLVTRDTPALRHMADLAEALHRSVHLVAQVAGTRGPEADRAARELEELDSSSSA
+TLMAFLTALRSAYVTPLPRQDLYRLASGVHATTRRVVSAGVLIQRADLEELPTHALDVLE
+TVGRQAELLARGAAEMRDLDALEATWMQLLRASRRTERIMVEWLADLGMDLLQRDYNRQR
+EVAWALHAALEALSRVNMDLGMVLVRES
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000256.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000256.fa
new file mode 100644
index 0000000000000000000000000000000000000000..adfca4f330c720c331f0eaea14761a25984f05ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000256.fa
@@ -0,0 +1,25 @@
+>0_109
+MARHRLPAGRGASSSASGVLRPHRPRLSEPQELTHFAGGEDPQEVAAAASRLAHALVAGG
+RAEEDPAIVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATTRDGERWAAW
+YRAGHAAYASRVVAGAVEPPGPAELRRLTDTILTGAYRSEIDVAFERAAAYARVVALGQV
+EHAEGSEAAAPDRAAALTRRAARLVSTADALEAAGRAFRDGSLD
+>1_2073
+MARHRLPAGRGASSSASGVLRPHRPRLSEPQELTHFAGGEDPQEVAAAASRLAHALVAGG
+RAEEDPAIVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATTRDGERWAAW
+YRAGHAAYASRVVAGAVEPPGPAELRRLTDTILTGAYRSEIDVAFERAAAYARVVALGQV
+EHAEGSEAAAPDRAAALTRRAARLVSTADALEAAGRAFRDGSLD
+>2_262
+MARHRQTTGRGASSSASGLVRPHRPRLSEPDELAHFAGGEDPQEVAAAASRLAHALVAGG
+RAEEDPEVVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATARDGERWAAW
+YRAGHAAHAARAVAGAVEPPGPDELRRLTDTILTGAYRSEIDVAFERAGAYGRVVALGQV
+EHAEAAEAADPALAAGLTRRAARLVSTSEALEEAARAFRNGSLD
+>3_204
+MAHHRAPAGRGASSTASGLVRPHRPRLTDPGLIADLADGEDPQEIAAAASRLAHALVAGG
+RAEEDPDVVARLVGLVREVGVETLAGLWADAPAVSLAGALWRLYALQEATARDGERWAAW
+YRAGHAAHAARAVAGAVEPPGPEELRRLTDTILTGAYRSELDVALERAGAYARVVALGQA
+EHAAAAEHADPAHAARLTLRAARMISTAEALEAAARSWRDGSLD
+>4_104
+MARHRLPAGRGASSSASGVLRPHRPRLSEPQELTHFAGGEDPQEVAAAASRLAHALVAGG
+RAEEDPAIVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATTRDGERWAAW
+YRAGHAAYASRVVAGAVEPPGPAELRRLTDTILTGAYRSEIDVAFERAAAYARVVALGQV
+EHAEGSEAAAPDRAAALTRRAARLVSTADALEAAGRAFRDGSLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000258.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000258.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a3b573eb7e53a8560c08d83203306ef0e83c2fc1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000258.fa
@@ -0,0 +1,30 @@
+>0_111
+MAKNSTIGRYASGKVKDFGLKSALDENGEPTEGFEKALSTVLAVQRPLVLKNIQRMAAKH
+PGESPERLAERLGQQYLTTVTGAGAAVGGTAIVPGIGTVAALGLSGAAVAGFMEATALYA
+QSLAELHGITTQDPQRAQALVMGLMLGDDAKELLREAAAKAGRPYDPQSSLNALAGTASG
+TGISAFVVDRLKRTFMRKMLLRQGAGFVGRAVPFGVGAVIGGVGNRAMGKAVMENAAELF
+GPLPMVIPGEIREGVAQGRAGGESAGAKDDGGVLGAIRRALPGGKDEKDDRQKKGKPAA
+>1_2075
+MAKNSTIGRYASGKVKDFGLKSALDENGEPTEGFEKALSTVLAVQRPLVLKNIQRMAAKH
+PGESPERLAERLGQQYLTTVTGAGAAVGGTAIVPGIGTVAALGLSGAAVAGFMEATALYA
+QSLAELHGITTQDPQRAQALVMGLMLGDDAKELLREAAAKAGRPYDPQSSLNALAGTASG
+TGISAFVVDRLKRTFMRKMLLRQGAGFVGRAVPFGVGAVIGGVGNRAMGKAVMENAAELF
+GPLPMVIPGEIREGAAQGRAAGESEGTKDYGGVFGAIRRALPGGKDEKDKPAA
+>2_257
+MAKNSMIGRYTSGKVKDFALKSALDENGEPTEGFEKVVSKVLGIQRPLVLKHIQNVAAKN
+PELTAEQIAERLGQQYLNTVTGAGAAVGGTAIVPGVGTVAALGLSAAATVGFMEATALYA
+QSLAELHGITMEDPQRAETLVMALMLGDDAKELLREAAAKAGRPFDPNASLNALAGSAAG
+TGGGAGISAFVMDRLKRTFMKKMLVRQGAGFLGRAVPFGVGAVIGGVGNRAMGKAVMENA
+QELFGPLPTVIPGEIREGAARQAQEDDGEGGVFAAIRRALPGGDDKKDAAKA
+>3_190
+MAKNSIIGRYASGKAKDFAMKSAFDENGNPTEGFEKLVFTTLDIQRPLVLKNIQRLHESH
+PGETPEQLAERLADQYVTASTGAGAAVGGTAIVPGIGTVAALGLSAAATVAFLEATALYA
+QSLAELHGLTTKDPARSKALVMAVMLGDDTKELLKDISRKSGVKNTGTPDSAAGLAAMMN
+GGAAGQAAGGAGLGAVAIEQLKKQFVKKVLVRQGAGFLGRAVPFGVGAVIGGVGNRAMAK
+AVVKNSRDLFGPLPAQIPGEIVAASAKGQDVGQSAEDGKGGLVSGLIKALPLGKKDEKKA
+>4_116
+MAKNSTIGRYASGKVKDFGLKSALDENGEPTEGFEKALSTVLAVQRPLVLKNIQRMAAKH
+PGESPERLAERLGQQYLTTVTGAGAAVGGTAIVPGIGTVAALGLSGAAVAGFMEATALYA
+QSLAELHGITTQDPQRAQALVMGLMLGDDAKELLREAAAKAGRPYDPQSSLNALAGTASG
+TGISAFVVDRLKRTFMRKMRLRQGAGFVGRAVPFGVGAVIGGVGNRAMGKAVMENAAELF
+GPLPMVIPGEIREGAAQGRADGTKDDGGVFGAIRRALPGGKDEKDDRQKKGKPAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000260.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000260.fa
new file mode 100644
index 0000000000000000000000000000000000000000..144d8a8d24c2a2aced4a8402903c7560cf0188d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000260.fa
@@ -0,0 +1,45 @@
+>0_117
+MATRADRGRPVHNPDIIGFTDAELNETPIRPKWNSLGPGIVAAATGVGAADLVATLTAGS
+RYGYMLLWAVILGVIFKIVLVEGVGRWYLSTGKTIFQGWRSLGSWTSWYFGPYILIWGFV
+YGATAMSSAALPLAALFPGVDMKVYAIGLGLVGLGLVWLNRYGLIEKLMAVLIGVMFLTV
+LLSAALTAPNVGDILAGLVPRIPSGDPDVMFYVLGLAGGVGGTITLGAYAYWLREKGWNV
+PKYMRVMKFDNATSYILTGIFVIATMIMGVELLHSAGLAISSGDRGLLDVGNVLAERYGQ
+AYSVVFLVGFFAASFSSLLGVWHGVSLMFADFWTNFRRPADELDQDDAPSLASKPGRFFL
+LWLTFPPMTLLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNKKEVPAQFRNGWIRNTL
+LGLTAAVFVAIGVNELWKALQPLIGG
+>1_2082
+MAHAVDPGRPVHNPDIVGFTDAELNETPIRPRWNSLGPGIVAAATGVGAADLVATLTAGS
+RYGYMLLWAVVLGVIFKIVLVEGVGRYYLSTGKTIFQGWRTLGAWTSWYFGPYILIWGIV
+YGATAMSSTALPLAALFPGVDSKVFAIASGLIGLGLVWLDRYRLIEWLMTVLIGVMFVTV
+LLSAALTVPNLGAILAGLVPRLPSGDPQAMFYVLGLAGGVGGTITLAAYGYWLREKGWNV
+PKYLKVMRFDNATSYILTGIFVIATMVMGVELLHSAGLAISSGDKGLLDVGDVLAERYGS
+AWSTVFLIGFFAASFSSLLGVWHGVSLMFADFWTNFRRPAEELDQDDAPSLSSKPGRFFL
+LWLTLPPMALLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNTKDVPRQFRNGWVRNTL
+LGLTAAVFVAIGVNELIKALQPVLGG
+>2_250
+MPHTADRGHPVHNPDIVGFTEAELNETPIKPRWNSLGPGIVAAATGVGAADLVATLTAGS
+RYGYMLLWAVVLGVIFKIVLVEGVGRWYLSTGKTIFQGWRQLGSWTSWYFGPYILIWGFV
+YGATAMSSTAIPLAALFPAVDAKVFAIAAGLIGLALVWLNKYGLIEKLMTALIGVMFVTV
+LISAALTAPNVGEILSGLVPRIPSGDPQVMFYVLGLAGGVGGTITLGAYAYWLREKGWNV
+PKYMKVMKFDNATSYVLTGIFVIATMIMGVELLHSAGLAISSGDKGLLDVGNVLAERYGQ
+VWSYVFLIGFFAASFSSLLGVWHGVSLMFADFWTNFRRPADELDQDDAPSLASKPARFYL
+LWLTILPMSLLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNRKDVPVQHRNGWIRNIL
+LGLTAAVFVAIGVNELIKALQSVLGG
+>3_184
+MSHTTPPGHGLVDRHHPVHDPDIVGFTEAELNETPIKPKWNSLGPGIVAAATGVGAADLV
+ATLTAGSRYGYMLLWAVVLGVVFKIVLVEGVGRYYLSTGKTIFQGWRGLGSWTSWYFGPY
+ILIWGFVYGATAMSSTALPLAALFPGVDSKVFAIASGLVGLGLVWLNRYGLVEKVMTVLI
+GVMFVTVLISAALTVPNLGDILGGLVPRIPSGDPDVMFYVLGLAGGVGGTITLGAYGYWL
+REKGWNTPKYMRVMRFDNTVSYVLTGVFVIATMIMGVELLHSAGIAISSGDKGLLDVGDV
+LAQRYGDVWATVFLIGFFAASFSSVIGVWHGVSLMFADFWTNFRRPADELDQDDAPSLAS
+KPGRFYLLWLTFPPMVLLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNSRRVPGKFRN
+GWVRNVLLALTTAVFLVIGGNELLKALKPLIGG
+>4_125
+MATRADRGRPVHNPDIIGFTDAELNETPIRPKWNSLGPGIVAAATGVGAADLVATLTAGS
+RYGYMLLWAVVLGVIFKIVLVEGVGRYYLSTGKTIFQGWRTLGAWTSWYFGPYILIWGIV
+YGATAMSSTALPLAALFPGVDSKVFAIAAGLIGLGLVWLDKYRLIEWLMTVLIGVMFVTV
+LLSAALTAPNLGEILAGLVPRLPSGDPQAMFYVLGLAGGVGGTITLAAYGYWLREKGWNV
+PKYLKVMRFDNATSYILTGIFVIATMVMGVELLHSAGLAISSGDKGLLDVGDVLAERYGS
+AWSTVFLIGFFAASFSSLLGVWHGVSLMFADFWTNFRRPAEELDQDDAPSLSSKPGRFFL
+LWLTLPPMALLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNTKDVPRQFRNGWVRNTL
+LGLTAAVFVAIGVNELIKALQPVLGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000262.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000262.fa
new file mode 100644
index 0000000000000000000000000000000000000000..17ff47ea0c8991e61aa3dd5c315ec8a58b2be83d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000262.fa
@@ -0,0 +1,23 @@
+>0_119
+MAVTVRPATSDDVEPLLRVKAQAWREAYGGLLPAAHLDAVDAGVPEQVPGWAALVGSDRE
+LWVADDGGRLLGMALAGPRRSQGGGLPDLELMALYVLAEAYGTGLGALLLDAVVGKRPAV
+LRVLAENPRAVAFYAKHGFAPEGGPEPMTGPWAGLHEQLMVRRG
+>1_2084
+MPESVTVRPAAPGDVEALLRVKARSWREAYGALLPSAYLDAIEARIPEDVPAWTALIGPD
+RDLWVADDGGRLLGVALAGPRRSAAETGRTGADDAAASPADLPDVELMVLYVLAEAYGTG
+LGARLLDAVVGERPAMLRVLAENPRAVAFYAKHGFAAVGAPEPMTGPWAGLHEQLMVRRR
+PHDGGAA
+>2_248
+MAVVVRPARREDAEALLRVKAQSWREAYGAHLPAEVFDRADARVPQDAPAWAALVGSDRD
+LWVAEDDDGGRLVGVALAGPSRIEDEGLPPRELMVLYVLAEAHGTGVGARLLDAVVGDGP
+AVLDVLAENPRARAFYAKHGFEDHGAPAPMDGAWAGLHEQRMVRRG
+>3_182
+MRETDGASDAVVRDVNPPSAPAPTVRPAGADDLPAVLAMKNAAWRETYAHLLEPGFLAAQ
+EAELPRAVEAWTRLLGEPGMEVWLAEGAGVVVGMAAAGPADDPALGPEGRELIALYVRAR
+LHGAGLGAALLRAAVGGRPARLDVLVGNERAIAFYERHGFVAVGEPAVLGGPWGDAREQR
+MVRR
+>4_127
+MPESVTVRPAAPGDVEALLRVKARSWREAYGALLPSAYLDAIEDRIPEDVPVWTALIGSD
+RDLWVADDGGRLLGVALAGPRRSAAETGRTGADDAAASPADLPDVELMVLYVLAEAYGTG
+LGARLLDAVVGDRPAVLRVLAENPRAVAFYAKHGFASVGAPEPMTGPWAGLHEQLMVRRL
+PHDGGAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000266.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000266.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34a54f06f9a11953a00206cdfa106ebb7a568603
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000266.fa
@@ -0,0 +1,25 @@
+>0_123
+MPDSPSARATGGETALVVIDVQHSYFEHPALAAQQAELTAAVVELLRTAREAGRPVFLVR
+TEHARDRSTWTLNMLADGEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSAFHGTGLAA
+ELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIASEEPALAAAMLDFLRDE
+MRQPLLGQDEALTLLRTGLVPDRG
+>1_2088
+MPDSPSARATGGETALVVIDVQHSYFEHPALAAQQAELTAAVVELLRTAREAGRPVFLVR
+TEHARDRSTWTLNMLADGEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSAFHGTGLAA
+ELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIASEEPALAAAMLDFLRAE
+MRQPLLGQDEALTLLRTGLVPDRG
+>2_244
+MPDSAPAPEPIAGERPSGGETALVVVDMQYSYFEHPDLAARQAELTEAVVELVRTAVEAG
+RPVVLVRTEHERDRSTWTLNMLEDGEGFAFPGTRQAAVLDEVARAARGAVEVVKTRDSAF
+HRTDLDAQLRRRGVGRLLLCGVSTHSCVFQTATDAFARDFHAATAVDAIASEDPRLSAAM
+LEFLRDEMRQPLLGREDALALLRTGLVPDQG
+>3_634
+MNTLQNPALIVVDVQRGFDDVEYWGSRDNPDCETNISSLLTHWRDRSWPIVFVRHDSTNP
+ESTLAVGTPGNEFKEVITGDPDLLVSKTVNSSFHGTPDLDDWLRAEGIEQVVICGITTNH
+CCETTARIAGNLGYDTYFAIDATHTFDRPALDGTVLPAATVSAMTAANLHGEFATVVSTR
+TLIDGNSYAPRYEQEK
+>4_131
+MPDSPSARATGGETALVVIDVQHSYFEHPALAAHQSELTAAVVELLRAAHEAGRPVFLVR
+TEHARDRSTWTLNMLADDEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSAFHGTGLAA
+ELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIASEEPALAAAMLDFLRDE
+MRQPLLGQDEALTLLRTGLVPDRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000268.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000268.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c29742037c4b9dd0235b3ac9dd57dbfde03e5a0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000268.fa
@@ -0,0 +1,59 @@
+>0_127
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG
+VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT
+SSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG
+QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVA
+PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV
+RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE
+HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPTRGVLAF
+TVTSGGGRHLGSGEPIPARTVLVMANLSTEPVDLPANHSRALFSLEEAEAVQDGRLAHDA
+AAWLLMD
+>1_2092
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG
+VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT
+SSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG
+QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVA
+PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV
+RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE
+HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPTRGVLAF
+TVTSGGGRHLGSGEPIPARTVLVMANLSTEPVDLPANHSRALFSLEEAEAVQDGRLAHDA
+AAWLLMD
+>2_240
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG
+VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT
+SSEHAWFQAALAAGPDSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG
+QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFLDQDRVHEVYRDWRRVLDSYGHEPMMVAEAWVA
+PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV
+RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE
+HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPARGVLAF
+TVTSGGGRHLGSGEPIPARTVLVMANLSTDPVDLPTGHSRALFSLEEAEAVQDGRLAHDA
+AAWLLMD
+>3_175
+MTTQRLTTPPSEARNRPETPWWVDAVVYQVYPRSFADGDGNGMGDLPGVTAKIPYLSRLG
+VDAIWLSPFYLSPQHDAGYDVADYRTVDPRFGTLADADALIDAAHAADIRVIVDLVPNHT
+SSEHPWFQAAMAAGPGSRERARYHFTEGRGEHGELPPSNWESTFGGGAWSRVTEADGTPG
+QWYLHLFDTTQPDLNWENPEVREEFESILRFWLDRGVDGFRVDVAHGLVKKPGYPDADHT
+RMGMVTDAGEDQDPDFDVDAFEPAMPFLDQDGVHEVYRQWRRVLDSYPHEPMMVAEAWVS
+PLPRTFRYVRPGEMHQAFNFTYLMAGWDAESLTSAIDRSFTEAEKVGAPNTWVLSNHDTV
+RHTSRYGLSDPTAYPAGITAEDEQPDEALGRRRARAAAMIELALPGSAYIYQGDELGLPE
+HTTLPAELREDPYFFRTGGAEPGRDGCRIPLPWAADEPALGFSGPDADAAPWLPQPDSFR
+VLAADRQVGVEGSHFELYRHLLQIRAELDLGTGTFAWSAEHHRPEQGVLAFTVSSGGGRH
+LGSGVPIPARTVLVMANIGDTPVALPGDHVRAQFSLPESEAVVDDRLAPDAAAWLLLR
+>4_135
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG
+VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT
+SSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG
+QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVA
+PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV
+RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE
+HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPARGVLAF
+TVTSGGGRHLGSGEPIPARTVLVMANLSTDPVDLPAGHSRALFSLEEAEAVQDGRLAHDA
+AAWLLMD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000269.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000269.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6700937c6561afa0d48cb4b8d4ff0e791d98d842
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000269.fa
@@ -0,0 +1,31 @@
+>0_128
+MTHDDGGPPPGVARGTAHLRVFQPLAAFPDAVQARLIAGGHRTRAEVEAEAAERARRRLA
+RPVADPFPEPGEDDLVRVLQDEHRSAFYCPDERGLRAEMAAAMLEETMLPRLHSAAIPPA
+ARAMNRGRALVALEDEWGLSPDPDAAVEDPQDEDGAPEHHRVQTRTATWGVPHGWLTVFD
+PEEPVQRLVDGERTAYRRAPIVAARERAGHAAAVLARHAPDAELIGELTVMVEWLGAFHP
+DSWVELDYGGLTRHVWPDDSVFDLWTLIDALEEGDEATAGVAQERLNRRWATVGMLARLT
+>1_2093
+MTHDDGGPPPGVARGTAHLRVFQPLATFPDAVQARLIAGGHRTRAEVEAEAAERARRRLA
+RPVADPFPEPGEDDLVRVLQDEHRSAFYCPDERGLRAEMAAAMLEETMLPRLHEAAIPPA
+ARAMNRGRALVALEDEWGLSPDPDAAGQDPQDEGGAPEHHRVQTRTATWGVPHGWLTVFD
+PEEPVKRLVDGERTAYRRAPIVAARERAGHAAAVLARHALDAELIGELTVMVEWLGAFHP
+DSWIELDYGGLTRHVWPDDSVFDLWTLIDALEEGDEATAGVAQERLNRRWAAVGMLARLT
+>2_238
+MVHDDGADGPAPGGGRVPGGAPPPGIAHGTAHLRVFQPLAAYPDAVQARLIAGAHRTRAE
+VEAEAAERARRRLARPVTDPFPEPGEDDLVRVLQDEQGSAFYCPDEFGLRAEMAAAQLEE
+TMLPLAYEAAVPTAARAMNRGRVLVALEEEWGLSPDPDADRAHPDEEDGPGRDEDGPSGR
+HRVQTRTATWGVPHGWLAVFDPEEPVRRLVDGERTAYRRAPALAALERAGHAAAVLSRHA
+PDAELIAELTVMVEWLGAFHPDSHVELDYGGLTRHVWPDDSVFDLWTLIDALGEGDEATA
+GVAQGRLNRRWAAVGMLARLT
+>3_172
+MRTAAANLRVFQPLSAYPDAVAARMVAAAHRTRAEVEAEAAERARRRLLRLPADPFPAPG
+EDDLVRVLERGGSAFYCPDELALRMEMAAEMLEASAPEALYAAAVPAAARAMNRGRALVA
+LEDEWGLSPDPDAPAPDDPQDAAHQDQDADAGTHRLQTRTSLWGVPHAWLAAFDPEEPAR
+RLVDGEDVAYRRTPVAEAVERVGHAAAVLAGAAPDAELLGELAVMIPWLQAFHPDAVLEL
+DYGRALTSLVWPDDSVFDLWTLLDALEEGDEVGAGMAQERLNRRWARVGMHAHDG
+>4_136
+MTHDDGGPPPGVARGTAHLRVFQPLAAFPDAVQARLIAGGHRTRAEVEAEAAERARRRLA
+RPVADPFPEPGEDDLVRVLQDEHRSAFYCPDERGLRAEMAAAMLEETMLPRLHEAAIPPA
+ARAMNRGRALVALEDEWGLSPDPDAAGQDPQDEGGAPEHHRVQTRTATWGVPHGWLTVFD
+PEEPVKRLVDGERTAYRRAPIVAARERAGHAAAVLARHAPDAELIGELTVMVEWLGAFHP
+DSWIELDYGGLTRHVWPDDSVFDLWTLIDALEEGDEATAGVAQERLNRRWAAVGMLARLT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000272.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000272.fa
new file mode 100644
index 0000000000000000000000000000000000000000..50b26207566535af04961a962ce7bc5b20452f0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000272.fa
@@ -0,0 +1,20 @@
+>0_131
+MSEIQHDDAVQHPSGLPLAHWLTLTEGLIAARVAESLEEHGLTRAQWQLLNTLTVAPQSR
+AELEAGFEEEQRGAVSGQIEELVESRWVTVEGDLYTLTATGRTAGARVGEAVEALRAEAT
+ADVPRDQIDDAVRVLRRIARNLGHPDA
+>1_2096
+MSEIPHDDAPVQHPSGLPLAHWLTLTEGLIAARVAESLEEHGLTRVQWQLLNTLTVAPQS
+RAELEAGFEEEQRGAVSGQIEELVESHWVTVEGDLYTLTATGRTAGARVGEAVEALRAEA
+TADVPRDQIDDAVRVLRRIARNLGHPDA
+>2_235
+MSEIPHDDAAVQHPSGLPLAHWLTLTEGLIAVRVAESLEEHGLTRAQWQLLNTLTVAPQS
+RAELEAGFEEEHRGAVSGQIEELVESRWVTVEGDLYTLTATGRTAGARVGEAVEALRAEA
+TADVPRDQIDDAVRVLRRIARNLGHPDA
+>3_169
+MTDNTQTPENRQTQAPRRDSHPSGLPLSHWLTVAEGLLAARVAASLEEHGLTRAQWQSLN
+ALTAAPLSAAEIGAGFEPEVRGAVVEQLDELVDAGWVTVEGDLFTLTSTGRTAGERVGEA
+VERLRGEATADLPAEHYEVTVATLRTIARNLGHPDA
+>4_139
+MSEIQHDDAVQHPSGLPLAHWLTLTEGLIAARVAESLEEHGLTRAQWQLLNTLTVAPQSR
+AELEAGFEEEQRGAVSGQIEELVESRWVTVEGDLYTLTATGRTAGARVGEAVEALRAEAT
+ADVPRDQIDDAVRVLRRIARNLGHPDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000279.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000279.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0988ed31dfe1a1069745ee165171112a6f489676
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000279.fa
@@ -0,0 +1,50 @@
+>0_139
+MDHGNGPPLVKNVTFFPKHVISSPVPSTVPRMMTRPLPEDSATVDTVALGRRVRHLRKQA
+GLTLDQLAERTGVSGSHLSLVENARREPRLSLVQRIAEVLGVPVEDLLTGRAPTRRAELE
+IEVERFARSEHYASLGLPPLRIGPRTPTEVLEVIAGLEAELRRRLEEQAATPEEARRANA
+QLRARMRAVDNHYPDLEAEAHRLLDAIGHTGGPLGLHAVSELAEHLGFTLRFVPDLPHST
+RSVTDLKHGRIHISGSRSSDHDRRTVVLQALAAAVLGHGEPRDYEDFLAQRVAVNYLAGA
+LLMPQRAASSLLRAAQKRRDLSVDDLKDAFGVSYEAAAHRFTNLATVDLGIRCHFQKVHE
+TGVIHKAYENDGIVFPADHTGAIEGQQACRKWGARQAFSRNDRFRAHAQYTDSPNGTFWC
+TSMIENGPDGLFALSVGTPFEHARYFRGADTRHRVTSTCPDPRCCRRPDPELEAAWGGHV
+WPAARMHAHLLAAMPTQTFPGVDEREVFEFLQAQEEREG
+>1_2104
+MMTRPLPEDSATVDTVALGRRVRHLRKQAGLTLDQLAERTGVSGSHLSLVENARREPRLS
+LVQRIAEVLGVPVEDLLTGRAPTRRAELEIEVERFARSEHYASLGLPPLRIGPRTPTEVL
+EVIAGLEAELRRRLEEQAATPEEARRANAQLRARMRAVDNHYPDLEAEAHRLLDAIGHTG
+GPLGLHAVSELAEHLGFTLRFVPDLPHSTRSVTDLKHGRIHISGSRSSDHDRRTVVLQAL
+AAAVLGHGEPRDYEDFLAQRVAVNYLAGALLMPQRAASSLLRAAQKRRDLSVDDLKDAFG
+VSYEAAAHRFTNLATVDLGIRCHFQKVHETGVIHKAYENDGIVFPADHTGAIEGQQACRK
+WGARQAFSRNDRFRAHTQYTDSPNGTFWCTSMIENGPDGLFALSVGTPFEHARYFRGADT
+RHRVTSTCPDPRCCRRPDPELEAAWGGHVWPAARMHAHLLAAMPTQTFPGVDEREVFEFL
+QAQEEREG
+>2_226
+MMTRPLPEDSATVDAVALGRRVRHLRKQAGLTLDQLADRTGVSGSHLSLVENARREPRLS
+LVQRIAEVLGVPVEDLLTGRAPTRRAELEIEVERFARSEHYASLGLPPLRIGPRTPTEVL
+EVIAGLEAELRRRLEEQAATPEEARRANAQLRARMRAVDNHYPDLEAEAQRLLDAIGHTG
+GPLGLHAVSSLAEHLGFTLSFVANLPHSTRSVTDLKHGRIHVSGGRASDHDRRTVVLQAL
+AAAVLGHGEPRDYEDFLSQRVAVNYLAGALLMPQRPASALLRAAQKRRDLSVDDLKDAFG
+VSYEAAAHRFTNLATVDLGIRCHFQKVHETGVIHKAYENDGLVFPADHTGAIEGQAACRR
+WGARQAFGRSDRFRAHTQYTDAPNGTYWCTSMVEHGPDGLFALSVGTAFEHARHFRGADT
+RHRITSTCPDPRCCRLPDPALEAEWGGHVWPAARMHAHLLAAMPTQAFPGVDEVEVFEFL
+ESQRDRTPGAPGADAPDGAGGVTP
+>3_803
+MATPTDPAHEPPRVDPLVLGRRLRHLRRVSGATLSDVAEKVGVTASHLSLVENGHREPRL
+TLLTALADVHGVGVEDLLTPEAPSRRAALEVAVERAQRGPLFQRLGLPALKIGPRTPDEV
+LEVIAGLQAELDRQMAERVSTPEEARRANSALREEMRACGNHYADLERRAQELREAVDVA
+DGPLTHHHVSALAEHLGFAVRFVPDLPHSTRSVTDLKNRRIYLARARRPDHDPRAVLLQA
+VCSSVLGHGEPADYADFLRQRVYTNYLAAAMMMPERGTVRALREAKERRDLSVDDLRDRF
+GVSWESAAHRFTNLATEHLGLTCHFAKVHESGVFHKAYENDGIPFPTDHIGAIEGQTACR
+HWTSRQVFSVADHLGAFPQYTDTPAGTYWSAAVVEPTSTGFYSLTVGVPFDDAKWFRGRE
+TSARTRSTCPDPKCCRLPSAELEAAWGGQAWPAARANAHLLAAMPGGAFPGVEEVQVFEF
+LQTQESRWPPEGSGAA
+>4_147
+MMTRPLPEDSATVDTVALGRRVRHLRKQAGLTLDQLAERTGVSGSHLSLVENARREPRLS
+LVQRIAEVLGVPVEDLLTGRAPTRRAELEIEVERFARSEHYASLGLPPLRIGPRTPTEVL
+EVIAGLEAELRRRLEEQAATPEEARRANAQLRARMRAVDNHYPDLEAEAHRLLDAIGHTG
+GPLGLHAVSELAEHLGFTLRFVPDLPHSTRSVTDLKHGRIHISGSRSSDHDRRTVVLQAL
+AAAVLGHGEPRDYEDFLAQRVAVNYLAGALLMPQRAASSLLRAAQKRRDLSVDDLKDAFG
+VSYEAAAHRFTNLATVDLGIRCHFQKVHETGVIHKAYENDGIVFPADHTGAIEGQQACRK
+WGARQAFSRNDRFRAHTQYTDSPNGTFWCTSMIENGPDGLFALSVGTPFEHARYFRGADT
+RHRVTSTCPDPRCCRRPDPELEAAWGGHVWPAARMHAHLLAAMPTQTFPGVDEREVFEFL
+QAQEEREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000282.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000282.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4465ed2f12b3863a319efd749dbed37d0b668a88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000282.fa
@@ -0,0 +1,39 @@
+>0_142
+MTHPAPARRRAPLAVGVAALALALAGCGSAGQSGEPASSTAAAPSGSAASAAAGSATESP
+TDPASAAASRVREALASESAEGTPRAEPRQAFETVGPGIKDGAATEAWKNTAAVRNDTVS
+VMDCTRDVLDQRTLDAVATHIPDSSNIEIVQLFASQDETHEFLTCVYNGYFEYSPGMPLA
+QVHYQHNLDGSRLEWCQEEPAAVADEYTFDPKTGKGLLALLRPGMVGGQDGAPLLPQRTA
+WACSEDGSEMVSVTMGSMEGFGDANGGLTQVKNSPVAQSTTLVTETRDHLADTVLKDAGD
+FQEVIKLSSPFFLNAQMDEETLAQAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPP
+RPFQGAAREAAESQRAAEASASASASPSPTKSASASASPSPSTSGD
+>1_2107
+MTHPAPARRRAPLAVGVAALALALAGCGSAGQSGEPASSTAAAPSGSAASAAAGSATESP
+TDPASAAASRVREALASESAEGTPRAEPRQAFETVGPGIKDGAATEAWKNTAAVRNDTVS
+VMDCTRDVLDQRTLDAVATHIPDSSNIEIVQLFASQDETHEFLTCVYNGYFEYSPGMPLA
+QVHYQHNLDGSRLEWCQEEPAAVADEYTFDPKTGKGLLALLRPGMVGGQDGAPLLPQRTA
+WACSEDGSEMVSVTMGSMEGFGDANGGLTQVKNSPVAQSTTLVTETRDHLADTVLKDAGD
+FQEVIKLSSPFFLNAQMDEETLAQAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPP
+RPFQGAAREAAESQRAAEASASASASPSPTKSASASPSPSTSGD
+>2_223
+MREARESASAEGTPRAQPRQALETLGPGIRDGAATTAWENTAAVRNDTVSVMDCTRDVLD
+QRTLDAVATHIPDGSNIEIVQLFAAQDETHEFLTCAYNGYFEYSPGMPLAQVQYQHNLDS
+TRLDWCEDEPATVADEYTFDPETGKGLLALLRPGMIGGQDGAPLMPQRTAWACSEDGTEL
+VSVTMGSMEGYGDANGGLTQVENSPVAGSTTLVTEARDHLADTVLKDASRFHEVIKLSSP
+FFLNASMDEESLAKAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPPRPFQGAAREA
+AESQRAAEASASAAEASASRAASGSGTPSPSSTPASRTPSPSGTGG
+>3_162
+MTHPTSAPHRAAAALGAAALALTLAGCSDSGQPSPASSTSTATAAAGSSASATGDPQSPA
+SAAASEIRAARASEKADGSERPQPREALETQGPGITSGAASAGWKSVAARYNDTVSVMDC
+TQDVLDQTTLDAVATHIPVANDIGIVQLFASRDQTHEFLTCQYQGSSSRSEGAPLVMVHY
+QHNLDGRRLEWCRPEAPVMADEYSYDESTRKGLLALLRPGMVGGADGAPLLPQRTAWACN
+EDGTQLVSVTFGAMKGYGSVNEGLTQVTNSPIANSTTLATQARDHLADTVLKDPSDFQAD
+IETSSPFFLNAQTDQETLDKAKGLPTGIIPQDQLSDQSTIDRPEGAPEPVAPGQPPRPFV
+GAARDAAESAAAESAASSSGSDSASPSDDGDGNPVVSESGTPSPSNTTD
+>4_150
+MTHPAPARRRAPLAVGVAALALALAGCGSAGQSGEPASSTAAAPSGSAASAAAGSATESP
+TDPASAAASRVREALASESAEGTPRAEPRQAFETVGPGIKDGAATEAWKNTAAVRNDTVS
+VMDCTRDVLDQRTLDAVATHIPDSSNIEIVQLFASQDETHEFLTCVYNGYFEYSPGMPLA
+QVHYQHNLDGSRLEWCQEEPAAVADEYTFDPKTGKGLLALLRPGMVGGQDGAPLLPQRTA
+WACSEDGSEMVSVTMGSMEGFGDANGGLTQVKNSPVAQSTTLVTETRDHLADTVLKDAGD
+FQEVIKLSSPFFLNAQMDEETLAQAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPP
+RPFQGAAREAAESQRAAEASASASASPSPTKSTSASPSPSTSGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000283.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000283.fa
new file mode 100644
index 0000000000000000000000000000000000000000..41b9105345b05a4f49d15f689ad3fc05d9557eaa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000283.fa
@@ -0,0 +1,20 @@
+>0_143
+MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR
+TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNRGFLRALYALGRAAAGIGESEEV
+ERIRTFLRDSDPTAAEQIEAGQGRARG
+>1_2108
+MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR
+TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNHGFLRALYALGRAAAGIGESEEV
+ERIRTFLRDSDPTAAEQIEAGQGRAQG
+>2_222
+MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDVVPVAPESSLVWALMAEDAWSEGR
+TVDSYAYARVGYHRGLDALRKAGWRGAGPVPYDHEPNRGFLRALYSLGRAAAGIGESEEV
+ERIRTFLKDSDPTAAEKIEATQGRSGS
+>3_161
+MSESLIGKNLMEPPATLLPEEPEVLARLDAGDLPEDLVPLAPESSLVWALMAEDAWSEGR
+AVDSYAYSRVGYHRGLDALRRAGWRGAGPVPWSHEPNRGFLRALYALGRAAAGIGESAEV
+DRIRTFLKDSDPTAAQQIEAAQA
+>4_151
+MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR
+TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNRGFLRALYALGRAAAGIGESEEV
+ERIRTFLRDSDPTAAEQIEADQGRAQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000284.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000284.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4fe31f38fd5a22cd812721a7ca57c4b80763a0a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000284.fa
@@ -0,0 +1,25 @@
+>0_144
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF
+LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG
+VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF
+VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG
+>1_2109
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF
+LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG
+VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF
+VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG
+>2_221
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEDEVVSRLGVTRTVDF
+LVPAGAGVRELFRRHASGDDPDALVDHVDAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG
+VPVIAYGLRTDFRTRCFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVNPATGAEHF
+VFEGDQVAIDGVEVTYESLCGSCYLAESGGRLG
+>3_160
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPAVDTKGDAAVVSRLGVTRAVDF
+LVPAGADVLALFRAHAAGDDPDALVDHVDAPPVACLLVDEAQFLEAGQVDDLLRIAVLED
+VPVMAYGLRTDFRTHSFPGSARLLELAHSLEELKTICRCGRKAVLNTRKVVDAATGRSRF
+VFEGDQVAIDGVEVTYESLCAACYLEESGGRLG
+>4_152
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF
+LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG
+VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF
+VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000287.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000287.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d3921ebe72ff2323055673e3b108d60737fe1af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000287.fa
@@ -0,0 +1,25 @@
+>0_170
+MSTAAPHTQHSDFPSPTPTRKGPSVGTWRPWAVLPWALALLALPLIALALRSNFGANGWM
+TVIYMVFGALPHELVLMVLVGSLFLLPRVNPQDEQRGGIRLGRLLHTLLGVSWGSFALAA
+IIFPDGGDHPDSGATTPVLMDLLGKSTAMDVGIVGGLALVAVSALTGLAVIVVCVVRRIR
+AVR
+>1_2117
+MSTAAPGTQHSDFASPTPTRKGPSVGTWRPWAVLPWALALLALPLIALALRSNFGANGWM
+TVIYMVFGALPHELALVLMVGSLFLLPRVNPQDEQRGGIRLGRLLHTLLGISWGSFALAA
+IIFPDGGDHPDSGATTPVLMDLLGKSTAMDVGLVGGLALVAVSALTGLAVIVVCVVRRIR
+AVR
+>2_213
+MSTAAPHTQHSDSASPAPTRKGPSVGTWRPWAVLPWALALLALPLIALALRSNFGANGWM
+TVIYMVFGALPHELFLMLMVGSLFLLPRVNPLDEQRGGIRLGRLLHTLLGVSWGSFALAA
+ILFPDAGDHPDSAATTPVLMDLLGKSTAMDVGSVAGLALAAVSALTGLAVIVVCVVRRIR
+AVR
+>3_159
+MAVPHPVMPPPGTPLPHQLRPAGPSVGTPRWLPAVLWIVAFALLPLCVIVGRFATENGGW
+LLFTYIMFGWMVQGGLGVLAAASLFLLPRVNPPVERRAGVRTGVVVHLLLGASWLTGLLG
+MLAFGDYGDAPGSETAPAPLVDLYGMDRAVEIGDAVGPPLVGISLLTGLAAVVLVVVRRL
+AAAVRS
+>4_167
+MSTAAPGTQHSEFASPAPARKGPSVGTWRPWAVLPWALALLALPLIALALRSDFGANGWM
+TVIYMVFGALPHELVLMVLVGSLFLLPRVNPQDEQRGGLRLGRLLHTLLGVSWGSFALAA
+IIFPDGGDHPESGATTPVLMGLLGTSTAMDVGIVGGLALVAVSALTGLAVIVVCVVRRIR
+AVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000290.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000290.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e56cf53b0f4c6fd17033122d546fb486f84c205
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000290.fa
@@ -0,0 +1,30 @@
+>0_173
+MRISVGQFGPVGDVEENLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA
+WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH
+RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK
+VEHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADEREAVATAEVTR
+ERIDEVREFLPSLANRRTDVL
+>1_2120
+MRISVGQFGPVGDVEANLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA
+WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH
+RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK
+VDHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADEREAVVTAEVTR
+ERIDEVREFLPSLANRRTDVL
+>2_210
+MRISVGQFGPVGDVEANLAVMARLAARAAGEGAELLVLPEEAMLGAREVGEEFPDAIAAA
+WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH
+RESDRISPGDGGVAAIELDGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK
+VEHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVVELADEREAVVTAEVTR
+ERIDEVRKFLPSLANRRTDVL
+>3_155
+MRIAVGQFGPTGRVEDNLEAMGRLAARAAAEGAGLLVLPEEAMLTFREVEDEFAHAVAGS
+WEPFTEGLARLARQHGLAIVAGGYEPSATDRPYNTLVAVDADGAVAGAYRKLHLYDAFEH
+RESELITPGDRGLVTVEVGGLTVGLQTCYDLRFPEVSRALALAGAQVLAIPAAWFAGEHK
+VDHWRTLLRARAVENTVWVAAADTASAATVGHSAIIDPLALTLAEADDDAAPETLLCADV
+TAERVEEVRRTVPVLANRRTDVLTPPVDVEPGG
+>4_170
+MRISVGQFGPVGDVEANLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA
+WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH
+RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK
+VDHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADEREAVVTAEVTR
+ERIDEVREFLPSLANRRTDVL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000291.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000291.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9276decb14edbf3e485200277221a7cd1d7f0098
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000291.fa
@@ -0,0 +1,20 @@
+>0_174
+MTINADGSHAVQPHTANAHTTPARPVRHAVVEEEVLEPLRPVDGWGFTNRVILVSVLVVI
+IGNVVRVLTGGLGDPNGSVALGETGHGWVVLVQSFMFGLVGGALAGAAGYLVVLLMGGAA
+RSVVRYVVGGVVGGFLGAVGLFAVFSNTVVYGSGVHLFWMLPVAGLLGGLWAGLVSSRR
+>1_2121
+MTINADGSHAVQPHAANAHTAPARPVRHAVVEEEVLEPLGPVEGWGFTNRVILVSVLVVI
+IGNVVRVLTGDLGDPNGSVALGETGHGWVVLVQSFMFGLVGGALAGAAGYLVVLLMGGAA
+RSVVRYVVGGVVGGFLGAVGLFAVFSNTVLYGAGLHLFWMLPVAGLLGGLWAGVVSSRR
+>2_209
+MTINADGSHAVQPHSANAHTAPASPARHAVVEEEVLEPLRPVDGWGFTNRVILVSVLVVI
+IGDVVRVLTGGLGDPNGSVALGETGRGWVVLVQSFMFGLVGGALAGAAGYLIVLLMGGAA
+RSVVPYVVGGVVGGFLGAVGVFAVFSNTALYGSGLHLYWMLPVAGLLGGLWAGVVSSRR
+>3_154
+MNTQAHGAHAVQTVGGTAAPQAPARRAVVAPEAVEPARPVDGWGFVNRILVVATVLIVAF
+ELWRAATGLLSDGPRVLGEDGVGWVAVLEAFMFALVGGAIAGAAGYGIVLLMGGAARSAA
+RYAIGGLIGGFLAAVGVIFVFSNTAALSVGGHLFWMLPLAGLIGGVWAGITSAKS
+>4_171
+MTINADGSHAVQPHAANAHTAPARPVRHAVVEEEVLEPLGPVEGWGFTNRVILVSVLVVI
+IGNVVRVLTGDLGDPNGSVALGETGHGWVVLVQSFMFGLVGGALAGAAGYLVVLLMGGAA
+RSVVRYVVGGVVGGFLGAVGLFAVFSNTVLYGAGLHLFWMLPVAGLLGGLWAGVVSSRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000292.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000292.fa
new file mode 100644
index 0000000000000000000000000000000000000000..60b105b8fc523267f5ab936a2c68db9463622a5f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000292.fa
@@ -0,0 +1,25 @@
+>0_175
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVATPPDSAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATHELAHLLGAADTPRERPADSPGKPKARS
+>1_2122
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPDSAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATGELAHLLGAADTPRERPADSPGKPKASS
+>2_208
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPASAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATDELAHLLGAADTPRERPADSPGKPKASS
+>3_153
+MPTTPPASTRTVDRALALLAAVVAQPRLSLAEAARATDLPASTALRLLRSLETAGFVDRQ
+EEGEYRPGARLIQLGARAFSREPLVRLARAPMDGVAEATGESVYLSLRNGAQEAVYIAIV
+EGTHSVRHASWVGRTVPLEGTAVGEVYRGEVPPGGYAHGGHSVEQDVTALSSPVVVGGRV
+VAALSALVPDYRCTAEHADRCGRALAGATTRLASALGEEAPPEDAD
+>4_172
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPDSAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATHELAHLLGAADTPRERPADSPGKPKASS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000295.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000295.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d04cd54c706f7c55eb01f8ab4bc847f855e673d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000295.fa
@@ -0,0 +1,40 @@
+>0_178
+MRSTLITDIAELTTVDPEGRVLTDAAVVVEDERIAWIGPAADAPEADDRVSVEGRAVLPG
+WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDARLAELVRGRVADAVA
+GGTTYLETKTGYGLTVEEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV
+GPMLAAVREHVGWVDVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE
+FGAASVDHVNHLSDADVEALAGTWADWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL
+LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGALGLRAQDRVG
+SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV
+>1_2125
+MRSTLITDIAELTTVDPEGRVLTDAAVVVEDERIAWIGPAADAPEADDRVSVEGRAVLPG
+WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDARLAELVRGRVADAVA
+GGTTYLETKTGYGLTVAEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV
+GPMLAAVREHVGWVDVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE
+FGAASVDHVNHLSDADVEALAGTWADWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL
+LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGAIGLRAQDRVG
+SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV
+>2_205
+MRSTLITDIAELTTVDPEGRVLTDAAVVVEDERIAWIGPAADAPDADDRVSVEGRAVLPG
+WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDDRLAELVRGRVADAVA
+GGTTYLETKTGYGLTVEEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV
+GPMLEAVREHAGWADVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE
+FGAASVDHVNHLSDTDVEALAGTWTGWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL
+LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGALGLRAQDRVG
+SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV
+>3_150
+MASTLITDIAELTTVDPEGRVLRDAAVVLDDEDVAWIGPAAQAPAADERVSVAGRAVLPG
+WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGLTMEATRAASDERLRELVLGRVADAVR
+GGTTYLETKTGYGLTVEEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDVEDYLDDVV
+GPMLEAVREHVGWVDVFCDTGAFDAAQTRRVLAAGVAAGLRARLHGNQIEQGPGVALAVE
+FGAASVDHVNHLSDADVEALAGTWSGWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL
+LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGAIGLRAQDRVG
+SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV
+>4_175
+MRSTLITDIAELTTVDPEGRVLQDAAVVVEDERIAWIGAAADAPDADDRVSVGGRAVLPG
+WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDDRLAELVRGRVADAVA
+GGTTYLETKTGYGLTVAEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV
+GPMLEAVREHAGWVDVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE
+FGAASVDHVNHLSDADVEALAGTWTGWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL
+LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGAIGLRAQDRVG
+SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000298.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000298.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2eb347a95e93cf5db2f44f4c9ce926024786325
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000298.fa
@@ -0,0 +1,20 @@
+>0_185
+MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGKEILGHRVYASLDGLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEVVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR
+>1_2132
+MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGKEILGHRVYASLDDLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEVVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR
+>2_197
+MSATHPERTWTGPSAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGQEILGHRVYASLDDLPVTPDLVEVFRKASDAPEMVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEIVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR
+>3_144
+MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGKEILGHRVYASLDDLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEIVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR
+>4_185
+MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGKEILGHRVYASLDDLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEVVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000299.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000299.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a732d53d8aeff21fb5ef4ca44ec00a6f6cfaee4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000299.fa
@@ -0,0 +1,49 @@
+>0_186
+MITQPALHATGRRRVTLCDVPTLPPARLARDNGADCPEASIERTPVADHEFGFRTQALHA
+GAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL
+EGGIGAVATASGMAAEFVTFAALAAAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS
+AEAADFEAALQPNTKTVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP
+IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG
+EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANAQAVAQWLDEDPRVS
+WVRYAGLPDHPHHARAQQLLPRGVGSVFSIGVAPAATDTDDGASGPEAGRATASRFISAL
+QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPEDLIRISVGIEDTEDILWDLDQ
+ALTEATGRTRDDDGAPAAPKEA
+>1_2133
+MITQPALHGTGRRRVTLCDVPTLPPAHLARDNGRDCPEASIERTPVADHEFGFRTQALHA
+GAVPDTVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL
+EGGIGAVATASGMAAEFVTFAALAAAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS
+AEAADFEAALQPNTKTVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP
+IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG
+EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANAQAVAQWLDEDPRVS
+WVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASGPEAGRATASRFISAL
+QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPEDLIRISVGIEDTEDILWDLDQ
+ALTEATGRTRDDDGAPAAPKEA
+>2_196
+MADHEFGFRTQALHAGAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRI
+GNPTVAAFEERVATLEGGIGAVATASGMAAEFVTFAALAGAGDHIVASSKLYGGTITQLD
+VSLRRFGVETTFVDSVEAADFEAALQPNTKAVYTEIVANPSGDVVDLPGLADVAHRHGVP
+LVVDATLTPPYLIRPIEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTE
+PVPSYGGVSWWGNFGEYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLAN
+ARAVATWLDEDPRVSWVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASG
+PEAGRATASRFISALQLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPADLIRIS
+VGIEDLEDILWDLDQALTEATGRTRDGAVVPAEQEA
+>3_143
+MITQPALHGTGLRRVTLCDVPTLPPAHLARDNGTDCPEASIERTPVADHEFGFRTQALHA
+GAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL
+EGGIGAVATASGMAAEFVTFAALAGAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS
+AEAADFEAALQPNTKAVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP
+IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG
+EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANARAVATWLDEDPRVS
+WVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASGPEAGRATASRFISAL
+QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPADLIRISVGIEDLEDILWDLDQ
+ALTEATGRTRDGAVVPAEQEA
+>4_186
+MITQPALHGTGRPRVTLCDAPTLPPAHLARDNGTDCPEASIERTPVADHEFGFRTQALHA
+GAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL
+EGGIGAVATASGMAAEFVTFAALAGAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS
+AEAADFEAALQPNTKAVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP
+IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG
+EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANAQAVAQWLDEDPRVS
+WVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASGPEAGRATASRFISAL
+QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPADLIRISVGIEDLEDILWDLDQ
+ALTEATGRARDGAVVPAEQEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000300.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000300.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf23140fe3e1e429b6965901164a729963826d7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000300.fa
@@ -0,0 +1,35 @@
+>0_187
+MTARTPLPSTLAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGIPDPCAPDGAAAL
+VRLTGGVVSHVSAALWHGLPLPPRLARPAGLHLTFDRSARTHRTDLDGVVSHRVRLPSDH
+VLELPDGQRVTTAARTWFDLAGMLRPHEVDWLIADGDHLVRPPWTPTGRADPVATVSELS
+EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP
+VVDLGYRGARLALQYDGAGHRTAQQQARDARRDAYCLEREWTTLRCTWEDQRAGFGRIVG
+LVRRRLARTR
+>1_2134
+MTARTPLPSTLAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGIPDPCAPDGAAAL
+VRLTGGVVSHVSAALWHGLPLPPRLARPAGLHLTFDRSARTHRTDLDGVVSHRVRLPSDH
+VLELPDGQRVTTAARTWFDLAGMLRPHEVDWLIADGDHLVRPPWTPTGRADPVATVSELS
+EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP
+VVDLGYRGARLALQYDGAGHRTAQQQARDARRDAYCLEREWTTLRCTWEDQRAGFGRIVG
+LVRRRLARTR
+>2_194
+MTARAPLPPALARAAFGVDELLDAGLPWDRTRAADLHRIWRGVYTAADPAALTWDRAAAL
+CRVTGGVISHTTAAAWHGIPLPRRLEASEELHLTVDRGRRQHRSARPGVVTHRLRLPPQE
+IRQVGGGLRVTSPERTWLDLAVLLRPWELDWLVVAGDHLVHHPWHPDGRRPSATTPALLD
+AALGRHVGRHGIRRAREALADVRVGADSAPETRLRLALIRAGLPEPALQIAVDPSDPRSP
+EADLGYRDARIALQYDGAAHRTPEQQARDARREAYCLELDWLPLRCTQEDLREGFIRVIG
+LVRRRLGPRGAFGATSRR
+>3_142
+MTARTPLPPALAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGVPDPCAPDGAAAL
+ARLTGGVVSHVSAALWHGLPLPPRLARPAGLHLTFDRSARTHRSDLGGVVSHRVRLPSDH
+VLELPDGQRVTTAARTWFDLAGMFRPHEVDWLIAAGDHLVRPPWTPTGRADPVATVPGLS
+EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP
+VVDLGYRAARLALQYDGAGHRTAQQQARDARRDAYCLEREWTTLRCTWEDQRAGFGRIVG
+LVRRRLARTR
+>4_187
+MTARTPLPSTLAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGVPDPCAPDGAAAL
+VRLTGGVVSHVSAALWHGLPLPPRLTRPAGLHLTFDRSARTHRTDLGGVVSHRVRLPSDH
+VLELPDGQRVTTAARTWFDLAGMLRPHEVDWLIAAGDHLVRPPWTPTGRAHPVATVPGLS
+EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP
+VVDLGYRGRAWPSSTTAPATARLSSRRGTPVGTRTASSGNGRPCAAPGRTSALGSGGSWG
+WSGVGSPARADPPPRPTRVELSRVPSNAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000306.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000306.fa
new file mode 100644
index 0000000000000000000000000000000000000000..04a7cbb81b70bdf4914735f8c1400fd8bc0252d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000306.fa
@@ -0,0 +1,27 @@
+>0_200
+MAAAPCLGRQQPQEENMQRRRAVRAAGLGVVGALALAGCASEPQSAGEAWHQARTQLDEA
+ETVRLETAYTTGRQGPHSVRWDIAGRLDGGDAESKGVMQVGRDSHITMESRQVGEDVFVR
+VDVDGSDVPDDVQVMYSDPQWRRVPAGEGQEPPLKALLDQVGFPAADALDGAEVRAEEVD
+WDDGTAYRYAVPEEVADAAMVEGDATRVHSFTVDDDGELVALTVDDGRATQQYALSDWNQ
+IEPAEAPEEVAE
+>1_2144
+MQRRRAVRAAGLGVVGALALAGCGSEPQSVGEAWHQARTQVDEAETVRLETAYTTGRQGP
+QSVRWDIAGRLDGGDAESKGVMQVGRDSHITMESRQVGEDVFVRVEVDGSDVPDDVQLMY
+ADPQWRRVSAGEGQEPPLKSLLDQVGFPAADALDGAEVRAEEVDWDGGTAYRYAVPEEVA
+DAAMAEGDATRVHSFTVDDDGELVALTVDDGRATQQYALSDWNQIEPAEAPEEVAE
+>2_173
+MQRRRAVRAVGLGVAGVLALAGCAAEPQSAGEAWQQARTQLDEAQTVRLETAHTTGRQGP
+NTVRWDIAGRLDGSNGDAKGVIQAGHESHMTMETRTVGEDSYVRVSIDGADFADDVQLAY
+ADPQWRRTPAGQEQERPLKELLEQIGLPSADALEGAEVRAEEVGWAGETAHRYAVPQEVA
+AAAMGQGDSTLLHSFTVDDDGGLLALTVDDGRSLRQYALSDWNEIDPAEAPEEVAE
+>3_119
+MQRRRAVHAAGLGVVAALTLAGCGTDQQDVGEAWQHARAQIDGAESVRMTMASVNDSQGP
+SVVAWDVAGPLEGADGTTTGRMQVGRDSWMTVRSVSADGKTWARVDTEGQDVPEQIASMY
+RTDGWTETQQSGQNALRATLDAVGLPAADALDGVDVQPEKVDWSGGTAYRYAMPGDVASA
+ARGDSQFSVRAFTVDEDGDLVGLRVEDGGVIQEFALSDWNEIEPAEAPEEAQH
+>4_200
+MAAAPCLGRQQPQEENMQRRRAVRAAGLGVVGALALAGCASEPQSAGEAWHQARTQLDEA
+ETVRLETAYTTGRQGPHSVRWDIAGRLDGGDAESKGVMQVGRDSHITMESRQVGEDVFVR
+VDVDGSDVPDDVQVMYSDPQWRRVPAGEGQEPPLKALLDQVGFPAADALDGAQVRAEEVD
+WDGGTAYRYAVPEEVADAAMAEGDATRVHSFTVDDDGELVALTVDDGRATQQYALSDWNQ
+IEPAEAPEEVAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000309.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000309.fa
new file mode 100644
index 0000000000000000000000000000000000000000..246d8b4bb733d525a3d3df2229194a712627d1f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000309.fa
@@ -0,0 +1,70 @@
+>0_203
+MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI
+GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA
+SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWL
+GEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARPAWQDELQADTFRSSEAGQDL
+PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGIGVA
+LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEA
+VRGLADGCQTLGIPVTGGNVSLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG
+QAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLLGELLVNMSRDGMIDAAHDVS
+GGGLAATLSEMVLRFGVGARVVLDEVLRRAGVDLFTALFSETQARAVVAVPRTEEVRFTD
+MTTARGYAAVRIGVVDADSAALEVQDAFTLPIAELREAWEATLPKHFG
+>1_2147
+MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI
+GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA
+SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWL
+GEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARPAWQDELQADTFRSSEAGQDL
+PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGIGVA
+LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEA
+VRGLADGCQTLGIPVTGGNVSLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG
+QAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLLGELLVNMSRDGMIDAAHDVS
+GGGLAATLSEMVLRFGVGARVVLDEVLRRAGVDLFTALFSETQARAVVAVPRTEEVRFTD
+MTTARGYAAVRIGVVDADSAALEVQDAFTLPIAELREAWEATLPKHFG
+>2_165
+MSQQFSIETVADAAANPDIEQPWAELGLKENEYAQIREILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI
+GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGLGNKVVLFGARTGGDGIGGASVLA
+SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFAGSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPDNVAAFEAVMAKWDVEYSWL
+GEVTGDGRLVITWDGEVIVDVDPRTVAHDGPVYERPYARPGWQDRVQADTFRASEAGADL
+PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTAMAAPDDAGVVRVDEETGMGVA
+LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPENPDVMWQFAEA
+VRGLADGCQVLGIPVTGGNVSLYNQTGATPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG
+QAIYLLGETADELDGSEFARLRGHLGGVPPKVDLAKERLLGELLVNMSRDGMIDAAHDVS
+GGGLAATLSEMVLRHGVGARVVLDEVLRRDGVDLFTALFSETQARAVVAVPRTEEVRFTD
+MTTARGYTVTRIGVVDADSAALEVQDAFTLPIAELREGWEATLPKHFG
+>3_114
+MSTQFTIETVEQAAANPDVAQPWAELGLKEDEYARIREILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGDTLTEEMKEHMMVGIGENAGVTDLGDGWAVTFKVESHNHPSFVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAVDHPDTARVVHGVVAGIGGYGNSLGLPNI
+GGEVAFDPSYQGNPLVNALAVGVLRHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA
+SESFDDGGKPAKRPSVQAGDPFAEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEHSWL
+GEVTGDGRLVITWDGETIVDVDPRTVAHDGPVYERPCHRPSFQDALQADTFRSSAAGQDL
+PATGEELKAAVVELMASPNMADVSWITRQYDRYVRGNTALASPDDAGVVRVDEETGMGVA
+VATDCNDRYAYLDPYAGAQLSLAEAYRNVTTTGAVPLAVTDCLNFGSPEDPEVMWQFAEA
+VRGLADACQVLGVPVTGGNVSLYNQTGGVAIHPTPTVGVLGRFDDVLRRTPSGFGTDADG
+QAVYLLGVTADELDGSEYANLRGHLGGVPPKVDLAQERLLGELLVNMSRDGMVDAAHDVS
+KGGLAATLADMVLRFGVGARIVLDEVVRRDGVDVFTALFSETQGRTVVSVPRTEEVRFTD
+MTTARGYTVTRIGVVDAQSDALEVQGQFTLPIAELREAWEATLPKHFG
+>4_203
+MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI
+GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA
+SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWL
+GEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARPAWQDELQADTFRSSEAGQHL
+PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGMGVA
+LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEA
+VRGLADGCQTLGIPVTGGNVSLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG
+QAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLLGELLVNMSRDGMIDAAHDVS
+GGGLAATLSEMVLRFGVGARVVLDEVLRRDGVDLFTALFSETQARAVVAVPRTEEVRFTD
+MTTARGYAAVRIGVVDADSAALEVQDAFTLPITELREAWEATLPKHFG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000310.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000310.fa
new file mode 100644
index 0000000000000000000000000000000000000000..321aee9b6ada1ef73780708e54edf5cc1ac5556d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000310.fa
@@ -0,0 +1,30 @@
+>0_204
+MTELPLIGDYSTPATPLSGARIGVITFPGTLDDVDALRAVRLAGAEPVSLWHADADPQRT
+LAGVDAVVIPGGFSYGDYLRAGAIARFAPMMDAVATAAGGPEGEADGLPVLGICNGFQIL
+TESHLLPGSMIKNDHLHFICRDQELVVESTDTVWTRDFEQGQTITVPLKNQDGQYVADET
+TLDALEAEGRVVFRYQGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVETGFGPDTAAGP
+RSGVDGLGFFTSVLTTLASRGGHA
+>1_2148
+MTELPLIGDYSTPTTPLSGARIGVITFPGTLDDVDALRAVRLAGAEPVSLWHADADPQRT
+LAGVDAVVIPGGFSYGDYLRAGAIARFAPMMDAVATAAGGPEGEADGLPVLGICNGFQIL
+TESHLLPGSMIKNDHLHFICRDQELVVESTDTVWTRDFEQGQTITVPLKNQDGQYVADET
+TLDALEAEGRVVFRYQGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVETGFGPDTAAGP
+RSGVDGLGFFTSVLTTLASRGGHA
+>2_164
+MTTDLPLIGDYSTPTTPLNGARIGVITFPGTLDDVDALRAVRLTGAEPVSLWHADEDPQR
+TLAGVDAVVIPGGFSYGDYLRAGAISRFAPMMDAVATAAGGPEGAADGLPVLGICNGFQI
+LTESHLLPGSMIKNDHLHFICRDQELTVENTDTAWTRDYERGQTITVPLKNQDGQYVADD
+ATLDALEAEGRVVFRYRGWNPNGSRRDIAGIANAAGNVVGLMPHPEHAVEPGFGPDTADG
+PRTGTDGLGFFTSVLTTLASRGGHA
+>3_113
+MTEIPLIGDYSTPSTPLNGARIGVITFPGTLDDVDALRAVRLTGAEPVSLWHAEADAAAT
+LATVDAVVIPGGFSYGDYLRAGAISRFAPMMGAVAQAAGGPEGSEDGLPVLGICNGFQIL
+TESHLLPGSMIKNDHLHFICRDQQLAVESTDTAWTRDFEQGEVITVPLKNQDGQYVADEK
+TLDALEAEGRVVFRYVGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVEAGFGPDTEAGP
+RSGTDGLGFFTSVLTTLATRGGAA
+>4_204
+MTELPLIGDYSTPTTPLSGARIGVITFPGTLDDVDALRAVRLAGAEPVSLWHADADPQRT
+LAGVDAVVIPGGFSYGDYLRAGAIARFAPMMDAVATAAGGPEGEADGLPVLGICNGFQIL
+TESHLLPGSMIKNDHLHFICRDQELVVESADTVWTRDFEQGQTITVPLKNQDGQYVADET
+TLDALEAEGRVVFRYQGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVEPGFGPDTAAGP
+RSGVDGLGFFTSVLTTLASRGGHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000314.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000314.fa
new file mode 100644
index 0000000000000000000000000000000000000000..06f9181f3bdd14b9d0211e09e56b8edde328f4c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000314.fa
@@ -0,0 +1,34 @@
+>0_210
+MILHITLPEDWAAARRTGRYTASTRGASIDDVGFLHASDDAAQVGVVGAAIYPDRPDAFV
+CGLDEDELAGAGLRVRREPGDPSDPHSAEFPHVYPDEAVSGHIPCSMLTPVTDPRADARV
+HREDSAEAAALLDAGWSVRSRSWGARLHLDDDADLAPYRGHVAAAEARGIEVRRLTAVDL
+PALRALDEEAAPRFPRTDGSRHEPLPDDLEARLSTPAGLAVGAFEGGVLIGFTLTFRSPD
+RWEVDRTAVASEHENRGVAKAVKAATLLATHARGGRQWGTGGAEANAASLRMNTALGFRL
+EPAWLGLTPPMTWEEFARAPASSSLDDKVT
+>1_2155
+MILHITLPEDWAAARRTGRYTASTRGASIDDVGFLHASDDAAQVGMVGAAIYPDRPDAFV
+VGLDEDELAGAGLRVRREPGDPSDPHSAEFPHIYPDEAVSGHIPCSMLTPVTDPRADARV
+HREDSAEAAALLDAGWSVRSRSWGARLHLDDDADLAPYRGHVAVAEARGIEVRRLTAVDL
+PALRALDEEAAPRFPHTDGSRHEPLPDDLEARLSTPEGLAVGAFQGGVLIGFTLTFRSPD
+RWEVDRTAVASEHENRGVAKAVKAATVLATHARGGREWGTGGAESNAASLRMNAALGFRL
+EPAWLGLTPPTTWEEFARAPASSSLDDKVT
+>2_1574
+MILHIALPEDWAAARAAGHYTVSTRGATVDRVGFLHASEDAAQVGIVGPAVYADRPDAVV
+LAMDEAALEAAGLTVRREPGVPGDPHSPLFPHVYGGPVPVGLMTPLPRADVDPRVVREDD
+AEAIRLQDAGWTPASTSWGARLHLADDADLAPYERRVAAVRAAGFQVRRLTPDDVGQVRR
+LDGETAADYPATAASSHSPLPEDLAVRLTLPGHRGYGAFRDGVLAGFTLLDRLDDRWDVD
+RTAVHPTGRRRGLAAAVKALSVLETHREDGARTWGTGGAGANAGSLAMNRKLGFELEPLW
+LALVPALTWPEAAATSGTP
+>3_599
+MILHLTLPEDWAAARAAGVYTASTRGAGIAEVGFLHASEDERQAGAVAAAFYADRPDAFL
+VALDEDALAAAGLEVRREPGNPADPQSELFPHVYGGPIPVALMRPLRPSLTLRPYAPDDA
+AATLDVFRAAVTGTAAAHYTPEQIRAWCPADVDADAWAARRAAAWTVVAVDGAGRVLGFA
+DLTADGVLDMLFVHPEAGGRGASHLLVGAVLAEARRRGLLRVDVRASRSARPVLEALGFT
+VDGEDPGNTVRGVVVPNTRMHADLAGSAGSPAPPGLWS
+>4_211
+MILHITLPEDWAAARRTGRYTASTRGASIDDVGFLHASDDAAQVGMVGAAIYPDRPDAFV
+VGLDEDELAGAGLRVRREPGDPSDPHSAEFPHIYPDEAVSGHIPCSMLTPVTDPRADARV
+HREDSAEAAALLDAGWSVRSRSWGARLHLDDDADLAPYRGHVAVAEARGIEVRRLTAVDL
+PALRALDEEAAPRFPHTDGSRHEPLPDDLEARLSTPEGLAVGAFQGGVLIGFTLTFRSPD
+RWEVDRTAVASEHENRGVAKAVKAATVLATHARGGREWGTGGAESNAASLRMNAALGFRL
+EPAWLGLTPPTTWEEFARAPASSSLDDKVT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000316.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000316.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7093315ce703f5f3f1e54fdffd73a8e2e38569ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000316.fa
@@ -0,0 +1,45 @@
+>0_214
+MSLIVQKFGGSSVADAAGIQRVARRIADTVRAGNRVCVVVSAMGDTTDELLDLAAELTQD
+APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMLTDTSYGRARIVKVNPHR
+VQEALDAGRVAIVAGFQGMSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY
+SADPRVVPTARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPLHVRSSFSDHEGTW
+IMPDPNDTITLQEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAVSNVNI
+DMIVQNISREGSGRTDISFTLPIVEGKDAMAALRAAQDRIGFQDIVSDPEIGKLSLIGAG
+MRSNPGVSATFFKALADAGVNVDLISTSEIRISVVTAESKLDDAVRAVHAAFGLDAEEEA
+TVYGGTGR
+>1_2178
+MSLIVQKFGGSSVADAAGIQRVARRIADTVRAGNRVCVVVSAMGDTTDELLDLAAELTQD
+APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMLTDTSYGRARIVKVNPHR
+VQEALDAGRVAIVAGFQGMSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY
+SADPRVVPTARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPLHVRSSFSDHEGTW
+IMPDPNDTITLQEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAVSNVNI
+DMIVQNISREGSGRTDISFTLPIVEGKDAMAALRAAQDRIGFQDIVSDPEIGKLSLIGAG
+MRSNPGVSATFFKALADAGVNVDLISTSEIRISVVTAESKLDDAVRAVHAAFGLDAEEEA
+TVYGGTGR
+>2_148
+MSLIVQKFGGSSVADAAGIQRVARRVADTVRAGHRVCVVVSAMGDTTDELLDLAAELTQD
+APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMMTDTSYGRARIVKVNPHR
+VQEALDAGGVAIVAGFQGVSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY
+SADPRVVPSARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPIHVRSSFSDHEGTW
+IMPDPNDTITLKEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAESNVNI
+DMIVQNVSREGSGTTDISFTLPIVEGKDAMAALRAAQERIGFQDIVSDKEIGKLSLIGAG
+MRSNPGVSATFFKALSDAGVNVDLISTSEIRISVVTAEDKLDDAVRAVHTAFGLDAEEEA
+TVYGGTGR
+>3_106
+MRLIVQKFGGSSVADAEGIQRVARRIVATQQAGNQVCVVVSAMGDTTDELLDLAAELTAD
+APAREMDILLSAGERISMSLLAMAIDAQGVPARSFTGSQAGMMTDAAYGRARIIEVNPHR
+VRAALDEGAVAIVAGFQGMSRESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY
+SADPRVVSSARKLPQLSSEETLELAASGAKVLHLRSVEYARRFGVPIHVRSSFSDHEGSW
+IMPDPNDTIHLKEGAPMEQPIVAGVAHDRSEAKVTIVGVPDVPGKAAEIFRVIAESNVNI
+DMIVQNVSRQDSGRTDISFTLPIVEGKAAIEALRAAQESIGFEEIVPNKEIGKLSLIGAG
+MRSNPGISATFFKALSDAGVNVDLISTSEIRISVVTSEDKLDDAVRAVHTAFGLDTDVEA
+TVYGGTGR
+>4_215
+MSLIVQKFGGSSVADAAGIQRVARRVADTVRAGNRVCVVVSAMGDTTDELLDLAAELTQD
+APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMLTDTSYGRARIVKVNPHR
+VQEALDAGRVAIVAGFQGMSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY
+SADPRVVPTARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPLHVRSSFSDHEGTW
+IMPDPNDTITLQEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAVSNVNI
+DMIVQNISREGSGRTDISFTLPIVEGKDAMAALRAAQDRIGFQDIVSDPEIGKLSLIGAG
+MRSNPGVSATFFKALADAGVNVDLISTSEIRISVVTAEDKLDDAVRAVHAAFGLDAEEEA
+TVYGGTGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000317.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000317.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e8954d74fd9bfbe0cc12e467701c8d83cc814b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000317.fa
@@ -0,0 +1,40 @@
+>0_216
+MSTAVATSIHDRRPPQPQPGGRLGAAQAVATVVGMELRQRLRSRGWYVLLGVFFVVVGAV
+TLGALGLRGLGVAEMEASGLEPELAEQQMRALGRTLFDGVLLFVLTLSLLVSPALAANAI
+SGDRAGGTLAITQVTLLRTGHLMAGKWLAAWIASAAFPAAALPWLAVAAVVGRVSPWAVL
+VGLVMILVEFGMIAGIGVAVSAIAGRTLFAVVVTYLIVAALTIGTLVAFGLSLQFLQTEV
+RANEADYGSTTAEPFTEAELEKMTPEEAEQAWAEWEAAHPELYDGIADRCVGPVTTRTIP
+DPRRSGWLLAANPYAVLADASPWEGGLLEDGTRAEPGPLNLLSVGLRWTQRDPVRDVECL
+DGELRGLDQSGVPDRQGTWPVWPLGLAMQGVLVAGLGWWGHRRLDTPAGRLPAGTRVA
+>1_2180
+MSTAVATSIHDRRPPQPQPGGRLGAAQAVATVVGMELRQRLRSRGWYVLLGVFFVVVGAV
+TLGALGLRGLGVAEMEASGLEPELAEQQMRALGRTLFDGVLLFVLTLSLLVSPALAANAI
+SGDRAGGTLAITQVTLLRTGHLMTGKWLAAWIASAAFLAAALPWLAVAAVVGRVSPWAVL
+VGLVMILVEFGMIAGIGVAVSAIAGRTLFAVVVTYLIVAALTIGTLVAFGLSLQFLQTEV
+RANDAEYGSMTAEPFTEAELEKMTPEEAEQAWAEWEAAHPELYDGIADRCVGPVTTRTIP
+DPRRSGWLLAANPYAVLADASPWEGGLLEDGTRAEPGPLNLLSVGLRWTQRDPVRDVECL
+DGELRGLDSTGVPDRQGTWPVWPLGLAMQGVLVAGLGWWGHRRLDTPAGRLPAGTRVA
+>2_146
+MSTVVADPTRQGPPPLRPPGGGRLSTASAVRTVVGMELRQRLRSRGWYVLLGVFFLVVGA
+VTLGALGLRATTLGDLQSQGMDPAAAEVQMRSAGQWLFDGVLLFVLTLSLLVSPVLAANA
+ISGDRAGGTLAITQVTLLRTGQLMAGKWIAAWIASAAFLVAALPWLAVAAVVGRVSPLFV
+LVGLLMILVEFGVITGIGVAVSAIAGRTLFAVVVTYLIVAALSIGTLVAFVLSLQFLQTD
+VRANMPEHDGMTMADPLEGQDVENMTQAEIDAAWAEWERQNPDAYDGIADACVGPVGVQS
+VPDPRRVGWLLAANPYAVLADASPWDPTGASMQFTPETGPLNMMSAALRLTQQDPAETTE
+CLDGQLRRIDTTSVPDREGTWPVWPLGLAMQAALTGGLLWWGHRRLDTPAGRLPAGTRVA
+>3_104
+MSAVLHTPPPAAAPAGGPTPLGSGRLGVVDALRTLVGMELRQRLRSRGWYILLGVFFLLV
+GGVTLGALGLHAWTGGNSPDSTMVFGRWLYDGVLLFVLTLCLLVSPALSANAISGDRSAG
+TLAITQVTLVSTWQLMLGKWLAAWIAAVAFLVAAAPWLIVAAVVGQVPPLAVLAGLAMIL
+VEFAVVTGIGVAVSAITGRTLFAVVVTYLLVAMMTIGSLIAFTISLQFIETRLQTNQVTY
+GYAEDAGSTKSCAGPLRDTTVPDPRRVAWLLAGNPYVVVADAVPLPELREDSAGEEFGAL
+NLISLGMRVAQIDPREYTDCVDGQVNEGSVTDSPVTLVDRTWPTWPLGMLLQGGFLAALL
+WWGRRRLDTPAGRLPTGTRVA
+>4_217
+MSTAVATSIHDRRPPQPQPGGRLGAAQAVATVVGMELRQRLRSRGWYVLLGVFFVVVGAV
+TLGALGLRSLGVTEMEASGLEPELAEQQMRALGRTLFDGVLLFVLTLSLLVSPALAANAI
+SGDRAGGTLAITQVTLLRTGHLMAGKWLAAWIASAAFLAAALPWLAVAAVVGRVSPWAVL
+VGLVMILVEFGMIAGIGVAVSAIAGRTLFAVVVTYLIVAALTIGTLVAFGLSLQFLQTEV
+RANDAEFGSMTAEPFTEAELEKMTPEEADQAWAEWEAANPELFDGIADRCVGPVTTRTIP
+DPRRSGWLLAANPYAVLADASPWEGGLVEDGTWAEPGPLNLLSVGLRWTQRDPVRDVECL
+DGELRGLDQSGVPDRQGTWPVWPLGLAMQGVLVAGLGWWGHRRLDTPAGRLPAGTRVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000320.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000320.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5cfa3237c998abe7eebbdd0b0ea9c6222ace982b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000320.fa
@@ -0,0 +1,35 @@
+>0_220
+MPAGRYAPSPTGSLHLGNLRTALVAWLAARATNRAFLLRVEDLDRVRSGAEADQRADLAA
+VGLDWDAEPVRQSERTALYDAAVAALRAVHGPDAVYECFCSRKDIAEATSAPHPRPDDGA
+PASGGAVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDVAKVAGLPAGETPRATAVD
+VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL
+CAARGEPTPAVEYLHVPLVLNAEGRRLAKRDGAVTLEDLSAQDPAWTPERVRDRLLESLG
+LPAGPLAAAVPAFDPAALPRVPWVFTGL
+>1_2184
+MPAGRYAPSPTGSLHLGNLRTALVAWLAARATDRAFLLRIEDLDRVRSGAEAGQRADLAA
+VGLDWDAEPVRQSERTALYDAAVAALRAAHGADAVYECFCSRKDIAEATSAPHPRPDDGA
+PASGGAVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDAAKVAGLPAGEIPRATAVD
+VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL
+CDGRGEPTPAVEYLHVPLVLNAEGRRLAKRDGAVTLEDLAAQDPAWTPERVRDRLLESLG
+LPAGPLAAAVPAFDPAALPRDPWVFTGL
+>2_143
+MPAGRYAPSPTGALHLGNLRTAIVAWLAARATDRTFLLRVEDLDRVRSGAEAAQLSELAA
+VGLDWDAEPVRQSERTGLYDDAVAALRAAHGADAVYECFCSRKDIAEATSAPHPAPADDD
+GAPGPAGAAPLRPPGFYPGTCRGLTAAQRAERRRVRPAALRIDAVQVAGLPEGEIPRAEA
+VDLLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSTPRQRWLAA
+ALCAARGEALPQTSYLHVPLVLNAEGRRLAKRDGAVTLEDLAAADPSWTPERVRDRLLSS
+LGLPPGPPADAVPAFARMLEDGSLPREPWMFDPAAFAGA
+>3_100
+MPAGRYAPSPTGTLHLGNLRTALVAWLAARATGRTFLLRIEDLDRVCSGAEAGQLADLAA
+VGLDWDGEPVHQSERTALYDAAVAALRAAHGADAVYECFCSRKDIAEATSAPHPRPDDGA
+PASGGTVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDAAKVAGLPAGEIPRATAVD
+VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL
+CVARGEPTPAVEYLHVPLVLNAEGRRLAKRDGAVTLGDLAAQDPAWTPARLRDRLLESLG
+LPAGPLAVAVRAFDPAALPRDPWVFTGL
+>4_221
+MPAGRYAPSPTGSLHLGNLRTALVAWLAARATDRAFLLRVEDLDRVRSGAEAGQRADLAA
+VGLDWDAEPVRQSERTALYDAAVAALRAAHGADAVYECFCSRKDIAEATSAPHPRPDDGA
+PASGGTVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDVAKVAGLPAGEIPRATAVD
+VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL
+CSARGEPTPAVEYLHVPLVLNAAGRRLAKRDGAVTLEDLAAQDPAWTPERVRDRLLESLD
+LPPGPLAAAVPAFDPAALPRDPWVFTGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000328.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000328.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fee422c156ef7d8600fde5dcd9023c6adae36ad3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000328.fa
@@ -0,0 +1,30 @@
+>0_229
+MKILVLAKQVPDTWQERELSLETGWVVRDGAAEPVPDEISERVMEVALGWRDAGADIEVV
+ALTVGPEDSSKTLRKMLAMGADSAVQITDDALVGSDAVQTARVIAAAVEKEGADLVLAGT
+VSTDGGTGVVPAMVAELLERPYLPHAEAPELADGELIGTVATSDADVRAAVALPAVASLT
+EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGEKI
+TDDGTAAERLVEFLAGRGLV
+>1_2193
+MKILVLAKQVPDTWQERELSLETGWVVRDGAAEPVPDEISERVMEVALGWRDAGADIEVV
+ALTVGPEDSSKTLRKMLAMGADSAVQITDDALVGSDAVQTARVIAAAVEKEGADLVLAGT
+LSTDGGTGVVPAMVAELLERPYLPHAEAPELADGELTGTVATSDADVRAAVALPAVAGLT
+EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGEKV
+TDDGTAAERLVEFLAGRGLV
+>2_124
+MKILVLAKQVPDTWQERELSLDTGWVVRDGAAEPVPDEISERVMEVALGWRDAGTDAEIV
+ALTVGPEDSSKTLRKMLAMGADAAVQVTDDALVGSDAVETARVIAAAVEREGADLVLAGT
+VSTDGGTGVVPAMVAELLDRPYLPHAEAPQLADGELTGTVATSDADVRAAVALPAVAGLT
+EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGAKV
+SDDGTAAQQLVDFLAGRGLV
+>3_89
+MKIAVLAKQVPDTWQERTLDMETGMAVRDGAAEPVPDEIGERVMEVALAAREAGLEAEIV
+AVTMGPADATKTLRKMLAMGADSAVHVVDDALDWSDAVQTARVLAAAVEHLGVDLVLAGS
+ESTDGATGVVPAMVAELLDRPLLPSVEAVEITPEEVRGVLVTEDARLRASVPVPAVVALT
+EKTAEPRFPNFKSIMAAKKKPLETLTLADLGLTAGPLDADRRSVMVSAAARRERAAGEKI
+VDDGTAGEQVAAFLAARGLV
+>4_230
+MKILVLAKQVPDTWQERELSLETGWVVRDGAAEPVPDEISERVMEVALGWRDAGADIEVV
+ALTVGPEDSSKTLRKMLAMGADSAVQITDDALVGSDAVQTARVIAAAVEKEGADLVLAGT
+LSTDGGTGVVPAMVAELLERPYLPHAEAPELADGELTGTVATSDADVRAAVALPAVAGLT
+EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGEKV
+TDDGTAAERLVEFLAGRGLV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000329.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000329.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9737ce385ff45a6a70f32c9a9bf8ed3eb7bca43c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000329.fa
@@ -0,0 +1,35 @@
+>0_230
+MSANVEETEMTTQTDAANSGQTVLVHAEIGADGALRPVVAELLGAAATVGVPEAVLVTGA
+EGRDAAVARLGEYGATRVHVLVADDAATTLGDAAVQALAAAAARTAPVAVLLSGSPESRA
+VAGRLSVRARGPVCTDAVGLRWADDEVIARHSVFGGDYLSESTGEGGPRIITMRPGAVAD
+RAPAVEAPEVVELAAAELGPVTAGARVLEVNARTQNSARPPLRGAKTVVAGGRGVGSEEG
+FAIVEQLADELGAAVGASRAAVDSGYTAAERQVGQTGVIVSPNLYIALGISGAIQHLAGM
+KTAKTIVAIDKNEDAEIFEHADFGVVGDIFQVVPQVIEQLRTRRG
+>1_2194
+MSANVEETEMTTQTDAANSGQTVLVHAEIGADGALRPIVAELLGAAATVGVPEAVLVTGA
+EGRDAAVARLGEYGATRVHVLVADDAATTLGDAAVQALAAATARTAPVAVLLSGSPESRA
+VAGRLSVRARGPVCADAVGLRWADDEVIARHSVFGGDYLSESTGEGGPRIITVRPGAVAD
+RAPAVEAPEVVELAAAELGPVTAGARVLEVNARTQNSARPPLRGAKTVVAGGRGVGSEEG
+FAIVEQLADELGAAVGASRAAVDSGYTAAERQVGQTGVIVSPNLYIALGISGAIQHLAGM
+KTAKTIVAIDKNEDAEIFEHADFGVVGDIFQVVPQVIEQLRTRRG
+>2_123
+MSANVEESEMTMQNDAANSGQTVLVHAELGADGALRPVVAELLGAAATVGVPEAVLVTGA
+ASQDAAVARLGELGAARVHVLVAEDAAGTLGDAAVQALAAVTARTAPVAVLLSGSPESRA
+VAGRLSVRARGPVCADAVALRWADDEVIARHSVFGGDFLSESTGEGGPRIITMRPGAVSD
+RAPAVASPEVVEVAAAELGAVTAGARVLETTRRVQQADRPALRGAKTVVSGGRGVGSEEG
+FAIVEELADALGAAVGASRAAVDAGYTAADRQVGQTGVIVSPNLYIALGISGAIQHLAGM
+KTAKTIVAIDKNEDAEIFEYADFGVVGDIFKVVPQVIEQLRARRG
+>3_88
+MTDLPVTPVLVLAELTAAGDLRPAVAEALGAAARVGVPHAVLVTDADADDALVARLGELG
+AAVVHTAVAQDPAELGTAQVAALAAAVDAVLPEAVVLPNTPESRAVAGRLAVRARGAVTA
+DAVGLHRADGEIVARHSVFGGDVLAESTVEGGPNIVTLRPGAVADRARPVAAPEVRPLDV
+AGRTVTAGARILSSEPAAPSADRPDLRTARAVVAGGRGVGSAEGFTTLVEPLADALGAAV
+GASRVAVDSGFTAPEGQIGQTGVTVAPDLYVALGISGAIQHLVGMKTSGTIVAVDSDEDA
+AIFEHADLGVVGDVNEVVPQLIAALAARRG
+>4_231
+MSANVEETEMTTQTDAANSGQTVLVHAEIGADGALRPIVAELLGAAATVGVPEAVLVTGA
+EGRDAAVARLGEYGATRVHVLVADDAATTLGDAAVQALAAATARTAPVAVLLSGSPESRA
+VAGRLSVRARGPVCADAVGLRWADDEVIARHSVFGGDYLSESTGEGGPRIITVRPGAVAD
+RAPAVEAPEVVELAAAELGPVTAGARVLEVNARTQNSARPPLRGAKTVVAGGRGVGSEEG
+FAIVEQLADELGAAVGASRAAVDSGYTAAERQVGQTGVIVSPNLYIALGISGAIQHLAGM
+KTAKTIVAIDKNEDAEIFEHADFGVVGDIFQVVPQVIEQLRTRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000330.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000330.fa
new file mode 100644
index 0000000000000000000000000000000000000000..db488c80b9e8c0062953b299c979df19e1a95d33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000330.fa
@@ -0,0 +1,52 @@
+>0_231
+MPKQRMAGYVPLKGAPAETEPAPAPAQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRR
+MAGYVPFAREAEWLGGAPAPAAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPD
+VAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMAGYVPFAREGEWFTELAAVGGPTAPE
+MVAQEVDAPEQATAEPTAEPAAAAPARPVVAELADVEPADAEPAVAAPVAAASAPEPAPT
+APDTRSAPPASAVQPPRAATGTPARTAETDAAESAVPSRLRKALPAVAGVVVLALLAVLA
+ARWLRSLDPVADFIATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHET
+RPPANFTPTKDGLFSARGNTPKKFSLTIWMHQALDALWLLNGLIFVVLLIATGHWARIVP
+TDPHVFQHALSAGIQYLSLDWPTENGWVHYNALQMLSYALVVFVAAPLAALTGWRMSSWF
+PTEAKGLNKAFPMEVARKVHFPVMVFFVAFIVVHVFLVAFTGLLTNLNHMYTSRGGATDA
+WGLVVFLVSVAVTAAAWFFLKPAFTAPVASRFGTVGR
+>1_2195
+MPKQRMAGYVPLKGAPAETEPAPAPGQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRR
+MAGYVPFAREAEWLGGAPAPAAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPD
+VAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMVGYVPFAREGEWFTELAAVGGPTAPE
+TAAQEVVAEPATAEPAAAEPADAEPAVAAPVAAAPAAEPAPTAPDTRSAPPASTAQPPRA
+APGAATGTPARAAETDAAESAAPSRLRKALPAVAGVVVLALLAVLAGRGLRSLDPVADFI
+ATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHETRPPANFTPTKDGLF
+SARGNTPKKFSLTIWMHQALDALWLLNGVIFVVLLIVTGHWARIVPTDPHVFQHAVSAGI
+QYLSLDWPTENGWVHYNALQMLSYSLVVFVAAPLAALTGWRMSSWFPTKATGLNKAFPME
+VARKVHFPVMVFFVAFILVHVFLVAFTGLLTNLNHMYTSRGGATDAWGLVVFLVSVAVTA
+AAWFFLKPAFTAPVASRFGTVGR
+>2_122
+MARRRRRPGGRSGLGHPAGAPAAAPAPIAASASPTQSPRPAEPAAAQPRLAEQDVAAAVA
+RPAAAAPVAVESDLVPLGQRRRMGGYVPLAREGEWFAELAAADAAPAGETAEPTVLEAAH
+DDAAPAAEAAVTEPAAPTTTAAAAAATTAAAQAPAAPAQPAAAAAAPTAPDTRSAPPASA
+AQPPRAEPAAASGRPARATKKTDAAEEAPAPSRLRKALPLVAGVVVLALVAVLAARWLRT
+LDPVADFIAAYDGHPALAEGTPVGMPPWLGWQHFLNMFLMVLIIRTGLQIRNETRPPANF
+TPKKDGAFSARGNTPKKFSLTIWTHQALDALWLLNGVVFVVLLFVTGQWARIVPTDPYVF
+HHAFSAGIQYLSLDWPTENGWVHYNALQMLSYTLVVFVAAPLAALTGWRMSSWFPTEAKG
+LNRAFPMEAARKVHFPVMLFFVLFILTHVFLVFFTGALKNLNHMYTSRGDATDAWGLVVF
+LVSVAVTAAAWFLLRPSFTAPAASKFGTVGR
+>3_87
+MPQRMQGYTEFRGEPWPPRDRVPQAPAPTTTPAVAADERRPGRRMVGYTAFRGEPWPPVR
+EAAQPAPAPAAAASPAEVTEAAAAAVPLEATAPAGIAVPGRRMAGYTAFRGEPWPPARVG
+AAPQAPEPAPMATVEPAVATGPTPTVEPVAAGAPETTPKPAPSTGRRVAAAVGGVVVLGL
+LAVLGARWLLTLPEVAAFVARYPGVPRHPEVTPVGIPAWLAWQHFLNLFLLVLVVRTGLQ
+VRHETRPPATFTPHQPGPFAPRSATGGTYSLTVWIHQALDALWLLNGLVFVVLLFATGHW
+MRLIPTDPQTPQHMVSTALQYLSLQWPEHDGWLHYNALQMVTYAGVVFVLAPLAALTGFR
+MSSWWPSRNTALSRGFPMELARRLHYPTMLAFVLFVVVHVVLVLFSGVLHELNAMFLARN
+AADAWGLAAFLVGCAVIAAGWVLLKPAIVAPVAERFGRVSR
+>4_232
+MPKQRMAGYVPLKGAPAETEPAPAPAQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRR
+MAGYVPFAREAEWLGGAPAPAAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPD
+VAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMAGYVPFAREGEWFTELAAVGGPTAPE
+MVAQEVVAEPATAEPAAAEPADAEPAVAAPVAAAPAAEPAPTAPDTRSAPPASTAQPPRA
+VPGAATGTPARAAETDAAESAAPSRLRKALPAVAGVVVLALLAVLAGRWLRSLDPVADFI
+ATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHETRPPANFTPTKDGLF
+SARGNTPKKFSLTIWTHQALDALWLLNGVIFVVLLIVTGHWARIVPTDPHVFQHALSAGI
+QYLSLDWPTENGWVHYNALQMLSYALVVFVAAPLAALTGWRMSSWFPTEAKGLNKAFPME
+VARKVHFPVMVFFVAFIVVHVFLVAFTGLLTNLNHMYTSRGGATDAWGLVVFLVSVAVTA
+AAWFFLKPAFTAPVASRFGTVGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000336.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000336.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1c67bcfaf9b8430aced6c738ac203b1868cb24d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000336.fa
@@ -0,0 +1,41 @@
+>0_242
+MTAIADRPVPAPGAPAVTPGLPHVDLLRLRDRLEPVERARLDAIEDHLQTRVRPHLTRYW
+DAEEFAFDLLPGLAELGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMI
+AGLGSERQKATWQGRLESFDALGAFCLTEPDHGSDIAGGLATTATRDGDEWVIRGAKRWI
+GAGTIADVALVWARDTADGEIKGFVVPTDTPGYEATKISGKMGLRIMQNADITLDVRLPA
+DAILPGATTFAATRALLRDSRMWVGWQGVGAQMGVLDVLRSYALRREQFGRPLAAFQLIQ
+AQIAEVAGNLAASAGMMLQVDALRQEGRMEMMHAAMAKATSTRLARSSAALARDALGGNG
+LLTEHEIAKIMGDVEAIYSYEGSYGMNTLIVGRALTGVSAFV
+>1_2205
+MTALADRPLPATGAPAVPPGLPHVDLLRLRDRLEPVERARLDAIEDHLQTRVRPHLTRYW
+DAEEFAFDLLPGLAELGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMI
+AGLGSERQKATWQGRLESFDALGAFCLTEPDHGSDIAGGLATTATRDGDEWVIRGAKRWI
+GAGTIADVALVWARDTADGEIKGFVVPTETPGYEATKISGKMGLRIMQNADITLDVRLPT
+DAILPGATTFAATRALLRDSRMWVGWQGVGAQMGVLDVLRSYALRREQFGRPLAAFQLIQ
+AQIAEVAGNLAASAGMMLQVDALRQEGRMEMMHAAMAKATSTRLARSSAALARDALGGNG
+LLTEHEIAKIMGDVEAIYSYEGSYGMNTLIVGRALTGVSAFV
+>2_110
+MTPHADLPHVDLLRLRDGLDPAERTRLEEVEEHLQTAVRPRLAPYWDAEEFAFDLLPGLA
+GLGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMIAHLGSDAHRDRWQA
+RLESFDALGAFCLTEPEHGSDVAGGLATTATLDGDEWVIRGAKRWIGAGMIADVALVWAR
+DTADGEIKGFVVPTDTPGYEATKITGKMGLRIMQNADITLDVRLPADAQLPGAATFDAAR
+DLLRDSRMWVGWQGFGAQMGLLDSLRSYALEREQFGRPLAKFQLIQSAIAEVAGNLAATS
+GMMLQVDALRQEGRMEMMHAAMAKATSTRLARASAALARDALGGNGLLTEYEVSKMMGDV
+EAIYSYEGSYGMNTLIVGRALTGVSAFV
+>3_78
+MTPSPTPSPASAEPAASPATGVLTVAAAVHPGHAAAPAAAVTDGLPDVDLFDLRSLLSAE
+ERAHLERIEAHLEEHVRPHLAEPWNTETLPMEMLPGLASVGLGELDFLGASRLFQNLVHV
+AIARVDLSFSALVGIHNELNIGSIERFGTEEQKQRWVPALRRFEALGAFCLTEPDHGSDI
+AGGVETTATPDGDGWILRGTKRWIGAGTVAAVALVWAKDVSDGEVKCFLVPTDAPGFSAS
+KITGKTGLRIMQNADMVFDDVRLGPEALLPGAGSFDATREMLRDSRAWVGWQGVGVQQGI
+LRTLREYALTRTQFGRPLAKFQLIQAAIAQVAGNLAAATGLMMQVQRLQDDGTLKMVHAA
+AAKATSTRLARESAALARDAMGGNGIVASYEMARFMGDVEAIYTYEGTQSINALLVGRAL
+TGVSAFV
+>4_242
+MTALADRPLPATGAPAVPPGLPHVDLLRLRDRLEPVERARLDAIEDHLQTRVRPHLTRYW
+DAEEFAFDLLPGLAELGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMI
+AGLGSERQKATWQGRLESFDALGAFCLTEPDHGSDIAGGLATTATRDGDEWVIRGAKRWI
+GAGTIADVALVWARDTADGEIKGFVVPTDTPGYEATKISGKMGLRIMQNADITLDVRLPA
+DAILPGATTFAATRALLRDSRMWVGWQGVGAQMGVLDVLRSYALRREQFGRPLAAFQLIQ
+AQIAEVAGNLAASAGMMLQVDALRQEGRMEMMHAAMAKATSTRLARSSAALARDALGGNG
+LLTEHEIAKIMGDVEAIYSYEGSYGMNTLIVGRALTGVSAFV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000344.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000344.fa
new file mode 100644
index 0000000000000000000000000000000000000000..277c6167f15a2a6cb98ba766548ec8c7fa44382f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000344.fa
@@ -0,0 +1,15 @@
+>0_256
+MDGMILINLKFTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYFLLEGF
+TDEGAQAHVASPHFQEGLDAMRPLLASTPQIISEQVGAEGFGPMGELQID
+>1_2220
+MDGMILINLKFTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYFLLEGF
+TDEGAQAHVASPHFQEGLDAMRPLLASTPQIISEQVGAEGFGPMGELQID
+>2_89
+MDRMILINLKYTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYLLIEGF
+TDEGAKAHVESPHFQEGIDAMRPLLASTPQIISEHVDAEGFGPMGELQID
+>3_60
+MILINLKFTVKPELADQWMDAVAKYIADVRSEPGNMFFEWYKPVEGGDNEFFLLEGFTDE
+GAQAHVASPHFQEGIDAMRPLLQSTPQIISEQIGAEGFGPMGEIQID
+>4_254
+MDGMILINLKFTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYFLLEGF
+TDEGAQAHVASPHFQEGLDAMRPLLASTPQIISEQVGAEGFGPMGELQID
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000347.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000347.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba2b0906704151d40621115106260d15e235d750
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000347.fa
@@ -0,0 +1,40 @@
+>0_259
+MTETLPTVEPEYDVATPLDTDFYLALADVSDAEKDVWRRARAFALEPDVLPRIREAWDRH
+EYPLDLVARLGQADLLRDGVPVDGLPEISRVAAGLAMMELSRLDGSIATMTGVQGGLAMR
+SIQLCGSEEQRAEHLPAMARGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLHGHKKW
+IGNGAAGGVTVVWARSAEDEKVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV
+PDADVLPEARSFKDTSRVLFATRVGVAWSALGKAVGCYEAAVHYAGQRVQFGRPLAAAQS
+VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASMAKYSATRAARSIAANARDLLGG
+NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV
+>1_2223
+MTETLPTVEPEYDVATPLDTDFYLALADVSDAEKDVWRRARAFALEPDVLPRIREAWDRH
+EYPLDLVARLGQADLLRDGVPVDGLPDVSRVAAGLAMMELSRLDGSIATMTGVQGGLAMR
+SIQLCGSEEQRAEHLPAMARGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLHGHKKW
+IGNGAAGGVTVVWARSAEDEKVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV
+PDADVLPEARSFKDTSRVLFATRVGVAWSALGKAVGCYEAAVHYAGQRVQFGRPLAAAQS
+VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASMAKYSATRAARSIAANARDLLGG
+NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV
+>2_86
+MTENLPTAEPEYDVAAPLDTDFYLALGDVSDDEKEVWRRARAFALEPDVLPRIREAWDRH
+EYPLDLVARLGAADLLRDGVPVDGLPEVSRVAAGLAMMELSRLDGSIATVAGVQGGLAMR
+SIQLCGSDEQRAELLPAMSRGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLRGHKKW
+IGNGAAGGVSVVWARSAEDEQVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV
+PDADVLPEARSFKDTSRVLFATRVGVAWSALGQAVGCYEAAVQYAGQRIQFGRPLAAAQT
+VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASLAKYSATRAARSIAANARDLLGG
+NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV
+>3_57
+MTETLPTAEPDYSTITGPLDTDAYAVFAELPDEDLALARAARAFLTPEVQKRLQEAWDTG
+EYPTELIAGLAEADLLRDGVAVEGKPAQSRLACGLAAMETSRIDGSLATVVGVQGGLAMR
+SIEMCGSDEQKAKYLPAMDRGELFGAFALTEPTHGSDSVSLQTTATKVEGGWRISGHKKW
+IGNGAAGGITVTWARSAEDGQVKGFIVQQDAEGYSAEVIRGKMSLRAIHQAHITYDDVFV
+PDEDVMPGAQSFKNTAAVLFATRLGVAWAAVGHALGCYEAAVQYAKQRVQFGRPLAESQI
+VQERLARMLSELTQVQLLVLRAARLEDAGKLTGPQASLAKYSATRTARSIAANARDLLGG
+NGILLENEVGKHFADIEAIHTYEGTETVQALIVGRDITGVGAFA
+>4_257
+MTETLPTVEPEYDVATPLDTDFYLALADVSDAEKDVWRRARAFALEPDVLPRIREAWDRH
+EYPLDLVARLGQADLLRDGVPVDGLPDVSRVAAGLAMMELSRLDGSIATMTGVQGGLAMR
+SIQLCGSEEQRAEHLPAMARGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLHGHKKW
+IGNGAAGGVTVVWARSAEDEKVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV
+PDADVLPEARSFKDTSRVLFATRVGVAWSALGKAVGCYEAAVHYAGQRVQFGRPLAAAQS
+VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASMAKYSATRAARSIAANARDLLGG
+NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000350.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000350.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a4323f906b0afd0927a1105f71b07838aadcffa1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000350.fa
@@ -0,0 +1,30 @@
+>0_266
+MTTPTGAIPSPHPRPFLLVQTRPEDDAAAAEVEAVQRLGGYPEGRLRVLRLDRVVQRPDV
+ATHGLDWEAELADVAAVILPGSPFTGSDPEETKSPVQRAVEAELGRMLDVVRRRDLPFLG
+CCYGVGTLGRHAGGVVDNAYGESAAPVEVTLTDEGAADPLLAGVPRTFAAYVGHKEAMSA
+LPPGAVLLAAGTDCPVQMFRLGTRQYATQFHPELDQAGILERLEIYRDHGYFAPGEYEPT
+VAGLAAVDPEHPRRILANFRTLFG
+>1_2232
+MTTPTGAIPSPHPRPFLLVQTRPEDDAAAAEVEAVQRLGGYPEGRLRVLRLDRVVQRPDV
+ATHGLDWEAELADVAAVILPGSPFTGTDPEETKSPVQRAVEAELGRMLDVVRRRDLPFLG
+CCYGVGTLGRHAGGVVDNAYGESAAPVEVTLTDEGAADPLLAGVPRTFAAYVGHKEAMSA
+LPPGAVLLAAGADCPVQMFRLGTRQYATQFHPELDQAGILERLEIYRDHGYFAPGEYEPT
+VAGLAAVDPEHPRRILANFRTLFG
+>2_71
+MSTPSAPQPAPSADAPPSGRPFLLIQTRPEDEAARAEEEAVRRLGGFAEHQLAALRLDRT
+LDADPDARQDWAALVAGHAGVILSGSPYTSSVPQETKDELQVAVELELGRMLDAVLDADA
+PFLGCCYGVGTLGAHAGGTVDGTHAEPAGPTDVTLTEAGAADPLLEGLPPRFTAYVGHKE
+GLTVPPPGAVVLATGEACPTQMFRLGRRQYATQFHPELDQVGLVERLRIYLHHGYVDPED
+AEDTFARIESTPAPVPPRILENFRRVFG
+>3_54
+MTETTAPAADAAAPRPFLLVQTRPEEDAAAAEAESVRRLGGYDDATLRVLRLDRRVLDAE
+GEAHAGAVDWEAELADVAGVILPGSPFTGSDPEESKSDLQVAVEAELGRLMALVLARQTP
+FLGCCYGVGTLGRAAGGVVDTTYRELPGPIDVALTSEGLRDPLLEGMPAEFAAYVGHKEA
+VRELPPGAVLLATGQACPVQMFRVGEHLYATQFHPELDQAGLLERLEIYADHGYFAAHEA
+DDMFAAIRAREAPIPPRILERFRAIYG
+>4_264
+MTTPTGAVPSPHPRPFLLVQTRPEDDAAAAEVEAVQRLGGYPEGRLRVLRLDRVVQRPDV
+ATHGLDWEAELADVAAVVLPGSPFTGSDPEETKSPVQRAVEAELGRMLDVVRRRDLPFLG
+CCYGVGTLGRHAGGVVDNAYGESAAPVEVTLTDEGAADPLLAGVPRTFAAYVGHKEAMSA
+LPPGAVLLAAGADCPVQMFRLGTRQYATQFHPELDQAGILERLEIYRDHGYFAPGEYEPT
+VAGLAAVDPEHPRRILANFRTLFG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000359.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000359.fa
new file mode 100644
index 0000000000000000000000000000000000000000..59e6c665abf47f3eb394067d05308493d2d8644b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000359.fa
@@ -0,0 +1,20 @@
+>0_281
+MGLALRAARAAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR
+AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHQVQVRAGVRSEESAALLRGFFAAQRD
+>1_2255
+MGLALRAARAAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR
+AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHRVQVRAGVRSEESAALLRGFFAAQRD
+>2_55
+MGLALDAARAAGEAGDVPIGAVLVAGDGTVLAAVGNEREQHHDPTAHAEVLALRRGARAL
+AEAGEADGWRLSDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHAVQVRAGVRAEESAALLRGFFAVQRG
+>3_34
+MGLALDAARTAGEAGDVPIGAVLVDGDGRVLAAVGNEREQHHDPTAHAEVLALRRGAAAL
+AARGDADGWRLAECTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHTVQVRAGVRGDECAALLVDFFAARRPGG
+>4_288
+MGLALRAARVAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR
+AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVIRDP
+RFNHQVQVRAGVRAEESAALLRGFFAAQRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000360.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000360.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4ba84b9f46a7cc72c1b66cecdf5419c4c942643
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000360.fa
@@ -0,0 +1,26 @@
+>0_282
+MDGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR
+IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY
+AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL
+GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE
+>1_2256
+MGGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR
+IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY
+AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL
+GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE
+
+>2_54
+MRVHLVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVEIQTPVAT
+TTGLRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTYAERLPAD
+LSGRHVFVLDPMLATGGTLIESIRFLYERGAARVTCICLLGAPEGIARLEESLGDVEVDL
+YLAAQDERLDENAYIVPGLGDAGDRLYGLAE
+>3_33
+MRLHVVDHPLVAHKLTVLRDERTPSMIFRQLTEELVMLLAYEATRGVAVTEVEVKTPVAT
+TVGTTLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTYAERLPAD
+LTGRHVFVLDPMLATGGTLIEAIRFLYERGAERVTCLCLLGAPEGVARLEEALGDVDVEL
+YLAAVDERLNEKSYIVPGLGDAGDRLYGLAE
+>4_289
+MGGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR
+IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY
+AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL
+GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000361.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000361.fa
new file mode 100644
index 0000000000000000000000000000000000000000..adef270a562dfd8614c34cce79d731133e7cb7c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000361.fa
@@ -0,0 +1,30 @@
+>0_283
+MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGTDAPDSQTAPTPVLAPNGIPGPQ
+AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGA
+EGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLTFK
+EFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR
+GQGYRFYRHPEVVVWAAPEYSI
+>1_0
+MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGTDAPDSQTAPTPVLAPNGIPGPQ
+AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGA
+EGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLTFK
+EFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR
+GQGYRFYRHPEVVVWAAPEYSI
+>2_53
+MGQSAGYVHISVRNAQRRADGMSRRGQARADLRLAGGTDAPAAQTAPTPVLAPNGIPGPQ
+AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGSESHAAVALAPSGA
+EGRDLEVVRQVLGDPTVQGGAHPDLAQAPAPVSTREPGVLIDLSRREVQLDGESLNLTYK
+EFELLNYLVENGERTVGREELLEALWHNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR
+GQGYRFYRHPEVVVWAAPEYSI
+>3_32
+MGETAGYVHISVRNAQRRANVSRARRGDLRLAGGTSHEPTPPQTAPTPVLAPSGIPGPQA
+VARENEARGFVIYVGMDELMASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGAA
+GRDLEVVRQVLGDPTVQGAARPDLAQAPAPVSTRQPGVLIDLSRREVQLDGEALNLTFKE
+FELLNYLVENGERTVGREELLDALWKNSDEVPNERTIDVHIRRLRAKLGRLANTVRTVRG
+QGYRFYRHPEVVVWAAPEYSI
+>4_290
+MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGTDAPDSQTAPTPVLAPNGIPGPQ
+AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGA
+EGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLTFK
+EFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR
+GQGYRFYRHPEVVVWAAPEYSI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000362.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000362.fa
new file mode 100644
index 0000000000000000000000000000000000000000..65ca05ea05ce624c2914ffba9b5d260a27aad49c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000362.fa
@@ -0,0 +1,20 @@
+>0_284
+MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLREHGLVPDAVVCSDA
+LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE
+LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR
+>1_1
+MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLREHDLVPDAVVCSDA
+LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE
+LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR
+>2_52
+MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLRENGLVPDAIVCSDA
+LRTRQTCVWVCERLGELAPTPYLDPRLYHADAAKALAIVNETEETTRSLLVVGHMPWVQN
+LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWVELDGRDAALTHFVVPGR
+>3_31
+MSPADAKTLVLLRHAKADWPAGVDDHDRPLAPRGHAQAPAAGDWLLEHGIAPEAAVVSDA
+LRTRQTWVWVAQRLGERAPTAYLDRRLYEADAARALAVVNETEETVRSLIVVGHMPWLQN
+LGMRLMSLDSDQDAALEMAEHLPTLGLQVFRVDTPWAELDGRDAALTHFAVPGR
+>4_291
+MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPTAGDWLREHDLVPDAVVCSDA
+LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE
+LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000364.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000364.fa
new file mode 100644
index 0000000000000000000000000000000000000000..349f909a31c811ecbeeb95b1b593cde293d11a9b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000364.fa
@@ -0,0 +1,20 @@
+>0_287
+MKLSAYTDVCLRVLMTLAAAEGERLTSQQIADRIQVPYNHVIKAVAELRRRGTIQVARGR
+LGGARITEAGLDQRVGELVRDLSPRAEVLDCAGHETGVPCPFAADCRLREALARAREAFM
+AELDLLTVRDLVRPGRAGATGPVSLGLPAMGSHAATV
+>1_4
+MKLSAYTDVCLRVLMTLAAAEGERLTSQQIADEIHVPYNHVIKAVAELRRRGTIEVLRGR
+HGGAMIAAAGLDQRVGELVRTLSSRDEVIDCAGRDSGVACPYAGDCRLRGALHRAREAFL
+AELDTLRIRDLVSAGPVGGPVLLGLPEIPVTH
+>2_49
+MKLNAYTDVCLRVLMTLAGDEGERLTSQQIADRIQVPYNHVIKAVAELRRRGAIDVARGR
+LGGATIAEAGLELRVGALVRDLAGWDEVIDCTGRESGVACPLAGDCRLRGALHRAREAFL
+AELDAVRVRDLVAAGPAAGPVLLGLPEIPLPADPRPRRRTCPAGA
+>3_27
+MKLTAFTDVCLRVLMTLGRDAGAKMTSQEIADRIGVPYNHVVKAVGELRRRGLVDVARGR
+AGGAVITEAGLDQRVGELVRALSGRPEVVDCEGLESGTPCPLLEACSLRGALARAREAFF
+AELDRQRVRDLVSLPAEFLGLRRLPGA
+>4_294
+MKLSAYTDVCLRVLMTLAAAEGERLTSQQIADRIQVPYNHVIKAVAELRRRGTIEVLRGR
+HGGAMIAAAGLDQRVGELVRSLSSRDEVIDCTGRDSGVACPYAGDCRLRGALHRAREAFL
+AELDTVQIRDLVSAGPVGGPVLLGLPEIPVAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000367.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000367.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b42da9e822724130f5789920cf1b1646519357f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000367.fa
@@ -0,0 +1,42 @@
+>0_290
+MPPTTPPPPAGPPAVPPSGPAPAAPGEAAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD
+DLGVPADRAALLVSASTLGLALSVVPWSVAGDRWGRRRAMVVSMVSASACALAGVLAPTF
+EAMLRLRLLEGMAHGGVAGLAVALLAEEVAPHAVAAAAGTYIAGTTLGGLSGRLLALPVA
+EASSWRGGMLAVTVVGVLCTVGFLAITPRARRFTPSPTSPATLVRIVRGHLRSPELVAVY
+LQGALLMGGFVALYNFVGYRLLGPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL
+PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS
+LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALASAVVVLRGRGTAPAR
+>1_7
+MPPTTPPPSAGPPAVPPSGPAPAAPGEPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD
+DLGVPADRAALLVSASTLGLAVSVVPWSVAGDRWGRRRAMVVSMVSASACALTGVLAPTF
+EAMLGLRLLEGMAHGGVAGLAVALLAEEVVPHAVAAAAGTYIAGTTLGGLSGRLLALPVA
+EASSWRGGMLTVTVVGVLCTVGFLAITPRARRFTPSPTSPATLVRIVRGHLRSPELVAVY
+LQGALLMGGFVALYNFVGYRLLDPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL
+PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS
+LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALVSAVVVLRGRGTAPAR
+>2_46
+MPPQPPPAGPPAVPPSGPAPLAPGDPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSADL
+GVGAHRAALLVSAGTLGLALSVVPWSMAGDRWGRRRAMVVSMVSASLFALAGVLAPTFEA
+MLGLRLLEGMAHGGVAGLAVALLAEEVAPRAVATAAGTYIAGTTIGGLSGRLIALPVAEA
+FTWRTGMLAVTVVGVACTAAFLAVTPQARRFTPSPTSVARLVRIVRGHLGSAELVAVYLQ
+AALLMGGFVALYNFVGYRLLGPPFSWAPTAAGLVFLAYLAGTWSSPRAGRLAARFGRLPV
+LTGATAAMAAGAALTLVPHPAVLVGALVLTTGAFFAAHSVASAWSGTAAPHGRAQSTSLY
+NLAYYAGSSLFGWLGGVFHESHGWTGTVLMVVALALTALAIAVVVLRGRGTAPARCAGAV
+RGAGRRGIRRISRGRLRRRRWPSGAGRARPRGPRGPAARASRPSAGRSRSRCPARRTPPA
+WSAPRPG
+>3_24
+MPPALPAPLEPGTPLYRRLLLGLFLAGVATFAQLYAPQGLLPLVSSDLGVPSHRAALLVS
+AGTLGLALSVVPWSLAGDRWGRRPVMVASLVSASVLALVGVFMPSIELLMGMRLLEGMAH
+GGVAGLAVTLLAEEVAPRVVPVAAGTYVAGTTLGGLSGRLLAMPVGEWAGWRAGMLAVTA
+AGAACTVAFLFVTPPARRSTPVRLSLARLGRIIGGHLRTPGLVALYLQAALLMGGFVALY
+NYIGYTLLAPPFGWPPTAVGLVFLAYLAGTWSSPRAGRLAVRVGRLKVLTGSTALMAVGV
+VLTLVPSPFVLVPALVVATGAFFAAHSVASGWAGTAAPTGRAQSTSLYNLAYYAGSSLFG
+WLGGVFHEGVGWAGTVFMVAGLAAVALVVALVVLRGREDAGPPPPSAVAEGAAA
+>4_297
+MPPTTPPPSAGPPAVPPSGPAPAAPGEPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD
+DLGVPADRAALLVSASTLGLAVSVVPWSVAGDRWGRRRAMVVSMVSASACALTGVLAPTF
+EAMLGLRLLEGMAHGGVAGLAVALLAEEVAPHAVAAAAGTYIAGTTLGGLSGRLLALPVA
+EASSWRGGMLAVTVVGVLCTVGFLAITPRARRFTPSPTSAAALVRIVRGHLSSPELVVVY
+LQGALLMGGFVALYNFVGYRLLDPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL
+PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS
+LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALASAVVVLRGRGTAPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000369.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000369.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d15226f333fc77906cc3d783f6a45c0a45ebcd8a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000369.fa
@@ -0,0 +1,31 @@
+>0_293
+MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+ITADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSYSVEHPAADHDGDVRR
+DDVRTDAGTAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRRDVTDADSVVVKDEHLNV
+GTERRASGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDVEVTTY
+EETPVVNKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDLDGRNDRKDRI
+>1_17
+MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+TTADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSAADHDGDVRRDDVRTD
+AGAAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRREVTDADSVVVKDEHLNVGTERRA
+SGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDVEVTTYEETPVV
+NKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDLDGRNDRKDRI
+>2_26
+MDRNMLDQLQNANVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+TTADGITVPFDKAFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSNVDHDRDVRHDDGLRA
+DAGTAGVAGTAGVAGVADRREDTVVDGDRRDVVDGDRRDLVDADRRDVVDGDRDSMVVKD
+EHLQVGTERQATGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDI
+EVTTYEETPVVNKTVEAEKVSLGKRQVQDTETVSEELRHEDVKIDGDATDRDLDGRTDRK
+DRI
+>3_22
+MDRNALDQLQNGHVFSTDGEKIGSVGQVYLDDVTNEPTFVTVKTGLFGAKETFVPLQQAQ
+TTTDGITVPFTKDFVKDAPNVDADGSLTPEEEQRIYEYYSMDYSAVDTHDRRDVRDAAAA
+GTAGGVVTDRERRDVVDADRRDVVDNDRRDLVDGDADSVVVKDEKLNVGTERRATGRVRL
+RKQSYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDIEVTTYEETPVVNKTVEA
+EKVSLGKRTVQDTETVSEELTHEDVKIDGDDVDGRRR
+>4_300
+MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+TTADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSAADHDGDVRRDDVRTD
+AGAAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRREVTDADSVVVKDEHLNVGTERRA
+SGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDVEVTTYEETPVV
+NKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDLDGRNDRKDRI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000370.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000370.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e447858a3001660b741dc7844b16f605e26eb1ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000370.fa
@@ -0,0 +1,61 @@
+>0_294
+MSEPLVADRRLAVVGAGPRGVMLLERILARLEGAAPDAHPRRLRIDVVDPYPPGPGRVWR
+TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVRRHQYPARAVY
+GRYLRHLYKDVVAGLRARPEVAEVVEHRAEATALHPRPDGGARLELRDPDGSVSVLDADA
+VVLCLGHQPAELSPGQMRMAAAARGRDELHYQGPQIPSDVDWETVEAGADVLVRGMGLNA
+FDLLAQLTQGRGGVYRRTGDGPGRALRYEPTGDEPRLHLMSRRGIPYLPKAEVDAFVPRG
+VTLSYLSDAAVDALTARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF
+LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYGSPFEDAVFASHEDYQRAV
+ADLMEQACVEAALGEESPFMMAVGALHAGRLRIKAWIAEGRIAEASRIRDVQGWFEPLVE
+GLASGPPLWRVEQMLAVHRAGLLTWAGPAPVVEAEEHAFTAHSPQVGAQDSLEPAVVEGA
+WLVEAMMPPNRVQAAASPLVRQMLADGVAAAGTWEDEEGVRVPATGFDVTARPYRLRAAD
+GTVHADVFVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAAAAAVLAG
+>1_18
+MSEPLVAERRLAVVGAGPRGVMLLERILARLEGAAPDAHPRRLRIDVVDPYPPGPGRVWR
+TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVRRHQYPARAVY
+GRYLRHLYKDVVAGLRARPEVVEVVEHRAEATALHPRPDGGARLELRDADGAVSALDADA
+VVLCLGHQPAELSPGQNRMAAAARGRDELHYQGPQIPSDVDWETVEAGADVLVRGMGLNA
+FDLLAQLTQGRGGVYRRTGDGPGRALRYEPSGDEPRLHLMSRRGIPYLPKAEVDAFVPRG
+VTLSYLSDAAVDALAARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF
+LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYGSPFEDAVFASHEDYQRAV
+AELMEQTCVEAALGEESPFMMAVGALHAGRLRIKAWVAEGRITEASRIRDVQGWFEPLVE
+GLASGPPLWRVEQMLAVHRAGLLTWAGPAPVVEAEEHAFTAHSPQVGAQDSLGPAVVEGA
+WLVEAMMPPNRVQAAASPLVRQMLADGVAAAGTWEDEEGVRVPATGFDVTARPYRLRAAD
+GTVHADVFVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAAATAVLAG
+>2_25
+MPDAQEAVRRLAVVGAGPRGVMLLERLLARLEGSAPGAHPARLRIDVVDPYPPGPGRVWR
+TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVQRHQYPARAVY
+GRYLRHLYQDVVAGLRARPEVADVVEHRAEVTALHPTPAGGARLELRDADGAASELAADA
+VVLCLGHQPAELSPGQARMAAAARGRDDLHYQGPQIPSDVDWDTVEPGARVLVRGMGLNA
+FDLLAQLTQGRGGVYRRTGDGPGRALAYEPSGREPRLHLMSRRGVPYLPKAEVDAFVPRG
+VTLSYLSDAAVDALSARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF
+LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYTAPFEDAVFASHEDYQRAV
+ADLMEQACVEAALGEESPFMMAVGALHAGRLRIKAWVAEGRIAEDSRIRDVQGWFEPLVE
+GLASGPPLWRVEQMLAVHRAGLLTWAGPVPVVDAEERAFSVRSPQVGAADSLGPAVVEGE
+WLVEAMMPPNRVQAASSPLIRGMLDDGVAAAGTWEDEEGVRVPAPGFDVTGRPHRLRAAD
+GAVHEDVYVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAVAQAVLAG
+>3_21
+MSPPSISEPTRAIAVVGAGPRGVMVLDRLLARLEAASEPRPTGSLAVHVVDPFPPGPGRV
+WRPDQDPLLLMNTPAFFPTACAADNPGLAPSSVSLSFDQWRLARPDRAAGLERTDYPPRA
+VYGRYLEDVVAAVLDALRARPEVVAVTVHAAQAVALRAAYEGGPVAAPESPSAWRLTLRP
+VDGTPPRELQADVVVLCLGHQDAEPSAAQRRLGEAADASPALHYRGPHLPAELDVDGIAP
+GATVLVRGMGLNAFDLQARLSEGRGGRFEPTGGEPGRALRYVPSGREPVLHLLSRRGLPY
+LPKAAVDAFVPRGVRMSYLTDTEAEALVARHGQLDLAEHLWPLLHRDVVRAYYATLARVH
+PERLGGPADAGRFVRELVGMFESAGRGAPVTARHGQELLHAFAPGMRFLDIRSWAAPFQG
+AVFDDAAAYQEAVAGVLEQACGEAAAGEDSPFMQAVGTLHAGRLRIKAWIAQGLLTDASR
+IRDVQGWFEPLVEGLASGPPLVRVEQMLALHRAGLLSWAGPGPQVEADAEAGVFRARSPQ
+VGADDAVAPAVTEAAWLVEAMMPPSRVEAAATPLVRQMLADGVAAVGRWEDEDGALRSSS
+GFDVTARPHRLRGADGTVREGVLVLGLQLSGVQWGTAIAAEAGADVRDRALFLADADAAA
+RVALGG
+>4_301
+MSEPLVAERRLAVVGAGPRGVMLLERILARLEGAAPDAHPRRLRIDVVDPYPPGPGRVWR
+TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVRRHQYPARAVY
+GRYLRHLYKDVVAGLRARPEVVEVVEHRAEATALHPRPDGGARLELRDADGAVSALDADA
+VVLCLGHQPAELSPGQNRMAAAARGRDELHYQGPQIPSDVDWETVEAGADVLVRGMGLNA
+FDLLAQLTQGRGGVYRRTGDGPGRALRYEPSGDEPRLHLMSRRGIPYLPKAEVDAFVPRG
+VTLSYLSDAAVDALAARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF
+LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYGSPFEDAVFASHEDYQRAV
+ADLMEQACVEAALGEESPFMMAVGALHAGRLRIKAWIAEGRIAEASRIRDVQGWFEPLVE
+GLASGPPLWRVEQMLAVHRAGLLTWAGPAPVVEAEEHAFTAHSPQVGAQDSLGPAVVEGA
+WLVEAMMPPNRVQAAASPLVRQMLADGVAAAGTWEDEEGVRVPATGFDVTARPYRLRAAD
+GTVHADVFVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAAATAVLAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000373.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000373.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6bd0d929a97dc475813e757f9b491b7061dd7ae3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000373.fa
@@ -0,0 +1,20 @@
+>0_298
+MRGPFARFRQERADDRELGTGLWRRAHDRLGRAMDRYWQVLAGQRGTDVLSPEERNGVVH
+AGNVLTERLPAVRALCVRLHRDHEGDGEHIPAEAADVHRELSRAAHELAATAQALALYRL
+GQGSAESVGRHAERTLGHLDRAEELGAGL
+>1_22
+MRGPFARFRQERADDRELGTGLWRRAHDRLSRALDRYWQVLEGQRGTDVLSPEERNGVVH
+AGNVLTERLPAVRALCVRLHRDHEGDGEHIPAEAADVHRELSRAAHELAATAQALALYRL
+GQGSAESVGRHAERTLGHLDRAEELGAGL
+>2_21
+MRGPFARFRQSCSDDRELGTGLWRRAHDRFVRAMDRYWQVLEGDRGPDLLRTEQRNGVVH
+AGNVLAERLPAVRALCVRLHRDHAGDGEHIPPEAADVHRELSRAAHELAATAQALAMHRL
+GQGSSDSVGRHAERTLAHLDRAEELAARL
+>3_17
+MIRGPFARFRQGRSDDRELGTGLWRRSHDRYVRALDRYWQVLEDGRSAGGFTPEERNGLV
+HAGNVLAERVPAVRALAARLHAAHPGDGEQHIPPVTAPVHRELSRASHELAAAAQAVAMF
+RRGVSGSEAVSRHAQRTLDHLDRAEGLAADL
+>4_305
+MRGPFARFRQERADDRELGTGLWRRAHDRLGRALDRYWQVLEGQRGTDVLSPEERNGVVH
+AGNVLTERLPAVRALCVRLHRDHEGDGEHIPAEAADVHRELSRAAHELAATAQALALYRL
+GQGSAESVGRHAERTLGHLDRAEELGARL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000377.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000377.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c629b386549178c3e9e63916a701df812b530fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000377.fa
@@ -0,0 +1,15 @@
+>0_302
+MHVALLFDHWLFRVLAIAALVLEVWALVDVVRRRPDDFARIGGRDRSFWLILTGVAAVVG
+LLGVLAGGGMGMFGLVAACVACVYLAGPRQDMGPALRR
+>1_26
+MHFALLVDHWLFRVLAIAALVLEVWALVDVVRRRPDDFARIGGRDRSFWLILTGVAAVVG
+LLGVLAGGGMGMFGLVAACVACVYLAGPRQDMGPALRR
+>2_17
+MHLALTFDQWLFRILAIVGLVLEVWAFLDALRRSPGDFARIGGRDKSFWMILTGVAAAVG
+VLGVLSGGGMGMFGLLAACVACVYLAGPRQEMGPATRR
+>3_13
+MHLAIVAGNWLFYALAVVAFLLELWAFADAARTSQETFLRTGGRTKGFWLALTGAAAAVG
+LVGVLLGPTGGFGILGLAAVCVASVYLAGPRDDLRFYGGRRGR
+>4_309
+MHFALLVDHWLFRVLAIAALVLEVWALVDVVRRRPDDFARIGGRDRSFWLILTGVAAVVG
+LLGVLAGGGMGMFGLVAACVACVYLAGPRQDMGPALRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000385.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000385.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab53af26817ae1b7907e51824556b92cf87dd830
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000385.fa
@@ -0,0 +1,50 @@
+>0_311
+MAQRFYDTRTAQVRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL
+RVTSVRNVTDIDDKILERSAASHEAGFEASDLYPAREPWWALAYRFEKAFDAAYLALGVR
+RPTYEPRATGHVPEMFALIERLMERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGTEFD
+IHGGGLDLRFPHHENELAQSAAAGDGFARLWLHNGLVTYGGEKMSKSVGNTISPEEMLGM
+ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR
+VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV
+PEGDDAAAGPVSDALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT
+WRLAD
+>1_35
+MAQRFYDTRTAQVRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL
+RVTSVRNVTDIDDKILERSAASYEAGFEASDLYPAREPWWGLAYRFEKAFDAAYLALGVR
+RPTYEPRATGHVPEMFALIERLMERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGTEFD
+IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVTYGGEKMSKSVGNTISPEEMLGM
+ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR
+VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV
+PEGDDAAAGPVSDALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT
+WRLAD
+>2_8
+MAQRFYDTRTAQIRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDVLIRWLEATGL
+RVTSVRNVTDIDDKILDRSAASHEEGFEPSALYPAREPWWALAYRFEKAFDAAYLALGVR
+RPTYEPRATGHVPEMFALIERLVERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKEGEPATAVWTSPWGAGRPGWHLECSAMATKYLGAQFD
+IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVAYGGEKMSKSVGNTISPEEMLGM
+ARPKAVRYFLGQAHYRSQLDYRPGALEEAEAAVERIENFTARARTAGAVPPAVDGALADR
+VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAAQDLESAAARLTEVEAMTAVLGLDDV
+PEGDGDGTGPAADALDSLVRSQIEARAQARAEKDWAAADRIRDALAAAGVVVEDGADGAT
+WRLAD
+>3_4
+MAQRFYDTRSAEIRDFVPLVPGQASVYYCGATVQGMPHVGHVRSAIVFDVLIRWLEATGL
+RVTSVRNVTDIDDKILDRSAASQEPGFEPSEMYPADEPWWALAFRFENAFDAAYLALGVR
+RPTYEPRATGHVPEMLALIERLIERGHAYPAADGSGDVYFDVRSWDRYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKEGEPVTAVWSSPWGAGRPGWHLECSAMSTKYLGGEFD
+VHGGGLDLRFPHHENELAQSAAAGDPFARFWLHNGLVTYQGEKMSKSVGNTISPQEMLAM
+ARPKAVRYFLGQAHYRSQLDYRPGALEEAEAAVERIENFVQRAAAALGAPELTAPLAEHV
+PAAFRAAMEDDLAVPQALAVLHEAVRAGNSALAAGDDAAARARLAEVAAMTAVLGLDDVP
+EASAGGSGPEAAALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGAQGATW
+HLAG
+>4_318
+MAQRFYDTRTAQIRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL
+RVTSVRNVTDIDDKILDRSAASHEAGFEASDLYPAREPWWALAYRFERAFDAAYLALGVR
+RPTYEPRATGHVPEMFALIERLIERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGAEFD
+IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVTYGGEKMSKSVGNTISPEEMLGM
+ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR
+VPAAFRTAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV
+PEGDDAAAGPVSDALDLLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT
+WRLAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000386.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000386.fa
new file mode 100644
index 0000000000000000000000000000000000000000..145ba3e4819a3913c09e0755888e409d27f72fcc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000386.fa
@@ -0,0 +1,35 @@
+>0_312
+MSTAPRSGGSRKPKGKKGPMKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA
+KRGPVKDQVRGRVKLTDETVSGRNPVLEALRAGIPAKALHVAVRIEMDDRVKEALRLCLE
+QGVPVLENTKPELDRLSGEAVHQGIVLQIPPYEYADATALALDALAKHEKGHLRTPPLLI
+ALDGITDPRNLGAIIRAGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLN
+TTLVDLHKAGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRMVREHCQQIVSIP
+IDSTMESLNASMAVGISLYEISVQRAGGR
+>1_37
+MSTAPRSGGSRKPKGKKGPMKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA
+KRGPVKDQVRGRVKLTDETVSGRNPVLEALRAGIPAKALHVAVRIEMDDRVKEALRLCLE
+QGVPVLENTKPELDRLSGEAVHQGIVLQIPPYEYADATALALDALAKHEKGHLRTPPLLI
+ALDGITDPRNLGAIIRAGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLN
+TTLVDLHKAGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRMVREHCQQIVSIP
+IDSTMESLNASMAVGISLYEISVQRAGGR
+>2_5
+MSTAPRSGGSRKPKGKKGPMKGTGGHGRKALEGKGPTPKAEDRVYHKAYRAKQLSERSAA
+KRGGPVRPSRPKLTDETVSGRNPVVEALRAGIPAKALHVAVRIEMDDRVKEALRLCLEQG
+VPVMENTKPELDRLSGEAIHQGLVLQIPPYEYADAMTLATDALEKHEKGHLRTPPLLIAL
+DGITDPRNLGAIIRSGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLNTT
+LVELHRAGYFVLGLDGGGDVSLPGLSLATEPLVLVVGAEGKGLSRMVREHCQQIVSIPIN
+SDMESLNASMAVGISLYEISVQRAGGR
+>3_3
+MSTAPRSGGSRAPKGKKGPQKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA
+KHGGGRVPVRDQVRGRVKLTDETVSGRNPVVEALRAGIPAKALHVATRIEVDDRVKEALR
+LCAENKVPVMENTRPELDRMSGEAVHQGLVLQIPPYQYADALTLGREAMEAQEKGHLRTP
+PLLIALDGITDPRNLGAIIRSASAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQA
+GNLNTTLVELHRMGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRMVREHCQQI
+VSIPIQSEMESLNASMAVGISLYEIAVGRAGGRPVAS
+>4_319
+MSTAPRSGGSRKPKGKKGPVKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA
+KRGPVKDQVRGRVKLTDETVSGRNPVLEALRAGIPAKALHVAVRIEMDDRVKEALRLCLE
+QGVPVLENTKPELDRLSGEAVHQGIVLQIPPYEYADATALALDALAKHEKGHLRTPPLLI
+ALDGITDPRNLGAIIRAGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLN
+TTLVDLHKAGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRLVREHCQQIVSIP
+IDSTMESLNASMAVGISLYEISVQRAGGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000387.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000387.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2de58032a4a0262be7425784a7ff3533c0ca2247
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000387.fa
@@ -0,0 +1,65 @@
+>0_316
+MKPDTQSATAADVRLQTVTGRIPVTDVQPVVLDGRFPAKAVVGEDIPVRATVFREGHDSV
+RATVRLLDPAGAEVQRVQMRPGRPGLDEVVATLRPAEPGLHQFVVEGWDDPVGTWKHAAT
+VKIAAGIDVELMLAEGAALFRRAAEDAERSAEDRAVFEEVVRGLEDESLIPAQRLASAES
+AEVSAVLHARPVREHLTSSELYPLDVQRELAGRGAWYEFFPRSEGARFDEASGTWSSGTF
+ATAADRLPAVARMGFQVVYLPPIHPIGTTHRKGPNNTLTAGPQDPGSPWAIGGPEGGHDA
+AHPDLGTVEDFEAFVAAAADEGLEVALDLALQCSPDHPWVTAHPEWFTTRVDGTIAYAEN
+PPKKYQDIYPLNFDNDPDGLAQAVLDVVRGWVARGVHIFRVDNPHTKPLWFWEWLIAKVR
+AEEPRVVFLAEAFTRPAMMHALGKVGFQQSYGYFTWRNTAEELAEYLQEISHETPAFYRP
+NLFVNTPDILTEYLQHGGPGAFRIRAVVAATASPLWGVYAGFELFEHVARPGAEEYIDNE
+KYEYRPRDWEGAEAAGASLAPYLTRLNEIRAAHPALGDLQNLTLHASTHPDLLVFSKTRS
+ARPEGAHRDAEAVTDAGPAEDTLIVVVTTNPHDVAEATLDLDLEALRLRPEDRDASGAVE
+VEDLLTGQRWRWGRTPYVRLDPHVEPAHVLRIVRNG
+>1_41
+MKPDTQSATAADVRLQTVTGRIPVTDVQPVVLDGRFPAKAVVGEDIPVRATVFREGHDSV
+RATVRLLDPAGAEVQRVQMRPGRPGLDEVVATLRPAEPGLHQFVVEGWDDPVGTWKHAAT
+VKIAAGIDVELMLAEGAALFRRAAEDAERSAEDRAVFEEVVRGLEDESLIPAQRLASSES
+AEVSAVLHARPVREHLTSSELYPLDVQRELAGRGAWYEFFPRSEGARFDEASGTWSSGTF
+GTAADRLPAVARMGFQVVYLPPIHPIGTTHRKGPNNTLTAGPQDPGSPWAIGGPEGGHDA
+VHPDLGTVEDFEAFVAAAADEGLEVALDLALQCSPDHPWVTAHPEWFTTRVDGTIAYAEN
+PPKKYQDIYPLNFDNDPDGLAQAVLDVVRGWVARGVHIFRVDNPHTKPLWFWEWLIAKVR
+AEEPRVVFLAEAFTRPAMMHALGKVGFQQSYGYFTWRNTAEELAEYLQEISHETPAFYRP
+NLFVNTPDILTEYLQHGGPGAFRIRAVVAATASPLWGVYAGFELFEHVARPGAEEYIDNE
+KYEYRPRDWEGAEAAGASLAPYLTRLNEIRAAHPALGDLQNLTLHASTHPDLLVFSKTRS
+ARPEGAHRDAEAVTDAGPAEDTLIVVVTTNPHDVVEATLDLDLEALRLRPEDRDASGAVE
+VEDLLTGQRWRWGRTPYVRLDPNVEPAHVLRVVRNG
+>2_1
+MSNSKQAAQSTPVPDVRLQTVTGRIPVTGVQPVVQDGRFPAKAVVGEDIPVRATVFGEGH
+DAVRATVRLLDPSGAEVQRVHMRPGRPGLDEFLATLRPSETGVHHFVVEGWHDPVGTWLH
+AATVKLAAGVDVELMLAEGAALFRAAAEDAERSAQDRAAFEETARVLADEGLVPAQRLAG
+AESAELAAVLGARPLREHVTSSELLPLDVQRELAGRGGWYEFFPRSEGARFDEAAGTWSS
+GTFTTAARRLPAVARMGFQVVYLPPIHPIGTAHRKGPNNTLTAGPQDPGSPWAIGAAEGG
+HDAVHPDLGTIADFEDFVAAAADEGLEVALDLALQCSPDHPWVAEHPEWFTTRVDGTIAY
+AENPPKKYQDIYPLNFDNDPEGLAQAVLEVVQGWVGRGVHIFRVDNPHTKPLWFWEWLIA
+RVRAEEPRVVFLAEAFTRPAMMHALGTVGFQQSYGYFTWRNTAAELAEYLEEISHETPAF
+YRPNFFVNTPDILTEYLQHGGPGAFRIRAVVAALANPLWGVYAGYELFEHVARPGAEESI
+DNEKYEYRPRDWEGAEAAGASLAPYLTRLNEIRAAHPALRDLQNLTLHRSTHQDLLVFSK
+TRTARPEGEHRDAEAVTDAGAHEDTVITVVTVNPHHVAEATLDLDLSALRLRPEDLDESG
+SFEVEDLLTGQRWRWGRTPYVRLDPHVEPAHVLRVVRHG
+>3_2
+MSTSKPRPAAHPAPPAPALPDVRRTTLTGRIPVSNVQPTVEEGRFPAKAIVGEDVPVRAN
+VYREGHDAVRATVRLLGPDGAEVQRVHMRPGRPGLDEAVATLRPSEPGVHHFVVEGWDDP
+VGTWRHNASVKLAAGVDVELMLDEGAALFRAAAQDPERGAADRAVFEEAVRGLEDASLAP
+VQRFAVTQSAEVSAVLDARPVRRWVTSSELYPLDVQRPLAGRGAWYEFFPRSEGARYDEA
+AGLWHSGTFRTAAERLPAVAAMGFQVVYLPPIHPIGVAHRKGPNNTLTAGPQDPGSPWAI
+GGEAGGHDAIHPGLGTFEDFDAFQERVRELGMELALDLALQCSPDHPWVTEHPEWFTHRV
+DGSIAYAENPPKKYQDIYPLNFDDDADGLARAVLDVVLGWVRRGVHIFRVDNPHTKPLWF
+WEWLIREVRAVEPEVVFLAEAFTRPAMMHGLGRVGFQQSYGYFTWRNTREELEEYLEEIT
+AETAGFYRPNFFVNTPDILTDYLQHGGPGAFKARAVIAATSNPLYGVYAGFELFEHVARP
+GAEEYIDNEKYEFRPRDWAGEEAAGRSLAPYLTRLNRIRAEHPALQDLQNLTLHSATDPE
+LLVFSKTRSALPEGDHRDAAAVTDAGSAEDTVVVVVACDPHRVAEATLRLDAEALRVRPE
+DRDEEGRFEVEELLTGARWRWDEQPYVRLDPAVEPAHVLRVVRRG
+>4_323
+MKPDTQSATAADVRLQTVTGRIPVTDVQPVVLDGRFPAKAVVGEDIPVRATVFREGHDSV
+RATVRLFDPAGAEVQRVQMRPGRPGLDEVVATLRPAEPGLHQFVVEGWDDPVGTWKHAAT
+VKIAAGVDVELMLAEGAALFRRAAEDAERSAEDRAVFEEVVRGLEDESLIPAQRLASAES
+AEVSAVLHARPVREHLTSSELYPLDVQRELAGRGAWYEFFPRSEGARFDEASGTWSSGTF
+ATAAGRLPAVARMGFQVAYLPPIHPIGTTHRKGPNNTLTAGPQDPGSPWAIGGPEGGHDA
+VHPDLGTVEDFEAFVAAAADEGLEVALDLALQCSPDHPWVTAHPEWFTTRVDGTIAYAEN
+PPKKYQDIYPLNFDNDPGGLAQAVLDVVRGWVARGVHIFRVDNPHTKPLWFWEWLIAKVR
+AEEPRVVFLAEAFTRPAMMHALGKVGFQQSYGYYTWRNTAEELAEYLQEISHETPAFYRP
+NLFVNTPDILTEYLQHGGPGAFRIRAVVAATASPLWGVYAGFELFEHVARPGAEEYIDNE
+KYEYRPRDWEGAEAAGASLAPYLTRLNEIRAAHPALGDLQNLTLHASTHPDLLVFSKTRS
+ARPEGAHRDAEAVTDAGPAEDTLIVVVTTNPHDVVEATLDLDLEALRLRPEDRDASGAVE
+VEDLLTGQRWQWGRTPYVRLDPHVEPAHVLRIVRNG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000390.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000390.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1fcdbf36d0c2b07aeb8397a4aa28da83a15a18f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000390.fa
@@ -0,0 +1,17 @@
+>0_319
+MTEQTPSLEHPQVRKNAERYEIVVDEAGTVAGYTVAIDYDTGDGPTQRIFPHTKVDHGYE
+GRGLASTLVREALKDTVAAGRRIVPVCPYVKDWVNEHDDVAGEVDPAGPEHLQFLESRQD
+>1_44
+MTEQTPSLEHPQVRKNAERYEIVVDDAGTVAGFTVAIDDDTADGPAQRIFPHTKVDHQYE
+GRGLASTLVREALKDTVAAGRRIVPVCPYVKDWVDEHDDVAGEVDPARPEHMQFLESRQD
+>2_2617
+MTENTPTLDAPQVRKVGEKYEIVVDGDGTVAGYTLAIDYEGTDGVAQRIFPHTKMAEEYG
+GRGLASVLVREALKDSVAAGFRIVPVCPYVKQWTQKHDDVAGDVDQARPEHLQFLEEHAR
+RRSEG
+>3_2428
+MTEQTSSLDHPQVRKNAEKYEIVVDADGTVAGYTLAIDYTAEDGTAEDGTEQRIFPHTKL
+EDAYEGKGLASTLVREALRDTEAAGRRIVPVCPYVKQWADKHADEVEGQVDQPRPEHLQF
+LEKHAQERKQG
+>4_326
+MTEQTPSLEHPQVRKNGERYEIVVDDAGTVAGFTVAIDDDTADGPAQRIFPHTKVDHEYE
+GRGLASNLVREALKDTVAAGRRIVPVCPYVKDWVDEHDDVAGEVDPARAEHLQFLESRQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000391.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000391.fa
new file mode 100644
index 0000000000000000000000000000000000000000..caff0bee4b08ac4e3e6d903abf2a33ad6a492e8c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000391.fa
@@ -0,0 +1,20 @@
+>0_320
+MTAADTPAPRQDPLAFFLDKAVPEAWHAVGPLASAARGAAEQAGLDRQLVELVNLRVSQL
+NGCVFCLDRHTRQGADAGLSVQRLGLLPAWREAGAVYSEQERAALELAEAVTDLPEQEQL
+NYVQASTAAVLTDAQYAAVQWVAIVMNLTNRISILSHHPVRRRDG
+>1_45
+MTAADTPAPRQDPLAFFLDKAVPEAWHAVGPLASAARAAAEQAGLDRQLVELVNLRVSQL
+NGCGFCLDRHTRQGADAGLSVQRLGLLPAWREAGAVYSEQERAALELAEAVTDLPEQEQL
+NYVQASTAAVLTDAQYAAVQWVAMVMNLTNRISILSHHPVRRRDD
+>2_2615
+MSAAENPATRKDPLAFYLDKAVPDAWKAVGGLAAAVRTAAEEAGLDRQLVELVNLRVSQI
+NGCGFCLDLHAREGAKAGLNAQRMALLPAWREAEAVYSEQERAALELAEAVTELPEQEQL
+HYVQASTAAALTDAQYAAVQWAAMVMNLTNRISILSHHPVRRRED
+>3_2426
+MSSPHDDAAPARKDPLAFYLDKAVPEAWVAVGGLAAAARRAAVEAGLDEQLMELVNLRVS
+AINGCAYCLDVHTRKGVGAGLSDQRRGLLSAWREAPEVYTELERAALELAEAVTELPEQE
+QQQYVQLSTHGVLTDAQYAAVQWLAIVMNVTNRISILSHHPVRRHDS
+>4_327
+MTAADTPAPRQDPLAFYLDKAVPEAWHAVGPLASAARDAAEQAGLDRQLVELVNLRVSQL
+NGCVFCLDRHTRQGADAGLSVQRLGLLPAWREAGAVYSEQERAALELAEAVTDLPEQEQL
+NYVQASTAAVLTDAQYAAVQWVAIVMNLTNRISILSHHPVRRRDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000394.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000394.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1c390ecfc4784ea6c5cd2c201441c0790a8f61c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000394.fa
@@ -0,0 +1,30 @@
+>0_323
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEEQRE
+MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA
+KFPQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVEDAPEHIAGYAVANDISMR
+GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFPADARVLTHVNGELRQEDRVADVVFSPAE
+LVSYASQLITLNPGDLILTGTPAGVALARRDAEGRRPWLRPDDVVEVEITGLGRQRNELV
+>1_48
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEERRE
+MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA
+KFAQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVEDAPEHIAGYAVANDISMR
+GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFSADARVLTHVNGELRQEDRVADVVFSPAE
+LVSYASQLVTLNPGDLILTGTPAGVALARRDAEGRRPWLRPDDVVEVEITGLGRQRNELV
+>2_2569
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPECRDVGEYLTAEPQEQRE
+MVESALRAAQEDRSLLLDTSTLVYDTLIPFPTKVFCVGLNYTNHIEETGQNQPEHPTLFA
+KFTQSLTGALDPVEVPEEDHLVDYEGELCIVIGEPGRRIAVEDAKEHIAGYAVANDVSMR
+GWQGRTSEWLQGKVWEASTPVGPWLVTPDELTADARIITRVNGVERQDDRIADVVFSPEE
+LVAYVSQMITLNPGDLIMTGTPAGVAVARKGADGRRPWLQAGDVVEVEITGLGRQRNELV
+>3_2420
+MKLATFRQPDSDASYPGATFAAVLTSFHPQDPQVAVRAVALPECRDVGEFLTAEPQEQKD
+MVREALEAAKEDHGLLLDVSTLVYDTLVPFPTKVFCVGLNYADHIRETGQEKPEHPTLFA
+KFAQSLTGALDPIEVPEEDHRVDYEGELCVVIGEPGRRIAVEDAKDHIAGYAVANDVSMR
+GFQGRTPEWLQGKVWEASTPVGPWLVTADEFPKDARIVTRVNGEVRQDGKVKDVVFSPAE
+LVSYVSQLVTLNPGDLIMTGTPAGVAVARRDGDGRRPWLRADDVVEVEITGLGRQRNELV
+>4_330
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEEQRE
+MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA
+KFPQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVADAPEHIAGYAVANDISMR
+GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFPADARVLTHVNGELRQEDRVADVVFSPAE
+LVSYASQLITLNPGDLILTGTPAGVALACRDAEGRRPWLRPDDVVEVEITGLGRQRNELV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000395.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000395.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d3b4f65ef1a929080dfc3a205bb924676b26633
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000395.fa
@@ -0,0 +1,35 @@
+>0_324
+MSTAPTHPPLDLDPTPATPIVLGTMAWGSVLPPPPDADPGVGPEGPAGEAQAEAAVERAR
+RALRAGIEAGVDLLDTADIYGAGRSEETVGRLLHELPYEERSALKVQTKCGIVLHETDPA
+GRRLTRYDSSPEHVRASLEGSLARLGEQRVDTLIIHRPDVLTPVADTVRAFLDAREAGLV
+GKLGVSNLGVGRVLEFQRELESQAADGTGLACVQVELGLHHRTLMEAVVLANHPDAPADA
+DAGRLGPVCAAEGIELQAWGPLGQGRFSSGDDGAAGAVGEVAAELGGSREAVVLAWLLRL
+PWDVRPVIGTQDPERVAACAEAAAAAEAMDSAQWHRLWTAARGAGLP
+>1_49
+MSTAPTHPPLDLDPTPATPIVLGTMAWGSVLPPPPDADPGVGPEGPAGEAQAEAAVERAR
+RALRAGIEAGVDLLDTADIYGAGRSEETVGRLLHELPYEERSALKVQTKCGIVLHEADPA
+GRRLTRYDSSPEHVRASLEGSLARLGEQRVDTLIIHRPDVLTPVADTVRAFLDAREAGLV
+GKLGVSNLGVGRVLEFQRELESQAADGTGLACVQVELGLHHRTLVEAVVLANHPDAPADA
+DAGRLGPVCAAEGIELQAWGPLGQGRFSSGDDGAAGVVGEVAAELGVSREAVVLAWLLRL
+PWGVRPVIGTQDPERVAACAEAASVAEAMDSAQWHRLWTAVRGAGLP
+>2_2568
+MAWGAAPAPAPAPGEGPALLASAGPEHAEAARERARGALRAGIDAGVDLLDTADIYGAGV
+SEETVGALLHELPYEERSALKVQTKCGIVLDEVDADGRPMVRYDSSPEYVRARLEGSLAR
+LGELRVDTLVIHRPDVLTPVADTVRAFLDAREEGLVGKLGVSNLGVGRTLEFQRELAAQS
+ADGTGLACVQVELGLHHRTLVESVILANHPGAAADADVADLGRVCAAEGIELQAWGSLGQ
+GRFSSGDDGAAGVVGEIARELDTSREAVVLAWLLRLPWGVRPVIGSQDPGRIAACADAAA
+AAEAMDSAQWHRLWTAARGAPLP
+>3_2419
+MTAQDTAPQTPAASPLILGTMGWGDVERARGALRAGLEAGIGLLDTADIYGAGASEETVG
+ALLAELDPAERTRLRVQTKSGIVLHEPGPDGTPAVRYDNSPAYLHERLALSLERLGLDRV
+DTLVVHRPDVLTPVSDTVRAFLDAREAGRVDALGVSNMGTRRVLEYQHALREVSADGTGL
+ACVQVELGLHHRMLVESVVLANHPAAAPDGGAGDLGEVCAGEGIEIQAWGPLGQGRFTRG
+SDGTVPADPAEQAALAAAGGAPAVVARVARELEVSREAVVLAWLLRLPWGVRPVVGTQDP
+ARIASCAQAADAAARMDGAQWHRLWTAARGETLP
+>4_331
+MSTAPTHPPLDLDPTPATPIVLGTMAWGSVPPPPPDADPGAGPEGPAGEAQAEAAVERAR
+RALRAGIEAGVDLLDTADIYGAGRSEETVGRLLHELPYEERSALKVQTKCGIVLHETDPA
+GRRLTRYDSSPEHVRASLEGSLARLGEQRVDTLIIHRPDVLTPVADTVRAFLDAREAGLV
+GKLGLSNLGVGRVLEFQRELESQAADGTGLACVQVELGLHHRTLVEAVVLANHPDAPADA
+DAGRLGPVCAAEGIELQAWGPLGQGRFSSGDDGAAGVVGEVAAELGVSREAVVLAWLLRL
+PWGVRPVIGTQDPERVAACAEAASVAEAMDSAQWHRLWTAARGRPLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000399.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000399.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b7cb130f19f0de048dfcb0e58f6aa0851a495ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000399.fa
@@ -0,0 +1,30 @@
+>0_329
+MARNTSGSHTSATDARARARQIQEEQRRKDRRRRTGVIWGSVLAAVLVIGLVVAFALTRN
+GDDAAAAGPIPAAANEQGGIELTSATGLAEGAGEREVDPSEIEVPKQAASSQPETLPNTE
+ARGDGEPTRIVLYADFNCVHCADFESSNAEQIEQWLEQGEVTVEYRMVDFLSAPNNQNYS
+ARAANAAYCVADQKPEAYNGFVAALFAAYDEHQGKGLDNAALTQLAQEQGVDISSCVEDG
+TFRSAVEHTTRQARVAGVAGTPTVFVDGKNWALDGEDKTFTDWAGAKIAD
+>1_54
+MARNTSGSHTSATDARARARQIQEEQRRKDSRRRTGVIWGSVLAVVLVIGLVVAFVLNRN
+GDDAAAAGPIPAVANEQGGIELTSATDLAEGAGEREVDPSKIEVPKQAASSQPETLPNTE
+ARGDGEPTRIVLYEDFNCVHCADFESTNGDQIEQWLEQGEVTVEYRMVDYLSAPNNQNYS
+ARAANAAYCVADQKPEAYNGFVSALFAAYDEHQGKGLDNAALTQLAQEHGADIASCVEDG
+TFRSAVEYTTRQARAAGVAGTPTVFVDGKNWALDGEDKTFIEWAGAKIAG
+>2_2563
+MARNTSGSHTSATDARARARQIQEQQRKKDGRRRTAVIWGSVLAAILVIGLIVAFALNRG
+GDEPAAAGPIPAAANEQGGIELTSATTLAEGAGAREVDASTVEVPEQGAAQQPETIPAAE
+APAEGEPSEIVLYADFNCVYCADFETSNAAQIEQWLEAGEVTVEYRMVDFRSAPNNQNYS
+ARAANAAYCVADQKPEAYNGFVTALFGTYQEHGGKGIDNAALTQLAQDNGADIASCVEDG
+TFRSAVEHTTRQAQAAGVGGTPTVFMDGENWAIGGPDQSFQEWAQSKISG
+>3_2415
+MASRNPAPSEVDARARARQMQVDQQKKARRRRTATIWGAVLAAVLVIGLIVGFVVKGNQG
+TEISATGPVPGVVNEEGGVEMTSATALADSGKSERQVDSSSVAVPETATAPEELTTIPAA
+GEPADGEPAQIVVYADFNCVHCAEFESQNSEQLQSWLRDGKATVEYRMVNFLSAPNNKNY
+SARSANAAYCVAAAKPEAYNEFTTGLFMAWEGHGGKGLSDDELIQRADALGVDIEGCLKD
+NTYRPAVEWATNKAKAASVAGTPTVFVNGKNWSTDGGDKSFVDWAKPMVEG
+>4_336
+MARNTSGSHTSATDARARARQIQEEQRRKDSRRRTGVIWGSVLAVVLVIGLVVAFVLNRN
+GDDAATAGPIPAVANEQGGIELTSATDLAEGAGEREVDPSKIEVPKQAASSQPETLPNTE
+ARGDGEPTRIVLYEDFNCVHCADFESTNGDQIEQWLEQGEVTVEYRMVDYLSAPNNQNYS
+ARAANAAYCVADQKPEAYNGFVSALFAAYDEHQGKGLDNAALTQLAQEHGADIASCVEDG
+TFRSAVEYTTRQARAAGVAGTPTVFVDGKNWALDGEDKTFIEWAGAKIAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000400.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000400.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1061aac1b23b12e276d6a2da76feb661d4e4cb78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000400.fa
@@ -0,0 +1,56 @@
+>0_330
+MQSSTPRSTRRIGALVAGAVLAGGTLTSSPALAAPSGAAPAAPAASPTVASPLAAAQVED
+PNADGYDSFIVTYKETAANAHAKGRANAWGKAAKEAGVSVKELRETALGSRVVTVDRKLD
+QAESAKFMADLKASGAVEAVEPDAILTATGLSPVDALYSQQWGFTGTHGMRVPGAWDRTT
+GSGATVAVIDTGITSHPDLDRNVVPGYDFISDSAAARDGGGRDSNPRDEGDWYAAGECGT
+AGASDSSWHGTHVAGTVAAVADSQGVVGVAPNAKIQPIRVLGKCGGSLSDIADAVVWAAG
+GTVAGVPANPNPADVINMSLGGSGMCGTTYQNAINAAVSRGVPVVVAAGNENQPAANVRP
+ANCQNTIVVAASTSQGARASFSNYGSAVDVTAPGANIISTVNNGATTPTTAGHAAYNGTS
+MATPHVAGLAALLLAAQPSLTPAQVESTLRSTARSMPVTCSAGCGAGLADASAAVSSLGG
+AQTEPGPAPVASLIVNGGFESGSTGWTGTPTGFVRTDAAKAASGQAFAQLNGVGRRNTTT
+VEQKVTVPASGATLTYALQVDTAETTASRSYDLLDVQVVTGATGTYTVASHSNLDKGGYA
+TRTVDLSRFAGTTVTLRFRGTEDSSAATTFRIDEVAVTAR
+>1_55
+MQSSTPRSTRRRIGALVAGAVLAGGTLTSSPALAAPSGGAPAAPAASPTAASPLAAAQAE
+DPNADGYDSFIVTYKETAANAHAKGRANAWGKAAKEAGVSVKELRETALGSRVITADRKL
+DQAESAKFMADLKASGAVEAVEPDALLTATGLSPVDALYSQQWGFTGSHGMRVPGAWDRT
+TGSGATVAVIDTGITSHPDLDRNVVPGYDFISDSAAARDGGGRDSNPRDEGDWYAAGECG
+TAGASDSSWHGSHVAGTVAAVADSQGVVGVAPNAKIQPIRVLGRCGGSLSDIADAVVWAA
+GGTVAGVPANPNPADVINMSLGGSGVCGTTYQNAINAAVSRGVPVVVAAGNENQPAANVR
+PANCRNTIVVAASTPQGARASFSNYGSAVDVTAPGANIISTVNNGATTPTTAGHAAYNGT
+SMATPHVAGLAGLLLATKPSLTPANVESTLTSTARSMPVTCSAGCGAGLADAARAVSSLG
+GSS
+>2_2554
+MKSSVQHSTRRRVGALLAGAVLAGGALTSSPAFAAPAEGARAEQAPRPVAAAPLATVDAA
+DPNADGYDSFIVTYKETAQNNNGKGRALAWGKAAKAAGVSVKELRETALGSHVVQADRKL
+DQSESARFMADLKASGAVEDVEPNAIMTATGLSPADALYSQQWGFTGTNGMRVPGAWDYN
+TGSGVTVAVLDTGITSHPDLDRNVVAGYDFISSSAAARDGNGRDSNPRDEGDWYAAGECG
+ASQPGNSSWHGTHVAGTVAAVTDTQGVVGVAPNAKIQPVRVLGKCGGSLADIADAIVWAS
+GGSVTGVPANANPADVINMSLGGSGTCGTTYQNAINAAVNRGVPVVVAAGNENQPAANAR
+PANCSNVITVAASTSQGARSSFSNYGSAVDVTAPGSSIISTINRGLTTPTTAGHASYNGT
+SMATPHVAGLTALMLAQQPGITPAQVESTLKSTARSMPVACSAGCGAGLVDATRAVAALG
+GGSTTPTPTGVIVNGGFESGATGWTGTPSDFVGNTAGYARSGSNYGVLNGYGRSNTGTVE
+QRVTVPASGASLSYWLQVGSDETTTRSQYDTLAVQVVDGSQTTTVKSHSNLEKGTSYAQH
+TVDLSAYKGKTVTLRFRGVEDYSNSTVFRIDDVAVTAK
+>3_2413
+MTALTSPSARRRVGSLLAAAVLAGTALTAAPTLAAAERPAEPARTSPAAAAPLADPNADG
+YDSFIVTYRETAANSTAQGRAKAWGRAAREAGVSVKELRETALGSRVIATDEKLTQEESA
+AFMADLRASGAVEAVEPNVIMTRAALSPADPYYADQWGFTGVNGMRVPGAWDVSTGTGAI
+VGVIDTGQTDHADLNANTVPGYDFISDATTARDGGGRDADPRDEGDWYLAGECGQSRASN
+SSWHGSHVAGTVAAVANTQGVVGVAPGAKVQHARVLGKCGGTLADIADAIVWSSGGSVPG
+VPANPTPVDVINMSLGGQGTCGTTYQNAINAAVGRGVPVVVAAGNENQSAANARPANCQN
+TITVAATDVNGNRASYSNYGSAVDVAAPGSGIISTVNAGTTTPTAGAYAQYNGTSMATPH
+VAGTVALMLAEDATLTPAEVESSLKTNSRPIPGVCAEGCGAGLVDAAKTLASLRGGTTDP
+HPVTPVPGAEKLVNGGFESGLTGWTATGRVAASSTAGLSATGSLHAALNGKGGTSTATLT
+QKAVLPAGAAATLSYAVRVDSAETTTARQWDKLTVSVSDGATTTTLRTHSNLDKGRGYLA
+QAADLSAYAGKTVTISFSGTEDGSGATTFRIDDVSVKAG
+>4_337
+MQSSPPRSTRRRIGALVAGAVLAGGTLTSSPALAAPSGDAPAAPAATPTAASPLAAAQVE
+DPNADGYDSFIVTYKETAATAHAKGRANAWGKAAKEAGVSVKELRETALGSRVIKADRKL
+DQAESAKFMADLKASGAVEAVEPDAILTATGLSPVDALYSQQWGFTGTHGMRVPGAWDRT
+TGSGVTVAVIDTGITSHPDLDRNVVPGYDFISDGRAARDGGGRDSNPRDEGDWYAAGECG
+TAGASDSSWHGTHVAGTVAAVADSQGVVGVAPNAKIQPIRVLGKCGGSLSDIADAVVWAA
+GGTVAGVPANPNPADVINMSLGGSGMCGTTYQNAINAAVSRGVPVVVAAGNENQPAANVR
+PANCRNTIVVAASTSQGARASFSNYGSVVDVTAPGANIISTVNNGATTPTTAGHAAYNGT
+SMATPHVAGLAALLLAEQPSLTPAQVESTLTSTARSMPVTCYAGCGAGLADATRAVSSLG
+GSS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000403.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000403.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02ac11d3fd5a72d0ded969b23294df8a81a610d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000403.fa
@@ -0,0 +1,15 @@
+>0_333
+MSHPTPVSPDPAPDEGARARARRDELTDLERAVLDLEAATWRYGGAKDHAVRERLGLSPT
+AYYQVLNGLLDREAALAYRPLLVTRLLRKRGTRSRARRGPADPAPSTPASRQEN
+>1_58
+MSHPTPVSPDPAPDEGARARARRDELTDLERAVLDLEAATWRYGGAKDHAVRERLGLPPT
+AYYQVLNGLLDREAALAYRPLLVTRLLRKRGTRSRARRGPADPAPSTPASRQEN
+>2_2551
+MPTSAPEPRRDALTPQERAVLDLEAATWRHGGAKDHAVRERLGLSPTAYYQVLNGLLDRE
+AALAYRPLLVARLLRKRGTRSRARRAPADPAPSTPASRQEN
+>3_2410
+MPDADPRPAAPADGPEPTPQDELTELEEAVLALEAQTWRHGGAKDHAIRERLQITPTAYY
+QVLNGLLERRAALARQPLLVSRLARSRGTRSRARRRPAPENSAPPASPQER
+>4_340
+MSHPTPVSPDPAPDEGARARARRDELTDLERAVLDLEAATWRYGGAKDHAVRERLGLPPT
+AYYQVLNGLLDREAALAYRPLLVTRLLRKRGTRSRARRGPADPAPSTPASRQEN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000404.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000404.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f47f541b21e2211195ab717fe01d8c77e1033bcc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000404.fa
@@ -0,0 +1,35 @@
+>0_334
+MAYQPDRFDEVPEYTDQRGAHRESFAVAGATATGGGRRLSPLLWVAGLVLLAGLFVGVVL
+PWLTGDRSEPVAAESSTTAPAAAPSTSASSVSSSASSASASTASATESATPSEDAVEASR
+SAAAAESSRAAQEAAAAEAAESSQAAASSRAAAEAQAAEASRSEAAAQSAEASRAAAEAQ
+AAEASRSEAAAQSAEASRSAAAVQAAESSRAAASRSAAAAEASRSQSAAASSSRAAAQSA
+AASSSRAAAQSAAVRGTHVTVYNATRTQGLAASYAQRLTGAGYTSVDAKNWSGYGIQSST
+VLYNGSANKAAAEAVGKELGFPVMQTPNLQVNGIAVVVTS
+>1_59
+MAYQPDRFDEVPEYTDQRGAHRESFAAAGATAAGGGRRLSPLLWVAGLVLLAGLFVGVVL
+PWLTGDRSEPVAAESSTTAPAVEPSPSTSTSASSESSSASSASASTASATESATPSEDTA
+EASRSAAAAAAESSRVAQEAAAAEAAESSRAAESSRAAAEAAESSRAAAEAQAAEASRSE
+AAAQSAEASRSAAAVQAAESSRAAASRSAAAAEASRSQSAAASSSRAAAQSAAASSSRAA
+AQSAAVRGTHVTVYNATRSQGLAASYAQRLTSAGYTSVDAKNWSGYGIQSSTVLYNGSAN
+KAAAEAVGKELGFPVMQTPNLQVNGVAVVVTG
+>2_2550
+MAYQPDRFDEVPEYTDQRGAHRASFAAPAGAAAAGGGARRFSPLLLVAGLVLLAGLFVGV
+VLPWLTGDRSEPVAAESSASSPAADPSTSSEPASPTEGAATTEPASPSEDAAAAEASRSQ
+AAAQSAAEQSAAEAAAASSRAAEEAAAAEASRSAEAAQAAEASRSAAAAAEASRSAGAAQ
+AAEASRSAEAAQAAEASRSAAAAAEASRSAEAAQAAEASRSAAAAAEASRSAEAAQAAEA
+SRSAAAQAAEASRSAAAQAAAAARSTNVTVYNATRTTGLAASYAQRLRSAGFTSVSAQNW
+GGYGIQSSTVLYNGSGNQAAAEAVAAELGFPVLQTPNLQVNGVAVVVTG
+>3_2409
+MAYPADRFDDVPEYTDQSGAHRESFAAAPAAAGAAGATAAGTEAAAGGGILKWLLAAAAA
+VLLVGLFLGLVLPRLNGGDDKPVAGAASSSSSSEPAADASSSSSDAPSSDASSSAGPDSA
+APAAPSSDAGAESAAAPSSDAAVESRAAAESSQAAAESSQAAADAQRSRDDAARAASESA
+QAAADASSADAAARERAASESAQAAADASRAAEASRSAEASRSAEASRSAEASRSAEASR
+SAEASRSAAASRSAAAQESADRAVKSTPVNVYNATRRNGLAASYADRLTGAGYTRVTADN
+WPGFRVTSNTVMYNGADKRAAAEAVGRELGMPVQQVPNLQVPGIAVVVVR
+>4_341
+MAYQPDRFDEVPEYTDQRGAHRESFAAAGATAAGGGRRLSPLLWVAGLVLLAGLFVGVVL
+PWLTGDRSEPVAAESSTTAPAVEPSTSASSESSSASSASASTASATESATPSEDTAEASR
+SAAAAAAESSRVAQEAAAAEAAESSQAAASSRAAAEAQAAEASRSEAAAQSAEASRSAAA
+VQAAESSRAAASRSAAAAEASRSQSAAASSSRAAAQSAAASSSRAAAQSAAVRGTHVTVY
+NATRTQGLAASYAQRLTGAGYTSVDAKNWSGYGIQSSTVLYNGSANKAAAEAVGKELGFP
+VMQTPNLQVNGIAVVVTS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000407.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000407.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21bde5fa7af5f747fc6c0c43a1f8c3b6f0afb954
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000407.fa
@@ -0,0 +1,59 @@
+>0_338
+MRARLDAAAARVRHPRAWLRGAWQGQSLRTKLVVMIAALMLALVAVTAVATAVLFRQEAV
+RQLDEDMAANRDTVSMYLANVAQTGEYYMPQLPILRFYGVVWDNEGARVVQTPVMPGADE
+PALPDITPAEALERGSASFEVPGTQPDSSGWRVQLYGLSSGDGTMAVALPLQSVTSSVER
+VTSIVVTIGLLATAGTVIVANLAVQRAFRTLNRVERTAAKIAAGDLSQRVESAAPDTEVG
+RLSRSLNAMLAHIESAFRDKEISEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREE
+EDVAAAMQRIESEATRMTRLVEDLLTLARLDEQRPLEHAPVDLLILAMDSMMDASVNAPD
+RKVTLVGPDGDRAAPAPILGDENRMRQVVVNLMANALRYTPAGTPIEIAVGTVDHLGGQA
+GADGAGRSSVIEIRDHGPGVSEEDRARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQH
+GGSVRLLETEGGGATFSVHLPWAPFEDEADEDVEDERLPARDTDDDAAGPPTGPLALAAP
+SGAGASAADAARSSRLLRAAERFRRASAERRRRASAPAQAPQADPPSPGEDDPAAERDAR
+P
+>1_63
+MRARLDAAAAHVRHPRAWLRGTWQGQSLRTKLVVMIAALMLALVAVTALATAALFRQEAV
+RQLDEDMAANRDTVSMYLANVAQTGEYYMPQLPILRFYGVVWDNEGARVVQTPVMPGADE
+PALPDITPAEALERGSASFEVPGTQPDSSGWRVQLYGLSSGDGTMAVALPLQSVTSSVER
+VTSIVVTIGLLATAGTVIVANLAVQRAFRTLNRVERTAAKIAAGDLSQRVESAAPDTEVG
+RLSRSLNAMLAHIESAFRDKEISEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREE
+EDVAAAMQRIESEATRMTRLVEDLLTLARLDEQRPLEHAPVDLLILAMDSMMDASVNAPD
+RKVTLVGPDGDRAAPAPILGDENRMRQVVVNLMANALRYTPAGTPIEIAVGTVDHLGGQA
+GADGAGRSSVIEIRDHGPGVSEEDRARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQH
+GGSVRLLETEGGGATFSVHLPWAPFEDEADEDVEDERPSARDTDDDAAGPPTGPLAQTAP
+SGAGASAADAARRSRLLRAAERFRRASAERRRRVSAPAQAPQADAPSPGGDDPAAGRDAR
+P
+>2_2546
+MSGRLDAAAARARLPRAWLSSAWRGQSLRTKLVMMITVLMLALVAVTAIATAALFRQEAV
+RQLDEDMAANRDTVSMYLANVAQTGEYYMPQLPILRYYGVVWDNDGDRVVQTPVVPGSDE
+PDLPSITPERALEIGSASFEVAGTQDESSRWRVQLYGLSSGDGTMAVALPLEGVRSSVER
+VTSLVVTIGLLGTAGTVIVANLAVQRAFRALNRVERTAAKIAAGDLTQRVESAAPDTEVG
+RLSRSLNAMLAHIESAFRDKEVSEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREE
+EDVAAAMQRIESEATRMTRLVEDLLTLARLDEQRPLELAPVDLLILAMDSMMDASVNAPD
+RKVTLVGLDGGRAGSAPIVGDENRMRQVVVNLMANALRYTPAGTPIEIAVGTVDPLGGPG
+AAGDGEGRTSVIEIRDHGLGVSEEDAARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQ
+HGGSVRLLETEGGGATFSVHLPWAPFEDDDDLEDEDDAGPVSESENAAEVSHTGPLGLVA
+PSGAGASVVDAARRSRLLRAGERFRRASAERRPRAGTPAQAPAEGAASPGEEEPGPAAPD
+RP
+>3_2405
+MGPRLGVAAARLRHPRTWLWGWWGARPLRTKLVVMITALMMVLVAVIALVTAVLFRTELL
+RQLDDDLSHNRDEVSIYLTTMSQTGGYYTPQQSILRFYGVVWDTSGRAVVSTPLMPGADG
+PALEGMTPEQVDAQGSASFEVPGTTAGSDGWRVQLYHLRSGEGSLAIALPLHGVRTSVER
+VVTLVVTIGLLGTAVSVVASNLLVERAFRALNRVERTAAKIAAGDLSQRVAYAPPSTEVG
+RLSRSLNAMLAHIETAFRDKEASEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGITRE
+EDVAAAMGRIESEAGRMHRLVEDLLTLARLDEQRPLEHEPVDLLVLGMDSMMDASVNAPD
+RKVSLVGLDGGPAGSAPLMGDENRMRQVVVNLMTNALRYTPEGTPIEIAVGTRDAFGGDS
+GVDGTRHSVIEIRDHGAGVSEEDAARIFERFYRADASRHRETGGTGLGLAIVAAIVAQHG
+GSVRLLETEGGGATFSVHLPWAALEDDADDDLDLEDDDARPGAGVPAGRPPTGGSTAAGS
+AGALETGQRRRLAWAGERFRRASAARRQAQAGTSPAQAARDGA
+>4_345
+MRARLDAAAARVRHPRAWLRGAWQGQSLRTKLVVMIAALMLALVAVTAVATAVLFRQEAV
+RQLDEDMAANRDTVSMYLANVAQTGEYYMPQLPILRFYGVVWDNEGARVVQTPVMPGADE
+PALPDITPAEALERGSASFEVPGTQPDSSGWRVQLYGLSSGDGTMAVALPLQSVTSSVER
+VTSIVVTIGLLATAGTVIVANLAVQRAFRTLNRVERTAAKIAAGDLSQRVESAAPDTEVG
+RLSRSLNAMLAHIESAFRDKEISEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREE
+EDVAAAMQRIESEATRMTRLVEDLLTLARLDEQRPLEHAPVDLLILAMDSMMDASVNAPD
+RKVTLVGPDGDRAAPAPILGDENRMRQVVVNLMANALRYTPAGTPIEIAVGTVDHLGGQA
+GADGAGRSSVIEIRDHGPGVSEEDRARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQH
+GGSVRLLETEGGGATFSVHLPWAPFEDEADEDVEDERPSARDTDDDAAGPPTGPLAQTAP
+SGAGASAADAARRSRLLRAAERFRRASAERRRRVSAPAQAPQADAPSPGGDDPAAGRDAR
+P
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000408.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000408.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e716a76727e2477be052b198881f29d3a259d1a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000408.fa
@@ -0,0 +1,14 @@
+>0_340
+MTSQDSPTRVAGMPRTSTLPAPAPADHRGGRGVVLVLGVAVTAVSALALVALLVAYFLAW
+PASPALFALALFGLPVGFGLMLLHVVLGAVRRSRP
+>1_65
+MTSQDSPTRVAGMPRTSTLPASAPAADPADHRGGRGVVLVLGVAVTAVSALALVALLVAY
+FLAWPASPALFALALFGLPVGFGLMLLHVVLGAVRRSRP
+>2_2544
+MLGVTVTAVSFVALLGLLAAYFFSWPAVPALYALAMFGLPVGFSLMLLHVVLGAVRRSRL
+>3_2403
+MPSPRTSPQPRPDAAPAPSGARRALRVLLTAGVVLTVVSGLGLLGALAAYFLHATPAFLP
+ALYAVSLFGLPLGFTLMVLHVVLSAVLRARS
+>4_347
+MTSQDSPTRVAGMPRTSTLPASAPAADPADHRGGRGVVLVLGVAVTAVSALALVALLVAY
+FLAWPASPALFALALFGLPVGFGLMLLHVVLGAVRRSRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000412.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000412.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5971227eee34a29f3c1ba8cf36c91fa97b38971c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000412.fa
@@ -0,0 +1,23 @@
+>0_344
+MTDLIDTTEMYLRTILELEEEGIPPLRARIVERLEHSGPTVSQTVARMERDGLVHVGMDR
+RLELTVAGRERAVSVLRKHRLAERLLADVIGLEWELVHEEACRWEHVMSDQVERRLLTLL
+ENPTETPYGTPIPPRPEQASAEDWSRDMGLAGTRLSEEAATAGRFRVRGLAEGVQTDPDL
+LAQLAGAGVTPGRVVRAEAARDAGYIRVEGEAEDGAAADGGALELAAATAAHVWVERLDG
+>1_69
+MTDLIDTTEMYLRTILELEEEGIPPLRARIVERLEHSGPTVSQTVARMERDGLVHVGTDR
+RLELTVAGRERAVSVLRKHRLAERLLADVIGLEWELVHEEACRWEHVMSDQVERRLLTLL
+ENPTETPYGTPIPPRPEQASAEDWSREMGLAGTRLSEEAATAGRFRVRGLAEGVQTDPEL
+LAQLAGAGVTPGRVVRAQAARDAGYIRVEGEAEDGAAADGGALELAEATAAHVWVERLDG
+>2_2540
+MGLAGTRLSEEAATPGRFRVRGLAEGVQTDPELLAQLAAAGVTPGRTVTAQAAIDPGYVR
+VEGEAADGAPESGALELAVETAAHVWVERLDA
+>3_2399
+MTDLIDTTEMYLRTILELEEEGTVPLRARIVERLEHSGPTVSQTVARMERDGLVHVGSDR
+RLLLTDEGRERAVAVLRKHRLAERLLSDVIGLDWAYVHDEACRWEHVMSDRVEQRLLEVL
+ENPTATPYGTPIPPRPEAQSAGEWSRDLGLAGEPLATAAATPGRFRVGSLSEGVQADPEL
+LAELQDAGVLPGGVLEAQPALEAGYVRVQGEGSAEALELSAGTAAHVWVQRL
+>4_351
+MTDLIDTTEMYLRTILELEEEGIPPLRARIVERLEHSGPTVSQTVARMERDGLVHVGADR
+RLELTVAGRERAVSVLRKHRLAERLLADVIGLEWELVHEEACRWEHVMSDQVERRLLTLL
+ENPTETPYGTPIPPRPEQASAEDWSRDMGLAGARLSEEAATAGRFRVRGLAEGVQTDPEL
+LAQLAGAGVTPGRVVRAEAARDAGYIRVEGEAEDGAAADGGALELAEATAAHVWVERLDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000414.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000414.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a03ef4fe4d4648e0124694c61460efe87cf97056
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000414.fa
@@ -0,0 +1,26 @@
+>0_347
+MSQKSRKSRPRPSRPAARPVAESPRSRPTLRDVHVREDLAAAAEREGSPAIPVSALIVTT
+LLVGAYLHLLVLQQMTQLSGGLAMPDSLLFYGQDHIRALSAVMDEDARGQLNWVHKTAGV
+IFPIAVALTVTAVGAWRLRPVGAKWAVFGLGVLFAVVDICENIAIEQAIAAGGPGTGLAA
+ALTLTRWVLLALLALAVAVMLWAGRRRRRGPAARED
+>1_72
+MSQKSRKSRPRPSRPAARPVAESPRSRPTLRDVNVREDLAAAAEREGSPAIPVSALIVTT
+LLVGAYLHLLVLQQMTQLSGGLAMPDSLLFYGQDHIRALSAVMDEDARGQLNWVHKTAGV
+IFPIAVALTVTAVGAWRLRPVGAKWAVFGLGVLFAVVDICENIAIEQAIAAGGPGTGLAA
+ALTLTRWVLLALLALAVAVMLWAGRRRRGRATRAA
+>2_2537
+MRGRGPALLDPAPGRQTGTGLGGWSAEVPPLSQKPRKPRKSRPSRASQSGARSGSSAARA
+AGGAERARPTLRDLNIREDLAAAGRQEGSPAIPVSALIVTTLLVGAYLHLLVLQQMTQLT
+GGLAMPDSMLFYGQDHVRALSAVMDDAARGQLNWVHKTAGVIFPIAVALTLAAVGAWRLR
+PAAAKWGALGVGVLFAVVDIAENIAIEQAIAAGGPGTGLAAALTLARWVLLALIALAIVV
+MLWAGRRRREPAARRR
+>3_2396
+MSKKQKKSRPARTGSSAAPTAEPRRAGLHDVSPRADLADAAQQEGSPAMLITALIGTTLF
+IGAYFHLLVLQQMTQLTGGLAMPDSMLFYGQDHVAALSAVMDDAARGQLNWVHKTAGVIF
+AVAVALTVAAVGAWRLKPVAAKWGALALGVLFAVVDIWEGLAIEAAIAAGGPGTGLAATL
+TAIRWVLLAVITVAVVVMLWAGRRRRPRT
+>4_354
+MSQKSRKSRPRPSRPAARPVAESPRSRPTLRDVNVREDLAAAAEREGSPAIPVSALIVTT
+LLVGAYLHLLVLQQMTQLSGGLAMPDSLLFYGQDHIRALSAVMDEDARGQLNWVHKTAGV
+IFPIAVALTVTAVGAWRLRPVGAKWAVFGLGVLFAVVDICENIAIEQAIAAGGPGTGLAA
+ALTLTRWVLLALLALAVAVMLWAGRRRRGRATRAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000416.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000416.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb7b3ef0423a31d0a4c9bd7519a0223f73ce962e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000416.fa
@@ -0,0 +1,40 @@
+>0_350
+MDLYEYQARDLFEAHGVPVLAGIVAQTPDEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVHQVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSALTGIDAETAQKIVTEAGFPEELRADVAEVIQKLWEVF
+EKEDATLVEVNPLVKTGDGTILALDGKVSLDDNAQFRHEDHAALVDERTEDPLEAKAKAN
+GLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEQHGGVKPANFLDIGGGANAEVMANGLD
+VILGDEQVKSVFVNVFGGITACDQVANGIVKALEILGDTATKPLVVRLDGNAVEEGRRIL
+QEANHPLVTLAATMDEGADKAAELAHSAN
+>1_75
+MDLYEYQARDLFEAHGVPVLAGIVAQTPDEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVHQVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSPLTGIDAETAQKIVTEAGFPEELRADVAEVIQKLWEVF
+EKEDATLVEVNPLVKTGDGTILALDGKVSLDDNAAFRHEGHAALVDERTEDPLEAKAKAN
+GLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEKHGGVKPANFLDIGGGANAEVMANGLD
+VILGDEQVKSVFVNVFGGITACDQVANGIVKALEILGDTATKPLVVRLDGNAVEEGRRIL
+QEANHPLVTLAATMDEGADKAAELAHSAN
+>2_2535
+MDLYEYQARDLFEAHGVPVLAGIVAQTPEEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVHQVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSPLTGIDAETAQKIVAEAGFPEELRADVADVIQKLWVVF
+EKEDATLVEVNPLVKTGDGKILALDGKVSLDDNAEFRHEGHAALVDERTEDPLEAKAKAN
+DLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEQHGGVKPANFLDIGGGANAEVMANGLD
+VILGDEQVKSVFVNVFGGITACDAVANGIVKALEILGDAATKPLVVRLDGNAVEEGRRIL
+QEANHPLVTLAATMDEGADKAAELAHSAN
+>3_2394
+MDLYEYQARDLFEKHGVPVLQGIVAETPEEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVNKVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSALTGLDQATADTIVAEAGFPEELRADVAAVIVKLGEVF
+KNEDATLVEVNPLVKTGDGTILALDGKVSLDDNAEFRQADHAGLVDKTTEDPLEAKAKAN
+DLNYVKLDGQVGIIGNGAGLVMSTLDVVAYAGENHGGVKPANFLDIGGGANAEVMAAGLD
+VILGDEQVKSVFVNVFGGITACDAVANGIVKALEILGDSATKPLVVRLDGNAVEEGRRIL
+QEADHPLVTLAATMDEGADKATELAHSAN
+>4_357
+MDLYEYQARDLFEAHGVPVLAGIVAQTPDEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVHRVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSALTGIDAETAQKIVAEAGFPEELRADVAEVIQKLWEVF
+EKEDATLVEVNPLVKTGDGTILALDGKVSLDDNAAFRHEGHAALVDERTEDPLEAKAKAN
+GLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEKHGGVKPANFLDIGGGANAEVMANGLD
+VILGDEQVKSVFVNVFGGITACDAVANGIVKALEILGDTATKPLVVRLDGNAVEEGRRIL
+QEANHPLVTLAATMDEGADKAAELAHSAN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000417.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000417.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0dbd57cb64413cc83f78cd200524d222935015b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000417.fa
@@ -0,0 +1,35 @@
+>0_351
+MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL
+PVFGTVKEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDTAEFFAL
+SQSKTGEDGKPKTRIIGPNCPGVITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE
+LRDFGFSTAIGIGGDPVIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV
+TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE
+ILQAQA
+>1_76
+MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL
+PVFGTVKEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDTAKFFAL
+SQSKTGEDGKPKTRIIGPNCPGIITPGEALAGITPATITGTGPIGLVSKSGTLTYQMMYE
+LRDFGFSTAIGIGGDPIIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV
+TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE
+ILEG
+>2_2534
+MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL
+PVFGSVTEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDSAKFFAL
+SQSKTGEDGKPKTRIIGPNCPGVITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE
+LRDFGFSTAIGIGGDPVIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV
+TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE
+ILQAQA
+>3_2393
+MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDEDGNAVEL
+PVFGSVAEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDSAEFFAL
+SQSKTGEDGKPKTRIIGPNCPGIITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE
+LKDFGFSTAIGIGGDPVIGTTHIDALEAFEADPETKAIVMIGEIGGDAEERAAEFIKANV
+TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETADLMRE
+IMKGL
+>4_358
+MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL
+PVFGTVKEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDSAEFFAL
+SQSKTGEDGKPKTRIIGPNCPGIITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE
+LRDFGFSTAIGIGGDPVIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV
+TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE
+ILQAQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000422.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000422.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d63feca2be8e2a91696ab97e3f3f894dc09e8a0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000422.fa
@@ -0,0 +1,20 @@
+>0_359
+MDAAETPDGPETAAHDGGRPAWQHRLLAGGEEPDPRFTLANERTFLAWVRTALALLAGGV
+AVEAFTGALFAPPVRVVLSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA
+GGVVLAVVVLLAAVVLPRG
+>1_92
+MDAAETPDGPETAAHDGGRPAWQHRLLAGGEEPDPRFTLANERTFLAWVRTALALLAGGV
+AVEAFTGALFAPPVRVVLSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA
+GGVVLAVVVLMLAVVLPRG
+>2_2519
+MDAAETPEGPEATAYDGGRPAWQHRLLAGGDEPDPRFTLANERTFLAWVRTALALLAGGV
+AVEAFTGALFAPPVRVALSTVLLVLAALLAVGAGARWLRVERAMRRGRPLPLPLIVPVLA
+GGVVLAVVVLMLAVVLPRG
+>3_2391
+MDAAETPDGPEAAAYDGGRPAWQHRLLAGGDEPDPRFTLANERTFLAWVRTALALLAGGV
+AVEAFTGALFAPPVRVALSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA
+GGVVLAVVVLMLAVVLPRG
+>4_365
+MDAAETPDGPETAAHDGGRPAWQHRLLAGGEEPDPRFTLANERTFLAWVRTALALLAGGV
+AVEAFTGALFAPPVRVVLSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA
+GGVVLAVVVLLAAVVLPRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000423.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000423.fa
new file mode 100644
index 0000000000000000000000000000000000000000..361f7f1f0bf6ce890d72075573fd29a9ab4f68c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000423.fa
@@ -0,0 +1,15 @@
+>0_360
+MRLHHDPGLQPERTVMSWGRTALALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAHADGIAREQARPALASVACMVALVVGLAALGITATLLHAA
+>1_93
+MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAHADGIARERARPALASVACMVALVVGLAALGITATLLHAA
+>2_2518
+MRLHHDPGLQPERTVMSWGRTVLALGVLSLMFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAQSRGIAGEWARPALASVAGMVALVVGLAALGITATLLHAA
+>3_2390
+MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAQADGIAREQARPALASVACMVALVVGLAVLGITATLLHAA
+>4_366
+MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAHADGIAREQARPALASVACMVALVVGLAALGITATLLHAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000428.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000428.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30083b8e99471b1a052715624157477da0c39b4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000428.fa
@@ -0,0 +1,20 @@
+>0_367
+MTQQHHDTDDAPSMQRPDPVAEPGDHLMFEHPDGEAVLVLDEDQVWRLLGRVGHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGPHPERNESQTD
+>1_100
+MTQQHHDTDDAPSMQRPDPVAEPGDHLMFEHPDGEAVLVLDEDQVWRLLRRVRHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGPHPERNESQTD
+>2_2512
+MTPQHHDTADAPSMQRPDPVAEPGDHLMFEHPDGEPVLVLDEDQVWRLLRRVRHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGTHPERNESQTD
+>3_2383
+MTEHTTPSMQRPDPAVGPGSMFPHPEGEPVLKLTDEQIWKLMRGVRHARLGLAVGGEPDI
+VPVNVRAVDGVVWFRTAPGSKLAELTVNPRVVVQADGILSDQAWSVLLHGTARRADTAEE
+IAEAESMGIRPWVPTIKDFYVKVEVDSATGRHFLLGEQPERDGAEPTD
+>4_373
+MTQQHHDTDDAPSMQRPDPVAEPGDHLMFEHPDGEAVLVLDEDQVWRLLGRVGHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGPHPERNESQTD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000432.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000432.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9eb932d47ff7144ffd5874ebc4c06f3a0c76850a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000432.fa
@@ -0,0 +1,37 @@
+>0_372
+MTLLSDHSRALLPGRGPLLCAADPHDGAARRRLERAWTRGVLVRLCPRVYISVSDWAALR
+PWDRTVVSAVALSIARPETVFTGLTAARLHGLGPAVEPPALELRAPSPGHHGAGPLTRRP
+FAPSLMAHDRRPPGLPRRRPRWGLPEADPAAPQRVEAVLSDGQSLGTVLADPLPTVLLVL
+GAATPFRDAVATLDALVRARPEEAARWARQAESRLGSAAALRRFERAWHFADARAESAGE
+SYSRAIVHELGFVPPTALQHRHRDANGREVARTDFWWEQVRVYGEFDGLGKYDLSFFDGD
+DTARRASIRREKEREVALQLVTRAGAHWTWGDLLRPDRLARILTAAGVPRSV
+>1_105
+MTPLSDHSRALLPGRGPLLSAADPHDGAARRRLERAWTRGVLVRLSPRVYISVSDWAALR
+PWDRAVVSAVALSIARPATVFTGLTAARLHGLGPAVEPPALELRAPSPGHHGCGPLTRRP
+LAPSLVAHDRRLPVPPRRRPRWGLPEAAPTGPQPVEAVLSDGQSLGTVLADPLPTVLLVL
+GAATPFRDAVAPLDALVRAWPEEAARWARQAESRLGSAAALRRFERAWHFADARAESAGE
+SYSRAIIHELGFVPPTALQHRHRDANGRGVARTDFWWEQVRVYGEFDGLGKYDLSFFDGD
+DTARRASIRREKEREVALQLVTRAGAHWTWGDLLRPDRLARILTAAGVPRSV
+>2_162
+MDDAPDPRLAPLRHDGHLLPGHGPLLRAAPGAPTRARKALARLWAQGVLVRLGAGLYVPL
+AHWCALAPWDRYTLACAGYALLHPAARFTGTTAAHLHGLPLAQTPPEIRLRSPAPGHRAR
+RPLAASAFSDLADARGRRLPAPPAVRWTWNGVQAPADDGGELRRRRLASGGPEGEAPPPG
+PLPPVTVEAALSDGTLLGPVTVDALPTVQLALGSGPVFREAVVPLDGLRRRLPGPSAAWA
+ERHADRLPTRAARERFERAWGFSDPRAESAGESLSRALIHELGFAAPHLQRTVFGRDGRA
+IGRTDFWWEEVDVVGEFDGIGKYDVDLHASAAERRQAITREKEREVALRRVCRDVARWTW
+ADLREPAGLEAELVRAGVPRRR
+>2_2507
+MTALADVADLRPGTGPLLHVARREDLAARRRLERAWTRGDLVRLAAGVYLPAPTWTALSP
+WDRSTASAAALALARPATVFTGLTAARLRGLPVALELPALDLRATSPGHRGAAPLTSRPF
+SPALLATGGRLPRPPRRRPRWGLPQAPGMAPEPVEIRLSDGTGLGWGLADASATLLLVLG
+AATPFRNAVAPLDVLLATHPEAQSWAQAAEEALPTRAARERFERTWSFAAAGSESAGESY
+SRALMHELGFASPTALQHRHRDATGREVARTDFWWADARVAGEFDGIGKYDLGLHRGDDA
+ARRASIRREKEREVALQLVTRAVAHWTWEDLRAPERLARILTAAGVPRTVCPEPTDAQRH
+HRRAERR
+>4_378
+MTLLSDHSRALLPGRGPLLSAADPHDGAARRRLERAWTRGVLVRLCPRVYISVSDWAALR
+PWDRAVVSAVALSIARPATVFTGLTAARLHGLGPAVEPPVLELRAPSPGHHGAGPLTRRP
+LAPSVVAHDRRLPVPPRRRPRWGLPEAAPAAPQPVEAILSDGQSLGTVLADPLPTVLLVL
+GAATPFRDAVAPLDALVRARPEEAARWARQAESRLKSAAALRRFERAWHFADARAESAGE
+SYSRASIHELGFVPPTALQHRHRDANGREVARTDFWWEQVRVYGEFDGLGKYDLSFFDGD
+DTARRASIRREKEREVALQLVTRAGAHWTWGDLLRPDRLARILTAAGVPRSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000434.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000434.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea559437868b443829788d8dcbf8eb85d9a3360b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000434.fa
@@ -0,0 +1,40 @@
+>0_375
+MRVVVVAESFLPHMNGVTNSILQVLRHLRERGDEAMVVAPAASWSAGWTQRAGAGEAPRE
+VEGFPVRTLPSVPLTGYTSVRVAAGTVGRLRGMLADFAPDVVHIASPFVLGWRAVQAAEE
+LGIPSVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNMATLTLAPSSFTVRQLHRQGVR
+RVHLWGRGVDSRRFHPAKRDEALRAELAPNGEKLVGFVGRLAHEKQVGDLRVLSDLPGTR
+LVVIGSGPLREQLERELPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS
+GVPVVAVGRGGPLDIVDASRTGWLYPPGELDELRRHVADLVYDDVKRAAFADAAWASVQG
+RTWPVLCEQLMGYYEKAIAVQERRRVELARRLLTAPALLAARVFG
+>1_108
+MRVVVVAESFLPHMNGVTNSLLQVLRHLRERGDEAMVVAPAASWSAGWTQRAGAGEAPRE
+VEGFPVRTLPSVPLTGYTSVRVAAGTVGRLRGMLADFAPDVVHIASPFVLGWRAVQAAEE
+LGIPSVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNMATLTLAPSSFTVRQLHRQGVR
+RVHLWGRGVDSRRFHPAKRDEALRAELAPNGEKLVGFVGRLAHEKQVGDLRVLSDLPGTR
+LVVIGSGPLREQLERELPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS
+GVPVVAVGRGGPLDIVDASRTGWLYPPGELDELRRHVADLVYDDVKRAAFADAAWASVQG
+RTWPVLCEQLMGYYEKAIAVQERRRVELARRLLTAPALLAARVFG
+>2_2505
+MVAESFLPHMNGVTHSILQVLRHLRERGDEAIVIAPAASWSAGWTQRAGEGQAPREVEGF
+PVHALPSVPLSGYSSVRVAAGTVGRLRGILTAFGPDVVHIASPFVLGWRAVQAAEELGIP
+SVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNTATLTLAPSSFTVRQLHAAGLRRVHL
+WGRGVDTRRFHPVKRDDALRAELAPHGERLIGFVGRLAHEKQVEDLRVLSDLPGTRLVVI
+GSGPLREQLERRLPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMASGVPV
+VAVGRGGPLDIVDPSRTGWLYPPGELDELRRHVADLAHDDVKRSAFAQAAWASVQGRTWP
+VLCEQLVGCYEKAVAVQDRRRRELARRLLAMPSQLTARVFG
+>3_2376
+MRVAVIAESFLPHMNGVTNSILQVLKHLRSRGDEAVVIAPAASWSAGWTQRAGAGQAPSE
+VEGFPVITLPSMPLSGYASVRVAAGTVLRLRSLLADFAPDVVHIASPFVLGWRAVQAAEE
+LGIPSVAVYQTEVPRYAAKYGAPWLEDVLWNHVTRLHNTATLTLAPSSFTLRQLHHVGVR
+RVHLWGRGVDSTRFHPAKRDEALRAELAPNGERLIGFVGRLAHEKQVADLRVLADLPDTR
+LVIIGSGPLRDQLERRLPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS
+GVPVVAVGRGGPLDIVDSSRTGWIYQPGDLGELRARVADLAYDDAKRAAFAEAAWASMQG
+RTWPVLCEQLVGYYEKAIHVQRRRRGELSRRLLGAPGAVASRAYRVFG
+>4_381
+MRVVVVAESFLPHMNGVTNSILQVLRHLRERGDEAMVVAPAASWSAGWTQRAGAGEAPRE
+VEGFPVRTLPSVPLTGYTSVRVAAGTVGRLRGMLADFAPDVVHIASPFVLGWRAVQAAEE
+LGIPSVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNMATLTLAPSSFTVRQLHRQGVR
+RVHLWGRGVDSRRFHPAKRDEALRAELAPNGEKLVGFVGRLAHEKQVGDLRVLSDLPGTR
+LVVIGSGPLREQLERELPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS
+GVPVVAVGRGGPLDIVDASRTGWLYPPGELDELRRHVADLVYDDVKRAAFADAAWASVQG
+RTWPVLCEQLVGYYEKAIAVQERRRVELARRLLTAPSLLAARVFG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000436.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000436.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff7efac1cd2fe50fa504e9e0b140b96da9907931
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000436.fa
@@ -0,0 +1,19 @@
+>0_377
+MSAPVPSSPPRPPQGAPDPGRVRTGRALLWQSVALLGMVLSFSLVLPWKLIALALGLVAL
+VLGVRVWVTSRGAERSGLPRAVASAGMAMALMGMTTAALPLLAWDATVQLEQCGASALTV
+RAQQACADEFTRQVEERTGVPQLRP
+>1_110
+MSAPVPSSPPRPPQGAPDPGRVRTGRALLWQSVALLGMVLSFSLVLPWKLIALALGLVAL
+VLGVRVWVTSRGAERSGLPRAVASAGMAMALMGMTTAALPLLAWDATVQLEQCGASALTV
+RAQQACADEFTRQVEERTGVPQLRP
+>2_2503
+MVLSLSLVLPWKLAALVLGLVALVLGVRVWLTSRGERRAGLPRAVAAGGMALALFGTTTA
+ALPLLAWDATVELERCTSSALTVRAQQACADAFTRAVEERTGVPQLRP
+>3_2374
+MSALPPVPPSAPDRRPADAAARARVGRLLVAQSAALLAMLGAFTLVLPFKVLTLAAALAA
+LVLGVLVFTASRRTAQSLVPRAAAGAGMALALMGLTVGVFPLLLWNETAGFERCTASAVT
+VRAQQTCADDFTATVERRTGVAQLGG
+>4_383
+MSAPVPSSPPRPPQGAPDPGRVRTGRALLWQSVALLGMVLSFSLVLPWKLIALALGLVAL
+VLGVRVWVTSRGAERSGLPRAVASAGMAMALMGMTTAALPLLAWDATVQLEQCSASALTV
+RAQQACADEFTRQVEERTGVPQLRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000438.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000438.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6d73007ec6d84be25e8952a6539bb85f372bbf5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000438.fa
@@ -0,0 +1,45 @@
+>0_379
+MSSATPPRPSADGAHPGPAPDVVAPDAALPTGEAVVQELPWRWSVQGRIFLIGGLGFMFD
+AWDVTLNGVMIPLLREEWALDKADAAWIGTANLIGMAVGAFLWGTIADRIGRKAAFAWTL
+AIFSVFTIAGALTDSLLWFALFRFVAGMGLGGTIPVDYALVGEFTPRRLRGRVLAAMDGW
+WPVGAALCGLVSAWLVGTWGDWRLPLLAMVLPALLVFVVRLGIPESPLFLMSRGREAQAR
+AVIDRMVAATGAPRRPYTMPPAEPARSSGVGAQLAAVWRFSPRITAVAWALFVAIMLVYY
+IALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATALIEVTGRRWLLAVSAVVASA
+LTVWLASVLDVPAAVLPLVLTFGFVVQVAIPVLYTYVSELYPTTLRASGFGWASAASRVG
+AGLGPLLFVGTLVPALGLPGAFAVTGGLVVLACAAMLALAPETRGRALEVSAD
+>1_112
+MSSATPPRPSADGAHPGPTPDVVSPDAALPTGEAVVQELPWRWSVQGRIFLIGGLGFMFD
+AWDVTLNGVMIPLLREEWALDKADAAWIGTANLIGMAVGAFLWGTIADRIGRKAAFAWTL
+AIFSVFTIAGALTDSLLWFALFRFVAGVGLGGTIPVDYALVGEFTPRRLRGRVLAAMDGW
+WPVGAALCGLVSAWLVGTWGDWRLPLLAMVLPALLVFVVRLGIPESPLFLMSRGREAQAR
+AVIDRMVAATGAPRRPYTMPPAEPARSGGVGAQLAAVWRFSPRITAVAWALFVAIMLVYY
+IALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATALIEVTGRRWLLAVSAVVASA
+LTVWLASVLDVPAAVLPLVLAFGFVVQVAIPVLYTYVSELYPTTLRASGFGWASAASRVG
+AGLGPLLFVGTLVPALGLPGAFAVTGGLVVLACAAMLALAPETRGRALEVSAD
+>2_2501
+MQGRIFLIGGLGFMFDAWDVALNGVMIPLLREEWALAPADAAWIGTANLIGMAVGAFLWG
+TIADRIGRKAAFAWTLAIFSVFTLAGALTDSLLWFAVFRFVAGVGLGGTIPVDYALVGEF
+TPRRLRGRVLAAMDGWWPVGAALCGLVSAWLVGTWGDWRLPLLAMVLPALLVFVVRLGIP
+ESPLFLMSRGREAEARKVIDRMVEATGAERREYVMPPVEQERAGGVLAQLAAVWRFSPRI
+TAVTWALFVAIMVVYYIALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATVLIEV
+TGRRWLLGVSAVVASALLVWLASVLGVPSAVLPLVLAFGFVVQIAIPVLYTYVSELYPTT
+LRASGFGWASAASRVGAGLGPLFFVGTLVPAMGLPAAFAVTGGLVLLACVAMLALAPETR
+GRALEVSAD
+>3_2371
+MPPTGSHAASAAPTGEQVVQELPWRWPVQGRIFLIGGLGFMFDAWDVTLNGVMIPLLTEE
+WGLSKADAAWIGTANLIGMAVGAFLWGTVADQIGRKAAFTWTLLIFSVFTLAGALTDSLL
+WFAVFRFMAGIGLGGTVPVDYALVGEFTPRRLRGHVLTAMDGWWPIGAALCGVVSAWLVG
+TWSDWRLPLLAMVLPALLVFLVRLGIPESPLYLMSRGREREARAVIDRMVERTGAEPRPY
+VMPAADSRAHGGLLAQLAAVWRFSPRITATAWLLFVAVMLIYYIALQWLPTFLIEAGFAQ
+SRAFITTSGMAAAGLVGVAVSAVLVEATGRRRLLAVSGVVASGLLVWLASVLGVPGAALP
+LVLAYGFVIQIAVPVLYTYVSELYPTTLRASGFGWASAASRVGAGLGPLFFVGTLVPALG
+LPGAFGVTAGLVVVAVLVMFAWAPETRGRALEVAED
+>4_385
+MSSATPPHPSADGAHPGPTSDVVAPDATLPTGEAVVQELPWRWSVQGRIFLIGGLGFMFD
+AWDVTLNGVMIPLLREEWALDKADAAWIGTANLIGMAVGAFLWGTIADRIGRKAAFAWTL
+AIFSVFTIAGALTDSLLWFALFRFVAGMGLGGTIPVDYALVGEFTPRRLRGRVLAAMDGW
+WPVGAALCGLVSAWLVGTWGDWRLPLMAMVLPALLVFVVRLGIPESPLFLMSRGRETQAR
+AVIDRMVAATGAPRRPYTMPPAEPARSGGVGAQLAAVWRFSPRITAVAWALFVAIMLVYY
+IALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATALIEVTGRRWLLAVSAVVASA
+LTVWLASVLDVPAAVLPLVLTFGFVVQVAIPVLYTYVSELYPTTLRASGFGWASAASRVG
+AGLGPLLFVGTLVPALGLPGAFAVTGGLVVLACAAMLALAPETRGRALEVSAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000445.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000445.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dfeb1e27123908730dc22857003056d478be788a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000445.fa
@@ -0,0 +1,45 @@
+>0_390
+MRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTNPDDGGQAKIAAQCTDAA
+NGRYRVETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFVPELAEPGFLAPVPEEMQ
+AYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAAGLDMSQPVTWDQLIEAA
+RSQDKDLAVQGARAESMTVWLNALIEGGGEQIVPNAEAPTDEVTTNLDSEAGRTAARIIS
+TIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATLGSVEEGSLPEDLPEDIG
+WAVYPRTVEGEDAAPPVGGINLGVGAKSEHQDLAWDAISCITTTEHQSQYFVENGNPPAD
+PAAYDAPEVAEKYPMADTIRESLELGAPRPQTPYYNEVSTAIQQRYAPPSGVSESTPAET
+DDFIQEVLRGERLL
+>1_119
+MRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTNPDDGGQAKIAAQCTDAA
+NGRYRVETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFVPELAEPGFLAPVPEEMQ
+AYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAAGLDMSQPVTWDQLIEAA
+RSQDKDLAVQGARAESMTVWLNALIEGGGEQIVPNAEAPTDEVTTNLDSEAGRTAARIIS
+TIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATLGSVEEGSLPEDLPEDIG
+WAVYPRTVEGEDAAPPVGGINLGVGAKSEHQDLAWDAISCITTTEHQSQYFVENGNPPAD
+PAAYDAPEVAEKYPMADTIRESLELGAPRPQTPYYNEVSTAIQQRYAPPSGVSESTPAET
+DDFIQEVLRGERLL
+>2_2492
+MRHDTRARQRRRATLAGAVVAGALILAGCAPAEQTPTLTWYTNPDDGGQAKIAAQCTDAA
+NGRYRIETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFVPELAEPGFLAPVPEEMQ
+AYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAAGLDMSQPVTWDQLIEVA
+RSQDKDLGVQGARAESMTVWLNALIEGGGEQIIPNAEAPTDEVTTNLDSEAGRTAARIIS
+TIGKEGLGSAGLPTQDENASMLLFQGNNGSFMVNWPFVWPATLGSVEEGSLPEDLPEDIG
+WAVYPRTVEDKDAAPPVGGINLGVGEKSEYQDLAWDAISCITTTEHQSQYFVENGNPPAD
+PAAYDAPEVAEKFPMADTIRESLELGAPRPQTPYYNEVSTAIQQRYAPPSGVSESTPAET
+DDFIQEVLRGERLL
+>3_2360
+MGDDGRHIRLASNEVPLVRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTN
+PDDGGQAKIAAQCTDAANGRYRIETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFV
+PELAEPGFLAPVPEEMQAYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAA
+GLDMSKPVTWDQLIEVARSQDKDLGVQGARAESMTVWLNALIEGGGEQIIPNAEAPTDQV
+TTNLDSEAGRTAARIISTIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATL
+GSVEEGSLPKDLPEDIGWAVYPRTVEDKDAAPPVGGINLGVGAKSEHQDLAWDAISCITT
+TEHQSQYFVENGNPPADPAAYDAPEVAEKFPMADTIRESLELGAPRPQTPYYNEVSTAIQ
+QRYAPPSGVSESTPAETDDFIQEVLRGERLL
+>4_393
+MRDDGRHIRLASIEVPLVRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTN
+PDDGGQAKIAAQCTDAANGRYRVETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFV
+PELAEPGFLAPVPEEMQAYAKDNALEGALAAASWKDEIVTVPFWANTQLLWYRKSVAEAA
+GLDMSQPVTWDQLIEAARSQDKDLAVQGARAESMTVWLNALIEGGGEQIVPNAEAPTDEV
+TTNLDSEAGRTAARIISTIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATL
+GSVEEGSLPEDLPEDIGWAVYPRTVEGKDAAPPVGGINLGVGAKSEHQDLAWDAISCITT
+TEHQSQYFVENGNPPADPAAYDAPEVAEKYPMADTIRESLDLGAPRPQTPYYNEVSTAIQ
+QRYAPPSGVTESTPAETDDFIQEVLRGERLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000447.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000447.fa
new file mode 100644
index 0000000000000000000000000000000000000000..387b29c3e22ea5a031f90559d384eb66042db84f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000447.fa
@@ -0,0 +1,45 @@
+>0_393
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDITDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPSEEEIDRKVRD
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGELQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKQKEGGHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDRGSTFDATLTHLEWLGHEQYGYIEFDPDPAVAEMLSSLAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPTTGENLTRDPEVGAELTRRAAEERRRQIEMAAERDA
+AEHEADAPRR
+>1_122
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDITDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPSEEEIDRKVRD
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGELQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKQKEGGHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDRGSTFDATLTHLEWLGHEQYGYIEFEPDPAVAEMLSALAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPTTGENLTRDPEVGAELTRRAGEERRRQIEMAAERDA
+AEHEADAPRR
+>2_2489
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDISDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPAEEEIDRKVRN
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGVLQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKEKDGVHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDQGSTFDATLTHLEWLGHEQYGYIEFDPDPAVAEMLSSLAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPKTGENLTRDPEVGAELTRRAAEERRRQIEVAAERDA
+AADREAADTRR
+>3_2357
+MASITLNHIEKTYDDGYHAISDVNLDIEDGEFVILVGPSGSGKSTLLRMIVGLEDISGGD
+LLIDGRRVNEAAPKDRNLAMVFQNYALYPHLSVYENIAFPLRLAKDGKLSEEELDRKVRD
+AARVLELQDHLDRKPANLSGGQRQRVAMGRAIVRDADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGVLQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPATVKEQGGQYVLSSPIGDIPVPAEKAQRAAGRDIVFMGLRPEFFEDAELVEDA
+KRPHGSEFDATLTHLEWLGHEQYGYIEFEPDPEVAELLSSLAKDLDADELRPVVVTTLSA
+ESAARPGVPTRLWVDTTRVHLFDPKTGENLTRDAEAGAELTRRTAEARRRQIEAAQARDA
+EGR
+>4_396
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDITDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPSEEEIDRKVRD
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGELQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKQKEGGHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDRGSTFDATLTHLEWLGHEQYGYIEFEPDPAVAEMLSALAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPTTGENLTRDPEVGAELTRRAGEERRRQIEMAAERDA
+AEHEADAPRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000448.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000448.fa
new file mode 100644
index 0000000000000000000000000000000000000000..221fa1e7d1fd6c654f4fd38e801b92c54dceab65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000448.fa
@@ -0,0 +1,20 @@
+>0_395
+MAHIITVAGATPRIHESVFLAPTAAITGDVEMAERSSAFYGVSARGDSAPIRVGAGTNLQ
+DNVVLHADEGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA
+LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKKNAATYLRLSAAHRDAVAG
+>1_124
+MAHIITVAGATPRIHESVFLAPTAAITGDVEMAERSSAFYGVSARGDSAPIRVGAGTNLQ
+DNVVLHADEGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA
+LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKKNAATYLRLSAAHRDAVAG
+>2_2488
+MAHIITVAGAGPRIHESVFLAPTAAITGDVEMAERSSAFYGVSARGDSAPIRVGERTNLQ
+DNVVLHADKGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA
+LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKVNAATYLELSAAHREATAER
+>3_2356
+MGHLVTVLGRTPRVDPSAFVARTAVLSGDVELGPRASAFYGVSARGDSAAIRVGEGSNLQ
+DNVVLHADAGFPCTLGAGVSVGHAAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA
+VVLEGTQVPPGSLVAGVPAKVRRGLTEEERASLTVNARTYLDLAAAHRAAEEAEQAGV
+>4_398
+MAHIITVAGATPRIHESVFLAPTAAITGDVEMAEHSSAFYGASARGDSAPIRVGAGTNLQ
+DNVVLHADEGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA
+LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKKNAATYLRLSAAHRDAVAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000450.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000450.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff261b6e9fd3e2ff1232fb99450618635dd6dbc1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000450.fa
@@ -0,0 +1,50 @@
+>0_398
+MTEYQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR
+PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL
+RFYSEEGNYDLVGNNTPIFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH
+QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA
+GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG
+TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP
+VNRPKNAVHNYAFDGQMWYDHTGDRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA
+LRADDDDFGQAGTLVREVFSAQEREDFVETVAGALKGVRQDVQARAFEYWKNVDTAIGQR
+IEDEVKRHEGDGIPGVEAGGEARI
+>1_128
+MTEYQKKTPHATGSTRQNGAPAISDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR
+PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL
+RFYTEEGNYDIVGNNTPIFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH
+QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA
+GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG
+TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP
+VNRPKNAVHNYAFEGQMWYDHTGDRSTYVPNSNGDSWSDETGPVDDGWEADGTLTREAQA
+LRADDDDFGQAGTLVREVFSDQERDDFVETVSGALKGVRQDVQARAFEYWKNVDATIGQR
+IEDEVKRHEGDGIPGVEAGGEARI
+>2_2484
+MTENQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLVETHQHFNRMNIPERR
+PHAKGSGAFGEFEVTEDVSKYTKALVFQPGAKTETLLRFSTVAGELGSPDTWRDVRGFAL
+RFYTDEGNLDVVGNNTPVFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNTPESAH
+QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNFSNEEAEAMA
+GKNADYHRQDLFESIAKGDYPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG
+TLTLNRNPENHFAQIESAAFNPGNMVPGVGLSPDRMLLGRSFAYHDAQLYRVGAHVNQLP
+VNRPKNEVHNYAFDGQMWYDHTGSRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA
+LRKDDDDFGQAGTLVREVFTDAERDAFVETVAGALDGVREDVQARAFQYWKNVDATIGQR
+IEDEVNKGQGDDIPGAAGGGEARI
+>3_2353
+MTEYQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR
+PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL
+RFYSEEGNYDIVGNNTPVFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH
+QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA
+GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISQKDYPRIKVG
+TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP
+VNRPKNAVNNYAFDGQMWYDHTGDRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA
+LRADDDDFGQAGTLVREVFSDQERDDFVETVAGALKGVRQDVQARAFEYWKNVDATIGQR
+IEDEVKRHEGDGIPGVEAGGEARI
+>4_401
+MTEYQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR
+PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL
+RFYSEEGNYDLVGNNTPIFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH
+QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA
+GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG
+TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP
+VNRPKNAVHNYAFDGQMWYDHTGDRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA
+LRADDDDFGQAGTLVREVFSAQEREDFVETVAGALKGVRQDVQARAFEYWKNVDTAIGQR
+IEDEVKRHEGDGIPGVEAGGEARI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000455.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000455.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18ccc35ef1ede2dd89b46d1546ff43634c8bd97e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000455.fa
@@ -0,0 +1,25 @@
+>0_404
+MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL
+VFAVVVYLQMRRGVRAAGRKVDTAMQNARADVAALRGREADAAAPAVAPPAPAADPLRDT
+KLDHSFKIAQVQVRVVREQLAAGAGMDREMVDRALETIDITASNARDMIKESRAGGAEGP
+VSGTVIG
+>1_134
+MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL
+VFAVVVYLQMRRGVRAAGRKVDTAMQNARADVAALRGREADAAAPAVAPPAPAADPLRDT
+KLDHSFKIAQVQVRVVREQLAAGAGMDREMVDRALETIDITASNARDMIKESRAGGAEGP
+VSGTVIG
+>2_2476
+MSQPLTTGSGETRRGPRAGLRVGSVGFAAMIVILIVAIMFAANQNDVIGWLVVAVAAGWL
+VFALVVFLQMRRGVQAAGRKVDAAMENARADVAALRGQGAAAAPQAAAHAPAGDPMRDTK
+LDHSFKIAQVQVKVVREQLAAGGAMDREMVDRALETIDITAANARDMIKESRGQGGSEGP
+VSGTVIG
+>3_2346
+MPQSIPSGSAGTRPARAGLTVGSTGFAVMVAVLLVAIVFAANANDLIGWLVVAIAAGWLV
+FAVVVFLQMRKGVREAGRKVDTAMQNARADVAALRAPQQPAPAAAVPAAAGDPMRDTKLE
+HSFKICQVQARVITQQLDAEGPLDREMVDRALETITITAQNARDMIKESARDAEGPVSGT
+VVS
+>4_407
+MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL
+VFAVVVYLQMRRGVQAAGRKVDTAMQNARADVAALRGRDADAAAPAVAPSAPAADPLRDT
+KLDHSFKIAQVQVRVVREQLAAGESMDREMVDRALETIDITASNARDMIKESRAGGAEGP
+VIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000457.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000457.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca7207ee5489b84d4045d0ed7e1e6321b3492d18
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000457.fa
@@ -0,0 +1,35 @@
+>0_406
+MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD
+FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV
+LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH
+VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP
+KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSGTPIPQLEEEFVGKMYGHLKV
+AVADAVVERLAPVRERALALLDDPAELDRILAAGAEKARAVATPVLEDVYAKVGFLPPLR
+>1_136
+MTMKKNSVQDVLAQDAAATAHLPGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD
+FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV
+LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH
+VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP
+KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILAAVSGTPIPQLEEEFVGKMYGHLKV
+AVADAVVERLAPVRERALELLADPAELDRILASGAEKARAVATPVLEDVYAKVGFLPPLR
+>2_2474
+MKKNSVQDVLAQDVSATAHLAGASDRHRVLSGMQPSADSLHLGNYLGALTNWVRTQDDFE
+AFFFIPDLHAITVPQDPAALAQRTRVAAAQFIAAGIDPERSTLFVQSQVPEHAQLAWVLT
+CMTGMGEAMRMTQFKDKSAKQGAEAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQHVE
+LTRDLAQRFNHRHGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINVMDDPKR
+TAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAMTDVPVAELEGRYVGRMYGHLKVDV
+ADAVVERLAPVKARTEELLADPAELDRILAAGAAKARAVATPVLEDVYAKVGFLPPLR
+>3_2344
+MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD
+FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV
+LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH
+VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP
+KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSDRPIPELEAEFEGKMYGHLKV
+AVADAVVERLAPVRERALGLLDDPAELDRILAAGAAKAREVATPVLEDVYARVGFLRPLR
+>4_409
+MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD
+FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV
+LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH
+VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP
+KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSGTPIPQLEEEFVGKMYGHLKV
+AVADAVVERLVPVRERALALLADPAELDRILAAGAEKARAVATPVLEDVYAKVGFLPPLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000459.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000459.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89aa919c90c993b80222713dcaa5b8f1ed095dff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000459.fa
@@ -0,0 +1,45 @@
+>0_408
+MKATDVAGTALANTMRSKLRTFLTVVAIVIGAFTLTLTTGLGAGINKYVDNVVEGFGKPG
+ELTVMKQQDMSSAGAASGSPQEYAEQDAAGGEMFGMPLLTQEDLAAIEDTEHVTEVKTYR
+VAEPEYIQGPDDRKWQTGFMGSSGEIDMLTFSAGRAPEAGAAEIVMPESWVEDLGAGDAE
+DLVGTELTVVAATPLQEHKSVTATVVGVTKAAASGAGTAPTPSESLEQEIYDITTEGLPE
+SQRDTYFQATAIVADPEANEDAVKQALADQGLLAQTLEEQLGVIRGIIDAVTWVLTGFAL
+IALLAASFGIINTLLMAVQERTREIGLMKALGMTGGKIFGLFTMEAVVIGLLGSLVGIGL
+GVAVGLIANQVLTTGPLSGVTGLVLFAVNPLALLLILLLIVAIAFIAGTLPALRAARKDP
+IEALRHE
+>1_138
+MKATDVAGTALANTMRSKLRTFLTVVAIVIGAFTLTLTTGLGAGINKYVDNVVEGFGKPG
+ELTVMKQQDMSSAGAASGSPQEYTEQDAAGGEMFGMPLLTQEDLAAIEDTEHVTEVKTYR
+VAEPEYIQGPDDRKWQTGFMGSSGEIDMLTFSAGRAPEAGAAEIVMPESWVEDLGAGDAE
+DLVGTELTVVAATPLQEHKSVTATVVGVTKAAASGAGTAPTPSESLEQAIYDITTEGLPE
+SQRNTYFQATAIVEDPEANEDAVKQALADQGLLAQTLEEQLGVIRGIIDAVTWVLTGFAL
+IALLAASFGIINTLLMAVQERTREIGLMKALGMTGGKIFGLFTMEAVVIGLLGSLVGIGL
+GVAVGLIANQVLTTGPLSGVTGLVLFAVNPLALLLILLLIVAIAFIAGTLPALRAARKDP
+IEALRHE
+>2_2472
+MKATDLAGTALANTMRAKLRTFLTVVAIVIGAFTLTLTSGLGAGINKFVDNMVEGFGSPD
+QLTVMKQVDPTSFAAGGAPQEYEPDEAAAGEMFGLPLLTAADLDRIRDTEHVTEVETARL
+VEPEYIEGEDGRQWQVPFMGSSFEIGALSLAAGREPAADAAEVTVPQDWVEALGGQTPED
+VLGQTVTLVAADPLGKQDGVEAEVVGVTEPMASGSGSGPVPSGEVETRLHEIQTAGLPEA
+QRDTFFSASVTVADMAANEAAVKAALAEEGYSAQTLEDQLGPIRGIIDAVTWVLNGFALI
+ALLAASFGIINTLLMAVQERTREIGLMKALGMTGRKIFGLFTMEAVVIGLLGSLIGVGLG
+VAVGVVANQVLTEGALSGVTGLVLYAVEPLSLALIVLLIVAIAFLAGTLPAARAARKDPI
+EALRYE
+>3_2342
+MKAPDLIRTALGNTARAKLRTFLTVIAIMIGAFTLTLTSGLGAGINKYVDNMVAGFGAPD
+ELTVSKPAGNQMAGMTGGAPTEYEDSAAAGEMYGMPLLTQEDLDRIGATEHVTGVETVRI
+VEVQDLRGADGRRWSVPMMGGTYEIGKLSVKAGREPAADGGAMELTVPTEWVESLGGTAP
+EDVLGQEVTLTTKTPLQQERTVQAEVVGVTERLPSGVGANPVPSAALEQGLHDIQTEGLP
+EEQRNTYFQATAIVEGMPGNEAAVKAALSEQGYQAQTLEDQLGSIRGIISAVTWVLNGFA
+LIALLAASFGIINTLLMAVQERTREIGLMKALGMTSGRIFGLFTLEAVVIGLLGSLLGVG
+LGVAVGVGVNAWLTTGGPLEDVAGLVLYAVDPLALLLIVLLIVAIAFVAGTLPAARAARK
+DPIEALRHE
+>4_411
+MKATDVAGTALANTMRSKLRTFLTVVAIVIGAFTLTLTTGLGAGINKYVDNVVEGFGKPG
+ELTVMKQQDMSSAGAASGSPQEYTEQDAAGGEMFGMPLLTQEDLAAIEDTEHVTEVKTYR
+VAEPEYIQGPDDRKWQTGFMGSSGEIDMLTFSAGRAPEAGAAEIVMPESWVEDLGAGDAE
+DLIGTELTVVAATPLQEHKSVTATVVGVTKAAASGAGTAPTPSESLEQEIYDITTEGLPE
+SQRDTYFQATAIVADPEANEDAVKQALADQGLLAQTLEEQLGVIRGIIDAVTWVLTGFAL
+IALLAASFGIINTLLMAVQERTREIGLMKALGMTGGKIFGLFTMEAVVIGLLGSLIGIGL
+GVAVGLIANQVLTTGPLSGVTGLVLFAVNPLALLLILLLIVAIAFIAGTLPALRAARKDP
+IEALRHE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000460.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000460.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c14db783b7b1c9e06a4da214adc327aa9f276746
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000460.fa
@@ -0,0 +1,26 @@
+>0_409
+MTTDRPNPDPNPEQPAVGSRYGTQPYAAPGYGAQPGSPYGIVPEPAAFPALLTLTLTSLA
+LYVLSSLPALFGGEESIERMRDSLRQSGLTPEQVEEIAPVVGASVTVGTIIVLLIGVALY
+ALVYFNLRGAKNWARILGIVVGILGTLSAVGGIFSFVTYPGIGGVLASVLSLALVIVNIL
+WLVKAFNPQVAAYTRQGRRA
+>1_139
+MTTDRPNPNPEQPAAGSRYGTQPYAAPGHGAQPGSSYGIVPEPAAFPALLTLTLTSLALY
+VLSSLPALFGGEESIERMRDSLRQSGLTPEQVEEIAPVVGASVTVGTIIVLLIGVALYAL
+VYFNLRGAKNWARILGIVVAILGTLSAVGGIFSFVTYPGIGGVLASVLSLALVIVNILWL
+VKAFNPQVAAYTRQGRRA
+>2_2471
+MSNQNPDFTNPAYNPANPPFEGESGQAGQAPQQGQPGQAAQYGQPGPYGQAPQYGQPGQY
+PATGTRYGTQPYGVDGRYGTVPEPRGFRTLLTLTLVSAALWVLSSLPAMFTMDDMMDVVM
+RDAASQPGVTAEDMEMVSSFMRTAGITSIVISLIIGLGLYALVYFNLRGVKNWARILGIV
+FAILGALAIFSGIGFLFSGSTMLILSGALTLAYAVVNIIWVITAFRSDVAEWFRQGRPAA
+A
+>3_2341
+MTDQNTPYPQNPQGGQPAPQYGQPGQAAPQYGQPGEGSRFGTQAYGAPGLQYGAPLAEPA
+KFRTLLKLTLASAVVYVLSALPGLFVDQDALVRDQLRAQGMSAEQIDQAMQNAGMFSAMA
+GIGAVVGLLIALGLYALVYFGLRAGKNWARVLGIVLAILGTLSAVFGLFSLGSFPAGVMI
+ASLVLSVLFIAVNVLWLVNAFNKDVAAYTKQGRLPAA
+>4_412
+MTTDRPNPDPNPEQPAAGGPGPYPGQNPAYGQPTAGSRYGTQPYAAPGYGAQPGSPYGIV
+PEPAAFPALLTLTLTSLALYVLSSLPALFGGEESIERMRDSLRQSGLTPEQVEEIAPVVG
+ASVTVGTIIVLLIGVALYALVYFNLRGAKNWARILGIVVAILGTLSAVGGIFSFVTYPGI
+GGVLASVLSLALVIVNILWLVKAFNPQVAAYTRQGRRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000461.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000461.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee5d498972fb5443aca4a6a9f4f6ad436095f34f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000461.fa
@@ -0,0 +1,20 @@
+>0_411
+MHPLDDDPHAATDRDPAPDRAALRPLRLFQTVTAVTGALSAAGVAGVLALQSTPGYARAV
+LEARSWGASEVTDADVAAFVTPAGAWPVAAAAVVLLAVVLLAGITRRIRAVRPVGSVLVV
+LGMLTAAFWMVDGGRMVQAGGGGPVVLGAVVGMLVSSAMWLRVAHRRETRDGFDG
+>1_141
+MMGGMHPLHDDPHETTERDPGPDRAALRPLRLFQTVTAVTGALSAAGVGGVLALQATPGY
+ARAVLEARSWGASEVTDADVAAFLTPAGAGPVAAAAVVVLTLVLLAGITRRIRAVRPVGS
+VLVVLGMLTAAFWMVDGGRMVQAGGGGPVVLGAVVGMLVSSAVWLRVAHRRETRDAFDV
+>2_2469
+MHTPDDAAADADDAAARAALHDRVVRRPLRRLLTLTAVTGALSALGTAGVLALQGAPGYA
+RAVLEARSWGRAAVTDADVASFLTPPWGVPAAVLGVLAVAALLMLGVARRVRAVRPVGTV
+AVGLGLLSAAFWMVDGGRMVAAGGAGPLVLAAVVAMFLACAVWLLTAHLRATRDAFDG
+>3_2340
+MRSDDVAPASARPSGLDDPAVRGPIRRYQAMTAGTGLVSAAAVAGVLGLQSDPGYAREVL
+QSRTWGQYEVSAQQVQDFLTPPGGAVLGAVGVLLTAALLVWGAQRLWGATRWLGTALAGV
+GLLSAVFWAVDGGRMAARGASGMAVLVAVGAMAVFCAVWLVTAHSKAVREAFLG
+>4_414
+MHPLDDDPHETTDPAPDLASLRPLRLFQTVTAVTGALSAAGVGGVLALQSTPGYARAVLE
+ARSWGASEVTDADVAAFLTPAGAWPVAAAAVVVLTLVLLAGITRRIRAVRPVGSVLVVLG
+MLTAAFWMVDGGRMVQAGGGGPVVLGAVVGMLVSSAVWLRVAHRRETRAAFDV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000468.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000468.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a58665fd8505509622d1b3db466c0077c6ab2fc9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000468.fa
@@ -0,0 +1,40 @@
+>0_418
+MGIATPSAARRRRLLLPAAALGVSGLLLTACGAPPEQSEASDSGAAESEAIATVDGVGSD
+NKDYKACIVSDEGGFDDRSFNQSSYEGLKAAEEAYGITTSEAESNEPSEYTPNVTAMVNG
+DCDAVIGVGFLLGDAMKPIAAQHSDTHFFGVDVTDGDFTDNFQKLTYDTAQAAFLAGYLA
+AGTTETGAVATYGGAEIPTVTIFMDGFARGVEHYNEVKDKDVKVLGWDKDAKTGSFTGDF
+ENVANGKTNTANFINEGADIVMPVAGPVGLGTLDAVREANQGGKDVKVIWPDSDGYESTK
+DGNLILTSVKKNMGQSVTDVIAADLKDEFSAEPYVGTLENKGVELAPFHDFEDTVPQELK
+DELKDLEAKIISGELKVGSEYSPEA
+>1_148
+MGIATPSAARRRRLLLPAAALGVSGLLLTACGAPPEQSEASGSGAAESEAIATVDGVGSD
+NKDYKACIVSDEGGFDDRSFNQSSYEGLKAAEKAYGITTSEAESNEPSEFTPNVTAMVNA
+DCDAVIGVGFLLGDAMKPIAAQHSDTHFFGVDVTAEGFSDNVQKLTYDTAQAAFLAGYLA
+AGTTETGTVATYGGMEIPTVTIFMDGFARGVEHYNEVKDKDVKVLGWDKDAKTGSFTGDF
+KNVANGKTNTANFINEGADIVMPVAGPVGLGTLDAVREANQGGKDVKVIWPDSDGYESTK
+DGNLILTSVKKNMGQSVADVIAADLKDEFSAEPYVGTLENKGVELAPFHDFEDTVPQELK
+DELKDLEAKIVSGELKVGSEYSPEA
+>2_2462
+MGTATPSAEGRRRLLLPAAVLGASALLLTACGQAPEASNSSEPAGSASATGAAAEVGSDN
+SDYTGCIVSDEGGFDDRSFNQSSYEGLKAAEEEFGIEIREAESNSVGEYVPNLNAMLDAD
+CNLVVAVGFQLGDTMKPIAEENAETKFVGVDVTAPGFPENVRNIIYDTAQGAFLAGYLAA
+GMTETGTVATYGGMEIPTVSIFMDGFARGVEHYNEVKGEDVRVLGWDTENRTGSFIGDFS
+NQNAGKTNTANFINEGADIIMPVAGPVGLGTIDAVKEANGGGKDVKVIWVDSDGYETTQD
+GEVILTSVMKRMGDAVKQVIAEDINDEFTSEAYVGTLENDGVALAPFHDFEDAVPQELKD
+ELEALEAGIVSGEIEVGSEDSPEA
+>3_2333
+MGIVSPLAGRRRLAVPAALLSSGLLLAGCGAPPAENSGSASGSGAAVSADAAAGSDNKDY
+KSCIVSDAGGFDDRSFNQSSYEGLKAAEEAYGIETNKAESKDASEFTPNVNAQVNAQCDS
+IIGVGYMLGDTIKPIAQKNPDIHFLGVDVTADGFSDNVKKLTYDTAQAAFLAGYVSAGMT
+KTGTVATYGGMEIPTVTVFMDGFAAGVEHYNEVKGKDVKVLGWDREAKTGSFTGDFDNQA
+NGKTNTANFINQGADIVMPVAGPVGLGTLDAVKEANAGGKSVAVVWPDSDGYESTKDGAL
+ILTSVVKNMGQSVSDVIGQDLKGEFSADPYVGTLENKGVELAPFHDFDSKVPQELKDEVQ
+TLQEDIISGKVKVDSEYSPKS
+>4_421
+MGIATPSAARRRRLLLPAAALGVSGLLLTACGAPPEQSEASDSGAAESEAIATVDGVGSD
+NNDYKACIVSDEGGFDDRSFNQSSYEGLKAAEEAYGITTSEAESNEPSEYTPNVTAMVNG
+DCDAVIGVGFLLGDAMKPIAAQHSDTHFFGVDVTDGDFTDNFQKLTYDTAQAAFLAGYLA
+AGTTETGTVATYGGAEIPTVTIFMDGFARGVEHYNEVKDKDVKVLGWDKDAKTGSFTGDF
+ENVANGKTNTANFINEGADIVMPVAGPVGLGTLDAVREANQGGKDVKVIWPDSDGYESTK
+DGNLILTSVKKNMGQSVTDVIAADLKDEFSAEPYVGTLENKGVELAPFHDFEDTVPQELK
+DELKDLEAKIISGELKVGSEYSPEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000469.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000469.fa
new file mode 100644
index 0000000000000000000000000000000000000000..14539fb8717576b14b5cbc6bc7463baf3a7d3b0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000469.fa
@@ -0,0 +1,50 @@
+>0_419
+MRLELRGISKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGEIL
+LDGEPVRFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRALGVLDLEATRRRI
+REISAQYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLG
+IIRQLREDGTAIVFISHKLREVKAVSDDITVLRRGRVVGTADPSAEAAELAALMVGRSVV
+LERRKTAPTLGEETFRVEDLSVVSPTGQVLLDAVSFAVRQGEVLAVAGVQGNGQTELTEA
+IMGLVKATGSVTLDGRELIGRSTRQIIRAGVGFVPEDRSTDGLVGPFSVAENMVLNRYDV
+APAGNAVQMRPAAVRALAERRVAEFDVRTQGVDLPVSSLSGGNQQKVVMARELVDGLRLF
+IASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVLELADRIAVMYHGRIVGIV
+PGDTSRETLGLMMAGQTPDDAALASGADVAAGTPGTAGEAPAAHPTTEGERP
+>1_149
+MRLELRGITKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGEIL
+LDGEPVRFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRALGVLDLEATRRRI
+REISAQYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLG
+IIRQLRADGTAIVFISHKLREVKAVSDDITVLRRGRVVGTAEPSAEAAELAALMVGRNVV
+LERRKTAPTLGEETFRVEDLSVVSPTGQVLLDAVSFAVRQGEVLAVAGVQGNGQTELTEA
+IMGLVKATGSVTLDGRELIGRSTRQIIRAGVGFVPEDRSTDGLVGPFSVAENMVLNRYDV
+APAGNAVQMRPAAVRALAERRVAEFDVRTQGVDLPVSSLSGGNQQKVVMARELVDGLRLF
+IASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVLELADRIAVMYHGRIVGIV
+PGDTSRETLGLMMAGQTPDDAALASGTDVAADTPGTAGAAPAAHPTTEGERP
+>2_2461
+MKLELRGITKRFGTFTANDSVDFVVRSGEVHTLLGENGAGKSTLMNVLFGLYDPTEGEIL
+VDDRPVRFAGPGEAMRAGIGMVHQHFMLVPVFTVAENIALGDEHTRAAGVLDLEATRRKI
+RAISDEYGFAVDPDAVVEDLPVGVQQRVEIIKALVRDAKVLILDEPTAVLTPQETDELLA
+IIDRLRQDGTAIVFISHKLREVKAISEHITVLRRGKVVGTAEPSASAAELAALMVGRQVS
+LNRAKTAPTLGEETFKVQDLTVVSPTGQVLVDHVSFAIRQGEILGVAGVQGNGQTELTEA
+IMGLHKATGSVTLDGRELVGRSTRQIIRAGVGYVPEDRSTDGLVGSFTVAENMVLNRFDR
+EPAGSALQLRPRAVRELAEARVQEFDVRTQGVVSPVSSLSGGNQQKVVMARELVDELRLF
+IASQPTRGVDVGSIEFLHERIVRERDNGTPVMIVSTELDEILELSDRIAVMYHGRIVGIV
+DGDASRETLGLMMAGQTPESLATETATTEEGPRA
+>3_2332
+MKLELRGITKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGQIL
+LDGEPVAFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRGAGVLDLEATRRKI
+REISDAYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLA
+IIRQLRADGTAIVFISHKLREVKAISDDITVLRRGRVVGTADPSASAAELASLMVGRDVV
+LNRRKTAPQLGEETFRVEHLTVVSPTGQVLVDDVSFGIRQGEVLAVAGVQGNGQTELTEA
+IMGLQAKAAGSIRLDGRELLGRSTRQIIHAGVGYVPEDRSTDGLVGSFSVAENMVLNRFD
+VAPAGSAVQLRPRAVRELAERRVEEFDVRTQGVDVPVSSLSGGNQQKVVMARELVDGLRL
+FIASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVRELADRIAVMYHGRIVDI
+VPGDASREHLGLLMAGQTAEDTHQEGARA
+>4_422
+MRLELRGITKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGEIL
+LDGEPVRFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRALGVLDLEATRRRI
+REISAQYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLG
+IIRQLRADGTAIVFISHKLREVKAVSDDITVLRRGRVVGTAEPSAEAAELAALMVGRNVV
+LERRKTAPTLGEETFRVEDLSVVSPTGQVLLDAVSFAVRQGEVLAVAGVQGNGQTELTEA
+IMGLVKATGSVTLDGRELIGRSTRQIIRAGVGFVPEDRSTDGLVGPFSVAENMVLNRYDV
+APAGNAVQMRPAAVRALAERRVAEFDVRTQGVDLPVSSLSGGNQQKVVMARELVDGLRLF
+IASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVLELADRIAVMYHGRIVGIV
+PGDTSRETLGLMMAGQTPDDAALASGADVAADTPGTTGAAPAAHPTTEGERP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000471.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000471.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a469d2105779a93a98f636886a5cdbd81fa0b1be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000471.fa
@@ -0,0 +1,45 @@
+>0_421
+MSATAARPHADVVRPEAAEPARVVVRHWTTPIALTILTLLALAVFALGAPEATATFRLSH
+ASDAVVLPDLTADPVLGGWLLVGLMAVLTAVAWLATLRSGRTPGWAAALFAVAFVAAFLI
+WVIGSADNTTVFLTGLIAGSFALAVPLIFGSMAGILAERSGVVNIAIEGQLLAGAFTAAV
+VGTATGSPWAGLVAAIVAGVLVSWLLAVFSIKYLVNQVIVGVVLNVLVAGLTSFLYSTVL
+TDGDTELNAPPHFPNLRIPGLADIPVLGPILFDQTILGYAMYLLVIALWFALFRTRWGLR
+VRAVGEHPKAADTVGIDVNRTRYAAVLLGGAVAGMGGAFFTLVSASSFTKEMTAGQGFIA
+LAAVIFGRWNPIGAFFAALLFGFATNMQYVLAILGTPVPSQFMAMLPYLVTVFAVAGLVG
+RSRGPAASGVPYVKE
+>1_151
+MSATAARPHADVVRPEAAEPARVVVRHWTTPIALTILTLLALAVFALGAPETTATFRLSH
+ASDAVVLPDLTADPVLGGWLLVGLMAVLTVVAWLATLRSGRTPGWAAALFAVAFVAAFLI
+WVIGSADNTTVFLTGLIAGSFALAVPLIFGSMAGILAERSGVVNIAIEGQLLAGAFTAAV
+VGTATGSPWAGLAAAIVAGVLVSWLLAVFSIKYLVNQVIVGVVLNVLVAGLTSFLYSTVL
+TGGDTELNAPPHFPNLRIPGLADIPVLGPILFDQTILGYAMYLLVIALWFALFRTRWGLR
+VRAVGEHPKAADTVGIDVNRTRYAAVLLGGAVAGMGGAFFTLVSASSFTKEMTAGQGFIA
+LAAVIFGRWNPIGAFFAALLFGFATNMQYVLAILGTPVPSQFMAMLPYLVTVFAVAGLVG
+RSRGPAASGVPYVKE
+>2_2459
+MSTAAQTNPVQPTPAGTGRAPSAEAPREGGTVVVRSWTTPIVFTVFTVLALVVFGLNAPD
+AAATFRVSTEADAFRIPDLVADGAGGGWIVTAILVVLTVLAWMRAARGRAVGAVLGISFA
+LVFVAGFLIWVVGSAANTSVFLTGLIAGSFALAVPLIFGSMAGILSERAGVVNIAIEGQL
+LAGAFTAALVGSMTGSPWAGLAAAVVAGVLVSVILAVFSIKYLVNQVIVGVVLNVLVAGL
+TGFLFSTVLSENSSGLNSPPRFETLRIPGLADIPVIGPILFEQTLLGYGMYLIVAVIYIG
+LFHTRWGLRVRAVGEHPKAADTLGINVLRTRYVNVLLGGAVAGMGGAFFTLVQSSSFSRE
+MTAGMGFIALAAVIFGRWNPIGAFFAALLFGFATNMQYVLAILGTPVPSQFMAMLPYLVT
+IFAVAGLVGRSRAPAASGVPYVKE
+>3_2330
+MSTAAPARESATPSERAGAASSGVVVRHWSTPVLLSVFTLVSLVVFALGASDSTAVFRIS
+EASDAVRLPDLLADPAVTGWALTAVMAAITAAAWVLTLRGRRLPGWAAGLFALAFTAAFL
+VWVVGAATNNEVFLTGLIAGSFTLAVPLIFGSMAGILSERSGVVNIAIEGQLLAGAFMAA
+VVGSLTGSPWAGLGAAIVAGVLVSWLLAVFSIRYLVNQVIVGVVLNVLVAGLTNFLFSTV
+LTADSDLNAPPRFPDLRIPLLADIPVIGPILFDQTILGYLMYAIVALLWFGLFRTRWGLR
+VRAVGEHPKAADTVGIDVNRTRYVNVLLGGAVAGMGGAFFTLVSASSFSKEMTAGQGFIA
+LAAVIFGRWNPIGAFFAALLFGFATNMQFVFAILGTPVPSPFMAMLPYLVTVFAVAGLVG
+RSRGPAAAGEPYVKE
+>4_424
+MSATAARPHADVVRPEAAEPARVVVRHWTTPIALTILTLLALAVFALGAPEATATFRLSN
+ASDAVVLPDLTADPVLGGWLLVGLMAVLTAVAWLATLRSGRTPGWAAALFAVAFVAAFLI
+WVIGSADNTTVFLTGLIAGSFALAVPLIFGSMAGILAERSGVVNIAIEGQLLAGAFTAAV
+VGTATGSPWAGLAAAIVAGVLVSWLLAVFSIKYLVNQVIVGVVLNVLVAGLTSFLYSTVL
+TGGDTELNAPPHFPNLRIPGLADIPVLGPILFDQTILGYAMYLLVIALWFALFRTRWGLR
+VRAVGEHPKAADTVGIDVNRTRYAAVLLGGAVAGMGGAFFTLVSASSFTKEMTAGQGFIA
+LAAVIFGRWNPIGAFFAALLFGFATNMQYVLAILGTPVPSQFMAMLPYLVTVFAVAGLVG
+RSRGPAASGVPYVKE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000472.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000472.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5ac778bcdda9aba0c2720df25e5933ab4491ffb5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000472.fa
@@ -0,0 +1,20 @@
+>0_422
+MADGQHTTTAPRVDWDRLRAAALAATEHAYVPYSGFRVGAAALTDDGRLVSGCNIENASY
+GLTLCAECALLAELRMGGGGRLAAFVCVDGAGVLTMPCGRCRQLLYEFRAPGLVLLTPAG
+ERGIDAVLPDAFGPADLERADRP
+>1_152
+MADGQHTTTAPRVDWDRLRAAALAATEHAYVPYSGFRVGAAALTDDGRLVAGCNIENASY
+GLTLCAECALLADLRMGGGGRLAAFVCVDGAGVLTMPCGRCRQLLYEFRAPGLVLLTPAG
+ERGIDAVLPDAFGPADLERADRP
+>2_2458
+MAAEGTTTAPGVDWDRLRRAALAATEHAYVPYSGFRVGAAALTEDGRLVTGCNIENASYG
+LTLCAECALLADLRMGGGGRLAAFVCVDGQGVLTMPCGRCRQLLHEFRAPDMVLLTPAGE
+RTMGQVLPDAFGPEDLERAAAR
+>3_2329
+MTGTTTPPACAAPVAEADWDRLRAAAADAMERAYAPYSGFRVGAAALTEDGRLVSGCNVE
+NAAYGVALCAECALVGQLHMTGGGRLRAFLCVGGDGRLITPCGRCRQLLWEFRAPGLAVL
+TAAGVTTVEALLPEAFGPDALEA
+>4_425
+MADGQHTTTAPRVDWDRLRAAALAATEHAYVPYSGFRVGAAALTDDGRLVSGCNIENASY
+GLTLCAECALLADLRMGGGGRLAAFVCVDGDGVLTMPCGRCRQLLYEFRAPGLVLLTPAG
+ERGIDAVLPDAFGPADLERADRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000475.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000475.fa
new file mode 100644
index 0000000000000000000000000000000000000000..181c9b3ca71b5f808d94b7641406c3813aaa9735
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000475.fa
@@ -0,0 +1,40 @@
+>0_425
+MTTTQLPDTASPSPLEVDLAVLPKVSLHDHLDGGLRVGTVLDLAREAGVEVPADTVEGLA
+EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH
+LAGGLSLDEAVEAVQAGLDEAVEADAAAGHAIRVGQLVTAMRHADRAQEIAELAVRHRAA
+GVVGFDIAGAEAGFPPSRFADTFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH
+GVRLAEDISVEYGGVDEDGEQLDELTGLVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA
+AAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLSELLDLQLNAAE
+AAFLSVDEREDLAEILVAGWGEVISGDAVGPVLEELDDEDEDD
+>1_155
+MTTTQLPDTASPSPLEVDLAVLPKVSLHDHLDGGLRVGTVLDLAREAGVEVPADTVEGLA
+EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH
+LAGGLSLDEAVEAVQAGLDEAVEAADAAGHVIRVGQLVTAMRHADRAQEIAELAVRHREA
+GVVGFDIAGAEAGFPPSRFADTFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH
+GVRLAEDISVEYGGVDEDGEQLDELTGIVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA
+AAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLSELLDLQLNAAE
+AAFLSVDEREDLAEILVAGWGEVISGDAVGPVLEELDDEDEDD
+>2_2455
+MTATQLPDTASPSPLEVDLAALPKVSLHDHLDGGLRVGTVLELATEAGVDVPADTVEGLA
+EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH
+LAGGLSLDEAVEAVQEGLDEAVDAAEAQGRLIRVGQLVTAMRHADRAQEIAELAVRHRER
+GVVGFDIAGAEAGFPPSRFAETFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH
+GVRLAEDISVEFGGVDEDGEQLDELTGLVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA
+EAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLAELLDLQLNAAE
+AAFLAVDEREDLAEILVAGWGEVISGDDAGPVLEELDEDDEDEDA
+>3_2326
+MTISSQTPADAAPSPLTIDLGALPKVSLHDHLDGGLRVATVLELAREAGVEVPADTVDGL
+ADWFAEHANGESLEKYLETFALTTSVMQTHEQLRRVAREFVEDLVADGVVYGEIRWAPEQ
+HLASGLTLDEAVEAVQEGLDEAVDAADEAGHVIRVGQLVTAMRHADRAQEIAELAVRHRD
+RGVVGFDIAGAEIGFPPSRFADTFTWLAQQHLPVTVHAGEAEGLSSIQDALVSGRALRLG
+HGVRIADDIQVEFGGLDEDGVPVDADTGIVDLGETAAWVRDRQIALEICPSSNLQTGAVD
+AAAGIAGHPIDLLVQLGFRVTVNTDNRLVSNVSLTDELYLLAETFGYSLSELLDLQLNAA
+EAAFLAVDEREDLAEILVSGWGEVISGAGGTVALEELEADTDDEADA
+>4_428
+MTTTQLPDTASPSPLEVDLAVLPKVSLHDHLDGGLRVGTVLDLAREAGVEVPADTVEGLA
+EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH
+LAGGLTLDEAVEAVQAGLDEAVEAADAAGHVIRVGQLVTAMRHADRAQEIAELAVRHREA
+GVVGFDIAGAEAGFPPSRFADTFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH
+GVRLAEDISVEYGGVDEDGEQLDELTGLVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA
+AAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLSELLDLQLNAAE
+AAFLSVDEREDLAEILVAGWGEVISGDAVGPVLEELDDEDEDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000484.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000484.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a70089a95c293f20c20b5925cc8557afff35b4f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000484.fa
@@ -0,0 +1,25 @@
+>0_438
+MLTVEKAHLLLTREDGRSESPSHHRVALAAAALADHRSAGIVTLEDVPVDRARVLVTAAG
+TTGDPVLDSSLGQVDALAGRPLVSTVAAGKPDLRKAVVAHLTETGRLTERKAFLATRHVP
+RGTERTELLAHLTAVVLDEAEPCDEDVLLLGVLQHLNLARRLLPGAHERYDRREMVRRIE
+TLTREDLLVQAVRRAVGGTCGTVTAAAAGSVA
+>1_165
+MLTVEKAHLLLTREDGLSESPSHHRVALAAAALADHRSAGIVTLEDVPVDRARVLVTAAG
+TTGDPVLDSSLAQVDALAGRPLVSTVAAGKPDLRKAVVAHLTETGCLTERKAFLATRHVP
+RGTERTELLAHLTAVVLDEAEPSDEDVLLLGVLQHLNLARRLLPGAHERYDRREMVRRIE
+ALTREDLLVQAVRRAVGGTCGTVTAAAAGSAA
+>2_2432
+MLTAEKTHLLLTREDGRSESPSHHGVALAAAALADYRAAGIVTVEDAPVDRARVLVTAAG
+VTGHPVLDARLGKVDALAGTPVTAAVAAGRPNLRKAVIARLTETGDLAEHKAFMATRHLP
+RGGTRAELLDRLTAVVLDEREATDEDVLLLGVLQHLNLAWRLLPGTHERYGRRELVRRVE
+SLTRSDLLVQAVRRAVGGTAAAVTAAAAGSLA
+>3_2316
+MLTSEKLHLLLTREDGRSLSPSHHGVALAAAVLADLRDAGIVSLEDAPVSRARVLVTGAG
+STDHPVLDALLPELDGLRGKKVAAVVGKGRPKARKPVVAHLVETGELVEHKALLNTRHTP
+VGPGRPALVAGLTSALDGDSPSDEDRLLLGVLHQLNVLRRVLPEAGAEGESRREQSRRLE
+RLTHDDLLVQAVGRTVSTAAAAAAAAG
+>4_438
+MLTVEKAHLLLTREDGLSESPSHHRVALAAAALADHRSAGIVTLEDVPVDRARVLVTAAG
+TTGDPVLDSSLGQVDALAGRPLVSTVAAGKPDLRKAVVAHLTETGRLTERKAFLATRHVP
+RGTERTELLAHLTAVVLDEAEPSDEDVLLLGVLQHLNLARRLLPGAHERYDRREMVRRIE
+ALTREDLLVQAVRRAVGGTSGTVTAAAAGSAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000485.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000485.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce4301361bcd34a818d9fc78dccd3a6cf913838c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000485.fa
@@ -0,0 +1,20 @@
+>0_439
+MTTSQSDAPWLTQEAYDRLSKELEYISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL
+EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG
+>1_166
+MTTSQSDAPWLTQEAYDRLSKELEYISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL
+EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG
+>2_2431
+MTTSQSDAPWLTQEAFDRLSKELEHISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAEDDEHL
+EVYSERSPLGEAINGAAKGDKVTYTAPNGKEIKVEIKDVKPYSG
+>3_2315
+MATTPSDAPWLTQEAFDRLSKELAHISGPGRQEIIERIEAAREEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGETQAADGVVTPGTVVTAVVAGDEMTFLFGNREIAADGEDL
+EVYSERSPMGEAINGAKQGDKVTYTAPNGKDIAVEITDVKPYQA
+>4_439
+MTTSQSDAPWLTQEAYDRLSKELEHISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL
+EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000487.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000487.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f6016605ae8fa9e04cdc71a1126e6073c2de1f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000487.fa
@@ -0,0 +1,20 @@
+>0_442
+MTPLSGLPLVLTALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVL
+RVMVRSVRRVQQRSPQAEAMLVERHQQHLPDEVRAGGEHLDADSEDRLRRLQEKYPGYLQ
+EPAPEPQAPDTGRD
+>1_169
+MTPLSGLPLVLTALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVL
+RVMVRSVRRVQQRSPEAEAMLVERHQQHLPDEVRAGGEHLDADSEDRLRRLQEKYPGYLQ
+APAPEPQAPDTGRD
+>2_2429
+MSPLSGLPLVLTALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVL
+RVMVRSVRRVQQRSPEAEAMLVDRHQQHLPEDVRELAPEDEERDAQDRLRHLQEKYPGYL
+QEPAPRPQSPDDGRS
+>3_2312
+MSLAPLALSAVSLAASVSPSAPMPAVPEPTLKPGLDKQDISPGIEGFLFTALMVVMAIIV
+FRLMVRSVRRVQQRSPEAEAMLVDRHQQHLPEEVREGGERLDGDAHDRIERLRRRYPGYL
+QDPTPEPESPDTGREPR
+>4_442
+MTPLSGLPLVLNALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVF
+RVMVRSVRRVQQRSPQAEAMLVERHQQHLPDEVRAGGEHLDADSEDRLRRLQEKYPGYLQ
+EPAPEPQAPDTGRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000488.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000488.fa
new file mode 100644
index 0000000000000000000000000000000000000000..65b33064a77ddc2615483c0b64aae576216349da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000488.fa
@@ -0,0 +1,26 @@
+>0_443
+MTPLRETDAARRLRWRIERIRDPDHPLYKPRLRGWIHAVMAPLTLAAGIVLIVLAPTATL
+RWASAVYAVTGLLLFAVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLALLAP
+DRARVLLTLVWVGAVAGVAFRVLWTDAPRWLYTPVYVALGLAALLYLGDFFAADAAAGWL
+IVAGGVAYITGAVCYALQAPTIHREWFGFHELFHAFTVAGFVCHAVAIYRAVLVVA
+>1_170
+MTPLRETDAARRLRWRIERIRDPDHPLYKPRLRGWIHAVMAPLTLAAGIVLIVLAPTATL
+RWASAVYAVTGLLLFAVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLALLAP
+DRARVLLTLVWVGAVAGVAFRVLWTDAPRWLYTPVYVALGLAALLYLGDFFAADAAAGWL
+IVAGGVAYITGAVCYALQAPTIHREWFGFHELFHAFTVAGFVCHAVAIYRAVLVVT
+>2_2428
+MDPLTPAREPEAARRLRWRIERIRDPEHPLFKPRLRGWIHAAMAPLTLAAGIVLIVLAPT
+ATLRWASAVYAVTGLLLFGVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLAL
+LPPGKAHLLLTLVWAGAVAGVAFRLLWTDAPRWLYTPVYVVLGLAALLYIGDFFAADVAA
+GWLIVAGGAAYIVGAVFYALRAPTIHREWFGFHELFHVFTVGGFVCHAVAIYRAVLVVA
+>3_2311
+MWEHGGMVTRAPSVENRTGRPLKWRIERIRDPEHPLYKPRLRGWVHAVMAPLVLVAGIVL
+IVLAPGATLTWACVVYVVTGLLLFGVSATYHLVQWNETVSRVLKRLDHTNIMLVIAGTYT
+PLSLAMLPADKAWTLVTAVWVGAALGVAFRLLWTDAPRWLYTPVYVALGLAAVVYLGDFF
+AASVPAAVLICAGGAAYIVGAVFYALKAPTIHREWFGFHELFHVFTVGGFVCHYIAVMMA
+VLAA
+>4_443
+MTPLRETDAARRLRWRIERIRDPDHPLYKPRLRGWIHAVMAPLTLAAGIVLIVLAPTATL
+RWASAVYAVTGLLLFGVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLALLAP
+DRARVLLTLVWVGAVAGVAFRVLWTDAPRWLYTPVYVALGLAALLYLGDFFAADAAAGWL
+IVAGGVAYITGAVFYALQAPTIHREWFGFHELFHAFTVAGFVCHAVAIYRAVLVVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000493.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000493.fa
new file mode 100644
index 0000000000000000000000000000000000000000..58b085406be14b9112b2aa0197301b5e427af1ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000493.fa
@@ -0,0 +1,45 @@
+>0_448
+MTAENTDQQFRIEHDTMGEVKVPVNALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA
+AAKANAELGIISQERADAIVAAADQVIAGDHDDQYPIDVFQTGSGTSSNMNTNEVLATLA
+TRALKEAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTAALVNDLVPALDHLAVSLEKKA
+EAFAGVVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIQSALPRVAEVPLGGTAVGTG
+INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNIAFSLMKINNDL
+RWMGSGPNTGLGEIAIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVALSSTNGA
+FELNVGIPVMAANLLESIRLLANTTRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV
+IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDKALDTMSMTHPE
+>1_175
+MTAENTDQQFRIEHDTMGEVKVPVNALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA
+AAKANAELGIISQERADAIVAAADQVIAGDHDDQYPIDVFQTGSGTSSNMNTNEVLATLA
+TRALKEAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTAALVNDLVPALDHLAVSLEKKA
+EAFAGVVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIQSALPRVAEVPLGGTAVGTG
+INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNIAFSLMKINNDL
+RWMGSGPNTGLGEIAIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVALSSTNGA
+FELNVGIPVMAANLLESIRLLANTTRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV
+IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDKALDTMSMTHPE
+>2_2423
+MTAQNPEQQFRIEHDTMGEVKVPIDALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA
+AAKANAELGVISQERADAIVAAADQVIAGEHDDQYPIDVFQTGSGTSSNMNTNEVLATLA
+TRALKDAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTGALINELIPALDHLAVSLEKKE
+KAFANIVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERVESSLPRVAEVPLGGTAVGTG
+INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNVAYSIMKINNDL
+RWMGSGPNTGLGEIFIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVSLSSTNGA
+FELNVGIPVMAANLLESIRLLANTSRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV
+IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDTALDTMSMTHPE
+>3_2306
+MTAQNTEQQFRIEHDTMGEVKVPVDALYRAQTQRAVENFPISGKTLEPAHIHALAQIKKA
+AAKANAELGVISQERADAIVAAADEVISGKHDGEYPIDVFQTGSGTSSNMNTNEVLATLA
+TRRLKDAGSSEEVHPNDHVNASQSSNDVFPTSVHVAVTGALVNDLKPALEHLAESLERKA
+EEFQGIVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIEASLPRVAEVPLGGTAVGTG
+INTPQGFSARVIELLAEETGLPITEARNHFEAQANRDGLVEASGQLRNIAYSFIKINNDL
+RWMGSGPNTGLGEIALPDLQPGSSIMPGKVNPVICEAAIMVAAQVIGNDTTISLSSTNGA
+FELNVGIPVMAANLLESIRLLANTSRVMADKMIDGIEANEERCTFLAGASPSIVTPLNKV
+IGYEAAAAIAKHAVKNKMTVREAVVDLGYVERGEVTEEQLDKALDTMSMTHPGE
+>4_448
+MTAENTDQQFRIEHDTMGEVKVPVNALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA
+AAKANAELGIISQERADAIVAAADQVIAGDHDDQYPIDVFQTGSGTSSNMNTNEVLATLA
+TRALKEAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTAALVNDLVPALDHLAVSLEKKA
+EAFAGVVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIQSALPRVAEVPLGGTAVGTG
+INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNIAFSLMKINNDL
+RWMGSGPNTGLGEIAIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVALSSTNGA
+FELNVGIPVMAANLLESIRLLANTTRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV
+IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDKALDTMSMTHPE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000506.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000506.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81b1dff44dfa23146521d58cb1de133ca860f37e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000506.fa
@@ -0,0 +1,40 @@
+>0_462
+MASHQAGRGRDERAGAEDFDSGLDYGAFVEDDAADDPNRTQALPAMGRDDDGGAQHTSAL
+SPEDLAALRGGDAAAADRRDAGRPAADADRDIVASRAVPEGGRRPLPGADELGPLSAAVG
+ARAAGSSAAAPVDRYPEDGTAAPVAQAAALQGPTPEERARLPKAGPRLAQVLLAILAPLA
+LVLATVRLVASPVFLWLEYHRPGFPADRFGFTLADRMHYGSAGLDYVTNLAGPRYLSSLT
+HQGAPLFTEVEVDHMTDVKTVLWIAAAALVVLLVVCALLIASLLRTSPGGVRRALFAGAV
+WLPLAVIALAVLAVLGWETFFAGFHSLFFADGTWTFSVRDALIRLYPQQFWVDAAVVVGL
+VTLLASLVTLVLTWPTRRRRELSADRREQLLRTRLRWAREDDAVVR
+>1_189
+MASHQAGRGRDERAGAEDFESGLDYGAFVQDDAADDPNRTQALPATGRDDDGGAQHTSAL
+SPEDLAALRGGDAAAADRRDADRPAPDADRDIVASRAVPESDRRPLPGADELGPLSAAVG
+ARAAGSSAAAPVDRYPEDGTAAPVAQAAALQGPTPEERARLPKAGPRLAQVLLAILAPLA
+LLLAAVRLVASPVFLWLEYHRPGFPADRFGFTLADRMHYGSAGLDYVTNLAGPRYLSSLT
+HQGAPLFTEVEVDHMTDVKTVLWIATAALVVLVVVCALLIASLLRTSPGGVRRALFAGAV
+WLPLAVIALAVLAVLGWETFFAGFHSLFFADGTWTFSVQDALIRLYPSQFWIDAAAAVGL
+ISLLTALLTLVFTWPTRRRRERTADQRSAFESTRLRWAREEDAQLR
+>2_2409
+MASHQAGRGREERAGAEDFESGLDYGAFAEDDAAEDPNRTQALPASGRDDAGVQHTSALS
+PEDLAALRGGDAAAADGRAERSAERGMPDARERDIVASRAVPSSDRRPLPGADELGPLSA
+AVGARSASGSSAADPADRYPQDASAAYAASSSAALQGPTPEERARLPKAGPRVAQVLLAI
+LAPLALLLAAVRFVASPAFLWLEYHRPGFPADRFGFDTGDRMHYGSAGLDYVTNLAGSRY
+LSSLTHQGEPLFTEAEVSHMTDVKVVLWIALAVLVALVVVCALLIAHLLRTSPGGVRRAL
+FAGALWLPLALIALAVLAVLGWEIFFAGFHSLFFADGTWTFSVRDALIRLYPEQFWVDAA
+LVVAAIAVIASLVTLVFTWPTRRRREMSADRRGQLLDTRLRWAREEDSPVR
+>3_2292
+MASHTPGRSDGAGSGSSDFESGLDYGAFVEDDDAQPTQALPRTTEEHGAQRTLAFDRDEL
+AAAAAGAGTGAGRSGAGSRAAGAAHGVAGEDITASRPAPAPAPSPASPWGADRYPSDATV
+PASAPAAADTRTPEERARLPKAGPRLAQVLLAVLAPLVLLLGAVRLVATPLFLWLEYHRP
+GFPADPYGFSTADRMTYGSAGLDYLHNLAGPRYLSELTFQGKPLLSEAAVSHMTDVKTVM
+WIATAVLVLLGLACLLLALYLRRTSPGGVRRALFAGALGLLVVIVVLAAMAATGWQGFFA
+GFHSLFFAEGTWTFSVSDPLIRLYPAQFWVDAAVAVAVLALIGIIAALVAGAPTRRRREM
+SQDRRAQLEATRLRWAREDAHGVR
+>4_462
+MASHQAGRGRDERAGAEDFESGLDYGAFVQDDAADDPNRTQALPAMGRDDDGGAQHTSAL
+SPEDLAALRGGDAAAADRRDAGRPAADADRDIVASRAVPEGDRRPLPGADELGPLSAAVG
+ARTAGSSTAAPVDRYPEDGTAAPVAQAAALQGPTPEERARLPKAGPRLAQVLLAVLAPLA
