diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000000.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000000.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16b81fa2caef61a7f5a82f6242ead8cf2155477a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000000.fa
@@ -0,0 +1,307 @@
+>NZ_CP042169.1_61
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGFTRLAYTEALEDERTVTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYT*
+>NZ_CP042169.1_1294
+MTHANAPLTPTGRLRMVQRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLASEGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRAHGRESEAGRASKRGAG
+RRVGYTYLHSAIDGFTRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNN
+YRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSERARREALQV
+WVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYI*
+>NZ_CP042169.1_1897
+MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLPSRPHRSPAQLDPVLV
+AQIHALRRERKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRLRDLTPAGEDLRQRPQ
+KITARGPGHMVHLDVKKIGKIPDGGGWRAHGRESEAGRASKRGAGRRVGYTYLHSAIDGY
+TRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVITDNGNNYRAVDFTAKVVSLGG
+RHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAVWVNHYNYHRPHTSCG
+DAPPASLAPARVNNVMPSYS*
+>NZ_CP042169.1_2012
+MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLPSRPHRSPAQLDPVLV
+AQIHALRRERKWSARRIHHHLVSEGHQVCLRTVGRWLHRAGISRLRDLTPAGEDLRRQPA
+RRITARGPGHMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRGPGRRVGYTYLHSAIDG
+FTRLAYTEALPDERAATTVSFFCRARAFFAAHGITVDRVITDNGNNYRAADFTAKVVSLG
+GRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSEQARREALAVWVNHYNYHRPHTSC
+GDAPPASLAPARVNNVMTSYI*
+>NZ_CP042169.1_2055
+MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLPSRPHRSPAQLDPEVV
+AQIQTLRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRLRDLTPAGEDLRQRPQ
+KITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPGRRVGYTYLHSAIDGF
+TRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIRIDRVITDNGNNYRAVDFTRKVVSLGG
+RHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAVWVNHYNYHRPHTSCG
+DAPPASLAPARVNNVMPSYI*
+>NZ_CP042169.1_2222
+MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLPSRPHRSPAQLDPEVV
+AQIQTLRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRLRDLTPAGEDLRQRPQ
+KITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPGRRVGYTYLHSAIDGF
+TRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIRIDRVITDNGNNYRAVDFTRKVVSLGG
+RHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAVWVNHYNYHRPHTSCG
+DAPPASLAPARVNNVMPSYN*
+>NZ_CP033200.1_11
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPEVVAQIQTLRRREKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYN*
+>NZ_CP033200.1_37
+MTHANAPLTPTGRLRMVHRHLNDGIPQSHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGRIPEGGGWRTHGRDSEAGRASKRGS
+GQRVGYTYLHSAIDGYTRLAYTEALEDERTVTTIGFYCRARAFFAAHGITVDRVVTDNGN
+NYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALQ
+VWVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYT*
+>NZ_CP033200.1_126
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLLDRP
+SRPRRSPAQLDPEVVAQIQTLRRREKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRAHGRESEAGRASKRGAG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYT*
+>NZ_CP033200.1_299
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRDSEAGRASKRGAG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVITDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSEQARREALQV
+WVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYT*
+>NZ_CP033200.1_339
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+SRPHHCPAQLDIAILAEIEALRRDQKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIPDGGGWRAHGRDCENARAAKRGPG
+RRVGYTYLHSAVDGFTRLAYTEALPDERAATTVSFFCRARAFFAAHGITVDRVITDNGAN
+YRAAEFTMKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVIYARPYTSEQARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYN*
+>NZ_CP033200.1_1085
+MVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGAGRRVGYTYLHSAIDGFTRLAYTEAL
+EDEKAVTTIGFFCRARAFFAEHGITVDRVITDNGNNYRAADFTAKVVSLGGRHHRIRPYT
+PRHNGKVERYNRLMVDEVLYARPYSSEQARREALQVWVNHYNYHRPHTSCGNAPPASLAP
+ARVNNVMPSYN*
+>NZ_CP033200.1_1123
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGAG
+RRVGYTYLHSAIDGFTRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNN
+YRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYS*
+>NZ_CP033200.1_1198
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRDSEAGRASKRGPG
+RRVGYTYLHSAIDGFTRLAYTEALEDERTVTTIGFFCRARAFFAAHGITVDRVITDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRPHTSCGDAPPTSLAPARVNNVMPSYN*
+>NZ_CP033200.1_1774
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPEVVAQIQTLRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIRIDRVITDNGNN
+YRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYI*
+>NZ_CP033200.1_1777
+MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLPSRPHRSPAQLDPVLV
+AQIHALRRERKWSARRIHHHLVSEGHQLCLRTVGRWLHRAGISRLRDLTPAGEDLRRQPA
+RRITARGPGHMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRGPGRRVGYTYLHSAIDG
+FTRLAYTEALPDERAATTVSFFCRARAFFAAHGIRIDRVITDNGNNYRAVDFTAKVVSLG
+GRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARREALAVWVNHYNYHRPHTSC
+GDAPPASLAPARVNNVMTSYT*
+>NZ_CP033200.1_1924
+MVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGPGRRVGYTYLHSAIDGFTRLAYTEAL
+EDERAATTVSFYCRARAFFAAHGITVDRVITDNGNNYRAADFTAKVVSLGGRHHRIRPYT
+PRHNGKVERYNRLMVDEVLYARPYTSEQARREALAVWVNHYNYHRPHTSCGDAPPTSLAP
+ARVNNVMPSYI*
+>NZ_CP033200.1_1927
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLLDRP
+SRPHRSPAQLDPEVVAQIQTLRRREKWSARRIHHYLVSEGHQLCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGAG
+RRVGYTYLHSAIDGFTRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNN
+YRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYS*
+>NZ_CP033200.1_2030
+MIHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLLDRP
+SRPRRSPAQLDPVLVAQIHALRRERKWSARRIHHHLASEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVITDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYS*
+>NZ_CP040019.1_38
+MVHLDVKKIGKIPDGGGWRAHGRDSQAGRASKRGAGRRVGYTYLHSAIDGFTRLAYTEAL
+EDERAVTTIGFFCRARAFFAAHGITLDRVITDNGNNYRAADFTAKVVSLGGRHHRIRPYT
+PRHNGKVERYNRLMVDEVLYARPYSSETARREAMQVWVNHYNYHRPHTSCGGAPPASLAP
+ARVNNVMPSYT*
+>NZ_CP040019.1_138
+MTTIGFFCRARAFFAAHGITVDRVVTDNGNNYRAADFTRKVVSLGGRHHRIRPYTPRHNG
+KVERYNRLMVDEVLYARPYTSEAARREALQVWVNHYNYHRPHTSCGDTPPASLAPVRVNN
+VMTSYT*
+>NZ_CP040019.1_218
+MTHANAPLTPTGRLRMVQRHLHEGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+CRPRRSPAQLDPALVTQILTLRRECKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAMTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARREALQV
+WVNHYNYHRPHTSCGNAPPASLAPARVNNVMPSYT*
+>NZ_CP040019.1_540
+MTHANAPLTPTGRLRMVQRHLIDGIPQSHVAAEFRVSRPTVATWVARYLAEGAAGLQDRS
+SRPHHCPDQLDAEVVTELETLRRDHKWSARRIHHHLLAQGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPAKKITARAPGHMVHLDVKKIGKIPDGGGWRAHGRDSQAGRASKRGA
+GRRVGYTYLHSAIDGFTRLAYTEALEDERAVTTIGFFCRARAFFAAHGITLDRVITDNGN
+NYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARREAMQ
+VWVNHYNYHRPHTSCGGAPPASLAPARVNNVMPSYS*
+>NZ_CP040019.1_676
+MTHANAPLTPTGRLRMVQRHLIDGIPQSHVAAEFRVSRPTVATWVARYLAEGAAGLQDRS
+SRPHHCPDQLDAEVVTELETLRRDHKWSARRIHHHLLAQGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPAKKITARAPGHMVHLDVKKIGKIPDGGGWRAHGRDSQAGRASKRGA
+GRRVGYTYLHSAIDGFTRLAYTEALEDERAVTTIGFFCRARAFFAAHGITLDRVITDNGN
+NYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARREAMQ
+VWVNHYNYHRPHTSCGGAPPASLAPARVNNVMPSYT*
+>NZ_CP040019.1_763
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLPSASRPGGSPRGAGAHGAPGREEDRKDPRGGGWRAHGRDSEAGRASKRGP
+GARVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFYCRARAFFAAHGITVDRVVTDNGN
+NYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARREALQ
+VWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT*
+>NZ_CP040019.1_1473
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGKIPEGGGWRAHGRDSEAGRASKRGP
+GARVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFYCRARAFFAAHGITVDRVVTDNGN
+NYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARREALQ
+VWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT*
+>NZ_CP040019.1_1479
+MVHLDVKKVGRIPDGGGWRIHGRNSDQARTAGRAKSAGAKRGYTYLHSAVDGFSRLSYTE
+PLTDEKGPTAAAFLARAKAWFAAHGISHIHRVITDNGACYRSADFARIVGNRTRHQKTRP
+YTPRHNGKVERYQRILAEELLYAREFESEEARDTAIGIWNIHYNYHRPHSGAGGHPPASR
+LRAGVTNVWPSYS*
+>NZ_CP040019.1_1710
+MTHANAPLTPTGRLRMVQRHLHEGIPQAHVAAEFRVSRPTVATWVARYRAEGEVGLQDRS
+CRPRRSPAQLDPALVTQILTLRRECKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARREALQV
+WVNHYNYHRPHTSCGNAPPASLAPARVNNVMPSYT*
+>NZ_CP040019.1_1741
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+CRVGYTYLHSAIDGYTRLAYTEALEDEKAMTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARREALQV
+WVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT*
+>NZ_CP040019.1_2291
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+CRVGYTYLHSAIDGYTRLAYTEALEDEKAMTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARREALQV
+WVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT*
+>NZ_CP040019.1_2294
+MAYTESLENEKATTAVAFLNRAREWFASHGITRIERVITDNGACYRSAAFTAALDGADHR
+RTRPYTPKHNGKVERYNRILAEEFLYARTWTSEEQREKALETWNLHYNYHRPHGVHDGKP
+PASATPSRVNNVLASYS*
+>NZ_CP040019.1_2425
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGKIPEGGGWRAHGRDSEAGRASKRGP
+GARVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFYCRARAFFAAHGITVDRVVTDNGN
+NYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARREALQ
+VWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT*
+>NZ_CP040019.1_2507
+MTHANAPLTPTGRLRMVQRHLHEGIPQAHVAAEFRVSRPTVATWVARYRAEGEVGLQDRS
+CRPRRSPAQLDPALVTQILTLRRECKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARREALQV
+WVNHYNYHRPHTSCGNAPPASLAPARVNNVMPSYT*
+>NZ_CP040019.1_2563
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGKIPEGGGWRAHGRDSEAGRASKRGP
+GARVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFYCRARAFFAAHGITVDRVVTDNGN
+NYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARREALQ
+VWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYN*
+>NZ_CP040019.1_2581
+MVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGAGRRVGYTYLHSAIDGFTRLAYTEAL
+EDERAATTVSFYCRARAFFAAHGIRIDRAVTDNGNNYRAAEFTRKVVSLGGRHHRIRPYT
+PRHNGKVERYNRLMVDEVLHARPYSSETARREALQVWVNHYNYHRPHTSCGNAPPASLAP
+ARVNNVMTSYT*
+>NZ_CP040019.1_2586
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+CRVGYTYLHSAIDGYTRLAYTEALEDEKAMTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARREALQV
+WVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYI*
+>NZ_CP097650.1_266
+MTHANAPLTPTGRLRMVQRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLASEGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVITDNGNN
+YRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYS*
+>NZ_CP097650.1_496
+MAQRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLPSRPHRSPAQLDPVLV
+AQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRLRDLTPAGEDLRQRPQ
+KITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGAGRRVGYTYLHSAIDGF
+TRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNNYRAADFTAKVVSLGG
+RHHRIRPYTPRHNGKVERYNRLMVDEVIYARPYSSEQARREALAVWVNHYNYHRPHTSCG
+DAPPTSLAPARVNNVMPSYN*
+>NZ_CP097650.1_772
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVTQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNN
+YRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRSHTSCGDAPPASLAPARVNNVMPSYT*
+>NZ_CP097650.1_847
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNN
+YRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYN*
+>NZ_CP097650.1_1131
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVTQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNN
+YRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRSHTSCGDAPPASLAPARVNNVMPSYI*
+>NZ_CP097650.1_1497
+MTHANAPLTPTGRLRMVQRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLASEGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVITDNGNN
+YRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYS*
+>NZ_CP097650.1_1521
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNN
+YRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALQV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYT*
+>NZ_CP097650.1_1942
+MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLPSRPHRSPAQLDPVLV
+AQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRLRDLTPAGEDLRQRPQ
+KITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGPGRRVGYTYLHSAIDGF
+TRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNNYRAADFTAKVVSLGG
+RHHRIRPYTPRHNGKVERYNRLMVDEVIYARPYTSEQARREALTVWVNHYNYHRPHTSCG
+DAPPTSLAPARVYNVMPSYS*
+>NZ_CP097650.1_2047
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+CRPRRSPAQLDPEVVAQIQTLRRREKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRPQKITARGPGRMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGFTRLAYTEALPDERAATTVSFFCRARAFFAAHGIRIDRVITDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYT*
+>NZ_CP097650.1_2051
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+CRPRRSPAQLDPEVVAQIQTLRRREKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRPQKITARGPGRMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGFTRLAYTEALPDERAATTVSFFCRARAFFAAHGIRIDRVITDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYNYLFGLLMVTRSPECALLGHGPDQRG
+WLLDTYLRGLRP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000001.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000001.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49e3ee49b015085e4b81a2ce737c27197cd3f14e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000001.fa
@@ -0,0 +1,231 @@
+>NZ_CP042169.1_167
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT*
+>NZ_CP042169.1_567
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT*
+>NZ_CP042169.1_580
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKLPVVAEHLDAARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAAGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVSNTGSEVNPDTAPALEFSA*
+>NZ_CP042169.1_581
+MTAPHILDPAGLLGEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPSSSRTAQR
+NGYRHRDLDTRVGTLDVAIPKLRSGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGVNALSKSQVSRMATELDEQVEAFRHRPLGVAGPFTFVAADALSMKVREGGRV
+VNAVVLLATGVNADGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHTGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAASVHAQFDRLLD
+YVSGKLPTVAEHLDAARADILAFTTFPKDVWTQVWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVTNTGDEVDPDTELTLGLSA*
+>NZ_CP042169.1_601
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVTDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDAVGIFPNR
+DAVIRLVGAVLAEQTDEWAEGRRYLGLELLARCSNQDPDTPSTTGASAEVMPTLA*
+>NZ_CP042169.1_690
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT*
+>NZ_CP042169.1_1029
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKLPVVAEHLDAARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAAGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVSNTGSEVNPDTAPALEFSA*
+>NZ_CP042169.1_1159
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKLPAVAEHLGDARADILAFTTFPKDVWTQVWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTPVEDTGSEVGTDTDTALELSA*
+>NZ_CP042169.1_1351
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQTLGITGLSKSQVSEMSKDLDAQVEAFRTRPLDAGPYRFVAADALVLKVREHGRVV
+KVAAMVATGINNDGYREILGLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLVE
+AAGAVFGTAQWQRCRTHYAANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMIDS
+LATHLPAAAEHLEGARDEVLTFTKFPKEVWKKIWSNNPNERLNKEIRRRTDVVGIFPSRV
+EVIRLLGAVLAEQHDEWTESRRYMSLELLTATDTMLAEAAAKAAAEQAALQVSDTMTDDP
+GHAALAA*
+>NZ_CP042169.1_1356
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT*
+>NZ_CP042169.1_1456
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVAGAWPGSGWSPLMPTPGSR
+TPSPRTCPVRCGNAAAPTTRRT*
+>NZ_CP042169.1_1974
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKLPAVAEHLGDARADILAFTTFPKDVWTQVWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTPVEDTGSEVGTDTDTALELSA*
+>NZ_CP042169.1_2008
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFSATGLWARPARSCSSPPTP*
+>NZ_CP042169.1_2009
+MFLAADALTMKVREGGRVVNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVA
+RGLAGVALVTSDSHRGLVEAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSV
+YDQPDGPAVHAQFERLLDYVQDRLPAVAAHLDAARQDILAFTSFPRDVWCQIWSNNPAER
+LNREIRRRTDAVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQE
+TVMSTEVMPTLQT*
+>NZ_CP042169.1_2170
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+INAVAMVATGVNADGRREVLGLRVATTETGAAWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT*
+>NZ_CP042169.1_2173
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGQASQSRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFERLLD
+YVQDRLPAVAAHLDAARQDILAFTSFPRDVWCQIWSNNPAERLNREIRRRTDAVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT*
+>NZ_CP042169.1_2175
+MVADCYLAGVSTRRMDKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFL
+AADALTMKVREGGRVVNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGL
+AGVALVTSDSHRGLVEAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQ
+PDGPAVHAQFERLLDYVQDRLPAVAAHLDAARQDILAFTSFPRDVWCQIWSNNPAERLNR
+EIRRRTDAVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVM
+STEVMPTLQT*
+>NZ_CP042169.1_2176
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPNGCSSAANGPSPH*
+>NZ_CP042169.1_2210
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFERLLD
+YVQDRLPAVAAHLDAARQDILAFTSFPRDVWCQIWSNNPAERLNREIRRRTDAVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT*
+>NZ_CP042169.1_2215
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKLPVVAEHLDAARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAAGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVSNTGSEVNPDTAPALEFSA*
+>NZ_CP033200.1_1093
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQTRHHGPVEIAGLRDE*
+>NZ_CP033200.1_1094
+MSKDLDAQVEAFRTRPLDAGPYRFVAADALVLKVREHGRVVKVAAMVATGINNDGYREIL
+GLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLVEAAGAVFGTAQWQRCRTHYA
+ANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMIDSLATHLPAAAEHLEGARDEV
+LTFTKFPKEVWKKIWSNNPNERLNKEIRRRTDVVGIFPSRVAVIRLLGAVLAEQHDEWTE
+SRRYMSLELLTATDTMLAEAAAKAAAEQAALQVSDTMTDDPGHAALAA*
+>NZ_CP040019.1_675
+MTAPHILDPAGLLREALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPGRATQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMATELDEHVESFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHTGLR
+EAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAQAVDAQFDRLLD
+YVSEKLPAVAEHLDAARADILAFTTFPKDVWTQVWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLHRCRLTPVSNTGDEVDTDTALELSA*
+>NZ_CP040019.1_705
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKLPVVAEHLDAARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVSNTGNEVNPDTAPALEFSA*
+>NZ_CP040019.1_879
+MTAPHILDPAGLLREALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPGRATQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMATELDEHVESFRHRPLGEALPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHTGLR
+EAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAQAVDAQFDRLLD
+YVSEKLLYGGRAPGRCPGGHPGLHDLPEGRVDAGLVEQSGRAAQPRDPPPHRRGGHLPQP
+GSHRQAGRCGAGRADR*
+>NZ_CP040019.1_2453
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKLPVVAEHLDAARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVSNTGNEVNPDTAPALEFSA*
+>NZ_CP040019.1_2620
+MTAPHILDPAGLLGEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPSSSRTAQR
+NGYRHRDLDTRVGTLDVAIPKLRSGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGVNALSKSQVSRMATELDEQVEAFRHRPLGVAGPFTFVAADALSMKVREGGPV
+VNAVVLLATGVNADGHREVLGLRVATSETGAAWNEFFADLVARGLAGLRLVTSDAHTGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAASVHAQFDRLLD
+YVSEKLPTVAEHLDAARADILAFTTFPKDVWTQVWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVTNTGDEVDPDTELTLGLSA*
+>NZ_CP097650.1_1300
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQTLGITGLSKSQVSEMSKDLDAPVEAFRTRPLDAGPYRFVAADALVLKVREHGRVV
+KVAAMVATGINNDGYREILGLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLVE
+AAGAVFGTAQWQRCRTHYAANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMIDS
+LATHLPAAAEHLEGARDEVLTFTKFPKEVWKKIWSNNPNERLNKEIRRRTDVVGIFPSRV
+AVIRLLGAVLAEQHDEWTESRRYMSLELLTATDTMLAEAAAKAAAEQAALQVSDTMTDDP
+GHAALAA*
+>NZ_CP097650.1_1941
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQTLGITGLSKSQVSEMSKDLDAQVEAFRTRPLDAGPYRFVAADALVLKVREHGRVV
+KVAAMVATGINNDGYREILGLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLVE
+AAGAVFGTAQWQRCRTHYAANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMIDS
+LATHLPAAAEHLEGARDEVLTFTKFPKEVWKKIWSNNPNERLNKEIRRRTDVVGIFPSRV
+AVIRLLGAVLAEQHDEWTESRRYMSLELLTATDTMLAEAAAKAAAEQAALQVSDTMTDDP
+GHAALAA*
+>NZ_CP097650.1_2143
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKLPAVAEHLGDARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTPVEDTGSEVGTDTDTALELSA*
+>NZ_CP097650.1_2160
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKLPAVAEHLGDARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTPVEDTGSEVGTDTDTALELSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000004.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000004.fa
new file mode 100644
index 0000000000000000000000000000000000000000..66f1ad015da3b3ddb904e893437b59bba1c7aecd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000004.fa
@@ -0,0 +1,192 @@
+>NZ_CP042169.1_356
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL*
+>NZ_CP042169.1_1350
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL*
+>NZ_CP042169.1_2013
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPLTQTS*
+>NZ_CP042169.1_2056
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL*
+>NZ_CP042169.1_2221
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL*
+>NZ_CP033200.1_342
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL*
+>NZ_CP033200.1_979
+MGRTQWPLTDVPRDRGGSFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIG
+TDLSHETISNITDAVSEEVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGV
+DLEGIKHVLGIWVQDTEGSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSM
+VQTCVVHLIRAAMRFVAYQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAA
+ATWANSWERFIPFLQFPPMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLA
+ICNIEDKRAAERARDRGKPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL*
+>NZ_CP033200.1_982
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVCKRP*
+>NZ_CP033200.1_1092
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL*
+>NZ_CP033200.1_1702
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL*
+>NZ_CP033200.1_1775
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL*
+>NZ_CP033200.1_1970
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL*
+>NZ_CP040019.1_219
+MVQTCVVHLIRAAMRFVAYQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSA
+AATWANSWERFIPFLQFPPMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWL
+AICNIEDKRAAERARDRGKPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL*
+>NZ_CP040019.1_220
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEAPKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYA*
+>NZ_CP040019.1_627
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEAPKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL*
+>NZ_CP040019.1_878
+MVQTCVVHLIRAAMRFVAYQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSA
+AATWANSWERFIPFLQFPPMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWL
+AICNIEDKRAAERARDRGKPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL*
+>NZ_CP040019.1_882
+MTDTADAQNPLAGVLSADQVDALVNAAEDLGEGRHGVEELLSRMTQAVLERALETEMSEH
+LGYEAGDPAGAGTGNSRNGKTTKSVQTLQGPGQITVPRDRNGSFEPVIVPKRSRRLGRVE
+DMILSLYARGMTTRDIGSHLEEIYGSKVSAATISRVTDVVADEVAQWQSRPLETVYPIVY
+IDAIWLKIRDGGVVTNKACHVAVGVDLEGRKQVLGLWLGVSEGAKFWANVLTEIRNRGTK
+DILILCCDGLSGLPAAVNSIYPETVVQTCVVHLLRSAMKYASYADRKTMAKDMRPIYTAA
+TVEAAQLALEAFAEIWQTKAPGAVLAWRTAWEDFIPFLAFTPEIRKVIYTTNQIESINYQ
+LRKITKTRGSFPSDEAAIKLVYLGIRNIETRRGGELGTGTQGWHQALNAFAVQFPNRLPL
+*
+>NZ_CP040019.1_1480
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEAPKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL*
+>NZ_CP040019.1_2058
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYGKGSEDASKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL*
+>NZ_CP083691.1_1793
+MSESTTEMTGPMIDPVTGEIIDQKDLAEQLLAQAKEQGVRLVGPGGLLNQLTKNVLETAL
+EAELTEHLGHDHGQTPIAANMRNGTRSKTVLTEIGPVEIEVPRDRDGSFEPVIVPKRKRR
+LDGTDQIVLSLSARGLTTGEIAVHFEEVYGAKVSKDTISRITEKVAGELAEWSSRPLDPL
+*
+>NZ_CP097650.1_112
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL*
+>NZ_CP097650.1_1498
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL*
+>NZ_CP097650.1_1500
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL*
+>NZ_CP097650.1_1826
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL*
+>NZ_CP097650.1_1919
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000006.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000006.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3e47078a834c28d378382d465469e3b4a9a8ccc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000006.fa
@@ -0,0 +1,100 @@
+>NZ_CP042169.1_150
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE*
+>NZ_CP042169.1_997
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE*
+>NZ_CP042169.1_1249
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE*
+>NZ_CP042169.1_1341
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETGDSQNVRTE*
+>NZ_CP042169.1_2021
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE*
+>NZ_CP033200.1_978
+MVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIK
+ICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWA
+GTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRH
+SSLGYLTPAEYARQCTHQMETDDSQNVRTE*
+>NZ_CP033200.1_1071
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE*
+>NZ_CP033200.1_1079
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE*
+>NZ_CP033200.1_1081
+MSERIACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINRFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE*
+>NZ_CP033200.1_1977
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMEIGDSQNVRTE*
+>NZ_CP040019.1_1192
+MACRLVGLSRSAYRRPLKGDTVADPDRALRQWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE*
+>NZ_CP097650.1_565
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVASRGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE*
+>NZ_CP097650.1_567
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVVDWAGTR
+TGLWADPVS*
+>NZ_CP097650.1_1206
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE*
+>NZ_CP097650.1_1295
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTH*
+>NZ_CP097650.1_1831
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLGHV*
+>NZ_CP097650.1_2151
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVASRGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000010.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000010.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad3e57a1d8eae6ce6c5ffce7d723293162cc4c48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000010.fa
@@ -0,0 +1,79 @@
+>NZ_CP042169.1_433
+MLHPTFATPDLTTFCRLDELGLVAVGQLIEPDRATIECRVVEDDPWCRKCGVEGVPRDTV
+TRRLAHEPFGHRPTTLLVRVRRYRCGHCRRTWRQDMTRAAAPRAKISRGGLEWALRGIVI
+DHLTVTRVAAGLGVSWSAANAAVLAEGKRRLIDDPARFDGVTTIGVDEHVWRHTRLGDKY
+VTVIIDLTPARNKTGPARLLDMVEGRSKAVFKQWLAARPADWAKRIEVVAMDGFAGFKTA
+AAEELPDAVPVMDPFHVVRLAGDALDVCRRRVQQDTTGHRGLKGDPLYKARRTLHTGASL
+LTDRQRARLDAVFASEEHIEVEATWGIYQRIVAAYREPDKKKAKAMMQEVIATISSGVPA
+ALVEVRKLGRTMKQRAGDILAFFDRPGTSNGPTEAINGRLEHLRGSALGFRNLTHYIARS
+LLEAGGFRPALHPRS*
+>NZ_CP042169.1_818
+MRRYRCSGCGYVWRQDTTASAEPRAKLSRRALRWALEGIVVQHLTVARVAEGLGVAWDTA
+NDAVLAEGKRVLIDEEHRFEGVKVVGVDEHVWRHTRRGDRYVTVIIDLTPVRDGTGPARL
+LNMVEGRSKQAFKTWLADRPQDWRDGVEVVAMDGFTGFKTAAVEELPDVVTVLDPFHVTR
+LAGEALDECRRRVQQAICGHRGRKGDPLYAARRTLSTGVDLLNDKQKDRLDTLFADDAHV
+EVEVTWSVYQRMIAAYRHENRRHGRELMARLIDSISTGVPKALVEITKLGRTLKKRAADV
+LAYFDRPSTSNGPTEAINGRLEHLRGSALGFRNLTNYIARSLLETGGFRPRLHPGFG*
+>NZ_CP042169.1_1349
+MSLLTDRQEEHLSVLFAHEKHAAVEAAWEIYQAMVAAYREFDRAKAKAKMEKVIAALSKK
+VPDTLEELGKLGRTLTKRAADVLAFFERLGTSNGPTEAINGRLEHLRGSALGFRNLTNYI
+ARSLLESGGFRPLLHPQMR*
+>NZ_CP033200.1_1091
+MSLLTDRQKEHLSVLFAHEKHAAVEAAWEIYQAMVAAYREFDRAKAKAKMEKVIAALSKK
+VPDTLEELGKLGRTLTKRAADVLAFFERLGTSNGPTEAINGRLEHLRGSALGFRNLTNYI
+ARSLLESGGFRPLLHPQTR*
+>NZ_CP040019.1_100
+MLILWRQRVWRCAEPGCARGTFVEQLPSLVAPRGSITTRAISWAIGQLRREHGTIAGLAR
+QLGTSWKTLWRAIRPELEHLADDESRFEGVTSLGVDEHIWHHVDRRRRGPRELTGMVDLS
+RDEHGRVRARLLDLVPGRSGKAYAGWLAERGDAFRRGVQVAALDPFAGYKTAIDQRLDDA
+TAVLDAFHVVKLGTQVVDEVRRRVQQATLGHRGRKGDPLYGIQTILRAGAEHLTDKQLAR
+LAAAIESDPAHEEVFVAWQCAQDLRAAYRSGNLADGRAIAERLADSLHTSPIPEVARLGR
+TLRRWRAAFLAYFTTNRSSNGGTEAINGIIELHRRLARGFRNRDNYRLRMLLAAGGLTP*
+>NZ_CP040019.1_492
+MVDLSRDEHGRVRARLLDLVPGRSGKAYAGWLAERGDAFRRGVQVAALDPFAGYKTAIDQ
+RLDDATAVLDAFHVVKLGTQVVDEVRRRVQQATLGHRGRKGDPLYGIQTILRAGAEHLTD
+KQLARLAAAIESDPAHEEVFVAWQCAQDLRAAYRSGNLADGRAIAERLADSLHTSPIPEV
+ARLGRTLRRWRAAFLAYFTTNRSSNGGTEAINGIIELHRRLARGFRNRDNYRLRMLLAAG
+GLTP*
+>NZ_CP040019.1_493
+MLILWRQRVWRCAEPGCARGTFVEQLPSLVAPRGSITTRAISWAIGQLRREHGTIAGLAR
+QLGTSWKTLWRAIRPELEHLADDESRFEGVTSLGVDEHIWHHVDRRRRGPKS*
+>NZ_CP040019.1_1073
+MLILWRQRVWRCAEPGCARGTFVEQLPSLVAPRGSITTRAISWAIGQLRREHGTIAGLAR
+QLGTSWKTLWRAIRPELEHLADDESRFEGVTSLGVDEHIWHHVDRRRRGPKS*
+>NZ_CP040019.1_1074
+MTRSGVACRSRRWTRSCGYKTAIDQRLDDATAVLDAFHVVKLGTQVVDEVRRRVQQATLG
+HRGRKGDPLYGIQTILRAGAEHLTDKQLARLAAAIESDPAHEEVFVAWQCAQDLRAAYRS
+GNLADGRAIAERLADSLHTSPIPEVARLGRTLRRWRAAFLAYFTTNRSSNGGTEAINGII
+ELHRRLARGFRNRDNYRLRMLLAAGGLTP*
+>NZ_CP083691.1_614
+MPEPTLYCRARGDYCTCCDLLVGLPGLHVLTAERDDHDRLVVTVESAPEPMGCRSCGVIA
+RGHGRIEVSLVDAPAFGRPVRIIWRKRRWLCPDPACEVGSFIEQDEKVAAPRAVLTTRAC
+RWAIEQIRREHASVNGIRRQLGTGWRTVWDSIQPLLQAADEDPSRFEGVAILGVDEHVWH
+HVSTKPIHHGGRGPKELTGMVDLTRDEGGRTRARLLDLVPGRSGRVYKDWLDQRGDAFRA
+RIEVATLDPFHGYKNAIDDQLEDARSVLDAFHVVKLATTVVDDVRRRVQQQIHGHRGRKS
+DPLYRVRNVLRAGAENLTDRQRDRLETAWAAHEQHIEVEIAWLCAQKVRSAYRQGTHAAG
+RAVAEKILATFTSCPIPEVARLGKTLNRWRREFLGYFDTNGASNGGTEAINGLIELHRRI
+ARGFRNRDNYRLRMLLIGGGLDMTHHTQR*
+>NZ_CP083691.1_622
+MPEPTLYCRARGDYCTCCDLLVGLPGLHVLTAERDDHDRLVVTVESAPEPMGCRSCGVIA
+RGHGRIEVSLVDAPAFGRPVRIIWRKRRWLCPDPACEVGSFIEQDEKVAAPRAVLTTRAC
+RWAIEQIRREHASVNGIRRQLGTGWRTVWDSIQPLLQAADEDPSRFEGVAILGVDEHVWH
+HVSTKPIHHGGRGPKELTGMVDLTRDEGGRTRARLLDLVPGRSGRVYKDWLDQRGDAFRA
+RIEVATLDPFHGYKNAIDDQLEDARSVLDAFHVVKLATTVVDDVRRRVQQQIHGHRGRKS
+DPLYRVRNVLRAGAENLTDRQRDRLETAWAAHEQHIEVEIAWLCAQKVRSAYRQGTHAAG
+RAVAEKILATFTSCPIPEVARLGKTLNRWRREFLGYFDTNGASNGGTEAINGLIELHRRI
+ARGFRNRDNYRLRMLLIGGGLDMTHHTQR*
+>NZ_CP083691.1_821
+MPEPTLYCRARGDYCTCCDLLVGLPGLHVLTAERDDHDRLVVTVESAPEPMGCRSCGVIA
+RGHGRIEVSLVDAPAFGRPVRIIWRKRRWLCPDPACEVGSFIEQDEKVAAPRAVLTTRAC
+RWAIEQIRREHASVNGIRRQLGTGWRTVWDSIQPLLQAADEDPSRFEGVAILGVDEHVWH
+HVSTKPIHHGGRGPKELTGMVDLTRDEGGRTRARLLDLVPGRSGRVYKDWLDQRGDAFRA
+RIEVATLDPFHGYKNAIDDQLEDARSVLDAFHVVKLATTVVDDVRRRVQQQIHGHRGRKS
+DPLYRVRNVLRAGAENLTDRQRDRLETAWAAHEQHIEVEIAWLCAQKVRSAYRQGTHAAG
+RAVAEKILATFTSCPIPEVARLGKTLNRWRREFLGYFDTNGASNGGTEAINGLIELHRRI
+ARGFRNRDNYRLRMLLIGGGLDMTHHTQR*
+>NZ_CP097650.1_1299
+MSLLTDRQKEHLSVLFAHEKHAAVEAAWEIYQAMVAAYREFDRAKAKAKMEKVIAALSKK
+VPDTLEELGKLGRTLTKRAADVLAFFERLGTSNGPTEAINGRLEHLRGSALGFRNLTNYI
+ARSLLESGGFRPLLHPQMR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000013.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000013.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb9cd345a50e3e5f938eb496fbc663b81435469c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000013.fa
@@ -0,0 +1,60 @@
+>NZ_CP033200.1_328
+MKELAAVGIPVAVTCRVLKLSRQPYYRWLADPVTDAELAEAYRANALFDAHQDDPEFGYR
+FLVDEAKEAGEVMCERSAWRICRDNGWWSVFGKKRGKNGKKPGPPVHDDLVERDFTAGGS
+NQLWLTDVTEHRTAEGKLYMCAIKDVFSGRIVGYSIDSRMKARLAVQALQNAVARRGDVA
+GCIVHSDRGSQFRSRKFVHALNRHGLVGSMGKVGAAGDNAAMESFFALLQKNVLDRRSWT
+TRDELRIAIVTWTERTYHRRRRQARLGRLTPIEYETMMKPAVTLPA*
+>NZ_CP033200.1_1721
+MYPLVSELAADQIPVAVSLRVLKLARQPYYRWRDQPVAVSEVEQAYRANALHAAHLNDPE
+FGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCGFGAKRGKYGTRPGPPVHDDHVRRDFS
+AEAPNRLWLTDITEHPTSEGKLYLCAIKDLYAGRIVGYSMAGRMQASLAVNALEQAVARR
+GGTDAVAGCIVHSDRGSQFRSALFQDALTTHGLIGSMGQVGAAGDNAAMESFFALLQKNV
+LDRRDWDTRDELRAGIITWIERTYHRRRRQVRLGRLTPVEYELIMDHTPADAA*
+>NZ_CP040019.1_690
+MMYPHVKELATDGIPVVVSVRMLKLARQPYCRWLENPLTRTDLDQAYRANALHAAHQNEK
+ALAHRSAS*
+>NZ_CP040019.1_2232
+MYPLVSELAADGVPVAVSLRVLKLARQPYYRWREKPVAVSEVEQAHRANALHAAHLNDPE
+FGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCAFGAKRGKNGRRPGPPVHDDRVRRDFS
+AEAPNRLWLTDITEHPTGEGKLYLCAIKDVHAGRIVGYSMAGRMQASLAVNALEQAVARR
+GGTDAVAGCIVHSDRGSQFRSALFQDALTAHGVIGSMGQVGAAGDNAAMESFFALLQKNV
+LDRRDWDTRDELRAGIITWIERSYHRRRRQVRLGRLTPVEYELIMDHTPADPA*
+>NZ_CP040019.1_2448
+MHDDRVRRDFSAEAPNRLWLTDITEHPTGEGKLYLCAIKDVHAGRIVGYSMAGRMQASLA
+GNALEQAVARRGGTDAVAGCIVHSDRGSQFRSALFQDALTAHGLIGSMGQVGAAGDNAAM
+ESFFALLQKNVLDRRDWDTRDELRAGIITWIERTYHRRRRQVRLGRLTPVEYELIMDHTP
+ADPA*
+>NZ_CP040019.1_2449
+MYPLVSELAADGVPVAVSLRVLKLARQPYYRWRDQPVAVSEVEQAHRANALHAAHLNDPE
+FGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCAFGGQARQERALYLALPCMMTASAGTS
+LPKLRTGCG*
+>NZ_CP040019.1_2565
+MYPLVSELAADGVPVAVSLRVLKLARQPYYRWRDQPVAVSEVEQAHRANALHAAHLNDPE
+FGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCAFGAKRGKNGRRPGPPVHDDRVRRDFS
+AEAPNRLWLTDITEHPTGEGKLYLCAIKDVHAGRIVGYSMAGRMQASLAGNALEQAVARR
+GGTDAVAGCIVHSDRGSQFRSALFQDALTAHGLIGSMGQVGAAGDNAAMESFFALLQKNV
+LDRRDWDTRDELRAGIITWIERTYHRRRRQVRLGRLTPVEYELIMDHTPADPA*
+>NZ_CP040019.1_2585
+MEQAHRANALHAAHLNDPEFGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCAFGAKRGK
+NGRRPGPPVHDDRVRRDFSAEAPNRLWLTDITEHPTGEGKLYLCAIKDVHAGRIVGYSMA
+GRMQASLAVNALEQAVARRGGTDAVAGCIVHSDRGSQFRSALFQDALTAHGVIGSMGQVG
+AAGDNAAMESFFALLQKNVLDRRDWDTRDDLRAGIITWIERAYHRRRRQVRLGRLTPVEY
+ELIMDHTPADPA*
+>NZ_CP083691.1_1847
+MHPLVRELAVDGIPVAVTCRVLKIARQPYYRWLASPVTPAELDEAYRANALFDAHKDDPE
+FGYRFLADEAREAGESMAERTAWRICSDMGWWSAFGKKRGRNGKKPGSPVHDDLCAVTDE
+KGRIRHQFNADAVNELWIGDITEHRTGEDRLYLCAFKDVYSNRIVGYSIDSRMKSSLAVT
+ALNNAVARRGEVAGCVVHTDRGSQCRSRKFVHALNRHGMVGSMGRVGATGDNAAMASFFA
+LLQKNVLERRSWATREDLRIAIVTWIERTYHRRRRQVALGRLTPIEYEAIMTTPASQAA*
+>NZ_CP097650.1_866
+MYPLVRELAVDGIPVAVTCRVLKIARQPYYRWLASPVTPAELDETYRANALFDAHKDDPE
+FGYRFLADEAREAGELMAERTAWRICSDMGWWSAFGKKRGRNGKKPGSPVHDDLCAATDE
+KGRIWHQFNADAVNELWIGDITEHRTGEGRLYLCAFKDVYSNRIVGYSIDSRMKSSLAVT
+ALNNAVARRGEVAGCVVHTDRGSQFRSRKFVHALNRHGMVGSMGRVGAAGDNAAMESFFS
+LLQKNVLDRRSWATREDLRIAIVTSIERTYHRRRRQAALGRLTPIEYEAIMTTPASQAA*
+>NZ_CP097650.1_1495
+MTYPLVAELADAGILVTVSCRVLKLARQPYYRWRNAPVRDADMLRAYRINALHDAHHDDP
+TFGYRYLADEARRAGWRMSRRTAWKLCSQAGILSSAQRRRRGKGKKTGPPVFDDHVQRVF
+RADAPNRLWLTDITEHRTSEGKLYCCAIKDVFSNRIVGYSISDRMTAKLAVDAVRNAVAR
+RGEVAGCILHADRGSQFRSRAMARELRRHDMVGSMGRVGAAGDNAAMESFWSLLQTNVLN
+QQRWTTRQELRLVIVVWIERKYHRQRAQDILGGLTPIEFEAKLAEPHTLAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000014.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000014.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a581bcbbf336f96dcfc4f65ce4651a4ddaf53b57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000014.fa
@@ -0,0 +1,97 @@
+>NZ_CP042169.1_153
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA*
+>NZ_CP042169.1_1033
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA*
+>NZ_CP042169.1_2004
+MNEAVPHFDLAIIGSGGGAFAAAIRATNLDKRVVMIERGTVGGTCVNTGCIPSKALLAAA
+EARHTAQDAGRFPGLTATAGPVDMEALIAGKRALVENVRSDKYVDLVADYGWELRHGNAV
+FTGTAADPALEVTAQDGTRETITAAHYLVATGSTPWAAPINGLDTVDYLTSTTAMELDEV
+PESLLVIGGGYVALEQAQLFARLGSKVTMLVRSRLASGEEPEASRALMSVFANEGIRVIR
+RSTVSSITQDTDGGIAAQADIAGGRETLRASKVLVATGRRPVTDGLNLAGVSVKTGDKGE
+VVVEDTLVSSNPRVWAAGDVTGHPEYVYVAASHGTLMVDNAFSDAGRAVDYSHLPRVTFT
+SPNLAVVGMTDKQARDAGIRCECRVVPLEYIPRAVVNRDTRGFIKMVADADTGRIVGITA
+VAKEAGDLAATGVYILQAGMTVDQVANLWSPYLTMAEGIKIVAQSFKTDVSKLSCCAA*
+>NZ_CP033200.1_285
+MPTKYDLAIIGSGGGAFAAAIRATTLGKSVVMIERGTLGGTCVNTGCVPSKALIAAADAR
+HSAADAADRFPGIATTAGPVDMPALIAGKQALVESLRGEKYADVADSYGWAVRRGDAAFA
+GTPDAPVLQVAGDDGSTETIEAGHFLVATGSRPWAPPIDGLDETGYLTSTTAMELTELPE
+SLLVLGGGYVALEQAQLFARLGSQVTVLVRSRLASKEEPEVSRTLEEVFADEGIRVVRRA
+LPTRVSRDAATGQAVVTADVAGGREEFRADQVLVALGRRPVTDGLGLDRVGVETGDLGEV
+VVSDRMQSSHPRIWAAGDVTGHPEFVYVAAHHGTLVAENAFADADRAVDYARLPRVTFTG
+PAIGAVGMTEKDVVAAGIRCDCRVLPLHHVPRALVNRDTRGFVKIVVDADTGKILGITAV
+AKDAGELAAAGVHVLGKTVAEVADAWAPYLTMAEGIRIAAKAFTTDPSLLSCCA*
+>NZ_CP033200.1_324
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTCGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA*
+>NZ_CP033200.1_333
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA*
+>NZ_CP033200.1_762
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPLPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTCGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA*
+>NZ_CP040019.1_707
+MTATANSRSYDLAMIGSGGAAFAAAIRATSLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPLPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA*
+>NZ_CP083691.1_2171
+MNEAVPHFDLAIIGSGGGAFAAAIRATNLDKRVVMIERGTVGGTCVNTGCIPSKALLAAA
+EARHTAQDAGRFPGLTATAGPVDMEALIAGERALVENVRSDKYVDLVADYGWELRHGNAV
+FTGTAADPALEVTAQDGTRETITAAHYLVATGSTPWAAPINGLDTVDYLTSTTAMDLDEV
+PESLLVIGGGYVALEHAQLFARLGSKVTMLVRSRLASGEEPEASRALMSVFANEGIRVIR
+RSTVSSITQDTDGGIAAQADIAGGRETLRASKVLIATGRRPVTDGLNLAGVSVKTGDKGE
+VVVEDTLVSSNPRVWAAGDVTGHPEYVYVAASHGTLMVDNAFSDAGRAVDYSHLPRVTFT
+SPNLAVVGMTDKQARDAGIRCECRVVPLEYIPRAVVNRDTRGFIKMVADADTGRIVGITA
+VAKEAGDLAATGVYILQAGMTVDQVANLWSPYLTMAEGIKIVAQSFKTDVSKLSCCAA*
+>NZ_CP097650.1_981
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPLPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDGHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000015.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000015.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d030baba64dbf19e29ec24a62b0324a22a2432e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000015.fa
@@ -0,0 +1,105 @@
+>NZ_CP042169.1_336
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIE
+KAVEAVTSELLSASREIETKDQIAATASISAADKQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENATLDLLGSARKVVITKDETTIVEGGGDAEQIAGRVAQIRSEIENTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFGGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKTLDDGHGLNAAT
+GEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM*
+>NZ_CP042169.1_1607
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVE
+LEDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKRGIE
+VAVAAVEQRLQENARPVEGKEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVVQA
+NKPLFVIAEDIEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGAQVVSP
+DLGMKLEQADLDVLGSARRITVTKDETTIVDGGGAPEDVEARIAQIKAEAAATDSDWDRE
+KLQERLAKLSGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+TVLDTDADVQALTGDAAVGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFNA
+KTGVYGDLIADGVIDPVKVTRSALANATSIAALVLTTETLVADKPADEDEAGHQH*
+>NZ_CP033200.1_61
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPCGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIE
+KAVEAVTSELLSASREIETKDQIAATASISAADKQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENATLDLLGTARKVVVTKDETTIVEGGGDAEQIAGRVAQIRSEIENTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFGGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKTLDDGHGLNAAT
+GEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM*
+>NZ_CP033200.1_1323
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVE
+LEDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKKGIE
+VAVAAVERRLQENARPVEGQEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVLQA
+NKPLFVIAEDIEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGAQVVSP
+DLGMKLEQADLDVLGSARRITVTKDETTIVDGGGAAEDVEARVAQIKAESAATDSDWDRE
+KLQERLAKLSGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+TALDTDADVQALTGDAAVGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFNA
+KTGVYGDLIADGVIDPVKVTRSALANATSIAALVLTTETLVADKPADEDEAGHQH*
+>NZ_CP040019.1_1216
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVE
+LDDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKKGIE
+VAVAAVEQRLQENARPVEGKEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDPYVLINSGKISNVQELLPVLEKVLQA
+SRPLFVIAEDIEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMLQDIAVLTGAQVVSP
+DLGMKLEQADLDVLGSARRITVTKDETTIVDGGGSAEDVEARVAQIKAESAATDSDWDRE
+KLQERLAKLAGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+SVLDTDADVQALTGDAASGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFNA
+KTGVYGDLIADGVIDPVKVTRSALANAASIAALVLTTETLVADKPEDEDEHQH*
+>NZ_CP040019.1_2557
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIE
+KAVDAVTAELLSASREIETKEQIAATASISAADKQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENATLDLLGTARKVVITKDETTIVEGAGDAEQIAGRVAQIRAEIENTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFGGLTLEGDEATGANIVKVAIEAPLKQIAFNAGMEPGVVADKVKTLQDGHGLNAAT
+GEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM*
+>NZ_CP083691.1_1126
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIARDVE
+LEDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPNEVKKGIE
+TAVAAVEKRLQENARPVEGKEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGYLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVLQA
+NKPLFVIAEDVEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGATVVSP
+DLGMKLEQADLDVLGSARRVTVTKDATTIVDGGGEAADVEARVSQIKAEVAATDSDWDRE
+KLQERLAKLAGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+SVLDEDAEVTALTGDAATGVEIVRKALKEPLRWIAQNAGEDGYVVVSKVAEMKPNEGFNA
+KTGVYGDLIADGVIDPVKVTRSALANAASIAALVLTTETLVADKVEDEDEHQH*
+>NZ_CP083691.1_2412
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPISLKRGIE
+KAVEAVTSELLSAAREIETKDQIAATASISAADAQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISTVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENASLDLLGTARKVVITKDETTIVEGAGDADQIAGRVAQIRSEIANTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFEGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKSLESGHGLNAAT
+GEYVDLMAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM*
+>NZ_CP097650.1_343
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIE
+KAVEAVTSELLSASREIETKDQIAATASISAADKQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENATLDLLGTARKVVVTKDETTIVEGGGDAEQIAGRVAQIRSEIENTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFGGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKTLDDGHGLNAAT
+GEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM*
+>NZ_CP097650.1_1537
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVE
+LEDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKKGIE
+VAVAAVERRLQENARPVEGQEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVLQA
+NKPLFVIAEDVEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGAQVVSP
+DLGMKLEQADLDVLGSARRITVTKDETTIVDGGGAAEDVEARVAQIKAEAAATDSDWDRE
+KLQERLAKLSGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+TVLDTDADVQALTGDAAVGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFNA
+KTGVYGDLIADGVIDPVKVTRSALANAASIAALVLTTETLVADKPADEDEAGHQH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000016.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000016.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed8b1aea023a90f33690f217e7dccfbf2c7c3c0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000016.fa
@@ -0,0 +1,90 @@
+>NZ_CP042169.1_957
+MTPTPSRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGVAP
+DHPRIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALDVP
+GVELAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLPT
+EIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEAS
+EKAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEQFLDEDGDGRVDGLRM
+RRMELDGSGGVRPTGETVDYPVQAVYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDADG
+APVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWRAQEPSEESVIELLESRG
+VPYTTWAGWHALDEHEKSLGVQATEAGPVARERVKVVDREEMTRISREGVLLGAGG*
+>NZ_CP042169.1_1718
+MTVRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGVAPDHP
+RIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAVLDVPGVE
+LAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLPTEIP
+DNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEASEKA
+IEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGLRMRRM
+ELDGSGGVRPTGETVDYPVQAIYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDADGAPV
+PGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLESREVPY
+TTWAGWHALDEHEKSLGAQATEAGPVARERVKVVDREEMTRISRDGASVPTA*
+>NZ_CP033200.1_681
+MTLTPSSSRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALD
+VPGVELAGSFGGADFAAWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDA
+ASEKAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTDETVDYPVQAIYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDA
+DGAPVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLES
+REVPYTTWAGWHALDEHEKSLGAQATEAGPVARERVKVVDREEMTRISRESVLLGAGG*
+>NZ_CP033200.1_1436
+MTVRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGVAPDHP
+RIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAVLDVPGVE
+LAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLPTEIP
+DNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEASEKA
+IEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGLRMRRM
+ELDGSGGVRPTGETVDYPVQAIYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDADGAPV
+PGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLESREVPY
+TTWAGWHALDEHEKSLGAQATEAGPVARERVKVVDREEMTRISRDGASVPTA*
+>NZ_CP040019.1_1088
+MTERPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGVAPDHP
+RIKGIVNALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAWLDVPGVE
+LAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLPTEIP
+DNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEASEKA
+IEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGLRMRRM
+ELDGAGGVRPTDETVDYPVQAVYRAVGYFGSPLDGVEFDAARGVVPNDEGRVLDADGVPV
+PGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDVDGLWTAQDPAEESVIDLLEAREVPY
+TTWEGWQALDAHEKSLGAQATEAGPVERERVKVVDREEMTRISREGAWAPTA*
+>NZ_CP040019.1_1864
+MTLTPSSPKPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVNALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAWLD
+VPGVELAGSYGGADFASWYDGHPDVPRHWPLDATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDE
+ASEKAIEENNQVRTMVGTLTNWLMEQEDREQSASRRLHLHFLQAPEQFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTGETVDYPVQAVYRAVGYFGSPLDGVEFDAARGVVPNDEGRVLDA
+DGVPVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLES
+REVRYTTWAGWLALDDHEKALGVQATEAGPVERERVKVVDREEMTRISRESVLLGAGG*
+>NZ_CP083691.1_1013
+MTERPDRPLRIAVVGAGPAGVYTADILTKEERDFQVSIDLFDRYPAPFGLIRYGVAPDHP
+RIKGIVTALHKVMDRGDIRFIGNVDVGTTVSLEDLRRLYDVVVFTTGAVRDAALDVPGVE
+LEGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLVTEIP
+DNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEASEKA
+IEENNQVRTMVGTLTNWLMEQEDRTEQASRRLHLHFLQAPEEFLDADGDGRVDGLRMRRM
+ELDGQGGITPTDETVDYDVQAVYRAVGYFGSPVPGVEFDDVRGVIPNAEGRVLDAAGHPV
+PGLYTSGWIKRGPVGLIGSTKGDSLETIKHLIEDEPGLYTAEDPSEQAVLDLLAERGVDY
+TTWEGWHALDAHEKALGAEATQAGPVERERVKVVDRAEMTRISRAGTGLA*
+>NZ_CP083691.1_1808
+MTPTPSSSRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVNALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALD
+VPGVELAGSFGGADFAAWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDE
+ASEQAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEQFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTGETVDYPVQAVYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDA
+DGAPVPGLYASGWIKRGPVGLIGHTKGDSLETITHLIEDEPGLWRAQEPSEESVIELLES
+REVPYTTWAGWHALDDHEKSLGAQATEAGPVARERVKVVDREEMTRISRKSILLGAGG*
+>NZ_CP097650.1_899
+MTLTPSSSRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVNALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALD
+VPGVELAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDE
+ASEKAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTDETVDYPVQAIYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDA
+DGAPVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLES
+REVPYTTWAGWHALDEHEKSLGAQATEAGPVARERVKVVDREEMTRISRESVLLGAEG*
+>NZ_CP097650.1_1647
+MTARPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGVAPDHP
+RIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALDVPGVE
+LAGSFGGADFAAWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLPTEIP
+DNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEASEKA
+IEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGLRMRRM
+ELDGSGGVRPTGETVDYPVQAVYRAVGYFGSPVEGVEFDEVRGVIPNAQGRVLDADGAPV
+PGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLESREVPY
+TTWAGWHALDDHEKSLGAQATEAGPVARERVKVVDREEMTRISRDGASVPTA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000019.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000019.fa
new file mode 100644
index 0000000000000000000000000000000000000000..392cd24fea37ce2d76b080708989cd9f52bf9113
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000019.fa
@@ -0,0 +1,27 @@
+>NZ_CP033200.1_329
+MPAPYPQEFRDDVVRVARSREEGVTLAQIAKDFGTHEMTLSKWMRQADVEDGAKPGTTKA
+ESAENRELKKRIRLLEQENEVLRRAAAYLSQANLPGKGSTRS*
+>NZ_CP033200.1_1722
+MPAPYPKEFRDDVVRVAQNREPGTHLKDIAKDFGISESCLTNWIRQADIEAGNIPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK*
+>NZ_CP040019.1_2231
+MPAPYPQEFRDEVVRVAQNREPGTQLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK*
+>NZ_CP040019.1_2450
+MPAPYPQEFRDDVVRVAQNREPGTHLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK*
+>NZ_CP040019.1_2566
+MPAPYPQEFRDDVVRVAQNREPGTHLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK*
+>NZ_CP040019.1_2583
+MPAPYPQEFRDDVVRVAQNREPGTQLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK*
+>NZ_CP083691.1_1846
+MSKPYPKEFRDDVVRIARNREPGVELSQIAKDFGIHFTTLYAWMKKADIEDGDRPGTTEA
+QYAELREAKRRIRTLEQEVEVLRRAAAYLSQAHLPGK*
+>NZ_CP097650.1_867
+MSKPYPKEFRDDVVRVARNRGPGVELSQIAKDSGIHVTTLYAWMKKADIEDGDRPGTTEA
+QSAELREAKRRIRTLEQEVEVLRRAAAYLSQAHPPGK*
+>NZ_CP097650.1_1494
+MPGPCPREFREDVVAVARSRESGVTIKQIATDFGVSEATLQNWLRQADVEDGNRPGQTAA
+DAAEARELKKRIRLLEQENEVLRRAAAYLSQANLRLGGSPK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000021.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000021.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a0db6414d3e4ebfc360aea11356877f32b54cf0b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000021.fa
@@ -0,0 +1,48 @@
+>NZ_CP042169.1_548
+MHAGWSLGAAAGAGLGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPVDSASAR
+GAADQSPAPSETSAPPAPAAQALPRRAAVAVLVPAVVIAMAGFGVEEFGNAWATLFLITE
+RGLDPAAAVLGASTLLGAQFVGRLAGDRTLAVLGRRGALTAGLGAVVVGLGLALAPLPGP
+VAVPAAFAGLALAGLGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGA
+LAGAVGLAPALTVFLGLAAVGTVLAARLPAAP*
+>NZ_CP042169.1_549
+MSEAPPHLPTADDGVARARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDPAAFGLL
+VIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAGAGHGAG
+TAAAWLLWVFAGLVLASGVLDAVVDTAQNAQGLQV*
+>NZ_CP033200.1_281
+MHAGWSLGAAAGAGLGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPVDSASAR
+GAADQSPAPSETSTPPAPAAQALPRRAAVAVLVPAVVIAMAGFGVEEFGNAWATLFLITE
+RGLDPAAAVLGASTLLGAQFVGRLAGDRTLAALGRRGALTAGLGAVVVGLGLALAPLPEP
+VAVPAAFAGLALAGLGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGA
+LAGAVGLAPALTVFLGLAAVGAVLAARLPAAP*
+>NZ_CP033200.1_282
+MSEAPPHLPTADDGVARARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDPAAFGLL
+VIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAGAGHGAG
+TAAAWPLWVFAGLVVASGVLDAVVDTAQNAQGLQV*
+>NZ_CP040019.1_2328
+MPSASPSSPAARRARAHPVARRDVVRARWAATLAFLTNGGMLGALIPHYPQAKAAFGLDA
+DAFGLLVVALAAGAAAAGSLPAPVLRRWGSRRVMLAGTVVMAVVVVAAGLVVDLSAPAQG
+RPWAGAVWLFAALLGVAGILDAVVDTAQNAQGLTVQTRLARPVLTSMHAGWSLGAGLGAG
+LGALAVGAGMPAGLHLGLNGAACVAVLVAAGRRFLPDDARPAPDADAPEGTAAPAPGPSP
+RRPARPPPPRPAPPPGWPCSP*
+>NZ_CP040019.1_2329
+MAGFGVEEFGNAWTALFLQSERGLDVAAAGLGASTLLLAQFVGRLVGDRVLHRLGRRRTL
+AGSLAVVVAALVLVLTAPAAPAVFAGLALAGLGCAVVVPTAYALGDEVPGLPPRTGLAVV
+SWLMRVAGIGLSPLVGLLATGLPLPAALAVFPALAVLGLVGTGVVGRRRRRP*
+>NZ_CP083691.1_2204
+MTSAPADTPRIDRRAATRSRWAATAAFFTNGALAAAMIPHYPQAKAAFGLDPAGFGLLVT
+VMTLGAACAGPAGAPILRRAGSRATVLWGSLAIAVVLTGAGLALDLGARSDAAGPWLGAY
+AAAVFASGLCDAVVDTAQNAQGLRAQHALGRPVLTSMHAGWSLGAAVGAALGAAAVGAGV
+PAGLHLGLNGAACVLLLALTLPRFLPDTPDHAPAPALLTADDPGPESEATPASHRHPWLL
+LAPIVVISMAGFSVEEFGNSWTSLFLQAERGLDPATAGLGASTLLGAQFLGRLTGDRVLA
+ALGRTRALTGGLAVVLAGLTVTLLVPTPAAMFTGLALAGLGSAVVVPTAFALADEVPGLP
+AQTGLAVVSWLMRLAGLGLSPLVGLLAGVLPLTAALGAFVVLAALGTVLALTLRAPRLAP
+DFR*
+>NZ_CP097650.1_550
+MSEAPPHLPTADDGFARARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDPAAFGLL
+VIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAGAGHGAG
+TAAAWPLWVFAGLVLASGVLDAVVDTAQNAQGLQVQTRLARPVLTTMHAGWSLGAAAGAG
+LGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPTDSASARDASDQSPAPSETST
+PPAPAAQALPRRAAVAALLPAVVIAMAGFGVEEFGNAWATLFLITERGLDPAAAVLGAST
+LLGAQFVGRLAGDRTLAALGRRGALTAGLGAVVVGLGLALAPLPGPVAVPAAFVGLALAG
+LGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGALAGAVGLAPALTVF
+LGLAAVGAVLAARLPAAP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000024.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000024.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fc3fd2d7d1d4f84499b6d9ae8fb72d2e9aa9a691
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000024.fa
@@ -0,0 +1,101 @@
+>NZ_CP042169.1_2241
+MSSDQRTASAPRHALPPQDGVPAVKVGTRVSRGPGRVTALDGLRGIAVLAVLVFHAWPTF
+LRGGFVGVDMFFVLSGFLITTGLVRGVDAGRGVALGTFWMKRVRRLIPAMLMALVGTTAL
+AWLAVDEFPAGLGRQWFGALTYTSNWVMILEGGDYFNRASPPLFEHLWSLAIEEQFYILW
+PLLLWGLLLLTWPPRSTVNSGRVADRRRILAVAVAAVASAAWMAWGSWHGFEQARLYFGT
+DTHAFGLLFGACVAIGLAHVPRPEHGGPEPRTSATRVAVAWGAVAVLAAGFALVDGGHAS
+TYRGVLAGLSAVVAFIVWHVVQGDRRDSLSRALGNGFLRWWGRRSYAAYLWHWPLLVIMR
+VMVPVDAPGWVEPVAAGAILLLTALIADLSTRLIEEPILHEGFRGAFGRWGAAARRAFTG
+GAGPIGQLAAAATALGLVAVPAAAVAAVVHSPAQTQLEQDIAQAEESLKAAEAAQQAARE
+SRAAEQSKRAEASASASPGSAAPGDAEGSAGATSSPGSSAEPSGLGLGDPAVTRPTYSKE
+QLTAALPPSELGTDVTLIGDSVSLSAAPTLMEELPGMLLEAEVGYQIWDAADELEKLKAD
+GQLSDVVVVALGANGTTHRGDWEKILAAVGEDRLLVLVVPHGPMDWIADVQVQMAAQAKA
+HPDRIVLADWDAAAKQHVTDFSADGVHPRADGQAMYAQLVRLTIEDRLGARR*
+>NZ_CP033200.1_1946
+MSSDQRTAPVPRHALSPQDGVPAVKVGTRVSRGPGRVTALDGLRGIAVLAVLVFHAWPTF
+LRGGFVGVDMFFVLSGFLITTGLVRGVDAGRGVALGTFWMKRVRRLIPAMLMALVGTTAL
+AWLAVDEFPAGLGRQWFGALTYTSNWVMILEGGDYFNRASPPLFEHLWSLAIEEQFYILW
+PLLLWGLLLLTWPPRSTVNSGRVADRRRILAVAVAAVASAAWMAWGSWHGFEQARLYFGT
+DTHAFGLLFGACVAIGLAHVPRPEHGGPEPRTSATRVAVAWGAVAVLAAGFALVDGGHAS
+TYRGVLAGLSAVVAFIVWHVVQGDRRDSLSRALGNGFLRWWGRRSYAAYLWHWPLLVIMR
+VMVPVDAPGWVEPVAAGAILLLTALIADLSTRLIEEPILHEGFTGAFGRWGAAARRAFTG
+GAGPIGRLAAAATALGLVAVPAAAVAAVVHSPAQTQLEQDIAQAEESLKAAQAAQQAARE
+SRAAEQTKRAEASASGAPGSAAPGDAEGSAGATPSPGSSAEPSGLGLGDPAVTRPTYSKE
+QLTAALPPSELGPDVTLIGDSVSLSAAPTLLEQLPGMLLEAEVGYQIWDAADEIEKLKAD
+GQLSDVVVVALGANGTTHRGDWEKILAAVGEDRLLVLVVPHGPMDWIADVQVQMEAQAKA
+HPDRIVLADWDAAAKQHVTDFSADGVHPRADGQAMYAQLVRLTIEDRLGARR*
+>NZ_CP040019.1_423
+MVRRDVWPTIAGVPSLTPSSPVRSAEERTDRGGGSRTRPLVHADRPGIRVSPGPGRIPAL
+DGLRGVAVLAVLVFHAWPALLPGGFVGVDMFFVLSGFLITTGLVRGVDGGRGLRLGPFWM
+RRVRRLVPSMVVALVCCTALAWLAVAEFPAGLGRQWLGALTYTSNWVMILSGSDYFAAAT
+PPLFEHLWSLAIEEQFYVLWPLVVAGLLTLFWPREPTLRGAFRADRARVLTVLALAAASA
+VWMAVGLRGGAPHTRLYFGTDTHAFGLLLGAAVALMLAHTRRPEHGGAVMRNPPVRSAIA
+WGLFAALLAAFVLVDGREDVTYLGVLAGLSLVVTLLLFHVVQGNRQDSFSRAMSGDVLRW
+WGRRSYAAYLWHWPLLVILRTALPVDAPAWVDPVAAGGVLVLTAGIADLSTRWMEEPIVQ
+RGFRGAFAHWRAGLRTATRGIGGKAAAGAAGLALVAVPVAAVAAVVHSPAETALQRQIAE
+AEAALEQARQAQAAARAEASARAEAERAGAAEEAVAKDSQEDAPGAGAGGDAGSAAPTAS
+STPSDTAAPSAGEDPAVEVAADPTASAEPEPTAEPEPEPPLTGDPSVTRPAFTGAELTEP
+MPPSSVGPDVTLLGDSVALSAAPELLAALPGIAVEAEVGFQVRDAAARLAELDAAGMLTD
+VVVVSLGANGNAELGDWDRILAAAGPERLLVLVVPHGPMDWIGPAQQEMAEQAALHPDRV
+VLADWDAASAHVDEWSADGVHPKGNGQGIYARLVRLTVEARLGLR*
+>NZ_CP040019.1_1808
+MAVLSVLVFHAGVTALPGGFVGVDVFFVISGFLITGLLLKEVDRTGRVGLAEFYARRARR
+ILPAALAVIVLTVAAGLLVYPVSEWTRLGSVAVASALSVVNWLFARESTDYFAQEEAASP
+FQHYWSLAVEEQFYLVWPLLLILVTVGVAALRRRGAGDAAPDADAGARRRPSAPVAARRV
+LLASAVIGLASFVHSVSYSASDPGAAYFVTTTRVWELALGAGLAAALVVLPVIRPAVRTV
+LGWAGLGMIAVSLVLITGAMAYPGSVALLPVVGSALVILAGAHEDGSTPGHPARLLATRP
+MQWVGDLSYSLYLVHWPVLTLAAWRFPDGRLPLWLGLILAVVSVGLAWALRRWVEVPAMH
+GSLLAGRRRALTRGGLGMAAVAAAGALVLAAGAALAPARPGEESPVAGARAVMDGQDPMA
+ALAAGMRIVPDPAVAKEDRSPRSAAGASSRTPRPRAWSPRRACWRTASPTRSATSGTAPC
+PTSWTGSTRTSCWSRAPGGRPWRRTPRRRWPRRGGS*
+>NZ_CP083691.1_376
+MTVSTSDHHAARPAPRHAQAALADGPAPRTGLRVSRGPGRITALDGLRGIAVLAVLVFHA
+WPEALPGGFVGVDMFFVLSGFLITTGLVRGVDAGKGLRLPSFWMRRIRRLVPAMVVALVA
+CTALAWLAVAEFPTGLGRQWLGALTYTSNWLMIFDGGDYFDRASPPLFEHLWSLAIEEQF
+YVLWPLIIGGLCLVVRPKRDTYASGRVADRRRILVVLVVALASAAGMVLGSLGGADQTRL
+YFGTDTHAFGLLLGACVSMGLAHVPRPEHGGPELRTGPARTAAAWLAVVVLFTGFALVDG
+TQDATYRGVLVGLAAVVAFIVWHVAQGDRRDSLSRALGNPFLRWWGRRSYAAYLWHWPLL
+VIMRIVVPVDAPSWAEPVAAGAVLLLTAGIADLSSRYFEEPILQKGFRGAFGGWGDAARR
+AFGGAFGPGGRLAAGATALALVAVPVAAVAAVAHSPAQTQLQEDIQAAEQSLQDAQAQQQ
+AQLEARRSAQAEKSKDAEAGGAEATGSAGASASPSGSTLGDPQVTRPEFTQEELTASLPP
+SDVGSRTTLIGDSVALSAAPALLEEMPGIVVDAKVGFQIWDAADKIRAMDREGTLGDVVV
+LSLGANGTAGRGDWDKIRQAVGPDRLLVVVVPHGPMSWIEDAQRKAVEQAEAHPDQVVLA
+DWEAASTYVPGWSADGVHPGHEGQGIYAQLIRLTVEERLGLR*
+>NZ_CP083691.1_2385
+MPRPVDTKASYFPGLDGLRALAVGLVVAYHLGVPGTDGGLLGVGVFFTLSGYLITSLLLR
+RHERHGDLDLKNFWIRRFRRLLPAVVLVLIAVLAATALVSPDLLGARLGQSVAALLYVAN
+WHTILSGRSYFDQAEGAGPLDHLWSLAVEEQFYLVWPLVLLGLLALTRRLGPDARRRVLA
+AATLVLGAVSFVLLAVFADPAGDSTRAYEGTDTRAGGLLWGAVLAFLWRPDRVARLTGRA
+SRVVVDLVGVLGLAGVLALSATTGQEDAALYTWGLAALTVATCAALLPLVHPGSWVARVL
+GIPPLQWIGARSYGIYLWHMPVVAFLPDRVLFGQPVLRGLLIVALTLVLAALSWRLVEDP
+IRRHGLVAALARARGVLGVGAVAVLASGALVLTAALPQTSAQEIAAQEPAAPAGDAVAHP
+ALDGRTSCTSVLHVGDSTSLASGNTDRTRIADPAQRITGRYEAVGVETVVEDIAGGRSTR
+EHIDGSADLNAPEAVAAGVSRLDAGGCVVVNVGLNDAATMTKDDAWDQAAARIDAVVDAA
+DGRPVLWVGPAIMPWSSRPYYEPAGAERFTRALVDATARHPDLRVHDWARESRSHPDWYL
+SDDANHNTEAGAVAKARSMAAALTAAFPAGRPASAEKVVLGE*
+>NZ_CP097650.1_564
+MTNPPVYPRGYRPRHAADGPDSTPAAARRRADWRPEIQGLRAVAVLLVVVFHIFTDRVSG
+GVDIFLFISAFFLTGSFTRKMESGRPLAVGRYWLHVFTRLMPMAVLTILTTLVAVATVYP
+LADRASWRTEALASALYVENWALAFNAVDYYAADNTSLSPFQHFWSLSVQGQVFILWPLL
+FLVSALVARRTGARPRAVLTTAFASVFVVSLLWSVTQTSQNQAFTYFDTRARLWEFALGS
+LLALALPFLHLGRRTRVFLGWAGLASMIAVGVVVDVQGAFPGWIALWPLMSATAVIVAGT
+SGSHFGVDRILASRPLTRLGDSAYALYLVHWPLLITYSVLTGSQKPGAAAGVALVLVSLG
+TAILLSARVERPLRAWGWPQTAAWRSAVVLGACAALVVAPVTLWRGAEAAESARVLEAAD
+RNNPGAAVLRPDYEPAGDPGAPVLPVVEGRYPFPEYPEECDPALEAQLTEVGAESCHVLV
+PQADPAGVVLMAGNSHVMQWSPALRRLGEERRLEVVSYTRGSCLVAPMEEQVDDSPKCPD
+FLADLNLVVEHVRPDVVFMQGTRSTYEDEEMLTPGMTGRMEEIAGTGAHVLALRDNPRFA
+AGSPTTCGTMHGVDAVTCRWTHAVLDPNTSPLAGLADAHPRIAQVQLNDMICPDRQCQPT
+VGNVHVYWDDNHLTPTYVETLAPVFIERVLAALEHDGMRLGR*
+>NZ_CP097650.1_2184
+MPAVKVGTRVSRGPGRVTALDGLRGIAVLAVLVFHAWPTFLRGGFVGVDMFFVLSGFLIT
+TGLVRGVDAGRGVALGTFWMKRVRRLIPAMLMALVGTTALAWLAVDEFPAGLGRQWFGAL
+TYTSNWVMILEGGDYFNRASPPLFEHLWSLAIEEQFYILWPLLLWGLLLLTWPPRSTVNS
+GRVADRRRILAVAVAAVASAAWMAWGSWHGFEQARLYFGTDTHAFGLLFGACVAIGLAHV
+PRPEHGGPEPRTSATRVAVAWGAVAVLAAGFALVDGGHASTYRGVLAGLSAVVAFIVWHV
+VQGDRRDSLSRALGNGFLRWWGRRSYAAYLWHWPLLVIMRVMVPVDAPGWVEPVAAGAIL
+LLTALIADLSTRLIEEPILHEGFRGAFGRWGAAARRAFTGGAGPIGRLAAAATALGLVAV
+PAAAVAAVVHSPAQTQLEQDIAQAEESLKAAQAAQQAARESRAAEQSKRAEASASASPGS
+AAPGDAEGSAGATSSPGSSAEPSGLGLGDPAVTRPTYSKEQLTAALPPSELGPDVTLIGD
+SVSLSAAPTLLEQLPGMLLEAEVGYQIWDAADEIEKLKADGQLSDVVVVALGANGTTHRG
+DWEKILAAVGEDRLLVLVVPHGPMDWIADVQVQMEAQAKAHPDRIVLADWDAAAKQHVTD
+FSADGVHPRADGQAMYAQLVRLTIEDRLGTRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000025.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000025.fa
new file mode 100644
index 0000000000000000000000000000000000000000..78ca9190772d74527b69df8b35b857ba0bd334ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000025.fa
@@ -0,0 +1,22 @@
+>NZ_CP042169.1_96
+MNFALDGRNYEIDLSKEHAAELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNAKRK*
+>NZ_CP033200.1_2065
+MNFALDGRNYEIDLSKEHAAELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNAKRK*
+>NZ_CP040019.1_279
+MNFALDGRNYEIDLSKEHADELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNARRK*
+>NZ_CP083691.1_601
+MATITTIADDFDNSTPAETTYFSVNGKEYAIDLNEEHRRELEDVLEEVAERLSKYTAVAR
+PLGKSSAPARKSSKSPSSRSGASYDAGAVRSWAEENGYKVADRGRISADVLEAYNASKKG
+*
+>NZ_CP083691.1_654
+MAIISTVADDFDGSTPAEAVRFSVAGRDYEIDLSKEHRAELDAIMAEFQDRLKKFTDVAR
+PAGRAASTGRTPARRSSGSGVDASTVRLWAVENGFDVKDRGRIPVEVMDAYRNRGKKG*
+>NZ_CP097650.1_91
+MNFALDGRNYEIDLSKEHAAELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNAKRK*
+>NZ_CP097650.1_1959
+MAIISTVADDFDGSTPAEAVRFSVAGRDYEIDLSKEHRAELDAIMAEFQDRLKKFTDVAR
+PAGRAASTGRTPARRSSGSGVDASTVRLWAVENGFDVKDRGRIPVEVMDAYRNRGKKG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000031.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000031.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bec27e643bf4660534bbd3479661423cb6f495f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000031.fa
@@ -0,0 +1,42 @@
+>NZ_CP042169.1_237
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEALEVAATIASKSKPASWMAKEAVNAAFETTLAQGIAFERRVFHA
+AFATADQKEGMDAFTAKREAGWQHR*
+>NZ_CP033200.1_85
+MSTGLHIETVDRIGIIRLDRPAELNALTFATVEEIAAQVQRWEVDGETDGVVITGSGQKA
+FAAGADIRELQHKSVQEMTARGMQHAMTALRESSLISVAAVNGLALGGGFELALSCDIRL
+ATPQASFGLPELGLGIIPGAGGTQLLTRYTNASVASYHILTGQPISADRAHQLGLVSELH
+EAEDLMAAAMEVIGTIASKGPLARQLAKRAIHGAAHAGMDSGLEIELLAQAAIFGTQERE
+EGLNAFLERRTPSFIPRPRPRKD*
+>NZ_CP033200.1_89
+MTDRIRTSVEQGVCTITLNRPGALNALENTMIATIVAELERAGADPDVRAILLRGEGKAF
+CAGDDLVDMGTEEHPESPDLVERYSRGYPAIVERMLTLEKPIVASVRRYALGAGLEMALA
+ADLIVAEPQAKLGLPFVLRGIAAGTSLLPKRAPVQLVQRMLYLGEMITAEDAHRMGVVGH
+LAEDEDVDELALATARRLAVGATRAIGLMKTALRTSETLSARDALAVQVGATAASVLTED
+FTEGKVAFTQKRDPEFGGR*
+>NZ_CP033200.1_2205
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEALEVAATIASKSKPASWMAKEAVNAAFETTLAQGIAFERRVFHS
+AFATADQKEGMDAFTAKREAGWQHR*
+>NZ_CP040019.1_116
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEAQEVAAAIASKSKPAAWMAKETVNAAFETTLAQGIAFERRVFHS
+AFATTDQKEGMDAFANKREAGWQHR*
+>NZ_CP083691.1_85
+MNEQNRTEAAEAEQPVIVGRDGRVGRIQLNRPKALNALNAATMEAVVAAAVEMDADPEVG
+AILLLGSAKAFAAGADIKEMKDKDAADMYAADWFRRWEDLARLRTPIVACVQGYALGGGC
+ELAMMADVLVAGRSAKFGQPEITLGVLPGMGGSQRLTKSVGKAKAMDMVLTGRMVEAEEA
+ERMGLVSRLVEDEDAVATAEEVAATIAGFSKPVAQMNKEVVLNAFETPLTQGLVFERRVF
+HGVFSSEDQAEGMAAFAEKRSPVWKHR*
+>NZ_CP097650.1_237
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDLEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEAKEVAAAIASKSKPAAWMAKETVNAAFETTLAQGIAFERRVFHS
+AFATADQKEGMDAFTAKREAGWRHR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000036.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000036.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f6c92540aa2f1b49b6d6f047c2b5fdbfabd7b124
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000036.fa
@@ -0,0 +1,74 @@
+>NZ_CP042169.1_809
+MGWEHEDPRFDARATGFANEPHRFGYIVEIDP*
+>NZ_CP042169.1_810
+MGRFKHEGANVIVADDGHVVAYMGDDERFDYLYKFVSKDIYRKNDRRHNMTLLNEGDLYV
+ARFSGTSDGEIDGSGRVPADGTFDGSGRWIPLVQGGRSTVEGMAVDQVLVFTRLAADRVG
+ATKMDRCEDVEPSPGSGKIYVACTNNSQRGVDGQATADEANPRTENRDGHIVEITEHRGD
+HTSTRFTWDLLMLCGDPSQGDATYFGGFPVDQVSPISCPDNLAFDTDGNLWISTDGAPDG
+IGYNDGLFKVAVEGRNRGQVAQFLSVPRDAETCGPVIHDDEAMVFVAVQHPGEEGSYTDI
+RSAFPDYVPSEARPGDGEVRGPRPSIVQVYRT*
+>NZ_CP042169.1_1725
+MLKRLLPMAGHTRGNRSAVTCELKCGNACAHPVPNTSANPTFQQIAETAISRRSALVGGT
+GLAAAVVIGSQVAQAPEALADNGRRPTGGGKLPFEPIAPVTRTVDTMTVPEGYDWGTVIR
+WGDPLFADSPEFDIEHQTGASQAAQFGYNNDYLNIITDGGNDRSGYLVSNHEYTNENIMF
+SPEYIASNFEDVVNVGLQAHGLSIVELKCAKRGAQWEYVRGGRRNRRITGTTEFEVRGPA
+AGHALLTTVEDPTGTRVLGTLNNCAGGTTPWGTVLSGEENFNQYFKGRGTAEEKRYGIST
+SATRRGWEKVHDRFDLTKPGYENEANRFGWVVEIDPEDPTSTPVKHTLLGRFKHEAGTAV
+ISPSGHAVVYSGDDERHDYLYKFVSAEKVREGDKKHNMRLMDKGTLYVAKFSGDSPAAQI
+DGRGTLPSDGAFDGSGEWIALADEKTSFVPGMSLAEVLVYTRLAADKMGATKMDRPEDVE
+TNPVTGKVYAALTNNTKRTAVDEANPVIGNRDGHVIEITERGGDHTSTTFTWVILLLAGD
+PAVSSSAYFAGYPKEKVSPISCPDNLAFDSEGNLWISTDGQPGTIGYADALHKVTLDGAE
+RGRVQQFLAVPRDAETCGPVIHDRDNSVFVNVQHPGEDGTWGAHTSYFPDFLSPTGPVQV
+GDKVAAPRPSVVQVFNATGNNGVGKGAGKEKGNKGKGNGNGNGKGNGNGKGPKG*
+>NZ_CP033200.1_1443
+MLKRLLPMAGHTRGNRSAVTCELKCGNACAHPVPNTSANPTFQQIAETAISRRSALVGGT
+GLAAAVVIGSQVAQAPEALADNGRRPTGGGKLPFEPIAPVSRTVDTMTVPEGYDWGTVIR
+WGDPLFADSPEFDIEHQTGASQAAQFGYNNDYLNIITDGGNDRSGYLVSNHEYTNENIMF
+SPEYIASNFEDVVNVGLQAHGLSIVDLKRAKRGAPWEYVRGGRRNRRITGTTEFEVRGPA
+AGHALLKTVEDPTGTRVLGTLNNCAGGTTPWGTVLSGEENFNQYFKGRGTAEEKRYGISA
+AATSRGWEKVHDRFDLTKPGYENEANRFGWVVEIDPEDPTSTPVKHTLLGRFKHEAGTAV
+ISPSGHAVVYSGDDERHDYLYKFVSAEKVREGDKKHNMRLMDKGTLYVAKFSGDSPAAQI
+DGRGTLPSDGAFDGSGEWIALADEKTSFVPGMSLAEVLVYTRLAADKMGATKMDRPEDVE
+TNPVTGKVYAALTNNTKRTAVDEANPVIGNRDGHVIEITERGGDHTSTTFTWVILLLAGD
+PAVSSSAYFAGYPKEKVSPISCPDNLAFDSEGNLWISTDGQPGTIGYADALHKVTLDGAE
+RGRVQQFLAVPRDAETCGPVIHDRDNSVFVNVQHPGEDGTWGAHTSSFPDFLSPTGPVQV
+GDKVAAPRPCVVQVFNATGNNGIGKGAGKEKGNKGKGNGNGNGKGNGKGNGNGKGPKG*
+>NZ_CP040019.1_1081
+MLKRLLPMAGHTRGNRSAVTCALKCGNACSHPMPNTSANTTFQEIAETAISRRAALGVGG
+GLAAAVVIGAQVAQAPEALADNGAAPRGGGKLDYRAIAPVPRTVDTVTVPEGYDWGTVIR
+WGDPLFADSEEFDILHQTGASQAGQFGYNNDYLNIISDGGNDRSGYLVSNHEYTNEYIMF
+PPAYIASNFTDVVDAAIEAHGLSIVDLKRAKQGAKWEYVRGGRRNRRITGTTPFTVTGPA
+AGHALLKTVEDPTGTRVLGTLNNCAGGTTPWGTVLSGEENFNQYFKGRGTAEEKRYGIGT
+GTTERRWEEVHDRFDLTAPGYENEANRFGWIVEIDPEDPASTPVKRTLLGRFKHEAGTAV
+VAPSGQAVVYSGDDERHDYLYKFVSAEKVVEGDKKHNMTLLDEGTLYVARFTGDSPASEI
+DGRGTLPSDGEFDGSGEWIALTTDKKSFVPGMSVAEVLVYTRLAADKMGATKMDRPEDVE
+TNPVNGKVYMALTNNTRRTAVDEANPVVGNRDGHVIELTERGGDHASTRFDWVILLLAGD
+PAVSSSVYFSGFPQEKVSPISCPDNVAFDSAGNLWISTDGQPGAIGFGDALHKVTLDGPE
+RGRVEQFLSVPRDAETCGPVVHDRDNSVFVNVQHPGENGMWGAQTSYFPDYLDPAGPVQV
+GDKVAAPRPSVVQVFDVTGNNGVGKGSGKDKGGKGKGNKGGKGKGPKA*
+>NZ_CP083691.1_1004
+MLKRLLPMAGHTRGNRSAVTCELKCGNACSHPIPNTSANETFHSVAERAISRRAALGVGG
+GLAAAVVIGANVAHAPEALADNGLRPAGGGKLDFTAIQPVQRTVDTMTVPEGYDWGTIIR
+WGDPLFADSEEFDIEHQTGASAAGQFGYNNDYLNIISDGGNHRRGYLVSNHEYTNENIMF
+SPEYIASNPEDVVNAGIESHGLSVVELERRKAGAKWEYVRGGRRNRRITGTTPFRVTGPA
+AGHDLLKTVEDPTGTRVLGTLNNCSGGTTPWGTVLSGEENFNQYFKGRGTAEEKRYGIST
+SATQRGWERFHDRFDLTKAGYENEAHRFGWVVEIDPEDPTSTPVKHTLLGRFKHEAGTAI
+ISESGHAVVYSGDDERHDYLYKFVSSKKVIEGNKKHNMTLMDEGTLYVAKFTGDSPASEI
+DGKGTLPSDGAFDGSGEWIALASHKKSYVPGMSLAEVLVFTRIAADKMGATKMDRPEDVE
+TNPVNGKVYAALTNNTKRTAVDETNPVIGNRDGHVLEITEKCGDHTSTSFNWVILLLAGD
+PKVSSSAYFAGYPKELVSPISCPDNVAFDSEGNLWISTDGQPGTIGYADALHKVTLDGPE
+RGRVQQFLAVPRDAETCGPVIHDRDNSVFVNVQHPGEDGNWGAHTSYFPDFLSPNGPVQV
+GDKVAAPRPSVVQVFNATGNNGIGKGSGNKKGNHGKGRGNSAFGHAQGHGPKK*
+>NZ_CP097650.1_1654
+MLKRLLPMAGHTRGNRSAVTCELKCGNACAHPVPNTSANPTFQQIAETAISRRSALVGGT
+GLAAAVVIGSQVAQAPEALADNGRRPTGGGKLPFEPIAPVTRTVDTMTVPEGYDWGTVIR
+WGDPLFADSPEFDIEHQTGASQAAQFGYNNDYLNIITDGGNDRSGYLVSNHEYTNENIMF
+SPEYIASNFEDVVNVGLQAHGLSIVELKRAKRGAPWEYVRGGRRNRRITGTTEFEVRGPA
+AGHALLTTVEDPTGTRVLGTLNNCAGGTTPWGTVLSGEENFNQYFKGRGTAEEKRYGIST
+SATRRGWEKVHDRFDLTKPGYENEANRFGWVVEIDPEDPTSTPVKHTLLGRFKHEAGTAV
+ISPSGHAVVYSGDDERHDYLYKFVSAEKVRDGDKKHNMRLMDKGTLYVARFSGDSPAAQI
+DGKGTLPSDGAFDGSGEWIALADEKTSFVPGMSLAEVLVYTRLAADKMGATKMDRPEDVE
+TNPVTGKVYAALTNNTKRTAVDEANPVIGNRDGHVIEITERGGDHTSTTFTWVILLLAGD
+PAVSSSAYFAGYPKEKVSPISCPDNLAFDSEGNLWISTDGQPGTIGYADALHKVTLDGAE
+RGRVQQFLAVPRDAETCGPVIHDRDNSVFVNVQHPGEDGTWGAHTSYFPDFLSPTGPVQV
+GDKVAAPRPCVVQVFNATGNNGIGKGAGKEKGNKGKGNGNGNGKGNGKGNGNGKGPKG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000039.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000039.fa
new file mode 100644
index 0000000000000000000000000000000000000000..14712a2d227bd7c9a1ac40ac915b94a85c15c2ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000039.fa
@@ -0,0 +1,48 @@
+>NZ_CP042169.1_1138
+MSSFETPQPPTARRRRRLLPLLSLGAAGLMLATACATGDDGADQPHSDTASASTSAAPER
+AAVGEGQGEPDALTGVTFTEGDGGAPTVEIDGEIDTDQPTTRVLTAGEGEQVQEGDVLKM
+SIAVVDPASGEVVAENFSGEPEAVPVDDQLKSMNPEIHEMLVGSGAGTIVAAYSPEYDVS
+VPQTESASPSASPSTQTQPAQLFVYKIDAILPKQAEGEEVTERDERLPDVTVDEQSGRPS
+IAKPDGEAPQELVVQPLIEGEGHEVGADDTVTVQYEGVTWSDGEVFDSSWETGQAITFSL
+NRVIEGWKEGLAGQKVGSRVLLSIPAEKAYGEQGSPPDIGENEPLLFVVDILDAQASATP
+SAN*
+>NZ_CP033200.1_867
+MSSFETPQPPTARRRRRLLPLLSLGAAGLMLATACATGDDGADQPHSDTASASTSAAPER
+AAVGEGQGEPDALTGVTFTEGDGGAPTVEIDGEIDTDQPTTRVLTAGEGEQVQEGDVLKM
+SIAVVDPASGEVVAENFSGEPEAVPVDDQLKSMNPEIHEMLVGSGAGTIVAAYSPEYDVP
+VPQTESASPSASPSTQTQPAQLFVYKIDAILPKQAEGEEVTERDERLPDVTVDEQSGRPS
+IAKPDGEAPQELVVQSLIEGEGREVGADDTVTVQYEGVTWSDGEVFDSSWETGQAITFSL
+NQVIEGWKEGLAGQKVGSRVLLSIPAEKAYGEQGSPPAIGENEPLLFVVDILDAQAPATE
+SAN*
+>NZ_CP040019.1_1681
+MTDGTPEIGDAEGEAPSEMVVQPLIRGEGPEVGPDDSVTVNYVGETWSEGTRFDSSWERG
+APISFSLNQVIPGWKEGLAGQPVGSRVLLSIPAEKAYGEQGSPPDIGPNEPLLFVVDILD
+AQAPSTPPTN*
+>NZ_CP040019.1_1682
+MSSFQTPETTTPRRRRRLLPLVSLGVAGLFLATACASGQDDTPEPQEDAASASQSAAPER
+AAVGEGQGEPDALEGLSFSEGEDGAPSVEVDGELATDQPTTRVLTAGEGDQVKEGDVLKM
+SIAVVDPASGDVLAENFTGDPESVPVDQQLKSMNPEMHDLLVRNGVGSVVAAYSPEREVP
+APPADGASPSASPPPRPSPPSSSCTRSSRSCPRRPRARRSPSATSGCPRSP*
+>NZ_CP083691.1_301
+MRPLLPLALTVLMLSAGLTGCAPSSPLDSVQVEEVTGQAQGRSVKFQTPVAVEEVSIRQL
+RAGTGAELDAGDAIVLKMDLFKGSDGTPIEAPFAGGPGQVIALDDQFKAQVPELHEALLQ
+AQEGTMLAYSSPQTAGAAGDESTAVEIYEVAQKIPTTIEGKTSPVPDGLPPITEDETGAP
+VVGPPQGQVPDELVAEYLIQGGGEPVQAGDTVIVHHLGMRWADAQVFDSSYQRGAPARFV
+LDNVIKGWQKGLIGKRTGSRVVLSVPVDQAYGTEAELGDNAPFPAGDLLFVIDILTTQPT
+PPVPTP*
+>NZ_CP083691.1_1578
+MNRAPSSAAAPRRRRPRTALSLSLAGLLLATACGAGESSDGSSSPASASSSAAAQGSEAT
+SSSAAPVEYGDPAALDGLTFTVGADGTPSATVGKAIESDKAVVKTLTKGTGATPKAGDVL
+RLSTALLDPATGKVLNENFTTQPEMVAVGSDPASMNPYVHKAVYGAPVGSDVAVYLPAPS
+SSASAPSGTEAAPAQLAVFRVQGVAEQLPQADERLPKVSVDPATGRPSIEKPTGSAPEEL
+VVEPLIQGEGPEVEDTDTVAVQYQGVTWSDGSTFDSSYERGTPATFSLDQVIAGWKEGLA
+GQKVGSRVLISVPSEKAYGAEGTPDGSIGKDEDLLFVVDILAAQPAAASSPAAPSGSTAP
+SGSSSASPSN*
+>NZ_CP097650.1_1087
+MSSFETPQPPTARRRRRLLPLLSLGAAGLMLATACATGDDGADQPHSDTASASTSAAPER
+AAVGEGQGEPDALTGVTFTEGDGGAPTVEIDGEIDTDQPTTRVLTAGEGEQVQEGDVLKM
+SIAVVDPASGEVVAENFSGEPEAVPVDDQLKSMNPEIHEMLVGNGAGTIVAAYSPEYDVS
+VPQTESASPSASPSTQTQPAQLFVYKIDAILPKQAEGEEVTERDERLPDVTVDEESGRPS
+IAKPDGEAPQELVVQPLIEGEGREVGADDTVTVQYEGVTWSDGEVFDSSWETGQAITFSL
+NQVIEGWKEGLAGQKVGSRVLLSIPAEKAYGEQGSPPDIGENEPLLFVVDILDAQASATP
+SAN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000040.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000040.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d935a60b8daaf8c218f389d848df07d8f2a9108a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000040.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1245
+MRKHLKTTVAAGVLGGALVFTGCSTGGDQDQGTPSTTSQHEGHGSSSDSGGMEHPMDGGP
+APEGIETAASPTYPVGTEVTLTADHMEGMDGANAMIAGAYDTYTYAVDFTPSAGGEPVKD
+HKWVVQQEIKDAGDERLADGTEVTLEAEHMEGMKGAKATIASSTEETVYMVDYESDGMTM
+TNHKWVVESELKPAS*
+>NZ_CP042169.1_1578
+MTMRFWTRTVAVTAASLLALTGCATGGEEAATSSSHGGHAGHAMDGGPAPEGIEPAADPA
+HPVGTEVTLMADHMPGMEGAAATVVGAYETTAYSVDYRPTTGGPEVTDHKWVVQEELEDA
+GAERLPDGAAVTLAADHMPGMQGAEGTVHSSTDETVYMVDYESDGMRMRNHKWVVESEIA
+SAG*
+>NZ_CP033200.1_974
+MRKHLKTTVAAGVLGGALVFTGCSTGGDQDQGTPSTTSQHEGHGSSSDSGGMEHPMDGGP
+APEGIETAASPTYPVGTEVTLTADHMEGMDGANAMIAGAYDTYTYAVDFTPSAGGEPVKD
+HKWVVQQEIKDAGDERLADGTEVTLEAEHMEGMKGAKATIASSTEETVYMVDYESDGMTM
+TNHKWVVESELKPAS*
+>NZ_CP040019.1_604
+MKTRRLTLAAVGILASAGLITGCSTADDAGPSASPSSGQSAATSSSQPASESGSASESAS
+GGGHMDHKMDGGPAPEGIAEAASPAHPVGSEITLTADHMPGMDGATARITGAFDTTAYSV
+DYTPTTGGEPVEDHKWVVHEELQDAGDAPLQVGDTAVMEAEHMAGMKGAEATVASVTDET
+VYMVDYTADGMTMTNHKWVVESEIQPKG*
+>NZ_CP083691.1_695
+MQRRLRTGLAAGALGVALVLAGCASGADDNQQTDPSATEEHQGHGGNNAESGDEEMEHPM
+DGGPAPEGIAEASEPTYPVGTEVQLTADHMEGMEGATATISGAFDTYTYSVNYTPAGGGD
+PVTDHKWVVQEEIEDAGDARLADGTEVTLLAEHMEGMEGVKAIIASSTDETVYMVDYETD
+GMKMTNHKWVVESEIQPAS*
+>NZ_CP097650.1_1202
+MRKHLMTTVAAGVLGGALVFTGCSTGGGQDQGTPSTTSQHEGHGSSSDSGGMEHPMDGGP
+APEGIETAASPTYPVGTEVTLTADHMEGMDGANATIAGAYDTYTYAVDFTPSAGGEPVKD
+HKWVVQQEIKDAGDERLADGTEVTLEAEHMEGMKGAKATIASSTEETVYMVDYESDGMTM
+TNHKWVVESELKPAS*
+>NZ_CP097650.1_1507
+MTMRFWTRTVAVTAAGLLALTGCATGGEEVATSSSHGGHAGHAMDGGPAPEGIEPAADPA
+HPVGTEVTLVADHMPGMEGAAATVVGAYETTAYSVDYRPTTGGPEVTDHKWVVQEELEDA
+GAERLPDGAAVTLAADHMPGMQGAEGTVHSSTDETVYMVDYESDGMRMRNHKWVVESEIA
+PAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000043.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000043.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a5327a3dbf328f4f667dd01d55e7fe97864f3060
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000043.fa
@@ -0,0 +1,97 @@
+>NZ_CP042169.1_1490
+MTQNSEHTPASADLDPTVAAIAEDIVTEDAAPVAPEQTFADFGVHPAIVEALEAKGIVHP
+FPIQAMTLPVALGGHDIIGQAKTGTGKTLGFGIPALQRAIGPGEPGWDGLEAKGTAGAPQ
+ALIVAPTRELAVQVAGDLTAAAARRPLRIATIYGGRAYEPQIEELQRGVEIVVGTPGRLI
+DLMRQRHLRLDLVNTVVLDEADEMLDLGFLPDVETLLAAVPAVRQTMLFSATMPGPVVAM
+ARRYMTQPTHIRAADPEDEGLTKKDIRQLVYRAHHMDKDELVARALQAEGRGRTIIFTRT
+KRTAARVADELTARGFAAGALHGDLGQGAREQALRAFRNGKVDILVATDVAARGIDVDDV
+THVFNFQAPEDEKTYVHRVGRTGRAGNKGVAVTLVDWEDMPRWSLIDKALGLGQPEPVET
+YSSSPHLFSDLGIPKGTKGRLPQAKRVLEGLEGETLEDLGGPEAKQRDGGRGRGREGGRS
+RDGERGGREGGRGGRGGRGRGGRSGEGRDAARGGSRGERSERSGRGRGEAPAEQRAEGRG
+RGRGEGRKRTASRSETPAARTSEPVAGVELTEARRAERAEARAEARRRRGGRSRTRRRNG
+EVVDG*
+>NZ_CP033200.1_1211
+MTQNSEHTPAPADVDPTVAEIAEDIVTEDAAPVAPEQTFADFGVHPKIVEALEAKGIVHP
+FPIQAMTLPVALGGHDIIGQAKTGTGKTLGFGIPALQRAIGPGEPGWDGLEAKGTAGAPQ
+ALIVAPTRELAVQVAGDLTAAAARRPLRIATIYGGRAYEPQIEELQRGVEIVVGTPGRLI
+DLMRQRHLRLDLVNTVVLDEADEMLDLGFLPDVETLLAAVPAVRQTMLFSATMPGTVVAM
+ARRYMTQPTHIRAADPEDEGLTKKDIRQLVYRAHHMDKDELVARALQAEGRGRTIIFTRT
+KRTAARVADELTARGFAAGALHGDLGQGAREQALRAFRNGKVDILVATDVAARGIDVDDV
+THVFNFQAPEDEKTYVHRVGRTGRAGNKGVAVTLVDWEDMPRWSLIDKALGLGQPEPVET
+YSSSPHLFSDLDIPKGTKGRLPQAKRVLEGLEGETLEDLGGPEAKQRDGGRGRGREGGRS
+RDGERGGRGRGGRSGEGRDRARGGGRGERTERSPRGRDEARAEGRGRGEAPAEQRAEGRG
+RGRGEGRERTASRPETPAARTPEPVAGVELTEARRAERAEARAEARRRRGGRTRTRRSNG
+EVVDG*
+>NZ_CP040019.1_1364
+MNRAHGASGPSRPPCRRPNRNASRHDPELRAHPRPGRRRPPQVADIAEEIVTEEAVETAP
+EQTFADFGVHPAIVQALEAKGIVHPFPIQAMTLPVALGGHDIIGQAKTGTGKTLGFGIPA
+LQRAIGPGEPGWDKLEAQGSAGAPQALIVAPTRELAVQVAGDLTAAAAQRPLRIATIYGG
+RAYEPQIEELQRGVEVVVGTPGRLIDLMRQRHLRLDLVNTVVLDEADEMLDLGFLPDVET
+LLGAVPAVRQTMLFSATMPGPVVAMARRYMTQPTHIRAADPEDEGLTKKDIRQLVYRAHH
+MDKDELVARALQAEGRGRTIIFTRTKRTAARVADELTARGFAAGALHGDLGQGAREQALR
+AFRNGKVDILVATDVAARGIDVDDVTHVFNFQAPEDEKTYVHRVGRTGRAGNKGVAVTLV
+DWEDMPRWSLIDKALGLGQPEPQETYSSSPHLFADLGIPKGTKGRLPKEKRVLEGLEGEV
+LEDLGGPESAPRGRGGRSRDGERDGGRGGRGGRGERGGRGGRSRDDERGGREGGRGGRGE
+RAGREGGRGRDAEQSSARGEEAGESKGRGRGGERAGREGGRGESTGRGRGGRSGESRTRG
+ESRTEASEARAAQPVAGVERTEARMAERAEARAEARRRRGGRTRTRRRNGEVVDG*
+>NZ_CP040019.1_1474
+MNLPLTDYQAKYYAHELQRSYANDHVGKLAGLLFDAQVEPKPHQIDAALFALQTPFLPGV
+ILADEVGLGKTIEAGIVISQYWAERRRSILIVAPSSLRQQWQQELYEKFLIPSAILDPKS
+KDSLLAAAGGRSAQVLICSYEFALRHETSLLKAWDLVVADEAHRLRNYWTGKTKAAEAVA
+HVVSGAHKTVLLTATPLQNKLEELYGLVSIFDPNYFYSLDAFRERYVKNRDLGGDDDLVE
+RVATVSKRTLRRDADKYIHFTKRLPLTVEFTPSPDEARLYDLVNDYLQRDELFAFAGSQR
+HLSALIIRKRLGSSTYAVASTLENIANRLAEEVAAGQRRDGRGGLVTADFTVDDEITSEE
+LEEAEEIEGAGPASRPSSSPLDESLLEAMRAEVAELRDYAALARSITENQKAVKLGEALD
+LGFERLRELGAPQKAIIFTDSTKTQEYIARSLREAGRGDGLVLFNGSNNGPEQTAIYQAW
+LKANQDGDLITGIAAVDRRKALVDYFRTEGTIMIATEAAAEGINLQFCSMLVNYDLPWNP
+QRVEQRIGRVHRFGQKHNVVVVNFSNKGNIAEQRILELLTNKFQLFSSVFGASDEVLGAI
+EDGLDFEKTISDILTRCRTADELDAAFRELEGQYASEISREMASAKAKVFDNLDPHVQDR
+LKAYDTQSGEVLNKFERLLLAVTRHELDRFATFEGDGRAFVLNESPVQDVPTGRYFFKSQ
+PLENAHQYRYASSLAQYVVDTSKGHETPARELTFSLGQSERVSSAIRALEGTSGELTVNL
+ATFRMKARDEDVSESYMLAGALTDDGQWLDEEYVADILDLACISVGEQPVAIDESRFTPH
+LDARRAELEKEVQGRNSRYYDQQEELLYRNQQDRKAEHEGKIREYRAKEKEARKLARQAD
+DPMEQLRLKKEARKWEQRAEEADEDFRDTRKKLRAEADKYLELIEQSLQGTQETEHLFTI
+RWRITT*
+>NZ_CP083691.1_273
+MKSIDNVNVKLGDDLKAEITAGSKVRIAASAFSIYAFEALREELEGLEELQFIFTDPAFS
+ASSIDGTPRREHRRYFIPPLDIESSLTGTEFEVRLRNRLTQRAIARECADWVRRKVRFRS
+NTSGKGMQPIIGVGDDAAYLPVQDFSTSALGYEAGGALSNVVGKFEGPLEAAGLLTVFDQ
+VWNDPSALEDVTSTVLERIEQVYAENSPRHIYFLILNSIFSDFLADLSEDALPNDRTGYR
+ETKVWRALYDFQRDAAESIIQKLETYNGCILADSVGLGKTFTALAVIQYYEKRNKSVLVL
+CPKKLAENWTTYNNNYVTNPFVEDRFNYDVLAHTDLSRTRGESLGVRLDRINWGNYDLVV
+IDESHNFRNATYGEDRDTRYQRLMEKVIREGVRTKVLMLSATPVNNRFNDLKNQLQLAYE
+GEEENLSQHLNLSTTIDGVFRGAQAAFNEWSKLPAEERTPGRILGMLDFDFFELLDAVTI
+ARSRKQIQRFYDTAAIGAFPTRLPPLSLQEPLSEDKSVPSYNDIFEQLQALNLAVYTPLA
+FVHASRRYKYETGPGEENTDNFRSGRGQAGRETGLKRLMTVNLLKRLESSVHAFRKTLVS
+IESQVDALHRRLESEALGPLRVDAPAVEEDILREDDDVAEALFALPGDLELDLNDVDVLS
+WTSALWHDRETLRELIGEMDKITPERDLKLQRLRRLIRDKATSPLNEGNRKVLVFSAFAD
+TADYLYEQLSPALSAAGLETGIITGGSHSARSTLDGAVDFQTLMTLFSPVSKNRSALMPE
+ETREVDVLIGTDVISEGQNLQDCDFLVNYDIHWNPVRIVQRFGRIDRIGSTNERIQLVNF
+WPDMDLDAYIQLKDRVENRMVMVDVTGTADDNVLTPQQEQDAAYRTAQLKRMREEVVELE
+DTQAGVSITDLGLNEFRSALMAYVREHGDLTRAPRGLHAVVPADPDAGLPAGVIFALHNL
+QADPAMHRGNRLHPYYLVYVGEDGATVLEHTKAKPLLDLLRSAAEKQSVPLADAVRAFNT
+ATAEGTDMAAYSALLTRAIESMVEADEEQDVASLFTAGPTTALTSAIRGLEDFELIAFLA
+VVDTAGTDA*
+>NZ_CP083691.1_1254
+MTENTAAAEAVAPTAPEQTFADFGVQEPIVRALSEKGIVHPFPIQAMTLPVALGGHDIIG
+QAKTGTGKTLGFGIPALQRAVGPDEAGWDTRVAAGAAGAPQALVVAPTRELAVQVAGDLV
+AAAKHRPLRIATIYGGRAYEPQIEELQRGVEVVVGTPGRLIDLLRQKHLRLDAVNTVVLD
+EADEMLDLGFLPDVETLLAAVPEVRQTMLFSATMPGPVIAMARRYMTRPTHIRASDPEDE
+GLTKKDIRQLVYRAHHMDKDELVARALQAEGRGRTIIFTRTKRTAARVAEELTNRGFAAG
+PLHGDLGQGAREQALRAFRNGKVDILVATDVAARGIDVDDVTHVINFQAPEDAKTYVHRV
+GRTGRAGHKGTAVTLVDWEDMPRWSLIDKALGLNQPEPVETYSSSPHLFSDLGIPKGTKG
+RLPKEKRVLAGLDAERLEDLGGPEAKEKAARGGRDERSGSRSGGRGERSGGRGGRAGGGS
+RASREDRPPREDRTPRGERAPRPEKTVKAERAPRAERAPRAEKADRPAAAERSEGASGER
+RRRTRTRRRGGDVIDG*
+>NZ_CP097650.1_1417
+MTQNSEHTPASADLDPTVAAIAEDIVTEDAAPVAPEQTFADFGVHPAIVEALEAKGIVHP
