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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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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