+LLLAAVRLVASPVFLWLEYHRPGFPADRFGFTLADRMHYGSAGLDYVTNLAGPRYLSSLT
+HQGAPLFTEVEVDHMTDVKTVLWIATAALVVLVVVCALLIASLLRTSPGGVRRGLFAGAV
+WLPLAVIALAVLAVLGWETFFAGFHSLFFADGTWTFSVRDALIRLYPQQFWVDAAVVVGL
+VTLLASLVTLVLTWPTRRRRELSADHREQLLRTRLRWAREDDAVVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000515.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000515.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c726f3937883ba0effea9985721c1c0eabfefd1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000515.fa
@@ -0,0 +1,50 @@
+>0_474
+MSQPSARPSAVIVLAAGQGTRMKSTTPKIMHAIGGRSLVGHALAAAWSLSPEHLVAVVRH
+ERARVAEHIETVAAQLGIDALAIADQDDVPGTGRAVELGLAALPADLEGTVVVTYGDVPL
+LTPETLARLVADHEADGNAVTVLTATLEDATGYGRIVRDAEGLVERIMEHKDALAHAEAT
+GDDSFVAIREVNSGIYAFDAALLRRTLPEISTDNVQGEKYLTDVLGMARAEGGRVASVGT
+DDVWEVEGANDRRQLSDLGRQLNDRVLRGWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG
+TQLHGATSVATGAVVGPDSTLTDTQVGEGAVVKRTDATEAVIGAGATVGPFTYLRPGTVL
+GEDGKIGAFYETKNVTVGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVNKHRTVIG
+AHVRTGSNTVFTAPVTVGDGAYTGAGAVVREDVPAGALALNAVSQRTLEGWVPAKRPGTS
+SAEAARAAGAEGSGAQG
+>1_204
+MSQPSARPSAVIVLAAGQGTRMKSTTPKIMHAIGGRSLVGHALAAAWSLAPEHLVAVVRH
+ERARVADHLETVAAQLGIDALAIADQDDVPGTGRAVELGLAALPADLEGTVVVTYGDVPL
+LTPETLARLVADHEADGNAVTVLTATLEDATGYGRIVRDAEGLVERIMEHKDALAHAEST
+GDDSFVAIREVNSGIYAFDAALLRRTLPEISTDNVQGEKYLTDVLGMARAEGGRVASVGT
+DDVWEVEGANDRRQLSDLGRQLNDRVLRGWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG
+TQLHGATSVATGAVVGPDSTLTDTQVGEGAVVKRTDATEAVIGAGATVGPFTYLRPGTVL
+GEDGKIGAFYETKNVTVGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVAKHRTVIG
+AHVRTGSNTVFTAPVSVGDGAYTGAGAVVRDDVPAGALALNAVAQRTIEGWVPAKRPGST
+SAQAARAAGAEGSGAQG
+>2_2397
+MPQSSVRPSAVIVLAAGQGTRMKSTTPKIMHPIGGRSLVGHALAAAHSLAPEHLVAVVRY
+ERDRVAEHIESVAEGLGIASLAIADQDEVPGTGRAVELGLAALPKDLEGTVVVTYGDVPL
+LTPETLERLVAAHEADGNAVTVLTAALEDATGYGRIVRDGEGLVERIMEHKDALAHAEST
+GDSSFVEIREVNSGIYAFDAALLRRTLPAISTDNVQGEKYLTDVLGMARAEGGRVASVGT
+DDVWEVEGANDRRQLSDLGRRLNDRVLRHWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG
+TQLHGATQVATGAVVGPDTTLTDTRVGERAVVKRTDATEAVIGADATVGPFTYLRPGTVL
+GEEGKIGAFYETKKVTIGRGAKLSHLGYAGDAEIGDYTNIGCGNITANYDGEKKHRTVIG
+AHVRTGSNTVFTAPVTVGDGAYTGAGAVVREDVPAGALALNAVSQRTIEGWVPAKRPGTS
+SAQAAQAADAQGDAPQG
+>3_2280
+MPQTAVRPSAVIVLAAGQGTRMKSATPKIMHAIGGRSLVGHALAAAQSLAPEHLVTVVRH
+ERDRVAAHIEEAAADLGVTGLAIADQDEVPGTGRAVELGLAALPEDLEGTVVVTYGDVPL
+LTPETLQRLVAAHEADGNAVTVLTATLADATGYGRIVRDADGLVERIMEHKDALAHAEAT
+GDSSYVEIAEVNSGIYAFDAALLRRTLPQLSTENVQGEKYLTDVLGMARAEGGRVASVGT
+DDVWEVEGANDRRQLSDLGRQLNERVLRRWMKDGVTVVDPSSTWVDVTVELAADVTLKPG
+TQLHGSTTVATGAVVGPDSTLVDTRVGERGTVKRTDATEAVIGDDATVGPFTYLRPGTVL
+GEEGKIGAFYETKKVTIGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVDKHRTVIG
+SHVRTGSNTVFIAPVTVGDGAYTGAAATVRQDVPAGALALNAVDQRNVDGWVVSRRAGTA
+SAEAAQAAGAVGRDQATEAAQD
+>4_473
+MSQPSARPSAVIVLAAGQGTRMKSTTPKIMHAIGGRSLVGHALAAAWSLAPEHLVAVVRH
+ERARVAEHLETVAAQLGIDALAIADQDDVPGTGRAVELGLAALPADLEGTVVVTYGDVPL
+LTPETLARLVADHEADGNAVTVLTATLEDATGYGRIVRDAEGLVERIMEHKDALAHAEST
+GDDSFVAIREVNSGIYAFDAALLRRTLPEVSTDNVQGEKYLTDVLGMARAEGGRVASVGT
+DDVWEVEGANDRRQLSDLGRQLNDRVLRGWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG
+TQLHGATSVATGAVVGPDSTLTDTQVGEGAVVKRTDATEAVIGAGATVGPFTYLRPGTVL
+GEDGKIGAFYETKNVTVGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVNKHRTVIG
+AHVRTGSNTVFTAPVTVGDGAYTGAGAVVREDVPAGALALNAVSQRTLEGWVPAKRPGTS
+SAEAARAAGAEGSGAQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000516.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000516.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76ba1f038bb2a075497908a33baebd6c333cd793
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000516.fa
@@ -0,0 +1,35 @@
+>0_477
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKDAGAKDVIIAATHPVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGVA
+>1_207
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKDAGAKDVIIAATHAVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGVA
+>2_2396
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADYIRTRVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKEAGAKDVIIAATHAVFSEPAAQRLGECGAREVVVTNTLPILEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGDA
+>3_2279
+MTELSRSEDKRLVLAAGRAHPGLAQEIAEALGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFVIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADYIRGQVEGEKVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVRILKEAGAKDVIIAATHAVFSDPAAQRLGESGAREVVVTNTLPIPEEKRFDNLTVLS
+IAPLIARAIREVFEDGSVTSLFDGDA
+>4_476
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKDAGAKDVIIAATHPVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000523.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000523.fa
new file mode 100644
index 0000000000000000000000000000000000000000..29c3524b480817e3d9bbdb2b20246416d8ef14f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000523.fa
@@ -0,0 +1,70 @@
+>0_485
+MIIERRLTPYLVFPEDSLLAALQKMTDNRERTVFVVDSHGFLVGSLTDGDVRRWLLAQPE
+ASLDVAAADVAHRDPATAPLGATPAEMREALPAGALHLPLLDERGRLTALAINREAELRI
+GGHRIGEGHPAFLIAEIGNNHQGDVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA
+TAGEDLGAQRTLDELAKFSLSAEDMVRVFDHVREAGVALMCTPWDAPSMRVLREYPVDGV
+KIASADLTNHGLLRDAAASGLPMVLSTGMSREEEIREAAALVRSFGVPFAMLHAQSTYPA
+PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVALAAVARGAAIIEKHFTVDRGLEGNDHK
+VSLLPEEFAQMVRQTRDIEESIGVGTERVVSTGEAMNRINLAKSLVAARPLRVGATITAD
+DVTVKSPGRGLQPNELPRLVGRTLHREMAEGDFFFAGDLTDTVPTGRQFEFRRPWGLPVR
+YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFSEPMPMGFTTHLPDIFSGDFLVDLASD
+DDAVWERSIAEVQRTIDITRDLKRWFPHEEEPIMVITMGGFTLDRHIRPEERLPKYERIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL
+>1_214
+MIIERRLTPYLVFPEDSLLAALQKMTDNRERTVFVVDSHGFLVGSLTDGDVRRWLLAHPE
+ASLDVAAADVAHRDPATASLGASPDEMREALPAGALHLPLLDERGRLTALAINREAELRI
+GGHRIGEGHPAFLIAEIGNNHQGDVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA
+TAGEDLGAQRTLDELAKFSLSAADMVRVFDHVREAGVALMCTPWDAPSMRVLREYPVDGV
+KIASADLTNHGLLRDAAASGLPMVLSTGMSREEEIRESVALVRSFGVPFAMLHAQSTYPA
+PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVALAAVARGAAIIEKHFTVDRGLEGNDHK
+VSLLPEEFAQMVRQTRDIEESIGVGTERVVSTGEAMNRINLAKSLVAARPLQAGVTITAD
+DVTVKSPGRGLQPNELPRLVGRTLHREMAEGDFFFAGDLTDTVPTGRQFQFRRPWGLPVR
+YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFREPLPMGFTTHLPDIFSGDFLVDLASD
+DDAVWERSIVEVQRTIDITRDLKRWFPNEEEPIMVITMGGFTLDRHIRPEERRPKYERIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL
+>2_2389
+MITERHLTPYLVFPEDSLLVALQKMTDNRERIVFVVDSHGFLAGSLTDGDFRRWLLANPG
+ASLEVAAVEAANRTPATGPVGASPAEVLAALPAGALHLPLLDERGRLAALAINRESELRI
+GEHRIGPGRPAFLIAEIGNNHQGSVDLARELVDLAVEAGADAVKFQLRDMDALYRQSGAG
+TAGEDLGAQRTLDELAKFSLPAEDMVRVFDHVRDAGVALMCTPWDAPSMRVLAQYPVDGV
+KIASADLTNHGLLRDAAAARLPMVLSTGMSREDEIKEAVELVRSSGVPFAVLHAQSTYPA
+PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVPLAAVARGASIIEKHFTVDRGLEGNDHK
+VSLLPEEFAQMVRQTREIEESIGVAAERVVSTGEAMNRINLAKSLVAARPLAAGETVTED
+AVTVKSPGRGLQPNELPRLVGRTLHRDMAEGDFFFAGDLTDTVPTGRQFEFRRPWGLPVR
+YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFTEPLPMGFTTHLPDIFSGDFLVDLASD
+DDAVWERSIAEVQRTIDITRDLKRWFPKEEAPIMVITMGGFTLDRHIAPAERQAKYDRIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL
+>3_2272
+MIIERHLTPYLVFPEDSLTVALQKMTDNRERIVFVVDTHGFLQGSLTDGDVRRWLLAHPG
+AALDSPAVAAANPSPATGLVGDAPSSVLAALPEGALHLPLLDERGHLTALAINRESELRI
+GSHRVGEGRPAFLIAEIGNNHQGSVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA
+TAGEDLGAQRTLDELAKFSLSVDDMVKVFDHTRAAGVALMCTPWDAPSMQVLADYPVDGV
+KIASADLTNHGLLRDAASRGIPMVLSTGMSREEEIQESAALVRSYGVPFAMLHAQSTYPA
+PYKDVNLAYLDRLAEIAQAPVGYSGHERGFHVALAAVVRGASIIEKHFTIDRSLEGNDHK
+VSLLPDEFAQMVRQTREIEESIGVAGERVVSTGEAMNRINLAKSLVAARSLTAGDVVAEA
+DVTVKSPGRGLQPNQLPQLVGRTLHRDLEEGDFFFAGDLTDSVPTGRQFEFRRPWGLPVR
+YHDYAALTKDCTPDFLEFHFSYKDLEIDIDTVFREPMPGGFTTHLPDIFAGDFLVDLASM
+DEQVWERSIAEVQRTIDITRDLKRWFPSEEAPIMVITMGGFTLDRHIRPEERQPKYERIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL
+>4_484
+MIIERRLTPYLVFPEDSLLAALQKMTDNRERTVFVVDSHGFLVGSLTDGDVRRWLVAHPE
+ASLDVAAADVAHRDPVTAPLGASPAEMREALPTGALHLPLLDERGRLTALAINREAELRI
+GGHRIGEGHPAFLIAEIGNNHQGDVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA
+TAGEDLGAQRTLDELAKFSLSAEDMVRVFDHVREAGVALMCTPWDAPSMRVLREYPVDGV
+KIASADLTNHGLLRDAAASGLPMVLSTGMSREEEIRESVALVRSFGVPFAMLHAQSTYPA
+PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVALAAVARGAAIIEKHFTVDRGLEGNDHK
+VSLLPEEFAQMVRQTRDIEESIGVGTERVVSTGEAMNRINLAKSLVAARPLQAGATITAD
+DVTVKSPGRGLQPNELPRLVGRTLHREMAEGDFFFAGDLTDTVPTGRQFQFRRPWGLPVR
+YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFTEPMPMGFTTHLPDIFSGDFLVDLASD
+DDAVWERSIAEVQRTIDITRDLKRWFPNEEEPIMVITMGGFTLDRHIRPEERLPKYERIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000524.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000524.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1fed2c2f0a530eb6235ef0558e7f2ebb8b2d3fbc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000524.fa
@@ -0,0 +1,35 @@
+>0_488
+MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAADGFDVVRL
+GGPGRLGYLRALRAWDRGRGKDDVVWCNGLLPATALAGRPRRIVHLHQVPEKPLLRVFSA
+LARPGALAVLAPSRFAADRIRGARVLHNWVPAPTTPQAGRARDADEPLTVGFLGRLSEDK
+GIVTLLEAAALLRKTDPGAFVFRVAGESRFVADDEAERLATALKAAGEDVQVLGWQDTAE
+FLASVDVLAVPSQWAEVFGLVTAEAMAAGVPVVASDAGAVPEVVGSEHPFVFPQRDAAAL
+ADRLQAVRAVDLGAVAHSQQRRWESLFSPEAGRAAVAELLDDLSL
+>1_217
+MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAADGFDVVRV
+GGPGRLGYMRALRVWDRGRGGDDVVWCNGLLPATALAGRPRRIVHLHQVPEKPLLRVFSA
+LARPGALAVLVPSRFAADRIHGARVLHNWVPGPTTPQAGRARGTDEPVTVGFLGRLSEGK
+GIVTLLEAAALLRRTDPGAFVFRIAGESRFVAEDEAERLATALKAAGEDVQVLGWQDTGE
+FLTSVDVLAVPSQWAESFGLVAAEAMAAGVPVVASDAGAVPEVVGSDHPFVVPQRDAAAL
+ANCLRAVRAVDLGEVAHSQRHRWASLFSPEAGRAAVAELLDDLSL
+>2_2387
+MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAANGFDVVRV
+GGPGRLGYLRALRAWDRDRGNDDVVWCNGLLPATALAGRPRRIVHLHQVPEKPLLRVFSA
+LARPGALAVLAPSRFAADRIRGARVLHNWVPGPTTPPARRARDADEPVTVGFLGRLSEDK
+GIVTLLEAAALLRKTDPGAFVFRVAGESRFVAEDEAERLATALKAAGEDVQVLGWQDTAE
+FLASVDVLAVPSQWAEVFGLVTAEAMAAGVPVVASDAGAVPEVVGNDHPFVFPQRDAAAL
+ADRLQAVRAGDLGAVAHSQRRRWASLFSPEAGRAAVAELLDDLSL
+>3_2269
+MTRRIWIAANQGEVGGGEVMLHHLATALHELGRDIAVVAPAAPSATAARLEADGFTVDRV
+GGPGRAGYMRALRRWHNGHREDVVWCNGLLPATALAGRPRRIVHLHQWLIRPRDRVLGTL
+AMRGALAVIAPSESVAREIPGCRVLHNWVPRPLPLSGAAPARRRPGEGGALRVGYLGRLS
+FDKGFHLLMDVAEELHREQPDEWRFFVAGEPRFTTGDDAREIRERLAASRAVTALGWQAP
+GDFLPTVDVLVVPSLAPESFGLVAAEAMAAGVPVAVSDSGALPEVAGDDHPLLFECDDHE
+ELAAALRRARQIDLAPLVAAQHRRWEALFSPEAGRAGVAALLEELHV
+>4_487
+MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAADGFDVVRV
+GGPGRLGYLRALRAWDRGRDGDDVAWCNGLLPATALAGRPRRIVHLHQVPEKPVLRVFSA
+LARPGALAVLVPSRFAANRIRGARVLHNWVPAPTAPQTRPARGADDPVTVGFLGRLSEDK
+GIVTLLEAAALLRKTDPGAFVFRVAGESRFVAEDEADRLATALKAAGEDVQVLGWQDSGE
+FLATVDVLAVPSQWAEVFGLVTAEAMAAGVPVVASDAGAVPEVVGSDHPFVVPQRDAAAL
+ANCLRAVRAIDLGAVAHSQRHRWESLFSPEAGRAAVAELLDDLSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000535.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000535.fa
new file mode 100644
index 0000000000000000000000000000000000000000..982489ddff45f554d8e0f415d69b01948c2a9823
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000535.fa
@@ -0,0 +1,30 @@
+>0_510
+MGERATRQRPAAPPSLDLEVRVRLAHARITHLLDRAGIRGLHLKGYATEPGVYPDHRRSS
+DVDLLVHPADATAVIELLRSHGWEPVATFSEGSIFQHAATLWHDQLGYVDVHRLFPGLGA
+SPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRESLPAE
+SWAALREEAHRLDAGAAWHVATGEAADGVDSRQLTLFAALHESQSGLELFRTRWRSAATA
+RERAVLVARTIPVNRPHLQMRLGRPVTRADLWREQRARLGALAGWAWTKAVRRDR
+>1_240
+MGEHATGQRPAAPPSLDLEVRVRLAHARITHLLERAGIRGLHLKGYATEPGVYPDHRRSS
+DVDLLVPPADAAAVIALLGSHGWEPVATFSQGSIFQHAATLWHDQLGYVDVHRLFPGLGA
+SPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRESLPAE
+SWAALREEARRLDAGAAWHVATGEAADGVDTRQLTLFAALHESQSGLELFRTRWRSAATV
+RERAALVARTIPVNRPHLQMRLGRPVTRADLWREQRARLGALAGWAWTKAVRRDR
+>2_2366
+MTETGTTDQRAAAQPALDLAVRVRLGHARIAYVMEEAELRGLHVKGYAAEPGVYRGRRSS
+SDVDLLVHPSDAAAAVELLASHGWAPVADFSEGSIFEHAATLWHDHLGYVDVHRLFPGLG
+TDAARTFDALWAERTTRVIAGRPVPVPGPVHQRLVVIVHAARDSHRGALDVRHIRDTSSP
+AEWDALRQEARRLHATAAWHVATGEDADGMDAHDLALFEALQDDESGLDLFRTRWRTAHS
+ARERARLVLHTLPVNRPHLQMRLGHAPTRADLWREQRSRATALARWAWTRGVRRGR
+>3_2247
+MTAAPAPLETRVRLAHARITHLMAAAGVRSLHIKGYAMGPGVYAGGRTSSDVDLLVHPAD
+LSHALDALTSHGWRRIADFAEGSVFEHAATLWHDQLGYVDVHRRLPGLGRSPVDAFEALW
+GERTTTVVAGHAVPVPSLRHQRLVVLVHGARDAGRGRFDVDHLRHTLDAGQWAELRVQAQ
+ILGAGAAWSIATGETDVAGVDEREALLLSAVRGDESGIRLLATRWHAARGWRERLHLLVR
+TVPVNRAHLQMRLGRPPTTADVLREQASRGAALTRWAAGKAVPRVGR
+>4_510
+MLAAMGERATGQRPAAPPSLDLEVRVRLAHARITHLLDRAGIRGLHLKGYATEPGVYPDH
+RRSSDVDLLVPPADADAVIALLGSHGWEPVATFSQGSIFQHAATLWHDQLGYVDVHRLFP
+GLGASPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRES
+LPAESWAALREEAHRLDAGAAWHVATGEAADGVDSRQLTLFAALHESQSGLELFRTRWRS
+AATVRERAALVARTIPVNRPHLQMRLGRPVTRADLWREQGARLGALAGWAWTKAVRRDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000540.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000540.fa
new file mode 100644
index 0000000000000000000000000000000000000000..195444346c94c0a304a9ab9bfc7e38e87e38a038
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000540.fa
@@ -0,0 +1,30 @@
+>0_516
+MTDQTSIPSPDSPLTGDHPGFAEARAAADTIARATGVAEHRVAVVLGSGWGEAAGLIGDE
+VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA
+AAAGARTVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLVGATFVDLTDLYSPRLRAI
+AREVDPSLREGVYVQFAGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGIS
+LVTNLGAGISETPLSHAEVVEAGQAAGPRIARLLADIVGRL
+>1_249
+MTDQTSIPSPDSPLTGDHPGFAEARAAADTIARATGVAEHRVAVVLGSGWGEAAGLIGEE
+VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA
+AAAGARTVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLAGATFVDLTDLYSPRLRAI
+AREVDPSLREGVYVQFAGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGIS
+LVTNLGAGISETPLSHAEVVEAGQAAGPRIARLLADIVGRL
+>2_2357
+MSEQTFSPSPASPLAGDHPGFDQARAAAAVIADATGVAEHRIAVVLGSGWGEAAGLIGEE
+VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA
+AAAGAKTVVLTNGCGGLDPEIAPGTPVLISDHLNLTGATPLVGATFVDLTDLYSPRIRQI
+AREVDPSLREGVYVQFSGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGMS
+LVTNLGAGISETALSHGEVVEAGQAAGPRISRLLADIVWRL
+>3_2239
+MSEQSTPTPTPASLARLAGDHPGFAEARAAAEAIAEATGCAEHRIAVVLGSGWGEAAELI
+GVERARIDLADVPGFHAPKVPGHNAVIRSVELADGSRALVFGSRTHFYESRDAQAVAHTV
+RTAAAAGAATVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLVGATFVDLTDVYSPRI
+RAIAQEVDPTLTEGVYVQFSGPQYETPAEVRMATALGGDLVGMSTALDAIAARHAGLEVF
+GISLVTNHGAGIQETPLSHQEVVEAGQAAGPRISRLLAEIVGRL
+>4_519
+MTDQTSIPSPDSPLTGDHPGFAEARAAADTIARATGVAEHRVAVVLGSGWGEAAGLIGDE
+VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA
+AAAGARTVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLVGATFVDLTDLYSPRLRAI
+AREVDPSLREGVYVQFAGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGIS
+LVTNLGAGISETPLSHAEVVEAGQAAGPRIARLLADIVGRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000541.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000541.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8dc4272fe9941dcfe8624477d6138995ebc8791a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000541.fa
@@ -0,0 +1,45 @@
+>0_517
+MEPVSEENSTFIPSLTIIGGGPGGYEAAMVAAKLGARVTLVERQGLGGAAVLTDVVPSKT
+LIAAADSMRRVGASVDLGVDLGGADVHADMGRVGHRILNLAHEQSSDIRAGLERVGVRVI
+DGVGRVVGPHEVSVRALDDADAGAEPEIITSDAILVAVGASPRELPTAVPDGERIFNWKQ
+VYNLKELPEHLIVVGSGVTGAEFASAYNRLGAKVTLVSSRDRVLPGEDADAAELLEKVFE
+GNGLRVVSRSRAESVERTETGVRVHLSGEGAEDTPSIEGSHALVAVGGVPNTAGLGLDDV
+GVKLTGSGHVLVDGVSRTSVPSIYAAGDCTGKLALASVAAMQGRIAVAHLLGDALKPLRP
+HLLASNIFTSPEIATVGVTQAQVDSGQYQADVLRLDFHTNPRAKMSGAEEGFVKIFARQG
+SGTVIGGVVVSPRASELIYALALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRI
+>1_250
+MEPVTEENSTFIPSLTIIGGGPGGYEAAMVAAKLGARVTLVERQGVGGAAVLTDVVPSKT
+LIAAADSMRRVGASVDLGVDLGGAEAHADMGRVGHRILNLAHEQSSDIRAGLERVGVRVI
+DGVGRVVGPHEVSVRALDDADAGAEPEIITSDAILVAVGASPRELPTAVPDGERIFNWKQ
+VYNLKELPEHLIVVGSGVTGAEFASAYNRLGAKVTLVSSRDRVLPGEDADAAELLEKVFE
+GNGLRVVSRSRAESVERTETGVRVHLSGEGAEDTPSIEGSHALVAVGGVPNTAGLGLDDV
+GVKLSGSGHVLVDGVSRTSVPSIYAAGDCTGTLALASVAAMQGRIAVAHLLGDALKPLRP
+HLLASNIFTSPEIATVGVTQAQVDSGQYQADVLRLDFHTNPRAKMSGAEEGFVKIFARQG
+SGTVIGGVVVSPRASELIYALALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRI
+>2_2356
+MVAAKLGARVTLVERQGVGGAAVLTDVVPSKTLIATADSMRRVGLAEDLGVDLGDAEPRA
+DMRQVDRRILDLAGEQSRDIRAALERRGVRVIDGVARVVGPNEVSVRTLQDADAEPEVIT
+SDAILVAVGASPRELPTAVPDGERIFNWKQLYAMTELPEHLIVVGSGVTGAEFASAYNRL
+GAKVTLVSSRDRVLPGEDADAAELLEKVFQDNGLTVVARSRAEAVERTETGVRVELSGEG
+AADTPYVEGSHALVAVGGIPNTAGLGLEDVGVELTESGHVKVDGVSRTTVPSIYAAGDCT
+GNLALASVAAMQGRIAVAHLLGDALKPLRPHLLASNIFTSPEIATVGVTQAQVDSGQYQA
+DVLRLDFATNPRAKMSGVQEGFVKIFARQGSGTVIGGVVVSPRASELIYALALAVTHKLH
+VDDLADTFTVYPSMSGSIAEAARRLHVRI
+>3_2238
+MNVTEENTTFLPSLTIIGGGPGGYEAALVAAKLGARVTVVERAGMGGSAVLTDVVPSKTL
+IATADSMRRVMAASGLGVDLGEAQPHADMHAVDRRILELAGQQSSDIHRALEKRGVRVVI
+GDAVVTGPHEVTVRRRGIEEGEEPEVITSDAILVAVGASPRELPTARPDSERIFNWKQVY
+ALQDLPEHLIVVGSGVTGAEFASAYNQLGAAVTLVSSRDRVLPGEDPDAAELLEDVFAQN
+GLDVAGRCRAESVERTETGVRVHLSGEGADGRPYIDGSHCLLAVGGVPNTAGLGLEEVGV
+ELTESGHVKVDGVSRTTVPSIYAAGDCTGQLALASVAAMQGRIAVAHLLGDALKPLRPHL
+LASNIFTSPEIATVGVTQAQVDSGQYQADVIRLDFATNPRAKMQGVSTGFVKIFARQGSG
+TVIGGVVVAPRASDLIYSLALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRV
+>4_520
+MEPVSEENSTFIPSLTIIGGGPGGYEAAMVAAKLGARVTLVERQGLGGAAVLTDVVPSKT
+LIAAADSMRRVGASVDLGVDLGGGDVHADMGRVGHRILNLAHEQSSDIRAGLERVGVRAI
+DGVGRVVGPHEVSVRALDDADAGAEPEIITSDAILVAVGASPRELPTAVPDGERIFNWKQ
+VYNLKELPEHLIVVGSGVTGAEFASAYNRLGAKVTLVSSRDRVLPGEDADAAELLEKVFE
+GNGLRVVSRSRAESVERTETGVRVHLSGEGAEDTPSIEGSHALVAVGGVPNTAGLGLDDV
+GVKLTGSGHVLVDGVSRTSVPSIYAAGDCTGKLALASVAAMQGRIAVAHLLGDALKPLRP
+HLLASNIFTSPEIATVGVTQAQVDSGQYQADVLRLDFHTNPRAKMSGAEEGFVKIFARQG
+SGTVIGGVVVSPRASELIYALALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000544.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000544.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6798eda427bdec33196460bf5f10492d63be28b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000544.fa
@@ -0,0 +1,55 @@
+>0_521
+MTQHTSEAAVDGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA
+DDELNARLLEDLAALELQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGA
+AGGFFPGLVERAEAADVVDDALAARIRSGADAAAQAYRDFADTLEAELRPHAPEADGVGI
+EYYRLASRDFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE
+RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLSKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK
+AFHTRALRLGGMGLDTLREALA
+>1_255
+MTQHTSEAAVDGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA
+DDELNARLLEDLAALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQSIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGA
+AGGFFPGLAERAEAADVVDDALAARIRSGADTAAQAYRDFADMLEAELRPHAPEADGVGI
+DYYRLASRVFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE
+RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLTKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK
+AFHTRALRLGGMGLDTLREALA
+>2_2350
+MTQNTPVAADRGARTPSAIDALAERYVADVLALHPDEATTLGFPGHETEYADFSPAGTRA
+DDELNARLLADLEALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVIEQARAHGA
+AGGFFPGLVERAEATDVVDAALAERIRAGADAAAQAYRDFADTLQAELRPHAPEADGVGI
+ELYRLGSRAFLGAEIDLEETYRWGQEELARIIAAQEADAERIKPGATIEEARALLDADPE
+RTLNGTAALQAWMQRLSDEAVQAMKAHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLEKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRTEHEEREGEGFDLK
+AFHTRALRLGGMGLDTLRAALA
+>3_2233
+MTQTTSAPEGARTPSAVDALAERHVAAYLALRPDEATSLGMPGHETEYPDLSPAGAAALD
+ELNRTTLEELAGLEPADDVDRVTVAAMRERLGLEREIHATGRTELNNIASEAQGIRAIFD
+LMPTDTAEQWGHIAGRLENLPAALRGYAESLLASRDAGHVAAVRQVEIVVEQARAHGAEG
+GFFPGLVERAEAADVVDAALAERIRTGAAGAAAAYAEFADTLEAELRPHAPEADAVGIEH
+YRLASRVFLGAEIDLEETYRWGQEELDRIIAAQEADAERIKPGATIEEARAILDADPART
+LTGTKALQEWMQRLSDEAVEAMKAHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSRPG
+RMWWSVPAGEEEFTTWAETTTVYHEGVPGHHLQIATAMMNRGTLNLWRRNFAWTSGHGEG
+WALYAEKLMEEFGFLDDAGDHLGMLDMQRMRAARVVFDIGYHCGFEMPASEGGGEWTPEK
+GYAFLEKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEAREGADFDLKAF
+HTRALRVGGMGLDTLREALA
+>4_524
+MTQHTSEAAADGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA
+DDELNARLLEDLAALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGG
+AGGFFPGLVERAEAADVVDDALAARIRSGADTAAQAYRDFAATLEAELRPHAPEADGVGI
+DYYRLASRVFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE
+RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLAKHLMISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK
+AFHTRALRLGGMGLDTLREALA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000550.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000550.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1c8c0fc0d29377b8c0e6d7da07aee041fa6f2a44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000550.fa
@@ -0,0 +1,35 @@
+>0_528
+MSARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSSGSDWVTDYDR
+RAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVRGLPQFCTSVA
+VTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADATTAGVDLPDR
+DAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRIGSAALDLCMV
+ADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAGDVDGSALAAM
+TGERA
+>1_262
+MSARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSSGSDWVTDYDR
+RAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVRGLPQFCTSVA
+VTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADATTAGVDLPDR
+DAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRIGSAALDLCMV
+ADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAGDVDGSALAAM
+TGERA
+>2_2341
+MSSPTRVAHVPSQPPGISGLLVVAKAAARAGADVLARRWTGHHPAVPLGREEIGAETKTS
+GSDWVTDYDRRAEQAVREVLVAYRPQDEITGEEYGATVPAEPSGLRWSIDPLDGTTNFVR
+GLPQFCTSVAVTGPVDEETAALLGVPAGTRRWLAGVVAAPALGRTWFASAGRGAFSTADA
+TTAGVDVPDRDAAPVRITGPAPGRSGRLLATGFGYDPARRAMQVRALAALLPAFGDVRRI
+GSAALDLCMVADGTLDAYAEFGTQEYDWAAGALIAEEAGVRVRRPASGDGTAHPDWMVAG
+DVDEAALAAAQEETA
+>3_2225
+MSAAPARPASPAGLLVIAKAAARAGADVLAERWAGHHPAVPLTSDELGADTKSSGSDWVT
+DYDRRAEDAVRAVLTGYRPHDEITGEEHGSTAPVEPSGYRWSIDPLDGTTNFIRGLPQFG
+TSVAVEGPVDEETAALLGVLPGSRRWLAGVVAAPALGRTWFASAGRGAFSTADATTAGVA
+VPDRDAAPVRLTGPVPGRSGRLLATGFGYHPGRRAMQLRALAALLPAFGDVRRIGSAALD
+LCMVADGTLDAYAEFGTQEWDWAAGALIADEAGVPVDRPASGDGTGHPDWMTAGDVDAAA
+LAAAKEATA
+>4_531
+MSARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSSGSDWVTDYDR
+RAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVRGLPQFCTSVA
+VTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADATTAGVDLPDR
+DAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRIGSAALDLCMV
+ADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAGDVDGSALAAV
+TGERA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000551.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000551.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a9611c9cfa42cda19a832a4583a5b0ddf4a2078
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000551.fa
@@ -0,0 +1,20 @@
+>0_529
+MRRIVGDPWFYPVLFVAGGLTFMIAGTRLQQVGMIVAGLVLAGYAVTYRWAVRVRSRPFA
+GAQAHVERGGVVVFWRPGCPFTRRLVKELTAQERDRAYWVNIWQEPAAATFLEGLHESRD
+GHPHQAVPTAWLRRRDYVVATDATRARLKDTLRQHAGGDA
+>1_263
+MRRIVGDPWFYPVLFVAGGLTFMIAGTRLQQVGMIVAGLVLAGYAVTYRWAVRVRSRPFA
+GAQAHVERGGVVVFWRPGCPFTRRLVKELTAQERDRAYWVNIWQEPAAATFLEGLHESRD
+GHPHQAVPTAWLRRRDYVVATDATRARLKDTLRQHAGGDA
+>2_2340
+MRRLVGDPWFWPVLFGSAGLVFLVWGTLRRDVVVLVAALAMLWMLRRHLPQLRVRSRPLA
+GAQAHVQDGGVVVFWRPGCQYCQALLRDLDPAQRDAVYWVNIWTDKDAVPVLRRLHAGRD
+GHAHEAVPTVWARRKDFVAADEASRSRLKDMLRDARPAGGPRTREEGPR
+>3_2224
+MRRLVGDPWFWPVLFGAAGVVFLVWGTVRRDVIAIVAGVAMLWMVWQYLPALRVRSCPMA
+GAQAHVDAGGVVVFWRPACRYCLALIKDLDPAQRAAVYWVNIWTDPDAVPVLHRLHATRD
+GHAHEAVPTVWSRRRDFVVKDEATRRRLTDMLGAVRHIPESGR
+>4_532
+MRRIVGDPWFYPVLFVAGGLTFMIAGTRLQQVGMIVAGLVLAGYAVTYRWAVRVRSRPFA
+GAQAHVERGGVVVFWRPGCSFTRRLVTELTAQERERAYWVNIWQEPAAATFLAGLHEARD
+GHPHQAVPTAWLRRRDYVVATDATRARLKDTLRQHAGGDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000561.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000561.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00b8413b89563f1ae7a207684f8fc638f192bf80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000561.fa
@@ -0,0 +1,25 @@
+>0_540
+MPLARLAGVNANPTPAVEPVVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPEHVT
+VAAVRAPLPLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTVSLL
+GFSQGMAMATSLLRLDPEAYACTVALSGFVVDPELDEPRLRELFTRDDDVARVRPKVFWG
+RGQEDPIISEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPRG
+>1_274
+MNANPTPAVEPVVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPEHFTVAAVRAPL
+PLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTVSLLGFSQGMAM
+ATSLLRLDPEAYACTVALSGFVVDPELTEPRLRELFTRDDDVARVRPKVFWGRGQEDPII
+SEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPRG
+>2_2327
+MNNDTANTAPSSETAPFTVRWSRPEGERTEDLLILLHGYGANEDDLFGLVPHLPERFTVA
+AVRAPMTLQPGGYAWFPLSQDPVTGEIGSDAASVRTAIEDLHAWVGAVREGFRTVSLLGF
+SQGMALATSLLRLDPTAYAATVALSGFVVDPTREESGLAGLFDGDDEVARVRPKVFWGRG
+QDDPIISEARVEASHAWLNAHVDLMKIVYAGLPHAINQQELGHVKEYLEHMVR
+>3_2210
+MNDTTPRDPAPFAVRWSRPEGERTEHLLVLLHGYGADEDDLFGLVPQLPEAFTALAVRAP
+MDLPQGGAAWFPLTQDPATGEIGSDAGAVRAAVEDLHAWLPGVSGGFRTVSLLGFSQGMA
+MATSLLRLDPAAYAATVALSGFVVDPLHVEPELEGLFPADETVDAVTPKVFWGRGQEDPI
+ISAQRVEESHGWLTAHTDLTKVVYAGLPHAISPQELGHVREYLTHVVL
+>4_543
+MPLARLAGVNANPTPAVEPVVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPEHVT
+VAAVRAPLPLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTVSLL
+GFSQGMAMATSLLRLDPEAYACTVALSGFVVDPELAEPQLRELFTRDDDVARVRPKVFWG
+RGQEDPIISEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000562.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000562.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4774d5c849fa2e8e9ba19fb28e1fa1a63525a880
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000562.fa
@@ -0,0 +1,15 @@
+>0_541
+MTETNAPDAQPLPIRDESIRLGQALKLASLVEDGAMARDVVTDGLVTVNGAVETRRGAQL
+HDGDVVEFAGEAFVVQAEQA
+>1_275
+MMDTMTETNAPDAQPLPIRDESIRLGQALKLASLVEDGAMARDVVTDGLVTVNGAVETRR
+GAQLHDGDVVEFNGEAFVVQAGQA
+>2_2326
+MMDTMTETNPADARPLPIRDASIRLGQALKLAALVEDGAMARDVVQDGLVTVNGAVETRR
+GAQLKDGDVVEFHGEAVVIEAGSAD
+>3_2209
+MTSSSDVQPLPIRDESIRLGQALKLASLVEDGAMARDVVQDGMVSVNGEVETRRGRQLHD
+GDVVEFNGEEIVVEAGQS
+>4_544
+MTETNAPDAQPLPIRDESIRLGQALKLASLVEDGAMARDVVTDGLVTVNGAVETRRGAQL
+HDGDVVEFAGEAFVVQAEQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000566.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000566.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9528b51d598c4fcb168156afb5bfb6f8c2f2b3d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000566.fa
@@ -0,0 +1,20 @@
+>0_549
+MSEQWSEKDIELANRLFDMARDGDTAQLKAYLDAGVSTRLRNHAGDSFLTLAAYHEHPDT
+VAMLIEAGAEIEHANDRGQRALTCATFKRDVASMRHLLAAGADPDAGTPSARQTAQMFAG
+ADLLAVLDGGGAAPPSEA
+>1_290
+MSEQWSEKDIELANRLFDMARDGDTAQLKAYLDAGVSTRLRNHTGDSFLTLAAYHEHPDT
+VAMLIEAGAEIEHANDRGQRALTCATFKRDVASMRHLLAAGADPDAGTPSARQTAQMFAG
+ADLLAVLDGGDAAPASEA
+>2_2308
+MTEQPQDPRQDQTAAEPAPEPAEALAAETTDAVAPEAAPGEAGQPSPEMLELAGRMFDAA
+RSGDAETLEAYIVAGLNPDLQNGKGDTFLTLAAYHDQPGVVEMLIRVGADVEKANDRGQR
+PLTCATFKGDVASMRLLLAAGADPDAGTPSARQTAQMFGGEEITAVLDEPR
+>3_2198
+MTEHQDTQGQHAPATPPAEPAVESAGPSPEMLELAGRMFDAARTGDVDTLEAYIVAGLNP
+DLQNGKGDTFLTLAAYHDQPAVVEMLIRVGADVEKANDRGQRPLTCATFKGDVASMCLLL
+AAGADPDAGTPSARQTAQMFGGERVAAVLDEAR
+>4_550
+MSEQWSEKDIELANRLFDMARDGDTAQLKAYLDAGVSTRLRNHAGDSFLTLAAYHERPDT
+VAMLIEAGAEIEHANDRGQRALTCATFKRDVASMRHLLAAGADPDAGTPSARQTAQMFAG
+ADLLAVLDREDAAPSSEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000571.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000571.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40bc8376e574be7150c0f44de9510ea3de4eeaf6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000571.fa
@@ -0,0 +1,60 @@
+>0_559
+MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY
+HCFGCGAHGDVISFLMELEHTTFTETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFE
+ANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHATQFGLGYAPQGWSHLLDHLRQRGFR
+DEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP
+LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVA
+RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKG
+DEAVRALIASRRPLFEFAIRAGLKDYDLDTVEGRAGALRHAVPIVAGIKDAVLRPGYERE
+LAGWLGLDPNAVHRAVAAAGRAPRRGPEPEARPAPADDGQAIGPQGRHGEAAAPAPRIVV
+PVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKMAGSAGAT
+PQRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELL
+GRLQRLGPEGDPAEFTRLNSELMELEARRRALRADD
+>1_301
+MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY
+HCFGCGAHGDVISFLMELEHTTFTETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFE
+ANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHAVQFGLGYAPQGWSHLLDHLRQRGFR
+DEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP
+LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVA
+RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKG
+DEAVRALIASRRPLFEFAIRAGLKDYDLNTVEGRAGALRHAAPIVAGIKDAVLRPGYERE
+LAGWLGLDPNAVHRAVAAAGRAPRRGPEPEARPAPADDGQAIGPTGRHGEAAAPAPKIVV
+PVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKMAGSAGAT
+PQRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELL
+GRLQRLGPEGDPAEFTRLNSELMELEARRRALRADD
+>2_2299
+MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY
+HCFGCGEHGDVISFLMELEHTTFTETVERLAARVGVELHYEDGGTGPDKAETGRRRRLLE
+ANKVADEFYRRALGSAEAQTGRDFLTQRGFTQEHAEQFGLGYAPQGWSHLLDHLRQKGFR
+DEELRASGLFSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP
+LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKMA
+RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTYVAVEPSGMDPCDLRMQQG
+DEAVRALIASRRPLFEFAIRAGLKDYDLDTVEGRAGALRHAAPIVAGIKDAVLRPGYERE
+LAGWLGLDPNAVHRAVAAAGRGQRRGGGSEPRREPERGPEPDQAPGQGRGPAPEGPSVGP
+QGRHGEAAAPAPQVLVPVDPRDPVARCERESLEVVLQHPTLLSAEQWTALYAARFTIPQY
+AAVHHGVKVAGSSGATPQRWVDAVRYAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIM
+NRLFALQIVHRKEELLGRLQRLGPDGDPAEFTALNSELMELEARRRALRADD
+>3_2193
+MVRMAGLIVRKDIDLVRERADLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGV
+GTYHCFGCGEHGDVISFLMEMEHTTFTETVERLAARAGVELHYEDGQGPDRAETSRRRRL
+LEANKLADEFYRARLAAPDAQPGRDFLTGRGFTQEHAEQFGLGYAPQGWSALLDHLRQQG
+FRDDELRASGLFSEGQRGLYDRFRGRLLWPIRDMTGNTIGFGARKLFEDDPGPKYLNTPE
+TPLYKKSQVLYGIDLAKRAIAKERQLVLVEGYTDVMAAHLSGVETAVATCGTAFGADHIK
+IARRLISDDGTGGEVIFTFDGDAAGQKAALKAFDEDHRFLAKTFVAVEPNGLDPCDLRMQ
+QGEEAVRALIASRRPLFEFAISAGLKDYDLNTVEGRAGALRHAAPIVAGIKDSVLRPGYE
+RELAGWLGMDPNVVSRAVAQELRGRRRGGPSGGSAERTPAPERAPEGANAGQAPGEEPAA
+PRPALIVPVDPRDPAARRERESLEVVLQHPTLLSAEQWTAFYQARFTIPQYAAVHHAVKV
+AGTAGATPSRWVDAVRDAAPGEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFSLQIV
+HRKEELLGQLQRLGPEGDHDEFMRLNAELMELETRRRALRADD
+>4_560
+MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY
+HCFGCGAHGDVISFLMELEHTTFMETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFE
+ANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHAVQFGLGYAPQGWSHLLDHLRQRGFR
+DEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP
+LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVA
+RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKG
+DEAVRALIASRRPLFEFAIRAGLKDYDLNTVEGRAGALRHAAPIVAGIKDAVLRPGYERE
+LAGWLGLGPNAVHRAVAAAGRAPRRGPEPEARPTPASDGQAVGPTGRHGEAAAPAPRIVV
+PVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKVAGSAGAT
+PQRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELL
+GRLQRLGPEGDPAEFTRLNSELMELEARRRALRADD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000578.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000578.fa
new file mode 100644
index 0000000000000000000000000000000000000000..637ab1d5cd13f06edf241b6639c963f06a8fa449
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000578.fa
@@ -0,0 +1,36 @@
+>0_616
+MDTTRFDDDLRAMLGEVESDRRGEPSDYLEDVAGQHVDGLAVAVCTVDGHQAAAGETEHA
+FALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGAILV
+HSLLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGRLPI
+SAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQTMSVMLTCGM
+YDASGQWVAEVGVPAKSGVSGALLGAVPGALGLAAWSPRLDEQGNSRRGIGLFEGLSARW
+DLHVLQHRGALRGLSGPR
+>1_362
+MDTTRFDDDLRAMLDEVESDRRGEPSDYLEDVAGQHVDGLAVAVCTVDGHQAAAGETEHA
+FALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGAILV
+HSLLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGRLPI
+SAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQAMSVMLTCGM
+YDASGQWVAEVGVPAKSGVSGALLGAVPGALGLATWSPRLDEQGNSRRGIGLFEGLSARW
+DLHVLQHRGALRGLSGPR
+>2_2270
+MDTTRLDDDLRAMLAEVESDRRGEPSDYLEDVAGQHVDGLAAAVCTVDGHQAAAGETDHA
+FALQSVSKALTYAVVLQEVGLDAVLERVGVEPSGEAFNHLSLHDDGRPYNPLINAGAIMA
+HALLPAGDHEERVALLVRRYSALAGAELEVSQDVLDAELTRADRNLGLAHLLADAGQLPV
+SAREAVAGYLAQCSVTVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQTMSVMLTCGM
+YDATGQWVAEVGVPAKSGVSGALLGAVPGALGIATWSPRLDERGNSRRGIGIFEGLSARW
+DLHVLQHRGALRGLRASR
+>3_2132
+MGIGSLIATMLPSSIAFLPACTGMVIGWRWLGLPLGPNARSSAHRDRPGARPRPGRPSTT
+VTGMDTTRFDDDLRAMLGEVESDRRGEPSDYLEDVAGQHVDGLAVAVCTVDGHQAAAGET
+EHAFALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGA
+ILVHSLLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGR
+LPISAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQTMSVMLT
+CGMYDASGQWVAEVGVPAKSGVSGALLGAVPGALGLAAWSPRLDEQGNSRRGIGLFEGLS
+SRWDLHVLQHRGALRGLSGPR
+>4_586
+MDTTRFDDDLRAMLDEVESDRRGEPSDYREDVAGQHVDGLAAAVCTVDGHQAAAGETEHA
+FALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGAILV
+HALLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGRLPI
+SAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQAMSVMLTCGM
+YDASGQWVAEVGVPAKSGVSGALLGAVPGALGIATWSPRLDEQGNSRRGIGLFEGLSARW
+DLHVLQHRGALRGLSGPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000580.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000580.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28be3372a7a97cb64bdc2fda09d08dee2c0ce825
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000580.fa
@@ -0,0 +1,35 @@
+>0_618
+MTARLLADVDTGIDDACALLHLVGAHRLGAGPELAAVTTTGGNATARDCALNTAAVLDLA
+GRADVEVAVGAETPLRRPAVTTPETHGDGGLGHARIVRRPERLSPRPAVDVWLDELRAHP
+GETAILCTAPLTNLALALRTEPRLPFLARGIVIMGGSFYHPGNTTPTAEWNTWVDPDAAK
+EVFAAVEGLPEDRLPIVCALETTERIEYTPALLDGLLADAGAHPVGWSADRPRVAGPDAA
+TGSPVLDVLADALRFYFEFHHDYDQGYIAHLHDLFAAQVAAGQARIATRATVVDVEADSE
+LLRGTTVHDTRDIWGRRPNAQLVTANDPAEVFAAFARAVGAVVAGERTLDGGSPAR
+>1_364
+MTARLLADVDTGIDDACALLHLVGAHRLGVGPELAAVTTTGGNATARDCALNTAAVLDLA
+GRADVEVAVGAETPLRRPAVTTPETHGDGGLGHARIVRRPERLSSRPAVDVWLDELRAHP
+GETTILCTAPLTNLALALRTEPRLPFLARGIVIMGGSFYHPGNTTPTAEWNTWVDPDAAK
+EVFAAVEGLPEDRLPIVCALETTERIEYTPALLDGLLADAGARPVGWSADRPRVAGPDAA
+TGSPVLDVLADALRFYFEFHHDYDQGYIAHLHDLFAAQVAAGQARIATRATVVDVEADSE
+LLRGTTVHDTRDIWGMRPNAQLVTANDPAEVFAAFARAVGAVVAGERTLDGGSPAR
+>2_369
+MGARILADMDTGIDDACALLQLVGAGAELAAVTTTGGNATARECALNTAALLDLMGRTDV
+EVAVGAEAPLQRPPETTPETHGDGGLGYARLAHRPERLSARSAVDVWVEELRARPGRTTI
+LCTAPLTNLALALRAEPALPELAAGVVIMGGAFYYPGNTTPTAEWNTWCDPDAAKEVFAA
+FEGLPEDRLPLLCPLETTERIEYTPALLDALLTGVGHAPTGWSVDRARHAGPQADTGSPV
+LDVLADALRFYFEFHHDYDQGYVAHLHDLFAAQVALGTAQIRTQATVVDVEADSDLLRGT
+TVHDDRHIWGRRPNARRVVDADPAGVFAAFAQAASAAARAGDDAGR
+>3_2130
+MAAVTARLLADVDTGIDDACALLHLVGAHRLGAGPELAAVTTTGGNATARDCALNTAAVL
+DLAGRADVEVAVGAETPLRRPAVTTPETHGDGGLGHARIDRRPERLSPRPAVDVWLDELR
+AHPGETTILCTAPLTNLALALRAEPRLPFLARGIVIMGGSFYHPGNTTPTAEWNTWVDPD
+SAKEVFAAVEGLPEDRLPIVCALETTERIEYTPALLDGLLADAGARPARWDVARPRVSGP
+AADTGHPVTDVLADALRFYFEFHHDYDQGYIAHLHDLVAAQVAAGQADVTLQATVVDVEA
+DSELLRGTTVHDDRRIWGRRPNARRVTGCDPRRVFEDFAQAVGALTGAGVG
+>4_588
+MAAVTARLLADVDTGIDDACALLHLVGAHRLGAGPELVAVTTTGGNASARDCALNTAAVL
+DLAGRADVEVAVGAETPLRRPAVTTPETHGDGGLGHARIVRHPERLSPRPAVDVWLDELR
+AHPGETTILCTAPLTNLALALRTEPRLPFLARGIVIMGGSFYHPGNTTPTAEWNTWVDPD
+AAKEVFAAVEGLPEDRLPIVCALETTERIEYTPALLDGLLADAGARPVGWSADRPRVAGP
+DAATGSPVLDVLADALRFYFEFHHDYDQGYIAHLHDLFAAQVAAGQARIATRATVIDVEA
+DSELLRGTTVHDTRDIWGRRPNAQLVTANDPAEVFAAFARAVGAVVAGERTPDGGAPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000581.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000581.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa64113564fb4d2430b18f618d238c4598b89786
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000581.fa
@@ -0,0 +1,35 @@
+>0_620
+MSHQAPPADASKVRAPRTAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELELAKRHVAAK
+GKKAGIGAGIAVVGLFFLALMVVALVVTLIGAFADPTFWFPALMVALAFLVLGLIFAGVG
+LMMVKGAMPLVPQEIVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAAREAERKK
+VEKEENKKARKNGEAAPHPDRADASEAEIRRRADLRRRHLGDIRSGLDEKTSVKGQLAAF
+AAQRKGRGVTPETAHATEQTAPFTGAARAGERTAEAEDYVKDNWQPLALLGASSAAFVAL
+AGRLRRR
+>1_366
+MSHQAPPADASKVRAPRTAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELELAKRHVAAK
+GKKAGIGAGIAVVGLFFLALMVVALVVTLIGAFADPTFWFPALMVALAFLVLGLIFAGVG
+LMMVKGAMPLVPQEIVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAAREAERKK
+VEKKENKKARKNGEAAPHPDRADASEAEIRRRADLRRRHLGDIRSGLDEKTSVKGQLAAF
+AAQRKGRGVTPETAHATEQTAPFTGAARAGERTAEAEDYVKDNWQPLALLGASSAAFVAL
+AGRLRRR
+>2_2267
+MSHQAPPADALKAGAPRPAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELALAKGHVVAK
+GKKAGIGAGVTVVGLFFLALVVVALVVALIGAFADPTFWFPALMVAAAFLVLGAIFAGIG
+LFMVKGAMPLVPQETVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAKRAEERRK
+VEKEENKKARKNGEAAPHPDRDEASEAEIRRRADLRRRHLGDIRSGLEEKTSVKGQLAAF
+AAQRKGRGVTPQTAHATDQTAPFTGAARAGEKAAEAEDYVKDNWQPLALLGASSAAFLAL
+AGRLRRR
+>3_2125
+MSHAAPTAAPRAPRPTTPVTPQTRASSLTDLLAAVVRLLPLQLKDELALAKGQAAAKGKK
+AGIGAALAVVGLFFLALMTIALVVALIGAFANPPFWFPALMVALVFLVLGLVLAGVGAMQ
+IKGAMPLVPQETVRNLEYDLGYLKEGNDFDPAEYDRLKAERAEAKRLEKQREAERKKVEK
+EENKQARKDGLAAPHPAKDDASEDEVRRRAELRRRHLGDIRSGLDEKTSVKGQVAAFTAQ
+RKLRGTTPDTAHATEQTAPFTTAARAGEQTAAAEDYVKERWQPLALLGASGTAFAVLASR
+LRGRKG
+>4_590
+MSHQAPPADASKARAPRTAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELALAKGHVAAK
+GKKAGIGAGVAVVGLFFLALMVVALVVTLIGAFADPSFWFPALMVALAFLVLGLIFAGVG
+LVMVKGAMPLVPQETVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAAREAERKK
+VEKEENKKARKNGEAAPHPDRDDATEAEIRRRADLRRRHLGDIRSGLDEKTNVKGQLAAF
+AAQRKGRGVTPETTHATEQTAPFTGAARAGERTAEAEDYVKDNWQPLALLGASSAAFVAL
+AGRLRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000582.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000582.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6979d3ec2216674ec4a45da1a86562afc8560e35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000582.fa
@@ -0,0 +1,40 @@
+>0_622
+MSDRPGIAADRPLKVLIAADTYPPHVNGAATFGHRLATALHARGHEVHVVMPRSDAGPDT
+VEHRPEATVHLLRSLPAPTHEYYRVVLPRHAKTSFRRIYREVQPDVVHAQCHYMIGEAAI
+NEAERRRIRIVSTNHFMPENLEPFLPFPQWFLDIVSRVSWKDMGRLMGKGAVVTTPTALA
+AQAMAEHAGLDNVLPVSNGIDASAYELQPGERVDHPGHPVVLFVGRLAVEKNVEVLIRAI
+AHLARTRPDLDVHAEIVGDGEQRDRIRATVDEEGAADRVLLRGHVSEEELRAAYLRADVF
+CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALAERIARIL
+DLSDAERAAMGEASHAKALHHSAQKTVDIFERLYRGATAAEVRALL
+>1_368
+MSDRPGIAADRPLKVLIAADTYPPHVNGAATFGHRLATALHARGHEVHVVMPRSDAGPDT
+VEHRPEATVHLLRSLPAPTHEYYRVVLPRHAKTSFRRIYREVQPDVVHAQCHYMIGEAAI
+NEAERRRIRIVSTNHFMPENLEPFLPFPQWFLDIVSRVSWKDMGRLMGKGAVVTTPTALA
+AQAMAEHAGLDNVLPISNGIDASAYELQPGEKVDHPGHPVVLFVGRLAVEKNVEVLIRAI
+AHLARTRPDLDVHAEIVGDGEQRDRIRATVDEEGAADRVLLRGHVSEEELRAAYLRADVF
+CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALAERIARIL
+DLSDAERAAMGEASHAKALHHSAQKTVDIFERLYRGATAAEVRALL
+>2_2265
+MSDRPGTAADRPLKVLIAADTYPPHVNGAATFCHRLATALHARGHEVHVVMPRGEAGPDT
+VEERPEATVHLLRAIPAPTHEYYRLVMPWHAKAAFRRIYREVQPDVVHVQCHYMVGEAAI
+NEAERRRIRMVSTNHFMPENLEPFLPFPQWFLDIVSRVSWRDMGRLMGKGAAVTTPTALA
+ARAMAEHAGLDNVLPVSNGIDAAAYELQPGETVDHPGHPVVLFVGRLAVEKNVEVLIRAI
+AHLARVRPDLDVHAEIVGDGEQRDRIRAAVESEGVADRVLLRGHVSDEELRAAYLRADVF
+CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALAERVARIL
+DLPEAERAAMGEASHAKAMHHSAQKTVDVFERLYRGATPAEVRELL
+>3_2123
+MTSSARPAQERPLTVVIAADTYPPDVNGAAVFCFRLASALHERGHRVHVIAARNEPGPDT
+VEERPEATVHRLESHRAFTHEYYRLVFPWHASRSIDRILAEVRPDVVHAQCHYMIGEAAI
+NVADRRRIRTVSTNHFMPENLEPFLPFPQWFLNIVSKNSWRDMGRLMGKGAAVTTPTALA
+AAAMAEHAGLDRVLPISNGIDASAYELAPGEVVERAAHPTVLFVGRLAVEKHVDVLVRAV
+AHLARTRPDLDVHAEIVGDGEQRTALDAVIAEEGVADRVRRLGHVSDAELHTAYLRADVF
+CQPGTAELQSLVSLEAMSASTPVVLADALALPHLVDDGVNGWLFPPGDHVALAERIARVL
+DLPEAGRAAMGEASHAKAVRHSQAKTVDLFERLYRGATPAEIRAAL
+>4_592
+MSDRPGIAADRPLKVLIAADTYPPHVNGAATFGHRLATALHARGHEVHVVMPRSDAGPDT
+VEHRPEATVHLLRSLPAPTHEYYRVVLPRHAKISFRRIYREVQPDVVHAQCHYMIGEAAI
+NEAERRRIRIVSTNHFMPENLEPFLPFPQWFLDIVSRVSWKDMGRLMGKGAVVTTPTALA
+AQAMAEHAGLDNVLPVSNGIDASAYELQPGERVDHPGHPVVLFVGRLAVEKNVEVLIRAI
+AHLARTRPDLDVHAEIVGDGEQRDRIRATVDEEGVADRVLLRGHVSEEELRAAYLRADVF
+CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALADRIARIL
+DLSDADRAAMGEASHAKALHHSAQKTVDIFERLYRGATAAEVRAML
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000583.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000583.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b013ec012e7b25fb537e8ea9e230f2f75a206b5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000583.fa
@@ -0,0 +1,30 @@
+>0_623
+MSVTSSHAAVRRAPRTAAASVALALGAAALTGVGTVSVAETAQAAETAYTVRSGDGWWII
+AQRTGVSMSRLQSLNGMTAATVLHPGMVLKTSGTATPTPAPAPSTSGSTYTVLAGDGWWI
+ISYRTGVSASILQSINGMSSSTMLHPGMVLKTTSVSTSSAPAVAPAPAPASKQAAVDYVR
+SAVRNPSSYYVWGGNGPSGFDCSGLTQQAMARAGISIPRRAGDQYLAAKSYVPISQAQPG
+DLVFYANQSTGRIYHTAMYMGGGQLAHALNEDAGLVFTSTTIMKSDMLAVAARY
+>1_369
+MSVTSSHAASRRAPRTAAASVALALGAAALTGVGTVSVAETAQAAETTYTVRSGDGWWII
+AQRTGVSMSTLQSLNGMTAATVLHPGMVLETSGTATPAPAPAPSTSGSTYTVLAGDGWWI
+ISYRTGVSASILQSINGMTSSTMLHPGMVLKTTSVSTSSAPALAPASAPASKQAAVDYVR
+AAVRNPSSYYAWGGNGPSGFDCSGLTQQAMAQAGISIPRRAGDQYLAAKSYVPISQAQPG
+DLVFYANQSTGRIYHVAMYMGGGQLAHALNEDAGLVFTSTTIMKSDMLAVAARY
+>2_2264
+MSVTSSRAASRRAPRTAAASLALALGAGALAGVGSVTAAETAQAVETTYTVRAGDGWWVI
+SQRTGVSMSTLQSLNGMTSATMLHPGMVLKTSGTAAPAPAPAPSASTYTVLAGDGWWIIS
+YRTGVSASVLQSINGMTSSTVLHPGMVLKTSVVASSAPAPAPAPVTNGKQAAVDFVRSTV
+QNPSSYYLWGGNGPYGFDCSGLTQQAMAKAGISIPRRAGDQYNAAKSYVPISQAQPGDLV
+FYANQSTGRIYHVAMYMGGGQLAHALNEDAGLLFTSTTIMKSDMLAVAARY
+>3_2120
+MPEALLTPARRPRAAAASLALALGAGAGVTAGAAVIAPQAVAAETYTVQAGDGWWIISQR
+TGVSMATLMQLNGMTSADMLHPGMVLKTSGTVTAAAGTYTVKAGDGWYAISRATGVPVST
+LTSLNGMTITSMLYPGMVLKTTGTPASTAPAPAPAPAPVVRQSSKQAAIDFAVAKVNDPN
+TYYAWGGNGPYGYDCSGLTKAAFAAAGITIPRVSHDQYVNAPAYAPLSQAQPGDLVFWAN
+QSTGRVYHVAVYIGNGKVAHALNTTDDLVITSTDVMTSNRLAVVGRY
+>4_593
+MSVTSPHAAARRAPRTAAASVALALGAAALTGVGTVSVAETAQAAETTYTVRSGDGWWII
+AQRTGVSMSTLQSLNGMTAATVLHPGMVLKTSGTATPAPAPAPSTSGSTYTVLAGDGWWI
+ISYRTGVSASVLQSINGMTSSTMLHPGMVLKTTSVSTSSAPAPAPAPASKQAAVDYVRSA
+VRNPSSYYVWGGNGPSGFDCSGLTQQAMARAGISIPRRAGDQYLAAKSYVPISQAQPGDL
+VFYANQSTGRIYHTAMYMGGGQLAHALNEDAGLVFTSTTIMKSDMLAVAARY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000584.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000584.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0c54131a298499ece4482ea5d2549b9c9fefda27
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000584.fa
@@ -0,0 +1,25 @@
+>0_625
+MTPRTHLPRPLPRPHIAGCVAAALLAWLVLASGVGGLDAVPRATSAPSGRDALLLVAASP
+AGPGSTAAPVAWHAPVAGAAPDDVLRAFVAPERPWGRGHRGVDLAVPSGAAIRAPAAGRV
+VFAGVVVDRPVLTLEHEDGTRSSLEPVEADVAVGAVVAAGDPVGRLAGAPPHCTRACVHW
+GVREPDGWRVGDAAFDRYLDPLVLIGWSGPSVLWPHAAPHPARP
+>1_371
+MTPRTLLPRPLPRPRIAGCVAAALLAWLVLALEMGDLGPASRATPAPSTRDALLLVAASP
+AGPGATAAPVAWHPPVAGAAPDDVLRAFVAPERPWSRGHRGVDLAVQTGAPIQAPAAGRV
+VFAGVVVDRPVLTLEHADGTRSSLEPVEADVAVGAVVDAGDPVGRLAGAPPHCPRACVHW
+GVREPDGWRVGDAAFDRYLDPLVLIGWSGPSVLWPHAAPHPARP
+>2_2262
+MTARSPAPRRARPAASPHRLLAVLLLCVLGLALAFALGPGIGAATPSSIRAEDGPTADAR
+LAVAATPARAWTAPAAGVRPGDVLRPFAAPERPWGRGHRGVDLAVSPGAAVLAPAAGTVV
+FAGTVVDRPVVTLEHADGTRSSLEPVEAAAPVGARLERGAPLGTVADAPAHCAVPCVHWG
+VRVPDGWRFGDATFDRYLDPLVLIGWSGPSVLWPHAAPPPAGPAPARE
+>3_2118
+MNEASTPPPRLRAAAVLAVALLATASAARAEDAPAAPPVTGALLAPTPGAGPSDVLRGFA
+GPERPWSRGHRGVDLATSSGLVTAPAAGTVRFVGSVAGRGVLTLAHPDGTLSSFEPVTSD
+LTAGQAVAAGQEVARVQEGAAHCPVRCVHWGVRREDAWAVGAARFDRYLDPLLLLGWSGP
+SVLWPVGDAG
+>4_595
+MTPRTLLPRPLPRPRIAGCVAAALLAWLVLALGMGDLGPVSRATPAPSTRDALLLVAASP
+AGPGATAAPVAWHPPVAGAAPDDVLRAFVAPERPWSRGHRGVDLAVQTGAPIQAPAAGRV
+VFAGVVVDRPVLTLEHEDGTRSSLEPVEADVAVGAVVAAGDPVGRLAGAPPHCTRACVHW
+GVREPDGWRVGEAAFDRYLDPLVLIGWSGPSVLWPHAAPHPARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000586.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000586.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2452e9e689b552eab7c5ee71bc513fe1439ba240
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000586.fa
@@ -0,0 +1,30 @@
+>0_627
+MANYTAADIKALRERTGAGMMDVKKALDEADGDAEKAIEIIRVKGLKGATKREGRSAAEG
+LVAATVENGVGVMIELNCETDFVAKADKFIALGDVVLRAAVASGATDVDGLLASEHEGRT
+LGDYVTEEGALLGEKVAVRRLARVEGAYVDAYLHKTSKDLPAQVGVLLAVDADSAEAKTA
+AHDIAVHVAAYSPTYLTREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK
+EIVLVDQPFAKDPKQTVGKVASDAGTNVTGFARFRVGN
+>1_373
+MANYTAADIKALRERTGAGMMDVKKALDEANGDAEKAIEIIRVKGLKGATKREGRSAAEG
+LVAATVENGVGVMIELNCETDFVAKADKFIALGDVVLRAAVASGATDVDGLLASDYEGRT
+LGDYVTEEGALLGEKVAVRRLARVEGAFVDAYLHKTSKDLPAQVGVLLAVDADSADAKTA
+AHDIAVHTAAYSPTYLTREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK
+EIVLVDQPFAKDPKQTVGKVASDAGTNVTGFARFRVGN
+>2_2260
+MANYTAADIKALRERTGAGMMDVKKALDEANGDAEKAIEIIRVKGLKGATKREGRSAAEG
+LVAATVENGVGVMIELNCETDFVAKAEKFITLGDVVLRAAVASGAADVESLLASEHEGRT
+LGDHVIEEGALLGEKVAVRRLARVEGALVDAYLHKTSKDLPAQVGVLLAVDADSAEAKTA
+AHDIAVHTAAYSPTYLSREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK
+EIVLEDQPFAKDPKQTVGKVASDAGTKVTGFARFRVGN
+>3_2116
+MANYTAADIKALRERTGAGMMDVKKALDEANGDADKAVEIIRVKGLKGATKREGRSAAEG
+LVAATVENGVGVMIELNCETDFVAKADKFISLGDVVLKAAVASGAADVDSLLASDHEGRT
+LGDYVTEEGALLGEKVAVRRVARVEGAHVDAYLHKTSKDLPAQVGVLLAVDADSDAAKTA
+AHDIAVHTAAYSPTYLTREDVPAETVENERRIAEESARAEGKPEQALAKIVEGRLTGFFK
+EGVLVDQPFAKDPKTTVGKVASEAGTAVTGYARFRVGN
+>4_597
+MANYTAADIKALRERTGAGMMDVKKALDEANGDAEKAIEIIRVKGLKGATKREGRSAAEG
+LVAATVENGVGVMIELNCETDFVAKADKFIALGDVVLRAAVASGATDVDGLLASDYEGRT
+LGDYVTEEGALLGEKVAVRRLARVEGAFVDAYLHKTSKDLPAQVGVLLAVDADSADAKTA
+AHDIAVHTAAYSPTYLTREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK
+EIVLVDQPFAKDPKQTVGKVASDAGTNVTGFARFRVGN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000587.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000587.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d154f3d1ad6c2f48d4070461a882848cb17146c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000587.fa
@@ -0,0 +1,30 @@
+>0_628
+METNRAPEDPTTAHAPQTSDDTGRRRVLLKLSGEVFGGGKIGVDPETVRGIAEQIAAAAD
+QVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVTTRVQSA
+IHMEQVAESYIPLRAIRHMQKGRVVIFGAGTGLPYFSTDTVAAQRALEVGADEVLMAKSG
+VDGVYTADPKKDPTAERLTHLTYDEALLRNIRVMDLTAMTMCKDNDLDMRVFGMEGPGNV
+TRALLGEPIGTTVTV
+>1_374
+METNRAPEDPTTAHAPQTSDDTGRRRVLLKLSGEVFGGGKIGVDPETVRGIAEQIAAAAD
+QVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVTTRVQSA
+IHMEQVAESYIPLRAIRHMQKGRVVIFGAGTGLPYFSTDTVAAQRALEVGADEVLMAKSG
+VDGVYTADPKKDPTAERLTHLTYDEALLRNIRVMDLTAMTMCKDNDLDMRVFGMEGPGNV
+TRALLGEPIGTTVTV
+>2_2259
+METNRAPEDPKTAHVPQTSDDTGRRRVLLKLSGEVFGGGKVGVDPETVRGIAEQIAVAAD
+RVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVSTRVQSA
+IHMEQVAESYIPLRAIRHMQKGRVVVFGAGTGLPYFSTDTVAAQRALEIGADEVLMAKSG
+VDGVYTADPKKDPSAELLTHLTYDEALLRNIRVMDLTAMTMCKDNNLDMRVFGMEGPGNV
+TRALLGEPIGTTVTV
+>3_2115
+MSPAQQPENHAVDAEDTGRRRVLLKLSGEVFGGGSVGIDPVTVRGIAEQIAEAAEQVEIS
+IVVGGGNFFRGAELSESGMDRRRADYMGMLGTVMNCLALQDFLLQAGVSTRVQSAIHMEQ
+VAESYIPLRAVRHMQKGRVVVFGAGTGLPYFSTDTVAAQRALEIGADEVLMAKSGVDGVY
+TADPKKDPTAQRLEHLTYDEALRKDIRVMDLTAMTMCKDNGLSMRVFGMEGPGNVTRALL
+GEEIGTSVTP
+>4_598
+METNRAPEDPTTAHAPQTSDDTGRRRVLLKLSGEVFGGGKIGVDPETVRGIAEQIAAAAD
+QVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVTTRVQSA
+IHMEQVAESYIPLRAIRHMQKGRVVIFGAGTGLPYFSTDTVAAQRALEVGADEVLMAKSG
+VDGVYTADPKKDPTAERLTHLTYDEALLRNIRVMDLTAMTMCKDNDLDMRVFGMEGPGNV
+TRALLGEPIGTTVTV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000590.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000590.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb70877ad683d1df69d01e1e07de2a8b10ae6f96
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000590.fa
@@ -0,0 +1,40 @@
+>0_632
+MTLVDHTRPTGGQSAGSPPPAGPAEAVMLQVLDTEGRRRPQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY
+FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH
+QELERQRREHALYLQQFGDEEAGA
+>1_378
+MTLVDHTRPTGGQSAGSPLPAGPAEAVMLQVLDTEGRRRPQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY
+FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH
+QELERQRREHALYLQQFDDEEAGA
+>2_2255
+MTLVDHTRPAGGEAATSPPPGEPAEAPMLQVLDAEGRRHAQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALREDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSGWDPQATGVATQQIIIGAQALHAVGYAMGVQRDQADAATIVY
+FGDGATSQGDVNEAMVFSASYRSPVVFFCQNNHWAISEPVKLQTRRSIADRPWGFGIPSL
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALESLVEDGAELLFDEIYAEPH
+QELERQRREHALYLQQFDDEEAGA
+>3_2110
+MTDVHLPEQDAPPRSDRPAEQLQVLTPDGRRSPSPELDPWLTDVDEEMLARLHRELTLVR
+RLDTEATHLQRQGRLALWPPLRGQEASQVGAAAALRPADHVFPSYRENGLCLLRGVEAGE
+LLRVWSGSSFSGWDPAATGVATQQLVIGAQTLHAVGYAMGVQRDAADVSTLVCFGDGATS
+EGDVHEAMVFAASYQAPVVFFCQNNHWAISEPVGLQARRSIADRAWGYGIPALRVDGNDV
+LAVLAAVRRGVDRAAAGAGPMFVEAVTYRMGAHTTADDPTRYQDPAELEAWARRDPLERL
+TAHLRDVGADADAVVDASEAAADDLAARMRADLDALPEEGPEALFAHVYAEPHQELARQQ
+RDLQLHLDGLDAGEEQA
+>4_602
+MTLVDHTRPTGGQSAGSPPPAGPAEAVMLQVLDAEGRRRPQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY
+FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH
+QELERQRREHALYLQQFDDEEAGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000591.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000591.fa
new file mode 100644
index 0000000000000000000000000000000000000000..456af99531ffaa4cfe5bec995147d3f61379a86b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000591.fa
@@ -0,0 +1,35 @@
+>0_633
+MSERMTFGRAINRGLQRALADDPKVLLMGEDIGALGGVFRITDGLQAEFGEDRVLDTPLA
+ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF
+GGGIGSPEHHSESPEAYFLHTAGLRVVSPSSPQEGYDLIRAAIASEDPVVYLEPKRRYHD
+KGDVDLDVAIPPMSPARILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS
+PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP
+PSKLEHLHLPDLDRILDGLDRALGRPNSLDSVDAFAAPETAEQFLAAQNAGEETR
+>1_379
+MSERMTFSRAINRGLHRALADDPKVLLMGEDIGALGGVFRITDGLQAEFGEDRVLDTPLA
+ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF
+GGGIGSPEHHSESPEAYFLHTAGLRVVSPSSPQEGYDLIRAAIASEDPVVYLEPKRRYHD
+KGDVDLDVAIPPMSPARILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS
+PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP
+PSKLEHLHLPDLDRILDGLDRALGRPNSLDSVDAFAAPETAEQFLAAQNAGEETR
+>2_2254
+MSERMTFGRAINRGLHRALADDPKVLLMGEDIGALGGVFRITDGLQDEFGEDRVLDTPLA
+ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF
+GGGIGSPEHHSESPEAYFLHTPGLRVVSPSSPQEGHDLIRAAIASDDPVVYLEPKRRYHD
+KGEVDLDADIPPMSTAKILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS
+PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP
+PSKLEHLHLPDLDRILDGVDRALGRPNSLDSVDAFAAPETAEQFLAAQTAGEETR
+>3_2109
+MSEQMTFGRALNRGLHRALADDPKVLLMGEDIGRLGGVFRITDGLQEEFGVDRVVDTPLA
+EAGIVGTAIGLALRGYRPVVEIQFDGFLYPAFDQIVANLAKLRARTRGRVAVPVTIRIPY
+GGGIGSPEHHCESPEAYFLHTPGLRVVSPSSPQAGYEMIRAAIASDDPVVFFEPKRRYHD
+KGPVDLDAAPGPLSVGRVLRPGADVTLVAYGPLVKTALQAAEVAEQEGVSVELIDLRSLS
+PLDTGLVEASVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLESPPVRVTGLDIPYP
+PATLEHLHLPDLDRILEGVDRALGRPNPQDAVDAFAPPQTAEDFLSARADSSEVPA
+>4_603
+MSERMTFGRAINRGLHRALADDPKVLLMGEDIGALGGVFRITDGLQAEFGEDRVLDTPLA
+ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF
+GGGIGSPEHHSESPEAYFLHTAGLRVVSPSSPQEGYDLIRAAIASEDPVVYLEPKRRYHD
+KGDVDLDVAIPPMSPARILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS
+PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP
+PSKLEHLHLPDLDRILDGLDRALGRPNSLDSVDAFAAPETAEQFLAAQNAGEETR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000593.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000593.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eda644dcbfd11a9d975e89716c2bac66e72db47c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000593.fa
@@ -0,0 +1,20 @@
+>0_635
+MAGTRDGDAVEPRPERSTAVLLRDVRPEDLDEFFLHQQDEQANLMSAFAPRNPRDRGVFD
+YHWAHLLGDEDTVVRTIEHEGRAVGALVCTQQDGVGELSFWTAQDYWGLGLTTAAVDRFL
+EEHTARPLRAHVPEDNVGSVKVLSRRGFETVGEEKVFSNARAEVITELVMELPAAD
+>1_381
+MLLRDVRPEDLDEFFLHQQDEQANLMSAFAPRNPRDRGVFDYHWAHLLGDEDTVVRTIEH
+EGRAVGALVCIQQDGVGELSFWTAQDYWGLGLTTAAVDRFLEEHTARPLRAHVPEDNVGS
+VKVLSRRGFETVGEEKVFSNARAEVITELVMELPAAD
+>2_2252
+MLLRDVRPEDLDEFFLHQQDEQASLMSAFAPRNPRDRGVFDYHWSSLLAAETAVVRTIEH
+EGRAVGAIVCTEHDGVGELSFWTAQDYWGLGLTTAAVDAFLREHTRRPLRAHVPEDNAGS
+VKVLSRRGFETVGQEKVFSNARAEVITELVMELPAGAE
+>3_2107
+MPLRDVRPDDLDAFFLHQQDERANLMSAFAPRNPSDRGVFDYHWAHLLGDDATEVRTIEH
+EGRPVGALVCTRVDGVDELSFWVAREFWGQGLTTSAVDEFLSTHRERPVRAHVPEDNLGS
+VKVLTRRGFREVGREKVFSNARAEVVEELVLELPGA
+>4_605
+MLLRDVRPEDLDEFFLHQQDEQANLMSAFAPRNPRDRGVFDYHWAHLLGDEDTVVRTIEH
+EGRAVGALVCTQQDGVGELSFWTAQDYWGLGLTTAAVDRFLEEHTARPLRAHVPEDNVGS
+VKVLSRRGFETVGEEKVFSNARAEVITELVMELPAAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000594.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000594.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b76a025b853e096bcab77769bed9e79ac19edca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000594.fa
@@ -0,0 +1,25 @@
+>0_636
+MPAADPASPAAPATPPTAREAAKARRRVDLLAAAARLFAARGFDAVRLEDIGAAVGISGP
+AIYRHFAGKAAVLTAILDTASQDLLDGGLAAEAQHAPGAETLRALIGFQADFALAQRDVI
+RVQDRDMSALPDGARTAITRTQRAYIDVWARQLQVVHPREDQATAVFRAQAVLGLLNSTP
+RSVRRTAADRAARRATLVAMAWAAATAPGPLSGED
+>1_382
+MPAVDPASPAAPATPPTAREAAKARRRVDLLAAAARLFAARGFDAVRLEDIGAAVGISGP
+AIYRHFAGKAAVLTAILDTASQDLLDGGLAAEAQHAPGAETLRALIGFQADFALAQRDVI
+RVQDRDMSALPDGARTAITRTQRAYIDVWARQLQVVHPHEDQATAVFRAQAVLGLLNSTP
+RSVRRTAADRAARRATLVAMAWAAATAPGPLSGED
+>2_2251
+MPAAVDPSAPAASAAAPTSRVAAKARRREDLLAAAARLFAARGFDAVRLEDIGAEVGISG
+PAIYRHFAGKAAVLVAILATASQDLLEGALATEREHDAGEDALRALIAFQTDFALAQRDV
+IRVQDRDMSALPEDERAAVTGTQRAYIDVWARQLRVVHPSEDQATAVFRAQAVLGLINST
+PRSVRRTAADRAARRATLVAMAWAAATAPGPAADRP
+>3_2106
+MPHAPDTAAPGPTGTPRERAKARRRAELLAAAARLFAAHGYEATRLEDIGAAAGISGPGI
+YRHFAGKAAVLVEILSSASLFLLDGAEAVAARGLSGAEAVHDLIAFHTDFALANRDVIRV
+QGRDMSSLPPADGAEITRVQRRYIDLWGAQLRRLHPGEDHATARFRTQALLGLINSTPFS
+VRRSRADRGARRDALIGMAWAAARTPGGTARPEPPVVP
+>4_606
+MPAVDPASPAAPATPPTAREAAKARRRVDLLAAAARLFAARGFDAVRLEDIGAAVGISGP
+AIYRHFAGKAAVLTAILDTASQDLLDGGLAAEAQHAPGAETLRALIGFQADFALAQRDVI
+RVQDRDMSALPDGARTAITRTQRAYIDVWARQLQVVHPHEDQATAVFRAQAVLGLLNSTP
+RSVRRTAADRAARRATLVAMAWAAATAPGPLPGGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000595.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000595.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21d8330d9ff5fdc3cf91374f4baaec1c46343394
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000595.fa
@@ -0,0 +1,60 @@
+>0_638
+MTENHAQGTPLFDTVLLANRGEIAVRVIRTLRRLGIRSVAVHSDADADARHVREADTAVR
+LGPAPARESYLDIDAVVDAARRTGAQAVHPGYGFLSENADFARALEAAGIVFVGPPVGSL
+DAMADKIRAKETVAAYDVPVVPGIQDPTLTDAQITAEAEHVGFPLLIKPSAGGGGKGMVA
+VRAAEELPGALASARRTARSAFGDDTLLLERLITAPRHVEVQVFADAHGATVHLGERECS
+LQRRHQKVIEEAPAPLLTGLAHGAELRERLGRAAVDAAVSVGYRGAGTVEFLVSDENPDE
+FFFMEMNTRLQVEHPVSEEVVRVRGQRLDFVELQLRIAAGEPLGFAQEDVSLDGAAVEAR
+VYAEDPANGFLPSTGPVLRWREPAGEGVRVDTLLLPSQGEERAFGTVLTIRDDEGALWEG
+LAAPDGAQPEITGFYDPMIAKLITRGADRTEALERLDAALADTVLFGVRSNLGWLRELAA
+RTDVRTGRLTTELIDGLEAWTAPALPEDLAALAAEALADVSEDAAAAEQRAAGTAWARAD
+GWRGAGAPQPGMRVRVGDEDRILTAPAADAEVDEDAGALAGVNLLAGDPRDPRSAWLHRD
+GAAWQVRRLTRAEVVEAARAAAAARRAPAGAASPEARTPMPGTVVAVSVATGDTVAAGQE
+LAVVEAMKMEHPVTAAVAGVVTVHVAEGDPVAAQALIAVVEPAENAAPEENA
+>1_384
+MTENHAQGTPLFDTVLVANRGEIAVRVIRTLRRLGIRSVAVHSDADADARHVREADTAVR
+LGPAPARESYLDIDAVVDAARRTGAQAVHPGYGFLSENADFARALEAAGIVFVGPPVASL
+DAMADKIRAKETVAAYDVPVVPGIQDPTLTDEQITAEAERVGFPLLIKPSAGGGGKGMVA
+VRAAEELPGALASARRTARSAFGDDTLLLERLITAPRHVEVQVFADAHGATVHLGERECS
+LQRRHQKVIEEAPAPLLTGLAHGAELRERLGRAAVDAAVSVGYRGAGTVEFLVSDENPDE
+FFFMEMNTRLQVEHPVSEEVVRVRGQRLDFVELQLRIAAGGPLGFAQEDVTLDGAAVEAR
+VYAEDPANGFLPSTGPVLRWREPAGEGVRVDTLLLPSRPAEERAFGSGPQTGPAAGAVDP
+VDVDGAQPEITGFYDPMIAKLIARGADRAEALDRLDAALADTVLFGVRSNLGWLRELAAR
+EDVRTGRLTTELIDGLEAWTAPALPEDLAALAAEALADVSEDAAAAEHRAAGTAWARADG
+WRGAGAPQPGMRVRVGDEDRILTAPAADAEVDEDAGGLAGVNLLAGDPRDPRSAWLHRDG
+AAWQVRRLTRAEVVEAARAAAAARRAPASAASPEARTPMPGTVVAVSVATGDTVAAGQEL
+AVVEAMKMEHPVTAAVAGVVTVHVAEGDAVAAQALIAVVEPTEHAAPAENT
+>2_1195
+MDLDARPLAGRKLLLLDGSRKSIEIVDEAHRLGVHVIVTDYNTPEQSPAKLAADQHFQVS
+TSDVDAVVDLIRREGVDGVLAGFSDRWLATYAEICAAAQVPCYATVDQIRLFTDKKRYKA
+MLEQFGVPTITGYSVDDATSGAIPEEAFPLIVKPADGSGSRGISVVASQSELQNGLDVAL
+NYSWTQDLVIERFLPGQEATVYWVFQDGDCRVSLMWHRHMHDFGPQDRYRLPVAYSSPSS
+LLPTYLADVAPSVQAMLRSAGVRDGIMFMQGLIHEGVFHTYDIGYRVTPTQEYRVVEELC
+GYNPLSMLIHYALTGTMGQPDLAAVAEPRHPGYGFNVSTLIRPGTVGAVTGLDDVAALRG
+ILSTTAAIDAGETLPEEGWGQLRQVAVRTVGVADSLDLLRQTMRQVDELIDVRDVDGASM
+VIHPDMPPQDLDAYVL
+>2_2249
+MTENPTQGAPLFHTVLVANRGEIAVRVIRTLRRLGIRSVAVHSDADAQARHVLEADEAVR
+LGPAPARESYLDIEAVVEAARRTGAQAVHPGYGFLSENADFARALEAAGIVFVGPPMASL
+DAMADKIRAKETVAAYDVPVVPGVADPTLDDAALAAEAQRVGFPLLIKPSAGGGGKGMVA
+VHAADELPAALASARRTARSAFGDDTLLLERLIAAPRHIEVQVFADAHGTTVHLGERECS
+LQRRHQKVIEEAPAPLLTGLAHGAELRERLGKAAVDAAVSVGYRGAGTVEFLVSDEDPDA
+FFFMEMNTRLQVEHPVSEEVVRVRGQRQDFVELQLRIAAGEPLGFAQDDIALEGAAVEAR
+VYAEDPANGFLPSTGPVLRWREPQGEGVRVDTLLLPAADAADPAAVDGGQPEVTGFYDPM
+VAKVITRGADRAEALDRLDAALADTVLFGVRSNLGWLRELAAREDVRAGRLTTELIDGME
+AWNAPTLPEDLAALAAEALEEASDDAAAAERHAAGSAWARADGWRGAGAPQPGMRVRVGD
+EDRVLHGPAADAETEEDESALAGLNLLAGDPRDPRSAWLHRDGAAWQVRRLTRAEVVEAA
+RAAAAARRAPGRAQRPPRPARPCRAPSSPSRWPPGTPWPSARSWPWSRP
+>4_608
+MTENHAQGTPLFDTVLVANRGEIAVRVIRTLRRLGIRSVAVHSDADADARHVREADTAVR
+LGPAPARESYLDIDAVVDAARRTGAQAVHPGYGFLSENADFARALEAAGIVFVGPPVASL
+DAMADKIRAKETVAAYDVPVVPGIQDPTLTDEQITAEAERVGFPLLIKPSAGGGGKGMVA
+VRAAEELPGALASARRTARSAFGDDTLLLERLITAPRHVEVQVFADAHGATVHLGERECS
+LQRRHQKVIEEAPAPLLTGLAHGAELRERLGRAAVDAAVSVGYRGAGTVEFLVSDENPDE
+FFFMEMNTRLQVEHPVSEEVVRVRGQRLDFVELQLRIAAGGPLGFAQEDVTLDGAAVEAR
+VYAEDPANGFLPSTGPVLRWREPAGEGVRVDTLLLPSRPAEERAFGSGPQTGPAAGAVDP
+VDVDGAQPEITGFYDPMIAKLIARGADRAEALDRLDAALADTVLFGVRSNLGWLRELAAR
+EDVRTGRLTTELIDGLEAWTAPALPEDLAALAAEALADVSEDAAAAEHRAAGTAWARADG
+WRGAGAPQPGMRVRVGDEDRILTAPAADAEVDEDAGALAGVNLLAGDPRDPRSAWLHRDG
+AAWQVRRLTRAEVVEAARAAAAARRAPAGAASPEARTPMPGTVVAVSVATGDTVAAGQEL
+AVVEAMKMEHPVTAAVAGVVTVHVAEGDAVAAQALIAVVEPTEHAAPAENT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000609.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000609.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e761b20e8607cb5a5bc1d1a2f1e7666b17064d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000609.fa
@@ -0,0 +1,20 @@
+>0_656
+MILDAWFWTGLVIGAVSFVVCVVMTAIRRHPADASILSVAAVELFTLVYAAAAAVRQLGG
+DTLNGPGWEFWGYILTALIVPVIAVGWAVTDKTRWSNLVLAVVGPTIAVMLHRMQVIWFG
+QW
+>1_402
+MILDAWFWTGLVIGAVSFVVCVVMTAIRRHPADASILSVAAVELFTLVYAAAAAVRQLGG
+DTLNGPGWEFWGYILTALIVPVIAVGWAVTDKTRWSNLVLAVVGPTIAVMLHRMQVIWFG
+QW
+>2_2231
+MILDAWFWAGLVIGAVSLAVCVAMTAIRRHPADSSILSVAAVELFLLVYAVAAAVRQLGG
+EGLNGPGWEFWGYVVTALLVPVIAVAWAVTDKTRWSNLVLAVVGPTVVVMLHRMQVIWFG
+QW
+>3_2091
+MILDAWFWTGAVVGGLSFVVCLAMTALRRHPADSSIVSVAAVELFLLVYGVVGAFRQLGG
+QPLNGPTWEFWGYVLTALLVPVIAVAWAVTDKTRWSNLVMAVAGPTVVVMLHRMQVIWFG
+QW
+>4_626
+MILDAWFWTGLVIGAVSFVVCVVMTAIRRHPADASILSVAAVELFTLVYAAAAAVRQLGG
+DTLNGPGWEFWGYILTALIVPVIAVGWAVTDKTRWSNLVLAVVGPTIAVMLHRMQVIWFG
+QW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000610.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000610.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e08582c0b0e3212a413216d5a85f8f8b6f79537d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000610.fa
@@ -0,0 +1,20 @@
+>0_657
+MAPSDGAPARNQGLGRIIVMVYAVFALSASARSLFQILTQFDAAPVAYTLSAVAAVVYIV
+ATFALARSGARAWAVALGAVLVELAGVVGVGLWTVLDPGMFAHDTVWSRFGAGYGYVPLV
+LPVVGLIWLLTHRPARPAEAGAL
+>1_403
+MAPSDGAPARNQGLGRIIVMVYAVFALSASARSLFQILTQFDAAPVAYTLSAVAAVVYIV
+ATFALARSGARAWAVALGAVLVELAGVVGVGLWTVLDPGMFAHDTVWSRFGAGYGYVPLV
+LPVVGLIWLLTHRPARPAEAGAL
+>2_2230
+MARTRTASGAARPGAAAPARNQGLGRIIVMVYAVFALSATARSLFQILTDVEAAPVAYSL
+SAFAATVYIVATLALARSGARAWAVALGAVLVELIGVVGVGLWTVLDPGLFAEETVWSRF
+GAGYGYVPLVLPVVGLAWLLAHRPSRPTAEEMAR
+>3_2090
+MVEQHPVADDGAPARPRRNQGLGRIIVMVYAVFALSASARSLFQILDHFWVAPFAYVLSA
+FAAVVYIVATLALARSGPTAWKVAVAAVGVELAGVVGVGLLTVLDPQLFADATVWSRFGA
+GYGYVPLVLPMVGLAWLLSHRPSREGRVR
+>4_627
+MAPSDGAPARNQGLGRIIVMVYAVFALSASARSLFQILTQFDAAPVAYTLSAVAAVVYIV
+ATFALARSGARAWAVALGAVLVELAGVVGVGLWTVLDPGMFAHDTVWSRFGAGYGYVPLV
+LPVVGLIWLLTHRPARPAEAGAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000616.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000616.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a068289eef104d4229d854011c99780be3d4190
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000616.fa
@@ -0,0 +1,45 @@
+>0_663
+MSVHREIPLDFDGVLADEGNGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSRDES
+PEGYGATHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDLPMA
+VEVLTDMLTSSLIDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRPIGG
+TPETIRAVTRDHVVGHYTHWYRPDELVVTAAGHLDHDEVCRLVLAALRASGWELTQGALP
+APRRAVDTAGAAASRVRTGTHTVTKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLGGGM
+SSRLFQEIRERRGLAYNTYSFSAGYSDAGYWGLYAGCQPDRVDEVAALMEAELDRMAEAD
+VTGEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLARVREVDAGQVR
+AVAARLAAGDRARVVVAPA
+>1_409
+MSVHREIPLDFDGVLADEGNGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSRDES
+PEGYGATHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDLPMA
+VEVLTDMLTSSLIDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRPIGG
+TPETIRAVTRDHVVGHYTHWYRPDELVVTAAGHLDHDEVCRLVLAALRASGWELTQGALP
+APRRAVDTAGAAASRVRTGTHTVTKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLGGGM
+SSRLFQEIRERRGLAYNTYSFSAGYSDAGYWGLYAGCQPDRVDEVAALMEAELDRMAEAD
+VTGEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLARVREVDAGQVR
+AVAARLAAGDRARVVVAPA
+>2_2216
+MAGMSIHREIPLDFTGVLADEGHGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSR
+DESPEGYGSTHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDL
+PMAVEVLTDMLTSSLLDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRP
+IGGTPETIRAVTREHVAGHYARWYRPDELVVTAAGNLDHDEVCRLVLAALQASGWELAPG
+ALPAPRRAVDTEGAAASRVLTGTHTVAKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLG
+GGMSSRLFQEVRERRGLAYSTYSFSAGYSDAGYWGLYAGCQPDRVDEVSALMEAELDRMA
+AEVVTEEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLERVRAVDAA
+QVRAVAARLAAGERARVVVAPA
+>3_2084
+MAGMTVQREIPLDFSGVLAEDRGAVVCRSVLPGGVRVLTESMPDQRSVTVGYWVAVGSRD
+ESPEGYGSTHFLEHLLFKGTPTRTAMDIASAFDRVGGESNAGTAKESTVYHAHVLDEDLP
+MAVEVLTDMVTSSLIDADELETERGVILEELAMDADDPVDVAHERLAAVLMDGHPLGRPI
+GGTPETIRAVTREHVVAHYRHWYRPQELVITAAGNLDHDDVCRLVLDALERSGWDLAEGA
+APAPRRTADAAGAGAVLAGTHTVAKQVEQANVIVGGQSLSTTDPDRFALGVMMSVLGGGM
+SSRLFQEIRERRGLAYSTYSFSAGYSDGGYFGLYAGCQPERVDEVAALMEAELERMAAAE
+VTAEELDRAHGQICGGTVLGMESTGARMSRLGRAELVTGEFVDLSASLARVRAVDAGRVR
+AVAARLAAGERARVVVAPA
+>4_633
+MSVHREIPLDFDGVLADEGNGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSRDES
+PEGYGATHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDLPMA
+VEVLTDMLTSSLIDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRPIGG
+TPETIRAVTRDHVVGHYTHWYRPDELVVTAAGHLDHDEVCRLVLAALRASGWELTPGALP
+APRRAVDTAGAAASRVRTGTHTVTKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLGGGM
+SSRLFQEIRERRGLAYNTYSFSAGYSDAGYWGLYAGCQPDRVDEVAALMEAELDRMAEAD
+VTGEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLARVREVDAGQVR
+AVAARLAAGDRARVVVAPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000618.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000618.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0bb7f7cdc826aa9e9a29625fe73f11fed763c0c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000618.fa
@@ -0,0 +1,20 @@
+>0_665
+MDWTDTWTLAEPSRTPDDGAVGPPAPAVRARRSTVMSKVWVGFVCLLVLLFAGFALNASV
+ALVRAPQPLAKAIGAGVILVVLVTVAVLAREVWFGRQTERLADQLEAEGGLPEDDLPRSP
+GGRIDREAADAQFELYRVEAEAAPRDWRARYRLALAYDASGDRRRAREAAREAVRLHRAG
+>1_411
+MAEPSRTPDDGAVGPTEHAARARRSTVMSKVWVGFVSLLVLLFAGFALNASVALVRAPQP
+LAKAIGAGVILVVLVTVAVLAREVWFGRQTERLADQLEAEGGLPEDDLPRSPGGRIDREA
+ADAQFELYRVEAEAAPRDWRARYRLALAYDASGDRRRAREAAREAVRLHRAG
+>2_2214
+MADRAPRPAEQTVADPAEHAARARRSTLMSKLWVGFVSLLVLFFASFAVYVAVAFIRAPQ
+LLAKGIGVGVIFVVLVTVAVLAREVWFGQQTERLADLLEAEGGLPEDDLPRSPGGRIDRA
+AADAQFEVYRVEAEAAPRDWRTRYRLALAYDASGDRRRAREAAREAVRLHRQG
+>3_2081
+MASTDPRPGVDREQAPRAGSSTGAKLWVLFVAALTLFFAFFVVRAAVVFIAAGGVLPAVI
+GVAVILVVLVGLGLLGREMLFGLQTERLARTLEAEGGLPADDLPRSPGGRIDRDAADAAF
+ADAADEVRAAPEDWRARYRLSLAYDAAGDRRRAREAARQAISLASRRG
+>4_635
+MAEPSRTPDDGAVGPTEHAARARRSTVMSKVWVGFVSLLVLLFAGFALNASVALVRAPQP
+LAKAIGVGVILVVLVTVAVLAREVWFGRQTERLADQLEAEGGLPEDDLPRSPGGRIDREA
+ADAQFELYRVEAEAAPRDWRARYRLALAYDASGDRRRAREAAREAVRLHRAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000623.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000623.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab35f490f4ee61c075e1d6b42c49dc9705a3bbbd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000623.fa
@@ -0,0 +1,22 @@
+>0_671
+MAGAQDVVHALAHAGRTVATGESLTAGLLAARLADVPGASAVLHGGVVAYQNAVKTGLLG
+VPEDLLARVGAVDADVARRMALGARAALGADVGVATTGVAGPEPHQGQPVGTVWLGLAVP
+DADANALDVLGGERDGAATAILLRLDGDRAAIREATVAAALQALTRLLAVRGH
+>1_417
+MAAARDVVHALADAGLTVATGESLTAGLVAARLADVPGASAVLHGGVVAYQNAVKTGLLG
+VPEDLLARVGAVDADVARRMALGARAALGADVGVATTGVAGPEPHQGQPVGTVWLGLAVP
+DADASALDVFGGERDGAATAILLRLDGDRAAIREATVAAALQALTRLLAGRGH
+>2_2207
+MAAQETVRALAGAGLTVATAESLTAGLVAARLADVPGASAVLQGGVVAYQNSVKAGLLGV
+PADLLERVGAVDPEVARRMAEGARAGLGADVGVATTGVAGPEPHQGRPVGTVWLGVAVPE
+RLTAALDGLGGERRGAATAIPLALDGDRRAIREATVAAALAALTRLGAPVGERATGEGAA
+GEPCAGA
+>3_2077
+MSTGVGAVAAEGEAADPARAAVRALTTAGLTVATAESLTAGLVAARLADVPGASAALQGG
+VVAYQNHVKAGLLGVDAGLLTARGAVDPEVARQMACGARRAAGADVGVATTGVAGPEPHQ
+GKPVGTVFVGVAVPAELAPALAGLDGEPGAGEAAPGEAGSGGSEAGVAAAAFALTLPGNR
+AEIRAATVETVLDLLAALGTTGRGMPDEAPALS
+>4_641
+MTTAAARDVVHALADAGLTVATGESLTAGLVAARLADVPGASAVLHGGVVAYQNAVKTGL
+LGVPEDLLARVGAVDADVARRMALGARAALGADVGVATTGVAGPEPHQGQPVGTVWLGLA
+VPDADASALDVLGGERDGAATAILLRLDGDRAAIREATVAAALQALTHLLAGPGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000627.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000627.fa
new file mode 100644
index 0000000000000000000000000000000000000000..56b3f061a10484e12f08716557f2f6af28473841
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000627.fa
@@ -0,0 +1,33 @@
+>0_679
+MTRSRRNVGGGAAHRSETTGRSGSASGASAFDDARDSDVGRMWLDLAGAPEPTSSDADAS
+DAARDAAPARDAGAPAEDVPDPAPGAAPDLGALLTRASDLPSPAPGAGPRSLPWSGREDT
+RADTERRGRRRAPAKRSGRTRPREDGRAPAEPAPQTDRPRRRPGPAPLPTAPREREEAAR
+EVVLRQLALGPRSRGQLERKLAERQAEPELIERVLDRFEEVRLVDDAAFAEVWVRSRHRS
+KGLARRALGHELQQKGVDREIAAEALEAIDGEDERAAALDLVRRRLRGRTVPGGASPEAR
+AERDKVTRRLVGMLGRKGYGGGLAFAVVKEVLAEHEE
+>1_422
+MTRSRRNVGGGAAHRSETTGRSGSASGASAFDDARDSDVGRMWLDLAGAPEPTSSDADAA
+RDAVPARDAGTPAGDGSDPAPGAAPDLGALLTRASDLPSPAPGAGPRALPWSGREDTRAD
+TERRGRKRATTPPRRGRPRDEGRPAVDPRPAVETDRPRRRPGPAPLPTAPREREEAAREV
+VLRQLALGPRSRGQLERKLAERQAEPELIERVLDRFEEVRLVDDAAFAEVWVRSRHRSKG
+LARRALGHELQQKGVDREIAAEALEAIDGEDERTAALDLVRRRLRGRTVPGGASPEARAE
+RDKVTRRLVGMLGRKGYGGGLAFAVVKEVLAEHEE
+>2_2202
+MTRARRDAGGGAARRSERNGRSGAASGASAFDDARDTDAARMWLELAGVPEADAPAAARS
+VDEPPAAPTDGPDDPPLATAENGSSAAPSGPAAAPDEAGPPDLGSLLGRASDLPSPAPGA
+AARVLPWSADARPERGGRGARGTSSEARRARRRTARLAAADVASAPEAASTPEEANARED
+ARPRRRPGPAPLPAEPREREEAAREVVLRQLALGPRSRGQLEAKLADREAEPELIARVLD
+RFEEVRLVDDAAFAEVWVRSRHRSKGLARRAIGHELRQKGVDRDVAAEALEAIDGEDERA
+AALELVRRRLRGRRVPAGNGPHARAERDKVTRRLVGMLGRKGYGGGLAFAVVKEVLGELE
+E
+>3_2073
+MPEDPREREEAARQVVLRQLAMGPRSRRQLERKLADREAEPELVERVLDRFEEVSLVDDA
+AFAEVWVRSRARGKRLSRRAISRELHDKGVDRDVAEEALAAIEPEDERQAALELVRSKMR
+GRPAPAADGPEGRAERDKVTRRLVGMLGRKGYGPGLAFGVVKEVLAELDEA
+>4_646
+MTRSRRNVGGGAAHRSETTGRSGSASGASAFDDARDSDVGRMWLDLAGAPEPTSSDADAA
+RDAVPARDAGTPAGDVPDPAPGVAPDLGALLTRASDLPSPAPGAGPRTLPWSGREDTRAD
+IERRGRKRATTPPRRGRPRDEGRPAVDPRPAVETDRPRRRPGPAPLPTAPREREEAAREV
+VLRQLALGPRSRGQLERKLAERQAEPELIERVLDRFEEVRLVDDAAFAEVWVRSRHRSKG
+LARRALGHELQQKGVDREIAAEALEAIDGEDERAAALDLVRRRLRGRTVPGGASPEARAE
+RDKVTRRLVGMLGRKGYGGGLAFAVVKEVLAEHEE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000628.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000628.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34cefca5c2b8573142a0332a53f16ad898451df0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000628.fa
@@ -0,0 +1,49 @@
+>0_680
+MTLTDPTPRTTPLAQDGAAARPHEGLTYEVRTFGCQMNVHDSERISGLLESTGYAPVAED
+AQADLVVFNTCAVRENADNRLYGNLGNLRAVKDAHPGMQIAVGGCLAQKDQAAIQRRAPW
+VDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEVFPSTLPTKRDSTHSGWVSISVGCN
+NTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAK
+LLRACGEIEGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDKVLKDMRRS
+YRSAKFLRILEKVRERIPHAAITTDIIVGFPGETEEDFAETMRVVEASRFSSAFTFQYSI
+RPGTPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATLVGTRQELLVTADSGSKAAER
+GRLSGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGD
+AWDRAQAESCGAPAPGTAGGSGATSLGMPTLRPRS
+>1_423
+MTLTDPTPRTTPLAQDGAAARPHEGLTYEVRTFGCQMNVHDSERISGLLESTGYAPVAED
+AQADLVVFNTCAVRENADNRLYGNLGNLRAVKDAHPGMQIAVGGCLAQKDQAAIQRRAPW
+VDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEVFPSTLPTKRDSTHSGWVSISVGCN
+NTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAK
+LLRACGEIEGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDRVLKDMRRS
+YRSAKFLRILEKVRERIPHAAITTDIIVGFPGETAEDFAETMRVVEASRFSSAFTFQYSI
+RPGTPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATLVGTRQELLVTADSGSKAAER
+GRLSGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGD
+AWDRAQAESCGAPAPGTAGGSGATSLGMPTLRPRS
+>2_2201
+MNVHDSERISGLLESTGYAPVPQDAQADLVVFNTCAVRENADNRLYGNLGNLRAVKDARP
+GMQIAVGGCLAQKDQATIQRKAPWVDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEV
+FPSTLPTKRDSTHSGWVSISVGCNNTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAV
+EVTLLGQNVNTYGVEFGDRGAFAKLLRACGQIEGLERVRFTSPHPAAFTDDVIDAMAETP
+NVMPQLHMPLQSGSDTVLKAMRRSYRSKRFLGILEKVRERIPHAAITTDIIVGFPGETEE
+DFQDTMRVVEASRFSSAFTFQYSIRPGTPAGEMADQVPKAVVQERFERLVALQDRISAEE
+MATLVGTRQELLVTADSGTKASERGRLSGRARDNRLVHFSVPAGAPTPRPGDFVTVTVTE
+AHPFFAVADPAPEDYSLRRSRAGDAWDRAQAESCGVPTPGASGGAGATSLGMPTLRPRS
+>3_2072
+MTLTDPTTHLPALGTAPDAHAGLTYEVRTFGCQMNVHDSERISGLLESTGYTPAEDGTQP
+DLVVFNTCAVRENADNRLYGNLGNLRPVKDAHPGMQIAVGGCLAQKDQATIQEKAPWVDV
+VFGTHNIGSLPALLERSRHNAEAEMEILESLEVFPSTLPTKRESTHSGWVSISVGCNNTC
+TFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAKLLR
+ACGEIDGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDKVLKDMRRSYRS
+AKFLRILEKVRERIPHAAITTDIIVGFPGETEEDFAETMRVVEASRFSSAFTFQYSIRPG
+TPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATLVGTRQELLVTADSGSKATERGRL
+SGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGDAWD
+RAQAESCGAPAPGAAGGSGATSLGMPTLRPRF
+>4_647
+MTLTDPTPRTTPLAQDGAAARPHEGLTYEVRTFGCQMNVHDSERISGLLESTGYAPVAED
+AQADLVVFNTCAVRENADNRLYGNLGNLRAVKDAHPGMQIAVGGCLAQKDQAAIQRRAPW
+VDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEVFPSTLPTKRDSTHSGWVSISVGCN
+NTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAK
+LLRACGEIEGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDKVLKDMRRS
+YRSAKFLRILEKVRERIPHAAITTDIIVGFPGETEEDFAETMRVVEASRFSSAFTFQYSI
+RPGTPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATLVGTRQELLVTADSGSKAAER
+GRLSGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGD
+AWDRAQAESCGAPAPGTAGGSGATSLGMPTLRPRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000637.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000637.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51fda72fb151f0fa2b06c415b2a00d185e1eb995
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000637.fa
@@ -0,0 +1,40 @@
+>0_692
+MTDLSSLPLRENLRGLSPYGAPQLDVPYMLNTNENTHPVPEEVATAIAERVAAVAGGLNR
+YPDREFTGLRRALAGYLGHGLTADHVWAGNGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTVFVDGGRAEDHTLSAEHAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAQNEAAGGPGAMVVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+LGYLAADPAVADALRLVRLPYHLSAVTQATAEAALDHVDALLRTVEDIKAQRDRIVSTLR
+GLGLRPSVSDSNFVFFGHLEDASDVWRRLLDRGVLVRDVGIPHHLRVTAGTEAETTAFLT
+ALAEVLGETGDRS
+>1_432
+MTDLSSLPLRENLRGLSPYGAPQLDVPYMLNTNENTHPVPEEVATAIAERVAAVAGGLNR
+YPDREFTGLRRALAGYLGHGLTADHVWAGNGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTVFVDGGRAADHTLSAEHAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAQNEAAGGPGAMVVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+LGYLAADPAVTDALRLVRLPYHLSAVTQATAEAALDHVDALLRTVEDIKAQRDRIVSTLR
+GLGLRPSVSDSNFVFFGHLEDASDVWGRLLDRGVLVRDVGIPHHLRVTAGTEPETTAFLT
+ALEEVLGETGHRS
+>2_2190
+MTDLSSLPLRENLRGLSPYGAPQLDVPHMLNTNENTHPVPQEVATAIAERVAAVAGGLNR
+YPDREFTALRRALARYLGHGLTEGHVWAANGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTAFVDGGRAADHTLSAERAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAENESAGGPGAMIVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+VGYLAADPAVADALRLVRLPYHLSAVTQATAEAALDHVDALLETVEDIKGQRDRIVATLR
+ELGLEPSVSDSNFVFFGRLEDAADVWRRLLERGVLVRDVGIPHHLRVTAGTEEETTAFLE
+ALEAVLAEIGHRR
+>3_2061
+MTDLSSLPLRDSLRGQSPYGAPQLDVPYMLNTNENTHPVPQAVAEAITARVAKVAGGLNR
+YPDREFTELREHLAAYLGHGITPEQVWAANGSNEVLQQILQAFGGPGRTLLSFLPSYSMY
+PLLANGTDTAFVDGGRAADHTLSAEHAAALVREHRPNVVFLASPNNPTGTALGLDVIEAI
+YAAQAQNEAEGGHGAMVVVDEAYAEFALAGTDSALTLLRGRERLIVTRTMSKAFALAGAR
+LGYLAADAAVADALRLVRLPYHLSAVTQATAIAALERVDELLETVEDIKGQRDRIVAELT
+GMGLVPAVSDSNFVFFGRLADAHAVWEALLERGVLVRDVGIPHHLRVTAGTEEETTAFLD
+ALREIVEQDPAVVSAVDAD
+>4_656
+MTDLSSLPLRENLRGLSPYGAPQLDVPYMLNTNENTHPVPEEVATAIAERVAAVAGGLNR
+YPDREFTGLRRALAGYLGHGLTADHVWAGNGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTVFVDGGRAEDHTLSAEHAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAQNEAAGGPGAMVVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+LGYLAADPAVADALRLVRLPYHLSAVTQATAEAALDHVDALLRTVEDIKAQRDRIVSTLR
+GLGLRPSVSDSNFVFFGHLEDASDVWRRLLDRGVLVRDVGIPHHLRVTAGTEAETTAFLT
+ALAEVLGETGDRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000638.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000638.fa
new file mode 100644
index 0000000000000000000000000000000000000000..32a3951b0ac220783d474a8ab09435df961458ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000638.fa
@@ -0,0 +1,25 @@
+>0_693
+MAAELISGRRARMTRTTSESDVYVEMDLDGTGRAEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMTGVPSTKGAL
+>1_433
+MAAELISGRRARMTRTTSESDVYVEMDLDGTGRAEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMTGVPSTKGAL
+>2_2189
+MAAELISGRRARMTRTTSESDVHVEMDLDGTGRAEISTSVPFYDHMLTALARHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMSGVPSTKGAL
+>3_2060
+MAAELMSGRRARMQRTTSESDVYVEMDLDGTGTSEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKRGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFEAITYHASICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRVHDVPSTKGAL
+>4_657
+MAAELISGRRARMTRTTSESDVYVEMDLDGTGRAEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKAALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMTGVPSTKGAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000640.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000640.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24f22e27c82dfc616d7c88ebc3c3a88660a5d864
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000640.fa
@@ -0,0 +1,10 @@
+>0_695
+MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA
+>1_435
+MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA
+>2_2187
+MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVAR
+>3_2058
+MPYWSVLYLGLGGILLGAAWSMRTQKAPTWAVVIALVLAAMAVAAAFLTV
+>4_659
+MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000642.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000642.fa
new file mode 100644
index 0000000000000000000000000000000000000000..691bcf5ee9b2540fa32b9dd335ce95190d97b137
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000642.fa
@@ -0,0 +1,35 @@
+>0_697
+MTGSHDDGGLARDDGLGPIDETVAVPHPAARELPGHIRAALDRMREKTAGENTADTAGVP
+WQGRDLSGPGVDGSANPLHVFDEDDGTSPAEWTAVMSALTDGSAGEREVTEVLARIRVFA
+AVVPTLAGDEDDVHDHADHTGHEHDVAAHGDKAADVALVTMRAPDGRQALPVFTNVPALT
+AWNPVARPVAVWLPRACLSAVDEGCELVVIDAGAEHTYVVRRPAVWSLAQQREWTPAYRD
+QEIADEIAEVADLVPNLLNLGLAPGSGVATHTGSGAVMNGGGAGPELQIVAMPTRDADAA
+GVRLMTATLKTLLADLPLLAERADSVEITVRRP
+>1_437
+MTGSHDDGGLARDEGLGPIDETVAVPHPAARELPGHIRAALDRMREKTAGENTADTAGVP
+WQGRDLSGPGVDGSANPLHVFDEDDGTSPAEWTAVMAALTDGSAGEREVTEVLARIRVFA
+AVVPTLAVDEDDVHDHTGHEHDVAAHGDKAADVALVTMRAPDGRQALPVFTNVPALTAWN
+PVARPVAVWLPRACLSAVDEGCELVVIDAGAEHTYVVRRPAVWSLAQQKEWTPAYRDQEI
+ADEIAQVADLVPNLLNLGLAPGSGVATHTGSGAVMNGGGAGPELQIVAMPTRDADATGVR
+LMTATLKTLLADLPVLAERADSVEITVRRP
+>2_2185
+MTHGHDDGAPAGVAGAGPIEETVAVPRPDSRELPGHIRAALDRMREKTAGPNTADTAGVP
+WEGRDLSGPGVDGSANPLHVFDEDDGTSPEEWTRVMAALTTGAAGEAEVTDVLSRIRVFA
+AVVPTLAVDEDDVHDHADHSGHEHDVAAHGDKAADVALVTMRAPDGRQALPVFTSVPALT
+AWNPIARPVAVWMPRACLSAVDEGCELVVVDAGAEHTYAVRRPAVWALAQQKPWTPSYRD
+QEIADEIAQVADLVPHLLNLGLAPGSGVATHTGSGAVMSGGGAGPELQIVAMPARDADAA
+GVRLMAATLKTLLADLPLLAERADSVEVTVRRP
+>3_2056
+MSSASSSEPAHDAEATVPVPAPGGRELPGHIRAAMERMRQKTARENTADTAGVPWAGRDL
+SGPGLEGSANPLHIFDEDDGTAPAEWARVMDALTEGTAGEAEVVDVLGRIRVFAAVVPTL
+AVDEADVHDHAAHSVHEHAQHEDAAHGDKAADVALVTMRAPDGRQALPVFTSVPALTAWN
+PLARPVAVWAPRACLSAVDEGCELVVVDAGAEHTYAVRRPAVWALAQQKPWTPSYLDQEI
+AEEIAGVADLVPNLLNLGLAPGPGVATETASGEVMNGGGSGTELTVLAMPARDADAAGIR
+LMTTTLAMLLGDLPLLAERADSVEITVRRP
+>4_661
+MTGSHDDGGLARDDGLGPIDETVAVPHPAARELPGHIRAALDRMREKTAGENTADTAGVP
+WQGRDLSGPGVDGSANPLHVFDEDDGTSPAEWTAVMSALTDGSADEREVTEVLARIRVFA
+AVVPTLAVDEDDVHDHADHTGHEHDVAAHGDKAADVALVTMRAPDGRQALPVFTNVPALT
+AWNPVARPVAVWLPRACLSAVDEGCELVVIDAGAEHTYVVRRPAVWSLAQQREWTPAYRD
+QEIADEIAEVADLVPNLLNLGLAPGSGVATHTGSGAVMNGGGAGPELQIVAMPTRDADAA
+GVRLMTATLKTLLADLPLLAERADSVEITVRRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000644.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000644.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7effb06fb4d89b8585cb362dd5606ad00f9e463f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000644.fa
@@ -0,0 +1,23 @@
+>0_699
+MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVVERR
+LKQDCGMSLADYNLLLLLYESPEGRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV
+ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLGDLAPGEAESLTRIFSRLGRRLEGL
+C
+>1_439
+MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVVERR
+LKQDCGMSLADYNLLLLLYESPEGRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV
+ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLGDLAPGEAESLTRIFSRLGRRLEGL
+C
+>2_2183
+MNSSSTPTPEPSETARHAWRAYFEATQMLSEMLERGLKKDSGMSLADYNLLLLLYEAPEG
+RLRMGELASGMVFSPSRITYQVKTLVARGLIERRAAECDRRGFEAVLTDEGRTAFRRAAA
+GHARQVDELFLSHLEPGEAETLERIFTRLGGRLEGLC
+>3_2054
+MTSSSTPAAEPTGPRAARHAWRAYFESTQMLQDQLERGLKAECGITLADYNLLLLLVESD
+GGRLRLGELASRMVFSPSRVTYQVKSLVARGLIERRRVECDRRGFEAVLTDAGRTAFRRA
+AVVHARQVDELFLDLLQPGEAEVLGRVFTRVGTALESRCAGRAAPSEPCGAQASNSADA
+>4_663
+MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVLERR
+LKQDCGMSLADYNLLLLLYESPEDRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV
+ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLVDLAPGEAESLTRIFSRLGRRLEGL
+C
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000648.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000648.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ce1eb1e2d3bc6e89654f5160ae65760af5cbd1e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000648.fa
@@ -0,0 +1,46 @@
+>0_703
+MDFGAYGRLLQDPRIRHLLAVGFIARFPHTAAGVILTLHVALTLGLGYGQAGLAGAAMTL
+GIAVGSPWRGRVVDAKGLRRALLPSVIAEAVIWPIVPWLPFWPMLLAVFLGGVFSLPIFS
+VVRQGLGVLTHGKDRQTAFALDSIVTETIFMMGPALGAVVAATWSSALGLTIVGLSSALG
+GILLMWFNPPTRSSQLAVVGPATEDPYTEEQDRQEAIAQAVTAAPMHVEMAAPSLATGAL
+PAITEAIPLVTGSLPVIAADGSGPTTAPRRARAERLRQWRRTHFSWVGPEVLGVLVVSMA
+AGIVMVGTEVSMVAELESQGAAASVGLVYAFWCGASAVGGLFYGAWGRQVHPYLLMALFA
+VATVPLALVDGVWALALASIPSGLLTAPTLASASSRLSHLVVEERRGEAMGFYGSAMTAG
+AAMGAPLAGVFIDGVAPSAGYVFAAAAGFVLVLLAALATVMRGRRPA
+>1_443
+MDFGAYGRLLQDPRIRHLLAVGFIARFPHTAAGVILTLHVALTLGLGYGQAGLAGAAMTL
+GIAVGSPWRGRVVDAKGLRRALLPSVIAEAVIWPIVPWLPFWPMLLAVFLGGVFSLPIFS
+VVRQGLGVLTHGKDRQTAFALDSIVTETIFMMGPALGAVVAATWSSALGLTIVGLSSALG
+GILLMWFNPPTRSSQLAVVGPATEDPYTEEQDRQEAIAQAVTAAPMHVEMAAPSLATGAL
+PAITEAIPLVTGSLPVIAADGSGPTTAPRRARAERLRQWRRSHFSWVGSEVLGVLVVSMA
+AGIVMVGTEVSMVAELESQGAAASVGLVYAFWCGASAVGGLFYGAWGRQVHPYLLMALFA
+VATVPLALVDGVWALALASIPSGLLTAPTLASASSRLSHLVEEERRGEAMGFYGSAMTAG
+AAMGAPLAGVFIDGVAPSAGYVFAAAAGFVLVLLAALATVARGRRSA
+>2_2176
+MGFIARFPHTAAGVILTLHVALTLDLGYGQAGLAAAAMTLGIAVGSPWRGRVVDAKGLRR
+ALLPSVIAEALIWPLVPWLPFWLMLVAVFFGGVFALPIFSVVRQGLGVLTHGRDRQTAFA
+LDSIITETIFMVGPALGAVVAATWSSALGLTIVGLSSALGGVLLMWFNPPTRSSQLAVVG
+PETEDPYTEDEDREEAVAQTVHGAPMHVEMTAPSLATGALPVVTEAIPLVTGALPVIAAD
+GSGPATPTPGLTRAERLRLWRARHFAWVGPEALGVLVVSMAAGLVMVGTEVTMVAELEHA
+GMAGSVGVVYAFWCGASAVGGLFYGAWGRQVHPYLLMGLLALLTLPMAFVDGLWALALAA
+IPSGLFTAPTLASASSRLSTLVPEERRGEAMGFYGSAMTAGAAMGAPLSGVFIDAIHPAA
+GYVFAGLAGAVLVLAAALVTLARRRRVGGTSA
+>3_2049
+MDFRAYGRLLQDPRIRNLLAVGFIARFPHTAAGVILTLHVAVTLGLGYGQAGLAAAAMTL
+GIACGSPWRGRAIDRDGLRRALLPSVVAEAVIWPVVPWLPFGFLLVAVFFGGLFAVPIFS
+VVRQGLGVLTHGADRQTAFTLDSIITELVFMVGPALGAVIAATGSTALGLTVVGLSGALS
+GALLMWFNPPTRSTQLAADGPSAGDPFTEEEDREQALSQAVHTAPVRATVAAADLATGAL
+PVVTEAVPIVTGSLPVIAADGSGPVSPAPRAGRHDDGRAADGLTRDERWRLWRVRHFGWV
+TPEVLGVLVVAMAAGIALVGTEVTMVAELEHAGQEASVGVVYAFWCGASALGGLFYGAWG
+RQVHPYLLGALFALAVAPMAFVDGLWALAWASVPSGLLTAPTLAAASSRISLLVSEERRG
+EAMGYYGSAMTAGSALGAPVVGLVIDGVGPGAGYVGAAGAAVVMIGAAAILTAARRRRSP
+ARG
+>4_667
+MDFGAYGRLLQDPRIRHLLAVGFIARFPHTAAGVILTLHVALTLGLGYGQAGLAGAAMTL
+GIAVGSPWRGRVVDAKGLRRALLPSVIAEAVIWPIVPWLPFWPMLLAVFLGGVFSLPIFS
+VVRQGLGVLTHGKDRQTAFALDSIVTETIFMMGPALGAVVAATWSSALGLTIVGLSSALG
+GILLMWFNPPTRSSQLAVVGPATEDPYTEEQDRQEAIAQAVTAAPMHVEMAAPSLATGAL
+PAITEAIPLVTGSLPVIAADGSGPTTAPRRARAERLRQWRRTHFSWVGPEVLGVLVVSMA
+AGIVMVGTEVSMVAELESQGAAASVGLVYAFWCGASAVGGLFYGAWGRQVHPYLLMALFA
+VATVPLALVDGVWALALASIPSGLLTAPTLASASSRLSHLVVEERRGEAMGFYGSAMTAG
+AAMGAPLAGVFIDGVAPSAGYVFAAAAGFVLVLLAALATVMRGRRPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000650.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000650.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a020cc125e77c72ca0747e6c3c4319578e244b5c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000650.fa
@@ -0,0 +1,40 @@
+>0_706
+MDAVRILEDEIREIVRRQGIDPQREHARVLTLIQDAAADYESRAMVSSLPDLEDPVAARQ
+DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARSGRSELTGIVLTEEEVQDLVEVML
+KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFIARARRLDDLVRGGSLT
+PTAARFLDAAVDAGMNILVSGATQAGKTTLLNCLASAIGPRERVITVEEIFELQIPVRDV
+VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI
+HANSAADALTKLCTLPLLAGENISRDFVVPTVATCIDVVVHCERDRQGRRRVREILTVGS
+RVEGGVIETSALFQRDAEGDLRLNEGANLEFEALARRGVDVHELVGLR
+>1_446
+MDAVRILEDEIREIVRRQGIDPQREHARVLTLIQDAAADYESRAMVSSLPDLEDPVAARQ
+DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARSGRSELTGIVLTEEEVQDLVEVML
+KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFIARARRLDDLVRGGSLT
+PTAARFLDAAVDAGMNILVSGATQAGKTTLLNCLASAIGPRERVITVEEIFELQIPVRDV
+VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI
+HANSAADALTKLCTLPLLAGENISRDFVVPTVATCIDVVVHCERDRQGRRRVREILTVGS
+RVEGGVIETSALFQRDAEGDLRLNEGANLEFEALARRGVDVHELVGLR
+>2_2171
+MDAVRILEDEIREVVRRQGIDPQREHARVIALIQDAAADYESRAEVSALPDLEDPAAARQ
+DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARAGRSELTGIVLTEEEVHDLVEVML
+KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFISRARRLEDLVRSGSLT
+PTAARFLDAAVDVGMNVLVSGATQAGKTTLLNCLASSIGARERVITVEEIFELQIPVRDV
+VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI
+HANSAADALTKLCTLPLLAGENISRSFVVPTVATCIDVVVHCERDWDGRRRVLEVLTVGA
+RVEDGVIETSTLFQRDSAGDLRLNEAASLEFDAFARRGVDVHELVGLR
+>3_2046
+MDAVRMLEDELRELVRRRGVDPRVEGHRIRTMIAEATLDYESRSLVSSLPPLEDPEAARQ
+ELFDRIAGLGPLQRLMDDPTVEEIWLNAPDQVYCARAGRSELTGIVLSEEQVRDLVELML
+KSSGRRLDLSMPFVDASLPDGSRLHVAIPDITRRHWAVNIRKFISRAHRLDDLVRSESLT
+TPAARFLDAAVDAGMNILVSGATQAGKTTMLNCLSASIGARERVITVEEIFELQIPVRDV
+VGLQCRQPNLEGTGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI
+HANSASDALTKLCTLPLLAGENISRNFVVPTVATCIDVVVHCERDREGRRRVREILTVGS
+RVEGGVIETSTLFRRDAHGDLVLNPSADLEFEAFARRGLDPRDLVEVR
+>4_670
+MDAVRILEDEIREIVRRQGIDPQREHARVLTLIQDAAADYESRAMVSSLPDLEDPVAARQ
+DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARSGRSELTGIVLTEEEVQDLVEVML
+KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFIARARRLDDLVRGGSLT
+PTAARFLDAAVDTGMNILVSGATQAGKTTLLNCLASAIGPRERVITVEEIFELQIPVRDV
+VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI
+HANSAADALTKLCTLPLLAGENISRDFVVPTVATCIDVVVHCERDRQGRRRVREILTVGS
+RVEGGVIETSALFQRDAEGDLRLNEGANLEFEALARRGVDVHELVGLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000653.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000653.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54843c1a121686f03577fb4b8592bae2f85fe453
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000653.fa
@@ -0,0 +1,15 @@
+>0_709
+MLHHHAITVLAALRALIHDDVRDERGDVPGWVMITLMSAVLVAGLLALALPALQGLFNQA
+ISQVSQGG
+>1_449
+MLHHHAITVLAALRALIHDDVRDERGDVPGWVMITLMSAVLVAGLLALALPALQGLFNQA
+ISQVSQGG
+>2_2145
+MLHHHVISILTALRGLLHDDVRDDRGDVPGWVMITLMSAVLVAALLTLALPALTDLFDQA
+ISQVTQGE
+>3_2043
+MLTNAYLTVVSALTSLLHDDARDERGDVPGWVMITLMSAALVVALLGLAMPALKAMFDQA
+ITQVNNAAG
+>4_673
+MLHHHAITVLAALRALIHDDVRDERGDVPGWVMITLMSAVLVAGLLALALPALEGLFNQA
+ISQVSQGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000662.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000662.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6e0a246b845b6c47db0487f878a5fc88a57dcfa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000662.fa
@@ -0,0 +1,20 @@
+>0_719
+MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDTYEAGMVLTGTEVKSLREGKASLVD
+GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL
+SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA
+>1_459
+MGKNSKGKATKQPAPGERQVIANNKKARHDYTILDTYEAGIVLTGTEVKSLREGKASLVD
+GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL
+SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA
+>2_2134
+MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDVYEAGLVLTGTEVKSLREGKASLVD
+GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL
+SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRIRNRRAGVA
+>3_2031
+MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDTYEAGMVLTGTEVKSLREGKASLVD
+GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL
+SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA
+>4_684
+MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDTYEAGMVLTGTEVKSLREGKASLVD
+GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL
+SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000664.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000664.fa
new file mode 100644
index 0000000000000000000000000000000000000000..06e3489447acd1b264645b7d865bcbf70fa42f41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000664.fa
@@ -0,0 +1,40 @@
+>0_724
+MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAEVGMVTTVDRGRYAVVLPERLDE
+RITAMRARELRRTPIATGDRVAVVGDLSGEEGTLARIVRVEERSTVLRRSADDSDEVERV
+VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPDALVAHYEAL
+DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER
+ATGHVNAVTGRGRHTSSSALALPLTGDDGVPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF
+DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED
+AASSED
+>1_463
+MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAQVGMVTTVDRGRYAVVLPDRLDE
+RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARIIRVEERSTVLRRSADDSDEVERV
+VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPDALVAHYEAL
+DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER
+ATGHVNAVTGRGRHTSSSALALPLTGDDGAPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF
+DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED
+AASSED
+>2_2130
+MGRRVDPGAWDESDVRVRPSKRGTRPRTKERPKHEDAVVGMVTTVDRGRYTVVLPERLDE
+RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARVVRVEERSTVLRRSADDSDEVERV
+VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAALMAHYESL
+DLEVMTSGAAVFEAETGDTALDGALVARVAERLQGHTSAFVGPSGVGKSTLLNALTGAER
+ATGHVNAVTGRGRHTSSSALALPLTDDDGVPLADTWVVDTPGIRSFGLGWVEPDRVVEAF
+DDLAGGLADCPRGCAHTADSPGCGLDGWVAAGHAGPSGAARLASLRRLLGNRLGPAGAED
+SASSED
+>3_2024
+MGRSLDPSAWDESHVRVRPSKRGTRPRTKQRPQHEDAQTGLVTTVDRGRYTVVLPGRAHA
+PVTAMRARELRRTPIATGDRVDVVGDLSGDEGSLARIVRVQERDTVLRRSADDSDAVERV
+VVANADTLMVMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAELVAHYEAL
+DLEVMTSGASRFEAESGDTDLDDGLVERVAERLAGHTAAFVGPSGVGKSTLLNALTGAGR
+ATGHVNAVTGRGRHTSSSALAMSLPGPDGEPVPDTWVVDTPGIRSFGLGWVEPDRVVEAF
+EDLAGGLEGCPRGCTHLADSPGCGLDAWVAEGHAGEAGPARLASLRRLLGNRTTAEAGGS
+ASSED
+>4_688
+MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAEIGMVTTVDRGRYAVVLPDRLDE
+RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARIVRVEERSTVLRRSADDSDEVERV
+VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAALVAHYEAL
+DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER
+ATGHVNAVTGRGRHTSSSALALPLTGDDGAPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF
+DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED
+AASSED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000668.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000668.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f406c209e993d495e145b0494eb9490b610d97c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000668.fa
@@ -0,0 +1,25 @@
+>0_728
+MHNRRIRIAAVGDQLLAGAGDARAIGWWGRVLARTQAPDVELENYVLAVPHETTEDLNER
+WWGEASRRFSEETENRLVVALSDADLDLEATSTARSRLNLANVLDTASQRNIPVLVVGPT
+PTLDEQRNARLAELNAAYLDVADRRNHVYVDTFTPLVGHEQWRSDLASGQGRPGQAGHGL
+IAWLVLHRGWYQWLGLPEPTA
+>1_467
+MHNRRIRIAAVGDHLLAGAGDARAIGWWGRVLARTQAPDVELENYVLAVPHETTEDLNER
+WWGEASRRFSEETENRLVVALSDADLDLEATSTARSRLNLANVLDTASQRNIPVLVVGPT
+PTLDEQRNARLAELNAAYLDVADRRNHVYVDTFTPLVGHEQWRSDLASGQGRPGQAGHGL
+IAWLVLHRGWYQWLGLPEPTA
+>2_2126
+MNDRRIRIAAVGDHLLAGAGDARAIGWWGRVLARTQAPGVELENYVLAVPHETTEDLNER
+WWGEASRRYSEDTENRLVVALSDADLDLEASSTARSRLNLANVLDTASQRGIPVLVVGPT
+PTLDEERNARLAELNAAYLDVADRRSHVYVDTFTPLQGHEQWRADLAAGEGRPGQAGHGL
+IAWLVLHRGWYQWLGLPEPTA
+>3_2020
+MQNRRIRIAAVGDHILAGAGDPRSIGWWGRVLARTAAPEVTLENYVLAVPHETTEQLNER
+WWGEASRRFSESAENRLVVALSDADLDLEASSSARSRLNLANVLDTASQRGITALVVGPV
+PTLDEARNDRLADLNTAYQDVAARRGHLYVDAFTPLRTHEQWRADLAAGDGVPGQAGHGL
+IAWLVLHRGWYQWLGVPEPTA
+>4_692
+MHNRRIRIAAVGDHLLAGAGDARAIGWWGRVLARTQAPDVELENYVLAVPHETTEDLNER
+WWGEASRRFSEETENRLVVALSDADLDLEATSTARSRLNLANVLDTASQRNIPVLVVGPT
+PTLDEQRNARLAELNAAYLDVADRRNHVYVDTFTPLVGHEQWRSDLASGQGRPGQAGHGL
+IAWLVLHRGWYQWLGLPEPTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000669.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000669.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ebde72e016d5bd400493c9a7b26fcf265029e51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000669.fa
@@ -0,0 +1,110 @@
+>0_729
+MPELTSDRLAQEFPGNERLVAEIYRKYREDSGSVDRQWAQIFARLEASAPAAEAEPKAAA
+KTEPKTAAKAEPKATAKVTEPKAATAPARGAQPKETSVSTGPKPKKTPAAQAVPSEPADT
+ATTTADEKQEKATVLKGMAKAVATNMDASLSMPTATTVRDLPAKVLIDNRVVINSHLART
+RGGKVSFTHFIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLPRPDGTRA
+LVVPNVKAAETLDFRGFWKAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGTVHSVPRL
+SQGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSGEFLKIVH
+GLLLGEDGFYDEVFHSLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN
+VDPLEYSMAYHPDLDIREHGLTLWDLDRKWPTGGFGGAGSLTLRKILGVLRDAYCRTIGV
+EYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE
+GGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA
+SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRLDLGGQRP
+DSFSVLPILVHGDAAFAGQGVVTEVLQLSQLPGYRTGGTIHVVVNNQVGFTTPPTQARSA
+VYSTDVAKTIQAPIFHVNGDEPESVVHVAQLAFEYRQRFNKDVVIDLVCYRRRGHNEGDD
+PSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADSALKDYQQQLERVFAETHEDAP
+ASGGEGLRPAEDRDAAPEAPASTAISAETLRAIGQAHIDVPEGFTVHPKLAALLERRAKM
+AVDGGIDWGFAELAAFGSLLMERVPVRLAGQDSQRGTFTQRHSVFHDRITGDTWAPLRHL
+SEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFVNGAQTIIDEFISSAD
+QKWSQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSTGANHFHLLREHA
+YARPRRPLIVFTPKQLLRLKAAANSVEDFTEGGFQPVIPDAGVDAKDVTRVLLVSGRLYY
+DLLARRQKSGDTSTAIVRVEQLYPLPLDEIRKALRAYPVADVTWVQDEPANQGPWPFMAL
+NLVPQLDVPVTLVSRPASAATSAGTKGRHDQELSTLLDAAFGR
+>1_468
+MPELTSDRLAQEFPGNERLVAEIYRKYREDSGSVDRQWAQIFARLEASAPAAEAEPKAAA
+KTEPKTAAKAEPKATAKVTEPKAATAPARGAQPKETSVSTGPKPKKTPAAQAVPSEPADT
+ATTTADEKQEKATVLKGMAKAVATNMDASLSVPTATTVRDLPAKVLIDNRVVINSHLART
+RGGKVSFTHLIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLPRPDGTRA
+LVVPNVKAAETLDFRGFWKAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGTVHSVPRL
+SQGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSGEFLKIVH
+GLLLGEDGFYDEVFHSLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN
+VDPLEYSMAYHPDLDIREHGLTLWDLDRQWPTGGFGGASSLTLRKILGVLRDAYCRTIGV
+EYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE
+GGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA
+SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRLDLGGQRP
+DSFSVLPILVHGDAAFAGQGVVAEVLQLSQLPGYRTGGTIHVIVNNQVGFTTPPTQARSA
+VYSTDVAKTIQAPILHVNGDEPESVVHVAQLAFEYRQRFNKDVVIDLVCYRRRGHNEGDD
+PSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADSALKDYQQQLERVFAETHEDAP
+ASGGEGLRPAEDRDAAPEAPASTAISAETLRAIGQAHIDVPEGFTVHPKLAALLERRAKM
+AVDGGIDWGFAELAAFGSLLMEGVPVRLAGQDSQRGTFTQRHSVFHDRITDETWAPLKHL
+SEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFVNGAQTIIDEFISSAD
+QKWSQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSTGANHFHLLREQA
+YARPRRPLVVFTPKQLLRLKAAANSVEDFTEGRFQPVIPDAGVDAKDVTRVLLVSGRLYY
+DLLARREKSGDTSTAIVRVEQLYPLPLEEIRKALRAYPDADVAWVQDEPANQGPWPFMAL
+NLVPQLDVPVTLVSRPASAATSAGTKGRHDQELSTLLDAAFGR
+>2_2125
+MLRKRRYTVPELTSDRLAQEFPGNERLVAEIYRKYRADSGSVDRQWAQIFARLEASAPAP
+AEKAPAQAAAKAAPKAEPQAEAKVTEPKAKPAPARGAQPKETSTSTGPKVKKTPAAQAVP
+SEPADPSKDAAKEEKQEKATVLKGMAKAVATNMDASLSMPTATTVRDVPAKVLIDNRVVI
+NSHLARTRGGKVSFTHLIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLP
+RPDGSRSLVVPNVKAAETLDFRGFWQAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGT
+VHSVPRLSKGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSG
+EFLKIVHGLLLGEDGFYDEVFHSLRIPYEPVRWAQDLQVNPEEQVGKVARVQQLIHAYRD
+RGHLMANVDPLEYSMPYHPDLDIREHGLTLWDLDRQWPTGGFGGASTLTLRKILGVLRDA
+YCRTIGVEYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIG
+QKRFSLEGGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYGQVFREFE
+GATPGGTSGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRL
+DLGGQRPDSFSVLPILVHGDAAFAGQGVVTEVLQLSQLPGYRTGGTIHVIVNNQVGFTTP
+PTQARSAVYSTDVAKTIQAPILHVNGDEPESVMHVAELAFEYRQRFNKDVVIDLVCYRRR
+GHNEGDDPSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADTALKDYQQQLERVFA
+ETHEGSASSGGEGIRPAEDRDQAPEAPETTAISAETLRAIGQAHIDVPEGFTVHPKLAAL
+LERRAKMAVDGGIDWGFAELAAFGSLLMEGVPVRLAGQDSQRGTFTQRHSVFHDRITGDE
+WAPLKNLSEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFINGAQTIID
+EFISSAEQKWAQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPTTGANHF
+HLLREQAYARPRRPLVVFTPKQLLRLKAAANSVEDFTEGRFQPVIPDAGVDPKKVTRVQL
+VSGRLYYDLLARRNKDGDETTAIVRVEQLYPLPLDELRAALEAYPQAEVVWVQDEPANQG
+PWPFMALNLLPQLDREVRLVSRPASASTSAGTKGRHDQELSTLLDAGFAR
+>3_2019
+MPELTSDRLSQEFPGNEDLVAQIYRKYREDQGAVDRQWAQIFARLEASQPQPEPAAAAPK
+ATSSATAEPAPAVKPAVKRGAATPADPQAAAKKSGPTDVSAPAQRKRSVSEAVPSEPARD
+AAAGASEKQDKATVLKGMAKAVATNMDASLSMPTATTVRDLPAKLLIDNRTVINSHLART
+RGGKVSFTHLIGYAVVRALKAMPSMNTLYEERDGKPTMVEPAHVNFGLAIDLPKPDGTRA
+LVVPNIKAAETLSFRQFWEAYDDLVKRGRANKLTMDDYAGTTVSLTNPGGIGTVHSVPRL
+SKGQAAIIGVGALTYPAAFQGAAESTLNSLAISKTITLTSTYDHRVIQGAGSGEFLKLIH
+GYLLGEDGFYDDVFHDLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN
+VDPLEYRMPTHPDLDIREHGLTLWDLDREWPTGGFGGADTLTLRRILGVLRDAYCRTVGV
+EYMHIQNPAERAWFQDKLERPYEKPSREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE
+GGESLIPLLDSILGDAADEGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA
+SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVARAKQDRLEAAGESG
+AAFPVLPILVHGDAAFAGQGVVTEVLNLSQLPGYRTGGTIHVVVNNQVGFTTSPAEGRSS
+VYATDVAKTIQAPILHVNGDEPESVLRVARLAYEYRQRFHKDVVIDLVCYRRRGHNEGDD
+PSMTQPRMYTLIEQKRSTRKLYVESLVGRGDITQEEADTALKDYQQQLERVFAETHAAET
+GQAVATTGLEPARDRDAARPAPSTTAISPDTLRRIGDVHLEVPEDFTVHPKLSQLLEKRA
+KMAVDGGIDWGFAELAAFGSLLMEGVPVRLSGQDSQRGTFTQRHSVFHDRVTDETWTPLN
+HLSESEAPFWVYNSLLSEYAVLGFEYGYSVERSDALVLWEAQFGDFINGAQTMIDEFISS
+AEQKWSQNSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSHGANHFHLLRE
+QAYSRPRRPLVVFTPKQLLRLKAAADPVEAFTQGGFRKVIGDASVDAAQVERVILVSGRL
+YYDLLARREKSGDTSTAIVRVEQLYPLPAEEIRAELAKYPGAQVRWVQDEPANQGPWPFM
+ALNLLPQLDREVTLVSRPALAATSAGTKGRHDEELSTLLDTAFGA
+>4_693
+MPELTSDRLAQEFPGNERLVAEIYRKYREDSGSVDRQWAQIFARLEASAAAAEAEPKAAA
+EAEPKAAARAEPKATAKVTEPKAATAPARGAQPKETSVSTGPKAKKTPAAQAVPSEPADT
+ATTTADEKQEKATVLKGMAKAVATNMDASLSMPTATTVRDLPAKVLIDNRVVINSHLART
+RGGKVSFTHLIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLPRPDGTRA
+LVVPNVKAAETLDFRGFWKAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGTVHSVPRL
+SQGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSGEFLKIVH
+GLLLGEDGFYDEVFHSLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN
+VDPLEYSMAYHPDLDIREHGLTLWDLDREWPTGGFGGASSLTLRKILGVLRDAYCRTIGV
+EYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE
+GGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA
+SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRLDLGGQRP
+DSFSVLPILVHGDAAFAGQGVVTEVLQLSQLPGYRTGGTIHVIVNNQVGFTTPPTQARSA
+VYSTDVAKTIQAPIFHVNGDEPESVVHVAQLAFEYRQRFNKDVVIDLVCYRRRGHNEGDD
+PSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADSALKDYQQQLERAFAETHEDAP
+TSGDEGIRPAEDRDAAPKAPASTAISAEMLRAIGQAHLDVPEGFTVHPKLAALLERRAKM
+AVDGGIDWGFAELAAFGSLLMEGVPVRLAGQDSQRGTFTQRHSVFHDRITGDTWAPLKHL
+SEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFVNGAQTIIDEFISSAD
+QKWSQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSTGANHFHLLREHA
+YARPRRPLIVFTPKQLLRLKAAANSVEDFTEGRFQPVIPDAGVDAKDATRVLLVSGRLYY
+DLLARRQKSGDTSTAIVRVEQLYPLPLEEIRKALRAYPDADVAWVQDEPANQGPWPFMAL
+NLVPQLDVPVTLVSRPASAATSAGTKGRHDQELSTLLDAAFGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000675.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000675.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b3583b0b2e31a3d9833cf91885d8757cbb20e356
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000675.fa
@@ -0,0 +1,20 @@
+>0_736
+MSTVSAPEPSPRAARPRATRQKAAVDRALDRIPDFVSAQELHARLQDQGERVSLATVYRT
+LQQQLDDGLVDVLRRDDGESVYRRCEDEGHHHHLVCRSCWTTVEVTAPHVEAWATAVAAE
+HGFTDADHTVEITGVCARCRTEGRTRGA
+>1_475
+MSTVSAPEPSPRAARPRATRQKAAVDRALDRIPDFVSAQELHARLQDQGERVSLATVYRT
+LQQQLDDGLVDMLRRDDGETVYRRCEDEGHHHHLVCRICWTTVEVTAPHVEAWATAVAAE
+HGFTDADHTVEITGVCARCRTEGRTRGA
+>2_2118
+MSAPDPGPRVVRPRATRQKAAVDRALETIPDFVSAQELHARLQEEGERISLATVYRTLQQ
+QLEDGQVDVLRREDGESVYRRCEARGHHHHLVCRLCWSTVEVTAPPVEAWAARIAAEHGF
+TEAEHTVEITGVCADCAATRAADAG
+>3_2012
+MSETPGRPSEAPAPRGRSTRQKAAVDGALDAAEDFVSAQELHARLRDAGERVSLATVYRA
+LQQRLDEGTVDMLRREDGESVYRRCAAEGHHHHLVCRVCWTTVEVTAPGVEEWAARMAAE
+HGFSDPDHTVEITGVCAECRAAGRG
+>4_700
+MSTVSAPEPSPRAARPRATRQKAAVDRALDRIPDFVSAQELHARLQDQGERVSLATVYRT
+LQQQLDDGLVDMLRRDDGESVYRRCEDEGHHHHLVCRICWTTVEVTAPHVEAWATAVAAE
+HGFTDADHTVEITGVCARCRAEGRTRAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000677.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000677.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dd4074ec96ccb2cee68c6ea6ff3088715fd8945a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000677.fa
@@ -0,0 +1,20 @@
+>0_738
+MATVFSRIIAGELPARFVWQDQTCVAFLSAAPLQPGHALVVPRAEVDEWVEVDPALVTHL
+TTVAQQIGKAQVAAFSARRAGLMIAGYEIPHLHVHVWPSTSLADFDLARVDNAPDPADLD
+DAAARLRAALRDLGHGEVVPQD
+>1_477
+MATVFSRIIAGELPARFVWQDQTCVAFLSAAPLQPGHALVVPRAEVDEWVEVDPALVTHL
+TTVAQQIGKAQVAAFSARRAGLMIAGYEIPHLHVHVWPSTSLADFDLARVDNAPDPADLD
+DAAARLRAALRDLGHGEVVPQD
+>2_2115
+MASVFSRIIAGELPARFVWQDETCVAFLSTGPLNPGHALVVPREEVDAWVDADPALVMHL
+MTVAQQLGKAQVRAFSAQRAGLMVAGYEILHLHVHVWPSNSLADFDLNRVDNSPDPAEMD
+DAAARLRAALRELGHGEVVPQD
+>3_2010
+MATVFSRIIAGELPARFVWQDEQCVAFLSLGPLAQGHTLVVPREEVDQWVDADPDLLAHL
+TRVAQAIGRVQVRAFGAQRAGLMVAGYEIPHLHVHVWPSNSMNDYDMARVDNAPEPESLD
+EAAAAIRAGLREDGHGDVVPQD
+>4_702
+MATVFSRIVAGELPARFVWQDQTCVAFLSAAPLQPGHTLVVPRAEVDEWVEVDPALVTHL
+TTVAQQIGKAQVAAFSARRAGLMIAGYEIPHLHVHVWPSTSLADFDLARVDNAPDPADLD
+DAAARLRAALRDLGHGEVVPQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000684.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000684.fa
new file mode 100644
index 0000000000000000000000000000000000000000..84b848e0fca2fa53762fe4f43c616d810f8e11ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000684.fa
@@ -0,0 +1,30 @@
+>0_747
+MHSPDPLLMTAAGRDDGGTGPGARRRARLAASRLYVCTDLQRFLRPDGTLDTAAFADFCA
+AAFRGGVDVIQVRDKAVDVAVELAAFATLVPLAREHGALSAANDRADVAALAGVDVFHTG
+QTDLTTAQCRALLGPDVVLGRSCHTEAQVRGARAEDGLDYFCTGPVWATPTKPGRAAVGL
+ELPTLAARLDAEDPAGARPWFAIGGVDADRLPEVRAAGAERIVVVRAVTQAEDPEAAART
+LRAGLPG
+>1_487
+MHSPDPLLMTAAGRDDGGTGPGARRRARLAASRLYVCTDLQRFLRPDGTLDTAAFADFCA
+AAFRGGVDVIQVRDKAVDVAVELAAFATLVPLAREHGALSAANDRADVAALAGVDVFHTG
+QTDLTTAQCRALLGPDVVLGRSCHTEAQVRGARAEDGLDYFCTGPVWATPTKPGRAAVGL
+ELPTLAARLDAEDPAGARPWFAIGGVDADRLPEVRAAGAERIVVVRAVTQAEDPEAAART
+LRAGLPG
+>2_2107
+MHSPDPLLMAAAGRDDGDTGPGTGRRARLAASRLYVCTDLQRFLRPDGTLDTVAFADFCA
+AAFRGGVDLIQVRDKAVDVAVELAAFAVLVPLARAHEALSAANDRADVAALAGVDVFHTG
+QTDLTTVQCRALLGPDVVLGRSCHTEAQVRAARAEDGLDYFCTGPVWATPTKPGRAAVGL
+ELPSHAARLDAEDPAGARPWFAIGGVDADRLTEVRAAGADRIVVVRAVTQAEDPEAAART
+LRAGLPG
+>3_2001
+MHSPDPLLMTAAGRDDGDTGPGAGRRARLAASRLYVCTDLQRFLRPDGTLDTAAFGGFCA
+AAFRGGVDLIQVRDKAVDVAVELAAFAVLIPLAREHGALSAANDRADVAALAGVDVFHTG
+QTDLTTAQCRALLGPNVVLGRSCHTPDHVRAARAEDGLDYFCTGPVWATPTKPGRAAVGL
+GLPTLAARLDAEDPAGARPWFAIGGVDAERLPEVRAAGAGRIVVVRAVTQAADPEAAARE
+LRAGLPA
+>4_714
+MHSPDPLLMAAAGRDDGGTGPGAGRRARLAASRLYVCTGLQRFLRPDGTLDTAAFADFCA
+AAFRGGVDVIQVRDKAVDVALELAAFAVLVPLAREHGALSAANDRADVAALAGVDVFHTG
+QTDLTTAQCRALLGPNVVLGRSCHTEAQVRAARAEDGLDYFCTGPVWATPTKPGRAAVGL
+GLPSLAARLDAEDPAGARPWFAIGGVDADRLPEVRTAGAERIVVVRAVTQAEDPEAAART
+LRAGLPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000687.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000687.fa
new file mode 100644
index 0000000000000000000000000000000000000000..372399b82f19d5a190f7804d1cf5912789a52a7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000687.fa
@@ -0,0 +1,30 @@
+>0_750
+MAEHRTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTVALRRWS
+ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP
+DVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL
+ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG
+FHARRAGRIPRREHALASSPMAGRVTAEEDER
+>1_490
+MAEHRTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTVALRRWS
+ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP
+DVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL
+ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG
+FHARRAGRIPRREHALASSPMAGRVTAEEDER
+>2_2104
+MAEHRTPPATPAIPPLRIGGYDLAARLIMGTGGITDLTALEGALVASGTTLTTVALRRWS
+ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP
+DVVETLEATELLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL
+ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG
+FHARRAGRIPRREHALASSPMAGRVTAEEDER
+>3_1998
+MAPHDTTERRRAREASTAVPPLRIGGYELSSRLIMGTGGITDLAALEGALVASETTLTTV
+ALRRWSTDARDGLIALLDRLGIDVLPNTAGCRTARDAVLTARLGREALETELVKVEVIAD
+DRTLLPDVVETLDATEQLAAAGFTVLAYTSDDPAMALRLEHAGAAAVMPLGSPIGSGLGI
+LNRTNLELIVSRAGVPVVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACR
+LALEAGYHAHRAGRIPRRLHALASSPMAGRIGGAEERA
+>4_717
+MAEHRTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTVALRRWS
+ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP
+DVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL
+ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG
+FHARRAGRIPRREHALASSPMAGRVTAEEDER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000688.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000688.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d6ede4daef92edcf4e2cf6b0cec20eed24f4053
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000688.fa
@@ -0,0 +1,40 @@
+>0_751
+MTAALDPAAREPRDLTALSDTQLERFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPV
+LTYLAAAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEH
+RERLTAANALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAP
+GGPLYRDVFPERPEPGEVPSCAQAGVLGVLPGIIGSLMAAEAIKLLSGVGEPLVGRLLSV
+DALTMRFRELRLVPDPERTPVTDLSAHADQAPRPDDAGAPGSAEACGAAGGEIAPAALAA
+LLADPARVASLTLLDVREDWERRLRRVEAPAAVADRHVPLEAVLAEPAALAPGRDRVLVV
+YCAAGARSARARDAVVGADPSAGGRVLSLAGGLAAWPA
+>1_491
+MTAALDPAAREPRDLTALSDTQLERFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPV
+LTYLAAAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEH
+RERLTAANALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAP
+GGPLYRDVFPERPEPGEVPSCAQAGVLGVLPGIVGSLMAAEAIKLLSGVGEPLVGRLLSV
+DALTMRFRELRLVTDPERTPVTDLSAHAAQAPRPDDAGAPGSAEACGAAGEEIAPAALAA
+LLADPARAASLTLLDVREDWERRLRRVEAPAAVADRHVPLEAVLAEPAAHAPGQDRVLVV
+YCAAGARSARARDAVVGADPSSGGRVLSLAGGLAAWPA
+>2_2103
+MTAAPDPADREPRDLTALSDTQLQRFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPV
+LTYLAAAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEH
+RERLTAANALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAP
+GGPLYRDVFPERPEPGEVPSCAQAGVLGVLPGIIGSLMAAEAIKLLSGVGEPLVGRLLSV
+DALTMRFRELRLVADPERTPVTDLSAHADQAPGSDDAGAPGSAEACGAAGGEIDPATLAA
+LLADPARAASLTLLDVREDWERRLRRVEVPAAVADRHVPLDAVLAEPAAHAPGPDRVLVV
+YCAAGARSARARDAVVAADPSAGERVLSLVGGLAAWPA
+>3_1997
+MSRPAGEPLVPEDRAPHSLDELSDTQLQRFARHLGLDGFGPEAQLALLRSRVLVVGAGGL
+GAPVLTYLAAAGVGEVHVVDDDVVDRSNLHRQVIHVETDLGRPKTASAAETMRGLHPEIR
+VVEHRQRLAAANALELVGAVDLVVDGSDNYATRYLVADAGEITGVPVVWGAILRFAGQVS
+VFAPGGPLYRDVFPEEPEPGDVPTCAQAGVLGVLPGIVGSLMAAEAVKLLAGVGEPLTGR
+LLSVDALTMRFSTLRLVPDPERTSVTDLSAHTVPRGGADPVESGEITPAGLAALLADPER
+AAALTLLDVREDWERGLARISAPAAAEDRHVRLDEVLADPAAHSPESGRTVVVYCAAGAR
+SARAREAVVAAAPEAADRVLSLAGGHAAWADRN
+>4_718
+MTAAREPRDLTALSDTQLERFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPVLTYLA
+AAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEHRERLT
+ATNALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAPGGPLY
+RDVFPERPEPGEVPSCAQAGVLGVLPGIIGSLMAAEAIKLLSGVGEPLVGRLLSVDALTM
+RFRELRLVPDPERTPVTDLSAHADQAPRPDDAGAPGSAEACGAAGGEIAPAALAALLADP
+ARAASLTLLDVREDWERRLRRVEAPATVADRHVPLEAVLAEPAALAPGQDRVLVVYCAAG
+ARSARARDAVVGADPSAGGRVLSLAGGLAAWPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000689.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000689.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e66d2cd184cfad00c483b4f2394a3e11b9d31bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000689.fa
@@ -0,0 +1,55 @@
+>0_752
+MKPEDLSALLSAVLTDAVDAGDLPAALREEITPARVKVERPRSREHGDWATNVALQLGKK
+AGMAPRDLAGLVAERLTDKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPEYGRND
+ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV
+FADSVLARLHGRDVPAGGYPGAYVQELADAVALEHPDVRELTDEAARPVVREAAYRLQMQ
+DIKDTLAAFDVHFDVFTSEQTLHDSGAIEQAVQRLREQGHVEDREGAVWLKTTDFGDDKD
+RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS
+TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVAA
+AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVETLNRTRLWLNDATAQV
+LANGLGLLGVSAPEKM
+>1_492
+MKPEDLSALLSAVLTDAVDAGDLPAALREEITPARVKVERPRSREHGDWATNVALQLGKK
+AGMAPRDLAGLVAERLTGKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPEYGRND
+ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV
+FADSVLARLHGRDVPAGGYPGAYVQELADAVALEHPDVRELTDEAARPVVREAAYRLQMQ
+DIKDTLAAFDVHFDVFTSEQTLHDSGAIEQAVQRLRAQGHIEDREGAVWLKTTDFGDDKD
+RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS
+TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVAA
+AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVETLNRTRLWLNDATAQV
+LANGLGLLGVSAPEKM
+>2_2102
+MKPEDLSALLSAVLTDAVDAGDLPAELREEITPARVKVERPRSREHGDWATNVALQLGKK
+AGMAPRDLAGLVAERLTGKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPDYGRNA
+ALVGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV
+FADSVLARLHGRDVPEGGYPGAYVQELADAVALEHPDVRELTDEAARPVVRQAAYRLQMQ
+DIKDTLAAFDVHFDVFTSEQTLHESGAIEQAVERLREQGHIEDREGAVWLKTTDFGDDKD
+RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS
+TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVAA
+AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVDTLNRTRLWLNDATAQV
+LANGLGLLGVSAPEKM
+>3_1995
+MKPEELSALIHAQLLAAVDAGELPAELREQLSADRVKVERPRSREHGDWATNVALQFAKQ
+AGMNPREFASALASRVGEQPGVATVDVAGPGFLNITLDAAAAGELARQIVEAGEAYGRNE
+ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIVRLLRASGADVTAEYYINDAGNQMNV
+FADSVLARMAGRDVPEGGYPGAYVKDLADAVATDHPQVRELTDDAARPVVRQAAYELQMQ
+DIKDTLAAFDVHFDVFTSETRLHESGAIQAAVDRLREQGHVEDREGAVWLRTTDFGDDKD
+RVMIRANGEPTYFAADAAYYLDKRDRGFEEKVYLLGADHHGYVGRLKAIAAAAGDDPEEN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVQWLGKDALRYDLARYPADSPITIDPELLRS
+QTNDNPVYYVQYAHARACGAARTAAAHGVDRCAFDASLLTDPTESELLAQLAEFPAVVAS
+AARLREPHRVARHLEVIAGAYHSWYAAQRIVPVPLEDGTPAPVEDVNRTRLWLNDAAAQV
+LRNGLGLLGVSAPETM
+>4_719
+MKPEDLSALLSAVLTDAVDAGDLPAALREEITPARVKVERPRSREHGDWATNVALQLGKK
+AGMAPRDLAGLVAERLTDKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPEYGRND
+ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV
+FADSVLARLHGRDVPAGGYPGAYVQELADAVALEHPDVRELTDEAARPVVREAAYRLQMQ
+DIKNTLAAFDVHFDVFTSEQTLHDSGAIEQAVQRLRAQGHVEDREGAVWLKTTDFGDDKD
+RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS
+TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVGA
+AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVETLNRTRLWLNDATAQV
+LANGLGLLGVTAPEKM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000690.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000690.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e515305f7d871aabadb95f7304b87c782eafac6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000690.fa
@@ -0,0 +1,50 @@
+>0_753
+MRTPQPAPASPLAPAWLPAPGDPDALVPGLWAAGVDRAADGELTVQGLRASALAAEFGTP
+LLVVDEDDFRARARAFRKGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS
+GGELAIALAAGIDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELTHLAALAAEAGR
+RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPASTDRDGNVAGRSPAAVAVAAALAA
+ESIELLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV
+DEPRPAAEIADALADDVQKTVERLGLACPRISLEPGRAISGPAGLTLYTVGVTKTVDVDA
+PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSARRTSEAEPVLSRVVGKHCESGDILV
+RDVYLPADLGRGDLLAVPATGAYTHVMSSNYNALARPAVVAVSGGQARVIIRRETQEDLF
+ARETDPRLAR
+>1_493
+MRTPQPAPASPLAPAWLPAPGDPDALVPGLWAAGVDRAADGELTVQGLRASALAAEFGTP
+LLVVDEDDFRARARAFRKGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS
+GGELAIALAAGIDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELTHLAALAAEAGR
+RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPASTDRDGNVAGRSPAAVAVAAALAA
+ESIELLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV
+DEPRPAAEIADALADDVQKTVERLGLACPRISLEPGRAISGPAGLTLYTVGVTKTVDVDA
+PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSARRTSEAEPVLSRVVGKHCESGDILV
+RDVYLPADLGRGDLLAVPATGAYTHVMSSNYNALARPAVVAVSDGQARVIIRRETQEDLF
+AREADPRLAR
+>2_2101
+MTTPQPAPASPLAPAWLPAPGDPDALAPGLWAAGVDRAADGELTVQGLRASALAVEFGTP
+LLVVDEDDFRARARAFREGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS
+GGELAIALAAGVDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELEHLAALAAEAGH
+RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPATTDRDGNVAGRSPAAVAVAAALAA
+ESIDLLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV
+DEPRPAAEIADALADDVQKTVERLGLACPRISLEPGRAISGPAGLTLYTVGVTKTVDADT
+PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSAARTSDAQAVLTRVVGKHCESGDVLV
+RDVYLPEDLGRGDLLAVPATGAYTHVMASNYNALTRPAVVAVAGGRARVIIRRETQEDLF
+AREADPRLGR
+>3_1994
+MNAGSVNLEETVTETAPQSAHPLAPAWLPAPADPDALAPLVWSSGVARDAAGELAVQGVP
+ASVLAERFGTPVLVLDEDDFRARARAFREGFDAAFESLCGGADVYFAGKSMLTLSTARWA
+AEEGLRVDTASGGELAIALRAGVLPEHIGLHGNNKSAAELATALDAGVGRIIVDSVDELE
+FLAALAAERGQIAPVMLRVTPGVHAHTHDFIATAHEDQKFGLSLTPSATGRDGNEAGVAP
+AAVAVRTALQADSIRLLGLHCHIGSQIFEADGFGLAAERVLGFLAEVKDEHGVELPELDL
+GGGHGIAYTAVDEPRPAAEIADALADDVQKAVERLGLTCPRISIEPGRAISGPAGLTLYS
+VGVTKTVDVDAPDDGTASRRYVAVDGGMSDNPRPVLYDADYTAALASRTSDAAPALSRVV
+GKHCESGDILVRDVWLPEDVARGDLLAVPATGAYTHSMSSNYNALLRPAVVAVRDGEARE
+IVRRETLDDLLRREVDPQNPA
+>4_720
+MTTPQPAPASPLAPAWLPAPGDPDALVPGLWAAGVDRAADGELTVQGLRASALAAEFGTP
+LLVVDEDDFRARARAFREGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS
+GGELAIALAAGVDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELTHLAALAAEAGR
+RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPASSDRDGNVAGRSPAAVAVAAALAA
+ESIDLLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV
+DEPRPAAEIADALADDVQKTVERLGLRCPRVSLEPGRAISGPAGLTLYTVGVTKTVDADA
+PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSARRTSEAEPVLSRVVGKHCESGDILV
+RDVYLPADLGRGDLLAVPATGAYTHVMSSNYNALARPAVVAVSGGQARVIIRRETQEDLF
+AREADPRLAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000693.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000693.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d1745f79a19c5b8d096ca1333ae1cd3b68219a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000693.fa
@@ -0,0 +1,35 @@
+>0_756
+MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVEGEGEA
+TLPRDGAHLILRLAREQLRGRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATVRLRLHERVVPVV
+AIPDTELSTHVARGVLPADVPHAVAAAQAGRAALLVHALAEDPALLPAATRDWLHQEPRA
+VAMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAASWRVL
+VPCVAVDGVRVESLHHG
+>1_496
+MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVEGEGEA
+TLPRDGAHLILRLAREHLRDRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATARLRLHERVVPVV
+AIPDTELSTHVARGVLPAEVPHAVAAAQAGRAALLVHALAEDPALLLAATRDWLHQEPRA
+VAMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAASWRVL
+VPCVAVDGVRVESLHHG
+>2_2098
+MPAPRTLAAGTAVVVAVPATSANLGPGFDSMGLALELRDEVSLTVVDGPDVAEVTGEGAD
+VLPRDGSHLILRLAHEHLRARGVRAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAADRRPPEALLEAATDFEGHPDNVAPALVGGATVSWTRDDDARPATAPLRLHERIVPVV
+AIPDTELSTHAARGVLPESVPHAVAAAQAGRAALLVHALAERPELLMAGTRDWLHQGPRA
+AAMPASAALVAGLRVRGHAAVVSGAGPTVLALCDGAEAAEQAAAAARALTADDVLAWRVL
+VPAVAADGVRVEPLHHG
+>3_1991
+MRELRDLTPGTGARVLAPATSANLGPGFDALGLALELRDEVTLTVVDGPDTAVVTGEGAA
+ELPTDGEHLVLRLAHAHLTRRRFRAPGLALTAVNRIPHARGLGSSAAAVVTAVLAAEALL
+PADERLSAAELLDVTARREGHPDNVAPALSGGASVSWHRDGGPGWATAAVALHPQITPVI
+GIPDVTLSTHAARAALPESVPHAVAAEQAGRAALLTLALASRPDLLLPATRDWLHQDARA
+SAMPPSAALVRGLREQGHAAVVSGAGPTVLVLAPTPADAERAAEAMRALAPETGAAWRVL
+VPGVAAEGARVEPLHHG
+>4_723
+MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVVGEGEA
+TLPRDGAHLILRLAHEHLRDRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATARLRLHERVVPVV
+AIPDTELSTHVARGVLPAEVPHAVAAAQAGRAALLVHALAEDPALLPAATRDWLHQEPRA
+VTMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAAAWRVL
+VPCVAVDGVRVESLHHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000694.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000694.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ed34849a2a98da90177d240f974d0824fb7ed05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000694.fa
@@ -0,0 +1,65 @@
+>0_757
+MTESTEQTTPTNGGGLASLKLAQLQALASQLGIAGGSRMRKADLVTAISDHQRGGSVADR
+DAAERAAQAPAAPAAEAAPAAASSQDAAPAAERPARRRSRRADADTSAPAAAQDGQPQAE
+AREDQTEQAPRETASDQDRSEGSETRDEGEGRPQSERRSRGRRAGDDDAQQGQDRRSDGA
+QGEDGADRRGDREDRDDNGRENGRGRNGRNGRDRDNGRDRENGRENNRDRENGRDGSREQ
+RGDKSEDGGRGDGGRGDRSRRDDRDDEGGRNRRNRRNRNERGRNRRGRGGPEVDETELTE
+DDVLQPVAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKYGLRKGDAVVGAIRAPRDG
+EKQQHHGGGSNRQKFNALVKISSVNGQPAVEHPQRVEFGKLVPLYPQERLRLETDPKLIG
+PRVIDLVSPIGKGQRGLIVSPPKAGKTMILQSIANAIKTNNPEVHLMMVLVDERPEEVTD
+MQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNLAA
+PASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGT
+GNMELRLSRHLAERRIFPAVDVNASGTRREEALLSQEEVKIMWKLRRVLSGLEQQQALDL
+LTNKIKDTASNAEFLMLVSKTTLGSKGDD
+>1_497
+MTESTEQTTPTNGGGLASLKLAQLQALASQLGIAGGSRMRKADLVTAISDHQRGGSVADR
+DAAERAAQAPAAPAAEAAPAAASSQDAAPAAERPARRRSRRADADTSAPAAAAQDGQPQA
+EAREDQTEQAPRETASDQDRSGGSEARDEGEDRPQSERRSRNRRRAGDDDAQQGQDRRSD
+GAQGEDGADRRGDREDRDDNGRENGRGRNGRNGRDRENGRDRENGRENNRDRENGRDGSR
+EQRGDKSEDGGRGDGGRGDRSRRDDRDDEGGRNRRNRRNRNERGRNRRGRGGPEVDETEL
+TEDDVLQPVAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKYGLRKGDAVVGAIRAPR
+DGEKQQHHGGGSNRQKFNALVKISSVNGQPAVEHPQRVEFGKLVPLYPQERLRLETDPKL
+IGPRVIDLVSPIGKGQRGLIVSPPKAGKTMILQSIANAIKTNNPEVHLMMVLVDERPEEV
+TDMQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNL
+AAPASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFK
+GTGNMELRLSRHLAERRIFPAVDVNASGTRREEALLSQEEVKIMWKLRRVLSGLDQQQAL
+DLLTNKIKDTASNAEFLMLVSKTTLGSKGDD
+>2_2097
+MTESTEQTTPTTGGGLAALKLAQLQALASQLGIPGGSRMRKADLVTAISDHQRGGSVADR
+AAAERAAKAAAAPAAEAAPAADKAAEQPAEAAERPARRRSRRADADTSAAAQSAESGKDQ
+AERRAEQPAEGRDAEGSQDSGDRAQDSGDRTQGERRSRGRRRAGDDDARGQDRRRQDGED
+AGQDQAHDSAEDRGGDREDGGRENGRGNRGRNGRDNGRDRENGNGRDRDNGNGRDRDGSR
+EQKQDKSEDGGRDGGRNDRNRRDDRDDEGGRGRRNRRNRNERGRNRRGRGGPDVDETELT
+EDDVLQPVAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKHGLRKGDAVVGAIRAPRE
+GEKPQHQGGGSNRQKFNALVKISSVNGQPAVEHPERVEFAKLVPLYPQERLRLETDPKQV
+GPRVIDLVSPIGKGQRGLIVSPPKAGKTMILQSIANAIKTNNPEVHLMMVLVDERPEEVT
+DMQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNLA
+APASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKG
+TGNMELRLSRHLAERRIFPAVDVNASGTRREEALLSPEEVKIMWKLRRVLSGLEQQQALE
+LLTNKIKDTGSNAEFLMLVSKTTLGAKGED
+>3_1990
+MTESPDQTTAGGGLASLKLAQLQALASQLGITGGSRMRKSDLVAAISDHQRGGSVADRDA
+AAQAAAAPAAQAEAAEAPAAEQAPRSRRRSRRADSDGAVAADQPAEATQAPADEQPAAET
+EDAPARAEASAESGAQEAGSGRSRRRRGDRAARDEQQDGAQDEKQESGRGAGEETRREQD
+GDEERAEGRSRSRRGRGDRDRGERQNADRQNGERANGERANGQGEDRSQGGRREDREEES
+GRGQGGDGQKRSDRGNGRREDRDEDGRRGRNRRNRNDRGRNRRSRGPEVDDVEVTEDDVL
+QPVAGILDVLDNYAFVRTSGYLPGEKDVYVSLAMVKKFGLRKGDAVVGAIRAPREGEKPH
+SGGGRNQKFNALVKVTTVNGQPAEENPQRVEFGKLVPLYPTERLRLESDHKLVGPRVIDL
+ISPIGKGQRGLIVSPPKAGKTMILQSIANAITRNNPEVHLMMVLVDERPEEVTDMQRSVA
+GEVIASTFDRPAEDHTTVAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNLAAPASGRI
+LSGGVDSAALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGTGNMELR
+LSRQLAERRIFPAVDVNASGTRREEVLLSPEEVKIMWKLRRVLSGLDTQQALELLTNKIK
+DTASNAEFLMLVSKTTLGSKGDD
+>4_724
+MTESTEQTTPTNGGGLASLKLAQLQALASQLGIAGGSRMRKADLVTAISDHQRGGSVADR
+DAAERAAQAPAAPAAEAVPAAASSQDAAPAAERPARRRSRRADADTSAPAAVAQDGQPQA
+EAREAQTEQGPRETASDQDRSGGSETRDEGEDRPQSERRSRGRRRAGDDDAQQGQDRRSD
+GAQGEDGADADRRGDREDRDDNGRENGRGRNGRNGRDRDNGRDRDNGRDRENGRDGSREQ
+RGDKSEDGGRGDGGRGDRSRRDDRDDEGGRNRRNRRNRNERGRNRRGRGGPEVDETELTE
+DDVLQPAAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKYGLRKGDAVVGAIRAPRDG
+EKQQHHGGGSNRQKFNALVKISSVNGQPAVEHPQRVEFGKLVPLYPQERLRLETDPKLIG
+PRVIDLVSPIGKGQRGLIVSPPKAGKTMILQSIANAIKTNNPEVHLMMVLVDERPEEVTD
+MQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNLAA
+PASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGT
+GNMELRLSRHLAERRIFPAVDVNASGTRREEALLSQEEVKIMWKLRRVLSGLEQQQALDL
+LTNKIKDTASNAEFLMLVSKTTLGSKGDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000697.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000697.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d65813da2bbece9106bdb8189171db2807abdbd1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000697.fa
@@ -0,0 +1,40 @@
+>0_761
+MRAYLVLVMVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG
+FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL
+GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV
+AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH
+HKLVDGGYTQAQAVGLLWLWAFLVAWGAVSLNFVDHMVVLPVLAVALAGAGYLTLHPIVE
+RRRADRNDAAAHPDERGDA
+>1_501
+MRAYLVLVMVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG
+FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL
+GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV
+AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH
+HKLVDGGYTQAQAVGLLWLWAFLVAWGAVSLNFVDHMVVLPVLAVALAGAGYLTLHPIVE
+RRRADRNDAAAHPDERGDA
+>2_2094
+MRAYLVLVVVTALACGALTPLMRRIGLRARVFTPVRQRDMHRRPIPKLGGVAMAAAVLVG
+LAVGGTVPFLQGIYADDAAMVGLLVAVAVVFVVGIADDLWDLRWWVKMAGQVCAGLAVAL
+GGIRIEAMPVGWIPVGSEAMQIALTVFAVVLTMNALNFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACLGFLPFNRFPARIFMGEVGAMLLGLLMAAAAV
+AVTADVKALDGMRFRNVPAYMPILLPIAVLALPLLDLALAVVRRTARGASPFSADRGHLH
+HKLVDGGYTHAQAVWLLWLWAFLVAWGAVSLNFVDDMIVLPVLGLALLGAGYLTLRTPVR
+RRRAGAPAAGPALDPEEGA
+>3_1986
+MRAYLLVAAVTALTCLALTPWVRRVGVRARAYTPHRDRDVHRAPVPKLGGVAMVAAVLAG
+LAVAGTVPFLGGIFTDASAMRGLLAALGIILVLGVVDDLVDLRWWAKLGGQSLAALAVAL
+GGIRIAALPVGWIHVGSEAVQVALTVFVVVLTMNAINFIDGLDGLAAGVALIGGSAFFVY
+SYLLTRTIDQFDYSNLATLLMALLIGACAGFLPYNRHPARIFMGESGALLLGLLLSTAAV
+AVTADLDALEGFRFRNVPAYMPVLLPIAVLALPLADLTISVIRRAAHGESPFGADRGHLH
+HRLVDGGFTHAQAVRVLWLWSFIVAWGVLSLNFADDAVVLLLAAAGLAVATWLTVHPLRA
+RAARPASRPDAQPKDQP
+>4_728
+MRAYLVLVVVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG
+FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL
+GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV
+AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH
+HKLVDGGYTQAQAVALLWLWAFLVAWGAVSLNFVDPMIVLPVLAVALAGAGYLTLHPIVE
+RRRAVRNDAAAHPDERGDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000698.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000698.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0422924417eb885db59748974ee5bf6db6adc1f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000698.fa
@@ -0,0 +1,20 @@
+>0_762
+MTGAGGRRRRRRWENRRGWWGILGWSLAAAGVALAITCAAWLLSVGGEAAGSALLGGGAV
+LALSALTGVTTALVWDRAREAALPVSVGLFVLKIAVFAVLLGVLPRPGWVRADAAAIAAL
+VTILVWQAAEVLVFARTRRGIYAD
+>1_502
+MTGAGGRRRRRRWENRRGWWGILGWSLAAAGVALAITCAAWLLSVGGEAAGSALLGGGAV
+LALSALTGVTTALVWDRAREAALPVSVGLFVLKIAVFAVLLGVLPRPGWVRADAAAIAAL
+VTILVWQAAEVLVFARTRRGIYAD
+>2_2093
+MSPRTAPDAAPRSARARRRPRRRRWENRRGWWGILAWSLAATAAAVAVVCAVALAAGGPD
+AAASALLGGGAVLVLSALTGATTALVWDRAREAALPVSVGLFVLKIAVFAVLLGTVPRPD
+WILPDAAAIAALVAILVWQGVEVLVFARTRRGIYAD
+>3_1985
+MTASARPARRRWENRAGWWGILRWCCAATAVGVLACGAVAAVLHGGPAGLSALTGGGAVL
+VLSALTGATTAVAWDRARAAALPLSVGAFVVKLVLYALLLATLRMPEWMSGTAVAVGALV
+GVVVWQAVEVLVFARTRRGIYAD
+>4_729
+MTGAGGRRRRRRWENRRGWWGILGWSLAAAGAALAITCAAWLLSAGGEAAGSALLGGGAV
+LALSALTGATTALVWDRAREAALPVSVGLFVLKIAVFAVLLGVLPRPGWVRADAAAIAAL
+VTILVWQAAEVLVFARTRRGIYAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000699.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000699.fa
new file mode 100644
index 0000000000000000000000000000000000000000..148389391988b640fd790d784539770b958e8a0b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000699.fa
@@ -0,0 +1,30 @@
+>0_763
+MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP
+RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFAIFFFVLLNNLFGAIPVLQL
+PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI
+VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL
+IMYLQAFVFTLLTAIYIQGAIDANDH
+>1_503
+MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP
+RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFAIFFFVLLNNLFGAIPVLQL
+PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI
+VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL
+IMYLQAFVFTLLTAIYIQGAIDANDH
+>2_2092
+MLTLVLANASFVPPTISDGNLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP
+QLVPGKAQWLAESGYSFVRNGIAKDILGEKNFRQWVPLLFAIFFFVLLNNLFGAIPVLQL
+PSFSHAGAAYGIALIVYAIWIGVGLKRHGIRYLKLAVVPSGVPSWILPLLVPLEIISNFI
+VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVIIGSVALYFLELL
+IMYLQAFVFTLLTAIYIQGAIDANDH
+>3_1984
+MLPLVLANAEFVPPSVSDAHLPDLLPWGAEYGTGFGKQMLLVLLSVVLITGFFAWAMRKP
+KLVPGRAQWIAESGYAFVRNGIGRDVMGEKHFKQWVPLLFAIFFFVLLNNLFGAIPLLQM
+PSFSHAGSAYAIALIVYAIWIGVGVKHHGVKYFKLAVVPSGVPGWILPLLVPLEFISNFI
+VRPLTHSLRLMAVMLAGHMIVMLAGAGAAFLITQTGNPLLAGTGVLVILASVALYLLEIL
+LMYLQAFVFTLLTALYIQGAIDANDH
+>4_730
+MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP
+RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFSIFFFVLLNNLFGAIPVLQL
+PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI
+VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL
+IMYLQAFVFTLLTAIYIQGAIDANDH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000701.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000701.fa
new file mode 100644
index 0000000000000000000000000000000000000000..769c2598f5a266bca668842ad47c7f872d2fe511
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000701.fa
@@ -0,0 +1,25 @@
+>0_765
+MISNGLILAAAEGANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGG
+LAKAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAEARRISE
+QAQAQIAAERQQAAAQLKGEVGSLATTLAGKIVGESLEDDARSQRVVDRFLADLDRHQSA
+GVAE
+>1_505
+MISNGLILAAAEGANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGG
+LAKAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAEARRISE
+QAQAQIAAERQQAAAQLKGEVGSLATTLAGKIVGESLEDDARSQRVVDRFLADLDRHQSA
+GVAE
+>2_2090
+MISNGLILAAGANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGGLA
+KAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAESTRISEQA
+QAQIAAERQQAASQLKGEVGTLATTLASKIVGESLEDDARSQRVVDRFLADLDRHQSAGV
+AE
+>3_1982
+MISNGLILASAEGANPLVPNPWEILVTTVGFAVLMFIVVKFVVPALEKSYTDRVEAIEGG
+LEKAEKAQAEANKMMADYEGQLADARQEANRIREEARTEGAQIVAEARERAAAEAARITE
+QAQTQIAAERTQAAAQLKGEVGTLATTLASKIVGESLDDDARSQRVVDRFLADLDRHQSA
+GVSE
+>4_732
+MISNGLILAAAEGANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGG
+LAKAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAEATRISE
+QAQAQIAAERQQAAAQLKGEVGSLATTLAGKIVGESLEDDARSQRVVDRFLADLDRHQSA
+GVAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000702.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000702.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c4857df98cb30686b54dce502817f1746d75c34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000702.fa
@@ -0,0 +1,30 @@
+>0_766
+MMTGASRDSLAASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH
+GLVDSLFGARVTPGALQVLKDLAGRRWSAERDLGDALETVAVHAAAAEAARGGHAGLAAL
+LGELLAFNRTVEDSHELQRALTDQHAPLEARAALAGRLLGESASPAGRLLVERAVSAPRG
+LKPSAAIRKAADAVAERQRQWIAEVTVARPLEAEQQERLALGLRRAFGRDLVMDVTVDPH
+VVGGVRVQVGDDVVDGSMASRLHDLQRRMAG
+>1_506
+MMTGASRDSLAASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH
+GLVDSLFGARVTPGALQVLKDLAGRRWSAERDLGDALETVAVHAAAAEAARGGHAGLAAL
+LGELLAFNRTVEDSHELQRALTDQHAPLEARAALAGRLLGESASPAGRLLVERAVSAPRG
+LKPSAAIRKAADVVAERQRQWIAEVTVARPLEAEQQERLALGLRRAFGRDLVMDVTVDPH
+VVGGVRVQVGDDVVDGSMASRLHDLQRRMAG
+>2_2089
+MMTGASRDSLTASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH
+GLVDSLFGARVTPGALQVIKDLAGRRWSAERDLGDALETVAAHAAAAEAGRGGHAGLAAL
+SGELLAFNRTVEDSHEVQRALTDQHAPVEARAALARRLLGESASPAGQLLVERAVAAPRG
+VKPAAAVRQAADVVAERQRQWIAEVTVARPLGAEQQERLALGLRRAFERDLVMDVTVDPH
+VVGGIRVQVGDDVVDGSMASRLNDLQRRMAG
+>3_1981
+MMTGASGDSLTASLESVRTVLDEGGVALARELFAALDVVDQQGALRRALTDPAWSTERRH
+GVLDSLFGGRVSPGALQVLKDLAGRRWSAERDFGDALEAVAADAAAGEAARGGHAGLAAL
+SGELLGFQRVFQDSHEVERALTDQRAPRESRSGLARRLLGAQASPAAVLLVERAVTDGRG
+VKPATALRSYADVVATRQRQWIAEVTVARPLEDGQRERLAAGLRRAFGRDLVLDVNVDPT
+VVGGIRVQVGDDVIDGSMASRLNDLQRRMAA
+>4_733
+MMTGASRDSLAASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH
+GLVDSLFGARVTPGALQVLKDLAGRRWSAERDLGDALETVAAHAAAAEAARGGHAGLAAL
+SGELLAFNRTVEDSHEVQRALTDQHAPLEARAALAGRLLGESASPAGRLLVERAVSAPRG
+LKPSAAVRKAADVVAERQRQWIAEVTVARPLEAEQQERLALGLRRAFGRDLVMDVTVDPH
+VVGGIRVQVGDDVVDGSMASRLHDLQRRMAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000707.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000707.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83c11fb376bc3fa31ad0b4cd768285b8c776a9ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000707.fa
@@ -0,0 +1,20 @@
+>0_771
+MQGPVLIASATVAAVIVLSALALVMRRRALARVTAAFPAVLEREGPGRERVIGVYDESRL
+RLTGRWRLSRERWSADRSRLQIDRLPADEAGRTVLELSAGARPVRVVVDPDDAGALRAWS
+EAGPSAASSFWRR
+>1_511
+MLIASATVVAVIVLSALALVMRRRALARVTAAFPAVLEREGPGRERVIGVYDESRLRLTG
+GWRLSRERWSADRSRLQIDRLPADEAGRAVLELSAGARPVRVVVDPDDAGALRAWSEAGP
+SAASSFWRR
+>2_2084
+MLIALAGVLAVFALSASALAVRRRALLRTSAAFPAVLQGHGRPRERVIGVYDETRLLFTG
+RWMIRRERWSVGRCDLQIDRLPVAEDGRAVLELDGGRGSVTVVVDPDDAGALRAWSEAGP
+SAASSFWRR
+>3_1976
+MRGPVLLLSGALAVFALLALAGWARHRALVRGPGRFAGVLVTDGGRRCRVVGCFRSHELV
+LSHHLLPERRLWSAERWRLEVDRLPAAEAGHTRLRITDASGRSDDAVDLEVEDDVAGAVR
+AWTEAGPSQAGQSWWRPPGAA
+>4_738
+MEGPVLIASATVVAVIVLSALALVMRRRALARVTAAFPAVLEREGPGRERVIGVYDESRL
+RLTGGWRLSRERWSADRSRLQIDRLPADEAGRAVLELSAGTRPVRVVVDPDDAGALRAWS
+EAGPSAASSFWRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000708.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000708.fa
new file mode 100644
index 0000000000000000000000000000000000000000..608fc0680006190f51f62f03bd2161f3b0d5b1a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000708.fa
@@ -0,0 +1,25 @@
+>0_772
+MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE
+PSPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA
+EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN
+RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF
+>1_512
+MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE
+PSPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA
+EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN
+RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF
+>2_2082
+MRLVIARCSVTYEGRLNAHLPPATRLLMVKADGAVLVHSDGGSYKPLNWMSPPATLHTTA
+PTAEQAEQGVVEVWRVQAAKSDDRLMILIEEILADQSHELGADPGLVKDGVEADLQRLLA
+EQIGLLGDGHTLVRREYMTAIGPVDILARDPEGGTVAVELKRRGDIDGVEQLTRYLELMN
+RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF
+>3_1974
+MRLVIARCSVTYEGRLNAHLPSATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE
+PTEEQAAAGVTQVWRVQAKKSDDRLLVLLEEVLADETHELGVDPGLVKDGVEADLQRLLA
+EQIGLLGDGHTLVRREYMTAIGPVDILAKGPGGQTVAVELKRRGDIDGVEQLTRYLDLMN
+RDPLLAPVTGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDADARLF
+>4_739
+MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE
+PFPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA
+EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN
+RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000710.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000710.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aeaf20dbb191783e33cd7248c42524a3ccbec953
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000710.fa
@@ -0,0 +1,43 @@
+>0_774
+MEEKEPASGPDAPSVADVRAPAEPEGAEQQPVGGIPVEPAGAAAAPPSHGPTPAGRRRRL
+RLGSVLRRRRPFLEEDRVDPEPDPADGAEDPAVAAVALESPVLTGFLLAVGVTLAIGIVS
+VLRTNGQLIVWIAAALFIALGLDPLVRRVESWGAPRWVGVLTAALGLAAVAGAFVALLVP
+TVIEQSTQLVQDLPAIIDGVMRAEWFVQLDEEFHLQEAVRAQTERLAADGVAITDLFGGL
+LGLGQTVLNAVFSVLVVVVLTLYFLSSLPHMKYWAYRLAPRSRRPRIEALSEQITSSVGH
+YVMGQSFVAALNGAVAFTALAIAGAPFAVLLAAIAAFMAFIPLVGAAIGGTLLTLVSLLT
+SWQTAAVFAAIYFVYLQIEAYVISPRVMARAVPVPAAVAVIAVIAGGALLGVLGALMAIP
+LAAALALLVREVFIPRQDAR
+>1_514
+MSLGPTVASRARRGQAGALTYAERVEEKETASGPDVAGVADVRGPAEPEGAEQPPVAGVP
+VEPVGVAAAPPSHGPTPAGRRRLPRLGSVLRRRRPFLEEDRVDPESVPVDGAEDPAVAAV
+ALESPVLTGFLLAVGVALAIGVVSVLRTNGQLIVWIAAALFIALGLDPLVRRVESWGAPR
+WVGVLTAALGLAAVAGAFVALLVPTVIEQSTQLVQDLPAIIDGVMTAEWFVQLDEEFHLQ
+EAVRAQTERLAADGVAVTDLFGGLLGFGQTVLNAVFSVLVVVVLTLYFLSSLPHMKYWAY
+RLAPRSRRPRIEALSEQITSSVGHYVMGQSFVAALNGAVAFTALAIAGAPFAVLLAAIAA
+FMAFIPLVGAAIGGTLLTLVSLLTSWQTAAVFAAIYFVYLQIEAYVISPRVMARAVSVPA
+AVAVIAVIAGGALLGVLGALMAIPLAVALLLLVREVFIPRQDAR
+>2_2080
+MEPVDPTAAPASAAPAPLPASGRVPRRRRRRGRLIPLRGVLRRRRPVFLAEDRVDPDPEH
+PEPEPTGEPPVTAVTVESPVATGFLLTVGVALALAVVWVLRTNGQLLVWIAAALFIALGL
+DPLVRRVESWGAPRWAGVLTAALGLAAVASAFVALLVPTVVEQSRQLVEGLPGTIEDVMT
+SAWFIELDQEFHIQEAVRAQTDRLTTDGAAVTDLFGGLLGIGQTVLNAFFSVFVVVVLTL
+YFLASLPHMKYWAYRLAPRSRRPQVERLSEKITSSVGHYVMGQSFVAALNGTVAFTALAV
+AGTPFAVLLAAFAAFMAFIPLVGAVIGGTVLTLLSLLTSWQTAAVFAAIYFVYLQIEAYV
+VSPRVMARAVAVPAAVAVIAVIAGGALLGVLGALMAIPLAAALSMLVREVFIPRQDAR
+>3_1972
+MDHIEDSPAPSGPSRGARRLRLGSLVRRREAFLPNERVDPLPPGSPDAAPAEPEVPELAL
+RAPVAAGFLLTMGVCLAAVLVWVVLENTQLLVWIAAALFIALGLDPVVRLVERWGAPRWV
+GVLLAALGLAAVAGAVVGMLVPAVVQQSTQLITGLPDTITQIMATPWFREVDRQLQIQHA
+VQSWLDGLTKDGAAVTQLFGGLVGIGQTVMNAVFSTIVVVVLALYFLASLPHLKYWGYRL
+APRSKRLRVEALGEEITLSVGHYVMGQTVVAVLNGTVAFIALSVAGGPFPVLLAFVAAVM
+AFIPLVGALIGGTILTAVCLLESWQAAALFAAIYFVYLQIEAYVVSPRVMARAVAVPAAV
+GVIAVIAGGTLLGVLGALMAIPTAAAVLLIVREVLIPRQDAR
+>4_741
+MSLRPTVASPARRGQAGALTYAERVEEKETASGPDAAGVADVRAPAEPEGTEQPPVAGIP
+VEPVGVAAAPPSHGPTPAGRRRLPRLGSVLRRRRPFLEEDRVDPESVPVDGAEDPAVAAV
+ALESPVLTGFLLAVGVALAIGVVSVLRTNGHLIVWIAAALFIALGLDPLVRRVESWGAPR
+WVGVLTAALGLAAVAGAFVALLVPTVIEQSTQLVQDLPAIIDGVMTAEWFVQLDEEFHLQ
+EAVRAQTERLAADGVAVTDLFGGLLGFGQTVLNAVFSVLVVVVLTLYFLSSLPHMKYWAY
+RLAPRSRRPRIEALSEQITSSVGHYVMGQSFVAALNGAVAFTALAIAGAPFAVLLAAIAA
+FMAFIPLVGAAIGGTLLTLVSLLTSWQTAAVFAAIYFVYLQIEAYVISPRVMARAVSVPA
+AVAVIAVIAGGALLGVLGALMAIPLAAALLLLVREVFIPRQDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000714.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000714.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a45733158fefa9e087d51c302efde92d6df7a62b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000714.fa
@@ -0,0 +1,15 @@
+>0_778
+MSVTGEPDLNDPFAPAGGGTSVLEREELRQEIEPGDHERFAHYVRKEKITESAVTGAPVI
+ALCGKVWVPGRDPNKFPVCPTCKEIYEGLREPQDGGDGDGGGKRGGWFGGRGRG
+>1_518
+MSVTGEPDLNDPFAPAGGGTSVLEREELRQEIEPGDHERFAHYVRKEKITESAVTGAPVI
+ALCGKVWVPGRDPNKFPVCPTCKEIYEGLREPQDGGDGDGGGKRGGWFGGRGRG
+>2_2076
+MSVTGEPDLTDPFSPAGGGTSVLEREQQLQDVEPGDHERFAHYVRKEKITESAVTGAPVI
+ALCGKVWVPGRDPQKFPVCPTCQEIYEGLREPQDGDDAGAGGGRRGGWFGGRGRG
+>3_1968
+MSISDPFQNDPLSPSGGGTSVLEREEQLQDVEPGDHERFAHYVRKEKIMESALSGEPVIA
+LCGKVWVPGRDPNKFPVCPLCQEIYDGLRDPQDGDDAGSGGGRRGGFFGRGRG
+>4_745
+MSVTGEPDLNDPFAPAGGGTSVLEREELRQEIEPGDHERFAHYVRKEKITESAVTGAPVI
+ALCGKVWVPGRDPNKFPVCPTCKEIYEGLREPQDGGDGDGKRGGWFGGRGRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000720.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000720.fa
new file mode 100644
index 0000000000000000000000000000000000000000..74a54b07b82ca9ec935ef1a0f2bda96503cc23ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000720.fa
@@ -0,0 +1,35 @@
+>0_785
+MSGQRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIAEVRA
+LALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAVAATR
+TGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETAREYT
+APLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEHPHS
+AAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRSTAFV
+PLGAEQEGVT
+>1_526
+MSGQRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIAEVRA
+LALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAVAATR
+TGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETAREYT
+APLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEHPHS
+AAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRSAASV
+RPGPEQEGVT
+>2_2069
+MSAPPQARPEVSASSPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTAHAPYGPRPIAQ
+VRALALGIMDELVDAGVKALVIACNSASAAVLRDARERYTGRHGIPVVEVIQPAVRRAVA
+ATRSGRIGVIGTQATVGSRAYDDSFSAAPHLQVTSAACPRFVEFVEAGITTGPELLATAQ
+EYTEPLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEH
+PHSAAGSGQDTRHRFAATGDPEHFQALARRFLGPEVGAVRRLDTVRERYPTAALAQLTPD
+LIARLGAEQERET
+>3_1959
+MSATADTAQTGAGPSSPIGVFDSGVGGLTVARAIMDQLPHEPIIYVGDTAHSPYGPRPIA
+QVRALALGVMDELVEAGVKALVIACNSASAAVLRDARERYTGRLGIPVVEVIQPAVRRAV
+AATRNGRVGVIGTQATVGSRAYEDSFSAAPHLQITSVACPRFVEFVEAGITTGPELLETA
+EEYVAPLKAAGVDTMVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRALVRHGLE
+HPHSAAGSAAAPEHRFAATGDPEHFAALARRFLGPEVGPVRQIQEIRERYPTAALTALTP
+DVLARLRAEMEEDGAR
+>4_754
+MSGQRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIAEVRA
+LALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAVAATR
+TGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETAREYT
+APLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEHPHS
+AAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRSAASV
+RPGPEQEGVT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000725.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000725.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9010c92da9ac996a66b3619fcb481c59b5e274e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000725.fa
@@ -0,0 +1,40 @@
+>0_790
+MSATAPEPTASSSTPLPGPEHADRVLALLAAGAAGDALGGVVEFTPASGIAAVHGPAGVT
+DAADLLAQEGAHALPITDDTQLTLYVLDGLLEWIEWQNDGVPADPAACVWLACLRWFATQ
+DGALPEGAPPAPPRWIDAHAELKVRRAPGTACLTGLAEPGMGLPGDPHNPGSKGCGTVMR
+SAPYGMVPGLEDPHVVSLARQGAVLTHGHPTAWVAAAAYALVIAALLRGLDLAAAVAHAR
+AWLDTLGEEAEETRAAVTAAVDLAGTVDADPGAPGALPTALGEGWVAEEALAIALYAALT
+AQAAHPADPAAALALALRIGVNHDGDSDSTASLAGQVLGAAHGTAVFGAHDPADRAAAEA
+SVPGWIAEREVVLEAARRWSAATT
+>1_531
+MSATAPEPTASSSTPLPGPEHADRVLALLAAGAAGDALGGVVEFTPASGIAAVHGPAGVT
+DAADLLAQQGAHALPITDDTQLTLYVLDGLLEWIEWQNDGVPADPAACVWLACLRWFATQ
+DGALPEGAPPAPPRWIDAHAELKVRRAPGTACLSGLAEPGMGLPGDPHNPGSKGCGTVMR
+SAPYGMVPGLEDPHVVSLARQGAVLTHGHPTAWVAAAAYALVIAALLRGLDLAAAVAHAR
+AWLDTLGEEAEETRAAVTAAVDLAGTVDADPGAPGALPTALGEGWVAEEALAIALYAALT
+AQAAHPADPAAALALALRIGVNHDGDSDSTASLAGQVLGAAHGTAVFGAHDPADRAAAEA
+SVPGWIAEREVVLEAARRWSAATT
+>2_2064
+MTETPAAPSLPGPEHATRVAALLAAGAAGDALGYTVEFDADAAVRARHGAEGLTTGEAAL
+AVVGGEALPISDDTQMTLYVLDGLLEWIEWQNDGQAADPAACVWLACLRWWATQHGGALP
+DGAPPVPPRWLEDHPELRARRAPGNACLSGLDSAAMGLPGDPRNPDSKGCGTVMRSAPYG
+MVPGLEDVHVVSFARQGAVLTHGHPTAWVAAAAYSLMIAALLRGAGLEDAVAHARVWVDS
+LDPAEGGETAAALASAVELAASPADDAGRPGTLPAALGEGWVAEEALAIAVHAALVAQAR
+HEDPADMLALALRIGANHAGDSDSTASLAGQLLGAAHGPAVFGADAAADGPAGLVPAWVA
+EREVVAEAARRWSAATT
+>3_1954
+MTDAAPSPRTDVSYPSRVLGLLAAGAAGDALGYAVEFDSVDRILGRLGAAGVTDGPALAA
+VSGVSALPVSGDTQMTLYVLDGMLEWIEWQNAGQASDPAACVWLACLRWLRTQDGALPDG
+APPAQDRWIDAHTELHAQRAPGMACLSGLRSSGMGVVPDPKNPDSKGCGAVMRSAPYGMV
+PGLEDHHVASFARQGAVLTHGHPTGWTAAAAFALTVSALFDGAELRGALEHPRTWLDSTG
+EDGAETRAALDGALAEAARAVEAGDDVGAPGTLPASLGEGWVAEEALAIAAYAALVAEAR
+AEDPAAALGLALRIGANHDGDSDSTAALAGQLVGARHGMAVFGSRGQDADSVPAWITERE
+VVAEAARRWIAATT
+>4_759
+MSATAPEPTASSSTPLPGPEHADRVLALLAAGAAGDALGGVVEFTPASGIAAVHGPAGVT
+DAADLLAQEGAHALPITDDTQLTLYVLDGLLEWIEWQNDGVPADPAACVWLACLRWFATQ
+DGALPEGAPPAPPRWIDAHAELKVRRAPGTACLTGLAEPGMGLPGDPHNPGSKGCGTVMR
+SAPYGMVPGLEDPHVVSLARQGAVLTHGHPTAWVAAGAYALVIAALLRGLDLAAAVAHAR
+AWLDGLGEEAAETRAAVTAAVDLAGTVDADPGAPGALPTALGEGWVAEEALAIALYAALT
+AQAVHPADPAAALALALRIGVNHDGDSDSTASLAGQVLGVAHGTAVFGAHDPADRAAAEA
+SVPGWVAEREVVLEAARRWSAATT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000727.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000727.fa
new file mode 100644
index 0000000000000000000000000000000000000000..93c27957f21ef6086d4ca1e8c4c4b1ac3bcf2fe8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000727.fa
@@ -0,0 +1,91 @@
+>0_792
+MRIHRMRLEGLGPYAQAQDVDFDRLNAGGLFLLDGPTGAGKSTVLAALCFALYGTVPGGR
+SAESLVTTLREPGAVIPEVQVEFTVQGRRFEVVRSPKHERPRRRRSAAGGATVTTQATVS
+LRERVAGEWTAPLTRADEVGQQIAAVLHLDAEQFMQVVLLPQGQFAQFLTAKSDERRALL
+RRLFGTQRFDGVEEHLRVETARLDTAVAVDADVARTARAQLAEALHEALGPDWHAPEPSP
+DTDDRLLALAAERAGRAHEDARADLATARAAEQRARVTARELETRGRDLAAAEAWASRRR
+DHDAEAETAAARRRAVDAHERAGRVLAAAQRATAAADAAGTASETVTEALAHVEDEPTAA
+AWLAAARADGAADAPASRQALGEAERAAEAVARAVQDRARMGELEQEAAAAAERRAEIGR
+DRAALVESRPEREAAVAAHRAAVERGTERLGAREAVDRAVSEAAARRTAAEAAAARAVEA
+ETAARAHREAQERRREAAERHVGLLRARYEQAASELAERLVPGEPCAVCGSPEHPAPAAT
+ADTAVTEADVRDAEQARTAADRAATDAETALRAAEQTLRTAREAAAGLAPEAAREALERA
+EAERAALDQAAKDLAADRRRLTAAEKTLAGADETAAALAAEDGRLAEAAAHRAARLTELR
+DAVEAARGDAETLDARRDQVTAARRVLAALAAAQDEDARARAVADETDQALTAALAEQHF
+DDVDAARAARLEETEAAARTAAVQEWHAERARLAELEASEPVRRGRALAEAGVEPPTEEQ
+TRAAAEALAAAEAASSSRATAVGRLDSLVATVRRQSAALTEVLERSAGLIAEHTRVRGLL
+DLVRGGGENLLKMPLTSYVLAGRLEEVAAAATERLLAMTDQRYSIEYSDAVGGRGNKGLE
+LVIRDHYVDETRHPATLSGGETFMASLALALGLADTVQAEAGGIELDTLFVDEGFGSLDA
+DTLDDVLDVVDTLRTGGRTVGLVSHVERMRQEIGVRLEVRKDRRGSSLAVHDGA
+>1_533
+MRIHRMRLEGLGPYAQAQDVDFDRLNAAGLFLLDGPTGAGKSTVLAALCFALYGTVPGGR
+SAESLVTTLREPGAVIPEVQVEFTVQGRRFEVVRSPKHERPRRRRSAAGGATVTTQATVS
+LRERVAGEWTAPLTRADEVGQQIAAVLHLDAEQFIQVVLLPQGQFAQFLTAKSDERRVLL
+RRLFGTQRFDGVEEHLRVETARLDTAVAVDADVARTARAQLAEALHEALGPDWHAPEPSP
+DTDDRLLALAAERAGRAHEDARADLATARAAEQRARVTARELETRGRDLAAAEAWASRRR
+DHDAEAETAAARRRAVDAHERAGRVLAAAQRASAAADAAGTASEAVTEALAHVEDEPTAA
+AWLAAARADGAADAPASRQALGEAERAAEAVARAVRDRDRMRELEQEAAAAAERRAEIDR
+DRAALVESRPEREAAVAAHRAVVERGTERLGAREAVDRAVSEAAARRTAAEAAAARAVEV
+ETAARAHREAQERRREAAERHVGLLRARYEQAASELAERLVPGEPCAVCGSPEHPAPAAT
+ADTAVTEADVRDAEQARTAADRAATDAETALRAAEQTLRSAGEAAAGLAPEAAREALERA
+ETERAALDQAAKDLAADRRRLTAAEKTLAGADETAAALAAEDGRLAEAAAHRAARLTELR
+DAVEAARGDAETLDARRDQVTAARRVLAALAAAQDEDARARAVADETGQALTATLAEQRF
+DDVDAARAARLEETEAADRTAAVQEWDAERARLAELEASEPVRRGRALAEAGVEPPTEEQ
+TRAAAEALAAAEAASSSRATAVGRLDSLVATVRRQSAALTEVLERSAGLIAEHTRVRGLL
+DLVRGGGENLLKMPLTSYVLAGRLEEVAAAATERLLAMTDQRYSIEYSDAVGGRGNKGLE
+LVIRDHYVDETRHPATLSGGETFMASLALALGLADTVQAEAGGIELDTLFVDEGFGSLDA
+DTLDDVLDVVDTLRTGGRTVGLVSHVERMRQEIGVRLEVRKDRRGSSLAVHDGA
+>2_2062
+MRIHRMRLQGIGPYAEAQDVDMDRLNDAGLFLLDGPTGAGKSTVLAALCYALYGSVPGGR
+SPESLVTTLRPPGAVVPEVLVEFTVQGRRFEVVRSPRHERLKKRRSASGKDTTPTPAAVS
+LREHVDGAWQEPLTRNDEVGVQVADVMHLDAAQFMQVVMLPQGRFAEFLTARSDERQRLL
+RRLFGTQRFDGVEEHLKAEAERLGSRAAADAKVAASAREQLREAVAAELGEDWHAPEPFP
+ATDEELVERTAERTREAVDAARAGRDAAAAEEAAARGTQAELRATGEALAAAAAWTERER
+AHREGAEAAAGDRTAVAAHERAGRVLGAADRSESARAAEDRAREADGTAQAAAAEDPLSA
+GWLEQARRDAAETPADDAAETSADAAALPRDAVALAERAVEEVVRAVRDRAAAERLEETE
+RTEAARRTQIVAEREAAEAERSGREEGLAAVREAVEAASARLGAQADVDRRVAEAEQGLA
+AAREAERHALAADAADRAREAARTGRDAAAQHRLGLLRSRYEQAAADLAADLEDGTPCAV
+CGSPEHPDPAPRVGTAVTEADVAAAEEGLAAAEAVLADAETARTAAHERVRASSAAAGGR
+TPAQAEEALAAARTEHAELAAVRKALAADRRRLRALETERDEAAAAETARTAEDARLQEA
+ARQRHERLLELRAGIERARGDAPDLDARGALVRAARGRLEALAGAVEVRERAVAVAADAD
+RALAAALREQEFEDVGAARAARLPAEDAAARTARVRAWDDEQARLAELAQSDAVRRGREL
+QDQQATAPTPEDLEAAAARLLEAERSRREQDEALGRRTAVAAAVERQAALLRGVLDRSAA
+LLAEHERVTGLLALVRGGGENRLKMPLASYVLAGRLEEVAAAATERLLAMTDGRYSIEYS
+DDSAGRGNKGLELVVRDHYVDETRHPSTLSGGETFMASLALALGLADTVQAEAGGVELDT
+LFVDEGFGSLDSDTLDDVLDVVDGLRSGGRTVGLVSHVERMKQEIPVRLAVTKEREGSSL
+AVHVDA
+>3_1952
+MRIHRMRLEGIGPYAEPQDLDLDPLNDAGLFLLDGPTGAGKSTVLAALCFALYGSVPGGR
+TPESLVTTLRPPGAVVPQVLVEFTVQGRRFEVLRSPRHARPKKRGGGTTATQASVSLRER
+VDGAWTAPLTRADEVGRQVAEVLRLDAAQFMQVVSLPQGRFAEFLTARSDDRQRLLRRLF
+GTQRFDGVEDRLKECAEALGTRVAADAAEAAGARAQLLEQARLELGEDWHAPDPAPEEGE
+DERLVELTRTRADAALAEARTAQQAADAAEAAARAAQDRLTADTEALRALAAWEGREREH
+RQAADHVAADRSAVALHERASHVLGAATRAEQTRAAHASTAERARAAAEAVAADALAAAW
+LDEAEDADAARRRADRETDALARAVRDRDALTRLEAEGTQADAERERLEDEARSAREKGK
+RRAAQIAELHDTVDAAAARLGAEDEVARRLAEATERAAAAGQAAERAVAQERARAARDER
+RDAQRGAAQARLDLLRSRFEQAAAELAAGLEDGSPCPVCGSAEHPDPAPRADGAVTEADV
+AAADRALEAADAALAEAEQALAAASEEHRAARERAGGQDVAAAEEALSAVRAEHEALAAA
+RTALATDRRALARRESEQRTADEAATARTAALARLSEAQARRTERAAELTAAVAAAQGDA
+ADLDARTAHVRTATRALSALVEAGDAAARAAAVAEDAAQALAGALAEQDFADVAAARAAA
+LPPDDAAARAARVRSWDVEEARLAEAAASEPLVRGRALREAGTSEPTAEEFAAAQETLRE
+ATAARTARAAVVGRREALVASLERQARRLRAVLERSSELLAEHERATGLLALVRGQGENR
+LKMPLASYVLAGRLEEVAAAATERLLAMTDRRYSIEYSDEATGRGNKGLELVIRDHYVDE
+TRHPSTLSGGETFMASLALALGLADTVQAEAGGVELDTLFVDEGFGSLDADTLDDVLDVV
+DGLRAGGRTVGLVSHVERMKQEIPVRLEVTKSRAGSTLAIHDGG
+>4_761
+MRIHRMRLEGLGPYAQAQDVDFDRLNAGGLFLLDGPTGAGKSTVLAALCFALYGTVPGGR
+SAESLVTTLREPGAVIPEVQVEFTVQGRRFEVVRSPKHERPRRRRSAAGGATVTTQATVS
+LRERVDGEWTAPLTRADEVGQQIAAVLHLDAEQFMQVVLLPQGQFAQFLTAKSDERRVLL
+RRLFGTQRFDGVEEHLRVETARLDTAVAVDADVARTARAQLAEALHEALGPDWHAPEPSP
+DTDDRLLGLAAERAGRAHEDARADLATARAAEQRARVTARELETRGRDLAAAEAWASRRR
+DHDAEAETAAARRRAVDAHERAGRVLAAAQRATAAADAAGTASETVTEALAHVEDEPTAA
+AWLAAARADGAADAPASRQALGEAERAAEAVARAVQDRARMGELEQEAAAAAERRAEIGR
+DRAALVESRPEREAAVAAHRAAVERGTERLGAREAVDRAVSEAAARRTAAEAAAARAVEA
+ETAARAHREAQERRREAAERHVGLLRARYEQAASELAERLVPGEPCAVCGSPEHPAPAAT
+ADTTVTEADVRDAEQARTAADRAATDAETALRAAEQTLRTAREAAAGLAPEAAREALERA
+EAERAALDQAAKDLAADRRRLTAAEKTLAGADETAAALAAEDGRLAEAAAHRAARLTELR
+DAVEAARGDAETLDARRDQVTAARRVLAALAAAQDEDARARAVADETDQALTAALAEQHF
+DDVDAARAARLEETEAAARTAAVQEWHAERARLAELEASEPVRRGRALAEAGVEPPTEEQ
+TRAAAEALAAAEAASSSRATAVGRLDSLVATVRRQSAALTEVLERSAGLIAEHTRVRGLL
+DLVRGGGENLLKMPLTSYVLAGRLEEVAAAATERLLAMTDQRYSIEYSDAVGGRGNKGLE
+LVIRDHYVDETRHPATLSGGETFMASLALALGLADTVQAEAGGIELDTLFVDEGFGSLDA
+DTLDDVLDVVDTLRTGGRTVGLVSHVERMRQEIGVRLEVRKDRRGSSLAVHDGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000728.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000728.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3cf1a33149f274370d2f3dd0cc347eb1fc84c0e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000728.fa
@@ -0,0 +1,98 @@
+>0_793
+MGALARFSLGRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVV
+DAQVGEPLETALQAVEGLESSRSTSQSGFNAVQLEFAYGTDLNRARSQVDRVVANLGPQL
+PEEAETSSFAGSVSDFPVVFLALSGDEDLNTLRRRAEDVLAPRLQKIDGVRGADVLGGTD
+ENVSVVPDPAALAAAGLTTSDITDALEENAGLFPVGQVTEGATTYPVQAGAAVEDLEGLR
+GIVVAPSGDGEPRTLDEVADVTLVAAAPTSLTRTDGVPTLSVSVTATPDADLVAVSQAVR
+DALPELASLVGGGADLTVVFDQAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSVRSTLV
+TAVSIPLSLLAALIGVAAFGYSLNTLTLGALTISIGRVVDDAIVVVENIRRHLGLGADRR
+TAILDGTREVATAITASTLVSVAVFLPIAFVGGLAGELFRPFAVTATVALLASLVVALTI
+VPVLCWWFLRSPRRGAETTAAPAVPGDRPVAAGGWLTRAYRPVLRWTQRHTVVTLAAALA
+LLAGTAALVPLIPTNLLGDSGQNSFVVTAEQEPGTSLETTAAAAERIERVLLDTDGVETV
+QWTAGTAAGPMGAFGGSSADRARFTVVTDPDADQVALQDGVRAELTGLDGVGDVSVSTQQ
+GPSGGQDIEVAVSAPDPQALTAAADQVAEALRPVEGAREVTTPASDLRPTFQVDVDTVAA
+ARLGLTEEAVAGQAAAALQAVPVGDVRFGFESFAVQLGDPEPVESLDALRQVPVETAEGP
+VPLADLAEVSRVSVPARVTSSNGERTAVVTVTPDDEDLGAVSRRVTQAVAELDLPEGVTA
+AVGGAAEQQAQTFRDLGLALLAAVATVYVVLVATFNSLRQPLVLLVSIPFAATGVFLALL
+ATGTPLGLSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMPLDEAIEVGALNRVRPVVM
+TALATVLAMTPMALGVTGHAGFISQPLAVAVVGGLVSSTLLTLVLVPVLYRLTEVRGERR
+LQEERRVAAAWEAQRVAAERAAKQERRAEQGSAAPSELDAGRLGRLRQRLRRRWRRA
+>1_534
+MGALARFSLGRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVV
+DAQVGEPLETALQAVEGLESSRSTSQSGFNAVQLEFAYGTDLNRARSQVDRVVANLGPQL
+PEEAETSSFAGSVSDFPVVFLALSGDEDLNTLRRRAEDVLAPRLQKIDGVRGADVLGGTD
+ENVSVVPDPAALAAAGLTTSDITDALEENAGLFPVGQVTEGATTYPVQAGAAVEDLEGLR
+GIVVAPSGDGEPRTLDEVADVTLVAAAPTSLTRTDGVPTLSVSVTATPDADLVAVSQAVR
+DALPELASLVGGGADLTVVFDQAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSVRSTLV
+TAVSIPLSLLAALIGVAAFGYSLNTLTLGALTISIGRVVDDAIVVVENIRRHLGLGADRR
+TAILDGTREVATAITASTLVSVAVFLPIAFVGGLAGELFRPFAVTATVALLASLVVALTI
+VPVLCWWFLRSPRRGAETTAAPAVPGDRPVAAGGWLTRAYRPVLRWTQRHTVVTLAAALA
+LLAGTAALVPLIPTNLLGDSGQNSFVVTAEQEPGTSLETTAAAAERIERVLLDTDGVETV
+QWTAGTAAGPMGAFGGSSADRARFTVVTDPDADQVALQDGVRAELTGLDGVGDVSVSTQQ
+GPSGGQDIEVAVSAPDPQALTAAADQVAEALRPVEGAREVTTPASDLRPTFQVDVDTVAA
+ARLGLTEEAVAGQAAAALQAVPVGDVRFGFESFAVQLGDPEPVESLDALRQVPVETAEGP
+VPLGDLAEVSRVPVPARVTSSNGERTAVVTVTPDDEDLGAVSRRVTQAVAELDLPEGVTA
+AVGGAAEQQAQTFRDLGLALLAAVATVYVVMVATFNSLRQPLVLLVSIPFAATGVFLALL
+ATGTPLGLSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMTLDEAIEVGALNRVRPVVM
+TALATILAMTPMALGITGHAGFISQPLAVAVVGGLVSSTLLTLVLVPVLYRLTEVRGERR
+LQEERRVAAEREAQRVAAERAAEQARRAEERWAAPSELDAGRLGRLRQRLRRRWRRA
+>2_2061
+MGALARFSLRRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVV
+DSLVGEPLETALQAVEGLESSGSTSQASFNSIQLQFAYGTDLNRARSQVDRVVSNLASQL
+PEEAETSSFAGSVSDFPVVFLALSGDEDLNELRRRAEAVLAPRLQKLEGVRGADVLGGTE
+EHVSVVPDPEALAAAGLSTQDITTALEENAGLFPVGQVTEGESTYPVQAGAAVEDLEGLR
+GIVVTPAEGGQGAAPQDRTADGGPVGGGGGPPADAEATPAAPAEPAGDGEPRTLGEVAEV
+SLQAAEPTSVTRTDGADTLSVSVTATPDADLVAVSEAVREALPELESVVGGGADLTVVFD
+QAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSLRSTLVTAVSIPLSLLAALIGVAVFGY
+SLNTLTLGALTISIGRVVDDAIVVVENIRRHLDLGADRRTAILIGTREVATAITASTLVS
+VAVFLPIAFVGGLAGELFRPFAVTATIALLASLVVALTIVPVLCWWFLRTPRRPAGDESP
+ADAAEGGAPAVPAGEHGHDAHPSAAGGWLARAYRPVLRWTQRHTVATLAGAVAVLAGTAA
+LVPLIPTNLIGDTGQNSFVVTADQEPGTSLEATAAAAGVIERTLLETEGVETVQWTAGTA
+GGPAGAFGGSSADRARFTVVTDENADQTALQDGVRADLAALEGVGEVSVSTQQGPGGGQD
+IEVSVSAPDPQALATAADEVAGALRGVEGAREVTTPAADVRPTFQVDVDTEAAARLGLTE
+EAVAGQAAAALQAVPVGDVRFGFEQFQVRLGDPDPVESLEALRQVAVQTGSGPVPLEELA
+SVERVDVPARVTSSNGERTAVVTVTPDDQDLGAVSRRVTEAVDGLALPEGVTATVGGAAE
+QQAATFRELGLALLAAIATVYVVMVATFNSLRQPLVLLVSIPFAATGVFLALLATGTALG
+LSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMGLDEAIEVGALNRVRPVVMTALATIL
+AMVPMALGLTGHSGFISQPLAVAVVGGLLSSTLLTLVLVPVLYRLTEARGERRIQAERAE
+QARRDEEARRRAAEAEQAAAEQAESARAGLLARRRTGGAPAASAAAGMADDGGRRPGPLG
+RLRARLGGLVGRARRA
+>3_1951
+MGALARFSLSRRALVALVTAFIAVFGVLSAGLLKRELIPSLELPVISVSTTYPGASPEVV
+DAEIGQPLEQALQAVEGLDSSASTSATSFNSVQLRFRYGTDLTRARSQVDRVISNLASQL
+PEEAQTTSFAGSVSDFPVVFLALSGDEDLNALKRRAEDVLVPRLQRIDGVRGAQVLGGTE
+EYVSVVPDAAKLAAAGLTTQDVTTALEENAGLFPIGQATSGTVTYPVQAGAPVGSVADLE
+QVTVTPGGGQSSTGAADQGAGAGAGGGPGAATGTPARLGDVAAVSMQAADPTSVTRTDGA
+PTLSLSVTATPDADLVAVSHAVADALPELESLAGSGAKLTVVFDQAPFIEQSIRTLFVEG
+LLGLAMAILVIAVFLLSARSTMVTAVSIPLSLLTALIGVAVFGYSLNTLTLGALTISIGR
+VVDDAIVVVENIRRHLGLGADKRTAILEGTREVATAITASTLVSVAVFLPIAFVDGLAGE
+LFRPFAVTTSIALLASLVVALTIVPVLCWWFLRAPRAAAAPGGAEGVSSPVEDAAQDTWL
+ARAYRPVLRWTQRHAVATLAGAAALLAGTVALAPLIPTNLLGDSGQNSFVVTAQQAPGTS
+LEATTAIAGRIEAALRDTPGVRTVQFTAGSAGGAMGAFGRGSADRATFTVVTDPDADQTA
+LQDEVRGRLAGLGDVGEVDVSAQQGPAGGQDITVSVTAPDPEALADGIDRVAEALRGLDG
+VLQASTPSSDVRPTFQVDVDTLAAAERGLTEKAVSGQVAAALQAVPAGTVRFGFQEFTVR
+LGDPDPVESLGALRAVPISTPSGPVPLSELADVRRADVPAQVTSSNGQRTAEVTVTPDPA
+DLGGVSRRVSDALEGVALPDGVEATVGGAATEQAKTFRDLGLALLAAIAAVYVVMVATFN
+SLRQPFVLLVSIPFAATGVVLALLASGTALGVATMIGLLMLVGIVVTNAIVLIDLINQYR
+RRHGMALDEAIERGALHRVRPVVMTALATVLAMTPMALGITGHAGFISQPLAVAVVGGLA
+SSTVLTLVLVPVLYRLTEARGERRIQAERAAREAEERELAEREARERELAEREAAARAVA
+GPAAAAHPAPAGRLSRRRGWRGWIRRATS
+>4_762
+MGALARFSLGRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVV
+DAQVGEPLETALQAVEGLESSRSTSQSGFNAVQLEFAYGTDLNRARSQVDRVVANLGPQL
+PEEAETSSFAGSVSDFPVVFLALSGDEDLNTLRRRAEDVLAPRLQKIDGVRGADVLGGTD
+ENVSVVPDPAALAAAGLTTSDITDALEENAGLFPVGQVTEGATTYPVQAGAAVEDLEGLR
+GIVVAPSGDGEPRTLDEVADVTLVAAAPTSLTRTDGVPTLSVSVTATPDADLVAVSQAVR
+DALPELASLVGGGADLTVVFDQAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSVRSTLV
+TAVSIPLSLLAALIGVAAFGYSLNTLTLGALTISIGRVVDDAIVVVENIRRHLGLGADRR
+TAILDGTREVATAITASTLVSVAVFLPIAFVGGLAGELFRPFAVTATVALLASLVVALTI
+VPVLCWWFLRAPRRGAETTAAPAVPGDRPVAAGGWLTRAYRPVLRWTQRHTVVTLAAALA
+LLAGTAALVPLIPTNLLGDSGQNSFVVTAEQEPGTSLETTAAAAERIERVLLDTDGVETV
+QWTAGTTAGPMGAFGGSSADRARFTVVTDPDADQVALQDGVRAELTGLDGVGDVSVSTQQ
+GPSGGQDIEVAVSAPDPQALTAAADQVAEALRPVEGAREVTTPASDLRPTFQVDVDTVAA
+ARLGLTEEAVAGQAAAALQAVPVGDVRFGFESFAVQLGDPEPVESLDALRQVPVETAEGP
+VPLGDLAEVSRVPVPARVTSSNGERTAVVTVTPDDEDLGAVSRRVTQAVAELDLPEGVTA
+AVGGAAEQQAQTFRDLGLALLAAVATVYVVMVATFNSLRQPLVLLVSIPFAATGVFLALL
+ATGTPLGLSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMTLDEAIEVGALNRVRPVVM
+TALATILAMTPMALGITGHAGFISQPLAVAVVGGLVSSTLLTLVLVPVLYRLTEVRGERR
+LQEERRVAAEREAQRVAAERAAEQARRAEERWAAPSELDAGRLGRLRQRLRRRWRRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000731.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000731.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4bc296da91e98ea79d2c8ac93c8756c721407311
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000731.fa
@@ -0,0 +1,20 @@
+>0_796
+MTDTTQHRLQPGDTAPAFTLQDQEGRPVSLRDSAGKHTIVYFYPAASTPGCTTQACDFRD
+SLASLTAAGYVVLGISPDPIGKIIRFAEQEGLTFPLLSDEDHAVAEAYGAWGEKKNYGRT
+FEGLIRSTIVVGPDGKVTHAQYNVKATGHVARLRRTLGLDEA
+>1_537
+MTDTTQHRLQPGDTAPAFTLQDQEGRPVSLRDSAGKHTIVYFYPAASTPGCTTQACDFRD
+SLASLTAAGYVVLGISPDPIGKIIRFAEQEGLTFPLLSDEDHAVAEAYGAWGEKKNYGRT
+FEGLIRSTIVVGPDGKVTHAQYNVKATGHVARLRRTLGLDEA
+>2_2050
+MSDTTQNRLQPGDIAPSFTLQDQDGRPVSLRDSAGKSTIVYFYPAASTPGCTTQACDFRD
+SLASLTAAGYVVLGVSPDPIGKIIRFAQKEGLTFSLLSDEDHAVAEAYGAWGEKKNYGRT
+YEGLIRSTVVVGPDGRVTHAQYNVKATGHVARLRRTLGLDEA
+>3_1948
+MTENTAAPARLSPGDVAPEFTLQDQDGRPVSLRDSAGKSTIVYFYPAASTPGCTTQACDF
+RDSLASLTAAGYRVLGISPDPIGKIIRFAQNEGLTFSLLSDEDHAVAAAYGAWGEKKNYG
+RTSEGLIRSTVVVGPDGKVTLAQYNVKATGHVARLRRELGLDD
+>4_765
+MTDTTQHRLQPGDTAPAFTLQDQEGRPVSLRDSAGKHTIVYFYPAASTPGCTTQACDFRD
+SLASLTAAGYVVLGISPDPIGRIIRFAEQEGLTFPLLSDEDHAVAEAYGAWGEKKNYGRT
+FEGLIRSTIVVGPDGKVTHAQYNVKATGHVARLRRTLGLDEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000732.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000732.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb8a2ff05ceb7cc03cfb812b05d373276a5ea764
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000732.fa
@@ -0,0 +1,24 @@
+>0_797
+MTRADGSAYVGPMDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLE
+MLLCPFDPTSTPDDHDRRAPGVAEDDPHGPVTEASADRADVVEVGLANVATVADTGSGYQ
+VETVTGFRTWFDVPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYATPE
+TDATDVTPPDLHGV
+>1_538
+MDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLEMLLCPFDPTSTP
+DDHDRRAPGVAEDDPHGPVTEASADRADVVEVGLANVATVADTGSGYQVETVTGFRTWFD
+VPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYATPETDATDVTPPDLH
+GV
+>2_2049
+MDSPTLQRRLRGVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLEMLLCPFDPTSTP
+DDAPADAPAADAPEEDPHGPVAEPSSHGTDVVGVALGNVATVADTGSGYQVETVTGFRTW
+FDVPEHARVPVGDLTEDGTAGLDQAEDAVDFHAFMTAFMDELDRLYAAPEAGGTDVTGPD
+LHAR
+>3_1947
+MDSPTLARRIRGAFDARVFNHGDYNLVYGQRSGGSLPLVIGYRHSPLEMLLCPLDPVEAV
+AAVPEEVALANVATVADTGSGYQVETVTGFRTWFEVVDRPRVPVGEASEDGLAELDQADD
+AADFHAFMTAFMDELDRLYAEPADPDLHPPQKSV
+>4_766
+MDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLEMLLCPFDPTSTP
+DDHDRRAPGVAEDDPHGPVTEASADRADVVEVGLANVATVADTGSGYQVETVTGFRTWFD
+VPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYATPETDATDVTPPDLR
+GV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000736.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000736.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ebc981db2cd3be8c38778ed12bbb71a9044c2beb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000736.fa
@@ -0,0 +1,20 @@
+>0_802
+MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ
+VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES
+LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRALAR
+>1_543
+MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ
+VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES
+LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRALAR
+>2_2046
+MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ
+VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES
+LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRALAR
+>3_1944
+MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTQVPGISRMTVVVDADAHLLEQ
+VTKQLNKLINVIKVVELAGDSSVQRDHLLVKVRADASTRGQVVQAADLFRAHVVDVAPDS
+LTFEATGTREKLEAFLEMMEPHGIRELVRSGTLALARGPRSMTDRALAR
+>4_772
+MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ
+VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES
+LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRAVAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000737.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000737.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7cf50744116586f6e2b2da42d8914e39e9d0db41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000737.fa
@@ -0,0 +1,35 @@
+>0_803
+MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSKSRAKAEA
+EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQKGDALFFAHGFNVRFGYIQA
+PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV
+IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM
+VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAQRFMDDQKAGA
+PEFKELRARGEAHPIEKTGRELRQMFSWLKDADDDYTEGTAAR
+>1_544
+MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSKSRAKAEA
+EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQEGDALFFAHGFNVRFGYIQA
+PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV
+IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM
+VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAKRFMDDQKAGA
+PEFKELRARGEAHPIEKTGRELRQMFSWLKDADDDYTEGTAAR
+>2_2045
+MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSKSRAKAEA
+EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQEGDALFFAHGFNVRFGYIQA
+PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV
+IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM
+VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAQRFMDDQKAGA
+PEFKELRAKGEAHPIEKTGRELREMFSWLKDADDDYTEGTAAR
+>3_1943
+MTAQKFYDDDADLSIIQGRTVAVIGYGSQGHAHSLSLRDSGVDVRIGLAEGSKSRAKAEA
+EGLRVVDVATAAAEADLIMILTPDQVQADVYDEHIAPNLQEGDALFFAHGFNVRFGYIQA
+PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEQDASGQAEALALSYAKAIGGTRAGV
+IKTTFTEETESDLFGEQAVLCGGASQLIQYGFEVLTEAGYQPEIAYFEVLHELKLIVDLM
+VEGGIAKQRWSISDTAEFGDYVSGPRVITPEVKDHMKEVLADIQNGAFAKHFMDDQKAGA
+PEFTELRAKGESHPIEKTGRELRQMFSWLKDTDDDYTEGTAAR
+>4_773
+MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSRSRAKAEA
+EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQEGDALFFAHGFNVRFGYIQA
+PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV
+IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM
+VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAKRFMDDQKAGA
+PEFKELRARGEAHPIEKTGRELRQMFSWLKDADDDYTEGTAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000738.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000738.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f97c4a44cea36f7a5129c08f89c9f812b95a88ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000738.fa
@@ -0,0 +1,50 @@
+>0_804
+MSAAQPVVLIAEELSPATVEALGPDFEIRRTDGADRARLLEDLRDVDAVLIRSATQMDAE
+AIAAAPQLKVIARAGVGLDNVDVPAATEAGVMVVNAPTSNIISAAELTCGHILAAARNIA
+AAHGSLKAGEWKRSKYTGVELYGKRLGVIGLGRIGALVAERMKAFGMEILAYDPYVTTAR
+AQQLGASLVELDELLERADVVTIHMPKTPETVGMIGDEQFARMKDTAIIVNVARGGLVDE
+DALARALEAGTIGGAGIDVFSSEPATDLAFFAHDSAVVTPHLGASTAEAQEKAGVAVAGS
+VRLALSGELVPDAVNVAGGAIHEDVRPGLPLAEKLGRVLTALVGEQSITAVEVEIAGEIS
+EHDVSAMRLAALKGVFTDIVSDQVSYVNAPVLAEQRGVECRLTTTAVSESYRNTVTVRAA
+TAQGAQTAVTGTLTGPRQVQKLVGVDRHELEVPLADHLLVFAYQDRPGVIGVLGQALGVQ
+GVNIAGMDVSRDDEGAALAVLTLDGALSGDTAATLAAAIGAARAAEVDLSV
+>1_545
+MSAAQPVVLIAEELSPATVEALGPDFEIRRTDGADRARLLEDLRDVDAVLIRSATRMDAE
+AIAAAPQLKVIARAGVGLDNVDVPAATEAGVMVVNAPTSNIISAAELTCGHILAAARNIA
+AAHGSLKAGEWKRSKYTGVELYGKRLGVIGLGRIGALVAERMKAFGMEILAYDPYVTTAR
+AQQLGASLVELDELLERADVVTIHMPKTPETVGMIGDEQFARMKDTAIIVNVARGGLVDE
+DALARALEAGTIGGAGIDVFSSEPATDLAFFAHDSAVVTPHLGASTAEAQEKAGVAVAGS
+VRLALSGELVPDAVNVAGGAIHEDVRPGLPLAEKLGRVLTALVGEQSITAVEVEIAGEIA
+EHDVSAMRLAALKGVFTDIVSDQVSYVNAPVLAEQRGVECRLTTTAVSESYRNTVTVRAA
+TAQGTQTAVTGTLTGPRQVQKLVGVDRHELEVPLADHLLVFAYQDRPGVIGVLGQALGVQ
+GVNIAGMDVSRDDEGAALAVLTLDGALSGDTAATLAAAIGAARAAEVDLSA
+>2_2044
+MSAAQPVVLIAEELSPATVEALGPDFEIRRTDGADRARLLEDLRDVDAVLIRSATRMDAE
+AIAAAPQLKVIARAGVGLDNVDVPAATAAGVMVVNAPTSNIISAAELTCGHILATARNIA
+AANRSLKAGEWKRSKYTGVELYGKKLGVIGLGRIGALVAERMRAFGMEILAYDPYVTTAR
+AQQLGATLVELDQLLERADFVTIHMPKTPETVGMIGDDQFARMKDTAVVVNVARGGLVDE
+DALARALDSGAIAGAGIDVFSTEPATDLAFFAQDSAVVTPHLGASTAEAQEKAGVAVAGS
+VRLALSGELVPDAVNVAGGVIHEDVRPGLPLAEKLGRVLTSLVGEQSLTAVEVEIAGEIA
+EHDVSAMRLAALKGVFTDIVSDQVSYVNAPMLAEQRGVECRLTTTPVSESYRNTVTLRAA
+TAQGTQVSVTGTLTGPRQIQKLVGVDRHELEVPLADHLLVFTYEDRPGVIGVLGQALGVQ
+GVNIAGMDVSRDDEGEALAVLTLDGALSGDTATALAAAIGASRVAEVDLSA
+>3_1942
+MSAAKPVVLIAEELSPATVEALGPDFEIRHTDGADRARLLADLPGVDAVLIRSATTMDAE
+AIAVAKDLKVIARAGVGLDNVEVPAATAAGVMVVNAPTSNIVSAAELTCGHILSVARNIA
+PANRALKAGEWKRSKYAGVELFEKKLGVIGLGRIGALVAERMKAFGMEILAYDPYISAAR
+AQQLGATLLDLDELLAQSDFITVHMPKTPETVGMISDAQFATMKDTAFIVNVARGGLIDE
+DALDRALESGAIAGAGVDVFSSEPATDLAFFRHDTAVVTPHLGASTAEAQEKAGVAVAKS
+VRLALAGELVPDAVNVAGGVIHEDVRPGLPLAEKLARVLRALAGERSLASVDVEVAGEIA
+VHDVKALRLAALKGVFTDVVSDQVSYVNAPVLAEQRGVGGQLTTAAEAGSYRNTVTVAAV
+TDEGERLSVTGTLTGPKQVEKLVGVGRHEMEVALAEHMLLFRYADRPGVVGVLGQSLGEQ
+GVNIAGMDVSRDEQGSALAVLTLDAALAPGTAPTLAAAIDADRAAEVNLAD
+>4_774
+MSAAQPVVLIAEELSPATVEALGPDFEIRRTDGADRARLLEDLRDVDAVLIRSATRMDAE
+AIAAAPQLKVIARAGVGLDNVDVPAATEAGVMVVNAPTSNIISAAELTCGHILAAARNIA
+AAHGSLKAGEWKRSKYTGVELYGKRLGVIGLGRIGALVAERMKAFGMEILAYDPYVTTAR
+AQQLGASLVELDELLERADVVTIHMPKTPETVGMIGDEQFARMKDTAIIVNVARGGLVDE
+DALARALEAGTIGGAGIDVFSSEPATDLAFFAHDSAVVTPHLGASTAEAQEKAGVAVAGS
+VRLALSGELVPDAVNVAGGAIHEDVRPGLPLAEKLGRVLTALVGEQSITAVEVEIAGEIA
+EHDVSAMRLAALKGVFTDIVSDQVSYVNAPVLAEQRGVECRLTTTAVSESYRNTVTVRAA
+TAQGTQTAVTGTLTGPRQVQKLVGVDRHELEVPLADHLLVFAYQDRPGVIGVLGQALGVQ
+GVNIAGMDVSRDDEGAALAVLTLDGALSGDTAATLAAAIGAARAAEVDLSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000744.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000744.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a653a56a57e1533cd4788f8563f7df3c5ea8b135
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000744.fa
@@ -0,0 +1,30 @@
+>0_822
+MRIARFVDQAEPTYGIVEGPADADPAELTVTALQGDPFFHGIQPTGTTHRLEDVRLVAPI
+IPRSKIVGVGRNWADHAKELGNEVPASPQFFLKPNTAVVGPNEPVTLPSWSDEVSYEAEL
+AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE
+LDVEPAGGLRITSRLDGETRQDGTTTDMVFGVRELVAAASEMFTLLPGDVILTGTPGGVG
+TVQEGQRVEAEVEGIGVLATVFRR
+>1_553
+MRIARFVDQAEPTYGIVEGPADADPAELSITALQGDPFFHGIQPTGTTHRLEDVRLVAPI
+IPRSKIVGVGRNWADHAKELGNEVPASPQFFLKPNTAVVGPNEPVTLPSWSDEVSYEAEL
+AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE
+LDVEPTGGLRITSRLDGETRQDGTTADMVFGVRELVAAASEMFTLLPGDVILTGTPGGVG
+TVQEGQRVEAEVEGIGILATVFRR
+>2_2036
+MRIARFVDQAEPTYGVVEGPADADLSELTITALQGDPFFHGIQPTSTVHRLEDVRLVAPI
+IPRSKIVGVGRNWADHAKELGNETPASPQFFLKPNTSVVGPGEPVTLPSWSDEVSYEAEL
+AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE
+LDVEPAGGLRITSRLDGQTRQDGTTADMVFGVRELVAAASEAFTLLPGDVILTGTPAGVG
+TVAEGQRVEAEVEGIGVLATVFRR
+>3_1930
+MRIARFVDQAEPTYGVVEGPADADLSALTVTALQGDPFFHGIQPTGTTHRLEDVRLVAPI
+IPRSKIVGVGRNWADHAKELGNEVPSSPQFFLKPNTSVVGPDEPVTLPSWSEEVSYEAEL
+AVVIGTICKDVPLSRVDDVVFGYTVANDLTARDAQRTDLQWARAKGFDGACPLGPWIETE
+LDVEQAGGLRVTSRLAGETRQDGTTADMVFGVKELVAAASEMFTLLPGDVILTGTPAGVG
+TVEAGQRVEAEVEGIGVLGTHVRR
+>4_781
+MRIARFVDQAEPTYGIVEGPADADPAELSITALQGDPFFHGIQPTGTTHRLEDVRLVAPI
+IPRSKIVGVGRNWADHAKELGNEVPASPQFFLKPNTAVVGPNEPVTLPSWSDEVSYEAEL
+AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE
+LDVEPTGGLRITSRLDGETRQDGTTADMVFGVRELVAAASEMFTLLPGDVILTGTPGGVG
+TVQEGQRVEAEVEGIGILATVFRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000745.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000745.fa
new file mode 100644
index 0000000000000000000000000000000000000000..251ce4e684440d933946788747b658979babe0a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000745.fa
@@ -0,0 +1,50 @@
+>0_823
+MTDATAPVSENAPAPFADVPQVDAETPVRVRFAPSPTGTPHVGLIRTVLFNWGWARHTGG
+TLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGQIYADVIE
+KLKAGGYIYPSYSSPEETEARHRAAGRDPKLGYDGHDRDLTDEQIAAFEAEGRAPVWRLR
+MPDEDITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLL
+SSTPRQIALYRALHAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQANLFLHRDNGFIPEG
+LLNYLGLLGWSLSADEDIFTPQQFVEHFDVHKVLANPARFDEKKAIAINGTHVRMLDVAD
+FRDRLVPYLHAAGLVGEHLTEREMQILTAAAPLVQERVQLLGEAVEMLAFLFTADRDVRT
+AEGALKGMPADLGAAVAAAREALAALPEDEFTTERIEAALRAALIDGLGLKPRQAFGPVR
+VAVTGRKVSPPLFESLEILGRDSALARLDRFAAEQGLDQGRPTDA
+>1_554
+MTDATAPVSENAPAPFVDVPQVDAETPVRVRFAPSPTGTPHVGLIRTVLFNWGWARHTGG
+TLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGQIYADVIE
+KLKAGGHIYPSYSSPEETEARHRAAGRDPKLGYDGHDRDLTDEQIAAFEAEGRAPVWRLR
+MPDEDITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLL
+SSTPRQIALYRALYAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQANLFLHRDNGFIPEG
+LLNYLGLLGWSLSADEDIFTPQQFVEHFDVHKVLANPARFDEKKAIAINGTHVRMLDVAD
+FRDRLVPYLHAAGLVGEHLTEREMEVLTAAAPLVQERVQLLGEAVEMLAFLFTADRDVRT
+AEGALKGMPADLGAAVAAAREALAALPEEEFTTERIEAALRAALIDGLGLKPRQAFGPVR
+VAVTGRKVSPPLFESLEILGRDSALARLDRFAAEQGLDQDQPTDA
+>2_2035
+MDAETPVRVRFCPSPTGTPHVGLIRTALFNWGWARHTGGTLVFRIEDTDAKRDSEESYQQ
+LLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGEIYAEVIEKLKAGGHIYPSYSSPEETEAR
+HRAAGRDPKLGYDGFDRDLTDEQVAAFEAEGRAPVWRLRMPDTDITFTDLVRGEITFKAG
+TVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLLSSTPRQIALYRALHAVGVAAY
+MPVFGHLPYVMGEGNKKLSKRDPQANLFLHREHGFIREGLLNYLALLGWSLSADEDIFTP
+EQFVEHFDVHKVLANPARFDEKKAIAINGSHVRMLDADDFRERLVPYLHAAGLVDAEPTE
+REREILAAAAPLVQERVQLLGEAVEMLAFLFTADADVATSEGALKGMPADLGAAVAAARD
+ALAALPEDGFTTERIEEALRAALIDGLGLKPRQAFGPVRVAVTGRKVSPPLFESLEILGR
+DSALARLDRFAAEQGLDQGLPTDA
+>3_1929
+MTEPTTASDTAAENAPAVFADVPQVDADTPVRVRFCPSPTGTPHVGLIRTALFNWGWARH
+TGGTLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGEIYAE
+VIEKLKAGGHIYPSYSTPEETEARHRAAGRDPKLGYDGADRDLSAEQVEAYEAEGRRPVW
+RLRMPDADITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGE
+DLLSSTPRQIALYRALHAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQSNLFLHRDRGFI
+PEGLLNYLALLGWSLSADEDIFTPEQFVEHFDIHKVLANPARFDEKKATAINGTHVRMLE
+PADFRARLVPYLQAAGLVGERLTEREERILDAAAPLVHERVALLGEAVDMLAFLFTPDAE
+IATAEGALKGMPADLPTAVAAAREALAGIDEAEFTTAAVEEALRAALIDGLELKPRQAFG
+PVRVAVTGKKVSPPLFESLEILGKESALARLDRFAAEQAAA
+>4_782
+MTDATAPVSENAPAPFVDVPQVDAETPVRVRFAPSPTGTPHVGLIRTVLFNWGWARHTGG
+TLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGQIYADVIE
+KLKAGGHIYPSYSSPEETEARHRAAGRDPKLGYDGHDRDLTDEQIAAFEAEGRAPVWRLR
+MPDEDITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLL
+SSTPRQIALYRALYAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQANLFLHRDNGFIPEG
+LLNYLGLLGWSLSADEDIFTPQQFVEHFDVHKVLANPARFDEKKAIAINGTHVRMLDVAD
+FRDRLVPYLHAAGLVGEHLTEREMEVLTAAAPLVQERVQLLGEAVEMLAFLFTADRDVRT
+AEGALKGMPADLGAAVAAAREALAALPEEEFTTERIEAALRAALIDGLGLKPRQAFGPVR
+VAVTGRKVSPPLFESLEILGRDSALARLDRFAAEQGLDQDQPTDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000746.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000746.fa
new file mode 100644
index 0000000000000000000000000000000000000000..544f54dc23963f3db851f83073283d19392e51a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000746.fa
@@ -0,0 +1,52 @@
+>0_826
+MSRRDTPALAPRLDALGEAAELAAGRLPEDVVAGADAVVRAAGERQALSAEHTVVGFFGA
+TGSGKSSLFNALTGRDLARVAATRPTTSEPLAAVWGVGRGQGLDPDAEHGDGTGEGGGAA
+ALLDWLGVRRRHLLDEAPVLDDGRPGFLGFGRRDGADATGLILLDLPDIDSVERGNREIT
+SRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSVRDRDVVLAS
+LRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQVAAIVAQRGAAAERLGADVAARAADLAA
+ASGEGEPAGVGPGDEQRLGRELAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRA
+DPLRRLHLMPESAAPRRDRDEVARDPALHRTSLPERSGTQRAVVDGAVRTLAAAAGAGAS
+EPWAAAIRRAGREHAEELPGAVDQAIAATDLGAGRGSWWHPVLDVLQWLALLTAVVGAGW
+LGVLALAGYLQFPLPPAPTVEGFPLPTLLLVGGLALGVLLALLAIPLTRWTAAARGRHAR
+RRLEEATTDVGRRLVVDPVRAEVDRFRAFRDALARASGAPVRRGRR
+>1_557
+MSRRDTPALAPRLDALGEAAELAAGRLPEDVVAGADAVVRAAGERQALSAEHTVVGFFGA
+TGSGKSSLFNALTGRDLARVAATRPTTSEPLAAVWGVGRGQGLDPDAEHGDGTGEGGGAA
+ALLDWLGVRRRHLLDEAPVLDDGRPGFLGLGRRDGADATGLILLDLPDIDSVERGNREIT
+SRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSVRDRDVVLAS
+LRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQVAAIVAQRGAAAERLGADVAARAADLAA
+ASGEGEPAGVGPGDEQRLGRELAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRA
+DPLRRLHLMPASTAPRRDRDEVARDPALHRTSLPERSGTQRAVVDGAVRTLAAAAGTGAS
+EPWAAAIRRAGREHAEDLPGAVDQAIAATDLGAGRGSWWHPVLDVLQWLALLTAVVGAGW
+LGVLALAGYLQFPLPPAPTVEGFPLPTLLLVGGLALGVLLALLAIPLTRWTAAARGRRAR
+RRLEEATTDVGRRLVVDPVRAEVERFHAFRDALARASGVPVRRGRR
+>2_2033
+MELSNREITSRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSV
+RDRDTVLASLRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQIAAIVERRGAAAERLGADV
+AARARDLDAASGEGEPAGVGPGDEQRLGRDLATAGGVPAVVRAVEGSYRLRSAKQTSWPV
+LRWMHSFRADPLRRLHLMPDRPAVRRDRDEVGRDPALHRTSLPERTGTQKAVVDGAVRTL
+VTAAAAGAPEPWAASVRRAGRAHAEQVPDAVDQAIAATDLGAGRGSWWHPVLNVLQWLAL
+LTAVVGAGWLGVLALAAYLQFPLPPAPVVEGFPIPTLLLVGGLALGVLLALLAIPLTRIT
+AASRGRRARRRLEEGTTDVGRRLVVDPVRAEVDRFHAFRDAVARAAGATARRGRR
+>3_1926
+MSRPAAPTLAQRLDALGTAAELARDRLPDAVVADAQAAVRAAEERQSLSAEHTVVGFFGA
+TGSGKSSLFNALTGRELAGVAATRPTTSEPLAAVWGVGRGENLDGEGGGAAALLDWLGVR
+RRHLLDDAPVLDGGRPVFLGLGHREGADATGLILLDLPDIDSVQRSHRDVTARLAGHVDV
+LVWVVDPEKYADAVIHRDFLATMASHAAVTLVLLNQVDRLTVTDRDAVLASLRRMLSGHG
+MGDVRVLPVSARTGEGLEEVGRQIAAIVSRRGAAAERLGADVSARARALDEASGPGEPAG
+AGDDDAVRLGRDLAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRADPLRRLHLL
+PERAVARRDRDPVDRDPALHRTSLPERTQTQRAVVEGAVRTLVTSASAGASEPWAASVRR
+AGREHLDELPAAVDHAIAGTDVEAGRGSWWWPVLDVLQWLALAVAVAGAGWLGAYALAAW
+LQFPLPPAPTTQGFPIPTLLLIGGLALGLLLALLAVPLTRLTAASRGRRARRRLEEAAVR
+VGRELVVDPVNAEAARHREFRSALAAAQGSGVRSRSRR
+>4_785
+MSRRDTPALAPRLDALGEAAELAAGRLPEDVVAGADAAVRAAGERQALSAEHTVVGFFGA
+TGSGKSSLFNALTGRDLARVAATRPTTSEPLAAVWGVGRGQGLDPDAEHGDGTGEGGGAA
+ALLDWLGVRRRHLLDEAPVLDDGRPGFLGVGRRDGADATGLILLDLPDIDSVERGNREIT
+SRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSVRDRDVVLAS
+LRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQVAAIVAQRGAAAERLGADVAARAADLAA
+ASGEGEPAGVGPGDEQRLGRELAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRA
+DPLRRLHLMPESAAPRRDRDEVARDPALHRTSLPERSGTQRAVVDGAVRTLAAAAGAGAS
+EPWAAAIRHAGREHAEELPGAVDQAIAATDLGAGRGSWWHPVLDMLQWLALLTAVVGAGW
+LGVLALAGYLQFPLPPAPTVEGFPLPTLLLVGGLALGVLLALLAIPLTRWTAAARGRRAR
+RRLEEATTDVGRRLVVDPVRAEVDRFHAFRDALARASGVPVRRGRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000749.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000749.fa
new file mode 100644
index 0000000000000000000000000000000000000000..48e30ce0edac07dd56a3c92a84736075228e9684
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000749.fa
@@ -0,0 +1,30 @@
+>0_829
+MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVIATGIARPTL
+HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV
+FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT
+PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD
+AVVSAATRLTELIRAGEA
+>1_560
+MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVIATGIARPTL
+HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV
+FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT
+PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD
+AVVSAATRLTELIRAGEA
+>2_2030
+MTAEPARAQADDDVLGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTL
+HRLAAALTHHRLVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV
+FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT
+PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRNHAD
+AVVAAATRLTELIRAGEA
+>3_1923
+MTTTPLPDAGADIGPALHVHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTLHR
+LAAALTHHRLVAKDLQGRYVLGSRLAELASAAGEDRLTSAAGPVLQWLRDACGESAQVFR
+RQADSRVCVASAERPWGLRDTIPVGTRMSMKAGSAAQVLLAWEDNERLVDGLVGAVFTPT
+VLAAVRRRGWAQSLAEREPGVASVSAPVRGPNGKVIAALSISGPLERLSRQPGRLHAGSV
+VAAADRLTELIRAGEA
+>4_788
+MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTL
+HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV
+FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT
+PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD
+AVVSAATRLTELIRAGEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000750.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000750.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5105278adca35bdb4e2ce485080089f82ce9f112
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000750.fa
@@ -0,0 +1,50 @@
+>0_830
+MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR
+PVRRPDLTIATEDHNTPTLDIDQPIADATSRTQIETLRANCAEFGVRLHPLGDAEQGIVH
+VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAVT
+VDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAGAR
+AGMVAPDETTFAYLKGRPHAPEGDDWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPFVT
+WGTNPGQGVSLNDTVPAPEDFADPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSCTN
+SRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM
+CLGMNPDQLSPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT
+PQEA
+>1_561
+MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR
+PVRRPDLTIATEDHNTPTLDIDQPIADPTSRTQIETLRANCAEFGVRLHPLGDAEQGIVH
+VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAVT
+VDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAGAR
+AGMVAPDETTFAYLKGRPHAPEGADWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPFVT
+WGTNPGQGVSLNDTVPAPEDFTDPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSCTN
+SRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM
+CLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT
+LQEA
+>2_2029
+MTSETTRPRTLAEKVWDEHVVVRGEGEGSSRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR
+PVRRPDLTIATEDHNTPTLEIDKPIADPTSRTQIETLRANAAEFGVRLHPLGDAEQGIVH
+VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAIT
+VDGTLRPGVTAKDVILAVIAKIGTGGGQGFVLEYRGEAIRSLSMEGRMTICNMSIEAGAR
+AGMVAPDETTFAYLKGRPHAPEGADWDAAVEHWRTLATDEGAEFDAEVVIDADELEPFVT
+WGTNPGQGVSLNGAVPAPEDFDDPVAQESARKALGYMDLTPGTPMKEVAVDTVFMGSCTN
+SRIEDLRAFAEVVKGRKKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM
+CLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT
+PQEA
+>3_1922
+MSTQTQTPRPRTLAEKVWDEHVVVRGEGEGARRTPDLLYIDLHLVHEVTSPQAFDGLRLA
+DRPVARPELTIATEDHNTPTLEIDRPIADETSRVQIETLRANAEEFGVRLHSLGDREQGI
+VHVVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLRLKPFRTMA
+ITVDGTLRPGVTAKDVILAVIAKIGTGGGQGYVLEYRGEAIRSLSMEGRMTLCNMSIEAG
+ARAGMVAPDDTTFEYLKGRPHAPQGADWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPF
+VTWGTNPGQGVSLNDAVPAPEDFSDPAAQEAARKALSYMDLTPGTPMKDVAVDTVFMGSC
+TNSRIEDLRAFAEVVKGRTKADGLRVMVVPGSARVRLQAMDEGLDKVFEDFGAEWRFAGC
+SMCLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPLVAAATAVLGRLASPSDLPA
+LENQEA
+>4_789
+MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR
+PVRRPDLTIATEDHNTPTLDIDQPIADATSRTQIETLRANCAEFGVRLHPLGDAEQGIVH
+VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAVT
+VDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAGAR
+AGMVAPDETTFAYLKGRPHAPEGDDWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPFVT
+WGTNPGQGVSLNDTVPAPEDFADPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSCTN
+SRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM
+CLGMNPDQLSPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT
+PQEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000755.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000755.fa
new file mode 100644
index 0000000000000000000000000000000000000000..66b44ebab0e615919f13bc93d6beeb3cd5daf5fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000755.fa
@@ -0,0 +1,40 @@
+>0_835
+MTATPAPEAAADARPRVLLLFGGRSSEHPISCVTAAGVLHAADRQRWDVVPVGVARSGLW
+SHDELDVASFRLDGDALPEVPEPEAPVSLRALPDGTVELTAADGSSLGPVDVVFPLLHGP
+WGEDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITARDWARD
+PEAALARAGALAYPLFVKPARAGSSFGITRVTEPAGLRAAVEEARRFDPKVVVEAGIVGR
+EIECAVLDGHGSAAPRASLPGEIVVAHDEGETQFYDFESKYQDTGTTQLSCPAELPEEEI
+ERLRALAIRAFEAVDGSGLGRCDFFFTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSY
+DDLISELLDLALERGVGLH
+>1_566
+MTATPAPEAAADARPRVLLLFGGRSSEHPISCVTAAGVLHAADRQRWDVVPVGVARSGLW
+SHDELDVASFRLDGDALPEVPEPEAPVSLRALPDGTVELTAADGSSLGPVDVVFPLLHGP
+WGEDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITARDWARD
+PEAALARAGALAYPLFVKPARAGSSFGITRVTEPAGLRAAVEEARRFDPKVVVEAGIVGR
+EIECAVLDGHGAAAPRASLPGEIVVAHDEGETQFYDFESKYQDTGSTQLSCPAELPEEEI
+ERLRALAIRAFEAVDGSGLGRCDFFFTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSY
+DDLISELLDLALERGVGLH
+>2_2024
+MLLLFGGRSSEHPISCVTAAGVLHAADPQRWDVVPVGVARSGLWSHDELDVAAFRLDGET
+LPEVPEPEAPVSLRTLPDGTVELTAEDGSSLGRVDVVFPLLHGPWGEDGTLQGMFESLGL
+PYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITDRDWARDPEAALARAGALAFPLF
+VKPARGGSSFGITRVSDPADLRAAVEEARRFDPKVVVEAGIVGREIECAVLDGHGSDAPR
+ASLPGEIVVKHDEGDLQFYDFQAKYQDDDAAQLSCPAELPEEQTRRLRELAVRAFEAVDG
+SGLGRCDFFHTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSYDALISELLDLALERGV
+GLH
+>3_1917
+MTQPPETAPGRRPRVLLLFGGRSSEHPISCVTAAGVLHAADRERWDVVPVGVAHSGLWSH
+GEVDAAAYALGDGELPSVPEPERPVSLRARADDAVELVGADGEDLGVVDVVFPLLHGPWG
+EDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAGGLEVGPWETITDRQWRNDPE
+AALERAGALDYPLFVKPARGGSSFGITKVDAPEDLRAAVEEARRFDPKVVVEAGILGREI
+ECAVLDGHGAESPRASLPGEIVVKGAESGHQFYDFEAKYQDASAAQLSCPAELPEEAIER
+LREQAVRAFEAVDGAGLGRCDFFYTPDGRWVVNEINTMPGFTSISMYPAMWERTGLPYGE
+LISELLDLALERGVGLH
+>4_794
+MTAIPAPEAAAGARPRVLLLFGGRSSEHPISCVTAAGVLHAADRQRWDVVPVGVARSGLW
+SHDELDVASFRLDGGALPEVPEPEAPVSLRALPDGTVELTAADGSSLGPVDVVFPLLHGP
+WGEDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITARDWARD
+PEAALARAGALAYPLFVKPARAGSSFGITRVTEPAGLRAAVEEARRFDPKVVVEAGIVGR
+EIECAVLDGHGSAAPRASLPGEIVVAHDEGETQFYDFESKYQDTGTTQLSCPAELPEEEI
+ERLRALAIRAFEAVDGSGLGRCDFFFTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSY
+DDLISELLYLALERGVGLH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000756.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000756.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5af8fd2c4b6670c1430f668e2b231e4962ba257
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000756.fa
@@ -0,0 +1,20 @@
+>0_836
+MESRRLRRLVPLLTAIALGATACTGRVATVEAAPHAADPACAPAMVAMPDALGDLDLRPT
+DSQATAVWGDPAAVVLRCGAEVPGPTTDRCISVDGIDWVVRDEDENWRITTYGRDPAVEV
+LFGKDQASSDTVMVGLSSAVAQIEPSGGCVGVQDATPVG
+>1_567
+MESRRLRRLVPLLTAIALGATACTGRVATVEAAPHAADPACAPAMVAMPDALGDLDLRPT
+DSQATAVWGDPAAVVLRCGAEVPGPTTDRCISVDGIDWVVRDEDENWRITTYGRDPAVEV
+LFGKDQASSDTVMVGLSSAVAQIEPSGGCVSVQDATPVG
+>2_2023
+MESRPLRPLRRLVPLLTAIALGATACSGRVATVEAAPDAANPECAPAMVAMPDALGDAAL
+RPTDSQATAVWGDPAAVVLRCGAPVPGPTTDRCISVDGVDWVIRDEDENWRIVTYGRDPA
+VEVLFGKDKASSDTVMVGLASAVAQIDADGGCVNLQDATPVG
+>3_1916
+MPRLPRPVILAPALAAAALGLTACSGPVVSVEAAPGAADPACAPAMVAVPDVLGGQDRRE
+TDSQATAAWGEPAAVVLRCGVPTPGPTTDRCVSVDDIDWVVRDEDDHWRITTYGRTPAVE
+AVFGKSEVSSDSVMTGLGSAVAQIPSQRRCVNIEDATPVG
+>4_795
+MESRRLRRLVPLLTAIALGATACTGRVATVEAAPHAADPACAPAMVAMPDALGDLDLRPT
+DSQATAVWGDPAAVVLRCGAEVPGPTTDRCISVDGIDWVIRDEDENWRITTYGRDPAVEV
+LFGKDQASSDTVMVGLSSAVAQIESSGGCVSVQDATPVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000768.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000768.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0faa3a687ae2c0f4813b6b9aee02cfc56fd94d9f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000768.fa
@@ -0,0 +1,40 @@
+>0_848
+MSHPPAASWTPEPLPRPEPPRDDAPPVARRRRRWPWVVGLLAVLLAALLGLGAWYTSSLG
+RTFDDHRQTVDVGALEQAAGNGPLNVLVLGSDSREGEGEQDMGQRSDTMMLVHIPADRRQ
+VYVMSVLRDSWVTVPGHGEAKINSAFDTGGYTLAVDTVELLLGVSIHHVLEVDFQGFRGV
+TNALGGVEVCNPRAFSSGQANPSYYPRGHILLQDTAALRYVRERHAFDDGDVTRVENQQR
+YLAGAMDRFLSPQILGNPARTTEVVATFSDHLGVDEGLTSGVIASLAWQLRDVRGEDVEM
+FTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDDVQRYVDEHEPTKEKKAQAAGGPAP
+VLTLLTGTTPAPVLGEDPCDD
+>1_579
+MSHPPAASWTPEPLPRPEPPRDDAPPVARRRRRWPWVVGLLAVLLAALLGLGAWYAGSLG
+RTFDDHRQTVDVGALEQAAGDGPLNVLVLGSDSREGEGEQDMGQRSDTMMLVHIPADRRQ
+VYVMSVLRDSWVTVPGHGEAKINSAFDTGGYALAVDTVELLLGVPIHHVLEVDFQGFRGV
+TNALGGVEVCNPQAFSSGQANPSYYPRGHILLQDTAALRYVRERHAFDDGDVTRVKNQQR
+YLAGAMDRFLSPQILGNPARTTEVVATFSDHLGVDEGLTSGVIASLAWQLRDVRGEDVEM
+FTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDDVQRYVDEHEPEKEKKAQAAGGPAP
+VLTLLTGTTPAPALGENPCDD
+>2_2011
+MSQPPAASWTPEPLPRPARSPEPPRPARRRRWPWVLGVLAAVLVVLLALGAWYAVSLART
+FDDHRQTVDAGALEQAGGGEPVNVLVLGSDSRGGEGEEDMGERSDAMMLVHLPADRSQVF
+VMSVLRDSWVEIPGHGEAKVNAAFDLGGYPLAVDTVEQLLGVPVHHVVEMDFQGFRGVTN
+ALGGVEVCNPVAFSSGQTSPSYYPRGPVLLQDTAALRYVRERHAFDDGDVSRVQNQQRYL
+AGAVERFLSPQILGNPARTTEVVATFSDHLGVDAGLTSGVVASLAWQLRGVRAGDVEMFT
+VPRAGFGYSPDGDSIVELDEAKLADLRSALKDDDVQRYVAEHESEDGQDASAAGADPAPV
+LALLAQPAPTPAVGEDPCAD
+>3_1904
+MTQPPQQPWIPPERPGGAADPLEGLRGPAPAAPPTSTPPATRRSGGGRARRRRPLRRFLA
+VLGVLALLLVVALGAYGLLLARTFDGHRQTVSAAAFADPGNDGPVNFLVLGSDSRAAEDS
+AETSQRSDTMMLVHVPADRRHVYVISVLRDSLVEIPGRGQRKANAAYELGGPELTAAMLD
+KLLGVPVHHLAELDFQGFRGMTTALGGVEVCNPHAFSSGQKNPSFYPRGRIELKDTAALR
+YVRERHAFPEGDVMRVQNQQRFVRGAVAAFLDPAVVLNPPRAVDVVAGLSDHLTVDEGLD
+SATLASLAWQLRGVDRSALTMFTVPRAGYGTSPDGQDVVLLDADRMAALRDALQRDDVES
+YLRAHDPEALAAGEDVQPALAAAPGATPLLTELAAAPPAGEGTLLGEDPCGG
+>4_807
+MSHPPAASWTPEPLPRPESPRDDASSVARRRRRWPWVVGVLAVLLAALLGLGAWYAGSLG
+RTFDDHRQTVDVGALEQAAGNGPLNVLVLGSDSREGEGEQDMGQRSDTMMLVHIPADRRQ
+VYVMSVLRDSWVTVPGHGEAKINSAFDTGGYALAVDTVELLLGVPIHHVLEVDFQGFRGV
+TNALGGVEVCNPQAFSSGQANPSYYPRGHILLQDTAALRYVRERHAFDDGDVTRVKNQQR
+YLAGAMDRFLSPEILGNPARTTEVVATFSDHLGVDEGLTSGVIASLAWQLRDVRGEDVEM
+FTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDDVQRYVDEHEPTKEKKAQAAGGPAP
+VLTLLTGTTPAPALGEDPCDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000770.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000770.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce3f3961382dfc208c9deed07dd3cdc691057e23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000770.fa
@@ -0,0 +1,41 @@
+>0_852
+MKKIETVAVIGLGYIGLPTAAILAENGVRVLGVDVSDRTVDAVNAGTVPFVEPDLAGFVA
+RGVEKGLLSASTTTPAADAYIVAVPTPFKDGHSPDLGYIEAAARGLAPQLTGDELVILES
+TSPPGATEYMAEVIFAERPELREAELDFAHCPERVLPGRVMVELVTNDRIVGGSTRRAAE
+RARDLYRTFCEGEILLTDTRTAEMAKLVENSFRDVNIAFANELSVICAEQGIDVWELIEL
+ANHHPRVNILQPGPGVGGHCIAVDPWFIVDAAPQTARLIRAAREINDGKPQWVIDQVKAA
+AFDVQQATGRAPVVAALGLAFKPNIDDLRESPALNIAAELAGQFSGSDVLVVEPHVTELP
+AALQGKDNVRLVAVDEALEAADIVVLLVDHSAFADLGDRVADKRVIDTRGQWRTDPSL
+>1_583
+MKKIETVAVIGLGYIGLPTAAILAENGVKVLGVDVSDRTVDAVNAGTVPFVEPDLAGFVA
+RGVEKGLLSASTTTPAADAYIVAVPTPFKDGHSPDLGYIEAAARGLAPQLTGDELVILES
+TSPPGATEYMAEVIFAERPELREAELDFAHCPERVLPGRVMVELVTNDRIVGGSTRRAAE
+RARDLYRTFCEGEILLTDTRTAEMAKLVENSFRDVNIAFANELSVICAEQGIDVWELIEL
+ANHHPRVNILQPGPGVGGHCIAVDPWFIVDAAPQTARLIRAAREINDGKPQWVIDQVKAA
+AFDVQQATGRAPVVAALGLAFKPNIDDLRESPALNIAAELAGQFSGSDVLVVEPHVTELP
+AALQGKDNVRLVAVDEALEAADIVVLLVDHSAFADLGDRVADKRVIDTRGQWRTDPSL
+>2_2008
+MTTQIKDVAVIGLGYIGLPTAAILAENGVRVHGVDVSQRTVDAVNAGTVPFVEPDLADFV
+ERNVKAGRLSASLKTPQADAYIVAVPTPFKDGHSPDLGYIEAAARGLAPQLRGGELVILE
+STSPPGATEHMAAVIREARPDLDGATLDFAHCPERVLPGRVMIELVTNDRIVGGSTPEAA
+QRAKQLYETFCQGEILVTDCVTAEMAKLVENSFRDVNIAFANELSLICSDLGIDVWELIE
+LANHHPRVDILQPGPGVGGHCIAVDPWFIVDAAPQTARIIRAAREINDGKPKWVVDQAKA
+AAFDVQQATGRAPVVAVLGLAFKPNIDDLRESPALNIATEVAQQFTGSRILVVEPHVEEL
+PAALAGRDNVELVPAEDGIREADVVLLLVDHDAFASLGTTTEGKKVIDTRGQWR
+>3_1901
+MMGTPPALRCRDVNARMGIQNVTQIKTVAVIGLGYIGLPTAAILAENGLTVHGVDVSPRT
+VDAVNAGKVPFVEPDLADFVERNVAAGRLDASLETPKADAYIVAVPTPFQGDHAPDLSYI
+EAAARGLAPQLTGDELVILESTSPPGATDHMADVIREVRPDLKDAPLDFVHCPERVLPGR