+FPIQAMTLPVALGGHDIIGQAKTGTGKTLGFGIPALQRAIGPGEPGWDGLEAKGTAGAPQ
+ALIVAPTRELAVQVAGDLTAAAARRPLRIATIYGGRAYEPQIEELQRGVEIVVGTPGRLI
+DLMRQRHLRLDLVNTVVLDEADEMLDLGFLPDVETLLAAVPAVRQTMLFSATMPGPVVAM
+ARRYMTQPTHIRAADPEDEGLTKKDIRQLVYRAHHMDKDELVARALQAEGRGRTIIFTRT
+KRTAARVADELTARGFAAGALHGDLGQGAREQALRAFRNGKVDILVATDVAARGIDVDDV
+THVFNFQAPEDEKTYVHRVGRTGRAGNKGVAVTLVDWEDMPRWSLIDKALGLGQPEPVET
+YSSSPHLFSDLGIPKGTKGRLPQAKRVLEGLEGETLEDLGGPEAKQRDGGRGRGRDGGRS
+RDGERGGRGRGGRSGEGRDRARGGGRGERNRGGRSGEGRDDARGGGRGERSGRGRGEAPA
+EQRAEGRGRGRGEGRERTASRSETPAARTSEPVAGVELTEARRAERAEARAEARRRRGGR
+SRTRRRNGEVVDG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000044.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000044.fa
new file mode 100644
index 0000000000000000000000000000000000000000..67ed3e6fccce539025fd48ddca4f9b7ddf38bafa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000044.fa
@@ -0,0 +1,66 @@
+>NZ_CP042169.1_1541
+MPVAPRPSDGAASSVFTPHQQRILAVLLIPIFMSLLAVSSINVALPALQRGLDASDAELQ
+WAISGYTLVFGMVLVPAGRAGDLFGRRRLFMVGLGVFALGALLSGLAPTGVLLVLARLVM
+GVGAGLLNPQVTGFIQSEFSGTSRARAFGALGAVVGVSVAVGPLLSGGLIAWLGGDLGWR
+ATFLVNVPIALGALVVARHWLPRTAPERARRPDLDPVGVVLLAGALVAVMLPFLDRELGP
+WRFVLVPVGIGLAALWTRWEARYARRGRAPMVDLRLFQTRSFACGALLIAIYFTGSTSMF
+VVIAMFMQNGLGYPALHAALIGLPSAVMSSVMSTVAGRVVLRTGRKIVVLGIALALLAVV
+GSIGVAWANREFGLSPWWLLLTLAILGAGQGLVVSPNQTLSLAEVPPRHSGTAGGVLQTG
+QRVGTAVGTAVIVGVFLGVASGADWDGAFMAAFTLVAGCMALALLVALADLRGPRTAAPR
+G*
+>NZ_CP033200.1_1264
+MPVAPRPSDGAASSVFTPHQQRILAVLLIPIFMSLLAVSSINVALPALQRGLDASDAELQ
+WAISGYTLVFGMVLVPAGRAGDLFGRRRLFMVGLGVFALGALLSGLAPTGVLLVLARLVM
+GVGAGLLNPQVTGFIQGEFSGASRARAFGALGAVVGVSVAVGPLLSGGLIAWLGGDLGWR
+ATFLVNVPIALGALIVARQWLPRTAPERARRPDLDPVGVVLLAGALVAVMLPFLDRGLGP
+WRFVLVPVGIGLAALWTRWEARYARRGRAPMVDLRLFQTRSFACGALLIAIYFTGSTSMF
+VVIAMFMQNGLGYPALHAALIGLPSAVMSSVMSTVAGRVVLRTGRKIVVLGIALALLAVV
+GSIGVAWANREFGLSPWWLLLTLAILGAGQGLVVSPNQTLSLAEVPPRHSGTAGGVLQTG
+QRVGTAVGTAVIVGVFLGVASGADWDGAFMAAFTLVAGCMALALLVALADLRGPRTAAPR
+G*
+>NZ_CP083691.1_627
+MLFASFMDLLDVTIVTVAAPHIAADLNASPAQLQWMLAAYTLALGSGLITGGRIGDDYGR
+RRVFLAALAAFAIASAACALAPTAGALIAVRAVQGLAGGFMVPQVFGIIRSSFEPAAMAK
+AFGAYGAVQGLASVAGPLIGGALADADLWGLGWRTIFWINIPIALVALVLGWRVLPDSRA
+AARSRLDGVGALLAAVGVLLVLLPLVQGRDWGWPTWGWALLAAGVLVLAGFLRYENALAR
+RGGEPVLDPDLLRVRPFVAGLAASVLFFGGLASFFLVVSIYLQAGTGRSAWDTGLVILPY
+AIGSMLTSGAGVALAARAGRALLLTGSLTLAASQALLWWLVRDGSTTPDYWPLAGAMFLG
+GLGLGLGAPILVNVVLAGVPGRRAGAAGGVLSTVNQIGGAVGVAVLGTVFFNAASSAGPA
+TAPAELFGDALAQVMPWQVATYLLAAVAMLALPKTAAPHQD*
+>NZ_CP083691.1_697
+MAGDCIRQIPRWGFVLSLAATILMMAAASAPSLFYPQIAERLGLIPVATTLVFAVYTFTL
+LAALLYLGPLSDHVGRRPVVAAGSLALALSVAMFWFAGSLAALLVARALQGLAAGLLIPA
+LSAMMIDFESPSHRNIAALWNTIGPMIGLGAGALGAALLLDLTSEPTTAVFGSLVLAFLI
+VATVVWSTPELVPKTQIRRGDLRPRFTVPPHLRRMFTVGVPVIIAGWATNGLFLALGADL
+VGSELGGSTHTQAGIVLFALAISGVTASSVLQRRSARTISLYATSALAFGTAVSIGALAL
+GSYPAYVASVAIVGSGFGTAFLGVLRTLMPHTASSERAAVMAVIYTVAYLAFGVPTIVAG
+LLVPVLTLSGTMTILGAIIIALSLVATVLRLRIPHPAAGPAEADDFPEPPTGSHRRSAPD
+REEQP*
+>NZ_CP083691.1_1217
+MNPSAGTSGGVFTARQRRVLAVLLVPVFMSLLAVSSINVALPSLQRGLGASDAELQWSIS
+GYTLAFGMVLVPAGRAGDLLGRARLFRIGVLGFGLGALLSGLAPSGLLLVLARVLMGVGA
+GLLNPQVSGFIQAEFEGQARARAFGALGSTVGVSVAAGPLLAGGLIAVLGGDLGWRATFL
+VNVPIALAAVLIARGWLPEESPAPAGRRDFDPVGVALLASALVAVMLPFLDRGLGPWRFA
+LLPLGAALAAGWAVWERGYRARGRAPMVDLSLFGLPGFRNGALMIGVYFTGSTSLFIVVA
+MFMQNGLGYGALQAALVGLPSAVCSSVMATVAGRLVLRAGRRLVVVGVSLVLAAVVGSIG
+VVAAHQAFGLSPWWLLATLGLFGMGQGLTVSPNQTLSLAEVPRPQSGTAGGILQTGQRVG
+TSVGSAVIVGVYLGVAGTGGPDRGFMAALGLIAVSIAAALAVAVADQRRRARQGGR*
+>NZ_CP083691.1_1792
+MPRPRLLLAVILLAQFVIPLSISGTAVALPAIASDLGSDPTPLQWVVNGFNVAFAVCTIV
+WGACSDRIGYTRSFRIGIAIAIAGGIVSMFAPNIAVLDAGRIIAGIGSAAVLTSAAPILS
+HLFEGKARAQAFALFGTINGLGLAAGPALSGLLLSAWGWQGIFAAHTIVLIVAFIGAARL
+PQLGRGGTSLREILDFSALKAPKFLAMTLVPIAGAIGFVTFLTYLPSALGAIHGLTAGVT
+GALMLVMTIPVLIAPVAVHRLMERSHLTPTAIVAVSFACLIVGGIGVLLLLRPDLPVALG
+VTPMILLGLGFGLPLGFVDAEALAAVPAERAGAASGVINLFRIGSEAVFVAAYGALLAAV
+ITTTLPGTTGELIASGSPGEPWIYHSGLMAAAGTMIGLVAIAGVTFLALTRAANRSAVTA
+RQVEVAR*
+>NZ_CP097650.1_1468
+MPVAPRPSDGAASSVFTPHQQRILAVLLIPIFMSLLAVSSINVALPALQRGLDASDAELQ
+WAISGYTLVFGMVLVPAGRAGDLFGRRRLFLVGLGVFALGALLSGLAPTGVLLVLARLVM
+GVGAGLLNPQVTGFIQGEFSGASRARAFGALGAVVGVSVAVGPLLSGGLIAWLGGDLGWR
+ATFLVNVPIALGALIVARQWLPRTVPERARRPDLDPVGVVLLAGALVAVMLPFLDRGLGP
+WRFVLVPVGIGLAALWTRWEARYARRGRAPMVDLRLFQTRSFACGALLIAIYFTGSTSMF
+VVIAMFMQNGLGYPALHAALIGLPSAVMSSVMSTVAGRVVLRTGRKIVVLGIALALLAVV
+GSIGVAWANREFGLSPWWLLLTLAILGAGQGLVVSPNQTLSLAEVPPRHSGTAGGVLQTG
+QRVGTAVGTAVIVGVFLGVASSADWDGAFMAAFALVAGCMALALLVALADLRGPRTAAPR
+G*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000049.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000049.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c789a1127b1a22900d3befacd4637eea9c27ab6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000049.fa
@@ -0,0 +1,70 @@
+>NZ_CP042169.1_1949
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRPHRLEIGQADGIQARSVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARPDYGWAFETLEDTNDGEHPVL
+VTLRRTVDAEENALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGVM
+DALADTDFPDIRTKCAIHSSSGSILLIPREGGHLSRMYVDLGEVPADDDHKVRQTPLEEI
+IRRAQQILRPYTLDVKEVAWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGLAPVELVPTYAEERKEIAKNLIDFDKEWSTLMATPTS
+ELGDPNEVAEFYTKTAEFPAGFMTEYQPSLLTTDATGQALAQGYPIGKRFKSALVERSCD
+TNVKHLGHLHRADGRWRVYVFADAASPRAEDSKVAAWAKAIEEDPRSFRNRHTPSDGPED
+ARFDIKVVYQQKQTEFAHPDVPSIFRPTTGSLGLHDLNNIFATCRPQHGEDIFEARGISR
+DGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN*
+>NZ_CP033200.1_1671
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRPHRLEIGQADGIQARSVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARPDYGWAFETLEDTNDGEHPVL
+VTLRRTVDAQGNALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGVM
+DALADTDFPDIRTKCAIHSSSGSILLIPREGGHLFRMYVDLGEVPADDNHKVRQTPLEEI
+IRRAQQILRPYTLDVKEVAWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGMAPVELVPTYSEERKEIAKNLIDFDKEWSTLMAKPTS
+ELGDPNEVAEFYTKTAEFPAGFMTEYQPSLLTTDATGQALAQGYPIGKRFKSGLVERSCD
+TNVKHLGHLHRADGRWRVYVFADTASPRAEDSKVAAWAKAIVEDPRSFRNRHTPSDGPED
+ARFDIKVVYQQKQTEFAHPDVPSIFRPTTGPLGLHDLNNIFATCQPKHGEDIFEARGISR
+DGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN*
+>NZ_CP040019.1_821
+MLFHHHGYVSTDPRVQPAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRSHRLEIGQADGIQARSVETFQAFGFASQIIDEAYDLTSMAFWNPSSEDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAAYMKNSPTRAEPDYGWSFESLEDSAEGEYPVL
+VTLRRTVDAQGEPLADPESGETRQVRAKYVVGADGAGSRVRKAIGHSLAGGASNHAWGVM
+DALAVSDFPDIRTKCAIHSSTGSILHIPREGGHLFRMYVDLGEVPADDNHKVRQTPIEEI
+IRRAQQIIRPYTLEVKDVAWHSVYEVGHRLTSGFDNRERVDHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGVAPAELVPTYSEERKEIAKNLIDFDKEWSTLMAKPTS
+ELGDPNEVADFYTKTAEFPAGFMTEYKPSILTTDATGQSLAAGFPIGKRFKSALVERSCD
+TNVKHLGHLHRADGRWRVYVFADAASPRSADSKVAAWAKAVEEDPRSFRNRHTPADGPQD
+ARFDVKVVYQQKQTEFAHPDVPAVFRPTSGDLRLLDLNNIFATCQPKHGEDIFEARGISR
+DGAVVVVRPDHYVSGVFGLDEVERLNEFFAGVLLDAS*
+>NZ_CP083691.1_757
+MLFHHHGYVSTDPRMKPAAGIGLDRPAELPDEMDVLIVGTGPAGMIAAAQLAMFPDVHTR
+IIERRGKRLEIGQADGIQARSVETFQAFGFASQIIDEAYDLTSMAFWNPSPEDEDAIVRT
+SLAEDDPHGVSEFPHLIVNQARILDWFAEFMKNSPTRATPDYGWEFVSLDDSDQDAERPV
+QVTLRRTVDAKGNPLAEGVAGEERVVRAKYVIGADGAGSRVRKAIGHSLSGDAANHAWGV
+MDVLADSNFPDIRTKCAIHSSSGSILHIPREGGHLFRMYVDLGEVPADDNHKVRQTPIEE
+VIRRAQQIIRPYTLDVKDVAWSSVYEVGHRLTSGFDNRERCTHPNVFLLGDACHTHSAKA
+GQGMNVSMQDGWNLAWKLGQVLSGIAPAELVPTYSEERKEIAKNLIDFDKEWSTLMAKPT
+SELGDPNEVAEFYTKTAEFPAGFMTEYRPSMLTTDAAGQELATGFPIGKRFKSAKVERSC
+DTNVKHLGHLHTADGRWRVYVFADAAAPHDADSKVAAWAEAVEEDPQSFRNRHTPAGAPQ
+DERFDLKVVYQQKQTEFAFPDVPAVFRPTTGPLGLHDLNNIFAVCRPEHAEDIFELRGVS
+RDGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN*
+>NZ_CP097650.1_166
+MFIAGDACHTHSAKAGQGMNVSMQDGWNLAWKLGQVLEGRSDASLLATYSEERQQIAENL
+IEFDKAWEGMMSKRPDELEDPQAVGRFYKDNAEFPNGFATQYPASSVTGEDTHQALAAGV
+PIGKRFESAAVRRVADTSPRQLGHLFEADGRWRLYAFADEDRTAVGELADWLADSPDSPV
+RRFTPESADLNSVFDAKVVYQQPYQEVELADVPALFLPKMGPYQLTDKEVVFAADLADDI
+FEARGIDRGGALIIQRPDMYVAHVLPLSAREEITAFFEQNMVSASV*
+>NZ_CP097650.1_167
+MRGAADPRRSLSTLPTTAVSEFPFLIVNQARVIDYFAEYAERGPQGQERTVRAKYVVGCD
+GSRSRVRDCTGIEVVRDPSAHAWSVMDVLLETDFPDNRQKCGIQSDKDGTILLIPREGGF
+LARFYVSLGSIDDAPRPRSGGGIRACSSPATPATPTPPRPARA*
+>NZ_CP097650.1_1888
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRPHRLEIGQADGIQARSVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARPDYGWAFETLEDTNDGEHPVL
+VTLRRTVDAQGNALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGVM
+DALADTDFPDIRTKCAIHSSSGSILLIPREGGHLFRMYVDLGEVPADDNHQVRQTPLEEI
+IRRAQQILRPYTLDVKEVAWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGMAPVELVPTYSEERKEIAKNLIDFDKEWSTLMAKPTS
+ELGDPNEVAEFYTKTAEFPAGFMTEYRPSLLTTDATGQALAQGYPIGKRFKSALVERSCD
+TNVKHLGHLHRADGRWRVYVFADAASPRAEDSKVAAWAKAIEEDPRSFRNRHTPSDGPED
+ARFDIKVVYQQKQTEFAHPDVPSVFRPTTGSLGLHDLNNIFATCRPTHGEDIFEARGISR
+DGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000050.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000050.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d27b418c63d0669e06dd0e013ba05488b86731a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000050.fa
@@ -0,0 +1,62 @@
+>NZ_CP042169.1_2033
+MSTDPRRQTPAPRGSDTGTPPLPEGRARWLVASNALDAGGRSATDVALDVLAVLLLGVGA
+DGMGVLMTLSGLGFLLLGVPLGIVVDRHLSPRLLAATGLAKAAVLGSLVAAWALDALTFG
+HLAAVMTLLGVLTVLAETTQTALVPRVVPATAVARLTARLESADAALVLIVPAAAGVLVG
+SLGAGPVLGIATAFLFAAAIVALRVRLRPSAAADVPDDDGDPGVADVLSRWARFGKDAAE
+GWTVLRRTPVLWLLTMGSVAANVGMALFAPVEAVWILTDLRLGPEFLGIQITAGAVGALT
+ASSLAGRAIDRLGERRCILLGSVGCAVAVGLHLLAYADRAHAGPWLLAGAALWGFMVLLG
+NITQAAVTARACPEGTLGRVTAMRRTLTRGSVPLATLAGGALGATLGVGWALAGWQVLAV
+VSLAAVVPAARWVDAGRDDVD*
+>NZ_CP033200.1_1750
+MSTDPRRQTPAPRGSDTGTPPLPEGRARWLVASNALDAGGRSATDVALDVLAVLLLGVGA
+DGMGVLMTLSGLGFLLLGVPLGIVVDRHLSPRLLAATGLAKAAVLGSLVAAWALDALTFG
+HLAAVMTLLGVLTVLAETTQTALVPRVVPATAVARLTARLESADAALVLIVPAAAGVLVG
+SLGAGPVLGIATAFLFAAAIVALRVRLRPSAAADVPDDDGDPGVADVLSRWARFGKDAAE
+GWTVLRRTPVLWLLTMGSVAANVGMALFAPVEAVWILTDLRLGPEFLGIQITAGAVGALT
+ASSLAGRAIDRLGERRCILLGSVGCAVAVGLHLLAYADRAHAGPWLLAGAALWGFMVLLG
+NITQAAVTARACPEGTLGRVTAMRRTLTRGSVPLATLAGGALGATLGVGWALAGWQVLAV
+VSLAAVVPAARHLGPRTAER*
+>NZ_CP040019.1_678
+MSTDPRRQTPAPRVPDTGTRPPPEGRARWLVASNALDAGGRSATDVALDVLAVLLLGVGA
+DGMGVLMTLSGLGFLLLGVPIGIVVDRHLSPRLLAATGLAKAAVLGSLVVAWALDALTFG
+HLAAVMALLGVLTVLAETTQTALVPRVVPATAVARLTARLESADAALVLIVPAAAGVLVG
+SLGAGPVLGIATSFLFAAAIVALRVRLRPSAAVDIPDDDGDPGVADVLSRWARFGKDAAE
+GWTVLRRAPVLWLLTMGSVAANVGMALFAPVEAVWILTDLRLGPEFLGVQITAGAVGALA
+ASSLAGRAIDRLGERRCILLGSVGCAVAVGLHLLAYADRAHAGPWLLAGAALWGFMVLLG
+NITQAAVTARACPEGTLGRVTAMRRTLTRGSVPLATLAGGALGATLGVGWALAGWQVLAV
+VSLAAVVPATRHLGPRTAER*
+>NZ_CP040019.1_1286
+MVSSPLTDDTTAPENAAPAKRLGRARWLVASNALDAGGRSATDVAIDVLAVLALGVGAAQ
+MGVLMTLSGLGFLLLGVPIGILVDRHLSPRLLVATDLAKAALLGTLVLAWALDALTFAHL
+AAVMALLGVLTVLAETTQATLVPRVVAPDTVSRLAARLESADAALGLIVPAAAGLLVAAL
+GAGPVLGIAAAFLAAAALVALKVRMNPAPVTEDTRDEETPAAAVVLTRWSRFWSEAAHGW
+TTLRRTPVLWLLTLNSMAGNIGMALFAPIEAVWVLTDLQLGPEFVGFQLTAGALGALTVS
+ALAPRAIDTLGEKGCILAGSAGCAAAVALHLAAFFDRAHAGPLLLAGAALWGFMVVLGNI
+TSGAIFARSCPEGTLGRVTAMRRTLTRGSVPLATLAGGALGAAFGPGWVLAGWQAMALLS
+LAFAFAATRLARRPQ*
+>NZ_CP083691.1_646
+MTRVSAWRSRDFRRLWGASTASALGGEIGELAMPVLALVWLGASAEELSWVRVATFLPYL
+VLPLWLGVLVDRWRRRPLMITAETVSGITLLGIAGAALAGWLTVPALVAAAAVLGAMSVL
+HMLADFSFTPQVVSRAALPDANAKMTATYSAIGIGGSGVGGALVQWLTAPFAVAINGAGR
+LLSVVLLRRIQTHEPPAEAPDTSARQQAREGFLALLRHRVVRALAAEATIWNLGNEVFML
+ALTVLIVDARDDGPLVLGLIFMAGGLGAFLGAGISARLTERFGYGRSLITAMLVGNTAPL
+IGVLFSSDTSVTSLVVLAAAFFASGFGTGIANSQAVTVRQVTVPEELRGRVNASYRMLSW
+GALAIGALLGGWLISAVGGWLAAALGTAAMAASTLPVALSPVRQMRDLDDGAPPAAE*
+>NZ_CP083691.1_2188
+MSSPLTDDTTAPENAARAKRLGHARWLVASNALDAGGRSATDVAIDVLAVLALGVGAAQM
+GVLMTLSGLGFLLLGVPIGILVDRHLSPRLLVATDLAKAALLGTLVLAWALDALTFAHLA
+AVMALLGVLTVLAETTQATLVPRVVAPDTVSRLAARLESADAALGLIVPAAAGLLVAALG
+AGPVLGIAAAFLATAALVALKVRINPAPVTEDTQDEETPAAAVVLTRWSRFWSEAAHGWT
+TLRRTPVLWLLTLNSMAGNIGMALFAPIEAVWVLTDLQLGPEFVGFQLTAGALGALTVST
+LAPRAIDTLGEKGCILAGAAGCAAAVALHLAAFFDRAHAGPLLLAGAALWGFMVVLGNIT
+SGAIFARSCPEGTLGRVTAMRRTLTRGSVPLATLAGGALGAAFGPGWVLAGWQAMALLSL
+AFAIAATRLARRPH*
+>NZ_CP097650.1_1973
+MSTDPRRQTPAPRTPDTGTPPPPEGRARWLVASNALDAGGRSASDVALDVLAVLLLGVGA
+DGMGVLMALSGLGFLLLGVPIGIVVDRHLSPRLLAATGLAKAAVLGSLVVAWALDALTFG
+HLAAVMALLGVLTVLAETTQTALVPRVVPATAVARLTARLESADAALVLIVPAAAGVLVG
+SLGAGPVLGTATAFLFAAAIVALRVRLRPSAAADVPDDDGDPGVADVLSRWARFGKDAAE
+GWTVLRRTPVLWLLTMGSVAANVGMALFAPVEAVWILTDLRLGPEFLGIQITAGAVGALT
+ASSLAGRAIDRLGERRCILLGSVGCAVAVGLHLLAYADRAHAGPWLLAGAALWGFMVLLG
+NITQAAVTARACPEGTLGRVTAMRRTLTRGSVPLATLAGGALGATLGVGWALAGWQVLAV
+VSLAAVVPAARWVDAGRDDVD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000052.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000052.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3abfdaacc5164822f2cbe67d834b832b982aa0b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000052.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_2104
+MSSEETVPVRVALVDDQALIRSGLAMLVDSQPDLTVVAEAGSGREAVASVSVAGADVVLM
+DVRMPEMDGIEATRALLRRPDAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAPPEELLA
+AIRTVHRGDAVIAPSTTRRLLTHMAPRLRSDQVRSAECEEQQAAVASLTPREHEVLVLMA
+QGAANLEIAAELVLSEATVKTHVGRVLAKLGARDRVQAVLIAHRAGLVQF*
+>NZ_CP033200.1_1829
+MSSEETVPVRVALVDDQALIRSGLAMLVDSQPDLTVVAEAGSGREAVASVSVAGADVVLM
+DVRMPEMDGIEATRALLRRPDAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAPPEELLA
+AIRTVHRGDAVIAPSTTRRLLTHMAPRLRSDQVRSAECEEQQAAVASLTPREHEVLVLMA
+QGAANLEIAAELVLSEATVKTHVGRVLAKLGARDRVQAVLIAHRAGLVQF*
+>NZ_CP040019.1_573
+MTTRVLLVDDQPLIRLGFAAILQSQDDIEVVGEAGDGAECLERAAALDPDVICMDVQMPR
+MDGIEATRALAEAGTRAAVLILTTFDRDDFLFETLEAGASGFLLKSAEAEHLIDAVRVLG
+RGDALLDPQVTRRVLRRMASAAPEGVDGPAGVGQPRDDDGAAPGQAEASDAVGKAGLTGR
+EAEILTLMARGLSNGEIAGQLFVGESTVKTHVSNVLMKLGARDRVHAVIWAFEHGVAG*
+>NZ_CP040019.1_582
+MSTDAENAPVRVALVDDQALIRSGLAMLVDSQPDLTVVAEAGSGREAVASVSVAGADVVL
+MDVRMPEMDGIEATRTLLQRPDAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAPPEELL
+AAIRTVHRGDAVIAPSTTRRLMAHMAPRLRSDHARTAECEHEQAAVESLTPREREVLVLM
+AQGSANLEIAGELVLSEATVKTHVGRVLAKLGARDRVQAVLIAHRAGLVQF*
+>NZ_CP040019.1_2532
+MVLPDAGVRGGVRVRTSRTGVVGDIRLVEGAVSGDLDSADLLLGGVNSLGETRQVARQGR
+DVPPFLLVAEATIVEELSGIDASGAAAVLAYPLDTVELASVAHGIAGSGPFLSPRLPQLS
+VEPLGEGLSAREAEVVVALGEGLSDAEIAQALCVSVKTVHTHVLNLRRKLGARNRAHAVS
+LARSVGPLGDACSEPGLVAAL*
+>NZ_CP083691.1_504
+MSPDDAQPTPIRVALVDDQALIRSGLAMLIDSQPDLTVVAQASDGREAAASVAVAGADVV
+LMDVRMPEMDGIEATRALLRRPDAPRVVVLTTFDLDEHVMDAIEAGASGFLLKDAPPEEL
+LAAIRTVHGGDAVIAPSTTRRLLAHMAPRLRQDAARSAECADEQAAVGSLTPREREVLVL
+MGQGAANPEIAAQLVLSEATVKTHVGRVLAKLSARDRVQAVLIAHRTGLVGF*
+>NZ_CP097650.1_2049
+MSSEETAPVRVALVDDQALIRSGLAMLVDSQPDLTVVAEAGSGREAVASVSVAGADVVLM
+DVRMPEMDGIEATRALLRRPDAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAPPEELLA
+AIRTVHRGDAVIAPSTTRRLLTHMAPRLRSDQVRSAECEEQQAAVASLTPREREVLVLMA
+QGAANLEIAAELVLSEATVKTHVGRVLAKLGARDRVQAVLIAHRAGLVQF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000060.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000060.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bab95727f18752c969c59f3c186cf1c5d9e49856
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000060.fa
@@ -0,0 +1,47 @@
+>NZ_CP042169.1_60
+MTPEWWMALAALVLLALLVVVVVVLAVRQVRLGVQHERTRLLVDALDARVGGVQRRLEEV
+PGIGTGRHEVALVLNPIKTHADRVRRELERLAEAEGLGEVLVLETQEDDPGTAMARQALD
+AGARLVIAAGGDGTVRTVAEQLAGTDVALGVVPLGTGNLLARNLDLPINDVEQCLRIAVG
+GRQRRIDTVDVRFTHEDGRVTRQTFTVIGGAGYDADIMGDTKDELKSLAGWLAYSEAGMR
+HLRGKRHEVTVALDGGQPRRFKVRTVMVANCGMLTGGVELLPQAKLDDGLLDVMVLSPRH
+ALDWARIAVKTVTRHRSSVPAMHTEQAQRVKVEFAEPMPSQLDGDATGVITALDARVQPD
+SLVVMLVAEDDASVRDDGVSAAAPVPEPAPHI*
+>NZ_CP033200.1_2029
+MTPEWWMALAALVLLALLVVVVVVLAARQVRLGVQHKRMRLRVDALDARVGGVQRRLEKV
+PGIGTGRHEVALVLNPIKTNAGQVRRELERLAEAEGLGEVLVLETQEDDPGTAMARQALG
+AGARLVIAAGGDGTVRTVAEQLAGTDVALGVVPLGTGNLLARNLDLPINDVEQCLRIAVG
+GRQRRIDTVDVRFTHEDGRVTRQTFTVIGGAGYDADIMGDTKDELKDLAGWLAYSEAGIR
+HLRGKRHEVTVALDGGQPRRFKVRTVMVANCGMLTGGVELLPQAKLDDGLLDVMVLSPRH
+ALDWARIAVKTVTRHRSSVPAMHTEQAQRVKVEFAEPMPSQLDGDATGVITALDARVRPD
+SLVVMLVAEDDASVRDDGVSAAAPVPEPAPHI*
+>NZ_CP040019.1_192
+MTPGSPDDDGAPAVRRRVLVLLNPHAGRRRSLARAQARLRTHPGLALDLVVPDPADHAAQ
+LAAGRTALADGVDAVVVRGGDGMVAAGVGLVGDHAEATGRRVPLGIVPAGTGNDLARAAG
+LHRRDPGAALEAVLRALEDPAAPVRRIDALRLTVTRAGAVVERRWAANSVNIGFDARVNA
+RANALGAVPGPLRYLAALGLEARAFAAVEMGLGLDDGPVRRERVALVSVQNGPTIGGGIP
+LAPGARLDDGRAEATVVGPLPTAGLALLFPLVYVRAHRLLRPLCTERARRVRVAVPDGVP
+VYADGDEVLPASHGGAAVEVEAVPGAVALLG*
+>NZ_CP040019.1_319
+MALVALVLGAVLAVAVIVLAVRHRGLAERHERTRGQLDAVEHRLDAAQRRLGELPGVDRP
+RQEIALVLNPVKARADEVRRTLEAMADREGLGSVLVLETEEDDPGTQMAKDALEAGVRLV
+IAAGGDGTVRTVAEQLTGTDVALGVVPLGTGNLLARNLDLPINDIEECLRIALTGRQRRI
+DTVDVRFTHEEGEVTRQTFTVIGGAGYDADIMADTKDELKDVAGWLAYSEAGMRHLRGKR
+HDVSISLDGGASRRFKVRTVMVANCGMLTGGVELLPEAKLDDGLLDVLVLSPRHALDWAR
+IAAKTVTRHGANIPVMHTEQAQRVKVEFADPMPSQLDGDATGHIVALDARVQPDSLVVML
+LDEKEASVHDDGRSEAAPVPEPAPHI*
+>NZ_CP083691.1_260
+MALAALVLAALFAVAVVVLGLRLRRLDGAHERTRGQLDAVEARLGDLRRRAGRAPGVDLP
+GPQVALVLNPVKARADEVRRAMEALAEKEGLGEVLVLETTEEDPGTAMTREALTAGVRLV
+VAAGGDGTVRTVAEQLAGTDVALGVMPLGTGNLLARNLDLPINDIEECLRIALTGRQRRI
+DTVDVRLTHEDGARTRQTFTVIGGAGYDADIMGDTKDELKDMAGWLAYSEAGMRHLRGRR
+HEVSITLDGGAVQRFKVRSVMVANCGMLTGGMELLPEAKLDDGLLDVLVLSPRHALDWVR
+IAAKTLTRHRASIPVMHTEQAQRVQVRFAEPMSSQLDGDATGDITALDARIQPDSLVVML
+GDEDDASVEDGGRSAEAPVPEPAPHI*
+>NZ_CP097650.1_55
+MALAALVLLAVLAVVVVVLAVRQVRLGVQHQRTRLLVDALDARVGGVQRRLEEVPGIGTG
+RHEVALVLNPIKTHADRVRRELERLAAAEGLGEVLVLETQEDDPGTAMARQALDAGARLV
+IAAGGDGTVRTVAEQLAGTDVALGVVPLGTGNLLARNLDLPINDVEQCLRIAVGGRQRRI
+DTVDVRFTHEDGRVTRQTFTVIGGAGYDADIMGDTKDELKDLAGWLAYSEAGIRHLRGKR
+HEVTVALDGGQPRRFKVRTVMVANCGMLTGGVELLPQAKLDDGLLDVMVLSPRHALDWAR
+IAVKTVTRSRSSIPVMHTEQAQRVKVEFAEPMPSQLDGDATGVITALDARVQPDSLVVML
+VAEDDASVRDDGVSAAAPVPQPAPRI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000063.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000063.fa
new file mode 100644
index 0000000000000000000000000000000000000000..884814be59c39a9deb3fd4b5c88456f3d0ada75d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000063.fa
@@ -0,0 +1,52 @@
+>NZ_CP042169.1_102
+MATKTAPKRAPGYRCTECGWTTVKWVGRCGECQSWGTVEEIGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVSEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGSPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLSAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFTVAEVGSIGEALATIPTWTGGGPAAHPEAGPGR*
+>NZ_CP033200.1_2071
+MATKTAPKRAPGYRCTECGWTTVKWVGRCGECQSWGTVEEIGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVSEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGSPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLSAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFTVAEVGSIGEALATIPTWTGGGPAARPEAGPGR*
+>NZ_CP040019.1_32
+MSPFDLEELDMTATAPDPLDGAFTAAWLTSQTFAPVEYVVPGLIPEGLTLLVAAPKVGKS
+WMVLDLAHAAATGGKALGSISVDRRPVLYLALEDGPRRLQSRLSMLGVDGGGPDLMFLTA
+LSASPVATVAAYLERHAQDRPLVILDTLGKVRGRDGGNDQYGRDYSQMSALKTLVDAVPG
+SSLIVVHHTNKGGREDFLEAVSGTQGLAGAADSILVIRRDRNQADGTINVTSRDAREGEY
+AVTFDGSRWHTVGADLAEAAAAAESKRATAGVGDDMARVIDAVSRHPGGVGVAQIVAMTE
+LPRATVDKYLSRAVAAERIVRVERGTYAPTPLSEVSDCQIGSDPDPLDF*
+>NZ_CP040019.1_272
+MATKTAAKRAPGYRCTECGWTTVKWVGRCGECQAWGTVEEVGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVAEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGGPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLAAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFTVAQVGSIGEALATIPTWTGAGAGA*
+>NZ_CP083691.1_218
+MATKSSTKRAPSYRCTECGWTTVKWVGRCGECQAWGTVEEAGGAATAGRTHASTVAQAAP
+RIRDVDATLASFRTTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAA
+GGGPRDVLYLTGEESAAQVRSRADRIGALADTLRLAAETDLGRALGQIEKTDPALVIVDS
+VQTLQSTEVEGVAGGVTQVREVAASLIRTAKEKGITTILVGHVTKDGSIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGTQEPVEGT
+CVTVTLEGRRPLVAEVQALLTPSGGGSARRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAIASAKLGAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFSVAQVGTLSEALGTIPSWTGQRSPGARS*
+>NZ_CP097650.1_97
+MATKTAPKRAPGYRCTECGWTTVKWVGRCGECQSWGTVEEIGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVSEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGSPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLSAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGEVPAGFTVAEVGSIGEALATIPTWTGGGPAARPEVGPGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000067.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000067.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24c3972b1b3066befb3c36953e74b53844a12cc8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000067.fa
@@ -0,0 +1,37 @@
+>NZ_CP042169.1_191
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEAFARIPQGVAVTFEVLGPLALSVAARPSWRSAAWAAL
+ALAGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAGYILLSRRAGTHLPGVQGLA
+LATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQVLRRMPTALFSL
+LTCLSPIAAALTAWAVRGQELTPLDLAGMLLVIAACAAAVWTSRSPGVAGGGRG*
+>NZ_CP033200.1_1980
+MAVAVYPLAFYTSIHWAGVAIGSVVSLASAPLASGLLERIVEYRRLSRWWMLAAALGGTG
+AALLCLSQLDQEAASSTATLAGVLLGLVAGATYATYSWAAHRLIHDGISRAASMGAVFGA
+GGALLLPVLVLTGAPLIATPQAFAVAAYMALVPMFLGYVLFGYGLTRVPASTATTITLTE
+PAIAAILAVAVVGERLTPVGWTGLGIIAAVLFILALTPTNTTADRHGRTPTSEAIQPALA
+PSPRRHNERTSPRDDAGRGSDVMWVSQTMRCQGATRPSRWEGVRGRFRKPYRLRPVSPDH
+GRATCGERTEIMRPARGLDARSVLAATMET*
+>NZ_CP033200.1_2143
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEAFARIPQGVAVTFEVLGPLALSVAARPSWRSAAWAAL
+ALAGIGVLGREGFSADGRIGGAGLDPVGVALALAAAACWAAYILLSQRAGTHLPGVQGLA
+LATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQVLRRMPTALFSL
+LTCLSPIAAALTAWAVRGQQLTPLDLAGMLLVIAACAAAVWTSRSPGVSGGARG*
+>NZ_CP040019.1_188
+MRLIPLVLLSLLCQQLGASVAGLMFGTTGPAGMVALRLAFSALVLLVLTRPRMRTLAGLS
+RRGWVAVVMLGVTMAGMNLLIYAAFDRIPQGVAVTFEVLGPLALSVLANRRWLSVVWAAL
+AFAGIALLGRDGFSAGMDGAGLDPLGVAFALAAAACWAGFILANRHAGTHLPGVQGLALA
+MVVGSAVAVPVGAADAGPVLLEPWVLAVGLGVALLSSSIPYGIEMQVLRTMPTGLFSLIT
+CLSPVVAALTAWAVRGQRLAVLDLGGMGLVVLACGAAVWAAERAARPSRRAPRTS*
+>NZ_CP083691.1_140
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEAFARIPQGVAVTFEVLGPLALSVAARPSWRSAAWAAL
+ALAGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAAYILLSRRAGTHLPGVQGLA
+LATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQVLRRMPTALFSL
+LTCLSPIAAALTAWAVRGQELTPLDLAGMLLVIAACAAAVWTSRSPGVAGGGRG*
+>NZ_CP097650.1_191
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEAFARIPQGVAVTFEVLGPLALSVAARPSWRSAAWAAL
+ALVGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAAYILLSRRAGTHLPGVQGLA
+LATAAGSLVALPVGVATAGTALLSPVVLGVGLAVALLSTAVPYGIDLQVLRHMPTALFSL
+LTCLSPIAAALTAWAVRGQELTPLDLAGMLLVIAACAAAVWTGRSPGVAGGGRS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000075.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000075.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8b6290613242a98fcc2423cbd9c55f6ad71007e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000075.fa
@@ -0,0 +1,47 @@
+>NZ_CP042169.1_271
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWHFQHLGAR
+AAGGFGIVVAEATAVTPEGRISAWDTGLWNDEQRDAWAPIAEFIASQGALPAIQLGHAGA
+KASTVPMHPGALAGQPILEGPDSWETLSPSGVATNSMEIRTHAMRVDEIRETVQAFADAA
+ERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVWPA
+DKVLGIRISGSDWVEGGWSIEETVRLAQELQGQVHWFDLSSAGIGDTYEGPQGPGYQVPL
+ATAVKEGTEGIVVSAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPNWPTAAALALDVP
+SEQVPMARQYFRAKW*
+>NZ_CP033200.1_191
+MPSLFDPLDVGALRLDNRIVMAPLTRQRAGEDGVPTELPAEHYAQRATAGLLVTEGAFPS
+FRSRAFPGQTGLADDAQTDGWRAVAQAVHEAGGHVFVQVMHGGRMCHPDLLRGAEPEAPS
+AIAPGVPVRGFSGKMEGPVPSALDTEELPRVVAEFADAARRAVEAGLDGVEVHGANGYLL
+HEFLAPSSNTREDAYGGSPENRARLTVEVVRAVAQAIGAERTALRISPEHNVQGTIEEDR
+ADVLATYDALLAGLADLDLAYLSVIHQDVAGDLAAHLRESFSGPLVLNSGFGAVTGLEEA
+RRIVEDGLADAVAVGRELIANPDLARRWREGLPLNEPDPTTFYTGGAHGYTDYPFVDGSP
+SS*
+>NZ_CP033200.1_2242
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWQFQHLGAR
+AAGGFGIVVAEATAVTPEGRISPWDTGLWNDEQRDAWAPIAEFIASEGALPAIQLGHAGA
+KASTVPMHPGAPAGQPILEGPDSWETLSPSGVATNSMEIRTHAMRVDEIRETVQAFADAA
+ERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVWPA
+DKVLGIRISGSDWVEGGWSIEETVRLAQELQGQVHWFDLSSAGIGDTYEGPQGPGYQVPL
+ATAVKEGTEGIVVSAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPNWPTAAALALDVP
+SEQVPMARQYFRAKW*
+>NZ_CP040019.1_66
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWQFQHLGAR
+AAGGFGIVVTEATAVTPEGRISPWDTGLWNDEQRDAWAPIAEFIASEGALPAIQLGHAGA
+KASTVPMHPGAPAGQPILEGPDSWETLSPSGVATNSMEIRTHAMRVDEIRETVQAFADAA
+ERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVWPA
+DKVLGIRISGTDWVEGGWSIEETVRLAQELQGQVHWFDLSSAGIGDTYEGPQGPGYQVPL
+ATAVKEGTEGIVVSAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPNWPTAAALALDVP
+SEQVPMARQYFRAKW*
+>NZ_CP083691.1_2295
+MPDLFDPLPLGGLTLPNRVTMAPLTRQRAGEDGVPGDLHVEYYRQRASAGLIVSEGVFPT
+VDSRAFPGQPGLEDEAQQAGWARVADAVHEAGGRIFVQVMHGGRMCHPDLLRGAEPVAPS
+AIAPGVPVRGFSGKTDGPVPRALETEELPGIAAAFASAARRAVDAGADGVEVHGANGYLL
+HEFTAASSNHRTDAYGGSPENRARLTVEVVRAVAAEIGAERTALRLSPEHDVQGVLEQDR
+ADVLATYGAILDGVADLDLAYLSLLHRDVAGDLVAALRARFGGPVLLNSGFSEVTGAAEA
+RRIVEGGLADAAVVGRALIANPDLVRRWREDRETNAPDPSTFYVGGAHGYTDYPSLEG*
+>NZ_CP097650.1_270
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWQFQHLGAR
+AAGGFGIVVAEATAVTPEGRISPWDTGLWNDEQRDAWAPIAEYIASEGALPAIQLGHAGA
+KASTVPMHPGAPAGQPILEGPDSWETLSPSGVATNSMEIRTHAMRVDEIRETVQAFADAA
+ERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVWPA
+DKVLGIRISGSDWIEGGWSIEETVRLAQELQGHVHWFDLSSAGIGDTYEGPQGPGYQVPL
+ATAVKEGTEGIVVSAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPNWPTAAALALDVP
+SEQVPMARQYFRAKW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000076.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000076.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3895529a874e014dac8a4bde70d7ea69455113cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000076.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_274
+MTGGDPAALMDALGAWFHPLTALLVALDAPIPPVPSEVVVIGSGALAAEGRVSPVAAVLA
+AWLGCWAGDVGLYALFRHGLADRLDRWAWWRRIHRGIRSLLVRVGPAGSLAGLSVLRFVS
+GGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSSSMVGLGWITGRATGLPWWASAMVGMVF
+GTLAGLMIAGIMAHRRRGRKG*
+>NZ_CP033200.1_2245
+MTGGDPAALMDALGAWFHPLTALLVALDAPIPPVPSEVVVIGSGALAAEGRVSPVAAVLA
+AWLGCWAGDVGLYALFRHGLADRLDRWAWWRRIHRGIRTLLVRVGPAGSLAGLSVLRFVS
+GGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSGSMVGLGWLTGRATGLPWWASAVVGMVF
+GTLAGLMIAGIMAHRRRGRKG*
+>NZ_CP040019.1_63
+MTVLTPAWFAASGGVPTMGAGAAAASGAGAWDPSALLDSLGAWFHPLTALLVALDAPIPP
+VPSEVFVIGSGALAAEGRVGLAAAVLTAWLGCWAGDVGLYALFRHGLADRLDRWAWWRRV
+HRGIRVLLVRVGPAGSLAGLSVLRFVSGGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSG
+WMVGLGWLTGRTTGLPWWASAVVGMVFGTLAGLIIAGVVARRRARKG*
+>NZ_CP083691.1_49
+MTDVTALLEGLGPWFHPLTFLLVALDAPVPPTPSEVLVIGSGSLAAAGRLGLATSVLTAW
+LGCWAGDVGLYALFRHRLTSVLDRWGWGRAVHAGIRRLMEKAGPASSLAGLFVLRFVSGG
+RTASMAAAGVAGVRWRPFLWLSGTGSLAWSVYMVGLGWITGSATGLPWWASAVVGVVLGT
+LLGAAVAAVIAWRRRGKEGA*
+>NZ_CP083691.1_434
+MPVLTNILDAASILHSLGPWTLGGIGSMVFIESGVLFPFLPGDSLLVTAAALHVELGIAL
+WAIILVAGLAAILGDQVGFYLGHRYGRRLFKDDARVLKTERLAQAEAFFERRGPLALVLG
+RFVPIVRTYVPVAAGTAGMPYRSFVGWNIGGAVAWVCSMVAVGALLGQIPGITKSIDGIM
+ILIIVISVAPIAIQALRARRKARRDAVMTEGQPVA*
+>NZ_CP097650.1_273
+MTGGDPAALMDALGVWFHPLTALLVALDAPIPPVPSEVVVIGSGALAAEGRVSPVAAVLA
+AWLGCWAGDVGLYALFRHGLADRLDRWAWWRRIHRGIRSLLVRVGPAGSLAGLSVLRFVS
+GGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSGSMVGLGWITGRATGLPWWASAVVGMVF
+GTLAGLMIAGIMAHRRRGRKG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000077.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000077.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ff5c06069df940cbdb5881cd3ef66a005e8d69e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000077.fa
@@ -0,0 +1,165 @@
+>NZ_CP042169.1_279
+MSGPAESAAGTATPAADVVLGRFTEPTRAWFTGAFETPTPAQLGAWDAISSGRHALVIAP
+TGSGKTLSSFLWALDSFVREPAAEGTAATRVLYVSPLKALGVDVERNLRAPLVGITQTAA
+HQGRPVPRVRVGVRSGDTPAAERRRLQQDPPDILITTPESLYLMLTSQARAALTGVRTVI
+VDEVHAVAGTKRGAHLAVSLERLDALLDAPVQRIGLSATVEPAAEVARFLGGTQPVTVVR
+PASAKRWDLTVTVPVPDLTDLSSPAAAHDLGPGSSTGGLGDEGAVTGGSIWPHVEERIVD
+LVAERRSTLVFANSRRLAERLTGRLNEIWEARAEAAAAAEHPDAVPGFRTPDPTGFHGPA
+QVAGQTGTGSGTVSDFARAHHGSVSKEQRAIVEEALKTGQIRCVVATSSLELGIDMGAVD
+QVIQVESPPSVASGLQRVGRAGHQVGEVSRGVFFPKHRGDLVDTAVVAERMTAGRIESLR
+IPANPLDILAQQTVAAVAVADLDAQEWFDLVRRSAPFATLPFSAYESVLDLLAGRYPSDE
+FAELRPRILWDRENGTLAARPGAQRLAVTSGGTIPDRGLFGVFLASDGGADGTPGGAAAG
+DTAESAGTASAGSARSGGRRVGELDEEMVYESRVGDVILLGATSWRIVDITADRVLVLPA
+YGQPGKLPFWRGDAAGRPAELGDAVGRFRRELDADPEAGRTRLGAAGLDPWAQDNLLAYL
+KDQREATGVLPTEQTLVVERFTDELGDWRVVLHSPYGMAVHAPWALAVGARLAQRYGLET
+GSGAAMAADDGIVLRIPLMDAEPPGAELFEFTAEELDEIVTAEVGGSALFAARFRENAAR
+SLLLPRRDPGRRTPLWQQRQRSAQLLDVARKHPRFPVILETVREVLQDVYDLPALKELAG
+RVSSRAVRLVEVTTTAPSPFSQSILFGYIAQFIYEGDSPLAERRAAALSLDPALLSELLG
+TEELRELLDAEVIAEVEAQLQRLAPDRRARGVEGVADLLRLLGPLSVAEAARRTRAEGEA
+EEAADEAAVAGMLAELERAGRAFRLRQDGVERFAAVEDAARLRDALGTPIPHGVPTAFLD
+PVDDPLGDLVGRYARTHGPFTAAEAGAALGLGGAVVLSVLQRLATERRVSTGAFRPEGTP
+GAASLDAEWCDAEVLRRIRMRSLAALRAEVEPVDQAAYARFLADWQHLRPRTGRDGAWRP
+PATLEGVDGVATVLDQLAGTPLPASAWESLVLPARVRDYAPALLDELLATGEYVWSGVGE
+ATGNDGWVALHPADAVDLTLRLPEPAEETPADAALRAAVLEVLAGGGAWFFPQLVERVRA
+VQAAAGDGGTGTAGGTGGPDPHRDPADLARGPAVLAALWGLVWDGRVGNDTFAPVRGLLS
+LGKTAHRTGRQTPRARTARTGGAAGAAAGRGLGGRLAGVRGRGRYAGLTSSEGGARGTAG
+LTAGTVGLSAAEQARSAGRWSLLPAAEQDPTIRAHATAELLLDRYGVITRGSVVAEEVPG
+GFAGQYRLLTRMEDAGQVRRGHFVDGLGGAQFSTGAVVDRLRGFQRDEEDAAVDTAPLAL
+ALAATDPANPYGAALDWPSVPAGPDGVVPTGHRPGRKAGAVVVLIAGRLALYMERGGRTL
+LAFTEESGELRAAAEALVWALRTGHTERLSLEKVNGGPVLGTPLAEALLAAGFYSSPSGI
+RFRN*
+>NZ_CP042169.1_1903
+MTTSVEGFSALDPVIQHHIVNTLRWPDLRPLQKASVASLLAGHDALLLAPTAGGKTEAAF
+FPVLTRAEREQWTGTSVLYVAPLKALLNNVESRAMEYTSWLGRSASVRHGDTTQAERRRQ
+GTERPDVLMTTPESLESMLISPTVNVTDFFSELRTIIVDEVHAFAGDDRGWHLLSVLERL
+SAVVRRPIQRIGLSATVGNPEELLTWLQGGNAAAGLPASVIAPPVDRTGAAAPELRLDFV
+GSEDNAATVISRLHGGEKRLVFAESRRTVELLGNALHERDVTTFLSHSSLSLSERRRSEQ
+AFAEAQDCVIISTSTLELGIDVGDLDRVLQLGAPSTVASFLQRLGRTGRRPGAQRNMLFL
+ELKPADLLRAAGLLLLHGEGYVEPIQPPPAPHHIVAQQILALTLQKGQLQRGAALAGLQA
+LGMSDSTTYRTIEDGLLEHGHLDSDGGLLFVGPETQRRYGGLYFRDLMAVFTVEAEFPVF
+HGRTEIGSVAPNWIATDPDDQPLLILAGRSWKVSFIDWKRHLVHVERSDRGLAPRWASPP
+RALSWALSDAMRRVLLGADPAGVVLTGRAQDALADHREAEGYTAAADHTVLASTADDLRW
+WTWGGAGANALLVAALEQVAPELLGEKLRFDNFSLRLRGDVDAASLGRALRQATSNFGGD
+LAGVDPLVDDAAVRGLKFHEMLPLDLARATLAARLADHTGVARVLERPVQMLRTAEDGRM
+WG*
+>NZ_CP033200.1_2257
+MSGPAETAAGAPTPAADVVLGRFTEPTRAWFTGAFEAPTPAQLGAWDAISSGRHALVIAP
+TGSGKTLSSFLWALDSFVREPAAEGTAATRVLYVSPLKALGVDVERNLRAPLVGITQTAA
+HQGRPVPRVRVGVRSGDTPAAERRRLQQDPPDILITTPESLYLMLTSQARAALAGVRTVI
+VDEVHAVAGTKRGAHLAVSLERLDALLDTPVQRIGLSATVEPAAEVARFLGGTQPVTVVR
+PASAKRWDLTVTVPVPDLTDLSSPAAAHDLGPGSSTGGLGDEGAVTGGSIWPHVEERIVD
+LVAERRSTLVFANSRRLAERLTGRLNEIWEARAEAAAAAEHPDAVPGFRTPDPTGFHGPA
+QVAGQTGTGSGTVSDFARAHHGSVSKEQRAIVEEALKTGQIRCVVATSSLELGIDMGAVD
+QVIQVESPPSVASGLQRVGRAGHQVGEVSRGVFFPKHRGDLVDTAVVAERMTAGRIESLR
+IPANPLDILAQHTVAAVAVADLDAQEWFDLVRRSAPFATLPFSAYESVLDLLAGRYPSDE
+FAELRPRILWDRENGTLAARPGAQRLAVTSGGTIPDRGLFGVFLASDGGADGAPGGAAAG
+DTAESASTASAGSARSGGRRVGELDEEMVYESRVGDVILLGATSWRIVDITADRVLVLPA
+YGQPGKLPFWRGDAAGRPAELGDAVGRFRRELDADPEAGRTRLAAAGLDPWAQDNLLAYL
+KDQREATGVLPTEQTLVVERFTDELGDWRVVLHSPYGMAVHAPWALAVGARLAQRYGLET
+GSGAAMAADDGIVLRIPLMDAEPPGAELFEFTAEELDEIVTAEVGGSALFAARFRENAAR
+SLLLPRRDPGRRTPLWQQRQRSAQLLDVARKHPRFPVILETVREVLQDVYDLSALKELAG
+RVSSRAVRLVEVTTTAPSPFSQSILFGYIAQFIYEGDSPLAERRAAALSLDPALLSELLG
+TEELRELLDAEVIAEVEAQLQRLAPDRRARGVEGVADLLRLLGPLSVAEAARRTRAEGEA
+EEAADEDAVAGMLAELERAGRAFRLRQDGVERFAAVEDAARLRDALGTPIPHGVPTAFLD
+PVDDPLGDLVGRYARTHGPFTAAEAGAALGLGGAVVLSVLQRLATERRVSTGAFRPEGTP
+GATGLDAEWCDAEVLRRIRMRSLAALRAEVEPVDQAAYARFLADWQHLRPRTGRDGAWRP
+PATLEGVDGVATVLDQLAGTPLPASAWESLVLPARVRDYAPALLDELLATGEYVWSGVGE
+ATGNDGWVALHPADAVDLTLRLPEPAEETPADAALRAAVLEVLAGGGAWFFPQLVERVRA
+VQAAGGDAGGAGRAVGPDPHRDPADLARGPAVLAALWGLVWDGRVGNDTFAPVRGLLSLG
+KTAHRTGRQTPRARTARTGGAAGAAAGRGLGGRLAGVRGRGRYAGLTSPEGGARGSAGLT
+AGTVGLSAAEQARSAGRWSLLPAAEQDPTIRAHATAELLLDRYGVITRGSVVAEEVPGGF
+AGQYRLLTRMEDAGQVRRGHFVDGLGGAQFSTGAVVDRLRGFQRDEEDAAVDTAPLALAL
+AATDPANPYGAALDWPSVPAGPDGVVPTGHRPGRKAGAVVVLIAGRLALYMERGGRTLLA
+FTEDPGELRAAAEALVWALRTGRTERLSLEKVNGGPVLGTPLAEALLAAGFYSSPSGIRF
+RN*
+>NZ_CP040019.1_59
+MSGPAETAAGAPTPAADVVLGRFTEPTRAWFTGAFEAPTPAQLGAWDAISSGRHALVIAP
+TGSGKTLSSFLWALDSFVREPAAEGTAATRVLYVSPLKALGVDVERNLRAPLVGITQTAA
+GLGRPVPRVRVGVRSGDTPAAERRRLQQDPPDILITTPESLYLMLTSQARSALAGVRTVI
+VDEVHAVAGTKRGAHLAVSLERLDSLLETPVQRIGLSATVEPASEVARFLGGTQPVTVVR
+PASAKRWDLTVTVPVPDLTDLSSPSAAHDLGPGSSPGGPGAEGGPGGAVTGGSIWPHVEE
+RIVDLVAERRSTLVFANSRRLAERLTGRLNEIWEARLEAAAAVEDPDAVPGFRTPGAGAG
+AASSTPATPSSSYPAQVAGQTGTGSGTVSDFARAHHGSVSKEQRAIVEEALKTGRIRCVV
+ATSSLELGIDMGAVDQVIQVESPPSVASGLQRVGRAGHQVGEVSRGVFFPKHRGDLVDTA
+VVAERMTAGRIEALRIPANPLDILAQQTVAAVAVADLDAQEWFDLVRRSAPFATLPLSAY
+ESVLDLLAGRYPSDEFAELRPRILWDRENGTLAARPGAQRLAVTSGGTIPDRGLFGVFLA
+SDGGPDGAPGGAAAGDTAESAGSARSGGRRVGELDEEMVYESRVGDVILLGATSWRIVDI
+TADRVLVLPAYGQPGKLPFWRGDAAGRPAELGDAVGRFRRELDADPAAGRERLAAAGLDA
+WAQDNLLAYLKDQREATGVLPTEQTLVVERFTDELGDWRVVLHSPYGMAVHAPWALAVGA
+RLAQRYGLETGSGAAMAADDGIVLRIPLMDAEPPGAELFEFTAEELEEIVTAEVGGSALF
+AARFRENAARSLLLPRRDPGRRTPLWQQRQRSAQLLDVARKHPRFPVILETVREVLQDVY
+DLPALKDLAGRVASRAVRLVEVTTPAPSPFSQSILFGYVAQFIYEGDSPLAERRAAALSL
+DPTLLAELLGTEELRELLDAGIIAEVEAQLQRLAPDRRARGVEGVADLLRLLGPLSAAEA
+ARRVRPEAGADDDGGAAAADVAAVGEMLAGLERAGRAFRLRQDGVERFAAVEDAARLRDT
+LGTPIPHGVPAAFLEPVDDPLGDLVSRYARTHGPFTAAEVGAALGLGGAVVLPVLQRLAT
+ERRVSTGAFRPDGAPGATGLDAEWCDAEVLRRIRLRSLAALRAEVEPVDQSAYARFLADW
+QHLRPRVGRDGAWRPPATLEGVDGVATVLDQLAGTPLPASAWESLVLPTRVRDYAPALLD
+ELLATGEYVWSGVAEAAGNDGWVALHPADAVDLTLRLPERPDGTGPDAAAPRDAALRADV
+REVLAGGGAWFFPQLVERVRAAQSARLGTGGPDGHGADLARGPAVLEALWGLVWAGEVGN
+DTFAPVRGLLSLGKTAHRTGRQTPRARTARTGGAGAGTAGRGLGGRLAGVRGRGRYAGLA
+SPDGGARGTAGPAAGMAGLSAAEQARAAGRWSLLPAAERDPTIRAHATAELLLDRYGVIT
+RGSVVAEEVPGGFAGQYRLLTRMEDAGQVRRGHFVAGLGGAQFSTGAVVDRLRGFQDDDG
+ADAPAAPRLDAFGLPLPAAPAEQRTPAALALAATDPANPYGAALDWPSVPAGPDGVVPTG
+HRPGRKAGAVVVLIRGELALYMERGGKTLLCFTQGAAELKAAAEALVWALRTGRTERLSL
+EKVNGGPVLGTPLAEAMLAAGFYSSPSGLRYRS*
+>NZ_CP083691.1_38
+MREDGGEGPAPEEAAPSPAAVPDADAVLARFSEPTRRWFTGAFAAPTAAQLGAWDAISSG
+RHALVVAPTGSGKTLSSFLWALDSFVREPAEPDVSATRVLYVSPLKALGVDVERNLRAPL
+IGITQTARSLGAPVPEVRVGVRSGDTPAAERRRLQQDPPDILITTPESLYLMLTSKARSA
+LSGVRTVIVDEVHAVAGTKRGAHLAVSLERLDALLDSPVQRIGLSATVEPAAEVARFLGG
+VQPVTVVRPVSAKRWDLTVTVPLPDMTDLSTPPPSALDAGRDGAAAGVPGEATGGSIWPH
+IEERIVDLVAPRRSTIVFANSRRLAERLTGRLNEIWEARQEAAAAVHDPDLVPGFRTPST
+AGEVLTDWLGTATGQTPAGAPRPPGGSAATSFPAQVAGQTGTGSGTVSDFARAHHGSVSK
+EQRALVEEALKTGRIRCVVATSSLELGIDMGAVDQVIQVESPPSVASALQRVGRAGHQVG
+EVSRGVFFPKHRGDLVDTAVVAERMAAGRIEALRIPQNPLDILAQQTVAAVALEDVDAEE
+WFDLVRRSAPFSALPHSAYESVLDLLAGRYPSDEFAELRPRILWDRELGELSARPGAQRL
+AVTSGGTIPDRGLFGVFLATEASDGAPGGAALGDTAESASGASSGSKRSGGRRVGELDEE
+MVYESRVGDVILLGATSWRIVDITADRVLVLPAYGQPGKLPFWRGDAAGRPAELGDAVGR
+FRRELDADPDAARDRLAAAGLDEWARENLLTYLADQRESTGRLPTEQALVVERFTDELGD
+WRVVLHSPYGMAVHAPWALAVGARLAQRYGLETGSGAAMAADDGIVLRVPLMDAEPPGAE
+LFEFSAEELEEIVTAEVGGSALFAARFRENAARALLLPRRDPGRRTPLWQQRQRSAQLLD
+VARKYPSFPVILETVREVLQDVYDLPALKDLAGRIASRAVQMVEVTTPAPSPFAQSILFG
+YVAQFIYEGDSPLAERRAAALSLDPALLAELLGTEELRELLDPEVIARVEAELQRTAPDR
+RVRGAEALADLLRIVGPLSVAEAAARTLPVEDAAPAPADEAAAGAPSAAHLAAVTAHLEG
+LERTGRAYRVRLNGEERFAAVEDAARLRDALGAPIPLGVPVAFHEPVEDPVGDLVSRYAR
+THGPFTAAEAGAALGLGGAVVLPVLQALASQRRVSQGAYRPDGTPGATGLEAEWIAAEVL
+QKVRRRSLAALRAEVEPVDQAAYARFLADWQHLRPRPGRPSPATLEGVDGVATVLDQLAG
+VPLPASAWESLVLPSRVRDYTPGLLDELLATGEYVWSGTADAPGNDGWVALHPADAVDLT
+LRRPEPPAQDVAAERLTARDHLLTVLAGGGAWFFGPLVERVRADAARAAEAEAGGEDGPR
+DPHAAAATLPRGPVILEALWDLVWAGRVGNDTFAPIRGLLSLGKTAHRTGRQTPRARTAR
+TGGAALSAAGTGGRGLGGRLAGVRGRGRYAGLAAPGSGAGAGTLPGAGLVGLSAAEEARA
+AGRWSLLPDPEPDPTIRAHAAAEVLLDRYGVITRGSVVAEEVPGGFAGQYQLLTRMEDAG
+QVRRGHFVDRLGGAQFSTGAVVDRLRSFQRDEDGPSPAEEEPAPRLDAFGMPVDESPRTD
+WSGWVADGVGGWTPAPQGHGAGMGTVGGAAGAREEPLPPALALAATDPANPYGAALDWPD
+LPAGPDGVAPTGHRPGRKAGAVVVLVHGALALYMERGGRTLLAFTQDGPVLRAAAQALVW
+ALRAARTDKLSLEKVNGGPLLGTPLAEALLAAGFYSSPSGIRYRS*
+>NZ_CP097650.1_285
+MSGPAETAAGAPTPAADVVLGRFTEPTRAWFTGAFEAPTPAQLGAWDAISSGRHALVIAP
+TGSGKTLSSFLWALDSFVREPAAEGTAATRVLYVSPLKALGVDVERNLRAPLVGITQTAA
+HQGRPVPRVRVGVRSGDTPAAERRRLQQDPPDILITTPESLYLMLTSQARAALAGVRTVI
+VDEVHAVAGTKRGAHLAVSLERLDALLDTPVQRIGLSATVEPAAEVARFLGGTQPVTVVR
+PASAKRWDLTVTVPVPDLTDLSSPAAAHDLGPGSSTGGLGDEGAVTGGSIWPHVEERIVD
+LVAERRSTLVFANSRRLAERLTGRLNEIWEARAEAAAAAEHPDAVPGFRTPDPTGFHGPA
+QVAGQTGTGSGTVSDFARAHHGSVSKEQRAIVEEALKTGQIRCVVATSSLELGIDMGAVD
+QVIQVESPPSVASGLQRVGRAGHQVGEVSRGVFFPKHRGDLVDTAVVAERMTAGRIESLR
+IPANPLDILAQHTVAAVAVADLDAQEWFDLVRRSAPFATLPFSAYESVLDLLAGRYPSDE
+FAELRPRILWDRENGTLAARPGAQRLAVTSGGTIPDRGLFGVFLASDGGADGAPGGAAAG
+DTAESASTASAGSARSGGRRVGELDEEMVYESRVGDVILLGATSWRIVDITADRVLVLPA
+YGQPGKLPFWRGDAAGRPAELGDAVGRFRRELDADPEAGRTRLAAAGLDPWAQDNLLAYL
+KDQREATGVLPTEQTLVVERFTDELGDWRVVLHSPYGMAVHAPWALAVGARLAQRYGLET
+GSGAAMAADDGIVLRIPLMDAEPPGAELFEFTAEELDEIVTAEVGGSALFAARFRENAAR
+SLLLPRRDPGRRTPLWQQRQRSAQLLDVARKHPRFPVILETVREVLQDVYDLPALKELAG
+RVSSRAVRLVEVTTTAPSPFSQSILFGYIAQFIYEGDSPLAERRAAALSLDPALLSELLG
+TEELRELLDAGVIAEVEAQLQRLAPDRRARGVEGVADLLRLLGPLSVAEAARRTRAEGEA
+EEAADEDAVAGMLAELERAGRAFRLRQDGVERFAAVEDAARLRDALGTPIPHGVPTAFLD
+PVDDPLGDLVGRYARTHGPFTAAEAGAALGLGGAVVLSVLQRLATERRVSTGAFRPEGTP
+GATGLDAEWCDAEVLRRIRMRSLAALRAEVEPVDQAAYARFLADWQHLRPRTGRDGAWRP
+PATLEGVDGVATVLDQLAGTPLPASAWESLVLPARVRDYAPALLDELLATGEYVWSGVGE
+ATGNDGWVALHPADAVDLTLRLPEPAEETPADAALRAAVLEVLAGGGAWFFPQLVERVRA
+VQAAAGDGGTGAAGGAVGPDPHRDPADLARGPAVLAALWGLVWDGRVGNDTFAPVRGLLS
+LGKTAHRTGRQTPRARTARTGGAAGAAAGRGLGGRLAGVRGRGRYAGLTAPEVGARGSAG
+LTAGTVGLSAAEQARSAGRWSLLPAAEQDPTIRAHATAELLLDRYGVITRGSVVAEEVPG
+GFAGQYRLLTRMEDAGQVRRGHFVDGLGGAQFSTGAVVDRLRGFQRDEEDAAVDAAPLAL
+ALAATDPANPYGAALDWPSVPAGPDGVVPTGHRPGRKAGAVVVLIAGRLALYMERGGRTL
+LAFTEEPGELRAAAEALVWALRTGRTERLSLEKVNGGPVLGTPLAEALLAAGFYSSPSGI
+RFRN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000081.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000081.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f5f968a194a7ca1e93c90e7035e0bef73dec6a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000081.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_340
+MQPQNPEARLLVVDDEPNIRELLSTSLRYAGFEVTAAANGREALDAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRAAGRHFPVVFLTARDGTEDKITGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTASLDDDAAVLRVDDLELDDDAHEVRRGGEVVELSPTEFKLLRYLMMNPNRVLSK
+AQILDHVWEYDFNGDASIVESYISYLRRKIDVGGREKMIHTKRGVGYMLRTADKR*
+>NZ_CP033200.1_65
+MQPQNPEARLLVVDDEPNIRELLSTSLRYAGFEVTAAANGREALDAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRSAGRHFPVVFLTARDGTEDKITGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTASLDDDAAVLRVDDLELDDDAHEVRRGGEVVDLSPTEFKLLRYLMMNPNRVLSK
+AQILDHVWEYDFNGDASIVESYISYLRRKIDVGGREKMIHTKRGVGYMLRTADKR*
+>NZ_CP040019.1_1230
+MIPVLLIEDEERIAAFVTKGMAAEGIAVTTAGTGAEGVGLAMTGAFELVILDLGLPDADG
+FDVLARIRRQDAHLPVIILTARSSAQDTVEGLTSGADDYMPKPFRFAELLARVRLRLRPG
+APAPEPTDTVMRHGDLELDPASHTARVDGRTVALSAREFALAEEFLRSPGQVLSREQLLD
+GAWGEDFESGSNVVDVYVRYLRAKIGAERILTVRGLGYRLAGEDELSG*
+>NZ_CP040019.1_2553
+MQSQNPEARLLVVDDEPNIRELLSTSLRYAGFEVTAAANGREALDAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRAAGRHFPVVFLTARDGTEDKITGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTASLDDDAAVLRVGDLELDDDAHEVRRGGEVVELSPTEFKLLRYLMMNPNRVLSK
+AQILDHVWEYDFNGDASIVESYISYLRRKIDVGGREKMIHTKRGVGYMLRAADKR*
+>NZ_CP083691.1_2408
+MQSQTPEARLLVVDDEPNIRELLSTSLRFAGFEVRAAGNGREALEAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRAAGRLFPVVFLTARDGTEDKVTGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTAPLDDDSAVLRVDDLELDDDAHEVRRGGEVVDLSPTEFKLLRYLMMNPNRVLSK
+AQILDHVWEYDFNGDASIVESYISYLRRKIDVGGRDKMIHTKRGVGYMFRTADKR*
+>NZ_CP097650.1_347
+MQPQNPEARLLVVDDEPNIRELLSTSLRYAGFEVTAAANGREALDAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRSAGRHFPVVFLTARDGTEDKITGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTASLDDDDAAVLRVDDLELDDDAHEVRRGGEVVELSPTEFKLLRYLMMNPNRVLS
+KAQILDHVWEYDFNGDASIVESYISYLRRKIDVGGREKMIHTKRGVGYMLRTADKR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000084.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000084.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4def6c00f36eb3661ff8b671d7249191fe94f0bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000084.fa
@@ -0,0 +1,42 @@
+>NZ_CP042169.1_392
+MSHVDTAPAASTPRAAEGRRPRRVKSQRAKSEARLGWLLAGPAFFVMLFVVLYPILQALY
+DSLFKYRLTAPGDREFVGLGNYGVILTDPVFWKGLGVTLLITVVTVVVELILGFLLALAM
+HHAIKQTRGLIRTIILVPYGIITVVSAFAWFYMFSIDSGYINAWFEWLPGVDADLNWFAQ
+GSTALFVIMLSEIWKTTPFISLLLLAGLAQVPGDLTEAASVDGASWWQRMKLVILPNMKA
+SIMVAVLFRAMDAFRIFDSIYIMTNGAYGTEVLSLLAYRTSIGRLEIGMGSAVSVILFLC
+VALMAVIAVKGFKVDLADRGGSK*
+>NZ_CP033200.1_121
+MSHVDTAPAASTPRAAEGRRPRRVKSQRAKSEARLGWLLAGPAFFVMLFVVLYPILQALY
+DSLFTYRLTAPGDREFVGLGNYGVILTDPVFWKGLGVTLLITVVTVVVELILGFLLALAM
+HHAIKQTRGLIRTIILVPYGIITVVSAFAWFYMFSIDSGYINAWFEWLPGVDADLNWFAQ
+GSTALFVIMLSEIWKTTPFISLLLLAGLAQVPGDLTEAASVDGASWWQRMKLVILPNMKA
+SIMVAVLFRAMDAFRIFDSIYIMTNGAYGTEVLSLLAYRTSIGRLEIGMGSAVSVILFLC
+VALMAVIAVKGFKVDLADRGGSK*
+>NZ_CP040019.1_2499
+MSHVDTAPAASTPRTAEGRRPRRVKSQRAKSEARLGWLLAGPAFFVMLFVVMYPILQALY
+DSLFKYRLTAPDDREFVGLGNYGVILSDPVFWKDLGVTLLITVVTVVVELILGFLLALAM
+HHAIKQTRGLIRTIILVPYGIITVVSAFAWFYMFSIDSGYINAWFEWLPGVDADLNWFAQ
+SNTALSVIMLSEIWKTTPFISLLLLAGLAQVPGDLTEAAAVDGASWWQRMKLVILPNMKA
+SIMVAVLFRAMDAFRIFDSIYIMTNGAYGTEVLSLLAYRTSIGRLEIGMGSAVSVILFLC
+VALMAVIAVKGFKVDLADRGGSK*
+>NZ_CP040019.1_2595
+MFTEVLPQQQVAPRPEAATAEPGIAESGIAESRTATDAPRPAKQKSRRTGRSFSIVPYLY
+VLPAVALLLLWTYLPLAQTFELSFYDWNLLPTKAKEPVGLENYATVLTLPEMQQALGNTV
+LYIGAFFLLSVALPVIFALLSKRVSGRAKTIYQALIFVPYLVTPVATSAIWRWLFAEEGG
+TIPAVAHFFGIDMGNVFREPGASMIAVMVIVGWQLLGFGVLVVSAGLSGISPDYEHAAGV
+DGARRWQITSRITLPLLSPSLVFLSLMTILLSAQWTFPMIDIITQGGPSGSSTNIYYLLY
+EFGFKNFDAGISAAAGVLFFIGFGLIALVFVELSEKLSFHDN*
+>NZ_CP083691.1_2363
+MSHVDTAPAASTPRAAEGRRPRRVKSARAKSEARLGWLLAGPAFFIMLFVVLYPTVQAFY
+DSLFKYRLTAPQDREFVGLGNYGVILSDPVFWKDLGVTVLITLVTVLVELVLGFLLALAM
+HHAIKQTRGLIRTIILVPYGIITVVSAFAWFYMFSIDSGFVNNWFDWVPGITSDLNWFAQ
+SGTALSVIMLSEIWKTTPFISLLLLAGLAQVPGDLTEAAAVDGASWWQRMKLVILPNMKA
+SIMVAVLFRAMDAFRIFDSIYIMTNGAYGTEVLSLLAYRTSIGRLEIGMGSAISVILFLC
+VALMAFTAVKVFKVDLADRGGSK*
+>NZ_CP097650.1_395
+MSHVDTAPAASTPRAAEGRRPRRVKSQRAKSEARLGWLLAGPAFFVMLFVVLYPILQALY
+DSLFKYRLTAPGDREFVGLGNYGVILTDPVFWKGLGVTLLITVVTVVVELILGFLLALAM
+HHAIKQTRGLIRTIILVPYGIITVVSAFAWFYMFSIDSGYINAWFEWLPGVDADLNWFAQ
+GSTALFVIMLSEIWKTTPFISLLLLAGLAQVPGDLTEAASVDGASWWQRMKLVILPNMKA
+SIMVAVLFRAMDAFRIFDSIYIMTNGAYGTEVLSLLAYRTSIGRLEIGMGSAVSVILFLC
+VALMAVIAVKGFKVDLADRGGSK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000089.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000089.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7e3db4743676a019c51a0158823eab3f4c99b06
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000089.fa
@@ -0,0 +1,56 @@
+>NZ_CP042169.1_474
+MIGSPGDESTALRMGSTARGRVLGRPWERGLPLLVLIVDVVAVLLATFVSAQLRFGGPRR
+TTLPGAEVIDYSVISLALSAAWVLALTIQGSRDIRILGVGSEEYKRVLQGTLYLFGTVAI
+LAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQRHRGRFRRRLLLVGGPKAVRH
+IFQTLDSEAGAGYAPVAAALPGYKARREDYLPIPVSTDLDTVEDVVALVEVRDVEAVVIT
+SGHSFVPGDVRRLGWELQERGVSLIMAPALVDVAGPRLHTQPLAGLPLIHLSTPRLSEGK
+AFAKRAFDVVASGLGLIAISPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSM
+VVDAEEIRQRLVSDGGDADVLFKMKDDPRITRVGKLIRRTSIDELPQLVNVLRGEMSLVG
+PRPHLPHEVEAYGQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGDL
+VILGRTVKAVVAADGAY*
+>NZ_CP033200.1_204
+MIGSPGDESTALRMGSTARGRVLGRPWERGLPLLVLIVDVVAVLLATFVSAQLRFGGPRR
+TTLPGAEVIDYSVISLALSAAWVLALSIQGSRDIRILGVGTEEYKRVLQGTLYLFGTVAI
+LAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQRHRGRFRRRLLLVGGPKAVRH
+IFQALDSEAGAGYAPVAAALPGYKARREDYLPIPVSTDLDTVEDVVAHVEERDVEAVVIT
+SGHPFVPSDVRRLGWELQERGVSLIMAPALVDVAGPRLHTQPLAGLPLIHLSTPRLSEGK
+AFAKRAFDVVASGLGLIAISPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSM
+VVDAEEIRQRLVSDGGDADVLFKMKDDPRITRVGKLIRRTSIDELPQLVNVLRGDMSLVG
+PRPHLPHEVEAYEQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGDL
+VILGRTVKAVIAADGAY*
+>NZ_CP040019.1_1199
+MLTPDSPYEERFAALNQSLRWEVADELRRANLARVDELHPPVTPRDTFYTRHGKRALDVG
+VSGAALLFSSPVIGALCLVTLKDLGQPVLFTQQRPGKHGKPFQMVKLRTMREAYDDQGKP
+LLGELRVTKTGRLIRRASLDELLNFWNIFKGDMSLIGPRPLVPEYVERFSRRHRQRLAVK
+PGLECPPPRPPQGPVTYDDQFENDCWYVENVSLKTDAWLTWRVLQTALDRRQNKARGSST
+RGSFMGYDADGTVITTAALPDWALNTVLERHGLLTSNSADARQEG*
+>NZ_CP040019.1_2405
+MFSSPGDESPALRTGSTARGRLLGRPWERGLPLLVFIVDVVAVLLATFVSAQLRFGGPRR
+TTLPGTEVIDYSVISLALSAAWVLALSIQGSRDIRILGVGSEEYKRVLQGTLYLFGTVAI
+LAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQRHLGRFRRRLLLVGGPKAVRH
+IFQALDSEAGAGYAPVAAALPGYKTRQEDYLPIPVSTDLDTVEDVVALVEVRDVEAVVIT
+SGHSFVPGDVRRLGWELQERGVSLIMVPALVDVAGPRLHTQPLAGLPLIHLSTPRLSEGK
+AFAKRAFDVVASGLGLIAISPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSM
+VVNAEEIKQRLVSDGGDADVLFKMKDDPRITKVGKFIRRTSIDELPQLVNVLRGDMSLVG
+PRPHLPHEVEAYEQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGDL
+VILGRTVKAVVAADGAY*
+>NZ_CP083691.1_2285
+MTSSAVTTSQTGRGGSSVHARVLGAPWERGLPRLVLLADVVAVVLAAFLSSELRFGTARN
+AAVPGAESVNYLLVGAVLSASWVVALGVDGSRDIRILGIGAEEYKRVLRGTLYLFGMIAI
+LAYAFAFEVARGYVALALPIGLLLLMLGRFLIRGWVARGRHRGAMRRRLLLVGGPQAVKY
+VHDTLDSEAGAGYKPIAAVLPGYRARDEGWLPIPVTTEVDGVDELVAQVREMDIEAVVIT
+SGHPFVPDDVRRLGWDLQERGISLIMAPALVDVAGPRLHTQPLAGLPLLHLSTPRLSRGK
+AFVKRSFDVVASGLGMLVISPLLLTVAIAVKATDGGPVLFRQERVGLRGEHFTMLKFRSM
+VVDAEEIKQQLMSDRGEEDVLFKMKDDPRITRVGRFIRRTSIDELPQLVNVLRGDMSLVG
+PRPHLPHEVEQYGQYVHRRFLVQPGITGLWQVSGRSDLSWEDAVRLDLYYVENWSVLGDL
+VILGRTVKAVLAADGAY*
+>NZ_CP097650.1_473
+MFASPGDESTTLRMGSTARGRVLGRPWERGLPRLVLVVDVVAVLLATFVSAQLRFGGPRR
+TTLPGAALVDYSVISLALSAAWVLALTIQGSRDIRILGVGTEEYKRVLQATLYLFGTVAI
+LAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQRHRGRFRRRLLLVGGPKAVRH
+IFEALDSEAGAGYAPVAAALPGYKARQEDYLPIPVSTDLDTVEDVVALVEVRDVEAVVIT
+SGHSFVPGDVRRLGWELQERGVSLIMAPALVDVAGPRLHTQPLAGLPLIHLSTPRLSEGK
+AFAKRAFDVVASGLGLIAISPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSM
+VVDAEEIRQRLVSDGGDADVLFKMKDDPRITRVGKLIRRTSIDELPQLVNVLRGDMSLVG
+PRPHLPHEVEAYEQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGDL
+VILGRTVKAVIAADGAY*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000091.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000091.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7312a697a4f830de41e48b881c4337245220f8a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000091.fa
@@ -0,0 +1,42 @@
+>NZ_CP042169.1_499
+MTPRGSCWSSLPVGARFRLWNTLDPMHLLVTGGAGFIGSNFVHHVVRETGHDVVVLDKLT
+YAGNRENLAGLPEDRVTLEVGDICDAALVDRLVAESDAVVHYAAESHNDNSLNDPSPFIQ
+TNIVGTFVLLEAARKHGKRFHHVSTDEVYGDLELDDPAKFTETTPYNPSSPYSASKAGSD
+HLVRAWVRSFGVQATLSNCSNNYGPYQHIEKFIPRQITNLIDGVRPRLYGQGVNVRDWIH
+TEDHSSAVLRILERGEIGRTYLIGADGEKNNREVVEILLELFDRPADDYDLVADRPGHDL
+RYAIDNTALRTELGWEPRFTDIRAGLADTVRWYRENEAWWRPAKAAVEATYRAQGQ*
+>NZ_CP033200.1_230
+MHLLVTGGAGFIGSNFVHHVVRETGHDVVALDKLTYAGNRENLAGLPEDRVTLEVGDICD
+AALVDRLVAESDAVVHYAAESHNDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVST
+DEVYGDLELDDPAKFTETTPYNPSSPYSASKAGSDHLVRAWVRSFGVRATLSNCSNNYGP
+YQHIEKFIPRQITNLIDGVRPRLYGQGVNVRDWIHTEDHSSAVLRILERGEIGRTYLIGS
+DGERNNREIVEILLELFDRPADDYDLVADRPGHDLRYAIDNTALRTELGWEPRFTDIRAG
+LADTVRWYRENEAWWRPAKAAVEATYRAQGQ*
+>NZ_CP040019.1_1197
+MRFVVTGAGGFLGSNVVRELLAETDHDVVAVSSQTDRELAAQLERAPYPALRRFPQVHPR
+TRLLEAGFLRDGDIVINCAFPWNRGGRAMADGLEYLTRLFQSAHAVALHTFVNVSSQSVY
+SQARTEAADESSPVECDTPYSTGKYAMELAAELVLPPKVLVNARMSSLIGPGYDVRIVNR
+FIARFLADEPVSIQGGDQVFDFMDVRDAARALIAVALAGPPEGSAALNIGSGAPRTLRDI
+AQTVADVVRTHTGHDPRIAWEPSAGDDRTLGLDSGLLRREYGFAPRHTLEDSALSILQAM
+TSAQSASVGETPTGSVEGGRR*
+>NZ_CP040019.1_2382
+MHLLVTGGAGFIGSNFVHHVVRETGHDVVVLDKLTYAGNRENLAGLPEDRVTLEVGDICD
+AALVDRLVAQSDAVVHYAAESHNDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVST
+DEVYGDLELDDPAKFTETTPYNPSSPYSASKAGSDHLVRAWVRSFGVQATLSNCSNNYGP
+YQHIEKFIPRQITNLIDGVRPRLYGQGVNVRDWIHTEDHSSAVLRILERGEIGRTYLIGS
+DGERNNREIVEILLELFDRPADDYDLVADRPGHDLRYAIDNTALRTELGWEPQFTDIRAG
+LADTVRWYRENEAWWRPAKAAVEAKYRAAGQ*
+>NZ_CP083691.1_2261
+MHLLVTGGAGFIGSNFVHHVVRETGHDVVVLDKLTYAGNRENLAGLPEDRVTLEVGDICD
+AALVDRLVAESDAVVHYAAESHNDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVST
+DEVYGDLELDDPAKFTETTPYNPSSPYSASKAGSDHLVRAWVRSFGVQATLSNCSNNYGP
+YQHIEKFIPRQITNLIDGVRPRLYGQGINVRDWIHTEDHSSAVLRILERGEIGRTYLIGS
+DGERNNKEIVEILLELFDRPADDYDLVADRPGHDLRYAIDNTALRTELGWEPQFTDIRAG
+LADTVRWYRENEAWWRPAKDAVEATYRAQGQ*
+>NZ_CP097650.1_499
+MRILVTGGAGFIGSNFVHHLVRETDHDVVVLDKLTYAGNRDNLVGLPESRVRLEIGDICD
+AALVDRLVAESDAVVHYAAESHNDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVST
+DEVYGDLELDDPAKFTETTPYNPSSPYSASKAGSDHLVRAWVRSFGVQATLSNCSNNYGP
+YQHIEKFIPRQITNLIDGVRPRLYGHGVNVRDWIHTEDHSSAVLRILERGEIGRTYLIGS
+DGERNNREIVEILLELFDRPADDYDLVADRPGHDLRYAIDNTALRTELGWEPRFTDIRAG
+LADTVRWYRENEAWWRPAKAAVEATYRAQGQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000095.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000095.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9522f2f414f7fbd6d42363e330763b9f72278431
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000095.fa
@@ -0,0 +1,36 @@
+>NZ_CP042169.1_588
+MSLGGFFAEMVQSGALLVAMPLAAIAGLVSFLSPCILPLVPGYLGYVSGLADPRRADNRR
+RVMTGVGLFILGFAAVFTFYGAAFGVIGGWLLQWQDALIRALGVFVVLMGLVLIGWLPFL
+QNTRRMSFQPKTGIVGAPLLGVVFGLGWTPCMGPTLSAVLALSTTTGDPWRGALLGFLYC
+LGLGIPFVLVAMGLDWVTRTLGFVRRHIRAFNIIGGILLVLVGVLMVTGIWTLWIYQLQN
+LAGTFTTPV*
+>NZ_CP033200.1_1726
+MSLGGFFAEMVQSGALLVAMPLAVVAGLVSFLSPCILPLVPGYLGYVSGLADPRRADNRR
+RVMTGVGLFIMGFAAVFTLYGAAFGVIGGWLLQWQDALIRALGVFVILMGLVLIGWLPFL
+QNTRRMSFQPRTGIAGAPLLGVVFGLGWTPCMGPTLSAVLALSTTTGDPWRGALLGFLYC
+LGLGIPFVLVAMGLDWVTRTLGFVRRHIRAFNIIGGVLLVLVGVLMVTGIWTLWIYQLQN
+LAGTFTTPV*
+>NZ_CP040019.1_385
+MGEYFAQTVQSGALLLAIPLAAIAGIVSFLSPCILPLVPGYLGYVSGLSDPTRPDNRRRV
+MTGVGLFILGFAAVFTLYGAAFGLIGGWLLRWQDLLIRILGVLVILMGLALMGMFTFLQR
+TTTPSFTPRTGLAGAPLLGLGFGLGWTPCMGPTLSAVLALSTTTGGAWRGALLGFVYCLG
+LGIPFVLVARGLGWVSTALGFVRRHMRAFNIAGGTLLVLVGVLMATGIWTVWIYQLQNLA
+GTFTTPV*
+>NZ_CP040019.1_2591
+MDVQQLVADGQLLVASVIALAAGLLSFLSPCVLPLVPGYLAYVSASAGAAPGEKPARGRL
+VLGSLLFVAGFTAVLVALLAAAGTVGVWLLEWEQLITRVMGAVVILMGLVFIGAFGFMQR
+TTKLRIKPRTGLLGAPLLGVVFAIGWTPCLGPTLAAIMTLSVQQGSVARSVVLALAYCIG
+LGLPFVLAAFGFGWMTQTMTFFKRHIRTVNLIGGVLLILIGLLMVTGLWSQMMYALQAVI
+GGYVTPL*
+>NZ_CP083691.1_2153
+MGEYFAQTVQSGALLLAIPLAAIAGIVSFLSPCILPLVPGYLGYVSGLSDPTRPDNRRRV
+MTGVGLFILGFAAVFTLYGAAFGLIGGWLLRWQDLLIRILGVLVILMGLALMGMLTFLQR
+TTTPSFTPRTGLAGAPLLGLGFGLGWTPCMGPTLSAVLALSTTTGGAWRGALLGFVYCLG
+LGIPFVLVARGLGWVSTALGFVRRHMRAFNIAGGTLLVLVGVLMATGIWTAWIYQLQNLA
+GTFTTPV*
+>NZ_CP097650.1_1949
+MSIGNYFAETVNSGALLIAAPLAMIAGIVSFLSPCILPLVPGYLGYVSGLSNPTHPDNRR
+RVLTGVGLFILGFAAVFTLYGAAFGTIGHWLVRWQDPMIRVLGVLVIVMGLVMVGKFSLF
+QRTLKPTLAPRTGLAGAPLLGVVFGLGWTPCMGPTLSAVLALSTTTGDPWRGALLGFLYC
+LGLGIPFLLAAAGINWVTTALSYIRRNIRVFNIIGGCLLVLVGVLMVSGLWMLWMYQLQN
+LAGTFTTPV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000099.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000099.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b1c201d4c873071427c3fe59d43a22aadd823b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000099.fa
@@ -0,0 +1,33 @@
+>NZ_CP042169.1_604
+MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYQWLAEPVSAREWSDAHAANAVLDAHAGDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVRVRCCHWFRRGSGKRPGPAVHDDLVRREFR
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLALDALQMALARR
+GGKAEVQGCRVHSDRGSQGGFNRSSQHPLGITGGMGDGKQGLGEEDQ*
+>NZ_CP033200.1_358
+MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFR
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLAVDALQMALARR
+GGKAEVQGCRVHSDRGSQFRARRFVETLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNV
+LNRRRWQSFDQLRLAIVSWIERTYHRRRRQARLRKLTPVEFEMVQSVQAAAAA*
+>NZ_CP040019.1_378
+MTYPVVKDLARDGIPVRLCCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFR
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLAVDALQMALARR
+GGKAEVQGCRVHSDRGSQFRARRFVETLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNV
+LNRRRWQSFDQLRLAIVSWIERTYHRRRRQAPLGRLTPVEFEMVQSVQAAAAA*
+>NZ_CP040019.1_397
+MTYPVVKDLARDGIPVRLCCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFR
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFLKRPGSDEDS*
+>NZ_CP083691.1_2139
+MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYPWLAEPVSAREWSDAHAANAVFDAHADDP
+EFGYRFLADELRGRGLDVSDHQVLKACRLVRVRCCHSIRRGSGKRPGPAVHDDLVRRQFR
+ADKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSIDRRMSSQLAVDALQMALARR
+GGKAGVQGCRVHSDRGSQFRARRFVETLRVNSLIGSMGRVGAAGDNAAMESFFALLQKNV
+LNRRRWDSFAQLRLAIVSWIERTYHRRRRQARLGKLTPVEFEMVQSVQAAAAA*
+>NZ_CP097650.1_582
+MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFA
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLAVDALQMALGRR
+GGKAEVQGCRVHSDRGSQFRARRFVETLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNV
+LNRRRWQSFDQLRLAIVSWIERTYHRRRRQARLGKLTPVEFEMVQSVQAAAAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000104.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000104.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f222114dffb0fb618a40255239bd436399e41fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000104.fa
@@ -0,0 +1,37 @@
+>NZ_CP042169.1_633
+MTSAVSTSPAPPRGGRDLKSAVLVGVGLLATALVGLFWLDWLLVLLVVALLVGAVSEIAT
+AVRGIGLDVPRPPLWVAAAVLPLTAWRWGVPALFIALVACLALVAVWTALTRRRPAGQFM
+LAGVFIVLWAPFLLSFAAALLDEPLGHRMVAVLLLMVVSNDTFGYIVGYRFGRTPIAPRI
+SPKKSWEGLAGSLAGSVLVGVVAVPLLVGQPWWVGAVLGVTTVAAATSGDFSESMVKREL
+GIKDMSSALPGHGGVMDRLDSLVFAAPVAYTVLALPLT*
+>NZ_CP033200.1_379
+MTSAVSTSPAPPRGGRDLKSAVLVGVGLLATALVGLFWLDWLLVLLVVALLVGAVSEIAT
+AVRGIGLDVPRPPLWVAAAVLPLTAWRWGVPALFIALVACLALVAVWTALTRRRPAGQFM
+LAGVFIVLWAPFLLSFAAALLDEPLGHRMVAILLLMVVSNDTFGYIVGYRFGRTPIAPRI
+SPKKSWEGLAGSLAGSVLVGVVAVPLLVGQPWWVGAVLGVTTVAAATSGDFSESMVKREL
+GIKDMSSALPGHGGVMDRLDSLVFAAPVAYTVLALPLT*
+>NZ_CP040019.1_153
+MVGLLGPTAGGLLLGVVGVLAAASVIAAVLRARMGARNPELIGNLVQRIGAWWAMVAVLA
+AVLALGETATLLLFLVLTWLSLREFLTISPTGRADHRTLVWLFFVVTPLHYWFVWEHWYG
+MFSVFIPVYAFLFLPVRAALAGRTEGFLRRAAAVQWAAMVCVYAVSHIPAVLQLPVAMEH
+GRHMAEGSAPGSGDEAGALLLLFLLLVVQGSDVFQYVWGKTLGRRPIAPSVSPNKTWEGF
+VGGVLTATALGAALSFLTPFPWWVAALFAFVSCLLGFGGGLVMSAIKRDRGIKDFGSLIP
+GHGGIMDRIDSLVFAAPVFFHLVRFFYA*
+>NZ_CP040019.1_2263
+MTTAVSTPAPPRGGRDLKSAVLVGVGLLVLALVGLVWLDWLLVLLVVALLVGAVTEVATA
+VRGIGLQVPRPPLWAAAVALPVSAWLWGVPALFVALAACLALLAVWTALTRHRPTGQFML
+AGVFIVLWAPFLLSFAVAMLDQPRGNLLVAITLLMVVSNDTFGYIVGYRFGRTPIAPRIS
+PKKSWEGLAGSLAGSALVGVVTVPLFVGQPWWVGAILAVTTVAAATSGDFSESMVKRELG
+IKDMSSALPGHGGVMDRLDSLVFAAPVAYTVLALPLT*
+>NZ_CP083691.1_2116
+MTPDATAPSPPRGGRDLRSAVLVGVGLLGTALVGLVWLPWLLVLLVVSLLVGAVNEVAVA
+IRQIGLDVPRPPLWVGATVMPLAAWTGGIPALFLALMASLVLMFAWTAVTRRRPTGQFML
+AGTFVLLWAPFLLSFAAALLDQPAGHMMVVCLVLMVVSNDTFGYMVGYRWGRTPIAPRIS
+PKKSWEGALGSLAGSVAVGSVLVPVLVGHPWWAGALLGALTVGAATAGDFSESMVKRELG
+IKDMSSALPGHGGIMDRLDSLVFAAPVAYAVLALPLS*
+>NZ_CP097650.1_602
+MTSAVSTSPAPPRGGRDLKSAVLVGVGLLATALVGLFWLDWLLVLLVVALLVGAVSEIAT
+VVRGIGLDVPRPPLWVAAAVLPLTAWRWGVPALFIALVACLALVAVWTALTRRRPAGQFM
+LAGVFIVLWAPFLLSFAAALLDEPLGHRMVAVLLLMVVSNDTFGYIVGYRFGRTPIAPRI
+SPKKSWEGLAGSLAGSVLVGVVAVPLLVGQPWWVGAVLGVTTVAAATSGDFSESMVKREL
+GIKDMSSALPGHGGVMDRLDSLVFAAPVAYTVLALPLT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000107.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000107.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f42de59f937870c4b268576300a93ca11ce0ba9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000107.fa
@@ -0,0 +1,22 @@
+>NZ_CP042169.1_723
+MLSGFCLALGTWSTVAAEAADAALARRWGAAARLWTAHLGLGLVAVVVGWGAGLGLHAVL
+AG*
+>NZ_CP042169.1_724
+MSGAGYEVFALFQVALLACLAAGGVLGALARRRLTDRLGPRGLLTANTTAALLLGVTVGL
+AVPELVYASGG*
+>NZ_CP033200.1_463
+MSGAGYEVFALFQVALLACLAAGGALGALARGRLTDRLGPRGLLTANTTAALVLGATVGL
+AVPELVYASESWGDGQGLMLVAAVSAVVSGFCLALGTWSTVAAEAADAALARRWGAAARL
+WTAHLGLGLVAVVVGWGAGLGLHAVLAG*
+>NZ_CP040019.1_2139
+MSPALMGASPWEWVLGLAVLAAGGALGALLRLTLQEHLPRRGVLAANTLAAGVLGFSLAL
+ALPSLVYASGLAGDPLGVAGLLVASLTAGFCLALGTWSTVAGQAADAVLAGRWGAAGRIW
+AAHLGLGLLAAAAGWGLGLGARLLVA*
+>NZ_CP083691.1_2030
+MSAGTVLLTVLLAGLAAAVGAGLRHLADHRWGGRGVLLANVTASALAGALFAIGFGPGSA
+DPEGPAGAALALGAAGAFVLALGTWSTVAFQAAQEVLAGRTRRAVRVWLVHLASGTAAAV
+VGVLAVGFLVR*
+>NZ_CP097650.1_687
+MSGAGYEVFALLQVALLACLAAGGALGALVRRRLTDRLGPRGLLTANTTAALLLGVTVGL
+AVPELVYASGGGGDGQGLVLVAAVSAVVSGFCLALGTWSTVAAEAADAVLARRWGTAARL
+WAAHLGLGLVAVVVGWGAGLGLHAVLAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000110.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000110.fa
new file mode 100644
index 0000000000000000000000000000000000000000..74c538dc187283b63243afcd4a6890a5aed6cd71
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000110.fa
@@ -0,0 +1,54 @@
+>NZ_CP042169.1_811
+MSLEFRTSEESPDVTRVVATHLPTRHGDFALLGYRDGRGTDHVALTLGDVAADDGELPLV
+RLHSECLTGDALGSYRCDCGEQLDAALQAIGAAGRGVLIYIRGHEGRGIGLLDKLRAYAL
+QDSGIDTVDANTHLGLPADARDYDQSAQILRELGVGKIRLLSSNPAKQEALEALGIHVEA
+RVRLNVADRPENSRYLSTKRARMRHDLPPERNAWDLLAGARVPTGPLTPQEEALVLRYGP
+LVEAGPRLVIGQLGQSLDGFIASRTGDACFVTGEADREHLHRLRALVDAVLVGAQTVAAD
+DCQLTVRAVNGADPARVVVDPHARIPLTAKVLTDPRSRTLWLVGSDASVPASLAPHVSVH
+RLETSTGFEPAAILQYLADQGLGRVLIEGGGLTVSGFLHAGVLDRLYLTSAPLLVGDGVP
+GIRFDGADALSGALSAPVRRFVLGDDVCTEFDFSAAKPASPAALHRADQENQPTGQD*
+>NZ_CP042169.1_1024
+MSEHIRLDPVPVAIAAIAAGRPVVVVDDADRENEGDLIYAAALATDEVTAFTVRHTSGVI
+CAPLPAGLADRLALPPMTTVNEDPKGTAYTVSVDAAAGVTTGISAADRTRTLRLLADPGA
+APGDLTRPGHVFPLRAVPGGVRARRGHTEAGVELCRLAGVAPVAAIAELVHDDGTMMRLP
+ALREFSDEHGLVLISIEDLVAHLEETTPALTAVPAEATLPTRHGLFRVSVHVDAETGAEH
+LLLVAGETDSERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALARAAAEGGAVLYLRGHE
+GRGIGLANKIRAYRLQEEGMDTVEANLALGLPAEARDWAGAAAVLTAAGHRRIRLVTNNP
+AKVAGLRAAGIDVVERVPAPTPVTEHNVVYLRTKRDRMAHALADRVLEPPTATGGPATPA
+DDPTTDPTHPTHQEDTP*
+>NZ_CP033200.1_753
+MSEHIRLDPVPAAIAAIAAGRPVVVVDDADRENEGDLIYAAALATDEVTAFTVRHTSGVI
+CAPLPAGLADRLALPPMTTVNEDPKGTAYTVSVDAAAGVTTGISAADRTRTLRVLADPGA
+APGDLTRPGHVFPLRAVPGGVRARRGHTEAGVELCRLAGVAPVAAIAELVHDDGTMMRLP
+ALREFSDEHGLVLISIEDLVAHLEETTPTLTAVPAEATLPTRHGLFRVSVHVDAETGAEH
+LLLVAGETDPERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALARAAAEGGAVLYLRGHE
+GRGIGLANKIRAYRLQEEGMDTVEANLALGLPAEARDWAGAAAVLTAAGHRRIRLVTNNP
+AKVAGLRAAGIDVVERVPAPTPVTEHNVVYLRTKRDRMAHALADRVLEPPTATGGPATPA
+DDPTTDPTHPTHQEDTP*
+>NZ_CP040019.1_1794
+MSDSIPLDAVPAAIAAFAAGRPVVVVDDADRENEGDLVYAAALATDAVTAFTVRHTSGVI
+CAPMPADLADRLALPPMTARNEDPKGTAYTVSVDAATEVSTGISAADRTRTLRILADPAA
+GPADLTRPGHVFPLRAVPGGVRARRGHTEAGVELCRLADVAPVAAIAELVHDDGTMMRLP
+ALREFADEHGLVLISIEDLVRHLEEEGPTPVPVPAEATLPTRHGVFRVSVHADAVTGAEH
+VLLVAKKAGEAGEADPERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALSRAGSEGGAVL
+YLRGHEGRGIGLANKVRAYRLQEQGLDTVEANIALGLPTEARDWAGAAAVLAAAGHTRVR
+LVTNNPAKVAGLQAAGIDVVERVPAPTPVTEHNLGYLRTKRDRMAHALADRVLEHPVAPG
+HEDPRHETPTHQEDTP*
+>NZ_CP083691.1_1681
+MSIDTAVEPAAPVDIRLDPVADAVAAIAQGRPVVVVDDADRENEGDLIYAAALATDAVTA
+FTVRHTSGVICAPLPAELADRLNLPPMTARNEDPKGTAYTVSVDAVAGVTTGISAADRTV
+TLRVLAGEESTAADLTRPGHVFPLRAVPGGVRARRGHTEAGVELCELADLPPVAAIAELV
+HDDGTMMRLPALREFADEHSLVLISIEDLVAHLHEHRPEQRVVPAEAALPTAHGDFRISV
+HPDTATGAEHVLLVADRPGSATGGDADAPVTVRVHSECLTGDVFGSLRCDCGPQLQAALD
+AAARDGGAVLYLRGHEGRGIGLTNKIRAYRLQEEGLDTVEANLALGLPAEGRAYAGAADL
+LREAGLTRIRLVTNNPAKVDALRAAGIDVVERVPAPTPVTEHNAAYLRTKRDRMHHELAD
+RDLGDA*
+>NZ_CP097650.1_970
+MSEHIRLDPVPAAIAAIAAGRPVVVVDDADRENEGDLIYAAALATDEVTAFTVRHTSGVI
+CAPLPAGLADRLALPPMTTVNEDPKGTAYTVSVDAAAGVTTGISAADRTRTLRVLADPGA
+APGDLTRPGHVFPLRAVPGGVRARRGHTEAGVELCRLAGVAPVAAIAELVHDDGTMMRLP
+ALREFSDEHGLVLISIEDLVAHLEETTPTLTAVPAEATLPTRHGLFRVSVHVDAETGAEH
+LLLVAGETDPERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALARAAAEGGAVLYLRGHE
+GRGIGLANKIRAYRLQEEGMDTVEANLALGLPAEARDWAGAAAVLTAAGHRRIRLVTNNP
+AKVAGLRAAGIDVVERVPAPTPVTEHNVVYLRTKRDRMAHALADRVLEPPTATGGPATPA
+DDPTTDPTHPTHQEDTP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000113.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000113.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24752d6db98b45157f91639bc7df1fb9aa864e98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000113.fa
@@ -0,0 +1,31 @@
+>NZ_CP042169.1_958
+MTTFAAAERARLADLLLEKGPDAPTLCGGWSTRDLAAHLWLRERRPDAFAALFIPPLSRH
+LDRLTAETTRRDYAEVVREWAAGPSALNPMRAADRHVNAAEHFIHLEDVRRGESATGGSL
+PAPRSFSPDEEDALYRSLRRMAPLFLRKSAAPVVLQGPGRAPVTVTRGAVALRAPVTVTG
+EVGELLLWASGRDAVHVELDGDASAAVRTAL*
+>NZ_CP033200.1_682
+MTTFAAAERARLADLLLEKGPDAPTLCGGWSTRDLAAHLWLRERRPDAFAALFIPPLSRH
+LDRLTAETKRRDYAEVVREWAAGPSALNPMRAADRHVNAAEHFIHLEDVRRGESSAGGSL
+PAPRPFSPDEEDALYRSLRRMAPLFLRTSTAPVVLQGPGRAPVTVTRGAVALRAPVTVTG
+EVGELLLWASGRDAVHVELDGDASAAVRTAL*
+>NZ_CP040019.1_1789
+MAAMADFPVTADRQGPDYAAASRAALVEALTAAGPGMPTLCAGWRTEHLAAHLALRDSSP
+TAPGLFLPPLAAVLERRTRALGDAHAGDRGYAELVARIGRGPLPAPADDGVRGRLRGLAA
+RARGSRPGRAVAGRVQLLEFFVHTEDVRRAQDRWAPRILADDYADALFTRLHARAALLYR
+GEETGVVLVRRARAGSRTDNAPLTARRPGPDGVGVRVTGPAGELAMHAFGRRGAALVTQD
+RFDADPAEDGPGAA*
+>NZ_CP040019.1_1863
+MTTFAAAERARLADLLLEKGPHAPTLCGGWSTRDLAAHLWLRESRPDAFAALFIPPLSCH
+LDRLTAETTRRDYVEVVREWALGPSALNPMRAADKHVNAAEHFIHLEDVRRGESAAGGSL
+PAPRSFSPDEEDALYRSLRRMAPLVLRTSTAPVVLQGPGRAPVTVTRGAVALRAPVTVTG
+EVGELLLWASGRDAVHVELDGDASAAVRTAL*
+>NZ_CP083691.1_1807
+MTTFAAAERARLADLLLEKGPHAPTLCEGWSTRDLAAHLWLRENRPDAMASMFVKPLAGH
+LDRLTAHTKRREYVDVVGEWSQGPASLNPMRVADRHVNAAEHFIHLEDVRRGEAVAGGVT
+PAPRDFTPSEEDALYRSLRRMAPLLLRKSAAPVVLQAPGRAPITVAREAVAVKAPVTVSG
+PVGELLFWASGRDAVHVDLDGDHAAVVRGGI*
+>NZ_CP097650.1_900
+MTTFAAAERARLADLLLEKGPHAPTLCGGWSTRDLAAHLWLRESRPDAFAALFIPPLSRH
+LDRLTADTKRRDYAEVVREWAAGPSALNPMRAADRHVNAAEHFIHLEDVRRGESSTGGSL
+PAPRPFSPDEEDALYRSLRRMAPLFLRKSAAPVVLQGPGRAPVTVTRGAVALRAPVTVTG
+EVGELLLWASGRDAVHVEIDGDASAAVRTAL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000119.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000119.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e07c197d607772a437920cf34f39225d2105fa95
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000119.fa
@@ -0,0 +1,54 @@
+>NZ_CP042169.1_1060
+MTPHTDAPEGPSLRRLADAAEDRLGEHGLALRDLGVLGPEDPAASHFAAAVERGFYETVP
+TGAALRQQLEAHAADGRRRLGVYAPGDDPAARRPAATFEDFVQPLTTSPGRTVDAWLITD
+VTVSPDARRRGVLRAMMLRSLADARDAGLCAAALTATEAAIYGRFGFGAATRWHAVRIDV
+SGAPAFTGAPAGGRVTVEEPREIPGLVDELYGRVLPATPGSVQRTSFSVPRWEDREASRN
+EGRGSGLYAAVHRDDDGRVQGVALYRFEGWEKEPPTITVTAFLAATADARRGLVHHLARL
+DLVERIEWGRAPEPGWLEALFVDERRVSRHRGSDDLYLRVLNLPAAMAARGWAGDGEVVV
+AVEDALGAIDGTWRLTVRQGRGAAERLGPAADAVGLDAGLRLDAARFSALWLGGHSRGAG
+AAVLAEAGVVAELRAGAAEAFDGLVRPSRPLHTLVGF*
+>NZ_CP033200.1_789
+MTPHTDTPEGPSLRRLADAAEARLGEHGLALRDLGVLGPEDPAASHFAAAVERGFYETVP
+TGAALRQQLEAHAADGRRRLGVYAPGEDPAARRPAATFEDFVQPLTTWPGRAVDAWLITD
+VTVSPDARRRGVLRAMMLRSLADARDAGLCAAALTATEAAIYGRFGFGAATRWHAVRIDV
+SGAPALTGAPAGGRVTVEEPREMPGLVDELYGRVLPATPGSVQRTSFSVPRWEDREASRN
+EGRGSGLYAAVHRDDDGRVQGVALYRFEGWEKEPPTITVTAFLAATADARRGLVHHLARL
+DLVERIEWGRAPEPGWLEALFVDERRVSRHRGSDDLYLRVLNLPAAMAARGWAGDGEVVV
+AVEDALGAIDGTWRLTVRQGRGAAERLGPAADAVRMGAGLRLDAARFSALWLGGHSRGAG
+AAVLAEAGVVAELRAGAAEAFDGLVRPSRPLHTLVGF*
+>NZ_CP040019.1_1765
+MSINPAAAAHAADATAAQDALARHGLVLRTLAPLSRGFDGADPARAEHPAHVRHTAAVEK
+GFYEEVPQGAAADQDLGVSADDAKVLRGVYLSADDPARREPVGTFVDWTSRLTTSPGAEL
+PVWMISNVTVSPGHRRRGILRAMMTASLEEAVAAGVPVAALTASESTIYGRFGFGAASTA
+RTVRVDVRGDVVLAADAAGRTDEDAGTVLREDPRELAGVVEALHDRVRRGTPGSVHRPTG
+HVIRWEDRSAAKNDGRGSGLFAAVHRDADGAVQGVALYRFDGWGKEPTTVSVEVFLAATD
+AAARQLWRYLTRLDLIERLRMTRCPDDGGLEQVLADRRRVRTKSVWDDLYLRVLDVPVCL
+GGRGYAPEVVGEVVLAVADAAGHAAGTWRLRVADGVGRAERLADDARADLALDVAHLSAV
+WLGGVRAGALVRAGVVDEREPGAAARLDALLAPAAAVHLLTGF*
+>NZ_CP040019.1_1766
+MTPRTDAPDAWLDPAPATAEALAAHGLELLRVPSPWETGDADPDAPFDHARRWADAPAVR
+RHTAVLQRNFHEVGDPDFALADRFIGVEQGDRRRLSGVYPQGADPAATDPVGTLVDFTKD
+LNVGDGRMLPAWCLTEVTVSPTHRRRGILRAMMTESLRRAHAARVPIALLTATEATLYRR
+FGFGVSTYHRSVWLDVTRGVQLRGRRPDGSFRFVEPTASGALIDGLWRRAFEAQAGSVER
+IRFHAARETDRDPRVGEGRPQGLRAVVYSAPDGEDLGVAVYRVTGSTAELVADDPVTATV
+VALWAATPEAHRALLEFLGNLDLVVRLRLPAVAADRLLEFLVLDESRIYTRGVHHHLWHR
+VLDVAACFEARPYLHEGAVTVTVEDDLGYAAGTWEIAAADGVGRVRPAPQDAAELTLDVA
+ELGSVLLGGVKAEMMREAGILLAHRPGAAADLDTLLRQARPPYSLTGF*
+>NZ_CP083691.1_1654
+MRPHTDLQPTATPRADAEVLAEQGLALVVAPGRAADPAFERHTTAVERGFYEQVPSGEAM
+AQLLEAGEADGRRMVDVLPLGADPATTRPVATFEDFRSELTVSPGVAVSAWLISGVTVDP
+GFRRRGLLRTMMTRSLADAVAAGVPVAALTASEAAIYGRFGFGAATRWRRARLDTRGDVR
+LRGAPSAGRVTREEPREVGALADELYQHVRRLTPGATQRPTMTAIGWEDRSRFKNDGKGS
+GLYAAVHRDAAGTAQGIALYRPQGWDVEPPTVTMELFLALTPDARRGLLTHLTSLDLIER
+IVWERAPEAGWPEALLEDERRLRTERDGDDLYLRILDVPAALGARADLGDGEVVVDVTDP
+LGHAAGAWRIRARDGVAEVTEAAEGEAELGLDVADLSAVWLGGHGSAGGVAARVATGLVR
+EVVPGAGARLDALLRPSVPVRSLVGF*
+>NZ_CP097650.1_1008
+MTPHTDAPEGPSLRRLADAAEDRLGEHGLALRDLGVLGPEDPAASHFAAAVERGFYETVP
+TGAALRQQLEAHAADGRRRLGVYAPGDDPAARRPAATFEDFVQPLTTWPGRTVDAWLITD
+VTVSPDARRRGVLRAMMLRSLADARDAGLCAAALTATEAAIYGRFGFGAATRWHAVRIDV
+SGAPAFTGAPAGGRVTVEEPREIPGLVDELYGRVLPATPGSVQRTSFSVPRWEDREASRN
+EGRGSGLYAAVHRDDDGRVQGVALYRFEGWEKEPPTITVTAFLAATADARRGLVHHLARL
+DLVERIEWGRAPEPGWLEALFVDERRVSRHRGSDDLYLRVLNLPAAMAARGWAGDGEVVV
+AVEDALGAIDGTWRLTVRQGRGAAERLGPAADAVRMGAGLRLDAARFSALWLGGHSRGAG
+AAVLAEAGVVAELRAGAAEAFDGLVRPSRPLHTLVGF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000125.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000125.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0cca54fb7bb5a22cdd37d00f00e4c505698144d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000125.fa
@@ -0,0 +1,56 @@
+>NZ_CP042169.1_1229
+MSAESSPLSAAAVDPEERRLEAALRPKHLDEFVGQMRVREQLDLMLASARLRDRAADHVL
+LSGPPGLGKTTLAMIVAAEMNAPLRLSSGPAIQHAGDLAAILSSLTEGEVLFLDEIHRMS
+RPAEEMLYMAMEDFRVDIVVGKGAGATSIPLELPPFTLVGATTRAGLLPGPLRDRFGFTG
+HLDFYTEVELERVLRRSALLLDMRLATEGYRQIARRSRGTPRIANRLLRRVRDWALVKGL
+AEVGAHDAAAALDMYEVDGRGLDRLDRSVLTALCTTFGGGPVGLSTLATAVGEEAETVET
+VAEPFLIREGMVARTPRGRVALPGAWEHLGLAAPEATPGP*
+>NZ_CP033200.1_958
+MSAESSPLSAAAVDPEERRLEAALRPKHLDEFVGQMRVREQLDLMLASARLRDRAADHVL
+LSGPPGLGKTTLAMIVAAEMNAPLRLSSGPAIQHAGDLAAILSSLTEGEVLFLDEIHRMS
+RPAEEMLYMAMEDFRVDIVVGKGAGATSIPLELPPFTLVGATTRAGLLPGPLRDRFGFTG
+HLDFYTEVELERVLRRSALLLDMRLATEGYRQIARRSRGTPRIANRLLRRVRDWALVKGL
+AEVGAHDAAAALDMYEVDGRGLDRLDRSVLTALCTTFGGGPVGLSTLATAVGEEAETVET
+VAEPFLIREGMVARTPRGRVALPGAWEHLGLAAPEATPGP*
+>NZ_CP040019.1_1589
+MSAEPSPLSGLAADPEERRLEAALRPKHLDEFVGQRRVREQLDLMLASARLRDRAADHVL
+LSGPPGLGKTTLAMIVAAEMNAPLRLSSGPAIQHAGDLAAILSSLTEGEVLFLDEIHRMS
+RPAEEMLYMAMEDFRVDIVVGKGAGATSIPLELPPFTLVGATTRAGLLPGPLRDRFGFTG
+HLDFYAEAELERVLRRSALLLDVRLASDGYRQIATRSRGTPRIANRLLRRVRDWALVKGV
+EQVEADHAAAALDMYDVDARGLDRLDRSVLTALCTTFGGGPVGLTTLATAVGEEAETVET
+VAEPFLIREGMVARTPRGRIALPGAWDHLGLASPEAGSGA*
+>NZ_CP083691.1_1482
+MSERPVTAFEADAEERRLEAALRPKHLDEFVGQARVREQLDLMLASARLRDRAADHVLLS
+GPPGLGKTTLAMIVAQEMNAPLRLSSGPAIQNAGDLAAILSSLTEGEVLFLDEIHRMSRP
+AEEMLYMAMEDFRVDIVVGKGAGATSIPLELPPFTLVGATTRAGLLPGPLRDRFGFTGHL
+EFYAIEELERVLRRSSALLDMRVETDGYRQIASRSRGTPRIANRLLRRVRDWALVKGLDT
+VDAEAASAALTMYEVDARGLDRLDRSVLTALCTTFGGGPVGLTTLATAVGEEAETVETVA
+EPFLIREGMMARTPRGRVALPGAWDHLGMTPPEAPLG*
+>NZ_CP097650.1_1186
+MSAESSPLSAAAVDPEERRLEAALRPKHLDEFVGQMRVREQLDLMLASARLRDRAADHVL
+LSGPPGLGKTTLAMIVAAEMNAPLRLSSGPAIQHAGDLAAILSSLTEGEVLFLDEIHRMS
+RPAEEMLYMAMEDFRVDIVVGKGAGATSIPLELPPFTLVGATTRAGLLPGPLRDRFGFTG
+HLDFYTEVELERVLRRSALLLDMRLATEGYRQIARRSRGTPRIANRLLRRVRDWALVKGL
+AEVGAHDAAAALDMYEVDGRGLDRLDRSVLTALCTTFGGGPVGLSTLATAVGEEAETVET
+VAEPFLIREGMVARTPRGRVALPGAWEHLGLAAPEATPGP*
+>NZ_CP097650.1_1828
+MSILRVHDGLFGLTFQQALDKASPGATIALTPGTYAEFESIPVGNLRIIGAGSRPEDVIL
+VTQLDVHGQISVENLTLQAPHFHNAVRLHGPTASAVFLYTAIQPEPTGQFPAVYSEGGAV
+TVRRSTLDQGPGGCALYVEGQGTATFEDSTTGTVNAVASTVTTVDSTHGAFHLSAASKVH
+ARGTLCLAPAEGMRGLVLTAFSVLKAERLTTDITYLELSLEDSALDVAEVSTSSDVDVHV
+MTSGGSHVQIPPDTVRVTDIDRQKAEQEVAERRQREEAAARRRAEEAAAEAAATGEAARQ
+AAAEAQAEARRQEEAKPRAVMWTAAQGADFTTVQDQLRPGDTLVLEEGDFHLPDPAIMLN
+CHIRGTGRADRIRLHGAVGIPNGATVRLENMLLVTPSTGNAVNVHAGGNATLTGVLVDPT
+KAEVFSPLCSSGGRLTLNEVRVVSEPTSYLADVLGTQGGVIVAEDSTFGIVRLESSARAT
+LTDCTANQLYVLGSGEALSLGTLRIPPTTPHLRALAVEEGGRGTIADLCVEEPCEVFVAG
+SLQIAHVSSAPHALHLITTDTALHSIPEDAIATAEEPSQTATADATLVEHPGENSTGDRE
+PSAGRGHDGADLADTNCDPMAQLSALTGLADVKNQVQTFIAEVRFAEARRQRGFAVRRQT
+LHSQFLGNPGTGKTTVARLLGRALHQAGVLSSDVFVEVTREDLVSEHIGGTGPKTRRILE
+SALGGILFIDEAYTLAEGGPQDFGREAIATLLAFMENHRDEFMVILAGYPEQMHAFFKAN
+PGLRSRVPLRFDFEDYSTAELVQMGLAALADDGFTVDPDAYRRTVAEAHRSSGDRSNGRW
+VRNLNDRLVRHMAHRVMAESGAAEDMVGVEDERLTQVDPADLHALLGRSTEDDTGVDHLL
+VELDEMVGLETVKAWVRGLVAQAEADERLRDAGVDLPRPTYHMVFAGSPGTGKTTVARLV
+GKLFHRLGILSTPQVVEASRERMVGRYIGHTEERTGLLLDEARGGVLFVDEAYQLDMPDS
+SNDFGKVAVETLITRLEDDRHSFIAIFAGYTDRMAQFLSLNPGLASRVPHNIEFPDYSPD
+DIAEIVVRTLRRTWSFDETVLRSAVAQGYAALPPESRANARQARNYADAISQAHKTWITE
+SSTDGDDIRHIRDATIIGVLAAEPTGQDQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000126.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000126.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b26916d8aca86d8b0100a1e23238cc9efbc77e52
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000126.fa
@@ -0,0 +1,42 @@
+>NZ_CP042169.1_1242
+MRHTRLGRSGLTVSVVGLGCNNLGRPGTATLEQAGTDDVVHAALDAGITFFDVADVYGAE
+PGLSEERLGRALGARRDEVVIGTKFGMDMGGVAGDDGGARGSRRYIVRAVEDSLRRLGTD
+WIDLYQFHTPDPATPIEETLRALDDLVRAGKVRYVGHSNRAGWQIAQAEYVARELGVERF
+VSAQNHYNLLDRRAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGDAPEGSRLSHVRQ
+HMVADADLEQLAGFGRFARERGITEVQAAIGWLAAQGPVSSVIAGATRAAQVVENAAAAD
+WLATAEDLAELDALFPGPEKVALF*
+>NZ_CP033200.1_971
+MRHTRLGRSGLTVSVVGLGCNNLGRPGTATLEQAGTDAVVHAALDAGITFFDVADVYGAE
+PGLSEERLGRALGARRDEVVIGTKFGMDMGGVAGDDGGARGSRRYIVRAVEDSLRRLGTD
+WIDLYQFHTPDPATPIEETLRALDDLVRAGKVRYVGHSNRAGWQIAQAEYVARELGVERF
+VSAQNHYNLLDRRAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGDAPEGSRLSHVRQ
+HMVADADLEQLAAFGRFARERGITEVQAAIGWLAAQGPVSSVIAGATRAAQVVENAAAAD
+WLATAEDLAELDALFPGPEKVALF*
+>NZ_CP040019.1_1574
+MRHTRLGRSGLTVSVVGLGCNNLGRPGTVTLEQDGTDAVVHAALDAGITFFDVADIYGAQ
+PGLSEERLGRALGARRDDVVIGTKFGMDMAGANGVDHDARGSRRYIVRAVEASLRRLGTD
+WIDLYQFHTPDPATPIDETLRALDDLVRDGKVRYVGHSNRTGWQIAQAEYVARELGTERF
+VSAQNHYNLLDRRAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGAAPEGSRLSHVRQ
+HMVADADLEQLAAFGEFARARGITEVQAAIGWLAAQGPVSSVIAGATRTGQVAENARAAD
+WEATEADLAELDALFPGPEKVALF*
+>NZ_CP083691.1_1468
+MRTVRLGRSGLTVSVVGLGCNNLGRPGTATMEQEGTDAVVHAALDAGITLFDVADVYGAR
+PGLSEERLGRALGSRRDEVVLATKFGMDMGGAAGADGGARGSRRYIVRAVEDSLRRLGTD
+WIDLYQFHTPDPATPIEETLRALDDLVRSGKVRYIGHSNRTGWQIAQAEHAAREIGVERF
+VSAQNHYNLLDRRAELEVLPASAEYGLGVLPYFPLANGLLTGKYSDGTAPAGSRLSHVRQ
+HMVEEADRGQLAAFGAFARERGITEVQAAIGWLAAQRPVASVIAGATRPGQIAENARAAD
+WEATPADLAELDALFPAPPPVALF*
+>NZ_CP083691.1_2033
+MSDMIYNRLGSSGLQVSQFSFGSWVTFGNQVDMGLAKDQLAAAKEGGVNFFDNAEVYAGG
+ESESIMGRAIAELGWKRHEYVVSTKLFWGIHGDVVNMKNTLNRKYLMQGIDGSLERLGLD
+FVDLVFCHRPDPHTPIEETVWAMSDMINRGKALYWGTSEWSADEIRAAWNIAERHHLHKP
+VMEQPQYNLLHRTKVEEEYARLYEDIGLGLTTWSPLASGILSGKYVDGVPEGSRGALKGY
+DFVKDSIADQETTAKVRQLVDIAAELDVTPAQLALAWTASNPRVSTVILGASSVAQVQEN
+LKALDVIELVTPEVRERLEAVFA*
+>NZ_CP097650.1_1199
+MRHTRLGRSGLTVSVVGLGCNNLGRPGTATLEQAGTDAVVHAALDAGITFFDVADVYGAE
+PGLSEERLGRALGARRDEVVIGTKFGMDMGGVAGDDGGARGSRRYIVRAVEDSLRRLGTD
+WIDLYQFHTPDPATPIEETLRALDDLVRAGKVRYVGHSNRAGWQIAQAEYVARELGVERF
+VSAQNHYNLLDRRAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGDAPEGSRLSHVRQ
+HMVADADLEQLAAFGRFARERGITEVQAAIGWLAAQGPVSSVIAGATRAAQVVENAAAAD
+WLATAEDLAELDALFPGPEKVALF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000131.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000131.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e001d3f91f4773183a8f7f5d702792612a373284
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000131.fa
@@ -0,0 +1,51 @@
+>NZ_CP042169.1_1403
+MPPGPGALLGGRRVRLLPAILALALGSFAIGTTEFAMMGLLPQAVADLGVGLEAGGVLIS
+MYALGVVIGAPLLAASFARVDRRVTSIVLMLLFVVGHVAAFLAPDMGSMMAARFVSGLPH
+GAYFSAAALAAADLAGPARRGQAVAWVMAGLSVANVLGVPGATALGQAVGWRWMFVIVAV
+CAALCVGATAWLVPSVPAPAGASVGRELRGLASGRLWATVAVGVIGFAGMFALYTYIAPL
+LTEVAGLEERWVPAVLALYGVGMVIGTLVSGALTDRDPVGTLRLSFGLSAVSLAAVALTA
+PWAPVMIVFLFCVAVSGSGIAPSLQVLLVDSAPTAPQLAGSLNHSALNMANAMGAWVGAA
+AIGAGASLRTPPLVGAGIALAGLVLAFLLVRRDVAASPGVRADDGGSPR*
+>NZ_CP033200.1_1145
+MPTPTPAADGAHDRSPRAPRPTRPDPSIPPTAPTGPGALLGGRRVRLLPAILALALGSFA
+IGTTEFAMMGLLPQAVADLGIGLEAGGVLISMYALGVVIGAPLLAASFARVDRRVTSIVL
+MLLFVVGHVAAFLAPDAATMMAARFICGLPHGAYFSAAALAAADLAGPARRGQAVAWVMA
+GLSVANVLGVPAATALGQSAGWRWMFVIVATCAALCVAATAWLVPPVPAPEGASVRRELR
+GLASGRLWATVAVGVLGFAGMFALYTYIAPLLTTVSGLDERWVPAVLALYGVGMVVGTLV
+GGALTDRDPVRTLRLSFALSAVFLLGVGLTAQWAPVMVVFLFLVAVSGSGIAPSLQVLLV
+DSAPTAPQLAGSLNHSALNMANAMGAWVGAAAIGAGASLRTPPLIGAAIALGGLVLALLL
+VRRTPAVGAVPHDGPSAATV*
+>NZ_CP040019.1_1426
+MTTPASGDPAASPSVSARPDPADAAGSPAAGAVGPQSLLGGRRVRLLPAILALALGSFAI
+GTTEFAIMGLLPQAVADLGIGLEAGGVLISMYALGVVVGAPLLAAAFARVDRRTTGIVLM
+LLFTVGHTGAFLAPDTATMMAARFVSGLPHGAYFSAAALAAADLAGPARRGQAIAWVMAG
+LSVANVVGVPAATAIGQAAGWRWMFVIVAACALACVAATAWLVPPVPAPEGASVRRELRG
+LASGRLWATVAVGVIGFAGMFALYTYIAPLLTEVAGLDERWVPAVLALYGIGMVVGTLVS
+GALTDRDPVGTLRLSFGLSAVSLLAVGLTAQWAPVMVLLLFCVAVSGSGIAPSLQVLLVD
+SAPGAPQLAGSLNHSALNMANAMGAWVGAAAIGAGASLRTPPLVGAAIALAGLVLAFVLV
+RRASPTSAATAADAR*
+>NZ_CP083691.1_1329
+MRLLPAILALALGSFAIGTTEFTMMGLLPEAVTDLGVGLETGGVLISMYALGVVVGAPVL
+AAALARMDRKLSSILLMGLFVVGHLASLLAPSLGALMAARFVSGLPHGAFFSAAALAAAD
+LAGPARRGQAIGWVMAGLSVANVVGVPAATALGQAAGWRWMFAVVAACALGCIAATALLV
+PRVPAPAGASVAAEIRGLASGRLWATVAIGVVGFAGMFCLYTYIAPLLTEVSGLHPRWVP
+AVLALYGVGMVIGTLVSGALTDRDPIRTLRWSFGVSALGLLAVSLTAPWWPALLVSLLVV
+ALSGSGIAPALQVLLVDAAPTAPQLSGSLNHSALNMANAMGAWVGAAAVGAGASLRMPSL
+IGAGIALVGLLMSVALLRRPASAPPGA*
+>NZ_CP083691.1_1741
+MSAVSNAPRPRLPWGALLALSASGFLAIFTETIPAGLLPELSRGLGVTESAAGQLVTLYA
+MGSVVAAIPLVAATQTVNRKKVLLAAVATLGAFNLVTAAAPWLPVILAARFVAGAAAALV
+WGVLAGFARSLVAPQLQGRALAVTGLGQPIALAGGVPLGSFAASVMDWRWVFVAISVAAG
+GLAVWIAAAVQNVEGSPRRQREPLRRVVMLPGVRLIFAVTGCWILAHNMLYTYAAPLLNR
+TDLRLDVGLGLFGVASMIGISLVGMVIDRALRLVSAICVTAMCLATTVWLLPQVGIALAV
+ASVVAWGLSFGGAPVLLQTALADRAGEHTDAAQSVFVTVFNLAVAGGGFMGGMLLASSGT
+AGIATTSAVLCLVAVGMIVLARAAFPAGHRHKDETDESVVAPSECSA*
+>NZ_CP097650.1_1352
+MPTPTPAADGAHDRSPRAPRPTRPDPSIPPTAPTGPGALLGGRRVRLLPAILALALGSFA
+IGTTEFAMMGLLPQAVADLGIGLEAGGVLISMYALGVVIGAPLLAASFARVDRRVTSIVL
+MLLFVVGHVAAFLAPDMGSMMAARFVSGLPHGAYFSAAALAAADLAGPARRGQAVAWVMA
+GLSVANVLGVPGATALGQAVGWRWMFVIVAVCAALCVGATAWLVPSVPAPAGASVGRELR
+GLASGRLWATVAVGVIGFAGMFALYTYIAPLLTEVAGLEERWVPAVLALYGVGMVIGTLV
+SGALTDRDPVGTLRLSFGLSAVSLAAVALTASWAPVMIVFLFCVAVSGSGIAPSLQVLLV
+DSAPTAPQLAGSLNHSALNMANAMGAWVGAAAIGAGASLRTPPLVGAGIALAGLVLAFLL
+VRRDVAARPGVRADDDGSPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000136.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000136.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d267bd4e07c3b4f448b71cb6f09fd11d7e245aaa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000136.fa
@@ -0,0 +1,48 @@
+>NZ_CP042169.1_1533
+MSLACVPHPGPVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKVLRGRFARGLTLRSGWV
+DGATDHTAKILADTLPSDTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATKPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYADVPVIAQWDDHETTNNWWPGEVLED
+PRYTQVRDVDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDM
+RTHKGENTPGLETHETPILGEEQLQWLIRGLRASTATWKVIANDLPLGLVVPDGTGQESL
+SNGDDGAPLGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWE
+FVAGPINAGSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRL
+INAAGRTVYSRTLTAA*
+>NZ_CP033200.1_1254
+MRLACVPHPGPVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKVLRGRFARGLTLRSGWV
+DGATDHTAKILADTLPSDTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATKPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYADVPVIAQWDDHETTNNW*
+>NZ_CP033200.1_1255
+MDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDMRTHKGENT
+PGLETHETPILGEEQLQWLIRGLRASTATWKVIANDLPLGLVVPDGTGQESLSNGDDGAP
+LGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFESFWEFVAGPINA
+GSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRLINAVGRTV
+YSRTLTAA*
+>NZ_CP040019.1_1318
+MKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWEFVAGPINAGSFGPNTLDGTFGPRLDF
+EAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRLINAVGRTVYSRTLTAA*
+>NZ_CP083691.1_1211
+MSLACVPHPGSVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKVLRGRFARGLTLRSGWV
+DGATDHTAKILADTLPSGTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATQPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYADVPVIAQWDDHETTNNWWPGEVLED
+PRYTQVRDVDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDM
+RTHKGENTPGLETHETPILGEEQLQWLIHGLRASTATWKVIANDLPLGLVVPDGTGQESL
+SNGDDGAPLGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWE
+FVAGPINAGSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRL
+INANGRTVYARTLTAA*
+>NZ_CP097650.1_1460
+MSLACVPHPGPVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKALRGRFSRGLTLRSGWV
+DGATDHTAKILADTLPSGTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATQPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYTDVPVIAQWDDHETTNNWWPGEVLED
+PRYTQVRDVDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDM
+RTHKGENTPGLETHETPILGEEQLQWLIRGLRASTATWKVIANDLPLGLIVPDGTGQESL
+SNGDDGAPLGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWE
+FVAGPINAGSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEGGREFRVRL
+INAAGRTVYSRTLTAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000137.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000137.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09cd39e396c5e8492feec9923496c44f55ee451d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000137.fa
@@ -0,0 +1,34 @@
+>NZ_CP042169.1_1535
+MIARLRAASAEDRLLLIGLPLLVAALLIGWTVWVRGAALDDVEARLLTWPTVLRLTAEHL
+ALVGVSTVLVVATAVPLGVLLSRPAARRFTPVAMGLANAGQAAPVIGVIVLLAMAWGFGF
+RVAVLALSLYAFLPVLANTLAGLRGVDPTVVEAARGMGMSPLQTLLRVELPLALPVIMAG
+LRTALVLLVGTGAFATFIDAGGLGLLIQTGIVLFRFPLLVSGAILVAALALMIEWIGRLV
+ETLATPRGLA*
+>NZ_CP042169.1_2193
+MISSLFSWFADPAHWAGPNGVPARVLEHLGYSVLALVIAAAIAFPVGVWIGHTGRGRRVV
+VALSSALRALPTLGLLTFLAIVLDIRLRQALIPTVMVLVILAIPPLLAGTYAGLQAVPRE
+VVHAARANGHSTGQLIGQVELPIALPMAVGGLRSATLQVIATTSVASYLGLGGLGRYLFD
+ALAVQDYVTMLAGAVLIAVLALLCDGLLLLVQRILTPAGLRARG*
+>NZ_CP033200.1_1257
+MIARLRAASAEDRLLLIGLPLLVATLLIGWTVWVRGAALDDVEARLLTWPTVLRLTAEHL
+ALVGVSTVLVVATAVPLGVLLSRPAARRFTPVAMGLANAGQAAPVIGVIVLLAMAWGFGF
+RVAVLALSLYAFLPVLANTLAGLRGVDPTVVEAARGMGMSPLQTLLRVELPLALPVIMAG
+LRTALVLLVGTGAFATFIDAGGLGLLIQTGIVLFRFPLLVSGAILVAALALMIEWIGRLV
+ETLATPRGLA*
+>NZ_CP040019.1_1316
+MIARLRAASAEDRLLLIGLPLLVAALLIGWTVWVRGAALDDVEARLLTWPTVLRLTAEHL
+ALVGVSTVLVVATAVPLGVLLSRPAARRFTPVAMGLANAGQAAPVIGVIVLLAMAWGFGF
+RVAVLALSLYAFLPVLANTLAGLRGVDPTVVEAARGMGMSPLQTLLRVELPLALPVIMAG
+LRTALVLLVGTGAFATFIDAGGLGLLIQTGIVLFRFPLLVSGAILVAALALMIEWIGRLV
+ETLATPRGLA*
+>NZ_CP083691.1_442
+MIADLFAWFADPAHWTGPGGVPARVAEHLGYSLLALAIAAVIALPAGVAIGHTGKGRRVV
+VAVSSALRALPTLGLLTFLAIVLQVGLRQALIPAVIVLVVLAVPPLLAGAYAGVHAVPRD
+VVVAARANGHSTRQLVSQVEVPLALPMIVGGLRSASLQVLATTSVAAYLGLGGLGRYLFD
+ALAVQDYTTMLAGAVLIALLALVSDAVLLLFQRLVTPA*
+>NZ_CP097650.1_1462
+MIARLRAASAEDRLLLIGLPLLVAALLIGWTVWVRGAALDDVEARLLTWPTVLRLTAEHL
+ALVGVSTVLVVATAVPLGVLLSRPAARRFTPVAMGLANAGQAAPVIGVIVLLAMAWGFGF
+RVAVLALSLYAFLPVLANTLAGLRGVDPTVVEAARGMGMSPLQTLLRVELPLALPVIMAG
+LRTALVLLVGTGAFATFIDAGGLGLLIQTGIVLFRFPLLVSGAILVAALALMIEWIGRLV
+ETLATPRGLA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000139.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000139.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d298df9d3d2789c377d76970b40ec7fa7ee2e9f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000139.fa
@@ -0,0 +1,59 @@
+>NZ_CP042169.1_1555
+MTATLVASGLAGGHGHRTLFEDLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQERERVPGETVAGYIARRTGCAEATREMDASASGLADPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARIQREWSSQGVRNAMKKSPDN
+DKLRRRANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSLQVNAGERIGITGPNGAGKSTLLRALLGRQAPDEGTAALGSSVQIG
+EIDQARSLLAGTVPLAAAVEALVPEMASGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER*
+>NZ_CP033200.1_1278
+MTATLVASGLAGGHGHRTLFEDLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQERERVPGETVAGYIARRTGCAEATREMDASASGLADPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARIQREWSSQGVRNAMKKSPDN
+DKLRRRANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSLQVNAGERIGITGPNGAGKSTLLRGLLGRQAPDEGTAALGSSVQIG
+EIDQARSLLAGTVPLAAAVEALVPEMASGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER*
+>NZ_CP040019.1_1253
+MPWEPVVRYIGLRAGSAETTAEMDLAATSLAGPDFTNVAANRVSAALARWLATGTTDLEK
+CIRIVLANLGLEMDDIPTGWVALEADVVVDTAGAMIVRFLYVHVVNRCFYASAYDDIRKV
+IARGVAVAGPAHWTGGTAPGLTWAGTSAQN*
+>NZ_CP040019.1_1268
+MTATLVASHLAGGHGHRTLFESLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQEHERVPGESVAAYIGRRTGCAAATAEMDEAAEALGAPDAGDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLERLERFVQELRGGVVLVSHDREFLARCVTRVLELDLAQHSN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKADLVSRARVQREWSSQGVRNAMKKSPDN
+DKLRRKANAESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGTAPRSSSVVATLNE
+AVFRQGSFTLGPVSLQVNAGERVGITGPNGAGKSTLLRGLLGRQDPDDGAASLGSSVQVG
+EIDQARSLLAGPTPLADAFEALVPEMASGEVRTLLAKFGLRADHVTRPVDELSPGERTRA
+GLALLQARGVNLLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER*
+>NZ_CP083691.1_1175
+MTATLVASGLAGGHGHRTLFDALDLTVAPGDVVGVVGANGAGKSTLLRILGGNLAPQTGT
+VSLAPSDAFVGWLPQEHERVSGETVAGYIARRTGCAEATREMDASAEALAGPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARTQREWSSQGVRNAMRKSPDN
+DKLRRKANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSLQVNAGERIGITGPNGAGKSTLLRGLLGRQAPDEGTAALGSSVQIG
+EIDQARSLLAGAVPLAAAFETLAPEMTSGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRLDRRW
+HVADGRVTER*
+>NZ_CP097650.1_1482
+MTATLVASGLAGGHGHRTLFEDLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQEHERVPGETVAGYIARRTGCAEATREMDASASGLADPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARIQREWSSQGVRNAMKKSPDN
+DKLRRRANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSRQVNAGERIGITGPNGAGKSTLLRGLLGRQAPDEGMAALGSSVQIG
+EIDQARSLLVGTVPLAAAVEALVPEMASGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000140.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000140.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9e9d67bfb9f97b3e5e77e43a9d2e5f45db533a6e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000140.fa
@@ -0,0 +1,52 @@
+>NZ_CP042169.1_1575
+MRDASAAAGPPVDCRTVALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVV
+NLPDERLPQLAEIFGSERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVV
+RAFDDGDVVHVDGKVDPASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEAL
+KAALAVLERGETIFAAKDKDKLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRD
+LVAPADAVFLDAKLESDLVELSEEEAAEMLEMAGQDESGLDQLARVGFSTLGLQTYLTAG
+PKETRAWTIPVGATAPEAAGVIHTDFQRGFIKAEIVSFDDLIAAGSMADAKAAGKVRMEG
+KDYVMKDGDVVEFRFNV*
+>NZ_CP033200.1_1292
+MRDASAAAGPPVDCRTVALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVV
+NLPDERLPQLAEIFGSERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVV
+RAFDDGDVVHVDGKVDPASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEAL
+QAALAVLERGETIFAAKDKDKLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRD
+LVAPADAVFLDAKLESDLVELSEEEAAEMLEMAGQDESGLDQLARVGFSTLGLQTYLTAG
+PKETRAWTIPVGATAPEAAGVIHTDFQRGFIKAEIVSFEDLIAAGSMADAKAAGKVRMEG
+KDYVMKDGDVVEFRFNV*
+>NZ_CP040019.1_1251
+MALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVVNLPDERLPQLAEIFGS
+ERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVVRAFDDGDVVHVDGKVD
+PASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEALKAALAVLERGETIFAA
+KDKDKLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRDLVAPADAVFLDAKLES
+DLVELSEEEAAEMLEMAGQNESGLDQLARVGFSTLGLQTYLTAGPKETRAWTIPVGATAP
+EAAGVIHTDFQRGFIKAEIVSFEDLIAAGSMADAKAAGKVRMEGKDYVMKDGDVVEFRFN
+V*
+>NZ_CP083691.1_764
+MSHAHHHGGGSSAAVLDSSLTRLGLVGSPNSGKSTLFNALTGLRVKTGNYPGVTVSRAEG
+VMVAEDGTRVVLEDLPGTYSLDPISPDEQVVADLLALDPADADHPQALLLVADATTLRRG
+LTMVAHALAVELPATLVLTFGDELALRGGSVDVTRLSRALGIPVLAATAGDARQREAVRA
+HLATDPAGWAVPPVAPPTDPAGIAAWIDSVLEAARYAVPRPDGRTRRIDDVLLHPVWGTL
+VFLVTMFAFFQVIFTVAAPLQALVEELFGWLGERAAALIPIEWLGRFVAEALIGGVGGVV
+VFLPQILLLFLMISLLESTGYMTRAAFLMDRVMSRFGLEGRSFVALLSSLACAVPGIMAT
+RSLPSARDRLATMMAAPSMTCSARLPVYVLLISLLVPSEVRWGPVGLQGLVMFALYLGGA
+TASMLTAAFWSRVVGRRQAAMPFYMEMPPYRLPKARTVVTSMWASAEGFLRKVTSIILVT
+TALLWVLLNVPVRSEEEMAGAGVAMDDPAAVAQYTIDHSAAAAVGKAVEPAFEPLGFDWR
+IDVGVLASLAAREVFVATLGQMAAAEDPEDPGDALASWTVTDDAGVERPLFTPDVVAALL
+VFFMLALQCMSTLAVMRRETGTWRWPLLAFGYYFTLAWLAAFAVRHVVLALT*
+>NZ_CP083691.1_1159
+MALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVVNLPDERLPQLAEIFGS
+ERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVVRAFDDGDVVHVDGKVD
+PASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEALKAALAVLERGETIFAA
+KDKDKLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRDLVAPADAVFLDAKLES
+DLVELSEEEAAEMLEMAGQDESGLDQLARVGFSTLGLQTYLTAGPKETRAWTIPVGATAP
+EAAGVIHTDFQRGFIKAEIVSFDDLIAAGSMNDAKAAGKVRMEGKDYVMKDGDVVEFRFN
+V*
+>NZ_CP097650.1_1502
+MGPPVDCRTVALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVVNLPDERL
+PRLAEIFGSERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVVRVFDDGD
+VVHVDGKVDPASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEALQAALAVL
+ERGETIFAAKDKDTLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRDLVAPADA
+VFLDAKLESDLVELSEEEAAEMLEMAGQDESGMDQLARVGFSTLGLQTYLTAGPKETRAW
+TIPVGATAPEAAGVIHTDFQRGFIKAEIVSFDDLIAAGSMNDAKAAGKVRMEGKDYVMKD
+GDVVEFRFNV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000141.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000141.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0217c659f7ed956833dfa7a57eacfb2a9e384009
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000141.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1587
+MTENANQNAPLTGKTVAFLATNGVEQVELTSPWEAVIAAGATPVLVSSKSGTITAMKSDW
+EHGESFEVNTTVKDAKAEDFHGLVMPGGTLNADTLRIDKDVQAFVRAFFEQHKPVAAICH
+APWTLIEAGVVDGRRLTSYASLESDLKNAGAQWVDEEVVVDNGLTTSRTPDDLDAFNAKL
+VEELGEGKHEDQTA*
+>NZ_CP033200.1_1303
+MTENANQNAPLTGKTVAFLATNGVEQVELTSPWEAVIAAGATPVLVSPESGTITAMQSDW
+DHGESFDVNTTVKDAKAEDFDGLVMPGGTLNADAMRVNKDAQAFVRAFFEQHKPVAAICH
+APWTLIEAGVVEGRRLTSYPSLKTDLKNAGAQWVDEEVVVDNGLTTSRSPEDLDAFNAKL
+VEELGEGKHEDQTA*
+>NZ_CP040019.1_1237
+MTENAAQNAPLTGKTVAFLATNGVEQVELTSPWEAVIAAGATPVLVSPESGTITAMQSDW
+DHGESFEVNTTVKDAKAEDFDGIVLPGGTLNADAMRVNKDAQAFVRAFFEQHKPVAAICH
+APWTLIEAGVVEGRKMTSYSSLKTDLKNAGAQWVDEEVVVDAGLTTSRSPEDLDAFNAKL
+VEELAEGKHEDQTA*
+>NZ_CP083691.1_1145
+MTENAVQNAPLTGKTVAFLATNGVEQVELTSPWEAVIAAGATPVLVSPESGTITAMQSDW
+DHGESFEVNTTVKDAKAEDFHGLVMPGGTLNADAMRVNKDAQAFVRAFFDQHKPVAAICH
+APWTLIEAGVVDGRRLTSYASLESDLKNAGAQWVDEEVVVDNGLTTSRSPEDLDAFNAKL
+VEELGEGKHEDQTA*
+>NZ_CP083691.1_1187
+MAVDLQGKRVTILAADGVERVELDQPREALDRAGARTEVLSVDEGEIKARENDLDPAGTF
+GVDGLVAEASGADYDALVLPGGTVNPDKLRIDEDAVAFVRDFAENGKPVVAICHGPWTLI
+EADVATGRTLTSFPSIRTDLRNDGANVVDQEVVVDKNLITSRSPEDLPAFSEAIVAQLAG
+TTTKEEETS*
+>NZ_CP097650.1_1516
+MTENAVQNAPLSGKTVAFLATDGVEQVELTSPWEAVIAAGATPVLVSPKSGTITAMKSDW
+EHGESFEVNTTVKDAKAEDFHGLVMPGGTLNADALRIDTDAQAFVRAFFEQHKPVAAICH
+APWTLIEAGVVDGRRLTSYASLESDLKNAGAQWVDEEVVVDSGLTTSRTPDDLDAFNAKL
+VEELGEGKHEDQTA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000146.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000146.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e73d7d179a5dfbade345f9b758c0bb30e124cb6a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000146.fa
@@ -0,0 +1,66 @@
+>NZ_CP042169.1_1742
+MSTAPRRRVTGYPSTSGDDVQLNTTTLIRHAARTHGDQEIVYRTPDGGWDRYTYAEAYER
+IRRAANAMTGLGVSPGDRVGVIDWNSRRHYELYWAIPGIGATMVQVNLRLAPEDLVHVLT
+DSGCTTVFVDESLLRHAEVIAPRLPEVTTWVVMTDRPLSEIETTLPGVRHYEDLLASASP
+DVDWPEVEETSAYGACYTTGTTGRPKGVFYSHRAIVLHSYALAASIGMTLRDATMIITPM
+FHGQAWGLPQAATLMANKIVLPGRYMAEDTAPLTDALIAEEVTITSGAPAIFQPMLAYIE
+TLDEKPDLSRLRMISGATEPSLSLMRGFRDLTGAEVVHAYGATETTPLVTVNRYKPGVLA
+RLDEPALMDLKRKQGLPLTNVDLRIVGPGDENLPFDGVSQGEICVRGPWVTTGYHGMSEA
+DAEGRFLDGYWRSGDVGTVDSDGYLKVTDRLKDVIKSGGEWISSIDMENLLTSHPAITEA
+AVVGLPHPKWQERPYVQVMLRPGATITLAEVHEHLSGAFASWQLPERVDVVTELPRTSVG
+KIDKKTIRGRHTDLYADASEAARPGGGAGDVEEGGRA*
+>NZ_CP042169.1_1994
+MQTTDTVLGTPSTMGDDEQLTTTRLLRDAARTFGDQQIIHTRGGGSRWQTTTYAAVWERV
+RRIAAALRAEGVGPGDRVGLLLWNDVRHLESYFSVPLLGATMVQLNLRLAPTDLAYVITH
+AQVGTIVVDETLLELAAALEPHLPDGVRWIVAGDGELPADWAGRDDVLSYEALLDGHEPL
+ETGGLPNVSERSASGACYTTGTTGRPKGVFYSHRATWLHAHAVVSTLGMTMADTALLLTP
+MFHAQCWGLPFAAVAVGARLVLPGRFNLTDTPWLTSTLVDHGVTVAPAAPAILMPMLHHL
+RTLETPPRMDGVRLLCGATEPPVAMMRGFDELTGAEVIHAYGATETSPIVSLNRMKPSLM
+DTLSEDERWNLKRFQGLVVVGVDVKITDPLGELLPPGEENVGEIRLRGPWVTTSYADNAE
+ATEAGFDDEGYWRSGDLGYLSPEGYLKVTDRLKDVVKSGGEWISSIDLENHIMTVPGVRD
+AAVIGVPHPQWEERPLALVVRDEDSDVDQDAVLAALAERFATWQLPDEVRFVTEIDRTGV
+GKVNKRKLRADYADALTSGR*
+>NZ_CP033200.1_1712
+MQTTDTVLGTPSTMGDDEQLTTTRLLRDAARTFGDQQIIHTRGGGSPWQTTTYAAVWERV
+RRMAAALRAEGVGPGDRVGLLLWNDVRHLESYFSVPLLGATMVQLNLRLAPTDLAYVITH
+AQVGTIVVDETLLELAAALEPHLPGGIRWIVAGDGELPADWAGRDDVLSYEALLDGHEPL
+ETADLPNVSERSASGACYTTGTTGRPKGVFYSHRATWLHAHAVVSTLGMTMADTALLLTP
+MFHAQCWGLPFAAVAVGARLVLPGRFNLTDTPWLTSTLVDHGVTVAPAAPAILMPMLHHL
+RTLETPPRMDGVRLLCGATEPPVAMMRGFDELTGAEVIHAYGATETSPIVSLNRMKPSLM
+DTLSEDERWNLKRFQGLVVVGVDVKITDPLGELLPPGEENVGEIRLRGPWVTTSYADNAE
+ATEAGFDDEGYWRSGDLGYLSPEGYLKVTDRLKDVVKSGGEWISSIDLENHIMTVPGVRD
+AAVIGVPHPQWEERPLALVVRDEDSGVDQDAVLAALAERFATWQLPDEVRFVTEIDRTGV
+GKVNKRKLRADYADALTSGR*
+>NZ_CP040019.1_1063
+MSTAPRRRVTGYPSTSGDDVQLNTTTLIRHAARTHGDQEIVYRTPDGGWDRYTYAEAYER
+IRRAANAMTGLGVSPGDRVGVIDWNSRRHYELYWAIPGIGATMVQVNLRLAPEDLVHVLT
+DSGCTTVFVDESLLRHAEVIAPRLPEVTTWVVMTDRPLSEIETTLPGVRHYEDLLASASP
+DVDWPEVEETSAYGACYTTGTTGRPKGVFYSHRAIVLHSYALAASIGMTLRDATMIITPM
+FHGQAWGLPQAATLMANKIVLPGRYMAEDTAPLTDALIAEEVTITSGAPAIFQPMLAYIE
+TLDEKPDLSRLRMISGATEPSLSLMRGFRDLTGAEVVHAYGATETTPLVTVNRYKPGVLA
+RLDEPALMDLKRKQGLPLTNVDLRIVGPGDENLPFDGVSQGEICVRGPWVTTGYHGMSEA
+DAEGRFLDGYWRSGDVGTVDSDGYLKVTDRLKDVIKSGGEWISSIDMENLLTSHPAITEA
+AVVGLPHPKWQERPYVQVMLRPGATITLAEVHEHLSGAFASWQLPERVDVVTELPRTSVG
+KIDKKTIRGRHTDLYADASEAARPGGGAGDVEEGGRA*
+>NZ_CP083691.1_713
+MNSATAPVLGTPSTMGDDEQLTTSRLFRDAARTYPDQSITHRTIDGEWKVTDYAATWERM
+QRVAAGLASLGVGPRDRVGLLLWNDLRHFECYFAVPLTGATMVQLNLRLAPQDLAYVIGH
+SGARTIVVDATLLPLAEALGPHLPEDTRWIVATDGALPDSWAGRADTMSYEDLIERSAPI
+EDAPDMDERSASGACYTTGTTGRPKGVFYSHRATWLHAFAIAANTGMTMDDTVMLLTPMF
+HAQCWGLPYASVAVGARVVLPGRFTMQDTALLTESLVEHGVTVAPAAPAILLPMLHYLEG
+MEETPHLPGLRFLCGATEPPVALMQGFDRLMGAEIIHAYGATETSPVVSVNRLRPALAER
+LSEDEQWDLKRYQGLVVTGVDVKVVDPMGQPLPPGERNVGEVMIRGPWITRSYFENPEAT
+EKGFDDEGYWRSGDVGHLSEEGYLKIADRMKDVVKSGGEWISSIDLENHLLTVPGVSEAA
+VVGVPHPTWQERPIALVVRTAGADLSEEQVKAALGARFASWQVPDRVLFVDELDRTSVGK
+LDKKRLRQVYADALAQGDGPGAPSA*
+>NZ_CP097650.1_1929
+MQTTDTVLGTPSTMGDDEQLTTTRLLRDAARTFGDQQIIHTRGGGSPWQTTTYAAVWERV
+RRMAAALHAEGVGPGDRVGLLLWNDVRHLESYFSVPLLGATMVQLNLRLAPTDLAYVITH
+AQVGTIVVDETLLELAAALEPHLPGGIRWIVAGDGELPADWAGRGDVLSYEALLDGQEPL
+ETADLPNVSERSASGACYTTGTTGRPKGVFYSHRATWLHAHAVVSTLGMTMADTALLLTP
+MFHAQCWGLPFAAVAVGARLVLPGRFNLTDTPWLTSTLVDHGVTVAPAAPAILMPMLHHL
+RTLETPPRMDGVRLLCGATEPPVAMMRGFDELTGAEVIHAYGATETSPIVSLNRMKPSLM
+DTLSEDERWNLKRFQGLVVVGVDVKITDPLGELLPPGEENVGEIRLRGPWVTTSYADNAE
+ATEAGFDDEGYWRSGDLGYLSPEGYLKVTDRLKDVVKSGGEWISSIDLENHIMTVPGVRD
+AAVIGVPHPQWEERPLALVVRDEDSDVDQDAVLAALAERFATWQLPDEVRFVTEIDRTGV
+GKVNKRKLRADYADALTSGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000152.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000152.fa
new file mode 100644
index 0000000000000000000000000000000000000000..032c6c250eff261315e15172f82ba04c69e11c0c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000152.fa
@@ -0,0 +1,60 @@
+>NZ_CP042169.1_1884
+MEATVEQITAAITALNDKYWYVVMALLFVAGVWFTIRTVGVQVRMLPEMLRSVTAKSQTG
+FENDGVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWLLAIIGGATAFVESTL
+AQLYKQKGSDGYFGGPAYYIRDGLGAKWLAAVFAVAITVTYGFVFNAVQSNSISESVQAN
+WGASSTTAWIVGLGLAALTGLVIFGGVRRLSAVTNVLVPVMATFYIFLALIVMVVNITEV
+PGMIALIVGHAFGLREVAGAAVGMTMVMQGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQ
+GFVQSLGVYFDTLIVCSATAFVILLSNPAYGRGEAIGMQVTQGALQQAVGAWAGPALTVI
+IFFLAWSSVLGNTYYGEANIRYLAGRHAGPAITVFRVLVLVCVVGGALGSVALVWNLADT
+FAALMATINLVAIIPLGGLAVKLLRDYERKLKAGMNPGFHISDLPEARNVALWRDEPKTS
+PLQD*
+>NZ_CP033200.1_1592
+MEATVEQITAAVTAFNDKYWYVVMALLFVAGVWFTIRTVGVQVRMLPEMLRSVTAKSQTG
+FENDGVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWLLAIIGGATAFVESTL
+AQLYKQKGADGYFGGPAYYIRDGLGAKWLAAVFAVAITVTYGFVFNAVQSNSISESVQAN
+WGASSTTAWIVGLGLAALTGLVIFGGVRRLSAVTNVLVPVMATFYIFLALIVMVVNITEV
+PGMIALIVGHAFGLREVAGAAVGMTMVMQGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQ
+GFVQSLGVYFDTLIVCSATAFVILLSNPAYGRGEALGMQVTQGALQQAVGAWAGPALTVI
+IFFLAWSSVLGNTYYGEANIRYLAGRHAGRAITVFRVLVLVCVVGGALGSVALVWNLADT
+FAALMATINLVAIIPLGGLAVKLLRDYERKLKAGMDPGFHISDLPEARNVALWRDEPKTS
+PLQD*
+>NZ_CP040019.1_903
+MEAITAAVSAFNDKYWYVVMALLFTAGVWFTIRTVGVQVRMLPEMLRSVTAGSQKGFEND
+GVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWVLAIIGGATAFVESTLAQLY
+KQKGPDGFYGGPAYYIRDGLRSKWLAAVFAVAITVTYGFVFNAVQSNSISESVQANWGVS
+TTTAWIVGVALAVITGLVIFGGVRRLSAVTNVIVPVMAVFYLVLALIVMAVNITEIPGLI
+ALIVGHAFGLQEVTGAAVGMAMVMMGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQGFVQ
+SLGVYFDTLIVCSATAFIILLSNPSYGDGEALGMAVTQGALQQAVGAWAGPALTVIIFFL
+AWSSVLGNTYYGEANIRYLAGKRADAAITVFRVLVLLCVVGGALGSVALVWNLADTFAAL
+MATINLVAIIPLGGLAVKLLRDYERKLKAGEDPGFHVSDLPEARNVALWQDTPETAPLQK
+*
+>NZ_CP083691.1_836
+MGALADAISAFNSKYWYLVMALLAFAGVWFTVRTVGVQVRMLPEMIRSVAAKSPEGGADD
+GVSPFRAFTISAASRVGTGNVAGVAIAIVLGGPGAVFWMWVMAILGGATAFVESTLAQLY
+KRKDRDGFFGGPAYYIRDGLGLKWLAALFAVAITVTYGFVFNAVQSNSISESVQANWGAS
+TTTAWIVGVALAVITALVIFGGVQRLSSVTNVIVPVMAVAYVLLAVVVMVINITEIPAMF
+ALIVRHALGFEQVAGAAVGMAMVMQGVRRGMFSNEAGMGSAPNAAAAAAVSHPAKQGFVQ
+SLGVYFDTLLVCSATAFIILLSNPEYGNTDALGMVVTQNALQQAVGAWAGPFLTVVIFFL
+AWSSVLGNTYYGEANIRYLAGERAPQWITAFRVLVLLCVVGGALGTVSLVWNLADTFAAL
+MATINLVAIIPLGGLAVKLLQDYERKLKAGEDPHFRLADLPEAKNVPLWGDEDAELMRTE
+QGHGAGAREELHHADRPGRGHGGGSHSA*
+>NZ_CP083691.1_2086
+MDAFVTAATDGLGELSGIIWGPFVLIPLLFLTGLYLTIRLGFVQFLRLGAGLHLGLLRRK
+DDGDAEGEISQFQALTTALAATVGTGNIVGVATAIAVGGPGALFWMWVTGVLGMASKYSE
+AFLAVRFRTTDDAGEKSGGPQYYLQRGIKGGLGKGLALFFSVAALLACFGIGNMTQGNSI
+AVNVDSAFGVPTWITGAVLAVMTMVVLVGGIKSIGKVTAGFVPVMIVFYVLGALWILIVN
+ASAIPSAFATIFTEAFTGSAAVGGFTGSAMIVAVQYGMARGIFSNESGMGSAAIAAAAAQ
+TTHPVRQGLVSMTQTFIDTIIVVTCTGLVLITTGTWTEGKATAATMTSDAFATGLPGNWG
+HWIVTIGLVMFAYSTILGWSYYGERQVERLFGTRLIMPFRVLFSLVVFFGCTTELDLAWT
+FSDVMNGLMAIPNLLGLLILSGLIARETRLYLKHDPKLVATEAQIRDFMAEDPGYREWLA
+QEKQLDRAHAEHLHPHATGGSSVR*
+>NZ_CP097650.1_1804
+MEATVEQITAAITALNDKYWYVVMALLFVAGVWFTIRTVGVQVRMLPEMLRSVTAKSQTG
+FENDGVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWLLAIIGGATAFVESTL
+AQLYKQKGSDGYFGGPAYYIRDGLGAKWLAAVFAVAITVTYGFVFNAVQSNSISESVQAN
+WGASSTTAWIVGLGLAALTGLVIFGGVRRLSAVTNVLVPVMATFYIFLALIVMVVNITEV
+PGMIALIVGHAFGLREVAGAAVGMTMVMQGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQ
+GFVQSLGVYFDTLIVCSATAFVILLSNPAYGRGEAIGMQVTQGALQQAVGAWAGPALTVI
+IFFLAWSSVLGNTYYGEANIRYLAGRHAGPAITVFRVLVLVCVVGGALGSVALVWNLADT
+FAALMATINLVAIIPLGGLAVKLLRDYERKLKAGMNPGFHISDLPEARNVALWRDEPKTS
+PLQD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000154.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000154.fa
new file mode 100644
index 0000000000000000000000000000000000000000..47b268c47511a41a7c018a44f7776f91bc31d636
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000154.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_1927
+MTPALISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGVIAAGLAV
+AGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVVGLFLGFAVGLFASQWARTR
+DARAALSSSIGALTAMGVGMLVEFCCALGSLTAVGVGALVHGLTA*
+>NZ_CP033200.1_1633
+MTPALISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGVIAAGLAV
+AGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVVGLFLGFAVGLFASQWARTR
+DARAALSSSIGALTAMGMGMLVEFCCALGSLTAVGVGALVHGLTA*
+>NZ_CP040019.1_859
+MTLAIVVSVLAVLLLIVGVVGTVYPILPGSMLILVTAVAWAWILGSGASWTFGLLAAGLA
+VAGMSASAVLTGRRLLRERVTRGPIAAGVVGAIVGFFVIPVVGLFIGFAVGLFGSQWART
+KDARAALASSWGALKAMGLGMLVELGCAMLALVSVGVGILVHFVF*
+>NZ_CP083691.1_793
+MTPALISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGLIAAGLAV
+AGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVAGLFLGFAVGLFASQWARTR
+DARTALSSSIGALTAMGVGMLVEFCCALGSLTAVGVGALVHGVTA*
+>NZ_CP083691.1_806
+MTFAILVSLLAVLLLIVGLVGTVYPVLPGSVLNAVVSLAWAWVLGSVASWTFGLIACAFS
+IAGMSASAALTGRRLVKERIPRGPILTGVAAAVVGFFVIPVVGVFVGFAAGLFGAEWARR
+RDARAALTSSWGALKAMGLGMLVEFGCAMVALASVGAGALVHVLSL*
+>NZ_CP097650.1_1854
+MTPALISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGVIAAGLAV
+AGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVVGLFLGFAVGLFASQWARTR
+DARAALSSSIGALTAMGVGMLVEFCCALGSLTAVGVGALVHGLTA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000155.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000155.fa
new file mode 100644
index 0000000000000000000000000000000000000000..66e45963a79a284a6021e361398489004db1254c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000155.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1929
+MSPQKTVGVLALQGDVREHVHVLESLGARTRPVRRPADLEGLDGIVLPGGESSVMDRLAR
+IMGMRDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVDS
+FEEDLDIPAVAAEPVHAVFIRAPAVLQAGEGVEVLASVPASRLSVPAADPGLDGDARLPV
+AVRQGHLLATAFHPEVTGDWSFHRAFLAGL*
+>NZ_CP033200.1_1635
+MSPQKTVGVFALQGDVREHVHVLEALGARTRPVRRPADLEGLDGIVLPGGESSVMDRLAR
+IMGLKDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVDS
+FEEDLDIPAVAAEPVHAVFIRAPAVLQAGEGVEVLASVPTSRLSVPAADPGLDGDARLPV
+AVRQGHLLATAFHPEVTGDWSFHRAFLAGLRPPRAPRR*
+>NZ_CP040019.1_856
+MSALLVGVFALQGDVREHVRVLEGLGARTRPVRRAADLTGLDGIVLPGGESSVMDRLAGL
+MGLKEPLADAIGAGLPAYGTCAGIILLAREIQNPAPGQGSLGVLDVTVRRNAFGAQVDSF
+EADLEVPAVSAEPVHAVFIRAPAVLRAGGEVEVLASVPASRLSAAPPELGLDDAAQVPVA
+VRQGRVLATSFHPEVTGDHSFHREFLRGL*
+>NZ_CP083691.1_791
+MSPQKTVGVFALQGDVREHVHVLESLGARTRPVRRPADLEGLDGIVLPGGESSVMDRLAR
+IMGLKDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVDS
+FEEDLDVPAVAAEPVHAVFIRAPAVVQAGEGVEVLASVPASRLSLPAADPGLDGDARLPV
+AVRQGHLLATAFHPEVTGDWSFHRAFLAGL*
+>NZ_CP083691.1_801
+MRAVQKTVGVFALQGDVREHVHVLEALGARTRPVRRPADLAGLDGIVLPGEESSVMDRLA
+RIMGLRDPLAEAVRAGLPVYGTCAGMILLAAGIENPAPGQGSLGVLDVTVRRNAFGSQAD
+SLEADLQVPAVSADPMHAVLIRAPAVVRVGEGVEVLASVPAARAVAASSSTAETDDGAPA
+ADLPVAVRAGNVSATSFHPEVTGDWSFHRAFLAGL*
+>NZ_CP097650.1_1856
+MSPQKTVGVFALQGDVREHVHVLEALGARTRPVRRPADLEGLDGIVLPGGESSVMDRLAR
+IMGLKDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVDS
+FEEDLDVPAVAAEPVHAVFIRAPAVLQAGEGVEVLASVPASRLSVPAADPGLDGDARLPV
+AVRQGHLLATAFHPEVTGDWSFHRAFLAGL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000156.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000156.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3cd9ebabc01bf666fa998dc255c20968c7c6139f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000156.fa
@@ -0,0 +1,54 @@
+>NZ_CP042169.1_1958
+MSHTVASPAAPVPARDRREERKVIAGTVVGTTIEWYDFFIFAQATALVFAALFFQPMGEN
+GSQIAAWVTLGISFLVRPLGAIVAGHLGDRFGRKLVLSLTLIGMGLATTLIGLLPTYAQI
+GVWAPILLVALRLLQGLSAGGEWGGAALLSVEHAPHGKRGLFGSAPQIGVPLGMILATGV
+LFIVRSTMSEEQFLTWGWRIPFLISVILIVVGYLIRKAVEESPVFKEMQQLKVDESAPLG
+ELFRHHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLVGGVGWFI
+FTLLGGWVSDKIGRKLTFVFGYGFLIVWAFPLFGLLNTASLPLFSLGLFVLTLGLGPSYG
+PQSAMYAEMFPARVRFSGVSIGYALGTIIGGAFAPLLADQLVKTGWENVAWYIIVISAIS
+LIAVLFVPKGIQDRELHDEQVVATRSNPVVPT*
+>NZ_CP033200.1_1680
+MSHTVASPAAPAPARDRREERKVIAGTVVGTTIEWYDFFIFAQATALVFAALFFQPMGES
+GSQIAAWATLGISFLIRPLGAIVAGHLGDRFGRKFVLSLTLIGMGLATTLIGLLPTYAQI
+GVWAPILLVALRLLQGLSAGGEWGGAALLSVEHAPHGKRGLFGSAPQIGVPLGMILATGV
+LFIVRSTMSEEQFLTWGWRIPFLISVVLIVVGYLIRKAVEESPVFKEMQQLKVDESAPLG
+ELFRHHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLVGGVGWFI
+FTLLGGWVSDKIGRKLTFILGYGFLIIWAFPLFGLLNTASLPLFSLGLFVLTLGLGPSYG
+PQSAMYAEMFPARVRFSGVSIGYALGTIIGGAFAPLLADQLVKTGWENVAWYIIVISAVS
+LIAVLFVPKGIQDRELHDEQVVATRSNPVVPA*
+>NZ_CP040019.1_121
+MAEFSAAPTAHPAESDTHVSPAQRRKAFVGAIAGHLIEWYDYGVYGFLAVYVAANFFKSE
+NPMVGILAAFAVFALSFFVRPLGGLFFGPLADKIGRRKTLMIVLGLMCGATAVIGMLPTY
+ATIGVFAPILLVLMRLVQGFSAGGEVSTISAFVAEYAVKGRRGFATSFLMVTAASGLLLG
+GVVANGLGAIIGTEAMAEWGWRLPFLLAGVLGVVAVFIRMKLEDSPEFRRLHSEGKTSKT
+PLRETLRYQRQLFLMGALITLLGSTFYLVLTYLTTYMRTILELTPGAIFWLVLLTGAAAA
+AFMPVGGAISDRMGDRRPMLAIGAVLVAGAVVWFFLTAPGTDGGLPLVPSLLALGITTGL
+YCGVPYATMTELMPAHVRSTGIALGYNVPVAVFGGSAPFIASWLINETGDVASPMYFFLL
+TAAIALVGVAMLRPTDLLGHEDVPVTGSIDAVGGKVTRTVAPRPKADAL*
+>NZ_CP040019.1_810
+MSHTTVAHGAEHPARTRDRAEERKVLAGTLVGTTIEWYDFFIYAQAAALVFAPLFFAPMG
+EQGAQIASWASLGISFLVRPLGAIVAGHMGDRFGRKLVLSLTLIGMGAATVLIGLLPTYA
+SIGIWAPILLVVFRLLQGFSAGGEWGGAALLSVEHAPRGKRGLFGSAPQIGVPLGMLLAT
+GVLFAVRASMTNEQFLAWGWRIPFLISVILIFIGYIIRKAVEESPVFKEMQQLKKDESAP
+LGELFRNHTKEVVLAALIFAANNAVGYLVIAWFSKYGQKNLGMAPNDTLIAALVGGFGWF
+IFTLFGGWISDKIGRKTAFVAGYALIIAWAFPMFQMMNTASLPMFAAALFILSIGLGPSY
+GPQSAMYAEMFPARVRFSGVSIGYAIGAIIGGAFAPLIADLLLNDGGWVPVAWYMIIISA
+VSLIAVLFVPKGIQDRNLHDEGVVVAETGTREPVA*
+>NZ_CP083691.1_748
+MSHTVASPAVAAARDPREERKVLAGTLVGTTIEWYDFFIFAQATALVFATLFFQPMGESG
+AQIAAWVTLGISFLVRPLGAIIAGHLGDKFGRKLVLSLTLIGMGAATTLIGLLPTYAQIG
+VWAPILLVLLRLLQGFSAGGEWGGAALLAVEHAPHGKRGLFGSAPQIGVPLGMILATGVL
+FLVRSTMSEEQFLTWGWRIPFLVSVLLIVVGYFIRKAVEESPVFKEMQQLKVDESAPLGE
+LFRHHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLVGGVGWFIF
+TLLGGWISDKIGRKTTFVIGYAILIAWAFPMFQLLNTASLLLFSLALFVLTMGLGPSYGP
+QSAMYAEMFPARVRFSGVSIGYAIGTIIGGAFAPLIADELVKSGWPSVAWYIIGISAISL
+IAVLFVPKGIQDRELHDEEVVATRSNPVVPA*
+>NZ_CP097650.1_1897
+MSHTVASPAAPVPARDRREERKVIAGTVVGTTIEWYDFFIFAQATALVFAALFFQPMGES
+GSQIAAWVTLGISFLVRPLGAIIAGHLGDRFGRKLVLSLTLIGMGLATTLIGLLPTYAQI
+GVWAPILLVALRLLQGLSAGGEWGGAALLSVEHAPHGKRGLFGSAPQIGVPLGMILATGV
+LFIVRSTMSEEQFLTWGWRIPFLISVALIVVGYLIRKAVEESPVFKEMQQLKVDESAPLG
+ELFRNHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLIGGVGWFI
+FTLLGGWISDKIGRKLTFVLGYGFLIVWAFPLFGLLNTASLPLFSLGLFVLTLGLGPSYG
+PQSAMYAEMFPARVRFSGVSIGYALGTIIGGAFAPLLADQLVKTGWENVAWYIIVISAIS
+LIAVLFVPKGIQDRELHDEQVVATRSNPVVPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000160.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000160.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6115cb5866a239c7670963c97cf5d5aa58181a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000160.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_2016
+MTTKRPSVLFVCVKNGGKSQMAAALMRHHAGDAIEVHSAGTRPGTALNAQSTEAIAEVGA
+DMSSAVPQPVTPELLRSVDHVIVIGDEAVIKPVEGMTAPVTTWYTDEPSQRGIEGMERMR
+LVRDDIDIHVRKLLTDLTQPST*
+>NZ_CP040019.1_720
+MSEPTTLDTHVLQRSAEHLAECYAGVFSPETVERYVFESYATLSRTAKVRTYLASTASHF
+ADNRLRALAQSEGKIASPVPQVLFVCVHNIGRSQIAAALLTHHAGDKVEVRSAGSLPGSE
+VHPLVVQALAERGIDLSGAYPKPLTDDVVRAADYVITMGCGDACPVYPGKRYLDWEIADP
+AAETPDGVRAIVDAIDTRVKALWDELRSAT*
+>NZ_CP040019.1_724
+MTAETTPETTKPSVLFVCVHNAGRSQMAAAYLQRLAGGRIEVRSAGSAPADTVNPAAVEA
+MAEEGIDISANQPKVLSEQAVKDSDVVITMGCGDACPFFPGKRYEDWKLDDPAGRGVEGV
+RPIRDEIKTRIQQLITELLPAESTAN*
+>NZ_CP040019.1_725
+MTTPESASRPSVLFVCAKNGGKSQMAAALMEHHAAGAVQVHSAGTKPGKSINALSAEVIA
+EAGADMSAGHPKPIDPDLLARVDRVVVLGDEARVEPVDGMAGTIVTWHTDEPSTRGIEGI
+ERMRLVRDDIDARVRTLLTELTGSPAS*
+>NZ_CP083691.1_472
+MTSDRPSVMFVCVHNAGRSQMAAAYAQHLSGGAVEVRSAGSAPADQVNPAVVEAMAEEGI
+DLSAERPKVLTPEAVQASDAVITMGCGDACPLYPGKRYEDWVLEDPAGRGVDAVRPIRDE
+IRGRVAGLLRELGVEPVA*
+>NZ_CP097650.1_1945
+MTTKRPSVLFVCVKNGGKSQMAAALMRHHAGDAIEVHSAGTRPGTALNAQSTEAIAEVGA
+DMSSAVPQPVTPELLRRVDQVIVIGDEAVIKPVEGMTAPVTTWHTDEPSQRGIEGMERMR
+LVRDDIDTHVRKLLTDLTGTAN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000161.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000161.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d647fc76fd12c9700637da15b914659e754fb360
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000161.fa
@@ -0,0 +1,42 @@
+>NZ_CP042169.1_2023
+MPDIIEFPLPASSDDPHWRAYCRLGDEYNHELIGTTEWDETPTDALIQAAAETDHTQRRY
+LAYVDGEAVGYARVLINHVDDPDAAALNVYVLPRHRGRGHGRALAERLVQDTAGLTRFET
+WPLTPRPVAGQRTLTPPNGAGAVPAEHPGVRLAQSYGFALVQIERVSRYDFADPGIDPAV
+ALAEAERVSSDYELHAWEGAADASLQDDLAVLKARMATDVPSGERTVVEQVWDAARVRRM
+DEQILTTGRLFRAVARHRATGRIVALSELVAPRSRPDGLIDQWDTIVLPEHRGHRLGMRV
+KAANLIAVRDALPEARAIITWNAEENRHMLDVNEALGFRPVLVEASMEAPAPLRRR*
+>NZ_CP033200.1_1739
+MPDIIEFPLPASSDDPHWRAYCHLGDEYNHELIGTTEWDETPRDALIQAAAETDHTQRRY
+LAYVDGEAVGYARVLINHVDDPDAAALNVYIHPRHRGRGHGRALAERLVLDTAGLTRFET
+WPLTPRPVAGQRTLTPPNGAGAVPAEHPGVRLAQSYGFALVQTERVSRYDFADPGIDPAV
+ALAEAEGVSSDYELHAWEGAADASLQDDVAVLKARMATDVPSGERTVVEQVWDAARVRRM
+DEQILTTGRLFRAVARHRATGRIVALSELVAPRSRPDGLIDQWDTIVLPEHRGRRLGMRV
+KAANLIAVRDALPGARAIITWNAEENRHMLDVNEALGFRPVLVEASMEAPAPLRRR*
+>NZ_CP040019.1_689
+MPDIIEFPLPASSDDPHWRAYCQLGDEYNHELIGTTEWDETPTDALIQAAAETDHTLRRY
+LAYVDGEAVGYARVLINHVDDPDAASLTVYVHPRHRGRGHGRALAERLVLDTAGLTRFET
+WPLTPRPAVGQRALTPPNGAGMVPAGHPGVRLAQSYGFALVQIERVSRYDFADPGIDPAV
+AVAEAERVSSGYELHAWEGAADASLQDDLAVLKARMATDVPSGERTVVEQVWDAARVRRM
+DEQILTTGRLFRAVARHRATGRIVALSELVAPRSRPDGLIDQWDTIVLPEHRGHRLGMRV
+KAANLIAVRDALPEARAIITWNAEENRHMLDVNEALGFRPVLVEASMEAPAPLRRR*
+>NZ_CP083691.1_599
+MPDIIEFPLPASSDDPHWRAYCQLGDEYNHELIGTTEWDETPTDALIQAAAETDYTQRRY
+LAYVDGEAVGYARVLINHVDDPDAASLNVYVHPRHRGRGHGRALAERLVQDTAGLTRFET
+WPLTPRPVAGQRALTPPNGAGVVPAEHPGVRLAQSYGFALVQIERVSRYDFADPGIDPAV
+ALAEAERVSSDYELHAWEGAADAALQDDLAVLKARMATDVPSGERTVVEQVWDAARVRRM
+DEQILTTGRLFRAVARHRATGRIVALSELVAPRSRPDGLIDQWDTIVLPEHRGHRLGMRV
+KAANLIAVRDALPEARAIITWNAEENRHMLDVNEALGFRPVLVEASMEAPAPLRRR*
+>NZ_CP083691.1_603
+MPDILEFPLPATADEAHWQAYCRLNRDHNHELLGTTEWDESPDDALLDAAAESDYTLRRF
+LALDDGTPVGNGRILVNHVDEPDAASLSVFIHPDHRRRGHGRALAERIAREADGFTRFET
+WPMTPLPAEGERALRPSSGAGAVPADHPGVRLALSYGFALGQVERVSRYDVLTPAVDPAD
+ALAEAERPGADYEVLTWEGPADEAVRADLAVLKERMATDVPSGDLTVAEQTWDAGRVRRQ
+EEQILLTGRLFRAAVRHRDTGRIVGVNELVAPRSRTSGLVDQWDTIVSPEHRGHRLGMRV
+KAANLVALRRALTEARAIITWNAEENRPMLDVNEALGFQPILVEAEMQAHGPLRRVVP*
+>NZ_CP097650.1_1962
+MPDIIEFPLPVSSDDPHWRAYCQLGDEYNHELIGTTEWDETPTDALIQAAAETDHTLRRY
+LAYVDGEAVGYARVLINHVDDPDAAALNVYVHPRHRGRGHGRALAERLVLDTAGLTRFET
+WPLTPPPVAGQRALTPPNGAGAVPAEHPGVRLAQSYGFALAQIERVSRYDFADPGIDPAV
+ALAEAERVSSDYELHAWEGAADASLQDDLAVLKACMATDVPSGERTVVEQVWDAARVRRM
+DEQILTTGRLFRAVARHRATGRIVALSELVAPRSRPDGLIDQWDTIVLPEHRGHRLGMRV
+KAANLIAVRDALPEARAIITWNAEENRHMLDVNEALGFRPVLAEASMEAPAPLRRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000162.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000162.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2b04ebcd31b0455c8edb67988dd8c8fa63ff6c47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000162.fa
@@ -0,0 +1,22 @@
+>NZ_CP042169.1_2037
+MTDTTTARPKRPAHRDDGPPVRGIGHLRHPAVSGGLIGVIGGGAFLFGGIAGLPAEHRAT
+LRGIAISLISFTLVVVLLRRRMLPTVPTPARGALRVYGIAVVAMLAFLPVTRLVALALDA
+PTAQIALVAAVVGGHFLPFARAFQAPVFWWIGGAMAALGLAGAALAALGDPVAGPAGAAA
+AGVAMLVIVAAQGLLASPRQD*
+>NZ_CP033200.1_1756
+MSHVMRGGTMTDTTTARPMRPAHFDDDPPVRGIGHLRHPVVWGGLIGVVGGGAFLFGGIA
+GLPAEHQGTLRGSAIALIGFTLVVVLLRRRVLPAVQAPARGASTGSPSSRCWRSSP*
+>NZ_CP033200.1_1757
+MLALLPVTRLVALALDAPTAQIALVAAVVGGHFLPFARAFQAPVFWWIGGAMAVLGLAGA
+VVAVLGDPVAGPAGAAEAGAAMLVIVAAQGLLASPRQD*
+>NZ_CP040019.1_669
+MSHVTRGGTMTDTTTARPMRPTHHDDDPPVRGIGHLRHPVVSGGLIDGAMAAQGLLASPR
+PD*
+>NZ_CP083691.1_539
+MERDSTHARGIAHPMHPAVLGAVVGMVGGSLFMLLSRPELPFPWPTVTLVAWIALLAAAA
+WAVFLAPRRLRDVGAPSRHAGPIYGLSVLGMVALIIASPHLVRALGIEAAQPAVVVMAVG
+LHFIPFASAFGARVFAWLGGSLTAIGLAGVIAAAVVGAPAGAVAAVLAGAAMLAFLAVDA
+RRGA*
+>NZ_CP083691.1_585
+MSHVMRGGTMTATTTARPMRPTHHDDDPPVRGVGHLRHPVVSGGLIDGAMAAQGLLASPR
+QD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000168.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000168.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7552b3793b3466cfe9178aea7f29b183a2236cb5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000168.fa
@@ -0,0 +1,42 @@
+>NZ_CP042169.1_2196
+MTAQTPATPAIPETMKAVVMRAPGDVVVEEVDTPRVAQPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSQAQYMRVELADGSLVKVPGGEPSDPDRLADYLAASDVLGTGWYAAVAAQAGPGKT
+IAVVGDGAVGLCAVLGAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQVRE
+LTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFGRQIHLEGGP
+APVRRFLPELIERIQSGEIQPGRVFTARRPIDDAAEAYQAMDERREIKVLLEV*
+>NZ_CP042169.1_2220
+MTTETPTLAAPEIPATMKAVVMRAPGDVVVEEVDTPRVAQPTDVVLKLAAACVCGSDLWP
+YRGHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVN
+AGEYTGSQAQYMRVELADGSLVKVPGGEPSDPDRLTDYLAASDVLGTGWYAAVAAQAGPG
+KTIAVVGDGAVGLCAVLAAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQV
+RELTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFGREIHLEG
+GPAPVRRFLPELIERIQSGEIQPGRVFTARRPIDDAAEAYQAMDERREIKVLLEV*
+>NZ_CP033200.1_1907
+MTAQTLATPAIPETMKAVVMRAPGDVVVEEVDTPRVAQPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSRAQYMRVELADGSLVKVPGGEPSDPDRLADYLAASDVLGTGWYAAVAAQAGPGKT
+IAVVGDGAVGLCAVLAAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQVRE
+LTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFAREIHLEGGP
+APVRRFLPELIERIQSGEIQPGRVFTARMPLDDAAEAYRAMDERREIKVLLEV*
+>NZ_CP040019.1_473
+MTAQTPATPAVPETMKAVIMRAPGDVVVEEVDTPRVAKPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSQAQYMRVELADGSLVKVPGGEPADPDRLADYLAASDVLGTGWYAAVAANAGPGKT
+IAVVGDGAVGLCAVLAAKTLGAEQVIAFSRHEDRAALAREFGADVIIAERGEEGAAKVKE
+LTNGYGAHGVCEAVGTQESMDQALASVRPGGHVGFVGVSHDQTIDGSRLFGLEIHLEGGP
+APVRRFLPELIERIQAGEIQPGRVFTARMPIDDAAEAYKAMDERREIKVLLEV*
+>NZ_CP083691.1_419
+MTAQTPTTPAIPETMKAVVMRAPGDVVVEEVDTPRVVQPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSQAQYMRVELADGSLVKVPGGEPSDPDRLADYLAASDVLGTGWYAAVAAQAGPGKT
+IAVVGDGAVGLCAVLAAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQVRE
+LTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFGREIHLEGGP
+APVRRFLPELIERIQSGEIQPGRVFTARMPLDDAAEAYRAMDERREIKVLLEV*
+>NZ_CP097650.1_2129
+MTAQTLATPAIPETMKAVVMRAPGDVVVEEVDTPRVAQPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSQAQYMRVELADGSLVKVPGGEPSDPDRLADYLAASDVLGTGWYAAVAAQAGPGKT
+IAVVGDGAVGLCAVLAAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQVRE
+LTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFAREIHLEGGP
+APVRRFLPELIERIQSGEIQPGRVFTARMPLDDAAEAYQAMDERREIKVLLEV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000169.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000169.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a5d4030df42318230e5b413e0582ecf4341a397c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000169.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_2209
+MDVTFTPLDPAGADRDALVALLTENAWPFHTRPRVTRPEAEKAVDGGAWEDEDHRTFWIE
+HPEHGRVGVVRLEDLTDPTPLFDLRVAERFRGRGLGAQILTALTRHVFETMPAVDRFEGQ
+TREDNVPMLRTFRRAGWVKEAHYRRGWPVDGGEPLASVAYAMLRQDWASGTTTPVPADVD
+APPPAGRKEGAAAGGRAPDWPLPTARLTLRPHREDDLGWLQEMYMQPVVVRHLLDEPWDE
+ATARAKLAKRITWDDLGGPSGAVSLVVEHAGVPVGDVILWLTDRERGVAEIGWALDPRHA
+GQGFAREAAAALLDLGFETSGLHRVVAQMDARNTASARLAETLGMRREAHHRQDLWSKGE
+WTDTLVYAMLASDRGVRGHL*
+>NZ_CP033200.1_1916
+MDVTFTPLDPAGADRDALVALLTENAWPFHTRPRVTRPEAEKAVDGGAWEDEDHRTFWIE
+HPEHGRVGVVRLEDLTDPTPLFDLRVAERFRGRGLGAQILTALTRRVFETMPAVDRFEGQ
+TREDNVPMLRTFRRAGWVKEAHYRRGWPVDGGEPLASVAYAMLRQDWASGTTTPVPADVD
+APPPAGRKEGAAAGGRAPDWPLPTARLTLRPHREDDLGWLQEMYMQPEVVRHLLDEPWDE
+ATARAKLAKRITWDDLGGPSGAVSLVVEHAGVPVGDVILWLTDRERGVAEIGWALDPRHA
+GQGFAREAAAALLDLGFETSGLHRVVAQMDARNTASARLAETLGMRREAHHRQDLWSKGE
+WTDTLVYAMLASDRGGGGPSMTANGLLRSPHAARDREGVDSRGSPGVRTEVLEDLQVEKP
+LVRAGGLGEHRLVGADVDDLPHTEAGGLLRLKDRQVSVAGDAVDLGEPPRGPHLVCRPHH
+GPHTTQRDRPGGAAVVVMGDDPACRGQGPSLTHSPGGQQDQLVDFPHGDRVTAAFLLPVR
+ERGAADGADGDVHGRSVGAGPHPGARGASSPVMLGIGLEARRVKARTTHPHRVHRIDAMT
+RTGAFTIAGLAAFAISTGILVLLLITGSETPRETMAFFALIIGCYALSALCFAAAKRVLL
+ALLSGALAVVSFPLALFIGYVVEMLQSQQ*
+>NZ_CP040019.1_453
+MDVTFTPLDPAGADRDALVALLTENAWPFHTRPLVTRPEAEEAVDGGAWEDEDHRTFWIE
+HPEHGRVGVVRLEDLTDPTPLFDLRVAERFRGRGLGAQILTALTRHVFETMPAVDRFEGQ
+TREDNVPMLRTFRRAGWVKEAHYRRGWPVDGGEPLASVAYAMLRQDWASGTTTPVPADVD
+APPPAGRKEGAAAGGRAPDWPLPTARLTLRPHREDDLGWLQEMYTQPEVVRHLLDEPWDE
+ATAREKLAKRITWDDLGGPSGAVSLVVEHAGVPVGDVILWLTDRERGVAEIGWALDPRHA
+GQGFAREAAAALLDLGFETSGLHRVVARMDARNTASARLAETLGMRREAHHRQDWWSKGE
+WTDTLVYAMLASDRG*
+>NZ_CP040019.1_625
+MAERFRGRGLGAQILAALTRHVFETMPAVDRFEGQTREDNIPMLRAFRRAGWVKEAHYRR
+GWPVEGGEPLASVAYAVLRQDWETGTTTPVPADVDVPSRRKRDVGAESNGHIPDWPMRTE
+RLTLRPHREDDLGWLQEMYAQPEVVRHLLDEPWDEPTARQKLVRRIEWNDLAGPSGVASL
+VIEHAGVPVGDVILWLTNRERGVAEIGWALDPRHAGQGFAREAAAAMLALGFEVHGLHRV
+VAQMDARNTASARLAEAIGLRREAHHRQDWWSKGKWTDTLVYATLSSDRD*
+>NZ_CP083691.1_403
+MDVTFTPLDPAGADRDALVALLTENVWPFHMRPRITRSEAEEAVDGGAWEDEDHRTLWIE
+HPEHGRVGVVRLDELTDPTPLFDLRVTERFRGRGLGAPILTALTRLVFETMPAVDRFEGQ
+TREDNVPMLRTFRRAGWVKEAHYRRGWPVEGGEPLASVAYAVLRQDWETGTTTPVPAEVD
+VPPQVEHGEGAAAVGPAPDWPLRTERLTLRPHREDDLGWLRDMYARPEVVRHLLDEPWDE
+ATARQKLAKRIAWDGLAGPSGAVSLVVEHRGVPVGDVILWLTDRERGVAQIGWALHPEHA
+GQGFAREAAAALLTLAFETYDLHRVVAQMDARNTASAQLAEAVGLRREAHHRQDWWSKGE
+WTDTLVYATLASDRG*
+>NZ_CP097650.1_2144
+MVRLEDLTDPTPLFDLRVAERFRGRGLGAQILTAITRHVFETMPAVDRFEGQTREDNVPM
+LRTFRRAGWVKEAHYRRGWPVDGGEPLASVAYAMLRQDWASGTTTPVPADVDAPPPAGRK
+EGAAEGGRAPDWPLPTARLTLRPHREDDLGWLQEMYTQPEVVRHLLDEPWDEATARAKLA
+KRITWDDLGGPSGAVSLVVEHAGVPVGDVILWLTDRERGVAEIGWALDPRHAGQGFAREA
+AAALLDLGFETSGLHRVVAQMDARNTASARLAETLGMRREAHHRQDLWSKGEWTDTLVYA
+MLASDRGVRGHL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000176.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000176.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ef5120b5cf06c48a3a22460b66db039fbb7d4a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000176.fa
@@ -0,0 +1,41 @@
+>NZ_CP042169.1_3
+MYLSHLTVADFRSYRWADLELTPGSTVLLGANGVGKTNLVEAIGYLGAQQSHRVSSDAQL
+VRFGRDRARIAGRVHRGSRAVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLSLVTGEPGGRRRLLDQLMVQLRPALGEAAADYERVLRQRNALLKSSRGSRRWGPEEDA
+TLAVWDEHLCAAGARLLHGRLHVLRLLARPLQEMYAALTNGSKAAAYAYESTVPLARGTH
+AEVPAVADLAVDMRRTLETQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRMAAYDVLVADDPDPDARPVLILDDVFAELDAARRRRLAALVHRAEQVIVTAAALE
+DVPEELTAHRVLIRQDAEGSEAVAAAAPVEGDIREPRREGGADG*
+>NZ_CP033200.1_1964
+MYLSHLTVADFRSYRWADLELTPGSTVLLGANGVGKTNLVEAIGYLGAQQSHRVSSDAQL
+VRFGRDRARIAGRVHRGSRAVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLGLVTGEPGGRRRLLDQLMVQLRPALGEAAADYERVLRQRNALLKAGRGSRRWGPEEDA
+TLAVWDEHLCAAGARLLHGRLHVLRLLARPLQEMYAALTNGSKAAAYAYESTVPLARGTH
+AEVPAVADLAVDMRRTLETQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRMAAYDVLVADDPDPDARPVLILDDVFAELDAARRRRLAALVHRAEQVIVTAAALE
+DVPEELTAHRVLIRQDAEGSEAVAAAAPVEGDIREPRREGGADG*
+>NZ_CP040019.1_405
+MHLSHLTVADFRSYRWADLELGPGSTVLLGANGVGKTNLVEAVGYLGSHQSHRVSSDAQL
+VRFGQDRARIAGRVHRGSRTVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLNLVTGEPGGRRRLLDQLMVQLRPALGEAAADFERVLRQRNALLKSARKARRWGPEEEA
+TLEVWDEHLCAAGARLLHGRLHVLRLLAHPLREMYGALTNGSKAATYAYESTVPLARGTH
+AEVPPVAELAADMRRALVAQRDEEQARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRLAAYDVLVADDPDPDGRPVLILDDVFAELDAARRRRLAALVGRAEQVIVTAAALE
+DVPAELAGPRVLIRQDAEGSEAVPAAAPVEGDIRAPRGAGGTEGEAPGARRGRRRRRRHA
+PADPAEDDPDG*
+>NZ_CP083691.1_358
+MHLSHLTVQDFRSYRWADLELSPGSTVLLGANGVGKTNLVEAIGYLGSHQSHRVSQDAQL
+VRFGQDRARIAGRVHRGARSVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLGLVTQDPGGRRRFLDQLMVQLRPALGQAAADYERVLRQRNALLKSARKARRWGAEEDA
+TLAVWDEHLCAAGARLLHGRLHVLRLLAHPLQEDYAALTNGSKTATYSYESTVPAARGTH
+VQAPPVAELAASMHAALVEQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRLAAYDVLVADDSDPEGRPVLILDDVFAELDAARRERLAGLVGRAEQVIVTAAALA
+DIPASLAGHRVLIRQDAEGSEAVAAAEPVEGDIRAPRPGAAPGAAASEAEEPEDGDARA*
+>NZ_CP097650.1_3
+MYLSHLTVADFRSYRWADLELTPGSTVLLGANGVGKTNLVEAIGYLGAQQSHRVSSDAQL
+VRFGRDRARIAGRVHRGSRTVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLSLVTGEPGGRRRLLDQLMVQLRPALGEAAADYERVLRQRNALLKSSRGSRRWGPEEDA
+TLAVWDEHLCAAGARLLHGRLHVLRLLARPLQEMYAALTNGSKAAAYAYESTVPLARGTH
+AEVPAVADLAADMHRTLEAQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRMAAYDVLVADDPDPDARPVLILDDVFAELDAARRRRLAALVHRAEQVIVTAAALE
+DVPEELTAHRVLIRQDAEGSEAVAAAAPVEGDIREPRREGGADG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000178.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000178.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d90585956cbbad75656acc472f0887e334c5588
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000178.fa
@@ -0,0 +1,65 @@
+>NZ_CP042169.1_5
+MPENPAEEPTAASAAPNPEAVPDAVGQPETPVKDRKVPGEYGASAITVLEGLEAVRKRPG
+MYIGSTGPRGLHHLVYEVVDNSVDEALAGYATGIDVTLQADGGVRVADDGRGIPVDLHPT
+EGRPTVEVVMTILHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSF
+ADGGVPQGELVKGEATDATGTVQTFYPDPEIFDSIEFDYETLRARFQQMAFLNRGLRITL
+TDERVQESNEVVDDEIAGEGAAGEDVAENGLAEDAEQEPQRRSVTYLYENGLLDYVQHLN
+SAKKVEYVHDNVIAFEAEDVSDGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEG
+FRAALTSLVNRYAREKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSE
+ARGFVSKAVTDHLGDWFERNPGPAKEIIRKAIMASHARLAARKARDNARRKSPLESFGMP
+GKLADCSSKDPERCEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGN
+AEIQSMITAFGTNIGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAG
+HVFLAQPPLYRIKWSNAPHDYVFSDEERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQ
+ELWDTTMDPEHRTLLQVTMEDAAAADAVFSMLMGEDVESRRTFIQQNAKDIRFLDV*
+>NZ_CP033200.1_1966
+MPENPAEEPTAASAAPNPEAVPDAVGQPETPVKDRKVPGEYGASAITVLEGLEAVRKRPG
+MYIGSTGPRGLHHLVYEVVDNSVDEALAGYATGIDVTLQADGGVRVADDGRGIPVDLHPT
+EGRPTVEVVMTILHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSF
+ADGGVPQGELVKGEATDATGTVQTFYPDPEIFDSIEFDYETLRARFQQMAFLNRGLRITL
+TDERVQESNEVVDDEIAGEGAAGEDVAENGLAEEAEQEPQRRSVTYLYENGLLDYVQHLN
+SAKKVEYVHDDVIAFEAEDVSDGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEG
+FRAALTSLVNRYAREKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSE
+ARGFVSKAVTDHLGDWFERNPGPAKEIIRKAIMASHARLAARKARDNARRKSPLESFGMP
+GKLADCSSKDPERCEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGN
+AEIQSMITAFGTNIGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAG
+HVFLAQPPLYRIKWSNAPHDYVFSDEERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQ
+ELWDTTMDPEHRTLLQVTMEDAAAADAVFSMLMGEDVESRRTFIQQNAKDIRFLDV*
+>NZ_CP040019.1_403
+MLAAPSPDAAPETPEAPALAKDRRVPGEYGASAITVLEGLEAVRKRPGMYIGSTGPRGLH
+HLVYEVVDNSVDEALAGYASGIDVTLQADGGVRVADDGRGIPVDLHPTEGKPTVEVVMTI
+LHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSFADGGVPQGELVQ
+GEATDATGTVQTFYPDPEIFDSIEFDWETLRARFQQMAFLNKGLRITLTDERVQEDNEVV
+DDEIAGEAAAEENAEQGLDEAAAQAPQRRQVTYLYENGLLDYVQHLNSAKKVDFVHEDVI
+AFEAEDAEAGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEGFRAALTSLVNRYA
+REKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSEARAFVSKAVTDHL
+GDWLERNPGPAKEVIRKAIMASHARMAARKARDNARRKSPLESFGMPGKLADCSSKDPSR
+CEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGNAEIQSMITAFGTN
+IGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAGHVFLAQPPLYRIK
+WSNAPHDYVFSDAERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQELWDTTMDPEHRT
+LLQVSMEDAAAADAVFSMLMGEDVESRRNFIQQNAKDIRFLDV*
+>NZ_CP083691.1_355
+MVDAAPEQPEQPSAPAPDTNPAHQVQEYGASAITVLEGLEAVRKRPGMYIGSTGPRGLHH
+LVYEVVDNSVDEALAGFADGIDVTLQADGGVRVQDNGRGIPVDIHPTEGKPTVEVVMTIL
+HAGGKFGGGGYAVSGGLHGVGISVVNALSTRVETEIRRQGHAWRMSFANGGIPQGELVKG
+EATEETGTVQTFWPDPEIFESVEFDYETLRARFQQMAFLNKGLRITLTDERVQEDNEVQE
+DEIVGEGTAGEDAAAENGLDDEQTPQRRCVTYLYEDGLLDYVKHLNSSKRAELVHEDVIA
+FDAEDAERGMALEVAMQWTTAYSESVHTYANTINTHEGGTHEEGFRSALTALVNRYAREK
+EILKAKDDNLSGEDIREGLTAVVSVKLSEPQFEGQTKTKLGNSEARGFVSKVVTDHLGDW
+LERNPGPAKDIIRKAVQASHARMAARKARDNARRKSPLESFGMPGKLADCSSKDPARCEV
+YIVEGDSAGGSAKQGRNPDTQAILPLRGKILNVERARLDKALGNAEIQSMITAFGTNIGE
+EFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAGHVFLAQPPLYRIKWSN
+APHDYVFSDEERDAAIEAGLARGWRYPKDNGVQRYKGLGEMNYQELWDTTMDPEHRTLLQ
+VTMEDAAAADQVFSMLMGEDVESRRNFIQQNAKDIRFLDI*
+>NZ_CP097650.1_5
+MPENPAEEPTAASAAPNPEAVPDAVGQPETPVKDRKVPGEYGASAITVLEGLEAVRKRPG
+MYIGSTGPRGLHHLVYEVVDNSVDEALAGYATGIDVTLQADGGVRVADDGRGIPVDLHPT
+EGRPTVEVVMTILHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSF
+ADGGVPQGELVKGEATDATGTVQTFYPDPEIFDSIEFDYETLRARFQQMAFLNRGLRITL
+TDERVQESNEVVDDEIAGEGAAGEDVAENGLAEEAEQEPQRRSVTYLYENGLLDYVQHLN
+SAKKVEYVHDDVIAFEAEDVSDGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEG
+FRAALTSLVNRYAREKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSE
+ARGFVSKAVTDHLGDWFERNPGPAKEIIRKAIMASHARLAARKARDNARRKSPLESFGMP
+GKLADCSSKDPERCEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGN
+AEIQSMITAFGTNIGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAG
+HVFLAQPPLYRIKWSNAPHDYVFSDEERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQ
+ELWDTTMDPEHRTLLQVTMEDAAAADAVFSMLMGEDVESRRTFIQQNAKDIRFLDV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000179.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000179.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2cff01e34d982ed178f4c4ce5fa91677a7646b65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000179.fa
@@ -0,0 +1,82 @@
+>NZ_CP042169.1_6
+MSDETTPQTPDEPVEGAPTPQPPQTGLDIEVEHYVLPEGAADKVEPVDLESEMKRSYLDY
+AMAVIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRAFNKSARVVGDVMGNYHPHGDTA
+IYDALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVD
+MQDNYDGKQQEPVVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEAT
+REELLEALLARVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVT
+ELPYMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLY
+KHTELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTAFRKRKAEERAHILR
+GLLKALDMLDEVIATIRRSASAEVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQ
+DEYDDLMAKIAEYNRILESPQRQREVISEELAEIVAKHGDDRRTEIMAGFDGDMSIEDLI
+PEEEMVVSITRGGYVKRTRIDQYRSQARGGKGVRGATLRGDDVVEHFLTVSTHHWLLFFT
+NFGRVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLVDYGRAPYLVLATRGGL
+VKKTPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISHKGQSLRFTATDEALR
+PMGRATSGVTGMKFRDDDSLLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRPQNRGGLGIK
+VAKLVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDR
+IVAVTLNNEQEMEAKADAEAEAGPDVPLDADIDPTDPVAAPEDALTQDAGEGADGGEQ*
+>NZ_CP033200.1_1967
+MSDETTPQTPDEPVEGAPTPQTGLDIEVEHYVLPEGAADKVEPVDLESEMKRSYLDYAMA
+VIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRAFNKSARVVGDVMGNYHPHGDTAIYD
+ALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVDMQD
+NYDGKQQEPVVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEATREE
+LLEALLARVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVTELP
+YMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLYKHT
+ELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTAFRKRKAEERAHILRGLL
+KALDMLDEVIATIRRSASADVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQDEY
+DDLMAKIAEYNRILESPQRQREVISEELAEIVAKHGDDRRTEIMAGFDGDMSIEDLIPEE
+EMVVSITRGGYVKRTRIDQYRSQARGGKGVRGATLRGDDVVEHFLTVSTHHWLLFFTNFG
+RVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLVDYGRAPYLVLATRGGLVKK
+TPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISRKGQSLRFTATDEALRPMG
+RATSGVTGMKFRDDDSLLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRLQNRGGLGIKVAK
+LVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDRIVA
+VTLNNEQEMEAKADAEAEAGPDVPLDADIDPTDPVAAPEDALTQDAGEGADGGEQ*
+>NZ_CP040019.1_402
+MSDETTPQTPDESAEVPETPETGQDVAVEQYVLPEGAADKVEPVDLESEMKRSYLDYAMA
+VIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRSFNKSARVVGDVMGNYHPHGDTAIYD
+ALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVDMQD
+NYDGKQQEPAVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEATREE
+LLEALLTRVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVTELP
+YMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLYKHT
+ELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTVFRKRKAEERAHILRGLL
+KALDMLDEVIATIRRSASADVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQDEY
+DELMARIAEYDRILESPQRQREVISEELGEIVAKHGDDRRTEIMAGYDGDMSMEDLIPEE
+EMVVSITRGGYVKRTRIDQYRSQGRGGKGVRGATLRGDDIVEHFLTVSTHHWLLFFTNFG
+RVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLTGYDRAPYLVLATRNGLVKK
+TPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISHKGQSLRFTATDEALRPMG
+RATSGVTGMKFRDDDALLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRLQNRGGLGIKVAK
+LVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDRIVA
+VTLNNEHEMEAQADAEAAEDPVSEGSAAAAGVLPEGEPEALVGAEATAGAAADADVRLDA
+DIDPTDPAAAPEGLFEEDADGEGADGGEQ*
+>NZ_CP083691.1_354
+MSDETTPGTAPGTPQDGHDADQTPQIGQDVAVEHYVLPEGAADKVEPVDLESEMKRSYLD
+YAMAVIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRSFNKSARVVGEVMGNYHPHGDT
+AIYDALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTV
+DMQENYDGKQLEPTVLPARFPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEA
+TREELLAALMQRIKGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVV
+TELPYMTNPDNLAAKIAEMVRDGKIAGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNL
+YKHTELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIEVIVRRTAFRKKKAEARAHIL
+QGLLKALDMLDEVIATIRRSASAEVAREALKTLLDIDDEQAQAILQMQLRQLAALESQKI
+QDEYDELMARIAEYTAILESPQRQREVVSDELGELVAKHGDERRTEIVAGFDGDMSIEDL
+IPEEEMVVTITRGGYVKRTRIDQYRSQARGGKGVRGAALRGDDVVEHFLTVSTHHWLLFF
+TNLGRVYRIKTYELQEAGRDAKGQHVANLLAFQPDERIAQIQPLAGYDGDAPYLVLATRN
+GLVKKTPLEDYDTNRQAGLIAIKLREGDELVSARVVSAQDDLLLISRQGQSVRFTATDEA
+LRPMGRATSGVTGMKFRGDDALLAMDVIRAGDEDSYVFTVTDGGFAKRTHVDEYRTQGRG
+GLGIKVARLVDDRGELAGGLVVGEDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVVFAKP
+DKRDRIVAVTLNNEDEIEATADERAAAEGAAPEAAGAADGAGVPLDAVNDQTDPAAAAEA
+EAAGEDADGGEQ*
+>NZ_CP097650.1_6
+MSDETTPQTPDEPVEGAPTPQTGLDIEVEHYVLPEGAADKVEPVDLESEMKRSYLDYAMA
+VIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRAFNKSARVVGDVMGNYHPHGDTAIYD
+ALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVDMQD
+NYDGKQQEPVVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEATREE
+LLEALLARVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVTELP
+YMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLYKHT
+ELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTAFRKRKAEERAHILRGLL
+KALDMLDEVIATIRRSASADVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQDEY
+DDLMAKIAEYNRILESPQRQREVISEELAEIVAKHGDDRRTEIMAGFDGDMSIEDLIPEE
+EMVVSITRGGYVKRTRIDQYRSQARGGKGVRGATLRGDDVVEHFLTVSTHHWLLFFTNFG
+RVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLVDYGRAPYLVLATRGGLVKK
+TPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISHKGQSLRFTATDEALRPMG
+RATSGVTGMKFRDDDSLLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRLQNRGGLGIKVAK
+LVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDRIVA
+VTLNNEQEMEAKADAEAEAGPDVPLDADIDPTDPVAAPEDALTQDAGEGADGGEQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000181.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000181.fa
new file mode 100644
index 0000000000000000000000000000000000000000..70938ee14c1e7a6c56d76662042418838efde0a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000181.fa
@@ -0,0 +1,10 @@
+>NZ_CP042169.1_8
+MGRLARVALVVSAAAAAYGARLWRENSARKDVWATATDDLPEDADGVEPAPED*
+>NZ_CP033200.1_1969
+MGRLARVALVVSAAAAAYGARLWRENSAGKDVWATATDDLPEDADGVEPAPED*
+>NZ_CP040019.1_400
+MGRLARVALVAGAAAAAYGARLWQQNREGKDIWATATDDLPEDAEGVEPAPED*
+>NZ_CP083691.1_352
+MRLARIATLVAGAAAAYGVRSWRQQREDKAVWASATDSLEPRKAPAEDGRGEDEETPQG*
+>NZ_CP097650.1_8
+MGRLARVALVVSAAAAAYGARLWRENSAGKDVWATATDDLPEDADGVEPAPED*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000183.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000183.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ddafbe4b9f4bd78be9c757852d6b8dfee27ebf6c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000183.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_12
+MARKTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG
+RRKAQDAKKEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH
+EVQQQFAAARKDAEKAAKKGRRRGGRKAKQLRRDGRQAAKGLRKDAKKAAKGARKDAQRS
+AALFSDRAGQAKDAAAAGGLTLAGLLATGLSALQEQGGKVAPQVQARLADAGDYAQRRKE
+EVLPVAAARLADGAAHARKTAHDVEVPDALEQALIKLTGDKAIVQRLRQGAEQYAGAAEK
+DLNRAAGRRASRSGGRAWIVAGMAAAAAGAGFALWRLTKPVQDPWTAPVPGPITANIPVV
+EANNPYAQQQKVVAEAGSAAAGQGVRVDTATPDPVAAANAKVLGVQPGQQR*
+>NZ_CP033200.1_1986
+MARTTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG
+RRKAQDAKQEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH
+EVQQQFAAARKDAEKAAKKGRHRGGRKAKQLRRDGRQAAKGARKDAQRSAALFSDRAGQA
+KDAAAAGGLTLAGLLATGLSALQEQGGKVGPQVQARLADAGDYAQRRKEEVLPVAAARLA
+DGAAHARKTAHDVEVPDALEQALIRLTGDKAIVQRLRKGAEQYAGAAEKDLNRAAGRRTS
+RSGGRAWIVAGMAAAAAGAGYALWRLTKPVQDPWTAPVPGPIAANIPVVEANNPYAQQQK
+VVAEAGSAAAGEGVRVDTAAPDPVAAANAKVLGVQPGQQR*
+>NZ_CP040019.1_369
+MARTTLNDEIQHDGGADTFVTRQTENLRHWAAPKLEAARTWGEYGAAFTGVGASVAAEEG
+RRAAHDAKQEYGPRVEKQAKRAGDAVADRYAKLAPAVATGAGVLQDVLHRLQEQAQEAGH
+EAQKQFADARKDAEKAAEKGRKRGAKKAKQVRRAGRGARKDVTKAARGARKDARQAGSFL
+ADRAGQAGSAAAAGGLTLAGALAAAVNALQEQGEKLAPQVQARLSDAGDYAQRRKEEVVP
+LAAARLADGAAHARKTAHDVQVPDAVEQALIALTGDKAIVRKLRKGAEQYAGSAEKDLNR
+AAGRKARSGGRGWILGGMALAAAGAGYALWRLTKPVQDPWTAPVPGPITANIPVVEANNP
+YAQQQKVVAESGSAAAGEGVRVDTAAPVTTAVPAQDPVAEANAKVLGTDR*
+>NZ_CP083691.1_350
+MARTTLSNEIEHNGSADTFFARQAENLRHWAAPQLENARAWAEVTTGFGQVGGKVAAAEG
+RRLAEEEVAPRVKDSAERVNAAAKGRYEKAAPVVATGLGAAGTVLQQLLEAAQDKAQQAG
+QQVQDLAEQAQKDAKKSAKRTRKDAKKAGKRVSKKADKAQSLFASKAGDAKGAAAAGGLN
+VAGLLAAAVAAAQDRGQELAPQVKGRVEQAAQYAQDRRAEYAPKAAASLAGVAGRAEKAA
+GDVTVPASVEQLLVKLTGDKNAVKHLRQDVQSRARETQKGLKKQARQESRRGGATGWIIA
+GMAAAAAGAGLAVWKLTKPVQDPWAAPVPGPITANIPVVQADGTVNPYAKQEQAVAEARA
+AQGGMVNVRPQVG*
+>NZ_CP097650.1_12
+MARTTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG
+RRKAQDAKKEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH
+EVQQQFAAARKDAEKAAKKGRRRGGRKAKQLRRDGRQAAKGLRKDAKKAAKGARKDAQRS
+AALFSDRAGQAKDAAAAGGLTLAGLLATGLSALQEQGGKVAPQVQARLADAGDYAQRRKE
+EVLPVAAARLADGAAHARKTAHDVEVPDALEQALIKLTGDKAIVKRLRQGAEQYAGAAEK
+DLNRAAGRRASRSGGRAWIVAGMAAAAAGAGFALWRLTKPVQDPWTAPVPGPITANIPVV
+EANNPYAQQQKVVAEAGSAAAGQGVRVDTATPDPVAAANAKVLGVQPGQQR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000184.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000184.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4799dfb3dbc68313a2d24d35dc73fffb7ba7a8e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000184.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_13
+MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA*
+>NZ_CP033200.1_1987
+MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA*
+>NZ_CP040019.1_368
+MARMANATHIATIKTNQGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGVGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEESQQVVDRLNAVATDPRDRPLEDVVIESVEIAEA*
+>NZ_CP083691.1_349
+MTRMTNATQIATIHTNQGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDQLNSVATDPRDRPLEDVVIESVEISEA*
+>NZ_CP097650.1_13
+MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000185.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000185.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34daad04803b9d4a219def21f62f94533eec6a83
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000185.fa
@@ -0,0 +1,34 @@
+>NZ_CP042169.1_14
+MSTTPSDPHGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS
+GVVAGPAPTVAPAGAAASVPARRRTGFTASPVTWILLAVTTVVYAAQWMTRDQASGVTEA
+LWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLALY
+VLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVFS
+FLLPGVAWQVHMGGLLTGAVVAVVFSLAGGLRPGRARVPSVGAQVAGLVVVAAALAALTV
+LGAARVTVAGLLG*
+>NZ_CP033200.1_1988
+MSTTPSDPYGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS
+GVVAGPAPTSPPAAGAAATVPARRRTGFAASPVTWILLAVTTVVYAAQWMTRDQASGVTE
+ALWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLAL
+YVLSAVGGAVFALWASDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVF
+SFLLPGVAWQVHVGGLLTGAVVAVVFSLAGGLRPGRARLPSVGAQVAGLVVVAAALAALT
+VLGAARVTVAGLLG*
+>NZ_CP040019.1_367
+MDCAAQGGAPAGTTTSPAAVGSPGPGGVGMAGAAGRGAPARRRTGLAAAPVTWTLIAVTV
+AAYVAQWATRDTVPGVTEALWYAGLYTSPFGLEPWRMATYALVHDLSGPTHLILNMLALW
+VIGRVLEPALGWWRFAALYVLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLVTRV
+RGGQVRSIAVLIGLNLVISFLLPGISWQVHVGGLITGAVVALVYSLAGGLRPGRASAPSA
+GAQAAGLVLVAAVLAVLTVLGADRIGLDAVLR*
+>NZ_CP083691.1_348
+MSTTPSDPHGPDVAEGTPPVCPRHPGRAAYVRCASCADPVCLDCQRPAAGGLTLCPDCAA
+RLAAGVPGPASGTTTSPAPASAGAGRGGVGAALRAAPVTWTLLAVTLLVYAGQWLTRGSR
+TGVTESLWYAGAYTSAIGMEPWRMLTYALVHDVSGPTHVALNMVALWVIGRVLELALGWW
+RFLALYLVSALGGAVFALWTADPLQPVVGASGAVYGLFAALFAVTRFRGGQVTSIAVLIG
+LNLVFSFLMPGISWQVHVGGLLTGAVAGALLVSAGGPPGRSAAADGTARRSSAGVHVAGL
+VLLAAVLAVLTLVGAARLSPAALLG*
+>NZ_CP097650.1_14
+MSTTPSDPHGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS
+GVVAGPAPTVAPAGAAASVPVRRRTGFAASPVTWILLAVTAVVYAAQWMTRDQASGVTEA
+LWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLALY
+VLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVFS
+FLLPGVAWQVHVGGLLTGAVVAVVFSLAGGLRPGRARVPSVGAQAAGLVVVAAALAALTV
+LGAARVTVAGLLG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000186.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000186.fa
new file mode 100644
index 0000000000000000000000000000000000000000..55d105d9b1b495da890e3797b6ca0781cad11a02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000186.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_15
+MAAPAGKRKDSARRKREELEAARRSRSAVRTDLGDVDPGPKPLSPVYKAVMFGLLILGLL
+WIIVYYLTQGLLPIVQIGGWNILVGFGIALVGFLMMSRWSE*
+>NZ_CP033200.1_1989
+MAAPAGKRKDSARRKREELEAARRSRSAVRTDLGDVDPGPKPLSPVYKAVMFGLLILGLL
+WIIVYYLTQGLFPIVQIGGWNILVGFGLALVGFLMMSRWSE*
+>NZ_CP040019.1_366
+MAAPSGKRKDSARRKHEELEDARRGARRGSSAVTTDLGDVDPGPKPLSPVYKAVMFGLMI
+VGLLWIVVYYLTQGLFPIVAIGGWNILVGFGIALVGFLMMSRWSE*
+>NZ_CP083691.1_347
+MATTSGKRKDSARRKRRELEQARSRRGRTASVSTDLGDVDATPAPLPRWYKAVMFGLLIL
+GLLWIVVYYLSQGLFPIPDAGGWNILIGFGIALVGFLMMSRWSE*
+>NZ_CP097650.1_15
+MAAPAGKRKDSARRKREELEAARRSRSAVRTDLGDVDPGPKPLSPVYKAVMFGLLILGLL
+WIIVYYLTQGLFPIVQIGGWNILVGFGIALVGFLMMSRWSE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000187.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000187.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f738d5ef84ea272a50d0eb32dd1122acff8d2cfa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000187.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_16
+MQSPEVSVLVVDNYDSFVYTLVGYLEQLGARTTVIRNDEVTPARALELAAEHTAVLISPG
+PGAPADAGVSLDLIRSAADGGRPLFGVCLGHQAIAEAFGATVTHAESLMHGKTSLVRHGE
+HPMFEGVPSPFTATRYHSLATVRPTVDEAVLEITAETEDGVVMGLAHRTAPLWGVQFHPE
+SVLTEGGYRMLGNWLESVGLSGAAERGGRLSPLVRQD*
+>NZ_CP033200.1_1990
+MQSPQVSVLVVDNYDSFVYTLVGYLEQLGARTTVIRNDEVTPARALELAAEHTAVLISPG
+PGAPADAGVSLDLIRSAADGGRPLFGVCLGHQAIAEAFGATVTHAESLMHGKTSLVRHGE
+HPMFEGVPSPFTATRYHSLAAVRPTVDEAVLEITAETEDGVVMGLAHRTAPLWGVQFHPE
+SVLTEGGYRMLGNWLESVGLSGAAERGGRLSPLVRQD*
+>NZ_CP040019.1_365
+MSGTVPSPEVSVLVVDNYDSFVYTLVGYLEELGARTTVIRNDEVDAARALELAAEHTAVL
+ISPGPGAPADAGVSLDLIRAAADGGRPLYGVCLGHQAIAEAFGATVTHAESLMHGKTSLV
+RHGDHPMFAGLPERFTATRYHSLAAVRSTVDEAVLQITAETEDGVVMGLAHRSAPLWGVQ
+FHPESVLTEGGYRMLGNWLESVGLTGAADRGGRLSPLVRGD*
+>NZ_CP083691.1_346
+MSTPPESAPTAVSVLVVDNYDSFVYTLVGYLQELGARTTVIRNDEVSPARALELAAQHDA
+VLISPGPGTPSEAGVSLDLIRSAADGGRPLYGVCLGQQAIAEAFGATVTHAESLMHGKTS
+VLTHTDHPMFAGVPARFTATRYHSLAAVRHTVDESVLEITAQTDDGVVMGLAHRTAPLWG
+VQFHPESVLTEGGYRMLGNWLESVGLVGAAERGGRLSPLVRAAD*
+>NZ_CP097650.1_16
+MQSPEVSVLVVDNYDSFVYTLVGYLEQLGARTTVIRNDEVTPARALELAAEHTAVLISPG
+PGAPADAGVSLDLIRSAADGGRPLFGVCLGHQAIAEAFGATVTHAESLMHGKTSLVRHGE
+HPMFEGVPSPFTATRYHSLAAVRPTVDEAVLEITAETEDGVVMGLAHRTAPLWGVQFHPE
+SVLTEGGYRMLGNWLGSVGLSGAAERGGRLSPLVRQD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000189.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000189.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6973709ca0b32b14dd0d774408b398b7b58a12dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000189.fa
@@ -0,0 +1,64 @@
+>NZ_CP042169.1_18
+MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEKGSAYLVMELVPGQPLSSILEKEKVLSPERTLRIIAQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPPLPDTVPAPV
+RALIMCMLSKDPKERPSDATALSEAADALRRKDTRGAVEAVPGLAVFLEEQGVADPSGAE
+TAPLDYDGLRTTHPRTEGIRTDGSPATAALPVTAAQPRTDDAARGPGAAGAAAVGAAGAA
+ASASTRDHEIAAVRDQQTRPGDVVDPGPPAGGGSAPARRRRANPWPLWALLGLVVFALLG
+ALLWPLLTGGRGDGGSAPATSQEESSVNVDPEAYKGRPVSEVRAELEGLGLAVREEDRDA
+QSPQGTVEEINPVGALQRGETVTLAVSTGEGVIPEGLVGQPVDSAIQTLRDRGFTVDRVD
+DPSADGADGEVVRVVPGEGERHRYDTHVQLIVATGGSDAAPTREASQPASEPVPSASEEP
+SSEPSPSASDEPSPSPTAESPTATADPEPTQEPTEEPTTPTGDPTTESSGESTAPTGEPT
+TDPSADARGAEASSADATPSA*
+>NZ_CP033200.1_1992
+MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRNTAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEEGSAYLVMELVPGQPLSSILEKEKVLSPERTLGIIAQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPPLPDTVPAPV
+RALIMCMLSKDPKERPSDATALSEAADALRRKDTCGAVEAVPGLAVFLEEQGVADPSGAE
+TAPLDYDGMRTTHPRAEGTRADGSPATAALPVTAAQPRTDDAARGPGAAGAAAVGAAGAA
+GAAGAVASTRDHEIAAVRDQQTRPGDVVDPAPPAGGGSAPARRRRANRWPLWALLGLVVF
+ALLGALLWPLLTGGRGIGGSAPATSQDESSVRVDPEAYRGRPVSEVRTELEGLGLAVREE
+DRDAQSPQGTVEEINPVGALRRGETVTLAVSTGEGVIPEGLVGQPVESAIQTLRDRGFTV
+DRVDDPSADGADGEVVRVVPGEGERHRYDTHVQLIVATGGSDAAPTREASQPASEPEPSA
+SEEPSTEPSPSASDEPSPSPTAESPTATADPEPTPEPSEEPTTPTGDPTTESSGESTAPT
+GESTTDPSADARGAEASSADATPSA*
+>NZ_CP040019.1_362
+MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEKGSAYLVMELVPGQPLSAILEKEKVLSPERTLRIIAQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDAPPPLPSTVPAPV
+RALIMCMLSKDPKERPTDATAASEAADALRRKDTRAAVEAVPGLAAFLAAEGVADPSGAE
+TAPLDYDGMRTAHPRPEGTRADGTPATAALPVTAAQPRTDDGARGSAATAAGAAGAAGLA
+GAAAAGARPANEEIAAVRDPQTRPSDVVQEAPPAGQGSAPVKRRRANRWPVFALLGLVLF
+ALLGALLWPWITGDRTPGGSTPSGTSQASSVSVDPEAYKGRPAAEVRAELERLGLVVREE
+DRDARNPRGTVEEVNPVGSLQRGETVTLAVSTGEGVVPDGLVGQPVDSAIQLLRDRGFTV
+DRVDDPSADGAEGEVVRVVPGEGQRHRYDTHVQLIVAGGAGGDEPAPTPEPSEPAEPTAE
+PSDEPTTEPTSEPTEEPTTEPTAPSEEPTEEPTEEPTTEPTSDPTGEPTGEPTADPTDDA
+GGSASPTAEESPTA*
+>NZ_CP083691.1_344
+MRPTSGITLGGRYALTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEKGSAYLVMELVPGQPLSAILEKDRTLSTDRTLSIIRQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDIYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPALPDTISAPV
+RALIMCMLSKNPKDRPANATALSEAAEALRRKDVAGAVAAVPTLAAFLADQGVHSTGGPG
+DAETTALDAAPRTAPQPTVPLGTTTEPAAPATAALPVAAARPDVAATRSPRAAEPARSVP
+AAAPADPAPRTAKPRRRNRWPLFALLALVAFAVLGALLYPLLSGESGAGAGASSSTGTDA
+QVEVDAAAYRGRPADEVRAELEGRGLAVEEEQRDANDPQGTVVEVTPTGTLRRGDTVTLA
+VSTGQGTIPQDLVGQPADTVVGILRDRGFSVDRVDDPNADGATGQVVRVVPGEGQTHRFD
+TPVQVIVAGGTGSSPVTQSVVTAPTAAPASESPAEPAPASSSSGDPAPSSAQPTPSEAST
+EPSPESPAPTSESAAPSTEPSAGTPSTPDASGPSSQGSDAGSPSTDPAG*
+>NZ_CP097650.1_18
+MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEEGSAYLVMELVPGQPLSSILEKEKVLSPERTLGIIAQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPPLPDTVPAPV
+RALIMCMLSKDPKERPSDATALSEAAEALRRKDTCGAVEAVPCLAVFLEEQGVADPSGAE
+TAPLDYDGMRTTHPRAEGIRTDGSPATAALPVTAAQPRTADDARGPGAAGAAAVGAAGAA
+GAAASTRDHEIAAVRDQQTRPGDVVDPGPPAGGGSAPARRRRANRWPLWALLGLVVFALL
+GALLWPLLTGGRGVGGSAPATSQEESSVHVDPEAYRGRPVSEVRTELEGLGLAVREEDRD
+AQSPQGTVEEINPVGALRRGETVTLAVSTGEGVIPEGLVGQPVESAIQTLRDRGFTVDRV
+DDPSADGADGEVVRVVPGEGERHRYDTHVQLIVATGGSDAAPTREASQPASEPEPSASEE
+PSTGPSPSASDEPSPSPTAESPTATADPEPTPEPSEEPTTPTADPTTESSGESTAPTGEP
+TTDPSADARGAGASSADATPSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000193.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000193.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d734378b7bb656b4d576037937feb86c2e77e065
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000193.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_22
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGA
+AGAGSSAVDRPAPASTPSPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRAVPVGPGTAIRIGKT
+VMELEA*
+>NZ_CP033200.1_1996
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGA
+AGAGSSAVDRPAPASTPSPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRALPVGPGTAIRIGKT
+VMELEA*
+>NZ_CP040019.1_358
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGV
+AGAGSSAVDRPAPASTPAPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRALPVGPGTAIRIGKT
+VMELEA*
+>NZ_CP083691.1_340
+MNELAVAVLRLGLLLALWILIISIVLSQGRDLVVGRRNKLRLEQARRDAGLVTAVPAAGA
+HAASADRPAPAATPAAERPAPVPPAPAPRLARTLRITEGPLAGQTVDLGGRPLLIGRAQD
+ADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTFVDGDPVTRTLPVGTSSTIRIGKTV
+MGLED*
+>NZ_CP097650.1_22
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGV
+AGAGSSAADRPAPASTPSPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRALPVGPGTAIRIGKT
+VMELEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000194.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000194.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b5bc4d7d50ae1cfb16661183873509a31b1a904
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000194.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_29
+MTVTLPAAITPSPAFQPVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA
+VAPKDKDQARADAVAWLTSGHTGWVRLNGYGSRWWEQDVEALAAALPAHLGGPVSEGGLA
+GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD
+TGLGESPMALAYTRSQFTIAAKATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL
+APEQCAAVNEGLSPSQEELAWAHEFLADFEADGGEIRNGSDLPRKARAEKILGLAAAFGV
+HSTRYPDQDNAITAPSDTYHY*
+>NZ_CP033200.1_2002
+MTVTLPAAITPSPAFQPVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA
+VAPKDKDQARADAVAWLTSGHTGWVRLNGYGSRWWEQDVEALAAALPAHLGGPVSEGGLA
+GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD
+TGLGESPQALAYTRSQFTIAAKATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL
+APEQCAAVNEGLSPSQEELAWAHEFLADFEADGGEIRNGSDLPRKARAEKILGLATAFGV
+HSTRYPDQDNAITAPSDTYHY*
+>NZ_CP040019.1_353
+MTMTLPAAITPSPAFQAVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA
+VAPKDKDRARADALAWLTSGHTGWVRLNGYGSKWWEDDVAALAEALPAHLGGPVAEGGLA
+GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD
+TGLGESPMALAYTRSQFTIAAKATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL
+APEQCAAVNEGLSPSQEELAWAHEFLADFEADGSEIRNGSDLPRKARAEKILGLAAAFGV
+HSTRYPDQDNAITAPSDTYHY*
+>NZ_CP083691.1_291
+MTVTLSPSPTQPFQPTPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDVEDSVA
+PADKAKALADTVEWLTSGHTAWVRLNGYGSKWWEDDVDALASALPAHLGGPVAEGGLAGV
+MLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRDTG
+LGESPMALAYTRSQFTIAAKATGLPGAIDGPTVGSTGAKLAEATAVTTEFGMTGKLCLAP
+EQCAAVNEGLSPSPEELAWAQEFLEEFAAAGGQIRNGSDLPRKARAEKIQALAAAFGVQL
+AHIPDQENRAAAPSDTYHY*
+>NZ_CP097650.1_28
+MTVTLPAAITPSPAFQPVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA
+VAPKDKDQARADAVAWLTSGHTGWVRLNGYGSRWWEQDVEALAAALPAHLGGPVAEGGLA
+GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD
+TGLGESPMALAYTRSQFTIAARATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL
+APEQCAAVNEGLSPSQEELAWAHEFLADFEADGGEIRNGSDLPRKARAEKILGLATAFGV
+HSTRYPDQDNAITAPSDTYHY*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000201.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000201.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a7bde55923073cfee946c811979a9fb04e2e758d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000201.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_40
+MGRVAQYCGVIGEALVDVVVSDTATPRVHVGGSPLNVAVGLSRLERPVLFAGRLGRDAHG
+DMVASHLRENGVRCLLEPDAAATSVATARLDPTGAASYEFELDWTLPPAAALARDFDDAA
+GGPLHHMHAGSIATMLAPGDAEVMALLERISAVTTISYDPNVRPTIVPDRAFARARAEES
+VRLADVVHASDEDIAWLYPDRPLRESLQAWQQMGPAFVVMTRGAEDIVAVTAHGVVERPI
+VPVDVADTVGAGDSFTAALLAALDDRSLLGAANRGRLHAMDPADVESVLIYASRASAITA
+SRPGADPPTRAELAD*
+>NZ_CP033200.1_2009
+MGRVAQYCGVIGEALVDVVVSDTATPRVHVGGSPLNVAVGLSRLERPVLFAGRLGRDAHG
+DMIASHLRENGVRCLLEPDAAATSVATARLDPTGAASYEFELDWTLPPAAALARDFDDAA
+GGPLHHMHAGSIATMLAPGDAEVMALLERISAVTTISYDPNVRPTIVPDRAFARARAEES
+VRLADVVHASDEDIAWLYPDRPLRESLQAWQQMGPAFVVMTRGAEDIVAVTAHGVVERPI
+VPVDVADTVGAGDSFTAALLAALDDRSLLGAANRGRLHAMDPADVESVLIYASRASAITA
+SRPGADPPTRAELAD*
+>NZ_CP040019.1_344
+MDVVVSDTATPRAHVGGSPLNVAVGLSRLGRPVLFAGRFGRDEHGDMIASHLRDNGVHCL
+LEQDAAPTSQATARLDPTGAASYEFELDWTLPPAEELAEEFAAAAGGRLRHMHAGSIATM
+LAPGDAEVMSLLERISADTTISYDPNVRPSIVPDRAFARARAEESVRLADVVHASDEDVA
+WLYPARPLVETLQAWQRMGPALVVMTRGAEDIVAVTRDGVVERPIVPVDVADTVGAGDSF
+TAALLAALDDRSLLGAENRERLNAMDPADVESVLIYASRASAITASRPGADPPTRDELAD
+*
+>NZ_CP083691.1_286
+MGLVAEYFGVVGEALVDVVLSDTATPRAHPGGSPLNVAVGLSRLGRPVRFAGRYGTDEYG
+DMVAAHLADNGVHCVLGADDAPTSVATARLDPTGAASYEFELDWTLPEAAELERLLTGAA
+GGRLLHVHAGSIATMLAPGDASVMGLLEAVQPTATISYDPNVRPSIVPDREFARARAEES
+VRLSDVVHASDEDVAWLYPDRPLMDSLRAWQQAGPALVVMTRGAEDIVAVTAEHVLEQPI
+VPVDVADTVGAGDSFTAALLGALDDRSLLGAENRGRLHAMDLADIRSVLIYAARASAITS
+SRPGADPPMRDELAD*
+>NZ_CP097650.1_35
+MGRVAQYCGVIGEALVDVVVSDTATPRVHVGGSPLNVAVGLSRLERPVLFAGRLGRDAHG
+DMIASHLRENGVRCLLEPDAAATSVATARLDPTGAASYEFELDWTLPPAAALARDFDDAA
+GGPLHHMHAGSIATMLAPGDAEVMALLERISAVTTISYDPNVRPTIVPDRAFARARAEES
+VRLADVVHASDEDIAWLYPDRPLRESLQAWQQMGPAFVVMTRGAEDIVAVTAHGVVERPI
+VPVDVADTVGAGDSFTAALLAALDDRSLLGAANRGRLHAMDPADVESVLIYASRASAITA
+SRPGADPPTRAELAD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000211.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000211.fa
new file mode 100644
index 0000000000000000000000000000000000000000..771f3db36f52d3146c5f7bc843b57013eccca1ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000211.fa
@@ -0,0 +1,65 @@
+>NZ_CP042169.1_55
+MVSFSHTDDGTSEAAWAEGGVGELPELRLPVWDAQTLLLVAVAHPDDETLAATGLIRSAL
+RDGARVHVLVATAGEASHPHSPTHTPEDLVRLRRDEMEHALDALAAGLPASAGPGSPARD
+RLTWASLALPDSGVAEHEDAVRDAVAAALDAHPGPAVLASHDPGDGHADHEAVGRAVGAV
+AGECDLPLYAFPIWFWHWADPADLPARRYRRLPLTDDDRAARRAALDAHASQVRPLSAAP
+GDEAILGPAVLAHHERPFEAHRVSGPDDADAHRAAAVFDRLYRAQEDPWRYLSSSYEARK
+RALTLAALPRPRYGTVVEAGASIGVLTADVAARADRVVGLEASSTAVERAAARLAGAPHA
+EVRRAVLPADWPADVAGADLVIASEIGYFLQPEELDALIDDADAALAPGGELLLCHWRHP
+IEGWPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVVVPAKDEQERLP
+AALAALAAALDRWEEHHAQGTAAVVVAADRCDDATVAAALEARAADPRIHVLELGEPTAG
+QAGVGRARLEGARRARALFPDVPAERLWLASTDADSRVPADWLLAQTVAAGHDEVLVLGT
+VDVHQGPLRQAWLRGYRHEEGHPHVHGANLGLPWSLYEAVGGFPPVAEHEDVGLAEAVRA
+LAGERDGGDGRRVRVIATDTTRVLTSSRLEGRTPGGFSGYLKAVGRPG*
+>NZ_CP033200.1_2024
+MVSFSHTDDGTSEAAWAEGGVGELPELRLPVWDAQTLLLVAVAHPDDETLAATGLIRSAL
+RGGARVHVLVATAGEASHPHSPTHTPADLVRLRRDEMEHALDALAAGLPASAGPGSPARD
+RLTWASLALPDSGVAEHEDAVRDAVAAALDAHPGPAVLASHDPGDGHADHEAVGRAVGAV
+AGECDLPLYAFPIWFWHWADPADLPARRYRRLPLTDDDRAARRAALDAHASQVRPLSAAP
+GDEAILGPAVLAHHERPFEAHRVSGPDDADAHRAAAVFDRLYRAQEDPWRYLSSSYEARK
+RALTLAALPRPRYGTVVEAGASIGVLTAAVAARAGRVVGLEASPTAVERAAARLAGAPHA
+EVRRAVLPADWPADVAGADLVIASEIGYFLQPEELDALIDDADAALAPGGELLLCHWRHP
+IEGWPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVVVPAKDEQERLP
+AALAALTAALDRWEEHHAQGTAAVVVAADRCDDATVAAALEARAADPRIHVLELGEPTAG
+QAGVGRARLEGARRARALFPDVPAERLWLASTDADSRVPADWLLAQTVAAGRDEALVLGT
+VDVRQGPLRQAWLRGYRHEEGHAHVHGANLGLPWSLYEAVGGFPPVAEHEDVGLAEAVRA
+LAGERDGGEGRRVRVIATDTTRVLTSSRLEGRTPGGFSGYLKAVGRPG*
+>NZ_CP040019.1_324
+MVSFSHTDAGTSEEAWAAAGVGALPVLESPAWDADTLLLVAVAHPDDETLGATGLIRSAL
+RGGARVHVLVATAGEASHPDSPTHAPEDLVRLRRAEMEHALDALAADLPGPGEDRRSALT
+WESLGLPDSGVAGREDAVRAAVVAALAAHPGPAVLASHDPGDGHADHEAVGRAVGELAGE
+RDLPLCAFPIWFWHWADPAELPARRYRRLALTDDDRAARRAALDAHASQVRPLSDAPGDE
+AVLGPQVLAHHDRPFEAHRLSGPDDADAHRAAAVFDRLYREHEDPWRYLSSPYEARKRAL
+TLAVLPRPRYGTVVEAGASIGVLTGEVAARADRVVGLEASPTAVERAAARLADTPHAEVR
+RAVLPGHWPDDVAGADLVIASEIGYFLQPEELDALVDDADAALAPGGELLLCHWRHPIEG
+WPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVIVPAKDEQERLPAAL
+AALGAALDRWEEHHAQGSAAVVVAADRCDDATVAAAVAARHADPRVHVLELGEPGPGEAG
+VGRARAEAARRARALFPDVPAQRLWLASTDADSRVPADWLLAQTTAAGPDGALVLGTVDV
+REGALRRAWVRDYRHEEGHPHVHGANLGLPWSLYEAAGGFPPVAEHEDVRLVEAVRALAE
+ARVRATDTTRVLTSSRLTGRTPGGFAGHLQEVGGEAVPRRGAQARP*
+>NZ_CP083691.1_264
+MVSFDHRDDGTAEAVWMAAGVGELPALPARAWTRADTLLVAVAHPDDETLGAAGLIRAAL
+RGGAAVHVAVATAGEASHPDSPTHTPADLVRLRRAEMDHALAALADGLGPDAGALTWESL
+ALPDGGLTDRPDEVRAALERVLAGRTPAEEGGGAVVLVSHDPDDGHGDHDAVGAAAAALA
+ADHDLELYAFPLWLWHWGAPEDLAPRRYRRLELAAGDDAARLAALDAHASQTRPLSAAPG
+DEAILPERMIAHFTRGFETYRRTAPDDADASRASAVFDRLYREHEDPWRYLTSPYEARKR
+ALTLAVLPRPRYGTVVEAGASIGVLTAALAERAERVVGLEASQVAVERAAAHLAEIPHAE
+VRRAVLPADWPADVGPAEEGAGAPADLVVASEIGYFLQPEELDALVDAADASLGAGGELL
+LCHWRQPITGWPLDGDAVHDRVAADPRWRLLSEHVEADLRLSVHARAAAATHAVAVVPAM
+DEAEHLPAGLDALSAALDLWEAQHTQGSAAVVTVVPADDAPTLEAAHAARARDPRIRVLE
+LAPGAGGVGRARAAAARHARGLFPDVPAEALWLASTDADTRVPADWLVGQPALAARRRAD
+GQVLVLGTVDLPAHADDDLAHRWRADYEHREDHPHVHGANLGLPWGLYERAGGFAEVAEH
+EDVRLAEAVRALGEDRVLATDRVRVHTSSRLEGRTPGGFAGFLRGLLEEGAAEG*
+>NZ_CP097650.1_50
+MVSFSHTDDGTSEAAWAEGGVGELPELRLPVWDAQTLLLVAVAHPDDETLAATGLIRSAL
+RGGARVHVLVATAGEASHPHSPTHTPEDLVRLRRDEMEHALDALAAGLPASAGPGSPARD
+RLTWASLALPDSGVAEHEDAVRDAVAAALDAHPGPAVLASHDPGDGHADHEAVGRAVGAV
+AGECDLPLYAFPIWFWHWADPADLPARRYRRLRLTDDDRAARRAALDAHASQVRPLSAAP
+GDEAILGPAVLAHHERPFEAHRVSGPDDADAHRAAAVFDRLYRAQEDPWRYLSSSYEARK
+RALTLAALPRPRYGTVVEAGASIGVLTADVAARADRVVGLEASPTAVERAAARLAGAPHA
+EVRRAVLPADWPADVAGADLVIASEIGYFLQPEELDALIDDADAALAPGGELLLCHWRHP
+IEGWPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVVVPAKDEQERLP
+AALAALTAALDRWEEHHAQGTAAVVVAADRCDDATVAAALEARAADPRIHVLELGEPTAG
+QAGVGRARLEGARRARALFPDVPAERLWLASTDADSRVPADWLLAQTVAAGRDEALVLGT
+VDVRQGPLRQAWLRGYRHEEGHAHVHGANLGLPWSLYEAVGGFPPVAEHEDVGLAEAVRA
+LAGERDGGDGRRVRVIATDTTRVLTSSRLEGRTPGGFSGYLKAVGRPG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000213.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000213.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5395b1d5296adc72202c13f3477746317530c9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000213.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_58
+MSAFETVDVNEIPADAAILDVREDDEWALGRAAGAQHIPLGQLPDRLEELDPDTDYYLIC
+RTGGRSARAAEFMTGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK*
+>NZ_CP033200.1_2027
+MSAFETVDVNEIPADATILDVREDDEWALGRAAGAQHIPLGQLPDRLEELDPDTDYYLIC
+RTGGRSARAAEFMTGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK*
+>NZ_CP040019.1_321
+MSAFETVDVNEIPADAAILDVREDDEWALGRAAGAQHLPLGQLPDRLEELDPDTDYYVIC
+RTGGRSARAAEFMVGRGYTAINVAGGSGAWLEAGKPMEADGGAEPTVK*
+>NZ_CP083691.1_262
+MSHFETVTVDQIPADAAILDVREDDEWALGRAAGAQHLPLGQLPERIEELDPDTDYYVIC
+RTGGRSARAAEYMVGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK*
+>NZ_CP097650.1_53
+MSAFETVDVNEIPADAAILDVREDDEWALGRAAGAQHIPLGQLPDRLEELDPDTDYYLIC
+RTGGRSARAAEFMTGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000222.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000222.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5f5876a86272ff77563e25ac7435e1942d42c47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000222.fa
@@ -0,0 +1,65 @@
+>NZ_CP042169.1_71
+MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQR
+VDLTLREPYKQDDRDLGKEVYFYFATARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGF
+MVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE
+IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVDAPDLEGRAKILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL
+AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVG
+GAAGGSSREYSEELAYLVDAEVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQE
+AIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRSRHDGGEQTPVGVEGTTVPVR
+PEGAPPSSLGGDAAGPGLPPHGGPSNTPGPGEGPTF*
+>NZ_CP033200.1_2040
+MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQR
+VDLTLREPYKQDDRDLGKEVYFYFATARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGF
+MVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE
+IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVDAPDLEGRAKILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL
+AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVG
+GAAGGSSREYSEELAYLVDAEVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQE
+AIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRSRHDGGQQTPVGVEGTTVPVR
+PEGAPPSSLGGDAAGPGLPPHGGPSNTPGPGEGPTF*
+>NZ_CP040019.1_306
+MKKLFNKPYIWILLGLLVLAVAIPLATSQTGRTMVDTNVGMAMLQDDKAAQARVVDGDQR
+VDLTLREPYSQDGRDLGKEVYFHFATARASDVVTAVDDSALDGYTDEPVRSNWLLSLLGF
+MIPFLLIALLFWFLLSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE
+IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVEAPDLEGRAKILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL
+AYALGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGNSEPFVG
+GGGGGSSREYSEELAYLVDAEVRGLLDGAHAEAHWVLTENRDVLDRLAYELLEKETLTQE
+AIAEIFRDVRKRPERDVWLASDERLPQDIPPVLSPSERRSRHEGGEQTPVGVEGTTVPVH
+PEGAPPSSLGGDAPTPGLPPHGGPSSSPGAGEGPTY*
+>NZ_CP083691.1_247
+MKKQFNKPYIWILLGLLVLGLVIPLTTAQSGRGMVDTNVGMALLRDDKVAQARVVDGEQR
+VDLTLREPLSQDGRDLGRDVYFQFSAARAQDVVRTVQDSSVDGYQDEPVRDSWLLSLLGL
+MIPFLLISLLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELHE
+IKEFLTEPERFHAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKANAPAIIFVDEIDAVGRSRGVGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVEAPDLDGRAKILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSRNNVIDNAALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPENDKYSVTRNELLDQL
+AYAMGGRVAEEVVFKDPSSGAANDIQKATETARKMVTDYGMSSKVGAVKLGSANTDPFLG
+GGGAASREYSEELAYLVDAEVRALLDGAHAEAHWVLTENRDVLDRLAAELLEKETLTQEQ
+IAEIFKDVRKRPERPLWLAADDRPPHDVPPVLTARERASRLEGEQPEAVGVEGTTVPDAP
+EGAPPTALGGAGGSAGGPGDLPGQHSPTPGPTY*
+>NZ_CP097650.1_65
+MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQR
+VDLTLREPYKQDDRDLGKEVYFYFASARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGF
+MVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE
+IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVDAPDLEGRARILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL
+AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVG
+GAPGGSSREYSEELAYLVDAEVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQE
+AIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRSRHDGGEQTPVGVEGTTVPVR
+PEGAPPSSLGGDAAGPGLPPHGGPSNTPGPGEGPTF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000224.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000224.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf924669144a20d7e4b281360e1d2a657f1abb32
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000224.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_74
+MSARDRIRLAGLSAVGHHGVFDHERRDGQPFVTDVVLHLDAGPAAAGDDLARTANYAEVA
+DTVVRLVTGEPVDLIETLADRIARAVLAEQPVVTAVEVTVHKPQAPIPHDFADAAVTVHR
+TREDLA*
+>NZ_CP033200.1_2043
+MSARDRIRLAGLSAVGHHGVFDHERRDGQPFVTDVVLHLDAGPAAADDDLARTANYAEVA
+DTVVRLVTGEPVDLIETLADRIARAVLAEQPVVAAVEVTVHKPQAPIPHDFADAAVTVHR
+TREDLA*
+>NZ_CP040019.1_303
+MSARDRIRLTGLSAVGHHGVFDHERRDGQPFVTDVVLHLNAGPAAAGDDLARTANYAEVA
+DTVVRLVTGEPVDLIETLAERIARAVLAEQPVVEAVEVTVHKPQAPIPHDFADAAVTVHR
+TRRDAS*
+>NZ_CP083691.1_244
+MSDVIRLTGLTATGRHGVFEHERRDGQPFTTDVALTLDAGPAAARDDLARTANYAEVAET
+VVRLVTGEPFDLIETLAVRIAEAVLAEQPVVTAVEVTVHKPQAPIPHDFTDVSVTVARRR
+GA*
+>NZ_CP097650.1_68
+MSARDRIRLAGLSAVGHHGVFDHERRDGQPFVTDVVLHLDAGPAAAGDDLARTANYAEVA
+DTVVRLVTGEPVDLIETLADRIARTVLAEQPVVAAVEVTVHKPQAPIPHDFADAAVTVHR
+TREDLA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000232.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000232.fa
new file mode 100644
index 0000000000000000000000000000000000000000..518794532ec22324def7d0927f154ecb281548d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000232.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_84
+MTTNTPKNAHGSSAEGRDAKDQAKDKAQQAAGEAQGQAKAVAQDAKDKAQDLAATAKHEA
+GQVKDEAADQVQSLVGSAQEQVGAQVQTQQERFAGQVRSYTDDLHRVVSGEQPQTDLVRQ
+GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA
+VQPDSAASTSPRRHTTRPDAVHADVTPHHLDSQAPAYSSDSLSQADGRVADGAGPRRAAG
+VGDTPYGTQAPVQQGLTAERPFDQTRPGGDA*
+>NZ_CP033200.1_2053
+MTTNTPKNAHGSSAEGRDAKDQAKGKAQQAAGEAQGQAKAVAHDAKDKAQDLAATAKHEA
+GQVKDEAADQVQSLVGSAQEQVGAQVQTQQERLAGQVRSYTDDLHRVVSGEQPQTDLVRQ
+GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA
+AQPDSTASTSPRRHETRPDAVHADVTPHHLDSQAPAYSSDSLSQADGRVADGAGPRRAAG