+VMVELVTNDRIVGGSTPAAAERARDLYRSFCEGEILLTDCRTAEMAKLVENSFRDVNIAF
+ANELSLICAEQGIDVWELIGLANHHPRVNILQPGPGVGGHCIAVDPWFIVDAAPQTARII
+RAAREINDAKPQWVIERAKAAAFDVQQKEGRPAVVAALGLAFKPNIDDLRESPALNIAAQ
+LADEFSGSTVLVSEPHVDELPAKLQGKENVRFVPAEQAVAEADVVLLLVDHDAFAGLGEQ
+TAGKRVIDTRGQWR
+>4_810
+MTTQIKDVAVIGLGYIGLPTAAILAENGVRVHGVDVSQRTVDAVNAGTVPFVEPDLADFV
+ERNVKAGRLSASLKTPQADAYIVAVPTPFKDGHSPDLGYIEAAARGLAPQLRGGELVILE
+STSPPGATEHMAAVIREARPDLDGVTLDFAHCPERVLPGRVMIELVTNDRIVGGSTPEAA
+QRAKQLYEAFCQGEILVTDCVTAEMAKLVENSFRDVNIAFANELSLICSDLGIDVWELIE
+LANHHPRVNILQPGPGVGGHCIAVDPWFIVDAAPQTARIIRAAREINDGKPKWVVDQAKA
+AAFDVQQATGRAPVVAVLGLAFKPNIDDLRESPALNIAIEVAQQFTGSRILVVEPHVEEL
+PAALAGRDNVELVPAEDGIREADVVLLLVDHDAFASLGATTEGKKVIDTRGQWR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000772.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000772.fa
new file mode 100644
index 0000000000000000000000000000000000000000..072914b25d6b42795a4f01b089b2b9609a987580
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000772.fa
@@ -0,0 +1,29 @@
+>0_863
+MSDTGDPRVPSGTAVLTVDGATLRRVGARPGLARYLASLWEYRSFILFDSRSRIAGANSV
+NALGRVWMVLNPILDGAAYFLVFGLLLGTGRGVPNFLGYLIIGVFLFRYTSSAITAGSRS
+ISTNLSIVRAFRFPRATLPIATNIRELMLFGPTLVVMLVLVLAIPPMEQITWRWLLLIPL
+LALQTLFNVGASLLLARYVARWSDLSNLIAFGTRIWLYVSAVFFSADRFADFPPMMTAMH
+LNPLFCVLDIARQSLLYASDADPMRWVVLAAWTAALLVVGTVVFWRAEETYGEER
+>1_594
+MADTGDPRVPSGTAVLTVDGATLRRVGARPGLARYLASLWEYRSFILFDSRSRIAGANSV
+NALGRVWMVLNPILDGAAYFLVFGLLLGTGRGVPNFLGYLIIGVFLFRYTSSAITAGSRS
+ISTNLSIVRAFRFPRATLPIATNIRELMLFGPTLVVMLVLVLAIPPMEQITWRWLLLIPL
+LALQTLFNVGASLLLARYVARWSDLSNLIAFGTRIWLYVSAVFFSADRFADIPPLMTAMH
+LNPLFCVLDIARQSLLYASDADPMRWIVLAAWTAALLVVGTVVFWRAEETYGEER
+>2_2000
+MSGTGMAASGPVNTVVVDAAPLGVVGARPSLRDYVLSLFRYRSFILFDSRSRISGANAVN
+TLGRLWMVLNPILDGGAYFLVFGVLLGTGRGIPNFIAYLIIGVFFFRYSSQAITAGSKAV
+SSNLTLVRAFRFPRATLVLATNLRALLEFVPTLAVMVVLILAIPPLEVFTWRWLLLVPLL
+ILQTLFNVGLSLVLARFVAHWPDLANMIAFGMRIWLYLSAVFFSVERFDGQPIVQTAMHL
+NPLYCVLDIARQSLLYGQDAEPHRWLVLAGWAALVAVVGLVVFWRAEETYGEER
+>3_1897
+MTDRVEATSPPVELRVDESRLERVGRRPSLGDYVTRLWRLRHYVRYDAVAAVQAQNRRHR
+LGNVWLLLNPILNGATYFLVFGVLLRTSLGVENFIGYLTVGVFMFTFTTRAVTALSRSLT
+ARNNVADAFQLPRAVLPLTALAREVLAYGFTLAAMLLAVLILPPHAQVTWWWLLFPVVVA
+LQLMLVAGVGLLLARAVSRVRDLSQIVGFGIRLWMYGSAVFYSFDRFVSQPNVLAVLQLN
+PMYQVLDISRDLLLYGRSPSPVAWGILAAWSVGLLVVGVVVFWLGEERYAKDLNR
+>4_814
+MLDAIFYWLIFGLLLRFDHGMDNFVAFVIVGVFMFQMTSAALTSGTRTIASNLSLTRAFR
+FPRMALPLADLVYDVLQRLPAIAVMFILVIAIPPHETPEWSWLVFPGVLGLHVILNFGIM
+LLLARLSTLLPDVSRMVPFVSRLLMYGSGVIFPITRFTDNHPALHAIIQLNPLYVLITMY
+RQVIIEGVTPPASSWAMLAAYAVCLTIVGGIVFWLGEESYGRDQYR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000773.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000773.fa
new file mode 100644
index 0000000000000000000000000000000000000000..72045616a133ca32f5cb497d3ca913aab751a2d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000773.fa
@@ -0,0 +1,40 @@
+>0_864
+MPKVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLN
+IIQPRQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAG
+LRSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAAEDIYVTGNTVIDALLE
+AVGHQVPFEDERLAELEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLP
+AHRNPVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPV
+LVMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYTAMSQAVNPYGDGRAAER
+TVSAIAELLGVGERLPAFDGGDPA
+>1_595
+MPKVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLN
+IIQPRQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAG
+LRSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAPEDVYVTGNTVIDALLE
+AVSHQVPFEDERLAGLEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLP
+AHRNPVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPV
+LVMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYSAMSQAVNPYGDGRAAER
+TVSAIAELLGVGERMPEFAPDDRG
+>2_2001
+MKVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLNI
+IQPRQTLNGVFARTLDGLDAILEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAGL
+RSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAPEDVYVTGNTVIDALLEA
+VGHQVPFEDERLAELEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLPA
+HRNPVVREAILPEIEGRANVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPVL
+VMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYTAMSQAVNPYGDGRAAERT
+VSAIAELLGVGERLPAFDGA
+>3_1898
+MPLKIMPIYGTRPEAIKMAPIVNALRADDRFECFTTVTGQHREMLDQVNAIFGITPDADL
+DIMRPNQTLNGIMSVMLEGLDELLVRERPDAVVVQGDTTTSTAGAIAAFYRGIPVVHAEA
+GLRSGDLFSPFPEEANRKITSQIASLHLAPTSVSRANLEREAIDSAAITVTGNTVIDALL
+ETVAQQLPFTDPRLAELAERRAADPQSRVLLVTTHRRENQGEAMRGVGRALARLAQSHPN
+LTIVLPAHRNPVVREAVLPTLEGIDSVIVTEPLPYGEFTRMMDLADVVLTDSGGVQEEAP
+SLGKPVLVMRDNTERPEAVHAGTVRLIGTDEERLVEETSLLLTDPDAYAAMAHAVNPYGD
+GRAGLRTVAAIAQLLGVGDRLDEFGA
+>4_815
+MPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLNIIQP
+RQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAGLRSF
+DILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAAEDIYVTGNTVIDALLEAVSH
+QVPFEDERLAELEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLPAHRN
+PVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPVLVMR
+ENTERPEAVTAGTVRLIGTDEEVVVTEVTRLVTDEAAYTAMSQAVNPYGDGRAAERTVSA
+IAELLGVGERLPAFDGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000774.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000774.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dea6bba8c3a6c04912666a5332a9ca120d2c0b5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000774.fa
@@ -0,0 +1,45 @@
+>0_867
+MPSSPPAARVPLPTEIKVMVAAAFVIAIGFGIIAPLLPQYAEMFASDFANPATAVAAVVS
+AFGLTRLLFAPVSGRLTNRLGETPVYMTGVLIVAASMFLIAFAQDYTQLLLYRALGGVGS
+TLFTVSAMAFLASKSPPTIRGRVSGAYASAFLIGNIVGPIVGSVLAVFGFRVPFLIYGTS
+LVIAAGIVFVMLRDTRLQDRARGETRPVMPLRAALGHRSYRAALTSMFANGWATFGVRNA
+ITPLFAASAFTGTALLGWGITEENRQLMAGLALSVFAAGNVLAVASSSRLSDLHGRKPLI
+LVGLAVMAVFTGAIGWLESPLLFLVSCALAGAGTGTLNAPQQAAVADLVGQDRKAGPVMS
+AAQMSGDLGAILGPLLVGLVVDAAGYGWGFVVTGAVIAVGALAWARAPETNLPVAPGGPR
+TGSLPKVDPDVDPCRMEGRELG
+>1_596
+MAVMPSSSARSSRVPLPREIKVLVAAAFIIAIGFGIIAPLLPQYAATFDASAVGVAAVVS
+AFGLTRLLFAPVSGKLTNRLGETPVYMTGVLIVAASMFLVAFAQTFPQLLLFRALGGVGS
+TLFTVSAMAFLARKSPPTMRGRISGAYASAFLIGNIVGPIVGSALSVFGYRAPFLIYGSS
+LVVAAALVFFLLKDTRLADRAVRDVRPAMPVREALSNPSYRAALVSFFANGWATFGVRNS
+VMPLFAATAFAGTGLLGWQVDGAMMAGLALSVFALGNVVAVSFSSRLSDVHGRKPLILTG
+LLVMAVTTGAIGWVGTPSLFLIACLVSGAGTGILNAPQQAAIADVVGQDRRSGSVMSSAQ
+MSADLGAIVGPLAAGLVVDVAGYGWAFVVTGAVILLGAIAWWRAPETNLPVVPGGPRTGA
+LPKIEPEDARPPHREDG
+>2_1998
+MPSSSSRTARAPLPREIKVLVAAAFIIAIGFGIIAPLLPQYAASFNASATAVAAVVSVFG
+LTRLLFAPLSGRLTNRLGETPVYMTGVLIVAASMFLIAFAQTFAQLLAFRAIGGVGSTLF
+TVSAMAFLARKAPPSMRGRVSGAYASAFLIGNIVGPIVGSALAVFGYRAPFLIYGTSLVI
+AAALVFFMLKDTRLADRAARDARPAMPVKEALENPSYRAALVSFFANGWATFGVRNSVMP
+LFAASAFAGSGLLGWQVDGALMAGLALSVFALGNVVAVTFSSRLSDMHGRKPLILTGLLV
+MAVTTGVLGWMQSPLLFLLACLVSGAGTGVLNAPQQAAIADVVGQGRRSGAVMSSAQMSA
+DLGAIIGPLLAGLVVDAAGYGWAFVLTGGVILLGALAWWRAPETNLPIVPGGPRTGSLPL
+VRPEDARVTPREDG
+>3_1895
+MPTTPSAARAPLPREIKVLVAAAFVIAIGFGIIAPLLPQYAERFASDFANPATAVAAVVS
+AFGLTRLLFAPLSGRLTNRLGETPVYMTGVLIVAASMYLIAFAQDYTQLLVFRGLGGVGS
+TLFTVSAMAFLASKSPPSMRGRVSGAYASAFLIGNIVGPIVGSVLSVFGYRVPFLIYGTS
+LVIAAAIVFFMLKDTRLHDRAAADSRPVMRLREALDHPSYRAALVSMFANGWATFGVRNA
+VTPLFAASAFTGTALLGWTVTQENQALMAGLALSVFAAGNVAAVTFSSRLSDVRGRKPLI
+LLGLAVMAVCTGVIGWMTSPLLFLVACLLAGAGTGTLNAPQQAAVSDLVGQGRKAGPVMS
+VAQMAADLGAISGPMLVGLVVDGAGYGWAFAVTGAVLAVGFLAWLRAPETNLPIVPGGPR
+TGSLPKIAPEDVAPPHHREA
+>4_816
+MAVMPSSSARSSRVPLPREIKVLVAAAFIIAIGFGIIAPLLPQYASSFNASATAVAAVVS
+AFGLTRLLFAPLSGRLTNRLGETPVYMTGVLIVAASMFLIAFAQTFEQLLLFRALGGVGS
+TLFTVSAMAFLAAKSPPTMRGRVSGAYASAFLIGNIVGPIVGSALAVFGFRAPFLIYGTS
+LVIAAGMVFVLLRDTRRADRGTGDPRPTMPLKEAFGLPSYRAALASFFANGWATFGVRNS
+VMPLFAATAFAGTGLLGWQVDGAFMAGLALSVFALGNVVAVTFSSRLSDVHGRKPLILTG
+LLTMAATTGVIGWMSSPALFLLACLLAGAGTGTLNAPQQAAIADVVGQGRRSGAVMSAAQ
+MSADLGAISGPLLAGLVVDTAGYGWAFVLTGGVILLGALAWWRAPETNLPIVPGGPRTGS
+LPLVRPEDARVTPREDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000780.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000780.fa
new file mode 100644
index 0000000000000000000000000000000000000000..516dafaed922d082465b08211e6324fe59d3af37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000780.fa
@@ -0,0 +1,25 @@
+>0_874
+MSPAAQDDLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGERLVVRDGAPGLPAELTVT
+RARWNKQILVVGFEESPDRNVAETLRGAQLFAVPAAPEESDEWYEEDLVDLEVRVDGERV
+GVVTALTTGAVQDLLHVALDGVEEEALVPFVEEIVPEIDPEAGVLVLTPPPGLLELATGE
+DEGAADGPTDADAED
+>1_602
+MSPAAQDDLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGERLVVRDGAPGLPAELTVT
+RARWNKQILVVGFAESPDRNVAETLRGAQLFAVPAVPEESDEWYEEDLVDLEVRVEGERV
+GVVTALTTGAVQDLLHVALDGVEEEALVPFVEEIVPEIDSEAGVLVLTPPPGLLELATGE
+DEGAVDGPADADAED
+>2_1992
+MSPAPQDGLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGATLTVRDGGPSLPAELTVT
+RARWNKQILVVGFEQSPDRNTAETLRGAQLFAAPAAPEESDEWYEDDLVDLEVRVDGRRV
+GVVTALTTGAVQDLLHVALDGVDEEALVPFVEEIVPEIDPEAGVLVLTPPPGLLELASGE
+AEQDDDAAASDAEADADAGREG
+>3_1889
+MSPAPQPAETEGQVRVARIGKPHGIRGEVTVQLFTDDPEARFAADSRLEVRQGPPGAPAA
+LTVTRARWNKAILVVGFAEVPDRNAAEALRGAQLYAAPLEKVEDDAWYEDDLLDLEVHVD
+GARVGVVTGLLTGTVQDLLQVRLDATGDDALVPFVEEIVPEVDQEAGVVVVAPPPGLLEL
+ASETTAGEG
+>4_822
+MSPAAQDDLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGERLVVRDGAPGLPAELTVT
+RARWNKQILVVGFAESPDRNVAETLRGAQLFAVPAAPEESDEWYEEDLVDLEVRVEGERV
+GVVTALTTGAVQDLLHVALDGVEEEALVPFVEEIVPEIDSEAGVLVLTPPPGLLELATGE
+DEDAADGPADADAED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000782.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000782.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5af6c171ef034fec5ff0d031adffa1871db88f4f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000782.fa
@@ -0,0 +1,15 @@
+>0_876
+MHILDSFDKKTLRDDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGHGVRETFRV
+RKVSFGIGVERVFPVHSPVIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRVDAK
+>1_604
+MHILDSFDKKTLRDDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGYGVRETFRV
+RKVSFGIGVERVFPVHSPVIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRADAK
+>2_1990
+MHILDSLDSNSLRSDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRNGYGVRETFRV
+RKVSFGVGVERVFPVHSPVIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRVDAK
+>3_1887
+MHILDSFDKASLREDIPAFGPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGHGVRETFRV
+RKVSFGVGVERVFPVHSPVIDKIEVLTKGDVRRAKLYYMRDRHGKAARIREKRADAK
+>4_824
+MHILDSFDKKTLRDDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGYGVRETFRV
+RKVSFGIGVERVFPVHSPIIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRVDAK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000787.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000787.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a4746d4cc3017e84e142d1e0169f30aea3beaea7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000787.fa
@@ -0,0 +1,20 @@
+>0_881
+MTGTAEQVGAQPPGERRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGELDIVA
+HHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVRAHAADRRGTPWRVDAVA
+VLVPRTGGIRFDLLQDVRP
+>1_609
+MTGTAERIGAQPPGDRRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGELDIVA
+HHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVRAHAADRRGTPWRVDAVA
+VLVPRTGGIRFDLLQDVRP
+>2_1985
+MTGTAEKVGADSPGGGRGSRAHTALGRFGEDAAARWLADRGYVIADRNWRGEAGELDLVA
+HHAGWWVGVEVKTRSGLAFGDPLESIDRRKLLRLHRLTAAWVRAHGEGRRAERWRVDAVA
+VLVPRTGGIRFDLLQDVRP
+>3_1882
+MVPLDTTTTTPAARRGSTAHTALGRYGEDAAARWLAERGYQIVARNWRGEDGELDLVARH
+GPWWVGVEVKTRSGLAYGDPLEAIGRRKLLRLHRLTAAWVREAAAREGRPLRSQQWRVDA
+VAVLVPRTGGVHFDLVQDVRP
+>4_829
+MTGTAEQVGAQPPGERRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGELDIVA
+HHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVRAHAADRRGTPWRVDAVA
+VLVPRTGGIRFDLLQDVRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000788.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000788.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7840fc5e4a4c155daa7487bf0a8f8218562f3425
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000788.fa
@@ -0,0 +1,50 @@
+>0_882
+MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE
+TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA
+RRQVTAPEPEPTRAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG
+ILPPLDRRTALECAALRSLRGGDARVRRRGGTSQGFDGEIDRTPPFEAPHHSASRSALVG
+GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ
+LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP
+ASETTSQVAVRVAAAADRQARRWATAAERGVVPPGLRRNAHVPAGVLRHGPYAVPRAARR
+PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA
+>1_610
+MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE
+TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA
+RRQVTAPEPEPARAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG
+ILPPLDRRTALECAALRSLRGGDARVRRRGGTAQGFDGDIDRTPPFEAPHHSASRSALVG
+GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ
+LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP
+ASETTSQVAARVAAAADRQARRWATAAERGLAPSGLRRNAHVPAGVLRHGPYAVPRAARR
+PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA
+>2_1984
+MSGIGRTRSISLSGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGAGHDLAIVLAAYAADGRVRGVEGPVFLAELGLDGALHRSPE
+TVAMVMASVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVILAFGGEPEGEAPQRRP
+VRPADDDGAPGLGPGAPDLSEVAGQAEARFALEVAAAGAHHLLLRGAPGAGKTMLAERLP
+GILPPLDRRTALECAALRSLRGADALARRGVGQGSAGTRAAGDLDRTPPFEAPHHSASMA
+ALVGGGANLARPGAVSLAHGGVLFLDEAPEFERRALESLRQPLESGEVLLHRARGTVAYP
+ARFQLVLAANPCPCGKGGGNGVECRCSVTERRRYGQRLSGPLLDRVDLQVTVRPVQARQL
+AGAPAAETSAQVAARVAEAARRQAERWARAAEEGLVAPGLRRNAHAPAGVLRHGPYAVPR
+AARRAADEAVDHGLLSARGHARVLRLAWTLADLRGAETPAPEDTDVALTLRHQEEDET
+>3_1881
+MSGIGRTRSISLTGLRGTVVDVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGAAHDLAIVLAAYAADGRVQGVDGPVFLAELGLDGTLHRAPE
+TVAMVMAAVDAGHDRVVVAADAVAEAELVPGARVRGFAHLHEAILAFGGRPDASVARPSG
+PSGTAGRGPAAGQEGPSGPVPDLAEVAGQAEARFALEVAAAGGHHLLLSGPPGAGKTMLA
+ERLPGILPPLDDRTALETAALRSLRGLEPSARGLRRTPPFEAPHHSASMAALVGGGTGLG
+RPGAVSLAHGGVLFLDEAPEFERRALDALRQPLESGEMIVHRAHGSVAYPARFQLVLAAN
+PCPCGFGSGTGAHCRCTSLQRRKYAARLSGPLLDRVDVQVSVRPVRADQLAAAPEAEPSR
+AVAARVAAAVAAQDARWAAAAREGSLPPGVCRNAHVPAALLRSGRFAVPPEARATADRAV
+DRGELSARGHGRVLRLAWTLADLRGASCPEAQDVEIALQLRIRSEEDR
+>4_830
+MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE
+TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA
+RRQVTAPEPEPTRAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG
+ILPPLDRRTALECAALRSLRGGDARVRRRGGTSQGFDGEIDRTPPFEAPHHSASRSALVG
+GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ
+LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP
+ASETTSQVAVRVAAAADRQARRWATAAERGVVPPGLRRNAHVPAGVLRHGPYAVPRAARR
+PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000789.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000789.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b1eb2e82f29216368a57ea8443f58cf4c12b05f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000789.fa
@@ -0,0 +1,44 @@
+>0_883
+MTTHVTPAADHVAGPRRPDAARLARAALTRLVEPGDALAVQTVTALGPERALALLTGRET
+IQPAERDLLADLAGAPDTLPRRWAAGLARWAPRAARLEPERDLVTLHRLGGGLLIPEDDA
+WPAALADLGEEAPLGLWFRGSGTLPPADRMLAVVGSREATAYGRTVTARCAAHAVQQGAC
+VISGGAYGIDGAAHRAALQAPAAPEDAADRDGVPPTVAVLAGGLDRFYPAGHEDLLRAVM
+AAGLLVSEMPPGASPTRYRFLQRNRVIAALAGAVLVVEARWRSGAQNTAGHAFGLGREVG
+VVPGPVTSPSSAGCHRLLQESPARLVTTEQEALALLGQGPARSGDTGGRTSARAAPEPAA
+RPTDGLTMEEALVHEALPLRQAVPADRITVSAGLALPTVLACLSRLQRAGLAERVEDRWR
+RG
+>1_611
+MTTYVTPAADHVAGPRRPDAARLARAALTRLLEPGDALAVQTVTALGPERALALLTGRET
+IQPAERDLLADRAGAPDTLPRRWAAGLARWAPRAARLEPERDLVTLHRLGGGLLIPEDDA
+WPAALADLGEEAPLGLWFRGSGTLPPADRMLAVVGSREATAYGRTVTARCAAHAVQQGAC
+VISGGAYGIDGAAHRAALQALAAPGDAADRDGVPPTVAVLAGGLDRFYPAGHEDLLRAVM
+AAGLLVSEMPPGASPTRYRFLQRNRVIAALAGAVLVVEARWRSGAQNTAGHAFGLGREVG
+VVPGPVTSPSSAGCHRLLQESPARLVTTEQEALALLGQAPARSGGAGGRASTRAAPEPAT
+RPTDGLTMEEALVHEALPLRQAVPADRITVSAGLALPTVLACLSRLQRAGLAERVEDRWR
+RG
+>2_1983
+MTADTAHDHPVAAAQGPDTQRPDAHRPDTQRPDAQRPDTQRPDAARIARAALTRLVEPGD
+ALAVHAVAALGPERALVLLTGREAIQPAERDLLAEHAGAPDTLARRWSAGLDRWAPRAAR
+LDPVRDLVALHRLGGGLLVPEDEAWPAALDDLGEAAPLGLWFRGPGTLPPASRALAVVGS
+REATAYGRAVTTRLAAHAVQQGVCVVSGGAYGIDGAAHRAALAAPVGPEDPDAHDGPGGA
+SDRVPPTVAVLAGGLDRFYPAGHEDLLREVMAAGLLVSEMPPGASPTRYRFLQRNRVIAA
+LAGAVLVVEARWRSGAQNTAGHAFGLGREVGAVPGPVTSPSSAGCHRLLQETPARLVTSE
+TEALALLDGGAPAPRPGGTGGGNTAPPGDAPAPPPGGTGEGTRRPPRPPPPPRPCGSRTG
+>3_1880
+MTTAGETAQNARPDGPRVARAALTRLVEPGDDLALATVAALGPERALTLLTGAARIEAAE
+RDLLADRLGQDAFARRWSAGLARWAPRSARLDPVRDLVALHRLGGGLLIPEDPAWPAGLD
+DLGDAAPVGLWFRGRGTLPPLPRALAVVGSREATAYGRQVTRDVVACASAAGVCIVSGGA
+YGIDGAAHEAALETAAAAGRRSGPGSHDDAAPGVPPTVAVLAGGLDRFYPAGHERLLRAV
+MEEGLLLSEMPPGATPTRYRFLHRNRLIAALSGAVVVVEARWRSGAQNTAGHAHGLGREV
+GAVPGPVTSPSSAGCHRLLQEGPTRLIADPAQALTLLEPPRPGEPPAASPATTTRGEASR
+SPGRPTDGLTVEELLVHEALPLRRAVPVDNLTSSAGLALPTVLAVLTRLEGRRLAERRGD
+LWRRAPE
+>4_831
+MTTHVTPAADHVAGPRRPDAARLARAALTRLVEPGDALAVQTVTALGPERALALLTGRET
+IQPAERDLLADLAGAPDTLPRRWAAGLARWAPRAARLEPERDLVTLHRLGGGLLIPEDDA
+WPAALADLGEEAPLGLWFRGSGTLPPADRMLAVVGSREATAYGRTVTARCAAHAVQQGAC
+VISGGAYGIDGAAHRAALQALAAPGDAADRDGVPPTVAVLAGGLDRFYPAGHEDLLRAVM
+AAGLLVSEMPPGASPTRYRFLQRNRVIAALAGAVLVVEARWRSGAQNTAGHAFGLGREVG
+VVPGPVTSPSSAGCHRLLQESPARLVTTEQEALALLGQGPARSGGAGGPSSTRAAPEPAA
+RPTDGLTMEEALVHEALPLRQAVPVDRITVSAGLALPTVLACLSRLQRAGLAERVEDRWR
+RG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000792.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000792.fa
new file mode 100644
index 0000000000000000000000000000000000000000..608782b8a4ff953ef1b1975aa44137d131d5851c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000792.fa
@@ -0,0 +1,40 @@
+>0_886
+MTRTAVITGLGATTPIGGDVPTFWSHALQGVSGARTMEHDWVEKYELPVTFAAELAVPTS
+EVLSKVEQKRQDPATQMATVAAREAWKDAGLEGAEVDGDRLAVAFGTGIGGVWTLLDGWD
+TLRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLVRS
+GQADVVICGAAEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV
+IESEEHAKARGARVYAELAGAGVSSDSHHITAPEPEGLGATRAMRAALRSADITPEDVCH
+VNAHATSTPKGDAPEYLAMRAVFGDHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH
+GQAPVTINLDHQDPEIPLNVVTGSPARLPEGPRVAVKNSFGFGGHNAVAVFRSV
+>1_614
+MTRTAVITGLGATTPIGGDVPTFWSHALQGVSGARTMEHDWVEKYELPVTFAAELAVPTS
+EVLSKVEQKRQDPATQMATVAAREAWKDAGLEGAEVDGDRLAVAFGTGIGGVWTLLDGWD
+TLRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLIRS
+GQADVVICGAAEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV
+IESEEHAKARGARVYAELAGAGVSSDSHHITAPEPEGLGATRAMRAALRSADIAPEDVCH
+VNAHATSTPKGDAPEYLAMRAVFGEHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH
+GQAPVTINLDHQDPEIPLNVVTGSPARLPEGPRVAVKNSFGFGGHNAVAVFRSV
+>2_1979
+MTRTAVITGLGATTPIGGDVPTFWSNALKGVSGARTMEHEWVEELGLPVTFAAELAVPTA
+DVLSKVEQKRQDPGTQMATVAAREAWRDAGLEGVELDGDRLAVAFGTGIGGVWTLLDGWD
+ILRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLIRS
+GQADVVICGASEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV
+VESEEHARARGARVYAELAGTGVTSDSHHITAPEPEGLGATRAMRAALKAADLTPEDVCH
+VNAHATSTPKGDAPEYLAMKAVFGDHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH
+GQAPVTINLENQDPEIPLNVVTGSPAQLPEGPRVAVKNSFGFGGHNAVAVFRSV
+>3_1877
+MTRTALITGLGATTPIGGDVPTFWANAQKGVSGAATMQHEWVEQYDLPVTFAAELAVPTS
+EVLSKVELKRQDPSTQMATVAAREAWADAGLADADVDPERLAVAMGTGIGGVWTILDAWD
+ALRERGPRRVMPMTVPMLMPNGAAGALSLEFGARAGARTVVAACAAGTEALDTALTLIRT
+GQADVVLCGATEAAVHPMPMAAFAAMQALSKRNDDPQSASRPYDVDRDGFVLGEGAGVMV
+VESEEHAAARGARVYARLAGTGVTSDSHHITAPEPEGLGATRAMRRALADAGLRPEDVGH
+VNAHATSTPKGDAPEYLAMKAVFGTGLDDVLVSATKSQTGHLLGASGAIESILSVLAVHH
+GVAPVTINLENQDPEIPLNVVTGTPAALPADRRVVVKNSFGFGGHNAVAVFTGV
+>4_834
+MTRTAVITGLGATTPIGGDVPTFWSHALQGVSGARTMEHDWVEKYELPVTFAAELAVPTS
+EVLSKVEQKRQDPATQMATVAAREAWKDAGLEGAEVDGDRLAVAFGTGIGGVWTLLDGWD
+TLRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLVRS
+GQADVVICGAAEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV
+IESEEHAKTRGARVYAELAGAGVSSDSHHITAPEPEGLGATRAMRAALRSADITPEDVCH
+VNAHATSTPKGDAPEYLAMRAVFGDHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH
+GQAPVTINLDHQDPEIPLNVVTGSPARLPEGPRVAVKNSFGFGGHNAVAVFRSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000793.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000793.fa
new file mode 100644
index 0000000000000000000000000000000000000000..48c03096016c10ba128b32db4ece1867ae2da349
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000793.fa
@@ -0,0 +1,15 @@
+>0_887
+MASKEEILAGLAEIVNEETGLDTAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDGAQA
+>1_615
+MASKEEILAGLAEIVNEETGLDAAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDGAQA
+>2_1978
+MASKEEILAGLAEIVNEETGLDTADVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDNAQA
+>3_1876
+MASKEEILAGLAEIVNEETGLETADVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDQAQA
+>4_835
+MASKEEILAGLAEIVNEETGLDTAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDGAQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000796.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000796.fa
new file mode 100644
index 0000000000000000000000000000000000000000..809faad2bd5fcb8b4d54bf17e97bbb0357bd72e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000796.fa
@@ -0,0 +1,40 @@
+>0_890
+MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA
+LQGFLTWFERPTSTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAER
+DQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRAT
+ALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDAR
+AVGEALAPWFAPGPVIVGPVVDSLVSAHVSARHTLAGLSAAAAHPRASRPTPAEDLLPER
+ALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRLK
+RVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGTGSD
+>1_618
+MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA
+LQGFLTWFERPTSTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAER
+DQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRAT
+ALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDAR
+AVGEALAPWFAPGPVIVGPVVDSLVSVHVSARHTLAGLSAAAAHPRASRPTPAEDLLPER
+ALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRLK
+RVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGAGSD
+>2_1975
+MPEPRSAASRPVSTEGRARLRSHLGALNTAVLQRLDATLPWYRGLTPDERSALGLVAQRA
+LQGFISWFDRPKTTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAER
+DQAPIREHVLHYSREVAFALADVYARAAEMRGAMDSRLEAVLLDAVLRGQDPDEIRHRAT
+ALGWRGDHRVMVMAGLAPGQDQPAFIPGLRRAAAKLDCDLLVGVQAERLVLVIGSVTDAQ
+VVGEALTPWFAPGPVILGPVVDSLVEAHVSARHTLAGLGAAPAHPRAIRPTPAEDLLPER
+ALLGDPTACEALVEGVYAPLADAGTALLDTVDAYGALGHSLEGTARELFVHANTVRYRLK
+RVAEVTGWDPLVPRDAYVLQTAVTLGRLAGSRPGVAEASA
+>3_1873
+MPAPRPSAPRRVSADGLARLRAHLGTFNTATLRRLDETLPWYRELTPDERSALGLIAQRA
+LQGFITSFERPQTTTVDVLRDVFGQSPTELTRAISLHRALQLIRTIVDVVETGVPDAVSE
+ADQPVVAEHVLHYSREIAFAIADVYARAAELRGAMDSRLEAVLLDAVLRGQEPDEIQHRA
+TAFGWRGGDGVMVMAGSARDGATAAFLPGLRRDAARLQCELLVGVQSRRLVLVVGSVSDP
+DAVAEALLPWFADGPVIVGPVVDSLLEAHVSAHHALAGLGAAAAHPRAGRPARSDDLLPE
+RALAGDATACAALVDGVYAALADAGPSLLETVDVYTACGHSLEGTARELYVHANTVRYRL
+RRAAEVTGWDPQRPRDAYVLQTAVALGRLSEGAPRL
+>4_838
+MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA
+LQGFLTWFERPTSTGHVLQDVFGPAPTDLTRAISLHRALQLIRTMVDVVETRVPELLAER
+DQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRAT
+ALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDAR
+AVGEALARWFAPGPVIVGPVVDSLISAHVSARHTLAGLSAAAAHPRACRPTPAEDLLPER
+ALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRLK
+RVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGTGSD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000798.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000798.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5cedefcca1fe1e4de6ba70a59c3331a0625338a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000798.fa
@@ -0,0 +1,20 @@
+>0_892
+MQAGSTPTSTDSALLAELALSRGDLVQEWGYDDDVDVTFRDALEDALGEELLTEDDQEPA
+DAVLFWWRADDGDVMDLADALVDAQRSLDAGPVWIMTPRKGRPGHVSPADVAEAASTAGL
+HATTGAGASEDWAAQKLVQKRGG
+>1_620
+MQAGSTPTSTDSALLAELALSRGDLVQEWGYDDDVDVTFRDALEGALGEELLTEDDQEPA
+DAVLFWWRADDGDVMDLADALVDAQRSLDAGPVWIMTPRKGRPGHVSPADVAEAASTAGL
+HATTGAGASEDWAAQKLVQKRGG
+>2_1973
+MEAGSTPTSTDSALLAELALAQGDLVQEWGYDDDVDFTFRDGLEDALGEELLTEEDQEPA
+DAVLYWWRAEDGDVTDLADALVDAQRSLDSGPVWLMTPRKGRAGHVNPADVQEAAGTAGL
+HATTGAGVSEDWAAQRLVQKRGG
+>3_1871
+METPSDGTSTHQELLDAYGLTAGELVQEWGYDDYIDFDFRDALEDALGEELLTEEDQEPA
+DAVLFWWRTDDGDVSDLTDALVDAQRSLDAGPVWLMTPRNGRPGHVSPTDVAEAAATAGL
+HVTTGAGGSADWAAVRLEKRGG
+>4_840
+MQAGSTPTSTDSALLAELALSRGDLVQEWGYDDDVDVTFRDALEDALGEELLTEDDQEPA
+DAVLFWWRADDGDVMDLADALVDAQRSLDAGPVWIMTPRKGRPGHVSPADVAEAASTAGL
+HATTGAGASEDWAAQKLVQKRGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000799.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000799.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20d1ab7369da8f7fb90fd0610630db340eb20f33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000799.fa
@@ -0,0 +1,20 @@
+>0_893
+MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL
+GWIGALAEDVAVDDVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF
+DVETGRPRRVSVLLDADGVEAARVVAAPGQARTRSEHEAATRDLLADR
+>1_621
+MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL
+GWIGALAEDVAVDEVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF
+DAETGRPRRVSVLLDADGVEAARVVAAPGQARTRGEHEAATRDLLVDR
+>2_1972
+MAEEPGAVPALRDDRGQDWPWPPTRGPEDAAAPRATWLVLLPGAFTPVCTGELGWLGELA
+TDLAADDVAVRVIACDAAPVLRRVREELGLPEDLVLLSDFWPHGAACAALDAFDAASGRA
+RRVSVLLDADGVEVSRVTAAPGRPRSRTEHEAATRALLGDR
+>3_1870
+MAEPALRDIHGTPWPWPPVVSGERAAWLVFLPGAFTPVCAGELAWLGPLAVELAAEDVGL
+RVVSCDAAPVLREVADRTGLPAECVLLSDFWPHGAAAARFGLLDETTGRPRRVSVLVDES
+GTELVRVRPGEPGGPRTAQAHRRAAEGALGRRR
+>4_841
+MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL
+GWIGALAEDVAVDDVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF
+DVETGRPRRVSVLLDADGVEAARVVAAPGQARTRSEHEAATRDLLADR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000801.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000801.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f759bae9d2138b2657b98a2315d2ee59045bb46d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000801.fa
@@ -0,0 +1,15 @@
+>0_895
+MTGAAYLVAAAVVAGLVTFCLRAVPFALLQPLRESVLAARLAVWMPAGVLTILALVMLLD
+AAALAPGEPVDGTRVAHALFAAAVTVVVHLLAGRRTLVSIAAGTLAYVLLVNLA
+>1_623
+MTGAAYLVAAAVVAGLVTFCLRALPFALLQPLRESVLAARLAVWMPAGVLTILALVMLLD
+AAALAPGEPVDGTRVAHALIAAAVTVVVHLLAGRRTLVSIAAGTLAYVLLVNLA
+>2_1969
+MTDAAYLVAVAVVAGAVTFALRALPFALLRPLRESVLAARLAVWMPAGVLTILAVVMLLD
+AAALAPGAPVDPRRVAHALIAAVVTVAVHLLGGRRTLLSIAAGTLAYVLLVNLA
+>3_1867
+MIDGVVHPGYIVAAALVAGGVTFLLRALPFVLLRPLRESRLVARLAVWMPAGILTILAVV
+MVLDSAALAPGDPVDWPRVGCTLAAGAVTVLVHLLGGRRTLLSIGAGTLAYVLLVNLAL
+>4_843
+MTGAAYLVAAAVVAGLVTFCLRALPFALLQPLRESVLAARLAVWMPAGVLTILALVMLLD
+AAALAPGEPVDGARVAHALIAAAVTVVVHLLAGRRTLVSIAAGTLAYVLLVNLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000812.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000812.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb393bd729959b3c2aa857244cf04fc0463f5a73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000812.fa
@@ -0,0 +1,30 @@
+>0_906
+MLILLPPSEGKTAPRSGAPLDLDALALADDAAVTGARADLLTRLAAVSAAPDALAALGVG
+ASLTGEVEANTRLASAPAAPGHRVFTGVLFDALDHASLSAAAKRRARASVLVFSALFGAT
+ALADRIPAFRLPVGAKLPGLPGLAAHWRPVLTPALDALAARDGGPVVDCRSGGYAAQWRA
+PAERTLAVDVFQLRDGERTVVSHFAKHTRGLVARALLEAGARETSTLERVADVVARAGDG
+HGWEVELARPSGAKPGALRVILPEG
+>1_634
+MLILLPPSEGKTAPRSGAPLDLDSLALADDAAVTGARADLLTRLAAVSAAPDALTTLGVG
+ASLAGEVEANTRLAVAPAAPGHRVFTGVLFDALDHASLSAAAKRRARLSVLVFSALFGAT
+ALADRIPAFRLPVGAKLPGLPGLAAHWRPVLTPALDALAARDGGPVVDCRSGGYAAQWRA
+PAEQTLAVDVFQLRDGERTVVSHFAKHTRGLVARALLEAGARETSTLDRVADVVARAGDG
+PGWEVELARPSGGKPGALRVILPEG
+>2_1957
+MLILLPPSEGKTAPRSGAPLRLEDLALAEHDAVTAARRDLLARLAEASAAPDALETLGVG
+ASLAGEVAANTSLATAPAAPGHRVFTGVLFDALDHASLSPGAKRRARDAVLVFSALFGAT
+SLADRIPAHRLSVGARLPGLPGLAAHWRPVLAPALDAVAQADGGPIVDCRSGGYAAMWKA
+PAERTATVDVFQLRGGEPTVVSHFAKHTRGLVARALLEAGARATGALDRAAEVVAAAGAG
+DVEGRRWDVELVAPSGAKPGSLRVVLPEA
+>3_1853
+MLILLPPSEGKTGPRSGRPLDLSSLTLADDDAVTAARAELLPRLAEASARPDALDILGVG
+ASLADEVAANTRLATAPSAPARKVYTGVLFEALDLTSLSPAAKRRAASDVLVFSALFGAT
+TPGDRIPAYRLPVGARLPGMPGLAAWWRPRLAPALDGYAEARGGVVVDCRSGGYAAQWKA
+PAERSLAVDVFQLRAGRRTVVSHFAKHTRGLVARALLEAGSRAAGTPATAADVVARAGDG
+GVPGQRWEVELVPPTGRKAGSLQVILPEE
+>4_855
+MLILLPPSEGKTAPRSGAPLDLESLALADDAAVTGARADLLTRLAAVSAAPDALTALGVG
+ASLAGEVEANTCLASAPAAPGHRVFTGVLFDALDHVSLSSAAKRRARASVLVFSALFGAT
+ALADRIPAFRLSVGAKLPGLPGLAAHWRPVLTPALDALAARDGGPVVDCRSGGYAAQWRA
+PAERTLAVDVFQLRDGERTVVSHFAKHTRGLVARALLEAGARETSTLERVADVVARAGDG
+HGWEVELARPSGAKPGALRVILPEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000813.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000813.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e6d4b801a528ced7c3b9d749640c6500b284d0bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000813.fa
@@ -0,0 +1,14 @@
+>0_907
+MTAMNVFGVVYPFVLLVIAAAVWLGIRSSGRERTHASAVEQRLRERTFTGQDRVTLEWPR
+DRRRPSLAKVVSIGESYGYRLLDKREREHVVELEFERILDDEGF
+>1_635
+MTAMNVFGVVYPFVLLVIAAAVWLGVRSSGRERTHASALEHRLRERTFTGQDRVTLEWPR
+DRRHPSLAKVVSIGESYGYRLLDKREREHVVELEFERILDDEGF
+>2_1955
+MTLEWPRDRRRPTPAKVVAIAESYGYRLLEKRERDHVIELDFERIRDDEGF
+>3_1852
+MQTIPVMGWVFPVVLLVIAAAFWLGVRSSGGARGDSDLERRLRERTFTGAPRARLEWPRD
+RRRPTLAQLVRIGASHGYRLVSRTEAEHVYILDFQRVEDDDL
+>4_856
+MTAMNVFGVVYPFVLLVIAAAVWLGIRSSGRERTHASAVEQRLRERTFTGQDRVTLEWPR
+DRRRPSLAKVVSIGESYGYRLLDKREREHVVELEFERILDDEGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000819.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000819.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a48990a05b49fc54cb0b117cc6ef5e24181b7612
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000819.fa
@@ -0,0 +1,55 @@
+>0_924
+MTSHPRSPAPSRPSGRWVGLLVGLTVVAAAVGVLTKQWCRVNGWAAPGVHAHMCYSDFAQ
+LFPTRGLSDGHFPFYTPLPPEQWMEYPALLAVVAGVTMWLVPASGDLHERTVTYFDVNAI
+GVVLCWIVLVVATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAGR
+PTLAGLLIGLGTATKLYPLFFFGAIFVLALRTGRWAGFVKAALAGAAAWLAVNLPFMLTA
+FDQWSRFYTFSGDRAVSFSSTWLALAWTGWSGETFTTLQNGLFLVCCVGIAYLALAARHR
+PRMAQLCFLIVASFILWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWME
+SARITSDGAFAGGAWWITAWYASGIVAHIVALVWLMTTVVKDILDPVRDPVRRTALDQGA
+PEIAPGVAEDPHAGVFTGARDRLLLPPAGLGLQPLGESAGR
+>1_646
+MTSHPRSPAPSRPSGRWVGLLVGLTVVAAAVGVLTKQWCRVNGWAAPGVHAHMCYSDFAQ
+LFPTRGLSDGHFPFYTPLPPEQWMEYPALLAVVAGVTMWLVPASGDLHERTVTYFDVNAI
+GVVLCWIVLVVATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAGR
+PTLAGLLIGLGTATKLYPLFFFGAIFVLALRTGRWAGFVKAALAGAAAWLAVNLPFMLTA
+FDQWSRFYTFSGDRAVSFSSTWLALAWTGWSGETFTTLQNGLFLVCCVGIAYLALAARHR
+PRMAQLCFLIVASFILWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWME
+SARITSDGAFAGGAWWITAWYASGIVAHIVALVWLMTTVVKDILDPVRDPVRRTALDQGA
+PEIAPGVAEDPHAGVFTGAPDRLLLPPAGRGLQPLGGSADR
+>2_1888
+MRRAGLAPTPAPPGLPERETAPPEPAVAVRQGTWAAVLIMVGSWGVGWLPMTPDSVFSGS
+TLLNPLRVNLPGVLASTLLLASGSLLLVRAWLVLGRSLRGRWEGHGRLVSRAAWQWSAPL
+MLALPIFSRDVFSYLQQGRLFALGLDPYTQGVSALPGWFMQGADSIWAESPSPYGPLFLL
+CAEAIWRVTGGQIELSVTAFRLLALAGLALCLWAVPRLAEAAGRCGAWAAWVCVANPLFL
+LYMIAGVHNDALMSGLMLAGIVLMVRVPRRRLHALWGIVLIALSVAIKPLTALVLPFVGL
+LLPTGWDRFRRADPGLRRRDRLGPWITTAAIALAVLTILGAGSRLWFGWVPAMLTSGDAA
+FPYAPVGVLGLLLGAAADGLAGLPARAVAGGFYTLMTLAALGFGAWLALRRRAPEPVSAA
+AAVLFVAVVTAPIVQPWYLLWVLPLLACALRPLPWGADHPRWLGWVTALAVLLLTGVGVV
+DQISVAQWLPVAAVRALTAVVVLAGIAWIVVRDPATAPLFPGRRRPPREVVEPREAVGPR
+EPGAPPGPPTAAPDAEFPPDALAADPDRRRRPAPDRRPARPGETVTSQPRRPADTRTGSA
+AAPPSPAALRPGPRWIGILVGLTAVAAVVGLLTKQWCRVNGWAAPGVHVHMCYSDFAQLF
+PTRGLSDGYFPFYTPLPPEQWMEYPALLAVVAGVTMWLVPDSGDLHERTVMYFDVNALGV
+VLCWVVLVIATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAHRPT
+LAGLLIGLGTALKLYPLFFFGAILVLALRTGRWRGLITSLAAGVAAWLAVNVPFMLTAFD
+QWSRFYTFSGDRAVSFSSTWLSLAWTGWSGETFSTLQNGMFALFCAGIAWLGLSARHRPR
+MAQLCFLIVASFLLWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWMESA
+RITSGGAFADGAWWITAWYASGIVAHIVALVWLMVTVVKDILDPSRDPVRRTALAQGAPT
+IAPGVAEDPHAGVYAGAPDRLVLPPAGRGLQPAEGATSGS
+>3_1838
+MSSHPRAADAAPRPAAGLRPAGRPSPRWIGVLIAVTAAAAVVGLLTKQWCRLNGWATPGV
+HVHMCYSDFAQLFPTRGLSDGYFPFYTPLPEEQWMEYPALLAVVAGASSWLVPSTGTLAE
+RTVTYFDVNAAGVVLCWMAVVVATAFTARGRSKDALLVAVAPGIILTSMLNWDLWAVMLA
+ALALWAWSEDRPVLSGLLLGLGAAMKLYPLFFFGALLVLALRTGRWRGFLGALAAGAAAW
+LAVNVPFMLTAFDQWSRFYTFSGDREVSFSSMWLAFTWTGLSGSAFSVISNGLFALCCVG
+VAYLGLSSRHRPRLAQLCLLIVAAFLLLGKVYSPQFVMWLIPLVVLATPRRKQFWIWQAA
+EFFHWAGVWMESARITSGGEFGGTWVTVWYASGIVLHMATLIWICVTVIRDIRDPERDPV
+RRSALEQGVEPLAPGVAEDPNAGVFTGAADRFLLPPAGHGLQPTR
+>4_870
+MTSHPRSPAPTRPSARWVGLLVGLTVVAAAVGVLTKQWCRVNGWAAPGVHAHMCYSDFAQ
+LFPTRGLSDGHFPFYTPLPPEQWMEYPALLAVVAGVTMWFVPASGDLHERTVTYFDVNAI
+GVVLCWIVLVVATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAGR
+PTLAGMLIGLGTATKLYPLFFFGAIFVLALRTGRWAGFVKAAVAGAAAWLAVNLPFMLTA
+FDQWSRFYTFSGDRAVSFSSTWLALAWTGWSGETFTTLQNGLFLVCCVGIAYLALAARHR
+PRMAQLCFLIVASFILWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWME
+SARITSDGAFAGGAWWITAWYASGIVAHVVALVWLMTTVVKDVLDPVRDPVRRTALDQGA
+PEIAPGVAEDPHAGVFTGARDRLLLPPAGRGLQPLGESAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000821.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000821.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3df326ebaf80866bc6a27fe270fb213180808f31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000821.fa
@@ -0,0 +1,24 @@
+>0_926
+MQDLITVRGFVATDPATRHTASGAAVTGFRLATTERRFDRETAEWVDAHTNWYSISAFGQ
+LGSNTAQSVKKGNPVIVTGRLRVRDWSSGERSGTSVDVVADAVGLDLGFGSAAFQRSQRA
+AVPRPESAPRDDDASGGRAGAVGDGFSAGLPDGFQGGDAPASPGPDESDAGAPGREPAAA
+GVA
+>1_648
+MQDLITVRGFVATDPATRHTASGAAVTGFRLATTERRFDREAAEWVDAHTNWYSISAFGQ
+LGSNTAQSVKKGNPVIVTGRLRVRDWSSGERSGTSVDVVADAVGLDLGFGSAAFQRSQRA
+AVPRPESAPRDDASGGRAGAVGDGFNVGLPDGFQGGDAPASPGPGEPDAEAPDREPAAAG
+VA
+>2_1886
+MQDIITVRGFVATDPVTRTTASGATVAGFRLATTERRFDREAGAWVDAHTNWYSVSAFGQ
+LGSNTAQSVRKGNPVIVTGRLRVRDWSTEERSGTTVDVVADAVGLDLAFGSAAFQRSQRA
+ASARPEGADEQDGQGQAGAVASAGPAEADGTAAGTGDGYVTELPPALRGGDAPATPPPPS
+SEEGDEADEADDDAHGVRALCGGVSAA
+>3_1836
+MQDTVTIRGFVATDPTTRHTASGAAVVGFRLASTERRFDRDAGMWVDAHTNWYSVSAFGQ
+LGSNTAQSVKKGNPVIVTGRLRVRDWSTEDRSGTSVDVVADAVGLDLAYGASAFMRNGRR
+ADAVERADAPVDADAGASLDAAPADGFGLALPPAFTGGDAPASSAEDAHEAAGALAVA
+>4_872
+MQDLITVRGFVATDPATRHTASGAAVTGFRLATTERRFDRETAEWVDAHTNWYSISAFGQ
+LGSNTAQSVKKGNPVIVTGRLRVRDWSSGDRSGTSVDVVADAVGLDLGFGSAAFQRSQRA
+AVPRPESAPRDDASGGRAGAVGDGFSAGLPDGFQGGDAPASPGPDESDAGAPEREPAAAG
+VA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000822.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000822.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fed3f96db98a9d9f0337bea2cdd183b84339e5fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000822.fa
@@ -0,0 +1,55 @@
+>0_927
+MAEFIYTMVKARKKVGDKLILDDVTMSFYPGAKIGMVGPNGAGKSTILKIMAGLDEPSNG
+EARLSPGYSVGILMQEPKLDESKTVLENVQEGVGEIYGKIQRYNQISEEMANPDADFDAL
+MGEMGELQSAIDAADAWDIDSQLEQAMDALRTPPGDEPVTNLSGGEKRRVALCKLLLEKP
+DLLLLDEPTNHLDAESVLWLEQHLASYPGAVIAVTHDRYFLDHVAEWIAEVDRGRLYPYE
+GNYSTYLETKRARLEVQGKKDAKLAKRLAEELDWVRSNTKGRQAKSKARLARYEEMAAEA
+EKTRKLDFEEIQIPPGPRLGTVVIEAKDLKKGFGDRVLIDGLSFSLPRNGIVGVIGPNGV
+GKTTLFKTIVGLEPLDGGELKIGETVKISYVDQSRSNIDPEKSLWEVVSDGLDYIKVGNV
+EMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLLLDEPTNDLDVETL
+TSLENALLEFPGCAVVVSHDRWFLDRVATHMLAYEGTAEDPANWYWYEGNFESYEANKVD
+RLGPEAARPHRMTHRKLTRD
+>1_649
+MAEFIYTMVKARKKVGDKLILDDVTMSFYPGAKIGMVGPNGAGKSTILKIMAGLDEPSNG
+EARLSPGYSVGILMQEPKLDESKTVLENVQEGVGEIYGKIQRYNQISEEMANPDADFDAL
+MEEMGELQSAIDAADAWDIDSQLEQAMDALRTPPGDEPVTNLSGGEKRRVALCKLLLEKP
+DLLLLDEPTNHLDAESVLWLEQHLASYPGAVIAVTHDRYFLDHVAEWIAEVDRGRLYPYE
+GNYSTYLETKRARLEVQGKKDAKLAKRLAEELDWVRSNTKGRQAKSKARLARYEEMAAEA
+EKTRKLDFEEIQIPPGPRLGTVVIEAKDLKKGFGDRVLIDGLSFSLPRNGIVGVIGPNGV
+GKTTLFKTIVGLEPLDGGELKIGETVKISYVDQSRSNIDPEKSLWEVVSDGLDYIKVGNV
+EMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLLLDEPTNDLDVETL
+TSLENALLEFPGCAVVVSHDRWFLDRVATHMLAYEGTAEDPANWYWYEGNFESYEANKVD
+RLGPEAARPHRMTHRKLTRD
+>2_1885
+MAEFIYTMVKARKKVGDKLILDDVTMSFYPGAKIGMVGPNGAGKSTILKIMAGLDEPSNG
+EARLSPEYTVGILMQEPKLDESKTVLENVQEGVGEIYGKIQRYNQISEEMASPDADFDAL
+MEEMGELQTAIDAADAWDIDSQLEQAMDALRTPPGDEPVTNLSGGEKRRVALCKLLLEKP
+DLLLLDEPTNHLDAESVLWLEQHLAAYPGAVIAVTHDRYFLDHVAEWIAEVDRGRLHAYE
+GNYSTYLETKRARLEVQGKKDAKLAKRLAEELDWVRSNTKGRQAKSKARLARYEEMAAEA
+EKTRKLDFEEIQIPPGPRLGTVVIEAKDLKKGFGDRVLIEGLSFSLPRNGIVGVIGPNGV
+GKSTLFKTIVGLEPLDGGELKIGETVKISYVDQSRANIDPEKSLWEVVSDGLDYIKVGQV
+EMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLLLDEPTNDLDVETL
+TSLENALLEFPGCAVVVSHDRWFLDRVATHMLAYEGTAEDPANWYWYEGNFESYEANKVE
+RLGPEAARPHRVTHRKLTRD
+>3_1835
+MSRFPPPPTSLERMAEFIYTMVKARKKVGDKLILDDVTMSFFPGAKIGMVGPNGAGKSTI
+LKIMAGLDEPSNGEARLSPGYSVGILLQEPKLDEDKTVLENVQQGVGEIYGKIQRYNAIS
+EEMADPDADFDALMEEMGQLQTEIDAADAWDLDSQLDQAMDALRCPPPEAQVSHLSGGEK
+RRVALCALLLSKPDLLLLDEPTNHLDAESVLWLEQHLSSYPGAVVAVTHDRYFLDHVAGW
+ICEVDRGRLYPYEGNYSTYLETKRQRLEIQGKKDAKLAKRLAEELDWVRSNAKGRQAKSK
+ARLARYEEMAAEAEKTRKLDFEEIQIPPGPRLGNVVIEATNLQKGFDGRTLIDGLSFSLP
+RNGIVGVIGPNGVGKTTLFKTIVGLEPLDGGDLKIGETVKISYVDQNRTNIDPEKSLWEV
+VSDGLDYIKVGNVEMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLL
+LDEPTNDLDVETLTSLENALLEFPGCAVVVSHDRWFLDRTATHMLAYEGTEENPANWYWY
+EGNFESYEANKVERLGPEAARPHRVTHRKLTRD
+>4_873
+MAEFIYTMVKARKKVGDKLILDDVTMSFYPGAKIGMVGPNGAGKSTILKIMAGLDEPSNG
+EARLSPGYSVGILMQEPKLDESKTVLENVQEGVGEIYGKIQRYNQISEEMANPDADFDAL
+MEEMGELQSAIDAADAWDIDSQLEQAMDALRTPPGDEPVTNLSGGEKRRVALCKLLLEKP
+DLLLLDEPTNHLDAESVLWLEQHLASYPGAVIAVTHDRYFLDHVAEWIAEVDRGRLYPYE
+GNYSTYLETKRARLEVQGKKDAKLAKRLADELDWVRSNTKGRQAKSKARLARYEEMAAEA
+EKTRKLDFEEIQIPPGPRLGTVVIEAKDLKKGFGDRVLIDGLSFSLPRNGIVGVIGPNGV
+GKTTLFKTIVGLEPLDGGELKIGETVKISYVDQSRSNIDPEKSLWEVVSDGLDYIKVGNV
+EMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLLLDEPTNDLDVETL
+TSLENALLEFPGCAVVVSHDRWFLDRVATHMLAYEGTAEDPANWYWYEGNFESYEANKVD
+RLGPEAARPHRMTHRKLTRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000824.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000824.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21f59cc7058ca6941ebd5bd54765b0af2ae9f3e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000824.fa
@@ -0,0 +1,37 @@
+>0_930
+MKHTFSLRTEWTGDRGSGTSGVRDYDRSVVIQDAAVGEIQASAARPFRGDDSKWNPETLL
+LGALAECHVLSYLHVAATSGVVVTGMTCGVEGELEVDGDGAGRFTAITLRPEVTLQDEAD
+RERAEALHAEAHRLCFIANSLSAPVAVEPVRPEALPTGAPTLPDHSARLGAPLAVLRPRV
+AKGPSRVTGLAERPTEVEPVMQEGTPAPVEQVRARDAAAGPAGATPGTPAAPGQAASFYD
+AVGGRPTFDRLTAEFYARVREDEILAPMYPQDDFEGAQRRLLMFLEQYWGGPRTYSEERG
+HPRLRMRHAPYRIDPAARNAWLRHMRAAVDTLELSPLHEAELWDYLERAAHSLQNSA
+>1_652
+MKHTFSLRTEWTGDRGSGTSGVRDYDRSVVIQDAAVGEIQASAARPFRGDDSKWNPETLL
+LGALAECHVLSYLHVAATSGVVVTGMTCGVEGELEVDGDGAGRFTAITLRPEVTLQDEAD
+RERAEALHAEAHRLCFIANSLSAPVAVEPVRPEALPTGTSTLPDHSARLGAPLAVLRPRV
+AKGPSRVTGLAERPTEVEPVMQEGTPAPVEQVRARDAAAGPTGATPGTPAVPGQATSFYD
+AVGGRPTFDRLTAEFYARVREDEILAPMYPQDDFEGAQRRLLMFLEQYWGGPRTYSEERG
+HPRLRMRHAPYRIDPAARDAWLRHMRAAVDTLELSPLHEAELWDYLERAAHSLQNSA
+>2_1881
+MKHTFALRTEWTGNRGTGTSGVRDYDRSVVIQDAAVGEIHASAARPFRGDDSKWNPETLL
+LGALAECHVLSYLHVAATSGLVVTGMACAAEGVLEVDGDGAGRFAAVTLRPEVALQDEAD
+RERADALHAEAHRLCFIANSLSAPVSVEPAVAGSGAAASGGPALPDHSSRLGAPLAVLRP
+RVAKRPSQVTGLAERPTEVEPVMKAGAPAPVDQMQARDAAAGRAASPATPAPAAETAAPG
+QAASFYEAVGGRETFDRLTAEFYARVREDELLSPMYPQDDFEGAQRRLLMFLEQYWGGPR
+TYSEERGHPRLRMRHAPYRIDPAARDAWLTHMRAAVDTLGLSPLHEAELWDYLERAAHSL
+QNSA
+>3_1828
+MKHTFSLRAEWTGDRGTGTTGVRDFDRSVVIQESEVGEIHASAARPFRGDAAKWNPETLL
+LGALAECHVLSYLHAAATGGLVVTGMTCAAEGTLEVDSDGAGRFASITLRPEVALRDEAD
+RARADELHAEAHRMCFIANSISAPITVEAGPGSSPTRGDGAALPDHSARLGAPLAVLRPR
+VANRPTRVTGLADRPTEAEPVVRADAPSGAEQARARDEATARGERPPSATPIATPAPGAT
+PAASPATAAPGQATSFYEAVGGHPTFEKLVHVFYQGVREDPLLAPMYPHQDWDGAEERLR
+MFLEQYWGGPRTYSERRGHPRLRMRHMPFTVDPAARDAWLRHMRAAVDAVELSPLHEAEL
+WDYLERAAHSLQNSA
+>4_876
+MKHTFSLRTEWTGDRGSGTSGVRDYDRSVVIQDAAVGEIQASAARPFRGDDSKWNPETLL
+LGALAECHVLSYLHVAATSGVVVTGMTCGVEGELEVDGDGAGRFIAITLRPEVTLQDEAD
+RERAEALHAEAHRLCFIANSLSAPVTVEPVRPEALPTGTPTLPDHSARLGAPLAVLRPRV
+AKGPSRVTGLAERPTEVEPVMQEGTPAPVEQVRARDAAAGPAGATPGTPAAPGQATSFYD
+AVGGRPTFDRLTAEFYARVREDEILAPMYPQDDFEGAQRRLLMFLEQYWGGPRTYSEERG
+HPRLRMRHASYRIDPAARDAWLRHMRAAVDTLELSPLHEAELWDYLERAAHSLQNSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000827.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000827.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf20b688ffe9810924136c83d997747c3016c42a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000827.fa
@@ -0,0 +1,31 @@
+>0_936
+MMHGSRPALRRAASALAGRRPLSLRGATVLVTGGASGIGRLIALGAARRGAGRVVVWDLD
+LQGAEAVAAEIRSQGADAQAERVDVTDAAAVEAAAARAGEVDVAVNNAGVVTGVRLEDAT
+EEGIRRTFEVNALAPYWLTRAVLPGMRARDRGAVVTVASAAGLVGVARQTDYSATKHAAV
+GFAESLAAELRKDGSRVTSLAVCPFYIDTGMFAGVRSRVPWLLPVLDPRHVAQEVLDAVE
+AGRTRLLLPRAVGLIAPLRALPAPVFDRAMDVLGVNATMDGFTGRRSRLFAGRETAR
+>1_659
+MHGSRPALRRAASALAGRRPLPLHGATVLVTGGASGIGRLIALGAAHRGAGRVVVWDLDL
+QGVEAVAAEIRSQGADARAERVDVTDAAAVEAAAAGAGEVDVAVNNAGVVTGAPLEDATE
+EGIRRTFEVNALAPYWLTRAVLPGMRARDRGAVVTVASAAGLVGVARQTDYSATKHAAVG
+FAESLAAELRKDGSRVTSLAVCPFYIDTGMFAGVRSRVPWLLPVLDPHHVAQEVLDAVEA
+GRTRLLLPRAVGLIAPLRALPAPVFDRAMDVLGVNATMDGFTGRRSRLFAGRETAR
+>2_1877
+MPRSRTPRPALRALAGALPRRRRLPLRGTAVLITGGASGIGRLMALGAARRGAARVVVWD
+LDLSAAEAVAAEARALGAEAVAERVDVTDAAAVEAAAARAGAVDVAVNNAGVVTGARLED
+ATEEGIRRTFEVNALAPYWLTRAVLPGMKARDRGAVVVIASAAGLVGVARQTDYSATKHA
+AVGFAESLSAELRKDGSAVTALAVCPFYIDTGMFDGVRSRIPWLLPVLRQEEVAEQVLDA
+VEAGRTRLPLPRAVGLLAPLRALPTPVFDRAMDVMGVNDTMDGFTGRRPAVDVPAPDPRV
+FAPDGAAR
+>3_1823
+MTPILNRLRGRRPLPLAGRAVLITGAGSGIGRLMALEAARRGAAVVHVWDRDDAAARTVA
+AEVAALGARGEAACVDVTDTAAVEAAAARAEAVDVLVNNAGVVTGTPLLETTEEGIRRTF
+EVNALAGYWTTRALLPGMLERGRGAVVTVASAAGLVGVARQTDYSASKHAAVGFAESLRA
+ELRRADAPVTSLVVCPFYISTGMFAGVRTKVPALLPILEPEAVAAQVVDAVEAGRERLVL
+PPAVQLIAPLRALPVPAFDRVMDVLGVNRAMDGFTGRR
+>4_879
+MMHGSRPALRRAASALAGRRPLSLRGATVLVTGGASGIGRLIALGAARRGAGRVVVWDLD
+LQGAEAVAAEIRSQGADAQAERVDVTDAAAVEAAAARAGEVDVAVNNAGVVTGVRLEDAT
+EEGIRRTFEVNALAPYWLTRAVLPGMRARDRGAVVTVASAAGLVGVARQTDYSATKHAAV
+GFAESLAAELRKDGSRVTSLAVCPFYIDTGMFAGVRSRVPWLLPVLDPRHVAQEVLDAVE
+AGRTRLLLPRAVGLIAPLRALPAPVFDLAMDVLGVNATMDGFTGRRSRLFAGRETAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000832.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000832.fa
new file mode 100644
index 0000000000000000000000000000000000000000..970d06401ff7c648e26aa6439d77c7d2eec6c50a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000832.fa
@@ -0,0 +1,25 @@
+>0_941
+MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL
+ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHDAD
+ILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIFD
+GAVALADFPYFYEIKRARTTDPQFD
+>1_664
+MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL
+ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHDAD
+ILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIFD
+GAVALADFPYFYEIKRARTTDPQFD
+>2_1872
+MSENTQPVVDFYFDPTCPFAWITSRWILEVEKVRDIQVKFHQMSLYMLNEGRDLPEDYRR
+STDRGLIPGRGTQHVGAEHPERLAEWYTALGTRIHNEGQKDYEAALTGAAVDLGLDPAPI
+LAATETDAEDERLREKQRAAEELVGNDVGTPVVSFNGTAFFGPVLTRIPRGEEAGRIFDG
+AVALAEYPYFYEIKRARTTDPQFD
+>3_1818
+MSENTAPVVDFYFDPTCPFAWITSRWILEVEKVRDLSVTFHQMSLYMLNEGRELPEDYRR
+HTDRGLMPGRATLHVGEHHPELLSDWYTAVGTRIHNEGNQDYEAVVTGAAAELGLDAAPI
+LEATRTDAADDDLRAKQRAAEELVGNDVGTPVVSFDGTAFFGPVMTRIPRGEEAGEIFDA
+AVRLAQFPYFYEIKRARTTDPQFD
+>4_884
+MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL
+ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHDAD
+ILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIFD
+GAVALADFPYFYEIKRARTTDPQFD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000833.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000833.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4d876327fd0d6b7fa276da72b04a205d5329c82d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000833.fa
@@ -0,0 +1,20 @@
+>0_942
+MRPTPDPAPAGRRACDSSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG
+VAELAVAGLLAVPRTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV
+PLIRAAGRVARS
+>1_665
+MRPTPDPAPAGRRACDSSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG
+VAELAVAGLLAVPRTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV
+PLIRAAGRVARS
+>2_1870
+MRRASAPRTDTAGATGTGARRMAAALAGMGVLHFARPKPFDGLIPPALPGPARAWTVGSG
+VAELAVAGMLAAPRTRRAGGRAAQALFLGVWPGNAWMAWRWRGRSWPWRALALGRLPLQV
+PMIRAAGRIARG
+>3_1817
+MKPTPDPAPAGRRASDGSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG
+VAELAVAGLLAVPHTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV
+PLIRAAGRVARR
+>4_885
+MRPTPDPAPAGRRACDSSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG
+VAELAVAGLLAVPRTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV
+PLIRAAGRVARS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000834.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000834.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b7c87b00abb33807775c8046c7458f7032149df8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000834.fa
@@ -0,0 +1,80 @@
+>0_943
+MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ
+VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY
+YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL
+SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP
+GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV
+FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR
+QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI
+RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL
+DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ
+IVGRWSRDEAFFNNVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP
+DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA
+AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLTRLAATVEQATRAFEAYDYARALNVTE
+QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW
+RAGSVHTAAWPGAADEVASLSFAASAGDAEVLPTVAQVLGGIRKAKSEAKVKQRTEVRSA
+VVTGPADWLEKLRGGLADLKAAGNIADLSLTQGEAGESAPLTVSDVQLAPVDDD
+>1_666
+MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ
+VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY
+YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL
+SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP
+GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV
+FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR
+QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI
+RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL
+DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ
+IVGRWSRDEAFFNNVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP
+DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA
+AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLTRLAATVEQATRAFEAYDYARALNVTE
+QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW
+RAGSVHTAAWPGAADEVAALSFAASAGDAEVLPTVAQVLGGVRKAKSEAKVKQRTEVRSA
+VVTGPTEWLEKLRGGLADLKAAGNIADLSLTQGEAGESAPLTVSDVQLAPVEDD
+>2_1869
+MAENTQGTDTPIDASTASTPAAGAVAVPDKPGLEGLEEKLTARWAQEGTYAFDPRTTREQ
+VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMTGKNVFYPMGWDDNGLPTERRVQNY
+YGVRCDPTKPYIEGYTPPAQPAKNQRDWDVVSRKNFIELCEELAVEDEKVFEDLFTRLGL
+SVDWSMTYRTIDDVSRAVSQRAFLRNVAAGDAYLSEAPTMWDVTFRTAVAQAELEDREVP
+GAYHRYPFTAADGTQVFIETTRPELLASCSALVAHPEDERYQPLFGTMVRSPLFDVEVEV
+KAHELAKPDKGSGIAMVCTFGDLTDVTWWRELQLPTRTLIGRDGRFAAETPEWISSEAGR
+AFYAESIAGKTVFSAKEAVVTALTEAGLMDGEPKKVQHAVNFYEKGDKPLEIVTSRQWYI
+RNGGRDADRREQLIARGRELDWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYRL
+DAEGEPVYDEPIVPEDAALPVDPVAETAPGFTEDQRDQPGGFTGDPDVLDTWATSSLTPQ
+IVGRWSRDEEFFANVFPFDLRPQGHDIIRTWLFSTVVRADALNGSVPWTDTALSGWILDP
+DRKKMSKSKGNVVVPTDILEEFGSDAVRYWASSARLGADTAYEVAQMKIGRRLAIKLLNA
+AKFVLNLGATRDAVVRTPDDAARVTNALDASLLARLATTVEQATAAFDAYDYARALNVTE
+SFFWQFTDDYVELIKDRAYGGHGEAEQASVVAALATTLDSLLRLLAPFQPFATEEVWSWW
+RTGSVHRAPWPGLESEAAGLRAAAEGGDPQVLAVVAQVLGRVRKAKSEAKVKQRTQVRTA
+TVRAAAAQLDALRGGLADLKGAGNVADVTLTEADGELEVTDIELAPAEEA
+>3_1815
+MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ
+VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY
+YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL
+SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP
+GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV
+FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR
+QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI
+RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL
+DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ
+IVGRWSRDDAFFSSVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP
+DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA
+AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLARLAVSVEQATRAFEAYDYARALNVTE
+QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW
+RAGSVHTAAWPGAADEVASLSFAASSGDAEVLPTVAQVLGGVRKAKSEAKVKQRTEVRSA
+VVTGPAEWLEKLRGGLADLKAAGNIADLSLTQGEAGEAAPLTVSDVQLAPVEDD
+>4_886
+MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ
+VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY
+YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL
+SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP
+GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV
+FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR
+QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI
+RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL
+DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ
+IVGRWSRDEAFFNNVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP
+DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA
+AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLARLAATVEQATRAFEAYDYARALNVTE
+QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW
+RAGSVHTAAWPGAADEVAALSFAASGGDAEVLPTVAQVLGGVRKAKSEAKVKQRTEVRSA
+VVTGPADWLEKLRGGLADLKAAGNIADLSLTQGEAGESAPLTVSDVQLAPAEDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000835.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000835.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4046f315c8f30e41eb921342238ff461f6ef58d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000835.fa
@@ -0,0 +1,30 @@
+>0_944
+MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG
+VSGDVVPAALDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGDGDRADWEWMYR
+VNVLGTLTMCQAFLPMLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE
+EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVMRPVAQAAQHKVIRR
+>1_667
+MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG
+VSGDVVPAALDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGVGDRADWEWMYR
+VNVLGTLTMCQAFLPMLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE
+EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVMRPVAQAAQHKVIRR
+>2_1868
+MDVSHTTENQSPRAAVVTGATTGIGRATALELARRGWRVYAVGRRAERLDALAAQAREEA
+VPGEVVPAPLDVTDEAAVAGLVARVDTDGGIDTLVNIAGGARGTDFVGAGNREDWEWMYR
+ANVLGTLAMCQAFLPGLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTAALRLE
+EAEHNVRVIEVLPGMVHTEEFSLMRLGGDAAAAEKVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVIRPVAQAAQHKVIRR
+>3_1814
+MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG
+VSGDVVPAPLDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGDGDRADWEWMYR
+VNVLGTLTMCQAFLPMLRTHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE
+EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVMRPVAQAAQHKVIRR
+>4_887
+MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG
+VSGDVVPAALDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGDGDRADWEWMYR
+VNVLGTLTMCQAFLPMLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE
+EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVMRPVAQAAQHKVIRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000836.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000836.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8fa1c5aaa10724f2c3d31d5b451af239c1953109
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000836.fa
@@ -0,0 +1,30 @@
+>0_945
+MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER
+VARAVPAGEAATSDVILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD
+AVARVHAAGRRAVVAAHLLAPGYFHDRLGEAGADAVTDPLLPHPLVARIALDRLRSALVE
+APRGAAGGR
+>1_668
+MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER
+VAQAVPAGEAATSDIILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD
+AVSRVRAAGRRAVVAAHLLAPGHFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE
+APRGAAGGR
+>2_1867
+MSAPVLHVIACAHGTHDAAGRVVIDGLRADLAALLDAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPDTIAAAPLAGAGDDVEPRLVAVLAER
+VAQAVPAGEAATSEVILAAAGTRAADGQAQVHALAAALARATGLPVTAAFGAAATPPVPD
+AVSRVRATGRRAVAAAHLLAPGYFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE
+APRGAAGGR
+>3_1813
+MSAPVLHVIACAHGTHDAAGRVVIDGLRADLAALLDAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPDTIAAAPLAGAEDDVEPRLVTVLAER
+VAQAVPAGEAATSDIILAAAGTRAADGQAQVHALAAALARATGLPVTAAFGAAATPRVPD
+AVARVRATGRRAVVAAHLLAPGYFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE
+APRGAAGGR
+>4_888
+MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER
+VARAVPAGEAATSDVILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD
+AVARVHAAGRRAVVAAHLLAPGYFHDRLGEAGADAVTDPLLPHPLVARIALDRLRSALVE
+APRGAAGGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000837.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000837.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dba2d92417351570a716a5883a842524880bd929
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000837.fa
@@ -0,0 +1,48 @@
+>0_946
+MTQVNETSRPARTPRRPSAKPHGQWKVDGTAPLNHNEEFKQQDDGLNVRERIEQVYAHEG
+FDSIPSDDLHGRFRWWGLYTQRRQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL
+RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG
+SPVAGIAADEIIDPTPVIREIADRWIGDLEISNLPRKFKTAITGHPSQDVVHEINDVSLI
+GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK
+ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP
+VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS
+VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA
+RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY
+VERVVRRYDEQREPGETFARWAHRVDEEALR
+>1_669
+MTQVNETSRPARTPRRPSAKPHGQWKVDGTTPLNHNEEFKQQDDGLNVRERIEQVYAREG
+FDSIPSDDLHGRFRWWGLYTQRRQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL
+RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG
+SPVAGIAADEIIDPTPVIREIADRWIGDLEVSNLPRKFKTAITGHPSQDVVHEINDVSLI
+GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK
+ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP
+VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS
+VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA
+RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY
+VERLVRRYDEQREPGETFARWAHRVDEEALR
+>2_1866
+MVLDVEGDRVDAVVAGLKELGLDPEPSVFRRSTIACTGLEFCKLAIVDTKDTATAAIAQL
+EERLADLADRLPERLSLHVNGCPNSCARIQTADIGLKGQLLPDDDGGQTPGFQIHLGGGL
+ASVDRAEAGLGRSVRGLKVRADGLVDYVERLVRRYDEQREPGETFARWAHRVDEEALR
+>3_1812
+MTQVNETSRPARTPRRPSAKPHGQWKVDGTAPLNHNEEFKQQDDGLNVRERIEQVYAREG
+FDSIPSDDLHGRFRWWGLYTQRKQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL
+RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG
+SPVAGIAADEIIDPTPVIREIADRWIGDLEVSNLPRKFKTAITGHPSQDVVHEINDVSLI
+GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK
+ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP
+VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS
+VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA
+RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY
+VERLVRRYDEQREPGETFARWAHRVDEEALR
+>4_889
+MTQVNETSRPARTPRRPSAKPHGQWKVDGTAPLNHNEEFKQQDDGLNVRERIEQVYAHEG
+FDSIPSDDLHGRFRWWGLYTQRRQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL
+RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG
+SPVAGIAADEIIDPTPVIREIADRWIGDLEISNLPRKFKTAITGHPSQDVVHEINDVSLI
+GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK
+ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP
+VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS
+VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA
+RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY
+VERVVRRYDEQREPGETFARWAHRVDEEALR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000838.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000838.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a388641085c9cd25fdcc639d9eb11535340566b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000838.fa
@@ -0,0 +1,30 @@
+>0_947
+MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL
+PHLVAQRMPGVDVLFLDTGYHFTETLATRDEVARRLAVTVVDVLPELTVAEQDERHGKDL
+FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA
+PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH
+V
+>1_670
+MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL
+PHLVAQRMPGVDVLFLETGYHFTETLATRDEVARRLDVTVVDVLPELTVAEQDERHGKDL
+FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA
+PWSLDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH
+V
+>2_1865
+MSTVPPTRPTEELERLQALAESGAAELGWDAPAAAVVDWAARHVDLRRAAVACSMADAVL
+PHLVAQRMPGVDVLFLETGYHFTETLATRDEVARRLDVTVVDVLPELTVAEQDERHGKDL
+FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA
+PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWTGTAKTECGIH
+V
+>3_1811
+MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL
+PHLVAQRMPGVDVLFLETGYHFTETLATRDEVARRLDVTVVDVLPELTVAEQDERHGKDL
+FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA
+PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH
+V
+>4_890
+MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL
+PHLVAQRMPGVDVLFLDTGYHFTETLATRDEVARRLAVTVVDVLPELTVAEQDERHGKDL
+FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHSMVKVNPVA
+PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH
+V
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000839.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000839.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b64400070510a56febed6ff6c764aa8f057ad27
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000839.fa
@@ -0,0 +1,35 @@
+>0_948
+MTLTHAPDPGTVSPAGPDVQDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK
+AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR
+NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY
+NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR
+PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA
+AMEDRKKDGYF
+>1_671
+MTLTHAPDPGTVSPAGPDVQDALEAEAIHIVREVVAEFERPAMLFSGGKDSVVMLHLAAK
+AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR
+NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY
+NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR
+PAENEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA
+AMEDRKKDGYF
+>2_1864
+MTLTHAPDPGTVSPAGPDVLDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK
+AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR
+NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY
+NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPPIYYAHEREVFRRDGMWRAVGEHSR
+PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA
+AMEDRKKDGYF
+>3_1810
+MTLTHAPDPGTVSPAGPDVQDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK
+AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR
+NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY
+NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR
+PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA
+AMEDRKKDGYF
+>4_891
+MTLTHAPDPGTVSPAGPDVQDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK
+AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR
+NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY
+NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR
+PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA
+AMEDRKKDGYF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000842.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000842.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68e32483e0f700dbb80055d1352e09a3f1818e90
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000842.fa
@@ -0,0 +1,35 @@
+>0_951
+MRTDTPTLDAPGRAPGAATDDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV
+LLVAIWQAFAWLAGARGEPITGPGDVVGAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV
+GVGLGLLLGQVSVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV
+VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA
+EIIAVGGPMGVGLGTLLHEGRAESDLAVVLCAVLAILAVGVLVELTAFGPAERRMLRRRG
+LLEGSTR
+>1_674
+MRTDTPTLDAPGRAPGAATDDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV
+LLVAIWQAFAWLAGARGEPITGPGDVVGAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV
+GVGLGLVLGQVGVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV
+VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA
+EIIAVGGPMGVGLGTLLHEGRAASDLAVVLCAVLTILAVGVLVELAAFGPVERRMLRRRG
+LLEGSTR
+>2_1861
+MRTDTPTLDAPGRAPGAAADDELRELDSGLDALQAVDSARRTGLAGWDWSRVLLPVAAVV
+LLVAIWQVAAWLAGARGEPITGPGDVLGAFGALWAQGLVQQAVATSVGRAVVGFALAVVA
+GVGLGLLLAQVGVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVILTGAVPAV
+VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA
+EIIAVGAPMGVGLGTLLHQGRTESDLAVVLCAVLAILAVGVLVELTAFGPVERRMLRRQG
+LLEGSTR
+>3_1807
+MRTDTPTLDAPGRAPGAAADDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV
+LLVAIWQVAAWLAAARGEPITGPGDVLRAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV
+GVGLGLLLGQVSVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV
+VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA
+EIIAVGGPMGVGLGTLLHQGRAESDLAVVLCAVLAILAVGVLVELTAFGPVERRMLRRQG
+LLEGSTR
+>4_894
+MRTDTPTLDAPGRAPGAATDDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV
+LLVAIWQAFAWLAGARGEPITGPGDVLGAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV
+GVGLGLVLGQVSVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV
+VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA
+EIIAVGGPMGVGLGTLLHEGRAASDLAVVLCAVLTILAVGVLVELAAFGPVERRMLRRRG
+LLEGSTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000845.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000845.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0ff893aeabe35d59b425311ac415073f29d2a50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000845.fa
@@ -0,0 +1,53 @@
+>0_956
+MRGDAPGTVEEVYRDLLARAPENKMQPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTST
+ARMVEAVLRAYGLRTGRYTSPHLQRVTERISIDGAPVADETFVRVWGEILPIVQTVDAEL
+EAAGEVPLTYFEAVTTLGFAVFADEPVEVVVLEVGLGGVTDATNVADAVVSVVTPISLDH
+TDLLGETEAEIAEEKAGIIKPGGALVSAAQERDAAQVLLEAAQAADVPFRFEGVEFGVLE
+RSLAVGGQQVSVRGLAAEYRDLFLPLLGEHQAQNLAVAVAALEMFLGGGERPLDEELLRE
+GLSQVTSPGRLEVLRTAPTLIVDAAHNPDGVRATARAVQEAFGFTRLSLVVGILQEKDAP
+GMLAALYRAFGDDVEDLAVTQSSSARAIPAGELARMAVDAGWPEDDVYATESVPDALEWA
+VGRAEALETSADELASGTGGGVLVLGSITLAAEVRTLVGEPRHAGPVTVAARGLDPADLL
+DAVGLADADEDDLDPEILELLEDRDDAGARRRPEEDR
+>1_679
+MRGDVPGTVEEVYRDLLARAPENKMQPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTST
+ARMVEAVLRAYGLRTGRYTSPHLQRVTERISIDGAPVADETFVRVWGEILPIVQTVDAEL
+EAAGEVPLTYFEAVTTLGFAVFADEPVEVVVLEVGLGGVTDATNVADAVVSVVTPISLDH
+TDLLGETEAEIAEEKAGIIKPGGALVSAAQERDAAQVLLEAARAADVPFRFEGVEFGVLE
+RSLAVGGQQVSVRGLAAEYRDLFLPLLGEHQAQNLAVAVAALEMFLGGGERPLDEELLRE
+GLSQVTSPGRLEVLRTAPTLIVDAAHNPDGVRATARAVQEAFGFTRLSLVVGILQEKDAP
+GMLAALYRAFGDDVEDLAVTQSSSARAIPAGELARMAVDAGWPEDDVYATESVPDALEWA
+VGRAEALETSADELASGTGGGVLVLGSITLAAEVRTLVGEPRHAGPVTVAARGLDPADLL
+DAVGLADADEDDLDPEILELLEDRDDAGARRRPEEDR
+>2_1856
+MSGAPAPQTVEQVYADLLARAPENAMEPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTS
+TARMIEAVLRSYGLRTGRYTSPHLQSVTERISIDGAPVSDETFVRVWGEILPIVQAVDAE
+LEAEGRPRLTYFEAVTTLGFAVFADEPVEVVVLEVGLGGITDATNVADGAVSVVTPISLD
+HTDLLGETEAEIAEEKAGIVKPGGALVSAVQERDAAQVLLEAARAADVPFRFEGVEFGVL
+ERSLAVGGQQVSVRGLAAEYRDLFLPLHGEHQAQNLAVAVAALEMFLGGGDRPLDEELLR
+EGLAQVASPGRLEVLRTAPTLIVDAAHNPDGVRATARAVQEAFGFTRLALVVGILREKDA
+PAMLEALFRAFGDDVEDLALTQSSSPRAIPAGDLARMAVDAGWPEADVFAAESVPDALEW
+AVGRAEALETSADELASGTGGGVLVLGSVTLAAEVRALVGEPRHAGPVTVAARGLDPADL
+PRRRRPGRGGRGRPGPRDPRAARGPRRRRLPPPHRGGPMSTPQPGTGRTPEEDERFGDES
+WRPERETRAQRAWRPGTRRRRRSVRALFTSTVLMLEAVVIFFLGMMLFGMNRDQPGAVWF
+IAGYTLLAAVAVLTCALVRRPVGIAIGWAIQAVLVLSGFWEYSMFVVGALFALTWAYAVI
+KGGGMDVENAERDRLQAEWEAEHGQ
+>3_1802
+MSAPAEGRVPGTVEEVYADLLARAPEHRMEPRLDPVRRVLALLGDPQHAAPVIHLTGTNG
+KTSTARMIEAVLRAYGLRTGRYTSPHLERVTERISVDGEPVADEDFVRVWGEILPMVHTV
+DAELEAAGEPRLTYFEAVTVLGFAVFADAPVEVVVLEVGLGGITDATNVADGAVSVVTPI
+SLDHTDLLGDTEAEIAEEKAGIIKPGGFLVSAAQDADAAQVLLEAARAADVPFRFEGVEF
+GVLERRLAVGGQQVDVRGLADEYRELFLPLHGAHQAENLAVAVAALEAFLGGGQRPLDVE
+LLREGLAQVTSPGRLEVLRTAPTVVVDAAHNPDGVAVTARAVQEVFSFTRLALVVGVLQE
+KDARTMLEVLHREFGDLISDVALTQSASPRAIPAGDLAALAVDAGWPEDDLFITESVPDA
+LEWAVGRAEAVETSADALASGTAGGVLVLGSITLAAEVRSLLGAPAHAGPVTVAARGMDP
+ADLLAAVGLEDDDADAVDPEVLELLDDREEHTR
+>4_899
+MRGDVPGTVEEVYRDLLARAPENKMQPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTST
+ARMVEAVLRAYGLRTGRYTSPHLQRVTERISIDGAPVADETFVRVWGEILPIVQTVDAEL
+EAAGEVPLTYFEAVTTLGFAVFADEPVEVVVLEVGLGGVTDATNVADAVVSVVTPISLDH
+TDLLGETEAEIAEEKAGIIKPGGALVSAAQERDAAQALLEAARAADVPFRFEGVEFGVLE
+RSLAVGGQQVSVRGLAAEYRDLFLPLLGEHQAQNLAVAVAALEMFLGGGERPLDEELLRE
+GLSQVTSPGRLEVLRTAPTLIVDAAHNPDGVRATARAVQEAFGFTRLSLVVGILQEKDAP
+AMLAALYRAFGDDVEDLAVTQSSSARAIPAGELVRMAVDAGWPEDDVYATESVPDALEWA
+VGRAEALETSADELASGTGGGVLVLGSITLAAEVRTLVGEPRHAGPVTVAARGLDPADLL
+DAVGLADADEDDLDPEILELLEDRDDAGARRRPEEDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000849.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000849.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20ecc9467c146efa343d2b9e4d8964918245f391
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000849.fa
@@ -0,0 +1,15 @@
+>0_961
+MVYAIVRAGGRQEKVSVGDLVTLDRVPAETGGSVELPALMLVDGDEVKAGADAAGVKVTA
+EVVSHSRGKKVVIMKYKNKTGYKKRQGHRSELSTVKITGIA
+>1_684
+MVYAIVRAGGRQEKVSVGDLVTLDRVPAETGGSVELPALMLVDGDEVKAGADAAGVKVTA
+EVVSHSRGKKVVIMKYKNKTGYKKRQGHRSELSTVKITGIA
+>2_1852
+MVYAIVRAGGRQEKVSVGDLVTLDRVPAETGGSVELPALMLVDGDKVTAGADAAGVKVTA
+EVVSHSRGKKVVIMKYKNKTGYKKRQGHRSELSTVKITGIA
+>3_1779
+MVYAIVRAGGRQEKVSVGDLVTLDRVPAEEGGSVELPALMLVDGDKVKAGADAADVKVTA
+EVVSHSRGKKIVIVKYKNKTGYKKRQGHRSELSTVKITGIA
+>4_904
+MVYAIVRAGGRQEKVSVGDLVTLDRVPAETGGSVELPALMLVDGDEVKAGADAAGVKVTA
+EVVSHSRGKKVVIMKYKNKTGYKKRQGHRSELSTVKITGIA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000852.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000852.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d0096ab51846567c29fb5b25f133996679050860
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000852.fa
@@ -0,0 +1,40 @@
+>0_964
+MSVRRTVVTRYPTPATRGSEDPQANPVTSRETMQAARRVVVKIGSSSLTTPDGLDVAAID
+RLVDVLAAERQKGTQVVLVSSGAIAAGFPHLGLSRRPKDTATQQASAAVGQSKLMAHYTT
+SFGRHDTEVAQVLLTAEELMRRTQYTNAHRALARLLTLDVMPIVNENDAVATREIRFGDN
+DRLAALTANLCKADLLVLLSDVDALYTGHPSNPDARRIPEVTSDDDLSGVDVRVPGSAGV
+GTGGMVTKVDAAGIAATTGIPTLLTSAANAGAAFAGEDVGTWFSATGRRRSARAAWLGLT
+AEVRGRLIIDDGAVAGAIDRGRSLLAAGITGCTGAFTPGDVVEIVDAHGRVRARGLVQYS
+SSQLPAMLGRTTADLREDLGAGYDGVVVHADDWVRLAPPQR
+>1_687
+MSVRRTVVTRYPTPATRGSEDPQANPVTSRETMQAARRVVVKIGSSSLTTPDGLDVAAID
+RLVDVLAAERQKGTQVVLVSSGAIAAGFPHLGLGRRPKDTATQQASAAVGQSKLMAHYTT
+SFGRHDTEVAQVLLTAEELMRRTQYTNAHRALSRLLTLDVMPIVNENDAVATREIRFGDN
+DRLAALTANLCKADLLVLLSDVDALYTGHPSHPDARRIPEVTSDDDLAGVDVRVPGSAGV
+GTGGMVTKVDAAGIAATTGIPTLLTSAANAGAAFAGEDVGTWFSATGRRRSARAAWLGLT
+AEVRGRLIIDDGAVAGAIDRGRSLLAAGITGCTGAFTPGDVVEIVDAHGRVRARGLVQYS
+SSQLPAMLGRTTADLREDLGAGYDGVVVHADDWVRLAPPQR
+>2_1849
+MSARRTVVTRYPTPATRGAEDPRANPVTTRDTMAAARRVVIKIGSSSLTTATGLDVAAID
+RLVDVIAELRGRGTQVVLVSSGAIAAGFPHLGLDRRPKDTATQQAAAAVGQGRLLAHYTH
+SFGRHETEVAQVLLTAEELMRRTQYTNAHRALARLLTLDVMPIVNENDAVATREIRFGDN
+DRLAALTANLVKADLLVLLSDVDALYTGHPSLPDSRRIPVVATDADLEGVDVHVPGSAGV
+GTGGMVTKVDAAGIAATTGIPTLLTSAPNAGSAFAGEDVGTWFEATGRRRSARAAWLGLT
+AEVRGQLVIDDGAVAGAIDRGRSLLAAGIIGLSGRFTPGDVVEILDATGRVLARGLVQYS
+SSQLPRMLGRSTSDLKEDLGAGYDGVVVHADDWVRLAPPRR
+>3_1776
+MARRPSTVHRHATPSSRGAEDPKANPVHTRADIGAARRVVIKVGSSSLTTGTGLNTDAID
+ALVELVARLRGRGTQVVLVSSGAIAAGFPALGLSRRPKDTATQQAAAAVGQNRLVAYYSQ
+SFARFDTTVAQVLLTAEELMRRGQYINAHRALARLLTLDVLPIVNENDAVATREIRFGDN
+DRLAALTANLVKADLLVLLSDVDALYTGHPSRPGSRRIDTVTAETDLGGVDVRTPGSAGV
+GTGGMVTKVDAAGIAATTGIPTLLTSAALASAALDGEDVGTWFSAAGRRRTARAAWLGLT
+AQVRGRLTIDDGAVAGAIDRGRSLLAAGITAAEGDFTAGDVVEIADAQGTVLARGLAAYS
+SSQLPRMLGRQTAQLKEEIGAGYDGVVVHADDWVRLAPTHSAFR
+>4_907
+MSVRRTVVTRYPTPATRGSEDPQANPVTSRETMQAARRVVVKIGSSSLTTPDGLDVAAID
+RLVDVLAAERQKGTQVVLVSSGAVAAGFPHLGLGRRPKDTATQQASAAVGQSKLMAHYTT
+SFGRHDTEVAQVLLTAEELMRRTQYTNAHRALSRLLTLDVMPIVNENDAVATREIRFGDN
+DRLAALTANLCKADLLVLLSDVDALYTGHPSNPDARRIPEVTSDDDLAGVDVRVPGSAGV
+GTGGMVTKVDAAGIAATTGIPTLLTSAANAGAAFAGQDVGTWFSATGRRRSARAAWLGLT
+AEVRGRLVIDDGAVAGAIDRGRSLLAAGITGCTGDFTPGDVVEIVDTHGRVRARGLVQYS
+SSQLPAMLGRTTADLREDLGAGYDGVVVHADDWVRLAPPQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000853.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000853.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d439bb9c94a1d6e5fddb47dbb443812db5f4266c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000853.fa
@@ -0,0 +1,45 @@
+>0_965
+MQTTESTAPQDQSGRQDAEAPTPEVEEAVRQRAEWARQAVPELAVAGRARKDAVLRHMAE
+ALRANTAAILTANREDRSRGRETGTSAAMLDRLKLDEARVEALALALETLAGLPDPVGTV
+VRGGPLPNGVRMSQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILRGGSAAESTNA
+VLIQVLREALVDQGFDANIIQGIDDLGRPGVAALMAARGAVDVLVPRGGRELIQRVVREA
+RVPVIETGEGNVHLYVDASAPKQMAVDIALNSKTHRTSVCNAAETLLLHRDAEETGREVL
+RALTRAGVLLHVDEAARAWLPTLADRGDHARDAVDATEEDWGTEYLDMEMAVRVVDSLGQ
+AIEHIGRWSTGHTEAIVTNDLAAAERFITEVDAAAVIVNASTRFTDGGELGLGAEVGIST
+QKMHARGPMGLEELTTTKWILRGDGQIRR
+>1_688
+MQTTESTAPQDQSGRQDAEAPTPEVEEAVRQRAEWARQAVPELAVAGRARKDAVLRHMAE
+ALRANTAAIITANREDRSRGRETGTSAAMLDRLKLDEARVEALALALETLAGLPDPVGTV
+VRGGPLPNGVRMSQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILRGGSAAESTNA
+VLIQVLREALVDQGFDANIIQGIDDLGRPGVAALMAARGAVDVLVPRGGRELIQRVVREA
+RVPVIETGEGNVHLYVDASAPKQMAVDIALNSKTHRTSVCNAAETLLLHRDAEETGREVL
+RALTRAGVLLHVDEAARAWLPTLADRGDHARDAVDATEEDWGTEYLDMEMAVRVVDSLGQ
+AIEHIGRWSTGHTEAIVTNDLAAAERFITEVDAAAVIVNASTRFTDGGELGLGAEVGIST
+QKMHARGPMGLEELTTTKWILRGDGQIRR
+>2_1848
+MENQESTAPQDQSAGQEAEAPSQEVVDAIRQRAEWARLAVPELATAGRTRKDAVLRHMAE
+SLRSNAAAIITANQEDRARGAEAGTSAALLDRLKLDEPRVEALALGLEALAALPDPVGAV
+VRGGTLPNGVRMTQTRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILRGGSAAQSTNA
+VLIQVLREALADQGFDPNVVQGIDDLGRPGVAALMATRGAVDVLVPRGGRELIQRVVREA
+RVPVIETGEGNVHLYLDASAPKDMAVEIALNAKTHRTSVCNAAETLLIHREAEETGREVL
+RALMRGGVLLHVDEAAKAWLPGPTDRGDHARDAVDATEEDWGTEYLDMDMAVRIVDSLDQ
+AIEHIGRWSTGHTEAIVTNDLAAAEQFITEVDAAAVIVNASTRFTDGGELGLGAEVGIST
+QKMHARGPMGLEELTTTKWILRGDGQVRR
+>3_1775
+MTTEHTETEPAERVQQTPTPEQGASADGRPGADVVAEVRSRSARARAAAPELARAGRERK
+DALLRSMADAVRAAAASILAANAEDLARGEENGTSAAMLDRLRLDEPRLESLAVALEDLA
+SLPDPVGAVVRGGDLPNGIHMQQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNAVLLRG
+GSAAEHTNAVLIQVLREALRDQGFESDLVQGIDDLGRPGVAALMSTRGAVDVLIPRGGRE
+LIQRVVAEARVPVIETGEGNVHLFIDASAPADMAVDIALNAKTHRTSVCNAAETLLLHKD
+AERAGREVLRALTRAGVLLHVDEASRARLPSPADRGQDAREPQAASDEDWGREYLDMEMA
+VRTVDSIDEAMEHVRRWSTGHTEAIVTNDLANADRWVSEVDAAAVIVNASTRFTDGGQLG
+LGAEVGISTQRMHARGPMGLEELTTTKWVLRGAGQVRR
+>4_908
+MQTTESTAPQDQSGRQDAEAPTPEVEEAVRQRAEWARQAVPELAIAGRARKDAVLRHMAE
+ALRANTAAILTANREDRGRGRETGTSAAMLDRLKLDEARVEALALALETLAGLPDPVGTV
+VRGGPLPNGVRMSQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILRGGSAAESTNA
+VLIQVLREALVDQGFDPNIIQGIDDLGRPGVAALMAARGAVDVLVPRGGRELIQRVVREA
+RVPVIETGEGNVHLYVDASAPKQMAVDIALNAKTHRTSVCNAAETLLLHRDAEETGREVL
+RALTRAGVLLHVDEAARAWLPTLADRGDHARDAVDATEEDWGTEYLDMEMAVRVVDSLDQ
+AIEHIGRWSTGHTEAIVTNDLAAAERFITEVDAAAVIVNASTRFTDGGELGLGAEVGIST
+QKMHARGPMGLEELTTTKWILRGDGQIRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000854.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000854.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad3fd67e87a59c32bf0c8b70b954adf1849db1dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000854.fa
@@ -0,0 +1,15 @@
+>0_966
+MLNTSLILAAAEGHHVVNELPMDPIWYGLLVFALLMAALAATMSMRSRALRLPEPTTAVQ
+HHGTGRGSHTSGH
+>1_689
+MLNTSLILAAAEGHHVVNELPMDPIWYGLLVFALLMAALAATMSMRSRALRLPEPTTAVQ
+HHGTGRGSHTSGH
+>2_1847
+MLNTSLVLAAAEGPHVVNELPIPTVWYGIIVFALLMAALLATMSMRSRALRLPEPTTAVQ
+HHGTGHGSHTPGH
+>3_1774
+MLNSALVLAAAEEGHHVVNELPIPPVWFGIIVFLLLMAGLLAILSMRSVGLRHAEPTTAV
+QHHGTHGTGSHSAGH
+>4_909
+MLNTSLILAAAEGHHVVNELPMDPIWYGLLVFALLMAALAATMSMRSRALRLPEPTTAVQ
+HHGTGRSSHTSGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000862.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000862.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75e5052e4e8e3aacb677ba8650d0ded5473327da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000862.fa
@@ -0,0 +1,31 @@
+>0_979
+MNTTVRRALWVVLVLLCLGLVFLALRGVLAVGAVPISAAPTLSATASATPSPSPSPSSAR
+FTPSPATTATPTPTPSPSSASPTREAAVPVETQELAGTPTPSEEPTPTEEPAPSEEPAPS
+EEPTPAAAAHLSGPAAPWDEVTATPVHVDVHQDGEQIVGAGIDLTQLDEGGDLDPEPQTV
+GWYGPPQWGTTPGERSRYAGVLAGHVVYHGVRDVFWNLGDVRAGAVVVVTYDDGTQAAFE
+ADSDAVSVEKEALTQDPANRWAWEPGGDDAKVTLITCDLVPGTGMAGNAFNNWVVQATRV
+A
+>1_702
+MNTTVRRALWVVLVLLCLGLVFLALRGVLAVGAVPISAAPTLSATASATPSPSPSPSSAR
+FTPSPAPTATPIPTPSPSSASPTREAAVPVETQELAGTPTPSEEPTPTEEPAPSEEPAPS
+EEPTPAAAAHLSGPAAPWDEVTATPVHVDVHQDGEQIVGAGIDLTQLDEGGDLDPEPQTV
+GWYGPPQWGTTPGERSRYAGVLAGHVVYYGVRDVFWNLGDVRAGAVVVVTYDDGTQAAFE
+ADADAVSVEKEALTQDPAHRWAWEPGGDDAKVTLITCDLVPGTGMAGNAFNNWVVQATRV
+A
+>2_1831
+MTGPAAPWESIDAAPVHVEVHQDGERIVGASVEHTQMNEAGELDPDPQTVGWYGAPQWGT
+DPGERSPYAGILAGHVVYYGVKDVFWNLDAVRAGDVVVLTYDDGSQAVFEADADAVSVEK
+EALTQDPANRWAWEPGGDDARLTLITCDLVPGTGMAGNAFNNWVVQATRVA
+>3_1726
+MSTTVKRAVWALLLLICLGVGAFALRGMFAFGDVPISAAPTVSARASTASSTPSAATGSP
+SSTSASASAGPSVPAATSASSAAASTTTPASPTSSTTTPASPTSSTTPASTEAAAPAVGA
+ASSTATASSSATPTGTDSRMTKPAASWERITAAPVHIDVYADGEQVVGAPVELVQTRDDG
+ELNPDPQMAGWYGPPQWTTTPGERSAHPGVIAGHVIHSGLKDVFWNLQTLKAGSIVVITY
+DDGTQAEFRTDFDVRSMDKDDLTQSPDYAWAWELPEAGNKVTLITCDLVDGSGMTGWSTN
+NWVTQATRIG
+>4_923
+MNTTVRRALWVVLLLLCLSLVFLALRGVLAVGAVPISAAPTLSATASVSPSSAATTREAA
+VPVETQELAGTPTPSEEPTPTEEPAPSEEPTPAAAAHLSGPAAPWDEVTATPVHVDVHQD
+GEQIVGAGIDLTQLDEGGDLDPEPQTVGWYGPPQWGTTPGERSRYAGVLAGHVVYHGVRD
+VFWNLGDVRAGAVVVVTYDDGTQAAFEADADAVSVEKEALTQDPSHRWAWEPGGDDAKVT
+LITCDLVPGTGMAGNAFNNWVVQATRVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000863.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000863.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e6602c73192a3da1281963cfa541a82c45aa7ff0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000863.fa
@@ -0,0 +1,33 @@
+>0_980
+MSRADIAPARVRPRRWSVAVGGALLSITLATGGCSVAEEPGQTGGTEAGNTYLEGVLASP
+SQTSADPLAADIQFAGLLLRNHRDAIQQSDQVLGKDGVDQEIRATAERMKSEHEERAGRL
+ESMLEGWGVPSDDVRGAGAESTPSAQPESTEDAEPTQIVGDELRAGLLSDREKNVLAAAE
+PEEAGRIYLLQMRRLYQGALTISATEAEDGSDDAAKELASSVVEGHRKELESLAATLGEM
+GVIGSSGARTAEPSGFTGPIKIEGTGADGGSVPSDFVPEPLQRVRSFRATQKPVLPSSSS
+PSSSSASGSASASGRDAEDQRGRDAASASPSPSPADTAQATPRPSSGASPSPSASR
+>1_703
+MSRADIAPARVRPRRWSVAVGGALLSITLATGGCSVAEEPGQTGGTEAGNTYLEGVLASP
+SQTSADPLAADIQFAGLLLRNHRDAIQQSDEVLGKDGVDQEIRATAERMKSEHEERARRL
+ESMLEGWGVPSDDVRGAGAESTPSAQPESTEDAEPTQIVGDELRAGLLSDREKNVLAAAE
+PEEAGRIYLLQMRRLYQGALTISATEAEDGSDDAAKELASSVVEGHRKELESLAATLGEM
+GVIGSSGARTAEPSGFTGPIKIEGTGADGGSVPSDFVPEPLQRVRNFRATQKPVLPSSSS
+PSSSSASGPASASGRDAEDQRGRDAASASPSPSPADTAQATPRPSSGASPSSSASR
+>2_1830
+MPVTGDELRAGLLSEREKNVLAAADAEDAGRIYLLQMHRVYQGALTISATEAESGTDEEA
+KALAASVVADHQEDMQRMVEVLADMGAIGADASHTALPSGYTGPIKIEGTGADGGPVPSD
+FVPEPVQRVQSFRATQRPVLPTSSSPGDAEDRRGRDSATASPSPTPADTARPSPSPSSAA
+SPSPSATTGSPSGTNR
+>3_1725
+MNRATDATAPVCPVRWSAAAGGLLGLSLVLAGCGTSAQPVPAGSGSNTYLEGVLATPSAT
+KADPLAADQRFVASLLQNQYQVVQEADHVLSRPDMDGEVRDMAQQHKDVANQRIGDLSSR
+LQAWGLEVPAAPEPLVDDTKPSGRPTGDPSEIQASKGQQAAADIRAGLLTASDQSALVTA
+DDDAAGRIYLLQVHRLLQGGVSLAGTESDEGTDEETKKIASDLIDADRPRMQRILEKLGE
+NGVVAAVPSPTAPNSGYQGPISLPSQAGGDGANVDYTPSALYEMWSTLPPPATSSSADGS
+STGPSPSAQPTPTPADTASPRPTPGASAQPGAASSTASTTGAASTRNG
+>4_924
+MSRADIAPARVHPRRWSVAVGGALLSITLATGGCSVVEEPGQTGDTEAGNTYLEGVLASP
+SQTSADPLAADIQFAGLLLRNHRDAIQQSDQVLGKDGVDQEIRATAERMKSEHEERAGRL
+ESMLEGWGVPSDDVRGAGAEATPSAQPESTEDAEPAEIVGDELRAGLLSDREKNVLAAAE
+PEEAGRIYLLQMRRLYQGALTISATEAEDGSDDAAKELASSVVEGHRKELESLAATLAEM
+GVIGSSGARTAEPSGFTGPIKIEGTGADGGSVPSDFVPEPLQRVRNFRATQKPVLPSSSS
+PSSSSASGSASASGRDAEDQRGRDTASASPSPSPADTAQATPRPSSGASPSPSASR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000871.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000871.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89f3f8fc3887e257f21d5c9fe61c461e510563d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000871.fa
@@ -0,0 +1,30 @@
+>0_991
+MSVAPRLRWAVQERTLGAVEDLDWAMGELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR
+DARLPGFAAAAAAARAHGFAPAVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF
+ADLFVRAFARMDVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV
+VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGI
+EVVAEQLAVLGARTSG
+>1_715
+MSAAPRLRWAVQERTLGAVEDLDWAMDELAVFRAAAAEGRALDGLIRVYVPEPTVAFGQR
+DARLPGFEAAAAAARAHGFEPVVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF
+ADLFVRAFARMDVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV
+VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAGLE
+VVDEQLAVLTAGTAG
+>2_1814
+MSAAPRLRWAVQERTLGATDDLDWAMDELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR
+DARLPGFEAAAAAARTHGFEPAVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF
+ADLFVRAFARMGVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV
+VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGL
+KVVDEHLAVLAAGTSG
+>3_1703
+MSAAPRLRWAVQERTLGAADDLDWAMGELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR
+DARLPGFEAAAAAARAHGFEPAVRRAGGRAAAYHHGCLVVDHLSQQEDATLTQQARFAEF
+ADLFVRAFARMGVPASVGEIPGEYCPGEFSVQGPAPAYPVKLAGSAQRVVKGAFLFSTHV
+VVSDPAPLRAVLVDVYRELGLGMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGL
+EVVDEQLAVLGAGTSG
+>4_935
+MSAAPRLRWAVQERTLGAVEDLDWAMGELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR
+DARLPGFAAAAAAARAHGFAPAVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF
+ADLFVRAFARMDVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV
+VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGI
+EVVAEQLAVLGARTSG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000873.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000873.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da3ef9013e135dc78d87303c5ac2cee7151336e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000873.fa
@@ -0,0 +1,25 @@
+>0_995
+MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV
+LTHGHDDHIRQVQEFRQMVDAPALLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR
+VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI
+RERLLSLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH
+>1_717
+MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV
+LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR
+VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI
+RERLLPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH
+>2_1812
+MARIDHLVTSGTFSLDGETFDVDNNVWLVGGAEQCIVIDPAHDASAVWKKVNGRQVLAIV
+LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR
+VLHTPGHSPGSVCLYAPALGEAGDDGGATGVVFSGDTLFQGGPGATGRSYSDFDTIIESI
+RERLFPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH
+>3_1701
+MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV
+LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR
+VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI
+RERLFPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH
+>4_937
+MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV
+LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDAVFPDEEPDGALAEGDVLRVAGVELR
+VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI
+RERLFPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000876.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000876.fa
new file mode 100644
index 0000000000000000000000000000000000000000..36b4966617229335fde88f6064bff0c9cdbc43d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000876.fa
@@ -0,0 +1,28 @@
+>0_1002
+MSLTAPGRALRRHRFAQAGTLSVALALALTACGGQSEPAESSTTSPSSAKPAVETSAPAS
+TSETAGVSSSPTATESGSGEYVPASADGPARSVPKPEMPADMKEETKEGAEAAIRYFWDV
+HYYAEQTGDTELLDSLYSEYCEFCQFSSNDLQMIYKDGGWYTGTEVQIDSILTHRSETGY
+VSTLLVTTGTGTGYTKGGVVPENGDVEAASKQPWIAEVSFNPESSHWIVDEMSYEGSIGS
+N
+>1_724
+MSLTAPGRALRRHRFAQAGTLSVALALTLTACGGQSEPAESSTTSPSSAKPAVETSAPAS
+TSATAGVSSSPTATESGSGEYVPASADGPARNVPKPEMPAAMKEETKEGAEAAIRYFWEA
+IYYTDQTGETADFDSTYSEYCELCQAVSDSTAQHYKEGGWSTGEHTSIKSLTLTPSEFGY
+TATLVRDASAVDVFDSQGVRDDSASGAETHDETWLADVVYEPSKGHWVIDEMQNQQDAQ
+>2_525
+MSFTAPRRVLRRHRLTQVGALGAGLALLLTACGGGSEPAESSSPAPTGSSSSPAEATTAS
+PSAESSPTTSPSGSVGSTAAAGSSGSGGAYVPASAEGPARNVPKPEMPAVTKEETQEGAE
+AAVEYFWEAAYYLQQTGDSEYQESVSSPTCKFCDLQRTSMEGHYRDGGWMKVEAVNIASM
+VTRPSANGYMSTLLLDMPKEEAFASQGGKAESIGTQPALEESPWIAETSFSEEAGHWVIE
+AMIAGGS
+>3_1697
+MTLPAPRRTLRRRRLARTGALSGALLLALTACAGGGADSGASSASTTTTAPAASSTSAAA
+SSSTGGASASESDATTSGAAGEYVPASSKGPAQNVPKPVMPAAVKENTPEGAEAAVKYWW
+EAVNYLQQTNDPEPLKSISMEECNLCSAHIKTIKRIYGDGGWATGENFAVNSVSMEKKKD
+FTLATVAISTDDSATFNADGVKVDQAPADAGTDAPWGVLLKFDSNKGQWVVREAEYDFQE
+G
+>4_943
+MSLTAPGRALRRHRFAQAGTLSVALALALTACGGQSEPAESSTTSPSSAKPAVETSAPAS
+TSETAGVSSSPTATESGSGEYVPASADGPARNVPKPEMPAAMKEETKEGAEAAIRYFWEA
+IYYTDQTGETADFDSTYSEYCELCQAVSDSTAQHYKEGGWSTGEHTSIKSLTLTPSEFGY
+TATLVRDASAVEVFDSQGVRDDSASGVETHDETWLADVVYEPSKGHWVIDEMQNHQDAQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000879.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000879.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4649abf0a934ac9b5a1db33335110207f0a92ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000879.fa
@@ -0,0 +1,65 @@
+>0_1005
+MSEPKNILLTVDGELREVTHGTTGLDLFREKPTTAVMRVDGLLWDLAREIPAGASVESVD
+ITEPEGLEVLRHSTAHVMAQAVQQLRPGAKLGIGPYITDGFYFDFDVDEPFTPEDLKQIS
+SLMQKIVKSGQTFRRRVVDEETARAEMAEEPYKLELLGKKDAADTAGEGASVEVGAGEIT
+IYDNVDRKTGDAVWCDLCRGPHLPSTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW
+ASKDDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR
+RRHTEAGYEFVYTPHITKQHLYEVSGHLDWYADGMFPPMHIDEVRDPETGEITRQGQNYY
+LKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSGVVHGLTRVRGMTQDDAHIYC
+TREQMKEELTTTLNFVLDLLKDYGLNDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA
+SGLQLVPDPGGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGTRQRP
+VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFNDYLDDVVAKLRAEGI
+RARLDDSSDRFPKKIRTAAKEKAPFVLIAGGEDREANAVSFRFRDGTQDNGVPVEEAIER
+IVKAVREREVTP
+>1_727
+MSEPKNILLTVDGELREVTHGTTGLDLFREKPTTAVMRVDGLLWDLAREIPAGASVESVD
+ITEPEGLEVLRHSTAHVMAQAVQQLRPGAKLGIGPYITDGFYFDFDVDEPFTPEDLKQIS
+SLMQKIVKSGQTFRRRVVDEETARAEMADEPYKLELLGKKDAADTAGEGASVEVGAGEIT
+IYDNVDRKTGDAVWCDLCRGPHLPSTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW
+ASKDDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR
+RRHTEAGYEFVYTPHITKQHLYEVSGHLDWYADGMFPPMHIDEVRDPETGEITRQGQNYY
+LKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSGVVHGLTRVRGMTQDDAHIYC
+TREQMKEELTTTLNFVLDLLKDYGLNDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA
+SGLQLVPDPGGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGTRQRP
+VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFNDYLDDVVAKLRAEGI
+RARLDDSSDRFPKKIRTAAKEKAPFVLIAGGEDREAGAVSFRFRDGTQDNGVPVEEAIER
+IVKAVREREVTP
+>2_1806
+MSEPNNILLTVDGQMREVAHGITGLELFRDQSTTVVMRVDGVLWDLSREIPGGASVESVD
+ITEQDGLDVLRHSTAHVMAQAVQQLRPDAKLGIGPYITDGFYFDFDVAEPFTPEDLRTLE
+KMMQKIINSGQAFRRRVVTEDEARAEMADEPYKLELLGKKNDAATAGEGASVEVGAGEIT
+IYDNVDRKSGDAVWCDLCRGPHLPQTKLISNAFALTRSAAAYWLGNQDNKQLQRIYGTAW
+PTKADLKAYQERLAEAERRDHRRLGSELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR
+RRHTEAGYEFVYTPHITKQHLYETSGHLDWYADGMFPPMQIDEQRDPETGEVTRQGQNYY
+LKPMNCPMHNLVFRSRGRSYRELPLRLFEFGAVYRYEKSGVVHGLTRVRGMTQDDAHIYC
+TREQMKDELTTTLNFVLDLLKDYGLDDFYLELSTRDPEKSVGSDEIWEEATRTLDEVARA
+SGLDLVPDPGGAAFYGPKISVQAKDAIGRTWQMSTIQLDFNLPERFDLEYQAPDGSRQRP
+VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFADYLGDVVKRLRAEGI
+RARLDDSSDRFPKKIRTASKEKVPFVLIAGGEDAEAGAVSFRFRDGSQDNGVPVDEAIER
+IVRAVREREATP
+>3_1693
+MSESNPILLTVDGEMREVTHAITGAELFKDQPTTVVMRVDGQLWDLSRELHGGEAVESVD
+ITEQDGLNVLRHSTAHVMAQAVQELRPDAKLGIGPFITDGFYFDFDVAEPFTPEDLKQLE
+KMMQRIVKSGQTFRRRVVTEDEARAEMADEPYKLELLGKKDDAEAAGEGATVEVGAGEIT
+IYDNVDRKSGDAVWCDLCRGPHLPTTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW
+PTKEDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR
+KRHAAAGYEFVYTPHITKQHLYEVSGHLDWYADGMFPPMQIDEVRDPETGQITKQGQNYY
+LKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSGVVHGLTRVRGMTQDDAHIYC
+TREQMKDELTTTLNFVLDLLKDYGLDDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA
+SGLELVPDPAGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGSRQRP
+VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFNDYLADVVATLKAEGI
+RVRLDESSDRFPKKIRTASKEKVPFVLIAGGEDAEAGAVSFRYRDGSQDNGVPVDEAVAR
+IVKAVREREVTP
+>4_946
+MSEPKNILLTVDGELREVTHGTTGLDLFREKPTTAVMRVDGLLWDLAREIPAGASVEAVD
+ITEPEGLEVLRHSTAHVMAQAVQQLRPGAKLGIGPYITDGFYFDFDVDEPFTPEDLKQIS
+SLMQKIVKSGQTFRRRVVDEETARAEMADEPYKLELLGKKDAADTAGEGASVEVGAGEIT
+IYDNVDRKTGDAVWCDLCRGPHLPSTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW
+ASKDDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR
+RRHTEAGYEFVYTPHITKQHLYEVSGHLDWYADGMFPPMHIDEVRDPETGEITRQGQNYY
+LKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSGVVHGLTRVRGMTQDDAHIYC
+TREQMKEELTTTLNFVLDLLKDYGLNDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA
+SGLQLVPDPGGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGTRQRP
+VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFNDYLDDVVAKLRAEGI
+RARLDDSSDRFPKKIRTAAKEKAPFVLIAGGEDREANAVSFRFRDGTQDNGVPVEEAIER
+IVKAVREREVTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000881.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000881.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b92bb89f74ba40fc585d5ffbc1f8618a628870a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000881.fa
@@ -0,0 +1,25 @@
+>0_1007
+MLDRHARDLTTRLFTPVAHTLLRAGVSPDTVTVVGTLGVSLGALVLFPLGHLFWGTLFIT
+AFVFSDLVDGIMAREAGSTGRWGAFLDSTLDRVQDAAVFLGLCLWGFGVGAAPAVGALSG
+ACLALGMLVSYVRAKAEALGWSAHVGIAERAERLVAALVVAGLTGLGLPPVVLAVTLGLL
+AAASLVTVGQRMAAVRRQARDDA
+>1_729
+MLDRHARGVTTRLFTPVARTLLRAGVSPDTVTVVGTLGVSLGALVLFPLGHLFWGTLFIT
+AFVFSDLVDGIMAREAGSTGRWGAFLDSTLDRVQDAAVFLGLCLWGFGVGAAPAVGALSG
+ACLALGMLVSYVRAKAEALGWDAHVGIAERAERLVATLVVAGLTGLGLPPVVLAVTLGLL
+AAASLVTVGQRMVAVRRQARDDA
+>2_1804
+MLDRHARGATTRVFTPVARALLRAGVSPDAVTVVGTLGVSLGALVLFPLGELFWGTLFIT
+AFVFSDLVDGIMAREAGTTGRWGAFLDSTLDRVQDAAVFLGLSLWGFGVGGEPAVGTLAA
+VCLALGMLVSYVRAKAEALGLTANVGIAERAERLVAALVLAGLTGLGLPPAFLAATLGLL
+AAASLVTVGQRVAAVRSQTRRAA
+>3_1691
+MLDRRARGTTTALFTPLARRLLRAGVTPDAVTVAGTVGVSAAALLLYPAGHLFWGTIVIT
+LFVFSDVLDGVMAREAGTTGPWGSFLDSTLDRVQDAAIFLALSWWGFGVGAHPAVGVLAG
+VCLALGMLVSYARAKAESLGFTAAGGIAERAERLIVTLVFAGLTGLGLPSAVLTAVLGLL
+ALASLITVAQRVAGVRRQSRTA
+>4_948
+MLDRHARGVTTRLFTPVARTLLRAGVSPDTVTVVGTLGVSLGALVLFPLGHLFWGTLFIT
+AFVFSDLVDGIMAREAGSTGRWGAFLDSTLDRVQDAAVFLGLCLWGFGVGAAPAVGALSG
+ACLALGMLVSYVRAKAEALGWDAHVGIAERAERLVATLVVAGLTGLGLPPVVLAVTLGLL
+AAASLVTVGQRMAVVRRQARDDV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000890.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000890.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc456fc0458938a2913e12990a6f0d73215bb000
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000890.fa
@@ -0,0 +1,25 @@
+>0_1016
+MTARPPRLHPSILSADFARLADDLARIPSADAVHVDVMDNHFVPNLTLGLPVVEAIRRAT
+DLPLDLHLMIEDADRWAPGYAEAGAESVTFHAEASAAPVRLARELRAAGAKAGMALRPAT
+AVEPYLDMLPELDMLLLMTVEPGFGGQAFLDVVLPKIRRARRALDGGPAPLALQVDGGVN
+RETIERAAEAGADVFVAGSAVFGAEDPDAALAGLRTAAARACH
+>1_744
+MTARPPRLHPSILSADFARLADDLARIPSADAVHVDVMDNHFVPNLTLGLPVVEAIRRAT
+DLPLDLHLMIEDADRWAPGYAEAGAESVTFHAEASAAPVRLARELRAAGAKAGMALRPAT
+AVEPYLDMLPELDMLLLMTVEPGFGGQAFLDVVLPKIRRARRALDGGPAPLALQVDGGVN
+RETIERAAEAGADVFVAGSAVFGAADPDAALVGLRTAAARACH
+>2_1793
+MSPRAPRLHPSILSADFAHLAEELGRIRGADAVHVDVMDNHFVPNLTLGLPVVEAIRRAT
+DLPLDIHLMIEDADRWAPGYAEAGAESVTFHAEASAAPVRLARELRAAGARAGMALKPAT
+PVEPYLDMLPELDMLLLMTVEPGFGGQAFLDVVLPKIRRARRALDGAAAPLALQVDGGVN
+AETIERAAEAGADVFVAGSAVFGAEDPDAAVDGLRRAAARACC
+>3_1682
+MSAHPCIHPSILSADFARLADELARIPGSDAVHVDVMDGHFVPNLTLGLPVVEAIRAATD
+LPLDIHLMIEDADRWAPAYADAGAESVTFHAEAARAPIVLARSLRAAGAQAGLAVRPATP
+IEPYLDLLPELDMLLIMTVEPGFGGQSFLDVTLPKIRRARQALDGAPVPVRLQVDGGVNR
+ETILRAAEAGADVFVAGSAVFGADDPGAAIAGLRDLAAGVAPACHTR
+>4_963
+MTARALRLHPSILSADFARLADELARIPSADAVHVDVMDNHFVPNLTLGLPVVEAIRRAT
+DLPLDLHLMIEDADRWAPGYAEAGAESVTFHAEASAAPVRLARELRAAGAKAGMALRPAT
+AVEPYLDMLPELDMLLLMTVEPGFGGQAFLDVVLPKIRRARRALDGGPAPLALQVDGGVN
+RETIERAAEAGADVFVAGSAVFGAEDPDAALAGLRTAAARACH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000891.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000891.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4c5a3d172063477c12c8c017d334f0dabd2cdcf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000891.fa
@@ -0,0 +1,25 @@
+>0_1017
+MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARRVWAWPVGILGNLILLTVFL
+ASLFTGADHATLLGQAGRQVMFIAVSVYGWARWRQARRGHAEDAPAITPEWAGWRGRVFL
+VTAMAVGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV
+PLLWSTGYYASAVMYAFYGAFTLIGFFVWLRATDRDKPAVETLLPDGPEGDVAR
+>1_745
+MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARRVWAWPVGILGNLILLTVFL
+ASLFTGADHATLLGQAGRQVMFIAVSVYGWARWRRARRGHAEDAPAITPEWAGWRGRVFL
+VTAMAVGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV
+PLLWSTGYYASAVMYAFYGAFTLIGFFVWLRATDRDKPAVETLLPDGPEGDVAR
+>2_1792
+MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARKVWAWPVGILGNLILLTVFL
+ASLFTGADHATLLGQAGRQVMFIAVSVYGWVRWNEARRGRSEHATAITPEWAGLGGRAFL
+VLGMLIGTLALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLVWVAVDVVGV
+PLLWSTGYYASAVMYAFYGAFTLVGFFVWLRAKDRDKPAVETLLPDGPEEHAAR
+>3_1681
+MQWLVDVFNWTIPVAGGGLLMREVVGNVFGLASALGGMARKVWAWPVGILGNLLLLTVFL
+ASLFNDAPHATLLGQAGRQVMFIAVSVYGWKRWRDAQRGRADHAPAITPEWAGWGNRAFL
+AVALVLGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV
+PLLWSSGYYASAVMYAFYGVFTLTGFFVWMRARDRDKPAVETLLPDGPAPEEAAR
+>4_964
+MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARRVWAWPVGILGNLILLTVFL
+ASLFTGADHATLLGQAGRQVMFIAVSVYGWVRWRQARRGHAEDAPAITPEWAGWRGRVFL
+VTAMAVGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV
+PLLWSTGYYASAVMYAFYGAFTLIGFFVWLRATDRDKPAVETLLPDGPEGDVAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000895.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000895.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b726fe687ce0d9fb80ae863d3cec77265b346ee3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000895.fa
@@ -0,0 +1,30 @@
+>0_1034
+MLRIAVPNKGALSESAREILTEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFCDAQVGDTAEEIMALGFGRSVFRLAAPVGSFTSAEQLAGKRIATSYDG
+LLSDYLARTGLDATVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMEVFGEPILDSE
+AVLIGRAGERPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEAATAVTPGLESPTVSPL
+RDETMVAVRSMVRKPDANRVMDELYALGARGILISAIHAIRL
+>1_762
+MLRIAVPNKGALSESAREILTEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFCDAQVGDTAEEIMALGFGRSVFRLAAPVGSFTSAEQLAGKRIATSYDG
+LLSDYLARTGLDATVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMEVFGEPILDSE
+AVLIGRAGERPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEAATAVTPGLESPTVSPL
+RDETMVAVRSMVRKPDANRVMDELYALGARGILISAIHAIRL
+>2_1787
+MLRIAVPNKGALAEAAREILQEAGYRQRRDSRELVLVDPENQVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFRDAQVDGGAEEIMALGFGRSVFRLAAPVGAFSSEAELSGKRIATSYDG
+LLSAYLERTGLDAEVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMETFGESILDSE
+AVMIARVGARPEGLDVLLRRLKGVLVARRWVMIDYDVRRELLEQATAVTPGLESPTISPL
+RDESMVAVRSMVRKADANRAMDDLYALGARGILISAIHAIRL
+>3_1673
+MLRIAVPNKGALSESAREILIEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFRDARVGETAEEIMALGFGKSVFRLAAPVGSFTSAEELAGRRIATSYDG
+LLTEYLAESGLDARVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMETFGEPILDSE
+AIMIARVGARPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEQATAVTPGLESPTVSPL
+RDESMVAVRSMVRKADANRAMDDLYDLGARGILISAIHAIRL
+>4_983
+MLRIAVPNKGALSESAREILTEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFCDAQVGDTAEEIMALGFGRSVFRLAAPVGSFTSAEQLAGKRIATSYDG
+LLSDYLARTGLDATVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMEVFGEPILDSE
+AVLIGRAGERPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEAATAVTPGLESPTVSPL
+RDETMVAVRSMVRKPDANRVMDELYALGARGILISAIHAIRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000897.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000897.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cd08c5b035b94fc69b9607865d0159334e603366
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000897.fa
@@ -0,0 +1,20 @@
+>0_1036
+MSISPPDDLVASVTFDDRGLVPAIAQQEGTGEVLMMAWMNEESLRATLETGWATYWSRSR
+GELWRKGETSGHLQRVRAVHADCDGDTLLLTVDQTGPACHTGTRTCFTGRELVMPPAAVD
+PEEAAR
+>1_764
+MSISPPDDLVASVTFDDRGLVPAIAQQEGTGEVLMMAWMNAESLRATLETGWATYWSRSR
+GELWRKGETSGHLQRVRAVHADCDGDTLLLTVDQTGPACHTGTRTCFTGRELVMPPAAVD
+PEEAAR
+>2_1784
+MSISSHHDLVASLAFDDRGLVPAIAQQEGTGEVLMMAWMNAESLRLTLETGWATYWSRSR
+GELWRKGETSGHLQRVLAVHADCDADTLLLTVDQTGPACHTGTRSCFTDRLLAEPAAPAG
+DQAEGAGR
+>3_1671
+MSPSDVVADLPPLIFDERGLIPAIAQQHDSGEVLMMAWMNEESLRRTLEDGWATYWSRSR
+QEYWRKGETSGHLQRVLAVAADCDGDTLLLTVDQTGPACHTGTTSCFTDRRFAAPTAADE
+DPQTEDAEAVR
+>4_985
+MSISPPDDLVASVTFDDRGLVPAIAQQEGTGEVLMMAWMNAESLRATLETGWATYWSRSR
+GELWRKGETSGHLQRVRAVHADCDGDTLLLTVDQTGPACHTGTRTCFTGRELVMPPAAVD
+PEEAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000900.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000900.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c45c96d2ecfa1409ee15dce7614ec1c39e46678b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000900.fa
@@ -0,0 +1,15 @@
+>0_1039
+MSHTANTAHTEPTTRRAARRGAVEDVVVTEDGLVLNDPTHLELPGHGNSPGAWAMVALVL
+VGFVAGCVGLLADWSVVVWIGVALMAVGVVVGIVAGKAGAGRGQHGH
+>1_767
+MSHTANTAHTEPTTRRAARRGAVEDVVVTEDGLVLNDPTHLELPGHGNSPGAWAMVALVL
+VGFVAGCVGLLADWSVVVWIGLALMAVGVVVGIVAGKAGAGRGQHGH
+>2_1781
+MSHTANTEHTTRRAARNGAVEDVVVTEDGRVLNDPTHLELPDHGNTPGGWAMVALVLVGF
+VAGCIGLLADWMIVVWIGVALIVVGVLVGIVAGRGGSARSGHRAH
+>3_1668
+MSHTEATVNHTAQAGAHAAGHTTGHTASREVVVTEDGRVLNDPTHAKVPGHGNSPAAWAM
+AGLVVLGFLAGCIGLLNDALVIVWIGVAVIVVGVLVGIVGGKAAGRSDH
+>4_988
+MSHTANTAHTEPTTRRAARRGAVEDVVVTEDGLVLNDPTHLELPGHGNSPGAWAMVALVL
+VGFVAGCVGLLADWSVVVWIGLALMAVGVVVGIVAGKAGAGRGQHGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000902.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000902.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3d7a61e68eaca9b415f5083695757494f0b8b9a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000902.fa
@@ -0,0 +1,45 @@
+>0_1041
+MSADRPSTEPAIEFEGPYQGQAGPYFGDYGGQWMPESLMAALQELTRTYEEARQDPAFEA
+ELRTLFRDYVNRPSLLSEVPRFAADTPGVRIFLKREDLNHTGSHKINNVIGQALLARRMG
+KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVVPVAIG
+ARTLKDAINEALRDWVASVDTTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQAGR
+LPDAVAACVGGGSNAMGLFHGFLDDPGVELYGFEAGGEGLETGRHAASITLGRTGVLHGA
+RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLHDTGRAVYEPVSDTECMDAFLRLTRT
+EGITPAIESAHALAGALRLARRWADEGLVGPDAPEGQERIIIVNLSGRGDKDVATAAAWF
+GLGTATEEKDPLEEMTPGEEQ
+>1_769
+MSADRPSTEPAIEFEGPYQGQAGPYFGDYGGQWMPESLMAALQELTRTYEQARQDPAFEA
+ELRTLFRDYVNRPSLLSEVPRFAADTPGVRIFLKREDLNHTGSHKINNVIGQALLARRMG
+KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVVPVAIG
+ARTLKDAINEALRDWVASVDNTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQAGR
+LPDAVAACVGGGSNAMGLFHGFLDDPEVELYGFEAGGEGLETGRHAASITLGRTGVLHGA
+RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLHDTGRAVYEPVSDTECMDAFLRLTRT
+EGITPAIESAHALAGALRLARRWADEGLVGPDAPEGEERIIIVNLSGRGDKDVATAAAWF
+GLGTAAEEKDPLEEMTPGEEQ
+>2_1779
+MSADRPSTEPTVEFEGPYQGQSGPYFGDYGGQWMPESLMAALQEVQRTYEEARQDPAFEG
+ELRTLFRDYVNRPSLLSDVPRFAADSPGVRIMLKREDLNHTGSHKINNVIGQALLARRMG
+KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVVPVAIG
+ARTLKDAINEALRDWVASVDTTHYLLGTVTGPHPFPAMVRYFHSVIGEEARQQVLAQTGR
+LPHAVAACVGGGSNAMGLFHGFLDDPEVELYGFEAGGDGLETGRHAASITLGRTGVLHGA
+RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLNDTGRAVYEPVTDTECMDAFLRLTRT
+EGITPAIESAHALAGALRLARRWADEGLVGPDTPEGEERIIVVNLSGRGDKDVATAAAWF
+GLGQADAEKDPLEELTPGEEQ
+>3_1666
+MTSTESVDVAGPFQDQPGPYFGRYGGQWMPESLMAALKEVADTYEAARQDPEFLAELEDL
+YANYVNRPSLLTEAPRFAAEVPGVRIFLKREDLNHTGSHKINNVIGQALLARRMGKTRLI
+AETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVIPVTIGARTLK
+DAINEALRDWVASVDTTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQTGRLPDAV
+AACVGGGSNAMGLFHGFLDDPEVELYGFEAGGDGVETGRHAASITLGRTGVLHGARTYLM
+QDEDGQTIDSHSISAGLDYPAVGPEHAFLNDTGRATYEPVTDTECMDALLRLTRTEGITP
+AIESAHALAGALRLARRWRDEGLVGEGTPEGEERIIIVNLSGRGDKDVATAAAWFGLGEA
+DEQKDPLEEMTPGEEQ
+>4_990
+MSADRPSTEPAIEFEGPYQGQAGPYFGDYGGQWMPESLMAALQELTRTYEQARQDPAFEA
+ELRTLFRDYVNRPSLLSEVPRFAADTPGVRIFLKREDLNHTGSHKINNVIGQALLARRMG
+KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVIPVAIG
+ARTLKDAINEALRDWVASVDNTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQAGR
+LPDAVAACVGGGSNAMGLFHGFLDDPEVELYGFEAGGEGLETGRHAASITLGRTGVLHGA
+RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLHDTGRAVYEPVSDTECMDAFLRLTRT
+EGITPAIESAHALAGALRLARRWADEGLVGPDAPEGQERIIIVNLSGRGDKDVATAAAWF
+GLGTAAEEKDPLEEMTPGEEQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000909.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000909.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f60742eccc89fb7ddec20bf1959a70dd084feb07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000909.fa
@@ -0,0 +1,77 @@
+>0_1048
+MLLTSLLLTLLSVVAAVPASRALGRDAGWVLAAPLLAAAGVLIAAWTGDVRTEHHPWIPA
+VGVDLDLRLNGLALVFAMIVLVIGAAILAYSSRYLSRDRTESRPGSFYLLMTAFAASMLL
+LVLADNIVVLFVAWEFTSFTSFFLIGRSGDHARDPAIRTLLVTVGGGLALLAAVALMAVR
+TGTASLSGVLASDVWSEAGFTTTVAVLLAVAAFTKSAQFPFQAWLPDSMVAISPVSAYLH
+AAAMVKAGIFLLLVFSPVLAGNPVWSALLIGSGLITALLGAVSAIRRHDLKGLLAYSTMS
+QLGLLVTAIGIGTPVALTAAIVHTVAHALFKSALFMLIGVVDHEAGTRDLRELAARHVRM
+PVTGTAIAVAALSMAGIPPLFGFISKEGLVEAALGTPGPAWLPVLVTAGIALTSVFTVAY
+SGRLVLGALGLWGPSPDGAAHSWPTGREDEVHEASATFWGVPVLAAAAGVALGLLPGVLD
+TPVSYAAEAASGAEVHAHLALWHGVNTALLVSAAIIVLGLLLVALRRPVERVASHAALPF
+SALDAVDEVRHRLIGVGAVVSRASGTLAPRPHLLIPALVLGLLAVAGVATIEDLPAVVGQ
+PSRWHDWVLVVLVGAGVIATIRAKTRIAAMVVVGVVGFGMTLWFLTLGAVDVALTQLMVE
+VLTVCVMVLLLRRLPARFSDEPTPRRMQAVLAASVAGVAATLGVLAFTGRSSMSEIAHFY
+LTQSYAQAGGTNVVNVILVDFRAVDTWGEMTVLGATALTIAALLLNRRPTPPQPSAVDMR
+SPLAHVRENLVHIRVFGRVFGVLIILLSAFLLLRGHYEPGGGFIAALVAGAGYALLYLAA
+DSDTAPELRWPYLAFIGSGIAVGTATGIVGYLTGKGFLGAAGVKVLDYGLSTTLAFDMGV
+YLAVIGLIVAAFSLLGPERPGEDPLRASSRDPGVAPAAPSSDPSAPTTTTAREEVTR
+>1_776
+MLLTSLLLTLLSVVAAVPASRVLGRDAGWVLAAPLLAAAGVLIAAWTGDVRTEHHPWIPA
+VGVDLDLRLNGLALVFAMIVLVIGAAILAYSSRYLSRDRTESRPGSFYLLMTAFAASMLL
+LVLADNIVVLFVAWEFTSFTSFFLIGRSGDHARDPAIRTLLVTVGGGLALLAAVALMAVR
+TGTASLSGVLASDVWSEAGFTTTVAVLLAVAAFTKSAQFPFQAWLPDSMVAISPVSAYLH
+AAAMVKAGIFLLLVFSPVLAGNPVWSALLIGSGLITALLGAVSAIRRHDLKGLLAYSTMS
+QLGLLVTAIGIGTPVALTAAIVHTVAHALFKSALFMLIGVVDHEAGTRDLRELAARHVRM
+PVTGTAIAVAALSMAGIPPLFGFISKEGLVEAALGTPGPAWLPVLVTAGIALTSVFTVAY
+SGRLVLGALGLWGPSPDGAAHSWPTGREDEVHEAPATFWGVPVLAAAAGVALGLLPGVLD
+TPVSYAAEAASGAEVHAHLALWHGVNTALLVSAAIIVLGLLLVALRRPVERVASHAALPF
+SALDAVDEVRHRLIGVGAVVSRASGTLAPRPHLLIPALVLGLLAVAGVATIEDLPAVVGQ
+PSRWHDWVLVVLVGAGVIATIRAKTRIAAMVVVGVVGFGMTLWFLTLGAVDVALTQLMVE
+VLTVCVMVLLLRRLPARFSDEPTPRRMQAVLAASVAGVAATLGVLAFTGRSSMSEIAHFY
+LTQSYAQAGGTNVVNVILVDFRAVDTWGEMTVLGATALTIAALLLNRRPTPPQPSAVDMR
+SPLAHVRENLVHIRVFGRVFGVLIILLSAFLLLRGHYEPGGGFIAALVAGAGYALLYLAA
+DSDTAPELRWPYLAFIGSGIAVGTATGIVGYLTGKGFLGAAGVKVLDYGLSTTLAFDMGV
+YLAVIGLIVAAFSLLGPERPGEDPLRASSRDPGVAPAAPSSDPSAPTTTTAREEVTR
+>2_1770
+MDEARHGLVRLGALVDRASGSVAPRVHLLIPACVLGAFALAGVFTVDDLPAVVGTPSRWH
+DWALVVLVGAGVVATIRAKTRISAMVVVGVVGFGVTLWFFTLGAVDVALTQLLVEVLTVC
+VMVLLLRRLPGRFRDEEAPRRVQAVVAATIAGVAATVGVLAFTGRSEMSEIAHFYLTQTY
+AQAGGVNVVNVILVDFRALDTLGEMTVLGATGLTVAALLLNRRPAPPQRSAVDLRSPLAH
+VRENLVHIRVFGRVFGVLIIALSVLLLLRGHYEPGGGFIAALVAGAGYALLYLAADHDTD
+RRLQWPYLTLIGGGIALGALTGVAGYLTGKGFLGAAGVKILGYGLSTTLAFDLGVYLAVL
+GLIVAAFSLLGPERSETEAGAEPDPTSPIADPAAEQTTGQTTEPTTAPGTAPTPAAAREE
+TSR
+>3_1659
+MLLTSLLLTLLAVVLAAPLGRTLGRDAGWVLALPLLTSAGALVSARAGGGGETVVERRPW
+IPSLGAHLDLRLDGLAFVFALLVLVVGAGILAYSSRYLPRDRDEARAGSFYTLMTAFAAS
+MLLLVLADNLVVLFVAWEFTSFASFLLIARSGDHARRPAIRTLLVTVGGGLCLLAAVALT
+AARTGTASLSGALASDAWADPGFAAPVAALLAVAAFTKSAQFPFQSWLPDSMVAISPVSA
+YLHAAAMVKAGIYLLLVFSPVLAGTPVWSALLIGSGLTTALLGAVSAIRRHDLKGLLAYS
+TMSQLGLLVTAIGVGTPTALAAAVVHTVAHALFKSTLFMLIGVVDHEAGTRDLRDLAARH
+VRMPVTGAAIAVAAASMAGLPPLLGFVSKEGLLDAALGAQGPAWLPGLVTAGIALTSVFT
+VAYSGRLVLGALGVWGTAPAGAADMWSAGRGEDVHEAPAAFWAVPVLGVVVTLVLGLVPG
+VLDEAVAAAATAAAGAPVHAHLALWHGVTPALLVSAGVIAAGLALVAARRPVERVASHAG
+LPFSGLGVVDGILRGAVSLGAAVSRVSGGIAPRAHLLMPALVLGAFAVAGVVASPDLPAV
+VGQPSRWHDWALVALVGVGVAATLRARTRIAAMVVVGTVGFGVTLWFFTLGAVDVALTQL
+MVEVLTVCVMVLLLRRLPARFSAESTPHRAGAVAAAVIAGVASTLSVLAFTGRREISDIA
+QYYLDRTYPDAGGHNVVNVILVDFRALDTLGEMTVLGVTGLTVAALLMNRRPAPPQPSAV
+DVRSPLAAVHENLVYARTFGRALGPIILVLSVLLLLRGHYEPGGGFIAALVGGAGYALLH
+LSADTDDEPRLRWPYLALIGGGVTLGTVAGLAGYLTGKGFLGSASVKVLGYSLGTTLAFD
+MGVYLAVLGLIVAAFRLLGPDNATADDAAPAPTTGGESAREEAAR
+>4_997
+MLLTSLLLTLLSVVAAVPASRVLGRDAGWVLAAPLLAAAGVLIAAWTGDVRTEHHPWIPA
+VGVDLDLRLNGLALVFAMIVLVIGAAILAYSSRYLSRDRTESRPGSFYLLMTAFAASMLL
+LVLADNIVVLFVAWEFTSFTSFFLIGRSGDHARDPAIRTLLVTVGGGLALLAAVALMAVR
+TGTASLSGVLASDVWSEAGFTTTVAVLLAVAAFTKSAQFPFQAWLPDSMVAISPVSAYLH
+AAAMVKAGIFLLLVFSPVLAGNPVWSALLIGSGLITALLGAVSAIRRHDLKGLLAYSTMS
+QLGLLVTAIGIGTPVALTAAIVHTVAHALFKSALFMLIGVVDHEAGTRDLRELAARHVRM
+PVTGTAIAVAALSMAGIPPLFGFISKEGLVEAALGTPGPAWLPVLVTAGIALTSVFTVAY
+SGRLVLGALGLWGPSPDGAAHSWPTGREDEVHEAPATFWGVPVLAAAAGVALGLLPGVLD
+TPVSYAAEAASGAEVHAHLALLHGVNTALLVSAAIIVLGLLLVALRRPVERVASHAALPF
+SALDAVDEVRHRLIGVGAVVSRASGTLAPRPHLLIPALVLGLLAVAGVATIEDLPAVVGQ
+PSRWHDWVLVVLVGAGVIATIRAKTRIAAMVVVGVVGFGMTLWFLTLGAVDVALTQLMVE
+VLTVCVMVLLLRRLPARFSDEPTPRRMQAVLAASVAGVAATLGVLAFTGRSSMSEIAHFY
+LTQSYAQAGGTNVVNVILVDFRAVDTWGEMTVLGATALTIAALLLNRRPTPPQPSAVDMR
+SPLAHVRENLVHIRVFGRVFGVLIILLSAFLLLRGHYEPGGGFIAALVAGAGYALLYLAA
+DSDTAPELRWPYLAFIGSGIAVGTATGIVGYLTGKGFLGAAGVKVLDYGLSTTLAFDMGV
+YLAVIGLIVAAFSLLGPERPGEDPLRASSRDPGVAPAAPSSDPSAPTTTTAREEVTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000917.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000917.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4fd1f9cfee99021718e7cfd5a01da3f1cd2f11f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000917.fa
@@ -0,0 +1,50 @@
+>0_1057
+MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY
+ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE
+KLTGN
+>1_785
+MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY
+ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE
+KLTGN
+>2_1760
+MTTTSNAPQVAINDIGTAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVESNEWMEGFESERAAWEQQY
+ADAQSRWEQHKEQVRRSFEEEANAGADTGAGMGGSSYSSEAPASDGGTLASDEALAALRE
+KLTGN
+>3_1650
+MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKVKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRQGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQDVTVEVLDVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDQLFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDDEGNYKYPEGFDVETNEWMEGFESERASWEQQY
+ADAQTRWEAHKEQVRRSLEEEAQAPAGNASTASSYSSEAPASDGGTLASDEALAALREKL
+TGN
+>4_1006
+MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY
+ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE
+KLTGN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000927.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000927.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f339ee9eca71f1b2f2a6437376de5e5c29d1ec11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000927.fa
@@ -0,0 +1,25 @@
+>0_1070
+MPETARNRLLHDLPAVTVRTCSVSEMDNNVYLLTSKTTGAQVLIDAAAEAEAIRDLIASA
+ADDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLR
+HGDTVGADGLRLEVVALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF
+RQLFTDVSDRIFDAFDDDVVVHPGHGASTTLGAERPHLPEWAERSW
+>1_798
+MPETARNRLLHDLPAVTVRACSVSEMDNNVYLLTSKTTGAQVLIDAAAEAEAIRDLIASA
+ADDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLR
+HGDIVGVDGLRLEVLALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF
+RQLFTDVTERIFDAFDDDVVVHPGHGASTTLGAERPHLPEWAERGW
+>2_1746
+MPETARNRLLHDLPAVTVRTSSVSEMDNNVYLLTSKTTGAQVLIDAADDAEAIRDLIASA
+AGDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLH
+HGDIVGADGLRLEVVALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF
+RQLFTDVSERIFDAFDDDVVVHPGHGASTTLGAERPHLPKWAERGW
+>3_1638
+MPATAEPRLLHDLPAVTVRAVSVSEMDNNAYVLTSKTTGAQVLIDAAAEPETLRDLLASA
+AADTPCELRLELIVTTHRHWDHVRALPALATVTGARTAAGEDDADAIAAETGVTPDVRLA
+HGSRTGAEGIELEVIALRGHTPGSVALAYRPEADEPAVLFTGDSLFPGGVGNTQGDAERF
+ASLIRDVEDRVFAAFDDDVVVHPGHGASTTLGAERPHLQEWRERGW
+>4_1020
+MPETARNRLLHDLPAVTVRACSVSEMDNNVYLLTSKTTGAQVLIDAAAEAEAIRDLIASA
+ADDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLR
+HGDIVGVDGLRLEVLALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF
+RQLFTDVTERIFDAFDDDVVVHPGHGASTTLGAERPHLPEWAERGW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000929.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000929.fa
new file mode 100644
index 0000000000000000000000000000000000000000..deb923ded6b61e61fac462ec05f8bf0c33c3baef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000929.fa
@@ -0,0 +1,30 @@
+>0_1074
+MTEETLQPEKPPTSEVLVIAGMSGAGRTTAAHALEDHGWDVVENMPPALFGTLAELIARS
+PEAFPRLAIVVDVRSRSYFEELYAALQHLANSGVEYRTVFLDAEDHVLLQRFEAGRRPHP
+MQGNARLLDGIRAERDVVEPLKARADVVVDTTELNVHGLATEITELFSESGPVTLRLTIM
+SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAAVADYVLSRPGVEDFLRTYVAM
+LGPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVHVQHRDMGRE
+>1_802
+MTEETLQPEKPPTSEVLVIAGMSGAGRTTAAHALEDHGWDVVENMPPALFGTLAELIARS
+PEAFPRLAIVVDVRSRSYFEELYAALQHLANSGVEYRTVFLDAEDHVLLQRFEAGRRPHP
+MQGNARLLDGIRAERDVVEPLKARADVVVDTTELNVHGLATEITELFSESGPVTLRLTIM
+SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAAVADYVLSRPGVEDFLRTYVAM
+LGPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVHVQHRDMGRE
+>2_1742
+MSEESLRPEKPPTSEVLVITGMSGAGRTTAAHALEDHGWYVVENMPPPLFITLADLVARS
+PEAFPRLAIVVDVRSRAYFPELHAALQQLENNGVEYRMVFLEADEHVLVRRFEAGRRPHP
+LQGNASLLDGIRAERDMLAELKARADVVVDTTELNVHGLATEITELFSVSGPVTLRLTLM
+SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAEVSDYVLTRPGVEDFLRSYTAM
+LAPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVQVQHRDMGRE
+>3_1634
+MSADEHLQPDKPPSSEVLVITGMSGAGRTTAAHALQDHGWYVVENMPPQLLGTLSDLVAR
+SPEAFPRLAIVVDVRSRSYFNELRTALQQLESTGVEFRTVFLEASDEVLVRRFEAGRRPH
+PLQGNARLLDGIQAEREILSELKERADIVVDTSALNVHGLATEVTQLFSEDGPVTVRLNV
+MSFGFKYGLPSDANFVADMRFVANPHWVPELRSKTGLDPEVSGFVLGQPGVQEFLSNYLA
+ALGPVVEGYRRENKHYATLAVGCTGGKHRSVAVAEELARRVAQWPRVSVHVDHRDVGRE
+>4_1024
+MTEETLQPEKPPTSEVLVIAGMSGAGRTTAAHALEDHGWDVVENMPPALFGTLAELIARS
+PEAFPRLAIVVDVRSRSYFEELYAALQHLANSGVEYRTVFLDAEDHVLLQRFEAGRRPHP
+MQGNARLLDGIRAERDVVEPLKARADVVVDTTELNVHGLATEITELFSESGPVTLRLTIM
+SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAAVADYVLSRPGVEDFLRTYVAM
+LGPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVHVQHRDMGRE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000935.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000935.fa
new file mode 100644
index 0000000000000000000000000000000000000000..532b7bcc0fbb8db046684ea7cdf50e116216e5a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000935.fa
@@ -0,0 +1,30 @@
+>0_1080
+MAEQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLSDADHDQEAVEVAVFPPFTGLRSVQ
+TLVTGDRLDLVYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDALV
+ARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEPV
+WAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDVD
+GALVGGASLDADEFAKIVRFDQA
+>1_808
+MAEQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLTDADHDQEAVEVAVFPPFTGLRSVQ
+TLVTGDRLDLVYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDALV
+ARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEPV
+WAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDVD
+GALVGGASLDADEFAKIVRFDQA
+>2_1735
+MAETAARVPLIAGNWKMNLDHREAVTLVQRLAWLLTDADHDHEDVEVAVFPPFTDLRAVQ
+VLVTGDRLDVAYGAQDLSPEDSGAYTGDVSGAFLAALGCRYAIVGHSERRTIHGEDDALV
+ARKAAAALRHGLSPVVCVGEGLDVRQAGRHVAHTVAQLEGSLVGLSAEDVARTVVAYEPV
+WAIGTGEVAGAGDAQEMCAALRARVGELHGDDVAAGLRILYGGSVKSTSAPELLAQPDVD
+GALVGGASLDAEEFARIVRFDQA
+>3_1628
+MSVVQPVRVPLIAGNWKMNLDHQEAVTLVQRLGWLLGDADHEQGNVEAAVFPPFTDLRSV
+QTLVAADRIGVAYGAQDVSAEDSGAFTGEVSGAFLAKLGCAYAIVGHSERRTLHHEDDAL
+VARKAAAALRHGLVPVVCVGEGLDVRQAGRHVEHTVAQLRGSLDGLSSEDVARVVVAYEP
+VWAIGTGEVASAADAQEMCAALRADLAERHGAEVAERVRVLYGGSVKSSSAPELLAQPDV
+DGALVGGASLDADEFARIVRSDAAH
+>4_1030
+MAEQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLTDADHDQEAVEVAVFPPFTGLRAVQ
+TLVTGDRLDLAYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDALV
+ARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEPV
+WAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDVD
+GALVGGASLDADEFAKIVRFDQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000938.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000938.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e44635a1c65ba446b6c2e94b141f44bf03c6583
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000938.fa
@@ -0,0 +1,50 @@
+>0_1083
+MAGESRTAPRNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPA
+FSLVGFGRRSWSDEEFADYVRAAVEASSRTTFDETVWDQFQGGLRFVSGAFDDEAAYVRL
+DEVLAELETSRGTRGNTAFYLSIPPDWFEAVSRHLADQGLADRSQPAEGPWRRVVIEKPF
+GHDLASAQELNAVIERVFPSDAVFRIDHYLGKETVQNILAFRFANRMFEPLWNAEHVDHV
+QITMAEDIGIGGRASYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRAEKEKVLE
+AVTVPDTPEGLAAASARGQYTSGWQGGERVTGFLDEEGFNPASVTETYAALKVGIRTRRW
+QGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHDGDEFGQNIIVIRVQPDEGVTIRFA
+SKVPGTQTEIRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIVD
+PFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRSWRRP
+>1_811
+MAGESRTAPRNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPA
+FSLVGFGRRSWSDEEFADYVRAAVEASSRTTFDETVWDQFQGGLRFVSGAFDDEAAYVRL
+DEVLAELETSRGTRGNTAFYLSIPPDWFEAVSRHLADQGLADRSQPAEGPWRRVVIEKPF
+GHDLASAQELNAVIERVFPSDAVFRIDHYLGKETVQNILAFRFANRMFEPLWNAEHVDHV
+QITMAEDIGIGGRASYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRAEKEKVLE
+AVTVPDTPEGLAAASARGQYTSGWQGGERVTGFLDEEGFNPASVTETYAALKVGIRTRRW
+QGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHDGDEFGQNIIVIRVQPDEGVTIRFA
+SKVPGTQTEIRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIVD
+PFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRSWRRP
+>2_1732
+MPGESKAAARNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPS
+FSLVGFGRRDWSDEEFAEYVRAAVEASARTTFDETVWDQFRGGLRFVSGAFDDEAAYVRL
+GEVLGELESSRGTRGNTAFYLSIPPDWFEDVSRHLADQGLADRSQPADGPWRRVVIEKPF
+GHDLASAQELNAVIERVFPPDAVFRIDHYLGKETVQNILAFRFANRMFEPIWNAEHVDHV
+QITMAEDIGIGGRAGYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRTEKEKILE
+AVQVPDTPAGLEAASARGQYTSGWQGGERITGFLDEEGFNPESVTETYAALKVGIRTRRW
+QGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHEGDEFGQNVIVIRVQPDEGVTIRFA
+SKVPGTQSEVRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIVD
+PFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRAWRRP
+>3_1625
+MRPEPGGPARRNPLRDPRDRRLTRIAGPSALVLFGVTGDLARKKLLPAMYDLAHRGLLPP
+SFSLVGFGRRDWSEAEFADYVRAAVEAGSRTAFNETVWDQFRGGLRFVSGAFGDADAYAR
+LDEVLTELESSRGTGGNTAFYLSIPPDWFEDVSRHLADQGLADRSQPADGPWRRVVIEKP
+FGHDLASAHELNAVIERVFPPDAVFRIDHYLGKETVQNILAFRFANRIFEPLWSAEHVDH
+VQITMAEDIGIGGRAGYYDGVGAARDVIQNHLLQLLALTAMEEPISFDAAHLRAEKEKVL
+AAVRVPCTPEGLEAASARGQYTSGWQGGEQVTGFLDEEGFNPASVTETFAALKVDIGTRR
+WQGVPFYLRAGKRLGRRVTEIAVVFKSPPHLLFPVHPGDEFGQNVIVIRVQPDEGVTIRF
+ASKVPGTQHEVRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQEEVELSWAIV
+DPFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRTWRRP
+>4_1033
+MAGESRTAPRNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPA
+FSLVGFGRRSWSDEEFADYVRAAVEASSRTTFDETVWDQFQGGLRFVSGAFDDEAAYVRL
+DEVLAELETSRGTRGNTAFYLSIPPDWFEAVSRHLADQGLADRSQPAEGPWRRVVIEKPF
+GHDLASAQELNAVIERVFPSDAVFRIDHYLGKETVQNILAFRFANRMFEPLWNAEHVDHV
+QITMAEDIGIGGRASYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRAEKEKVLE
+AVTVPDTPEGLAAASARGQYTSGWQGGERVTGFLDEEGFNPASVTETYAALKVGIRTRRW
+QGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHDGDEFGQNIIVIRVQPDEGVTIRFA
+SKVPGTQTEIRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIVD
+PFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRSWRRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000939.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000939.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a989fda7973bd8fec0249368c6404ab0c0d544b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000939.fa
@@ -0,0 +1,50 @@
+>0_1084
+MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED
+SRALVPDIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ
+LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW
+DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY
+LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL
+EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR
+>1_812
+MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED
+SRALVPDIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ
+LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW
+DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY
+LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL
+EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR
+>2_1731
+MSTLGLSATGSALEAIDRHLPTLLEDRVASRLGAQDAGLWGEAAREESARRLGWIDLFED
+SRALVRHIDALSRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVMEAAFREAGIDPRSRLVAVTDPGSPLHAECES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLTADDADNPGLQ
+LGAALGGTAPLRDKLVFTDHGSGIDGLPAWAEQLIAESTGKDGTGLLPVVVADGDPETGW
+DAPDMLQVQLVGEDAPAAPAHGVQVSGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KTAARSLLDAPARERTADRTVDGVELSGPEAVVSAADLAGVLRATADLVPENGYLAVHAY
+LSRHDDAELEEVRADLARLAGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQVTGDADLDV
+EVPGRPFSLGRLIAAQAAGDARVLVEHGRPVVTLHLPHRAAGIDAIRTAARAR
+>3_1624
+MSTFGLTATGAALDAVDRHVPALVAERFASRLAAEDADLWGPDARDEAAKRLGWISLFEE
+SRTVAAEAAALAEELRGQGLTRVVLAGMGGSSLAPEVIAATAGAELEVLDSTDPQQVAAV
+LDHDLERTVLVVSSKSGSTVETDSQRRIVEAALAAEDIDPASRIVVVTDPGSPLEEASVE
+AGYRAVFTADPTVGGRYSALTAFGLVPAALAGVDVESLLDEAEDVLDLVTADDADNPALQ
+LGAAIGGTEPLRDKLVIQDLGSGIDGFGDWVEQLIAESTGKDGTGLLPVVVRPGDPETAW
+EAPDLLKVTLVSESEESPAGGDGVRLHGSLGALLLTWEAATAVAGRLLGINPFDQPDVEA
+AKAAARELLDSPAEEAEPGTVIHGVEVSGPESVTSADDLRGVLAAVRELVPEDGYLAVHA
+YLDRHADVDLAGIRADLASALGRPVTFGWGPRFLHSTGQYHKGGPRNGVYLQVTGDAALD
+VEVPGRPFTLGRLIAAQAAGDADVLRRLGRPVVTLRLRDRSAGIAALRTAAREA
+>4_1034
+MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED
+SRALVPHIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ
+LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW
+DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY
+LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL
+EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000943.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000943.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cde6384672cf725a631b63712025f62325c72ad1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000943.fa
@@ -0,0 +1,35 @@
+>0_1088
+MSTTTPAAGTAPAGLAARLPQRLTKATMALAVASLASEIGIIVTGGAVRLTGSGLGCPTW
+PKCSPESLTNTPEMGIHGYIEFGNRTLTFVLVVIAAAMFLSLWNLRGTHRSPFWLSVGLL
+AGIPAQALVGGVVVLTNLNPWWVAGHFIVSSIMVAVATLLVVRIAAERRAGRAGVPLVDG
+ATTVRSRAAAWAAFALTWAAVYLGTVVTGTGPHSGDPGSPRHEFDPLLVTRIHVIPVYLL
+LAAALVLFFTVRRAAGASRLQRAAVLRLLLALVFQAAVGYTQHFTGLPIGVVLLHMLGSA
+LLVASATEAWDRQVARYVTAGPGAAVETATPARTVAAG
+>1_816
+MSTTTPAAGTAPAGLAARLPQRLTKATMALAVASLASEIGIIVTGGAVRLTGSGLGCPTW
+PKCSPESLTNTPEMGIHGYIEFGNRTLTFVLVVIAAAMFLSLWNLRGTHRSPFWLSVGLL
+AGIPAQALVGGVVVLTNLNPWWVAGHFIVSSIMVAVATLLVVRIAAERRAGRAGVPLVDG
+ATTVRSRAAAWAAFALTWAAVYLGTVVTGTGPHSGDPGSPRHEFDPLLVTRIHVIPVYLL
+LAAALVLFFTVRRAAGASRLQRAAVLRLLLALVFQAAVGYTQHFTGLPIGVVLLHMLGSA
+LLVASATEAWDRQVARYVTAGPGAAVETATPARTVAAG
+>2_1727
+MASLASEIGIIVTGGAVRLTGSGLGCPTWPKCTPESLTNTPEMGIHGYIEFGNRTLTFVL
+VVIAAAMFLSLWRLRRTHRSPFWLSVGLLAGIPAQAVVGGIVVLTELDPWWVAGHFIVSS
+VMVAVATLLVIRIGAERRAGRAGVRIVDGVTTGASRAAAWAAFAFTWAAVYLGTVVTGTG
+PHGGDPDAPRHAFDPLLVTRVHVIPVYLLIAAALVLLFTVRRAEGASRLQRAAVLRLLLA
+IAVQAAIGYTQHFTGLPVVLVILHMLGSALLVAAATEVWDRQRSRYVTAGPAALLDADPT
+PVTANAR
+>3_1620
+MTASPTTARPAAGGSSARRPPDRVTGVTVGLALASLISQMVIVVTGGAVRLTGSGLGCPT
+WPKCTPESLTTTAEMGIHGIIEFGNRTLTGVLGVIALLMIATLWRLRRSHRQAFTLSLLL
+LAGIVLQAVVGGVTVWMHLDPRIVGVHFVISGALIALATMLWVRLRAEHRHGAGAPVADG
+TTTPASRTASRVAYAALWLALVVGTLVTGTGPHSGDPAAARHGFDALMITRLHVVPVYIT
+VAATLVLLWQVLRTPGSGAGQRVAAWSLLGAVLLQGLLGYWQHFTGLPVGVVAAHLAGAT
+VAVVAGTLAWQRQTSRYRAPAVA
+>4_1038
+MSTTTPAARTAPAGLAARLPQRLSKATMALAVASLASEIGIIVTGGAVRLTGSGLGCPTW
+PKCSPESLTNTPEMGIHGYIEFGNRTLTFVLVVIAAAMFLSLWNLRGTHRSPFWLSVGLL
+AGIPAQALVGGVVVLTNLNPWWVAGHFIVSSIMVAVATLLVVRIAAERRAGRAGVPLVDG
+ATTGRSRAAAWAAFALTWAAVYLGTVVTGTGPHSGDPGSPRHEFDPLLVTRAHVVPVYLL
+LAAALVLFFTVRRAAGASRLQRAAVLRLLLALVFQAAVGYTQHFTGLPIGVVLLHMLGSA
+LLVASATEAWDRQVARYVTAGPGAAVETATPARTVAAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000944.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000944.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e3778187c912b4fdb60b03c5b586a87ceeb3a97b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000944.fa
@@ -0,0 +1,30 @@
+>0_1089
+MSTPVVDHRAPAGTGAHAGAAPLAARVLRQAGYETGTALRNGEQLLVTVVLPLLALVGVH
+VTGLLDAPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALATTPLGTLGLV
+AGKALAVVALLLVQVSVIGGVGLALGWRPDPEGILPALVALALGAAAFTALGLLLAGTAR
+PEATLAVANLLWVLFGAVGGTVFPARVPGVDLLPSGALGTALRAALLDGAWSPVPLLVLT
+LWGAVAVAAALRWFRWRP
+>1_817
+MSTPVVDHRAPAGTGAHAGAAPLAARVLRQAGYETGTALRNGEQLLVTVVLPLLALVGVH
+VTGLLDAPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALATTPLGTLGLV
+AGKALAVVALLLVQVSVIGGVGLALGWRPDPEGILPALVALALGAAAFTALGLLLAGTAR
+PEATLAVANLLWVLFGAVGGTVFPARVPGVDLLPSGALGTALRAALLDGAWSPVPLLVLT
+LWGAVAVAAALRWFRWRP
+>2_1726
+MSAPIAPGSAEPRTAGQVPEPGTAPHAGAAPLATRVLRQAAYETGTALRNGEQLLVTVVL
+PLLALVGVHVTGLLDEPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALAT
+TPLGTLGLVAGKALSVVALLLVQVAVIGGVGLALGWRPEAAGILPAVVALALGAAAFTAL
+GLLLAGTARPEATLAAANLLWVLFGAVGGTVFPSRVPGVDLLPSGALGSALRAALVDGAG
+APIPLLVLALWCAVAVAAALRWFRWRP
+>3_1619
+MSAPAAPIPASHAGAAPLGARILAQARYETVTALRNGEQLLVTLVLPLLALVGVHVTGLL
+DAPGRNGLDLAVPGVLALAVISAAFTATAISTGFERRYDVLAALATTPLGTGGLVAGKAA
+AVAAVLLLQTIVIGGVGLALGWSPDPAGIPPAVVALLLGAAAFTALGLLLAGTARPEATL
+AVANLVWVLLGALGGTVFPSRWAWMDLLPSGALGTALRSALQDGAWAPSALAVLAAWTVM
+AVAAALRWFRWRP
+>4_1039
+MSTPVVDHRAPAGTGAHAGAAPLAARVLRQAGYETGTALRNGEQLLVTVVLPLLALVGVH
+VTGLLDAPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALATTPLGTLGLV
+AGKALAVVALLLVQVSVIGGVGLALGWRPDPEGILPALVALALGAAAFTALGLLLAGTAR
+PEATLAVANLLWVLFGAVGGTVFPARVPGVGLLPSGALGTALRAALLDGAWSPVPLLVLT
+LWGAVAVAAALRWFRWRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000948.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000948.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a12d0e5297c312a7bac4ce83f6e84495e20387a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000948.fa
@@ -0,0 +1,40 @@
+>0_1093
+MTDTVENTQRTMIPGMGEEGEKLTAAQNPAARAGGRERNAAGSRADRLSSFELSDFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPAVTVAEQAGVTVETVARDDARVGSVLTP
+DDRVSAAAWNSVSEATVVTISGEVAEPVRIDVVGSSADPAAMHLTVLVEENAQADVVIAH
+RGTAVLAQNVEFDVRRDARLNVVALQAWEGDAVHVSAQQASVATNAHFKHVAVSYGGGVV
+RLTPTARFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPDCVSNVLYKGALQGTDARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGISETEARRLIVRGFLNEIIQKIGIGDVEDELTAVMEDELRIAQL
+>1_821
+MTDTVENTQRTMIPGMGEEGEKLTAAQNPAARAGGRERNAAGSRADRLSSFELSDFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPAVTVAEQAGVTVETVARDDARVGSVLTP
+DDRVSAAAWNSVSEATVVTISGEVAEPVRIDVVGSSADPAAMHLTVLVEENAQADVVIAH
+RGTAVLAQNVEFDVRRDARLNVVALQAWEADAVHVSAQQASVATNAHFKHVAVSYGGGVV
+RLTPTARFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPDCVSNVLYKGALQGTDARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGISETEARRLIVRGFLNEIIQKIGIGDVEDELTAVMEDELRIAQL
+>2_1722
+MTDTVENTQGSMIPGMGEEGEKLTVAQTSAPRAGAPERNAAGSRADRVSSYELADFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPSVTVAEQVGVRVETVARDDARVGSVLTP
+DDRVSAAAWNSVAQATVVTVSGEVAEPVRIDVVGSSAEPAAMHLTVIVEENAQADVVLAH
+RGTAVLAQNVEFDVRRDARLNVVSLQAWEDDAVHVSAQQASVATNARFKHVAVSHGGSVV
+RLTPTSRFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPRCVSNVLYKGALQGADARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGISETEARRLIVRGFLNEIIQKIGVRDVEDELTAVMEDELRIAAL
+>3_1615
+MENTERNMIPGMGEEGETLAGGQDAGAPVATRGQGQSRADRVSSKDLADFPVLTGREEDW
+RFTPLERLGGLHLPGGDDARLTGAAPAVTVSETAGVSVETVGRDDARVGSVLTPDDRVSA
+AAWTSFAEATVVTVSGEPGEPVRIEVTGSGVEPAAQQLTLIAEENAHADVVLTHRGSAVL
+AQNVEFEVRRGASLNVVSVQAWDDDAVHVGAHQASVARDAHLKHVTVTHGGSLVRLTPTA
+RFSDERGEAEMYGLYYADAGQHLENRLFVDHNRPNCVSNVLYKGALQGQDAHTVWVGDVL
+IRTEAEGTDSYEKNENLLLTDGARADSVPNLEIETGVIEGAGHASATGRFDETQLFYLMA
+RGIPESEARQLIVRGFLNEILQKIGIADVQDELTAVMEEELRVTAL
+>4_1043
+MTDTVENTQRTMIPGMGEEGEKLTVAQNPAARAGGRERNAAGSRADRLSSFELSDFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPAVAVAEQAGVTVETVARDDARVGSVLTP
+DDRVSAAAWNSVSEATVVTISGEVAEPVRIDVVGSSADPAAMHLTVLVEENAQADVVIAH
+RGTAVLAQNVEFDVRRDARLNVVALQAWEGDAVHVSAQQASVATNAHFKHVAVSYGGGVV
+RLTPTARFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPDCVSNVLYKGALQGTDARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGIPETEARRLIVRGFLNEIIQKIGVGDVEDELTAVMEDELRIAQL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000953.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000953.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ebf287391ee13cdc2e36c72970898832bf965504
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000953.fa
@@ -0,0 +1,35 @@
+>0_1098
+MSIPAPMTDPTARDAERLPALRFGFLATGPWILGFVVCVLFAFLCHALAQWQWDRRVEVQ
+HRVNRVLENYDDDPVPFAEASRLFTAFQTDDEWTPVTLTGEYLVDETLIVRNRPRAGQPG
+YEVLVPFRTDEGPVVVVDRGWLPVGNSPGQPDAVPAPPAGHAEVVVRVKPGEPALDRDAP
+DGQVPSIDLAEIADTVGGPVAGTAYGIMVTEDPAVEPMPQKLVEPTLDEGPHLSYAIQWY
+LFAAMGFGVWGYSAWMRARNDRADALDDAADDGLLSAHRVPRAKPARRRRDGRLTDEEAE
+DALFD
+>1_826
+MSTPAPMSAPTARDAERLPPLRFGFLATGPWILGFVLCILFAFLCHALAQWQWDRRVEVQ
+HRVNRVLENYDDDPVPFAEASRLFTAFQTEDEWTPVTLTGEYLVDETLIVRNRPRAGQPG
+YEVLVPFRTDEGPVVVVDRGWLPVGNSPGQPDAVPAPPAGHAEVVVRVKPGEPALDRDAP
+DGQVPSIDLAEIADTVGGPVAGTAYGIMVTEDPAVESMPQKLVEPTLDEGPHLSYAIQWY
+LFAAMGFGVWGYSAWMRARNDRADALDDAADDGLLSAHRVPRAKPARRRRDGRLTDEEAE
+DALFD
+>2_1716
+MTAPAPATGFRRDPGSARPPRLRFDFLATPPWILGFVLCILFAFACHYLAQWQWERRVQV
+QHQVNRVLENYDDAPVPFAQASRMFTDFDAQDEWTPVTLSGEYLAEETLVVRNRPRAGRP
+GYEVLVPFRTDEGPVVVVDRGWLPVGNTPGRPDAVPAPPAGPAEVVVRVKPGEPALDRDA
+PEGQVPSIDLAEIRGHVGGPVADTAYGIMVEEDPAVQDLPQKLVEPTLDEGPHLSYAIQW
+YLFAAMGFGVWGYSAWMRARNDRADALEGVRDDGMLTARRAPRPKPVRRRRDGRPTDEEA
+EDALFD
+>3_1610
+MTPAPAPTDTPDAPGAERLPPLRFGFLASGPWILGFVVCILFAFLCHGLAQWQWDRRVQV
+MHDVNRVLANYDDDPVPFAEAPRLFTDFDSEDEWTPVTLTGRYETDETLVVRNRPRAGAP
+GYEVLVPFVTEEGVTVIVDRGWLPIGSQPGRPDAIPAPDPAAGEVVVRVKPGEPALDRDA
+PEGQVPSIDLAAIERILGRPIADTAYGLMVSESPAAATVPNQLVAPTLDEGPHLSYAIQW
+YIFAAMGFAVWGYSAWMKARNDRADALEDAEDDGLLAARRAPRPKARRRRRGGRPSDEEV
+EDALQEDVLRDRPGQASEIRSR
+>4_1048
+MSTPAPMSAPTARDAERLPPLRFGFLATGPWILGFVLCILFAFLCHALAQWQWDRRVEVQ
+HRVNRVLENYDDDPVPFAEASRLFTAFQTEDEWTPVTLTGEYLVDETLIVRNRPRAGQPG
+YEVLVPFRTDEGPVVVVDRGWLPVGNSPGQPDAVPAPPAGHAEVVVRVKPGEPALDRDAP
+DGQVPSIDLAEIADTVGGPVAGTAYGIMVTEDPAVESMPQKLVEPTLDEGPHLSYAIQWY
+LFAAMGFGVWGYSAWMRARNDRADALDDAADDGLLSAHRVPRAKPARRRRDGRLTDEEAE
+DALFD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000954.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000954.fa
new file mode 100644
index 0000000000000000000000000000000000000000..109d29706967663233fb6c71a4ca8032af8afb65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000954.fa
@@ -0,0 +1,20 @@
+>0_1100
+MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMRVYLVQMLVRTACFVAAL
+FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLRAVPAQGPALAPRPDDTAAPEPVV
+LTGDLVDDPRDRAPRALGRGSSSAGSPGLPGRGGA
+>1_828
+MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMKVYLVQMLLRTACFVAAL
+FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLRAVPAQGPALAPRPDDTAAPKPVV
+LTGDLVDDPRDRAPRALGRGSSSAGGPGLPGRGAA
+>2_1715
+MTSSAAGSRAGRPARAGRSTGPQVQGVTTASAARSEDREARMKVYLVQMLIRTVCFGAAL
+FTTGWWQLLFILGAVALPYVAVVQVNNAGPRQAGSLRAVPAEGPELTARPADAPGPASPV
+VLTGDVVDDPREVGPRALPPGSPSEGARRLPGRGAA
+>3_1608
+MAAIVREPDAVQGVTTAAAPRSADRDARTRVYVVQMAVRTACFIAALFTHGWWQILFILG
+AVVLPYVAVVRVNNTGPREAGRRRDVARTAPAVPALPAEPSPVPTGPVVLVGEVVEDDDP
+AARRALPAGSPGETGRGRP
+>4_1050
+MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMKVYLVQMLLRTACFVAAL
+FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLHAVPAQGPALAPRPDDTAAPKPVV
+LTGDLVDDPRDRAPRALGRGSSSAGGPGLPGRGAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000956.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000956.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aba6b513546fb58aab13cc8c44ea147e3d2598af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000956.fa
@@ -0,0 +1,30 @@
+>0_1103
+MSTLRRLVVTADPALLVTDAPPAGVPDDAERLTDDGLLGWRFAADEWAAAPEPGSGWDVL
+TVPATVAAAPAPLVVTDVDSTLIRQEVIELLAAHAGREAEVAEVTERAMRGELDFAASLH
+ARVEALAGLPVGVVADVVRAIRPTDGALALIEAVTAAGGRVCAVSGGFTQVLAPLAEAWG
+VHAYCANELEVQDGHLTGKVLGDVVDRAAKAAMLRAWAEDAGLTPEQAVGVGDGANDIDL
+LEAAGCGVALCAKPILREHADVVVDVPSFTPLRWLLGL
+>1_831
+MSTLRRLVVTADPALLVTDAPPAGVPDDAERLTDDGLLGWRFAADEWAAAPEPGSGWDVL
+TVPATVAAAPAPLVVTDVDSTLIRQEVVELLAAHAGREAEVAEVTERAMRGELDFAASLH
+ARVEALAGLPVGVVADVVRAIRPTDGALALIEAVTAAGGRVCAVSGGFTQVLAPLAEAWG
+VHAYCANELEVRDGHLTGKVLGDVVDRAAKAAMLRAWAEDAGLTPEQAVGVGDGANDIDL
+LEAAGCGVALCAKPILREHADVVVDVPSFTPLRWLLGL
+>2_1712
+MSTLRRLVVTADPALLADRTPPAGVPDDAERLLEDGLLGWRFAADEWAAAPEPGPGWAVH
+TLPAAVAEAPVPLVVTDVDSTLIRQEVIELLAAHAGREAEVAAVTERAMRGELDFAASLH
+ARVEALAGLPVGVVDDVVRAIRPTAGALALIEAVTAAGGRVCAVSGGFSQVLAPLAQAWG
+VHAYCANELEVHDGHLTGRVAGDVVDRAAKAAMLRAWAEDAGLSPEQAVGVGDGANDIDL
+LDAAGAGVALCAKPVLREHADVVVDVPSFTPLRWLLGL
+>3_1605
+MTQARHLLYRAVPAGTDSPVAPAWAPLPADAEHLAADGLAGLRWEGSVPSAEEATALPED
+WALASLPQSVAAAPTPLVVTDVDSTLIQQEVIELLAAHTGREAEVAAVTERAMRGELDFA
+QSLHARVEALAGLPASVVDDVVARVRPTDGAVELIAAVNAAGGRVCAVSGGFTQVLAPLA
+EAWGVHAYCANELEVRDGHLSGKVLGDVVDRAAKAAMLRAWAEDAGLSPEQAVGVGDGAN
+DIDLLEVAGCGVALCAKPILREHADVVIDVPSFTPLRWLLGL
+>4_1053
+MSTLRRLVVTADPALLVTDAPPAGVPDDAERLTDDGLLGWRFAADEWAAAPEPGSGWDVL
+TVPATVAAAPAPLVVTDVDSTLIRQEVVELLAAHAGREAEVAEVTERAMRGELDFAASLH
+ARVEALAGLPVGVVADVVRAIRPTDGALALIEAVTAAGGRVCAVSGGFTQVLAPLAEAWG
+VHAYCANELEVRDGHLTGKVLGDVVDRAAKAAMLRAWAEDAGLTPEQAVGVGDGANDIDL
+LEAAGCGVALCAKPILREHADVVVDVPSFTPLRWLLGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000963.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000963.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f562e7d90328c750be8343856a1f9e6150a0e41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000963.fa
@@ -0,0 +1,40 @@
+>0_1112
+MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP
+GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID
+TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP
+DTAELAHEVNELISELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE
+DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR
+>1_840
+MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP
+GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID
+TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP
+DTAELAHEVNELIAELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE
+DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR
+>2_1700
+MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGEPRDPDYHGARVLTYPNPP
+GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANMAGHLGKLMHGVPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAEKTAYLGADAVIAVSDGMRRDILACYPEVDPEKVHTVHNGID
+TEAWTPQTETDALEKYGIDPTRPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP
+DTPELAHEVNGLIAELRRTREGVVVIEGMIPRREVTQILSAATVFACPSVYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVQDGETGLLVPIEQVADGTGAPADEDAFAADFAAALTRVLE
+DPERATAMGEAGRARAIEHFSWEAIAERTIEVYEAVLR
+>3_1597
+MRIDIVTKEFPPTIYGGAGVHVAELTRVLSSRADVHVHAFGGAREPDYHGATVTSYAQPA
+GFESANGAVQTLVTDLDIVGDLDGADVIHSHTWYANMAGHLGGLMHGVPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAESTAYHGAAAVIAVSEGMRRDILRCYPDVDPAKVHTVHNGID
+TQLWTPQTGTDALTKYGIDPDRPSVAFVGRITRQKGVPHLLRAALQLPEDVQLVLCVGAA
+DTPELAREVEGLIGRLRAEREGVVVVEGMIPRGEVTQILSAATVFACPSIYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVDDGVTGLLVPVEQADDGTGTPVDEEKFAADLAKALSTVLA
+DPERATAMGEAGRARAIEHFSWETIADRTMEVYAAVAR
+>4_1062
+MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP
+GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID
+TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP
+DTAELAHEVNELISELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE
+DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000964.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000964.fa
new file mode 100644
index 0000000000000000000000000000000000000000..70be84a1cb38225acfbb99926acf3a3375adbc2c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000964.fa
@@ -0,0 +1,65 @@
+>0_1113
+MTVHEKLAPQSSTPSTEVPSDVAEIAPERPTPGSLDAAALEEALLGRWAAERRESRELVK
+DPALWRDPLLGMDEHRARVLRQLGVLVERNAVHRAFPREFGGEDNHGGNLAAFGDLVLAD
+PSLQIKAGVQWGLFSSAILHLGTAEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIATT
+ATYDEATQEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITRGVNHGVHCFYVPIRDEE
+GAFLPGVGGEDDGLKGGLNGIDNGRLHFTQVRIPRTNLLNRYGDVAEDGTYSSPIASPGR
+RFFTMLGTLVQGRVSLSLAATTASFLGLHGALAYAEQRRQFKASDPQREEVLLDYQNHQR
+RLIDRLARAYADAFASNELVEKFDDVFSGRSDTDVDRQELETLAAAVKPLTTWHALDTLQ
+EAREACGGAGFLAENRVAQMRADLDVYVTFEGDNTVLLQFVGKRLLTDYSKEFGRLNVGA
+VSRYVVHQASDALHRAGLHKAVQSVADGGSERRSANWFKDPAVQHELLTERVRAKTADIA
+GTLSGARGKGQAAQAEAFNTRQHELIEAARNHGELLQWEAFTRALEGITDETTKTVLTWL
+RDLFALRLIEDDLGWFVAHGRVSSQRARALRGYVNRLAERLRPFALELVESFGLEPEHLR
+MAVATDAETQRQEEAHAWFTARRAAGEEPEDEKAVRAREKAARGRRG
+>1_841
+MTVHEKLAPQSSTPSTEVPSDVAEIAPERPTPGSLDAAALEEALLGRWAAERRESRELVK
+DPALWRDPLLGMDEHRARVLRQLGVLVERNAVHRAFPREFGGEDNHGGNLAAFGDLVLAD
+PSLQIKAGVQWGLFSSAILHLGTAEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIATT
+ATYDEATQEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITRGVNHGVHCFYVPIRDEE
+GAFLPGVGGEDDGLKGGLNGIDNGRLHFTQVRIPRTNLLNRYGDVAEDGTYSSPIASPGR
+RFFTMLGTLVQGRVSLSLAATTASFLGLHGALAYAEQRRQFKASDPQREEVLLDYQNHQR
+RLIDRLARAYADAFASNELVEKFDDVFSGRSDTDVDRQELETLAAAVKPLTTWHALDTLQ
+EAREACGGAGFLAENRVAQMRADLDVYVTFEGDNTVLLQLVGKRLLTDYSKEFGRLNVGA
+VSRYVVHQASDALHRAGLHKAVQSVADGGSERRSANWFKDPAVQHELLTERVRAKTADIA
+GTLSGARGKGQAAQAEAFNTRQHELIEAARNHGELLQWEAFTRALEGITDETTKTVLTWL
+RDLFALRLIEDDLGWFVAHGRVSSQRARALRGYVNRLAERLRPFALELVESFGLEPEHLR
+MAVATDAETQRQEEAHAWFTARRAAGEEPEDEKAVRAREKAARGRRG
+>2_1699
+MTVHEKLAPQSPTHTTEVPSDVAEIAPEHPEPGSLDSAALQDALLGAWAEDRRTARALVR
+DPRLHRDPLLGMDEHRERVLGQLGVLVENGAVHRMFPKEFGGDDNHGGNIAAFADLVLGD
+PSLQIKAGVQWGLFAAAILHLGTEEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIGTT
+ATYDEAAGEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITKGVNHGVHCFYVPIRDED
+GAFLPGVGGEDDGLKGGLNGIDNGRLHFDQVRVPRTNLLNRYGDVAEDGTYSSPIESPGR
+RFFTMLGTLVQGRVSLSLAATTASFLGLHGAIAYGEQRRQFNASDPEREEVLLDYQNHQR
+RLVDRLARAYADAFASNELLERFDGVFSGRADSDADRQELETLAAAIKPLATWNALDTLQ
+ETREACGGAGFMARNRIPQMRADLDVYVTFEGDNNVLLQLVGKRLLTDYSHEFGRLNVGA
+VSRYVVAQASDAIHRAGLHKAVQSVSDGGSERRSANWFKDPEVQRDLLTDRVRAKTADIA
+GTLAGVRGKTQAEQAAAFNTRQHELIEVARNQGELLQWEAFTRAVQATRDESTRTVLTWL
+RDLFALRVLEEDLGWLVAHGRLSSQRARSLRGYVNRLAERLRPFALELVEAFGLEPEHLR
+MDIATQAEAERQAEAHAWFEARRAAGEEPEDEKAVRAREKAARGRRG
+>3_1596
+MTDIRTDAASAAEALPATDAVPHDVAEIAPEDPTPGALDAAALQDLLLGSWAEAHRTARG
+LVKDERLHRDPALGMDEHRARVLDQLGILVEEKAVHRAFPADLGGQDDHGGSIAAFANLV
+LADPSLQIKAGVQWGLFSSAILHLGTREHHEKWLPGAMDLSMPGAFAMTEIGHGSDVASI
+ATTATYDEATQEFVIHTPFKAAWKDYLGNAALHGRAATVFAQLITKGVNHGVHCFYVPIR
+DESGAFLPGVGGEDDGLKGGLNGIDNGRLHFDHVRVPRTHLLNRYGDVAEDGTYSSDIAS
+PGRRFFTMIGTLVQGRVSLSLAASIASFMGLHGALAYAEQRRQFGGPEGSETLLLDYQNH
+QRRLIDRLARTYADLFAANELLEKFDHVFSGAGDTDKDREELETLAAAIKPLTTWNALDT
+LQEAREATGGMGFMAGRNRLPHLRADLDIFVTFEGDNNILLQLVGKRLLTDYSAEFGKLN
+VGAVSRWAASEASDALHRVGLHKAAQSVHDRGDQRRAANWFKDPQVQRDLLTDRVRTRVA
+DIASTLGSARGKSKAEQAAAFNSRQHELIEVARHHGELLQWEAFTRQVESLPAGQTRTVL
+TWLRDLFALRLIEDDLGWLVAHGRVSSARARVLRGYVNRLAERLRPFALELVEAFGLEPE
+HLRMEIATDAESVRQQEAADWFAARRAAGEEPVHEKTLHAGKR
+>4_1063
+MTVHEKLAPQSSTPSTEVPSDVAEIAPERPTPGSLDAAALEEALLGRWAAERRESRELVK
+DPALWRDPLLGMDEHRARVLRQLGVLVERNAVHRAFPREFGGEDNHGGNLAAFGDLVLAD
+PSLQIKAGVQWGLFSSAILHLGTAEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIATT
+ATYDEATQEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITRGVNHGVHCFYVPIRDEE
+GAFLPGVGGEDDGLKGGLNGIDNGRLHFTQVRIPRTNLLNRYGDVAEDGTYSSPIASPGR
+RFFTMLGTLVQGRVSLSLAATTASFLGLHGALAYAEQRRQFKASDPQREEVLLDYQNHQR
+RLIDRLARAYADAFASNELVEKFDDVFSGRSDTDVDRQELETLAAAVKPLTTWHALDTLQ
+EAREACGGAGFLAENRVAQMRADLDVYVTFEGDNTVLLQLVGKRLLTDYSKEFGRLNVGA
+VSRYVVHQASDALHRAGLHKAVQSVADGGSERRSANWFKDPAVQHELLTERVRAKTADIA
+GTLSGARGKGQAAQAEAFNTRQHELIEAARNHGELLQWEAFTRALEGITDETTKTVLTWL
+RDLFALRLIEDDLGWFVAHGRVSSQRARALRGYVNRLAERLRPFALELVESFGLEPEHLR
+MAVATDAETQRQEEAHAWFTARRAAGEEPEDEKAVRAREKAARGRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000965.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000965.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d4b6530eed9045290057771f376d9a04050af38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000965.fa
@@ -0,0 +1,45 @@
+>0_1115
+MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLVA
+RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEALGTLA
+NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLNTAKTMKDRLRALAQLRPGQLVP
+EPAGAGEPRTGMSMGEHQALTTHKWGITRQTQDELAAASHRNLGAAYAAGYMDDLVTPFH
+GLARDNNLRPDSTPEKLAGLKPAFGRQLGDEATMTAANSTPLTDGASAVLLSSEEWAAER
+GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV
+LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH
+EKGEGSLGLISVCAAGGQGIVALLRGR
+>1_843
+MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLVA
+RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEAVGTLA
+NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLTTAKTMKDRLRALAQLRPGQLVP
+EPAGAGEPRTGMSMGEHQALTTHKWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFH
+GLARDNNLRPDSTPEKLAGLKPVFGRQLGDEATMTAGNSTPLTDGASAVLLSSEEWAAER
+GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV
+LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH
+EKGEGSLGLISVCAAGGQGIVALLRGR
+>2_1698
+MTQPETTARPAVAGGALRPAVVVGGNRIPFARANTAYAEVGNQEMLTAALEGLVARFGLQ
+GERVGQVSAGAVLKHPRNFNLTREAVLGSALASDTPAADLQVACATGMEAIGTLADKIRL
+GRIDSAIGGGVDSISDAPVSLSDGARRALLRLNAAKTMKDRLAALKDLRPGHLAPEPAGA
+GEPRTGMSMGDHQALTTHRWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFRGLDRD
+NNLRPDSTPEKLAGLKPAFGRHLGEEATMTAGNSTPLTDGASAVLLSSEDWAAERGLPVL
+AEFVDVENAAVDFVDGDEGLLMSPAYAVPRLLARHGLTLQDLDFVEIHEAFAGTVLSTLA
+AWEDEEYCRERLGLPGALGSVDRAKLNVHGSSLAAGHPFAATGGRIVALLSKMLHEKGEG
+SLGLVSVCAAGGQGIVALLRGR
+>3_1594
+MSTESPRVPAETARPAIAGGELRPAVVVGSNRIPFARAFTAYAEVGEQEMLTAAIDGLVA
+RLGLQGERLGQVSAGAVMKHPKDFNLTREAVMGSALSSETPAADIQVACATGMEAIGTLA
+DKIRLGRIDSAIGGGVDSISASPMTVSESARRVLLQLNSAKTVKDRLKALSSLRPGQLVP
+EPAAAGEPRTGMSMGEHQALTTHQWGITRQAQDELAAASHRNLGASYASGYQDDLVTPFR
+GLAKDNNLRPDSTVEKLAGLKPAFGRHLGDEATMTAGNSTPLTDGASAVLLSSEDWAVQR
+NLPVLAEIVDMENAAVDFVDGEDGLLMSPVYAVPRLLARHGLTLDDLDFVEIHEAFAGTV
+LATLAAWEDEEFGRTRLGLPGAYGSVDRAKLNVNGSSLAAGHPFAATGGRIVGLLSKMLH
+EKGEGSLGLVSVCAAGGQGIVALLRGR
+>4_1065
+MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLIA
+RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEALGTLA
+NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLNTAKTTKDRLRALAQLRPGQLVP
+EPAGAGEPRTGMSMGEHQALTTHKWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFH
+GLARDNNLRPDSTPEKLAGLKPAFGRQLGDEATMTAANSTPLTDGASAVLLSSEEWAAER
+GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV
+LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH
+EKGEGSLGLISVCAAGGQGIVALLRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000969.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000969.fa
new file mode 100644
index 0000000000000000000000000000000000000000..142c863dd53e38f6bb817398bf3ea56a5b24123a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000969.fa
@@ -0,0 +1,45 @@
+>0_1119
+MVENIVNPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMAEAGMTPRF
+FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV
+DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA
+ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG
+GHEWPLVYTKTTRALLEQVAEIMGVDFDEADPTPQLDALGQARSWVAGTLRTSSNPTGLT
+AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPEVTIAPEHRDVALETPFSGDLV
+ELMIASLQAEDPEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHAIDE
+RVPVDALEFGCRVLERMLEPR
+>1_847
+MVENIVNPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMAEAGMTPRF
+FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV
+DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA
+ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG
+GHEWPLVYTKTTRALLEQVAEIMGVDFDETDPTPQLDALGQARSWVAGTLRTSSNPTGLT
+AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPDVTIAPEHRDVALETPFSGDLV
+ELMIASLQAEDSEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHAIDE
+RVPVDALEFGCRVLERMLEPR
+>2_1693
+MIQNAHDTPVSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAALCARLMEEAGMRPRL
+FESSPGRVSVVGHLPGWDEDAPGLVVHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV
+DMKGMDAMVLSVLLHLTRTGRRPRRPLTVAFFADEEAGGVYGARWLVEHHPELFDGCTEA
+ISEVGGFSTEVHGSRAYLVQTAEKGIAWLNLRAEGAPGHGSAPHPDNAVTRLAGAMTRIG
+GHEWPLVYTKTTRALLEQVAEIMGVDFDEQDPTPQLDALGQARSWVAGTLRTSSNPTGMT
+SGYKHNVIPSTATGTVDARLLPGEEEAALATLQELAGPGVSIEPEHRDVALETPFSGDLV
+ELMVASLQAEDPGAEVLPFMLGGGTDNKSLARLGITGYGFAPMRLPADLAFTSLFHGIDE
+RVPVDALEFGCRVLERMLEPR
+>3_1590
+MDASTPSTAPSTADADVVEICRDLIRIDTTNHGGGRSVGEPEAAELCAAWMRKAGMEPEL
+IESAPGRVSVVGRLEGWDPEAPGLVLHGHTDVVPAEPDEWTVDPFGAEFRDGMIWGRGAV
+DMKGMDAMILSVLVHLARTGRRPRRPVVVAFFSDEEAGGVFGAQWLVAHRPELFAGCTEA
+ISEVGGFSTDVAGTRAYLVQTGEKGLAWLNLRAQGAPGHGSAPHTDNAVTRLAGAMERIG
+RHPWPLTYTKTTRQLLEEVAEITGTPFDERDPTPQLQALGHARDWVAGTLRTSSNPTGLT
+AGYKHNVIPSTATGTVDVRLIPGEEEQTLAELADLAGDGIEISPEHQDTGLEVPFSGDLV
+ERMASALDAEDPGAHVLPFMLGAGTDNKSLHRLGIAGYGFSPLQLPSGLEFTRLFHGIDE
+RVPVESLRFGCRVLEHVLEPRA
+>4_1069
+MVENIENPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMTEAGMTPRF
+FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV
+DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA
+ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG
+GHEWPLVYTKTTRALLEQVAEIMGVDFDETDPTPQLDALGQARSWVAGTLRTSSNPTGLT
+AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPDVTIAPEHRDVALETPFSGDLV
+ELMIASLQAEDPEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHGIDE
+RVPVDALEFGCRVLERMLEPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000974.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000974.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b165de2f89c8d4bdce5078581e5d24b05aa730b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000974.fa
@@ -0,0 +1,35 @@
+>0_1124
+MTDATSEDQPDDALGPLRTHLTATVDALEAGRRAPTVLLLAFEGWNDAGEAATGALGALR
+EQWDAADAGRVCDGEFYDYQVTRPLVRRDADGLGTLDWPAVTLHEAFLDREGRPVAGEAA
+PPDGVRVLLAVGVEPNVRWRAFLEELFTAADAHDVDAVVTLGALLADVPHTRPLRARPTS
+PLVDVRVAVGADRPVYEGPTGIIGVIADEAARRGLPSLSLWGTVPHYVAQAPSPKTLLGL
+VEAVEDLLHVSVSTRGLEDDARAWQRGVDELAAEDPDVAAYVRQLEEAQDTQQLPEASGE
+SIAREFERYLRGRGGR
+>1_852
+MTDATSEDQPDDVLGPLRTHLTATVDALEAGRRAPTVLLLAFEGWNDAGEAATGALGALR
+EQWDAADAGRVCDGEFYDYQVTRPLVRRDADGLGTLDWPAVTLHEALLDREGRPVAGEAA
+PPDGVRVLLAVGVEPNVRWRAFLEELFTAADARDVDAVVTLGALLADVPHTRPLRARPTS
+PLVDVRVAVGADRPVYEGPTGIIGVIADEAARRGLPSLSLWGTVPHYVAQAPSPKTLLGL
+VEAVEDLLHVSVSTRGLEDDARAWQRGVDELAAEDPDVAAYVRQLEEAQDTQQLPEASGE
+SIAREFERYLRGRGGR
+>2_1688
+MTDASSADQPDDALGPLRTHLTATVDDLEAGLRAPTVLLLAFEGWNDAGDAASGALDALR
+EQWDAAEAGRICDGEFYDYQVTRPVVRRDADGLGTLEWPAVRLHEAQLDAQGRPVAGEAA
+PPDGVRVLLAVGVEPNVRWQAFAEELFAAAAARQVDAVVTLGALLADVPHSRPLRARPTS
+PLVDVRVAVGADRPAYEGPTGIVGVIADEAARRGLPSVSLWGAVPHYVAQAPSPKTLLGL
+VEAIEDLLHVSVSTCELEDDAQAWQRGVDELAAEDPDVAAYVRQLEEAQDTQQLPEASGE
+AIAREFERYLRGRGGR
+>3_1585
+MDEQTDPGSLDGAPSPEDRLGALRAHLTATVPEVEDGSRPPAVLLLAFEGWNDAGEAATG
+ALAELSAQWEAAPAGVVCDGEYYDYQVTRPVVHRDADGLGTLEWPALRVHEARLDAHGAP
+VPDGEAVPADGLRVLLASGVEPNVRWRAYVEELLRWAEAEGVDAVLTLGALLADVPHSRP
+LRARPTSPLVAVRVAVDAGLPAYEGPTGIVGVVTDEAARRGTASLSLWGAVPHYVAQAPS
+PKTLLGLVEAVEDLLHVELLTHALRDDAQAWQRGVDELAREDPEVASYVRRLEESQDAQE
+LPEASGEAIAREFERYLRGRGRD
+>4_1074
+MTDATSEDQPDDVLGPLRTHLTATVDALEAGRRAPTVLLLAFEGWNDAGEAATGALGALR
+EQWDAADAGRVCDGEFYDYQVTRPLVRRDADGLGTLDWPAVTLHEALLDREGRPVAGEAA
+PPDGVRVLLAVGVEPNVRWRAFLEELFTAADARDVDAVVTLGALLADVPHTRPLRARPTS
+PLVDVRVAVGADRPVYEGPTGIIGVIADEAARRGLPSLSLWGTVPHYVAQAPSPKTLLGL
+VEAVEDLLHVSVSTRGLEDDARAWQRGVDELAAEDPDVAAYVRQLEEAQDTQQLPEASGE
+SIAREFERYLRGRGGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000985.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000985.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dea6fa7e144e37096e3127911dd1a9b08b3d9f1d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000985.fa
@@ -0,0 +1,65 @@
+>0_1136
+MTPPAPRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLTDTAFEKLFQRDRR
+VLRAVGVPLETLEPAGLDEGEAGVRHRVVRDALLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFQPATDLTGDDELAGYHTLMPRADPRLEALTQAVADEAVLRFPYRDARG
+RATRRTVRAWYLTLVRGRWYLTGWDLDRGAERSFRLTRMEGEPRRVERATDAPGRPEDHD
+HAGLVARLAGQADAERVRVWLAPGRGQGVRAVGEPAEPRVEDGAAPGPDWELWEAPAGPR
+EDGLAAEIGGLLGRAVPSAAHPDLTDRVRAGLAAAAEAHAGPADPALLEVPLAAPVRRRA
+RDSSEDLVGRLLDIVGLANRAGGVDRAELRARLGITDERLDADLETLRYCGMPERDFPGF
+QFEVAEVGGRVHVERAADLAGPVRLTRPEAHSLVAALQTVADLPVLDEADREAARSAQRR
+IRAAVLDAGAPDADDADDAALREAEAHTAGEPPVAVAAHWDVAVDPATVRTLLAAVAERA
+VVHLTYRSVHADALTERDVEPLALVQDGARLYLQAWCRRAEDHRVFRVDRISAPAPTGET
+FAPRARPARWRVHPDDTAGVPVLLRWAHPVRDAAAGYRPDAQADLPDGDRLTRVHLTDAA
+VAAALVGRHGGAVEVLAPADLRTSVADALGDALAALPAR
+>1_864
+MTPPAPRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLTDAAFEKLFQRDRR
+VLRAVGVPLETLEPAGFDEGEAGVRHRVVRDALLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFQPATDLTGDDELAGYHTLMPRADPRLEALTQAVADEAVLRFPYRDARG
+RATRRTVRAWFLTLVRGRWYLTGWDLDRAAERSFRLTRMEGEPRRLERATDAPGRPEDHD
+HADLVARLAGQADAERVRVWLAPGRGQGVRAVGEPAEPRVEDGAAPGPDWELWEAPAGPR
+EDGLAAEIGGLLGCAVPSAAHPDLTDRVRAGLAAAAESHAGPADPALLEVALAAPVRRRA
+RDSSEDLVGRLLDIVGLANRAGGVDRAELRARLGITDERLDADLETLRYCGMPERDFPGF
+QFEVAEVGGRVHVERAADLAGPVRLTRPEAHSLVAALQTVADLPVLDEADREAARSAQRR
+IRAAVLDAGAPDADDADDAALREAEAHTAGEPPVAVAAHWDVAVDPATVRTLLAAVAERA
+VVHLTYRSVHADALTERDVEPLALVQDGARLYLQAWCRRAEDHRVFRVDRISAPAPTGET
+FAARARPARWRVHPDDAAGVPVLLRWAHPVRDAAAGYRPDAQADLPDGDRLTRVHLTDAG
+VAAALVGRHGGAVQVLAPADLRASVADALGDALVALPAR
+>2_1675
+MAPPASRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLSDAAFEKLFQRDRR
+VLRAVGVPLETLEADSFEEEAQGVRHRVVRDAMLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFAPTPDLAADDELAGYHALTPRADPRLEALTQAVAEEAVLRFPYRDARG
+RESRRTVRAWFLTLVRGRWYLTGWDADREAERSFRLTRMEGEPRRVERAASLPGRPADHD
+HADLVARLAGQADAERVRVWLAPGRGQGVRAVGARVDPRAEDGAAPGDGWELWEAPAGTH
+EDGLAAEVGGLLGRAVPSAAEPDLARRVADALAAAARAHAGPAAPALLEAPLAPPVRRRA
+RDSSEDLVGRLLDIVGLANRADGVDRAELRARLGVTEERLDADLETLRYCGMPERDFPGF
+QFEVDEEGGRVHVRRAADLAGPVRLTRPEGHSLVAALQTVADLPVLDDADRAAARSAQRR
+IAEAVLDAGGAAASAADDEALAEAEAGTAPTPAPGGAVAAHWDVAVDPETVRTLLAAIAE
+RRVLRLDYRSVHADALSERDVEPLAVVQDGARLYLRAWCRSAGEDRVFRVDRIGAATATG
+EAFAPRARPARWRVHPDEAAGTPAVLRWAHRVRDAASGYRPEAQADLPDGDRLTRVRLTD
+ADVAAALVGRHGGAVEVLYPAAMRAHVKDALDRAVDALAAR
+>3_1573
+MSAHGSTAEPAERIISLLWLLLHEPLGYTREQIRRLVVGYEGLTDGAFEKLFQRDRRALR
+AVGVPLETVGDPDDEAGPRLRVDRDALLLQDVDFTVDERRALVRARRLWGDSPLRDDVVR
+AVGVLFHPGEVGGDDALEGFRTVMPRTDPRVAALSEAAAEQSVVRFSYRDAAGALTERTV
+RAWLLTLVRGRWYLTGWDADRAAERSFRLTRMESDPVVLDAGAASPAGEAPTLPAGHDHA
+ALRARLAGRAEAETVRVWLAPGRGQGFRVAGRPVPATAADGPAPGPDWELWECPSGPSED
+GAVAEAAVAVGQVLFSTVEAAAGRALAADLAAAAAVHAGDPDPAWRDVPLTAPTRRRSRA
+SSEDLVGRLLDIVGLANRAEGIGRDELQERLGVTARELDADLEVLRYCGMPEREFPGFQF
+DVEDEGGRVRVHQSSELAGPVRLTLPEAHALVAALQTVAEMTVLTPEDREAARSAQRRIR
+ASLADAGQSHAGSADAEAPRDGTGKEPGAVVAHWDVVADPDTVRTLLDAVAERAVVHLRY
+HGVRSDAVTERDVEPLAVVQDRTRLYLQAWCRRAGGPRVFRVDRIGALHRTGETFRARRV
+PAWDPRPAGDGVEAVVRWAHEVRDAADAYAPAAAATLDSGDRLTRVLLADDDAAVGLAAR
+HGGRVEILAPAALRGAVRGRLEAAARRAAGAVA
+>4_1086
+MTPPAPRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLTDAAFEKLFQRDRR
+VLRAVGVPLETLEPAGFDEGEAGVRHRVVRDALLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFQPATDLTGDDELAGYHTLMPRADPRLEALTQAVADEAVLRFPYRDARG
+RATRRTVRAWFLTLVRGRWYLTGWDLDRGAERSFRLTRMEGEPRRVERATDAPGRPEDHD
+HAGLVARLAGQADAERVRVWLAPGRGQGVRAVGEPAEPRVEDGAAPGPDWELWEAPAGPR
+EDGLAAEIGGLLGRAVPSAAHPDLTDRVRAGLAAAAETHAGPADPALLEVALAAPVRRRA
+RDSSEDLVGRLLDIVGLANRAGGVDRAELRARLGVTDERLDADLETLRYCGMPERDFPGF
+QFEVAEVAGRVHVERAADLAGPVRLTRPEAHSLVAALQTVADLPVLDEADREAARSAQRR
+IRAAVLDAGAPDADDADDAALREAEAHTAGEPPVAVAAHWDVAVDPATVRTLLAAVAERA
+VVHLTYRSVHADALTERDVEPLALVQDGARLYLQAWCRRAEDHRVFRVDRISAPAPTGET
+FAPRARPARWRVHPDDAAGVPVLLRWAHPVRDAAAGYRPDAQADLPDGDRLTRVHLTDAA
+VAAALVGRHGGAVEVLAPADLRTSVADALGDALAALPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000986.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000986.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d83cf68b6c360f9cc8f6047e55c51ed5dc86d548
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000986.fa
@@ -0,0 +1,15 @@
+>0_1137
+MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEGKGTTDERSGA
+GSTAADEPVEGRVVERDETDPRDPR
+>1_865
+MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEGKGTTDERSGA
+GSTAADEPVEGRVVERDETDPRDPR
+>2_1674
+MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEDKGAKDGKDAR
+SGSGSTAADEPVEGRVVERDETDVRPRDER
+>3_1572
+MRFTPTHLIVLIIVVLLLFAAPKLPALARNLGQSMRIFSSEVKQMKEENTTKKAEGAATA
+DAPSQGAGSTAAEPVEGRVVDRDVRDDR
+>4_1087
+MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEGKGTTDERSGA
+GSTAADEPVEGRVVERDETDPRDPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000989.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000989.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d9546259873d088e81bf4de6fd2624827f9dd2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000989.fa
@@ -0,0 +1,39 @@
+>0_1140
+MSAHLLTRGIIHSTTDPYAQALLVRDGMIAWLGADDSADRVADPGDERRDLDGAVVVPVF
+VEPLARPADARDALSRGTAVVTVLAGPEDTGAAPADEDVQTVVYRHADRVDAEAAGVWLP
+VGTDTDPATLTGLLTASTQAGEQAYLVPDGGADAGPAAQDVALTALRSVAEELGTAALGR
+VRHRLVVTHPVTAEDRAFLAAAGVSATVVPDADGVLHAPVASLLADAVTVCLGAGPAGDP
+WAAVRSALSHPDPDERISARSAFAAATRTPLRALPDAPAARLSVAPRLSVSAPAVFGVWD
+ADAVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRIAAEDVARDAHDA
+ATPA
+>1_868
+MSAHLLTRGIIHSTTDPYAQALLVRDGMIAWLGADDSADRVADPGDERRDLDGAVVVPVF
+VEPLARPADARDALSRGTAVVTVLAGPEDTGAVPADEDVQTVVYRHADRVDAEAAGVWLP
+VGTDTDPATLTGLLTASTQAGEQAYLVPDGGADAGPAAQDVALTALRSVAEELGTAALGR
+VRHRLVVTHSVTAEDRAFLAAAGVSATVVPDADGVLHAPVASLLADAVSVCLGAGPAGDP
+WAAVRSALSHPDPDERISARSAFAAATRTPLRALPDAPAAGLSVAPRLSVSAPAVFGVWD
+ADAVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRIAAEDVARDAHDA
+ATPA
+>2_1671
+MGRVTAHLLTTGIIHSVTDPYAQALLVRDGVIAWLGADDSAERVADPADARTDLDGAVVV
+PAFVEPLARPEDARDALSRGTAVVTVLAGPAGDVAPAEGVQAVVYRHAEGPAEGAVGVWL
+PVAADADAADLAAALAEATRAGEQAYLVPAADAAGHGDAEAPAAAQAAAIAALRRVAEEL
+GAPALGRVRHRLVVTSPVTAEDRAFLASVAVSATVVPAADGTLRAPVASLLADAVPVALG
+AGPGRDPWAAVRAALSHPEEAERISARSAFAAATRTPLRALPDAADADLVAAPRLAVSAP
+GVFGVWEAEAVAVQSPDGRVAAWSTDTRAGTPLLPALDDQTPLPRWRATWVGGRIAAEAA
+DGDARGTGDHA
+>3_1569
+MSSTLFLNGIVHSASDPYATAALVSDGVVAWLGDDSSADRVADPDVPRVDLAGAVLAPAF
+VEPGGPSVDPAQALRHGVAIVTVLAEPGQTAQALQAAADPALQTVVYRAADTVDAEAAGV
+WLPAEGEALAALVVASTRAGEQVHLVPPAGGDPSEGQAAALAALRSAAEELGAPALGRVR
+HRVVLTAPITAEDRALLAAISASVTVGPEADGLLRAPLGTLLAEGVPVCLSTAGEAGPWA
+AVRAALSHPDEAERISARSAFTAATRTPLRVLPDAPGATVQAAPRLTVSAPATFAVWEAD
+AVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRPAAVEVADA
+>4_1090
+MSAHLLTRGIIHSTTDPYAQALLVRDGMIAWLGADDSADRVADPGDERRDLDGAVVVPVF
+VEPLARPADARDALSRGTAVVTVLAGPEDTGAAPADEDVQTVVYRHADRVDAEAAGVWLP
+VGTDTDPATLTGLLTASTQAGEQAYLVPDGGADAGPAAQDVALTALRSVAEELGTAALGR
+VRHRLVVTHPVTAEDRAFLAAAGVSATVVPDADGVLHAPVASLLADAVTVCLGAGPAGDP
+WAAVRSALSHPDPDERISARSAFAAATRTPLRALPDAPAARLSVAPRLSVSAPAVFGVWD
+ADAVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRIAAEDVARDAHDA
+ATPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000991.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000991.fa
new file mode 100644
index 0000000000000000000000000000000000000000..138af093f98a657448d216028841c5929b82f437
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000991.fa
@@ -0,0 +1,15 @@
+>0_1142
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEEVDA
+>1_870
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEDVDA
+>2_1669
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAEAEGKPVRTHWDMLRERRSLEELQETYALQLNKLRASRGEDVDA
+>3_1567
+MSDRSLRGMRLGAQSLESEAGVEPAPRQRVEYRTEDGEQVFVTFAQEAEVPTTWTSKTGK
+EALRVDGEKPEENPGKPVRTHWDMLLERRSMEELEETFQIQLKKLHASRGEAV
+>4_1092
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEEVDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000993.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000993.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bbe6270574edc2ecc79389436b316e1902ca489c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000993.fa
@@ -0,0 +1,20 @@
+>0_1144
+MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV
+EPGAPEVAPGDEVTVLRIDGATLVVRPLPRIDWEADGA
+>1_872
+MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV
+EPGAPDVAPGDEVTVLRIDGATLVVRPLPRIDWQADGA
+>2_1667
+MDWIEANAGWLWLVAAAGLIGVELLTLDLVFLMIAAGAGAAGVVALAGGPLPLQLAAFAV
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITAEAGTLTVDGDTWSARV
+EDGAPDAAPGAEVTVLRVEGATLVVRPLPQIDWEDGRS
+>3_1565
+MEWIEANADWLWLVLALGLVGAELLSLDLVLAMLAAGALSAGVAALAGAPLGLQLGVFVV
+VSLLTLVAVRPAAMRRLHPDPAVGASWLDGLSGRRLTATGPVTDEGGRIDVDGETWSARV
+EPGAAPAAHGQGVTVLRVEGAHLILRPDPVIDWDAPAHD
+>4_1094
+MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV
+EPGAPEVAPGDEVTVLRIDGATLVVRPLPRIDWEADGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000996.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000996.fa
new file mode 100644
index 0000000000000000000000000000000000000000..349d31663111411996112760662a8a900e3d9e9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000996.fa
@@ -0,0 +1,24 @@
+>0_1147
+MVSVHLVPIRPTAATADDAQRLSAALLDDPRPGAAVISAAWHIDETDAAPGDGELAVTLD
+GMAAGVGLALWAVRSGSWAVLLDTEGNYDKQSALSHITAGERRRARRAPGRLVLPHGRRP
+GRASETGREADLRCAEATLQLVATVERRRSDDQHAAGRLVEAGASQREAAAELGISQQAV
+HSRLRHGLWHESRTAVAAVLPLLERLSADPGE
+>1_876
+MVFVHLVPIRPTAATADDARRLAAVLLDDPHPDASVAAAVWRGDEGNPDADAAPGDGELA
+VVVESMAAAVGLALWAVRTGSWAVLLDPEDALDKDSLLSYLTPAERRRARRAPGRLVLPH
+GRRPGRASETGREADLRCAEATLQLVATVERRRSDDQHAAGRLVEAGASQREAAAELGIS
+QQAVHSRLRHGLWHESRTAVAAVLPLLERLSADPGE
+>2_1663
+MIVLHLLPLTAPDAADAAWTRVGDELNRPGAVSSLVMPFDRQGEGSEARLVGGMDSGVEA
+VGILLSLVRSGAWAVVVEVAEGRAAGESLLQREAERARRANGHCAVLGPSGPSAAWIEPA
+LQLLGALERRRSEPQQDAGRRVEAGASQREVAAELQVSQQAVHARLRGGLWNETRALAGA
+TADALDVLARRGDRVSDGGASPSTSERG
+>3_1560
+MVPVAVRCGSAGAAGRWAASIPGARRLGREGGRDLIVHADDAAAAVALMLAVRRAGAGAV
+GAGVAIEQVEGALRRARRRPGGIAVSRVPGSTGTEEERGLLEAGLGVLLTLESRRSAPQQ
+AAGVLIEAGRSQREAAADLGVSQQAVQQRLRAGLWEETRTLLDALLPMARRVLEA
+>4_1101
+MVSVHLVLIRPTTATAEDARRLATALRDDPRPDAAVTAAMWLGDESDPVDDDAAPHDGEL
+AVVLDDAAAAVGLALWAVRTGSWAVMLDPEGGSDKDSALSYLTPAELRRARRAPGRLVLP
+AGGRPGRASESGREADLRCAEATLQLVAAVERRRSADQHAAGRLVEAGASQREAAAELGI
+SQQAVHSRLRHGLWHVSRTAVAAVLPLLERLSTDPGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000997.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000997.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b0fc7d94104a0acf5d3699e4cc5aea862b7fd02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000997.fa
@@ -0,0 +1,20 @@
+>0_1148
+MTSSPTARRAAPAEHRDPRGALPALAVDLLLTLLFVALGQGQHSTERGPLGLLVTAAPFL
+AGLLLMTGVTAGHRTWARAWPHGVIVWLGTVAVGMLLRVAFGLGGAPVSFVLVALGVLGV
+LLLGRRAVTAWLVRRTRR
+>1_877
+MTSSPTARRAVPAEHRDPRGAQPALAVDLLLTLLFVALGQGQHATERGPLGLLVTAAPFL
+AGLLVMTGLTAGHRTWARVWPHGVIVWLGTVAVGMVLRVAFGLGGAPVSFVLVALGVLGV
+LLLGRRAVTAWLVRRTRR
+>2_1662
+MADTLSENRSETMAQTGGMTDSPTRRHSPASPPSPLWAATALAVDAVLVVVFVALGQDQH
+TTDRGLGGLLATALPFLLGLVAATVLTAGHRTWHRVWPHGVAVWLGTVAVGMALRVLWDQ
+GGAPLSFVLVALGVLGVFLLGRRAVTAWVIRRRARV
+>3_1559
+MSTTPLPQDSSPAAHPSDRRRGSAPWVAFALDAALVVLFVALGQREHATDRGGLALVTAA
+APFLLAWVAGTALAGGPRTWARVWPQGVVVWAVTVAAGMGLRVLWGLGGAPVPFVLVASA
+VLAVFLLGRRWASTLLAHRATDRASRAS
+>4_1102
+MTSSPTARRVVPAEHRAPRGALPALAVDLLLTVLFVALGQGQHSTERGPVGLLVTAAPFL
+AGLLLMTGLTSGHRTWARVWPHGVIVWLGTVAVGMVLRVAFGLGGAPVSFVLVALGVLGV
+LLLGRRAVTAWLVRRTRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000998.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000998.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7de6470c596b15b6b21933dd58941e0bedcb84e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000998.fa
@@ -0,0 +1,15 @@
+>0_1149
+MVTAIVLIKTDKSSIPETAETLAALEGVGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL
+SKVDGIQDTETMLAFRAYSSEDLGEGWALGFDS
+>1_878
+MVTAIVLIKTDKSSIPETAETLAALEGVGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL
+SKVDGIQDTETMLAFRTYSSEDLGEGWALGFDS
+>2_1661
+MVTAIVMIKTDKSSIPETAETLAALEGIGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL
+SKVEGIQDTETMLAFRTYSSEDLGEGWALGFED
+>3_1558
+MVTAIVMITTDKSTIPETAQAIASLEGVSSVYSVTGAWDLVAMVKLKRYEDLADVIADQL
+SKVDGIEDTETMLAFRTYSTEDLEEGWALGFDG
+>4_1103
+MVTAIVLIKTDKSSIPETAEALAALEGVGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL
+SKVDGIQDTETMLAFRTYSSEDLGEGWALGFDS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000999.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000999.fa
new file mode 100644
index 0000000000000000000000000000000000000000..73931764b7046929f1f00d23deb1863bfff3687b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000999.fa
@@ -0,0 +1,35 @@
+>0_1150
+MSTPENTAAVLGTSWPEVFRALTVGEDLSDDVAAWAMGEMMAGDATEGQVGGFLLALAAK
+GVTVPELRGLTEAMVQAANPVHVPGETLDVVGTGGDRLGTVNLSTMSSLVAAGAGARIVK
+HGNRGASSTAGAADVIEALGVDLSMPTRKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ
+LGVPTVFNFLGPLSNPAQVTAQALGCSSQAMVPLLAQVLADRGVRGFVFRGADGRDKITT
+SGPSTVMEVRDGVRTHELDPRELGIDLAPVQALAGRDGAYNATLVRALLAGEKGPIRDAV
+LLNAAAGLTAWDRGADAPLMERLAANMARAAESIDSGAARDVLDRWVAFSRS
+>1_879
+MSTPENTAAVLGTSWPEVFRALTVGEDLSDDVAAWAMGEMMAGDATEGQVGGFLLALAAK
+GVTVPELRGLTEAMVQAANPVHVPGETLDVVGTGGDRLGTVNLSTMSSLVAAGAGARIVK
+HGNRGASSTAGAADVIEALGVDLSMPTRKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ
+LGVPTVFNFLGPLSNPAQVTAQALGCSSEAMVPLLAQVLADRGVRGFVFRGADGRDKITT
+SGPSTVMEVRDGVRTHELDPRELGIDLAPVQALAGRDGAYNATLVRALLAGEKGPIRDAV
+LLNAAAGLTAWDRDADAPLMERLAANMARAAESIDSGAARDVLDRWVAFSRS
+>2_1660
+MSIPNTTAAAPETTWPDVFRALTFGEDLSDEAAAWAMGEMMAGDATEGQVGGFLLALAAK
+GVTVPELRGLTEAMVQAARPVQVTGETLDIVGTGGDRLGTVNLSTMSSLVAAGAGARIVK
+HGNRGASSTAGAADVIEALGVDLSMPREKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ
+LGVPTVFNFLGPLSNPAQVSAQALGCSSEVMVPLLARVLADRGVRGFVFRGSDGRDKITT
+SGPSTVIEVRHEVTAHELDPRDFGIELAPVEALAGRDGAYNATLVHALLAGEKGPIRDAV
+LLNAATGLTAWDTEAQGPLADRLAANMARAAESLDSGAARDVLDRWVAFSRS
+>3_1556
+MRETVTHTWPEVFRRLTLGQDLDDAAAEWAMGEMMSGDATEGQVGAFLLALAAKGETVPE
+LRGLTDAMVAKARRVHVSGETLDIVGTGGDRLGTVNLSTMSSLVAAGAGARIVKHGNRGA
+SSTAGAADVIEALGVDLSMPPAKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQLGVPTV
+FNFLGPLSNPAQASAQALGCSSEEMVPLLAQVLADRGVRGFVFRGSDGRDKITTSGPSTI
+MEVRGGVTAHEIDPRDFGIELAPVEALAGRDGAYNATLVRGLLAGEHGPIRDAVLLNAAA
+GLTAWDVEAEGPLMDRLRTNMARAAESIDSGAAADVLERWVQFSRS
+>4_1104
+MSTPENTAAVLGTSWPEVFRALTVGEDLSDDVAAWAMGEMMAGDATEGQVGGFLLALAAK
+GVTVPELRGLTEAMVQAANPVHVPGETLDVVGTGGDRLGTVNLSTMSSLVAAGAGARIVK
+HGNRGASSTAGAADVIEALGVDLSMPTRKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ
+LGVPTVFNFLGPLSNPAQVTAQALGCSSEAMVPLLAQVLADRGVRGFVFRGADGRDKITT
+SGPSTVMEVRDGVRTHELDPRELGIDLAPVQALAGRDGAYNATLVRALLAGEKGPIRDAV
+LLNAAAGLTAWDRDADAPLMERLAANMARAAESIDSGAARDVLDRWVAFSRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001001.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001001.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1faae33cb23c3a81c72328fcad25a00f474be47c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001001.fa
@@ -0,0 +1,30 @@
+>0_1152
+MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDISEGEKLF
+NANCASCHGTGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAQVKPNQFNDEQTA
+QLAAYVASLGAGPAVPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA
+PSLQGVEEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLALGSLG
+PVSEGLFIWTAGLALIIGFMVWLTSRSS
+>1_881
+MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDITEGEKLF
+NANCASCHGMGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAPAKPNQFNEEQTA
+QLAAYVASLGAGPAIPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA
+PSLQGVDEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLTLGSLG
+PVSEGLFIWTAGLALIIGFMVWLTSRSS
+>2_1658
+MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDITEGEKLF
+NANCATCHGMGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAPAKPNQFNEEQTA
+QLAAYVASLGAGPAIPEDEYLDINNEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKFA
+PSLQGVEEKYIYEAMETGPQNMPVFSDANIKPEDKRDIIAYLKTIENQGSPGGLSLGSLG
+PVSEGLFIWTAGLALIIGFMVWLTSRSS
+>3_1554
+MKALSQNRRHPLVGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAAAADDITAGEKLF
+NANCASCHNMGATGTADGPSLVGVGAAAVDFQVGTGRMPMQMNGPQAQRKPNQFSEEQTA
+QLAAYVASLGAGPAVPADEDLDPNAEGVNIAKGGDLFRINCAMCHNAAAAGGALTRGKFA
+PSLEGVSEKHIYEAMETGPQNMPVFSDANLKPEDKRDIIAYLKTIEANGSPGGLQLGSLG
+PVAEGLFIWTAGLALIVGFMVWLTSRSS
+>4_1106
+MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDISEGEKLF
+NANCASCHGTGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAQVKPNQFNDEQTA
+QLAAYVASLGAGPAVPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA
+PSLQGVEEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLALGSLG
+PVSEGLFIWTAGLALIIGFMVWLTSRSS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001003.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001003.fa
new file mode 100644
index 0000000000000000000000000000000000000000..55cee4415b48574c116cf98522878d538521e760
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001003.fa
@@ -0,0 +1,55 @@
+>0_1154
+MSTTVNEFQPATSTGRIANFVDTRTGMSPIVKFFARKIFPDHWTFMFGEVALYSFVILLL
+SGAFLTFFFDPSMSEVVYNGAYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALM
+FVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAGFTGYSLPDEVLSGNGLRIID
+GILKSLPLVGTYLSAFFFGGEFPGHSVIGRLYALHIMIVPAAILLLIGIHLFMVVVHKHT
+QYPGPGRTEDNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQ
+AGTQPDWYIGVFDGALRLMPGMIGDYSFLWNIPMPWGSSVSLPMGVLVPLIPVGVLLVGM
+CAWPWIERWITKDDTEHHLLDRPRNAPARTGIGVAAVVWYCVMWAAASSDLIATHFHLSL
+NDVLYVLRALFFLGPVIAFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPEGGFHERHRP
+LTDYELYRLVAFEDRRPVPAIPGRNGKVGALEKARAGLNRMFYQERVAPVSREELVEART
+HGQHGHEEHPVELGHGSDAPRLER
+>1_883
+MSTTVNEFQPATTTGRIANFVDTRMGMSPIVKFFGRKIFPDHWTFMFGEVALYSFVILLL
+SGAFLTLFFDPSMSEVVYDGAYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALM
+FVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAGFTGYSLPDEVLSGNGLRIID
+GILKSLPLVGTYLSAFFFGGEFPGHSVIGRLYALHIMIVPAAILLLIGIHLFMVVVHKHT
+QYPGPGRTEDNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQ
+AGTQPDWYIGVFDGALRLMPGMIGDYSFLWNIPMPWGSSVSLPMGVLVPLIPVGVLLVGM
+CTWPWIERWITKDNTEHHLLDRPRNAPARTGIGVAAVVWYCVMWAAASSDLIATHFRLSL
+NDVLYVLRALFFLGPVIAFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPEGGFHERHRQ
+LTDYELYRLVSFEDRRPVPAIPGRNGKVGMLEKARAGLNRMFYQDRVAPVSREELVEART
+HGQHGHEEHPVELEHGSHAPHLDR
+>2_1656
+MSTTVNEFQPATSTGRIANFVDTRMGMSPIVKFFARKIFPDHWTFMFGEVALYSFVILLL
+SGAFLTFFFDPSMSEVVYNGAYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALL
+FVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAGFTGYSLPDEVLSGNGLRIID
+GILKSLPIVGTYLSAFFFGGEFPGHSIIGRLYALHIMVVPAAILLLIGIHLFMVVVHKHT
+QYPGPGRTENNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQ
+AGTQPDWYIGVFDGALRLMPGMIGDFSFLWNIPMPWGSSVSLPMGVLVPLIPIGVLIVGM
+CAWPWIERWITKDDTEHHLLDRPRNAPTRTGIGVAAVIWYCVMWAAASSDLIATHFRLSL
+NDVLYALRTLFFLGPVIGFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPDGGFHERHRQ
+LTDHELYRLVSFEDRRPVPALPNRSGKVGMIEKARAGLNRMFYQDRVAPVTREELVEARA
+HGHHGVEDGGHHELGADPSSHNPKIDG
+>3_1552
+MSTATHEYQPATGTGRLANFLDTRVGLSPIVKFFGRKTFPDHWTFMFGEVALYSFVILLL
+SGAFLTFFFDPSMSHVTYDGAYAPLRGIEMSAAMASALDISFDIRGGLFMRQLHHWSALL
+FVASMSVHMLRIFFTGAFRRPRELNWVVGCFLLMAGWAAGFTGYSLPDDVLSGNGLRIID
+GILKAMPLVGSYLSAFLFGGEFPGYSVIGRLYALHIMIVPAIILLLIAVHLFMVVVHKHT
+QYPGPGRTENNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINSIWIYGPYDPSPVS
+AGTQPDWYIGPFDGALRLMPGMIGDFSFLWNIPMPWGSRVSLPMGVLTPLIPVGVILVGM
+ISWPWIERWITKDDREHHLLDRPRNAPARTGIGVGMMIMWCTMWAAASSDLIATHFHLSL
+NDVLYFLRALFILGPILGFIVTRRICISLQRRDRETVLHGHESGVVEMSPEGGFSERHRQ
+LTDYEMYRLVSFEDRRPVPATPGRNGKVSGAERMRAGLNRMFYQERVAPVSREELVEART
+HGHGEHVGAVQGGSHSAELGH
+>4_1108
+MSTTVNEFQPATTTGRIANFVDTRMGMSPIVKFFGRKIFPDHWTFMFGEVALYSFVILLL
+SGAFLTLFFDPSMSEVVYDGAYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALM
+FVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAGFTGYSLPDEVLSGNGLRIID
+GILKSLPLVGTYLSAFFFGGEFPGHSVIGRLYALHIMIVPAAILLLIGIHLFMVVVHKHT
+QYPGPGRTEDNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQ
+AGTQPDWYIGVFDGALRLMPGMIGDYSFLWNIPMPWGSSVSLPMGVLVPLIPVGVLLVGM
+CTWPWIERWITKDNTEHHLLDRPRNAPARTGIGVAAVVWYCVMWAAASSDLIATHFHLSL
+NDVLYVLRALFFLGPVIAFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPEGGFHERHRQ
+LTDYELYRLVSFEDRRPVPAMPGRNGKVGALEKARAGLNRMFYQDRVAPVSREELVEART
+HGQHGHEDGGHHELGADPSSHNPKIDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001004.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001004.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bade6fe3b0d087984685a1523518635ea8389ec1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001004.fa
@@ -0,0 +1,20 @@
+>0_1156
+MKVAANIFWVIGLFFVGAGTLYGFWNEWTEWAGIPAIYALGGMSWMIAWYLNAAERKYGV
+GPADDEDGQIVEYAGTYGTFAPWSWWPLGLGLACAIIVTGLAVGWWVFVIGIIAGAYFTF
+GWVYEFSRGKFAH
+>1_884
+MKVAANIFWIIGLFFIAAATLYGFWVEWTEWAGIPAIYAVGGMSWMIAWYLNVTERKYGV
+GPADDADGQIADYAGTYGTFAPWSWWPLGLGLACAIIVTGLAVGWWIFIIGVIAGAYFTF
+GWVYEFSRGKYAH
+>2_1654
+MKVAANIFWIIGLFFIAAATLYGFWVEWTEWAGIPAIYAVGGMSWMIAWYLQSTEKKFGL
+GPADDEDGEITDYAGTYGTFAPWSWWPLGLGVACAILITGLAVGWWVFIIGAVAAAYFTF
+GWVYEFSRGKYAH
+>3_1551
+MKIASNIFWIIGAFLVAVATLYGFWVKWTEWAGIPAIYALGAMCWMIAWYVQSTDKRHGL
+GPADDEDGEIVEYAGTYGTFAPSSWWPLGVAVACAMLVTGLAVGWWIFALGVIAGVYFTF
+GWVYEFSRGKYAH
+>4_1113
+MKVAANIFWVIGLFFVGAGTLYGFWNEWTEWAGIPALYALAGMSWMIAWYLNAAERKYGV
+GPADDEDGQIVDYAGTYGTFAPWSWWPLGLGLACAIIVTGLAVGWWVFIIGVIAGAYFTF
+GWVYEFSRGKFAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001006.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001006.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5c3192ab13f8adc6b91153f80ccabafa38f5df7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001006.fa
@@ -0,0 +1,31 @@
+>0_1158
+MGTTALLVLTGCSAEVQRGWYPGTRDTTNHNAQLTDLWVNSWIAAMVVGLLVWGAMIWCM
+VAYRRRKNDQGFPKQTAYNVPLETMFTAIPILTVFTLWGFTDRVQTEVDRPVDDSPLTVT
+VYGKQWSWDFNYSYEQEDGEVIEAHYSGIQAQLDGTEGVRDTLPVLYLPNDVPVHFELKS
+RDVVHSFWIPQFLQKRDMVPGKTNHLYLTPQELGSYDGKCAELCGEFHSEMLFNVEVVDE
+AEFVQRLEEMESGQVGEEYSRNPNNNPDGAGTMERDLQTPRGGGSH
+>1_886
+MGTTSLLVLTGCSAEVQRGWYPGTRDTTNHNAQLTDLWVNSWIAAMVVGLLAWGAMIWCM
+VAYRRRKNDQGFPKQTAYNVPLETMFTAIPILMVFTLWGFTNRVQTEVDRPVDDSPLTVT
+VYGKQWSWDFNYSYEQENGEVIEAHYSGIQAQLDGTEGVRDTLPVLYLPNDVPVHFELKS
+RDVAHSFWIPQFLQKRDMVPGKTNHLYLTPQELGSYDGKCAELCGESHSEMLFNVEVVDE
+AEFVQRLEEMEPGQVGDEYSRNPNNNPDGAGTMERDLQTPRGGGSH
+>2_1652
+MGTTALLVLTGCSAEVQRGWYPGTRDTTNHNAQLTDLWVNSWIAAMVVGLLAWGAMIWCM
+VAYRRRKNDQGFPKQTAYNVPLETMFTIIPILMVFTLWGFTNRVQTEVDRPVDDSPLTVT
+VYGKQWSWDFNYSYEQENGEVVEANYSGIQAQLDGTEGVRDTLPVLYLPKDVPVHFELKS
+RDVAHSFWIPQFLQKRDLIPGKTNHLYLTPQELGSYDGKCAELCGEFHSEMLFNVEVVDE
+AEFVDRLAEMEPGLVGDEYSRNPNNNPDGAREMERDLQTPRGGGSH
+>3_1549
+MRAQNDAGRRTRRRLTAGALGATALVALTGCSAEAQRGWLPGTDNTTNHNAQLTDLWVNS
+WIAALAVGLIAWGAMIWCMIAYRRRKNDQGFPRQTAYHMPIETMFTVIPILMVFTLWGFT
+DRVQAEVDTPIDDSPLTVTVYGKQWSWDFNYSYEKDGQTREAHFQGVQAQLDGSDGKRET
+LPTLYLPKDVPVHFELKSRDVAHSFWIPQFLQKRDMLPGKTNNLYLTPQEIGRFDGKCAE
+LCGEFHSEMLFNVEVVDEATFVQKMNEMEPGLVGDELNRNPNQNPDGARNMEVDLQTPRG
+GGNH
+>4_1115
+MGTTALLVLTGCSAEVQRGWYPGTRETTNHNAQLTDLWVNSWIAAMAVGLLAWGAMIWCM
+VAYRRRKNDQGFPKQTAYNVPLETMFTAIPILMVFTLWGFTDRVQTEVDRPVDDSPLTVT
+VYGKQWSWDFNYSYEQENGEVIEAHYSGIQAQLDGTEGVRDTLPVLYLPNDVPVHFELKS
+RDVAHSFWIPQFLQKRDMVPGKTNHLYLTPQELGSYDGKCAELCGEFHSEMLFNVEVVDE
+AEFVQRLEEMEPGQVGDEYSRNPNNNPDGAGTMERDLQTPRGGGSH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001008.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001008.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f5cbfafeac94b554102f1b368d1aa236b867bb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001008.fa
@@ -0,0 +1,45 @@
+>0_1160
+MTDITSRAPQDAALVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRAQLERSAEAVA
+GLLREAGLQDVEIVSEIRDDGRPGGPAVIGEKPGTSDKPTVLFYAHHDVQPIGDEDLWDT
+PPLVATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAGSPTF
+RTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP
+VLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAGRGPV
+ADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSMRLGPGMEPAEAFEALRTHLEAQS
+AAVLGAEITVTAGEFGQPFTTDTSAPAAAAMMAALEDAWGVEPRAIGMGGSIPFTADLAE
+VFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA
+>1_888
+MTDITSRAPQDAALVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRTQLERSAEAVA
+GLLRAAGLQHVEIVTETRDDGRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDEDLWDT
+PPLVATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAGSPTF
+RTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP
+VLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAGRGPV
+ADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSLRLGPGMDPAEAFEALRTHLEAQS
+AAVLGAEITVTAGEFGQPFTTDTSATAAAAMMAALEDAWDVEPRAIGMGGSIPFTADLAQ
+VFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA
+>2_1650
+MTETTPPVRDDAALVAAVRDAVDARFPQTLQTLTDLVAIPGIAWDSADRAQLERSSEAVA
+ALLRQAGLQGVEIVTETREDGRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDEALWDT
+EPLVATEKGGRLYGRGAADDKAGIMVHLAALAALKDVLPDAGVGVRVFIEGEEEAGSPTF
+RTFLENHRARLEADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP
+VLDAVVLLSRLIATLHDADGAVAVPGLEPRRSASLDYPEDVFRADAGVLDSVTLAGRGPV
+ADRLWNAPALSVIGIDVPSVAESSNTIQPQARAKFSLRLGPGMDPAEAFEALKAHLEAQS
+AAVLGAEITVEAGEFGQPFDTDTSDPLAAAMMGALGDAWGVAPKEAGMGGSIPFTADLAE
+VFPDATILITGVEDPDSRAHSANESLHIEDFRRAVVAEALWFARLAG
+>3_1547
+MTQSTQNTPVGAAPDPELVSAIRAAVDRRFPETLQSLKDLVSIPGIAWDSMDREPLERSA
+AAVADLLRTAGLEGVETAVEERADGRPGGPAVIGGRPAVGDKPTVLLYAHHDVQPLGEEG
+LWDTPPLVATERDGRLYGRGAADDKAGIMVHLAALAALDEVCPDAGVGVRVFIEGEEEAG
+SPTFRPFLERHRDRLAADAIVVADSSNWAVGEPALTTSLRGVVSATVTVRALDHAVHSGM
+FGGPVLDAVVLMSRLIATLHDADGAVAVPGLEPRHHADVDYPEDAFRADSGILPGTRLAG
+RGALADRLWNGPALSVIGLDAPSVDTSSNTIQPAARAKISLRLGPGMDPAASLDALRAHL
+EAQSDAVLGAEITVEPGELGQPFSTDTSAPAAAAMMGALGAAFATPARETGLGGSIPFTA
+DLKELFPEATILITGVEDPDSRAHSANESLHLEDFRRAIVAEALWLAAMGA
+>4_1117
+MTDITSRAPQDAALVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRTQLERSAEAVA
+GLLREAGLQEVEIVTETRDDDRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDEDLWDT
+PPLEATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAGSPTF
+RTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP
+VLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAGRGPV
+ADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSLRLGPGMEPAEAFEALRTHLEAQS
+AAVLGAEITVTAGEFGQPFTTDTSAPAAAGMMAALEDAWGVEPRAIGMGGSIPFTADLAE
+VFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001014.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001014.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0430ced5faaed88e35111ae56bcf3ba16244608f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001014.fa
@@ -0,0 +1,35 @@
+>0_1167
+MTDLVDPARAADGFRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH
+REDFQLVLVDTPGLHRPRTLLGERLNDLVAETLNEVDAVGMCLPADEAIGPGDRFIAQQL
+SYLHRTPVVAVVTKTDKVGPEQLMAQLVAVTALGDEVLGPENGGEGFAAVVPVSAVAGRQ
+VDDVLGVFAGLLPAGPPLYPDGELTDEPEAVMVAELIREAALEGVRDELPHSVAVMVEEM
+SLREDRPADRPLMDVWANVFVERDSQKGIIIGKGGSRLREIGAQARAGIERMLGTKVHLD
+LRVKVAKEWQRDPKQLGRLGF
+>1_895
+MTDLVDPARAADGFRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH
+REDFQLVLVDTPGLHRPRTLLGERLNDLVAETLNEVDAVGMCLPADEAIGPGDRFIAQQL
+SYLHRTPVVAVVTKTDKVGPEQLMAQLVAVTALGDEVLGPENGGEGFAAVVPVSAVAGRQ
+VDDVLGVFAGLLPAGPPLYPDGELTDEPEAVMVAELIREAALEGVRDELPHSVAVVVEEM
+SLREDRPADRPLMDVWANVFVERDSQKGIIIGKGGSRLREIGAQARAGIERMLGTKVHLD
+LRVKVAKEWQRDPKQLGRLGF
+>2_1644
+MTDLVDPARAADGHRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH
+REDFQLVLVDTPGLHRPRTLLGQRLNDLVAETLGEVDAVGFCLPADEAIGPGDRFIAQQL
+AHLHRTPVVAVVTKTDKVGPEQLMAQLLAVTALGEEVLGPENGGEGFAAVVPVSAVAGRQ
+VDDVLEVLRGLLPEGPPLYPDGELTDEPEAVMIAELIREAALEGVRDELPHSVAVVVEEM
+ALREGRPDDRPLMDVWANLFVERDSQKGIIIGKGGSRLREIGARARAGIERMLGTKVHLD
+LRVKVAKEWQRDPKQLGRLGF
+>3_1540
+MTSLLDPAVPEGHRSGFACLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVHR
+PDFQLVLVDTPGLHRPRTLLGERLNALVQETLSEVDVVGFCLPADEKIGPGDRFIAQQLA
+ALRRTPVVAIVTKTDKTDPQRVAEQLLAVTALGDEVLGPENGGRGFAAVVPVSAVAGRQV
+EDVESVLAQLLPDGPPLYPDGELTDEPEAIMVAELIREAALEDVRDELPHSVAVVVEEMN
+PREGRPEERPLLDVYANVFVERDSQKGIIIGKGGSRLRAIGTQARTGIERMLGTPVHLDL
+RVKVAKDWQRDPKHLNRLGM
+>4_1124
+MTDLVDPARAADGFRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH
+REDFQLVLVDTPGLHRPRTLLGERLNDLVAETLNEVDAVGMCLPADEAIGPGDRFIAQQL
+SYLHRTPVVAVVTKTDKVGPEQLMAQLVAVTALGDEVLGPENGGEGFAAVVPVSAVAGRQ
+VDDVLGVFAGLLPAGPPLYLDGELTDEPEAVMVAELIREAALEGVRDELPHSVAVVVEEM
+SLREDRPADRPLMDVWANVFVERDSQKGIIIGKGGSRLREIGAQARAGIERMLGTKVHLD
+LRVKVAKEWQRDPKQLGRLGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001017.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001017.fa
new file mode 100644
index 0000000000000000000000000000000000000000..abf4cf4fb83eba44ea1e35156cefa5aa9ed96584
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001017.fa
@@ -0,0 +1,35 @@
+>0_1170
+MSRPRDPEVIRPIVTVPPTTPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVFPTV
+DVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGRGAG
+QLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQALQAK
+EVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGTIEV
+APLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGTQSG
+LAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARGPAERSQKRGGARRGR
+>1_898
+MSRPRDPEVIRPIVTVPPTTPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVFPTV
+DVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGRGAG
+QLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQALQAK
+EVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGTIEV
+APLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGTQSG
+LAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARGPAERSQKRGGARRGR
+>2_1641
+MVRTLGPQDALLRILGGVFPAVDLTVRDQRLEMAGPVPDVASVRRVVEDLRSIARRDQAV
+TPEVMEQVVTHVRGAAAGRGAGQLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGI
+GPAGTGKTYLAMAKAVQALQAKEVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYD
+ALHDMIEPESIPRLMEAGTIEVAPLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGF
+GARMVVTGDTSQVDLPRGTRSGLSQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYD
+AARGAEPAPRGGRGHRGR
+>3_1537
+MIRPIVSDPSSHVVLPPVSVPGAESVSFESAELMVRTLGAHDALLRILAGVYPDVEVTVR
+DQSLGMSGPPRHVAQARRIVEDLRSLARRDAPVTPDVVEQVVSLVRDGETGRASGTLHLD
+SILSGRGRKIRAKTLHQQDYVEAIDRATIVFGLGPAGTGKTYLAMAKAVQALQAKEVTRI
+ILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMESGTIEVAPLAY
+MRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGVRSGLAEAV
+EVLEGVDGLEMVRFDSSDVVRHSLVSAIVDAYDGARGSGSAADPRPAGRGAQRGRSGRGR
+>4_1127
+MSRPRDPEVIRPIVTVPPTTPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVFPTV
+DVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGRGAG
+QLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQALQAK
+EVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGTIEV
+APLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGTQSG
+LAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARGPAERSQKRGGARRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001018.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001018.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6ff4c54f4f593e0e932ded4ba303a1604acb99ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001018.fa
@@ -0,0 +1,30 @@
+>0_1171
+MTAPLFHLEPGALAGASAGAEVVFDGAEARHAAAAMRLAPGEAVLLADGSGTLGHGTVLA
+AAPDAVSVRLDAVAEEPAPTPALVLVQALAKGDRDLMAVQAAVELGVDAVVPWEAERSIV
+RWKGPKAAKARQKWADTARAAAKQARRARVPAVRDHVSGTAVAGLARDDDGGRLVLVLHE
+DAEHGVSAVPAERLSAAVEIAVVVGPEGGIGPAELEACVAAGAVPVRLGPHVLRASTAGP
+AALAVLQHRLGRW
+>1_899
+MTAPLFHLEPGALAGASAGAEVVFDGAEARHAAAAMRLAPGEAVLLADGSGTLGHGTVLA
+AAPDAVSVRLDAVAEEPAPTPALVLVQALAKGDRDLMAVQAAVELGVDAVVPWEAERSIV
+RWKGPKAAKARRKWADTARAAAKQARRARVPAVRDHVSGTAVAGLAWDDDGGRLVLVLHE
+DAEHGVSAVPAERLSAAVEIAVVVGPEGGIGPAELEACVAAGAVPVRLGPHVLRASTAGP
+AALAVLQHRLGRW
+>2_1640
+MTAPLFHLEPGALTGAVPGAEVSFGGPEARHAAASMRLAPGESVLLADGSGVRGHGTVLA
+AAPDAVTVRLDAVDEEPAAVPALVLVQALAKGDRDLMAVQAAVELGVDAVVPWEAERSIV
+RWKGPKAEKARQKWADTARAAAKQARRARVPEVRGHVSGTGVAGLASAPDDGARLVLVLH
+EDAERGLSEVPVERLREAAEIAVVVGPEGGVGPAELEACTAAGAVPVRLGPHVLRASTAG
+PAALAVLAHRLGRW
+>3_1536
+MTAPLFLLDAGALAGVAPGAEVAFTGAEARHAAASMRLGAGESVLVADGSGARASCVVVD
+AAPSAVTVRVESLEHDAAPRPALVLVQALAKGDRDLMAVQASTELGVDAVVPWEAERSIV
+RWKGAKAAKAHQKWEDTVRAAAKQARRARVPEVRPVVSGTAVAALAGPDRLLLVLHEDAD
+LGLGGLPDADLEAAAEVALVVGPEGGVSPAELDACTAAGAVPVRLGPHVLRASTAGPAAL
+AVLQHRLGRW
+>4_1129
+MTAPLFHLEPGALAGASAGAEVVFDGAEARHAAAAMRLAPGEAVLLADGSGTLGHGTVLA
+AAPDAVSVRLDAVAEEPAPTPALVLVQALAKGDRDLMAVQAAVELGVDAVVPWEAERSIV
+RWKGPKAAKARQKWADTARAAAKQARRARVPAVRDHVSGTAVAGLAWDDDGGRLVLVLHE
+DAEHGVSAVPAERLSAAVEIAVVVGPEGGIGPAELEACVAAGAVPVRLGPHVLRASTAGP
+AALAVLQHRLGRW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001019.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001019.fa
new file mode 100644
index 0000000000000000000000000000000000000000..335f794dcb37a7251ab1f6217940960adf21d340
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001019.fa
@@ -0,0 +1,40 @@
+>0_1172
+MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPDPEAAEQFKRISHAYEVLSDEGRR
+RAYDTTGNENGQAGFPGGFGGAGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT
+ARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLLGT
+VMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP
+GGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLDPG
+VQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVHGA
+PQAKGMFARLRENLRNL
+>1_900
+MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPDPEAAEQFKRISHAYEVLSDEGRR
+RAYDTTGNENGQAGFPGGFGGAGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT
+ARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLLGT
+VMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP
+GGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLDPG
+VQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVHGA
+PQAKGMFARLRENLRNL
+>2_1639
+MTDHYATLGVSRDASTEEIRRAYRKLARTHHPDVNPDPESAEQFKRISHAYEVLSDEGRR
+RAYDTTGNENGQSGFPGGFGGGGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT
+APIDLEDAVFGGEQTITLDTAVRCKRCEGSCCEPGTEPETCQTCQGHGMIQRPMRSLLGT
+VMATEACPACQGFGTVIPDPCHECAGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP
+GGGPNGDLYVEIAVRPHETFRREGDHLATTVTVPMAAAALGTTVTLATLDGEQTVRLEPG
+VQSGHVETLAGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRELLERLAELRGEEVVHGT
+PPARGMFARLRENLRNL
+>3_1535
+MADHYATLGVSRDASAEEIKRAYRKLARQHHPDVNPSEEAAEEFKRISHAYEVLSDEDKR
+RVYDQTGNENGTAGGFGGGGFGGAGFGGFADIFETFMNAAGTPGGGRGPMPRARRGQDAL
+VTARIELRDAVFGGEATLQLDTAVTCERCSGTCCEPGTHPETCSTCQGQGMTQRPVRSML
+GTIMAAETCPVCRGFGTVIPHPCTECSGQGRVRVQQPLTIRIPAGVDDGTRIHLAGRGEA
+GPGGGPNGDLYVEVQVRPDEVFRREGDHLATTVTVPMAAAALGTSVTLETLDGPQEVDIE
+PGTQSGHVETLRGLGVGRLRGAGRGDLKVDVVVTTPTDVTDEQRALLEQLAGLRGEEVVH
+GAPPQSKGMFARLRENLKNL
+>4_1130
+MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPGPEAAEQFKRISHAYEVLSDEGRR
+RAYDTTGNENGQAGFPGGFGGAGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT
+ARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLLGT
+VMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP
+GGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLDPG
+VQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVHGA
+PQAKGMFARLRENLRNL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001028.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001028.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d4a84f0981638043d337889c0adb865118ea1f2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001028.fa
@@ -0,0 +1,31 @@
+>0_1182
+MSPSHRLCDDPPAFAPDPAAVPDVDTAGPHAASRWERTPPRGPVLRWRPALLAVTVLLVA
+AAAWWAVAWLTTPAPPAAVPAAAAGAGIPQTGAPSAASTAAGTDARTPEAGPSGEASGSA
+GSTPLRVHVVGEVARPGVVSLAPGSRVADAVRAAGGPTRHARAERINLAAPLDDGQQVLV
+PSAHTPQDALDRVAGAAQAQPTPTTGGAGATGEPGGAEPRGTVDLNTADAAGLQTLPGVG
+PATAEKIIAHRETVGPFTGLQDLDAVPGIGPATLDRLRDLVSW
+>1_910
+MRDAPDSATGPQTARMSPSHRLCDDPPAFAPDPAPAAAPDVDTAGPHAASRWERTPPRGP
+VLRWRPALLAVTVLLVAATAWWAVAWLTTPAPPAAIPAAAAGAGIPQTDAPSTAPSAAGT
+DARTSEAGPSGEASGPAGSGPLRVHVVGEVARPGVVSLAPGSRVADAVGAAGGPTRHARA
+ERINLAAPLDDGQQVLVPSARTPQDALDRVAGAAQAQPTPTTGRAGGGGEPGGAESGDTV
+DLNTADATELQTLPGVGPATAEKIIAHRETVGPFTGLQDLDAVPGIGPATLDRLRDHVSW
+>2_1629
+MSHPHRLAPDAALSDDPRRGRPASDLVPVPPALAARGPSAWERVPPRGRVLRWRPALLAV
+TVLLVAAAAWWAVAWLTSPAPPSPAPAASAVEARVEPETEDGPDAADAAPPSDGAGPAAE
+PSGGSGPVATLLRVHVVGEVERPGVVSLAPGARVADAVRAAGGATREARTERINLAAPLA
+DGRQVLVPSARTPEEDLARVAGGQDGPGGPEGGAAGTAPDAAASAPAGPARAGGSGGAGA
+GPVDLNAADAVALQTLPGVGPATAEKIIAHRETVGPFTGLQDLDAVPGVGPAALERLRDR
+VTW
+>3_1526
+MDTKTLTPAVDEPDWEDPPPRGPLLRWRTAGAGLTLVAILGLTWWLVAWLTAPAPPDAVP
+AGAVGSASAAGSAAHEASAAPLRATAATPEGQDGGGRSAAAANPSGRVRVHVVGQVRRPG
+VVELPAGARVADAVAAAGGARELARTDRINLAAPVVDGQQVVVPDAQTAVEPAAVAGEAP
+DGGPTPRTGSGASAADGSGGGPATVDLNTADLAALQTLPGVGPATAEKIIAQRESVGPFS
+GLQDLDAVPGIGPATLDRLKDHVTW
+>4_1140
+MSPSHRLCDDPPAFAPDPAPAAAPDVDTAGPHAASRWERTPPRGPVLRWRPALLAVTVLL
+VAATAWWAVAWLTTPAPPAAIPAAAAGAGIPQTDAPSTAPSAAGTDARTSEAGPSGEASG
+PAGSGPLRVHVVGEVARPGVVSLAPGSRVADAVGAAGGPTRHARAERINLAAPLDDGQQV
+LVPSARTPQDALDRVAGAAQAQPTPTTGRAGGGGEPGGAESGDTVDLNTADATELQTLPG
+VGPATAEKIIAHRETVGPFTGLQDLDAVPGIGPATLDRLRDHVSW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001030.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001030.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e0d573486968f90512883d7b8e575b30d93e4f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001030.fa
@@ -0,0 +1,75 @@
+>0_1184
+MSQTPDSAVPATPSIPADAEYSFRDVEARWAGYWEQAGTFAPREDGSETRTVVDMFPYPS
+GDLHMGHAEAFAMGDVVARHWMQRGFDVLHPIGWDSFGLPAENAAIKRDAHPAEWTYANI
+ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRRGLAYRKDSPVNWCPQDQTV
+LANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI
+GRSEGAHVDFQVEDGPVVTVFTTRPDTLHGATFMVVAADAPLAAELAGDDVRAELEAYRE
+DLKKVSDIDRQATDRPKSGVFLGRHAVNPLTGERLPIWASDYVLADYGTGAIMAVPAHDQ
+RDLDFARAMGLPVRTVLDTGEEDPAVSGVATTGEGILVNSGELDGLDKTAAIARAIEIVQ
+ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPDCGEVLVPEDQLPVTLPTDLKGEQLA
+PKGQSPLAAATSWVEVDCPQCGGPARRDTDTMDTFVDSSWYMLRYASPNDDARVFDPEAL
+RRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNDGKAMSK
+SLGNGVDLGDQLDQFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRLARDVRA
+TGTPAGTDPADGAVALRRVTHRTVHEAQQLLDDGKFNVVVAKTMELVNAARKEIDAGAGA
+ADPAVREAAEAVAVLLSLVAPYTAEDMWVLLGHEPSVIRAGWPAVDEALLVEDTVTAVVQ
+VKGKVRDTLEVPADITAEDLEARARASQKVRNFIGDAQIVKVIVREPKLVNLVIR
+>1_912
+MSQTPDSAVPATPSIPADAEYSFRDVEARWAGYWEQAGTFAPREDGSETRTVVDMFPYPS
+GDLHMGHAEAFAMGDVVARHWMQRGFDVLHPIGWDSFGLPAENAAIKRDAHPAEWTYANI
+ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRRGLAYRKDSPVNWCPQDQTV
+LANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI
+GRSEGAHVDFQVEDGPVVTVFTTRPDTLHGATFMVVAADAPLAAELAGDDVRAELEAYRE
+DLKKVSDIDRQATDRPKSGVFLGRHAVNPLTGERLPIWASDYVLADYGTGAIMAVPAHDQ
+RDLDFARAMGLPVRTVLDTGEEDPAVSGVATTGEGILVNSGELDGLDKTAAIARAIEIVQ
+ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPDCGEVLVPEDQLPVTLPTDLKGEQLA
+PKGQSPLAAATSWVEVDCPQCGGPARRDTDTMDTFVDSSWYMLRYASPNDDARVFDPDAL
+RRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNGGKAMSK
+SLGNGVDLGDQLDEFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRLARDVRA
+TGAPAGTDPAGGAVTLRRVTHRTVHEAQQLLDDGKFNVVVAKTMELVNAARKEIDAGAGA
+ADPAVREAAEAVAVLLSLVAPYTAEDMWVLLGHEPSVVRAGWPAVDEALLVEDTVTAVVQ
+VKGKVRDTLEVPADITAEDLEARARASQKVRNFIGDAEIVKVIVREPKLVNLVIR
+>2_1627
+MFPYPSGDLHMGHAEAFAMGDVVARHWMQRGYDVLHPIGWDSFGLPAENAAIKRDAHPAE
+WTYANIETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRKGLAYRKDSPVNWC
+PQDQTVLANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLA
+MQRNWIGRSEGAHVDFQIEDGPQITVFTTRPDTLHGATFMVVAADAPLAAELADESVRAE
+LEAYREELKKVSDIDRQATDRPKTGVFLGRHAINPLNGERLPVWASDYVLADYGTGAIMA
+VPAHDQRDLDFARAMGLPVRAVLDTGEENPAVSGVATTGDGTLVNSGELDGLDKTAAIAR
+AIEIVEGRGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCEACGEVLVPEDQLPVTLPTDL
+NGEQLAPKGQSPLAAATSWVEVACPDCGGPARRDTDTMDTFVDSSWYTLRYASPNDDTQV
+FDPEAVRRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNG
+GRAMSKSLGNGVDLGAQLDEFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRL
+ARDVREAGTPADADPATGSVALRRVTHRSVHEAGQLLDDGKFNVVIAKTMELVNAARKEI