+VGDVPYGTQAPVQQGLTAERPFDQTRPGGDA*
+>NZ_CP040019.1_291
+MTTNTPKNAHGSSAEGRDAKDQAKDKAQQAAGEAQGQAKAVANDAKDKVQDLAATAKHEA
+GQVKDEAADQVQSLVGSAQEEVGAQVQTQQERLAGQVRSYTDDLHRVVSGEQPQTDLVRQ
+GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA
+AQPDAAAPTAPRRRDTRPEAVHADVTPHHLDSQAPAYSSDSLSQADGRVASGAGPRRAAG
+VGDTPYGVEAPEQHGLTAERPFDRSQPGGRA*
+>NZ_CP083691.1_236
+MAKNHSARAADPQQSETRQKAEAAAGAAQDQAAGVAQDAKAHAQDLAQSAQQEAVAVKDE
+AVQHAKSLAGSLQDQAAQQASTQQGRLAEQSRGITDDLHRLLSGEQPQGDAVRQAVAAVA
+DRAETLTQRLETAQPMDLVDDVRRFAARRPGTFLAIALGAGVLAGRMTRGVRDASQDGPA
+SLSSAPRTPQHRRELEPQGVQADVTPHHLDSQIPAHTGDDAPRPVSDTAAGLPYGTEPLP
+TIDPLTGEPVAEDPYDQTRDGGRA*
+>NZ_CP097650.1_79
+MTTNTPKNAHGSSAEGRDAKDQAKGKAQQAAGEAQGQAKAVAHDAKDKAQDLAATAKHEA
+GQVKDEAADQVQSLVGSAQEQVGAQVQTQQERLAGQVRSYTDDLHRVVSGEQPQTDLVRQ
+GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA
+AQPDSTASTAPRRHETRPDAVHADVTPHHLDSQAPAYSSDSLSQADGRVADGAGPRRAAG
+VGDVPYGTQAPVQQGLTAERPFDQTRPGGDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000235.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000235.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2ece188e5efc6ba5874f87cc9695eee047173b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000235.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_87
+MTPLDRVPDQRPVPAGTGLTLEDALPAPVTAEADGVSARPRLARTVAEMRSALRELVAHA
+TDDGDAEPVTVGLIPTMGALHGGHAALVRRARAENDVVAVSIFVNPLQFGDPADLEHYPR
+TLDADLDLLAAAGADVVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGASRPGHFDGVAT
+VVAKLWNIVRPAVPALRSYFGQKDAQQLTVLRRLATDLDIDVDVRAVPIVRSPEGLALSS
+RNTRLDAAGLEHALVLSRALRSLADAAAAGEPVDVQAARRMVEDEPGVELDHLVVVDRDT
+FAELGPELLCQPLRREALALVAAHVPPVRLIDTMVLPVAGPLP*
+>NZ_CP033200.1_2056
+MTPLDRVPDQRPVPAGTGLTLEDALPAPVTAEADGVSARPRLARTVAEMRSALRELVAHA
+TDDGDAEPVTVGLIPTMGALHGGHAALVRRARAENDVVAVSIFVNPLQFGDPADLEHYPR
+TLDADLDLLAAAGADVVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGASRPGHFDGVAT
+VVAKLWNIVRPAVPALRSYFGQKDAQQLTVLRRLATDLDIDVDVRAVPIVRSPEGLALSS
+RNTRLDAAGLEHALVLSRALRSLADAAAAGEPVDVQAARRMVEDEPGVELDHLVVVDRDT
+FAELGPELLCQPLRREALALVAAHVPPVRLIDTMVLPVAGPLP*
+>NZ_CP040019.1_288
+MTPLDRVPDRTPVPPRTGLTLEDQVPEAGGTRPRLTTTKADFRAAVAELVGRAAAEDPGE
+EVSVGLVPTMGALHGGHAALARQARSENDVVAASIFVNPLQFGDRADLEHYPRTLEADLD
+LLGAVGVDVVFAPSVDEMYPGHPDAPIVSVSAGRMGEVLEGASRPGHFDGVCTVVAKLWN
+LSMPPAPAVLRSYFGQKDAQQLAVLRRLAHDLDVAVDVRAVPIVRSPEGLALSSRNTRLD
+EAGLHAALVLNRALTRLEEAAVAGRVLDVQAAREEVAAEPGVTLDHLVVVDRETLEELGA
+ELLCQPLRRDALALVAAHVPPVRLIDNRVLPAAGPLP*
+>NZ_CP083691.1_233
+MTPLDRTPDRRPVPAGTGLTLEDALPVADGARRPRLARTVAEARAALRELTAAAGQERGG
+APVVVGMVPTMGALHGGHAALIRQARAENDVVVASIFVNPLQFGDPADLENYPRTLEADL
+DLLGAAGADLVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGVSRPGHFDGVVTVVAKLW
+NIVRPAVPALRSYFGQKDAQQLAILRRLAHDLDVDVEVRAVPIVRSPEGLALSSRNTRLD
+ADGLEHALVLSRALRALVDAAEAGEPIDVRAARQMVSDEPGVTLDHLVVVDRETLEELGP
+ELLCQPLRREALALVAAHVPPVRLIDNMVLPAAGPLP*
+>NZ_CP097650.1_82
+MTPLDRVPDQRPVPAGTGLTLEDALPAPVTAEADGVSARPRLARTVAEMRSALRELVAHA
+TDDGDAEPVTVGLIPTMGALHGGHAALVRRARAENDVVAVSIFVNPLQFGDPADLEHYPR
+TLDADLDLLAAAGADVVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGASRPGHFDGVAT
+VVAKLWNIVRPAVPALRSYFGQKDAQQLTVLRRLATDLDIDVDVRAVPIVRSPEGLALSS
+RNTRLDAAGLEHALVLSRALRSLADAAAAGEPVDVQAARRMVEDEPGVELDHLVVVDRDT
+FAELGPELLCQPLRREALALVAAHVPPVRLIDTMVLPVAGPLP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000241.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000241.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d7849a0c159d71b4779f2a6331a8a7615a9a6bf1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000241.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_93
+MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD
+VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE
+GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMEVVFAPRPPAH
+REVAAAELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDADVIAKMKDDAVLVN
+TARGPVVDEAALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA
+AMAELAARNAIAMATGAEAPALVNPEVRG*
+>NZ_CP033200.1_2062
+MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD
+VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE
+GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH
+REVAAEELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDAEVIAKMKDDAVLVN
+TARGPVVDEVALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA
+AMAELAARNAIAMATGAEVPALVNPEVRG*
+>NZ_CP040019.1_282
+MSPRFLLMTEIPEPGLGMLREAGEVTLGSEVGGNDALPALAASGDYDVVVCALAQKFDAD
+VLAQARLKGIANYAVGYNNVDVAAATEAGIAVGNTPDVLTDATADIALLLILGVSRRAHE
+GEAMMRAGEFTGWRADLLVGKDVKGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH
+REVAPEELGELAGRVEQVRWEELVERSDFLSLHVPLTADTEHLVDADVLARMKDDAVLIN
+TARGPVVDEAALVEALRAGRLFGAGLDVYEDEPAMAPGLAELDNVMLLPHLGSATRDTRA
+AMAELTARNAIAMATGGEVPALVNPDVRR*
+>NZ_CP083691.1_227
+MSPRFLLMADLPEPGLGMLREAGEVVRGGDVGGNAALADLCASGEYDVVVGALDQRYDAD
+LLARARVKGIANYAVGFDNVDVPAATEHGILVGNTPDVLTAATADIALLLILGVTRRAVE
+GERMMREGRFEGWRADMLVGKDVVGATLGLAGFGRIGRAVAERALAFGMEVVFAPRPPAH
+REVPAEELGDLAGRVRQVRWEELVETADVLSLHVPLTEDTRHLVDEDVIARMKDDAVLVN
+TARGPVVDEAALVTALREGRLFGAGFDVYEDEPAMAEGLAELPNVMLLPHLGSATRDARA
+AMAELTARNAIGMATDGEAPALVNPEARG*
+>NZ_CP097650.1_88
+MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD
+VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE
+GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH
+REVAAEELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDAEVIAKMKDDAVLVN
+TARGPVVDEVALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA
+AMAELAARNAIAMATGAEVPALVNPGVRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000243.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000243.fa
new file mode 100644
index 0000000000000000000000000000000000000000..149485e8496dbb7452242a46f6bc675dadcef5c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000243.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_95
+MAAFWDYFSVLAPSIGLGLIFWLVMRSLLRSDTGERESQARRLSGADARAAREEAEAREW
+AARRRAEGGPGADPEDRAR*
+>NZ_CP033200.1_2064
+MADFWDYFSVLAPSIGLGLIFWLVMRSLLRSDTGERESQARRLSGADARAAREEAEAREW
+AARRRAEGGPGADPEDRAR*
+>NZ_CP040019.1_280
+MATFWEYFSVLAPSIGLGLIFWLVMRSLLRSDTAERESMGRRSTGEDARAAREEADAREW
+ARRRGGDDVPRRGDDSR*
+>NZ_CP083691.1_225
+MAAFWEYFSVLAPSVGIGLVFWLVMRSLLRSDTAEREARQRRGEDARAAREEAEAREWAA
+RRRGDAPAGPGGAERP*
+>NZ_CP097650.1_90
+MAAFWDYFSVLAPSIGLGLIFWLVMRSLLRSDTGERESQARRLSGADARAAREEAEAREW
+AARRRAEGGPGADPEDRAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000244.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000244.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6220337b6060f27631e9593099743e84d4970821
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000244.fa
@@ -0,0 +1,80 @@
+>NZ_CP042169.1_97
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG
+DVPETLRDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVAEPSVEDAT
+EILRGLRDRYEAHHKVSITDGALKAAAGLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLGDERREKEQAWRTGADADV
+ATVDEDLIAEVLSKSTGIPVFKLTEEETDRLRNMEDELHRRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVEIVDLFVSRLGKRLAEQDLSIELTQSAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFAFSGGREALEGADLAELESG
+AGDPVDADRSV*
+>NZ_CP033200.1_2066
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG
+DVPETLRDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVAEPSVEDAT
+EILRGLRDRYEAHHKVSITDGALKAAAGLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLGDERREKEQAWRTGADADV
+ATVDEDLIAEVLSKSTGIPVFKLTEEETDRLRNMEDELHRRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVQIVDLFVSRLGKRLAEQDLSIELTQSAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDTTGEGEGAELTFAFSGGREALEGADLAELEPG
+AGDPVDADRSA*
+>NZ_CP040019.1_278
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVKLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG
+DVPETLKDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVPEPSVEDAT
+EILRGLRDRYEAHHRVSITDGALKAAATLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLEDERRQKEEAWRTGADSDV
+ATVDEELIAEVLSKSTGIPVFKLTAEETDRLRTMEDELHKRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVEIVDLFVSRLGKRLAEQDLSIELTQAAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFGFSGGREALEGAELPELEPG
+SGETVEAGRSA*
+>NZ_CP083691.1_224
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLAAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGSEGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAQEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIERG
+DVPETLKGKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVPEPSVEDAT
+QILRGLRDRYEAHHKVSITDGALSAAASLADRYISDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEVKAYEERIAEVKAQKEAAIDGQDFEGAARLRDQEKQLEEEREQKEQAWRAGQDAAV
+ATVDEDLIAEVLSLSTGIPVFKLTEEETDRLRNMEAELHQRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHADLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSSTDTSTGYERMKGKVREELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVEIVDLFVSRLAKRLAEQDLSIELTPAAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFAFAGGRAALEGDDAAEPAAL
+PAAADAPVEGREAPGADVPRGDDAGQDGPEAGGALGARLD*
+>NZ_CP097650.1_92
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG
+DVPETLRDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVAEPSVEDAT
+EILRGLRDRYEAHHKVSITDGALKAAAGLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLGDERREKEQAWRTGADADV
+ATVDEDLIAEVLSKSTGIPVFKLTEEETDRLRNMEDELHRRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVEIVDLFVSRLGKRLAEQDLSIELTQSAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFAFSGGREALEGADLAELEPG
+AGDPVDADRSV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000247.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000247.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c3ea395906e1a811d44b2e8673a82e3a3824adae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000247.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_100
+MPAPAPLVPPTVDVPHLHDAMLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL
+PRWREWLERWPTPADLAAAPTADVLTAWDRLGYPRRALRLQEAARAVVGRHDGRVPADPA
+ALRALPGIGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA
+LMPEDPARANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA
+GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGRLGSHRPDDAQWARCVAGLVSDGLLAR
+DDDGGLTFPA*
+>NZ_CP033200.1_2069
+MPAPAPLVPPTVDVPRLHDAVLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL
+PRWREWLERWPTPADLASAPTADVLTAWDRLGYPRRALRLQEAARAVVERHDGRVPADPA
+ALRALPGVGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA
+LMPEDPARANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA
+GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGRLGSHRPDDAQWARCVAGLVSDGLLAR
+DDDGGLTFPD*
+>NZ_CP040019.1_274
+MPAHETAVPPSVDVPRLHDAVLDWFAVHARDLPWRSPDCPPWGVLVSEIMLQQTPVARVL
+PRWHAWLERWPTAADLAAAPTADVLTAWDRLGYPRRALRLQEAARAIVERHSGEVPADPA
+ALRALPGIGEYTAAAVSSFAFGLPETVVDTNVRRVIARAVGGQALPGRSLTRAEMRRAHA
+LMPEDPDRAQAWNAGVMELGALVCTARSPACERCPLADACAWVAAGSPPPEQAPRGQAWA
+GTDRQVRGAVMAAVREHGRVAGDGLRAVVVAGGRLGAHRPGDAQWERCVAGLLADGLLAR
+DDDGALAFPS*
+>NZ_CP083691.1_220
+MPAHDDAAPRPDLTALQDEVLDWFAAHGRDLPWRDPDCPPWGVLVSEIMLQQTPVVRVLP
+RWRAWMERWPTPADLAAAPTADVLTAWDRLGYPRRALRLQEAARAIVERHGGEVPADPAA
+LRALPGIGEYTAAAVSSFAFGIPETVVDTNVRRVLARALRGEGLPGRTLTRAEMAAAHAA
+LPADEHRANRWNAAVMELGALVCTARSPACDRCPIRARCAWVAAGSPAPEVARRGQAWVG
+TDRQVRGAVMAAVREHGRVPRGGLREAVDGTGRLGAHTPDDAQWERAVAGLLGDGLLVAH
+DDGALAFPA*
+>NZ_CP097650.1_95
+MPAPAPLVPPTVDVPRLHDAVLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL
+PRWREWLERWPTPADLASAPTADVLTAWDRLGYPRRALRLQEAARAVVERHDGRVPADPA
+ALRALPGVGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA
+LMPEDPTRANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA
+GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGWLGSHRPEDAQWARCVAGLVSDGLLAR
+DADGGLTFPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000248.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000248.fa
new file mode 100644
index 0000000000000000000000000000000000000000..73bc8082baec563e2577f83f0d3a667483938886
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000248.fa
@@ -0,0 +1,31 @@
+>NZ_CP042169.1_101
+MPSRPTSPGSKPSPAVYRRRRLVAALLALVLLLLVGWAVVALVRAGIGAFSSEDADPSAA
+PTPVHSPSPAPATDAESSSASPTVALEDAAECQPSDLRIAASADRSEYQRGEEAELRLGI
+TNLSSTPCRTDVGTARQEFTIRTAEGDDVFSTRICQADPAEAQRVLYPHEELTAVYRWSG
+RASSQDCGRLGALAEPGPHLLTVSLGDVTSRPVALKILEELAPGAQDSSSSAAPSSATPS
+SATPSSSGSASPSGSASDPASASTTDPSPSSSR*
+>NZ_CP033200.1_2070
+MPSRPTSPGSKPSPAVYRRRRLVAALLALVLLLLVGWAVVSLVRAGIDAFSSEDADPSAA
+PTPVHSPSPAPATDAESGSASPTVALEDAAECQPSDLRIAASADRSEYQRGEEAELRLGI
+TNLSSTPCRKDVGTARQEFTIRTAEGDDVFSTRICQADPAEAPRVLYPHEELTAVYRWSG
+RASSQDCGRPGALAEPGPHLLTVSLGDVTSRPVALKILEELAPGAQDSSSSAAPSSATPS
+SATPSSSGSASPSGSASDPASASTTDPSPSSSR*
+>NZ_CP040019.1_273
+MPSRPSSPGPKPSAAVYRRRRLVAALLALILLLLVGWGLWSLIRLGMGALSGDDAEPSVS
+APPTPVHSPSPAPPSGATPGSAAPTVALEDAAECQPSDLRLVASADKAQYLRGEEAVLRL
+GVTNLSSSPCRADVGTARQEFTVRTAEGDDVFSTRVCQADPTSSERVLTPHEELTAVYRW
+SGHASNEDCGTPGALAAAGPHLLTVTLGEQTSRPVALRIQEEAAPGAWDGASSGAPASGS
+PAPSTPASPSASPSATGSAPAASSPAPASGSPAASTPATPSASPSR*
+>NZ_CP083691.1_219
+MPSASPAPRPRPSAAVLRRRRVVAGCLAAAFLLLVGWGIGALVNALLPSGRPDAEPSAAP
+TPVSSPTPAAARSLDAQAGQTQDPASVESCAPMDLRLVAAADRERYAPGEEAVLRLEVTN
+LSGRPCRTDVGTAQQEFRVTDASEQQVMSTRVCQADPTHEDVVLEPRDQKAAVYRWNGRA
+SSADCARLGPAVEPGEYRLTVTLGEVTSRPVALTVTDGTKSAAPASSPAASSAAPGPSAT
+TAPASAETSSASPSASSSSAQPSSPAPRASEPTSSAPTSSPAGSGRASSSPAAPSSSAAS
+PTR*
+>NZ_CP097650.1_96
+MPSRPTSPGSKPSPAVYRRRRLVAALLALVLLLLVGWAVVSLVRAGIDAFSSEDADPSAA
+PTPVHSPSPAPATDAESGSASPTVALEDAAECQPSDLRIAASADRSEYQRGEEAELRLGI
+TNLSSTPCRTDVGTARQEFTIRTAEGDDVFSTRICQADPAEAPRVLYPHEELTAVYRWSG
+RASSQDCGRLGALAEPGPHLLTVSLGDVTSRPVALKILEELAPGAQDGGSSATPSSATPS
+SSGSASPSASASAPASASASASASASASASPSAAPATTTDPSPSPSR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000249.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000249.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33432fec0ab1ce7c4f5d401b1dd79cce105ea7ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000249.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_103
+MTDRFATATGTVPMVDPQTRGERLGRFLRRRARAGWSRVRSSVGQAALVAVCAVGAYWFA
+EAVLGHQQPLFASTALLIALGFQREPKLRKVAEVAVGCTVGILIGDLLMVGLGRGLWQAS
+VVLFVSVMVARFLDSGATFTMQMSLQSVLVVLLPTGTGGPFVRSQDAIVGGVLALLVTFL
+SPQDVRRPAVRQLGGLYDSIATVLRDLSRALRENDSRTAWMALVASRGTHTTLEALRKEL
+RVTHEQTVFNPLHRSSRSFVEDAVNAADRSDLAVRSLRIVARRVVSVLDEGVFDDDDRER
+LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASALDPHQLGGGSVHGEAL
+VMLLRPMMVDLIEATGAEHDEARGYLPRV*
+>NZ_CP033200.1_2072
+MTDRFATATGTVPMVDPQTRGERLGRFLRRRARAGWSRVRSSVGQAALVAVCAVGAYWFA
+ETVLGHQQPLFASTALLIALGFQREPKLRKVAEVAVGCTVGILIGDLLMVGLGRGLWQAS
+VVLFVSVMVARFLDSGATFTMQMSLQSVLVVLLPIGTGGPFVRSQDAIVGGVLALLVTFL
+SPQDVRRPAVRQLGGLYDSIATVLRDLSRALREDDSRTAWMALVASRGTHTTLEALRKEL
+RVTHEQTVFNPLHRSSRSFVEDAVNAADRSDLAVRSLRIVARRVVSALDEGVLDDDVRER
+LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASALDPHQLGGGSVHGEAL
+VMLLRPMMVDLIEATGAEHDEARAYLPRV*
+>NZ_CP040019.1_271
+MSDRFATATGTVPMVAPESRGARLRRFLRRRSRAGWSRVRSSVAHAALMAVCAVGAYWFA
+ETVLGHHQPLFSSTALLIALGFQREPTLRKVAEVAVGCTVGILIGDLLLAALGRGLWQAT
+VVVFVSVMVARFLDSGATFTMQMSLQSVLVVLLPAAQGGPFARSADALVGGLLALVVTFL
+SPQDVRRGTARHLEGLYDSMATVLRDLSRALRQEDSRTAWMALVACRGTQGTLESIRAEL
+KMAQEQATFNPLQRGSRSFVSDAANAADRSDLAVRSLRIVARRVVSVLDEGAFDDDHRER
+LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASRLDPRELGGGSLHGEAL
+VMLLRPMMVDLLEATGAPHDEARAYLPRV*
+>NZ_CP083691.1_212
+MTDRHATATGTLPAVPAAAGPSGVGRFLRRRARAGWSRLRSSVGHAALMAVCAVGAYWFA
+ETVLGHAQPLFAATALLIALGFQREPRVRKVAEVAFGCTLGILIGDLMMAALGRGLWQAV
+LVVFVSVLAARFLDSGATFTMQMSLQSVLVVLLPLNADGPFARSADALVGGLLALLVTLL
+SPRDPTRLPARQLRGLYESMASVLRELSAALRAEESRTAWMALVECRRTQSTLEDVRKEL
+KVTREQTVLNPLQRPARDAADVMAVAADRSDLAVRSLRIVARRVVSILDHGAVDGDHRER
+LAAWFDDAADAVEILHRSLAEPQAEGRHRSLDVARDALGASASWLDPHELAGGTVHGEAL
+VMLLRPMMVDLIEATGASHAEALTYLPRV*
+>NZ_CP097650.1_98
+MTDRFATATGTVPMVDPQTRGERLGRFLRRRARAGWSRVRSSVGQAALVAVCAVGAYWFA
+EAVLGHQQPLFASTALLIALGFQREPKLRKVAEVAVGCTVGILIGDLLMVGLGRGLWQAS
+VVLFVSVMVARFLDSGATFTMQMSLQSVLVVLLPTGTGGPFVRSQDAIVGGVLALLVTFL
+SPQDVRRPAVRQLGGLYDSIATVLRDLSRALRENDSRTAWMALVASRGTHTTLEALRKEL
+RVTHEQTVFNPLHRSSRSFVEDAVNAADRSDLAVRSLRIVARRVVSALDEGVLDDDVRER
+LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASALDPHQLGGGSVHGEAL
+VMLLRPMMVDLIEATGAEHDEARGYLPRV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000250.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000250.fa
new file mode 100644
index 0000000000000000000000000000000000000000..324eeee2ffcbac24e2a333464af6e5b72f670bb3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000250.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_104
+MKALRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEQGTTSEVQGNLVGAGASS
+QEAAMTAWTQGVTETAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKEEEAESAKEN
+CGDEGAFHVPAYISPIAVAYNLPGVDDVKMDAETIAKVFSGEIKNWNDEAIAAQNEGVEL
+PDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQGTKGVVGLAS
+QTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSIELDRATDES
+GVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPISEDTRKKAM
+ERIEAISVKG*
+>NZ_CP033200.1_2073
+MKALRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEQGTTSEVQGNLVGAGASS
+QEAAMTAWTQGVTETAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKEEEAESAKKN
+CGDEGAFHVPAYISPIAVAYNLPGVDDVKMDAETIAKVFSGEIKNWNDEAIAAQNEGVEL
+PDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQGTKGVVGLAS
+QTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSIELDRATDES
+GVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPISEDTRKKAM
+ERIEAISVKG*
+>NZ_CP040019.1_270
+MKALRFGRSAALLSVAALALTACGGNGGGDASSSAPAGGSSSAAAEGSGAAAASGTLIGG
+GASSQEAAMTAWSEGVKATSPELTVQYSPDGSGAGREGFLGGAFSFAGSDAALKEDEAEQ
+AKQICGDNGAFHVPAYISPIAIAYNLEGVDEVKMDAETIAKVFSKEITTWNDPAIAEQNE
+GVELPDTPITVVHRSDDSGTTENFTAYLTEAAGDAWKYDEVETWPSEITAESAQGTRGVV
+GQAAQTDGAITYADASAVGELGTVAVKVGEEYVPYSSDAAAKTVSASVQNEDGSIELDRA
+TTEAGVYPIVLVSYHIYCNQYQNQETADQVKAFASYVVSEDGQKAAEEAAGNAPIGAETR
+DAAVERIEAITAG*
+>NZ_CP083691.1_211
+MKALRFGRSAALLSVAALALTACGGGNDSASSSSSAASSSAAGSSSASSSAAGSSSASSS
+AAESSSASGSSSAAQGGYAIDVPTASGTLMGSGASSQEAAMTAWTEGVKATSPELQVQYS
+PDGSGAGRKAFLSGAATFAGSDAALKDEEKTQAQEVCGPDGAFHVPAYVSPIAVAYNLEG
+VDSLNLDADTIAKIFSKKITKWNAPEIAALNEGVELPDTAITVVHRADESGTTENFTAYL
+DQVAPEAWTYGKVKEWPGDITAESAQGTKGVVSQAAATNGAITYADESGVGSLKTAKVGK
+DGKFAEISPEAAAKIVADGKKQDDGSIELDRANAGEGVYPIVLVSYHIFCNQYGDQETVD
+QVKAFASYVISEDGQKAAQEASKSAPLDAELAKEAKTRIDAIKVG*
+>NZ_CP097650.1_99
+MKAHRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEHASGSAGGEQGTTSEVQG
+NLVGAGASSQEAAMTAWTQGVTEIAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKE
+EEAESAKENCGDEGAFHVPAYISPIAVAYNLPGVDEVKMDAETIAKVFSGEIKNWNDEAI
+AAQNEGVELPDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQG
+TKGVVGLASQTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSI
+ELDRATDESGVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPI
+SEDTRKKAMERIEAISVKG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000251.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000251.fa
new file mode 100644
index 0000000000000000000000000000000000000000..05decc8d803e11832aaa264b62e73709a18a4160
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000251.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_105
+MSSTTNEAAPKPSSLRGPRRGAAGDKLLSGGALAAAVLILLVLAFVAVFLLTEAWPALQP
+GAELVSADSFFQYVWPLMAGTVMVSIIALLIATPVAIGVALFISHYAPPRIAQSVGFVID
+LLAAIPSVVYGVWGWLTLAPLMVPIYGWLNENLGFIPFFGGSATTTGRTLLTSGVVLAVM
+VLPIITALCREIFTQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIISSIMLGLGRALG
+ETMAVTMVLSGGVFSWSLVESGRNQTIPSEIALNFPEAFNMRLHELIAAGLMLFIITLAV
+NMIARAIVNKHKEFSGAN*
+>NZ_CP033200.1_2074
+MSSTTNEAAPKPSSLRGPRRGAAGDKLLSGGALAAAVLILLVLAFVAVFLLTEAWPALQP
+GAELVSADSFFQYVWPLMAGTVMVSIIALLIATPVAIGVALFISHYAPPRIAQSVGFVID
+LLAAIPSVVYGVWGWLTLAPLMVPIYGWLNENLGFIPFFGGSATTTGRTLLTSGVVLAVM
+VLPIITALCREIFTQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIISSIMLGLGRALG
+ETMAVTMVLSGGVFSWSLVESGRNQTIPSEIALNFPEAFNMRLHELIAAGLMLFIITLAV
+NMIARAIVNKHKEFSGAN*
+>NZ_CP040019.1_269
+MTSPATEAPPRATTLKSSRGGAAGDKVFSGLSLAAGVLILLTLAFVAIFLVVRSLPALFP
+DAYGTQLKSADTFFQYVWPLMAGTIMAAVIALLLATPVAVGVALFISHYAPPKIAQPVGY
+VIDLLAAIPSVIYGIWGWLTLAPVMVPIYQWLNEYLGFIPFFGGPVTGTGRVIMTSGVVL
+AVMILPIITALCREIFRQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIVSSVMLGLGR
+ALGETMAVTLVLSAGGFSLSLIEEGRNATIPSEIALNFPEAYGIRLNELIAAGLMLFVIT
+LVVNMTARWIVNKHKEFSGAN*
+>NZ_CP083691.1_210
+MSHTATEAAPSSSALKSSRAGAAGDKVFSGLALAAGVLILLILAFVAIFLVSEAWPALFP
+AEGANLESGDSFWGYVWPLMAGTVMAAIIALLLATPVAVGVALFISHYAPPKIAQPVGYV
+IDLLAAIPSVVYGIWGWLTLAPLMVPIYEWLNEYLGWLPFFGGSVTSTGRVLMTSGIVLA
+VMVVPIITALCREIFSQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIVSSIMLGLGRA
+LGETMAVTMVLSPGKFSPSVIEEGRNATIPSEIALNFPEAYGIRLNELIAAGLMLFVITL
+VVNMVARWIVNKHKEFSGAN*
+>NZ_CP097650.1_100
+MSSTTNEAAPKPSSLRGPRRGAAGDKLLSGGALAAAVLILLVLAFVAVFLLTEAWPALQP
+GAELVSADSFFQYVWPLMAGTVMVSIIALLIATPVAIGVALFISHYAPPRIAQSVGFVID
+LLAAIPSVVYGVWGWLTLAPLMVPIYGWLNENLGFIPFFGGSATTTGRTLLTSGVVLAVM
+VLPIITALCREIFTQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIVSSIMLGLGRALG
+ETMAVTMVLSGGVFSWSLVESGRNQTIPSEIALNFPEAFNMRLHELIAAGLMLFIITLAV
+NMIARAIVNKHKEFSGAN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000255.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000255.fa
new file mode 100644
index 0000000000000000000000000000000000000000..db3d9123281274c48a0a1b7575c440c4dca9a840
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000255.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_109
+MSPRMPWLVTRDTPALRHMADLAEALHRSVHLVAQVAGTRGPEADRAARELEELDSSSSA
+TLMAFLTALRSAYVTPLPRQDLYRLASGVHATTRRVVSAGVLIQRADLEELPTHALDVLE
+TVGRQAELLARGAAEMRDLDALEATWMQLLRASRRTERIMVEWLADLGMDLLQRDYNRQR
+EVAWALHAALEALSRVNMDLGMVLVRES*
+>NZ_CP033200.1_2078
+MSPRMPWLVTRDTPALRHMADLAEALHRSVHLVAQVAGTRGPEADRAARELEELDSSSSA
+TLMAFLTALRSAYVTPLPRQDLYRLASGVHATTRRVVSAGVLIQRADLEELPTHALDVLE
+TVGRQAELLARGAAEMRDLDALEATWMQLLRASRRTERIMVEWLADLGMDLLQRDYNRQR
+EVAWALHAALEALSRVNMDLGMVLVRES*
+>NZ_CP040019.1_265
+MSPRMPWPVTRDTPALRHIVDLAEALRRSVHLVAQVAGARGPEADRTARELEDLDAASTA
+SLMSFLTALRSAYVTPLPRQDLYRLAGGVHAATQRVVSAGVLIQRADLEHLPAHALDVLE
+TVGRQAELLGRSTTELRDLDALEATWMQLLRASRRTERIMVQWLADLGMDLLQRDFNRQR
+EVAWALQSALEALGRVNTDLGMVLVRES*
+>NZ_CP083691.1_206
+MTPRPAWLVTRDSPALGHLTDLCDTLGRAVRAVAQAVAADGSERDRVERDLSALDAAATA
+ALMAFLTALRSAYVTPVPRPDLYRLADGVKTAAHRVVGAGVLVHRADLDALPRNAVELLE
+TLGRQAELLAHGTRQLRDLDALEDTWMQLERGIRRMERLMVDWLAALGTDLLQRDYNRQR
+EIASALRDAVLALDRVNTDLGVVLVRES*
+>NZ_CP097650.1_104
+MSPRMPWLVTRDTPALRHMADLAEALHRSVHLVAQVAGTRGPEADRAARELEELDSSSSA
+TLMAFLTALRSAYVTPLPRQDLYRLASGVHATTRRVVSAGVLIQRADLEELPTHALDVLE
+TVGRQAELLARGAAEMRDLDALEATWMQLLRASRRTERIMVEWLADLGMDLLQRDYNRQR
+EVAWALHAALEALSRVNMDLGMVLVRES*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000256.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000256.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd15270f74c256d0341d4e85798c898a32164708
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000256.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_110
+MARHRLPAGRGASSSASGVLRPHRPRLSEPQELTHFAGGEDPQEVAAAASRLAHALVAGG
+RAEEDPAIVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATTRDGERWAAW
+YRAGHAAYASRVVAGAVEPPGPAELRRLTDTILTGAYRSEIDVAFERAAAYARVVALGQV
+EHAEGSEAAAPDRAAALTRRAARLVSTADALEAAGRAFRDGSLD*
+>NZ_CP033200.1_2079
+MARHRLPAGRGASSSASGVLRPHRPRLSEPQELTHFAGGEDPQEVAAAASRLAHALVAGG
+RAEEDPAIVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATTRDGERWAAW
+YRAGHAAYASRVVAGAVEPPGPAELRRLTDTILTGAYRSEIDVAFERAAAYARVVALGQV
+EHAEGSEAAAPDRAAALTRRAARLVSTADALEAAGRAFRDGSLD*
+>NZ_CP040019.1_264
+MARHRQTTGRGASSSASGLVRPHRPRLSEPDELAHFAGGEDPQEVAAAASRLAHALVAGG
+RAEEDPEVVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATARDGERWAAW
+YRAGHAAHAARAVAGAVEPPGPDELRRLTDTILTGAYRSEIDVAFERAGAYGRVVALGQV
+EHAEAAEAADPALAAGLTRRAARLVSTSEALEEAARAFRNGSLD*
+>NZ_CP083691.1_205
+MAHHRAPAGRGASSTASGLVRPHRPRLTDPGLIADLADGEDPQEIAAAASRLAHALVAGG
+RAEEDPDVVARLVGLVREVGVETLAGLWADAPAVSLAGALWRLYALQEATARDGERWAAW
+YRAGHAAHAARAVAGAVEPPGPEELRRLTDTILTGAYRSELDVALERAGAYARVVALGQA
+EHAAAAEHADPAHAARLTLRAARMISTAEALEAAARSWRDGSLD*
+>NZ_CP097650.1_105
+MARHRLPAGRGASSSASGVLRPHRPRLSEPQELTHFAGGEDPQEVAAAASRLAHALVAGG
+RAEEDPAIVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATTRDGERWAAW
+YRAGHAAYASRVVAGAVEPPGPAELRRLTDTILTGAYRSEIDVAFERAAAYARVVALGQV
+EHAEGSEAAAPDRAAALTRRAARLVSTADALEAAGRAFRDGSLD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000260.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000260.fa
new file mode 100644
index 0000000000000000000000000000000000000000..032370da15d7194a23360d5e98437db05deaa5f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000260.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_114
+MIAHRGASAAFPEHTRAAMLHALAVGADGLECDVQLTRDREVVCWHDPTVDRTSDGRGAV
+ADHTLDRLRGLDVVSWHARRPGAEPATTTAPPAVYGGAGEQVLTLADLLAIAAAADRPLR
+LAVELKHPSPFGHELEERVLRELLRAGWDPETGRLGQVQVSLMSFHPDALRHVAPLAGTD
+PLCPLMDLMPTELPTRLARGPLSRAAVRAAARQSLAGSEALVWRGRAGMAGPSVAYVREH
+LADVKAWLAAGRRLRVWTVDEREDADSLLAQGVQELTTNRPEDVLRWVRERAAARRERMP
+TGA*
+>NZ_CP033200.1_2083
+MPALVIAHRGASAAFPEHTRAAMLHALAVGADGLECDVQLTRDREVVCWHDPTVDRTSDG
+RGAVADHTLDRLRGLDVVSWHARRPGAEPATTTAPPAAYGGAGEQVLTLADLLAIATAAD
+RPLRLAVELKHPSPFGHELEERVLRELLRAGWDPETGRVGQVQVSLMSFHPDALRHVAPL
+AGTDPLCPLMDLMPTELPTRLARGPLSRAAVRAAARQSLAGSEALVWRGRAGLAGPSVAY
+VREHLADVKAWLAAGRRLRVWTVDEREDAEFLLAQGVQELTTNRPEDVLRWVRERAAARR
+ERVPTGA*
+>NZ_CP040019.1_257
+MPALVIAHRGASAAFPEHTRAAMLHALEAGADGLECDVQLTRDREVVCWHDPTVERTSDG
+RGAVADHTLARLRALDVLAAPARGTGSTERTTTALPAAYGGAGEQVLTLAELLGIATAAG
+RPVRLAVELKHPSPFGHELEERVLRELLRAGWDPETGRVGQVRVSLMSFHPDALRHVAPL
+AGTDPLCPLLDLVPRDVPSRLARGPLGRAAVRSAVRGSLAGSEAMVWGGRAGMAGPSVAY
+VREHLADVKAWLAAGRRLRVWTADAREDVDFLLAHGVQEITTNRPAEVLDWVREHAAARR
+EPAPARA*
+>NZ_CP083691.1_188
+MTGVLPLVIAHRGASAAFPEHTRAAMLHALAVGADGIECDVQLTRDRQVVLWHDPTVDRT
+SDGRGPLADHTLAQLRALDVVSWHQGMGGDAPGDAAGRVPAVYGRRDEQVLTLADLLRMV
+LAADRPLRLAVELKHPSPFGHELEERVLRELVAAGWDAETGLMGQVRVSLMSLHPGALQY
+LAPLTGPDALCPLIDLVPDEIPSRLARGPLSRAAVRATVRQSLADAETMVWRGRAGLAGP
+SVAYVRSHLADVKAWLASGRRLRVWTVDEREDALFLAAQGVQELTTNRPADVLRWVTQAA
+TSASPGAISGRDMPSPAAR*
+>NZ_CP097650.1_119
+MPALVIAHRGASAAFPEHTRAAMLHALAVGADGLECDVQLTRDREVVCWHDPTVDRTSDG
+RGAVADHTLDRLRGLDVVSWHARRPGAEPATTTAPPAAYGGAGEQVLTLADLLAIATAAD
+RPLRLAVELKHPSPFGHELEERVLRELLRAGWDPETGRVGQVQVSLMSFHPDALRHVAPL
+AGTDPLCPLMDLMPTELPTRLARGPLSRAAVRAAARQSLAGSEALVWRGRAGLAGPSVAY
+VREHLADVKAWLAAGRRLRVWTVDEREDAEFLLAQGVQELTTNRPEDVLRWVRERAAARR
+ERVPTGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000266.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000266.fa
new file mode 100644
index 0000000000000000000000000000000000000000..418c094ee92eb21661359afbcc24de1343bfee33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000266.fa
@@ -0,0 +1,19 @@
+>NZ_CP042169.1_123
+MDHRPSPEQPAATWMSEQEFDDAVSAALTRIPDELARLLTNVVVVVEDEYEPQRWEDPAT
+ELFGLYEGVPLTERAEFAWQMPDRIVVFRGPLTRHCTSRAELEDEITVTVMHEVGHFFGI
+SEERLHELGWG*
+>NZ_CP033200.1_2093
+MDHRPSPDQPAATWMSEQEFDDAVSAALARIPDELARLLTNVVVVVEDEYEPQRWEDPAT
+ELFGLYEGVPLTERAEFAWQMPDRIVVFRGPLTRHCTSRAELEDEITVTVMHEVGHFFGI
+SEERLHELGWG*
+>NZ_CP040019.1_246
+MSEQEFDDAVSAALTRIPDELARLLTNVVVVVEDEYEPQRWENPDTELFGLYEGVPLTER
+AEMPWQMPDRIVVFRGPLTRHCTSRAELEHEITVTVMHEVGHFFGIDEERLHELGWG*
+>NZ_CP083691.1_180
+METWMSEEEFDAAVDAALLRIPDELARLLTNVVVIVEDEYEPQRWEDPDTELFGVFEGFS
+LAERAEAAWQLPDRIVIFRGPLTRHCRSRAELEHEITVTVMHEVGHFFGISEERLHELGW
+G*
+>NZ_CP097650.1_131
+MDHRPSPEQPAATWMSEQEFDDAVSAALTRIPDELARLLTNVVVVVEDEYEPQRWEDPAT
+ELFGLYEGVPLTERAELAWQMPDRIVVFRGPLTRHCTSRAELEDEITVTVMHEVGHFFGI
+SEERLHELGWG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000269.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000269.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8bce46e09c99a2083c4964e5f6a6094c8059513e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000269.fa
@@ -0,0 +1,59 @@
+>NZ_CP042169.1_128
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG
+VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT
+SSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG
+QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVA
+PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV
+RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE
+HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPTRGVLAF
+TVTSGGGRHLGSGEPIPARTVLVMANLSTEPVDLPANHSRALFSLEEAEAVQDGRLAHDA
+AAWLLMD*
+>NZ_CP033200.1_2098
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG
+VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT
+SSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG
+QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVA
+PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV
+RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE
+HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPTRGVLAF
+TVTSGGGRHLGSGEPIPARTVLVMANLSTEPVDLPANHSRALFSLEEAEAVQDGRLAHDA
+AAWLLMD*
+>NZ_CP040019.1_241
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG
+VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT
+SSEHAWFQAALAAGPDSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG
+QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFLDQDRVHEVYRDWRRVLDSYGHEPMMVAEAWVA
+PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV
+RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE
+HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPARGVLAF
+TVTSGGGRHLGSGEPIPARTVLVMANLSTDPVDLPTGHSRALFSLEEAEAVQDGRLAHDA
+AAWLLMD*
+>NZ_CP083691.1_176
+MTTQRLTTPPSEARNRPETPWWVDAVVYQVYPRSFADGDGNGMGDLPGVTAKIPYLSRLG
+VDAIWLSPFYLSPQHDAGYDVADYRTVDPRFGTLADADALIDAAHAADIRVIVDLVPNHT
+SSEHPWFQAAMAAGPGSRERARYHFTEGRGEHGELPPSNWESTFGGGAWSRVTEADGTPG
+QWYLHLFDTTQPDLNWENPEVREEFESILRFWLDRGVDGFRVDVAHGLVKKPGYPDADHT
+RMGMVTDAGEDQDPDFDVDAFEPAMPFLDQDGVHEVYRQWRRVLDSYPHEPMMVAEAWVS
+PLPRTFRYVRPGEMHQAFNFTYLMAGWDAESLTSAIDRSFTEAEKVGAPNTWVLSNHDTV
+RHTSRYGLSDPTAYPAGITAEDEQPDEALGRRRARAAAMIELALPGSAYIYQGDELGLPE
+HTTLPAELREDPYFFRTGGAEPGRDGCRIPLPWAADEPALGFSGPDADAAPWLPQPDSFR
+VLAADRQVGVEGSHFELYRHLLQIRAELDLGTGTFAWSAEHHRPEQGVLAFTVSSGGGRH
+LGSGVPIPARTVLVMANIGDTPVALPGDHVRAQFSLPESEAVVDDRLAPDAAAWLLLR*
+>NZ_CP097650.1_136
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG
+VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT
+SSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG
+QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVA
+PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV
+RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE
+HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPARGVLAF
+TVTSGGGRHLGSGEPIPARTVLVMANLSTDPVDLPAGHSRALFSLEEAEAVQDGRLAHDA
+AAWLLMD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000272.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000272.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a92853d655c6039c3f001b9654029b4a8fab53c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000272.fa
@@ -0,0 +1,33 @@
+>NZ_CP042169.1_131
+MRELQQRIIAQQGVLPEIDPAAEVERRVAFLADYLAATGASGFVLGISGGVDSTVGGRLA
+QLAVERRRAQLGVTDAVALGGPDTTPPGEAGVGADVVPSRENPRFTAVRLPYKVQHDEAD
+ARAAMDFVGADQDVTLNIAEAVQGLAAAFAEAVGEPISDYNQGNVKARIRMTAQYAVAGA
+HGQLVIGTDHAAEAVTGFYTKFGDGGADVLPLAGLNKRQVRALGRELGAPEPLWNKVPTA
+DLLDGTPGQTDEAELGMTYEDIDDYLEGKDVPTEVAEKLEGIWLRSRHKRTTPVTIHDDW
+WR*
+>NZ_CP033200.1_2101
+MRELQQRIIAQQGVLPEIDPAAEVERRVAFLADYLAATGASGFVLGISGGVDSTVGGRLA
+QLAVERRRAQLGVPDAVALGGPGTTPPGEAGVGADVVPSRENPRFTAVRLPYKVQHDEAD
+ARAAMDFVGADQDVTLNIAEAVQGLAAAFAEAVGEPISDYNQGNVKARIRMTAQYAVAGA
+HGQLVIGTDQAAEAITGFYTKFGDGGADVLPLAGLNKRQVRALGRELGAPEPLWNKVPTA
+DLLDGTPGQTDEAELGMTYEDIDDYLEGKDVPTEVAEKLEGIWLRSRHKRTTPVTIHDDW
+WR*
+>NZ_CP040019.1_237
+MRELQQQIIAEQGVRPQIDPAQEIERRVEFLVDYLEATGAAGFVLGISGGVDSTVGGRLA
+QLAVERRRARLGAPDAVALGGPEAPRGAPAADEAPSPQRPQFTAVRLPYRQQKDEADARA
+AMDFVDADREITLDIAAGVEGIASAFVEATGDEIADFDKGNVKARMRMVAQYALAGAHRQ
+LVIGTDHAAEAVTGFYTKFGDGGADVLPLSGLNKRQVRALGRELGAPEHLWNKVPTADLL
+DGNPGRTDEDELGMTYEHIDDYLEGGDIPEEAAEKLEGIWLRSRHKRTMPVTVHDDWWR*
+>NZ_CP083691.1_171
+MPEPYAGAMRELQQQIIAEMGVRPEVDPAAEVEARVRFLVDYLEATGASGFVLGISGGVD
+STTAGRLAQLAVERRRAELGTEAGDDAAPSRENPRFTAVRLPYRVQADEADATAAMDFVG
+ADGRVTLNIAEAVAGMASAFQEATGEPISDYNQGNVKARMRMVAQYAIAGAHGQLVIGTD
+HAAESITGFFTKFGDGGADVLPLAGLDKRQVRAVAKELGAPEHLWAKVPTADLLDGSPGR
+ADEDELGLSYEHIDDYLEGREIPEEAAEKLEGVWRRSRHKRTTPVTIHDDWWR*
+>NZ_CP097650.1_139
+MRELQQRIIAQQGVLPEIDPAAEVERRVAFLVDYLAATGASGFVLGISGGVDSTVGGRLA
+QLAVERRRAQLGVTDAVALGGPGTTPPGEAGVGADVVPSRENPRFTAVRLPYKVQHDEAD
+ARAALDFVGADQDVTLNIAEAVQGLAAAFAEAVGEPISDYNQGNVKARIRMTAQYAVAGA
+HGQLVIGTDQAAEAITGFYTKFGDGGADVLPLAGLNKRQVRALGRELGAPEPLWNKVPTA
+DLLDGTPGQTDEAELGMTYEDIDDYLEGKDVPTEVAEKLEGIWLRSRHKRTTPVTIHDDW
+WR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000273.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000273.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d0c56913dc7f86e3118235e749c2cefcf2c16928
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000273.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_132
+MSEIQHDDAVQHPSGLPLAHWLTLTEGLIAARVAESLEEHGLTRAQWQLLNTLTVAPQSR
+AELEAGFEEEQRGAVSGQIEELVESRWVTVEGDLYTLTATGRTAGARVGEAVEALRAEAT
+ADVPRDQIDDAVRVLRRIARNLGHPDA*
+>NZ_CP033200.1_2102
+MSEIPHDDAPVQHPSGLPLAHWLTLTEGLIAARVAESLEEHGLTRVQWQLLNTLTVAPQS
+RAELEAGFEEEQRGAVSGQIEELVESHWVTVEGDLYTLTATGRTAGARVGEAVEALRAEA
+TADVPRDQIDDAVRVLRRIARNLGHPDA*
+>NZ_CP040019.1_236
+MSEIPHDDAAVQHPSGLPLAHWLTLTEGLIAVRVAESLEEHGLTRAQWQLLNTLTVAPQS
+RAELEAGFEEEHRGAVSGQIEELVESRWVTVEGDLYTLTATGRTAGARVGEAVEALRAEA
+TADVPRDQIDDAVRVLRRIARNLGHPDA*
+>NZ_CP083691.1_170
+MTDNTQTPENRQTQAPRRDSHPSGLPLSHWLTVAEGLLAARVAASLEEHGLTRAQWQSLN
+ALTAAPLSAAEIGAGFEPEVRGAVVEQLDELVDAGWVTVEGDLFTLTSTGRTAGERVGEA
+VERLRGEATADLPAEHYEVTVATLRTIARNLGHPDA*
+>NZ_CP097650.1_140
+MSEIQHDDAVQHPSGLPLAHWLTLTEGLIAARVAESLEEHGLTRAQWQLLNTLTVAPQSR
+AELEAGFEEEQRGAVSGQIEELVESRWVTVEGDLYTLTATGRTAGARVGEAVEALRAEAT
+ADVPRDQIDDAVRVLRRIARNLGHPDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000277.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000277.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc35361eb9c86e1df9a84748fabfd9e0bb1402fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000277.fa
@@ -0,0 +1,23 @@
+>NZ_CP042169.1_136
+MAIENWQHDLNIGTVVRTANAFNAAGVHIIGRRRWNRRGAMVTDRYLHVRHHETVAAFTE
+WAAGEGLPVLGVDLFPESVPVETFDFPRACVLVFGQEGPGLSAEVRAASSAVLSIAQYGS
+TRSINAGVAAGIAMHAWIRQHAAVP*
+>NZ_CP033200.1_2106
+MLDHYRYWSLEAIVADLDARRHPFHVAIENWQHDLNIGTVVRTANAFNAAGVHIIGRRRW
+NRRGAMVTDRYLHVRHHETVAAFTEWAAGEGLPVLGVDLFPESVPVETFDFPRACVLVFG
+QEGPGLSAEVRAASSAVLSIAQYGSTRSINAGVAAGIAMHAWIRQHAAVP*
+>NZ_CP040019.1_232
+MGPGTSENSPETREKREEREGREEREVGVGPWEGPWPEDPRYDPELLRDGDRRNVVDGYR
+YWTLEAIVADLDARRHPFHVAIENWQHDLNIGTVVRTANAFNAAGVHVIGRRRWNRRGAM
+VTDRYLHVRHHATVEEFTAWAAAEGLPVLGVDLFPESVPLESFELPRECVLVFGQEGPGL
+SEEVRAASAAVLSIAQYGSTRSINAGVAAGIAMHAWVRQHGGVPTSSS*
+>NZ_CP083691.1_166
+MGSGEGVDAREVGREVGAPPWEGPWPEDPRYDPALLRDGDRRNVADRYRYWTVEAIVADL
+DRTRHPFHVAIENWQHDLNIGTVVRTANAFNAAGVHIIGRRRWNRRGAMVTDRYLHVHHH
+ETVEAFTAWAAGEGLPVLGVDLFPESVPVETFDFPRACVLVFGQEGPGLSEEVRAASEAV
+LSIAQYGSTRSINAGVAAGIAMHAWIRQHGGPAPV*
+>NZ_CP097650.1_144
+MPREVGVGPWLGPWPEDPRYDPELLAHGDRRNVLDRYRYWRLEAIVADLDARRHPFHVAI
+ENWQHDLNIGTVVRTANAFNAAGVHIIGRRRWNRRGAMVTDRYLHVRHHETVAAFTEWAA
+GEGLPVLGVDLFPESVPVETFDFPRACVLVFGQEGPGLSAEVRAASSAVLSIAQYGSTRS
+INAGVAAGIAMHAWIRQHAAVP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000279.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000279.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b3cb8ac7f789aeeda4080b5787b763511f27d8de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000279.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_139
+MPIASPEKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF
+SGSSVKDMVAGSLAFAAFAREVAKKHSVNIALHTDHCPQDKLEDFVLPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL
+YTTVADGIATVEALGLGENGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGR
+ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG
+EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG*
+>NZ_CP033200.1_2109
+MPIASPEKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF
+SGSSVKDMVAGSLAFAAFAREVAKKYSVNIALHTDHCPQDKLEGFVLPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL
+YTTVADGIATVEALGLGEHGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGK
+ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG
+EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG*
+>NZ_CP040019.1_229
+MPIASPDKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF
+SGASVKDMVTGSLAMAAFAREVAKNYSVNIALHTDHCPKDKLDAFVMPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGKELLARTHANKQILEVEIGVVGGEEDGVAHEINDKL
+YTTVEDGIATIEALGLGEQGRYLTALTFGNVHGVYKPGNVKLRPQILEDIQKAVGEKFGK
+ERPFDLVFHGGSGSAAQEIADSVSYGVVKMNVDTDTQYAFSRPVAGHMFENYAGVLKVDG
+EVGDKKMYDPRVWGAKAEEAMAARVVQACQELNSAGTSIG*
+>NZ_CP083691.1_164
+MPIASPDKYAEMIDAAKNGAFAYPAINVTSSQTLNAAVRGFAEAGSDGIIQVSTGGAAYF
+SGSSVKDMVAGSLAMAAFAREVAKKYSVNIALHTDHCPKDKLDGFVKPLLDASEAEVKAG
+RDPLFNSHMWDGSAETLEENLRIAQELLARTHANKQILEVEIGVVGGEEDGVANEINDKL
+YTTVEDGIATIEALGLGENGRYLTALTFGNVHGVYKPGGVKLRPQILQDIQQAVGEKFGR
+QRPFDLVFHGGSGSAAQEIADSVSYGVVKMNVDTDTQYAFSRPVAGHMFENYDGVLKVDG
+EVGNKKMYDPRVWGAKAEDGMAARVVQACQELNAAGKSIG*
+>NZ_CP097650.1_147
+MPIASPEKYAEMIDAAKNGAFAFPAINVTSSQTLNAAIRGFAEAGSDGIVQVSTGGAAYF
+SGSSVKDMVAGSLAFAAFAREVAKKYSVNIALHTDHCPQDKLEGFVLPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL
+YTTVQDGIATVEALGLGEHGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGK
+ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG
+EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000281.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000281.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee44ee49feed6bc5644aff29b4352bfcb117f701
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000281.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_141
+MTTQPHHSTPASAEQLQHDWDNNPRWAGVERSFTAEDVVRLRGRIQEEHTLARRGAEKLW
+TQLKDENARGEFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYP
+ANSVPQVVRRINNALLRADQIEHAEGVSSVEDWLVPIVADAEAGFGGPLNAYELMKSMIT
+AGASGVHWEDQLASEKKCGHLGGKVLIPTGQHIRTLNAARLAADVADVPSVIIARTDAEA
+ATLITSDVDERDAEFITGERTAEGFYKVRNGVEPCIARAKAYAPHADLIWMETGTPDLEL
+ARKFAEAVKAEFPDQMLAYNCSPSFNWKKNLDDDTIAKFQRELGAMGYTFQFITLAGFHA
+LNHSMFDLAKGYNERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAVSTAINPDS
+STVALAGSTESGQFH*
+>NZ_CP033200.1_2111
+MTTQPHHSTPASAEQLQHDWDNNPRWAGVERSFTAEDVVRLRGRIQEEHTLARRGAEKLW
+TQLKDENARGEFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYP
+ANSVPQVVRRINNALLRADQIEHAEGVSSVEDWLVPIVADAEAGFGGPLNAYELMKSMIT
+AGASGVHWEDQLASEKKCGHLGGKVLIPTGQHIRTLNAARLAADVADVPSVIIARTDAEA
+ATLITSDVDERDAEFITGERTAEGFYKVRNGVEPCIARAKAYAPHADLIWMETGTPDLEL
+ARKFAEAVKAEFPDQMLAYNCSPSFNWKKNLDDDTIAKFQRELGAMGYTFQFITLAGFHA
+LNHSMFDLAKGYNERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAVSTAINPDS
+STVALAGSTESGQFH*
+>NZ_CP040019.1_226
+MTTQPHHSTPASAEQLQHDWDHNPRWAGIERTYSPDDVVRLRGRIQEEHTLARRGAEKLW
+TQLKDENARGDFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYP
+ANSVPQVVRRINNALLRADQIEHAEGVSSVEDWLVPIVADAEAGFGGPLNAYELMKSMIT
+AGASGVHWEDQLASEKKCGHLGGKVLIPTGQHIRTLNAARLAADVADVPSVIIARTDAEA
+ATLITSDVDERDAEFITGERTAEGFYKVRNGVEPCIARAKAYAPHADLIWMETGTPDLEL
+ARKFAEAVKAEFPDQMLAYNCSPSFNWKKNLDDDTIAKFQRELGAMGYTFQFITLAGFHA
+LNHSMFDLAKGYHERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAVSTAINPDS
+STVALAGSTESGQFH*
+>NZ_CP083691.1_803
+MTEQTVQQIAQEIQKDWDTNDRWTHIERTHTAEDVAKLRGRVQEEHTLARRGSEKLWEQL
+TSEHAKGEFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYPANS
+VPAVVRRINNALLRADQIEWSEGIKTVEDYLVPIVADAEAGFGGPLNAYELMKGMIASGA
+SGVHWEDQLASEKKCGHLGGKVLIPTGQHVRTLNAARLAADVAGVPSVIIARTDAEAATL
+ITSDVDERDAEFITGERTAEGFYKVKNGVEPCIARAKAYAPYSDLIWMETGTPDLELARK
+FAEAVKSEFPDQMLSYNCSPSFNWKKNLDDATIAKFQRELGAMGYTFQFITLAGFHALNH
+SMFDLAKGYNERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAISTAVNPESSTV
+ALKESTEAGQFH*
+>NZ_CP097650.1_149
+MTTQPHHSTPASAEQLQHDWDNNPRWAGVERSFTAEDVVRLRGRIQEEHTLARRGAEKLW
+TQLKDENARGEFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYP
+ANSVPQVVRRINNALLRADQIEHAEGVSSVEDWLVPIVADAEAGFGGPLNAYELMKSMIT
+AGASGVHWEDQLASEKKCGHLGGKVLIPTGQHIRTLNAARLAADVADVPSVIIARTDAEA
+ATLITSDVDERDAEFITGERTAEGFYKVRNGVEPCIARAKAYAPHADLIWMETGTPDLEL
+ARKFAEAVKAEFPDQMLAYNCSPSFNWKKNLDDDTIAKFQRELGAMGYTFQFITLAGFHA
+LNHSMFDLAKGYNERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAVSTAINPDS
+STVALAGSTESGQFH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000282.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000282.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dca5deece31128f77edb869547977284bdad8dbe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000282.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_142
+MSPQTTTPTLHEIHADDVREHTPLPHDVSTQAIPVVIPEGAAPVVTVHGPVDGRQAEILT
+DEALAFLGRLHRLAEDRRRRLLEEREYTRRRITDGWNPHYLRSTRRVREDDSWRVAPLAP
+GLQDRRVEITGPVDRKMTINALNSGASGWLADFEDSSTPSWDRMLDGQVNLFDAIRDQID
+FTSPEGKEYRLRERELTDRPTIIVRPRGWHLLEDHIRVDGEPMAGALVDFGLYFFHNADE
+LIRRGHGPYFYLPKLESHLEARLWNCVFVAAQDELGIPQGTIRATVLIETITAAFQMEEI
+LYQLRNHAAGLNAGRWDYIFSIIKNFRDRGAEFVLPDRSEVTMTQPMMRAYTEQLVRACH
+RRGASAIGGMSAVIPDRRNEEANAAALEKVRADKAREAGDGFDGSWVAHPDLVPVAREEF
+DAVLGEAPNQIRTRRREDVEPDEAALLDVAATTGSVTEAGVRMNIEVGIRYIESWLRGNG
+AAAIHGLMEDAATAEISRSQIWQWAHNGTGVQLTEGGVRTANRGWMEQLIREEHARILAG
+PLPEGHRFEDAVRVFCESALPPEYPAFLTLGAYRRHFASQDDAAAKA*
+>NZ_CP033200.1_2112
+MSPQTTTPTLHEIHADDVREHTPLPHDVSTQAIPVVIPEGAAPVVTVHGPVDGRQAEILT
+DEALAFLGRLHRLAEDRRRRLLEEREYTRRRITDGWNPHYLRSTRRVREDDSWRVAPLAP
+GLQDRRVEITGPVDRKMTINALNSGASGWLADFEDSSTPSWDRMLDGQVNLFDAIRDRID
+FTSPEGKEYRLRERELTDRPTIIVRPRGWHLLEDHIRVDGEPMAGALVDFGLYFFHNADE
+LIRRGHGPYFYLPKLESHLEARLWNCVFVAAQDELGIPQGTIRATVLIETITAAFQMEEI
+LYQLRNHAAGLNAGRWDYIFSIIKNFRDRGAEFVLPDRSEVTMTQPMMRAYTEQLVRACH
+RRGASAIGGMSAVIPDRRNEEANAAALEKVRADKAREAGDGFDGSWVAHPDLVPVAREEF
+DAVLGEAPNQIRTRRREDVVPDEAALLDVAATTGSVTEAGVRMNIEVGIRYIESWLRGNG
+AAAIHGLMEDAATAEISRSQIWQWAHNGTGVQLTEGGVRTANRGWMEQLIREEHARILAG
+PLPEGHRFEDAVRVFCESALPPEYPAFLTLGAYRRHFAGQDDAAAKA*
+>NZ_CP040019.1_225
+MTTTTVTSGRHHAAPALHHTDEPVDTAAHTPLPHDVSTQALPVVAPAGAAPVVTVHGPVT
+DRQAEILTEDALAFLGRLHRVAEDRRRRLLEEREFTRQRITEGWDPHFLRATKRVREDDS
+WRVAPLAPGLKDRRVEITGPVDRKMTVNALNSGATGWLADFEDSSTPSWERMLDGQVNLY
+DAIRGRIDFTSPEGKEYRLRGAELTDRPTIIVRPRGWHLTDDHLRVDGEPMAGGLVDFGL
+YFFHNAAELVRRGHGPYFYLPKLESHLEARLWNCVFVAAQDALGIPQGTIRATVLIETIT
+AAFQMEEILYQLRNHAAGLNAGRWDYIFSLIKNYRDRGPAYVLPDRAEVTMTQPMMRSYT
+EQLVRACHRRGASAIGGMSAVIPDRRDQAANEVAFAKVREDKTREARDGFDGSWVAHPDL
+VPVAREVFDEVLGEAPNQIRTRRREDVEPDEAGLLDVAATTGSVTEAGVRRNIEVAMRYV
+ESWLRGQGAAAIHGLMEDAATAEISRSQIWQWAHNRTAVALEDGGTRTASREWMEQLVRE
+EHARILAGPLPEGHRFEDARRVFCESALPPEYPAFLTLGAYRRHFSAERA*
+>NZ_CP083691.1_802
+MMTLQTTHSDTTVNGVRVLGEPVPGQDRVLTSAALEFLAALHRGVEGRRRELMDERAARR
+RRIAEGETLDFLPATRKVREDDSWHVAPLAPGLRDRRVEITGPVDRKMTINAMNSGAKCW
+LADFEDSSTPSWENVIAGQVNLQDAIRRTISLTTPEGKEYTLGGVQLVDRPTIIVRPRGL
+HLMEDRILVDGQPVSGALADFALYFFHNAKELLRRGRGPYFYLPKTESHLEARWWNCVFV
+RAQDLLEIPQGTIRATVLIETITAAFEMEEILYQLRNHAAGLNAGRWDYIFSVIKTFRER
+GEDFVLPDRSEVTMTQPMMRAYTELLVRTCHRRGASAIGGMAAQIPNRKDPEANAAALEK
+VRSDKTREAGDGFDGSWVAHPDLVPVAMEVFDAVLKDLPNQIRTRRREDVVPDAAALVDI
+KSTTGSITEQGLRMNIEVGIRYVESWLRGNGAAAIHNLMEDAATAEISRSQIWQWIRTGS
+TARLTDGGERTVTREWVEQVTEEEFGRIERTEGDRFDDAREIFTSVALAEDFPDFLTLPA
+YERFLSAEARRRAGHGA*
+>NZ_CP097650.1_150
+MSPQTTTPTLHEIHADDVREHTPLPHDVSTQAIPVVIPEGAAPVVTVHGPVDGRQAEILT
+DEALAFLGRLHRLAEDRRRRLLEEREYTRRRITDGWNPHYLRSTRRVREDDSWRVAPLAP
+GLQDRRVEITGPVDRKMTINALNSGASGWLADFEDSSTPSWDRMLDGQVNLFDAIRDQID
+FTSPEGKEYRLRERELTDRPTIIVRPRGWHLLEDHIRVDGEPMAGALVDFGLYFFHNADE
+LIRRGHGPYFYLPKLESHLEARLWNCVFVAAQDELGIPQGTIRATVLIETITAAFQMEEI
+LYQLRNHAAGLNAGRWDYIFSIIKNFRDRGAEFVLPDRSEVTMTQPMMRAYTEQLVRACH
+RRGASAIGGMSAVIPDRRNEEANAAALEKVRADKAREAGDGFDGSWVAHPDLVPVAREEF
+DAVLGEAPNQIRTRRREDVVPDEAALLDVAATTGSVTEAGVRMNIEVGIRYIESWLRGNG
+AAAIHGLMEDAATAEISRSQIWQWAHNGTGVQLTEGGVRTANRGWMEQLIREEHARILAG
+PLPEGHRFEDAVRVFCESALPPEYPAFLTLGAYRRHFAGQDDAAAKA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000290.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000290.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b04f205b7355ce8acd7369fe210e87157f707a18
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000290.fa
@@ -0,0 +1,70 @@
+>NZ_CP042169.1_173
+MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAA
+QGCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGA
+HGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGT
+WDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW
+NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDP
+DFHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMT
+LNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWNQLPIN
+RPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER
+AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLA
+QQVADGLGIPVPAPTETPADVQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQG
+IHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPGLDQKAG
+AADPEAVDPRVIKVLQEMWRHSKAILALEPAEAVLAAAQVSGKGVESAADGASAVSRLTE
+LLPAHRVWDRFPTTGRLAD*
+>NZ_CP033200.1_2125
+MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAA
+QGCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGA
+HGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGT
+WDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW
+NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDP
+DFHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMT
+LNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWNQLPIN
+RPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER
+AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLA
+QQVADGLGIPVPAPTETPADVQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQG
+IHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPSLDQKAG
+AADSEAVDPRVVKVLQEMWRHSKAILALEPAEAVLAAAQVSGKGVESAADGASAVSRLTD
+LLPAHRVWERFPTTGRLAD*
+>NZ_CP040019.1_212
+MTTQQPDIPGTPGPRTPDLEERTAPTSSDDAAMPAPDQRGPASVSPTGQDTGADPATAAQ
+GCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGAH
+GMFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGTW
+DLVGNNMPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTIWN
+MSDRGIPRSFRMMEGFGVHTYRLIAADGSTVLVKFHWKPKLGVHSVTWEEALITNGADPD
+YHRRDLADAIEAGAFPEWELGVQVFEDTEEQMFEGIDLLDPTKLVPEELVPVQPLGRMTL
+NANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWTQLPINR
+PHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHALIEHPEPLPASVKERA
+HAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLAQ
+QVADGLGIPVPAPTETPADVQPSPVLSQIGGVWPLDGRQVGVVVGESVDEKELDALVQGI
+HGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPGLDEKAGA
+AASEAVDPRVVKVLQEMWRHSKAILALEPAEGVLAAAQVSGKGVESAADGASAVSRLTEL
+LPAHRVWERFGTTGRFAD*
+>NZ_CP083691.1_157
+MAEQPKIPGTPGPITPDLEEHTALTDPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAAQ
+GCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGAH
+GVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGTW
+DLVGNNMPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTIWN
+MSDRGIPRSFRMMEGFGVHTYRLIAADGSTVLVKFHWKPKLGVHSVTWEEALITNGADPD
+YHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELVPVQTLGLMTL
+NANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWTQLPINR
+PHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHALIEHPEPLPASVKERA
+HAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEETIRVRQLQNLGAIDPRLAQ
+QVADGLGMPVPAPADAPADVQPSAALSQVGGTWPLDGRQVGLVVGPQVDEKELGDAVQGI
+HGAGMVPLVIAPKGGPVAGEVVAQRAYLTAASIELDAVVVLGATPPAGDAQHGLDAKAAA
+DAPDAVDPRVAKLVQEAWRHAKAIVAVGEGTSVLDELGLTGTPGVLTVDAGADAVAQLKE
+LMPAHRVWERFPTTGRLAD*
+>NZ_CP097650.1_170
+MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAA
+QGCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGA
+HGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGT
+WDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW
+NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDP
+DFHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMT
+LNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWNQLPIN
+RPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER
+AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLA
+QQVADGLGIPVPAPTETPADVQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQG
+IHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPGLDQKAG
+AADSEAVDPRVVKVLQEMWRHSKAILALEPAEAVLAAAQVSGKGVESAADGASAVAALKQ
+LLPAHRVWDRFPTTGRLAD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000291.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000291.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed9c6069015b458080d17458c94891c26ae5d6e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000291.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_174
+MRISVGQFGPVGDVEENLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA
+WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH
+RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK
+VEHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADEREAVATAEVTR
+ERIDEVREFLPSLANRRTDVL*
+>NZ_CP033200.1_2126
+MRISVGQFGPVGDVEANLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA
+WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH
+RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK
+VDHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADEREAVVTAEVTR
+ERIDEVREFLPSLANRRTDVL*
+>NZ_CP040019.1_211
+MRISVGQFGPVGDVEANLAVMARLAARAAGEGAELLVLPEEAMLGAREVGEEFPDAIAAA
+WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH
+RESDRISPGDGGVAAIELDGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK
+VEHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVVELADEREAVVTAEVTR
+ERIDEVRKFLPSLANRRTDVL*
+>NZ_CP083691.1_156
+MRIAVGQFGPTGRVEDNLEAMGRLAARAAAEGAGLLVLPEEAMLTFREVEDEFAHAVAGS
+WEPFTEGLARLARQHGLAIVAGGYEPSATDRPYNTLVAVDADGAVAGAYRKLHLYDAFEH
+RESELITPGDRGLVTVEVGGLTVGLQTCYDLRFPEVSRALALAGAQVLAIPAAWFAGEHK
+VDHWRTLLRARAVENTVWVAAADTASAATVGHSAIIDPLALTLAEADDDAAPETLLCADV
+TAERVEEVRRTVPVLANRRTDVLTPPVDVEPGG*
+>NZ_CP097650.1_171
+MRISVGQFGPVGDVEANLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA
+WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH
+RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK
+VDHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADEREAVVTAEVTR
+ERIDEVREFLPSLANRRTDVL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000294.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000294.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8fd0c29d101efdf21ee2e8ab3eed1b5243682b2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000294.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_177
+MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEF
+RELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLQGTLTLTGGCGGM
+GGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIDKAVERVMQAKNDGEAVSV
+GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVD
+AGYSRAAEVAKERGVRVPMEATIRD*
+>NZ_CP033200.1_2129
+MAEGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEF
+RKLEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLQGTLTLTGGCGGM
+GGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIDKAVERVMQAKRDGEAVSV
+GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVD
+AGYSRAVEVAAERGVRVPMEATIRD*
+>NZ_CP040019.1_208
+MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEF
+RKLEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLKGTLTLTGGCGGM
+GGAQPLAVTLNGGACLIVDVSEGRLRRRMGKRYLDEVVTDIDKAVERVMQAKRDGEAVSV
+GLVGNAAEVFPELLERQKRGEIEIDIVTDQTSAHDPLSYLPIEIDEADWQAEAEGDPETF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGLADGTELAAAKLEALLTNDPGMGVIRHVD
+AGYSRAAEIAAERGVRVPMEATIRD*
+>NZ_CP083691.1_153
+MAAGFTQHDPSRTIRAPRGTELNAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAFDAIVETLKDLEEDETLLVQSGKPVGVFRTNVWAPRVLIANSNLVGDWADWKTF
+RELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKKYDGTLKGTLTLTGGCGGM
+GGAQPLAVTLNGGVCLIVDVSEERLRRRMGKRYLHEVETDIDAAIARVMQAKRDGEAVSV
+GLVGNAAEVFPELLKRQKAGEVEIDIVTDQTSAHDPLSYLPIEIEEKDWHAEAEADPDTF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGLADGTELAAAKLTALLTNDPGMGVIRHVD
+AGYSRAVEVAAERGVRIPMEPTVRD*
+>NZ_CP097650.1_174
+MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVVKTNVWAPRVLIANSNLVGDWADWKTF
+RELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLKGTLTLTGGCGGM
+GGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIERAVERVMQAKRDGEAVSV
+GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDAALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVD
+AGYSRAAEVAKERGVRVPMEATIRD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000298.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000298.fa
new file mode 100644
index 0000000000000000000000000000000000000000..80514a8da4c65891e45ec2519bb4fffbe270109e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000298.fa
@@ -0,0 +1,36 @@
+>NZ_CP042169.1_185
+MTSELPSSSLSPAWTGRTDGDTPEHLRWHQVVRPADGRGEPTTPQRDPGAGAPTSGARST
+ALIGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG
+ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVAAGTRVGILNLDAH
+FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRALFDTARERGVTWVTDE
+QAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAAVAPGVSAPAGFGVPYEVIHACALE
+ATQSGKLALADVVELNPALDVDGRTAKAAARLIHTIVSRHRTDASLLA*
+>NZ_CP033200.1_2137
+MTSELPSPSLSPAWTGRTDGDTPEHLRWHQVVRPADGRGEPTTTQRHPGAGAPTSGARST
+ALVGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG
+ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVGAGTRVGILNLDAH
+FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRALFDTARERGVTWVTDE
+QAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAAVAPGVSAPAGFGVPYEVIHACALE
+ATQSGKLALADVVELNPALDVDGRTAKAAARLIHTVVSRHRTDASLLA*
+>NZ_CP040019.1_199
+MTSELPSPSLSSAWAGRTDGDAPEHLRWHQVVRPADGRGEPTTTQRHPGAGAPTSGARST
+ALVGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG
+ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVGEGTRVGILNLDAH
+FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRVLFDTAREHGVTWVTDE
+QAQIADVTGVRRWVRSFIDAVDVLYLTVDLDVLPAAVAPGVSAPAGFGVPYEVIHACAVE
+AATSGKLALADVVELNPSLDVDGRTAKAAARLIHTIVSRHRTDASLLA*
+>NZ_CP083691.1_146
+MSGVVRPSLRTRPSMAWNGAMTADRASELPSAALSPAWTGRTDGDAPEHLRWHQVVRSAD
+GGAPAQTVDAAPARSTALVGFASDEGVRRNHGRVGAEDGPDALRGALASLAYLEGTGALV
+DAGDVSVDRGDDDAPGELEAGQAELATVVSGLLNAHDLAVVLGGGHETAYASITGLTGST
+RVAAGTRVGILNLDAHFDLREAPRPSSGTPFLQALRDAEEAEHQLSYAVVGISEANNTRA
+LFDTARERGVTWVTDEQAQTADVTGVRRWVRSFIDAVDVLYLTIDLDVLPAAVAPGVSAP
+AGFGVPYEVIHACTLEATQSGKLALADVVELNPALDVDGRTAKAAARLIHTIVSRHRTDA
+SLLA*
+>NZ_CP097650.1_185
+MTSELPSSSLSPAWTGRTDGDTPEHLRWHQVVRPADGRGEPTTTQRHPGAGAPTSGARST
+ALIGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG
+ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVGAGTRVGILNLDAH
+FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRALFDTARERGVTWVTDE
+QAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAAVAPGVSAPAGFGVPYEVIHACALE
+ATQSGKLALADVVELNPALDVDGRTAKAAARLIHTIVSRHRTDASLLA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000299.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000299.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee873c6623964a93f387c982a5051619da17a167
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000299.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_186
+MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGKEILGHRVYASLDGLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEVVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR*
+>NZ_CP033200.1_2138
+MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGKEILGHRVYASLDDLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEVVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR*
+>NZ_CP040019.1_198
+MSATHPERTWTGPSAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGQEILGHRVYASLDDLPVTPDLVEVFRKASDAPEMVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEIVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR*
+>NZ_CP083691.1_145
+MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGKEILGHRVYASLDDLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEIVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR*
+>NZ_CP097650.1_186
+MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGKEILGHRVYASLDDLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEVVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000300.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000300.fa
new file mode 100644
index 0000000000000000000000000000000000000000..06a9480617f34220335cddbc1652611abd88be6f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000300.fa
@@ -0,0 +1,49 @@
+>NZ_CP042169.1_187
+MITQPALHATGRRRVTLCDVPTLPPARLARDNGADCPEASIERTPVADHEFGFRTQALHA
+GAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL
+EGGIGAVATASGMAAEFVTFAALAAAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS
+AEAADFEAALQPNTKTVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP
+IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG
+EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANAQAVAQWLDEDPRVS
+WVRYAGLPDHPHHARAQQLLPRGVGSVFSIGVAPAATDTDDGASGPEAGRATASRFISAL
+QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPEDLIRISVGIEDTEDILWDLDQ
+ALTEATGRTRDDDGAPAAPKEA*
+>NZ_CP033200.1_2139
+MITQPALHGTGRRRVTLCDVPTLPPAHLARDNGRDCPEASIERTPVADHEFGFRTQALHA
+GAVPDTVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL
+EGGIGAVATASGMAAEFVTFAALAAAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS
+AEAADFEAALQPNTKTVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP
+IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG
+EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANAQAVAQWLDEDPRVS
+WVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASGPEAGRATASRFISAL
+QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPEDLIRISVGIEDTEDILWDLDQ
+ALTEATGRTRDDDGAPAAPKEA*
+>NZ_CP040019.1_197
+MADHEFGFRTQALHAGAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRI
+GNPTVAAFEERVATLEGGIGAVATASGMAAEFVTFAALAGAGDHIVASSKLYGGTITQLD
+VSLRRFGVETTFVDSVEAADFEAALQPNTKAVYTEIVANPSGDVVDLPGLADVAHRHGVP
+LVVDATLTPPYLIRPIEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTE
+PVPSYGGVSWWGNFGEYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLAN
+ARAVATWLDEDPRVSWVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASG
+PEAGRATASRFISALQLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPADLIRIS
+VGIEDLEDILWDLDQALTEATGRTRDGAVVPAEQEA*
+>NZ_CP083691.1_144
+MITQPALHGTGLRRVTLCDVPTLPPAHLARDNGTDCPEASIERTPVADHEFGFRTQALHA
+GAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL
+EGGIGAVATASGMAAEFVTFAALAGAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS
+AEAADFEAALQPNTKAVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP
+IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG
+EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANARAVATWLDEDPRVS
+WVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASGPEAGRATASRFISAL
+QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPADLIRISVGIEDLEDILWDLDQ
+ALTEATGRTRDGAVVPAEQEA*
+>NZ_CP097650.1_187
+MITQPALHGTGRPRVTLCDAPTLPPAHLARDNGTDCPEASIERTPVADHEFGFRTQALHA
+GAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL
+EGGIGAVATASGMAAEFVTFAALAGAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS
+AEAADFEAALQPNTKAVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP
+IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG
+EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANAQAVAQWLDEDPRVS
+WVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASGPEAGRATASRFISAL
+QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPADLIRISVGIEDLEDILWDLDQ
+ALTEATGRARDGAVVPAEQEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000302.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000302.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aeb02fdcd49fb733c440dbfcc9f898cb211b1722
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000302.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_189
+MPDDVAVRLLLIADTHIPRRARALPAQVWAEVARADVVLHAGDWVTEDVLDDLDARAARL
+VGVWGNNDGPKLRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS
+HIPWDTVAGPDTANPGLRLLNPGSCTDRRRQPVCTLMRAVVRGGRLEDVELVSVDRTP*
+>NZ_CP033200.1_2141
+MPDDVAVRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDARAARL
+VGVWGNNDGPGPRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS
+HIPWDTVAGPETANPGLRLLNPGSCTDRRRQPVCTLIRAVARDGRLEDVELVPVDRTP*
+>NZ_CP040019.1_194
+MTTETRLLLLADTHIPPRARAMPAQVWDEVARADVVLHAGDWVEESVLDELEARSRRLVG
+VWGNNDDGALRARLPEVARVEIGGVRIAMVHETGAARGRERRMAEAFPDADVLVFGHSHI
+PWDTVAGPETANPGLRLLNPGSPTDRRRQPVCTLMRAVVRDGGLADVELVPVDRTP*
+>NZ_CP083691.1_142
+MTTRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDAQAARLVGVW
+GNNDGPRLRARLPEVARVEIGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHSHIPW
+DTVAGPETANPGLRLLNPGSCTDRRRQPVCTLMRAVVRGGRLEDVELVPVDRTP*
+>NZ_CP097650.1_189
+MPDDVAVRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDARAARL
+VGVWGNNDGPGPRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS
+HIPWDTVAGPETANPGLRLLNPGSCTDRRRQPVCTLIRAVARDGRLEDVELVPVDRTP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000303.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000303.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f91b2b2b1f6ceb470ec3b7a4ccac478b9aa8d38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000303.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_190
+MPHPPRPTPDDVPAAERAALRRGRLRPWLPFLLAAALCLALLGWALVALPGLPERVPTHW
+GVDGRPDAWEDASFGTVATGPLIGLGVTGFLALVSAMVTVLVPTDPGLSPWRRVRQAGVH
+RGVQECLGWSCVLIVLVLAPTTAEVLAAGAWTMPWWILPLTLTVLMVGVFPAMRASTRRW
+TRWSDRVAAELGYRPTAAERAEDEVWTPLGLKRDPDDPAVFPTKRPGYGVGVTVNLATPA
+GRWLVRGFVVVVIVGLPLALWLGAFAAR*
+>NZ_CP033200.1_2142
+MPHPSRPTPDDVPAAERAALRRGRLRPWLPFLLAAALCLALLGWALVALPGLPERVPTHW
+GVDGRPDAWEDTSFGTVATGPLIGLGMTGFLALVSAMVTALVPTDPGLSPWRRVRQAGVH
+RGVQECLGWPCVLIVLVLAPMTAEVLAAGAWTMPWWLLPLTLTVLMVGVFPAMRVSTRRW
+TRWSDRVAAELGYRPTAAELAEDEVWTPLGLKRDPDDPAVFPAKRPGYGVGVTVNLATPA
+GRWLVRGFVAVFIVGLPLALWLGAFAAR*
+>NZ_CP040019.1_193
+MARYVPAPAPEPVPAAEEAALRQGRARPWWPYLLTAAVSVALLVWTVVAYPGLPEQVPVR
+WGIDGRPDRWEDTTFGTVAFGPIFGLGMTAFLALIAAMIPAMTGVHGATSAWRRVRQEGV
+NRGVREGMGWIALLSLLMTAPTTAEVLSAGAWRMPWWLMPLLLTALMVGVFGALRATLGR
+WTRWADGVAADLGHRPTPEELAEDKTWTPLGMKDDPEDPTVFPAKRPGYGVGTTINIGTR
+AGRLLVYGFVAVFMVALPLATWIGAYLAR*
+>NZ_CP083691.1_141
+MPHPPRPTPDDVPAAERAALRRGRWIPWLPYLLTAAVSAGLLVWAIVALPGLPDRVPVHW
+GIDGRPDAWEEKSFGTVAFGPLLGLGMTALLAFCAALTPAMTATPQDASPWRRVRQEGVN
+RGVREALGWLTLLIALATAPSTVEVLSNGAWRPAWWLMPLVLTLVMLGTVGVFGPALRRW
+TGWADRTAQDLGYRADFAELAEDAKWTPLGLKNDPEDPSAFPAKREGYGVGATVNLATTT
+GRLLVYGFVALFVIGLPAALWIGAFLNR*
+>NZ_CP097650.1_190
+MTHPPHPVPADVPAAERAALRRGRLRPWLPFLLAAALCLALLGWALVALPGLPERVPTHW
+GVDGRPDAWEDASFGTVATGPLIGLGMTGFLALVSAMVTALVPMDPGLSPWRRVRQPGVH
+RGVQACLGWSCVLIVLVLAPTTAEVLAAGAWTMAWWLLPLTLTVLMVGIFPAMRAGTRRW
+TRWADRVAADLGHRPTAAELAEDEVWTPLGLKRDPEDPAVFPAKRPGYGVGVTVNLATPA
+GRWLVRGFVAVFIVGLPLALWLGAFAAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000306.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000306.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d4bad28c0829291421eaf5479e3cd8f018361573
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000306.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_197
+MSAALTTPAATTGPEARERSGHDDGDTGARRRQRPRVLDRPGARAVVGLAAPAVLLVLWW
+AVTAAGLLSAVQLPSPGAVLSAGVNLLERGDLWLHVGISTQRVLLGFLLGAALGLAVGSA
+LGLSRWADALFAPLIGALRAVPSLAWVPLLILWMQIGEESKVTLIAIGAFFPVFTTVYAA
+LRHVDPHLVEAGRAFGYHGLSLLRTVQLPAVVPAVFSGLRLALAQAWLFLVAAELIASSM
+GLGFLLTDSQNNGRTDRLILAIILLAVLGKLTDWLLGLLERRALRRWA*
+>NZ_CP033200.1_2148
+MLDRPGTRAAVGLAAPAVLLVLWWAVTAAGLLSAVQLPSPGAVLSAGVNLLERGDLWLHV
+GISTQRVLLGFLLGAALGLAVGSALGLSRWADALFAPLIGALRAVPSLAWVPLLILWMQI
+GEESKVTLIAIGAFFPVFTTVYAALRHVDPHLVEAGRAFGYHGLSLLRTVQLPAVVPAVF
+SGLRLALAQAWLFLVAAELIASSMGLGFLLTDSQNNGRTDRLILAIILLAVLGKLTDWLL
+GLLERRALRRWA*
+>NZ_CP040019.1_189
+MTVLDRPGGRTAVGLIVPALLLLLWWALTAAGVFSGVQLPPPAWVAEAAVDLAARGTLWH
+HIAISVQRVLVGFLIGGALGLLVGSVLGLSRWADALLAPTIGALRAVPSLAWVPLLILWM
+QIGEESKVTLIAIGAFFPVFTTVYAALRHVDPHLVEAGRAYGYHGVRLLGTVQLPAVVPA
+MFSGLRLALAQAWLFLVAAELIASSMGLGFLLTDSQNNGRTDRLILAIILLAVLGKISDW
+LLGFVERWAVRRWA*
+>NZ_CP083691.1_131
+MSTALTTPAATTGPEARERSGHDDGGTGARRRQRSRVLDRPGARAVVGLAAPAVLLVLWW
+AVTAAGLLSAVQLPSPGAVLSAGVNLLERGDLWLHVGISTQRVLLGFLLGAALGLAVGSA
+LGLSRWADALFAPLIGALRAVPSLAWVPLLILWMQIGEESKVTLIAIGAFFPVFTTVYAA
+LRHVDPHLVEAGRAFGYHGLSLLRTVQLPAVVPAVFSGLRLALAQAWLFLVAAELIASSM
+GLGFLLTDSQNNGRTDRLILAIILLAVLGKLTDWLLGLLERRALRRWA*
+>NZ_CP097650.1_199
+MLDRPGTRAAVGLAAPAVLLVLWWAVTAAGLLSAVQLPSPGAVLSAGVNLLERGDLWLHV
+GISTQRVLLGFLLGAALGLAVGSALGLSRWADALFAPLIGALRAVPSLAWVPLLILWMQI
+GEESKVTLIAIGAFFPVFTTVYAALRHVDPHLVEAGRAFGYHGLSLLRTVQLPAVVPAVF
+SGLRLALAQAWLFLVAAELIASSMGLGFLLTDSQNNGRTDRLILAIILLAVLGKLTDWLL
+GLLERRALRRWA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000314.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000314.fa
new file mode 100644
index 0000000000000000000000000000000000000000..63487b2d6936b5210e923e48d6be0f4d6264b31f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000314.fa
@@ -0,0 +1,10 @@
+>NZ_CP042169.1_208
+MDRELRTPPELEGVDWHDDAPRRPRPIVTLVAWIAILGLVLSVGAGIFSAF*
+>NZ_CP033200.1_2157
+MDRELRTPPELEGVDWHDDAPRRPRPIVTLVAWIAILGLVLSVGAGIFSAF*
+>NZ_CP040019.1_157
+MDRSNEIPPELQGLDWGEDDAPRRRRPLITLVAWLCIIGLVLGVAAGLFSIL*
+>NZ_CP083691.1_110
+MADLPPELEFAEFDDDPRPSAPSPWVRVLAVVVLLGLVGSLAAGLFGGI*
+>NZ_CP097650.1_208
+MDRELRTPPELEGVDWHDGAPRRPRPIVTLVAWIAILGLVLSVGAGIFSAF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000318.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000318.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b671db4ef58b49f9425d17ac7f7854d498795ff3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000318.fa
@@ -0,0 +1,41 @@
+>NZ_CP042169.1_217
+MSTAVATSIHDRRPPQPQPGGRLGAAQAVATVVGMELRQRLRSRGWYVLLGVFFVVVGAV
+TLGALGLRGLGVAEMEASGLEPELAEQQMRALGRTLFDGVLLFVLTLSLLVSPALAANAI
+SGDRAGGTLAITQVTLLRTGHLMAGKWLAAWIASAAFPAAALPWLAVAAVVGRVSPWAVL
+VGLVMILVEFGMIAGIGVAVSAIAGRTLFAVVVTYLIVAALTIGTLVAFGLSLQFLQTEV
+RANEADYGSTTAEPFTEAELEKMTPEEAEQAWAEWEAAHPELYDGIADRCVGPVTTRTIP
+DPRRSGWLLAANPYAVLADASPWEGGLLEDGTRAEPGPLNLLSVGLRWTQRDPVRDVECL
+DGELRGLDQSGVPDRQGTWPVWPLGLAMQGVLVAGLGWWGHRRLDTPAGRLPAGTRVA*
+>NZ_CP033200.1_2186
+MSTAVATSIHDRRPPQPQPGGRLGAAQAVATVVGMELRQRLRSRGWYVLLGVFFVVVGAV
+TLGALGLRGLGVAEMEASGLEPELAEQQMRALGRTLFDGVLLFVLTLSLLVSPALAANAI
+SGDRAGGTLAITQVTLLRTGHLMTGKWLAAWIASAAFLAAALPWLAVAAVVGRVSPWAVL
+VGLVMILVEFGMIAGIGVAVSAIAGRTLFAVVVTYLIVAALTIGTLVAFGLSLQFLQTEV
+RANDAEYGSMTAEPFTEAELEKMTPEEAEQAWAEWEAAHPELYDGIADRCVGPVTTRTIP
+DPRRSGWLLAANPYAVLADASPWEGGLLEDGTRAEPGPLNLLSVGLRWTQRDPVRDVECL
+DGELRGLDSTGVPDRQGTWPVWPLGLAMQGVLVAGLGWWGHRRLDTPAGRLPAGTRVA*
+>NZ_CP040019.1_147
+MSTVVADPTRQGPPPLRPPGGGRLSTASAVRTVVGMELRQRLRSRGWYVLLGVFFLVVGA
+VTLGALGLRATTLGDLQSQGMDPAAAEVQMRSAGQWLFDGVLLFVLTLSLLVSPVLAANA
+ISGDRAGGTLAITQVTLLRTGQLMAGKWIAAWIASAAFLVAALPWLAVAAVVGRVSPLFV
+LVGLLMILVEFGVITGIGVAVSAIAGRTLFAVVVTYLIVAALSIGTLVAFVLSLQFLQTD
+VRANMPEHDGMTMADPLEGQDVENMTQAEIDAAWAEWERQNPDAYDGIADACVGPVGVQS
+VPDPRRVGWLLAANPYAVLADASPWDPTGASMQFTPETGPLNMMSAALRLTQQDPAETTE
+CLDGQLRRIDTTSVPDREGTWPVWPLGLAMQAALTGGLLWWGHRRLDTPAGRLPAGTRVA
+*
+>NZ_CP083691.1_105
+MSAVLHTPPPAAAPAGGPTPLGSGRLGVVDALRTLVGMELRQRLRSRGWYILLGVFFLLV
+GGVTLGALGLHAWTGGNSPDSTMVFGRWLYDGVLLFVLTLCLLVSPALSANAISGDRSAG
+TLAITQVTLVSTWQLMLGKWLAAWIAAVAFLVAAAPWLIVAAVVGQVPPLAVLAGLAMIL
+VEFAVVTGIGVAVSAITGRTLFAVVVTYLLVAMMTIGSLIAFTISLQFIETRLQTNQVTY
+GYAEDAGSTKSCAGPLRDTTVPDPRRVAWLLAGNPYVVVADAVPLPELREDSAGEEFGAL
+NLISLGMRVAQIDPREYTDCVDGQVNEGSVTDSPVTLVDRTWPTWPLGMLLQGGFLAALL
+WWGRRRLDTPAGRLPTGTRVA*
+>NZ_CP097650.1_218
+MSTAVATSIHDRRPPQPQPGGRLGAAQAVATVVGMELRQRLRSRGWYVLLGVFFVVVGAV
+TLGALGLRSLGVTEMEASGLEPELAEQQMRALGRTLFDGVLLFVLTLSLLVSPALAANAI
+SGDRAGGTLAITQVTLLRTGHLMAGKWLAAWIASAAFLAAALPWLAVAAVVGRVSPWAVL
+VGLVMILVEFGMIAGIGVAVSAIAGRTLFAVVVTYLIVAALTIGTLVAFGLSLQFLQTEV
+RANDAEFGSMTAEPFTEAELEKMTPEEADQAWAEWEAANPELFDGIADRCVGPVTTRTIP
+DPRRSGWLLAANPYAVLADASPWEGGLVEDGTWAEPGPLNLLSVGLRWTQRDPVRDVECL
+DGELRGLDQSGVPDRQGTWPVWPLGLAMQGVLVAGLGWWGHRRLDTPAGRLPAGTRVA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000328.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000328.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d7a8260afd34c6bf901c578938e32c5d7e00a3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000328.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_229
+MSPAAPPTAPPAAEDRPRVPAVPASSLVLVRPGAGGEISVFTVRRAGTMAFSAHATAFPG
+GRVDPADDLSDRLWEGTDLADWGRRLGLPHEPADAHGTLAELDPAEGAGRVLAAAVRETF
+EETGVLLARDAVTGTPVDPARVAAFPDELRDAVERHEVDFGELLDREGLRPDAGALVPWS
+RWITPHGGPRRYDTFFFAVHLPQGQSPERMSSEAASHGWASPAELLRRFRVGKVNLMAPT
+WWQLRTLVDAGEDVHAGRSRFEPLEGVMLVAGQGPVFPHADEYLRDLTAFRAAAQVEESK
+DNIL*
+>NZ_CP033200.1_2198
+MSPAAPPTAPPAAEDRPRVPAVPASSLVLVRPGAGGETSVFTVRRAGTMAFSAHATAFPG
+GRVDPADDLPDRLWEGTDLADWGRRLGLPHEPVDAHGTLTELDPAEGAGRVLAAAVRETF
+EETGVLLARDAVTGTPVDPARVAAFPDELRDAVERHEVDFGELLDREGLRPDAGALVPWS
+RWITPHGGPRRYDTFFFAVHLPHGQSPERMSSEAASHGWASPAELLRRFRAGEVNLMAPT
+WWQLRTLVDAGEDIHAGRSRFEPLEGVMLVAGQGPVFPHADEYLRDLMAFRAAAQVEESK
+DNIL*
+>NZ_CP040019.1_126
+MSPAAPSADPADGDRPDVPAVPASSLMLVRPEQDGDTSVFALRRAGSMAFSAHATAFPGG
+RVDPADDLPDALWEGTDLAAWGRRLGLPHEPVDALGTLAALDPAEGAGRVLAAAVRETFE
+ETGVLLARDTATGAPVDPDRVAALPEDLRDAVERHEVDFGDLLRDEGLRPDAGALVPWSR
+WITPHGGPRRYDTFFFAVHLPAGQSPERMSSEAAEHGWASPAELLRRFRAGEVNLMAPTW
+WQLRTLDDAGEDVHAGRSRFEPLEGVMLVAGQGPAFSHADEYLRDLAAFRAAAHVEESKD
+NIL*
+>NZ_CP083691.1_91
+MDAAQTSSSETLPVEATPARAAASLLLLRDGAAGLEVFHVHRAGTMAFSAHATAFPGGRV
+DPSDDALPVPGADLAAWARRLGLEDRPVETQPEDDPARVAARFLAAVVRETFEETGVLLA
+RAADGGPVPPEAAAALAGRREDVEAHAADLGALLAEHGLAADVSGLRAWQRWITPLSVPR
+RYDTAFFLVAVPAGQDPDRLTTEATEHGWARPADLITAFQAGDVNLMAPQWAQLRALMDL
+PDVEAALRAGAAAEPVPVVQLASEASPEERTREFSHAAEYREHLRSFRTHDRVQDTPDNV
+L*
+>NZ_CP097650.1_230
+MSPAAPPAEPSAAEDRPRVPAVPASSLVLVRPGAGGEISVFTVRRAGTMAFSAHATAFPG
+GRVDPADDLPDRLWEGTDLAEWGRRLGLPHEPVDAHGTLTELDPAEGAGRVLAAAVRETF
+EETGVLLARDAVTGTPVDPARVAAFPDELRDAVERHEVDFGELLDREGLRPDAGALVPWS
+RWITPHGGPRRYDTFFFAVHLPQGQSPERMSSEAASHGWASPAELLRRFRAGKVNLMAPT
+WWQLRTLVDAGEDIHAGRSRFEPLEGVMLVAGQGPVFPHADEYLRDLTAFRAAAQVEESK
+DNIL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000330.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000330.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb8f0173fd8a15d13540ad31508d4fa9e73e5939
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000330.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_231
+MSANVEETEMTTQTDAANSGQTVLVHAEIGADGALRPVVAELLGAAATVGVPEAVLVTGA
+EGRDAAVARLGEYGATRVHVLVADDAATTLGDAAVQALAAAAARTAPVAVLLSGSPESRA
+VAGRLSVRARGPVCTDAVGLRWADDEVIARHSVFGGDYLSESTGEGGPRIITMRPGAVAD
+RAPAVEAPEVVELAAAELGPVTAGARVLEVNARTQNSARPPLRGAKTVVAGGRGVGSEEG
+FAIVEQLADELGAAVGASRAAVDSGYTAAERQVGQTGVIVSPNLYIALGISGAIQHLAGM
+KTAKTIVAIDKNEDAEIFEHADFGVVGDIFQVVPQVIEQLRTRRG*
+>NZ_CP033200.1_2200
+MSANVEETEMTTQTDAANSGQTVLVHAEIGADGALRPIVAELLGAAATVGVPEAVLVTGA
+EGRDAAVARLGEYGATRVHVLVADDAATTLGDAAVQALAAATARTAPVAVLLSGSPESRA
+VAGRLSVRARGPVCADAVGLRWADDEVIARHSVFGGDYLSESTGEGGPRIITVRPGAVAD
+RAPAVEAPEVVELAAAELGPVTAGARVLEVNARTQNSARPPLRGAKTVVAGGRGVGSEEG
+FAIVEQLADELGAAVGASRAAVDSGYTAAERQVGQTGVIVSPNLYIALGISGAIQHLAGM
+KTAKTIVAIDKNEDAEIFEHADFGVVGDIFQVVPQVIEQLRTRRG*
+>NZ_CP040019.1_124
+MSANVEESEMTMQNDAANSGQTVLVHAELGADGALRPVVAELLGAAATVGVPEAVLVTGA
+ASQDAAVARLGELGAARVHVLVAEDAAGTLGDAAVQALAAVTARTAPVAVLLSGSPESRA
+VAGRLSVRARGPVCADAVALRWADDEVIARHSVFGGDFLSESTGEGGPRIITMRPGAVSD
+RAPAVASPEVVEVAAAELGAVTAGARVLETTRRVQQADRPALRGAKTVVSGGRGVGSEEG
+FAIVEELADALGAAVGASRAAVDAGYTAADRQVGQTGVIVSPNLYIALGISGAIQHLAGM
+KTAKTIVAIDKNEDAEIFEYADFGVVGDIFKVVPQVIEQLRARRG*
+>NZ_CP083691.1_89
+MTDLPVTPVLVLAELTAAGDLRPAVAEALGAAARVGVPHAVLVTDADADDALVARLGELG
+AAVVHTAVAQDPAELGTAQVAALAAAVDAVLPEAVVLPNTPESRAVAGRLAVRARGAVTA
+DAVGLHRADGEIVARHSVFGGDVLAESTVEGGPNIVTLRPGAVADRARPVAAPEVRPLDV
+AGRTVTAGARILSSEPAAPSADRPDLRTARAVVAGGRGVGSAEGFTTLVEPLADALGAAV
+GASRVAVDSGFTAPEGQIGQTGVTVAPDLYVALGISGAIQHLVGMKTSGTIVAVDSDEDA
+AIFEHADLGVVGDVNEVVPQLIAALAARRG*
+>NZ_CP097650.1_232
+MSANVEETEMTTQTDAANSGQTVLVHAEIGADGALRPIVAELLGAAATVGVPEAVLVTGA
+EGRDAAVARLGEYGATRVHVLVADDAATTLGDAAVQALAAATARTAPVAVLLSGSPESRA
+VAGRLSVRARGPVCADAVGLRWADDEVIARHSVFGGDYLSESTGEGGPRIITVRPGAVAD
+RAPAVEAPEVVELAAAELGPVTAGARVLEVNARTQNSARPPLRGAKTVVAGGRGVGSEEG
+FAIVEQLADELGAAVGASRAAVDSGYTAAERQVGQTGVIVSPNLYIALGISGAIQHLAGM
+KTAKTIVAIDKNEDAEIFEHADFGVVGDIFQVVPQVIEQLRTRRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000331.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000331.fa
new file mode 100644
index 0000000000000000000000000000000000000000..731822561319ec2d96a09bef4026259f2236866b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000331.fa
@@ -0,0 +1,52 @@
+>NZ_CP042169.1_232
+MPKQRMAGYVPLKGAPAETEPAPAPAQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRR
+MAGYVPFAREAEWLGGAPAPAAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPD
+VAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMAGYVPFAREGEWFTELAAVGGPTAPE
+MVAQEVDAPEQATAEPTAEPAAAAPARPVVAELADVEPADAEPAVAAPVAAASAPEPAPT
+APDTRSAPPASAVQPPRAATGTPARTAETDAAESAVPSRLRKALPAVAGVVVLALLAVLA
+ARWLRSLDPVADFIATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHET
+RPPANFTPTKDGLFSARGNTPKKFSLTIWMHQALDALWLLNGLIFVVLLIATGHWARIVP
+TDPHVFQHALSAGIQYLSLDWPTENGWVHYNALQMLSYALVVFVAAPLAALTGWRMSSWF
+PTEAKGLNKAFPMEVARKVHFPVMVFFVAFIVVHVFLVAFTGLLTNLNHMYTSRGGATDA
+WGLVVFLVSVAVTAAAWFFLKPAFTAPVASRFGTVGR*
+>NZ_CP033200.1_2201
+MPKQRMAGYVPLKGAPAETEPAPAPGQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRR
+MAGYVPFAREAEWLGGAPAPAAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPD
+VAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMVGYVPFAREGEWFTELAAVGGPTAPE
+TAAQEVVAEPATAEPAAAEPADAEPAVAAPVAAAPAAEPAPTAPDTRSAPPASTAQPPRA
+APGAATGTPARAAETDAAESAAPSRLRKALPAVAGVVVLALLAVLAGRGLRSLDPVADFI
+ATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHETRPPANFTPTKDGLF
+SARGNTPKKFSLTIWMHQALDALWLLNGVIFVVLLIVTGHWARIVPTDPHVFQHAVSAGI
+QYLSLDWPTENGWVHYNALQMLSYSLVVFVAAPLAALTGWRMSSWFPTKATGLNKAFPME
+VARKVHFPVMVFFVAFILVHVFLVAFTGLLTNLNHMYTSRGGATDAWGLVVFLVSVAVTA
+AAWFFLKPAFTAPVASRFGTVGR*
+>NZ_CP040019.1_123
+MARRRRRPGGRSGLGHPAGAPAAAPAPIAASASPTQSPRPAEPAAAQPRLAEQDVAAAVA
+RPAAAAPVAVESDLVPLGQRRRMGGYVPLAREGEWFAELAAADAAPAGETAEPTVLEAAH
+DDAAPAAEAAVTEPAAPTTTAAAAAATTAAAQAPAAPAQPAAAAAAPTAPDTRSAPPASA
+AQPPRAEPAAASGRPARATKKTDAAEEAPAPSRLRKALPLVAGVVVLALVAVLAARWLRT
+LDPVADFIAAYDGHPALAEGTPVGMPPWLGWQHFLNMFLMVLIIRTGLQIRNETRPPANF
+TPKKDGAFSARGNTPKKFSLTIWTHQALDALWLLNGVVFVVLLFVTGQWARIVPTDPYVF
+HHAFSAGIQYLSLDWPTENGWVHYNALQMLSYTLVVFVAAPLAALTGWRMSSWFPTEAKG
+LNRAFPMEAARKVHFPVMLFFVLFILTHVFLVFFTGALKNLNHMYTSRGDATDAWGLVVF
+LVSVAVTAAAWFLLRPSFTAPAASKFGTVGR*
+>NZ_CP083691.1_88
+MPQRMQGYTEFRGEPWPPRDRVPQAPAPTTTPAVAADERRPGRRMVGYTAFRGEPWPPVR
+EAAQPAPAPAAAASPAEVTEAAAAAVPLEATAPAGIAVPGRRMAGYTAFRGEPWPPARVG
+AAPQAPEPAPMATVEPAVATGPTPTVEPVAAGAPETTPKPAPSTGRRVAAAVGGVVVLGL
+LAVLGARWLLTLPEVAAFVARYPGVPRHPEVTPVGIPAWLAWQHFLNLFLLVLVVRTGLQ
+VRHETRPPATFTPHQPGPFAPRSATGGTYSLTVWIHQALDALWLLNGLVFVVLLFATGHW
+MRLIPTDPQTPQHMVSTALQYLSLQWPEHDGWLHYNALQMVTYAGVVFVLAPLAALTGFR
+MSSWWPSRNTALSRGFPMELARRLHYPTMLAFVLFVVVHVVLVLFSGVLHELNAMFLARN
+AADAWGLAAFLVGCAVIAAGWVLLKPAIVAPVAERFGRVSR*
+>NZ_CP097650.1_233
+MPKQRMAGYVPLKGAPAETEPAPAPAQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRR
+MAGYVPFAREAEWLGGAPAPAAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPD
+VAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMAGYVPFAREGEWFTELAAVGGPTAPE
+MVAQEVVAEPATAEPAAAEPADAEPAVAAPVAAAPAAEPAPTAPDTRSAPPASTAQPPRA
+VPGAATGTPARAAETDAAESAAPSRLRKALPAVAGVVVLALLAVLAGRWLRSLDPVADFI
+ATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHETRPPANFTPTKDGLF
+SARGNTPKKFSLTIWTHQALDALWLLNGVIFVVLLIVTGHWARIVPTDPHVFQHALSAGI
+QYLSLDWPTENGWVHYNALQMLSYALVVFVAAPLAALTGWRMSSWFPTEAKGLNKAFPME
+VARKVHFPVMVFFVAFIVVHVFLVAFTGLLTNLNHMYTSRGGATDAWGLVVFLVSVAVTA
+AAWFFLKPAFTAPVASRFGTVGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000332.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000332.fa
new file mode 100644
index 0000000000000000000000000000000000000000..872466cacd5777075bd4ba7c2ad92e5a8a76dcd6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000332.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_233
+MICRVATGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA
+AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA
+AAVTAGDEDGPLLECWTRPLAWDAAGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMA
+EFVAAGRLPRGAETRVPMPGLLAARPESLPTADPDVRPAVDAAATAGARFAPKPELANPS
+GAVHGGAMTLRAVTAAQAAMPDRERYDVQAVRVVFVRPGHGEMVALTRVRHAGRSLRLVD
+VDLVPVGADGVPVADKPMVQVQVTFRAARS*
+>NZ_CP033200.1_2202
+MISRVAAGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA
+AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA
+AVAAGDEDGPLLECWTRPLSWDAAGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMAE
+FVAAGRLPRGAETRVPMPELLAARPESLPTADPDTRPAVAAAPTAGARFAPKPELANPSG
+AVHGGAMTLRAVTAAQAAMPDRERYDVQAVRVVFVRPGHGEMVALTRVRHAGRSLRLVDV
+DLVPVGADGVPVADKPMVQVQVTFRATRS*
+>NZ_CP040019.1_120
+MRWHGDRAAASGVTALTNILGHPIICDAAGRGRSASVLTVQNSLRPAADSPTGPRAHASG
+RTEQLFGIRRHAAMPERDGALNPAAFEAGPWCLDLDGRPTGAAATVIMDNATAVAVHHAA
+PGVETVVTTELQINVLAPLPAFDAAAITEGRAEGPLLECWTRPLSWDAGGGVGRAWLEDA
+EGRRIVEATGWFQAVPTGAPEHRAAFTAAADLPRGPETRVPMPGLLAARPETLPPAARAG
+RPAVTAAVAPGARFAPKPELANPSGAVHGGAMTLRAVVAAQAAMPDRELYDVQAVRVVFT
+RPGHGEMVALTRVRHAGRSLRLVDVDLVPVGEDGAPVAEKPMVQVQVTFRAAR*
+>NZ_CP083691.1_87
+MDEITLNPDADARWRGPRRLLLGRPEQLAGLRRRETAEIQGDTLHPGDWEVGPWVRDLDG
+RPTGAAACVAADNLTAVALHWAAAEAYDAMVTTQLQVNVLRPLPVFDPADPADRPRLRML
+GTPLSTDALGGCARGVIVDDDGTAYVEATGWFQATPGPMSLALEAFREHAALPVAEADRA
+DLPAVTAVVADSVPAPRPGERPAVSQEMTAGLRFRAEPLLDNPGGMTHGGIQCLRAVLAA
+QAALPDRLEYDVQAVQVVFARPGLGEQVALTRVRHAGRSLRIVEVELVGVDPETGAPQAG
+RPSILAQVSFRAAQG*
+>NZ_CP097650.1_234
+MISRVAAGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA
+AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA
+AAVTAGDEDGPLLECWTRPLAWDAGGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMA
+EFVAAGRLPRGAETRVPMPELLAARPESLPTADPDTRPAVAAAPTAGARFAPKPELANPS
+GAVHGGAMTLRAVTAAQAAMPDRERYDVQAVHVVFVRPGHGEMVALTRVRHAGRSLRLVD
+VDLVPAGADGVPVADKPMVQVQVTFRAARS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000336.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000336.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6cd163f849b39b981b144fae25f4ce53a6e6b837
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000336.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_241
+MKKPPLAQDPIREAARNWERHGWGDVARPMAAITSIMRAQQILLGRAQAALKPYGLTFAR
+YELLALLNFSRENRMRMSKASALLQVHPTSVTNAVDRLEAAGLVERTPHESDRRALVLAL
+TDEGRRVAVAATETLNAEVFGRSGFGPADVDTLIDVLGRFRAEAGDFQVDGPDAGAPATA
+EHTSS*
+>NZ_CP033200.1_2209
+MKKPPLAQDPIREAARNWERHGWGDVARPMAAITSIMRAQQILLGRAQAALKPYGLTFAR
+YELLALLNFSREKRMRMSKASALLQVHPTSVTNAVDRLEAAGLVERTPHESDRRALVLAL
+TDEGRRVAVAATETLNAEVFGRSGFDPADVDTLIDVLGRFRAEAGDFEADGPDAGAPATA
+EHTSS*
+>NZ_CP040019.1_113
+MKNAPLPQDPIREAARNWERHGWGDVARPMAAVTSIMRAQQILLGRTQAALKPFGLTFAR
+YELLALLNFSREKRMRMSKASALLQVHPTSVTNAVDRLESAGLVERTPHESDRRALVLAL
+TDEGRRVAVAATETLNEEVFGRTGFDEADVDALIDVFGRFRAGAGDFEADGADTTTERPS
+A*
+>NZ_CP083691.1_81
+MSTRDPLPQDPIREAARNWEHHGWGEVAAPMAAVTAIMRTQAILLARTQAVLKPFGLTFA
+RYELLALLNFSRERRQLMSKAGALLQVHPTSVTNAVDRLEAAGLVERQPHETDRRALLLA
+LTDEGRRVADAATEALNAEVFGATGFTDDDVAALNEILGRFRAGSGDFEA*
+>NZ_CP097650.1_241
+MKKPPLAQDPIREAARNWERHGWGDVARPMAAITSIMRAQQILLGRAQAALKPYGLTFAR
+YELLALLNFSREKRMRMSKASALLQVHPTSVTNAVDRLEAAGLVERTPHESDRRALVLAL
+TDEGRRVAVAATETLNAEVFGRSGFDPADVDTLIDVLGRFRAEAGDFEADGPDAGAPATA
+EHTSS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000339.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000339.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8aecf49591bcba11b9a71ef39d12b5ef92bf8002
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000339.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_248
+MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKYGSELAEHKAVRTSAGLFDLSHMGEIRV
+TGPEAGAMLDHALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEAGSEPDYLVV
+PNAGNIAAVHTALNQRASGWDAVVEDESSTTALVAVQGPQAERILARAMPEAAAQLAELK
+YYGHLTLTVPTDAGDVTAVVARTGYTGEDGFELFLPAASTAEAGDRGSAVWNTMLSAADE
+AGVELTLCGLASRDSLRLEAGMPLYGNELDTGHQPHASGVGFAVPASKEADFVGRSALVG
+RDDVEEVLVGLQGAGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDLAA
+EGTSLQVDLRGRGEPFTVVATPFYRRER*
+>NZ_CP033200.1_2218
+MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKYGSELAEHKAVRTSAGLFDLSHMGEIRV
+TGPEAGAMLDHALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEAGSEPDYLVV
+PNAGNIAAVHTALNQRASGWDAAVEDESSTTALVAVQGPQAERILARAMPEAAAQLAELK
+YYGHLTLTVPTDAGDVIAVVARTGYTGEDGFELFLPAASTAEAGDRGSAVWNTMLSAADE
+AGVELTLCGLASRDSLRLEAGMPLYGNELDTGHQPHASGVGFAVPASKEADFVGRSALVG
+RDDVEEVLVGLQGAGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDLAA
+EGTSLQVDLRGRGEPFTVVATPFYRRER*
+>NZ_CP040019.1_105
+MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKHGSELAEHKAVRTAAGLFDLSHMGEVRV
+TGPQAGAMLDYALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEDGSEPDFMVV
+PNAGNIAAVHTALNQRASGWDATVEDQSSTTSLVAVQGPKAEAILAQAMPEAAEQLAALK
+YYGHLTLTVPTEAGDVTAVVARTGYTGEDGFELFLPASSTQEAGDRGSAVWNAVLKAAEA
+ADVELTLCGLASRDSLRLEAGMPLYGNELDTAHQPHASGVGFAVPASKEADFVGKAALVG
+KDDAEEVLVGLRGEGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDVAA
+EGTSLQVDLRGRGEPFTVVATPFYRRER*
+>NZ_CP083691.1_73
+MTESTRNSPLHPVHEAAGASFTDFGGWNMPLKYGSELAEHKAVRESAGLFDLSHMGEVRV
+SGPESGAMLDHALSSSISVLKPGRAKYALCLTDAGTVLDDLIVYRTDSGAEGEDQEFLVV
+PNAGNISAVVTALTQRASGWDVEVHDESSTTALVAVQGPQSEAILARLMPASAQELAELK
+YYGHVTLTVPTAAGDVQAVVARTGYTGEDGFELFLPASSTAEAGDRGSAVWSAVVKAAEE
+AGIALTPCGLASRDSLRLEAGMPLYGNELDTAHQPHASGVSFAVPASKEGDFVGKAALVG
+KDEVEEVLVGLKGEGRRAARHGYSVLDADGAVIGEVTSGAPSPTLGHPVAMARIRREHAA
+EGTSVQVDLRGRGEPFTVVPLPFYTRAR*
+>NZ_CP097650.1_247
+MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKYGSELAEHKAVRTSAGLFDLSHMGEIRV
+TGPEAGAMLDHALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEAGSEPDYLVV
+PNAGNIAAVHTALNQRASGWDAVVEDESSTTALVAVQGPQAEKILARAMPEAAAQLAELK
+YYGHLTLTVPTDAGDVIAVVARTGYTGEDGFELFLPAASTAEAGDRGSAVWNTMLSAADE
+AGVELTLCGLASRDSLRLEAGMPLYGNELDTGHQPHASGVGFAVPASKEADFVGRSALVG
+RDDVEEVLVGLQGAGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDVAA
+EGTSLQVDLRGRGEPFTVVATPFYRRER*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000347.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000347.fa
new file mode 100644
index 0000000000000000000000000000000000000000..163188fcfff14a66e1806ec959b468e336b25bc1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000347.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_259
+MARMTTPAEDTLTALIHLLDREGYDAVTADQLARQAGMSRASFFRHLGGKEEVVFADHAA
+LLARLDDFLRGTSLGVREALEEAVLQVFRHHTADPDRARARSRLLRGSQSLRTRELLTSH
+RYTELFSGWLATALPDTPARGGVAVGLAAAVVAVHNRALRAWLHAPADDAEAGLRADLAE
+VIARLTAEPAEAERTLAAVRRLLG*
+>NZ_CP033200.1_2228
+MARMTTPAEDTLTALIHLLDREGYDAVTADQLARQAGMSRASFFRHLGGKEEVVFADHAA
+LLARLDDFLRGTSLGVREALEEAVLQVFRHHTADPDRARARSRLLRGSQSLRTRELLTSH
+RYTELFSGWLATALPDTPARGGVAVGLAAAVVAVHNRALRAWLHAPADDAEAGLRADLAE
+VIARLTAEPAEAERTLAAVRRLLG*
+>NZ_CP040019.1_88
+MARMSTPAEDTLTALIHLLDREGYDAVTADQLAREAGMSRASFFRNLGGKEEVVFADHAT
+LLAHLEELLRGTGLGVREALDEAVLQVFRHHTRDPERAQARARLLRGSQALRTRELLTSH
+RYEELFSAWLADALPDTPARGGVAVGLAAAVVAVHNRALRAWLHSPDDDAEAGLRADLAE
+VVARLTAEPSAAERTLEAVRRLLG*
+>NZ_CP083691.1_59
+MNPMTAVPEDTLTALIHLLDRQGYDDVTVDQLAREAGMSRASFFRHVGGKEEVVFADHEQ
+LLPRLEDLLHSTSLPLPTALREAGLQVFRHHVQHPERARARARLLRGSRALRTRELLASH
+RYEQLFSRWLAERLPDTPTRGSVAVGLAAAVVAVHNAALRGWLHAEAPDPTAAEAALGAQ
+LDEVILRLTREPGEAEVRLAAVRALLD*
+>NZ_CP097650.1_257
+MARMTTPAEDTLTALIHLLDREGYDAVTADQLARQAGMSRASFFRHLGGKEEVVFADHAA
+LLARLDDFLRGTSLGVREALEEAVLQVFRHHTADPDRARARSRLLRGSQSLRTRELLTSH
+RYTELFSGWLATALPDTPARGGVAVGLAAAVVAVHNRALRAWLHAPADDAEAGLRADLAE
+VIARLTAEPAEAERTLAAVRRLLG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000350.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000350.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c9878551f6a1afa7b827fc02f693786dabdb81a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000350.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_262
+MPDTPQPPAVPAHPDHFGFEVTHRLETPGHDGAPLGRTGVITTPHGRIQTPAFIPVATQA
+TVKAVLPESMKDLGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTDSGGFQVM
+SLGSGFKKVIDMKGPGAPEGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRHRFTPEVS
+VGIQHNLGADIMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVRAARPYQA
+LFGVIQGAQYEDLRRKACRDLAGMRAEFPAAGELDGVTSGFDGYGVGGALEKENLGTIVG
+WCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDGRYNLPGA
+KYRRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLLSIHNERFTVSLVDRIRAAM
+QDGTLAELKAETLGRYYAPKG*
+>NZ_CP033200.1_2233
+MPDTPQPPAVPAHPDHFGFEVTHRLETGGADGAPLGRTGVITTPHGRIQTPAFIPVATQA
+SVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTDSGGFQVM
+SLGSGFKKVIDMKGPGAPEGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRHRFTPEVS
+VGIQHNLGADIMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVRAARPYQA
+LFGVIQGAQYEDLRRKACRDLAGMRAEFPAAGELDGVTSGFDGYGVGGALEKENLGTIVG
+WCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDGRYNLPGA
+KYRRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLLSIHNERFTVSLVDRIRAAM
+QDGTLAELKAETLGRYYAPKG*
+>NZ_CP040019.1_79
+MPDTSPGPAPSSSSSGAPAHPSHFGFEVTHRLEAGGVDGAPLGRTGVISTPHGQIQTPAF
+IPVATQATVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTD
+SGGFQVMSLGSGFKKVIDMKGPSAPDGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRH
+RFTPEVSVGIQHRLGADVMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVR
+AARPYQALFGVIQGAQYEDLRRKACRDLAAMRADFPSAGELDGVTSGFDGYGVGGALEKE
+NLGTIVGWCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDG
+RFNLPGAKYRRDFGPLDPACDCYTCAHYSRAYIRHLFKAKEMVAHTLISIHNERFTVSLV
+DRIRAALQDGTYAELKEETLGRYYAPKG*
+>NZ_CP083691.1_56
+MPETSAPGTAGPTSSSAVTSDPAHPDHLGFEVRERLDAPGADGIALGRTGVLRTPHGEIQ
+TPAFIPVATQATVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGP
+TFTDSGGFQVMSLGSGFKKVIDMKGPAAPEGQGADDAVAPGKERLANVDDDGVWFKSHLT
+GDRHRFTPERSLQIQHNLGADVMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARL
+TAERAGRPYQGLFGVIQGAQYEDLRRKACRDLSGMTAEFAAAGERPATAHGFDGYGIGGA
+IEKENLGTIVGWCAQELPEDRPRHLLGISEPDDLFRAVENGADTFDCVSPTRVARTGAFY
+TRDGRYNLPGATYKRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLISIHNERFT
+VSLVDRIRASIQAGTFAELKAETLGRYYAPKG*
+>NZ_CP097650.1_260
+MPDTPQPPAVPAHPDHFGFEVTHRLETGGADGAPLGRTGVITTPHGRIQTPAFIPVATQA
+SVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTDSGGFQVM
+SLGSGFKKVIDMKGPGAPEGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRHRFTPEVS
+VGIQHNLGADIMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVRAARPYQA
+LFGVIQGAQYEDLRRKACRDLAGMRAEFPAAGELDGVTSGFDGYGVGGALEKENLGTIVG
+WCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDGRYNLPGA
+KYRRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLLSIHNERFTVSLVDRIRAAM
+QDGTLAELKAETLGRYYAPKG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000351.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000351.fa
new file mode 100644
index 0000000000000000000000000000000000000000..87b6623df5ea0d0b28d6751752ced4a8cbdeb3b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000351.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_267
+MTTPTGAIPSPHPRPFLLVQTRPEDDAAAAEVEAVQRLGGYPEGRLRVLRLDRVVQRPDV
+ATHGLDWEAELADVAAVILPGSPFTGSDPEETKSPVQRAVEAELGRMLDVVRRRDLPFLG
+CCYGVGTLGRHAGGVVDNAYGESAAPVEVTLTDEGAADPLLAGVPRTFAAYVGHKEAMSA
+LPPGAVLLAAGTDCPVQMFRLGTRQYATQFHPELDQAGILERLEIYRDHGYFAPGEYEPT
+VAGLAAVDPEHPRRILANFRTLFG*
+>NZ_CP033200.1_2238
+MTTPTGAIPSPHPRPFLLVQTRPEDDAAAAEVEAVQRLGGYPEGRLRVLRLDRVVQRPDV
+ATHGLDWEAELADVAAVILPGSPFTGTDPEETKSPVQRAVEAELGRMLDVVRRRDLPFLG
+CCYGVGTLGRHAGGVVDNAYGESAAPVEVTLTDEGAADPLLAGVPRTFAAYVGHKEAMSA
+LPPGAVLLAAGADCPVQMFRLGTRQYATQFHPELDQAGILERLEIYRDHGYFAPGEYEPT
+VAGLAAVDPEHPRRILANFRTLFG*
+>NZ_CP040019.1_72
+MSTPSAPQPAPSADAPPSGRPFLLIQTRPEDEAARAEEEAVRRLGGFAEHQLAALRLDRT
+LDADPDARQDWAALVAGHAGVILSGSPYTSSVPQETKDELQVAVELELGRMLDAVLDADA
+PFLGCCYGVGTLGAHAGGTVDGTHAEPAGPTDVTLTEAGAADPLLEGLPPRFTAYVGHKE
+GLTVPPPGAVVLATGEACPTQMFRLGRRQYATQFHPELDQVGLVERLRIYLHHGYVDPED
+AEDTFARIESTPAPVPPRILENFRRVFG*
+>NZ_CP083691.1_55
+MTETTAPAADAAAPRPFLLVQTRPEEDAAAAEAESVRRLGGYDDATLRVLRLDRRVLDAE
+GEAHAGAVDWEAELADVAGVILPGSPFTGSDPEESKSDLQVAVEAELGRLMALVLARQTP
+FLGCCYGVGTLGRAAGGVVDTTYRELPGPIDVALTSEGLRDPLLEGMPAEFAAYVGHKEA
+VRELPPGAVLLATGQACPVQMFRVGEHLYATQFHPELDQAGLLERLEIYADHGYFAAHEA
+DDMFAAIRAREAPIPPRILERFRAIYG*
+>NZ_CP097650.1_265
+MTTPTGAVPSPHPRPFLLVQTRPEDDAAAAEVEAVQRLGGYPEGRLRVLRLDRVVQRPDV
+ATHGLDWEAELADVAAVVLPGSPFTGSDPEETKSPVQRAVEAELGRMLDVVRRRDLPFLG
+CCYGVGTLGRHAGGVVDNAYGESAAPVEVTLTDEGAADPLLAGVPRTFAAYVGHKEAMSA
+LPPGAVLLAAGADCPVQMFRLGTRQYATQFHPELDQAGILERLEIYRDHGYFAPGEYEPT
+VAGLAAVDPEHPRRILANFRTLFG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000360.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000360.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e770d431b0a8fed126d7f131809a38714fe96b1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000360.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_282
+MGLALRAARAAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR
+AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHQVQVRAGVRSEESAALLRGFFAAQRD*
+>NZ_CP033200.1_2261
+MGLALRAARAAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR
+AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHRVQVRAGVRSEESAALLRGFFAAQRD*
+>NZ_CP040019.1_56
+MGLALDAARAAGEAGDVPIGAVLVAGDGTVLAAVGNEREQHHDPTAHAEVLALRRGARAL
+AEAGEADGWRLSDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHAVQVRAGVRAEESAALLRGFFAVQRG*
+>NZ_CP083691.1_35
+MGLALDAARTAGEAGDVPIGAVLVDGDGRVLAAVGNEREQHHDPTAHAEVLALRRGAAAL
+AARGDADGWRLAECTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHTVQVRAGVRGDECAALLVDFFAARRPGG*
+>NZ_CP097650.1_289
+MGLALRAARVAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR
+AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVIRDP
+RFNHQVQVRAGVRAEESAALLRGFFAAQRS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000364.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000364.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d9fd21bb11aef68fb3bc3eb7de7257171710a14a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000364.fa
@@ -0,0 +1,60 @@
+>NZ_CP042169.1_286
+MADNATTSFADRALADAPTDYAQLREWVAQIAELTQPDSVQWVDGSEEERDRLADELVAA
+GTLTRLAEDKFPNSFAAFSDPADVARVEDRTFICSEKEEDAGFTNNWMDPAKMHGILDDA
+FTGAMRGRTMYVIPFVMGHLDAEDPKYGVEITDSAYVVLSMRIMARIGQDVLDKMSREQA
+FYVPAVHSVGAPLEPGEQDVPWPCNETKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR
+IASVMARDEAWLAEHMLILKLTNPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLG
+DDITWIRAGKDGEFRVINPETGYFGVAPGTGWSTNPNAMRAISKGNSIFTNVALTDDGGV
+WWEGMTDEVPEHLTDWRGNDWTPEFGTPAAHPNSRFCTPIEQTDMLADEYRDPRGVKLDA
+ILFGGRRKTTVPLVTEAFDWEDGILKGATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA
+GDYLAHWVRESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGKAE
+AEETPIGLVPAAGSLDLSGIEVSAEDLEDALKVDAAEWAEENELIEQWLGRFGESLPAVV
+RERFEAQKARFAQA*
+>NZ_CP033200.1_3
+MADNATTSFADRALADAPTDYAQLREWVAQIAELTQPDSVQWVDGSEEERDRLADELVAA
+GTLTRLAEDKFPHSFAAFSDPADVARVEDRTFICSEKEEDAGFTNNWMDPAKMHGILDDA
+FTGAMRGRTMYVIPFVMGHLDAEDPKYGVEITDSAYVVLSMRIMARIGQDVLDKMSREQA
+FYVPAVHSVGAPLEPGEQDVPWPCNETKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR
+IASVMARDEAWLAEHMLILKLTNPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLG
+DDITWIRAGKDGEFRVINPETGYFGVAPGTGWSTNPNAMRAISKGNSIFTNVALTDDGGV
+WWEGMTDEVPEHLTDWRGNDWTPESGTPAAHPNSRFCTPIEQTDMLADEYRDPRGVKLDA
+ILFGGRRKTTVPLVTEAFDWEDGILKGATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA
+GDYLAHWVRESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGKAE
+AEETPIGLVPAAGSLDLSGLEVSAEDLEDALKVDAAEWAEENELIEEWLGRFGESLPQAI
+RDRFEAQKQRFAQA*
+>NZ_CP040019.1_52
+MADNATTSFADRALQDAPTDYAQLREWVAQVAELTQPDAVQWVDGSEEEYARLADELVAA
+GTLTRLAEDKFPNSFAAFSDPADVARVEDRTFICSEKEEDAGFTNNWMDPEKMHGILDDV
+FAGSMRGRTMYVIPFVMGHLDAEDPKYGVELTDSAYVVLSMRIMARIGQDVLDKMSREQA
+FYVPAVHSVGAPLEPGQEDVPWPCNSTKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR
+IASVMARDEAWLAEHMLILKLTSPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLG
+DDITWIRAGKDGEFRVINPETGYFGVAPGTGWSTNPNAMRAIAKGNSIFTNVALTDDGGV
+WWEGMTDEVPEHLTDWRGNDWTPASETPAAHPNSRFCTPIEQTDMLADEYRDPKGVKLDA
+ILFGGRRKTTVPLVTESFDWEDGILKAATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA
+GDYLAHWVEESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGRAD
+AVETPIGHVPSPEALDLTGIDVSAEDLEDALKVDAEEWAKENELIEEWLGRFGESLPAMV
+RERFEAQKERFARA*
+>NZ_CP083691.1_30
+MADNATTSFTELATKDAPTDYAQLREWVAGIAELTQPDAVHWVDGSQEEYDRLAAELVAA
+GTLTKLNEKKLPNSYAAFSDPADVARVEDRTFICSEKEEDAGFTNNWMDPKEMHGILDDA
+FAGSMRGRTMYVIPFVMGHLDAEDPKYGVEITDSAYVVLSMRIMARIGQDVLDKMSREQA
+FYVPAVHSVGAPLEPGEQDVPWPCNETKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR
+IASVMARDEAWLAEHMLILKLTNPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLG
+DDITWIRAGKDGEFRVINPETGYFGVAPGTGWSTNPNAMRAISKGNSIFTNVALTDDGGV
+WWEGMTDEVPEHLTDWRGNDWTPESGTPAAHPNSRFCTPIEQTDMLADEYRDPRGVKLDA
+ILFGGRRKTTVPLVTEAFDWEDGILKGATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA
+GDYLAHWVKESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGKAG
+AEETPIGLVPAAGSLDLSGIEVSAEDLEDALKVDAAEWAEENELIEEWLGRFGESLPQAI
+RDRFEAQKARFAQA*
+>NZ_CP097650.1_293
+MADNATTSFADRALADAPTDYAQLREWVAQIAELTQPDSVQWVDGSEEERDRLADELVAA
+GTLTRLAEDKFPNSFAAFSDPADVARVEDRTFICSEKEEDAGFTNNWMDPAKMHGILDDA
+FTGAMRGRTMYVIPFVMGHLDAEDPKYGVEITDSAYVVLSMRIMARIGQDVLDKMSREQA
+FYVPAVHSVGAPLEPGEQDVPWPCNETKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR
+IASVMARDEAWLAEHMLILKLTNPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLG
+DDITWIRAGKDGEFRVINPETGYFGVAPGTGWSTNPNAMRAISKGNSIFTNVALTDDGGV
+WWEGMTDEVPEHLTDWRGNDWTPESGTPAAHPNSRFCTPIEQTDMLADEYRDPRGVKLDA
+ILFGGRRKTTVPLVTEAFDWEDGILKGATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA
+GDYLAHWVRESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGKAE
+AEETPIGLVPAAGSLDLSGLEVSAEDLEDALKVDAAEWAEENELIEEWLGRFGESLPQAI
+RDRFEAQKQRFAQA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000369.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000369.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb5d7c7c601f1ad4cc0b18baf7df21b1ac21b322
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000369.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_293
+MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDIGPERARLAAGLLDED
+AHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPAQEPDATSAGA
+AGPVPADHEEPHRDDTAPAETPGPERPGQDSSGRGEPDAQTPDREPSDAVAEDDARQDTD
+HASAAPRPTATPADELTTLTVPAEWTAAPAEEELPFEVEVMRGTESVRLSSRDLPPWLRD
+QLSAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMREHRGEG*
+>NZ_CP033200.1_10
+MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDIGPERARLAAGLLDED
+AHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPVQEPDATSAGV
+AGPVPGGHGEPHRDDAAPADTPGPKRPGQDSSGRGEPDAQTPDRETSDAVAEDDARQDSD
+HASAAPRPTAPSADELTTLTVPAEWTAAPAEEELPFEVEVMRGTESVRLSSRDLPPWLRD
+QLAAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMRERRGEG*
+>NZ_CP040019.1_45
+MEYLVPVLAVVLIGALAFAVSRWMSAARDRQTAGPRTPSGRPLEIGPERARQAAALLDED
+AHRRVYGHIAQSRVMEAVRDYRAHTGRSLKDAVMDVQSLAVHPQVYSVPATEQEAPEEAE
+VRDPRTRPTPPEPARDEAADGERQGTERADVVEEGADDPAADDEPRPEAESDLSAEEGRV
+DDGAASGTEPRPGTSEPARADELTALTVPADWSAAPAEEEPPFEVEVMRGMDSVRLSSQD
+LPPWLRDQLSAMVRDGNLESAAVQLSSHSQLSVPEAYELLRRMRERRGED*
+>NZ_CP083691.1_24
+MEYLVPILAVVVIGGITLLVARRLSGRSQAPTRSATGTGADTVEASPERARTAARRLDEA
+THRAVYGHIAQGRPFEAVRDYRRATGRGVRDAILDIQSLTLHPQVWSLPVQAEPADDASP
+AAADMPSGPPRGPSDGRGRDGESSARPRLRRAEPSEAGPAPDAEPAPGGDAAADPEADGA
+TSRRPGRQAPEELTTLTVPEGWTADPAPEEPPFEVEVMRGEESVRLASQDLPPWLRDQLS
+AMVRDGNLESAAVQLSSHSSLSVPEAFELLRRMKERREGRG*
+>NZ_CP097650.1_300
+MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDIGPERARLAAGLLDED
+AHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPVQEPDATSAGV
+AGPVPDDHGEPHRDDAAPAETPGPKRPGQDSSGRGEPDAQTPDREPSDAVAEDDAQQDTD
+HASAAPRPTATPADELTTLTVPAEWTAAPAEEELPFEVEVMRGTDSVRLSSQDLPPWLRD
+QLSAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMRERRGEG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000370.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000370.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e2cb136e0cec8e459454e6d5f6792df1d459b60
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000370.fa
@@ -0,0 +1,31 @@
+>NZ_CP042169.1_294
+MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+ITADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSYSVEHPAADHDGDVRR
+DDVRTDAGTAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRRDVTDADSVVVKDEHLNV
+GTERRASGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDVEVTTY
+EETPVVNKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDLDGRNDRKDRI*
+>NZ_CP033200.1_18
+MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+TTADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSAADHDGDVRRDDVRTD
+AGAAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRREVTDADSVVVKDEHLNVGTERRA
+SGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDVEVTTYEETPVV
+NKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDLDGRNDRKDRI*
+>NZ_CP040019.1_27
+MDRNMLDQLQNANVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+TTADGITVPFDKAFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSNVDHDRDVRHDDGLRA
+DAGTAGVAGTAGVAGVADRREDTVVDGDRRDVVDGDRRDLVDADRRDVVDGDRDSMVVKD
+EHLQVGTERQATGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDI
+EVTTYEETPVVNKTVEAEKVSLGKRQVQDTETVSEELRHEDVKIDGDATDRDLDGRTDRK
+DRI*
+>NZ_CP083691.1_23
+MDRNALDQLQNGHVFSTDGEKIGSVGQVYLDDVTNEPTFVTVKTGLFGAKETFVPLQQAQ
+TTTDGITVPFTKDFVKDAPNVDADGSLTPEEEQRIYEYYSMDYSAVDTHDRRDVRDAAAA
+GTAGGVVTDRERRDVVDADRRDVVDNDRRDLVDGDADSVVVKDEKLNVGTERRATGRVRL
+RKQSYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDIEVTTYEETPVVNKTVEA
+EKVSLGKRTVQDTETVSEELTHEDVKIDGDDVDGRRR*
+>NZ_CP097650.1_301
+MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+TTADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSAADHDGDVRRDDVRTD
+AGAAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRREVTDADSVVVKDEHLNVGTERRA
+SGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDVEVTTYEETPVV
+NKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDLDGRNDRKDRI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000372.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000372.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b3b8d7a5276e6e2c50b0d84c13dde41fa2e80c2b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000372.fa
@@ -0,0 +1,84 @@
+>NZ_CP042169.1_296
+MTPLPRFAARTAVTTAALALLAPAVALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVE
+LYNPTDQPINLDGWSLQYRSAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQA
+DLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQVPGVADVLGYGATNTFETAAAG
+APSANSDPKSLTRTNGVDTDDNSADFTVTGQVTPTNAAATGGEPTPEPEPQPTPSERITI
+AQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVY
+SPDTVGSVTLGDHVQVTGEAAEHYGLTQIKVAADGVLPVAEPGAVAPTPVEFPLEEADRE
+ALEGMVLAPQGDWTVTDNYSLNQYGSLGVVPGTKPLDNPTSVARPGAEAQAVAAANAQQL
+IVLDDGASTNFMRSPGNQNPLPYLDADQPVRVGAGLEFSTGVILDWRFDAWSFQPLGHLT
+DATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCGAYRDRAGTP
+VTTNGCLPRGAYTPEAFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVE
+ALNAQAGEQRWAYVASPSARPALADEDVIRSAFIYQPAEVTPLGESVILDDQTNFDNARE
+PMAQLFRAADGTAEGAAGTEFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRVGQAEA
+LVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYVSQGALTGEYSYAFGGAVGS
+LDGIYASPSAAAAITGQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGL
+QLDAPVTEPTPEPEPEPTPGETCDGVTDPRGVPGKPANSVREWLRCIGATPGHGGDHPGK
+GHGGDHPGKGRGPVRP*
+>NZ_CP033200.1_20
+MTPLPRFAARTAVTTAALALLAPAVALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVE
+LYNPTDQPINLDGWSLQYRSAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQA
+DLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQVPGVADVLGYGATNTFETAAAG
+APSANSDPKSLTRTNGVDTDDNSADFTVTDQVTPTNAAATGGEPTPEPEPQPTPAERITI
+AQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVY
+SPDTVGSVTLGDHVQVTGEAAEHYGLTQIKVAAGGVLPVAEPGAVAPTPVEFPLEEADRE
+ALEGMVLAPQGDWTVTDNYSLNQYGSLGIVPGTTPLDNPTSVARPGAEAQAVAAANAQQL
+IVLDDGATTNFMRSPGNQNPLPYLDADQPVRVGAGLEFTTGVILDWRFDAWSFQPLGHLT
+DATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCSAYRDRAGTP
+VTTNGCLPRGAYTSEAFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVE
+ALNAQAGEQRWAYVASPATRPALADEDVIRSAFIYQPAEVTPVGESVILDDQTNFDNARE
+PMAQLFRAADGTSEGAAGTDFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRVGQAEA
+LVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYLSQGALTGEYSYAFGGAVGS
+LDGIYASPSAATAITGQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGL
+QLDAPVTEPTPEPEPSPGETCDGVTDPRGVPGKPANSVREWLRCVGATPGHGGDHPGKGH
+GPEHPGKGRGPVRP*
+>NZ_CP040019.1_25
+MTQRTFRLSRPAVALAALTLLAPAVVAGPAHAAPTGDGLVINEVYTNGGSANAVFTHKFV
+ELYNPTDTPISLDGWSLQYRSATGTAAPNGVVALSGTVPAKGHFLIQGGSNGTTGAALPR
+PDLNAGGAFNPAGARGTVVLSDQAGALTALPVGSVTTGQAEGVADLLGYGTSNTFETAAA
+GAPSSNSDPKSLTRTDGVDTDDNAADFTVTAQVTPTSSTGEAPVDPIPDPEPDPEPAPAL
+TIAQIQGDGAATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGSAEDATPGASDGLF
+VYSPDTVGSVALGDHVQVTGEAAEHYGLTQVRVGAAGVTPVAEPAAVAPTAVDFPLSEAD
+REALEGMLLAPTGEWTVTDNYDLNQYGSLGIVPGTEPLPNPTSVAAPGAEAQAVAADNAS
+RLIVLDDGASTNFMRSPGNENPLPYLDADRPVRVGAGLDFTTGVILDYRFDAWSFQPLGH
+LTDATAAAVQPVAVEDTRPEEASPEAVGGNVSVGSFNVLNYFTALGQDFPGCRAYTDRFG
+EPVTTNGCLPRGAYTPEAFARQQEKIAAAIDGLDASVVALEEIENSAKFDLDRDRALAHL
+VDALNAQAGEQKWAYVASPADRPALSEEDVIRNAFVYQPAEVTPVGESVILRDEVNFDNA
+REPLAQHFRAADGTEAGVAGTDFVAVTNHFKSKGGSGAAGDNADSGDGQGAYNGDRTRQA
+QALVAFAEQVADDAGTDRVLLLGDFNAYEKEDPIRVLEEAGYVSQGALTGEYSYTFDGAV
+GSLDGVYASPAASAVVTGQDIWMINANESVALEYSRHDYVAEDLYAPDQWRSSDHNPLLV
+GLQLDAPVVEPEPQPGAGHPGKGKGLDKGAGHPGKGKGLDKGAGHPGHGRVPEAARP*
+>NZ_CP083691.1_21
+MPTPRLRLVRTAATLAAATLLAPAVLALPAQASPAGDSLVINEAYTNGGSAGALFTHKFV
+ELYNPTDQPISLDGWSLQYRSATGTTAPSTTVALSGTVPAKGHFLIQGGSNGATGAALPT
+PDLTTSFNPAGTKGTIVLADQAGTVAGLPTGSVVTDQVAGVADVLGYGATNTFETAASGA
+PAANSDPKSIARTGGADTDDNAADFTVAADVTPQNAAGGGTAPVDPVDPVDPTPAPAPSV
+TVAEIQGTGATSPLEGRRVSTTGVVTAVYSTGGYDGFYIQTAGTGGAEDATPGASDGVFV
+YAPAEVGSVTLGQTVTVTGDVAEYYGLTQVKAEAGGVRQAAEAGAPVTARELAFPLTEAE
+KEAHEGELLAPAGAWTVTDNYDVNQYGSLGLAPGTSPLPNPTSVALPGADAQAVAADNAQ
+RLIVLDDGASTNFFRSPGNQNALPYIDADAPARVGSAVDFRTPVILDYRYGAWSFQPLGH
+LTDANKAEVQPVDIADTRPAEAVREDLGGNVTVGSFNVLNYFTTLGEDVPGCGYYADKDG
+APVSTKGCLPRGAYTEEAFLEQQAKIATAINGMDTSVVALEEIENSEKFGLDRDHALAHL
+VDALNAQAGYAKWAYVASPTVRPALADEDVIRSAFIYQPAEVTPVGESVILDDQVNFANA
+REPMAQAFRVADGSAGGVVGTEFVAITNHFKSKGGSGATGDNVDTGDGQGAYNGDRTRMA
+QALVAFAEQMKVQAGTDRVLLMGDFNSYEKEDPIRVLEAAGYISQGAKTGEYSYTFDGAV
+GSLDGIYASPAADATVTGQDIWMINANESVAFEYSRDNYVGEEFYAPDQWRSSDHNPVLV
+GLQLDAPAAPVVPTPGTRPTPPADQCALITSPRGAKASAGFSASEWMRCAGVHPGKGRGR
+G*
+>NZ_CP097650.1_303
+MTPLPRFAARTAVTTAALALLAPAVALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVE
+LYNPTDQPINLDGWSLQYRSAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQA
+DLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQVPGVADVLGYGATNTFETAAAG
+APSANSDPKSLTRTNGVDTDDNSADFTVTDQVTPTNAAATGGEPTPEPEPQPTPAERITI
+AQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVY
+SPDTVGSVTLGDHVQVTGEAAEHYGLTQIKVAAGGVLPVAEPGAVAPTPVEFPLEEADRE
+ALEGMVLAPQGDWTVTDNYSLNQYGSLGIVPGTTPLDNPTSVARPGAEAQAVAAANAQQL
+IVLDDGATTNFMRSPGNQNPLPYLDADQPVRVGAGLEFTTGVILDWRFDAWSFQPLGHLT
+DATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCSAYRDRAGNP
+VTTNGCLPRGAYTSEAFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVE
+ALNAQAGEQRWAYVASPATRPALADEDVIRSAFIYQPAEVTPVGESVILDDQTNFDNARE
+PMAQLFRAADGTSEGAAGTDFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRVGQAEA
+LVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYLSQGALTGEYSYAFGGAVGS
+LDGIYASPSAATAITGQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGL
+QLDAPVTEPTPEPEPSPGETCDGVTDPRGVPGKPANSVREWLRCVGATPGHGGDHPGKGH
+GPEHPGKGRGPVRP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000373.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000373.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da86396de9ec6d6ec4a93c7ae046a299a21232e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000373.fa
@@ -0,0 +1,72 @@
+>NZ_CP042169.1_297
+MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSADYIGT
+QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA
+GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN
+ELYATTTGAGLKGNEVLDEVAAVNAVADELEAQDAADVIVASYHDGAAGAGELAAERAAR
+AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG
+EVTGLTPRLLARSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY
+QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF
+TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG
+WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG
+YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV
+GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG
+ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKDADHPGKGRVK
+GEDHPGKGRGVQRGAATHPVFSAQAWLTAAGLPR*
+>NZ_CP033200.1_21
+MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSADYIGT
+QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA
+GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN
+ELYATTTGAGLKGNEVLDEVAAVNAVADELEAQDAADVIVASYHDGAAGAGELAAERAAR
+AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG
+EVTGLTPRLLARSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY
+QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF
+TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG
+WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG
+YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV
+GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG
+ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKGADHPGKGRVK
+GEDHPGKGRGVQRGAATHPVFSAHAWLTAAGLPR*
+>NZ_CP040019.1_24
+MSSLFRRHAVATAACTVLVLAPASAAPALAVETVAADETTISLLSFNDFHGALSSDFSGT
+QFADTVEDYRTAFEAQHGERSVLLTSAGDLIGGSASVSNVQQDDPTIDVMNALGLSALAA
+GNHEFDRGLDDLQDRVIPRAEFPVLAANFVDPDTLEPILASHAIFDVNGVSVAVIGAVPN
+ELYATTTGAGLQGNTVLDMVEAVNGVAAELEASGAADVIVASYHEGAAGAGDLAAELGKR
+EVFRSMVEDTHPAVDVIFNGHTHQLYQYETAGDGVARPVLQAGASGSNLAAVELTVDAAG
+EVTAVASRLLDRSTQDPAEAAAESAVTAEVYAIEQEAVAVFEDMQSQVVADLDGSLTTDY
+QKRLDEGGTWRAGGTRSAETTLGNWVADATKQTALNADPEVDLGVVNPGGLRSEILVDAF
+TGGGTFSPKPADLIGKLTLGELLDVAPFGNSISYFDIPGSSIELALEQNWRDDVRTFTLG
+WSENLTWTYDESRPQGEKVTGVWIDGEPLEQDAIYTVATQSFLADDTWVALGDPTAAPDG
+YTAFATGREDFVDLGVLDTQAISDYARLQASAEGAVGPDFAKKGVPVSGAPETVAAGEEI
+VLTLGDLVIDSDDAPAAAEVAVAFEAADGTVTELGSVTVPAGSEEVTLSGIAAPAEAGAG
+ELRMTVRYADGTETIVRHALEVTASEAPVEPTEPTDPTVPADPSEPADPADPTVPADPSE
+PADPADPSDPTDPAAPVEGDDDGDDRDEEHTVPSTVETGDASAWWLAGFGALLGAALLRG
+RRALGLTASSTPAGR*
+>NZ_CP083691.1_20
+MSSIFSRRTAATLACTTLVLAPAAAPALAADASGERTISVLSFNDFHGALSEDFKGTQFA
+DTVEDYRTAFEAQHGEGSTLLTSAGDLIGGSASVSNVQQDNPTIDVMNALGLASLTAGNH
+EFDRGLDDLQGRVADRADFPVLSANFVDPNTKAPVLTSHKVFDVDGVRVAVIGASPNELY
+ATTTGAGLQGNLVVDMVDAVNAVATGIEAADEADVIIASYHDGAAGAAADLSAELGNRAT
+FDAMVERTVPAVDVIFNGHTHQLYQYQTDNGGVPRPIMQAAASGADLAAVELTVDAAGEV
+TAVTPRMLPRSTQDPAEAAAESPVTARVYEIEQQAVDVFTDMQSQVIADLSGSITTDYAT
+RIAAGMGWKAGGTRTAETTLGNWVADSLKHSVSAAEPGVDLGVVNPGGIRSELLVDQTNA
+GGVFSPKPEQLVGKLTMGEVMDVAPFGNTLTYFDLPGSSIKEALEQNWRDGERTFTLGWS
+SNLTWTYDDARAQGDKVTGVWIDGEPLQADRMYTVAAQSFLADDTWVKLGDPSKAPDGYT
+AFATGRQGFVDLGVLDTTAVLSWARAQDAADGAAHPDYAKKGVPVTGAPASVEGGQDVVL
+TLGDLVIDSDGAPAATAVDVAFQGADGAVTELGTVEVPAGQESVTLSGITAPQTAGAGEL
+VMTVRYADGTTAVVRHALEVTASAAPVDPSTPAEPTQPGEPSDPAEPTTPGEPTPSAQPT
+APVEPTAPVEPSAPAEPTAPVEPTAPAESPEPTPTAQPSTPAEPTAPTPSAPAEDGGEHA
+VPGKVQTGDQAIWLVAALGALGAGALVAVRRRAAAR*
+>NZ_CP097650.1_304
+MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSGDYIGT
+QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA
+GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN
+ELYATTTGAGLKGNEVLDEVAAVNAVADELAAQDAADVIVASYHDGAAGAGELAAERAAR
+AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG
+EVTGLTPRLLTRSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY
+QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF
+TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG
+WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG
+YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV
+GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG
+ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKGADHPGKGRVK
+GEDHPGKGRGVQRGAATHPVFSAHAWLTAAGLPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000386.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000386.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa484e796cf41898237f2918411df431976ea007
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000386.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_312
+MAQRFYDTRTAQVRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL
+RVTSVRNVTDIDDKILERSAASHEAGFEASDLYPAREPWWALAYRFEKAFDAAYLALGVR
+RPTYEPRATGHVPEMFALIERLMERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGTEFD
+IHGGGLDLRFPHHENELAQSAAAGDGFARLWLHNGLVTYGGEKMSKSVGNTISPEEMLGM
+ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR
+VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV
+PEGDDAAAGPVSDALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT
+WRLAD*
+>NZ_CP033200.1_36
+MAQRFYDTRTAQVRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL
+RVTSVRNVTDIDDKILERSAASYEAGFEASDLYPAREPWWGLAYRFEKAFDAAYLALGVR
+RPTYEPRATGHVPEMFALIERLMERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGTEFD
+IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVTYGGEKMSKSVGNTISPEEMLGM
+ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR
+VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV
+PEGDDAAAGPVSDALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT
+WRLAD*
+>NZ_CP040019.1_9
+MAQRFYDTRTAQIRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDVLIRWLEATGL
+RVTSVRNVTDIDDKILDRSAASHEEGFEPSALYPAREPWWALAYRFEKAFDAAYLALGVR
+RPTYEPRATGHVPEMFALIERLVERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKEGEPATAVWTSPWGAGRPGWHLECSAMATKYLGAQFD
+IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVAYGGEKMSKSVGNTISPEEMLGM
+ARPKAVRYFLGQAHYRSQLDYRPGALEEAEAAVERIENFTARARTAGAVPPAVDGALADR
+VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAAQDLESAAARLTEVEAMTAVLGLDDV
+PEGDGDGTGPAADALDSLVRSQIEARAQARAEKDWAAADRIRDALAAAGVVVEDGADGAT
+WRLAD*
+>NZ_CP083691.1_5
+MAQRFYDTRSAEIRDFVPLVPGQASVYYCGATVQGMPHVGHVRSAIVFDVLIRWLEATGL
+RVTSVRNVTDIDDKILDRSAASQEPGFEPSEMYPADEPWWALAFRFENAFDAAYLALGVR
+RPTYEPRATGHVPEMLALIERLIERGHAYPAADGSGDVYFDVRSWDRYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKEGEPVTAVWSSPWGAGRPGWHLECSAMSTKYLGGEFD
+VHGGGLDLRFPHHENELAQSAAAGDPFARFWLHNGLVTYQGEKMSKSVGNTISPQEMLAM
+ARPKAVRYFLGQAHYRSQLDYRPGALEEAEAAVERIENFVQRAAAALGAPELTAPLAEHV
+PAAFRAAMEDDLAVPQALAVLHEAVRAGNSALAAGDDAAARARLAEVAAMTAVLGLDDVP
+EASAGGSGPEAAALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGAQGATW
+HLAG*
+>NZ_CP097650.1_319
+MAQRFYDTRTAQIRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL
+RVTSVRNVTDIDDKILDRSAASHEAGFEASDLYPAREPWWALAYRFERAFDAAYLALGVR
+RPTYEPRATGHVPEMFALIERLIERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGAEFD
+IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVTYGGEKMSKSVGNTISPEEMLGM
+ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR
+VPAAFRTAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV
+PEGDDAAAGPVSDALDLLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT
+WRLAD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000390.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000390.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c7284793aca93d3214fc6c331aa878e08f1dae3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000390.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_319
+MSWWPFPRPSASPSPDDDGAPAAAELEEAVAALRQLLRAERHRLRPDSWALAWEMVEQAA
+EYAPAWTRLQRTRPVETQELVLALTGRLEPLLCDFLALPDSEKPTHADAVHARLREQGTE
+HGRLRRRLTRALTARLRAGEEL*
+>NZ_CP033200.1_44
+MSWWPFLRSSASPSPDDDGAPAAAELEEAVAALRRLLRAERHRLRPDSWALAWEMVEHAA
+EYGPAWTRLQRTRPVETQELVLALTGRLEPLLRDFLALPDSEKPAHADAVHARLREQSTE
+HGRLRRRLTRALTARLRAGEEL*
+>NZ_CP040019.1_2628
+MAWWPFRGPSGAPRDDDASTAGRASLEAAVHSLRALMTAERHRLRPDSRDLAWTITERAA
+EYGPAWDRVSAQRPAEAQELLLLLSHRLEPALRDFLDLPDSQKPRHADELHGRLSELQTE
+AQRLGRRLTRALSSRLRARGEL*
+>NZ_CP083691.1_2436
+MAWWARRRLSSSGPAPLGKPPLVAAEELRRLTDELSEILQRESARIRPDAAAVLRSFLNR
+SRALLPAWDRTAPARSAEALAAYELLRDRVLPGLQDWLCLPDHLKPVHADDLLADAQAWE
+GDLSHHAARLTQVLTARGRAVRELDERQ*
+
+>NZ_CP097650.1_326
+MSWWPFLHSSASPSPDDDGAPAAAELEEAVAALRRLLRAERHRLRPDSWALAWEMVEHAA
+EYGPAWTRLQRTRPVETQELVLALTGRLEPLLRDFLAIPDSEKPAHADAVHARLREQSTE
+HGRLRRRLTRALTARLRAGEEL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000391.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000391.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ecda5a73f7d7d77c0eb67a99851585da424c8810
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000391.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_320
+MTEQTPSLEHPQVRKNAERYEIVVDEAGTVAGYTVAIDYDTGDGPTQRIFPHTKVDHGYE
+GRGLASTLVREALKDTVAAGRRIVPVCPYVKDWVNEHDDVAGEVDPAGPEHLQFLESRQD
+*
+>NZ_CP033200.1_45
+MTEQTPSLEHPQVRKNAERYEIVVDDAGTVAGFTVAIDDDTADGPAQRIFPHTKVDHQYE
+GRGLASTLVREALKDTVAAGRRIVPVCPYVKDWVDEHDDVAGEVDPARPEHMQFLESRQD
+*
+>NZ_CP040019.1_2625
+MTENTPTLDAPQVRKVGEKYEIVVDGDGTVAGYTLAIDYEGTDGVAQRIFPHTKMAEEYG
+GRGLASVLVREALKDSVAAGFRIVPVCPYVKQWTQKHDDVAGDVDQARPEHLQFLEEHAR
+RRSEG*
+>NZ_CP083691.1_2433
+MTEQTSSLDHPQVRKNAEKYEIVVDADGTVAGYTLAIDYTAEDGTAEDGTEQRIFPHTKL
+EDAYEGKGLASTLVREALRDTEAAGRRIVPVCPYVKQWADKHADEVEGQVDQPRPEHLQF
+LEKHAQERKQG*
+>NZ_CP097650.1_327
+MTEQTPSLEHPQVRKNGERYEIVVDDAGTVAGFTVAIDDDTADGPAQRIFPHTKVDHEYE
+GRGLASNLVREALKDTVAAGRRIVPVCPYVKDWVDEHDDVAGEVDPARAEHLQFLESRQD
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000392.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000392.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce4f09ce665b93c498e7206d063e3ee9b99c3dce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000392.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_321
+MTAADTPAPRQDPLAFFLDKAVPEAWHAVGPLASAARGAAEQAGLDRQLVELVNLRVSQL
+NGCVFCLDRHTRQGADAGLSVQRLGLLPAWREAGAVYSEQERAALELAEAVTDLPEQEQL
+NYVQASTAAVLTDAQYAAVQWVAIVMNLTNRISILSHHPVRRRDG*
+>NZ_CP033200.1_46
+MTAADTPAPRQDPLAFFLDKAVPEAWHAVGPLASAARAAAEQAGLDRQLVELVNLRVSQL
+NGCGFCLDRHTRQGADAGLSVQRLGLLPAWREAGAVYSEQERAALELAEAVTDLPEQEQL
+NYVQASTAAVLTDAQYAAVQWVAMVMNLTNRISILSHHPVRRRDD*
+>NZ_CP040019.1_2623
+MSAAENPATRKDPLAFYLDKAVPDAWKAVGGLAAAVRTAAEEAGLDRQLVELVNLRVSQI
+NGCGFCLDLHAREGAKAGLNAQRMALLPAWREAEAVYSEQERAALELAEAVTELPEQEQL
+HYVQASTAAALTDAQYAAVQWAAMVMNLTNRISILSHHPVRRRED*
+>NZ_CP083691.1_2431
+MSSPHDDAAPARKDPLAFYLDKAVPEAWVAVGGLAAAARRAAVEAGLDEQLMELVNLRVS
+AINGCAYCLDVHTRKGVGAGLSDQRRGLLSAWREAPEVYTELERAALELAEAVTELPEQE
+QQQYVQLSTHGVLTDAQYAAVQWLAIVMNVTNRISILSHHPVRRHDS*
+>NZ_CP097650.1_328
+MTAADTPAPRQDPLAFYLDKAVPEAWHAVGPLASAARDAAEQAGLDRQLVELVNLRVSQL
+NGCVFCLDRHTRQGADAGLSVQRLGLLPAWREAGAVYSEQERAALELAEAVTDLPEQEQL
+NYVQASTAAVLTDAQYAAVQWVAIVMNLTNRISILSHHPVRRRDG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000394.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000394.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf634d21308982b0e1271245a3010ad26803a427
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000394.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_323
+MSSSEAAAPAHALPRVVGILGAGRAGTALARAIARIPRLSPGTAAPRVMVAGTRRPAAVQ
+RHLTIYAPEAVAVSAEDLAAEAELVVVAVPREALDDVDPLALAGPATRAVVDLTNTWGDE
+PVPAWLDDDAAPGTTRIAERWAAAGLRVPVVRAFSEISHHDLGDAGRATAPRRALAVGTE
+PADATADPAAVAAARDTVIALVTAMGFDAVPYTGLDRAGVLEPGAAGFGTAHDAGRLAAL
+LADAPTG*
+>NZ_CP033200.1_48
+MSSSEAAAPADALPRVVGVLGAGRAGTALARAIARIPRLSPGTAAPRVMVAGTRRPAAVQ
+RHLTIYAPEAVAVSAEDLAAEAELVVVAVPREALDDVDPLTLAGPATRAVVDMTNTWGDE
+PVPAWLDDDGAPGTTRIAERWAAAGLRVPVVRAFSEISHHDLGDAGRATAPRRALAVGTE
+PADATADSAAVAAARDTVIALVTAMGFDAVPYTGLDRAGVLEPGAAGFGTAHDAGRLAAL
+LADAPIG*
+>NZ_CP040019.1_2578
+MSSSEPAAPAALPRAVGILGAGRAGTGVARAIARIPRLSPGLPEVRALVAGTRRPSAVQR
+HLTVYAPAAQAVAAEELAARAEVIVVAVPREDLDDVDPLALAGPGVRAVVDMTNTWGEEL
+LPAWLEAGPDDAPGTARIAARWAAAGLEVPVVRALSEVSHHDLDVHGRAAAPRRALAVGT
+VPAADASDPGAVVAARDAVAALVTAMGFDAVPYEGLERAAVLEPGGAGFGVAHDARELAA
+LLGAGPRG*
+>NZ_CP083691.1_2429
+MPHDAAPRPDQPAAFESLPASVGILGAGRAGTALARAIARIRVLHPGTAAPRVVLAATRS
+PAAVRRHLAIHAPGAEAAHPGDLATDTELTVVAVPREELDEVDPAWLAGPRTLAVVDMTN
+TWGDELVPDWLAAAAAPGLPTMPGSAAIAAHWAEAGLTAPVVRAFSEVSHHELDRDGRAQ
+PPLRALGVGADSPGPARAAVAALVTAMGFEPVEYAPLARAAALEPGTRAFTRPLPADELA
+RELA*
+>NZ_CP097650.1_330
+MSSSEAAPADALPRVVGILGAGRAGTALARAIARIPRLSPGTAAPRVMVAGTRRPAAVQR
+HLTIYAPEAVAVSAEDLAAEAELVVVAVPREALDDVDPLALAGPATRAVVDLTNTWGDEP
+VPDWLDGDGSPGTARIAARWAAAGVRVPVVRAFSEISHHDLGDAGRATAPRRALAVGTEP
+ADTAADPAAVAAARDTVVALVTAMGFDAVPYTGLDRAGVLEPGAAGFGTAHDAGRLAALL
+ADAPTG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000395.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000395.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28fe73e77b65639378223b5ac9bd6fa7bae42bf2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000395.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_324
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEEQRE
+MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA
+KFPQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVEDAPEHIAGYAVANDISMR
+GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFPADARVLTHVNGELRQEDRVADVVFSPAE
+LVSYASQLITLNPGDLILTGTPAGVALARRDAEGRRPWLRPDDVVEVEITGLGRQRNELV
+*
+>NZ_CP033200.1_49
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEERRE
+MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA
+KFAQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVEDAPEHIAGYAVANDISMR
+GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFSADARVLTHVNGELRQEDRVADVVFSPAE
+LVSYASQLVTLNPGDLILTGTPAGVALARRDAEGRRPWLRPDDVVEVEITGLGRQRNELV
+*
+>NZ_CP040019.1_2577
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPECRDVGEYLTAEPQEQRE
+MVESALRAAQEDRSLLLDTSTLVYDTLIPFPTKVFCVGLNYTNHIEETGQNQPEHPTLFA
+KFTQSLTGALDPVEVPEEDHLVDYEGELCIVIGEPGRRIAVEDAKEHIAGYAVANDVSMR
+GWQGRTSEWLQGKVWEASTPVGPWLVTPDELTADARIITRVNGVERQDDRIADVVFSPEE
+LVAYVSQMITLNPGDLIMTGTPAGVAVARKGADGRRPWLQAGDVVEVEITGLGRQRNELV
+*
+>NZ_CP083691.1_2425
+MKLATFRQPDSDASYPGATFAAVLTSFHPQDPQVAVRAVALPECRDVGEFLTAEPQEQKD
+MVREALEAAKEDHGLLLDVSTLVYDTLVPFPTKVFCVGLNYADHIRETGQEKPEHPTLFA
+KFAQSLTGALDPIEVPEEDHRVDYEGELCVVIGEPGRRIAVEDAKDHIAGYAVANDVSMR
+GFQGRTPEWLQGKVWEASTPVGPWLVTADEFPKDARIVTRVNGEVRQDGKVKDVVFSPAE
+LVSYVSQLVTLNPGDLIMTGTPAGVAVARRDGDGRRPWLRADDVVEVEITGLGRQRNELV
+*
+>NZ_CP097650.1_331
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEEQRE
+MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA
+KFPQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVADAPEHIAGYAVANDISMR
+GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFPADARVLTHVNGELRQEDRVADVVFSPAE
+LVSYASQLITLNPGDLILTGTPAGVALACRDAEGRRPWLRPDDVVEVEITGLGRQRNELV
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000398.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000398.fa
new file mode 100644
index 0000000000000000000000000000000000000000..10118a6572f35662fefa341c0bbaa3d22de9b7a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000398.fa
@@ -0,0 +1,75 @@
+>NZ_CP042169.1_327
+MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDV
+VDPTRLDAARGGAEGLDAVARAAHEAGMGVLVDIVPNHVGVATPQANPAWWDVLTHGPEA
+AHAAWFDVDWAAGGGSLLIPVLGDGPDGDADAELNRLVVDEGRLRYWDNVYPLAPGSLEA
+AEAETGLRAAEVFAEADPAKESTAERARLARAVHDRQHYRLVGWRRGDAELNYRRFFTVT
+TLAGVRVDEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEGYL
+VVEKILEPGEALPADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVVRA
+KHDVATGSLAAETARLVREVRAVHALGAHPDEDVAAAFAAVLARLPVYRTYLPVGLAVLE
+GALADAAEAEPALAAVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSFYRYTRWAN
+LNEVGGDPSHVALSLADFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEPDR
+WAAELAELRRLHPLGHPDAERLLWESIVGVWPTDGTAPEEERILGFLQKASREAALATSW
+TDQDPEFEARLAALAAAVTSPEGPARGVLQAVADRIAEPGLVVQLGHKLVQLAAPGVPDV
+YQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVAAVLRTRRD
+RPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGETVVTVPAGRWED
+AVTGHPVHPDARGAVRLDELLSTLPVALLVPAHAPSDRRERTAP*
+>NZ_CP033200.1_52
+MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDV
+VDPTRLDAARGGAEGLDMVARAAHEAGMGVLVDIVPNHVGVATPRANPAWWDVLTHGPEA
+AHAAWFDVDWAAGGGSLLIPVLGDGPDGDADAELNRLVVDEGRLRYWDNVYPLAPGSLEA
+AEAETGLRAAEVFAEADPASEPTAEQARLARAVHERQHYRLVGWRRGDAELNYRRFFTVT
+TLAGVRVDEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEGYL
+VVEKILEPGEALPADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVVRA
+KHDVATGSLAAETARLVREVRAVHALGAHPDEDVAAAFAAVLARLPVYRTYLPVGLAVLE
+GALADAAAAEPGLADVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSFYRYTRWAN
+LNEVGGDPSHVALSLADFHSAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEPDR
+WAAELAELRRLHPLGHPDAERLLWESIVGVWPTDGTAPEEERILGFLQKASREAALATSW
+TEQDPEFEARLAALAAAVTSPEGPARGVLQAVADRLAEPGLVVQLGHKLVQLAAPGVPDV
+YQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVAAVLRARRD
+RPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGETVVTVPAGRWED
+AVTGHPVHPDARGAVRLDELLSTLPVALLVPAHAPSDRRERTAP*
+>NZ_CP040019.1_2574
+MSTSTERPVPSSTYRLQVGPDLPLESVAGLVPYLRRLGVGWLYLSPILEAEPGSDHGYDV
+VDPTRLDAARGGAEGLEAVARAAREAGLGVLVDIVPNHVGVATPEANPAWWDLLAHGSEA
+AHAPWFDVDWTAGEGRVLLPVLGDGPDGEAEAELDRLVVETGDDGGRLRHWDTRYPLAPG
+SLAAAEEETGLRAADVFAGAEPAHEPTPERARLARAVHARQHYRLIGWRRGDAELNYRRF
+FTVTTLAGVRVEDPEVFDAVHAEPARWVREGLVQGLRVDHPDGLADPAGYVRRLRSHVLP
+EGYLVVEKILEPGEELPADWDVDGTTGYDALGEVERVFMHPVAAGGPNEDERRRRDWDEV
+VAEAKRDVATGSLVAETARLVREVRGVHALGAHADEDVAAAFAAVLSRLPVYRTYLPVGL
+AVLERALADAGEAEPALAPVLADLGPELADPDSPVARRFQQTSGMVMAKGVEDRSFYRWT
+RWANLNEVGGDPAHVQLSLDAFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAE
+EPDRWAGELAGLRALHPLGDEGAERLLWESIVGVWPTDGTAPSTERILGFLQKASREAAL
+STTWTDQDPEFEGRLEDLARAVTAPDSPARGAVQAVADRIAEPGLVVQLGHKLVQLAAPG
+VPDVYQGTELPVPSLVDPDNRRPVDFHARADLLDRLDAGHVPGLDDADAAKLAVVAAVLR
+ARRDRPELFTRHRRLDVSGPAAEHAVAFDRGGALAVATRWPVHLAAAGGWGETVVTLPPG
+RWEDAVTGRPVHPDARGAVRLDELLSTLPVALLVPARAEEATP*
+>NZ_CP083691.1_2422
+MSHTDAVSAPASTYRLQVGPDLPLDSVAGLVPYLRRLGVDWLYLSPILAADPGSDHGYDV
+VDPARVDPARGGPEALAALAAAAHEAGMRLLVDVVPNHLGVATPLANPAWADLLAHGPEA
+AHAAWFDVDWEAGDGRVLLPVLGDGPEGDPRGAEAGLDQLIVDPSAGEHGVLRHWDTAYP
+LAPGSLAAAEEETGLRAAEVFAGADPAAPTDDAARLGRAVHDRQHYRLVHWRRGDAELNY
+RRFFTVTTLAGLRVEDPEVFDATHVEIGRWVSEGLVHGLRIDHPDGLTDPGAYLRALRER
+VLPEGYLVVEKILEPGEDLPAAWPVDGTTGYDALGELERVFMPADPDGPAADDAARAAWE
+ALIAEAKRDVATGSLAAETARLVREARAAVVLGAHSDEALTEAFADVLASLDVYRTYLPV
+GAERLAAAVARARAAHPEPADVLDDVARVLADPDSPVARRFQQTSGMVMAKGVEDRSFYR
+WTRWANLNEVGGDPAHLDLPLAGFHALQRARQASWPTTMTALTTHDTKRSEDVRARITAL
+AEEPASWEDALARLRTAHPLDAPGLEELVWESIVGVWPTDGTAPEADRLEEFLLKSAREG
+QEHTSWTAQDDAYEGRLRALAADVVAPDSAARAVVQEIADRIAEPGLTVQLGRKLVQLAA
+PGVPDVYQGTEIPFPTLVDPDNRRAVDFEARADLLDRLDAGHAPTLDEPEAAKLLVVSRA
+LRARRDRPELFHGYRPLDVDGPAAAHLIAFSRGGALALATRLPLTLAAAGGWRETVVSLP
+PGRWRCAVTGRAVTPDARGAVRVDDVLSQLPVALLLPEEETA*
+>NZ_CP097650.1_334
+MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDV
+VDPTRLDAARGGAEGLDMVARAAHEAGMGVLVDIVPNHVGVATPPANPAWWDVLTHGPEA
+AHAAWFDVDWAAGDGSLLIPVLGDGPDGNADAELDRLVVDAEGGRLRYWDNVYPLAPGSL
+EAAETETGLRAAEVFAAADSAKEPTAEQARLARAVHDRQHYRLVGWRRGDAELNYRRFFT
+VTTLAGVRVEEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEG
+YLVVEKILEPGETLPADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVV
+RAKHDVATGPLAAETARLVREVRAVHALGAHPDEDVAAAFAAVLARLPVYRTYLPVGLAV
+LEGALADAAEAEPGLADVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSFYRYTRW
+ANLNEVGGDPSHVALSLADFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEP
+DRWAAELAELRRLHPLGHPDAERLLWESIVGVWPTDGTTPEEERILGFLQKASREAALAT
+TWTDQDPEFEARLAALAAAVTSPEGPARGVLQAVADRIAEPGLVVQLGHKLVQLAAPGVP
+DVYQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVAGVLRAR
+RDRPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGQTVVTVPAGRW
+EDAVTGHPVHPDARGAVRLDELLSTLPVALLVPAHAPSDRRERTAP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000399.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000399.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a976acb564e3d43f1de5a44fbdc018d77dae834
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000399.fa
@@ -0,0 +1,64 @@
+>NZ_CP042169.1_328
+MTEPRPADAPAPGLHPIGSDPVDPAAAERAAVEAARAVPYAVWAPHAESVELVLVDTEPG
+ALRYAEDRWPVAAVVAMDPAAGGWWTPTEDPLAALGLDAAQPPADPGYGYRVDGADPVPD
+PRSRRQPDTVHGPSRRDVAGRSVAWPDEGWAGPPGVESDPTVLQGGGLRGAVLYELHVGT
+FTAEGTLDAAIARLPHLTDLGVTHVELLPVNSFSGPRNWGYDGVAWFAVDESYGGPAAYR
+RFVAAAHAAGLGVVQDVVHNHLGPSGNYLPVFGPYLGPGGTGWGDGLNLDGADSDEVRRF
+VLDNVRFWLEEMRVDGLRLDAVHALRDTRAVHLLEEMAALADGIAARAGRPVPLLAESDL
+NDPRLVLPRQAGGLGLAAAWNDDVHHALHVAATGETHGYYADFAPLEAVAKVMERTYFHD
+GTRSTFRGRDHGRAVPDAVPNHAWVASIQNHDQVGNRAGGDRTAAALSEGALAAEAALLL
+TGPHVPMLFMGEEFAASTPWPFFTSFREPELGDAVRQGRRREFAAHGWDPADVPDPQDPA
+TRDAAVLDWAEAAGGTDGQGRGVRVLAAYRTLIGLRRTLPQLTDPRRDRVRAEVDAARRH
+VRLTRAGEDADVVLLVALGAEPLPVPADLTRAELLAGHGDHGPLGPGTVPAAVPAPGFLL
+LRR*
+>NZ_CP033200.1_53
+MTEPRPADAPAPGLHPIGSDPVDPAADERAAVEAARAVPYAVWAPHAESVELVLVDTEPG
+ALRYAEDRWPVAAVVAMDPAAGGWWTPTEDPLAALGLDAAQPPADPGYGYRVDGADPVPD
+PRSRRQPDTVHGPSRRDVAGRSVAWPDEGWAGPPGVESDPTVLQGGGLRGAVLYELHVGT
+FTAEGTLDAAIARLPHLTDLGVTHVELLPVNSFSGPRNWGYDGVAWFAVDESYGGPAAYR
+RFVAAAHAAGLGVVQDVVHNHLGPSGNYLPVFGPYLGPGGTGWGDGLNLDGADSDEVRRF
+VLDNVRFWLEEMRVDGLRLDAVHALRDTRAVHLLEEMAALADGIAARAGRPVPLLAESDL
+NDPRLVLPRQAGGLGLAAAWNDDVHHALHVAATGETHGYYADFAPLEAVAKVMERTYFHD
+GTRSTFRGRDHGRAVPDAVPNHAWVASIQNHDQVGNRAGGDRTAAALSEGALAAEAALLL
+TGPHVPMLFMGEEFAASTPWPFFTSFREPELGDAVRQGRRREFAAHGWDPADVPDPQDPA
+TRDAAVLDWAEAAGGTDGQGRGVRVLAAYRTLIGLRRTLPQLTDPRRDRVRAEVDAARRH
+VRLTRAGEDADVVLLVALGAEPLPVPADLTRAELLAGHGDHGPLGPGTVPAAVPAPGFLL
+LRR*
+>NZ_CP040019.1_2573
+MTRTRPDSDTAGLRPLGEDRVDPAAAERAAVDAARATPYAVWAPDAETVELVLVTAEPGA
+LHDAEDRWPAAAVVAMDPAAGGWWTPVEDPLAALGLDTAAEDADPGYGYRVDGSDPVPDP
+RSRRQPDTVHGPSRRDVAGQAFAWPDEDRAGQADPAEPQGGGLRGAVLYEMHVGTFTAEG
+TLDSAIERLPHLADLGVTHVELLPVNSFSGPRNWGYDGVAWSAVDESYGGPAAYRRFVAA
+AHAAGLGVVQDVVHNHLGPSGNYLPVFGPYLGPGGTGWGDGLNLDAAHSDEVRRLVLDNV
+RFWLEDMRVDGLRLDAVHALRDGRAVHLLEEMAALADEVAARTGRPVPLMAESDLNDPRL
+VLPREAGGLGLAAAWNDDVHHALHVAATGETHGYYADFAPLEAVAKVMERTYFHDGTRST
+FRGRDHGRPVPDHVPNHAWVASIQNHDQVGNRAAGDRTSAVLSEGSLAAEAALLLAGPHV
+PMLFMGEEFAAATPWPFFTSFREEELGEAVRQGRRREFAAHGWDPAQVPDPQDPATRDSA
+VLDWSETEGDGRGARVLAAYRTLIGLRRTLPQLTDPRRDRVRAEVDAPRRHVRLTRAGEE
+ADVVLLAALGEEPLPVPADLAGAELLAGHGDDGPLAPGRAPAAVPAPGFLLLRR*
+>NZ_CP083691.1_2421
+MSTPAGRPAADLPVDPLDSPLPVDPLDSPLPVDPLDPAGAERAAVAAARATPYAVWAPHA
+EAVELVLVDAAAGDLHDTADRWPVTSAHALERGPGGWWLPGADARAAAAALQDGNPGYGF
+RVDGADPVPDPRSRRQPDTVHGPSRRDLEAADFPWTDADWTGPAGVEKDPAAPQGGGLRG
+AVLYELHVGTFTPDGTLDSAIERLPHLVDLGVTHVELLPVNSWSGDRNWGYDGVAWNAVD
+ESYGGPEAYRRFVDAAHAAGLGVVQDVVHNHAGPSGNYLNVLGPYLTDHGTGWGDGPNLD
+GPDSDEVRALILDNVRLWLEEMHVDGLRLDAVHALVDTRAVHLLEEMAVLADGIAARAGR
+PVPLMVEWDRNDPRVVLSRSAGGLGLAGAWDDDVHHALHVAATGETHGYYADFAPLEAVA
+KVMERVYFHDGTRSTFRGHDHGRPVPASVPSHAFVVSIQNHDQVGNRAAGDRTAAALTEG
+ALAAEAALLLAGPFTPMLFMGEEFAATTPWPFFTAHREPELAQAVREGRRREFGAHGWAA
+HEVPDPQDPATRDGAVLDWSALEPAPRGHSGAPSEAEAAAGAAPGGPGRGARILEAYRGL
+LAARRALPALTDPDRSRTRVTVEPGARHVRMDRLAADGSGDAVLLTALGDEPMSVPDDLK
+DAVLVAGHGDAGPLGSSGRPWEVPGSVPAPGFLLLHRAPAAQG*
+>NZ_CP097650.1_335
+MTEPRPADAPAPGLHPIGSDPVDPAAAERAAVDAARAIPYAVWAPHAESVDLVLVDTEPG
+ALHDAEDRWPVAAVVAMAPAAGGWWTPTEDPLAALGLDAAQPPADPGYGYRVDGADPVPD
+PRSRRQPDTVHGPSRRDVAGRVFAWPDEGWAGPPGVESDPAAPQGGGLRGAVLYELHVGT
+FTAEGTLDAAIARLPHLRDLGVTHVELLPVNSFSGPRNWGYDGVAWFAVDESYGGPAAYR
+RFVAAAHAAGLGVVQDVVHNHLGPSGNYLQVFGPYLGQGGTGWGDGLNLDGADSDEVRRL
+VLDNVRFWLEEMRVDGLRLDAVHALRDARAVHLLEEMAALADGIAARAGRPVPLVAESDL
+NDPRLVLPREAGGLGLAAAWNDDVHHALHVAATGETHGYYADFAPLEAVAKVMERTYFHD
+GTRSTFRGRDHGRAVPDAVPNHAWVASIQNHDQVGNRAGGDRTAAALSEGALAAEAALLL
+TGPHVPMLFMGEEFAASTPWPFFTSFREPELGDAVRQGRRREFAAHGWDPADVPDPQDPA
+TRDAAVLDWAEAAGGTDGQGRGVRVLAAYRTLIGLRRTLPQLTDPRRDRVRAEVDAARRH
+VRLTRAGEDADVVLLVALGAEPLPVPADLTRAELLAGHGDHGPLGPGTVPAAVPAPGFLL
+LRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000400.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000400.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9edbb43f3889292c458b2aefdb18e98a9dd0e3ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000400.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_329
+MDTVETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV
+RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV
+TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG
+FAAHLVDAETGELRERLSNGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV
+ASYRRLWDELTGPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH
+AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV
+PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT
+TTMLRAVPPADAD*
+>NZ_CP033200.1_54
+MDTAETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV
+RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV
+TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG
+FAAHLVDAETGELRERLSNGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV
+ASYRRLWDELTEPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH
+AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV
+PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT
+TTMLRAVPPADAD*
+>NZ_CP040019.1_2572
+MSERIVTVDTVETPSPDDRLTVTGAPSGDASEDPATALLALPWSTALEDWPEDVLAALPR
+GISRHVVRFARVGGGVVAVKETTEDLAFREYRLLRRLEGSPAPSVVPVAVVTGRTDGRGE
+PLPAALVTRYLHFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVL
+FRRDAGGFAAHLVDAETGELRERLSTGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPA
+ATPELFVDAYRRLWDELTGPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMML
+AAPVEVHAGYHRRRLTRLTGLQVQENQARRLLVDIEAARRAWDPFLDLEGAAHRWVVEVF
+DPVVRSVPLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRVRRDED
+AVALHPTTTMLRTVPPADED*
+>NZ_CP083691.1_2420
+MDEHEQPRTDPADRLTVTAAPSGDASEDPATSLLALPWERPLEDWPAEVLAALPRGISRH
+VVRFARMGAGVVAVKETTEELAFREYRLLRELEDRPSPSVVPVAVVTGRTREDGTALPAA
+LVTRHLRFSLPYRAVFSERMERRTLVRLMDALALLLVELHLEGFFWGDVSLSNVLFRRDA
+GGFAAHLVDAETGELRERLSTGQREHDLDVARVNIGGELLDLHASGLADPDVDAIATPDL
+FVESYRQLWQQLTEPTVFPRGEPWRMDRRFRRLTELGFEVEEYSLRAADAPGMMVAQPTD
+VNSGYHRRRLERLTGLHVQENQARRLLVDIEAARRSWDPFMDMDHAAHRWVIEVFDPVVR
+SVPLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLDEAVDSYVETVLRARRDEDALALH
+PTTTMLRAVPAPEADPEG*
+>NZ_CP097650.1_336
+MDTAETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV
+RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV
+TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG
+FAAHLVDAETGELRERLSTGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV
+ASYRRLWDELTEPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH
+AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV
+PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT
+TTMLRAVPPADAD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000401.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000401.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de04ed88dd8c2c547717c406d2207fa0cc5c32ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000401.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_330
+MARNTSGSHTSATDARARARQIQEEQRRKDRRRRTGVIWGSVLAAVLVIGLVVAFALTRN
+GDDAAAAGPIPAAANEQGGIELTSATGLAEGAGEREVDPSEIEVPKQAASSQPETLPNTE
+ARGDGEPTRIVLYADFNCVHCADFESSNAEQIEQWLEQGEVTVEYRMVDFLSAPNNQNYS
+ARAANAAYCVADQKPEAYNGFVAALFAAYDEHQGKGLDNAALTQLAQEQGVDISSCVEDG
+TFRSAVEHTTRQARVAGVAGTPTVFVDGKNWALDGEDKTFTDWAGAKIAD*
+>NZ_CP033200.1_55
+MARNTSGSHTSATDARARARQIQEEQRRKDSRRRTGVIWGSVLAVVLVIGLVVAFVLNRN
+GDDAAAAGPIPAVANEQGGIELTSATDLAEGAGEREVDPSKIEVPKQAASSQPETLPNTE
+ARGDGEPTRIVLYEDFNCVHCADFESTNGDQIEQWLEQGEVTVEYRMVDYLSAPNNQNYS
+ARAANAAYCVADQKPEAYNGFVSALFAAYDEHQGKGLDNAALTQLAQEHGADIASCVEDG
+TFRSAVEYTTRQARAAGVAGTPTVFVDGKNWALDGEDKTFIEWAGAKIAG*
+>NZ_CP040019.1_2571
+MARNTSGSHTSATDARARARQIQEQQRKKDGRRRTAVIWGSVLAAILVIGLIVAFALNRG
+GDEPAAAGPIPAAANEQGGIELTSATTLAEGAGAREVDASTVEVPEQGAAQQPETIPAAE
+APAEGEPSEIVLYADFNCVYCADFETSNAAQIEQWLEAGEVTVEYRMVDFRSAPNNQNYS
+ARAANAAYCVADQKPEAYNGFVTALFGTYQEHGGKGIDNAALTQLAQDNGADIASCVEDG
+TFRSAVEHTTRQAQAAGVGGTPTVFMDGENWAIGGPDQSFQEWAQSKISG*
+>NZ_CP083691.1_2419
+MASRNPAPSEVDARARARQMQVDQQKKARRRRTATIWGAVLAAVLVIGLIVGFVVKGNQG
+TEISATGPVPGVVNEEGGVEMTSATALADSGKSERQVDSSSVAVPETATAPEELTTIPAA
+GEPADGEPAQIVVYADFNCVHCAEFESQNSEQLQSWLRDGKATVEYRMVNFLSAPNNKNY
+SARSANAAYCVAAAKPEAYNEFTTGLFMAWEGHGGKGLSDDELIQRADALGVDIEGCLKD
+NTYRPAVEWATNKAKAASVAGTPTVFVNGKNWSTDGGDKSFVDWAKPMVEG*
+>NZ_CP097650.1_337
+MARNTSGSHTSATDARARARQIQEEQRRKDSRRRTGVIWGSVLAVVLVIGLVVAFVLNRN
+GDDAATAGPIPAVANEQGGIELTSATDLAEGAGEREVDPSKIEVPKQAASSQPETLPNTE
+ARGDGEPTRIVLYEDFNCVHCADFESTNGDQIEQWLEQGEVTVEYRMVDYLSAPNNQNYS
+ARAANAAYCVADQKPEAYNGFVSALFAAYDEHQGKGLDNAALTQLAQEHGADIASCVEDG
+TFRSAVEYTTRQARAAGVAGTPTVFVDGKNWALDGEDKTFIEWAGAKIAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000403.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000403.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4bfe4fd2d3506112cb285dad02d2877856d82bab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000403.fa
@@ -0,0 +1,59 @@
+>NZ_CP042169.1_332
+MEQEGTQEPARFDPLIAEPPAVPTLIPVLRPAGAEDAAAVGDLALDPEDPGLLDLDPAES
+AHPAAVAVEPTEPLPPVVRPAAADPAPAPAPEPEPEESAEPDAETLPEPAADAPLTEPPL
+SEQVPTSVLAPAEADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENL
+PTQALVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDV
+ETSIIVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVH
+RLVEEIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALG
+MVSTWLVFWLKIQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLL
+PTARFVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLVGFEQLDLAEAGT
+LSYPPLLLLGLVVAAGMADAVVEQSRWPQILACGLVSGAGFGAYLAAQQVGVSDRLVPAV
+AAAAVGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFN
+AAVIVVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG*
+>NZ_CP033200.1_57
+MEQEGTQEPARFDPLIAEPPAVPTLIPVLRPAGAEDAAAVGDLALDPEDPGLLDLDPAES
+AHPAAVAVEPTEPLPPVVRPAAADPAPAPAPEPEPEESAEPDAETLPEPAADAPLTEPPL
+SEQVPTSVLAPAEADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENL
+PTQALVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDV
+ETSIIVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVH
+RLVEEIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALG
+MVSTWLVFWLKIQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLL
+PTARFVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLVGFEQLDLAEAGT
+LSYPPLLLLGLVVAAGMADAVVEQSRWPQILACGLVSGVGFGAYLAAQQVGVSDRLVPAV
+AAAAVGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFN
+AAVIVVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRR*
+>NZ_CP040019.1_2561
+MLAPADADGALPAPDVLPEPDVTVPDPVVPVGPPEKRGRRRGRKAREVFVENLPTQALVL
+ADRLHSSPYGRRMRSTLQQRREAETHALEARTTLDFALKLGETMFSFGAASLDVETSIIV
+VTQAYGILETEVDLTNQSISLNYAPDSSRGESPYTLQRVVRSSSVNFEGLVAVHRLVEEI
+ADGRLDRAEAQRRLVEIRHQPKPFPPVFEILFAGVFVACFIPFIGGNWTGSLLGMISTWL
+VFWLKIQADRARFPEIFSTMFGAIVATVIALAAFALELPVNPAVVIAGGIMMLLPTARFV
+TAVQDAINGFPVTAAGRFLSALLVFTGVMAGIMVAVALGDLAGLEHLDLAEAGTLQHPPL
+LLLALVTAAGMSDAVVEQSRWPQILACGLVSGAGYGVFLAAQQLGIGDRLVPAAAATAVG
+FLGRLVAQRIAAPALVIVLPSMLFLLPGLMMFRSVYGFTVETGSTLLGLAGLFNAAVIVV
+AIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG*
+>NZ_CP083691.1_2416
+MGAEPRRGPAQGTGPLGPDRNPRKDPVRSVDPLAPQDGSPEDGGVPQGARRAGTRPDAAG
+SAPAEPAVHVALLPVLRPADARTPAGASDGDAPAGDGVDLAAAPAREPGPEDVLPPVLAP
+VAAPTVPVETLPTPEPAPAPEEEPTPAADAPLTAPPLSEPVPTSVLAPAEGDAPTAQEAA
+AAVPDVVVPDPLKQHGPEEPRGRRRRRRTREDHRAVFEEVLPTQAIVLVDRLQASPYGKR
+MRSTLRQRRDTEAAALEARTTLDFALKLGETMFGFGATSLDVETSIIVVTQAYGIHETEV
+DLTNQAISLNYAPDSSRGEVPYTLQRVVRTYSTNFEGLVAVHRLVEEISDGTLERAEAQR
+RLVEIRRRPKPYPPAVEILLAGVFVACFIPFIGGTWQGSLLGMVSTWFVFWLHTRTSVFL
+PEIYSVMIGAFLATLIALGAYALHVPVNPAIVVAGGIMMLLPTSRFVTAVQDAINGFPVT
+AAGRFISAMLVFIGIMAGIMVAVGLTDMLGIARLDLAATQSTAYPTTLLLALVVAATACD
+AVVERSGWRTLLASCAVTAAAFAAHTVVAGLGVSAQLLPAAAAAMVGFAGRIVALRVGAP
+PIVVVVPAILFLLPGFAVFRGLYEFTVESASTMAGLAGIVNALVIIVGIGAGAVFGDTLA
+RPVTERLSPARSTPGPEGHTR*
+>NZ_CP097650.1_339
+MEQEGTQEPARFDPRIAEPPAVPTLIPVLRPAGAEDAAAVGDLAIDPEDPGLLDLDPAES
+AHPAAAAVAVEPTEPLPPVVRPAAADPEPEPEEPAEPEAETLPEPAADAPLTEPPLSEQV
+PTSVLAPADADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENLPTQA
+LVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDVETSI
+IVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVHRLVE
+EIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALGMVST
+WLVFWLKVQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLLPTAR
+FVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLLGFEQLDLAEAGTLSYP
+PLLLLGLVMAAGMADAVVEQSRWPQILACGLVSGAGFGAYLAAQQVGVSDRLVPAVAAAA
+VGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFNAAVI
+VVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000406.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000406.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ae1c4ad52ef82ada8379a8c16cb778cb3d11037
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000406.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_335
+MAYQPDRFDEVPEYTDQRGAHRESFAVAGATATGGGRRLSPLLWVAGLVLLAGLFVGVVL
+PWLTGDRSEPVAAESSTTAPAAAPSTSASSVSSSASSASASTASATESATPSEDAVEASR
+SAAAAESSRAAQEAAAAEAAESSQAAASSRAAAEAQAAEASRSEAAAQSAEASRAAAEAQ
+AAEASRSEAAAQSAEASRSAAAVQAAESSRAAASRSAAAAEASRSQSAAASSSRAAAQSA
+AASSSRAAAQSAAVRGTHVTVYNATRTQGLAASYAQRLTGAGYTSVDAKNWSGYGIQSST
+VLYNGSANKAAAEAVGKELGFPVMQTPNLQVNGIAVVVTS*
+>NZ_CP033200.1_60
+MAYQPDRFDEVPEYTDQRGAHRESFAAAGATAAGGGRRLSPLLWVAGLVLLAGLFVGVVL
+PWLTGDRSEPVAAESSTTAPAVEPSPSTSTSASSESSSASSASASTASATESATPSEDTA
+EASRSAAAAAAESSRVAQEAAAAEAAESSRAAESSRAAAEAAESSRAAAEAQAAEASRSE
+AAAQSAEASRSAAAVQAAESSRAAASRSAAAAEASRSQSAAASSSRAAAQSAAASSSRAA
+AQSAAVRGTHVTVYNATRSQGLAASYAQRLTSAGYTSVDAKNWSGYGIQSSTVLYNGSAN
+KAAAEAVGKELGFPVMQTPNLQVNGVAVVVTG*
+>NZ_CP040019.1_2558
+MAYQPDRFDEVPEYTDQRGAHRASFAAPAGAAAAGGGARRFSPLLLVAGLVLLAGLFVGV
+VLPWLTGDRSEPVAAESSASSPAADPSTSSEPASPTEGAATTEPASPSEDAAAAEASRSQ
+AAAQSAAEQSAAEAAAASSRAAEEAAAAEASRSAEAAQAAEASRSAAAAAEASRSAGAAQ
+AAEASRSAEAAQAAEASRSAAAAAEASRSAEAAQAAEASRSAAAAAEASRSAEAAQAAEA
+SRSAAAQAAEASRSAAAQAAAAARSTNVTVYNATRTTGLAASYAQRLRSAGFTSVSAQNW
+GGYGIQSSTVLYNGSGNQAAAEAVAAELGFPVLQTPNLQVNGVAVVVTG*
+>NZ_CP083691.1_2413
+MAYPADRFDDVPEYTDQSGAHRESFAAAPAAAGAAGATAAGTEAAAGGGILKWLLAAAAA
+VLLVGLFLGLVLPRLNGGDDKPVAGAASSSSSSEPAADASSSSSDAPSSDASSSAGPDSA
+APAAPSSDAGAESAAAPSSDAAVESRAAAESSQAAAESSQAAADAQRSRDDAARAASESA
+QAAADASSADAAARERAASESAQAAADASRAAEASRSAEASRSAEASRSAEASRSAEASR
+SAEASRSAAASRSAAAQESADRAVKSTPVNVYNATRRNGLAASYADRLTGAGYTRVTADN
+WPGFRVTSNTVMYNGADKRAAAEAVGRELGMPVQQVPNLQVPGIAVVVVR*
+>NZ_CP097650.1_342
+MAYQPDRFDEVPEYTDQRGAHRESFAAAGATAAGGGRRLSPLLWVAGLVLLAGLFVGVVL
+PWLTGDRSEPVAAESSTTAPAVEPSTSASSESSSASSASASTASATESATPSEDTAEASR
+SAAAAAAESSRVAQEAAAAEAAESSQAAASSRAAAEAQAAEASRSEAAAQSAEASRSAAA
+VQAAESSRAAASRSAAAAEASRSQSAAASSSRAAAQSAAASSSRAAAQSAAVRGTHVTVY
+NATRTQGLAASYAQRLTGAGYTSVDAKNWSGYGIQSSTVLYNGSANKAAAEAVGKELGFP
+VMQTPNLQVNGIAVVVTS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000408.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000408.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff05c177800598bdf1a4d743db2445967061f2ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000408.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_338
+MSIVQIDVEDLRAKSGAVEGSIGRLQAEVSTMEANLRQLQDTWRGQAAANFQGVLTEWRA
+TQQRVEESLAGIRRAMDAAATQYQDAETANAAMFRF*
+>NZ_CP033200.1_63
+MSIVQIDVEDLRAKSGAVEGSIGRLQAEVSTMEANLRQLQDTWRGQAAANFQGVLTEWRA
+TQQRVEESLAGIRRAMDAAATQYQDAETANAAMFRF*
+>NZ_CP040019.1_2555
+MSIVQIDVEDLRAKSGAVEGSIGRLQAEVGAMEAHLRQLQDTWRGQAAANFQGVLTEWRA
+TQQRVEESLAGIRRAMDAAAQQYQDAEAANAAMFRH*
+>NZ_CP083691.1_2410
+MTIVQIDVEDLRAKSGAVEGSIARLQTEVNTMEANLRQLEGTWRGQAAANFQGVLTEWRA
+TQARVEESLGGIRRAMDLAATQYSDTEAANAAMFRL*
+>NZ_CP097650.1_345
+MSIVQIDVEDLRAKSGAVEGSIGRLQAEVSTMEANLRQLQDTWRGQAAANFQGVLTEWRA
+TQQRVEESLAGIRRAMDAAATQYQDAETANAAMFRF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000410.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000410.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e87c95e185ef4319e5119eccbc022dce03ae78c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000410.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_341
+MTSQDSPTRVAGMPRTSTLPAPAPADHRGGRGVVLVLGVAVTAVSALALVALLVAYFLAW
+PASPALFALALFGLPVGFGLMLLHVVLGAVRRSRP*
+>NZ_CP033200.1_66
+MTSQDSPTRVAGMPRTSTLPASAPAADPADHRGGRGVVLVLGVAVTAVSALALVALLVAY
+FLAWPASPALFALALFGLPVGFGLMLLHVVLGAVRRSRP*
+>NZ_CP040019.1_2552
+MLGVTVTAVSFVALLGLLAAYFFSWPAVPALYALAMFGLPVGFSLMLLHVVLGAVRRSRL
+*
+>NZ_CP083691.1_2407
+MPSPRTSPQPRPDAAPAPSGARRALRVLLTAGVVLTVVSGLGLLGALAAYFLHATPAFLP
+ALYAVSLFGLPLGFTLMVLHVVLSAVLRARS*
+>NZ_CP097650.1_348
+MTSQDSPTRVAGMPRTSTLPASAPAADPADHRGGRGVVLVLGVAVTAVSALALVALLVAY
+FLAWPASPALFALALFGLPVGFGLMLLHVVLGAVRRSRP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000412.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000412.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c68cdb220c79ca676c9bfd1dbaa5c08b5f3703f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000412.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_343
+MTTHDDAPRVDHRSPDAEPAEERTAVPPARGRAPRRDELLAADVDTARAGLAGLAAPDEV
+GEHVDVLVDDDRLLTHRFACRLPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGSLVAP
+PWVPYAERVNEEERERLKAVAEGRVPGAPAPDAEGDGTPEAAARG*
+>NZ_CP033200.1_68
+MTTHDDAPRVDHRSPDAEPAPAEERAAVPPARRRAPRRDELLAAAVDAARAGLAGLAAPD
+EVGEHVDVLVDDDRLLTHRFACRMPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGSLV
+APPWVPYAERVNEEERERLKAVAEGRVPGAPAPEAEGDGTLGAAALG*
+>NZ_CP040019.1_2550
+MTDREDATPVEQEQAAPAAEEAVVKAPPARRRAPRRDDLLAAAVDEARAGLAGLAAPEEV
+GEHVDVLVDDDRLVTHRFESRLPGYAGWLWYATIARAPRSRLVTVCETGLVAGEGALVAP
+PWVPYAERVSEEERERLRAVAEGRVPGAAAPAGQPAPEGDGKG*
+>NZ_CP083691.1_2405
+MTEHSDTPGQTDTSGQTHTPEQAPAVAPAGPAADAAPAASARAPRRRAPKRDELLAAAVD
+EARAALTELAEEGQVGPHLGVTVDDDRLMTHRFAAEVPGYTGWVWYSTIARAPRAKKVTV
+CETGLEAGEGAVVAPAWVPYADRVSAEERERLAAVAEGRVPDAG*
+>NZ_CP097650.1_350
+MTTHDDAPRVDHRSPDAEPAPAEERAAVPPARRRAPRRDELLAAAVDAARAGLAGLAAPD
+EVGEHVDVLVDDDRLLTHRFACRMPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGALV
+APPWVPYAERVNEEERERLKAVAEGRVPGAPAPETAPDDRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000414.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000414.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b0327d3eb5d1d96db9640240242bcb92199a79f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000414.fa
@@ -0,0 +1,26 @@
+>NZ_CP042169.1_345
+MTDLIDTTEMYLRTILELEEEGIPPLRARIVERLEHSGPTVSQTVARMERDGLVHVGMDR
+RLELTVAGRERAVSVLRKHRLAERLLADVIGLEWELVHEEACRWEHVMSDQVERRLLTLL
+ENPTETPYGTPIPPRPEQASAEDWSRDMGLAGTRLSEEAATAGRFRVRGLAEGVQTDPDL
+LAQLAGAGVTPGRVVRAEAARDAGYIRVEGEAEDGAAADGGALELAAATAAHVWVERLDG
+*
+>NZ_CP033200.1_70
+MTDLIDTTEMYLRTILELEEEGIPPLRARIVERLEHSGPTVSQTVARMERDGLVHVGTDR
+RLELTVAGRERAVSVLRKHRLAERLLADVIGLEWELVHEEACRWEHVMSDQVERRLLTLL
+ENPTETPYGTPIPPRPEQASAEDWSREMGLAGTRLSEEAATAGRFRVRGLAEGVQTDPEL
+LAQLAGAGVTPGRVVRAQAARDAGYIRVEGEAEDGAAADGGALELAEATAAHVWVERLDG
+*
+>NZ_CP040019.1_2548
+MGLAGTRLSEEAATPGRFRVRGLAEGVQTDPELLAQLAAAGVTPGRTVTAQAAIDPGYVR
+VEGEAADGAPESGALELAVETAAHVWVERLDA*
+>NZ_CP083691.1_2403
+MTDLIDTTEMYLRTILELEEEGTVPLRARIVERLEHSGPTVSQTVARMERDGLVHVGSDR
+RLLLTDEGRERAVAVLRKHRLAERLLSDVIGLDWAYVHDEACRWEHVMSDRVEQRLLEVL
+ENPTATPYGTPIPPRPEAQSAGEWSRDLGLAGEPLATAAATPGRFRVGSLSEGVQADPEL
+LAELQDAGVLPGGVLEAQPALEAGYVRVQGEGSAEALELSAGTAAHVWVQRL*
+>NZ_CP097650.1_352
+MTDLIDTTEMYLRTILELEEEGIPPLRARIVERLEHSGPTVSQTVARMERDGLVHVGADR
+RLELTVAGRERAVSVLRKHRLAERLLADVIGLEWELVHEEACRWEHVMSDQVERRLLTLL
+ENPTETPYGTPIPPRPEQASAEDWSRDMGLAGARLSEEAATAGRFRVRGLAEGVQTDPEL
+LAQLAGAGVTPGRVVRAEAARDAGYIRVEGEAEDGAAADGGALELAEATAAHVWVERLDG
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000415.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000415.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a49e09c62d4d4d3ea9c9a7e6013b95818f1dbc43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000415.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_346
+MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR
+VPHTDAAPVSRKGVLRRDGHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNGAK
+ADRSLEALGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA*
+>NZ_CP033200.1_71
+MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR
+VPHTDAAPVSRKGVLRRDGHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNGAK
+ADRSLEALGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA*
+>NZ_CP040019.1_2547
+MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR
+VPHTDAAPVSRKGVLRRDAHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNALK
+ADRSLESMGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA*
+>NZ_CP083691.1_2402
+MRTLVLNAGYEPVSVVSDRRALLLVATGKASVLEDGDAPMHSPTRAWGRPLVILLHQYVR
+VPHADAAAVSRKGVLRRDGHRCAYCGAHATTVDHVHPRSRGGQNTWENLVACCLRCNSAK
+ADRSLDALGWRLRVVPTRPCGVQWRLRELERPAPAWEGWLQFAA*
+>NZ_CP097650.1_353
+MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR
+VPHTDAAPVSRKGVLRRDGHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNGAK
+ADRSLEALGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000416.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000416.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af6ad252ecd22a58c340a9ad2e85385b4bbb7e42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000416.fa
@@ -0,0 +1,26 @@
+>NZ_CP042169.1_348
+MSQKSRKSRPRPSRPAARPVAESPRSRPTLRDVHVREDLAAAAEREGSPAIPVSALIVTT
+LLVGAYLHLLVLQQMTQLSGGLAMPDSLLFYGQDHIRALSAVMDEDARGQLNWVHKTAGV
+IFPIAVALTVTAVGAWRLRPVGAKWAVFGLGVLFAVVDICENIAIEQAIAAGGPGTGLAA
+ALTLTRWVLLALLALAVAVMLWAGRRRRRGPAARED*
+>NZ_CP033200.1_73
+MSQKSRKSRPRPSRPAARPVAESPRSRPTLRDVNVREDLAAAAEREGSPAIPVSALIVTT
+LLVGAYLHLLVLQQMTQLSGGLAMPDSLLFYGQDHIRALSAVMDEDARGQLNWVHKTAGV
+IFPIAVALTVTAVGAWRLRPVGAKWAVFGLGVLFAVVDICENIAIEQAIAAGGPGTGLAA
+ALTLTRWVLLALLALAVAVMLWAGRRRRGRATRAA*
+>NZ_CP040019.1_2545
+MRGRGPALLDPAPGRQTGTGLGGWSAEVPPLSQKPRKPRKSRPSRASQSGARSGSSAARA
+AGGAERARPTLRDLNIREDLAAAGRQEGSPAIPVSALIVTTLLVGAYLHLLVLQQMTQLT
+GGLAMPDSMLFYGQDHVRALSAVMDDAARGQLNWVHKTAGVIFPIAVALTLAAVGAWRLR
+PAAAKWGALGVGVLFAVVDIAENIAIEQAIAAGGPGTGLAAALTLARWVLLALIALAIVV
+MLWAGRRRREPAARRR*
+>NZ_CP083691.1_2400
+MSKKQKKSRPARTGSSAAPTAEPRRAGLHDVSPRADLADAAQQEGSPAMLITALIGTTLF
+IGAYFHLLVLQQMTQLTGGLAMPDSMLFYGQDHVAALSAVMDDAARGQLNWVHKTAGVIF
+AVAVALTVAAVGAWRLKPVAAKWGALALGVLFAVVDIWEGLAIEAAIAAGGPGTGLAATL
+TAIRWVLLAVITVAVVVMLWAGRRRRPRT*
+>NZ_CP097650.1_355
+MSQKSRKSRPRPSRPAARPVAESPRSRPTLRDVNVREDLAAAAEREGSPAIPVSALIVTT
+LLVGAYLHLLVLQQMTQLSGGLAMPDSLLFYGQDHIRALSAVMDEDARGQLNWVHKTAGV
+IFPIAVALTVTAVGAWRLRPVGAKWAVFGLGVLFAVVDICENIAIEQAIAAGGPGTGLAA
+ALTLTRWVLLALLALAVAVMLWAGRRRRGRATRAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000417.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000417.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76b57e8163aef47a772ac7c1c6db209005b3cba7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000417.fa
@@ -0,0 +1,79 @@
+>NZ_CP042169.1_350
+MADLFSALGRTHLNLDRTRRPADPETALPGLVPPAVTRAAADPEAWGVDARPAAPSHTPE
+SLVAGLNPQQAAAVTHTGAPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEILAITFTN
+KAAAEMRERVAGLIGPTAQRMWISTFHSSAVRLLRNEAANIGLKSTFTIYDSADSLRLVT
+TVAKQHELDPKRFAPKALLNRISSLKNELVEADDYAATVAEGDPWGRAVAAVYRDYTARL
+RQANALDFDDLIGVTVHMFEAFPRVLDNYRRRFRHVLVDEYQDTNHAQYRLIRLLAGPAG
+DPEGVETPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAVTIKLEQNYRSTQTILD
+AANAVIERNPDRRPKRLWTAEGEGPAIVGYAAENESAEAEWIATTIDRLQDEDGIRPADV
+AVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRI
+LNEPKRGIGDRAEGAVAAWAERNRSTFSAALRDAENAPGMAARSLKAVRGFVQMMDDLGQ
+VAESAGPATVLEAVLEQSGMLAALRESEDVQDESRADNLGELVAVVRSFETTHPDGTLSD
+FLEQVALVADADQLPTAPDVEGEALAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPH
+ARSMTDEKELAEERRLAYVGLTRARRRLFLTRAEARSLWGQHQFNPPSQFLGEIPETLID
+WEREGTTRSAGSLSLTGAGTSRYAGRFGGGRPAWRSRDDDGARPQRLTRGDEPADLTVPS
+AVVRGKAPSRVQPQKEIVALSPGDRVSHATFGEGRVDAVAGAGDKTVATVTFDATGAQKR
+LLLRYAPLTKVEG*
+>NZ_CP033200.1_75
+MADLFSALGRTPLNLDRTRRPADPETALPGLVPPAVTRAAADPEAWGEDARPAAPAHTPE
+SLVAGLNPQQAAAVTHTGAPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEILAITFTN
+KAAAEMRERVAGLIGPTAQRMWISTFHSSAVRLLRNEAANIGLKSTFTIYDSADSLRLVT
+TVAKQHELDPKRFAPKALLNRISSLKNELVEADDYAATVAEGDPWGRAVAAVYRDYTARL
+RQANALDFDDLIGMTVHMFEAFPRVLDNYRRRFRHVLVDEYQDTNHAQYRLIRLLSGPAD
+DPEGVETPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAATIKLEQNYRSTQTILD
+AANAVIERNPDRRPKRLWTAEGEGPAIVGYAAENESAEAEWIATTIDRLQDEDGIRPADV
+AVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRI
+LNEPKRGIGDRAEGAVAAWAERNRSTFSAALRDAENAPGMAARSLKAVRGFVQMMDDLGQ
+VAESAGPATVLEAVLEQSGMLAALRESEDLQDESRADNLGELVAVVRSFETTHPDGTLSD
+FLEQVALVADADQLPTAPDVEGEALAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPH
+ARSMTDEKELAEERRLAYVGLTRARRRLFLTRAEARSLWGQHQFNPPSQFLGEIPEALID
+WEREGTTRSAGSLSLTGAGTSRYAGRFGGGRPAWRSRDDDGARPQRLTRGDEPADLTVPS
+AVVRGKAPSRVQPQKEIVALSPGDRVSHATFGEGRVDAVAGAGDKTVATVTFDATGAQKR
+LLLRYAPLTKVEG*
+>NZ_CP040019.1_2544
+MPTAVTRAAADPEAWGGDPESWGRDAAPAHTPDSLVAGLNPQQSAAVTHTGAPLLIVAGA
+GSGKTRVLTHRIAWLLATGRARPHEILAITFTNKAAAEMRERVSGLIGPTAQRMWISTFH
+SSAVRLLRNEAANIGLKSTFTIYDSADSLRLVTTIAKLHELDPKRFAPKALLNRISSLKN
+ELVEADDYASTVAEGDPWGRAVAAVYRDYTARLRQANALDFDDLIGMTVHMFEAFPRVLD
+NYRRRFRHVLVDEYQDTNHAQYRLIRLLAGPAGEPEGVDTPGGELTVVGDSDQSIYAFRG
+ADIRNIVEFEQDFTDAVTIKLEQNYRSTQTILDAANAVISNNPDRRKKDLWTAEGAGAAI
+VGYAAENESAEAEWIASTIDRLQDEDGIRPADVAVFYRTNAQSRALEERLVTRGIPYRVI
+GGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRILNEPKRGIGDRAEGAVAAWAERNRTTF
+SAALRDAEHAPGMATRSLKAVNGFVQMMDDLAQVAESAGPATVLEAVLEQSGMLAALRES
+EDLQDESRADNLGELVAVVRSFEKTTPDGTLSDFLEQVALVADADQLPTAPDVEGESLAE
+AQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPHARSMTDEKELAEERRLAYVGLTRARRR
+LFLTRAEARSLWGQHQFNPPSQFLGEIPEALIDWEREGAVRSAGSLSLTGAGTSRYAGRF
+GSGGGRPAWRSRDDDGGARPQRLTRGDEPTDLTVPSAVVRGRAPSRVQPQKEIVALSPGD
+RVSHATFGQGRVDAVAGAGDKTVATVTFEDSGAQKRLLLRYAPLTKVED*
+>NZ_CP083691.1_2399
+MADLFSSLGRDPLFAPRTRPADPETALPGLVPTAVTRAADPEAGAWGAGRDAGAPSAGPL
+TPEGLVEGLNPQQAAAVQHTGSPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEVLAIT
+FTNKAAAEMRERIAGLIGDTARRMWISTFHSSCVRILRNEAANIGLKSTFTIYDSADSLR
+LVTQIAKVQDLDPKRFAPKALLSRISALKNELVDPEDHASRVAEGDPWGRAVAAVYTEYT
+ARLRQANALDFDDLIGMTVHMFEAFPRVLDGYRRRFRHVLVDEYQDTNHAQYRLIRLLSG
+PAGEPEGVDTPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAATIKLEQNYRSTQT
+ILDAANAVIAHNPDRRKKDLWTAEGEGPRIIGYAAENESAEAEWIASTIDRLQDEEGIRP
+ADVAVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNV
+RRILNEPKRGIGDRAEGAVAAWAERNRVPFFTALRDAENAPGMATRSLKAVQGFVQLMDD
+LAQVAESAGPATVLEAVLEQSGMLAALRESEDLQDESRADNLGELVAVVRAFEKGTPGGT
+LTDFLEQVALVADADQLPAAPDVEGEELAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGV
+FPHSRSLTDEKEMAEERRLAYVGITRARRRLHLSRAEARSLWGQHQFNPPSQFLGEIPDE
+LIEWERAGTDRSFGGLTSLAGAGTSRYANRFSGGGSGSARRGSMTGAWGDRAAGGVGGGL
+ASNRPQRLTRGEEAADLTVPSSVVRGRAPSRVQPQKEVVALSAGDRVEHATFGAGRVDAV
+AGTGDKTVATVTFDATGAQKRLLLRYAPLTRVEG*
+>NZ_CP097650.1_357
+MADLFSALGRTPLNLDRTRRPADPETALPGLVPPAVTRAAADPEAWGEDARPAAPAHTPE
+SLVAGLNPQQAAAVTHTGAPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEILAITFTN
+KAAAEMRERVAGLIGPTAQRMWISTFHSSAVRLLRNEAANIGLKSTFTIYDSADSLRLVT
+TVAKQHELDPKRFAPKALLNRISSLKNELVEADDYAATVAEGDPWGRAVAAVYRDYTARL
+RQANALDFDDLIGMTVHMFEAFPRVLDNYRRRFRHVLVDEYQDTNHAQYRLIRLLAGPAG
+DPEGVETPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAVTIKLEQNYRSTQTILD
+AANAVIERNPDRRPKRLWTAEGEGPAIVGYAAENESAEAEWIATTIDRLQDEDGIRPADV
+AVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRI
+LNEPKRGIGDRAEGAIAAWAERNRSTFSAALRDAENAPGMAARSLKAVRGFVQMMDDLGQ
+VAESAGPATVLEAVLEQSGMLAALRESEDLQDESRADNLGELVAVVRSFETSHPDGTLSD
+FLEQVALVADADQLPTAPDVEGEALAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPH
+ARSMTDEKELAEERRLAYVGLTRARRRLFLTRAEARSLWGQHQFNPPSQFLGEIPEALID
+WEREGTTRSAGSLSLTGAGTSRYAGRFGGGRPAWRSRDDDGARPQRLTRGDEPADLTVPS
+GVVRGKAPSRVQPQKEIVALSPGDRVSHATFGEGRVDAVAGAGDKTVATVTFDATGAQKR
+LLLRYAPLTKVEG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000418.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000418.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6fb2ef78c8b3ccfdfa6c6cc4f9770d98ca5637bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000418.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_351
+MDLYEYQARDLFEAHGVPVLAGIVAQTPDEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVHQVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSALTGIDAETAQKIVTEAGFPEELRADVAEVIQKLWEVF
+EKEDATLVEVNPLVKTGDGTILALDGKVSLDDNAQFRHEDHAALVDERTEDPLEAKAKAN
+GLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEQHGGVKPANFLDIGGGANAEVMANGLD
+VILGDEQVKSVFVNVFGGITACDQVANGIVKALEILGDTATKPLVVRLDGNAVEEGRRIL
+QEANHPLVTLAATMDEGADKAAELAHSAN*
+>NZ_CP033200.1_76
+MDLYEYQARDLFEAHGVPVLAGIVAQTPDEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVHQVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSPLTGIDAETAQKIVTEAGFPEELRADVAEVIQKLWEVF
+EKEDATLVEVNPLVKTGDGTILALDGKVSLDDNAAFRHEGHAALVDERTEDPLEAKAKAN
+GLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEKHGGVKPANFLDIGGGANAEVMANGLD
+VILGDEQVKSVFVNVFGGITACDQVANGIVKALEILGDTATKPLVVRLDGNAVEEGRRIL
+QEANHPLVTLAATMDEGADKAAELAHSAN*
+>NZ_CP040019.1_2543
+MDLYEYQARDLFEAHGVPVLAGIVAQTPEEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVHQVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSPLTGIDAETAQKIVAEAGFPEELRADVADVIQKLWVVF
+EKEDATLVEVNPLVKTGDGKILALDGKVSLDDNAEFRHEGHAALVDERTEDPLEAKAKAN
+DLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEQHGGVKPANFLDIGGGANAEVMANGLD
+VILGDEQVKSVFVNVFGGITACDAVANGIVKALEILGDAATKPLVVRLDGNAVEEGRRIL
+QEANHPLVTLAATMDEGADKAAELAHSAN*
+>NZ_CP083691.1_2398
+MDLYEYQARDLFEKHGVPVLQGIVAETPEEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVNKVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSALTGLDQATADTIVAEAGFPEELRADVAAVIVKLGEVF
+KNEDATLVEVNPLVKTGDGTILALDGKVSLDDNAEFRQADHAGLVDKTTEDPLEAKAKAN
+DLNYVKLDGQVGIIGNGAGLVMSTLDVVAYAGENHGGVKPANFLDIGGGANAEVMAAGLD
+VILGDEQVKSVFVNVFGGITACDAVANGIVKALEILGDSATKPLVVRLDGNAVEEGRRIL
+QEADHPLVTLAATMDEGADKATELAHSAN*
+>NZ_CP097650.1_358