+DGGAGAADPAVREAAEAVAVLLSLVAPYTAEDMWVMLGHEPSVVRAGWPAVDESLLVEDT
+VTAVVQVKGKVRDTLEVPADITAEDLEARARASQKVRTFIGDAEIVKVIVREPKLVNLVI
+R
+>3_1524
+MSQTPESAAPATPQVPEDAEYAFSEVEARWAGYWEQAGTFTPRGDGSATRTVVDMFPYPS
+GDLHMGHAEAFAMGDVLARYWLQRGYDVLHPIGWDSFGLPAENAAIKRNAHPAEWTYANI
+ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRKGLAYRKDSPVNWCPQDQTV
+LANEQVVDGKCERCGAEVTKRELNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI
+GRSEGAHVDFQVEDGPAVTVFTTRPDTLHGATFMVVAADAPLALELVDDEHRAALEAYRE
+ELKKASDIERQATDRPKTGVFLGRHAVNPLTGERLPMWASDYVLADYGTGAIMAVPAHDQ
+RDLDFARAMDLPVRTVVDTGEEDPAVSGVATTGEGTLVNSGELDGLSKADGIARAIEIVQ
+ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPEHGEVLVPEDQLPVLLPTDLKGGQLA
+PKGQSPLAAAEEWVNVPCPECGAPARRDSDTMDTFVDSSWYFLRYASPWDEQQVFDPELV
+KTWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNGGKAMSK
+SLGNGVDLGQQLDEFGVDAVRTTMVFASPPEDDVDWADVAPAAAGKFLARAWRLARDVRA
+AGTPAGDPAQGSAALRRVTHRTVHEAAALVEDHKFNVVVAKTMELVNATRKEIDGGAGAA
+DPAVREAAEAVAILLSLVAPYVAEDMWAMLGHEPSVVRAGWPAVDESLLVEDTVTAVVQV
+KGKVRDQLQVPADVSAADLEAAARASAKVRAFIGDAEIVKVIVREPKLVNLVIR
+>4_1142
+MSQTPDSAVPATPSIPADAEYSFRDVEARWAGYWEQAGTFAPREDGSETRTVVDMFPYPS
+GDLHMGHAEAFAMGDVVARHWMQRGFDVLHPIGWDSFGLPAENAAIKRDAHPAEWTYANI
+ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRRGLAYRKDSPVNWCPQDQTV
+LANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI
+GRSEGAHVDFQVEDGPVVTVFTTRPDTLHGATFMVVAADAPLAAELAGDDVRAELEAYRE
+DLKKVSDIDRQATDRPKSGVFLGRHAVNPLTGERLPIWASDYVLADYGTGAIMAVPAHDQ
+RDLDFARAMGLPVRTVLDTGEEDPAVSGVATTGEGILVNSGELDGLDKTAAIARAIEIVQ
+ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPDCGEVLVPEDQLPVTLPTDLKGEQLA
+PKGQSPLAAATSWVEVDCPQCGGPARRDTDTMDTFVDSSWYMLRYASPNDDARVFDPDAL
+RRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNGGKAMSK
+SLGNGVDLGDQLDEFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRLARDVRA
+TGAPAGTDPAGGAVTLRRVTHRTVHEAQQLLDDGKFNVVVAKTMELVNAARKEIDAGAGA
+ADPAVREAAEAVAVLLSLVAPYTAEDMWVLLGHEPSVVRAGWPAVDEALLVEDTVTAVVQ
+VKGKVRDTLEVPADITAEDLEARARASQKVRNFIGDAEIVKVIVREPKLVNLVIR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001031.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001031.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2534e00755c30432f7e7aac04687004feffe9a9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001031.fa
@@ -0,0 +1,43 @@
+>0_1185
+MQHPVALRSLKIALAFVGLLVGAGFATGAEVIQYFVGFGWIGIVGAGLAGLLVTAGGAVI
+LQLGSVFLAADHKVVFRSVSHPVMARILDVVVTVTLFAIGVVMLAGAGSTLAQQFGWPTW
+AGSTLMTLLVLVTGMLDVEKVSAIISLITPLVVVAVVAGFVHVLVTRDGGFTAHESLAVQ
+ATTPVDPWWLSSVNYFGLVVVMAVSMCLVIGGSITHPREAFLGGLTGGLMYTALLLMAST
+LLYLGYAEIGRADVPMLRLFASIAPWLGWAMVVVIYLMIFNTAIGMFYALGRRLTADRPG
+RYRPVFAGVTLLAFAVSFVGFGDLINVVYPALGHLGIVLALVLLVWWLTHRRQISAESGL
+RLRLLALLRLREHPEKTFTAQHAVQLQEAVGDSVAAPDAVTEALEDEVAQVLEEDDALTS
+EGARPGPDAGPERPAGGSHSA
+>1_913
+MQHPVALRSLKIALAFVGLLVGAGFATGAEVIQYFVGFGWIGIVGAGLAGLLVTAGGAVI
+LQLGSVFLAADHKVVFRSVSHPVMARILDVVVTVTLFAIGVVMLAGAGSTLAQQFGWPTW
+AGSTLMTLLVLVTGMLDVEKVSAIISLITPLVVVAVVAGFVHVLVTRDGGFTAHESLAVQ
+ATTPVDPWWLSSVNYFGLVVVMAVSMCLVIGGSITHPREAFLGGLTGGLMYTVLLLMAST
+LLYLGYAEIGRADVPMLRLFASIAPWLGWAMVVVIYLMIYNTAIGMFYALGRRLTADHPG
+RYRPVFAGVTLLAFAVSFVGFGDLMNVVYPALGHLGIVLALVLLVWWLTHRRQISAESGL
+RLRLLALLRLREHPEKTFTAQHAVQLQEAVGDSVAAPGAVTEALEDEVAQVLEEDDAVTP
+DEVHPGPDAGPERPAGGSHSA
+>2_1626
+MVFRSVSHPVMARILDVTVTVTLFAIGFVMLAGAGSTLAQQLGWPTWAGAGLMTALVLVT
+GMLDVEKVSAIISLITPLIILAVVAGFVHVLLTHEGSFTANEALAVQAATPVAPWWLSSV
+NYFGLVVVMAVSMCLVIGGSITNPREAFAGGLTGGVLYTVLLLLASVLLYLGYAEIGRAD
+VPMLQLFASIAPWLGWTMVVVIYLMIYNTAIGMLYALGRRLTAERPGRYRPVFIGVTLLA
+FAVSFVGFGDLMNVVYPALGYLGIVLALVLIAWWVLHRRQISAESGLRLRLRALLRLREH
+PEKTFTAQHAVLLQEAADESVAATAVVTEAVEEEVVQAIEADEPYGDPRRS
+>3_1523
+MQKSAALRSVQLALAFVGLLVGAGFATGAEVIQYFVGFGEVGIGGALLAGVLVAVGGAVA
+LQLGSLFLAADHKVVFRSVSHPVMARILDAVVTVTLFAIGFVMLAGAGSTLAQQLGWPVW
+AGAALMTAMVIVTGMLDVEKVSAIIGMITPLIIIAVVAGFAYVVATHEGPFTVNDSLAVQ
+AVTPVSPWWLSSINYFGLVVVMAVSMCVVIGGSTSSPREAFVGGLVGGVVYTVLLVLASV
+LLYLGYAELGTADVPMLQLFASIHPALGWAMVVVIYLMIYNTAIGMFYALGRRLTAERPG
+LYRPAFVGVTLAAFAVSFLGFGDLMNYVYPALGYLGIVLAVVLLVWWAAHRDDIAAESGL
+RLRLLALLRLREHPEKTFTRQHAVILQETAEESVAPTETVTEMMEADAVAVIEAEDPDLL
+PAADETAGRGGADHGGADGSAAARG
+>4_1143
+MQHPVALRSLKIALAFVGLLVGAGFATGAEVIQYFVGFGWIGIVGAGLAGLLVTAGGAVI
+LQLGSVFLAADHKVVFRSVSHPVMARILDVVVTVTLFAIGVVMLAGAGSTLAQQFGWPTW
+AGSTLMTLLVVVTGMLDVEKVSAIISLITPLVVVAVVAGFVHVLVTRDGGFTAHESLAVQ
+ATTPVDPWWLSSVNYFGLVVVMAVSMCLVIGGSITHPREAFLGGLTGGLMYTALLLMAST
+LLYLGYADIGRADVPMLRLFASIAPWLGWAMVVVIYLMIFNTAIGMFYALGRRLTADRPG
+RYRPVFAGVTLLAFAVSFVGFGDLMNVVYPALGHLGIVLALVLLVWWLTHRRQISAESGL
+RLRLLALLRLREHPEKTFTAQHAVQLQEAVGDSVAAPGAVTEALEDEVAQVLEEDDALTS
+GGARPGPDAGPERPAGGSHSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001032.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001032.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e2248a41302da6e4752b5a813fcdefe7a33c520e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001032.fa
@@ -0,0 +1,34 @@
+>0_1186
+MPVPTPPAAPGPPVRLRDLLRPPAAPADPRVLTGHVARTPRRRTLAVPDPVRRTPSSVAV
+WEYAPVPEAAPGSRGAPEGDPAAAPLVFVHGFRGDHHGLALLADALPEHPIHSIELPGFG
+DSEPFPHAEHTVAHHADAVAAGVAALGLPAAPVLVAHSYGTTVAAELAVRDPSRWARLVL
+LNPIAEPALQASASVTSRVLAAVAEGYYEVAARLPERPARLLLGAPPVVWVTTLATTRTR
+DRDVLAYTHDQHRRHFSGFASARMLSEAYRASSTGSVADVAARLTLPVLLVAGREDPLGS
+VPAQKALAAAIDAGGGTAELHVLDGVGHLLHYERPAACAALIRDWLRRAGR
+>1_914
+MPVPTPPAPPGPPVRLRDLLRPPAAPADPRVLTGHPARTPRRRTLAVPDPVRRTPSSVAV
+WEYAPVPVAAPGSPGALEGDAAAAPLVFVHGFRGDHHGLALLADALPEHPIHSIELPGFG
+ASEPFPRAEHTVAHHADAVAAAVVALGLPAAPVLVAHSYGTTVAAELVAREPSRWGRLVL
+LNPIAEPALQASASATSRVLAAVAEGYYEVAARLPERSARLLLGAPPVVWATTLAMTRTR
+DRDVLAYTHDQHRRHFSGFASARMLSEAYRASSTGSVADVAARLTLPVLLVAGREDPLGS
+VPAQEALAAAIDAAGGTAELHVLDGVGHLLHYERPAACAALIRDWFRRAGR
+>2_1625
+MHGFRGDHHGLALLADALPERAITSIELPGFGDSEPFPDAEHTVAHHADAVAAVLAAMPP
+SQRPVLVAHSYGTVVGAELVARDPGRWDRLALLNPIAEPALDASASWTSRGLAALARGYY
+ELAARLPERAGRLVLGAAPVVWVTTLAMSRTPDRRVLAYTHDQHRRYFSRFASARMLSES
+YRASSTGTVADAADRLRLPVLLVAGREDPLGSVPAQEALAAAIEAGGGRAELHVLDGVGH
+LLHYERPGECAALLRAWAARGR
+>3_1522
+MPAPHDADPASPAGPRPIRPWHRLRIPAPTTPPRALTGHDVRVPRRRDVAVPDPISGAPL
+SVAVWQHDAAPSSGASVAGAARPHLVFVHGFRGDHHGLQLLADCLPEFGVSSVELPGFGA
+SDPFPDAEHTVAHHADALAAAVAALGLDAPPVLVAHSYGTVVAAHLVQRDSGAWPALALL
+NPIAEPALDASGSRADRLLAGVAEAYYEAAARLPERVSRLLLGAPPVVWVTTQAMSRTRD
+RDVLAYTHDQHRRFFSGFASARMLSESYRASSTGTVAQAADRLDLPVLLVAGREDPLGSV
+AAQEALAARIAAAGGVPELHVLDGVGHLLHYERPAACARLLREWLAAGA
+>4_1144
+MPAPTPPAAPGPPVRLRDLLRPPAAPADPRVLTDHPARTPRRRTLAVPDPVSGTPSSVAV
+WEYAPVPEAAPGSPSGLKGDTAAAPLVFVHGFRGDHHGLALLADALPEHPIHSIELPGFG
+ASEPFPHAEHTVAHHADAVAAVVAALGLPAAPVLVAHSYGTTVAAELVARDPSRWGRLAL
+LNPIAEPALQASASVTSRVLAAVAEGYYEVAARLPERSARLLLGAPPVVWVTTLAMTRTR
+DRDVLAYTHDQHRRHFSGFASARMLSEAYRASSTGSVADVAARLTLPVLLVAGREDPLGS
+VPAQEALAAAIDAGGGTAELHVLDGVGHLLHYERPAACAALIRDWLRRAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001034.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001034.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa25d7fd960e4a049da32bda7c55a49671324fdc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001034.fa
@@ -0,0 +1,40 @@
+>0_1188
+MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK
+VAVETLTTTGLVQVAGEVNTSAYVEIPKIVRETILDIGYDSSANGFDGAQCGVNISIGQQ
+SSDIFAGVSRSLETREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL
+TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEEH
+VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK
+IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL
+>1_916
+MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK
+VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ
+SSDIFAGVSRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL
+TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEEH
+VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK
+IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL
+>2_1623
+MTDAAQPSPARHADPYTGVGGGELRLFTSESVTEGHPDKICDQISDAILDAILAADPAAK
+VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ
+SSDIFAGVTRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL
+TAVRRQENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHDWVGQEQLRKDVEEH
+VIRPVIERSGLDTSGMRVIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTAVVPEER
+IIQAVNEVFDLRPAAIVKELNLLRPIYRKTAANGHFGRDDADFTWERTDRVERLRAAAGL
+>3_1520
+MSDTPTPTPSAAAQPYRGVGGGDLRLFTSESVTSGHPDKMCDQISDAILDAILAADPSAK
+VAVETLSTTGLVQVAGEVNTSAYVEIPHIVRETILDIGYDSSANGFDGAQCGVNVSIGQQ
+SSDIFAGVSRSLEAREQGSADEVDEQGAGDQGIMFGYATNETPSYMPTPIYLAHRLSERL
+TAVRRQENTPMPYLLPDGKTQVTVGYDADHRPRTVETVVVSTQHHDVVTQEQLRADVAEH
+VIRPVIERSGLDVSNARFIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYALRWVAKNVVAAGLAGRAEFQVAYAIGSARPVGLYVDTFGTNAVPEET
+IIAAVNEVFDLRPAAIVKSLNLLRPIYRKTAAHGHFGRDDADFTWERTDKVEELRRAAGV
+>4_1146
+MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK
+VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ
+SSDIFAGVSRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL
+TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEKH
+VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK
+IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001041.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001041.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ae2bc555f6fb8ec1d64df49cee5d06500dd04eeb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001041.fa
@@ -0,0 +1,40 @@
+>0_1195
+MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT
+SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR
+AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE
+HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG
+DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG
+RVAITSQNHGFAVAAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP
+ESAAGPNDTLDLFDRFVQLLTEHRAATTPATEGA
+>1_923
+MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT
+SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELETFGVVGIREVDTR
+AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE
+HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG
+DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG
+RVAITSQNHGFAVDAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP
+ESAAGPNDTLDLFDRFVQLLTEHRAATTPATEGA
+>2_1616
+MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT
+SPHIGNTGVNDTDRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR
+AITRRLRTEGSMRAGVYSGEHAGRPEAELLAEVREQPSMAGARLAETVTTEQPYVIEPAA
+HGWEGEPLAEIAALDLGIKAATPRHLASRGIRVHVLPATAGLEEIRAVSPDGVFLSNGPG
+DPATADAQVALLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVMDNATG
+RVAITSQNHGFAVDAPLGEPVEAPETRYGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP
+ESAAGPNDTLDLFDRFVRMLTEHRDAAAPAATEGA
+>3_1513
+MSTPTPETALLVLEDGTVHRGRAYGARGSTLGEAVFTTGMTGYQETLTDPSYARQIVVQT
+APHIGNTGVNDEDAESRAIWVAGYVVRDAARRPSNWRSQRTLDEELAAHGVVGIQDVDTR
+AITRALRTEGSMKAGIFSGEAAQRPEAELLAEVREQPSMAGARLAETVSAPSAYVVEPSD
+HGWDGEPIADVAALDLGIKAATPHHLAARGIRVHVLPADSDFAAIQAVRPDGVFMSNGPG
+DPATADAQVAVLREVLDAGLPYFGICFGNQIFGRALGFGTYKLPFGHRGPNQPVMDKATG
+RVEITSQNHGFAVDAPIGEVVEAPEARYGRVEVSHWSLNDDVVEGLRLLDRPAFSVQFHP
+EAAAGPHDSLGLFDRFAHTLTERRAAAPSATPEGA
+>4_1153
+MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT
+SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR
+AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE
+HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG
+DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG
+RVAITSQNHGFAVAAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP
+ESAAGPNDTLDLFDRFVQLLTEHRAATTPATEGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001048.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001048.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f291d5e36283de423ff6af09f144ea40a55023a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001048.fa
@@ -0,0 +1,25 @@
+>0_1202
+MTDTPGTAPAPGPDPSTRPVPGPVTVCPWEGMTGALEARLTAAATVAAAADEDPAARPAR
+RVVLVGPMGAGKTTVGRALAAVTGLPFVDSDELFTQVHGPIPEFFAEHGEAAFRAEEARV
+IGHVLGRPTPCVLSCGGGAVLHPGTRRALAGPDSDVVYLAVGEEEALRRVGGGAGRPVLA
+GDPAGTWRRILAEREGLYREVADLVLDTTGLTAAEAAWRIVGDAHRPRRSESHP
+>1_930
+MTDTPGTAPAPGPDPSTRPVPGPVTVCPWEGMIGALEARLTAAATVAAAADEDPAARPAR
+RIVLVGPMGAGKTTVGRALAAVTGLPFVDSDELFTQVHGPIPEFFAEHGEAAFRAEEARV
+IGHVLGRPAPCVLSCGGGAVLHPGTRRALAGPDSDVVYLAVGEEEALRRVGGGAGRPVLA
+GDPAGTWRRILAEREGLYREVADLVLDTTGLTAAEAAWRIVGDAHRPRRSESHP
+>2_1608
+MPGPVSLCAWEAMTGALEARLATAAAAADGAPAPRIVLVGPMGAGKTTVGRALAATTGLP
+FVDADELFVQVHGPIPEFFAARGEAAFREEEARVIAHVLGRPSPCVLSCGGGAVLHPATR
+RALRGPGSDVVHLAVDEAVALRRVGGGAGRPVLAGDPAGTWRRILAEREPFYREVADLVV
+DTTGLTAAEAAWRIVEGVHRPRRSESHP
+>3_1505
+MSAQPAPTDGVPSWEAMVRGLDGRLAETSRDPGPVVVLVGPMGAGKTTVGRALAEATGRV
+FVDSDALFEDAFGSIPAYFTSRGEPEFRRQEERVIAHVLAHPAPCVLACGGGAVLSAATR
+ARLADPRAVVVSLQVAEPEALRRLGGGAGRPVLAGDPAGRWKAVLAERAPLYAEVADLTL
+DGTGHRPGDIASRIVEAIPTLPRRHTRP
+>4_1160
+MTDTPGTAPAPGPDPSTRPVPGPVTVCPWEGMIGALEARLTAAATVAAAADEDPAARPAR
+RIVLVGPMGAGKTTVGRALAAVTGLPFVDSDELFTQVHGPIPEFFAEHGEAAFRAEEARV
+IGHVLGRPAPCVLSCGGGAVLHPGTRRALAGPDSDVVYLAVGEEEALRRVGGGAGRPVLA
+GDPAGTWRRILAEREGLYREVADLVLDTTGLTAAEAAWRIVGDAHRPRRSESHP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001050.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001050.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1dee21fa654e391c8997e3bad020c5b8b5ed5090
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001050.fa
@@ -0,0 +1,35 @@
+>0_1204
+MRPVLRAAVLGRPIAHSLSPVLHAAAYRVLGLDVDYGRRDLGEDEVLAFAAEHLGAPGAA
+DGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANTLVRDHPAAPGVVHAEN
+TDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLGANAVLFGVRDAARAAE
+VTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAAHVPADAALPPLLDAAY
+DPWPSVLAAAWSREGGPVASGLSMLLHQGVEQVRLFTARPRAAAGMPEPDWAAVTRAAAD
+ALGPAAG
+>1_932
+MRPTLRAAVLGRPIAHSLSPVLHAAGYRVLGLDVDYGRRDLGEDEVLAFAAEHLGAPGTA
+DGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANTLVRDHPSAPGVVHAEN
+TDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLGADAVLFGVRDPARAAE
+VTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAAHVPAGAALPPLLDAAY
+DPWPSVLASAWSREGGPVASGLSMLLHQGIEQVRLFTARPRAAAGMPEPDWAAVTRAAAD
+ALGPAAG
+>2_1606
+MGAPSDVRAEASAGAPAAPRLRAAVLGRPIAHSLSPVLHGAAYGVLGLDVDYRRRDLGED
+EVGAFVAGRLGAPRTADGGDAAARGEDWLGCSVTMPLKRAVVGCAGRVSERVRLLGTANT
+LVRDHPEHPGLVSAENTDVDGILGALASAGLAERGSGGAVGILGNGGTATAAVLAAATLG
+ADEVVFGVRDAARAAEVTALADALGLAWRTVGQPELAAAAPGLRAVVATLPPRAADPLAA
+HVPVGAALPPLLDAAYDPWPSALASAWTEAGGAVASGLSMLLHQGVEQVRLFTARPRAAA
+GMPEPDWAAVTRAAARALGPAAG
+>3_1503
+MAGATFRAAVLGRPIAHSLSPVLHAAAYRALGLDVDYGRADLGEEEVGPWLAARLGAPGS
+AARPAGPSGGDWLGVSVTMPLKPAVVPLADELSARVRELGVANTLVRDHPDHPGSLLAHN
+TDVDGIVRALAERGLDAGAGGGAVGILGNGGTATAAVAAASLLRAETVVLGVRDAGRARD
+VVALADRLGLGVRVEAQDALVRQAADLRAVVATLPPRAADPLADKVPAGVLPPLLDAAYD
+PWPSAIARAWSAAGGGVASGLSMLLHQGVEQVRLFTERPRRAAGGVEPDWAEVTAAASRA
+LGLPGR
+>4_1162
+MRPTLRAAVLGRPIAHSLSPVLHAAGYRVLGLDVDYGRRDLGEDEVLAFAAEHLGAPGTA
+DGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANTLVRDHPSAPGVVHAEN
+TDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLGADAVLFGVRDPARAAE
+VTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAAHVPAGAALPPLLDAAY
+DPWPSVLASAWSREGGPVASGLSMLLHQGIEQVRLFTARPRAAAGMPEPDWAAVTRAAAD
+ALGPAAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001052.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001052.fa
new file mode 100644
index 0000000000000000000000000000000000000000..72b1415afe0fe37e9309c8e40dcfa19b4e103bd6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001052.fa
@@ -0,0 +1,85 @@
+>0_1207
+MKSQEIARRWTAFFESRGHRVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRVV
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKETAIPMAWELLTSSVEDGGFGLD
+PERLWVTVYREDDEAERIWREDVGVRPERIQRMGKEDNYWHTGQPGPGGPCSEIFYDRGP
+AYGVDGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDVAGELEHKNIDTGLGLERLAMI
+LQGVENMYETDQVRPVLDRAAQLAGRSYTSTEDPADPHYDDDVRLRMVADHVRSALMLIS
+DGVRPGNEGRGYVLRRLIRRVVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERI
+ARIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPDAFELHDTYGFPIELTLEIAE
+EAGVAVDEAGFRALMAEQRDRARADAKAKKSGHTDTAVYQRLRAEGQTHFTGYTEHTTES
+VVRGLLQNGEEVPSAGAGTELELVLDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPV
+KGLSVHRVKVLDGEVAAGAQALGAIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGS
+FNKEGYLRFDFRWAESLSAGARSEVEDVVNIAIRDDHTVLTQEMSLEEARALGAMSLFGE
+KYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSELSEMFKAPAEELKDRIGATLDRLKAAEKQVAELRAQALQAQAGQLAAQAR
+DVTTSGGTSVRVLAHHAGDVAGDQLRSLALDLRARIESAGGNAAGTPVFVALTAEAKGRP
+LVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQGGGQDVTRVGDALDAVVAAV
+RAA
+>1_935
+MKSQEIARRWTAFFESRGHRVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRVV
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKETAIPMAWELLTSSVEDGGFGLD
+PERLWVTVYREDDEAERIWREDVGVRPERIQRMGKDDNYWNTGQPGPGGPCSEIFYDRGP
+AYGVDGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDIAGELEHKNIDTGLGLERLAMI
+LQGVENMYETDQVRPVLDRAAQLAGRSYTSTEDPADPHYDDDVRLRMVADHVRSALMLIS
+DGVRPGNEGRGYVLRRLIRRVVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERI
+SRIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPDAFELHDTYGFPIELTLEIAE
+EAGVAVDEAGFRALMAEQRDRARADAKAKKAGHTDTAVYQRLRAEGQTHFTGYTEHTTES
+VVRGLLQNGEEVASAGAGTELELVLDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPV
+KGLSVHRVKVLDGEVAAGAQALGAIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGS
+FNKEGYLRFDFRWAEALSAGARSEVEDVVNIAIRDDHAVLTQEMSLEEARALGAMSLFGE
+KYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSELSEMFKAPAEELKDRIGATLDRLKAAEKQVAELRAQALQAQAGQLAGQAQ
+DVTTSAGTSVRVLAHHVGDVAGDQLRSLVLDLRARIESAGGNAAGTPVLVALTAEAKGRP
+LVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQGGGQDVTRVGDALEAVVAAV
+RAA
+>2_1603
+MKSQEIARRWIAFFESKGHQHVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRAV
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKEKAIPMAWELLTTSVEDGGYGLD
+PERLWVTVYEEDDEAARIWEESVGVRPERIQRMGKDDNYWNTGQPGPGGPCSEIFYDRGP
+EYGADGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDVAGELENKNIDTGLGLERLAML
+LQGVENMYETDQVRPVLDRAAELSGREYTSTEDPTDPHYEDDVRLRMVADHVRSALMLIG
+DGVRPGNEGRGYVLRRLIRRVIRALRLMGVTEPVLPELLPVSRDAMKGSYPVVADEFERI
+SRIAYAEEKAFLRTIAAGTARLDAAVGQARTAGGGIAGADAFELHDTYGFPIELTLEIAE
+ESGVAVDEAGFRALMAEQRDRARADAKAKKSGHTDTALYQRLRAEGQTHFTGYTEHTTES
+VVRGLLLDGEEVASASAGTELEVILDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPV
+RGLSVHRVKVLDGEVPAGAEALGAIDLQRRLDGEKAHSGTHLVHAALHQVLGPEATQSGS
+FNKEGYLRFDFRWAESLSAGARSEVEDVVNIAIRDDHTVLTQEMSLEEARALGAMSLFGE
+KYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSELSEMFKAPAEELKDRIAASMDRLKAAEKQIAELQAKALQAQAGELAAQAQ
+DVTTASGVSVRVLARHVGEVAGDQLRGLVLDLRSRIESAGGNAAGTPVLVALTGEAKGRP
+LVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQGGGQDVTRVGDALDAVVAAA
+RAA
+>3_1500
+MKSHEIARRWTAYFEKQGHLVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRAT
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKEKAIPMAWELLTTSVEDGGYGLD
+PERLWVTVYEEDDEAARIWREDVGVRPERIQRMGKADNYWNTGQPGPGGPCSEIFYDRGP
+EYGVEGGPEADDTRYIEIWNLVFMQYRLSQVRSKYDFDVAGELEHKNIDTGLGLERLAMI
+LQGVENMYETDQVRPVLDRAAELAGKSYTSTEDPADPHYDDDVRLRMVADHVRSALMLIS
+DGVRPGNEGRGYVLRRLIRRVVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERI
+SRIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPDAFELHDTYGFPIELTLEIAE
+EAGVAVDEAGFHALMAEQRDRARADAKAKKSGHTDTAVYQRLRAEGQTHFTGYTEHTTES
+VVRGLLQNGEEVASAGAGTELELVLDATPFYAESGGQAADTGVITGDGFSLEVLDVQAPV
+KGLSVHRVKVLDGEVPVGAEAVGRIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGS
+FNKEGYLRFDFRWAEAVSAMARSEIEDVVNIAIRDDHQVLTQEMSLDEARAMGAMSLFGE
+KYGDRVRVVEINGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSDLSEMFKAPADQLKDRITATMDRLKAAEKQVADLQAKALQAQAGTLAAQAQ
+DVTTTSGASVKVLAHHAGEVAGDQLRSLVLGLRSRIESAGGNAAGTPVLVALTGEAKGRP
+LVVVATNEAARGAGLKAGAMVKLATAALGGGGGGKDDVAQGGGQDVTAVAAALDAVLDAV
+RDA
+>4_1164
+MKSQEIARRWTAFFESRGHRVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRVV
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKETAIPMAWELLTSSVEDGGFGLD
+PERLWVTVYREDDEAERIWREDVGVRPERIQRMGKDDNYWNTGQPGPGGPCSEIFYDRGP
+AYGVDGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDIAGELEHKNIDTGLGLERLAMI
+LQGVENMYETDQVRPVLDRAAQLAGRSYTSTEDPADPHYDDDVRLRMVADHVRSALMLIS
+DGVRPGNEGRGYVLRRLIRRVVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERI
+SRIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPDAFELHDTYGFPIELTLEIAE
+EAGVAVDEAGFRALMAEQRDRARADAKAKKAGHTDTAVYQRLRAEGQTHFTGYTEHTTES
+VVRGLLQNGEEVASAGAGTELELVLDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPV
+KGLSVHRVKVLDGEVAAGAQALGAIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGS
+FNKEGYLRFDFRWAEALSAGARSEVEDVVNIAIRDDHAVLTQEMSLEEARALGAMSLFGE
+KYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSELSEMFKAPAEELKDRIGATLDRLKAAEKQVAELRAQALQAQAGQLVGQAQ
+DVTTSAGTSVRVLAHHVGDVAGDQLRSLVLDLRARIESAGGNAAGTPVLVALTAEAKGRP
+LVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQGGGQDVTRVGDALEAVVAAV
+RAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001054.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001054.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c293d245a721e2cb281e2dbb127b493757ea3fa3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001054.fa
@@ -0,0 +1,25 @@
+>0_1209
+MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL
+RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEQRLDALVLRAGFARTIQQARQLVVHR
+HIMVDGKRVDVPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL
+RATLTRRPKRSEVPVTCEEQLVVEYYAR
+>1_937
+MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL
+RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEQRLDALVLRAGFARTIQQARQLVVHR
+HILVDGKRVDVPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL
+RATLTRRPKRSEVPVTCEEQLVVEYYAR
+>2_1600
+MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL
+RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEMRLDALVLRAGFARTIQQARQLVVHR
+HIMVDGKRVDIPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL
+RATLTRRPKRSEVPVTCEEQLVVEYYAR
+>3_1498
+MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL
+RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEMRLDALVLRAGFARTIQQARQLVVHR
+HIMVDGKRVDIPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIEKL
+RATLTRRPKRSEVPVTCEEQLVVEYYAR
+>4_1166
+MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL
+RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEQRLDALVLRAGFARTIQQARQLVVHR
+HILVDGKRVDVPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL
+RATLTRRPKRSEVPVTCEEQLVVEYYAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001056.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001056.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e31315ac11812012d37030344184a3400aef2f5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001056.fa
@@ -0,0 +1,45 @@
+>0_1211
+MDDLFSAAHTGADDDGPAGTVAAPHPGAPLAVRMRPRTLDDVLGQRHLMRPGSPLRKLAE
+PDPDSAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRE
+RDLYGRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLL
+TLRPLTDDDIVGLLDRAVTQERGLNGAVVLEDDARDYLVRMAGGDARRALTVLEAAAGVA
+LDKAREAGRAGEGAVAVTEEDAAQAMDHHVQRYDKDGDQHYDVISAFIKSIRGSDVDASM
+HYLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVATAQAVQLIGMPEGRIILAQ
+AVTHLATAPKSNASYTAVNEAIADVRAGHTGAVPAHLRDAHYPGAAALGHGQGYVYSHDE
+PHAVARQQYAPDPLVGRDYYRPKPIGHEKRLTEQVAALRRIIRGD
+>1_939
+MDDLFSAAHNGADDDGPAGTVAAPHPGAPLAVRMRPRTLDDVLGQRHLMRPGSPLRKLAE
+PDPDSAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRE
+RDLYGRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLL
+TLRPLTDDDIVGLLDRAVTQERGLNGAVVLQDDARDYLVRMAGGDARRALTVLEAAAGVA
+LDKAREAGRAGEGAVAVTDEDAAQAMDHHVQRYDKDGDQHYDVISAFIKSIRGSDVDASM
+HYLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLIGMPEGRIILAQ
+AVTHLATAPKSNASYTAVNEAIADVRAGHTGAVPAHLRDAHYPGAAALGHGQGYVYSHDE
+PHAVARQQYAPDPLVGRDYYRPKPIGHEKRLTEQVAALRRIIRGD
+>2_1598
+MADLFSAAHESDDDGPSGTVAAPRASAPLAVRMRPRTLEEVLGQRHLMRPGSPLRKLAEP
+DPGSPAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRER
+DLYDRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLLT
+LRPLTDEDIVGLVERAVADERGLNGAVDLADDARDYVVRMAGGDARRALTVLEAAAGVAL
+DKARQAGADEDAGGDGGARAGAAAPVTVTEEDAAQAMDHHVQRYDKDGDQHYDVISAFIK
+SIRGSDVDAALHWLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLI
+GMPEGRIILGQAVTHLATAPKSNASYAAVNEALADVRAGGTGQVPPHLRDAHYPGAAALG
+HGKGYVYSHDEPHAVARQQYAPDPLVGKDYYRPKPIGAEKRLVDQVAALRRITRGE
+>3_1496
+MDDLFSAAHADPDDDAPVTASGRARASAPLAVRMRPRSLDEVLGQAHLKQPGSPLRKLAE
+PAASAQAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQARR
+EREMYDRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLL
+LTLRPLDDTDLAALVDRAVADERGLNGTVEPTPNARDYVVRMAGGDARRALTVLEAAAGV
+ALDRAEARGETTGPGSAPVEVTEEDAAQAMDAQVQRYDKDGDQHYDVISAFIKSIRGSDV
+DAAMHWLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLIGMPEGRI
+VLGQAVTHLATAPKSNASYTAVNEAIADVRAGGTGVVPAHLRDSHYPGAKALGHGQGYVY
+SHDEPHAVARQQYAPDPLVGRDYYRPKPIGHERQLGPQVDALRRIIRGD
+>4_1168
+MDDLFSAAHNGADDDGPAGTVAAPHPGAPLAVRMRPRTLDDVLGQRHLMRPGSPLRKLAE
+PDPDSAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRE
+RDLYGRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLL
+TLRPLTDDDIVGLLDRAVTQERGLNGAVVLQDDARDYLVRMAGGDARRALTVLEAAAGVA
+LDKAREAGRAGEGAVAVTDEDAAQAMDHHVQRYDKDGDQHYDVISAFIKSIRGSDVDASM
+HYLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLIGMPEGRIILAQ
+AVTHLATAPKSNASYTAVNEAIADVRAGHTGAVPAHLRDAHYPGAAALGHGQGYVYSHDE
+PHAVARQQYAPDPLVGRDYYRPKPIGHEKRLTEQVAALRRIIRGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001057.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001057.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e602f1facb654d4d1a4a6060937cb420df13fd4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001057.fa
@@ -0,0 +1,25 @@
+>0_1212
+MSPAAPRADHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD
+AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD
+PAPESAAALAALDHGDGRPAGPDRTALEGRLLWTRCATGVADSPLTPARLDRALGVRGTA
+RNLTTVRVLAGLPAGDRPRRTARGASGDVDIRGTPRAGRDVTVRSHPCDGVTPSSASLP
+>1_940
+MSPAAPRTDHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD
+AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD
+PAPEAAAALAALDHGDDRPAGPDRTALEGRLLWMRCAAGVADSPLTPARLDRALGVRGTA
+RNLTTVRVLAGLPSED
+>2_427
+MSEHPASPTHVLLLRAVNVGGRNRVPKADLAELAAEAGLADVAVHLNSGNVLGTPDTGDH
+VDDVAARLRALLAERLGVDTSVHAAARTELSALVDGLLASDLLAPGETLDSVDPKTVHLV
+LLDTVPHPEAGEALAAVDAGDDRAVVVGRGVWVRYAGPSHSSHLGLPRIERAASGDAPPA
+QRRVGTARNLATVRVLAGR
+>3_1495
+MSRAAPRTDHTHVLLLRGINVGRSNRVSNARLAAWAEAARARDVTTHLASGNVLFRLPDA
+DDDAGPAFLRAFRDAALADDGPDVPLILTTPAELRGALAMHDRLPWSGGEAKLTQLTVLA
+ESPRDGAAEALAGLDHGSGRAAGPDRSALEGRFLWIRSPGRISDSPLTPARLEKALGVTG
+TARNLATVRVLAGMA
+>4_1169
+MSPAAPRTDHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD
+AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD
+PAPEAAAALAALDHGDDRPAGPDRTALEGRLLWMRCAAGVADSPLTPARLDRALGVRGTA
+RNLTTVRVLAGLPSED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001062.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001062.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71542f3920a458494cf4315013b8ee439af65f99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001062.fa
@@ -0,0 +1,45 @@
+>0_1217
+MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE
+VYAVSRLAEDEEVAAGRREPKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ
+KVWRGERPQEGRAREFTQADIDVVGDGALSPRYDADVALVMAEALGALPIGDFLIRVNNR
+KLAEGFYRGIGLEDTAGVLRSIDKLEKVGPEEVARLLQEEVGASPEQAAQALALADIRTS
+DTSFVERVRALGVTHELLEEGLTELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET
+VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQQMAVASRSVPTAV
+YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFMGRDDAG
+ARVHEVKDIRSGEQHAVDPADWTPPTEDLLPQITRTQD
+>1_945
+MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE
+VYAVSRLAEDEEVAAGLRDPKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ
+KVWRGERPQEGRAREFTQADIDVVGDGALSPRYDADVALVMAEALGALPIGDFLIRVNNR
+KLAEGFYRGIGLEDTAGVLRSIDKLEKVGPEEVARLLQEEVGASPEQAAQALALADIRTS
+DTSFVERVRALGVTHELLEEGLTELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET
+VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQQMAVASRSVPTAV
+YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFMGRDDAG
+ARVHEVKDIRSGEQHAADPADWTPPAEDLLPQVARAQD
+>2_1592
+MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE
+VYAVSRLAEDEEVAAGRREAKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ
+KVWRGERPQEGRAREFTQADIDVVGDGELSPRHDADVALVMAEALGALPIGDFLIRVNNR
+KLAEGFYRGIGLTDAAGVLRSIDKLEKIGADEVARLLQEEVGASPEQARQALALAAIRTE
+DVSFVEQVRALGVSDPLLEEGLAELADVVETLHRRAPGRAVADLSIARGLDYYTGTVYET
+VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQEMAQASRSVPTAV
+YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFLGRDDAG
+ARVHEVKDIRSGDQHPADPADWTPPSEDLLPQVTRTESTEG
+>3_1487
+MSRKQSLSGFHEWLPAERIVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE
+VYAVSRLAEDQEVAEGVREAKDPSDPKRLALHFDLTVPFARYVTENAGHLAFPFRRHQIQ
+KVWRGERPQEGRAREFTQADIDVVGDGELSPRYDADVALVMAEALGALPIGDFRIRVNNR
+KLAEGFYRGIGLEDAAGVLRSIDKLEKVGAEEVARLLQEEVGATAEQAAQALKLAEIRTP
+DTAFVEQVRALGVEDPLLEEGLAELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET
+VLVGHEQLGSICSGGRYDALATKGNRAFPGVGLSIGVTRLVMRMLSQEMAVASRAVPTVV
+YVALTHDDDWSRAQDVAAGLRGRGIAAEVAVSAEKFGKQIKYADRRGIPFVWFLGAEGAS
+DEVKDIRSGEQVPADAATWAPPAEDLVPQVTESPRAED
+>4_1174
+MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE
+VYAVSRLAEDEEVAAGLRDPKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ
+KVWRGERPQEGRAREFTQADIDVVGDGALSPRYDADVALVMAEALGALPIGDFLIRVNNR
+KLAEGFYRGIGLEDTAGVLRSIDKLEKVGPEEVARLLQEEVGASPEQAAQALALADIRTS
+DTSFVERVRALGVTHELLEEGLTELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET
+VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQQMAVASRSVPTAV
+YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFMGRDDAG
+ARVHEVKDIRSGEQHAADPADWTPPAEDLLPQVARAQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001066.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001066.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a44b9d59e36db9ef9ae09bf6f55eb264718cfcb5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001066.fa
@@ -0,0 +1,35 @@
+>0_1221
+MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF
+TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG
+VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL
+AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP
+LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL
+>1_949
+MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF
+TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG
+VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL
+AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP
+LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL
+>2_1588
+MNRFADWGNALYSGRVSYPFVQRWRLWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF
+TVSQTAATDIAAGERAVTDVLAGGHATVTNIAPGTVRVQTEQLDDAQTRQVAANLQDAYG
+VGQDQVTSTFVGPTWGAAVSQQALLGLVIFVVLVTLFMAFYFRTWKMSLAAVIGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGQEEDPERTFEQNVNL
+AVNQTLVRSITTSIVGILPVGSILFIGAGLLGAGTLRDIALAIFVGIIVGTLSTLFIQAP
+LYALLRRGDEDVRDHDARAAARAARENRGDTVTDPDVAPWEDGARL
+>3_1483
+MNRFADWGNALYSGRISYPFVRKWKTWFLIAAALLAVAFGLTALRGGFNLGIDFRGGSEF
+TVSDAASSELDPGRAAVTDVVAGAEPTVTQVAPGTMRVQTEQLDDAQTRQVAQNLQQAYG
+VTGDHVTSTFVGPTWGQAVSQQAVIGLVIFVVLVTLFMALYFRTWKMSLAAVVGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTRGVEEDPDRTFDGSVNL
+AVNQTLVRSITTSIVGLLPVGSILFIGAGLLGAGTLRDISLAIFVGIIVGTLSTLFIQAP
+LYALLRRGDADVVAHDARVGADHDEREQEEDLADARGAVL
+>4_1178
+MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF
+TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG
+VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL
+AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP
+LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001069.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001069.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa1af3ccbf18e8dc87f0a51cdcc580cc1e7805c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001069.fa
@@ -0,0 +1,25 @@
+>0_1225
+MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLSTLHEGRPGAVQTHLVVKEDALTLY
+GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA
+RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT
+VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR
+>1_953
+MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLATLHEGRPGAVQTHLVVKEDALTLY
+GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA
+RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT
+VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR
+>2_1584
+MIASLSGTVEHVALDRAVIAVGGFGVQFSATPQTLATLHEGRTGSVQTHLVVKEDALTLF
+GFADRHEREVFEVLITANGVGPRLALAVLSVHHPEAVRRAVTEEDENALTRVPGVGPKLA
+RKIIVELSGRLTPTGEQVPAPEEPAAPETPEAAWHADVVQAMTGLGWSEKEALKAVEATV
+AARPELDEARDVAALLRATLRDVGTAGTVRGGR
+>3_1479
+MIASLSGTVEHVGLDHAVIAVGGVGLSFSATPQTLSHLHEGRDGAVQTHLVVKEDSLTLF
+GFADRAEREVFEVLLGANGVGPRLALAILAVHRPEAVRRAVTDEDEKALTLVPGIGPKMA
+RKIIVDLAGRLAPTGEVEPEAAVVEPEAAADAWHADVVQAMTGLGWSEKEAAKAVAATVA
+THPDVDASGDVAALLRATLRDVGAAAAVRGGRRA
+>4_1182
+MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLATLHEGRPGAVQTHLVVKEDALTLY
+GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA
+RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT
+VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001072.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001072.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9449b1832d721732e4728bea05a19d12a2f8c7ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001072.fa
@@ -0,0 +1,65 @@
+>0_1228
+MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAAT
+APTFENTVRALELSGQLLRRSAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPR
+LAARVASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAREELRGINTELASLSAAYTRR
+LVADTAARAVLVTDRERLAGLSEDDLAAAAGAAAEAGHGDGDAAAGPWLLTLSLFTSQPW
+LASLQDEGMRREVFEASTGRGGSGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRA
+APSTAAVEELLAAMAPRAMANARADAATAAAHAGRADAEVAPWDWPALSAGYAREEFAVD
+ADALRPYFELDRVLTEGVFAAATALYGLTFAERPELARHLYRPGIRVFEVTGEDGAGVGL
+FVADLFARPTKSGGAWMHTVRDRADALGERPVVFTTMNVPAPAAGRPALLTLDETTTLFH
+EFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVETGEPLPA
+GTLERLEAADLWGEGHRTVEYLGATLVDWAWHSLTEETVDAATADPAAFERRVLTEAGID
+PDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLDADAVEWFREHGGMTRENGRRFADEL
+LSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA
+>1_956
+MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAAT
+APTFENTVRALELSGQLLRRSAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPR
+LAARAASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAREELRGINTELASLSAAYTRR
+LVADTAARAVLVTDRERLAGLSEDDLAAAAGAAAEAGHGDGDAAAGPWLLTLSLFTSQPW
+LASLQDEGMRREVFEASTGRGGSGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRA
+APSTAAVEELLAAMAPRAMANARADAATAAAHAGRTDAEVAPWDWPALSAAYAREEFAVD
+ADALRPYFELDRVLTEGVFAAATALYGLTFAERPELARHLYRPGIRVFEVTGEDGAGVGL
+FVADLFARPTKSGGAWMHTVRDMADALGERPVVFTTMNVPAPAAGRPALLTLDEATTLFH
+EFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVESGEPLPA
+GTLERLEAADLWGEGHRTVEYLGAALVDWAWHSLTEETVDAATADPAAFERRVLTEAGID
+PDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLDADAVEWFREHGGMTRENGRRFADEL
+LSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA
+>2_1581
+MTPTPASSVLPADHPLATPSELPYGLPDFSAVTDAQLAEAVRAGMAAQRAEVEQILGAAT
+APTFENTVRAFELSGQLLRRSAAMFFTLVSADGTDARQGLAEELSPELAAHEDALLLDPR
+LAERVAAIDGAGLTGEDARLLEVLRRRLDLAGAGLGEAERAELGRINTELAGLTAAYTRR
+LVADTAERAVLVTDRERLAGLSEDDLASAAAAAREAGHGGADGEGGDEAGPWLLTLSLFT
+SQPWLASLEDEALRREVFEASVGRGAAGDHETLSTAMEVVRLRLRKARLLGSASWAEHAL
+KDRAAPSTTAVEELLATMAPRAMANARTDAATAAAHAGRVGGAVAPWDWPALSAAYARER
+FAVDAGALRPHFELDRVLHAGVFAAATALYGITFEERPELAGRLYRPGIRVFEVRDEDGA
+GVGLFVADLFARSTKSGGAWMHTVRDAADALDERPVVFNTMNVPAPAPGRPALLTLDEAT
+TLFHEFGHALHGLLAKGEYVSLSGTHVPRDVVEFPSQVNEVWLREPALLAEYARHVETGE
+PLPAGTLERLEAADLWGEGYRTVEYLGATLVDWAWHSLTEDTVEAATADPAAFERRVLTE
+AGIDPELVPPRYGTGYFKHIFGNDYAAGYYSYIWAEVLDADAVEWFREHGGMTRENGRRF
+AEELLSRGETRDLLESYRAFRGRDAELEPLLRRRGLVDAAA
+>3_1476
+MTQITHRLPAGHPLLSPSPLPHGLPDFAAVSDADLATGMRQGMAEQRAEVEEILSSPEAP
+TFENTVRALELSGALLRRVAPMFSTLVGSDGTDARQALAEELSPELAAHEDAILLDPRLS
+ARVAAVDDAGLAGEDARLLERTRTRLEIAGAGLDEAGRAELARLNGELATLSAAYTRRLV
+ADTAARAVLVTDRERLAGLRADDLAAAAERAAAEAGHRRADAAEGAGPWLLTLSLFTSQP
+WLADLEDAGLRREVFEASVGRGSSGEHETLTTAMRIVRLRLEKARLLGAASWAEHALRDR
+AAPSVAAVEGLLGSLTGPAMANARRDAEAVAEGDAPVVPWDWPFLSAAHAREAFDVDAGA
+LRPWFELDRVLTRGVFAAATALYGLRFAEREDLAGHLYRPAIRVWEVTDEDGRGVGLFVG
+DFFARPTKSGGAWMHNVVDASAALGTRPVVFCTMNVPAPAEGRPALLTLDEATTLFHEFG
+HVLHGLLAEGEYPSLTGTAVPRDTVEFPSQVNEVWLREPSLLADYARHVETGAELPTGTL
+ERLEAADLWGEGYRTVEYLGATLLDWAWHTLTEDTVDAATADPAGFERRVLTEAGIDVDL
+VPPRYGTGYFKHVFGNDYAAGYYSYIWAEVLDADAVEWFREHGGLTRENGRRFAEELLSR
+GDTRDVLESYRAFRGRDAELEPLLRRRGLLPEGA
+>4_1185
+MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAAT
+APTFENTVRALELSGQLLRRSAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPR
+LAARAASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAREELRGINTELASLSAAYTRR
+LVADTAARAVLVTDRERLAGLSEDDLAAAAGAAAEAGHGDGDAAAGPWLLTLSLFTSQPW
+LASLQDEGMRREVFEASTGRGGAGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRA
+APSTAAVEELLAAMAPRAMANARADAATAAAHAGRTDAEVAPWDWPALSAAYAREEFAVD
+ADALRPYFELDRVLTEGVFAAATALYGLTFAERPELARHLYRPGIRVFEVTGEDGAGVGL
+FVADLFARPTKSGGAWMHTVRDMADALGERPVVFTTMNVPAPAAGRPALLTLDEATTLFH
+EFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVESGEPLPA
+GTLERLEAADLWGEGHRTVEYLGAALVDWAWHSLTEETVDAATADPAAFERRVLTEAGID
+PDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLDADAVEWFREHGGMTRENGRRFADEL
+LSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001073.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001073.fa
new file mode 100644
index 0000000000000000000000000000000000000000..972f10ee6efec8f0f6c2735a354755b865a874d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001073.fa
@@ -0,0 +1,44 @@
+>0_1229
+MAARPRRPRPHPADLPPALAAAVTVAARRAGSRESRVRRAGRLVRRGVTGSVRGGVAVAS
+PVARWAPPVLSVAAAYAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV
+ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF
+TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIAPYPSEDGEPRPAEGLWAVMVHGRGARR
+NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD
+VVLFGWSMGGAVVLQTVDRSALAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ
+WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP
+DLVRFVRFHQARHTREQNVDPRKWDTAVRGWLRAVLSAPRPGGRGR
+>1_957
+MAARPRRPRPHPADLPPALAAAVTVAARRAGGRDSRVRRAGRLVRRGVTGSVRGGVAVAS
+PVARWAPPVLSVAAASAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV
+ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF
+TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIEPDPSEDGEPRPAEGLWAVMVHGRGARR
+NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD
+VVLFGWSMGGAVVLQTVDRSPLAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ
+WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP
+DLVRFVRFHQARHTREQNVDPRKWDTTVRGWLRAVLSAPRPGGRGR
+>2_1580
+MRTGVKAASPLARWTPPVLSVLASSAFVLAGASSALAGVFARTVVTPVRRHTETTAVLAV
+VDTPTGPEVILKADEYTTVPGVYSLTFDGGAGCARIGRISSFDPRDGTVQRVVEEVYFGD
+LAAATRGRLTGFVYPTPADAGLDAEEVLVPVPGGHAPAWLVGPDPDDDGAARPAAGIWAI
+MVHGRGARRNEGIRTVPTAQRLGMTSLLISYRNDGDAPDAADSRYGLGTTEWEDVEAAIR
+YALDNGASDVVLFGWSMGGAVVLQAVDRSDLAPQVRGVVLTGPVVDWVDVLQHQARLNRI
+PEAVGVLGQWLLSNRAGRFITGLAAPVDLKSLDWVTRAEHVRVPTLIIHSEDDEYVPVGP
+SQDLAERNPGLVRFVRFHQARHTREQNVDPKRWDTTVRGWLRAVLNADRPGAAER
+>3_1475
+MACPRRHSPRLRARPDLRDALLGSLRGSAAVARPAARLAPAAASVAASAAFVLAGASAGL
+AGVFARTVVTPVRSRPEHTAVLAVLDTGDGMDVILPADEHTTVPGTYSLTFHGGEGCARI
+GAIRSYDPRDGTVQRVVEEVYSGDLRSAVRGRFTAFIWPGPAEAGLEAADVEVPVPGGAA
+PAWRIDPPPAEDGEERAGEGMWAVMVHGRGAVRNEGLRAVPTAARLGMTSLLVSYRNDGD
+APDAEDARYGLGTTEWEDVEAAVRYALDHGARDVVLFGWSMGGAVVLQTADRSDLTSRVR
+GIVLTGPVVDWMDVLRHQARLNRIPEGIGLLGQWLLSNRAGRLVTGLAAPVDLKALDWVT
+RADHVRVPTLILHSEDDEYVPVGPSQDLAERNPALVRFVRFHQARHTREQNVDPVKWDRS
+VRGFLRAVLTAPRPGAVSPPGAPQAPSGSSPRRRSSGSSSASRPRNAR
+>4_1186
+MAARPRRPRPHPADLPPALAAAVTVAARRAGGRDSRVRRAGRLVRRGVTGSVRGGVAVAS
+PVARWAPPVLSVAAASAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV
+ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF
+TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIEPDPSEDGEPRPAEGLWAVMVHGRGARR
+NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD
+VVLFGWSMGGAVVLQTVDRSPLAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ
+WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP
+DLVRFVRFHQARHTREQNVDPRKWDTTVRGWLRAVLSAPRPGGRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001076.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001076.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c40c936545938f323fef1597f9a3317a461359a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001076.fa
@@ -0,0 +1,42 @@
+>0_1232
+MTDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTGPVAVDAERASGIRY
+GQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQDLPCLAEQGLRPDR
+LFDTELAARVAGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPEAMLTYAALDVELLV
+PLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQTLRRPVQRAVLKRL
+WEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHGRAASREAPRWIAAI
+RAGVEDAERGDAPAAQIRTGDGPPPPRAWKDRDPVADRRLRTAKARVARRAEQLGMPTEN
+LLTPDTLRRICWTPPAPITPETVDAFLTERGARPWQVENVGAIVTVALLDPDPAGA
+>1_960
+MTDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTGPVAIDAERASGIRY
+GQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQDLPCLAEQGLRPDR
+LFDTELAARVSGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPEAMLTYAALDVELLV
+PLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQTLRRPVQRAVLKRL
+WEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHGRAASREAPRWIAAI
+RAGVEDAERDDAPAAQIRTGDGPPPPRAWKDRDPVADRRLRTAKARVARRAEQLGMPTEN
+LLTPDTLRRICWTPPAPITPETVDAFLTERGARPWQVENVGAIVTVALLDPDPAGA
+>2_1576
+MTDVPEPAEPDATPRLIAEPADGVPRVTDTPAGLEACAAALAAGTGPVAVDAERASGIRY
+GQRAMLVQLKREGAGIWLVDPEALDGLEPLQEALSGVEWILHAASQDLPCLAEQGLRPDR
+LFDTELAARVAGLPRVGLAAVLESMLGVTLAKEHSAADWSVRPLPEAMLAYAALDVELLV
+PLRAAMLELLEAEGKREWAEQEFEHVRTAPAPGPRADPWRRTSGSQTLRRPVQRAVLKRL
+WEAREDLARHRDVAPGRLIPDRSLIAAAESQPRTVPALRQTSGFHGRAASREAPPLDHRD
+PRRRRGRRARRRPARPGARRGRPAPAPGVEGPRPARRPPPEDRQGARGPARRAAGPAHGE
+PAHPGHPAPALLGAAAAADARGRGRVPPRARGPALAGGPGGRGGHRGPAGPGPRRGLSRG
+GRRADAAVGRGPTHR
+>3_1471
+MTSPTSPAVATSPDPSDRPGGEQAAPTLVAEPAGGVPVVTDTPAGLAACAAALAAGTGPV
+AVDAERASGIRYGQRAFLVQLKRAGAGIWLVDPEAFEDLAPLDEALRGVEWVLHAASQDL
+PCLADCGMRPDLLFDTELAARLAGLPRVGLAAVLESQLGLTLAKEHSMADWSTRPLPVDW
+LNYAALDVELLVELRDALAVLLEEQGKLAWAEQEFEHVRTTPPAAPRQDPWRRTSGMAAL
+KRPVQLAVLRRLWQAREDLAQHRDLAPGRLLPDSALVAAASTLPRTVPELRATRGFHGRS
+AAREAPRWITAIRAGIEDAAAGQAPPRHGPGSDAPPPPRAWRDRDPLADRRLTTAKPRIA
+RAAEALGMPPENLLTPDTLRRVCWTPPETITPETVAAALAERGARPWQVEQTSAIITVAL
+LDPDPARDR
+>4_1189
+MTDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTGPVAVDAERASGIRY
+GQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQDLPCLAEQGLRPDR
+LFDTELAARVSGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPEAMLTYAALDVELLV
+PLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQTLRRPVQRAVLKRL
+WEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHGRAASREAPRWIAAI
+RAGVEDAERGDAPAAQIRTGDGPPPPRAWKDRDPVADRRLRTAKARVARRAEQLGMPTEN
+LLTPDTLRRICWTPPAPITPETVDAFLTERGARPWQVENVGAIVTVALLDPDPAGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001079.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001079.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2dd553269c8cd139d1f871ace031a9b2d66fc15e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001079.fa
@@ -0,0 +1,21 @@
+>0_1235
+MTTQDSPLTPNSSRSACCGGHARPDTSRRTVLGRGAAVAAAGAGALALTGCTDQLREKDT
+AQDHYTGSDAVDALPAAELPVGASREVQVQGRTLMMHRVDETTVTAFTNVCTHQGCLLQV
+VDRQEGPAYACPCHGSHFDVTSGKPFGGPARQALMDYDAAVVDDRIVVKL
+>1_963
+MTTQDSPLTPNSSRSGCCDDHARPDTSRRTVLGRGAAVAAAGAGTLALAGCTDRLREKDT
+AQDHYTGSDAVDALPAAELPVGASREVQVQGRTLMMHRVDETTVTAFTNVCTHQGCLLQV
+VDRQEGPAYACPCHGSHFDVTSGKPFGGPARKALMDYDAAVVDDRIVVKL
+>2_1572
+MTAQDSTPTPDPSAVAPPSAPAGCCGGRAAADAARPEASRRTVLGRGAAVAAAGAGALAL
+SGCTEQLREKENAQDHFAGADAVEALPAADLPVGAAREVEVEGRTLMMHRVDETTVTAFT
+NVCTHQGCLLQVVDRAEGPSFACPCHGSHFDVQTGKPFGGPARQPLMDYEAVVDGDRIVV
+KL
+>3_1468
+MTSQDPAPHTSASPCCSGCSAEPAGSSRRSVLGAGSLVALAGAGSVVLSGCTQQLKDEAA
+AGDHHVGSETTDAMALAELPVGGTTSVQVQGRTLLLHRADESTVTAFSNVCTHQGCLVQV
+VDRPEGTAYACPCHGSNFDVATGEPFGGPAKAPLTDYQAAIEGDRIVVKL
+>4_1192
+MTTQDSPLTPNSSRSGCCDDHARPDTSRRTVLGRGAAVAAAGAGTLALAGCTDRLREKDT
+AQDHYTGSDAVDALPAAELPVGASREVQVQGRTLMMHRVDETTVTAFTNVCTHQGCLLQV
+VDRQEGPAYACPCHGSHFDVTSGKPFGGPARKALMDYDAAVVDDRIVVKL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001083.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001083.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8168d57ea8d5fe98f049950c8d7439278698b024
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001083.fa
@@ -0,0 +1,80 @@
+>0_1247
+MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIK
+ALAAWDPNAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE
+LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG
+NMSPEFGSTAAIFPIDEVTLDYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLE
+LDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQDEAGEGRPSKLVDVAMPDGRQ
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY
+YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIID
+ASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKSTYVRKPPYFEGMTMQPDPVSD
+ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS
+GITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA
+>1_979
+MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIK
+ALAAWDPNAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE
+LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG
+NMSPEFGSTAAIFPIDEVTLDYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLE
+LDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQDEAGEGRPSKLVDVAMPDGRQ
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY
+YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIID
+ASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKSTYVRKPPYFEGMTMQPDPVSD
+ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS
+GITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA
+>2_1567
+MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAEKLPYSLKVLLENLLRTEDGANVTAEQIK
+ALASWNPDAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE
+LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGSIPAGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG
+NMSPEFGSTAAMFPIDEVTLDYLRLTGRTAEQVDLVEAYTKEQGMWHDPSSEVKYSEYLE
+LDLSTVVPSISGPKRPQDRIELSDSKDQFRKDLHNYATQDEAGEGRPSKLVDVSMEDGRQ
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY
+YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDSEGNDVFLKDIWPDPTEVQKIID
+ESIDTEMFTSQYGTIFDGDERWQSLETPSGSTFEWDEQSTYVRKPPYFEGMTMQPDAVSD
+ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGKYLLENGVERKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQDGAPQAYVYDAAQNYAAAGTPLVVLGGKEYGSGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS
+GITALNEGTTPKTVKVTATGGDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA
+>3_1463
+MTTVDSFGSKGVLDVNGSEYEIFRLNAVEGAQKLPYALKVLLENLLRTEDGANVTAEQIK
+ALASWDPTAEPDTEIQFTPARVIMQDFTGVPCIVDLATMREAIADLGGDPSRVNPLSPAE
+LVIDHSVQIDSFGNDAAVERNMDIEYQRNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARAVMVRDVDGVKRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGQIPAGATATDVVLTITEQLREHGVVGKFVEFYGEGVGAVPLANRATIG
+NMSPEFGSTAAMFPIDDVTLDYLRLTGRSEEQVALVEAYTKEQGLWHDPSAEVQYSEYLE
+LDLSTVVPSISGPKRPQDRIVLSDSKDQFRKDLHNYATQDEAGEGRPSKLVDVHMEDGRE
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLTAKPWVKTSVAPGSRVVTDY
+YEKSGLNASLDALGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDCDFENEALGTDQDGNDVFLKDIWPDPAEVQRIID
+ESIDTEMFTSQYGTIFDGDERWQSLETPTGKTFEWDEASTYVRKPPYFEGMPAQPEPVQD
+IAGARVLLKLGDSVTTDHISPAGSFKSDTPAGQYLLANGVERKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQDGAPQAYVYDAAQNYAAAGTPLVVLGGKEYGTGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPAGESADSLGLTGTETFAIS
+GIAELNEGRTPKTVKVTATAEDGKVTEFDAVVRIDTPGEADYYRNGGILQYVLRQIAAKA
+>4_1204
+MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIK
+ALAAWDPNAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE
+LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG
+NMSPEFGSTAAIFPIDEVTLDYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLE
+LDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQDEAGEGRPSKLVDVAMADGRQ
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY
+YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIID
+ASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKSTYVRKPPYFEGMTMQPDPVSD
+ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS
+GITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001085.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001085.fa
new file mode 100644
index 0000000000000000000000000000000000000000..97ce048949fe6d5d26016c9d3a1914973d49b3bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001085.fa
@@ -0,0 +1,61 @@
+>0_1249
+MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGT
+SALALGPAVGWAVVAVMLLIVVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDF
+VFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLLAALRGVRLSRWVLPVLVSVF
+VALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT
+GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAA
+GAEVTPDRAPAPVLAQLADTVYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAE
+DGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTALLVQLYVIGVLLAFTLAQAG
+MLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL
+GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPS
+SLEAVVVDAERAATLEVIDAWERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLT
+MVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSVPWQVHEGQGS
+>1_981
+MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGT
+SALALGPAVGWAVVAVMLLIVVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDF
+VFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLLAALRGVRLSRWVLPVLVSVF
+VALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT
+GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAA
+GAEVTPDRAPAPVLAQLADTVYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAE
+DGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTALLVQLYVIGVLLAFTLAQAG
+MLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL
+GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPS
+SLEAVVVDAERAATLEVIDAWERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLT
+MVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSVPWQVHEGQGS
+>2_1565
+MATLSSLLRRGLLGRPVASHDVAEPRMSRWQALPVTSSNALSSLAYAPDEIVLTLVAAGT
+AALALGPLVGWGVVVVMLLIVASFRAAVAAVPQGGIYQMARTKLGPRAGVVASAALLLDF
+VFTAAVSVAAFAHFAAALLPGLGLESRVLVACAALVGVLLTSLRSARLSRWALPVLVSAF
+VALTALLVAAGLWQEGQGLLGRAATSGWTQEGAGIGGTVGAVATALLALRAFSAGSVLLT
+GVEVPVSSSSAMARPAVATVRWVLAVMALTLGALTLGVMHLAQRTGVVVALDPARLRDAA
+GRPVAEADTPAPVIAQLADTVFGPGSVLSLATIAATALLLLFAARSAFRSFPALASRLAE
+DGYLPRQLRVRGDRLVHTWGVLALGAAALALVLLFRAQTALLVQLYVIGVLLAFTLAQAG
+MLRLWRRRLAQTPGARARAAVRLRLTITAVAWVVTALAGVVVLVTRFAQGAWVALLAIVL
+GSLVMGRIRRHYEDVGRELAPDPEDDARALPSRVHVVVVVSTLNRPALRALAYARATRPS
+SLEAVVVDAERAVTEDVIDAWSRAGLPVPLTVVAAPYRDTVVPLVRHLRERRRRSPRDLT
+MVFIPEYVVRPGWRTLMHNRTATRQKRRLQREAGVMIGSVPWQIHEGQGDGQRSTTV
+>3_1461
+MSTPPSTLRRLLLGRPVASGARPAPRRGRWLALPATASNALSSLAYAPDEVILTLVASGT
+GALALGPLVGWAVVAVMVLIVLAFRAAVVAVPRGGIYRMARTKLGPRSGVVAAAALLLDF
+VFTAAVSVAAFAHHASALVPALRGHVGIVSAVALVLVLVSALRGERGSGALVTVLVAAFV
+GLLGTLVAVGLWQSGQGTLAAAPSAGLHVDGAGLGPVGDAATALLALRAFSAGSVLLSGV
+EVPLSATDRMARPAVRTARWVLTVLAVVVGTLTVGVMHLAQRTGVVVALHPDRLRTADGA
+PLAPDTAPAPVVAQLAETVFGAGSPGAVATVAVTSLLLLVAARGAFRSFPTLTARLAEDG
+WLPRQLRVRGDRMVHTGGTLALATATLLLLVLFRGRTALLVQLYVIGVLLAFALALVGML
+RLWRLKLAHTPGARARASVRVKLVVTAVGLGATALAGVVVLVTRFAQGAWVALLAIGVSA
+VVMGRIRRHYRAVEAELAPDPQDDARALPSRVHAVVVVSTLNRPALRALAYARATRPATL
+EAVVVDADRRQTERVVEDFARAGLPVPLTVIAAPYRDTVVPLVRHVRGRRLRSPRDLTMV
+FIPEHVVRGGWRRLLHNRTASRQKARLQREAGVMVGSVPWQIREGDPHRPVEGGIVACAA
+PGDVPEGVESS
+>4_1206
+MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGT
+SALALGPAVGWAVVAVMLLIVVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDF
+VFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLLAALRGVRLSRWVLPVLVSVF
+VALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT
+GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAA
+GAEVTPDRAPAPVLAQLADTVYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAE
+DGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTALLVQLYVIGVLLAFTLAQAG
+MLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL
+GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPS
+SLEAVVVDAERAATLEVIDAWERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLT
+MVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSVPWQVHEGQGS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001086.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001086.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a4c1b2e6c8b47044e7f0bf914fe03f9e8539c8c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001086.fa
@@ -0,0 +1,25 @@
+>0_1250
+MAHYVIVGGGRVGTRLAAALDAAGHGVALVDRDPRTVEGLAPGFSGELVAGVGFDRSALL
+AAGIDRAQGLAAVTADDNTNIIAARVARETFHVDHVVARIYDADRARLYQRLGIPTVASI
+QWTADQVLHRLLPAGTADAEHRDASGRLLVTELVPHSSWWGRRLTDVESTVGMRIAYLTR
+LGDGQLPRPGDRLQEGDVLHAVYPVDRRDRVEAALQGEARVPDGTDEDEEGRA
+>1_982
+MAHYVIVGGGRVGTRLAAALDAAGHGVALVDRDPRTVEGLAPGFSGELVAGVGFDRSALL
+AAGIDRAQGLAAVTADDNTNIIAARVARETFHVDHVVARIYDADRARLYQRLGIPTVASI
+QWTADQVLHRLLPAGTADAEHRDASGRLLVTELVPHSSWWGRRLTDVESTVGMRIAYLTR
+LGDGQLPRPGDRLQEGDVLHAVYPVDRRDQVEAALQGEARVPDGTDEDEEGRA
+>2_1564
+MAHYVIVGGGRVGTRLACALDAAGHSVALVDRDPRTVDGLVPGFSGELVAGVGFDRAALL
+AAGVDRAQGLAAVTAEDNTNIIAARVARETFHVEHVVARIYDADQAKVYQRLGIPTVASI
+QWTADQVLHRLLPAGTADVERRDASGRLLVTGLVPHPSWWGRRLTDVESGAGLRIAYLTR
+RGEGLLPRPGDRLQEGDLLHAVYPVDRRDQVEAALQGEAVRSDRDAEDEDEEGRA
+>3_1460
+MAHYVIVGAGRVGTRLAGALDTAGHSVAVIERSPELTAGLGPDFGGTVVAGIGFDRDALR
+RAGIEQAQGLAAVTTEDTTNVIAARVARETFGVQHVVARIYDAQRARVFQRLGIPTVASV
+EWTADQVLHRLLPAGTAEPSRRDASGRLAMGDYMPHRSWWGSPLHAVEAAVGARIAYLTR
+YGEGVLPSPDGVLQEGDVLHVAYPAARRDRVEAALQGEAGDVRAGEDEDQEEDA
+>4_1207
+MAHYVIVGGGRVGTRLAAALDAAGHGVALVDRDPRTVEGLAPGFSGELVAGVGFDRSALL
+AAGIDRAQGLAAVTADDNTNIIAARVARETFHVDHVVARIYDADRARLYQRLGIPTVASI
+QWTADQVLHRLLPAGTADAEHRDASGRLLVTELVPHSSWWGRRLTDVESTVGMRIAYLTR
+LGDGQLPRPGDRLQEGDVLHAVYPVDRRDQVEAALQGEARVPDGTDEDEEGRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001088.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001088.fa
new file mode 100644
index 0000000000000000000000000000000000000000..06b50114ce7ab062b308c54050cc47fccdd30161
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001088.fa
@@ -0,0 +1,25 @@
+>0_1252
+MTEPRGPVTAAPDGAGPLPSRARLDERGRLDALGSVGGWRGIVEASLPTLVYMVGYVATQ
+QVWPSGVAAVAVALVLGVARLVQRQSPVQVLAGLAVVVLSVVVSLTTGQARDYYLWGFVT
+NAAYGLAFAVSVLVGWPAAGLVLGLVRAEGTRWRAHRRRRRAYAAATWILVAVFALRLAV
+QVPLYLGDAVTALGVARLVMGLPLYALGLWLAWSVSSPGQDDGVPADSAASERP
+>1_984
+MTEPRGPVTAAPDGAGPLPSRARLDERGRLDALGSVGGWRGIVEASLPTLVYMVGYVATQ
+QVWPSGVAAVAVALVLGVARLVQRQSPVQVLAGLAVVVLSVVVSLTTGQARDYYLWGFVT
+NAAYGLAFAVSVLVGWPAAGLVLGLVRAEGTRWRAHRRRRRAYAAATWILVAVFALRLAV
+QVPLYLGDAVTALGVARLVMGLPLYALGLWLAWSVSSPGQDDGVPADSAASERP
+>2_1562
+MTEPRGPESPAPDVAGALPSRARVDEQGRLDALASVGGWRGIVEASLPTLVFMAGYVVSQ
+QVWPSGVAAVAVALVLGAVRLVQRQSPVQVLAGLAVVVLSVVVALTTGQARDYYLWGFVT
+NAAYGLAFALSVVVGWPAAGLVLGLVRGEGTHWRRSPRRRRAYATATWILVAVFTLRLAV
+QVPLYLADAVTALGVARLVMGLPLYALGLWLAWSVSAPAPGEDDGLRPAAEDEPAPGRA
+>3_1458
+MSAHPRPDHGPDAAPSAAEGLQALGARTRVDEDGRIDALATVGGVRGIVEASLPTLVFLV
+VFLLAGQVWTAGAAALGVAAVMTAARLAQRQSAAQALAGLLVVGVSVVLALTRGEARDFY
+LWGFVTNIAYGLALPLSAALGWPLAGLLFGMVRGEGLHWRADPARRRAYGIATLIVAAVS
+WLRLAVQAPLYLADAATALGVARVVMGLPLYALGLWLAWSVSTPRPGAPPLRRDPAAG
+>4_1209
+MTEPRGPVTAAPDGAGPLPSRARLDERGRLDALGSVGGWRGIVEASLPTLVYMVGYVATQ
+QVWPSGVAAVAVALVLGVARLVQRQSPVQVLAGLAVVVLSVVVSLTTGQARDYYLWGFVT
+NAAYGLAFAVSVLVGWPAAGLVLGLVRAEGTRWRAHRRRRRAYAAATWILVAVFALRLAV
+QVPLYLGDAVTALGVARLVMGLPLYALGLWLAWSVSSPGQDDGVPADSAASERP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001090.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001090.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c97518f86a7f714e3c8026f298fbb64846fc0c1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001090.fa
@@ -0,0 +1,30 @@
+>0_1254
+MIFGRNRTVRHEQVSLPAELLEERDLEIAAAPEAADVGPHDVATRPDPAGMIDLGSLRLR
+AVQGMKLRLDVEDATKRIVAATVSLGRSALQVQAFSAPRRTGLWDDLRAELHDSLSTTAH
+ATVQEQTGRFGIEILTRVPAALPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAFQPEAAE
+PLEQVFSDLVVVRGDEPLPPRELLPLRPPPNARPLQRRRPAPDEGRDVLADTATGPGDGA
+APEATALPERGPEITETR
+>1_986
+MIFGRNRTVRHEQVSLPAELLEERDLEIAAAPEAADVGPHDVATRPDPAGMIDLGSLRLR
+AVQGMKLRLDVEDATKRIVAATVSLGRSALQVQAFSAPRRTGLWDDLRAELHDSLSTTAH
+ATVQEQTGRFGIEILTRVPAALPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAFQPEAAE
+PLEQVFSDLVVVRGDEPLPPRELLPLRPPPNARPLQRRRPAPDEGRDVLADTATGPGDGA
+APEATALPERGPEITETR
+>2_1560
+MIFGRNRKVRHEQVSLPEELLEERDHEVAALPEAAETGPHDVATRPDPAGAIDLGSLRMR
+AVQGMKLRLDVEDSTKRIVAATITLGRSALQVQAFSAPRRAGLWDEVREELRDSLDTTPN
+ATVQEQAGRFGTEILTRVPAALPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAFQPEAAA
+QLEQVFSDIVVVRGDEPMPPRELLPLRPPANARPVQRRRPGAARDAGRDVLADTERGPQE
+APALPERGPEITEIR
+>3_1456
+MIFGRNRNVRHEQVAVPEQLKDERDRLVEARPAPAAEGDRGPFDVEAAPSGRPSVDLGAL
+RVPAVQGMQLRLDVEDATQRIVAVTVTLERSALQIQAFSAPRAAGVWDDLRAEIKEALVG
+TPGAQVQEQSGGFGPEVLTRIPATLPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAYLPD
+AARALEDVFAGVVVVRGDAPLPPRELLPLRPPADAQPVRRRPRPHAGGEPDVHARRPDDA
+PETGAETLPERGPEITEIR
+>4_1211
+MIFGRNRTVRHEQVSLPAELLEERDLEIAAAPEAADVGPHDVATRPDPAGMIDLGSLRLR
+AVQGMKLRLDVEDATKRIVAATVSLGRSALQVQAFSAPRRTGLWDDLRAELHDSLSTTAH
+ATVQEQTGRFGIEILTRVPAALPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAFQPEAAE
+PLEQVFSDLVVVRGDEPLPPRELLPLRPPPNARPLQRRRPAPDEGRDVLADTATGPGDGA
+APEATALPERGPEITETR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001100.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001100.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc70f23f8eec278472326587b8030cbc9abea817
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001100.fa
@@ -0,0 +1,50 @@
+>0_1265
+MDPLDLARWQFGITTVYHFLMVPLTIGLGLVVAVMQTLWVRTGREQYLRMTKFWGKLFLI
+NFIMGVATGIVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGVWIFGWGRV
+PRRLHLAAIWCAVIGAHLSAYFIMTANAFMQHPVGYEVVDGRPVLNDIGAVLANPIVLTH
+FPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDEHGRVVVGTTGSKARDRLDHRVWI
+TSLRAGAAVAIVGFLGTAFTGHAQAQQMIEFQPTKMASAEAACHDGTAFSVLTLGDLGAG
+DRTTCTDVTTVIELPGLLSYLAYEDFTTPVPGLNSLLPDFEERYGTHLPDDPLYGERAGA
+PIDYQPLMEVTYWGFRLMITFGGLGALAGALTLWMTRRGTVPDSRGWTATAVASIGAPFA
+ANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSAQEVLASLIVLVGIYAVL
+LVVEVVLMVRYVRGGVPAGMPELTADEHRDPDEDRHDRDDVLAFAY
+>1_997
+MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVATGKDHYLRMTKFWGKLFLI
+NFIMGVATGLVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGIWIFGWDRI
+PRRLHLAALWCAVLGINLSAYFIMVANGFMQHPVGYEVVDGRPVLNDLGAVLTNPIVLTH
+YPHTIFGSWAVAGGFLVGIAWYHLWKRRRDGIDVVDEAGRVVVGDAGTAARDRTDHRVWL
+TSLRAGAAVALIGFVGTAFSGHAQAQQMIHFQPTKMAAAEAACHDGTAFSVLTLGDVRSG
+GATTCEDVQGVIEVPGLLSYLAYEDFTTPVRGINTLLPEFEQKYGTHLPDSELYGDRAGS
+EISYLPLMEVTYWGFRLMILFGGLGALAALGALWFSRRGTVPASRGWMRLAVASIGAPFA
+ANMTGWVFTEMGRQPFVVYPNPAMGVDQVYMFTAAAVSPGVTGEEVLVSLIVLVGIYAVL
+LGVEVFLLTRFVRGGVPAAMPELTAAEHSDEQKRDRDDVLAFAY
+>2_1549
+MDPLDLARWQFGITTVYHFLMVPLTIGLGLVVAVMQTLWVRTGREQYLRMTKFWGKLFLI
+NFIMGVATGIVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGVWIFGWGRV
+PRRLHLAAIWCAVIGAHLSAYFILTANAFMQHPVGYEVVDGRPVLNDIGAVLANPIVLTH
+FPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDEHGRVVVGTTDSKARDRLDHRVWI
+TSLRAGAAVAIVGFLGTAFTGHAQAQQMIEFQPTKMASAEAACHDGTAFSVLTLGDLGAG
+DRTTCTDVTTVIELPGLLSYLAYEDFTTPVPGLNSLLPDFEERYGTHLPDDPLYGERAGA
+PIDYQPLMEVTYWGFRLMITFGGLGALAGALTLWMTRRGTVPDSRGWTATAVASIGAPFA
+ANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSAQEVLASLIVLVGIYAVL
+LVVEVVLMVRYVRGGVPAGMPELTADEHRDPDEDRHDRDDVLAFAY
+>3_1445
+MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVRTGREHYLRMTKFWGKLFLI
+NFIMGVATGLVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGMWIFGWDRL
+PRRLHLAAIWCAVIGAHLSAYFIMAANAFMQHPVGYEVVDGRPVLNDIVAVLTNPIVLTH
+FPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDAEGRVVVGTTGSKARDALDHRVWI
+TSLRAGAAVVIVGFLGTAFTGHAQAQQMIHYQPTKMASAEAACHDGTAFSVLTLGDVNTP
+GATTCDDVTGVIEIPGLLSFLAYSDFTTPVPGITTLLPQFEARYGTQLPDDPMYGERAGQ
+EISYLPLMEVTYWGFRLMITFGGLAALAGALTLWMTRKGTVPDSKPWMITAVASIGASFA
+ANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSGEEVLTSLIVFVVLYAVL
+LVVEVALLARYVRGGVPAGMPELTADEHRDPDDDRHDRDDVLAFAY
+>4_1222
+MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVATGKDHYLRMTKFWGKLFLI
+NFIMGVATGLVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGIWIFGWDRI
+PRRLHLAALWCAVLGINLSAYFIMVANGFMQHPVGYEVVDGRPVLNDLGAVLTNPIVLTH
+YPHTIFGSWAVAGGFLVGIAWYHLWKRRRDGIDVVDEAGRVVVGDAGTAARDRTDHRVWL
+TSLRAGAAVALIGFVGTAFSGHAQAQQMIHFQPTKMAAAEAACHDGTAFSVLTLGDVRSG
+GATTCEDVQGVIEVPGLLSYLAYEDFTTPVRGINTLLPEFEQKYGTHLPDSELYGDRAGS
+EISYLPLMEVTYWGFRLMILFGGLGALAALGALWFSRRGTVPASRGWMRLAVASIGAPFA
+ANMTGWVFTEMGRQPFVVYPNPAMGVDQVYMFTAAAVSPGVTGEEVLVSLIVLVGIYAVL
+LGVEVFLLTRFVRGGVPAAMPELTAAEHSDEQKRDRDDVLAFAY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001104.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001104.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b2a8639b7f5117e52fec937e604a1ea181b21211
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001104.fa
@@ -0,0 +1,66 @@
+>0_1271
+MSGPRSRLDRPLSSTERPAPVPANTEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHC
+LWEIIDNSVDEALAGFGQSIEITLHPDGSVEVEDNGRGIPVDVEPRTGLSGVEVVFTKLH
+AGGKFGGGSYAASGGLHGVGASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRP
+SPDAPFEPSTDASPLDVVGKAKRGQTGTRVRYWADEQIFVKDATFSAEELQARARQTAYL
+IPGLRITVKDLRRRPGTPGADGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGTFK
+ERVPVLGEDGRTSMQDVQRTCEVDVALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAAL
+LKVFRAQVEANARRLKAGSDKVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRI
+VSQVVEKQLTARLTSTARAQKQQVHTLLEKVVAEMKSRISARTHKENQRRKNALETSTMP
+AKLADCRSNDVASSELFIVEGDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILAN
+AECAALIQVVGGGAGRSFDLDAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAG
+RVYAAVPPLHRIEAVTRGVKEREVIYTYSEQELHATLARLEREGRSYREPIQRYKGLGEM
+DADQLAETTMDPRHRMLRRVNIAEVEAAERVFDLLMGSAVAPRKDFIVSHADELDRARID
+A
+>1_1001
+MPANTEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGFGQSI
+EITLHPDGSVEVEDNGRGIPVDVEPRTGLSGVEVVFTKLHAGGKFGGGSYAASGGLHGVG
+ASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRPSPAAPFEPSTDASPLDVVGK
+AKRGQTGTRVRYWADEQIFVKDATFSAEELQARARQTAYLIPGLRITVKDLRRRPGTPGA
+DGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGTFKERVPVLGEDGRTSMQDVQRT
+CEVDVALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAALLKVFRAQVEANARRLKAGSD
+KVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRIVSQVVEKQLTARLTSTARAQ
+KQQVHTLLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVASSELFIVE
+GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILANAECAALIQVVGGGAGRSFDL
+DAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVYAAVPPLHRIEAVTRGVK
+EREVIYTYSEQELHATLARLEREGRSYREPIQRYKGLGEMDADQLAETTMDPRHRMLRRV
+NIAEVEAAERVFDLLMGSAVAPRKDFIVSHADELDRERIDA
+>2_1542
+MPANSEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGYGQSI
+EITLHPDGSVEVEDSGRGIPVDVEPRTGLSGVEVVFTKLHAGGKFGGGSYAASGGLHGVG
+ASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRPSPDAPFEPSTDASPLDVVGK
+AKRGQTGTRVRYWADEQIFIKDAAFSADDLHARARQTAYLIPGLRITVKDLRRRPGTPGA
+EGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGSFKERVPVLGEDGRTAMQDVQRT
+CEVDLALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAALLKAFRTQVESNARRLKAGSD
+KVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRIVAQVVEKELTARLTATARAQ
+KQQVHVLLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVASSELFIVE
+GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILANAECAALIQVVGGGAGRSFDL
+DAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVFAAVPPLHRIEAVTKGVK
+EREVIYTYSEQELYATLARLEKEGRSYKEPIQRYKGLGEMDADQLAETTMDPRHRTLRRV
+NIAEVEAAERVFDLLMGSSVAPRKDFIVSHADELDRERIDA
+>3_1438
+MPANTEYSARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGFGQSI
+DVTLHPDGSVEVADNGRGIPVDVEPRTGLTGVEVVFTKLHAGGKFGGGSYAASGGLHGVG
+ASVVNALSSRLDVQVVRGGKVHQLSFRRGEPGRFQDGSRPTPDAPFEPAADAAPLDVVGK
+AKRGQTGTRVRYWADEQIFTPDATFSMEDLQARARQTAYLIPGLRIAVTDLRRLTGTAGE
+AGPVQEVYQYDGGIAEFVDHLTPAKPVTDVWRIQGSGTFTERVPVLGEDGRTQMQDVQRT
+CEVDVALRWDVGYETVFRSFVNIIATPKGGTHQSGFESALLKVFRAQVEAGARRLKAGSD
+RPDKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTPAVRRIVARVVEKELTALLTSTARGQ
+KQQVGALLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVAASELFIVE
+GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILSNAECAALIQVVGGGAGRGFDL
+DAARYGKVILMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVYAAVPPLHRIEAVTRGKK
+EREVIYTYSEAELHEVLARLEAEGRTYREPIQRYKGLGEMDADQLAETTMDPRHRMLRRV
+TISEVEAAERVFELLMGSSVAPRKAFIVSNADELDRERIDA
+>4_1226
+MPANTEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGFGQSI
+EITLHPDGSVEVEDNGRGIPVDVEPRTGLSGVEVVFTKLHAGGKFGGGSYAASGGLHGVG
+ASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRPSPDAPFEPSTDASPLDVVGK
+AKRGQTGTRVRYWADEQIFVKDATFSAEELQARARQTAYLIPGLRITVKDLRRRPGTPGA
+DGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGTFKERVPVLGEDGRTSMQDVQRT
+CEVDVALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAALLKAFRAQVEANARRLKAGSD
+KVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRIVSQVVEKQLTARFTSTARAQ
+KQQVHTLLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVASSELFIVE
+GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILANAECAALIQVVGGGAGRSFDL
+DAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVYAAVPPLHRIEAVTRGVK
+EREVIYTYSEQELHATLARLEREGRSYREPIQRYKGLGEMDADQLAETTMDPRHRMLRRV
+NIAEVEAAERVFDLLMGSAVAPRKDFIVSHADELDRERIDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001111.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001111.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a2e5660a309199d6ee78d815e8b9f58f0f1edac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001111.fa
@@ -0,0 +1,60 @@
+>0_1278
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL
+VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER
+ASTDQGSDGAPSAGGEASEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD
+TEIPSPVAGTLLEIRAEEDDTVEVGAVLALVGSGSAGGGSAPSEGSSGQDEASAEEIEDK
+ATEAEAPEETEEAAEAAGAEKSEKTPEASPSEEASRRESAERDSAQAESAEAPSATEPGQ
+GYVTPLVRRLAHQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAA
+APSSAPAAASAPAASSSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSAQLTQVHEVDVTR
+IVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASEDIA
+IAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVG
+ALFDTPIINQPQVAILGIGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAG
+RFLRTLRQRLEGGEFANELGL
+>1_1008
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL
+VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER
+ASTDQGSDGAPSAGGEASEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD
+TEIPSPVAGTLLEIRAEEDDTVEVGAVLALVGSGSAGGGSAPSEGSSGQDEASAEEIEDK
+ATEAEAPEETEEAAEAAGAEKSEKTPEASPSEEASRRESAERDSAQAESAEAPSATEPGQ
+GYVTPLVRRLAHQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAA
+APSSAPAAASAPAASSSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSAQLTQVHEVDVTR
+IVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASEDIA
+IAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVG
+ALFDTPIINQPQVAILGIGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAG
+RFLTTLRQRLEGGEFANELGL
+>2_1535
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLQEIL
+ADEDETVEVGAPLATIGDGDGGGSSESDDDAQAEESEEPAAEEAQEDEEQQEPEGEPAPE
+ERSSTQDSEEKSSGGASGGDASEVTLPALGESVTEGTVTRWLKAVGDEVEVDEPLLEVST
+DKVDTEIPSPVAGTLLEIRAEEDETVEVGAVLALVGSGSAGGSSDSSDDSAKDDSAPDEA
+SAEEIEDKATEAETGEETEEAAQDAGEEKEEKAPEASASENASREESAEQEKAAAADAPE
+ATSPGQGYVTPLVRRLAHQNDVDLSTVRGTGVGGRIRKQDVLAAALAQQAGSAESAPAQE
+QGSKEQAAAASSAPAVASSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSTQLTQVHEVDV
+TRIVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASED
+IAIAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGS
+VGALFDTPIINQPQVAILGTGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGAD
+AGRFLTTLRQRLEGGEFANELGL
+>3_1431
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL
+VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER
+ASTDQGSDEAPSAGGEDSEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD
+TEIPSPVAGTLVEILANEDDTVEVGAVLARVGSGAAPAASQDPAPAADTASPEEIEDKAT
+EAPTGEQTEEAAEQAGDVKQEQAPAASPAETASAAPAASAPAAETSASEPGPGYVTPLVR
+RLAKQNGVDLSTVRGTGVGGRIRKQDVLAASLANQASSGSASPAAAEEQQTPAAASAPAP
+AAVRGETEKAPRIRQVIAQRMRESLDLSTQLTQVHEVDMTRIVQLRGKAKASFQEKNGVK
+LTYLPFITQAVTEALKQHPKLNASFSEDNKEITYHASEDIAIAVDTDRGLLVPVVKDAGT
+LNLAGLAQKIADVAERTRTNKINPDELSGGTFSITNIGSVGALFDTPIINQPQVAILGTG
+AIVKRPMVVADADGNDTIAIRHMMYLSLTYDHRLVDGADAGRFLQTLKARLEGGEFAAEL
+GL
+>4_1233
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL
+VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER
+ASTDQGSDEAPSAGGEASEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD
+TEIPSPVAGTLLEIRAEEDDTVEVGAILALVGSGSAGGGSAPSEGSSGQDEASADEIEDK
+ATEAEAPEETEEAAEAAGAEKSEETPEASPSEEASRRESAERDSAQGESAEAPAATEPGQ
+GYVTPLVRRLAHQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAA
+APSSAPAAASAPAASSSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSTQLTQVHEVDVTR
+IVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASEDIA
+IAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVG
+ALFDTPIINQPQVAILGTGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAG
+RFLTTLRQRLEGGQFADELGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001114.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001114.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2aabe1978fc8ad93f102207a070f18c8c574e2fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001114.fa
@@ -0,0 +1,25 @@
+>0_1281
+MPETLLPPLRLLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE
+DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF
+GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG
+IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA
+>1_1011
+MPETPLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE
+DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF
+GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG
+IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA
+>2_1532
+MPETLLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE
+DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF
+GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG
+IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA
+>3_1428
+MPHALLPPVRVLGLAPDLIDYEEGWALQRTLHADVVAGRSDGEILLLEHEAVYTAGRRTE
+DADRPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEEVLIRTAAEF
+GVTAVRVDGRAGIWITAREGDPRPDRKLGAIGLSIHDGVSMHGFSFNCSNSLTPYETIIA
+CGIADASTTTLSVETGREVTPVDVLPVLVRHLEDLGPEHIALTPTEGTPA
+>4_1236
+MPETLLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE
+DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF
+GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG
+IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001117.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001117.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9bf3d7d8c19cbd05e66b8a0f59fe14ce427f6856
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001117.fa
@@ -0,0 +1,21 @@
+>0_1284
+MARRAPDPAQEPEPTRRDEPLITRRDLAGWVDGPGGGLAGGRWPGDLLGLPEHGPTSMAT
+AARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATMHILGITLLATTVGKAVCRTQVVR
+LGGRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHDKVAGTVEIRM
+>1_1014
+MARRAPDPAQEPEPTRRDEPLITRRDLAGWVDGPGGGLAGGRWPGDLLGLPEHGPTSMAT
+AARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATMHILGITLLATTVGKAVCRTQVVR
+LGGRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHDKVAGTVEIRM
+>2_1529
+MARRAPDPAQEPEPTRRDEPLITRRDLAGWVDGPGGGLAGGRWPGDLLGLPEHGPTSMAT
+AARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATMHILGITLLATTVGKAVCRTQVVR
+LGGRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHDKVAGTVEIRM
+>3_1425
+MSCVFPACNASSGPDYPGGVAHRASDPAPRDRSERDAAGRAEPLISRADLAGWIDGPGGG
+RAGGRWPGDLLGLPEHGPASMATAARRAGALMIDWALALVVSNLAFGGDAIATLLVFAAM
+HVVGLTLLATTVGKALCRIQVVREGTGGTAPVHRVLIRTALLCLVLPAVVVGPDGRGMHD
+RVAGTVELHM
+>4_1239
+MVAHYAGGVARRAPDPQDRTETTGRAEPLITRRDLAGWVDGPGGGRAGGRWPGDLLGLPE
+RGPASMATAARRMGALVLDWFIALGISWLAFDADAIATLLVFAAMHVIGLTLLATTVGKA
+VCRIQVVRVGGRPAGLLRILLRTALLCLVLPAVVVGPDGRGMHDKLADTVEIRM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001119.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001119.fa
new file mode 100644
index 0000000000000000000000000000000000000000..910fdb40262f83a76c7220b02973c10aba413a25
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001119.fa
@@ -0,0 +1,95 @@
+>0_1287
+MSSLSTTGALPAVPDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRA
+LLLWVRLAEREPRVHHALRDPETTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAAT
+APALAQPDPADGEPWGDASATLRRLLLDSVGADPDTDRPVAAVTGKDAAVALRRAYRRQL
+AAIALRDLDSAEPTAAMPSVGRWLADLAGATVDAALAVSRAVLTEREGPVVDRVDLAVIG
+MGKCGAGELNYVSDVDVVFAHAVREAADGADPDAEVPDGPRAAALAAELAAGIGRVIQGA
+APEPGLWEVDANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGER
+YIAEIWPRVWESSSRDGFVESVRAMRARVLDTLAPAEREREIKLGPGGLRDVEFTAQLLQ
+LVHGRADESLRVRGTLDAVRALHAASYITTRDARAFDEHYRWLRTLEHRIQLVHLRRTHL
+MPVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALS
+AEDVRLSAEAVRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGAD
+PDGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLSGSRFVGDLLEHSPEAVAWVG
+DDRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVALADISGLLDLE
+AVTGALSDIDQVTVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVH
+RPRPGVDEGRAREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGRQGPLVRTLD
+SYREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAGDLTTADAREIRRIKA
+RVEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGTLPALRAIARH
+GLLPEAEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTAGGELE
+ERYLRVTRLARQVFETRFYGL
+>1_1017
+MSALPDAATADAPDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRAL
+LLWVRLAEREPRVHHALRDPGTTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAATA
+PALAQPDPTAGEPWGDASAALRRLLLDSVGADPDADRPLAAVTGKDAAVALRRAYRRQLA
+AIALRDLDSAEPTAAMPSVGRWLADLAGATVDAALAVSRAVLTEREGPVVDRVDLAVIGM
+GKCGAGELNYVSDVDVVFAHAVREAADGADPDAQVPDGPRAAALAAELAAGIGRVIQGAA
+PEPGLWEVDANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGERY
+IAEIWPRVWESSARDGFVESVRAMRARVLDTLAPAEREREIKLGPGGLRDVEFTAQLLQL
+VHGRADESLRVRGTLDAVRALHAASYVTTRDARAFDEHYRWLRTLEHRIQLVHLRRTHLM
+PVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALSA
+EDVRLSAEAVRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGADP
+DGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLSGSRFVGDLLEHSPEAVAWVGD
+DRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVALADISGLLDLEA
+VTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVHR
+PRPGVDEGRAREQAEEVVRTLMALLQKPVAPPLPGERRLEVDADLRPEGRQGPLVRTLDS
+YREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAQDLSAADAREIRRIKAR
+VEAERLPRGADPARHVKLGRGGLSDVEWLVQSMQLKHAGQIEDLRVTGTLPALRAIARHD
+LLPESEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTTGGELEE
+RYLRVTRLARQVFETRFYGL
+>2_1526
+MSALPDAATADAPDRRALAQAGVADARRVQSLLASPEFEGADVAPLVKRLGHAADPDRAL
+LLWVRLAEREPRVHRALRDPETTARLLRLLGASEALGEFLIRRPEHLDLVLEPESAAATA
+PALAQPDPADGEEWADEPAALRRLLLEAVEADPDADRPRAGLTGADAAVALRRAYRRQLA
+AIALRDLDSADPAAVMPSVGRWLADLAGAAVDAALAVSRATLAEREGPAVDRVDLAVIGM
+GKCGARELNYISDVDVVFVHELLDPGPDAAGEAGADGADGEASDAVDGTRAAVLAAELAA
+GIGRVIQAAAPEPGLWEVDANLRPEGKDGALSRTLDSHAEYYRRWAHGWEFQALLKARPI
+AGSADLGARYLERIWPRVWESSAREGFVDSVRAMRSRVLETIAPAEREREIKLGSGGLRD
+VEFTAQLLQLVHGRADESIRVRGTLDAVRALHEASYISTRDAAAFDEHYRWLRTLEHRIQ
+LVHLRRTHLMPVKDEALRIVARSLRGAQETGPATGEDLQAAFTRVRRAVRGLHETVFYRP
+LLSTTAALSDDEVRLSAEAVRERLAALGYRDPKGALRHIEALTQGVSRRAAIQRQLLPAM
+LGWFAEGADPDGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLAASRFVGDLLEH
+SPEAVAWVGDDRELEPRGTVQLWRQADARLDRRIEAQETPAAVRHVRQVRRSETLRVALA
+DISGLLDLEAVTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYG
+SDLDALFVHRPRPGVDEGRAREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGR
+QGPLVRTLDSYREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAGDLTTAD
+AREIRRIKARVEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGTL
+PALRAIARHGLLPEAEVAVLEEAWLLASRIRAAVLLWTGKVGDVLPTNMRDLEAIARLSG
+VGTAGGELEERYLRVTRLARQVFEARFYGL
+>3_1422
+MAPTPDSHVPGPRRALVHAGVADLTRAERLLSSPELAEQDADAALAALAHAADPDSALLL
+YIRLAERDPQVHRVLAEADRARDLLRLLGASEALGEFLIRRPEHLDLVLDPARAAATAPA
+LAQQDPTDGGDWHDEPAALRALLLEAVGADPAADQPVAGLTGADASVALRRAYRRQLTAI
+ALADLASREPTLVMPAVGRWLADLAGAALEAALAVSRAELRAREGAAVDCVELAVIGMGK
+CGARELNYVSDVDVVFVHDVLEPGAPDAPSAQEAARLAAELAAGISRVLSGPAPEPGLWE
+VDANLRPEGRDGALSRTLDSHVEYYRRWAHGWEFQALLKARPVAGSPALGERYVAAVWPR
+VWESSAREGFVENVRAMRTRVLDTIARDERDREIKLGAGGLRDVEFTAQLVQLVHGRADE
+SVRVRGTLDALRVLHAASYISSRDMRAFDAAYRWLRLLEHRIQLVHLRRTHLMPVKEGPR
+RVVARSMRGAGDVHPVAGDDLQDRFSRVRREVRALHETVFYRPLLSTTAALSDEDVRLSA
+DAVQARLSALGYRDPRRALAHIEALTRGVSRRAAVQRQLLPAMLGWFADGADPDAGLLAF
+RRLSESLGSSPWFLRMLRDSTDAARRLCLVLAGSRRVGDLLEHAPESVAWIGETRELAPR
+GLSALTSEVTARLDRRSPEESAAQVIRHVRQIRQREILRTALADITGVVGLEEVGHALAD
+VDQAAVQGALRVAGQAVLDGADPLTEVVVVAMGRQGGREIAYGSDLDAMFVHRPLAGADE
+TAAAAQAEAVARQLMALLQQPAAPPLPSEQPLDVDADLRPEGRQGPLVRTLDSYREYYAR
+WAEVWERQALLRARVVAGPAGLAEEFTAWADGVRYGDELSAGDAREIRRIKARVEAERLP
+RGADPARHVKLGRGGLSDVEWLVQSLQLRHAHDEPELRVTGTLPALRALARLDLLPPSEA
+ALLEEAWLLATRVRSALVLWTGKGSDVLPTNARDLGALARLAGDACGGGVAFEERYLRVT
+RQARQVFEQRFYGL
+>4_1242
+MSALPDAATADAPDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRAL
+LLWVRLAEREPRVHHALRDPGTTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAATA
+PALAQPDPTAGEPWGDASAALRRLLLDSVGADPDADRPLAAVTGKDAAVALRRAYRRQLA
+AIALRDLDSAEPTAAMPSVGRWLADLAGAAVDAALAVSRAVLTEREGPVVDRVDLAVIGM
+GKCGAGELNYVSDVDVVFAHAVREAADGADPDAQVPDGPRAAALAAELAAGIGRVIQGAA
+PEPGLWEVDANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGERY
+IAEIWPRVWESSARDGFVESVRAMRARVLDTLAPAEREREIKLGPGGLRDVEFTAQLLQL
+VHGRADESLRVRGTLDAVRALHAASYVTTRDARAFDEHYRWLRTLEHRIQLVHLRRTHLM
+PVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALSA
+EDVRLSAEAVRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGADP
+DGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLSGSRFVGDLLEHSPEAVAWVGD
+DRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVALADISGLLDLEA
+VTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVHR
+PRPGVDEGRAREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGRQGPLVRTLDS
+YREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAGDLTTADAREIRRIKAR
+VEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGTLPALRAIARHG
+LLPEAEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTAGGELEE
+RYLRVTRLARQVFETRFYGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001121.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001121.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d8d614d0997e6e2c61fb1af9f230ba8521014ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001121.fa
@@ -0,0 +1,31 @@
+>0_1290
+MSAPQSPRQPDDTAPYGPPAPSRYRTVHLQRAKDEGRRFAMLTTYDAMTAALFDEAGVEV
+LLVGDSVGNTVLGHPTTLPVTLDQMILFTQAVVRGAERALVVADLPFGSYEASPRQAVES
+AVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVMAHIGFTPQSEHVLGGYRVQGRGAG
+AVERMTASARALEAAGAFAVLMEMVPSDVAAAVDAALRVPTVGIGAGPGTTGQVLVWQDM
+LGLREGRVPRFVRQYARLHEVVGDAVRAYRADVLDGAFPAPEHGFQG
+>1_1019
+MSAPQSPRQPDDTAPYGPPAPSRYRTVHLQRAKDEGRRFAMLTTYDAMTAALFDEAGVEV
+LLVGDSVGNTVLGHPTTLPVTLDQMILFTQAVVRGAERALVVADLPFGSYEASPRQAVES
+AVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVMAHIGFTPQSEHVLGGYRVQGRGAG
+AAERMTASARALEAAGAFAVLMEMVPSDVAAAVDAALRVPTVGIGAGPGTTGQVLVWQDM
+LGLREGRVPRFVRQYARLHEVVGEAVRAYRADVLDGAFPAPEHGFEG
+>2_1524
+MLTAYDAMTAALFDEAGIEVLLVGDSVGNTVLGHSSTLPVTLDQMILFSQAVVRGAQRAL
+VVADLPFGSYEASPQQAVESAVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVIAHIG
+FTPQSEHVIGGYRVQGRGEGAVEAMTASARALEAAGAFAVLMEMVPSDVAAAVDAALRVP
+TVGIGAGPGTTGQVLVWQDMLGLREGRTPRFVRQYARLHEVIGAGVRAYRRDVLDGAFPA
+PEHGFEA
+>3_1420
+MDSRTVTPPASSPAASEAAAPYGGAATAAAAAPVEAPARYRTVHLQRAKDEGRRFAMLTT
+YDAMTAALFDEAGVEVLLVGDSLGNTVLGHGSTLPVTLEDMIVFSAAVARGARRAFVLAD
+LPFGSYEASPEQAVRAGVRLMKEAGVHGVKVEGDERFAPHIAAMVAAGVPVMGHIGFTPQ
+SEHVLGGYRVQGRGEGAAERLIASARALEDAGAFAVLMEMVPSDVAAAVDAALRVPTVGI
+GAGPKTTGQVLVWQDMLGLGAGRTPRFVKRYADLRAVMGDAVRAYRADVLSGAFPDPAHA
+FES
+>4_1244
+MSAPQSPRQPDDTAPYGPPAPSRYRTVHLQRAKDEGRRFAMLTTYDAMTAALFDEAGVEV
+LLVGDSVGNTVLGHPTTLPVTLDQMILFTQAVVRGAERALVVADLPFGSYEASPRQAVES
+AVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVMAHIGFTPQSEHVLGGYRVQGRGAG
+AAERMTVSARALEAAGAFAVLMEMVPSDVAAAVDAALRVPTVGIGAGPGTTGQVLVWQDM
+LGLREGRVPRFVRQYARLHEVVGEAVRAYRADVLDGAFPAPEHGFEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001132.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001132.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6431db2a60f6fd5cd9fa4048e2f5a9050cb1294b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001132.fa
@@ -0,0 +1,30 @@
+>0_1302
+MTAAEGPAGTARVPAGPFVHRETVRTATGAVHVAWTSVAAGNLALHVVPPDEAEGLARVS
+AARRALERVMGVPEGATLYLDQVHSADVVWADGPGRGGASAPVADAAVSRDGSRPLAVMV
+ADCLPVVVVDETTGATAVAHAGRRGLLDGVLEATVDRLLSLRPEADRTGPGLRAWIGPGV
+CGRCYEVPAAMRDEAAARLPATAATTSWGTPALDLPAGAAEVLRARGVATATIDVCTRED
+ERLFSHRRAPGEGRFAGLVWRADPDATVPRGDA
+>1_1031
+MTAAGGPAGTARVPAGPFVHRETVRTATGAVHVAWTSVAAGNLALHVVPPDEAEGPARVS
+AARRALERMMGVPEGATLYLDQVHSADVVWADGPGRGGAPAPVADAAVSRDGSRPLAVMV
+ADCLPVVVVDETTGATAVAHAGRRGLLDGVLEATVDRLLSLRPETDRTGPGLRAWIGPGV
+CGRCYEVPAAMRAEAAARLPATAATTSWGTPALDLPAGAAQVLRARGVATATIDVCTRED
+ERLFSHRRAPGEGRFAGLVWRADPDATTPRGEA
+>2_1512
+MTAAEGPVGTVPVPAGPFVHREAVATAGGTVHVAWSGVAAGNLGLHVVADEDAAGRRAVG
+EARRGLERAMGVPVGSTLYLDQVHSADAVWADGPGWGEEAGPTADAAVSRDGGRALAVMV
+ADCLPVVLVDEATGATAVAHAGRRGLVDGVLEGTVDRLLSLRPADRRDAPGLRAWIGPGV
+CGRCYEVPEQMRAEAAERVPATAATTAWGTPGLDLPAGAVAILRGRGADVAVVQACTLED
+ERLFSHRRAPGQGRFAGLVWRADEDASTPTRAA
+>3_1408
+MSLAGGPVGTQPVPSGPFVHREDLRADARGRVAHVAWTSAEAGSLAFHILGAEQEQARAD
+VVAARHRVEDAMGVPRGSVFYLEQVHSVDVVTAGPGWEEGFAPTADASVSPDGHTPLAVM
+VADCLPVVFVDGLTGATAVAHAGRRGLLDGVLENTVDALLALRPEGSAGAFGLKAWIGPG
+ISGESYEVPQAMQDEAVARIPELEATTSWGTPALALASGAQAVLRARGVAVERIALDTFT
+DERVFSHRRAPGRGRFAGLVWTTPADVDQDHDAGDARG
+>4_1256
+MTAAEGPAGTARVPAGPFVHRETVRTATGAVHVAWTSVAAGNLALHVVPPDEAEGLARVS
+AARRALERAMGVPEDATLYLDQVHSADVVWADGPGRGGAPAPVADAAVSRDGSRPLAVMV
+ADCLPVVFVDETTGATAVAHAGRRGLLDGVLEATVDRLLSLRPETDRTGPGLRAWIGPGV
+CGRCYEVPAAMRTEAAARLPATAATTSWGTPALDLSAGAAQVLRARGVTTATIDVCTRED
+ERLFSHRRAPGEGRFAGLVWRTDLDATTPRGEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001137.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001137.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dafe602041b9feb9ebc8b92c7a14cc697f283c4a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001137.fa
@@ -0,0 +1,45 @@
+>0_1307
+MSPIELRPVRPRAADDAPEHRERILRRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV
+LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVLKALAWPAFGVAVILLA
+LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV
+LPGGLLLLVLVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSVLGILALTLLAP
+HRMVRVQAWMGDCSDATDPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT
+ILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQAAVNIAMVS
+GVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLPV
+IPTPALQEPR
+>1_1036
+MSPIELRPVRPRADDDAPEHRERLLHRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV
+LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVFKALAWPAFGVAVILLA
+LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV
+LPGGLLLLGLVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSVLGILALTLLAP
+HRMVRVQAWMGDCSDATDPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT
+ILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQASVNIAMVS
+GVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLPV
+IPTPALQEPR
+>2_1507
+MSPTELHPVRTPADEEETEARSRPLQRLWRLVEGRRALDLSVLLIGGSTFLLTALGLVMV
+LSSSSVEAIGTGGGSYGLFLRQTMWAVAGLAALLLFSRLPIGWIKALAWPAFGLAVVLLS
+LVAFTPLGVTVGGNTNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALVPV
+LPGGLLLIGLVMAGSDLGTAIILALVLAAVLFVAGTHHGVFIAFSAVTVVGAIALTLLAP
+HRMVRVQAWLGDCSDASDPCFQPDHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT
+ILGEELGLVGTLGVLLAYLALAVGMYRVAAGTTSPFIRLATWGIMAWLVGQAFVNIAMVS
+GVIPVVGVPLPFISYGGSALTLSLTAVGIVLAFARHERRRAEEPDARPDADDPDTDPLPV
+IPAPASQES
+>3_1403
+MPSTATRPEASSRASARTAVRPRLAGFWGALEGRRALDWAALLIGLCTAVLTVLGLVMVL
+SASSVEAISSSGGSYGLFLRQGGWALGGAVLLAVLRRLPVDLYRRLAWAAYLFAFLLLAL
+VAFTPLGKEVNGNTNWLQLGPVTFQPSEAAKLAMALWAAAVLQRKERLVHLVSHALVPVL
+PFGVALILLVLKGRDLGTALILAFILAVILFVAGTPGRVFAVLAGIGVVAALGMTVFAAN
+RMERVQAWLFGCEGLQGDPCMQPDHGIYALASGGWWGVGLGQSRQKWNYIPEAENDFIFT
+ILGEELGLVGTLLVLACFVGLAVGMYRVAAGASSTFVRLATWGILAWIVGQAAMNIAMVT
+GLLPVVGVPLPFISYGGSALTLSLAAVGVVLSFARHERDLLPAAEASAADPASSASPQES
+R
+>4_1261
+MSPIELRPVRPRADDDAPEHRERLLPRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV
+LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVFKALAWPAFGVAVILLA
+LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV
+LPGGLLLLILVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSMLGILALTLLAP
+HRMVRVQAWMGDCSDATDPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT
+ILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQAAVNIAMVS
+GVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLPV
+IPTPALQEPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001140.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001140.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5564b5719c8c70afcd6ace5baac485cef6c66f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001140.fa
@@ -0,0 +1,55 @@
+>0_1311
+MTTPSDPPAPLTPAQQDAAFRPSHTPAAAWPALAQALAEAGIAAHVHGAAPADGVTGVSL
+DSRVVRPGDLYVAVPGARAHGAAFAATALEAGAVGVLTDAAGRALLAEQGLADVPVLEVD
+AVRTAAGTVAARVYGGGGDTGPRLLGVTGTNGKTTTSFLAAALLEALGRRSGIVGTILIR
+AGEREVPSTLTTPEATQLHALMALMREEEVDTAVMEVSSHAVAYQRIAGLRYAVAGFTNL
+TQDHLDMHGSMQEYFAAKAGLFDPARTDHAVITLDGGEGPRWGVAMARAAGAPVTTLALG
+PAAPTPGALAEHDPGLRADWEVAELAPDGLGHRFTLRHAATGRELRASVGLPGRFNVANA
+ALAVLLVLHAVGEEHLDALAAVLDVPAGEGPLAAAVPGRMEVVGREPDAVVDFAHNPDGM
+VQALRSLADARAAAGTRGRTLIVFGSAGDRDRDKRPVMGAIAARAADVLIVTDDTPHSED
+PAPIRAHILAGARAEADRIAREEGRTVVIEEVADRATAIRRAVELAGPQDGILLAGRGHE
+TTMDYDGELVPLDDRVALREALAARVAAASASGSGPAREGKVIES
+>1_1040
+MTTPSDPPAPLTPAQQDAAFRPSHTPATPWPALAQSLAGAGIAAHVHGAAPADGVTGVSL
+DSRVVRPGDLYVAVPGAHAHGAAFAARALEAGAVGVLTDAAGRALLAEQDLADAPVLEAD
+AVRTAAGTVAARVYGGGGDAGPRLVGVTGTNGKTTTSFLAAALLEALGHRSGIVGTILIR
+AGEREVPSTLTTPEATQLHALMALMREEQVDTAVMEVSSHAVAYQRIAGLRYAVAGFTNL
+TQDHLDMHGSMQEYFAAKAGLFDPARTDHAVITLDGGEGPRWGVAMARAAGAPVTTLALG
+PAAPTPGALAEHDPGVRADWEVAELAPDGLGHRFTLRHAATGRELRASVGLPGRFNVANA
+ALAVLLVLHAVGEEHLDALAAVLDVPAGEGPLAAAVPGRMEVVGREPDAVVDFAHNPDGM
+VQALRSLADARAAAGTRGRTLIVFGSAGDRDRDKRPVMGAIAARAADVVIVTDDTPHSED
+PAPIRAHILAGARAEADRIAREEGRTVVIEEVADRAAAIRRAVELAGPQDGILLAGRGHE
+TTMDYDGELVPLDDRVALREALAAGAAVASASVSGPVREGKVIES
+>2_1504
+MSSQPAQPQPLTPAQQDDAFRPSRTPATPWDELTRALQAAGVAARTHGRGPAAGVTGACL
+DSRVVRPGDLYVALPGARSHGADFARAAVDAGAAGVLTDAEGRARLAEQGLDGSAVIEVD
+SVRTAAGVVAARVYGGGQDAGPRLIGITGTNGKTTTSFLAAALLEALDRRSGVIGTILIR
+AGGREVPSTLTTPESTQLHALMALMREEQVDTAVMEVSSHAVAYQRIAGLRYAVAGFTNL
+TRDHLDMHGSMEEYFEAKAGLFDPERTARAVITVDGGEGPRWGLSMARAVRTPVTTLALG
+PAAPHPGALAEEDPDFRADWEIAELVPDGLGHRFTLRHGATGRALRASVGLPGRFNAANA
+ALAVLLVLYAVGEEHLDALAAVLDVPAGEGPLAAAVPGRMEVVGRAPDAVVDFAHNPDGM
+VQALRSLADAREAAGRSGRTLIVFGSAGDRDREKRPIMGEIAARAADVVIVTDDTPHTED
+PAPIRAQILEGARAEAARLLQAEGRTVLVEEVADRAVAIRRAAELAAPQDGILVAGRGHE
+TTMDYDGELVPLDDRQALREALAARAAAASPRASDPGSGAPRGGKVDES
+>3_1399
+MTDDAPQTTAPLTPAEQDAAFRPAAVTPVAWAEVAAALRAAGQDVRERSAAAAPAVTGAA
+LDSRVVRPGDLYVALPGARAHGAAFAAAAREAGAAGVLTDGDGVALLAEQGLDDLPVLEV
+ESVRAAAGVAAARIYGGGPDAGPRLLGVTGTNGKTTTSFLAASIVEALGERSGIIGTILT
+RAGDRQVPSTLTTPESAQLHALMALMRQEGVDTAVMEVSSHAVEYRRIAGLHYAVAGFTN
+LTQDHLDQHGTMEGYFRAKLGLFEADRTDRAVVVLDGGEGPRWGVKTARRAGAPVTTLAL
+GAASPTPGALAEEHPDVVPDWQVTDLVADGLGHRFALVHAATGRRLPASVGLPGLFNVAN
+AALAALMVLESIGEDRLDELAAVLDVPAGTGPLAAAVPGRMEVVGREPDAVVDFAHNPDG
+MVQALRALGDARAAAGRAGRTLIVFGAAGDRDATKRPLMGRIAAEHADVVIVTDDTPHTE
+DPAPIRAQLLEGAREEAARAAAAGREVRVEEFADRAAAIRRAAELAAPEDGILVAGRGHE
+TEMDYDGTLVPLDDRVALRDALAARRPGDAQEPGVAGGKVAGK
+>4_1265
+MTTPSDPPAPLTPAQQDAAFRPSHTPATPWPALAHALAEAGIAAHVHGAAPADGVTGVSL
+DSRVVRPGDLYVAVPGARAHGAAFAATALEAGAVGVLTDAAGRALLAEQGLVDVPVLEVD
+AVRTAAGTVAARVYGGGGDAGPRLVGVTGTNGKTTTSFLAAALLEALGRRSGIVGTILIR
+AGEREVPSTLTTPEATQLHALMALMREEEVDTAVMEVSSHAVAYQRIAGLRYAVAGFTNL
+TQDHLDMHGSMQEYFAAKAGLFDPARTDHAVITLDGGEGPRWGVAMARAAGAPVTTLALG
+PAAPTPGALAEHDPGLRADWEVAELAPDGLGHRFTLRHAATGRELRASVGLPGRFNVANA
+ALAVLLVLHAVGEEHLDALAAVLDVPAGEGPLAAAVPGRMEVVGREPDAVVDFAHNPDGM
+VQALRSLADARAAAGTRGRTLIVFGSAGDRDRDKRPVMGAIAARAADVLIVTDDTPHSED
+PAPIRAHILAGARAEADRIAREEGRTVVIEEVADRATAIRRAVELAGPQDGILLAGRGHE
+TTMDYDGELVPLDDRVALREALAARVAAASASGSGPAREGKVIES
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001141.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001141.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d7699575c9f18ebbdd3c62b7ece35d56c582eda
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001141.fa
@@ -0,0 +1,57 @@
+>0_1312
+MRTRILLLLVFVLLGGLALRLVYVQGIDPTGQAAAAMDQRLTHQETLPQRGSILDRDGDV
+LAASVRRYDIVVDQRLVKDFNEWDREARETVLVDVDSRLASLAEVLGMSEEEVREATIGS
+RPYAVVRRSVTPEVRDAAMALNVPGLLSEAVDRRTYPNGSVAGSIIGFMGGDGTALEGLE
+LSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAVDGADLRLTVDKDAQWFAQETLGAL
+AAEYEAEWANAVVMDVKTGDVIVMADSTTVDPADPDATEGNFRTSTVMSTPYEPGSTGKA
+LPIAAAVDAGKVTATDGFTVPGSQDFDGQTIRDFSPHPTFDMTVAGIYARSYNTGTVQIA
+EKITDEQRYEYMRSFGVGQPIDLGLPQQAGSVLVPPEQWDGRQRLTTAFGQGYTQTTLHT
+AQMYQALANGGVLIPARLIDATVDGDGAEKRWESSAEPHRVVSEETAAQMLRMMETVVTQ
+GTSKAAAIPGYRVGGKSSTAEAASDTGTYDGYNLGFTAVAPLDDPRFVVSVSMHRPPSKQ
+GSRDVSVAAATIMEYMLRQADVPATGAEPNDYRVFVDDPQDRPW
+>1_1041
+MRTRILLLLVLVLLGGLALRLVYVQGIDPTGQAAAAMDQRLTHQETLPQRGSILDRDGDV
+LAASVRRYDIVVDQRLVKDFNEWDREARETVLVDVDSRLASLAEVLGMSEEEVREATIGS
+RPYAVVRRSVTPEVRDAAMALNVPGLLSEAVDRRTYPNGSVAGSIIGFMGGDGTALEGLE
+LSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAVDGADLRLTVDKDAQWFAQETLGAL
+AAEYDAEWANAVVMDVKTGDVIVMADSTTVDPADPDATEGNFRTSTVMSTPYEPGSTGKA
+LPIAAAVDAGKVTATDGFTVPSSQDFDGQTIKDFSPHPTFDMTVAGIYARSYNTGTVQIA
+EKITDEQRYEYMRSFGVGQPIDLGLPQQAGSVLVPPEKWDGRQRLTTAFGQGYTQTTLHT
+AQMYQALANGGVLIPARLIDATVDGEGAEKRWESSAEPHRVVSEETAAQMLRMMETVVTQ
+GTSKAAAIPGYRVGGKSSTAEAASDTGTYDGYNFGFTAVAPLDDPRFVVSVSMHRPPSKQ
+GSRDVSVAAATIMEYMLRQADVPATGAEPNDYRVFVDDPQDRPW
+>2_1503
+MTDRPAFSSPRGGSTVGPAPGLPDARIRGLLLLVLVLLGGLALRLVYVQGVDPTGQAAAA
+MDKRLTHQETLPERGSILDRDGDVLASSVRRYDMVVDQRLVKDFNEWDREARKTVLVDVD
+SRLASLAEVLELPEEQVREATIGSRPYNVVKRSVTPEMRDAAMALKVPGLLAEPVDRRVY
+PNGSVAGSIVGFMGGDGTPLEGLELSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAV
+DGADLRLTLDKDAQWFAQETMGALAAEHDAEWANAVVLDAKTGDVLVMADSTTVDPADPE
+GTEPYFRSSTVMSTPYEPGSTGKALPIAAALDAGAVTATDGYTVPSSQEFDGQTIRDFAP
+HETYDMTVAGIFARSYNTGTVQVAEEISDELRYEYMRSFGVGKPIDLGLPRTAGGVLVPP
+GEWDGRQRLTTAFGQGYTQTTLHTAQMYQAMANGGVMEPARLIDATVDGDGAEKRWEPAA
+EPHRVVSEATAADMLRMMETVVTQGTSKAAAIPGYRVGGKSSTAEAASDTGRYDGYNFGF
+TAVAPLDDPRFVVSVSMHRPPSQLGSRAVTSAAAQIMEHMLRQADVPADGAAPQDYDVFV
+DDPQDRPW
+>3_1398
+MPVSRSRVSGAGSRTAPPIGTARVRSRTVLLLLLALVTVLGLRLVWVQGIDASGAAATAM
+SERLKTQEIRPERGAITDRDGAVLASTVRRYDIVVDQRLVKDFKEWDAEKRQSVLVSIDS
+RLSSLAEALGMSEDEVRAAAIGDRPWAVLKRSVTPEVRDRVLALKVPGVLADAVDRRTYP
+SGAVAGSLVGFMSSDGTPLEGLEKSQDAVLSGTPGTRTFEVGATGIRIPNAPEDVTPAVD
+GATLRLTLDKDAQWYAQEAMARLADTYSAQWANAVVMDAKTGEVLALADSATVDPGDPQA
+ADARARTPGVVYTPYEPGSTGKTATMAAALDMGLVTPETGLEVPDRLELKGQPPIRDASP
+HETYTMTVAGVYARSYNTGTVMVAEKMSDEQRYEYMRSFGIGRPIDLGLPQPARSVLAAP
+GDWDGRQRLVTAFGQGYTVTTLHTAQMFQAIANGGVLEPARLIAATVGADGTEHRWDPGV
+ASRRVVSEQTAEEMLRMMETVVTQGTSTVAQLPGYRVGGKSSTAQVAGETGTYDGYNYGF
+TAVAPLDDPRYVVSVSMNRPSAGGSSKVVAAAAADVMQHMLRQGGVPPGGAEPDDYRVFV
+DDPQERPW
+>4_1266
+MRTRILLLLVFVLLGGLALRLVYVQGIDPTGQAAAAMDQRLTHQETLPQRGSILDRDGDV
+LAASVRRYDIVVDQRLVKDFNEWDREARETVLVDVDSRLASLAEVLGMSEEEVREATIGS
+RPYAVVRRSVTPEVRDAAMALNVPGLLSEAVDRRTYPNGSVAGSIIGFMGGDGTALEGLE
+LSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAVDGADLRLTVDKDAQWFAQETLGAL
+AAEYEAEWANAVVMDVKTGDVIVMADSTTVDPADPDATEGNFRTSTVMSTPYEPGSTGKA
+LPIAAAVDAGKVTATDGFTVPGSQDFDGQTIRDFSPHPTFDMTVAGIYARSYNTGTVQIA
+EKITDEQRYEYMRSFGVGQPIDLGLPQQAGSVLVPPEQWDGRQRLTTAFGQGYTQTTLHT
+AQMYQALANGGVLIPARLIDATVDGDGAEKRWESSAEPHRVVSEETAAQMLRMMETVVTQ
+GTSKAAAIPGYRVGGKSSTAEAASDTGTYDGYNLGFTAVAPLDDPRFVVSVSLHRPPSKQ
+GSRDVSVAAATIMEYMLRQADVPATGAEPNDYRVFVDDPQDRPW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001147.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001147.fa
new file mode 100644
index 0000000000000000000000000000000000000000..767f7ed866711d33f58ced5da1c16f7a7abddd85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001147.fa
@@ -0,0 +1,40 @@
+>0_1318
+MPADVAVPRPRPADQDRFRAAVADALDRLLAEHRDLARDVHPLTAPLVDAIADLTAGGKR
+LRAVLAWLGWRAAGGEAEDPRIAEAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRRFE
+SLHREAGWRHAAEHFGVSAAILAGDVALGMSETAFARVLAGTPREDRARAELERMRFGVM
+AGQYLDVVAEMAPAARDAREAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDGLVTAFA
+RVSLPFGMAFQYRDDLLGVFGDPATTGKPAGDDLREGKQTVLIARAVELLAPDEAAALDA
+DLGDPDLGADRVAHWQGVLEACGARRAVEERVAALSHEAAGAVAGLLAHGVPEDVSAELT
+QLIDAYTSRRH
+>1_1047
+MPADVAVPRPRPRPADQDRFRAAVADALDRLLAEHRELARDIHPLTAPLVDAIADLTAGG
+KRLRAVLAWLGWRAAGGEAEDPRIAEAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRR
+FESLHREAGWRHAAEHFGVSAAILAGDVALGMSETAFARVLAGTPREDRARAELERMRFG
+VMAGQYLDVVAEMAPAARDAREAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDGLVTA
+FARVSLPFGMAFQYRDDLLGVFGDPATTGKPAGDDLREGKQTVLIARAVELLAPDEAAAL
+DADLGDPDLGADRVAHWQAVLEACGARRAVEERVAALSHEAAGAVAGLLAHGVPEDVSTE
+LTRLIDAYTPRRH
+>2_1497
+MPVDAAVTRPRPADQDRFRAAVAEELTRTLDEHRERARAVHPLTVPLVDAVGDLAAGGKR
+LRAVLGWLGWRAAGGDPENPRIARTGAALELFQAAALIHDDILDRSDTRRGMPSVHRRFE
+AEHRASGWRHDAGHFGVSAAILAGDVALGMSETAFAAALEGAGRPARARDEFERMRFGVM
+VGQYLDVAAEMAPPATDPAEAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDALVAAFA
+EVSLPFGLAFQYQDDLLGVFGDPAATGKPAGDDLREGKRTVLIARAVALLSPADAAALDA
+DLGDPGLSAERIAHWQRALEECGARQAVTDRVAALSARAAEAVGALEAHGVPADVRAELT
+ALIEAATTRRH
+>3_1392
+MPTPETASVSDFRAAVAERLTAVLDGHARGAARIHPDADPVVEAVSVLTSGGKRLRAVLC
+WLGWRAAGGSPTDPRAAVAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRRFEARHREH
+GWRHEAEHFGVSAAILAGDVALALSDSMFSRAIEGTPRAERARREMERMRFEVMVGQYLD
+VAAEMAPPAADPAAAERAARAVVEHKSARYSAVHPLALGALLAGADDDLVAAFEAVSLPF
+GMAFQLQDDLLGVFGDPAHTGKPAGDDLREGKRTVLVARAEALLPRGEAAALDAELGDPA
+LSAERVAHWQRRLEEVGARTAVADEVDRLSAEARRGLERLAALGVGTDVRGELAELIDAY
+TVRTA
+>4_1272
+MPADVAVPRPRPADQDRFRAAVADALDRLLAEHRERARDVHPLTAPLVDAIADLTAGGKR
+LRAVLAWLGWRAAGGEAEDPRIAEAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRRFE
+SLHREAGWRHAAEHFGVSAAILAGDVALGMSETAFARVLAGTPREDRARAELERMRFGVM
+AGQYLDVVAEMAPAARDAREAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDGLVTAFA
+RVSLPFGMAFQYRDDLLGVFGDPATTGKPAGDDLREGKQTVLIARAVELLAPDEVAALDA
+DLGDPDLGADRVAHWQAVLEACGARQAVEERVAVLSHEAAGAVAGLLAHGVPEDVSAELT
+RLIDAYTSRRH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001150.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001150.fa
new file mode 100644
index 0000000000000000000000000000000000000000..066325f036df6c1b472d2be80e90354ae0e6aed4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001150.fa
@@ -0,0 +1,45 @@
+>0_1322
+MTEDPREKILAFGTAISEGAADIPGLDHWRSLPIAQAPSWADEADHRAAVAELSALPPLV
+FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM
+PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEQARRHDARRMVQAYHTS
+ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA
+MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR
+NPIGVKLGPTTTVADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE
+PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRELGTHPGGMHVELTGDDVAEC
+LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERRAPRA
+>1_1051
+MTEDPREKILAFGTAISEGAADIPGLDHWRSLPIAQAPSWADEADHRAAVAELSALPPLV
+FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM
+PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEQARRHDARRMVQAYHTS
+ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA
+MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR
+NPIGVKLGPTTTTADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE
+PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRELGTHPGGMHVELTGDDVAEC
+LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERRAPRA
+>2_1492
+MTEDPREKILAFGTAISEGAADIPGLDHWRSLPVAQAPSWADEAEHRAAVAELSQVPPLV
+FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM
+PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEEARRHDARRMVQAYHTS
+ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA
+MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR
+NPIGVKLGPTTSAADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE
+PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRALGTRPGGMHVELTGDDVAEC
+LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERVAPRR
+>3_1388
+MHEDPRDQIMAFGTAISEGAAPDPALDAWRELPIKQAPTWADEDDFRAAVAELSQVPPLV
+FAGEVDVLRTRLADVARGQAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM
+PVVKMGRIAGQYAKPRSSDTETRDGVTLPSFRGEIVNGFEFTEEARRHDARRMVTAYHTA
+SSTLNLVRAFTQGGFADLRSVHQWNRGFMENPAYAQYEQIAAEIDRAVRFMDAAGADFEA
+MRRTEFYAAHEALLLDYERALTRLDSRTGLPYATSAHFLWIGERTRDVDGAHVDFLSRVR
+NPIGVKLGPTTTVDDVRALADRLDPEREPGRLTFITRMGADKVRDVLPGIVAGVRDEGLQ
+PVWVTDPMHGNTVTAANGYKTRRFEDVMDELTGFFEVHRELGTHPGGMHVELTGDDVAEC
+LGGSDPVDEADFDEHYETLCDPRLNHQQSLELAFKVTDALAHPHQD
+>4_1276
+MTEDPREKILAFGTAISEGAADIPGLDHWRSLPIAQAPSWADEADHRAAVAELSALPPLV
+FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM
+PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEQARRHDARRMVQAYHTS
+ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA
+MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR
+NPIGVKLGPTTTVADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE
+PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRELGTHPGGMHVELTGDDVAEC
+LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERRAPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001151.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001151.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b9c6bebe1db7b4d7f831de4eacc226bd0cb04b30
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001151.fa
@@ -0,0 +1,25 @@
+>0_1323
+MSTFYWSAKTFAVAPATRLLFRPWVKGLGNVPAEGPAILASNHLSVSDSVFMPAMLDRQV
+HFLAKHEYFTGPGVKGWVTRRFFEAANQLPMDRSGGEASLRSLDAGLEALREGRLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDRVQPIGHVLPRIRRLGMIFGEPL
+DFSDRAEAVGDPRVLREVTDEIMEAIRRLSGQEYVDTYAADVKAGRTAAPPRARD
+>1_1052
+MSTFYWSAKTFAVAPATRLLFRPWVKGLANVPAEGPAILASNHLSVSDSVFMPAMLDRQV
+HFLAKHEYFTGPGVKGWVTRRFFEAANQLPMDRSGGEASLRSLDAGLAALREGRLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGVPVVPIAMIGTDRVQPIGHVLPRIRRLGMIFGEPL
+DFSGRAAAADDRRVLREVTDEIMEAIRRLSGQEYVDTYAADVKAGRVAAPPRAGD
+>2_1491
+MSTFYWSAKTFAVAPATRLLFRPWVKGLGNVPAEGAAILASNHLSVSDSVFMPAMLERQV
+HFLAKKDYFTGAGPKGWITRKFFEATNQLPMDRSGGEASLRSLDAGLEALREGRLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDQAQPIGRTLPRIRRIGMIFGEPL
+DFSDRAEGVTDARVLRAVTDEIMEAIRRLSGQEYVDAYAADVKSGRVPAPPRARD
+>3_1387
+MSAFYWSAKTFVVAPATRLLFRPWVKGLSHVPAEGPAILASNHLSVSDSVFMPAMLDRQV
+HFLAKQEYFTGRGAKGWATKKFFEATNQLPMDRSGGAASLRSLEAGLECLREGKLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDRVQPIGRILPTLRRLGMIFGEPL
+DFSHLQGREGDHRALRQVTDEIVEAIRRLSGQDYVDVYAADVKSGRVAVPPRAGRD
+>4_1277
+MSTFYWSAKTFAVAPATRLLFRPWVKGLGNVPAEGPAILASNHLSVSDSVFMPAMLDRQV
+HFLAKREYFTGPGVKGWVTRRFFEAANQLPMDRSGGEASLRSLDAGLEALREGRLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDQVQPIGHVLPRIRRLGMIFGEPL
+DFSDRAEAVGDPRVLREVTDEIMEAIRRLSGQEYVDTYAADVKAGRTAAPPRARD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001158.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001158.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d33b253f8ff9c12f68ffde4ef2de08755f326eea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001158.fa
@@ -0,0 +1,30 @@
+>0_1330
+MIDPRPLPDAVPTARPAGRLGIGEVVAALEAEFPGVTASKVRFLEDRGLVLPERTPAGYR
+RFRPEDVDRLRFVLALQRDHFLPLKVIADHLAALDRGERPTGLPGTAAVPASSDAARLGR
+EVAGGRRSWTRAELAAESGAGEELLAELDQYSLLPVDPDGGYPSHAMDVARAAVVLAGHG
+LEPRHLRPLRAAADRELGLVERAVAPLQARRDAGTRPRVARSAREIAQASLRLHAALVAV
+GLEQWDD
+>1_1059
+MTDPRPRPDAVPTARPAGRLGIGEVVASLEVEFPGVTASKVRFLEDRGLVLPERTSAGYR
+RFRPEDVDRLRFVLALQRDHFLPLKVIADHLAALDRGERPTGLPGTAAAPASSDAERLGR
+EVAGGRRSWTRAELAAESGAGEELLAELDQYSLLPVDPDGGYPSHAMDVARAAVVLAGHG
+LEPRHLRPLRAAADRELGLVERAVAPLQARRDAGTRPRVARSAREIAQASLRLHAALVAV
+GLEQWDD
+>2_1484
+MTEPQHADAGPRTRPAGRLGIGEVVAALKSDFPGVSASKVRFLEDRGLVLPERTPAGYRR
+YRPEDVDRLRFVLTVQRDHFLPLKVIAAQLAALDRGEVPADLPGGVVAPGASDASRLGRE
+VAAGRRGWTRSELAEESGAGEELLAELDQYSLLPADEDGAYSSHAMEVARAAVVLAGHGL
+EPRHLRPFRAAADRELGLVERAVAPLQARRDANMRPRVARSAQEIAQASLRLHSALVAEG
+LEQWDDGAVG
+>3_1379
+MSAPHEPSAAPPPAGAALGIGDLVAALEPSFPGVSASKVRFLEDRGLVRPERTAAGYRRY
+RPADVDRIRLVLTLQRDRFLPLKVIREHLDALDRGERPEDLGEAPAAAQEAVRLGHGIAD
+PDRRWTRAELAREAEVPAPLVDELDQYALLPRAEDGLHPPAALGVVRAAGRLAAHGIEPR
+HLRPFRAAADRELGLVQSAVAPLATRRDAGTRERAARTAEEIATACLALHAALVRAGLES
+LDG
+>4_1284
+MTDPRPRPDAVPTARPAGRLGIGEVVASLEVEFPGVTASKVRFLEERGLVLPERTSAGYR
+RFRPEDVDRLRFVLALQRDHFLPLKVIAEHLAALDRGERPTGLPGTAAAPASSDAERLGR
+EVAGGRRSWTRAELAAESGAGEELLAELDQYSLLPVDPDGGYPSHAMDVARAAVVLAGHG
+LEPRHLRPLRAAADRELGLVERAVAPLQARRDAGTRPRVARSAREIAQASLRLHAALVAV
+GLEQWDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001159.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001159.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40d78d4d5dfded5076f3b2da904cb8b2ee9d5fad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001159.fa
@@ -0,0 +1,20 @@
+>0_1331
+MNQPGREPDLSTSAINLTELAPLVSADLTREESDAIRALPAGSALLLAHEGPDQSARFLL
+DKDVVSVGRHPDADIFLDDVTVSRRHAEFRAEDGGHRLVDLNSLNGTFVNHDRVDEILLR
+SGMHVQIGKYRLTYYAAPARG
+>1_1060
+MNQPGREPDLSTSAINLTELAPLVSADLTREESDAIRALPAGSALLLAHEGPDQSARFLL
+DEDVVSVGRHPDADIFLDDVTVSRRHAEFRAEDGGHRLVDLNSLNGTFVNHDRVDEILLR
+SGMHVQIGKYRLTYYAGPARG
+>2_1483
+MNQPGREPDLSTSSINLTELAPLVAADLSAEESDAIRALPAGSALLLADGGPEKAARFLL
+DQDVVTVGRHPDADIFLDDVTVSRRHAEFRAEAGGHRLVDMNSLNGTFVNHDRVDDVLLR
+SGTHVQIGKYRLTYFTSTQRG
+>3_1378
+MTQQEPSLHTSSISLTDLAPVAETGLSPEETAAVRALPAGAALLVAHEGPDAGARFLLDT
+PVVTVGRHPESDILLDDVTVSRRHAEFRAVDGGHELVDLSSLNGTYVNNDRVDQVRLRTG
+MQLQIGRYRLSYHAAEPA
+>4_1285
+MNQPGREPDLSTSAINLTELAPLVSADLTREESDAIRALPAGSALLLAHEGPDQSARFLL
+DEDVVSVGRHPDADIFLDDVTVSRRHAEFRAEDGGHRLVDLNSLNGTFVNHDRVDEILLR
+SGMHVQIGKYRLTYYAGPARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001164.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001164.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a34337c0356a2f4daa3d44357d851a64b122caa8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001164.fa
@@ -0,0 +1,40 @@
+>0_1357
+MSAPAESAAKLGDGPAGIPQPVLVRGTGLLGASIGIGLSAAGVDVRLHDPSPAALAVAAD
+IRAGRPARLDAEGDDLDVAPGLVVVAAPPDVTADVVVDSLRRWPAAVVVDIASVKEAVAA
+GVRAAVDDGRLAPQDADRYLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTHPGALA
+AGRALARTLQATPYRMAARAHDESVALISHLPQIAASLVASRLQDTPDQALALAGNGLRD
+TTRIAASDPQLWVQILSGNAGRIVPALHGLRADLDRLIRTLEDPSAPGARLDMAQLIAEG
+NAGRARVPGKHGAPPQAFAVVTVIVDDAPGQIAALLDEVGRTDVNVEDLRLEHASGHRVG
+MVEISVLPGRRDELVAALTAAGWKVV
+>1_1096
+MSAPAESAAKLGDGPAGIPQPVLVRGTGLLGASIGIGLSAAGVDVRLHDPSPAALAVAAD
+IRAGRPARLDAEGDDLDVAPGLVVVAAPPDVTADVVVDSLRRWPAAVVVDIASVKEAVAA
+GVRAAVDDGRLAPQDADRYLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTHPGALA
+AGRALARTLQATPYRMAARAHDESVALISHLPQIAASLVASRLQDTPDQALALAGNGLRD
+TTRIAASDPQLWVQILSGNAGRIVPALHGLRADLDRLIRTLEDPSAPGARLDMAQLIAEG
+NAGRARVPGKHGAPPQAFAVVTVIVDDAPGQIAALLDEVGRTDVNVEDLRLEHASGHRVG
+MVEISVPPGRRDELVAALTAAGWKVV
+>2_1461
+MSAAAETAAAVPGALPAGIPQPVLVRGTGLLGASIGIGLSAAGADVLLHDLSPAALAVAA
+DIGAGRPMRIDDDGADAGPAPALVVVAAPPDVTADVVVDSLRRWPEALVLDIASVKEAIA
+AGVRAAVDDGRLGPSDPDRHLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTLPAAV
+QAGRALALALRATPYRMDARAHDESVAMISHLPQIAASLVAARLQDTPDQALALAGNGLR
+DTTRIAASDPQLWVQILSGNAERIVPALHGLRDDLDRLIRTLEAPGAPGSRLDMARLIAE
+GNAGRARVPGKHGAPPQAFAVVTVIVDDTPGQIAAVLDEVGRTDVNVEDLRLEHASGHRA
+GMVDISVLPGRRDELVAALSAAGWKVV
+>3_1372
+MIPAEGGAGPAGLSGPVLVRGTGLLGASIGLGLRAAGADVLLDDPSPTALAVARDIGAGA
+VVDLDDPALAPGLVVVGAPPDVTPAVVVDSLRRWPHAVVTDIASIKGAILAEVREAATRG
+DIAPGDVARYLPGHPMAGSERSGPVAARGTLFTASPWVLCPAAETDPAALAAGEALARTL
+QATVHRMSAADHDASVALISHLPQIAASLVASRLQDAPDPSLALAGNGLRDTTRIAASDP
+HLWVQILAGNAPQIVPTLHGLREDLDRLIGTLEAPSAPGARLDVARLIAEGNAGRARIPG
+KHGAPPQAFALVTVIVDDTPGQLAALFEEIGRAGVNVEDIRLDHASGYRVGMVDVSVLPG
+RKDELVSALTDAGWKVV
+>4_1306
+MSAPAESAAKLGDGPAGIPQPVLVRGTGLLGASIGIGLSAAGVDVRLHDPSPAALAVAAD
+IRAGRPARLDAEGDDLDVAPGLVVVAAPPDVTADVVVDSLRRWPAAVVVDIASVKEAVAA
+GVRAAVDDGRLAPQDADRYLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTHPGALA
+AGRALARTLQATPYRMAARAHDESVALISHLPQIAASLVASRLQDTPDQALALAGNGLRD
+TTRIAASDPQLWVQILSGNAGRIVPALHGLRADLDRLIRTLEDPSAPGARLDMAQLIAEG
+NAGRARVPGKHGAPPQAFAVVTVIVDDAPGQIAALLDEVGRTDVNVEDLRLEHASGHRVG
+MVEISVLPGRRDELVAALTAAGWKVV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001174.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001174.fa
new file mode 100644
index 0000000000000000000000000000000000000000..67d3881e5dfd93597b86264d23f122d80f1f33d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001174.fa
@@ -0,0 +1,40 @@
+>0_1372
+MPYTPGRRILVLTHTGREDAISAALQATRMFAEEGLVTVMLEQDVAAIRAAAGDPPEFAP
+ETLGVDCELEDITLGLVLGGDGSVLRAADFVRGYNVPLLAVNLGHVGFLAESERTDLHRT
+VQAIASESYVVIERMALDVVVHVEGREVARTWALNEASVEKSHRERMLEVVVSVDNSPLT
+SFGCDGVVLATPTGSTAYAFSAGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD
+VLTRTRETGVLWCDGRRTVELPPQARVEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG
+WRGPVTAQERAGVLHEVETVEPRHAGPRPDVVEPATMPLSVPSPADIQRHRDRGARHPGE
+DA
+>1_1112
+MPYTPGRRVLVLTHTGREDAISAALQATRMFAEEGLVSVMLEQDVAAIRAAAGDPPEFAP
+EALGVDCELEDITLGLVLGGDGSVLRAADFVRGHNVPLLAVNLGHVGFLAESERTDLHRT
+VQAIASESYVVIERMALDVVVLVEGREVARTWALNEASVEKSHRERMLEVVVSVDNSPLT
+AFGCDGVVLATPTGSTAYAFSGGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD
+VLTRTRETGVLWCDGRRTVELPPQARIEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG
+WRGPVTAQERAGVLHAVETVEPRHAGPRPDVVEPATMPLSVLSPADIQRHRDRGARHPGE
+DA
+>2_1449
+MPHNPGRRVLVLAHTGREDAISAALQATRILEEEGLVSVMLEQDVAAIRENADAPAGFAP
+QTLGVDCGLEDIVLGLVLGGDGSVLRAADFVRGYDVPLLAVNLGHVGFLAESERTDLQRT
+VQAIASEAYVVIERMALDVVVRVEDREVARTWALNEASVEKSNRERMLEVVISVDNAPIS
+SFGCDGVVLATPTGSTAYAFSGGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD
+VLTRTRETGVLWCDGRRTVELPPQARIEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG
+WRGPVTAQEREAVLREVETVEPRHAGPRPDVVEPATMPLSVLSAADIQRYRDRGARYPGE
+DA
+>3_1357
+MSETPSRRVLVLAHTGRADAIAAALQATAMLAEEGLDTVMLAEDVAAILESGTDAVGFRP
+LTLGRDCTLDDVQLGLVLGGDGSVLRAADFVRGHGIPLVAVNLGHVGFLAESERTDLHRT
+VKAIADGAYVVIERMALDVTVRVEGREVARTWALNEASVEKSNRERMLEVVVSVDDSPLT
+SFGCDGVVLASPTGSTAYAFSAGGPVVWPGVEALLCVPISAHALFSRPLVVGPHSTVAVD
+VLTRTRETGVLWCDGRRTVELPPRARIEVTRSAEPVRLARLRPTPFAERLVRKFRLPTEG
+WRGPVTEADRRTGPLAEVETVEPRHAAPRPDVVPPPSEPLTVLSPEALARYRGRDGREGD
+RTS
+>4_1321
+MPYTPGRRVLVLTHTGREDAISAALQATRMFAEEGLVSVMLEQDVAAIRAAAGDPPEFAP
+EALGVDCELEDITLGLVLGGDGSVLRAADFVRGHNVPLLAVNLGHVGFLAESERTDLHRT
+VQAIASESYVVIERMALDVVVLVEGREVARTWALNEASVEKSHRERMLEVVVSVDNSPLT
+AFGCDGVVLATPTGSTAYAFSGGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD
+VLTRTRETGVLWCDGRRTVELPPQARIEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG
+WRGPVTAQERAGVLHAVETVEPRHAGPRPDVVEPATMPLSVLSPADIQRHRDRGARHPGE
+DA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001175.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001175.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5b7d12d3a79a76dbe1fb3d20561f4799c6f9a07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001175.fa
@@ -0,0 +1,30 @@
+>0_1373
+MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPADRVAADATLRLRDPGPR
+YVSRAAHKLVSALEAFPDVGVAGRRALDAGASTGGFTQVLLERGAERVAAVDVGHNQLAP
+PVRADPRVLVREGLNIRDLTAEDIDGPVDLVVSDLSFISLRLVLAPLASVCRPGAELLLM
+VKPQFEVGRRALPRSGVVTDPDARRHAVVGVTAAALGAGLAPRGLARSGLAGQDGNAEFF
+LRLRRPDATAADNPAGGTSPAPPAGERAAGWVRGAHIDWS
+>1_1113
+MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPSDRVAADATLRLRDPGPR
+YVSRAAHKLVSALEAFPDVAVAGRRALDAGASTGGFTQVLLERGAERVAAVDVGHDQLAP
+PVQADPRVLVREGLNVRDLRAEDIDGPVDLVVSDLSFISLRLVLAPLAGVCRPGAELLLM
+VKPQFEVGRRALPRSGVVTDPDARRDAVAGVAAAALGAGLAPRGLTRSGLAGQDGNAEFF
+LRLHRPDATAADDPAGRTSPATPADERAAGWVRGAHIDWS
+>2_1448
+MAEAVRADVALAARGLARSRTEASALIRAGQVLVDGRPVRRASERVAPTASLTLADDGPR
+WVSRAAHKLVSALEAFPDVAVRGRRALDAGASTGGFTQVLLEGGAARVAAVDVGHGQLVD
+LVRTDPRVLVREGLNVRDLTVQDVEGEVDLVVSDLSFISLRLVMDALAGVCRPGADLLLM
+VKPQFEVGRAALPRTGVVTDPAARRDVVAAVAAAALDSGLELRGLARSGLPGQDGNVEFF
+LRLRRPAADAAGAPGTGLDDDAPAAEAVAAAWTAAAEVDWA
+>3_1356
+MGEARRADVALAADGLARSRTEAAALVKEGVVLVDGTPVRRPSQPVASGAVLSLLDQGPR
+WVSRAAHKLVSALEAFPVPVAGRRALDAGASTGGFTQVLLERGAARVAAVDVGHGQLVQE
+LRADPRVLVREGLNVRDLTATDVEGSVDLVVSDLSFISLRLVLDALAGVCRPDADLLLMV
+KPQFEVGRAALPRTGVVTDPRARRSAVEGVVAAALGTGLAARGVARSGLPGQDGNVEFFL
+HLRAPAAPRDGGAVAGDADEDERRRRAAALVAAADVDWS
+>4_1322
+MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPSDRVAADATLRLRDPGPR
+YVSRAAHKLVSALEAFPDVAVAGRQALDAGASTGGFTQVLLERGAERVAAVDVGHDQLAP
+PVRADPRVLVREGLNVRDLRAEDIDGPVDLVVSDLSFISLRLVLAPLAGVCRPGAELLLM
+VKPQFEVGRRALPRSGVVTDPDARRDAVAGVAAAALGAGLAPRGLTRSDLAGQDGNAEFF
+LRLHRPDATAADDPAGRTSPATPADERAAGWVRGAHIDWS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001179.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001179.fa
new file mode 100644
index 0000000000000000000000000000000000000000..64623d0ee09977d5e3a22ef9e1b0758294fc1ef9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001179.fa
@@ -0,0 +1,70 @@
+>0_1377
+MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFAS
+LYEDRLAQLYAVDDRLVFGRLDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAG
+AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLGEDGVRADAQGALLAAVTARR
+TGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG
+VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDA
+VAHAVAQRQRLLVEPRRLMIDGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRE
+LAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCWMPLTPEKLIGDLLTREDLLR
+AAAPWLSDAEVGALLRPADAPWTEADVPLLDEAAELLGRLDTPGRGGESAAQHERNLENA
+RASLENMHQTLADLGVDGVVDAEQLAAANEARGVRRTTAETAAHDRTWTYGHVVVDEAQE
+LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSP
+ARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGDVAALALDAVEAERDRVPEAL
+TAVIAPAERTGELLTALRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVLPERI
+VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE
+>1_1118
+MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFAS
+LYEDRLAQLYAVDDRLVFGRLDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAG
+AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLGEDGVRADAQGALLAAVTARR
+TGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG
+VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDA
+VAHAVAQRQRLLVEPRRLMIDGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRE
+LAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCWMPLTPEKLIGDLLTREDLLR
+AAAPWLSDVEVGALLRPADAPWTEADVPLLDEAAELLGRLETPGRGGESAAQHERNLENA
+RASLENMHQTLADLGVDGVVDAEQLAAANETRGVRRTTAETAAHDRTWTYGHVVVDEAQE
+LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSP
+ARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGDVAALALEAVEVERDRVPEAL
+TAVIAPAGRTGELLTVLRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVSPERI
+VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE
+>2_1444
+MTDAVSVRQSELELERARVAERYARLDALREEKERQLAAVRRTGLEGSLQNHSERDAFAS
+LYEDRLAQLLAVDDRLVFGRLDLDPERAGDPDEERYIGRIGLTTEEHERLLVDWRAAEAG
+AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDVLDPDLLGQEGVRADAQGALLAAVTARR
+TGRMGDIVATIQAEQDEVIRAPLAGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG
+VLIVGPSTAFMRYIERVLPSLGETGVVMASLGTLMPGVQAGPERDLDAAAVKGRLEMAQV
+IAHAVAQRQRLLAQPRRLMIEGTAVKLKPAAVRRARDRARATGKPHNEARVTFVKILVRE
+LAEKLSKKLEKSSGAPVQRDLLLEDVRTSRDVRVALNLCWMPLTPQKLVGDLLTREHLLR
+AAAPWLSDGEVGALLRPADAPWTEADVPLLDEAAELLGRLEAPAKGGESAAQHERNLENA
+RASLENMHQTLADMGVDGVVDAEQLAAANEARAVRRTTAETAAHDRTWTYGHVVVDEAQE
+LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLEPEFGDRWRLEELTVNYRSP
+ARVMRWASQVAQAAGLEVSRPRAVREGEHAPRLTVRPGADLVALTLDAVAGERDRVPEGL
+VAVITAAAHAPELLAALRERWGRARVDTAPLPGVEIVVATPWETKGLEFDAVVLAAPERL
+VDDARGVVGDLYVAMTRATQSLSVVSTAAVAALPAGLADPPA
+>3_1351
+MTDTVSSRQAELELERERVAVRYARLDALRAEKEEQLARVRRSGLQGSVQNHSERDAFAS
+LYEDRLAQLYAVDERLVFGRLDLDADDAGDVEQRYIGRIGLTDEGQERLLVDWRAQEAGA
+FYQATAARRLGVGRRRHLLLRGREVRDFEDDVLDPSLIAEGAAGAQSQGALLAAVTARRT
+GRMGDIVATIQAEQDEVIRADTSGALVVQGGPGTGKTAVALHRAAYLLYTHRDRLAKSGV
+LVVGPSNAFMRYIERVLPSLGETGVVMASLGTLMPGVQAGPDRSARAAELKGRLEMADVV
+AAAVAQRQRLIPETRRLEIEGTVVKLKPAMVRRARDRARATGKPHNEARTTFVKILVREL
+AEKLRKKLEKSSGVPVQRDLLLEDVRTARDVRVALNLCWMPLTPQKLVGDLLTKEHLLRA
+AAPGLSDGDVAALLRTDPDAWVESDVPLLDEAAELLGELEEPHRPGESEAQHRRNVENAQ
+ASLENMHQTLAELGVDGVVDAEQLAAANEVRAVRRTTAEQAAHDRTWTFGHVVVDEAQEL
+SPMQWRLLARRCPLKSFTVVGDIAQASRRGGARSWKDVLGPEFGDRMRLEELTVNYRSPA
+RITRWAAQVAQAAGLEISSPEAVREGEHEPLLTVEPGADPTRLAQRVVEAERGRVGDGLV
+AVIVPADDAAEHLTHLQDRWGSLVDRAPAPGVEVVVVTARETKGLEFDAVVLVSPERIVA
+DADGVVGDLYVAMTRCTQSISVVSGAAEEELPAGLMPVPA
+>4_1326
+MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFAS
+LYEDRLAQLYAVDDRLVFGRLDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAG
+AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLGEDGVRADAQGALLAAVTARR
+TGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG
+VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDA
+VAHAVAQRQRLLVEPRRLMIDGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRE
+LAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCWMPLTPEKLIGDLLTREDLLR
+AAAPWLSDAEVGTLLRPADAPWTEADVPLLDEAAELLGRLETPGRGGEFAAQHERNLENA
+RASLENMHQTLADLGVDGVVDAEQLAAANEARGVRRTTAETAAHDRTWTYGHVVVDEAQE
+LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSP
+ARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGDVAALALDAVEVERDRVPEAL
+TAVIAPAGRTGELLTVLRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVSPERI
+VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001181.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001181.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6cba34504a5cc052359dcea29c54ed59d0f743fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001181.fa
@@ -0,0 +1,40 @@
+>0_1379
+MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAQRNDLPIVTTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFERGVPTALDGRALSPLEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+HVDQRWTELVYDGQWYSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIFGLSAKTASEREQRLRGSDDLQDVARLSND
+>1_1120
+MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADAREEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAERNDLPIVTTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFERGVPTALDGRALSPLEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+QVDQRWTELVYDGQWYSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIFGLSAKTASEREQRLRGGDDLQDVARLSND
+>2_1442
+MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTRDKAIDYAERNELPIVTTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFSPAPDVVTIAFERGVPTALDGRALSSLEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+TVDQRWTELVYDGQWFSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIFGLSAKTASERDQRLRGGDDLKDVARLANS
+>3_1349
+MKDRIVLAYSGGLDTSVAIGWIGEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAERNELPIATTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFEQGVPTALDGRALSALEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+QVDQRWTELVYDGQWFSPLKKSLDTFIDDTQKHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIYGLSAKTASEREQRLGGAADLADVARLSND
+>4_1328
+MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAERNDLPIVTTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFERGVPTALDGRALSPLEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+HVDQRWTELVYDGQWYSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIFGLSAKTASEREQRLRGGDDLQDVARLSND
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001182.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001182.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea93726e2591830c727b3c4b20f4e41c5e903476
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001182.fa
@@ -0,0 +1,33 @@
+>0_1380
+MDTMTLFTTSATRSRRATASIVAGMTLAGAAAVGFSAPAQAATVDTWDRLAECESSGTWD
+INTGNGFYGGVQFTLSSWQAVGGEGYPHQASKAEQIKRAEILQDLQGWGAWPLCSQKLGL
+TQADADAGDVDAAPVAVERTATVQRQSAADETAADQAAAEQAAADQAAAEQAAADQAAAE
+RWAAKQAAADQAAAERWAAKQAAAEQAAADKAAAQRAAAAEKAAAQKAAAAEKAAAQKAA
+AAEKAAAQKAAAAEQAAAAEQAVVAEAETIVVKSGDSLWKLANEYEVEGGWTALYEANKG
+AVSDAAVIYVGQELVLPQA
+>1_1121
+MDTMTLFTTSATRSRRATASIVAGMTLAGAAAVGFSAPAQAATVDTWDRLAECESNGTWD
+INTGNGFYGGVQFTLSSWQAVGGEGYPHQASKAEQIKRAEILQDLQGWGAWPLCSQKLGL
+TQADADAGDVDATEAAPVAVERTATVQRQSAADEAAAEQAAAEQAAADQAAAERWAAEQA
+AADQAAAERWAAEQAAAEQAAAERWAAKQAAAEQAAADKAAAQRAAAAEKAAAQKAAAAE
+KPAAQKAAAAEKAAAQKAAAAEQAAAAEQAVVAEAETIVVKSGDSLWKLANEYEVEGGWT
+ALYEANKGAVSDAAVIYVGQELVLPQA
+>2_1441
+MDTMTLFTSTRTRRTTASVAAGMTLMGAAAVGFSAPAQAATEETWDAIAFCESTNRWDIN
+TGNGFYGGLQFTLSSWQGVGGQGYPHQASKAEQIKRAEMLQDLQGWGAWPKCAAGLTQAD
+ADATDAAPVAVERTSSVQRQAAAEQAAAEEAAAEQAAAEEAAAEQAAAEQWAAEQAAAEQ
+AAAERAEAKRAAAAEKAAAKKAAAAERAAAHQAAAEQAVVAEAETIVVKAGDSLWKLAAE
+HEVEGGWTALYEANKDTVSDAAMIYVGQELVLPQA
+>3_1348
+MTFFTTSSRRATATALTGMTLVGAAAAFAAPAQAASVETWDKIAACESNGNWAINTGNGY
+YGGLQFSLTSWRGVGGTGYPHEASKAEQIKRAEILQDMQGWRAWPVCSVKAGLSGADTAP
+DAYSTTPVQRQSTQASASAAQDWAAEQSAAEQRAAEKAAAQRAAAAAHTPKSVLKAAEKA
+NTENATELAAAEDTVFVKPGDSLWKIAKTHKVAGGWKALHEANKDIIEDASVIYVGQELV
+LPTA
+>4_1329
+MDTMTLFTTSATRSRRATASIVAGMTLAGAAAVGFSALAQAATVDTWDRLAECESNGTWD
+INTGNGFYGGVQFTLSSWQAVGGEGYPHQASKAEQIKRAEILQDLQGWGAWPLCSQKLGL
+TQADADAGDVDATEAAPVAVERTATVQRQSAADEAAAEQAAAEQAAADQAAAERWAAEQA
+AADQAAAERWAAEQAAADQAAAERWAAEQAAAEQAAADKAAAQRAAAAEKAAAQKAAAAE
+KAAAQKAAAAEQAAAAEQAVVAEAETIVVKSGDSLWKLANEYEVEGGWTALYEANKGAVS
+DAAVIYVGQELVLPQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001188.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001188.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09b978f6b08d3e34f787f0f5b1fba0cea92f632e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001188.fa
@@ -0,0 +1,35 @@
+>0_1386
+MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE
+TTAEVLAGHDVVILALPHGASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH
+AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT
+SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMPR
+GILATATARLRPGVAAADVRAAWAAAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD
+ERAGRVIVCAVLDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP
+>1_1127
+MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE
+TTADVLAGHDVVILALPHEASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH
+AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT
+SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMSR
+GILATATARLRPGVAAADVRAAWAAAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD
+ERAGRVIVCAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP
+>2_1434
+MTHTVAVSGASGYAGGEALRLLAGHPDVAVGAITAHSNAGERLGALQPHLHSLADRVLEE
+TTADVLAGHDVVILALPHGASGALAAQIAERSPETLVIDAGADHRLESAADWEAFYGSEH
+AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT
+SGAGKAAKPHLLGSEVMGGMSPYGVGGGHRHTPEIEQGLSQAAGERVQISFTPTLAPMAR
+GILATATARLRPGADPAAVRGAWERAYADERFVHLLPEGLWPATKSVLGSNHVQMQLAVD
+ERAGRVIVTAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP
+>3_1342
+MTFTVAVSGASGYAGGEVLRLLAGHPEVQIGAISAHSNAGERLGSLQPHLHALADRVLDD
+TTADVLAGHDVVVLALPHGASAAVAAELAERSPRTLVIDAGADHRLESAADWERFYGTDH
+AGTWPYGLPELPGQRERLAGATRIAVPGCYPTTSILALAPGFAAGLLETRDVVIVAASGT
+SGAGRAAKPHLLGSEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVQISFTPTLAPMPR
+GILATATARLKEGVTADRVRAAWEDAYGPERFVHLLPEGQWPTTKAVVGSNHVVMQLAVD
+PHAGRVIVTAALDNLTKGTAGGALQSMNIALGLPEQLGLEIQGVAP
+>4_1335
+MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE
+TTAEVLAGHDVVILALPHGASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH
+AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT
+SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMSR
+GILATATARLRPGVAAADVRDAWAEAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD
+ERAGRVIVCAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001204.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001204.fa
new file mode 100644
index 0000000000000000000000000000000000000000..437e0d9cd8e326e8f2829e49aed3f8f9eff2f6c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001204.fa
@@ -0,0 +1,15 @@
+>0_1406
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS
+>1_1147
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS
+>2_1416
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS
+>3_1319
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRTCEVIDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS
+>4_1355
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001206.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001206.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a9d985829e412c845f8eb4d82e569be3055ee3e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001206.fa
@@ -0,0 +1,51 @@
+>0_1408
+MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDLAELLAIARSGLVDAVLVAGDTESLT
+AAFLEETARLPRPVGVAALSEVRTERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEG
+RRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPGLTDPWRGADEPDDAGPGAAPAA
+ATPDGGPATADEGADPAPSPEEGEPAGPARESLVTVVWGPTGAPGRTTVAVNLAAEHAVA
+GRNTLLIDLDTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADL
+TVLTGLTRVDRWPELRPAAVSALIAAARERWDRVVVDVGFGLEQDEELSFDVPAPQRNGA
+TLAALAAADEVIAVGGPDAVALPRLVRGVEELAEVAPAARLRVVVNRLRPAAAGVAPRGQ
+VEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPA
+RRGRHRARPSQTIAAVSSDAARDATDTGRPARRRTLIPWSVRSRRTP
+>1_1149
+MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDIAELLAIARSGLVDAVLVAGDTESLT
+AAFLEETARLPRPVGVAALSEVRAERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEG
+RRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPGLTDPWRDADEPDDAGPGAAPAA
+ATPDDGPATAGEGADPAPSPEEGEPTAPARESLVTVVWGPTGAPGRTTVAVNLAAEHAMA
+GRNTLLVDLDTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADL
+TVLTGLTRVDRWPELRPAAVSALIAAAREHWDRVVVDVGFGLEQDEELSFDVPAPQRNGA
+TLAALAAADEVIAVGGPDAVALPRLVRGVEELAEAAPAARLRVVVNRLRPAAAGVAPRGQ
+VEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPA
+RRGRHRARPSQTIAAVSSDAARDATDPGRPARRRTLIPWSVRSRRTP
+>2_1414
+MTVRIALATTVLPGLDHIGPLERHQTRITVVRRAEDLAELLAIARSGLVDAVLVAGATEA
+VTGAFLEELARLPRPVGAAAISEVRAERRRLRALGVPCVRADAGPEPLAAAVVEAALAAA
+DGRRARADAVAEDEGGEDPVDGLDGIELTYGVLDDDPRLGPPLLGGDPERSAVSAARPEA
+GAGDEAVDDGRRGGRAGDDLVPADAAQGGVTRDGVAQDRAQDGFARDDAQDFAAWDADAA
+GRSVPDVDRPDPRDPDGDAAEHAEDRPDVEASGTPGDARVIVVWGPTGAPGRTTVAVNLA
+AEHAVAGRSTLLVDLDTYGPSVGAHLGLTEESAGVARAVRRADHGPLGPADLEAAGVRVR
+VAGAELTVLTGLTRVDRWPELRPSALTSLLAAARGRWERVVVDVGFGLEQDEELSFDVPA
+PQRNGATLAALAAADEVLAVGGPDAVSLPRLVRGTEELVEAAPEARLRVVVNRLRPAAAG
+VSPRSQVEAVWSRYASAGIPLAAFLPWDPAAADRALLGGQVLAEAAPNSALRRALAELAD
+VDPRGARRTGRRRRPTGQGPAGAARRHPQDEGAARPSRRRTLMPWSARSRRTP
+>3_1317
+MRVALATTLMPGRDHVGPLEQAQAEVTVVRRAEDLAELLAAARSGLVDAVLVAGDLSALA
+RGFVDEVREAPRPVAVVAMGEVRAERERVRTLGVPCLSADADPLALAAAVQSAVRARLTG
+ARPELGSETPPADPPAPAPGTPDGGDPEAVRVAAVRDREGTPRLPEPNPVRVDALAASEV
+DALFTEETSPVAAADEAGPASPDAAGPDAVTASPADTAPEDGPEGGPERGRTGRTVAVWG
+PTGAPGRTTVAVNLAAESAVAGLRTLLVDLDTYGPSVGVHLGLTEETAGLARAVHRAERG
+SVTREDLVDAAVRVRVAGGDLDVLTGLTRPDRWPEVRPGALREVLQAARDGWDRVVLDLG
+FCVEEDEELSFDVPAPQRNGATLAGLAAADRVLVVGGADAVAMPRLLRAVEALPAGVEQD
+RVRVVVNRVRPQASGVAPQAQVAGVWERYGPPIPLVAQLPWDPGAADRALLGGQVLAEAA
+PGSALRAAVLELARLDPAVAARTQSAGRGRRPAVRGLRRRLAPWSAPSPRTP
+>4_1357
+MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDIAELLAIARSGLVDAVLVAGDTESLT
+AAFLEETARLPRPVGVAALSEVRAERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEG
+RRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPGLTDPWRDADEPDDAGPGAAPAA
+ATPDDGPATAGEGADPAPSPEEGEPTAPARESLVTVVWGPTGAPGRTTVAVNLAAEHAMA
+GRNTLLVDLDTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADL
+TVLTGLTRVDRWPELRPAAVSALIAAAREHWDRVVVDVGFGLEQDEELSFDVPAPQRNGA
+TLAALAAADEVIAVGGPDAVALPRLVRGVEELAEAAPAARLRVVVNRLRPAAAGVAPRGQ
+VEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPA
+RRGRHRARPSQTIAAVSSDAARDATDPGRPARRRTLIPWSVRSRRTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001211.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001211.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d1f08ce904248ffba99d96e7755ba863f1097989
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001211.fa
@@ -0,0 +1,20 @@
+>0_1413
+MTTLATRPRAASDRRTADTLLHGPAHSPAVLPRGEEIARRARTEQGREELRRVRSLAAVI
+AVACVEVETGRRALRDLSAWLSPEVLDKLTRRMELLGAVAPTGPGRRPSAAVPPRTPKSA
+PRPVGARVCEVAPGRVEASATVLWEGRARAFALRLERRLSRWKVTSVEIG
+>1_1154
+MTALATRPRTASARRTADTLLHGPAHSPAVLPRGEEIARRARTEQGREELRRVRSLAAVI
+AVACVEVETGRRALRDLSAWLSPEVLDKLTRRMELLGAVAPTGPGRRPSAAVPPRTPASA
+PRPVGARVCEVAPGRVEASATVLWEGRARAFALRLERRLSRWKVTSVEIG
+>2_1409
+MIAVACVEVETGRRALRDLSAWLSPEVLDKMTRRMDLLGLAEQDRPRARSAAAGVSRAPA
+AAPRPVGARVCEVAPGRVEASATVLCDGRARAFALRLERRISRWKVTSVEIG
+>3_1312
+MTHSVRADRTMIRTSADRPAHRPAQEDPMTTLAPALAHGPTRPRPVSRTAPSRRDTESAL
+LRGPARRMSAVPTGEDLVRRAEQEDDREELRRLRSLAAVVAVACVETEAGRRPVRDLAGW
+LAPETYEKMCRRVDLLERTGTRPPSGSAPRPVGARVCAVRPGAVEASATVLVAGRARAVA
+LRIERRLSRWKVTHLEIG
+>4_1362
+MTTLATRPRAASDRRTADTLLHGPAHSPAVLPRGEEIARRARTEQGREELRRVRSLAAVI
+AVACVEVETGRRALRDLSAWLSPEVLDKLTRRMELLGAVAPTGPGRRPSAAVPPRTPASA
+PRPVGARVCEVAPGRVEASATVLWEGRARAFALRLERRLSRWKVTSVEIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001212.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001212.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3e822eab92f9ba224065eca4772f1c924dd6854d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001212.fa
@@ -0,0 +1,85 @@
+>0_1414
+MPSIIDRVLKISDNRVLKRMQATVDAVNLLEDDFRALSDAELRAETDTLRARHADGESLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL
+SGRGVHVVTVNDFLASYQADLMGRVFRFLGMQTGVIVAGQTPAVRREQYAADITYGTNNE
+FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA
+RLVRRLEADTDYEVDHKKRTVGILGPGIEKVEDHLGITNLYETQNTTLIQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYEKLAGMTGTAETEAAEFTSTYGLGVVVIPPNRERQRVDRNDVVYKNEKVKFDAV
+VDDIAERHAKGQPVLVGTTSVEKSEYLSTLLAKRGVRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLAQAEAAVED
+AHRAVIEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA
+QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLKYDDVMNRQREAIYTDR
+RSILEGEDLQDRVRRFVEDAVGNIVDAATEEGHATDWDLDQLWRDLAELYPVGISQEDVL
+DEVGGRGRLKAEVLKRELVSDALLAYEDREAQVGSEALREAERRVVLATIGRRWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAAIREDAVRTLFQAQISAAPASTSLP
+GVQDARAVTMAPQISVEGIDAPQQPAQLRFTGPSEDGQSAVTRSGTDSGATVAAGTNRRS
+RRQAERRGRRG
+>1_1155
+MPSIIDRVLKISDNRVLKRMQATVDAVNLLEDDFRALSDAELRAETDTLRARHADGESLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL
+SGRGVHVVTVNDFLASYQADLMGRVFRFLGMQTGVIVAGQTPAVRREQYAADITYGTNNE
+FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA
+RLVRRLEANTDYEVDHKKRTVGILGPGIEKVEDHLGITNLYETQNTTLIQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYEKLAGMTGTAETEAAEFTSTYGLGVVVIPPNREPQRVDRNDVVYKNEKVKFDAV
+VDDIAERHAKGQPVLVGTTSVEKSEYLSTLLAKRGIRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLAEAEAAVED
+AHRAVIEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA
+QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLKYDDVLNRQREAIYTDR
+RSILEGEDLQDRVRRFVEDAVGNIVDAATEEGQATDWDLDQLWRDLAEIYPVGVSQEDVL
+DEVGGRGRLTAEVLKRELVSDALLAYEDREAQVGSEALREAERRVVLATIGRHWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAAIREDAVRTLFQAQISAAPAPTSLP
+GVKDARAVTMAPQISVEGIDAPQQPAQLRFTGPSEDGQSAVTRSGTDSGATVAAGTNRRS
+RRQAERRGRRG
+>2_1408
+MPSIIDRVLKISDNRVLRRMQGTVDAVNLLEEDFRALSDAELRAETDTLKARHADGESLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL
+TGRGVHVITVNDFLASYQAELMGRVFRFLGMETGVVVAGQLPAVRREQYAADITYGTNNE
+FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA
+RLVRRLEEGSDYEVDHKKRTVGVLGPGIEKVEDHLGIANLYETQNTTLIQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYDKLAGMTGTAETEAAEFTSTYGLGVVVIPPNRERQRVDRNDVVYKNEKVKFDAV
+VEDIAERHERRQPVLVGTTSVEKSEYLSTLLAKRGIRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPQVLAEAEAAVED
+ANREVLEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA
+QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLKYDDVMNRQREAIYADR
+RSILEGEDLKDRVRRFVEDAVGNIVDATTEEGHAADWDLDQLWRDLSELYPVGITQEDVL
+EEVGGRGRLKAEDLRRELVSDALLAYEDREAQVGSEALREAERRVVLSAIGRRWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAGIREDSVSTLFKAQITAAPAPTSLP
+GIKDARGLTMTPQISVEGVEAPQRPSQLRFTGPSEDGQGAVTRAGTETGATVEAGTNRRS
+RREAERRERRS
+>3_1311
+MPSIIDRVLKISDNRVLKRMRGTVDAVNLLEDDFRALSDAELRAETDSFKKRLADGETLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGLALHQGNIAEMKTGEGKTLVATAPAYLNAL
+TGKGVHVVTVNDFLASYQADLMGRVYRFLGMETGVIVSGQDPATRRAQYAADITYGTNNE
+FGFDFLRDNMAWSKEELVQRGHHFAIVDEVDSILIDEARTPLIISGPAQGDISRWYGEFA
+RLVRSLERGTDYEVDEKKRTVGVLEPGIEKVEDHLGIANLYESQNTTLVQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLAGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYEKLSGMTGTAETEAAEFTSTYGLGVVVIPPNREKQRVDRNDLVYKNEKVKFDAV
+VKDIAERHATGQPVLVGTTSVEKSEYLSTLLTKAGVRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLEQAEAAVQD
+AREKVREAGGLYVLGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDDLMRNFNPGAA
+QRIMNSASIPDDMALEFKMVSSAIQNAQSQVEGRNAEQRKNVLKYDDVMNRQREAIYADR
+RAILEGDSLGERVRGFVEDAVGAVVDAATEEGAPVDWDLEKLWETLREVYPVGISPEDVL
+EQVGGRGRLKAADLKRELVSDALLAYDDREAQVGSEALREAERRVVLAMIGRHWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGFTMFQAMLAAIKEDSARTLFHAQIAAAPAPTQLP
+GVKDARAMTMVPQISVEGVETPRQPARLHLSGPSEDGEGVEEKDLAADGAQTPAGANRAS
+RRAEARRRRRGED
+>4_1363
+MPSIIDRVLKISDHRVLKRMQATVDAVNLLEDDFRALSDAELRAETDALRARHADGESLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL
+SGRGVHVVTVNDFLASYQADLMGRVFRFLGMQTGVIVAGQTPAVRREQYAADITYGTNNE
+FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA
+RLVRRLEADTDYEVDHKKRTVGILGPGIEKVEDHLGITNLYETQNTTLIQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYEKLAGMTGTAETEAAEFTSTYGLGVVVIPPNRERQRVDRNDVVYKNEKVKFDAV
+VDDIAERHAKGQPVLVGTTSVEKSEYLSTLLAKRGVRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLAEAEAAVED
+AHRAVIEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA
+QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLQYDDVMNRQREAIYTDR
+RSILEGEDLQDRVRRFVEDAVGNIVDAATEEGHATDWDLDQLWRDLAELYPVGISQEDVL
+DEVGGRGRLKAEVLKRELVSDALLAYEDREAQVGSEALREAERRVVLATIGRRWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAAIREDAVRTLFQAQISAAPAPTSLP
+GVKDARAVTMAPQISVEGIDAPQQPAQLRFTGPSEDGQSAVTRSGTDSGATVAAGTNRRS
+RRQAERRGRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001213.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001213.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c75794b5bb233e192017da30a1cdfc2d1e8f897c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001213.fa
@@ -0,0 +1,25 @@
+>0_1415
+MTMDVSYIARNLRLPESFRDHVVERTERLQPLAEGADTLEVRVTKSSHHKHSDETVRVEL
+TVRGPRDVVRAEADADDKLVAFDQAATRLAERLRRLRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPSGAALAAEEAAEQDAPEVGTPVRIRQKAFPATPMSVDEAVDAMELVGHDFFLFQN
+AETGVPSVVYRRRGWSYGVIRLDESLPQDHVSASEGERAYQARED
+>1_1156
+MTMDVSYIARNLRLPESFRDHVVERTERLQPLAEGADTLEVRVTKSSHHKHSDETVRVEL
+TVRGPRDVVRAEADADDKLVAFDQAATRLAERLRRMRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPSGAALAAEEAAEQDAPEVGTPVRIRQKAFPATPMSVDEAVDAMELVGHDFFLFQN
+AETGVPSVVYRRRGWSYGVIRLDESLPQDHVSASEGERAYQARED
+>2_1407
+MTMDVSYIARNLSLPESFRDHVAERTERLHTLAEGAETLEVRVTKSSHHKHSDETVRVEL
+TARGPREVVRAEADADDKQVAFDMAVTRLAERLRRMRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPNGAQMAAEDAAREQDIPEEGTPVRIREKAFPATPMTVDEAVDAMELVGHDFFLFQ
+NSETGVPSVVYRRRGWSYGVIRLDESLPADHVSATEGERAYQAREA
+>3_1309
+MTLDVSYIARGITLSDRFREHVEERLEKIEPLAEGAETLEVKVSRSSHHRHSDEGMRVEL
+TLRGAREVVRAEGDADDKAAAFDAALSRIAERLRRMRDRRKDRRHGKGSAASRGAGEIPF
+VPPLPAVGQADAPADEAPESGTPVSIRAKRFPATPMSVDRAVDAMELVGHDFYLFQDETT
+GVPSVVYRRRGWSYGVISLDESLPAHHVAPVEGERVYQASREADAE
+>4_1364
+MTMDVSYIARNISLSESFRDHVVERTERLQPLAEGADTLEVRVTKSSHHKHSDETVRVEL
+TVRGPRDVVRAEADADDKLVAFDQAATRLAERLRRMRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPSGAALAAEEAAEQDAPEVGTPVRIRQKAFPATPMSVDEAVDAMELVGHDFFLFQN
+AETGVPSVVYRRRGWSYGVIRLDESLPQDHVSASEGERAYQARED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001216.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001216.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9333b178e3c743560f5659684b580c7a3a92b9d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001216.fa
@@ -0,0 +1,25 @@
+>0_1419
+MGKAKILVVDDDEALAEMIGIVLRNDGFEPAFAADGTSALPAFHRERPDLVLLDLMLPGI
+DGIEVCRLIRDESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLHIGDLEIDVAGHEVTRGGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG
+>1_1160
+MGKAKILVVDDDEALAEMIGIVLRNDGFEPTFAADGTSALPAFHRERPDLVLLDLMLPGI
+DGIEVCKLIRAESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLHIGDLEIDVAGHQVTRAGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG
+>2_1403
+MSRAKILVVDDDEALAEMIGIVLRNDGFEAAFAADGTAALPAFHRERPDLVLLDLMLPGM
+DGIEVCKLLRSESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLQIGDLEIDVAGHQVTRDGAAISLTPLEFDLLVALARRPRQVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG
+>3_1305
+MSKARILVVDDDEALAEMIGIVLRNDDFEPSFAVDGTSALPAFRSARPDLVLLDLMLPGI
+DGIEVCKQIRAESDVPIIMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEQRPAEALAIGDVRIDVAGHQVSRGGAPISLTPLEFDLLVALARKPRQVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRAKVEPDPENPTVVLTVRGVGYKAGQV
+>4_1368
+MGKAKILVVDDDEALAEMIGIVLRNDGFEPAFAADGTSALPAFHRERPDLVLLDLMLPGI
+DGIEVCRLIRDESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLHIGDLEIDVAGHEVTRGGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001217.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001217.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba5c65902409048fd852569d2811e62eb8abc8c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001217.fa
@@ -0,0 +1,40 @@
+>0_1420
+MTEAAHDDGATGPVALGGTPWRGTDVAEAQRVTLGELGADHWPVLPELPDRGPGADATGR
+SAALLQQLAVDLQPHGWRVSPPGAAGSGRDRRRAVSLWREDAHRWADTAGAEGAVVERLA
+VRVRGPLSLLACLWLPGGERVLGDHGARRDVAESYLEGLQDALPRLRRATGAGRLGVVVD
+EPWAAAVLAGTLPTASGYRTVRSLPREEARGLWRAALDGLTALPDVARVWLAPGRRAASP
+GAELPGPAALSTLTGESLPRPDAAADAPAPAPVSLVVGVGALDDGADGTPGTREAWEAAA
+GWADIGRGLTLAPEPGVRPVEVVRTWERLGVDPGRVGDVGLTAAGLHDPVVLHTLRRDAE
+ELTARLAELRG
+>1_1161
+MTEAAHDDGATGPVALGGTPWRGTDVAEAQRVTLGELGADHWPVLPELPDRGPGADATGR
+SAALLQELAVDLQPHGWRVSPPGAAGSGRDRRRAVSLWHEDAHRWADTAGAEGAVVERLA
+VRVRGPLSLLAGLWLPGGERVLGDHGARRDVAESYLEGLQDALPRLRRATGAGRLGVVVD
+EPWAAAVLAGTLPTASGYRTVRSLPREEARGLWRAALDGLTALPDVARVWLAPGRRAASP
+GAELPGPAALATLTGESLPRPDAAADAPVPAPVSLVVGVGALDDGADGTPGTREAWEAAA
+GWADIGRGLTLAPEPGVRPVDVVRTWERLGVDPGRVGDVGLTAAGSHDPAVLRTLRRDAE
+ELTARLAELRG
+>2_1402
+MPEAHDDGARPVALGGSPWAGTDAAEAQRVTLGELGAEHWPVLPELPSRGPGADATGRSA
+ALLSELAVDLQPHGWRVSPPGAAGSGMDRRRAASFWREDAHRWADTAGAEGAVVERLAVR
+VRGPLSLLGGLWLPGGERVLADHGARRDVAASYLEGLLEAVPRLRAATGAAGLGLLVDEP
+WAAAVLAGALPTASGYRTVRSLPRDEARGLWRELLAGLTALPGVASVWLAPGRRTASAAD
+VPATAELAALAGECLPAAGGEDDDAGAPVRLVVPVGDLDDGPDGTAGTRAAWESAAGWAD
+AGRGLTLSPAAHLRPADVVTTWERLGADPAHLRGTGLTAPGRHDATVLRRLRTDAAELAA
+RLDDALG
+>3_1304
+MPEASDDVGAVRVAALGGAPWRGTDAAEAQLATLGELGAEHWPVLPELPDRGPGADATGR
+SAALLHELAVDLQPHGWRVSPPGVVGSGMDRRRAASFWREDAHRWADTAGAEGAVVERLG
+VRLRGPLSLLGSLWLPGGERVLVDHGARRDVAASYVEGLRDAVPRLAAATGARTLGVVLD
+EPWAAAVLAGALPTASGYRTVRSVPRDEVRALWRDALAALADLPGVGRVWLAPGRRSAGV
+DVPLPDVSALAALAGESLPAAAPSADDDAPAPTRVDLVVPVGALDPGPDGTGGTRAGWET
+AAGWTDAGRGLTLSTATGVRPADVARTWERLGADPGHLAGVGLTVPGPHDAAVLGRLRAD
+AEELAARVGELLG
+>4_1369
+MTEAAHDDGATGPVALGGTPWRGTDVAEAQRVTLGELGADHWPVLPELPERGPGADATGR
+SAALLQELAVDLQPHGWRVSPPGAAGSGRDRRRAVSLWREDAHRWADTAGAEGAVVERLA
+VRVRGPLSLLAGLWLPGGERVLGDHGARRDVAESYLEGLQDALPRLRRATGAARLGVVVD
+EPWAGAVLAGTLPTASGYRTVRSLPREEARGLWRAALARLTALPDVARVWLAPGRRAASP
+GAELPGPAALATLTGESLPRPDAAADAPARAPVSLVVGVGPLDDGADGSPGTREAWEAAA
+GWADVGRGLTLAPEPGVRPVDVVRTWERLGVDPGRVGDVGLTAAGPHDPAVLRTLRRDAE
+ELAARLAELRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001218.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001218.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d900b8c0dfe41846e2217e125adf20af27bd255c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001218.fa
@@ -0,0 +1,20 @@
+>0_1421
+MSPDYDPHASSLPGTADPAVLDELFAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHD
+LPPSDPGREAAQIARLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALAAEGRPDAEAEP
+GESPGDADD
+>1_1162
+MSPDYDPHASSLPGTADPAVLDELFAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHD
+LPPSDPGREAAQIARLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALAAEGRPDAEAEP
+GESPGDADD
+>2_1401
+MSPDYDPHASSLTGRTDPEVLAELYAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHE
+LPPSDPGREAAQIERLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALASGAGPEAPAGD
+PAADSLPDGTRTDAGDDPRRGGADA
+>3_1303
+MSHDYDPHASSLAGTADQDILEELYEIRGSIDNIDASLVYLLAERFKFTQRVGRLKARHA
+LPPSDPGREAAQIERLQDLARDADLEPEFAEKFLNFIIAEVIRHHRAIAEDEAPVARPAE
+ASDAGSADA
+>4_1370
+MSPDYDPHASSLPGTADPAVLDELFAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHD
+LPPSDPGREAAQIARLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALAAEGRPDAEAEP
+GAGSGDADD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001220.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001220.fa
new file mode 100644
index 0000000000000000000000000000000000000000..50d5f15132aa3fa0084fe6dc2e24ba6aece39212
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001220.fa
@@ -0,0 +1,41 @@
+>0_1423
+MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLRLEEARERIAAAL
+GAHPTEVILTSGGTEADNLAIQGLYRARRAAAPERTRIVLTGIEHHAVLDVVDWLAAHEG
+AEPVLVPVDDDGRVDLAAWGAALATAPERTALATLMWANNEIGTVQPVAEAARLAADHGV
+PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALLVRRDVTLEAVVHGGGQER
+RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP
+ATGQALSPGTRRLPGNVHITVPGRTADALLFSFDMAGLDTSSGSACTAGVAEPSHVVAAL
+PGRTEADARATQRFTLGRTTTPAEAAALIDALRTLLGPGV
+>1_1164
+MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLHLEEARERIAAAL
+GAHPPEVILTSGGTEADNLAVQGLYRARRAVAPERTRIVLTGIEHHAVLDVVDWLAAHEG
+AEPVLVPVDDDGRVDLAAWGAALAAAPERTALATLMWANNEIGTVQPVAEAARLAADHGI
+PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALFVRRDVTLEAVVHGGGQER
+RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP
+ATGEPLPPGTRRLPGNVHITVPGRTADALLFSFDMAGLDTSSGSACTAGVAEPSHVVAAL
+PGRTEADARATQRFALGRTTTPAEAAALIDALRTLLGPGV
+>2_1399
+MPSAATPRPLGERVHLDHAATTAVRPSALAALAEAAALPGNPASLHASGRRAKLALEQAR
+EAVAAALGAHPSEVVLTSGGTEADNLAVQGLFRARRAADPQRLRIVLTGAEHHAVLDAVD
+WLAAHEGAEPVIVPVDADGVVDLAAWEAALAAAPERTALAALMWANNEIGTVQPVAEAAR
+IAAAHGVPLHTDAVQAVGAVPVDFAASGAATLAVSGHKAGAPVGVGALLVRRDVALTPVV
+HGGGQERRLRSGTVSVALAAALAAALTEAVAEQPAEAVRLGVLRDRVIEAVEALETVVLT
+GPRDADPATGEPLPPGTRRLPGNVHVTVPGRTADALLFTFDTAGLDTSSGSACTAGVAEP
+SHVVAALPGRTEADARATQRFTLGRTSTSADVDALIAALRALAPAPRRGAPTPKGAPTTK
+EESR
+>3_1301
+MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLHLEEARERIAAAL
+GAHPTEVILTSGGTEADNLAVQGLYRARRAAAPERTRIVLTGIEHHAVLDVVGWLAAHEG
+AEPVLVPVDDDGRVDLAAWGAALAAAPERTALATLMWANNEIGTVQPVAEAARLAADHGV
+PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALLVRRDVTLEAVVHGGGQER
+RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP
+ATGEPLPPGTRRLPGNVHITVPGRTADALLFFFDMAGLDTSSGSACTAGVAEPSHVVAAL
+PGRTEADARATQRFTLGRTTTPAEAAALIDGLRTLLGPASRLDRPSVVERGVRP
+>4_1372
+MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLHLEEARERIAAAL
+GAHPSEVILTSGGTEADNLAVQGLYRARRAVAPERTRIVLTGIEHHAVLDVVDWLAAHEG
+AEPVLVPVDDDGRVDLAAWGAALAAAPERTALATLMWANNEIGTVQPVAEAARLAADHGI
+PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALFVRRDVTLEAVVHGGGQER
+RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP
+ATGEPLPPGTRRLPGNVHITVPGRTADALLFSFDMAGLDTSSGSACTAGVAEPSHVVAAL
+PGRTEADARATQRFALGRTTTPAEAAALIDALRTLLGPGV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001222.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001222.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b9631ea9d388e575943ff82534630463ffe68c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001222.fa
@@ -0,0 +1,30 @@
+>0_1427
+MRRLTETGPGLDDDALRTALAAPAAEDTGPGPWVRVVFIASADGAATLDGRAGGLGSPAD
+QRLLSLSRHDADVVLVGAGTIRAEGYEGALLSEEDRRRRAEAGGPADPPVAVVSGSLDLD
+PASAFFTAAPVRPWILTSRAALAAEPERAAALAARADVLAVGEEHVDPQTVVATLHARGA
+RVVHCEGGPRLFGSLAAAGLVDEVHLTVAPLLAGPAAGRVLTGEDGPGLPARLQLVQVLH
+DDGMLFLRLHHERHASPGPDPTP
+>1_1168
+MRRLTETGPGLDDDALRTALAAPAAEDTGPGPWVRVVFIASADGAATLDGRAGGLGSPAD
+QRLLSLSRHDADVVLVGAGTIRAEGYEGALLSEEDRRRRAEAGGPADPPVAVVSGSLDLD
+PASAFFTAAPVRPWILTSRAALAAEPERAAALAARADVLAVGEEHVDPQTVVATLHARGA
+RVVHCEGGPRLFGSLAAAGLVDEVHLTVAPLLAGPAAGRVLTGEDGPGLPARLQLVQVLH
+DDGMLFLRLHHERHASPGPDPTP
+>2_1397
+MRRLAAVGPELSDEDLLALRRAPSTQDAPGPWVRAVFVSSLDGATALDGRSGTLGSPADR
+RQFALARTDADVILVGAGTVRAEGYAGPLVDAAARARRAARGLPEHPAVAVVTGSLDLDP
+DGEFFRAAPVRPWVIASERAVAAQPERAAALAEVADVLTAGVRDVEPRELLALLAGRGAR
+VVHCEGGPTLLGALAAAGAVDELLLTLSSLLAGGAGPRLIPAVEGIGLPARMLPHHVLTQ
+DGDLYLRLLHERHAALLADAPGLDGRAGTGR
+>3_1297
+MRLLTATGPEIDDDALLALRRAPAPDLVPGPWVRAVFVSSLDGAATLDGRAGGLGSPADQ
+RQFTLARTDADVVLVGAGTVRAEGYEGPLVGPAARARREEAGLPAHPGIAVVSGALGLDP
+DGDFLRQAPVRPLILTTQTALERCPDRAEALAARADVVASGAEVVEAPALVDALTARGHR
+VLHCEGGPRLFGTLAAADLVDELLLTISPLLAGGDGPRVLSGGDGPGLPTRLRPHHVLTE
+DGELYLRLVHERHAAVLAEAPGLEADPADADPAPGAP
+>4_1376
+MRRLTETGPGLDDDALRTALAAPAAEDTGPGPWVRVVFIASADGAATLDGRAGGLGSPAD
+QRLLSLSRHDADVVLVGAGTIRAEGYEGALLSEEDRRRRAEAGGPADPPVAVVSGSLDLD
+PASAFFTAAPVRPWILTSRAALAAEPERAAALAARADVLAVGEEHVDPQTVVATLHARGA
+RVVHCEGGPRLFGSLAAAGLVDEVHLTVAPLLAGPAAGRVLTGEDGPGLPARLQLVQVLH
+DDGMLFLRLHHERHASPGPDPTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001225.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001225.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e236043c09b6e767509ff4246ebd225f94835cf2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001225.fa
@@ -0,0 +1,47 @@
+>0_1430
+MQTPDASEPHADRPDDAGQPALDTLLRRSAEGDRAAFSAFYDATVPWVHGLAEAMFGPGD
+DAAAATVRTYLTAWEEASEAGLDLSEQDDATHRERQVFTWLEVLAHRVMTSLRRAGGSAA
+ERGRRPGPAGPAALPEDLMDRVDPDAFEAVRLAWLGGCTDREVADRLDLPADRARTLLRD
+GVRQVVAARRDITQDAARPSAPAPATGPALGADVREDVDAGRALELADLSAVHALDTAGH
+TAAFSAVQRRGGELARWRSRVDGARQAVAWAFRSVTAEPPSALLDEVLRRLPAQDVGMDL
+IGDESTPAGPPRDRLRWLKVTALLLLAALVLGIGGWTVWSQFTRPGIVHRIDQSKDLFTT
+SEYPAQDGGTVQAFLSREQNSGYLTISGMPQLPEGQSYQLWLYPSDGTAPASLGTYDANG
+FGEPVTFRGLDRFAAMGISVEPSSGSEVPTSEPIVGVDLDPTAQTGPRYGGRPSTN
+>1_1171
+MQTPDASEPHVDRPDDAGQPALDTLLRRSAEGDRAAFSAFYDATVPWVHGLAEAMFGPGD
+DAAAATVRTYLTAWEEASEAGLDLSERDDATHRERQVFTWLEVLAHRVMTSLRRAGGSAA
+ERGRRPGPAGPAPLPEDLVGRVAPDAYEAVRLAWLGGCTDREVADRLGLPADEARTLLRD
+GVRQVVAARRDLTQDAARPSAPAPATGPALGADVREDVDAGRALELADLSAVHALDTAGH
+TAAFSAVQRRGGELARWRSRVDGARQAVAWAFRSVTAEPPSALLDEVLRRLPAQDVGMDL
+IGDESAPAGPPRDRLRWLKVTALLLLAALVLGVGGWTVWSQFTRPGIVHRIDQSKDLFTT
+SEYPAQDGGTVQAFLSREQNSGYLTISGMPQLPEGQSYQLWLYPSDGTAPASLGTYDANG
+FGEPITFRGLDRFAAMGISVEPSSGSEVPTSEPVVGVDLDPTAQTGPRYGGRPSTN
+>2_1394
+MQTPDASEPRADRSAAAGAPALDTLLRRSAEGDRAAFSAFYDATVPWVHGLASAMFRSAD
+DAAEATTLTYLTAWEEASEAGLDLSEHDAASHRERQVFTWLEVLAHRVMTTLLRSDGLPE
+AGHGLLPDRAGPGSAGPAERPEDLDSRVDPAAFEAVRLAWLGGLSDRQVAARMGRPVAES
+RTLLRDGVRQVVEAHRALTRDAADRSPETSARPALATSVREDVEAGHALELADLSAVHAL
+ETAGHTAAVSAVQRRGGDLPRWRSRVDGARQAVAWAFRSVTAEPPSAVLDDVLRRLPAQD
+VGMDLIGEEAAPARPPKDRLRWLKITVMVLLAALVLGVGAWTVWSQFTRPGIVHRVDQSE
+DLFTTSENPARDGGTAQAFLSRDQNSGYVTVSGMPQLPDGQAYQVWLYPDDGTAPASLGT
+FDANGFGEPVTFRGLDRFAAVGITVEPSSGSEVPTTDTLVGVDLDPTAHTGPRYGGRPST
+N
+>3_1294
+MQTPQHPETPGADASTAPQQPSRRGVDELLHASARGDRAAFSAFYDATVPWVHGMATAMF
+RSRRDAAEATAQTYLAAWSEAPEAELDLSDRDAAAARERRVFAWLEVLAHRVMTGLLRTD
+ALPEQGRRLLPERAGLGTGGPTALPATLEGSVSPETHRAVRLAWLGGRTDAQVAEALDVP
+VDRARTLLRDGVQELVAAHRADQGLPAPVAGARPALAATTREDVDAGRGAELADLSALHA
+LDAAGHTAAAAAAQQRGAGELALWRTRVDAGRRAVAWAFRDVVAEPPSDLLDGVLRRLPA
+QDMGLELVEETAAPRGAAERRRGLKTVLLGLLALVVLALGVYAGWSQFSRDGITHRVHGA
+KDLYTTSEYPAAGGGTMQGFLSDSENSGYVTVSGMPQLEDGQTYQVWLYPKDGSAPSSLG
+TYDADGFDDPISFRGLDRFAAVSMTVEPSGGSPEPTADDVLLGLDLDPSNQSGPQYGGMP
+SNN
+>4_1379
+MQTPDASEPHADRPDDAGQPALDTLLRRSAEGDRAAFSAFYDATVPWVHGLAEAMFGPGD
+DAAAATVRTYLTAWEEASEAGLDLSERDDATHRERQVFTWLEVLAHRVMTSLRRAGGSAA
+ERGRRPGPAGPAPLPEDLVDRVAPDAYEAVRLAWLGGCTDREVADRLGLPADQARTLLRD
+GVRQVVAARRDLTQDAARPSAPAPATGPALGADVREDVDAGRALELADLSAVHALDTAGH
+TAAFSAVQRRGGELALWRSRVDGARQAVAWAFRSVTAEPPSALLDEVLRRLPAQDVGMDL
+IGDESAPAGPPRDRLRWLKVTALLLLAALVLGVGGWTVWSQFTRPGIVHRIDQSKDLFTT
+SEYPAQDGGTVQAFLSREQNSGYLTISGMPQLPEGQSYQLWLYPSDGTAPASLGTFDANG
+FGEPVTFRGLDRFAAMGISVEPSSGSEVPTSEPVVGVDLDPTAQTGPRYGGRPSTN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001229.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001229.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6bdb3e1ce53b12a415f0f6e0f1e0325352889a9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001229.fa
@@ -0,0 +1,30 @@
+>0_1434
+MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI
+EDDYREDQDASRSWGQKALAASQKADDFRAKGDTASADKFDNLAKVAIERQMDFERQAKS
+AEPTIASQREIVERLKTGLDQMKVKRQQLVAKRDELTARAKSAHAQSAVADAVKSIDLLD
+PTSEVSRFEEKVRREEARVRGQQEIAASSLDAQFESLEDLGEKTEVEARLAALKAGGAGQ
+AALTSGDVDADETLTLDYAAEGTAEETGTARG
+>1_1175
+MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI
+EDDYREDQDASRSWGQKALAASQKADDFRTKGDTASADKFDNLAKVAIERQMDFERQAKS
+AEPTIASQREIVERLKTGLDQMKVKRQQLVAKRDELTARAKSAHAQSAVADAVKSIDLLD
+PTSEVSRFEEKVRREEARVRGQQEIAASSLDAQFESLEDLGEKTEVEARLAALKAGGAGQ
+AALTSGDVDADETLTLDYAAEGTAEETGTARG
+>2_1390
+MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI
+EDDYREDQDAARSWGQKALAASQKADDFRTKGDAASAEKFDNLAKVAIERQMDSERQAKS
+AEPTITSQREIVERLKTGLDQMKVKRQQLVSKRDELTARAKSAHAQSAVADAVKSIDLLD
+PTSEVSRFEEKVRREEARVRGQQELAASSLDAQFESLEDLGEKTEVEARLAALKSGGAGQ
+SALTAGGSEGSDLALDYGAETTAEQGAEQTRVERG
+>3_1290
+MVKQSILGRITTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMM
+EDDYREDQEAARSWGQKALAASQKADEFRTKGEAANADKFDNLAKVAIERQMDAERQAKT
+AEPTITSQREIVDRLKTGLDQMKVKRQQLVSKRDELTARSRTAEAQTKVNEAVKSIDIMD
+PTSEISRYEEKVRREEARVRGQQELAASSLDAQFESLEDLGEQTEVEARLAALKSGSAPS
+ALTAGSEELTLDYSGAETGTQTGTAERA
+>4_1383
+MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI
+EDDYREDQDASRSWGQKALAASQKADDFRTKGDTASADKFDNLAKVAIERQMDFERQAKS
+AEPTIASQREIVERLKTGLDQMKVKRQQLVAKRDELTARAKSAHAQSAVADAVKSIDLLD
+PTSEVSRFEEKVRREEARVRGQQEIAASSLDAQFESLEDLGEKTEVEARLAALKAGGAGQ
+AALTSGDVDADETLTLDYAAEGTAEETGTARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001241.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001241.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb813f54106e6f9297bbd0524cc81c5eba662135
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001241.fa
@@ -0,0 +1,25 @@
+>0_1469
+MTWHESIRAGFDLETTGRDPRTALIVTATLVMVDEQGRAASSAEWLVDPGVPIPAEAAEV
+HGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARHHGLTPL
+EARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALAARY
+EQLRVAPVDLHERQVRWKAEQAESFEQYLRRKDPQATVSRHWPVEAER
+>1_1188
+MTWHESIRAGFDLETTGRDPRTALIVTATLVMVDEQGRAASSAEWLVDPGVPIPAEAAEV
+HGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGLTPL
+EARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALAAQY
+EQLRVAPADLHERQVRWKAEQAESFEQYLRRKDPQATVSRHWPVDAER
+>2_1377
+MSPVNWHQSIRAGFDLETTGRDPRSALIVTATLVMVDAQGRATASAEWLLDPGVPIPAEA
+AEVHGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGL
+APVEARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALA
+ERHEQLRVDPAELHERQVRWKAEQAESFEEYLRRKDPQATVSRDWPVESGR
+>3_1277
+MSWNEQIRAGFDLETTGRDPRQARIVTATIVMVDAAGKAVSSAEWLLDPGVPIPEEAAAV
+HGVTTERARAEGLEARRGVSEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGVAPL
+EPRPVVDPYVVDKQVDRFRKGKRTLGAVSEHYDVVLEDAHTSAADALAAVQVMDELVRRH
+PKADLPLDELHAAQARWKAEQAESFEEYLRRKDPQATVSRAWPVEPDV
+>4_1396
+MTWHESIRAGFDLETTGRDPRTALIVTATLVMVDEHGRAASSAEWLVDPGVPIPAEAAEV
+HGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGLTPL
+EARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALAARY
+EQLRVAPTDLHERQVRWKAEQAESFEQYLRRKDPQATVSRHWPVEAER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001243.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001243.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6df4ca4a0a2e6e613f1c11834437a429b9d973e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001243.fa
@@ -0,0 +1,35 @@
+>0_1471
+MSFPLHRPRRLRRSAAMRRLAAETRLHPAELILPAFIKEGAAEPVPIASMPGVVQHTADS
+LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRDVKAEVGDGLVVMSDL
+CLDEFTDHGHCGVLTAEGAVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA
+LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALLEVALDLE
+EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV
+LSIRRAGADSVLTYWAAELGRWMKEGSL
+>1_1190
+MSFPLHRPRRLRRSAAMRRLVAETRLHPAELILPAFIKEGAAEPVPIASMPGVVQHTADS
+LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRDVKAEVGDGLVVMSDL
+CLDEFTDHGHCGVLTAEGTVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA
+LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALLEVALDLE
+EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV
+LSIRRAGADSVLTYWAAELGRWMKEGSL
+>2_1375
+MSFPLHRPRRLRRSAAMRRLVAETRLHPAELILPAFIKEGAPEPIAIASMPGVVQHTSDT
+LKAAAAEAAELGLGGIMLFGVPETRDAVGSISLDPEGVLNQAIRDVKSEVGDALVVMSDL
+CLDEFTDHGHCGVLTEDGAVDNDATLEIYAQMGVAQAEAGADVLGPSGMMDGQVRVIREA
+LDAAGHVDTGILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRTEALHEVALDLE
+EGADMVMVKPAMSYLDIVRDVAELADVPVSAYQISGEYAMIEAAAANGWIDRKASIVESV
+LSIRRAGADTVLTYWATELGRWMKEGSL
+>3_1275
+MSFPLNRPRRLRQSAAMRRLVAETRLHPNELILPAFIKEGAAEPVPIASMPGVVQHTTDT
+LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRDVKAEVGDGLVVMSDL
+CLDEFTDHGHCGVLTAEGTVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA
+LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALREVALDLE
+EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV
+LSIRRAGADSVLTYWAAELGRWMKEGSL
+>4_1398
+MSFPLHRPRRLRRSAAMRRLVAETRLHPAELILPAFIKEGAAEPVPIASMPGVVQHTADS
+LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRGVKAEVGDGLVVMSDL
+CLDEFTDHGHCGVLTAEGTVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA
+LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALLEVALDLE
+EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV
+LSIRRAGADSVLTYWAAELGRWMKEGSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001249.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001249.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0568ae68da01b3f331e4f04d57101dd0150a00ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001249.fa
@@ -0,0 +1,45 @@
+>0_1477
+MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDALLLASFGGPE
+GQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAIEAELAARGLD
+LPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDMGMAMEQTGLT
+GKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHSIPTSDAAAAG
+PRGLAADLRAQAGAEPGDEGADVYSAQHLDVAREILAGVPEAADVPWSLVYQSRSGPPSV
+PWLEPDINDAMEHLAGEGAETDAQGRAVAGFVVVPLGFVSDHMEVVWDLDTEAKETAEGL
+GVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRPDCCVKVMRDGS
+TRPTTSAVDAAVRGLAEHEAGAAAPAEEA
+>1_1197
+MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDALLLASFGGPE
+GQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAIEAELAARGLD
+LPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDMGMALEQTGLT
+GKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHSIPTSDAAAAG
+PRGLAADLRAQAGAEPGDEGADVYSAQHLDVAREILAGVPEAADVPWSLVYQSRSGPPSV
+PWLEPDINDAMEHLAGEGAETDAQGRAVAGFIVVPLGFVSDHMEVVWDLDTEAKETAEGL
+GVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRPDCCVKVMRDGS
+TRPTTSAVDAAVRGLAEHEAGAAAPAEEA
+>2_1369
+MSTAPENAAAASPAPEPRADAPVHAGPRAGVAPTLRAPEEAAAGVDFDVCGVMAPKEYDA
+LLLASFGGPEGQDDVIPFLRNVTRGRGIPDERLEEVATHYRANDGVSPINAQNRALKAAI
+EAELAARGLALPVYWGNRNWEPYVPDTLERMHADGHRRILTVTTSAYSCYSSCRQYREDM
+GMALRRTGLEGVVDLDKTRQYFNHPGFIEPFRDGLRADLASLREELGEDARIHVLFATHS
+IPTSDAAAAGPRGLAADLRAQAGAEPGEEGADVYSAQHLDVAREILAGVPEAADVPWSLV
+YQSRSGPPSVPWLEPDINDAMEHLAGEDAEADAAGRAVAGFVVVPLGFVSDHMEVLWDLD
+TEARQTAADLGVAFRRSPTPGTDPRFVSGLVDIVEERMGRREGRASLGCFGAWYDVCRPD
+CCSKVMRDGTVRPTTSAVDADVRGLAEHEAGTAPAGRTEES
+>3_1261
+MTAVPTHRVPEDARRPVHEPERAAAGVDYDACGAMAPKAYDALILASFGGPEGQEDVIPF
+LRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALISAIEAELVRRGLELPVYFGNR
+NWEPYFPDALQRAYDDGHRRILTVTTSAYSCYSSCRQYREDMGLAMERTGLEGKVDLDKT
+RQYFNHPGFVEPFAEGLRADLASLREEVGEDARVHLLFATHSIPTADAAAAGPRGLAAAL
+REQAGGEPGDVEGADAYSAQHLDVIREVLARVPEAEGVDWSLVYQSRSGAPHVPWLEPDI
+NDALEALAGPDAPADADGRALAGVVVVPVGFVSDHMEVVWDLDTEAKDTAAELGVAFRRT
+PTPGTDPRFVSGLVDIVEERLGRREGREAVGCFPAWYDVCRPDCCVKVMRDGSVRPTTSA
+VDAPVRGLAEHRGEQDGADDAGAQDS
+>4_1404
+MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDALLLASFGGPE
+GQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAIEAELAARGLD
+LPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDMGMAMEQTGLT
+GKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHSIPTSDAAAAG
+PRGLAADLRAQAGAEPGDEGADVYSAQHLDVAREILAGVPEAADVPWSLVYQSRSGPPSV
+PWLEPDINDAMEHLAGEGAETDAQGRAVAGFVVVPLGFVSDHMEVVWDLDTEAKETAEGL
+GVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRPDCCVKVMRDGS
+TRPTTSAVDAAVRGLAEHEAGAAAPAEEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001257.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001257.fa
new file mode 100644
index 0000000000000000000000000000000000000000..78b8cf01a9000ad0f4c555f8376d791fd2d64d56
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001257.fa
@@ -0,0 +1,30 @@
+>0_1486
+MAAMARYDLHTHSTESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWAEAAQAARETGL
+TLVPGMEMSCTSADGVSVHVLSYLHDPEDPALLREVGRARDARLTRAQEMVRRLGADFSI
+TWELVQEHAAENATIGRPHLADALVTIGAVPDRSAAFREILAGRSKYYVPHFAPDPAEAV
+ALIRAAGGVPVFAHPRARMRGRVVGDEVFEQMAEAGLAGVEVEHRDNPAEERTWLRAFAD
+RHGLFVTGSSDYHGTGKPNPIGEHTTGAEVLAEIERQGTGTAIIRG
+>1_1206
+MAAMARYDLHTHSTESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWAEAAHAARETGL
+TLVPGMEMSCTSADGVSVHVLSYLHDPEDPALLREVGLARDARLIRAQEMVRRLGADFPI
+TWELVQEHAAENATIGRPHLADALVTIGAVPDRSAAFREILAGRSKYYVPHFAPDPAEAV
+ALIRAAGGVPVFAHPRARMRGRVVGDEVFEQMAEAGLAGVEVEHRDNPAEERTWLRAFAD
+RHGLFVTGSSDYHGTGKPNPIGEHTTGAEVLAEIERQGTGTAIIRG
+>2_1360
+MSRYDLHTHSVESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWEAAAEAALAEGIAFV
+PGMEMSCMAADGTSVHVLSYLHDPADPSLLREIGTARSARLTRAQEMVHRLARDYPITWE
+LVQEHAAEGATIGRPHLADTLVTLGVVEDRSAAFAHILTGRSKYYVPHYAPDPAIAVELI
+RSAGGVPVFAHPRAVTRGRVVGVEVIEEMIDAGLAGLEADHRDNPEEERSWLREVAARHD
+LFVTGSSDYHGTGKPNLLGEFSTGEDVLAEIERQGTGAAVVRG
+>3_1252
+MSTARYDLHTHSTESDGTEPAADVVHAAALAGLDGLALTDHDTTAGWAAAADAARETGLL
+LVPGMEMSCMAADGTSVHLLSYLHDPADPSLLAELGASRDARLTRAQSMTDRLAEDFPIT
+WDLVREHASENATIGRPHIADALVTIGAVPDRSAAFSSILRGGSKYYVPHYAVDPVEAVR
+LVRAAGGVPVFAHPRARLRGRIVGDDVLEAMIEAGLAGLEADHRDNPEQERTWLRETATR
+HGLFVTGSSDYHGAGKPNLIGEFTTGPEVLAEIEHQGTGAAVVRG
+>4_1413
+MAAMARYDLHTHSTESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWAEAAHAARETGL
+TLVPGMEMSCTSADGVSVHVLSYLHDPEDPALLREVGLARDARLIRAQEMVRRLGADFPI
+TWELVQEHAAENATIGRPHLADALVTIGAVPDRSAAFREILAGRSKYYVPHFAPDPAEAV
+ALIRAAGGVPVFAHPRARMRGRVVGDEVFEQMAEAGLAGVEVEHRDNPAEERTWLRAFAD
+RHGLFVTGSSDYHGTGKPNPIGEHTTGAEVLAEIERQGTGTAIIRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001258.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001258.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb85c3225dd328ec41e7cb3ebe759ef08fe21bee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001258.fa
@@ -0,0 +1,50 @@
+>0_1487
+MTDAAQHPAQTTPDQPAATPEAGADGTGAVNPQPLAERVDNRSQRPASNAFRDFMASDWA
+PSSQALPDPDASAPYAARRRAAVSARFPGERIVVPAGRLKVRSNDTDYRFRAHSAFAHLT
+GLGVDHEPDAVLVLEPTDPGAGDDGTDHTATLYFRPLAGRDTEQFYADSRSGEFWIGPRP
+TLAGLAARTGLRTAGLEELESAVTKNVAADGTAVRLLAETDQDVDALLAAVRTEAGVDLA
+AAAEADAQTAEFLSELRLVKDAWEVDRMRASVAATIAGFEDVVRALPRAVGHDRGERVVE
+GAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGAVRPGELLLLDAGVEDDSLYTADI
+TRTLPVSGTFTDVQRRIYQAVLDAADAAFAIVRPGIRFRELHAEAMRVLVDRLDGWGLLP
+VSAEVALSDEGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEPGLYF
+KEEDLAVPEEYRGIGVRIEDDILVTEDGAENLSAALPRTPDEIEAWMARLQA
+>1_1207
+MTDAAQHPAQTTPDQPAATPEAGADGTGAVNPQPLAERVDNRSQRPASNAFRDFMASDWA
+PSSQALPDPDASAPYAARRRAAVSARFPGERIVVPAGRLKVRSNDTDYRFRAHSAFAHLT
+GLGVDHEPDAVLVLEPTDPGAGDDGTDHTATLYFRPLAGRDTEQFYADSRSGEFWIGPRP
+TLAGLAARTGLRTAGLEELESAVTKNVAADGTAVRLLAETDQDVDALLAAVRTEAGVDLA
+AAAEADAQTAEFLSELRLVKDAWEIERMRASVAATIAGFEDVVRALPRAVGHDRGERVVE
+GAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGAVRPGELLLLDAGVEDDSLYTADI
+TRTLPVSGTFTDVQRRIYQAVLDAADAAFAIVRPGIRFRELHAEAMRVLVDRLDGWGLLP
+VSAEVALSDEGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEPGLYF
+KEEDLAVPEEYRGIGVRIEDDILVTEDGAENLSAVLPRTPDEIEAWMARLQA
+>2_1359
+MTDAAQHPAQHADQDRPQDPAATPEAGVDAEGAVSPQPLAQRVENRSQRPSSDAFRAFMG
+ADWAPSSDELPAQDASAPHAARRRAAVSARYPGERIVVPAGRLKVRSNDTDYRFRAHSAF
+AHLTGLGVDHEPDAVLVLEPTDPGAGDGGSDHAATLYFRPLAGRDTEQFYADARAGEFWI
+GPRPTLAGLAARTGLRTAGLEELESAVTKNVCADGTAVRLLREADQDMDALLAGVRAEAG
+MDAEAAASADAQVAEFLSELRLVKDAWEVERMRASVAATIAGFEDVVRALPRAVGHDRGE
+RVVEGAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGTVREGDLLLLDAGVEDDSLY
+TADITRTLPVSGSFTDVQRRIYQAVLDSADAAYAIVRPGIRFREIHAEAMRVLVERLADW
+GLLPVSAEVALSEDGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEP
+GLYFKEEDLAVPEEYRGIGVRIEDDILVTEDGAENLSAALPRTPDEIEAWMARLQA
+>3_1251
+MTDASAQQNDDLAPEAAADSGAALSPQPLAERVENRSQKPTSDAFRAFMASQWAPASREL
+PGPDASAPFAARRRAAVSAMFPGERIVVPAGRPKVRSNDTDYRFRAHSAFAHLTGLGVDH
+EPDAVLVLEPTDAGAGDAGTDHAATLYFRPLAGRDTEQFYSDPRAGEFWIGPRPTLAELA
+ARTGLRTAGLEELENAVTKDVAATAVRLLREADQDMDAVVAAARADAGVDAQAAGAADAA
+LAEALSELRLVKDEWEVERMRASVASTIAGFEDVVRALPRAVGHARGERVVEGAFFARAR
+EEGNDLGYDTIAASGNNATVLHWIRNTGRVREGELILVDAGVEDDSLYTADITRTLPVSG
+TYSDVQRRVYQAVLDAADAAFALVKPGIRFREIHAEAMRVLAGRLHGWGLLPVSPEEALS
+EAGQHHRRWMPHGTSHHLGLDVHDCAQARRELYLDAVLEPGMVFTIEPGLYFKAEDLAIP
+EEYRGIGVRIEDDILVTEDGAENLSAALPRTPEDVEAWMARLQG
+>4_1414
+MMGGMTDAAQHPAQTAPDQPAATPEAGADGTGAVNPQPLAERVDNRSQRPASNAFRDFMA
+SDWAPSSDALPDADASAPYAARRRAAVSARFPGERIVVPAGRLKVRSNDTDYRFRAHSAF
+AHLTGLGVDHEPDAVLVLEPADPGTGDDGTDHTATLYFRPLAGRDTEQFYADSRSGEFWI
+GPRPTLAGLAARTGLRTAGLEELESAVTKNVAADGTAVRLLAETDQDVDALLAAVRTEAG
+VDLTAAAEADAQTAEFLSELRLVKDAWEVERMRASVAATIAGFEDVVRALPRAVGHDRGE
+RVVEGAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGAVRPGELLLLDAGVEDDSLY
+TADITRTLPVSGTFTDVQRRIYQAVLDAADAAFAIVRPGIRFRELHAEAMRVLVDRLDGW
+GLLPVSAEVALSDEGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEP
+GLYFKEEDLAVPEEYRGIGVRIEDDILVNEDGAENLSAALPRTPDEIEAWMARLQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001261.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001261.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b1ba606b182e36a925b696f65005a2e09b1f2eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001261.fa
@@ -0,0 +1,45 @@
+>0_1490
+MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM
+TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR
+NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA
+DLADMLHDMSEKRRVEVASELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD
+DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA
+MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEPV
+SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDAETRP
+AT
+>1_1210
+MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM
+TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR
+NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA
+DLADMLHDMSEKRRVEVASELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD
+DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA
+MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEPV
+SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDAETRP
+AT
+>2_1356
+MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAVPPFATGLVIEVPGKKRVFVPM
+TRVTSMDSGQIITTGLINLRRFSRRGAEQTVAADLFDRRVRLTDGSGEAFLEDIGLEQQR
+NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLDWDEARWTGQAEPQAATSFLAAHEDLKPA
+DLADMLHEMPEKRRVEVARELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD
+DAADLLHELPDSQQELLLERMEPEEAEDVRRLLEYEEGTAGSVMTPVPVILPPEATVAEA
+MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAVGNIMDKDLEPV
+SDLAPIAHVTRELATYNLTSIPVVNEHHRVVGAVSVDDVLDHILPDDWRAMDHDDHDPRP
+AA
+>3_1248
+MNSPRIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGRGARSAATGLVIEVPGKKRVFVPM
+TRVTSMDSGQIITTGLINLRRFSRRGAEQTVAGDLFDRRVHLTDGSGRAVVEDLGIEQQR
+NGDWLVTDYYVRRDDGRTAFGRPRGEHLLVSWDEVAWGAAAEPQGASSFVAAHDDLKPAD
+LADMLHEMTDKRRVEVANELQDERLADVLQELPDDDQVQILSHLDIERAADVLEEMDPDD
+AADLLNELPDSQQELLLELMEPEDAEDVRRLLEYEEDTVGSIMTPVPVVLPPEATVAEAM
+ATIRQQEISPALASLVIVARPPLETPTGRYLGVVHFQRLLRYPPPEAIGNIMDKDLEPVS
+DMDSVAHVTRELATYNLTSIPVVNAQHRVVGAVSVDDVLDHILPEDWRAMDPEDHPETEG
+QD
+>4_1417
+MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM
+TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR
+NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA
+DLADMLHDMSEKRRVEVARELQNERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD
+DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA
+MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEAV
+SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDAETRP
+AT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001263.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001263.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8c68de03f6da2df6a66f1308c116df0c2c6051aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001263.fa
@@ -0,0 +1,40 @@
+>0_1492
+MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI
+AACPLRGTIQTDVAAAVAVVPGCESVDVRVGVMEPERRLALQDALRATRPTNPFGEGTLT
+RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM
+ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL
+DVFGTGGGAEVAERLSGVLDTQVPLLGTVPLDPALRAGGDAGEPVVVSAPESPAGRALTQ
+IAQRVAVRPRGLAGRRLPVTPR
+>1_1212
+MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI
+AACPLRGTIQTDVAAAVAVVPGCESVDVRVGVMEPERRLALQDALRATRPTNPFGEGTLT
+RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM
+ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL
+DVFGTGGGAEVAERLSGVLDTQVPLLGTVPLDPALRAGGDAGEPVVVSAPESPAGRALTQ
+IAQRVAVRPRGLAGRRLPVTPR
+>2_1354
+MSDLGLHVPEVRTDLERRVLDRLATVQDPEIRRPVTELGMVESVVETAPGTVEVTVLLTI
+EACPMRGTIQGDVAAAVADVPGCDAVDVRTGVMSPERRLALQDALRAARPANPFGEGSLT
+RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTASPTKLDRM
+ILPPVVRDVKVISIGMFLDEDRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQAVAGVIENMGPMTLPDGTVL
+DVFGAGGGQEVAERLERVLGSAVPLLGSVPLDPALRRGGDAGDPVVLSAPDSPAGRALAG
+VAERLAVRPRGLVGRRLPLSPR
+>3_1246
+MSAPALPRPEVRTPLEAAVLAALDGVVDPEIRRPITELGMVRSVAETGGGHVAVEVLLTI
+AGCPLKGTIQADVAAAVADVPGCAGVDVRLGVMTPTERAALQEALRGARPANPFAEDSLT
+RVLAVASGKGGVGKSTVTANLAVALAGRGLSVGLIDADVHGYSIPGLLGVQASPTRVGEL
+ILPPVSRGVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELVVVTTPQHAAAQVAARAGQLAAQTGQRVAGVVENMGPMALPDGTVL
+DVFGAGGGQEVADRLSGALGTSVPLLGTVPLDPALRRGGDAGEPVVVSAPESPAAAALQE
+VAARLAVRPGSLRGRGLPVSPR
+>4_1419
+MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI
+AACPLRGTIQTDVAAAVADVPGCGSVDVRVGVMEPERRLALQDALRAARPTNPFGKDTLT
+RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM
+ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL
+DVFGTGGGAEVAERLSGVLGTQVPLLGTVPLDPALRAGGDAGDPVVVSAPESPAGRALAE
+IAQRLAVRPRGLAGRPLPFTPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001266.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001266.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51c8c1fffb6d1d0a6c0288755c141ac812503c00
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001266.fa
@@ -0,0 +1,10 @@
+>0_1496
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQA
+>1_1216
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQA
+>2_1350
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQG
+>3_1242
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEAKELQQCLEGVTQA
+>4_1423
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001267.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001267.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4f49e5cf2db7ee248e573fb18ea81ff55fe8cdf7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001267.fa
@@ -0,0 +1,18 @@
+>0_1497
+MRAPLGGEGRRVSGPQWIVLVAVLVVVLAALAAALAGRLTLRADDPAGRTPGHPVLLPER
+PRAADVDLLRLAVAVPGYQRDQVDAVLLRLRDALAQCEDEVTALRARVAELEAADPSRSD
+PAGRA
+>1_1217
+MRAPLGGEGRRVSGPQGIVLVAVLVVVLAALAAALAGRLTLRADDPAGRTPGHPVLLPER
+PRAADVDLLRLAVAVPGYQRDQVDAVLLRLRDALAQREDEVTALRARVAELEAADPSRSD
+PAGRA
+>2_1349
+MSTPLWIAVIAALVVVVAALAAAAAGRLTLRAGEPAGQAPVHPVALPERPRADDVAFVRL
+AVAVPGYQRDQVDAVLLRLRDALADHEDEVAALRARLAELEADAARDAERTGPR
+>3_1241
+MTQPIWIAVLVVAVVAVAALAAAALGRALPRPADPAGQAPPHPVLLPEHPRAADVDRLRL
+ATAVPGYQRDQVDEVLARLRAALAADEERIAALEARLGEGDGVGR
+>4_1424
+MRAPLGGEGRRVSGPQGIVLVAVLVVVLGALAASLAGRLTLRADDPAGRTPGHPVLLPER
+PRAADVDLLRLAVAVPGYQRDQVDAVLLRLRDALAQREDEAAALRARLAELEAADPSRSD
+PAARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001280.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001280.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8d97b398eb6a056a786ef1232f4c73d317d23cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001280.fa
@@ -0,0 +1,40 @@
+>0_1512
+MTTNNSSMTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHRAAMISLIVL
+VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD
+TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSLLMRLTDLIIVI
+PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA
+KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA
+FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGGGAHRRLRFFGRRAAATEAGAT
+TAGGLAAAPTAGRIEAPVEEAGGSARISDADEDGQR
+>1_1232
+MTTNNSSMTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHRAAMISLIVL
+VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD
+TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI
+PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA
+KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA
+FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAGAHRRPRFFGRRAAATEAGAT
+TAGGLAAAPTAGRIEAPVEAAGGSARISDADEDGQR
+>2_1335
+MTTNNSSTTGAQLDEKQIFDLAEAEDAKLRVKAGKSYSQGALVRKRFFRHKAAMISLIVL
+VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD
+TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI
+PLLVLAAVLGQMASGANMGILPLALVLGLVTWTSLARLVRGEVLSLREKEFVAAAVAMGA
+KPGRVIGKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISLYQNS
+FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAAAGRKRGLFSRRAAKTDAGAT
+TAGGLGTAPTARDGEADDLIADPDAPEHRRGGAGGPAGGVGQ
+>3_1227
+MTMSHSAQQNPRSTSPAVVDLAEAEDLKLQQKTGKSYSQGALIRMRFFRHKAAMVSLVVL
+AFIALMAFTSIGFAGIPGWWDESYSAASTVVDGGRPTLSVVPQFLGGEGLRWGAHPFGQT
+STGTDFFALVMRGTQQSLIIAFIVGLISTAIGALVGAASAYFGGWVDSVLMRLTDLIIVI
+PLLVLAAVLGKMAGGLQLGILPLAFVLGIVSWTSLARLVRGEILSLREKEFVAAAVAMGA
+KPGRIIGKHLLPNTIGVIVVNATFAIAGAVLLETSLSYLGFGVKSPDSSLGLLISDYQTA
+FTTRPWLFWWPGMTILAIALSVNFLGDGLRDAFDPRQSGSGRRKRGLFSRRAAVTEATPT
+TAGGLQASPASAPAGHADVVTDSRGLDAPAAWTVTDADGTSRPAGDDVDTTEGDAR
+>4_1439
+MTTNNSSTTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHKAAMISLIVL
+VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD
+TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI
+PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA
+KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA
+FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAGAHRRPRFFGRRAAATEAGAT
+TAGGLAAAPTAGRIEAPVEEAGGSARISDADEDGQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001282.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001282.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d4bb1b59f1a96cf578279df67c657e871bc5aa10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001282.fa
@@ -0,0 +1,60 @@
+>0_1514
+MKYTKLSAAAALAAGSALILSACAPGGGNAGDSSSNSASGASQGGDSGAGNVIEGDKGQK
+LTAEASGPGKADLGDVKTQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVADRMFSSFWY
+FGTDGSIIPDKDFGTYEKTSDDPLTVKYTISDDAKWSDGTPVTAGDFIVHWAANNDTIKA
+EGAETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEILISTALPAHIVAKEA
+GMSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGPYKFKDGGWQAGQ
+SITLEANPEYWGTPAATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLEGLGED
+VNVQTGDQLTWEHVDYNRGEGSVFADSPELREAFALCLPRQQIVDNLIKPIYADAQVMNL
+REVFPFQDKYQEVVDAAYPKEMDQPNIEKAKELVEKSGVSKPTVRLGYQAGNQRRTETVA
+LIKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALFAWAGSGQKASGANIYQSDGAQNQQ
+SYNNPEVDAAWDKLATSLDENEQLEQVKTIEKLLWEDFQAIPLYAHPGLVGHKADVANVR
+DTAAQSGALWNVEQWVRVQE
+>1_1234
+MKYTKLSAAAALAAGSALILSACAPGGGNAGDSSSNSASGASQGGDSGAGNVIEGDKGQK
+LTAEASGPGKADLGDVKTQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVADRMFSSFWY
+FGTDGSIIPDKDFGTYEKTSDDPLTVKYTISDDAKWSDGTPVTAGDFIVHWAANNDTIKA
+EGAETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEILISTALPAHIVAKEA
+GMSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGPYKFKDGGWQAGQ
+SITLEANPEYWGTPAATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLEGLGED
+VNVQTGDQLTWEHVDYNRGEGSVFADSPELREAFALCLPRQQIVDNLIKPIYADAQVMNL
+REVFPFQDKYQEVVDAAYPKEMDQPNIEKAKELVEKSGVSKPTVRLGYQAGNQRRTETVA
+LIKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALFAWAGSGQKASGANIYQSDGAQNQQ
+SYNNPEVDAAWDKLATSLDENEQLEQVKTIEKLLWEDFQAIPLYAHPGLVGHKADVANVR
+DTAAQSGALWNVEQWVRVQE
+>2_1333
+MKYTKLSAAAALAAGSALILSACAPGGGDDADNTASSGNGGASGSASQGGEAGAPEVTEG
+DKGQKLTAPVDGPGMADLGDVETQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVADRMF
+SSFWYFGTDGSIIPNKDFGTYEKTSDDPLTVKYTISDDAKWSDGTPVTAGDFIVHWAANN
+ETVKAEGSETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEILISTALPAHI
+VAKEAGMSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGPYKFKDGG
+WQAGQSITLEANPEYWGTPAATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLE
+GLGDDVNVQTGDQLTWEHVDFNRGEGSVFADSPELREAFALCLPRQQIVDNLIKPIYADA
+QVMNAREVFPFQENYQEVVDAAFPEEMDQPNIEKAKELVEKSGVSKPTVRLGYQAGNQRR
+TETVALIKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALYAWAGSGQKASGANIYQSDG
+AQNQQSYNNPEVDAAWDKLATSLDEDEQLEQVKTIERLLWEDFQAIPLYAHPGLVGHKAD
+VANVRDTAAQSGALWNVEQWVRVQE
+>3_1225
+MKHTKLSAAAALAFGSALVLSACAPAGPAASGSSSNGGGSSAASGSSAASGSDAAGGVTT
+GEKGEKLTAPADGPGMADLGDVKTEEGSVAYSVGKDDFLSYNGVQANTYSTYNSAIVDRL
+FSGFYYFGTDGTIVRNEEFGTFEKISDDPLKVKYTINEDATWSDGTPVTAADFIVQWAAD
+NPNIVDESGKADPKTGQKPQLFESITSEPGKYIPEAPEGDPKGKEFTVTYAEPYADWEIL
+ITTALPAHVIAKGADMSLDDLVAAAKAKDSTKLVPAAKFWNNGWDFNPGELPSADMIPSM
+GPYKIKDGGWVAGQSITLEANDKYWGTPAATKNLVIKFAAPETHVQALQNKELDVIEPQA
+TVDTVSQLEGLGDSVNIQKGDQLTWEHLDFNRGTGSTFADSKELREAFALCVPRQQIVDN
+LVKPINPDATVMNAREVFPFQDNYQEVVDAAYPKEMDQPNIEKAKELVAKSGVSKPTVRL
+GYQAGNQRRAETVKLIKASCDQAGFDVQDANSNVFFKEVMPTGDYDVALYAWSGSGQKAS
+GANIYQSDGEQNQQSYSNKTVDEAWDKLAGSLDEKEQLEQVKVIEKALWEDFQAIPLYAH
+PGVVAHQADLANVRDTVAQQGALWNVEQWKRVS
+>4_1441
+MKYTKLSAAAALAAGSALILSACAPGGGNADDSSSNGSGASQGGDSGAGNVVEGDKGQKL
+TAEASGPEMADLGDVETQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVVDRMFSSFWYF
+GTDGSIIPNEDFGTYEKTSDDPLTVKYTISDDAKWSDGTPVTAGDFIFHWAANNDTVKAE
+GSETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEILISTALPAHIVAEEAG
+MSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGSYKFKDGGWQAGQS
+ITLEANPEYWGTPPATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLEGLGDDV
+NVQTGDQLTWEHVDYNRGEGSVFADSPELREAFALCLPRQQIVDNLIKPIYADAQVMNLR
+EVFPFQDKYQEVVDEAYPKEMDEPNIEKAKELVEKSGVSTPTVRLGYQAGNQRRTETVAL
+IKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALYAWAGSGQKASGANIYQSDGAQNQQS
+YNNPEVDAAWDKLATSLDENEQLEQVKTIEKLLWEDFQAIPLYAHPGLVGHKADVANVRD
+TAAQSGALWNVEQWVRVQE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001286.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001286.fa
new file mode 100644
index 0000000000000000000000000000000000000000..250174d8ed43e48648da1be129460744f2f2dcc5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001286.fa
@@ -0,0 +1,31 @@
+>0_1519
+MTEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNAVNYLSRD
+PARARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATFRANPARL
+VLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG
+IPLTAAEDAGFEKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRWRRYNATR
+ERLFEMERQGRAYLFAPETMPIANGERSVAKLAAAHELGLDQVRREMPAIRAFLGLPASR
+>1_1239
+MTEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNAVNYLSRD
+PARARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATFRANPARL
+VLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG
+IPLTAAEDAGFEKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRWRRYNATR
+ERLFEMERQGRAYLFVPATMPISNGERSVAKLAAAHELGLDQVRREMPAIRAFLGLPASR
+>2_1326
+MRTPMTSNVTDTALLFEGGGMRASLTSAVVAELLRERIHVDFVAGISAGSSNSVNYLARD
+PERARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATFQANPARL
+VLVGFDAVTGQTRWWDRSDMGTLADLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG
+IPVTAAEEAGFEKLFVVMTRERSYVKRPERFPAFYQRTFRRYPAVAEALISRWRRYNETR
+ERLFEMERQGRAYLFVPESMPVSNGERSVAKLAAAHELGLAQVRREMPAIREFLGL
+>3_1220
+MAEQQDHTAEALTSNVTDTALLFEGGGMRASHTSAVVAELLRAGVHVDFVAGISAGSSNA
+VNYLARDPLRARQAFVDFADDPRFGNWRTFLRGKGMFNAEYIYEHAGLPEADLPYDFAAY
+RANPARLALAGFDAVTGETRWWGREDMTTLQDLMVRVRASSTMPILMPPVHLEDTVYVDG
+ALGVDGGIPVTAAEEAGLAKLLVVMTRERSYVKRPERFPAFYQRAFRRYPAVAEALVTRW
+QRYNATRERLFEMEREGTAYLFVPEVMPVSNGERSVAKLAAAHELGLAQARREMPAIKEF
+LGL
+>4_1446
+MTEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNAVNYLSRD
+PARARRSFVDFADDPRFGNWLSFLRGKGLFNAEYIYEHAGLPEADLPYDFAAFRANPARL
+VLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG
+IPLTAAEDAGFKKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRWRRYNATR
+ERLFEMERQGRAYLFAPETMPIANGERSVAKLAAAHELGLDQVRREMPAIRAFLGLPASR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001289.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001289.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce193b1832af88d1e50588e0ef3e06013d7451e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001289.fa
@@ -0,0 +1,35 @@
+>0_1522
+MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL
+PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG
+HADDEEPAVERGPEAEDTVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL
+ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV
+GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTETATSAVWGLLWGSVALGVV
+LLVGRLRGNKAAPAH
+>1_1242
+MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL
+PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG
+HADDEEPAVERGPEAEETVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL
+ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV
+GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTDTATSAVWGLLWGSVALGVV
+LLVGRLRGKKAAPAH
+>2_1323
+MSGLVALLDDVAALARLAAASVDDVAAGAAKASAKAAGVVVDDAAVTPQYMAGAAANREL
+PMIWRITKGSLRNKLLIILPALLLLDWLAPWVLPWLLLAGGTYLAYEGAHKVWGKLTGHS
+PERDEPAVEKGPEAEDKVVRGAITTDFILSAEIMVISMNEVADVDFWLKAVILVVVAILI
+TAVVYGAVALIVKMDDVGLHMTQNGRTAGGRRFGAGLVKAMPHVLTAITVIGTVAMLWVG
+GHIVLVELAALGVPWPYDVQHGIVHAVEAAGGFVAWLVETLTSALWGLIWGSLALGVVLV
+VNRLRGKKDTLAH
+>3_1217
+MSGLVALLDDVAALARLAAASVDDVAAGAAKASAKAAGVVVDDAAVTPQYMEGAAAQREL
+PMILRIVRGSLRNKLVFILPGLLLLDWLAPWALPWLLLAGGTYLSFEGAEKVWHKLTGHH
+EPQEDTPAVEQGPEAEDKVVRGAITTDFILSLEIMVISMNEVSDQGFWMKAAILAIVAVV
+ITVAVYGAVALIVKMDDVGLHMHENAHTSGARRFGLGLVKAMPVVMGVISVIGTVAMLWV
+GGHIVLMELATLGLPWLYELQHTIVHAVEGAGSVIAWLVETLTSAIWGLVWGSLVVAVVG
+LVRRLRT
+>4_1449
+MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL
+PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG
+HADDEEPAVERGPEAEDTVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL
+ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV
+GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTDTATSAVWGLLWGSVALGVV
+LLVGRLRGKKAAPAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001294.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001294.fa
new file mode 100644
index 0000000000000000000000000000000000000000..91d41a1752bfc71a935af6feabb41c7bb813ddf0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001294.fa
@@ -0,0 +1,43 @@
+>0_1533
+MSRSHSDALDASGPDSGGAVAVPRRRFGLLPRILVAIVAGVLVGLVAPTWLVQAFATFNG
+LFSNFLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLVGGFGALLVCLLVFP
+LILTPGSFEGMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTMLPRGALHESFD
+QLRSIIERVVMGLIVPLLPVYIFGVFLNMTAAGEVFKVITTFLGVILLVFGLTVVLLLLQ
+YVVAGTIAGRNPFTALKTMLPAYATALGTSSSAATIPVTLRQTLLLGVRRPIASFVVPLC
+ATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLGVTMIAAPGVPGGAIVAASGL
+LTSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMIVDKIAGDRLIEDSEDEGLER
+LDDEGAATGADAG
+>1_1254
+MSRSHSDALDASGPDSGGAVAVPRRRVGLLPRILVAIVAGVLVGLVAPTWLVQAFATFNG
+LFSNFLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLVGGFGALLVCLLVFP
+LILTPGSFEGMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTMLPRGALHESFD
+QLRSIIERVVMGLIVPLLPVYIFGVFLNMTAAGEVFKVITTFLGVILLVFGLTVVLLLLQ
+YVVAGAIAGRNPFTALKTMLPAYATALGTSSSAATIPVTLRQTLLLGVRRPIASFVVPLC
+ATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLGVTMVAAPGVPGGAIVAASGL
+LTSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMIVDKIAGDRLIEDSEDEGLER
+LDDEGAATGADAG
+>2_1310
+MSHASSGAAAPSDRAPQGAVSESCRRRRFGLLPRILVAIVAGVLVGLVAPTWLVQAFATF
+NGLFSNVLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLFGGFGALLVCLLV
+FPLILTPGSFEAMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTMLRRGALHEG
+FDQLRSIIERVVMGLIVPLCATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLG
+VTMVAAPGVPGGAIVAASGLLSSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMI
+VDKIAGDRLIEDSEDEGLERLDDEEAATGADAG
+>3_1209
+MSHAAPSSSVPPAPPSSSATDGTAAPEKAPRRGLRRLGLLPRVLLGIVLGVVVGLVSPEW
+LTRTAVTGTSLFSAFLGFIVPVLIVALVAPAIAELGRGAGRWLSVTAAIAYGSTLFGGFL
+SLGVALALFPRILTPGSISGVTDPSEGGATPFFEIAMDPPFGVMTALLLSFVLGIGMTLI
+PRGVLQQGFEELRTIIERVVTGIVVPLLPFYIFGIFLAMAASGGVFEVIGTFLGVILIVF
+ALTVVLLLVQYAVAGVIAHRNPLTALKAMMPAYATALGTSSSAATIPVTLRQVVSLGVRQ
+PIAAFVVPLAATIHLAGSTVKIVAFSTAVIILTGGQVDVGLMVGFIFMLGITMVAAPGVP
+GGAIVAASGLLSSMLGFTEPQVALMVATYIAIDSFGTATNVTGDGAIALIMDRIAGDRIA
+ADPGVAEESPAA
+>4_1460
+MSRSHSDALDASGPDSGGAVAVPRRRFGLLPRILVAIVAGVLVGLVAPTWLVQAFATFNG
+LFSNFLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLVGGFGALLVCLLVFP
+LILTPGSFEGMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTMLPRGALHESFD
+QLRSIIERVVMGLIVPLLPVYIFGVFLNMTAAGEVFKVITTFLGVILLVFGLTVVLLLLQ
+YVVAGAIAGRNPFTALKTMLPAYATALGTSSSAATIPVTLRQTLLLGVRRPIASFVVPLC
+ATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLGVTMVAAPGVPGGAIVAASGL
+LTSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMIVDKIAGDRLIEDSEDEGLER
+LDDEGAATGADAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001296.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001296.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6c6aea18a286872be3222b7a7260b5ddc1adb5ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001296.fa
@@ -0,0 +1,20 @@
+>0_1537
+MAEPRPGDVRVTPGPGAPRGLVIPAGELVERFSHASGPGGQGVNTADSRVQLSLDLAATS
+ALDDVQRARVLARLAPRLAGTVLTVSVAEHRAQRRNRVAARERLAALLREALAPPTPRRA
+TKPTRGSRRRRLEAKHRRSEVKRTRRRPGLD
+>1_1259
+MAEPRPGDVRVTPGPGAPRGLVIPAGELVERFSHASGPGGQGVNTADSRVQLSLDLAATS
+ALDDVQRARVLARLAPRLAGTVLTVSVAEHRAQRRNRVAARERLAALLREALAPPTPRRA
+TKPTRGSRRRRLEAKHRRSEVKRTRRRPGLD
+>2_1275
+MADLRVEPGPGAPRGLVIPAAELMERFSHASGPGGQGVNTADSRVQLSLDLATTTALDES
+QRARALAVLGPRLAGTVLTVAAEEHRAQRRNRVAARERLAAMLREALIPETPRRATRPTR
+GSRRRRLEAKRQRSETKQLRRRPGV
+>3_1195
+MDDLRVPPGPGVPRGLRIPAAELSERFSHGSGPGGQGVNTADSRVQLSLDLAATTALTDA
+QRIRLLEGLAPRLAGTVLTVDAAEHRAQRRNRTAARERLAALLREALVPETPRRATKPTR
+GSQRRRLQAKARRSEVKQSRRRPRMD
+>4_1464
+MAEPRPGDVRVTPGPGAPRGLIIPAGELVERFSHASGPGGQGVNTADSRVQLSLDLAATS
+ALDDVQRARVLARLAPRLAGTVLTVSVAEHRAQWRNRVAARERLAALLREALAPPTPRRA
+TTPTRGSRRRRLEAKRRRSEVKRTRRRPGLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001302.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001302.fa
new file mode 100644
index 0000000000000000000000000000000000000000..219c5a456c13afa4c7484a94e6e870ec15a1c8af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001302.fa
@@ -0,0 +1,20 @@
+>0_1546
+MDAAPTPSLALEDQLCFALHRAARAVTRGYGPLLSRLGLTYPQYLVMLTLWQAEGDASAE
+TEASTPDAGALGVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDEG
+RALRASARTVPVDALTRIPLDTTERQVLMDLLNRITEAAGPR
+>1_1268
+MDAAPTPSLALEDQLCFALHRAARAVTRGYGPLLSRLGLTYPQYLVMLTLWQAESDASAE
+TEASTSDAAGALGVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDE
+GRALRASARTVPVDALTRIPLDTTERQVLMDLLNRITEAAGPR
+>2_1268
+MDAAPTPSLALEDQLCFALHRATRAVTRGYGPLLSRIGLTYPQYLVMLTLWQVEGDASAE
+TEAPTPGAGALAVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDEG
+RALRASARTVPADALTRIPLDATERQVLMCLLNRITEAVGPR
+>3_1178
+MDAAPTPSLALEDQLCFALHRATRAVTRGYGPLLSRLGLTYPQYLVMLTLWQVEGDASAE
+TDAPTPGAGALAVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDEG
+RALRESARTVPADALTRIPLDATERQVLMGLLNRITEAAGPR
+>4_1473
+MDAAPTPSLALEDQLCFALHRAARAVTRGYGPLLSRLGLTYPQYLVMLTLWQVESDASAE
+TEASTSDAAGALGVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDE
+GRALRASARTVPVDALTRIPLDTTERQVLMDLLNRITEAAGPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001306.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001306.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b1248cae891fc112b4906ff600af5a20e464dac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001306.fa
@@ -0,0 +1,20 @@
+>0_1557
+MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI
+LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLVDAHPLTD
+DDADPALEADAEAVRVRMPVGAARAFARRTREVVDAGRPVCSDCGQPIDPDGHDCTFPDS
+>1_1278
+MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI
+LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGGIGLGWDPTTAQVLIDAHPLSD
+DDADPALEADAEAVRVRMPVGAARAFARRTREVVDAGRPFCSDCGQPIDPDGHDCTLPDS
+>2_1262
+MTESPAHVHEFDWPDRVVIGTIGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMLDEI
+LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLIDAHPLSD
+DDADPALEVDAEAVRVRMPVGAARAFARRTREVVDAGRPICSDCGQPIDPDGHDCTLPDS
+>3_1168
+MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI
+LDDLMALDGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLIDAHPLTD
+DDADPVLETDAEAVRVRMPVGAARAFARRTREVVDAGRPICSDCGQPIDPDGHDCTLPDS
+>4_1483
+MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI
+LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLIDAHPLSD
+DDADPALEADAEAVRVRMPVGAARAFARRTREVVDAGRPICSDCGQPIDPDGHDCTLPDS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001307.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001307.fa
new file mode 100644
index 0000000000000000000000000000000000000000..64f3c451e16de3855b03cd7d5838d44dc34ae66a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001307.fa
@@ -0,0 +1,30 @@
+>0_1558
+MSAADVPAGELMSGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAATLAR
+REVAASLVSEALGWDIVPRTWLRDGPFGKGMVQLWQEQDPEQDAVDLFPADEVPASGWLT
+VLEGEDEGGNRLVLAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRHGVDHGLTFH
+VQDKLRTVLWGWLGEALSEEERDGVARVLDGLDGELGQGLAELLGAEEVEALAARCAQLL
+DDGIFPAPSGLTPAVPWPLF
+>1_1279
+MSAADVPAGELVAGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAGTLAR
+REVAASLVSEALGWDIVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPAGQVPASGWLT
+ILEGEDADGNRLVLAHEDSAALRRMAVFDVIVNNADRKGAHILAMPGGHRHGVDHGLTFH
+VADKLRTVLWGWLGEELSEEERDGVGRVLDGLDGELGRGLAELLSAEEVQALAERSAGLL
+DDGRFPAPSGLTPAVPWPLF
+>2_1261
+MSAADVPAGELVAGELTLTGRITTASNATFLGAIGDTSVVYKPVAGEAPLWDFPAGTLAR
+REVAAYLVSEALGWDIVPRTWLREGPFGEGMVQLWQEQDPEQDAVDLFPADEVPASGWLT
+ILEGEDEGGNRLALAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRYGVDHGLTFH
+VADKLRTVLWGWLGEALSEEERDGVARVLDGLDGELGRGLVQLLSAEEVEALAERCAQLL
+DDGVFPAPSGLTPAVPWPLF
+>3_1167
+MSAADVPAGELVDGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAGTLAR
+REVAAHLVSEALGWEIVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPADEVPAAGWLT
+ILEGEDEEGRRLALAHENSAALRRMAVFDVIVNNADRKGAHILAMPGGHRYGVDHGLTFH
+VAGKLRTVLWGWLGEALSEEERDGVGRVLDGLDGELGRGLAELLSAEEVEALAERGARLL
+DDGIFPAPSGRTPAVPWPLF
+>4_1484
+MSAADVPAGELVSGELTLTGRITTASNATFLGAVGDTPVVYKPVAGEAPLWDFPAGTLAR
+REVAAHLVSEALGWDVVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPADEVPASGWLT
+ILEGEDEDGNRLALAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRHGVDHGLTFH
+VEDKLRTVLWGWLGEALSDEERDGVARVLDGLDGELGRGLAELLSAVEIGALAERSAGLL
+DDGTFPAPSGLTPAVPWPLF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001308.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001308.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5ec26a5f27f16acfc2f316cac6dcf18708874f02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001308.fa
@@ -0,0 +1,61 @@
+>0_1566
+MARRAAKAKPAKTLEQTLWDAADKLRGNQEPSEYKHVVLGLVFLKYVSDRFEERREQLKD
+ELAAEGIKPERIESFLEDRDEYASQNVFWVPSLARWGYVQSVAKQPEIGQQIDQAMDLIE
+KENPSLRGVLPRNYGRDGLDKRRLGELVDLIGSIGFTETDDHGADDVLGRVYEYFLGQFA
+GKETGKDAGAFYTPRSVVKTLVEMLEPFKGRVYDPAVGSGGMFVQSAEFVKAHGGKRTDI
+SVYGQEFTDTTWKLAKMNLALRGVEADMGSHSADSFTEDLHLDLRADYVIANPPFNVSDW
+WDAKLADDPRWKYGTPPKGNANFAWVQHFLHHLAPHGTAGFVLANGSLSSKSSGEGEIRQ
+RLVEAGLVDCIVAMPDKLFFNTGIPVSLWFISKGRDGNGHRARKGEVLFIDARKLGAMQS
+RRLRVLSDDDIAQIADTYHEWRNHDGCYEDVPGFAKSATIGEIEKHEFVLTPGRYVGAAE
+AEVDDEPIDEKIERLTNELLAEFERGRELENEVRLRMGSLS
+>1_1599
+MTIPATRGAASAPHRSPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMAPH
+REFFAELAAKGHPDFVLDNLVESRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQ
+NVADLFTYYEFDKTVAKLDEHDRLFLVLQQFASIDLSPETVSNAEMGTLFEDLIRRFAAA
+SNETAGEHFTPRDAVKLLVDLLTANDDDVLTGYPVRTVYDPTAGTGGMLSVLDERLRRMN
+PNAEVRLFGQELNDQSYAICKSELLGKGQAADGIARGDTLKNDAHMTERFDYVLSNPPYG
+GDWKASRAAVEKEIAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLN
+GSPLFTGGAGSGPSEIRRWLLESDLVDVIVALPTDMFYNTGIATYVWVLDNNKPADRRGR
+AQLIDARTFFTKLRRNVGSKNKELSKADRQRVLDIYRDFDAQSEANAEFSKVLTAQDFGY
+REITVERPLQLRFEVEDATIAAALATKPADKLPDDGRSALEAALASLRGRVWDHQPTFVL
+DLKKALKEHGVTAGAPLVKALTGAIGVHDPKAEVVTNKKGEPEPDTSLRDTELVPFGRDI
+HEYFEAEVAPHVPGAWIDESKTKIGYEIPFTRLFYTYVPPRPLEEIDADLKQLTAEIIEL
+LQEVER
+>2_880
+MTTPATPGAASAARRSPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMAPH
+REFFAELAAKGHPDFVLDNLVESRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQ
+NVADLFTYYEFDKTVAKLDEHDRLFLVLQQFASIDLSPDTVSNAEMGTLFEDLIRRFAAA
+SNETAGEHFTPRDAVKLLVDLLTANDDDVLTGYPVRTVYDPTAGTGGMLSLLDERLRRMN
+PNAEVRLFGQELNDQSYAICKSELLGKGQDADGIARGDTLKNDVHLTERFDYVLSNPPYG
+GDWKASRTAVEKEIAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLN
+GSPLFTGGAGSGPSEIRRWLLESDLVDAIVALPTDMFYNTGIATYVWVLDNNKSAERRGR
+VQLIDARTFFTKLRRNVGSKNKELSKADRQRVLDIYRDFDAQSEANAEFSKVLTAQDFGY
+REITVERPLQLRFEVEDATIAAALATKPVDKLPDDGRSALETALASLRGRVWDHQPTFVL
+DLKKALKEHGVTAGAPLVKALTGAIGVHDPEAQIVTNKKGEPEPDTSLRDTELVPFGRDI
+HEYFAAEVAPHVPGAWIDESKTKIGYEIPFTRLFYTYVPPRPLDEIDAELKQLTAEIIEL
+LQEVER
+>3_819
+MPSPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMAQHREFFAELAAKGHP
+DFVLDNLVQSRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQNVADLFTYYEFDK
+TVAKLDEHDRLFLVLQQFASIDLSPETVSNAEMGTLFEDLIRRFAAASNETAGEHFTPRD
+AVKLLVDLLTANDDDVLTGYPVRTVYDPTAGTGGMLSLLDERLRRMNPNAEVRLFGQELN
+DQSYAICKSELLGKGQDADGIARGDTLKNDAHLTERFDYVLSNPPYGGDWKASRTAVEKE
+IAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLNGSPLFTGGAGSGP
+SEIRRWLLESDLVDAIVALPTDMFYNTGIATYVWVLDNNKSAERRGKVQLIDARTFFTKL
+RRNVGSKNKELSTADRQRVLDIYRDFDAQSEANAEFSKVLTAQDFGYREITVERPLQLRF
+EVEDATIAAALATKPADKLPVDGRSALGAALASLRGRVWDHQPTFVLDLKKALKEHGVTA
+GAPLVKALTGAIGVHDPKAEVVMNKKGEPEPDASLRDTELVPFGRDIHEYFEAEVVPHVS
+GAWIDESKTKIGYEIPFTRLFYTYVPPRPLEEIDAELKQLTAEIIELLQEVER
+>4_1820
+MTTPATRGAASAPHRSPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMDPH
+REFFAELAEKGHPDFVLDNLVQSRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQ
+NVADLFTYYEFDKTVAKLDEHDRLFLVLQQFASIDLSPDTVSNAEMGTLFEDLIRRFAAA
+SNETAGEHFTPRDAVKLLVDLLTANDDDVLTGYPVRTVYDPTAGTGGMLSLLDERLRRMN
+PNAEVRLFGQELNDQSYAICKSELLGKGQDADGIARGDTLKNDAHLTERFDYVLSNPPYG
+GDWKASRTAVEKEIAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLN
+GSPLFTGGAGSGPSEIRRWLLESDLVDAIVALPTDMFYNTGIATYVWVLDNNKPADRRGR
+VQLIDARSFFTKLRRNVGSKNKELSTADRQRVLDIYRDFDAQSEDNAEFSKVLTAQDFGY
+REITVERPLQLRFEVEDATIAAALATKPVDKLPDDGRSALESALASLRGRVWDHQPTFVL
+ELKKALKKHGVTAGAPLAKALTGAIGVHDPDAEVVKDKKGEPEPDTSLRDTELVPFGRDI
+HEYFEAEVAPHVPGAWIDESKTKIGYEIPFTRLFYTYVPPRPLEEIDAELKQLTAEIIEL
+LQEVER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001309.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001309.fa
new file mode 100644
index 0000000000000000000000000000000000000000..61a29f6f0bc9e88ca6c2a453ad024cee6344cd3d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001309.fa
@@ -0,0 +1,20 @@
+>0_1572
+MARPIDPFREMERLVNGLTPRATGTVSMPMNLYREGDVFVAEVELPGVDPASIDVDVEER
+TLTVRAERKEDPAREDRRWLTRERSAGTFARQLTLGEGLALDRIQADYSDGVLTLTIPVA
+EQAKPRKISVTHGGAAPVAGQTVEGETAETTGE
+>1_1288
+MARPIDPFREMERLMTGFARTSGAASMPMNLYREGDVFVAEVELPGVDPSSIDVDVEERT
+LTVRAERKEAPAGEDRRWLTKERPAGTFARQLNLGQGLALDKIEADYSDGVLLLTIPVAE
+QAKPRKIQVKHTGSAAQVEGEAVEGEAVEGSAAEASGE
+>2_1246
+MARPIDPFREMERPFREMERLVNGLTRTSGTASMPMNLFREGDRFVAEVELPGVDPASID
+VDVEERTLTVRAERKESPAGEDRRWLTRERSAGTFARQLTLGEGLALDRIEADYEDGVLT
+LTIPVAEQAKPRKISVKHSGAGAGAGQTVPGETAEVEERSAEQEAAQNGGAPQA
+>3_1157
+MARPIDPFREMERPFREMERLVNGLTTRATGTASMPMNLYREGDAFVAEVELPGVDPASI
+DVDVEERTLTIRAERKEAAASEGRQWLTRERSSGTFARQLTLGQGLALDRIEADYRDGVL
+VLSIPVAEQAKPRKIQVKHSAADQVEGQEVAGQESVQDSAAVEAPQQPSGE
+>4_1501
+MARPIDPFREMERLVNGLTPRATGTVSMPMNLYREGDVFVAEVELPGVDPASIDVDVEER
+TLTVRAERKEDPAREDRRWLTRERSAGTFARQLTLGEGLALDRIQADYSDGVLTLTIPVA
+EQAKPRKISVTHGGTAPVAGQTVEGETAETTGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001312.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001312.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b1fcb10be0303a9a9c3d0a585aaec487d52987f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001312.fa
@@ -0,0 +1,42 @@
+>0_1576
+MEILSLLLALTLGLVLGALLGAWLMWRRAADGGEEARRAQAELAALRTEHQGAREALAAA
+RAEQRALTAARAEDAERQRAESQVMSTLAPLGQRLAALQEQVSVLERDRASQFGRLGEQL
+RAAAATDRDLLNQTTSLMATLKSTSARGHWGEAQLRRVVEAAGMLHHVDFTEQATLSGRD
+GERLRPDLVVSLPGGKAMAVDAKAPIGDALAAEALADEPGEEAYERRQALAAQHAAAVRR
+HVDQLSAKSYWDGLEHSPELVLCFLPAESLLAAALDADPGLLDHAFSRNVALVAPVSLLT
+ALKSVAYAWRQDTLAENAHTVVASAKDLYERLGTLGTHLDRMGGSLKTAVDRYNQLVGSV
+ESRVLPAARRLRDADPGLAPTPDIRTLESAPRPLAAPELVAGVEEDELRRRRAESAREA
+>1_1291
+MEILSLLLALILGLVLGALVGAWLMWRRAAGGGEEARRAQAELAALRTEHQGAREELAAA
+RAEQRALTAARAEDAERQRAESQVMSTLAPLGQRLAALQEQVGVLERDRASQFGRLGEQL
+RAAAATDRDLLNQTTSLMATLKSTSARGHWGEAQLRRVVEAAGMLHHVDFTEQATLSGKD
+GERLRPDLVVSLPGGKAMAVDAKAPIGDALAAEALADEPGEEAYERRQALAGQHAAAVRR
+HVDQLSAKSYWAGLEHSPELVLCFLPAESLLAAALDADPGLLDHAFSRNVALVAPVSLLT
+ALKSVAYAWRQDTLAENAHTVVASAKDLYERLGTLGTHLDRMGGSLKTAVDRYNQLVGNV
+ESRVLPAARRLRDADPGLAPTPDIRTLESAPRPLAAPELVAGVEEDELRRRRAESAREA
+>2_1241
+MDILSLLLALALGLVVGALTGAWLMWRRAAGGGEEARRAEQELAALRVEHQGAREELAAA
+RAEHRAVAAARAEDVERQRSEARVLSTLTPLGQQLTALQEQVGVLERDRAAQFGRLGEQL
+RAAAATDRDLLNQTTSLMATLRSTSARGHWGEAQLRRVVEAAGMLHHVDFSEQSTLSGRD
+GERLRPDLLVSLPGGKSMAVDAKAPIGDALAAEALADEPGEEAWERRQALAAQHAAAVRR
+HVDQLSAKAYWAGLEHSPELVLCFLPAESLLAAALDADGGLLDHAFSRNVALVAPVSLLT
+ALKSVAYAWRQDTLAENAHTVVASAKDLYERLGTLGTHLDRMGGSLKTTVDRYNQLVGNV
+ESRVLPAARKLREADPGLAPTPDIRTLESAPRVLSAPELVEGVEQDELRRRREDPAREEA
+VREDPAREA
+>3_1150
+MDFLTLVITLALGLLVGAAVGAWLMWRRMDGAADGSAGAELDALRREHAAVREELAGARA
+ESRALTQQRAEDAERARTDARVLETLAPLGRQLGALQEQVGVLERDRAAQFGRLGEQLRT
+AAANDRDLLNQTASLMATLKSTSARGHWGEAQLRRVVEAAGMLHHVDFSEQTTMTGRDGE
+RLRPDLLVSLPGGKTLAVDAKAPIGDALAAGALAEEPGEEAAERRAALNARHAAAVRRHV
+DALSAKAYWTGLERSPELVLCFLPAESLLAAALDADGALLDHAFSRNVALVAPVSLLTAL
+KSVAYAWRQERLAENAQLIVSGARELYDRLGTMGSHLDRMGGSLRAAVDGYNRLVGNVES
+RVLPAARTLREADPGLPALADVRSVDNAPRPLTAPELVDGDGPVDEGWTPAGSAAAEDRP
+EPAPAFEESPLWEDDEWTEDAAWDTDRRTA
+>4_1505
+MEILNLLLALILGLVLGALVGAWLMWRRAAGGGEEARRAQAELAALRTEHQGAREELAAA
+RAEQRALTAARAEDAERRRAESQVMSTLAPLGQRLAALQEQVSVLERDRASQFGRLGEQL
+RAAAATDRDLLNQTTSLMATLKSTSARGHWGEAQLRRVVEAAGMLHHVDFTEQATLSGRD
+GERLRPDLVVSLPGGKAMAVDAKAPIGDALAAEALADEPGEEAYERRQALAAQHAAAVRR
+HVDQLSAKSYWDGLEHSPELVLCFLPAESLLAAALDADPGLLDHAFSRNVALVAPVSLLT
+ALKSVAYAWRQDTLAENAHTVVASAKELYERLGTLGTHLDRMGGSLKTAVDRYNQLVGNV
+ESRVLPAARRLRDADPGLAPTPDIRTLESAPRPLAAPELVAGVEEDELRRRRAESAREA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001320.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001320.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5c263e8342493dca0a3884aeec368c515f40a54
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001320.fa
@@ -0,0 +1,38 @@
+>0_1585
+MSRPAHRRPTALAASALALSLALGACARQADAPPTPSASGTPITVVHGGEGLEGAVAAVL
+ARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAVAADPAVALPSPPPPTSTP
+SSTPTGTEAGPSADAVPTPSATASTAVPSPTALPVGDPAADAQAAGRVLETLLAEETAAA
+GTPQDEAPAVLSSSAGVLRLTAVVTQTTAARLELESITDLNGWCESLTAVAPPPLTAAAD
+PDAATALRARLDRLAGCRPETWLADTEDPSAALVADEAQVALLTDTDPEIDANTLVPLED
+DGRVLPEGRLTAVGSAATLDDDAERRIAEVMSALDGDGLRELERLTTGADPLPAAEAAQY
+WLVDHGLEDAPEDWFVPRGSWF
+>1_1300
+MSRPAHRRPTALAASALALSLALGACARQADAPPTPSASGAPITVVHGGEGLEAAVAAVL
+ARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAAAADPAAALPSPPTPTPTP
+TPTGTEAGTSTGTVPTPSATASTAAPSPTALPVGDPAADAPAAGRVLETLLAGQTAAAGT
+PQDEAPAALSSSAGVLRLTAVVTQTTAARLELESITDLNGRCESLTAVAPPALTSAADAA
+TALRARLDRLAGCRPETWLADTEDPTAAVVADEAQVALLTGTDPEIDANTLIPLEDDGRV
+LPEGRLTAVGSAATLDDDAERRIAEVMSALDGDGLRELERLTTGADPLPVAEAAQYWLVD
+QGLEDAPEDWFVPRGSWF
+>2_1231
+MPTASESSDAADASATPEPTPLPDGEPAADAAEAGRVVERLLQGDAEAGASPEPGDAVAV
+LGSSAGVLRLSAVVTATTAARLELDALEDLNGRCEGLTAALPAGLAGDPQANAALHARLD
+RLAGCRPGTWREEDASAAAVVVADQAQLGLLSATDPEIPASMLVPLEDPERVLPEGRLAA
+VGAPDALDDDAQRRIEEVLSALDEDGLRELERITTGADALPPAEAARYWLVDQGLEDVPE
+GWFMPRDSWF
+>3_1141
+MTRPAERPRTSRVRAAAGASALSLALALSGCGAPRAGAPADPTGAPVTVVHTSDPLDSAV
+AAVVARHLRHRGHPVTLEDAGDATPWSAAAGDTVAVVDTLRLALQADPAAVLPPEPEDAA
+ASRAAAAPTPSESSLEPIDPSAPARVPATGSATPSPTPLASGLPAADADAAQAVVDAALS
+RVAAGADAAAPTPAASRSAATPTGPSPRVLADSAGTLRLAAVVTATTASREGLDSIDDLD
+GRCGDLTLAVPAALAAAVSDGLLAHRLDDFAGCRPADWRTDAADVGPAVVADAAQVGLTY
+RTDPDIPPNGLVLLEDPDRVLPEGRIAVVGERETLDDDAQSALGEVMDRLDDDGIAELAR
+LTEGGDALPADEAAQYWLVSQRLEDAPEDWVVPADPWF
+>4_1514
+MSRPAHRRPTALAASALALSLALGACARQADAPPTPSASGTPITVVHGGEGLEGAVAAVL
+ARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAAAADPAAALPSPPSPTSTP
+SSTPTGTEAGTSADAVPTASTAAPSPTALPVGDPAADAPAAGRVLETLLAEETAAAGTPQ
+AEAPAVLSSSAGVLRLTAVVTQTTAARLELESITDLNGRCESLTAVAPPTLTAAADADAA
+TALRTRLDRLAGCRPETWLADTEDPTAAVVADEAQVALLTGTDPEIDANTLVLLEDDGRV
+LPEGRLTAVGSAATLDDDAERRIAEVMSALDGDGLRELERLTTGDDPLPVAEAAQYWLVD
+HGLEDAPEDWFVPRGSWF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001321.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001321.fa
new file mode 100644
index 0000000000000000000000000000000000000000..032c4ed3cc4d824d622387901f05180a24090deb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001321.fa
@@ -0,0 +1,20 @@
+>0_1586
+MSTTPAAPDAAGAHPAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIELGES
+PEEACLREVWEETGHTAELTGLLGVTTGTIPVEKRLRGEPLPLLTVQVLYTARITGGVLR
+PEVGGSSTDARWFDLAELSELRTASWVTEALARAGVDT
+>1_1301
+MSTTPAAPDAAGAHPAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIELGES
+PEEACLREVWEETGHTAELTGLLGVTTGTIPVERRLRGEPLPLLTVQVLYTARITGGVLR
+PEVGGSSTDARWFDLAELSGLRTASWVTEALARAGVAT
+>2_1230
+MSPTPVPDAEPARADAPAGPFQTRAGAYALIVDGGRVLLSSWQGPEHLVWTLPGGGIELG
+ESPEEACRREVWEETGHTAELTGLLGVTTGVIPAERRLRGEALPLLTVQVLYTARITGGV
+LRPEVGGSSTDARWFDLAGLDAVRTAPWVREALARAGAAA
+>3_1140
+MSAASPTAASTAPGPFETRAGAYALIVEDGRVLMSAWAGPTGIVWTLPGGGIELGESPEE
+ACVREVEEETGHTAELTGLLGVTTGTIPVERRLRGEPLPLLTVQVLYTARLTGGVLRPEA
+DGSSVDAAWFALDGLADVRTSAWVDRALALAGLAADDAAGTAR
+>4_1515
+MSTTPAAPDAAGAHPAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIELGES
+PEEACLREVWEETGHTAELTGLLGVTTGTIPVEKRLRGEPLPLLTVQVVYTARITGGVLR
+PEVGGSSTDARWFDLAELSELRTASWVTEALARAGVDT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001322.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001322.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac76774d3b361e2036be56aa928ca4f22edb71b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001322.fa
@@ -0,0 +1,60 @@
+>0_1587
+MDTPQDPPHRDDPSGGPVEPAVDAALDRVRALLRQARGTAAPDAPTALDARGWWELSLEA
+ALRDEPRESARLADSGLAALGPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR
+HLGRPRQAELESQLGAALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH
+RVHTGDLDAALELARRVIAVLGGLRAAGALLPTGSWSSAHLLLARLHLWRGEHAEADAAA
+AVVTALPAARAVLASATTVRAIAAHELDRPTAALDLALEAAERMASVGLRRGAASAAALA
+GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL
+VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA
+GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL
+LEEALALVRDAGADWQVADYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA
+ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE
+LDALREGLGAD
+>1_1302
+MDTPQDPPRRDDPSGGPVEPAVDAALDRVHALLRQARVIAAPDAPTALDARGWWELSLEA
+ALRDEPRESARLADSGLAALVPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR
+HLGRPRQAGLESQLGAALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH
+RVHTGDLDTALELTRRVIAVLGGLRAAGALLPIGSWSSAHLLLARLHLWRGEHAEADAAA
+AVVTVLPAARAVLASATTVRAIAAHELDRPTAALDLAFEAAERMASVGLRRGAASAAALA
+GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL
+VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA
+GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL
+LEEALALVRDAGADWQVADYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA
+ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE
+LDALREGLGAD
+>2_1229
+MDAPQQTPAPADVGPTAVLARVRTLLAEARTSGAPEDAVDAAPVDHDARQWWELSLEAAL
+RDEPRESARCAESGLAALGPGEDGVRLSLLRALAVAADRLGDETGLTRWVEARAALLRTL
+GRPRQAALETQLGASLVREPDGFEAAVLAGVVEEEPGVPGEDPGDTVLPEAALALAVHRV
+HASDLDGALAAARRAVESLRGLRAAGAVLPVGSWSSAHLLLSRLHLWRGEHAEADEAAAV
+VTSLPAARAVLASATTVRAIAAHEQDRPTAALALALDAADRMARVGLRRGAASAAALAGR
+VAGDLEGHEEAAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRPDEAEPLLARLVR
+REAAQGHDVEQARALVDLGHAHHDQDRSENALPLWREAAGLFEAHGRWEDAARTLLAAGA
+LVNRERDELTRPSALDLFERAVAAARRAVDEDPAVLPAALHAHGYLLCESGRPEGLELLD
+EAVALVREAEAPWQVADYTDTRARALWSLEQGAEAVSTALHAADLFTAAQDPEGAAQAEL
+FAASVVAEDGSPEQAATLFRLVSESTQSTLVRLGALTGLHQCLSAVGDHDGAARVRDDLD
+AVREQLGAD
+>3_1139
+MAEDAPALLAGRDPLAAVEALLAAARDDAALPLPAGSDAPSLRERALEALLREDPASAAR
+AAEDGLDAPGGQDPALRLALLRLRATAAAHAGDEPALEEWTARRADLLRRLGRPRQADLE
+VQLGASLLREPDAFEATVLAGVAEDERGRITADPAALEDTVLPDALLALCAQRVQAHDLD
+AALEAAEEALAVIRAQETAGVVLGEAAEPHALLMLARLHLWREEHRASDDAARAVLARPC
+AAVVRASATLVRALAAHGQDRPEAALDFALRAAEAMSRAGLRRGAASAAALVGRVAGARA
+DRQDLAVAAWELSCVHAEKAEAPEAPSLAYWWAHQLLIAGRAEEAEPVLTALVRREAAAG
+DEAAQARALVDLGHACHELDRPSEALPLWREAAELFTRRGHHADAAHTLLAAGALCHRDP
+HDAAHAGALDLFEQAVDAARRSEGDSAVLASALHALGYLRCETGRGDGLELIDEAIALAE
+GSGAAWQKADYLDTRARSLWALHRGDDAVSAALTSADLFTDAGDPSGAAQAELFAAHVVA
+EDGRPEQAATLFRLVSESTHSDLVRLGALTGLQQCLAALGEHAEADRVRADADAVRRALG
+GRD
+>4_1517
+MDTPQDPPHRDDPSGGPVEPAVDAALDRVRALLRQARGTAAPDAPTALDARGWWELSLEA
+ALRDEPRESARLADSGLAALGPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR
+HLGRPRQAGLESQLGGALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH
+RVHTGDLDAALELARRVIAVLGGLRAAGALLPTGSWSSAHLLLARLHLWRGEHAEADAAA
+AVVTALPAARAVLASATTVRAIAAHELDRPTAALDLALEAAERMASVGLRRGAASAAALA
+GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL
+VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA
+GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL
+LEEALALVRYAGADWQVANYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA
+ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE
+LDALREGLGAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001328.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001328.fa
new file mode 100644
index 0000000000000000000000000000000000000000..678275d21755fa3410ac69ef6ec59995b1ddfbc8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001328.fa
@@ -0,0 +1,15 @@
+>0_1593
+MPADGAPRRRGPRRADAPGTGPASADGREPRLPGMPRLIGQAGTSPATAPTGDVAGVESG
+PAEAERDRWLREQRPPHWG
+>1_1308
+MSADGAPRRRGPRRADAPGTGPAAADGREPRLPGMPRLAGQAGTSPVTAPTGDVAGVESG
+AAEAERDRWLREQRPPHWG
+>2_1221
+MGAEVPDPAPRRRGPRRADAPGTGPASADAPEPRLPGVGAGTDGARGAEGVRGAGGVRGA
+VGVRGAAGEPTADERDRWLLEQRPPHWG
+>3_1133
+MRTTPTASPEPGRRRGHRRADAAGTGPASADGPEPTLPEPTLPGPALPGAQTAGDATPSR
+PAVSRGRAVTSAAGADRPQPADELGRWLLEQRPPHWG
+>4_1523
+MSADGAPRRRGPRRADAPGIGPAAADGREPRLPGMPRLAGTSPATAPTGDAAGVESGPAE
+AERDRWLREQRPPHWG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001330.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001330.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b9d7818cf059749402af38d084588bd32dee219a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001330.fa
@@ -0,0 +1,50 @@
+>0_1595
+MTQNAPHPDTPAPLSDVMPTVLVLDFGAQYAQLIARRVREANVYSEVVPASTPAAQILER
+KPAALILSGGPSSVYEPGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVAQTGTREYG
+STRLDSVDADSVLFAGQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDRERRIY
+GVQWHPEVGHSSHGQRVLEQFLHVGAGLGADWTVSNVIEEQVERIREQIGDKRAICGLSG
+GVDSAVAAALVQRAIGDRLTCVYVDHGLMREGESAEIEQAFGEAHGGARLVMVDAREDFL
+SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPDATEVRFLVQGTLYPDVVESG
+GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG
+LGIRIIGEVTQERLDLLRRADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY
+GHPVVLRPVTSEDAMTADWARIPDDVLSRISNRITNEVDGVNRVVLDVTSKPPGTIEWE
+>1_1310
+MTQNAPHPDTPAPLSDVMPTVLVLDFGAQYAQLIARRVREANVYSEVVPASTPAAQILER
+KPAALILSGGPSSVYEPGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVAQTGTREYG
+STRLDSVDADSVLFADQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDRERRIF
+GVQWHPEVGHSSHGQRVLEQFLHVGAGLGADWTASGVIEEQVERIREQIGDKRAICGLSG
+GVDSAVAAALVQRAIGDRLTCVYVDHGLMREGESAEIEQAFGEAHGGARLVMVDAREDFL
+SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPDATEVRFLVQGTLYPDVVESG
+GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG
+LGIRIIGEVTQERLDLLRRADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY
+GHPVVLRPVISEDAMTADWARIPDDVLSRISNRITNEVDGVNRVVLDVTSKPPGTIEWE
+>2_1219
+MTENAPHSDAPAPLSDVMPTVLVLDFGAQYAQLIARRVREANVYSEVVPASTPAAQILER
+RPAALILSGGPSSVYEPGAPTLDPALLEAGVPVLGLCYGFQSIAHALGGTVAKTGTREYG
+STRLDSVDADSVLFAGQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDAERRIY
+GVQWHPEVGHSSHGQQVLEHFLHQGAGLGSDWTASNVIEEQVERIREQIGDKRAICGLSG
+GVDSAVAAALVQRAIGDRLTCVYVDHGLMRQGESAEIEQAFGEAHGGARLVMVDAREDFL
+SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPEATEVRFLVQGTLYPDVVESG
+GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG
+LGIRIIGEVTQERLDLLRSADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY
+GHPIVLRPVTSEDAMTADWARIPDDVLSRISNRITNEVDGVNRVVLDVTSKPPGTIEWE
+>3_1131
+MTQNEPTRDQPAPLHDVLPTVLVMDFGAQYAQLIARRVREANVYSEVVPSSTPAQEILDR
+RPAALILSGGPSSVYEAGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVARTGTREYG
+STRLESADGGSVLLAGQDAAQVVWMSHGDAVTEAPEGFAVTAVTAGAPVAAFEDRERRIF
+GVQWHPEVGHSERGQEILANFLTEGAGLSQDWTAENVIEEQVARIREQIGDARAICGLSG
+GVDSAVAAALVQRAIGDRLTCVYVDHGLMRQGESDEIERAFGEAHGGAKLVMVDAREDFL
+AALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESAHDPNAPEVRFLVQGTLYPDVVESG
+GGDGTANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG
+LGIRIIGEVTQERLDLLRQADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY
+GHPVVLRPVTSEDAMTADWARIPSEVLSRISNRITNEVDGINRVVLDVTSKPPGTIEWE
+>4_1525
+MTQNAPHPDTPTPLSDVMPTVLVLDYGAQYAQLIARRVREANVYSEVVPASTPAAQILER
+EPAALILSGGPSSVYEPGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVAKTGTREYG
+STRLDSVDADSVLFADQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDRERRIY
+GVQWHPEVGHSSRGQRVLEQFLHVGAGLGADWTASGVIEEQVERIREQIGDKRAICGLSG
+GVDSAVAAALVQRAIGDRLTCVYVDHGLMREGESAEIEQAFGEAHGGARLVMVDAREDFL
+SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPDATEVRFLVQGTLYPDVVESG
+GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG
+LGIRIIGEVTQERLDLLRRADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY
+GHPVVLRPVTSEDAMTADWARIPDDVLSRISNRITNEVDGINRVVLDVTSKPPGTIEWE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001334.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001334.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e12f3dd6baf362f3850f1ab8fc4acdb6ce7f400
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001334.fa
@@ -0,0 +1,50 @@
+>0_1599
+MARTRVAGLTPGHRIAETPVPKGVFVTTTSTGPSPEPVHSSSDPFGFFGLTYDDVLLLPN
+ATDVIPADADPGTRLTRNIRLNIPIVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ
+ARHVDTVKRSESGMIKDPVTIGPDATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT
+RFIPREEWATRTVDTAMTRMPLVTAQEGVSRAETIRLFSQNRVEKLPLVDDAGRLTGLIT
+IKDFDKAEQYPDAAKDDEGRLRVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV
+LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV
+PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGADSVMLGSLLAGTAESPGDLV
+FYQGKQFKTYRGMGSLGAMQTRNGTRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPVA
+SVVHQLVGGLRQTMFYTGASTVTDLKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR
+>1_1314
+MARTRVAGLTPGHRIAETPVPKGAFVTNTSTGPSPEPVHSSSDPFGFFGLTYDDVLLLPN
+ATDVIPADADTGTRLTRNIRLNIPIVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ
+ARHVDTVKRSESGMIKDPVTIGPDATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT
+RFIPREEWATRTVDTAMTRMPLVTAQEGISRAETIRLFSQNRVEKLPLVDDAGRLTGLIT
+IKDFDKAEQYPDAAKDDEGRLLVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV
+LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV
+PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGADSVMLGSLLAGTAESPGDLV
+FYQGKQFKTYRGMGSLGAMQTRNGTRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPIA
+SVVHQLVGGLRQTMFYTGASTVADLKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR
+>2_1215
+MARTRVAGLTPGHRIAETPVPKGAFVTTTSTGPSSEPVHSSADPFGFFGLTYDDVLLLPS
+ATDVIPAEADTSTQLTRNIRLNIPVVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ
+ARHVDTVKRSESGMIKDPVTIGPKATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT
+RFIPHEEWETRTVDTAMTRMPLITAREGISREETIRLFSQNRVEKLPLVDEAGRLTGLIT
+IKDFDKAEKYPDAAKDDEGRLRVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV
+LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV
+PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGAESVMLGSLLAGTAESPGDLV
+FYQGKQFKAYRGMGSLGAMQTRNGKRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPIA
+SVVHQLVGGLRQTMFYTGASTVDELKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR
+>3_1127
+MSTSTGPSSDPVYASEDPFGFFGLTYDDVLLLPNATDVIPADADTSTQLTRNIRLNIPVV
+SAAMDTVTEAPLAIAIARQGGMGIIHRNLSIEDQAKHVDTVKRSESGMISDPVTIGPKAT
+LAELDELCAQYRVSGLPVVAEDMTLLGIITNRDTRFIPHEEWDTRTVDTAMTRMPLITAQ
+DGISREEVLHLFSQNRVEKLPLVDDAGRLTGLITIKDFDKAEKYPDAAKDDEGRLRVGGA
+VGFFGDGWERAMTLVEAGVDALVVDTANGHTHGVLDMIARLKKEKAAAHVDVIGGQAATY
+AGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGVPQITAIYEAAKATRPAGVPLIADGGL
+QHSGDIGKALVAGADSVMLGSLLAGTAESPGDLVFYQGKQFKAYRGMGSLGAMQTRNGTR
+SFSKDRYFQADVPDEDKLIPEGIEGQVPYRGPIASVVHQLVGGLRQTMFYTGAPTIVDLK
+ENGRFVRITTAGLKESHPHDIMMTVEAPNYRSK
+>4_1529
+MARTRVAGLTPGHRIAETPVPKGAFVTNTSTGPSPEPVHSSSDPFGFFGLTYDDVLLLPN
+ATDVIPADADTGTRLTRNIRLNIPIVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ
+ARHVDTVKRSESGMIKDPVTIGPDATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT
+RFIPREEWATRTVDTAMTRMPLVTAQEGISRAETIRLFSQNRVEKLPLVDDAGRLTGLIT
+IKDFDKAEQYPDAAKDDEGRLLVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV
+LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV
+PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGADSVMLGSLLAGTAESPGDLV
+FYQGKQFKTYRGMGSLGAMQTRNGTRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPVA
+SVVHQLVGGLRQTMFYTGASTVADLKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001339.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001339.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86d3b4f7a40e5ed15dfd383eb059fd2ce7b66425
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001339.fa
@@ -0,0 +1,35 @@
+>0_1607
+MTLDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVVVTAALIVVS
+LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE
+WAGLGLLVTMVLVPGAGLVTRMAGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA
+VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL
+GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRMNL
+PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG
+>1_1322
+MILDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLAGIVVTAVLVVVS
+LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE
+WAGLGLLVTMVLVPGAGLVTRMAGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA
+VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL
+GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL
+PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG
+>2_1208
+MTDLHPGVADARTRLPEPGPGERVCWVPPTVLRPQRSRWQRTWPLLAGVAVTVLLAVVSL
+FVGVYDVGAEGGREMFAITRVPRTVALVLAGAAMAMCGLIMQLMTQNRFVEPSTTGTTEW
+AGLGLLVTMILIPGASIVTRMTGAVLFAFVGTMVFFLFLRRVRLQSSLIVPIVGIMLGAV
+VGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLVVCVAVFVIADRFTVAGLG
+KDVATNVGLNYNAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNIVSMVRGDNLRTNLP
+WVVMVGIWVVIVCDLIGRTVIAPFEVPISLILGLVGAVVFLGLLIRQAKHG
+>3_1120
+MTLDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVLVTAALIVVS
+LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE
+WAGLGLLVTMVLVPGSGLVTRMVGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA
+VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL
+GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL
+PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG
+>4_1537
+MILDVRHHVADAPPRLEELGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVVVTAALIVVS
+LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE
+WAGLGLLVTMVLVPGAGLVTRMVGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA
+VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFLIADRFTVAGL
+GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL
+PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001340.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001340.fa
new file mode 100644
index 0000000000000000000000000000000000000000..687a7dce5cc3d235b63504f5bcbfbb70e86618b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001340.fa
@@ -0,0 +1,36 @@
+>0_1608
+MPRSVSAPRLARLALTSVAALALVGCSAGGAATGSSSASASGESSASASAAGGSSAASGG
+IAAGVTVTDMSGAEVTLPEEVDSVIATDNRAFRTLDDWGVELSAAPKQIMYKGEGGPSYL
+QDDSVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVVDTDFDVTQTP
+MDEGLKELTTLLGEATGHEADAEKLIADFDAATQRAKDAYDPEQTVMGLIASGGELSYVA
+PSTGRAIGPFFDMLELTPALEQSGTDNHQGDDISVEAIAKSNPDWLIVMDRDAAIGEENA
+TAAELIERSEALQDVTAVKEGNIVYLPADFYVAEDIQNHTTVMEDLAKAFEGAQ
+>1_1323
+MPSSARAPRLARLALTSVAALALVGCSAGGAATGSSSASASGESSASASASGESSASASA
+AGGSSAASGGIATGVTVTDMSGAEVTLPEEVDSVIATDNRTFRTLDDWGVELSAAPKQIM
+YKGEGGPSYLQDDSVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVV
+DTDFDVTQTPMDEGLKELTTLLGEATGHEADAEKLIADFDAATQRAKDAYDPEQTVMGLI
+ASGGELSYVAPSTGRAIGPFFDMLELTPALEQSGTDNHQGDDISVEAIAKSNPDWLIVMD
+RDAAVGEENATAAELIERSEALQDVTAVKEGNIVYLPTDFYVAEDIQNHTTVMEDLAKAF
+EGAQ
+>2_1207
+MQRSPRTPRLKALALASVAALALVGCSAGGAAEGPASGSADTGSAAGSGSASAPAGDGVA
+AGATVTDMSGAEITLPEEIDSVITTDNRTFRTLDEWGVELSAAPKQLMFKGEGGPGYLQD
+DEVADIGNHREPDMEVFVTAEPDVVFNGQRFNERKAEIDELTGDAAVIDTDFDPKQKPMD
+EGLKELTTLLGEATGHQDDAAALNKEFDDAVAKAKGAYDSEQTVMGLISTGGELSYVAPG
+TGRSIGPMFDILGLTPALEQAGSDNHQGDDISVEAIAQSNPDWLIVMDRDAATGEANATA
+AELIERSEALKDVTAVKEGNIVYLPQDFYVAEDIQNYTTVMDDLAKAFEGAR
+>3_1119
+MRTARLSTAAALASLAALTLAGCGAGGPAAEGSSPASSAASSSPASSAASSSATAGGVAA
+GVTVTDMSGTEVTLPEEVDSVIATDNRIFRTLDDWGVELSAAPKQIMYKGEGGPSYLQDD
+SVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVVDTNFDVTQTPMDE
+GLKKLTTLLGEATGHEADAEKLIADFDAATQLAKDAYDPEQTVMGLIASGGELSYAAPST
+GRSIGPFFDMLDLTPALDQSGTDNHQGDDISVEAIAKSNPDWLIVMDRDAAVGEENATAA
+ELIERSEALQDVTAVKEGNIVYLPADFYVSEDIQNHTTVMEDLAKAFEGAQ
+>4_1538
+MPRSARAPRLARLALTSVAALALVGCSAGGAATGSSSASASGESSASASASGGSSAASGG
+IATGVTVTDMSGAEVTLPEEVDSVIATDNRIFRTLDDWGVELSAAPKQIMYKGEGGPSYL
+QDDSVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVVDTNFDVTQTP
+MDEGLKELTTLLGEATGHEADAEKLIADFDAATQRAKDAYDPEQTVMGLIASGGELSYVA
+PSTGRAVGPFFDMLELTPALEQSGTDNHQGDDISVEAIAKSNPDWLIVMDRDAAIGEENA
+TAAELIERSEALQDVTAVKEGNIVYLPADFYVAEDIQNHTTVMEDLAKAFEGAQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001341.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001341.fa
new file mode 100644
index 0000000000000000000000000000000000000000..441383d236220b712f3ba7095c06c59fe5e33d0e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001341.fa
@@ -0,0 +1,43 @@
+>0_1609
+MARPRPAARPSRPSAAASEEDDTALAPVLESEGRALLDSLAGYREADALAVSSRLRAAGH
+PPERVAAALTQAALRSRAEARLGPEARRMLFTRDGLEQATRPLVAGLHADRLAAAGARRV
+ADLGCGLGLDARAFADRGLDVVAVERDAVVAAAAEVNLAGHRGARVVHGDAVAWARAHVP
+AEADAVWLDPARRQVGGGGSARVFDPEAFSPPLSVVTDIAATGVPVGVKLGPGLPHEAVP
+AGAEAEWVSVDGDVVEAALWFNAAARPGVRRAARVMTVHGGKTTTAQLVSGADFGDSPEV
+EAVGEEGMAGLVGAVLHEPDGAVIRAGLVTDLAVSWPVPTRQLDPHLAYLVAPEPVHDGL
+ARAHRIEAVHGFHLASLRRWAKETGVGRLDVKKRGIRETPEEVRRAVLGGAKPGRRGGAG
+RHATLVLARVGRSRFALEVTPLD
+>1_1324
+MARPRPASRSPRPTAAASEADDTALAPVLEPEGRALLDSLAGYREADALAVSSRLRAAGH
+PPERVAAALTQAALRSRAEARLGPEARRMLFTRDGLEQATRPLVAGLHADRLAAAGARRV
+ADLGCGLGLDARAFADRGLDVVAVERDAVVAAAAEVNLAGHRGARVVHGDAVAWARAHVP
+AEADAVWLDPARRQVGGGGSARVFDPEAFSPPLSVVTDIAATGVPVGVKLGPGLPHEAVP
+EGAEAEWVSVDGDVVEAALWFNAAARPGVRRAARVMTVRGGETTTAQLVSGADFGDSPEV
+EAVGEEGMAGLVGAVLHEPDGAVIRAGLVTDLAASWPVPTRQLDPHLAYLVAPEPVRDGL
+ARAHRIEAVHGFHLASLRRWAKETGVGRLDVKKRGIRETPEEVRRAVLGGAKPGRRGGAG
+RHATLVLARVGRSRFALEVTPLD
+>2_1206
+MLTQADLRARAVPRLGPDARGMLFTRDGLEQATRPVVAALHAQRMAAAGARTVADLGCGL
+GLDARAFADAGLGVVAVERDAVVAAAAEVNLTDRPGARVVHGDAVPWAREHVPAQADAVW
+LDPARRQVGGGGSARVFDPEAFSPPLSVVEELAATGVPVGVKLGPGLPHEAVPAGAEAEW
+VSVDGDVVEAALWFNAAARPGVRRAARVIDTRGGQATTAELVSGADFGDSPGVEAVGEEG
+MPGLVGRCSTSRTAPSSGPGSSRTWRSPGRRRPASWTRTWPIWWPPSTRPTRWPGRTGST
+RSTISTSSLCAGGRRRRGSAAWT
+>3_1118
+MARSQRPARPSRPRPRPADRPGRPRAAESAADATRLEPVLDPAGRVLLDGLGDVSGQDPL
+ALSSRLRAAGHDADTVAAALTQAGLRHAGRAKLGALADGMLLTRDGLEQATRAVVAEHRA
+RRLQEAGVRSLADLGCGIGADALVYARAGLDVTAVERDPTVAAAAAANLATLAPAGAASV
+VTGDAEAWAAAHADEVDALWLDPARRRLGSSGTARVFDPEAFSPPLSFVLGLADGGRPVG
+VKLGPGLPHEHVPAAAEAEWVSVDGDVVEVTLWFGPLAQAPGRRTATLLDTRGSAVHRLV
+PAAASSPAVEAVGEEGVDGLVGQVLLEPDGAVIRAGLVTDLAVELGPAVRLLDPHLAYLV
+APDAAPHPLARGYRVLAVHEFRTKALARWARETGVGRLDVKKRGVRETPEQVRAAVLGRG
+TPGGRHATLVLARVGERRVAFEVEPLPAG
+>4_1539
+MARPRPASRSPRPTAAASEADATALTPVLEPEGRALLDSLAWYREADALAVSSRLRAAGH
+PPERVAAALTQAALRSRAEARLGRQARRMLFTRDGLEQATRPLVAGLHADRLAAAGARCV
+ADLGCGLGLDARAFADRGLDVVAVERDAVVAAAAEVNLAGHRGARVVHGDAVAWARAHVP
+AEADAVWLDPARRQVGGGGSARVFDPEAFSPPLSVVTDIAATGVPVGVKLGPGLPHEAVP
+AGAEAEWVSVDGDVVEAALWFNAAARPGVRRAARVMTVRGGETTTAQLVSGADFGDSPEV
+EAVGEEGMAGLVGAVLHEPDGAVIRAGLVTDLAASWPVPTRQLDPHLAYLVAPEPVHDGL
+ARAHRIEAVHGFHLASLRRWAKETGVGRLDVKKRGIRETPEEVRRAVLGGAKPGRRGGAG
+RHATLVLARVGRSRFALEVTPLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001342.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001342.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a59632e93508c1f59d7dc2d8d5c77343c10c91b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001342.fa
@@ -0,0 +1,40 @@
+>0_1610
+MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRALHVTEGLAEDDVNPHMTSELL
+QNTVELVTGVHERVDAATADLGRIAARVADAAAERGISLFCQGTHPFADAIAQPSTPSER
+YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD
+TGYQSQRTLLFQQLPTAGLPFQFQEWEGFERCVAQMEQVGMIADVTECRWDVRAVPRLGT
+VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD
+ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA
+LAGPPAAGEDADDAVAPLRAVVLDAAARTRASLDGRAG
+>1_1325
+MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRTLHATEGLAEDDVNPHMTSELL
+QNTVELVTGVHERVDAATADLGRIAARVADAAAARGISLFCQGTHPFADAIAQPSTPSER
+YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD
+TGYQSQRTLLFQQLPTAGLPFQFQEWEGFERCVAQMEQVGMIADVTECRWDVRAVPRLGT
+VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD
+ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA
+LAGPPAAGEDTDDAVAPLRAVVLDAAARTRASLDGRTG
+>2_1205
+MNLPFADSTQSTLGIEWEVALVDAATGDLRSEAPAILHELHKEAGLAEGEDHPHVTGELL
+QNTVELVTGVHEAVPTAVAELGTIAARVARAAADRGLALYCQGTHPFGEAMTQPITPKER
+YGRMVDLTQYWGRQMLIFGVHVHVGLDDPAKAMPAVNRLISRFPHLLALSASSPFWVGAD
+TGYQSQRTQLFQQLPTAGLPFQFETWAEFEACVQQMTDVGMVEDVTECRWDVRAVPRLGT
+VEMRACDGMATLEEIAAVAAYTQCLVHELSADVERGRHMEILPPWYTQENKWRASRYGMD
+ATVIVDAAGTQVPLAEHLGADLERLAPIAEELGCAAELAHARVLMEHSPADRQRAVEAEA
+LAGPPAEGESAHDAAAPLRAVVLDAAARTRESLERVGG
+>3_1117
+MSLPFADSAQSTLGIEWELALVDPLTGDLRSEAPGILEELRAEAGLDADADHPHVTGELL
+QNTVELVTGVHGSVPDAVADLGGIAARVQRAAADRGLALFCQGTHPFGEAMTQPITPKAR
+YGRMVDLTQYWGRQMLIFGVHVHIGLDDRAKAMPAVNRLISRLPHLLALSASSPFWVGAD
+TGYQSQRTQLFQQLPTAGLPFQFETWEGFEHCVEQMTGVGMVEDVTECRWDVRAVPRLGT
+VEMRVCDGMATLEEIGAVAAYAQCLVHELSAQVEDDEPVAILPPWYTQENKWRAARYGLE
+ATVITDDAGTQVPLAEHLAADLERLAPVAEELGCAAELAHARVLMEHSPADRQRRVAAEA
+AAGPPRTGEDPADPVAPLRAVVRDAADRTRESLRAFQG
+>4_1540
+MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRALHVTEGLAEDDVNPHMTSELL
+QNTVELVTGVHERVDAATADLGRIAARVADAAAERGISLFCQGTHPFAEAIAQPSTPSER
+YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD
+TGYQSQRTLLFQQLPTAGLPFQFQEWEDFERCVAQMEQVGMIADVTECRWDVRAVPRLGT
+VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD
+ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA
+LAGPPAAGEDADDAVAPLRAVVLDAAARTRTSLDGRTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001343.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001343.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0287c4fe4949ebfb254a15b94ec1faf13809ce3d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001343.fa
@@ -0,0 +1,40 @@
+>0_1611
+MRALTWQGKRNVVVEDVPDPRIQEPTDAIIEVTSTGICGSDLHLYEVLGPFMDAGDVIGH
+EPMGIVREVGSEVTHIRPGDRVVVPFTISCGRCWMCQRGLQSQCETTQVREQGCGAALFG
+YSRLYGSVPGGQAELLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYANVPDGG
+TLAVLGLGPIGQLAARIGVHLGYRVIGVDPVPERRAMAARHGIEVLDADGGEAEVLRERT
+GGRGPDAVLDAVGMEAHASPVGHAAHTAVGLLPDALGRAAMKTAGVDRLSALHTAIDAVR
+RGGTVSISGVYGGMKDPMPMLTLFDKQVTLTMGQCNVRRWVDDLLPLLDDPSDPLGVLDL
+TTHTAPLEDAPALYETFQKKEDGCVKVVLKP
+>1_1326
+MRALTWQGKRNVAVEDVPDPRIQEPTDAIIEVTSTGICGSDLHLYEVLGPFMDAGDVIGH
+EPMGIVREVGSEVTHIRPGDRVVVPFTISCGRCWMCQRGLQSQCETTQVREQGSGAALFG
+YSRLYGSVPGGQAELLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYANVPDGG
+TLAVLGLGPIGQLAARIGVHLGYRVIGVDPVPERRAMAARHGIEVLDADGGEAEVLRERT
+GGRGPDGVVDAVGMEAHASPAGHAAHTAVGLLPDALGRAAMKTAGVDRLSALHTAIDAVR
+RGGTVSLSGVYGGMKDPMPMLTLFDKQVTLTMGQCNVRRWVDDLLPLLDDPSDPLGVLDL
+ATHTAPLEDAPALYETFQKKEDGCIKVVLKP
+>2_1204
+MRALTWQGKRNVAVEDVPDPRIQEPTDAIVEITSTGICGSDLHLYEVLGPFMDAGDVIGH
+EPMGIVREVGAEVTHIKPGDRVVVPFNIACGRCWMCERGLQSQCETTQVREQGSGAALLG
+YSRLYGSVPGGQAEYLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYAQVPRGG
+TLAVIGLGPIGQLAARIGVHQGLRVIGVDPVPERRAMAARHGVEVLDSSDGGVAELLREC
+TQGRGPDGVVDAVGMEAHGSPVAKAAHTVVGLLPDALGRAAMKTAGVDRLDALHTAIDAV
+RRGGTVSLSGVYGGMQSPMPLLTMFDKQVTLAMGQCNVRRWVDDLLPLLDDPSDPLGVLD
+LTTHTAPLEDAPALYETFQKKEDGCIKVVLKP
+>3_1116
+MRALTWQGKRSVSVEDVPDPRIQEPTDAIIKVTSTGICGSDLHLYEVLGPFMDKGDVIGH
+EPMGIVEEVGSAVTNLSPGDRVVIPFNISCGHCWMCQHGLQSQCETTQVKEQGSGAALLG
+YSRLYGSVPGGQAEYLRVPHADYGPIKVPHTGPDTQWLFLSDVVPTAWQAVQYANVSKGD
+TLAVLGLGPIGQMSARIGVHLGCRVIAVDPVPERRHMAARHGVEVLDMEGSGTGVPDLLR
+QATGGRGPDGVVDAVGMEAHGAPVAAAAQTAAGMLPGPLARAAVKTSGIDRLTALHTAIE
+SVRRGGTVSLSGVYGGMQDPMPLLTMFDKQIQFTMGQCNVRRWVDDLLPLMDDPSDPLGV
+LDLVTHTAPLEDAPAMYEKFQKKQDGCIKVVLTP
+>4_1541
+MRALTWQGKRNVTVEDVPDPRIQEPTDAIIEVTSTGICGSDLHLYEVLGPFMDAGDVIGH
+EPMGIVREVGSEVTHIRPGDRVVVPFTISCGRCWMCQRGLQSQCETTQVREQGSGAALFG
+YSRLYGSVPGGQAELLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYANVPDGG
+TLAVLGLGPIGQLAARIGVHLGYRVIGVDPVPERRAMAARHGIEVLDADGGEAEVLRERT
+SGRGPDGVVDAVGMEAHASPAGHAAHTAVGLLPDALGRAAMKTAGVDRLSALHTAIDAVR
+RGGTVSLSGVYGGMKDPMPMLTLFDKQVTLTMGQCNVRRWVDDLLPLLDDPSDPLGVLDL
+TTHTAPLEDAPALYETFQKKEDGCIKVVLKP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001345.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001345.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa696d8cb7532fd7589a0425f0f766d931c6a6c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001345.fa
@@ -0,0 +1,20 @@
+>0_1613
+MRTRTLTRRAALTGLLGSAALGFTACTSSGYPADPDGTLDRVTGGVLRVGVVHHPPHVDV
+SGAEPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHA
+SITRDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR
+>1_1328
+MTITRRAALAGLLGGAALGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDASGA
+EPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHASIT
+RDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR
+>2_1202
+MTITRRAALTGLLGGAVLGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDASGA
+EPVGPEPDLIRGFAAAHDAEIAWTVSGEEALLTALEKGDVDLVAGGLTSDSPWTTHASLT
+RDYAEAAGPDGEPVKLVMAVPPGENQMLAALEAHLDAQAREAGR
+>3_1114
+MQTPRRTLLTGALAAAGVVLTGCTSSGYPADPDGTLDRITGGTLRVGASHHPPHVDAAGA
+EPQGPEPDLVRAFAAERDARVEWTVSGEEALMTALKQGDLDLVVGGLTKKSPWTTDAGLT
+RPYAETTGPDGEKAELVMAVPLGENQFQSALERFLDAHGEEAGA
+>4_1543
+MTITRRAALAGLLGGAALGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDASGA
+EPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHASIT
+RDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001347.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001347.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e62e1dd4625dc9aaf223f8dba6ec742507d6986
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001347.fa
@@ -0,0 +1,40 @@
+>0_1616
+MTGPLTRLEPMPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIP
+EIAARAHLEALVPTIRRALDTADVTLADLDAIAVTSGPGLAGALMVGVAGAKALATALGT
+PLYGINHLVAHVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISAEVELLGST
+IDDAAGEAYDKVARLIGAGYPGGPVIDRLAAQGDPTAFRFPRGLTAGKFVGSAEEPGPHR
+HDWSFSGLKTAVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLM
+LGGGVAANSRLRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWF
+GADPGQPVEVVSV
+>1_1331
+MPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIPEIAARAHLEA
+LVPTIRRALDTADVTLADLDAIAVTSGPGLAGALMVGVAGAKALATALGTPLYGINHLVA
+HVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISSEVELLGSTIDDAAGEAYD
+KVARLIGAGYPGGPVIDRLAAEGDPTAFRFPRGLTAGKFVGSAEEPGPHRHDWSFSGLKT
+AVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLMLGGGVAANSR
+LRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWFGADPGQPVEV
+VSV
+>2_1183
+MTGPLTRLEPMPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIP
+EIAARAHLEALVPTVRRALEAADVGLKDLDAIAVTSGPGLAGALMVGVAGAKALATALDT
+PLYGINHLVAHVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISSEVELLGST
+IDDAAGEAYDKVARLIGAGYPGGPVIDRLAAQGDPTAFRFPRGLTAGKFVGSAEEPGPHR
+HDWSFSGLKTAVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLM
+LGGGVAANSRLRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWF
+GADPGQPVEVVSV
+>3_1112
+MAPMSATATAPLVLGIESSCDETGVGIARGTALLAHEVASSVEEHVRFGGVIPEIAARAH
+LEALVPTVRRALDAAGVTLDEVDAIAVTSGPGLAGALMVGVAGAKALAVAADKPLYGINH
+LVAHVGVGLLDGVRPADWDDLPRDLGALLVSGGHTEILQVDRISSDVTLLGSTIDDAAGE
+AYDKVARLIGAGYPGGPVIDRMAQEGDPKAFRFPRGLTAGKFVGTAEEPGPHRHDWSFSG
+LKTAVSRAVEQFEAQGLEVPRTDIAASFQEAVADVITAKAVRACREHGLTHLLLGGGVAA
+NSRLRGLLADRCRSAGIELVVPPVNLCTDNGAMVAALGARLVADGVAPSDLAFGADPGQP
+VSAVSAA
+>4_1546
+MTGLLTRLEPMPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIP
+EIAARAHLEALVPTIRRALDTADVTLADLDAIAVTSGPGLAGALMVGVAGAKALATALGT
+PLYGINHLVAHVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISSEVELLGST
+IDDAAGEAYDKVARLIGAGYPGGPVIDRLAAQGDPTAFRFPRGLTAGKFVGSAEEPGPQR
+HDWSFSGLKTAVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLM
+LGGGVAANSRLRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWF
+GADPGQPVEVVSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001350.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001350.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab9256d23f424e5a55663f34ba7ac97dc5cc6950
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001350.fa
@@ -0,0 +1,25 @@
+>0_1619
+MSDHAIPAPGATLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS
+VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDAPAASAGEGEDGIVTDFS
+DEDGGQAEELRSAVVTGRGPRWAGVVLP
+>1_1334
+MSDHAIPAPGATLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS
+VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDAPAAPAGEGEDGIVTDFS
+DEDGGQAEELRSAVVTGRGPRWVGVVLP
+>2_1180
+MSRHEPPAPDPALPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAT
+VDRSVTVVEWGRGLAESLAGFPEDPDASWLDVEIVRARGGEDPAPAGPGADDGGIVTDFS
+DEDGEQAEELRSAVVTGYGPRWAGVRLP
+>3_1109
+MIAGRRAEQPLPAPVWERRVPLDGAAGTREFGAALAGVLRAGDVLILTGELGAGKTTLTQ
+GLGAGLGVREGVISPTFVLSRIHPSLADGPDLVHVDAYRLRSAGELTDLDLEATADRSVT
+VVEWGRGMAESLAGFPEDPEASWLDVEVLRARGGADLPDGPAGGDAAPDAPVIVTDFSDE
+EGEAAEEVRTAVVRAHGPRWAAVALP
+>4_1549
+MSDHEFPAPGPTLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS
+VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDGPAASAGEEDGIVTDFSD
+EDGGQAEELRTAVVTGRGPRWAGVVLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001352.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001352.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7b4a86039d993a6af8ee56856a9d3aa9242ee97
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001352.fa
@@ -0,0 +1,50 @@
+>0_1621
+MTADDLTRIAVTGSAVRTAEEPLLAAGRGPELMRAAAWALAEHAAALLRERGPVAGTTVA
+ALVGPGNNGGDALFALAFLRRRGVAAVAVPVRRDDDGAPRWHAEGWAALRAAGGRRADAV
+PPEAALVVDGVLGTGFTGEYELPAAARALPAEALVLACDVPSGVDADTGEVRGEALRAAA
+TVTFGALKSGLVLGEGAGRAGTVHVADIGLGPHLPTSPAARLGVMDEAAARAAHPAPAAA
+AHKYTRGVVAVVAGSERYPGAAVLASAGALHTGAGMVHHAGPQTTRDLVLAAHPEALVSA
+EGPEPSRADAWVAGPGLDTEHDARRRWAGVLAALEERPEAALLADASALDLVTAAELRSL
+RAAGTPVVLTPHAGEWSRLRERVPADGADAADPLAALRAWTAEHGATVLLKGPRTLVVAP
+DGEAWAVTGGGPDLAMGGTGDVLSGAIGAVLAADVARRSRARRAGEDPGPAPTARLAAAA
+AWLHAQAGAEQARAGRITTATLPAALGARVARLWWPDDAEPEAVR
+>1_1336
+MTADDLTRIAVTGSAVRTAEEPLLTAGRGPELMRAAAWALAEHAAALLRERGPVAGATVA
+ALVGPGNNGGDALFALAFLRGRGVAAVAVPVRRDDDGAPRWHAEGWAALRAAGGRRADAV
+PPEAALVVDGVLGTGFTGEYELPAAARALPAEALVLACDVPSGVDADTGEVRGEALRADT
+TVTFGALKSGLVLGEGAARAGTVHVVDIGLGPHLPTSPAARLGVMDEAAARTAHPAPAAE
+AHKYTRGVVAVVAGSERYPGAAVLASAGALHTGAGMVHHAGPQTTRDLVLAAHPEALVSA
+EGPEPSRADAWVAGPGLDTEHDARRRWAGVLAALEERPEAALVADASALDLVTAAELRSL
+RAAGTPVVLTPHAGEWSRLRERVPADGADAADPLAALRAWTSEHGATVLFKGPRTLVVAP
+DGEAWVVTGGGPDLAMGGTGDVLSGAIGAVLAADVARRSRARRAGEDPGPAPTARLAAAA
+AWLHARAGADQARAGRITTATLPTALGARVAHLWWPDDAEPEAVR
+>2_1178
+MSVEELRRVAVAGSAVRAAEAPLLAAGRGPAMMRDAAWALAEHAAALLRARGPVAGTTVA
+ALVGPGNNGGDALFALAFLRRRGVAAVAVPVRHDDDGAPRWHAEGWAALRAAGGRRADAV
+PAAAALVIDGMLGTGFAGELTLPPAARALPRDAVVLACDVPSGVDADTGEVRGEALRADA
+TVTFGALKTGLLVGEGAALAGEVHPVDIGLGPQLPTSPAARLYLADEAAVRAAHPAPAPD
+AHKYTRGLVAVAAGSPRYPGAAVLSCSGALHAGAGMVHHAGPEATRDRVLAEHPEALVSA
+EGPAPDRADAWVAGPGLDTQDDARRRWEGVLSALAERPEAALVADASALELVTAAQLRAL
+REGGTPVVLTPHAGEWARLRERLPADGADAADPLAALRSWSAAHGATVLLKGPRTLTVQP
+DGEAWLVADGGPELAMGGTGDVLAGALGAVLAADVARRSRARRAEQAPGPVPTAALAAAA
+AWLHARAGAEQARAGRLTTRTLPAALGAVTARLWRAGDENGRTRG
+>3_1107
+MRAHTGTDVRAAERPLLDEGRGEALMRTAAWGLAEHVAAELRARGPVAGATVAALVGPGN
+NGGDALWALAFLRRRGVEAVAVPVRRNEAGEPVWHAAGWAALQAAGGRRSTAVPARAAVV
+VDAMLGTGARGGFTLPEPARHLPSGAAVVACDLPSGVDADTGAVPGEALAADLTVTFGAS
+KTGLLLGAGPGRAGRVVCVDIGLGPHLPADPAAGLHVVDDDAVARLHPVPARDAHKYTRG
+VVGVVAGSERYPGAAVLAVGGVLAGGAGMAHHGGPARAGDLVLAAHPAALTSADGPAPER
+ADAWVLGPGLGDGDGARERVRATVAAVLASGADGDRGPAALVVDASALDLVTGEDLAALA
+AVDARTVITPHAGEWARLRDRLPVPAADAVDVDEDGAGELARLRAWTAARGVTVLLKGPA
+SLAVAPDGQAWLMRDGGPQLGVAGTGDVLAGALGAVLAAETARARRGGDERHGAARGGRP
+SPAALAAAAAWLHARAGVRQAADGRATADTLPAALGDVVARRWWENDAHGRRP
+>4_1551
+MTADDLTRIAVTGSAVRTAEEPLLAAGRGPELMRAAAWALAEHAAALLRERGPVAGATVA
+ALVGPGNNGGDALFALAFLRRRGVAAVAVPVRRDDDGAPRWHAEGWAALQAAGGRRADAV
+PPEAALVVDGVLGTGFTGEYELPAAARALPAEALVLACDVPSGVDADTGEVRGEALRADA
+TVTFGALKSGLVLGEGAARAGTVHVVDIGLGPHLPTSPAARLGVMDEAAARTAHPAPAAE
+AHKYTRGVVAVVAGSERYPGAAVLASAGALQTGAGMVHHAGPQTTRDLVLAAHPEALVSA
+EGPEPSRADAWVAGPGLDTEHDARRRWAGVLAALEERPEAALVADASALDLVTAAELRSL
+RAAGTPVVLTPHAGEWSRLRERVPADGADATDPLAALRAWTAAHGATVLLKGPRTLVVAP
+DGEAWVVTGGGPDLAMGGTGDVLSGAIGAVLAADVARRSRARRAGEDPGPAPTARLAAAA
+AWLHAQAGADQARAGRITTATLPTALGARVARLWWPDDAEPESVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001353.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001353.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e5ea1f084552b3fa1405a9825516aeb1e9da1f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001353.fa
@@ -0,0 +1,19 @@
+>0_1622
+MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP
+GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA
+AEEESA
+>1_1337
+MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP
+GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA
+AEEESA
+>2_1177
+MIVGVGMDVVDVPRFRAQLERTPALRERLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP
+GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEAQGITHWHLSLSHDGDVAAAYVVAERRA
+GEDGA
+>3_1106
+MIVGIGVDVVDVPRFERQLARTPALRERLFTEEERDLSLRSLAARFAAKEAIAKALGAPP
+GMMWHHCSIPRPAHGDGRPEVRLTDSVRDRADELGVTHWHLSLSHDGDVAVAYVVAERHD
+>4_1552
+MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAVAKAMGAPP
+GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA
+AEEESA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001358.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001358.fa
new file mode 100644
index 0000000000000000000000000000000000000000..805485d839ea1ee09481fca8e8d3f24dccb7a135
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001358.fa
@@ -0,0 +1,20 @@
+>0_1630
+MLQGFKDFIMKGNVLDLAVAVIIGAAFGKIVNALVEAVLMPLIAAAVGSPNFDSFAVLTV
+NGNDVKFGVLLTAIVNFLLIAAAVYFAIVMPMNKMIEARNRRLGIDPAEEEVPADVAVLT
+EIRDLLAERRGGPTSGTTTL
+>1_1344
+MLQGFKDFIMKGNVLDLAVAVIIGAAFGKIVNALVEAVLMPLIAAAVGSPNFDSFAVLTV
+NGNDVKFGVLLTAIVNFLLIAAAVYFAIVMPMNKMIEARNRRLGIDPAEEEVAADVAVLT
+EIRDLLAERRGGPTSGTTTL
+>2_1169
+MKGNVIDLAVAVVIGAAFGAVINAVVDSVLMPLIAALFAAPSFDDWLVLDINGVLVKFGV
+VLTAVVNFLLIAAAIYFAIVLPMNKMIERRNRRLGIDPAEEEVPEDVALLTEIRDLLSAQ
+RGGAAGTTHTTL
+>3_1100
+MKGNVVDLAVAVVIGAAFGKVVTALVDSVLMPLIAALFKAPSFDSWLVLNLNGVDVKFGV
+VLTAIVNFLLIAAAVYFCIVLPMNTMIERRNRRLGITPAEDEVAPDVAVLTEIRDLLARQ
+NGAPRV
+>4_1559
+MLQGFKDFIMKGNVLDLAVAVIIGAAFGKIVNALVEAVLMPLIAAAVGSPNFDSFAVLTV
+NGNDVKFGVLLTAIVNFLLIAAAVYFAIVMPMNKMVEARNRRLGIDPAEEEVPADVAVLT
+EIRDLLAERRGGPTSGTTTL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001364.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001364.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c87b6b07da24a3548a6f7a7ce3f6f4ac1fd53519
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001364.fa
@@ -0,0 +1,31 @@
+>0_1637
+MSEQHRPDAPTAPGEPPSVRVRLGLAYDGGTFHGWARQPGLDSVQGALEDGLERILRRPV
+RTVVAGRTDAGVHARGQVVHLDLTETEWAGLTRGRPGLEPATSLIRRLGGVLSGWGGAVV
+VHGARRAPAGFDARFSALWREYEYRIDDAPAARDPRTRGFTHWHGAALDDRLMALEADAV
+LGLHDFLSFCRPRAGATTIREVQHLEVRRDEDGVVRVRIRADAFCHNMVRAIVGALLQVG
+EGAREPGWLAHRVARPARDSEVRLAPPGGLTLLAVGYPDEAEELHRRAEGTRAKRTL
+>1_1354
+MSEQHRPDAPSAPGEPASVRVRLDLAYDGGTFHGWARQPGLDSVQGALEDGLERILRRPV
+RTVVAGRTDAGVHARGQVVHLDLTETEWAGLTRGRPGLEPATSLTRRLGGVLSGWGGAVV
+VHGARRAPAGFDARFSALWREYEYRIDDAPAARDPRTRGFTHWHGAALDDRLMALEADAV
+LGLHDFLSFCRPRAGATTIREVTHLEVRRDEDGVVRVRIRADAFCHNMVRAIVGALLQVG
+ERAREPGWLAHRVARPARDSEVRLAPPGGLTLLAVGYPDEAEELHRRAEGTRAKRTL
+>2_1162
+MTEQPAPSAPRPSAAGEEPVRVRLDLAYDGGAFRGWARQPGLDSVQGALEDGLERILRRP
+VRTVVAGRTDAGVHARGQVVHLDLAEGEWAGLTRGRPDLEPGASLARRLGGVLSGWDGAV
+VVHGARRAPAGFDARFSALWREYEYRIDDAPDRRDPRTRAFTHWHGAALDERLMALEADA
+VLGLHDFLSFCRPREGATTIREVQDLRVARDEDGSVRVRIRADAFCHNMVRAVVGALLQV
+GEGSREPGWLGLRVATPARDSQVRLAPPRGLTLLAVGYPEDGEGLRRRAEGTRARRTL
+>3_1093
+MVGMPDDALPAAPVEPRPEPTTGLPREGEVRLRLDLAYDGSDFRGWAAQPGLATVQGALE
+GALETIVRRPVRTVVAGRTDAGVHARGQVVHCDLTEAEWSALARGRADVDPADALVRRLQ
+GVLRPWQGAVVVRGARRAPDGFDARFSALWRAYEYRISDRPETRDPLARHGVLWHGARVD
+ERLMAVEAGALLGLHDFLSFCRPREGATTVREVQDAEVVRTPDGLVRVRLRADAFCHSMV
+RTIVGALLEVGEGRRTPGWTAARVAGPVRDSAARLAPAHGLTLLEVGYPETGEELRARAE
+GTRARRAPLADLG
+>4_1566
+MSEQHRPDAPSAPGEPASVRVRLDLAYDGGTFHGWARQPGLDSVQGALEDGLERILRRPV
+RTVVAGRTDAGVHARGQVVHLDLTETEWAGLTRGRPGLEPATSLIRRLGGVLSGWGGAVV
+VHGARRAPAGFDARFSALWREYEYRIDDAPAARDPRTRGFTHWHGAALDDRLMALEADAV
+LGLHDFLSFCRPRAGATTIREVKHLEVRRDEDGVVRIRIRADAFCHNMVRAIVGALLQVG
+EGAREPGWLAHRVARPARDSEVRLAPPGGLTLLAVGYPDEAEELRRRAEGTRAKRTL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001365.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001365.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d4b75a2748ae729e33001aafbceec1a5c6f3ca4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001365.fa
@@ -0,0 +1,30 @@
+>0_1638
+MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL
+PARRKVQGLIAAKNRTNKAVVHELFTVIGPAMAERNGGYTRITKIGNRHGDNAPMAVIEL
+IMDPISGKQAVVREAEQAAASAPAAPAESTPVEAVDPAATEEVTVAESQETAAEIDGAVP
+TTEDGSAPAEATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGEAAQK
+MA
+>1_1355
+MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL
+PARRKVQGLIAAKNRTNKAVVHELFTVIGPAMAERNGGYTRITKIGNRQGDNAPMAVIEL
+IMDPISGKQAVVREAEQAAASAPAAPAESTPVEAVDPAATEEVTVAESQETAAEIDGAVP
+TTEDGSAPAEATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGEAAQK
+MA
+>2_1161
+MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL
+PARRKVQGLIAAKNRTNKSIVHELFTVIGPAMAERNGGYTRITKIGNRQGDNAPMAVIEL
+IMEPISGKQAVVREAEQAAASAPAAETAPVQETAPVEAVDPAAAEDVTVAESQEAAAEID
+GAVATTEDGSAPEGASIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGE
+AAQKMAD
+>3_1092
+MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPHAERLITIAKKGDL
+PARRKVQGIIAAKSRTNKSIVHELFTVIAPAMAERNGGYTRITKIGNRQGDNAPMAVIEL
+VMEPVSGKQAVVREAEQAAASAPAAAPVEETPVEVVDPAATEEVTVAESEETAAEIDGAV
+ATTEDGSAPEGATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGEAAQ
+KMA
+>4_1567
+MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL
+PARRKVQGLIAAKNRTNKAVVHELFTVIGPAMAERNGGYTRITKIGNRHGDNAPMAVIEL
+IMDPISGKQAVVREAEQAAASAPAAPAESTPVEAVDPAATEEVTVAESQETAAEIDGAVP
+TTEDGSAPAEATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGEAAQK
+MA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001368.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001368.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a373deee2343a5f66251697ff272189a034188dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001368.fa
@@ -0,0 +1,20 @@
+>0_1641
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK
+>1_1358
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK
+>2_1158
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK
+>3_1089
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDRDIRVKDLTDDQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK
+>4_1570
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001369.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001369.fa
new file mode 100644
index 0000000000000000000000000000000000000000..049e361127f3d0d232693bcbfbf32584b7a9c8e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001369.fa
@@ -0,0 +1,10 @@
+>0_1642
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG
+>1_1359
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG
+>2_1157
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG
+>3_1088
+MKVQPSVKRICDKCQVVRRKGRVLVICENPRHKQRQG
+>4_1571
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001371.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001371.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20187aacae838b08b75b02f168fac424a42695df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001371.fa
@@ -0,0 +1,30 @@
+>0_1644
+MIGRRSLELKTAPQLQAMQRAGVVLSEALDATLAAAAPGVTTAELDAVFAGVLAERGATS
+NFLGYYDFPASICTSVNDEVVHGIPGDRVLQTGDVLKVDGGAIVDGWHADSARTVILGSS
+EAGTAGPADERLSAITREALWVGIAAFASATHVGDIGDAIDDFVSAQPGEELGILEEYVG
+HGIGSAMHLPPDVFNYRTGHRGPKIRPGLALAIEPMLVRGSIDTKVLADDWTVVTLDGAR
+ASQWEHSVCRHDGGVWVLTAPDGGASELARFGVVPVPPGE
+>1_1361
+MIGRRSLELKTAPQLQAMQRAGVVLSEALDATLTAAAPGVTTAELDAVFAGVLAERGATS
+NFLGYYDFPASICTSVNDEVVHGIPGDRVLQTGDVLKVDGGAIVDGWHADSARTVILGSS
+AAGTADPADERLSAITREALWVGIAAFASATHVGDIGDAIDDFVSAQPGEELGILEEYVG
+HGIGSAMHLPPDVFNYRTGHRGPKIRPGLALAIEPMLVRGSIDTKVLADDWTVVTLDGAR
+ASQWEHSVCRHDGGVWVLTAPDGGASELARFGVVPVPPGE
+>2_1155
+MVGRRSLELKTTPQLQTMRRAGVVLSEALDATLAAAAPGVTTAELDAVFAGVLAEHGATS
+NFLGYYDFPATICASVNEEVVHGIPGDRVLQAGDVLKVDGGAIVDGWHADSARTLVLGSS
+EAGTADEGDERLSAITREALWVGIAAFATAKHVGDIGDAIDDFVSAQPGEPLGILEEYVG
+HGIGSSMHMPPDVFNYRTGHRGPKVRPGLALAVEPMLVRGGIETRVLEDDWTVVTVDGAR
+ASQWEHSVCRHAGGLWVLTAPDGGASELERFGVVPVPPGE
+>3_1086
+MFSRRSIELKTTPQLQTMQRAGVVLSEALDAAVAAAAPGVTTAEVDAVFADVLAQHGATS
+NFLGYYGYPATVCASVNEEVVHGIPGERVLQQGDVLKIDGGAIVDGWHSDSARTLILGSS
+EAGTADPEDERLSEITRQALWVGIAAFAQARHVGEIGDAVDDFVTSQPGAPLGILEDYVG
+HGIGSAMHLAPDVFNYRTGHRGPKVQHGMALAIEPMLVRGGIETRTLEDEWTVVTTDGAR
+ASQWEHTVCRHPGGVWVLTAPDGGAAELAAHGVVPVPPGE
+>4_1573
+MIGRRSLELKTAPQLQAMQHAGVVLSEALDATLTAAAPGVTTAELDAVFAGVLAERGATS
+NFLGYYDFPASICTSVNDEVVHGIPGDRVLQTGDVLKVDGGAIVDGWHADSARTVILGSS
+AAGTADPADERLSAITREALWVGIAAFASATHVGDIGDAIDDFVTAQPGEELGILEEYVG
+HGIGSAMHLPPDVFNYRTGHRGPKIRPGLALAIEPMLVRGSIDTKVLADDWTVVTLDGAR
+ASQWEHSVCRHDGGVWVLTAPDGGASELARFGVVPVPPGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001385.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001385.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e51ee5ec4754329b1f7c98eb6bcef2b2597c886a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001385.fa
@@ -0,0 +1,20 @@
+>0_1658
+MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR
+GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVTEDVAREALRL
+AIHKLPLKARIIRREGGE
+>1_1375
+MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR
+GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVTEDVAREALRL
+AIHKLPLKARIIRREGGE
+>2_1141
+MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR
+GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVSEEVAREALRL
+AIHKLPLKARVIRREGGE
+>3_1072
+MLIPRRVKHRKQHHPKRSGMAKGGTTVTFGEWGIQALSPAYVTNRQIEAARIAMTRYIKR
+GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVSEEVAREALRL
+AIHKLPLKARIIRREGGE
+>4_1587
+MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR
+GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVTEDVAREALRL
+AIHKLPLKARIIRREGGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001393.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001393.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c393316bc2d25f40e14885cdab0b3f67e0b2e5c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001393.fa
@@ -0,0 +1,15 @@
+>0_1666
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL
+>1_1383
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL
+>2_1133
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL
+>3_1064
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL
+>4_1595
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001397.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001397.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff87be69dc1a3653021a993c3444120e040f3132
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001397.fa
@@ -0,0 +1,65 @@
+>0_1670
+MAQDVLTDLHKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGGATTDWMEQEKE
+RGITITSAAVTCFWNDHQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGARPLVMQLPIGAENDFVGVVDL
+LSMKAFVWPGDAKGDVTMGASYETREIPAELQEKAEEYRNELVEAVAETSEELMEKYLEG
+EELTVEEIQAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGSVKGHAV
+NDEEEVLEREASKEAPFSALAFKIATHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPANPIILESMTFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVNALVPLS
+EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE
+>1_1387
+MAQDVLTDLHKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGGATTDWMEQEKE
+RGITITSAAVTCFWNDHQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGARPLVMQLPIGAENDFVGVVDL
+LSMKAFVWPGDAKGDVTMGASYETREIPAELQEKAEEYRNELVEAVAETSEELMEKYLEG
+EELTVEEIQAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGSVKGHAV
+NDEEEVLEREASKEAPFSALAFKIATHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPANPIILESITFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVNALVPLS
+EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE
+>2_1129
+MAQDVLTDLNKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGASTTDWMEQEKE
+RGITITSAAVTCFWNDNQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVNRLGARPLVMQLPIGAENDFVGVVDL
+LSMKAFVWPGDAKGDVTMGAEYETREIPAELQEKAEEYRAQLVEAVADTSEELMEKYLEG
+EELTTEEIQAGVRHLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGAVKGHDV
+KDEEVELEREASKDAPFSALAFKIASHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDAAHPIILESMTFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTADGEIYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVKALVPLS
+EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE
+>3_1060
+MAQDVLTDLNKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGASTTDWMEQEKE
+RGITITSAAVTCFWKNNQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGAKPLVMQLPIGSESDFIGVVDL
+LTMKAFVWPGDAKGDVTMGAEYETQEIPADLQEKAEEYRTQLLEAVADTSEELMEKYLEG
+EEISEEEIVAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGAVKGHAV
+GDEEQVLEREPSKEAPFSALAFKIASHPFFGTLTFIRVYSGRLEGGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPQNPIILESMTFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNDETGQTEIGGMGELHLDVFVDRMRREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPVLLEPLMAVEVRTPEEFMGDVVGDLNSRRGQIQSMEDATGVKVVNALVPLS
+EMFGYIGDLRSRTQGRAVYSMTFHSYSEVPKNVADEIIQKSQGE
+>4_1599
+MAQDVLTDLHKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGGATTDWMEQEKE
+RGITITSAAVTCFWNDHQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGARPLVMQLPIGAENDFVGVVDL
+LSMKAFVWPGDAKGDVTMGASYETREIPAELQEKAEEYRNELVEAVAETSEELMEKYLEG
+EELTVEEIQAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGSVKGHAV
+NDEEEVLEREASKEAPFSALAFKIATHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPANPIILESMTFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVNALVPLS
+EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001400.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001400.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ff6df45ac42a720bdd577e04e4d6d9e86cd3ade
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001400.fa
@@ -0,0 +1,115 @@
+>0_1673
+MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC
+ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL
+APKDLEKVIYFAAYMITSVDEEARHRDLANLQAEYDQETRVLADQRDSDIAAVAADLEKD
+LAKLESEGAKAAEKKKARDAADKTMAQIRKRADADLDRKEQVWDRFKNLKVADLEGDEGL
+YRAMRDKYGQYFEGSMGAEAIQRRLQTFDLEAESEMLRETIKTGKGQRKTRALKRLKVVN
+AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL
+GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK
+RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR
+PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ
+MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDEVGAGN
+LYATVGEAIMAFDGGDLHLNAPARIGVEGFVPSADVPAPEGWSEGEIALIETTLGKVLFN
+ELLPDDYPWLDKQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS
+DITSDFDKAAIMEGYEEQAQRVQQQYDKGLIADDERRSELIDIWNKATDEVAAAMKDGLP
+ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH
+GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTERGLSVTIAAPNADGELVAHE
+QVENSAFARTLAQDVTGEDGTVLASAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT
+CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ
+ELFEARTPKGVAPISEVAGRVTIEDTETSVRLLLTPDDGSEEIAYPVLRRARILVADGEH
+VPVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR
+ITVIESGDTDLLPGELTDRARFVAANRAAVAEGRQPASGRDELMGITKASLATDSWLSAA
+SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA
+SPAGFADFDYPGLDQSLGENDFHAVSLDDYGRGGDFRA
+>1_1390
+MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC
+ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL
+APKDLEKVIYFAAYMITSVDEEARHRDLANLQAEYDQETRVLADQRDSDIAAVAADLEKD
+LAKLESEGAKAAEKKKARDAADKTMAQIRKRADADLDRKEQVWDRFKNLKVADLEGDEGL
+YRAMRDKYGQYFEGSMGAEAIQRRLQTFDLEAESEMLRETIKTGKGQRKTRALKRLKVVN
+AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL
+GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK
+RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR
+PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ
+MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDEVGAGN
+LYATVGEAIMAFDGGDLHLNAPARIGVEGFVPSADVPAPEGWSEGEIALIETTLGKVLFN
+ELLPDDYPWLDKQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS
+DITSDFDKAAIMEGYEEQAQRVQQQYDKGLIADDERRSELIDIWNKATDEVAAAMKDGLP
+ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH
+GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTERGLSVTIAAPNADGELVAHE
+QVENSAFARTLAQDVTGEDGTVLASAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT
+CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ
+ELFEARTPKGVAPISEVAGRVTIEDTEASVRLLLTPDDGSEEIAYPVLRRARILVADGEH
+VPVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR
+ITVIESGDTDLLPGELTDRARFVAANRAAVAEGRQPASGRDELMGITKASLATDSWLSAA
+SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA
+SPAGFADFDYPGLDQSLGENDFHAVSLDDYDRGGDFRA
+>2_1126
+MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC
+ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL
+APKDLEKVIYFAAYMITSVDEEGRHRDLANLQAEYDQETRVLADQRDADIAAVAADLEKD
+LAKLESEGAKAAEKKKARDAADKTMSQIRKRADAELDRKEQVWDRFKNLKVADLEGDEGL
+YRTMRDKYGQYFEGSMGAEAIQRRLQTFDLAAESEMLRETIKTGKGQRKTRALKRLKVVN
+AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL
+GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK
+RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR
+PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ
+MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDAVGAGN
+AYATVGEAVMAFDGGDLHLNAPVKIGVDGFVPSTAVPAPEGWSEGELAVIETTLGKVLFN
+ELLPADYPWLDTQATKGSLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS
+DITSDFDKAAIMEGYEEQALRVQQQYEKGLIADDERRSELIDIWNKATDEVAAAMKDGLP
+ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH
+GARKGLADTALKTANSGYLTRRLVDVSQDVIVREEDCGTERGLSVTIAVPNADGELVAHE
+QVENSAFARTLAQDVTGEDGSVLASGGADVGDVLIDQLVGAGVSEIKVRSVLTCESAVGT
+CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ
+ELFEARTPKGVAPISEVAGRVTIEDTDASVRLLLTPDDGSEEIAYPVLRRARILVADGEH
+VAVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR
+ITVIESGETDLLPGELTDRARFVAANRSAVAEGRQPASGRDELMGITKASLATDSWLSAA
+SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA
+SPAGFADFDYPGLDQQLGESDFHAVSLDDYGRGGDFRS
+>3_1056
+MTTENPFGLMRIGLATADDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC
+ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL
+APKDLEKVIYFAAYMITSVDEEARHRDLPNLQAEHDQETRVLEDQRDADIAAVAADLEKD
+LAKLEAEGAKAAEKKKARDAADKTMAQIRKRADAELDRKAQVWDRFKNLKVADLEGDEGL
+YRAMRDKFGAYFEGSMGAEAIQRRLQTFDLAAESELLRETIKTGKGQRKTRALKRLKVVN
+AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL
+GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK
+RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNVKSAKRMVERFR
+PQVWDVLEEVISEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ
+MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRAEGKGAGR
+QFATVGEAVMAFDNGELHLNAPATIGVEGFVPSAAVAAPEGWTEGEVALIETTLGKVIFN
+DLLPADYPWLDTQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS
+DITSDFDKASIMQGYEDQAQRVQAQYDKGLIADDERRSELIDIWNKATDEVAAAMKAGLS
+ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH
+GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTGRGLSVTIAEPNHDGELVVRE
+QVENSAFARTLAQAVTAEDGTVLAEAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT
+CAKCYGRSMATGKLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ
+ELFEARTPKGVAPISEVAGRVTIEDTDASVRLILTPDDGSEEIAYPVLRRARLLVADGEH
+VAVGTQLVAGAVDPKQVLRVLGPRAAQRFLVQEVQDVYQSQGVGIHDKHVEVIVRQMLRR
+ITVIESGETDLLPGELTDRSRFVAANRAAVAEGKQPAAGRDELMGITKASLATDSWLSAA
+SFQETTRVLTQAAMEGKEDPLLGLKENVIIGKLIPAGTGLDRYTQTTVEPTEEAKANLFA
+APVGFADFDYPGLDQPLGEAEFHAVSLDDYGRGGDFRA
+>4_1602
+MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC
+ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL
+APKDLEKVIYFAAYMITSVDEEARHRDLANLQAEYDQETRVLADQRDSDIAAVAADLEKD
+LAKLESEGAKAAEKKKARDAADKTMAQIRKRADADLDRKEQVWDRFKNLKVADLEGDEGL
+YRAMRDKYGQYFEGSMGAEAIQRRLQTFDLEAESEMLRETIKTGKGQRKTRALKRLKVVN
+AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL
+GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK
+RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR
+PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ
+MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDEVGAGN
+LYATVGEAIMAFDGGDLHLNAPARIGVEGFVPSADVPAPEGWSEGEIALIETTLGKVLFN
+ELLPDDYPWLDKQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS
+DITSDFDKAAIMEGYEEQAQRVQQQYDKGLIADDERRSELIDIWNKATDEVAAAMKDGLP
+ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH
+GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTERGLSVTIAAPNADGELVAHE
+QVENSAFARTLAQDVTGEDGTVLASAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT
+CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ
+ELFEARTPKGVAPISEVAGRVTIEDTETSVRLLLTPDDGSEEIAYPVLRRARILVADGEH
+VPVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR
+ITVIESGDTDLLPGELTDRARFVAANRAAVAEGRQPASGRDELMGITKASLATDSWLSAA
+SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA
+SPAGFADFDYPGLDQSLGENDFHAVSLDDYGRGGDFRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001402.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001402.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e141562f25add668d15aab88689cba213d353c3b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001402.fa
@@ -0,0 +1,20 @@
+>0_1675
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK
+DEFDVVLEAAGDKKIGVIKEVRAITSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE
+GAGATVTLK
+>1_1392
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK
+DEFDVVLEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE
+GAGATVTLK
+>2_1124
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAAGAAGGDAAAAEEKD
+EFDVVLESAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLEG
+AGATVTLK
+>3_1054
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAMAAAGAPAGGDAAAAEEKD
+EFDVILEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLEG
+AGATVTLK
+>4_1604
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK
+DEFDVVLEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE
+GAGATVTLK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001403.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001403.fa
new file mode 100644
index 0000000000000000000000000000000000000000..06a2f9f31ef6a612ecffb031ed70f252f23dcc46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001403.fa
@@ -0,0 +1,20 @@
+>0_1676
+MATSAKESAVAELTDLFRESSAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA
+AKDAGLEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI
+KQLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAAQGEAA
+>1_1393
+MATSAKESAVAELTDLFRESSAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA
+AKDAGLEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI
+KKLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAAQGEAA
+>2_1123
+MATSAKESAVAELTDLFRESNAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA
+AKEAGVEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI
+KKIADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAQQGEAA
+>3_1053
+MATSAKESAVAELTDLFRSSSAAVLTEYRGLTVSELKQLRDSIRQDATYSVAKNTLTEIA
+AKEAGVEGLDAHLAGPTAIAFVTGDPVTVAKALRDFAKDHDKLVLKGGYMDGQPLDEAGI
+EKLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTARTVEALRAQQDQAA
+>4_1605
+MATSAKESAVAELTDLFRESSAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA
+AKDAGLEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI
+KKLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAAQGEAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001405.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001405.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ddddd2f671eecccc7acba45ac8e408057beff864
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001405.fa
@@ -0,0 +1,20 @@
+>0_1678
+MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI
+TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA
+NDVQAAAKIIAGTARSMGITVEG
+>1_1395
+MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI
+TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA
+NDVQAAAKIIAGTARSMGITVEG
+>2_1121
+MAPKKKVSGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI
+TVYEDRSFTFITKTPPAAELIKKAAGVAKGSATPHTAKVGKLTQAQCEEIAQTKMEDLNA
+NDVKAAAKIIAGTARSMGITVEG
+>3_1051
+MAPKKKVAGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATEAQRGNVIPVEI
+TVYEDRSFTFITKTPPAVELIKKAAGVQKGSSTPHTAKVGTLTQAQCEEIAQSKMEDLNA
+NDVKAAAKIIAGTARSMGITVEG
+>4_1607
+MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI
+TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA
+NDVQAAAKIIAGTARSMGITVEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001406.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001406.fa
new file mode 100644
index 0000000000000000000000000000000000000000..39954baeb22c947d5380b5b4b74b058d87a57c77
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001406.fa
@@ -0,0 +1,30 @@
+>0_1679
+MSEQELDRQPAEESVPMSEDAVAEETAETAQDAGTPVEDALDEVAGSGDETAEATVQEAD
+LAVAEGEDAPTPVEEQSDDEPAVDPAEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEAR
+ILTQDMEDSIYEIEVPMEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGV
+TGFVGNDAHHPQPLSLDEVYDMLAPSVIQEAARAAEKAGLAVPAAAESGAPAAPAIHVDF
+EVGESVTVNDGPFETLPATISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKAI
+>1_1396
+MSEDAVAEETAETAQDAGTPVEDALDEAAGSGDETAEATVQEADLAVAEGEDAPTPVEEQ
+ADDEPAVDPAEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARILTQDMEDSIYEIEVP
+MEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGVTGFVGNDAHHPQPLSL
+DEVYDMLAPSVIQEAARAAEKAGLAVPALVESGAPAAPAIHVDFEVGESVTVNDGPFETL
+PATISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKAI
+>2_1120
+MSEQELDRQAAEESVSVQEDGAVEETVETAQDAPAPAEDAAGETAVDGEEAAEATEATAQ
+EADPAAVEQAEEEPAVDPGEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARILSQDME
+DAIYEIEVPMEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGVTGFVGND
+AHHPQPLSLDEVYDMLAPSVIQEAARAAEKAGLAVPASAESGAAAAPAIHVDFEVGESVT
+VNDGPFETLPATISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKVI
+>3_1050
+MSEQELDRQDVEETAVAEDSTALEAPVEDTAAEEAEQTVQEADLAIAEGDQDAAEAPSAE
+ELDAAGQAPAQPDVEAAEQLRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARIQTQDMEDS
+IYEIEVPMEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTSGVTGFVGNDAH
+HPQPLTLDEVYDMLAPSVVQEAVREAEKAGLVPVAVAESGAAGAPAIHVDFEVGESVTVD
+DGPFETLPATISEIKPETQQLVVLVSIFERETPVTLSFNQVTKVI
+>4_1608
+MSEDAVAEETAQDAGTPVEDALDEPAGSGDETAEATVQEADLAVAEGEDAPTPVEEQSDD
+EPAVDPAEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARILTQDMEDSIYEIEVPMEE
+VVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGVTGFVGNDAHHPQPLSLDEV
+YDMLAPSVIQEAARAAEKAGLAVPAAAESGAPAAPAIHVDFEVGESVTVNDGPFETLPAT
+ISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKAI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001409.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001409.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8efe52dcc1b5da01ba736798386c71b92c4078ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001409.fa
@@ -0,0 +1,25 @@
+>0_1682
+MTDPAPRTAVNVDDHAIFRSGLRADLDPDRLAIVGEAGDVDEAVRAVLDLAPDVVLLDVH
+LPGGAGGGGAEVAERVLARRPAQRFLALSVSDAAEDVVAVIRAGARGYITKTASGAEVAD
+AAVRVADGDAVFSPRLAGFVLDAFRGTAPASPPVPAAATSGAAAPDEDLDRLSAREREVM
+RLIARGYTYREAGAELFISDRTVETHVSSVLRKLQLSNRHELTRWAARRGYA
+>1_1399
+MTDPAPRTAVIVDDHAIFRSGLRADLDPDRLAIVGEAGDVDEAVRTVLDLVPDVVLLDVH
+LPGGAGGGGAEVAERVLARRPAQRFLALSVSDAAEDVVAVIRAGARGYITKTASGVEVAD
+AAVRVADGDAVFSPRLAGFVLDAFRGTAPASPPVPAAATSGAAAPDEDLDRLSAREREVM
+RLIARGYTYREAGAELFISDRTVETHVSSVLRKLQLSNRHELTRWAARRGYA
+>2_1117
+MSVPAPRTAVIVDDHAIFRSGLRADLDPARLAIVGEAGDVDEAVRAVLELAPDVVLLDVH
+LPGGAGGGGAEVAERVLARRPAQRFLALSVSDAAEDVVAVIRAGARGYITKTASGAEVVD
+AAVRVAGGDAVFSPRLAGFVLDAFRGAAAPAAAPASPAVPDEDVDRLSAREREVMRLIAR
+GYTYREAGAELFISDRTVETHVSSVLRKLQLSNRHELTRWAARRGYA
+>3_1047
+MTVHADPVVPTAVVVDDHAIFRSGLRADLDASRLRIVGEAGDVDEAVRVVLQLAPDVVLL
+DVHLPGGAGGGGAEVASRVLAERPGQRLLALSVSDAAEDVVAVIRAGARGYITKSAAGAE
+VVEAALRVAGGDAVFSPRLAGFVLDAFRGLPTESAPAGPAPSEGDLDRLSAREREVMRLI
+ARGYTYREAGAELFISDRTVESHVSSVLRKLQLSNRHELTRWAARHGWA
+>4_1611
+MTDPAPRTAVIVDDHAIFRSGLRADLDPDRLAIVGEAGDVDEAVRTVLDLAPDVVLLDVH
+LPGGAGGGGAEVAERVLARRPAQRFLALSVSDAAEDVVAVIRAGARGYITKTASGAEVAD
+AAVRVADGDAVFSPRLAGFVLDAFRGTAPAPPLVPAAAASGAAAPDEDLDRLSAREREVM
+RLIARGYTYREAGAELFISDRTVETHVSSVLRKLQLSNRHELTRWAARRGYA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001410.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001410.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2383b92e2ad3b9ef35a63adc67c17a67203bd4b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001410.fa
@@ -0,0 +1,42 @@
+>0_1683
+MPTPSAPAPAPRPPLMRHGADRPVSGVAAGLARHLGMPAGRVRAALALLSLLGGAGLALY
+VWLWLLVPEEGPDGAPAADAPTLRGRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLG
+LAVDWALVGPVAVLVIGLGLAWMQLDLAGGPRAGRSGRLVRLVLGTALVLLAVLAIVLGA
+VSSGELWRALLAAVAMLAGAALVAMPYVLAWLRRRDAERTAFAVQAQRAEIAAHLHDSVL
+QSLALIQRRAQDADAVARVARAQERELRQFLALDSRGGPHSLAEALEQHAAAVEDAHGAR
+VEVVAVGRAAGAWLEPLAAAAREAMQNAARHAGDAQVFAEAGEDDRGRTVAEVFVRDRGP
+GFDLPTVPADRLGVRESILGRMGRAGGTARIRSGPGGTEVHLTLAEPEGARARTGQEHP
+>1_1400
+MPTPSAPAQAPRPPLMRHGADRPVSGVAAGLARHLGVPVGRVRAALALLSLMGGAGLALY
+VWLWLLMPEEGPDGAPAADAPTLRGRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLG
+LAVDWALVGPVAVLVIGLGLAWMQLDLAGGPRAGRSGRLVRLVLGTALVLLAVLAIVLGA
+VSSGELWRALLAAVAMLAGAALVAMPYVLAWLRRRDAERTAFAVQVQRAEIAAHLHDSVL
+QSLALIQRRAHDADAVARVARAQERELRQFLALDSRGGPRSLAEALEEHAAAVEDAHGSR
+VEVVAVGRAAGAWLEPLAAAAREAMQNAARHAGDAQVFAEAGEDDHGRTVAEVFVRDRGP
+GFDLHTVPADRLGVRESILGRMERAGGAARIRSGPGGTEVHLTLTEPEGARARAGQEHP
+>2_1116
+MPASAVPPSAPSGRAGPRRAAADDARTRPIGADPRTSEARASGTRAPLMRHRADRPVSGV
+AAGAARHLGLSPRTARAGFAVLALAGGAGLALYVWLWLLMPEEGADGAPTGEAPSLRGRA
+PEVLERVREGGWPVLLAAVVLGVGVITIADGLGLAVDWALVGPVAVLVIGLGLAWMQLDL
+AGGPPAGRVGRVVRLALGTALVLLAVLAIVLGGVTSGDLWLGLLVAVALIAGVAMVAMPY
+ALSWLRRRDAERTAFAVQAQRAEIAAHLHDSVLQSLALIQRRAHDPEAVARAARAQEREL
+RRFLALDDRGGHDSLAATLREHAAAVEDAHGRRVEVVAVGEASGAWLEPLTAAAREAMLN
+AARHAGDAQVFAEVAEDDDGRTVAEVFVRDRGPGFDPGAVPADRLGVRESVVGRMERAGG
+AARIRSGPGGTEVHLTLTRPDRVPPHAAQERP
+>3_1046
+MPAPAIPPPADLSARPALLRHAADRPVSGVAGGVARHLGLDPRLARAGFAVLALAGGAGI
+ALYAWLWLLMPEEGPDGAPAGPAPTLRGRAPEVLERLREGGWPILLAVVVLGVGVLTVAD
+GLGVPVDWALVGPVAVLVIGLGLAWMQLGAADGPEGGRWARRARLGLGTALVLLGVLAIV
+VGAVTAGDLWLGLLVAVALLAGGALVAMPFVLARRRRRDEERTGAAVRAQRDEIAAHLHD
+SVLQSLALIQRRADDPETVARVARAQERELRQFLALDSARAHGTLAEAVEDHAAAVEDAF
+GRRVEVVSVGEASGPWLEPLASAAREAMVNAARHAGDVQVFVEVSEDDGGRTLAEVFIRD
+RGTGFDLADVPADRLGVRESILGRMRRAGGTARIRSGPSGTEVQLSLADPGAPGVGLREG
+RGRA
+>4_1612
+MPTPSAPAPAPRPPLMRHGADRPVSGVAAGLARHLGMPAGRVRAALALLSLLGGAGLALY
+VWLWLLMPEERPDGAPAADAPTLRGRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLG
+LAVDWALVGPVAVLVIGLGLAWMQLDLAGGSRAGRSGRLVRLVLGTALVLLAVLAIVLGA
+VSSGELWRALLAAVAMLAGAALVAMPYVLAWLRRRDAERTAFAVQAQRAEIAAHLHDSVL
+QSLALIQRRAQDADAVARVARAQERELRQFLALDSRGGPHSLAEALEQHAAAVEDAHGAR
+VEVVAVGRAAGAWLEPLAAAAREAMQNAVRHAGDAQVFAEAGEDERGRTVAEVFVRDRGP
+GFDLHTVPADRLGVRESIVGRMERAGGTARIRSGPGGTEVHLTLTEPEGARARTGQEHP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001411.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001411.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8352ac3977a86b70c84027322d835dff1d0d74d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001411.fa
@@ -0,0 +1,36 @@
+>0_1684
+MTSTHDPFTGPGPHVAPDGAAAGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG
+VAERYRIDPLLARGVFVAVCMVSAGLGLLAYAAAWAVLPDPDGRVQFGRLRRGEWQDATV
+AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLVGLGALAVLVWWLVTRWDGRAQARVAPG
+RVPDADQPAHAVPRPAWYVGGGPRERAAEVTDPHGFRPEWIDPATGTWRDHVHSRERRAA
+TRLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP
+TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG
+>1_1401
+MTSTHDPFTGPGPHVAPDGAASGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG
+VAERYRIDPLLARGVFVAVCMVSAGLGLLAYAAAWAVLPDADGRVQFGRLRRREWQDATV
+AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLLGLGALAVLVWWLVTRWDGRAQARVAPG
+RAPDADQPSHAVPRPAWYVGGGPRERAAEVTDPHGFHPEWIDPATGTWRDHVHSRERRAA
+ARLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP
+TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG
+>2_1115
+MRRSDSSWVGGVLAGVAERYRVDPLLARGVFVALCVVSAGFGLLAYAVAWALLPDGDGTV
+HYGRLRRGEWQDATVAIAVIGGIGVLNVVLGAGFTLLAPVVGGPGSLLGLAAVAVLVWWL
+VTRWDGSTQSRVGPAPASEPEASGRAAARPAWYLRRDDARAAASRQDAHGFRADWLDPET
+GTWRSPVHSRELRAAARLAEEEQAAPAGPSGRGSAVVAAPRRLSPAVQAVTYAVAALAAA
+AAVGASLLVGVGSLTLLAVPAIVAALAVIAPVMLAALLTGRRPGSLAPASGILVGAAALQ
+VAVAVAVL
+>3_1045
+MDTAHDPFPAPRSSPATRPLPPGPASDARSRSAGTDGPAPDGLEVLPVWLRRPVEGWGVR
+RSRSSWVGGVLAGVAERYRIDPLLSRGVFVALCVVSAGIGLLGYALAWAVLPDADGRVHY
+GRLRRGEWSDAPVAIAAIAAIGALNVVLGAGFTLIAPVLGGPGSLIGLTALAVLVWWLVT
+RWDGEGERRMAPAQPARDAAARPAAEPSWYLRRHRPESATVDAHGFRSDWIDPETGSWRE
+QPHSREHRAAARLAEAQVRAAGQAAGRRPAGTGRGSHSAVKPLLGRGTRIATCVVAAGVA
+LAVSLAMVLGNVSTSATLFPVWPALAALGVMAAVMTAGLLRGRRPGLLAPLSGILVGVVA
+LQVCAHLLFTPLP
+>4_1613
+MTSTHDPFTGPGPHVAPDGAAAGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG
+VAERYRIDPLLARGVFVAVCMISAGLGLLAYAAAWAVLPDADGRVQFGRLRRGEWQDATV
+AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLVGLGALAVLVWWLVTRWDGRAQARVAPG
+RVPDADQPAHAVPRPAWYVGGGPRERAAEVTDPHGFRPEWIDPATGTWRDHVHSRERRAA
+ARLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP
+TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001416.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001416.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24d39fdd8a7d29a25d79c303154a3925d373d9f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001416.fa
@@ -0,0 +1,10 @@
+>0_1689
+MDTLLALEIFFLALVVLAGLGMAAVAAVVISGLFKGQR
+>1_1406
+MDTLLALEIFFLALVVLAGLGMAAVAAVVISGLFKGQR
+>2_1109
+MDTLLALEIFFLALVVLAGLGMAAVAAVVVGGLFKGQR
+>3_1039
+MDSIVALEIFFLVLVVLAGLGMAAVAALVVGGLFKGQR
+>4_1618
+MDTLLALEIFFLALVVLAGLGMAAVAAVVISGLFKGQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001417.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001417.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a05fd35cb1f60ba1146f980a4ea1ccb749775ace
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001417.fa
@@ -0,0 +1,30 @@
+>0_1690
+MAREVRPAVARPGPSRCAPGRMGQVMRLSMALSAAVAALVLGGAALLGPVPAALAAAVVI
+LVIAWGWPRQMGAPARLSLSVTLAVAGGAAVLLMLLWPPLEDGHSGAWTLFEPLAVVVAW
+STMASFVVQLVRGTGRPLRLESTVATMGGAFMAVVTACWVAVSRWTDTPAVAGLVITLAV
+TVAAVSLVGLTPWMQGRPGVLALVVIPLGTVLAWPVSALAGVGARDRPAVTAAALAVAVL
+VSLTAATAPSSRPRPEDRPVGTTLRPRRAGYALALAPVGAAGVVAHVMVGFLA
+>1_1407
+MAREVRPAVARPGPSRCAPGRMGQVMRLSMALSAAVAALVLGGAALLGPVPAALAAAVVI
+LVIAWGWPRQMGAPARLSLSVTLAVAGGAAVLLMLLWPPLEDGHSGAWTLFEPLAVVVAW
+STMASFVVQLVRGTGRPLRLESTVATMGGAFMAVVTACWVAVSRWTDTPAVAGLVITLAV
+TVAAVSLVGLTPWMQGRPGVLALVVIPLGTVLAWPVSALAGVGARDRPAVTAAALAVAVL
+VSLTAATAPSSRPRPEDRPVGTTLRPRRAGYALALAPVGAAGVVAHVMVGFLA
+>2_1108
+MMRLSMALSAAVAALVLGGATLLGPVPAAVAAMAVILVIAWGWPRQMGAPARLSLSVTLA
+AVGLVAVLLMLLWPPIEDGRSGAWTLFEPLAVALAWSTMASFVVQLVRGTGRPLRLESTV
+ATMGGGLIAVMTACWVAVSRWTDAPAVAGLVLTLAISVAAFSLIGLIPGVQGRPGVLALV
+VVPLGALLAWPVSALLGVGPQDRAAVVAAVVAVATLVSLTAATAPSARPRPEDRPVGTTL
+RPRRAGYALALAPVGAAGVVAHVMVGFLA
+>3_1038
+MMRLSMALSAALAALVLGGAALLGPVPAAVAACLVIAVIAFGWPRQMGAPARLSLTLTML
+VAGVLGVLVMVLWPRGDAGPRGAWALFEPLAVVLAFGTMASFIVQLVRGTGRPLRLESTV
+TTMGGVLVCLLAASWVPLAHHREAPGATGLVVTLAATLIVTSLIGLTPFMQGRPRVLALV
+MVPASGVVAALVSLLLGAPAHTAWVYAAAALGTAGLVSLTAAAAPSSRPLPEDRVVGTTL
+SPRRAGYALAMAPVGAAGVVGHVMLGFLA
+>4_1619
+MMRLSMALSAAVAALVLGGAALLGPVPAALAAAVVILVIAWGWPRQMGAPARLSLSVTLA
+VAGGIAVLLMLLWPPLEDGHSGAWTLFEPLAVVVAWSTMASFVVQLVRGTGRPLRLESTV
+ATMGGAFMAVVTACWVAVSRWSDTPAVAGLVITLAVTVAAVSLVGLTPWMQGRPGVLALV
+VIPLGTVLAWPVSALAGVGARDRPAVTAAALAVAVLVSLTAATAPSSRPRPEDRPVGTTL
+RPRRAGYALALAPVGAAGVVAHVMVGFLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001418.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001418.fa
new file mode 100644
index 0000000000000000000000000000000000000000..79e707577d5b84b1c307aad19791cb2e02d6ee72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001418.fa
@@ -0,0 +1,35 @@
+>0_1691
+MAEHPTPTTSDADGMPRVVTPRPEEASAVLDLADRAGAADGHPPLSDQTRVLLARGGQLW
+WGATRGPDGAIDGAAVLVPEGTAAVLELVVDPTARRTGRGTVLADAAAAAVRDLAREETT
+SVWAHGMLPGAVRLARRHGLEPVRELRRMRLSHAALAALPEVRLADGVALRGFVPGQDEQ
+AWLDVNAAAFADHPEQGSLTRADLDDRMAEDWFDADGLLLAAREADGRLLGFHWTKVEPD
+AGADGPRVGEVYAVGVSPDAQGLGLGRALTLAGLHRMAEQGVDVVDLYVDADNTAAVTLY
+ASLGFELFAADAQYRRP
+>1_1408
+MAEHPTPTTSDADGMPRVVTPRPEEASAVLDLADRAGAADGHPPLSDQTRVLLARGGQLW
+WGATRGPDGAIDGAAVLVPEGTAAVLELVVDPTARRTGRGTVLADAAAAAVRDLAREETT
+SVWAHGMLPGAVRLARRHGLEPVRELRRMRLSHAALAALPEVRLADGVALRGFVPGQDEQ
+AWLDVNAAAFADHPEQGSLTRADLDDRMAEDWFDADGLLLAAREADGRLLGFHWTKVEPD
+AGADGPRVGEVYAVGVSPDAQGLGLGRALTLAGLHRMAEQGVDVVDLYVDADNTAAVTLY
+ASLGFELFAADAQYRRP
+>2_1107
+MAENPVPATPTDPAAPRVSEPRPDEVDAVLALADRAQAADGHPPLSDQTRVVLARGRQRW
+WGVVREADGSVSGAAVLAPEGGEDSGSVLELVVDPEARRAGRGAALADAAAAAVRERGLE
+STTSVWAHGMLPGSDALARRHGLEPVRELRRMRLPHEALADLPQPQLADGVALRGFVPGR
+DEQAWLDANAAAFADHPEQGGLTRADLEDRMAEDWFEAEGLLLAVREEDDALLGFHWTKV
+EPQAGPGPRVGEVYAVGVTPATQGLGLGRALTLAGLHRMAGQGVDVVDLYVDADNAAAVR
+LYESLGFGLFAADAQHRRP
+>3_1036
+MSEQPASPALPPTPGVVSPGTPSDVDAALALADRAHRSDGHPPLNDQTRAVLARDAQRWW
+GLTRDEAGAVTGVAVLAPEGEAAGPGVVELAVDPAHRGAGLGAALAEAAADAVRERGEAR
+RTSAWAHGALPGALALARRHGLEPVRELRRMRLDPAGLGALPPTRLPEGVTLRGFVPGRD
+EDAWLALNAAAFADHPEQGSLTRADLDAREAEDWFEAAGLLLAEDAEGTPVGYHWTKVTP
+AEAGAPSEGEVYAVGISPAAQGRGLGRALTLAGLHHMAGRGVDAVDLYVDADNVPAVRLY
+ESLGFALAAADVQLRPAR
+>4_1620
+MAEHPTPTTSDADGMPRVVTPRPEEASAVLDLADRAGAADGHPPLSDQTRVLLARGGQLW
+WGATRGTDGAIDGAAVLVPEGAAAVLELVVDPTARRTGRGTVLADAAAAAVRDLAREATT
+SVWAHGMLPGAVRLARRHGLEPVRELRRMRLSHAALAALPEVRLADGVALRGFVPGQDEQ
+AWLDVNAAAFADHPEQGSLTRADLDDRMAEDWFDADGLLLAAREADGRLLGFHWTKVEPD
+AGADGPRVGEVYAVGVSPDAQGLGLGRALTLAGLHRMAEQGVDVVDLYVDADNTAAVALY
+ASLGFELFAADAQYRRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001419.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001419.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35b8fdb60bb144f8447be4c8add795f08d8c6f33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001419.fa
@@ -0,0 +1,35 @@
+>0_1692
+MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPGGLEVMVIHRPRYDDWSWPKGK
+LDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPGKRGARQSKEVWYWAAEVDGQRA
+LPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRAASRGRLRTVPLLVLRHAKAKPRS
+SWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSSPWRRCVETLAPLVKSSRLALKTK
+GAFTETTAREKPQKTRKVMAELMGRSRPLVVCTHRPVLPTLFEVVEDAAAGRTDRVLRAL
+PTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD
+>1_1409
+MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPGGLEVMVIHRPRYDDWSWPKGK
+LDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPGKRGARQSKEVWYWAAEVDGQRA
+LPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRAASRGRLRTVPLLVLRHAKAKPRS
+SWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSSPWRRCVETLAPLVKSSRLALKTK
+GAFTETTAREKPQKTRKVMAELMGRSRPLVVCTHRPVLPTLFEVVEDAAAGRTDRVLRAL
+PTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD
+>2_1106
+MPSTPTERVARWSTEDRAADGPRAEVLAAGVVPWRRTPGGRLEVLVIHRPRYDDWSWPKG
+KLDPGETLPQCAVRELREEVGLALRPGIPLCVTEYEVSGKRGARLTKEVWYWAADAGAQR
+AVPDGDEVDEVRWVRPEEAEALLTNETDREPLELLVRADSRGRLRTLPLLVLRHAKAKPR
+SSWSRAEQERPLAATGRRQALAVEGLVAAWAPDRLVSSPWRRCVETLAPLVKSSRLPLKT
+KGAFTETAAKEKPKKTRKAMHELLGRQRAQVVCTHRPVLPVLFEVVEDAARRQERVLRAM
+PREDPWLRPGAVLVVHRSLDGDVVAVEAYDPWDD
+>3_1035
+MTRPLSWDGIPDPIPPEDPRTMSAHPDDRAAAWSTPDGAVTAPGAEVLAAGMIPWRPGAE
+GLEVLVIHRPRYDDWSWPKGKVDDGETLPEAAARELAEEVALTLRPGLPLAVTRYDVPDR
+KGKGMLSKEVWYWAGEATGQRPTPDGDEVDEARWVSSARAREMLSNATDLEPLDRLERAD
+ARGHLRTVPLLVLRHAKAKPRSSWSRAEQERPLAATGRRQAHSVARLIAVWRPERVVSSP
+WRRCVETLAPFVKATRLPLKTKSAFTETTAREKPKKTRRAFRDLLARRRPQVLCLHRPVI
+PSILEEVDDAAARPASDVLAALPRRDPHLRPGGVLVLHQGLDAKGAVVAAEVYDPWSD
+>4_1621
+MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPGGLEVMVIHRPRYDDWSWPKGK
+LDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPGKRGARQSKEVWYWAAEVDGQRA
+LPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRAASRGRLRTVPLLVLRHAKAKPRS
+SWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSSPWRRCVETLAPLVKSSRLPLKTK
+GAFTETTAREKPKKTRKVMAELMGRSRPLVVCTHRPVLPTLFEVVEDAAAGQADRVLRAL
+PTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001422.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001422.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b19d8e54c9ae0980979ee8a20691bf22cf60f44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001422.fa
@@ -0,0 +1,25 @@
+>0_1695
+MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR
+TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPNFGAALAAAAEADGCDT
+VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPPLDARWRRTAVDPAPDAWLDSASG
+PRHRFERWERD
+>1_1412
+MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR
+TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPNFGAALAAAAEADGCDT
+VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPPLDARWRRTAVDPAPDAWLDSASG
+PRHRFERWERD
+>2_1103
+MRSDPMSRATRPTEPAIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR
+TWESFPARFRPLPGRTNIVVSRTLTASEEAGAELRAAGAVVVPDFGAALAAAAEADGCDT
+VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPVLDPRWRRTAVDPAPDAWLDSASG
+PRHRFERWERD
+>3_1029
+MARHHDDGARPRQTIAMIWAQTPDGVIGADGTMPWHLPEDLARFKALTLGHPVIMGRRTW
+DSFPARVRPLPGRTNIVVSRTLTATPEAGEAVRAAGAVVVPDFGAALTAADEADGLDLVW
+VIGGATLYEQALDVATRAEITVVDVDAPGDTHAPALDSRWRLVAADPSPDGWLDSAAGPR
+RRDERWERD
+>4_1624
+MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR
+TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPDFGAALAAAAEADGCDT
+VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPLLDARWRRTAVEPAPDAWLDSASG
+PRHRFERWERD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001423.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001423.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ad4107a3577e8a3d326c08c3e121dfd61ba4d2f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001423.fa
@@ -0,0 +1,15 @@
+>0_1696
+MAPTDSDQRLLSPQAVSFLALVALPVLAFVCAVFGLILVLQGKTIAGLVFLLVLTQVFAV
+GGLIAWNRRKRAQQGR
+>1_1413
+MAPTDSDQRLLSPQAVSFLALVALPVLAFVCAVFGLILVLQGKTIAGLVFLLVLTQVFAV
+GGLIAWNRRKRAQQGR
+>2_1102
+MAPTDPQDRLFTPQAVTFLALVACPVLAFVCAVMGLILVLQGKTIAGLVFLIVLTQVFAV
+GGLIAWNKRKRAQQGR
+>3_1028
+MADLPSDEKAPLLDAQAVTFLTLIAFPVLAFVCAVMGLILVLQGKVVAGVVFLVVLTQVF
+AAGGLITWNRRRRDRSGR
+>4_1625
+MAPTDSDQRLLSPQAVSFLALVVLPVLAFVCAVFGLILVLQGKTIAGLVFLLVLTQVFAV
+GGFIAWNKRKRAQQGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001425.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001425.fa
new file mode 100644
index 0000000000000000000000000000000000000000..138a067f0ea7bfa1cd756efc8c870b323776d2a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001425.fa
@@ -0,0 +1,40 @@
+>0_1698
+MSERLADHTTTRVGGPARAWVTARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADAGFP
+GTVVRLAFEGIHVLDGPLPGEGETPPAGDGARSADHEGEAVVVRIAAGHPWDDAVAWTVA
+HGLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVALRAWDREAGDVVELTPADLRFGY
+RDSVIKRSMLETGAPSPRWIVLSIDLRLRRASSDAEPTAPVRYGQLAAALDVEEGAHAPL
+AVVRREVLALRAAKGMVSDPADPDTWSTGSYFTNPIVPASVRASLPDGAPAFAAGQAEDG
+TPLVKLSAAWLIDRAGFAKGFGLPEVAPREGGPDGRGADGTGLAGGRASVSTKHTLAMTN
+RGDATTEDVLTVARTVRDGVRERFGVELHPEPMIIGTSL
+>1_1415
+MSERLADHTTTRVGGPARAWVTARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADAGFP
+GTVVRLAFEGIHVLDGPLPGEGETPPAGDGARSADHEGEAVVVRIAAGHPWDDAVAWTVA
+HGLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVALRAWDREAGDVVELTPADLRFGY
+RDSVIKRSMLETGAPSPRWIVLSIDLRLRRASSDAEPTAPVRYGQLAAALDVEEGAHAPL
+AVVRREVLALRAAKGMVSDPADPDTWSTGSYFTNPIVPASVRASLPDGAPAFAAGQAEDG
+TPLVKLSAAWLIDRAGFAKGFGLPEVAPREGGPDGRGADGTGLAGGRASVSTKHTLAMTN
+RGDATTEDVLTVARTVRDGVRERFGVELHPEPMIIGTSL
+>2_1100
+MSERLAEHTTTRVGGPARAWETARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADAGFP
+GTVVRLAFEGIEVRAGDEAHGGDADDQDPAAGGDRAGEAVVVRVAAGHPWDDAVAWTVEH
+GLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVSLRAWDREAGQVVELGAEELEFDYR
+DSIIKRSMLETGAPSPRWIVLSIDLRLRRASGAAEPTAPVRYGQLASALDVAEGTHAPLA
+VVRREVLALRAAKGMVSDPQDPDTWSTGSYFTNPIVPAAVRASLPEGAPAFAAGRAADGT
+ELVKLSAAWLIDHAGFAKGFGLPDVAPREGGPDGRGADGAGLAGGRASVSTKHTLAMTNR
+GDASTEDVLTIARTVRDGVKARFGVDLHPEPMIIGTSL
+>3_1026
+MSERLSDHTTTRVGGPARAWVEARTEAEAVAAVRAADAAGEPLFVLGGGSNTLMADAGFE
+GTVVHMGFTGVEVLPAEGAADGAGDVVVRVAAGHVWDEAVAWTVEHGLAGVEALSGIPGS
+AGATPVQNVGAYGADVSQVLVSLRAFDRAAGQVVELSAEDLRFGYRDSVIKRSMFEDGSP
+SPRWIVLSIDLRLRRAEEGAEPTAPVRYAQLARALEVEEGADVSLAQVREHVLALRASKG
+MVSDAADHDTWSTGSYFTNPIVPATVRVTLPEGAPAFAAGTDEDGTPLVKLSAAWLIDHA
+GYGKGFGLPDAPRREGDADGSGPDGRGLAGGRAALSTKHTLAVTNRGGASTEDVLTVARA
+VRDGVKARFGVDLHHEPMIIGTRL
+>4_1627
+MSERLADHTTTRVGGPARAWVTARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADSGFP
+GTVVRLAFEGIGVLDGPVPGEGEAPPVGDGARLADHEGEAVVVRVAAGHPWDDAVAWTVA
+HGLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVALRAWDREAGDVVELTPADLRFGY
+RDSVIKRSMLETGAPSPRWIVLSIDLRLRRASSDAEPTAPVRYGQLAAALDVEEGAHAPL
+AVVRREVLALRAAKGMVSDPADPDTWSTGSYFTNPIVPASVRASLPDGAPAFAAGQAEDG
+TPLVKLSAAWLIDRAGFAKGFGLPEVAPREGGPDGRGADGTGLAGGRASVSTKHTLAMTN
+RGDATTEDVLTVARTVRDGVRERFGVELHPEPMIIGTSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001429.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001429.fa
new file mode 100644
index 0000000000000000000000000000000000000000..69e187d9f354aa1a752ae2d9f6e9e964a443ccda
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001429.fa
@@ -0,0 +1,66 @@
+>0_1702
+MSDILDPQTTAEVAPELAEAEQEATGTVPQVDAAPEAPAEPAAPEAPAEPAGPTFLDLGL
+DARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTD
+VTGRADTPQVLVLAPTRELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQ
+VVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDRILASTPDTKQTALFS
+ATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEEHDG
+VIAFVRTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAAR
+GLDVERISHVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQ
+VEEMAVPSVADVNAARKRRFADGITRTLERASEEELAVFGEIVAAYVDEHEAEPARVAAA
+LGMMAQGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPAREPAA
+GNVTYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEA
+AANAEINGRRLGLRKDTGRPTRAERDGEDRGERRGGFRKDRGERGERGGFRGDRDGGQRG
+GYRKDRDDRGSREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR
+>1_1419
+MSDILDPQTTAEVAPELAEAEQEATGTVPQVDAAPEAPAEPAAPEAPAEPAGPTFLDLGL
+DARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTD
+VTGRADTPQVLVLAPTRELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQ
+VVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDRILASTPDTKQTALFS
+ATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEEHDG
+VIAFVRTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAAR
+GLDVERISHVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQ
+VEEMAVPSVADVNAARKRRFADGITRTLERASEEELAVFGEIVAAYVDEHEAEPARVAAA
+LGMMAQGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPAREPAA
+GNVTYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEA
+AANAEINGRRLGLRKDTGRPTRAERDGEDRGERRGGFRKDRGERGERGGFRGDRDGGQRG
+GYRKDRDDRGSREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR
+>2_1096
+MSDALDPQTTPEAQVDAAELAEARQEAAEAAAPKAETPETAAAATETDSAPEAETAEEPE
+APAEPAGPTFLDLGLDARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTG
+AFALPALARLAETADVNGRADTPQVLVLAPTRELALQVADAFDSYAKHLEDVSVLAVYGG
+SPYGPQLAGLRRGAQVVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDR
+ILASTPDTKQTALFSATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWK
+LEAFTRILETEDHDGVIAFVRTRAGTEELAQKLNRAGFKAVAISGDIAQKQREKTVEDLK
+AGRVDILVATDVAARGLDVERISLVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPR
+ERFLLKQIERTTRQQVEEMAVPAVKDVNAARKRRFADGITRTLERASEEELAVFGEIVAA
+YVEEHDAEPSRVAAALGMMAQGGRPLLAKEQEIPTGPRGRKERDGGRDGGREHGTADGRG
+SRGPAREPAAGNATYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELP
+ADLTPAQLEAAANIEISGRRLGLRKDTGRPTRAERDGDERRGGFRKDRGERGGHGGHRGG
+FRKDRDERGFRGDREERGGFRGDRDDRGDRGGFRKDREDRGGFRKDREDRGDRGGFRKDR
+EDRGGFRKDRDERGGFRGGKAGGRKPRWGAQERSDRGPRR
+>3_1022
+MTPHETIPADDQAPVDLTEFDPELAETTAEAPAAEQDADDAEADAEPAGPTFLSLGLDAR
+VLAAVEDLGYQRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETQDVNG
+RSQAPQILALAPTRELALQVAEAFESYAKHLDDVSVLAVYGGAPYGPQLAGLRRGAQVVV
+GTPGRVIDHLERGNLDLSQLQTLVLDEADEMLRMGFAEEVDRILAETPDSKQTALFSATM
+PPAIRRISAQYLNDPEEVAVARQSTTGTNIRQRYLQIAHQWKFEAMTRILETEDHEGVIA
+FVRTRAGTDELAQRLNQAGFSAVAISGDVAQKQREKTVDDLKAGRVDILVATDVAARGLD
+VERISLVVNYDIPQDAESYVHRIGRTGRAGRSGDAVLFMTPRERFLLKQIERTTRQEVEE
+MQVPTVAQVNEARTRGVVAGIGRTLETASEADLDTYARMVAEYVEANDVDPARAAAALAL
+MAQGGRPLLTEADEVPAGGRVRRDRDRDDRRERGDRSERGDRDGRGSRGPRREPAAGNAT
+YWIGVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHALVELPADLTAAQLDAAANT
+EINGRRLNLRKDTGRPTRAERDGDGERGHRGPREDRGGFRRDRGDRGGFRRDRGERPERG
+GFRKDRDDRGPREDRGGFRHDRDDRGGRPGARKPRWGSDDRRDRGPRR
+>4_1631
+MSDILDPQTTAEAAPELAEAEQEATGTVPQVDAAEPAAPEAPAGPAGPTFLDLGLDARVL
+AAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTDVTGRA
+DTPQVLALAPTRELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQVVVGT
+PGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDRILASTPDTKQTALFSATMPP
+AIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEEHDGVIAFV
+RTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAARGLDVE
+RISHVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQVEEMA
+VPSVADVNAARKRRFADGITRTLERASEEELAVFGEIVAAYVDEHEAEPARVAAALGMMA
+QGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPAREPAAGNATY
+WIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEAAANAE
+INGRRLGLRKDTGRPTRAERDGEDRGGFRKDRGERGERGGFRGDRDGGQRGGYRKDRDDR
+GSREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001433.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001433.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef25ea9a13104de2a2ede58a7b8a906c9bae9326
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001433.fa
@@ -0,0 +1,50 @@
+>0_1706
+MQYAENVLELIGHTPLVKLHSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEEAEREGL
+LGPGGTVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLSAYGAELVVTPTAV
+DPTSEESYYGVADRLVREIPGAYQPNQFFNPAAPASHYETTGPEIWEDTAGRVTHVVMGA
+GTGGTITGTGRYLKEVSADRPSGAVRVIGADPSGSVYSGGAGRPYFVEGVGEDMWVDNYD
+PAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARELGPEDVMVIVLPD
+SGRGYLAKIFNDPWMDERGFDYDVRETVLPAWARGRTRSAVPQTDDDGATGAAGGAGTPV
+EALEHADAEPATRAGAPAEADRWSATAGELLTEKADLFPGSVPTLVTAAPTTSVADAVAT
+MNRYGVDALPVILEPRHDLRIGEVRGTVSSAALADALAEGRATAQTPVADVMGPVLPCLG
+ARTPLRAVARRLAQDPVLLVLEAGRVQGVVTLHDVLAHVTA
+>1_1423
+MQYAENVLELIGHTPLVKLHSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEEAEREGL
+LGPGGTVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLSAYGAELVVTPTAV
+DPTSEESYYGVADRLVREIPGAYQPNQFFNPAAPASHYETTGPEIWEDTAGRVTHVVMGA
+GTGGTITGTGRYLKEVSADRPSGPVRVIGADPSGSVYSGGAGRPYFVEGVGEDMWVDNYD
+PAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARELGPEDVMVIVLPD
+SGRGYLAKIFNDPWMDERGFDYDVRETVLPAWARGRTRSAVPQMDDDGATGAAGGAGTPV
+EVLEHADAEPATRAGAPAEADRWSATAGELLTEKADLFPGSVPTLVTAAPTTSVADAVAT
+MNRYGVDALPVILEPRHDLRIGEVRGTVSSAALADALAEGRATAQTPVADVMGPVLPCLG
+ARTPLRAVARRLAQDPVLLVLEAGRVQGVVTLHDVLAHVTA
+>2_1092
+MQYAENVLELIGHTPLVKLNSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEDAEKAGK
+LAPGGTVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLTAYGAEIVVTPTSV
+APESEESYYGVANRLERDIPGAYQPNQFFNPAAPASHYETTGPEIWEDTAHRVTHVVIGA
+GTGGTITGTGRYLKEVSADRESGPVRVIGADPSGSVYSGGTGRPYFVEGVGEDMWVDNYD
+PAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARDLGPKDVMVIVLPD
+SGRGYLAKIFNDPWMDERGFDYDVQDTVLPEWARGRTRSAAPEADDDGAQGAAGGAGTPV
+EALEQADAAAGADAGQVADAPAEADRWAATAGELLAEKADLFPGSVPTLVTASPTTSVAD
+AVATMNRYGVDALPVVAEPRHDLRIGEVRGTVSAAALGEALAAGRVHPGTPVAEAMGPVL
+PCIGARTPLRAVARRLAQDPTLLVLSAGRVAGVVTLHDVLAHVTA
+>3_1018
+MGAVNEINPAPAHGQPRWAENVLDLIGRTPLVKLNRVTEGVEATVLVKVEYLNPGGSVKD
+RIALRMLEEAERDGKLAPGGTVVEPTSGNTGVGLALVAQQKGYRAVFVTPDKVGQEKRDV
+LTAYGAEIVVTPTSVEPSSDESYYGVANRLEKEIPGAFQPNQFFNPAAPASHYETTGPEI
+WEDTAGTVTHVVIGAGTGGTITGTGRYLKEVSADRASSPVRVIGADPEGSVYSGGTGRPY
+FVEGVGEDMWPGNYDPSVPDEVIAVSDDAAFEMTRRLAAEEGLLVGGSSGMAVVAGLQAA
+RELGPDDVMVIVLPDSGRGYLAKIFNDDWMDERGFHYAQEETVLPAWAQGRTRSAVATAP
+SDSREGARGGVGTPVEAPGEGSPQDGAATATPAPGSRWDASLADVLADKEDLFPGSVPTL
+VTASPDTTVADAVATLARYGVDALPVIAEPRHDLRINEVRGTVSAPALAAALAAGRVQPG
+SAVSDVMEPALPSVGAAMTLRAAARRLQEDPILLVMDAGIVQGVVTLHDVLVYATA
+>4_1635
+MQYAENVLELIGRTPLVKLHSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEEAEREGL
+LGPGGTVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLSAYGAELVVTPTAV
+DPTSEESYYGVADRLVREIPGAYQPNQFFNPAAPASHYETTGPEIWEDTAGRVTHVVMGA
+GTGGTITGTGRYLKEVSADRPSGPVRVIGADPSGSVYSGGAGRPYFVEGVGEDMWVDNYD
+PAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARELGPEDVMVIVLPD
+SGRGYLAKIFNDPWMDERGFDYDVRETVLPAWARGRTRSAVPQTDDDGATGAAGGAGTPV
+EVLEHADAELATRAGAPAETDRWSATAGELLTEKADLFPGSVPTLVTAAPTTSVADAVAT
+MNRYGVDALPVILEPRHDLRIGEVRGTVSTAALADALAEGRATAQTPVADVMGPVLPCLG
+ARTPLRAVARRLAQDPVLLVLEAGRVQGVVTLHDVLAHVTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001436.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001436.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16b1c9d491d14d9dbd0ba4cefbea2b99bc13d36f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001436.fa
@@ -0,0 +1,20 @@
+>0_1710
+MASDSTFDVVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMRASSEERVK
+AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEATMKEGIDQPTAKKITKLIRDEGPK
+SVKAQIQGDELRVSSKSRDDLQSVIAMLKDFEDADLQFVNFR
+>1_1427
+MASDSTFDIVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKASSEERVK
+AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEATMKEGIDQPTAKKITKLIRDEGPK
+SVKAQIQGDELRVSSKSRDDLQSVIAMLKDFEDADLQFVNFR
+>2_1088
+MASDSTFDVVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKASSEERVK
+AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEASMKEGIDQPTAKKITKLIRDEGPK
+SVKAQIQGDELRVSSKSRDDLQEVIAMLKDFEDADLQFVNFR
+>3_1015
+MASDSTFDVVSKVDKQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKANSEERVK
+AVLDVFESKLVKRGISLKSLDCGEPFASGKETRMEASIKEGIDQPTAKKITKLIRDEAPK
+SVKAVIQGDELRVSSKSRDDLQETIALLKTFEDADLQFINFR
+>4_1639
+MASDSTFDVVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKASSEERVK
+AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEATMKEGIDQPTAKKITKLIRDEGPK
+SVKAQIQGDELRVSSKSRDDLQSVIAMLKDFEDADLQFVNFR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001440.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001440.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9581992123ebca0586f08e2013d856ef7f85002e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001440.fa
@@ -0,0 +1,20 @@
+>0_1715
+MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW
+RRSAGADAPEGEWQDEGGTFSEFLTDLLAWTFEDPEDDGEGLDR
+>1_1432
+MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW
+RRSAGADAPEGEWQDEGGTFSEFLTDLLAWTFEDPEDDDEGPDR
+>2_1083
+MPAKPPAPVHLPAFQRLVPDLLGDAWAEDDGLSPADVEARLGQSPAAGQLGAGFMVPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDAEETVVWGLPVDNLALPDPLVW
+RRSSGAEAEEGDWQDEGGTFSEFITDLLAWTFEDPEDDDGRDER
+>3_1009
+MPAKPPAPVYLPGFQRLVPDLLGDTWAKDDGLAPADVEARLAESPAAEQLGTGFMVPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDEGETVVWGLPVDNLALPDPLVW
+RRDTGADAEEGDWQDEGGTFSEFITDLLVWTFEDPEDDAAEDAR
+>4_1644
+MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW
+RRSAGADAPEGEWQDEGGTFSEFLTDLLAWAFEDPEDDDEGPDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001443.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001443.fa
new file mode 100644
index 0000000000000000000000000000000000000000..024e4243bff42e89ae156f55085c2f06c4fa0795
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001443.fa
@@ -0,0 +1,45 @@
+>0_1718
+MTDTPTSPAPDSTSAVVRRADVLISGCGPAGATAAAHLAAAGLDVVVLEKTAHPREKVCG
+DGLTPQAVRELQLLGVPHRGEPGDDGGWRVIRGLRLRAGERSVDVPWAPTQTWPDYALTR
+TRRDFDALLADLARTRGAEVRERHAVTGVVRDEAGRVVGLDAELIAPNGRKTGETARFTA
+PIVLACDGVSARAAVSAGLHRREDRPMGVAVRAYYTAGAAVDGAIPAPPGDRGEWMESWL
+RLPDAEGNPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLKSWTGALTADWGIA
+EQTRTSRILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARLAADLAV
+QAHAAGTDGAADAILSRYPVITQHLWGRHFALGARFARLIGDPRVMKAALGAGMAAPPLL
+RAAVKVMGNTVDARGGDAVDRAVRVLEALTPALTTAGGAPLGRLAR
+>1_1435
+MTGTPTSPAPASTPAVVRRADVLISGCGPAGATAAAHLAAAGLDVVVLEKTAHPREKVCG
+DGLTPQAVRELQLLGVPHRGEPGDDGGWRVIRGLRLRAGERSVDVPWAPTQTWPDYALTR
+TRRDFDALLADLARTRGAEVRERHAVTGVVRDEAGRVVGLDAELIAPNGRKTGETARFTA
+PIVLACDGVSARAAVSAGLHRREDRPMGVAVRAYYTAGAAVDGAIPAPPGDRGEWMESWL
+RLPDAEGNPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLKSWTGALTADWGIA
+EQTRTSRILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARLAAELAV
+QAHAAGTDGAADAILSRYPVITQHLWGRHFALGARFARLIGDPRVMKAALGAGMAAPPLL
+RAAVKVMGNTVDARGGDAVDRAVRVLEALTPALTTAGGAPLGRLAR
+>2_1080
+MTAAPSSSPSESAPPPVVRRADVLISGGGPAGATAAAHLAAAGLDVVVLEKTAHPREKVC
+GDGLTPQAVRELQLLGVPHRGEPGDDGGWQVIRGLRLRAGERSVDVPWPETRSWPDYALT
+RTRRDFDALLADLARERGAEVRERHAVTSVVRDDAGRVCGLDAELIAPNGRKTGETARFE
+APVVLSCDGVSARAAVSAGIHRREDRPMGVAVRAYYTAGPAADGAVPAPPGDRGEWMESW
+LRLPDAQGRPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLKSWSGALTPDWGI
+SEQTRVSKILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARIAADLA
+VQAHAAGSDAAADTVLSRYPVITQHLWGRHFALGARFARLIGDPRVMRASLGAGMAVPPL
+LRAVVKVMGNTVDPERGDAVDRAVRVLEALTPALTTADSAPLGRLAR
+>3_1005
+MTEHPTPAAAPVVRRADVLISGAGPAGATAAAHLAAAGLDVVVLEKSAFPREKVCGDGLT
+PQAVQEIRNLGIEHQGGPGDDGGWHAVRGLRLRAGERSVDVPWPATQSWPDYALTRTRKD
+LDALLADTARARGAEVRERHAVTGVTRDDAGRVDGLEAELIAENGRKTGERVRFAAPLVL
+ACDGVSARAAVSMDVHRRTDRPMGVAVRAYYTAGPVGADGAVPRPPGDRVDWMESWLRLP
+DEHGNPLPGYGWLFPLADGTVNVGLGILDTSPLFGKLDYRALLKQWSGALSEDWGISEET
+RTSKILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARIAADLAVQAH
+AAPNTPAADAVLARYPVITQHLWGRHFRLGTVFARLIGEPRVMRAALATGMAVPPLLRTV
+ARVMGNVVDPSGGDAVDRAVRILESVTPSLTTADAPGVGRLAR
+>4_1647
+MTGTPTSPAPASTPAVVRRADVLISGCGPAGATAAAHLAAAGLDVVVLEKTAHPREKVCG
+DGLTPQAVRELQLLGVPHRGEPGDDGGWRVIRGLRLRAGERSVDVPWAPTQTWPDYALTR
+TRRDFDALLADLARTRGAEVRERHAVTGVVRDEAGRVIGLDAELIAPNGRKTGETARFTA
+PIVLACDGVSARAAVSAGLHRREDRPMGVAVRAYYTAGAAVDGAIPAPPGDRGEWMESWL
+RLPDAEGNPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLRSWTGALTADWGIA
+EQTRTSRILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARLAADLAV
+QAHAAGTDGAADAILSRYPVITQHLWGRHFALGARFARLIGDPRVMKAALGAGMAAPPLL
+RAAVKVMGNTVDARGGDAVDRAVRVLEALTPALTTAGGAPLGRLAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001447.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001447.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb7bf8f15c1190ffd01affa82ae3b6e4f4aca487
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001447.fa
@@ -0,0 +1,35 @@
+>0_1725
+MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITIRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK
+AELDLDQLRAEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA
+AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA
+>1_1442
+MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITLRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK
+AELDLDQLRAEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA
+AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA
+>2_1074
+MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTKRFGEERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPMTIRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRAAIRLDDPVVFMEPKKMYWTK
+AELDLEDLRAEFEERWGRVEEKKEHGEAWARAAVVRAGSDVTLVSYGPSVPTCLAAARAA
+EEEGLSVEVVDLRTVNPLDEDTMVASVSKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA
+>3_998
+MANLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTQRFGDERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQVASHVAKMRNRTKGGAPMPIVIRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYLMLRSAIRLDDPVVFMEPKKMYWTK
+ADLDLDELRAEFDEQWARAQEKTAQGEAWARAAVVRQGADVTLVSYGPSVPTCLAAAQAA
+AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNVDRILDAIDDLNWDLDAEEARA
+>4_1654
+MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITIRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK
+AELDLDQLREEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA
+AEEGLSVEVVDLRTVNPLDEDTMTASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLGAEEARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001450.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001450.fa
new file mode 100644
index 0000000000000000000000000000000000000000..64b80a7c55bcdfab36c9c25637eb8c827cf53829
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001450.fa
@@ -0,0 +1,49 @@
+>0_1728
+MASRTASPPPSPAPSPAAPRGALDRYFRITERGSSVGQEFRGGLATFLAMSYIVVLNPLI
+LSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWARHPFAVAAGLGVSAFVSITIATTPG
+LTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPESLKSGIVVGIGLFIALIGLVNAGFV
+RRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLLTAVLVIRKVRGAILIGIVVATILAN
+VLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTAPDLHLLGSVDLFGAFTSVGGLMASL
+LVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPDLNRVLAADALAVAVGGAASGSAHQI
+FVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLIHLVPFEAVAPALVVVGFMMCQHVVQ
+IDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVAYAVIRTGQGRGREVHPLLWFVALAF
+VAYFGLGVVRAALGLN
+>1_1446
+MASRTASPPPSPAPSPAAARGALDRYFRITERGSSVGQEFRGGLATFLAMSYIVVLNPLI
+LSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWARHPFAVAAGLGVSAFVSITIATTPG
+LTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPEALKSGIVVGIGLFIALIGLVNAGFV
+RRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLLTAVLVIRKVRGAILIGIVAATILAN
+VLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTAPDLHLLGSVDLFGAFTSVGGLMASL
+LVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPDLNRVLAADALAVTVGGGASGSAHQI
+FVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLIHLVPFEAVAPALVVVGFMMCQHVVQ
+IDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVAYAVIRTGQGRGREVHPLLWFVALAF
+VAYFGLGVVRAALGLN
+>2_1068
+MGQEFRGGLATFLAMSYIVVLNPLILSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWA
+RHPFAVAAGLGVSAFVSITIATTPGLTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPE
+ALKSGIVVGIGLFIALIGLVNAGFVRRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLL
+TAVLVIRKVRGAILIGIVAATILANVLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTA
+PDLHLLGSVDLFGAFTSVGGLMASLLVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPD
+LNRVLAADALAVAVGGGASGSAHQIFVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLI
+HLVPFEAVAPALVVVGFMMCQHVVQIDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVA
+YAVIRTGQGRGREVHPLLWFVALAFVAYFGLGVVRASLGLN
+>3_995
+MSSRTTGATPPGTAPSNPASPAGPRSGLDRFFGISALGSSVGQEVRGGIATFLAMSYIVV
+LNPLILSGPDSTGAVLGIPRVAAATALVAAVATLAMGLWARHPFALASGLGVNAFLAITV
+ATTPGLTWPDVMGLVVIAGLVMVVLVATGFRTAVFNAVPEALKTAIVVGIGLFIALIGLV
+NAGFVRRLPDAAGTTVPVGLGTGGELAGWPVLVFIVGLLVTAILVIRNVRGAILVGIVTA
+TVLANILEAVFHIGPSVGADGSHNPTGWALVAPSLPEWAAPDLSLLGSARPFGAFEAVGG
+LMGALLVFAILLSVFFDAMGSTVGLAREAGSMDEHGNVPRLNRVLMVDALAVTGGGAASA
+SAGQIYVESGTGIGEGARTGLASVVTGLMFVATIFLTPLIHLVPFEAVAPALVVVGFMMC
+SQVVRIDWTDWGAALPAFLTFILMPFTYSIANGIGAGMIAYAVIRTGQGRAREVHPLLWV
+VAAAFVLYFGMGVFRGILGLA
+>4_1658
+MASRTASPPPSPAPSPAAPRGALDRYFRITERGSSVGQEFRGGLATFLAMSYIVVLNPLI
+LSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWARHPFAVAAGLGVSAFVSITIATTPG
+LTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPEALKSGIVVGIGLFIALIGLVNAGFV
+RRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLLTAVLVIRKVRGAILIGIVAATILAN
+VLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTAPDLHLLGSVDLFGAFTSVGGLMASL
+LVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPDLNRVLAADALAVTVGGGASGSAHQI
+FVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLIHLVPFEAVAPALVVVGFMMCQHVVQ
+IDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVAYAVIRTGQGRGREVHPLLWFVALAF
+VAYFGLGVVRAALGLN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001451.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001451.fa
new file mode 100644
index 0000000000000000000000000000000000000000..534c0d2a2e2df7d08ef3240273e0b63f569218e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001451.fa
@@ -0,0 +1,70 @@
+>0_1739
+MPQTTSHAPVPPSASAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD
+QAPLREAIVGEIKARTVETDRSVPARRDGWWYFVRTREGAEYPIHCRVPARDTGDLEADW
+TPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPDATRVAYAVDHTGDERFTLRV
+REIATGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVRAHVLGTDPAEDVLLHE
+EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLAD
+VEPVTDADGVRRLLVVHDRALDDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVK
+VDGVMVTLTHAALAVRRETTPRVVVAELDAVLAGQAAHWREPAFDEELYACHLSATAAES
+PFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPSSVTGE
+DVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGG
+GELGRRWYEDGKKLAKRHSFTDFVDATRHLVGLGWADPARVACMGGSAGGLLMGAVLNLA
+PELYRACLAVVPFVDALTTILDPELPLSALEWEEWGNPIEDAAVYAAMRAYTPYENVRAV
+DYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQATPLAEGGAPILLRTEMDGGHGGA
+SGRYQGWEDTAWEYAFLLTALGATARIV
+>1_1447
+MPQTTSHAPVPPSASAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD
+QAPLREAIVGEIKARTVETDRSVPARRDGWWYFVRTREGAEYPIHCRVPARDTGDLEADW
+TPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPDATRVAYAVDHTGDERFTLRV
+REISTGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVKAHVLGTDPAEDVLLHE
+EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLAD
+VEPVTDADGVRRLLVVHDRALDDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVK
+VDGVMVTLTHAALAVRRETTPRVVVAELDAVLAGQAAHWREPAFEEELYACHLSATAAQS
+PFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPSSVTGE
+DVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGG
+GELGRRWYEDGKKLAKRHSFTDFVDATRHLVDLGWADPARVACMGGSAGGLLMGAVLNLA
+PELYRACLAVVPFVDALTTILDPELPLSALEWEEWGNPIEDAAVYEAMRAYTPYENVRAV
+DYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQATPLAEGGAPILLRTEMDGGHGGA
+SGRYQGWEDTAWEYAFLLTALGATARID
+>2_1057
+MPQTTSHAPVPPSVSAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD
+QAPLRAAIFGEIKARTVETDRSVPSRRDGWWYFARTKEGAEYPVHCRVPAADTGDLEADW
+TPPVVTPDAPLEGEQVILDGNAEAEGHPFFALGGLHISPDSTRVAYAVDHTGDERFTLRV
+REIATGEDLPDVVENIAHGVRFDRSGARVLYTVWDDSWRPYQVKAHVLGTDPAQDQLLYE
+ESDPGMWTGFTGTADRTQLLIGVGNSEVSETHVVDLPESPDAPLPAPRLLIPRAWGMLAD
+VEPVTGADGVRRLLVVHDRTVARQDAADAGADAPAPNGMLSLVAEADVADRGAWRTVVPH
+REDVKVDGVMVTLTHAALAVRRETTPRVVVAPLDSVLAGEAADWREPAFEEELYACHLAS
+TAAESPFLRLAYTSWISPARVLDVSAATGEVHLRRETEVPGYDPSLYVAERVWAPASEPS
+SVTGEPVRIPVTVIRRKDVAADGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVYAVA
+HVRGGGELGRRWYEDGKKLAKRHSFTDFVDATRHLVDLGWADPARVACTGGSAGGLLMGA
+VLNLAPELYRACLAVVPFVDALTSILDPELPLSALEWEEWGNPIEDPEVYAAMRDYTPYE
+NVRAVDYPTIAAVTSLHDTRVLYVEPAKWVARLRRTVTSDQATPLAEGGAPVLLRTEMDG
+GHGGASGRYQGWEDTAWEYAFLLTALGATQRVD
+>3_993
+MYETSLPTPPRAAARPTARTVHGETFTDDFEWMRAKTEQEVLDHLQAENAYTEAATADQA
+DLRAAIYGEIKAHTVETDQSVPARRDGWWYFVRTVEGKDYAVHCRVPAQDTGDALADWTP
+PVVPADAALPGEQVILDGNAEAAGHPFFSLGGMHISPDGALAAYAVDLAGDERYTLRVRE
+IATGTDLPDVVRNIAPGVRFDRSGTRLIYTVWDETWRPYQVRVHTLGTDAAEDAVLYEES
+DPGMWTGFDASADRTQLLIGVGNSEVSETWAVDLPVDASPLPAPRVLVPRTARMLADVEP
+FDMDGRRRLLIVHDRLADGTTAPNGMLSIVDEADVADRDAWRPVVPHADDVRVDGVLVTR
+THVGLAVRRDTTPRVLIAPLEGLREGSAPAWTEPSFDEELYMCRLAGVNLDSPFLRLSYA
+SWTTPARVLDVVAATGEVRLRREVEVPGFDREDYVAERWWAPASEPSSLTGEQVRIPLTV
+IRRRDVAQDGTAPAVVYGYGSYEMSMDPVFGVARLSLLDRGVVYVVAHVRGGGELGRAWY
+EDGKKAAKRHSFTDFVDATRFVADSGWVDPARIACTGGSAGGLLMGAVLNLAPELYRACL
+AVVPFVDALTSILDPDLPLSALEWEEWGNPIEDPEVYATMKAYTPYENVRAVDYPAIAAV
+TSLNDTRVLYVEPAKWVAQLRRTVTSDQTTPIAAGGSPILLRTEMDGGHGGASGRYQGWE
+DTAWEYAFLLTALGATARVD
+>4_1659
+MPQTTTHAPVPPSVAAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD
+QAPLREAIVGEIKARTVETDRSVPARRDGWWYFVRTREGAEYPIHCRVPARETGDLEADW
+TPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPDATRVAYAVDHTGDERFTLRV
+REIATGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVKAHVLGTDPAEDVLLHE
+EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLAD
+VEPVTDADGVRRLLVVHDRALDDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVK
+VDGVMVTLTHAALAVRRETTPRVVVTELDAVLAGQAAHWREPAFDEELYACHLSATAAES
+PFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPSSVTGE
+DVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGG
+GELGRRWYEDGKKLAKRHSFTDFVDATRHLVDLGWADPARVACMGGSAGGLLMGAVLNLA
+PELYRACLAVVPFVDALTTILDPELPLSALEWEEWGNPIEDAAVYAAMRAYTPYENVRAV
+DYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQARPLADGGAPVLLRTEMDGGHGGA
+SGRYQGWEDTAWEYAFLLTALGATRRVV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001454.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001454.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b79214a3b570431a13cc0bcdbed05606adb0e8aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001454.fa
@@ -0,0 +1,40 @@
+>0_1742
+MPATADALARATDALAAAFDGGAPVELTADGAVLPRPEARDSRRCGDPDAVAVVRTSGST
+GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP
+GPFTPAAFATGAAALPDDAGPRLISLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL
+DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVTAAVAPDGPDAPPRVRLAGPMV
+AAGYLDDPARTAAHFVPAADGARAFLTEDTGILSPTDDGGVRLAVTGRLDDVVITGGVKV
+SAAAVTAALEAHPGVAAAHVAGVPDPEWGARLCAAVVPVRPAAAPDEAVLRAHVRAALGA
+AAVPKTWLLLEALPLLSTGKTDRQALAARFTAG
+>1_1450
+MPATADALARATDALAAAFDGGDPVELTADGAVLPRPEARDSRRCGDPDAVAVVRTSGST
+GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP
+GPFTPAAFATGAAALPDNAGPRLVSLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL
+DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVTAAVAPDGPDAPPRVRLAGPMV
+AAGYLDDPARTAAHFVTAVDGARAFLTEDTGILSPTDDGGVRLAVTGRLDDVVITGGVKV
+SAAAVTAVLEAHPGVAAAHVAGVADPEWGQRLCAAVVPADPASPVGENALRAHIRDALGA
+AAVPKTWLALDALPLLSTGKTDRQALAARFTAAG
+>2_1051
+MPATADALARATDALAAAFDGGDPVELTADGAVLPRPEARDPRRCGDPDAVAVVRTSGST
+GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGIAVLSRSIAAGTAPVALPP
+GPFTPAAFATGAAALPDHAGPRLVSLVPTQLARLLAADTDPAGRTALRSFDRVLVGGARL
+DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVAVAVAPDGPDAPPRVRLAGPMV
+AVGYLDDPARTAAHFVPAADGARAFLTEDTGVLSPTDDGGVRLAVTGRLDDVVITGGVKV
+SAAAVTAVLEAHPGVAAAHVAGVADPEWGQRLCAAVVPADPASPVGENALRAHIRDALGA
+AAVPKTWLALDALPLLSTGKTDRQALAARFAAAG
+>3_988
+MPATADALARATDALAAAFDGGAPVELTADGAVLPRPEARDPRRCGDPDAVAVVRTSGST
+GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP
+GPFTPAAFATGAAALPDDAGPRLVSLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL
+DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVAVAVAPDGPDAPPRVRLAGPMV
+AAGYLDDPARTAAHFVPAADGARAFLTEDTGVLSPTDDGGVRLAVTGRLDDVVITGGVKV
+SAAAVTAVLEAHPGVAAAHVAGVPDPEWGARLCAAVVPAHPAAAPDEAVLRAHVRAALGA
+VAVPKTWLVLDALPLLSTGKTDRQALAARFTAG
+>4_1664
+MPATADALARATDALAAAFDGGAPVELTADGAALPRPEARDPRRCGDPDAVAVVRSSGST
+GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP
+GPFTPAAFATGAAALPDDAGPRLVSLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL
+DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVAAAVAPDDPDAPPRVRLAGPMV
+AAGYLDDPARTAAHFVTAADGTRAFLTEDTGVLSPTDDGGVRLAVTGRLDDVVITGGVKV
+SAAAVTAVLEAHPGVAAAHVAGVPDPEWGARLCAAVVPAHEAAAPDEAVLRAHVRAALGA
+AAVPKTWLVLEALPLLSTGKTDRQALAARFTAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001455.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001455.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e8e8f699ca9059fa6a7c468cd7dbbb4048c0b868
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001455.fa
@@ -0,0 +1,30 @@
+>0_1743
+MAATLSQWVAAARPRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN
+DYSDGIRGTDDERVGPFRLTVSGLVPAARVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV
+GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSGLAWAGAIGCG
+LISTALLMANNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL
+LLVPIGGLLAIRPIRTVLRADDRRALIPVLRATGVIGIVYAITFTLGALL
+>1_1451
+MAATLSQWVAAARLRTLPMAIAPVIVGSAAAAELGRFHLGAALLALVVSLALQVGVNYAN
+DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFASFGLAGLAGLGLILLSGHWWFLLV
+GVACVVAAWYYTGGKKPYGYLGLGEVFVFVFFGLVAVLGTTYTQAGQVSGLAWAGAIGCG
+LISTALLMANNIRDIPTDRAVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPWL
+LLVPLGGLLAIRPVRTVLRAQDRRALIPVLRATGVIGIVYALTFTLGVLL
+>2_1050
+MAATLSQWVAAARLRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN
+DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV
+GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSRLAWAGAIGCG
+LISTALLMANNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL
+LLVPIGGLLAIRPIRTVLRADDRRTLIPVLRATGVIGIVYALTFTLGVLL
+>3_987
+MAATLSQWVAAARLRTLPMAVAPVIVGSAAAHALDQFRPGRALLALVVSLALQIGVNYAN
+DYSDGIRGTDDARVGPFRLTVSGLVPAKTVKHAAFACFGVAAVAGLALVALSGTWWLLIV
+GVASIVAAWYYTGGKKPYGYMGLGEVFVFVFFGLVAVLGTTYTQALAVNGLAWAGAVGCG
+LISTALLMANNIRDIPTDREVGKMTLAARIGDGPARASYVAMLAVAVVLPLLFTGAHPWL
+WLVLAAGAVAVKPCLTVLHAHERAALIPVLKATGIVGVVYAAAFALGVAL
+>4_1665
+MAATLSQWVAAARPRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN
+DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV
+GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSGLAWAGAIGCG
+LISTALLMVNNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL
+LLVPIGGLLAIRPIRTVLRADDRRALIPVLRATGVIGLVYAITFTLGVLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001456.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001456.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25e6eae674024c3d539e109ee11e8c7d3387f2ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001456.fa
@@ -0,0 +1,15 @@
+>0_1744
+MRIFFYGLVRVVLFVALWALFYYVMDLWMIFAVIAAAILAFAVSYLFLDRLRTGATEDLS
+AAWEGRPGRRGRTETADADAEDAYTEGRFRE
+>1_1452
+MRILYYGLLRVALFFVLWWVGLQLGLGMVMATLAAAILTFAVSYLFLGRLRRGATQDLSA
+AWEGRPGRRGRTEAADAEAEDAYTQGRFRE
+>2_1049
+MRILYYGLLRVALFFVLWWVGLQLGLGMVMATLAAAILTFAVSYLFLGRLRRGATQDLSA
+AWEGRPGRRGRTEAADAEAEDAYTEGRFRE
+>3_986
+MRLFLYGLVRVVLFFVIWALCYYVFGLGMLFSTLAAVILTFAVSYLFLTRLRLDASTDLQ
+NAWEGRPSRRGRTEAADAAAEDAYTDGRFPG
+>4_1666
+MRIFFYGLVRVVVFVALWALFYYVMDLGMIFGVIAATILTFAVSYLFLGRLRAGATEDLS
+AAWEGRPGRRGRTETADADAEDAYTEGRFRE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001464.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001464.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e64362c10bcc120c6ed6d18c7fa7c578b5f7bd3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001464.fa
@@ -0,0 +1,25 @@
+>0_1756
+MADTPQRTDPNAPVLVVGLGRFGAATAEELVAQGREVLAVERDPVLVQRYAPSLTHVVEA
+DATDSEALRQLGAQDFSTAVVGVGTSIEASVLITVNLVDLEIPHIWVKAISEAHGTILKR
+IGANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLAESHVRSKY
+GVTVVGVKTPGEDFTYAQPDTRVGPRDTLIVSGHTDLIDRFAARP
+>1_1464
+MADTPQRTDPNAPVLLVGLGRFGAATAEELVAQGREVLAVERDPVLVQRYAPSLTHVVEA
+DATDSEALRQLGAQDFSTAVVGVGTSIEASVLITVNLVDLEIPHIWVKAISEAHGTILKR
+IGANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLAESKVRSKY
+GVTVVGVKTPGEDFTYAQPDTRVGPRDTLIVSGHTDLIDRFAARP
+>2_1038
+MADPQRTDPNAPVLVVGLGRFGAATAEELVAQGREVLAIERDPVLVQRFAPSLTHVVEAD
+ATDPEALRQLGAQDFSTAVVGVGTSIEASVLITANLVDLEIQHIWVKAISEAHGTILKRI
+GANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLGESNVRSKYG
+VTVVGVKTPGEDFTYAQPDTRVGARDTLIVSGHTDLIDRFAARP
+>3_974
+MADQPRTDPNAPVLVIGLGRFGAATAEELVTQGREVLAIERDPVLAQRFAPTLTHVVEAD
+ATDAEALRQLGAQDFDVAVVGVGTSIEASVLITANLVDLEIPHIWVKAISDAHGTILKRI
+GAQHIIFPEKDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPTETVGFTLEESNVRQKYG
+VTIVGVKTPGEDFTYAQPHTRVGPRDTLIVSGHTDLIDRFAARP
+>4_1678
+MADTPQRTDPNAPVLVVGLGRFGAATAEELVAQGREVLAVERDPVLVQRYAPSLTHVVEA
+DATDPEALRQLGAQDFSTAVVGVGTSIEASVLITVNLVDLEIPHIWVKAISEAHGTILKR
+IGANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLAESHVRSKY
+GVTVVGVKTPGEDFTYAQPDTRVGPRDTLIVSGHTDLIDRFAARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001467.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001467.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b85014fdb31a1bc70ea65065b056337c640d1ab6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001467.fa
@@ -0,0 +1,35 @@
+>0_1759
+MRLGVLDIGSNTVHLLLVDAHPGARPVAYAEHKRSLPLIRYQDADGAITEEGQRELVDFV
+REAAAFAEEHRAEDMISFCTSAIRESANGAAVLARVQAETGVHLSELTGDQESAMTYFAV
+RRWQGWDAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWVPEDPPSPKAVK
+KLRKHVEKRLEEAYTVFPRIESPVVVTATSKTFRSLARITGAAPSAAGPFVKRHLRADDL
+HLWVNRLAAMTIAERAELPGVSDVRAHQVFAGAIVALTAMRTFGIAQLEICPWALREGLI
+LNRLDALMLEGHLTRDGLPGVGHVNLNPDTLLPGLSLGVR
+>1_1467
+MRLGVLDIGSNTVHLLLVDAHPGARPVAYAEHKRSLPLIRYQDADGAITEEGQRELVDFV
+REAAAFAEEHRAEDMISFCTSAIRESANGAAVLARVQAETGVHLSELTGDQESAMTYFAV
+RRWQGWGAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWVLEDPPSPKAVK
+KLRKHVEKRLEEAYTAFPRIESPVVVTATSKTFRSLARITGAAPSAAGPFVKRHLRADDL
+HLWVNRLAAMTVAERAELPGVSDVRAHQVFAGAIVALTAMRTFGIAQLEICPWALREGLI
+LNRLDALMLEGHLTRDGRPGVGHVNLNPDTLLPGLSLGVR
+>2_1031
+MRLGVLDIGSNTVHLLLVDAHPGARPSAYAEHKRSLPLIRYQDAEGAITEEGQHELVDFI
+REAVAFAEEHRAEDMISFCTSAIRESANGAEVLARVDREAGVHLAELSGDQESAMTYFAV
+RRWQGWDAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWLPEDPPSPKAVK
+KLRKHVEKRLEEAFAAFPPVEAPVAVTATSKTFRSLARLTGAAPSAAGPYVKRHLRADDL
+HLWVNRLAAMTAAERADLPGVSEVRAPQVLAGAIVALAAMRTFGIAQLEICPWALREGLI
+LNRLDALMLEGHLTHDGLPGVGHVNLNTDTLLPGLRLGVR
+>3_970
+MRLGVLDIGSNTVHLLLVEARAGARPTPYAEHKRSLPLIRYLDESGAINEEGQDELVGFI
+GEAVAFAEEHRAEDMISFCTSAIREAENGPAVLARVEAETGVHLSELSGEQEASMTYFAV
+RRWQGWGVGSILNFDIGGGSFEIAYGQDELPSHAVSLPLGAGRLTRERLPDDPPSPKAVK
+KLHKHVSREIEAVFADFPPLEAPYVVTATSKTFRSLARLTGAAPSAAGPYVKRHLRADDL
+QLWVNRLAAMTWEQRAELPGVSEVRAPQVLAGALVALAAMRTFGVAQLEICPWALREGLI
+LNRLDALMLEGHLTREDGLGVGHVNLNTDSLLPGLSLGVR
+>4_1681
+MRLGVLDIGSNTVHLLLVDAHPGARPVAYAEHKRSLPLIRYQDADGAITEEGQRELVDFV
+REAAAFAEEHRAEDMISFCTSAIRESANGAAVLARVQAETGVHLSELTGDQESAMTYFAV
+RRWQGWGAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWVLEDPPSPKAVN
+KLRKHVEKRLEEAYTAFPRIESPVVVTATSKTFRSLARITGAAPSAAGPFVKRHLRADDL
+HLWVNRLAAMTVAERAELPGVSDVRAHQVFAGAIVALTAMRTFGIAQLEICPWALREGLI
+LNRLDALMLEGHLTRDGRPGVGHVNLNPDTLLPGLSLGVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001468.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001468.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b8404d4a5f391a8b500c71568c18a225268de7a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001468.fa
@@ -0,0 +1,85 @@
+>0_1760
+MSTSSASVTAPVPEGKKLVIVESPAKSKSIAKYLNAVGSGWVVDSSVGHIRDLPKPSDLP
+ADMKKGPFGKFAVDTEHGFTPYYVVHPDKKKKVAELKRELKDAEALYLATDADREGEAIA
+WHLLDTLKPTVPVYRMTFGEITQEGVRRGLENIRELDTALVDAQETRRILDRLFGYELSP
+VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAHYWGVEGTFTVAEGAQAADAVGSS
+FTARLSTVDGERVATGRDFDDAGRLKASAGKKVTHLDEAGARSLAEGLRGADFTVDSVED
+KPYTRRPAAPFTTSTLQQEAARKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQ
+AARRQATELYGADAVPAQPRVYAKRNETAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL
+YELIWKRTVASQMADAKGYTATLRLSATAQDGRLAQFSASGTVITFKGFLDAYEEGRDAE
+VDGENAEAKDRRLPQVAQGERLTGDPIEATGHETSPPARYTEASIVAELERREIGRPSTY
+APTISTIMDRGYVSKRGTALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGE
+LGREAWLQTFYFGAPAAETEKGVEGLKHVVDNLGEIDARAVNSLPITEDITLRVGQYGPY
+LERSLPADAEAGATPPRANVPEDLAPDELTPAKAEELFATAQPSERELGTDPETGRTIVA
+KDGRYGPYVTEVIPEMTEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFTSMSV
+DTVTLEQALQLMSLPRVVGADAEGEVITAQNGRFGPYLKKGSDSRSLESEDQIFSITQEQ
+ALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRFGPYITDGVTNITVPRGRRPE
+ELTAEEAYQLLADKRAKGPATRGGAKKPAARKAPAKKTTARKKA
+>1_1468
+MSTSSASVTAPVPEGKKLVIVESPAKSKSIAKYLNAVGSGWVVDSSVGHIRDLPKPSDLP
+ADMKKGPFGKFAVDTEHGFTPYYVVHPDKKKKVAELKRELKDAEALYLATDADREGEAIA
+WHLLDTLKPTVPVYRMTFGEITQEGVRRGLENIRELDTALVDAQETRRILDRLFGYELSP
+VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAHYWGVEGTFTVAEGAQAADAVGSS
+FTARLSTVDGERVATGRDFDDAGRLKASAGKKVTHLDEAGARSLAEGLRGADFTVDSVED
+KPYTRRPAAPFTTSTLQQEAARKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQ
+AARRQATELYGADAVPAQPRVYAKRNETAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL
+YELIWKRTVASQMADAKGYTATLRLSATAQDGRLAQFSASGTVITFKGFLDAYEEGRDAE
+VDGENAEAKDRRLPQVAQGERLTGDPIEATGHETSPPARYTEASIVAELERREIGRPSTY
+APTISTIMDRGYVSKRGTALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGE
+LGREAWLQTFYFGAPAAETEKGVEGLKHVVDNLGEIDARAVNSLPITEDITLRVGQYGPY
+LERSLPADAEAGATPPRANVPEDLAPDELTPAKAEELFATAQPSERELGTDPETGRTVVA
+RDGRYGPYVTEVIPEMTEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFTSMSV
+DTVTLEQALQLMSLPRVVGADAEGEVITAQNGRFGPYLKKGSDSRSLESEDQIFSITQEQ
+ALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRFGPYVTDGVTNITVPRGRQPE
+ELTAEEAYQLLADKRAKGPATRGGAKKPAARKAPAKKTTARKKA
+>2_1030
+MPTTPASVTASVPEGKKLVIVESPAKSKSIAKYLNAVGEGWVVDSSVGHIRDLPKPSDLP
+ADMKKGPFGKFAVDTENGFAPYYVVHPDKKKKVTELKRELKDAVALYLATDADREGEAIA
+WHLLDTLKPKVPVYRMTFGEITKEGVRRGLENIRELDTHLVDAQETRRILDRLFGYELSP
+VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAAYWGVEGTFTVAPGAQAADAVGSS
+FTARLSTVDGERVATGRDFDDAGALKASAGKKVTHLDEAAASSLAQGLRGADFTVDAVED
+KPYTRRPAAPFTTSTLQQEASRKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQ
+AARRQATELYGQDAVPAQPRVYAKRNESAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL
+YELIWKRTVASQMADAKGYTATLRFSATAQDGRAAQFSASGTVITFKGFLDAYEEGKDAE
+TEDEKAEAKDRRLPQVAEGERLVGEPIEATGHETSPPARYTEASIVAELERREIGRPSTY
+APTISTIMDRGYVSKRGNALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGE
+LGREAWLQTFYFGAPASETGKGVEGLQQVVENLGEIDARAVNSLPITDEITLRVGQYGPY
+LEKPLPADAEAGSTPPRANVPEELAPDELTPAKAEELFATAKPSERELGTDPETGRAVVA
+KDGRYGPYVTEVIPEMTEEQLQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFSSMSV
+DTVTLEEALRLMSLPRVVGADAEGEVITAQNGRFGPYLKKGTDSRSLESEDQIFTITQEQ
+ALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRFGPYVTDGVTNITVPRGRQPE
+ELTAEEAYQLLADKRAKGPATRKAPARKPAARKAPAKKSAPKKKA
+>3_969
+MPTASASTSSSVPQGKKLVIVESPAKSKSIAKYLNAVGEGWVVDSSVGHIRDLPKPSDLP
+ADMKKGPYGKFAVDTEHGFTPYYVVHPDKKKKVTELKRELKDAEALYLATDADREGEAIA
+WHLLDTLKPKVPVYRMTFGEITKEGVRRGLENIRELDTHLVDAQETRRILDRLFGYELSP
+VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVAAQYWGVEGTFTVGPDAKADGAAGSS
+FTARLSTVDGARVATGRDFDDAGRLKESAGKKVAHLDEAAAASLAEGLDGKDFTVDSVED
+KPYTRRPAAPFTTSTLQQEASRKLRMSARVTMQVAQRLYENGYITYMRTDSVNLSQEAVQ
+AARRQATELYGQESVPTQPRVYAKRTENAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL
+YELIWKRTVASQMADAKGYTATLRFSAQAEDGRTAQFAASGTVITFKGFLDAYEEGRDAE
+PEEEKDAKDRRLPQVAEGETLTGAPIQPTGHETTPPARYTEASIVAELERREIGRPSTYA
+PTISTIMDRGYVSKRGSALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGEL
+AREAWLQTFYFGADSADTQKGVEGLKHVVENLGEIDARQVNSLPVTEDITLRVGQYGPYL
+ERRLPEGAAEGTAPERANVPEDLAPDELTPAKAEELMAAGGADERELGVDPETGRTVVAK
+DGRYGPYVTEVIPEMGEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFKTMSVD
+TVTLEQALQLMSLPRIVGADAEGEVITAQNGRFGPYLKKGTDSRSLESEDQIFTVTQEQA
+LEIYAQPKQRGRGTAKPPLAEFGEDPVSGKKVTVKEGRFGPYVTDGVTNITVPRGRAPEE
+LTAEEAYQLLADKRAKGSAKKPAAKKPAARKPAAKKTTTSTTTRKKA
+>4_1682
+MSTSSASVTAPVPEGKKLVIVESPAKSKSIAKYLNAVGSGWVVDSSVGHIRDLPKPSDLP
+ADMKKGPFGKFAVDTEHGFTPYYVVHPDKKKKVAELKRELKDAEALYLATDADREGEAIA
+WHLLDTLKPTVPVYRMTFGEITQEGVRRGLENIRELDTALVDAQETRRILDRLFGYELSP
+VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAHYWGVEGTFTVAEGAQAADAVGSS
+FTARLSTVDGERVATGRDFDDAGRLKASAGKKVTHLDEAGARSLAEGLRGADFTVDSVED
+KPYTRRPAAPFTTSTLQQEAARKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQ
+AARRQATELYGADAVPAQPRVYAKRNETAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL
+YELIWKRTVASQMADAKGYTATLRLSATAQDGRLAQFSASGTVITFKGFLDAYEEGRDAE
+VDGENAEAKDRRLPQVAQGERLTGDPIEATGHETSPPARYTEASIVAELERREIGRPSTY
+APTISTIMDRGYVSKRGTALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGE
+LGREAWLQTFYFGAPAAETEKGVEGLKHVVDNLGEIDARAVNSLPITEDITLRVGQYGPY
+LERSLPADAEAGATPPRANVPEDLAPDELTPAKAEELFATAQPSERELGTDPETGRTVVA
+RDGRYGPYVTEVIPEMTEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFTSMSV
+DTVTLEQALQLMSLPRVVGADAEGEVITAQNGRFGPYLKKGSDSRSLESEDQIFSITQEQ
+ALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRFGPYVTDGVTNITVPRDRQPE
+ELTAEEAYQLLADKRAKGPATRGGAKKPATRKAPAKKTTARKKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001470.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001470.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6eeae869097258601c1b9cae54ddee69e3beb9e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001470.fa
@@ -0,0 +1,35 @@
+>0_1762
+MSTAALSRIALYYRFTPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK
+RYVRGTREHPAFRDLEVKWSDGSAADFPRLSVKLKPELVAFGAPERVTVDADGVVGTGER
+LTPAQVDALVAERAGSANPVRFLDGRNTVEAAIGRFDGAVVPDAHTTRDLLAAVDSGALD
+HLKDAPLITYCTGGVRCEVLSALLKDRGFAEVYQLDGGIVRYGEARGDAGLWRGELAVFD
+RRLSTRFTADAETIGRCVTCEAPTSALRNCADPACTTLEVRCAACAVDDPERRCPVCVHH
+PHPAERTEA
+>1_1470
+MSTAPLSRIALYYRFTPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK
+RYMRGTREHPAFRDLEVKWSDGSAADFPRLSVKVKPELVAFGAPERVTVDADGIVGTGER
+LTPVQVDALVAERAGTANPVRFLDGRNTVEAAIGRFDGAVVPDAHTTRDLLAAVDSGALD
+HLKDAPLITYCTGGVRCEVLSALLKDRGFAEVYQLDGGIVRYGEARGDAGLWRGELAVFD
+RRLSTRFTADAETIGRCVTCHAPTSALRNCADPACTTLEVRCAACAVDDLEHRCPFCAHR
+PHPAERTEA
+>2_1027
+MSPAPVSRIALYYRFAPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK
+QYVKGTREHPALKDLEVKWSDGSAADFPRLSVKVRPELVAFGVPERITVDEHGVVGTGER
+LTPERLEALVAERAGTENPVRFLDGRNTVEAQIGRFDGAVVPAAHTTRDLLAAVDSGSLD
+HLRDAPLVTYCTGGVRCEVLSALLKDRGFREVYQLDGGIVRYGEAFGDAGLWRGELAVFD
+RRIALRFSEDAETIGRCVTCEAPTSALRNCSDPACTTLEVRCAACAAADPDRRCPVCTER
+SAA
+>3_967
+MTAAAPAAPTPLPAPGGPGRIALYYRFTPLADPEAVRLWQRTLAVSLGLAGRIIVSPQGI
+NGTVGGPAEAVKRYVRGTREHPAFRGLEVTWSDGSAADFPRLSVKVRPELVAFGAPERIR
+VDEHGVVGTGEHLPADQLHALVAERAAQGRPVRFLDGRNSVEAAIGRFEDAVIPAAHTTR
+DLLEAVDSGSLDHLKDQPVVTYCTGGVRCEVLSALLKDRGFSEVYQLDGGIVRYGEAHGD
+AGLWHGRLAVFDRRLSLAFTDGAETLGRCVTCGGATSHLANCADPACTTLQVRCPDCVAA
+HPDHVCPRCLERTPA
+>4_1684
+MSTAALSRIALYYRFTPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK
+RYVRGTREHPAFRDLEVKWSDGSAADFPRLSVKLKPELVAFGAPERVTVDADGVVGTGER
+LTPAQVDALVAERAGSANPVRFLDGRNTVEAAIGRFDGAVVPDAHTTRDLLAAVDSGALD
+HLKDAPLITYCTGGVRCEVLSALLKDRGFAEVYQLDGGIVRYGEARGDAGLWRGELAVFD
+RRLSTRFTADAETIGRCVTCEAPTSALRNCADPACTTLEVRCAACAVDDPERRCPVCVHH
+PHPAERTEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001473.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001473.fa
new file mode 100644
index 0000000000000000000000000000000000000000..475d192d8ca622c55d4df2e73ff2abbdbcce5b4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001473.fa
@@ -0,0 +1,20 @@
+>0_1765
+MTRGRAPARGERGSGTVSVLGTAALGAGLLLAVAALGQASATGSRAAGAADLAALAASDA
+RRGLSDHEPCVLAGRTAERNGAAVVACEVREDGTVRVAVELARAPLPAATADAVAGPPRS
+QAPGAASVAPPEDPPEAPPPEPSVEASAGTR
+>1_1473
+MTRGRAPVRGERGSGTVSVLGTAALGAGLLLAVAALGQASVTGARAAGAADLAALAASDA
+RRGLSDHEPCVLAGRTAERNGAAVVACEAREDGTVRVAVELARAPLPAATADAVAGPPRS
+QAPGAGSADPPEAPPPEPSVEASAGTR
+>2_1024
+MTGRAPGGVPRGAASETGSGTVSVLGTAALGAGLLLAVAALGQASVAGAQAAGAADLAAL
+AASDARRGLSAGEPCLVAGQTAARNRAVVVECEVRENGTVRVSVERGRAPLPPALAAAVA
+GPPRLQAPQAVPEDPLPDASSPSTPTPSSVPPSVSPDPSATTGTR
+>3_964
+MSGTATALGTALLGAGLLTGVLAVGHASATAARASGAADLAALAASDARRGLGAVPDAGV
+LEPCPLAEESARRNGAEVTECVLLPDGSVRVAVVIAADPLPASTAVAVAGPPVGPRGPVA
+GPGRDDAPEDAPDTPGAPPEAATP
+>4_1687
+MTRGRAPARGERGSGTVSVLGTAALGAGLLLAVAALGQASVTGSRAAGAADLAALAASDA
+RRGLSDHEPCVLAGRTAERNGAAVVACEVREDGTVRVAVELARAPLPAATADAVAGPPRS
+QAPGAASVAPPEAPPEPSLEASAGTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001474.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001474.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e27207fbb2d7b81ccedcfc785c3d215a09d00ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001474.fa
@@ -0,0 +1,19 @@
+>0_1766
+MTEHPTSASPSGRRTGARTAGRPRALRGGETGAVTAEYAVLLPVIAFVLVSVLLAGAAAV
+QQVRGQDAAASAARILARGDDEAAARDAVARMAGDDASLSHTVEGGWVTVEVVQPGPGPL
+AWAEVLTLTAHAAAPDQRPGTPAAGPEDRS
+>1_1474
+MTEHPTSAPPSARRTGARTAGRPRGLRGGETGAVTAEYAVLLPVIAFVLVSVLLAGAAAV
+QQVRGQDAAASAARILARGDDEAAARDAVARMAGDDASLSHTVEGGWVTVEVVQPGPGPL
+AWAEALTLTAHAAAPEQRPGTPAAGPEDRS
+>2_1023
+MTAEYAVLLPVIAFVLAAVLLAGAAAVQQVRGQDAATAAARILARGDGEAEARRAVARMA
+GDDAALAHTADGGWVAVEVSQPGPGPLAWAEALTLTARAAAPQQHPGAAVDPDGGRT
+>3_963
+MADLPAEAPRPGRLRGARAGASGTVAFRDAERGEGERGAVTAEYAVLLPAAVAVLVAVLL
+AGVAAVHQVRAQDAAASAARILARGDAESLARDAVGRMAGGDAALEARTAEGWVTVTVTR
+PGPGPLAAVTLSAEAVAPVQATSPTPPGRTPGITAPTGEAAP
+>4_1688
+MTEHPTSASPSGRRTGARTAGWPRALRGGETGAVTAEYAVLLPVIAFVLVSVLLAGAAAV
+QQVRGQDAAASAARILARGDDEAAARDAVARMAGDDASLSHTIKGGWVTVEVVQPGPGPL
+AWAEALTLTAHAAAPDQRPGTPAAGPEDRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001477.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001477.fa
new file mode 100644
index 0000000000000000000000000000000000000000..95322ea2785a110a278eb1d24f3bb8b62fbdba1d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001477.fa
@@ -0,0 +1,44 @@
+>0_1769
+MRPFVPAAPARPPRGRRRRPAPPEGGRRFPWPRTGPAEPERTQVAAPPLAAPAAGPDGLD
+AAVVRRRVAEARASAADGAEPPLAPLIAEALDVPIDDPRVAALVDELDGFGPLAPWVRTP
+GVTDVLVDGAGAVWTDGDGGLVRRPDRLDPETARALAVRLLHRAGRRLDAAVPLADARVG
+GVRVHAVLPPVSGGGTLLSLRIPAAATPSLAALADGWPDGALWADALEALVRDRATVLVS
+GATGAGKTTLLSAALGRVPGDERIVVVEDTAEAAPDHPHVVALQCRAANAEGAGEVGLAE
+LVRHALRMRPDRLVVGECRGAEVADVLTALNTGHQGAWGTLHANAAAEVPARLTAMASLA
+GWRPETVAAQARAGVDAVLHIARDGHGRHPVELAVPDLRADGFALLPALTWRPGTEATGG
+RTVEGPGMPALAARLAGRSGR
+>1_1477
+MRPFVPAAPARPPRGRRRRPAPPEGSRRFPWPRTDPAEPERTQVAAPPLAAPAAGPGGLD
+AAVVRRRVAEARASAADGAEPPLAPLIAEALDAPIDDPRVAALVDELDGFGPLAPWVRTP
+GVTDVLVDGAGAVWTDGDEGLVRRPGRLDPETARALAVRMLHRAGRRLDAAVPLADARVG
+GVRVHAVLPPVSGGGTLLSLRIPAATTPSLAALADGWPDGALWADALEALVRDRATVLVS
+GATGAGKTTLLSAALGRVPGDERIVVVEDTAEAAPDHPHVIALQCRAANAEGAGEVGLAE
+LVRHALRMRPDRLVVGECRGAEVADVLTALNTGHQGAWGTLHANAAAEVPARLTAMASLA
+GWRPETVAAQARAGVDAVLHVARDGHGRHPVELAVPDPRADGFALLPALTWRPGTEATGG
+RTVEGPGVPALAARLAGRSGR
+>2_1020
+MRRRVAEARAAAAEGQEPALAPLVAEAIGVSATDPRVAALVDELDGFGPLAGWVRAPGVT
+DVLVDGSGAVWTDGAEGLLRRPQRLDPHAAQALAMRLVHRAGRRLDAAVPLADARVDGVR
+VHAVLPPVSGGGTLLSLRIPAARTPSLAELAAGWPDGDLWGEALEALVRDRASVLVSGAT
+GTGKTTLLAAALGCVPGDERILTVEDTAEAAPEHPHVVALQCRAANAEGAGAVGLAELIR
+HALRMRPDRLVVGECRGAEVADFLTALNTGHQGAWGTLHANGAADVPARLTAMGSLAGWG
+PDTVAAQARAGVDAVVHLVRDRHGRHPVELAVPDPDARGFALLPALTWTPGPGPGDGSTA
+EGPGLRALAARLAGRGSR
+>3_960
+MPAWVPDAPRPARRPALLPAGLSLPAPLLPDLRRVGRRRPGSDRGEPAHVGPDPDARLRR
+AVAEAQARADPHAPPPLRETVSRALADLAAEDGDTPPSGCPRPAGLRDPDAVLEELVGFG
+PLAPWVRRTGVTDVLVDAAGSVWTDGVEGLVRRPLILPEPTARALAVRLIGLAGRRLDPA
+CPVADARVDGVRVHAVLPPVSGGGTVLSLRVPAAEPPSLDALAADWPDGERWRDAVVALV
+RGRASVLVSGATGTGKTTLLAAALGLAGADERIVLVEDTAEAAPAHPHVISLQARAPTAD
+GAGEVTLAELIRQALRMRPDRLVVGECRGPEVADLLTALNTGHQGAWGTLHANAAADVPA
+RLAAMGALAGWSASAVAAQARAGVDAVLHVRRDGRGRHPVELAVPAPAAHPDAPLSVLPA
+LTWDGGGTRAGPGLEVLEARLSGRGHG
+>4_1691
+MRPFVPAAPARPPRGRRSRLAPPEVGRRFPWPRTGAAEPERTQVAAPPLAAPAAGPCGLD
+VAAVRRRVAEARASAADGAEPPLAPLIAEALDAPIDDPRVAALVDELDGFGPLAPWVRTP
+GVTDVLVDGVGAVWTDGDEGLVRRPGRLDPETAGALAVRLLHRAGRRLDAAVPLADARVG
+GVRVHAVLPPVSGGGTLLSLRIPAATTPSLAALADGWPDGALWADALEALVRDRATVLVS
+GATGAGKTTLLSAALGRVPGDERIVVVEDTAEAAPDHPHVVALQCRAANAEGAGEVGLAE
+LVRHALRMRPDRLVVGECRGAEVADVLTALNTGHQGAWGTLHANAAAEVPARLTAMASLA
+GWRPETVAAQARAGVDAVLHLARDGHGRHPVELAVPDPRADGFALLPALTWRPGTEAAGG
+RTIEGPGVPALAARLAGRSGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001480.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001480.fa
new file mode 100644
index 0000000000000000000000000000000000000000..baf39edd590f087160765cd266fbe4f41847f8c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001480.fa
@@ -0,0 +1,60 @@
+>0_1773
+MDEQIPTFPPPAEFAAQAVAGADLYEEAAEDRLAYWARRAREVLHWEQDFTDVLDWSDAP
+FAKWFVGGTTNAAYNALDRHVEAGHGDRVAIHFEGEPGDTRTYTYADLAAEVRRAANAFE
+SLGVTKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSSDALRSRVDDAEAKLVVT
+ADGSFRRGKPSMLKPAVDQALSAPGHTAEHVLVVRRNEAEVEMTEGRDLWWHDVVDAQSD
+EHELVWHDAEHPLYILYTSGTTGKPKGILHTTGGYLVQAAATHHDTFDLHPESDVFWCTA
+DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKYGVSILYTAPTAIRTFM
+KWGRHIPDEYDLSSLRVLGSVGEAINPEAWRWYHEVIGAGRCPIVDTWWQTETGAHMLTP
+LPGVTTLKPGSAQRPVPGVVLEVVDELGEPMTDTSAGFLVVREPWPSMLRGIWGDRERFK
+ETYWSRFPGMYFAGDGARYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPSVAES
+AVVGAKDETTGEAVVAFVLLTAVAVAADRDVAEVEEELRQHVGKDIGPIAKPKRVLVVPE
+LPKTRSGKIMRRLLKDVAEGRDPGDSTTLADPTVMQRIVETLAPKA
+>1_1481
+MDEQIPTFPPPAEFAAQAVAGADLYEEAAEDRLAYWARRAREVLHWEQDFTDVLDWSDAP
+FAKWFVGGTTNAAYNALDRHVEAGHGDRVAIHFEGEPGDTRTYTYADLAAEVRRAANAFE
+SLGVTKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSSDALRSRVDDAEAKLVVT
+ADGSFRRGKPSMLKPAVDQALSAPGHTAEHVLVVRRNEAEVEMTEGRDLWWHDVVDGQSD
+EHELVWHDAEHPLYILYTSGTTGKPKGILHTTGGYLVQAAVTHHDTFDLHPESDVFWCTA
+DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKYGVSILYTAPTAIRTFM
+KWGRHIPDEYDLSSLRVLGSVGEAINPEAWRWYHEVIGAGRCPIVDTWWQTETGAHMLTP
+LPGVTTLKPGSAQRPVPGVVLEVVDELGEPMTDTSAGFLVVREPWPSMLRGIWGDRERFK
+ETYWSRFPGMYFAGDGARYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPSVAES
+AVVGAKDETTGEAVVAFVLLTAVAVAADRDVAEVEEELRQHVGKDIGPIAKPKRVLVVPE
+LPKTRSGKIMRRLLKDVAEGRDPGDSTTLADPTVMQRIVETLAPKA
+>2_1015
+MDEQIPTFPPPAEFAAQAVAGADLYEEAAEDRLAYWARRAREVLHWEQDFTEVLDWSDAP
+FAKWFVGGTTNAAYNALDRHVEAGNGDRVAVHFEGEPGDTRTYTYAELASEVRRTANAFE
+SLGVAKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSADALRSRVDDAEAKLVVT
+ADGSFRRGKPSMLKPAVDEALSAPGHSVQHVLVVRRNEAEVSLVEGRDLWWHDVVPAQSD
+EHELVWHDAEHPLYILYTSGTTGKPKGILHTTGGYLVQTAATHHDTFDLHPETDVYWCTA
+DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKYGVSILYTAPTAIRTCM
+KWGRQIPDEYDLSSLRVLGTVGEAINPEAWRWYHEVIGGGRCPIVDTWWQTETGAHMLTP
+LPGVTTLKPGSAQTPVPGVTLEVVDEIGEPMKDTSAGFLVAREPWPSMLRGIWGNPERFK
+ETYWSRFPGMYFAGDGARYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPSVAES
+AVVGAADETTGEAVVAFVLLTEEAAAAGRDVAEVEEELRQHVGRDIGPIAKPKRVLVVPE
+LPKTRSGKIMRRLLKDVAEGRDPGDATTLADPTVMQRIVETLAPGA
+>3_956
+MDETRATYPPSEQFAAQAVAGADLYEEAAADRLAYWARRAREHLHWEQDFTQVLDWSDAP
+FARWFADGTTNAAYNALDRHVEAGRGDRTAIVFEGEPGDTRTYTYADLAAEVRRAANAFE
+SLGVAKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSADALRSRVDDAEAKLVVT
+ADGSFRRGRPSMLKPAVDQALSAEGHTVEHVVVVRRNEADVDWTEGRDLWWHDVVPTASD
+EHEVVWHEAEHPLFILYTSGTTGKPKGILHTTGGYLVQTAATHHDTFDLHADTDVYWCTA
+DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKHGVTILYTAPTAIRTFM
+KWGRQIPDGYDLSSLRVLGTVGEAINPEAWRWFHDVIGGGRCPIVDTWWQTETGAHMLTP
+LPGVTELKPGSAQRPVPGVVLEVVDELGEPMEGSTAPGFLVAREPWPSMLRGIWGDPERF
+KETYWSRFPGMYFAGDGAQYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPKVAE
+SAVVGAADETTGEAVVAFVLLTEEATAAGEDVEAVQEELRQHVGKDIGPIAKPKRVLVVP
+ELPKTRSGKIMRRLLKDVAEGRRPGDATTLADPTVMDRITEAVGS
+>4_1695
+MDEQIPTFPPPAEFAAQAVAGADLYEEAAKDRLAYWARRAREVLHWEQDFTDVLDWSDAP
+FAKWFVGGTTNAAYNALDRHVEAGHGDRVAIHFEGEPGDTRTYTYADLAAEVRRAANAFE
+SLGVTKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSSDALRSRVDDAEAKLVVT
+ADGSFRRGKPSMLKPAVDQALSAPGHTAEHVLVVRRNEAEVEMTEGRDLWWHDVVDGQSD
+EHELVWHDAEHPLYILYTSGTTGKPKGILHTTGGYLVQAAVTHHDTFDLHPESDVFWCTA
+DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKYGVSILYTAPTAIRTFM
+KWGRHIPDEYDLSSLRVLGSVGEAINPEAWLWYHEVIGAGRCPIVDTWWQTETGAHMLTP
+LPGVTTLKPGSAQRPVPGVVLEVVDELGEPMTDTSAGFLVVREPWPSMLRGIWGDRERFK
+ETYWSRFPGMYFAGDGARYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPSVAES
+AVVGAKDETTGEAVVAFVLLTAVAVAADRDVAEVEEELRQHVGKDIGPIAKPKRVLVVPE
+LPKTRSGKIMRRLLKDVAEGRDPGDSTTLADPTVMQRIVETLAPKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001483.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001483.fa
new file mode 100644
index 0000000000000000000000000000000000000000..840dcb85fee4bd265e0e915eb045302701f8ffaf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001483.fa
@@ -0,0 +1,54 @@
+>0_1776
+MSSTVSAPATAPKRTREEFAGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI
+ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWA
+IMYTWFSVDQRWGDDPETFLMGDYLQVADDPSPSFDVVSGVFWPMLAVWVITLLIMGFGV
+RRGVALASMVGIPLLIVMFLVLVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI
+FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS
+VSEVAGSGIGLAFIAFPTLISQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKL
+GWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFANNFGIVGAALLSVLLVTGALG
+SARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF
+GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPV
+ATTRKEL
+>1_1484
+MSSTVSAPATAPKRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI
+ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWA
+IMYTWFSVDQRWGEDPETFLMGDYLRVADDPSPSFDFVSGVFWPMLAVWVITLLIMGFGV
+RRGVALASMVGIPLLIVMFLILVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI
+FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS
+VSEVAGSGIGLAFIAFPTLISQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKL
+GWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFANNFGIVGAALLSVLLVTGALG
+SARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF
+GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPT
+AATRKEL
+>2_1012
+MSSTVSAPAAAPTRTREEFAGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI
+ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTESVGWWQVLICVVIAVYYAAIIGWA
+IMYTWFSVDQRWGADPETFMMGEFLQVSETPNPTFDVVSGVFWPMLAVWVITLLIMGFGV
+RRGVAMASMIGIPLLVVMFLVLVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI
+FFSLSVGFGIMITYASYLKKRTNLTSSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS
+VADVAGSGIGLAFIAFPTLISQAPVGALIGVLFFGSLVLAGFTSLISILEVVISAVKDKL
+GWGRWTATIIVVGLAGVVSMALFSTTSGLHMLDTMDAFANNFGIVGAALVSVLLVTGVLG
+SARRVTAHLNAVSSFKLGRGYVLLIGVLMPIVLAYIWLSWIMKVISEGYGGYPGDFLGVY
+GWGVAIGSVVLAVVLSLIPWSRKSNLYAEEMETEIHGDLIPHNAVPEGTTPTGAIPLVPA
+DHTRKEL
+>3_954
+MSTSTGATAAPSRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYEHGGGAFVIPYLVA
+LLTAGIPLLFLDYAIGHRFRGSAPMAFRRMSRWTEAIGWWQVLICAVIGVYYAAIIAWSI
+MYTWFSLDQRWGDDPEGFLFSTYLQQVKDPNPSFDIVPGVFWPMVAVWGVLLLIMGLGIR
+RGVALASMIGIPLLVVMFVVLVIISLTLPGAMQGLDALFTPNWAALKEPGVWIAAYGQIF
+FSLSVGFGIMITYASYLKKRTNLTASGLVVGFSNSGFEILAGIGVFSALGFMAQASGVQV
+SEVAGSGIGLAFIAFPTLITQAPAGALIGVLFFASLVIAGFTSLISILEVVVSAVKDKLG
+WGRWTAVLVVVGISAVISISLFSTTTGVAMLDTMDAFANNFGIVGAALVAVIAVMWIARR
+GGELVAHLNSVSSFRVGRVYRILVGVVMPVLLGWMWIEWIRENAATPYGGYPTDFLAVYG
+WGLAIGSVVLAVLLSLIPWSHKSSLHAEESVNEIDHTAPVASKES
+>4_1698
+MSSTVSAPATAPKRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI
+ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWA
+IMYTWFSVDQRWGEDPETFLMGDYLRVADDPSPSFDFVSGVFWPMLAVWVITLLIMGFGV
+RRGVALASMVGIPLLIVMFLILVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI
+FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS
+VSEVAGSGIGLAFIAFPTLISQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKL
+GWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFANNFGIVGAALLSVLLVTGALG
+SARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF
+GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPA
+ATTRKEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001485.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001485.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a164016d0a2cbb4ba2bfb20b5651d3049a7b200
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001485.fa
@@ -0,0 +1,31 @@
+>0_1779
+MSADPAGLLLPVPGQEEDLTRQWLDRRFRQVRPARPGSSVVLVRDGDDGPEVFLRHRAGR
+TPLGRVGLPGGALIESDADSCPWYGPEPSQWARTFGTTDRRRARQHVVAAVRELHDEAGV
+LLAGRSDTDVVSTARIETWGGGRSSLEEGSESLPHLLAARGLGVRADLLRPVMRWRSAPH
+VHRRFDTAVFATMTPPLQSAPASEEPGPELQAWVSARRALAGPLRLPGPAGAEGTAPFDQ
+VATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDDGTPRMRVKRATRD
+>1_1487
+MSADPAGLLLPVPEQEEDLTRQWLDRRFRQVRPARPGSAVVLVRDGDDGPEVFLRHRAGR
+TPLGRVGLPGGALIESDADLCPWYGPEPSQWAHTFGTTDRRRARQHVVAAVRQLHDEAGV
+LLAGRSDTDVVSTARVETWGGGRSSLEEGSESLPHLLASRGLGLRADLLRPVMRWHSAPH
+VHRRFDTAVFATTTPPVQSAPASEEPGPELQAWVPACRALAGPLRLPGPAGAEGTAPFDQ
+VATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDDGTPRMRVERATRD
+>2_1009
+MVLVRDGEDGPEVFLRHRPGRTPLGRVGLPGGALSEADADACAWFGPDPAHWARVLGTTD
+RRCARQQVVAAVRELHDEAGVLLAGRTDADVVLDARGETWGGGGSSLEEGAESLPRMLAA
+RGLGLRTDLLRPVARWHSAPHAHRRFDTAVFAAAVPPLQRPLERPETAPALQAWVSARRA
+VAGPVPLPGPAGEEGVAPLDQVATPLTQVLVRRVAAHRTAAAFLLSLTQGAGHGPVPEYR
+LVTEAGDDGAPRMRVERVTRD
+>3_951
+MSAEPDAPRVRVPGHEEELTRQWLAQRHRQVRPARPASAVVLVRDGADGVEVLLRHRSGR
+TPLGRIGLPGGSLVDSDADPCTWYGPAPDEWARALGLADRRRVRQHVVAAVRELFEESGV
+LLAGPADMDLVQDARGETWGASRSSLEEGDESLPRLLGDRGLGLRTDLLRGVGRWLSAPH
+SPRRFDTVVFAAALPPQQELVHRPEGPVLQGWFSARRLLSEPAALPGPDGWLGESGVVAL
+EEVSTPMTQLVLRRVAEHRTAAGFLLSPAGCRGPVPVVKLRTEAEHDDLATGTLYTVAER
+VDPVG
+>4_1701
+MSADPAGLLLPVPEQEEDLTRQWLDRRFRQVRPARPGSAVVLVRDGDDGPEVFLRHRAGR
+TPLGRVGLPGGALIESDADLCPWYGPEPSQWAHTFGTTDRRRARQHVVAAVRQLHDEAGV
+LLAGRSDTDVVSTARVETWGGGRSSLEEGSESLPHLLASRGLGLRADLLRPVMRWHSAPH
+VHRRFDTAVFATTTPPVQSAPASEEPGPELQAWVPACRALAGPLRLPGPAGAEGTAPFDQ
+VATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDDGTPRMRVERATRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001487.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001487.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f6849bafce6689c88b9c41550d3ac340fafb8faa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001487.fa
@@ -0,0 +1,10 @@
+>0_1781
+MTQQTQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGNNPVAYLKRPKAA
+>1_1489
+MTQQTQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGNNPVAYLKRPKAA
+>2_1007
+MTEQTKWEYATIPLLIHATKQILDQWGEDGWELVAVVPGPDGPNPVAYLKRPKAA
+>3_949
+MTQRIQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGANPVAYLKRPKDA
+>4_1703
+MTQQTQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGNNPVAYLKRPKAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001489.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001489.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5effcf13d4d93af58212459ed8d1fafd7bc1bcc4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001489.fa
@@ -0,0 +1,35 @@
+>0_1783
+MPPAASPTRRMLRSAAPAAVGMAATAGLGLAWGLAEAEARTVRTHRLAVLPAGSAPLRVL
+HLSDIHLLPRHRAKRAWLRGLDALEPDLVVNTGDNVSAAASVPLVLDALGPLLARPGVFV
+PGSNDYYAPKAANPLRYFAGPSRMDEDRPRLPSDVLFGAFRAAGWADLTNRGAALAVPTR
+AGTTLEVLAAGTDDPHLGLDAWAGFPGAAPDENAGRPGDDGRFRLGVTHAPYRRVLDAMT
+ADGADLLLAGHTHGGQVCVPFLGALVTNCDLPRRQASGVSTWTAAGRTVPLEVSAGLGTA
+PSAPVRFACRPEAVVLDLVPRG
+>1_1491
+MPPAASPTRRMLRSAAPAAVGMAATAGLGLAWGLAEAEARTVRTHRLAVLPAGSAPLRVL
+HLSDIHLLPRHRAKRAWLRGLDALEPDLVVNTGDNVSAAASVPLVLDALGPLLARPGVFV
+PGSNDYYAPKAANPLRYFAGPSRMDEDRPRLPSDVLFGAFRAAGWADLTNRGAALAVPTR
+AGTTLEVLAAGTDDPHLGLDAWAGFPGAAPDENAGRPGDDGRFRLGVTHAPYRRVLDAMT
+ADGADLLLAGHTHGGQVCVPFLGALVTNCDLPRRQASGVSTWTAAGRTVPLEVSAGLGTA
+PSAPVRFACRPEAVVLDLVPRG
+>2_1005
+MRPSATAPRRLVRAGSRAAVGMGTAAALGLAWGLVEAEARVVRTHRLAVLPAGADPVRVL
+HLSDIHLLPRNRSRMAWLRGLDALEPDLVVNTGDNISAAASVPLVLDALGPLLRRPGVFV
+PGSNDYYEPKPANPFRYFAGPSRMDEDRARLPTEALFGAFRAAGWADLTNRGSVLSVPTR
+AGTVLEVLAAGTDDPHLGLDAWGGFPAPAPAPAPAPGDAAASGPASAHDDGAARPGGDGR
+FRLGVTHAPYRRVLDAMTVDGADLLLAGHTHGGQVCLPGFGALVTNCDLPRAQASGVSTW
+TAAGRTVPLEVSAGLGTAPSAPVRFACRPEAVVLELLPCA
+>3_947
+MTDAPGPRLRRLTHTAAWAAGGASALGAGALVWGRVEAEARVVRTHTVPVLPAGARPLRV
+LHLSDIHLLPRHRRRLEWLCSLADLEPDLVVDTGDNISSAASIPLLLDALAPLLAVPGVF
+VPGSNDYFTPKPANPLRYLRGPSELEASRSRLPTEDLFSAFRAAGWTDLTDRAADVVVGS
+GPDAVRIRAAGTDDPHLGLDRWPGFDLADEGAAGDAPLLRLGVTHAPYRRVLDAMTADGA
+DLLLAGHTHGGQVCLPFAGALVTNCDLPRSQASGLSSWTAAGRTVPLEVSAGIGTAPSAP
+VRTFCRPEAVVLDLVPRA
+>4_1705
+MRPAASPARRMFCAAAPAAAGLAATAGLGLAWGLAEAEARTVRTHRLAVLPAGSAPLRVL
+HLSDIHLLPRHRAKRAWLRGLDALEPDLVVNTGDNVSAAASVPLVLDALGPLLARPGVFV
+PGSNDYYAPKAANPLRYFAGPSRMDADRPRLPSDVLFGAFRAAGWADLTNRGAALAVPTR
+AGTTLEVLAAGTDDPHLGLDAWAGFPGSAPDGGAGRPGDDGRFRLGVTHAPYRRVLDAMT
+ADGADLLLAGHTHGGQVCVPFLGALVTNCDLPRRQASGVSTWMAAGRTVPLEVSAGLGTA
+PSAPVRFACRPEAVVLDLVPRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001490.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001490.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e26d7899814dda7e72a233eafd983c618b0abaab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001490.fa
@@ -0,0 +1,61 @@
+>0_1784
+MTRATSPDASSLRDALGGIAPYLEGVRARWVLGLASATAAGLVALAIPQVIHLLVDTVFT
+QTVLAGPSSPDSRADVWRAAGLLTVLGLAEAAFIGLRRYFILPPAAGVENRARIALFERL
+QRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVDVVTIAVGLVLLFLLSWQLA
+LLYLAAAVPIMWASFGFRNDFRAASRLSQDQAGDLATSVEESVHGIRVLKAFGRGAHALD
+GFRGRARTLQGTEVHKASVLARFIALIVALPETVLGLGLALGLWLVATGELTVGALAAYF
+ATAAVLAGPVESVGQLMGMTLSARTAIDRHVDVLATPVDIASPTGEAAVVPPATGALAFR
+GVRFRWPDADPGRGERDLLDGVDLELVPGETMALVGATGAGKSTLLQLVPRLLDVTAGSV
+CVDGVDVRRMPLEELRRRVSVAFEDATLFSATIRQNVLLGAPADVLADGLHSPAADALLD
+LALETAQAGFVADLADGVETEIGEEGLSLSGGQRQRIALARAIAARPDVLVLDDPLSALD
+VRTEETVTARLREVLDGTTTLIVAHRPSTVALADRVAVLADGRIEDVGTHPELLARSAVY
+RHIISSRPEEQA
+>1_1492
+MTRATSPDASSLRDALGGIAPYLEGVRARWVLGLASATAAGLVALAIPQVIHLLVDTVFT
+QTVLAGPSSPDSRADVWRAAGLLTVLGLAEAAFIGLRRYFILPPAAGVENRARIALFERL
+QRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVDVVTIAVGLVLLFLLSWQLA
+LLYLAAAVPIMWASFGFRNDFRAASRLSQDQAGDLATSVEESVHGIRVLKAFGRGAHALD
+GFRGRARTLQGTEVHKASVLARFIALIVALPETVLGLGLALGLWLVATGELTVGALAAYF
+ATAAVLAGPVESVGQLMGMTLSARTAIDRHVDVLATPVDIASPTGEAAVVPPATGALAFR
+GVRFRWPDADPGRGERDLLDGVDLELVPGETMALVGATGAGKSTLLQLVPRLLDVTAGSV
+CVDGVDVRRMPLEELRRRVSVAFEDATLFSATIRQNVLLGAPADVLADGLHSPAADALLD
+LALETAQAGFVADLADGVETEIGEEGLSLSGGQRQRIALARAIAARPDVLVLDDPLSALD
+VRTEETVTARLREVLDGTTTLIVAHRPSTVALADRVAVLADGRIEDVGTHPELLARSAVY
+RHIISSRPEEQA
+>2_1004
+MTRTATRPLPLREALQVVAPYLQGVRGRWVLGLLSAMAAGLVALAIPQVVQVLVNTVFAE
+AAPGTAGTADPAAGVWWAAGALALFGLAEALFIWLRRFFILPPAADVENRARISIYRRLQ
+RLPVAFHDAWASGQLLSRAQGDLALLRRWIAFGSVMLVVETVTIVVGLVLLFVMSWQLAL
+LYLVAAVPIMIRSFRFRTDFRAASRLSQDQAGDLATTVEESVHGIRVLKAFGRGPDALDG
+FRGEAETLQGTEVHKASVLAKFISLTVSLPELVLGVALGLGLYLVAVGDLTVGALAAYFA
+TTAVLARPVEGVGQLMGMTLSAKTAIDRHLEVMRVPVAVASPAGTDAAEEEATSRAVASS
+AAEDSPVVTDGLPPSSGRLAFRDVVFRYPDAPEDSRPLLAGVDLELTPGETMALVGVTGS
+GKSTLVQLVPRLLDVTAGVVEVDGTDVRAYPLDELRRRVSIAFEDATLFSDTVRANVLLG
+APAEVTADGLDSPRAQALLDLALDTAQAGFARDLPAGVDTEIGEEGLSLSGGQRQRIALA
+RAIAARPDVLVLDDPLSALDVRTEEAVTGRLREVLAGTTTLIVAHRPSTVALADRVAVLQ
+DGAIHDVGTHAELLARSAAYREIITTGAAEDRSLAGLADAAHDDAALAAATDAARPPAGA
+ARPPAGRTAGREETR
+>3_946
+MTRTTTAAAPLPLRDAVRGIAPYLEGVRTRWVLGLLSALAAGLVALAIPQVIRLLVNTVF
+AAPTTPGAPAAEDATASVWWAVGGLALLGAAEALFIWLRRFFILPPAADVENRARIAVYR
+RLQRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVETVTLVVGVGLLFWLSWP
+LALVYLAAALPIMWRSYGFRNDFRTASRLSQDQAGDLATTVEESVHGIRVLKAFGRGPHA
+LEGFRGEAQTLQGTEVHKAGVLASFIAFTVSLAEVMLGVALALGVWLVATGQMTVGALAA
+YFATTAVLARPVEGIGQLLGMTLSAKTAIDRHLEVMRQPVSIASPPGTDPAEEAATGASV
+GEDPDPAVADAPVDVSALPPSRGGLAFRGARFRHPDTPDDAPDLLAGVDLELVPGETMAL
+VGLTGSGKSTLLQLVPRLRDVTGGVVEVDGVDVRDYPLEELRRRVSIAFEDATLFSDTVR
+ANVLLGAPAAEVADGPDSPAAEALLELALDTAQAGFVADLPQGVDTPIGEEGLSLSGGQR
+QRLALARAIAARPDVLVLDDPLSALDVRTEEAVTARLREVLAGTTTLIVAHRPSTVALAD
+RVAVLQDGRIADVGTHADLLARSGAYRQIITTDREDAR
+>4_1706
+MTRATSPAASSLRDALGGIAPYLEGVRARWVLGLASATAAGLVALAIPQVIHLLVDTVFT
+QTVLAGPSSPDSRADVWRAAGLLTVLGLAEAAFIGLRRYFILPPAAGVENRARIALFERL
+QRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVDVVTIAVGLVLLFLLSWQLA
+LLYLAAAVPIMWASFGFRNDFRAASRLSQDQAGDLATSVEESVHGIRVLKAFGRGAHALD
+GFRGRARTLQGTEVHKASVLARFIALIVALPETVLGLGLALGLWLVATGELTVGALAAYF
+ATAAVLAGPVESVGQLMGMTLSARTAIDRHVDVLATPVDIASPTGEAAVVPPATGALAFR
+GVRFRWPDADPGRGERDLLDGVDLELVPGETMALVGATGAGKSTLLQLVPRLLDVTAGSV
+CVDGVDVRRMPLEELRRRVSVAFEDATLFSATIRQNVLLGAPADVLADGLHSPAADALLD
+LALETAQAGFVADLADGVETEIGEEGLSLSGGQRQRIALARAIAARPDVLVLDDPLSALD
+VRTEEAVTARLREVLDGTTTLIVAHRPSTVALADRVAVLADGRIEDVGTHPELLARSAVY
+RHIISSRPEEQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001491.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001491.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ae19c9487602b7b7fbe99377d341661b97801d4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001491.fa
@@ -0,0 +1,50 @@
+>0_1788
+MKTLVLGNGGREHALLTALSRDPQVSALHAAPGNAGMADLATLHAVEATDPAAVVELARE
+LGADLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGS
+RVCTTAAEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAEACFAAGGTVVIED
+FLDGPEVSLFVICDGEDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFTDEVM
+DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLETPLGG
+LLADAAAGRLGADRRLEWSDDVAVDVVMASAGYPASSSTGDVITGLADAAALEGVHVIHA
+GTAASGEDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI
+TVPGTGGAK
+>1_1495
+MKTLVLGNGGREHALLTALSRDPQVSALHAAPGNAGMADLATLHAVEATDPAAVVELARE
+LGADLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGS
+RVCTTAAEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAEACFAAGGTVVIED
+FLDGPEVSLFVICDGEDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFTDEVM
+DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLETPLGG
+LLADAAAGRLGADRRLEWSDDVAVDVVMASAGYPASSSTGDVITGLADAAALEGVHVIHA
+GTAASGEDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI
+TVPGTGGAK
+>2_1000
+MKTLVLGNGGREHALLAALSRDPQVGELHAAPGNAGMAALAALHAVEATDPDAVVALARE
+LAADLVVVGPEAPLAAGVSDALREAGFAVFGPSRAAAQLEASKAFAKEVMAAAGVPTAGS
+RTCATAEEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAQACFDAGGTVVIED
+FLDGPEVSLFVVCDGTDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFAEEVM
+DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLTTPLGG
+LLADAAAGRLGADRALEWSDDVAVDVVMASAGYPATSSQGDVITGLTDAEALEGVHVIHA
+GTATSGDDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI
+AVPAAVGQAGQAGEDAR
+>3_943
+MKILVLGNGGREHALLRALSRDPQVGELHAAPGNAGMADAAVLHPVTATDPEAVVALARD
+LAVDLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGA
+RVCATEAEVDAALTAFGAPHVVKDDGLAAGKGVVVTSDRAAALDHARACLSAGGTVVVED
+FLDGPEVSLFVLCDGEHAVPLTPAQDFKRIHDGDAGPNTGGMGAYTPLQWLPEGFVDEVM
+ERVARPVLAEMSRRDTPFAGVLFIGLAVTENGPEVIEFNVRFGDPETQSVLARLETPLGQ
+LLADAAAGRLGADRELRWSDDVAVDVVLASAGYPASSHSGDVIAGLEDALALEGVDVLHA
+GTARTEDGDVVTAGGRVLAVVGRGATLEQARERAYAGVAKIRFDGAQHRTDIAIKAERGE
+ITVPERRRGYAGAEALELPGWRHVYSGKVRDLYEPADAEPGTSETLLVVASDRISAYDFV
+LEPPIPGKGAVLTRLSLWWFEQLAGVANHVVSTDVPAEVAGRAMVVKRLDMHPIECIARG
+YLTGSGLAEYREHATVTGIPLPDGLVDGSRLEPPIFTPSAKAEVGEHDENITFEQTVERV
+GAPTAEALRAATLEVYTRAEAIARKAGIILADTKVEFGADPVTGELVLGDEVLTPDSSRF
+WDAEAYEPGRAQASFDKQFVRDWLTSPESGWDRTSGEEPPALPADVVERTRARYVEAYER
+LTGRRFEA
+>4_1709
+MKTLVLGNGGREHALLTALSRDPQVSALHAAPGNAGMADLATLHAVEATDPAAVVELARE
+LGADLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGS
+RVCTTAAEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAEACFAAGGTVVIED
+FLDGPEVSLFVICDGEDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFTDEVM
+DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLETPLGG
+LLADAAAGRLGADRRLEWSDDVAVDVVMASAGYPASSSTGDVITGLADAAALEGVHVIHA
+GTAASGEDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI
+TVPGTGGAK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001494.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001494.fa
new file mode 100644
index 0000000000000000000000000000000000000000..10a900f5fad6be7ad45e06747078ef78d33a18c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001494.fa
@@ -0,0 +1,45 @@
+>0_1791
+MSVAPRAAVPPAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPEASSGPFPAT
+TLVLLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVAHHGDFAWVA
+FPLFFVVLHVVDRVARQAWVRHVVGPALVVAMAVVVVAGMAAGAGGVRVPAVIGPLVGAA
+VAVVLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLTQG
+LASIVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGTGAPSLIEAL
+ERAVAGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLANVGAHAGARRAR
+VTLGYLGDELTVDVADDGAGFDPAVVAARPRAGAAGADPGAGTGVGLASVRERLAAVGGE
+ATVESAPGEGTVVALRVPLVAAGAGRSADPEQTESEETA
+>1_1498
+MSVAPRAAVPPAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPDASGPFPATT
+LVLLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVGHHGDFAWVAF
+PLFFVVLHVVDRVARQAWVRHVVGPALVVAMAAVVVAGMAAGAGGVRVPAVIGPLVGAAV
+AVVLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLTQGL
+ASIVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGTGAPSLVEALE
+RAVTGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLANVGAHAGARRARV
+TLGYLGDELTVDVADDGAGFDPAVVVARARAGAAGADPGAGTGVGLASVRERLAAVGGEA
+TVESAPGEGTVVALRVPLAAAGAGRSADPEQTESEETA
+>2_997
+MPTTRPSADTAGAPAETGAAAVLAGLRVALHVAFAVLLAVGLGRALADLSRTGAPAPAVL
+ALTGCTALLAGVYLAGTLVERRRWGRGEDVGRGPALLWLALVLALWGLLVAQHRDFAWVA
+FPLFFVALHVVARTARTAMARRIAGPVLVAAMAAVVVAGMAAGVDEGVRPAAVIGPLVGA
+AVAVVLSGAYRALHQESERQRDVAEQLRAAQAELARTQHRAGVGEERERLAREIHDTLTQ
+GLASIVLVSRAAQDALDAQDPALARTRMETVRTTAAENLDESRRFVRDLRATGGASLVAA
+VERAVAGFAERQAAAGTPVAADVEVVGTPVPLAEAVEAALLRAVQASLANVAAHARATRA
+RVTLAWMPGELAVDVADDGVGFRPEAVVTGDAGTQGTGAGTQGARAGRASRPGAGTGVGL
+ASVRERLAGVGGHASVESAPGEGTVVALRVPLPAAAGRAEEDEGRERG
+>3_940
+MRTSDPADGPRGANGTAALLSGLRVAVHVGFAVLLALALVRALAGPDAGARLTGRPALAL
+VGLTVVLAGVYLTGTVAERRLHAAGRAPGRTAAGTWLAVLLGVWALAVLRHPDMMWVAFP
+LFFVALHAVHVILGRPRLALACVAAMTVVVVVASLERGTAPGAVLGPAVGAAVAVVVFHA
+CRLLVVESERQRSVAEQLRATRAELAASERHAGVLAERERLAREIHDTLTQGLASIVLVS
+RAAQDAVRAGDAALADERLETVRTTAAENLAESRAFVRGLRAPVDGVQGGADRAGSALEA
+ALGAAVRGFRARRQALGRPVEAELAVVGEPVAVGEAVETVLVRAAQSSLANVDQHARTDR
+CRVTLTWMDGEVALDVADDGVGFDPEAARARASRAAVSDPAAPRPAEEGTGVGLAGLAER
+VAGVGGRVDVESAPGQGCVVAVRIPVPRQHERRGA
+>4_1712
+MSVAPRAAAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPEASSGPFPVTTLV
+LLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVAHHGDFAWVAFPL
+FFVVLHVVDRVARQAWVRHVVGPALVVAMAVVVVAGMAAGAGGVRVPAVIGPLVGAAVAV
+VLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLTQGLAS
+IVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGTGAPSLIEALERA
+VTGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLANVGAHAGAHRARVTL
+GYLGDELTVDVADDGAGFDPAVVAARPRAGAAGADPGAGTGVGLASVRERLAAVGGEATV
+ESAPGEGTVVALRVPLVAAGAGRSADPEQTESEETA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001496.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001496.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ba3490c06a90c2811984cd16bab12581b36e2d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001496.fa
@@ -0,0 +1,35 @@
+>0_1794
+MTHATVAPAGETLALSDAVELVETVRNGFVESRTAGAAVVTGPDGRVLAGLGPADALIYP
+RSTLKPFQAVASLRHGAALEGEALSIACGSHRGTLRHQALAERMLADAGLDASALQCPPA
+WPADTSEVVAQVRRDGESAAATPLAFNCSGKHAGFLAACAASGHDVATYLDPAHPLQREV
+DAVIAEYCGEPVAHTGVDGCGAPAAVISLAGLARGIGRVAAAPGRADADPHAAAVATAML
+EHPWAVHGETSSNTVVMRELGLLAKAGADGVLVMAAPDGTAVAVKALDGGTRAGDLVALA
+LLARFAPDHVDRATLPGVLAAVVPPVLGRGEPVGEIRLAAPVRDLVGDVLPAFEARA
+>1_1501
+MTHATIAPAGETFALSDAVELVETVRNGFVESRTAGAAVVTSPDGRVLAGLGPADALIYP
+RSTLKPFQAVASLRHGAALEGEALSIACGSHRGTLRHQALAERMLADAGLDASALRCPPA
+WPADTSEVVAQVRRDGESAAATPLAFNCSGKHAGFLAACAASGHDVATYLDPAHPLQREV
+DAVIAEYCGEPVAHTGVDGCGAPAAVISLAGLARGIGRVAAAPGRADADPHAAAVATAML
+EHPWAVHGETSSNTVVMRELGLLAKAGADGVLVMAAPDGTAVAVKALDGGTRAGDLVALA
+LLARFAPDHVDRATLPGVLAAVVPPVLGRGEPVGEIRLAAPVRDLVGDVLPTFEARA
+>2_994
+MTQTPSATFALADAVELVHVVRNGFVESRTPGAAVVTGPDGTVLAALGPVDALIYPRSTL
+KPFQAIASLRHGARLEGQEVAIACGSHRGTAAHRELAARILAEAGLSAADLQCPPDYPAD
+AAEIVRFAQDLEHGAEKTPLAYNCSGKHAGFLAACVAAGHEVGTYLEPDHPLQAEVERVI
+EEYCGEPVAHTGTDGCGAPAAVLSLTALARGIGKVASAPSRRDAEIHAATVANAMLEHPW
+AVHGQSSSNTVVMRELGLLAKLGADGVMVMAAPDGTAVAVKALDGGTRAGNLVALALLAQ
+FAPDHVDADRLPAVLETVAPKILGKGEPVGAVRLARPVLDLLD
+>3_937
+MTQTSAAPAGQTFALADAVELVEVVRGGFVESRTAGAAVVTGPDGEVLAALGPADALVYP
+RSTLKPFQAIASLRHGARLEGEALAIACGSHTGSEAHQQLAARVLADHGLAPEALQCPSA
+LPEVAGEVARLAAQAGTAEIATPLAYNCSGKHAGFLAACAASGHDVGTYLDPEHPLQREV
+DAVIAEYCGEPVAHTGVDGCGAPAAVVSLAGLARGIGAVSKAPGREGAEPHAAAVARAML
+AHPWAVQGPGKANTVVMEELGLVAKLGADGVMVMGAPDGTAVAVKALDGGTRAGNLVALA
+LLGRFAADQVDAGRLAEVSARVAPSILGRGAPVGEVRLAAPVRQLVGA
+>4_1715
+MTHATVAPAGETFALSDAVELVETVRNGFVESRTAGAAVVTGPDGRVLAGLGPADALIYP
+RSTLKPFQAIASLRHGAALAGEALSIACGSHRGTLRHQALAERMLADAGLDASALRCPPA
+WPADTSEVVAQVRRDGEAAAATPLAFNCSGKHAGFLAACAASGHDVATYLDPAHPLQREV
+DAVIAEYCGEPVAHTGVDGCGAPAAVISLAGLARGIGRVAAAPGRADADPHAAAVATAML
+EHPWAVHGETSSNTVVMRELGLLAKAGADGVLVMAAPDGTAVAVKALDGGTRAGDLVALA
+LLARFAPDHVDRATLPGVLAAVVPPVLGRGEPVGEIRLAAPVRDLVGDVLPAFEARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001497.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001497.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9dd33a61fc6a6ac612559eadfa407fe0ccefe27c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001497.fa
@@ -0,0 +1,20 @@
+>0_1795
+MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRATAVRFALEELATRVPGN
+SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTTWEDATAAGGVRASGV
+RADLGAHLPLVRP
+>1_1502
+MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRAMAVRFALEELATRVPGN
+SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTSWDEATAAGGVRASGV
+RADLGAHLPLVRP
+>2_993
+MTTGSVPRRRIPVPEGHAALTSWARTHAQDPAAAAALPRSTRATAVRFALEELATRVPGN
+AVEVRVPPFGVAQAIPGPRHTRGTPPNVVEMDAVTWLSLATGLLGWADAVGTGAVRASGT
+RADLGAHLPLIRP
+>3_936
+MTTGSVPKRRVPVVEGHAALTAWARAHAEDPAAAAALPRSTRATAVRFALEELATRAPGN
+SVEVRVPPFGVAQCIPGPRHTRGTPPNVVETDPVTWLSLATGLTRWNDAVASGAVRASGV
+RADLAGHLPLVRP
+>4_1716
+MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRAMAVRFALEELATRVPGN
+SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTTWEDATAAGGVRASGV
+RADLGAHLPLVRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001498.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001498.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce9540f3734e0e35c3fe4ecd38abc53274a2a30a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001498.fa
@@ -0,0 +1,20 @@
+>0_1796
+MTSAPEPTPDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYSGIPL
+SFSETFGFASLLSMLGTSVLGLLVWLLLDRRSRSTARTVVLERTDDPAVADVRLDRVDAG
+APPARTTPTERTPEQ
+>1_1503
+MTSAPEPTPDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYSGIPL
+SFSETFGFAALLSMLGTGVLGLIVWLLLDRRSRSTARTVVLERTDDPAVADVRLDRVDAG
+TPPARTTSTERTPEQ
+>2_988
+MTTGPERSQHQHAYTVRRAPRLAAVLAVALALGLVIALVITTAVHGSPTPPADPYSGIPL
+SFSETFGFAALLSMLGTGVLGLVVWLLLDRRSRATTRTVVLERTDDPAAADIRLDRSAAD
+ALRSRTAPTERTPEQ
+>3_933
+MTSGPERSTPSAPQQQEYVLRRAPRLSAAVIVSALVGVVLALLGTAAVHAGPQPPADPYS
+GMPLSFASTFGYMVVAAVLACLVLGLLVWLLLDRRSRRTQRTVLLERTDDPAAADVALPR
+PEAVAPAARPAADPSDGRTPEQ
+>4_1717
+MTSAPEPTPDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYSGIPL
+SFSETFGFASLLSMLGTSVLGLLVWLLLDRRSRSTARTVVLERTDDPAVADVRLDRVDAG
+APPARTTPTERTPEQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001502.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001502.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4f41d13f8923efd1bbc63d3d772e316e73d13392
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001502.fa
@@ -0,0 +1,35 @@
+>0_1800
+MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLMEESRPLVITGAGVSTDS
+GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNEAHRILARWA
+AEGRIAGVLTQNVDGLHAEAGRAAGMPEDRLIELHGDLARVACLNCGATESRRDLDLRLE
+AANPGYLERVAIDPDAVNPDGDVSLDQHWVEEFTMVGCRVCGSVKLKPDVVYFGESVPPA
+RRAAAEAMADDGGTVLAVGTSLAVMSGYRFVLRAERAGHETGLINLGPTRADAKARWRWR
+APVADALAWLDARL
+>1_1507
+MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLMEESRPLVITGAGVSTDS
+GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNEAHRILARWA
+AEGRIAGILTQNVDGLHAEAGRAAGMPEDRLIELHGDLARVACLNCGATESRRDLDLRLE
+AANPGYLERVAIDPDAVNPDGDVSLDQHWVEEFTMVGCRVCGSVKLKPDVVYFGESVPAA
+RRAAAEAMADDGGTVLAVGTSLAVMSGYRFVLRAERAGHETGLINLGPTRADAKARWRWR
+APVADALAWLDARL
+>2_983
+MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLLEETRPLVITGAGVSTDS
+GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNAAHRILAGWA
+VRGLVSGILTQNVDGLHAQAAAEAGAPEDRLIELHGDLARVVCLHCGATESRRDLDVRLE
+AANLGYLERVSIDPEAVNPDGDVTLDRHWVDEFAMVGCLRCGSVELKPDVVYFGESVPVA
+RREAAEAMADDGGAVLAVGTSLAVMSGYRFVLRAERAGKDTGLINLGSTRADPKASWRWR
+APVADALAWLDSRL
+>3_927
+MTPVRHPSQDGHQAALRSIARVVGETAPLQDPETASRGLLRMLEAGRPLVITGAGVSTDS
+GIPDYRGPNGTLHRHRPMTYQEFRDDPAARHRYWARSFVGWRHMDEAAPNAAHHVLADWV
+RRDVVAGIVTQNVDGLHAQAFAAAGAAPSRLIALHGDLARVVCLQCGAMEDRTSLDARLA
+AANPGYLEAVTVDPDAVNPDGDVTLDQRWVDAFTMVGCRVCGSVQLKPDVVYFGENVPPA
+RRDAARALAEEADSVLAVGTSLAVMSGFRFVLDAERAGKEVGVITLGPTRADPKAQWRWR
+TRVAEALAWLDARL
+>4_1721
+MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLMEEFRPLVITGAGVSTDS
+GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNEAHRILARWA
+AEGRIAGILTQNVDGLHAEAGRAAGMPEDRLIELHGDLARVACLNCGATESRRDLDLRLE
+AANPGYLERVAIDPDAVNPDGDVSLDQHWVEEFTMVGCRVCGSVKLKPDVVYFGESVPAA
+RRAAAEAMADDGGTVLAVGTSLAVMSGYRFVLRAERAGHETGLINLGPTRADAKARWRWR
+APVADALAWLDARL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001505.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001505.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d232124e3652bd0e69f0ef760c6d05fc7ed4985
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001505.fa
@@ -0,0 +1,80 @@
+>0_1803
+MDAKFTTKSQEALSAAAMNASTAGNPQVEPAHLLKALMDQRESVAVAVLKAAGADPDAVS
+TAASSAIRRLPSTQGSTVAQPQFSRAALQVVQNARTQAEQRSDEFVSTEHLLLGVAADSG
+EAGEALRSNGASLEALAAALTLVRGDSRVTTQDPETTFQSLEKYGTDLTEIARSGKLDPV
+IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL
+DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK
+PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVFVGEPSVDDTIAILRGLKERYEAH
+HKVAIADSALVAAATLSHRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD
+RLTMEELALEGETDPASIERLDALRAEKADREEELTALTARWDAEKATLNQAGDLRAKVD
+ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSATEPMVSEEVTADD
+IAEVVSAWTGIPAGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN
+RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG
+YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI
+LTSNLGSQFLVDPTLDEAAKRESVMSVVRGAFKPEFLNRLDEIVQFDALTVAELTRIVDL
+QVESLQARLTDRRLTLEVSDAAKAWLAATGFDPAYGARPLRRLVQREIGDRLARGILAGE
+IADGDTVVVDRVEGENGLTVTRKG
+>1_1510
+MDAKFTTKSQEALSAAAMNASTAGNPQIEPAHLLKALMDQRESVAVAVLKAAGADPDAVS
+TAASSAIQRLPSTQGSTVAQAQLSRAALQVVQNARTQAEQRSDQFVSTEHLLLGVAADPG
+EAGEALRSNGASLEALAAALTQVRGDSRVTTQDPETTFQSLEKYGTDLTELARSGKLDPV
+IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL
+DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK
+PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVYVGEPSVDDTIAILRGLKERYEAH
+HKVAIADSALVAAAALSDRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD
+RLTMEELALEGETDPASVERLEALRAEKADREEELTALTARWDAEKATLNEAGDLRAKVD
+ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSSTEPMVSEEVTADD
+IAEVVSAWTGIPSGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN
+RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG
+YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI
+LTSNLGSQFLVDPTLDEAAKRESVMSVVRAAFKPEFLNRLDEIVLFDALTVDELTRIVDL
+QVESLQARLTDRRLTLEVSDAAKAWLAETGFDPAYGARPLRRLVQREIGDQLARGILAGE
+IADGDTVVVDRVEGENGLTVTRKG
+>2_977
+MDAKFTTKSQEALSAAAMNASTAGNPQIEPAHLLKALMDQRESVAVAVLKAAGADPDAVS
+TAASSAIRRLPSTQGSTVAQAQLSRAALQVVQNARTQAEQRSDQFVSTEHLLLGVAADPG
+EAGEALRSNGASLEALAAALTQVRGDSRVTTQDPENTFQSLEKYGTDLTEVARSGKLDPV
+IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL
+DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK
+PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVYVGEPSVDDTIAILRGLKERYEAH
+HKVAIADSALVAAATLSHRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD
+RLTMEELALEGETDPSSVERLEALRAEKADREEELTALTARWDAEKATLNEAGDLRAKVD
+ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSTTEPMVSEEVTADD
+IAEVVSAWTGIPAGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN
+RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG
+YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI
+LTSNLGSQFLVDPTLDEAAKRESVMSVVRAAFKPEFLNRLDEIVQFDALTVAELTRIVDL
+QVESLQARLTDRRLTLEVSDAAKAWLAETGFDPAYGARPLRRLVQREIGDRLARGILAGE
+IADGDTVVVDRAEGEEGLTVASA
+>3_925
+MNPSPQFTTKSQEALSAAAMNASTASNPAVEPAHLLKALMDQRDSVAVAVLKAAGADPDV
+VSVAASTAIHGLPKASGATVSEARLSPAAGAVVKAAQQQASAHGDEYVSTEHLLLGLAAD
+GGEAGRALTDAGASLAALQAAFTQVRGDERVTTPDPEATFQSLEKYGTDLTAVARSGKLD
+PVIGRDQEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLI
+SLDLGAMIAGAKYRGEFEERLKSVLEEIKKSDGQIVTFIDEIHTVVGAGASEGAMDAGNM
+LKPMLARGELRLIGATTLDEYRENIEKDPALERRFQQVYVGEPSVDDTIAILRGLKERYE
+AHHKVAIADSALVAAATLSDRYISGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDALRRQ
+VDRITMEELALDGESDPGSVERLAGLRAEKADKEEELRALTARWEAEKASLNEAGDLRAR
+VDELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAQEGQQGDVEAMVSENVTA
+DDIAEVISAWTGIPAGRMLASETEKLLSMEEHLGDRLIGQKDAVRAVSDAVRRARAGIAD
+PNRPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHAVSRLVGAPPGY
+VGYDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVI
+LILTSNLGSQFLVDQTMPEQARKDAVMDVVRAAFKPEFLNRLDEIVTFDALGVEDLARIV
+DLQVASLGERLQQRRLTLDVTDAAREWLALTGYDPAYGARPLRRLVQREIGDQLARALLS
+GAVQDGDTVVVDRAGEDTADGLTVAARRA
+>4_1724
+MDAKFTTKSQEALSAAAMNASTAGNPQVEPAHLLKALMDQRESVAVAVLKAAGADPDAVS
+TAASSAIRRLPSTQGSTVAQPQFSRAALQVVQNARTQAEQRSDEFVSTEHLLLGVAADSG
+EAGEALRSNGASLEALAAALTLVRGDSRVTTQDPETTFQSLEKYGTDLTEIARSGKLDPV
+IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL
+DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK
+PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVFVGEPSVDDTIAILRGLKERYEAH
+HKVAIADSALVAAATLSHRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD
+RLTMEELALEGETDPASIERLDALRAEKADREEELTALTARWDAEKATLNQAGDLRAKVD
+ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSATEPMVSEEVTADD
+IAEVVSAWTGIPAGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN
+RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG
+YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI
+LTSNLGSQFLVDPTLDEAAKRESVMSVVRGAFKPEFLNRLDEIVQFDALTVAELTRIVDL
+QVESLQARLTDRRLTLEVSDAAKAWLAATGFDPAYGARPLRRLVQREIGDRLARGILAGE
+IADGDTVVVDRVEGENGLTVTRKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001508.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001508.fa
new file mode 100644
index 0000000000000000000000000000000000000000..908a491beeb97f8973c44cb51247e1291f45fdf9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001508.fa
@@ -0,0 +1,30 @@
+>0_1806
+MTRIHSRLLGAVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDV
+PYPPFEFEENGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI
+TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV
+QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVESLPTGEQLGMAVGPQKAQL
+GSAVNRALQELRNDGTVAELQERWFGQAQEDYR
+>1_1513
+MTRIHSRLLGAVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDI
+PYPPFEFEEKGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI
+TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV
+QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVESLPTGEQLGMAVGPQKAQL
+GSAVNRALQELRNDGTVAELQERWFGQAQEDYR
+>2_974
+MGLTASAALLTGCAVLGGDSGVAGVVSDDDLSTTYNLVQPGVLTVCSDIPYPPFEFELDG
+ELTGYDIQLVHAIAEELELGVNVIDSSFEAIESGASLTGCDLNASSISITEQRQRAMAFT
+LPYLDDDLVLVAATDSGITDVESAKGRRVGVQAATTGDAYAKENGLNPIEFEDGGMQVQA
+LQAGTVDALLGNQSVILYSLKDDERFEVVENLPTGEQLGMAVAPQNAQLGSAVNRALQQL
+RNDGTVAELQERWFGLAQEDYR
+>3_913
+MPRTPSRALGAVGAGLSAALLSGCAVIGGDAGTTGPLAEDDLRATYRLHEPGVLTVCADV
+PYPPFEFEQDGQLTGYDIDLTRKLAETMDLQLKVVDTSFEAIESGASLTGCDLNASAISI
+TEPRQHVMAFTLPYLDDDLVLVARKDSGITDVASAQGKRVGVQTATTGEEYAQSQGLDTV
+QFEDGGMQVQALQAGTVDALLGNQSVLLYSLKDDPRFGVVESLPTGEQLGMGVAPDNALL
+GSAVNRALQTLRNDGTVAELQQKWFGTAQKDYQ
+>4_1727
+MTRIHSRLLGTVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDV
+PYPPFEFEENGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI
+TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV
+QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVELLPTGEQLGMAVGPQKAQL
+GSAVNRALQELRNDGTVAELQERWFGQAQEDYR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001510.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001510.fa
new file mode 100644
index 0000000000000000000000000000000000000000..70091c8271ed38670532da3d8596a4fdbba6aad5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001510.fa
@@ -0,0 +1,30 @@
+>0_1808
+MAQQNPITGSFGAVAAADAAGVHVAGLNKSFGANHVLRGIDLDVAPGEVVCLIGPSGSGK
+STLLRCVNLLEKPDSGVVTVGEFTVTDEDVDLDVLRRHVGMVFQQFNLFPHLSVLENCTV
+AQLKVLKRGKAEAVDIARRQLARVGLAELEDRYPDQLSGGQQQRVAIARALAMDPQLMLF
+DEPTSALDPETVGDVLAIMRQLARDGMTMLVVTHEMGFAREVADRVVFMDGGVVVEAGPA
+AAVISDPQQPRTQDFLRRVLHPTEIDL
+>1_1515
+MAQQNPITGSFGAVAAADAAGVHVAGLNKSFGANHVLRGIDLDVAPGEVVCLIGPSGSGK
+STLLRCVNLLEKPDSGVVTVGEFTVTDEDVDLDVLRRHVGMVFQQFNLFPHLSVLENCTV
+AQLKVLKRGKAEAVDVARRQLARVGLAELEDRYPDQLSGGQQQRVAIARALAMDPQLMLF
+DEPTSALDPETVGDVLAIMRQLARDGMTMLVVTHEMGFAREVADRVVFMDGGVVVEAGPA
+AAVISDPQQPRTQDFLRRVLHPTEIDL
+>2_972
+MAQQTPQPAASAVDAAGVHVADLNKSYGSNHVLRGIDLDVAPGEVVCLIGPSGSGKSTLL
+RCVNLLEKPDSGRITVGEFDVTDEDVDLDALRRHVGMVFQQFNLFPHLSVLENCTVAQVK
+VLKRSKAEAAEVARRQLARVGLAELEDRFPDQLSGGQQQRVAIARALAMDPQLMLFDEPT
+SALDPETVGEVLAIMRQLARDGMTMLVVTHEMGFAREVADRVVSMDAGVVVETGPAAALI
+ADPQQPRTQDFLRRVLHPTEIDL
+>3_911
+MTEQTASPRPSDAGTAAGVHIAGLHKSYGSNHVLRGIDLDVAPGEVVCLIGPSGSGKSTL
+LRCVNLLEVPDSGGVQVGEFTVTDPDVDLDRLRQHVGMVFQQFNLFPHLTVLENCTVAQV
+KVLKRSAAEAADTARRQLARVGLGELEGRYPDQLSGGQQQRVAIARALSMDPRLMLFDEP
+TSALDPETVGDVLAIMRKLAREGMTMLVVTHEMGFAREVADRVVFMDGGVVVEQGPASAV
+ITDPQEPRTQDFLRRVLNPAGVDI
+>4_1729
+MAQQNPITGSFGAVAAADAAGVHVAGLNKSFGANHVLRGIDLDVAPGEVVCLIGPSGSGK
+STLLRCVNLLEKPDSGVVTVGEFTVTDEDVDLDVLRRHVGMVFQQFNLFPHLSVLENCTV
+AQLKVLKRGKAEAVDVARRQLARVGLAELEDRYPDQLSGGQQQRVAIARALAMDPQLMLF
+DEPTSALDPETVGDVLGIMRQLARDGMTMLVVTHEMGFAREVADRVVFMDGGVVVEAGPA
+AAVISDPQQPRTQDFLRRVLHPTEIDL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001513.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001513.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b048a9897ed710855b38391760db4e40083da86c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001513.fa
@@ -0,0 +1,47 @@
+>0_1811
+MHPVLPSPRRGRAALGLAAVALVALSACARTEPQPEPAPATTAASALPSMDMAPFTVEVP
+SHDLERVPEASVAVLEGEDPDHHGAWLQVSGAPAWTDAMAGAVRDQIDQYRRDTDPSADP
+RLEIQPQLAVVAEDIAAARLLATERRGTDSVSTSHVIWYSAREDRVLETADLFTPDGWDA
+FRAEVRQRMANDPDVIGSRLDSAVDAPEQVENRRVWDAVVFLPDGSLMLEADQASMAPAA
+AGVLTVRIPRDTATAWLSDLGHVAADAASAPADLRLPDRSTPTPEEQQPEPAPEPEPETS
+SWTEEATGAPVPPPSAPADTAAPTPSVTTPVPSSTAPSSSAPAPTRSATPSSPSSPPTSS
+SPSGTGSGSPTPSTPDPTPTSATPTPTSPTPTSPSPSGPSTSASGPSTSAPATDPAPDPT
+ESAPEPTATTASASASPTSGDRSSSTP
+>1_1518
+MHPVLPSPRRGRAALGLAAVALVTLSACARTEPQPEPAPATTAASALPSMDMAPFTVEVP
+SHDLERVPEASVAVLEGEDPDHHGAWLQVPGAPAWTEAMAEAVRAQIDQYRRDTDPSADP
+RLEIQPQLAVVAEDIAAARLLATERRGTDSVSTSHVIWYSAREDRVLETADLFTPDGWDA
+FRAEVRQRMANDPDVIGSRLDSAVDAPEQVENRRVWDAVVFLPDGSLMLEADQASMAPAA
+AGVLTVRIPRDTATAWLSDLGHVAADAASAPADLRLPDRSTPTPEEQQPEPAPEPEPETS
+SWTEEATGAPVPPPSAPADTAAPTPSVTTPVPSSTAPSSSAPAPTRSATPSSPSSPPTSS
+SPSGTGSGSPTPSTPDPTPTSATPTPTSPTPTSPSPSGPSTSASGPSTSAPATDPAPDPT
+ESAPEPTATTASASASPTSGDRSSSTP
+>2_969
+MSTPASPSARRARAALGLAAVALVALSACARTEPAPEPAPSTASATALPPMDMAPFTVDV
+PSLDLDRVPGASIAVLEGTDPDHRGAWLQVPEAPAWTEAMAGSVRGQIDAYRRDTDRGAD
+PRLEVQPRLAVVGEDIAAARLLSTETRGTDSVSSSHVVWYSAREDRVLETRDLFTDEGWD
+AFRTEVRQRMKNDPDVVRERLASAVDSPELVENRRIWDAVVLLPDGSVMLEADQASMAPA
+AAGVLTVRIPRDTAAPWLSDLGDAATDAARTPADLRLPDRSTPSPSTSAPEPAESSWTPE
+ATGAPVPPRVPVPDPTTTAPSVDPGGDRDPSTSSAPPSSRPGTTAPSPVAGPQHPGPHHP
+GPHHLRADRPGARPLDDDGAPAPGADQPDAHADADPVDSHADADAHDAHPDPDRDGDHGP
+ADRPGAGARAGADDAAAERHERLRPRDPGRAGLSRPTPGCPGRPRTGACPARRRPAPPPH
+GLT
+>3_908
+MHRLSPASTVRLRAGAGLLALGMLGLTACGSGDDAASSSPAPSSAAATQELPSMDMAPFT
+LDVPSLDLDKVPGASLAVIQGQDPEYHAAWLQVPGAPAWTQAMDESVRGLVAQYQRDTDR
+TASPVLDVQPRLAVAGRDVAAARLLSTERRGDRSVSAVHVVWYAAREDRVLSTEDLFTAD
+GWAAFRREVGARMAGDPAVVQDRLRSAVDAPAQVENVRVWDALTFLPDGSALLEVDQAAM
+SPADAGVLTARIPADTVRPWLSALGVSAQDAARSPEALVLPERPSAAPASEGGDAAVPAP
+GQPSSDGATTSAPGQGSVPPAPGLPGAPAPGTPGTASQGGGSPGTAPQDTGSQHTGSQGT
+GSQGTGASAPGASPSATRGDAGPAPTSSSAAPAPTGTGAPAPAPLPMPAPTTSSATPSGP
+APAPTGGTPAPSPTTVAPTEPSPSADPTTSEPAPSSDPAPAPTDTASPAPTASSPSTPAD
+VTGTATASGPLPATGGSTDPVTPTPAA
+>4_1732
+MHPVLPSPRRGRAALGLAAVALVTLSACARTEPQPEPAPATTAASALPSMDMAPFTVEVP
+SHDLERVPEASVAVLEGEDPDHHGAWLQVPGAPAWTEAMAEAVRAQIDQYRRDTDPSADP
+RLEIQPQLAVVAEDIAAARLLATERRGTDSVSTSHVIWYSAREDRVLETADLFTPDGWDA
+FRAEVRQRMANDPDVIGSRLDSAVDAPEQVENRRVWDAVVFLPDGSLMLEADQASMAPAA
+AGVLTVRIPRDTAAPWLSDLGHVAADAASAPADLRLPDRSTPTLEEQQPEPETSSRTQEA
+TDAPVPPPSAPADTAAPTPSATTPVPSSTVPSSTAPSSSVPTSTGSATPSSPTSPASSSS
+PSGTGSGSPTPSTPDPSPTSATPTPTSPSPSGPSTSAPATAPAPDPTESAPEPTATTASA
+PAPPTSGDRSSGTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001515.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001515.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d1fe43ed9ba856408b274a0772d49ccb96efe98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001515.fa
@@ -0,0 +1,35 @@
+>0_1813
+MQERLRADMARRDGLGRQARSALDGIVHALKPEGMDPHLPARHLLDYVLEGPDGPRAVVA
+AGDPATATHLTWLVSGMGIRPQTALWGTAREAAHLAAAQRAAGAPRPVVIGWLGYPAPTP
+WRVVLDGPGRRGGAMLAADVRAWWEFLRHGPGEDDDVAPALRARGTAVHGAVEAHSYGSL
+VAAHALRLLADRGLQPDDAEAPWPAERPVEALVVSGTVGLPAALAARSAHLGLRSGRTFR
+ALAPGDLLARVGRAVGRRRDWTDAAVLPVAPRPGLAGAAVRGHRTARWSPTAPEDAPRGY
+RDAGSVTLAATARVTAGLPLSPVPDGADPAGPVAPA
+>1_1520
+MQERLRADMARRDGLGRQARSALDGIVHALKPEGMDPHLPARHLLDYVLEGPDGPRAVVA
+AGDPATATHLTWLVSGMGIRPQTAMWGTAREAAHLAAAQRAAGAPRPVVIGWLGYPAPTP
+WRVVLDGPGRRGGAMLAADVWAWWEFLRHGPGEDDDATLALRARGTAVHGAVEAHSYGSL
+VAAHALRLLADRGLQPDDAEAPWPAERPVEALVVSGAVGLPAALATRAAHLGLRSGRTFR
+ALAPGDLLARVGRAVGRRRDWTDAAALPVAPRPGLAGAAVRGHHTARWSPTASEDAPRGY
+RDAGSVTLAATARVTAGLPLSPAPDGADPAGPVAPV
+>2_967
+MARRDGLGRQARSALDGIVHALKPEGMDPHLPARHLLDYVLDGPDGPRAVVAAGDPATAT
+HLTWLVSGMGIRPHTAMWGTAREAAQLAAAQRAAGAPRPAVLAWLGYAAPTPWRILLDGP
+GRRGGERLADDVAAWWDFARTGAGETEDRAGEPDDDRPSLRARGTALHGAVEAHSYGSLV
+AAHALRLLAERGLQPDDVEVLDDTDGGADADAGAQDTARPAERPVEALVVSGAVGLPAAF
+AARAGRLGLPPGRVFRAQAPGDVLARVGRALGRRRDWTDAVLLPVTPRPGLEGGAVHGHR
+TARWSPAAGTDAPRGYRDPGTVTLAATARVTAGLPLPPEPA
+>3_905
+MDLPEQARAAAARLDADRARARDGRLSARQLAALDGAEHALRRDSMDAAIPERVLVDWDL
+DAPDGPVAAVAVGELERPTHLTWQVSGMGIAASTAAWGSAREAGQLLLAQRAAGAPRPCV
+VAWLGYPAPPWWRTLDDGLARRGGARLAEAVRETRPGPSHGAGTAVHTAIEAHSYGTLVA
+THALEGLAAGDPPLTVDALALSGALGLPRRLAGRLEALGLAAGRVFEARAPGDRLAWLGR
+TLAGRAPWPEAVALPVAADPAAGLAGVRGHNTARWRPEDGDDGAPRGYRDPGSVTLAALA
+RVTAGLPVAGGGPRSGQRRA
+>4_1734
+MAARSRVRERLRADMARRDGLGRRARSALDGIVHALKPEGMDPHLPARHLLDYVLDGPDG
+PRAVVAAGDPATATHLTWLVSGMGIRPQTAMWGTAREAAHLAAAQRAAGAPRPVVIAWLG