+MDLYEYQARDLFEAHGVPVLAGIVAQTPDEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVHRVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSALTGIDAETAQKIVAEAGFPEELRADVAEVIQKLWEVF
+EKEDATLVEVNPLVKTGDGTILALDGKVSLDDNAAFRHEGHAALVDERTEDPLEAKAKAN
+GLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEKHGGVKPANFLDIGGGANAEVMANGLD
+VILGDEQVKSVFVNVFGGITACDAVANGIVKALEILGDTATKPLVVRLDGNAVEEGRRIL
+QEANHPLVTLAATMDEGADKAAELAHSAN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000428.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000428.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d1be2d8b8d7281f62a5db926d32a0b4aec8507f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000428.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_364
+MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV
+TLCQVLGASPGDVLDAPEVTVVRLADAPAVNLGGEGIRERLITPRGSRDLQILRADIAPR
+GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTFPGREPHSWANPDDRPAV
+VLWTLVGHA*
+>NZ_CP033200.1_97
+MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV
+TLCQVLGASPGDVLDAPEVTVVRLADAPAVSLGGEGIRERLITPRGSRDLQILRADIAPR
+GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTFPGREPHSWANPDDRPAV
+VLWTLVGHA*
+>NZ_CP040019.1_2523
+MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV
+TLCQVLGASPGDVLDAPEVTVVRLSDAPAISLGGEGIRERLITPRGRRDLQILRADIAPH
+GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTLPGREPHSWANPDDRPAI
+VLWTLVGHA*
+>NZ_CP083691.1_1720
+MKSLPLHPTPTTPQVGRRLRALREQARISLADLAQVTGLSKGFLSRVERDLTSPSVASLV
+AVCQALGTSPGHVLDAPEVTVVRGGEAPAISLGGQGITESLLSPPGLRPLQVIRAEIAPG
+GTGEDELYTVDCEVESVHVVSGRLTLRTVDGAHALAAGDTATFSGQEPHSWQNPDPDSPA
+LVLWILAGRT*
+>NZ_CP097650.1_370
+MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV
+TLCQVLGASPGDVLDAPEVTVVRLADAPAVNLGGEGIRERLITPRGSRDLQILRADIAPR
+GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTFPGREPHSWANPDDRPAV
+VLWTLVGHA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000432.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000432.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f91e48a69b3d416e7445e63bdaa041497aae1d70
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000432.fa
@@ -0,0 +1,41 @@
+>NZ_CP042169.1_371
+MPAASDAPTPAPRRGRLAPSGDPTPVENVATHLQEGWNRWHRARALRAGNVPTVMAFTGY
+GSTSWVRILSRVVIASDEEFMNGRRLSKVVADGVRGWRNFVAPPMAYAEVEVQVGDLRTT
+VRTDRMGVVDVVLDVELEPGWQTATLHVGGQEEHAVMDLYICEPGARIGLVSDIDDTVVV
+TSLPRPLLAAWNSFVIDEHARTPTPGIAVLLRRIAELEPKAPVLYLSTGAWNVAQTLTRF
+LGRNLYPLGALLLTSWGPTRDRWFRSGQEHKRVQLERLAEQFPDIQWILVGDDGQHDPEI
+YAEFAQRHPDRVKAIVIRQLTPSQALLAGGRAEDTRRSTPGIPWCYGPDGATLSNQLEDL
+GILPVEFVDVQPEAWREDILGDDEAPATLDAAAQRDDRSTDEEAAR*
+>NZ_CP033200.1_104
+MPAASDAPTPAPRRGRLAPSGDPTPVENVATHLQEGWNRWHRARALRAGNVPTVMAFTGY
+GSTSWVRILSRVVIASDEEFMNGRRLSKVVADGVRGWRNFVAPPMAYAEVEVQVGDLRTT
+VRTDRMGVVDVVLDVELEPGWQTATLHVGGQEEHAVMDLYICEPGARIGLVSDIDDTVVV
+TSLPRPLLAAWNSFVIDEHARTPTPGIAVLLRRIAELEPKAPVLYLSTGAWNVAQTLTRF
+LGRNLYPLGALLLTSWGPTRDRWFRSGQEHKRVQLERLAEQFPDIQWILVGDDGQHDPEI
+YAEFAQRHPDRVKAIVIRQLTPSQALLAGGRAEDTRHSTPGIPWCYGPDGATLSNQLEDL
+GILPVEFVDVQPEAWREDILGDDEAPATLDAPGQRDGRPADEEAAR*
+>NZ_CP040019.1_2517
+MSAVSDAAPVSPRRTRLAALGDPTPVENVATHLQEGWNRWHRSRALRAGHVPTIMAFTGY
+GSTSWVRILSRVVIAPDEEFLNGRRISKVVADGVRGWRNFVAPPMAYAEVEVEVGGTRTT
+VRTDRMGVVDAVLDVEMEPGWRTATLHVGDDEHVTMDLYICHPDARIGLVSDIDDTVVVT
+SLPRPLLAAWNSFVIDEHARTPTPGMAVLLRRVAELEPKAPVLYLSTGAWNVAQTLTRFL
+GRNLYPLGALLLTSWGPTKDRWFRSGQEHKKTQLERLAEQFPDIKWILVGDDGQHDPEIY
+ADFAQRHPDRVAAIVIRQLTPSEALLAGGRAEDTRRSTPGIPWCYGPDGASLSNQLEDLG
+ILPVGFVDVQPEGWKEDILGDDEVLSAAEHGAAALGDEADAPDTAAEPRVPAGEAAVGDG
+AADEAEAAEAGGSR*
+>NZ_CP083691.1_2384
+MPASESASIAAQNDPARRQRLAAAGGPTPAENVATHLQEQWNRWHRSRALRRGFVPTVMA
+FTGYGTTSWVRVLSRVVLAKDEDFLNGRRLSKVVADGVHGWRNFVAPPMAYAEVEVEVGD
+LVTTVRADRMGVVDVVLDVELEPGWRTAVLRVGDEEEVTTDLYIASPDAKVGLVSDIDDT
+VVVTSLPRPLLAAWNSFVIDEHARTPTPGMAVLLRRIAAAEPMAPVLYLSTGAWNVAQTL
+TRFLGRNLYPLGALLLTSWGPTKDRWFRSGQEHKVTQLERLAQQFPDLQWILVGDDGQHD
+PEIYADFATKHPDKVKAIVIRQLTPSEALLAGGRAEATRHSTPGIPWCYGPDGAALSNQL
+EDLGILPVDFVDVHPEGWLEDILGEDEASAAGRDGDEHGVHGGRADQDEARDVDVSAQD*
+>NZ_CP097650.1_377
+MPAASDAPTPAPRRGRLAPSGDPTPVENVATHLQEGWNRWHRARALRAGNVPTVMAFTGY
+GSTSWVRILSRVVIASDEEFMNGRRLSKVVADGVRGWRNFVAPPMAYAEVEVQVGDLRTT
+VRTDRMGVVDVVLDVELEPGWQTATLHVGGQEEHAVMDLYICEPGARIGLVSDIDDTVVV
+TSLPRPLLAAWNSFVIDEHARTPTPGIAVLLRRIAELEPKAPVLYLSTGAWNVAQTLTRF
+LGRNLYPLGALLLTSWGPTRDRWFRSGQEHKRVQLERLAEQFPDIQWILVGDDGQHDPEI
+YAEFAQRHPDRVKAIVIRQLTPSQALLAGGRAEDTRHSTPGIPWCYGPDGATLSNQLEDL
+GILPVEFVDVQPEAWREDILGDDEAPATLDAAAQRDGRSADEEAAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000436.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000436.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc6301720187ea70ca6ba765e0eef4c7ce70605d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000436.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_376
+MRVVVVAESFLPHMNGVTNSILQVLRHLRERGDEAMVVAPAASWSAGWTQRAGAGEAPRE
+VEGFPVRTLPSVPLTGYTSVRVAAGTVGRLRGMLADFAPDVVHIASPFVLGWRAVQAAEE
+LGIPSVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNMATLTLAPSSFTVRQLHRQGVR
+RVHLWGRGVDSRRFHPAKRDEALRAELAPNGEKLVGFVGRLAHEKQVGDLRVLSDLPGTR
+LVVIGSGPLREQLERELPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS
+GVPVVAVGRGGPLDIVDASRTGWLYPPGELDELRRHVADLVYDDVKRAAFADAAWASVQG
+RTWPVLCEQLMGYYEKAIAVQERRRVELARRLLTAPALLAARVFG*
+>NZ_CP033200.1_109
+MRVVVVAESFLPHMNGVTNSLLQVLRHLRERGDEAMVVAPAASWSAGWTQRAGAGEAPRE
+VEGFPVRTLPSVPLTGYTSVRVAAGTVGRLRGMLADFAPDVVHIASPFVLGWRAVQAAEE
+LGIPSVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNMATLTLAPSSFTVRQLHRQGVR
+RVHLWGRGVDSRRFHPAKRDEALRAELAPNGEKLVGFVGRLAHEKQVGDLRVLSDLPGTR
+LVVIGSGPLREQLERELPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS
+GVPVVAVGRGGPLDIVDASRTGWLYPPGELDELRRHVADLVYDDVKRAAFADAAWASVQG
+RTWPVLCEQLMGYYEKAIAVQERRRVELARRLLTAPALLAARVFG*
+>NZ_CP040019.1_2513
+MVAESFLPHMNGVTHSILQVLRHLRERGDEAIVIAPAASWSAGWTQRAGEGQAPREVEGF
+PVHALPSVPLSGYSSVRVAAGTVGRLRGILTAFGPDVVHIASPFVLGWRAVQAAEELGIP
+SVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNTATLTLAPSSFTVRQLHAAGLRRVHL
+WGRGVDTRRFHPVKRDDALRAELAPHGERLIGFVGRLAHEKQVEDLRVLSDLPGTRLVVI
+GSGPLREQLERRLPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMASGVPV
+VAVGRGGPLDIVDPSRTGWLYPPGELDELRRHVADLAHDDVKRSAFAQAAWASVQGRTWP
+VLCEQLVGCYEKAVAVQDRRRRELARRLLAMPSQLTARVFG*
+>NZ_CP083691.1_2380
+MRVAVIAESFLPHMNGVTNSILQVLKHLRSRGDEAVVIAPAASWSAGWTQRAGAGQAPSE
+VEGFPVITLPSMPLSGYASVRVAAGTVLRLRSLLADFAPDVVHIASPFVLGWRAVQAAEE
+LGIPSVAVYQTEVPRYAAKYGAPWLEDVLWNHVTRLHNTATLTLAPSSFTLRQLHHVGVR
+RVHLWGRGVDSTRFHPAKRDEALRAELAPNGERLIGFVGRLAHEKQVADLRVLADLPDTR
+LVIIGSGPLRDQLERRLPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS
+GVPVVAVGRGGPLDIVDSSRTGWIYQPGDLGELRARVADLAYDDAKRAAFAEAAWASMQG
+RTWPVLCEQLVGYYEKAIHVQRRRRGELSRRLLGAPGAVASRAYRVFG*
+>NZ_CP097650.1_382
+MRVVVVAESFLPHMNGVTNSILQVLRHLRERGDEAMVVAPAASWSAGWTQRAGAGEAPRE
+VEGFPVRTLPSVPLTGYTSVRVAAGTVGRLRGMLADFAPDVVHIASPFVLGWRAVQAAEE
+LGIPSVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNMATLTLAPSSFTVRQLHRQGVR
+RVHLWGRGVDSRRFHPAKRDEALRAELAPNGEKLVGFVGRLAHEKQVGDLRVLSDLPGTR
+LVVIGSGPLREQLERELPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS
+GVPVVAVGRGGPLDIVDASRTGWLYPPGELDELRRHVADLVYDDVKRAAFADAAWASVQG
+RTWPVLCEQLVGYYEKAIAVQERRRVELARRLLTAPSLLAARVFG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000439.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000439.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54abe8337b043ec2db940a332027bf120f58cbda
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000439.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_379
+MRIVALVSGSGTNLQAVLDAVASGALDMEIAAVGADVADAGGLERARAHGIETFVVSPKD
+HADRRAWDEALADAVAAYAPDWVVCSGFMRILGAPLLERFDGRILNTHPALLPSFPGAHG
+VRDALAHGVKVTGCTVHVVDAGVDTGPILAQAAVPVLDTDTEAELHERIKVQERALLLRV
+LGELSRR*
+>NZ_CP033200.1_112
+MRIVALVSGSGTNLQAVLDAVASGALDMEIAAVGADVADAGGLERARAHGIETFVVSPKD
+HADRRAWDEALADAVAAYAPDWVVCSGFMRILGAPLLERFDGRILNTHPALLPSFPGAHG
+VRDALAHGVKVTGCTVHVVDAGVDTGPILAQAAVPVLDTDTEAELHERIKVQERALLLRV
+LGELSRR*
+>NZ_CP040019.1_2510
+MRIVALVSGSGTNLQAVLDAVASGALDVEIAAVGADVADAGGLERARAHGIETFVVSPRD
+HADRHAWDVALADAVAAHEPDWVLCSGFMRILGAPLLERFEGRILNTHPALLPSFPGAHG
+VRDALAHGVKVSGCTVHVVDAGVDTGPILAQAAVPVLDTDTESELHERIKVQERALLLRV
+LGELSRR*
+>NZ_CP083691.1_2377
+MRILALVSGSGTNLQAVLDAVASGALPLEVAAVGSDVPGVQGLARAEAAGIPTFTVAPAD
+HPDRAAWNVALAEAVAAYEPDWVVCSGFMRILGAPLLEAFPGRIVNTHPALLPSFPGAHG
+VRDALAYGVKVTGCTVHLVDAGVDTGPILAQAAVPVLDTDTEEVLHERIKVQERVLLLRV
+LGELAAGRSPRQA*
+>NZ_CP097650.1_385
+MRIVALVSGSGTNLQAVLDAVASGALDVEIAAVGADVADAGGLERARAHGIETFVVSPKD
+HADRRAWDEALADAVAAYAPDWVVCSGFMRILGAPLLERFEGRILNTHPALLPSFPGAHG
+VRDALAHGVKVTGCTVHVVDAGVDTGPILAQAAVPVLDTDTEAELHERIKVQERALLLRV
+LGELSRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000441.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000441.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a8994d3e2f4dc964c314dc3fa05653fcf79a47e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000441.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_381
+MLEDTRTPSKERPLVTSAQPTTTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVST
+GSTAQRIAAAGVPVTEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVTQLRELEV
+EPFDLVVVNLYPFVDTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEV
+VQAAQSGGFDLRARRRLAALAFAHTAAYDNAVAAWTAAHFGEDTHADEIPVFPPYAGFSL
+ERAQILRYGENPHQPAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPVP
+AVAIVKHANPCGVAVTDEGTDIAQAHAKAHACDPVSAFGGVIAANRPVTAAMAAQAKDVF
+TEVVVAPSFEPEALEILTAKKNLRLLSLPEGFVRDAVEAKQVSGGMLLQITDAVDADGDD
+PATWTLAAGPAADEATLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLA
+VERANTLGAAQTGGQDVSTAGGAENVSGDGAPERARGAVAASDAFFPFADGLQILLDAGV
+RAVVQPGGSVRDEEVVAAAEAAGVTLYLTGARHFFHG*
+>NZ_CP033200.1_114
+MTSAQPIPTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVSTGSTAQRIAAAGVPV
+TEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVTQLRELEVEPFDLVVVNLYPFV
+DTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEVVQAAQSGGFDLRAR
+RRLAALAFAHTAGYDNAVAAWTAAHFGEDTDADEIPVFPPYAGFSLERAQILRYGENPHQ
+PAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPVPAVAIVKHANPCGVA
+VTDEGTDIAQAHAKAHACDPVSAFGGVIAANRPVTAAMAAQVKDVFTEVVVAPAFEPEAL
+EILSAKKNLRLLSLPEGFLRDAVEAKQVSGGMLLQIADAVDADGDDPATWTLAAGPAADE
+AVLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVSSAGGAENVSGEGAPERARGSVAASDAFFPFADGLQILIDAGVKAVVQPGGSVRDEE
+VVAAAEAAGVTLYLTGARHFFHG*
+>NZ_CP040019.1_2508
+MTSAQPTTTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVSTGSTAQRIAAAGVPV
+TEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVAQLRDLEVEPFDLVVVNLYPFV
+DTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEVVQAAQSGGFDLRAR
+RRLAALAFAHTAGYDNAVAAWTAAHFAEDTEQDDVPIFPPYAGFSLERAEILRYGENPHQ
+PAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPAPAVAIVKHANPCGVA
+VTDEGADVAQAHAKAHACDPVSAFGGVIAANRPVTAVMAAQVKDVFTEVVVAPSFEPEAL
+QILTAKKNLRLLALPEGFVRDAVEAKQVSGGMLLQIADAVDADGDDPATWTLAAGAAADE
+ATLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVTTSEVTTAGGAENVSGEGAPERARGAVAASDAFFPFADGLQILIDAGVRAVVQPGGS
+VRDEEVVAAAEAAGVTLYLTGARHFFHG*
+>NZ_CP083691.1_2373
+MSSAPSVTTVLDEVPLKRALISVYDKTGLEELATGLHAAGVQLVSTGSTAQRIAAAGVPV
+TEVSEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVAQLADLDVEPFDLVVVNLYPFV
+ETVRSGADEDAVVEQIDIGGPSMVRAAAKNHASVAVVVDPARYVDVVAAAQAGGFDLRTR
+RRLASLAFAHTAAYDNAVAAWTAAHFGEDAEDEDAPVFPPYAGFSLERAATLRYGENPHQ
+PAALYVDHEAAPGIAQAELLHGKAMSYNNYVDADAAVRAAFDHAVPAVAIVKHANPCGVA
+VAGEGEDVAVAHAKAHACDPVSAFGGVIAANRPVTRAMAEQVAPIFTEVVVAPSFDEDAL
+EVLTAKKNLRLLALPEGFARDAVEAKQVSGGMLMQIADAVDADGDDPRTWTLAAGEAADE
+ATLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVSSAGGAENVSGEGAPERARGAVAASDAFFPFADGLQILVDAGVKAVVQPGGSVRDQE
+VVDAANAAGITMYLTGARHFFHG*
+>NZ_CP097650.1_387
+MTSAQSIPTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVSTGSTAQRIAAAGVPV
+TEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVTQLRELEVEPFDLVVVNLYPFV
+DTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEVVQAAQSGGFDLRAR
+RRLAALAFAHTAGYDNAVAAWTAAHFGEDTDADEIPVFPPYAGFSLERAQILRYGENPHQ
+PAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPVPAVAIVKHANPCGLA
+VTDEGTDIAQAHAKAHACDPVSAFGGVIAANRPVTAAMAAQVKDVFTEVVVAPAFEPEAL
+EILSAKKNLRLLSLPEGFLRDAVEAKQVSGGMLLQIADAVDADGDDPATWTLAAGPAADE
+AVLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVSSAGGAENVSGEGAPERARGSVAASDAFFPFADGLQILIDAGVKAVVQPGGSVRDEE
+VVAAAEAAGVSLYLTGARHFFHG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000442.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000442.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b978188075e214a8058a58a8b4b5f26af975a2ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000442.fa
@@ -0,0 +1,70 @@
+>NZ_CP042169.1_383
+MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFKDVLPEDQRT
+ADALAELGELVKSPEANVIKLPNISASVPQLRAAIKELQADGYALPEYPDEPKTDEEKDA
+KARYDSVKGSAVNPVLREGNSDRRAPKAVKAYAKRFPHSMGEWTPDSKTAVATMGADDFR
+ANEQSVTLPAADVLTIEFTGEDGKTTVLKEGLKVLKGEVVDGTFMSAKALDAFLAEQVKR
+AKEEGILFSAHLKATMMKVSDPVIFGHVVKAYFSELFEKYGEQLAAAGLSANNGLAAIEG
+GLDKLDAETAEGVRAAIAAAYENGPDVAMVNSAKGITNLHVPSDVIVDASMPAMIRTSGR
+MWNKDDQTQDTLAVIPDSSYAGVYQAVIDDCKANGAYDPTTMGTVPNVGLMAQKAEEYGS
+HDKTFIMDAAGTVAVKNSAGETLLSHDVEAGDIWRACQTKDVPVRDWVKLAVTRARASQT
+PAVFWLDETRAHDRELIKKVEEYLKEHDTEDLDIRILSPVEAAKLSVERIRRGEDTISVT
+GNVLRDYNTDLFPILELGTSAKMLSVVPLLNGGGLFETGAGGSAPKHVQQLVEENHLRWD
+SLGEFLALAVSFEHEAVANENHRARVLADTLDAATGTLLIEGKSPKRKVGELDNRGSHFY
+LALYWARELAKQTEDAELAAAAKPVAEELEAQEETILGELNGVQGSPVDLGGYYWPELEK
+VTSVMRPSATLNAIVDKLSV*
+>NZ_CP033200.1_115
+MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFKDVLPEEQRT
+ADALAELGELVKTPEANVIKLPNISASVPQLRAAIKELQAHGYALPEYPDEPKTDAEKDA
+KARYDSVKGSAVNPVLREGNSDRRAPKAVKAYAKRFPHSMGEWTPDSKTAVATMGADDFR
+ANEQSVTLPAADVLTIEFTGEDGKTTVLKEGLKVLKGEVVDGTFMSAKALDAFLAEQVKR
+AKEEGILFSAHLKATMMKVSDPVIFGHVVKAYFSELFEKYGEQLAAAGLSANNGLAAIEG
+GLDKLDAETAEGVRAAIAAAYENGPDVAMVNSAKGITNLHVPSDVIVDASMPAMIRTSGR
+MWNKDDQTQDTLAVIPDSSYAGVYQAVIDDCKANGAYDPTTMGTVPNVGLMAQKAEEYGS
+HDKTFIMDAAGTVAVKNSAGETLLSHEVEAGDIWRACQTKDVPVRDWVKLAVTRARASQT
+PAVFWLDETRAHDRELIKKVEEYLKEHDTEGLDLRILSPVEATKLSVERIRRGEDTISVT
+GNVLRDYNTDLFPILELGTSAKMLSIVPLLNGGGLFETGAGGSAPKHVQQLLEENHLRWD
+SLGEFLALAVSFEHEAVANENHRAQVLADTLDAATGTLLIEGKSPKRKVGELDNRGSHFY
+LALYWARELAKQTEDAELAAAAKPIAEELEAQEETILAELNGVQGSPVDLGGYYAPEMEK
+VTSVMRPSATLNAIVDKLSV*
+>NZ_CP040019.1_2505
+MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFRDVLPEDQRT
+ADALAELGELVKSPEANVIKLPNISASVPQLRAAIKELQEDGYALPEYPDEPKTDEEKDA
+KARYDSVKGSAVNPVLREGNSDRRAPKAVKNYAKMFPHSMGEWTPDSKTAVATMGADDFR
+SNEKSVTMPADDTLTIEFTGEDGKTTVLKEGLKVLAGEVVDGTFMSAKALDAFLAEQVKR
+AKEEGILFSAHLKATMMKVSDPVIFGHVVKAYFSELFEKYGEQLEAAGLNPNNGLAAIEG
+GLDKLDAETAEGVKKAIAAAYEEGPDVAMVNSAKGITNLHVPSDVIVDASMPAMIRTSGR
+MWNKDDQTQDTLAVIPDSSYAGIYQAVIEDCKKHGAYDPTTMGTVPNVGLMAQKAEEYGS
+HDKTFILESAGTVAVKNAAGETLISHDVEAGDIWRACQTKDVPVRDWVKLAVTRARASQT
+PAVFWLDETRAHDRELIAKVEEYLKEHDTEGLDLRILSPVEAAKLSVERIRRGEDTISVT
+GNVLRDYNTDLFPILELGTSAKMLSVVPLLNGGGLFETGAGGSAPKHVQQLVEENHLRWD
+SLGEFLALAVSFEHEAVANENHRAQVLADTLDAATGTLLIEGKSPQRKVGELDNRGSHFY
+LALYWARELAKQTEDAELVAAAKPVAEELEAQEETILAELNGVQGSPVDLGGYYWPELEK
+VTSVMRPSATLNAIVDKLSV*
+>NZ_CP083691.1_2370
+MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFNDLLPEEQRV
+NDALAELGELVKTPEANVIKLPNISASVPQLRAAIKELQADGYALPEYVDDPQTDKEKDA
+RKRYDSVKGSAVNPVLREGNSDRRAPKAVKNYAKKFPHSMGAWTADSKTAVATMGQDDFR
+SNEKSVTMPKDDVLSIEFTGQDGTTKILKEGLKVLEGEVVDGTFMSAKALDAFLAEQVTR
+AKEEGVLFSAHLKATMMKVSDPVIFGHVVKAYFADLFAQYGEQLAAAGLDPNNGLAAIEA
+GLDKLDAETAEGVRKAIADAYQNGPDVAMVNSDKGITNLHVPSDVIVDASMPAMIRTSGH
+MWDKDGAERDTLAVIPDSSYAGIYQVVIDDCKANGAYDPTTMGTVPNVGLMAQKAEEYGS
+HDKTFVMEADGTVEVKDSAGEVLFSHEVEAEDIWRACQTKDVPVQDWVKLAVTRARASQT
+PAVFWLDETRAHDRELIKKVEQYLQGHDTEGLDLRIMSPVEATKFTVERMRRGEDTITVT
+GNVLRDYNTDLFPILELGTSAKMLSIVPLINGGGLFETGAGGSAPKHVQQLVGENHLRWD
+SLGEFLALAVSFEHEAAHNGNHRAQVLADTLDAATGILLIEGKSPERKAGQLDNRGSHFY
+LALYWAQELAKQTADAELAAAAKPVAEELEAQEETILAELNGVQGSPVDLGGYYAPSMDK
+VSEVMRPSATLNGIIATLGA*
+>NZ_CP097650.1_389
+MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFKDVLPEEQRT
+ADALAELGELVKSPEANVIKLPNISASVPQLRAAIKELQADGYALPEYPDEPKTDEEKDA
+KARYDSVKGSAVNPVLREGNSDRRAPKAVKAYAKRFPHSMGEWTPDSKTAVATMGADDFR
+ANEQSVTLPAADVLTIEFTDEDGETTVLKEGLKVLKGEVVDGTFMSAKALDAFLAEQVKR
+AKEEGILFSAHLKATMMKVSDPVIFGHVVKAYFSELFEKYGEQLAAAGLSANNGLAAIEG
+GLDKLDAETAEGVRAAIAAAYENGPDVAMVNSAKGITNLHVPSDVIVDASMPAMIRNSGR
+MWNKHDQTQDTLAVIPDSSYAGVFQAVIDDCKANGAYDPTTMGTVPNVGLMAQKAEEYGS
+HDKTFIMDAAGTVAVKNSAGETLLSHDVEAGDIWRACQTKDVPVRDWVKLAVTRARASQT
+PAVFWLDETRAHDRELIKKVEEYLKEHDTEDLDIRILSPVEAAKLSVERIRRGEDTISVT
+GNVLRDYNTDLFPILELGTSAKMLSVVPLLNGGGLFETGAGGSAPKHVQQLVEENHLRWD
+SLGEFLALAVSFEHEAVANENHRARVLADTLDAATGTLLIEGKSPKRKVGELDNRGSHFY
+LALYWARELAKQTEDAELAAAAKPIAEELGAQEETILAELNGVQGSPVDLGGYYWPELEK
+VTSVMRPSATLNAIVDKLSV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000443.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000443.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e4e5ce69cca378b87c570d28f9e0f596f5a0bd89
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000443.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_384
+MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPEDSEPPAAAIGRLLETLMDR
+LVALDPETADREMNPRPVEPRPGASQPVADALAAYAAGDVAALDALDVTQPGTAFRQRAW
+RELRGIAPGSPATYGGLAERCGAPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY
+GTAAKQALLAHEAAHAG*
+>NZ_CP033200.1_116
+MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPGDSEPPAAAIGRLLETLMDR
+LVALDPETADREMNPRPVEPRPGVSQPVADALAAYTAGDVAALDALDVAQPGTAFRQRAW
+RELRGIAPGSPATYGGLAERCGAPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY
+GTAAKQALLAHEAAHAG*
+>NZ_CP040019.1_2504
+MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPEGAEPHAAAIGRLLEALMDR
+LEALDPATADREMNPRPVEPHPGVSQPVADALAAYAAGDVAALDALEVAQPGTAFRQRAW
+RELRGIAPGSPATYGGLAERCGTPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY
+GTAAKRALLAHEAAHAG*
+>NZ_CP083691.1_2368
+MTHPPAFLPELRWTAATLPGTSLALVAVYSPEDDAVRASGVAVPEGAEPPAAAIGRLLLE
+LMDRLEELAPETAAREMDPRPVEPREGLDQTVADALAAYAAGDVDALDGLAVVQPGTAFR
+QASWEALRSITPGSPVAYGELATRAGAPKAVRAAGGACAANLAAVVVPCHRVVPASGGVG
+SYLYGSAAKAALLAHEAAHAPA*
+>NZ_CP097650.1_390
+MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPEDSEPPAAAIGRLLETLMDR
+LVALDPETADREMNPRPVEPRPGVSQPVADALAAYAAGDVAALDALDVTQPGTAFRQRAW
+RELRGIAPGSPATYGGLAERCGAPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY
+GTDAKQALLAHEAAHAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000447.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000447.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f37da7c8b12569183f3aca0d56c2993e63e5b7c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000447.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_391
+MRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTNPDDGGQAKIAAQCTDAA
+NGRYRVETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFVPELAEPGFLAPVPEEMQ
+AYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAAGLDMSQPVTWDQLIEAA
+RSQDKDLAVQGARAESMTVWLNALIEGGGEQIVPNAEAPTDEVTTNLDSEAGRTAARIIS
+TIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATLGSVEEGSLPEDLPEDIG
+WAVYPRTVEGEDAAPPVGGINLGVGAKSEHQDLAWDAISCITTTEHQSQYFVENGNPPAD
+PAAYDAPEVAEKYPMADTIRESLELGAPRPQTPYYNEVSTAIQQRYAPPSGVSESTPAET
+DDFIQEVLRGERLL*
+>NZ_CP033200.1_120
+MRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTNPDDGGQAKIAAQCTDAA
+NGRYRVETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFVPELAEPGFLAPVPEEMQ
+AYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAAGLDMSQPVTWDQLIEAA
+RSQDKDLAVQGARAESMTVWLNALIEGGGEQIVPNAEAPTDEVTTNLDSEAGRTAARIIS
+TIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATLGSVEEGSLPEDLPEDIG
+WAVYPRTVEGEDAAPPVGGINLGVGAKSEHQDLAWDAISCITTTEHQSQYFVENGNPPAD
+PAAYDAPEVAEKYPMADTIRESLELGAPRPQTPYYNEVSTAIQQRYAPPSGVSESTPAET
+DDFIQEVLRGERLL*
+>NZ_CP040019.1_2500
+MRHDTRARQRRRATLAGAVVAGALILAGCAPAEQTPTLTWYTNPDDGGQAKIAAQCTDAA
+NGRYRIETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFVPELAEPGFLAPVPEEMQ
+AYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAAGLDMSQPVTWDQLIEVA
+RSQDKDLGVQGARAESMTVWLNALIEGGGEQIIPNAEAPTDEVTTNLDSEAGRTAARIIS
+TIGKEGLGSAGLPTQDENASMLLFQGNNGSFMVNWPFVWPATLGSVEEGSLPEDLPEDIG
+WAVYPRTVEDKDAAPPVGGINLGVGEKSEYQDLAWDAISCITTTEHQSQYFVENGNPPAD
+PAAYDAPEVAEKFPMADTIRESLELGAPRPQTPYYNEVSTAIQQRYAPPSGVSESTPAET
+DDFIQEVLRGERLL*
+>NZ_CP083691.1_2364
+MGDDGRHIRLASNEVPLVRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTN
+PDDGGQAKIAAQCTDAANGRYRIETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFV
+PELAEPGFLAPVPEEMQAYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAA
+GLDMSKPVTWDQLIEVARSQDKDLGVQGARAESMTVWLNALIEGGGEQIIPNAEAPTDQV
+TTNLDSEAGRTAARIISTIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATL
+GSVEEGSLPKDLPEDIGWAVYPRTVEDKDAAPPVGGINLGVGAKSEHQDLAWDAISCITT
+TEHQSQYFVENGNPPADPAAYDAPEVAEKFPMADTIRESLELGAPRPQTPYYNEVSTAIQ
+QRYAPPSGVSESTPAETDDFIQEVLRGERLL*
+>NZ_CP097650.1_394
+MRDDGRHIRLASIEVPLVRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTN
+PDDGGQAKIAAQCTDAANGRYRVETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFV
+PELAEPGFLAPVPEEMQAYAKDNALEGALAAASWKDEIVTVPFWANTQLLWYRKSVAEAA
+GLDMSQPVTWDQLIEAARSQDKDLAVQGARAESMTVWLNALIEGGGEQIVPNAEAPTDEV
+TTNLDSEAGRTAARIISTIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATL
+GSVEEGSLPEDLPEDIGWAVYPRTVEGKDAAPPVGGINLGVGAKSEHQDLAWDAISCITT
+TEHQSQYFVENGNPPADPAAYDAPEVAEKYPMADTIRESLDLGAPRPQTPYYNEVSTAIQ
+QRYAPPSGVTESTPAETDDFIQEVLRGERLL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000450.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000450.fa
new file mode 100644
index 0000000000000000000000000000000000000000..636380de75b61967bc2ae2bea8eba8795a0ee754
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000450.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_396
+MAHIITVAGATPRIHESVFLAPTAAITGDVEMAERSSAFYGVSARGDSAPIRVGAGTNLQ
+DNVVLHADEGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA
+LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKKNAATYLRLSAAHRDAVAG*
+>NZ_CP033200.1_125
+MAHIITVAGATPRIHESVFLAPTAAITGDVEMAERSSAFYGVSARGDSAPIRVGAGTNLQ
+DNVVLHADEGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA
+LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKKNAATYLRLSAAHRDAVAG*
+>NZ_CP040019.1_2496
+MAHIITVAGAGPRIHESVFLAPTAAITGDVEMAERSSAFYGVSARGDSAPIRVGERTNLQ
+DNVVLHADKGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA
+LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKVNAATYLELSAAHREATAER*
+>NZ_CP083691.1_2360
+MGHLVTVLGRTPRVDPSAFVARTAVLSGDVELGPRASAFYGVSARGDSAAIRVGEGSNLQ
+DNVVLHADAGFPCTLGAGVSVGHAAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA
+VVLEGTQVPPGSLVAGVPAKVRRGLTEEERASLTVNARTYLDLAAAHRAAEEAEQAGV*
+>NZ_CP097650.1_399
+MAHIITVAGATPRIHESVFLAPTAAITGDVEMAEHSSAFYGASARGDSAPIRVGAGTNLQ
+DNVVLHADEGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA
+LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKKNAATYLRLSAAHRDAVAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000455.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000455.fa
new file mode 100644
index 0000000000000000000000000000000000000000..527c8373f7813090dd6ff3b5695f753fbb828af1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000455.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_402
+MSHTTLHASPGDASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAGKSTTMRM
+LAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYGRYFGLPY
+SYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPTTGLDPQ
+ARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAELIREHASR
+EVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQRLVDEGA
+LPAPVTTLTRRASLEDVFLILTGRTLVD*
+>NZ_CP033200.1_132
+MSHTTLHASPGPASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAGKSTTMRM
+LAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYGRYFGLPY
+SYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPTTGLDPQ
+ARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAELIREHASR
+EVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQRLVDEGA
+LPAPATTLTRRASLEDVFLILTGRTLVD*
+>NZ_CP040019.1_2488
+MSHATPASPSPSQSPADAPDAGPAPVIRARGLRKQYGDFHAVKGIDLDVRPGECFGLLGP
+NGAGKSTTMRMLAGTSQRTAGELSILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENI
+LIYGRYFGLPYSYLRPKADELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFL
+LDEPTTGLDPQARHILWDRLYRLKERGTTLLLTTHYMDEAEQLCDRLVVVDGGQIMAAGT
+PAALIREHAAREVLEARFGADRNEAAARTVQARAGDGVVHRVEVLPDRVLVYAAHADDLH
+AVVQGLVDDGALPAPVTTLTRRASLEDVFLILTGRTLVD*
+>NZ_CP083691.1_2354
+MTRTTSSPSPAAPAGGGAAPVILARGLRKQYGDFHAVQGIDLDVRPGECFGLLGPNGAGK
+STTMRMLAGTSQRTGGELRILGIDPEEDGPAVRARLGVVPQQDNLDEDLTARENILIYGR
+YFGLPYSYLRPKAEELLAFAQLTDKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPT
+TGLDPQARHTLWDRLYRLKERGTTLLLTTHYMDEAEQLCDRLVVVDAGRIMAAGTPASLI
+REHASREVLEARFGTDRNATAARLLRESLPGLHRLEVLPDRVLLYTEHADTLQQDLDRLV
+AEGHVTAPVTQLTRRASLEDVFLILTGRTLVD*
+>NZ_CP097650.1_405
+MRLCCRLVSPTTLHAPPGPASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAG
+KSTTMRMLAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYG
+RYFGLPYSYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEP
+TTGLDPQARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAEL
+IREHASREVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQ
+RLVDEGALPAPATTLTRRASLEDVFLILTGRTLVD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000461.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000461.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b56ceaead56bbcfae29d9d2f690d1c9c010a09c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000461.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_409
+MKATDVAGTALANTMRSKLRTFLTVVAIVIGAFTLTLTTGLGAGINKYVDNVVEGFGKPG
+ELTVMKQQDMSSAGAASGSPQEYAEQDAAGGEMFGMPLLTQEDLAAIEDTEHVTEVKTYR
+VAEPEYIQGPDDRKWQTGFMGSSGEIDMLTFSAGRAPEAGAAEIVMPESWVEDLGAGDAE
+DLVGTELTVVAATPLQEHKSVTATVVGVTKAAASGAGTAPTPSESLEQEIYDITTEGLPE
+SQRDTYFQATAIVADPEANEDAVKQALADQGLLAQTLEEQLGVIRGIIDAVTWVLTGFAL
+IALLAASFGIINTLLMAVQERTREIGLMKALGMTGGKIFGLFTMEAVVIGLLGSLVGIGL
+GVAVGLIANQVLTTGPLSGVTGLVLFAVNPLALLLILLLIVAIAFIAGTLPALRAARKDP
+IEALRHE*
+>NZ_CP033200.1_139
+MKATDVAGTALANTMRSKLRTFLTVVAIVIGAFTLTLTTGLGAGINKYVDNVVEGFGKPG
+ELTVMKQQDMSSAGAASGSPQEYTEQDAAGGEMFGMPLLTQEDLAAIEDTEHVTEVKTYR
+VAEPEYIQGPDDRKWQTGFMGSSGEIDMLTFSAGRAPEAGAAEIVMPESWVEDLGAGDAE
+DLVGTELTVVAATPLQEHKSVTATVVGVTKAAASGAGTAPTPSESLEQAIYDITTEGLPE
+SQRNTYFQATAIVEDPEANEDAVKQALADQGLLAQTLEEQLGVIRGIIDAVTWVLTGFAL
+IALLAASFGIINTLLMAVQERTREIGLMKALGMTGGKIFGLFTMEAVVIGLLGSLVGIGL
+GVAVGLIANQVLTTGPLSGVTGLVLFAVNPLALLLILLLIVAIAFIAGTLPALRAARKDP
+IEALRHE*
+>NZ_CP040019.1_2480
+MKATDLAGTALANTMRAKLRTFLTVVAIVIGAFTLTLTSGLGAGINKFVDNMVEGFGSPD
+QLTVMKQVDPTSFAAGGAPQEYEPDEAAAGEMFGLPLLTAADLDRIRDTEHVTEVETARL
+VEPEYIEGEDGRQWQVPFMGSSFEIGALSLAAGREPAADAAEVTVPQDWVEALGGQTPED
+VLGQTVTLVAADPLGKQDGVEAEVVGVTEPMASGSGSGPVPSGEVETRLHEIQTAGLPEA
+QRDTFFSASVTVADMAANEAAVKAALAEEGYSAQTLEDQLGPIRGIIDAVTWVLNGFALI
+ALLAASFGIINTLLMAVQERTREIGLMKALGMTGRKIFGLFTMEAVVIGLLGSLIGVGLG
+VAVGVVANQVLTEGALSGVTGLVLYAVEPLSLALIVLLIVAIAFLAGTLPAARAARKDPI
+EALRYE*
+>NZ_CP083691.1_2346
+MKAPDLIRTALGNTARAKLRTFLTVIAIMIGAFTLTLTSGLGAGINKYVDNMVAGFGAPD
+ELTVSKPAGNQMAGMTGGAPTEYEDSAAAGEMYGMPLLTQEDLDRIGATEHVTGVETVRI
+VEVQDLRGADGRRWSVPMMGGTYEIGKLSVKAGREPAADGGAMELTVPTEWVESLGGTAP
+EDVLGQEVTLTTKTPLQQERTVQAEVVGVTERLPSGVGANPVPSAALEQGLHDIQTEGLP
+EEQRNTYFQATAIVEGMPGNEAAVKAALSEQGYQAQTLEDQLGSIRGIISAVTWVLNGFA
+LIALLAASFGIINTLLMAVQERTREIGLMKALGMTSGRIFGLFTLEAVVIGLLGSLLGVG
+LGVAVGVGVNAWLTTGGPLEDVAGLVLYAVDPLALLLIVLLIVAIAFVAGTLPAARAARK
+DPIEALRHE*
+>NZ_CP097650.1_412
+MKATDVAGTALANTMRSKLRTFLTVVAIVIGAFTLTLTTGLGAGINKYVDNVVEGFGKPG
+ELTVMKQQDMSSAGAASGSPQEYTEQDAAGGEMFGMPLLTQEDLAAIEDTEHVTEVKTYR
+VAEPEYIQGPDDRKWQTGFMGSSGEIDMLTFSAGRAPEAGAAEIVMPESWVEDLGAGDAE
+DLIGTELTVVAATPLQEHKSVTATVVGVTKAAASGAGTAPTPSESLEQEIYDITTEGLPE
+SQRDTYFQATAIVADPEANEDAVKQALADQGLLAQTLEEQLGVIRGIIDAVTWVLTGFAL
+IALLAASFGIINTLLMAVQERTREIGLMKALGMTGGKIFGLFTMEAVVIGLLGSLIGIGL
+GVAVGLIANQVLTTGPLSGVTGLVLFAVNPLALLLILLLIVAIAFIAGTLPALRAARKDP
+IEALRHE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000462.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000462.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92d2ed7c46664fbfd859836f4812a3c1062e6c38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000462.fa
@@ -0,0 +1,26 @@
+>NZ_CP042169.1_410
+MTTDRPNPDPNPEQPAVGSRYGTQPYAAPGYGAQPGSPYGIVPEPAAFPALLTLTLTSLA
+LYVLSSLPALFGGEESIERMRDSLRQSGLTPEQVEEIAPVVGASVTVGTIIVLLIGVALY
+ALVYFNLRGAKNWARILGIVVGILGTLSAVGGIFSFVTYPGIGGVLASVLSLALVIVNIL
+WLVKAFNPQVAAYTRQGRRA*
+>NZ_CP033200.1_140
+MTTDRPNPNPEQPAAGSRYGTQPYAAPGHGAQPGSSYGIVPEPAAFPALLTLTLTSLALY
+VLSSLPALFGGEESIERMRDSLRQSGLTPEQVEEIAPVVGASVTVGTIIVLLIGVALYAL
+VYFNLRGAKNWARILGIVVAILGTLSAVGGIFSFVTYPGIGGVLASVLSLALVIVNILWL
+VKAFNPQVAAYTRQGRRA*
+>NZ_CP040019.1_2479
+MSNQNPDFTNPAYNPANPPFEGESGQAGQAPQQGQPGQAAQYGQPGPYGQAPQYGQPGQY
+PATGTRYGTQPYGVDGRYGTVPEPRGFRTLLTLTLVSAALWVLSSLPAMFTMDDMMDVVM
+RDAASQPGVTAEDMEMVSSFMRTAGITSIVISLIIGLGLYALVYFNLRGVKNWARILGIV
+FAILGALAIFSGIGFLFSGSTMLILSGALTLAYAVVNIIWVITAFRSDVAEWFRQGRPAA
+A*
+>NZ_CP083691.1_2345
+MTDQNTPYPQNPQGGQPAPQYGQPGQAAPQYGQPGEGSRFGTQAYGAPGLQYGAPLAEPA
+KFRTLLKLTLASAVVYVLSALPGLFVDQDALVRDQLRAQGMSAEQIDQAMQNAGMFSAMA
+GIGAVVGLLIALGLYALVYFGLRAGKNWARVLGIVLAILGTLSAVFGLFSLGSFPAGVMI
+ASLVLSVLFIAVNVLWLVNAFNKDVAAYTKQGRLPAA*
+>NZ_CP097650.1_413
+MTTDRPNPDPNPEQPAAGGPGPYPGQNPAYGQPTAGSRYGTQPYAAPGYGAQPGSPYGIV
+PEPAAFPALLTLTLTSLALYVLSSLPALFGGEESIERMRDSLRQSGLTPEQVEEIAPVVG
+ASVTVGTIIVLLIGVALYALVYFNLRGAKNWARILGIVVAILGTLSAVGGIFSFVTYPGI
+GGVLASVLSLALVIVNILWLVKAFNPQVAAYTRQGRRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000463.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000463.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bca4812955fd326e2a4930f4d2380730c4fded3d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000463.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_412
+MHPLDDDPHAATDRDPAPDRAALRPLRLFQTVTAVTGALSAAGVAGVLALQSTPGYARAV
+LEARSWGASEVTDADVAAFVTPAGAWPVAAAAVVLLAVVLLAGITRRIRAVRPVGSVLVV
+LGMLTAAFWMVDGGRMVQAGGGGPVVLGAVVGMLVSSAMWLRVAHRRETRDGFDG*
+>NZ_CP033200.1_142
+MMGGMHPLHDDPHETTERDPGPDRAALRPLRLFQTVTAVTGALSAAGVGGVLALQATPGY
+ARAVLEARSWGASEVTDADVAAFLTPAGAGPVAAAAVVVLTLVLLAGITRRIRAVRPVGS
+VLVVLGMLTAAFWMVDGGRMVQAGGGGPVVLGAVVGMLVSSAVWLRVAHRRETRDAFDV*
+>NZ_CP040019.1_2477
+MHTPDDAAADADDAAARAALHDRVVRRPLRRLLTLTAVTGALSALGTAGVLALQGAPGYA
+RAVLEARSWGRAAVTDADVASFLTPPWGVPAAVLGVLAVAALLMLGVARRVRAVRPVGTV
+AVGLGLLSAAFWMVDGGRMVAAGGAGPLVLAAVVAMFLACAVWLLTAHLRATRDAFDG*
+>NZ_CP083691.1_2344
+MRSDDVAPASARPSGLDDPAVRGPIRRYQAMTAGTGLVSAAAVAGVLGLQSDPGYAREVL
+QSRTWGQYEVSAQQVQDFLTPPGGAVLGAVGVLLTAALLVWGAQRLWGATRWLGTALAGV
+GLLSAVFWAVDGGRMAARGASGMAVLVAVGAMAVFCAVWLVTAHSKAVREAFLG*
+>NZ_CP097650.1_415
+MHPLDDDPHETTDPAPDLASLRPLRLFQTVTAVTGALSAAGVGGVLALQSTPGYARAVLE
+ARSWGASEVTDADVAAFLTPAGAWPVAAAAVVVLTLVLLAGITRRIRAVRPVGSVLVVLG
+MLTAAFWMVDGGRMVQAGGGGPVVLGAVVGMLVSSAVWLRVAHRRETRAAFDV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000468.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000468.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c0de68646a833a294513d84d82a255e5f120ac3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000468.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_417
+MSTDPNLTDAPREAAPGTALSRFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR
+ATWDRLAPLAAGMLVVTGEAHREAVCTQLPALAETDLVLEPSPKDSAAAIGLAAAILSLR
+DPDTIMGSFAADQVISPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL
+RVAGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG
+LMEIARAWETPERDEVMARVWPELTKTAIDYAVAEPAAAVGDVAVIPGSFTWDDVGDFAA
+IARLNPVRDASGITVIGDTPRVYSDDASGVVVTDTKRVIALIGIEDVVVVDTEDALLVTT
+TEHAQEVKKAVEALKAEGVDEVL*
+>NZ_CP033200.1_147
+MSTDPNLTDAPREAAPGTALSRFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR
+ATWDRLAPLAAGMLVVTGEAHREAVCMQLPALAETDLVLEPSPKDSAAAIGLAATILSLR
+DPDTIMGSFAADQVISPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL
+RVAGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG
+LMEIARAWETPERDEVMARVWPELTKTAIDYAVAEPAAAVGDVAVIPGSFTWDDVGDFAA
+IARLNPVKDASGITVIGDTPRVYSDDASGVVVTDTKRVIALIGIEDVVVVDTEDALLVTT
+TEHAQEVKKAVEALKAEGVDEVL*
+>NZ_CP040019.1_2472
+MSTDPNLTEAGREDAPGSALSRFHVVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR
+ATWDRLAPLAAGMLVVTGAAHRDAVCGQLPDLDTADLVLEPSPKDSAAAIGLAAAILSLR
+DPDTIMGSFAADQVIAPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL
+AVPGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG
+LMEIAHAWETERRDEVMERVWPELTKTAIDYAVAEPAAAVGDVAVIPGAFTWDDVGDFAA
+IARLNPVKDASGITVIGDTPRVYSDDASGVVVTDTRRVIALIGIEDVVVVDTEDALLVTT
+TDHAQEVKKAVEALKAEGVDEVL*
+>NZ_CP083691.1_2339
+MSIDPTAAQSAPSQPSASALERFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR
+ATWDRLAPLAGGIMVVTGRAHEDAVCRQLPDVGAADLVLEPEPKDSAAAIGLAAAILWLR
+DSDTIMGSFAADQVIGPVDVFQDAVRQAVETAATGRIVTIGITPTHAATGFGYIRTGRRL
+SVAGAPDAHDVAAFVEKPDQRVAERYVASGRYLWNAGMFVAPVALMLQHLEANEPELHAG
+LTEIARAWETPERDAVMARVWPGLKKTAIDYAVAEPAATAGDVAVIPGAFTWDDVGDFAA
+IARLNPVKDGSGVTVIGDTPRVYSDSATGVVVTDTSRVIALIGVEDVVVVDTGDALLVTT
+TEHAQDVKRTVESLKAQGADDVL*
+>NZ_CP097650.1_420
+MSTDPNLTDAPREAAPGTALSRFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR
+ATWDRLAPLAAGMLVVTGGAHREAVCMQLPDLAETDLVLEPSPKDSAAAIGLAAAILSLR
+DPDTIMGSFAADQVISPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL
+RVAGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG
+LMQIARAWETPERDEVMARVWPELTKTAIDYAVAEPAAAVGDVAVIPGSFTWDDVGDFAA
+IARLNPVKDASGITVIGDTPRVYSDDASGVVVTDTKRVIALIGIEDVVVVDTEDALLVTT
+TEHAQEVKKAVEALKAEGVDEVL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000469.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000469.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b8ef81d4a5455e551e6e9c41eff3d9b36054ec5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000469.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_418
+MTTSDSVLTGPRPTSVPSVGPVVAELEDEIVSFRRDLHRHPELSYEEYRTTDRIVELLSG
+YGLSPVRMESTGAYVDVGEGPVVLALRADIDALPVEEETGLPYVSVNDGVAHACGHDMHT
+AVMAGVAVALGRILRGATADADLRAVGERVHGTVRVIFQPAEERLPGGSLAVLRQGILDD
+VPRILAAHCDPQVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA
+VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGALLDE
+VVRQVAAPYGVHVQLEHVRGVPPVHNTEGETALIETAARRELGSRAIVLTPQSMGGEDFA
+WMTQKVPGSMLRLGTRSPGGPIYDLHRGDYAPDERAIGVGMRVFTAAALQVLTGEDHH*
+>NZ_CP033200.1_148
+MTTSDSVLTGPRPTSVPSVGPVVAELEDEIVSFRRDLHRHPELSYEEYRTTDRIVELLSG
+YGLSPVRMESTGAYVDVGEGPVVLALRADIDALPVEEETGLPYVSVNDGVAHACGHDMHT
+AVMAGVAVALGRILRGATADPDLRAVGERVHGTVRVIFQPAEERLPGGSLAVLRQGILDD
+VPRILAAHCDPQVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA
+VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGALLDE
+VVRQVAAPYGVHVQLEHVRGVPPVHNTEGETALIETAARRELGSRAIVLTPQSMGGEDFA
+WMTQKVPGSMLRLGTRSPGGPIYDLHRGDYAPDERAIGVGMRVFTAAALQVLTGEDHH*
+>NZ_CP040019.1_2471
+MTTSDSVLSDQRPASLPSVASVVAELEAEVVAFRRDLHRHPELSYEEYRTTDRIMELLTG
+YGFSPVRMESTGAYVDIGEGPVVLALRADIDALPLEEETGLPYVSVNDGVTHACGHDMHT
+AVMAGAALVIGRILRGATADPALRTAGERARGSVRVIFQPAEERLPGGSLSVLRQGILDG
+VPRILAAHCDPAVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA
+VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGDLLDE
+VVTQVAAPYGVQVQLEHVRGVPPVHNTDAETALIETAARRELGARAIQLTPQSMGGEDFA
+WMTQRVPGSMLRLGTRTPGGPVYDLHRGDFTPDERAIGVGMRVFAAAALQALVGEEGH*
+>NZ_CP083691.1_2338
+MTTSESVVTGTAPRLAPPSVAPVVQQLEEHVTAFRRDVHRHPELSYEEYRTTDLIVETLA
+EYGLNPVRLEGTGAYVDLGEGPVVLGLRADIDALPVEEETGLPYVSVNDGVAHACGHDMH
+TAVMLGTALTLGRILRGAAPTAELRAVGERARGRVRVIFQPAEERLPGGSLAVIRQGVLE
+GVPRVLAAHCDPHFDVGTIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQI
+AVNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDAGVWEEAGALLD
+EVVTQVASPYGVQVQLEHIRGVPPVDNAEAETALIEDAARRELGAHAIALTPQSMGGEDF
+AWMTQKVPGAMLRLGTRTPGGPTYDLHRGDYAPDERAIGVGMRVFAAAALDVLAGPAR*
+>NZ_CP097650.1_421
+MTTSDSVLTGPRPTSVPSVGPVVAELEDEIVSFRRDLHRHPELSYEEYRTTDRIVELLSG
+YGLSPVRMESTGAYVDVGEGPVVLALRADIDALPVEEETGLPYVSVNDGVAHACGHDMHT
+AVMAGVAVALGRILRGATADPDLRAVGERVHGTVRVIFQPAEERLPGGSLAVLRQGILDD
+VPRILAAHCDPQVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA
+VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGALLDE
+VVRQVAAPYGVHVQLEHVRGVPPVHNTEGETALIETAARRELGSRAIVLTPQSMGGEDFA
+WMTQKVPGSMLRLGTRSPGGPIYDLHRGDYAPDERAIGVGMRVFTAAALQVLTGEDHH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000471.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000471.fa
new file mode 100644
index 0000000000000000000000000000000000000000..53855b2ff136807a05bf514477f5000c35b97f11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000471.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_420
+MRLELRGISKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGEIL
+LDGEPVRFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRALGVLDLEATRRRI
+REISAQYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLG
+IIRQLREDGTAIVFISHKLREVKAVSDDITVLRRGRVVGTADPSAEAAELAALMVGRSVV
+LERRKTAPTLGEETFRVEDLSVVSPTGQVLLDAVSFAVRQGEVLAVAGVQGNGQTELTEA
+IMGLVKATGSVTLDGRELIGRSTRQIIRAGVGFVPEDRSTDGLVGPFSVAENMVLNRYDV
+APAGNAVQMRPAAVRALAERRVAEFDVRTQGVDLPVSSLSGGNQQKVVMARELVDGLRLF
+IASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVLELADRIAVMYHGRIVGIV
+PGDTSRETLGLMMAGQTPDDAALASGADVAAGTPGTAGEAPAAHPTTEGERP*
+>NZ_CP033200.1_150
+MRLELRGITKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGEIL
+LDGEPVRFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRALGVLDLEATRRRI
+REISAQYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLG
+IIRQLRADGTAIVFISHKLREVKAVSDDITVLRRGRVVGTAEPSAEAAELAALMVGRNVV
+LERRKTAPTLGEETFRVEDLSVVSPTGQVLLDAVSFAVRQGEVLAVAGVQGNGQTELTEA
+IMGLVKATGSVTLDGRELIGRSTRQIIRAGVGFVPEDRSTDGLVGPFSVAENMVLNRYDV
+APAGNAVQMRPAAVRALAERRVAEFDVRTQGVDLPVSSLSGGNQQKVVMARELVDGLRLF
+IASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVLELADRIAVMYHGRIVGIV
+PGDTSRETLGLMMAGQTPDDAALASGTDVAADTPGTAGAAPAAHPTTEGERP*
+>NZ_CP040019.1_2469
+MKLELRGITKRFGTFTANDSVDFVVRSGEVHTLLGENGAGKSTLMNVLFGLYDPTEGEIL
+VDDRPVRFAGPGEAMRAGIGMVHQHFMLVPVFTVAENIALGDEHTRAAGVLDLEATRRKI
+RAISDEYGFAVDPDAVVEDLPVGVQQRVEIIKALVRDAKVLILDEPTAVLTPQETDELLA
+IIDRLRQDGTAIVFISHKLREVKAISEHITVLRRGKVVGTAEPSASAAELAALMVGRQVS
+LNRAKTAPTLGEETFKVQDLTVVSPTGQVLVDHVSFAIRQGEILGVAGVQGNGQTELTEA
+IMGLHKATGSVTLDGRELVGRSTRQIIRAGVGYVPEDRSTDGLVGSFTVAENMVLNRFDR
+EPAGSALQLRPRAVRELAEARVQEFDVRTQGVVSPVSSLSGGNQQKVVMARELVDELRLF
+IASQPTRGVDVGSIEFLHERIVRERDNGTPVMIVSTELDEILELSDRIAVMYHGRIVGIV
+DGDASRETLGLMMAGQTPESLATETATTEEGPRA*
+>NZ_CP083691.1_2336
+MKLELRGITKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGQIL
+LDGEPVAFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRGAGVLDLEATRRKI
+REISDAYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLA
+IIRQLRADGTAIVFISHKLREVKAISDDITVLRRGRVVGTADPSASAAELASLMVGRDVV
+LNRRKTAPQLGEETFRVEHLTVVSPTGQVLVDDVSFGIRQGEVLAVAGVQGNGQTELTEA
+IMGLQAKAAGSIRLDGRELLGRSTRQIIHAGVGYVPEDRSTDGLVGSFSVAENMVLNRFD
+VAPAGSAVQLRPRAVRELAERRVEEFDVRTQGVDVPVSSLSGGNQQKVVMARELVDGLRL
+FIASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVRELADRIAVMYHGRIVDI
+VPGDASREHLGLLMAGQTAEDTHQEGARA*
+>NZ_CP097650.1_423
+MRLELRGITKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGEIL
+LDGEPVRFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRALGVLDLEATRRRI
+REISAQYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLG
+IIRQLRADGTAIVFISHKLREVKAVSDDITVLRRGRVVGTAEPSAEAAELAALMVGRNVV
+LERRKTAPTLGEETFRVEDLSVVSPTGQVLLDAVSFAVRQGEVLAVAGVQGNGQTELTEA
+IMGLVKATGSVTLDGRELIGRSTRQIIRAGVGFVPEDRSTDGLVGPFSVAENMVLNRYDV
+APAGNAVQMRPAAVRALAERRVAEFDVRTQGVDLPVSSLSGGNQQKVVMARELVDGLRLF
+IASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVLELADRIAVMYHGRIVGIV
+PGDTSRETLGLMMAGQTPDDAALASGADVAADTPGTTGAAPAAHPTTEGERP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000472.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000472.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49d548e436d17515f2bf756a62714deee5882c7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000472.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_421
+MSTAAPQRPAPASDPRVRPAPADSALRRILSGNGTVTALAILLSLLISGLLIIAVDEDVR
+DAAGYFFARPGDLLSAAWAAFAGAFAALFRGAVFNYRASDATGMLYPLTETLTVATPLII
+ISLGIAIAFRAGLFNIGGQGQFIFGAMFATWFGVHLHLPAGVHLLLVVVMGVLGGVLWGS
+VVGVLKAWTGAHEVILTIMLNYVAVNLLAYLLNTPVLRAPATTNPVSAPLDRSAMFPRLL
+GTDFRLHWGFFVALLAVLFTWWLMQRSTLGFRLRAVGANPDAARTAGISVKGSYVAAMAI
+SGGLAGLAGATHVAGTESTLNTSVAGSFGFDAITVALLGRSHPVGVLFAGLLFGALRAGG
+VTMQTETGVPVDIVLVVQSVIVLLIAAPPLVRAIFRLPAPGAARARRAADPVTQPAVAGA
+ALTGAGGHAAAPSTGVQEAAAAAVADPQAPTTQPTDTAPTHRPHEQKGDAR*
+>NZ_CP033200.1_151
+MSTAAPQRPAPASDPRVRPAPADSALRRILSGNGTVTVLAILLSLLISGLLIIAVDEDVR
+DAAGYFFARPGDLLSAAWAAFAGAFAALFRGAVFNYRASDATGMLYPLTETLTVATPLII
+ISLGIAIAFRAGLFNIGGQGQFIFGAMFATWFGVHLHLPPGVHLLLVVVMGVLGGVLWGS
+VVGVLKAWTGAHEVILTIMLNYVAVHLLAYLLNTPVLRAPGTTNPVSAPLDRSAMFPRLL
+GTDFRLHWGFFVALLAVLFTWWLMQRSTLGFRLRAVGANPDAARTAGISVKGSYLAAMAI
+SGGLAGLAGATHVAGTESTLNTSVAGSFGFDAITVALLGRSHPVGVLFAGLLFGALRAGG
+VTMQTETGVPVDIVLVVQSVIVLLVAAPPLVRAIFRLPAPGAARARRAADPVTQPAVAGA
+AVTGAGGHAAAPSTGVQAAAATAVADPQAPTTQPTDTAPTHRPHEQKGDAR*
+>NZ_CP040019.1_2468
+MSQNPPQTPASEPVQPPGGAPVPAAGVTGADAPPAPERGSQESVLREILSGNAMVTALAI
+VLSLAISAVLIIVTSPDVIDAAGYFFARPMDTLSAAWTVVSDAYLALFRGSIVNYRADSF
+ADMIRPLTETLTVATPLIIASLGVAIAFRTGLFNIGGQGQFLIGAAFATVGGVYLDLPLG
+VHLLLVIVMGALGGLLWGAVVGLLKAYTGAHEVILTIMLNYVALHLVSYLLNTPFLRRAG
+TNNPISEQFPDSAAFPALLGDGFRLHWGFVMALVLTFLAWWMLERSTLGFRLRAVGANPA
+AARTAGISVKGGYVAAMAIAGALAGLGGVAHISGTEKVLTSGIAGQFGFDAITVALLGRS
+HPVGVLFAGLLFGALRAGGVTMQTQTGVPIDIVLVVQSFIVLLIAAPPLVRAIFRLPAPG
+SVRARANADVVTQPALAGAAVPGAAAEAVPAETGSATTSKGEGR*
+>NZ_CP083691.1_2335
+MSTAVASRPAGARTQEDGSALRRLASSNGAVTVLAVLLSLVISAVLIVVTDEDVQDAAGY
+LFARPQDALTAAWKAVSGAYAALFRGAVFNYEADTFTDMVRPLTETLTVATPLIIISLGV
+AVAFRAGLFNIGGQGQFIFGAMVATWTAVHLPLPFGLHLLVVLLAGVVGGVLWGAVVGVL
+KAWTGAHEVILTIMLNYVAVNVLAYLLNTPVLRRAGTTNPVSEFLPESGMFPKLLGDGYR
+LHWGFVLALLVTAFTWWLMSRSTLGFRLRAVGANPAAARTAGMSVKGTYVAAMAISGGLA
+GLAGMTHVSGTENALNTSVAGSYGFDAITVALLGRSNPVGVLFAGLLFGALRAGGVTMQT
+ETGVPIDIVLVVQSMIVLFIAAPPLVRGLFRLPAPGAARARRTADVVTQPAVAGAAVPGA
+AGLASVPSAQTQDAAATAVAADPADPVAGTGPHREKGQDL*
+>NZ_CP097650.1_424
+MSTAAPQRPAPESDPRARPAPADSALRRVLSGNGTVTALAILLSLLISGLLIIAVDEDVR
+DAAGYFFARPGDLLSAAWAAFAGAFAALFRGAVFNYRASDATGMLYPLTETLTVATPLII
+ISLGIAIAFRAGLFNIGGQGQFIFGAMFATWFGVHLHLPAGVHLLLVVVMGVLGGVLWGS
+VVGVLKAWTGAHEVILTIMLNYVAVNLLAYLLNTPVLRAPGTTNPVSAPLDRSAMFPRLL
+GTDFRLHWGFFVALLAVLFTWWLMQRSTLGFRLRAVGANPDAARTAGISVKGSYLAAMAI
+SGGLAGLAGATHVAGTESTLNTSVAGSFGFDAITVALLGRSHPVGVLFAGLLFGALRAGG
+VTMQTETGVPVDIVLVVQSVIVLLIAAPPLVRAIFRLPAPGAARARRAADPVTQPAVAGA
+AVTGAGGHAAAPSTGVQEAAATAVADPQAPTTQPTDTAPTHRPHEQKGDAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000475.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000475.fa
new file mode 100644
index 0000000000000000000000000000000000000000..32ef9411001a55d952aa5b9d47766c4e7ab80428
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000475.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_424
+MTAQPQAEPFDAVEVIRTKRDRGTLSPEQIDWVVDAYTRGVVADEQMSALAMAILLNGMD
+RAEIARWTDAMIASGERMDFGGLTTPDGRPLATADKHSTGGVGDKITLPLAPLVASFGVA
+VPQLSGRGLGHTGGTLDKLEAIPGWRADLSNEAMLRQLSEVGAVICAAGSGLAPADKRLY
+ALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELARTMVDLG
+RDAGVDTSALLTDMSVPLGRTAGNALEVRESVEVLAGGGPADVVELTVALAAAMLAGAGV
+TDVDPAEHLANGRAMDVWNRMIEAQGGDPRAALPTAAHTEDVVAETDGVLTELDAMAVGL
+AAWRLGAGRERQGQAVQAAAGVEVHVRPGERVARGQKVLTLHTDTPERFERAKAALAGGW
+AVGELDDAAARTLRERSVILDRIG*
+>NZ_CP033200.1_154
+MTAQPQAEPFDAVEVIRTKRDRGTLSPEQIDWVVDAYTRGVVADEQMSALAMAILLNGMD
+RAEIARWTDAMIASGERMDFGGLTTPDGRPLATADKHSTGGVGDKITLPLAPLVASFGVA
+VPQLSGRGLGHTGGTLDKLEAIPGWRADLSNEAMLRQLSEVGAVICAAGSGLAPADKRLY
+ALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELARTMVDLG
+RDAGVDTSALLTDMSVPLGRTAGNALEVRESVEVLAGGGPADVVELTVALAAAMLAGAGV
+TDVDPAEHLANGRAMDVWNRMIEAQGGDPRAALPTAAHTEDVVAETDGVLTELDAMAVGL
+TAWRLGAGRERQGQAVQAAAGVEVHVRPGERVARGQKVLTLHTDTPERFERARAALAGGW
+SVGELDDDAARALRERSVILDRIG*
+>NZ_CP040019.1_2465
+MTAQQQAEPFDAVEVIRAKRDRQTLSPEQIDWVVDAYTRGVVADEQMSALAMAILLNGMD
+RAEISRWTDAMIASGERMDFSGLTAPDGRVLPTADKHSTGGVGDKITLPLAPLVASYGVA
+VPQLSGRGLGHTGGTLDKLEAIPGWRADLTNEQMMRQLSEVGAVICAAGSGLAPADKRLY
+ALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELARTMVDLG
+RDAGVDTVALLTDMSVPLGLTAGNALEVRESVEVLAGGGPADVVELTVELARAMLAGAGV
+TDVDPAQNLANGKAMDVWHRMIEAQGGDPRADLPTAAHTEDVVAEADGVLAELDAMAVGL
+AAWRLGAGRERQGQPVQAGAGVELHVRPGERVARGQKVMTLHTDTPERFARAKAALEGGW
+AVAEKGEAEAAALRDRSVILDRIG*
+>NZ_CP083691.1_2332
+MTTTSMPAQPAAPEAFDAIEVIRLKRDGHRLDPERIDWVVDAYTRGVVAPEQMSALAMAI
+LLNGMDREEIARWTAAMIASGERMDFSGLSAPDGRRLATADKHSTGGVGDKITLPLAPLV
+ASYGVAVPQLSGRGLGHTGGTLDKLESIPGWRADLTNDQMMRQLGEVGAVVCAAGAGLAP
+ADKKLYALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELAR
+TMVDLGRDAGVDTSALLTDMSVPLGLTAGNALEVRESVEVLAGGGPADVVELTVELARAM
+LAGAGVTDVDPAENLANGKAMDVWHRMIQAQGGDSHAELPAARHQETVTADADGVLTELD
+AMAVGLAAWRLGAGRERQGEPVQAGAGVELHARPGDAVRAGQPLMTLHTDTPERFDRARA
+ALAGGWAVTAADEAEAAALRSRSVILDRIG*
+>NZ_CP097650.1_427
+MTAQPQAEPFDAVEVIRTKRDRGTLSPEQIDWVVDAYTRGVVADEQMSALAMAILLNGMD
+RAEIARWTDAMIASGERMDFGGLTTPDGRPLATADKHSTGGVGDKITLPLAPLVASFGVA
+VPQLSGRGLGHTGGTLDKLEAIPGWRADLSNEAMLRQLSEVGAVICAAGSGLAPADKRLY
+ALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELARTMVDLG
+RDAGVDTSALLTDMSVPLGRTAGNALEVRESVEVLAGGGPADVVELTVALAAAMLAGAGV
+TDVDPAEHLANGRAMDVWNRMIEAQGGDPRAALPTAAHTEDVVAETDGVLTELDAMAVGL
+AAWRLGAGRERQGQAVQAAAGVEVHVRPGERVAQGQKVLTLHTDTPERFERARAALAGGW
+AVGELDDVDARTLRERSVILDRIG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000476.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000476.fa
new file mode 100644
index 0000000000000000000000000000000000000000..680ec85f2d783196c4da29f13902676ce36795f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000476.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_425
+MLAWLEGAILHASAQWWVLPLTLLLCLLDGIVPIFPSESVLVALGAIVRDGHPFSLWALW
+GVGFAGAFLGDVAAYAIGRAVGVERFRWMRLRRVRATVEVARHHLHSHGALLLFTARFIP
+GGRVALNFTAGATRYPPVRFVALDLLSTASWAAYSIMIARLTAGWLENPVLQIAVSVTGA
+ALVGLLLDRLLKALLRRRLGAGVKGLTLAEQEALR*
+>NZ_CP033200.1_155
+MLAWLEGAILHASAQWWVLPLTLLLCLLDGIVPIFPSESVLVALGAIVRDGHPFSLWALW
+GVGFAGAFLGDVAAYAIGRAVGVERFRWMRLRRVRATVEVARHHLHSHGALLLFTARFIP
+GGRVALNLTAGATRYPPVRFVALDLLSTASWAAYSIMIARLTAGWLENPVLQIAVSVTGA
+ALVGLLLDRLLKALLRRRLGAGVKGLTLAEQEALR*
+>NZ_CP040019.1_2464
+MLEWIEETVLHAAAQWWMLPLTLALCLLDGIVPVFPSESVIVALAAIVRDGQPFSLWALW
+AVGFAGAFLGDILAYAIGRAVGVDRFRWMRTPRVRASVAVARHHLNGHGALLLFTGRFIP
+GGRVAINLTAGAIRYPLHRFVVLDLLSTAAWSAYSIMIARLTTGWLDNALLQIAVSVTGA
+ALVGVLLDRALKAVLRRRLGTGVKGLRQAEDEALR*
+>NZ_CP083691.1_2331
+MVQALEQAILAGASHPWALPLAALLCLLDGLVPVFPSESVLVALASIVEDGRPFPLAALW
+AAGFVGAFLGDVAAYGAGRGVGVTRFRWMRHGRVRRTIVMARRNLDSHGALLLFTARFIP
+GGRVAVNLAAGAMHYSPWRFVGLDLVSTALWSVYSIAIARLTVGWLDSTVLRMAVAVLGA
+ALVGLLLDRAVKALLRRRLARDGHRLGADEQAALR*
+>NZ_CP097650.1_428
+MLAWLEEAILHASAQWWVLPLTLLLCLLDGIVPIFPSESVLVALGAIVRDGHPFSLWALW
+GVGFAGAFLGDVAAYAIGRAVGVERFRWMRLRRVRATVEVARHHLHSHGALLLFTARFIP
+GGRVALNLTAGATRYPPVRFVALDLLSTASWAAYSIMIARLTAGWLENPVLQIAVSVTGA
+ALVGLLLDRLLKALLRRRLGSGVKGLTLAEQEALR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000478.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000478.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e123e72f5ae8226199fb4f434f1377e6506d1645
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000478.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_427
+MDRLVAVVEALRDHCPWTAALTHADLAEYLVEEAYEAVAEIESRDAAAWADVPARRADGA
+YPALAAELGDVLFQVVLHAAVSRAPGAPAETAGFRVDDAADALTAKMIRRNPLVLTPEGG
+LRPAEELAAVTPEAVELAWERVKAQERAAAGLSPAAPAHDDGGTGPGLDVGDIPARLPAL
+AAAANVVDRAARQEPDPLAAHVPAPAAEAGERPAAGWPDEAALGAELFALVRRARAAGLD
+PERALRTTVARVRAGDWSALRPSG*
+>NZ_CP033200.1_157
+MDRLVAVVEALRDHCPWTAALTHADLAEYLVEEAYEAVAEIESRDAAAWADVPARRADGA
+YPALAAELGDVLFQVVLHAAVSRAPGAPAETAGFRVDDAADALTAKMIRRNPLVLTPEGG
+LRPAEELAAVTPEAVELAWERVKAQERAAAGLSSAAPAHGDGGTGPGLDVGDIPARLPAL
+AAAAKVVDRAARQEPDPLAAHVPAPAAEAGERPAAVWPDEAALGAELFALVRRARAAGLD
+PERALRTTVARVRAGDWSALRPSG*
+>NZ_CP040019.1_2462
+MDRLVAVVEALRDHCPWTAALTHGDLAEYLVEEAYEAVAEIEARDAAAWADVPARRADGA
+YPALAAELGDVLFQVVLHAAVSRPPGAPVSSAGFRVADAADALTVKMIRRNPLVLTPEGA
+PRSAEELARVTPEAVELAWEEVKAQERAAAGETASGEAEQAGGPASDPGFGGIPARLPAL
+AAAAKVVDRAARQPADPLARHAPLSGDPDSGHRAGHAAPDDGDPGWGDEAALGAELFALV
+RRARAAGLDPERALRGTVARVRSGDWDALRPPTAG*
+>NZ_CP083691.1_2329
+MSDAVDRLVATTEALRTHCPWTRALTHRSLTQYLVEEAYEALAEIEARTDAEWADVPARR
+ADGSYPALAGEMGDVLFQVVLHAAVSRAPDAPAPAAGFRLDDAADALTAKLVRRNPLVFT
+PDGAVRPPAELEGITPEAVELAWERVKRAERAAAEGGGAPDGPTGAPRPDDVGLGGIPAH
+LPALAAASAVVDRAARQDVDPLAGHVPLPERTGEAWEDEAALGAELFETVRRARAAGLDP
+ERALRGAIACVRAGDWDALRR*
+>NZ_CP097650.1_430
+MDRLVAVVEALRDHCPWTAALTHADLAEYLVEEAYEAVAEIESRDAAAWADVPARRADGA
+YPALAAELGDVLFQVVLHAAVSRAPGAPAESAGFRLDDAADALTAKMIRRNPLVLTPEGG
+LRPAEELAAVTAEAVELAWERVKARERAAAGLSPAAPAHDDGGTGPGLDVGDIPARLPAL
+AAAAKVVDRAARQEPDPLAAHVPAPAAEAGERPAAGWPDEAALGAELFTLVRRARAAGLD
+PERALRATVARVRAGDWAALRPSG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000484.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000484.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8f919f6b0a36032c4fa789c216a5a815152d3ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000484.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_437
+MSSTLAAQTKINKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA
+TLLAPVFQAMRRIKVPGVAAALLCVLLLVVVVVGLMGLAGQQIVQGFAELGDQLGQAVDD
+AIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATVMNSAVSLGSTAVNIGAGLFIALFSLIF
+FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL
+GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV
+LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTPEELTE
+RTGHALEPGGAEDETAGSHRYRPSAHDDAALASEADAGTRHGDDA*
+>NZ_CP033200.1_164
+MSSTLAAQTKIDKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA
+TLLAPVFQAMRRIKVPGVAAALLCVLLLVVVVVGLMGLAGQQIVQGFAQLGDQLGQAVDD
+TIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATVMNSAVTFGSTAVNIGAGLFIALFSLIF
+FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL
+GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV
+LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTPEELTE
+RTGHALEPGGAEDEAAGSHRYRPSAHDDAALASEADAGTRHGDDA*
+>NZ_CP040019.1_2442
+MSSTLAAQTKINKDVPYGLTVAAAWSWRLVAVLVGLGILWWLLSFVSLVLIPVLVAALLA
+TLLAPLFEGMRRIGIPGIAASLLCVVLLIVVVVGLVVVAGQQIAQGFSDLGDKLTQAVDG
+AIAWLASIGVELPTAGGGLEGLWQTLRDNSGTLLDSAMTFGSTAVNIGAGFFIALFSLIF
+FLYDGDRIWRFILVFVPKAHRATVGRAGQTGWRALGNYVRVQIFVAFVDAVGIGLGALIL
+GVPLAIPLAVLVFLASFIPMIGATVTGAIAVLFALMSNGLVNALLMLGVVLLVQQIESNV
+LQPLVMGKAVALHPLAVFLAVAAGSAVLGLAGAVFAVPVLAFVNSFIRALTADPPEQLTD
+RSDQALAPGSAADEAVGSHVFEPTKHDDAALASEDDAGTSGDLR*
+>NZ_CP083691.1_2322
+MSSTLSTDAKLEKDIPYGLTVAAGWSWRVIAVAAMLWVVWHFAGFASLVIIPVLVAALLA
+VLLAPIYRALRRARIPGVLAAVLSIVLLLAAVVLLAWVAGLELVQGFSDLSDQLGASVEH
+LVTWVQGMGVPVSFDAAALDNVWSTVKDNSGVLVDGALAFGSTAANVLTGLFIALFTLIF
+FLFDGERIWRFLLAFVPHTSRSRVDVAGRTGWNALGSFVRVQIVVAFIDAVGIGLGAWLL
+GVPLALPVAVIVFLFSFVPTIGAIASGALACVLALTANGLVNALLMLGVVILVQQIESNL
+LQPLIMGRAVSLHPLAVFLGVAAGGVALGLVGAVFAVPLLAFANAFVQALRAKGPGEEIL
+PGEKVFRPSDEVIAAARRDAKLDPKLDPTSFDDDSGPDGDVEDGRTGSTRTELKP*
+>NZ_CP097650.1_437
+MSSTLAAQTKIDKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA
+TLLAPVFQAMRRIKVPGIAAALLCVLLLVVVVVGLMGLAGQQIVQGVAQLGDQLGQAVDD
+AIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATLMNSAVSFGSTAVNIGAGLFIALFSLIF
+FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL
+GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV
+LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTPEELTE
+RTDHALEPGGAEDEAAGSHRYRPSTHEDAALASEADAGTRHGDGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000487.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000487.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9829fd1de68b311e9bba8f77ab51c92c6815962d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000487.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_440
+MTTSQSDAPWLTQEAYDRLSKELEYISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL
+EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG*
+>NZ_CP033200.1_167
+MTTSQSDAPWLTQEAYDRLSKELEYISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL
+EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG*
+>NZ_CP040019.1_2439
+MTTSQSDAPWLTQEAFDRLSKELEHISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAEDDEHL
+EVYSERSPLGEAINGAAKGDKVTYTAPNGKEIKVEIKDVKPYSG*
+>NZ_CP083691.1_2319
+MATTPSDAPWLTQEAFDRLSKELAHISGPGRQEIIERIEAAREEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGETQAADGVVTPGTVVTAVVAGDEMTFLFGNREIAADGEDL
+EVYSERSPMGEAINGAKQGDKVTYTAPNGKDIAVEITDVKPYQA*
+>NZ_CP097650.1_440
+MTTSQSDAPWLTQEAYDRLSKELEHISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL
+EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000488.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000488.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9114f6a9c9a57333afdb2507161cc3aa7a22092a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000488.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_441
+MSHHAPAVRAQDPTLANRYGTDHTRPGRRRLWAGLGGLGLVVAVLLSVWIGLNMSVGAIE
+YKDVGFTIEDDGHATVTFQASVPEGVQAECDVLVTDSHAAPVGFRTVRLETLPADRRDSP
+SDAQQRYTVDVRTVVRGDSGVVETCRKV*
+>NZ_CP033200.1_168
+MSHHAPAVRAQDPTLANRYGTDHTRPGRRRLWAGLGGLGLVVAVLLSVWIGLNMSVGAIE
+YKDVGFTIEDDGHATVTFQASVPEGVQAECDVLVTDSHAAPVGFRTVRLETLPADRRDSP
+SDAQQRYTVDVRTVVRGDSGVVETCRKV*
+>NZ_CP040019.1_2438
+MSHHAHAVHAQDPTLANRYGTDQDRPSRRRLWVGLGVLGLLGAVLLAVWLGLNLSVGNIE
+YKDVGYTIEDDGNATVTFQVLVPEGVQAECDVLVMDSHAAPVGFRTVRLVSVPQDQRDTP
+SDAQQVYTVDVRTVVRGDSGVVEACRKL*
+>NZ_CP083691.1_2318
+MSSTPAPAASAPETTLATRYGVGQRRDRRRLWTVLGAVALVLAVATAVAVALGNSVGRVE
+AEDVGYRIDDAAHAAVTFQVTLPRGVEAAACDLKVMDARYAPVGFHTVRVSAGPDHPAGE
+TVTYTADVRTVGRGVTGVVEGCRPA*
+>NZ_CP097650.1_441
+MSHHAPAVRAQDPTLANRYGTNHTRPGRRRLWAGLGGLGLVVAVLLSVWIGLNMSVGAIE
+YKDVGFTIEDDGHATVTFQASVPEGVQAECDVLVTDSHAAPVGFRTVRLETLPADRRDSP
+SDAQQRYTVDVRTVVRGDSGIVETCRKV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000493.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000493.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6acb524a438777e0ee1e0442c2c40507ae2a97cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000493.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_446
+MHRPSPGLPDLPGGPAPAPTLAERAGGRLLGAVAPTAVLIAAMWVAQFVLIFLGRVIIPG
+VGLIPRRLDGLDGVLFSPVLHAGWAHLIGNTTALLVLGPLAALVSRRPVALLVCAWLGSG
+LLTWVIGTPGVHIGASGIVYALIAFLIVYGVAVRRIGAVVVSVLVALTHLGSSLIGLLPA
+PGISWTGHLAGAVVGVLLGLWWGRADRQVPNRR*
+>NZ_CP033200.1_173
+MSMHRPSPGLPDLPGGPAPAPTLAERAGGRLLGAVAPTAVLIAAMWVAQVVLIFLGRVII
+PGVGLIPRRLGGLDGVLFSPVLHAGWAHLIGNTTALLVLGPLAALVSRRPVALLVCAWLG
+SGLLTWVIGTPGVHIGASGIVYALIAFLIVYGIAVRRIGAVVVSVLVALTHLGSSLIGLL
+PAPGISWTGHLAGAVVGVLLGLWWGRADRQVPNRR*
+>NZ_CP040019.1_2433
+MSMHRPTPRLPERGAVPAARPAPSLAERVSGRLVAVIAPTLLLVAALWVVQIALVFFGRL
+VIPSLGLIPRSVTGLDGILFSPLLHAGWGHLIGNASALILLGPLAALISGRPLALLAAAW
+LGSGVLTWVIGSPGVHIGASGIVYALVAFLVVYGIAVRRVVPVVVSVLVALTHLGSSLIG
+LLPAPGVSWTGHLAGAVVGVLLGLWWGRGDRRPRHADI*
+>NZ_CP083691.1_2313
+MPLPDRRPADDAVPAPRPSLTQAAAQGLVRTVAPTAVLVAAMWVMFLVSIVGGSTLIGGL
+GLIPRRAAGLDGILFSPLLHGGWRHLVGNTTALLVLGPVAAAVSRRPLALLAAAWLGSGA
+LTWVIGTPGVHVGASGIVYALIAFLLVYGVVARRVLAVVVAVAVAAAHLGSSLLGLLPQP
+GVSWTGHLAGAVVGVGLALLWGRADRPARAPLGP*
+>NZ_CP097650.1_446
+MHRPSPGLPDLPGGPAPAPTLAERAGGRLLGAVAPTAVLIAAMWVAQFVLIFLGRVIIPG
+VGLIPRRLDGLDGVLFSPVLHAGWAHLIGNTTALLVLGPLAALVSRRPVALLVCAWLGSG
+LLTWVIGTPGVHIGASGIVYALIAFLIVYGVAVRRIGAVVVSVLVALTHLGSSLIGLLPA
+PGISWTGHLAGAVVGVLLGLWWGRADRQVPNRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000494.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000494.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8fe86d5f5f0f9c8e576e3cb1235058dc2957a27a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000494.fa
@@ -0,0 +1,49 @@
+>NZ_CP042169.1_447
+MVAELVEHAQTRQEPSSRPGQARAEAGAAEATGLRTYVVDTSVLLSDPRALLHFAEHEVV
+LPLVVVSELEAKRADPDLGYDARTALRLLDDLRGRHGALDQPVPITPEGGTLRIELNHVS
+VDVLPLGIRGTDNDSRILAVAKALADEGAMVTVVSKDLPMRVKAAAMGLAADEYRHELVR
+DSGWRGTVSLSVAQERLDALYDDGEVDLAGVPLGTLTGTGVETGPEEAPAEADRLPVNTG
+LVLTAPRGSALARVGEGGRACLVRGDRDVFGLHGRSAEQRLAIELLTDPSVGIVSLGGRA
+GTGKSALALCAGLDAVMERREHRRVVVFRPLYAVGGQDLGYLPGSEGDKMGPWAQAVFDT
+LGALVSPSVVDEVVDRGMLEILPLTHIRGRSLHDAWVIVDEAQSLERNVLLTVLSRMGRN
+SKVVLTHDVAQRDNLRVGRHDGIAAVVERLKGHPLFGHVTLTRSERSPIAALVTDLLEEG
+RA*
+>NZ_CP033200.1_174
+MVAELVEHAQTRQEPSSRPGQARAEAGAAEATGLRTYVVDTSVLLSDPRALLHFAEHEVV
+LPLVVVSELEAKRADPDLGYYARTALRLLDDLRGRHGALDQPVPITPEGGTLRIELNHVS
+VDVLPLGIRGTDNDSRILAVAKALADEGATVTVVSKDLPMRVKAAAMGLAADEYRHELVR
+DSGWRGTVSLSVAQERLDALYDDGEVDLAGVPLGTLTGTGVETGPGEAPAEADRLPVNTG
+LVLTAPRGSALARVGEGGRACLVRGDRDVFGLHGRSAEQRLAIELLTDPSVGIVSLGGRA
+GTGKSALALCAGLDAVMERREHRRVVVFRPLYAVGGQDLGYLPGSEGDKMGPWAQAVFDT
+LGALVSPSVVDEVVDRGMLEILPLTHIRGRSLHDAWVIVDEAQSLERNVLLTVLSRMGRN
+SKVVLTHDVAQRDNLRVGRHDGIAAVVERLKGHPLFGHVTLTRSERSPIAALVTDLLEEG
+RA*
+>NZ_CP040019.1_2432
+MVAERVEHGRALTGTTEARPDAAGAAGHAAAARTGAADAVVAPDARETGLRTYVVDTSVL
+LSDPRAVLRFAEHEVILPLVVVSELEAKRADPDLGYFARTALRLLDDLRGRHGALDRAVP
+ISPEGGTLRVELNHVSTDVLPLGIRGTDNDSRILAVAKAFADEGRDVTVVSKDLPMRVKA
+AAMGLSADEYRHELVRDSGWRGTVTLTVEQELLDALYDDGEASLAGVPVDGTDGVGAGVE
+ADGTGAGGSGVDRTGAEGPGAAVLPVNTGLVLLAPRGSALARVAEGGRALLVRGDQDVFG
+LHGRSAEQRLAIDLLTDPAVGIVSLGGRAGTGKSALALCAGLDAVMERREHRKVVVFRPL
+YAVGGQELGYLPGSEGEKMGPWAQAVFDTLGALVSPSVIDEVVDRGMLEVLPLTHIRGRS
+LHDAWVIVDEAQSLERNVLLTVLSRMGRNSKVVLTHDVAQRDNLRVGRHDGIAAVVERLK
+GHPLFGHVTLTRSERSPIAALVTEMLEDGRG*
+>NZ_CP083691.1_2312
+MTLQADGTGRHGRGTGETGAEVREGAASDGRRSYVVDTSVLLSDPRALVRFAEHEVVLPL
+VVVSELEGKRQDPDLGHAARHALRLLEDLRVRHGSLEDAVPFTAQGGTLRVELNHVSTDV
+LPFGIRGTDNDSRILAVAKALADEGRDVTLVSKDLPMRVKAAAMGLAADEYRHELVRDSG
+WRGAVSLRVDEDRLDSLYDDGRMGLHGIPLDEVAGSGVDAVPGEPAPTAVDLPVNTGLSL
+TSPRAAGLARVREGGVATLVRGDADVFGLHGRSAAQRLAIDLLTDPSVGIVSLGGRAGTG
+KSALALCAGLEAVMERREHRRVVVFRPLYAVGGQDLGYLPGTEGEKMGPWAQAVFDTLSA
+IVSPSVIDEVVDRGMLEVLPLTHIRGRSLHDSWVIVDEAQSLERNVLLTVLSRMGRDSKV
+VLTHDVAQRDNLRVGRHDGIAAVVETLKGHPLFGHVTLTRSERSPIAALVTELLEEGED*
+>NZ_CP097650.1_447
+MVAELVEHAQTRQEPSSRPGQARAEAGPAEATGLRTYVVDTSVLLSDPRALLHFAEHEVV
+LPLVVVSELEAKRADPDLGYYARTALRLLDDLRGRHGALDQPVPITPEGGTLRIELNHVS
+VDVLPLGIRGTDNDSRILAVAKALADEGATVTVVSKDLPMRVKAAAMGLAADEYRHELVR
+DSGWRGTVSLSVAQERLDALYDDGEVDLAGVPLGTLTGTGVETGPEEAPAEADRLPVNTG
+LVLTAPRGSALARVGEGGRACLVRGDRDVFGLHGRSAEQRLAIELLTDPSVGIVSLGGRA
+GTGKSALALCAGLDAVMERREHRRVVVFRPLYAVGGQDLGYLPGSEGDKMGPWAQAVFDT
+LGALVSPSVVDEVVDRGMLEILPLTHIRGRSLHDAWVIVDEAQSLERNVLLTVLSRMGRN
+SKVVLTHDVAQRDNLRVGRHDGIAAVVERLKGHPLFGHVTLTRSERSPIAALVTDLLEEG
+RA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000497.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000497.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83546f856034345748f8bd81f68f19c6dedc4c1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000497.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_450
+MTPHTRPETTPAPDVVVPTSDLTPAEAWEVLAEGNRRFVAGEPSHPNQNAERRSDLTAGQ
+APVAVIFGCADSRLAAEIIFDLGLGDVFVVRTAGHVIDDAVLGSIEYGVDVLEIPLVIVL
+GHNSCGAVTATVESYISGTMPRGFVRPLVERIIPSVLAGRRRGLEEVDEFVAEHVDQTCD
+HLLETSQSVRAAVESGRTAVVGLTYSLSEGTARPGRVHGDLAV*
+>NZ_CP033200.1_177
+MTPHTRPETTPAPDVVVPTSDLTPAEAWEVLAEGNRRFVAGEPSHPNQNAERRSDLTAGQ
+APVAVIFGCADSRLAAEIIFDLGLGDVFVVRTAGHVIDDAVLGSIEYGVDVLEIPLVIVL
+GHNSCGAVTATVESYISGTMPRGFVRPLVERIIPSVLAGRRRGLEEVDEFVAEHVDQTCD
+HLLETSQSVRAAVESGRTAVVGLTYSLSEGTARPGRVHGDLAV*
+>NZ_CP040019.1_2429
+MSTENTATAAAAAHDDGAAGSRPTPQEAWETLAEGNRRFVAGDPGHPNQNAERRSTLTSG
+QEPIAVIFGCSDSRLAAEIIFDVGLGDVFVIRTAGQVIDDAVLGSLEYSVDVLKIPLIVV
+LGHDSCGAVTATVESYISGDMPPGFIRSLVERITPSVLAGRRRGLEEIDDFVAEHVDQTC
+DRLVETSQAVRDAVEAGRTAVVGLTYSLAGGTAQPGRVLGALQV*
+>NZ_CP083691.1_2309
+MTTAAETTPARPTPAEAWRTLQEGNRRFVAGTPGHPNQDSERRHGLTEGQAPIAVIFGCA
+DSRLAAEIIFDVGLGDVFVVRTAGHVVDDAVLGSLEYAVDSLDVPLIIVLGHDSCGAVTA
+TVESYISGTMPAGFVRSLVERITPSVLAGRRRGLEEVDDFVAEHVDQTCDRLLETSQSVR
+AAVEAGRTAVVGLTYSLAEGTASPGRVHGRIEA*
+>NZ_CP097650.1_450
+MTPHTRPETTPAPDVVVPTSDLTPAEAWEVLVEGNRRFVAGEPSHPNQNAERRSDLTAGQ
+APVAVIFGCADSRLAAEIIFDLGLGDVFVVRTAGHVIDDAVLGSIEYGVDVLEIPLVIVL
+GHNSCGAVTATVESYISGTMPRGFVRPLVERIIPSVLAGRRRGLEEVDEFVAEHVDQTCD
+HLLETSQSVRAAVESGRTAVVGLTYSLSEGTARPGRVHGDLAV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000506.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000506.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77415f76d706f5e865d80a1781308b52f558e27b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000506.fa
@@ -0,0 +1,22 @@
+>NZ_CP042169.1_460
+MARMTASASSDPLDPLPFRAGDAAGAEPGVEGGPAEAGVSSPTGRGGRDRRGRGLRHPRP
+FGARSERGRGEALLTAVEKAVDRLGSLDAPGLRHVTARVERIPDRLDERLRELHAGRERD
+EEALFARAERQGRDGVLITLFERPLRDAADPADLEGAVYGVALSRCADALGVDPQVLDPS
+WGRG*
+>NZ_CP033200.1_187
+MARMTAPASSDPLDPLPFRAGDAAGAEPGVEGGPAKAGVSSPAGRGGRDRRGRGLRHPRP
+FGARSERGRGEALLTAVEKAVDRLGSLDAPGLRHVTARVERIPDRLDERLRELHAGRERD
+EEALFARAERQGRDGVLITLFERPLRDAADPADLEGAVYGVALSRCADALGVDPQVLDPS
+WGRG*
+>NZ_CP040019.1_2419
+MDRLAALEAPGLRHVTARVERIPDRLDERLRALRAGAERDEETLFARAERQGQDGVVITL
+FERPLRDAADPEDLDGAVYGVALSRCAEALGVDPQVLDPGWGRA*
+>NZ_CP083691.1_2299
+MARMPADPLAPLPPLPPARRDGRGPRPGLRRDVRGRGLRHPLPFGARAGRGRADALMDAV
+EKAVDRLAGLQAPGLRRVAARLERIPDRLDERLALQRARAVADEEGLFGRAERDGADGVV
+ITLFERPLTESADPADLEEAVYAVALSRCAAALGVDPQVLDPSWGRA*
+>NZ_CP097650.1_460
+MARMTASASSDPLDPLPFRAGDAAGAEPGVEGGPAEAGVSSPAGRGGRDRRGRGLRHPRP
+FGARSERGRGEALLTAVEKAVDRLGSLDAPGLRHVTARVERIPDRLDERLRELHAGRERD
+EEALFARAERQGRDGVLITLFERPLRDAADPADLEGAVYGVALSRCADALGVDPQVLDPS
+WGRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000512.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000512.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f5ca76be1df65f4cd265ea96fd368e22ebd2ad4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000512.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_466
+MPEGRIVLAATPIGNLGDASARLRDLLAEADVIAAEDTRTARRLCAGLGVTPAGRVVAHH
+EHNEAASAQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVTCAPGPSAVT
+TALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLADALAVVAEVL
+GAERPVCVARELTKLHEEVVRGTAAGVHAWAAERHAGEGIRGEIVLVIGPAAPGAEGEAS
+EADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAARG*
+>NZ_CP033200.1_195
+MTGRIVLAATPIGNLGDASARLRELMAEADVIAAEDTRTARRLCAGLGVTPAGRVVAHHE
+HNEAASTQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVTCAPGPSAVTT
+ALALSGLPTDRFAFDGFVPRKDGDRRRWLTSLLTEARTVVAFESPQRLADALAVVVEVLG
+AERPVCVARELTKLHEEVVRGTAADVHAWAAERHAGEGIRGEIVLVIGPAAPGAEGEASE
+ADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAARS*
+>NZ_CP040019.1_2412
+MTPRPTDLPSPSGRIVLAATPIGNLGDASARLRELLAEADVIAAEDTRTARRLCQGLGVT
+PAGRVVAHHEHNEAASTQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVT
+CAPGPSAVTTALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLAD
+ALAVVVEVLGAERPVCVARELTKLHEEVVRGTAAEVHAWAAERHAGEGIRGEIVLVIGPA
+SPDAASAGGATEADAVAEVGVLVDSGTRLKEAVATVAAAHGLRSRTLYQAVLAARG*
+>NZ_CP083691.1_2292
+MSLPAASGRIVLAATPLGNLGDATGRLRELLATADVIAAEDTRNTRRLCQGLGITPAGRL
+MAHHEHNEAASAAGLLERVRAGETVVMVSDAGMPTVSDPGFRLVEAAVAAGLPVTCAPGA
+SAVTTALALSGLPSDRFAFDGFLPRKDGERRRRLEEIRTDPRTVVYFESPQRTASALAVI
+AEVLGGARPVCVARELTKLHEEVVRGTADELVAWAVEREAGEGIRGEVAIVVGPAAPDAG
+AGADEADVLAEVAALTDSGTRLKEAVAAVAAAHGLRSRELYQAVLDARRG*
+>NZ_CP097650.1_466
+MPEGRIVLAATPIGNLGDASARLRDLLAEADVIAAEDTRTARRLCAGLGVTPAGRVVAHH
+EHNEAASAQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVTCAPGPSAVT
+TALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLADALAVVVEVL
+GAERPVCVARELTKLHEEVVRGTAAGVHAWAAERHAGEGIRGEIVLVIGPAAPGAEGEAS
+EADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAARG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000515.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000515.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf9fc6a6f02bd30729e1d952fd0959cd61295e6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000515.fa
@@ -0,0 +1,34 @@
+>NZ_CP042169.1_471
+MVQPSPHPAPAPLLSAADVRRIAAELDLRPTKQWGQNFVIDPNTIRRIVQAADVTADEHV
+LEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAARLPRTAAEFRPGAEDALAVLHADAMTLS
+EQALAEVRPAAAAGGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG
+PGSKVYGVPSAKAAWYADVRKAGTIGTQVFWPAPRIHSGLVAFTRREPPTGGASRREVFA
+VVDAAFAQRRKTLRAALASWAGSPQAAEDALVAAGVDPRARGEALDIAAFARIAEHGPRR
+AAEVSA*
+>NZ_CP033200.1_201
+MVQPSPHPAPAPLLSAADVRRIAAELDLRPTKQWGQNFVIDPNTIRRIVQAADVTADEHV
+LEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAARLPRTAAEFRPGAEDALAVLHADAMTLS
+EQALAEVRPAAAAGGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG
+PGSKVYGVPSAKAAWYADVRKAGTIGTQVFWPAPRIHSGLVAFTRREPPAGSTSRREVFA
+VVDAAFAQRRKTLRAALASWAGSPQAAEDALVAAGVDPRARGEALDIAAFARIAEHGPRR
+AAEEVVA*
+>NZ_CP040019.1_2408
+MIDPNTIRRIVQAAGVGPDEHVLEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAERLPHTV
+QEFRPASADALAVLHADALRMTAADLDAVRPAAAPGGPTALVANLPYNVAVPVLLHALAE
+LPGLRHGLVMVQEEVADRLAAGPGSRVYGVPSAKAAWYAQVDKAGTIGTQVFWPAPRIHS
+GLVAFTRREPPTSAVSRAETFAVVDGAFAQRRKTLRAALAGWAGSPQAAEDALVAAGVDP
+RTRGEALGIEAFARIAEHGPRRAAGEGSA*
+>NZ_CP083691.1_2288
+MVPPPDAPATAPLLSAADVRRLAAELDLRPTKQWGQNFVIDPNTIRRIVAAADLAPDEHV
+LEIGPGLGSLSLGLLDAASAVTAVEIDPVTAARLPATAAEFRPERAADLAVLHADAMTLT
+AEGLDSVRPAGAASGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG
+PGSRVYGVPSAKAAWYADVRKAGVIGTQVFWPAPRIHSGLVAFTRREPPTQAVDRREVFA
+VVDAAFAQRRKTLRAALATWAGSPALAEEALVAAGVDPKARGEALDIAAFARIAEHRPEA
+AS*
+>NZ_CP097650.1_470
+MVQPSPHPAPAPLLSAADVRRIAAELDLRPTKQWGQNFVIDPNTIRRIVQAADVTADEHV
+LEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAARLPRTAAEFRPGAEDALAVLHADAMTLS
+EQALAEVRPAAAAGGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG
+PGSKVYGVPSAKAAWYADVRKAGTIGTQVFWPAPRIHSGLVAFTRREPPAGGASRREVFA
+VVDAAFAQRRKTLRAALASWAGSPQAAEDALVAAGVDPRARGEALDIAAFARIAEHGPRR
+AAEEVVA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000520.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000520.fa
new file mode 100644
index 0000000000000000000000000000000000000000..820c338ec849493e5158bb6f09addb8d352a93f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000520.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_479
+MAERVEPAHGEDGGAVAAPQPHRPRLPFWASLLLNVVVALAVVAVVQALWVKVYSVPSGS
+MENTLEVGDRMLVNRTAYPDGAADAQDVVVFTANEDWAHPMPPEGAVENAVRTFGDLTGI
+GRSHEQALVKRVIGTAGQTVECCTAEGAVTVDGEPLDEPYIHNDLPFIRDELDCESEVMS
+ARCFGPVTVPEDSMLVLGDHRSNSADSVIACRGIPADQAGDCARFVTREDIVGEVFVTVW
+PPTHWGGH*
+>NZ_CP033200.1_209
+MAERVEPAHGEDGGAVAAPQPHRPRLPFWASLLLNVVVALAVVAVVQALWVKVYSVPSGS
+MENTLEVGDRMLVNRTAYPDGMADAQDVVVFTANEDWAHPMPPEGAVENAVRTFGDLTGI
+GRSHEQALVKRVVGTAGQTVECCTAEGAVTVDGEPVDEPYIHNDLPFIRDELDCESEVMS
+ARCFGPVTVPEDSMLVLGDHRSNSADSVIACRGIPADQAGDCARFVTREDIVGEVFVTVW
+PPTHWGGH*
+>NZ_CP040019.1_2402
+MAERVEPVRGEDGDDGSVAAPERRRSRLPGWASVLLNVVVAIAVVAVVQALWVKVYSVPS
+GSMEQTLEVGDRMLVNRTAYPDGMAASQDVVVFNANEDWAQPLPPEGPVENAVRTFGDIT
+GIGRSHDQALVKRVVGTEGQTVECCTSEGRVTVDGQPLDEPYLHNDLPFAPGRLDCESDV
+MSARCFGPITVPEDSMLVLGDHRSNSADSVIGCRGLPAEQAEGCARFVTREDVVGEVFVT
+IWPPSNWGGH*
+>NZ_CP083691.1_2282
+MAHTPDAVPARDEAACDEAVRDDAAPAPASSAAAPGRRRRVQLPFWASVLLNVAVALLVV
+SVVQALWVKVYSVPSGSMEQTLQVGDRMLVNRTAYPDGVAERQDIVVFDANETWGVDTVG
+EEGPVEGAVRTFGDLTGIGRSHENALVKRVIGLPGETVECCTSQGAVTVGGTPLEEDYLY
+EDLPFVPGTLDCTTTPRSSRCFGPVTVPERSMLVMGDHRSNSADSVYQCRGLTAEQAGDC
+AHFVRDEDVVGRVFSTVWPPSNWSGH*
+>NZ_CP097650.1_478
+MAERVEPAHGDDVDGGAVAAPQPHRPRLPFWASLLLNVVVALAVVAVVQALWVKVYSVPS
+GSMENTLEVGDRMLVNRTAYPDGAADSQDVVVFTANEDWAHPMPPEGAVENAVRTFGDLT
+GIGRSHEQALVKRVVGTAGQTVECCTAEGAVTVDGEPLDEPYIHNDLPFIRDELDCESEV
+MSARCFGPVTVPEDSMLVLGDHRSNSADSVIACRGIPADQVGDCARFVTREDIVGEVFVT
+VWPPTHWGGH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000522.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000522.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f14349414f9c7e4693fb04a00ab9c90ac739154
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000522.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_482
+MAAQSTTAAVTVVIPHYGDPAPTLALVDRLLTDPGDALAAVVVSDDASPTPYPEAHDPRL
+TVVRRERNGGFGANVNTGLAAVTTELALVLNSDAEITGAQIDALVVAAAPYQPAVVSPQV
+VNEDGTPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAATRSASPVAVDWVM
+GAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSDPL
+RRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNALRQARGVDVDARAVLRDEHAL
+VWKGQRR*
+>NZ_CP033200.1_211
+MAAQSPTAAVTVVIPHYGDPAPTLALVDRLLTDPGDALAAVVVSDDASPTPYPEAHDPRL
+TVVRRERNGGFGANVNTGLAAVTTELALVLNSDAEITGAQIDALVAAAAPYQPAVVSPQV
+VNEDGTPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAATRSASPVAVDWVM
+GAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSDPL
+RRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNVLRQARGVDVDARAVLRDEHAL
+VWKGKRR*
+>NZ_CP040019.1_2400
+MAAQSTAAAVTVVIPHYGDPAPTLALVDRLLADPGDALAAVVVSDDASPTPYPEAHDPRL
+TVVRRERNGGFGANVNTGLSEVDTDLALVLNSDALITGEQIDALVAAAAPFQPAVVSPQV
+VNEDGSPQWSGRHFPTVLHQGVEWLTPLARFRHLPLLHEAVGHDVAAARSAAPVAVDWVM
+GAVMLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRDRGVASIVVPSVRVEHGMHGSSDPL
+RRRGWLVDSRFRYARKFGRPRALKAVLTAATGVNYAVNRVRQARGTDVDAAAVLRDEHAL
+IWKGTRR*
+>NZ_CP083691.1_2280
+MPASRIAPSVTVVIPHYGDPEPTRALVDALLAAPGRSVAGVVVSDDASPEPYPQPAPGRE
+GLTVVRREANGGFGANVNTGLAEVRTELALVLNSDAEITGEQIDALVEAARPYQPAVVSP
+QVVNEDGSPQWSGRHFPTVTHQTVEWLTPLARFRHLPALHEAVGHDVRAAEADSPVAVDW
+VMGAVMLLPMAEVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSVVVPSVRVVHGLHGSSD
+PLRRRAWLVDSRFRYARKFGRPRLLRGALTAATGVNWAVNRVRQTRGTDVDANAVFRAER
+DLIWKGTRR*
+>NZ_CP097650.1_481
+MTAQSPTAAVTVVIPHYGDPAPTLALVDRLLSDPGDALAAVVVSDDASPTPYPEAHDPRL
+TVVRRERNGGFGANVNTGLAAVTTELALVLNSDADITGAQIDALVAAAAPYQPAVVSPQV
+VNEDGSPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAAARSASPVAVDWVM
+GAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSDPL
+RRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNALRQARGVDVDARAVLRDEHAL
+VWKGRRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000523.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000523.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fdae0bc044c01481fa7ff2fc6bca9dee092100ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000523.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_483
+MSATGYTVPAPPDARGGRSPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYATLG
+MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSEIL
+EAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA
+LPQVPRRDELVFVGSRYPNRVELLARLAAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP
+AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE
+VLVFEDADHLIELGRRVVADPAWGARIREAGRRRSHAEHTFAHRAAMAQGWWA*
+>NZ_CP033200.1_212
+MSATGYTVAAPPEARGGRSPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYATLG
+MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSEIL
+DAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA
+LPEVPRRDELVFVGSRYPNRVELLTRLAAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP
+AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE
+VLVFEDADHLIELGRRIVADPAWGARIREAGRRRSHVEHTFAHRAAMAQGWWA*
+>NZ_CP040019.1_2399
+MSGTGYTVPARGARGTGRAERLFLVSPAFHGYHRSIARAWAAQGFDVTVHCYDAYATVPM
+KLRNKALLELPQKAGVDRTAARVAWDTERAVAALRAARPDRVLVIKGDSLGEAFWSEVVE
+AGLPRLLWLYDDLSRHDYSPEFLRAIGPVLSYARSEAEQLAGEGVDAHYLPNGFDPDMAL
+PSLPRREELVFVGSRYPNRVELLTTLAEAGVPVRAYGRQWSHHPVDRLRTWEVTRPALPA
+ERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYEPGEEV
+LVFENPEHLVELGRRVVAEPSWGERIREAGRSRSHAEHTFAHRAALAQEWWT*
+>NZ_CP083691.1_2279
+MSAGTYTIAARGERPVSGRPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYADLG
+MKLRNKLALELPQKAGLDRTAARVAWDTDRAVAALRAAAPDRVLVIKGDSLGDAFWDEVT
+GRALPRMLWLYDDLSRHDYSMDFLRGIGPVLSYARSEAESLAAQGVDAHYMPNGFDPEMV
+LPAVPRTEELVFVGSRYPNRVELLRALASAGVPVRAYGRQWSHHPVDRLRTWELSRPDLP
+AERDIPLAEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRPDVAEFYVPGEE
+VLVFEDTEHLVELGRRIVAEPAWGDRIRAAGRRRSHAEHTFSHRARMAQEWWA*
+>NZ_CP097650.1_482
+MSATGYTVPAPPDARGGRSPERLFLVSPAFHGYHRSIASAWAAQGFDVAVHCYDAYATLG
+MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSAIL
+DAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA
+LPQVPRRDELVFVGSRYPNRVELLSRLTAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP
+AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE
+VLVFEDADHLIELGRRVVADPAWGARIREAGRRRSHAEHTFAHRAAMAQGWWA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000524.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000524.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e09b77d365845c68fe38756ab19a41500b4c3c55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000524.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_484
+MTDAPLFWRSEDLPRWHAWQRAQWPLTRRAADTARSTVRGVAGALTRRRSTGDDAPRLLL
+PAGDVHTLVALESFGPTQLAALASPVAALATARPEAAAGVGWVLPAGDAPALPGAVGHRE
+HAATADVVTDRLPGLRRVLVAGEYLPSGRAAVRWARQRGARVGVVQHGLLAVSTPPVPRD
+ATLYAFTSADADWWTQGRADVEAVAVGSALLEQARRAAPAPSDTAGDGPGVFLGQLHGAE
+LPRRDFAAAAEQYVRATGAAYRPHPAERDRLSRGQHAAWRRAGVRIDDAGAPLVATRGPV
+AAVFSTGILEAAQAGRPAWAVHPDPPAWLEGFWRRYGMTRWRPGRTPEPTPPLASPTADP
+AAAIAEHVWKESA*
+>NZ_CP033200.1_213
+MTDAPLFWRSGDLPRWHAWQRAQWPLTRRAADTARSTVRGVAGALARRGSTGDDVPRLLL
+PPGDVHTLVALESFGPTQLAALASPVAALATARPEAAAGVGWVLPAGDAPALPGAAGHRE
+HAATADVVTDRLSGLRRVLVAGEYLPSGRAAVRWARQRGARVGVVQHGLLAVSTPPVPQD
+ATLYAFTSADADWWTQGRADVEAVPVGSALLEQARRTAPALSGAGDDGPGVFLGQLHGAE
+LPRRDFAAAAEQYVRATGAAYRPHPAERDRLSRGQHAAWRRAGVRIDDAGAPLVATRGPV
+AAVFSTGILEAAQAGRPAWAVHPDPPAWLEGFWRRYGMTRWRPGRVPEPTPPLASPTTDP
+AAAIAEHVWKESA*
+>NZ_CP040019.1_2398
+MSGVGSGDVPLFWRPEDLPAWQRWQRAQWPASRRLADTARRLARAGRGALAAGRGAAPAP
+ESGLRLVLPAGDVHTLVGVESAAPTQRAALVEPVRALAEGRAGHAAADAARTAAGVGWVV
+PADVVAAQLPDLPGSDALSVHAVDDVMVAERLGGLRCVLVAGEYLPAGRAAVRWARERGA
+RVGVVQHGLLAVSTPPVPRDVALYAFTDHDAHWWTQGRTDVQAVAVGSALLEAARRMASH
+AVADAVPRAAGPGVFLGQLHGAELPRTDFARAAQEYVRATGAAYRPHPAERDRLSLAQHE
+AWRKAGMRIDATAGPLASTAGPVAAVFSTGILEAAQAGRPAWAVHPDPPAWLEGFWERYG
+MTRWRPGVETEPTPPLASPSADPAAAIAAHLWKETA*
+>NZ_CP083691.1_2278
+MTRAVAQPPLFWRAEQLDAWRRWQRTQWPLARRAADLVRGGVARSRGAVQAPDAGLRLLL
+PAGDVHTLIAVESAGPTQRAALVEPTRALAEGRTGLDAAARTRLLGGVAWVVPADVAGAL
+LPDLPAAAQLTGHAADPDTVGTRLAGLERVLVAGEYLPAGRAAVRWAHERGASVHVVQHG
+LLAVSTPPVPRDATLYAFTARDADWWTQGRADVRAVPVGSALLEAARRGAASADPTATGS
+TGPGPGLFLGQLHGAELPRAQFAAAAEQYVRTTGAVYRPHPAERDRLSRAQHARWEGAGI
+AVDRSGAPLTQTAGPVAAVFSTGILEAAQTGRPAWAVHPDPPRWLVEFWDRYGITRWMPG
+ADPTPTPALVAPTADPAAAIARDLWKEHA*
+>NZ_CP097650.1_483
+MTDAPLFWRSEDLPRWHAWQRAQWPLTRRAADTARSTVRGVAGALTRRRSTGDDAPRLYL
+PAGDVHTLVALESFGPTQLAALASPVAALATARPEAAAGVGWVLPAGDAPALPGAVGHRE
+HAATADVVTDRLSGLRRVLVAGEYLPSGRAAVRWARQRGARIGVVQHGLLAVSTPPVPQD
+ATLYAFTSADADWWTQGRADVEAVPVGSVLLEQARRTAPALSGAGDDGPGVFLGQLHGAE
+LPRRDFAAAAEQYVRATGAAYRPHPAERDRLSRGQHAAWRRAGVRIDDAGAPLVATRGPV
+AAVFSTGILEAAQAGRPAWAVHPEPPAWLEGFWRRYGMTRWRPGRTPEPTPPLASPTADP
+AAAIAEHVWKESA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000535.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000535.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e91a84dce5d3b8c6a5883a3cec442e3aea9015c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000535.fa
@@ -0,0 +1,37 @@
+>NZ_CP042169.1_508
+MSALWAVALIMLLSGTAKLRSGEDVQATFTRLRVPRPFAAPALARAFPWLELLLAAALLQ
+PFTPLRPVVGLAAVALFAAFLALVVRAQDDGVSCGCFGEASAAPISRTTVVRNVVFLVLA
+VLALVEGIVSLAVHGAGLAWQPLTAFGAGAWAWALLVTVLLTTAAFLAGRESVPAAPDAA
+PATPEAPATPEAPDAADPVGEAEPERRPFPDAVVVADGEYTGLHRLVQDGAVVALRLSTG
+CGSCARVIERLDEFKDALGPVRLRVLMPQRAPGADGAIRSGAVDASLVLADPDGAASQAI
+GLHSFPTAVLLGTDRLTAGGPVGGADDVLAFLEEIREIMTTELPAATDGSTATPEVRA*
+>NZ_CP033200.1_238
+MSALWAVALIMLLSGTAKLRSGEDVQATFTRLRVPRPFAAPGLARAFPWLELLLAAALLQ
+PFTLLRPVVGLVAVVLFAAFLALVVRAQDDGVSCGCFGEASAAPISRTTVVRNVVFLALA
+VLALAEGIVSLAVHGAGLAWQPLTAFGAGAWAWALLVSVLLATAAFLAGRESVPAAPDAV
+PAMPTPEAPAAVDPAAVDPADGDPADAAEPERHPFPDAVVVADGEYTGLHRLVADGAVVA
+LRLSTGCGSCARVIERLDEFTDALGPVRLRVLMPQRAPGAEGAIHSGAVDASLVLADPAG
+AASQALGLYSFPTAVLLGTDRLTAGGPVGGADDVLAFLEEIREIMTTELPAATDGSTATP
+EVRA*
+>NZ_CP040019.1_2376
+MPALWAVALILLLSGTAKLRSGEDVQATFTRLRVPRPFAAPALARAFPWLELLLAAALLQ
+PFTQLRPVVGLVAVALFAAFLALVVRAKGDGVSCGCFGEASAAPISRTTVVRNVVFLVLA
+VLALAEGIVSLAVHGGGLAWQPLTAFGAGAWAWALLVSVLLATAAFLAGRESVPAAPDAA
+PAASTPEAPAAVDPADGAEPERHPFPDALVIEDGRYTGLHALASRGAVVALRLSAGCGSC
+SRVIARLDEFRASLGPVRLRVLMPQHEAGATPSASTGAIPEDLVVDDPNGAAARGLGLTS
+YPMAVLLGTDLLTAGGPVGGADDVLAFLEEIRDIMAAEAPAAPAAPARSPASDTPTPEVR
+A*
+>NZ_CP083691.1_2254
+MSALWAVALIMLFSGAAKLRSREDVGAVFTRLKVPAPWNDARLARAFPWLELLLALALVQ
+PFTVLRPLVGLAAVALFVAFLVLVVRATGDGVSCGCFGEASAAPITGQTVVRNVLFLLLA
+VMALFEGVASLAVHGIATEWLPLTAFGEDVTAWTVVVTLLLAAAAVLVGRESVPAAASAV
+PVPAAGVPGSAAPAPAEGQGDEPERRPFPVAAVQQGGAFVTLHQLVIPGAVVALRLSVGC
+GSCSAVIARLPELVERLGPIRVRVLMPQTVPGGELRHGTIPAELVLEDPAGAAAGGLGLT
+GFPSAVLLGADGMTAGGPVFGADEVIAFLEEIGEIVATELPAAAEGSHRP*
+>NZ_CP097650.1_508
+MSALWAVALIMLLSGTAKLRSGEDVQATFTRLRVPRPFAAPGLARAFPWLELLLAAALLQ
+PFTLLRPVVGLVAVALFAAFLALVVRAQDDGVSCGCFGDASAAPISRTTVVRNVVFLALA
+VLALAEGIVSLAVHGAGLAWQPLTAFGAGAWAWALLVSVLLATAAFLAGRESVPAAPDAV
+PATPTPEAPAVADPADGAEPERHPFPDAVVVADGEYTGLHRLVQDGAVVALRLSTGCGSC
+ARVIERLDEFKDALGPVRLRVLLPQYAPGAEGAIRSGAVDASLVLADPAGAASQALGLHS
+FPTAVLLGTDRLTAGGPVGGADDVLAFLEEIREIMTTELPAAMDGSTATPEFRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000540.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000540.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1896d5bea4a9e7cf364cbe8e54c6526adbe09646