+YPAPTPWRVVLDGPGRRGGAMLAADVRAWWEFMRHGPGEDDAAAPALRARGTAVHGAMEA
+HSYGSLVAAHALRLLADRGLQPDDAEAPWPAERPVEALVVSGAVGLPAALAARAAHLGLR
+SGRVFRALAPGDLLARVGRAVGRRRDWTDAAVLPVAPRPGLAGAGVRGHHTARWSPTAPG
+DAPRGYRDAGSVTLAATARVTAGLPLPPVPDGADPAGPVAPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001518.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001518.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0314c2fb76bae484b4c48434c6b2d801d75408e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001518.fa
@@ -0,0 +1,25 @@
+>0_1816
+MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETGEPRVSAESAAEQAEDGDALAQAER
+ILDEAGAQAGTEAPQPEASDREAELEADLRRLQAEYVNYKRRVDRDRDLARDAGVLKAVT
+ALLPVLDDIDAARAAGDLTDGPFAAIATKLDTALAGLGLERHDQEALAGVEFDPAVHEAV
+MRQPHAEVPADHVVQVFRNGYVRDGRVLRAAQVMVSAGDE
+>1_1523
+MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETGEPRVSAESAAEQAEDGDALAQAER
+ILDEAGAEAGTQAPQPAASDREAELETDLRRLQAEFVNYKRRVDRDRDLARDAGVLKAVT
+ALLPVLDDIDAARAAGDLTDGPFAAIATKLDTVLAGLGLERHDQAALAGVEFDPALHEAV
+MRQPHAEVPADHVVQVFRNGYVRDGRVLRAAQVMVSAGDE
+>2_963
+MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETGEPRVSAESAAEQAEDGDALTQAER
+ILDEAGAQAGTEAPQPAASDREAELETDLRRLQAEYVNYKRRVDRDRALAQDLGVLKAVT
+ALLPVLDDLDAARAAGDLTDGPFAAIATKLDTALAGLGLERHDQEALAGVEFDPSVHEAV
+MRQPHAEVPADHVVQVFRNGYVRDGRVLRAAQVMVSAGDE
+>3_902
+MSENQNETPSPEEPVIRDRRRIDPETGQARTPGAGEDTVPAQEQGQAPQDSGDALSQAEQ
+ILDEAGAAAEAEALPAAGSDREAELLEDLRRLQAEYVNYKRRVDRDRDVAKEQGVLKAVT
+ALLPVLDDLDAARAAGDLEDGPFAAIAAKLMTALEGLGLEREDQEALAGVEFDPVRHEAV
+MRQPHAEVPADHVVQVFRNGYARDGRVLRAAQVMVSAGQD
+>4_1737
+MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETDEPRVSAESAAEQAEDGDALAQAER
+ILDEAGAQAGTEAPQPEASDREAELEADLRRLQAEFVNYKRRVDRDRDLARDAGVVKAVT
+ALLPVLDDIDAARAAGDLTDGPFAAIATKLDTALAGLGLERHDQEALAGVEFDPAVHEAV
+MRQPHAEVPADHVVQVFRNGYLRDGRVLRAAQVMVSAGDE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001521.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001521.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d87cd55195dbfd8ef1b0a0d5114e6a5a45eceb4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001521.fa
@@ -0,0 +1,99 @@
+>0_1822
+MATLLYRLGLGAARRPLLVILAWVLALALAVGGFLAFGGTLSSTVTIPGTPTAQVTDRLK
+EEFPEASRGRGQVVFTTEDGSPLTDAQREQITALLDDVAEQPAVEGVVNPFEAQAQQDDA
+RTRLDEGRTELADGEQRLADGRQEIEDGRAELERRTAEADAAEQRLAEAAAQLEEGQAKL
+DAARADLEERGLDALPAEALAPLREAEQQVAEGQEQLDAGRAELEEQAERLEAGQAKLDA
+QRQELEAAQAELDARWAELEAGQAELDARAEQLAAGRAELEQARDAALAEAEAAGIPAEQ
+VTEQFADQEAQLAAAEAQLAAGQDQADAARAQLEAAQAEADAGAEQLAAAQAEADDGAAR
+LAAGRQQLQESEAELEAGREQVAAGRQQALDAAEAELDAQQQKIDEGRAEYERGVAELED
+GRAQLAAGAERLDQAEADLADGRAELEDGRVEAERGERTLALAEDFRTVSEDGSTAVGIV
+TFTTPTLDVTAEDKEAVTGALTGADIDGVAVHPSQELNATAPSLLGPGEVVGLVVAAIVL
+VVMLGTLVGAGLPLVNALVGVGVGAAGALAFSSAVEMISVTPVLGVMLGLAVGIDYALFI
+VNRHRQELRRGTGLHESIALANGTSGNAVVFAGITVIVALVGLNVTGIPFLGLMGTVGAV
+CVAVAVLVAVTLTPALLSLAGMRILSKKERARLADEGPASVAEGSAAVRRAGRRSTMSTP
+AAIASALAAVALLVLVALPVGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVV
+TVDLPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVST
+EELVRDLRATEPAGEASNLGVAGMTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRS
+ILVPLIATGGFVLSMFAAMGGVVAIYQWGWLGSVFGVHNPGPVLSFLPTIMIGVLFGLAM
+DYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPM
+GFGLAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERAHAPAQ
+PSVPAPDGGAHRA
+>1_1529
+MATLLYRLGLGAARRPLLVILAWVLALALAVGGFLAFGGTLSSTVTIPGTPTAQVTDRLK
+EEFPEASRGRGQVVFTTEDGSPLTDAQREQITALLDDVAEQPAVEGVVNPFEAQAQQDDA
+RTRLDEGRTELADGEQRLADGRQEIEDGRAELERRTAEADAAEQRLAEAAAQLEEGQAKL
+DAARADLEERGLDALPAEALAPLREAEQQVAEGQEQLDAGRAELEEQAERLEAGQAKLDA
+QRQELEAAQAELDARWAELEAGQAELDARAEQLAAGRAELEQARDAALAEAEAAGIPAEQ
+VTEQFADQEAQLAAAEAQLAAGQDQADAARAQLEAAQAEADAGAEQLAAAQAEADDGAAR
+LAAGRQQLQESEAELEAGREQVAAGRQQALDAAEAELDAQQQKIDEGRAEYERGVAELED
+GRAQLAAGAERLDQAEADLADGRAELEDGRVEAERGERTLALAEDFRTVSEDGSTAVGIV
+TFTTPTLDVTAEDKEAVTGALTGADIDGVAVHPSQELNATVSSLLGPGEVVGLVVAAIVL
+VVMLGTLVGAGLPLVNALVGVGVGAAGALAFSSAVEMISVTPVLGVMLGLAVGIDYALFI
+VNRHRHELRRGTSLHESIALATGTSGNAVVFAGITVIVALVGLNVTGIPFLGLMGTVGAV
+CVAVAVLVAVTLTPALLSLAGMRILSKKERARLADEGPASVAEGSAAVRRAGRRSTMSTP
+AAIASALAAVALLVLVALPVGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVV
+TVDLPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVST
+EELVRELRATEPAGEASNLGVAGMTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRS
+ILVPLIATGGFVLSMFAAMGGVVAIYQWGWLGSVFGVHNPGPVLSFLPTIMIGVLFGLAM
+DYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPM
+GFGLAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERGHAPAA
+EAASAPAPEAGRTPAVDGGAHRA
+>2_956
+MAKLLYRLGLGAARRPLTVILAWVLALALAVGGFLAFGGTLSTNVTIPGTPTAQVTDRLQ
+DEFPEASRGMGQVVFTTEDGQPFTDAQRDAVAALLDEVAGQDAVDAVVDPFEVQAQQDDA
+RTALADGRQEIADGEQALVDGREQVDAGRAEIEEGRAQADAGEQELADAAAQLEDGQVQL
+DAARADIEARGLDALPAEALAPLREAEQQIADGQAELDAGRAEIEEQAARLAAGQAEIDA
+NREQLEAGQAELDARWGELDAAQAQLDAQREELEAGRAQLEQALAAALEQAEAAGIPAEQ
+VTAQFAEQQAQLEAGQAQLDAAQEQADAGREQLVAAQAEADAGAEQLAEAQAQADAGAEQ
+LAAGREQLEAAEAELESGREQLAAGRQQALDAAAAELDAQQARIDEGRAQHEQGVADLEA
+GRAELAAGAERLDQAEADLATGRTELEDGRVAAERGERSLALVGGYRSVSEDGSTAVGIV
+SFSQPSLDVTAEEKEAVTGALTGADIDGVAVHPSQELNATVPSILGPGEVVGLIVAAIVL
+VVMLGTLVGAGLPLVNALVGVGVGAAGALAFSSVVEMISVTPVLGVMLGLAVGIDYALFI
+VNRHRQELKRGTALHEAIALANGTSGNAVVFAGITVIIALVALNVTGIGFLGLMGTVGAV
+CVAVAVLVAVTLTPALLSLAGTRILSRKERARLADEGPASAAEGSAAVRRAGRRSTMSTP
+AAIASALAAIALLVLVALPFGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVV
+TVDLPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVST
+EELVRELRATEPAGEASNLGVAGMTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRS
+ILVPLIATGGFVLSVFAAMGGVVAIYQWGWLGSVFGVHNPGPVLSFLPTIMIGVLFGLAM
+DYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPI
+GFGLAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERGHAPAA
+EAASAPAPEAGRTPAVDGGAHRA
+>3_895
+MATLLHRLGLASARRPWAAILAWLIALALAVGAFLAFSGTLTTAVTIPGTPTAQVTDRLK
+EQFPDAAKGTGQVVFATEDGSAFTEAQRRAVSDALRGVEGQDAVDSVVDPFDVARQQDEA
+RTALEDGRRQIAEGEQKIAENEKALEDGRAQLAEAKDKAEAGQKELDAAAAQLDAGQEKL
+DAARADLEARGLDALPAEATAPLTEAQQKLDAGQAEYDAGVAALEEQRPALEAAEAEIAK
+QEAALEQAQARFEAGRAQAIAQAEAAGATPEQAAAAVDARLAPEREKLDAGAAQLEEARA
+RTEAGRAEFDAGEEKLAAAAAELEQGRAQLAAGREKALTAARAELDAQQQKIDAGRAEHE
+QGVRELEAGRAEIAQNEAKLADGPAQLEQARKDLAAGREKADRGQRMLTLTDGYRVVSED
+GSAALGTVAFDRPSLDVTTEQKTAVIDALADADIPGVRAIPTQALNATMPSLIGPGEVVG
+LAVAALVLVLMLGTLVGAGLPLVNALIGVGVGAAGALAFSGVVEMMSVTPVLGIMLGLAV
+GIDYALFIVNRHRLELKRGTPLHASIALANGTSGNAVVFAGITVVIALVALNVTGIPFLG
+LMGTVGAVCVAVAVLVAVTLTPALLSLAGMRILSRKERARRAAEAAPVADDAAAPSGSHA
+AAPVSRSAARAVRDARRRRRMSTPAAVATVLASAAALIVVAIPFGSMRLGLPDGASEPVG
+SDSQVSYELIADEFGEGYNGPLVVTVDLPSGLDETTAEDAQVQVGEQLKGLEHVAAVVPA
+GFNQDRTTAMFQVLPEEGPNAISTGDLVHTLRDTEPAGEASNLGVAGVTSGFIDVSEKLS
+AALPLYLGVVVGLSLLIMILVFRSILVPLIATGGFVLSVFAAMGGVVAIYQWGWLGGLFN
+VHAPGPVLSFLPTIMIGVLFGLAMDYQLFIASGMREAYAHGQPARDAVMTGLRAGRAVVT
+AAAIIMISVLGGFVFSHDAMIRPIGFGLAFGVLLDAFVVRLLLMPALMHLLGDAAWWLPK
+WLDRILPDVDVEGAGLERHGAAGEAADAAPVGADRA
+>4_1743
+MATLLYRLGLGAARRPLLVILAWVLALALAVGGFLAFGGTLSSTVTIPGTPTAQVTDRLK
+EEFPEASRGRGQVVFTTEDGSPLTDAQREQITALLDDVAEQPAVEGVVDPFEAQAQRDDA
+RTRLDEGRAELADGEQRLADGRQEIEDGRAELERRTAEADAGEQRLAEAAAQLDEGQAAL
+DAARADLEERGLEALPADALAPLREAEQKVADGQEQLDAGRAELEEQAERLEAGQAEIDA
+QRQELEAGQAELGDRWTELEAGQAELDAQAEQLAAGRAELEQARDAALAEAEAAGIPAEQ
+VAAQFADQEAQLAAGEAQLAAGQDQADAARAQLEAAQAEADAGAEQLAAAQAEADDGAAR
+LAAGRQQLQESEAELEAGREQVAAGRQQALDAAEAELDAQQQKIDEGRAEYERGVAELED
+GRAQLAAGAERLDQAEADLADGRAELDDGRVEAERGERTLALAEDFRTVSEDGSTAVGIV
+TFTTPTLDVTAEDKEAVTGALTGADIDGVAVHPSQELNATAPSLLGPGEVVGLVVAAIVL
+VVMLGTLVGAGLPLVNALVGVGVGAAGALAFSSAVEMISVTPVLGVMLGLAVGIDYALFI
+VNRHRQELRRGTGLHESIALANGTSGNAVVFAGITVIVALVGLNVTGIPFLGLMGTVGAV
+CVAVAVLVAVTLTPALLSLAGMRILSKKERARLADEGPASVAEGSAAVRRAGRRSTMSTP
+AAIASALAAVALLVLVALPVGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVV
+TVDLPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVST
+EELVRDLRATEPAGEASNLGVAGMTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRS
+ILVPLIATGGFVLSMFAAMGGVVAIYQWGWLGSVFGVHNPGPVLSFLPTIMIGVLFGLAM
+DYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPM
+GFGLAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERAHAPAQ
+PSVPAPDGGAHRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001527.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001527.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a40442f1e125778a252e3b92ac3edca80493f67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001527.fa
@@ -0,0 +1,55 @@
+>0_1828
+MSIGTLPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWD
+TGVAAVHLGGWPAPLGISLVVDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIF
+HPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTMGGTAQRIRAGVTYVVVSVLS
+SVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP
+DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA
+QTDIKRILSFILVSHIGYMIFGLGLATEAGLAATVYYVAHHITVQTALFLVTGLIENRAG
+TANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGKVGLLRGGVEQATPLAYTLVG
+VSLLVSLLTLLVVVRVWTRAFWRRVEDVEHPPAQLVAAYERAVARGERPRPLEPGLVLPT
+TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHD
+ARK
+>1_1535
+MSIGSVPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWD
+TGVAAVHLGGWPAPLGISLVVDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIF
+HPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTMGGTAQRIRAGITYVVVSVLS
+SVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP
+DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA
+QTDIKRILSFILVSHIGYMIFGLGLATEAGLAATVYYVAHHITVQTTLFLVTGLIENRAG
+TANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGKVGLLRGGVEQATPLAYTLVG
+VSLLVSLLTLLVVVRVWTRAFWRRVEDLEHPPAQLVAAYERAVARGERPRPLEPGLVLPT
+TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHD
+ARK
+>2_950
+MSIGSVPMTDLAPLAVMMPVLGAAVTFMLVRRPRAQVVVTVAALVLTLLLNCLLLAAVWE
+GGVASVHVGGWPAPLGITLVVDRLSALMLVVSALITLAVLLYASAQGMVNRDEGGPVSIF
+HPTFLILVAGVFNAFLAGDLFNLYVGFEILLTASYVLLTMGGTAQRIRAGITYVVVSVIS
+SVVFLIAIAMVYAATGTVNMADLAVKLGELPSDVQMVLHVLLLVGFGIKAAVFPLSFWLP
+DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA
+QTDIKRILSFILVSHIGYMIFGLGLATQMGLAATVFYVGHHITVQTALFLVTGLIENRAG
+TANIDRLGSLAKVSPFISVLFLIPALNLGGIPPFSGFLGKVGLLRGGVEQGTGLSYTLVG
+VSLLASLLTLLVVVRVWTRAFWRKVEDVEHPPAQLVAAYERTIDRGLRPRRLEPGLVLPT
+AALVVMTLAFTVLAGPLFDLADAAATDMLDRTPYIASVLDEAAAERAAETLSHDPTEVHD
+ARH
+>3_889
+MLGSTPLTDLAPLAVMLPVLGAAITFALVGRARAQVVVTVSALTLTLVLDCLLLADVWTG
+GVAVVELAAWPAPVGITMVVDRLSALLLVVSSLITLAVLLYASAQGLINKDEGGPVSIFH
+PTFLVLVAGVSNAFLAGDLFNLYVGFEILLTASYVLLTLGGTEARIRAGITYVVVSVISS
+VLFLIAIAMIYAATGTVNMADLAVKLGELPHDLQLVLHVMLLAGFGIKAAVFPLSFWLPD
+SYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPAEHVNGLLMGVAALTMLVGILGALAQ
+SGLKRILSFILVSHIGYMVFGLALATQVGLAATVYYVGHHITVQTALFLVTGLIEQRAGT
+ASIDRLGSLAKVSPLLGVLFLVPALNLGGIPPFSGFLGKVGLIRGGVEDGGVLAWVLVGV
+SLLVSLLTLLVLVRAYTRAFWRKVEDVEHPTPQLVAAYERVTRRGLRPKPLSRGLVLPTA
+GLVAMTLAFTVFAGPLYDLADRAAVDMLERSPYISAVLGPEAADRAAVTLSHDPSEVHDA
+GR
+>4_1749
+MSIGTLPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWD
+TGVAAVHLGGWPAPLGISLVVDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIF
+HPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTMGGTAQRIRAGVTYVVVSVLS
+SVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP
+DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA
+QTDIKRILSFILVSHIGYMIFGLGLATEAGLAATVYYVAHHITVQTALFLVTGLIENRAG
+TANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGKVGLLRGGVEQATPLAYTLVG
+VSLLVSLLTLLVVVRVWTRAFWRRVEDVEHPPAQLVAAYERAVARGERPRPLEPGLVLPT
+TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHD
+ARK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001528.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001528.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de6ce02f58a26a900ff4dd27b8089277522d808f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001528.fa
@@ -0,0 +1,24 @@
+>0_1829
+MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIVLINNGAIMLLFLSSGGTGLAPLFV
+RGRDPHEYADTLPQALILTAIVIGFAVIAFLTAMIYRSWLLVREDEVEVDAEDVKIARMP
+AWDAEDDAELVEESSEFLDDAADPNAHYEHATESRPHVRHASPTPPAHPGPASAVRAHRA
+DGGPRP
+>1_1536
+MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIMLINNGAIMLLFLASGGVGLAPLFV
+RGRDPHEYADTLPQALILTAIVIGFAVVAFLTAMIYRSWLLVREDEVEVDAEDVKIARMP
+AWDAEDDAELVEESSEFLDDAADPNAHYEHATEARPQVQHATPAPQAPTGSGAASRGRRP
+EGGERA
+>2_949
+MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIMLINNGAIMLLFLASGGVGLAPLFV
+RGRDPHEYADTLPQALILTAIVIGFAVTAFLTAMIYRSWLISREDEVEVDAEDVKIASQG
+AWDAEDDSELVEEHSEFMDASTDPNAHYEHTTEARPQVQHVIPAPPTAAGSREAARGRRP
+EGGERA
+>3_888
+MTPTVDLALLAVMGVLFATGIYLLLERSLTRILVGVMLINNAAVVLLFLTSGGAGLAPLY
+DADTAPEDYADMLPQALILTAIVIGFATTAFLTAMIYRSWQLRREDDVATDVEDVKIAAQ
+SGWDAEDDSVLTEEDSEFMDDASDPNAEYEFATAAAPRARAVRPGRATVQGGGGRP
+>4_1750
+MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIVLINNGAIMLLFLSSGGTGLAPLFV
+RGRDPHEYADTLPQALILTAIVIGFAVVAFLTAMIYRSWLLVREDEVEVDAEDVKIARMP
+AWDAEDDAELVEESSEFLDDAADPNAHYEHATEARPQVQHATPAPQAPTGSGAASRGRRP
+EGGERA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001531.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001531.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6fe3675d5c3586050304a0719fe3cf8d1940d514
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001531.fa
@@ -0,0 +1,25 @@
+>0_1832
+MLLSDRDIRAELDSGRVGLDPLDPAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQKQDEL
+TRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGFIDP
+GFSGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSSAQSPYGTGANQNRYQGQRGPTAS
+RAHRDFHLTRIER
+>1_1539
+MLLSDRDIRAELDSGRVGLDPLDPAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQEQDEL
+TRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGFIDP
+GFSGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSAAQSPYGTGANQNRYQGQRGPTAS
+RAHRDFHLTRIE
+>2_946
+MLLSDQDIRAELASGRVGLDPLDEAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQEQDEL
+TRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGFIDP
+GFTGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSPAASPYGTGANQNRYQGQRGPTAS
+RAHLDFHLTRIDR
+>3_885
+MASVLLSDRDIRAELSSGRIGLDPLELSMVQPASVDVRLDRFFRLFDNHRYAHIDPAQPQ
+EELTRLVEVEPDQPFVLHPGEFVLGATYEQITLPDDVAARLEGKSSLGRLGLLTHSTAGF
+VDPGFTGHVTLELSNVATLPITLWPGMKIGQLCFFRMSSPAESPYGSGGNLNRYQGQRGP
+TASRSHQDFHLTRIPR
+>4_1753
+MLLSDRDIRAELDSGRVGLDPLDPAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQEQDEL
+TRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGFIDP
+GFSGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSSAQSPYGTGANQNRYQGQRGPTAS
+RAHRDFHLTRIER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001533.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001533.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6cc355c7365d5dd7d37f0579fc761e4a34e8a808
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001533.fa
@@ -0,0 +1,20 @@
+>0_1839
+MTTLIVTSSAHGSTREIAERVAEVLRTSQAVPTVVEDVEGAAAWLATADAVIVAAPVYTG
+SFAADARAFLDTRRAELTDLPLVILASGGAPELARPVREKLESYGPREVAYFRGALFEER
+LGRLEKLKLKLSRNEHYGDFRDWDAIEAWAKTLPGAGVR
+>1_1546
+MTTLIVTSSAHGSTREIAERVAEVLRTSQAVPTVVEDVEGAAAWLATADAVIVAAPVYTG
+SLAADARAFLDTRRAELADLPLVILASGGAPELAPPVREKLESYGPREVAYFRGALVEER
+LGRLEKLKLKLSRNEHYGDFRDWDAIEAWAKTLSGAGVR
+>2_939
+MTTLIVTSSAHGSTREIAERVAEVLRTSQSVETVVEDVAGAAAWLATADAVIVAAPVYEG
+SLAAEARHFLDSRRAELADKPLLFLASGGGYELDPKVREKLESYGPREIAFFRGALVEER
+LGWLEKLKLKVSRNENYGDYRDWDAIEAWAKSLSGHGVR
+>3_880
+MTALIVTASRHGSTREIAERVAEVLRTTAQTDTVVEDVAGAAAWLDTADAVVVAAPVYGD
+KLEKSAKAFLDSRRAELSQKSLVILYSGASPVPNRALADQLGTYGARDVKYLRGALVEER
+LGALEKLQIKLVKGRYGDFRDWNAVEHWAKGLSAHGVN
+>4_1760
+MTTLIVTSSAHGSTREIAERVAEVLRTSQAVPTVVEDVKGAAAWLATADAVIVAAPVYTG
+SLAADARAFLDTRRAELADLPLVILASGGAPELARPVREKLESYGPREVAYFRGALVEER
+LGRLEKLKLKLSRNEHYGDFRDWDAIEAWAKTLSGAGVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001534.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001534.fa
new file mode 100644
index 0000000000000000000000000000000000000000..003a4ecd0ca543867ca431084619f2d0202a3deb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001534.fa
@@ -0,0 +1,65 @@
+>0_1840
+MMVGMTAPQTPNPVPSADAPAAVPRAATRVRASELVGRGWLNTGGEQVTLEDLRGKVVLL
+DFWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYAIEHPV
+LDDPELTTWQAYSARAWPTLVVVDPEGYIAAHLSGEGHVAGLYGLVRELVAEHEAKGTLH
+RGSGPYVPPAPVARDLSFPGKAVSLGGRGSRPGSFLVSDTGHHRLLEVAEDLTTVLRAFG
+GGDPATADAGQAELAFPTPGEKGHADGGPDEALFNEPQGLALLPEDVAERVGYDVVVADS
+VNHRLRGLRLSDGHVSTLAGNGVQKLIDSERAKEAAAVDDEGDIAVDLADLPGEPTAISL
+SSPWDVVWHPALGRVVIAMAGTHQLFDFDPVTGALAVHAGTALEGLLDGDAGRAWFAQPS
+GLSVGADGALWVADSETSAVRWVRTGEDGRREVGTAVGAGLFDFGHVDGEADRARLQHPL
+GVTALPDGSVLIADTYNGAIRRYAPAGEDAAGRAVPATVTTVARGLLEPSDVLVEHDADG
+NDTAIVVVESNAHRLTRLAVPEEFLTVDEGARQTQRPRTPVVAGDLDLTIGFAAPTGQKL
+DDRWGDPTQLKISSSPEELLLEGAGTSTGLHRTLRLNPEVEEGVLHITARAAACDGEKGQ
+PIPDHAACHLYQQDWGIPVTVHTPDRAPEGAETRLDLDLRGIH
+>1_1547
+MMVDMTAPQTPNPAPTADAPAAVPRAATRVRASELVGRGWLNTGGEQVSLEDLRGKVVLL
+DFWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYAIEHPV
+LDDPELTTWQAYSARAWPTLVVVDPEGYIAAHLSGEGHVAGLYGLVRELVAEHEAKGTLH
+RGSGPYVPPAPVARDLSFPGKAVSLGGRGSRPGTFLVSDTGHHRLLEVAEDLTTVLRAFG
+GGDPATADAGQAELAFPTPGEKGHADGGPDQALFNEPQGLALLPEDVAQRVGYDVVVADS
+VNHRLRGLRLSDGHVSTLAGNGVQKLIDSERAKEAAAVDDEGDVAVDLADLPGEPTAISL
+SSPWDVVWHPALGRVVIAMAGTHQLFDFDPVTDALAVHAGTALEGLLDGEAGRAWFAQPS
+GLSVGADGTLWVADSETSAVRWVRTGEDGRREVGTAVGAGLFDFGHVDGEADRARLQHAL
+GVTALPDGSVLIADTYNGAIRRYAPAGEDAAGRAVPATVTTVARGLLEPSDVLVEHDADG
+NDTAIVVVESNAHRLTRLAVPEEFLTVDEGARQTQRPRTPVVAGDLDLTIGFAAPTGQKL
+DDRWGDPTQLKVSSSPEELLLEGAGTSTGLHRTLRLNPEVEEGVLHITARAAACDGEKGQ
+PIPDHAACHLYQQDWGIPVTVHTPDRAPEGAETRLDLDLRGIH
+>2_938
+MMVGMTDPQTPPAVSPDAAPSDAAPAAVPRAASRVRASELVGRGWLNTGGEQVTLEDLRG
+KVVILDFWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYT
+IEHPVLDDPELTTWQAYSARAWPTLVVVDPEGYIAAHLSGEGHVAGLYSLVRELVAEHEA
+KGTLHRGSGPYVPPAPVARDLKFPGKAISLAGRGTAPGTFLVADTGHHRLLEVAEDLTTV
+LRAVGGGDPAGAGEEQAGLAFPTPGEKGHADGGPEQALFNEPNGLALLPEDVAERVGYDV
+VVADTVNHRLRGLRLADGGVSTVAGNGVQKLIDSERAKEASAGDAEDVAVDLSDLPGEPT
+AISLSSPWDVAWDPAAGRVVIAMAGTHQLFDFDPVAGALAVHAGTGLEGLLDGDAGSAWF
+AQTSGLSLGPDGTLWAADSETSAVRWLRTGEDGRREVGTAVGTGLFDFGFVDGEAAQARL
+QHPLGVTALPDGSVLIADTYNGAVRRYAPAGEDAAGRPVAAAVSTVARGLQEPSDVLVEH
+DADGAPAAIVVVETNAHRLVRLAVPEEYLTVDEGARQTQRPRTPMVAGDVDLAIGFAAPS
+GQKLDDRWGDPTQLKVSSSPEELLLEGAGTSTGLSRTLRLNPAVAEGVLHITARAAACDG
+EKGQPIPDHAACHLYQQDWGIPVTVHAPEGAPEGAETRLDLDLRGIH
+>3_879
+MRRPLPADARRAWAMMEGMTEQQTSAPSVPRSGSRVRASSLVGRRWLNTGGTEVSLEDLR
+GKVVILDFWTFCCINCLHVADELRPLEEEFSDVLVTVGVHSPKFEHEADPDALDAAVERY
+DIAHPVLDDPTLVTWQAYSARAWPTLVVVDPEGYIVAHLSGEGHVAGLYSLVRELVAEHE
+AKGTLHRGSGPYVAPAPVARDLKFPGGAVSLEGRGSRPGSFLVADTGHHRIVELAADLTT
+VLRAIGGGDPAEAPAEAADLAFPTPATRGHRDGGPETALFSEPNGLLLLPEDVAARAGVD
+VVVADTVNHRLRGIDLATGEVTTLAGNGVQKLIDSERVREAAAGDESAAADLSDLPGDPT
+GISLSSPWDVAWDAAAGRVIVAMAGTHQLFSYDPVARVLAVHAGTGLEGLLDGPADTAWF
+AQTSGLSFAQDGTLWLADSETSAVRWLRTAEDGTRQVGTAVGTGLFDFGYVDGAPEQARL
+QHPLGVTALPDGSVLVADTYNGAIRRYAPAAEDAAGRPVEAAVSTVTRELKEPSDVLVEP
+GEDGAPAEIVVVETGAHQLVRISVPAEYLTVDEGARQTARPSTDVAAGDLDLSVGFAAPA
+GQKLDDRWGDPTQLKVSSSPEELLLDGAGTSVGLTRTLRLNPAVAEGVLHITARAAACDG
+EKDGPIPDSAACHLYQQDWGIPVRVHAADQAPDGAETRLDLDLRGIH
+>4_1761
+MMVDMTAPQTPNPAPTADAPAAVPRAATRVRASELVGRGWLNTGGEQVSLEDLRGKVVLL
+DFWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYAIEHPV
+LDDPELTTWQAYSARAWPTLVVVDPEGYIAAHLSGEGHVAGLYGLVRELVAEHEAKGTLH
+RGSGPYVPPAPVARDLSFPGKAVSLGGRGSRPGTFLVSDTGHHRLLEVAEDLTTVLRAFG
+GGDPATADAGQAELAFPTPGEKGHADGGPDQALFNEPQGLALLPEDVAQRVGYDVVVADS
+VNHRLRGLRLSDGHVSTLAGNGVQKLIDSERAKEAAAVDDEGDVAVDLADLPGEPTAISL
+SSPWDVVWHPALGRVVIAMAGTHQLFDFDPVTSALAVHAGTALEGLLDGEAGRAWFAQPS
+GLSVGADGTLWVADSETSAVRWVRTGEDGGREVGTAVGAGLFDFGHVDGEADRARLQHAL
+GVTALPDGSVLIADTYNGAIRRYAPAGEDAAGRAVPATVTTVARGLLEPSDVLVEHDADG
+NDTAIVVVESNAHRLTRLAVPEEFLTVDEGARQTQRPRTPVVAGDLDLTIGFAAPTGQKL
+DDRWGDPTQLKISSSPEELLLEGAGTSTGLHRTLRLNPEVEEGVLHITARAAACDGEKGQ
+PIPDHAACHLYQQDWGIPVTVHTPDRAPEGAETRLDLDLRGIH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001540.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001540.fa
new file mode 100644
index 0000000000000000000000000000000000000000..42aedcea6cb46a4d2e99f50a292e5db1249c4815
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001540.fa
@@ -0,0 +1,25 @@
+>0_1846
+MRSAVAAAPWAPSGLEDPRPRVVRGPARLARGWAGALAMTALAALFHTAAEPGHGFPEVG
+VVAFAAVLAAPLCTALAGRALSLWRTAAAVAIAQGLFHVLYGLAAGGPAVAPAAGVDPAH
+LGHARPGTGALLAPGEALSSAPTGHLTDLRMLAAHVIAAVLTVLVLRRGEALVLTIAERV
+VAAVCPPPAAHGPLPTPARVRVPVPPALRPATSLALLSSPGRRGPPFALAA
+>1_1553
+MRSAVAAAPWAPSGLEDPRPRVVRGPARLARGWAGALAMTALAALFHTAAEPGHGFPEVG
+VVAFAAVLAAPLCTALAGRALSLWRTAAAVAIAQGLFHVLYGLAAGGHAVAPAAGVDPAH
+LGHARPGTGALLASGEALSGAPTGHLTDLRMLAAHVIAAVLTVLVLRRGEALVLTIAERV
+VAAVCPPPAAHGPLPTPARVRVPVPPVLRPATSLVLLSSPGRRGPPFALAA
+>2_932
+MRSAVDAAPHAFGRPHPAPGRVVRGPARLARGVAGALAMTVLAALFHAAAVPGAGLPDVR
+VAAFAAVLAAPVCTALAGRALSLWRTAAAVAVAQGLFQVLYGIAAGGHAVAPAAGVDPAH
+LHHAAAAAGPLVSVSAGPAAGHVHAAEPLMLAAHAAAAVLTVLVLRRGEALVLAVAERVL
+QAVLPRAASAGPLPLPSPARVPALPAPRPTESLVLLGTPGRRGPPFALAA
+>3_873
+MGTPTPVPSRAVAGPARVLRGAAGALAMTLLAALFHSAAASTPLPAPALLLFSAVLAAPV
+CTLLAGRALSLWRTAAAVAVAQGLFHALYSVAAGGRSVATAAGVAPAHLAHSHVGAARPL
+LTVDAASETSAHAAHAGTPGMLLAHLAAAALTVAVLRHGERMLVAAAERVLQAAPVWRLL
+VALAAGLLPTPRPVRVPAWRAPSAPAAVVVLASPGRRGPPAFALAA
+>4_1767
+MRSAVAAAPWAPSGLEDAPPRVVRGPARLVRGWAGALAMTALAALFHTAAEPGHGFPEVG
+VVAFAAVLAAPLCTALAGRALSLWRTAAAVAIAQGLFHVLYGLATGGHAVAPAAGVDPAH
+LGHAHPGAGALLAPGEALSGAPTGHLTDLRMLAAHVIAAVLTVLVLRRGEALVLTIAERV
+VAAVCPPPAAHGPLPTPARVRVPVPPALRPATSLALLSSPGRRGPPFALAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001545.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001545.fa
new file mode 100644
index 0000000000000000000000000000000000000000..817962e041e2b790ab79e5a3aff573ab58bf7d75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001545.fa
@@ -0,0 +1,30 @@
+>0_1851
+MSHTSEQSSPLADQVPPGGPDEPHAAEGVHARLNWLRAGVLGANDGIVSVAATVVGVAGA
+TTALTPVLLAGAAAVVGGAFSMALGEYVSVSSSSDSQKSLIAKERRELEEDPEGELEELV
+QLYEADGLSRATAEAAARELTEKDALAAHLRMELGMAEEDVVSPWAAAGASFLSFLVGAL
+LPFLTVVLAPVDFRIPLTFGVTLVALAVTGWVGARLGDAPALRAAVRVVLGGALALGLTL
+AVGSLLGASVA
+>1_1558
+MSHTSEQSSPLADQLPPGGPDEPHAAGGVHARLNWLRAGVLGANDGIVSVAATVVGVAGA
+TTALTPILLAGAAAVVGGAFSMALGEYVSVSSSSDSQKSLIAKERRELEEDPEGELEELV
+QLYEADGLSRATAEAAARELTEKDALAAHLRMELGMAEEDVVSPWAAAGASFLAFLVGAL
+LPFLTVVLAPVGLRVPFTFGVTLVALAVTGWVGARLGDAPALRAAVRVVLGGALALGLTF
+AVGSLLGASVA
+>2_923
+MNESTAPSEPTVRDDVAASSGHDRPEPHAGGGLHERLNWLRAGVLGANDGIVSVAATVVG
+VAGATTAVAPVAIAGVAAVVGGAVSMALGEYVSVSSSSDSQKALIAKERRELAEDPEGEL
+EELVGLYEAEGLSRATAENVARELTEKDALKAHLRAELGMDETGVVSPWSAAGASFVAFL
+LGALLPFLTIILAPVDIRVALTFVTTLVALAGTGYAGAWLGGAPPVRAMLRVVIGGALAL
+ALTFAVGAWLGTTVA
+>3_865
+MSHSTAPAAPSSYPDEPHAQTGVHARLNWLRAGVLGANDGIVSVAATVVGVAGATTAVTP
+VLLAGTAAVVGGAVSMALGEYVSVSSSSDSQKAMIAKERRELAEDPEGELEELVGLYEAE
+GLSRDTAEQVARELTANDPVTAHLRMELGMAEEDVVSPLAAAGASFIAFLVGALLPFLAI
+LLSPVGVRVPVTFGVTLVALAVTGYLGAWLGNAPAVRAMVRVVVGGALALALTFGVGTWL
+GVGVA
+>4_1772
+MSHTSEQSSPLTDQVPPGGPDEPHAAGGVHARLNWLRAGVLGANDGIVSVAATVVGVAGA
+TTALTPILLAGAAAVVGGAFSMALGEYVSVSSSSDSQKSLIAKERRELEEDPEGELEELV
+QLYEADGLSRATAEAAARELTEKDALAAHLRMELGMAEEDVVSPWAAAGASFLAFLVGAL
+LPFLTVVLAPVGLRVPFTFGVTLVALAVTGWVGARLGDAPALRAAVRVVLGGALALGLTF
+AVGSLLGASVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001550.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001550.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d352b752c5d930f5a0c54f9cd84d8d4cf54302f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001550.fa
@@ -0,0 +1,20 @@
+>0_1863
+MSGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI
+LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRD
+RR
+>1_1570
+MSGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI
+LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRD
+RR
+>2_917
+MSGSVRVSGAVRVDAWLWAVRVYKTRSAATAAVRGGHVRVNDEPVKAAHTLAVGDRVRVR
+KDQRERILEVTGLIGTRVGAPVAVTNYIDHSPPPIPRELLAVPHRERGAGRPTKRDRRKL
+DELRGRASDERS
+>3_853
+MGAVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI
+LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRA
+STGRG
+>4_1784
+MSGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI
+LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRD
+RR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001551.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001551.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d70970f33b594eb35ed60d3bc2e76e4c6c6192d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001551.fa
@@ -0,0 +1,17 @@
+>0_1864
+MTLVEYTRRHPDADHLDPEKESVLEEAVGTGTQQITVDAQQGAVLRVIVLCPSDATGETE
+ILTSRGGGGTKTWMAGSEALCGGWSAATPPVDEAGPMTFTVTVDNDKPFRMVLTAPSA
+>1_1571
+MTLVEYTRQHPDADYLDPEKESVLEEAVGTGTQQITVDAQQGAVLRVIVMCPSDATGETE
+ILTSRGGGGTKTWMAGSEALCGGWSAATPPVDEAGPMTFTVTVDNDKPFRMVLTAPSA
+>2_916
+MPHRRRRPCVPVALSVAAALGLSLSACASTTTAGVGSQSPAPSSAAGAASSAAGTSSAAP
+TTSAALTTSGTAAEIAGDEAAAQAQDDAATRTALNRAVAEDGIPYAELDPSLTPVPDGAS
+ILWEGLAVGAQSLRVDARAGEEYTVVLLCAEQDGSRRSLVMATVPGEDFSDVMAESPGCG
+HWSAGLPAREADGPLTLTGVVPDGGPFRMVVYRSEG
+>3_849
+MTLEEYTRQNPDSDYLHPETESVLQEKVGTGTQQITVDAQEGAVLRVILLCPSDATGKTD
+IHTSRGAEGEKTWMAGSEALCGGWSAATPPVEKAGPMTFSATVDNDKPFRMVLTAPAA
+>4_1785
+MTLVEYTRRHPDADHLDPEKESVLEEAVGTGTQQITVDAQQGAVLRVIVLCPSDATGETE
+ILTSRSGGGTKTWMAGSEALCGGWSAATPPPVDEAGPMTFTATVDNDKPFRMVLTAPSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001560.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001560.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c966262c7f8c0f6f3dcee0bfc5de728865cc9a73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001560.fa
@@ -0,0 +1,55 @@
+>0_1875
+MSALTEVAAPGTDLPRRRARGRGDGLGPWWLVAAVLPVAFLLVFFAWPVAAMLWRGIGGD
+ADAFTGAVDLTAFGETLARERTWRILGQTLGMAAAGTVVSVALGLPTAFVLHRRRVPGRA
+VLRALVLVPFVLPTVVVGVAFRALLAPGGPLGFTGLDQTTTAVVLAMVFFNVSVVVRQVG
+ALWNALDPRQTEAARTLGASPWRAFRTVTLPQLAPAIAASAALVFLFCASAFGIVQTLGR
+PGYGTLESEIWVQTSVYLDLRTAAVFSVLQFAVVLVAVVVSGVTAARTQRALRLRETPPA
+RLTRADAVPVAVMLAVVALVVAPILTLVVRSFHTRHGWGLGNYRLLSTSAGSGFVGGSTP
+ARALEQSLRVAVDATLVTLVVAVPLALLLTRPFRSRAALAAQRALDGALLLPLGVSAVTV
+GFGFVVSLRAAFPELAASGVLVPLAQAVVALPLAVRALVPVLAAVDPRLREAARTLGAGP
+WRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLASPSAPTLPVLIARLLGRPGADN
+YGMALAAATVLAVLSAGIMLVCERLRPRGPAGAGGL
+>1_1582
+MSALTEVAAPGTDLPRRRARGRGDGLGPWWLVAAVLPVAFLLVFFAWPVAAMLWRGIGGD
+ADAFTGAVDLTAFGQTLARERTWRILGQTLGMAAAGTVVSVALGLPTAFVLHRRRVPGRA
+VLRALVLVPFVLPTVVVGVAFRALLAPGGPLGFTGLDQTTTAVVLAMVFFNVSVVVRQVG
+ALWNALDPRQTEAARTLGASPWRAFRTVTLPQLAPAIAASAALVFLFCASAFGIVQTLGR
+PGYGTLESEIWVQTSVYLDLRTAAVFSVLQFAVVLAAVVVSGVTAARTQRALRLRETPPA
+RLTRADAVPVAVMLAVVALVVAPILTLVVRSFHTRHGWGLGNYRLLSTSAGSGFVGGSTP
+AQALEQSLRVAVDATLVTLVVAVPLALLLTRPFRSRAALAAQRALDGALLLPLGVSAVTV
+GFGFVVSLRAAFPELAASGVLVPLAQAVVALPLAVRALVPVLAAVDPRLREAARTLGAGP
+WRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLASPSAPTLPVLIARLLGRPGADN
+YGMALAAATVLAVLSAGIMLVCERLRPRGPAGAGGL
+>2_904
+MDGPARGGGLLTVGLTSVPAPVGGPGAPPGAPGPAASGGRRRRRTAGGDGIGAWWLLAAV
+VPVAFLLVFFAWPVGAMLWRGVSAEGVLDLGAFAEVLGRERTWRIVGQTLGMAAAGTVLA
+VALGLPAAFVLHRRAFPGRAALRAVITVPFVLPTVVVGVAFRALLAPGGPFGWTGLDQST
+AAVVLAMVFFNVSVVVRQVGALWASLDPRQAEAARTLGSSGWRAFRTVTLPQLAPALASS
+AALVFLFCASAFGIVQTLGRPGVGTLESEIWVQTVVYFDLGTAAVFSTLQFLVVLAAVLV
+SGATARRTRRALRLRDAPVRRLTRADAAPVAVTLATALLVLAPLATLLVRSFHSSEGWGL
+RNYRLLASSPGAGFSGGVTPAQALEHSLRIALDATLLTLLIGVPLALLLTRPVRSAAGRR
+AQRGLDGALLLPLGVSAVTVGFGFVVSLRAEAPALAASGALVPIAQAVVALPLVVRSLVP
+VLGAVDPRLREAARTLGAGPLRVLATVDGPFLLRGLGVAAGFAFAVSLGEFGATSFLSSP
+DYQTLPLLIVKLLGRPGADNYGMALAAATVLAVLSAGTMMACERLGPRAAASRGGI
+>3_839
+MPTPAPARGRRRATLRPPRGRRAAGDGLAPLWLLSAAVPVAFLLVLFAWPVAAMLWRGVA
+SVDAAGDPTGGLDLSAFAQTLGAPRTWRILGNTLGLAAAGTAASVALGVPTAFALHRRAF
+PGRGLARAVVTVPFVLPTVVVGAAFRALLAADGPLGWTGLDQTSTAVVMAMVFFNVSVVV
+RQVGGLWAALDPRQAEAARTLGASPWRAFRTVTLPQLAPAVAGAAALVFLFCASAFGIVQ
+TLGRPGPGTLETEIWAQTTVYLDLRTAAVLSTVQLAVVLAAILASGAAAARARRALRLGE
+APARPLTRADAVPAAVTLAVLALVVAPILALLAGSLHSAEGWGLRNYRLLATSPGTGFAG
+GVTPAQALEQSLRTAVDATVVTLVVAVPLALVLTRPVRSRAGRAAQRALDGALLLPLGVS
+AVTVGFGFIVSLRATAPDLAASGALVPLAQSVIAVPLAVRALVPVLGAVDPRLREAARTL
+GAGPWRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLAAADRPTLPVLIARLIGRP
+GADNHGMALAAAVVLAVLSAGALLACERLRPRGAAPSGGL
+>4_1795
+MSALTEVAAPGTDLPRRRARGRGDGLGPWWLVAAVLPVAFLLVFFAWPVAAMLWRGIGGD
+ADAFTGAVDLTAFRETLARERTWRILGQTLGMAAAGTVVSVALGLPTAFVLHRRRVPGRA
+VLRALVLVPFVLPTVVVGVAFRALLAPGGPLGFTGLDQTTTAVVLAMVFFNVSVVVRQVG
+ALWNALDPRQTEAARTLGASPWRAFRTVTLPQLAPAIAASAALVFLFCASAFGIVQTLGR
+PGYGTLESEIWVQTSVYLDLRTAAVFSVLQFAVVLAAVVVSGVTAARTQRALRLRETPPA
+RLTRADAVPVAVMLAVVALVVAPILTLVVRSFHTRHGWGLGNYRLLSTSAGSGFVGGSTP
+AQALEQSLRVAVDATLVTLVVAVPLALLLTRPFRSRAALVAQRALDGALLLPLGVSAVTV
+GFGFVVSLRAAFPELAASGVLVPLAQAVVALPLAVRALVPVLAAVDPRLREAARTLGAGP
+WRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLASPSAPTLPVLIARLLGRPGADN
+YGMALAAATVLAVLSAGIMLVCERLRPRGPAGAGGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001562.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001562.fa
new file mode 100644
index 0000000000000000000000000000000000000000..42733573db99723c23152d21b8a58dc985e75e2d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001562.fa
@@ -0,0 +1,20 @@
+>0_1877
+MTPPAPRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAGVLGVQASALYWHVPDKQSLLAR
+VADRIVAEAEETVRARRVTDLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLHRLLT
+EAADTPEDGERALALLLGTVSLRQQRAQAQALGVATGPDVQRHRTDPL
+>1_1584
+MTPPAPRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAAVLGVQASALYWHVPDKQSLLAR
+VADRIVAEAEETVRARRITDLAGRAEAAEAALLRHRDGADLVLSALALGLGGLGLHRLLT
+EAADTPEDGERALALLLGTVSLRQQRAQAQALGVPTGPDVQRHRTDPL
+>2_902
+MSSPPRAGSSRGRLSATDVVDAAVGILQDFGMGDLSMRRVASVLGVQASALYWHVPDKQT
+LLARVADRIVAEAEEAVRHRGIADLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLH
+ALLTEAAPTPEEGERALALLLGGVSLRQQRAQAEALGVRVGPDVQRHRTDPL
+>3_837
+MSTSSARGRLSAEDVVDAAVGILQDFGMGDLSMRRVASMLGVQASALYWHVPDKQTLLAR
+VADRIVADVERACAARRVEDLAGRAEEAEAVLLRHRDGADVVLSALALGLGGLGLHRLLV
+DAAHTPEEGERALAALLGTAALRQQRNQAAALGLRLGPDVQARRTGAL
+>4_1797
+MTPPAPRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAGVLGVQASALYWHVPDKQSLLAR
+VADRIVAEAEETVRARRVTDLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLHRLLT
+EAADTPEDGERALALLLGTVSLRQQRAQAQALGVATGPDVQRHRTDPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001568.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001568.fa
new file mode 100644
index 0000000000000000000000000000000000000000..42574746216f3404888d347371946479fc9f2eb6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001568.fa
@@ -0,0 +1,30 @@
+>0_1887
+MSTAPTPSSSDDAPAVLVETRPGVVRLTLNRPAKGNALGLTMAREVLAAIAAAEADESVH
+VLTLTGAGRIFCGGGDVQAMAAAPAGPERRAMIQELGEAAGEVAVALTGSRLLVLAGVNG
+TAAGAGLGLMLGGDVVLVREDAQLVTAFSALGMTPDTGVSYWLPRVLGPVRATQLLLGGR
+RLNGTEAVGWGLATEAAAGDAFAARLAELEDELVAGPAHTYGPTKALTRGADVEALRAHV
+RQEAASIAAASEHPEAVRRVEAFAGR
+>1_1592
+MTTAPTPSPHDDAPAVLVETRPGVVRLTLNRPAKGNALGLTMAREVLAAIAAAEADESVH
+VLTLTGAGRIFCGGGNVQAMAAAPAGPERRAMIQELGEAAGEVAVALTGSRLLVLAGVNG
+TAAGAGLGLMLGGDVVLVREDAQLVTAFSALGMTPDTGVSYWLPRVLGPVRATQLLLGGR
+RLNGTEAVAWGLATEAVAGGAFAARLAELEDDLVAGPAHTYGPTKALARGADVEALRAHV
+RQEAASIAAASEHPEAVRRVEAFAGR
+>2_891
+MSGDGGAADVATVRVEARPGVVRLTLDRPAQGNALSLAMARELTAAVRASEADPDVHVLT
+LTGAGRFFCGGGDLAAMGAASPAERPAVLRELADAASEVALALVRSRLLVVAGVNGTAAG
+AGLGLVLNADVVLVGDDALLLAAYAGIGLVPDTGVSWWLPRAVGPVRAAELTLRGRRLTG
+AEAVEWGVASEAVSGDEFEARLAALEDELAAGAVHAYGPTKALLRGPEIVGYAEHLDRET
+AAISAASGHPEAVRRVDAFLRR
+>3_828
+MTTAPTPSSSDDAPAVLVETRPGVVRLTLNRPAKGNALGLTMAREVLAAIAAAEADESVH
+VLTLTGAGRIFCGGGDVQAMAAAPAGPERRAMIQELGEAAGEAAVALTGSRLLVLTGVNG
+TAAGAGLGLMLGGDVVLVREDAQLVTAFSALGMTPDTGVSYWLPRVLGPVRATQLLLGGR
+RLNGAEAVAWGLATEAVAGDAFAARLTELEDELVAGPTHTYGPTKALARGADAEALRAHV
+RQEAASIAAASEHPEAVRRVEAFAGR
+>4_1807
+MSTAPTPSSSDDAPAVLVETRPGVVRLTLNRPAKGNALGLTMAREVLAAIAAAEADESVH
+VLTLTGAGRIFCGGGDVQAMAASPAGPERRAMIQELGEAAGEVAVALTGSRLLVLTGVNG
+TAAGAGLGLMLGGDVVLVREDAQLVTAFSALGMTPDTGVSYWLPRVLGPVRATQLLLGGR
+RLNGAEAVAWGLATEAVAGDAFTARLAELEDELVAGPAHTYGPTKALARGADVEALRAHV
+RQEAASIAAASEHPEAVRRVEAFAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001569.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001569.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b1c887acef018d78690e6fe897becda7d279fb4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001569.fa
@@ -0,0 +1,15 @@
+>0_1888
+MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAAYNAVYRRTTVG
+LGDVLKMFK
+>1_1593
+MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAAYNAVYRRTTVG
+LGDVLKMFK
+>2_887
+MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAAYNAVYRRTTVG
+LGDVLKMFR
+>3_827
+MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAAYNAVYRRTTVG
+LGDVLKMFK
+>4_1812
+MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAARNAVYKRTTFG
+LGDVLRMFR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001571.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001571.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8a5d75af75cce6e6b73e7dc4b570368d029d901
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001571.fa
@@ -0,0 +1,40 @@
+>0_1903
+MTSHTDPSHPAAHPVSRRTLLGGAGLVVASAALLSTPAGTAHAATGPTPFTLGVASGDPW
+PDGVVLWTRLAVDPLALDGLGGMPDQSFRVEYQVATDEGFRKVVRSGAVTTDRAQGYAVH
+VTLTGLRPGTEYFYRFRALGHLSRVGRTVTAPARGSNPSRLTMTVASCANWEHGYFTAYG
+HMAAERPDLMVHLGDYYYEIMPYGYPVSSGVPRAHRNGESRTLAQYRARMAQYKTDPHLQ
+DAHAAAPWLVIFDDHELENNWADETPEIWDPSFLARRAAAFQAYYENMPLRASSVPRGID
+MQLYRRIHWGDLATFHLLDTRQYRSDQANLDLVKVVDADARDSRRTITGAAQEAWLREGF
+ETSVARWDLITQQVPFVQYDRTSGPLLWGDMDTWDGYVASRDRVVSAWTAAGVRNPVVLT
+GDIHEAFASDIKQDFNDLSSESVGVELITTSITSGGDGSDAAAEALAWNPHIKFNNDLRG
+YLRVDLSAQLLEARFRVVDYVSELGSSVRTRAVFGVGDGEHRLHRIA
+>2_874
+MPLRASSVPRGIDMQLYRRIHWGDLATFHLLGTRQYRSDQANLDLVKVVDADARDPRRTI
+TGAAQEAWLREGFETSVARWDLITQQVPFVQYDRISGPLLWGDMDSWDGYVASRDRVVSA
+WTAAGVRNPVVLTGDIHEAFASDIKRDFNDLSSESVGVELITTSITSGGDGSDAAAEALA
+WNPHIKFNNDLRGYLRVDLSAHMLEARFRVVDYVSELGSSVRTRAVFGVGDGEHRLHRIA
+>3_422
+MSSPSPTLSRRRLLGLSGASAAVLALGVNAPDAAHAEPLPQRDGLFGLGVASGYPRPDGA
+VLWTRLAPEPLAENGHGGMPLRSVPVKWEVARTADFRRIVARGTALAQPELAHSVHPRVE
+GLAPGTEHFYRFVVGPQTSPVGRFVTLPAAGAATDDYTVGLISCQAWYHGHFAAHRHLAQ
+EEDLDLTVFLGDYIYEYGITAANLWRQGAEVTPAHAVEIETLEQYRLRYALTKSDPHLQA
+LHARAAAVAIWDDHEVQNNYVGAASSTGIPEELFAHRIAVAYRAFYENLPVDIDALPEGP
+ESDIVAGLDVGALARISLLDTRQFRDAPPADAADRERENRTMLGAAQERWVTERLRTSQS
+QWNVLAGGVVLAPISDDRTDQWDGYPAARRRLLTEMKRAGNAVMLTGDIHKHVAAELRGE
+SAGLPAGPAGVELVTTSAASDGDGAKTDKYTPDWVRHDYVRHYDGRRGYLHLRFTPAQLT
+SSFWVVPWVESDDTAPKELSARFTTPAGSSRLIEA
+>3_815
+MAAAALISTPAGTAHAAAGPNPFTLGVASGDPWPDGFVIWTRLATMPLNRDGFGGMPDAS
+FTVEWQVSRHADFRSTVRTGTTTTSRAQGYAVHVTLTGLRAGTEFFYRFRCNGHLSRTGG
+AVTAPALGSMPGHLTATEAERLIRAAGFAPVRLGGIDESIRMEVTGELHPFGGLDGTLPT
+TANVEQLRG
+>4_1830
+MSSHTDPAHPTAHPVSRRTLLGGAGLVVASAALLSTPAGTAHAATGPTPFTLGVASGDPW
+PDGVVLWTRLAVDPLALDGLGGMPDQSFRVEYQVATDEGFRKVVRSGAVTTDRTQGYAVH
+VTLTGLRPGTEYFYRFRALGHLSRVGRTVTAPARGSNPSSLTMTVASCANWEHGYFTAYG
+HMAAERPDLMVHLGDYYYEIMPYGYPVSSGVPRAHRNGESRTLAQYRARMAQYKTDPHLQ
+DAHAAAPWLVIFDDHEVENNWADETPEIWDPNFLARRAAAFQAYYENMPLRASSVPRGID
+MQLYRRIHWGNLATFHLLDTRQYRSDQANLDLVKVVDADARDSRRTITGAAQEAWLREGF
+ETSVARWDLITQQVPFVQYDRSSGPVLWGDMDSWDGYVASRDRVVSAWTTAGVRNPVVLT
+GDIHEAFASDIKQDFNDLSSESVGVELITTSITSGGDGSDAAAEALAWNPHIKFNNDLRG
+YLRVDLSAQLLEARFRVVDYVSELGSSVRTRAVFGVGDGEHRLHRIA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001572.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001572.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2566b4e4915a107f9e8af9748b4acb37581fbfe5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001572.fa
@@ -0,0 +1,36 @@
+>0_1906
+MHEDEGRRRHYGHFYGLEDLPEDDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP
+PAFEAQPDEVAHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPEDAAVVRIPVVYD
+VSRFPWQVTLRNWKFAPGAAERPGEDPPVVPYHDLRVLAEAATGRRREVAPAAIREAAAA
+SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTLLTRVAERVAERLPGDVAVQPV
+PASRVLLGGVRAPLEAPVVEALDLDAAPTEDWTVAGQTVPAEQLRQTHLDWYAQNPQAVE
+VGMRKYADQLRLLGLTG
+>1_1611
+MNEDEGRRRHYGHFYGLEDLPEGDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP
+PAFEAQPDEVEHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPKDAAVVRIPVVYD
+VSRFPWQVTLRNWKVAPGAAERPGEDPPVLPYHDLRVLAEAATGRRRQVAPAAIREAAAA
+SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTLLTRVAERVAGHLPGDVAVQPV
+PASRVLLGGVRAPLEAVVVEALDLDAEPTEDWTVAGQTIPAEQLRQTHLDWYAQNPQAVE
+VGMRKYADQLRLLGLAA
+>2_873
+MHEDEGRRRHYGHFYGLEDLPEGDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP
+PAFEVQPDEVEHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPEDAAVVRIPVVYD
+VSRFPWQVTLRNWKFAPGAAERPGEDPPVVPYHDLRVLAEAATGRRREVAPAAIREAAAA
+SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTVLTRVAERVAEHLPGDVAAQPV
+PAARVLLGGVRAPLEAVVVEALDLDAEPTEDWTVGGETIPAEQLRQTHLDWYAQNPQAVE
+VGMRKYADQLRLLGLAA
+>3_814
+MSEETPMDDQTRTAGAEPGDEGVQVRGAAERAPSSDLPADEGRRRHYAHFYGLEPLPEGE
+LLTVMGGCQAEATRLLLCGEPGRAEGGTPASVRVPPMFELGPDDLPHLLALLKRTTVLVV
+KPVRDDYQGLPLGLGQLESLLPAGARSIRVPALYDSSRFPWLVTLRHPTRPWEDPPVVPY
+HDLRTVAEAAAEAGLIPWPAALGGPGEAGAYDAGPRLPLSAEALRGLAAESVARLRAREE
+HFGTVRVSDAVADERGVGFHTVNHPDNPLLEALARTVLAELGVDKEVHAPDRLLLGHVLA
+PIEEQVVDALGLQTAPRAAWRVGGAEVSDAEVRRAHLGWFRANPEALAPGLERHGALMRE
+LGLLA
+>4_1833
+MNEDEGRRRHYGHFYGLEDLPEGDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP
+PAFEVQPDEVAHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPEDAAVVRIPVVYD
+VSRFPWQVTLRNWKFAPGAAERPGEDPPVVPYHDLRVLAEAATGRRREVAPAAIREAAAA
+SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTLLTRVAERVAERLPGDVAVQPV
+PASRVLLGGVRAPLEAVVVEALDLDAEPTEDWTVAGQTVPAEQLRQTHLDWYAQNPQAVE
+VGLRKYADQLRLLGLTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001573.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001573.fa
new file mode 100644
index 0000000000000000000000000000000000000000..268fd4ad59fb00f741ad51d710b8016e23e4ce75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001573.fa
@@ -0,0 +1,45 @@
+>0_1908
+MSAAVSVVVPYYRAQADLDRLTAALAAQRGVTGGLQLVVADDGSPVPPRVDPGLPFDVVT
+VRQQDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAALAAVAEAPRDAAVVGRR
+RHLAEAWLERAWADGWRPGHEVPADALLAEPAWLRDGYRATDDLRRADSTGYRYVISAVL
+TVAREVYEDAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA
+EAARVKAREALVLVSRIPATTSRGHGLSLAGPLRAEARVRVPEGADGAAAAVVAVDAVLR
+AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAAPEDLPPTPARGDLDAVRSVPDW
+SVDVQVPLRPAAAGARPDTDAVAAWLLRLERAGVERVEVLGEPGERAERDVLAVLTCARA
+RWRPRRGGTARVWRVPASRLGWAPVAAVPDLEAWWGGWG
+>1_1613
+MSAAVSVVVPYYRAQADLDRLTAALAAQRGLTGGLQLVVADDGSPVPPRVGPGLPFDVVT
+VRQQDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAALAAVAEAPRDAAVVGRR
+RHLAEAWLERAWVDGWRPGDEVPADARLAEPAWLREGYRATDDLRRADSTGYRYVISAVL
+TVAREVYADAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA
+EAARVKAREALVLASRIPATTARGHGLSLAGPLRVEARVRVPEGADGAAAAVVAVDAVLC
+AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAASQDLPPTPARGDLDAVRSVPDW
+SVDVHVPLRPAAAGARPDADAVAAWLLRLERAGVERVEVLGEPGERAERAVLAVLTCARA
+RWRRRRGGTARVWRVPASRLGWAPVATVPDLEAWWGGWG
+>2_871
+MSAAVSVVVPYYRAQADLDRLTAALAAQRGVTGGLQLVVADDGSPVPPMVGPDLPFDVVT
+VRQQDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAAVAAVAEAPRDAAVVGRR
+RHLAEAWLERAWADGWRPGHEVPADARLADPAWLREGYRTTDELRRADSTGYRYVISAVL
+TVAREVYEDAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA
+EAARVKAREALALASRIPATTARGHGLSLAGPLRVEARVRVPERADGAAAAVVAVDAVLR
+AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAASQDLPPTPARGDLDAVRSVPDW
+SVDVRVPLRPAAAGARPDADAVAAWLLRLERAGVERVEVLGEPGERAERAVLAVLTCARA
+RWRRRRGGTSRVWRVPASRLGWAPVAAVPDLEAWWGGWG
+>3_813
+MTAPVAGREAAAETAGPEASVPEVSVVVPHYRAPADLERVVAALAAQDHPASRLQLVVAD
+DGSPEPPVLPAGLPFEAVVVAQEDHGFRASAARALGASAAEGRILAFLDGDMLPEPGYLT
+AACAAPAASVDAVVVGRRRHLDPALLESGWRPGEPVPEAARLPEPAWLAEAYQRSGDLAA
+ADSTSYRYVISAVLTVAREVYADAGGFDPAFVGYGGEDWELAHRLWRVGGAFRHQPAAVA
+WQAGEDFGGRGDAAERTAVKQREALRLAARITATTARGHGLSLPGPLRVGARVRAEASGD
+AAAVVGVDALLAAAPGARVGVTGLGSGAARAALADPRVWIMDGGGEAARADLPPAPARGD
+LGAVRGIPDWSCDVRTPLRPAAPGARPDAARAADWLLRLERAGVERVEVLGEPQAAEEPG
+EAGRGERPVLAVLTCSRALWRSRRGGDSRVWRVPAARLGWAPVARDVDLEAWWGGWG
+>4_1835
+MSAAVSVVVPYYRAQADLDRLTAALAAQRGLTGGLQLVVADDGSPVPPRVDPGLPFDVVT
+VRQPDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAALAAVAEAPRDAAVVGRR
+RHLAEAWLERAWAHGWQPGHEVPADARLAEPAWLREGYRATDDLRRADSTGYRYVISAVF
+TVAREVYEDAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA
+EAARVKAREALVLASRIPATTARGHGLSLAGPLRVEARVRVPEGADGAAAAVVAVDAVLC
+AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAADEDLPPTPARGDLDAVRSVPDW
+SVDVHVPLRPAAAGARPDADAVAAWLLRLERAGVERVEVLGEPAEPGERAVLAVLTCARA
+RWRHRRGGTARVWRVPASRLGWAPVATVPDLEAWWGGWG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001574.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001574.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df86b3db6a7f0284194b420b73ee42ed9a0d9dfc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001574.fa
@@ -0,0 +1,40 @@
+>0_1909
+MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALQRVGAEVELLTAEDVAAFRGLV
+PLLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPAGTTLTLHDIPQPAEGDGRYRR
+RGEAYARLAQAVAGVVVSSQHERALLADLVDVAADVVPLPVQDRRAAAARAEPVVPESMA
+GLDQDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSAGHDDLVAELT
+RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGR
+YTEEMERLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPERTWLDPAVDLSPGAEGCARMLF
+DVLRRVHRWT
+>1_1614
+MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALRRVGAEVELLTAEDVAAFRGLV
+PVLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRR
+RGEAYARLAQAVDGVVVSSQHERALLADLVDVAADVVPLPVEDRRAAAARAEPVVPESMA
+GLDRDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSAGHDDLVAELT
+RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGR
+YTEEMERLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPERTWLGPGVDLSPGAEDCARMLF
+DVLRRVHRWT
+>2_870
+MESQPQGRVLYVIVGPPEHGVVRHARQTAAALRRVGAEVELLTAEDVAAFHGLVPLMAEA
+RSLGAAVHLDVTDALFGPTAAAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRRRGEAYA
+RLARHAAGVVVSSQHERALLAELVDADADVVPLPVEDRRAEAARAESVVPENMAGLDQDV
+VLFGFVYPGKGHALALEALTELHRQWGPNSGAPRRLTALGPVSAGHDDLVAELTRDAEAR
+GLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGRYTEEME
+RLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPEHTWLDPAVDLSPGAEDCARMLFDVLRRV
+HRWT
+>3_812
+MTSHAQGRVLYLSVGSRGHGVVHHGLLTAEELAQVGLDVESLHTEDATGFVGLAPVLARA
+REARRAVHVDVTDSLFGPSPAAAADTLSRILPDGATVTLHDVPQPAEGEARFLERAEAYV
+RIAQAAAGVVVSSEHERALLHAIVDVDAHVVPLPVEDRRAAREAVRLPEALEGLDRDVVI
+FGHLYPGKGHAEAIDALAELDRQWGPSPHRPRRVTALGAVAARHEFLVDELTARAEVSGL
+QFRVTGFVPDEVLDPALRAAAVPLAAHHNVSASGSLASWMSVGRRPIVPAGRYTQEMARL
+RPGTLRIVQVGTSGPEYALAEAVAEAVEEPSRTWQARGTSLAPGPRACARMLAAALADVH
+GWAWPR
+>4_1836
+MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALRRVGAEVELLTAEDVAAFRGLV
+PVLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRR
+RGEAYARLAQAVDGVVVSSQHERALLADLVDVAADVVPLPVEDRRAAAARAEPVVPESMA
+GLDRDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSIGHDDLVAELT
+RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRTIASAGR
+YTEEMERLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPERTWLDPAVDLSPGAEDCARMLF
+DVLRRVHRWT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001575.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001575.fa
new file mode 100644
index 0000000000000000000000000000000000000000..724fb2220aba5ad51030c497e9ab759043488162
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001575.fa
@@ -0,0 +1,64 @@
+>0_1910
+MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPGAPAHQWWPPRALHAEWLAEHR
+PDVLHVHFGFEHFSPAQLAAALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGR
+ADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVAQGDDDAPGAEPGLLPPDASDD
+GDGAAAPARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQDTVQDEDAL
+AALRAGCAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAV
+ADIGHIADQSGAWLTPDSLAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVA
+AAHVAVYREALARARGALPGVSVLVITGHRDEHLARVIAGLERSHRRPDQVVVVFMGQPD
+GRVPATDLPVTVGHVAAEAGLPLAQARNRAAELATGEILVFLDVDCIPAAETVGVLATEV
+AAHPGSVVMGRPRYLRPGWTRDVGEADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHL
+VWTLILALRRADLARIGGFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMT
+PPLHHLEDILVNARRFRQVHGRWAMEGWLRAFADAGLIAWDPEGERLELLRHPTEAELTA
+ARRDDAAY
+>1_1615
+MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPDAPAHQWWPPRALHAEWLAEHR
+PDVLHVHFGFEHFSPAQLAAALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGR
+ADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVAQGDDDAPGLLPPDASDDGDGA
+PVPARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQDTVQDEDALAALR
+AGCAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAVADIG
+HIADQSGAWLSPDSLAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVAAAHV
+AVYREALARARGALPSVSVLVITGHRDEHLARVIAGLERSHRRPDQVVVVFMGQPDGRVP
+ATDLPVTVGHVAADAGLPLAQARNRAAELAIGEILVFLDVDCIPAAETVGVLATEVAAHP
+GSVVMGRPRYLRPGWTRDVGEADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHLVWTL
+ILALRRADLARIGCFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMTPPLH
+HLEDILVNARRFRQVHGRWAMEGWLRAFADAGLIAWDPEGERLELLRHPTEAELTAARRD
+DAAY
+>2_869
+MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPGAPAHQWWPPRALHAEWLAEHR
+PDVLHVHFGFEHFNPAQLAAALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGR
+ADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVSQGDDDAPGLLPPDASDDGAAA
+PARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQATVQDEDALAALRAG
+CAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAVADIGHI
+ADQSGAWLAPDSLAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVAAAHVAV
+YREALARARGALPSVSVLVITGHRDEHLARVIAGLERSHRRPDQVVVVFMGQPDGRVPAT
+GLPVTVGHVAAEAGLPLAQARNRAAELATGEILVFLDVDCIPAAETVGVLATEVAAHPGS
+VVMGRPRYLRPGWTRAVEEADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHLVWTLIL
+ALRRADLARIGGFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMTPPLHHL
+EDILVNARRFRQVHGRWAMEGWLRAFADAGLIAWDPEGERLELLRTPTADELAVARRDDA
+AY
+>3_811
+MSLTVQHVPAGHPYARSVRPLDGAAAPDVEFWPDPPVPGAAEGVWWPPRALDPAWIAEHR
+PDVLHVHFGFEHFTPEQLRAALDAQHAHGGAVVVTVHDLQNPHLQDQDPHRARLRVLLDA
+ADAVITLTPGAAAAVEAASGRAPLVLPHPHVVPLDALPDDGAADGERPGVDRPARLLMHA
+KDLRAQVDPVGLLPVLAAARDALAARGLAVEVTVDVQDGVRDEAALAELEAGAEAHGFAL
+WRHARLDDAELHAALRDADVSVLPYRVGTHSGWVEMCRDLGVPVAVAEVGHIADQARAWT
+TPELLAAFDPDDPASLADALAALLTAAPDARAAAPAARAAQRRRVAAAHVAVYRQALAVR
+RGTAATVSVLVITGHRDAHLARVLAGLERSHRRPDQVVVVFMGQPDGAVPATDLPVTVGH
+VAADHGLPLATARNRAAELATGEVLVFLDVDCIPAADTVGVLAAEVAAHPGSLVMGAPRY
+LAPDWTAALAAEGVDADAAPTDGDLRRHAVPHRARTHLRPGPSEEWALVWTLVMAIGAAD
+LARIDGFDEGFAGYGAEDTDLAFRARDAGLTLRISPAEAFHQHHGVHRPPLHHVADIVVN
+ARRFRTLHGTWPMGGWLAAFAERGLIRWDPDGDLLELVREPTPDDVAAARVDDAAY
+>4_1837
+MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPGAPAHQWWPPRALHAEWLAEHR
+PDVLHVHFGFEHFSPAQLAAALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGR
+ADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVAQGDDDAPGALPPDASDDGDGA
+AAPARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQDTVQDEDALAALR
+AGCAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAVADIG
+HIADQSGAWLSPDSLAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVAAAHV
+AVYREALARARGALPGVSVLVITGHRDEHLARVIAGLERSHRRPDQVVVVFMGQPDGRVP
+ATDLPITVGHVSAEAGLPLAQARNRAAELATGEILVFLDVDCIPAAETVGVLATEVAAHP
+GSVVMGRPRYLRPGWTRDVGEADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHLVWTL
+ILALRRADLARIGGFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMVPPLH
+HLEDILVNARRFRQVHGRWAMEGWLRAFADAGLIAWDPEGERLELLRHPTEAELTAARRG
+DAAY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001577.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001577.fa
new file mode 100644
index 0000000000000000000000000000000000000000..914d791e0522df58475734c5484cf965792c0b28
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001577.fa
@@ -0,0 +1,38 @@
+>0_1912
+MRISVLTHMLHPIRSPYEGGLEMHTAMTVEHLVRRGHDVTVYAREGTRVPGDVVAVLPAE
+GAGPGRAGARVREEAARRACALILDDDSDAVLNNSLSPAPLELLRARPVVTVLHTPATLA
+EVLAVVDAPGWTAPDHHRWASVSASNALAWQHRLPRVDVVPNGIELHQWVSDAVPVRGRA
+VWSGRITAEKGLHVAIDAARIAGMELHFAGPISDEEYHAREVVPRLGPDTVYHGHLDHHA
+LPHMLATGEVFLATPLWAEPFGLAVVEAMALGVPVAALLSGAMGEIVAPQAGALAVHHTA
+QELAVSIRHARRKDRGRVRAWACRFSAETMVEGYVDLLEQAAEDARDLAAAEDAYGFDPH
+GVPRPSADAADLESL
+>1_1617
+MRISVLTHMLHPIRSPYEGGLEMHTAMTVEHLVRRGHDVTVYAREGTRLPGDVVAVLPAE
+GAGPGRAGARVREAAARRACALILDDDSDAVLNNSLSPAPLELLRARPVVTVLHTPATLA
+EVLAVVDAPGWTAPDHHRWASVSASNALAWQHRLPRVDVVPNGIELHHWVSDAVPVRGRA
+VWSGRITAEKGLHVAIDAARIAGMELHFAGPISDEEYHAREVVPRLGPDTVYHGHLDHHA
+LPHMLATGEVFLATPLWAEPFGLAVVEAMALGVPVAALLSGAMGEIVAPQAGALAVHHTA
+QELAVSIRHARRKDRGRVRAWACRFSAETMVEGYVDLLEQAAEDARDLAAAEDAYGFDPQ
+GVPRPSADAADLESL
+>2_867
+MRISVLTHMLHPIRSPYAGGLEMHTAMTVEHLVRRGHDVTVYAREGTRLPADVVPVLPAE
+GAGPGKEGDRLREEATRRACEMVLADDSDAVLNNSLSPAPLELLRERPMITVLHTPATLA
+EVLAVVDHPDWRAPQHHRWASVSASNALAWQHRLPRVDVVPNGIELHHWVSDAVPVRGRA
+VWSGRITAEKGLHVAIDAARIAGMELHFAGPISDEEYHAREVVPRLGPDTVYHGHLDHQT
+LPHMLATGEVFLATPLWAEPFGLAVVEAMALGVPVAALLSGAMGEIVAPQAGALAVHHTA
+QELAVSIRHARRKDRGRVRAWACRFSAETMVEGYLDLLEQAAEDARDGELV
+>3_809
+MRIDVLTHPLHPIRSPYEGGLEMHTAMTVEHLVAAGHQVRVHARAGTRIPGADVVSLLAA
+APDAPGAEGQAVREGALAGACQRILADAPDAVLNNSLSPQPLIRLRSLPMLTVLHTPATL
+EPVLEVTDAPGWTPPAHHRWASVSVSNALAWRHRLPSVDVVPNGIDLDRWVSDRAPVPGR
+AVWSGRITPEKGLHMAIDAARAVGMELHAAGPVSDPAYYAERVAPRLGEDVVHHGHLDHT
+ALPDLLATGEVFLSTPLWAEPFGLATVEAMALGVPVAALLTGAMGEIVAPQAGALAVHHS
+VEALADAIRYARRKDRARVADWARRFSADTMVAGYLDLLEQAVADHADDAELRKVPA
+>4_1839
+MRISVLTHMLHPIRSPYEGGLEMHTAMTVEHLVRRGHDVTVYAREGTRLPGDVVAVLPAE
+GAGPGRAGARVREAAARRACALILDDDSDAVLNNSLSPAPLELLRARPVVTVLHTPATLA
+EVLAVVDAPGWTAPDHHRWASVSASNALAWQHRLPRVDVVPNGIELHHWVSDAVPVRGRA
+VWSGRITAEKGLHVAIDAARIAGMELHFAGPISDEEYHAREVVPRLGPDTVYHGHLDHHA
+LPHMLATGEVFLATPLWAEPFGLAVVEAMALGVPVAALLSGAMGEIVAPQAGALAVHHTA
+QELAVSIRHARRKDRGRVRAWACRFSAETMVEGYVDLLEQAAEDARDLAAAEDAYGFDPQ
+GVPRPSADAADLESL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001580.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001580.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a4ab73c1859301ca1b7dc3d7e3449496520a0238
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001580.fa
@@ -0,0 +1,54 @@
+>0_1918
+MSTAPTRVRLGMPTVRPVHGEGEILLNTPFPESAREQLGNGQMRANIRRATHTIRAKRAG
+VVEELPDWQELRAAGSALKQSVMADLPALLERLESEVTARGGVVHWARDAAEANRIITEL
+VTAKGVDEVIKVKSMATQEIGLDAALEHAGVAAVETDLAELIVQLGHDRPSHILVPAIHR
+NRREIRDIFRREMPDTDESLTSEPADLAEAARRHLREKFLSTKVAISGANFGVAETGTLS
+VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGV
+TEGDGPQEFHLVLLDNGRSAVLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPG
+PIGAILSPQLTGVDAGENGTLPYASTLCGACYDVCPVAIDIPSILIHLRDEDVQATHAAR
+KALRTEKDAAAGPLARAKAAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA
+GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRTALDGVAGLDRQEDEH
+VEEDGR
+>1_1623
+MSTAPTRVRLGMPTVRPVHGEGEVLLKTPFPESAREQLGNDQMRANIRRATHTIRAKRAG
+VVEELPDWQELRAAGSALKQSVMADLPALLERLESEVTARGGVVHWARDAAEANRIITEL
+VTAKGVDEVIKVKSMATQEIGLDAALEHAGVAAVETDLAELIVQLGHDRPSHILVPAIHR
+NRREIRDIFLREMPETDESLTSEPADLAEAARRHLREKFLSTKVAISGANFGVAETGTLS
+VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGV
+TEGDGPQEFHLVLLDNGRSAVLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPG
+PIGAILSPQLTGVDAGENGTLPYASTLCGACYDVCPVAIDIPSILIHLRDEDVQATHAAR
+KALRTEKDAAGGPLARAKTAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA
+GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRTALDGVAGLDRQEDEH
+VEEDGR
+>2_860
+MTRTALGMPAVRPAHGHGNIVLDEPFPSAARTQLGNAQMRANIHHATHTIRGKRARVVGE
+LPDWAELRQAGSALKQQVMADLPALLEQFEQRVTERGGVVHWARDAEEANRIITGLVKAK
+GVDEVIKVKSMATQEIDLEHALQAEGIAAVETDLAELIVQLGHDKPSHILVPAIHRNREE
+IREIFVREMPETDESLTSDPSALADVARVHLREKFLTTSVAISGANFGVAETGTLTVVES
+EGNGRMCLTLPETLITVMGIEKIVPTFQDLEVFLQLLPRSSTGERMNPYTSMWTGVTPGD
+GPQEFHLVLLDNGRSAVLSDPEGRPALHCIRCSACMNVCPVYEQTGGHAYGSVYPGPIGA
+ILSPQLTGVQEGANGSLPYASSLCGACYDVCPVAIDIPSILVHLRDQDVRATHARKKEET
+RVPLPSQMDLMMKGARTVMSSGTAMSLAERGLPLGRLAAGRDATLGWLPGIAGGWTDQRD
+VPSPPRQSFRNWWRGNAEHTEERVARDGGRRDVAAEDETTTTDGQEQR
+>3_796
+MSTAPTRVRLGMPTLRPVHGEGEILLKTPFPESAREQLGNGQMRANIRRATHTIRAKRAG
+VVGELPDWQELRAAGSALKQSVMADLPALLERLESEVTARGGVVHWARDAAEANRIITEL
+VTAKGVDEVIKVKSMATQEIGLDAALAQAGVAAVETDLAELIVQLGHDRPSHILVPAIHR
+NRREIRDIFLREMPETDESLTSEPADLAEASRRHLREKFLSTKVAISGANFGVAETGTLA
+VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGV
+TEGDGPQEFHLVLLDNGRSAVLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPG
+PIGAILSPQLTGVDAGENGTLPYASSLCGACYDVCPVAIDIPSILIHLRDEDVQATHAAR
+KALRTEGDGDAGPLARAKAAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA
+GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRTALDGVAGLDRQEDEH
+VEEDGR
+>4_1845
+MSTAPTRVRLGMPTVRPVHGEGEILLNTPFPESAREQLGNGQMRANIRRATHTIRAKRAG
+VVEELPDWQELRAAGSALKQSVMADLPALLERLESEVTARGGVVHWARDAAEANRIITEL
+VTAKGVDEVIKVKSMATQEIGLDAALEHAGVAAVETDLAELIVQLGHDRPSHILVPAIHR
+NRREIRDIFLREMPETDESLTSEPADLAEAARRHLREKFLSTKVAISGANFGVAETGTLS
+VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGV
+TEGDGPQEFHLVLLDNGRSAVLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPG
+PIGAILSPQLTGVDAGENGTLPYASTLCGACYDVCPVAIDIPSILIHLRDEDVQATHAAR
+KALRTDEDAAAGPLARAKAAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA
+GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRVAMDGVAGLDRPEDEH
+VEEDGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001592.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001592.fa
new file mode 100644
index 0000000000000000000000000000000000000000..676ada357691c0bba1a9310c1196ddb0a0f59dc0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001592.fa
@@ -0,0 +1,40 @@
+>0_1933
+MTNLESRQKTSSGFFVTKEVPIDPENPLPTPTSEAPDILRSASMELVVTDLAQSREFYVD
+VLGLVVTEEDEETVYLRSMEEFIHHNLVLRQGETAAVAAFSYRVRTPEDLDKAVAFYEEL
+GCRVERRKDGFVKGVGDSVRVEDPLGFPYEFFHDVEHVERLAWRYDLYTPGALVRLDHFN
+QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF
+ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD
+PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASRVLDLDGNLQPLVSRTDDSEMAVTIGAD
+GFSYTREGQGEESLPEWKQGEYKLGNQL
+>1_1638
+MTNLESRQKTSSGFFVTKEAPIDPENPLPTPTSEAPDILRCASMELVVTDLAASREFYVD
+VLGLVVTEEDEETVYLRSMEEFIHHNLVLRQGETAAVAAFSYRVRTPEDLDKAVAFYEEL
+GCRVERRKDGFVKGVGDSVRVEDPLGFPYEFFHDVEHVERLAWRYDLYTPGALVRLDHFN
+QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF
+ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD
+PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASRVLDLDGNLQPLVSRTDDSEMAVTIGAD
+GFSYTREGQGEESMPEWKQGEYKLGNQL
+>2_844
+MSNYAGRTRTSVGTYVGQEGPVKTDNPIPTPKAEAPDVLRCASMELVVTDLEKSRQFYVD
+VLDLVVTEEDEDTVYLRSMEEFIHHNLILRKGEIAAVAAFSYRVRTPEDLDKAVAFYTEL
+GCRVERNKDGFVKGVGDSVRVEDPLGFPYEFFYEVDHVERLAWRYDLYSPGALVRLDHFN
+QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVAF
+ATHEKHNILAICDKLGSLRMSDAIERGPGRHGVSNAFYLYLRDPDGHRVEIYTQDYYTGD
+PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASLVLDLDGNVKEVVARTDDSEMAVTIGAD
+GFSYTRAEEGEDSMPEYKKGEYKLGNQL
+>3_783
+MSNLESRKKTSSGFFVTEEAPITPANPLPTPKAEAPDILRCASMELVVTDLAASRHFYVD
+VLGLVVTEEDEETVYLRSMEEFIHHNLILRKGETAAVAAFSYRVRTPEDLDKAVAFYTEL
+GCRVERNKDGFVKGVGDSVRVEDPLGFPYEFFFETEHVERLAWRYDLYTPGALVRLDHFN
+QVTPDVPRAAKFMQDLGFRVTEDIQDEQGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF
+ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD
+PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASRVLDLDGNLQPLVARTDDSEMAVTIGAD
+GFSYTREDEGEESMPEYKQGEYKLGNQL
+>4_1860
+MTNLESRQKTSSGFFVTKEVPIDPENPLPTPTSEAPDILRCASMELVVTDLAASREFYVD
+VLGLVVTEEDEETVYLRSMEEFIHHNLVLRQGETAAVAAFSYRVRTPEDLDKAVAFYEEL
+GCRVERRKDGFVKGVGDSVRVEDPLGFPYEFFHDVEHVERLAWRYDLYTPGALVRLDHFN
+QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF
+ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD
+PDNPVVTWDVHDNQRRDWWGTPIVPSWYTDASRVLDLDGNLQPLVSRTDDSEMAVTIGAD
+GFSYTREGQGEESMPEWKQGEYKLGNQL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001595.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001595.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81e2d380732c485b4339357179ee9c0407f5f48b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001595.fa
@@ -0,0 +1,44 @@
+>0_1938
+MSHDVEAPAGVPGSVAVVGGGVAGFAVVRELRRRGFAGEIALVDPQGVPYDRPPLSKEFL
+TGDADARRLLLAPPTWFAEHGVELVEDAAVRVVPGGVHPDGGPAPHRVETASGRVLEADA
+VVLATGGRPRALDVAGADHPDLITLRTRSDAEALRDRLTFGAEVAVVGGGFTGAEVAAAA
+RRSLAAVTLVTGTDAPARAAVGPALAARLHRMHVEHGVAVEVGRAAWIEHRDADGGAALP
+AAHRLHLHDGRTVDADVVVLAGGTVPDTALAEDAGLEVADGVLTDAMGRTTVPGILAVGD
+AARARESAWATSRHWEPALRSGAAAAAALLGEQTDAPGAPWFWSDRYDAHVEAVGDMTVP
+AGGRIVDREVRGVVVASFALAADGTLRGAASIDDPMTVKAARRIIDRGIVVDAAALADPA
+VPVKSLARG
+>1_1643
+MSHDVEAPAGVPGSVAVVGGGVAGFAVVRELRRRGFAGGIALVDPQGVPYDRPPLSKEFL
+TGDADAHRLLLAPPAWFAEHGVELVEDEAVRVVPGGVHPDGGPAPHRVETASGRVLDADA
+VVLATGGRPRALDVAGADHPDLITLRTRADAEALRDRLTFGAEVAVVGGGFTGAEVAAAA
+RRSLAAVTLVTGTDAPARAAVGPALAARLHRMHAEHGVAVEVGRAAWIEHRDADGGAALP
+AAHRLHLHDGRTVDADVVVLAGGTVPDTALAEDAGLEVADGVLTDAMGRTTVPGILAVGD
+AARARESAWAPSRHWEPALRSGAAAAAAILGEEADAPGAPWFWSDRYDAHVEAVGDMTVP
+AGGRIVDREVRGTVVASFALAADGTLRGAASIDDPMTVKAARRIIDRGIVVDAAALADPA
+VPVKSLARG
+>2_839
+MSGDVDARAGAPASVVVVGGGVAGFGAVRELRRRGHTGSLALVEPQGVPYDRPPLSKDYL
+TGETDAHRLLFAPPSWFAEHDVELVEEAAVRLTPGGAHPDGDPVPHRVELASGRVLEAEA
+VVLATGGRPRPLDVEGATHPDLITLRTRADADALRERLHFGAEVAVVGGGFTGAEAASSA
+RQALAGVTLVTATDAPALRAVGPALAARLHRMHAEHGVAVEVGRVARIEHRDDDGGAALP
+AAHRLHLGDGRTVDADVVVLAGGTVPDTALAEEAGLEVADGILVDEAGRTSVPGILAVGD
+TARATGSAWGPSPHWEPALRSGAAAAAALLGEEPEPPGAPWLWSDRHGCHVEAVGDMAVP
+PGGASVDREARGAAVASFVLDAEGRMRGAASIDDPMTVKAARRIIDRGIVVDPQALADPT
+VPLKSLARG
+>3_776
+MTVPASVLVVGGGVAGFGTVRELRRRGFEGKLTLVDPQGLPYDRPPLSKDFLTGETDAHR
+LLFAPPAWFAEHAVELVTARVDRMDLTGEHPAAVLDDGTVRAADAVVLAPGGRPRPLDVP
+GGDRPGVLVLRTRADAEAIAARLHFGARVVVVGAGLTGSEVASAAREAMAEVTLVSASPA
+PAAAAVGPALAARLHALHAARGVDVVQGRVLRIEHADDAPGLDAPHRVHVALADGGEAAL
+DADLVVAAVGILPDAALAAEAGLELAVDGGILVDAAQRTSDPRVLAVGDAARRRDAAYAA
+PAMHWEPALQDAADAAAALLGEDLPERGAPWFWSDRHGVHVEGVGAMRPPEGGRIVDREV
+RGTVVASFALAADGAMVGAASVDDPMAVKAARRIVDRGIVVDPERLADPSVPVKALLRG
+>4_1865
+MSHDVEAPAGVPGSVAVVGGGVAGFAVVRELRRRGFAGGIALVDPQGVPYDRPPLSKEFL
+TGDADAHRLLLAPPAWFAEHGVELVEDEAVRVVPGGVHPDGGPAPHRVETASGRVLDADA
+VVLATGGRPRALDVAGADHPDLITLRTRADAEALRDRLTFGAEVAVVGGGFTGAEVAAAA
+RRSLAAVTLVTGTDAPARAAVGPALAARLHRMHAEHGVAVEVGRAAWIEHRDADGGAALP
+AAHRLHLHDGRTVDADVVVLAGGTVPDTALAEDAGLEVADGVLTDAMGRTTVPGILAVGD
+AARARESAWAPSRHWEPALRSGAAAAAAILGEEADAPGAPWFWSDRYDAHVEAVGDMTVP
+AGGRIVDREVRGTVVASFALAADGTLRGAASIDDPMTVKAARRIIDRGIVVDAAALADPA
+VPVKSLARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001596.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001596.fa
new file mode 100644
index 0000000000000000000000000000000000000000..621f2dd4391d1e9db1712a3c6ef4a24bb985376f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001596.fa
@@ -0,0 +1,15 @@
+>0_1939
+MAEPIHIGAAADVPEGEAIVVPAATAGTRDDVAVFHTDAGEFHAIDDTCTHEDASLAEGW
+LEDDRVECPLHAAQFCLRTGEALCLPATKGVGVHRVEEREGQLYLVPGA
+>1_1644
+MAEPIHIGAAADVPEGEAIVVPAATAGTRDDVAVFHTDAGEFHAIDDTCTHEDASLAEGW
+LEDDRVECPLHAAQFCLRTGEALCLPATKGVGVHRVEEREGQLYLVPGA
+>2_838
+MAEPIHIGAAADIPEGEAVVVPAATAGTSDDVAVFHAEDGAFYAIDDTCTHEDASLAEGW
+LEGTQVECPLHSAQFCLKSGEALCLPATRPVGTHPVQERDGQLYLTPGA
+>3_775
+MSREINVGPASAVPEGESLLVPNDTTGTKDHIGVFHAEDGAFYAIDNTCTHQDYALSEGF
+VEDCRVECPLHGASFDLRTGEALSLPATKPVGTHRVEERDGDLWLTVEDGE
+>4_1866
+MAEPIHIGAAADVPEGEAIVVPAATAGTRDDVAVFHTDAGEFHAIDDTCTHEDASLAEGW
+LEDDRVECPLHAAQFCLRTGEALCLPATKGVGVHRVEEREGQLYLVPGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001605.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001605.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f39317a26831c067dd35f17bd40b1ead67692ddb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001605.fa
@@ -0,0 +1,40 @@
+>0_1951
+MTETTDAPTTGKRRATFNTLEVSELRRLTEDSVEVTFAVPEELADDYDYVPGQYVALRKE
+LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGTFSTWANESLEVGEKIDVMNPQGAFTSRT
+HVTSLNDAQKVAAEKVAEKKDTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS
+AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD
+EWFLCGPFELVQLTRETLAARGVPEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI
+EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA
+LEKDEVEKGYVLTCQTRPTSDSITLDFDA
+>1_1672
+MTETTDVPTTGKRRATFNTLEVSELRRLTDDSVEITFAVPEELADDYDYVPGQYVALRKE
+LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGKFSTWANESLEVGEKIDVMNPQGAFTSRT
+HVTSLNDAQKVAAEKVAEKKDTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS
+AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD
+EWFLCGPFELVQLTRETLAARGVSEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI
+EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA
+LEKDEVEKGYVLTCQTRPTSDSITLDFDA
+>2_811
+MTETTVTPATGKRRATFNTLEVSELRRLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE
+LDGQEVRRSYSICAIPKRGEIRVAVKKDIGGKFSTWANEVLEVGEKIDVMNPQGAFTSRS
+HVTSLNDAEKVAAEKVAQNKNTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS
+AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDAEKLTTLLDRVIDVDGTD
+EWFLCGPFELVQLARETLSARGVDEDDVRFELFTTGRPENPQGHSGRVVEADPSGDNVTI
+EFNLDGLSGKVESPKSAHETILNAALRVRSDVPFACAGGVCGTCRAKVTDGEYEMDENYA
+LEKDEVEAGYVLTCQTRATSDSITVDYDA
+>3_749
+MTETTDAPITGKRRATFNTLEVSGLRKLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE
+LDGAELRRSYSICAVPQRGEIRVAVKKDLGGTFSTWANEVLEVGEKIDVMNPQGAFTSRT
+NVTSMNDPEAVAAEAVKQDQTHLVALAAGSGITPIMAIAKSVLAASDSARFDLIYANRSA
+MDVMFAEEIGDLKDKYPARFTVNHVLSREQRVAPLLSGRIDDEKLNTLLDRVIDVENTDE
+WFLCGPFELVQLARDTLSERGVAEDDVRFELFTTGKPEAPQGQSGRGVEADPSGDNVTIE
+FNLDGLSAKVESPKSAHETILNAALRVRSDVPFACAGGVCGTCRAKVTEGEFTMEENYAL
+EKDEVEQGYVLTCQTRPTTDSIKVDFDA
+>4_1890
+MTETTAAPTTGKRRATFNTLEVSELRRLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE
+LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGKFSTWANESLEVGEKIDVMNPQGAFTSRT
+HVTSLNDAQKVAAEKVAENKDTHLVAFAAGSGITPIMAIAKAVLAASESSRFDLVYANRS
+AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD
+EWFLCGPFELVQLTRETLAARGVSEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI
+EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA
+LEKDEVEKGYVLTCQTRPTSDSITLDFDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001607.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001607.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f17d7303fa7946de784cb41148360f422cb47665
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001607.fa
@@ -0,0 +1,40 @@
+>0_1955
+MSAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTVKAVIEDAGIDPSVVDDVILGNAN
+GAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAGGVE
+SMSRAPWVMEKPTTAFAKPGAAFDTAIGWRFVNPRFADGEFGEKFTFSMPETAEEVGEVD
+GITREDADAFAARSHERALAAIEAGRFADEIVPVVVTGRKGAETVVDTDEGPRPGSTPEV
+LASLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLAPEI
+MGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAIALG
+HPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVERV
+>1_1675
+MSAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTIKAVIEDAGIDPSVVDEVILGNAN
+GAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAGGVE
+SMSRAPWVMEKPTTAFAKPGAAFDTAIGWRFVNPRFADGEFGEKFTFSMPETAEEVGEVD
+GITREDADAFAARSHERALAAIEAGRFADEIVPVVVTGRKGAETVVDTDEGPRPGSTPEV
+LASLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLAPEI
+MGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAIALG
+HPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVEKV
+>2_787
+MTTPSPQPQALLVGGKRTAVGRYGGALSAVRPDDLAALTIKQVIEDAGIDPAAVDEVILG
+NANGAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAG
+GVESMSRAPWVMEKPTTAFAKPGAAFDTSIGWRFVNPRFADGEFGEKFTFSMPETAEEVG
+EVDGITREDADAFAARSHGRAIAAIEAGRFKDEIVPVTVKGRKGAETVVDTDEGPRPGST
+PEVLAGLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLA
+PEIMGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPEIVNADGGAI
+ALGHPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVEKV
+>3_746
+MSAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTVKAVIEDAGIDPSVVDDVILGNAN
+GAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAGGVE
+SMSRAPWVMEKPTTAFAKPGAAFDTSIGWRFVNPRFADGEFGEKFTFSMPETAEEVGEVD
+GITREDADAFAARSHERALAAIEAGRFADEIVPVVVTGRKGAETIVDTDEGPRPGSTPEV
+LAGLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLAPEI
+MGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAIALG
+HPLGSSGSRLVVTLLGRMEREGADKGLATMCVGVGQGSAMLVEKV
+>4_1893
+MSAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTIKAVIEDAGIDPSVVDEVILGNAN
+GAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAGGVE
+SMSRAPWVMEKPTTAFAKPGAAFDTAIGWRFVNPRFADGEFGEKFTFSMPETAEEVGEVD
+GITREDADAFAARSHARALAAIEAGRFADEIVPVVVTGRKGAETIVDTDEGPRPGSTPEV
+LAGLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLAPEI
+MGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAIALG
+HPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVERV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001608.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001608.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0845a156f144036f76d1050d80d82ca78962ff9b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001608.fa
@@ -0,0 +1,30 @@
+>0_1956
+MTDFSHFSALHVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESTREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRLSKRVFHLPRGAHPHVDEIAQA
+ILFESDAKFERMQAFLDRKKK
+>1_1676
+MDDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESKCEPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPEALLDAADALADRIAQQDPLAVRLSKRVFHLPREAHPHVDEIAQA
+ILFESEAKFERMQAFLDRKKK
+>2_786
+MTDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESKREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPEALEVAAHALADRIAKQDPLAVRISKRVFHLPREAHPHVDEIAQA
+ILFESEAKFDRMQAFLDRKKK
+>3_745
+MADFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESKREPGRFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETGLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRISKRVFHLPREAHPHVDEIAQA
+ILFESQAKFERMQAFLDRKKK
+>4_1894
+MTDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESTREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRLSKRVFHLPREAHPHVDEIAQA
+ILFESEAKFERMQAFLDRKKK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001613.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001613.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af3994f5d090cbc7e994dcbaa64cfacf9140de26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001613.fa
@@ -0,0 +1,65 @@
+>0_1962
+MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHART
+VGQQALGALTIHERALKLKELALYLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTF
+SGKGRRELPNSNVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP
+AFVAGVPTVVKPATPTGYVAQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF
+TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK
+AGQKCTAIRRVIVPQDRVEAVTAALTERLAAKVVLGDPRVEGTTMGALASKEQQGEVRGA
+VQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFEDARTPEVHSVEAFGPVTSVIG
+YTDVADAVALAALGSGSLVATVATNDGETARAFAAGIGAHHGRVHVLNRQTATTTTGHGA
+PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRE
+DVEAGTAVHPFYKSLAELTVGDQFASGLRTVTLEDITAFAEETGDRFYAHTDEEAAMANP
+FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITP
+RVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG
+>1_1682
+MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHART
+VGQQALGELTIHERALKLKELALFLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTF
+SGKGRRELPNSTVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP
+AFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF
+TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK
+AGQKCTAIRRVIVPQDRVEAVTAALTERLAAKVVLGDPRVEGTTMGALASKDQQGEVRGA
+VQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFEDARTPEVHSVEAFGPVTSVIG
+YTDVADAVALAALGSGSLVATVATNDGETARAFAAGIGAHHGRVHVLNRQTAATTTGHGA
+PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRE
+DVEAGTAVHPFYKSLAELTVGDQFASGLRTITLEDITAFAEETGDRFYAHTDEEAAMANP
+FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITP
+RVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG
+>2_778
+MTVTLPSLPEILPSYVNGAWWTPQSPSKVTDVTDANTGERLTGVSTDGLDTAAAIEHART
+VGRKSLGELTIHERALKLKELALYLNSRIQELYDVSFATGATQRDHAFDVDGGIGTLFTF
+SGKGRRELPNSNVITDGPVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP
+SFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSLQLISGSARDLLDHLDYRDHVSF
+TGSAATAQTLRKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK
+AGQKCTAIRRVIVPQDRVDAVVEALSARLGKVVLGDPRVEGTTMGALASKEQQGEVRGAV
+QRLVDAGGQVRLGGPDASTGDADAESGAFFAPTVLSFEDARTPEVHAVEAFGPVTSVVGY
+TDVEDAVALAALGSGSLVATVATDDGETARAFAAGIGAHHGRVHFLNRQTATTTTGHGAP
+VPVLVHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRED
+VEAGTAVHPFYKSLAELTVGDQFASGLRTVTLQDITDFAEETGDKFYAHTDEEAAMANPF
+FPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITPR
+VSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG
+>3_739
+MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGELMARVSTDGIDTAGAIEHART
+VGQRNLGELTIHERALKLKELALYLNSRIQELYDLSFATGSTQRDHAFDVDGGIGTLFTF
+SGKGRRELPNSNVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP
+AFVAGVPTVVKPATPTGYVTEACVRMMVESGVLPEGSIQLISGSARDLLDHLDYRDHVAF
+TGSAGTAQTLRQHENVLNGGVRFTAETDSLNAAILGPDAGVDTPEFEAFVKVVFQEMTVK
+AGQKCTAIRRVIVPEAMVEDVTAALTERLSSTVVLGDPRAEGTTMGALASKEQQSEVRKA
+VQTLVDAGGQVRLGGPEGSTGDADAEAGAFFAPTVLTFADADTPQVHSVEAFGPVTSVIG
+YTDVADAVRLAALGSGSLVATLATNDGATASEFIAGIGAHHGRVHVLNRQTAKTTTGHGA
+PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAVQGSPDMLTAITGVWHQGAAAQTATRE
+DVEAGKAKHPFYKALDELQIGDQFASGLRTVTIEDITAFAESTGDKFYAHTDEEAAMANP
+FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLDDLRFITPVTYDDAIRVTLTAKRITP
+RVTDEYGEVAWDCRLHNQKDELVAQYDVLTLVAKTWPMPEAEPKA
+>4_1900
+MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHART
+VGQQALGALTIHERALKLKELALYLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTF
+SGKGRRELPNSTVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP
+AFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF
+TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK
+AGQKCTAIRRVIVPQDRVEAVTAALTERLAAKVVLGDPRVEGTTMGALASKEQQSEVRGA
+VQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFEDARTPEVHSVEAFGPVTSVIG
+YTDVADAVALAALGSGSLVATVATNDGETARAFTAGIGAHHGRVHVLNRQTATTTTGHGA
+PVPVLVHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRE
+DVEAGTAVHPFYKSLAELTVGDQFASGLRTVTLEDITAFAEETGDRFYAHTDEEAAMANP
+FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITP
+RVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001615.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001615.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c8f98d4418db20c008ec2d1d9dc2e88273e9acb3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001615.fa
@@ -0,0 +1,33 @@
+>0_1964
+MTTSRLPLLGALAVGALALAGCAGGGAEPSSPAPSSASSTTTAASSASPAASSSTAPTSP
+AASASTASMGGASASGSLSLEMPPALDGQRTLAVQAAVQRAAGPGSEVGLSAASPLERQT
+ELRQRAAGLEQTVDAGASPASTRSAEQQACLDATRSDLERDAEAGAADLGLTAQPETAAT
+TGGGPTSTPVPSFTASPDAEVTPLGVRVTVYPTEEAARAALEDARAAAQACTGVDLAGLG
+VESVTRTEHEGGTAYTALPAPGGSVYSHLTAVQDGARTVAVAQADADGGVPADAEDRAAS
+IVADVLAALDGEG
+>1_1684
+MTTSRLPLLGALAVGALALAGCAGGGGAEPSSPAPSSASSTTTAASSAPTSPAASSSTES
+TGAAESTAGASASGSLSLEMPPALDGQRTLAVQAAVQRAAGPGSEVGLSAASPLERQTEL
+RQRAAGLEQAVDAGASPASTRSAEQQACLDATRSDLERDAEAGAADLGLTAQPETAATTG
+GGPTTTPAPSFTASPDAEVTPLGVRVTVYPTEEAARAALEDARAAAQACTGVDLAGLDVE
+SVTRTEHEGGTAYTALPAPGGSVYSHLTAVQDGARTVAVAQADADGGVPADAEDRAASIV
+ADVLAALDGEG
+>2_776
+MTPSRLPLLGVLAVGALALAGCAGGGAEPSSPAPSPASSSASPTTTAASSASTSPAASAS
+ASSTPTATALSLDLPEELSGESATRLRAVVQDAAGPAAELGQTFSSPLERRAALEEDAAI
+VDALEEDAGDDAGRRACVDATRAAREADQASGAAQAAWYAQPQTASTTGGSTDGTAASGR
+PGLQVEPLGVQVAVYPDEATARSVAEAARDAAEACEGQEMSSMGVSSVEPLTGAPGETAF
+TVVPVSGSIIYAVSTVVQVGDRVYAVSQGEDGAGVPEGAEERAVALVEDLEAALEG
+>3_738
+MTHMTAVPSRRLRAGFALGAAALVLTGCAGGGGSASSSTAAGSPTAGGAGSSVTSPAASS
+SAASSSALSLSMPDRFGNEARTGLTEAVTAAAPEGFEVTTRSVSPLERKTDLEDQATILT
+DGPLEPAAEGSSASPTYTEAQQRCADAAAERFRTEAAAGGAQLRSDAMPTVAGGGYTSVR
+ADVVAYPDVSAAVAALADGSAPIELCTDVQVPGAEQPTDIAPVTGIGDEAVGGELAGGRW
+LAVRRGTDVVSVMVAGPGETAPAGAADQARALAEQVLEAVPAG
+>4_1902
+MTTPRLPLLGALAVGALALAGCAGGGGAEPSSPAPSSASSTTTAASSASTSPAASSSTAP
+TSPAASASTESTAGASASSSLSLEMPPALDGQRTLAVQTAVQRAAGPGSEVGLSAASPLE
+RQTELRQRAAGLEQAVDAGASPAPTRSAEQQACLDATRSALERDAEAGAADLGLTAQPET
+AATTGVGPTTTPAPSFTASPDAEVTPLGVRVTVYPTEEAARAALEDARAAAQACTGVDLA
+GLGVESVTRTEHEGGAAYTALPAPGGSVYSHLTAVQDGARTVAVAQADADGGVPADAEDR
+AASIVTDVLAALDGEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001626.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001626.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb698e3c5eeb5a5b0bfa850d48fe1c2b9e3799d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001626.fa
@@ -0,0 +1,79 @@
+>0_1992
+MASPSPASAHPSAPESGTGLGFTGVEGITGLTASEVAEREAAGLVNVQSRDTSRSLGQIL
+RVHVFTLFNLAIALCAVVVILMGRWLDLLFSLAAVANVVIGVVQEYSAKRKLDRIALLHQ
+DDVLVIRDGARVPLPMAQIVRDDVVVLRRGDQVPVDGEVLVSDGLDMDEALLTGENDPVP
+KTPGDAVLSGSAVVAGAGLVRATAVGSASHAARLSAEARRYSAIHSELRGALEKVARWLT
+IALVPIIAVIVHGQMTAVGGWSLALSQPREAALEPALIASVAAVTSMIPQGLALMTTIAF
+AVSALKLAQQEVLIQEQPAVEVLARVDTVCLDKTGTLTEGGVRFDRLAAPASADASPDAH
+DDGAPAEVGDGARAVLAWFGADPDVNPTAAALREPFTAVPAVDPAAQVAFSSARRWSAVA
+FGPEAGAAAGTWLLGAPEALVDERLLGPDAAEAVRAQVHADADAGRRVLLLARTDEPLIG
+DALPAGGVPVAVVTFRENVRPDAAETLGYFHAQGVRAVVISGDSPRTVAAVAREVGLEVA
+GQAYDGRTLPDDPDALADVMEEHSVFGRVSPDQKKAMVQALQSRGHVVAMTGDGVNDALA
+LKTADLGIAMGNAAPATKAVSRMVLLDGRFDRLPRVLGEGRQVIANMERLAHIYLTKTTY
+ALLFGVVFSLFAWQFPLLPRQASTVDFIMIGAPTFFLALLPNPRRYVPGFLGRALRFAIP
+SGAVILLSMVALQTYVRLTAGDVDLARQQAAFMITLTLVGLWVLSVMSRPLSARVVVLIL
+AMYAVLAAVVLVPVSRWYHQMEVPPTDVLVAALVIAAVGCGLIELIHQVHRRHVARMLAA
+AGA
+>1_1709
+MASPSPASAHPSAPESGTGLGFTGAAGITGLTAAEVAEREAAGLVNVQSRDTSRSLGQIL
+RVHVFTLFNLAIALCAVVVILMGRWLDLLFSLAAVANVVIGVVQEYSAKRKLDRIALLHQ
+DDVVVIRDGARVPLPMARIVRDDVVVLRRGDQVPVDGEVLVSDGLDMDEALLTGENDPVP
+KTPGDAVLSGSAVVAGAGLVRATAVGSASHAARLSAEARRYSAIHSELRGALEKVARWLT
+IALVPIIAVIVHGQMTAVGGWSLALSQPREAALEPALIASVAAVTSMIPQGLALMTTIAF
+AVSALKLAQQEVLIQEQPAVEVLARVDTVCLDKTGTLTEGGVRFDRLTAPASADASPDAH
+DDGAPAEVGDGARAVLAWFGADPDVNPTAAALREPFTAVPAVDPAAQVAFSSARRWSAVA
+FGPEAGAAAGTWLLGAPEALVDERLLGPDAAEAVRAQVHADADAGRRVLLLARTDAPLIG
+DALPAGGVPVAVVTFRENVRPDAAETLDYFHAQGVRTVVISGDSPRTVAAVAREVGLEVA
+GQAYDGRTLPDEPGELAAVMAEHDVFGRVSPDQKKAMVQALQSRGHVVAMTGDGVNDALA
+LKTADLGIAMGNAAPATKAVSRMVLLDGRFDRLPRVLGEGRQVIANMERLAHIYLTKTTY
+ALLFGVVFSLFAWQFPLLPRQASTVDFIMIGAPTFFLALLPNPRRYVPGFLGRALRFAIP
+SGAVILLSMVALHAYVRLTAGDVDLARQQAAFMITLTLLGLWVLSVMSRPLSARVVVLIL
+AMYAVLAAVVLVPASRWYHRMEVPPTDVLVAALVVAALGCGLIEVIHQVHRRHVARVLAA
+AGA
+>2_751
+MTPPAPAPPPAAAPGALSGVSGLTSAEVAEREAAGLTNRQSKDTSRSLAEILRVHVLTLF
+NLAIALCAVVVISLGRWLDLLFSLAAIANVVIGVVQEYSAKRKLDRIALLHQDDAVVVRD
+GARVSLPMARIVRDDVVVLRRGDQVPVDGEVLASDGLDLDEALLTGENDPVPKAPGDAVL
+SGSSVVAGTGLMRATAVGPASHAARLSAEARRFSAIRSELRGALEKVARWLTIGLVPIIA
+VIVHGQMTAVGGWAHALAQPREAALEPALIASVAAVTSMIPQGLALMTTIAFAVSALKLA
+QHEVLIQEQPAVEVLARVDTVCLDKTGTLTEGGVRFHELLAPASASPSTSTSTDDDGAPA
+DVDAAARAVLAWFGADPDANPTAAALHEPFADAPPHEPADHVAFSSARRWSAVAFGPEVG
+AATGTWLLGAPEALLGDADARPGEAGTGRDDVAAVRAQADALSDEGLRVLLLARTDAPLA
+GNALPAGRVPAAVVTFRENVRPDAAETLGYFHAQGVRTVVISGDSPRTVAAVAREVGMDV
+PGHARDGRTLPEDPEALADVMAEHDVFGRVSPDQKKAMVAALQSRGHVVAMTGDGVNDAL
+ALKTADLGIAMGNAAPATKAVSRMVLLDGRFDRLPAVLGEGRQVIANMERLAHIYLTKTT
+YALLFGVVFSLLAWQFPLLPRQASTVDFIMIGLPTFFLALLPNPRRYVPGFLGRALRFAI
+PSGVVILLSMVALQVYVRLAADHVDLAQQQTAFMITLTLVGLWVLSVMSRPLTRRVVLLV
+LAMYAVLAAVVLVPASRWYHQMEVPPADVLVAALVIAAVGCALIELIHQVHRRHVARVLA
+AAGA
+>3_116
+MTHTPPSPAPAADAGPAALAGLTSAQVAERVAAGRVNVQPKDTSRSFGTILRSHVLTLFN
+LVIALCATVIVVLGRWFDLLFSLAAVANVVIGVVQENSARRALDRIALLHQDGVLVVRDG
+ARREVRIEEVVLDDVVVLRRGDQVPVDGAVLTSEGLDVDESLLTGESDPVPKAPGDAVLS
+GSAVVAGTALVRATAVGADSHAAKLAVQARRFTRAHSELRAALEKVARWLTIALVPIVAV
+ILHGQVTAAGGWSRVLGSEDQPALEAALVATVAAVTAMIPQGLALMTTISFALAALKLAR
+RAVLIQEQPAVEILARVDTVCLDKTGTLTEGGIVFHGAHAPVGAPALPHDDDAAVALDPG
+ARAVLAWFGADPDANPTAAALREPFPAAPASSPTGVVPFSSVRRWSAVTFGPDADAAHPG
+MAGTWLLGAPEALADAAHLGPERTAALTEACTAPADRGLRTVLLCRASDAPAGETLPAGR
+EPVAVLTFAEDVRPDAAQTLGYFREQGVAVKVISGDSPRTVAAVARAVGMEVPGDAVDGR
+TLPADPAELADVLESHEVFGRVAPEQKQAMVAALQSRGHVVAMTGDGVNDALALKTADLG
+IAMGNAAPATKAVSRMVLLDGRFDRLPDVLREGRQVIANMERLAHIYLTKTSYALLFGLV
+FSLLAWPFPLLPRQASTADFLMIGAPTFFLALLPNPRRYVPGFLRRALLFAVPAGVTIVA
+AMLAVSWYARHLSSKPVDTAQLQTASLITLTLLGLWVLTCISRPLRPLMCGVVAGMYALL
+AAAVLVPASRWYHQMELPAPDLLAASLAIALGGCVVVEAVHRIHHARVTVPGRRAAEG
+>4_1927
+MASPSPASAHPSAPESGTGLGFTGVAGITGLTAAEVAEREAAGLVNVQSRDTSRSLGQIL
+RVHVFTLFNLAIALCAVVVILMGRWLDLLFSLAAVANVVIGVVQEYSAKRKLDRIALLHQ
+DDVVVIRDGARVPLPMAQIVRDDVVVLRRGDQVPVDGEVLVSDGLDMDEALLTGENDPVP
+KTPGDAVLSGSAVVAGAGLVRATAVGSASHAARLSAEARRYSAIHSELRGALEKVARWLT
+IALVPIIAVIVHGQMTAVGGWSLALSQPREAALEPALIASVAAVTSMIPQGLALMTTIAF
+AVAALKLAQQEVLIQEQPAVEVLARVDTVCLDKTGTLTEGGVRFDRLTAPASADASPDAH
+DDGAPAEVGDGPRAVLAWFGADPDVNPTAAALREPFTAVPAVDPVAQVAFSSARRWSAVA
+FGPEAGAAAGTWLLGAPEALVDEWHLGPDAAEAVRAQVHADADAGRRVLLLARTDEPLIG
+EALPAGGVPVAVVTFRENVRPDAAETLDYFHAQGVRTVVISGDSPRTVAAVAREVGLEVA
+GQAYDGRTLPEDPGALADVMAEHDVFGRVSPDQKKAMVQALQSRGHVVAMTGDGVNDALA
+LKTADLGIAMGNAAPATKAVSRMVLLDGRFDRLPRVLGEGRQVIANMERLAHIYLTKTTY
+ALLFGVVFSLFAWQFPLLPRQASTVDFIMIGAPTFFLALLPNPRRYVPGFLGRALRFAIP
+SGAVILLSMVTLQTYVRLTAGDVDLPRQQAAFMITLTLLGLWVLSVMSRPLSARVVVLIL
+AMYAVLAAVVLVPASRWYHQMEVPPTDVLVAALVIAALGCGLIEIIHQVHRRHVARVLAA
+AGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001628.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001628.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b478a3ffbd298f808c28d38f941d9c9f9af1ee2f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001628.fa
@@ -0,0 +1,25 @@
+>0_1995
+MLSLYIHGDSPLHHARAGLKTGLFAVWVLALTLLPLSRWTAGAAVVGAVTAYLVGFGLRR
+GAAMIASDLHALWLFYVVLFAAQWIFTDAFAAGLMVARVLGLVLTAQVLTRTTRIADMAG
+VAEAMLRPVERIPWAGPRLARAGFRADRVGLAMGLVLSSIGHLRALAEQIRHAQAARGVR
+MAPWAWALPLLVLSFKHADDVGDALAARGID
+>1_1712
+MLSLYIHGDSPLHHARAGLKTGLFAVWVLALTLLPLSLWTAGAAVVGAVTAYLVGFGLRR
+GAAMIASDLRALWLFYVVLFAAQWIFTDAFAAGLMVARVLGLVLTAQVLTRTTRIADMTG
+VAEAVLRPVERIPWAGPRLARAGFRADRVGLAMGLVLSSIGHLRALAEQIRHAQAARGVR
+MAPWAWALPLLVLSFKHADDVGDALAARGID
+>2_746
+MISLYVPGDSPLHRAPAGLKLALFAAWALAVTLAPPTPWTAGAAVGMALAAYLTGFGPRR
+GAAMLGRDLRALWVFYAFLFAAQWLFADLTAAALMVGRVLGLVLAAQVLTRTTRIAELVG
+VAEAVLAPVERIPWLGPRLARVGLRPERVGLAMGLVLASIGHLRSVAEQVRQAQASRGVR
+MAPWAWVLPLLVLSVKHADDVGDALAARGIE
+>3_710
+MLSLHVPGDSPLHRCPAGAKVAALAVWALVVTLAPVSALTAGASVVVGVGAYLLGFGLRR
+GVRLLAADLRGLWVFYAVLFAAQWLFTDLPTAALTTARVLGLVLAAQVLTRTTRIAEMAG
+VAEAVLGPVTRIPWLGPRLARAGVRPDRVGLAMGLVLASVGHLRGLAEQIRAAQAARGVR
+MAPWAWVLPLLVLSLKHADDVGDALAARGID
+>4_1930
+MLSLYIHGDSPLHHARAGLKTGLFAVWVLALTLLPLSLWTAGAAVVGAVTAYLVGFGLRR
+GAAMIASDLRALWLFYVVLFAAQWIFTDAFAAGLMVARVLGLVLTAQVLTRTTRIADMTG
+VAEAVLRPVERIPWAGPRLARAGFRADRVGLAMGLVLSSIGHLRALAEQIRHAQAARGVR
+MAPWAWALPLLVLSFKHADDVGDALAARGID
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001632.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001632.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b47b5d369af1948c9e0d879281b24c33d3903de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001632.fa
@@ -0,0 +1,29 @@
+>0_2019
+MNLDQLQALRAIADEGSFEAAAYELDVSASAVSQRIRALEREVGQVLLRRGTPCEPTEAG
+IGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPADVLGTWFGPVLAEAADWEDTVLD
+LHVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAGPLGSMRYVPLASPALLARHAADDVV
+DLGAMPMMRYNAKDDLQRLALSGAGLDIAPPTHLAPSFDGFHRSVRAGLGWGMLVDAQAV
+EDVRAGRLVRVPGLDDVLVPLYWQAATLPVTRLVRLTRAVREAAQRTLERG
+>1_1734
+MPKLCFMNLDQLQALRAIADEGSFEAAAYELGVSASAVSQRIRALEREVGQVLLRRGTPC
+EPTEAGVGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPADVLGTWFGPVLAEAADW
+DDTVLDLHVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAEPLGSMRYVPLASPALRARH
+AAGDVVDLGAMPMMRYNAKDDLQRLALSGAGLDVAPPTHLAPSFDGFHRSVRAGLGWGML
+VDAQAVEDVRAGRLVRVPGLDDVLVPLYWQAATLPVTRLVRLTRAVREAAQRTLERG
+>2_686
+MNLDQLQVLLRRGTPCEPTEAGVGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPAD
+VLGTWFGPVLAEAADWDDLVLDLHVEDQDHSAQLLRRGEVLAAVTTEPQPVQGCAAEPLG
+SMRYVPLVAPALLARHAAGDVVDLGAMPMMRYNVKDDLQRLALSDAGLDVAPPTLPVTRL
+VRLTRAVREAAQRTLEPG
+>3_597
+MNLDQLQALRAIADEGSFEAAAYELGVSASAVSQRIRALEREVGQVLLRRGTPCEPTEAG
+VGLVRVARHMRVLEQEAWAGLGRMAAGRSVTSLAVPADVLGTWFGPVLAEAADWDDTVLD
+LRVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAEPLGSMRYVPLASPALLARHAAGDVV
+DLGAMPMMRYNAKDDLQRLALSGAGLDVAPPTHLAPSFDGFHRSVRAGLGWGMLVDAQAV
+EDVRAGRLVRVPGLDDVLVPLYWQATTLPVTRLARLTQAVREAAQRTLERG
+>4_1958
+MPKLCFMNLDQLQALRAIADEGSFEAAAYDLGVSASAVSQRIRALEREVGQVLLRRGTPC
+EPTEAGVGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPADVLGTWFGPVLAEAADW
+DDTVLDLHVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAEPLGSMRYVPLASPALLARH
+AAGDVVDLGAMPMMRYNAKDDLQRLALSGAGLDVAPPTHLAPSFDGFHRSVRAGLGWGML
+VGAQAVEDVRAGRLVRVPGLDDVLVPLYWQAATLPVTRLVRLTRAVREAAQRTLERG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001634.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001634.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3bed641f6debbf56b451fc8b2efc063861f9be05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001634.fa
@@ -0,0 +1,20 @@
+>0_2021
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQQRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG
+>1_1737
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQQRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG
+>2_683
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQRRKRGERRAALSDLVGEASSAGLYGQNAESYREALRQARADLRGERG
+>3_594
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQQRKRGERRAALSDLVAEASSAELYDQKAESYREALRQARADLRGERG
+>4_1961
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQRRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001637.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001637.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd7e2f3d8d310edc1b026552bbca689ede6e8420
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001637.fa
@@ -0,0 +1,35 @@
+>0_2024
+MSHATLVPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGTDRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAVTSPGTEEPDGFGDLHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQEHFVGPHRDLLERWAAAHAARDNEETR
+>1_1740
+MSHATLVPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGTDRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAVTSPGTEEPDGFGDLHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQEHFVGPHRDLLERWAAAHAARDNEETR
+>2_680
+MSHATLAPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGADRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAATSPGTEEPDGFGDKHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEASRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLVATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQAHFVGPHRDLLERWAAAHAARDTEETR
+>3_591
+MSHATLVPSTVPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGADRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERETG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAATSPGTEEPDGFGDLHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQEHFVGPHRDLLERWAAAHAARDTEETR
+>4_1964
+MSHATLVPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGADRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAATSPGTEEPDGFGDLHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQAHFVGPHRDLLERWAAAHAARDTEETR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001638.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001638.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49462bda311a98e3ab8854b3c1a38c7d0406d207
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001638.fa
@@ -0,0 +1,45 @@
+>0_2025
+MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHALAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPPSSAVPRPA
+PAHHRTTRARTPERTR
+>1_1741
+MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHALAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPPSSAVPRPA
+PAHHRTTRARTPERTR
+>2_679
+MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGERAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHDLAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAVGRGTPSSSAVPRPA
+PAHHRTTRVRTPERTR
+>3_590
+MTAVHHPTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDTTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHDLATRQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGTPSSSAVPRPA
+PAHHRTTRVRTPERTR
+>4_1965
+MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHALAARQMDGFGGIVSIRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPSSSAVPRPA
+PAHHRTTHARTPERTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001641.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001641.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c95707614917f6cf53a32e4ce35c9656613e8a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001641.fa
@@ -0,0 +1,29 @@
+>0_2031
+MHPDPAETNRRAYDDARVVALYDLDNPPGEDHAYFRRAAEESGARRIVDLGCGTGSLTVT
+LAGDDRAVVGIDPAEAMLRVARARPGGDRVEWRRGTAELIEPASADLVIMSGNVAMHLIG
+QDWHDALQRIAAGLVPGGRLLFETRNPVRRAWEDWQQEPTERTTAAGRLVESEATSTPDA
+DGVVVHRWRTEYSDEGVVREGEEHLQFRSVEQVTQDLAAAGLAVDRVWSDWHGRPFDEAE
+HPLMIIEARPQGA
+>2_668
+MHPDPAETNRRAYDDARVVALYDLDNPPGEDHAYFRRAAEESGAQRIVDLGCGTGSLTVT
+LTGDDRAVVGIDPAEAMLRVARARPGGDRVEWRRGTAELIEPASADLVIMSGNVAMHLIG
+QDWHGALRRIAAGLVPGGRLLFETRNPVRRAWEDWQQETTERTTAAGRLVESEATSAPDA
+DGVVVHRWRTEYSDEGVVREGEEHLQFRSVEQVTEDLAAAGLAVDRVWSDWHGRPFDAAE
+HPLMIIEACPQGA
+>3_396
+MTPSDPNGATYDDARLAALYDHDNPPGEDHAYFRQVADESRARRIVDLGCGTGSLTVTFA
+GEGRAVVGIDPAEAMLAVARARPGGNAVTWRQGTAELIEPASADLVVMSGNVAMHLIGEV
+WHATLRRVATGLVPGGRLVFETRNPVLRAWEDWSHGPTERTTPAGRLLETETVTAPDADG
+VVLMRSRTVFLADGALVEAEQRLQFRSAAQVRADLDAVGLTVERISGDWHRTPFDDATDR
+LMGVEARKA
+>3_585
+MHLDPAETNRRAYDDDRVVALYDLDNPPGEDHAYVRRAAEESGARRIVDLGCGTGSLTVT
+LTGDDRAVVGIDPAEAMLRVARARPGGDRVEWRRGTAELIEPGSADLVIMSGNVAMHLIG
+QDWHGALRRIAAGLVPGGRLLFETRNPVRRAWEDWQQEPTERTTAAGRLVESEATSAPDA
+DGVVVHRWRTEYPDEGVVSEGEEHLQFRSVEQVTQDLAAAGLAVDRVWSDWRGRPFDAAE
+HPLMIIEACPQGA
+>3_917
+MTDTNPSRGTDTYAHGHQPSVLASHATRTADNSCGYFLDRVRPGQRILDIGCGPGSITLD
+LAALVGDEGRVTGVDFSAEAIAAARLAAADRGDVVTEFLVGDVFELDLEPASFDVVHAHQ
+VMQHLTDPVAALEAMARFVKPGGILAAGRRLRAWAHQADLHVVLARSSAWSYATTESAAW
+WGNSQAERVTSSSFAQRAADQGVTPEQLTAMADDWRTWGQHPDAWFFLPHGEIIAVPSPH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001649.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001649.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c62d3c5ed48407f0af09f0e85039b6474a5acf6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001649.fa
@@ -0,0 +1,36 @@
+>0_2046
+MGEARTGGEAALSGVTAELDAALRHAAAQAPGSAAFAELLDSLHVHVGAGKLIRPRLVEL
+GWRLATADPVPPSGRAAVDRLGAAFELLHTALLVHDDVIDRDVLRRGQPAVHASARHRLE
+ARGVPAADAAHAGVAVALIAGDVLLTQAFRLAATCAADTARAAEAAAVVFDAAAVTAAGE
+LEDVLLGLSRHTGEEPDPDRILAMQRLKTAHYTVGAPLRAGALLAGADPDLARAMGEAGA
+DLGAAYQVIDDVLGVFGDPGETGKSADGDLREGKATVLTAHGRRIPAVRALLDAGPATPA
+DIEAARRALEAAGAREHALDVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS
+>1_1764
+MGEARTGGEAALSGVTAELDAALRHAAAQAPGSAAFAELLDSLHVHVGAGKLIRPRLVEL
+GWRLATADPVPPSGRAAVDRLGAAFELLHTALLVHDDVIDRDVLRRGQPAVHASARHRLE
+ARGVPAADAAHAGVAVALIAGDVLLTQAFRLAATCAADTARAAEAAAVVFDAAAVTAAGE
+LEDVLLGLSRHTGEEPDPDRILAMQRLKTAHYTVGAPLRAGALLAGADPDLARAMGEAGA
+DLGAAYQVIDDVLGVFGDPGETGKSADGDLREGKATVLTAHGRRIPAVRALLDAGPATPA
+DIEAARRALEAAGAREHALDVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS
+>2_654
+MSAGREGVVAELEAALSRAAGLAPESAAFAELLAGLRTHAGAGKLIRPRLVELGWRAAAD
+GPVPAAERPAVDRLGAAFELLHTGLLVHDDVIDRDVVRRGERTVHEATRRRLAARGVPEA
+EAAHAGTAVALIGGDVLLVEALRLAMTCTPDPGRAAPVAAVVLDAATASAAGELEDVLLG
+LARHTGEEPEPERILAMQRLKTAHYTVSAPLRVGGAAGGGGSRRRRGAGEAAAPTWAWPT
+RWWTTCSGCSAPRSRPASPPTATCARARPPCSPRTAAATPPSAPCSTPAPATPEELEAAR
+RALEAAGAREHALQVAEELTRRAAEHLAVLPLGEAACAEFADACHAVLTRSS
+>3_571
+MNPLAAGIGGAAPWSASAATPGLDDAGRARAAVRAELDRVFAETPLCADAPDSFHLLWAR
+LREAVSGGKLVRPRLVDLGWRTVRRAPASSGVPRGGTGEEEAADLRAVARVGAAFELLHA
+ALIVHDDVIDRDDLRRGRPTVAEQYRRDAVRDGVPAGEAEHVGRSAGIIAGDLLLTAAFR
+LAAASGARVRAAEAAESVFRAASAAAAGELEDVLLALHRHTGHHPEAGRILTMERLKTAG
+YSFEEPLRAGALLAGADPAHAEALAEAGALLGVAYQVVDDVLGTAGDPAVTGKPHDADLR
+EGKATLLTAHGRRDPRARAALDRVARAERHGEDLGELAAAVAEARAALVDAGSVEHALGV
+AEELVDQARALLDALPMAPAERAEFAATCGQILQREA
+>4_1987
+MGEARTGGEAALSGVTAELDAALRHAAAQAPGSAAFAELLDSLHVHVGAGKLIRPRLVEL
+GWRLATADPVPPSGRAAVDRLGAAFELLHTALLVHDDVIDRDVLRRGQPAVHASARHRLE
+ARGVPAADAAHAGVAVALIAGDVLLTQAFRLAATCAADTVRAAEAAAVVFDAAAVTAAGE
+LEDVLLGLSRHTGEEPDPDRILAMQRLKTAHYTVGAPLRAGALLAGADPDLARAMGEAGA
+DLGAAYQVIDDVLGVFGDPGETGKSADGDLREGKATVLTAHGRRIPAVRALLDAGPATPA
+DIEAARRALEAAGAREHALDVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001652.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001652.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6dbe27db3c936d32a7c026c40b837fd6fa0cf34e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001652.fa
@@ -0,0 +1,20 @@
+>0_2052
+MTGAPILPLLVLNGPNLNLLGTREPEVYGTATLDDVRALTEARAAEHGLTVDFRQSNHEG
+ELIDWIQEARTSHAGVLINPAAYSHTSIAIRDALAAVDRPIAEVHISNIHRREAFRHHSH
+VSAVADVVIAGAGVQGYTLAVDWLAAAVRR
+>1_1770
+MTGAPILPLLVLNGPNLNLLGTREPEVYGTATLDDVRALTEARAAEHGLTVDFRQSNHEG
+ELVDWIQEARTSHGGVLINPAAYSHTSVAIRDALAAVDRPIAEVHISNVHRREAFRHHSH
+VSAVADVVIAGAGVQGYALAVDWLAAAVRR
+>2_649
+MRETGASPRTFVRETGASVVVRSYTGPMTTAPSALPLLVLNGPNLNLLGTREPEIYGSDT
+LDDVRSRTEARAAGHGLAVDFRQSNHEGELVDWIQEARTSHAGILINPAAYSHTSVAIRD
+ALSAVGRPIVEVHISNIHRREPFRHHSHVSAVADAVIAGAGVLGYELGIDWLAAAVRR
+>3_566
+MTDSMPAATAARLPLLVLNGPNLNMLGTREPEKYGFETLEDVRALTAARAAEHGLEVDFR
+QSNHEGELVDWIQEARTGFSGILINPAAYSHTSVAIRDALAAVPVPIVEVHITNIHAREE
+FRHHSVVSAVATTVIAGAGTQGYALGVEVLAARLAR
+>4_1991
+MTATPALPLLVLNGPNLNLLGTREPEVYGTATLDDVRALTEARAAEHGLTVDFRQSNHEG
+ELIDWIQEARTSHAGVLINPAAYSHTSIAIRDALAAVDRPIAEVHISNVHRREAFRHHSH
+VSAVADVVIAGAGVQGYALAVDWLATTVRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001654.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001654.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34429911aa98d3487129f366aafd4b48aa2ea5e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001654.fa
@@ -0,0 +1,45 @@
+>0_2054
+MSDYQPRRPGSKPTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGHQLS
+APKRREAATAERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKERQEKA
+KEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMETDRGD
+TIKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTAEIVE
+QIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPSPEG
+LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID
+AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW
+TASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD
+>1_1773
+MSDYQPRRPGSKSTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGHQLS
+APKRREAATAERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKERQEKA
+KEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMETDRGD
+TVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTAEIVE
+QIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPSPEG
+LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID
+AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW
+TASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD
+>2_647
+MSDYQPRRPGSNPAPARRTDRAGKPALGRPKRGLIDESEARQLAEDRERMRRAGVGHQLS
+APKRREAATAERPQVMPQTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLAERQAKA
+KEIGLPAFRAKQLSVHYFERYTTDPEQMTDLPKDKREVIAEAFFPPLLTEVRRMETDRGD
+TVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTAEIVE
+QIVRANQVIAEGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPAPEG
+LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID
+AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW
+TASEKDVTREFVERLNAAGIPTTLRDTRGKEIDGACGQLAAGDEDA
+>3_564
+MEGMSDYTPRRPGSKPTPARQKDRAGKPALGRPRRGMIDEPEARQLAEDRERMHRAGVGH
+QLSAPPRRAAEVDADRPQVMPKTEGWQQPMGPDGRPQLQFKQPRVSQPPQHLADMTLAER
+QAKAKEIGLPAFRAKQLSVHYFEHFTTDPEQMTDLPKGKREEIAEAFFPPLLTEVRRLTT
+DRGDTVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTA
+EIVEQIVRANQVIAEGGLGGTRRDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDP
+APEGLGMSARHVTLSTVGLVPAIKKLAQEGVPLTFALSLHAPDDELRDELIPVNARWKAD
+EAIDAAYEYFLATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTP
+GSIWTASEKDVTREFVDRLNAAGIPATLRDTRGKEIDGACGQLAADDEDVAARA
+>4_1993
+MSDYQPRRTGSKPTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGHQLS
+APKRREAATAERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKERQEKA
+KEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMETDRGD
+TVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSPAEIVE
+QIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPSPEG
+LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID
+AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW
+TASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001656.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001656.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51e6b41f9f849bf5b2bb17e06a01ec9fac28386a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001656.fa
@@ -0,0 +1,40 @@
+>0_2057
+MSVRSLLPDLGTSATGTPEAAVPPFARAVLWAHGDDAWRGEGGWTVLLDGPDRLRRLSAL
+WQAAVAGRPDPTAPLRGWISSTFADDSPEPAVLRIPADLRRATPSGVRDVAQHVDADALA
+AAVAADRGARLLADGEVPLPADVADLAWDDAGYAAGVRELLTRMADSGGELAKVVISRTM
+TVPADDADLWRAIGELRREYPQTWVFAVGGLLGATPEVLATRHAGLVGSRVLAGSMPRGA
+DEEEDAALRERLASDPRLAEEHRWAARSVLDALAPVVDLADDDPAPTVLTLPNVHHLATS
+VRGRLRDGRGTVLDVVAALHPTAAVGGTPTPDAVRVIAEVEPVDRGRYAGPVGWLDQDGD
+GEIALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKFLPMRRALGVAED
+>1_1776
+MGAMSVRSLLPDLGAPATGAPEAAVPPFARAVLWAHGDDAWRGEGGWTVLLDGTDRLRRL
+SALWQTAVAGRPDPTAPLRGWISSTFADDSPEPAVLRIPADLRRATPSGVRDVAQHVDAD
+ALAAAVAADRGARLLADGAVPLPAGVADRAWDDAGYAAGVRELLTRMADSGGELAKVVIS
+RTMTVPADDADLWRAIGELRREYPQTWVFAVGGLLGATPEVLATRHAGLVGSRVLAGSMP
+RGADEEEDAALRERLASDPRLAEEHRWAARSVLDALAPVVDLADDDPAPTVLTLPNVHHL
+ATSVRGRLRDGRGTVLDVVAALHPTAAVGGTPTPDAVRVIAEVEPVDRGRYAGPVGWLDQ
+DGDGEIALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKFLPMRRALGVAED
+>2_644
+MSVPTLLPELGTAAAEAAVPPFARAVLWAHGDAAWRGDDGWTVLVDGPDRLRRLSALWQA
+AVAGREDPAAPVRGWVSAPFSDDSVEPAVLRVPARLRRSTASGIRETPQHVDAAALADAV
+AADGGGRLLPDGEVPLPADTSESAWDDAGYAAGVRELLARMAASDGALAKVVISRTLTVP
+ADDADLWRAIRALRREYPQTWVFAVGGLLGATPEILATRHAGLVGSRVLAGSLPRGEDEA
+EDAALRARLATDPRLGEEHRWAARSVLDALAPVVDLADPDPAPTVLTLPNVHHLATSVRG
+RLRDGRGTVLDVVAALHPTAAVGGTPTPEAVRVISEVEPVDRGRYAGPVGWLDQDGDGEI
+ALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKLLPMRRALGIDLD
+>3_562
+MPPVPSVAVAALAARALSPSGSAAGRVPAFARAVVWAREDTVRVGVGGHTVLLDGPDRLR
+RLSALWRAAVAARPEPASPALAWVSSAFDDASPVPSVLRVPARVLQAGPDGVVEVPVAMP
+REALAAAVAACPGARLTEAGEVPLPADDPALAWDDAGYAAGVEEVVARMEASAGALSKVV
+VSRTETVPAGEDRLWAAVDALRAEYPQTWTFAVGGLVGATPEMLATRRDGVVASRVLAGS
+LPRGVDEGDDARLRARLAADPRLLREHHWAARSVLDALAPVVELEDAHPAPFVLTLPNVH
+HLATDVRGRLRPGEGAVLDVVAALHPTAAVGGTPTAEALEVIRAVEPVDRGRYAGPVGWL
+DQDGDGEIALALRCGQQVPGGVRLQAGGGIVPGAAAEEEVVEVGVKLLPMRRALGVA
+>4_1996
+MGAMSVRSLLPDLGTPATGTPEAAVPPFARTVLWAHGDDAWRGEGGWTVLLDGTGRLRRL
+SALWQAAVAGRPDPTAPLRGWISSTFADDSPEPAVLRIPADLRRATPSGVRDVAQHMDAD
+ALAAAVAADRGARLLADGAVPLPADVADRAWDDAGYAAGVRELLTRMADSDGELAKVVIS
+RTMTVPADDADLWRAIGALRREYPQTWVFAVGGLLGATPEVLATRHAGLVGSRVLAGSMP
+RGADEEEDAALRDRLASDPRLAEEHRWAARSVLDALAPVVDLADDDPAPTVLTLPNVHHL
+ATSVRGRLRDGRGTVLDVVAALHPTAAVGGTPTPDAVRVIAEVEPVDRGRYAGPVGWLDQ
+DGDGEIALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKFLPMRRALGVAED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001658.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001658.fa
new file mode 100644
index 0000000000000000000000000000000000000000..367b1e94b245554be9a44d9aaac8e80d1caf3428
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001658.fa
@@ -0,0 +1,18 @@
+>0_2059
+MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE
+DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA
+LGRLLR
+>1_1778
+MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE
+DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA
+LGRLLR
+>2_642
+MSTLPTTTDAHDGADPCAGAHPPHAAHRDKDAHLTRLRRIEGQVRGIHRMVDEDVYCIDI
+LTQVAAVTKALQAMSLNLTSEHLRHCVAEAAVEAEASGRTELIDEKVAEATAAIGRLLR
+>3_560
+MEHDRHAGPGYSPQREAYLKRLKRIEGQVRGIHRMVEEDVYCIDVLTQVAAATKALHAVS
+LGLVEDHLRHCVAEAAVQAEAEGRTELIDEKVAEATAALGRLLR
+>4_1998
+MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE
+DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA
+LGRLLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001661.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001661.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92eeb61d70a0baf2de928a11e991f74a95efe3c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001661.fa
@@ -0,0 +1,14 @@
+>0_2064
+MSAGQGATTAGPVIESVELHVAAGAEAAFEAAVAEAEPLFRDGGATSFALSRQVEDPARY
+RLLIGWRTLEDHTVAFRESDSFLAWRALVTPHLAQLPAATHWSAV
+>1_1783
+MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAEPLFRDKGATSFALSRQVEDPARY
+RLLIGWRTLEDHTVAFRESDAFLAWRALVTPHLAQPPAATHWSAV
+>2_637
+MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAAELFRGARATSFALTRQVEDPARY
+RLLIGWRTLEDHTVGFRESEAFGQWRALVTPHLAQPPAATHWESVAAAF
+>3_555
+MEDPARYRLLIGWRTLEDHTVGFRESDAFLAWRALVTPHLAQPPAATHWSAV
+>4_2003
+MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAEPLFRDGGATSFALSRQVEDPAHY
+RLLIGWRTLEDHTVAFRESDAFLAWRALVTPHLAQPPAATHWSAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001665.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001665.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5094589fc1eac35a39b70b79d7b22672ba548193
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001665.fa
@@ -0,0 +1,50 @@
+>0_2068
+MTVYAFPGTEGAKVEFKSRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID
+AALDAAWKAAPAWGATSPAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADVP
+LAIDHFRYFAGAIRAQEGRLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL
+AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT
+GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMANDDAYWDKAQEGFTLFALNQGE
+VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG
+RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA
+MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE
+NHLMMLDHYQQTKNLLVSYSEDKLGFF
+>1_1787
+MTVYAFPGTEGAKVEFKSRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID
+VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADVP
+LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL
+AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT
+GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMAADDAYWDKAQEGFTLFALNQGE
+VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG
+RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA
+MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE
+NHLMMLDHYQQTKNLLVSYSEDKLGFF
+>2_633
+MTVYAFPGTEGAKVEFKPRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID
+VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADVP
+LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL
+AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT
+GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMANDDAYWDKAQEGFTLFALNQGE
+VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKIISYLDIG
+RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA
+MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE
+NHLMMLDHYQQTKNLLVSYSEDKLGFF
+>3_550
+MTVYAFPGTEGAKVEFKPRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID
+VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAIRETLNADLP
+LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL
+AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT
+GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMANDDAYWDKAQEGFTLFALNQGE
+ICTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG
+RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA
+MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE
+NHLMMLDHYQQTKNLLVSYSEDKLGFF
+>4_2007
+MTVYAFPGTEGAKVEFKSRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID
+VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADLP
+LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL
+AAGNAVVIKPAEQTPASVMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT
+GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMAADDAYWDKAQEGFTLFALNQGE
+VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG
+RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA
+MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE
+NHLMMLDHYQQTKNLLVSYSEDKLGFF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001668.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001668.fa
new file mode 100644
index 0000000000000000000000000000000000000000..afc3559b4b313d726cf302efcb05879c17e36403
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001668.fa
@@ -0,0 +1,25 @@
+>0_2071
+MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAVRRAFAAEA
+RGDVEPGRAPASFYVGVDENGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAAR
+LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVEADLDGAPFPVPQLRFD
+VPTTAA
+>1_1790
+MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAIRRAFAAEA
+RGDVEPGRVPASFYVGVDEAGHLVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAAR
+LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVEADLDGAPFPVPQLRFD
+VPTTAA
+>2_630
+MLPDPSPTVTVDGLLLRPLRTADEIAAREADAELHREGFDFLMAGTRSFPAIRRAFAADA
+RGDVEPGRVPASFYVGVDEAGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAVR
+LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVETGLDGAPFPEPKLRFD
+VPTTAA
+>3_547
+MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAIRRAFAAEA
+RGDVEPGRVPASFYVGVDENGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAVR
+LLRGALTLLAAHGVSTALLTCDETNTASVATIRACGGVLRDRVEAGLDGAPFPVPKLRFD
+VPTTAA
+>4_2010
+MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAVRRAFAAEA
+RGDVEPGRAPASFYVGVDENGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAAR
+LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVEADLDGAPFPVPQLRFD
+VPTTAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001670.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001670.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b61559d829388f1f39526e36eb0df64235f3e52c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001670.fa
@@ -0,0 +1,30 @@
+>0_2073
+MLSAPTLTRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA
+VRGRELRGRLAEVWALAAVDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAVE
+RLAAMAALALAETAMDGELVRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRSY
+RARLAEAAEAAPATDPAGPEEAEAPEAVADEAAPADKPRQETEKEKKERKKAEKKAEKKA
+RKKAEKKARKKKSDKKKD
+>1_1792
+MLSAPTLSRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA
+VRGRELRGRLAEVWALAAGDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAVE
+RLAAMAALALAETAMDGELTRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRSY
+RARLAEAAESAPAADPAGPEEAEAPEAVVDSEAAADEPRRETKKEKKERRKAEKKARKKA
+EKKAGKKKSDKKKD
+>2_620
+MLSPRTLARLSSVAAFLNTAPGPRGGQEAPERFTAATQLPALVPELQEGEVRLRLAAAAA
+VRARELRERLTRVWALAATDESAAVERVNELLAEAGPLRLTAGGDVVGLAPAQVPADAVE
+RLAAMATLALAETAMDGELARLRVCEGEDCENALVDGSRNRSKRFCDEANCANRTHVRSY
+RARLAEAAEAAPATDPAGPEEAEGTEAVVDEAAPADEPLQETEKEKKERRKAQKKARKKA
+EKKAGKKKSDKKKSDKKKD
+>3_544
+MLSPHTLARLASISAFLNTAPGVRGGQEAEERLTAGTQLPALVPELQEGESRLRVAAAAR
+TRAHELRARLTELWAAADAEDVPAAVAAVNELLAETGPLRLEVSDGSADLAPAQVPADAV
+ERLTAMAALALTEAALEGELTRLRVCAGEDCENTLVDASRNRSKRFCDAANCANRTHVRS
+YRARLAEAEDTQADVEAADAAPLPEVAPEADPQDATDLEAIEAAEGVESAVQEPVKKDST
+KDKKSKSEKKARRAAKKKAEKESEAAAEGKKGKREKSKKSEKHKKKAAKD
+>4_2012
+MLSAPTLSRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA
+GRGRELRGRLAEVWALAAVDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAVE
+RLAAMAALALAETAMDGELTRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRSY
+RARLAEAAESAPAADPAGPEEAEAPEAVVDSEAAADEPRRETKKEKKERRKAEKKARKKA
+EKKAGKKKSDKKKD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001675.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001675.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d91a01062c1e39fc675441456b7c169384ab12b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001675.fa
@@ -0,0 +1,20 @@
+>0_2079
+MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTYAMYLSPGYYT
+DFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDLREEMADSGMH
+SREIVDPDGHQWEFVTA
+>1_1798
+MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTYAMYLSPGYYT
+DFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDLREEMADSGMH
+SREIVDPDGHQWEFVTA
+>2_614
+MALFSQPVFINLPTTDTERIREFWTSLGAQAIEDFSDENSVCIELTESTFAMYLSPGYYT
+DFIGDREIADCMTTNSALMALTVGDAAAVDALADRAIEAGAAEVPLPVDLREEMVDSGMH
+SREIVDPDGHQWEFVTA
+>3_539
+MRTRWSTVLVMALFSQPVYINLPSTDTERIREFWTSMGADIDEDFSDENSVCVQLTESTF
+AMYLSPGFYTDFIGDREIADCLTTNSVLLQLTAPDRGAVDALVRAAVEAGGSEVPLPDEL
+QEDMTATGVHSRQVVDPDGHQWEFMAA
+>4_2018
+MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTYAMYLSPGYYT
+DFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDLREEMADSGMH
+SREIVDPDGHQWEFITA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001676.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001676.fa
new file mode 100644
index 0000000000000000000000000000000000000000..899fc88277430893cedb56da4442a04921f8c490
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001676.fa
@@ -0,0 +1,50 @@
+>0_2080
+MPAPAATTTTTPPATPRERQSVLRTLRTPRWLGTEVLAAVVVALALIPEAIAFSIIAGVD
+PRVGLFASFTMAVTTAIVGGRPAMISAATGAVALVVAPLSHAYGVGHLLAAIILGGVIQI
+LLGVFGVARLMRFVPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALAIVVLLP
+RLTTAVPATLVAVVVVTALVMAAGLAVPRVGDRGALPDALPVLGLPDVPLTWETLRLILP
+FSVGIAFVGLLESLLTAKLVDDITDTRSDKTRESWGQGVANVVSGLFGGMGGCAVVGQTM
+MNVKANGARTRISTFLAGVFLLVLVVAFGGFVAQIPMAALVGVMMFVAAATFDWHSVRPA
+TLRAMPRSETAVMVVTVAATVLTHNLAIGVGVGVLAALVLFAQRVSRLVTVVREVHDDGD
+AVTYRVHGALFFASSNDLYSQFEYALDPPRVVIDMSAAHVWDASTVAALDSVLTKYARHG
+IHAEVTGLNEASAAMHARLTGRLGA
+>1_1799
+MPALPAAPPPALTPLQRQSVLRTLRSPRLLGTEVLAAVVVALALIPEAIAFSIIAGVDPR
+VGLFASFTMAVTTAIVGGRPAMISAATGAVALVVAPLSHAYGVGHLLAAIILGGVIQILL
+GVFGVARLMRFVPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALAIVVLLPRL
+TTAVPATLVAVVVVTALVMAAGLAVPRVGDRGALPDALPVLGLPDVPLTWETLRLILPFS
+VGIAFVGLLESLLTAKLVDDITDTRSDKTRESWGQGVANVVSGLFGGMGGCAVVGQTMMN
+VKANGARTRISTFLAGVFLLVLVVAFGGFVAQIPMAALVGVMMFVAAATFDWHSVRPATL
+RAMPRSETAVMVVTVAATVLTHNLAIGVGVGVLAALVLFAQRVSRLVTVVREVHDDGDAV
+TYRVHGALFFASSNDLYSQFEYALDPPRVVIDMSAAHVWDASTVAALDSVLTKYARHGIH
+AEVTGLNEASAAMHARLTGRLGA
+>2_698
+MTPASTASARVAAPPNSREPSPEQLQSVRLTLRSPGRLKTEVLAGLVVALALIPEAIAFA
+LIAGVDPQVGLFAAATMAMTIAFVGGRPAMVSAATAATALVVAPLVASHGLDHLIAAVIL
+AGGLQVVLGLLGVAKLMRFVPRSVMVGFVNALAILIFTSQLPDLMGVPWLVYPLTALGLA
+IILLLPRVTTAVPAPLVAIVVVTVIVLLAGADVPTVGDKGRLPDSLPALLVPDVPFTLET
+LQLLFPYALGMAVVGLLESLMTAKLVDDITDTRSSKTRESWGQGVANVVSGLFGGMGGCA
+MVGQTMINVKASGARTRISTFMAGVFVLILSVTLGDVVALVPMAALVAVMIFVSLATFDW
+HSIRPSTLAFMPKSETAVMLVTVAATVLTHNLAIGVGLGVLAAMVMFAQRVSHLATVTRT
+LEGQGRDAVARYRVQGELFFASSNDLYTQFDYAGDPARVVIDFSQAHLWDASTIAALDAV
+EEKYRRHGATVEITGLNVASRAMRARMSGRLGGGH
+>3_537
+MPASPAAPPPALTPLQRQSVLRTLRTPRWLGTEVLAAVVVALALIPEAIAFSIIAGVDPR
+VGLFASFTMAVTTAVVGGRPAMISAATGAVALVVAPLSHAHGLDHLIAAIILGGLIQVAL
+GLLGVARLIRFIPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALGIVLLLPRL
+TTAVPSTLVAIVVVTALVMAAGWSVPRVGDRGELPDALPGLFVPDVPLTWETLRLILPFS
+VGMAVVGLLESLLTAKLVDDVTDTRSDKTRESWGQGVANIVSGLFGGMGGCAVVGQTMMN
+VKANGARTRISTFLAGVLLLVLVVALGDLVGQIPMAALVGVMVFVAGAAFDWHSVRPATL
+RAMPRSETAVMLLTVLATVVTHNLAIGVGVGVLTAMVLFAQRVSRLARVERVVTDDNGGT
+AVYRVHGELFFASSNDLYSQFEYALDPPRVVIDLSAAHVWDASTVAALDAVVTKYAQHGI
+AAEVTGLNEASAAMHARLTGRTGA
+>4_2019
+MPALPAAPPPALTPPATPRERQSVLRTLRTPRWLGTEVLAAVVVALALIPEAIAFSIIAG
+VDPRVGLFASFTMAVTTAIVGGRPAMISAATGAVALVVAPLSHAYGVGHLLAAIILGGVI
+QILLGVLGVARLMRFVPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALVIVVL
+LPRLTTAVPATLVAVVVVTSLVMAAGLTVPRVGDRGALPDALPALGLPDVPLTWETLWLI
+LPFSIGMAFVGLLESLLTAKLVDDITDTRSDKTRESWGQGVANVVSGLFGGMGGCAVVGQ
+TMMNVKANGARTRISTFLAGVFLLVLVVAFGGFVAQIPMAALVGVMMFVAAATFDWHSVR
+PATLRAMPRSETAVMVVTVAATVLTHNLAIGVGVGVLAALVLFAQRVSRLVTVVREVHDD
+GDAVTYRVHGALFFASSNDLYSQFEYALDPPRVVIDMSAAHVWDASTVAALDSVLTKYAR
+HGIHAEVTGLNEASAAMHARLTGRLGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001677.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001677.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b609f66895fb4dc36a494ebfabfd2e19d0c580b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001677.fa
@@ -0,0 +1,40 @@
+>0_2082
+MNLRTLLREALTAARTAPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPAARV
+LTVTDSGGTGFLTGATVATLAGLDSAEAALARDMPVDTVNAAIGAGGTRVAVTHVVGTVD
+RGVELTRGRLPGPGEVVVPEAKLAELGLAQPSGALESGDGRQWAVVGAFEALTPFEDLAD
+YAIAVPAAPASLVVQQVRVLAPDTAGTRAMQDSALAVIDPDPRSSQVQTARALAAGNATI
+TGELAGLGRSLLLLILGAGAFFVAIVVLADVLIRRRDLGRRRTLGIGRADLVLLVAVRTA
+APAVLGAVVGAGTGYAVVVGQGGALGLDFVAGVAVLAALTAVVASLLPAAFAAFRDPVRV
+MRTA
+>1_1800
+MNLRTLLREAVTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPGARV
+LTVTDTGGTGFLTGATAATLAGLDTAEAALARDSPMDAVNTGIGRGGARVAVTNVVGTLD
+RGIVLTRGRLPAPGEVVVPEAKLAELGLAQPSGAIEATDGGQWAVVGAFQAQDPFQDLDG
+YALTVPAAPDALVMQQVRVLAADTAGTRAMQEAALAVIDPDPRASSIQTARALSAGNQVI
+TGELAGLGRSLLLLILGAGAFFVSIVVLADVLIRRRDLGRRRTLGIGRGDLILLVAVRTA
+VPALLGAVLGSGAGYAVVAGQGGTLGVDFVAAVAVLAALTALLASLAPAAFAAFRDPVRV
+MRTA
+>2_611
+MNLRTLLREALTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPAARV
+LTVTDSGGTGFLTGATVTTLAGLDAAEAALARDMPVDTVNAAIGAGGTRVAVTHVVGTLD
+RGVELTRGRLPGPGEVVVPEAKLAELGLAQPSGALESGDGRQWAVVGAFEARTPFEDLDG
+YALAVPATPASLVVQQVRVLALDTAGTRAMQDSALAVIDPDPRSSQVQPARALAAGNETI
+TGELAGLGRSLLLLILGAGAFFVAIVVLADVLIRRRDLGRRRTLGIGRADLVLLVAVRTA
+APAMRGAAVGAGAGHGLVLAQGSALGSAFVVGAAVLAVLTAVVASLLPAAFAAFRDPVRV
+MRTA
+>3_536
+MNLRTLLREAVTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPGARV
+LTVTDTGGTGFLTGATAATLAGLDTAEAALARDSPMDAVNTWIGRGGARVAVTNVVGTLD
+RGIELTRGRLPAPGEVVVPEAKLAELGLAQPSGAIEATDGRQWAVVGAFQAQDPFQDLDG
+YALTVPAAPDALVMQQVRVLAADTAGTRAMQEAALAVIDPDPRASSIQTARALSAGNQVI
+TGELAGLGRSLLLLILGAGAFFVSIVVLADVLIRRRDLGRRRTLGIGRGDLILLVAVRTA
+VPALLGAVLGSGAGYAVVAGQGGTLGVDFVAAVAVLAALTALLASLAPAAFAAFRDPVRV
+MRTA
+>4_2020
+MNLRTLLREAVTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPGARV
+LTVTDTGGTGFLTGATAATLAGLDTAEAALARDSPMDAVNTGIGRGGARVAVTNVVGTLD
+RGIVLTRGRLPAPGEVVVPEAKLAELGLAQPSGAIEATDGRQWAVVGAFQAQDPFQDLDG
+YALTVPAAPDALVMQQVRVLAADTAGTRAMQEAALAVIDPDPRASSIQTARALSAGNQVI
+TGELAGLGRSLLLLILGAGAFFVSIVVLADVLIRRRDLGRRRTLGIGRGDLILLVAVRTA
+VPALLGAVLGSGAGYAVVAGQGGTLGVDFVAAVAVLAALTALLASLAPAAFAAFRDPVRV
+MRTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001678.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001678.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2500a4f2a2b6f2476ccbd877b6ec6ae6dac45445
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001678.fa
@@ -0,0 +1,25 @@
+>0_2083
+MNAELSVADLRFAYTRGAEELFDGLTHRFTPGAVTALTGPSGRGKSTLLYVLGLMLTPSA
+GVVRLGDVDASALPDRRRARLRATSVGFVFQDAELDPSRPILDSVVEPGLYAGLSRRELE
+GRARILLERFGLGHRAEHRPGQVSGGQAQRVAVCRALVNTPAVVLADEPTGNLDPDNASL
+VLDALAEAAGEGRTVVVATHDPAVVARADEVVRL
+>1_1801
+MTGPATPGTPAAPVVPAALAVEDLRFAYTRAAEELFDGLTHAFTPGAVTALTGPSGRGKS
+TLLYVLGLMLTPTSGVVRLGDVDASTRPDRERSRLRATSVGFVFQDSELDPSRPILDSVV
+EPGLYAGLERQTLEDRARALLERFGLAHRADHRPGQVSGGQAQRVAVCRALVNAPAVVLA
+DEPTGNLDPDNAGLVMDALADAAAEGRTVVVATHDPAVVARADEVVRL
+>2_610
+MNAELSVADLRFAYTRGAEELFDGLTHRFTPGAVTALTGPSGRGKSTLLYVLGLMLTPSA
+GVVRLGDVEASALPDRRRARLRATSVGFVFQDAELDPSRPILDSVVEPGLYAGLERRVLE
+ERARALLERFGLGHRAEHRPGQVSGGQAQRVAVCRALVNTPAVVLADEPTGNLDPDNASL
+VLDALAETAAEGRTVVVATHDPAVVARADEVVRL
+>3_535
+MTGPATPGTPAAPGTPAALAVEDLRFAYTRAAEELFDGLTHAFTPGGVTALTGPSGRGKS
+TLLYVLGLMLTPTSGVVRLGDVDASTRPDRERSRLRATSVGFVFQDSELDPSRPILDSVV
+EPGLYAGLERQTLEDRARALLERFGLAHRADHRPGQVSGGQAQRVAVCRALVNAPAVVLA
+DEPTGNLDPDNAGLVMDALADAAAEGRTVVVATHDPAVVARADEVVRL
+>4_2021
+MTGPATPGTPAAPVVPAALAVEDLRFAYTRAAEELFDGLTHAFTPGAVTALTGPSGRGKS
+TLLYVLGLMLTPTSGVVRLGDVDASTRPDRERSRLRATSVGFVFQDSELDPSRPILDSVV
+EPGLYAGLERQTLEDRARALLERFGLAHRADHRPGQVSGGQAQRVAVCRALVNAPVVVLA
+DEPTGNLDPDNAGLVMDALADAAAEGRTVVVATHDPAVVARADEVVRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001681.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001681.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7bc18364160df6757207c381d7bf2323a474dc06
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001681.fa
@@ -0,0 +1,65 @@
+>0_2086
+MSEHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLVVVALMVLV
+AVVLNVWAPHVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTP
+GEGIDFTELGRLILIVLGMYLVAQTFMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSY
+FDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMMFWLSWQLALIALIAL
+PVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNE
+ELYEAAFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN
+QPLGQIAGMSNMLISGVASAERIFELLDEPEETPDGTPARTPARTFVRETAPSEGTFVRE
+TAPSAASGPDVVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNLVAEPGQTVAIVGPTGA
+GKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRSELRAATGMVLQDAVLFGGTIRENIRYG
+RLDATDEEVVAAAKATYVDRFVHTLPEGYDTVIEHDASNVSAGERQLITIARAFLAQPSL
+LILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVMEHGDIVEQGS
+HAELLAAKGAYHRLYMSQFKGGEDDDGAASRDDAR
+>1_1805
+MSEHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLVVVALMVLV
+AVVLNVWAPHVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTP
+GEGIDFTELGRLILIVLGMYLVAQTFMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSY
+FDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMMFWLSWQLALIALVAL
+PVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNE
+ELYEAAFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN
+QPLGQIAGMSNMLISGVASAERIFELLDEPEETPDGTPARTPDGTFVWETAPSESAFVRE
+TAPSAIPGPDGVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNFVAEPGQTVAIVGPTGA
+GKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRGELRAATGMVLQDAVLFGGTIRENIRYG
+RLDATDEEVVAAAKATYVDRFVHTLPDGYDTVIEQDAANVSAGERQLITIARAFLAQPSL
+LILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVMEDGDIVEQGS
+HDQLLAARGAYFRLYRSQFQGGEQAEEQDDDGAPAAREDAR
+>2_604
+MSGTEKHGSTAAPQGEVGELTDAEIAAFQEAGVTDEWGEGPPRKAKAFWPSAMRLLGLFA
+PERTGLILVSLMVLVAVVLNVWAPHVLGQAMDVIFGGLISRDMPAGLTREQVIEGLRGQG
+QGQAADMLSGMAFVPGQGIDFAELARLILIVLGMYVVAQLFMWLQGRVLNDLVMRIVFRL
+REDIEAKLNRLPLSYFDTRQRGDLLSRTTNDVDNVQQAMQQAFATLVYSVLTIIGIVGMM
+FWLSWQLALIALIALPVAGVMVGVIGSKSQKLFTAQWRETGRLNGHIEESFTGHELVTVF
+GRQADMAERFDERNEAMYEASFKAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMT
+LGAVTAFIQYSREFNQPLGQVAGMSNMLISGVASAERIFELLDEDEQDSDAEVARRASDD
+DVAEPADASVRETGASADDDVAHLPQPVAGRVEFEHVRFSYTEAKPLITDLNLVAEPGQT
+IAIVGPTGAGKTTLVNLIMRFYEVDGGRILVDGVDTRTVSREELRSHTGMVLQDAVLFGG
+TIRENIRYGRQDATDEEVVAAAKATFVDRFVHTLPEGYDTVIEQDASNVSAGERQLITIA
+RAFLAQPSLLILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVME
+HGDIVEQGNHAELLAARGAYHRLYMSQFKGGEDDGGGAASGEDAR
+>3_530
+MSEQLTDQEIVELQESGATDEWGGGPGRKAKAFWPSAKRLLGLFRTEKAGLALVAAMVLV
+AVVFNVWAPHVLGRAMDVLFGGVISKGMPAGVSREQVIEGLRGQGQGQAADMLSGMDFTP
+GQGIDFDALARLILTVLGMYVVAQGFMWLQGRVLNDVVMRIVFRLREQIEAKLNRLPLSH
+FDTRQRGDLLSRATNDVDNVQQAMQQAFATLVYSVLTIFGIVGMMFWLSWELALIALIAL
+PVAGVVVGVVGKKSQALFTAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAERFDERND
+AMYEASFKAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN
+QPLGQVAGMSNMLISGVASAERIFELLDEPEEEPDDVVAARADDDVAHLPQPVAGRVEFE
+HVRFSYTEAKPLITDLNLVAEPGQTIAIVGPTGAGKTTLVNLIMRFYEVDGGRILLDGVD
+TRRVPRQELRAATGMVLQDAVLFGGTIRENIRYGRLEATDEEVLAAAKATYVDRFVHTLP
+DGYDTVIEQDASNISAGERQLITIARAFLAQPSLLILDEATSSVDTRTEVLVQQAMAALR
+NDRTSFVIAHRLSTIRDADVILVMEHGDIVEQGSHEELLAARGAYHRLYTSQFRGGEDEH
+HDDGAPASR
+>4_2025
+MSEHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLAVVAVMVLV
+AVVFNVWAPRVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTP
+GEGIDFTELGRLILIVLGMYLVAQTFMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSY
+FDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMMFWLSWQLALIALVAL
+PVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNE
+ELYEAAFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN
+QPLGQIAGMSNMLISGVASAERIFELLDEPEETPDGTPARTPDGTFVWETAPSESAFVRE
+TAPSAIPGPDGVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNFVAEPGQTVAIVGPTGA
+GKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRGELRAATGMVLQDAVLFGGTIRENIRYG
+RLDATDEEVVAAAKATYVDRFVHTLPDGYDTVIEQDAANVSAGERQLITIARAFLAQPSL
+LILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVMEDGDIVEQGS
+HDQLLAARGAYFRLYRSQFQGGEQAEEQDDDGAPAAREDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001690.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001690.fa
new file mode 100644
index 0000000000000000000000000000000000000000..22b3dee3148b97147a44c0051e6fe07652b02611
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001690.fa
@@ -0,0 +1,46 @@
+>0_2098
+MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG
+MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSLSLLMVPLTVYNLAANAPRSVSVAGL
+LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPLAMVIMAIGCGLMVLTAWAFGDVVR
+NRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYA
+AAAKPALAVTALETIGQTGRSALADMRQLLGVLRETGETVAGVPGVTDDDARRPAADVVA
+SPDGRGTRLPPGRRPQPRLADLPALVETMRLSGLEVSLLETGTPRRTLPAGGELAAYRIV
+QEALTNTLRHGGPDADAFVTLAWTAHGLDLQIDDDGCGAAADPATRGSGQGLRGAAERTA
+LFGGTLETGPRVGAGYRVSAHLPYSAV
+>1_1822
+MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG
+MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSMSLLMVPLTVYNLAANAPRSISVAGL
+LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPLAMVIMAIGCGLMVLTAWAFGDVVR
+NRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYA
+AAAKPALAVTALETIGQTGRSALADMRQLLGVLRETGETVAGVPGVTDDDARRPAADVVA
+SPDGRGTRLPPGRRPQPRLADLPALVETMRLSGLEVSLLETGTPRRTLPAGGELAAYRIV
+QEALTNTLRHGGPDADAFVTLAWTAHGLDLQIDDDGCGAAADPATRGSGQGLRGAAERTA
+LFGGTLETGPRVGAGYRVSAHLPYSAV
+>2_581
+MNPLHRIDQWMRAHPVRTDVLVSVLLFAVLGLTPWVMLGSLAGPTPGSIVASILIALALI
+APWAFRRVRPVASAAAVAAAAVAHLVAGPEFSLALVLVPMTVYNLAANAPRWASFTGLVA
+ALLGGVANGIRVGLFPDPAMRPDGVYEPVDPSLEALLVMVFGCAAVVLTAWAFGDVVRHR
+RLAVRALEDRNRRLETMALQERRLAASDERNHIAREMHDIVAHSLQVIISQADGARYAAA
+AKPELAVATLDTIGLTGRAALADMRQLLGVLRETGETVAGVPGVAPDDGAPGPAAGASDE
+GAAGAADEGAAGAADEGAAGAGTAGAGTTPGAGRTRLPADVASRDGRGARQPPGHRPQPT
+LADVPALIETMRLSGLEVSLLETGAPRRPLPPGGELAAYRIVQEALTNTLRHGGPQASAF
+LTLAWTGRGLDVQSDDDGRGADADPGTRGSGHGLRGVAERVALFGGTVETGPRAGAGYRV
+SAHLPYSAV
+>3_504
+MNPLRRLDVLLRRHPVRTDVTAAVLLTLVLVLAPLVMLGGGVGSPAAWQTAGTVVAGLLM
+TGAWGLRRVRPVAAAGVTVAGALLHLAVGPEFTIALAMVPATVYNLAAIGPRWASLAGLA
+TGLAGGLANGLKVWLFPPRFTTPDGVQVQSPAEPVAMVVMAVLCGMAVLTAWAFGDVVRN
+RRLAVQALEDRARRLETQALQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYAA
+AAKPELAVETLETIGQTGRSALADMRQLLGVLRGPAEPTGGPDRARRDPAAPDGHRAPPG
+LADLPALFQTLRLSGLEISLLEQGSPRRDLPAGGELTAYRTVQEALTNTLRHGGEGAHAF
+LTLRWTARGLEIQADDDGRSQADAETTGSGQGLRGIAERVALFGGTMEAGPRVGAGWRVW
+AELPYADV
+>4_2043
+MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG
+MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSLSLLMVPLTVCNLAANAPRSVSVAGL
+LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPLAMVIMAIGCGLVVLTAWAFGDVVR
+NRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYA
+AAAKPALAVTALETIGQTGRSALADMRQLPGVLRETGETVAGVPGVTDDDTRRPADPAPD
+RADPTGTRPDVVAAPDGRGARLPPGRRPQPRLADLPALVETMRLSGLEVSLLETDTPRRA
+LPAGGELAAYRIVQEALTNTLRHGGPDADAFVTLAWTARGLDLQIDDDGRGAAADPATRG
+SGQGLRGAAERTALFGGTLETGPRVGTGYRVSAHLPYSAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001691.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001691.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8fa11a0875b79d2d9f8319863f25280689cb3e28
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001691.fa
@@ -0,0 +1,14 @@
+>0_2100
+MTGSILDHPAPTTSRASDPAAERAQRDSECVAFFVALVTAAVVMLGLSLFTGVEGLLRLA
+LTAGAGLLAGAVAWATARPVLEDDAPGD
+>1_1824
+MTGSILDHPTPTTSRASDPAAEQAQRDSECVAFFVALVTAAVVMLGLSLFTGVEGLLRLA
+LTAGAGLLAGAVAWATARPVLEDDAPGD
+>2_578
+MTAAVVILGLSLFTQVEGLPRLLVTAASGLLAGAVTWSVTQPVLEDEVLHG
+>3_502
+MSAAPAPSPAAPAVPPVTAVPPAAREPEGTSPSDRERERGDAECLAFFLALVTAALVMAG
+LALATDLGPLLRVLLSLGASGLAGALTLAFTRPSLED
+>4_2045
+MTGSILDHPAPTTSRASDPAAERAQRDSECVAFFVALVTAAVVMLGLSLFTGVEGLLRLA
+LTAGAGLLAGAVAWATARPVLEDDAPGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001694.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001694.fa
new file mode 100644
index 0000000000000000000000000000000000000000..05bedc217fed896cb2dc88a51b64518a60510c76
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001694.fa
@@ -0,0 +1,60 @@
+>0_2106
+MTSLLRILRFAPQLNRLYLGIAVSSVLAAVLALATPFLIGAATDRIVAAVAGETDVAEAV
+TAVTWLAVAFLAVEVATTLVVSVGGYWGDVMAARMRTILSTRYFEQLLHLPQRYFDTAIT
+GRVVNRLNRTINELTQFLQFFANNAFTMLITTAAVLVITAFYWWPLAILLAVVFPVYMWL
+TARTSTKWQVWEGEKNTEVDIASGRFAEVVSQMSVVRAYNRQDHELSGFRDRFLRTVGIT
+RQQSRFWHGMDAGRRLALNVAFGAMYLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSM
+SFLVDSAQRAVAGSKDYFEVLAEERERAGGAALAVAGASAESAGADAPRVPAEPRADVVP
+GAPDVPADVPAVRFDEVSFAYDADASRPVLDRVSFDIPRGARVALVGESGGGKSTIAHLL
+LGLYPVTSGRIEVFGQDVAGLDLAVLRGRIATVFQEPSLFSGTVRENIAYADPDASDERV
+RAAAEAAYAHRFVEAFDDGYEQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSA
+LDTKSERLVQAALEELMVGRSSLIVAHRLSTIASVDRIVTLRGGQVQEIGTPAELAESGG
+IYAQLLELQRAGTQEARKMLKEYGLSG
+>1_1831
+MTSLLRILRFAPQLHRLYLGIAVSSVLAAVLALATPFLIGAATDRIVAAVAGETDVAEAV
+TAVTWLAVAFLAVEVATTLVVSVGGYWGDVMAARMRTILSTRYFEQLLHLPQRYFDTAIT
+GRVVNRLNRTINEITQFLQFFANNAFTMLVTTAAMLVITAFYWWPLAILLAVVFPVYMWL
+TARTSAKWQVWEGEKNTEVDVASGRFAEVVSQMSVVRAYNRQDHELTGFRDRFLRTVEIT
+RQQSRFWHGMDAGRRLALNVAFGAMYLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSM
+SFLVDSAQRAVAGSKDYFEVLAEERERAGGAALAAASASAESAGADAPRVPAEPRADVVP
+GAPDVPADVPAVRFDEVSFAYDADASRPVLDRVSFDIPRGARVALVGESGGGKSTIAHLL
+LGLYPVTSGRIEVFGQDVAGLDLAVLRGRIATVFQEPSLFSGTVRENIAYADPDASDERV
+RAAAEAAYAHRFVEAFDDGYEQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSA
+LDTKSERLVQAALEELMVGRSSLIVAHRLSTIASVDRIVTLRGGQVQEIGTPAELAESGG
+IYAQLLELQRAGTQEARKMLKEYGLSG
+>2_567
+MLAAVLTLATPFLIGAATDRIVAAIAGETTVEDAVVAVTWLAVAFLAVEVTTTLVVSVGG
+YWGDVMAARMRTILSTRYFDQLLHLPQRYFDTAITGRVTNRLNRTINELTQFLQFFANNA
+FTMLITTTAVLVITAFYWWPLAILLAIVFPVYMWLTAKTSAKWQVWEGEKNIEVDMASGR
+FAEVVSQMSVVRAYNRQDHELAGFRERFTRTVGITRKQSRFWHGMDAWRRLALNVVFGAM
+YLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSMSFLVDSAQRAVAGSRDYFEVLAEER
+ERAGGAGPQGRGAAAVAAGQPRADDDGGTDVRWGGAAPSRPAQPRADVVPGDGTGGMPAG
+PSADVVPAVRFDEVSFAYDPDASRPVLDRVSFEIPQGQRVALVGESGGGKSTIAHLLMGL
+YPVTGGRIEVFGQDVAELDLAELRERIAAVFQEPSLFSGTVRENIAYADPAASDERVRAA
+AEAAYAHRFVEAFDDGYEQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSALDT
+KSERLVQGALEELMVGRSSLIVAHRLSTIASVDRIVTLRGGRVQEVGTPAELAESGGIYA
+QLLRLQKAGTKEARKMLKEYGLSG
+>3_495
+MRALLRILRFAPQLNPLYLGIAVCSVLAAALSLATPFLIGAATNRIVDAIAGRSTLDDAV
+AAVTWLALAFLAVEVATTAVVSVGGYWGDVMAARMRAALSGRYYDHLLHLPQRYFDTAIT
+GRIVNRLNRSITELTQFLQFFSNNAFTMLITTAAVLVITAFYWWPLAVLLAVVFPVYMWL
+TAKTSAKWQGWEGEKNTEVDIASGRFAETVAQMNVVRAYNRQDHELAGFTERFRRTVGIT
+RKQSRFWHGMDAGRRLALNLVFGVMYLIVFVRTARGLFSVGDMVILLQLMNMARQPIFSM
+SYLVDSAQRAVAGSKDYFGVLAEERERSGGAALPAGLGSAEAPTTTTATGVVVRDRAEAP
+TGAPVRAGADVPAVRFADVTFAYDPEAERPVLDGVTFDIPQGAKVALVGESGGGKSTLAH
+LLMGLYPVGSGRVEVFGRDVAGLDLAVLRGQVAAVFQEPFLFSGTIRENIAYADPDASGE
+RVRAAAKAAFADGFVEEFEHGCEQLIGERGLRLSGGQKQRIAVARAVLKDAPVLVLDEAT
+SALDTKSERLVQSALDDLMVGRSSLIVAHRLSTIASVDRIVTLRGGRVQEVGTPAELAQS
+GGIYAQLLRLQKAGTKEARKLLKEYGLSG
+>4_2052
+MTSLLRILRFAPQLHRLYLGIAVSSVLAAVLALATPFLIGAATDRIVAAIAGETGVAEAV
+TAVTWLAVAFLAVEVATTLVVSVGGYWGDVMAARMRTILSTRYFEQLLHLPQRYFDTAIT
+GRVVNRLNRTINELTQFLQFFANNAFTMLITTAAVLVITAFYWWPLAVLLAVVFPVYMWL
+TARTSAKWQVWEGEKNTEVDIASGRFAEVVSQMGVVRAYNRQEQELSGFRDRFLRTVGIT
+RQQSRFWHGMDAGRRLALNAAFGAMYLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSM
+SFLVDSAQRAVAGSKDYFEVLAEERERAGGAVLAVASADAPRVPAEPRADVVAGAPDVPA
+DVPAVRFDEVSFAYDADASRPVLDRVSFDIPRGAKVALVGESGGGKSTIAHLLLGLYPVT
+SGRIEVFGQDIAGLDLAALRGRIATVFQEPSLFSGTVRENIAYADADASDERVRAAAQAA
+YAHRFVAAFDDGYDQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSALDTKSER
+LVQAALDELMVGRSSLIVAHRLSTIASVDRIVTLRAGRVEEVGSPAELAESGGIYAQLLE
+LQRAGTQEARKMLKEYGLSG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001695.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001695.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a94b29485942389bed0d99fb5327946e143bc084
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001695.fa
@@ -0,0 +1,31 @@
+>0_2108
+MARTWDGSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA
+LLVLGAGGVGVVAERWPWLVPALTVAGVVYLLGFAAGALRSAWRGDRTLSTAAADVEGTG
+HGPDRIDLAVLTGELPLIDPVTGRLAEREPAGAGVGHHDDGAPGFGAPSGGGSVTVRQRV
+QPRRVALDRPQTPLPRIILLALSVSLVNPHAILDTVVMMGTFAQTFGAAKWAYVGGAVAA
+SLVWFTALGWGGTKLAPSMDSARTWRIVDAVVGVLMLGIAVKVGLTLL
+>1_1833
+MARTWGDSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA
+LLVLGAGGVGVVAERWPWLVPALTVAGVVYLLAFAVGALRSAWRGDRTLTTAAADAAGTG
+HGPDRIDLAVLTGELPLIDPATGRLAEREPAGAGVGQHDDGAPGVGAPSGGGSVAARQRV
+QPRRVALDRPQTPLPRIILLALSVSLVNPHAILDTVVMMGTFAQTFGAAKWTYVGGAVAA
+SLVWFTALGWGGTKLAPSMDSARTWRIVDAVVGVLMLGIAVKVGLTLL
+>2_565
+MTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLIVCFLGDVALLALGAAGIGVV
+AERWPWLVTALTVAGVVYLVWFAAGALRSAVRGQRTLAAAAEAEGPAVGLTDGEIAALTG
+ELPLIDPATGRLSADFTGRTAEGRAVPVGAGVGMGRGHDPLGDESRTVGGIPVGNPRLCG
+TRPGERGADGRSGGVAVKQRVQPRRVVLSAPQTPLPRIVLLALSVSFLNPHAVLDTVVMM
+GTFAQTYGPGKWVYVGGAVAASLVWFTALGWGGTRLAPYMNTPRTWRIVDAAVGVLMLVI
+AAKVGLTLL
+>3_492
+MTVFSAGFLTYLALIVAIGAQTLFLLRQVVRGDRAWTAIGVCFLSDIVLLLAGAAGVGAA
+AERAPWLVPALTVAGVAYLVWFGVSALRSAHRGDRTLAGAAAEVEDDAWAPTAEEVAAMT
+GSLPVVAAGPDAGADAATAPAGTGGGVALRTRPVSTTAPASAAPRPALTPLPRLVLLCLS
+VSLLNPHAILDAVVMMGTFAQGYGADKWLYVAGAVASSALWFLVLGWGGAKLAPLMNTPR
+TWRIVDGAVGVVVLGIAGKVALTLF
+>4_2054
+MARTWDGSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA
+LLVLGVGGVGVVAERWPWLVPALTVAGVVYLLAFAVGALRSAWRGDRTLTTAAADGAGTG
+HGPDRIDLAVLTGELPLIDPATGRLADREPAGAGVGRHDDGAPGVGAPSGGGSVAVRQRV
+QPRRVALDRPQTPLPRIILLALSVSLVNPHAILDTVVMMGTFAQTFGAAKWVYVGGAVAA
+SLVWFTALGWGGTKLAPSMDSARTWRIVDAVVGVLMLGIAVKVGLTLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001698.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001698.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fe78a0aee7a2f1e93cf2633e0f21a770c4574f61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001698.fa
@@ -0,0 +1,35 @@
+>0_2114
+MAPSPLSRRSLLASGGVGLTLLLAACSTGPAGGSASSSSAGASSSDAAGGDAAFPRSIEH
+VYGTTEIPQRPTRVATVSWVNQDVTLALGVVPVGMAAVEFGGNAEKSTDWFDAKLAETEG
+AQKPVQWSEASGIDAEAIAAVKPDVILAVYSGITQEDYDRLSKIAPTVAYPKDVPAYGTS
+WQQSTEVIGRVLGKEQEAEELIADLEQQIKDAGEKHADLQGASFVYGTIDPAAADQISIY
+TDVDNRPKFLELLGMEQAPVVTENSPEDQAFFFTWSPERADELESDVFVSWAAQDSVREA
+IESDPLLGSIPAVKAGALVLQTDEQEVLSVSAISPLSIPFALEKVVPPIAEAAKTAQG
+>1_1839
+MAPSPLSRRSLLASGGVGLTLLLAACSTGPAGGSASSSSAGASSSDAAGGDAAFPRSIEH
+VYGTTEIPQRPARVATVSWVNQDVALALGVVPVGVAAVEFGGNAEKSTDWFDAKLAETEG
+AQKPVQWSEASGIDAEAIAAVKPDVILAVYSGITQEDYDRLSKIAPTVAYPKDVPAYGTS
+WQQSTEVIGRVLGKEQEAEELIADLEQQIKDAGEKHAGLQGASFVYGTIDPAAADQISIY
+TDVDNRPKFLELLGMEQAPVVTENSPEDQAFFFTWSPERADELESDVFVSWAAQDSVREA
+IESDPLLGSIPAVKAGALVLQTDEQEVLSVSAISPLSIPFALEKVVPPIAEAAKTAQG
+>2_559
+MATVSWVNQDVALALGVVPVGMAAVEFGGNAEKSTDWFDAALEKVEGAERPVTWSEAAGI
+DAEAVASVRPDVILAAYSGLTREDYDRLSKIAPVVAYPKDVPAFGTPWQQSTRMIGQALG
+KDAEAEALVEDVEGRIAAAAQKHPDLKDATFVYGTVDPTAADQISVYTLVDNRPRFLESL
+GMKQAPVVAENSPKDQAFFFTWSPERADELESDVLVSWALDASVADAIEADPLLSALPAV
+QKDGLVLQVDQQEVLSVSAISPLSIPFALERIVPPIAEAAARSRG
+>3_487
+MPQSPSRRSVLAAGGSGLALLLAACSTGPAGSSVPSSSPASSAGSAAASSSASGSAAYPL
+TVEHVYGTTEIPARPERVATVSWVNQDVALALGVVPVGVPAVEFGGNADKSTDWFDAKLK
+ELGGPTPVQWSEADGIDAEAIAAVKPDVILAVYSGLTREDYDRLSKIAPVVAYPKDVPAF
+GTSWQQSTEVIGRVLGKEREAAALVADLERQIADAGAEEDGLAGASFIYGTLDPAAADQI
+SIYTAADNRPKFLELLGMELAPVVAENAPEDGAFFFTWSPERADELESDVFVSWAASADV
+ADAIEADPLLGAIPAVEKGGLVLQVDQQEVLSVSAISPLSIPYALEKVVPPIAEAARAAK
+G
+>4_2060
+MAPSPLSRRSLLASGGVGLTLLLAACSTGPAGGSASSSSAGASSSDAAGGDAAFPRSIEH
+VYGTTEIPQRPARVATVSWVNQDVALALGVVPVGMAAVEFGGNAEKSTDWFDAKLAETEG
+AQKPVQWSEASGIDAEAIAAVKPDVILAVYSGITQEDYDRLSKIAPTVAYPKDVPAYGTS
+WQQSTEVIGRVLGKEQEAEELIADLEQQIKDAGEKHAGLQGASFVYGTIDPAAADQISIY
+TDVDNRPKFLELLGMEQAPVVTENSPEDQAFFFTWSPERADELESDVFVSWAAQDSVREA
+IESDPLLGSIPAVKAGALVLQTDEQEVLSVSAISPLSIPFALEKVVPPIAEAAKTAQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001700.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001700.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38332686de17101781945146edce9e688ebc5f49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001700.fa
@@ -0,0 +1,36 @@
+>0_2116
+MSLQCTAPDDVVARLRRADRRRLGGACAGLAVAVLVLALLRVVWGTYQVTVPDLVRILGG
+ETIPGASFIVLEEKLPRAVAAVLTGAALGAAGALYRRTLRNPLASPDILGVTQGAAAAVV
+LGMLATAGQTGGGSDLMRAATALIGGLAAVVAVFATARSVGGERFVVAGIAVAAAGQAVV
+AGAMLSLAQHDLQSATVWIAGSLNGVTWGRIALLAGVLVVALPLAGVLHARLAPADVGPD
+LAHALGARPRPTSAAALGLGAVLAAVATAVVGPLAFVALLATPVARGLTRGLPSLPAAAL
+TGAALVLLADLVAGEAVPLLTGAALPTGVLTGAAGAPLMLWLLLCQGRTPGGVRSA
+>1_1841
+MNLQHTAPDDVVARLRRSDRRRLGRACAGLAVAVLVLALLRVVWGTYQVTVPDLVRILGG
+ETIPGASFIVLEEKLPRAVAAVLTGAALGAAGALYRRTLRNPLASPDILGVTQGAAAAVV
+LGMLATAGQTGGGSDLMRAATALIGGLVAVAAVFATARSVGGERFVVAGIAVAAAGQAVV
+AGAMLSLAQHDLQSATVWIAGSLNGVTWGRIALLAGVLAAALPLAGALHTQLAPADVGPD
+LAHALGARARPTSAAALGLGAVLAAVATAVVGPLAFVALLATPVARGLTRGLPSLPAAAL
+TGAALVLLADLVAGEAVPLLTGAALPTGVLTGAAGAPLMLWLLLRQGRTPGGVRPA
+>2_557
+MSGRGSATLEHAVARVRAARRRDARRVGTALAVLTAAVLALVLLRLTWGAYMVAVPDLVR
+ILTGTTIPGASFIVTEEKLPRAAAAVLAGAALGAAGALYRRGLGNPLASPDVLGVTSGAA
+AGAVLWQAAATGTGGTTDAARAAAALAGGLIAALAVLLAARGTGGERFVVAGIAVAAGAQ
+AVVAGTMVTLAEHDLQAAALWVSGSLTGVTWGRIGLLAAAVALALPLAAWLHGRLEPADT
+GEDLAHALGARPRRTRPAALLLGAVLAAAATAAVGPLAFVALLATPLARGLAGGRPSLAA
+AALAGAVLVLAADLLAAEAVALLADGTRLPTGVLTGAAGAPLMMTLLIRAGRRGERTA
+>3_485
+MSARRETTTPGRRDAAPGGDAPETVRALRRADARRVAGVVLGLAVLTAGLMLLRVTWGTY
+QVTVPDLVRILGGERIAGASFIVWEEKLPRAVAATLTGAALGAAGALYRRTLRNPLASPD
+VLGTTAGAAAGVVLTLTASAGQAGGSSDLARAGAALLGALAAGAAVLLAARSVGGQRFVV
+AGVGVAAAGQAIVSGAMLSLSEHDLASATRWIAGSLNGVTWGRIGLLAAVLALALPAAGW
+LHRRLAPADVGDDLAHALGARPRTTAALALTVGAVLAAAATATVGPLSFVALLATPLALG
+LTRGRPSLPAAALTGAGIVLLADVLGTEALGLIADGAALPTGVLTGAAGAPLMLALLLRA
+GRSSEGTR
+>4_2062
+MSVQRTASDDVVARLRRSDRRRLGGACTGLAVAVLVLALLRVVWGTYQVTVPDLVRILAG
+ETIPGASFIVLEEKLPRAVAAVLTGAALGAAGALYRRTLRNPLASPDILGVTQGAAATVV
+LGMLATAGQTGGGSDLMRAATALIGGLVAVAAVFATARSVGGERFVVAGIAVAAAGQAVV
+AGAMLSLAQHDLQSATVWIAGSLNGVTWGRIALLAGVLAAALPLAGALHTQLAPADVGPD
+LAHALGARARPTSAAALGLGAVLAAVATAVVGPLAFVALLATPVARGLTRGLPSLPAAAL
+TGAALVLLADLVAGEAVPLLTGAALPTGVLTGAAGAPLMLWLLLRQGRTPGGVRPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001701.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001701.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a868b4b233eca04172f8cdfa227b673adc5d7826
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001701.fa
@@ -0,0 +1,32 @@
+>0_2117
+MTAPPLTVPSPAAPRAGAADDVAIRLRGLTLGYGPASAPPIVADLDLDVPAGRVTAIIGA
+NGCGKSTLLRGLTRQLAPRAGSIEVLGRDAARVSARDYARTVALLPQHPVAPEGMTVAQL
+VARGRHPHRGLLGGRAAGDDAAIASALERTDLVELADREAGTLSGGQRQRAWLALVLAQQ
+TPVVLLDEPTSYLDLSHQVEVLDLVRALPDPRGGGRATVVAVLHELNLAARSADHIVAMA
+AGRVVAQGTPGEVIVPEVLAEVFGLDADVVADPLLGHPVVLPRGDGDRR
+>1_1842
+MTAPPLTVPSPAAPRAGAADDVAIRLRGLTLGYGPASAPPIVEDLDLDVPAGRVTAIIGA
+NGCGKSTLLRGLTRQLAPRAGSIEVLGRDAARVSARDYARTVALLPQHPVAPEGMTVAQL
+VARGRHPHRGLLGGRAAGDDAAIASALERTDLVELADREAGTLSGGQRQRAWLALVLAQQ
+TPVVLLDEPTSYLDLSHQVEVLDLVRALPDPRGGGRATVVAVLHELNLAARSADHIVAMA
+AGRVVAQGTPGEVIVPEVLAEVFGLDADVVADPLLGHPVVLPRGDGDRR
+>2_556
+MTPPHPAAAPAERPGADPATGPAQDPALRLRGVRLGYGRPDTPDTVGPVDLDVPAGRVTA
+LIGANGCGKSTLLRGLTRQLPLRGGSAEVLGRDLGAYSAREYARTVALLPQHPVAPEGMT
+VAQLVQRGRHPHRGLFGTTGADDDAAVARALRHTDLEKLADREVAELSGGQRQRAWLALV
+LAQRTPVLLLDEPTSYLDLAHQVEVLDLVRGLTRPDGDEEPVTVVAVLHELSLAARVADR
+LVALRDGRVAAAGTPAEVLTPAVLAEVFDLDADVRPDPLLGHPVVLPRGAADRGAPLPSP
+TTQETR
+>3_484
+MTSSPPTPAAPSTAPAPALRLRGVELSYGPASAPPTVGPVDLDVPAGQVTAVIGANGCGK
+STLLRGLTRQLPLRAGTVDVLGRDAAGMSARDYARTVALLPQQPVTPEGLTVAQLVERGR
+HPWRGLLGGRAAGDDAAVAAALARTGLVDLAARDAATLSGGQRQRAWLALVLAQQTPVVL
+LDEPTSYLDLAHQVEVLDLVRTLPDPRAVGARTVEAAGGVVGGGAGTEAGPPPRATVVAV
+LHELSLAARAADHVVAMAGGRVVATGTPAEVIVPEVLAEVFGLDADVVPDPLLGHPVVLP
+RGRGDRA
+>4_2063
+MTAPPLTVPSPAAPRAGAADDVAIRLRGLTLGYGPASAPPIVEDLDLDVPAGRVTAIIGA
+NGCGKSTLLRGLTRQLAPRAGSIEVLGRDAARVSARDYARTVALLPQHPVAPEGMTVAQL
+VARGRHPHRGLLGGRAAGDDAAIASALERTGLVELAEREAGTLSGGQRQRAWLALVLAQQ
+TPVVLLDEPTSYLDLSHQVEVLDLVRALPDPRGGGRATVVAVLHELNLAARSADHIVAMA
+AGRVVAQGTPGEVIAPEVLAEVFGLDADVVADPLLGHPVVLPRGDGDRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001707.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001707.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83ec865002439422223c2e5e42ec8d5bef01f972
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001707.fa
@@ -0,0 +1,20 @@
+>0_2124
+MTQPTTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLAEEARVRALAAWATTT
+ASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRCVLCDAV
+FVQVDPAAGRPVAVSDEERAAFERVLIPAED
+>1_1849
+MTQPTTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLAEEARVRALAAWATTT
+ASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRCVLCDAV
+FVQVDPAAGRPVAVSDEERAAFERVLIPAED
+>2_547
+MNGQDGGQGRTTTDGATGREAPVPFETEIQVRWSDEDRYGHVNNARLLTLTEEARVRATR
+AWSGVTPGRDVHRVVRAMEVQYEAPVVYGPELTAKVWIARIGTSSYTLRHELWQDGRRCV
+LCDAVFVHVDPETGRSVALAEDERVTLERVLIPAEADAT
+>3_473
+MSDSQPRPYEGVLDLRWSDMDLYGHVNNVRILTLTEEARVRALKAWDEGDVGRDVMRVVR
+AMTTEYERPVEYGPELTAKVWVRALGRTSYTLHHELWQEGVRCVTCDAVMVHLDPETGAP
+LPHDDARRARLQAVLVPAEG
+>4_2070
+MTQPTTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLTEEARVRALAAWATTT
+ASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRCVLCDAV
+FVQVDPAAGRPVAVSDEERAAFERVLIPAED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001708.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001708.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3809687a15b439e04c02269e8255e9c548da9509
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001708.fa
@@ -0,0 +1,30 @@
+>0_2125
+MEQDPSPDAPAPSADVEALRGTPVSELTQLTPAASGALERLRRDVERFDLEYRSALLQVE
+ARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLSLDLDALRTNVTDIAGARV
+IVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPIHLSTGTIPVTV
+EMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVAADLDTRMERLHDQVQETD
+RDDDAAAAWEDDGGPAFEDEPTVEPGEARPGDAPGASTA
+>1_1850
+MEQDPSPDAPAPSADVEALRGTPVSELTQLTPAASGALERLRRDVERFDLEYRSALLQVE
+ARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLSLDLDALRTNVTDIAGARV
+IVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPIHLSTGTIPVTV
+EMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVAADLDTRMERLHDQVQETD
+RDDDAAAAWEDDGGPVFEDEPAAGPGEARPGDDAPGASTV
+>2_545
+MEQDRDPEESSQSTAIETLRGTPVSELTHLPPAMAGALDRLRRDVERFDLEYRSALLQVE
+ARLEVLRDEFTHLHDYNPIEHIVTRVKTPESILRKAASRGLSMDLDALRSNVTDIAGARV
+IVSFARDVYEVFRLFTRQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPVHLSTGSIPVTV
+EMQFRTSAMDFWATLEHKINYKFDGAVPPDITTELIAAARVAADLDTRMERLSDQVRQTD
+KDDDAAASWEDDGGPAFEDEGDDDGPDGDAPGTSTG
+>3_472
+MPRDVDHPPPADDPAPVERPAPGGRGVTSASTALEALRATPLTDLTQLPGEVADALASLR
+TDFERFDLEYRSALLQVETRLETLQDEFTHLHEYNPIEHIATRVKSPESLLRKAASRGLS
+LDLDALRSGVTDIAGARVIVSFTEDVYRVFRQFTSQPDIRVLEVEDYIRDPKPSGYRSLH
+CLVQVPVHLTTGTVPVTVELQFRTIAMDFWASLEHKINYKFAGHVPPAITTELAAAARVA
+HDLDARMERLHQAVHDAGAGPDEHDDEDDWVGHA
+>4_2071
+MEQDPSPDAPAPSADVEALRGTPVSELTQLTPAASGALERLRRDVERFDLEYRSALLQVE
+ARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLSLDLDALRTNVTDIAGARV
+IVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPIHLSTGTIQVTV
+EMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVAADLDTRMERLHDQVQETD
+RDDDAAAAWEDDGGPAFEDEPAAGPDGTDPGEARPGDDAPGASTV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001712.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001712.fa
new file mode 100644
index 0000000000000000000000000000000000000000..42201ea70091109d6e0f70fcd28c5657bace338e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001712.fa
@@ -0,0 +1,75 @@
+>0_2134
+MLFRYELRRFRRGLPLLALLFIFLVPAIYGALYLSANWDPYGAMDRLPVAIVNEDEPVQR
+GDTTLRTGADMTERLKDDRAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG
+GTPQQAQITLRRDDANGFVIGSVTNASQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD
+AADGAAQLADGTASAEDGASRLEDGIVQAHDGSGKLAEGAGQLATGAGDLADGAAQADDG
+AQRLAEGAASAQDGAGRLADGLDQAREGSQALADGAGQLAENAPALRQGATDLSDGLAQL
+QTGSAELTDGATQVADGTQQLYDTVVPGLDQVIERQDAVAADVAAVDEDVQRVAEVAGTA
+EDGAGARIADAQTALAALAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA
+AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF
+ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA
+GQLESGATELDGGLAQLQDGAGELRAGLGTLDDGAHELASGLSDGADRVPALTEDERDEA
+ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGRRNPV
+AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL
+GTPGSALLLVLLVLQLASTGGTYPAEVLPGFFQALHPFMPMSYSIEAFRNAISGGPDQRF
+WVPVVVLMGIGAAALALDVLVVRRRRRFRMKDLHPALQA
+>1_1858
+MLFRYELRRFRRGLPLLALLFIFLVPAIYGALYLSANWDPYGAMDRLPVAIVNEDEPVQR
+GDTTLRTGADMTERLKDDRAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG
+GTPRQAQITLRRDDANGFVIGSVTNASQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD
+AADGAAQLADGTASAEDGASQLEDGIVQAHDGSGKLAEGAGQLATGAGDLADGAAQADDG
+AQRLAEGAASAQDGAGRLADGLDQARGGSQALADGAGQLAENAPALRQGATDLSDGLAQL
+QTGSAELTDGATQVADGTQQLYDTVIPGLDQVIERQDAVAADVAAVDEDVQRVAEVAGTA
+EDGAGARIADAQAALAELAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA
+AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF
+ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA
+GQLESGATELDGGLAQLQDGAGELRAGLGTLDDGAHELASGLSDGVDRVPALTEDERDEA
+ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGRRNPV
+AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL
+GTPGSALLLVLLVLQLASTGGTYPAEVLPGFFQALHPFMPMSYSIEAFRNAISGGPDQRF
+WVPVVVLMGIGAAALALDVLVVRRRRRFRMKDLHPALQA
+>2_531
+MLFRYELRRFRRGLPLLALLFILLVPAIYGALYLSANWDPYGAMNRLPVAIVNEDEPVQR
+GDTTLRTGADMTARLKEDHAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG
+GTPQQAQITLRRDDANGFVIGSVTASSQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD
+AADGAAQLADGSASAVDGASQLEDGIVQAHDGSGRLAEGAGQLATGAGDLADGAAQADDG
+AQRLAEGATSAQDGAGRLADGLDQAREGSQALADGAGQLAENAPALRQGATDLSDGLAQL
+QTGSAELTDGATQVADGTQQLYDTVVPGLDRVIERQDAVAADVAAVDEDVQRVAEVAGTA
+GDGAGARIADAQAALAALAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA
+AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF
+ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA
+GQLESGATELDDGLAQLQDGAGELHTGLRTLDDGAHELASGLSDGVDRVPALTEDQRDEA
+ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGHRNPV
+AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL
+GTPGSALLLVLLILQLASTGGTYPAEVLPGFFRALHPFMPMSYSIEAFRNAISGGLDQHF
+WVPVVVLMGVGAAALALDVLVVRRRRRFRMKDLHPALQA
+>3_461
+MLFRYELRRFRGVLPTIALLFIVLVPTIYGALYLSANWDPYGNLSSLPVAIVNEDRPVES
+DGKTLTTGADITEELVDQHTFDWHETTRDDAEAGLRDGRYYLVMEIPEGLSADLVSANTS
+DPQQAHITLRRNDANGFVIGSVTSSSQSKIENAVDKAAVEAYFKAVFENLATIRQGMADA
+RDGAGRLADGAGQADDGAAQLADGIVQAHDGSGQLAQGASDAQDGAGQLADGAGQLKDGA
+DQLAAGATSAKDGAVQLQTGIGQAREGSQKLADGAGQIAAKVPDLRDGATALSNGLTQLD
+TGSADLADGAHQVADGTQQLYDTVIPGLDAVIERQDKVASDVATVNQDVQTLNDAVATAG
+SGAGGDIDTASEQLQALAESNPDIAVAPEYAALQQSLTDAKEKAGSATSTAQDVADRSAA
+VNSRVQGFVSEDVAGNAKADITKLNDGAHAVAEGADTLHAGIGQANTGAQALADGVGRFA
+DALDQLAAGATALDDGLAQLEDGSGRLVDGLGKLETGAGDLADGAGRLDQGAGELQTGLG
+KLSDGATSLDSGLAQLETGSGDLKTGLDSLSDGATQLHDGLASGTDKIPALSEDAADEAA
+LVMSRPVQVDMDVLNPAGVYGRGVAPLFFSIALWVFGIAAFNVMRPVNGRLLAGRRNPLL
+LALSAWLPVGLLSVVGSLVMLAATVPLGIDPVHPWHLVGLVVFTALAFSLFAHLVMTALG
+TPGSAVLLVTLILQLGSAGGTYPADVLPPFFRWVSPLMPMTHSINAIRYALSGGQPAQFW
+GAVAFLAVFGAACLFLDMAVVRRRQRFRMKDLHPALEK
+>4_2079
+MLFRYELRRFRRGLPLLALLFIFLVPAIYGALYLSANWDPYGAMDRLPVAIVNEDEPVQR
+GDTTLRTGADMTERLKDDRAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG
+GTPQQAQITLRRDDANGFVIGSVTNASQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD
+AADGAAQLADGTASAKDGASQLEDGIVQAHDGSGKLAEGAGQLATGAGDLADGAAQADDG
+AQRLAEGAASAQDGAGRLADGLDQARGGSQALADGAGQLAENAPALRQGATDLSDGLAQL
+QTGSAELTDGATQVADGTQQLYDTVVPGLDQVIERQDAVAADVAAVDEDVQRVAEVAGTA
+EDGAGARIADAQAALAALAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA
+AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF
+ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA
+GQLESGATELDDGLAQLQDGAGELHTGLGTLDDGAHELASGLSDGVDRVPALTEDERDEA
+ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGRRNPV
+AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL
+GTPGSALLLVLLILQLASTGGTYPAEVLPGFFQALHPFMPMSYSIEAFRNAISGGLDQRF
+WVPVVVLMGIGAAALALDVLVVRRRRRFRMKDLHPALQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001718.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001718.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6988259ccb688d7655e8bd44d055f2a659ec6c74
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001718.fa
@@ -0,0 +1,27 @@
+>0_2141
+MPPAPTARLRFREMADADLDHLAGLLADPVVMRFYPAPRTRAEAAAWIAGNRRRYAQDGH
+GLWIIETHDDGGPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACRDHAR
+DVLGHHELVAIIHPENTASRRVAERIGMTVVGEDRTGAPEARAALGLEARTVLGMRLRPG
+A
+>1_1865
+MPPAPTARLRFREMADADLDHLAGLLADPVVMRFYPAPRTRAEAAAWIAGNRRRYAQDGH
+GLWIIETHDDGGPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACRDHAR
+DVLGHHELVAIIHPENTASRRVAERIGMTVVGEDRTGAPEARAALGLEARTVLGMRLRPG
+A
+>2_523
+MLPAPTARLRFREMTEADLDAMAALLGDPAVMRFYPAPRTREQAAEWIAGNRRRYAQDGH
+GLWVIETLPEHSDDGEPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACR
+DHARDALGHHELVAIIHPENSVSRRVAEKIGLREAEQDFTGAAEARETMGLASRTVMAMR
+F
+>3_455
+MTQPIPRHPDPGNTGTDALDDVVREHMLLLRRAVHGLGAYRRPEALDRSAVLLLARLEAQ
+GPMTMAELAAAFGLDVSTLQRQIGAAQRAGFVERFRDPAGGQARLHRATDAGRAALEGEL
+AARRAAVAEVTRSWPAPDVAALARLLRRFNEGSEELREQPWPRERPEAPGAAAVPAGTAR
+LRFREMTEADLDVLVGLLGDPEVMEFYPAPKTRAEVADWIAWNRRSYAEHGHGLWIVETH
+AGAFVGECGLTWQRVNGERRLEVGYHVAPVLQGRGYATEAAAACRDHARDVLGAPELVAI
+VHPENTASRRVAEKIGMEVLEEDRTGVDASYLEAIGAEARTVLGMRLA
+>4_2086
+MPPAPTARLRFREMADADLDHLAGLLADPVVMRFYPAPRTRAEAAAWIAGNRRRYAQDGH
+GLWIIETHDDGGPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACRDHAR
+DVLGHHELVAIIHPENTASRRVAERIGMTVVGEDRTGAPEARAALGLEARTVLGMRLRPG
+A
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001719.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001719.fa
new file mode 100644
index 0000000000000000000000000000000000000000..846e245397b29e468d7c5b8004bfab059d8341ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001719.fa
@@ -0,0 +1,37 @@
+>0_2145
+MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN
+LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF
+RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA
+LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI
+DATPSQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAEPAQGEDD
+DGAPSPILAADHLARVVLGAEPRVVTQLAERVLAPLDEVSEAKRAVLEETLLAWLTHWGQ
+RAPIAAELGVHPQTVGYRVGRLRELFGEALEDPDARFDLEIVLRARRDGVG
+>1_1869
+MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN
+LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF
+RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA
+LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI
+DATPSQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAEPAQGEDD
+DGAPSPILAADHLARVVLGAEPRVVTQLAERVLAPLDEVSEAKRAVLEETLLAWLTHWGQ
+RAPIAAELGVHPQTVGYRVGRLRELFGEALEDPDARFDLEIVLRARRDGVG
+>2_521
+MTSPRPESDWRPPWQDLPADLPGRLAHALPGIMERIIQTVPDQIPAYAAARDGRYGKNLT
+LGVTTALEQLMSLPGTSRPALSAQSRELMARLGAGEFREGRSMDALLGAYRTSARIVFRD
+LSAECARLGMDMSVVIELGESIWAYIDELSAVSAQAYAEAQSAQAGVRELHRTALAAALV
+RGGAEEKEVERLAALADWRVPARLAVVALPPDAGQAVRARLGRGGLVVERDSEVVAVVGA
+DAPARRRRLLRILAGTAAVVGPAVEWPLAPHSYRVARTLAGQEAARRAAEQRAAARPEGD
+GSAADGPGAEEAVGFEPVGGADPAPGTPILAEEHLARVVLGAEPRVVAELAERVLAPLAE
+LTDAKRAVLEQTLLSWLVHWGQRAPIAAELSVHPQTVGYRVARLRELFGDALEDPDARFD
+LELVLRARAGGMAA
+>3_452
+MVLSAPPRSPVVTRRLLAALQGTGAVVGPEVDALEVARSLHVARAVLARRDALSGVAPGA
+AVLAEEHLADVVLGAEPEALRRLSERVLAPLDGLSDAKRATLEATLAAWLAHRGARGPMA
+AELNVHPQTVGYRVGRLRELFGGALDDADARFDLELALRSRRGQG
+>4_2090
+MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN
+LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF
+RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA
+LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI
+DATPSQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAEPAQGEDD
+DGAPSPILAADHLARVVLGAEPRVVTQLAERVLAPLDEVSEAKRAVLEETLLAWLTHWGQ
+RAPIAAELGVHPQTVGYRVGRLRELFGEALEDPDARFDLEIVLRARRDGVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001723.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001723.fa
new file mode 100644
index 0000000000000000000000000000000000000000..03d7b607cb154d8548e4f3d96aa69fbd5cf28d7c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001723.fa
@@ -0,0 +1,25 @@
+>0_2159
+MKHEIVLTRGDLTLRPLTPDDGPALRELVDAAMWAGNSAPLPVDGAAMSAHLAELSEREG
+TFAFAVEQGGELVGRTSLYDLVPGLRVEVGHTVYARRVWGTSVNPGCKLLLFGHAFEEWA
+LERVALRCDHRNARSHAAIARLGATFEGTLRRFRPAADGTIADVDYFSVVREEWPAVRGG
+LEARLAA
+>1_1883
+MKHEIVLTRGDLTLRPLSPTDGPALRELVDAAMWAGNSAPLPVDGAAMSAHLAELIEREG
+AFAFAVEQGGELVGRTSLYDLVPGLRVEVGHTVYARRVWGTSVNPGCKLLLFGHAFEEWA
+LERVALRCDHRNARSHAAIARLGATFEGTLRRFRPAADGTIADVDYFSVVREEWPAVRAG
+LEARLTA
+>2_497
+MSHDLHLTHGPIRLRPLTPDDAPRLRAIVDEASWAGMSTPLPETDAAMAEHLRELMGRPG
+LQAFAVERDGEFVGRTALYDPVPTVRVDVGHTVYARPVWGTEVNPACKLLLLGHAFEELG
+VARVGLRCDHRNTRSHRAILRLGATFEGTLRAFRRAADGTVADADHFSVTAPEWPAVRAG
+LETRLGA
+>3_445
+MPAAQLPADLLLEHGAVRLRPLTLDDAPRLRALVDAGSWAGMSSPLPTSDEAMAAHLAQL
+MAREDLTAFAVERDGEFVGRTAYYEHVPGVRVDVGHTIYAREVWGTEVNPACKLLLLRHA
+FEALGVERVGLRCDHRNTRSHRAILRLGATFEGTLRAFRPAADGTVADVDYFSVLAAEWP
+AVRAGLEARLAGSAPAD
+>4_2099
+MKHEIVLTRGDLTLRPLSPTDGPALRELVDAVMWAGNSTPLPVDGAAMSAHLAELIEREG
+TFAFAVEQGGELVGRTSLYDLVPGLRVEVGHTVYARRVWGTSVNPGCKLLLFGHAFEEWA
+LERVALRCDHRNARSHAAIARLGATFEGTLRRFRPAADGTIADVDYFSVVREEWPAVRAG
+LEARLAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001729.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001729.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5097ec7a8d6055945b6e1bcc4597276a2de8cc7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001729.fa
@@ -0,0 +1,50 @@
+>0_2186
+MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLTDMVGQLARGGSSSAGISSF
+QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR
+GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW
+VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQVPAMFGLIFSS
+ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD
+TLFVCTMTGLMILATNSFNVLGPDGESLLAEHVPGVEEGPAWVQIAIDEALPAFGPSFVA
+IAVFLFSFTTLLSFAFYAETNVAYLIPNKTAQRAVIAIARLLLAGSMVFGSVQTSAFVWS
+LADFGVGLYTWVNIVALILLSPVAIRLFKDYDRQRRAGQDPVLDPAAIGVRNARLWEQIH
+AAYQQTGDLDRAMEHVADTAPDTRAITVVPRREG
+>1_1899
+MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLRDMVGQLVRGGSSSAGISSF
+QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR
+GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW
+VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQVPAMFGLIFSS
+ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD
+TLFVCTMTGLMILATNSFNVLGTGEGPPIVEHLPGVEEGPAWVQIGIDVVLPSFGPSFVA
+VAVFLFAFTTLLSFAFYAETNLAYLIPNKKAQRICIAAARLLLAASMVIGSVQTSAFVWS
+LADFGVGLYTWVNILALVLLSPVAIRLLKDYDRQRRAGQDPVLDPAAIGVRNAHLWEQIH
+AAYQQTGDLDRAMEHVADTAPDTRAITVVPRREG
+>2_481
+MEQFLAGANAIMWSLPMVFGLLALGLYFTIRMGAPQLRRIPDMIGQLVRGGSSSAGISSF
+QAFAMALGGRIGVGNIAGVATAISLGGPGALFWMWVTALLGAPVALAESSLAQLYKHKVR
+GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVITGPQIQANAVTAATTQAWGWDPLW
+VGLAMAVLFCVIVFGGMHRLGRTVGLVVPFMAAAYIIVGVVVVALMWQQVPAMFGLIFTS
+AFAADSLYAGMLGAAISWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAFVD
+TLFVCTVTGLMILSTNSFNVLGPDEETVLVEHVPGIEAGPAWVQTAIDSVIPAFGPAFVA
+VAVFLFSFTTLLSFAFYAETNLAYLIPNKSVQRACIAVARLGLAASMVFGAVQTSTLVWS
+FADFGVGLYTWVNILALVLLSPVAIRLMKDYDRQRRAGQDPVLDPRAIGVRNATLWEQIH
+DEYERTGDVTAALDHVADTAPDTRAISVVRSHGERGQG
+>3_420
+MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLKDMVGQLVRGGSSSAGISSF
+QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR
+GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW
+VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQVPAMFGLIFSS
+ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD
+TLFVCTMTGLMILATNSFNVLGPDGESLLAENVPGVEEGPAWVQIAIDAALPAFGPSFVA
+IAVFLFSFTTLLSFAFYAETNVAYLIPNKTAQRAVIAIARLLLAGSMVFGSVQSSALVWA
+FADFGVGLYTWVNIVALILLSPVAIRLFKDYDRQRRAGQDPVLDPAAIGVRNARLWEQIH
+AAYQQTGDLDRAMEHVADTAPDTRAITVVRGGPERGEG
+>4_2119
+MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLTDMVGQLARGGSSSAGISSF
+QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR
+GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW
+VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQIPAMFGLIFSS
+ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD
+TLFVCTMTGLMILATNSFNVLGPDEESLLAEHVPGVEEGPAWVQIAIDEALPAFGPSFVA
+IAVFLFSFTTLLSFAFYAETNVAYLIPNKTAQRAVIAIARLLLAGSMVFGSVQTSAFVWS
+LADFGVGLYTWVNIVALILLSPVAIRLLKDYDRQRRAGQEPVLDPHAIGVRNARLWEQIH
+AAYQQTGDLDRAMEHVADTAPDTRAITVVPRREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001730.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001730.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a1ef6656861cb2b4bd94d5a20ea74d2ae8c43af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001730.fa
@@ -0,0 +1,29 @@
+>0_2193
+MMGPSHAATGAAAWLALTHWQSPIAVLHLPAELQLLGAVTTAGAAMISDWDHPRATVVHA
+LPPLTEWLSRGIRHVAGGHRRGTHSLVGVAAFTAIATAAASIQVPIAGHVYTPGQGVIAA
+FLAAVAAKALRLLPNRGWRAAWALGILVAVSATVLSDGLWWIPASVAVGVSVHILGDALT
+NNGVALLWPLSPEPPARLWWWQSSGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLVP
+LAARGVAALF
+>1_1904
+MMGPSHAATGAAAWLALTHWQSPIAALHLPAELQLLGAVTTAGAAMISDWDHPRATVVHA
+LPPLTEWLSRGIRHVAGGHRRGTHSLVGIAAFTAVATAAASIQVPIAGHVYTPGQGVIAA
+FLAAVAAKALRLLPNRGWRAAWALGILVAVSATVLSDGLWWIPASVAVGVSVHILGDALT
+NNGVALLWPLSPEPPTRLWWWQSSGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLIP
+LAARGVAALF
+>2_459
+MGPSHAATGAAAWLALTHWQSPIAVLHLPAELQLLGAVTTAGAAMISDWDHPRATVVHAL
+PPLTEWMSRGIRHVAGGHRRGTHSLVGIAAFTAIATAAASIQVPIAGHVYTPGQGVIAAF
+LAAVAAKALRLLPNRGWRAAWALGILVAGAATVLSDGLWWIPASVAVGVSVHILGDALTN
+NGVALLWPLSPEPPARLWWWQSSGRFRLPLLGRTGSWREWAFVSVVTAFTVVRAVRLVPL
+AARGVAGLLGAGAPS
+>3_415
+MSTPPAALALFLPRGPPAGPRGCGDAAWLALTHGQSPVGVRHLPAELQLLGAVTTAGAAM
+ISDWDYPRATAIATAAASIHVPIAGHVYTPGQGVIAAFVAAVAAKALRLLPNRGWRAAWP
+LGILVAVSATVFSDGLRWIPVSVAVGVSVHILGDALTNNGVALLWPLSPEPPARLWWWQS
+SGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLVPLAARGAALF
+>4_2125
+MMGPSHAATGAAAWLALTHWQSPIAVLHLPAELQLLGAVTTAGAAMISDWDHPRATVVHA
+LPPLTEWLSRGIRHVAGGHRRGTHSLVGIAAFTAIATAAASIQVPIAGHVYTPGQGVIAA
+FLAAVAAKALRLLPNRGWRAAWALGILVAVSATVLSDGLWWIPASVAVGVSVHILGDALT
+NNGVALLWPLSPEPPARLWWWQSSGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLLP
+LAARGVAALF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001731.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001731.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d9563c6733ad66216021c1f44bc758f67cc8a1d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001731.fa
@@ -0,0 +1,30 @@
+>0_2194
+MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMNGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM
+VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG
+>1_1905
+MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM
+VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG
+>2_458
+MNGAELADSLAEAWDALLHTPLFGIALTLAVAVLARRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPIAVGVTVGSLTAM
+VSAVLIVRLMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVFAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG
+>3_414
+MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLARRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTAGSLTAM
+VSAVLIVRVMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG
+>4_2126
+MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM
+VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001732.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001732.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8dacf365c4e1cd1e919035a69374f4396bb0fb2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001732.fa
@@ -0,0 +1,17 @@
+>0_2195
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ
+HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTDKEDAQ
+>1_1906
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ
+HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTDKEDAQ
+>2_457
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTTSHHLLQ
+HLPLLFVPAGVGVVAVLGLIGEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTNKKENA
+Q
+>3_413
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVITASHQLLQ
+HLPLLFVPAGVGVVAVLGLIQEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTNKKEDA
+Q
+>4_2127
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ
+HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTDKEDAQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001733.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001733.fa
new file mode 100644
index 0000000000000000000000000000000000000000..166cde934bd51b29bb37304b2fe380c5b6554540
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001733.fa
@@ -0,0 +1,30 @@
+>0_2196
+MHPITLARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTEAGISRT
+PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH
+AATGGSVDAARRLLDGHAEICAQLAAGRAADAQRALQAHLDAAGSGVVPGLPPVGPSEAG
+EPR
+>1_1907
+MHPITLARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTEAGISRT
+PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH
+AATGGSVDAARRLLDGHAEICAQLAAGRAADAQRALQAHLDAAGSGVVPGLPPVGPSEAG
+EPR
+>2_456
+MHLIILARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVRLSTEAGISRT
+PAREALLQLESWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH
+AATGGSVDAARRLLDGHAEICAQLAAGCAADAQRALQAHLDAAGTGVVVPGLPTVSQPEA
+GEPR
+>3_412
+MHLIILARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTDAGISRT
+PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIAMCGNAAFDEIMGTFAPRLARLIH
+AATGGSVDAARRLLDGHVQICAQLAAGRAADAQRALQAHLDAAGAGVVVPGLLPVGSSEA
+GEPR
+>4_2128
+MHPITLARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTEAGISRT
+PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH
+AATGGSVDAARRLLDGHAEICAQLAAGRAADAQRALQAHLDAAGSGVVPGLPPVGPSEAG
+EPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001734.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001734.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2081eeff02f4e6edac3876d42314ba91d11e0420
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001734.fa
@@ -0,0 +1,55 @@
+>0_2207
+MPTLRTVPLSAATREDHLARLRATSPEAPLDILVVGGGSTGVGAAFDAATRGLDVGIVEA
+RDWASGTSSRSSRLMHGGLRYLEMLDVKLVYEALRERDLLLTQTAPHLVRPLRFVFPFFH
+KVIDRGFIGAGVTMYDAMQSLGRRRAMGAHRHLSRRSMAATFPSLDDEKIVGAVEYADAQ
+FDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGDDGRVQGVRVREETSGEEFDVHARAVI
+LAGGVWTQEQQELAGADGGLEVLASKGAHITVPRDRIRADAATGVITKTEKSVLFLIPWD
+EYWVIGTTDTPWAEDVAHPATTADDIDYILEHANAVLKEDLTRDDVVATYAGLRPLLQPV
+TGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTYRAMAEDVVDFVVRETHPTRPSLTERI
+PVLGGLGYSEIEAEADRIAADYGLDEARVDRLLFRYGTVLRHVLDLIDADPSLSVPLAEA
+PRYLRAEIVYAARAEGVVHLDDVIERRTRLSTEVRDRGVAAAEEIASLVAPELGWDEERI
+AGEIRAYKNLVAARLRGETAHDDVTAAAALAAADADAAPTP
+>1_1911
+MPTLRTVSLSAATREDHLARLRATSPEAPLDILIVGGGSTGVGAAFDAATRGLDVGIVEA
+RDWASGTSSRSSRLMHGGLRYLEMLDVKLVYEALRERDLLLTQTAPHLVRPLRFVFPFFH
+KVIDRGFIGAGVTMYDAMQSLGRRRAMGAHRHLSRRSMAATFPSLDDEKIVGAVEYADAQ
+FDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGDDGRVQGVRVREETSGEEFDVHARAVI
+LAGGVWTQEQQELAGADGGLEVLASKGAHITVPRDRIRADAATGVITKTEKSVLFLIPWD
+EYWVIGTTDTPWAEDVAHPATTADDIDYILEHANAVLKEDLTRDDVIATYAGLRPLLQPV
+TGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTYRAMAEDVVDFVVRETHPTRPSLTEHI
+PVLGGLGYSEIEAEADRIAADYGLDEARVDRLLFRYGTVLRHVLDLIDGDPSLSVPLAEA
+PRYLRAEIVYAARAEGVVHLDDVIERRTRLSTEVRDRGVAAAEEIASLVAPELGWDEERI
+AGEIRAYKNLVAARLRGETAHDDVTAAAALAAADAAPVHGKEPVHGHDLPA
+>2_444
+MGGGSTGVGAAFDAATRGLDVGIVEARDWASGTSSRSSRLMHGGLRYLEMLDVKLVYEAL
+RERDLLLTQTAPHLVRPLRFVFPFFHKVIDRGFIGAGVTMYDAMQSLGRRRAMSAHRHLS
+RRSMAATFPSLDDEKIVGAVEYADAQFDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGD
+DGRVQGVRVREETSGEEFDVHARAVILAGGVWTQEQQELAEADGGLEVLASKGAHITVPR
+DRIRADAATGVITKTEKSVLFLIPWDEYWVIGTTDTPWAEDVAHPAATADDIDYILEHAN
+AVLKEDLTRDDVIATYAGLRPLLQPVTGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTY
+RAMAEDVVDFVVRETHPTRPSLTERIPVLGGLGYSEIEAEADRIAADYGLDEARVDRLLF
+RYGTVLRHVLDLIDADPSLSVPLAEAPRYLRAEIVHAARAEGVVHLDDVIERRTRLSTEV
+RDRGVAAAEEIASLVAPELGWDEERIAGEIRAYKSLVAARLRGETAHDDVTAAAALAAAD
+AASTH
+>3_476
+MPTLRTVELSPATRADHLARLRAADADHPLDVLVVGGGSAGVGAAFDAATRGLDVGIVDA
+GDWAGGTSSRSSRLMHGGLRYLEMLDVKLVYEALRERDLLLTRTAPHVVRPLRFVFPLEH
+ARDRGWIGAGVGVYDAMQSVGRRRAVGGHRHLGRKALAETFPGLDPEAAVGAVEYADAQF
+DDARLALLLVRSAVDLGAAALNHAPVVGYLKDGAGAVVGARVRESLTGEELQVHARAVIL
+AGGVWTQEQQELAGVDGGLEVLASKGVHVTVPRERIAAEPGVGVITRTEKSVLFVIPSDE
+HWIIGTTDTPWRQDVDHPAATAADVDYVLEHANAVLSEDLTRADVVAVYAGLRPLLQPAA
+GADDASTKVSREHTVTELAPGLTAVAGGKWTTYRAMAEDTVDFAVRDLFPTRPSLTAHTP
+VLGGLGYAEIAARAAEIAAERGFDAARVDRLLRRYGTLLPHVLALVDADPALGEPLPGGE
+AYLRAEVVYAARAEGAVHLDDVLERRLRLSTEVPDRGADAASEAAALVADVLGWDAARRD
+AEVAAYRALVAARRRAEGLDDDAAAAAELAAAGERAGVVPVTSRETVTPEEKGGAR
+>4_2140
+MPTLRTVSLSAATREDHLARLRATSPEAPLDILIVGGGSTGVGAAFDAATRGLDVGIVEA
+RDWASGTSSRSSRLMHGGLRYLEMLDVKLVYEALRERDLLLTQTAPHLVRPLRFVFPFFH
+KVIDRGFIGAGVTMYDAMQSLGRRRAMGAHRHLSRRSMAATFPSLDDEKIVGAVEYADAQ
+FDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGDDGRVQGVRVREETSGEEFDVHARAVI
+LAGGVWTQEQQELAEADGGLEVLASKGAHITVPRDRIRADAATGVITKTEKSVLFLIPWD
+EYWVIGTTDTPWAEDVAHPATTADDIDYILEHANAVLKEDLTRDDVVATYAGLRPLLQPV
+TGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTYRAMAEDVVDFVVRETHPTRPSLTEHI
+PVLGGLGYSEIEAEADRIAADYGLDEARVDRLLFRYGTVLRHVLDLIDADPSLSVPLAEA
+PRYLRAEIVYAARAEGVVHLDDVIERRTRLSTEVRDRGVAAAEEIASLVAPELGWDEERI
+ADEIRAYKNLVAARLRGETAHDDVTAAAALAAADAAPTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001742.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001742.fa
new file mode 100644
index 0000000000000000000000000000000000000000..abcaacde41f8ce22985cfecc1a9de5898b7bba99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001742.fa
@@ -0,0 +1,25 @@
+>0_2230
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW
+REAAENVAESLTKGMRVIVQGRLRARSYDDRDGNRRTSWELDVDEVGPALRFATAKVTRA
+QRGGGGGGGFGGGQQGGGFGGAPAGGGFGGNSDGGFGGAQQGGGWGGQQQGGGQAAPQDP
+WSGGGGGGWDTPSSNEPPF
+>1_1933
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW
+REAAENVAESLTKGMRVIVQGRLRARSYDDRDGNRRTSWELDVDEVGPALRFATAKVTRA
+QRGGGGGGGFGGGQQGGGFGGAPAGGGFGGNNDGGFGGAQQGGGWGGQQQGGGQAAPQDP
+WSGGGGGGWDTPSSNEPPF
+>2_429
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW
+REAAENVAESLTKGMRVIVQGRLKARSYDDRDGNRRTSWELDVDEVGPALKFATAKVTRA
+QRSGGGGGGGFGGGQQGGGFGGAPAGGGFGGNNDGGFGGAPQGGGWGGQQQGGGQAAPQD
+PWSGGGGGGGWDTPSSNEPPF
+>3_382
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDEEALFVRCSVW
+REAAENVAESLTKGMRVIVQGRLKANSYQDREGNKRTSWELQVDEVGPALKFATAKVTRS
+QRGGGGGGGFGGGQQGGGFGGSPQGGGGFGGGQQQSGGWGQPSGGGQSAPAQDPWSGSGG
+GGWDTPSNGEPPF
+>4_2171
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW
+REAAENVAESLTKGMRVIVQGRLRARSYDDRDGNRRTSWELDVDEVGPALRFATAKVTRA
+QRGGGGGGGFGGGQQGGGVGGAPAGGGFGGNNDGGFGGAQQGGGWGGQQQGGGQAAPQDP
+WSGGGGGGWDTPSSNEPPF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001743.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001743.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5903ca37e358c2fe10a000398e3e823f4bd29484
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001743.fa
@@ -0,0 +1,15 @@
+>0_2231
+MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDNIDVWGRRKTAYEIQKKSEAIY
+VVVNFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE
+>1_1934
+MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDNIDVWGRRKTAYEIQKKSEAIY
+VVVNFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE
+>2_428
+MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDKVDVWGRRKTAYEIQKKSEAIY
+VVVDFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE
+>3_381
+MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVEKIDVWGRRKTAYEIQKKSEAIY
+VVVDFTAEPAATQELDRVLNLNETILRTKIIRPEEQKISAE
+>4_2172
+MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDNIDVWGRRKTAYEIQKKSEAIY
+VVVNFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001745.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001745.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2046aebc0a9ad961fbbe7c9aab71f281797515ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001745.fa
@@ -0,0 +1,16 @@
+>0_2233
+MDIMIAVAVGVFLLVAWTVGGWAIVRMGFTRDGDAARTPAHDDGAARPAHPGAAADPATD
+PHVIWREQMKAATAASGAPCVCPPPPREGGAAEAGTSAPPSSPDCPIHRWDYA
+>1_1937
+MDIMIAVAVGVFLLVAWTVGGWAIVRLGFTRDGDAARAPAHDDGAARPAHRGPAADPATD
+PHVIWREQMKAATAASGAQCVCPPPREGGAAEAGTSAPPSSPDCPIHRWDYA
+>2_424
+MEIMIVVAVGVFLMVAWTVGGWVIVRMGFTRDSDAASRAGSQDDDGTRPVPDGPVPVDPA
+SDPNAIWREQMKAATAASGAACTCPRRPVGTPSESPAGSGEQGAAVDSAVDRALDPAADH
+AAVDPSPDCPIHRWDYA
+>3_378
+MPNEVLLVAGVGAALFVLWAVGGWLIVRMGFTRDRDRLPDGPGHASALPDGDGAPSPGRL
+PADPAQDPHAAWREQMKAATVASGARCTCEDGAVPDPDCPVHRWDYA
+>4_2175
+MDIMIAVAVGVFLLVAWTVGGWAIVRMGFTRDGDAARTPAHDAHDDGAARPAHPGAAADP
+ATDPHVIWREQMKAATAASGAQCVCPPPREGGAAEAGTSTPPSSPDCPIHRWDYA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001747.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001747.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8c15d18d91b716b547d10a2ee4c18c8355c1e1ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001747.fa
@@ -0,0 +1,40 @@
+>0_2235
+MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGDYHVSDLEFVAAFDV
+DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESDVEPVDV
+AQALRDAKVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG
+VPIVGDDIKSQIGATITHRVMAKLFQDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE
+R
+>1_1939
+MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGVYHVSDLEFVAAFDV
+DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESEAEPVDV
+AQALRDAEVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG
+VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE
+R
+>2_422
+MATTPIRVAIAGVGNCATSLIQGVEYYRDAKATDTVPGLMHVQFGDYHVSDLQFVAAFDV
+DAKKVGLDLSEAILASENNTIKLADVPHADVTVQRGPTLDGLGKYYAETIEESDAEPVDV
+AQALRDAQVDVLVCYLPVGSQLATEHYAQTAIDAGVAFVNALPVFIAGTPEWADKFTAAG
+VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAKLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGTGGPILSASSYFMKSPPVQHNDDEARELVEAFIRGDIE
+R
+>3_376
+MAENPIRVAIAGVGNCATSLIQGVEYYKDAQASDTVPGLMHVQFGDYHVSDLEFVAAFDV
+DAKKVGLDLSEAILASENNTIKISDVPATGVTVQRGPTLDGLGKYYRETIEESSAEPVDV
+VQALKDAKVDVLVSYLPVGSEEADKFYAQCAIDAKVAFVNALPVFIAGTQEWADKFTEAG
+VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAELAEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHADDEAHELVEAFIRGDIE
+R
+>4_2177
+MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGDYHVSDLEFVAAFDV
+DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESEAEPVDV
+AQALRDAKVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG
+VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE
+R
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001750.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001750.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ea572b9a676077c5d1c4d3105e42cd5cc18f3ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001750.fa
@@ -0,0 +1,61 @@
+>0_2241
+MPQPIAVGAVLGGRYRITQHVVTSADQDMVFLGTDQVLNRRVTVLVASRENATQVASSAR
+ELATGERTDDVQVLDLGLSEGRTYLIAGGDPDPDVLLGLAYPQELYVEPFQTDSLGSELF
+GESRTGDPHAYDDDEAYYTDLDRRLRADEDEAQRRPGFLNRLSERLAERVRPSDGTAAKA
+AAGASALAAADAATRKQQEERERAEREAAERAERERKEAAERAERERKEAAERAERERKE
+AEEKARAEREAAERAERERKEAAERAERERREAEERAEEERRAEAERARRQAEQEAEERA
+AREREAEQARLAAEREEAERRELERRAEARRRAEEERAREAAEREAEKRAAQEREAAERE
+AQAGTAALPAVAAGAAAAQAPDADADGATPPTEPVESVAAEKTDPPEPVAPDTEAIPVRR
+QRPVPRRAIVAESAPTAHEESRGTAAPVAAGAGVATAAGAAAAGSTAAAAAPDAQAAPAT
+TGGGDGATVADPGDGHGRTRGGGPLALLLVLGLLAALVVGGVLLAQNLRGGPAPQAASSE
+SESASSESASDTPSPSESTSPSPTPSSESAAAAPQPVQALRSVPDLPEHEAEHDADLSNL
+IDGDPTTVWRTFAYARPNFGGYVESMNLVVQLEERTEVNEVTLQSTGATGGAWFAYIADS
+PEGANAKEIGNGTFDQDTVSIPVPFEGTEAEAEYVIVSLTSLPQLEGTTSDLPFGLRLGE
+IAVR
+>1_1945
+MPQPIAVGAVLGGRYRITQHVVTSADQDMVFLGTDQVLNRRVTVLVASRENATQVASSAR
+ELATGERNDDVQVLDLGLSEGRTYLIAGGDPDPDVLLGLAYPQELYVEPFQTDSLGSELF
+GESRTGDPHAYDDDEAYYTDLDRRLRADEDEAQRRPGFLNRLSERLAERVRPSDGTAAKA
+AAGASALAAADAATRKQQEERERAEREAAERAERERKEAEEKARAEREAAERAERERKEA
+AERAERERREAEERAEEERRAEAERARRQAEQEAEERAAREREAEQARLAAEREEAERRE
+LERRAEARRRAEEERAREAERREAEKREAQEREAAEREAQEREAAEREAQAGTAALPAVA
+AGAAAAQATDADADGATPPTEPVEPVESVAAEKTDPPEPVAPDTEAIPVRRQRPVPRRAI
+VAESAPPVHEESRSTAAPVAAGTATGATAAAAGSTSAAAAPDALAAPATTGGDDGATVAD
+PGDGNGRTRGGGPLALLLVLGLLAALVVGGVLLAQNLRGGPAPQAAAASSESASSESASD
+TPSPSESTSPSPTPTSESAAAAPQPVQALRSVPDLPEHEAEHDADLSNLIDGDPTTVWRT
+FAYARPNFGGYVESMNLVVQLEERTEVNEVTLQSTGATGGAWFAYIADSPEGANAKEIGN
+GTFDQDTVSIPVPFEGTEAEAEYVIVSLTSLPQLEGTTSDLPFGLRLGEIAVR
+>2_417
+MAPGAAETDTVETRADEPAAAEPESTATAPAEDVDPEPTAPAPVVPASTAPDSAPDTEAI
+PVRRQRPVPRRAMVVEPTTPDADRSPDAQRSRGAGAPLAAAGAGAVAAAGATAASAAAAG
+AAPSATSAPSTASAAPEATAAGTSPADGDGGAPVDPDQGGSRRGGWPLALLLLAVLVGAL
+VLGGVLLAQNLRGAPHRAGRPARLPHRDRRGARTRRQPPPTQSDEASPTEASPTESSPAA
+STSASPTESETAAAAPQPARALRMVPDLPAHESEHDGELPNLIDGDPSTAWRTFAYARPN
+FGGYVESMNLVVELEDRAEVNEVTLQSTGATGGAWFAYIADSPEGENAREIGNGTFDQDS
+VTVPVPFDGAEAEAEYVIVSLTSLPRLDGTTPDLPFGLRLGEIGVR
+>3_370
+MPQPLAVGSVLGGRYRITDHVVTSADQNMVFQGADQVLNRRVTVLVASPENATQVAASAR
+ELATGERQDDVQVLDLGLSEGRTYLIAGGNPDPDVLLGLAYAQELYVEPFQTDSLGSEIF
+GESRTEQAHEYDDDDAYYADLDRRLRADQKQSQRRPGFLNRISEKLNERVRPADGTAAKA
+AAGASALAAADAATKAQLAEQERAEREAREAQERAEREEAQEAERREREAQERAERERLE
+RAAAAQAEKDRAAREAAEAEAAARREREAQRHAEAETRRREEEAAAAAALAAAAPAADAD
+PADAPTQAVPVTEPASTPEAVPAPVRRPRPAPRRALPAVASAAAVAASVSAEEGASAAEA
+APAESVAPEAVPTATATSSAAIAVAEAEPAVTEHREEAHAAPVAGGAGAGAPAAGATAAP
+ARSTSGKGWLMVLGLLALLALAGLAGLFLLGQNTRSVEPAPSASASSAAPSTAQASSAPP
+AASSSAAPTASSSAAPSTEPAPSTSAAAPAPTAAPQAVAVTRQVPEMPELEAPNDATLAN
+LIDGDPNTAWQSYTYARPNFGGYVGSMNLVVQLQERTTISEVQLENRGATGGKWIAYVAN
+TAQGGEGDARVIGQGTFDEDSITIPVDIAENQGQYVILSITGLPQLEGAGQRPYGLQLTE
+IGVR
+>4_2183
+MPQPIAVGAVLGGRYRITQHVVTSADQDMVFLGTDQVLNRRVTVLVASRENATQVASSAR
+ELATGERTDDVQVLDLGLSEGRTYLIAGGDPDPDVLLGLAYPQELYVEPFQTDSLGSELF
+GESRTQDPHAYDDDEAYYTDLDRRLRADEDEAQRRPGFLNRLSERLAERVRPSDGTAAKA
+AAGASALAAADAATRKQQEERERAEREAAERAERERKEAEERARAEREAAERAERERKEA
+AERAERERREAEERAEEERRAEAERARRQAEQEAEDRAAREREAEQARLAAEREEAERRE
+LERRTEARRRAEEERAREAERREAEKRAAQEREAAEREAEKREAQAGTAALPAVAAGAAA
+AQTTDADADGATPPVEPVEPVEPVAAEKTDAPEPVAPDTEAIPVRRQRPVPRRAIVAESA
+PPVHEESRSTAAPVAAGAATGATAAAAGSTSAAAAPDALAAPATTEGDDGATVADPGDGN
+GRTRGGGPLALLLVLGLLAALVVGGVLLAQNLRGGPAPQAAAASSESESASSESASDTPS
+PSESTSPSPTPTSESAAAAPQPVQALRSVPDLPEHEAEHDADLSNLIDGDPTTVWRTFAY
+ARPNFGGYVESMNLVVQLEERTEVNEVTLQSTGATGGAWFAYIADSPEGANAQEIGNGTF
+DQDTVSIPVPFEGTEAEAEYVIVSLTSLPQLEGTTSDLPFGLRLGEIAVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001751.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001751.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dd138315fc40eafe9d18f8df6a6607e791a19fff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001751.fa
@@ -0,0 +1,15 @@
+>0_2243
+MSTITVTDADFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLEDMAVEHEGKAVIAKLNVD
+ENPAIAARYGVTSIPLVVGFQNGEKVAESVGAKPKAALEKEFSALLG
+>1_1947
+MSTITVTDADFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLEDMAVEHEGKAVIAKLNVD
+ENPAIAARYGVTSIPLVVGFQNGEKVAESVGAKPKAALEKEFSALLG
+>2_415
+MSTINVTDTDFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLDEMAVEHEGKAVIAKLNVD
+ENPATAARFGVTSIPLVLGFQGGEKVAESVGAKPKAALEKEFSALLG
+>3_368
+MSTINVTDADFQAKVLDSELPVLVDFWAEWCGPCRMLGPVLDELAAEHEGEVLVAKLNVD
+ENPASAARYGVTSIPLVLGFQGGEKVAESVGAKPKAQLEKEFAALLG
+>4_2185
+MSTITVTDADFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLEDMAVEHEGKAVIAKLNVD
+ENPAIAARYGVTSIPLVVGFQNGEKVAESVGAKPKAALEKEFSALLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001754.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001754.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6c297815ec615d64e644524d0c0aadb2e01d9dfc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001754.fa
@@ -0,0 +1,25 @@
+>0_2247
+MSAENVTPAPEAEDAVVETPAGQGSRVAEQDGAAVSEAVRRLEEEGDVAADYVEELLDIA
+DLDGDIDIEVRDGRTYVSVVSEDHDERLDGLVGPDGRTLEALQELVRLAVLAATGHRSRL
+ILDVCGHRERRNVALRTAAQAAVERVRVGEGPVHLEPMGAYERKIVHDVVADAGLTSESE
+GEGARRHVVISADD
+>1_1951
+MSAENVTPASEAEDAVVETPVGQGSRVAEQDGAAVSEAVRRLEEEGDVAADYVEELLDIA
+DLDGDIDIEVRDGRTYVSVVSEDHDERLDGLVGPDGRTLEALQELVRLAVLAATGHRSRL
+ILDVCGHRERRNVALRTAAQAAVERVRAGEGPVHLEPMGAYERKIVHDVVADAGLTSESE
+GEGARRHVVISADD
+>2_410
+MSAENVNPAAEAEDAVVETTPAPDAPQAPAAEERTGSDAAVAAGEGAESSAAESASDGVR
+RLEEEGDVAADYVEELLDIADLDGDIDIEVRDGRTYVSVVSEDHDERLNALVGRDGKTLE
+ALQELVRLAVLAATGHRSRLILDICGHRERRDADLRETAQDAVERVRAGEGPVHLSPMGA
+YERKIVHDVVADAGLASASEGEGARRHVVISADA
+>3_364
+MTAEHEGPLADAAEDSPAVEAPVEATAPDAAVDEQAEAVRRLEEEGDVAADYVEELLDIA
+DLDGDIDIEVRDGRTYVSVVPGEDDEDDRLADLVGPDGKALEALQELVRLAVLTATGHRS
+RLILDIAGHRRRRDAELRTLAGEAVERVRSGAGEVHLDPMGAYERKIVHDVVAEAGLASE
+SEGEGPRRHVVISG
+>4_2189
+MSAENVTPAPEAEDAVVETPAGQGSRVAEQDDAAVSEAVRRLEQEGDVAADYVEELLDIA
+DLDGDIDIEVRDGRTYVSVVSEDHDERLDGLVGPDGRTLEALQELVRLAVLAATGHRSRL
+ILDVCGHRERRNVALRTAAQAAVERVRAGEGPVHLEPMGAYERKIVHDVVADAGLTSESE
+GEGARRHVVISADD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001756.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001756.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24098e9f1c386568dfafadf1ce0505fa8bad6eba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001756.fa
@@ -0,0 +1,20 @@
+>0_2249
+MTVTPSPFVVLEPSREWGPLRALPSALLAGLLTVYRAVVSPLYGPVCRFFPSCSAYGLEA
+VHVHGAVKGSWLAARRIGRCHPWNDGGVDPVPPGHRRWPPGRQPRILTLNHPPIPPDLPQ
+ED
+>1_1953
+MTVTPSPFVVLEPSREWGPLRALPSALLAGLLTVYRAVVSPLYGPVCRFFPSCSAYGLEA
+VHVHGAVKGSWLAARRIGRCHPWNDGGVDPVPPGHRRWPPGRQPRILTLNHPPIPPDLPQ
+ED
+>2_408
+MAVTPSPFTVLEPSREWGPVRALPSALLAGLLTVYRAVVSPLYGQVCRFFPSCSAYGLEA
+VHVHGAVKGSWLAARRIGRCHPWNDGGVDPVPPGHRRWPPGRQPRILTLNHPPIPPDLPQ
+ED
+>3_362
+MPASSPYTVLEPSHEWGPLRALPSTLLAWLLTAYRAVVSPLYGPVCRFFPSCSAYGLEAV
+HVHGAVRGSWLTARRLLRCHPWNDGGVDPVPPGRRRWPPGREPRIFALNHPPIPPDPSQE
+D
+>4_2191
+MTVTPSPFVVLEPSREWGPLRALPSALLAGLLTVYRAVVSPLYGPVCRFFPSCSAYGLEA
+VHVHGAVKGSWLAARRIGRCHPWNDGGVDPVPPGHRRWPPGRQPRILALNHPPIPPDLPQ
+ED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001757.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001757.fa
new file mode 100644
index 0000000000000000000000000000000000000000..42cc3ac2d231a35b15711b46db8e655dbd003241
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001757.fa
@@ -0,0 +1,20 @@
+>0_2250
+MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDQTRSTPPSAPRPRAGFVVSKAV
+GNAVTRNRVRRRLRAVVADQMRTAPLRELPVLVQVRALPAAAEADFALLRRETVGALGKA
+LKPHLPAASEHA
+>1_1954
+MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDQTRSTSPSAPRPRAGFVVSKAV
+GNAVTRNRVKRRLRAVVADQMRLPPLRDLPVLVQVRALPAAAEADYALLRRETVGALGKA
+LKPHLPAASEHA
+>2_407
+MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDHTRSTSPSVPRPRAGFVVSKAV
+GNAVTRNRVKRRLRAVVAEQMRAAPLRELPVLVQVRALPPAAEADHALLRRETVGALAKA
+LRPHLPAVPRDEA
+>3_361
+MLPRDRRVRTPEEFRRIRRTGSRAGRSTVVVSVAADTDPARPGATSQPRRPRAGFVVSKA
+VGNSVVRHRVTRRLRALLRAELDSPALRDRALLIQVKALPAAVDADHATLRRDVHGALGA
+AVRKLDQADRSR
+>4_2192
+MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDQTRSTSPSAPRPRAGFVVSKAV
+GNAVTRNRVKRRLRAVVADQMRLPPLRDLPVLVQVRALPAAAEADYALLRRETVGALGKA
+LKPHLPAASEHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001760.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001760.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eba8b3dcbc26645957fa511b2a96cd304af683dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001760.fa
@@ -0,0 +1,45 @@
+>1_288
+MVELVALRKTNEVAAYVRASMDRKGDRWTVDTQLRKIRALAEAKDWNVVEVYEDNAVSAT
+KKRRAGTRWAEMLDDARAGRFSMVVAVDMDRLLRSTKDLNTLIDLGLRVVTVDGEIDLST
+ADGEFRATMLAALARFEARRKAERQIRSNERRRAEGIPASTWKAFGWTREGELIEEEAAA
+VRRAFDAFLGEPSLSIRRIREDLNSAGHLTARGSEFSVDAVRYLLANSLYAGFIRHYKTG
+ELYPVQGEAFPPIVGEQTWRAAVAKLEDNVRRSARQGNQPKYLLSTIGLCGKCGATLVSG
+TNSRKQPTYRCGEQFHLTRQREPVDAMVTEAVLTRLSSVDVHDLVMPQEAAGPDREELLT
+ERNALVERVKELSPLLRDIHQPVLEITAAINDVKARIDEIDAELLDRSVSVAAKLLAEVD
+EPVGTAERREVVESKWKALDMDRRRMLVDELVTVTIEPIMPGHVKFDPDLVRIEPRRD
+>1_2175
+MRAAIYLRISLDRHGDGLAVERQREDCKRIIAQRGWEHVATYEDPSVSASSRTVTRPGYE
+RMVRDWQAGRFDAVVCWDLDRLTRQPRQLEDWIDAAEQRGLHLVTANGEADLGTDAGRMF
+ARIKAAVSRQEVDRKSARQVRAAQQRAELGKGWGPRRPFGFAEDKVTHDPAEAAVVRRMY
+DDFNAGVGQREICRRLAAEGVRTSTGREWTQPALRQFLRNPRNAGLRAYRGEIIGPAEWA
+PLVSESVYRAALDRMDAPTKRVGGSGAKHLLIGVARCGVCDSPVGTNYTATHKRQYACRA
+GHVARSAEAVDAYVSEVAVGVLSTRGAAAFTRHDDAGQVELSAEADRIRARQEALAVEFA
+DGTLTAAQLRAANARMAERLEQVTAAMVAAEGNAALRPLLEAESVAAGWERLDIPRRRAV
+IDTLMNVRILRTSQGSRFDPASVEITPRTG
+>2_2146
+MVSVVGGRVDYSVVGLQNPMRISEMPGKTAKITVSGRMPNTRGSITRTGYSYSMTSKRAV
+IYTRISRDDRGVEAGVTRQEEDCRAKAAGLGFEVVRVYTDNDIGASTRSRKVRPEYAQML
+EAARRGAFGAILAYSTSRLTRRPREAEDLIDLVERHGVQIKTVVSGDWNLETADGRAVVR
+TLAAWDAAEAERTAERVARACEQRAAEGRTHGAVPYGWTRDADGTEHLHPERAQVIRDAA
+AHVLEGGSLRSFTLDLNARGVGSPRGGKWTAPQLKQLLLRERNAGRLVRRDPNNPRHRPV
+VGKGIWPQILDEETHDRLVAHLTDPTRRKSRGSELKHMMSGILICGVCGARCRLMPGGKS
+PDGTPRPPSYGCRECFGVKRRVAQVDEWVSYMARVRLAEKDAPALLAGDDEGARKAQRER
+DEARAKLDRAADAYAEGLIDSHQLTRISANLHKKREDAEARLARARPLGGLSFDRGASPV
+QVWRRAPVAVRRTLVEMMMTVTLLPGGRGSRFDPEQHLRIVMNDLKTSVSDILVTSGTVP
+DRPTGSEDSDPPRRE
+>2_2148
+MQVEEDDRRVVAVVEDPVREPVVCEAARRVLAGESLNSIARALNERGAPTAATDREEASR
+LWTASKVRQMLQRPGYAGLRVYRGEGVGKAAWEPLIEREQWDELQALFESSRAAQGPQDH
+RAAYLLTGIARCGVCGSKLVRRATRSGKVVRKDGTVAPKRRYDTYACAAGIDRAGAGFHV
+SMSMVHLDDYVSRLVVERLSRPDVLECLAGTEGTQSDERVALRAEIAGYREHLERARAYA
+AEHLRMDLLIDQEARLQPKIDTAERRLRELAAVDPEVRRLAEAADVRATWDALDLEGQRH
+VVRVRMTPSVLPRTRPGRRGLDPERVDVTWLSDCLESP
+>2_2320
+MVELVSLRKTNEVAAYVRASMDRKGDRWTVETQLRKIRALAEAKDWEVVEVYDDNAVSAT
+KKRRAGTRWAEMLDDARAGRFSMVVAVDMDRLLRSTKDLNTLIDLGLRVVTVDGEIDLST
+ADGEFRATMLAALARFEARRKAERQIRSNDRRRAEGIPASSWKAFGWTREGELIEAEADA
+VRRAFDAFLGEPSLSIRRIREDLNSAGHLTARGSAFSVDAVRYLLANPLYAGYIKHYASG
+ELYPVQGDAFPPIVGEQTWRAAVAKLEDNVRRSARQGNQPKYLLSTIGLCGKCGATLVSG
+TNSRKQPTYRCGEQFHLTRQREPVDAMVTEAVLTRLSSVDVHDLVMPQEDDGPDREALLT
+ERNALVERVKELSPLLLDVRQPVLEITEAIRGGKARIDQIDAEILDRSVSVAAKLLGDVD
+ESLGTMERREVVESKWKALDMDRRRMLVDELVTVTIEPIAPGHVKFDPDLIRIEPRRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001765.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001765.fa
new file mode 100644
index 0000000000000000000000000000000000000000..42de3f21d509e6bda54507f6d3a3761d8d8046e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001765.fa
@@ -0,0 +1,34 @@
+>1_2080
+MSVNLPPSPGGGPTEHAVEHALAPVEAGATQATTEAAADTRGTSVWGAAFQRLRRNPAAI
+AGAVIVLLFVLVAVLAPVLAPYAGTATPGMREIRPTHVPGPGEVAGYPLGLDRFGGDVLS
+KLIWGAQASLLIGVVSTAFGLAGGMLLGLLAGTFGGWVDSVVMRVVDILLSVPNLLLAVS
+IAAILGQTPFAVMIAIGVAQVPVFARLLRSSMLTQKGSDYVLAAQTLGLSRGRITMSHVL
+PNSLGPVIVQATLTLATAVIDAAALSFLGLGGGRPETAEWGRMLTYAQAELGINPWLAFL
+PGLCIAITALGFTLLGESLREALDPTSRRR
+>2_80
+MTAVLTSSQTPPPPSDSSAAASPVSLVPATRRPRRADLGLAFALTGAAVLLVAALWPQLL
+ATHDPRALDLAAPLQAPSLDHWFGTDQNGRDLYSRIVHGTGPSLLIGLGAAAVGVGLGML
+LGIVAAFGGRWADAAVSRTVEVLFAFPSLLLALMLITVYGPSVSTLILAVGVGTAPGYAR
+LVRGQVLAVRGSAYVQAAEVIGHPPMTILLQHIVPNAVRPLVAVFMLGVGQAIVWASGLA
+FLGFGVAPPSPEWGALLEAGRPYITAAWWLEIFPGLAVLATALTATALGRHLEARLQGET
+R
+>2_253
+MSVNLPPSPGSGPAEHAVDHALAPVEAGATQETTEAAADARGTSVWGAAFQRLRRNPAAI
+AGAVIVALFVLVAVLAPVLAPYAGTDTPGMREIRPTHVPGPGEVDGYPLGLDRFGGDVLS
+KLIWGAQASLIIGVVSTAFGLVGGMLLGLLAGTFGGWVDSVVMRTVDILLSVPNLLLAVS
+IAAILGQTPFAVMIAIGVAQVPIFARLLRSSMLTQKGSDYVLAAQTLGLSRGRITMSHVL
+PNSLGPVIVQATLTLATAVIDAAALSFLGLGGGRPETAEWGRMLTYAQAELGINPWLAFL
+PGLCIAIAALGFTLLGESLREALDPTSRRR
+>3_126
+MTSAPAVAAEPTPAASATPSDPAGARRRARPRLGLLLSAGFLVVVLLAALFPSLLAPGDP
+FAGASGATLEPPGPGHWLGTDHLGRDLYTRVVHGTGLTVATAAAAVAGALVVGGTLGLAS
+GYVGGVADTLLMRVVDVLLSIPSLLLSLAVVAGLGFGPVQVAVAVGIGSVASFARIGRAQ
+ALRISQAPFVEAAPSFGTRRILVLLHHVVPNAVGPLVSLAVLEFGSALLAVSALSFLGYG
+EPRPAAEWGGLISDGRSYLAVAPWLTALPGLVIAATVLALQQVATSPAPADAPR
+>4_121
+MSVNLPPSPGGGPTEHAVEHALAPVEAGATQATTEAAADTRGTSVWGAAFQRLRRNPAAI
+AGAVIVLLFVLVAVLAPVLAPYAGTATPGMREIRPTHVPGPGEVAGYPLGLDRFGGDVLS
+KLIWGAQASLLIGVVSTAFGLAGGMLLGLLAGTFGGWVDSVVMRVVDILLSVPNLLLAVS
+IAAILGQTPFAVMIAIGVAQVPVFARLLRSSMLTQKGSDYVLAAQTLGLSRGRITMSHVL
+PNSLGPVIVQATLTLATAVIDAAALSFLGLGGGRPETAEWGRMLTYAQAELGINPWLAFL
+PGLCIAITALGFTLLGESLREALDPTSRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001771.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001771.fa
new file mode 100644
index 0000000000000000000000000000000000000000..36f87f12f4bad377b34f36cb0aa62d3ec79f9ed9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001771.fa
@@ -0,0 +1,36 @@
+>0_37
+MSEHQQHVGRRDPRISDEAIERGRRAHELDRAHVFHSWSAQRDLNPMTILDAEGSWVWDG
+EGRPMVDFSGQLVFTNVGHRHPKIVAAIREQAETLATVAPQHVNDARSEAARLITEWLPE
+SINHVFFTNAGAEANDHAVRMARLHTGRHKVLSAYLSYHGATRLTANLTGSLRRVGSDSA
+SDGVVHFQPAYTYRSAFGSENDEQEAERALAHLRDVIELEGPSTVAAVVLEAVPGTAGIF
+MPPPGYMAGVKELCREHGILLIIDEVMVGFGRVGEWFGHQLTGVTPDIVTFAKGVNSGYV
+PLGGVAMSDDVYESFATTPYPGGLTYSGHPLACAAAVAAITAMEEECMVANAKRIGEEII
+GPRLAEIAAAHPSVGDVRGAGAFWAVELVKDRQTRERLAPLGQVAPVMGRMMAEAKDRGL
+LLFMAENRFHLCPPLNISDEDLRFGLDVLDQVLALADEEVAAG
+>1_2001
+MSEHQQHVGRRDPRISDEAIERGRRAHELDRAHVFHSWSAQRNLTPMTILDAEGSWVWDG
+EGRPMVDFSGQLVFTNVGHRHPKIVAAIREQAETLATVAPQHVNDARSEAARLITERLPE
+SINHVFFTNAGAEANEHAVRMARLHTGRHKVLSAYLSYHGATRLTANLTGSLRRVGSDSA
+SDGVVHFQPAYTYRSAFGSESDEQEAERALAHLRDVIELEGPSTVAAVILEAVPGTAGIF
+LPPPGYMAGVKELCREHGILLIIDEVMVGFGRVGEWFGHQLTGVTPDIVTFAKGVNSGYV
+PLGGVAMSDDVYESFATTPYPGGLTYSGHPLACAAAVAAITAMEEEGMVAHAKRIGEEVI
+GPRLAEIAAAHPSVGDVRGAGAFWAVELVKDRQTRERLAPLGQVAPVMGRMMAEAKDRGL
+LLFMAENRFHLCPPLNISDEDLRFGLDVLDQVLALADEEVAAG
+>1_2114
+MTAPAEAGLLDRDAAHLWHPYGAAGARQLYAVRGARGVHLDLEGPGGERHRAIDAMASWW
+SVVHGHGHPALVEALTRQAAAFPHVMFGGLTHAPAVDLAERLVAHTPAALEHVFLADSGS
+VSVEVALKLALQYQATRGRPSRRRFLTVRGGYHGDTAAPMGVCDPVDGMHAAFTSLVARH
+LFLPRPPAARWVPEGFAAAPTAPDAAPAGHWEADDAALAAWEDEARAFTAAHADEIAGVI
+LEPVLQGAGGMRVYDPRCLTVLRELCDEHGLLLIADEIATGFGRTGRWLACEGAGVAPDV
+LCLGKALTGGTMTGAAMLCTAEVAETVSRRERGMPGALLHGPTFMGNPLMCAVASASLDL
+LTDPRDGWAAQVPRVEAGLRAGLAAAADLPAVTDVRVLGAVGVVELDRTVDVEPVTRAAV
+ARGAWVRPFRRLVYVMPPYVSTDDDVATICAAVTGAVEEVCA
+>4_32
+MSEHQQHVGRRDPRISDEAIERGRRAHELDRAHVFHSWSAQRDLNPMTILDAEGSWVWDG
+EGRPMVDFSGQLVFTNVGHRHPKIVAAIREQAETLATVAPQHVNDARSEAARLITERLPE
+SINHVFFTNAGAEANEHAVRMARLHTGRHKVLSAYLSYHGATRLTANLTGSLRRVGSDSA
+SDGVVHFQPAYTYRSAFGSESDEQEAERALAHLRDVIELEGPSTVAAVILEAVPGTAGIF
+LPPPGYMAGVKELCREHGILLIIDEVMVGFGRVGEWFGHQLTGVTPDIVTFAKGVNSGYV
+PLGGVAMSDDVYESFATTPYPGGLTYSGHPLACAAAVAAITAMEEEGMVAHAKRIGDQII
+GPRLAEIAAAHPSVGDVRGAGAFWAVELVRDRQTRERLAPLGQVAPVMGRMMAEAKDRGL
+LLFMAENRFHLCPPLNISDEDLRFGLDVLDQVLTLADEEVAAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001772.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001772.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5175bbf6162ba33a64e3cdd216f45222a6bea0c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001772.fa
@@ -0,0 +1,40 @@
+>0_44
+MDTSAPRTSPSTPPASAAHITPEGGSLRRTLKSRHLTMIAMGGAIGTGLFVASGNTIATA
+GPGGALAAYVAIGFMVFLLMQSLGEMSTYLPVSGAFEEYSTRFVSPSFGFAIGWNYWYNW
+AITVAAELVAAALIMRYWLPDVPSWIWSATFLALLFGLNALSTRAYGESEFWFSLIKVAT
+VVIFLVLGVLMIVGILGGSSPGFHNWTDGEAPFVGGGAGILAIFMVAGFSFQGTELVGVA
+AGEAEDPEKNVPKAIRTVFVRILLFYVGAITVVGFLIPYTSPHLLGSDVEDISISPFTLV
+FENAGVLAAASVMNAVILTAILSAGNSGLYASTRMLWALADSGKAPRFLAKVNRRGVPMN
+ALYATTAVGAACFLTTFIGDGAAYVWLVSASGLAGFIVWMGIAWSHYRFRRAYVAQGHDP
+KDLPYRAFLFPLGPIVALVMCAVVILGQNYQAFMGDVDLVAVASAYIGLPLFLALWLGHK
+LVTGSKPVRYEDADLTRVLD
+>1_2008
+MDTSAPRTSPSTPAASAAHATHEGGSLQRTLKSRHLTMIAMGGAIGTGLFVASGNTIATA
+GPGGALVAYVAIGFMVFLLMQSLGEMSTYLPVSGAFEEYSTRFVSPSFGFAIGWNYWYNW
+AITVAAELVAAALIMRYWLPDVPSWIWSAIFLALLFGLNALSTRAYGESEFWFSLIKVAT
+VVIFLVLGVLMIVGILGGSSPGFHNWTDGEAPFVGGGAGILAIFMVAGFSFQGTELVGVA
+AGEAEDPEKNVPKAIRTVFVRILLFYVGAITVVGFLIPYTSPHLLGSDVEDISISPFTLV
+FENAGVLAAASVMNAVILTAILSAGNSGLYASTRMLWALADSGKAPRFLAKVNRRGVPMN
+ALYATTAVGAACFLTTFIGDGAAYVWLVSASGLAGFIVWMGIAWSHYRFRRAYVAQGHDP
+KDLPYRAFLFPLGPIVALVMCAVVILGQNYQAFMGDVDLVAVASAYIGLPLFLALWLGHK
+LVTGSKPVRYEDADLTRVLD
+>3_282
+MNPTDSPRTAGPAGSTAAAASPEPHTGLKRTLAARHLMMIAMGGAIGTGLFVASGNSIAT
+AGPGGALLAYVVIGFMVFLLMQSLGEMATYLPVSGAFEEYATRFVSPSFGFAIGWNYWYN
+WAITVAAELVAAALVMRYWFPDVPSWAWSALFLALLFGLNALSTRAYGESEFWFSLIKVV
+TVVVFLVLGVLMIVGVLGDAAVGTDNWTTGEAPFVGGAPGILAIFLVAGFSFQGTELVGV
+AAGEAEDPERTVPKAIRTVFWRILLFYVGAITVIGFLIPYTSPNLLGSDIEDIAISPFTL
+VFENAGVLAAAAVMNAVILTAILSAGNSGLYASTRMLWALADSGKAPRFLAKVNRRGVPM
+NALVVTTAVGALCFLTTFIGDGAAYVWLVSASGLAGFIVWMGIAWSHYRFRKAYVAQGND
+ITDLPYRAALFPLGPIVALLLCTVVILGQNYEAFLNGVDLVAVASAYIGLPLFLALWIGH
+KLVTGSKGVRPEEADLTRGRA
+>4_39
+MDTSAPRTSPSTPAASAAHATHEGGSLQRTLKSRHLTMIAMGGAIGTGLFVASGNTIATA
+GPGGALVAYVAIGFMVFLLMQSLGEMSTYLPVSGAFEEYSTRFVSPSFGFAIGWNYWYNW
+AITVAAELVAAALIMRYWLPDVPSWIWSAIFLALLFGLNALSTRAYGESEFWFSLIKVAT
+VVIFLVLGVLMIVGILGGSSPGFHNWTDGEAPFVGGGAGILAIFMVAGFSFQGTELVGVA
+AGEAEDPEKNVPKAIRTVFVRILLFYVGAITVVGFLIPYTSPHLLGSDVEDISISPFTLV
+FENAGVLAAASVMNAVILTAILSAGNSGLYASTRMLWALADSGKAPRFLAKVNRRGVPMN
+ALYATTAVGAACFLTTFIGDGAAYVWLVSASGLAGFIVWMGIAWSHYRFRQAYVAQGHDP
+KDLPYRAFLFPLGPIVALVMCAVVILGQNYQAFMGDVDLVAVASAYIGLPLFLALWLGHK
+LVTGSKPVRYEDADLTRVLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001775.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001775.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0aae73bcdd6d23a74e89c7a8ab335c7060285a87
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001775.fa
@@ -0,0 +1,20 @@
+>0_55
+MTDPHASHDPRREAARPSWYGSEAGAGSSGTGSSAAGWPDAPAGDADRAAWDRAPSYAEQ
+EGQTRPAYGQPYGYGQDANTVPAYGYGQGTPGHGFGAPLQPGQTEGIGRSVASMILGIIS
+VVGGFTFLLPPIVGVVLGHIGLKREPHGRGMAIAGLVMNYVSLALLLLAVVFLVILVIAG
+MSLGDYTST
+>1_2019
+MTDPHASHDPRREAARPSWYGSEAGAGSSGTGSSAAGWPDAPAGDADRAAWDRAPSYAEQ
+EGQTRPAYGQPYGYGQDANTVPAYGYGQGTPGHGFGAPLQPGQTDGVGRSVASMILGIIS
+VVGGFTFLLPPIVGVVLGHIGLKREPHGRGMAIAGLVMNYVSLALLLLAVVFLVILVIAG
+ISLGDYTST
+>2_321
+MTEPHPAHDPHRRADGGQPSWYGGGASGGGSSAASWPDGPAADADRAGWEQAPSYAEQQA
+APAYGGDAGHGQDGYAPAGYAPAPGHGRPAYGFGAPLAPGQTEGTGRSVASMILGIVSIV
+GGFTLVVPPIVGVILGHLGLKREPNGRGMAIAGLVMNYLSLAFVLLGVVLLTILVAAGMA
+ASEYSTY
+>4_50
+MTDPHASHDPRREAARPSWYGSEAGAGSSGTGSSAAGWPAAPTGDADRAAWDRAPSYAEQ
+EGQTRPAYDQPYGYGQDANTVPAYGYGQGTPGHGFGAPLQPGQTEGIGRSVASMILGIIS
+VVGGFTFLLPPIVGVVLGHIGLKREPHGRGMAIAGLVMNYVSLALLLLAVVFLVILVIAG
+ISLGDYTST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001779.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001779.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e91b22e534ace4a46ab42a7b37a86e63d98b2f8e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001779.fa
@@ -0,0 +1,28 @@
+>0_113
+MIAHRGASAAFPEHTRAAMLHALAVGADGLECDVQLTRDREVVCWHDPTVDRTSDGRGAV
+ADHTLDRLRGLDVVSWHARRPGAEPATTTAPPAVYGGAGEQVLTLADLLAIAAAADRPLR
+LAVELKHPSPFGHELEERVLRELLRAGWDPETGRLGQVQVSLMSFHPDALRHVAPLAGTD
+PLCPLMDLMPTELPTRLARGPLSRAAVRAAARQSLAGSEALVWRGRAGMAGPSVAYVREH
+LADVKAWLAAGRRLRVWTVDEREDADSLLAQGVQELTTNRPEDVLRWVRERAAARRERMP
+TGA
+>1_2077
+MPALVIAHRGASAAFPEHTRAAMLHALAVGADGLECDVQLTRDREVVCWHDPTVDRTSDG
+RGAVADHTLDRLRGLDVVSWHARRPGAEPATTTAPPAAYGGAGEQVLTLADLLAIATAAD
+RPLRLAVELKHPSPFGHELEERVLRELLRAGWDPETGRVGQVQVSLMSFHPDALRHVAPL
+AGTDPLCPLMDLMPTELPTRLARGPLSRAAVRAAARQSLAGSEALVWRGRAGLAGPSVAY
+VREHLADVKAWLAAGRRLRVWTVDEREDAEFLLAQGVQELTTNRPEDVLRWVRERAAARR
+ERVPTGA
+>3_187
+MTGVLPLVIAHRGASAAFPEHTRAAMLHALAVGADGIECDVQLTRDRQVVLWHDPTVDRT
+SDGRGPLADHTLAQLRALDVVSWHQGMGGDAPGDAAGRVPAVYGRRDEQVLTLADLLRMV
+LAADRPLRLAVELKHPSPFGHELEERVLRELVAAGWDAETGLMGQVRVSLMSLHPGALQY
+LAPLTGPDALCPLIDLVPDEIPSRLARGPLSRAAVRATVRQSLADAETMVWRGRAGLAGP
+SVAYVRSHLADVKAWLASGRRLRVWTVDEREDALFLAAQGVQELTTNRPADVLRWVTQAA
+TSASPGAISGRDMPSPAAR
+>4_118
+MPALVIAHRGASAAFPEHTRAAMLHALAVGADGLECDVQLTRDREVVCWHDPTVDRTSDG
+RGAVADHTLDRLRGLDVVSWHARRPGAEPATTTAPPAAYGGAGEQVLTLADLLAIATAAD
+RPLRLAVELKHPSPFGHELEERVLRELLRAGWDPETGRVGQVQVSLMSFHPDALRHVAPL
+AGTDPLCPLMDLMPTELPTRLARGPLSRAAVRAAARQSLAGSEALVWRGRAGLAGPSVAY
+VREHLADVKAWLAAGRRLRVWTVDEREDAEFLLAQGVQELTTNRPEDVLRWVRERAAARR
+ERVPTGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001780.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001780.fa
new file mode 100644
index 0000000000000000000000000000000000000000..785e66c64dd488a9cafa9b08169cd661af28c2a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001780.fa
@@ -0,0 +1,29 @@
+>0_115
+MLVLVINSGSSSLKYQLRELADDGTDAPVPVLAQGLVERIGVPGSGVPDHAAALEQVEAE
+LAEATGGRTIDAAGHRVVHGGERFTAPARVTNEVIRAIERLAPLAPLHNPAAAQGLRAMA
+ERWPDMPQVVVFDTSFHQTMPREAWQYALPDEVYTEHGIRRYGFHGTSDDLVTGLAAEHL
+GIPRGEFRAVVLHLGNGASATAIRDGVSVDTSMGYTPLAGLVMGTRSGDLDPSVVTHLMR
+NHGYDAEELDTLMNRRSGLLGLAGEADMRQVLENAASGDGRARNALDVASYRLAKYVGGY
+HVAVGGAQAIVFTAGIGENSAPFRARVLDRLEALGVAYDAEANRARVAGPHTISAPESAI
+PVLVVPTDEEQAIARLTWELAR
+>2_251
+MLHLGNGASATAIRDGASVDTSMGFTPLAGLVMGTRTGDLDPSVVTHLMRTQGHSAEEMD
+TLMNKESGLLGLAGHADMRQVVEAADAGDRRARTAPDVASYRLAKYVGGYHVAVGGAQAI
+VFTAGIGENSAPFRARVVERLGALGVELDAAANEAGLSAAGDDGVAVISAPGSAIPVLVI
+PTDEEQAIARLTWELTRG
+>3_186
+MTASPATMTLPTVSARQLPEDALLVLVVNSGSSSLKYQVRELTPDGRDTDQPVVLKGLVE
+RIGVAGSDVPDHAAALERVEAEITAVVGSRRLAAAGHRVVHGGERFQRPELVTNEVIRAI
+ERLAPLAPLHNPAAAQGLRAVAQRWPDLPQVVVFDTSFHQSMPREAWQYAIPDELYTEHG
+IRRYGFHGTSHDLVTGLAAEHLGLERSEFDGVVLHLGNGASATAIRGGRSIDTSMGYTPL
+AGLVMGTRSGDLDPSIVTHLITAHGMSAEDVDAMLNKESGLLGLSGNADMRQVLEAAEAG
+HRASRDALRIASYRLAKYVGGYHVAVGGAKAIVFTAGIGENSAPFRARVLDRLEPLGVRY
+DHARNMVRGDEPRTISTDDSAIPVLVVPTDEEMAIAQLTHHVVEQAEAWTLG
+>4_123
+MLVLVINSGSSSLKYQLRELADDGTDAPVPVLAQGLVERIGVPGSGVPDHAAALEQVEAE
+LAEATGGRTIDAAGHRVVHGGERFTAPARVTNEVIRAIERLAPLAPLHNHAAAQGLRAMA
+ERWPDMPQVVVFDTSFHQTMPREAWQYALPDEVYTEHGIRRYGFHGTSHDLVTGLAAEHL
+GIPRGEFRAVVLHLGNGASATAIRDGVSVDTSMGYTPLAGLVMGTRSGDLDPSVVTHLMR
+NHGYDAEELDTLMNRRSGLLGLAGEADMRQVLENAASGDGRARNALDVASYRLAKYVGGY
+HVAVGGAQAIVFTAGIGENSAPFRARVLDRLEALGVAYEAEANRARVAGPHTISAPESAI
+PVLVVPTDEEQAIARLTWELAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001787.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001787.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ea8792e42a412a2d8fbe0bf170939a18483938c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001787.fa
@@ -0,0 +1,25 @@
+>0_192
+MKTPARLAVGMLAASGLLLTGCASDPTLDESWPEIRQKVVDAESLRLRVEGTAADKEEEK
+DDASASAAPSASLGTDASQSLNVDLAGATDDSHLKGTMNMDMGAATMDIEVLRRDADVFF
+KLKADGDDLPQEMGMFSTLVGDRWIKTSADQAAQMDISLQEIMSDLEEDMPAADAFDGKD
+LKAEEVELEGRTYLKYALPEEHHEFGRTMLIDPESTTLYRLEDVNSEDEDVDANATFTEW
+NAVEAPEAPAKEDVFDLAELQELAG
+>2_179
+MKSSLLTATGLPRAAAVLAAAGLLLTGCAADPTLDENWPEIRQKVVDAQSLRLQMDGEAA
+PDAEGSGQDSEITAAAADLSGATDDSHLKGTMDMDMGADSVDMEILRLGEEVFLKMAADG
+DGVPAEMAMFEQLVGDRWMLMPADEADSMAGISLKEIMDDLEADMPAAEAFDGKDLKAEK
+VELDGQEYLKYALPEEFHDFARTMYVHPDDETLHRLEGTGGEDAEADTTATFSEWNAVQA
+PERPAEDQIVDMAALQGLTG
+>3_115
+MTPRLSRASLTALLGAGALALSACGGDPAPAASSSAEAASSSAAGPTVSTSPNGSDAAAS
+SSSESAASESSASDVPAGQAPEAEVVWKDIQQGLDEAESVHILAEIDGGSGSEVQRVDLA
+GDVAGTTVQGSVTGDSADFTGTMDFIHVGGQTYLKMDGSGGGDASRMAEALDGRWLVDTQ
+GMIPVDEMNPQVFLDEMKQEFSTVTDAELAAMEGEVVQVDGEEMYRYSDDSSWTMTVDKD
+NHVREFRDTKSSGEGTVTMDRWNQVTPAAAPPAAEQVTMDELSQEIASSGAGSSAGATAS
+ATVDG
+>3_135
+MKSPKIAAAALLATGGLLLSACATQPTLEESWPEVRQKVVDAQSLHLKMDGTAKEDASGS
+ASASSSSDIQSGTIDLAGATDDSHLKGTVAAKMGDGEVNMDILRLGQDVYMRINKAEGGQ
+APEGMDAFQQIVGDRWMLMPADQASGMGELSLGTVMDDLEEDMPAADAFNGKDVKAEEVD
+LDGRKVLKYALPEEHKDFGRTMYVDKETKELYRLEDVNSVESEADATATFTEWNAVQAPE
+RPAEDEVFDMQKLSEGLAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001792.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001792.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac8619ca98be13d5601624db4fa4d5f5f045a345
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001792.fa
@@ -0,0 +1,31 @@
+>0_234
+MDVLAEAGELGLGGIYVGEEHGGTGLARTDAILIFEELAKADPAFAAYISIHNMVAWMID
+SFGSDEQRARWIPDLVGMEHLASYCLTEPGAGSDAAALKTRAVRDGDHYVLNGVKQFISG
+AGSSGYYVVMCRTADTGARGISAVVVHKDTPGLSFGPSEKKMGWHTQPTRQVIFEDVRVP
+VADRLGEEGDGFRIAMKGLNGGRLNIGACSIGGGLAALDKATRYLKERSAFGEPLTTKQA
+LVFELADMSVKLETAHTMLMRAADALDRNDPDTVRLCAMAKLVATESGYEAADTALQLHG
+GYGYLHEYGVEKLVRDLRVHRILEGSNEIMRMIVGRGLIG
+>1_2197
+MFPITDDQKALVDAVRDFAEQRVAPHALDWDAEKHFPVDVLAEAGELGLGGIYVGEEHGG
+TGLERTDAILIFEELAKADPAFAAYISIHNMVAWMIDSFGSDEQRARWIPDLAGMEYLAS
+YCLTEPGAGSDAAALKTRAVRDGDHYVLNGVKQFISGAGASDCYVVMCRTADTGARGISA
+VVVHKDTPGLSFGPNEKKMGWHTQPTRQVIFEDVRVPVADRLGEEGDGFRIAMKGLNGGR
+LNISACSIGGGLAALDKATRYLKERSAFGEPLTTKQALVFELAEMAVKLETAHTMLMRAA
+DALDRNDPDTVRLCAMAKLVATEHGYEAADTALQLHGGYGYLHEYGVEKLVRDLRVHRIL
+EGSNEIMRMIVGRGLIG
+>2_118
+MFPITDDQEALVDAVRDFAQQRVAPHALEWDAEKHFPVDVLAEAGELGLGGIYVGEEHGG
+TGLERKDAILIFEELSKADPAFAAYISIHNMVAWMIDSYGNDEQRAQWIPELMSMEHLAS
+YCLTEPGAGSDAAALKTRAVRDGDDYVLNGVKQFISGAGSSDYYVVMCRTADTGAKGISA
+VVVHKDTPGLSFGPNEKKMGWHTQPTRQVIFEDVRVPVANRLGEEGDGFRIAMKGLNGGR
+LNIGACSIGGGLAALDKATRYLKERSAFGEPLTTKQALVFELADMAVKLETAHTLLMRAA
+DALDRNDPDTVRLCAMAKLVATESGYEAADAALQLHGGYGYLHEYGVEKLVRDLRVHRIL
+EGSNEIMRMIVGRGLIGG
+>4_234
+MFPITDDQKALVDAVRDFTEQRVAPHALDWDAEKHFPVDVLAEAGELGLGGIYVGEEHGG
+TGLERTDAILIFEELAKADPAFAAYISIHNMVAWMIDSFGSDEQRARWIPDLAGMEHLAS
+YCLTEPGAGSDAAALKTRAVRDGDHYVLNGVKQFISGAGASDCYVVMCRTADTGARGISA
+VVVHKDTPGLSFGPNEKKMGWHTQPTRQVIFEDVRVPVAGRLGEEGDGFRIAMKGLNGGR
+LNIGACSIGGGLAALDKATRYLKERSAFGEPLTTKQALVFELADMSVKLETAHTMLMRAA
+DALDRNDPDTVRLCAMAKLVATEHGYEAADTALQLHGGYGYLHEYGVEKLVRDLRVHRIL
+EGSNEIMRMIVGRGLIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001798.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001798.fa
new file mode 100644
index 0000000000000000000000000000000000000000..995aa0cb2ef06df15f7b05a083d93fbeb8b0c5ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001798.fa
@@ -0,0 +1,20 @@
+>0_267
+MTGSAPAQLRPLRATDAPAVLAAFHAGTVGMADPAEVTDDASARAYVDGLVQAEGTDAVA
+VVERGTDTLIGLVAVVRDEAHGTGALTAWLHQGWRGDAIMSRAATTVADAELAEGGLERI
+ELAHRADSPTAGAVARAAGLRHEGTQRGRLRTGGRRLDVHLYGRLAADPLPEERVRPLPW
+ASDARPWADR
+>1_2233
+MTGSAPAQLRPLRPTDVPAVLAAFHAGTVGMADPAEVTDEASARAYVDGLVQAAETDAVA
+VVERGTDTLIGLVAVARDEAHGTGALTAWLHQGWRGDAIMSRAATTVTDAELAEGGLERI
+ELAHRADSPTAGAVARAAGLRHEGTQRGRLRAGGRRLDVHLYGRLAADPLPEERVRPLPW
+ASDARPWADR
+>2_70
+MTGTARAQLRPLHSDDADAVFEGFRSDPVGMARQGDVSDEASARFYVDRMLESEATDAVA
+VVDPATDRLIGLVSVVRDEENRSGWFSYWLNSAWRGDAIMARAAATVADAELAEGGLERL
+ELGHRANNPTSGSVARAAGFLHEGTQRGHFLIDGRRQDVHLYGRLPSDPQPAEKVRPLPW
+ASDERPWSGR
+>4_266
+MTGSAPAQLRPLRPTDVPAVLAAFHAGTVGMADPAEVTDEASARAYVDGLVQAAETDAVA
+VVERGTDTLIGLVAVARDEAHGTGALTAWLHQGWRGDAIMSRAATTVTDAELAEGGLERI
+ELAHRADSPTAGAVARAAGLRHEGTQRGRLRAGGRRLDVHRYGRLAADPLPEERVRPLPW
+AADARPWADR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001799.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001799.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4db2beba2a3a356fd45d867bded7d51f431a529a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001799.fa
@@ -0,0 +1,28 @@
+>0_276
+MPEGDSLVRVAHRLRPVLEGRVLTHADLRVPRHATADLTGWTVAEVLPRAKYLLMRLTPP
+AARPGARPLTLISHLKMEGRWLVSALDARWGAPAWQVRAVLETAEHRVLGAQLGLLTLVP
+TADETTVLGHLGPDLLDPAWDTPDDGAALLAEGMRRLTARPERPVGLALLDQRLVSGIGN
+IYRCETLLLAGIDPHRPIGEVEDVAGLVLLARDLLRANVPPAAPATGARRRTTGVRPNPG
+RPFGVEVLVPAGPPLGTAPGRTPGARGGGAPSYWVYGHDRAPCLRCRGPVRQEDYGSAED
+DARRLWWCPHCQG
+>1_2249
+MPEGDSLVRVAHRLRLVLEGRVLTHADLRVPRHATADLTGWTVAEVLPRAKYLLMRLTPP
+AARPGARPLTLISHLKMEGRWLVSAVDARWGAPAWQVRAVLETAEHRVLGAQLGLLTLVP
+TADEATVLGHLGPDLLDPAWDTPDDGAALLAEGVRRLTARPERPVGLALLDQRLVSGIGN
+IYRCETLLLAGIDPHRPIGEVEDVAGLVLLARDLLRANVPPAAPAAGARRRTTGVRPNPA
+RPFGVEVLVPAGPSPGTAPGRTPGARGGGAPSYWVYGHDRAPCLRCRGPVRQEDYGSPED
+DARRLWWCPHCQR
+>3_39
+MPEGDSLVRAAHRLRPVLAGRVLTHADLRVPQLATARLTGWTVSEVEPRGKWLLMRLTPP
+ADRPDAAPHTLVSHLKMEGRWMVTGRDARWPAPAWQVRAVLETAEHRAVGAQLGRLELAP
+TAEEDRLLGHLGPDLLDPAWDDPARGAELLAEGVRRLTARPERPVGLALLDQRTTCGIGN
+IYRCESLLLAGLDPHRPVAAVPDVSGLLTLARDLLRANVPPAAPFIGWPRTTTRVRPDPS
+GPYGLRVVVEDRGFPGGLPGGPVPDDAPHASATSTSGAGLGRRGDLPRGPHYWVYGHRTT
+PCGRCGGPVTFEEYGSPEDDERQLWWCRTCQR
+>4_282
+MPEGDSLVRVAHRLRPVLEGRVLTHTDLRVPRHATADLTGWTVAEVLPRAKYLLMRLTPP
+TARPGARPLTLISHLKMEGRWLVSAIDARWGAPAWQVRAVLETAEHRVLGAQLGLLTLVP
+TADEAAVLGHLGPDLLDPAWDTPDDGAALLAEGVRRLTARPERPVGLALLDQRLVSGIGN
+IYRCETLLLAGIDPHRPIGEVEDVAGLVLLARDLLRANVPPAAPAAGARRRTTGVRPNPA
+RPFGVEVLVPAGPSPDTAPGRTPGARGGGTPSYWVYGHDRTPCLRCRGPVRQEDYGSPED
+DARRLWWCPHCQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001801.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001801.fa
new file mode 100644
index 0000000000000000000000000000000000000000..465f6958d13b31c7a6b88eb030f41f6e79fa74f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001801.fa
@@ -0,0 +1,36 @@
+>0_291
+MALALVLVGCAAPQGDEGTAAGSSGATDAAVSSPASVDGSEASSSQGRSSDAASSPAAAS
+SGEGSPSAAADPAGPAVPLAARSHEGVPMRAFTAEERPPQFVLFSFDGGRQDARWKTFLD
+AAADSDAKFTVFQSAINLIETANRENYTAPGNTPGYVGTEFGGDEAEVAQRIENINTAHA
+AGHEIGTHYAGHLCALATYGGDKWSTAEWEQEYGSFRDILSDPAAYNPGSSLPALEVTPE
+DVKGGRLPCLDGQWDQLVPMWKDNGLEYDTSRAAAASGVAWPYQEDGIWEFEMPMTWSPV
+LAEKGAASPFVMAMDYNFWISGNGGRDIPEDVARLTDFQYRTYRYMYDSALAGNRAPLVF
+GNHFNDWGLNAFNPAVEKVMREVCVEEDTYCVTYQQMIAWLELQDPEVLAAWRDQARSAT
+GTDAEALGW
+>1_8
+MSFPRRSARTVDTPSPRRRRWWGTSVALALVLAGCAAPQGDEGTAAGSSGATDAAVSSPA
+SANGSEASSSQGRSSDAASSGEGSPSAAADPAVPLAARSHEDVPMRAFTAEERPPQFVLF
+SFDGGRQDARWKTFLDAAADSDAKFTVFQSAINLIETANRENYTAPGNEPGYVGTEFGGD
+EAEVAQRIENINTAHAAGHEIGTHYAGHLCAPTRYGADQWSTAEWKQEYGSFTDILSDPG
+AYNPGSSLPALEVTPDDVKGGRLPCLDGEWDQLVPMWKDNGLEYDTSRAAAASGVAWPYQ
+EDGIWEFEMPMTWSPVLAEKDAASPFVMAMDYNFWISGNGGKDIPEDVARLTDFQYRTYR
+YMYDSAFAGNRAPLVFGNHFNDWGLNAFNPAVEKVMREVCVEEDTYCVTYQQMIAWLELQ
+DPEVLAAWRDQARSATGTDAEALGW
+>2_45
+MPLHRQPAPFRARRVWGTSVALALVLAGCAAPQEGDAQGAASETSSSSAPAPSASAPSDA
+GPASPSGSTGTDASETAAAPSSSASGDSAGPTASADPATPLAARSHEGVPMRAYAADERP
+PQFVLFSFDGGRQDARWKTFMDAAEDSGAKFTVYQTGINLIESANRENYAAPGNEPGYVG
+TELGGDAAEVAQRIGNINAAHAAGHEIGTHYNGHLCSPTPHGGDKWTTAEWEQEYSTFEE
+IITDPGAFNPGSALPALDITPEDIKGGRPPCLDGQWDQLVPMWKEHGLVYDTSRSASATG
+VAWPYQEDGIWQFEMPIVWSPVLAEQGKPSPLVMAMDYNFWISGNGGKDDPADTARLTAF
+QHRTYRYMFSSAHAGNRAPLVFGNHFNDWGLNAFNPAVEQTMREVCDEPDTYCVTYQQMV
+DWLELQDPAVLEAWRAQPRSATGDDAAALG
+>4_298
+MSFPRPSARTVDTPSPRRRRWWGTSVALALVLAGCAAPQGDEGTAAGSSGATDAAVSSPA
+SADGSEASSSQGRSSDAASSQAASSFGEGSPSAAADPADPALPLAARSHEGVPMRAFTAE
+ERPPQFVLFSFDGGRQDARWKTFLDAAADSDAKFTVFQSAINLIETANRENYTAPGNEPG
+YVGTEFGGDEAEVAQRIENINTAHAAGHEIGTHYAGHLCAPTRYGADQWSTAEWKQEYGS
+FTDILSDPGAYNPGSSLPALEVTPDDVKGGRLPCLDGEWDQLVPMWKDNGLEYDTSRAAA
+ASGVAWPYQEDGIWEFEMPMTWSPVLAEKDAASPFVMAMDYNFWISGNGGKDIPEDVSRL
+TDFQYRTYRYMYDSAFVGNRAPLVFGNHFNDWGLNAFNPAVEKVMREVCVEEDTYCVTYQ
+QMIAWLELQDPEVLAAWRDQARSATGTDAEALSW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001804.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001804.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1818f93c4e30da0f4097466672a0d2c73b7c5e79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001804.fa
@@ -0,0 +1,24 @@
+>0_315
+MLEISQVSKTFFPNTVNERRALQGIDLHLAEGDFVTVIGSNGAGKSTILNTIAGKLLPDT
+GTVAVGGKDVTRMPDHRRAASIGRVFQDPTAGTAPNLTIEENMALAWRRGHARGLSRGVS
+RARRAMFRDELTKLELGLENRLTAKVGLLSGGQRQALSLLMATFSGPKILLLDEHTAALD
+PSRAELVTRLTRQVVAEHRLTTLMVTHNMSQALEVGNRLIMMHDGRIILELDEQEKAGRT
+PADLLAEFAKIKGAVVDDKTMLS
+>1_40
+MLEISQVSKTFFPNTVNERRALQGIDLHLAEGDFVTVIGSNGAGKSTILNTIAGKLLPDT
+GTVAVGGKDVTRMPDHRRAASIGRVFQDPTAGTAPNLTIEENMALAWRRGHARGLSRGVS
+RARRAMFRDELTKLELGLENRLTAKVGLLSGGQRQALSLLMATFSGPKILLLDEHTAALD
+PSRAELVTRLTRQVVAEHRLTTLMVTHNMSQALEVGNRLIMMHDGRIILELDEQEKAGRT
+PADLLAEFGKIKGAVVDDKTMLS
+>2_2
+MLEISQVSKTFFPNTVNERRALQGIDLHLAEGDFVTVIGSNGAGKSTILNTIAGKLLPDT
+GTVKVSGKDVTRMADHRRAAWIGRVFQDPTAGTAPNLTIEENMALAWRRGHTRGLARGVS
+RSRRGLFREELTKLELGLEDRLTAKVGLLSGGQRQALSLLMATFSGPKILLLDEHTAALD
+PSRAELVTRLTQQVVAEHRLTTLMVTHNMSQALEVGNRLIMMHDGRIILELDEAQKAGRT
+PADLLAEFAKIKGAVVDDKTMLS
+>4_322
+MLEISQVSKTFFPNTVNERRALQGIDLHLAEGDFVTVIGSNGAGKSTILNTIAGKLLPDT
+GTVAVGGKDVTRMPDHRRAASIGRVFQDPTAGTAPNLTIEENMALAWRRGHARGLSRGVS
+RARRAMFRDELTKLELGLENRLTAKVGLLSGGQRQALSLLMATFSGPKILLLDEHTAALD
+PSRAELVTRLTRQVVAEHRLTTLMVTHNMSQALEVGNRLIMMHDGRIILELDEQEKAGRT
+PADLLAEFGKIKGAVVDDKTMLS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001810.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001810.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e08d9328b5716278e7f82de4568dc7197b0001eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001810.fa
@@ -0,0 +1,20 @@
+>0_410
+MASDHRPPHPVSPHPDDLDGGGRPVVGPDEARRRIAGHSGPDARPLIRPDARTPGVFRAL
+LGLTVASAVLYAASTLRNLLPGAAQDIADSLPEGSAQSPAMTAEAIEGALTGSVWFATLL
+GLAVYAIVLVGLTRRSNAARIMGALFASIAIFVTLLGTIRLFVFPAGDVVLPLVLGGLFA
+LVNAAWLVCAFNPGLATTFLRRRA
+>1_140
+MASDHRPPHPVSPHPDDLDGGGRPVVGPDEARRRIAGHSGPDARPLIRPDARTPGVFRAL
+LGLTVASAVLYAASILRNLLPGAAQDIADSLPEGGAQSPAMTAEAIEGALTGSVWFATLL
+GLAVYAIVLVGLTRHSNTARIMGALFASIAIFVTLLGAIRLFVFPAGDVVLPLVLGGLFA
+LVNAAWLVCAFNPGLATTFLRRRA
+>2_2470
+MASDPRPPNPASPDPASPDGFRPGDGRPVVGPEDARRRIAGHSGPHARPLIRPNERTPGV
+FRALVGLTVASAAVYVVSLLLGLRPGAAEEIAATLPADASRSPAMTAESIQAALTGSVWV
+AVLLGLGVYALVLVGLLRRSNTARIVGAIVAALAVFVTLLGAIRLFVFPAESVVAPLLLG
+LLFALVNAAWLVCAFNPGLATTFVRRDAGPRRPA
+>4_413
+MASDHRPPHPVSPDSDDLDGGGRPVVGPDEARRRIAGHSGPDARPLIRPDARTPGVFRAL
+LGLTVASAVLYAASILRNLLPGAAQDIADSLPEGGAQSPAMTAEAIEGALTGSVWFATLL
+GLAVYAIVLVGLTRHSNTARIMGALFASIAIFVTLLGAIRLFVFPAGDVVLPLVLGGLFA
+LVNAAWLVCAFNPGLATTFLRRRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001812.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001812.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c1961d5f53072c69a945caa6d2e245dc02a76f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001812.fa
@@ -0,0 +1,20 @@
+>0_454
+MTATPQTPAQPLQDDAPVVSVVMGSDSDWPVMSAAAEALRELDVPVEVGVVSAHRMPHEM
+VEFGARAHERGIRVIVAGAGGAAHLPGMLAAVTPLPVIGVPVKLKSLDGMDSLLSIVQMP
+AGVPVATVSIDGARNAGLLAARILASADTAEGDRLRAALAEHADELNAQARAKGARLRER
+MAADR
+>1_181
+MTATPQTPAQPLQDDAPVVSVVMGSDSDWPVMSAAAEALRELDVPVEVGVVSAHRMPHEM
+VEFGARAHERGIRVIVAGAGGAAHLPGMLAAVTPLPVIGVPVKLKSLDGMDSLLSIVQMP
+AGVPVATVSIDGARNAGLLAARILASADTAEGDRLRAALAEHADELNAQARAKGARLRER
+MAADR
+>3_2300
+MTAEQTTQPTSDAPCTRPLQEEAPVVSVVMGSDSDWPVMGQAVEALRELGVPVEVGVVSA
+HRMPHEMVDFGARAHERGIRVIVAGAGGAAHLPGMLAAVTPLPVIGVPVKLRSLDGLDSL
+LSIVQMPAGVPVATVSVDGARNAGLLAARILAAGTDDGAAHLRAALQDVAAGLNAQARAK
+GARLHERAADGA
+>4_454
+MTATPQTPAQPLQDDAPVVSVVMGSDSDWPVMSAAAEALRELDVPVEVGVVSAHRMPHEM
+VEFGARAHERGIRVIVAGAGGAAHLPGMLAAVTPLPVIGVPVKLKSLDGMDSLLSIVQMP
+AGVPVATVSIDGARNAGLLAARILASADTAEGDRLRAALAEHADELNAQARAKGARLRER
+MAADR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001822.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001822.fa
new file mode 100644
index 0000000000000000000000000000000000000000..99ac71a89682666b61cca488319b47f567372f32
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001822.fa
@@ -0,0 +1,29 @@
+>0_600
+MASKDWARKISDVPEGTRRQWRADRALRAPMRSPGRPQPSREVQRQFWRVIATGVTTVEA
+SLTVGVSWPVGARWFRHAGGMTPLSLAEPTGRYLSFAEREEIAILHAQGQGVRQIARTLG
+RDPGTISRELRRNCATRSGKQEYRATVAQWKAQEAARRPKPAKLATNQRLHDYVQARLNG
+VVLGPDGVAVPGPVGPGFKGRKMKPRRADRRWSTAWSPEQISHRLRLEFPDDVSMRISHE
+AIYQSLFIQGRGALKRELVACLRTGRALREPRARTRNKPQGHVTEDVVFSKRPPEAADRA
+VPGHWEGDLIIGTERSAIGTLAERKSRATILVHLPRLEGWGERPPVKNGPSLGGYGAEAM
+TAALIKAMATVPEQLRQSLTWDRGKELAGHVQFTMATGTKVFFADPHSPWQRPTNENTNG
+VLRQYFPKGTDLSRWSAEDLAAVAYTLNNRPRKVLDWKTPAEVFAEQLRSLSTHGVATTG
+>2_716
+MASKDWARKISDAPEGARRQWRADRALRAPMRSPGRPQPSREVQRQFWRVIATGVTTVEA
+SLSVGVSWPVGARWFRHAGGMTPLPLAEPTGRYLSFAEREEIAILHAQGHGVRQIGRALG
+RDPGTISRELRRNCATRSGGKEYRATVAQWKAQQAARRPKPAKLATNQRLHDYVQARLNG
+VVLGPDGVAVQGPVGPGFKGRKMKPRRADRRWSTAWSPEQISHRLRLEFPDDVSMRISHE
+AIYQSLFVEGRGALKRELVGCLRTGRALREPRARTRNKPQGHVTEDVVFSKRPPEAADRA
+VPGHWEGDLIIGLQRSAIGTLAERKSRATILVHLPRLQGWGEQPPVKNGPSLGGYGAAAM
+SAALTKAMTGLPQQLRQTLTWDRGGELAGHAQFTMATGTRVFFADPHSPWQRPTNENMNG
+LLRQYFPKGTDLSRWSADDLAAVAYTLNNRPRKVLGWKTPAEVFAEQLSSLETSGVATTT
+>2_728
+MRISHEAIYQSLFVEGRGALKRELVGCLRTGRALREPRARTRNKPQGHVTEDVVFSKRPP
+EAADRAVPGHWEGDLIIGLQRSAIGTLAERKSRATILVHLPRLQGWGEQPPVKNGPSLGG
+YGAAAMSAALTKAMTGLPQQLRQTLTWDRGGELAGHAQFTMATGTRVFFADPHSPWQRPT
+NENMNGLLRQYFPKGTDLSRWSADDLAAVAYTLNNRPRKVLGWKTPAEVFAEQLSSLETS
+GVATTT
+>2_731
+MASKDWARKISDAPEGARRQWRADRALRAPMRSPGRPQPSREVQRQFWRVIATGVTTVEA
+SLSVGVSWPVGARWFRHAGGMTPLPLAEPTGRYLSFAEREEIAILHAQGHGVRQIGRALG
+RDPGTISRELRRNCATRSGGKEYRATVAQWKAQQAARRPKPAKLATNQRLHDYVQARLNG
+VVLGPDGVAVQGPVGPGFKGRKMKPRRAEVKSLEVV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001824.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001824.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7097752ad660eb92a126c1a98618911252736696
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001824.fa
@@ -0,0 +1,24 @@
+>0_604
+MTPLTRRTLIAGGLTLLGAGTLTACAAPNPATSPAAGTGTQGTGTAITHVHALTRDPESG
+EVLLATHQGLFRLQDGELTQVGPVVDFMGFTLTPEGRYLASGHPAPRTDLPEPLGLAEST
+DRGQSWTVLSRGGASDFHALAAGPNGVLGFDGQLRASTDGLTWQSLEIPVAPASLAISPK
+TGTVLATTETGMLRSTDHGATWTTLDTPQLMHLVAWADDTTAVGAGTEGHLLTSTDAGDT
+WTASDRPVGTATALGTGITDDGQTEALLVVGSTVLSTTDGGNTTESLL
+>2_385
+MTPLTRRTLIAGGLTLLGAGTLTACAAPNPATSPAAGTGTQGTGTAITHVHALTRDPESG
+EVLLATHQGLFRLQDGELTQVGPVVDFMGFTLTPEGRYLASGHPAPNTDLPEPLGLAEST
+DRGQSWTVLSRGGQSDFHALAAGPNGVLGFDGQLRASTDGLTWQSLEIPVAPASLAISPQ
+TGTVLATTETGMLRSTDHGATWTTLDTPQLMHLVAWADDTTAVGAGTEGHLLTSTDAGDT
+WTASDRPVGTATALGAGITDDGQTEALLVVGSTVLSTTDGGNTTESLL
+>3_2148
+MTPLTRRTLIAGGLTLLGAGTLTACAAPNPATSPAAGTGTQGTGTAITHVHALTRDPEYG
+EVLLATHQGLFRLQDGELTQVGPVVDFMGFTLTPEGRYLASGHPAPRTDLPEPLGLAEST
+DRGQSWTVLSRGGASDFHALAAGPNGVLGFDGQLRASTDGLTWQSLEIPVAPASLAISPQ
+TGTVLATTETGMLRSTDHGATWTTLDTPQLMHLVAWADDTTAVGAGTEGHLLTSTDAGDT
+WTASDRPVGTATALGTGITDDGQTEALLVVGSTVLSTTDGGNTTESLL
+>4_577
+MTPLTRRTLIAGGLTLLGAGTLTACAAPNPATSPAAGTGTQGTGTAITHVHALTRDPESG
+EVLLATHQGLFRLQDGELTQVGPVVDFMGFTLTPEGRYLASGHPAPRTDLPEPLGLAEST
+DRGQSWTVLSRGGASDFHALAAGPNGVLGFDGQLRASTDGLTWQSLEIPVAPASLAISPQ
+TGTVLATTETGMLRSTDHGATWTTLDTPQLMHLVAWADDTTAVGAGTEGHLLTSTDAGDT
+WTASDRPVGTATALGTGITDDGQTEALLVVGSTVLSTTDGGNTTESLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001825.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001825.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e1faebbea8c76c28914ebdc328a12a1ab5bf432
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001825.fa
@@ -0,0 +1,12 @@
+>0_607
+MTESARTPLPGATNGCSCCAPAADATAPAGHQSADPTGTSAGDATYQVEGMTCGHCVGSV
+AEAVSALDGVDDVRVELVAGGASPVTVTGPASADSVRTAIEAAGYRVRI
+>2_388
+MTESARTPLPGATNGCSCCAPAADATAPAGHQSADPTGTSAGDATYQVEGMTCGHCVGSV
+AEAVSALDGVDDVRIELVAGGASPVTVTGPASADSVRTAIEAAGYRVRI
+>3_2145
+MTESARTPLPGATNGCSCCAPAADATAPAGHQSADPTGTSAGDATYQVEGMTCGHCVGSV
+AEAVSALDGVDDVRIELVAGGASPVTVTGPASADSVRTAIEAAGYRVRI
+>4_574
+MTESARTPLPGATNGCSCCAPAADATAPAGHQSADPTGTSAGDATYQVEGMTCGHCVGSV
+AEAVSALDGVDDVRVELVAGGASPVTVTGPASADSVRTAIEAAGYRVRI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001826.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001826.fa
new file mode 100644
index 0000000000000000000000000000000000000000..705d159af8e62fb8765b2b084825c99dd914725b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001826.fa
@@ -0,0 +1,28 @@
+>0_610
+MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA
+LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG
+HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH
+SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHYWTIELTRPAEKQEV
+LETFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVALWEDILTVDGNELYYTY
+TVDNQAIVIPENIDAIRALTGTVDDGGESIRCTDRALGVRQDFVRSSVAAR
+>2_391
+MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA
+LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG
+HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH
+SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHYWTIELTRPAEKQEV
+LEAFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVALWEDILTVDGNELYYTY
+TVDNQAIVVPENIDAIRALTGTVDDGGESIRRTDRALGVRQDFVRSSVAAR
+>3_2142
+MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA
+LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG
+HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH
+SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHNWTIELTRPAEKQEV
+LEAFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVVLWEDILTVDGNELYYTY
+TVDNQAIVVPENIDAIRALTGTVDDGGESIRRTDRALGVRQDFVRSSVAAR
+>4_571
+MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA
+LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG
+HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH
+SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHYWTIELIRPAEKQEV
+LEAFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVALWEDILTVDGNELYYTY
+TVDNQAIVVPENIDAIRALTGTVDDGGESIRRTDRALGVRQDFVRSSVAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001832.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001832.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c9295b01b92ed418c52e1bb361ab412a741df3d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001832.fa
@@ -0,0 +1,17 @@
+>0_640
+MTERVEIEQRGRYADELAVGQVYLHRPGRTLTEADNVLFTTLTMNPQALHLDHAYAADQP
+FGRPLVNSMLTLSTLVGLAVGQTTQGTLVAQLGLGEIAFPKPVFHGDTLYGRSEVTAIRE
+SSSRPGQRIVTFAMTGENQHGDVVVRAQRTCLMWTAQAHAEAKAKAADAAGTGERA
+>1_386
+MTERVEIEQRGRYADELAVGQVYLHRPGRTLTEADNVLFTTLTMNPQALHLDHAYAADQP
+FGRPLVNSMLTLSTLVGLAVGQTTQGTLVAQLGLGEIAFPKPVFHGDTLYGRSEVTAIRE
+SSSRPGQRIVTFAMTGENQHGDVVVRAQRTCLMWTAQAHAEAKAKAADAAGTGERA
+>2_2246
+MGRAEPGAAPERVEIVQRGRYADELAVGQVYLHRPGRTLTEADNVLFTTLTMNPQALHLD
+HAFAQTQSFGRPLVNSMLTLSTLVGLAVAQTTQGTLVAQLGLGEIAFPAPVFHGDTLYGR
+SEVRAVRESSSRPGQRIVTFAMTGENQHGDVVVRAERTCLMWTEAAHADARAQAAADAAE
+ERA
+>4_610
+MTERVEIEQRGRYADELAVGQVYLHRPGRTLTEADNVLFTTLTMNPQALHLDHAYAAAQP
+FGRPLVNSMLTLSTLVGLAVGQTTQGTLVAQLGLGEIAFPKPVFHGDTLYGRSEVTAIRE
+SSSRPGQRIVTFAMTGENQHGDVVVRAQRTCLMWTAQAHAEAKAKAADAAGTGERA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001833.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001833.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37532190d8f51ee5641b8f7588fb2dfac529b16e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001833.fa
@@ -0,0 +1,24 @@
+>0_641
+MSALTLGPAVMFTPADRPERYATALERADAVILDLEDAVIPEARPAARDAVAAAWAGRAT
+GGVDGGPLDEDRVVVRVNPAGTADHDADLAMLAGTGWRTLMLAKAESAAQVDGVVAALGP
+QTRVVALCETAAGILAAAELAAHPHVGALMWGAEDLVASMGGSSSRTPEGAYRSVVQHAR
+ATVLLAAAAHGAAAWDAVHLDLGDEAGLAAEAEDAAALGCTATVCLHPRQVPVVRSAYTP
+APEAVERARRVLAAAEGRHGAFELDGTMVDEVVLAQARAVLRRADAARPAGA
+>1_387
+MSALTLGPAVMFTPADRPERYATALERADAVILDLEDAVTPDARPTARDAVAAAWAGRAT
+GGVDGGPLDEDRVVVRVNPAGTADHDADLAMLAGTGWRTLMLAKAESAAQVDGVVAALGP
+QTRVVALCETAAGILAAADLAAHPHVGALMWGAEDLVASMGGSSSRTPEGAYRSVVQHAR
+ATVLLAAAAHGAAAWDAVHLDLGDEAGLAAEAEDAVALGCTATVCLHPRQVPVVRSAYTL
+APEAVERARRVLAAAEGRHGAFELDGAMVDEVVLAQARAVLRRADAPRPASA
+>2_2245
+MSALALGPAVMFTPADRPERYAKALERADAVILDLEDAVTPDARPAARDAVRAAWEGRAA
+GGADGGPLDVARVVVRVNPAGGADYTADLAMLAETGWRTLMLAKAESAAQVDGLVAAMGE
+DVRVVALCETAAGVLAAAELAAHPNVGALMWGAEDLVASMGGSSSRTADGAYRSVVTHAR
+AAVLLAAAAHGAAAWDAVHLDLADEAGLAAEAEDAVALGCAATVCLHPRQVPVVRSAYTP
+AAEAVERAHRVLSEAEGRRGAFELDGAMVDEVVLAQARAVLRRAEAAGAAAG
+>4_611
+MSALTLGPAVMFTPADRPERYATALERADAVILDLEDAVTPDARPTARDAVAAAWAGRVT
+GGVDGGPLDEGRVVVRVNPAGTADHDADLAMLAGTGWRTLMLAKAESAAQVDGVVAALGP
+QTRVVALCETAAGILAAADLAAHPHVGALMWGAEDLVASMGGSSSRTPEGAYRSVVQHAR
+ATVLLAAAAHGAAAWDAVHLDLGDEAGLAAEAEDAVALGCTATVCLHPRQVPVVRSAYTP
+APEAVERARRVLAAAEGRHGAFELDGAMVDEVVLAQARAVLRRADAARPASP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001836.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001836.fa
new file mode 100644
index 0000000000000000000000000000000000000000..105f99fb541b15ba093f108ce6ecb537ee3ce0fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001836.fa
@@ -0,0 +1,24 @@
+>0_713
+MIRFLHGIGGRPAHFEPLADALGAVADLAASPALPGHPGTDAGGQGRPRAARPATDADPV
+LDAARTWAAQAGPVPGLLIGHSTGGVIALRAVADGLVRPRALVVIDSNVPVTDTALAARA
+AKARLAARPDWRSVLRASLARDLLVPEPWRERILTDLDATPDHPMRELWAAVLAADTRAL
+WAGITVPTLYVRSTRDVHQRDLDAVTQHATVVDVSTGHWPHVTEPEAVAAAIRRWHTTGV
+HPTR
+>1_453
+MIRFLHGIGGRPAHFQPLADALDAAADLAASPALPGHPGTDAGGQDRPRSARPAIEADPV
+LDAARTWAAQAGPVPGLLIGHSTGGVIALRAVADGLVRPRALVVIDSNVPVTDIALAARA
+AKARLAARPDWRSVLRASLARDLLVPEPWHERILADVDATPDHPMRELWAAVLAADTRTL
+WAGITVPTLYVRSTRDVHQRDLDAVTQHTTVVDVGPGHWPHVAEPGAVAAAIRRWHTTGV
+HPTR
+>2_2141
+MIRVLHGIGGRPGHLAPLLDALGHGSTEDAADASPALLGHGDAVPAAPAPTGGAADPAAG
+ADHDWILAAARDWAARAREGAGPDLLIGHSTGGVIALRALAEGLVRPRGLVVIDSNVPVD
+AAALAARADKARLAAAPDWRDRLRASLARDLVAPKPWPARILADLDATADHPMRALWSAV
+LTADPRPLWAAASVPVLYVRSTRQVHQADLDKLTDRARVVDVSAHAGGHWPHLADPAGVA
+RAIRDWRAETGA
+>4_677
+MIRFLHGIGGRPAHFQPLADALGAAADLAASPALPGHPGTDAGGQDRPRAARPAIEADPV
+LDAAHTWAAQAGPVPGLLIGHSTGGVIALRAVADGLVRPRALVVIDSNVPVTDPALAARA
+AKARLAARPDWRSVLRASLARDLLVPEPWHERILADLDATPDHSMRELWAAVLAADTRAL
+WSSLTVPTLYVRSTRDVHQRDLDAVTQHATVVDVGPGHWPHVAEPEAVAAAIRRWHATVA
+AQPSHH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001839.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001839.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0dd2835cdd30acdff2b7c7b9e5a9900f05f6a93
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001839.fa
@@ -0,0 +1,48 @@
+>0_825
+MRARETMAHVPHTDQNAPDLGVDTAVRRVREHLAALELPFETVTAGQDRAERERTLHQID
+DYVLPRLDSLDAPLLAVVGGSTGAGKSTLVNALVGHEVSRSSALRPTTRQPLLLHNPADA
+HWFTGPRVLPDLARVSVHRDAAAGPVEPDQSAMDTVALVAEPALPSGIALVDAPDIDSVA
+DQNRALARQLLEAADLWIFTTTAHRYADAVPWQLLDEAAARDITVAVVLGRVPEGAAEDI
+TPDLRRMLTERGLADARIHVIPETRFDERGLLPQEHVAGLRAWLETLAADAQARGAVARR
+TVDGVLGQLAARVADLARAEEEQRHAADLLARIVGDSTDQAVGRVREATSDGTLLRGEVL
+SRWQDFVGTGEFFRGVETTIGRLRDRLGALVRGRPAPPEEVETALETGLHAVMVEAAAAA
+AEQIERRWASEPAGRALVAGRDLGALAPDTSARAADVVRDWQSDVLALVQEEGAGKRTRA
+RLAATGVNGAAVALMIISFASTGGLAGIEVGIAGGAAVVGQKLLESIFGEDAVRRMARRA
+DELLEHRVRAFLETVLADRFLPLLHLEREPQATEELRALVPVLRRGVAAGVDGPTGPEHV
+PSAAEAGEEPR
+>1_556
+MAHVPHTDQNAPDLGVDTAVRRVREHLAALELPFETVTAGQDRAERERTLHQIDDYVLPR
+LDSLDAPLLAVVGGSTGAGKSTLVNALVGHEVSRSSALRPTTRQPLLLHNPADTHWFTGP
+RVLPDLARVSVHRDAAAGPVEPDQSAMDTVALVAEPALPSGIALVDAPDIDSVADQNRAL
+ARQLLEAADLWIFTTTAHRYADAVPWQLLDEAADRDITVAVVLGRVPEGAAEDITPDLRR
+MLTERGLADARIHVIPETRFDERGLLPQEHVAGLRAWLETLAADAQARGAVARRTVDGVL
+GQLAARVADLARAEEEQRHAADLLARIVGDSTDQAVGRVREATSDGTLLRGEVLSRWQDF
+VGTGEFFRGVETTIGRLRDRLGALVRGRPAPPEEVETALETGLHAVMVEAAAAAAEQIER
+RWASEPAGRALVAGRDLGALTPDASARAADVVRDWQSDVLALIQEEGAGKRTRARLAATG
+VNGAAVALMIISFASTGGLAGIEVGIAGGAAVVGQKLLESIFGEDAVRRMARRADELLEL
+RVRAFLETVLADRFLPLLHLEREPQATEELRALVPVLRRGVAAGVDGPTEPEHAPSAAEA
+GEESR
+>3_1927
+MESTDLTSPSAAAPIGVDTAVRRVRAHLDALELPFATATVGADRAEAERTRHQIDDYVLP
+RLDSLDAPLLAVVGGSTGAGKSTLVNALVGHEVSRSSALRPTTRQPLLLHHPDDAHWFTG
+SRVLPDLARVTVHRSASAGPVEPDSQAMDTVALVAEPSLPQGIAIVDAPDIDSVADQNRA
+LARQLLEAADLWIFTTTAHRYADAVPWELLDQAAARDITVAVVLGRVPQGAGEAIAPDLR
+RMLVEHGLPEAPIHVIPETRFGEDGLLPAEHVADLRAWLTSLAEDAQARSAVARRTVDGV
+LTQLAVRVEALAEAEHGQQETAARLAGIVADSTELALETVHRATSDGTLLRGEVLARWQD
+FVGTGEFFRGLESAVGRVRDRLGALVRGRPAPPEEVEDALETGLHAVLVEAVASAVEQVE
+RRWRSEPAGRALVEGRDLGSLPAGTSERAATLVREWQGDVLALIQEEGAGRRTRARLAAF
+GVNGAAVALMVISFASTAGLSGIELGIAGGAAAVGQKLLESIFGEDAVRRMARRASELLD
+ERVRVLLEDVVGGRFLPLLRLERDAEDTAALRALVPTLRRGVAAGVDGPQPDAAPDAPRR
+EAADAAIEEDAR
+>4_784
+MRARETMAHVPHTDQNAPDLGVDTAVRRVREHLAALELPFETVTAGQDRAERERTLHQID
+DYVLPRLDSLDAPLLAVVGGSTGAGKSTLVNALVGHEVSRSSALRPTTRQPLLLHNPADA
+HWFTGPRVLPDLARVSVHRDAAAGPVEPDQSAMDTVALVAEPALPSGIALVDAPDIDSVA
+DQNRALARQLLEAADLWIFTTTAHRYADAVPWQLLDEAAARDITVAVVLGRVPEGAAEDI
+TPDLRRMLTERGLADARIHVIPETRFDERGLLPQEHVAGLRAWLETLAADAQARGAVARR
+TVDGVLGQLAARVADLARAEEEQRHAADLLARIVGDSTDQAVGRVREATSDGTLLRGEVL
+SRWQDFVGTGEFFRGVETTIGRLRDRLGALVRGRPAPPEEVESALETGLHAVMVEAAAAA
+AEQIERRWASEPAGRALVAGRDLGALTPDTSARAADVVRDWQTDVLALIQEEGAGKRTRA
+RLAATGVNGAAVALMIISFASTGGLAGIEVGIAGGAAVVGQKLLESIFGEDAVRRMARRA
+DELLERRVRAFLETVLADRFLPLLHLEREPQATEELRALVPVLRRGVAAGVDGPTGPEHA
+PSAAEAGEEPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001847.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001847.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e8067d52a9512f108f8917ea6bb044a056f6f279
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001847.fa
@@ -0,0 +1,12 @@
+>0_1022
+MNEKQLEPDLSLRAQRRKPTPAPQTQAPGAVIPAEPATTSDPAGGYAPLARRGAPTVALN
+VRVPEAIRDAVRREAATNPATPSQAAVIEALGHV
+>1_750
+MNEKQLEPDLSLRAQRRKPTPAPQTPAPGAVIPAEPATTSDPAGGYAPLARRGAPTVALN
+VRVPEAIRDAVRREAATNPATPSQAAVIEALGRV
+>3_2177
+MNEKQLEPDLSLRAQRRKPTPAPHTPAPGAVIPVEPATASDPAGGYAPLARRGAPTVALN
+VRVPEAIRDAVRREAATNPATPSQAAVIEALVRAHLMN
+>4_969
+MNEKQLEPDLSLRAQRRKPTPAPQTPAPGAVIPAEPATTSDPAGGYAPLARRGAPTVALN
+VRVPEAIRDAVRREAATNPATPSQAAVIEALGHV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001848.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001848.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8f7179115e5ff42e9572836e2ee765eb189f9f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001848.fa
@@ -0,0 +1,28 @@
+>0_1031
+MHGPLIVMLVTTALIVLSAIFVIMEFSLLGARRHRLEAEAGRSRAARAALKGVDELTLML
+AAAQLGITLCTFALGAITKPAVDAWLGPVLEDWGIPAAAAGTASFVLSLLAVTFLHLVIG
+EMAPKSWAIAHPETAAKAVAVPARAFVWTVRPLLLLANRLANRLVTLSGVTPVDQAAVGG
+YDAAAIRQLVEHSAAAGTLDRQNHEALAGALDLQTLTLGDLLPQGQHPVKVAPDADVEAV
+QNAAACSGHLRILVQPDHTPESVPGVVHVRDTLTMEPSAPIQPLIQQALTLPSTTPLHEA
+LASMRRNSRQLAAVTQDNRFTGVVTLTDVLRGVLPRAA
+>1_759
+MHGPLIVMLVTTALIVLSAIFVIMEFSLLGARRHRLEAEAGRSRAARAALKGVDELTLML
+AAAQLGITLCTFALGAITKPAVDAWLGPVLEDWGIPAAAAGTASFVLSLLAVTFLHLVIG
+EMAPKSWAIAHPETAAKAVAVPARAFVWTVRPLLLLANRLANRLVTLSGVTPVDQAAVGG
+YDAAAIRQLVEHSAAAGTLDRQNHEALAGALDLQTLTLGDLLPQGQHPVKVAPDADVEAV
+QNAAACSGHLRILVQPDHTPESVPGVVHVRDTLTMEPSAPIQPLIQQALTLPSTTPLHEA
+LASMRRNSRQLAAVTQDNRFTGVVTLTDVLRGVLPRAA
+>2_2271
+MTQSPVFVILATIALIALSALFVIMEFSLLAARRHRLEAEAGTSRAARAALRSVDELTIM
+LAGAQLGITLATFALGAITKPAVDAWLGPVLTGWGLPAAVAGTASFFLSLLLVTFLHLVV
+GEMAPKSWAIAHPEFAAKAVAGPARAYVWAVRPLLAFANAVANRLVAASGVTPTDRAAVG
+GHDADSIRQLVEHSASSGALDEQAHGQISGALDLQDATVGDLVSPPRDLVTVPADATAED
+VQAASVASGHLRILVRPADGPDDGVPGVVHVRDTMVLGPREPVAPLVQEALTLPVDTALH
+EASSAMRAAGRQLAVVTSEGRTVGVVTLTDLFRRVLPVSG
+>4_980
+MHGPLIVMLVTTALIVLSAIFVIMEFSLLGARRHRLEAEAGRSRAARAALKGVDELTLML
+AAAQLGITLCTFALGAITKPAVDAWLGPVLEDWGIPAAAAGTASFVLSLLAVTFLHLVIG
+EMAPKSWAIAHPETAAKAVAVPARAFVWTVRPLLLLANRLANRLVTLSGVTPVDQAAVGG
+YDAAAIRQLVEHSAAAGTLDRQNHEALAGALDLQTLTLGDLLPQGQHPVKVAPDADVEAV
+QNAAACSGHLRILVQPDHTPESVPGVVHVRDTLTMEPSAPIQPLIQQALTLPSTTPLHEA
+LASMRRNSRQLAAVTQDNRFTGVVTLTDVLRGVLPRAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001854.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001854.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a3231a1bfbe0447f1ac1730ca586119f0abee9df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001854.fa
@@ -0,0 +1,20 @@
+>0_1114
+MNPVTSTARDGRSVRWDRHRAERRLELVRAARSAVHALGAHASMEEIASHAGTSKTVYYR
+YFGDREGLRLAVSERVTAHMERRLLEVADEPVSEPEALRRMVEVYLTVAATSPEVYAFAV
+APSPAAAEAPVLGPFLERVYAMLESGLARGMAARGHAPAPADPLALWPRAAVGLVRAAAE
+TWLRTPAAGRIPVEAMARAIADWLLTGLIGAAPGAALEPAAADAVRARPHSRTGASS
+>1_842
+MNPVTSTARDGRSVRWDRHRAERRLELVRAARSAVHALGAHASMEEIASHAGTSKTVYYR
+YFGDREGLRLAVSERVTAHMERRLLEVADEPVSEPEALRRMVEVYLTVAATSPEVYAFAV
+APSPAAAEAPVLGPFLERVYAMLESGLARGMAARGHAPAPADPLALWPRAAVGLVRAAAE
+TWLRTPAAGRIPVEAMARAIADWLLTGLIGAAPGAALEPAAADADRARPHSRTGASS
+>3_1595
+MLVRAARAAVHELGPTASMDEIAAHAGTSKSVFYRYFGDRAGLRQAVAERVTASMERRLR
+EAAVDAPDGVSALHRMVAECLSVAASSPAVYAFAVTQGGAADGTGPDLGPFFERIAALLA
+EGLARTLPAADAGPGTTLVLWPRVAVGTVRAAVEAWLATEESVRPDPVRTAHDVAGWLLA
+GLRSADPSASPAADTHTPTQQGEPS
+>4_1064
+MNPVTSTARDGRSVRWDRHRAERRLELVRAARSAVHALGAHASMEEIASHAGTSKTVYYR
+YFGDREGLRLAVSERVTAHMERRLLEVADEPVSEPEALRRMVEVYLTVAATSPEVYAFAV
+APSPAAAEAPVLGPFLERVYAMLESGLARGMAARGHAPAPADPLALWPRAAVGLVRAAAE
+TWLRTPAAGRIPVEAMARAIADWLLTGLIGAAPGAALEPAAADADRARPHSRTGASS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001855.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001855.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca5804d0caafa5938347b73445f0dac6e0c2535e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001855.fa
@@ -0,0 +1,24 @@
+>0_1165
+MSGSGSSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIIEALTPEHGLVRAVAKGVRKT
+SSRLGSVVEPFMHSTLQLARGRGELHIVSQAQLLHPYATMLAADYDAYTVAGALAEAVER
+VPAVDDDGRRAQYRLFHGALAALARGAHDPRLILHSFLLRALAQAGWAPTFDRCARCGAP
+GPHTALHVGLGGAVCPACRPPGAAHPAPETFDLLSALAAGGWATADASGAPARREAAGIV
+AAYLQFHAERRLVSLSVLDQDLGLPAPRVERRP
+>1_893
+MSGSGSSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIIEALTPEHGLVRAMAKGVRKT
+SSRLGSVVEPFMHSTLQLARGRGELHTVSQAQLLHPYATMLAADYDAYTVAGALAEAVER
+VPAVDDDGRRAQYRLFHGALAALARGAHNPRLILHSFLLRALAQAGWAPTFDRCARCGAP
+GPHTALHVGLGGAVCPECRPPGAAHPAPETFDLLSALAAGDWATADTSGAPARREAAGIV
+AAYLQFHAERRLVSLSVLDQDLGLPAPRVERRP
+>3_1542
+MSGARHGGYSANSFRTEAIVLRTHRLGEADRIVEAITPEHGVLRCVAKGVRKSSSRFGSV
+VEPFMHSTLQVARGRGELHTITQAQLLHPYATAVAADYEAFAVAAALAEGVERIPALDAD
+GRRAQYLLFHGALAALARRAHDPRMILHSFLLRTLTQAGWAPTFDRCARCGAPGPHTAVN
+VALGGAVCAEHRPPGSASPAPETFALLTALTAGDWAVVDTAGPLARREAAGIVSAYLQFH
+AERRLVALSVLDQEIAPPAPRAERSA
+>4_1122
+MSASGSSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIIEALTPEHGLVRAVAKGVRKT
+SSRLGSVVEPFMHSTLQLARGRGELHTVSQAQLLHPYATMLAADYDAYTVAGALAEAVER
+VPAVDDDGRRAQYRLFHGALAALARGAHDPRLILHSFLLRALAQAGWAPTFDRCARCGAP
+GPHTALHVGLGGAVCPECRPPGAAHPAPETFDLLSALAAGDWATADASGAPARREAAGIV
+AAYLQFHAERRLVSLSVLDQDLGLPAPRVERRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001857.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001857.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac7ee9bdad4256a483e62e306096e7aa6c60d00c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001857.fa
@@ -0,0 +1,34 @@
+>0_1205
+MTGDHQHARREDHWDDLLDDEADVHDDLDVFGFAHEEADEADVGAPSQPVGAAGPRRPRT
+FLRRRGTGSHPASRVDRGAGRRRTALVLGTVLVAFAVVVGLIVRGFLSGPDHTAVEGDEV
+TFSVEPGEDLGSVAARLDRAGIVGSARAFERAARDTGSGLVRSGDFVLRERMPAAEALAV
+LQGATDGAVHYVLVERGRRLTEVLDAVAEATGLPREELEAAAQDPTRYGVPGEAGTLEGW
+LDAGEYRLPVDATAGQVLDALVRPTLAELEALDVRDPAEQQRVLTIASILEAEALPQDYQ
+QVAGAIENRLAPDNTETHGLLQIDATVTYGLGVRSLSFTSGQRQDASNPYNTYVHPGLPP
+GPIGMPSDAAVEAALDPAETDAYYWVTTDIGTGHTEFSRTYEEHQQHVRTLQRYCASNPG
+VC
+>1_933
+MTGDHQHARREDHWDDLLGDEADVHDDLDVFGFAHGEADEADLGVPSQPVDAAGPCRPRT
+FLRRRGSGSHPAPRVDRGAGRRRTALVLGTVLVAFAVVVGLIVRGFLGGPDHTAVEGDEV
+TFSVEPGEDLGSVAARLDRAGIVASARAFERAARDTGSGLVRSGDFVLRERMPAAEALAV
+LQGAADGAVHYVLVERGRRLTEVLDAVAEATGLPREELEAAAHDPTRYGVPGEAGTLEGW
+LDAGEYRLPVDATAEQVLDSLIRPTLAELDALDVRDPAEQQRLLTIASILEAEALPQDYR
+QVAGAIENRLAPDNTETRGLLQIDATVTYGLGVRSLSFTSGQRQDASNPYNTYVHPGLPP
+GPIGMPSDAAVEAALDPAETDAYYWVTTDIGTGHTEFSRTYEEHQQHVRTLQRYCASNPG
+VC
+>2_1605
+MNRPPEHDWDDLPGDEADPDDDLDVFGFVHEDADDDPDEARRLGAPAAAAGGRRRGLLRR
+RGTGSHPAAPGRSRRGSRLRGGIALGAAALAFLAVVVLVVQGFLGGADHDGIEGEELTFS
+VEPGEDLASVARRLDSAGVVASARAFERAAEDSASGVVRAGDFVMRERMPAADALAVLQG
+TADGAVHYVLVERGRRLTEVLDALAESTGLPREELAAATQDPARYGVPAEAQTLEGWLDP
+GEYRLPVEASAEEVVDALVRPVLADLAELGVDDPDEQRRVLTVASLLEAEALPRDYRTVA
+GVIENRLAPDNTETRGLLQIDAAVTYGLGVRSLSFSAGQRQDASNPYNTYVHPGLPPGPI
+GMPSDAAVAAALDPADTDAYYWVTTDIATGHTEFSRTYEEHQEHVRTLQRYCASNPGVC
+>3_1502
+MSAPPPPPWREDETDDDLDVFGLVDHGEDEPEPEPERVERQPAPPRPVGRARRPRVRTGG
+SHRLRAIGRNLAVERPRGAVVLAVAALAVVLVAALLVVLFSRPADRQAVSGDRVTFTVEP
+GEDLASVAARLDERGIVASDRAVLDAAEDSGQTSIGAGEYVLREQMPAADALAVLQGRAE
+GASHYVVVGRGRWLSEVLDGLAQSTGLPRADFEAAAEDPTRYGVPEQAPSLEGWLDPGEY
+YPPVGADAEQVLAELVKPRLAHLRAQGVTDPAEQQRIVTIASILEAEALPKDYPRVAGVI
+DNRLNDPDAETRGLLQVDSTVNYGLGRRNLQFSAAQRADESNTYNTYQHTGLPPGPIGMP
+SDAAIEGAVHPEPSEDLYWVTTDIATGHTEFSRTYEEHSVHQEEFRRYCAQNPGVC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001858.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001858.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b4e3a6e0fa6d386b19d8b710941958e70eb907fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001858.fa
@@ -0,0 +1,12 @@
+>0_1242
+MTTETAADETGTDAGAHRHGYISDKDRYRNRMKRIEGQARGITKMIDDEKYCIDILTQVS
+ALTRALQGVATGLLDDHLKHCVLDAAKKGDEDAAIAKIQEATDAINRLVRS
+>1_970
+MTTETAADETGTDAGAHRHGYISDKDRYRNRMKRIEGQARGITKMIDDEKYCIDILTQVS
+ALTRALQGVATGLLDDHLKHCVLDAAKKGDEDAAIAKIQEATDAINRLVRS
+>3_692
+MSVDNDSHQHGYISDKERYLGRMKRIEGQARGIAKMIDEEKYCIDILTQVSALTRALQGV
+ATGLLDDHLKHCVLDAAKLSDEAAVEKIQEATDAINRLVRS
+>4_1199
+MTTETAADETGADTGAHRHGYISDKDRYRNRMKRIEGQARGITKMIDDEKYCIDILTQVS
+ALTRALQGVATGLLDDHLKHCVLDAAKKGDEDAAIAKIQEATDAINRLVRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001861.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001861.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5618a9f1fb4490c852dd83d19f063047b2f28e80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001861.fa
@@ -0,0 +1,32 @@
+>0_1309
+MIGLLIGGVLGLVLSAVGTPLFIRFLVKRGYGQFVRDDGPTTHKTKRGTPTMGGAVIIGS
+MVLAYLITHGLLAVFGVDFGGPTASGLILLLLTVGMAFVGFVDDFTKITKQRSLGLTPRG
+KIILQALIGTAFAVLALNFPDERGLTPASTAISFARDIPWLDLAFAGPAIGVILFVIWSN
+LITTATTNAVNLTDGLDGLATGATAMITGAYVLISLFQSSQSCALEGTRGCYEVRDPMDL
+ALLAAILTGSLLGFLWWNTSPAKIFMGDTGSLGLGGALAGFAIFTRTEILVAVLAGLMVA
+ITLSVIIQVGWFKVSGGKRVFLMAPLQHHFELKGWAEVTVVVRFWLLSLMCVTVGLAIFY
+GDWLIRQGGLAGVTP
+>1_1038
+MIGLLIGGVLGLVLSAAGTPLFIRFLVKRGYGQFVRDDGPTTHKTKRGTPTMGGAVIIGS
+LVLAYLITHGLLAVLGVDFGGPTASGLILLLLTVGMAFVGFVDDFTKITKQRSLGLTPRG
+KIILQALIGTAFAVLALNFPDERGLTPASTAISFARDIPWLDLAFAGPASGVILFVIWSN
+LITTATTNAVNLTDGLDGLATGATAMITGAYVLISLFQSSQSCALEGTRGCYEVRDPMDL
+ALLAAILTGSLLGFLWWNTSPAKIFMGDTGSLGLGGALAGFAIFTRTEILVAVLAGLMVA
+ITLSVIIQVGWFKVSGGKRVFLMAPLQHHFELKGWAEVTVVVRFWLLSLMCVTVGLAIFY
+GDWLIRQGGLAGVTP
+>3_1401
+MIGLLIGGVLGLILSGLGTPLFIRYLVKRGYGQQVRDDGPQTHKSKRGTPTMGGFVIISA
+LVLGYLLTHGILALLGSELAGPTASGWIVLLLTVGMAFVGWIDDYTKIAKQRSLGLTPKG
+KIILQGLIGTAFAVLALLFPNADGVTPASTAVSFVRDIPWLELAFAGPVVGVVLFVIWSN
+IITTATTNAVNLTDGLDGLAAGATAMVTGAYVLVSLFQASQSCGLTEGAEACYVVRDPMD
+LGLLAAVLTGALLGFLWWNTSPAKIFMGDTGSLGLGGALAGLAILSRTEILVVILAGLMV
+AITLSVIIQVGWFKISGGKRVFLMAPLQHHFELKGWAEVTVVVRFWLISLVCVIIGLALF
+YGEWLLQHGALQAVAR
+>4_1263
+MIGLLIGGVLGLVLSAVGTPLFIRFLVKRGYGQFVRDDGPTTHKTKRGTPTMGGAVIIGS
+MVLAYLITHGLLAVFGVDFGGPTASGLILLLLTVGMAFVGFVDDFTKITKQRSLGLTPRG
+KIILQALIGTAFAVLALNFPDERGLTPASTAISFARDIPWLDLAFAGPAIGVILFVIWSN
+LITTATTNAVNLTDGLDGLATGATAMITGAYVLISLFQSSQSCALEGTRGCYEVRDPMDL
+ALLAAILTGSLLGFLWWNTSPAKIFMGDTGSLGLGGALAGFAIFTRTEILVAVLAGLMVA
+ITLSVIIQVGWFKVSGGKRVFLMAPLQHHFELKGWAEVTVVVRFWLLSLMCVTVGLAIFY
+GDWLIRQGGLAGVTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001862.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001862.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd6ff03e51c70a3a605f9472fda39ce9f5e30b2c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001862.fa
@@ -0,0 +1,17 @@
+>0_1334
+MSVTSEIARARSLIRVVPDHPSPGVAFQDITPLLADARALRECVEALVAPFEGRFDLVAG
+LEARGFLLAGAAAVLTGTGLVPLRKAGRLPAPAARADYTLEYGTASIEVSEDLRAGSRVL
+LLDDVLATGGTLAAGRRLIEARGAEVVGAACLLELRALGGRAVVPDTHVLFAA
+>1_1063
+MSVTSEIARARSLIRVVPDHPSPGVAFQDITPLLADARALRACVEALVAPFEGRFDLVAG
+LEARGFLLAGAAAVLTGTGLVPLRKAGRLPAPAARADYTLEYGNASIEVSEDLRAGSRVL
+LLDDVLATGGTLAAGRRLIEARGAEVVGAACLLELTALGGRAVVPDTHVLFAS
+>3_1850
+MSGVALSAAGRQAADVPGLERAATLFRSVPDFPTDGVVFQDITPVLADPAALRAVVEAMI
+APFEGAYDAVAGLDARGFLLAGFAAALTGTGVIPLRKAGKLPVSVAHVDYALEYGAASLE
+APPELAVPGVRVLILDDVLATGGTLAAARDLAERCGAEVAGSAVVLEVEGLGGRERCPDA
+LTLFSA
+>4_1288
+MSVTSEIARARSLIRVVPDHPSPGVAFQDITPLLADARALRECVEALVAPFEGRFDLVAG
+LEARGFLLAGAAAVLTGTGLVPLRKAGRLPAPAARADYTLEYGTASIEVSEDLRAGSRVL
+LLDDVLATGGTLAAGRRLIEARGAEVVGAACLLELRALGGRAVVPDTHVLFAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001863.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001863.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7fea83e79d844d5008653348a53de84bc62d6e62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001863.fa
@@ -0,0 +1,24 @@
+>0_1356
+MTEHTRDDVAPAPLVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHCLNEGV
+DLADAEAVAAAAVAMDLDQSTDPDVEAVRVGGTDVTEAIRGPEVTDTVSTVAVVIPVREE
+LHRRQRAAIAAAGRMVAEGRDITTVVAPDAHARVLLTASEAVRTARRSGQLAAAGETGVD
+AGTLHRQVAGRDARDATVSTFDRPADGVALVDSTELDFEQTVAAVLAAVEDQAGIPAVKG
+GRR
+>1_1095
+MTEHTRDDVAPAPLVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHCLHEGV
+DLADAEAVAAAAVAMDLDQSTDPDVEAVRVGGTDVTEAIRGPEVTDTVSTVAVVIPVREE
+LHRRQRAAIAAAGRMVAEGRDITTVVAPDAHARVLLTASEAVRTARRSGQLAAAGETGVD
+AGTLHRQVAGRDARDATVSTFDRPADGVALVDSTELDFEQTVAAVLAAVEDQAGIPAVKG
+GRR
+>3_1373
+MTEHTQHDDAARPALVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHVLDSG
+VDLADPDAIAGAARAMDLRQSTDPDVESVVVGGTDVTDAIREDRVTDVVSTVAVVIPVRE
+ELQRRQRAAIAGAGRIVAEGRDITTVVAPDAHARVLLTASAEARMARRSGQLQRAGAGER
+DAATLERQVSGRDARDSAVSTFDRPAEGVALVDSTELDFEQTVAAVLAAVQDQAGVDAVP
+GR
+>4_1305
+MTEHTRDDVAPAPLVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHCLHEGV
+DLADAEAVAAAAVAMDLDQSTDPDVEAVRVGGTDVTEAIRGPEVTDTVSTVAVVIPVREE
+LHRRQRAAIAAAGRMVAEGRDITTVVAPDAHARVLLTASEAVRTARRSGQLAAAGETGVD
+AGTLHRQVAGRDARDATVSTFDRPADGVALVDSTELDFEQTVAAVLAAVEDQAGIPAVKG
+GRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001875.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001875.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb8b118d8d419abb85c0c5424494b6820d507b51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001875.fa
@@ -0,0 +1,28 @@
+>0_1529
+MTTPRATLPSRRRGRTPARAALAALGLAASLVLSGCGLSTAGGYLPSGTPAGDVAGIDLE
+GAHVAVGSKNFNEGVVLGKITAILLRSAGADVEDLTNMPGSLSARQAQVAGVVDVEWDYT
+GTAWITYLGHTDPIPDAQAQWAAVRDEDAQQGLVWLPPAELDNTYTLSVRQDRAEELGLE
+TLADIKDLPTEEQSFCVSAEFAARNDGFLPMLEAYGIERPTGSRLRQMDIGAVFAAVADG
+SCTFGEAYSTDGRIAALDLTTLQDPLSFFPKYNAAPIVREEVLAQHPEIADLLAPVTARL
+DNATAARLNARVDVDGEEPTQVAWDWLREEGLITD
+>1_1250
+MTTPRATIPSRRRGRTPARAVLAVLGLAASLVLSGCGLSTAGGYLPSGTPAGDVAGIDLE
+GAHVAVGSKNFNEGVVLGKITAILLRSAGADVEDLTNMPGSLSARQAQVADVVDVEWDYT
+GTAWITYLGHTDPIPDPQAQWAAVRDEDAQQGLVWLPPAELDNTYTLSVRQDRAEELGVE
+TLADIKDLPTEDQSFCVSAEFAARNDGFLPMLEAYGIERPTGSRLRQMDIGAVFAAVADG
+TCTFGEAYSTDGRIAALDLTTLQDPLSFFPKYNAAPIVREEVLAQHPEIADLLAPVTARL
+DNATTARLNARVDVDGEEPTQVAWDWLREEGLITD
+>2_1314
+MTTPRATLPSRRRGRTPARVALAALGLAASLVLSGCGLSTAGGYLPSGTPAGDVAGIDLE
+GAHVAVGSKNFNEGVVLGKITAILLRSAGADVEDLTNMPGSLSARQAQVAGVVDVEWDYT
+GTAWITYLGHTDPIPDAQAQWAAVRDEDAQQGLVWLPPAELDNTYTFSVRQDRAEELGLE
+TLADIKDLPTQDQSFCVSAEFAARNDGFLPMLEAYGIERPTGSRLRQMDIGAVFAAVADG
+SCTFGEAYSTDGRIAALDLTTLQDPLSFFPKYSAAPIVREEVLAQHPEIADLLAPVTARL
+DNATAARLNARVDVDGEEPTQVAWDWLREEGLITD
+>4_1456
+MTTPRATLPSRRRGRTPARAALAALGLAASLVLSGCGLSTAGGYLPSGTPAGDVAGIDLE
+GAHVAVGSKNFNEGVVLGKITAILLRSAGADVEDLTNMPGSLSARQAQVAGVVDVEWDYT
+GTAWITYLGHTDPIPDAQAQWAAVRDEDAQQGLVWLSPAELDNTYTFSVRQDRAEELGLE
+TLADIKDLPTEDQSFCVSAEFAARNDGFLPMLEAYGIERPTGSRLRQMDIGAVFAAVADG
+SCTFGEAYSTDGRIAALDLTTLQDPLSFFPKYNAAPIVREEVLAQHPEIADLLAPVTARL
+DNATAARLNARVDVDGEEPTQVAWDWLREEGLITD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001876.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001876.fa
new file mode 100644
index 0000000000000000000000000000000000000000..162f326124ef6129904ffc6faf49980ebeddf44d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001876.fa
@@ -0,0 +1,20 @@
+>0_1532
+MSEFLASRWPDILFRAWQHGWLVLQALAIATVLAIALAVIATRIKALTPIANAFTAVGLT
+LPSFALIGVLIPLVGIGTVPAVVVVVFYALLPILRNALVGLRGVDPEVLEAARGMGMGPV
+ALFTRVRLPLAWPVILTGIRVAGQLGMGVAAVAAYVLGPGLGSYIFTGLVSLGGANALNY
+ALVGTLGIVVVALVLDGLLVLLGRLTISKGLRA
+>1_1253
+MSEFLASRWPDILFRAWQHGWLVLQALAIATVLAIALAVIATRIKALTPIANAFTAVGLT
+LPSFALIGVLIPLVGIGTVPAVVVVVFYALLPILRNALVGLRGVDPEVLEAARGMGMGPV
+ALFTRVRLPLAWPVILTGIRVAGQLGMGVAAVAAYVLGPGLGSYIFTGLVSLGGANALNY
+ALVGTLGIVVVALVLDGLLVLLGRLTISKGLRA
+>2_1311
+MSEFLASRWPDILFRAWQHGWLVLQALAIATVLAIALAVIATRIKALTPIANALTAVGLT
+LPSFALIGVLIPLVGIGTVPAVVVVVFYALLPILRNALVGLRGVDPDVLEAARGMGMGPV
+ALFTRVRLPLAWPVILTGIRVAGQLGMGVAAVAAYVLGPGLGSYIFTGLVSLGGANALNY
+ALVGTLGIVVVALLLDGLLVLLGRLTISKGLRA
+>4_1459
+MSEFLASRWPDILFRAWQHGWLVLQALAIATVLAIALAVIATRIKALTPIANAFTAVGLT
+LPSFALIGVLIPLVGIGTVPAVVVVVFYALLPILRNALVGLRGVDPEVLEAARGMGMGPV
+ALFTRVRLPLAWPVILTGIRVAGQLGMGVAAVAAYVLGPGLGSYIFTGLVSLGGANALNY
+ALVGTLGIVVVALVLDGLLVLLGRLTISKGLRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001877.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001877.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bbfaae246369342f09e179bc85c77af57d0bde59
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001877.fa
@@ -0,0 +1,40 @@
+>0_1534
+MTATRSGGAATSRLNAKVVGISVAAALGGFLFGFDTSVINGAVDALAGEFGLGAGLTGFA
+VSSALIGCALGAWFAGPIANRRGRVPVMVIAAILFLVSAIGSGLAFGVVDLIFWRVVGGL
+GVGAASVIAPAYIAEVSPAHVRGRLGSLQQLAIVLGIFAALLTDALFATMAGGAAQPFWL
+GVDAWRWMFLAEAVPAVLYGLFALKLPESPRYLVARGRTDEAAEVLHEFTGVDRVNLMIE
+DIRRSLDSERRESLADLRGPSAGLQPIVWIGILLSVFQQAVGINVIFYYSTTLWRSVGFG
+ESDALTVTVITSVTNIAVTLIAIALVDRVGRRPMLIAGSAGMTVSLGLMALAFSFAQTGG
+AESVSLPQPWSTVALVAANAFVVFFGATWGPLVWVLLGEMFPNRIRAGALAVAAAAQWAA
+NFTVSTTFPWLADIGLTLAYGLYAVMAALSLAFVAAFVPETKGKTLEEMSDVVVRSPGQR
+RAVRAEAERDLRG
+>1_1255
+MTATRSGGAATSRLNAKVVGISVAAALGGFLFGFDTSVINGAVDALAGEFGLGAGLTGFA
+VSSALIGCALGAWFAGPVANRRGRVPVMVIAAILFLVSAIGSGLAFGVVDLIFWRMVGGL
+GVGAASVIAPAYIAEVSPAHVRGRLGSLQQLAIVLGIFAALLTDALFATMAGGAAQPFWL
+GVDAWRWMFLAEAVPAVLYGLFALKLPESPRYLVARGRTDEAAEVLHEFTGVDRVNLMIE
+DIRRSLDSERRESLADLRGPSAGLQPIVWIGILLSVFQQAVGINVIFYYSTTLWRSVGFG
+ESDALTVTVITSVTNIAVTLIAIALVDRVGRRPMLIAGSAGMTVSLGLMALAFSFAQTGG
+AESVSLPQPWSTVALVAANAFVVFFGATWGPLVWVLLGEMFPNRIRAGALAVAAAAQWAA
+NFTVSTTFPWLADIGLTLAYGLYAVMAALSLAFVAAFVPETKGKTLEEMSDVVVRSPGQR
+RAVRAEAERDLRG
+>2_1309
+MTATRSGGAATSRLNAKVVGISVAAALGGFLFGFDTSVINGAVDALAGEFGLGPGLTGFT
+VSSALIGCALGAWFAGPIANRRGRVPVMVIAAILFLVSAIGSGLAFGVVDLIFWRMVGGL
+GVGAASVIAPAYIAEVSPAHVRGRLGSLQQLAIVLGIFAALLSDALFATMAGGAAQPFWL
+GVDAWRWMFLAEAVPAVLYGLFALKLPESPRYLVARGRTDEAAEVLHEFTGVDRVNLMIE
+DIRRSLDSEHRESLADLRGPAAGLQPIVWIGILLSVFQQAVGINVIFYYSTTLWRSVGFG
+ESDALTVTVITSVTNIAVTFIAIALVDRVGRRPMLIAGSAGMAVSLGLMALAFSFAETGG
+AESVSLPQPWSTVALVAANAFVVFFGATWGPLVWVLLGEMFPNRIRAGALAVAAAAQWAA
+NFTVSTTFPWLADIGLTLAYGLYALMAALSLAFVAAFVPETKGKTLEQMSDIVVRSPGQR
+RAGRAEAERDLRG
+>4_1461
+MTATRSGGAATSRLNAKVVGISVAAALGGFLFGFDTSVINGAVDALAGEFGLGAGLTGFA
+VSSALIGCALGAWFAGPIANRRGRVPVMVIAAILFLVSAIGSGLAFGVVDLIFWRVVGGL
+GVGAASVIAPAYIAEVSPAHVRGRLGSLQQLAIVLGIFAALLTDALFATMAGGAAQPFWL
+GVDAWRWMFLAEAVPAVLYGLFALKLPESPRYLVARGRTDEAAEVLHEFTGVDRVNLMIE
+DIRRSLDSERRESLADLRGPSAGLQPIVWIGILLSVFQQAVGINVIFYYSTTLWRSVGFG
+ESDALTVTVITSVTNIAVTLIAIALVDRVGRRPMLIAGSAGMTVSLGLMALAFSFAQTGG
+AESVSLPQPWSTVALVAANAFVVFFGATWGPLVWVLLGEMFPNRIRAGALAVAAAAQWAA
+NFTVSTTFPWLADIGLTLAYGLYAVMAALSLAFVAAFVPETKGKTLEEMSDVVVRSPGQR
+RAVRAEAERDLRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001880.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001880.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35678b599919f73eeaf01132bd29bf323fdafa6f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001880.fa
@@ -0,0 +1,28 @@
+>0_1571
+MRLRFNDYRDKPAVDPRYFTDPEGHDMAVAVAGIRLAREIVSQPAMAAWAGRELAPGEQA
+QTDEEIADYVRRTHNTVYHPVGSVRMGADDDAMSPLDARLRVKGVTGLRVADASVMPEHV
+TVNPNITCVMIGEKAAQLILADRA
+>1_1287
+MRLRSNDYRDEPVVDPRYFTDPEGHDMAVAVASIRLAREIVSQPAMAAWAGRELAPGEQA
+QTDEEIADYVKRTHNTVYHPGGSVRMGADDDAMSPLDARLRVKGVTGLRVADASVMPEHV
+TVNPNITCFMIGEKAAQLILADRA
+>2_799
+MTAEPLTTDAPDDGTPAHESDVLVIGAGSAGCVLARRLLDAGRTVTLVEAGDQDVNPDID
+DVSRLGFLWESEVDWNYRTTPQPGLAGRSLHLPRGKVMGGSHALNATIWVRGDAWDYDTW
+AAEHGCTGWSWQDVLPYFKAIENTALGEDAVRGRDGLLDISTDYPHHPIQQAMYDATVQE
+GVPENPDYNSGDVEGVGWMQLNVRDGKRFNTWRAYLKPVADHEGLTLVTGAQARRLLLDG
+TRVTGAEFDRDGETLTITADEVVLCAGALGSPEILLRSGVGPADHLREVGVDVAHDLPGV
+GRNLHDHLLVPVVGVTEKEAPAPEVAVAQVHYFAKSDPALPVADTQPIFFSVPMYTNTAG
+DPMVGPETGFSLLAGIVRPLSRGSLTLSGPAPEDPVQVDLGAYTAPEDLQAMLFSLRQCR
+RIAAQPALAEGWGATEIHPGPNVGDTDEELIAYIRNTTTTYHHQVGTCAMGSGEDAVVDP
+ATLRVYGLEGLRVADASIMPQVTSGNTNAPSVMIGERAAAMITGVEPF
+>4_1500
+MTTTTPDASTPQPDTPVYDYIVVGGGSSGAALAARLSEDPQISVALLEAGPTDVDLDEVL
+ELRRWPELLESGLDWDYPIEPQENGNSFMRHSRAKVLGGCSSHNSCIAFWPPREDLDQWE
+AMGATGWGAEHTLPLVKKLENNRAEGDHRGHDGPVELMDVPADDPAGVALLEAAAQAGIP
+TTTFNTGETVVKGANWFQINRKQDGTRASSSVSYLHPILDRENLDILTDHWVSEVLFDDD
+RRAYGVRHVADRHGRQAEIHARAEVILSAGAINTPKLLMLSGIGPAEHLAEHGLDVRVDA
+PGVGSNLQDHPEAVISWESKQPMYRDATQYWEIGIFSPTKEGLDRPDLMMHYGSVPFDMH
+TYRQGYPTADETFCLTPNVTHAKSRGTVRLRSNDYRDKPAVDPRYFTDPEGHDMAVAVAG
+IRLAREIVSQPAMAAWAGRELAPGEQAQTDEEIADYVRRTHNTVYHPVGSVRMGAEDDAM
+SPLDARLRVKGVTGLRVADASVMPEHVTVNPNITCFMIGEKAAQLILADRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001886.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001886.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d79470759e007f0d6981b62c84d1288c5b6560dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001886.fa
@@ -0,0 +1,20 @@
+>0_1722
+MTRVPPAHGHRPALRDSTGSAHGPGVEPGARPRLSAEDLLAARDALAPFGRLSRQEPIEW
+AAEEPLAPDLADFYRYVGPEWLEIDTLGLPVMFFPLDRLWDEQAGYRWNPRTGALLVDWN
+DDWTVVAKQGADPFIHAASTGQVLMAPGDEGWEDRLDEPRPVFRDLTEMTRALAAVGTAW
+ARFDDPFTADWHLTEEVTAAVVAGLEGVLGAHDRAVDLARALGYLGAV
+>1_1439
+MTRVPPAHGHRPALRDSTGSAHGPGVEPGARPRLSAEDLLAARDALAPFGRLSRQEPIEW
+AAEEPLAPDLADFYRYVGPEWLEIDTLGLPVMFFPLDRLWDEQAGYRWNPRTGALLVDWN
+DDWTVVAKQGADPFIHAASTGQVLMAPGDEGWEDRLDEPRPVFRDLTEMTRALAAVGTAW
+ARFDDPFTADWHLTEEVTAAVVAGLEGVLGAHDRAVDLARALGYLRAV
+>3_1001
+MDRHLLPAGPGEVTPRPRIALDPARLHAARAALSVFGPVHRQEPIEWAAEEPLAPDLAEF
+YREVGPDWVEIDTLGLPLLMFPLERLWDEQAGYRWNHRTGAMLADWNEDWTVVAKQGAEP
+FIHEAATGHVLMAHGEEGWEDRLGEPVPVFRDVAEMTLALCAAGAAWAGSDDPFTADWHV
+RPEVTSAVVDGLEQVLGDRARAVDVARRLGHLRAA
+>4_1651
+MTRVPPAHGHRPALRDSTGSAPGPGVEPGARPQLSAEDLLAARDALAPFGRLSRQEPIEW
+AAEEPLAPDLADFYRYVGPEWLEIDTLGLPVMFFPLDRLWDEQAGYRWNHRTGALLVDWN
+EDWTVVAKQGADPFIHAASTGQVLMAPGDEGWEDRLDEPEPVFRDLAEMTRALAAVGTAW
+ARFDDPFTVDWHLTEEVTTAVVAGLEAVLGAHDRAVDLARALGYLRAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001890.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001890.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e722a11e666b4ce299a1780a6e30fc23c3042d2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001890.fa
@@ -0,0 +1,18 @@
+>0_1818
+MAEKNAAEYTVPGLSLSTGRRTAEILQGRLHALNDLQLTLKHAHWNVVGPGFIGVHEMLD
+PQIELVRGMVDVVAERIATLGVSPAGTPGALVAARTWDDYTLGRASTLEHLAALDLVYDG
+VVTDHRAAIDATEDLDPVTQDILIDQVAQLELFQWFMRSFLTTDDGRLSSAGTTTEAAAA
+GRVKGAQSAPAPKAGRTKKSDAKKSKKK
+>1_1525
+MAEKNAAEYTVPGLSLSTGRRTAEILQGRLHALNDLQLTLKHAHWNVVGPGFIGVHEMLD
+PQIELVRGMVDVLAERIATLGVSPAGTPGALVAARAWDDYTLGRASTLEHLAALDLVYDG
+VVTDHRAAIDATEDLDPVTQDILIDQVAQLELFQWFMRSFLTTDDGRLSSAGTTTEAAAA
+GRVKGAQSAPAPKAGRTKKSDAKKSKKK
+>2_961
+MAAKKNDAAFTVPGLALKDGHRVAEILQGRLHALNDLQLTLKHAHWNVVGPGFIGVHEML
+DPQIETVRAMVDVVAERIATLGVSPEGTPGALVAARTWDDYALGRASTLEHLAALDLVYD
+GVVTDHRAAIETVGELDPVSEDMLIGQVAELELFQWFMRSFLTTVDGDLSHAGATREIVA
+AARVSGAQKAPAPKKGAAKKAPAKKK
+>3_900
+MDSRARASTDPGLSVEDGHHVAEVLPVRLHALNDLQLTLKHAHWNVVGPGVIGVHEMPGP
+QIEKVRAMVDAIAELELFPRSMRSFPATDDGELSHADALREAEAAKQK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001891.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001891.fa
new file mode 100644
index 0000000000000000000000000000000000000000..36116d3db840c7fc9b7244f055e170f619306d81
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001891.fa
@@ -0,0 +1,57 @@
+>0_1819
+MPTPPDLSAFRTPAATGRPPRGLRLGLAAALAVVWFAVLGLGGPVFGRIGDVSSNDQATF
+LPASAESTRAGQEAAAFQDGEAVPAVVVGPASTADPAAAFPALADLAGRLGEVPGVTDVA
+GPIPSDDGAAVQFLAFVDSSAGAERPVADVVADLREVVADPAAADPALAGTVAADTEWHV
+GGPAGLVAELGGAFAGIDGLLLLVALAVVFVILVAVYRSVLLPVLVLLTAVAALCGAIVA
+VYGMALAGWIQLNGQAQGILSILVIGAATDYCLLLVARHREELLVRADVGEALRAAVRGS
+FGAITASASTVALALLILMASDLNSTRSLGPVAATGVAFAWLAALTLLPALLRLTGRAAF
+WPTIPSPERARRRAQRRAARGRAFTPPLDGAGRPVAGLEEDHGVWTRVGAVVARRPRLVW
+VATTVVLLALCGGLLQLRADGVAQEDVLLGDSDARQAQALLSEHFDAGAGAPAQILAPAG
+DAEAVLAAVAEDPGVAEAEVTTDAPEAAAGPPPGVTDAEGGAGAASAPEPQPRVVDGRVL
+VSATLADPGESLAAQQTVARLRDRLADLPATGEILVGGPAAQALDTNVTTQRDLRVVIPL
+ILAMLLVILAVLLRSLLAPVLLVAATVVSFGAALGVSALVFRHVFGFEDADPTVPLYGFV
+FLVALGIDYTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPL
+MFMVQLAFIVAFGVLLDTLIVRSLLIPALVRDIGPKVWWPAKVD
+>1_1526
+MPTPPDLSAFRTPAATGRPPRGLRLGLAAALTVVWFAVLGLGGPVFGRIGDVSSNDQATF
+LPASAESTRAGQEAAAFQDGEAVPAVVVGPASTADPAAAFPALADLAGRLGEVPGVTDVA
+GPIPSDDGAAVQFLAFVDSSAGAERPVADVVADLREVVADPAAADPALAGTVAADTEWHV
+GGPAGLVAELGGAFAGIDGLLLLVALAVVFVILVAVYRSVLLPVLVLLTAVAALCGAIVA
+VYGMALAGWIQLNGQAQGILSILVIGAATDYCLLLVARHREELLVRADVGEALRAAVRGS
+FGAITASASTVALALLILMASDLNSTRSLGPVAATGVAFAWLAALTLLPALLRLTGRAAF
+WPTIPSPERARRRAERRAARGRAFTPPRDGAGRPVAGLEEDHGVWTRVGAVVARRPRLVW
+VATTVVLLALCGGLLQLRADGVAQEDVLLGDSDARQAQALLSEHFDAGAGAPAQILAPAE
+DAEAVLAAVAEDPGVAEAEVTTDAPEAAAGPPPGALDAEGGAGAASAPEPQPRVVDGRVL
+VSATLADPGESLAAQQTVARLRDRLADLPTSGEILVGGPAAQALDTNVTTQRDLRVVIPL
+ILAMLLVVLAVLLRSLLAPVLLVAATVVSFGAALGVSALVFRHVFGFEDADPTVPLYGFV
+FLVALGIDYTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPL
+MFMVQLAFIVAFGVLLDTLVVRTLLIPALVRDIGPKVWWPAKVD
+>2_960
+MRTPPDLSALRSPDARRAAGSADPDSAAGRPEGLGASAAGRDGERTDGRTGDRTGERTAG
+RPSAWLRFGLAAALFVVWFAVMGLGGPTFGKIGDVSSNDQSTFLPASAESTRAGEEAAAF
+RDGEAVPAVIVAEADLSDPAQAFPALGGLAETLRGVDGVTDVAGPIPAEDGEAVQFLAFV
+DSSDGAEREVADVVEDLKGILADPAAADADLADTVAADADWHLGGPAGLATELGGAFAGI
+DGLLLLVALVVVFVILVIVYRSVLLPILVLLTAVGALCAAILAVYGMAVAGWIQLNGQAQ
+GILSILVIGAATDYCLLLVARHREELLVREEVTASLLAAVRGSFGAITASASTVALALLI
+LLVSDLNSNSSLGPIAATGILFAWLAALTLLPALLQLAGRAAFWPTVPSPENARRRATRR
+AERGRAFVQPEDAAGRPLAGLEEDHGVWTKVGAAVARRPRPVWLATLAVLLVMSAGLLQL
+QASGVAQEDVLLGESDSRQAQALLTEHFDAGSGAPAQIVAPAEDADAVLAAVEADPGVAE
+ASVTTDEAPAPAGPPPGVTGGGEGTPAEGGAGRPEAAPQPDPEPKVVDGTVLISATLADP
+GESLAAQATVERLRAELADVGSGGEVLVGGPAAQALDTNTTSQRDLVVVIPLILAMLLVI
+LSMLLRSILAPVLLVAATVISFGAAMGVSALVFRHVFGFENADPTVPLYGFVFLVALGID
+YTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPLMFMLQLAF
+IVAFGVLLDTLVVRTLLIPALVRDIGPKVWWPARAE
+>4_1740
+MPTAPDLSAFRTPAAPGRPSRGLRLGLAAALAVVWFAVLGLGGPVFGAIGDVSSNDQATF
+LPASAESTRAGEEAAAFQDGEAVPAVVVGPASTADPAAAFPALADLAGLLGEVPGVVDVA
+GPIPSEDGAAVQFLAFVDSSAGAERPVADVVADLREVVADPAAAAPALAGTVAADTEWHV
+GGPAGLVAELGGAFAGIDGLLLLVALVVVFVILVAVYRSVLLPVLVLLTAVAALCGAIVA
+VYGMALAGWIQLNGQAQGILSILVIGAATDYCLLLVARHREELLVRAEVGEALRAAVRGS
+FGAITASASTVALALLILMASDLNSTRSLGPVAATGVAFAWLAALTLLPALLRLTGRAAF
+WPTIPSPERARRRTERRAARGRAFTPPRDGAGRPIAGLEEDHGVWTRVGTVVARRPRPVW
+VATTVGLLALCGGLLQLRADGVAQEDVLLGDSDARQAQALLSEHFDAGAGAPAQILAPAG
+DAEAVLAAVAEDPGVAEAEVTADAPEAAAGPPPGVTDAEGGAGAASAPEPQPRVVDGRVL
+VSATLADPGESLAAQQTVARLRDRLADLPTSGEILVGGPAAQALDTNVTTQRDLRVVIPL
+ILAMLLVILAVLLRSLLAPVLLVAATVVSFGAALGVSALVFRHVFGFEDADPTVPLYGFV
+FLVALGIDYTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPL
+MFMVQLAFIVAFGVLLDTLVVRTLLIPALVWDIGPKVWWPAKAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001892.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001892.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac426750991271795333b24204456d04a6437ad5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001892.fa
@@ -0,0 +1,16 @@
+>0_1820
+MIKQPWGLARLPAMTTQPPSAPAEHLAVVHALRVFSESAEHAVDEAGRGVGLHRTDLRAL
+AYLMARAAAGEPVTASDLGAHLHLTRASATALVDRLAAAGHVRRHRDEGDRRRVLVEHTD
+TARRDGQRAFEPMSQRLSAALEGFSAAELRAAVRVLEAATAALTDPAPEDP
+>1_1527
+MIKQPWGLARLPAMTTQPPSAPAEHLAVVHALRVFSESAEHAVDEAGRGVGLHRTDLRAL
+AYLMARAAAGEPVTASDLGAHLHLTRASATALVDRLAAAGHVRRHRDEGDRRRVLVEHTD
+TARRDGQRAFEPMSQRLSAALEGFSAAELRAAVRVLEAATAALTDPAPEDP
+>2_959
+MTPQPAAAPAEHVAVVHALRAFSEGAEHAVDEAGRGIGLHRTDLKALAHLMRCADEDRPV
+TATDLGAHLHLTRAATTAVVDRLVASGHARRRRDDVDRRRVLVEHTDSARRDGAAAFLPM
+SLRISGALTPFTAEELRAALRVIEAATAALQAPPDAPAAPVPG
+>4_1741
+MTTQPPSAPAEHLAVVHALRVFSESAEHAVDEAGRGVGLHRTDLRALAYLMARAAAGEPV
+TASDLGAHLHLTRASATALVDRLAAAGHVRRRRDEGDRRRVLVEHTDTARRDGQRAFQPM
+SQRLSAALEGFSVAELRAAVRVLEAATAALTDPTPEDP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001894.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001894.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2b8949d4f6ac3011581ea82ead8cd6c450b8acf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001894.fa
@@ -0,0 +1,14 @@
+>0_1834
+MAGRWRAGAALTIRGEFSIVIAGPVLTRYADAFGRSRARAATRRVRAREVAAADPVH
+>1_1541
+MAGRWRAGAALTIRGEFSIVIAGPVLTRYADAFGRSRARAATRRVRAREVAAADPVH
+>3_883
+MHGTTLALVELGAVLFLLGVLGRLAARIGMSPVPLYLLGGLLIGVGGLLFSGADPSGTLR
+SPVAAIGDFSSLAAEIGVVLLLLTLGLEYSARELMTGLRGSWRSGLLDVALNFTPGAAAG
+WLLGWGPVGAVVLGGITYISSSGIIAKVLNDLGRVGNRETPVMLSVLVFEDLAMAVYLPL
+MTALVAGSAFAAGLRAVGIALVVVAAVLFTALRFGPQISRLVYSPEQETFLLKVLGLALL
+VAGVAGALQVSAGVGAFLLGIAISGAAAKQARSVLEPLRDMFAALFFVLFGMNVDPRTLP
+PVLLGALALAVVTAATKVATGYLAARAAGIGVAGRWRAGATLTIRGEFSIVIAGLATASG
+TLPAEVSAFATAFVLILAVAGPLLTRSADGFGRRRAAAARVREARRARQAPLV
+>4_1755
+MAGRWRAGAALTIRGKFSIVIAGPVLTRYADAFGRSRARAATRRVQAREVAVADPVH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001896.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001896.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3f711971e87412a53a7b9b8992e6cab0922da5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001896.fa
@@ -0,0 +1,18 @@
+>0_1838
+MSPSARRPAASSRPARPRPTTAPFALPDRPGWVRLAAGAVVPGVIAAAAALAALQVFVLN
+PLAAAPGDRGLGRIYADLSAAGQLGVPFVLSAVILAAGLGVAAVLWFLTWRREEVDPLAV
+LALGLASLVAASPAYFMASFGPGMALADTYGIGGADHSPWAWPIYVVSMLALTGLVAVVV
+LLLRGPAGGLGAPRRRA
+>1_1545
+MSPSARRPAASSRPARPRPTTAPLALPDRPGWVRLAAGAVVPGVIAAAAALAALQVFVLN
+PLAAAPGDRGLGRIYADLSAAGQLGVPFVLSAVILAAGLGVAAILWFLTWRREEVDPLAV
+LALGLASLVAASPAYFMASFGPGMALADTYGVGGGDHSPWAWPIYVVSMLALAGLVAVVV
+LLLRGPAGGLGAPRRRA
+>2_941
+MAGEGALPFLLPALLCAAGLGVAAILWFLVWRREEVDPLAVLALGLASLVAATPAYFFAS
+FGMGMALADTYGIGGADHSPWARPIYVLSALALAALVAVVVLLLRGPAGGRATPRPTR
+>4_1759
+MSPSARRPAASSRPARPRPTTAPLALPDRPGWVRLAAGAVVPGVVAAVAALAALQVFVLN
+PLAAAPGDRGLGRIYADLSAAGQLGVPFVLSAVILAAGLGVAAILWFLTWRREEVDPLAV
+LALGLASLVAASPAYFMASFGPGMALADTYGIGGGDHSPWAWPIYVVSVLALAGLVAVVV
+LLLRGPAGGLGAPRRRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001901.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001901.fa
new file mode 100644
index 0000000000000000000000000000000000000000..446359e59caf5e55a2e8c969907c70888fc0ab52
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001901.fa
@@ -0,0 +1,24 @@
+>0_1857
+MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAQTCRDAVAAG
+VTIGAHVGYRDLAGFGRRFLDCTPTELADDVLYQIGALDALARAAGGQVRYVKPHGALYN
+TIVRHEAHAQAVVDGVRAFGSDLPLLLLPGSVALDKAAAAGLRGVAEAFADRGYNPDGTL
+VSRREPGAVLHDEDDVAARMVRLATEGVVAAVDGTDVRVDAESICLHGDTPGAVAMAAAV
+RRALEGAGVSIKAFA
+>1_1564
+MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAQTCRDAVAAG
+VTIGAHVGYRDLAGFGRRFLDCTPTELADDVLYQIGALDALARAAGGQVRYVKPHGALYN
+TIVRHEAHAQAVVDGVKAFGSDLPLLLLPGSVALDKAAAAGLRGVAEAFADRGYNPDGTL
+VSRREPGAVLHDEDDVAARMVRLATEGVVAAVDGTDVRVDAESICLHGDTPGAVAMAAAV
+RRALEGAGVAIKAFA
+>3_859
+MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAATCRAAVAAG
+VTIGAHVGYRDLAGFGRRFLDCSPTELADDVLYQIGALEALAGAAGATVRYVKPHGALYN
+TIVHHEEHAQAVVDGVAAFGADLPLLLLPGSVALEKAEKAGLRGVAEAFADRGYTPQGTL
+VSRREPGAVLHDEDEVAARMVRLATEGVVTAVDGSDVRVAAESICVHGDTPGAVSMAAAV
+RRALEDAGVTIASFA
+>4_1778
+MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAQTCRDAVAAG
+VTIGAHVGYRDLAGFGRRFLDCTPTELADDVLYQIGALDALARAAGGRVRYVKPHGALYN
+TIVRHEAHAQAVVDGVRAFGSDLPLLLLPGSVALDKAAAAGLRGVAEAFADRGYNPDGTL
+VSRREPGAVLHDEDDVAARMVRLATEGVVAAVDGTDVRVDAESICLHGDTPGAVAMAAAV
+RRALEGAGVSIKAFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001906.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001906.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e76f8e35fdf164a318fb828778d58ce059edb5d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001906.fa
@@ -0,0 +1,8 @@
+>0_1916
+MTVGLTLYVLMWPVLVLAVLVSIARGFFADWAAARREGRSII
+>1_1620
+MTVGLTLYVLMWPVLVLAVLVAIARGFVADWAAARRQGRSII
+>2_862
+MTLGLTLYVLMWPVLVLAVLASIAAAFFKDWREARREGRSII
+>4_1842
+MTVGLTLYVLMWPVLVLAVLVAIARGFVADWAAARREGRSII
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001907.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001907.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8c1703cadc9172c75da9f828f0dd178f18ae23cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001907.fa
@@ -0,0 +1,16 @@
+>0_1926
+MMAWIDGLPLLWSIGFFWMLAILRTLIVFSLGRGLASGVERTRWFARVMEGPVYVRAQRF
+IQRHGVWAIPFCYLTVGIQTAVIGSAGVARMPWRRFLPAAALGTFLWGVVYGTVGMAVVW
+AVIGAALGEGRGVLALVLILAAVAAFVVWRRRRTLRRHGAG
+>1_1631
+MMAWIDGLPLLWSIGFFWMLAILRTLIVFSLGRGLASGVERTRWFARVMEGPVYVRAQRF
+IQRHGVWAIPFCYLTVGIQTAVIGSAGVARMPWRRFLPAAALGTFLWGVVYGTVGMAVVW
+AVIGAALGEGRGVLALVLILAAVAAFVVWRRRRTLRRHGAG
+>2_851
+MMAWIDGLPLLWSIGFFWMLAILRTLIVFSLGRGLASGVERTRWFARVMEGPVYVRAQRF
+IQRHGVWAIPFCYLTVGIQTAVIGSAGVARMPWRRFLPAAALGTFLWGVVYGTVGMAVVW
+AVIGAALGEGRGVLALVLILAAVAAFVVWRRRRTLRQHGAG
+>4_1853
+MMAWIDGLPLLWSIGFFWMLAILRTLIVFSLGRGLASGVERTRWFARVMEGPVYVRAQRF
+IQRHGVWAIPFCYLTVGIQTAVIGSAGVARMPWRRFLPAAALGTFLWGVVYGTVGMAVVW
+AVIGAALGEGRGVLALVLILAAVAAFVVWRRRRTLRRHGAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001908.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001908.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00b67cf33dd24409309ff1d0926fe86fb10fded6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001908.fa
@@ -0,0 +1,24 @@
+>0_1935
+MPVRHNPQPLFRDLFTPEAVAARGGRPAAGMFLSSGDPTTAEICAGAGLDYLLIDAEHAP
+LTLQDVLAQLRTIAGYRVPTLVRVPALDTVAIKQFLDLGAQSLLVPMVDDAAMARRAVAA
+ARYPDGSAEGGVRGVGSALARSGRWNRIPGYLPGAADHVSVIVQIETAAGVRNADEIAAV
+DGIDGVFIGPSDLSASLGLLGQQSHPDVVAAVEEVITKVKAAGKIVGVNAFVPAQADAYA
+AAGADYVNVGADVALLARAAEALADRWCPAPSNAAADGQSAPRASY
+>1_1640
+MPVRHNPQPLFRDLFTPEAVAARGGRPAAGMFLSSGDPTTAEICAGAGLDYLLIDAEHAP
+LTLQDVLAQLRTIAGYRVPTLVRVPALDTVAIKQFLDLGAQSLLVPMVDDAAMARRAVAA
+ARYPDGSAEGGVRGVGSALARSGRWNRIPGYLPGAADHVSVIVQIETAAGVRNADEIAAV
+DGIDGVFIGPSDLSASLGLLGQQSHPDVVAAVEEVITKVKAAGKIVGVNAFVPAQADAYA
+AAGADYVNVGADVALLARAAEALADRWCPAPSNAAADGQSAPRASY
+>3_779
+MPVRLNAQPLVRDLFTPEARAARGGRPAAGMFLSSGDVTAAEICAGAGMDYLLIDGEHAP
+LSLESVLAQLRAVAGYGVPVMTRVPSLDAVLVKQFLDLGAQTLLVPMVDTAEQAAEAVRA
+VRYPPHGVRGVGSALARSGRWNRIDGYLTHDADHVGLFVQIETAAGVENARSIAETSGVD
+GIFVGPSDLSASMGLIGQQTHPDVVAAVQSVIAAANAAGTVVGVNAFAEPQARAYAEAGA
+DFVNVGADVALLARAAEALADTWCPTPEAAADDDAGSRASY
+>4_1862
+MPVRHNPQPLFRDLFTPEAVAARGGRPAAGMFLSSGDPTTAEICAGAGLDYLLIDAEHAP
+LTLQDVLAQLRTIAGYRVPTLVRVPALDTVAIKQFLDLGAQSLLVPMVDDAAMARRAVAA
+ARYPDGSAEGGVRGVGSALARSGRWNRIPGYLPGAADHVSVIVQIETAAGVRNADEIAAV
+DGIDGVFIGPSDLSASLGLLGQQSHPEVVAAVEEVIAKVKAAGKFVGVNAFVPAQADAYA
+AAGADYVNVGADVALLARAAEALADRWCPAPSDAAGDGEGAPRASY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001909.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001909.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea9c331f19a405b0ce7a8a1c391d2c5d2635cf3e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001909.fa
@@ -0,0 +1,28 @@
+>0_1936
+MPRRPAPLPPSIDPAAFTVDDARRAGVTWSRLQSSDLRRLRHGIYGPAGPAAASVREWTM
+DEVRAYQRRHPGVVVSHETAARLHGLTVPARLLAPGAVHVSVGTSGGRPVQAGLVPHRIE
+VPEGQRMTRGGVLVTTPARTLWDLCAARSALTERDVVAAGDALLCPPWLPGGGRGAPAYT
+PEELVRSLAERGRFRGRGLARAALARMRVGADSPRETRLRLALVDAGLPEPEVQCRLDPS
+DRRAPTVDLGYRQWRLALQYDGEHHRTAEQQARDVLRDRWCADHDWLSIKVMWADARDDY
+ADVVARVRRRAAEFGG
+>1_1641
+MPRRPAPLPPSIDPTAFTVDDARRAGVTWSRLQSSDLRRLRHGIYGPAGPAAVSVREWTM
+DEIRAYQRRHPDVVVSHETAARLHGLTVPARLLAPGAVHVSVGTSGGRPVQASLVPHRIE
+VPEGQRMTRGGVLVTTPARTLWDLCAARAALTERDVVVAGDALLCPPWLPGGGRGDPAYT
+PEELVRSLAERGRFRGRGLARAALARMRVGADSPRETRLRLALVDAGLPEPEVQCRLDPS
+DRRAPTVDLGYRPWRLALQYEGEHHRTAEQQARDVLRDRWCADHDWLSIKVMWADARNDY
+ADVVARVRRRAAAFGG
+>3_778
+MPLRPVALPDSLISGPFTTRELLAAGAPAQRVRSPDLRRVAHGIHRPRSASGSTGDATAA
+ERGWLPEEVRAYQRMVPHAVVSHTTAARLHGLPLPAWAADERDVHLTFTAGAGRTRRRGL
+VAHQAGIPALDVALVAGVRVTTPPRTLWDLCSLHPRLSVEDLVVVADAVMAPGWDDEHGF
+LPGEHSAAALREALGRRGRFRGVRAAREVAERMREDVASPMETRTRLALVDQGLPEPEVQ
+VRLWGEDGAKGPVVDLAFPQWRVVVQYEGARHRTREQQERDVRRDRWCADHGWTVIKVVA
+ADVHAGLGPVAARILRLARQ
+>4_1863
+MPRRPAPLPPSIDPAAFTVDDARRAGVTWSRLQSSDLRRLRHGIYGPAGPAAVSVREWTM
+DEVRAYQRRHPDVVVSHETAARLHGLTVPARLLAPRAVHVSVGTSGGRPVQAGLVPHRIE
+VPQGQRMMRGGVLVTTPARTLWDLCAARSALTERDVVVAGDALLCPPWLPGGGRGAPACT
+PEELVRSLAERGRFQGRGLARAALARMRVGADSPRETRLRLALVDAGLPEPEVQCRLDPS
+DRRAPTVDLGYRPWRLALQYEGEHHRTAEQQARDVLRDRWCADRDWLSIKVMWADARDDY
+ADVVARVRRRAAAFGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001911.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001911.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1923620c22e42100f388f9dd73ecf45f07960f90
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001911.fa
@@ -0,0 +1,40 @@
+>0_1971
+MTELTGQASEAGTIDRLMAGWVADVETPDACAAHLLCDRWPADAVAFRFVAEDMSAVDLT
+FGELADRSRRLATGLAARGVTRGDRVPVMMSKREELVITLLALWRLGAVHVPLFTAFAAG
+AARMRIEGAAARLVVAEPRQAEKLTDIPGIEIIRTGPEWDALADSAPLAEDVAVGGDGPI
+ALLFTSGTTGRPKGVPVPLRAAAAFAVYLTCAVDLRPEDLFWNAADHGWAYGLYYGIVGT
+LVLGATSVQYRGAFSPATMVEVIRSQDVTNLAGAPTMFRALAKAGEVTEDAPLRLRRVST
+AGEPLPPSVLEWGRAALGTEIRDHYGQTELGMVICTPAHPELAAPPRPGSMGVPLPGIAA
+EIRDGQIAIDAASPMFWFPGYLGEPEKTAERFTPDGRWYLTGDTARQDDDGWFFFSSRDD
+DVILAAGYRIGPFDVESVLIDHPRVQEVAVVGLPDPEGVRGEEVVAFVVPAGAVADPDAL
+AAELQAKVRDEYSKHAYPRRVHFVDRLPKTPSGKLQRFLLRQGATD
+>1_1689
+MTERTGQAHEAGTIDRLMAGWVADVETPDACAAHLLCDRWPADAVAFRFVAEDMSAVDLT
+FGELADRSRRLATGLAARGVTRGDRVPVMMSKREELVITLLALWRLGAVHVPLFTAFAAG
+AARMRIEGAAARLVVAEPRQAEKLTDIPGIEIIRTGPEWDALADSAPLAEDVAVGGDGPI
+ALLFTSGTTGRPKGVPVPLRAAAAFAVYLTCAVDLRPEDLFWNAADHGWAYGLYYGIVGT
+LVLGATSVQYRGAFSPATMVEVISSQDVTNLAGAPTMFRALAKAGEVTEDAPLRLRRVST
+AGEPLPPSVLEWGRAALGTEIRDHYGQTELGMVICTLAHPELAAPPRPGSMGVPLPGIAA
+EIRDGQIAIDAASPLFWFPGYLGEPEKTAERFTPDGRWYLTGDTARQDDDGWFFFSSRDD
+DVILAAGYRIGPFDVESVLIDHPRVQEVAVVGLPDPEGVRGEEVVAFVVPAGAVADPDAL
+AAELQAKVRDEYSKHAYPRRVHFVDRLPKTPSGKLQRFLLRQGAAG
+>2_770
+MTERTGQASEAGTIDRLMAGWVADVETPDACAAHLLCDRWPADAVAFRFVAEDMSAVDLT
+FGELADRSRRLATGLAARGVTRGDRVPVMMSKREELVITLLALWRLGAVHVPLFTAFAEG
+AARMRIEGAAARLVVAEPRQAEKLTDIPGIEIIRTGPEWDALADSAPLAEDVAVGGDGPI
+ALLFTSGTTGRPKGVPVPLRAAAAFAVYLTCAVDLRPDDLFWNAADHGWAYGLYYGIVGT
+LVLGATSVQYRGAFSPATMVEVIRSQGVTNLAGAPTMFRALAKAGEVTEDAPLRLRRVST
+AGEPLPPSVLEWGRSALGTEIRDHYGQTELGMVICTLAHPELAAPPRPGSMGVPLPGIAA
+QIRDGQIAIDAASPLFWFPGYLGEPEKTAERFTPDGRWYLTGDTARQDDDGWFFFSSRDD
+DVILAAGYRIGPFDVESVLIDHPRVQEVAVVGLPDPEGVRGEEVVAFVVPAGAVVDPDAL
+AAELQAKVRDEYSKHAYPRRVHFVDRLPKTPSGKLQRFLLRQGAAD
+>4_1907
+MTERTGQAHEAGTIDRLMAGWVADVETPDACAAHLLCDRWPADAVAFRFVAEDMSAVDLT
+FGELADRSRRLAAGLAARGVTRGDRVPVMMSKREELVITLLALWRLGAVHVPLFTAFAAG
+AARMRIEGAAARLVVAEPRQAEKLTDIPGIEIIRTGPEWDALADSAPLAEDVAVGGDGPI
+ALLFTSGTTGRPKGVPVPLRAAAAFAVYLTCAVDLRPEDLFWNAADHGWAYGLYYGIVGT
+LVLGATSVQYRGAFSPATMVEVIRSQDVTNLAGAPTMFRALAKAGEVAEDAPLRLRRVST
+AGEPLPPSVLEWGRAALGTEIRDHYGQTELGMVICTPAHPELAAPPRPGSMGVPLPGIAA
+EIRGGQIAIDAASPLFWFPGYLGEPEKTAERFTPDGRWYLTGDTARQDDDGWFFFSSRDD
+DVILAAGYRIGPFDVESVLIDHPRVQEVAVVGLPDPEGVRGEEVAAFVVPAGAVADPDAL
+AAELQAKVRDEYSKHAYPRRVHFVDRLPKTPSGKLQRFLLRQGAAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001914.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001914.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c7f7be6f5a7e83d2e28710b9befbea24ea640ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001914.fa
@@ -0,0 +1,32 @@
+>0_1985
+MTTKDSRTRSLIDVDVLEYHRLLTPEQQEKLGEIRAALAEIVTPHVAEAWSRDEFPHEIA
+RRVGELGYNHISGMTEDPLFRGHLMAELARADISLSVYFALHNDLVGATLEALGSEEQKQ
+TWLPGLYAMEYTGCFALTEPEHGSDVAGGMATTARREGDEWVINGAKRWIGNGTMSRIAI
+VWARDEEDDQVKGFIVETDTPGYEATKIEHKTAVKIVQNADITFTDVRIPAENKLEKANT
+FADTNVILLGSRNGLGWQAVGAQQGILDAARRYALERTQFGRPIAGHQLVQSLLVQIAAN
+LAATLGMAHRAVQLEAAGEVSMTQASLVKLKTSQMCRESAALGRQMMGGNGILADVGLGR
+FFCDVEAIFTYEGTYEVNSLIVGRGLTGHSAFL
+>1_1702
+MTTTDSRTRSLIDVDVLEYHRLLTPEQQEELTEIRAALAEIVTPHVAEAWSRDEFPHEIA
+RRVGELGYNHISGMTEDPLFRGHLMAELARADISLSVYFALHNDLVGATLEALGSEEQKQ
+TWLPGLYAMEYTGCFALTEPEHGSDVAGGMATTARREGDEWVINGAKRWIGNGTMSRIAI
+VWARDEEDDQVKGFIVETDTLGYEATKIEHKTAVKIVQNADITFTDVRIPAENKLEKANT
+FADTNVILLGSRNGLGWQAVGAQQGILDAARRYALERTQFGRPIAGHQLVQSLLVQIAAN
+LAATLGMAHRAVQLEATGEVSMTQASLVKLKTSQMCRESAALGRQMMGGNGILADVGLGR
+FFCDVEAIFTYEGTYEVNSLIVGRGLTGHSAFL
+>3_716
+MTTTDSRTRSLIDVDVLEYHRLLTPEQQEKLTEIRAALAEIVTPHVAEAWSRDEFPHEIA
+RRVGELGYNHVSGMTEDPLFRGHLMAELARADISLSVYFALHNDLVGATLEALGSEEQKQ
+TWLPGLYAMEYTGCFALTEPEHGSDVAGGMATTARREGDEWVINGAKRWIGNGTMSRIAI
+VWARDEEDDQVKGFIVETDTPGYEATKIEHKTAVKIVQNADITFTDVRIPAENKLEKADT
+FADTNVILLGSRNGLGWQAVGAQQGILDAARRYALERTQFGRPIAGHQLVQSLLVQIAAN
+LAATLGMAHRAVQLEAAGEVSMTQASLVKLKTSQMCRESAALGRQMMGGNGILADTGLGR
+FFCDVEAIFTYEGTYEVNSLIVGRGLTGHSAFL
+>4_1920
+MTTTDSRTRSLIDVDVLEYHRLLTPEQQEKLTEIRAALAEIVTPHVAEAWSRDEFPHEIA
+CRVGELGYDHISGMTEDPLFRGYLMAELARADISLSVYFALHNDLVGATLEALGSEEQKQ
+KWLPGLYAMEYTGCFALTEPEHGSDVAGGMATTARREGDEWVINGAKRWIGNGTMSRIAI
+VWARDEEDDQVKGFIVETDTSGYEATKIEHKTAVKIVQNADITFTDVRVPAENKLEKANT
+FADTNVILLGSRNGLGWQAVGAQQGILDAARRYALERAQFGRPIAGHQLVQSLLVQIAAN
+LAATLGMAHRAVQLEAAGEVSMTQASLVKLKTSQMCRESAALGRQMMGGNGILADVGLGR
+FFCDVEAIFTYEGTYEVNSLIVGRGLTGHSAFL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001915.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001915.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51428256fae649c21fdd80d2fd74568ec405716c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001915.fa
@@ -0,0 +1,56 @@
+>0_1987
+MSEHMITWDQDADGVVTLTMDDPQARVNTMNERYQDAMDAVVDRLEAERDTVTGVVLTSA
+KKTFFAGGDLDSLAQAGPEDVESVFALTQRVKGQLRRLETLGRPVVAAINGTALGGGLEI
+ALACHRRIAVDDPGLKVGLPEVTLGLLPGGGGITRLVRMVGVERALMEWLLQGTARDARA
+AMEKGIIDEVVTDPADLVPAAKRWILEHRDDADAAAKPWDVKGFRIPGGTPAQASFASRL
+PAFAATLRRQLHGADLPAPKAILSAAVEGSQVDFDTASRIETRYFVSLVTGHTSSAMIQA
+FHSDMQALRSGAALGGPSRERSTITTAAVLGAGMMGVGIAHALALNGVDVMLKDVSLEAA
+ERGRERVGALLEGRVAKGRMSREDADAVLARVQPTEDYQDLAHVDAVIEAVFEDVELKDS
+VFAEVEKVVGPDTLLCSNTSTLPITLLQGPRERSQDFIGLHFFSPVDRMKLVEIIRGEQT
+SQRTVERAYDLVQQIRKLPILVNDGRGFYTSRVYGTLVLEAAALVEEGVDAQRIERAARH
+AGFPASPLAMMDEVSLTLIQHIRREEEKAVAEAGGERPVRPGERVVERMVDEFGRPGRAQ
+GAGFYEYPEEGPKHLWPGLAEHFATGADVPEQDLQDRLLYRMAIETARCFDDGVLTDAPS
+ANLGGVFGIGFPPHTGGPVTFMTHREGGPAAFVARADELADRYGERFRPGDTLRQRAERG
+EGPGR
+>1_1704
+MSEHMITWDQDTDGVVTLTMDDPQARVNTMNERYQDAMDAVVDRLEAERDTVTGVVLTSA
+KKTFFAGGDLDSLAQAGPEDVESVFALTQRVKGQLRRLETLGRPVVAAINGTALGGGLEI
+ALACHRRIAVDDPGLKVGLPEVTLGLLPGGGGITRLVRMVGVERALMDWLLQGTARDARA
+AMEKGILDEVVTDPADLVPAAKRWILEHRDDADAAAKPWDVKGFRIPGGTPAQASFASRL
+PAFAATLRRQLHGADLPAPKAILSAAVEGSQVDFDTASRIETRYFVSLVTGHTSSAMIQA
+FHSDMQALRSGAALGGPSRERSTITTAAVLGAGMMGVGIAHALALNGVDVMLKDVSLEAA
+ERGRERVGALLEGRVAKGRMSREDADAVLARVQPTEDYQDLAHVDAVIEAVFEDVELKDS
+VFAEVEKVVGPDTLLCSNTSTLPITLLQGPRERSQDFIGLHFFSPVDRMKLVEIIRGEQT
+SPRTVERAYDLVQQIRKLPILVNDGRGFYTSRVYGTLVLEAAALVEEGVDAQRIERAARH
+AGFPASPLAMMDEVSLTLIQHIRREEEKAVAEAGGERPVRPGERVVERMVDEFGRPGRAQ
+GAGFYEYPEQGPKHLWPGLAEHFATGADVPEQDLQDRLLYRMAIETARCFDDGVLTDAPS
+ANLGGVFGIGFPPHTGGPVTFMTHREGGPAAFVARADELADRYGERFRPGGTLRQLAERG
+EGPGR
+>3_714
+MTENTITWDQDAEGVVTLTMDDPTAKVNTMNGHWQESMRAAVERLEQERESITGVILTSA
+KKTFFAGGDLDQLGPSGPEDAEDVFAMTEHVKSLLRRLEKLGRPVVAAINGAALGGGLEI
+ALACHRRVAVDDPRIKVGLPEVTLGLLPGGGGITRLVRMLGLEKALMDWLLQGTQYRPAQ
+AKEKGVIDELVSSPEELLPAARRWILEQGAAAAKAREGGPEETDEALGAPSYAVKPWDRK
+GFRLPGGTPQQPQLASRLPAFAATLVKTLHGADLPAPRAILSAAVEGAQVDFDTASRIET
+RYFTSLVTGRVSTAMVQAFHTEMGAIRAGAGLGERVSERHTIATAAVLGAGMMGAGIAHA
+LATSGIDVVLKDVSKENAERGKAHCADLVGKAVARGRMDQSAADEVLGRIRTTDDYADIA
+GVDAVIEAVFEDFDLKSEVFAEVEKVVGRQTLLCSNTSTLPITQLQGPRERAADFVGLHF
+FSPVDRMKLVEIIRGEQTSQETVERAYDLVQQIRKVPILVNDGRGFYTSRVFGTLVLEAA
+AMVEEGVDPQRVERTARQAGFPGAPLAMLDEVSLTLTQHVRREAEKAAEAAGTERAEQPG
+ERVVDRMVEEFDRPGRARGAGFYEYPAEGPKHLWPGLREHFAAEVDVSDEDLKDRFLYRM
+ALETAACFEAGVLTDTASADIGGILGIGYPPHTGGPATFATNRPGGLADFVSRADALADA
+YGERFRPSDWLRERAAAGQGLA
+>4_1922
+MSEHMITWDQDADGVVTLTMDDPQARVNTMNERYQDAMDAVVDRLEAERDTVTGVVLTSA
+KKTFFAGGDLDSLAQAGPEDVESVFALTQRVKGQLRRLETLGRPVVAAINGTALGGGLEI
+ALACHRRIAVDDPGLKVGLPEVTLGLLPGGGGITRLVRMVGVERALMEWLLQGTARDARA
+AMEKGIIDEVVTDPADLVPAAKRWILEHRADADAAVKPWDVKGFRIPGGTPAQASFASRL
+PAFAATLRRQLHGADLPAPKAILSAAVEGSQVDFDTASRIETRYFVSLVTGHTSSAMIQA
+FHSDMQALRSGAALGGPSRERSTITTAAVLGAGMMGVGIAHALALNGVDVMLKDVSLEAA
+ERGRERVGALLEGRVAKGRMSREDADAVLARVQPTEDYQDLAHVDAVIEAVFEDLELKDS
+VFAEVEKVVGPDTLLCSNTSTLPITLLQGPRERSQDFIGLHFFSPVDRMRLVEIIRGEQT
+SPRTVERAYDLVQQIRKLPILVNDGRGFYTSRVYGTLVLEAAALVEEGVDAQRIERAARH
+AGFPASPLAMMDEVSLTLIQHIRREEEKAVAEAGGERPVRPGERVVERMVDEFGRPGRAQ
+GAGFYEYPEQGPKHLWPGLAEHFATGADVPEQDLQDRLLYRMAIETARCFDDGVLTDAPS
+ANLGGVFGIGFPPHTGGPVTFMTHREGGPAAFVARADELADRYGERFRPGDTLRQRAERG
+EGPGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001918.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001918.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8fec779221e7afcadbf75ecfcdc9870a78efd55d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001918.fa
@@ -0,0 +1,39 @@
+>0_2001
+MSEHFDVAVLGLGPGGEVAADRLLKAGKNVVVFERELIGGECAYWACIPSKTVLRPPEAR
+TEVQRAAGVSGAELDWAATAKYRDYMIRNLDDQAQVDGYIKEGAVVIKDEARITGPGRIQ
+AGDREITAEHIIIATGSDAVIPPLDGIDQITAWTNRETYTTSTLPERAVIIGGSAVGVET
+ATFLARFGVAITLIHCGERLLDREGPRVGELAHQYLQEAGIDIRLATSAVQARREGADSI
+IELQTRDGDPAGEVAADVVIFGTGRTPRTEGLGFEHAGVTLGDHGEIQIDDHCRAGENTW
+AIGDVTGIMPFTHVAKYQGRIAADAILGRPHPATYDGIPRVVFTDPEIAGAGLTQEQATK
+QGIRTIATELDLADAIARPWTYEQDSRGHLGLLADADRKILIGAWAVGPMAGEWIHHASL
+AIRTQLPIDTLLDQVAQFPTYHEAYQVALEQLDLTP
+>3_2170
+MSEHFDVAVLGLGPGGEVAADRLLKAGKNVVVFERELIGGECAYWACIPSKTVLRPPEAR
+TEVQRAAGVSGAELDWAATAKYRDYMIRNLDDQAQVDGYIKEGAVVIKDEARITGPGRIQ
+AGDREITAENIIIATGSDAVIPPLDGIDQITAWTNRETYTTSTLPERAVIIGGSAVGVET
+ATFLARFGVAITLIHCGERLLDREGPRVGELAHQYLQEAGIDIRLATSAVQARREGADSI
+IKLQTRDGDPAGEVAADVVIFGTGRTPRTEGLGFEHAGVTLGDHGEIQIDDHCRAGENTW
+AIGDVTGIMPFTHVAKYQGRIAADAILGRPHPATYDGIPRVVFTDPEIAGAGLTQEQATK
+QGIRTIATELDLADAIARPWTYEQDPRGHLGLLADADRKILIGAWAVGPMAGEWIHHASL
+AIRTQLPIDTLLDQVAQFPTYHEAYQVALEQLDLTP
+>3_2370
+MTEDLAPTTGPDDATPGAPDEEAVDVVVIGAGPVGENAAQYAHTAGGLEVALVEADLLGG
+ECSYWACMPSKALLRPLEVAGAAAHLGGLTDPDIDLPGLLARRDEWRSHLDDAGQVEWAE
+DAGLRVVRGHGRLAGPRRVEVLGDDGAPARVLRARHAVVVATGSTAVVPGELRGVSPWTS
+RDATGVREVPGRLAIVGGGVVAVEAATWMAALGSDVQLLVRGDRLLSGQEPVASRLVLEG
+LVDAGVRVRFGTSVERAERADVHAESDVGVPHGGPVRLTLAGSGETLEVDELLVAAGRRP
+ALDGLGLEALGLSAEDLQDESGTAVVPASDGAAPWLYAVGDVTGGPALTHWGKHRARLLG
+ERIAALATGRPAPSGEEAGEGVPEAVPQVVFTSPQVARVGVTEAQAREEGGEGELRVVDV
+PLTSAAGAALLRDDAAGRAVLVLRGDRVVGATFVGFEVAELLHAATVAIVGEVPLDRLRH
+AVAAYPTASEVWLRLVEEALGRG
+>3_2384
+MSSVIPDTARPSSGHAGVHRADVVVLGHGLAGLVAACELLEAGRSVVLVDQERAADLGGQ
+AWWSFGGLFLVDSPEQRRLRVRDSVDLAWSDWRETAGFTGGDDALPRAWAEAYVHFAAGE
+KRAWLRERGHRLFPVVGWAERKVPAPGVGGNSVPRFHITWGTGPGIVEPFAAVVEQAAFD
+GRLTYLPRHRVTELVTQNGAVCGVRGDRLADDDGARGTSSSRTVTGAFEVRAQAVLIASG
+GIGADHDAVRAAWPDRLGTPPERMLSGVPAYVDGSGVAAARAVGAHMLHPDRMWHYTEGV
+ANWDPVWPGHGIRILPGPSSLWLDAAGRRLPHPRWPGFDTLGALGEICRPGGARRAEGAD
+HTWFVLNERIIGREFALSGSEQNPDLTGRSLGHVLGRATQGVPAPVRAFLDHGEDFVQAA
+TVEELVDQMNELQDRTGGGGPRVELHAVRQAVAEHEDGAARAGVDPQLDAVRRARQYLGD
+RLIRTAAPHRLTDPAAGPLIAVRLRTLTRKTLGGLHTDLRGRVLDELGGPVPGLYAAGEA
+AGFGGGGMHGFRALEGTFLGGCLFSGRTAGRALAEDVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001919.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001919.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25d536ab242f829b0793232cb33e915489542029
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001919.fa
@@ -0,0 +1,16 @@
+>0_2029
+MVTRPVLQQPVVDAVDIRSVAEFYRELLGLHYRTGDELADGREPDSADWLVLLDDDGRRV
+LTFQRTEELKPSTWPSPEVPMQLHLDFTVPDRESLDAAHDHALRLGGRLVLDRSDDEDEP
+LYVFADPAGHPFCVFVG
+>1_1748
+MVTRPVLQQPVIDAVDIRSVAEFYRELLGLHYRAGDELADGREPDSADWLVLLDDDGRRV
+LTFQRTDELKPSTWPSPEVPMQLHLDFTVPDRDSLDAAHDHALRLGGRLVQDRSDDEDEP
+LYVFADPAGHPFCVFVG
+>2_670
+MITHPALQQPVIDAVDIRSVAEFYRELLGLHYRAGDELADGREPDSADWLVLLDDDGRRV
+LTFQRTEELKPSTWPSPEVPMQLHLDFTVPDRDSLDAAHDHALRLGGRLVQDRSDDEDEP
+LYVFADPAGHPFCVFVG
+>3_587
+MVSRPVLQQPVIDAVDIRSVADFYRELLGLHYRTGDELADGREPDSADWLVLLDDDGRRV
+LTFQRTEELKPSTWPSPEVPMQLHLDFTVPDRDSLDAAHDHALRLGGRLVLDRSDDEEEP
+LYVFADPAGHPFCVFVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001920.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001920.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c37bc6f6a283c0ae74bf446fd0605f91f14311fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001920.fa
@@ -0,0 +1,16 @@
+>0_2030
+MTDADLDDMFRLLGDAEVMRYYPRAKSRNEVRRWINWSKDNYATHGFGLWVIEHRTTGDF
+IGDCGLTWQNVDGQEVLEVGYHVLPEHQGQGLATEGASACLRHGFETLDATMVTAIINPD
+NMASRRVAERIGMTVWKSTRDPRGAPIVVYSSHGHEA
+>1_1749
+MTDADLDDMCRLRGDAEVMRYYPRAKSRNEVQRWINWSKDNYAKHGFGLWVIEHRTTGDF
+IGDCGLTWQNVDGQEVLEVGYHVLPERQGQGLATEGASACLRHGFETLDATMVTAIINPD
+NMASRRVAERIGMTVWKRTRDPSRAPIVVYSSHGQEA
+>2_669
+MTDADLDDMCRLLGDAEAMRYYPRAKSRNEVQRWINWSKDNYAKHGFGLWVIEHRTTGDF
+IGDCGLTWQNVDGQEVLEVGYHVLPERQGQGLATEGASACLRHGFETLDATMVTAIINPD
+NMASRRVAERIGMTVWKSTRDPSGAPIVVYSSHGQEA
+>3_586
+MTDADLDDMCRLLGDAEVMRYYPRAKSRNEVQRWINWSKDNYAEHGFGLWVIEHRATGDF
+IGDCGLTWQNVDGQEVLEVGYHVLPERQGQGLATEGASACLRYGFETLCATMVTAIINPD
+NMASRRVAERIGMTVWKSTRDPSGAPIVVYSSHGQEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001922.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001922.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e79ad4c5ce78637f3d8b7b41f8df2f4e03323750
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001922.fa
@@ -0,0 +1,24 @@
+>0_2039
+MTPARPTVSVVVPVLDDAEHLRVCLALLAAQSRPALEVVVVDNGCVDDSAVLARAAGARV
+VHEPRRGVPAAAAAGLDAAVGELLVRCDADTRMPADWLERIVARFDADSGLDALTGPGTF
+HDQPGLRGRVRAALYTGAYRWGAGAAVAATPVWGSNCALRAEAWQAVRTRVHRERGDVHD
+DLDLSFQLALAGRRIRFDPDLRVEVAGRIFHSLRQRVRQGRMAVTTLQVNWARLSPGRRW
+LRRAARSRPRPHWGRGPDGQSRD
+>1_1757
+MTPARPTVSVVVPVLDDAEHLRVCLALLAAQSRPALEVVVVDNGCVDDSAVLARAAGARV
+VHEPRRGVPAAAAAGLDAAVGELLVRCDADTRMPADWLERIVARFDADSGLDALTGPGTF
+HDQPGLRGRVRAALYTGAYRWGAGAAVAATPVWGSNCALRAEAWQAVRTRVHRERGDVHD
+DLDLSFQLALAGRRIRFDPDLRVEVAGRIFHSLRQRVRQGRMAVTTLQVNWARLSPGRRW
+LRRAARSRPRPHWGRGPDGQSRD
+>2_661
+MSGGRPAGALTVSVVIPVLDDAAHLRECLRHLARQTRPADEVIVVDNGSADESSAVARKA
+GARVVAEPLRGISAAAAAGYDAAVGDVILRCDADTRPPPDWVARAAGRFEAEPDLAALTG
+PGTFYDQPRLLARLRSRAYGAAYRFGAGAAVAGTALWGSNLGLRAEAWRAVRGRVHRRRP
+DVHDDLDLSFHLGLADVGSVVHDRRLHVGAAGRIFTSLPARVRQLRMAVTTLRLNWALLS
+PGMRWVRRARRSR
+>4_1980
+MTPARPTVSVVVPVLDDAEHLRVCLALLAAQSRPALEVVVVDNGCVDDSAMLARAAGARV
+VHEPRRGVPAAAAAGLDAAVGELLVRCDADTRMPADWLERIVARFDADPGLDALTGPGTF
+HDQPGLRGRVRAALYTGAYRWGAGAAVAATPVWGSNCALRAEAWQAVRTRVHRERGDVHD
+DLDLSFQLALAGRRIRFDPDLRVEVAGRIFHSLRQRVRQGRMAVTTLQVNWARLSPGRRW
+LRRAARSRPRPHWGRGPDGQSRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001925.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001925.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d73eb33425fb41f54f8ca0f070c172857719973
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001925.fa
@@ -0,0 +1,24 @@
+>0_2055
+MRPDRHSAPTSAAALAREAAILAGAGAAILLQVAHRPVGAGVAGHSRFTEDPMRRLRHTL
+AYIYAVTLPEAAPARDAVVDRVRAAHGSVRGVDAGGRPYDAADPDAQLWVAATLYAMGEQ
+VRRRMWGALDAEDADRLYRGYAPLATSLEVPASAWPVDRAAFADYWDDRVARLEVTDDAR
+RVAADLFSGQGVPAPLRAAMPLARFVTAGLLPGRVRAGLGWSWTGRDSVREARLWGLART
+LYRPLPATVRGVVVRWVLRGLPRTRKPRGAVDVEATRREVRPVWENGADV
+>1_1774
+MRPDRHSAPTSAAALAREAVILAGAGAAILLQVAHRPVGAGVAVHSRFTEDPMRRLRHTL
+AYIYAVTLPEAAPLRDAVVDRVRAAHRPVRGLDAGGHPYDAADPDAQLWVAATLYAMGEQ
+VRRRMWGALDAEDADRLYRGYAPLATSLEVPASAWPVDRAAFADYWDDRVARLEVTDDAR
+RVAADLFSGQGVPAPLRAAMPLARFVTAGLLPGRVRAGLGWSWTGRDSVREARLWGLART
+LYRPLPATVRGVVVRWVLRGLPRMPELGDAVAVRATRRDVRSVWENGGDV
+>2_646
+MPREAHGPVSAAGLAREAAILAGAGAAILLQVAHRPVAAGVAAHSRFTEDPMRRLRHTLG
+YIYAVTLPEAAGARDAVVARVRAAHAPVRGADHEGRPYNAADADAQLWVAATLYWAGEQV
+RRRLWGALDPADADRLYRGFAPLATSLEVPAAAWPADRAAFAAYWDARIAGLEVTDDARA
+VAADLFSGRGVPAPLRAALPLARFVTAGLLPARARAGLGWDWSRRDSIREARLWVLTRTL
+YRPLPAAVRGVVVRGILRGLRRMSEAGGPAS
+>4_1994
+MRPDRRSAPTSAAALAREAVILAGAGAAILLQVAHRPVGAGVAVHSRFTEDPMRRLRHTL
+AYIYAVTLPEAASLRDAVVDRVRAAHRPVRGVDAGGHPYDAADPDAQLWVAATLYAMGEQ
+VRRRMWGALDAEDADRLYRGYAPLATSLEVPASAWPVDRAAFADYWDDRVARLEVTDDAR
+RVAADLFSGHGVPAPLRAAMPLARFVTAGLLPGRVRAGLGWSWTGRDSVREARLWGLART
+LYRPLPATVRGVVVRWVLRGLPRTRKPRGAVDVEATRREVRPVWENGADV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001930.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001930.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2b306029c97660b610d4014dd3e88038962efe3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001930.fa
@@ -0,0 +1,16 @@
+>0_2110
+MTDIRRTATALTLGAAVVTGLGAPAAVAQTTAPATETATTAPASESPAPQEEEKDDNGNW
+GLWGLAGLLGLAGLAGRRKREVHAEPVRRDHHVAGAHRDHDVHRVDDRAGDVRTEGADAR
+RREADGTLGDATRRPGTGDAR
+>1_1835
+MTDIRRTATALTLAAAVVTGLGAPAAVAQTTAPATEAATTAPASESPAPQEEEKDDNGNW
+GLWGLAGLLGLAGLAGRRKREVHAEPVRRDHHVGGAHRDHDVHRVDDRAGDVRAEGADTR
+RPGTGDAR
+>3_490
+MADIRKTATALTLSAAVLVGAGAPAATAAESSTAPATETATTAPASSQSPEPEQTEEKDD
+NGNWGLWGLAGLLGLAGLAGRGKKREVVHAQPVREAPRVQPTHTENHHVDTTRVQDGVRD
+AGHRAGGTDGTPGNGR
+>4_2056
+MTDIRRTATALTLGAAVVTGLGAPAAVAQTTAPATETATTAPASESPAPQEEEKDDNGNW
+GLWGLAGLLGLAGLAGRRKREVHAEPVRRDHHVAGAHRDHDVHRVDDRAGDVRTEGADAR
+RREADGTLGDATRRPGTGDSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001932.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001932.fa
new file mode 100644
index 0000000000000000000000000000000000000000..161222048ac18425d6b8cc78fc861209718ca5e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001932.fa
@@ -0,0 +1,24 @@
+>0_2126
+MPSTAVPPRDSGAASTLPARTGHRGVSILRTAALVLVVAAFVWLALTVRLPGVDELRAQL
+DGFGWWSWLAFTVLYAAVALTPIPVTIMAVTAGVLFGAIEGTVLSVVGALLGSLGAYGIA
+RAVGREVVLRWLGRHAETVERRLEDTGFLALLTLRVAPGLPYWPVNYGAGALAVPLGIFA
+GSTAVGVIPGQLSLVAMGAFAVRPGVVNGVLLGVGWLTVGGLTLWAVRHWRRAARSAEEP
+ENPQSGHDTPSPRRRRGVS
+>1_1851
+MPSTAVPPRDSGAASTLPARTGHRGVSILRTAALVLVVAAFVWLALTVRLPGVDELRAQL
+DGFGWWSWLAFTVLYAAVALTPIPVTIMAVTAGVLFGAIEGTVLSVVGALLGSLGAYGIA
+RAVGREVVLRGLGRHAETVERRLEDTGFLALLALRVAPGLPYWPVNYGAGALAVPLGIFA
+GSTAVGVIPGQLSLVAMGAFAVRPGVVNGVLLGVGWLAVGGLTLWAVRRWRRAARAAEGP
+AGSEGPESPRSGQDTPSPRARRGVS
+>2_544
+MPSSAAPPSDAASSRPDRRGSSGSVGTASRTLLLVVVMALFIWLATSVRLPDIDTLRDRL
+ASFGFWSWLVFVLAYAGVALTPVPVTLMALTGGVLFGAVQGSVLSVAGALLGSIGAYWIA
+RALGRDVILRGLGRHADTVEEHLEDAGFLALLTLRVAPGLPYWPVNYGAGALGVPSGMFV
+GSTAVGVIPGQVSLVALGAFAVHPGVLNGVILGAGWLAVGVLTVWAARHWRRAANHDDGE
+GGED
+>4_2072
+MPSTAVPPRDSGAASTLPARTGHRGVSILRTAALVLVVAAFVWLALTVRLPGVDELRAQL
+DGFGWWSWLAFTVLYAAVALTPIPVTIMAVTAGVLFGAIEGTVLSVVGALLGSLGAYGIA
+RAVGREVVLRWLGRHAATVERRLEDTGFLALLTLRVAPGLPYWPVNYGAGALAVPLGIFA
+GSTAVGVIPGQLSLVAMGAFAVRPGVVNGVLLGVGWLAVGGLTLWAVRRWRRAARAAEGP
+AGSEGPESPRSGQDTPSPRARRGVS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001937.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001937.fa
new file mode 100644
index 0000000000000000000000000000000000000000..91f94ecfaaba861af1c9fb43ac19d805edfd4701
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001937.fa
@@ -0,0 +1,28 @@
+>0_2146
+MVGPSLFSRLASTLLHPLAPQDVLSLLDPVHSSRQLRGVVTSVTRETPGTATIAFRPGPG
+WRAHDAGQWARIGVDVDGVRQWRSYSLSAPAGADPEITVSDIGLVSGTLVRHTKPGDVLF
+LDIPEGDFTLPDEPRPLLMLTAGSGLTPVMSMIRTLVPTRRDADVVLIHSSRTPEDALFR
+EELAELADQFPGLRVVHHHTAETGRLDLSSPAQLEGLCPDWRERAGYACGPAGFLDDAEA
+LWRREAAADLTIERFQADFAPGVAGAGGRVVFEHADVEVDAPGDVPLLVVAEEAGVAAPA
+GCRMGICHACLTPLRSGRVTDLRTGQVHGEPGELVQTCVSAAAGPLSLSL
+>1_1870
+MVGPSLFSRLASTLLHPLAPQDVLSLLDPVHSSRQLRGVVTSVTRETPGTATIAFRPGPG
+WRAHDAGQWARIGVDVDGVRQWRSYSLSAPAGADPEITVSDIGLVSGTLVRRTKPGDVLF
+LDVPEGDFTLPDEPRALLMLTAGSGLTPVMSMIRTLVPARADADVVLIHSSRTPEDALFR
+EELAELADQFPGLRVVHRHTADEGRLDLSSPAELEDLCPDWRDRAAYACGPAEFLDDAED
+LWRREAGEDLRIERFRADFAAGVAGAGGRVVFEHADAEADAPGDVPLLIVAEEAGVAAPS
+GCRMGICHACLTPLRSGQVTDLRSGEVHGEPGELIQTCVSAAAGPLSLDL
+>2_520
+MAGPSLLSRLASTLLHPLTPQDVLGLLDPVHSSRQLRGVVTSVRRETPGTATIAFRPGPG
+WRLHDAGQWARIGVDVDGVRQWRSYSLSAPAGADPEITVSDIGLVSGTLVRRTVPGDVLF
+LDVPEGDFTLPEEPRPLLMLTAGSGLTPVMSMIRTLVPARRDADVVLVHSSRTPETALFR
+EELAELADQFPCLRVVHRHTADEGRLDLSSPAELEALCPDWRERAAYACGPAPFLDDAED
+LWRREAGGELRIERFRADFAPGVAGAGGRVVFEHSDAEADAPGDVPLLIVAEEAGVAAPA
+GCRMGICHACLTPLRSGQVTDLRSGEVHGEPGDLVQTCVSAAAGPVSLDL
+>4_2091
+MVGPSLFSRLASTLLHPLAPQDVLSLLDPVHSSRQLRGVVTSVTRETPGTATIAFRPGPG
+WRAHDAGQWARIGVDVDGVRQWRSYSLSAPAGADPEITVSDIGLVSGTLVRRTKPGDVLF
+LDVPEGDFTLPDEPRALLMLTAGSGLTPVMSMIRTLVPARADADVVLIHSSRTPEDALFR
+EELAELADQFPGLRVVHHHTAETGRLDLSSPAQLEGLCPDWRERAGYACGPAGFLDDAEA
+LWRREAAADLTIERFQADFAPGVAGAGGRVVFEHADAEADAPGDVPLLIVAEEAGVAAPS
+GCRMGICHACLTPLRSGQVTDLRSGEVHGEPGELIQTCVSAAAGPLSLDL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001938.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001938.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7b9cbbb3122eb4b3e21f624c7bea222fbdd7e62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001938.fa
@@ -0,0 +1,27 @@
+>0_2148
+MSIPQDSGRPRPDAPTSPLAAALAQQETDPLRWEEDPAPPRRRRSFGRWMRELGWRHAVG
+VLASAFALFPLLYVLSASLDPTGTMASSNRLFSSFSGQNYVDLFSDPNRPFGRWFLNTMV
+IGVITSVMTVFLGALAAYAFSRMRFTGRRVGLLTLLLVQMFPQLLAVVAIFLLLTYIGNL
+VPVLGIGSQLGLILVYLGGALGVNTYLMYGFFNTIPPSLDEAAKLDGASHARIFFSIILR
+LVTPILAVVALLSFITTVSEFVIASVVLTDPSAQTLAVGLYGYVSETRSENWGVFAAGAV
+LAALPVMALFLFLQRYIVSGLTAGGVKG
+>1_1872
+MSIPQDSGRPRPDAPTSPLAAALAQQETDPLRWEEDPAPPRRRRSFGRWMRELGWRHAVG
+VLASAFALFPLLYVLSASLDPTGTMASSNRLFSSFSGQNYVDLFSDPNRPFGRWFLNTMV
+IGVITSVMTVFLGALAAYAFSRMRFTGRRVGLLTLLLVQMFPQLLAVVAIFLLLTYIGNL
+VPVLGIGSQLGLILVYLGGALGVNTYLMYGFFNTIPPSLDEAAKLDGASHARIFFSIILR
+LVTPILAVVALLSFITTVSEFVIASVVLTDPSAQTLAVGLYGYVSETRSENWGVFAAGAV
+LAALPVMALFLFLQRYIVSGLTAGGVKG
+>2_517
+MSIPQDPSARAPQGQAAPAAASPLAAALAQQEIDPLRWEDGAPPPRRRRSFGRWLRELGW
+RHVVGVLASAFALFPLLYVLSASLDPTGTMASSNSLFSSFSGQNYVDLFSDPSRPYGRWF
+VNTMVIGLVTSFSTVFLGALAAYAFSRMRFAGRRVGLLTLLLVQMFPQLLAVVAIFLLLT
+YIGDLVPVLGIGSQLGLILVYLGGALGVNTYLMYGFFNTVPASLDEAAKLDGASHVQIFF
+SIILRLVTPILAVVGLLSFISTVSEFVIASVVLTDPAAQTLAVGLYGYVSETRSENWGVF
+AAGAVLAAVPVMALFLFLQRYIVSGLTAGGVKG
+>2_2586
+MTFTLLAPHQSAAISEAGIEQAARDLTRARTLGRIGLVPAFAILTVLAVISIFPIYWMFV
+TAFRPAEQMLSTNPLPGPFSLENFQYVWDTIPILSMLGNTFVMALVIAIGQLFVAILASY
+GFSRWTFRGQKILFLLFVGSWLVPFQVTMIPNYVRIAEMGLLNNMVGVILPQLAAAFAVM
+MLKQHLDSFPRELLDASDMDGRSPWRTLWEVVVPNLRPALAALAIMLFISAWNEYLWPSL
+IMQGSNDLIQVGVRSFLGSEGNNWGAVMAASALACLPIFLIYIFLQRYVVDAFVRSGLK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001939.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001939.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7393a9cea219b7adacee57d63e128ddd96ab1154
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001939.fa
@@ -0,0 +1,30 @@
+>0_2152
+MASVTFRSASRQYPGSPRPAVDSLDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEELSHG
+SILIGDRDVTDVDPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPADERRRRVEDAA
+KLLDLTEYLDRKPKALSGGQRQRVAMGRAIVRDPQVFLMDEPLSNLDAKLRVQTRAQIAN
+LTRRLGTTTVYVTHDQTEAMTMGDRVAVLKEGRLQQVDTPRNLYERPMNVFVAGFIGSPA
+MNIFRMPATHEGVHWGETVIPVPREDLADAGTAVDLGVRPENLVVSDDAAGLPVEVDTVE
+ELGADAYVYGHATIGGEERLITLRTVGYTAPEKGSVVHVVPDPERVHLFHAETGERLNR
+>1_1876
+MASVTFRSASRQYPGSPRPAVDSLDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEELSHG
+SILIGDRDVTDVDPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPADERRRRVEDAA
+KLLDLTEYLDRKPKALSGGQRQRVAMGRAIVRDPQVFLMDEPLSNLDAKLRVQTRAQIAN
+LTRRLGTTTVYVTHDQTEAMTMGDRVAVLKEGRLQQVDTPRNLYERPMNVFVAGFIGSPA
+MNIFRMPATHEGVHWGETVIPVPREDLADAGTTVDLGVRPENLVISDDAAGLPVEVDTVE
+ELGADAYVYGHATIGGEERLITLRTVGYTAPEKGSVVHVVPDPERVHLFHADTGERLNR
+>2_513
+MASVSFRSATRQYPNAPRPAVNRLDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEELSSG
+SIHIGDRDVTDVDPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPADERRRRVEDAA
+KLLDLTEYLDRKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRAQIAQ
+LTRRLGTTTVYVTHDQTEAMTMGDRVAVLKDGTLQQVDTPRSLYEKPVNVFVAGFIGSPA
+MNIFRMPVAADGVHWGESVIPVDRATLADAGQSVDLGVRPENLEITDRGGLAVEVDTVEE
+LGADAYVYGHATIGGEERLITLRTVGYTAPEKGSVVHVVPDPERVHLFHAETGERLNR
+>2_2591
+MARLVLNQITREFGDFVATDRVSLEVDDGDFLVLLGPSGCGKTTLLRMIAGLLEPSSGSI
+EVDGDDITALPARKRDLAMVFQSYALYPHLTVEKNLAFPLRVRKLPKAEIAARVRAAAEA
+VEIDHLLSRKPKELSGGQRQRVALARALVREPKAFLMDEPLSNLDAKLRTATRRELAALH
+RRLGATFVYVTHDQVEAMTMATKIALLNGGRIEQYGTPEQLYDTPSSVFAAGFLGSPAMN
+LLDATLTTTDGRITAFAPGVEAVLWEGATPERDVVLGVRPEHLSVFAGGAPEAVPTAGAA
+LRGTVELVENLGREQLVHCRVGDERVTVSCAREEAWQAGELVVIAAPLTRLHLFDRRSGR
+RLEWRPAAQSEAPLRAAMAPSAGRPQENASRFRAARGGATAPASRSADVRSTEEAAQSEA
+SLRTATR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001940.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001940.fa
new file mode 100644
index 0000000000000000000000000000000000000000..153cad34800940a05e40e48681ca7ae7e35ff2b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001940.fa
@@ -0,0 +1,16 @@
+>0_2153
+MEHIDETALPAPEDRVVSATRHVDAPAGVVFELIADPSRQPEWDGNDNLAEAAPGQRVTA
+VGDVFVMTLQKGVDRANHVVEFEEGRRIAWKPSEVGGEPFGQLWRWEVEGDDEGGCRVTH
+TYDWTALTDPKRVQKALRTGEGQLRASIDRLAELAERQG
+>1_1877
+MEHIDETALPAPEDRVVSATHHVDAPAGVVFELIADPSRQPEWDGNDNLAEAAPGQRVTA
+VGDVFVMTLQKGVDRANHVVEFEEGRRIAWKPSEVGGEPFGQLWRWEVEGDDEGGCRVTH
+TYDWTALTDPKRIQKALRTGEEQLRASIDRLAELAERQD
+>2_512
+MEHIDETALPAPQDRVATASREVDAPAGVVFELIADPARQPEWDGNDNLAGAEPGQRVTA
+AGDVFVMTLRKGVDRANHVVEFEEGRRIAWKPSEVGGEPFGQLWRWEVEGIRDEPRCRVT
+HTYDWTELTDPGRIRRALRTGPEQLRASIDRLAELARTQPQA
+>4_2093
+MEHFDETALPAPEDRVVSATRHVDAPAGVVFELIADPSRQPEWDGNDNLAEAAPGQRVTA
+VGDVFVMTLQKGVDRANHVVEFEEGRRIAWKPSEVGGEPFGQLWRWEVEGDDEGGCRVTH
+TYDWTALTDPKRIQKALRTGEEQLRASIDRLADLAERQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001941.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001941.fa
new file mode 100644
index 0000000000000000000000000000000000000000..faae2c47777e108962e5d328d3b4a38f35fb4d41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001941.fa
@@ -0,0 +1,32 @@
+>0_2157
+MQIAEQERIASPTFVLAWVVSFLQFLAFYALVTTMAVYAVRQFAASDAGAGLASSAFVIG
+ATLSRVVTGHVVDRFGKRRVLVVALVAVALSCTLYLVASSLPALVAVRMLHGASYAFAST
+AVMALAQAAIPDGRRAEATGHLALGTTLATAIGPALGLFLAGSIGYVWLFRATLGITVVS
+LVLGLLVREAPAAAGVDGERAAGEVPLEHPAPAVGFRLRSVLHPAVLPISGFMLLVGLSY
+AGILTYLNAYSVERGLTAGAGLFFLAYAAAMLVMRLTLGTLQDRRGDDAVVYPALLCFTA
+ALLVLAFATRDWQVVLAGALSGLGYGTLMPAAQAIAVNAVPSHQLGAGISTLMLFADVGL
+GLGPVLLGGLVASAGYGAMYAALAGVLVVAAGYYFVMHGRRHGRRETVARA
+>1_1881
+MQIAEQERIASPTFVLAWVVSFLQFLAFYALVTTMAVYAVRQFAASDAGAGLASSAFVIG
+ATLSRVVTGHVVDRFGKRRVLVAALVAVALSCTLYLVASSLPALVAVRMLHGASYAFAST
+AVMALAQAAIPDGRRAEATGHLALGTTLATAIGPALGLFLAGSIGYVWLFRATLGITVVS
+LVLGLLVREAPAAADVDGERAAGEVPLEHPAPAVGFRLRSVLHPAVLPISGFMLLVGLSY
+AGILTYLNAYSVERGLTAGAGLFFLAYAAAMLVMRLTLGTLQDRRGDDAVVYPALLCFTA
+ALLVLAFATRDWQVVLAGALSGLGYGTLMPAAQAIAVNAVPSHQLGAGISTLMLFADVGL
+GLGPVLLGGLVASAGYGAMYAALAGVLVVAAGYYFVMHGRRHGRRETVARA
+>3_456
+MHHPVTAPAEAAPRIVTPVFAVAWLVNFAQYLTFYLLATTMALYAVKQFGAGDAAAGFAS
+SAFVVGATVARIFAGHVVDSLGRRRMLLVSLSVVTLACAAYLPASSLGLLVAVRLVHGAM
+YAVASTAVMTLAQSVIPASRRAEGTGYFALGTTLATALGPAAGLMLVSAAGYPGMFWATT
+AVAAVGLAFGLALRVPDEPASARPHLVRGFRLGGILHPAVVPIGVFMLLVGVAYAGVITY
+LNGYAEQRGLGAGAGLFFLAYALVTLVMRFVLGRVQDRRGDNAVVGLGLVCFAASLVLLA
+VARQDAVVVLAGALCGLGYGTLMPAAQAIAVRLVPPHQMGTGISTLYLGVDVGIGLAPLP
+LGALLAAGGYLWMYLVLAGFVVLAGVYYVLVHGRTPAARAVAR
+>4_2097
+MQIAEQERIASPTFVLAWVVSFLQFLAFYALVTTMAVYAVRQFAASDAGAGLASSAFVIG
+ATVSRVVTGHVVDRFGKRRVLVVALVAVALSCTLYLVASSLPALVAVRMLHGASYAFAST
+AVMALAQAAIPDGRRAEATGHLALGTTLATAIGPALGLFLAGSIGYAWLFRATLGITVVS
+LVLGLLVREAPAAADVDGERAAGEAPLEHPAPAVGFRLRSVLHPAVLPISGFMLLVGLSY
+AGILTYLNAYSVERGLTAGAGLFFLAYAAAMLVMRLTLGTLQDRRGDDAVVYPALLCFTA
+ALLVLAFATRDGHVVLAGALSGLGYGTLMPAAQAIAVNAVPSHQLGAGISTLMLFADVGL
+GLGPVLLGGLVASAGYGTMYAALAGVLVIAAGYYFVMHGRRHGRRETVARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001942.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001942.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e823eaba4b5166401af79efc0c2b8eb04a997179
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001942.fa
@@ -0,0 +1,20 @@
+>0_2160
+MTITAIDTSSLTTEAAAVLAATPGMRYAEFLTAAPAVPGIVAVVADESARAALGLTPAAG
+DVLAVDVADESLQCREVRAAFQSGRTGGSPLRQAFAALLAGELGLDVERTSPGAAGAGFA
+LTPESEETLTAWMREHLTLRAWVAQDASALEGVAREVAADLAPALQPGALEAPVAQRVAA
+MRASARRSATL
+>1_1887
+MTITAVDTPSLTAEAAAVLAATPGMRYAEFLTAAPAVPGIVAVVAEESARAALGLTPAAG
+DVLAVDVADESLQCREVRAAFQSGRTGVSPLRQAFAALLAGELGLDVERTSPGAAGVGFA
+LTPESEETLTAWMREHLTLRAWVAQDASALEGVAREVAADLAPALQPGALEAPVAQRVAA
+MRASARRSATL
+>2_498
+MTITAAETQSLTAEATAVLAAMPGVSYAQFLAEAPEVPGIVAVVADQAARARLGVEAEET
+GLLAVTVAPYGLRARDVRAAFQSGRTAVSPLRQALAALLEDELGLDVERTSPGAAGAGFT
+LTPESEDALTAWMRAHLTLRAWATQDASVLADVADQVNADLAPALALDGVAAPSAHLRER
+LAAMTAAARRSATI
+>4_2100
+MTITAVDTPSLTTEAAAVLAATPGMRYAEFLTAAPAVPGIVAVVAEESARAALGLTPAAG
+DVLAVDVADESLQCREVRAAFQSGRTGVSPLRQAFAALLAGELGLDVERTSPGAAGAGFA
+LTPESEETLTAWMREHLTLRAWVSQDASALEGVAREVAADLAPALQPGALEAPVAQRVAA
+MRASARRSATL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001951.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001951.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e89dcf25813cd8ecbc5b44693bf4de35c532858
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001951.fa
@@ -0,0 +1,12 @@
+>0_2237
+MAEKKTEKNGAPMGPGTSNIKDPEVYEALRREGASEEKAARIANASARDGRDEVAERGGE
+AGSYEDWTKDELAKRARELDIEGRSTMTKDELIEALRNH
+>1_1941
+MAEKKAEKNGAPMGPGTSSIKDPEVYEALRREGASEEKAARIANASARDGRDEVAERGGE
+AGSYEDWTKDELEKRARELDIEGRSTMTKDELIEALRDH
+>2_925
+MATQKKSESDTPQIKDPEMYEALRRDGASKEKAARISNAAARDGREEVAERGGESESYEE
+WTVDELEDRAKELDLTGYSDKRKDELIAMLREH
+>4_2179
+MAEKKTEKNGAPMGPGTSNIKDPEVYEALRREGASEEKAARIANASARDGRDEVAKRARE
+LDIEGRSTMTKDELIEALRDH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001956.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001956.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2fa059126b56182e2506e88f09a5afa91a27fc91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001956.fa
@@ -0,0 +1,36 @@
+>1_243
+MTVGHGAHGPRHSDPRYVALQTEREKHARAAARGTSVWSADQDAAVPREPLRIPELLLGA
+LLAMEAFSVPLGPVALPLNEAGMLLLLALALCRRSRRDVSALGLTAVLAAAVLLFLAIVS
+VSQGIPDLEWLRRWVRMAALVGLVGCIAGGRLSLRSLAVGLGAAMALNVPLFYAGLVPAP
+YGSFLTGILADKNVAGLYYAAMPVLALALVRTRRWKLILLVAAAVCVVLTGSRTSMAGFA
+CAVLWLWLTPRMGAGLRLVLLAVLAWAVAFAEENLARIAFFADRTGTDWLRSNIQAETAV
+RVAETPWYGRGLTTAYVDFGGATWHYHNSYAGLYTEGGVVLLLAVLGAYAFFGLRLFSAR
+LRTPSRVAVEAAAVVVFVSATQLGEVFITIPSMLVVAAGVTLWLDERDAPLESEVLERRR
+RRVLAAARRGQHAPSSGGHAVPDL
+>2_2363
+MAVRHQTRGPVDTDPRYRALLEARAAQERQAARGTAAWSRDDATGLPREPLRIPELILGA
+LLAMEAFGVRLGPLGVPLNEAAMLLLLFLALCRRSRRDTSALGLSAVLAGAVMVFLAVVS
+VNQGIPDMEWLRRWVRIAALVGLVGCIAGGRLDLRSVLTGLLAAMAANVPLFYAGVVPTP
+YGSFLTGFLADKNVAGLYYAAMPVLALAVVRSRRWKLAILLAAAVCLFLTGSRTSMAGFG
+VALVWLAVTPRLAAGLRVVLLVVLGWAVGFAEENLSRLEVFGDRTGTDWLRGTIQAATEA
+KAATTPWHGRGLTEAYVTIGRDTWLYHDSYAGLFTEGGVVLLVAVLGAYAFFGLRLFSTR
+LRTPSRVAVEAAAAVVFVTATQLGEVFITIPGMLIVAAGVSLWLRERDAPLESEVRERRR
+RQVLAAARRGSTPESSADLAAPGSA
+>3_2244
+MPPHLPSGPALQDPRYQAVLAERGRREAATARGVSVLTAEDAAGPRTSLRVPELLLGFLL
+AMEAYTLPAGGVPVPLNEAAMMVLLGLALCRRAKRRASALGVAALLAVLVGVYLAAVSLA
+MGVPDAVWLRRLVRMAALTALVGCFAARRVDLRSVLTGLLAAMAVNVPLFYAGLVPAPYQ
+GFLTGFLADKNVAGLYYAAVPVLALTFVRRPGVRLLLLSASGLCVFLTGSRTSLAGFACA
+LVWVVLTPRMGPVLRVALLALLAWAVGFAEENLARVGVYSDREGTDWFRSVIQTATGVKV
+EATPWTGQGLAQSFVELDAGRFLFHNSYAALYVEGGVVLTAAMLTAYAVYGLRLGATRLR
+TPSRVAVEAAAVVVLVTATQLGEVFVSIPSMLILAAGATLAITEADAPLDAQARARREER
+TLRQAAARGH
+>4_513
+MTVGHGAHGPRHSDPRYVALQAEREKHARAAARGTSVWSAGQDAAAPREPLRIPELLLGA
+LLAMEAFSLPLGPVALPLNEAGMLLLLALALCRRSRRDVSALGLTAVLAAAVLLFLAVVS
+VSQGIPDLEWLRRWVRMAALVGLVGCIAGGRLSLRSLAVGLGAAMALNVPLFYAGLVPAP
+YGSFLTGVLADKNVAGLYYAAMPVLALALVRTRRWKLILLVAAAVCVVLTGSRTSMAGFA
+CAVLWLWLTPRMGAGLRLVLLAVLAWAVAFAEENLARIAFFADRTGTDWLRSNIQAETAV
+RVAETPWYGRGLTTAYVDFGGATWHYHNSYAGLYTEGGVVLLLAVLGAYAFFGLRLFSAR
+LRTPSRVAVEAAAVVVFVSATQLGEVFITIPSMLVVAAGVTLWLDERDAPLESEVLERRR
+RRVLAAARRGQHAPSSGGHAVPDL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001961.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001961.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a02a6a1a957096b9d0d182109c1720a79b362aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001961.fa
@@ -0,0 +1,80 @@
+>1_1597
+MAIHNESELETYICEYLEQHDWLYSPNDAGYDRKNAIFPEDVHAWLAENQPEDYGRIVKA
+DAPASAQQAQRDQITTRLIDVLNKPQDTGVGGTLNVLRKGFKVGTSATLRMAEPRPATNL
+NPAAVASYERMRLRVMRQVHFNPATNQSVDLVLFVNGLPVATIELKTDSTQSIGHAKKQY
+RDRNPKATPLFGFGTRAVVHFAVSNREVWMTTKLAGKDTFFLPFNQGDDGHAGNPLNPNG
+SSTAYLWERILQRDTWLEILQKFVFLKKETVEDEHGRSRRKSTLIFPRFHQWEAVTTMLA
+AVREEGAGASYLIEHSAGSGKTNTIAWTAHRLLSTYGVDEQRVFDSVIVVTDRTVLDDQL
+QEAVRQIERTSGTVVAVDRKNLGGEATSKSALVKQTLLQGNRIIVVTLQTFPAVLELLKG
+DSTLAGRTYAVIADEAHSSQTGSAAAKLKRVLTPDEQADLDDGGEADTESILAAEVAATG
+RPQNISFFAFTATPKDKTLQMFGRPSGEYDEKGQEIPASFHRYTMQQAIEEEFILDVLKN
+FTNYDTAFKLALAGQQGEFRPEGDRAAVGKPTTEVDQTEASKKLMRWVKLHPTNIAQKVK
+IIVEHFRANVAGLLDGQAKAMVVTDSRAAAVRYKRQMDQYIQDMGYTDVGTLVAFSGEIT
+DDEFGLEKVTERSMNPSVTGDLAKAFDGDGYQVMIVANKYQTGFDQPKLCALYVDKKLSG
+VLAVQTLSRLNRAAPGKDTTYVLDFVNSEDDIQAAFEPYYAGAKLEAVTDPNLIHDLGTK
+LDAAGVYDWDEVDAFAEVWVAWKPGSGQEGLQAALEPVAYRFRKELAHARMNQDETRVNE
+LVLVRKDMRSFVSLYDFLSQIYEFGDTEHYKRALFLRHLVQLVGDQPGGEELIDLSDVQL
+VSIRQKKTSSGDIGLTGGAALKGTTAVGGGQVREEQRGPLEEVIEKINEIFAGEGVDASP
+SQQEAWVSALVAPLMEDEKLLGQAGANSLEQFLASPNLERSAMGAVYANEDAFAKMTDIV
+GRGGDPSKMIVAAIGEYLYWKVRSEGTGPVDVAHGRSAVFADETAPSQGTSVDERARATP
+SRVRKGS
+>2_882
+MAIHNESELETYICEYLQSHGWLYSANDEGYDRKNAIFPEDVHAWLVENQPEDYGRIVKA
+DAPASAQQAQRDQITTRLVDVLNKPQDTGVGGTLNVLRKGFKVGTSATLRMAEPRPATNL
+NPAAVASYERMRLRVMRQVHFTGAHESESVDLVLFVNGLPVATIELKTDSTQSIGHAKKQ
+YRDRNPKATPLFGFGTRAVVHFAVSNREVWMTTKLAGKDTFFLPFNQGDDGHAGNPLNPN
+GGSSTAYLWERILQRDTWLEILQKFVFLKKETVEDEYGRSRRKSTLIFPRFHQWEAVTKM
+LAAVREEGVGKSYLIEHSAGSGKTNTIAWTAHRLLSTYGVDEQRVFDSVIVVTDRTVLDD
+QLQEAVRQIERTSGTVVAVDRKNLGGEPTSKSALVKQTLLQGNRIIVVTLQTFPAVLELL
+KGDSTLAGRTYAVIADEAHSSQTGSAAAKLKRVLTPDEQADLEDGGEADTESILAAEVAA
+TGRPQNISFFAFTATPKDKTLQMFGRPSGEYDEKGQEIPASFHRYTMQQAIEEEFILDVL
+KNFTNYDTAFKLALAGQQGEFRPEGDRAAVGKPTTEVDQTEASKKLMRWVKLHPTNIAQK
+VRIIVEHFRANVAGLLDGQAKAMVVTDSRAAAVRYKRQMDQYIQDMGYTDVGTLVAFSGE
+ITDDDFGLEKVTERSMNPPVTGDLAKAFDGDGYQVMIVANKYQTGFDQPKLCALYVDKKL
+SGVLAVQTLSRLNRAAPGKDTTYVLDFVNSEDDIQAAFEPYYAGAKLETVTDPNLIHDLG
+TKLDAAGVYDWAEVDAFAEVWVVWKPGSGQEGLQAALEPVAYRFRKELAHARMNQDETRV
+NELVLVRKDMRSFVSLYDFLSQIYEFGDTEHYKRALFLRHLVQLVGDQPGGEELIDLSDV
+QLVSIRQNKTSSGDIGLTGGTALKGTTAVGGGQVHEKQRGPLEDVIEKINEIFAGEGVDA
+SPSQQEAWVSALVAPLMEDEKLLGQAGANSLEQFLASPNLERSAMGAVYANEDAFAKMTD
+IVGRGGDPSKMIVAAIGEYLYLTVRGEGAGPVDVAHGRSAVFADETAPSQGTSVDERASA
+TPSRVRKGN
+>3_822
+MAIHNESELETYICEYLERHGWLYSANDDGYDRKNAIFPEDVHAWLAENQPEDYGRLVKA
+DAPASAQQAQRDQITTRLIDVLNKPQDTGVGGTLNVLRKGFKVGTSATLRMAEPRPATNL
+NPAAVASYEHMRLRVMRQVHFNPATNQSVDLVLFVNGLPVATIELKTDSTQSIGHAKKQY
+RERNSKATPLFGFGTRAVVHFAVSNREVWMTTKLAGKDTFFLPFNQGDDGHAGNPLNPNG
+GSSTAYLWERILQRDTWLEILQKFVFLKKETVEDEYGRSRRKSTLIFPRFHQWEAVTTML
+AAVREEGAGKSYLIEHSAGSGKTNTIAWTAHRLLSTYGADEQRVFDSVIVVTDRTVLDDQ
+LQEAVRQIERTSGTVVAVDRKNLGGEATSKSALVKQTLLQGNRIIVVTLQTFPAVLELLK
+GDSTLAGRTYAVIADEAHSSQTGSAAAKLKRVLTPDEQADLEDGGEADTESILAAEVAAT
+GRPENISFFAFTATPKDKTLQMFGRPSGEYDEKGQEIPASFHRYTMQQAIEEEFILDVLK
+NFTNYDTAFKLALAGQQGEFRPEGDRAAVGKPTTEVDQTEASKKLMRWVKLHPTNIAQKV
+KIIVEHFRANVAHLLDGQAKAMVVTDSRAAAVRYKRQMDQYIHDMGYTDVGTLVAFSGEI
+TDDDFGLEKVTERSMNPSVTGDLAKAFDGDGYQVMIVANKYQTGFDQPKLCALYVDKKLS
+GVLAVQTLSRLNRAAPGKDTTYVLDFVNSENDIQAAFEPYYAGAKLETVTDPNLIHDLGT
+KLDAAGVYDWDEVDAFADVWVAWKPGSGQEGLQAALEPVAYRFRKELAHARMNHDETRVN
+ELVLVRKDMRSFVSLYDFLSQIYEFGDTEHYKRALFLRHLVQLVGDQPGGEELIDLSDVQ
+LVSIRQKKTSSGDIGLTGGAALKGTTAVGGGQAREKQRGPLEEVIEKINEIFAGEGVDAS
+PSQQEAWVSALVAPLMEDEKLLGQAGANSLEQFLASPNLERSAMGAVYANEDAFAKMTDI
+VGRGGDPSKMIVAAIGEYLYWKVRGEGAGPVDVAHGRSAVFADETAPSQGTSVDERASAT
+PSRVRKGN
+>4_1817
+MAIHNESELETYICEYLEQHGWLYSPNDDGYDRKNAIFPEDVHAWLAENQPEDYGRLVKA
+DAPASAQQAQREQITTRLVDVLNKPQDTGVGGTLNVLRKGFKVGTSATLRMAEPRPATNL
+NPAAVASYERMRLRVMRQVHFNPATNQSVDLVLFVNGLPVATIELKTDSTQSIGHAKKQY
+RDRNPKATPLFGFGTRAVVHFAVSNREVWMTTKLAGKDTFFLPFNQGDDGHAGNPLNPYG
+GSSTAYLWERILQRDTWLEILQKFVFLKKETVEDEHGRSRRKSTLIFPRFHQWEAVTTML
+AAVREEGAGKSYLIEHSAGSGKTNTIAWTAHRLLSTYGADEQRVFDSVIVVTDRTVLDDQ
+LQEAVRQIERTSGTVVAVDRKNLGGEATSKSALVKQTLLQGNRIIVVTLQTFPAVLELLK
+GDSTLAGRTYAVIADEAHSSQTGSAAAKLKRVLTPDEQADLEDGGEADTESILAAEVAAT
+GRPQNISFFAFTATPKDKTLQMFGRPSGEYDEKGQEIPASFHRYTMQQAIEEEFILDVLK
+NFTNYDTAFKLALAGQKGEFRPEGDRAAVGKQTTEVDQTEASKKLMRWVKLHPTNIAQKV
+KIIVEHFRANVAGLLDGQAKAMVVTDSRAAAVRYKRQMDQYIQDMGYTDVDTLVAFSGEI
+TDDEFGLEKVTERSMNPSVTGDLAKAFDGDGYQVMIVANKYQTGFDQPKLCALYVDKKLS
+GVLAVQTLSRLNRAAPGKDTTYVLDFVNSEDDIQAAFEPYYAGAKLETVTDPNLIHDLGT
+KLDAAGVYNGDEVDVFADVWVAWKPGSGQEGLQAALEPVAYRFRKELAHARMNQDETRVN
+ELVLVRKDMRSFVSLYDFLSQIYEFGDTEHYKRALFLRHLVQLVGDQPGGEELIDLSDVQ
+LVSIRQKKTSSGEIGLTGGAALKGTTAVGGGQVREKQRGPLEEVIEKINEIFAGEGVDAS
+PSQQEAWVSALVAPLMEDEKLLGQAGANSLEQFLASPNLERSAMGAVYANEDAFVKMTDI
+VGRGGDPSKMIVAAIGEYLYWKVRSEGAGPVDVAHGRSAVFVDETAPSQGTSVDERASAT
+PSRVRKGN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001962.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001962.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ef7637c47306d09d2bec1d2df73a68c90786c79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001962.fa
@@ -0,0 +1,14 @@
+>1_1598
+MARIVEVMTRETAKIDALIAKAERFIELAQERRAALITAAVTGQIEIPTED
+>2_881
+MAGLNQRIISVLALPKPSLKEQREIAEHLDRETAKIDALISKAERFIELAQERRAALITA
+AVTGQIEIPTED
+>3_821
+MCSRYLGYLVLSSFFLEQVNASTYGTKMPRANWDFIKTIEVWAPDFDTQRCIADYLDRET
+ATIDALIAKQVELMNRLRERRQAVIDRAFVSTSEIVILRRHLVLNDSGAWGEDPTGADDV
+AVLRSTEQTVDGYWAISDPALRTLSQTERQNTRLREGDLIVTKTSGSFKHVGKTTLVDNE
+VAEGGYGFGNFMQRLRLKSTMIPKFLWWFMRTDQARSWINLVATTSTGLMNLNGSTLGRM
+EVPLPSLVEQREIADHLDRETAKIDALIAKAERFIELAQERRAALITAAVTGQIEIPTED
+>4_1819
+MAGLNQRIISVLALPKPSLKEQREIAEHLDRETAKIDALIAKAERFIELAQERRAALITA
+AVTGQIETTSELHRRW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001969.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001969.fa
new file mode 100644
index 0000000000000000000000000000000000000000..baaf36381bf9b4b50573c2b4430e221d588b439c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001969.fa
@@ -0,0 +1,16 @@
+>1_1656
+MSAEQPIGHDMDRTSQEVLDAGMAVRREVLGDAHVDRAEARKDATTEDFQNLITRYAWGT
+IWTRPGLDRRMRSAVTISAMVAGGYWDECAMHPRAALRNGLTREEIQEILLQTAVYASVP
+AANIAFKLAQEDADLAEGRPL
+>2_827
+MSGGRTEHAGGADAGQTPLGHQMERTSQEILDAGMAVRREVLGDAHVDRAEATKDATTDD
+FQNLISRYAWGTIWTRPGLDRRMRSAVTITAMVSGGYWEECAMHLRAALRNGLSRDEIKE
+ILLQAAIYSSVPAANVAFKLAQEVFAQVDEDLAAGRPL
+>3_761
+MGEQPIGHDMDRTSREVHDAGMAVRREALEDAHVDRAEANKDAATEDFQNLITRYAWGTV
+WTRPGLDRRMRSAVTITAMVAGGYWDECAMHLRAALRNGLSREEVQEILLQTAVYCSVPA
+ANIAFTLAQRVFAEVDADLAAGRPL
+>4_1874
+MSAEQPIGHDMDRTSQEVLDAGRAVRREVLGDAHVDRAEARKDATTEDFQNLITRYAWGT
+IWTRPGLDRRMRSAVTISAMVAGGYWDECAMHPRAALRNGLTREEIQEILLQTAVYASVP
+AANIAFKLAQEDADLAEGRPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001973.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001973.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b680d6354e0d9aa4f530010d4c884988b20a76be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001973.fa
@@ -0,0 +1,12 @@
+>1_1807
+MRTADAETQRKILNRLKRARGQLDAVIREVEGEGRCKDVVTQLSAVSTALDRAGFAIVSA
+AMQYCLADPEKAEDEEKLTVAELEKLFMTLA
+>2_599
+MRSADPETQRKILNRLKRARGQLDAVIREVEGEGSCRDVVTQLSAVSTALDRAGFAIVSS
+AMKNCVADPERAREDESLTVEELEKLFLSLA
+>3_524
+MRTADAETQRKILNRLKRARGQLDAVIREVEGEGSCRDVVTQLSAVSTALDRAGFAIVSS
+AMKNCVADPEKAREDEGLTVEELEKLFLSLA
+>4_2027
+MIPLPATVTKEVAVRTADAETQRKILNRLKRARGQLDAVIREVEGEGRCKDVVTQLSAVS
+TALDRAGFAVVSSAMQYCLADPEKAEDEEKLTVAELEKLFMTLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001975.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001975.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8bc9a360ce797e8cb74f6f5451e9cb97f79f170f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001975.fa
@@ -0,0 +1,19 @@
+>1_1900
+MSPLMTVGEFALATGLSAKALRFYDERGLLAPADVDAHSGYRCYAPGQIRTAAQIRVLRA
+AGLTVDDVRSVLADPASLPARLETHAAELRRRRDLEDRALALAVAGVYAAPDPDDDGGPA
+RPGPVAERTVGPTPWAGVVQRVALDEAGEESTTERANAAFVTLFQALAEAGSAPAGPLWT
+ALRPVPGAADVVETVLAVPLSGPAPAGLRVDGHEVVAGTLPRRVERYVDVRADTGEVDLL
+DDAPGGALPHPDLLGLMDAFDMEDAGAAPEIRQILADPEAGHIELAVTVREEAGAGQG
+>2_1299
+MAVEEQRLALPVDGELPEGFAVQGLRIASGVLPRREEAAVTVRVLD
+>3_419
+MSPLMTVGEFALATGLSAKALRFYDERGLLAPADVDAHSGYRRYEPGQIRTAAQIRVLRA
+AGLTVDDVRSVLADPASLPARLEAHAAEVRRRRDLEDRALALAAAGVYAAPDPDDDGGPA
+RPGPVAERTVGPTPWAGVVQRVALDEAGEEATTERANAAFATLFQALAEAGSAPAGPPWT
+ALRPVPSAADVVETVLAVPLSGPAPAGLRVDGHEVVTGTLPRRVERYVDVRADAGEVDLL
+DDAPGGALPHPGLLGLMDAFDVEDAGTAPEIRQILADPEAGHVELAVTVREEAGAGQG
+>4_2120
+MSPLMTVGEFALATGLSAKAHAAELRRRRDLEDRALALAVAGVYAAPDPDDDGGPARPGP
+VAERTVGPTPWAGVVQRVALDEAGEESTTERANAAFATLFQALAEAGSAPAGPLWTALRP
+VPGAADVVETVLAVPLSGPAPAGLRVDGHEVVAGTLPRRVERYVDVRADTGEVDLLDDAP
+GGALPHPDLLGLMDAFDMEDAGAAPEIRQILADPEAGHIELAVTVREEAGAGQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001976.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001976.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e6164005b30f5de40ac6fcb19575f4641d7fda72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001976.fa
@@ -0,0 +1,36 @@
+>2_186
+MTASRLIPPAVDPASLPRDLPGLRAHFRPVVEEIARGALERDRARLLPFEAVRALGCAGF
+SVLRVPREAGGPDVDVRTVTALLVDLAAADSNVAHLYRSHLGFLDALRFQPQPVRDRWHA
+LVLAGATVGNASTERGGNALGTLNTRLTAPAGGDDDGAPGAAWTLTGTKYYATGSIFSSH
+TRVSAAVVRADGSLAPGRGFAVVPVDAPGVCLEDDWDGFGQRLTGTGTAVFEDVAVDPRD
+VLERIPGSPEAVHEAAWFQLILLAVLAGIARAARDDAAARVAARVRTFNTGLGVPFREDP
+LIQEAVGRIAAKASAAEAVVLAAADALDASLAAGAATGADRWGFTGPVPPAFAEAELAVE
+HAQITVPELALGAAQELFLTGGASDTSVAKGLDRHWRNAQTVATHNPIAFRARAVGDYWI
+NGTLPEGLNAIGDAPAAPSSSAVDAAQPAPEPAEAGAR
+>3_138
+MPLTDPTDAPTPLGTVPPLVRPADLPRDLAGLRRHFAPVFARVAEGSRERDRRRILPFAE
+VRALNEAGFATLRVPAEAGGPGVDVRTAVALLIDLAEADANVAHLYRSHLGFLDSLRFQP
+AAVRERWHARILAGATVGNASTEKGGNALGTLNTVLTPPAAGDGPWTLTGTKFYATGSIF
+SSHTRVSAAQTDADGHPAPGRRFAVVPVEAPGVRLDDDWDGFGQRLTGTGTAVFDGVAVP
+PQDVLDRVPGSAEAVYEAAWFQLILLAVLAGIARAARRDAADAVAARVRTFNTGLGLPFR
+EDPLIQEAVGRIAAKAFTAEAAVLSAADALDAALADHDAGRTGSGAPEEVPASFTWAELA
+VEHAQVTVPELALGAAQELFLTGGASATSTAKGLDRHWRNAQTVATHNPIAFRARAIGDY
+WINGTVPEGLNAIGDAPAASAPLGDAPAPGEAAR
+>3_580
+MTTPVLDRPAPTSAADAPDTAELRARFAPVFARIAANEARRRDAAVPPHAAVRLLAETGF
+TALRLPRERGGSDATLTQLLDLLVDLAAADANLPQALHGHFMFTEQVARDVHPRLTDWWL
+DEVAAGKVFANALVDPPAATGLPGVTARRDPRDPEAFLLTGTKQYSTGTLLADWTLVAAH
+DDAGALQPLVVEVAGPGVEARDDWDGIGQRGTASGTTVYTDAPAPAWRRVDLERPAAAPG
+YPFLWLILAATQAGIAQRALDDFAEILRRRSRSYQHAASASPAHDPVLQHQLGAAAAQVR
+ALRSVVLGAVPALEAAYTAAAGAAPAIGAAATESPDDGAAEAFEAAHTEAWVAAASASSV
+AADLTLRLTSDLFETAGASAVVAGPGLDRHWRNARVLASHTPLPHRRRQIGECLLHGTPA
+PHSADAVETASSTDADPSRDSVSPSPSTPAATKEQ
+>4_191
+MPLTDPTDASAPPAATPVPLGAVPPLERPADLPRDLAGLRRHFAPVFARIAEGSRERDRR
+RILPFEEVRALNEAGFATLRVPAEAGGPGVDVRTAVALLIDLAEADANVAHLYRSHLGFL
+DSLRFQPEAVRERWHARILAGATVGNASTEKGGNALGTLNTVLTPAPAGDGPWTLTGTKF
+YATGSIFSSHTRVSAAQTDADGRPAPGRRFAVVPVEAPGVRLDDDWDGFGQRLTGTGTAV
+FDGVAVPPQDVLDRAPGSAEAVYEAAWFQLILLAVLAGIARAARRDAADAVAVRVRTFNT
+GLGLPFREDPLIQEAVGRIAAKAFTAEAAVLSAADALDAALADHEAGRTGSGAPEEVPAS
+FTWAELAVEHAQVTVPELALGAAQELFLTGGASATSTAKGLDRHWRNAQTVATHNPIAFR
+ARAIGDFWINGTVPEGLNAIGDAPAASAPLGADAPASGEAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001977.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001977.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fc3f0394513a154c3678f149549fa0987e187926
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001977.fa
@@ -0,0 +1,13 @@
+>2_694
+MSAAFDHIRRDDGEHVGYLEMTDDGLFVPRDRLRRVCGDPMELEEAEELLDAVGLRVLAE
+DWLLDAADGGAARRVRIREITWDTVTVAPVLDDAAVALSVDLARAEVLTLPTDRLRPADG
+>3_404
+MAGQDAGSLARRRGYADRMTDFDHLRAEDREHVGYIEMTDDGAFVPYDLLRRRRGEPGGL
+EEAEAVLDEIGLRLLAEDWILDADGDEPLCVRILEVTRDAVVVAPALDSAAVAKSLDLTA
+TVRLPLPTARLRQA
+>3_680
+MTTIFDHLRADDREHVGYIEMTDDGLFIPYDLLRRRCGEPMELAEAEELLDTVGLQALGE
+QWLLRTEGDAWVPVDIREFSRESVTVAPRLDDRAVAKALDLTATVMLSLPTDRLRSAE
+>3_703
+MTTVLDHLRADDREHVGYIEMTDDGLFIPYDLLRRRCGEPMELAEAEELLDTVGLQALGE
+QWLLRTEGDAWVPVGIQEFSRESVTVAPRLDDRAVAKALDLTATVMLSLPTDRLRSAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001981.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001981.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f65268f9ee3f94767822e1712ca6e5411871b724
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001981.fa
@@ -0,0 +1,24 @@
+>2_2286
+MTDFKWRHFQGDVILWAVRWYCRYPISYRDLEEMLAERGISVDHTTIYRWVQCYAPEMEK
+RLRWFWRRGFDPSWRLDETYVKVRGKWTYLYRAVDKRGDTIDFYLSPTRSAKAAKRFLGK
+ALRGLKHWEKPATLNTDKAPSYGAAITELKREGKLDRETAHRQVKYLNNVIEADHGKLKI
+LIKPVRGFKSIPTAYATIKGFEVMRALRKGQARPWCLQPGIRGEVRLVERAFGIGPSALT
+EAMGMLNHHFAAAA
+>2_2291
+MTDFKWRHFQGDVILWAVRWYCRYPISYRDLEEMLAERGISVDHTTIYRWVQCYAPEMEK
+RLRWFWRRGFDPSWRLDETYVKVRGKWTYLYRAVDKRGDTIDFYLSPTRSAKAAKRFLGK
+ALRGLKHWEKPATLNTDKAPSYGAAITELKREGKLDRETAHRQVKYLNNVIEADHGKLKI
+LIKPVRGFKSIPTAYATIKGFEVMRALRKGQARPWCLQPGIRGEVRLVERAFGIGPSALT
+EAMGMLNHHFAAAA
+>2_2581
+MTDFKWRHFQGDVILWAVRWYCRYPISYRDLEEMLAERGISVDHTTIYRWVQCYAPEMEK
+RLRWFWRRGFDPSWRLDETYVKVRGKWTYLYRAVDKRGDTIDFYLSPTRSAKAAKRFLGK
+ALRGLKHWEKPATLNTDKAPSYGAAITELKREGKLDRETAHRQVKYLNNVIEADHGKLKI
+LIKPVRGFKSIPTAYATIKGFEVMRALRKGQARPWCLQPGIRGEVRLVERAFGIGPSALT
+EAMGMLNHHFAAAA
+>2_2592
+MTDFKWRHFQGDVILWAVRWYCRYPISYRDLEEMLAERGISVDHTTIYRWVQCYAPEMEK
+RLRWFWRRGFDPSWRLDETYVKVRGKWTYLYRAVDKRGDTIDFYLSPTRSAKAAKRFLGK
+ALRGLKHWEKPATLNTDKAPSYGAAITELKREGKLDRETAHRQVKYLNNVIEADHGKLKI
+LIKPVRGFKSIPTAYATIKGFEVMRALRKGQARPWCLQPGIRGEVRLVERAFGIGPSALT
+EAMGMLNHHFAAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001982.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001982.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1481730b4f4901a0dc703562bc014e1b422400fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001982.fa
@@ -0,0 +1,25 @@
+>3_296
+MDRCNRARAMGSRAAQSGRRRCHDDDGAMGALVRVHAAQSCSRSRVHPASGSRRRNPHHP
+PSRTSAAVPDTATPVPCPAPPRLHRPRPRAGPDPRAHHLTRVTTDRTGVADTPRHDRCRT
+PEGHARRGMGGLVQDHRFSTACTPCADAAGEVEQAPSMTIAARHQACRYTSTARSATEHR
+SGETSTELAARLLAEAPQRDWRLRDLAALVHLSASQLGRAFTQRFGMPPMRYLAHIRAHR
+LAELLVETDLPIGVAMTKVGWRSRGHAARQFTDVVGISPSEYRRTAIGRTLTETSPWPSA
+TQGSPVAPGRESLEKSPP
+>3_392
+MPTTFSDQRKLSVVLFEGFELLDVFGPVQLFGSLPDVAIEYVGPHTGPVISSKGARVVAD
+LAYEDLARPDILMVPGGQGTRTLVDDAGFLAWLGQAGSRADLVASVCTGSALLAAAGLLE
+GYSATSNKRAFTWASGFGDDVDWRPRARWVHDRDRWTSSGVAAGMDMATGMIADLYDADT
+ARAVTLRAEYEPHTDSTRDPFADVYRLG
+>3_638
+MRHVVTIACPGTALFDVGIPSRVFGAARTANDEPAYDVTIASPTGAGPLLTKDGVSVDLP
+GVDQIKETDTVVVASSDALLDPLVRRDMASALAPFLLQGQAVRPGVRVAAVCSGAFLLGE
+LGLLDHRTATTHWRLADQLAKLFPSTHLQTESLYIEDDGVLTSGGVAAGIDLCLHMIRQD
+YGVRIANDVARSCVVAPFREGGQAQYVQTPVPRSADPSMNDLVHWLLETLDQRHTLEDIA
+HRGHMSTRTFERRFRREHGTSPGQWLTAARIQRAKELLESTDLPVERIAELVGLGTASNL
+RTHFTRCVGRTPQAYRRSFTAGSNSTNVSGQYS
+>3_1736
+MDRCHRARAMGSCAAQSRRRRCHDDDRAMGALVHLHVAQSCSRSRVHPTSGRRRRNHHHP
+PPRTPATAPGAATPVPRPGPPRLHRSRTWARPDPRTHHHTRLSTGGTGVADTPGRERCRT
+AERLARRGMGGLVQDHGLLATAPPHAVVLRKAAAMSTEPSWRVCPDETTPSHACPTETAA
+HHAARLLAQDPGRDWRLRDLADLVHLSTSQLGRAFSQRFGMPPIQYLAHVRAHRLAELLI
+ETDLPIGVAMAQVGWRSRGHAARQFTAIVGVSPSAYRRTATQRASLRCPCCGQRNELPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001986.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001986.fa
new file mode 100644
index 0000000000000000000000000000000000000000..50b8dedd695ce20e25e7128512c784375b033455
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001986.fa
@@ -0,0 +1,15 @@
+>0_10
+MSTTLTLFGHSAVRLEKAGRRLAFDPGAFSDAAVLDGADAVLVTHGHPDHVVPEQLARAV
+AGTEAHVWAPRDLTGPLAEAGLDAGHVHTAVPGETFEAAGFRVEVLGGEHAVIHAEVPRP
+VNVSYLVDGAVLHPGDSFTVPDADVEVLLLPAAAPWLRIADVVDQMRAIAATHTRPIHDG
+ILSEDGKGVVDGVLSGLAEGVTDYRRLAPGEPWTF
+>1_1979
+MSTTLTLFGHSAVRLEKAGRRLAFDPGAFSDAAVLDGADAVLVTHGHPDHVVPEQLARAL
+AGTEAHVWAPRDLTGPLAEAGLAAGRVHTAVPGETFEAAGFRVEVLGGEHAVIHAEVPRP
+VNVSYLVDGAVLHPGDSFTVPDADVEVLLLPAAAPWLRIADVVDQMRAIAATHTRPIHDG
+ILSEDGKGVVDRVLSGLAEGVTDYRRLAPGELWTF
+>4_10
+MSTTLTLFGHSAVRLEKAGRRLAFDPGAFSDAAVLDGADAVLVTHGHPDHVVPEQLARAV
+AGTEAHVWAPRDLTGPLAEAGLDAGHVHTAVPGETFEAAGFRVEVLGGEHAVIHAEVPRP
+VNVSYLVDGAVLHPGDSFTVPDADVEVLLLPAAAPWLRIADVVDQMRAIAATHTRPIHDG
+ILSEDGKGVVDGVLSGLAEGVTDYRRLAPGEAWTF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001988.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001988.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0f8731224947a841eb2c6b9f639f178d9613c61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001988.fa
@@ -0,0 +1,21 @@
+>0_24
+MSSTSPDGPPRRRTGIGRIVFSVIAVLTVLAASAFSIRSASGGNDIRTNLTLIAPAAAGG
+GWDSFQRELQQTMRVNGLVNNVQVVNIPGAGGTIALGQLTTLEDANNLMVGGTGQIAAHA
+ARGTGPELSQVTAVSRVVEEYSLVVVPADSPYQSMDDLVTAWRADPAHVAWTGGGSFDQL
+VMADIARTADVPVADTTYIPSDGGGEAIQALLNGTAQASAGGFADIYPQVEAGRLRALGV
+VAAEPLAGVEEIPTLRSQGYDVTLTNWRALFAPPGISAEERTELEALIAEAVDTPEWKEA
+VQRNYWNPVPLSGTELEEFIAAEKERIGTLTEEIK
+>1_1993
+MSSTSPDGPPRRRTGIGRIVFSVIAVLTVLAASAFSIRSASGGNDIRTNLTLIAPAAAGG
+GWDSFQRELQQAMRVNGLVNNVQVVNIPGAGGNIALGQLTTLEDANNLMVGGTGQIAAHA
+ARGTGPELSQVTAVSRVVEEYSLVVVPADSPYQTMDDLVTAWRVDPAHVAWTGGGSFDQL
+VMADIARTAGVPVADTTYIPSDGGGEAIQALLNGTAQASAGGFADIYPQVEAGRLRALGV
+VAAEPLAGVEEIPTLRSQGYDVTLTNWRALFAPPGISAEERTELEALIAEAVDTPEWKEA
+VQRNYWNPVPLSGTELEEFIAAEKERIGTLTEEVK
+>4_24
+MPSTSPDGPPRRRTGIGRIVFSVIAVLTVLAASAFSIRSASGGNDIRTNLTLIAPAAAGG
+GWDSFQRELQQTMRVNGLVNNVQVVNIPGAGGNIALGQLTTLEDANNLMVGGTGQIAAHA
+ARGTGPELSQVTAVSRVVEEYSLVVVPADSPYQSMDDLVTAWRADPAHVAWTGGGSFDQL
+VMADIARTADVPVADTTYIPSDGGGEAIQALLNGTAQASAGGFADIYPQVEAGRLRALGV
+VAAEPLAGVEEIPTLRSQGYDVTLTNWRALFVPPGVSAEERTELEALIAEAVDTPEWKEA
+VQRNYWNPVPLSGAELEEFIAAEKERIGTLTEEIK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001992.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001992.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c16c2eb03503ad9bf6cccaf7845385eb818b10c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001992.fa
@@ -0,0 +1,39 @@
+>0_116
+MPQGIFVSTTSTGAGKSLVSLGLADSLYRRSGTVGYFRPVVPGDDVETDPMVLLMREQYG
+LSPEQARGGLTAAEARTLMAEGRGDEVQQRCVEQYDAMRAAGGVVVVEGTDLISPDPAAD
+LDLNAQLARNLGTPVVAVVSGADLTPEQAADVVDLARRTLDDAGVELLAVMVNRADPRDL
+DAVGAAVRPGRHAWPVYVLPELTELAHPSVAEVADALGLEQMAGQETLDRDVAEVKAVSM
+EGGNFLEVLREGALVIVSGDRSDAILATVASSLTPDFPTPSGMILTNGILPNRQLQRLYL
+GAAFPVFVTHDDTFTTAAKVSRVRSELSSAQPRKTAAALGTWHQRVDGDELLARFDLPRT
+DVVTPLRFLHELISRARADRRRIVLPEGEDARVLRAAEILQRRDVCDLVVLGPAAAVREL
+ASREGVDLSGIELVDPADSPDLERYAQEYARLRAHKGVDAERAREVMQEGAYFGTMMVHL
+GDVDGMVSGAAHTTANTIRPALEFVKTKPGVSIVSSVFFMLLPDRALVYGDCAVNPDPDA
+QQLADIAVASAATAAQFGVDPRVAMLSYSTGASGSGQSVDKVRAATELVRERAPELKVEG
+PLQYDAAVNASVAASKMPGSEVAGQATVFVFPDLNTGNNTYKAVQQSSGAVAVGPVLQGL
+NKPVNDLSRGTTVEDIVNTVAITAIQAQAQG
+>3_185
+MPQGILVTTTTAGAGKSLVSLGLADSLYRRSGTVGYFRPVVPGDDVEADPMVLLMREQFG
+LTAEQARGGITAAEARSLMAEGRGDELQERCVEVYDRMARECGVVVVEGTDLTGADAAAD
+LELNAGLALNLSTPVVAVVSGAGLGAQEAADAVDLTRHALAEAGADLLAVMVNRADAGRL
+DEIAEAIRPGRRSWPVYVLPELPELAHPSVAEVAAALDLEQVAGRPTQDRDVTEVKAVSM
+EGGNFLEVLREGALVIVSGDRSDAILATLASSLTPDFPTPSGMILTNGILPNAQLQRLYQ
+DAAFPVLATDDDTFGTAADVSRVRSELSSAQPRKTAAALGTWHQRVDGDELLQRIDLPRT
+DVVTPLRFLHDLIERARADRRTVVLPEGEDARVLRAAEILQRRDVCDLVVLGGEAEVREL
+ASREGVDLTGITLVDPATSEDRERYAAEYRRLRSHKGVDLERAREVMLEGAYYGTMMVHL
+GDADGMVSGAAHTTANTIRPALEFVKTKPGVSIVSSVFFMLLPDRALVYGDCAVNPDPDA
+RQLADIAAASAETAAQFGVDPRVAMLSYSTGASGSGDAVDKVRAATELVRAAHPELKVEG
+PLQYDAAVNASVAASKMPGSEVAGQATVFVFPDLNTGNNTYKAVQQSSGAVAVGPVLQGL
+NRPVNDLSRGTTVEDIVNTVAITVIQAQTGSPQPTPKDAP
+>4_124
+MPQGIFVSTTSTGAGKSLVSLGLADSLYRRSGTVGYFRPVVPGDDVETDPMVLLMREQYG
+LSPEQARGGLTAAEARTLMAEGRGDEVQQRCVEQYDAMRAAGGVVVVEGTDLISPDPAAD
+LDLNAQLARNLGTPVVAVVSGADLTPEQAADVVDLARRTLDDAGVELLAVMVNRADPRDL
+DAVGAAVRPGRHAWPVYVLPELTELAHPSVAEVADALGLEQMAGQETLDRDVAEVKAVSM
+EGGNFLEVLREGALVIVSGDRSDAILATVASSLTPDFPTPSGMILTNGILPNRQLQRLYL
+GAAFPVFVTHDDTFTTAAKVSRVRSELSSAQPRKTAAALGTWHQRVDGDELLARFDLPRT
+DVVTPLRFLHELISRARADRRRIVLPEGEDARVLRAAEILQRRDVCDLVVLGPAAAVREL
+ASREGVDLTGIELVDPADSPDLERYAQEYARLRVHKGVDAERAREVMQEGAYFGTMMVHL
+GDVDGMVSGAAHTTANTIRPALEFVKTKPGVSIVSSVFFMLLPDRALVYGDCAVNPDPDA
+QQLADIAVASAATAAQFGVDPRVAMLSYSTGASGSGQSVDKVRAATELVRERAPELKVEG
+PLQYDAAVNASVAASKMPGSEVAGQATVFVFPDLNTGNNTYKAVQQSSGAVAVGPVLQGL
+NKPVNDLSRGTTVEDIVNTVAITAIQAQAQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001993.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001993.fa
new file mode 100644
index 0000000000000000000000000000000000000000..39a254257fb9a75777edc399aa8c28143862227f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001993.fa
@@ -0,0 +1,20 @@
+>0_158
+MEYTKKWLPLEAQVERLVQRGLEVDDLTRALRLLESVGYYRVTGYLYPFLESEKQVDDQG
+HTKIRVLNRYQPGTALHHAEEIIDFDRQLRMLVMEGVERIEVAVRMRIGYVLGRTSPFAH
+ENPTCFDDSFTRANTDSRDPRPSKQVLWLERVKQRRDGSDEQFVAHFRQKYDDHMPVWAL
+TELLELGHLSNLYQGMLQKDAEEVATAFGIPQKKMMGSWLASLNYVRNVAAHHARLFNRK
+LQNAPSRPAAGMVPLLDHLREPAAPKGDFGTYNALAIIAYMLRPIEAERSWAPRLAELFR
+TFPTSHALSVQSMGVPEDWHTLDLWRG
+>1_337
+MGYYRVTGYLYPFLESEKQVDDQGHTKIRVLNRYQPGTALHHAEEIIDFDRQLRMLVMEG
+VERIEVAVRMRIGYVLGRTSPFAHENPTCFDDSFTRANTDSRDPRPSKQVLWLERVKQRR
+DGSDEQFVAHFRQKYDDHMPVWALTELLELGHLSNLYQGMLQKDAEEVATAFGIPQKKMM
+GSWLASLNYVRNVAAHHARLFNRKLQNAPSRPAAGMVPLLDHLREPAAPKGDFGTYNALA
+IIAYMLRPIEAERSWAPRLAELFRTFPTSHALSVQSMGVPEDWHTLDLWRG
+>1_1973
+MRYSKPHLPYDQQVRLLASRGLNVGREGDAVRALKRIGYYRLSAYTYPMRAFTTDDAGTV
+HRSDDFVEGACLSDAVALHDFDHRLRRTLLPAIQSLEIALRTKVGYHLGKHGPLAHLDRS
+GLDPQRCDAVSRGPDHTGTKYDTWRSEYDSLQRKAGREDYMVHFATKYDGDVPVWAATEF
+MTMGCLIGLYRMMQPKDARRIAEEVGVKNPQVLFGWLKALNVLRNHCAHNARIWNRSTVY
+PPDKINRRMVEEELHHLVSADTNKVYFLTAVLAYLLRHVDPDSRFASDLRTTMGKFPSVL
+GWTPGHTMGFVDGWSTEALWSIH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002009.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002009.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b400a613739e14152ad0a0251b28c0057d7805a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002009.fa
@@ -0,0 +1,15 @@
+>0_505
+MLIVCTGNVCRSAYASRALQGRLAALVPGRVEVGSAGSQPNQALTVPPPLVRLGAEAGVA
+GLADHRPAALQPFMVAEADLVLAAAQEHMRFALREVPQAVARVFTVLELAALVRILDARN
+GRDWIPAGRGVRAFAAEAAHHRALARSSAQPLDVVDPFRGPVEGYAEMIRIMDPALETIA
+DALARAVTPTP
+>1_235
+MLIVCTGNVCRSAYASRALQGRLAALVPGRVEVGSAGSQPNQALTVPPPLVRLGAEAGVT
+GLEGHRPAALQPFMVAEADLVLAAAQEHMRFALQEVPQAVARVFTVLELAALVRAMDQRD
+GRDWIPAGRGVRAFAAEAARHRALARSTAQPLDVVDPFRGPVEGYAEMIQIMDPALETIA
+DALARAVTPTP
+>4_505
+MLIVCTGNVCRSAYASRALQGRLAVLAPGRVEVGSAGSQPNQALTVPPPLVRLGAEAGVT
+GLEGHRPAALQPFMVAEADLVLAAAQEHMRFALQEVPQAVARVFTVLELAALVRAMDQRD
+GRDWIPAGRGVRAFAAEAARHRALARSTAQPLDVVDPFRGPVEGYAEMIQIMDPALETIA
+DALARAVSLAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002014.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002014.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f4041704d3eedfe0cb8a7c1f6a437fefe06e5061
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002014.fa
@@ -0,0 +1,11 @@
+>0_588
+MTMIKEPGVSPTAGLGPAAALFHGFSDPTRLAILRHLATGEHKVRELTEHLGLAQSTVSA
+HLACLTGCGLVSSRPVGRASLYSLAAEPELLEVLAAAERLLTVTGHAVELCPHSGPAATG
+ALPHDAGH
+>1_1723
+MSPAAGLGPAAALFHGFSDPTRLAILRHLATGEHKVRELTEHLGLAQSTVSAHLACLAGC
+GLVASRPVGRASLYALAAEPELLQVLAAAERLLTVTGHAVELCPHSGTPGPDGPAAA
+>3_686
+MIQEKGATLDEVATVAYAHLFQAFAEPTRLAIVQHLASGEHRVRDLVEHMGLAQSTVSKH
+VGFLVECGLATMRPEGRSTWYSLAQSELLRTLIAAAERLLDATGTQALLCTHLRLPHTHH
+ASDTDKK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002022.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002022.fa
new file mode 100644
index 0000000000000000000000000000000000000000..085de751eb8439d5e0326aa95725c0804efff7a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002022.fa
@@ -0,0 +1,9 @@
+>0_911
+MTATTHILLRAEGFSCPSCVRKIEKALDALPGVTGAQVHFETQRIEVDHDPQTTTAQDLV
+EAVAKVGYTARPSAF
+>1_639
+MTPTTRTLLRAEGFSCPSCVRKIEKALDALPGVTGAQVHFETQRIEVDHDPQTTTAQDLV
+EAVAKVGYTARPSAF
+>2_1950
+MTATTHTLLRAEGFSCPSCVRKIEKAVDALPGVTGSKVHFETQRIEVDHDAERTSVQDLV
+DAVDRVGYRARPSVF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002027.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002027.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb27ede1a4ba54d0835f4e240cd2236805360df5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002027.fa
@@ -0,0 +1,14 @@
+>0_1243
+MPLAIVAPIQSSRSRLRICAALTGLATSAVLLLSGFADAGPSADAGSDHSLVVEHNLDGL
+NAREIIKRLDSTKVTDRSSEFIASIEPDQLVLTDDQNNQTTVPMPEDEFYVSIAPYRSQT
+HECYFHSLTTCTGELANTDVHVTVVEATSGETLLDETLTTYDNGFVGVWLPRGIDATLTV
+SAEGRTAKKAISTRPDDPTCLTGLQLA
+>1_971
+MVEHNLDGLNAREIIKRLDSTKVTDRSSEFIASIEPDQLVLTDDQNNQTTVPMPEDEFYV
+SIAPYRSQTHECYFHSLTTCTGELANTDVHVTVVEATSGETLLDETLTTYDNGFVGVWLP
+RGIDATLTVSAEGRTAKKAISTRPDDPTCLTGLQLA
+>4_1200
+MPLAIVAPIQSSRSRLRICAALTGLATSAVLLLSGCADAGPSADAGSDHSLVVEHNLDGL
+NAREIIKRLDSTKVTDRSSEFIASIEPDQLVLTDDQNNQTTLPMPEDEFYVSIAPYRSQT
+HECYFHSLTTCTGELANTDVHVTVVEATSGETLLDETLTTYDNGFVGVWLPRGIDATLTV
+SAEGRTAKKAISTRPDDPTCLTGLQLV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002028.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002028.fa
new file mode 100644
index 0000000000000000000000000000000000000000..50351797a740eeec32fe5b58d32ecedb39ae9fab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002028.fa
@@ -0,0 +1,20 @@
+>0_1246
+MGAGAEAGAGPLFIPQCRDRPTLGPDGPRACLTMKPGEGRHPRRHGPGSRCSPTPPQAGR
+AGLSPMPSRWSTPSSTGTGASIPWRDLPEIYGPWLSRVDLARPHGRRGHVGHGAGNTDRR
+SGCRNRDRLVGLGGLHDRPRPSAREEHHPAHRGLDRTTRNPREEPADHGLGRSRSGLSTK
+THQLVDGAGREGVLLAGDRHPSARRWHQGRPPQPADQQGHRRRRGSAGGRPVGLDSEAYT
+GRNVIERQDAHLKQWPGLASRYDEYAIVYWAAVVLNAVLAWSTALSDTPEWRVRTDRRSR
+SSAREARRGSAPAGMSVRTWTERIPRNAHRETE
+>1_978
+MGAGAEAGAGPLFIPQCRDRPTLGPDGPRACLTMKPGEGRHPRRHGPGSRCSPTPPQAGR
+AGLSPMPSRWSTPSSTGTGASIPWRDLPEIYGPWLSRVDLARPHGRRGHVGHGAGNTDRR
+SGCRNRDRLVGLGGLHDRPRPSAREEHHPAHRGLDRTTRNPREEPADHGLGRSRSGLSTK
+THQLVDGAGREGVLLAGDRHPSARRWHQGRPPQPADQQGHRRRRGSAGGRPVGLDSEAYT
+GRNVIERQDAHLKQWPGLASRYDEYAIVYWAAVVLNAVLAWSTALSDTPEWRVRTDRRSR
+SSAREARRGSAPAGMSVRTWTERIPRNAHRETE
+>4_1203
+MKPGEGRHPRRHGPGSRCSPTPPQAGRAGLSPMPSRWSTPSSTGTGASIPWRDLPEIYGP
+WLSRVDLARPHGRRGHVGHGAGNTDRRSGCRNRDRLVGLGGLHDRPRPSAREEHHPAHRG
+LDRTTRNPREEPADHGLGRSRSGLSTKTHQLVDGAGREGVLLAGDRHPSARRWHQGRPPQ
+PADQQGHRRRRGSAGGRPVGLDSEAYTGRNVIERQDAHLKQWPGLASRYDEYAIVYWAAV
+VLNAVLAWSTALSDTPEWRVRTDRRSRSSAREARRGSAPAGMSVRTWTERIPRNAHRETE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002034.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002034.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f571066a64327810133f54106c7b4d18bc8a748
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002034.fa
@@ -0,0 +1,9 @@
+>0_1348
+MSEEQWDEAAFRASIPAAREKVEFAARFCEIGPSQPRWDSHRPVVELIFYLCKLDYDIKV
+LLLPS
+>1_1090
+MSEEQWDEAAFRASIPAAREKVEFAARFCEIGPSQPRWDSHRPVVELIFYLCKLDYDIKV
+LLLPS
+>4_1297
+MSEEQWDEAAFRASIPAAREKVEFAARFCEIGPSQPRWDSHRPVVELIFYLCKLDYDIKV
+LLLPS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002038.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002038.fa
new file mode 100644
index 0000000000000000000000000000000000000000..67977f8129d8ce2ad9a9f56ec917fc5388ce6f78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002038.fa
@@ -0,0 +1,8 @@
+>0_1561
+MRLVWDRSAWEDYTHWQTTDRKVLNRINTLIDAALRDPFEGIGKPEQLKYGAAGAWSRRI
+TEEHRLVYLVDGEDLIILQARYHY
+>1_1281
+MRLVWDRSAWEDYTHWQTTDRKVLTRVNTLIDAALRDPFEGIGKPEQLKYGAAGAWSRRI
+TEEHRLVYLVDGEDLIILQARYHY
+>3_1164
+MTRKPSGPFGPPLAPASAAAIARRAAGAWSRRITAEHRLVYLVDGEDLIILQARYHY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002044.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002044.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d0b22aebae702491552cc52382cff92e46e8c981
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002044.fa
@@ -0,0 +1,21 @@
+>0_1837
+MTIRAGIVGYGNLGRSVEKLVKLQPDMELVGIFSRRTGLDTDTPVLPAERAAEHAGEIDV
+LFLCLGSATDIPEQAAGYARHFTTVDTYDNHQLIPRHRAEMDAAAREGGHVAMISTGWDP
+GLFSVNRVLGAALFPQPQQNTFWGKGLSQGHSDAVRRVPGVRRGVQYTIPSEEAIAEARA
+GRGAEITGASAHVRECYVVADEADHAAITEAITTMPDYFAPYETTVHFISEEEFERDHQG
+MPHGGHVVTSGDLGGSRSAVEFVLELESNPDFTAAAQVAYGRAAARLKAQGETGARTVLE
+VAPYLLSPTGLDELIRRDV
+>1_1544
+MTIRAGIVGYGNLGRSVEKLVKLQPDMELVGIFSRRTGLDTDTPVLPAERAAEHAGEIDV
+LFLCLGSATDIPEQAAGYARHFTTVDTYDNHQLIPRHRSEMDAAAREGGHVAMISTGWDP
+GLFSVNRVLGAALFPQPQQNTFWGKGLSQGHSDAVRRVPGVRRGVQYTIPSEEAIAEARA
+GRGAEITGASAHVRECYVVADEADHAAITEAITTMPDYFAPYETTVHFISEEEFERDHQG
+MPHGGHVVTSGDLGGSRSAVEFVLELESNPDFTAAAQVAYGRAAARLKAQGETGARTVLE
+VAPYLLSPTGLDELIRRDV
+>4_1758
+MTIRAGIVGYGNLGRSVEKLVKLQPDMELVGIFSRRTGLDTDTPVLPAERAAEHAGEIDV
+LFLCLGSATDIPEQAAGYARHFTTVDTYDNHQLIPRHRAEMDAAAREGGHVAMISTGWDP
+GLFSVNRVLGAALFPQPQQNTFWGKGLSQGHSDAVRRVPGVRRGVQYTIPSEEAIAEARA
+GRGAEITGASAHVRECYVVADEADHAAITEAITTMPDYFAPYETTVHFISEEEFERDHQG
+MPHGGHVVTSGDLGGSRSAVEFVLELESNPDFTAAAQVAYGRAAARLKAQGETGARTVLE
+VAPYLLSPTGLDELIRRDV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002047.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002047.fa
new file mode 100644
index 0000000000000000000000000000000000000000..102d96ba5e3f85d7baf888ee090e81318b34f7d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002047.fa
@@ -0,0 +1,9 @@
+>0_1902
+MTTAVRTCAASACAFNAETSCSALAITVAGSDRTPGCGTFVQLDVRRPVTEGASTVGACH
+RLECTYNADLACTAEGIEVTDVATCATYTID
+>1_1606
+MTTAVRTCAASACAFNAETSCNALAITVAGSDRTPGCGTFVQLDVRRPVTEGASTVGACH
+RLECTYNVDLACTAEGIEVTDVATCATYTID
+>4_1829
+MTTAVRTCAASACAFNAETSCNALAITVAGSDRTPGCGTFVQLDVRRPVTEGASTVGACH
+RLECTYNADLACTAEGIEVTDVATCATYTID
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002051.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002051.fa
new file mode 100644
index 0000000000000000000000000000000000000000..23e496a59e12f5d3bc47d6a9740ebcff8b232dd7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002051.fa
@@ -0,0 +1,30 @@
+>0_1981
+MTPTTSTPATFHDTRVDQQFIAGQWRDGASGDRASDINPYTDDVVAEFALATAEDLDEAY
+RAAAAAQEEWAAMPPKDRAAVLRRAAEILEERRDEVIDWLVKEAGSTRIKADSEVSLAIA
+ITQEAASFPTRVHGKIFDSNTPNRETRVYRKPIGVVGVISPWNFPLHLSQRSVAPALALG
+NAVVLKPASDTAVTGGTLIARVFEEAGLPAGVLSVVVGSGSEIGDAFVTHPVPRLISFTG
+STVVGKQVAANAVTGDTIKKVALELGGNAPLVVLDDADLDAAVDQAVLGGYLHSGQICMS
+VQRVIVDESVYDEFLPKYEGAVKALKVGDPAEEGVLVGPIINDSQVESLRKKIASAEADG
+ARALVGGEIQGRVVPPFVWVDATADMDIAREEIFGPMTVVLKAHDEAHALELANDHEYGL
+SSAVFTQDLDRGLRFANGLAAGMSFINEMTVQDEAHVAFGGARNSGLGRFNGEWALEEFT
+TDHTIGVTRVG
+>2_758
+MSPTTHAAATFHSNDVSKQFIAGQWRDGAAGSTKQDLNPYDDAVVAEFALASEADLDEAY
+RAAADAQKEWAAVAPAKRAAVLRRAAELLEERRAEIVDWLVKESGSTVIKANIEVSLAVG
+ITQEAASFPTRVHGTIHPSNTPDREMRVYRKPIGVVGVISPWNFPLHLSQRSVAPALALG
+NAVVIKPASDTPVTGGTLIARLFEEAGLPAGVLSVVVGAGSEIGDAFVKHPVPRLISFTG
+STPVGKQVGANAVSGDHIKKVTLELGGNAPVVVLDDADLDAAVEQSVTGGYLHSGQICMS
+VQRVIVDEKVYDEFLPKYEGAVKSLKFGDPREEGVLVGPVVNDQQLETLKKKIASAEADG
+ARALVSGEIEGRVVPPFLWVGAEPDMEIARDEIFGPMTVVLKARDEAHALELANDHEFGL
+SSAVFTQDLDRGLRFADGLAAGMSFINEMTVQDEAHVAFGGARNSGLGRFNGEWAIEEFT
+TAHTIGVKRLG
+>3_726
+MTPTTHASGTFLGNDVGKQFIAGQWRDGAAGSTKQDVNPYDDSVVAEFALASEADLDEAY
+RSAAEAQKGWAETGPKERAAVMRRAAELLEEHRDEVVDWLVQEAGSTVIKANIEVSLAIA
+ITEEAATFPTRVHGKIFDSNTSNRESRVYRSPIGVVGVISPWNFPLHLSQRSVAPALALG
+NAVVIKPASDTPVTGGTLIARLFEQAGLPAGVLSVVVGAGSEIGDAFVKHPVPRLISFTG
+STPVGKQVAANAVLGENIKKVALELGGNAPLVVLDDADLDTAVEQAVTGGYLHSGQICMS
+TQRVIVDAKVYDEFLPKYEQAVKALKVGDPRGEGVLVGPIINDSQVEGLQKKIASAEADG
+ARALVGGEVEGRVVPPFVWVDVDPDMEIAKEEIFGPMTVVLKARDEEHALELANHHEFGL
+SSSVFTQDTGRGVRFAQRVAAGMTFVNEMTVQDEAHVAFGGARNSGLGRFNGEWAVEEFT
+TDHTIGVTTVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002052.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002052.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a4a2c26ffd56e613dbb083a4193455a9fb3aa7c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002052.fa
@@ -0,0 +1,21 @@
+>0_1982
+MSEPIGLRDAAIEWLKMRSLDGQVPLTREDIGDFRWNGEPFPLISTQNGIRKPAGFDAAL
+SFYTVYRPKGHARPYEDEIGDDGLMRYKWQGTNPRLPANQGLFRAYERGLPLIWFVGVGM
+SPARFQVVAPVYVVGREDERHQIVFAPMEPEDYSPELMHESVLEASLKRYLRREVKIRVH
+QPHFRSTVLAAYDNHCAVCNFAHPELLDAAHIVPDREVHGLPTVVNGLAMCRIHHGAFDN
+HFLGITPDFTVEIRQDLLDEVDGPMLRHGLQDLHGRKLMKLPTRRADRPCRENLAWAYER
+FREATVADVA
+>2_756
+MVEPAGLRNDAIRWLAERTLDGQLSVTREDLADYRWDGEKFPLISTMQGIRRPAGWSATL
+SIRTAFRRSGETRPYEDEIGDDGLIRYKWRGDNPQQPENVGLRNAMHQRLPIIWFIGISM
+NPAQYQVISPVYILGEEPERQQFVMAPFAEEDYVPDLMTGSVMESSLKRYLKRETTVRLH
+QPLFRSTVLAAYGNHCSVCNFAHPELLDAAHIVPDREVHGLPTVTNGIALCKIHHAAFDR
+RFLGLRPTQGRPVVEIQQDLLDEVDGPMLRHGLQDLHGKPVMTMPKRRVDYPSNENLAWA
+YAEFTRAGRAA
+>3_724
+MVEPDGLRETAIQWLIERTLDRQVSLTREDIADFRFQGEPFRLIPSYQGIWKPARFEATL
+SIVTTYRAPGQERPYNDALGEDGLHRYKWRGDNPNHPENVGLRRAMERQLPIMWFTGVGG
+KPPQYQVTAPVYIVNEERDRQQFVLAPLEDASEIPERGEGSEMVTALRRYMKRETVVRLH
+QPVFRSTVLVAYEDHCAVCNFAHSELLDAAHIVPDSEEEGVPDVTNGMALCKIHHAAFDR
+RFLGIRPTKDVPVVEIRQDLLDEVDGPMLRHGLQELHGKPLMKVPSRRADRPGTDKLVWA
+YERFLNATAADVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002053.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002053.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb6c6554f67ec4e0e28ccb1dc0ecee379e6e307b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002053.fa
@@ -0,0 +1,25 @@
+>0_2012
+MLTTSTTSHPVAIIGAGPIGLAAAAHLAERGLPFLILEAGTAAGAAIAEWGHTRLFSPWQ
+YNLDAAAQRLLEAAGWTAPDADVLPTGHELREHYLEPLAQLPQLAESIRYGARVTAVSRA
+GIDKTRTARREETPFLVRIQTTDGHSEDVLASAVIDASGTWSTPNPLGQAGLLAPGEQQA
+RAAGHITAPLPDVQGRDRDRFAGKRVMVTGAGHSAANTLLDLADLEADTTIIWAARTADL
+TRVYGGGDQDELAARGALGSRLRQLVDSGRIAVLTSFTITRFRADDTLTVHAVTPDGERE
+VSVDVLVPATGFRPDLGMLSELRLALDPAVEAPSQLEPLIDPEFHSCGSVEPHGERVLAH
+PETNFYIVGMKSYGRAPTFLMATGYEQVRSIAAALAGDRKAADAVHLELPETGVCTTDLG
+GGCDAPATAGDACCSSPQLIELPLGR
+>2_719
+MEDVHARAVIDASGTWTTPNPLGQAGLPAPGEAEALAAGQITAPLPDVLGADQARFAGQH
+VLVVGAGHSAANTLLELGTLAQDTPGTRISWAVRSADVARVYGGEDRDELAARGALGTRL
+RHLVETGTIQVHPSFTITAFTTTGLGMMVQASTPAGEEHLVVDVVVPATGFRPALGMLSE
+LRLELDPAVEAPRQLGPLIDPEFHSCGSVTPHGEKMLAHPEPGFYIAGMKSYGRAPTFLM
+ATGYEQVRSIAAALAGDRTAADNVELQLPETGVCSTDLGGSCDAPAPATAADTADQGCCA
+PAPQTLPAPASRLPVLLPVQAATCC
+>4_1941
+MLTTATNPHPIVVIGAGPIGLAAAAHLAERGLPFLILEAGTAAGAAIAEWGHTRLFSPWQ
+YNLDAAAQRLLEADGWTAPDADALPTGHELREQYLEPLAQLPQLAESIRYDARVTAVSRA
+GIDRTRTTRREETPFLVRIETADGHSEDVLASAVIDASGTWSTPNPLGQAGLLAPGEQQA
+HAAGHITAPLPDVQGRDRDRFAGKRVMVTGAGHSAANTLLDLADLEADTTIIWAARTADL
+TRVYGGGDQDELAARGALGSRLRQLVDSGRIEVLTSFTITRFRADDTLTVHAVTPDGERE
+VSVDVLVPATGFRPDLGMLSELRLALDPAVEAPSQLGPLIDPEFHSCGSVEPHGERVLAH
+PETNFYIVGMKSYGRAPTFLMATGYEQVRSIAAALAGDRKAADAVHLELPETGVCTTDLG
+GSCDAPAPAGDACCSSPQLIELSVGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002054.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002054.fa
new file mode 100644
index 0000000000000000000000000000000000000000..39f2390a6872663f97d29fdee30daaa4a60ee988
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002054.fa
@@ -0,0 +1,14 @@
+>0_2035
+MGGASATLRTRGLGRHGRNARVLASHNPLIYRARLLGDRAVNGTPLERHYRLGG
+>3_579
+MTTTTDRTDTISRPADVGTADSGVPTTAHPADRPQFLAARARLAPVFAWLAETAAERDRE
+RVTDREATDRLAAAGFPGLRVPEDAGGAGLTFPEAARLYVELAEADSNVLQALRVHVVNV
+ETVLGSPDGPRRERWLHRFATGETVANATTEIGNRTGHYETRLTTRPDGSAVVNGRKAYS
+TGTLYADWTIVVVEDEDGAERAATVRSDAPGVTLHDDWDGFGQRLSASGTTEFTDVVVDP
+EELTPVGQSLDDGSSIFASQAIFQFVHLVGLTGIARAVVRDAAAYVAGRTRGFSHGAAPR
+PGDDPQVLQVVGELEAAAFGAQAALDAVVGPLDRALRAEAAGAPLAEAEVDAVYTAVYAA
+QQVIARAALDAATRLFEVGGASATLRTRGLDRHWRNARVLASHNPLIYRARLLGDRAVNG
+TPLERHYRLGG
+>4_1976
+MRLIHNKDCCGWFAIRRGASARHTGGADGAPPSREPARDALERAATRLFEVGGASATLRT
+RGLDRHGRNARVLASHNPLIYRARLLGDRAVNDTPLERHYRLGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002055.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002055.fa
new file mode 100644
index 0000000000000000000000000000000000000000..56ddcce1066a063501c7256f032cb2936f0ffb09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002055.fa
@@ -0,0 +1,15 @@
+>0_2092
+MDAKPTRLRKKATREEILASLPVQARVRPSRWLLLWLIVVVCIAVFVWVIFRPPEDVSAG
+FGVWRVASFIGLALALAVLPAATMGLFRPRHVTFDERRVWTRDWSVDWADVKEVRAVAPE
+SEHTMKVALKVDERLWNEGGLRKANRWDSGRPLQGGGLTRAQPLVLTQPALAPSALTLLQ
+VFVELKKRNRRAGSPR
+>1_1816
+MDAKPTRLRKKATREEILASLPVQARVRPARWLLLWLIVVVCIAVFVWVIFRPPEDVSAG
+FGVWRVASFIGLALALAVLPAATMGLFRPRHVTFDERRVWTRDWSVDWADVKEVRAVAPE
+SEHTMKVALKVDERLWNEGGLRKANRWDSGRPLQGGGLTRAQPLVLTQPALAPSALTLLQ
+VFVELKKRNRRAGSPR
+>4_2036
+MDAKPTRLRKKATREEILASLPVQARVRPARWLLLWLIVVVCIAVFVWVIFRPPEDVSAG
+FGVWRVASFIGLALALAVLPAATMGLFRPRHVTFDERRVWTRDWSVDWADVKEVRAVAPE
+SEHTMKVALKVDERLWNEGGLRKANRWDSGRPLQGGGLTRAQPLVLTQPALAPSALTLLQ
+VFVELKKRNRRAGSPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002057.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002057.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ae6166d431db41a6811c6f5fffbf94fbb2fdb10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002057.fa
@@ -0,0 +1,21 @@
+>0_2105
+MRVPGPFPAHLQDAPFTRAQALAAGVSGSRLRSRDVERVAHGHYRWIGPVTGATPPARPL
+ATELSRLQDLAAMRPDVVVTGESVARLLGWPLPDDVKARVRPTVLRSRTRRVLREPGVRT
+RLVDLDRVLVRRDRLHGLRWTSHADTWFHLATVLDRDALVAVGDRLAREDERRGKVALAT
+RRELGAALERHTGEAGIVRAREALALVRTGSDSPAETELRLALMAAGLPEPDLQIELWDP
+DYSLWHPASADLGYRRWRIAIHYEGKTHDGAAQVGKDTRRDAVFLRQGWLNIRVAGTDRW
+RGFVETAGLVRAAIAERGGLDAGGAEDRLRN
+>1_1830
+MRVPGPFPAHLQDAPFTRAQALAAGVSGSRLRSRDVERVAHGHYRWIGPVTGATPPARPL
+ATELSRLQDLAAMRPDVVVTGESVARLLGWPLPDDVKARVRPTVLRSRTRRVLREPGVRT
+RLVDLDRVLVRRDRLHGLRWTSHADTWFHLATVLDRDALVAVGDRLAREDERRGKVALAT
+RRELGAALERHTGEAGIVRAREALALVRTGSDSPAETELRLALMAAGLPEPDLQIELWDP
+DYSLWHPASADLGYRRWRIAIHYEGKTHDGAAQVGKDTRRDAVFLRQGWLNIRVAGTDRW
+RGFVETAGLVRAAIAERGGLDAGGAEDRLRN
+>4_2051
+MRVPGPFPAHLQDAPFTRAQALAAGVSGSRLRSRDVERVAHGHYRWIGPVTGATPPARPL
+ATELSRLQDLAAMRPDVVVTGESVARLLGWPLPDDVKARVRPTVLRSRTRRVLREPGVRT
+RLVDLDRVLVRRDRLHGLRWTSHADTWFHLATVLDRDALVAVGDRLAREDERRGKVALAT
+RRELGAALERHTGEAGIVRAREALALVRTGSDSPAETELRLALMAAGLPEPDLQIELWDP
+DYSLWHPASADLGYRRWRIAIHYEGKTHDGAAQVGKDTRRDAVFLRQGWLNIRVAGTDRW
+RGFVETAGLVRAAIAERGGLDAGGAEDRLRN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002062.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002062.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6324df5e87ad3af59dcb051ea3f76070f30a09b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002062.fa
@@ -0,0 +1,33 @@
+>0_2149
+MSPSSTASDRSDAATAALDDAARRTGPGRRRRADARGTEGLGGTLAKIVLLGLVDAFAAF
+LLFQLAAAGDWVVFALTLAVTIGINWIYLRRGGLPAKYLAPGLFFLMLFQVFVVVYSSYV
+AFTNYGAGHNSDKAAAIEIIQRSSSIRVPDSPVYDITVLEEGGDLYLLTLRDGEPVLGGA
+DQALEPVEAQMQDGEPVGVEGYTTLRFGDLLQRQDQVARLKVPLSDDAADGTLETRDGSR
+GYVYAPRLEYDEARDTFTDLESGVEYRDNGEGQFQADDGSTLQTGWRVFVGLDNFTRAFT
+DPELRDPLLRVTVWTFAFAFLSVATTFAVGLLLAIAFNRSDMRGKKVYRVMMILPYAFPA
+FLSGLVWAGLLNPEFGFVNTVFFGGADIPWLTDPWLARLSVLVVNLWLGFPYMFLVTTGA
+LQSLPEDVDEAARMDGAGPWRIFRSIKLPLLLVSVAPLLISSFAFNFNNFNIIYMLTGGG
+PRFPDAGSNIGATDLLITVVYKTAFSGVGRDYGLASALSIVIFLIVATISAISFRQTKAL
+EEIDK
+>1_1873
+MSPSSTASDRSDAATAALDDAARRTGPGRRRRADARGTDGLGGTLAKIVLLGLVDAFAAF
+LLFQLAAAGDWVVFALTLAVTIGINWIYLRRGGLPAKYLAPGLFFLMLFQVFVVVYSSYV
+AFTNYGAGHNSDKAAAIEIIQRSSSIRVPDSPVYDITVLEEGGDLYLLTLRDGEPVLGGA
+DQALEPVEAQMQDGEPVGVEGYTTLRFGDLLQRQDQVARLKVPLSDDAADGTLETRDGSR
+GYVYAPRLEYDEARDTFTDLESGVEYRDNGEGQFQADDGSTLQTGWRVFVGLDNFTRAFT
+DPELRDPLLRVTVWTFAFAFLSVATTFAVGLLLAIAFNRSDMRGKKVYRVMMILPYAFPA
+FLSGLVWAGLLNPEFGFVNTVFFGGADIPWLTDPWLARLSVLVVNLWLGFPYMFLVTTGA
+LQSLPEDVDEAARMDGAGPWRIFRSIKLPLLLVSVAPLLISSFAFNFNNFNIIYMLTGGG
+PRFPDAGSNIGATDLLITVVYKTAFSGVGRDYGLASALSIVIFLIVATISAISFRQTKAL
+EEIDK
+>2_516
+MSTSSTTSARPDAPHEDPADAGRRGLRGRRADRGPDGTAGTLVKIALLGLVDAFAAFVLF
+QLAAAGDWVVFAVTLAVTLLINWIYLRRGGLPAKYLAPGVFFLVLFQVFVVVYSSYIAFT
+NYGAGHNSDKPAAIEIIQRSSSIRVPDSPVYPVSVLEQGGDLHLLTVRDGQAVLGGADEP
+LAPVEAQMDGAEAVAVDGYTTLKFGDLLSRQDQVTQLKVPLSDDPADGTLETRDGSRAYV
+YSPRLEYDEAQDTFTDLESGVVYRDNGEGRFQADDGSTLQTGWRVFVGVDNFAKAFTDPS
+LRDPLLRVLVWTFAFAFLSVVTTFALGLLLAIAFNRADMRGKNVYRVLMILPYAFPAFLS
+GLVWAGLLNPEFGFVNNVFFGGADIPWLTDPWLARFSVIVVNLWLGFPYMFLVTTGALQS
+LPEDVDEAARMDGAGPWRIFRSIKLPLLLVSVAPLLISSFAFNFNNFNIIYMLTGGGPRF
+ADAATNIGATDLLITVVYKTAFSGVGRDYGLASALSIVIFLIVATISAISFRQTKALEEI
+DS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002063.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002063.fa
new file mode 100644
index 0000000000000000000000000000000000000000..abca389c4676bfcf22b2f7e43b83d6ee49fb6af1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002063.fa
@@ -0,0 +1,27 @@
+>0_2150
+MQSTTTGGLFRRPLSLTLTAAFSALALTACGGGSSAPASSSPAGATEQGTATASPSQDLS
+EAGASTITMWVDQNRQEPLQAVAEDFKEDTGITVELVVKDNSTMKDDFITQNPTGEGPDV
+IVGAHDWIGSLVQNGTIEPLELGERAGDFVESSVQAVTYEGQTWGVPYSVENIAILRNTE
+LAESTPASFDEMIAEGRKAVDAGEAEYPFVVGLDAVNGDPYHLYPFQTSMGAPVFKQAED
+GSYDTGSLAMGGPEGEAFAEKLAEYGESGVLNPNMTADIAKEQFNSGNAAYFITGPWNIE
+EAEAAGVDFEVEAIPSMGDQPAQPFVGVNAFFVSSESENQLAANEFVVNYLSTEAAQDAL
+FAEGKRPPALTASFDKAASDETVKAFGEIGENGVPMPAAPEMGAVFEFWGGAEMSIIKGE
+GDPVQTWQKMISDIEGRIGQ
+>1_1874
+MQSTTTGGLLRRPLSLTLTAAFSALALTACGGGSSAPASSSPAGATEQGTAAASPSQDLS
+EAGATTITMWVDQNRQEPLQAVAEDFKEDTGITVELVVKDNSTMKDDFITQNPTGEGPDV
+IVGAHDWIGSLVQNGTIEPLELGDRAGDFVESSVQAVTYEGQTWGVPYSVENIAVLRNTE
+LAESTPASFDEMIAEGQKAVDAGEAEYPFVVGLDPVNGDPYHLYPFQTSMGAPVFKQAED
+GSYDTGSLAMGGAEGEAFAEKLAEYGESGVLNPNMTADIAKEQFNSGNAAYFITGPWNVE
+EAEAAGVDFEVEAIPSMGDQPAQPFVGVNAFFVSSESENQLAANEFVVNYLSTEAAQDAL
+YAEGKRPPALTASFDKAASDETVKAFGEIGENGVPMPAAPEMGAVFEFWGGAEMSIIKGE
+GDPVQTWQKMISDIEGRIGQ
+>2_515
+MTSTTPRAALRRPLGLTLTAAFSALALTACGGGGGTAASSSPAAGGSASSSAAGGSDQGA
+ASSSSAGQDLTEAGAATITMWVDQNRQKPLQAVAEDFKEDTGITVELVVKDNSKMKDDFI
+TQTPTGEGPDVIVGAHDWIGSLVQNGTIAPLELGDTADAFSETSVQAVTYDGQTWGVPYS
+VENLAILRNTALAEETPASFDEMIAEGQKAVDAGDADYPFVVGLDPVNGDPYHLYPFQTS
+MGAPVFEQQEDGSYDVSSLAMGGAEGQAFAEKLAEYGESGVLNPNMTADIAKEQFNAGKA
+AYFITGPWNVDEAEEAGVDFAVEEIPSMGDQPAQPFVGVNAFFVSAESENQLAANEFVVN
+YLSSEEAQDALYAEGKRPPALTASFEKAAVDETVKAFGEIGEDGVPMPAAPEMGAVFEFW
+GGAEMSIIKGEGDPAQTWDKMISDIEGRIGQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002064.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002064.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2417bbb68a327b69c7e40b4bfafda6187f54da89
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002064.fa
@@ -0,0 +1,22 @@
+>0_2151
+MVGIKDVARMAGVSTATASRALTGSGPVAAATRTRVQEAVATLGYVADSAASSLASGRTR
+NIGLVTPSVHRWFFAAVLEGAADELVRHGYDLTLYDVGQDPERRSTVISDLLPRRRLDAL
+ITLSFRLSVFEFAGLERLGRPVIAIGGRLPAGETLPDWFTAVQVDHARAARMATEHLLEL
+GHRDIAYVGRVDEDIEFQVSTERTRGFLHALAATGVRTPADWMVPADFTIGGTYHQARAL
+LADPRRRPTAVMCISDEMAMGTWMAAHSLGLRVPEDVSVMGLDGHPEAARLGISTVDQNP
+LEQGRRAVRLALGALDGAAHPHRIMHHLALRPRASTAPP
+>1_1875
+MVGIKDVARMAGVSTATASRALTGSGPVAVATRTRVQEAVATLGYVADSAASSLASGRTR
+NIGLVTPSAHRWFFAAVLEGAADELVRHGYDLTLYDVGQDPERRSTVISDLLPRRRLDAL
+ITLSFRLSMFELAGLERLGLPVIAVGGRLPAGETLPDWFTAVQVDHARAARMATEHLLEL
+GHRDIAYVGRVDEDIEFQVSTERTRGFLHALAATGVRTPADWMVPADFTIGGTYHQARAL
+LADPRRRPTAVMCISDEMAMGTWMAAHSLGLRVPEDVSVMGLDGHPEAARLGISTVDQNP
+LEQGRRAVRLALGALDGAAHPHRIMHHLALRPRASTAPP
+>2_514
+MVGIKDVARMAGVSAATASRALTGSGPVASSTRTRVQEAVAALGYVPDAAASSLASGRTR
+NIGLVTPSVHRWFFAAVLEGAADELVRRRYDLTLYDVGQDHDRRSAVLTDLLPRRRLDAL
+VTLSFRLSPFELDGLARLGRPVVAVGGRLPSGEALPEWFTAVQVDDARAARMATGHLIEL
+GHREIAYMGRVADDIEFQVSTERTRSFLDALAAAGLRTPADWMLPADFTIGDAYHRARAL
+LADPEHRPTAVLCISDEMAMGTLMAAQSLGLRVPEDVSVMGLDGHPDAARLGISTVDQTP
+VDQGRRAVRLALGALDGTPTRPASSTTWPCNPGRAPRRRERRAGSRPRRRRPPSTPPSPR
+IVGHVPARERTPPWPP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002065.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002065.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ead0d6ab0bde496da7aab550f0de953c788d6c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002065.fa
@@ -0,0 +1,12 @@
+>0_2156
+MMQSSEGAWVDPVEGIMYEHMLLLRVATQGVAPYGRSSALERSATVLLARLEAGGAMSIA
+ELAEAFDLDVSTVHRQVAAAMKAGLVERVVDPDGGSARLHRPTEEGRARLAAELSSRADN
+VAQIVSSWPAEDVVEFSRLLRRFNEGAEERRGHPWPRPQTGPGAEDPRL
+>1_1880
+MMQTSEGAWADPVRGIMYEHMLLLRVATQGVAPYGRSSALERSATVLLARLEAGGAMSVA
+ELAEAFDLDVSTVHRQVAAAMKAGLVERVADPDGGSARLHRPTEEGRARLAAELSSRADN
+VAQIVASWPAEDVVEFSRLLRRFNEGAEERRGHPWPRPQTGPGAEDPRP
+>4_2096
+MMQSSEGAWVDPVEGIMYEHMLLLRVATQGVAPYGRSSALERSATVLLARLEAGGAMSIA
+ELAEAFDLDVSTVHRQVAAAMKAGLVERVADPDGGSARLHRPTEEGRARLAAELSSRADN
+VAQIVSSWPAEDVVEFSRLLRRFNEGAEARRGHPWPRPQTGPGAEDPRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002067.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002067.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c4703004bbda78db6e54ec96de043092aa0c832
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002067.fa
@@ -0,0 +1,18 @@
+>0_2182
+MTLPTPSGRWTTTARPAFAVAAALSLGGNLLSLWIGSWKSSDLPADAGYAGVLEGGWEHM
+LNQPTYFTFLSNFLVGLTSLLLALRLHRPGTLFRVLRVTGVVCIVITGVVFNVLLRDADP
+MTAVERFNDTLQHIVTPILTPVLWAVFGPRRQITWRVVWLSTLIPLAWLAFTLLRGPWLD
+WYPYTILDVPRLGYDGVAVYVVAILVFFVAVAALLRVADGLLARAGVGVGAGAEAEARVE
+ARPSP
+>1_1895
+MTLPTPSGRWTTTARPAFAVAAALSLGGNLLSLWIGSWKSSDLPADAGYAGVLEGGWEHM
+LNQPTYFTFLSNFLVGLTSLLLALRLHRPGTLFRVLRVTGVVCIVITGVVFNVLLRDADP
+MTAVERFNDTLQHIVTPILTPVLWAVFGPRRQITWRVVWLSTLIPLAWLAFTLLRGPWLD
+WYPYTILDVPRLGYDGVAVYVVAILVFFVAVAALLRVADGLLARAGVGVGAGAEAEARVE
+ARPSP
+>4_2115
+MTLPTPSGRWTTTARPAFAVAAALSLGGNLLSLWIGSWKSSDLPADAGYAGVLEGGWEHM
+LNQPTYFTFLSNFLVGLTSLLLALRLHRPGTLFRVLRVTGVVCIVITGVVFNVLLRDADP
+MTAVERFNDTLQHIVTPILTPVLWAVFGPRRQITWRVVWLSTLIPLAWLAFTLLRGPWLD
+WYPYTILDVPRLGYDGVAVYVVAILVFFVAVAALLRVADGLLARAGVGVGAGAEAEARVE
+ARPSP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002069.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002069.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ecb3b51baaf50011020d740288fd246c9cb7960
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002069.fa
@@ -0,0 +1,12 @@
+>0_2201
+MRNGQSGAGPPATAPSPRSTRDVDVGWVPRFDVDVLEAALRPVHERPRWEEWGQIAAPTL
+LITGENGYVPAGELDEMRRRRPDVRHVQVPGAGRDVHLDAPERVAELVRGFAA
+>3_400
+MSGLGRRSAGPVTREDGTRLHVLDSGGSGPALLLLHGLAGYAREWAQVAERLAAACRVVA
+FDQRGHGSSTRRPADLSRTAHVGDVVAVADALGLQRFTLVGQSMGAHTALLAAAAHPARV
+GRLVLIEGGVGGEGPEATAGVIDWFRAWPIPFATVDDAVAHLGGGPAARVWAEGLEETDA
+GGVPRFDVDVLEAALRPVHERPRWEEWGQIAAPTLLITGENGYVPAGELDEMRRRRPDVR
+HVQMPGAGHDVHLDAPERVAELVRGFAA
+>4_2133
+MRNGQSGARPPAIAPSPRSTRDVDAGWVPRFDVDVLEAALRPVHERPRWEEWGQIAAPTL
+LITGENGYVPAGELDEMRRRRPEVRHVQVPGAGHDVHLDAPDRVAELVRGFAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002072.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002072.fa
new file mode 100644
index 0000000000000000000000000000000000000000..84e42a6de1acf10541d6fe5d084782a01f7d2045
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002072.fa
@@ -0,0 +1,15 @@
+>0_2208
+MGTIFLYEIAGTAILLLLGVGVVANVVLSKTKGNGGGWLLISFGWGLGVFAGVYVAAATG
+AHLNPAVTVGLLVSGAEEYAPGIAVTLGTTLAYFAAQLIGAFLGAALAWLAYRDHYQTET
+DQGAILGTFATGPEIRNPLWNMVTELIATFVLVFVVLLFGSTPSGLGPLAVALLVVAIGA
+SLGGPTGYAINPARDLGPRLFHAVAPIRHKGGSDWGYAWVPIVGPLVGAVLAGLAAPLFV
+>1_1912
+MGTIFLHEIAGTAILLLLGVGVVANVVLTKTKGNGGGWLLISFGWGLGVFAGVYVAAATG
+AHLNPAVTVGLLVSGAEEYAPGIAVTLGTTLAYFAAQLIGAFLGAALAWLAYRDHYQAET
+DQGAILGTFATGPEIRNPLWNMITEVIATFVLVFVILLFGSTPSGLGPLAVALLVVAIGA
+SLGGPTGYAINPARDLGPRLFHAVAPIRHKGGSDWGYAWVPIVGPLVGAVLAGLAAPLFV
+>4_2141
+MGTIFLYEIAGTAILLLLGVGVVANVVLTKTKGNGGGWLLISFGWGLGVFAGVYVAAATG
+AHLNPAVTVGLLVSGAEEYAPGIAVTLGTTLAYFAAQLIGAFLGAALAWLAYRDHYQAET
+DQGAILGTFATGPEIRNPLWNMVTEVIATFVLVFVILLFGSTPSGLGPLAVALLVVAIGA
+SLGGPTGYAINPARDLGPRLFHAVAPIRHKGGSDWGYAWVPIVGPLVGAVLAGLAAPLFV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002076.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002076.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d60707747bdba330f1e45cf1e353e3097e8af092
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002076.fa
@@ -0,0 +1,18 @@
+>1_228
+MRAVGAVKASILRTVRRGAPVSWAPEWMGLGNLLYQGLWAYEGASLGEPRFVLLPENRVG
+VIELFPRLREKRFLRRSHVPFTAQRVRPWENEERSTGRFAPPLLEDFIRDDLLPGSAVSP
+ATDSYDDAIVVNVRRGDYYSVERHRAQFGMDQEKYLRSALAEAVRTQGPVGRIVVISDGL
+DWCRDHVNDLLSEFAPVEYEDGDIAHDLKAIIHAKRLIITNSTFSYWGGYIGDVLNPGRQ
+VIAPWFFSRTENGGRSHLLAPSWTVIEGDF
+>2_2377
+MKFLDKSKSRALKAIRRGDPVSWVPDWMGLGNILYQGLWAFEGDDRQEGRRVLLHPKREA
+AVALFPTLRGRYFVTRDRVPFTARRVMPWREESPEPIPYQPAELPGFIREVLLPGSPVAA
+VPDGLSEDDVVINVRRGDYYSVPQHEAEFGMDQVAYVRAAISRAAAVSGPIGRILVISDG
+LDWCRENLGPVLEPHGPVIYEDGDLFHDLRTIVHARRLVITNSTFSYWGGYIGDELHPGR
+LVIAPALFSHNLNGGRAHQLKPSWTVLEDGCWDRAR
+>4_491
+MNRLLDMKSNALSAIRRGRPIAWVPEWMGLGNLLYLGHWAYEGSAEDEDRRVLLHADRGA
+AVGIFPRLRERLFVRREDVRFTDRRVMPWSGAATRQRPDHIPAQAHEAFIRDLLLPDSPV
+ATPPHCLKGMLVVNVRRGDYYSVKDHQDDFGMDQVEYIKAALKTSVAAHGSPDGIAVVSD
+GLDWCKEALGGVLEAVAPTTYVDGDLTHDLGTIVHAERLIITNSTFSYWGGYIGDVLSPG
+REVIAPWFFSRSQDGGRATQLRPHWTALEGDFY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002077.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002077.fa
new file mode 100644
index 0000000000000000000000000000000000000000..951812c69b1b7e6dee3e6764e45914b59835a984
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002077.fa
@@ -0,0 +1,9 @@
+>1_308
+MPKKFDPEVKDRAVRMVLDRVEEAGSVTKAVALVSPKVDVGRETLRRWVCQHRVDAGLKD
+GPTSDDLAELKRLRGEVKRLREDNEILRKASIFFAGELDPRNR
+>2_2222
+MPKKFDPEVKDRAVRMVLDRVEEAGSVTKAVALVSPKVDVGRETLRRWVCQHRVDAGLKD
+GPTSDDLAELKRLRGEVKRLREDNEILRKASIFFAGELDPRNR
+>3_1787
+MPLPFEFERMLFMPKKFDPEVKDRAVRMVLDRVEEAGSVTKAVALVSPKVDVGRETLRRW
+VCQHRVDAGLKDGPTSDDLAELKRLRGEVKRLREDNEILRKASIFFAGELDPRNR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002079.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002079.fa
new file mode 100644
index 0000000000000000000000000000000000000000..728cd6112bfc2416c2839200f0ca4b1ce9cb5f8e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002079.fa
@@ -0,0 +1,15 @@
+>1_342
+MQAMSLDEITPVAQDYLKAIWSATEWGDAPLSTKSLAARMGTTAPNVTETVKRLAAQGLV
+EYQPYKPVTLTGKGCEHAIAMVRRHRLLESFLAASLGYSWDEVHAEAERLEHAASDELIE
+RIDQMLGHPTHDPHGDPIPTPVGQRERPAHAVRLDAAEPGFYRVLRISDADPQRLIRFQQ
+AGIVPDSVVEVAEAGHFRLRVVAVGPVELIETDAAAIWLVPSSTRG
+>3_655
+MQAMSLDEITPVAQDYLKAIWSATEWGDAPLSTNSLAARMGTTAPNVTETVKRLAAQGLV
+EYQPYKPVTLTGKGREHAIAMVRRHRLLESFLAATLGYSWDEVHAEAERLEHAASDELIE
+RIDQMLGRPTRDPHGDPIPTPEGQRAQPAHAVRLDVAEPGFYRVLRISDADPQRLVRFQQ
+AGLVPGTVVEVTEAGHSRLRVVAVGPVELIETDAAAIWLVPSATRG
+>4_1952
+MQAMSLDEITPVAQDYLKAIWSATEWGDAPLSTNSLAARMGTTAPNVTETVKRLAAQGLV
+EYQPYKPVTLTGKGREHAIAMVRRHRLLESFLAATLGYSWDEVHAEAERLEHAASDELIE
+RIDQMLGRPTRDPHGDPIPTPEGQRAQPAHAVRLDVAEPGFYRVLRISDADPQRLVRFQQ
+AGLVPGTVVEVTEAGHSRLRVVAVGPVELIETDAAAIWLVPSATRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002082.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002082.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5449b29daecec62e55cc3694f1ac2bacf15f2d7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002082.fa
@@ -0,0 +1,36 @@
+>1_520
+MPVSAPSPSSSRPAVLGFAARYPWVLATLVVVALTLGLHLAGAEDPARWIASAYALVVAA
+WTSVGMVRDLMRGHWGVDILAVTAIVATVLVGEHLAAVLVCLMLTGGEALEDYAAGRARR
+DLSALLDRAPQRAHRLGPDGSVEDVPVEEVRAGDRLLVRPAEVLPVDGTVASAEDGGEVA
+VDLDESSLTGESLPVTHRTGSAVMSGALNGTRAFVLEATASAADSQYAAIVSLVQQAAES
+RAPMVRLADRYAVPFTAVAYLIAGLAWWLSQDPVRFAEVLVVATPCPLLIAAPVAFLGGM
+SRAATSGVIVKSGGTIEALGSVQTVGFDKTGTLTAGRPELVGVRPAAGFAQDELLRLAAS
+AEQYSVHVLADAIRAAAEERGLSLATAQDATEEATHGVVAVLEGRRVVVGKRAYVTQAAP
+DTVTADLAPGQSAVYVAVDGAFAGVLLLADRIRPESAATVQALHRLGARQVLMLTGDAEA
+TGRHIAREAGIDEVHADLLPADKVRLLSERPERPVMMVGDGVNDVPVLAAADVGVAMGAR
+GSTAASESADVVVLADDVSKVAVAVAAGQRTLQVATQSIWVGIALSLVLMVIAATGAIPA
+LVGALFQELVDVVAIVNALRAMKPGPHEAERLGDLAAAPARGERQAVSA
+>2_781
+MTRLSRFARSYPLVAVTLAVLALVLGLHAAGLDAAAAVIATVYVAGHIAWAAVGMVREVL
+RGHFGLDILAVVAMTASLLVGEHLAALIIVLMLTGGEALEDFAAARARRELTALLEKAPQ
+TAHLLGADGEAREVPAAQVRPGDELLVKPNEVVPVDAELLSAEAAFDESSLTGESLPSAK
+AAGDAVLSGSVNGTAAVRVRATAAAADSQYQRIVELVEQAHEQKAPVVRLADRFALPFTA
+VSLAIAGVAWWASGDPVRFAEVLVLATPCPLLIAAPVAFLGGMSQASRRGVIVKGGGVLE
+SLAHARAVAFDKTGTLTHGRPRLQRVEPAEGFTADAVLAAAAAAEAYSTHVMAEAVVRAA
+DDAGLARLSARGGTEEGTRGVRALVRGTDGGAGAGTGTDTHEPGAAVEVRVGKLAFVREV
+APDAPEARFAPGETAAYVSVDGRHAGTLVLADALRENAGETVAALRAEGFERAVMLTGDN
+EHTARSLAAEAGLDDVAHSLLPEDKVRLLAELQPRPVIMVGDGVNDAPVLAAADVGIAMG
+ARGSSAAGESADVVITRDDIGRTVEAVRIGRHTYRIALQAVLLGVALSVGLMLVAAFGHI
+PAVAGALTQELVDLACILYALRARTSPRGTPQGAAARARGRAPQEAARA
+>4_748
+MPVSAPSPSRPAVLGFAARYPWVLATLVVVALTLGLHLAGAEDPARWIASAYALVVAAWT
+SVGMVRDLMRGHWGVDILAVTAIVATVLVGEHLAAVLVCLMLTGGEALEDYAAGRARRDL
+SALLDRAPQRAHRLGPDGSVEDVPVEEVRAGDRLLVRPAEVLPVDGTVASAEDGGEVAVD
+LDESSLTGESLPVTRRTGSAVMSGALNGTRAFVLEATASAADSQYAAIVSLVQQAAESRA
+PMVRLADRYAVPFTAVAYLIAGLAWWLSQDPVRFAEVLVVATPCPLLIAAPVAFLGGMSR
+AATSGVIVKSGGTIEALGSVQTVGFDKTGTLTAGRPELVGVRPAAGFAQDELLRLAASAE
+QYSVHVLADAIRAAAEERGLSLATAQDATEEATHGVVAVLEGRRVVVGKRAYVTQAAPDT
+VTADLAPGQSAVYVAVDGAFAGVLLLADRIRPESAATVQALHRLGARQVLMLTGDAEATG
+RHIAREAGIDEVHADLLPADKVRLLSERPERPVMMVGDGVNDVPVLAAADVGVAMGARGS
+TAASESADVVVLADDVSKVAVAVAAGQRTLQVATQSIWVGIALSLVLMVIAATGAIPALV
+GALFQELVDVVAIVNALRAMKPGPHEAERLGDLAAAPARGERQAVSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002084.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002084.fa
new file mode 100644
index 0000000000000000000000000000000000000000..99e3c69b8bfc2ce7858b1f9f3657458808bd3584
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002084.fa
@@ -0,0 +1,46 @@
+>1_1066
+MTVSMRVMSAGDGYKYLLRSVAAADGDRSLSTPLTRYYAEEGTPPGRWLGSGLTGLGDGQ
+LAVGDQVSEAQLQLLIGMGRDPITGEPLGRAFPQYAPVADRIERRVDELPDELGPAGRAE
+AVAQIEAEEASRGTRRAVAGFDYTFSVPKSVSVLWAVADAGTQALIAEAHHDAVAEVVD
+>2_2594
+MTVSMRVMSAGDGYKYLLKSIAAGDGDRSLSTPLTRYYAEAGTPPGFWMGSGLGRLGHGD
+LVEGGQVSEAQLALLVGMGHDPITGEPLGRAYQQFASITERIKQRVDALDPELGPATRAQ
+EVAAIEAEEAERGTRRAVAGYDFTFSVPKSVSTIWAVADAGTQALIADAHHAAVAELVAF
+LEREVAATRVGATGPDGAVAHVDVAGVVAAAFDHYDSRAGDPQLHTHVVVSNKVLTVQDG
+RWRTLAGRPMHSVVVAVSELYNAALADQLTRVLGVEWEARERGRDRNPAWEIEGVPDELV
+TEFSTRSRHIEAEKDRLIAGYVAKHGRQPSARTVLKLRAQATLATRPEKQVRSLADLTAE
+WRQRAGRVLRRDANGWARTFTASTADAPRRVLRADDVPLDVVREVGQTVMETVGEKRSTW
+TRWNLHAEASRQLMGWRFASIQDREAITGLVVDAAEHASLRLTPPELASSPLQFRRVDGT
+SRFRPHASTLFSSEVLLAAEDRLLARAATTAGPVVPLETVERIARKPDARGRVLGEDQAA
+ALAAIAVSGRVVDVLVGPAGAGETTAMNGLRRAWEKEHGTGSVIGLAPSAVAAQVLADDL
+GIATENTAKWWQNHLMYGTTFTAGQLVIIDEASLAGTMSLDRLTHEAEKAGAKVLLVGDW
+GQLQSPGAGGSFAMLVHARDDAPELTDLHRFTNEWEKTTSLQLRHGRAEAIDALIEHGRI
+TGGDEEAMIDAAYTEWRADLAAGRASILVTETHATVTELNARARADRIIDGTVNPTRELP
+LRDGTAVSEGDLVITRENDRRLRNGRTWVRNGSRWTVTGVREDGSVIIRPAGRRFGGGIV
+LPADYVAEHLDLGYAITAHRAQGVTTDTAHAVVTATTTRENFYVSMTRGAHSNHAYVTVD
+REDAEHAVPHPGDNPNVTARSILYGVLQHIGAELSAHETVAAEQDRWGSIAQLAAEYDTI
+AQAAQHDRWATLLAASGITAEQIEDVLGSDAYGALSAELRHAEANHHDLDALLPRLVAAR
+SLDDADDIASVLHARVARATARPAGSGRTRKAPRLIVGLIPHAGGQMADDMRRALDERRE
+LIEGRADAVLRGYLTDEEPWTADLGAAPRGDKQKAAWWRAARTVAAYRDRYGITDDRTPL
+GPTPESTSQKIDAIRARAALNRAQAIAHEGTTADAVRPATTSRPAPSL
+>3_1735
+MVWVTVSMRVMSAGDGYKYLLRTVAAGDGDRSLSTPLTRYYAEAGTPPGRWLGSGVTALG
+NGEIAPGAQVSEAQLQLLVGMGRDPITGVPLGRAYPVYSSTADRVADRVNQLDPALGAVE
+RGRRVAQIEAEEAARGSRRAVAGFDFTFSVPKSASVLWAVADAGTQALIAQAHHEAVAAV
+VAFMEREVAATRTGATAGDGAVAQVDVTGLIATAFDHFDSRAGDPHLHTHVVISNKARTV
+LDGKWRSLDGRPMHAAVVALSELHEAVFADHMTRTLGVSWEPREMGRDRNPSWAITDVPE
+ELAAEFSTRARQIEVEKDRLVAEYVATHGRQPSDATVIRLRAQATLGTRPDKQLRSLAEL
+TAEWRTRASQQLGVDATVWARTITVGERQMLLRADDVPLDLIGQVGRSVVEVVGEKRSTW
+RRWNLMAEAARQTMGWRFATVEDREAITAMVADAAEHASLRLTPPELTTSPVEFRRLDGT
+SVFRPKHSTVFSSDTLLAAEDRLLQRTRATTGQSVDLATVEAITGRPDAEGRVLGRDQAA
+ALASVAVSGRVVDVLVGPAGAGKTTAMNALRRAWETEHGAGSVVGLAPSAVAAQVLADDL
+RIATENTAKWWTTHQHTGATFHAGQLVIIDEASLAGTLSLDRITQAAEEAGAKVLLVGDY
+AQLQSVDAGGAFSLLIHDRDDAPELVDVHRFTHDWEKTASLELRHGRAPVIDTYLAHDRI
+HDGDAEAMTDAAYTAWRHDRQAGLVSVLIAETRENVTALNVRARADLILDGTLKPGPEIT
+LSDGSAAGVGDTIITRRNDRRLRNRHGWVRNGQTWTITAVHDDGSITIRPPGTRFGNSIV
+LPADYVAEHVDLGYAVTAHRAQGITTDTAHVLVEPTTTRENLYVAMTRGRESNKAYVILD
+RPDDHATAHPGDSPDATARTVLYGVLQHSGAELSAHETITAEQDRWGSIAQLAAEYETIA
+AAAQHDRWTTLVRGSGLTGDQAQAVIDSDAFSALTAELRRAEANHHNVDTLLPRLIRARG
+FADADDIASVIHHRLANATTRPAGSGRTRQAPRLIAGLIPEATGPMTPDMQQALTERRHL
+IETRAEAVLDTALHTHEPWVTALGPIPTSGRERQQWRRRAVVVAAYRDRYQITDPTPLGA
+QPEDTAQRIDRARAETAVRTLTRPTMEDERGRPAAQATRHLDL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002087.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002087.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d7f766a38e823421adcafbf73a54b07602f7d7b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002087.fa
@@ -0,0 +1,10 @@
+>1_1603
+MKISDRVRAMRKELLLTQQQLADLAGVSDATVRQIERGTGKSTLKSVLSVMEVLGLELEV
+TG
+>3_194
+MSRQPASVPLTSALDTAPFGREMRALRRGAGLTQAQAADRMGVSLRWLKYLEAGTRRPRL
+QDVGRVAVMDPLTGRMATSVLQTLTPAGKITPSGPRLSLAHLARLAGWPLEPMDPSVSDA
+VTPEALAVVADVLDAAHALLDQADPHMEDLEALAATRNVSAVVHRLDHVYAALAAEDAR
+>3_817
+MAQPHPSPLVPVGERVRAARREMGLTQQELADLAGVSDATVRQIEHGTGKGTLGSLMAVL
+EVLGLHLEVNG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002091.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002091.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4d2c701ccad06b179ab7cc69ed01a6f9f575f555
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002091.fa
@@ -0,0 +1,18 @@
+>1_1660
+MSIAAQAKDDDTFDSAHVLDPAATRDSQGQISEEIAAVHAQAQGETQPRLDFPPYRSSVF
+RHPTKSLVHADPETVELWSPAFGHRDVHPLEADLTVGQNGEPIGERIKVRGRVLDDDGRP
+VRHQLVEIWQANAAGRYVHKRDQHPAPLDPNFTGIGRTLTGADGTYEFTTIKPAPYPWKN
+HRNAWRPAHIHFSLFGTDFTQRMITQMYFPGDPLFPLDPIYQGITDQAARDRLVATYDHS
+VTSHEWNTGYWWDIVLTGSHRTWMEDEEGDH
+>2_823
+MSDPVQKQDDDTFDNARVLDPAATQDSQEQISEEMAAVHGQASGETQPRLDFPPYRSSVF
+RHPTKSMAHADPESIELWSPAFGHRDVHQLESDLTVGQNGEPIGERIKVRGRVLDGQGRP
+VRGQLVEIWQANAAGRYVHKRDQHPAPLDPNFTGVGRTITDDRGFYEFTTIKPAPYPWKN
+HHNAWRPAHIHFSLFGTDFTQRMITQMYFPGDPLFSLDPIYQGITDQKARDRLVATYDHS
+VSEHEWNTGYYWDIVLTGSHRTWTEDEEGDH
+>4_1878
+MSIAAQAKDDDTFDSAHVLDPAATRDSQGQISEEIAAVHAQAQGETQPRLDFPPYRSSVF
+RHPTKSLVHADPETVELWSPAFGHRDVHPLEADLTVGQNGEPIGERIKVRGRVLDDDGRP
+VRHQLVEIWQANAAGRYVHKRDQHPAPLDPNFTGIGRTLTGADGTYEFTTIKPAPYPWKN
+HRNAWRPAHIHFSLFGTDFTQRMITQMYFPGDPLFPLDPIYQGITDQAARDRLVATYDHS
+VTSHEWNTGYWWDIVLTGSHRTWMEDEEGDH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002094.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002094.fa
new file mode 100644
index 0000000000000000000000000000000000000000..710f2eb6205c6858b8a129d1aeb01bbb716d17c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002094.fa
@@ -0,0 +1,23 @@
+>1_1698
+MAHQAMQRGRRRMVHLTGLFAGIGGIEQGFHNALGSKVETDLLCESWAPAQIVLKNRFPG
+AELHPDVRELASLPEATDILSAGFPCQDLSQAGRTAGIRGEQSGLVTHLFELLRRRISAG
+RRLPTLLIENVPNMLALDKGAAMEFLVQEMETLGYSWAYRVVDTRFTGLPQRRRRVIVVA
+SVNLNPSEVLFADEAASRPDDHYSSDAFGFYWTEGKGGLGWAPDAIPTLKGGSTIGIASP
+PAIWVRGAEDATRALVVPREAEMESLQGFPRGWTDLDFGLSAARTRGTRSKLLGNAVSVR
+VAEWVARRVFAPGEVVCPSVDWGSSRQWPNAAAGMGGKRWRVEASEFPTLEPYEHLLEHV
+DVSSAPALSRRAVSGFRSRLLQGNLGRYPGFREAVAEADRALTEDQLITKLEA
+>2_2161
+MALTSVEVCAGAGGQALGLEAAGFKHLACVEYDKHACTTLRTNRPQWNTVEADLLEWSGA
+AYAGKTDLFAGGVPCPPFSKAGKQLGEADERNLFPRALDLIEEIGPRAVMLENVRGLLDP
+QFQEFRDGVDARLESMGYVPSWRLLNASDYGVSQLRPRVILVALKEPWAQHFTWPEPNKK
+PAPSVGELLAPLMAANGWEGAKAWAARADRIAPTLVGGSHKHGGPDLGPTRARAAWAALG
+VEGRTIAAEAPEPGFEGMPRITVQMGGMVQGFPADWQFTGAKTHGWRQVGNAFPPPVAAA
+VGKQIRKALKAAN
+>4_1916
+MAHQAMQRGRRRMVHLTGLFAGIGGIEQGFHNALGSKVETDLLCESWAPAQIVLKNRFPG
+AELHPDVRELASLPEATDILSAGFPCQDLSQAGRTAGIRGEQSGLVTHLFELLRRRISAG
+RRLPTLLIENVPNMLALDKGAAMEFLVQEMETLGYSWAYRVVDTRFTGLPQRRRRVIVVA
+SVNLNPSEVLFADEAASRPDDHYSSDAFGFYWTEGKGGLGWAPDAIPTLKGGSTIGIASP
+PAIWVRGAEDATRALVVPREAEMESLQGFPRGWTDLDFGLSAARTRGTRSKLLGNAVSVR
+VAEWVARRVFAPGEVVCPSVDWGSSRQWPNAAAGMGGKRWRVEASEFPTLEPYEHLLEHV
+DVSSAPALSRRAVSGFRSRLLQGNLGRYPGFREAVAEADRALTEDQLITKLEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002096.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002096.fa
new file mode 100644
index 0000000000000000000000000000000000000000..932abf6cd62fc83860efcf19e897516b98a2fcd6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002096.fa
@@ -0,0 +1,22 @@
+>1_1727
+MVNANEYEPLELSHLHPAAQPVARLPAAERVQRIRADRWIGYPKAVEAVERLETMLGWPA
+KQRMPNLLLVGPTNNGKSMIIERFRRQHPPSSEPDREQVPVVCVQMPSEPSPLRFYTAIL
+SVLGAPLRPRPRLVELERLALSLLREVGARMLVVDELHNVLAGRGDTRREFLNLLRFLGN
+ELRIPLVGVGTREAYLAVRSDDQLENRFEPFVLPLWEADDQARSLLASFAASFPLRKPSV
+IDTEDMARYLLARSEGTIGELAHLLTAAAVAAVESGLEAIDHRTLTMANYTGPTERRRVF
+ERELL
+>3_618
+MDALLWHTQALTPAPAPPEPVLLREFSTLSTQDQDEYWTRMHRWMCASTLDCDRTAAIRR
+GMDRVLQRNEYARSGAKTIIGLSAPNGVGKSTFIKSYAQDRYQRMMHDQPVDKLPSRTDS
+GGSPSHWIPQVYITLRAASEVPDVNAAILSYLGYPIMGRTTKDTTLLVHAVARHGVKLLI
+LDDAHMLRAKQARARDVLDYVKFLNTMMGERDGTLVLVGANMEGGPVYQDPQVAARLHAF
+ALQPYTVQQDTTERVAWQQLLAGAEKKFMPYLDSATEGTLTRELAGQIWARTQGHLGDTH
+QLITTALLDAFDQGDTTLVSEHLQGVRLSARAEAAEADLAREATLTSRREQNRKAKR
+>4_2157
+MNSHDWHHQAVTSQPSGLKPITVRKFERLNQQEQNEHWTALNRWMAAQPIDCPRVRQTST
+RMQAEVLRNEYAPRGAKTIIGLSAANGVGKSTLIKRLAHQLYRETVPTTDPGILPTRTVG
+TGATVDWIPQVYITLRAASRIQEVNTALLSFLGYPTIGQTRATTTRVVEAIRTHGVQLLI
+LDDAHMLKTSQADARDVLDYLKFLNTELGELGGTMILVGANLEDSDVYADAQIATRLAPL
+QLQPHAIFPVSERARFQAMLRGVEEKFMCHLDTATTGTLTNELAGEIWQRTQGYLGDIHR
+LITTVILETFDAGEDVITRERLRAVPLSARATAAEASLREAATQRSRRTENRRKKKAGST
+PPAQTPSQDAAGSSSDSPTAAVPETKE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002106.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002106.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71ab0999cc3f91b1ca961bc0f92eeefc1dfdf366
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002106.fa
@@ -0,0 +1,13 @@
+>2_552
+MPDLQPVPTLADVPELGDGVVTLHPADARHAPALGALLRDADVQVLTGSVHSTAQAAAIA
+RGEAHAGPTPERLAEIYAGWAADEDRAVWTVEAEGAVLGEILLMDLDAGNRACGLRLWLA
+GAGRDRGVGTRALTLVLEHAFTTVGLHRVGLEVYDHNPRARHVYARLGFVHEGTLRQALL
+LDGEWIDCHVVGLLAHEWHARRAAPSSD
+>3_480
+MTPDPSVDASPQAAPTVAVTADPGRAPADDAGPDERRPSEPTRVQALFYSPPELTDGRIT
+LRPAGADDAAALYPLLQDRETLLLTGSTHSSARADRIVSGEIQPWGSPEKLAEDYDAWSV
+ADDRAVWVIEEDATIVGEMVLMDLDPPNISCALRLWITGATDRGIGTAALTLALDWAFRT
+VELHRVSLDVFEHNPRAIHVYEKLGFVREGTMREALWQDGRWIDSLGMGILRREWLARQD
+G
+>3_642
+MVDNLRAVQLYLQCGFVVEGLRRTSLIRDGGSVDEYAMAQLVLSSGSESAVVDK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002108.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002108.fa
new file mode 100644
index 0000000000000000000000000000000000000000..254066e8d393b79e895d278986e766843925c8ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002108.fa
@@ -0,0 +1,26 @@
+>2_743
+MTLAHPASRPMPATSPATPGATPPDPAARLVPLRGADHAAVLAEAVRVRASGGIPVVGDE
+RWPAALMAAQVEHAAATLRDLAVRDPRAAAEIAWAAFTSGSTSRPRVVLRTEASWRAGHR
+VAADWLGLRPGEELLVAVHPVSSMAVHAASLCGALGARLRVTARARLSAADLAGPVVLDA
+TPSQLVDALDLLDDGAPSTLRVALIGGDRLPAGARDRAAAHGIRVAHFYGSAEASFVAVD
+LDGAGLRPLPDVRLRIADGADDAGPAGPNTPDPNTPRARTGLLELRSDQLAAPDDSRLSS
+GAPRWREDGWLTTGDRATWDPDAGVLEVHGRADDVILTAGATVAAADVEAELAAARDGSG
+RPVASGVLVVGVPDRRLGERVCAVVEPARGQDPEAALQMLKTAARAGLSPAARPRRWVLV
+DRLERTGSGKIRRALPAATRHAAGRQDHA
+>3_706
+MSPLAPVPDPAARLAFLADADHAAVLAEAVAVRARGGVPVVGDERWPADLRAAQREHAVV
+QLRRLAARDPDLAARVGWAAFTSGSTSRPRVVLRTDDSWRAGHPHVAAWLGLAPGEAMLT
+AVHPVSSMALHAAAWCAATGHRLAVSPHARLTAADLTGPAALTATPSQLTDALDLLDDGA
+PSTLRVALVGGDRLPAGARERAAAHGLRTVHYYGAAEASFVAVDLDGSGLRPLPGVELEV
+AEPDVLADADGPRTGVLRVASPQLAVPDDSRLASGAPRWDAEGRLTTGDRVTWDPAAGIL
+TVHGRADEVVLTAGATVSAADVEAELAAVAGPDGRPVAAGVLVLGVPDPRLGQRVAAAVE
+PAPGVAPEDALAALQGVARARLSPAARPRRWVAVGRLERTGSGKIRRVTPPELRP
+>4_1933
+MIPPVRLPPSDDDVAPAVSRLAPLRGADHEAVLRRALEARTAGLVPLVGDERWSVAQWQA
+GVGHAEALLAELTARAPDRAARIGWAAFTSGTTGRPRVILRTADSWRTGHRLVEDWLGLE
+PGESLLVPVHPVSSMAVNAADLCAHVGARLLVPSRARLRAADVTGGAAAVHCTPAQLADL
+CDLLAAVRAASAPAGPRVVLVGGDRLPGQLRERAAALGLRVVHYYGSAEASFVAVDPDGS
+GLRALPGVRLEIREGVLHVRSDQLAEPDGTRLTDGTPRWGADGWLCTGDRAQIDDDGVLH
+LRGRADDAILTGGATVIPAEVEAELLRATVRRESTASGGDSAPHAVPVCTAVLVQGEPAP
+RLGSLVVAHVEPAPGLPADVVLAALKEHARTHLPPAARPRRWQVVDRLERTGSGKIRRMA
+PDVAAIPDPPGGSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002109.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002109.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8a78184b73b3c6065bf58a4e6acc03fceecf955
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002109.fa
@@ -0,0 +1,20 @@
+>2_744
+MVASALTGGDPALPGIGPVAAVREVLDAAGIALAEVAVVEVVEAYAAQVWAVLDELGLSA
+EAGAARADDWGVDPRVNAEGGALAFGHPWGASGAVAATHAVRRLQSCPPGSSALVTCAVG
+GGMGVALVLDVA
+>3_707
+MSAVGLDAAPVWITAVSRTPVTARSRAQAHLGAGELAAGPVGEVAAGTHPAAVVLGNGAG
+PGGNVARIAALAAGLGVATPGWTVDAQCGAGLVAVAQAAGHAVATGRACVGGGVESPSTA
+PERSIDGVSYAQAPMVPAGWDDPGMTAAADALAAARGIGRARQESFAARSHVLALAGGLR
+LPDDDGPRRLDAAALARFRAVTPGADPATAVTGATAARIADGAAAVLVTPHSAVVRETDG
+VSTASVRGVDVLRPCRVLSWSLTGVDPALPGLGPVSAVRDALDAAGRTLEGVAVVELVEA
+YAAQVLAALDDLGLTGASGTSAPGASGPATAHDPWGVDPRVNAAGGALALGHPWGASGAV
+AVVHAVRRLQAEPPGAVGLAACAVGGGMGAAMVLEVA
+>4_1932
+MTTTPGLWITAAARTAFTARSRGQAGLDAGALSAQAVAAVTGPAAADVAAVVLGNCTGPG
+GNLGRIAALAAGLGEHTPGWSVDAQCGAGLAGVLQAAQHAAFTGRPCVGGGVESPSTAPQ
+RSRDGVPYTQAPMVPSGWPDPGMTAAADALAAADAMPRARQEAFAARSHALALAAAGLRR
+IERVPGAPDDDGPRRLDARALARFTPVHPDADPAAAVTGGTAARIADGAAAVLVVPCERS
+PVGRDEPAGGLRPVRIVGAEIRGGDPALPGIAPVAAVERALAAADWRLGEVAVVEVVEAY
+AVQALATLDRLGLTDHARPGPASLGSDRQGLDDWGVDRRVNAAGGALALGHPWGASGAAA
+VVRAVHRLQGQPPGARAVVACAVAGGLGITMLLEVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002113.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002113.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e81ffb84aa870e2ace010ddf12d8f4731fadf9c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002113.fa
@@ -0,0 +1,16 @@
+>2_1272
+MSSPTGGSTAADASPRNRAPGGLLNRFLNVIEWSGNKLPDPIIIFAALCALTLAASAVAG
+LSGWSAVHPGTGETLVATNLLSTEGMRVVIGDAAKTFGAFAPLGQVLIIMLGIGVAERSG
+WFEVGLTQSMTSAPKGLIIPAIALIGLLGNIAGDAAPIVLPPLAALIFLKLGWHPIAGIA
+LAYAAATGGFAANLMIGMSDALVQGFTQEAAVIIDPDIETTVPMNWWFIAASVVVLLPVL
+WLVTSKIAIPRLGSYQATDDVEAGDMEVTDVQRRANRWALVALALFAALVVAACIPQGSF
+LRNAETGSLTTDAPLMNGIGLILAVAFFLPGLVYGVRAKTITGSSDVARMMVESMATMAS
+FIVVVFFASQLLSYVSASNMGAILAIRGAELLQGQDGIVLILGIIAISAVVNLFVGSASA
+KWAILAPIFIPMMMLLGYHPAFTQMVYRIGDAVTNPITPMFPYFALVLTYAQRYDKKLGI
+GTFISTLVPYSLAMGLVWTVMMVVWYLLGWPMGPDGPIHLPTP
+>3_1182
+MTSPTGGSTAADASPRKHTPGGLLNRFLNVIEWSGNKLPDPIIIFAALCALTLAASAVAG
+LSGWSAVHPGTGETLVATDLLSTEGMRVVIGDAAKTFGAFAPLGQVLIIMLGIGVAERSG
+WTICAATTWCGTTRPAPRWSRSCARTCSRAR
+>4_585
+MGIGSLIATMLPSSIAFLLAWTGMVIGWMWLALPLGPNAPVQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002116.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002116.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a071fe6082aae0808fa8dd42be6b3a4496c83742
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002116.fa
@@ -0,0 +1,17 @@
+>2_2378
+MSQPTAAGFRFYDAFNGSAADPSPHFNVARYRAHYPGPPTPGQAGCAISHFRVLESFASS
+LGHEDGVALVSEDDVLMPPETEAVLEGILKDDSFEIAVLADRGPTNPSLAFQRLLMTEAE
+LSLLSRPIVCGGRIRRLGRFEGNPYMAALYLVTRSGARKLASGLVDDAGGPWTIADDWPL
+FRDRYGLDIRVLRPGLVTYMGGSTTRDAESLARDALSAAGDGRPLTRLKTAVGLRSRSRA
+ARLVVRATLRDIATR
+>3_2223
+MPDIVDYRVIALADSTRLEGFLAQPLGRRFRPFEAVDARKGYGPEDFDAEGFEVRFGRPP
+LNGEVGCTLSHMSVLREFAVEDGAVTDVLVVAEDDARFSRFTSEVLNRLLETSAVRGLVV
+LADPYGPVDMRGRLGAPTLEDKLQQSLLRRRLRPLAGAPRFAVGRWSRGLVGTGFYLVSR
+DAAKYDIAWRLRHRRGGAR
+>3_2258
+MGQITDRYVISLEGSPRREAFFSQPGVADFVVWDAFDGRTGAGRDRFDVVAFERRAGRPP
+EGGEIGCTLSHAGLLADFAAGLGRPDDLMLVAEDDVVFTPDFEAVLGRVARTRGWGWTLL
+AQGLEDPFRDPFWAKSRDRAPQSLLAKPVGPPSSPWRYRLGNWDGELWGTGLYLVTREAA
+RALTDHATREGLSWAADDYVTWHAAAGVKVWILLPTIAGWVGESEINATTRPHLQIQSYA
+AHPMGRQAWSRRVSRFRAGARIAWKEMRGDTRPWAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002117.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002117.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5362f66630c563fbdddf155451c8dc46dcb7da5c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002117.fa
@@ -0,0 +1,9 @@
+>3_315
+MPQKYTPEFKAKALKLIEERVRAEQCSAWVACTAVGEALGGISPHTLRNWWKQDRVDHGE
+APGLSTAEAEEIKKLRRENLELRRANEILRKASAFFAAELDRPTTR
+>3_399
+MQLIEERIRAKQCSGWAACAAVGEALGGISPHTLRNWWKQSHVDRGETPGVSTDEFEEMR
+RLRRENLELRRANEILRKASAFFAAEHDRPTTR
+>3_648
+MPQKYTPEFKARALELIEERIRAEQCSGWGACVAVGEALGGISPHTMRNWWRQGRIDRGG
+APGVSTDESEEMRRLRRENLELRRANEILRKASAFFAAELDRPTTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002119.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002119.fa
new file mode 100644
index 0000000000000000000000000000000000000000..827ec123b8464db726be505df0b4a0872338dd05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002119.fa
@@ -0,0 +1,6 @@
+>0_157
+MNPELEQALRLATDPPGGVSLEALEDLVRDDPTTWWDISEAATHLNVTAHTLRYYERIGM
+VSVPRDDAGHRRYDSPAIRRLVFITRMRTAGMPIADLQHYLALGRV
+>1_335
+MNPELEQALRLATDPPGGVSLEALEDLVRDDPTTWWDISEAATHLNVTAHTLRYYGRIGM
+VSVPRDDAGHRRYDSPAIRRLVFITRMRTAGMPIADLQHYLALGRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002122.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002122.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a1e67822864c79b8a83dd06c9d642ccb0d8bfec8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002122.fa
@@ -0,0 +1,14 @@
+>0_181
+MSQQDLATAVGLERTMVNRIEGGQRKVTALELASIADALGTRMQSFFTEPAPALVSHRSA
+QGLDTTESAVDHLLAELLADVEFLHGLHPIEGFGVRDPWEQPKSVHEADDMAARAREHVG
+YTATEPVKDLQAHLATAGLLLFSRNFGVDAADAGTVLLAEGGISLVNSTPKVGRRRLSAV
+HELGHYLLADEYTVDWRTAHTGPDIEGRLDRFARAFLLPAAVLLQEWPAAAHSGDVRTAA
+VKIAGTYLVDMSTLARRLHDLELVDASTANDIRAVQTTQTDIITHDLYPSDEMAGTTQPR
+VYQKHVIALFEAEKLSRERTLDLLDGTFDDDDLPDLPPRQEQEIWEYVS
+>2_202
+MVNRIEGGQRKVTALELAAIADALQARMQSFFTDPAPSIVSHRSAQGLDATESAVDHLLT
+ELAAAVEFLHGLRPIQGLATREPWEPPTSTEAVEDMAARARAEAGYGPDEPAKNLQDHLA
+TAGLLLFSQDFGADAADAGSVLLEEGGVAIVNSAPKVGRRRLSAVHEFGHYLLADEYTVD
+WRTAHTGPDIEGRIDRFARAFLLPATAMASVWPRAVTANGTRTAAVTIAGSYLVDMSTLA
+RRLRDLDLVDASTANDIRAVQTTQTDIVTHDLYPSHELEGLTQPRTYQKHVLALFEAEKI
+SRDRALGLLGGTFTDADLPELPPRQEQEIWEYVS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002123.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002123.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3e523cff7c18c3d737b967c64ec47b8d3f8c011a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002123.fa
@@ -0,0 +1,5 @@
+>0_183
+MAPHSSTPLFAVGYGKIEKVRTNFPDAFRDQKVTSQLKHFIDSTTSLTFHWGSLSIGTLR
+PWGR
+>4_183
+MAPRSSTPLFVIGYGKIKKVRTDFPNAFRDQKVTSQLKHFIDSTTALTFH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002124.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002124.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46607e87debe86a9000fc298a346ecab9e5657c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002124.fa
@@ -0,0 +1,16 @@
+>0_245
+MATQARDGRFSNEVLPQDERPSRFGPGLIIAASFIGPGTITTSIVTGAEQGFVLAWAVVF
+SILATIVLQEMSGRLGLATRMSLGHALREVFSSVPARLVMAILVVAAIGIGGASYAGGDT
+VGTALALTSVTGLSQPVVVIGIVLTIGILLWTGSYKLIERVLTVMVGLLGLLFIVTAVLV
+QPPIGDLLMGMFIPRLPPGTALLAVALIGTTVVPYNLFLHASLVQEKWGPGLDSRESLRA
+ARTDTAVSISVGGVITLAVMATAFGGMYVKGMQAETGRDLASALEPLLGDAAGWVFAAGM
+FAAGFTSAVAGPLGAAYAIAGTLGQDTDLRSVPARIVWGAVLAIGAVIALTGTNPTEVIV
+IAQAANGLLLPIVAVFLMVVMNSRRLMGSHRNGPLANALGGLVCLVVIGLAVYQLGGLAG
+LWD
+>1_2210
+MAILVVAAIGIGGASYAGGDTVGTALALTSVTGLSQPVVVIGIVLTIGILLWTGSYKLIE
+RVLTVMVGLLGLLFIVTAVLVQPPIGDLLMGMFIPRLPPGTALLAVALIGTTVVPYNLFL
+HASLVQEKWGPGLDSRESLRAARTDTAVSISVGGVITLAVMATAFGGMYVKGMQAETGRD
+LASALEPLLGDAAGWVFAAGMFAAGFTSAVAGPLGAAYAIAGTLGQDTDLRSVPARIVWG
+AVLAIGALIALTGTNPTEVIVIAQAANGLLLPIVAVFLMVVMNSRRLMGSHRNGPLANAL
+GGLVCLVVIGLAVYQLGGLAGLWD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002125.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002125.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45f0041c421c7202223e0719b7f9a48d75beb3cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002125.fa
@@ -0,0 +1,5 @@
+>0_250
+MKTRALLASALLLASTLVGAPAAAASAASAEDDVVTTLGLGKGTAEWTCRHFGIWCD
+>2_101
+MKLRSLAASTLLLASVLVGAPAATATSTPAAPTTGPAVTAPTGDQSGTDGLNKGAKEWAC
+RNFGVWCD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002128.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002128.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f66611d29ce286f9f26bad491ca5f057c74aa777
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002128.fa
@@ -0,0 +1,6 @@
+>0_479
+MADYHGFYRDELGIDVLAVRPNLAGWEGESSIQDDEHVGWRAANDAEIPPVGVADFLREW
+RHRALRKARSTKFDLHWRLRMSQQR
+>4_478
+MADYHGFYRDELGIDVLAVRPNLAGWEGESSIQDDEHVGWRAANDAEIPPVGVADFLREW
+RHRALRKARSTKFDLHWRLRMSQQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002132.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002132.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6ec00c1f13eb49d2481e167d6eebc8503b83e5e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002132.fa
@@ -0,0 +1,20 @@
+>0_571
+MATMIQESMDSEYDDVRFPQERTQGLILGLTLEQVIVVLAGVLIGMAFILRGGPAMFVGI
+GLMAVIGAFGATRFRGRSLPGWVWVAAQYLRRGATDQLEYRQGMAPAHVLELVDGEPQAP
+VSEAGPQAQRDAKGRIKPGEPARFRLPGVAGELMVYAMPNGAGFVWDPRAREAVVCAKVM
+TTRGFDLESFDAQEERSLSWGSSLAALSRLPGVVRIQASDQTTLISGAAVEDFYESKQEG
+AGRTGASIDPFLDQAFRELMKEAQSMPVHEQWLTLVVSPSKITSQVKALGGGTPALMEHM
+LKLMTTVESTLPRSGTQVTAWHSPRTLAGLSRSAFDPDASVMVSTMKADGKTAGTAPSSA
+GPMAVEVHAGHMVTDGNYHRTYKVSELPQNLARLGFLDELVFAGDFRHTVSVFLAPVERG
+AAVRSVQRRKTDWHTNSRLMNKLGRIGSLEHDQSLEDVEREEAELRRRHTGVEVVVLVTV
+TGASRSELESAAAEVVASGITAECELRPVWMEQDAAFVAGALPFGRMKL
+>3_1755
+MSSRKKNNSHEPEATGSELVPVKFSRLTRRGILLGLSAAQLVTVGIAIATIITALYAGGG
+MWLAYTAPVWATAVLLTWVPVAGRPVIEWVPVAGWWVYRTTIGQLLYRRRIVTPRPAGTL
+ALPGDQARLREYEDPTTGAGMIHDPHQNTLTVVCEITHPAFVLLDPAEQERRVTAWGRVL
+ATVCRSGRIATLQILERTLPDSGTGLAEWWTTHGQPDDTSWAATTYAELINRAGPAGERH
+ATTLSLSLDMRNAARQIRTAGGGIRGAAAVLRQEMNTLTAALRSADLTPSGWLTPGQIAV
+ILRSAYDPAIAATLERHGEIGHDLATAGPVAVNETWSRIRTDSAHHAVLWISEWPRSMVY
+PGFLSPILLSSGIQRSFSLICTPMRSDQAARDIRKKKVEHISDQAQRAKIGQIEDASQTA
+EYHDVLQQEADLTAGHGILRYTGLITVTATTIEDLDAHVAALEQAAIQANCETRLLAGQQ
+AKAFTAAALPLCRQV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002133.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002133.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2db33acb9b0dc93257f66ae3438d4bba9ef1f210
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002133.fa
@@ -0,0 +1,18 @@
+>0_572
+MREEPKVDLFQIIEPGKMSLREARVAQRKMKMAQAQAQRLRNREAREERFPQPQWGKAGP
+RGARQLRGLRTLAPRPVRTTTHTAATAYPFVAGPGLGARGLMIGKDMHGGGAFCFDPWAL
+YEAGIISGMSMMLFGQVGTGKSSLAKSLAVRQVLAGRKLSVASDKKGEWTRVVKGLGGSV
+IQVGPGLDTRLNPLDPGTRPSTDVQGEPMTDRAWASMVRTRRMSILVALVKILTDREMTS
+PEHHVLSAGLDAAVAVADAEGRPPIIPDVIRALDAARTDPDAMKAEAASVTMMTLGRVSS
+GDLAGMFDGETTVVLDEQACATSIDTSALLGASPEAVRVVNACAGAWTEAMVTTRDGGQR
+IVIYEEGWDNISSEADLRRMVEQWKLSRAYGIFNVLVLHKIADLDMAGDQSSKMAAMARS
+LLADADVKVIYRQDRSALKITTSEMELSDRERSLVRSLPKGTGLWRLGDSSFEVQNVLTR
+AELPLFDTDERMDKAKEAVA
+>3_1761
+MAEGGLGSDGVFVGQDLYSGGSFVYDPWVLYARGIITAPNLVLAGIVGSGKSSLAKSLYT
+RSLPFGRRVYVPGDPKGEHTAVAEAVGGKAIVLGHGLHTRLNPLDEGHRPGGLTDQEWAS
+TVASRRRDLIGALAETVLARGLTPLEHTAIDLALTATVAENEVPILPMVVDHILTPSHDP
+GGRLAEDGRLVGHALRRLVAGDLAGLFDGPSTVAFDPDLPMISLDLSRVTENSTLISVLM
+TCSSAWMESALLDPNGGQRWVIYDEAWRLMSHPALLKRMDAHWRLARHYGIANMLIFHKL
+SDLDNVGDEGSAMRSLANSLLANAETRIVYRQESDQLGPTATALGLTGTEQTLLPNLGVG
+QGLWRIKNRSFVIQHQLHPGELELFDTSSRLTAGVK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002134.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002134.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d82857216ed05154842200e964fb8cf3b940e1e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002134.fa
@@ -0,0 +1,15 @@
+>0_573
+MRRERGNNSVLEGDNPAETALIWLIGPAVLLYGAYLLAGFLAGRIHCGAATKPDSLFAPL
+GFLVGEHDPAAFGATAQGCTATTGGVIGWLIGLGVLALVLIGVAVTAWSRYQQSDKKFIK
+ELREREGLARSAEITKTVGRKSVLSRVKKVRPSIKKPAITDGAMRLGKAEGVDVFASYEE
+SVVLIGPPRSGKGVHLLIGAILDAPGPVITTSSRADNLGATAELRKKKGPVALFDPQGLT
+GQPSTLKWSPITGCEEPRVANQRAASLIGASGLGSSSSNAEWQAPAITIMECLLHAAALG
+ERTVDDLMRWGNNPAEAKEAVKILTEHPKAALNWNLVLKGIIEGDPKLLQSKWFGVEGAV
+KGLSVPEVRDVLRPNRFEETLDIDKFLTECGTLYIVGTKTGGSSAGPFLIAMMDAITERA
+RELAAKSPGNRLDPPLSLVLDEIANISGAWPGLTQLMADGGGVGISPFAVFQSMAQARNE
+WGEQQAQALFDAATVKVQLGGASNVSDLEQFAKLAGQRKIMRTSKSRGKDHTSVSEQIHD
+TEVVSVAELRRLPFGWGVLLNRNGRPILMQMTRWWDRKDGKQIKEAAGRYSKALLAELES
+KDPAPSTPTDADRAEDSVAALDPVPETAPAIPVR
+>3_2191
+MLEAIARTSKSCGKDHTSVSEQIHDTEVVSVAELRRLPFGWGILLNRNGRPILMRMTRWW
+DRKDGKQIKEAAGRYSKALLAELESKDPAPSSTPTDADRAEESVAASDPVPEAAPAIPVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002135.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002135.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6673e18b273284f6e6d22a8d22bb48f07216b4ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002135.fa
@@ -0,0 +1,8 @@
+>0_574
+MGRFGLHRTGSAEYKRYLRSQAWGYRRVRWFADCRQAGQEPACQVCGITLTRAGTLDLHH
+VSYKGVGQDEEGRWQAREAHNDLMPLCRDHHQRLHQIMDGKKEFFGWDRRRATIVIVARM
+VRQSQA
+>3_2190
+MGRFGLYRTGSAEYKRYLRSQAWGYRRVRWFADCRQAGQEPACQVCGVTLTEAGTLDLHH
+VSYKGVGQDEEGRWQAREAHNDLMPLCRDHHQRLHQIMDGKKEFFGWDRRRATIVIVVRM
+IRQSQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002136.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002136.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b329362e9e87a0a48ee78b34230e8ed7841bc106
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002136.fa
@@ -0,0 +1,18 @@
+>0_576
+MIPVKDLIKAREDWDFEREVALDEQSSVERELASANGHLSRLKEALIERGLASLLWGAQH
+EDVASVPDLVQDTSEAVLAAQMYLADWLVLPDSAVRHLEDIDTAPEAYNWGNKAWRGFRA
+LAAYAQDRASGWDKGGFWEWCASGPVLGWPATSKKLSMTESEGVQTSGKFKGTRDFKVDP
+AVDSSGEITMLAHLKISEGGGNLAPRVYFYDDTNGATKKVHIGLVGPHYLVPNKSTN
+>4_179
+MAVGYRAIFAVSPREDALAIARESVHSWLVDKLNRARPEVRQQALELDFNAPFAVQLSDE
+IHVSNTRAHGDNGQLQQLIRLDESSAPGETWRVNITADRNDVGGVRQQTIMVELDPLHLD
+AETAVMRAAPPRFVREMLTQHVLRSGTTVLTATPKALRGSEGGREAYRAVIDPLRQAQAV
+IAAQPPGSDMTIWQAAVASLTRQAMGITTALTLDKDALDQFNRRLPRNLQLQPGEVRTFA
+PHVDLDDPADSLRHRSLGPGTFARHIKPRVKDGVTVPEVDPTFASVHARRARMYALEQPL
+PDSIRSMRQQVRTGELREERDRAAGLVTGFSTVRVRPAAPAPAASPHRPGAGKRPSPTPT
+SGRLGASGAIPVPRPLPPSQEKVAEASSATPVAPAEAPQASAPSSITPVPAWQKTLVQLV
+WSTLGTEEITKEAIELLAEQLAASGRREQVADEQIANAVREAEIAAAQHDDLRARLEDAE
+LAAAAEQEERESLAREVEHLRRKAIEAERYEDLVVPEATDEEAKPSTFDDLIERIQSERF
+TTHEYVVFTGDMKKVNEVEAIDIVGRHLSSCWEFVLTLEGYARAKKDGFNGGVHQYLTSG
+EVDGKRCSPGKHASLESESVKSNAAQRRERLLPVPKNVDRSGAVHMWAHFKCSKDGTKSP
+RMHYYDDTDNTGKIYIGYIGPHLTNRQTSSM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002137.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002137.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eaa60fa9828127af24ba677022246fe5c1991329
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002137.fa
@@ -0,0 +1,6 @@
+>0_805
+MVSMSRPPEPRPAPAPTARAAAARPATPPGVQGRWARRAAGGLIGVSVLLAAWSFALPFV
+FGLGPRQVPWWREVFGLIRIQGVVGV
+>1_546
+MSRPPEPRPAPAPTARAAAARPATPPGVQGRWARRAAGGLIGVSVLLAAWSFALPFVFGL
+GPRQVPWWREVFDVNHEANLTAWWSSGLLLLGAAGFTTVGLVRRALGRTGGGACSRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002138.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002138.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f81ccfb4e9f2c955fa929ee0bd1b3ab5030b6415
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002138.fa
@@ -0,0 +1,12 @@
+>0_850
+MPAGKSIRRVARAGARLLPPEQRRRVRRTGGALLRRLPPQVAEEVRGVFGIRWGDRPAHA
+RPADALGLAGGPARTRPGSASLTGRGAAAVGADPEAAARLERVLGLADTSRTERGGRAVG
+VVAAPDVRAALAAAGHRVVPLVPGTAAAVAERVEAVVVDVDGVDGPWAGALDAAGAALYL
+ELRGAVSAAAARGVTVWVLSRGRHQHRLGALALLHAEDVIVVEAGADRTPLHFTEDPGDA
+PQGIADVLAACPEESA
+>1_581
+MPAGKSIRRVARAGARLLPPEQRRRVRRTGGALLRRLPPQLAEEVRGVFGIRWGAPPAHA
+RPADALGLAGGQARARPGNASLTGRGAAAVGADPEAAARLERALGLADTSRTEQGGRAVG
+VVAAPDVRAALATAGHRVVPLVPGTAGAVAERVEAVVVDVDGVDGPWAGALDAAGAALYL
+ELRGAVSAAAARGVTVWVLSRGRHRHRLGALALLHAEDVIVVEAGADRTPLHFTEDPGDA
+PQGIADVLAACPEESA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002140.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002140.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de43729ae582fba52ee59265404280074b623672
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002140.fa
@@ -0,0 +1,14 @@
+>0_857
+MSVLRTGLIGLGMMGRHHARVMRSIEGTELVAVADAMGDPHGVAGDLPLYDSVQGLIDHG
+VDAVMCAVPTGLHEEVGLALAEAGVHVMVEKPIAHSTEAGTRLVHAFDEAGLVGAVGHIE
+RFNPALQEMRRRIQAGELGRVLQITTVRQGGFPARIADVGVVKDLGTHDIDLTAWLADSP
+FTRVAAETMTNSGREHEDMVVANGRLECGAITSHVVNWLSPVKIRQTVVTGELGAFVADT
+VHADLTFQANGSVRTRWDAVSAFRGVSEGDVTRLAIEKPEPLHTEHEAFRDAILGVRQEH
+VSMAEGLATLRVAEAMIASAHTGESIRL
+>1_588
+MSVLRTGLIGLGMMGRHHARVMRSIEGTELVAVADAMGDPHGVAGDLPLYDSVQGLIDHG
+VDAVMCAVPTGLHEEVGLALAEAGVHVMVEKPIAHSTEAGTRLVHAFDEAGLVGAVGHIE
+RFNPALQEMRRRIQAGELGRVLQITTVRQGGFPARIADVGVVKDLGTHDIDLTAWLADSP
+FTRVAAETMTNSGREHEDMVVANGRLECGAITSHVVNWLSPVKIRQTVVTGELGAFVADT
+VHADLTFQANGSVRTRWDAVSAFRGVSEGDVTRLAIEKPEPLHTEHEAFRDAILGVRQEH
+VSMAEGLATLRVAEAMIASAHTGESIRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002141.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002141.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f23cff07458781925634064c6ddb70ed3e3e41a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002141.fa
@@ -0,0 +1,26 @@
+>0_859
+MSTVLLLTTGTGPAEGLLLQDLRDSGHVVDVLDVASHAWLRRRPGLAPAPLYPWTGTHAL
+RAAGAQIAREMRRVTAAGAYDAILASGLGAAGFAARHVEEEFIPLLRRGDLDFSAARRHA
+EEDFAALTRAVDRLFLADEWEFDKALSKGSRSAHLRHPRVGLAPQTLAPLAAEAETPRVV
+VLHPEHVDADRLAAQMEALQTAVDTVPGASLRSLSASALYRTRDLAAGRAFDAVAATRLG
+GATHVVLVGSSRDHAAVGELLVGTGFAERLVVEDTIGSGAWAAGHPGVRTGRGLRLVTEL
+AAALHGGPETHSAVDTVDGGTTDLLSAYRAAMTGRVDRTFEDLAVLRHDGPLDVFFSTSP
+LEDRTDGARPQRVRNMNDALSEPAAALRLSSVPGVFDRRLRVLDEALAAGRPLGLLYGEN
+STSPIPVDRVTAALADVMARFSAGGGTSVWFVRDLHWLDEIDGYLEDADARRDVQERGLA
+EFDAMAEAAYRLAAPSAESGAGFDALLARHGRGPVDWLPLPPAVSPANTVPADAPAIGEE
+GVTLLYAGGVGGIYGLGQYLTAVGTLDPQVRLDFVVRAGERSVLEDMLAEHGLADRPGLR
+ITTVPLEWYVPATRTVVGVVLLGGKYARFSFPYKTMSLIERGYPVLCFADMGIADFLERN
+RVGLGVARSSEAIRAGIVTLVRDGAPGMAEAQRSQSWAVRVATARAALED
+>1_590
+MSTVLLLTTGTGPAEGLLLQDLRDSGHVVDVLDVASHAWLRRRPGLAPAPLYPWTGTHAL
+RAAGAQIAREMRRVTAAGAYDAILASGLGAAGFAARHVEEEFIPLLRRGDLDFSAARRHA
+EEDFAALTRAVDRLFLADEWEFDKALSKGSRSAHLRHPRVGLAPQTLAPLAAEAETPRVV
+VLHPEHVDADRLAAQMEALQTAVDTVPGASLRSLSASALYRTRDLAAGRAFDAVAATRLG
+GATHVVLVGSSRDHAAVGELLVGTGFAERLVVEDTIGSGAWAAGHPGVRTGRGLRLVTEL
+AAALHGGPETHSAVDTVDGGTTDLLSAYRAAMTGRVDRTFEDLAVLRHDGPLDVFFSTSP
+LEDRTDGARPQRVRNMNDALSEPAAALRLSSVPGVFDRRLRVLDEALAAGRPLGLLYGEN
+STSPIPVGRVTSALADVMARFSAGGGTSVWFVRDLHWLDEIDGYLEDADARRDVQERGLA
+EFDAMAAAADRLAAPSAESGAGFDALLARHGRGPVDWLPLPPAVSPANTVPADAPAIGEE
+GVTLLYAGGVGGIYGLGQYLTAVGTLDPQVRLDFVVRAGERSVLEDLLAEHGLADRPGLR
+ITTVPLEWYVPATRTVVGVVLLGGEYARFSFPYKTMSLIERGYPVLCFADMGIADFLERN
+RVGLGVARSSEAIRAGIAALVRDGAPGMAEAQRSQSWAARVATARASAED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002147.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002147.fa
new file mode 100644
index 0000000000000000000000000000000000000000..611a98e5570306f269b73cbec809db5f9d8281fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002147.fa
@@ -0,0 +1,16 @@
+>0_920
+MATIQTRTNKAGRTTYRVGFYEAGRFQWLPALAREAGAQRVKAIVEDPRQGPTVARRILE
+AQVDSAPGMPTLAEFFPRYIEHRGLRCTPGTLAGYEAEAARTFLPRLGELPVDMIDRRTV
+AEWIRWQLQQPTARWRAVAARAAAATPPRPEPPLATVSPKTVRNAHALLSAVLGLAVQEG
+ILPANPARGADLPDDDVEEERGIFSRAEWARFYAAISESYQPLLIVLLVTGARWGEATAL
+QVRDLDVAASVIHVRRAWKKGKEGAVLGVPKTARGRRTIMLPDWAVETLEPLAAGRAADE
+FLLTVPGGGVIHRTNFVERHWKPALAAAGIAKHLTPHSLRHTFASWALMDGVPAQVVQHR
+LGHESLQTTSRVYAHLLLDAQRAAVDAIGWEPPPGA
+>2_1891
+MATISTRTSKKGVTTFRVGYYEGGRFRQMPAMLSETGARRIKAIIEDPAQGPDVARRLLE
+AHADGAEDVPTLAQCLDRYVEARAVRCSEGTLAGYRREAARTFLPRLGQLPVTAIDRPAV
+QDWIRWQMTQPTARSRAAAERAARAGTPAPSLEPVSPKTVRNAHSLLSSILYLAVQDGLI
+PTNPAHGQDLPADDVEEEKDIFTRPEWDRFYRAMTPHFQPLLALLITSGARWGEATALQV
+RDLDVDAGVIHVRRAWKKGAQGVVLGTPKTQRGRRAIMLPDHVVAMLTPLAAGRPPEDFL
+LTSPTGRVIHRTNFVERHWKPALAAAGITKDLSPHSARHTFASWALMEGVAPQIVQHRLG
+HESLETTSRRYAHLLLDAQRAAVDAIGWRPSPGT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002149.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002149.fa
new file mode 100644
index 0000000000000000000000000000000000000000..95077126bae96d9a7fb3affb59eb53235832f751
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002149.fa
@@ -0,0 +1,12 @@
+>0_933
+MPLTASTVTRTVSVDGASVTCHDSVTPGELDRPLVLVHGTGGTTASHFGHLFPMMATRTR
+VIAVDWAPTADPAADLTVDLLVGQVRAVVDELLGPDAAFDLLGYSLGAVVAGQLAADLGR
+RVENLVLVAGWATTDVHQRLRNEVWRHLYATSPDALARYTAFCGLSPLALRSLTPAMLDG
+ALASLTADEFTARQMDLNARVDVADRLSAVTARTLIVSCAEDIMVPPHHQYELLGIIDDA
+RLTTMTSGHAFFLERPAELMQIVDLYLREPDRHPAGAIIPETHA
+>1_655
+MPLTASTVTRTVSVDGASVTCHDSVTPGELDRPLVLVHGTGGTTASHFGHLFPMMATRTR
+VFAVDWAPPADPAADLTVDLLVGQVRAAVDELLGPDAAFDLLGYSLGAVVAGQLAADLGR
+RVENLVLVAGWATTDVHQRLRNEVWRHLYATSPDALARYTAFCGLSPLALRSLTPAMLDG
+ALASLTADEFTARQMDLNARVDVADRLSAVTARTLIVSCAEDIMVPPHHQYELLGIIDDA
+RLTTMTSGHAFFLERPAELMQIVDLYLREPDRHPAGAIIPETHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002152.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002152.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1415092f3afd6156f4bcce93218ff606bb519ad7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002152.fa
@@ -0,0 +1,13 @@
+>0_1341
+MIRVEAGMSTARFCQLFDMPERTWRRWQAKARTGTAVKGPWPQPGRQAARELVVKHALAH
+PAWGHRKIWAMVRHDGHVVSEATVLRILRDEGLILPAQYQRERRKLAERRKAAFATEPSG
+PNQVWQLDFSEFETTTGGTWRLAGCRDYWSKYEHPFHVSPTGNQHDAIDAIELALADYEA
+MFGHPLVEACPVDPETGELLPVVTIVTDNGGPFRSFRFESFIAAHPELHHVRTRVKTPGQ
+NGSRERGFGTLKYERLYLDEIDDAIVLAERAEDYRIEYNELRPHEAISWNRPKEVHLGLA
+DPTTPTFKTKEILPTT
+>1_1082
+MVKHALAHPAWGHRKIWAMVRHDGHVVSEATVLRILRDEGLILPAQYQRERRKLAERRKA
+AFATEPSGPNQVWQLDFSEFETTTGGTWRLAGCRDYWSKYEHPFHVSPTGNQHDAIDAIE
+LALADYEAMFGHPLVEACPVDPETGELLPVVTIVTDNGGPFRSFRFESFIAAHPELHHVR
+TRVKTPGQNGSRERGFGTLKYERLYLDEIDDAIVLAERAEDYRIEYNELRPHEAISWNRP