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000540.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_513
+MDALRLVSIAAVVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVWGRFRS
+LMVPYLVWAALMSVAAFAWFADDPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFTTVL
+RRFLERFPSAVAWAVGLAGLAWAHLVPDSAIARTPLGVGLALPCLLFVLSGEMFRRRVQP
+HVRRHRTLIGVGLVLLGMVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFGSTV
+ERLLRSFARRTGTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALALAL
+SWLAGLALLATPLSKPFTGARRRWHPVHRLRHVEPPHPVTSALPRVTTASERTHP*
+>NZ_CP033200.1_246
+MVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVWGRFRSLMVPYLVWAAL
+MSVAAFAWFADDPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFTTVLRRFLERFPSAV
+AWAVGLAGLAWAHLVPDSAIARTPLGVGLALPCLLFVLSGEMFRRRVQPHVRRHRTLIGV
+GLVLLGMVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFGSTVERLLRSFARRT
+GTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALALALSWLAGLALLAT
+PLSKPFTGARRRWHPVHRLRHVEPPHPVTSALPRVTTASERTHP*
+>NZ_CP040019.1_2368
+MDALRLVSIAAVVLGHAYLADLTFSRYLEIWRMPLFFFLTGYFWTRGRPVARDARGRFKA
+LMVPYLVWAVVMSAAALAWFGDDPERLQRLMAAGWYGGADQEPPWWAFWFISVLFFATVL
+RRFLERFPTAVAWGVGLAGLAWAYLVPESAIARTPLGVGLALPCLLFILSGEAFRRRVQP
+RIRRHRTLLGLALVGLGLAAVALGLEPHNIKFGGFGTPLLTPLVGVLMSAGMVLVFGAAV
+ERILREFARRTGSGQALRRVITALVRTGTVVVLLHGWVLMWVMRQGVEDNLLKFVLALGI
+SWLVGLALLATPLSKPLTGARRRWFPLHRLRGEEPPHPPTSALPRVTTASERTHP*
+>NZ_CP083691.1_2246
+MDALRLVSISAVVLGHAYLADLTFSPYLEIWRMPLFFFLTGYFWTRGRPWAADALSRFRS
+LMVPYLLWSVLMTLVVLSWSRRSQIDGVTLADLVSAGWYGGADQPPPWWAFWFISVLFFV
+ALLRRALERAPSWAGWAVALAGLAAAELVPESAIARTPLGIGLAAPCLFYVLAGEAFRRR
+VQPRIRRHRTLIGVALVAAGVGAVALGLPPHNIKWGGFGLFPWTPLTGIAMAAGMVLVFG
+AFVERRLRAFARDTGTGRAIRAGITALTRTGTVVVLLHGLVLMEAMRVGIEDNLMKFVVA
+LTVSWAVGLALLATPLARPLTGVPQQWFPFGREAGA*
+>NZ_CP097650.1_516
+MDALRLVSIAAVVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVRGRFRS
+LMVPYLVWAALMSVAAFAWFADDPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFTTVL
+RRFLERFPSAVAWAVGLAGLAWAHFVPDSAIARTPLGVGLALPCLLFVLSGETFRRRVQP
+HVRRHRTLIGVGLVLLGLVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFGSTV
+EGLLRSFARRTGTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALALAL
+SWLAGLALLATPLSKPFTGARRRWHPVHRLRRVEPPHPVTSALPRVPTASERTHP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000541.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000541.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d8ea3291bf2d3763be9c540d54aa708693498eee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000541.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_514
+MIRNGKAIDHSNVGGVWGSLIAFIVAFGAFLGCLYAMGFWSLESVWIPGLIALALATVAF
+MIPKAFLGRSDTVDTTAIHTRPVVEHAASGAAHR*
+>NZ_CP033200.1_247
+MIRNGKAIDHSNVGGVWGSLIAFIVAFGAFLGCLYAMGFWSLESVWIPGLIALALATVAF
+MIPKAFLGRSDTVDTTAIHTRPVVEHAASGAHAVETGAAHR*
+>NZ_CP040019.1_2367
+MIRNGKAIDHSNVGGVWGSLIAFLVAYVAFLGSLYAMGFWTLENAWVPGLIALALAMVTF
+MIPQVFLGRSDTVDTAAIHTRPVAVEHPVSGAHAVETGAARRH*
+>NZ_CP083691.1_2245
+MIRNGKAIDHSNQGGFGGSAIAWLVTYAIFLAAVYAMGFWDFTHVWIPGLIALALAFLTM
+FIPKQLLGRGDTVDAVAIHAARPAEIHAPRGTGAVHH*
+>NZ_CP097650.1_517
+MIRNGKAIDHSNVGGVWGSLIAFIVAFGAFLGCLYAMGFWSLESVWIPGLIALALATVAF
+MIPKAFLGRSDTVDTTAIHTRPVVEHAASGAHAVETGAAHR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000544.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000544.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc2c309e83dff9bf2e6a673619a40b24e845d51e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000544.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_517
+MTDQTSIPSPDSPLTGDHPGFAEARAAADTIARATGVAEHRVAVVLGSGWGEAAGLIGDE
+VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA
+AAAGARTVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLVGATFVDLTDLYSPRLRAI
+AREVDPSLREGVYVQFAGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGIS
+LVTNLGAGISETPLSHAEVVEAGQAAGPRIARLLADIVGRL*
+>NZ_CP033200.1_250
+MTDQTSIPSPDSPLTGDHPGFAEARAAADTIARATGVAEHRVAVVLGSGWGEAAGLIGEE
+VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA
+AAAGARTVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLAGATFVDLTDLYSPRLRAI
+AREVDPSLREGVYVQFAGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGIS
+LVTNLGAGISETPLSHAEVVEAGQAAGPRIARLLADIVGRL*
+>NZ_CP040019.1_2364
+MSEQTFSPSPASPLAGDHPGFDQARAAAAVIADATGVAEHRIAVVLGSGWGEAAGLIGEE
+VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA
+AAAGAKTVVLTNGCGGLDPEIAPGTPVLISDHLNLTGATPLVGATFVDLTDLYSPRIRQI
+AREVDPSLREGVYVQFSGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGMS
+LVTNLGAGISETALSHGEVVEAGQAAGPRISRLLADIVWRL*
+>NZ_CP083691.1_2242
+MSEQSTPTPTPASLARLAGDHPGFAEARAAAEAIAEATGCAEHRIAVVLGSGWGEAAELI
+GVERARIDLADVPGFHAPKVPGHNAVIRSVELADGSRALVFGSRTHFYESRDAQAVAHTV
+RTAAAAGAATVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLVGATFVDLTDVYSPRI
+RAIAQEVDPTLTEGVYVQFSGPQYETPAEVRMATALGGDLVGMSTALDAIAARHAGLEVF
+GISLVTNHGAGIQETPLSHQEVVEAGQAAGPRISRLLAEIVGRL*
+>NZ_CP097650.1_520
+MTDQTSIPSPDSPLTGDHPGFAEARAAADTIARATGVAEHRVAVVLGSGWGEAAGLIGDE
+VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA
+AAAGARTVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLVGATFVDLTDLYSPRLRAI
+AREVDPSLREGVYVQFAGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGIS
+LVTNLGAGISETPLSHAEVVEAGQAAGPRIARLLADIVGRL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000549.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000549.fa
new file mode 100644
index 0000000000000000000000000000000000000000..688b8ed6d9e9eb60e3d707482333052207a25453
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000549.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_523
+MSALLGPGAPDENDESTQATPASADPLQLSGPELEPEEMAALAAVLEAAAAARAEAARLA
+AAAADPRPLDRTLRRRGDLGLWARPGRGQWRQGAGPQ*
+>NZ_CP033200.1_257
+MSALLGPGAPDENDASTQATPAPADPLQLSGPELEPEEMAALAAVLEAAAAARAEAARLA
+AEAADPRPLDRTLRRRGDLGLWARPGRGQWRQGAGPQ*
+>NZ_CP040019.1_2356
+MSAAHEPRTPNAAGTPDDAAAEPTTADPLQLRGVELDPEEMAALTAVLAHARAAEAEAAR
+AAAEAADPRPLDRTLRRRGDLGLWARPGRGQWRRGAGLQ*
+>NZ_CP083691.1_2235
+MSAALPDDAADREVQDPEPMRLTGSSLEPEEMAALTAVLAQMRAQGGAAVPQAGRSGRLR
+RPDRSLVRRGDLGLWARPGEDQWRRAAGRR*
+>NZ_CP097650.1_526
+MSALLGPGAPDENDESTQATPASADPLQLSGPELEPEEMAALAAVLEAAAAARAEAARLA
+AAAADPRPLDRTLRRRGDLGLWARPGRGQWRQGAGPQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000551.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000551.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b9038f99a4d96a0975fa4c34afab24a45cc45f08
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000551.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_526
+MRLEPGEQVMVRTRTHPRALLRPAAVLVAVAFLLGLAVGVLARPDLPGLVAANRAVLEAA
+AWVVAALVLLPGTVRPLWRWVFRRTVLTDRRILQGAGIGGSGAAMPLVSIADVQRRRRGS
+GAGDLHILFQEPARQVHWRLRDVPEAARFEEALAHLTRQARTATWPAPVPTGDLR*
+>NZ_CP033200.1_260
+MRLEPGEQVMVRTRTHPRALLRPAAVLVAVAFLLGLAVGVLARPDLPGIVAANRAVLEAA
+AWVVAALVLLPGTVRPLWRWVFRRTVVTDRRILQRAGVGGSGAAMPLVSIADVQRRRRGS
+GAGDLHILFQEPARQVHWRLRDVPEAARFEEALAHLTRQARTRTWPAPVPTGDLR*
+>NZ_CP040019.1_2352
+MRLEPGEQVMVRTRTHPRALLRPAAVLVTVAFLLGLAMGVLARPDLPGILTQNRALLETA
+AWAVAVLALLPGVLLPVLRWATRRTVVTSRRIVQRTGLGGGADVAMSLVSIADVQRRRRG
+SGAGDLHILFQERARQVHWRLRDVPEAARFEEALAHLTRQARVASWPAPAPTGGPR*
+>NZ_CP083691.1_2232
+MRLEPGEQVVVRTRSHPRVLVGTAARLTGTAFLLGLAMGLLARPGLPSPLRAAVPWLEAV
+VWAAAVVAVLVGVVRPLLRWATRATVLTSERLVQRPGLGAGPEAAMPLVSIADVQRRRRG
+ASSGDLHILFQDPLRQVYWRLADVPEAERFEQVLAETTRAARDRARPAMPAWGGVL*
+>NZ_CP097650.1_529
+MRLEPGEQVMVRTRTHPRALLRPAAVLVAVAFLLGLAVGVLARPDLPGIVAANRAVLEAA
+AWVVAALVLLPGTIRPLWRWVFRRTVLTDRRILQGAGVGGSGAAMPLVSIADVQRRRRGS
+GAGDLHILFQEPARQVHWRLRDVPEAARFEEALAHLTRQARTATWPAPVPTGDLR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000552.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000552.fa
new file mode 100644
index 0000000000000000000000000000000000000000..287b433bf7a87bd4658951fd5986054c179f1e59
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000552.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_527
+MSRPETPDTAPLPIVPPAEDETARDVEERSAEPAGWTSAMRTLDAGLVVGPRAYTSREVA
+QRLGVSMASARKIWRALGYPTSPEGHKAFTEADIEAFESVLTLVRSGTLNEDTAISLARS
+IGQMTDRMVVWQIEALVEDKIASEGLTDPEARRAVVDMLPDMVGPLEKSMRIVYRRQLNR
+AVQRLTVRVEAGLAASAEGRDGSESDAPLPLARAVGFADMVSYTTLSRTMDDRTLARMVL
+RFESLAAETISAGGGWLVKTIGDEVMFNAETPEAGAAIALSLAETIAADEELPSARVALT
+WGRVLSRMGDIYGPTVNLAARLTSLADPGTVLVDAMTAAALSRDERFVLVPQPPRIVRGF
+GEVRPSLLLDGSAQTLLAD*
+>NZ_CP033200.1_261
+MSRPETPDTAPLPIVPPAEDETARDVEERSAQPAGWTSAMRTLDAGLVVGPRAYTSREVA
+QRLGVSMASARKIWRALGYPTSPEGHKAFTEADIEAFESVLTLVRSGTLNEDTAISLARS
+IGQMTDRMVVWQIEALVEDKIASEDLTDPEARRAVVDMLPDMVGPLEKAMRIVYRRQLNR
+AVQRLTVRVEAGLAASAQGRDGSESDAPLPLARAVGFADMVSYTTLSRTMDDRTLARMVL
+RFESLAAETISAGGGWLVKTIGDEVMFNAETPEAGAAIALSLAETIAADEELPSARVALT
+WGRVLSRMGDIYGPTVNLAARLTSLADPGTVLVDAMTAAALSRDERFVLVPQPPRIVRGF
+GEVRPSLLLDGSAQTLLAD*
+>NZ_CP040019.1_2351
+MSRAETPETAPLPIIAPDGSGPAEAPRRKDPHDERRADRHEDRRGEAAADRLEEVDAPPP
+GAGWTTAMRTLDAGLVVGPRAYTAREVAQRMGVSTASARKIWRALGYPTSPEGHKAFTEA
+DVEAFESVLELVRSGALNEDAAISLARSIGQMTDRMVVWQIEALVEDKIVSEGLTDPEAR
+RAAVDLLPEIVTPLERAMQIVYRRQLNRAVKRLTVRVEAGLAASEEGRDGSESDSPLPLA
+RAVGFADMVSYTTLSRTMDDRTLARMVQRFETLSAEIISAGGGWLVKTIGDEVMFNAETP
+ETGAAIALALAEAIAADDELPSARVALTWGRVLSRMGDIYGPTVNLAARLTSLADPGTVL
+VDAMTAAALSRDERFVLVPQPPRIVRGVGEVRPSLLLNGSAQTLLAD*
+>NZ_CP083691.1_2231
+MTRDTHHDAVPETAPLPVQAPAGAADPAVGRRESDALHHGWTSAIRTLDAGLLDRPRSYS
+RREAAQRLGISSVSARKIWRALGYPTVKDEEKVFSAEDIDAFEQVLSLVRDGMLNEDTAI
+SLARSVGQMTDRMVVWQIEALVEDQIAAEGKTDPEARRAAVEMLPGLVEPLEKVMRIVYR
+RQLTNAVQRLTVRVEAGLAASERGRDGSEDDAPLPLARAVGFADMVSYTTLSRTMGERTL
+ARTVQRFESKAAEIIAAGGGWLVKTIGDEVLFNAETPEAGATIALALAEAMADDDQLPAA
+RVSLAWGRVLSRLGDIYGPTVNLASRLTSLADPGTVLVDAMTAAALSRDERFVLVPQPPR
+IVRGFGEVRPSLLMNGAAQPLIAD*
+>NZ_CP097650.1_530
+MSRPETPDTAPLPIVPSAEDETARDVEERSAQPAGWTSAMRTLDAGLVVGPRAYTSREVA
+RRLGVSMGSARKIWRALGYPTSPEGHKAFTEADIEAFESVLTLVRSGTLNEDTAISLARS
+IGQMTDRMVVWQIEALVEDKIASEDLTDPEARRAVVDMLPDMVGPLEKAMRIVYRRQLNR
+AVQRLTVRVEAGLAASAQGRDGSESDAPLPLARAVGFADMVSYTTLSRTMDDRTLARMVL
+RFESLAAETISAGGGWLVKTIGDEVMFNAETPEAGAAIALSLAETIAADEELPSARVALT
+WGRVLSRMGDIYGPTVNLAARLTSLADPGTVLVDAMTAAALSRDERFVLVPQPPRIVRGF
+GEVRPSLLLDGSAQTLLAD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000554.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000554.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e95a18d63b0045e69e46f84464c93d3b7e23db7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000554.fa
@@ -0,0 +1,75 @@
+>NZ_CP042169.1_529
+MSTPKESAAQPDPQDIPAADLREEYEDLVERVRAARTAYYQRDAPEISDAEYDALYRRLE
+DLEALHPELVANDSPTQEVGGEVSEAFAPVRHGARMYSLEDLFSIEELEVWFRRAAQALT
+QVRPGVAPRWLVEVKIDGLAVALRYRDGRLVQAATRGDGVTGEDVTANVRTIGDIPHELS
+GEGWPAEFEVRGEVFMSSAAFAELNARRAEEGQTPFANPRNAAAGALRQKDPAVTAQRPL
+AMFVHGIGSVEAFGLESQHEVYDALAGWGLPVSPYTRVVEGADEEALAAVVAVIEEYGRR
+RHELIHEIDGIVVKADAFADQRYLGHTSRVPRWAAAYKYPPEEVHTLLRDIAVSVGRTGR
+VTPFAVLEPVTVAGSTVSLATLHNQDVVKAKGVLIGDTVVVRKAGDVIPEVVGPVLPLRE
+KAIEAGRELREFVMPAHCPSCGTPLAPAKEGDVDLRCPNARSCPAQLAGRVEHLASRGAF
+DVEALGEEAARWLVQGPGEDPAEHEGQVRPEGPGPITAEAQIFDLASGTPEEITGPRGED
+GLTDLQRSLGEVRVWREGRTKVDGRMVPSGVFTLKPYFFTAGTAKKPSAPTANTLRLFDE
+LEKAKSQPLWRTLVALSIRHVGPTAARSLATAFGSMAALRAAAEAGDRDRLAEIDGVGPI
+IADALIEWFAEDWHREIVDRWAAAGVVMEDEQDESTPRTLEGLTVVVTGSLEGFSRDSAK
+EAILVRGGRASGSVSKKTDFLVAGEAAGSKLDKAQSLGVPVLDEAGFTALLAGGPDAVRP
+ADTDDAPDGAAEGEASA*
+>NZ_CP033200.1_263
+MSTPKESAAQPDPQDIPAADLREEYEDLVERVRAARTAYYQRDAPEISDAEYDALYRRLE
+DLEALHPELVANDSPTQEVGGEVSEAFAPVRHGARMYSLEDLFSIEELEVWFRRAAQALT
+QVRPGVAPRWLVEVKIDGLAVALRYRDGRLVQAATRGDGVTGEDVTANVRTIGDIPHELS
+GEGWPAEFEVRGEVFMSSAAFAELNARRAEEGQTPFANPRNAAAGALRQKDPAVTAQRPL
+AMFVHGIGSVEAFGLESQHEVYDALAGWGLPVSPYTRVVEGADEEALAAVVAVIEEYGRR
+RHELIHEIDGIVVKADAFADQRYLGHTSRVPRWAAAYKYPPEEVHTLLRDIAVSVGRTGR
+VTPFAVLEPVTVAGSTVSLATLHNQDVVKAKGVLIGDTVVVRKAGDVIPEVVGPVLPLRE
+KAIEAGRELREFVMPAHCPSCGTPLAPAKEGDVDLRCPNARSCPAQLAGRVEHLASRGAF
+DVEALGEEAARWLVQGPGEDPAEHEGQVRPEGPGPITAEAQIFDLASGTPEEITGPRGED
+GLTDLQRSLGEVRVWREGRTKVDGRMVPSGVFTLKPYFFTAGTAKKPSAPTANTLRLFDE
+LEKAKSQPLWRTLVALSIRHVGPTAARSLATAFGSMAALRAAAEAGDRDRLAEIDGVGPI
+IADALIEWFAEDWHREIVDRWAAAGVVMEDEQDESTPRTLEGLTVVVTGSLEGFSRDSAK
+EAILVRGGRASGSVSKKTDFLVAGEAAGSKLDKAQSLGVPVLDEAGFTALLAGGPDAVRP
+ADTDDAPDGAAEGEASA*
+>NZ_CP040019.1_2349
+MSTAKESAAQPDPQDIPAAGLREEYEDLVERVRAARTAYYQEDAPELSDAEYDVLYRRLE
+DLEALHPELVSNDSPTQEVGGEVSEAFAPVRHGARMYSLEDLFSVEELEVWFRRAADALT
+QVRPGVAPRWLVEVKIDGLAVSLRYKDGRLVQAATRGDGVTGEDVTANVRTIGDIPHELS
+GEGWPAEFEVRGEVFMSSAAFAELNARRAEEGQTPFANPRNAAAGALRQKDPAVTAQRPL
+AMFVHGIGSVEAFGLDSQHEVYDALAGWGLPVSPYTRRVEGADEEALAAVVAVIEEYGER
+RHELIHEIDGIVVKADAFADQRYLGHTSRVPRWAAAYKYPPEEVHTLLRDIAVSVGRTGR
+VTPFAVMEPVTVAGSTVSLATLHNQDVVKAKGVLIGDTVVVRKAGDVIPEVVGPVLPLRE
+KAIEAGRELREFVMPAHCPSCGTALAPAKEGDVDLRCPNARSCPAQLAGRVEHLASRGAF
+DVEALGEEAARWLVQGPGEDPAEHEGHVRPEGPGPITAEAQIFDLASGTPEEITGPRGED
+GLTDLQRSLGAVRVWREGRTKVDGRMVPSGVFTLKPYFFTAGTAKKPSAPTANTLRLFDE
+LEKAKSQPLWRTLVALSIRHVGPTAARSLATAFGSMAALRAAAEAGDRDRLAEIDGVGPI
+IADALIEWFAEDWHREIVDRWAAAGVVMEDEQDESTPRTLEGLTVVVTGSLEGFSRDSAK
+EAILVRGGKASGSVSKKTDFLVAGEAAGSKLDKARQLGVPVLDEAGFTALLAGGPEAVAD
+ATGEADDDAGAEGE*
+>NZ_CP083691.1_2229
+MSTAQTPREPEHGGLEPTPDQVPERDLREQHAELVERIRAARTAYYQDDAPEISDAEYDR
+LYRALEDLEALHPELASNDSPTQEVGGEASEAFAPVRHGSRMYSLEDLFSLEELETWFLR
+AAGSLAEVRPGRAPRWLVEVKIDGLAVALRYRRGRLVQAATRGDGVTGEDVTRNVMTIAD
+VPQTLTGEGWPEEFEVRGEVFMPSRAFAELNERRAEEGQAPFANPRNAAAGALRQKDPAV
+TAQRPLSMFVHGIGTVEAFGADGQEEVYGMLAGWGLPVSPYTRVVEGADEAALTRVVDVI
+EEYGRRRHELVHEIDGIVLKADAFADQRYLGHTSRVPRWAAAYKYPPEEVHTRLLDIAVN
+VGRTGRVTPFAVMEPAQVAGSTVSMATLHNQDVVKAKGVLIGDMVVLRKAGDVIPEVVGP
+VLPVRERLLAQGEDLREFVMPADCPSCGTPLAPAKEGDVDLRCPNARSCPAQVAGRVEHL
+AGRGAFDVEALGEEAARWLVIGHGPDPAEHEGMVLPEGAGPITAEAQLFDLASGTPEEVT
+GPRGEDGLTDLQRSLGDVRVWREGRTKVDGRMVPSGVFSLKPYFFTAGTAKKPAAPTANT
+LRLFDELEKAKTAPLWRVLVGLSIRHVGPAAARSLATAFGSMTALRAAAEAGERDRLAEI
+DGVGPIIADALIEWFAQDWHREIVDRWAAAGVVMEDEQDADTPRTLEGVTVVVTGSLEGF
+SRDSAKEAILVRGGKASGSVSKKTHFLVAGEAAGSKLEKAEQLGVPVLDEAGFVRLLAEG
+PAAFPSEDADAETVDAAAEGESA*
+>NZ_CP097650.1_532
+MSTPKESAAQPDPQDIPAADLREEYEDLVERVRAARTAYYQRDAPEISDAEYDALYRRLE
+DLEALHPELVANDSPTQEVGGEVSEAFAPVRHGARMYSLEDLFSIEELEVWFRRAAQALT
+QVRPGVAPRWLVEVKIDGLAVALRYRDGRLVQAATRGDGVTGEDVTANVRTIGDIPHELS
+GEGWPAEFEVRGEVFMSSAAFAELNARRAEEGQTPFANPRNAAAGALRQKDPAVTAQRPL
+AMFVHGIGSVEAFGLESQHEVYDALAGWGLPVSPYTRVVEGADEEALAAVVAVIEEYGRR
+RHELIHEIDGIVVKADAFADQRYLGHTSRVPRWAAAYKYPPEEVHTLLRDIAVSVGRTGR
+VTPFAVLEPVTVAGSTVSLATLHNQDVVKAKGVLIGDTVVVRKAGDVIPEVVGPVLPLRE
+KAIEAGRELREFVMPAHCPSCGTPLAPAKEGDVDLRCPNARSCPAQLAGRVEHLASRGAF
+DVEALGEEAARWLVQGPGEDPAEHEGQVRPEGPGPITAEAQIFDLASGTPEEITGPRGED
+GLTDLQRSLGEVRVWREGRTKVDGRMVPSGVFTLKPYFFTAGTAKKPSAPTANTLRLFDE
+LEKAKSQPLWRTLVALSIRHVGPTAARSLATAFGSMAALRAAAEAGDRDRLAEIDGVGPI
+IADALIEWFAEDWHREIVDRWAAAGVAMEDEQDESTPRTLEGLTVVVTGSLEGFSRDSAK
+EAILVRGGRASGSVSKKTDFLVAGEAAGSKLDKAQSLGVPVLDEAGFTALLAGGPDAVRP
+AGTDDATDDAAEGEASA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000561.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000561.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5a63ada7cb4e2ad4da33583daf2e21e8dc58566
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000561.fa
@@ -0,0 +1,31 @@
+>NZ_CP042169.1_537
+MPATPRTSRTPAVRPAPALPAPSARTVRWEIAIVLGLSLGKSAVYAIVQLIDKATQAPLG
+EQTTVLNPALADRWAFDLTYQLLGIGFALVPVALVLHLMHLRGRNPFRVLGLDLRRPGRD
+LAWGLGLFAAIGLGTLGVYAAGRALGITTAIVGSALGESWYQVPVLLLSALRHGLLEEVI
+VGAWLVDRLGYLQRLRAAGLARDPAPAVPSSWVSAEGLYLPTRAAVVVLALALLRGAYHL
+YQGIGPGVGNALMGVVFALVFLRVRRVMPLVIAHTLLDAVGFVGYPLLARAGLLG*
+>NZ_CP033200.1_271
+MPATPRTSRTPAGPAVRPAPALPAPSARTVRWEIAIVLGLSLGKSAVYAIVQLIDKATQA
+PLGEQTTVLNPALADRWAFDLTYQLLGIGFALVPVALVLHLMHLRGRNPFRVLGLDLRRP
+GRDLAWGLGLFAAIGLGTLGVYAAGRALGITTAIVGSALGESWYQVPVLLLSALRHGLLE
+EVIVGAWLVDRLGYLQRLRAAGLAHDPAPAVPSSWVSAEGLYLPTRAAVVVFALALLRGA
+YHLYQGIGPGVGNALMGVVFALVFLRVRRVMPLVIAHTLLDAVGFVGYPLLARAGLLG*
+>NZ_CP040019.1_2338
+MSLPVPPALASPVPTALPAPSARTVRWEIAIVLGLSLGRSAVYAVVQLIDKATQAPLGDQ
+TTVLNPTVDDRWAFDLTYQLLGIAFALVPVLLVLHLMHLRGRNPFRTLGLDLRRPGRDLA
+WGVGLFAVIGLGTLGVYAAGRALGLTTAIVANAMDESWYQIPVLLLSALRHSLLEEVIVG
+AWLVDRIGYLQRLKAAGLDRDPVPAVPAAPARRTGAPSSSWTTPEGLFLPTCVATALLAL
+ALLRGAYHLYQGVGPGIGNALMGVVFVLVFLRVRRVMPLVVAHFLLNAVGFVGYPLLARA
+GLLG*
+>NZ_CP083691.1_2218
+MTATARPEHAAGRRGPGAPALPAPSARTVRWEIAIVLGLSLGRSAVYAVVQLIDQATRAP
+LGDQTTVLNPTVADRWAFDLTYQLLGIAFSLVPVLLVLHLLWLRGRHPFRVLGLDLRRPG
+RDLAWGLGLFTVIGVGTLGVYAAGRALGITTAIVANAMDESWYQVPVLLLSAARHALLEE
+VIVGAWLIDRLGYLQRLREAGLGASSSWAGTEGLFLPLRTWPVVLSLALLRGAYHLYQGV
+GPGIGNALMGAVFVLVFLRVRRVMPLVLAHFLLDAVGFVGYPLLARAGLLG*
+>NZ_CP097650.1_540
+MPATPRTSRTPAVRPAPALPAPSARTVRWEIAIVLGLSLGKSAVYAIVQLIDKATQAPLG
+EQTTVLNPALADRWAFDLTYQLLGIGFSLVPVALVLHLMHLRGRDPFRVLGLDLRRPGRD
+VAWGLGLFAAIGLGTLGVYAAGRALGITTAIVGSALGESWYQVPVLLLSALRHGLLEEVI
+VGAWLVDRLGYLQRLRAAGLARDPAPAVPSSWVSAEGLYLPTRVAVVVLALALLRGAYHL
+YQGIGPGVGNALMGVVFALVFLRVRRVMPLVIAHALLDAVGFVGYPLLARAGLLG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000562.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000562.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9328949f51871b488b867fd5bb3207a23793c492
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000562.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_538
+MDHVSYAAGPEGLDATVARIAETLGIERIKGGVHPRFGTQNALFPMAGRQYLEVVEALDH
+PASLSAPFGQLVRARTEQGGGWMSWAVATTDIGRFERRLGREAVPGNRRFPDGRELSWRQ
+IGVKGTLADPQLPFILRWADGQEDMHPSQAAEPQATIERLNIAGSPERLAEWLGDDEDGQ
+VQDVNIEYVAPSGTPGIVSVTFRTPKGEVTL*
+>NZ_CP033200.1_272
+MDHVSYAAGPEGLDATVARIAETLGIERIKGGVHPRFGTQNALFPMTEGQYLEVVEALDH
+PASLSAPFGQLVRARTEQGGGWMSWAVATTDIGRFERRLGREAVPGNRRFPDGRELSWRQ
+IGVKGTLADPQLPFILRWADGQEDMHPSQAAEPQATIERLNIAGSPERLAEWLGDDEDGQ
+VQDVNIEYVAPSGTPGIVSVTFRTPKGEVTL*
+>NZ_CP040019.1_2337
+MDHVSYAAGPEGLDATVARIAEALGVERIKGGIHPRFGTQNALFPMAGGQYLEVVEALDH
+PASLSAPFGQLVRSRSEQGGGWMSWAVSTTDIGRFERRLGREAVPGNRRFPDGRELSWRQ
+IGIKGTIADPQLPFIMRWADGQEDMHPSQAAEAQASIERLSIAGSPDRLAEWLGGEGEDA
+HVEDLNVEYVAPSGTPGIVSVTFRTPRGDVTL*
+>NZ_CP083691.1_2217
+MNTCRMDHVSYAAGPEGLDATVARIAERLGVERVKGGIHPRFGTQNALFPMTGNQYLEVV
+EALDHPASLSAPFGQLVRTRSEQGGGWMSWAVTTNDIGRFERRLGREAVPGNRRFPDGRE
+LSWRQIGVKGTLADPQLPFILRWADGQEDMHPSQAAPAQASIARLSIAGSPDRLREWLGG
+TEDDEVADVSVDYVAPSGTPGIVSVTFSTPKGEVTL*
+>NZ_CP097650.1_541
+MDHVSYAAGPEGLDATVARIAETLGIERIKGGVHPRFGTQNALFPMTEGQYLEVVEALDH
+PASLSAPFGQLVRARTEQGGGWMSWAVATPDIGRFERRLGREAVPGNRRFPDGRELSWRQ
+IGIKGTLADPQLPYILRWADGQEDMHPSQAAEPQATIEHLNIAGSPERLAEWLGGEDEDG
+QVQDVNIEYVAPSGTPGIVSVTFRTPKGEITL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000566.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000566.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a5369121b950c45b16ead00eca7303f292d4bf4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000566.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_542
+MPLARLAGVNANPTPAVEPVVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPEHVT
+VAAVRAPLPLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTVSLL
+GFSQGMAMATSLLRLDPEAYACTVALSGFVVDPELDEPRLRELFTRDDDVARVRPKVFWG
+RGQEDPIISEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPRG*
+>NZ_CP033200.1_276
+MNANPTPAVEPVVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPEHFTVAAVRAPL
+PLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTVSLLGFSQGMAM
+ATSLLRLDPEAYACTVALSGFVVDPELTEPRLRELFTRDDDVARVRPKVFWGRGQEDPII
+SEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPRG*
+>NZ_CP040019.1_2333
+MNNDTANTAPSSETAPFTVRWSRPEGERTEDLLILLHGYGANEDDLFGLVPHLPERFTVA
+AVRAPMTLQPGGYAWFPLSQDPVTGEIGSDAASVRTAIEDLHAWVGAVREGFRTVSLLGF
+SQGMALATSLLRLDPTAYAATVALSGFVVDPTREESGLAGLFDGDDEVARVRPKVFWGRG
+QDDPIISEARVEASHAWLNAHVDLMKIVYAGLPHAINQQELGHVKEYLEHMVR*
+>NZ_CP083691.1_2213
+MNDTTPRDPAPFAVRWSRPEGERTEHLLVLLHGYGADEDDLFGLVPQLPEAFTALAVRAP
+MDLPQGGAAWFPLTQDPATGEIGSDAGAVRAAVEDLHAWLPGVSGGFRTVSLLGFSQGMA
+MATSLLRLDPAAYAATVALSGFVVDPLHVEPELEGLFPADETVDAVTPKVFWGRGQEDPI
+ISAQRVEESHGWLTAHTDLTKVVYAGLPHAISPQELGHVREYLTHVVL*
+>NZ_CP097650.1_545
+MPLARLAGVNANPTPAVEPVVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPEHVT
+VAAVRAPLPLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTVSLL
+GFSQGMAMATSLLRLDPEAYACTVALSGFVVDPELAEPQLRELFTRDDDVARVRPKVFWG
+RGQEDPIISEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000573.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000573.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e9833fb6812f8009c85d51ead8fd6384715086e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000573.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_553
+MAEPTTPEPAAGAPAAPSSPWTGAAHQPVLFGPEGRPPYAGRAVQTPGYPPWDRERWLPE
+PPKSSYRSDFERDRARVLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGR
+SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF
+ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT
+RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA
+EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH
+GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLDATGDRYLEPM
+FTFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI*
+>NZ_CP033200.1_294
+MAEPTTPVPAAGTPAAPSSHWTGAAHQPVLFGPEGRPPYAGRAVQTPGYTPWDRERWLPE
+PPKSSYRSDFERDRARVLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGR
+SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF
+ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT
+RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA
+EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH
+GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLEATGDRYLEPM
+FTFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI*
+>NZ_CP040019.1_2312
+MAEGWAGPAHQPVLFGPQGRPPYAGRAVQTPGYTPWDRERWLPEPPKSSYRSDFERDRAR
+VLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGRSLGCDPDLVDTACLSH
+DLGHPPFGHNGEKALDALSADVGGFEGNAQTLRLLARLEQKKLFEDGSSAGLNLTRAALD
+AACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFREGVSGSRKSMEAQVMDLADDIS
+YSVHDVEDGVVNAAFQLKWLAIPEHRERVVETTRQWYLPLTDPAEVDEALARLEATDVWV
+SEMDGSRRALAAMKDMTSQLIGRFCTAAFDATRQVFGNEPLTRHGADVVVPAETETEIAV
+MKGIAAAYVMASEQRQPLYARQRELLAELVELLDASGDRYLEPMFAFDWREAADEAARRR
+VVLDQVASLTDSTALEWHHTLVQGAEFTRVWI*
+>NZ_CP083691.1_2199
+MAEPQPTLFGPADRPPYAGRPVPTPGYTDWDRRRWLAEPPKSSYRSDFERDRARVLHSAA
+LRRLGAKTQVVAPDLDDFSRTRLTHSLEVAQIGRELGRSLGCDPDLVDTACLSHDLGHPP
+FGHNGEKALDAVAEAAGGFEGNAQTLRLLARLEQKKSFPDGSSAGLNLTRAALDAACKYP
+WVREDAPLRPDGKRSRKFGVYADDLPVFEWFRQGVHGARKSMEAQVMDLADDISYSVHDV
+EDGVVNSAFQLRWITEPGERRARVLETTRDWYLPGGDLEEIDAALTRLESQDVWMGEMDG
+SRRALAGMKDMTSQLIGRFCTAAFDATREVFGNEPLTRHAADVVVPAHTEHEIAVMKGIA
+AAFVMTSEQRQPLYARQRDLLTELVDLLMTTGDRYLDPMFAADFQDAADDAARARVVIDQ
+VASLTDSTAIEWHRTLVRGETFQRVWL*
+>NZ_CP097650.1_554
+MAERTTPAPADGAPAAPSSPWTGAAHQPVLFGPEGRPPYAGRAVQTPGYTPWDRERWLPE
+PPKSSYRSDFERDRARVLHSAGLRRLGDKTQVVAPDADDFARTRLTHSLEVAQVGRELGR
+SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF
+ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT
+RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA
+EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH
+GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLDATEDRYLEPM
+FAFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000576.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000576.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eae3d573bbf85e6e299c7917fe1dbde9c972bc29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000576.fa
@@ -0,0 +1,60 @@
+>NZ_CP042169.1_561
+MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY
+HCFGCGAHGDVISFLMELEHTTFTETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFE
+ANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHATQFGLGYAPQGWSHLLDHLRQRGFR
+DEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP
+LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVA
+RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKG
+DEAVRALIASRRPLFEFAIRAGLKDYDLDTVEGRAGALRHAVPIVAGIKDAVLRPGYERE
+LAGWLGLDPNAVHRAVAAAGRAPRRGPEPEARPAPADDGQAIGPQGRHGEAAAPAPRIVV
+PVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKMAGSAGAT
+PQRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELL
+GRLQRLGPEGDPAEFTRLNSELMELEARRRALRADD*
+>NZ_CP033200.1_303
+MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY
+HCFGCGAHGDVISFLMELEHTTFTETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFE
+ANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHAVQFGLGYAPQGWSHLLDHLRQRGFR
+DEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP
+LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVA
+RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKG
+DEAVRALIASRRPLFEFAIRAGLKDYDLNTVEGRAGALRHAAPIVAGIKDAVLRPGYERE
+LAGWLGLDPNAVHRAVAAAGRAPRRGPEPEARPAPADDGQAIGPTGRHGEAAAPAPKIVV
+PVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKMAGSAGAT
+PQRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELL
+GRLQRLGPEGDPAEFTRLNSELMELEARRRALRADD*
+>NZ_CP040019.1_2305
+MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY
+HCFGCGEHGDVISFLMELEHTTFTETVERLAARVGVELHYEDGGTGPDKAETGRRRRLLE
+ANKVADEFYRRALGSAEAQTGRDFLTQRGFTQEHAEQFGLGYAPQGWSHLLDHLRQKGFR
+DEELRASGLFSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP
+LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKMA
+RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTYVAVEPSGMDPCDLRMQQG
+DEAVRALIASRRPLFEFAIRAGLKDYDLDTVEGRAGALRHAAPIVAGIKDAVLRPGYERE
+LAGWLGLDPNAVHRAVAAAGRGQRRGGGSEPRREPERGPEPDQAPGQGRGPAPEGPSVGP
+QGRHGEAAAPAPQVLVPVDPRDPVARCERESLEVVLQHPTLLSAEQWTALYAARFTIPQY
+AAVHHGVKVAGSSGATPQRWVDAVRYAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIM
+NRLFALQIVHRKEELLGRLQRLGPDGDPAEFTALNSELMELEARRRALRADD*
+>NZ_CP083691.1_2196
+MVRMAGLIVRKDIDLVRERADLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGV
+GTYHCFGCGEHGDVISFLMEMEHTTFTETVERLAARAGVELHYEDGQGPDRAETSRRRRL
+LEANKLADEFYRARLAAPDAQPGRDFLTGRGFTQEHAEQFGLGYAPQGWSALLDHLRQQG
+FRDDELRASGLFSEGQRGLYDRFRGRLLWPIRDMTGNTIGFGARKLFEDDPGPKYLNTPE
+TPLYKKSQVLYGIDLAKRAIAKERQLVLVEGYTDVMAAHLSGVETAVATCGTAFGADHIK
+IARRLISDDGTGGEVIFTFDGDAAGQKAALKAFDEDHRFLAKTFVAVEPNGLDPCDLRMQ
+QGEEAVRALIASRRPLFEFAISAGLKDYDLNTVEGRAGALRHAAPIVAGIKDSVLRPGYE
+RELAGWLGMDPNVVSRAVAQELRGRRRGGPSGGSAERTPAPERAPEGANAGQAPGEEPAA
+PRPALIVPVDPRDPAARRERESLEVVLQHPTLLSAEQWTAFYQARFTIPQYAAVHHAVKV
+AGTAGATPSRWVDAVRDAAPGEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFSLQIV
+HRKEELLGQLQRLGPEGDHDEFMRLNAELMELETRRRALRADD*
+>NZ_CP097650.1_562
+MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY
+HCFGCGAHGDVISFLMELEHTTFMETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFE
+ANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHAVQFGLGYAPQGWSHLLDHLRQRGFR
+DEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP
+LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVA
+RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKG
+DEAVRALIASRRPLFEFAIRAGLKDYDLNTVEGRAGALRHAAPIVAGIKDAVLRPGYERE
+LAGWLGLGPNAVHRAVAAAGRAPRRGPEPEARPTPASDGQAVGPTGRHGEAAAPAPRIVV
+PVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKVAGSAGAT
+PQRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELL
+GRLQRLGPEGDPAEFTRLNSELMELEARRRALRADD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000580.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000580.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5377126a988acd77ff0971335551e7fbf7cc6016
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000580.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_612
+MKRTMTLTALALASALTLTACGTGAQDENAGAEASATAASSAPAATPAATATATPSTTAT
+GSAEEVSAEHNDADVMFAQMMIPHHQQAVEMSEMLLAKDDVPAEVAAFAQKVIDAQGPEI
+KRMNSMLTAWGQDPVDTDGMDGMEGMDHGGMSGMMSEEDMTALDQAQGTEAARLYLEQMT
+AHHKGAVDMAKDEAKDGQNPQAVQLAEQVIADQEAEITEMQQMLDKL*
+>NZ_CP040019.1_392
+MKRTMTLTALALASALTLTACGTGAQDENAGAEASATATSSAPAATPAATATATPSTTAT
+GSAEEVSAEHNDADVMFAQMMIPHHQQAVEMSEMLLAKDDVPAEVAAFAQKVIDAQGPEI
+KRMNSMLTAWGQDPVDTDGMDGMEGMDHGGMSGMMSEEDMTALDQAQGTEAARLYLEQMT
+AHHKGAVDMAKDEAKDGQNPQAVQLAEQVIADQEAEITEMQQMLDKL*
+>NZ_CP040019.1_737
+MSTETSAAGRAGHSVRLVVLATVIVLILGAAGWALGRLTAPVTSFPSAASPEAGFARDMQ
+VHHLQAVEMSFLVRDRTEDPEIRQLAYDIARTQQHQAGQMYGWLSIWGLPQASPEPAMAW
+MDEDAGHSSPHDTGQQSTAMPGMATAAQLEALTDAEGSEAEQLYLELMISHHQAGTTMAQ
+AVLDRTDNEAVRALAQSIATSQQTEIRYLEQLLRTR*
+>NZ_CP083691.1_2146
+MKRTMTLTALALASALTLTACGTGAQDENAGAEASATATSSAPAATPAATATATPSTTAT
+GSAEEVSAEHNDADVMFAQMMIPHHQQAVEMSEMLLAKDDVPAEVAAFAQKVIDAQGPEI
+KRMNSMLTAWGQDPVDTDGMDGMEGMDHGGMSGMMSEEDMTALDQAQGTEAARLYLEQMT
+AHHKGAVDMAKDEAKDGQNPQAVQLAEQVIADQEAEITEMQQMLDKL*
+>NZ_CP097650.1_574
+MKRTMTLTALTLASALTLTACGTGAQDENAGAEASATATGSAPAATPAATDTATPSATES
+ATSSATGSAEEVSAEHNDADVMFAQMMIPHHQQAVEMSEMLLAKDDVPAEVAAFAQKVID
+AQGPEIERMNAMLTAWGQDPVDTDGMDGMEGMDHGGMSGMMSEEDMTALDQAQGTEAARL
+YLEQMTAHHKGAVDMAKDEAKDGQNPQAVQLAEQVIADQEAEITEMQQMLDKL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000581.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000581.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a6b4b2dcc442bb23ac423f881ad47b1381d7f18
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000581.fa
@@ -0,0 +1,23 @@
+>NZ_CP042169.1_614
+MDSEKYQRVRNGAGFVAALDQSGGSTPAALHLYGIDKDAYSGPEEMFDLVHQLRTRIITS
+PSFDGERVMGAILFENTMNRQVEGSPTGDYLWNSKGIVPFLKIDQGLAPEQQGAQLMKPI
+PHLDDLLSRAVEKHMFGTKMRSVIKLPGDGVGSVVEQQFGLARQILVTGLVPIIEPEVDI
+RSPRKAEVEDQLKAAILAQLDKLGDDQSVILKVTLPERADFYREFVDHPRVIRVLALSGG
+YTRAQATTLLARNHGVIASFSRALTEGLSTAQSPAQFNAVLDEAINAIATASRT*
+>NZ_CP040019.1_394
+MLCILPLDQSLHQTRSDSDFYREFVDHPRVIRVLALSGGYTRAQATTLLARNHGVIASFS
+RALTEGLSTAQSPAQFNAVLDEAINAIATASRT*
+>NZ_CP083691.1_2143
+MDSEKYQRVRNGAGFVAALDQSGGSTPAALHLYGIDKDAYSGPEEMFDLVHQVRTRIITS
+PSFDGERVMGAILFENTMNRQVEGSPTGDYLWNSKGIVPFLKIDQGLAPEQQGAQLMKPI
+PHLDDLLSRAVEKHMFGTKMRSVIQLPGDGVGSVVEQQFGLARQILVTGLVPIIEPEVDI
+RSPRKAEVEDQLKAAILAQLDKLGDD*
+>NZ_CP083691.1_2144
+MTLPERADFYREFVDHPRVIRLLALSGGYTRAQATTLLARNHGVIASFSRALTEGLSTAQ
+SPAQFNTVLDEAINAIATASRT*
+>NZ_CP097650.1_572
+MDSEKYQRVRNGAGFVAALDQSGGSTPAALHLYGIDKDAYSGPEEMFDLVHQVRTRIITS
+PSFDGERVIGAILFENTMNRQVEGSPTGDYLWNSKGIVPFLKIDQGLAPEQQGAQLMKPI
+PHLDDLLSRAVEKHMFGTKMRSVIKLPGDGVGSVVEQQFGLARQILVTGLVPIIEPEVDI
+RSPRKAEVEDQLKAAILAQLDKLGDDQSVILKVTLPERADFYREFVDHPRVIRVLALSGG
+YTRAQATTLLARNHGVIASFSRALTEGLSTAQSPAQFNAVLDEAINAIATASRT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000582.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000582.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2af80b56df6b98732bedeb0f5824ff8e118b90d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000582.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_615
+MTHHVSAMLDTYPKNVGNIDRQKLAECIQACFECAQTCTACADACLAEDMVADLRQCIRL
+NLDCADVCAATGRMLSRQTGNNVETTRALLEACRAACKTCGDECESHAQMHEHCKVCAEA
+CRRCEQACADLLVTLG*
+>NZ_CP040019.1_1957
+MTHHVNAMLDTHPKDLGGIDRQKLAECIEACFACAQTCTACADACLSEDMVAELRQCIRL
+NLDCADVCAATGAVLTRQTGEDASTVRALLEACRAACRSCGEECASHAGMHEHCAVCAEA
+CRRCEQACADLLAALG*
+>NZ_CP083691.1_2142
+MTHHVSAMLETYPKEVGNIDRQKLAECIQACFECAQTCTACADACLAEDMVADLRQCIRL
+NLDCAEVCAATGRVLSRQTGTNVETTRALLEACRAACKTCGDECESHAQMHEHCKVCAEA
+CRRCEQACADLLVTLG*
+>NZ_CP097650.1_571
+MTHHVSAMLDTYPKNVGNIDRQKLAECIQACFECAQTCTACADACLAEDMVADLRQCIRL
+NLDCADVCAATGRMLSRQTGNNVETTRALLEACRAACKTCGDECESHAQMHEHCKVCAEA
+CRRCEQACADLLVTLG*
+>NZ_CP097650.1_862
+MTHHVSAMLETHPKDLGGVDRRKLAECIEACLACAQTCTACADACLSDDMVAEMRRCIRL
+NLDCADVCGATAAVLTRQTGEDASTVRALLEACRTACRACGDECASHAEMHEHCKVCAES
+CRRCEQACADLLASLG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000583.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000583.fa
new file mode 100644
index 0000000000000000000000000000000000000000..99ba931fb845e99673887082038a212e8550a6e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000583.fa
@@ -0,0 +1,36 @@
+>NZ_CP042169.1_619
+MDTTRFDDDLRAMLGEVESDRRGEPSDYLEDVAGQHVDGLAVAVCTVDGHQAAAGETEHA
+FALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGAILV
+HSLLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGRLPI
+SAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQTMSVMLTCGM
+YDASGQWVAEVGVPAKSGVSGALLGAVPGALGLAAWSPRLDEQGNSRRGIGLFEGLSARW
+DLHVLQHRGALRGLSGPR*
+>NZ_CP033200.1_365
+MDTTRFDDDLRAMLDEVESDRRGEPSDYLEDVAGQHVDGLAVAVCTVDGHQAAAGETEHA
+FALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGAILV
+HSLLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGRLPI
+SAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQAMSVMLTCGM
+YDASGQWVAEVGVPAKSGVSGALLGAVPGALGLATWSPRLDEQGNSRRGIGLFEGLSARW
+DLHVLQHRGALRGLSGPR*
+>NZ_CP040019.1_2276
+MDTTRLDDDLRAMLAEVESDRRGEPSDYLEDVAGQHVDGLAAAVCTVDGHQAAAGETDHA
+FALQSVSKALTYAVVLQEVGLDAVLERVGVEPSGEAFNHLSLHDDGRPYNPLINAGAIMA
+HALLPAGDHEERVALLVRRYSALAGAELEVSQDVLDAELTRADRNLGLAHLLADAGQLPV
+SAREAVAGYLAQCSVTVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQTMSVMLTCGM
+YDATGQWVAEVGVPAKSGVSGALLGAVPGALGIATWSPRLDERGNSRRGIGIFEGLSARW
+DLHVLQHRGALRGLRASR*
+>NZ_CP083691.1_2135
+MGIGSLIATMLPSSIAFLPACTGMVIGWRWLGLPLGPNARSSAHRDRPGARPRPGRPSTT
+VTGMDTTRFDDDLRAMLGEVESDRRGEPSDYLEDVAGQHVDGLAVAVCTVDGHQAAAGET
+EHAFALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGA
+ILVHSLLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGR
+LPISAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQTMSVMLT
+CGMYDASGQWVAEVGVPAKSGVSGALLGAVPGALGLAAWSPRLDEQGNSRRGIGLFEGLS
+SRWDLHVLQHRGALRGLSGPR*
+>NZ_CP097650.1_588
+MDTTRFDDDLRAMLDEVESDRRGEPSDYREDVAGQHVDGLAAAVCTVDGHQAAAGETEHA
+FALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGAILV
+HALLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGRLPI
+SAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQAMSVMLTCGM
+YDASGQWVAEVGVPAKSGVSGALLGAVPGALGIATWSPRLDEQGNSRRGIGLFEGLSARW
+DLHVLQHRGALRGLSGPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000584.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000584.fa
new file mode 100644
index 0000000000000000000000000000000000000000..021268c31385f067896254927774407fc51c1554
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000584.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_620
+MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLRVDKQRQPEPGLDVKTDPVPDIGLDSYR
+GMGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA
+VALPGDLMDADYRASLVDEAAQRLGGLDILVNNAGKQFISDDLTDLTDEQVHETFQINIM
+SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQLGPKGI
+RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSNPIGRAGQPVEMAPAYVFLASGESSYVNG
+ETLNANGGTPTP*
+>NZ_CP033200.1_366
+MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLRIAKQRQPEPGLDVKTDPVPDIGLDSYR
+GMGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA
+VALPGDLMDADYRASLVDEAAQRLGGLDILVNNAGKQFISDDLTDLTDEQVHETFQINIM
+SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQLGPKGI
+RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSTPIGRAGQPVEMAPAYVFLASGESSYVNG
+ETLNANGGTPTP*
+>NZ_CP040019.1_2275
+MTTPEKKDAAAATPVQDSQLAHDDPRTRHPKLDAPEQRQEEPGLDVKTEPVPDIGLDSYR
+GLGRLEGRKALITGGDSGIGAAVAVAYAREGADVAIAYLPEEQPDADRVLAAIEAAGRTA
+VALPGDLMDAGYREGLVEEAATALGGLDILVNNAGKQIISESLEDLTDQQVLETFQVNIL
+SMFTLSRAALTHMGPGSTIINTTSVQAYNPNPMILDYAATKAAINNFTKGLAQQLGERGI
+RVNAVAPGPVWSVLQVSYGQPKEKLPVFGHDTPTGRGGQPVEMAPAYVFLASGESSYVNG
+ETLNANGGTPTP*
+>NZ_CP083691.1_2134
+MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLHITKQRQPEPGLDVKTDPVPDIGLDSYR
+GAGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA
+VALPGDLMDVDYRASLVDEAAQRLGGLDILVNNAGKQFISDDLVDLTDEQVHETFQINIM
+SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQLGPKGI
+RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSTPLGRAGQPVEMAPAYVFLASGESSYVNG
+ETLNANGGTPTP*
+>NZ_CP097650.1_589
+MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLHITKQRQPEPGLDVKTDPVPDIGLDAYR
+GAGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA
+VALPGDLMDADYRAALVDEAAQRLGGLDILVNNAGKQFISDDLTDLTDEQVHETFQINIM
+SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQVGPKGI
+RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSTPIGRAGQPVEMAPAYVFLASGESSYVNG
+ETLNANGGTPTP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000586.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000586.fa
new file mode 100644
index 0000000000000000000000000000000000000000..94562b214013bb13fa94c36e6aa6ff4bd9ec46ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000586.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_623
+MSHQAPPADASKVRAPRTAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELELAKRHVAAK
+GKKAGIGAGIAVVGLFFLALMVVALVVTLIGAFADPTFWFPALMVALAFLVLGLIFAGVG
+LMMVKGAMPLVPQEIVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAAREAERKK
+VEKEENKKARKNGEAAPHPDRADASEAEIRRRADLRRRHLGDIRSGLDEKTSVKGQLAAF
+AAQRKGRGVTPETAHATEQTAPFTGAARAGERTAEAEDYVKDNWQPLALLGASSAAFVAL
+AGRLRRR*
+>NZ_CP033200.1_369
+MSHQAPPADASKVRAPRTAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELELAKRHVAAK
+GKKAGIGAGIAVVGLFFLALMVVALVVTLIGAFADPTFWFPALMVALAFLVLGLIFAGVG
+LMMVKGAMPLVPQEIVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAAREAERKK
+VEKKENKKARKNGEAAPHPDRADASEAEIRRRADLRRRHLGDIRSGLDEKTSVKGQLAAF
+AAQRKGRGVTPETAHATEQTAPFTGAARAGERTAEAEDYVKDNWQPLALLGASSAAFVAL
+AGRLRRR*
+>NZ_CP040019.1_2273
+MSHQAPPADALKAGAPRPAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELALAKGHVVAK
+GKKAGIGAGVTVVGLFFLALVVVALVVALIGAFADPTFWFPALMVAAAFLVLGAIFAGIG
+LFMVKGAMPLVPQETVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAKRAEERRK
+VEKEENKKARKNGEAAPHPDRDEASEAEIRRRADLRRRHLGDIRSGLEEKTSVKGQLAAF
+AAQRKGRGVTPQTAHATDQTAPFTGAARAGEKAAEAEDYVKDNWQPLALLGASSAAFLAL
+AGRLRRR*
+>NZ_CP083691.1_2128
+MSHAAPTAAPRAPRPTTPVTPQTRASSLTDLLAAVVRLLPLQLKDELALAKGQAAAKGKK
+AGIGAALAVVGLFFLALMTIALVVALIGAFANPPFWFPALMVALVFLVLGLVLAGVGAMQ
+IKGAMPLVPQETVRNLEYDLGYLKEGNDFDPAEYDRLKAERAEAKRLEKQREAERKKVEK
+EENKQARKDGLAAPHPAKDDASEDEVRRRAELRRRHLGDIRSGLDEKTSVKGQVAAFTAQ
+RKLRGTTPDTAHATEQTAPFTTAARAGEQTAAAEDYVKERWQPLALLGASGTAFAVLASR
+LRGRKG*
+>NZ_CP097650.1_592
+MSHQAPPADASKARAPRTAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELALAKGHVAAK
+GKKAGIGAGVAVVGLFFLALMVVALVVTLIGAFADPSFWFPALMVALAFLVLGLIFAGVG
+LVMVKGAMPLVPQETVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAAREAERKK
+VEKEENKKARKNGEAAPHPDRDDATEAEIRRRADLRRRHLGDIRSGLDEKTNVKGQLAAF
+AAQRKGRGVTPETTHATEQTAPFTGAARAGERTAEAEDYVKDNWQPLALLGASSAAFVAL
+AGRLRRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000587.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000587.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7683882076d2cde0e8ab2ef2aa44589bf6e0c989
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000587.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_625
+MSDRPGIAADRPLKVLIAADTYPPHVNGAATFGHRLATALHARGHEVHVVMPRSDAGPDT
+VEHRPEATVHLLRSLPAPTHEYYRVVLPRHAKTSFRRIYREVQPDVVHAQCHYMIGEAAI
+NEAERRRIRIVSTNHFMPENLEPFLPFPQWFLDIVSRVSWKDMGRLMGKGAVVTTPTALA
+AQAMAEHAGLDNVLPVSNGIDASAYELQPGERVDHPGHPVVLFVGRLAVEKNVEVLIRAI
+AHLARTRPDLDVHAEIVGDGEQRDRIRATVDEEGAADRVLLRGHVSEEELRAAYLRADVF
+CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALAERIARIL
+DLSDAERAAMGEASHAKALHHSAQKTVDIFERLYRGATAAEVRALL*
+>NZ_CP033200.1_371
+MSDRPGIAADRPLKVLIAADTYPPHVNGAATFGHRLATALHARGHEVHVVMPRSDAGPDT
+VEHRPEATVHLLRSLPAPTHEYYRVVLPRHAKTSFRRIYREVQPDVVHAQCHYMIGEAAI
+NEAERRRIRIVSTNHFMPENLEPFLPFPQWFLDIVSRVSWKDMGRLMGKGAVVTTPTALA
+AQAMAEHAGLDNVLPISNGIDASAYELQPGEKVDHPGHPVVLFVGRLAVEKNVEVLIRAI
+AHLARTRPDLDVHAEIVGDGEQRDRIRATVDEEGAADRVLLRGHVSEEELRAAYLRADVF
+CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALAERIARIL
+DLSDAERAAMGEASHAKALHHSAQKTVDIFERLYRGATAAEVRALL*
+>NZ_CP040019.1_2271
+MSDRPGTAADRPLKVLIAADTYPPHVNGAATFCHRLATALHARGHEVHVVMPRGEAGPDT
+VEERPEATVHLLRAIPAPTHEYYRLVMPWHAKAAFRRIYREVQPDVVHVQCHYMVGEAAI
+NEAERRRIRMVSTNHFMPENLEPFLPFPQWFLDIVSRVSWRDMGRLMGKGAAVTTPTALA
+ARAMAEHAGLDNVLPVSNGIDAAAYELQPGETVDHPGHPVVLFVGRLAVEKNVEVLIRAI
+AHLARVRPDLDVHAEIVGDGEQRDRIRAAVESEGVADRVLLRGHVSDEELRAAYLRADVF
+CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALAERVARIL
+DLPEAERAAMGEASHAKAMHHSAQKTVDVFERLYRGATPAEVRELL*
+>NZ_CP083691.1_2126
+MTSSARPAQERPLTVVIAADTYPPDVNGAAVFCFRLASALHERGHRVHVIAARNEPGPDT
+VEERPEATVHRLESHRAFTHEYYRLVFPWHASRSIDRILAEVRPDVVHAQCHYMIGEAAI
+NVADRRRIRTVSTNHFMPENLEPFLPFPQWFLNIVSKNSWRDMGRLMGKGAAVTTPTALA
+AAAMAEHAGLDRVLPISNGIDASAYELAPGEVVERAAHPTVLFVGRLAVEKHVDVLVRAV
+AHLARTRPDLDVHAEIVGDGEQRTALDAVIAEEGVADRVRRLGHVSDAELHTAYLRADVF
+CQPGTAELQSLVSLEAMSASTPVVLADALALPHLVDDGVNGWLFPPGDHVALAERIARVL
+DLPEAGRAAMGEASHAKAVRHSQAKTVDLFERLYRGATPAEIRAAL*
+>NZ_CP097650.1_594
+MSDRPGIAADRPLKVLIAADTYPPHVNGAATFGHRLATALHARGHEVHVVMPRSDAGPDT
+VEHRPEATVHLLRSLPAPTHEYYRVVLPRHAKISFRRIYREVQPDVVHAQCHYMIGEAAI
+NEAERRRIRIVSTNHFMPENLEPFLPFPQWFLDIVSRVSWKDMGRLMGKGAVVTTPTALA
+AQAMAEHAGLDNVLPVSNGIDASAYELQPGERVDHPGHPVVLFVGRLAVEKNVEVLIRAI
+AHLARTRPDLDVHAEIVGDGEQRDRIRATVDEEGVADRVLLRGHVSEEELRAAYLRADVF
+CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALADRIARIL
+DLSDADRAAMGEASHAKALHHSAQKTVDIFERLYRGATAAEVRAML*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000591.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000591.fa
new file mode 100644
index 0000000000000000000000000000000000000000..742b7b4e1956e8c684e36a3d9dcea214aaab6aab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000591.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_630
+MANYTAADIKALRERTGAGMMDVKKALDEADGDAEKAIEIIRVKGLKGATKREGRSAAEG
+LVAATVENGVGVMIELNCETDFVAKADKFIALGDVVLRAAVASGATDVDGLLASEHEGRT
+LGDYVTEEGALLGEKVAVRRLARVEGAYVDAYLHKTSKDLPAQVGVLLAVDADSAEAKTA
+AHDIAVHVAAYSPTYLTREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK
+EIVLVDQPFAKDPKQTVGKVASDAGTNVTGFARFRVGN*
+>NZ_CP033200.1_376
+MANYTAADIKALRERTGAGMMDVKKALDEANGDAEKAIEIIRVKGLKGATKREGRSAAEG
+LVAATVENGVGVMIELNCETDFVAKADKFIALGDVVLRAAVASGATDVDGLLASDYEGRT
+LGDYVTEEGALLGEKVAVRRLARVEGAFVDAYLHKTSKDLPAQVGVLLAVDADSADAKTA
+AHDIAVHTAAYSPTYLTREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK
+EIVLVDQPFAKDPKQTVGKVASDAGTNVTGFARFRVGN*
+>NZ_CP040019.1_2266
+MANYTAADIKALRERTGAGMMDVKKALDEANGDAEKAIEIIRVKGLKGATKREGRSAAEG
+LVAATVENGVGVMIELNCETDFVAKAEKFITLGDVVLRAAVASGAADVESLLASEHEGRT
+LGDHVIEEGALLGEKVAVRRLARVEGALVDAYLHKTSKDLPAQVGVLLAVDADSAEAKTA
+AHDIAVHTAAYSPTYLSREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK
+EIVLEDQPFAKDPKQTVGKVASDAGTKVTGFARFRVGN*
+>NZ_CP083691.1_2119
+MANYTAADIKALRERTGAGMMDVKKALDEANGDADKAVEIIRVKGLKGATKREGRSAAEG
+LVAATVENGVGVMIELNCETDFVAKADKFISLGDVVLKAAVASGAADVDSLLASDHEGRT
+LGDYVTEEGALLGEKVAVRRVARVEGAHVDAYLHKTSKDLPAQVGVLLAVDADSDAAKTA
+AHDIAVHTAAYSPTYLTREDVPAETVENERRIAEESARAEGKPEQALAKIVEGRLTGFFK
+EGVLVDQPFAKDPKTTVGKVASEAGTAVTGYARFRVGN*
+>NZ_CP097650.1_599
+MANYTAADIKALRERTGAGMMDVKKALDEANGDAEKAIEIIRVKGLKGATKREGRSAAEG
+LVAATVENGVGVMIELNCETDFVAKADKFIALGDVVLRAAVASGATDVDGLLASDYEGRT
+LGDYVTEEGALLGEKVAVRRLARVEGAFVDAYLHKTSKDLPAQVGVLLAVDADSADAKTA
+AHDIAVHTAAYSPTYLTREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK
+EIVLVDQPFAKDPKQTVGKVASDAGTNVTGFARFRVGN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000593.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000593.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83bb4deab70f983936f0b44295d0d9e4dffaa4ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000593.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_632
+MIQETLQSAEEQMDRTIEATREDFASVRTGRANPGLYSKVMVDYYGSFTPLQQLASFTTT
+DARTLLITPFDQSALRNIEKALSESEVGANPSNDGKVIRIVMPELTEERRKEYVKLVKSK
+AEEHKISVRNARRKAKEAMDKAVKDGEVGEDEGARGEKELDALTKRHVELIDEMAKNKEQ
+ELLEV*
+>NZ_CP033200.1_378
+MIQETLQSAEEQMDRTIEATREDFASVRTGRANPGLYSKVMVDYYGSFTPLQQLASFTTT
+DARTLLITPFDQSALRNIEKALSESEVGANPSNDGKVIRIVMPELTEERRKEYVKLVKSK
+AEEHKISVRNARRKAKEAMDKAVKDGEVGEDEGARGEKELDALTKRHVELIDEMAKNKEQ
+ELLEV*
+>NZ_CP040019.1_2264
+MIQETLQSAEEQMDRTIEATREDFASVRTGRANPGLYSKVMVDYYGSYTPLQQLASFTTT
+DARTLLITPFDQSALRNIEKALSESEVGANPSNDGKVIRVVMPELTEERRKEYVKLVKSK
+AEEHKVSVRNARRKAKDALDKAVKDGEVGEDEGARGEKDLDAMTKKHVDLIEEMAKNKEQ
+ELLEV*
+>NZ_CP083691.1_2117
+MIQETLTSAQEQMERTIEATREDFASVRTGRANPGLYSKVMVDYYGSFTPLQQLASFTTT
+DARTLLITPFDVSALRNIEKALSDSEVGANPSNDGKVIRVVMPELTAERRKEYVKLVKNK
+AEEHKVSVRNARRKAKEAIDKLVKDKEIGEDEGARGEKDLDALTKKHTDLIEEMAKKKEA
+ELLEV*
+>NZ_CP097650.1_601
+MIQETLQSAEEQMDRTIEATREDFASVRTGRANPGLYSKVMVDYYGSFTPLQQLASFTTT
+DARTLLITPFDQSALRNIEKALSESEVGANPSNDGKVIRIVMPELTEERRKEYVKLVKSK
+AEEHKISVRNARRKAKEAMDKAVKDGEVGEDEGARGEKELDALTKRHVELIDEMAKNKEQ
+ELLEV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000594.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000594.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6513f73bb142cabb6eb8ae3f883a2eb4258f231
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000594.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_634
+MTPRTTPDAEPVFELVEQDEIGYETTHVDAFMARAREARDGGAPLTAEEVRQARFATVNG
+GYATDEVDDELDRLEEELAAAERQAFVAERGDEDWAADLEERVAELVARADRAPAERFRR
+PSRADAVSYDVDQVDALVDRLRVTLAGAEDSTDPGAEGGLTADDVRRASFGEAEGAAGYE
+EGQVDAYLDAAVDVLLRRA*
+>NZ_CP033200.1_380
+MTPRTTPDAEPVFELVEQDEIGYETTHVDAFMARAREARDGGAPLTAEEVRQARFATVNG
+GYATDEVDDELDRLEEELAAAERQAFVAERGDEDWAADLEERVAELVARADRAPAERFRR
+PSRADAVSYDVDQVDALVDRLRVTLAGAEDSTDPGAEGGLTADDVRRASFGEAEGAAGYE
+EGQVDAYLDAAVDVLLRRA*
+>NZ_CP040019.1_2262
+MTTRRPQDAEPPFELVEQDEIGYETSHVDAFLARAREAREGGAPLTADEVRQARFATVNG
+GYATDEVDDELDRLEGELAAAEREAFVSERGDEDWSADLEERVAELVARADRAPAERFRR
+PSREDATSYDVDAVDALVDRLRVTLAGAEGAAAPDARGGLTADDVRRASFGEAEGDRGYE
+EGQVDAYLDAAVDVLLRRA*
+>NZ_CP083691.1_2115
+MTPTSPEARADFEHVGPDEIGYEPAHVDAFLERARRAEAGEGDLTAEDVRQARFATVNGG
+YAADQVDDELDRLEEVLMGREREDAVGDGAWDRELAERSQELLGRADRAPAERFRRPSAD
+DAQSYDVDDVDALVDRLRATLTDGSDELTADDVRRAGFASAQGGDGYDEAQVDAYLDAAV
+DVLLRRG*
+>NZ_CP097650.1_603
+MTPRTTPDTEPVFELVEQDEIGYETTHVDAFMARAREARDGGAPLTAEEVRQARFATVNG
+GYATDEVDDELDRLEEELAAAERQAFVAERGDEDWAADLEERVAELVARADRAPAERFRR
+PSRADAVSYDVDQVDALVDRLRVTLAGAEGSTDPDAEGGLTADDVRRASFGEAEGAAGYE
+EGQVDAYLDAAVDVLLRRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000595.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000595.fa
new file mode 100644
index 0000000000000000000000000000000000000000..216e39887d4621c0452ec2e47e427d2f0e6fc39d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000595.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_635
+MTLVDHTRPTGGQSAGSPPPAGPAEAVMLQVLDTEGRRRPQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY
+FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH
+QELERQRREHALYLQQFGDEEAGA*
+>NZ_CP033200.1_381
+MTLVDHTRPTGGQSAGSPLPAGPAEAVMLQVLDTEGRRRPQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY
+FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH
+QELERQRREHALYLQQFDDEEAGA*
+>NZ_CP040019.1_2261
+MTLVDHTRPAGGEAATSPPPGEPAEAPMLQVLDAEGRRHAQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALREDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSGWDPQATGVATQQIIIGAQALHAVGYAMGVQRDQADAATIVY
+FGDGATSQGDVNEAMVFSASYRSPVVFFCQNNHWAISEPVKLQTRRSIADRPWGFGIPSL
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALESLVEDGAELLFDEIYAEPH
+QELERQRREHALYLQQFDDEEAGA*
+>NZ_CP083691.1_2113
+MTDVHLPEQDAPPRSDRPAEQLQVLTPDGRRSPSPELDPWLTDVDEEMLARLHRELTLVR
+RLDTEATHLQRQGRLALWPPLRGQEASQVGAAAALRPADHVFPSYRENGLCLLRGVEAGE
+LLRVWSGSSFSGWDPAATGVATQQLVIGAQTLHAVGYAMGVQRDAADVSTLVCFGDGATS
+EGDVHEAMVFAASYQAPVVFFCQNNHWAISEPVGLQARRSIADRAWGYGIPALRVDGNDV
+LAVLAAVRRGVDRAAAGAGPMFVEAVTYRMGAHTTADDPTRYQDPAELEAWARRDPLERL
+TAHLRDVGADADAVVDASEAAADDLAARMRADLDALPEEGPEALFAHVYAEPHQELARQQ
+RDLQLHLDGLDAGEEQA*
+>NZ_CP097650.1_604
+MTLVDHTRPTGGQSAGSPPPAGPAEAVMLQVLDAEGRRRPQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY
+FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH
+QELERQRREHALYLQQFDDEEAGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000606.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000606.fa
new file mode 100644
index 0000000000000000000000000000000000000000..523d993f47af913e8df3831c532525c8f214e64e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000606.fa
@@ -0,0 +1,34 @@
+>NZ_CP042169.1_650
+MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL
+AGPRGGAAGTLFLGIDDDAPGAGALRAAVWIGSNVVPVAASEAPDAGWAPGDAEALGAAA
+AALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLGTAGGIDPNPHVVQAQP
+HDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIHTGRVFIDPGPRDAGGPLRFKA
+DIGLLSSRCAQIQGVWMAPAARGRGLAASAMAAVVDYVRLQAPVVSLYVNAYNTPALRTY
+ERVGFERRGTFATVLY*
+>NZ_CP033200.1_396
+MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL
+AGPRGGAAGTLFLGIDDDAPGAGALRAAVWIGSNVVPVAASEAPDAGWAPGDAEALGAAA
+AALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLGTAGGIDPNPHVVQAQP
+HDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIHAGRVFIDPGPRDAGGPLRFKA
+DIGLLSSRCAQIQGVWMAPAARGRGLAASAMAAVVDYVRLQAPVVSLYVNAYNTPALRTY
+ERVGFERRGTFATVLY*
+>NZ_CP040019.1_2245
+MTRLPPVPRWSPSTDRQVRAATGGRVRLLTDADTPALAALSARAPVSNVFVDSLLEAGRL
+AGPRGGAAGTLFLGIDAGEGRDDDGAPVAGLRAALWVGSNVVPVAAAETPDAGWAPGDAE
+ALGAAAVALRRRYGSLYGPAEPVLAVGSALAAAGHRARSVREDQPLLVLGADGAAETSPH
+VVQAHPRDFERVLPASAAMFEEELGFSPFLGGAAQYRDRVERLIRAGRVFIDPGPADAGG
+PLRFKADIGLLSSRCAQIQGVWMAPAARGRGLAAAAMAAVVEYVRLQAPVVSLYVNAYNT
+PALRTYERVGFERRGTFATVLY*
+>NZ_CP083691.1_2103
+MDLAAASDGRVRVLTDADTPALTALAAADPVANVHAASLLEAGRLAGPRGGRADGTLFLG
+VEDPDRPGALRSACWVGSTVVPLAGHDDDVPALAASVAALRRRFASVYGPAVTVLAVGRT
+LRDAGHRPRAVREEQPLMVHARTPGDLVPDPAVRAAAPGEWESVVPASAAMFEEELGFSP
+FLTGAAQYRDRVRRLVADGRVFTAPGEPVVDDPTSGVRFKADIGLLSASCVQVQGVWLHP
+SRRGRGEAAPAMAAAVALMARRAPAVSLYVNGFNTPALRTYERVGFERVGTFATVLY*
+>NZ_CP097650.1_619
+MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL
+AGPRGGAAGTLFLGIDDDAPGAGGLRAAVWIGSNVVPVAASEAPDAGWAPGDAEALGAAA
+AALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLGTAGGIDPNPSVVQAQP
+RDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIQAGRVFIDPGPRDAGGPLRFKA
+DIGLLSSRCAQIQGVWMAPAARGRGLAVSAMAAVVDYVRLQAPVVSLYVNAYNTPALRTY
+ERVGFERRGTFATVLY*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000609.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000609.fa
new file mode 100644
index 0000000000000000000000000000000000000000..93d30ee426d9e7120ab7aa7098a35cb1169db963
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000609.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_653
+MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGTAEHRTVEVVLDRASGTQGLSLDDV
+ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSVDGA
+APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD
+ADAAAGEDTAEHTEA*
+>NZ_CP033200.1_399
+MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGTAEHRTVEVVLDRASGTQGLSLDDV
+ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSVDGA
+APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD
+ADAAAGEDTAEHTEA*
+>NZ_CP040019.1_2242
+MDSTDRHDDAASLRARVEEALASADVVVEEVRVAGAAAHPTVEVVVDRASGTEGLSLDEL
+AGLSGRVSAALDALGDHVPGVGAGEYLLELTTAGVDRPLTQPRHFARNVGRLVEVAVDGG
+EPFTARLLAADEDAVELAEVRPGAKKGMKAKELPAQRVELARLGPAVVQVEWTPAQQAAD
+AAAAGEQTAEHTEA*
+>NZ_CP083691.1_2100
+METVPAALTELVEGAVSHRGVVVESVRVAGAADAPTVEVVLDRLEGTEGLSLDEVAELSG
+LVSDALDACGDEVPGVGAGEYLLEVSTAGVDRPLTGPRHWLRNVGRLVEVSIDAALPVTA
+RVLGVEASGVELEVVRPGAKKGMPAKVLPAEHVDFSRLGPGQVQVEWSTAAEQSGAEQTA
+EQTEA*
+>NZ_CP097650.1_622
+MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGAAEHRTVEVVLDRASGTQGLSLDDV
+ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSIDGA
+APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD
+ADAAAGEDTAEHTEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000615.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000615.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33564285173fa7137253de99add83ad429c1d66d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000615.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_660
+MAPSDGAPARNQGLGRIIVMVYAVFALSASARSLFQILTQFDAAPVAYTLSAVAAVVYIV
+ATFALARSGARAWAVALGAVLVELAGVVGVGLWTVLDPGMFAHDTVWSRFGAGYGYVPLV
+LPVVGLIWLLTHRPARPAEAGAL*
+>NZ_CP033200.1_406
+MAPSDGAPARNQGLGRIIVMVYAVFALSASARSLFQILTQFDAAPVAYTLSAVAAVVYIV
+ATFALARSGARAWAVALGAVLVELAGVVGVGLWTVLDPGMFAHDTVWSRFGAGYGYVPLV
+LPVVGLIWLLTHRPARPAEAGAL*
+>NZ_CP040019.1_2236
+MARTRTASGAARPGAAAPARNQGLGRIIVMVYAVFALSATARSLFQILTDVEAAPVAYSL
+SAFAATVYIVATLALARSGARAWAVALGAVLVELIGVVGVGLWTVLDPGLFAEETVWSRF
+GAGYGYVPLVLPVVGLAWLLAHRPSRPTAEEMAR*
+>NZ_CP083691.1_2093
+MVEQHPVADDGAPARPRRNQGLGRIIVMVYAVFALSASARSLFQILDHFWVAPFAYVLSA
+FAAVVYIVATLALARSGPTAWKVAVAAVGVELAGVVGVGLLTVLDPQLFADATVWSRFGA
+GYGYVPLVLPMVGLAWLLSHRPSREGRVR*
+>NZ_CP097650.1_629
+MAPSDGAPARNQGLGRIIVMVYAVFALSASARSLFQILTQFDAAPVAYTLSAVAAVVYIV
+ATFALARSGARAWAVALGAVLVELAGVVGVGLWTVLDPGMFAHDTVWSRFGAGYGYVPLV
+LPVVGLIWLLTHRPARPAEAGAL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000616.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000616.fa
new file mode 100644
index 0000000000000000000000000000000000000000..afd0082c568724c406da5f8887ec160276e8f769
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000616.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_661
+MRVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARARDALAVAVTFTPHPRA
+VHHPEVPHVDIISPEQRVVLLDEAGLDAVLLQRYTLEFADQSPEEFVRGMLVHGLHAAVV
+VVGHDVRFGRGNTGDVAEMVRLGARYGFEVEAVEEFPAEHGAEPERRCSSTWVREALAAG
+DVAQAAAVLGRHHVLAGEVVHGFARGRELGFPTANLETDVQGMIPADGVYAGWVHDAHGG
+VWPAAISIGSNPTFEDVSRVVEAHVIDRHDERVEDFDLYGQHIEVEFVARLRGMVAYEGV
+EKLVAQITQDVDEARAILATTPSDR*
+>NZ_CP033200.1_407
+MRVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARARDALAVAVTFTPHPRA
+VHHPEVPHVDIISPEQRVVLLDEAGLDAVLLQRYTLEFADQSPEEFVRGMLVHGLHAAVV
+VVGHDVRFGRGNTGDVAEMVRLGARYGFEVEAVEEFPAEHGAEPERRCSSTWVREALAAG
+DVAQAAAVLGRHHVLAGEVVHGFARGRELGFPTANLETDVQGMIPADGVYAGWVHDAHGG
+VWPAAISIGSNPTFEDVSRVVEAHVIDRHDERVEDFDLYGQHIEVEFVARLRGMVAYEGV
+EKLVAQITQDVDEARAILATTPSDR*
+>NZ_CP040019.1_2235
+MLVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARERDALAVAVTFSPHPRS
+VHRPDEPHVDILGPQQRAVLLSETGLDALLMQRYTLEFADQSPEEFVLSMFVRGLNAAVV
+VVGHDVRFGRGNVGDFAEMVRLGALHGFEVEAVEEHPAEIGDEPERRCSSTWVREALAAG
+DVAQAAAILGRHHTLDGEVVHGFARGRELGFPTANLAPEAEGMIPADGVYAGWVHDVQGE
+AWPAAISIGSNPTFEGVSRVVEAHVIDRPEERVEDFDLYGQHIEVEFVQRLRGMVAYEGV
+EKLVAQMTQDVEQARAILAATPSDR*
+>NZ_CP083691.1_2092
+MLVWNSMAEVPTDLPRTVVALGNFDGVHRGHRAVLERVVEIAHERGQLAVAVTFTPHPRV
+VHQPGLEHVEILSPEQRAVRLDETGIDALFLQHYTLEFAAQTPEEFVTSMFVRGLNAAAV
+VVGRDVRFGRDNAGDFAEMVRLGGVHGFDVVAVEDLPAEDGDGERRCSSTWIRELLAAGD
+VAHAAEVLGRNHVVAGAVVHGFARGRELGFPTANLEADAAGMIPADGVYAGWVHDAHGSV
+WPAAVSIGSNPTFEGVSRVVEAHVIDRPEEPVEDFDLYGQQIEVEFVERLRGMVAYEGVE
+KLVAQMHQDVDQARAVLAAAPQPAGRV*
+>NZ_CP097650.1_630
+MRVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARARDALAVAVTFTPHPRA
+VHQPEVPHVDIISPEQRVVLLEEAGLDAVLLQRYTLEFADQSPEEFVRGMLVHGLHAAVV
+VVGHDVRFGRGNTGDVAEMVRLGARYGFEVEAVEEFPAEHGAEPERRCSSTWVREALAAG
+DVAQAAAVLGRHHVLAGEVVHGFARGRELGFPTANLETDVQGMIPADGVYAGWVHDAHGG
+VWPAAISIGSNPTFEDVSRVVEAHVIDRHDERVEDFDLYGQHIEVEFVARLRGMVAYEGV
+EKLVAQITQDVDEARAILATTPSDR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000617.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000617.fa
new file mode 100644
index 0000000000000000000000000000000000000000..274d602ffde7b978b18c515b24dc635a8268c192
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000617.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_662
+MSAPEPGAPPAVPNLPGRPARARRAGPNPFETGGEHYDAVRPSYPAAAVDRVLAGTADGA
+DVVELGAGTGLFTRLLAARPADRVRTVTALEPSASMRAVLEREVAAGTGGRVRAVPGTGE
+ATGLPAASADVVVAAQAWHWMDPAAASAEAARVLRPGGRLAAVWNQLDTAVPWVHRLTRI
+MHAGDVHAARPEQRRFAAPFGAEEHARWAWTQPMTAAGLHGLMASRSYWLRADERIRSRM
+TANLDWYLHEHLGHAADAVLQVPYVTVAWWAAPVRGGRPR*
+>NZ_CP033200.1_408
+MSAPEPGAPPAVPNLPGRPARVRRAGPNPFETGGEHYDAVRPSYPAAAVDRVLAGTADGA
+DVVELGAGTGLFTRLLAARPADRVRTVTALEPSASMRAVLEREVAAGTGGRVRAVPGTGE
+ATGLPAASADVVVAAQAWHWMDPAAASAEAARVLRPGGRLAAVWNQLDTAVPWVHRLTRI
+MHAGDVHAARPEQRRFAAPFGAEEHARWAWTQPMTAAGLHGLMASRSYWLRADERIRSRM
+TANLDWYLHEHLGHAADAVLQVPYVTVAWWAAPVRGGRPR*
+>NZ_CP040019.1_2234
+MTGPGPGVPRLPGRPARARREAGNPFADAGGEHYDAVRPSYPAEAVAWVLEGLGQGLDRG
+LDVVEVGAGTGLFTRSLTALPVERVRSVAAVEPAASMRAVLERDVAAGSDGRVRAVPGTA
+EATGLPEASADVVVAAQAWHWVDPAAGSAEAARVLRPGGRLAAVWNQLDTAVPWVHRLTR
+IMHAGDVHAARPELRRFAAPFGAEEHARWTWTLPQTAADLHGIMASRAYWLRASETTRAK
+MSANLDWYLHEHLGHGPDEAIVVPYVSVAWQASST*
+>NZ_CP083691.1_2091
+MSERGLPDSGAAPRPAGGYVPALPSRPAITRTGGVNPFEVSPEQGEQYDAVRPSYPAAAV
+DWVLDGLGAGLDVVETGAGTGLFTRRLAERPAERVRSVAAVEPSEAMRAVLERDVAAGSA
+GRVRAVDGTGEATGLADGCADVVVAAQAWHWMDAERASAEAARVLRPGGRLAAVWNQLDV
+TVPWVHRLTRIMHAGDVHAAAPERRRFAAPFGPEEHARWSWSLTTTPAGLHALMASRSYW
+LRAREGTRARMTANLDWYLHEHLGHAAGEELTLPYVTVAWRAPAPAR*
+>NZ_CP097650.1_631
+MSAPEPGASPAVPNLPGRPARARRAGPNPFETGGEHYDAVRPSYPAAVVDRVLAGIADGA
+EVVELGAGTGLFTRLLAARPADRVRTVTALEPSASMRAVLEREVAAGTGGRVRAVPGTGE
+ATGLPAASADAVVAAQAWHWMDPAAASAEAARVLRPGGRLAAVWNQLDTAVPWVHRLTRI
+MHAGDVHAARPEQRRFAAPFGAEEHARWAWTQPMTAAGLHGLMASRSYWLRADERIRSRM
+TANLDWYLHEHLGHAADAVLQVPYVTVAWWAAPVRGGRPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000618.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000618.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d05ac1c3ac380840f54e59acac7f22105cb68baf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000618.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_663
+MSTPPVPHSPAPSSFPLRPPAPPLDLPLIGHGYPALLRTPRARWWNPLASFGLVLAGLVG
+LLVLGGVLGALALIATSGPALLGAADPTDVTDLDLYSAPMVLLNNLLLAALIGVALLAVA
+LGHPVAARFVHSVEGRVRWRWLARCVVVLTPLFLAYVLGAWALDGAPTAPRAQDWVWLLV
+MAFVLTPFQAAGEEYLFRGWLLLAVGTWIRRPVVAAAVTAVLSAATFSLAHGSLDPWILL
+DLAAFAVAAVLLTWRTGGLEAAVALHVVNNVVIIAVGTLVGTVEDSYVGAETAGSPAATL
+LSVAVVAVATALLLWQARRAGIARTVPVTVGARP*
+>NZ_CP033200.1_409
+MSTPPVPHSPAPSSFPLRPPAPPLDLPLIGHGYPALLRTPRARWWNPLASFGLVLAGLVG
+LLVLGGVLGALALIATSGPALLGAADPTDVTDLDLYSAPMVLLNNLLLAALIGVALLAVA
+LGHPVAARFVHSVEGRVRWRWLARCVVVLTPLFLAYVLGTWALDGAPTAPRAQDWVWLLV
+MAFVLTPFQAAGEEYLFRGWLLLAVGTWVRRPVVAVAVTAMLSAAAFSLAHGSLDPWILL
+DLAAFAVAAVLLTWRTGGLEAAVALHVVNNVVIIAVGTLVGTVEDSYVGAETAGSPAATL
+LSVAVVAVATALLLWQARRAGIARTVPVTVGARP*
+>NZ_CP040019.1_2227
+MTTASPPPPPPRGRLAPAAAPTPPGRRLDLPIIGAEYPQLLRTPRSRWWHPLLSAGLVLG
+SVLVLLAVLTLPMMLALVSEVGWDVFASADPADLARVEEALFSAPMMLLNNLMLAAFIGI
+AVLAVAVCHPVAARFVHSVQGRIRWRWLLRAHLVLLPLFLVYVLGTWALDGAPTAPRAED
+WVWLVVMAFLLTPLQAAGEEYLFRGWLLLAIGSWFRRPLPAIVLAAAVSAVTFSLAHGSF
+DPWILLDLSVFAVAAVLLTWRTGGLEAAVALHVVNNVVVIVFGTLAGTVNESFVDVETTG
+SPLATLVSAAVIALSTALLLWQARRAGIARTVPVSVGARP*
+>NZ_CP083691.1_2090
+MRTPRARWWNPLASFGMVLLGVGVLTVLLTVPMALVLFQQLDPGELWSAEGPSEASLELA
+LFSAPMVLLNNLLLAALTGVALLAVLVAHPVKARFLHSVEGRVRWRWLLRAHLVLLPLFL
+VYVLGTWALDGARVAPRPEDWGWLLAMALLVTPFQAAGEEYLFRGWTMLALGTWIRRPGV
+AVAVTAAVSAVAFALAHGSLNPWILLDLGVFAVAAVLLTWRTGGLEAAVALHVVNNVVIL
+AFGTVTGLATESYVTASTQGDPLATLVSAAVTALATVLLLWQAKRAGVARTVPSAVGARP
+*
+>NZ_CP097650.1_632
+MSTPPVPHSPAPSSFPLRPPAPPLDLPLIGHGYPALLRTPRARWWNPLASFGLVLAGLVG
+LLVLGGVLGALALIATSGPALLGAADPTDVTDLDLYSAPMVLLNNLLLAALIGVALLAVA
+LGHPVAARFVHSVEGRVRWRWLARCVVVLTPLFLAYVLGAWALDGAPTAPRAQDWVWLLV
+MAFVLTPFQAAGEEYLFRGWLLLAVGTWIRRPVVAAAVTAVLSAATFSLAHGSLDPWILL
+DLAAFAVAAVLLTWRTGGLEAAVALHVVNNVVIIAVGTLVGTVEDSYVGAETAGSPAATL
+LSVAVVAVATALLLWQARRAGIARTVPVTVGARP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000620.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000620.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8ac82b318a695194b50871e4e1d85012be75e93
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000620.fa
@@ -0,0 +1,70 @@
+>NZ_CP042169.1_665
+MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH
+SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA
+SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDALAETADAIESSQIEA*
+>NZ_CP033200.1_411
+MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH
+SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA
+SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGGSAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDALAETADAIESSQIEA*
+>NZ_CP040019.1_2225
+MEGPEITFAEAVIDNGAYGKRTIRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASVSTQLSGLPFSGPIGGVRMALVDDGAGKRQWVAFPKH
+SQLQDAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGASAPTEEVVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFKDYEDDAFEAVEKLATDRLTEIFSIGDKQTRESA
+SDAYHVEVMDELAGEDKPFAERRGEIAKAYGSVTKQVVRQRILKDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETSKRYLHHYNFPPYST
+GETGRVGSPKRREIGHGALAERAMVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGAFVSLTPGKDGLLHVSELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDADAETADAIESSQTEA*
+>NZ_CP083691.1_2088
+MEGPEITFAEAVIDNGRHGTRTVRFETGRLAQQAAGSAMVYIDEETSMLSATTVGKHPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFTKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALLDDGSGQRQWVAFPKH
+SQLEDAVFNMAVAGRVAGDDVAIMMVEAEAGENAWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLAARAGKAPVEVPVFKDYEQDAYDAVEKIATDRLTEIFSIADKQEREAA
+SDAYHLEVIEELAGEGKDFAERKGEVAKAYGSLTKQIVRRRILKDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETSKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAHVAGIAMGLVSAEVEGQTQYAALTDILGAEDAFGDMDFKVAGTSEFVT
+AIQLDTKLDGIPASVLAGALTQAREARLHILSVLEAAIDQPDELAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGAFVSLTPGKDGLLHISELRKLNEGKRVEDVEDVLGVGQKVQVEITK
+IDDRGKLSLAPVVADEDAAAGESREEDEEA*
+>NZ_CP097650.1_634
+MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH
+SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA
+SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDALAETADAIESSQIEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000627.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000627.fa
new file mode 100644
index 0000000000000000000000000000000000000000..735087a8acf962f73f3393de970b50e86a3d2f99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000627.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_673
+MSAAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWGGDSLVARWVALALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT
+LMRFVVIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPVVGGWWPWAGWVVIGAATVLTV
+LTGLEYVKDAWVLRRDALAAQRGA*
+>NZ_CP033200.1_419
+MSTAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWGGDSLVARWVALALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT
+LMRFVVIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPLVGGWWPWAGWVVIGAATVLTV
+LTGLEYVKDAWVLRRDALAAQRGA*
+>NZ_CP040019.1_2214
+MSTGGEAERVSAWNLPNILTSVRILMVPLFAWALWAGGPWGGDSATARWIAVALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGAALVLFSLLGELWWWVTVVILVREWGIT
+LMRFVVIRYGVMPAGRGGKLKTVLQAVGIGLLLMPLAPVVGGWWPWVGWTVIGAATVLTV
+LTGLEYVKDAWILRRDALAAPRGA*
+>NZ_CP083691.1_2081
+MNAQPERVSAWNLPNILTTVRILMVPFFVWAVWAGGPWGQDSLTARWIAVALFAAAMYTD
+KLDGDIARSRGLITDFGKIADPIADKLLTGSALVLFALLGELWWWVVIVILVREWGITAM
+RFVVIRYGVMPAGRGGKLKTVLQAVGIGLLLMPLAPVLGGWWPWLGWTVIGAALALTVVT
+GVEYVRDAVRLRADWLASHPEARR*
+>NZ_CP097650.1_642
+MSTAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWSGDSLLARWVALALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT
+LMRFVMIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPLVGGWWPWAGWVVIGAATVLTV
+LTGLEYVKDAWVLRRDALAAQRAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000629.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000629.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d8047a952dbfeb4ccd6c097fba2f46bbd35ea6a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000629.fa
@@ -0,0 +1,17 @@
+>NZ_CP042169.1_676
+MPLLRHEIGDVLRDVRQLQGRTLREVSHDARVSLGYLSEVERGQKEASSELLASICQALD
+IPLSYLLREVSDRLVEQEGMVVPDTLPDDLTDPSLGSLAGR*
+>NZ_CP033200.1_422
+MPLLRHEIGDVLRDVRQLQGRTLREVSHDARVSLGYLSEVERGQKEASSELLASICQALD
+IPLSYLLREVSDRLVEQEGMVVPDTLPDDLTDPSLGSLAGR*
+>NZ_CP040019.1_2211
+MMRHPVQAHGITRWVDDQPRPRATTPDIKERSMPLLRHEIGDVLRDVRQLQGRTLREVSH
+DARVSLGYLSEVERGQKEASSELLASICQALEIPLSYLLREVSDRLVDQEGIQVPDTLPE
+DLTDAADPSLGTLAGR*
+>NZ_CP083691.1_2079
+MMRHPVQAHGITRWVDSQPRPSQPTPELKERSMPILRHEIGDVLRDVRQRQGRTLREVSH
+DARVSLGYLSEVERGQKEASSELLASICDALQIPLSFLLREVSDRLAEQEGVVVPDTVPA
+DMAEDGAADVAPLAVR*
+>NZ_CP097650.1_645
+MPLLRHEIGDVLRDVRQLQGRTLREVSHDARVSLGYLSEVERGQKEASSELLASICQALD
+IPLSYLLREVSDRLVEQEGMVVPDTLPDDLTDPSLGSLAGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000634.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000634.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f1756501fba0730b25d3d8f0696eb1ddbd0cd72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000634.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_684
+MPAAASRPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTQAER
+EGVPHHLLDVLDVGQEASVAAFQSAVRDLFAQIRARGRTPILVGGSGLYVRAALDVLEFP
+PTDPALRAELEARAQREGLAGLRAELASLDPVSAERLQDARRIVRALEVCRLTGRPFSAF
+MPERTYAPEVAPVVQLGLRLDRAELHRRIAARVERMLAEGLLDEVRRLDVPGPDGLRQGP
+TASRAIGYAQMLAVLDGELTEAEAADQTVVATRRFARRQETWFRADPRVVWLDAQDEDVV
+AEALAVVAGDAT*
+>NZ_CP033200.1_427
+MPAAAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTPAER
+EGVPHHLLDVLDVGQEASVAAFQSAARDLFDQIRARGRTPILVGGSGLYVRAALDVLDFP
+PTDPALRTELEARAQREGLAGLRAELAALDPVSAERLQDARRIVRALEVCRLTGRPFSAF
+MPERTYAPEVAPVVQLGLRLDRSELHQRIAARVERMLAEGLLDEVRRLDVPGPGGLRQGP
+TASRAIGYAQMLAVLDGELTEAEAAEQTVVATRRFARRQETWFRADPRVVWLDAQGEDVV
+AEALAVVAGGAA*
+>NZ_CP040019.1_2206
+MRAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDIGTAKVTEAEREG
+VPHHLLDVLDVGQEASVAAFQSAARGVFEDVRSRGRTPILVGGSGLYVRAALDVLEFPPT
+DPEVRAAVEAELAERGEAALRAELAAVDPESAAKVADARRLVRALEVHRITGRPFSAFMP
+RREHDPSVAPVVQIGLSLERAVLHERIEARVERMLAAGLLDEVRALDVPGPDGLRQGPTS
+ARAIGYAQMLAVLDGTLTPEQAAEQTVVATRRFARRQETWFRADPRVHWVDALAPDVVAQ
+ALAVVAGS*
+>NZ_CP083691.1_2074
+MSAAAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTQAER
+EGVPHHLLDVLDVGQEASVAAFQSAARDLFDQIRARGRTPILVGGSGLYVRAALDVLEFP
+PTDPALRAELEARAQREGLTGLRAELAALDPASAERLRDARRIVRALEVCRLTGRPFSAF
+MPERTYAPEVAPVVQLGLRLDRAELHQRIAARVERMLAGGLLDEVRRLDVPGPDGLRQGP
+TASRAIGYAQMLAVLDGELTAAEAAEQTVVATRRFARRQETWFRADPRVVWLDAQGEDVV
+AAALAVVAGDAT*
+>NZ_CP097650.1_650
+MPAAAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTPAER
+EGVPHHLLDVLDVGQEASVAAFQSAARDLFDQIRARGRTPILVGGSGLYVRAALDVLDFP
+PTDPALRTELEARAQREGLAGLRAELAALDPVSAERLQDARRIVRALEVCRLTGRPFSAF
+MPERTYAPEVAPVVQLGLRLDRAELHRRIAARVERMLAGGLLDEVRRLDVPGSEGLRQGP
+TASRAIGYAQMLAVLDGELTEAEAAEQTVVATRRFARRQETWFRADPRVVWLDAQGEDIV
+AEALAVVAGDAT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000636.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000636.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12f08a0eaa11afb3dd1ab3916ae127068a223fd5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000636.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_686
+MVAVSSASHYFDADPSAPERRRTVRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA
+PPARGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNLVALRP
+EDVPEGAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG
+RMLEERAPGRFTAERADSVKGFRILRVARAR*
+>NZ_CP033200.1_429
+MVAVSSASHYFDADPSAPERRRTLRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA
+PPATGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNVVALRP
+EDVPEDAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG
+RMLEERAPGRFTAERADSVKGFRILRVVRAR*
+>NZ_CP040019.1_2202
+MVAVTSPAHYFSPDPGTPERRRSVDVELAGRRVTLQTANGVFSPDGIDKGTAALLSAVPA
+PPARGAFLDVGAGWGPLALTLALASPEAEVTGVEVNERSLALARDNAAAVGASNARFLTP
+EQIPDDARFDLIWSNPPIRIGKAALHDLLAQWLPRLAPGGEAWLVVQKNLGADSLLPWIA
+GMLQEQAPGEFTATRAATVKGFRILRISRAAESSS*
+>NZ_CP083691.1_2071
+MDAVTSPAHYFSPDPGTPERRRRVDVEIAGRRVTLQTANGVFSPDGIDKGTAALLSAVPA
+PPARGAFLDVGAGWGPLALTLALTSPEAEVTGVEVNERSLALARDNAAAVGAQNARFLTP
+EQVPDDARFDLIWSNPPIRIGKAALHDLLAQWLPRLAPGGEAWLVVQKNLGADSLLPWIS
+GMLQERAPGEFTATRAATVKGFRILRISRAAESSS*
+>NZ_CP097650.1_652
+MVAVSPASHYFDADPSAPERRRTLRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA
+PPATGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNVVALRP
+EDVPEDAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG
+RMLEERAPGRFTAERADSVKGFRILRVVRAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000637.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000637.fa
new file mode 100644
index 0000000000000000000000000000000000000000..238cc352d88f8be29558f64be0bc59c27b16bffd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000637.fa
@@ -0,0 +1,37 @@
+>NZ_CP042169.1_687
+MGRTQWPLTDEFAGQRVVIVGMGVSATQLLAEISTVADTLWVTRREPRWQDSAAPGALAE
+SVRGVDERTRAGLPPGSVVGATGMHRSSWVREAESRGVLVRHPMFTAVEPDGVRMPDGSF
+EPADVILWATGFRPAIRHLAPLRLRTPAGGIRVAGGRALDEPRLFLLGYGPSQSTVGANR
+AGRDAVRAILADLAGPASG*
+>NZ_CP033200.1_430
+MGVECTGRRVWATGAPAPGPLTTRTYPAGMTASPSPAPPRPGRTGRATVVVIGAGQAGLS
+AAYHLRRRGFVGLGPNDDGAAGVPDDAPGTFVVLDAETAPGGAWQHRWDSLTMATVNHIH
+ELPGDPVPPADPAAHANTLLPAYFADYEARFALPIRRPVRVRRVERIGEPGRARGFFVRT
+DGAPGTWRADFVVNATGTWTSPRWPSVPGMRSFRGRQLHTRDYVSKDEFAGQRVVIVGMG
+VSATQLLAEISTVADTLWVTRREPQWQDSAAPGALAESVRGVDERTRAGLPPGSVVGATG
+MHRSSWVREAETRGVLVRHPMFMAVEPDGVRMPDGSFEPADVILWATGFRPAIRHLAPLR
+LRTPAGGIRVAGGRALDEPRLFLLGYGPSQSTVGANRAGRDAVRAILADLAGPASG*
+>NZ_CP040019.1_2201
+MRTILAADRRRRHPSPVGEHAPAVPTLGRMTPHPDRHVTVLVVGAGQAGLSAAHHLRRRG
+FQPVGPGEAPRPAPEGSPGTFAVLDAEDRPGGAWLHRWDTLTMGSVNHIHELPGHPVPPA
+DPAARANAVLPAYFAEYEERFDLRVHRPVRVSRVERIGEPGAAEGFRVHTDAGTWTCGFL
+VNATGTWTSPHWPAVPGRREFRGRQLHTHDYRDPEEFARRRVVVVGMGVSATQHLAEVSR
+VADTLWVTRREPRWIDDPDPGHLAESVEGVDERTRLGLAPRSVVSATGMFRSDWVREAQA
+RGVLERHPMFERIEPDGVRMPDGSLERADVILWATGFRPAVRHLAPLRLRTPDGGIRAAH
+GRALDEPRLFLIGYGPSQSTVGANRAGRDAVRAILADLRAAGAA*
+>NZ_CP083691.1_2070
+MTPHPDRHVTVLVVGAGQAGLSAAHHLRRRGFLPVGPGEAPGPAPGGSPGTFAVLDAEDR
+PGGAWLHRWDTLTMGSVNHIHELPGHPVPPADPDAQANAVLPAYFAEYEERFDLRVHRPV
+RVSRVERIGEPGAAEGFRVHTDTGTWTCGFLVNATGTWTSPHWPAVPGRREFRGRQLHTH
+DYRGPQEFAGRRVVVVGMGVSATQHLAEVSRVADTLWVTRREPRWIDDPDPGHLAESVEG
+VDERTRLGLAPRSVVSATGMFRSDWVREAQARGVLERHPMFERIEPDGVRMPDGSLERAD
+VILWATGFRPAVRHLAPLRLRTPDGGIRAAHGRALDEPRLFLIGYGPSQSTVGANRAGRD
+AVRAILADLRAAGAA*
+>NZ_CP097650.1_653
+MGVECTGRRVWATGAPAPGPLTTRTYPAGMTASPSPAPPRPGRTGRATVVVIGAGQAGLS
+AAYHLRRRGFVGLGPNDDGAAGVPDDAPGTFVVLDAETAPGGAWQHRWDSLTMATVNHIH
+ELPGDPVPPADPAAHANTLLPAYFADYEARFALPIRRPVRVRRVERIGEPGRARGFFVRT
+DGAPGTWRADFVVNATGTWTSPRWPSVPGMRSFRGRQLHTRDYVSKDEFAGQRVVIVGMG
+VSATQLLAEISTVADTLWVTRREPQWQDSAAPGALAESVRGVDERTRAGLPPGSVVGATG
+MHRSSWVREAETRGVLVRHPMFMAVEPDGVRMPDGSFEPADVILWATGFRPAIRHLAPLR
+LRTPAGGIRVAGGRALDEPRLFLLGYGPSQSTVGANRAGRDAVRAILADLAGPASG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000638.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000638.fa
new file mode 100644
index 0000000000000000000000000000000000000000..316423a4953b0f56adb7df0bdd102728e93c0efb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000638.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_691
+MTEKNQHTPGPQGAHGSEDEIQAVIDRILAADDARRASEREATGRGSADSVVADHEDAPD
+AGTPDRSGALAGRALALDEGEDGHTDADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQ
+LRLERVVLAGVWTEGSAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKA
+QELAEIVALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQ
+VELAQLEYLLPRLRGWGESMSRQAGGRAAAGEGIGSRGPGETKIELDRRRIRTRMAKLRR
+DIAGMKPAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTV
+RKAMTPDGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHIVDGSHPDPEGQIA
+AVRSVFAEVHAHRIPEIIVLNKADAADPAVIARIRAKEPHAVVVSARTGEGIDELERAIA
+ATIPRPDVRLELLIPFTRGELVSRLHSADAEILAEGYEEGGTRLSVLVREDIAPDFAEFV
+VEADAL*
+>NZ_CP033200.1_431
+MTEKNQHTPGPQGAHGSEDEIQAVIDRILAADDARRASEREATGRGSADGAAAEHRDAPD
+AGTPDRSGALAGRALALDEGEDGHTDADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQ
+LRLERVVLAGVWTEGSAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKA
+QELAEIVALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQ
+VELAQLEYLLPRLRGWGESMSRQAGGRAAAGEGIGSRGPGETKIELDRRRIRTRMAKLRR
+DIAGMKPAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTV
+RKAMTPDGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDGSHPDPEGQIA
+AVRSVFAEVDAHRIPEIIVLNKADAADPAVVARIRSKEPHAVVVSARTGEGIDELERAIA
+ATIPRPDVRLELLIPFTRGELVSRLHSADAEILAEGYEEGGTRLSVLVREDIAPDFAEFV
+VEADAS*
+>NZ_CP040019.1_2200
+MTEEKNPTPAGGSEDEIQAVIDRILAADDARRSAAQGRADTPGRADAETAGDADAGTPDR
+TSALAGRALALAEGGDGHTAADGDQDELAARHSLRRVQGLSTELEDMTEVEYRQLRLERV
+VLAGVWTEGTAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATYLGKGKAQELAEI
+VALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQVELAQL
+EYLLPRLRGWGESMSRQAGGRAAGGEGIGSRGPGETKIELDRRRIRTRMAKLRKDIAGMK
+PAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTVRKAMTP
+DGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDGSHPDPEGQISAVRSVF
+AEVDAHRIPEIIVLNKADAADPAVVARIRAKEPHTVVVSARTGEGIEELERAIAATIPRP
+DVRLELLIPFTRGELVSRLHSEDAEILAEGYEEGGTRLSVLVRQDLAPEYEDYVVDPAAS
+*
+>NZ_CP083691.1_2068
+MTEEKNPTPAGGSEDEIQAVIDRILAADDARRATEREAAGRGSADSAAADHEGAPDRSGA
+LAGRALALAEGGDGHTAADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQLRLERVVLA
+GVWTEGTAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKARELADVVAL
+TGADTVIVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHATSREGRAQVELAQLEYL
+LPRLRGWGESMSRQAGGRAAGGEGIGSRGPGETKIELDRRRIRTRMAKLKKDIAGMKPAR
+EAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVQNALFATLDPTVRKAVTPDGI
+GYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDASHPDPEGQIAAVRSVLREV
+DAQSVPEIIVLNKADAAEPDVIARIRAKEPHTVVVSARTGEGIPELESAISATIPRPDVR
+LELLVPFTDGQVVSRLHSVDAEILSETYEETGTRLTVLVRRDIAADLEGYRVDAAAGDDA
+QEAASA*
+>NZ_CP097650.1_654
+MTEKNQHTPGPQGAHGSEDEIQAVIDRILAADDARRASEREATGRGSADSVVADHEDAPD
+AGTPDRSGALAGRALALDEGEDGHTDADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQ
+LRLERVVLAGVWTEGSAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKA
+QELAEIVALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQ
+VELAQLEYLLPRLRGWGESMSRQAGGRAAAGEGIGSRGPGETKIELDRRRIRTRMAKLRR
+DIAGMKPAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTV
+RKAMTPDGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDGSHPDPEGQIA
+AVRSVFAEVDAHRIPEIIVLNKADAADPAVVARIRSKEPHAVVVSARTGEGIDELERAIA
+ATIPRPDVRLELLIPFTRGELVSRLHSADAEILAEGYEEGGTRLSVLVREDIAPDFAEFV
+VEADAS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000640.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000640.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb3581834884407d26c40923d3a912da69498351
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000640.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_693
+MSTTDDQPAARAPLTDRQRRIVQTIRDAIADHGYPPSMREIGDAAGLASLSSVTHQLGRL
+ERHGYIRRDPGRPRALEVLLDVDGTPLGEAASPAAAPSSRVTAIPAWHTGADEADSVPVP
+WVGRIAAGGPVLAEQQVEDVMAIPRRLTGEGELFMLRVTGDSMVDAAICDGDWVVVRRQE
+TAENGDIVAALLDDEATVKTFRRRDGHTWLLPQNTAYEPILGDHATVMGRVVTVLRSL*
+>NZ_CP033200.1_433
+MSTTDDQPAARAPLTDRQRRIVQTIRDAIADHGYPPSMREIGDAAGLASLSSVTHQLGRL
+ERHGYIRRDPGRPRALEVLLDVDGTPLGEAASPAAAPSSRISAIPAWHTGADEADSVPVP
+WVGRIAAGGPVLAEQQVEDVMAIPRRLTGEGELFMLRVTGDSMVDAAICDGDWVVVRRQE
+TAENGDIVAALLDDEATVKTFRRRDGHTWLLPQNTAYEPILGDHATVMGRVVTVLRSL*
+>NZ_CP040019.1_2198
+MATTDEQPAPLTDRQRRIVQTIRDAIAEHGYPPSMREIGDAAGLASLSSVTHQLGRLEQH
+GYIRRDPGRPRALEVLLDVDGTPLGEAAPPAAAAPSGLPAIPAWHTGAEDADTVPVPWVG
+RIAAGGPVLAEQQVEDVMAVPRRLTGEGELFMLRVTGDSMVDAAICDGDWVVVRRQETAE
+NGDIVAALLDDEATVKTFRRRDGHTWLLPQNTAYEPILGDHATVMGRVVTVLRAL*
+>NZ_CP083691.1_2066
+MATSPTPPPGGAQPLTDRQRRIVRTIRQAIAERGYPPSMREIGDAAGLASLSSVTHQLGQ
+LERFGYLRRDPGRPRALEVLRDEDGAAAVADAAPGAPEIPSWHTGASEDATVEVPWVGRI
+AAGGPILADQQVEDVMAVPRRLTGEGDLFMLRVVGDSMVDAAICDGDWVVVRRQETAENG
+DIVAALLDDEATVKTLRRRDGHTWLLPQNTAYEPILGDHATLMGRVVTVLRAL*
+>NZ_CP097650.1_656
+MSTTDDQPAARAPLTDRQRRIVQTIRDAIADHGYPPSMREIGDAAGLASLSSVTHQLGRL
+ERHGYIRRDPGRPRALEVLLDVDGTPLGEAASPTAAPSSRVSAIPAWHTGADEADSVPVP
+WVGRIAAGGPVLAEQQVEDVMAIPRRLTGEGELFMLRVTGDSMVDAAICDGDWVVVRRQD
+TAENGDIVAALLDDEATVKTFRRRDGHTWLLPQNTAYEPILGDHATVMGRVVTVLRSL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000642.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000642.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0451353f7b59522cfd5fdc6a376a8dc63537ce8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000642.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_695
+MTDLSSLPLRENLRGLSPYGAPQLDVPYMLNTNENTHPVPEEVATAIAERVAAVAGGLNR
+YPDREFTGLRRALAGYLGHGLTADHVWAGNGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTVFVDGGRAEDHTLSAEHAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAQNEAAGGPGAMVVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+LGYLAADPAVADALRLVRLPYHLSAVTQATAEAALDHVDALLRTVEDIKAQRDRIVSTLR
+GLGLRPSVSDSNFVFFGHLEDASDVWRRLLDRGVLVRDVGIPHHLRVTAGTEAETTAFLT
+ALAEVLGETGDRS*
+>NZ_CP033200.1_435
+MTDLSSLPLRENLRGLSPYGAPQLDVPYMLNTNENTHPVPEEVATAIAERVAAVAGGLNR
+YPDREFTGLRRALAGYLGHGLTADHVWAGNGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTVFVDGGRAADHTLSAEHAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAQNEAAGGPGAMVVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+LGYLAADPAVTDALRLVRLPYHLSAVTQATAEAALDHVDALLRTVEDIKAQRDRIVSTLR
+GLGLRPSVSDSNFVFFGHLEDASDVWGRLLDRGVLVRDVGIPHHLRVTAGTEPETTAFLT
+ALEEVLGETGHRS*
+>NZ_CP040019.1_2196
+MTDLSSLPLRENLRGLSPYGAPQLDVPHMLNTNENTHPVPQEVATAIAERVAAVAGGLNR
+YPDREFTALRRALARYLGHGLTEGHVWAANGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTAFVDGGRAADHTLSAERAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAENESAGGPGAMIVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+VGYLAADPAVADALRLVRLPYHLSAVTQATAEAALDHVDALLETVEDIKGQRDRIVATLR
+ELGLEPSVSDSNFVFFGRLEDAADVWRRLLERGVLVRDVGIPHHLRVTAGTEEETTAFLE
+ALEAVLAEIGHRR*
+>NZ_CP083691.1_2064
+MTDLSSLPLRDSLRGQSPYGAPQLDVPYMLNTNENTHPVPQAVAEAITARVAKVAGGLNR
+YPDREFTELREHLAAYLGHGITPEQVWAANGSNEVLQQILQAFGGPGRTLLSFLPSYSMY
+PLLANGTDTAFVDGGRAADHTLSAEHAAALVREHRPNVVFLASPNNPTGTALGLDVIEAI
+YAAQAQNEAEGGHGAMVVVDEAYAEFALAGTDSALTLLRGRERLIVTRTMSKAFALAGAR