+KEVHLGLADPTTPTFKTKEILPTT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002154.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002154.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf946e1d4854db44993de4da431114dbbb08f6c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002154.fa
@@ -0,0 +1,9 @@
+>0_1440
+MTTTTPKTARQLRAEWQAEIARREAEIVAAERAEARRIDEALRRAGRARVAAVETLYEML
+GIDEQTKTRTRRDGSVQTVRADLDEAERAERLVAAVAALLEGAAGTRSAPAGGAEAVPDE
+AAQMVPEEPSGALAPLPPAAGGESAEPDPEEDEAHASDDAEEPVSDEGDEAAREEDAYAE
+EPAYGTVSDDLHEAGWQA
+>2_2151
+MTTTKTARQLRAEWQAEIARREAEIAAAEREEDRRTDEALRRAGRARVAAVEILYELLGV
+DEQTTTRTRRDGSIQTVRVDRDETERAERLVDAVRALLAHCDGLRSAPAESAPTSAPLPS
+PAGLDATVSGREQTAHAESESTSDEGWAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002159.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002159.fa
new file mode 100644
index 0000000000000000000000000000000000000000..193a12eada39fcf87857f9d005d6005293f927f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002159.fa
@@ -0,0 +1,8 @@
+>0_1456
+MTTPQFSVDRTRRPVATYRAISTKDAASTQRDGEAVLEVRELSSRSGQREAEVLFHDGQW
+QLCDPEHDLVPGFTFDAFPEHPFLAEAYGETWNGWDTPVVRREVLADILTALELSHRWEG
+DVTVLEVDDYEDRIVPRLDGLYDLQQAGWTVQQVELG
+>2_2164
+MTTTPPPVDRTRRPVATYRAISSRDASSTQRDGEAVLEVRRFAARDGHAEAEVLFGDGQW
+QLCDPERDLIPAFEFDAFPDHPFLAVEYGEDWNGWATPVVTRETLADVLAALELAHRWEG
+STAVLEIEDYEDRIEARADGLYDLAQAGWTVQQVEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002162.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002162.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca732a79317953f18d2ef820d75ce53647635766
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002162.fa
@@ -0,0 +1,10 @@
+>0_1553
+MFSASVIDDATGVNMGIGFLGVALAFGLTVVAMAYAVGHISGGHFNPAVTLGAALAGRLP
+WKLTVPYWIAQLVGGVAAGGVLLAIASGRPGYSLAENGLATNGYGELSPAGYSMGAVFLT
+EVLLTAVFLYVILGATDRRAPSGFAPLAIGLTLTLIHLISIPVSNTSVNPARSFGVALFA
+GGDALGQVWLFFVAPLLGAAVAGLSYRFVFPNTSRVTEELPEPAADGTRDAV
+>1_1275
+MAYAVGHVSGGHFNPAVTLGAALAGRLPWKLTVPYWIAQLVGGVAAGGVLLAIASGRPGY
+SLAENGLATNGYGELSPAGYSMGAVFLTEALLTAVFLYIILGATDRRAPSGFAPLAIGLT
+LTLIPLISIPVSNTSVNPARSFGVALFAGGDALGQVWLFFVAPLLGAAVAGLSYRFVFPN
+SSRMTEELPEPAADGTRDAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002166.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002166.fa
new file mode 100644
index 0000000000000000000000000000000000000000..983b12d3ae6daf037a2fcdf28e58cba935e5f918
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002166.fa
@@ -0,0 +1,12 @@
+>0_1729
+MTGTRVATERHDTALVLTLDGPDRLNAVTPTAMEALHTALGEAGRDPAIRAVILTGRGRA
+FCAGADLRDDLDPEATMRAANRVVETIRAVDVPVIAAVNGPAVGYGAALAAAADLAVAAD
+DAYLLLPFTGIGLVPDGGSSVTIARAVGRALAAEMALTGRRLGAEEARAAGLFSRVVPGP
+DLAGVAHALADAVAERPRRAVALAKAALNAADAEVVGRALEREARDQVELIRSAEFAQRS
+AAFRR
+>2_1067
+MTGTRVATERHDTALVLTLDGPDRLNAVTPTAMEALHTALGEAGRDPAIRAVILTGRGRA
+FCAGADLRDDLDPEATMRAANRVVETIRAVDVPVIAAVNGPAVGYGAALAAAADLAVAAD
+DAYLLLPFTGIGLVPDGGSSVTIARAVGRALAAEMALTGRRLGAEEARAAGLFSRVVPGP
+DLAGVAHALADAVAERPRRAVALAKAALNAADAEVVGRALEREARDQVELIRSAEFAQRS
+AAFRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002167.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002167.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eae3552541ac971da0cdc431d073668b6b1f9746
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002167.fa
@@ -0,0 +1,8 @@
+>0_1730
+MTAQATDGRHAEDFTVGEECDLGTYEVTEQEVIAFASHWDPQDIHIDPGHAETGGRYGGL
+IASGLHTLAILQRLQVLGRREHWNVIAGQGIDRLRFRRPVRPGDVLSGHSRVIDVRLEPE
+WRRGLVVFDVRALNQEGKEVLTMEMAAYLEMRSEATAGRRA
+>2_1066
+MTAQATDGRHAEDFTVGEECDLGTYEVTEQEVIAFASHWDPQDIHIDPGHAETGGRYGGL
+IASGLHTLAILQRLQVLGRREHWNVIAGQGIDRLRFRRPVRPGDVLSGHSRVIDVRLEPE
+WRRGLVVFDVRALNQEGKEVLTMEMAAYLEMRSEAPAGRRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002169.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002169.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cac07dbef5d57919a7abde1e71e456213b8687db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002169.fa
@@ -0,0 +1,16 @@
+>0_1734
+MSTAPSSRDAVIVDAVRTPVGRRGGALRDWHPLDLLAHTLDHLVRHSGADADALDDLIAG
+CALQRGEQAGNVARNALLGAGLPIGLPGTTIDRQCGSGQQAVHFAAQGVRSGEYDWAIGC
+GVESMSRVDLGPLFAPGGPRGEWYGTRSLARFEGNLPAQGPSAELIVEKWGLTRERLDAY
+SVQSHRRAAEATREGRFTDSLVPIDGLDRNGDTVALTADEGIRADVDPQKVAALAPVFSP
+DGAITAGNSSQLSDGAAALLVAERGAAEAAGLRPKARILSMAVAADDPVLQFTAILAATR
+RALDQAGLDITDIDLVEVNEAFAPVPLIFMDEFGYPEDQLNVNGGSIAIGHPLGSTGARL
+LTQLTDELHRRQARYGLLTVCEGGGMANATILERF
+>2_1062
+MSTAPSSRDAVIVDAVRTPVGRRGGALRDWHPLDLLAHTLDHLVRHSGADADALDDLIAG
+CALQRGEQAGNVARNALLGAGLPIGLPGTTIDRQCGSGQQAVHFAAQGVRSGEYDWAIGC
+GVESMSRVDLGPLFAPGGPRGEWYGTRSLARFEGNLPAQGPSAELIVEKWGLTRERLDAY
+SVQSHRRAAEATREGRFTDSLVPIDGLDRNGDTVALTADEGIRADVDPQKVAALAPVFSP
+DGAITAGNSSQLSDGAAALLVAERGAAEAAGLRPKARIVSMAVAADDPVLQFTAILAATR
+RALDQAGLDITDIDLVEVNEAFAPVPLIFMDEFGYPEDQLNVNGGSIAIGHPLGSTGARL
+LTQLTDELHRRQARYGLLTVCEGGGMANATILERL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002177.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002177.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6db6521f6d4a97ca8a8510bbb492c9987098243
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002177.fa
@@ -0,0 +1,10 @@
+>0_2000
+MNNISEVTDRLASNETGMEPWLWMPLLKLLALGDPVDVSDLAAATGRAGEEVRTALKAMG
+DTEYDGSGRIIGQGLTQRPTQHRFEVNGEQLYTWCALDTLIFPTLLGASARIESSHQATG
+TPVRVAVTAMGVTSVEPATAVVSLVNPEDISSVRSSFCNQVHFFASPDDAAPWLETHPGG
+TIMPVKEAYELGSSMAEKMLTHTPGPATDQVSNGVQSCAC
+>3_2169
+MNNISEVTDRLASNETGMEPWLWMPLLKLLALGDPVDVSDLAAATGRAGEEVRTALKAMG
+DTEYDGSGRIIGQGLTQRPTQHRFEVNGEQLYTWCALDTLIFPTLLGASARIESSHQATG
+TPVRVAVTAMGVTSVEPATAVVSLVNPEDISSVRSSFCNQVHFFASPDDAAPWLETHPGG
+TIMPVKEAYELGSSMAEKMLTHTPGPATDQVSNGVQSCAC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002180.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002180.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff3275ee22ea3f17babf4cf45b0d772a2e4bce43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002180.fa
@@ -0,0 +1,16 @@
+>0_2169
+MSAGRITVVKGDERLASIPLERVSAVVVHGNVDLSGALLRELMWRGLPCVWCTGAGRVVG
+WTNGVKPPNGGARFRQFAASAEGRVDIAREFVVAKVANQATILRRFGGMPAVVKRLRSAT
+RLASTATSTGQLFGIEGRAAAEYFAGFPGLLAPGVDAGVAESFPGRVGRGATDPLNIALN
+YGYGMLLSEVIRAVLACGLDPHAGVLHSSGRNKPALALDLMEEFRPPVVDSAILAAFNNG
+ELGRLSFTHVLGGARLTQS
+>4_2105
+MDEKAPKVAQIQQGVADHARVDVPTTREAQTMRGIDVRDPSLGLHGRVDRVERLPSGRLR
+VVEHKATPVKRAVRINDANRLQLVLQTMALESQGNTVEDAEVYFTTHHRRVPVEISAADR
+KAARDAVASARSVVNGETAPAPLLGDPRCMRCSHASVCLPEERQEEEVLSRIVPPDPAGE
+TLHLTVPGSRASMSAGRITVVKGDERLASIPLERVLAVVVHGNVDLSGALLRELMWRGLP
+CVWCTGAGRVVGWTNGVKPPNGGARFRQFAASAEGRVDIAREFVVAKVANQATILRRFGG
+MPAVVKRLRSATRQASTATSTGQLFGIEGRAAAEYFAGFPGLLAPGVDAGVAESFPGRVG
+RGATDPLNIALNYGYGMLLSEVIRAVLACGLDPHAGVLHSSGRNKPALALDLMEEFRPPV
+VDSAILAAFNNGELGRLSFTHVLGGARLTQTGRRKVIAAVERRLGTEFKHPVFGYRVTWR
+RAIEVQARMFLGVLDGSQEVYKGVRVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002183.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002183.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c08911ff3c50528a33cd79baccedf2a9eba30f43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002183.fa
@@ -0,0 +1,20 @@
+>0_2175
+MGGLVISADFPLGVYTGHGPDGGAERFPDVARLFSALVQAAAAGTLSTGDPEAPFTAESL
+AALDWLEEHPPDALVLPGHTPVAPGVRRFAYRKEGVFLKEVGKTNYKVTGRPVSDGTALG
+GPVQWVWDDGPSGTDTQVCSTLEQLCADVPHLGEASSPVRLTVHEGEGLPAPTHRRDRNA
+SLRAVPGAVRQAMPSPGRRAELDRAHAATTLGRKPSASGDKHTTSAVPHATLPPRDHLRS
+GIFAPVEHHEPDVPWTQVLAVPVIGANSTVPEERYVSVCVALHRALVSRLGPDAPPEITG
+RYAPSVAPPANRVALHLAPGDLPNLPFSDGRDRFLVLVPRGMPGPALGMLASALAGVRRV
+VTSEHQLTVAPEEIEVYDGTEFWKAPTEGAVRTWDAQPAVVVERRLKSKPPIRDVDLAAA
+WSLGNVLRDVEPAFATKDPVARHAAVVESGAQLRGRAFRTLTPTAYVHRTDRRSPIEPFR
+LTLTLSTAVPDRAILALGQSRHLGCGLLVPTDIPGSTQERS
+>4_2108
+MGGLVISADFPLGVYTGHGSDGGAERFPDVARLFSALVQAAAAGTLSTGDPEAPFTAESL
+AALDWLEEHPPDALVLPGHTPVAPGVRRFAYRKEGVFLKEVGKTNYKVTGRPVSDGTALG
+GPVQWVWDDGPSGTDTQVCSTLEQLCADVPHLGEASSPVRLTVHEGEGLPAPTHRCDRNA
+SLRAVPGAVRQAMPNPGRRAELDRAHAATTLGRKPSASGDKHTTSAVPHAALPPRDHLRS
+GIFASVEQHEPDVPWTQVLAVPVIGANSTVPEERYVSVCVALHRALVSRLGPDAPPEITG
+RYAPSDAPPANRVALHLVPGDLPALPFSDGRDRFLVLVPRGMPGPALGMLASAVAGVRRV
+VTSEHQLTVAPEEIEVYDGAQFWKAPPEGAVRTWDAQPAVVVERRLKSKPPIRDVDLAAA
+WSLGNVLRDLEPAFTTKDPVARHAAVVESGAQLRGRAFRTLTPTAYVHRTDRRSPIEPFR
+LTLTLSTAVPDRAILALGQSRHLGCGLLVPTDIPGSTQERS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002184.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002184.fa
new file mode 100644
index 0000000000000000000000000000000000000000..042aee1d672e35b469a728b62a0658a644762ae5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002184.fa
@@ -0,0 +1,16 @@
+>0_2176
+MSDFDTLSLEDLLAACAPGGSTSLLSETPLRPAGGPGAVIAPAKVIEGRGEPTYAYERRM
+ELDEAGQPRPVWTVVVDSKQSVSNRDEDAIISARRDQGTPEGEALRKVPTIEVRYGEAVE
+SDLSLPHRAFDGHIRAATLDGAPVTQTEAYRALRDATKLDARALLDAAPTALVLGAWDST
+RKSHQGRYQSCMTGEIIGVLADQDQEGGAPRTNRRAAGRVDPVAASVKPSAKDVEALVKA
+QAGELSAKLQDKVLAEAKKKGETGSSMSTLGLGHIPPVLGELGGVACRSIMRRRLLSFSA
+LRQLRFGGTTEQDVACRALLAAYALLGMALSDRELHLRANCHLVESDEPTVTLDLRYGKS
+RALAPITDEVAVQVFEAALAHAKSVAGVEWNGQTIQLVGDPAILGAASTDDVEV
+>4_2109
+MSDFDTLSLEDLLAACAPGGSTSLLSETPLQPAGGPGAVIAPAKVIEGRGEPTYAYERRM
+ELDEAGQPRPVWTVVVDSKQSVSNRDEDAIISARRDQGTPEGEALRKVPTIEVRYGEAVE
+SDLSLPHRAFDGHIRAATLDGAPVTQTEAYRALRDATKLDARALLDAAPTALVLGAWDST
+RKSHQGRYQSCMTGEIIGVLADQDQEGGAPRTNRRAAGRVDPVAASVKPSAKDVEALVKA
+QAGELSAKLQDKVLAEAKKKGETGSSMSTLGLGHIPPVLGELGGVACRSIMRRRLLSFSA
+LRQLRFGGTTEQDVACRALLAAYALLGMALSDRELHLRANCHLVESDEPTVTLDLRYGKS
+RALAPITDEVAVQVFEAALAHAESVAGVEWNGQTIQLVGDPAILGAASTDDAEV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002187.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002187.fa
new file mode 100644
index 0000000000000000000000000000000000000000..32b054611fd0a696d7f0dd196a85588d6eecc962
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002187.fa
@@ -0,0 +1,12 @@
+>0_2199
+MPDLPACLEREPLTRAVVTGYAAKVTAEDRAVQRDAFIAAMVWGYGRVGYGPSRVERIMA
+QPGFEEQLADVTRITLEQGGPAAFEHIRQQRKSGVGCLKHLGAAFGTKYLYFLTKAHRES
+DIAPVLDSVVRAWFAEHAKDVDVRIGGGWTYPRKYATYVETMQAWGEELKIPADDVERLI
+FLQQQDATQEPWRESWSSAAADPEAGELLEALRLALADLGAGDDAEPHLQALEDVIADAE
+DRAPDEA
+>4_2131
+MPDLPACLECEPLTRAVVTGYAAKVTAEDLAVQRDAFIAAMVWGYGRVGYGPSRVERIMA
+QPGFEEQLADVTRITLEQGGPAAFEHIRQQRKSGVGCLKHLGAAFGTKYLYFLTKAHRES
+DIAPVLDSVVRAWFAEHVKDVDVRIGGGWTYPDRYRTYVTTMQAWGEELKIPADDVERLI
+FLQQQDATQEPWRESWSSAAADPEAGELLEALRLALADLGARDDAEPHLQALEDVIADAE
+DRAPDEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002190.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002190.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ae1161e3f35e515bd56cdd6c22fa5820d827875
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002190.fa
@@ -0,0 +1,16 @@
+>1_16
+MATPRKLPRGITLNPSGRYRVKLYAQDREFSLGTFAALADAKAALAVAQGEVARGTFIPP
+AERRRALKAEAEAASARAAAESRTVRQLADAFLAWKEGAGLAWGSVYTYRRHLEGHFLPE
+FGDRAVGAVTTVDLNAWLDRLESDHGASVAPEVHGTVTALFKFAAGQARDLPRGFTPWIT
+ASPVPALTRTRRREHRQVTILAPSELARLSELMTYPEDRALILTAGWCALRIGEALALRR
+RHVVTDDAGRLMLRIETQVQARGRGLYEAPPKSEAGRRTIYVPALAREALTAHLAQHVGA
+TAEALLFSRRGGGNRLNNPNTIGKRLKSAVDLLNREREDAGAEPLGRFTFHGLRHTGLTR
+MGQQGATEAELMAFAGHSDPKAVRIYQHAERNRLAALADRMTGEDA
+>2_27
+MPKPQRLPRGVDRLPGGGYRARLTVDGYQHTIGSFATLGDARAALDIARGEKARGTFVPP
+AVTRARLKAEKEARRAQAAADSRTVRDMAEAWLSWQTERGLKLGSVYTYRRHLEAHFLPT
+FGDRPVGEVTALDLNAWLDALEESKGHAGAAQIHRVVAALFKWATGDAAELPRTFTPWLL
+TSPVPPLAARRLRRPNLPQRNRETLTDAELSALADLMPEADRLAVLLSGWCALRIGEVLA
+LRRRHVTTDPDGTAWVRVESQVQARGSGVREESPKSDAGRREVPVPPVIAADLAAHLDTH
+AAPGPDGLLFPRVGGGNGLNNPNTVRKRFNAALAALNAQRAEAGENPVENFTWHGLRHTA
+LTRLGQAGATTAELKAYAGHSDGKSVEVYQHAERRRLAALIQDV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002191.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002191.fa
new file mode 100644
index 0000000000000000000000000000000000000000..44600827fc81884cb4c75e8f48f0c474a51d7d83
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002191.fa
@@ -0,0 +1,16 @@
+>1_81
+MSDRLRDLVLAFAGGTASASQVDLILEAGGLDDDLVQAVSRLRQEGRLARRQREAARILV
+DAATLITGARDMDEILELICRRTRLLLDSDMAYVSLNDVDQGQTYIRTTDGVLTSAYRNL
+RMPLGTGILGQAAGGATVSQTGDYLDDTSFPHIPAVDEAVRGEGVVSILAATLRVRGRRI
+GALLVADRRPRTYTPDEVDLITQTAGLSAVALSRNEEMRDLQTALDDLTVAREEIESKNV
+LLSRLGRLDQELFSVLREEASPADLAEVIGQAIGTEVKALFPADLPAHRTPAAPVVSEHP
+CQDSPNGMATLVRAFTGHRELGALEAHGSLDRDERFLFERGATALTALLLAQERGWATQM
+QQQHRLVKDLENASTETWRSVAGRLAPHRLQEGGTVRVLAVRTEQLQDTRMALRELLARR
+GGVSSIRYEVLRVISPNLTGRELHELLVSRDRSAAVCEQEALLMPEDIRVSLQGVQRTVR
+AMAALNITGVADPRWDLGLTGLAVAQLPPATVDRLVYRALEPLLSYDRQQGTELTHTAWS
+FLECDGRVSVAAERLHIHPNTLRQRIGRIGTLLGEDWHQGSHRTDLHLALRLHRVQSASR
+TG
+>3_818
+MAFLGPGEHFRDLPGAFRTLENALAVSRVAGGLHAVDASTVGAVGMVLAGAGEASKDVTA
+RPLAPLRDLPPQRASALRETALAYLDAGTNVAETSRRLFLHRNTVLQRLEQLGAVLGPDW
+HTPPRSLDLHLALLSAARDDGGAPGAPPVRSQPRRRAEELRRPRSPAARC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002193.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002193.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5861a1ba74dc7bf06be6d057708f400afe74a2fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002193.fa
@@ -0,0 +1,12 @@
+>1_227
+MRSLMRMRTPRDIAAGVLATVRRADPPVIWGAEPMNGGNFLYLWATAWARRRETGRPWLV
+RYKPKMEPWLTEFPALRDLTVREEDVSFRQERTVEWGQQTYQDWFFRDLLDFARERLLTS
+SGFQVRLKQVDRGAVVVNVRRGDYYSDPVHRANFGFDVAGYVRAAVARVPRDEAGRIILV
+SDDVDWCRENLGFLSAWGEVGTIPGEHDMFNDLAQLAGGRHLVLANSTFSYWGGYLASAM
+PVNDRPQSVQAPLHFNRLYARGESPLLLPQWQAIPDDAFI
+>2_2380
+MARCDLAAARGRALSLVRTQQPFVIWGAEPMNGGNYLYLWATAWARQRHTGEQWLVRHKP
+KMDPWLEEFPLLRALTVDEADVGWRQRRTVEWGQQAGQDFRFKDLRDFARELLLASESFR
+SRMAARPGDAMVVNVRRGDYYADAGLRAVFGFDIPGYVHAALRRIPAERQERVVVVSDDP
+DWCAANLGFLGRERSVVFMPTPHDMFEDLAQLAVARDLILANSTFSYWGGYLASARSAQE
+RPRTVFAPLHFNRLYSDGESPLLLPEWTAIPDDEFSTPDRIQGEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002198.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002198.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6c359ee926ea948272cc11706a68ffe45396bea6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002198.fa
@@ -0,0 +1,6 @@
+>1_289
+MTRKHLGFLNFGHWIHRPGAEPDARQALDDVVAMAVAAEDAGLDGAWLRVHHFQRMFSSP
+FPILAAMAARTERISLGTGVIDLR
+>2_2310
+MTKKHLGFLNFGHWIHRDPVGGRPAEPDATAALDDVVQMAVDAEAAGLDGAWIRIHHFQR
+MFSSPFPILTAMAARTQRIHLGTGVIDLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002201.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002201.fa
new file mode 100644
index 0000000000000000000000000000000000000000..858deb2f86ae40b82ce1e3773351af600e0871e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002201.fa
@@ -0,0 +1,8 @@
+>1_315
+MLLPLLGRLRVARPVGRPRTRPEAVLGDKAYSSRAIRTHLRARRIKAVIPEPADQQGHRR
+RRGSAGGRPVGLDSQAYKGRNVIERQYAHLKQWRGLATRYDKYAIVYRAAVVLNAVLAWS
+KRLSDMP
+>3_2180
+MLLPLLGRLRVARPVGRPRTRPEAVLGDKAYSSRAIRTHLRARRIKAVIPEPADQQGHRR
+RRGSAGGRPVGLDSQAYKGRNVIERQYAHLKQWRGLATRYDKYAIVYRAAVVLNAVLAWS
+KRLSDMP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002203.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002203.fa
new file mode 100644
index 0000000000000000000000000000000000000000..99a4d6fb3f5be50757fe9ccc39d1393a6aba2bd6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002203.fa
@@ -0,0 +1,6 @@
+>1_358
+MSVTKGLLVRLEALPGKEDEVQEFLGIGRGLVEEEPATVAWFAIRLGPSSFGIFDVFPDD
+AGRDAHLSGAVAKALGEQTGKLFSEPTIEKLDVLASKLPA
+>3_1187
+MSVTKGLLVRFDALPGKEDDVKDFLDSGRALVAEEPATIAWFAIRLGPSSFGIFDVLPED
+AGRDAHLSGPVAVALGGQTGAGALFSEPTIEKLDVLGSKLPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002205.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002205.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb4bd9a685f08d4a3cc260dffc40db9a6fb6eafa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002205.fa
@@ -0,0 +1,34 @@
+>1_734
+MSADAWTGTATGDVAGRCHRDAHGVPTLVAASLPELAYLQGWHVATERAWQVDCEHRRVT
+GMGAEVFGPPAVANDVAARQMDLDGAARRAFDALDDAEDRAWFTRFADGVNAGLDAGARR
+APEFAAHGVKPLPFDPHTALALHLGYNVWLTNAPAALFRTLLAERFPALAAALISPRPDA
+DGSNAWAVRVGAEGAPLVAADPHRLLELPGVYQQVRLVVEAERPRDRVDVVGLAFPGVPG
+VPHVGQSEHVAWVTTSAMVSSLEMVLEDAPEGPEVLDARTERVHVRGGDPVDVRVAHTPR
+GRLVDVPGAGPVSMRFPAWDRADTGLPSARRLLTAASAAEACAVLDGHVEPVNRVIVADR
+RTVLTRHAGAVRRRDRRSAWGAARASALGRGSADGSLDQRWVRWPAPAAADDVVVAANEP
+HPDTACLTVDACAPWRSRRIREALEALAPQERTVDAMAALQTDTRTPGAPRAWLADAVDA
+LVADGVLAAESVPAWAGDAAAGSAAARWWLLVEHEVAAALIAHLPPASRALLGGPWAPWG
+DAAAWVGAALAERGPEPLRAALGITASTRDLVRAAVAAVDDAAEPPGPDGAARTWGEAHA
+LTPFLFTHEHPGGPDEPGLADVLDTIGSVRVGGTADAVCATSHAPGLAVGTHRGPVARVV
+FDLGDRTRSRWVVPFGASGLGGGHVTDQLDAWAAGRLLPVPSRPVPPSAGSGVAPARSVP
+GGAPPGRIVAEVGVGALGLTMTRVRPALDAPLIHALVTEPRAEFYGMRGHSVQDVEEVYD
+FLEFQPTHANHLVWHGGTLVALVQTYDPRAEEVGGAYEVRDGDLGFHFITAPGGLQGRAR
+ATAYRSIVDWLGARPGTRRLVIEPDVRNTRAVKTARALGFTVDREVELPGKRAALCFRDV
+R
+>4_953
+MSADAWTGTATGDVAGRCHRDAHGVPTLVAASLPELAYLQGWHVATERAWQVDCEHRRVT
+GMSAEVFGPPAVANDVAARQMDLDGAARQAFNALDDAEDRAWFTRFADGVNAGLDAGARR
+APEFAAHGVKPLPFDPHTALALHLGYNVWLTNAPAALFRTLLAERFPALAAALISPRPDA
+DGSNAWAVRVGAEGAPLVAADPHRLLELPGVYQQVRLVVEAERPRDRVDVVGLAFPGVPG
+VPHVGQSEHVAWVTTSAMVSSLEMVLEDAPEGPEVLDARTERVHVRGGDPVDLRVAHTPR
+GRLVDVPGAGPVSMRFPAWDRADTGLPSARRLLTAASAAEACAVLDGHVEPVNRVIVADR
+RTVLTRHAGAVRRRDRRSAWGAARASALGRGSADGSLDQRWVRWPAPAAADDVVVAANEP
+HPDTACLTVDACAPWRSRRIREALEALAPQERTVDAMAALQTDTRTPGAPRAWLADAVDA
+LVADGVLAAESVPAWAGDAAAGSAAARWWLLVEHEVAAALIAHLPPASRALLGGPWAPWG
+DAAAWVGAALAERGPEPLRAALGVAASTRDLVRAAVAAVGDAAEPPGPDDTARTWGAAHA
+LTPFLFTHEHPGGPDVPGLADVLDTIGSVRVGGTADAVCATSHAPGLAVGTHRGPVARVV
+FDLGDRTRSRWVVPFGASSLGGGHVTDQLDAWAAGRLLPVPSGPVPPSAGSGVAPARSVP
+GGAPPGRIVAEVGVGALGLTMTRVRPALDAPLIHALVTEPRAEFYGMRGHSVQDVEEVYD
+FLEFQPTHANHLVWHGGTLVALVQTYDPRAEEVGGAYEVRDGDLGFHFITAPGGLQGRAR
+ATAYRSIVDWLGARPGTRRLVIEPDVRNTRAVKTARALGFTVDREVELPGKRAALCFRAV
+H
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002208.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002208.fa
new file mode 100644
index 0000000000000000000000000000000000000000..84d70f4b0e9f19707de19f32a2538861f6d3e93a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002208.fa
@@ -0,0 +1,18 @@
+>1_737
+MSPASTSPRRVLAIGLGPFNLSLAALAHPLPDVEVEVVESRDAFVWHPGMMLPGAQIQVP
+FLADLVTFADPTSPYSFLAYLKAMGRLHRFYIRGSWYPLRREFSDYCAWVAAQLPGIAYA
+TTVTAVRWDDQADEFVVEAASAAGTSTHRADHVVVGTGTVPSLPAPLARVAEESARVGAS
+PVVHTGEYMGRREDIAGAGSVLVVGSGQSAAECALDLLNAGHPDLTWVTRSPRFFGMEVG
+QLTLELTSLDYERHFATLPRARRDEINASHRSLYKGISEYTIEDVYHALYERQVGPLDPA
+RLWPGTSVTDARLVAGPGAPRVEVTLRDEETGVTGGHVVDRVVAGTGYRHPDHPFLEPVR
+HLLRAEDGRTTANADHAIDVSGRRIFVHNTAEQPLGLTGPDLGMAAEHSGRILSTIAGRQ
+VYAQAESIAFQDFGAVAAGVR
+>4_956
+MSPASTSPRRVLAIGLGPFDLSLAALAHPLPDVEVEVVESRDAFVWHPGMMLPGAQIQVP
+FLADLVTFADPTSPYSFLAYLKAMGRLHRFYIRGSWYPLRREFSDYCAWVAAQLPGIAYG
+TTVTAVRWDEQADEFVVEAASAAGTSTHRADHVVVGTGTVPSLPAPLARVAEEAVRVGAS
+PVVHTGEYMGRREDIVEAGSVLVVGSGQSAAECALDLLNAGHPDLTWVTRSPRFFGMEVG
+QLTLELTSLDYERHFATLPRARRDEINASHRSLYKGISEHTIEDVYHALYERQVGPLDPA
+RLWPGTSVADARLVAGQGAPRVEVTLRDEETGVTARHVVDRVVAGTGYRHPDHPFLEPVR
+HLLRVEDGRTTANADHAIDVSGRRIFVHNTAEQPLGLTGPDLGMAAEHSGRILSTIAGRE
+VYAQAESIAFQDFGAVAAGVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002211.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002211.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0e237cd697d32c1d8a776df24fec46e029e9a50f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002211.fa
@@ -0,0 +1,10 @@
+>1_1572
+MRRDIKKKRAALSAAVVVAGLLTAAPSAGAAPTPAGEDTPSLDAYCAEEYWTNTSVTSNI
+FKQSHSSYSSVSGAPGVTLTIATGRTFGVSGDITGELSGDVSAILAGVSAKVGTRVGVNY
+SSTNTVSGSWKVPSTYTNGGKLAIGAKRAQGTWSRQMLNKSCNVVTLRSGSFYTPWQQFY
+FQHYRL
+>3_848
+MRMNIKKKLAALASGTVVAASLMVAPAAGAATTPGDGEAVSPDAYCAEEYWTNTSVTSNT
+FKQSYSSYSSVSGAPGVTLTIATGRTFGVSGDITGEVSGDVSAILAGVSAKVGTRVGVSY
+SSTNTVSGTWKVPSTYTNGGKLAIGAKRAQGTWNRQMLNRACNVVTLRSGSFYTPWQQFY
+FQHYKL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002212.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002212.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7aa62d0814549fa36bf93172fded4aa861dea880
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002212.fa
@@ -0,0 +1,12 @@
+>1_1600
+MLLAYIDEIGEPGAYVGPDHPRSRTSPAFGYAGFVMPESAARGFGAKFTALKRQLFASEI
+DRAKHPGRWEFKGANLFRPDTPARFPQQLRVFDALVRSVVVDHGGKLFYYADEKQRGTPK
+QIGLDVEKREADAMRETLNRLARHAHHHGHNLMVIIDQINEKTRVERVASMYAHIFSRAG
+DFPEMRCIVEPPMHVDSSLSSNVQFADWVAAAVTRAVDHQLNDSSKYAWVTDPQRLASMR
+GSFTYESKLHLWNRGVQDINHSELFHRERRLAPTPHGQLLGASVDPAAAEKMAKIWRSGR
+>4_1822
+MPESAARGFGAKFTALKRQLFASEIDRAKHPGRWEFKGANLFRPDTPARFPQQLRVFDAL
+VRSVVVDHGGKLFYYADEKQRGTPKQIGLDVEKREADAMRETLNRLARHAHHHGHNLMVI
+IDQINEKTRVERVASMYAHIFSRAGDFPEMRCIVEPPMHVDSSLSSNVQFADWVAAAVTR
+AVDHQLNDSSKYAWVTDPQRLASMRGSFTYESKLHLWNRGVQDINHSELFHRERRLAPTP
+HGQLLGASVDPAAAEKMAKIWRSGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002218.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002218.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0dc0090b105557f1c95fa44afb51b44e86dc9c52
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002218.fa
@@ -0,0 +1,6 @@
+>1_1811
+MSIRYPLGYVENERKVYPQGYARERVSPGGDGEGRHDQETSAGGVSQMISLRIGRQNYRN
+VWLTRQGA
+>4_2031
+MSIRYPLGYVENERKVYPQGYARERVSPGGDGEGRHDQETSAGGVSQMISLRIGRQNYRN
+VWLTRQGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002219.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002219.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6858f7433ca32ad64bdf6df24792984f134b88b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002219.fa
@@ -0,0 +1,10 @@
+>1_1903
+MTTLQRLRAEVARRYAALGLPAWPDPHPDGAPPREEEYSRVTDPQRYRIAAARARVWAEV
+LAEAGAVVVPDPVRGIPLDEAGRADLAAPVDRALRVAPPAGVDGASPWWLLETDVPQDDD
+GGVLPVIRVAVGAPRQVHALLPDCGCDACDPGSDELLEAVDQAVVRADGTAEALGRVPGW
+SFEALTDACRDLAAGGRPRLPRGTRRWCGRAK
+>3_416
+MTARARVWAEVLAETGAVVVPDPVRGIPLDEAGRADLTVPVDRALRVAPPAGVDGASPWW
+LLETDVPQDDDGGVLPVIRVAVGAPGQVHALLPDCGCDACGPGSDELLEAVDQAVASAVG
+TGVNLRGRHGLRRRDWHVHWRSDGTAEGQGRVPGWPFEALKDACRDLAAGGRPRLPRGTE
+ATVRAGWFPEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002222.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002222.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6659724a792a1c96c63ed10b4b7c8d15ee5f7fdf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002222.fa
@@ -0,0 +1,10 @@
+>1_1935
+MSESTSAAPQPSQSVPSRRRVASSLAWAVPTVVAAAAAPAEAASPLPRIDRVFQLTLAPG
+VPWTEPKVSPCASTLFTNPTRLSVTTDNSAFYYRITNLRADSTVTDVTASVLVQKSVVDK
+LSNGLTWTSETKDWSNPTLDVSGAKYIDNGIEYYRYYSTLRTAVPAPVSGTITLPRIQWY
+SNCSTNLLTQAQSTGVMANGRGSAVVNGTPLVNVGTYVRLTPRPAG
+>4_2173
+MSESTSAAPQPSQSVPSRRRVASSLAWAVPTVVAAAAAPAEAASPLPRIDRVFSIRRATT
+AAVPGASVSACGSGSTRLSVTTDDVNTYYRIANVRTGSTVTDVTASVLVQKDMVDAMETG
+KNPTTFTWTSSATPSWSTPVREVSGTGSPVLYTNNGIQYYRYVSKLSTPVPAPVSGTITL
+PIIGWYSNCSTTLAGVSVNGRGSAVVNGTPLVNVGTYRQL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002223.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002223.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85b945b86a2caae9b7dbcff33d5173b215f3d350
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002223.fa
@@ -0,0 +1,4 @@
+>1_1972
+MRVTSPQTLISAVFEAAERATNDLTHLIPDLDRDRAEYAVASVLLEEAWLSNR
+>4_1100
+MRATNQQALITAVFEAAERATDSITHLVPDLDRDRAEYALVSVLLEEAWVAQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002226.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002226.fa
new file mode 100644
index 0000000000000000000000000000000000000000..56ca12951549bf621c67aacd20e7f45b6868df62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002226.fa
@@ -0,0 +1,6 @@
+>1_2158
+MGDYYQDNAARVLAHIGAHHDADPGPLADTGRAHHGDMHAGVVVGQDGTIHAHTRRDASG
+TYRVHLPGEDVPVDLWAARERRVIGPTVHVPLWRIFSGQGVP
+>2_41
+MAGYYTTNAARVLAQVGAHHDADPGPLADAGRAHHGDMHAGVILGMDGTIHAHTIRDARG
+THRVHETGAEWAADLWAARNARRIGPTVHVPLWRVFSGPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002229.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002229.fa
new file mode 100644
index 0000000000000000000000000000000000000000..afb9bd96319b2085a19691ef655ad454678baace
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002229.fa
@@ -0,0 +1,21 @@
+>1_2171
+MTSPLDIEDVDLSETTRQRPDYFHPDLYAEQPPAERPGEKHRGQLRIAHRLAEAHSGRLM
+YVNGLGWHVWDGQRWAPDETAAAERAVHDVLRSALAESHDGDRNLREDVRRCETAAGIRG
+VLDIAATLEGVRVAVDALDADPHLLNVANGTLDLRTRTLRPHDPADRLTRVCRGAWTAGE
+SDGMWSDFLARVLPDDAERAYFQRVIGQAVFGAVREHLFPVLTGTGANGKGTAYTAIAHA
+LGDYAAIIDPDLLMTSARGPGGPEMMQLFGARLVIGSETEEGKPLDAALMKRLTGGDPIT
+ARHLYQAPVTWEPSHQFLYVTNHLPKVKGNDPAVWRRVRVLPFDVVIPPADRDPALPERL
+REAADAVVTWAVRGWWDYLDAGGMGEPEAVKAATDAYAVQSDAVRRFIADACVIAPGASA
+RTRELHTAWTAWAAADGAEPLAEKKFGAELDRLGYPTTRTRAGSVRQGIGLLADDD
+>2_2150
+MSVRESRPTQADETALKAFTGAEDEVTNFDGVVSYEEEPPAGFLAEPRSGLSPTARPDTE
+EHAEAVLAGLSSLSATDSEILQLATTHFVERMWDGTPGTTRHLLDLCAAVARRLGDRKHD
+GAPRFYAPRALPVSAVAAMLAHLHRYCVVDLGLPASDGVAPLLVRYADDGPLEGTYSRVT
+EASLYVDALALEPESSPKQMEELFARLAARSQVVHRCSDPNLVPVANGIFDYRTKTLREF
+DPELVFLFKAATRYVDAPPMPMIVQPDGTDWNPVDWMASLAPDPEVRHLLWEVTGALLRP
+LNAWDKWLALISPEGRNGKGTLLAMWRALLGPDAHKSATLASFGADFPDIEGLNEKSAIL
+TDENDVGRYLESSATLKSIVTGDVLSAPVKHSKAVPVAFQGLMVQCMNDLPRAKDKSSSF
+YRRLLAVPMEANFTEATENKAIKHDYVQRPEVLEWVLHHVLVEMEAFTSFSEPAACAALK
+DDVRDANDPVRVFVAEFIDQFAWDLVPTTFAHDLYKAWLVRRWPNTHPVNEAEFIRQVSG
+HMAEYGWEHKKNVRVSSRMHSHEPLINEYDLRAWMNPAYNGPDPVKRAAPLLKPSYRGWV
+RIEP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002232.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002232.fa
new file mode 100644
index 0000000000000000000000000000000000000000..06dbcd90ed5c1b93539c3ebecfe7329337fc07c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002232.fa
@@ -0,0 +1,8 @@
+>1_2243
+MQTFDGLDEFERAVGTHLGHSRWRTVTQEQVDLFADTTDDHQWIHVDPERAARGPFGSTV
+AHGFLTLALLPSMVREIYRVEGMAMVVNYGSDRVRFPHPTPVGARIRAGAELTRLDRGPQ
+GALAMVTTTVEIEGVAKPACVSDSLFLLRPGKDAS
+>4_276
+MQTFDGLDEFERAVGTHLGHSRWRTVTQEQVDLFADTTDDHQWIHVDPERAARGPFGSTV
+AHGFLTLALLPSMVREIYRVEGMAMVVNYGSDRVRFPHPTPVGARIRAGAELTRLDRGPQ
+GALAMVTTTVEIEGVAKPACVSDSLFLLRPGKDAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002234.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002234.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e2fed3a1fbddfd0a957cbb7958b4bcdb2af49f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002234.fa
@@ -0,0 +1,16 @@
+>1_2245
+MPEAVIVSAVRSPIGRARKGSLRDLRADDMAAQMVTAALDRVPELDRAEVEDLILGCGAP
+GGEQGGNLGRVVAVLAGLPSVPGTTITRFCSSSLQSTRMAFHAIRAGEGDVFVSAGVESA
+SRLDRGASDEDTRNPAFRSAWERSARRAEGDAPVWTDPAEEGELPDVYIAMGQTAENVAQ
+LRGVSRQAQDEYAVRSQQLTEKSQASGFWDREISPLVLPDGIRVTRDDSPRAGTTLEAVS
+QLNPVFRPDGTVTAGNACPLNDGAAALVVMSDTRAAELGLTPLARIVSTGLSALSPEIMG
+LGPVEASRQALARAGMSIDDVDLVEINEAFAAQVLPSAEDLGIPLDKLNVNGGAIALGHP
+WGMTGARITATLLNSLREHDKHIGLETMCVGGGQGMAMVIERLS
+>4_278
+MPEAVIVSAVRSPIGRARKGSLRDLRADDMAAQMVTAALDRVPELDRAEVEDLILGCGAP
+GGEQGGNLGRVVAVLAGLPSVPGTTITRFCSSSLQSTRMAFHAIRAGEGDVFVSAGVESA
+SRLDRGASDEDTRNPAFRSAWERSARRAEGDAPVWTDPAEEGELPDVYIAMGQTAENVAQ
+LRGVSRQAQDEYAVRSQQLTEKSQASGFWDREISPLVLPDGIRVTRDDSPRAGTTLEAVS
+QLNPVFRPDGTVTAGNACPLNDGAAALVVMSDTRAAELGLTPLARIVSTGLSALSPEIMG
+LGPVEASRQALARAGMSIDDVDLVEINEAFAAQVLPSAEDLGIPLDKLNVNGGAIALGHP
+WGMTGARITATLLNSLREHDKHIGLETMCVGGGQGMAMVIERLS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002249.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002249.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba462721fb0dfab5ff46842ea25c17b45a501ca7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002249.fa
@@ -0,0 +1,6 @@
+>2_275
+MADMGNKFDKLKGDAKEGLGKATGDDRLRAEGKTESTAAGAKDAVQNAGDKVKDAAAGIK
+DGLSKDR
+>3_222
+MADMGNTFDKLKGDAKGAVGEATGDSHLEAEGRTESAAASAKDAARSAGDAVKGAAEGVK
+NAVSRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002254.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002254.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3cc13e3b921184f905ee1f3eb199128ac4793947
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002254.fa
@@ -0,0 +1,8 @@
+>2_335
+MAPRPTPIRSVLQVFALDCPDPPALAAFYAGLLGWRVVEDRPDDEWVNVLPPEHEPQTMK
+LAFQLVPDHREPTWPEGDVPQQAHLDFHVPALAEAVPLAEAAGARRHPVQPAEDGSWVVF
+TDPAGHLFCLCQA
+>3_2421
+MDTQNAPVARLAMITLDAPDAAALGTFYQAVLGWPVAYEGDGVVMLAGPGGVNLGIGTVE
+DYTAPRWPDTGRKQYHLDLAAEDVAAAAARCVALGATRPDHQPGETWTVLLDPAGHPFCV
+TDAANWG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002256.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002256.fa
new file mode 100644
index 0000000000000000000000000000000000000000..124d5fbea0115b8e40f51cbdb9fc9bf881cfc990
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002256.fa
@@ -0,0 +1,6 @@
+>2_378
+MWVHHLDVSYRAVKSRPASARALRDTILIEELKRIHAENYGVYGVRKMHHAMRRAGWEIG
+RDQVARLMKLASVEGVRRGRKPIITRPAGEPDARPDLVERCFTAERPNQLWGLP
+>3_646
+MSYRAAKTRPASTRALRDEILIKEIRRVHAENYCVYGVRKMHHAMRRAGWEIGRDQVRRP
+GGSGRIHCPRRSLRRACLFRFPQIAIEHHWPVRERE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002257.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002257.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09349984a0743bedd88569ea6f8b3f89f77672f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002257.fa
@@ -0,0 +1,4 @@
+>2_379
+MIAFIDEHRDQFGVEAICRTLRATECGFITST
+>3_647
+MIAFIDEHRERFGVEAICRVLSATECGFITST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002261.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002261.fa
new file mode 100644
index 0000000000000000000000000000000000000000..daad75f3b8bf604f9e57db10cf8f4b7907420cac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002261.fa
@@ -0,0 +1,12 @@
+>2_466
+MVTHTDLMTIGEFSSLSRLSVRMLRHYDAHGVLVPEHVDAHSGYRRYAPAQLRDAADIRN
+LRDVGLGVSAITALLAARGTSTWTDALALQRCTLVEELHAARERLSLIDRMLTPGEIPMT
+IQLNRTAVPAMTVVALRGTVPSYSDEGRLWERLMPALQQQGIRPVGPCGVIEHDDEYREA
+DVDLSVYCPVAPGTRAEGPLVVLQLPERDCLVAHVIGPYTQISQAHDLIVQRMEAEGLAA
+RQDGTLASNVFNRYLVTPDQAAPEDLVTEVCRPLA
+>2_2621
+MSRRMLRHWEQEGLLSPALVDPVTGYRRFQATQLGRIRAIAELRDLGFSLSEIRQLLDPQ
+IAHSSLERILMQQADRLRDQITEASARLAQVQHRVDTIQKKAQEISMNLSLTPLPELSLQ
+GASTTVLDETDIGSAVARLRDLVPHDQGDLILLFDGTSPDQITVTAATADGATTPGLQPV
+SAPLAPQGATVTFPTPPSSVADAWVLIDAELEKRGLASGGVYRQIISPDGSTTLQAAVHA
+RD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002269.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002269.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27aad75f11e854ada787a62472c38cb41bc2898f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002269.fa
@@ -0,0 +1,11 @@
+>2_505
+MSLFETADDRVSVDVWSDVMCPFCLIGDRLLGQAADRAGHPVQVRYHSYQLQPDLPADRT
+RPVLDMLVDAKRMPREQVEEMDRQITARGAEVGVEFRQDIALAVNTRDAHRLSHVAAEQG
+LQHAMVQALFRAYFTQGRNVADHEVLADLAAEVGLDRQAALDALASDAHADTVDADVEAA
+RRLGIGGVPFFVVDGKYAISGAQPLEVFERALAAAWADKADGAPPAG
+>3_63
+MKVTVYSDVACPWCYIGKRRFETALAGFEHAEQVEVEWRSYQLDPTLPERSDLTEVEYLT
+RMKGLAEPQVRRMLDHVVMQAAGEGLTYDMDAIVVANSFPAHRVIQRARAVSAEAASALE
+EALFAAHFERGQDIGDAAVLAELGAAAGLSAEQVEEALTDERWAEAVRADLAEARAVGVT
+GVPFFVLDGKYAVSGAQPPELFAQALAQTWAERAPLRAFTPAAAADDDDAPLIGQACGPD
+GCA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002270.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002270.fa
new file mode 100644
index 0000000000000000000000000000000000000000..916c5be38c21ea0900f11ba6e3e7eebc67df1ab4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002270.fa
@@ -0,0 +1,8 @@
+>2_534
+MPHDSARWLDEEERRAFLALMSVTMRLEPALDAQLRRDADLTHFEYSVMANLSESEGDTR
+RMSELAWLSAGSLPRLSQVVTRLERRGLVKRTPDPTDGRYTLAVLTPEGRAVVEESAPGH
+VEEVRRVVLDPLTRAQVKQLAAIGKRIVGVLDPEDRCLED
+>3_458
+MSDAARPASDPVADTAPESVVPWLDDEERHAFLALMSVVLRLEPTLDAQLRREAGISHFE
+YTVLASLSEAEGGQRRMSELAYLSSGSLPRLSQVVTRLEKRGWVERRPDPEDGRYTLAVL
+LDEGREVVVAAAPGHVAEVRRAVVDPLTRAQLRQLTAIGRRIMGVIDPEDRCLED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002281.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002281.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f96bc83986bb424862ed4ad2b83da936ad59ecfe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002281.fa
@@ -0,0 +1,10 @@
+>2_695
+MTQRRTRWRSAASQDAEYRAHWKAAASADVGTPDALTWAVLGDSAAVGVGAARVEESYVA
+QVAAGVAERTGRPVRVLNLAVSGATAAHVLADQLPLLPADGVDAVTCVVGGNDVAWPVRF
+RVDRFAAPLEKIAQRLPAGATLGTVPVFRIPPYESRVECANAAVRVIAARHGLGVADVHA
+ATRRTSLRHQVSMLSHDLFHPNGAGYRDWARAVLPEVLRQVRGEAPTR
+>4_1972
+MPSPSGWQAQHDADYRAHWHALAARADPDALTWVVLGDSAAVGIGAESVERTYVAQVAER
+VAAETGRPVRVVNLAVSGAMAKDVLADQLPLMPASGVDAVTCVVGGNDVTWAWRFREAAF
+EEPLEAIARALPAGATLGLVPTFRIPPFEARVRRANTVVRRVAARHGLGVADVHAATWRR
+NLRHQVSRLARDLFHPNGAGYEDWAAAVAPEVLRQVRGQAPAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002285.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002285.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ce35d9ff008c6ed316996479e9610615abf2947
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002285.fa
@@ -0,0 +1,14 @@
+>2_755
+MAGGEAAVAWILGALRRELGAANLGEEDLEIVVERDRVWGSLWTVTAQGRRFWFKRPHAC
+LRREVPLRRVLSARAPGELLSTVAACAETGWQLTADQGPVLAQRAREDGPSHYVELARSL
+ARVQKSLTAADVAELRNIGLPVFETGDAVARLDEQLGWFSGLPAGHPAQCTAAERERAIE
+GMSVLVERWAVDARMLEGVVPELSVDHNDLHGGNAFVTAEGVRLSDWGDTVLAHPFASLR
+ALLVPVRNVFETEAMEQIRGAYLAEWGLGEDVGDVLDLAMMLAVPQRLSCWSALADADAW
+AEYAEYIAPLWREIGTPVAEVEVP
+>3_2348
+MTGTGVLDVAGRTAARDWIAGVLDLPAAALTVRVVRERSWGDVWRLSSPAGVHWFKAPHP
+RLRGEVPLRALLESRAAERVLPLVAADHERGWQLTADAGRTLAALARDDAGAPRPGEVAR
+LYAGLAGALAAMQEAVGEDDLRGRGLTEFDPAKAELSLLRELAPFRALPAAHPAHCTAEE
+EARAVAVRAALAMRWEDCGGPADPLGLDHNDLHGGNAFLGADGRVLVSDVGDAVLGHPGA
+SLRALLVPVRAEHGADAAETVRTAWLAARGQDHAAGRERLELAMLLAVPQRLRAWGALRS
+PETWAAYAEWITALWRDIGTPVDQLTTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002286.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002286.fa
new file mode 100644
index 0000000000000000000000000000000000000000..53d78f19e80f680dcff51783af86773c2b4faebd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002286.fa
@@ -0,0 +1,15 @@
+>2_808
+MATPAGAVGKGPNHNPRSTVNTSILATHAELVAQLQKEDARQDAMELTVIGQSVKGRDIH
+LASWISDPENPTILFLTQQHGNEQLTTEGAMAFIKSLGTGKMRSVLDDVNVLVVPMANPD
+GAMGDVDFSLEDYIASGDRNLTRYNANEVDLNRDHVAKTQPETRALHENVLGAYDIDYMI
+DLHHQGTRSAVDGELVSGSILYPTSPNVAPDVVEDSQRLGSVVYDAVEQYGWGNLGRYVG
+GTAETIARNGVAAEYGIATLLFEMRGMSDHEYESYVLGQRSNGYLIKQTVVTLEATTKAI
+ADGSIETADIGLWNTLPEQRTLPLAAE
+>2_1964
+MSPLTSPSLSRRGALGVLASAVALPLVAAPPAQAAGSMPTPSDTPPLAAIRDLADMLREL
+RKLERTSRGAIRVTTLAEVGTAEAHSEQGRDLYVALVGHGPRHVWLQGRIHGNEPYGLEA
+TLDVLASLGGNGSPAYRRMREEFTVHVIPMYNPDGSEANTRGTTLWDREADAPLLVGRGR
+PRTVDLNRDWGVGRFQARESRAWYEYWTMVKPEFALDIHHQWLKQDWVTGEDVTLSLGVS
+LAPGGPTLPGIRGGEYDRLARQLAGHVWLETLHRGHISTDRYDVGENTVIDIHGGVVSAM
+MMGLDWNGLNPTGHSNVAIFFETSGNTNSLGHKARGKLVQQNVLAVTAALDGMATGAVQR
+VDPAVWDRIPHTPVKYYSTDYAGLIPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002289.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002289.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5bd10a65fcfbfab908c41c3dfa7ef49d0e49f21
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002289.fa
@@ -0,0 +1,14 @@
+>2_864
+MPDSPAPPGAAPSELVPRAFAERIARRPADPLLAAAGGEAVSGEAWLARLPHLVEERLAA
+WNLTLDPDAPGAPWTGHGALVLPVRRHTLRPAVLKLTWPHLEARHEHLALRLWDGAGAVR
+LHAASPPDGALLLERLDADWPLTLEPVLDACVAVGGLLRALDRPATPQFDAVAVKAERWD
+GTLAAPVAAVPRRLQVQARSHLRRLVDSAPEPRLVHEDLHDGNVLAPLPDDGPSGAAPDA
+RRGHVARRGRWLAIDPKPVAGEGAYAVAPIVWNRPEVTAAAHNARIHVRLRADVVAEAAG
+LDEERVRAWTFVRLVLNAVDAAHEGPSADEWRARMIALAGHFAS
+>3_807
+MPASPPEILVPIPPEFAADIADRPADPLLAAAPDAAAQPLSGEQWLARLPRILAGRLTAW
+DLTLDPDVPGAPWAGTSALVVPVRLPTRRPAVLKVTWPHLEARHEHLALRLWDGAGAVRL
+HAADPRDGALLLERLDAGRPLSAEPILDACEVVGGLLRTLARSATPQFDAVADRGARWLD
+TLAAPVAQVPRRLQVQARSHLRDLLDSAPPPRLLHEDLHDGNVLAAPSPADGGEAARGPW
+LAIDPKLVAGEPAYAVAPIVWSRPEATARAHHARVHVRMRADVVAEAAGLDGERVRAWTF
+VRLVLRAVDAAGRGEAGDEVRARMITLAGHFAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002293.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002293.fa
new file mode 100644
index 0000000000000000000000000000000000000000..11d2664b7ad5dec5940aeb3893ece4937f779bd4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002293.fa
@@ -0,0 +1,10 @@
+>2_890
+MPSRRPPERPVVGPAAPDVAPSRPVPGSCQRALVRRSPLILAAVVLLVSAAVLAARGETE
+AAGLSVQIAMVVPVPIALERAHRVRLPTALHAMYAALLLVAPWVGAALGGYDAWPWWDAL
+VHFYSGVPIALGCVFLLGVAAARRGLVLPPGLEALLVMALHSLVALAWEIAEFTADQALG
+AQTQKGNTDTMTDMIVGTLGALIVAFALYAHRTRGRFAWLSRFTGA
+>4_1808
+MTPHLDTHPDARPDPGSRQRALVRRSPLILAAVVLLAGAAVLAAQGHREAAGLSLQIVTV
+VPVPIALERAHRVRLPTALHAMYAALLLVAPWVGAALGGYDAWPWWDALVHFYSGVPIAL
+GCVFLLGVAAARRGLVLPPGLEALLVMALHSLVALAWEIAEFTADQALGAQTQKGNTDTM
+TDMIVGTLGALIVAFALYAHRTRGRFAWLSRFTGARTDLAGGPAQPPPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002295.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002295.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9082acf548739e1db7b2fbfcddd69cab7fb32350
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002295.fa
@@ -0,0 +1,8 @@
+>2_924
+MSEPERTRPETTPDGHHIVVDGRKWRAQDPHIPEALAGELVKGLMAARRLVRTDPTTARP
+RVQDAKVALGERGDPWWEPTPEGTRERLAAAMRTLLRQRDEGKTICPSDAARVAGGEAWR
+DLMDEARAVAAELHAAGAVEVRQRGERVDSAAARGPIRLAAGPQLG
+>3_1201
+MTGEPITPSDPEHSGPERTGPEHTPDGHFIIVDGRRWRATDPDIPEALRAELVKELMAAR
+RLVKSRGDAARVRVQDAKVALGERGDPWWEPTEQGRRDRLAAAMRTLLRQRGEDRTICPS
+DAARVVGGEDWRDLMPVAREVAGTLAEEGVVVVTRKGAAVDVATARGPVRIAAGPALET
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002296.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002296.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea6b19c4eeb49badff211935237bbf619d8635de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002296.fa
@@ -0,0 +1,10 @@
+>2_927
+MTPADHRPEPDTAPEPEAFPALEDPYRRSLLTNEQRNAWAALSAASLGLVSQMESDLHRD
+AGLTPFEFHLLYVLGAEEVSREAEGTMPMSRAAQLVDSSLSRLSHVVRRIEERGWVERRP
+SAEDARVTLVGLTPEGRRRMEAAVPVYDRMVCRVFVDHVAEEDLAEVTRLSMRLLAGLRE
+GHWLLDAMDPHGSRRAGVAGADAGADAGAVTGATGESEEDSEGRPAS
+>3_868
+MTKDAHHEKDANAHPPLPPLPPVWLKDAGCSGADLAAWIALLQAASALQARVESDMHRGA
+GVTPFEAHFLAVLKEAGGEPLAMSRAAHLVDSSLSRLSHVVRRLEARGWVERLPSPEDAR
+VTLVRLMDEGRRRIDAAAGPHRALMEDVFVTALDAADRQEAARLSLKLLGVLRPGHWLFT
+EPTGPDEGADPDAASHVGEPLTSS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002299.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002299.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6ca1ad32c2e3ade0872ab89a9c5b69e32776b60e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002299.fa
@@ -0,0 +1,10 @@
+>2_984
+MDPVSTPTDPHRHPAPDARVRVQAGDAVVADGPLWARAALFAVPAVWLGLLIGISLIEAP
+LKFTAPGITIPLGLGIGRRVFFAMNLVEVVLAVVLLVALARVLGRPRGLTVPGPGRLWLG
+GLTAAGLLAVKAVAIRPFLNRRTDRVLAGVDDGGSSWHYLYIAVDGLLILTVVALIVAVA
+RHLLVRTTAA
+>3_929
+MSVPPHPTPAPDAPRPLPGAAPREAGNAVVVGGPRGARALLLAVPGVWLGLLVGISLIEA
+PLKFTAPGITIPLGLGIGRRVFFAMNLVEAVLAVVLLVALAKSLGRPRELTAPGPGRLWL
+GGLTAAGLLAVKAVFIRPFLNRRTDMVLAGVDDGGSLWHYAYVAVDGLLILTVIALIVLA
+ARHLLPASPGAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002303.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002303.fa
new file mode 100644
index 0000000000000000000000000000000000000000..937492bc6c6a4b76ad8a27a41a98e7e99a169bd5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002303.fa
@@ -0,0 +1,10 @@
+>2_1018
+MTKIAIITGSTRPNRLNRQVADWVLERANGRGDAAEYELVDIADFDLPLLDEPMPAAWQQ
+YANEHTKAWSAKIAEFDGFVFVTPEYNHSLAPALANALSYLNAEWANKAAGIVGYGSAMG
+VRATEHLRAILSELQVAHVQKHGMFSLFTDFKDFAEFQPTELQAASVDPMFDQLLSWTEA
+MKTVRQG
+>2_1296
+MRLGIVIGSVREGRFGAQVGAWVEEVARGLDTGGRDAEWDVLDVAAFDLPIMTDEGWAQD
+EDGPAEVHRWRDAVAACDGFVFISPEYNRNIPGAFKNAFDLLSAQWKDKALALVAYGGLG
+GVRATEAWRFTVAAYNMHVVGDSVQLVRRADFPDETFARTEHHDKTLSRVLTRLVDLTEA
+TAALRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002307.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002307.fa
new file mode 100644
index 0000000000000000000000000000000000000000..11f34d1537238ccf73f28c9318b5d4aa4acd154b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002307.fa
@@ -0,0 +1,10 @@
+>2_1247
+MVKKLEQNMGADAMRAATGRDHAGWRAVLQDAGAQQWSHPRIAAYLVEEHGVDGWWAQGI
+TVDYEQAHQGRLPGQQADGTFSVGLTRTVPGERLEALARVEAAVSAVHGEPHGRNLTASQ
+PVVRWRLPDGGRLAAAAQAPNKTGTPVNLTMQRLPDAAAVEPTRRALEELLEAARSGEGP
+VATPGR
+>3_2005
+MSTSPARGANLNAIAEATGLTFEDWAAWLDARGARDLTVHAEIVGLVLERMRSGETAEVG
+SPEWWAQGVTVAYEQHIGRRRPGQRADGTFAVTASRILEGTREEVHARAVGAVRAALSDG
+GALRGVGLAKEPTESATATRLFWRAVLADGTRAELATEPRPQTAGKPAKAAVVATHSRAA
+SAEEAAAWKAFWRNLPAAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002311.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002311.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d92ca9a47b89145ebdd59edb25e1f6b4017b399
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002311.fa
@@ -0,0 +1,8 @@
+>2_1294
+MDNVGIAVRDLEEAVAFFEDLGLTVLGRDEVSGEFAETAVGLEGNHAKIALLATPDGHGK
+VELMQYLNPEPVEAEPTRPNEIGMHRIAFAVDDLDAALAAAVRHGCRPLRGVARYEDAFL
+LTYVRGPSGILVMLAQELKAGE
+>3_1203
+MGIRFENVGIAVEDLEEAVDFFQGLGLVVVGRDEVQGEWADTAVGLDGNHARIALLTAPD
+GGPGVELFEYLHPEALPTPDTLPHMIGMHRVAFRVDDLDAALAACDRRGYAPLRGVADYE
+GVFRLTYVRGPSGIVVMLAQATGEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002312.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002312.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7529b6f9d164960f9bd6c732126103b5d08e446f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002312.fa
@@ -0,0 +1,37 @@
+>2_1472
+MKNSTASGSGFQFDASQPYQLDAIASVVDLFDGQPKDAEKLVTTLRSAAVLPESDQAALD
+IDLTQEVGAVGNSLVLDRDLILANLQRVQDRNGLEVAPALAGDALDFDIEMETGTGKTYV
+YLRTIFDLAVRYNFTKFVILVPSVAIREGVSTSIRLMREHFENLYKPQGVTFDASIYSGK
+SAEEVQSFATSTNVQILIMTIDSIRGNANTRIIHQTRDKLNGLRPIDYLKATHPVVIMDE
+PQNMESQLSQSAVGELDPVFTLRYSATHKKQRNVVYRLDPVDAHDLGLVKQIVVAEVAQQ
+GADATPYIKLVEVRREPSWSARLELSCRKADGSLERRIVSVKQHQELSDARLTNNPIYEG
+WRINEMSIEPAYVDLTLHGFLYEGESIGASAGAIYREMIRETVREHLRKESMLRAKGIKV
+LSLFFVDKVASYLGDGTNNDDANGDFVQWFDEVFVEERAKNARYQELLPQAPSKLRRAYF
+AQIKGKKGAPNAFVDSDERRQGAREDDAYELIMQQKERLLDENEPVRFIFSHSALREGWD
+NPNVFQICTLREMGAETERRQTLGRGLRLPVAKTEDGYTRVADRGVATLTVVANESYTKF
+ADALQREYKEAGVEIGRVRRAEFSKIPLQDENGALTDDQFGYQRSVLVWEHLKDKGFIDK
+DGAVTSKFQPNQLGFDLGLPVDFAWAESIIIELVERANIGKYVKPVSKRQPRMLNKQLYS
+NPEFEEFWETISQKTTYRVRVGRDQLIENAVRAIREAPQIDALRIQVTRAGVKVLRGGAK
+GEELGTRSADLKGSYDLPDIITELQEVTSLTRKTIVDILIGSGRLGEFIGNPNDFIAMTK
+RALQSELAKIVVDGIQYERIAGSVYELRELQRDGAEEKERFLDQMYKVQHTQKTDFDYVV
+FDSDVERQFAELLDSREDIKLFMKLPAKFKIDTPVGPYNPDWAIIKQEDGEDRIYMIRET
+KSTLDDSKLRPTELAKIKSAKRHFEAIGIDDYARAVPGKWNL
+>3_276
+MKLQFSTKQYQTDAVASVVDVFSGQPRDPGPQYQIDPGRRASTGEDAAVALTGYRNAEIA
+LSLSALLEGIQRVQRAQNLPVSTRLATSAAAPGRPNLDVEMETGTGKTYVYIKTMMEMHR
+RYGWTKFIVVVPSVAIREGVKKTFDITAQHFQQEYGTRPQTFVYDSSRLHEIEAFSSNGG
+VQVMIINIQAFNSSSKDNRRIYDVLDDFQSRRPIDVISANRPIVIIDEPQKIGAAKSLSS
+LANFNALMVLRYSATHEVDHDKVHRLDALDAFNQKLVKRIEVRGLTVRGLSGTTAYLHVS
+DIEVRQGKNPRARVETEMQSAAGTIRRKLAWVTKGTSLHDLSGGLEAYQGLTVVDVDARR
+NVVELSNGDLIESGQLADHDVTEDTKRRIQIREVISAHFHREREMFRRGIKVLSLFFIDE
+VAKYRDYDREDTLGDYARMFEEEYVEARDAVLGELETEDDAAYRDYLRRDEVSAVHEGYF
+SVDNKSRRMVDGKVAGRGDEKGQSTDTDAYDLILRDKERLLSLKEPVRFVFSHSALREGW
+DNPNVFTMGMLKRSDNEVSRRQEIGRGLRLAVDQHGVRMDDPATVHEINRLTVVTDESYT
+DFVTGLQTEIAKSLKGRPRKASVAYLTGKTLTTHEGEILTLNKEMAELLHRHLIRNGYVD
+DDDLLTQQYLNEREAGTLAMPSNEKLLGVVDFCWPLLDALHTGVDIVEPSRAMKRLPVNR
+HNLERQEFQRLWERINRKAVYRVQFDSEELVQKAVTALDEKLRVTGLTYTVETGVQGEDL
+EAEHFRSGQGFTSSAITTQKESATSGSRVRYDLLGEIAERTTLTRRTVSAILRGIRPDTF
+AAFPKNPEQFLTEAGKLINEQKAAMVIEHLAYSPLEDTYDISVFSENQTSQDFTLASEKL
+EKHVYDYVVTDSDVEKRFVTQLDASTEVAVYAKLPGGFTIPTPVGDYNPDWAIAFDEEDT
+HVRHVYFVAETKGTSSSFELRGMEDAKIRCARKFFDALNRKNAGDVRYDVVTDYNGLMDL
+VKGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002317.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002317.fa
new file mode 100644
index 0000000000000000000000000000000000000000..05798eb40f2a2b1de65e76bdd2927ef2a83bdcf7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002317.fa
@@ -0,0 +1,10 @@
+>2_1971
+MTTPAPTSRSDWAEYNAAQAGRGRIRPLTARAVDALAADADLGARHAVELGCGAGVEARH
+LLALGLTVSTIDADPSIAPAMAALAAGGALDHRTGRIEDWDPLPAADLVLANAALPFVPR
+HAFDAVWSRIRAALAPGGVLAVDLFGAEDDWSSNAGTYLTRPEVEDLVRGLEVVELTERS
+ERGPAFSGPKHWHVFTVIARARRRPSDRSPV
+>3_1266
+MGDTALMIATPTSSSDWNSYNAARAGTSAVRPLTERALTALRATHQNLSGLRAVELGSGA
+GIEARRLLQEGLTVHTIDVDASVEERMHELTSLGVLEHRTGLIEEWDPLPLADLILANAS
+LPFIPRAHFAPVWERLRQALLPGGILAVDLFGCEDTWASDQGTYLTLQEVERLLDALEVI
+ELNERNEEGRSFDGIKHWHTFTVIARRTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002334.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002334.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76df9395e59a94a536542e337b9f93f8ab633360
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002334.fa
@@ -0,0 +1,12 @@
+>3_293
+MRQDAGAQTVGNVVSTIAVSAGTGALAGSVLPGLGNVVGFAAGVVSGVAMAVPVADTDGD
+GQKDSVAEMAGDVAEGAWNWIRGK
+>3_321
+MTTSYVTKVGMSEWESADSMDQLAHGVTVAASSLAEVVSDQDATWQSLGNHYEGDGEGDL
+VNGFFVPVENAARVVLAAEALDKAFLDFSNALRGLWADRRVFETEVDTYNSMYGAQAIET
+LPPGVDSWRAALASMPADLERRYQQAASTCASAVRTIDIEALDLDSVSEGRPGQLGREIV
+AEAAKNALPLDPENPSTSALGLLDVARVREPWLRFDDVIPETWQARFMGLNVGPLGASVY
+AGGAAMVRAAQTRSWAPLRNVPLAMSMTMRNYSNDMAALALRYEDPRKFRRPTWPAFKSQ
+FLDGLPVTGFIRSTVPLWGKRTPATVGAPAPAMAGAYRVESRGAFRLNAGVKGLGAAGTL
+VGAGLTYRDEYDQQLRENQAETPGASREEVESEARQDAGAQTAGNVLSTIAVSAGTGALA
+GSVLPGPGNVVGFAAGVVSGVAMAVPVKDTDGDGQKDSVAEVAGDLAEGAWNWIRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002335.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002335.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26f0027a36ed835e867ea6bfd28b5c56cc5a1349
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002335.fa
@@ -0,0 +1,5 @@
+>3_309
+MTQTPTPHLAGPSPVKVGLLVLAICAVGGVIIGAVAGLTDGGSVENMFIGAVYAGFIGFF
+LPGLPAALIAGLVAAARGRRRG
+>3_329
+MDQDVATEAEQTVSEDGAVYAGVIGLFLPAALIAALVAAARGRRRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002339.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002339.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bd32455021a49fdf6ca52a57471c4f3a088e17f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002339.fa
@@ -0,0 +1,12 @@
+>3_331
+METFWGLTTPAWTAIYTLLTAGLLVAAIVAGLYAKRQWETARDAQVEATRPYVLVTLEPG
+ERSMAMVDFVIRNIGVRPAYNVTISIEPHLLRAREEGGNEMAAMRLLHEPTAMIPPGQVT
+RMFYDRMSDRSGRDDLPVHHTAVVSYVDSSGREWTDTFDLDLRVLEGGMFHSYDDLHTVS
+QTLKKMARTLDRSRVLKEGEMDVVAVTENRADHQVRTLLEEYHRQVEIANLHRGKPGYVD
+RVRSFDARAESIAEQLRALGVSVQGAPQD
+>4_1098
+MDDTFWGMSATGWTAYYTLLTAGLLLVAIAAALYARNQVQIARAAQREATRPYIIVTAEP
+SPIGWRVMDLVIRNIGQRPAYNVKVSLTPEPVRANETPGAPISEVQWLREPIPMLAPGQE
+LRTFYDAMEERLNSGRSDLPTSHDYSVEYDEGTVAAKKGKRDHRDSGVVDLNAMAGAMQP
+DVYNIHHVASALRDIKKEVAKMNRSGTYIQPASEVRDILDQRGPRTKPRSTVPGPLPAER
+SALRRLYDRFTGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002340.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002340.fa
new file mode 100644
index 0000000000000000000000000000000000000000..447805069213282fda8ec04c64e6821c2113120c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002340.fa
@@ -0,0 +1,20 @@
+>3_408
+MGKVRGDQAVQSLQPHKVLDSDSSHGRLIRQQGERVPTDGDFTLSDRAQKEIVKLFIASE
+SSLEGRTIGEWFSEDFFESNFWTYWATMFAFETWHSLAEMRRYLLRFVHAIDGLADFSAL
+KFNRYDQYDSMVKPLLAYLEPHGVDFRYSTTVRDVRVETADGKVRAERLLLTVDGVQQEQ
+EVGEDDLVSVTNGSITESTTYGDHHTPAPSTTEPGGSWTLWENLAEQSPLFGRPGVFYRG
+LPERSWFVSATATVESREVEEHIERLTQRPLHDGKVNTGGIVTATDSPWMLSFTVHRQPH
+FPTQRPDQTIVWIHALYSDTEGAYVKKPVTECTGEEITQEWLYHLGVPEDRIPEPAAQES
+VNTVLVYMPFITSYFMPRRAGDRPAVMPEGSMNLAFIGNFAESPTRDTVFTTEYSVRTAM
+EAVYTLFDVERGVPEVFASATDLRELI
+>3_1162
+MQYTAGNYEAFARPRPAQHAQETKAYIVGSGLAGLAAAVFLIRDAGVPGANVTILEKGEI
+AGGALDGLDVPEKGFVIRGGRELENHMECLWDMMRSIPSLELEDASVLDEFYWLNKDDPN
+YSLRRATVRRGEDAGHEGRFDLPKRAQKDLLKIFLAERAEMEGKRIDEVMGREFLDSPFW
+MYWRTMFAFEEWHSALEFKLYLHRFIHHIGGLPDFTALKFTKYNQYESFVLPLMHYLTEH
+GVVFRSGTEVLDVDFAHRNGEIRATAIRCRRDGAEETIELGEHDLALMTIGSLVDNSDEG
+DHHTPAALNEGPAPAWDLWKRIAKKDPAFGRPEVFCSSIEETKWESATVTTLDERIPAYI
+ERIAQRDPFSGRVVTGGIVTAEDSSWLLSWTVNRQPHFKKQPKDQIVVWVYGLFVDVDGD
+YVKKPLAQCTGEEITQEWLYHLGVPVEEIPELAATGARCVPVMMPYVTSFFMPRRAGDRP
+QVVPEGAANFAFLGQFAETGRDTIFTTEYSVRTGMEAVYELLDVERGVPETWGSTYDVRD
+LLEASARMRDGKKVEMPGPAALRGYLRGKLEHGEIGQLLEEHGLI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002341.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002341.fa
new file mode 100644
index 0000000000000000000000000000000000000000..977e0c313a51923d11eace5667de7b02cdab0b57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002341.fa
@@ -0,0 +1,4 @@
+>3_603
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVISEPADQ
+>4_973
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002342.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002342.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30d380bd979f09b51e3f8ad817f5ff1fbb06ff50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002342.fa
@@ -0,0 +1,12 @@
+>3_611
+MAINWRRAQYLLAEDLTDIPVRYIDELFGSNGIALGPENPQDVDTSVRRARMRRYLTTLD
+LDTNRADQQRFADVMAERYRKIALVHQHGNTDETQWKLERWTTLLRAAGFQVDTTALSVT
+WPPGPQMGTLAPDVLAHLNDPSAIEDHLERIHTTIDSDPRLAVATARSLMESTAKIVLTS
+RDKTYTATESLTKLVSRAQASLGMSPKDLGGEQPEVRRLLQSLQGIAAPISTLRNDTNVH
+HGAEVVPQWVRPRHARLVLGAAQLWCQTVLETLSDPTAPWRVTDAAAQR
+>3_679
+MAINWRRAQYLLAEDLTDFPVRYIDELFDGNGIALGPENPQDVDTSVRRARMRRYLTTLD
+LDINRADQQRFADVLAERYREIALVHQHGNTGETQWNLDRWTTTLQAAGFRVDTTALSVT
+WPPDPQMGTLAPDVLAHLNDPSAIEDHLERIHTTIDSDPRLAVATARSLMESTAKIVLTS
+RGETYTATESLTKLVSRAQTSLGMSPKGLGGEQPEVRQLLQSLQGIAVPISTLRNDTNVH
+HGAEVVPQWVRPRHARLVVGAAQLWCQTVLETLSDPTAPWRVVDAAAQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002345.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002345.fa
new file mode 100644
index 0000000000000000000000000000000000000000..743c4fa19202cf6a713e5e9feddabce7ca369367
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002345.fa
@@ -0,0 +1,28 @@
+>3_619
+MNFSVDLNIGDRVLTDAGPARVKSMWALGVELETINEPAKLVPWTDLIIRPTIDGQAQAV
+DAALHPWWDQLPEKVQQDAIFKMECVLEILTGFRSGLASLAQPHEPVVPFGPFSQASVSA
+QCEAMARLVSFEKSADRELMRRVQDGELDSPGVTPRAVHHWVRRWQASGLRGLVDGRALR
+SAQGFGALDPRFLKIAEQEFARFDGSASATNRQEIHRRIQVRMHAEGITDAHLPQRLVSD
+YLSHRFAQLGKTTRAHRSRRHRKISSTASAALHHLGHCATDVTRADNLVYDEFTGKPMSV
+EIATIMSVPARVIVAVRVFPKSVSATEVALLLYDAMRPQSMLIDQDGASDWRWCGVPTSL
+QLPEQASPLANDPASGLGEHAIPAMTPTHLRMDNGSIFRSEQLRRLALHWSITLSHSRGT
+RPTDNPHIERFHETLQRFYQQLPGYKGRNVSERGSWTGVVAEAPLLTAADLERRLRQFIA
+LDYHRRPHTGLTLPGAPEVNISPLEMFDWILATTGRIHVPQHPDLIYQFLPTRWLTPGHA
+GVEYKNMTYDAAVLDEFRSKIPGRFRDEDAKVPFHYDPRDATRLWFRHPDTDRIHEIPWR
+NRHLLHAPLTDVVRDEARRRIRARGGPKALTGALIDRQLIEEIGHLAHTRADETWTTTMA
+ASRMRFDQARRDHDEAALAHRLTTPEAPTDLEHGGRHLRLVPPDAMPDRTATNGLAGLFE
+PWPDYAQEI
+>4_2158
+MRAQMSAPIQAGDSILTEHGPVEVIAPQSTGLLVRAPGGQETLITHAQVIPRRFQNGTIA
+GVMASLYPLWDQLDQAVRDDALFKLECVNEVNTGYRRGVASLALEGEPFYPFGPGWGVSL
+RARYQAMARLVSLEKRVDRVLMRRVYDGEVQRPEIGLRTLQSWGESFEEHGLRGLIDGRA
+LRKVQDFGVIDVRYRQAADEVFGQFDGEISAVNQQEIQRRIYALLRQRGQSDVQVPDRLE
+SDFLRHYYRRLGKGTRAHRSRSLRKIATTSSAALHHPGYCASDVTRADNLVTDEYTGKPI
+SVEICTIISVPTRVVVALRVFPRSVTSFELGLVLYDAMRPFSMVAADGAIDDWRWCGVPT
+GLQMSAPQCPRHVKEDEGPLGVHYIPAVTPVEMHTDHGSTYISDQFRTLLQQFGITLSLT
+RGGRPTDNPHIERFHETLQRAYQQLPGYKGRNVSERGSVVGVQADEPLLTARQLEAYLRA
+FVAVDYHRRPHTGLIWPGTEEQALTPLEMFDAMLASTGRLHYPQHPDLIYQFLPIRWLTI
+RHAGVEYKNMAYDAEVLDEFRDCRAGAFRDKDAAAPFHYDPRDTTRLWFRHPETDRIHEI
+PWRGRHLLYAPMVEIVRDQALAQIRRRAGRRHSAKVSMLELIDEIGQLATAPRDETWAHK
+LSAARMRWDQGQRDHDEVAHARALQQAHVPKPRTSRAGRDHLLSLPGGRTEDTPPAGFGL
+ADLSEPWPDYPEEHDELA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002349.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002349.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a35038a83c2e070bac47c608b35e691b0df45146
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002349.fa
@@ -0,0 +1,10 @@
+>3_650
+MDLAPSSSPTIELSWHADLTPGQLDDLNRLFAAEYLEDFGEWDPDQPYGYAPHDMHVIAT
+LDAQTVGHIGWARRSITVGDHHVTIAGVGGVLVTPSGRGHHLGQRLMRAAVDSMRAHSDA
+EFGYLGCHESVVPFYVSCGWRRIVAAERYIGLNGQPSESAQGDPLLVMPLRNAKQPWSAG
+EIDLQGRPW
+>3_682
+MDLVPSSSLKIELTWHTDLTPGQLDDLNRLFAAEYREDYGEWDPDQPYGYAPHDMHVIAT
+LDAQTVGHIGWARRSIAVGARPVTIAGVGGVLVAPSGRGHHVGQRLMRSAVDSMRVHSDA
+EFGYLGCDESVVPFYVSCGWQRIVAAERSIGRGGQPTQSTQGEPLLVMPLRGTEQLWPAG
+EIDLRGRPW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002351.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002351.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1aa4b3fff61a30d7b4c03c48c22b74fd19adbabc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002351.fa
@@ -0,0 +1,4 @@
+>3_652
+MPRRDSHQDLRQKLEAVETKISHHLFQSPGIAESLRIVDQSTGKEADAVDAVLTSRGPA
+>4_1955
+MPRRDSHQDLRQKLEAVETKISHHLFQSPGIAESLRIVDQSTGKEADAVDAVLTSRGPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002354.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002354.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dd915ee3ac425125e4e5c46cdf198ee651c0bd50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002354.fa
@@ -0,0 +1,9 @@
+>3_718
+MTKSLISSAVVVLLILLVTVLTDASTWLVGLLSGLACLAGAWCAPLFQSGSPYGGTFFGG
+WQSRWDGPKAVQLLAAGAAVAVSVVLNLFGGGVPAVVGIIVALLVGALIPVPGDPAGGGH
+GADPEDARPA
+>3_720
+MRMTPARVASAAVLAVLTLVCLLLMLDTWSFMGALLVSLIGAVLFVAGAWFAPLARSGDA
+LGGTPLRPWQAGFDGPKTTQVAGGGLVALLVALVTGGAPLVGPILGVVAAVIGGRFLRIP
+SHAQVVAAVGPEVAEASEHLPGEHHDAAPADSVADPDTDPVPVPATEAADSEKPRHEHAA
+DVSPETAPVPVIHPADAEHPHGSHAAMAHPDPVDDVPGDGEPTTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002355.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002355.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9e4ebae946452e0273a5a488e835767753a390db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002355.fa
@@ -0,0 +1,7 @@
+>3_919
+MHGEERSTRAALERAGHVGLASRIGLDGTLVPPDGRAGPGAPDAAGVGYASRVPEQRIIA
+RRSLGNAPTRPDGLRLASLAALGEEQFSTHMLAASGGDPFDTSTEESALEDLLEIIEGAG
+DHFDPHAWYVVGDGEGEIGVVLPQPLPDKPGTGTVFYVAVLPSRRGRGKGRQLHQFGLSE
+LARRGCTEYVGSTSVDNAPMVAVFQANGCELEH
+>3_1270
+MAVLPSRRGQGMGRRLHALGLAELARRGARKYIGSTGRKKAAMVAVSRANDCIVEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002360.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002360.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37243396a8a016dc81c221c26ce0de846edafdd5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002360.fa
@@ -0,0 +1,16 @@
+>3_1173
+MTEPVTYTPDIEHSVDREEDLTREILAQMGAAQRRTAGEHKHAHRDAHAKSHAVLKATLE
+VHEGLAPELAQGIFARPGTYEAVARLSSAPGDIHTDRTPAPRGWALKVLGVEGKRLLPDL
+DSHNQDFLMVNFPTLAFGTVARYQEMLGLLEKNSQSPELLQRLTTGAARVVRGAVETVGG
+TPSATLEGLGRDNAHVLGETYFTQGALRYGDHVAKISLAPASANVRALTGQDMKVKDFSS
+ISEIVADFFSRESAEYVLRAQLATDAERMPVEDASVLWDEEEAPHQPVATLRIEAQESYS
+HPRRVYGDDALTFNPWNGVVEHQPLGSIMRVRKRAYEQSTRFRHEFNDRPAPEPTSLDEI
+PD
+>4_1478
+MTEPVKYTPDIEHSVDREEDLTREILAQMGAAQRRAAGEHKHAHRDAHAKSHAVLKATLE
+VHEGLAPELAQGIFARPGTYEAVARLSSAPGDIHTDRTPAPRGWALKVLGVEGKRLLPDL
+DSHNQDFLMVNFPTLAFGTVARYKEMLSLLEKNSQSPELLQRLTTGAARVVRGAVETVGG
+TPSATLEGLGRDNAHVLGETYFTQGALRYGDHVAKISLAPASENVRALTGQDMKVEDFSS
+ISEIVADFFSRESAEYVLRAQLATDPERMPVEDASVLWDEEEAPHQPVATLRIEAQESYS
+HPRRVYGDDALTFNPWNGVVEHQPLGSIMRVRKRAYEQSTRFRHEFNDRPAPEPSSLDDI
+PD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002361.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002361.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce86813aebe8ae9b8e95e136e5f69c7525c5c3fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002361.fa
@@ -0,0 +1,12 @@
+>3_1748
+MRIAVTTPMGHVGRHVTSMLIRSGVRPLLLARRPENVTPGLRKHADIVKANSTDPAQVTA
+ATQGVDAIYWVDPSVMSSDPLADYTLATEALVKAVTANGIGRVVFQSSIGAEKRHGVGEI
+DGLAGTEVALDTLDVDVTHLRCGYFFTNLLLDIDAVRQGQLTTVLPLDQPMSWVAPRDIA
+EVASLTLLNTQWHGHRVQAVHGPQDLSWRQVAETLTAHVGHQVHAEQITDTEMLQRYLAA
+GMAPMMADAILGMSTGLRDGFRPEQPRTLATTTPTTLTSWIHEELIPVL
+>3_1782
+MRIAVTTPTGNVGTHLTGMMIRAGVRPLLLARTPSKIPIDLLTHVDVVEADSTDPEQVVK
+ATRGVDAIYWVDPSTASADPLADYARATQAIVAAVEANTIARVVFQSSVGAEKRHGVGEI
+DGLAATEVALDRLDADVTHLRCGYFFTNLLLSMEDVRQGRLRTVLPLDHQFSWVSPRDIA
+EVAALTLLNPSWHGHRVQAVHGPQDLSWNDVAALLTDLTGRHVQAEQISDDLMRQQYLTA
+GMPPAMADAVLGMSTGLRDDFHPEQLRTATSTTPTSLAGWMQEELIPAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002372.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002372.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9fd225a2a7bfa24bc24169de645e1fecba8d23a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002372.fa
@@ -0,0 +1,2 @@
+>0_162
+MVGQTVAYVRVSSAEQNLDRQLEAVGECDRIFEDKISGSSRAKRTGLAELMTYVRAGGTW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002373.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002373.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d22bb53c116321578a8f05c8904646685ff0cbd7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002373.fa
@@ -0,0 +1,3 @@
+>0_165
+MSSSRDAVLVVRAAGGRWKVENFFAAHPKTSETESLWDFTVPALLEAADRAGVHIEATAM
+NEKLARHYKRKIPDLRRLGVVCTGQVKLLRVPRPHPTS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002376.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002376.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e3bdc1527c5d7e9ae5b902b736197077c8338bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002376.fa
@@ -0,0 +1,7 @@
+>0_387
+MRKLIFYPNLSKGGVSAVIRGRAQAEPDVQFDAVFLHDRGGSDAFSDMANVHVRLIQESR
+SGPYLTHLAHQFDYESVSVLSHPATANVLSALDHVAVTYEFHSSSIPVIEKELGALELDR
+LAAVVVPSQIMAREIQPLLPRRLRFRLAVEPNLVDVETFGEQGSAQFLADSGFGDGPGTI
+PLLWVGRFDQGKAYAHFLRVIAALPQEYVGHVVVSLEDDPHRAERFFAEAAGLGVLERVR
+LYLNLTPQALGEFYRSVRDADGWLVSTSLKESFGYAVAEATNAGLRVAASDLPVWDLFAG
+TGLVHRVPSGSIADLVRVIREGAPVSAGAATAW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002377.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002377.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18c46902b82c0ab2c24c29b21983ee11a9b33550
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002377.fa
@@ -0,0 +1,6 @@
+>0_388
+MDYFDRIQNRLEGREAGVPGWLGAKNATRQFAAQIGIRTPEQLFKGPLSDLERFDFPERC
+IVKPGFASTSIGVHLLERRGAELWDLVKDEPVTVPGLIETLREIEGRYDLSPDDGEFLVE
+ELLSDRRGVTPPADVRCYMFQGECGFVLVEDHIAGPAAASYFNGDFSPMTDVHDRFGVHP
+GVTHLESIVDAAEPPAGAEELLAVARRVSTAVPSAFCRVDLYDTPAGPVLGEITFYPGTF
+FYKNRKVMAPEEAARLGKMWDAAEKRLAGSLLIDAPKRN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002378.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002378.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e5893fbf73a5b38f21e3e7b71a067fcb9916dbba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002378.fa
@@ -0,0 +1,9 @@
+>0_494
+MVIQLVSLTVLARFLEPAEFGVYGMAITFIGFTTLFRDLGLSSAAIQVKSLPIQLRTNLW
+WINTGTGAILALLTLATAPLIAAFYREPQVAFVVAFMAPTMLLAGAAVQYRASLARDLRL
+GAAAAIDVTGALLGLIVSVGVALAGGGVWALVLPQLVSGVVTLAGVIFVSRWLPGLPRRG
+HGTRQLVRFGGAMFVSQALTYTHRTYDVLLLGRLHGADWTGQFNRAAQMSRMPMGMIAAP
+FSKVALATMAPHQEDVHALGALARRGQVLLALPVLLAAGGLVAAAEPLVSLVLGDGWGQA
+VPFLQLIAMSEALALMASVGGWLMAARGQGSKLIRLGVISTVIKVSTVSLGSLWGPYGIV
+AGVVVAQVILWPLSLVLTGRMSGVSTREALVDSYVLVGVTASATAAGWYAGRTHIVPGGP
+VVDIVAVVVTMLATLALAAALVAPFRRDVQTFLQTVRSGVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002380.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002380.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e2676c69271b4a06d3b43e96822bf19989ce335
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002380.fa
@@ -0,0 +1,6 @@
+>0_496
+MRITTREEALAAAGSRYAPVSAGGRSADDAGVMVGKPCEVAGRRQLDAANGVDSPVLLSF
+FCAGTPSQDATEVLLEREGIQRDEPLMDLWYRGRGWPGDFTALTRDGRRATVDYASSWGG
+ALGPTVQWRCRLCVDGVGEFSDITAGDFWDADERGYPVFDDAAGMSALIARTPRGLQIVQ
+DAVAAGRLHVEPMDLQALLRVQRYQVERRKYMLGRLVGNRLSGGHNPRYRGFGLLTLVSR
+SPRRVLHEVRGTIERAAKRRGGRGPS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002382.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002382.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83d0d3b79372b04fed8cee8a0d30a57b69f7292a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002382.fa
@@ -0,0 +1,3 @@
+>0_561
+MSNHTRCVRSNLAAEISRRDLTQARAAALAGLTPDGLSKRMSGQVEFRLGELLELARVLG
+VPFATLVAGIDAADEQLAEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002390.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002390.fa
new file mode 100644
index 0000000000000000000000000000000000000000..314fc8ec449148aa1c1c6818fe425036b5410869
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002390.fa
@@ -0,0 +1,3 @@
+>0_593
+MSARVKISGNLERELQRAVQDTMTTLAKDYQRMLDQLGQQYAGAPVEEIKAVLRTRWSRI
+SGTISDPELSIYAQHISEGTPITVRTS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002393.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002393.fa
new file mode 100644
index 0000000000000000000000000000000000000000..17b501e011bc3010481c61244d0f09c7cdc6495d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002393.fa
@@ -0,0 +1,3 @@
+>0_597
+MMSSQKDTATLKVQDVHQLQAIAEAAARIAEQLAGEGAAESVRDAIRAVDDQLGDYAGHW
+DEYAAVNDWSSTIKGGLGNHVKAVPATDLF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002398.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002398.fa
new file mode 100644
index 0000000000000000000000000000000000000000..629dc302c6635db595671b4528d5bfa334a8403b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002398.fa
@@ -0,0 +1,4 @@
+>0_812
+MYRLTVRDHVMIAHSLPDPFFGPAQALHGATLVVEVTWRRRELGPQSVVMDIGAATSMLS
+EVLEPLRYTNLDEHPAFAGRLSTTEAIAGHISDELRRHFDTTEFAGMEVLLREHPDAWAA
+HDVDFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002399.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002399.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fbfff8f63cdd604a20cf9be9833fc5fce61f8d67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002399.fa
@@ -0,0 +1,6 @@
+>0_813
+MRSLYSGVSRGTEMLVYRGEVPPEVAGRMRAPFQEGEFPFPVKYGYLSVGVVEQGPDDLL
+GRRTFCLYPHQDRYVVPVDALTVIPDDVPSRRAVLAGPVETALNALWDAPPCIGDRIAVI
+GGGMIGASLAVLLSRFPLGRLQLVDTDPVKRDMARAMGIEAVEPEALQAECDIIYHASTT
+EAGLAQGLERLGDEGELVELSWFGSHVPAVPLGTSFHARRLRITASQVSTIGRARRYRRT
+HAARMDLVMHMLQDPVFDALISGESGFADLPGAIAGLAQGELPTLCRAIRYPDPGPRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002400.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002400.fa
new file mode 100644
index 0000000000000000000000000000000000000000..58a071e5a516d9bdaf6c7f5065d26b85d1a908a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002400.fa
@@ -0,0 +1,6 @@
+>0_814
+MRHPTTPFRRQAMVDVLCTVVGSVGLGVTLVHFGKTSAWGSVAAIASGLTLVSVAVVTMV
+RRNPLFSTLADRVTLSRAVLGGGCATIVMLAALDTAPHRSWWLVLLAAPAVLLDAVDGRV
+ARHTGTASAQGSRLDMETDAALLLVLTVPLAFTIGPWVLAIGLMRYAFVVLSWFRPAWRE
+PLDFSQFRRVVAAIQAVVLVVALVPVVPLTGACIILALSLALLLTSFLRDIITLERGTSS
+RGDREPTRVGRTCSSHADLSDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002406.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002406.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c8f7ff6848bfe0447908cb1ca25d15856c68cca2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002406.fa
@@ -0,0 +1,19 @@
+>0_1438
+MTAPAVHEASQKRLLGTQHAAKTPSQTPLAAAAYGGTPVAAAADGWTIEYVTDSATSQKY
+PARFAVLTKTVGRAGCTGSTTSFGAYPSVAAMGTGRDAIVVGFDTEFVSAEEVDEQRGWV
+GEDVHVVRRIVSYQFAAIDPTDPSRLRLAVVLPQEYHGPRGPRTARLSFEKALEIAVTAL
+GLHEHPLASGWSSQGVPRAEVVDKKGETRPGWWFNGRAGVSRALPIALVAHWQQADLTTF
+VDRRKAHNTWNAAYPERARKVSTRAGLDSRRGRWLDSSTSDILRAVISASAGMVSPTPVR
+MVLAGANKRWARPVEVSIRDTMAQSGAQPLRALGEAVGVAKLDVPGDWIARMDDYLLKDP
+VAFMDYAANDAIIALEYVSQVYGDHQEVPLTLPTAAARAVKGLMSGEIEARPDTFDDFNA
+VFGGLVKVAKNVEATTGVENQLDFYKKRELQPIDGAAATWIHASAMAFRGGYNMSAELGL
+FEQVTHDLDLQSCYPTSSATIWDVDYLHPDGVILRTVNNVELGLDDFAEGGPLTPFVGFV
+SFEFPESVAFPCLPVPAEGSMIYPRTSGGARGVWAVGPEVWLALTLGAKVTCQIGHFGRT
+LRTSDGEPSRLLRGAYKTLLDDRARAKREFGKSSFQQGVLKLMANSPYGKLAQGVMGQRG
+WDAWAQERDAVGGSAITSPWHASMTTGLVRAVLLAVLNQLHDRGYATPSCTTDGFITDAE
+LSVVDGLDLFGLGQLWRDSREALTGSREMWERKHFQTDLLNVTTRANFSRQPGGVLAHGG
+YKLPEGIVPDSQEDRDHMYDLMVSRDGALPVTMKVFPSMEELTRIENRLDFAPKVVHKQQ
+TIEFDRKRRPVPEGMTAHMVMVGEQVFEVAHVRTVPWESPEDALRGRSVDQGLKRWDEEL
+GEPVWTRSPVRRTRAQWQDYFKRLERLLDEDGRVAEAERLDRIAKGIVIAHRQEVVHIPW
+LGSDRPLAERLDAFEDFGLPRPRERFWSHARSKTERQIEIDLEAIAPYVAEMKAVDPFES
+ETFLQEVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002408.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002408.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d763fed99bce7e2a1d09a61ddd3544dabc7c1915
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002408.fa
@@ -0,0 +1,6 @@
+>0_1445
+MTAEPLRPNDAIAPLPTVEGGFKTVMADPPWRFQNRTGKVAPEHRRLDRYSTLSLDDICA
+LPVQDVVADDAHLYLWVPNALLPDGMRVMQEWGFRYVSNIVWAKRRKDGGPDGRGVGFYF
+RNVTELILFGVRGRMRTLPPARSQVNMIETRKREHSRKPDEQYGLIEACSPGPYLEMFAR
+KAQPGWTAWGDESGADSAPRGQVHKGYAGGAIEAPFVEPHVRLDEAVADALAEDLKTKYE
+AGASVQELVESTGYTTTRVRGLLKKANTQMRPRGRKTKQAEALFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002409.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002409.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e8b8968eda34d8422efe8a3c50e09240fe72c5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002409.fa
@@ -0,0 +1,12 @@
+>0_1446
+MSPFPSPGRISFTKFTSPEGITDVLAGVVPGVTTAAEVLQDLAAAKLADPLWDDLLSYDP
+PFEPGKSRAAGSQVAVDNELLRACREGREDRFLLLWAQLILADPRLDAIVREVFTDSTGK
+LVPEMVNASKLGAALTARHAADPDEPHDTKAVSNLLSLLERCRLVEPVKHGKTIVGVERV
+LPTAHAVPAVVRLIGERLAERGFGAQPGRELDLALALGANAWLNLTASEFRDAFDGKTPP
+AAQPQSVPGALPEDLKVIATLLRRKGQVLLQGPPGAGKTYVARRYVDWVSAGRRADSRLQ
+SIVEALPDDRRTVPAIADEIVSRGLSAVWDIVQFHPGYEYTDFVRALVAQPHGQGVTFVA
+QHRIFSLVCAVGAELARRGYELEMVLILDELNRGDIPSIFGELLYALEYREEPVASPYTV
+DGTPSLTVPHNVRVIGTMNTADRSIAVIDYALRRRFTPIDLEASDSPIRGYTGFDDETAR
+EAALYLYERTRDALSEASQGLQVGPSYFLAEPDGEDGSIAVLATRFVYEVLPLLDEYTLE
+GEVDASRVESLRQELGLGQRAKQWDQGAALAAHLVAGQPWKPAAADPEVGEPEEALSVDL
+GGPLADGGDAPASGEDTRDQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002411.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002411.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e333af7b63d0bc6e67849697ee7b57dcf5d4d6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002411.fa
@@ -0,0 +1,2 @@
+>0_1448
+MSGQKGQLVGYERVSSVDQNLAWQLEALAGADRIFEEKASAKDRERPVLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002419.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002419.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a75425930ae2562aa75f14b8e17f86e2c60099f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002419.fa
@@ -0,0 +1,17 @@
+>0_1896
+MTRSTRRGTAGRITGAAVRSVIADAQRQGYAPSEDTPAVVGIYADPAGVAELGDVVVDGA
+AVTVLPAASTLAALDQVHHAPRGSWSALVTNRPEEDLGVGVLSALVGGVLRTPDLWETVR
+TDFAATGLEPALYGVPESMSVALGILQVTPDGGWPVVPGGALTRDHALGAVARAHLGLPQ
+RSLDLAGLLSWSVRPGLTTSIARLRETGTQALADVVLTWISDQAGDPRLAQLVRRLLLDG
+TPDLLVPLGLVLDVLVPRADRAGTTSAGDVDRLNAVLAVRGVPSRSLTRWADAALDEIER
+LLGSEDASTASEALLAAEALLDRIGATDAALQSAVLPTGLRHRQRLVAEAVAAATTVPAG
+YDGTPAELHAAASAGLDAVERAWSWLGSHRLVGVASAHVPAVRHLPVLESAVRLTRWLAA
+ERPEPTGLAALALRQAGESAWVDAAVARAHRGVTDTALSHALDSVLAAVRTVRDAEDRAF
+ALAWAAQTPHDLATDTGYGTAPDAVGLIEHTVRDHVVPLARHAPVLVLLVDGMSTGVATV
+LIDALLAEAGASWDEALLPGLTRRHAAVAALPTLTEVSRTAFFTGTVQRGGQAQEKAGFA
+ALMDAAGLGATELFHKAELQSAPDARTFSDEVAFALQDVDGHRVVAAVLNSIDDALDKSD
+PGGTDWTPDAVRHLRDLLDAARMAGRAVLLTSDHGHVVERRAGTLRSTPDATSARSRGPV
+PPPHEDEVLVTGPRVAGGSAVLPSSERLRYTALKAGYHGGATPAEAVVPVAVLVPDSAKH
+LLTAGSDSGLRVAPPQHPAWWAGSTHVPVPPPEAVTGPVPPAVHEPTPAAPPATAGAVSP
+EAGTTPVSAPASAAVEDAGLGAAVVASPVFQDQRETAGAVLLADAAVAAAVSALDAAPGQ
+RLPLAELGAVMGVPRSMAGGAFAQLTMLLNVEGYPVVSTVPGAVRLDRALLREQFELD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002424.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002424.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8a243315ac8c87735d1511798bbc326d43cba47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002424.fa
@@ -0,0 +1,7 @@
+>0_1977
+MSTGLRGTQVITLGTAGGPRWWRHGGGTPRAGISTAVVVGGAVYLIDCGYGAGRQLVRAG
+YGLDDVEAVFLTHLHSDHIVDLTAIALFSTFEITQDDRDAIRLIGPGDRGALYPTSPHTT
+AAPTPLTPHDPTPGTAETLRRIVAAHATDLNERILDSLRPSPLDRIHAHDIVLPSNIAFD
+PDAEQPPAMDPFVVFEDSRVRVSAILVEHPPVAPAYGYRFDTDEGSVVVSGDTAATDNMR
+RLADRASLLLHEAIDLDWLVAKFPDPESPQAHAIRSHHERAHTSVADALRIADDAAVGSL
+ALHHLVPGTSGASLGRQLEGHHPFSSTVPSDLQVIPLASR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002435.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002435.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00ee6cd979a51a663f4ce1c57ba9d6f658b57bd6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002435.fa
@@ -0,0 +1,3 @@
+>1_78
+MAGGPLGVFLAAHLRRAKRRFGLRWILTLALWCLFWVLGLLMGEARPWAGAVTAVGIMTV
+TVGGAVWELRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002436.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002436.fa
new file mode 100644
index 0000000000000000000000000000000000000000..460e187b21fd50dcbdf1db37c5ec6e7e48ba2aa5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002436.fa
@@ -0,0 +1,3 @@
+>1_85
+MSSSPQTMLSGSFFPISRFRLISATVLLIMSIVALTPWSFETRIGGMALINILLTAVMLY
+GLVVLIIDLMVTRETAAARTVSTEERHD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002438.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002438.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e19d36867bb55f98ca12c8a4ff47021517bca81d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002438.fa
@@ -0,0 +1,2 @@
+>1_196
+MLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002439.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002439.fa
new file mode 100644
index 0000000000000000000000000000000000000000..95672962d69199ccbbaaac1b6b5edc4167c65c6a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002439.fa
@@ -0,0 +1,4 @@
+>1_220
+MDILHSARRLKHRLWLAQKHGAHVVTEGRDLIYRMSSAVSPARYDAARYELDFTALTGRN
+TSWKPDRPIPRVVWCVWSGTNAMSANRAACLQSIREVQHDLDVRLVTPDTLHEVVVNGHP
+LHPSYEHLSDVHR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002447.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002447.fa
new file mode 100644
index 0000000000000000000000000000000000000000..22e85d2f190196408d049c93c565bc57a9eec8f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002447.fa
@@ -0,0 +1,3 @@
+>1_359
+MVARCLVDADQGSQFRSGLLQDALTRHGLIGTMGQVGPAGDNAAMESFFALLQKSVIDRG
+RWATRDESIMDPTPAHAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002448.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002448.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4317258fc92760c44f83677bce7f245e6bc30c85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002448.fa
@@ -0,0 +1,5 @@
+>1_482
+MTTTSASQGYRTINPATGELLKSFDNATDQQIADALDASQAAYEQWSRKSVAERAAVVKR
+ISELLAERSKDIAALITTEMGKSLGAAVGEVRYSAQIFGYYADEAEELLADQPIKQFSGQ
+EAFVQRLPLGPLLGIMPWNFPVYQVARFVAPNLVLGNTILLKHAEINPQVAQLLEELFTE
+AGLPEGVYQNVFATHD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002449.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002449.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7348fea2fa31e7e846a33c9251d40a2fc8fbebc1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002449.fa
@@ -0,0 +1,2 @@
+>1_642
+MPGGVVPVALAVAALALALFEGLERHREKVRRSAWT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002450.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002450.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d0cb936d60f183170e2572338395c9b7a3a0fc3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002450.fa
@@ -0,0 +1,7 @@
+>1_1067
+MLHLLVDTSTWLDLSKRRDGQRWIVALRVLVHQGEVELIVPPLVIDEYERNRERVEASMT
+ASVAQRFKLIRQDLDDYGGTDTEQALSTIEDLARHAPLIGAMTTRNFDEVLELLRGGRTV
+EPTESERHAVVERGLVKQAPFHRSRNSIADALLIELYASAVAGVDLAREPHAFVTSNSED
+FSLPHGDKRQPHPDIAATFALGGSTYALGVDGLNEVLLAHFGPEIEALFADTDFVEEPRR
+LDEIVEAETRLFDRVWYHRSLQHEYRLQDANNHVEIEQLRAIAGPGRKRVEETCNLPGEL
+GPYTDFELGMLNGKLSALRWVLGSEWDFLDT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002455.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002455.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee16250ec2c41514845eea6b17a634fc40bd75ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002455.fa
@@ -0,0 +1,4 @@
+>1_1351
+MAENTSPTPDPRTRGEHGTEHAAQAPFAVTRDYAAEVDEIRELGRKLGGEKKTPTPDPQA
+WREGYPYKTKLSRKSYERRKRELQIELLKMQLWVKETGQKVLIIFEGRDAAGKGGAICQG
+PLSSAHRRPVFLPAGGHQNCPLVASWFARLGGGAGHRDGISSVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002457.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002457.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f44ebe67eb8db2f40834ed8840789839197a4ed2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002457.fa
@@ -0,0 +1,6 @@
+>1_1602
+MGNRRRLRIRASRGRSKRCRPPHPKNSSGPGSQASGVRLLSARMRPTATPPCSERLRHHA
+LSPEPLELRVGDRGSAPGRVQAESVRHARPSAHHPAPHGGGHGPAPARSRGIPRSDRTGL
+AGWSRRRRAPTRHRPGWGCEKSRDDPLRRAASSTPPAAGCEVRLWQVKWPFTLPTRKRDM
+SIPARLSHVLGVSLNGCVAVHNMQLRAFSPFLDRLSLAPIPAARALGSRLAHQSRRVFSC
+ALSDSSSSCPSCSWPPAVPVRRDRGRLAPNPHCPRLLRRCRRRPPPRRAPCS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002458.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002458.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f632dc14768c9b26ebef879e30d1c070bb0480b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002458.fa
@@ -0,0 +1,6 @@
+>1_1604
+MTFRPTHYRLTTAALGVALALTLTSCGTAQDAGSSSEPATATVVDSALTRIKEAGTLRVC
+STGDYPPFTEQTESGDWKGIDVDMARDLAETMGVEPEFVKTSWKTLMDDYTSGACDVAVG
+GISLNPERAEQVYFTVPTQEDGKTPITRCEDVEKYDTVAEINQPGVRSIFPEGGTNEKFA
+REHYPQGELLTHDNLTVFDALAAGEADVMTTDRSEVLYIDHEYPELCAANPDEPFDYFQK
+GYMLPQGDEVFKHYVDQWLAIALKDGTYEGFAEPWVGDVELSLED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002460.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002460.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d69fa87dbf83d927f58abf4219fbb438bfefc5d0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002460.fa
@@ -0,0 +1,8 @@
+>1_1726
+MSTRWPVHPAPVTGEALTSWLRRIAHRYGAEVEDLVLDTGFCISRPGDLDVAAPEEFINQ
+LAGRTRTGTDTIRAMTLGGQTPWLLDQLEPAAEAYTTYTRQLAVLLPRGRRRDRTVEDWR
+AWLPTDAGWQHRACPRCTMESTPPCPYQLAWLVPLMLSCPVHHCRLERHNGPVGYHDFWH
+VSPGRPEPRPVGAAIRSMDQRTWQALTTGSVALPRHRVHAGLWFRLLRTLLDELGATIIE
+CGAPGRLTRQVWDRTGHPVRAGQGPWRPYEELSDQRQLQSLEAAATAIHLFETRAMTCPG
+REAEVFLPQPDISRDPGSTEQTTDPTAIRWQEIKKNFQAVVEEARTTPETARQLFNFCTM
+YRRDNDEVIQGVRSNFTELGIPSDYLSP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002461.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002461.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7eac816c6ca89aed88daa08dfa51dd84d384ce8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002461.fa
@@ -0,0 +1,2 @@
+>1_1884
+MTLAELEEGQVLVTSTVMSVGPCMGGHMNDVASDVAPFEVDAPSTAAGSAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002462.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002462.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b69a43db2a5ee69d46783d50ace1606abd565e6a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002462.fa
@@ -0,0 +1,3 @@
+>1_1885
+MKYSFQANEANGAPQQAVLNGWHTNDLLGIQAKIAGDQRDQSHRLTALVFFLGLGLLGDL
+VLRNAEAFRESKGS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002464.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002464.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e33f919cadd0558865a213d6f1875d9a08264c23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002464.fa
@@ -0,0 +1,2 @@
+>1_1920
+MKYGLCAYKWVICRAIAIRSIFFTKLNPTAAIRGFLVIFGMGFAARPVGAFRLSILDDL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002465.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002465.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fc52e54ee080835767a4621261c784f9d8f4a8c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002465.fa
@@ -0,0 +1,11 @@
+>1_1922
+MSKFHVDQIATRIRELYSTDYWDANLSDVNNLSRLLARYAVDLTIPESSDSGNQRIVEVI
+DGGEDRGIDAIGIDFVSQLVVLVQSKWRQDGSGTMDLAGLLKFRRGVETLLGIRTDNVPV
+SASPEMRMAVSDILKKPGTRMRFIAVTTAQEELPTQQQESMNELLSSVNEGGASEPIASF
+VHLGQGALFDSIVEREPMDLDLNMQIFNWGKIDEPRRMVYGRVDAAQIAQWYRDHEHKLF
+AENIRLVIPRSDINDGIRKTLTSEPENFAYFNNGITMVVRDMQVAPAGSATREAGYFTAK
+GVSIVNGAQTVSTIGRISKSEGSLDFLEAASVMIRCIVVSDEEAEFGRLVTRYANTQNDV
+STQDFAFLDAEQHRLKSEIKVMGFEYLLRSGEDVLTESSDKRIDVRSAAIALACAHRDVE
+LSVLVKREISQLFSDRYRTIFNPSTDPRLLVSSVLVNQVVENKLGELEPLTEGVKNGVII
+HGKRVISHLILRGIGTTNLSSSEFAIENYDSWIEDECERIVAALVENFPDNSYPGNVFKN
+TIRVRALLNESSLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002467.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002467.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c16fee2846f066cf1fbc6b0921e0c994277ed0a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002467.fa
@@ -0,0 +1,3 @@
+>1_1975
+MKDRGRLLGIAAISVTSLLWGTTGTAATFAPDAGPLAIGAAALGIGGLLQAAIAIPALRR
+A
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002469.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002469.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26388b2e0f1f255d3edc25d50de8e2e4ebba1f9e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002469.fa
@@ -0,0 +1,5 @@
+>1_2116
+MRIEVVTGTDTDVGKTWGTAALAARALVAGLRVHVDKPVQTGVAPGEAGDVETVRDLVAA
+AAASGALDAAAPARLTVSEGARVGPAMAPVDAVAHAGEGTPPLPPLGEQLGRWRGLAAGV
+DHLLIEGAGGITVAWTEADEGPVDAVRALRAAGLDAGLTVVARPGLGTQNHARLTVEHAA
+ARGVAPERILVSGVAADPDPVERANLVFLARLAGAHGAVLETVPRGTPPRVMSVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002470.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002470.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d1ab74c311013855c22e02c2cb61b7bdee07611
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002470.fa
@@ -0,0 +1,4 @@
+>1_2128
+MFGAYADRVGRKRSLFAAMMITALGSLIIAFTPTYGTVGVLASVILVIARLLQGLAHGGE
+MGTSVTYLVERAPQGRRGLFGATSWVSVVVGTILATLVGLAVNTLLSHEQVASWGWRVAF
+GIGGVLGLYALYLRRSLTESEHFTAAQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002473.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002473.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81dda5dded6110da8025d159dcbc62288451cc45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002473.fa
@@ -0,0 +1,4 @@
+>1_2160
+MLTSRRIVASTLALSALLLTGCQGDPESTRSSTFPSDDYVTVTVRGQWLPPNGTTVRREK
+GKVLLNVDRETVDSNLNALLPSSPSGKWYEASYMLTRGSLVEAYVSLPGAVPGMTTACEL
+EVDGVTLDRSELVAGSGNTAICSARLPAK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002474.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002474.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1bbb8b11d44748c839db086f82796a7df9db0900
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002474.fa
@@ -0,0 +1,3 @@
+>1_2161
+MTGVESPEAGRVEVSTDLTDPRTENSTEADQAKAICEAAADVEGVDYVNVTESDGTSWVL
+FGHPRYPAGECTEV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002478.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002478.fa
new file mode 100644
index 0000000000000000000000000000000000000000..581ef21d8cd3d73dccc824f02bf629392dcb1923
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002478.fa
@@ -0,0 +1,4 @@
+>1_2165
+MTGPSTDGVRGGRQTWAQWYYSGAPTAQDMADRRHADTARAERARLDAEALNARHAEPRP
+DPAARLRIALTNLGPSMVPPGAGPTLADVNAAIRREAGPDRALHQQMLDLHFTQQARRRA
+AGNH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002479.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002479.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff88a5e2ff6c5570e14582b20b2409f71da33eab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002479.fa
@@ -0,0 +1,4 @@
+>1_2166
+MKHPHITHAEAEAQAHPLPLEDQITYWKARGRALERAAQRAQTHPRPEDAAPETAPTPTG
+PDPVQLEMLEARMEAAAARRGIDPDPLLPYLRAEPFMNEDGRVERAAVETFFQQLADARD
+ARMVRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002480.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002480.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c7a1fdc1b03fe6dd43f854476d598c603877006
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002480.fa
@@ -0,0 +1,3 @@
+>1_2168
+MTRLFRSHATYWTKNRRTARRAQALPAVQIDPEGREVPGVALITDAHPRVVLTVDEMRAL
+ALALIDAAEVARQQLAPAEPEQTEKAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002481.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002481.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89b546bc058dac47cb96fb039265c174591334ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002481.fa
@@ -0,0 +1,3 @@
+>1_2169
+MSTRRAYTEDDVARFMDLARGGRDRHRPTTGTRELTDRRPIPRDWPAMTNADGSPSAPLP
+TADPEKE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002487.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002487.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f1f1ea0cfb5f057398b89023bad0b7b9729f5492
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002487.fa
@@ -0,0 +1,2 @@
+>2_34
+MSTTSRPTPKHAATTAPERIAAELAYLRNECDSIRHALNRSRERA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002490.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002490.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b79eefd63cf9d218ac893d0b61148b731d4e8234
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002490.fa
@@ -0,0 +1,3 @@
+>2_39
+MTVMTPIGDSVREVRATSAGDLPLHAYELRNRDFLVVQLPTGAVLAVPSDSVPPIERDLW
+EDAELRRSLWRGFDDAVCGRVTPLEDVLAELDFDLSSED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002492.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002492.fa
new file mode 100644
index 0000000000000000000000000000000000000000..03a76abd73d32ea6a6c75d50039cb89cceffc659
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002492.fa
@@ -0,0 +1,2 @@
+>2_42
+MNHLTDAECRAELERALDEVDALVRVTEPANAFMDALGRSETWTRFLTLPHAVPTTGAC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002493.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002493.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3754091f1403cedf14da6893f3d7690fb03c478
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002493.fa
@@ -0,0 +1,2 @@
+>2_43
+MNQPTRTLPQLLQPVARAATYTAVTVAGFFMLSWPSIFTGAM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002497.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002497.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4df9333680f1be3d1adab59f0ade37744c0b9483
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002497.fa
@@ -0,0 +1,6 @@
+>2_93
+MPLLTRTVDPRSSDVLSLANSPVLWVFALGVFAVIIVQSALYVRAARRAAPGLGIERAEL
+STAFRSGAVASVGPSLAVVVVAIALLALFGTPAVLVRIGLIGSAAFETGAAKIAAESAGA
+PLGGPGYDQHVFALAFITMSLAGAGWMVATLLFTPLLKRGSARLSDVNPVVLTVIPAAAL
+LGAFAGLTLGEFPKSPVHVITTAVSAAVMLLLLLVARALKADWLKEWALGISIIVGLAAA
+YLAHQALLAPAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002499.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002499.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4101015ee888ba5ce6bb78a7ed866dbd7a00c0d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002499.fa
@@ -0,0 +1,4 @@
+>2_98
+MSQEPVIRRDRLEAPSRILPMTDVAAPPRSAVAPWAPIVAAGVVAAMHIWKLPGVMDQVR
+ADLGMSLVDVGVLMGIVQVASLLLGLAAGGWGSSWVLTVGASLLGLALTPLALRAPRARG
+PRGMRSARRSGPRPPGRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002500.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002500.fa
new file mode 100644
index 0000000000000000000000000000000000000000..93643888316690f2d9a1ea8bc7030726dee4e4b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002500.fa
@@ -0,0 +1,6 @@
+>2_117
+MTPEEFPPIHSQHAVVLDWVGPRWAGHLRYAVHLSEQSLAPGETELRDLWPDGAGLCWLG
+GPAVGPGPWPRNAEGAPLSHVLTLDLRTVAGASDHQGKAVWPAGRLREGLPVSGHLQVFH
+DLQTYGGDPEDGDRAGWAVTWTPEAEDGLRPALVEAPDDDGAPDPVCQLVLPYAGFTLPS
+SLDVAVTDPRDADRLEELDDALREAWTVQRGLDPTWAIPTSHVYGHGWTGDALAGGEILP
+EVLPLEEGDEHRLVLDVESWTTLQGWFGDAGHLEVWMRQSDLERGAFDRAWCLIRTD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002503.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002503.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a79f30078f109fa7c171bfe52778638fb01402c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002503.fa
@@ -0,0 +1,8 @@
+>2_132
+MKITRIEAIPYAIPYTRPLKFASGEVQTADHVLVRVHTEDGIVGEADAPPRPYTYGETQV
+SIKNVLEEVFAPHVVGLSVFDRSQIHAVMRRTIHNQVAKGALDIALWDAMGKALKTPVTT
+LLGGWTDSMRVSHMLGFKPAQELLDEARRFGEEHGITTFKLKTGRRPLSLDIEACHVLRE
+GLGDDVDLYLDANRGWTANEAMEVLRRTEGLGLSLLEEPCDAKEAMSRRRLVEKSPIPVV
+GDESVPTAGDASRELLSGGCNAICIKTARSGFTEAQEILGLCTGLGVDVTMGNQIDTQVG
+SLATVTFGAAFEATSRRAGELSNFLDMADDLLAEPLQIRDGRIAVRHVPGVGAAIDEDKL
+TRYRTDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002505.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002505.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83809bfa10947f39003111bf2456904fbf3ce2aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002505.fa
@@ -0,0 +1,6 @@
+>2_154
+MPGPQGTDRRAIPQRSTRWAARLADLMHAAGLTPNRVSVGSVLFAAVGAAALVAAGHAAT
+GDGARAGWFVLAAACIPLRLNMLDGMLAVEKGLHSPTGDLFNEVPDRVADMLLLAGAGYA
+AAGAWLVPGWGAGLDVGVLLGWTAAAAAVLTAYVRSLGAANGVGNFFEGVLPKPHRMWVL
+AAACLLSLLEPLLPVPRGTVLALALAVIAAGSVLTVARRLRLIAAALRERADAAPARPAG
+ERTAGLPTDGGERA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002506.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002506.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34211498227d856bedef194306ba515d2286e92b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002506.fa
@@ -0,0 +1,5 @@
+>2_155
+MPRRQPAADRSALLDHALAAAAGFAEATFFVVVPDVWTSRVAFERPRRGLATAASALAGA
+LAGGAVTHAVSRRAGAARTRSWLTALPGISDGMVDTVEARVGAGGHLALITGPSRGIPYK
+VFARCYGVDAARPGRGLGALLLASVPARLPRFLLVTGGVGLLGARLRRRAPGLGRRGRGV
+LFWTGWGAFYAWYLPAVTRAYRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002514.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002514.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1afcec5e4ca71ea30ab4898a6914c76e423bbf17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002514.fa
@@ -0,0 +1,3 @@
+>2_227
+MVAGLPWFAWIAIVAILVWGTLQVVQLVTGRALPGEEMKKEVEELRTRLDANEGRRPAGE
+LPARADAEGSDLERRIERLEARADRREARDREHDDWDRRAGELG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002516.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002516.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16adaaf6f331f3c8dc0ddd6a9f423b9d95e0295f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002516.fa
@@ -0,0 +1,10 @@
+>2_260
+MTASSSPASPSRRALGALRGAVPPPRLVRLPRAAREGGAGREGGGVRGHDDGAPGPGAGR
+RTTWSGSASWTPAETARPGSVAEVADVVRRAAAAGRRVKPIGAGHSFSPIAVTDGVQLEL
+DALSGLTGVDRAAGRVRVLAGTPLHRLGPLLGAHGLALANMGDIDRQSLAGALSTSTHGT
+GLGFTGYGGMVTGLRLVTADGAVRWLDVRTEPELFQAARVGLGALGVVVEAEIQAVPAFL
+LRAEERSEPLEDVVASFVERSRAADHLEFYWFPGTSVALTKENTRLPLGSGLDPVPPLRA
+AVMDRILANGLFEATCRLGARVPRLVPALNAAAARGVDRRTYTDVSHRVFVADRAVRFRE
+MEYAPPLERFTEAFTGLRALLADRARGGGPVSFPVEVRTAAADDVWLSTAHGRESVYLAV
+HRYHREDPADCFRAVEELFLGLGGRPHWGKEHTRDAAWAAEAYPRFGDFLAQRDAVDPGR
+VFANDHLDRVLGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002520.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002520.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49b1f96e61b0bcc6f7ce59aa68907df92cfbf29f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002520.fa
@@ -0,0 +1,6 @@
+>2_310
+MTHPRTAPAPLAAVAGSLGLCLSAAVLAGAPALAAPTSTPAAGQARQQPVVVMDHSGSML
+NADADAEGTTRVDAAKAATKDLIRAAPGETPVSAALQQAADALEEKEKGTIVLVSDGQPS
+CDTPPACEDAAQLTEHLTTRTTRALHGYEAAGTPITGGSSLAEAPLLLPGPATDTLASHA
+RPEQIGHRLGTDDFADGDVTGLPQEAGPGFLTTAAQFRERFPDEAAAAPPPGPGPWTPSA
+CSPWPAAPS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002521.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002521.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18fb7a44b731cf9e60f3358badba05cfad171518
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002521.fa
@@ -0,0 +1,4 @@
+>2_313
+MLRRAWSGLVGPLGAARSAGVVGAATAAGLVAGTETAARCGPGVGAFVGVTAVDLVGGMV
+AFQLRPTREHYARTSLSRRMALAAAHVQCFALPIVGEGTWSAAAGRWAGVVVSTALLQCA
+VPAAHRRPAGLVLAAGLTTADVALAGPRQRWLGPVWFTKLVAGHATLPDPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002527.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002527.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1f6d7eaaf961cec71db3ee3b1567eef933cad4e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002527.fa
@@ -0,0 +1,7 @@
+>2_362
+MALLAALLASTLRGTVEVPATVGLTQEQAEAALEDAGLVPLVSSTHSSEAPAGTVISSDP
+PEGTELDRGTQVGLRVSRGLEGVVLPGSLRGLSEDAVRRELQRLGLTVSSVQYQDDGRLE
+RGMLARTDPALSTSVPPGSSVVLHLSSGTVRVPDVVGMSAEDARRQLALSAPELRVRIQD
+EDGAATETGTVVSQDPGADARVDNRSSLTLTASTWVEATAEPTPPPSPSAEVPPPVRPSA
+PPSSSTPPSSSAPPSEEPEPSEEPEPSASPTPTPSETVDPTPSDSPSPSPSPDPTTPTPS
+PTRTTTPTEDPSPTPTLSDPAPTLTPDPEPSIDPPPSD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002528.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002528.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cde7131276c84f0f1491dcdc15557410889d5e83
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002528.fa
@@ -0,0 +1,4 @@
+>2_374
+MPRTTLTFGGLLIAVGIISYAVTGFISWTALIPAFLGLLIAICGLIALKNTTIGLSIALV
+ISVLGVLGTSMNVLKVGELISGQAERPLAIVASTVTFVLLIVYIVTGVRLFLTARRGDKA
+EATTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002531.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002531.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6326339a9ff36e2fd06b462b89082cbe360c7e1f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002531.fa
@@ -0,0 +1,7 @@
+>2_437
+MVARVGSENIELVDPGTEDSEIRPAKYLPGRRSIGVHLKMREESFARRFVSVQVNRDGGV
+IVIPFLEKWKKVRCVSLNYPLPGHPVVDPTSAVRVGDGSRAKLHYHRSGYTSVQPQDPPG
+EAPRLGVHLAPLDSIHQLPVFTVAARIPSKFPRLERAKRGDLIHATSMLGVRSLLVAGVL
+YDRSQVAPKSIGGYDSATPLTFTSGDPNVMILDLSGYGLNSVLALFFVASPVDLADTSCD
+ATVASYGSAESSGSNGVAIMAGGGYPHTFRIGDIPPLESFHSNTDLDPRVRSFSFEPSLN
+YDEIFYSE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002533.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002533.fa
new file mode 100644
index 0000000000000000000000000000000000000000..081e5e75c97c8c0db788241d3705bc14361218cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002533.fa
@@ -0,0 +1,3 @@
+>2_439
+MDAMLTGAEVQATASADQLASGLLRNDESTKFLDGVVPMLLNFRLPPEAIASLVIGQTFV
+GNTHYGRQTIYCDGGHEVVLRERTRRAGPMSAKASTSRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002534.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002534.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c9db55c0fec28879671de1480b57ade8dc1bd72e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002534.fa
@@ -0,0 +1,3 @@
+>2_447
+MEGFRVRAGKEERAREWIAFLRENPEAFRETLEPERMYVETIFSETVGDALYLWWYTLQG
+EDGAELSDSTHWLDERHAAYWRECIDPDEPSLLLIPEVHMSPERLEDAMRPLGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002537.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002537.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08d41a66ae8eceeeeedae7fbde4aec4d2b412ba3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002537.fa
@@ -0,0 +1,4 @@
+>2_453
+MDNLRAMAALFGVSVDHLLDGTGDGAAPAVLRHPVDVASLEPYKPAGRPLGAKSHRAVRE
+AFPDAVIYPLARMRSNNRVQEFLEWGLMLAFDTPYGLFGLSDSLSNRDAYYLVEEKNRHV
+LARVTPKAVEGKELPEPVEGRTFTVGADRFRRTSRPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002540.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002540.fa
new file mode 100644
index 0000000000000000000000000000000000000000..57a30d956b3fa1ec1b59dbfb674639c5023215ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002540.fa
@@ -0,0 +1,5 @@
+>2_462
+MTPDSDDAATPPATDAAHTAGAAPTLWEGDLGTLGEQSRRALLELLQGPYLSGRRRPQLW
+QALIADEAAIRSRLHDLFLDVVIDQHDEFAFTRRVATDEIAVPAALRSKSMTFLDTAMLL
+VLRQHLLTAAGERRVIVGRDEVFEQLAVYQQGDDSGWARRLNSSWTKMLNSFSVLQQLED
+DRAEVSPVLKVMIGPEEARAFTELYREIAAGQNDDDADVTTQEDDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002546.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002546.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c071f9a430fea18e6c44e08fffb9b1e1b1af931
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002546.fa
@@ -0,0 +1,3 @@
+>2_469
+MCGACGRGVASPTTALLNEHGLKRRALARLRGELAPGCRLTLEGDAWTLIRRSGRGEHHA
+DVEGLIASLEGGAAGDWVGAEPPREVVAAVTAGMVARARRRSD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002550.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002550.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e8c3dd333aee828207af3649469c4b9de52d5d04
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002550.fa
@@ -0,0 +1,2 @@
+>2_477
+MPFDQVTAEHAAAEGDRTLASWRAEHERFWRAHAASGFAPDMPVVCEAFRVVHRRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002554.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002554.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76f8a327369a7f1b0f5182b815a428e72c7cb49d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002554.fa
@@ -0,0 +1,6 @@
+>2_486
+MGVYVAGGGLGIVVSGLALPWALNSFPDDVGWRVGWGLLGAVGLVAWAVAARAARRVPAP
+APRAAGSRAPVRGMVPLLVGYTLFGMGYIAYMTFIVALLRGDGATDQQVAVFWVVLGLAA
+VAGGFAWAPVVERLQGGRAPALLMVVVALGAGLPLLWAGPVPALASAVLFGGTFLALVGS
+VTHSAQRVLPAAQVADGIGLLTTVFALGQSVGPVLSGVLADSADGVRAGIALSVAIVVLG
+AVAFLPQRRVLPEAATTAGGAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002555.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002555.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5996174e4baeefe3155082727af252492a113f8e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002555.fa
@@ -0,0 +1,5 @@
+>2_493
+MPAATLDDLRRARRVLFHGVTGAGKSTAAVRLGAVLDLPVTLVDEELGWLPGWVIRTPEA
+QVALAEPILAGERWVLDSAYRFYREAAVARADVVVGLDYSRAATFARLLRRTVRRAATAE
+PVCNGNTETWGRALGPESILRWHAQTFEAKRAWIRAREADDAGTPVLRLTHPRQWERTLA
+ALAAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002564.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002564.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb71ac21a4a70f074ec588b1ed0428626cc8bc91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002564.fa
@@ -0,0 +1,3 @@
+>2_579
+MTGTTLDRPTPTSVSTSVEPRTGAHAVARTLADTAADAAPAVRTPVPPLPPTRPRPPSRP
+GATASASRSSSPW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002567.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002567.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee1fefe0c282a3edcd796c657a870699f91f7c92
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002567.fa
@@ -0,0 +1,10 @@
+>2_588
+MNAAPRTGEAAVARPDAWPAPASFSDSPRYVLARWITDLPAMAIGLVGSLTWIAQWPAPW
+GPLVQALMLLWVASLVLGPVVRWRTARFHVSADGVQVDSGLLSRRSESLPWDLVTSVDHR
+QPWAFQLLGITEVTCTQTGEDGSRVRLDGLAPADLAAFQRHADAAAALGRSAPAAPSRVE
+DVAASRVDDDGAPADRASTGQVDAPTGQAAAAPAAVVHRTTLADLLVLSLVYGQVLLLVP
+PVAFGLMELTDVLDLTERLESLLFSGLGSWPTALLIVALAVVVGLVATVVKFHGFTVLAT
+PEGRLRIRYGLVSTHERVITPGAVQGVVWHRNAAEQLLGRARLSVLTLDSAAQLGGNLVL
+PSMPVERARAIVAEHLPEFAGTDRRLSTGLATPAVNLVSLLALAAAFAGTWVLTAQTWGW
+PWPLAAGACLAAAAVVAGIIAVAPARLYADPAAGLFLTRRITVGERVTAVRATRLHGISA
+HHLHHARTPRGRRTAWLPTVFYFAGAPRRAMALVAAPEAVEALQAMVRHSSVPLRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002568.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002568.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7547c73b67d2f260a603f81136bf7bfcd7ce132d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002568.fa
@@ -0,0 +1,5 @@
+>2_589
+MLDHPNAAPSPEDAPAASARPAGDAGVTRLPRLALRVWQATTCATALPIAAVLAAVALWW
+DHPVGGPVLWILVALTAAVALADLAVVNRVRHRSYSYTVDEDEVYIAKGALVRHTVDVAV
+PQVLSVHVVRGPLQRALGLATVRFVSVVDAESLGPVELAEAQRVKEVVLRGLAARRQESA
+TALVAAGEVAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002573.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002573.fa
new file mode 100644
index 0000000000000000000000000000000000000000..42a36ebd6bb05d8a2790b3fa31c4be15bdd7b82e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002573.fa
@@ -0,0 +1,3 @@
+>2_607
+MGTVGDSYDNALAESVNGLYKAELIHAKRIWESVEAVELATMGWVHWWNTTRLHEALDYL
+TPAEVEAAYTHDQDSAPVAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002574.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002574.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f38247b6a4b28feb2eaaa8b8b802c3cc651122b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002574.fa
@@ -0,0 +1,8 @@
+>2_612
+MRPSSSRALAMLAAASLTALTAAPAQAAPAASTGAPSSSSKHAFEFGVIGDVPYGQAQVE
+RFPDMIDELSAQAGELEFLAHVGDIKAGSAECSDAYFWMIRGEFDRLALPLVLTPGDNDW
+TDCHRKNNGSYDPLERLDTFRDVFYPRADRTLGDTSMRLDAQDEIGLPENAHWREQRVEF
+GVVNVQGSQNSTLPWSGLGLTEQTPEQRAEVAARDAANHALIRDLFTDAERTNARGVVLM
+LQADMFEPRLAEGGVISPEDAAASQAFTKTVRLIADLSREFGKPVYLINGDSHRYTADAP
+LAAGSPWLDVYGVAPVANLQRVTVEGDATSNEWTRFTVAPNSAGKGKNAQQPLLTWERVP
+YTF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002575.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002575.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28c785af0a5bab4cea55f6a7de601c6e86894f2c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002575.fa
@@ -0,0 +1,2 @@
+>2_613
+MGAAHVWDASTVAALDSVLTKYAQHGIHAEVTGLNEASTAMHARLTGRLGT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002576.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002576.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dd56751d7fdaf6cfaab78df4c462b3e3e3a4d856
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002576.fa
@@ -0,0 +1,4 @@
+>2_628
+MIESTPAGRVSERSAPRVVLGLVLLVLIVPVVIAVFMAVYAVAEFVQGGHAPVGAPPLLV
+SVGQILAVACASVCGIRFARSRTTRARWGWTAAVVALLVLAAWPVLVGGIGLVGREACEV
+RPAPFWCE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002579.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002579.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8512b3551707841544f82702d6175db5afcda25d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002579.fa
@@ -0,0 +1,6 @@
+>2_690
+MVSRSSHPDTETAPGRVRIRTDDGVVLLRCARGAQGEPPRLGLEDSGSTFGLALHAERCA
+APVPGVRVEVTRSGLFAERSPAGTVLLPDDGGEPLWLSAPERSAAGQILLGVVEALRAEV
+LPGHVSVPPVPAPRARVERIARWDEVLAPNGLAGGLAPGERPSQAQQALGGAWRLVLDAA
+PDLPVEARLWLAHREQVAGEKVVRLTATWHGPGADVPWHVELHVSHRLGEGQTEFLVIDG
+STQEEWTIADAVHVPGVPLTWRVHPAPRPDTAGRTGEGLYALIDALAHACPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002583.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002583.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b175e01e4e27f4ecd83a3d7625fd32451c5a03ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002583.fa
@@ -0,0 +1,5 @@
+>2_712
+MELLTPILQAIGLFVATNIDDIIVLSLFYARGAGQRGTTRKILLGQYLGFGGILLAAVVI
+SLGARSFLPEDALPYFGLIPLALGLYAAWRAWRNRGDDDDDEAKVADKQVGVLTVAAVTF
+ANGGDNIGVYVPVFATASTTAIIAYCLVFLALVGLLVLAAKYVATRRPIAEILERWEHIL
+FPLVLIGLGIVILLEGGAFGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002590.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002590.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b5dcaab4059a955c97bdf9815310cc0f56dc3ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002590.fa
@@ -0,0 +1,3 @@
+>2_738
+MMHVPSMLKAYPKDLGEVDKVKLAACIAASVECAQACTACADACLSEDMVGQLATCIRTN
+LDCADICVTTGNVLSRHTGYDPNVTPAVLEACRIAAKTCADECEAHAEMHEHCGLSPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002592.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002592.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9949df2931af7a2f00a1c7fade575dd79f030b17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002592.fa
@@ -0,0 +1,4 @@
+>2_766
+MLLPPLDEFLRILIVTPLAYVAVVVLLRISGKRSLAKLNAFDMIVTVALGSVLASTVTAS
+GTVLVAGLTGFTVLLLLQVIVSWLTSRRRVQTSLVRSEPTLLVRHGRLLTDAVAEARLTE
+DEVRQAVRSQGIGGLDQVAAVCLESDGTLSVIPTSSLGDESALADVGAW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002596.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002596.fa
new file mode 100644
index 0000000000000000000000000000000000000000..69a05940129a50b431f01c09b93703d007a3e69f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002596.fa
@@ -0,0 +1,4 @@
+>2_783
+MGLAAAPRPSRRIDDGGRQVLDLGGLSAVVEHYGRAHTRTDLTVLVPEAGVLDAVLQRLE
+APAARSSRNEPCGMAPTTGEVGAIPQGSFHGEVRVVPGHGAVVDATLVRAQREALAAAPP
+G
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002599.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002599.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2400da4b71ec29b0245f574e258d490099d3b3bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002599.fa
@@ -0,0 +1,6 @@
+>2_797
+MNAALGFIGLGTMGLPMALNLAKGGFDVVGYDAFEGARTAAAEGGIALASSPRDLAERGV
+TAVISMVRDEAQNREVLLGADGVMAARPQGLTVVVMSTLDPDAMNRLAADVEDAGEATVI
+AAAVSGGQSGALEGTLSIMASGPQAAVDAAGPWFAAMGQETFYYGAEPGNSQVAKLANNL
+MLGVVMNGVAEALRFAAAYGLPQDELLRLAQASTGDSWVVRHWDAVRDWTRETALEVLRK
+DLKAAHLQGLEREIPMPFNALASTELIRAWDTLPAAADEETCR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002600.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002600.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ce02a2a14ed3a0d95234ffb752d614c45b87c66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002600.fa
@@ -0,0 +1,4 @@
+>2_798
+MTTHDLTASNPEQTERERFDRGMARMMELVGDGAGTFDHAKLVESYRDVDPELSDYIVSF
+AFGDIYSRTSLSKQQQTLVTISTLVGRGAEPQLKLHINVGFTVGLTREEIVGALIHCIPY
+VGFPHVLNALSLLKEVEAERAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002601.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002601.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e65ad07f92e655900363914e2848244ff70bb175
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002601.fa
@@ -0,0 +1,4 @@
+>2_800
+MTALASTLPRRGRPRIRTEAGPPAGALAGPLAGALALAAAPVHGVVLVAHSHGLVTTVVL
+LAMTAWCALCGARLLRRRGRTAEAATLRMLLVSAAAMVLAHAAMIAGLPGVGGGHHHGGG
+AADTAGPDVGAARAMLGVIVLELGVGLTTALALRRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002606.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002606.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee310c2fae3c40b1f633977c592afdf04565c779
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002606.fa
@@ -0,0 +1,4 @@
+>2_843
+MDETTPRILADVAELTADPAGAAPGAAWRLEQEPRDLDANVVRLPPGGRNEPFDGPALDI
+LVHVVAGSGLLHTADQDVPIRAGQVLWLPRQSRRGFTAGPEGLAWLTVHRRKPGLGIGRR
+LEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002615.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002615.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bad80783df96ab6a9ef04e008543d60973a467f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002615.fa
@@ -0,0 +1,3 @@
+>2_992
+MRRFTAFTSALLMASGMLAAAPVAMAASIYEHRDYSGAAQGGENVNKLGTMNDKTSSIRV
+YGKTVTFYEHAYLSGNALRLWSDASNLREYQYPFAPTLSWNDRISSWYTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002616.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002616.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27b326654b9a6342d85516be100599edd9dc7747
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002616.fa
@@ -0,0 +1,5 @@
+>2_1029
+MSAAELVRRWESAAQPAPTVVDVGSVLADHYRARPLDNAVFACGHLQSDDELRPDTDKML
+WTITDPVTLLRCARHAFGSLDAYLSHLESEQQEEDEAIQAEDGIERADVAYWSALEGRIP
+EEDHPYGLALTQHALGQRVTAILEVEDGAVTGFKVEGVLGRMVDEHLEGLVGYPAPGSGY
+DEAVPLMRRGDPGDEMFLQHLRQAARFGLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002622.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002622.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12073b52072299642e7177b05147f1f0092b766c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002622.fa
@@ -0,0 +1,10 @@
+>2_1191
+MKSVRKPPATATPGGAGPLVVPVVVTLLVLAAVMLIDPQMRAWSMPVSLWIAAVGFAAAR
+IHDRIMLLALLATYAFFLLGKPIMMGYFGYDGLGWYAEVEDHLILTLSLGLLGIVAGYLL
+YPRAIIALLDRRRRRARSAAREEARRQFSARFASAAELAYWATLPFALAHVITNIRTASQ
+AGYTGLYVSGQSGFASVTAYGNFANTVALCVFLAALASTRRTWVVLITAFTAQALVMVTG
+DRGNFGTFLLMVFAYLVYRARHQDAALIPLRPLMLIGGAAVTALVPVFLLVGANRDGAEG
+SDTLSGFLYGQGSSLNVIEYGLRYESRLPDGHYLMSFASQGILRLILGGDGGLAGNTVAY
+AQSGTSLSHSLSYITLGDLYLTGRGVGSSFLAEGFADYGYGGVLLVAVAYGLLVAWIDAF
+APGSVLANAVRLLSIPAIVFAPRGSASGFLADVLSPVTVAVLLGTWFVALLLKDRRREGA
+PRITPRVVSTTHVGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002628.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002628.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8a95a914e63f62e114ff5635a03143721c160ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002628.fa
@@ -0,0 +1,3 @@
+>2_1252
+MAVFDVIVNNADRKGDHLLTVPSSHRHGVDHGLTFHVGDKVRTVLWGWLSEELSEEECDG
+VVPVVAGLDGELGRGLAELLSAEGVEAAAERCTRLLDDGRFPTPSGWPPTVPWPVF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002631.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002631.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f83ee59ce75da8c8a29fe4a232b1a290c3e04062
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002631.fa
@@ -0,0 +1,5 @@
+>2_1274
+MIITVAGEHRAAHPPELGTLTVRIAVEDADAAAGMAALTREADRLTAEVDALRQAEPSPV
+VASAVQAPGTRSWRPWNERGEALPPRHEASVRASVTFDDVGALAGCASRWGERDGWSLDE
+VAWSLTDAVRARLEAAALRAAVADARRRAEAIAAECGTGRVTVLDVADAGLLPGGGAPEP
+RVEAMVRAFGKDAGEGVAVAPEDVEVLVRLHARFEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002634.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002634.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4875d76805fa146a6a937b645976d8601e6934db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002634.fa
@@ -0,0 +1,3 @@
+>2_1281
+MGKRETSKRRFLMMAVLLCLAGAAIITFTDLPWRGLIGAGLSLTGIALLMAGVIAGTRAK
+ETHSPEGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002637.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002637.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f1192ea862364dc72155d43cf35e8f9cd558a03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002637.fa
@@ -0,0 +1,4 @@
+>2_1298
+MAYEQKTTVTDVPVEEYLATVEPARRQEQGFALLRMFREETGAEAVMWGPSMIGFGHVRF
+TYPTGHSGEMFQVGFSPRKSALSLYGLTTYGSHADLLARLGKHKVGKGCLYINKLEDVDE
+AVLREMIRVGWGDDESFVDSHDGTVIERLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002639.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002639.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9dfd87d7a6e89f33e804a016ce5fc9555f740627
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002639.fa
@@ -0,0 +1,5 @@
+>2_1301
+MALEDIQRHLAWKLQGIPQDGDLLGAAGAPAHLTYWGDLQCPHCRDFVNHDLMELVHQEV
+RAGVVTLRYRPLETATRDRGEFVAQQAAAWAAGRQGRLWEFMETFHLSQQEADSGYVTDR
+FLRAIADEIPELDLERWERDRRTDLTDHLVESERQARAAGVTGSPGLVLEADGRRRGPLR
+PTIHDLLDAVDELLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002642.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002642.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d046fb740e73b667e11e82e42b824df4896bfa45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002642.fa
@@ -0,0 +1,8 @@
+>2_1307
+MQTETADLIASLSFELEKKYRHLSDHPAEGHSVDGVEEVELSPRRLRRAKTSYTARAFRQ
+RARGEEHQGYGLRRGRGVTPKAGDLVLARIATIGHHKRLESYNSRRRNLFVGDEVIVAYG
+DRYAPDQFLAEVPRNLNYTNLVAAGGMASRVIEKHENIDPATVLEPLGLITRGGEVVSLS
+DTAPHEITPWAQARKTLGEDGPTVVVVFGSSMNSGKSTTVGCLVNGLVNAGLTVHAGKAT
+GTGAGNDAGLFRDAGAEKVVDFTDFGLPSTFRLSFECIKDIMFSMTSVLSQGDPDVVVIE
+IADGIYQGETAALVADPEFGELADKVLFACGEALSAAAGVGLLQRAGLPLVAVSGLLTSA
+PLIAREASAVVDVPVIPTYDLCEADVTLRTLGLDAETVGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002645.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002645.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9be73f08cf628ba35f0318045b5dd8145e9881ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002645.fa
@@ -0,0 +1,4 @@
+>2_1331
+MSLWPLRAYAGSHLSGTDAPKFRLDSFPLSTYPMFSEHRGRSTHVPHVIGLTAEGERVIP
+HHRHFGTGGLNQTRKQVARAFRRGDAAVVVQDYADALARQHEALGGAVPTGSGPGSTRRR
+REAAIVTVEAVRSRFRFDEYMAGQRLPQREQVLARCAVGGRAEAVQGRRDAAQLGREAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002648.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002648.fa
new file mode 100644
index 0000000000000000000000000000000000000000..177ce89f658e28467942d4b5342a0ab03b0b76d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002648.fa
@@ -0,0 +1,6 @@
+>2_1440
+MSAPALAVPRSAVAGPRARRRPLAVGAALCLALAGCAAPGVPAGEDPDTLGGRWTELNES
+LDSARSVAVTARWARPAAVVTLAGSLEADGAYRGTSTGAEGAVEAVHADGVTYLRGEGAG
+DALDGVDPGRWLALPGPAQDLVSPAELIAQVRAELPDTLAPEDAAVEGREVTVDGERLEL
+FSGVRLDGAGPVDLYLDARGRLARVARSADATADATAAPSSRSGAAPTSNASPDPAGALL
+PRVESVDFDDWDAVPPVVAPPAADVWDRPGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002652.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002652.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2d2fcded52262bcaa5c75f6e158e06cbf3d7819
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002652.fa
@@ -0,0 +1,5 @@
+>2_1467
+MSSYQQQRESRSRIIFTVLIIAVSVAITYGFIRLTLPSITGQNPTTNDSSNQTTQKQEEK
+KDLPRGDAKRVADLDRLATALKTYKERHGGYPMSTGTCAGGTFDSDADLGFLADLEREAV
+IDAIPRDPAGIAKSTKTGQGANATTTADDRDTMYGAKHYLYYSNGTKFALIASVDDADAI
+PDDAAGVYLAEGDREWFDGSGLIADWHWSRNVYVVSNQKLAEAAGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002653.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002653.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f92011d8529bf6ece6dfb6649811245986bff82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002653.fa
@@ -0,0 +1,10 @@
+>2_1468
+MRLAPDLTPVGWFLFGAMVLLILTYLYFWWMVIKASAHKHVSREKVTNRKLTASLAHAKR
+KGNTHRFLIQITTKGGALSVVQRGIDNVLAGVARYPVLQKVVWVEIITEDANEVAALQTR
+YRNAVIPVTPYLLPTDYRTPKDTHLKAPALEYMVEQHRASPTESYVVHYDEESVFTPDNL
+ARLVHRLSRHPVGISEGMISYGLDWNETTLLNKTMESNRPFGCHECYSVMTSPPPMHLHG
+SNLVVRQDLENQIGWDIGNLDGSALIAEDLVFGLAAYLKFGKDVFGWHHTEMIEQPPFTL
+KAAYKQRERWVFGAMQALAHIRQQPDWMRLSRKDRWHINVIIRLRVLTYALGFPVSLLAL
+GSNVVILLILAAEAVREGTITVVAPELTVYGIVTSIGLVLWLAGTQLGLFYNLRYTGMTR
+LQRLRDHVLVLLVTPFAGVIDTAGPLVAVLKWLAGIREVAWKPTPKLAVPSRETTPKRVA
+AAEVAAGEKAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002654.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002654.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0c6c7cc6d289279fa27360b401829859cbc63abf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002654.fa
@@ -0,0 +1,11 @@
+>2_1473
+MRAVEVQIHNFRSIHDARIRLEPLSLIAGANNAGKSNIIDAIRLFYGDLKWDDARDKPKV
+ASGDAEAWVEVEFKPTENELAQLKDDYKSADGTFRVRNYVSPSTGADGKARSGYYAYEND
+NLSNNLFYGAKNVGSGKVGHIVYIPAVSKIDENTKLTGPSALRELVAEVLNKVVADSPAY
+KHLTEAFGTFEGSIKAQASADGQSLESLEKEVTDEITSWEASFSLAVQSIQPEEILKTLI
+KPQLIDETHGGEIDQARFGAGFQRHLIYTLIKLAAKHANPPKVLSSEKKEFTPQLTWILF
+EEPEAFLHPSQEEVLHDSLLKLVRDGTTQVLLTTHSSRFVSRSMDDLTRLIRLRRDAGVT
+TSYQLTQPELDQLFSDALVADDSILPHGTSSADVNKAAMMASLKTELWMQSTRTTAFFSQ
+RVVLVEGPSETAIYSYLTSRGIMEPPVRGLAIIDCMGKYNIHRFVAILSAFGIDHSVLYD
+GDNGGAYDAEVTQAISGAKTTFTKRITRFVNDLETELGIAPLPRNQSSRKPQYALYNLES
+GLVDQVKLEALKQEFVDLATAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002655.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002655.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed6f7c27d54dcac4ef15342d1921a338651a30f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002655.fa
@@ -0,0 +1,9 @@
+>2_1474
+MHEIKCPHCGKTFTVDEAGYADIVKQVRDSEFEKQLHERLELADQDKQKALELAETKAAS
+ELQKAAAAKDTEIQELKAKLETGDVQQKLAVTEALAAIEKDRDSLATELAQVKQEKQSAV
+ELAEAKALAELQKAAASKDSEIQELKSKLDSIETAKKLELAEAVSAVEKERDALRTGLEK
+AELEKQLAEKSLKDKYETQLKDRDDAIERLKDLKAKLSTKMVGETLEQHCEIEFNKIRAT
+AFPRAYFEKDNDARTGSKGDFIFRDFNDAETEIVSIMFEMKNESDGTATKHKNEDFFKEL
+DKDRNEKGCEYAILVSLLEPENEYYNTGIIDVSHRYPKMYVIRPQFFIQMITLLRNAAIN
+SLKYKTELALVKAQNIDITNFENELDAFKTAFGKNFDLASRRFHTAINEIDKSIDRLQKA
+KEALLGSERNLRLANDKAQDVTIKKLTRRNPTMAAKFAELEGPAHSGSE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002656.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002656.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7585350a28e1593a5bfd919c5522f5ca556ae04
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002656.fa
@@ -0,0 +1,5 @@
+>2_1478
+MTPQKQVHSDILKRLVATSGVIHLSWKGFSIGSLSGRRVLYAWPDRKHLNGLWDVEADAL
+AVIEWNEDETAEWIEDANPVQLFHGRTLEPRPVEESTDRQEPLPNGVDGILEHIAAMAAC
+YSSGLKWNEEDKLKADMMNRPERWAPITVEQVRTKCRALGMRPDDVDTVAGFLQRRKEGR
+RFNVQSSYRTFHFN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002666.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002666.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b915977f669ee1de25b6b108e3628d61bc78778b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002666.fa
@@ -0,0 +1,9 @@
+>2_1753
+MTAAPDAAQVADGGAALAARQRRVVRTLAASQVFSGLGNGSALAVGSVLAVELTGNAALG
+GTTTMMISAAGALAALPLARLALARGRRTALTVAYLVAALGAACMLAAPGIGGFGLLLAG
+SFGVGLGAAGNLQARFAATDLATPARRGRDLGLVVWSITIGAVAGPNLIGPGAVLARAVG
+LADTAGVFLFSVAGMLAAVAILQAGLRPDPLALRREAGLGGVASPQPPRLRAGVGAVVGD
+PRIRVGVAAVVVGHAVMVGVMAMTPVHLSRTHGAGAGGSDTLVIIGVVISLHIAGMYALS
+PVWGWAADRWGRLAATAAGFAGLLAATLVGAVGAASTGAVTAALVLLGLGWGAVTVAGSA
+WVSEVATGPRRVLVQGVTDSGMGAAAAVTAGLSGLVLARWGFTGLTVAAGLLSAALLVWV
+LRARWRYENADEVSPISDIVTS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002668.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002668.fa
new file mode 100644
index 0000000000000000000000000000000000000000..853d56ecda2120a177973bc0cb8dd68241827437
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002668.fa
@@ -0,0 +1,2 @@
+>2_1777
+MTALASLASPAALAPLAAFPAPPPGTASRSAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002670.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002670.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27209ce9b44d1e2175c09ac7d3da40cc6ed0eac5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002670.fa
@@ -0,0 +1,11 @@
+>2_1807
+MIAEDVDRAREAVEQALAAVAAPRWQDVPGGALLPDLLVQAETLSRTVAALQTALAGHLA
+EAYEHEADRQEVLGIPPGKGPHRDAADCLRDTVRIDRRTAQRRLRRAAATRPRRDFVTAP
+LADPALPEVAAVLSEGAADEAACDAVIETLTRARTDLALAAVPQDEADALLAAGESLLAA
+QLHHADLDGMRRLCARWRQHLDAVVLPDSGIPTEAELRAAQGLFHRGRRRGLHRWDLHLT
+DTQHEVLQTVAAAATNPRARGAGPSGQVDAPAGSPDLDPRTRGQRQADTLVSALQAALAL
+ATPGVLPATAGHRPQVLVTIDHETLLRRVRTASGTAAVLSEAEFTGPIDPREIRRIACDA
+EIIPAVLGGEGEILALGRSRRLFTRAQRRAVTARDGGCAAPGCTLPASWCEIHHIGHWED
+GGRTDVDNGVLLCSHHHHAVHAGWWTVAVVAGIPWFTPARHLDPRPDAPGGTGTTGSTAR
+RRPRAPGERHRRRRRRRRNRQGQWNRRTRRDGQDGQVGQVGQGQTEPVRPGPAAPPRPPV
+RRLPPPWTVLSPPWRPPGRRRPRHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002674.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002674.fa
new file mode 100644
index 0000000000000000000000000000000000000000..91e293df55221b99712708c491de562b3dc401f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002674.fa
@@ -0,0 +1,7 @@
+>2_1826
+MLRANDSGNADGTGVLVTSPDADCIPVSDPADPSALHWLDVATTTRETNSLMETGPLLSM
+EELPATLALMDGARGYTEYIWSSGITEPWMWHAYTGPDKEGTVRTRIALLDFMGPEQYEA
+TSGARYAAPGLDGDALRPTDWALLRAHGLGGDDEDGVRQGPRPSRPASRTRARRRPVTTT
+PRTTTPTRSPRPWRPATAPRGGSPPSARPRRACWSASARDSAWSDPGCSHLVARTTRRLQ
+IARTASREHNPAGERWEAASTSPDGGHRSPVAAVVACAGRALIPSGSTSSVRGEGDTPTR
+RGGARDFRHRKRGTRVLHRLWTSGGGLGVSRMAVRIARGARMWTVWGGTGDP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002675.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002675.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37e0f4818950e96b549e3168bd3303427e6937d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002675.fa
@@ -0,0 +1,4 @@
+>2_1828
+MPSVLFVLSASGHWTLKDGTRYETGFWAEEFVVPHDVFADAGWDVAVATPGGVAPTVDQT
+SLGLTGGAPWKTARLKRDLERLAPVLDRPVDLASVDEAGHDVVFYPGGHGPLAERILADA
+EARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002678.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002678.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e57d9609fb8d5cff67f96be686ffb6d64b6e7ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002678.fa
@@ -0,0 +1,5 @@
+>2_1894
+MFERFDLRPLARPHFQSLIDPGRRRISFGTTAIIFLLPLAVGILGGWAVPIPGAAPADAS
+GGAPAPASSAASAVFTALPGAAGTLVAGFLAAFVLLMNLRIKLDDSPQLPRTPAQLRSIS
+TAAMSSLYLTTVSGSALIVSLCLAIFGAPLAAIAPLAFRALVGLVLGLFTHILVNAITVL
+RRVAGAYYVLYKGEIRRVPVRGVPEHDKRAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002679.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002679.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca637967b530d61d4fd9adeb99f521a650fe6aa0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002679.fa
@@ -0,0 +1,7 @@
+>2_1895
+MSVRRRYPYGFRVWTFSLEQARERDSEAGPETVPLLPLQTESAKGMLLGALQVLQTEGLK
+IHDQKQHRIVEIHDATAQGFILLKIEGGRAGSKFTVKDERGQERGEVREEDSLVWPGRVL
+IAFSSNDARQGFMVHETYSGRTHSEVTRLRLYAHLLARHNVSLHTAHDLADNMAWDQVLK
+DDAARIEEIEFTVKAPDDVTIGEDTRPRKMSVAYQVEPAPVDRFLRKGSRTSVTDLVNSV
+GSLPHPDSFEEGEAVVEIATAHGTRRLQIGRRPYPFTRLIKSPYQVDDVEFLHEVTPDLL
+ELAARLDMALPQPFLPTDSLRPNP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002681.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002681.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b33824764d3d89b0ca33d4d25c991422ac2e1e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002681.fa
@@ -0,0 +1,6 @@
+>2_1898
+MTALTPFQYGATAVRTAVVDGEPHFVAADLCAVLEIGRQQDATRYLDADEKRGCLVDTPS
+GPQTMVVVTEAGMYSLVLRSRKPEAKAFKRWLTHEVLPAIRKTGAYSVQRELTEDEIIHR
+ALTLTVAKVEALEAKVAEDAPKVAAWESIVSSAGSWSYNDAAKVLCESGQIEIGEKRLVK
+ALVDWGYLYRDARGRPHVYQRYVEQGLFVVKARTYRDLVSGEVRESAAPQVRLTGKGLGV
+VRSRLTNQPAFELLGIRVVKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002683.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002683.fa
new file mode 100644
index 0000000000000000000000000000000000000000..302ea0b1faaba26dbda8cc54dc2f2926ee52dc5d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002683.fa
@@ -0,0 +1,3 @@
+>2_1900
+MTTAAAPFYVENLRRAREARTARAAERTAARLEDLEDLAAARVAREAAARRAGFPSVGAL
+ERFCYRVGRHDLIKSLPLQRSAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002684.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002684.fa
new file mode 100644
index 0000000000000000000000000000000000000000..129c4e50dd81b554bdff003a48118cbd7f52ddd3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002684.fa
@@ -0,0 +1,3 @@
+>2_1901
+MTAAVAQTVEVPAVLTTSDLAARWQVSEEWVQDAAKAGRIPGFKVGRAWRFRVDAVLAHE
+EAEQAALSPANVFALAPGAVARRARRATA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002691.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002691.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8ab4b7fdb2d4df3c63f51c880d6d8fdbf89c041
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002691.fa
@@ -0,0 +1,2 @@
+>2_1909
+MGDCECGRRGVLLDRELDLCILCRNRLDSAPAKEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002693.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002693.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba1065e698551d857cde53ca331c25b0d304fc91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002693.fa
@@ -0,0 +1,4 @@
+>2_1911
+MSITREAAAALADLHAANPTMQDVAGTWQEDAVAYVAALWDAEVGRAAKEGTFLPAFASH
+TAGMRRLIAAVVAAAREDLAEAERAQHGALAAVLNRVEFQQARAAIGELPDDVAAWQTTE
+HHALITTITRELEDPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002696.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002696.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5022e5ad0527fb33206dd92baf025c25d0f5437
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002696.fa
@@ -0,0 +1,9 @@
+>2_1914
+MPWLKVSDASAMHPIALAAMEAEDADERLVNELFGYVARCAVMSAQHEQDYVVTLATARV
+TAGGDARFKVLAAAAERAGYWTRTTVKDASGAERPAFRLVEEKDLFHMLLKKERAWETQR
+RADVANPELTVPVRLRDGDGCRWCGKSVAWRDRKSGRGATYDHVKPGQGAASPEDLVVAC
+RACNGARKDEENTSFSRTLMAPPFRPLYGPDTLAFLAEHDVVPEQQDTATAAERQSQRET
+APTPTTAAPATAAGSTARTATAAPRQGVRETADGQERRRGAQVRDVDGQAADAAAAHAQR
+EADARRAEAERERRLDAWLADHGISVAPAPATALSPLDVEEADWAPSEGDAGPPGGPDLQ
+IPADRQAEGSGFPGTGRDGSGREGPGLDVSGTGGARDGSGLDGGSAGSGRRRRRRGRRGG
+RGRGGEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002698.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002698.fa
new file mode 100644
index 0000000000000000000000000000000000000000..62578e5dcbace19ab12e7dfa65f40f2da62567bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002698.fa
@@ -0,0 +1,3 @@
+>2_1916
+MTNWDDADQVNDELLGRMERPDGCTCDLEYTTDYKGRILHIYWSLELTCHHHYPRTAAQL
+ERLNSCPKQEGEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002700.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002700.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c108c2b8599a3ea92a6e832891f70a6ab77e342
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002700.fa
@@ -0,0 +1,3 @@
+>2_1918
+MATSRTGTSEYKRWRSYVLREAERSGQHRCPYCGVTLDYRTGRLPHSAEPDHVTAWSAGG
+TNTVDNGRAICRRCNQSKGARAAPRPRAVQAAAPLRVSRRH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002701.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002701.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86a90730627da202f0c8df3d5facdb67917e6310
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002701.fa
@@ -0,0 +1,4 @@
+>2_1919
+MATANRWVRWALRPRGGRLTKVPLTVHGRHASSTRAATWTRRPAAAASRVGAGLGYVLGD
+GVGCYDLDGALDRGRLKDWARDALAAIPEPALFVEVSQSGTGLHVFVVAPPGPGTVTRHA
+GGAVERYTTGRYIAMTGVPFDVPDGLLRWATPLDAALVAARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002702.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002702.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2fb5f74d2526562810f3c4938b36952b92b32564
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002702.fa
@@ -0,0 +1,4 @@
+>2_1920
+MPLKFTLTTVRGRQVDVVVYGTRRQMRRAAQRWNGAELAPDVRGVTQGFTKPCNPQAVVR
+INQQDLSRRVIDHELVHAAQAIYGHDYGEAIEAHPLEHWTHFNETFAFTVTELQAAIYTA
+LAAHGLEPGISYEEGQPYG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002703.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002703.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6fd55e950728d302b0854f9339dcd39660a830ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002703.fa
@@ -0,0 +1,4 @@
+>2_1921
+MADAPAGLGDRGLTIWERYAGVDAGVDALALEAARAADRLDELDNVIQGKGVLKLMQFRL
+RDLPDLDADEPTWRVEVQFQSVLAEARQQQAGFSAMIGRLAAMEAPKGAAAPTAAHAAAV
+QAGGNVTPLQAARSAATR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002707.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002707.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6c0b483d5e3f9e5ea126ae3d042a3987d1e10c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002707.fa
@@ -0,0 +1,5 @@
+>2_1925
+MRRSFNPLLAGVLRFIEAGAQHGAAATPPPSPATVAAQTTPKSEPATGDADGDQGESPTE
+AGLSEAGKKAIKAERTARRTAEERVRELEAELAAQKNQEPATGSTQRNQEPATGAAPEAA
+TAAGADEDLRAKLRTAEQENWRHRALADHAIPRELVELLAGESEEEVRARAALLSRHVTA
+APLDPVPKSGVQTDASLPGSIAEYRRRIVKPNS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002708.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002708.fa
new file mode 100644
index 0000000000000000000000000000000000000000..10dbf9bfd8c06f783840341178c7666f9de409e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002708.fa
@@ -0,0 +1,3 @@
+>2_1926
+MPMLHRQNIGSGRKNWLGSAHGVNHAQTATLDVSTFTAAADHPEGRIPSGTPVNAADRTA
+VVKWDPAAGGGALGFLIDDVDVVDGEAVPCAVLLHGAVVVEELPVEFTVPTAPTAFIFE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002710.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002710.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d66478e82d0e4b4ee7c973ed74362cd8db36a4c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002710.fa
@@ -0,0 +1,3 @@
+>2_1928
+MIVTHTTTVLRDGEPVVLLAGQHVPAWAEDLVGAHLLAESAAPAEPVEGAEPAEPVEGAE
+PAEPVEGAEPGPADAGEPKPPVAVAVVDAEAEKPAPRRRAPRKKPAEDLEPDFTRPPTEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002713.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002713.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5180e5b011263ed4828d17996e7145bf5f50902d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002713.fa
@@ -0,0 +1,3 @@
+>2_1931
+MTTAGLRRVPGVRRYRALADGVRGLGTSSVVAEASLSAAERIAARARSTGEGEYQAYPTS
+VRAGWANEERAGARVVETRRVPSDARQRVLVTALRGSTTGGGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002718.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002718.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e5b8f18defb1855084ba12a3b9db5d2376957f27
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002718.fa
@@ -0,0 +1,4 @@
+>2_1936
+MFGVDLAAWVAAGRWLGVLELIHSLPRSSRLREAQLNDPDVAADLLELQEAQDEPEEWAP
+ALAETSLITDLLSALIGEVRSLRSEQTAIASGKKPRPVKPIPGPRTALETAKALRAEKYA
+AETLSRFGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002720.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002720.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34d1fc277d386e9fcc0facacab292fcaaa7b9775
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002720.fa
@@ -0,0 +1,14 @@
+>2_1938
+MAWSGAGSWASVSGRRMRLIWSATMSPTTVTAATSSVSVTVTHTLQTSAAIDDPSTAFVL
+SGGLGASTTSPYVRIGSLSGGSQVVSTRTVSVPLAYGKAQTLSWSASMSGLAYIPTTAKV
+SGSVPVPARPLAAPAAPSGVGVTRSSDTRHVITWTRNSPGSASAPYQNQVIQRSADNAAT
+WKTVATVGNVSSWTDTTTTAGRRYQWRVAAKNTGGTSAFASSPVVYTTPAAPTAVKAVRQ
+GMDVLVSWVKSVSPHSRSEIAWRQEGGAWQYPGWTSTGTSYVITSPDPSKPLQYAVRAEV
+ESQGVTLGSPYLWSSWVQLLALPAAPTNLSPALADAALPITLSWRYNSTDSSEQSAREIR
+WRPLGADAWKGIPKATAADSTHVVPAGLWEPGTVEWQVRTWGAHADPSPWSTPQLTRVAQ
+APSVTITSLQDGPLAASQAKIVYSFFDPEGDEQTAGSVQILDDEGSIVYQRTWTSASRGL
+TPPVRLQDGRSYTIRVRARAASGLWSEWDQVTVAVDYPEPPVGVLTAEWLPDSAAVMLTV
+AVPPPAEGEVEATSAEIWRSVDGGDWLRIAAGLPLDTALVDPTPHTSRTTAYRLTTVSDL
+PSTAEAAPVLVAPDPQGWIWLNSGPGWSRQVRMRDNARTGPSWSRASERHHMAGAKLPIA
+VRGEQRERSVSVSVRLAPNPDGGCTYAELEQFLDDADLPILYRDAKGRRWFADVSEVSGS
+EERILEEASFTVYEIDHVEAEAEAVEQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002722.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002722.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e2bcb12e4e8f97e515da3c651832a2db967a556f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002722.fa
@@ -0,0 +1,3 @@
+>2_1940
+MAGLVQALAGPQEAAKTPGLRVSDGVVVSTNPVRVRQAGADPSTDPLAPLSLVPAADLSV
+GARVLLLHRGTQKILLGRTYPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002724.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002724.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27a7046e2bdd8988c7ffc2f44aefc43d86b052e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002724.fa
@@ -0,0 +1,6 @@
+>2_1942
+MVFLFTLALAAVGAGVVTLARGDAAAAEAGLSRAALVLEGANTIGTSRILGTGAVILLVV
+ALAATTTRRWQRVVCLAVGSGLAATMLATGSRGPLLGVALGIAVVLLVSPSLRGRRVRGL
+LAVALAAAAAYWWSASRSAESVDRALGWITGDRDTSTQARQQLWDIAFDHAKRDPFGVGW
+GGFADLDSVPSDLPYPHNFVLEVLVEGGWLVGGAAVIFVIASLWRLTRQATTPAGAAVLA
+LGIFTVTNAMASGDINDNRLMWTILSSAWVSTRLSQPQSQFASPYPISAVRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002726.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002726.fa
new file mode 100644
index 0000000000000000000000000000000000000000..583c842f17e58c1ad7bf14fbccc1e4352711430b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002726.fa
@@ -0,0 +1,4 @@
+>2_1944
+MSIPETIILALIAAAASVAAAAAGRGYTRRSKQLEAETARLAAEREREAARLAAEEARWT
+RLEADVERLAAEVQALRQENEQLRRENAAERAARGDAEDTIRDHEELIEDLLVHLIVRQD
+WEDSGSTPPPPVLSWRILAALRKRRAAMTGPIPLAHDQTTPTSQED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002728.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002728.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b24e2aede605d0592f32844c66d2ec34d993ef26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002728.fa
@@ -0,0 +1,3 @@
+>2_1946
+MTKNAILRYFTYDHLTRSPLRDVSKLFHDLAGTLDAQLPDGPEKSTALRKLLESKDAAVR
+SALDIEGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002731.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002731.fa
new file mode 100644
index 0000000000000000000000000000000000000000..43a47a6bfa24962a3044324efeb9c893588dc1b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002731.fa
@@ -0,0 +1,3 @@
+>2_1982
+MRVTDGLSVEEALVHEALPLRQAVPVDRITVSAGLALPTVLASLSRLQRAGLARRVEDRW
+RRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002732.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002732.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9aba68316c23e5c627ccd7cf1e01c3eb6b1c4e8d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002732.fa
@@ -0,0 +1,5 @@
+>2_2003
+MTTTGRGSHRAYDSDRDRLLDVIGRAGTPPVDETTFRVDPLALTGHDQTTGPLSGAVVAE
+TVLVVACDALTAEIEQHHRVMHGAPGMTEAQDRRALVDRMVIDFDAFAGGVWSGTDSPHR
+HGVLLDLHTTAVRIRKRGGVVYVVPPADGSADQTRLPGLRVDHDLWLPDTEGAPVSRLLV
+AVRRHAGLMPREDDDQIGELHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002733.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002733.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c74a623c804df80e4956131035f7cad6a3a5d368
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002733.fa
@@ -0,0 +1,9 @@
+>2_2004
+MVRAAIAGEKDAARLLDQVVDLVASALARIAGSDETYRRELFDRLTVDPSGWAVPWDRLR
+APASTLSVLYNFQPFADTGSSVASKRLRVFGHTSDVIACSFLHHKKVDPTIGMISRPYLA
+RRRYLEMRPSWASWHAFADFAVQARDQADAWIAAGTRYERLYTRANWAPSHYAGALIHEA
+HPELIWTAEFSDPLSLDVQGKRRGDLLDRSDPMLARLTAPVEADFGRIPDEHFSIFGLAE
+ILPYALADSILFTNEHQMAEMLDHIYSPALRERVQGRAEVSHHPTLAPEYYDARPVTYEV
+DPTMVNVAYFGEFYVTRGITDITLAMAMLPQHIRDRIRLHVFTNFVPEGGLATRPPGFSK
+AQFDALVRRAQDGVGAHGMEHLVRFNASLPYLDFLAVTRQFDYLVVNDAQSGSRHTRNPF
+LPSKWSDYRGSQAEVWALVEDGSMLSTMPTALQTPLGDPAAARDVLWDRVEAKQEERR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002735.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002735.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e8379cfb9db79eef335a5f8dd416a2ebd3e2ae6e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002735.fa
@@ -0,0 +1,7 @@
+>2_2006
+MNPYQQLLYRGMAAQDIVTTPVLSVDGFNPLLAVRAETSGVGVHLHWLNPVLAGARNGAD
+ARARVDRFLERVDEFIDADGRVVWTVHNVLPHDAVHLEQERRLQQGVADRAHLVHVMHPD
+TADVLGESLRWDSARTVVAPHPSYAGAYPDTVRRDEARGVLGIHEDEVVYVALGAIKAYK
+GIDTLLDAFDQLCREDATPRRLVVAGPVDTSPHTRALVKRLRTNPRVLVQAGPVPGDRVQ
+YLLRSADMAVLPHLRALNSGGALLGPTYGLPVLAARVGVLPAVLQPEFTEFFQDHTVPGM
+TAGLRAADRLLGAEARDAASDFARQHDPDLIGERFAQVLRARLWAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002746.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002746.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d1216d1b02101c5cf129e770e0480b7632b33d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002746.fa
@@ -0,0 +1,3 @@
+>2_2158
+MTTDTRLVHIITLTGQDYDDAVRVAETEGGSVDAVARHLAQWDHGAEADDAALLWPEDMP
+TRADLGCQPHQLHAARVGGLGYLVQIDHGLRMYALYRPTLTQEAAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002751.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002751.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ada3975b8201a91f8ccf92b6a09c5ec1667ca36
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002751.fa
@@ -0,0 +1,5 @@
+>2_2168
+MSGQKGQVVGYARVSTADQNLDRQLEALGGADRIFEEKASAKDRERPVLAEMLAYVREGD
+TVVVKSPDRLARSTRDLLDLLSELKAKGVAVRFTDSPALDTGTAQGTFMLTVLGAVAELE
+RELIAERRAEGIALAKKAGKYDRGPKLSAEQIAVARQRVTEGVPKAVVARDLGVSRQTLY
+DALAGRGRYAATA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002753.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002753.fa
new file mode 100644
index 0000000000000000000000000000000000000000..41027a059a7242907e8d2da0b97a553d14fc425e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002753.fa
@@ -0,0 +1,9 @@
+>2_2175
+MPRRGWDSVTVPGAVSGWRALSDRFGALPFERLGAAAVAHAEDGWIVPPIVAQDWGRAAT
+VLGELPEFAATFLPGGAAPREGERVRMPDHAVTLREILATGGESFYTGPLAARIVAHAEA
+GGALSAQDLAAHEVDWADPRSVSWGGHELYEIPPNSQGLAACVAAAVLEVLGGQHRNPDS
+ADGVHLQVEAMKQALAVLHAEVADPDWMRLGPSELLEPERIAALAARVDPERAGAAVSAP
+PTAGGTIYLSVGDRSGMMVSLIQSNYDGFGSGLVVPGTGIALHDRGAGFSLVPGHPNEVG
+GGKRPLNTIIPGFLTAGGEPVAAFGVMGGPMQPQGHVRVMHRLLVGQDVQSALDAPRWFV
+EGSGELKLEAGWGGDVARRLGDLGHPVTRTGPGDRTYGGGQVVRRLPGGDYAGGSDPRKD
+GHAVAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002754.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002754.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5efe43b842abbe78302950c454f0ea80cf10152d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002754.fa
@@ -0,0 +1,4 @@
+>2_2177
+MADPRVLQQPSVRSEVHRRTLCEPVTPWGPARARAPAADWDAVTAALAEPSPEEWYCYDT
+DNRDTPLAGPQVIEDWSVLTAVLRETAELSTADGWVEGFEPPQGGGWTTDQAAATLRLWV
+TRRFRRGDARLTDVPRHPDS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002761.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002761.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5a8e37401ae2c31c1e71bea6859ab4a163aef71
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002761.fa
@@ -0,0 +1,3 @@
+>2_2275
+MSNQRHTTADVAAFESWLSVFRRPQTVNNRVHYATRLETWATAHGCTPWTLDTTQISAWL
+STVGK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002764.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002764.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e11f820f0e6609c626d335a38966729b40eddeac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002764.fa
@@ -0,0 +1,3 @@
+>2_2295
+MPKKYTPELRERAVRMVLERQAAEGGPRSHSIRAIAPQVGVGEETLRMWCNRHGHEVAPV
+PAGESPAEEIRRLKRELAEARRANEILKAASAFFARELDRPTTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002765.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002765.fa
new file mode 100644
index 0000000000000000000000000000000000000000..151f4d20a9fd3250755eec65a067617fc87e3c28
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002765.fa
@@ -0,0 +1,3 @@
+>2_2311
+MKVELLHIADCPNTGIAEANARAALDALGLGAVPVELVTIGTEAEAANTGFGGSPTILVD
+GIDLFPTTLVHSLACRVYVAENGFAGAPAATQIDEALRDRMQGGESDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002769.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002769.fa
new file mode 100644
index 0000000000000000000000000000000000000000..692cce0383b4a4915bfb31198612f19b4118fbb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002769.fa
@@ -0,0 +1,6 @@
+>2_2406
+MPVEPRICITSGGDEIRLRSYINHAIYAREHGLDYRLETGIDPQIVTKFDYKVAILRRLL
+PRYDWLVWMDDDAFFTDFEADNLRRLISEAERDDISLVIAEGPTEPNGFWSRINTGVMLL
+RNDETAHSIVESTSTADLATVRAWWDDDRDGLFTHGDQDQMWWAIQTGGHADRVRIVGHR
+ELNSRGHYYEDSLTDAFVMHFTGYPDKELGIARFADRFDIGQEIVPEPLLDKYHVRVRSP
+LRGARRAWRERSVDTLAAVKYRLRPHKDRIRHVAGFLPPAVRRRWPLGHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002770.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002770.fa
new file mode 100644
index 0000000000000000000000000000000000000000..67beebc182234c4769928bb3a57888f3250543ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002770.fa
@@ -0,0 +1,6 @@
+>2_2437
+MAVGGEHRLGLAGTCRHHYRDRLVFFGGPVSQDRVQRAELRTAEADARFGLLDETEPPRQ
+RRCYGVAVLGFLLVSAWTLAEPPQLVAVDVLSLDESHVGTPSSQVHEVPLQLHYYLVWTP
+NVVARFAQSCVVGCRLWRRRELPVRSWPDGDRGSGLFHHTPRPQNAPSRRRPRVRQRPLR
+ASCPARTAAQLLDAQAHPDRDDAPRHLPVQRSDAQSCDVCRTAAPAHRPARRWRTSQPAQ
+PDSGRSNGFKDGANSPRPGHADPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002773.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002773.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7eb2d9102715f731a5afeaf949dfd18fd9c918c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002773.fa
@@ -0,0 +1,8 @@
+>2_2443
+MKTNIFAHGFSDNHAVSFGASRKGRVWSNEQARDIHDWVRWASQVGPTITDTSISLDSVM
+SGFLLPEPARERPPLVPLSIEWPYQLVSTFSDRRKVSHEDQAFSLLDTELSLTDHTADQP
+LRFEVKTPSWSLEFEFEFHEDGPPTIRPVSDDGQVVTPSGVGSLAAFLTGHGLLVTFEDE
+VVLVEQGFLLKPERERRLFPIDAVETIDWSGVNIRRESQGAERDPATIQHRAIQALSAED
+EWEVVLDDDGTGELADIALLRRTDDVLEVLLVHCKYSSSDTPAARINDLYDVCGQSMKMN
+RAKSMSELLTKRLFRREQERQNAGKSGLIVGDIETLAAIVFEARYRLLKVTVAIVQPGMS
+KSAASEDMRSLLGATDRFLAETYGMKLRVIASA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002774.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002774.fa
new file mode 100644
index 0000000000000000000000000000000000000000..605c7793cf4f15a2ea14da3e3cf5c20475233669
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002774.fa
@@ -0,0 +1,22 @@
+>2_2444
+MPVLRSLGPAYQEDLHGRNAAVLLDVLTDKSATAAKNIALAGHYGSGKSSVILGVQDGLD
+ERKIKWVNLSLSTLGIDDTKRARIQQDGSLAPLTNLIQKEIVKQLLYRKPPSDMPGSRYF
+RIDSFKPWPALMWGGVVAVGFFVIAVLLGLVSRIQDVAPASVINSHSWVAWATVGALGAF
+VGGVWFLGLRVLQNRIRVESVSAGGAAVKLSAKENSYFDEYLDEIVYFFQRTKTKVAIFE
+DLDRFKDPHIFETLRELNTVLNNSEQIKSRPIQFVYAVRDSIFEELQVDAESDGEGTKTS
+ALHASALESAPSANRTKFFDLVVPMVPFITHRSARDLLAAEFAKADHQPSTALVNLVGAH
+LTDMRVIRNIRNEYEIYRASVLGENGLKGLTADRLFAMMVYKNLHLEDFEAIRLGTSKID
+EAHRAFHKMVEYQTRHQAMRSKTTQNRVRTKALWDKHAQAAGERLQEVLPIVYRATGRGG
+KPVLRYQSQDYQLSDLTSGDFWKSLYENRDSVHLLRPGYGGIELSFDELISLTGNGTDGL
+DDAVDADVAHLQRDSRVALETKDFVMKATMAELIARTDLVMPTTDGDERNLDSIVSELLS
+PLGRDLLTKGHIDENFTLYCSDYHDIAISVSAMNFILHCVQSDRAAPHFHFDEASSIEAV
+EREMGSRFLDGESVFNVEVFDYYLPARPERLDKAMDKLAVRSGDDSSFLDAYLIDGKSRD
+VLISRLAPRWDGVFIHLAEKAPLELDVVATLVDAAITCAAKDTEYEASDQVAEFVSEHYA
+QMQAFVGETDAAKATDVMALLRRLGAQIGDLGVLGQTQRQAAVAAGLYPVTRMNLSVALD
+ESTGLALDVMNAADDSVYRHVLSNLDDYLDVLQDHEVTVDSPDAFVAVLGDVADAAEFAV
+RTVAARAADSCEVVDLTDLDDGAWGHVVSAGRFAPTVWNVSQFVSKFGVNEELIENLGTL
+NLTKAEEVDEEPRLGLAYALANSGALDSAATVRLLGQLNLPDGLDPERLSDVGLALLPTL
+LEKDLVPDTADTYALVSDRPFAFREEYFAASKQLASYVCELELSSDDLARVMRSRRLAPP
+VKRAIAHDVEFITDRLSRQSVIAFCEWASKGNDVSVELLVKLAEAGAPAEHVLGLLEPYL
+PNIELGLLDQILLGLGDDYEPLTRTGHHRPRLKDRAGTEELLKALQSRGRVSSFGREKLI
+GGIRVNMRH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002776.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002776.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b1d33da23544adaf50e58591b81b1ac42cfc8fd9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002776.fa
@@ -0,0 +1,4 @@
+>2_2452
+MSPRRPRVPRVDPATGAPRRAAQDAAVEPTTAPQEPAAEPRGADSRPAPSEDAGTPAAPS
+PSAAPGTGQGDGSAPSAEPERPATAEVIDLQRAQDRRQGGQAAPEHAAGSHAAGSHAAGT
+QPVEDRRAGVNAARPAASSPARPAARRPRPAPRRALS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002780.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002780.fa
new file mode 100644
index 0000000000000000000000000000000000000000..995031a6e8dd1ee894b9abcf9154c1a5bb1d3a1f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002780.fa
@@ -0,0 +1,6 @@
+>2_2527
+MSEPSPGGEVVAVAGHPIHVRRCSEPGRPWVLLESALGCPCTEWAWVQSHLACRGINSLA
+WDRPGIGATRPAGRTADATARHVARLEALMQQEGIDDAVLVGHSVGALLVRAFAASRPER
+VRGLVLVEGTHPRQRERSPREADLITAMERGLAIGAPTCFQDAREASAGLPTGLHDWTAR
+AASGRSADTAALRELRRVGEWSRRVASAGVGAAIPVHVLSAGRAVEADSAHRVLQQELAA
+LGAGPAEPIVVPDVGHQDIVMEEQPASAVAAVAERAVRSAEGHGAPPPDERSQENT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002782.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002782.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf1c4fd006f20c6899da17a34cec5f6a586b3343
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002782.fa
@@ -0,0 +1,2 @@
+>2_2559
+MATEQGYQRIVDKNTKPFIRLNDLIASLEQKAQEFGIHDAAAEADAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002783.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002783.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc74ea1c946fa8b3bbd122660528c361fee21c57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002783.fa
@@ -0,0 +1,4 @@
+>2_2560
+MTEKLLASAQARTRECTRAVLATVKELEASQSAITLKGVAARAGVSRNFIYTTPDVLAAV
+QKAAERQRPKLPSEPAPTAPSSDASLRTRLAAALAHNECLQQEIDRLTATNQALVEEVIE
+LQNPAPKNVTSIRKRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002784.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002784.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21b8c0d1203efa2ed81a0197bf2fe9caccad55cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002784.fa
@@ -0,0 +1,9 @@
+>2_2561
+MKQSAYFGKFLADRVNLDDTRLGHLDSRVKAIVAELMKDVQLGQHVRRWEKQGSWAQRTI
+IRPRKNDEFDADILLHLNEVPGWEPKDYLRHTRGALRRSQRYREMVRKKNRCVRIGYAND
+CHVDVVPTIKLSDGRQVIVNWKDNAFEDTNPQGFTDWLKQQDDITRGNLRKCVRLLKFIR
+DSKDSFDIPSVILTLLLGKQVTKEGADERYADVPTTLVTLLTDLHLYLQRLPDDGTMPPI
+HLPKCPGPSLNHRWDDPTKIRNFRLVVGRYAAWASTAHAAADSKAILDGWQTLFGKDFSP
+DGQLEPRQVSAAAFAKTSGTRHNREVPQEEFIEHKFTFAPTHDAEIIARVLPRTGFRHGL
+LAVLGFVPKGSRIEFEFRSDAPGPYRVYWKVRNFGSEVGNQWRGHLMEGGYSPHHQEPSA
+ITGKHWIQAYAVQDGKVIAWAHCAVPIR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002786.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002786.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dac9dad66291f2adba350f6505064621b00dbf8d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002786.fa
@@ -0,0 +1,4 @@
+>2_2574
+MWEHHRSYVTYTRISPPWHAATAKTTPLVLTPLRIALWDRDRHGHPVQPGELIAHSDAGS
+QYTSLRFAEHLAAEGIAASIGTVADAYDNALMECVIGLYKTECITTTIFHNGPYKTIADV
+EYATAGWVEWYNNRRLHSSLAMTTPAEYETAYYAALNRELAPT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002787.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002787.fa
new file mode 100644
index 0000000000000000000000000000000000000000..942d4da7b26d00807f6050b616df8050c4676ec9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002787.fa
@@ -0,0 +1,2 @@
+>2_2576
+MMYPLVSELAADGVPVAVSLRVLKLARQPYYRCPSPFLRWSRPTGPTPCTPLT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002790.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002790.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1332c32e18d8348e3f1cddee33437d595de98d32
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002790.fa
@@ -0,0 +1,9 @@
+>2_2590
+MRLRRFAAASAIAAVAALTLASCSSGGATTESATAVVPELAADQQVEIVFESYNLAQAGV
+WTDTINQLIGEFEDANPNIKVTGQAPQGSSSAINTIDTVGSVQKQLLAGNPPDVAQLTFD
+TLDFTATELGAKPLSDIVTPEELAEAFEGEHPMHPNARVLADWDGKTVGMPYVFSTPVLF
+YNATALEEAGVTDPDFSTWDSVEQIAAQVTAHTGKPSIDVSCVIKGGNWCMQGLFKSNGA
+QVLSDDRSTIEFGSEAAIETVERFREMYDAGVLRNTDTNGTYEGLPKGDVSMILISSALQ
+GGFMQAAEAGGWKLDAAPMPAFDGQEAVPTNSGSALFVLSDDPAKQRAGWELIKFMTSDR
+AYELISSQIGYPPLRTGLIEEGGVLYDWAQANPLIQPNIEQLDRMQPWLSYPGNSYSQVD
+TLLAEAIEEAVFYGKSAADTLPDAAERAQALIK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002801.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002801.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad2a6f516d5830d23ad5041f6f30882db6b00c06
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002801.fa
@@ -0,0 +1,3 @@
+>2_2608
+MNENTREVILHVADDPADVQRALDAAAGLHAAGLGVRVRVIVNGPALAGLTGTDAVQVPE
+HTEVAACSVGLGRRGIDPGELRPEVGTVPSAVTAIVHAQLADAAYIRI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002804.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002804.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3f6a5cdbe542fea5599f12721d31106ebdc9de2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002804.fa
@@ -0,0 +1,3 @@
+>2_2618
+MAIVVRIDVELARRKMPVGEFAERVGITPANVAVLKNGRAKAVRLSTLERMCEVLGCQPG
+DLLEWVPDAAAAPGPGAAPANDDDGRPGTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002812.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002812.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad732253bc48ffea4c4a678b9fd12b61f01927fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002812.fa
@@ -0,0 +1,4 @@
+>3_75
+MVNRTAKRAGWDYDALAFLMGFLGAAAGGFAVAFLQLLGAEGLDAFLGLTVLFGIGPVHA
+LVAALVSPPLLAGLRRVHPRWLHVLIAGGVQAGIAAGVASLWLQNADARHLPGYVLTSGV
+LLAVAWAWALRRSAWRPAGGPADGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002816.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002816.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a32bec81682044b9289ba13dd665e9fc4b505bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002816.fa
@@ -0,0 +1,9 @@
+>3_174
+MSAADSLYSRLVTRDPEAEAALPGQVRRDLPANGLRLVGANTLQSSGDQIVDAGTVLPWL
+FAVLGVPAGLAGLLKPVRESLSMLPQALLTPVVLRARRRTRVFAAGAAVQAAAVAVMAAV
+AAVGHGAGAGVVILAALAVFSLGRCLCSIASKDVQGRTVPKGQRGQLTGWSTTASGLVAI
+TLGLGIRLLGGDALSAGRLAGLLAGGALLWVGVALVYLRIREPREDPEESGGAHDDAGAA
+AVLRRSWALLRDDRPFRSFVTVRSMLLVTSLSPPFLVMLALQAGTDALAGLGGFVIASGV
+ASLIGGRLFGRAADRSSRRLMGSTAGAASAVLVAALALTSWPGLPASAAGAVLVAAYFLV
+TLLHTGVRTGRKTYLVDMASGDTRTLYTAVSNTAMGVILLVVGAVSSAIAAVTVPGALLF
+LAVLGVGGVVGGARLPEVSQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002817.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002817.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8484a6f45ed338ffbb0159df387aaab9eee501e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002817.fa
@@ -0,0 +1,3 @@
+>3_189
+MWAAAVAAPVLFLLTMVVLGSLTQGSVSLGAPLLIAPLVLAVPVIALQVAILQPAGPRPA
+PPTAPAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002820.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002820.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ebcc193565ea6cdcd250d76bf91172df2346c5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002820.fa
@@ -0,0 +1,2 @@
+>3_195
+MSTTTAHPAEPTPAALVARVNLAEPDGKDHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002823.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002823.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4812f4d5d6bee68b1ecd14e69c6f51d78c515290
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002823.fa
@@ -0,0 +1,5 @@
+>3_198
+MGASNVIAAYTYWRDRLSHRDLHALVFMAVTALDSDRPPVYYGGWEAVARALGLDLEGNP
+ASAKRTTVKALTALTEAGAITSSGTARAGIRAEYALNLAPGTTYVPSGRGRNVTWTARPT
+TARGTAMDPQVGTVVDPQRGTVVDPLQGDRGGPRRGTAMDPPKRTQEPHGGTREEPPEEP
+PITSQPNPGTRVRESDAMNDDRTPSKAEQEARLLAWAAEHYTEDPNALTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002830.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002830.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e85f945d5ac5ef3bf26f146b2c3e810e75dbb92
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002830.fa
@@ -0,0 +1,4 @@
+>3_216
+MGTKTSGVAPRDHPPFANSDDGYAWQSNWCDRCIHDQPAREGRYEDACGIWYIAECGQTP
+GEWLRQPGQRYGDQYHCIEFRSEDDGPEPPTDPEPTPPGQGELLPMEPYLGVKMFADVAA
+EVATVSTTS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002832.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002832.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a676d6abce09d00d8c6759f88178af10d799aa8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002832.fa
@@ -0,0 +1,15 @@
+>3_256
+MATAATRESGTVGGTSPGPAGRVLAGALRWLRGVPATWTLLLFTALGPLLPLVDPARPGS
+LPHAPHEVATSLLFAPHPLAWALALVGVAVLGPPAEREAGSGPFAARVVLGHTASVLAVL
+GLLWAVRQVDPAWGAVLRSDAIAGPWAGLIVAFLASSGSWDSRWRRRLLTLALPVTAATV
+LFSGAPEDASLLTAVLLGGWLGRRRARRLGTDAAPVGSRSERRVLVATAVAAVVLGTFLA
+AGSPHLVGPLAGTRALFAASTVSPDMVAAACADDDRIRECARGTYILTATGPGAVLLAAL
+PLVLQLVLADGLRRGRRAALQGTLVLQSVLAALAAAHLGLAAWAVAAGPRDYPTDPSLIT
+RLILPVLVPLGVLALVLAHRGLFQARAPHGAYRRLRAVPILALAVVAMIVAVGLAVPEQF
+SPRPGVGALLADGLIALLPSTALTVLTPAALPSGPVARFLLEWLPLVPWLAGIWLLWRAQ
+HPLGGPVAQPGEAAEAARALAAEDATMAWMGTWEGCRLWRSPTHAGAVAYRVHQDVALTV
+GDPYSSARDRAVVTRQFAEFCVAHSLVPALYSVHPVTAQAVESRGWFGVQVAEEAVIRLG
+GVTFGGKRFQDLRTARNRAKKEGITARWTTWAEAGDDLRAQIRAISAAWVADKELPEMGF
+TLGGLAELDDPAVRLLLAEDEDGRLHGVTSWLPVHDAGRLVGLTLDFMRRAEGGFRPVVE
+FLLAQAVLDAQEEGLALVSLSGAPLARSQPDPSADVAPAQTGALDRLLDQLGHGLEPVYG
+FRSLHAFKEKFGPESVPLRLCVPDPAELPRVGAALTRAYLPTLTLGDLVRAGQDLRRREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002833.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002833.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9bb7bf8421823ed3aab89279afdf845cb2a08348
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002833.fa
@@ -0,0 +1,5 @@
+>3_273
+MPDVLYAWPSAARVGRRVPKESLYGAGHVSPAVRELFVSSVDRITWDYKLAGGTIGISGT
+PEVPEIQVFRVRAKGDDVPDQVLAAIDRAVQQPVFFEVTRGLDDAEVRLGATYKIAGSAP
+AAEYARTAWLPACAPRRPIPTGVDMAQVYAQVLRPLLGVRMEPGERPQAIAARLVALREL
+ERRHAAVASRHRRERQFNRKVELRKELKGIEQEMEQWR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002835.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002835.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aeb8477d979ee6298204a189fc0bad7249d513d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002835.fa
@@ -0,0 +1,8 @@
+>3_277
+MPLTLTPNESAQRALHLMAARLEPIIARTLAPHLGGLEWTAFLDVMDDVKGKPSYPYNRM
+DPQPQLRILTERLGNLGYPFGAGRSRMVSALGSQLRIARNMVAHNAEIEPLDAWRVADAA
+SLLLGELGDAEGAQELAAWRDQILRLDAPADDEPDHESGEDLHDGEGGAQEAAKEVTAPD
+AEVFRIQTNEPSPTVGAGLRHERQPYDPWIPGAAGEKSVLDGVRSQHNKDLLRSVLEEIV
+EHEGPIHIDRLATLAGRSFGFGRLETKRKDLLKRHVRKCPGLQVRGEWVWGDSVDPDQWT
+EFRPNDSTSERKFVEIAPQELRNASAFLRTLHPKDDQATHERRVLQTFGRRNKSKAIREH
+LARALD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002839.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002839.fa
new file mode 100644
index 0000000000000000000000000000000000000000..802cd18fb02a7942d5f08e981d2b18e7252b8644
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002839.fa
@@ -0,0 +1,5 @@
+>3_304
+MPPSATRATVEGHLSRVATPIFEGVAAGVEMADRIMRTVPNRDNYPAFRSMATRIGAREH
+WINQGLGPGWHIAGNPAMQAQTLLVNPAAGIEMRFLRERRRSYPGGVPVAGHNAARREAW
+SQSPLPFTLSGDPSTQEAIDEIILLLLWDMTTDGDIQVRVVHPLEPGVYGRAVPVDMEFQ
+VQPGGTLFSRLSYEGDDQNENLFAHIDRADNEGDGMNGLFGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002840.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002840.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6eb8d046b8d6e63279b7d3b889b4b56258123926
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002840.fa
@@ -0,0 +1,2 @@
+>3_305
+MVLAVISGIRHKVVDNTDPKALGGSSRVQERVF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002841.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002841.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d123b4103e6f0e245a6c100dd3435a6def84a7b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002841.fa
@@ -0,0 +1,8 @@
+>3_308
+MSRHHGTLTTGALLALALTACGTTTPAPALSSTGTSSTAAPTSAATTSDSPSSSASEPAV
+GGPKTARAFGPATWAIKPEIDTIALAKAHVYGNRVLLHTATETVAYDPQGQEVWRLTRDS
+QTPPAIVPMSPTVIGLVTTGSSDNSGLAQSKPQTQVQVVDLADGSTVAEHTLDAVTNTAN
+PTAPGLSLASPDGGSEVITPDGAIRTLEDVDMAGAVGDTVITSKDEVIGTDTWSSEAFWD
+EPQYTNAAVAAANTTDLLLIEGQFGVEKTNVLVDAATGTEYARPKCGAGAFYKPMVSSPN
+GDWNVSYGAVISPDHKVTCIGGGEDEKAVDLIAVTDQGRAFGTTTEGPTLLVDARPGAEP
+TTEELAPGTVLPSGVVGGNLAVHWDPSTGVLSANPIQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002842.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002842.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c65a5d10d09492c1cf0b00b2114af0ed8caee736
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002842.fa
@@ -0,0 +1,3 @@
+>3_314
+MFTHGSGFVKPPAPNGRPESHLFASRKPDSHNSSDTRNEACAECLSACPEYPTCSTCNQS
+TFHAHVDNPSSEIVKCRGNNAPITYTGKQSTINGNPTHINALKIDPTGVVPVESKNNA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002843.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002843.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4224828e1cb86921f05018a0c204d992790f9a30
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002843.fa
@@ -0,0 +1,3 @@
+>3_317
+MPRPYPPEFRARAIALVREGRQVKQTAQALGIHEVTLHTWLRQDDIDHGRRSGLSSRESA
+ELRAARGRVRQLEQEIAILRRAATWLDEEGGVDPKGRTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002853.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002853.fa
new file mode 100644
index 0000000000000000000000000000000000000000..03f1ad8c376bac3e0702ff9deacb9f3420a20c6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002853.fa
@@ -0,0 +1,6 @@
+>3_350
+MEGIRNTTHTPALGRDDARTDGGGPLSWVEGRPASERPPGGWGPSRAPADGDVPAGDRTL
+WEDGRAPGQRGRWWVWLLRHLAAAVACGAALVITAGAVMAELFAVADAAAPYGSLPLLAA
+AAAAVGWALMLVVLLALLIVGVFGGWGLGGTLFRASGPGVWSVWDGEALTEAMGAMAAAS
+TGLGRSSSESAAQATRSPRWRRFLRWTGHAVRWVLVALLVLAAGAAAVLGAMGPSPTTLV
+VWGSAAGLVVAAVLVGCGVIGLEPGPDRSPHTRW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002855.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002855.fa
new file mode 100644
index 0000000000000000000000000000000000000000..663d052a76d612197aa951e73c0a73c505b2c2ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002855.fa
@@ -0,0 +1,10 @@
+>3_390
+MLKVSDVFVPGKLPKYTYNPRENSKIEDQLKDYLDELGAILAISGPTKTGKTVLVSRLVQ
+NRIWIDGGLVGSIEDFYRLVVDRAGEFTTIEVAGADEYTATDETSGEANLLGAGKFAAKD
+ATGLSTTNSKSASVNRPASQVATDALRVSGHVLVIDDFHYIEPAVQTAIIRFLKPLVMND
+VPVVLMSTFHRVGDAVRAESDMNGRLATIKIDFWSTEELMQIASLGFEKLKIIDDPTVSS
+ILAENSFGSPQLMQTFCRELCKFNGIKTQQEHPVPLAPPEQWRTFFEAAIDVEESAAWFE
+TFLAGTKLRGKKRNIYDLVNGQRHDKYGVILSGFNSTLPPLTFTSARLMEEIQVLVAGQA
+PRSSDVSAGLSNISKMAFGDSEVVDETDLSEGVEEGLTTSTSLSSLDHAPASSPLSADSR
+SNLRFANAKKRPVLEYLEKGNTSSVYILDPFFAFYVKWHAPQALSEHAKLRNVAAMDSLE
+S
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002857.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002857.fa
new file mode 100644
index 0000000000000000000000000000000000000000..749f373447768f78aa6529ec838df0df9798c27c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002857.fa
@@ -0,0 +1,5 @@
+>3_397
+MSQRPACPYLPLPRATTLRDALVYTRASMSRLPDVVHGSLPLRRLMEAARPVLTAATSLL
+PLQDVLAAAAGAVLALSALLWAVLFLHRLLLCRGWHGHLVYTTDGRTAFLTIRSTSQGWE
+LSDHVATRSAKGDGRGLREALAPALRNAADAAGAPILVTAANRTLADLYRQEEPELREVG
+TTLLGRVRLVRPPRRAILPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002861.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002861.fa
new file mode 100644
index 0000000000000000000000000000000000000000..859d1bbf5afe669d45e0c66214f9e6ddab82615b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002861.fa
@@ -0,0 +1,4 @@
+>3_428
+MFAGAAAVTLGAGGCAVPETVVWGPDGAAVKSATRDVIAAAQRGGDGLPACPGVSVVTGD
+PAAWRGAGAGEPERPGPDLPAELTRGGEPAWVINVEAGAEAAAPGARVPGSLAFSDLADG
+GLCLSGLDWANVGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002862.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002862.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f9e3fb64634cb7bd823f5daf8773411b9976481b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002862.fa
@@ -0,0 +1,4 @@
+>3_429
+MSTLSETHVIDFPGFPTVVVHSPGQAMGTLPQFMDTAFRALGAAVQRGACAPAGPAFSKY
+RGLTGGSGEAPESADRGRRSIDPAVGLRTRGPGALVPDPEFVAGQLDWPVSKAKTEVDAT
+PGRSGVSRAWACLSQSRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002866.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002866.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e4d7aab02149592edcf0b168fe1f0842f744ce3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002866.fa
@@ -0,0 +1,5 @@
+>3_453
+MKKTATGLTLAAALSLTAFAAAPAQADEPIFENCAEARAAGYGNFTSEHATFRHLNDIDN
+DGVVCEGPNSPYGPNGPAVAKPSPKPAARPQASLPSHVTQPDAIDNQYTYPDCKDVFAAG
+LANLPKSSKYYHADLDADLDGIGCEVNGDDAWVPAAIKAKYAPATAARAEESAAAEAPQV
+TVVPEGTPKTGPEGVALAPFALGAVALAGVAGAGVVARRRQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002867.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002867.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b136e9d218553edaef49a5af335306160912dd16
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002867.fa
@@ -0,0 +1,4 @@
+>3_454
+MPDDVLPASRPTRVRVPSLGIDSSLIELGLQDDRTVEVPPTAPGSPAGWYENSPTPGSRG
+PAVLLGHVSDTEDGTGVFGHLRDIQPGALVEVDRADGTTAVFRVDRAVSYDRGGFPKDEV
+YGNTDDAQLRLITCDSYNAWTGHWDNNFVAFATLVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002870.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002870.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eec01206e410e8130ef6fe94d015c541a1064414
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002870.fa
@@ -0,0 +1,3 @@
+>3_510
+MSTSLVALDSAATRRSVGVAASLSVIGLIVGGVTLAWVAGSLGISASAASQIVNAVQVGG
+LALTLVGAAFGFGVGSAFVATVRWYILRKGKAVAIA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002872.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002872.fa
new file mode 100644
index 0000000000000000000000000000000000000000..396d0c80a0f536b996ff409cc203b0d1ba56632c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002872.fa
@@ -0,0 +1,5 @@
+>3_513
+MSSSSPALPVTALRFPEHSAPRPGVPGADAPAGPRTRGAVSWGVYLAVCAVAGLRLPAIL
+EATRDRIAAEAGADAGGGFVDLALGVTGVLAVVAFVIVFALYVSTARLLERHTLAPAPGS
+VVGAHTLALGCTLLSVHGAALLTGTLAPVPVRLGIAVAASAAAVALLRGQLPTGSAPRRV
+AAAATVLLLSALSVAF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002877.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002877.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c2ffab5a413608e75fd39e53f16bd8b21548af4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002877.fa
@@ -0,0 +1,3 @@
+>3_554
+MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAEPLFRDGARRPSHCPDRWRTRRAT
+GC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002880.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002880.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ce85e9d91a296986ee07962295404e0a33cc32a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002880.fa
@@ -0,0 +1,5 @@
+>3_605
+MDAGDEVYVRDDHNAYGFVPNLTYSDLMRIASFAKTLGYDTKIRDLGYTLEEVQKRLRED
+GPSAFLRLKRIQEDVSPKAPAKQAIQYVAERLDRLAPQDELLITDPYLFSSSARKDIEAY
+SQSVADLIAPLLANSAKLIAIVDKDASHREVRDAVLDRLAAARDVTDIRVVESKDFHDRF
+WIADRCRGVIMGTSLYKIGRKIFFMDTLSESDIAAVLAEADATLAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002882.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002882.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0857c1c02a11ae2ab5cd3996c8ed95fcd2f06c49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002882.fa
@@ -0,0 +1,6 @@
+>3_607
+MNTDRDACAYLEEILREVTPDEEARKKAASHRASLEDWLKKDLDIIRMRETGSWHHGTAI
+SRHSDVDYFVTMRGSRPSASWSALEELRSSLALGVSSAIVRTDRPAVNLMYFDSGPSVEI
+TPAYFRDTDDYDIPDPGGTGWIQSNPAVHLDYVNDAQKKTSSRAKSLIRLVKTWKARNSV
+PLSSFYLEMRVAKYALSNPTIIYDWDLRSFFKSLEGDGLREMNDPTNYGRRISTGASSLV
+DTIAAKYDIEQAVRSSSLALKAAQDGNPSLGVAHWRRLFGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002884.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002884.fa
new file mode 100644
index 0000000000000000000000000000000000000000..72488738c16a7d9ef6546ffc47333ac681de6a8c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002884.fa
@@ -0,0 +1,5 @@
+>3_615
+MTHQPPAEPAIIPSDTTHDQTADRKRARQWLKTLNVSPNPELVEGLIPLVSLYPKKSVLG
+FYAGRLLKKGKLPTEEAVLKLLWGQLEQIIYSIKALESRTGRDPFITPEQETEILQWVDN
+FWAQHGEGPLWSELAENFHWSRTQQNRLIHYLAARGLVTFSFAPRSLKTVRGATTIPSLE
+GPGSGS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002901.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002901.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6a53a59eefa9e33605c22fdfaf351197f4b5173
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002901.fa
@@ -0,0 +1,4 @@
+>3_689
+MPRFSRLTPETAVGASRDLLGDLVERHGQVGDMVSTMAHSPAVLGGYLDLSKAMRRAKLD
+RKVSELVSIAVQSKQGCGMCLASHISAARSLGVSDDEIALAQQGTAMTSPVAAMIALGLQ
+VYREPTSITDEQIDELRGYGYSDREISDVVGVVSLNILTGAFNLVAGLTPGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002902.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002902.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea64ae08374f6f60e361a190cceb473df3d4f810
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002902.fa
@@ -0,0 +1,4 @@
+>3_690
+MTMKEVEHAHATYDTPHLNAAVGVFALLANLVSVKMILAIRDIEVSANHLADIVDLPVDQ
+TSHELHRLESAGIVSRQRRESRDFYLLNGVHAGALAEAAIFHAEHQQQERTRAGSPTSNL
+RPN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002904.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002904.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d26ef82a01562035685fb6eebc2f6d1e9a3d00c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002904.fa
@@ -0,0 +1,3 @@
+>3_698
+MTTTTPTTETHLDTCPAGGDGDASVHGYISDKTKYRNRLRRLEGQIRGIDRMVDEDRYCI
+DILTQISAVTRALENVALGLLDDHLKHCVLDAALAGGPVSEQRLGEASEAIARLVRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002906.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002906.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e721a4640a518c0e24b3598777c2424d65c0720
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002906.fa
@@ -0,0 +1,7 @@
+>3_701
+MKAGGRLALYGAGLVVAFGGAFGLAGAVIPDSFAAAWAEGSGVNAHGEGHGDAAQETAEP
+ALNGVSASADGFVLSPVQAPTAAGEDGDLSFQILDESGEPVTEYTTAHEKDLHLIAVRTD
+GAGFQHVHPELDTSTGTWSVPWTWDEAGTYRVYADFTPAGEEAEGITLTRAIEVAGDFTP
+VETEAQPTDEVDGYTVSLNGDLTAGTSSELTISVERDGQPVTTLEPYLGAFGHLVALREG
+DLAYLHVHAEGDQPQAGDTAGPDIGFAAEAPTADRYLLYLDFQVDGQVHTAEFVIDAEHG
+DGTKTDDSHSDGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002910.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002910.fa
new file mode 100644
index 0000000000000000000000000000000000000000..022c3cdc0947d84c55f6b2f1fdfd8ea665c18340
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002910.fa
@@ -0,0 +1,6 @@
+>3_737
+MRSAPAALTAAALALSGALSLAGCGTDGAASGGSGGTDVASTAASSSEAPWAGRAQVDAV
+ARAVEEGTGAQMTVLDVYSRAEYRDAMERHLATVYGDEVALSQARDASQACVDANRAAAQ
+SEAESGARGLAGAGSARGQSSTDTAGYVNLTVTDFPDVEAARRSWDRHAQVRADCAGQTG
+WLGVVDARGADWPGGEAVVYEKRIPGPDGAEVRMRTAHVLDGRRQYVLNRRLDASEAGTM
+GGGDDVGILHRVAAALPAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002911.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002911.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4db8e5883337d3bfbf0ac7a90cead21a18f0d383
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002911.fa
@@ -0,0 +1,4 @@
+>3_762
+MALTLPITQSLSTRDVTGGVRADAPAARTLADLPLGTPGVVAGVCDAARPDVARRLFDLG
+FMPGAVVSGVRRAPLGGPVVVRVADYELTLRRDQARCVVLAGPGDVTSGACPAEDRGCRG
+CAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002913.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002913.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35504ab07f8283feae80153fa4af0bc2a478b9e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002913.fa
@@ -0,0 +1,3 @@
+>3_766
+MTGPGLWDDFMVYASREAMKAPSRTEPDGEKNTRCHKTPIKLYRMVNGKPQYVKTRHPRV
+AVSMYNKVVVTSYPTSTPSC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002920.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002920.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b75dddbfaa74cda3688d1c2b477ca91350873fcf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002920.fa
@@ -0,0 +1,4 @@
+>3_884
+MDMHETPLPGIGVRRELDTTSGRRIGVVTHRDGQTDLILSDRDDPDACAASIPLAADEAA
+ALGALLAGPRLVAQLEEEHADLPGVSTRQLILPHESPYAGEELGSTRMRTRTGVSIVAVV
+RAGVTHPSPGPDFLLEGGDLVIVVGTGEGVRQAEKLLTV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002921.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002921.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf9015b02aa016f087a2ddf0cdad1342d23390ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002921.fa
@@ -0,0 +1,5 @@
+>3_896
+MTDQNPHQEPADVVAGGPSDAEEVTLDPEIAEHWELWSRVIGTMALPRLQQLQREFPEIR
+SAMLCTADGMNLRSLGVPQADVGRLAALNSSMYAVASSQAEIVSSGAASPQQAMVSLSTG
+HGHVVLASFVQPPLGQLPLSVSADTAQLGFLVVRAREAAVGIQEWLTQEQAKDASLPETR
+PSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002927.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002927.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98940a811680e72c610c6cbdd31be3588c5ed5ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002927.fa
@@ -0,0 +1,3 @@
+>3_921
+MTSAQVASPTPLSPGHRFTWANGGTTIRSRVEVVRPGHDLTWTGIALWLVAVHRNVIETL
+PDGQARLTSTESMAGVAAALLMPEEKLQQQLQAFVEAIAAEAERRSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002930.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002930.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e193a0b86318058ba1ccebba88eb1118b30c7133
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002930.fa
@@ -0,0 +1,5 @@
+>3_953
+MTTAPTWIDAVLALVLLLALASGLRRGLALTLGSALGLLAGVAAAVLFAVPLGGLVPDPA
+WRPLAVVAAGVLLVVLGQGIGLRIGAAVRRALGRGALSRADGLLGGVAGLAVAAVVIALA
+APVARPLLPADAADEAGRSRVVAAAEHLTPEPVRQAAADLGTQARLFVAEAIAPVLPEPG
+LGGREAVRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002931.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002931.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e14f3925010d8f8626c72f6f13753bfe17284ca0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002931.fa
@@ -0,0 +1,3 @@
+>3_958
+MWTHALTGLLAGLALIVAIGAQNAFVLRQGVRREHVGLVVLVCLLSDAVLIAAGTAGVGV
+LVTAVPWLLEALRWGPCCGSPLSATVLACWPRPSPARPPGGCSTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002935.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002935.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c15fa9af1fa5985330c14bf8b3db89a314098f56
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002935.fa
@@ -0,0 +1,5 @@
+>3_1010
+MTIERSSAPSGGPLPRGIQHIGVTVPDLDAATRFLADGLGAKVAYDGLRPEDEPRSGPEV
+ERQLGLPAGAEIRRQRMLVIGEGPGLEMFEVSGEQRPASGLSDLGLNHISLYCDDIDGSL
+ARLVAAGGEALSEVHGNSRHEDTPGNGSVYVRAPWGMLIELQTIPGGHTYPADAEAEVWM
+PRPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002936.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002936.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d336931a52338bbd3a25b0efd2e74804b48d28f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002936.fa
@@ -0,0 +1,8 @@
+>3_1031
+MTLDIPLWPVLLLGLTVVGVLALAARRGPRRSARTTARQHLGLWALLALVLTGALLGPWA
+YVGLWAGDGGLSWVQADGAPTRGTVELVESAVPAELLTPGIAAVALLPALWLVGLAALAQ
+VTWPRETGPRRRAALRSRSWRHLLSRRVLVILGGATVLAAAGIAAMAGLPAVDGVQLSVH
+TGPESTQFRASADSQPAGADVAPWFAAAAATVLAAVAGVVLVVHRRGALGGLSPREDLAA
+RRIAVDRSARIGAALLAWNGLAGLLAAGAHAQARDAAGLLGDLAGRWAEGGIDVAGVTAA
+VRAQDTPDAGVSAAVLAATALIAAVLIFARPRAEERILQDGPDADPVATGGDSASGGDSA
+SGGLDRLPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002941.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002941.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b7eb9903aed40bb8f7d3f5da97400467f5518886
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002941.fa
@@ -0,0 +1,2 @@
+>3_1160
+MSLAPADAFIGWLPQEHERVPGETVAGYIARFTGRLKAELVKNI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002945.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002945.fa
new file mode 100644
index 0000000000000000000000000000000000000000..959519cb142f693c88c5378f0261cdb6d1e4770d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002945.fa
@@ -0,0 +1,4 @@
+>3_1196
+MQPQDLIADAAHRALDLAAPVLDGLSAEAAHTRPGGAGNSIAWLLWHAARQMDVQTVALR
+GGTTVWEAGGWARRLGVERDAQDFGLGDTAEDVSALRVTDVPALGEHLEACVDALVTWTS
+SLTTEDLGEVVDTYEGEPVTRGVRIVSMIDDAAVHVGQAAYARGLVDGWRFAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002946.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002946.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c9f62632677e8d4a4e20d40b4f05073594d56c8d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002946.fa
@@ -0,0 +1,3 @@
+>3_1199
+MRRITTWLLATLAGLVLLFSYHTSTDPNASATASQGTSVHMVSGASFTSAAYEQSLQSAL
+DRAHL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002952.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002952.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a76ac5670fe4fe6597c6aa815b967b66440c6409
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002952.fa
@@ -0,0 +1,9 @@
+>3_1310
+MSSRRAATAPPGSAPGGAVPVWSASRARRVVLGAQGLAGPRPAASARRVAGVAARLGVVQ
+VDSVDVLARAHLMPFHSRLEDVDPAHVAALTEGRGRRFTEAWAHEASIVPATSRAALTLL
+QGRRWPLATALPEDRRTAAAADIRALLAAHGPLTAREVRDRRASPCGPGTSWGWNWSEDK
+RVLEHLFAEGSLASAGRTASFERRYALPELLWPQGESGRAPVPPEPAAGGDARLAAALQL
+TRIALRAQGVGVADEIADHHRAPVTLTRRALEVLADRGEALEVRLDLGGTRPVPAWADPT
+ARTPRRAGACTLLNPFDPAVFHRPRVERLFGVRYRLGIYTPVDRRVRGYYPLLLLQGERL
+TAQADLGAVRRGPDPRLELRGAWSEDPAAHPGPAGPAPTPDEVADALAEEALRAARWRGL
+PRVVVPEGAPGDLTPRVRRALLERDGGRVPPGP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002959.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002959.fa
new file mode 100644
index 0000000000000000000000000000000000000000..516076eb8f24d3d2c2a7129c45b152f7a2024e5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002959.fa
@@ -0,0 +1,4 @@
+>3_1675
+MPRALIVVWALLIVPVLFCLVVVGGSAVAHASSSAGPATLRSALPLGAALLTAVAGTAAA
+RHARAPAARSVLTVAVALLLLAVAAPLVLSLFAAGTEEWCEGQPGGRGGAPITSEADVPL
+LCR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002965.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002965.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18aed52fb5db2bbecbdb17affd9245e6f48da27a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002965.fa
@@ -0,0 +1,10 @@
+>3_1731
+MAVTQWPIEMAELSSLVLDPRNVRVRAGRGDGLAHADDEHAEQAIAKYMVEAEDLFDLMR
+DILRDGYLDNEIPVVVRDADKFIVAEGNRRTTALKIIANPKLLGNPMSLRVERMKARYPD
+HDSPTSIRVMIAPTWEAAQPLLARLHTGQPKKSWIREQQAIFYHAQLSDEVTVDDLRVRY
+PSEASTIPKKIRMGEMREVIRRLKYDDSSLRDFVMNSELKMTTFEYAYTPKKLHSALGLE
+FTKDGLLVSKDISDGQRRGLIYLLGRFKDKSLNTRSPELIAKNATEHEEFSKLLRGIVEG
+TPLEASTEDEGATKDHTNNQDGEPGEASGERNSAAPDDISRDEGRHRGTSETDEASTSGD
+ATASRGPNRGDTKSRLNMEGFEYQGTSPGMRRRFEELRRLDVRDFPNATHDLLRTVLECS
+IKDYFQSKGQPLPPGKTIGACIGELAREFQGNPKMTALINSINRKGRLTAEQYAGTTPSL
+NASNHELDHFAVGPDVHAAWDRIQPILKEIVGTKKQS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002976.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002976.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5954075440e4445ece1c5dac1314c34bcced7d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002976.fa
@@ -0,0 +1,10 @@
+>3_1754
+MGVCDLPVISGVCETAGEAAASLVSAPFDWLAQAMGSAAGWLFEAVWNVFDATTLVDITS
+DGYLSVYNLLFGIAVFVMLLFFCLQLITGLIRRDPTALTRAALGLAKSVLGSFVVITLTG
+LLLEVVDQLCVGIVQAAGETTESMGEKITILAGGLTAINIAAPGVGAIITIFLAGLAITS
+AAIVWLSLLVRKALLLVAIVFAPLALSGSSWDATRGWISKWAMFVVALICSKLVLVVMFL
+VAITQVAAPIDGDLSSISDPLAGVVLMAMAAFAPYLTYRFISFVGFDMYHAIGAEQDAKN
+SLNRPIPLPDRQPGNPQQVLDGNNSGNGGGGGKQPPKPSSPNPSASQGGTEAGAGTGGAA
+GSGASGSGAASGGSAAAAGPAAAAVIGVQVAKDAATAGPKAGAELGQQAETAADAADHTP
+TPNGGAGNGGNTPPAPAPGGTPPQPGTPPASTQPTPPSTPSSQPPGSSSHGGGEQVSPSA
+PVPNPPPADNPPPPSSAWKEPQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002978.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002978.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec7f3f85c5cf666890adc53ddec380f2d44eca85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002978.fa
@@ -0,0 +1,6 @@
+>3_1760
+MATFVDPVADAAEAYEGLRGLAHATRAFEDPADTYRVLGEVSGSVRLLRQVLDQLSRAHA
+EHRDIAFTDDRVPAEAVALAAADELHQAADGLDEVADRVMRAHEASGRIAWHTHTSLEPE
+RSQRWVNVVFLQGTEADEVLELIDVQGVQAGIAHLAQWDFGDETTGAAFVNGEVYHELPA
+GQWDCTFEADGYVLTYNPQMGYVGLVREHPDTAPDPSHDGDVVAARDAFSGVTSEPSRRA
+AAGTDWFAPKAGGAAASSSVGRSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002979.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002979.fa
new file mode 100644
index 0000000000000000000000000000000000000000..32e680588186fea8b240155fe01baefd3f915e21
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002979.fa
@@ -0,0 +1,4 @@
+>3_1762
+MPKLPALRHRRNDPSEAVPVVLRHVVITVDITGTLTVTVDQQPHLPQAGEVWGRGDFGAI
+LDDLTEQRRIPVRVDVYESDGSHFTDIIHAHRPRRAPEPEPDDPAAADEEAAADTPAPPT
+DDPGRLVGFLPGETVFLGQIVEEVAADENGTITPPDTALGPVVVVGRASGTVIVQETR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002981.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002981.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16f3dc198974598e22898a83a59b246f18877926
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002981.fa
@@ -0,0 +1,4 @@
+>3_1764
+MAIRTQESLSGFIASDPQLTYTERGDARFYARYGQENFQREEDGTFTKLEPSFGNLVLYR
+ATAERAFQRFTKGDQFVAEGYAHDYTYERDGQRIAGEEFVAKKIGHDTARTRYDVDRTPR
+QALERQAAGQAFEPPQHHQATPATDSLSM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002990.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002990.fa
new file mode 100644
index 0000000000000000000000000000000000000000..10084c95a36d726392ac5cf73c45b16b4abc37d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002990.fa
@@ -0,0 +1,4 @@
+>3_1816
+MNSLPLHPLMVHLPVILIPLTVLMALPAVLSRRWFQWSAPLTLAFSLAAAVGSVLTAATG
+EQLAASDGEASALLWQHAQLGEKTRNLAMLLFLLLLVWTALSWHRSPAALRRIGERIPAL
+HLVLAVLVLLVGVAEVVVAVQAGHAGAQLVWQGEGSGTQSGGGLGTGGGRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002994.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002994.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d17757e86c5e1f9a80ec145ffdab7c8725cf4f41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002994.fa
@@ -0,0 +1,9 @@
+>3_1866
+MPRLHSAHDTADNAPGARALSGVGAARHRALRPAAVLFTAGLLLTGCAGPDGAPAGGSPE
+AGASTTEDAGASSGTAGGSAGGQSGASESRAEGSPPVDPADFPASNTTKLTRVETIKDPG
+LTPKSIVSNQHGLAIANNMMYRHNVMLFDTRSREVVQTLEDTVDTDAMGIDGLSGVVNGS
+PVEAAWTQDGRYAYVSNYQLTGGEGTGVKPDDNCTAGSAISPSLVYRYSVEEKKWDAAYR
+VGRVPKYLALSPDDSRLLVSNWCDATLSVLDAETGELQHTIPLDTMPRGIVVLPDNKTAY
+VVAMWADKLYRVDLDAGTAELVMNTGPQPRHLSLSPDGKTLYMTVAGADRIVKLDAATGK
+VLASASAGDEPRSMDVSRDGTALYVVNYEASTLTKIDAETLEILDTAPAGENTVGVTYDD
+PTGQVWVANYGGTVDVYDDTDGVGPGAAGSAQPTADAPGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002996.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002996.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b4c9ad7e68aa11edb5d6a5b67ad2b6818fa91a86
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002996.fa
@@ -0,0 +1,6 @@
+>3_1899
+MKKITRSLASVAAALGLAGAGLVAAPAAQAADLTCSGIISGRTMTGDITVPGGATCTIRS
+STVTADYVYVAPNATLITENSSVSGFISVERGATLRATEGSLGDVLADSQKLIRIHGTSV
+GSLNVSQGGTVTTTRMRVRDDAYFHGMGGTVSHSWGRFSNYVSQYGSARNRFMIRSSVVG
+ADVSVQQSGHVLVGRNTVYGNIFVHDNRGTIYIEGNRADLYLSCDGNRYQPTGGNNTAWD
+KWGQCAAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003003.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003003.fa
new file mode 100644
index 0000000000000000000000000000000000000000..accd04053ac852275b5ef4b2b8e1f95daf30d031
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003003.fa
@@ -0,0 +1,6 @@
+>3_1996
+MMGPSHAVTGAAGWLALTGPLADLAGVYVGPQVQLVGALTTAGAALISDWDHPRATIATA
+LPPLSTVLARFIRRAAGGHRRGTHSFVGLAAFTAVTWVLTPLTVTVGSVTFSAGQGVVAA
+FLAAVAARILRVAPGPVTGWAVGLAAGALAGTTAPGATWLTVSVALGVGLHIVGDMLTTR
+GVALLWPALPDPPVPTPFWLPGGRFRLPLLGRAGSWREWVVATACTVYVVGAVSAVVRAL
+LAAADPAAWPLPGPFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003008.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003008.fa
new file mode 100644
index 0000000000000000000000000000000000000000..520deb4ae1488a128038cb589a3acb79098eefee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003008.fa
@@ -0,0 +1,7 @@
+>3_2124
+MYLVPILCALTGALFLALGSERQASGVRALERGDGARPGRGGALRLLTSPVWLVGGVLML
+AGIVLNVIALAWAPLTVVQPLGAVAVVVTTLVHARVAGLRVDPATWRAVAACTLGSAAFV
+VVTVQATLPNPVPDADQETLTAWIAAGVVVVGLVAALALRGRRSALVPIVAAGVLYGFVA
+VCVRMSAVRLVDGRPPAWGVLAVLVAGAVLGVWFVQTAYRHGPPDLVVAGLTVVDPMVGV
+LVGVLVLGEMRPDAPWWVGPCLLAAAAVATVGIVRLSRSHPDVLARREERRVADTPGETT
+P
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003009.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003009.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8fbb6afe75f0e463d38121a3009e324d9f03fa66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003009.fa
@@ -0,0 +1,5 @@
+>3_2153
+MYVVPVEQLADRGVIRTALDDFGHAWGQRIDRWRADGQTHTEKSFAQQFWSDLLRAFGVI
+PERIDLFERGAARASTGGAGYIDFFWSGVALGEAKSLGANLDVAHAQALDYLAGGSIGQH
+EWPKYVLVTDFARIRVERLGDAGWVAEFGVEDAADHVDQLMFLAVMSREVVEPAGRCGSD
+RGVDSVMIVEVHPPRQRGPAFGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003010.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003010.fa
new file mode 100644
index 0000000000000000000000000000000000000000..796350c5806b4c8d220d2bd6865dc7adf48cb47c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003010.fa
@@ -0,0 +1,3 @@
+>3_2158
+MRLPRPSDYIAMMIPYITLHKPAEVAALAAKDLCLVDVGNHTASEVEESVIFHPGARISV
+AIKQSFHMSMLQEH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003014.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003014.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f081391a8618d03432eefc085df3284adfb04cb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003014.fa
@@ -0,0 +1,3 @@
+>3_2175
+MDTLTGSRHKNLKELHPGSSGRSEIRILFAFDPRRQAILLVAGDKAGAWKKWYATNIPLA
+EERLDAHLHALRSTPPGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003016.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003016.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef6abdc9b3be9bd2891bd0f08c37673e4ade64f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003016.fa
@@ -0,0 +1,4 @@
+>3_2181
+MTLTLIPPTTPDEATQQLAQLQGTTVALAVLRRVQLVKAAEVGVTQQQLAGALGRAQSSI
+SEYLTRARTSLADRPATHPLWPAEVIDLYAAGLLPRDEVLAYLASYPYIDPAPTDDPAYT
+VTQPGEFGEVAAAHWNDKLSDTDYANLYDLLHADD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003021.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003021.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b40e59fc0ef546cd7926c7598a2d814b4b08cd8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003021.fa
@@ -0,0 +1,8 @@
+>3_2204
+MERRVMAPRPGWERTIASQGLVFDETVHPDGTVTHYWNESACYALTMAEVEHLEQASERL
+HAMSLEAARFLADEQSVPGSPWRALGIPREAAQLAVDSLNAGEPSLYGRFDLVYSGPDAP
+TKLLEYNADTPTGLVEAAVCQWFWKEDVFGDAVDQWNGIFEALTDRWRRIAPPEADGTPA
+RVHFAHTELDETGEDAMTVAVLRDAAEQAGVRGESLLMSQIGFDTERLRFVGADLRYLRR
+IFKLYPWEDMVTERFGPRLKLDDEVRWIEPPWKMLLSTKALTAALWHLYPGHELLLPTFL
+NDRGGLREWVRKPLHGREGAGIEIRSRAGDVSSAAGRWGAEGHVYQQFHGLPDFPAPDGA
+PNRPVLGTWMVGDECFGVGIRESDGPVTDALCRFVPNIIDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003023.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003023.fa
new file mode 100644
index 0000000000000000000000000000000000000000..545489dcf6fbb688b5309ac390bff7f1b6096f3d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003023.fa
@@ -0,0 +1,5 @@
+>3_2217
+MRPLTLTVKNTFQGSHIRFGSQFGTENTNLAVQSGIIGGAANPLSLHQSPLSNSATSDSR
+VDANKTVTTFTFDRPVTSLAFSITDIDSTRNDFADAVAVTSAAAFTSSKADSSSSGLQGV
+GTVADPWRPWTTDNPVNNSATNGNVTVRFTSQVTSFQIHYWNQTAASYASVDGDQKIFIS
+NLSLTYNACA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003027.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003027.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0c5ce43c4328df7ce342b3795023a2ce08a6fe85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003027.fa
@@ -0,0 +1,6 @@
+>3_2265
+MESTPPVPPLPDGRVGIVIPVYNTGSLALGAAHSARVALGSTENVVVVDDGSKHPDTLAV
+LDSLRVEGFHVIRQPNGGVSSARNTGIQQVTTPYVIALDSDDEIMPEAPHAMAEILDRHS
+DVTIVTGGAFEVVDGAEHLSSPPDGPVTRSAMRAATVLAMASMFRRSDWEAVGGFPEGLS
+VGEDWVFWMRLLRTGGKVEILDIPIARRHLGEHQVTRGYIDPRQSTQAAALVRSENSDLY
+AGQEVELIERLNAAELQLAAYRHAYRHVDRFKAGIRSLLGRARAKR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003028.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003028.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fe9973a9bde271490068ea8e5e9b609e4d23186f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003028.fa
@@ -0,0 +1,2 @@
+>3_2266
+MWIIRQGKDFQEEVLVFITAKIFIESPHRLCICPPHHLAYLKKALVEELP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003036.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003036.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a9ec69ef66baca8926ad127808a3fccf040632a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003036.fa
@@ -0,0 +1,4 @@
+>4_110
+MTSKPSIDDVAAAIFEHFDRPITTMKLQKLAYLAQGWNLAFRGDPMFDGKFEAWVNGPVS
+RELYRKHRGEFARSRWPEGNPKALSDEDRIILDAVIDNYGGLSGAELSDLTHVAGTPWHR
+ARAVSNAGPSEPSRQPLDEALIRTHFRQLLGLDDPEYESNTNGEPPPNTGHYHAFSY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003037.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003037.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0cfbda14e05c619bad43e524e9be97d0d41f212
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003037.fa
@@ -0,0 +1,2 @@
+>4_112
+MFASFVATVLRNVCGVIFLNPMASRAICYCFR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003041.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003041.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d97c40827c7a2851575abf98c47582337d05f9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003041.fa
@@ -0,0 +1,6 @@
+>4_156
+MVADEDMDRQDACMGHNDALDGLASVRKAFALLDVVATDSRGMTAKEIAAALQMPLPTVY
+RMLKTLVASGHVVHLREESRYGLGYKLHALDTSLRRQVGTPPAVARLIQELHSRADAAAY
+YAVHRGEDIVVAYVVDSPAHPRITPMGFGFNKAAHATAFGKVLLSAMDAERRAIYLQRHG
+QPALTAATTTDPGQLEDQLEQVTRRGIAVEREEFVQGACCMAAPVLSSTGQTVGSVAVSM
+DPAYFSSHSAQMAVLLRDTAGRVGRALRGASLLQDIAAI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003042.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003042.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca79912ed47e608dcf89849b2a878e687d7c068b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003042.fa
@@ -0,0 +1,3 @@
+>4_157
+MIFIVVKFTVKPDWSDRWLDLTSSFTRDTRHEPGNLWFEWSRSVENPNEFILVEAFEDDA
+AEAHVNSEHFQNAMQQMRQALVETPRIISRQIEGNTWDRMGELAID
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003050.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003050.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9461e73a65e22c742477a1844c2043c24c9773f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003050.fa
@@ -0,0 +1,3 @@
+>4_1099
+MTQQHPKDPLQADWEALAEVFEAEDREDRRAEAQRRREGLPEPKRDIRTFDGFASGGAAP
+RA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003051.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003051.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2571349b063504da7aae343cd24e43220dbc4c69
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003051.fa
@@ -0,0 +1,6 @@
+>4_1112
+MATSGKKHWPPMGRTQWPLTSVSRTARMLGCAASTSSPSGSSASTSRPPPCRPGPRDRVV
+PRPGPCEVEAGEGLHELTNGDRWTRLGAGPPTGDGEEAAGRAPRPGSRSCRSQDASPVAR
+GLRIIPRSRPRRRPRGPATRACPRDVVGRSTPGGRCDRDLRPVHAPATVQTPVPSSSASW
+ELSPGLGGFGPLDTRFPSRGAWRGSRFPDESVREGSRFPHESAGAQRPGARRRRAGPPKR
+TGPPSSSAPVALRDRPEVSGRTCPERTRRPTRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003055.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003055.fa
new file mode 100644
index 0000000000000000000000000000000000000000..230c92a9a3888d4819bd3f59eed6ec00e35379a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003055.fa
@@ -0,0 +1,3 @@
+>4_1496
+MVTADDEGLAAAFERMGEILGRMNEGENPSEYVRRGPAIIAEHVQAIAESLKDADAFDVI
+ELMRMREMPMILEGYGRVNLSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003057.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003057.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc4f1925d29e1a5824716ba46bb9fe373d146234
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003057.fa
@@ -0,0 +1,4 @@
+>4_1818
+MSSRGNVIKRWGDKGGVGASDGSDARVVEFILNKPTKNFTCTGQYASAPENGVMVAIPAE
+LTLASGAEAAGFRGDFLHPVQFRFVGTDGKTASIDMQTSAALQCVDEKDAPNFNIGDGET
+TSGLITLDLPASEGTLILDNALMDSGWEWEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003059.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003059.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c314e1f3c2513a13bf3a2ab34e299d394d7244af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003059.fa
@@ -0,0 +1,2 @@
+>4_1970
+MTMGPSEAAAGALAMLGYVSWLRGEGSLTDDQLALAKARAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003062.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003062.fa
new file mode 100644
index 0000000000000000000000000000000000000000..73e6a12a6ea8f40b7e07013cdf3d76a234a4dced
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003062.fa
@@ -0,0 +1,8 @@
+>4_2121
+MAGMIITGLLLGLVLGFVFQRGRFCVTGAFRDLFTIRSTRWLTAFMVIVAVQSVGVFALD
+ALGVITLEAETFPWLGTIIGGLIFGFSIVLAGGCATGTYYRAGEGLVGSWFALIFYIVGA
+TAFRKGPLAGTTEAVRSVETQTGSFQQLTGLSPWVFVALLVAGVGLAVRHHLRREAAMTR
+FRLPAAKTGLAHVLTEKAWHPFVTAAIIGVLAILAWPLSWATGRESGLGITGPSANIGAF
+IGTGELELVDWGVLMVTGLLIGSFIAAKASGEFRVRVPDAQTTVRSIIGGLGMGWGAAWA
+GGCTIGNAMVNTATFSFQGWTALVFMVLGTGLAAKLFILNHRGKGTTPAPTSGSGLTSAE
+GAAADAGAARPVKLTPIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003067.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003067.fa
new file mode 100644
index 0000000000000000000000000000000000000000..940bd3f68cb624f1874539c6a0fb2b2fcdc49d4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003067.fa
@@ -0,0 +1,5 @@
+>4_2151
+MRDLVYYIATSLDGYIAAPDGDFSAFPQDPVTLKTLFDRYPETCPAHARAALGVDGPARR
+FDTVIMGYRTYEPALTVGLPGGAYPHLNQIVVTHRPLPKAPNLTAISGDVSEHIAHLKTL
+PGRDIWLCGGADVAAQLIEHIDELQLKVNPIALGTGIPVLPFDGKPHSFHLAECEQQPGE
+VLLLTYRAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003068.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003068.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c00c610de698b9597fb4f688f1b12a39a2afac8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003068.fa
@@ -0,0 +1,8 @@
+>4_2152
+MNPLRPLTIPTYRWLFAAMVLTIFAQGAWALYLAMQTLDLGATPATLSGVVVWSGIGLLA
+GSLPAGVLADRMPNKSVIVGVLSLNLAIATATSTVAVFGMVAFWMLAASAFFIGVSTAFF
+FPAYTALVPVLVESDDLMAVNGLEGATRPLVGQALAPAAVGAVIGVSMPAAGGYLIAAAL
+AVALLAALQLPAPTPAESEADASAASPIGDLLDGFGYAARTRWVRTSVLFAAVMGLVVTG
+PLEVLLPALMRSSHENGPALYGAVLAALGVGGLVGSLLAGSWCTPERFLPAMIGAWALGC
+LPLTIPALTSNPWAIGVGLAIYGALIGIGMVIWGTVLQEHVPLEMLGRVASLDFFISIAF
+MPLSIALTGLLSRHIDTHTLFISAGLVPLVTAVLLATLGQLRMPRTTVGVAGGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003069.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003069.fa
new file mode 100644
index 0000000000000000000000000000000000000000..caada20abef5836ade1bfdb15e605578bb06997a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003069.fa
@@ -0,0 +1,3 @@
+>4_2160
+MNPECVSLCAWPSKDQRGRPSNYCSRACRELTKRTRQRLSWECDVLEEALAEKELSWNQE
+RILQRALGHRKWALGRYPARDE