+LGYLAADAAVADALRLVRLPYHLSAVTQATAIAALERVDELLETVEDIKGQRDRIVAELT
+GMGLVPAVSDSNFVFFGRLADAHAVWEALLERGVLVRDVGIPHHLRVTAGTEEETTAFLD
+ALREIVEQDPAVVSAVDAD*
+>NZ_CP097650.1_658
+MTDLSSLPLRENLRGLSPYGAPQLDVPYMLNTNENTHPVPEEVATAIAERVAAVAGGLNR
+YPDREFTGLRRALAGYLGHGLTADHVWAGNGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTVFVDGGRAEDHTLSAEHAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAQNEAAGGPGAMVVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+LGYLAADPAVADALRLVRLPYHLSAVTQATAEAALDHVDALLRTVEDIKAQRDRIVSTLR
+GLGLRPSVSDSNFVFFGHLEDASDVWRRLLDRGVLVRDVGIPHHLRVTAGTEAETTAFLT
+ALAEVLGETGDRS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000644.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000644.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fbc0e177eb474e86147d95321b6fe0831ea0f4b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000644.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_697
+MARPTTVPGVRPRVAVLDYGSGNVHSALRAVERAGAEVELTRDPQAVQEADGLLVPGVGA
+YASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERTAGMGEWPGVVAE
+LPAEVLPHMGWNTVRPPEGSALFAGIEDERFYFVHSYGVLEWEFDQTISAMRPPQVTWAH
+HGADFIAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL*
+>NZ_CP033200.1_437
+MARPTTVPGVRPRVAVLDYGSGNVHSALRAVERAGAEVELTRDPQAVQEADGLLVPGVGA
+YASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERTAGMGEWPGVVAE
+LPAEVLPHMGWNTVRPPEGSALFAGIEDERFYFVHSYGVLEWEFDQTISAMRPPQVTWAH
+HGADFIAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL*
+>NZ_CP040019.1_2194
+MARPTSVPGVRPSVAVLDYGSGNVHSAVRALERAGADVELTRDPEAVQSADGLLVPGVGA
+FASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERAEGMGEWPGVVEA
+LPAEVLPHMGWNTVRPPEGSALFAGIEDERFYFVHSYGVLRWEFDQTISAMRPPQVTWAH
+HGADFVAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL*
+>NZ_CP083691.1_2062
+MASPTSVPGVRPTVAVLDYGSGNVHSAVRAVEHAGARVELTKDPDAVLGADGLVVPGVGA
+FASVMEALRSSGGTRWIGRRVAGGRPVLGICVGHQVLFEAGVEHGVRTEGMGEWPGVVEP
+LPAATVPHMGWNTVRPAEGSALFAGIEDERFYFVHSYAVQSWEFDQGNEAMRPPQVTWSH
+HGADFIAAVENGPLSATQFHPEKSGDAGQALLRNWLETL*
+>NZ_CP097650.1_660
+MARPTTVPGVRPRVAVLDYGSGNVHSALRAVERAGAEVELTRDPQAVQEADGLLVPGVGA
+YASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERTAGMGEWPGVVAE
+LPAEVLPHMGWNTVRPAEGSALFAGIEDERFYFVHSYGVLEWEFDQTISAMRPPQVTWAH
+HGADFIAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000648.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000648.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e8ffd0f4e1773cbb4aa9fee6bc5f06828c5ef6c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000648.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_701
+MRTRTLTGVATAALGAVVVAGAGPALAQTTLTQGSAITAPAGACSLTIVDDATAYTAAHC
+GAGQWQIGSTVRDVDGTAIGTVSALPGDSGVDAVRVALADDVDVVGDWSTRPASSIGVGE
+TVYTHGSSVPLGAPNTVSHTQTFEAATVCDDAYADQVALDTASTYAGDSGGAVYDAQQRV
+VGVISGIAPVTFDAEGNVVGCDAQAMSSIMVPVESLDALDASAAPAAETAAAAETAPAAE
+TAPAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIAAELKARAEAAAEEEAAEA
+APAAEAPVAEAAAPGVTDVVAAPAEGVAYGTQVVAQTDQGGFASVTVTAYDADGTVLGQD
+GLDLTGEYRAWLPVPAEVPAGGSVVVTVVDAAGAATDATVTLGGQLVG*
+>NZ_CP033200.1_441
+MRTRTLTGVATAALGAVVVAGAGPALAQTTLTQGSAITAPAGACSLTIVDDATAYTAAHC
+GAGQWQIGSTVRDVDGTAIGTVSALPGDSGVDAVRVALADDVDVVGDWSTRPASSIGVGE
+TVYTHGSSVPLGAPNTVSHTQTFEAATVCDDAYADQVALDTASTYAGDSGGAVYDAQQRV
+VGVISGIAPVTFDAEGNVVGCDAQAMSSIMVPVESLDALDASAAPAAETAAAAETAPAAE
+TAPAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIAAELKARAEAAAEEEAAEA
+APAAEAPVAEAAAPGVTDVVAAPAEGVAYGTQVVAQTDQGGFASVTVTAYDADGTVLGQD
+GLDLTGEYRAWLPVPAEVPAGGSVVVTVVDAAGAATDATVTLGGQLVG*
+>NZ_CP040019.1_2190
+MRTRTLTGVATAALGAVVVAGAGPALAQTVITQGSALSAPAGACSLTIVDDATAYTAAHC
+GAGQWEVGSPVLDAEGVQIGTVSGLPGTSGVDVVRVALAEDVEVVGEWSTRPAASVEVGE
+TVFTHGSSVPLGAPNSLSHTQTFDAATVCDDAYSDQMALDVASTYPGDSGGAVYDAQQRV
+VGVISGVAPVTFDEEGNVVGCDAQSLSSIMVPVESLDAVGQETAAPAAVEPAAAEAPATE
+VTETPAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIRAELIERAEAEAAAEAP
+AEQPAAEAPVAEAVVAGTEDVVAAPAEGVAYGTQVMAETSQGGFASVTVTAYDADGTVLG
+VDGLDLTGEYRAWMPVPAEVPAGGSVVVTVVDAAGDATDTQVTLGGQLIG*
+>NZ_CP083691.1_2058
+MKKTTLTGATTAALGAVVVAGAGSALAATPLTQGAALSVPAGECSITLVSDTTAFTAAHC
+GAGQWTVGSAVHAADGARIGSVSALPGSTGVDVVKIALDEDVDVVGDWSTRPAASVKPGE
+TVYTQGSSVPLGSPNSISDPETYDIAETCGDVYTDQVSLDAATTRPGDSGGAVYDAKQRV
+VGVVSGLAPVSFDEEGRAVGCDAASLSTIMVPAESLKAVAAAPAKATAPAPTVGKHGVIL
+KAPTAPAAKAPAAEKKAPAAKAPAAEKKAAPAPTLGKHGVSAETATAGTTTLKVAPEDGI
+DFRTRVQATTKTGGFSYMAVTAYDAAGKQIGHLHLHSDGQPMTWINTPAQVPAGGHIEVQ
+LKDAAGQPTDATVTLGGVPVN*
+>NZ_CP097650.1_664
+MRTRTLTGVATAALGAVVVAGAGPALAQTTLTQGSAITAPAGACSLTIVDDATAYTAAHC
+GAGQWQIGSTVRDVDGTAIGTVSALPGDSGVDAVRVALADDVDVVGDWSTRPASSIGVGE
+TVYTHGSSVPLGAPNTVSHTQTFEAATVCDDAYADQVALDTASTYAGDSGGAVYDAQQRV
+VGVISGIAPVTFDAEGNVVGCDAQAMSSIMVPVESLDALDASAAPAAETAAAAETAPAAE
+TAPAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIAAELKARAEAAAEEEAAEA
+APAAEAPVAEAAAPGVTDVVAAPAEGVAYGTQVVAQTDQGGFASVTVTAYDADGTVLGQD
+GLDLTGEYRAWLPVPAEVPAGGSVVVTVVDAAGAATDATVTLGGQLVG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000650.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000650.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e8df82b9408a07c7e9ecf537c32dad7f6d38ecf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000650.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_703
+MTTPGAPDASAPFTPQARHLAVVSGGSGDPSQTRMLAERMAESASAALSEHGVVPQIHLI
+TLRELAVDIAQALVTFAISPALRAALDEVAQADAVIAVSPTYKASYSGLFKSFWDLAEPT
+SVVGVPVLLGATGGTARHSLMIDTAMRPLFAYLKARIVPTAVFAASDDWGEAAGVQASMR
+TDPLQSRIRAAGRDLAEITLSRPPRARAAAPADIDLEVTPFEQLLNPGP*
+>NZ_CP033200.1_443
+MTTPGAPDASAPFTPQARHLAVVSGGSGDPSQTRMLAERMAESASAALSEHGVVPQIHLI
+TLRELAVDIAQALVTFAISPALRAALDEVAQADAVIAVSPTYKASYSGLFKSFWDLAEPT
+SVVGVPVLLGATGGTARHSLMIDTAMRPLFAYLKARIVPTAVFAASDDWGEAAGVQASMR
+TDPLQSRIRAAGRDLAEITLSRPPRARAAAPADIDLEVTPFEQLLNPGP*
+>NZ_CP040019.1_2188
+MIGQGAFEATDPLMPQARHVAVVSGGSGDPSQTRMLAERMAEAASAALSEHGVVPEIHLI
+TLRELATDIAQAMVTFAVSPALRAALDEVQQADAVIAVSPTFKASYSGLFKSFWDLVDDE
+SLIGVPVLLGATGGTVRHSLMIDTALRPLFAYLKSRIVPTAVFAASDDWGEADGAQASTR
+TDPLRSRIRSAGRDLAEILLNRPPRARAAAPETLDLEVTPFEQLLNPDA*
+>NZ_CP083691.1_2056
+MSTSAFESTDPFTPGARHIAVVSGGIGDPSQTRKLADRLARASADALSAAGVVPEIHVVS
+LRELATDLGAGMVTTARSPALLDAVAQVEHADAVIAVSPTFKASYSGLFKSFVDLIDDEA
+LVGVPVLLGATGGTARHSLMIDQAMRPLFAYLKARIVPTAVFAASDDWGRADGQNDSTRT
+TPLDARIRAAGEDLAEVLRHRPARVRPAADATDDDLEVIPFDQLLHPGR*
+>NZ_CP097650.1_666
+MTTPGAPDASAPFTPQARHLAVVSGGSGDPSQTRMLAERMAESASAALSEHGVVPQIHLI
+TLRELAVDIAQALVTFAISPALRAALDEVAQADAVIAVSPTYKASYSGLFKSFWDLAEPT
+SVVGVPVLLGATGGTARHSLMIDTAMRPLFAYLKARIVPTAVFAASDDWGEAAGVQASMR
+TDPLQSRIRAAGRDLAEITLSRPPRARAAAPADIDLEVTPFEQLLNPGP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000651.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000651.fa
new file mode 100644
index 0000000000000000000000000000000000000000..660b1f323dbdc853edaea9f1638d4a37119cdbd4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000651.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_704
+MQFGVFTIGDITADPTNGTAPTEHQRIKDTVKIARHAEQAGFEVFATGQHHNPPFVAPGN
+PPTLLAYLAAQTETLQLSTATTLITTMDPVRLAEDYAYLQHLADGRVDLTMGRGNTGPVY
+PWFGKDIRQGIQLAVENYNLLYRLWHEETVDWSGNHRTPLQDFTLTPQPLDGVAPFVWHG
+SIRSPEIAEQAAYYGDGYFHNNIFWNKEHVIQMVRLYRQRYEYYGHGKAHQAYVALGGQA
+YMAKNSQDAVAEFRPYFDNAPVYGHGPSLEDFSRMTPLTVGSPQQVIERTLTFRDWVGDY
+QRQMFLIDHAGLPTDTVLRQIDLFGEEVLPVLRKEFDALKPDDVPAAPTHEFLVARARRG
+EAPVPGGKEGSQAQLDRAAAAEQRATADAAKGGAAQ*
+>NZ_CP033200.1_444
+MQFGVFTIGDITADPTNGTAPTEHQRIKDTVKIARHAEQAGFEVFATGQHHNPPFVAPGN
+PPTLLAYLAAQTETLQLSTATTLITTMDPVRLAEDYAYLQHLADGRVDLTMGRGNTGPVY
+PWFGKDIRQGIQLAVENYNLLYRLWHEETVDWSGNHRTPLQDFTLTPQPLDGVAPFVWHG
+SIRSPEIAEQAAYYGDGYFHNNIFWNKEHVIQMVRLYRQRYEYYGHGKAHQAYVALGGQA
+YMAKNSQDAVAEFRPYFDNAPVYGHGPSLEDFSRMTPLTVGSPQQVIERTLTFRDWVGDY
+QRQMFLIDHAGLPTDTVLRQIDLFGEEVLPVLRKEFDALKPDDVPAAPTHEFLVARARRG
+EAPVPGGKEGSQAQLDRAAAAEQRATADAAKGGAAQ*
+>NZ_CP040019.1_2187
+MQFGVFTIGDVTQDPTTGTTPTEHQRIKDTVRIAQHAAQAGFEVFATGQHHNPPFVAPGN
+PPTLLAYLAAMTTDLQLSTATTLITTMDPVRLAEDYSYLQHLADGRVDLTMGRGNTGPVY
+PWFGKDIRQGIPLAVENYNLLYRLWHEETVDWSGKFRSPLQNFTLTPQPLDGVAPFVWHG
+SIRSAEIAEQAAYYGDGFFYNNIFWNKEHVIQMVRLYRQRYEYYGHGKAHQAYVALGGQA
+YMAKNSQDAVKEFRPYFDNAPVYGHGPSLEQFSSMTPLTVGSPQQVIERTLGFRDWVGDY
+QRQMFLIDHAGLPTDTVLKQIDIFGEEVLPVLRKEFAALKPDDVPEAPTHEFLVERARRG
+EAPVPGGKEGSQAQIDRAAAAEKRAAAKAGEGA*
+>NZ_CP083691.1_2055
+MQLGIFTIGDITADPTTGTTPTEHQRIKDTVTIARHAEQAGFDVFATGQHHNPPFVAPGN
+PPTLLSHLAAVTETMTLSTATTLITTMDPVRLAEDYSYLQHLADGRVDLTLGRGNTGPVY
+PWFGKDIRQGVNLAVENYNLLYRLWHEETVDWSGQFRTPLQDFTLTPQPLDGVAPFVWHG
+SIRSPEIAEQAAYYGDGFFHNNIFWNKEHIIRMVRLYRQRFEHYGHGKAHQAYVGLGGQA
+YMAKNSQDAVKEFRPYFDNAPVYGHGPSLEDFTSMTPLTVGSPQQVIERTLSFRDWVGDY
+QRQMFLIDHAGLPTDTVLKQIDLFGEEVLPVLREEFAALKPDDVPEAPTHEFLVERARRG
+EAPVPGGREGSPAHAAREAARAKQAEQQKKKEDAR*
+>NZ_CP097650.1_667
+MQFGVFTIGDITADPTNGTAPTEHQRIKDTVKIARHAEQAGFEVFATGQHHNPPFVAPGN
+PPTLLAYLAAQTETLQLSTATTLITTMDPVRLAEDYAYLQHLADGRVDLTMGRGNTGPVY
+PWFGKDIRQGIQLAVENYNLLYRLWHEETVDWSGNHRTPLQDFTLTPQPLDGVAPFVWHG
+SIRSPEIAEQAAYYGDGYFHNNIFWNKEHVIQMVRLYRQRYEYYGHGKAHQAYVALGGQA
+YMAKNSQDAVAEFRPYFDNAPVYGHGPSLEDFSRMTPLTVGSPQQVIERTLTFRDWVGDY
+QRQMFLIDHAGLPTDTVLRQIDLFGEEVLPVLRKEFDALKPDDVPAAPTHEFLVARARRG
+EAPVPGGKEGSQAQLDRAAAAEQRATADAAKGGAAQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000660.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000660.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed5befaa1e29f42f4323c1858c4111ed9c547b16
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000660.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_714
+MRSVNDVRDERGAATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFASVAAADQAVKAVVAE
+ADHPSAGAAHATVELTLADYGVGAGQYDLTVGCDQGGCGTLEPGEVVAVRVDVGVPVPLT
+PAAWSLTPVTVGSDARQTVPRF*
+>NZ_CP033200.1_454
+MRSVNDVRDERGAATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFASVAAADQAVKAVVAE
+ADHPSAGAAHATVELTLADYGVGAGQYDLTVGCDQGGCGTLEPGEVVAVRVDVGVPVPLT
+PAAWSLTPVTVGSDARQTVPRF*
+>NZ_CP040019.1_2149
+MPIASDVRDERGSATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFASVAAADQAAKVVVSG
+TEGRSAAQAHAAVRLTLADFGIDYGAYELDLGCSAGDCVSLDPGEVVQARVDVEVPIPLT
+PADWSLAPVTVGSDARQAVPRF*
+>NZ_CP083691.1_2044
+MPSATDARHGPTHAPWRGTDLADDVGSATVEFLGLSLILLIPLAYLMLFVSQVQAAAFGA
+LASADQAARVMVSGEGGNPGQAEGTIPLTLADYGFDAADAEWSVACDVGGCGTLEPGEVV
+DVTVAISLDPPLLPDGWVSVDIATVDSHSRARMPRF*
+>NZ_CP097650.1_677
+MRSVNDVRDERGAATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFASVAAADQAVKAVVAE
+ADHPSAGAAHATLELTLADYGVGAGQYDLTVGCDQGGCGTLEPGEVVAVRVDVAVPVPLT
+PAAWSMTPVTVGSDARQTVPRF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000661.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000661.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb631c0b6fa8ed4ceaff757f892dfee288aa8b53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000661.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_715
+MRRRLTARLGHDDGQTTVLTVGLCAVLVALMLVMLAVTTVQLQHRRLQSLADSAAIAGAE
+ELGFRLGEDPGVVLSDDDVAASASAHLAAVGAQEAVPGLGGMNARVADDGTTVVVTLDAR
+ADLFAMTGPFAGTLPLSVPLEATGSSRTSLAR*
+>NZ_CP033200.1_455
+MSRRLTARLGHDDGQTTVLTVGLCAVLVALMLVMLAVTTVQLQHRRLQSLADSAAIAGAE
+ELGFRLGEDPGVVLSDDDVAASASAHLAAVGAQEAVPGLGGMNARVADDGTTVVVTLDAR
+ADLFAMTGPFAGTLPLSVPLEATGSSRTSLAR*
+>NZ_CP040019.1_2148
+MRALSALRRDDGQTTVLTVGLCALLIGLMLVMLAATTVQLQHRRLQSLADGAALAGAEEL
+GFRLGEDPGVVLDDGDVAASAAAHLDAVDAASSVHGLGGMAAGVADDGATVTVRLDAEVD
+LLAAAGPFAGMLPLSVPIQATGDSRTSLSR*
+>NZ_CP083691.1_2043
+MTRRHRSRPQRRPDRRHGAHERGEITVLTLGLSAIVVGLLLVVLSATLVLIQARKVQSLA
+DGAALAGAEQLAFQLDADPRVVLEPGSVQASVNEHLDAVGARESVPGLESVSAQVAGDGA
+TVVVRARAKVTLVPSGAGWLADLIPASVPVSAEGSSRTVLTR*
+>NZ_CP097650.1_678
+MRRPLTARLGHDDGQTTVLTVGLCAVLVALMLVMLAVTTVQLQHRRLQSLADSAAVAGAE
+ELGFRLGEDPGVVLSDGDVAASASAHLAAVGAREAVPGLGGMSARVAEDGTTVVVTLDAR
+ADLFAMTGPFAGTLPLSVPLEATGSSRTSLAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000662.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000662.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24d05bcf3db55b0274d222084b03f9109aed5b72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000662.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_717
+MADTDFSAEIDSLRHTLASIEQVSDLDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS
+HRQTDLKRITSLESRIEDLETMVELAAEEDEPSLLDDANQELTSIRKALEELEVVTLLSG
+EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF
+EVNAPYAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHLPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLLRKA
+EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGHIDDFVDAGI
+RWRAEQVKAAQED*
+>NZ_CP033200.1_457
+MADTDFSAEIDSLRHTLASIEQVSDLDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS
+HRQTDLKRITSLESRIEDLETMVELAAEEDEPSLLDDANQELTSIRKALEELEVVTLLSG
+EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF
+EVNAPFAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHLPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLLRKA
+EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGHIDDFVDAGI
+RWRAEQVKAAQED*
+>NZ_CP040019.1_2145
+MADTDFSAEIDSLRHTLASIEQVSDIDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS
+HRQADLKRITSLESRIEDLETMVELAAEEDEPSLLDDANDELASIRKSLEELEVVTLLSG
+EYDPRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF
+EVNAPFAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHIPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLQRKA
+EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGAIDAFVDAGI
+RWRAEQAKAAQED*
+>NZ_CP083691.1_2039
+MADTDFSAEIDALRHTLASIEQVSDVEKMTAEVAELEKEAAAPDLWDDPEAAQKVTSKLS
+HRQADLKRIKSLADRIDDLETMVELAAEEDEPSLLDDANVELTSIRKALEELEVVTLLNG
+EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQKGWSTKVMDTSYAEEAGLKSATF
+EVNAPFAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHIPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLVRKA
+EEDAKKKEMAGDIKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGAIDDFIDAGI
+RWRAEQVKAAQED*
+>NZ_CP097650.1_681
+MADTDFSAEIDSLRHTLASIEQVSDLDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS
+HRQTDLKRITSLESRIEDLETMVELAAEEDEPSLLDDANQELTSIRKALEELEVVTLLSG
+EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF
+EVNAPYAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHLPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLLRKA
+EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGHIDDFVDAGI
+RWRAEQVKAAQED*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000664.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000664.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18f6d40293a64e4075ced2843765544e0b407c4a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000664.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_719
+MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV
+YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV
+AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA
+RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGA
+LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTILATVGAPGQTAGPDSSQLH
+SQPSDAINAAVRKQGWDVADLDFIEINEAFGAVAVQSLRDLDYPHEKTNIHGGAIALGHP
+IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR*
+>NZ_CP033200.1_459
+MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV
+YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV
+AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA
+RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGA
+LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTILATVGAPGQTAGPDSSQLH
+SQPSDAINAAMRKQGWDVADLDFIEINEAFGAVAVQSLRDLDYPHEKTNIHGGAIALGHP
+IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR*
+>NZ_CP040019.1_2143
+MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALECAGVAPEDVDMV
+YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLVRLGEADVVV
+AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA
+RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGA
+LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAYAEEKGLTILATVGALGQTAGPDSSQLH
+SQPSDAINAAMRKQGWDVADLDFIEINEAFGAVAVQSLRDLDYPHEKTNIHGGAIALGHP
+IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR*
+>NZ_CP083691.1_2037
+MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV
+YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV
+AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA
+RAEQDEVAAASHQRAARAQSQGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGS
+LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTVLATVGAPGQTAGPDSSQLH
+SQPSDAINAAVRKQGWDVADLDFIEINEAFGAVAVQSLRDLGYPHEKTNIHGGAIALGHP
+IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR*
+>NZ_CP097650.1_683
+MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV
+YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV
+AGGQESMTNAPHLLPGARTGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA
+RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEIPQRKGDPLVVSQDEGVRPDTTAESLGA
+LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTILATVGAPGQTAGPDSSQLH
+SQPSDAINAAVRKQGWDVADLDFIEINEAFGAVAVQSLRDLGYPHEKTNIHGGAIALGHP
+IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000667.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000667.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2468c7263298e730a2bcb58e109fa267e8ca77dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000667.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_722
+MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDTYEAGMVLTGTEVKSLREGKASLVD
+GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL
+SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA*
+>NZ_CP033200.1_462
+MGKNSKGKATKQPAPGERQVIANNKKARHDYTILDTYEAGIVLTGTEVKSLREGKASLVD
+GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL
+SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA*
+>NZ_CP040019.1_2140
+MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDVYEAGLVLTGTEVKSLREGKASLVD
+GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL
+SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRIRNRRAGVA*
+>NZ_CP083691.1_2034
+MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDTYEAGMVLTGTEVKSLREGKASLVD
+GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL
+SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA*
+>NZ_CP097650.1_686
+MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDTYEAGMVLTGTEVKSLREGKASLVD
+GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL
+SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000668.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000668.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ffcf7e1514bbdda72b682c42bd7a48693a448d0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000668.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_726
+MERPENPATRGRDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVTDADRAAE
+ESIRSTLSRARARDGVVGEEFGGSLSRSGRQWVVDPIDGTKNFVRGVPVWATLIALLIDG
+EPVVGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRITVSGVDRVEDASLSFSSIEGWRER
+GSIRAFLQLTSDVWRVRGFGDFWSYMLVAEGAVDIAAEPELELHDMAALVPIVREAGGRF
+TSLDGEDGPFGGHALATNGLLHDDVLARLRAGDETEDSA*
+>NZ_CP033200.1_465
+MERPENPATRGRDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVTDADRAAE
+ESIRSTLSRARARDGIVGEEFGGSLSRSGRQWVVDPIDGTKNFMRGVPVWATLIALLIDG
+EPVVGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRITVSGVDRVEDASLSFSSIEGWRER
+GSIRAFLQLTSDVWRVRGFGDFWSYMLVAEGAVDIAAEPELELHDMAALVPIVREAGGRF
+TSLDGEDGPFGGHALATNGLLHDDVLARLRAGEEAEGGA*
+>NZ_CP040019.1_2137
+MERPENPANRGRDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVTDADRAAE
+ESIRSTLSRARARDGIVGEEFGGSLSRSGRQWVVDPIDGTKNFVRGVPVWATLIALLVDG
+EPVVGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRISVSGVDDVADASLSFSSIEGWRER
+GAIREFLQLTSDVWRVRGFGDFWSYMLVAEGAVDIAAEPELELHDMAALVPIVREAGGRF
+TSLDGEDGPFGGHALATNGLLHEDVLARLRPSGGGED*
+>NZ_CP083691.1_2028
+MDQTWNAARDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVSDADRAAEESI
+RSTLSRARARDLILGEEFGGNLSRTGRQWVVDPIDGTKNFVRGVPVWATLIALLIDGEPV
+VGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRIQVSDVDRVEDASLSFSSIEGWRERGAV
+REFLQLTSDVWRVRGFGDFWSYMLLAEGAVDVATEPELALHDMAALVPIVREAGGRFTSL
+DGEEGPFGGHALATNGLLHDEVLRRLTPGQD*
+>NZ_CP097650.1_689
+MERPENPATRGRDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVTDADRAAE
+ESIRSTLSRARARDGIVGEEFGGSLSRSGRQWVVDPIDGTKNFVRGVPVWATLIALLIDG
+EPVVGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRITVSGVDRVEDASLSFSSIEGWRER
+GSIRAFLQLTSDVWRVRGFGDFWSYMLVAEGAVDIAAEPELELHDMAALVPIVREAGGRF
+TSLDGEDGPFGGHALATNGLLHDDVLARLRAGDETEGGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000671.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000671.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f385b4e0bbfef7ae26955539bfa17fe6a86bb9b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000671.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_729
+MSAALLTHPSRTVDWPAMSTDNSRPEFARPEDAPEHDRADIDVAAESEQQRRARFERDAL
+EFVDQLYSAALRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTNTYINLY
+RKRQRQPLEADNPEVEDWQMARAAEHTSGGLRSAETEALDRLPDSQVKDALQAIPEEFRL
+AVYFADVEGFAYKEIAEILDVPIGTVMSRLHRGRKQLRERLADYAAARGIKAQPKKKTGR
+GGTKQTETSTKEATR*
+>NZ_CP033200.1_468
+MSAALLTHASRTVDWPAMSTDNSRPEFARPEDAPEHDRADIDVAAESEQQRRARFERDAL
+EFVDQLYSAALRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTNTYINLY
+RKRQRQPLEADNPEVEDWQMARAAEHTSGGLRSAETEALDRLPDSQVKDALQAIPEEFRL
+AVYFADVEGFAYKEIAEILDVPIGTVMSRLHRGRKQLRERLADYAAARGIKAQPKKKTGR
+GGTKQTETSTKEATR*
+>NZ_CP040019.1_2134
+MTTALMARPDRDVDWRVMSTDNNLPEIARPADAPEHDRADIDVAAEDEQQRRARFERDAL
+EFVDQLYSAAMRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTNTYINLY
+RKRQRQPLEADSPEVEDWQMARAAEHTSSGLRSAETEALDHLPDSEVKDALQAIPEEFRL
+AVYFADVEGFAYKEIAEILDVPIGTVMSRLHRGRKQLRERLADYAAERGIKAQPKKTGRG
+AAKKTETSTKEATR*
+>NZ_CP083691.1_2025
+MAATLLERPVLTGSRGAAVDWPAMSTQNSTPEIARPADAPALDLPGIDVDAESEAQRRAR
+FERDALEFVDQLYSAAMRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTN
+TYINLYRKKQRQPLEADTDTVEDWQMARAAEHTSSGLRSAETEALDHLPDSEVKDALQAI
+PEEFRLAVYFADVEGYAYKEIAEILDIPIGTVMSRLHRGRKQLRERLTDYAGERGMGPKG
+RTAQETSTQEEKR*
+>NZ_CP097650.1_692
+MSAALLTHPSRTVDWPAMSTDNSRPEFARPEDAPEHDRADIDVAAESEQQRRARFERDAL
+EFVDQLYSAALRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTNTYINLY
+RKRQRQPLEADNPEVEDWQMARAAEHTSGGLRSAETEALDRLPDSQVKDALQAIPEEFRL
+AVYFADVEGFAYKEIAEILDVPIGTVMSRLHRGRKQLRERLADYAAARGIKAQPKKKTGR
+GGTKQTETSTKEATR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000675.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000675.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b828448d5d2af8ffe6dd15d99ed4b007e3e326e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000675.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_733
+MRFLTDPAVDLTYNDVFLVPSHSDVASRMDVDIAPDDGTGATIPLVSANMTAVTGRRMVE
+TMARRGGLGILPQDIPADVIRDVVRRVKAAHPVADTALTVGPQDTVLDLLHLVDRRNHGA
+VCVVDAHGGLLGVVRPQDCEDVDRFTSAASVMHPPAVTLTLAELGGTDGAPDKDALRAAF
+ERLHAAHQEMAPVVDPAVGTAAPVLRGVVTAAGLLRSSLFTPGLDDDGRLRVGAAVGING
+AVGEKAAVLVEAGVDVLVVDTAHGHQQTMLDALAAVRALDPGVPVVAGNVVSGDGVRDLV
+AAGADIVKVGVGPGAMCTTRMQTAVGRPQFSAVLECAAAARELGARVWADGGVKHPRDVA
+LALAAGASSVMIGSWFAGTLESPGDLVHGPDGRRYKESFGMASARAVQHRTRHEDAFTKA
+RKAMFEEGISSSRMYVDPRRPSVEDLLDTITSGVRSSLTYAGAHDLAEFRERAVVGLQSA
+AGYEEGRPVASSW*
+>NZ_CP033200.1_472
+MRFLTDPAVDLTYNDVFLVPSHSDVASRMDVDIAPDDGTGATIPLVSANMTAVTGRRMVE
+TMARRGGLGILPQDIPADVIRDVVRRVKAAHPVADTALTVGPQDTVLDLLHLVDRRNHGA
+VCVVDAHGGLLGVVRPQDCEDVDRFTSAASVMHPPVVTLTLAELGGTDGAPSKDALRAAF
+ERLHAAHQEMAPVVDPAVGTAAPVLRGVVTAAGLLRSSLFTPGLDDDGRLRVGAAVGING
+AVGEKAAVLVEAGVDVLVVDTAHGHQRTMLDALAAVRALDPGVPVVAGNVVSGDGVRDLV
+AAGADIVKVGVGPGAMCTTRMQTAVGRPQFSAVLECAAAARELGARVWADGGVKHPRDVA
+LALAAGASSVMIGSWFAGTLESPGDLVHGPDGRRYKESFGMASARAVQHRTRHEDAFTKA
+RKAMFEEGISSSRMYVDPRRPSVEDLLDTITSGVRSSLTYAGAHDLAEFRERAVVGLQSA
+AGYEEGRPVASSW*
+>NZ_CP040019.1_2130
+MRFLTSPTVDLTYNDVFLVPSHSEVTSRLDVDIAPDDGTGATIPLVSANMTAVTGRRMVE
+TMARRGGLGILPQDIPVEVIAEVVRRVKSAHPVADTALTVGPQDTVLDLLHLVDRRNHGA
+VCVVDADGGLLGVVRPRDCEDVDRFASAASVMQPASVTLTPAELGEAGGADGGQALRAAF
+DRLNAAGQDMAPVVEPAAGSAAPALRGVVTAAGLLRSSLFTPSLDDAGRLRVGAALGVNG
+AVGDKAAALVEAGVDVLVVDTAHGHQQSMLDALAAVRALDAPVPVVAGNVVSADGVRDLV
+EAGADIVKVGVGPGAMCTTRMQTAVGRPQFSAVLECSAAARDLGARVWADGGVKHPRDVA
+LALAAGASSVMIGSWFAGTLESPGDLVHGPDGRRYKESFGMASARAVQHRTRHEDAFTKA
+RKAMFEEGISSSRMYVDPRRPSVEDLIDTITSGVRSSLTYAGAQDLAQFRERAVVGVQSA
+AGYEEGRPVASSW*
+>NZ_CP083691.1_2021
+MRLMHEPAVDLTYNDVFLVPSHSEVGSRTAVDIAPDDGTVGSVPLVSANMTAVTGRRMAE
+TLARRGGLGVLPQDVPVDVVAKTVAAVKAAHAVADTALTVDAHATVLDVLHLVDRRAHGA
+VCVVDDDGRLLGVAGAEDCGDVDRFASVVSVMRTPSVLLSPADLEGPDAPRAAFEVLHAA
+GRPLAPVVEDPVADRPVLRGVVTGQGLVRSSLAAPALDASGRLQVGAALGVNGDVGSRAA
+ALLAAGADVLVVDTAHGHQRVMRDALAAVRALDPEVPVVAGNVVTAEGVRDLVAAGADVV
+KVGVGPGAMCTTRMQTAVGRPQFSAVLECAAAAREVGARVWADGGVKHPRDVALALAAGA
+SQVMIGSWFAGTLESPGDLVQGSDGRRYKESFGMASARAVEHRTRDEDAFSRARKAMFEE
+GISSSRMYVDPRRPSVEDLVDGITAGLRSSLTYAGAANLAQFRERAVVGVQSAAGYEEGR
+PVPASW*
+>NZ_CP097650.1_696
+MRFLTDPAVDLTYNDVFLVPSHSDVASRMDVDIAPDDGTGATIPLVSANMTAVTGRRMVE
+TMARRGGLGILPQDIPADVIRDVVRRVKAAHPVADTALTVGPQDTVLDLLHLVDRRNHGA
+VCVVDAHGGLLGVVRPQDCVGVDRFASATSVMHPPAVTLTLAELGGTDGAPSKDALRAAF
+ERLHAAHQEMAPVVDPAVGTAAPVLRGVVTAAGLLRSSLFTPGLDDDGRLRVGAAVGING
+AVGEKAAVLVEAGVDVLVVDTAHGHQRTMLDALAAVRALDPGVPVVAGNVVSGDGVRDLV
+AAGADIVKVGVGPGAMCTTRMQTAVGRPQFSAVLECAAAARELGARVWADGGVKHPRDVA
+LALAAGASSVMIGSWFAGTLESPGDLVHGPDGRRYKESFGMASARAVQHRTRHEDAFTKA
+RKAMFEEGISSSRMYVDPRRPSVEDLLDTITSGVRSSLTYAGAHDLAEFRERAVVGLQSA
+AGYEEGRPVASSW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000677.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000677.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f9181aca3fb4b4be1b51e84c20c89c44350bcecc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000677.fa
@@ -0,0 +1,36 @@
+>NZ_CP042169.1_735
+MNGDVVGLLWLVVLLAANAFFVAGEFAVMGARRAQIEPRAEAGSRQAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVVPMAALGVPSAAADVTAFVLALLVVTFLHVTL
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPVVAALNWTANLVLHALRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHRAGDVMVPLERVVTVPEGITPHDFE
+WTVGRVGFSRFVVEDPDGGYTGYLHLKDVLTVGPSGHDEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGILFLEDVLEELVGEINDVTQSPRRFRPA*
+>NZ_CP033200.1_474
+MNGDVVGLLWLVVLLAANAFFVAGEFAVMGARRAQIEPRAEAGSRQAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVVPMAALGVPSAAADVTAFVLALLVVTFLHVTL
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPVVAALNWTANLVLHALRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHRAGDVMVPLERVVTVPEGITPHDFE
+WTVGRVGFSRFVVEDPDGGYTGYLHLKDVLTVGPSGHDEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGILFLEDVLEELVGEINDVTQSPRRFRPA*
+>NZ_CP040019.1_2128
+MNEDVIGLLWLVVLLVANAFFVAGEFAVMGARRSQIEPKAEAGSRPAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVGPMTALGVPDAAADVTAFVLALLVVTFLHVTF
+GEMVPKNAAVSFADRAVMILARPLVGLSKLLHPIVTVLNWAANVVLRAFRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHTAGDVMVPLEKVVTVPEGITPHDFE
+WTVGRVGYSRFVVEDPDGGYTGYLHLKDVLTVGPSGHEEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGVLFLEDVLEELVGEINDVTQSPRRFRPA*
+>NZ_CP083691.1_2019
+MSQDVVGLLWLAVLLAANAFFVAGEFAVMGARRSQIEPRAEAGSRQAQVALFAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLAAPMEALGLPLAAADVVAFVLALLIVTFLHVTM
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPLIVVLNWAANTVLRAFGIEPKDEVASS
+FTLEEVQTIVAESTRSGTLEDESGVLHSALEFSSYTAGDVMVPIEKVVSVPEDVTPQQFE
+WAVGRVGYSRFVVEDSQGGYAGYLHLKDVLAGGPSRYADPVPVTRVRSLANVRVADEVED
+ALGLMQRTGSHLARVISEDGATVGVLFLEDVLEELVGEIHDVTQSPRRFRPTTGSHAAPE
+PTRMRDLPAR*
+>NZ_CP097650.1_698
+MNGDVVGLLWLVVLLAANAFFVAGEFAVMGARRAQIEPRAEAGSRQAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVVPMGALGVPAAAADVTAFVLALLVVTFLHVTL
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPVVAALNWTANLVLHALRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHRAGDVMVPLERVVTVPEGITPHDFE
+WAVGRVGFSRFVVEDPDGGYTGYLHLKDVLTVGPSGHDEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGILFLEDVLEELVGEINDVTQSPRRFRPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000687.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000687.fa
new file mode 100644
index 0000000000000000000000000000000000000000..11bc65219585c047bd64bab9aa3fa47e4c45bf43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000687.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_748
+MSHVTESSPAHPGRAEESAPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG
+TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLSITTSLLGTLVI
+MLAGAGAAVHTAFGLPSLVGSLVMATVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW
+GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA
+GAGLGALGLVVMAGAVMAAMTAHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT
+AVSCLYGGVERIALLSSMRRVPGWVIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGLVI
+IVMLVVTWIVERSTVRRRAARAARA*
+>NZ_CP033200.1_488
+MSHVTESSPAHPGRAEESTPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG
+TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLCITTSLLGTLVI
+MLAGAGAAVHTAFGLPSLVGSLVMAAVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW
+GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA
+GAGLGALGLVVMAGAVMAALTVHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT
+AVSCLYGGVERIALLSSMRRVPGWAIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGIVI
+IVMLIVTWIVERTTVRRRAARAARA*
+>NZ_CP040019.1_2115
+MSPVTESSPAHRGRAEESAPLRPTSRLGIAATFIGTTIGAGYASGNEILQYFVSFGFWGG
+TLALVIAGALFFLLSAIVLKMAQKLRTTDIHRLVNPTTSRVPTWFADLCITASLLGTLVI
+MLAGAGAAVNTSFGLPTMVGSLLMAAVCVLSVLAGISGLVRVQAVVVPLIIVVAVGVAWW
+GLANPGAPVEDVASLVTSSPLINQWWMSGILYVAFNFQLAYAVLAPIGRDSSSSGRTLVA
+GAGLGAVGLVVMAGAIMFAMAAHAHLIGRADLPMVELAAMIGGWAALVYTVILLLAQFTT
+AVSCLFGGVERIALLSPLRRVPGWAIAVATALAATLLSSVGFSDLVGTVYPVLGYAGIAI
+IVMLIITWIAERTLVRRRAARAARA*
+>NZ_CP083691.1_2006
+MSHVAQSTHENRPAQDGGNGLRPMSALGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG
+TGALVIAGVLFFLLSAIVLKMAQQLRTTDIHRLVNPTSSRIPTWFADLCITASLLGTLVI
+MFAGAGAALDTWLGLPAWAGAALMAAVCVLTVLGGISGLVKVQGLVVPLIILVAVGVAWW
+GLTHPGAGADDVASLVTSSPLINTWWMSGILYVAFNFQLAYAVLAPIGKGSSSPGTSLVA
+GAGLGAIGLVVMAGAIMAAMGAHATLIGRAELPMVELAGMVAPWVAAVYTVILLLAQFTT
+AVSCLFGGVERIALLSPLRDVPGWLIAVVTAVVAVLLSSVGFSDLVGIVYPVLGYAGIAI
+VAMLIATWILDRTLVRRRAARADRA*
+>NZ_CP097650.1_714
+MSHVTESSPAHPGRAEESAPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG
+TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLCITTSLLGTLVI
+MLAGAGAAVHTAFGLPSLVGSLVMAAVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW
+GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA
+GAGLGALGLVVMAGAVMAAMTAHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT
+AVSCLYGGVERIALLSSMRRVPGWVIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGIVI
+IVMLVVTWIVERSTVRRRAARAARA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000688.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000688.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f6ac12667e66cb2eb5b3eed80772298141fe5867
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000688.fa
@@ -0,0 +1,31 @@
+>NZ_CP042169.1_749
+MTSAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITAQNTQGVQAVHPLPVD
+VVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVVLDPVMVASSGDALTA
+VGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAARGLAAEHGVTVLLKG
+GHLDETEAPEAAAAEVPDAVVRVGGAVHEVRGPRVTTRASHGTGCTLSSALATLAGAGLS
+WDDALERAKPWLADAMRAGEALAVGDASRPTWHGPVDHGHAQRG*
+>NZ_CP033200.1_489
+MTPAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITAQNTQGVQAVHPLPVD
+VVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVVLDPVMVASSGDALTA
+VGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAARGLAAEHGVTVLLKG
+GHLDETEAPEAAAAEVPDAVVRVGGAVHEVRGPRVTTRASHGTGCTLSSALATLAGAGLS
+WEDALERAKPWLADAMRAGEALAVGDASRPTWHGPVDHGHAQRG*
+>NZ_CP040019.1_2114
+MLSIAGSDSGGGAGVQADLKTIAVWGGYGMTAITAITAQNTQGVQAVHPLPVDVVRAQLD
+SIAADIAVDAVKIGMLGTAELMGAVAGWLEETRPAVVVLDPVMVASSGDALTAVGDDDGR
+AAWSRLLRAAHLVTPNLPELARLTGRDSTDWEAALDAAGGLAAEHEVTVLLKGGHLDEAA
+AAEVPDAVVRVAGAVHEVRGPRVATRASHGTGCTLSSALATLAGAGLSWEDALERAKPWL
+ADAMRAGEALAVGDASRPTWHGPVDHGHARRG*
+>NZ_CP083691.1_2005
+MAPSPSTPPSSSPAAEGPAVPRVLSIAGSDSGGGAGIQADLKTIAEWGGYGMTAITAITA
+QNTQGVQAVHPLPAEVVRAQLDSVASDIAVDAVKVGMLGTAELMRVVADWLEEARPAVVV
+VDPVMAATSGHALTPVGDAEAHAAWGRLLRAAHLVTPNLPELARLAGRPLDSWAAALDAA
+RELAAAHAVTVLAKGGHLADLTRADPEGAEAGDDPDAEGGVPDALVRPDGSVHEVRGPRV
+ESGATHGTGCTLSAALATLAAGGLGWEDAIERAKPWLAQAMVAGEALAVGDRTRPTWHGP
+VDHGHARRG*
+>NZ_CP097650.1_715
+MTSAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITAQNTQGVQAVHPLPVD
+VVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVVLDPVMVASSGDALTA
+VGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAARGLAAEHGVTVLLKG
+GHLDETEAPEAAAAEVPDAVVRVGGAVHEVRGPRVTTRASHGTGCTLSSALATLAGAGLS
+WEDALERAKPWLADAMRAGEALAVGDASRPTWHGPVDHGHAQRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000689.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000689.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3bc6cf655b92d1881e8647834fe907945be4002b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000689.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_750
+MHSPDPLLMTAAGRDDGGTGPGARRRARLAASRLYVCTDLQRFLRPDGTLDTAAFADFCA
+AAFRGGVDVIQVRDKAVDVAVELAAFATLVPLAREHGALSAANDRADVAALAGVDVFHTG
+QTDLTTAQCRALLGPDVVLGRSCHTEAQVRGARAEDGLDYFCTGPVWATPTKPGRAAVGL
+ELPTLAARLDAEDPAGARPWFAIGGVDADRLPEVRAAGAERIVVVRAVTQAEDPEAAART
+LRAGLPG*
+>NZ_CP033200.1_490
+MHSPDPLLMTAAGRDDGGTGPGARRRARLAASRLYVCTDLQRFLRPDGTLDTAAFADFCA
+AAFRGGVDVIQVRDKAVDVAVELAAFATLVPLAREHGALSAANDRADVAALAGVDVFHTG
+QTDLTTAQCRALLGPDVVLGRSCHTEAQVRGARAEDGLDYFCTGPVWATPTKPGRAAVGL
+ELPTLAARLDAEDPAGARPWFAIGGVDADRLPEVRAAGAERIVVVRAVTQAEDPEAAART
+LRAGLPG*
+>NZ_CP040019.1_2113
+MHSPDPLLMAAAGRDDGDTGPGTGRRARLAASRLYVCTDLQRFLRPDGTLDTVAFADFCA
+AAFRGGVDLIQVRDKAVDVAVELAAFAVLVPLARAHEALSAANDRADVAALAGVDVFHTG
+QTDLTTVQCRALLGPDVVLGRSCHTEAQVRAARAEDGLDYFCTGPVWATPTKPGRAAVGL
+ELPSHAARLDAEDPAGARPWFAIGGVDADRLTEVRAAGADRIVVVRAVTQAEDPEAAART
+LRAGLPG*
+>NZ_CP083691.1_2004
+MHSPDPLLMTAAGRDDGDTGPGAGRRARLAASRLYVCTDLQRFLRPDGTLDTAAFGGFCA
+AAFRGGVDLIQVRDKAVDVAVELAAFAVLIPLAREHGALSAANDRADVAALAGVDVFHTG
+QTDLTTAQCRALLGPNVVLGRSCHTPDHVRAARAEDGLDYFCTGPVWATPTKPGRAAVGL
+GLPTLAARLDAEDPAGARPWFAIGGVDAERLPEVRAAGAGRIVVVRAVTQAADPEAAARE
+LRAGLPA*
+>NZ_CP097650.1_716
+MHSPDPLLMAAAGRDDGGTGPGAGRRARLAASRLYVCTGLQRFLRPDGTLDTAAFADFCA
+AAFRGGVDVIQVRDKAVDVALELAAFAVLVPLAREHGALSAANDRADVAALAGVDVFHTG
+QTDLTTAQCRALLGPNVVLGRSCHTEAQVRAARAEDGLDYFCTGPVWATPTKPGRAAVGL
+GLPSLAARLDAEDPAGARPWFAIGGVDADRLPEVRTAGAERIVVVRAVTQAEDPEAAART
+LRAGLPG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000690.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000690.fa
new file mode 100644
index 0000000000000000000000000000000000000000..663d92c90c8bc6dc50911086f050d8425e1e11b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000690.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_751
+MHVAVVGAGIIGLTAAVRLRAAGHAVTLIAPELDAAGRPHAVAGATHAAAGMLAPLAETQ
+FSQDDLAPLLQAGWEAYPALVDLLAAFTDVETGFLAQGAWIVAADPSDARAWDHVLEHAS
+ILGRRVEPVSVRALRRAEPALAPGLAAGFDAPDDHQVDPRRLAAACVAALRAETGPDGGP
+LPVGAGPAARFVAGRVTAAGPEGEGVRLTLADGGVLTADGAVLAAGLGHRGIGGAATAVE
+VPLRPVHGDVLRLRVRPEQLLPGESHLITRTVRGLVHGRQVYLVPRADGTLVVGASARED
+GLAGTSAGAVLDLLADAAAILPAVRECELVEITTAARPGTPDDAPRVLTVPEAPGAVVAT
+GFHRHGILLAPWAAGRILELLHARLKEIA*
+>NZ_CP033200.1_491
+MHVAVVGAGIIGLTAAVRLRAAGHAVTLIAPELDAAGRPHAVAGATHAAAGMLAPLAETQ
+FSQDDLAPLLQAGWEAYPALVDLLAAFTDVETGFLAQGAWIVAADPSDARAWDHVLEHAS
+ILGRRVEPVSVRALRRAEPALAPGLAAGFDAPDDHQVDPRRLAAACVAALRAETGPDGGP
+LPVGAGPAARFVAGRVTAAGPEGEGVRLTLADGGVLTADGAVLAAGLGHRGIGGAATAVE
+VPLRPVHGDVLRLRVRPEQLLPGESHLITRTVRGLVHGRQVYLVPRADGTLVVGASARED
+GLAGTSAGAVLDLLADAAAILPAVRECELVEITTAARPGTPDDAPRVLAVPEAPGAVVAT
+GFHRHGILLAPWAAGRILELLHARLKEIA*
+>NZ_CP040019.1_2112
+MHVAVVGAGIIGLTAAVRLRAAGHAVTLIAPELDAAGRPHAVAGATHAAAGMLAPLAETQ
+FSQDDLAPLLQAGWEAYPALVGLLAVFTDVETGFLAQGAWIVAADPSDARAWDHVLEHAS
+ILGRRVEPVSVRALRRAEPALTPGLAAAFDAPDDHQVDPRRLAAACVAALRAETGPDGGP
+LPAGAGPAARFVAGRVTAADPEGEGVRLTLADGGVLTADGAVLAAGLGHRGIGGAATAVE
+VPLRPVHGDVLRLRVRPEQLLPGESHLITRTVRGLVHGRQVYLVPRADGTLVVGASARED
+GLAGTCAGAVLDLLADAAAILPAVRECELVEITTAARPGTPDDAPRVLTVPEAPGAVVAT
+GFHRHGILLAPWAAGRILELLHARLKEIA*
+>NZ_CP083691.1_2003
+MHVAVVGAGIIGLTAAVRLRAAGHAVTLIAPELDTAGRPHAVAGATHAAAGMLAPLAETQ
+FSQDALAPLLHAGWKGWPLLVDLLAGFSDVGTGFRTEGSWIVAADPSDVLAWEHVLAHAS
+ALGRRVEPVAVRALRRAEPALAPGLAAGFDAPDDHQVDPRRAAAACLAALVAEAGPDGGP
+LPAGAGPAARLVSGTVTSADPVGSGVGLTLADGGILTADGAVLAAGLGHRGIGGAATAEV
+PLRPVHGDVLRLRVRPEQLLPGEDHLITRTVRGLVHGRQVYLVPRADGTLVVGASAREDG
+LAGTSAGSVLDLLADAAAILPAVRECELAEVTTAARPGTPDDAPRVEVVPGAPVVVATGF
+HRHGILLAPWAAGRVLDLLTALPKETA*
+>NZ_CP097650.1_717
+MHVAVVGAGIIGLTAAVRLRAAGHAVTLIAPELDTAGRPHAVAGATHAAAGMLAPLAETQ
+FSQDDLAPLLQAGWEAYPALVDLLAAFTDVETGFLAQGAWIVAADPSDARAWDHVLEHAS
+ILGRRVEPVSVRALRRAEPALTPGLAAGFDAPDDHQVDPRRLAAACVAALRAETGPDGGP
+LPTGAGPAARFVAGRVTAADPEGEGVRLTLADGGVLTADGAVLAAGLGHRGIGGAATAVE
+VPLRPVHGDVLRLRVRPEQLLPGESHLITRTVRGLVHGRQVYLVPRADGTLVVGASARED
+GLAGTSAGAVLDLLADAAAILPAVRECELVEITTAARPGTPDDAPRVLAVPEAPGAVVAT
+GFHRHGILLAPWAAGRILELLHAHLKEIA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000693.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000693.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a085b374d2789a62193e7997789bb5b6f131bea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000693.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_754
+MTAALDPAAREPRDLTALSDTQLERFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPV
+LTYLAAAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEH
+RERLTAANALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAP
+GGPLYRDVFPERPEPGEVPSCAQAGVLGVLPGIIGSLMAAEAIKLLSGVGEPLVGRLLSV
+DALTMRFRELRLVPDPERTPVTDLSAHADQAPRPDDAGAPGSAEACGAAGGEIAPAALAA
+LLADPARVASLTLLDVREDWERRLRRVEAPAAVADRHVPLEAVLAEPAALAPGRDRVLVV
+YCAAGARSARARDAVVGADPSAGGRVLSLAGGLAAWPA*
+>NZ_CP033200.1_494
+MTAALDPAAREPRDLTALSDTQLERFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPV
+LTYLAAAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEH
+RERLTAANALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAP
+GGPLYRDVFPERPEPGEVPSCAQAGVLGVLPGIVGSLMAAEAIKLLSGVGEPLVGRLLSV
+DALTMRFRELRLVTDPERTPVTDLSAHAAQAPRPDDAGAPGSAEACGAAGEEIAPAALAA
+LLADPARAASLTLLDVREDWERRLRRVEAPAAVADRHVPLEAVLAEPAAHAPGQDRVLVV
+YCAAGARSARARDAVVGADPSSGGRVLSLAGGLAAWPA*
+>NZ_CP040019.1_2109
+MTAAPDPADREPRDLTALSDTQLQRFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPV
+LTYLAAAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEH
+RERLTAANALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAP
+GGPLYRDVFPERPEPGEVPSCAQAGVLGVLPGIIGSLMAAEAIKLLSGVGEPLVGRLLSV
+DALTMRFRELRLVADPERTPVTDLSAHADQAPGSDDAGAPGSAEACGAAGGEIDPATLAA
+LLADPARAASLTLLDVREDWERRLRRVEVPAAVADRHVPLDAVLAEPAAHAPGPDRVLVV
+YCAAGARSARARDAVVAADPSAGERVLSLVGGLAAWPA*
+>NZ_CP083691.1_2000
+MSRPAGEPLVPEDRAPHSLDELSDTQLQRFARHLGLDGFGPEAQLALLRSRVLVVGAGGL
+GAPVLTYLAAAGVGEVHVVDDDVVDRSNLHRQVIHVETDLGRPKTASAAETMRGLHPEIR
+VVEHRQRLAAANALELVGAVDLVVDGSDNYATRYLVADAGEITGVPVVWGAILRFAGQVS
+VFAPGGPLYRDVFPEEPEPGDVPTCAQAGVLGVLPGIVGSLMAAEAVKLLAGVGEPLTGR
+LLSVDALTMRFSTLRLVPDPERTSVTDLSAHTVPRGGADPVESGEITPAGLAALLADPER
+AAALTLLDVREDWERGLARISAPAAAEDRHVRLDEVLADPAAHSPESGRTVVVYCAAGAR
+SARAREAVVAAAPEAADRVLSLAGGHAAWADRN*
+>NZ_CP097650.1_720
+MTAAREPRDLTALSDTQLERFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPVLTYLA
+AAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEHRERLT
+ATNALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAPGGPLY
+RDVFPERPEPGEVPSCAQAGVLGVLPGIIGSLMAAEAIKLLSGVGEPLVGRLLSVDALTM
+RFRELRLVPDPERTPVTDLSAHADQAPRPDDAGAPGSAEACGAAGGEIAPAALAALLADP
+ARAASLTLLDVREDWERRLRRVEAPATVADRHVPLEAVLAEPAALAPGQDRVLVVYCAAG
+ARSARARDAVVGADPSAGGRVLSLAGGLAAWPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000696.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000696.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b9968ad8bcc75b645cec6bad37dc416c80b37fa1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000696.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_757
+MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRDTGATRDW
+QADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKALLAQHGEEL
+YAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFILDRMDSEGAD
+FDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVAGITAITAED
+NAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN
+AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDPAEAHTSFMV
+VLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRARQRDLDATVE
+ALAALDVVHEVASVLRVEGN*
+>NZ_CP033200.1_497
+MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRDTGATRDW
+QADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKALLAQHGEEL
+YAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFILDRMDSEGAD
+FDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVAGITAITAED
+NAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN
+AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDPAEAHTSFMV
+VLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRARQRDLDATVE
+ALAALDVVHEVASVLRVEGN*
+>NZ_CP040019.1_2106
+MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRNTGATRDW
+QADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKALLAQHGEEL
+YAAAAATGAQLSFEAAVAGAIPILRPLRDSLAGDRVTRVMGIANGTTNYILDKMDSEGAG
+FDEALAEAQRLGYAEADPTADVEGHDAAAKAAILATLAFGAPYTLDQVAVSGITAITAED
+NEAAADAGYVIKLLAIAERARAADSAEGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN
+AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVAELPALDPAEAVTSCLV
+VLRVADEPGVLRRVAGVFEEQGVSIETLRQVQSDRDDAPGASLRLITHRARQRDLDATVE
+ALAALDAVHEVASVLRVEGN*
+>NZ_CP083691.1_1996
+MAEPTASAAQTAPAPARDALRVALLGGGTVGSQAARILTEDAAVLADRVGVRLELTGIAV
+RDTAAVRDWQADPSLYTTDAEALVDGADLVIELMGGIEPARSLIRRALQVGTSVVTGNKA
+LLAEHGEELYRLASETGAQLSFEAAVAGAIPILRPLRDSLSGDTVNRVMGIANGTTNFIL
+DRMDTEGASFADALAEAQRLGYAEADPTADVGGFDAAAKAAILATLAFGSSYTLDQVSVE
+GITEVTAEDNAAAADAGYVIKLLAIAERDTARDGTAGAILRVHPTLIPREHPLGSVRGAY
+NAVFVEAENAGQLMFYGPGAGGAPTASAVMGDAVAIGQRIVRGGPARLRTPVAALPALDV
+SEARTSCMVVLRVADQPGVLRRVAGVFEEHGVSIETLRQVQGADDAAGASLRLITHRARQ
+RDLDDVVAELTTLDAVHEVASVLRVEGN*
+>NZ_CP097650.1_723
+MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRDTGATRDW
+QADPALYTTDAEALVDGADVVIELMGGVEPARTLILRALAAGTSVVTGNKALLAQHGEEL
+YAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFILDRMDSEGAD
+FDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVAGITAITAED
+NAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN
+AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDPAEAHTSFMV
+VLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRARQRDLDATVE
+ALAALDVVHEVASVLRVEGN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000699.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000699.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71036e5a8af8f2988ee2cba0a6451073b50f2f96
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000699.fa
@@ -0,0 +1,65 @@
+>NZ_CP042169.1_760
+MTESTEQTTPTNGGGLASLKLAQLQALASQLGIAGGSRMRKADLVTAISDHQRGGSVADR
+DAAERAAQAPAAPAAEAAPAAASSQDAAPAAERPARRRSRRADADTSAPAAAQDGQPQAE
+AREDQTEQAPRETASDQDRSEGSETRDEGEGRPQSERRSRGRRAGDDDAQQGQDRRSDGA
+QGEDGADRRGDREDRDDNGRENGRGRNGRNGRDRDNGRDRENGRENNRDRENGRDGSREQ
+RGDKSEDGGRGDGGRGDRSRRDDRDDEGGRNRRNRRNRNERGRNRRGRGGPEVDETELTE
+DDVLQPVAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKYGLRKGDAVVGAIRAPRDG
+EKQQHHGGGSNRQKFNALVKISSVNGQPAVEHPQRVEFGKLVPLYPQERLRLETDPKLIG
+PRVIDLVSPIGKGQRGLIVSPPKAGKTMILQSIANAIKTNNPEVHLMMVLVDERPEEVTD
+MQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNLAA
+PASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGT
+GNMELRLSRHLAERRIFPAVDVNASGTRREEALLSQEEVKIMWKLRRVLSGLEQQQALDL
+LTNKIKDTASNAEFLMLVSKTTLGSKGDD*
+>NZ_CP033200.1_500
+MTESTEQTTPTNGGGLASLKLAQLQALASQLGIAGGSRMRKADLVTAISDHQRGGSVADR
+DAAERAAQAPAAPAAEAAPAAASSQDAAPAAERPARRRSRRADADTSAPAAAAQDGQPQA
+EAREDQTEQAPRETASDQDRSGGSEARDEGEDRPQSERRSRNRRRAGDDDAQQGQDRRSD
+GAQGEDGADRRGDREDRDDNGRENGRGRNGRNGRDRENGRDRENGRENNRDRENGRDGSR
+EQRGDKSEDGGRGDGGRGDRSRRDDRDDEGGRNRRNRRNRNERGRNRRGRGGPEVDETEL
+TEDDVLQPVAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKYGLRKGDAVVGAIRAPR
+DGEKQQHHGGGSNRQKFNALVKISSVNGQPAVEHPQRVEFGKLVPLYPQERLRLETDPKL
+IGPRVIDLVSPIGKGQRGLIVSPPKAGKTMILQSIANAIKTNNPEVHLMMVLVDERPEEV
+TDMQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNL
+AAPASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFK
+GTGNMELRLSRHLAERRIFPAVDVNASGTRREEALLSQEEVKIMWKLRRVLSGLDQQQAL
+DLLTNKIKDTASNAEFLMLVSKTTLGSKGDD*
+>NZ_CP040019.1_2103
+MTESTEQTTPTTGGGLAALKLAQLQALASQLGIPGGSRMRKADLVTAISDHQRGGSVADR
+AAAERAAKAAAAPAAEAAPAADKAAEQPAEAAERPARRRSRRADADTSAAAQSAESGKDQ
+AERRAEQPAEGRDAEGSQDSGDRAQDSGDRTQGERRSRGRRRAGDDDARGQDRRRQDGED
+AGQDQAHDSAEDRGGDREDGGRENGRGNRGRNGRDNGRDRENGNGRDRDNGNGRDRDGSR
+EQKQDKSEDGGRDGGRNDRNRRDDRDDEGGRGRRNRRNRNERGRNRRGRGGPDVDETELT
+EDDVLQPVAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKHGLRKGDAVVGAIRAPRE
+GEKPQHQGGGSNRQKFNALVKISSVNGQPAVEHPERVEFAKLVPLYPQERLRLETDPKQV
+GPRVIDLVSPIGKGQRGLIVSPPKAGKTMILQSIANAIKTNNPEVHLMMVLVDERPEEVT
+DMQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNLA
+APASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKG
+TGNMELRLSRHLAERRIFPAVDVNASGTRREEALLSPEEVKIMWKLRRVLSGLEQQQALE
+LLTNKIKDTGSNAEFLMLVSKTTLGAKGED*
+>NZ_CP083691.1_1993
+MTESPDQTTAGGGLASLKLAQLQALASQLGITGGSRMRKSDLVAAISDHQRGGSVADRDA
+AAQAAAAPAAQAEAAEAPAAEQAPRSRRRSRRADSDGAVAADQPAEATQAPADEQPAAET
+EDAPARAEASAESGAQEAGSGRSRRRRGDRAARDEQQDGAQDEKQESGRGAGEETRREQD
+GDEERAEGRSRSRRGRGDRDRGERQNADRQNGERANGERANGQGEDRSQGGRREDREEES
+GRGQGGDGQKRSDRGNGRREDRDEDGRRGRNRRNRNDRGRNRRSRGPEVDDVEVTEDDVL
+QPVAGILDVLDNYAFVRTSGYLPGEKDVYVSLAMVKKFGLRKGDAVVGAIRAPREGEKPH
+SGGGRNQKFNALVKVTTVNGQPAEENPQRVEFGKLVPLYPTERLRLESDHKLVGPRVIDL
+ISPIGKGQRGLIVSPPKAGKTMILQSIANAITRNNPEVHLMMVLVDERPEEVTDMQRSVA
+GEVIASTFDRPAEDHTTVAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNLAAPASGRI
+LSGGVDSAALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGTGNMELR
+LSRQLAERRIFPAVDVNASGTRREEVLLSPEEVKIMWKLRRVLSGLDTQQALELLTNKIK
+DTASNAEFLMLVSKTTLGSKGDD*
+>NZ_CP097650.1_726
+MTESTEQTTPTNGGGLASLKLAQLQALASQLGIAGGSRMRKADLVTAISDHQRGGSVADR
+DAAERAAQAPAAPAAEAVPAAASSQDAAPAAERPARRRSRRADADTSAPAAVAQDGQPQA
+EAREAQTEQGPRETASDQDRSGGSETRDEGEDRPQSERRSRGRRRAGDDDAQQGQDRRSD
+GAQGEDGADADRRGDREDRDDNGRENGRGRNGRNGRDRDNGRDRDNGRDRENGRDGSREQ
+RGDKSEDGGRGDGGRGDRSRRDDRDDEGGRNRRNRRNRNERGRNRRGRGGPEVDETELTE
+DDVLQPAAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKYGLRKGDAVVGAIRAPRDG
+EKQQHHGGGSNRQKFNALVKISSVNGQPAVEHPQRVEFGKLVPLYPQERLRLETDPKLIG
+PRVIDLVSPIGKGQRGLIVSPPKAGKTMILQSIANAIKTNNPEVHLMMVLVDERPEEVTD
+MQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNLAA
+PASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGT
+GNMELRLSRHLAERRIFPAVDVNASGTRREEALLSQEEVKIMWKLRRVLSGLEQQQALDL
+LTNKIKDTASNAEFLMLVSKTTLGSKGDD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000700.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000700.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ebe4a6fce1c8fbea4c6b15d0ec550aed3f93918d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000700.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_761
+MFDSEQRREAVDRLLAEHRELTARLSDPAVHQDPALARRLNRRFAELGAVVTAHRAWSAA
+AEELADARELAAAGDDDAAAFAAEVPGLEAAEAEAAERLRRLLIPRDPDDARDVILEIKG
+GEGGEEAALFAGDLLRMYLRYADSRGWKTEVLSATHSDLGGYKDVHVAVRGSAADPADGV
+YARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVHLDPNDLKVDVFRSSG
+PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAEQDAEDS
+AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVIASCLALDEER
+RLAALGGDA*
+>NZ_CP033200.1_501
+MFDSEQRREAVDRLLAEHRELTARLSDPAVHQDPALARRLNRRFAELGAVVTAHRAWSAA
+AEELADARELAAAGDDDAAAFAAEVPGLEAAEAEAAERLRRLLIPRDPDDARDVILEIKG
+GEGGEEAALFAGDLLRMYLRYADSRGWKTEVLSATHSDLGGYKDVHVAVRGSAADPADGV
+YARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVHLDPNDLKVDVFRSSG
+PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAEQDAEDS
+AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVIASCLALDEER
+RLAALGGDA*
+>NZ_CP040019.1_2102
+MFDSEERREAVDRLLAEHRELTARLSDPAVHQDPVLARRLNRRFAELGAVVTAHAAWREA
+AAELADARELAAAGDDDAAAFAAEVPCLEEAETAAAERLRRLLIPRDPDDARDVILEIKG
+GEGGEEAALFAGDLLRMYLRYAESRGWKTEVLSATHSDLGGYKDVHVAIRAGATDPAEGV
+FARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVRIDPNEVKTDVFRSSG
+PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAAMRVLRSRLLERRRAEQDAEDS
+AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVVASCLALDEER
+RLAALGGDA*
+>NZ_CP083691.1_1992
+MFESVERLLAEHRELAGQLSDPALHADAARARRVGRRYAELGAVVAAHREWEQAVADRDD
+ARELAAAPGEDAAAFAAEVPALEAAADEAAERLRRLLIPRDPDDGRDVILEIKGGEGGEE
+AALFAGDLLRMYLRYAESRGWRTEVLSATHSDLGGFKDVHVAVRGSAQDPAEGVYARLKH
+EGGVHRVQRVPVTESAGRIHTSAAGVLVLPEADAPDEVQIDPNDLKTDVFRSSGPGGQSV
+NTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAERDAEDSAARSAQ
+VRTMDRSERIRTYNFPENRIADHRTGFKAHNLDAVLDGALDPVIDSCVALDEQRRLARLG
+EEAR*
+>NZ_CP097650.1_727
+MFDSDQRREAVDRLLAEHRELTARLSDPAVHQDPALARRLNRRFAELGAVVTAHRAWSAA
+AEELADARELAAAGDDDAAAFAAEVPGLEAAEAEAAERLRRLLIPRDPDDARDVILEIKG
+GEGGEEAALFAGDLLRMYLRYAESRGWKTEVLSATHSDLGGYKDVHVAVRGSAADPADGV
+YARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVHLDPNDLKVDVFRSSG
+PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAEQDAEDS
+AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVIASCLALDEER
+RLAALGGDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000701.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000701.fa
new file mode 100644
index 0000000000000000000000000000000000000000..837e1099621c28c570759bc5fb7da05127779a25
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000701.fa
@@ -0,0 +1,34 @@
+>NZ_CP042169.1_763
+MTDVSDFIDVSDPAALENAVARAREVLADRGCVVLPTDTVYGIGADAFSPLAVAVLLAAK
+GRGRTMPPPVLIADRRVMAGLAYDVPEEAEALAERFWPGALTLILKSQPTLTWDLGETRG
+TVALRVPDDAVARELLYAVGPMAVSSANRTGMDAATTADAARSMLGESVALYLDAGPRES
+RDPSTIVDCTVTPFRVARQGSVPLEELRAVVPDLLAEGEEPPVAADRIAAEDAAAARPAD
+REA*
+>NZ_CP033200.1_503
+MTDVSDFIDVSDPAALENAVARAREVLADRGCVVLPTDTVYGIGADAFSPLAVAVLLAAK
+GRGRTMPPPVLIADRRVMAGLAYDVPEEAEALAERFWPGALTLILKSQPTLTWDLGETRG
+TVALRVPDDAVARELLYAVGPMAVSSANRTGMDAATTADAARSMLGESVALYLDAGPRES
+RDPSTIVDCTVTPFRVARQGSVPLEELRAVVPDLLAEGEEPPVAADRIAAEDAAAARPAD
+REA*
+>NZ_CP040019.1_2101
+MSAADESEPWGQALRRATGLLAEAGVDSPRVDAELLLAHVLGLGRGELLARVFAGAAGTA
+GEAERFAALVARRARREPVQHLTGVAFFHGLDLAVGPGVFLPRPETELLVDAVLAELTAR
+PAAATVVDLCTGSGAIAAAVSAWAQEHGRDVAVIAVELDDEAAGWARRNLEPRGVYMRQG
+DALVALPELEGRVDVVVSNPPYVPEAETPVQAEARLDPARALYGGDAAGLRIPQAIAHRA
+TELLVPGGLFAMEHHETQGPALLGALDADPRFTGVCVHQDLTGRDRFLTARRSCEAAAAA
+EDGRMADVSDFIDVSDPAALEDAVARAREVLGDCGCVVLPTDTVYGIGADAFSPRAVAVL
+LAAKGRGRTMPPPVLISDRRVLAGLAYDVPDEAEALAERFWPGALTLILKSQPTLTWDLG
+ETRGTVALRVPDDAVARELLYAVGPMAVSSANRTGMPAATTAEEARGMLGESVDLYLDAG
+PREDRAPSTIVDCTVTPFRVARQGAVPLEALRELVPDLLAEGEEPPVPADRLAAEPVAEA
+PAPTPAPDGDDAADRAGREA*
+>NZ_CP083691.1_1990
+MSEFIDVSDPSDLTAAVERARAVLADRACVVLPTDTVYGIGADAFSPTAVAVLLAAKGRG
+RTMPPPVLISDRSVMAGLAYDVPEAAEELAERFWPGALTLILRSQPTLTWDLGETRGTVA
+LRVPDDAVTRELLYAVGPMAVSSANRTGMPAATTARGAEEMLGESVALYLDGGERATQEP
+STIVDCTVTPFRVARQGAVSLEALRAVVPDLVAEGEEPPVPAELTTPPAAPEA*
+>NZ_CP097650.1_729
+MTDVSDFIDVSDPAALENAVARAREVLADRGCVVLPTDTVYGIGADAFSPLAVAVLLAAK
+GRGRTMPPPVLIADRRVMAGLAYDVPEEAEALAERFWPGALTLILKSQPTLTWDLGETRG
+TVALRVPDDAVARELLYAVGPMAVSSANRTGMDAATTADAARSMLGESVALYLDAGPRES
+RDPSTIVDCTVTPFRVARQGSVPLEELRAVVPDLLAEGEEPPVAAERIAAADDAAAARPA
+DPEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000708.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000708.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6921a9ce1e54dc2e0c8df9334833d6818aa76492
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000708.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_770
+MITKHREQGLQMAELTINADDVRNALNEFAASYEPSGTDRTEVGRVISAADGIARVEGLP
+SVMANELLRFENGIQGLAQNLDTREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDAFLG
+RVVDPLGQPIDDLGPIEAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQ
+LIIGDRQTGKTAIAVDTILNQKANWESGDVEKQVRCVYVAVGQKASTIAGVRATLEEHGA
+LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL
+RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI
+TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM
+FASDLDPATRRQLARGERLMELLKQPQYSPYPVEEQVVSIWAGSKGHLDEVPVQDVLRFE
+REFIDHLRRHTSVLTDIASTGKLEDGTVSALESAVAEFSKGFQSSEEGGVRAGHEEHRAI
+EQDQVAQEQITKQKR*
+>NZ_CP033200.1_510
+MITKHREQGLQMAELTINADDVRNALNDFAASYEPSGTDRTEVGRVISAADGIARVEGLP
+SVMANELLRFENGIQGLAQNLDTREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDAFLG
+RVVDPLGQPIDDLGPIEAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQ
+LIIGDRQTGKTAIAVDTILNQKANWESGDVEKQVRCVYVAVGQKASTIAGVRATLEEHGA
+LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL
+RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI
+TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM
+FASDLDPATRRQLARGERLMELLKQPQYSPYPVEEQVVSIWTGSKGHLDEVPVQDVLRFE
+REFIDHLRRHTSVLTDIASTGKLEDGTVSALESAVAEFSKGFQSSEDGGVQAGHEEHRAI
+EQDQVAQEQITKQKR*
+>NZ_CP040019.1_2094
+MAELTINADDVRNALNDFAASYEPSGTDRTEVGRVISAADGIARVEGLPSVMANELLRFE
+NGIQGLAQNLDAREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDGFMGRVVDPLGQPID
+DLGPIQAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQLIIGDRQTGKT
+AIAVDTILNQKANWESGDVDKQVRCVYVAVGQKASTIAGVRATLEEHGALEYTTIVASPA
+SDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLLRRPPGREAYPG
+DVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISITDGQIFLQSDL
+FNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSMFASDLDPATRR
+QLARGERLMELLKQPQYSPYPVEEQVVSIWAGSKGHLDEVPVEDVLRFEREFIDHLRRRG
+SVLTDIGSTGKLEDGTVSALESEIAEFKKGFQSSEDGGVHAGHEEHRAIEQDQVAQEQIT
+KQKR*
+>NZ_CP083691.1_1983
+MITKHREQGLQMAELTINADDVRNALNDFAASYEPSDTTRTEVGRVISAADGIARVEGLP
+SVMANELLRFSNGILGLAQNLDAREIGVVVLGEFQDIREGMEVQRTGEILSVPVGDGFLG
+RVVDPLGHPLDDLGPIEAEGRRALELQAPTVTQRKSVHEPLQTGMKAIDAMIPIGRGQRQ
+LIIGDRQTGKTAIAVDTILNQKANWQTGDVDKQVRCVYVAVGQKASTIAAVRSTLEEHGA
+LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL
+RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI
+TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM
+FASDLDPATRRQLARGERLMELLKQPQYSPYPVEDQVVAIWAGSKGHLDDVAVEDVLRFE
+REFLDHLRRKDVVLGEIASTGKLEDETVSALEREIDAFKKGFQASGHDGVAAGHEEHAAI
+GQDQVVQEQITKQKR*
+>NZ_CP097650.1_736
+MITKHREQGLQMAELTINADDVRNALNDFAASYEPSGTDRTEVGRVISAADGIARVEGLP
+SVMANELLRFENGIQGLAQNLDTREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDAFLG
+RVVDPLGQPIDDLGPIEAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQ
+LIIGDRQTGKTAIAVDTILNQKANWESGDVEKQVRCVYVAVGQKASTIAGVRATLEEHGA
+LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL
+RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI
+TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM
+FASDLDPATRRQLARGERLMELLKQPQYSPYPVEEQVVSIWAGSKGHLDEVPVQDVLRFE
+REFIDHLRRHTSVLTDIASTGKLEDGTVSALESAVAEFSKGFQSSEDGGVQAGHEEHRAI
+EQDQVAQEQITKQKR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000710.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000710.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c05db7e9b70a73ddd551408a1349b87b8a924eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000710.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_772
+MTATITDQGTGTPTGGATGRVSRVIGPVIDAEFPANAMPEIYNALTTEIDLNGQRRTVTF
+EVAQHLGDNMVRAISLQSTDGLVRGTDVVDTGAPISVPVGDAVKGHIFNVLGETLDMPTS
+QLQAEDRWPIHRPAPNFASLEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI
+QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMDEADVLKDTALVFGQMDEPPGTRLRV
+ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL
+QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA
+STSRILDPQYVGQEHYDVAIRVKQILQKNKELQDIIAILGVDELSEEDKITVGRARKIEQ
+FLSQNTYTAKQFTGVEGSTVPVKDTVEGFKAIADGDLDHVAEQAFYNVGGLDDVEREWAK
+IQAEG*
+>NZ_CP033200.1_512
+MTATITDQGTGTPTGGATGRVSRVIGPVIDAEFPANAMPEIYNALTTEIDLNGQRRTVTF
+EVAQHLGDNMVRAISLQSTDGLVRGTDVVDTGAPISVPVGDAVKGHIFNVLGETLDMPAS
+QLQAEDRWPIHRPAPNFASLEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI
+QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMEEADVLKDTALVFGQMDEPPGTRLRV
+ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL
+QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA
+STSRILDPQYVGQDHYDVAIRVKQILQKNKELQDIIAILGVDELSEEDKITVGRARKIEQ
+FLSQNTYTAKQFTGVEGSTVPVKDTVEGFKAIADGDLDHVAEQAFYNVGGLDDVEREWAK
+IQAEG*
+>NZ_CP040019.1_2092
+MTATITDQGTGTPTGGATGRVSRVIGPVIDAEFPANAMPEIYNALTTEIDLNGQRRTVTF
+EVAQHLGDNMVRAISLQSTDGLVRGTDVVDTGAPISVPVGDAVKGHIFNVLGETLDVETS
+SLNFEERWPIHRAAPNFASLEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI
+QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMDEADVLKDTALVFGQMDEPPGTRLRV
+ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL
+QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA
+STSRILDPQYVGQDHYDTAIRVKQILQKNKELQDIIAILGVDELGEEDKITVARARKIEQ
+FLSQNTYTAKQFTGVEGSTVPIKDTVEGFKAIADGDLDHIAEQAFYNVGGLDDVEREWAK
+IQAEG*
+>NZ_CP083691.1_1981
+MTATFTDQGTGTPTAGATGRVARVIGPVIDAEFPANAMPEIYNALTATVELAGQTRVVTF
+EVAQHLGDNMVRAISLQSTDGLVRGADVQDTGAPISVPVGDAVKGHLFNVLGETLDMPIS
+ELDVQERWPIHRPAPSFAALEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI
+QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMDEADVLKDTALVFGQMDEPPGTRLRV
+ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL
+QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA
+STSRILDPQYVGQEHYDVATRVKQILQKNKELQDIIAILGVDELSEEDKITVSRARKMEQ
+FLSQNTYTAKQFTGVEGSTVPIKDTVEGFKAIADGDLDHVAEQAFYNVGGLDDVEREWAK
+IQAEG*
+>NZ_CP097650.1_738
+MTATITDQGTGTPTGGATGRVSRVIGPVIDAEFPANAMPEIYNALTTEIDFNGQRRTVTF
+EVAQHLGDNMVRAISLQSTDGLVRGTDVVDTGAPISVPVGDAVKGHIFNVLGETLDMPTS
+QLQAEDRWPIHRPAPNFASLEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI
+QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMDEADVLKDTALVFGQMDEPPGTRLRV
+ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL
+QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA
+STSRILDPQYVGQDHYDVAIRVKQILQKNKELQDIIAILGVDELSEEDKITVGRARKIEQ
+FLSQNTYTAKQFTGVEGSTVPVKDTVEGFKAIADGDLDHVAEQAFYNVGGLDDVEREWAK
+IQAEG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000714.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000714.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ae0fda20a3b17ab30c049699d56b7fdf6d69dac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000714.fa
@@ -0,0 +1,16 @@
+>NZ_CP042169.1_776
+MPRSNRPRRSSAPRRSERGASGASRRSRPSPGRSDPLQELLGLDAGYSRQSGSDGGWHVR
+QIPAWRAVKDYTCPGCGRVIRQGQAHLVAWRADWIMGDEDAGEDRRHWHPVCWRTRPSR*
+>NZ_CP033200.1_516
+MPRSNRPRRSSAPRRSERGASGVSRRSRPSPGRSDPLEELLGLDAGYSRQSGSDGGWHVR
+QIPAWRAVKDYMCPGCGRVIRQGQAHLVAWRADWIMGDEDAGADRRHWHPVCWRTRPGR*
+>NZ_CP040019.1_2087
+MADPLKELLGLDPGYSHQSGGDGGWHVRQIPSWRAVKDYTCPGCGRVIRQGQAHLVAWRS
+DWIMGDEDAGADRRHWHPVCWRTRVGR*
+>NZ_CP083691.1_1976
+MVTMPRSNRPRRSAAPRRGEGAAGGASRRSRPGPGRADPLEELLGMDPGYSHQSGSDGGW
+HVRDIPSWRAVKDYTCPGCGRTIRQGQAHLVAWRSDWIMGDEDAGADRRHWHPTCWRTRA
+SR*
+>NZ_CP097650.1_742
+MPRSNRPRRSSAPRRSERGASGASRRSRPSPGRADPLEELLGLDAGYSRQSGSDGGWHVR
+QIPAWRAVKDYTCPGCGQVIRQGQAHLVAWRADWIMGDEDAGADRRHWHPVCWRTRPGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000718.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000718.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6180a4ae03b3cc0de379d2f75b06635be7547235
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000718.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_780
+MALTLVRLRWTLTLNQWRRSPFTLVVSVLGALYVLGMAAVAVTLLVTGLPALPDEARGAT
+TVLVAAVVVLAWLVIPPFVTGVDATLDPHSFVLFPVPARTLIAGLVLSAFTTPAGLATLA
+VLVGLGASWWDRPAALAAGLAGGALTAVTAVAIGSGLAGLLAAYASRRRVRDVVSVLLFI
+PLMLGGVALSRAVASFEDFLAIAPQVARGAAWTPFGAGPAAAWAAAEGRGAAAALHLAVA
+AAWCLAALALWHLAVRRTVEPVAVGGGGSRRVGAGADPTPLRWLGRPATGPRTAIAARAQ
+RYWLADPRYAAGLIIIPLMAVVLWFTGGLASGGGLGPGLLLILGPMTAWSLAYSISADIA
+YDHTAFHLHVVSGVRGVDDRWGRVLGLAGWGVPMILLVTTATVAAAGDWSLLAPMLGLAL
+GLFGTTAGLSAFLSARFVYPVPKPGDSPFKTPQGAAMRTMLVQGASMLVSLALAVPFLVP
+FIVRLATGAAVWGWVTVALGFAWGAVALWLGVRLGARWYDRAQAETYQAVAAF*
+>NZ_CP033200.1_520
+MALTLVRLRWTLTLNQWRRSPFTLVMSVLGALYVLGMAAVAVTLLVTGLPALPDEARGAT
+TVLAAAVVVLAWLVIPPFVTGVDATLDPHSFVLFPVPARTLIAGLVLSAFTTPVGLATLA
+VLVGLGASWWDRPAALAAGLAGGALTAVTAVAIGSGLAGLLAAYASRRRVRDVVSVLLFI
+PLMLGGVALSQAIASFEDFLAIAPQVARGAAWTPFGAGPAAAWAAAEGRGAAVALHLAVA
+AAWCLAALALWHLAVRRTVEPVAVGGGRSRRVAAGADPMPLRWLGRRATGPRTAIAARAQ
+RYWLADPRYAAGLIIIPLMAVLLWFTGGMAAEGGPGLGLLLILGPITAWSLAYSISADIA
+YDHTAFHLQVVSGVRGVDDRWGRVLGLAGWGVPMILLVTTATVAAAGDWSLLAPMLGLAL
+GLFGTTAGLSAFVSARFVYPVPKPGDSPFATPQGAAMRTMLVQGAAMLVSLALAVPFLVP
+FVVRLVTGAAVWGWVTVALGLAWGAVALWLGVRLGARWYDRAQAETYQAVAAF*
+>NZ_CP040019.1_2083
+MALTLVRLRWALTLNQWRRSTFTLVLAVLGALYVLGLAVFVVVMLVTFLPDAWVVDRGTV
+TVIVASALALGWLLIPPFITGVDATLDPHSFVLFPVRARTLIAGLTLSAFTTPSGLATLI
+VMLGTGLSWWDIPAALAAALVGGALTAVTAVASGYGLAGLMAAYAGRRRVREVLSIALLI
+PVMLSGVIVAQTLDSLGDLFDVAPRVAAVAAWTPFGAGPAAAWAVAEGQGLRAAAHLLVA
+AAWCLAALALWHLAVRRTVEPVAVGGGSAREAGRADGAPLRWLGRPATGPRTAIAARAQR
+YWLRDPRYAAGLVMIPVLAAVLWFASTAGGDAGPGLGMLTMLGPVSAWALAYSISADIAY
+DHTAFHLHVVSGVRGADDRWGRVMGLAGWGVPALVVLTVATTAAADRWDLLPALLGLTLG
+LFGVTAAMSAFVSARFVYPVPKPGESPFKTPQGATMRIMLVQGAAMLVVVPLAVPVVVPF
+VVALVTQSAVWGWATLAVGLAWGAVALWLGVRMGAAWYDRAQAETYQAVAAF*
+>NZ_CP083691.1_1972
+MALTLTRLRWALTLNGWRRSTLTLVLSVLGALYFFGMAAMAVAALVVGLPEAELPVRGAV
+TVLVAAVVVLLWTILPPLVTGVDATLDPSSFVLFPVPARTLVAGLLLSTFTTPIGALTLL
+GLLGVAASWWDTPAALAAAAVGAVLSAVTAVCLGYGVTGLMSSFTGRRRVREAISLLVLI
+PLMLGGVALSRVMQSIDDLLWLGPVLANAAVWTPFGAGLGAGWAAAEGRWGLAGLRLLVA
+LAWAVAAAALWMLAIRRTVEPAAVGSTDSAAPRGDRATDLRWLGRPATSARTAIAARAQL
+YWFKDPRYMASLVTVPLMFVLLWFMGTSGPEGATAILLAAGPVTAWALGYSLSADIAYDH
+TAFHLHVLAGVKGIDDRLGRVMGLLGWALPVVAGVTLATVAMHGDWSVLPAILGVSLGVL
+GACLGLSALVSARWVYPVPKPGDSPLKTPQGAAMRIMLVQGTSLLVTLVLLVPMAVPFVV
+LLVTGAAVWSWVTLAVGLAWGALALWLGVRAGAAWYDRAQAETLQAVQSW*
+>NZ_CP097650.1_746
+MALTLVRLRWTLTLNQWRRSPFTLVMSVLGALYVLGMAAVAVTLLVTGLPALPDEARGAT
+TVLAAAVVVLAWLVIPPFVTGVDATLDPHSFVLFPVPARTLIAGLVLSAFTTPVGLATLA
+VLVGLGASWWDRPAALAVGLVGGALTAVTAVAIGSGLAGLLAAYASRRRVRDVVSVLLFI
+PLMLGGLALSRAIASFEDFLAIAPQIARGAAWTPFGAGPAAAWAVAEGRGAAVALHLAVA
+AAWCLAALALWHLAVRRTVEPVAVGGGRSRRVAAGADPTPLRWLGRPATGPRTAIAARAQ
+RYWLADPRYAAGLIIIPLMAVLLWFTGGMAGEGGPGLGLLLVLGPITAWSLAYSISADIA
+YDHTAFHLHVVSGVRGVDDRWGRVLGLAGWGVPMILLVTTATVAAAGDWSLLAPMLGLAL
+GLFGTTAGLSAFVSARFVYPVPKPGDSPFATPQGAAMRTMLVQGAAMLVSLALAVPFLVP
+FVVRLVTGAAVWGWITVALGLAWGAVALWLGVRLGARWYDRAQAETYQAVAAF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000720.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000720.fa
new file mode 100644
index 0000000000000000000000000000000000000000..59c60873388580f87d561cf86d3d5d4d1748dc13
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000720.fa
@@ -0,0 +1,60 @@
+>NZ_CP042169.1_782
+MADGRSLTSGTPDGSVQHDLFHIGEDLPPAMPERAAWGTAPKLRQWQQEALERYLQTAPQ
+DFLTVATPGAGKTTFALRVAKILLDSGVVQRLTVVAPTDHLKRQWADNAARVGIAIDPNF
+KNADGRHGAEYRGVALTYAQVANKPVLHRNRTEAAKTLVILDEIHHGGDALSWGEGIREA
+FEPATRRLSLTGTPFRSDTASIPFVRYELGADGIERSKADYTYGYGPALRDHVVRPVIFM
+AYSGQMRWKTSTGEVMEAQLGEAATKDITASAWRTALDPAGEWIPSVLRAADRRLSEVRR
+NVPDAGGLVIASDHQDARAYAAQLEALTGQRPAVILSDDKGASDRIEEFAASDERWMVAV
+RMVSEGVDVPRLCVGVYATSTSTPLFFAQAVGRFVRSRRRGETASVFLPSVPALMLLANE
+MELERDHALDRKEGAVEVEDLEDAPEEDLIAEANRAESGSDALTREKFEALESRASFDKV
+LFDGGEFGLGGAVGSEEEQDFLGIPGLLDAEQVSALLRQRQAEQIQRRPRAQAAEPADVV
+DHRRMKELRSELSKTVSAWATRSGQPHGVIHNRLREISGGPAVAQASREQLEKRLSTLRG
+WFVGRT*
+>NZ_CP033200.1_522
+MADGRSLTSGTPDGSVQHDLFHIGEDLPPAMPERAAWGTAPKLRQWQQEALERYLQTAPQ
+DFLAVATPGAGKTTFALRVAKILLDSGVVQRLTVVAPTDHLKRQWADNAARVGIAIDPNF
+KNADGRHGAEYRGVALTYAQVANKPVLHRNRTEAAKTLVILDEIHHGGDALSWGEGIREA
+FEPATRRLSLTGTPFRSDTASIPFVRYELGQDGIERSKADYTYGYGPALRDHVVRPVIFM
+AYSGQMRWKTSTGEVMEAQLGEAATKDITASAWRTALDPAGEWIPSVLRAADRRLTEVRR
+NVPDAGGLVIATDHQDARAYAAQLEALTGQRPAVILSDDKGASDRIEEFAASDERWMVAV
+RMVSEGVDVPRLCVGVYATSTSTPLFFAQAVGRFVRSRRRGETASVFLPSVPALMLLANE
+MELERDHALDRKEGAVEVEDLEDAPEEDLIAEANRAESGSDALTREKFEALESRASFDKV
+LFDGGEFGLGGAVGSEEEQDFLGIPGLLDAEQVSALLRQRQAEQIQRRPRAQAAEPADVV
+DHRRMKELRSELSKTVSAWAARSGQPHGVIHNRLREISGGPAVAQASREQLEKRLSTLRG
+WFVGRT*
+>NZ_CP040019.1_2081
+MAERRSSASGTPDGAVQHDLFHIGEDLPPAMPERAAWGTAPKLRQWQQEALEKYLETGPQ
+DFLAVATPGAGKTTFALRVAKILLDSGVVQRLTVVAPTDHLKRQWADNAARVGIAIDPNF
+KNADGRHGSEYRGVALTYAQVANKPVLHRNRTEAAKTLVILDEIHHGGDALSWGDGIREA
+FEPAARRLALTGTPFRSDTSTIPFVEYVDGPDGLSRSKADYTYGYGPALRDHVVRPVLFM
+AYSGQMRWKTSTGEVMEAQLGEAATKDITASAWRTALDPKGEWIPAVLRAADRRLSEVRR
+GVPDAGGLVIATDHEDARAYAAQLEALTGQRPALILSDDKGASDRIEEFAASDERWMVAV
+RMVSEGVDVPRLCVGVYATSTSTPLFFAQAVGRFVRSRRRGEVASVFLPSVPQLMLLANE
+MELERDHALDRREGGVDVEDLEDAPEEDLLAQANREESGSDALLRGKFEAMESRASFDKV
+LFDGGEFGLGGAVGSEEEQDFLGIPGLLDAEQVSALLRQRQAEQVQRRPKAPAKEPADVV
+DHRRMKELRSELSKTVSAWSARSGTPHGVIHNRLREVSGGPAVAQASRDQLEKRLSTLRG
+WFVGRT*
+>NZ_CP083691.1_1970
+MAEGRSETSGAPTPDGIQPDLFHVGEDLPPALPERAAWGTAPKLRQWQQEALEKYLREAP
+QDFLAVATPGAGKTTFALRVAKILMDSGVVQRLTVVAPTDHLKRQWADNAARVGLAIDPN
+FKNADGRHGPEYRGVALTYAQVANKPVLHRNRTEAARTLVILDEIHHGGDARSWGEGIRE
+AFEPASRRLSLTGTPFRSDDAYIPFVRYERGEDGFERSRADYTYGYGPALRDHVVRPVIF
+LAYSGQMRWKTSTGEVMEAQLGEAATKDITASAWRTALDPAGEWIPSVLRAADRRLTEIR
+RGIPDAGGLVIASDHEDARAYAAQLQAVTGQAPAVILSDDKGASDRIEEFAASDERWMVA
+VRMVSEGVDVPRLCVGVYATSTSTPLFFAQAVGRFVRSRRRGEVASVFLPSVPQLMLLAN
+EMELERDHALDRREGAVTVEELEDLSQAPEEDLIAEANRAERGSETLTRASFEALESRAS
+FDKVLFDGGEFGLGGDVGSEEELDFLGIPGLLDAEQVSELLRQRQNEQIRRKPAAAPKES
+RDVVDHRRMKELRAELSTTVSAWSARSGQPHGVIHNRLREISGGPAVAQASREQLEKRLE
+TLRGWFVGRR*
+>NZ_CP097650.1_748
+MADGRSLTSGTPDGSVQHDLFHIGEDLPPAMPERAAWGTAPKLRQWQQEALERYLQTAPQ
+DFLAVATPGAGKTTFALRVAKILMDSGVVQRLTVVAPTDHLKRQWADNAARVGIAIDPNF
+KNADGRHGAEYRGVALTYAQVANKPVLHRNRTEAAKTLVILDEIHHGGDALSWGEGIREA
+FEPATRRLSLTGTPFRSDTASIPFVRYELGQDGIERSKADYTYGYGPALRDHVVRPVIFM
+AYSGQMRWKTSTGEVMEAQLGEAATKDITASAWRTALDPAGEWIPSVLRAADRRLSEVRR
+NVPDAGGLVIATDHQDARAYAAQLEALTGQRPAVILSDDKGASDRIEEFAASDERWMVAV
+RMVSEGVDVPRLCVGVYATSTSTPLFFAQAVGRFVRSRRRGETASVFLPSVPALMLLANE
+MELERDHALDRKEGAVDVEDLEDAPEEDLIAEANRAESGSDALTREKFEALESRASFDKV
+LFDGGEFGLGGAVGSEEEQDFLGIPGLLDAEQVSALLRQRQAEQIQRRPRAQAVEPADVV
+DHRRMKELRAELSKTVSAWAARSGQPHGVIHNRLREISGGPAVAQASREQLEKRLSTLRG
+WFVGRT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000722.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000722.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a58b10fe3f280a2681357c4a9c40e5dd6e1616b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000722.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_785
+MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE
+RHAASLRELPASVGRLQPGDPAIPTIFLED*
+>NZ_CP033200.1_526
+MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE
+RHAASLRELPASVGRLQPGDPAIPTIFLED*
+>NZ_CP040019.1_2078
+MSQNPVTSAPQTPDDWRIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTSL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTQTGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDRRGRATAEVVGVNRGAAPDADDRPLLHRFVHAGELAAGWTGPEAVTRAAE
+RHAASLRELPATVGRLQPGDPAIPTIFLED*
+>NZ_CP083691.1_1965
+MTQNASAPAPSAAPWHVPTSLMTDHYELTMLCAARRAGTAERRSRFELFSRRLPDGRRYG
+VVAGTGRILEGLSRFRFSTAEVDFLADHSVVDDATLQWLADFRFSGDITGYAEGEVYFPH
+SPVLQVESTFAEACILETYLLSILNYDSAVASAASRMASAAQGRPCIEMGARRIHEEAAV
+AAARAAVIAGFAATSNLEAGRRYGVRTVGTAAHSFTLLHDSERAAFEAQVAALGRDTTLL
+VDTYDVEQGVRTAVEVAGRALRNVRLDSGDLVQQAHEVRELLDSLGNTETGIMVTSDLDE
+YAIASLRSAPVASYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASHGG
+RKDAVRRRDARGRAVAELVGVNRAPAADADDRPLLHTFVKDGELQEGWTGPEAVTRAAER
+HAASLAELPRAAARLQPGEALIPTIFQED*
+>NZ_CP097650.1_753
+MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE
+RHAASLRELPASVGRLQPGDPAIPTIFLED*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000725.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000725.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b0008aca42de06f34fe7f99aa3cb249481e8f3d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000725.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_788
+MSGQRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIAEVRA
+LALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAVAATR
+TGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETAREYT
+APLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEHPHS
+AAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRSTAFV
+PLGAEQEGVT*
+>NZ_CP033200.1_529
+MSGQRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIAEVRA
+LALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAVAATR
+TGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETAREYT
+APLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEHPHS
+AAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRSAASV
+RPGPEQEGVT*
+>NZ_CP040019.1_2075
+MSAPPQARPEVSASSPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTAHAPYGPRPIAQ
+VRALALGIMDELVDAGVKALVIACNSASAAVLRDARERYTGRHGIPVVEVIQPAVRRAVA
+ATRSGRIGVIGTQATVGSRAYDDSFSAAPHLQVTSAACPRFVEFVEAGITTGPELLATAQ
+EYTEPLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEH
+PHSAAGSGQDTRHRFAATGDPEHFQALARRFLGPEVGAVRRLDTVRERYPTAALAQLTPD
+LIARLGAEQERET*
+>NZ_CP083691.1_1962
+MSATADTAQTGAGPSSPIGVFDSGVGGLTVARAIMDQLPHEPIIYVGDTAHSPYGPRPIA
+QVRALALGVMDELVEAGVKALVIACNSASAAVLRDARERYTGRLGIPVVEVIQPAVRRAV
+AATRNGRVGVIGTQATVGSRAYEDSFSAAPHLQITSVACPRFVEFVEAGITTGPELLETA
+EEYVAPLKAAGVDTMVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRALVRHGLE
+HPHSAAGSAAAPEHRFAATGDPEHFAALARRFLGPEVGPVRQIQEIRERYPTAALTALTP
+DVLARLRAEMEEDGAR*
+>NZ_CP097650.1_756
+MSGQRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIAEVRA
+LALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAVAATR
+TGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETAREYT
+APLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEHPHS
+AAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRSAASV
+RPGPEQEGVT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000727.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000727.fa
new file mode 100644
index 0000000000000000000000000000000000000000..edf9b328eb448983d9d4e8faec7d689133546d39
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000727.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_790
+MSSPAPTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGNTRVLCTASFTEGVPRWLK
+GEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILAKGAAVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGAPFTRAELDTLLDLALIGTGELAR
+IQAETLAAATEDRA*
+>NZ_CP033200.1_531
+MSSPAPTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGNTRVLCTASFTEGVPRWLK
+GEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILAKGAAVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGAPFTRAELDTLLDLALIGTGELAR
+VQAETLAAATEDRA*
+>NZ_CP040019.1_2073
+MTSPASTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGDTRVLCTASFTQGVPRWLK
+GEGTGWVTAEYAMLPRATNERNQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILRKDAEVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGVPFSRAELDTLLDLALTGTGELAR
+IQAETLAGAAGSAEAQA*
+>NZ_CP083691.1_1960
+MTESSPSTSPSVTRQDGRAVDELRPITITRGFSRQAEGSALIEFGGTRVLCTASFTEGVP
+RWLKGEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALG
+ENTIVLDCDVLDADGGTRTASITGAYVALAEAVAWAQGRGILKKDARVLTDSVSAVSVGI
+IDGVPMLDLPYVEDVKAETDMNVVVTGSGDFVEVQGTAEGVPFRRAELDVLLDLALAGTA
+ELSRIQAETLAGDVAGRA*
+>NZ_CP097650.1_758
+MSSPAPTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGNTRVLCTASFTEGVPRWLK
+GEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILAKGAAVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGAPFTRAELDTLLDLALIGTGELAR
+IQAETLAAATEDRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000731.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000731.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be26d373a54dc205e6a0c239392f6693b753e163
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000731.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_794
+MILLHTSDWHLGRSFHGTGLLEAQEEVLDALVATVTERGVDAVLLAGDVYDRALPPADAV
+RLLDRTLTRLHAAGAQVVLTSGNHDSAVRLGFGGGLLAAAGVHVRADAVELDRPVLLTEP
+GVDGGAGQTVAVYGIPYLEPRHQGPAWGVEPHHTAVLTEAVRRVHADLAARRAETPEPVA
+AVVLAHLFAAGGHGSESERDIGEGEHVEPDAPPEMLVGTLGQVPVSVFDGLDYAALGHLH
+GRQRLAEHVRYSGSPLPYSFSEAGHRKGGWLVHVTGGAVTDVEAVDWDAGRRLAVLSGPI
+EDLLESPEFAWAEQCWVQVTVTDDERPERALERLKTRFPSVLVFRHEPAGGRRARERTYA
+QVLRQAPSDHALAVGFVDHVRQRPASGAEQDLLRDALEAARAGEVRA*
+>NZ_CP033200.1_535
+MILLHTSDWHLGRSFHGTGLLEAQEEVLDALVATVTERGVDAVLLAGDVYDRALPPADAV
+RLLDRTLTRLHAAGAQVVLTSGNHDSAVRLGFGGGLLAAAGVHVRADAAELDRPVLLTEP
+GVDGGAGQTVAVYGIPYLEPRHQGPAWGVEPHHTAVLTEAVRRVHADLAARRAETPEPVA
+AVVLAHLFAAGGHGSESERDIGEGEHVEPDAPPEMLVGTLGQVPVSVFDGLDYAALGHLH
+GRQRLAEHVRYSGSPLPYSFAEAGHRKGGWLVHVTGGAVTDVEAVDWDAGRRLAVLSGPI
+EDLLESPEFAWAEQCWVQVTVTDDERPERALERLKTRFPSVLVFRHEPAGGRRARERTYA
+QVLRQAPSDHALAVGFVDHVRQRPASEAEQDLLRDALEAARAAEVRA*
+>NZ_CP040019.1_2069
+MLLLHTSDWHLGRSFHGTGLLEGQRQVLDALVDTVRERGVDAVLLAGDVYDRALPSADAV
+ALLDATLARLREAGAQVVLTSGNHDSAVRLGFGAGLLSAAGVHVLTDPARLDEPVLLEDA
+AGERAAVYGVPYLEPRHLGQAWEVDPTHTGVMTEAVRRIRADLEDRRAGSPTPLAGVVLA
+HLFAAGGDASDSERDIGAGGSSWPASPAPADPAGRDAGCGAEPEGLVGTLGQVPVTVFDG
+LDYAALGHLHGRQTMAEHVRYSGSPLPYSFSEAKHVKGGWLVHVHGGAVTEVEPVDWRAG
+RRLAVLADRIGPLLDSPEYAFAENRWVQATVTDPERPEKALERLRSRFPHLLVFRHEPEG
+GRPERVRTYAQALRQAPTDLALTTGFVDHVRGRPASAEESALLDDALTASRTREAQA*
+>NZ_CP083691.1_1956
+MLLLHTSDWHLGRSFHGTGLLDSQRRVLAQLVDTVRERGVDAVLLAGDVYDRALPAADAV
+TLLDETLAALRAAGSQVVLTSGNHDSAIRLGFGSALMAAGGVHVRTDPERLAEPVLLEDA
+AGERAAVYGIPYLEPRHLGEAWGVDPHHTAVMTEAVRRVLADLEERRAADGPLAGVVLAH
+LFAAGAEGTESERDIGEGPHTDAHGTAPEGLVGTLGQVPVSVFSGLDYAALGHLHGRQTM
+APHVRYSGSPLPYSFSEARHTKGGWLVHVAGGAVTEVESVDWDAGRRLAVLEDRIQPLLD
+SPGYAWAEDRFVQATVTDPERPEKALERLRSRFPHLLVFRHEPEGGHAARERTYAQALRQ
+APDDLALTTGFVDHVRGRPASEAERELLDEALTASRIGEAQA*
+>NZ_CP097650.1_762
+MILLHTSDWHLGRSFHGTGLLEAQEEVLDALVATVTERGVDAVLLAGDVYDRALPPADAV
+RLLDRTLTRLHAAGAQVVLTSGNHDSAVRLGFGGGLLAAAGVHVRADAAELDRPVLLTEP
+GVDGGAGQTVAVYGIPYLEPRHQGPAWGVEPHHTAVLTEAVRRVHADLAARRAETPEPVA
+AVVLAHLFAAGGHGSESERDIGEGEHVEPDAPPEMLVGTLGQVPVSVFDGLDYAALGHLH
+GRQRLAEHVRYSGSPLPYSFSEAGHRKGGWLVHVTGGAVTDVEAVDWDAGRRLAVLSGPI
+EDLLESPEFAWAEQCWVQVTVTDDERPERALERLKTRFPSVLVFRHEPAGGRRARERTYA
+QVLRQAPSDHALAVGFVDHVRQRPASGAEQDLLRDALEAARAGEVRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000736.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000736.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b39c4233fb84231806d6ef99d0fbf8acdc5695d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000736.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_799
+MTDTTQHRLQPGDTAPAFTLQDQEGRPVSLRDSAGKHTIVYFYPAASTPGCTTQACDFRD
+SLASLTAAGYVVLGISPDPIGKIIRFAEQEGLTFPLLSDEDHAVAEAYGAWGEKKNYGRT
+FEGLIRSTIVVGPDGKVTHAQYNVKATGHVARLRRTLGLDEA*
+>NZ_CP033200.1_540
+MTDTTQHRLQPGDTAPAFTLQDQEGRPVSLRDSAGKHTIVYFYPAASTPGCTTQACDFRD
+SLASLTAAGYVVLGISPDPIGKIIRFAEQEGLTFPLLSDEDHAVAEAYGAWGEKKNYGRT
+FEGLIRSTIVVGPDGKVTHAQYNVKATGHVARLRRTLGLDEA*
+>NZ_CP040019.1_2056
+MSDTTQNRLQPGDIAPSFTLQDQDGRPVSLRDSAGKSTIVYFYPAASTPGCTTQACDFRD
+SLASLTAAGYVVLGVSPDPIGKIIRFAQKEGLTFSLLSDEDHAVAEAYGAWGEKKNYGRT
+YEGLIRSTVVVGPDGRVTHAQYNVKATGHVARLRRTLGLDEA*
+>NZ_CP083691.1_1951
+MTENTAAPARLSPGDVAPEFTLQDQDGRPVSLRDSAGKSTIVYFYPAASTPGCTTQACDF
+RDSLASLTAAGYRVLGISPDPIGKIIRFAQNEGLTFSLLSDEDHAVAAAYGAWGEKKNYG
+RTSEGLIRSTVVVGPDGKVTLAQYNVKATGHVARLRRELGLDD*
+>NZ_CP097650.1_767
+MTDTTQHRLQPGDTAPAFTLQDQEGRPVSLRDSAGKHTIVYFYPAASTPGCTTQACDFRD
+SLASLTAAGYVVLGISPDPIGRIIRFAEQEGLTFPLLSDEDHAVAEAYGAWGEKKNYGRT
+FEGLIRSTIVVGPDGKVTHAQYNVKATGHVARLRRTLGLDEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000738.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000738.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b035d76708134002600b7baf2c93304130d8ef9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000738.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_801
+MLTRLRGMDSAASTPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIG
+IASSWNEITPCNLSLDRLAQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSRE
+VIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDG
+TERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALGMS
+LPGSAAAPSADRRRDAFARRSGKAVVNMLRQGITARDIMTKPAFENAIAVTMAFGGSTNA
+VLHLLAIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDE
+GLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDAMHPNGGIAILHGSLAPEGAVVK
+SAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITGAI
+KGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLL
+VDEAELAARRESWEPVEPKFTTGVLGKYAKLVHSAAEGAYLG*
+>NZ_CP033200.1_542
+MLTRLRGMDSAASTPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIG
+IASSWNEITPCNLSLDRLAQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSRE
+VIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDG
+TERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALGMS
+LPGSAAAPSADRRRDAFARRSGKAVVNMLRQGITARDIMTKPAFENAIAVTMAFGGSTNA
+VLHLLAIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDE
+GLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDAMHPNGGIAILHGSLAPEGAVVK
+SAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITGAI
+KGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLL
+VDEAELAARRESWEPVEPKFTTGVLGKYAKLVHSAAEGAYLG*
+>NZ_CP040019.1_2054
+MDTAASTPRTPSAAPDMKPRSRDVTDGMERAASRGMLRAVGLGDADFAKPQIGIASSWNE
+ITPCNLSLDRLAQAAKEGVHADGGFPLEFGTVSVSDGISMGHEGMHFSLVSREVIADSVE
+TVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSTMPGHARLSDGTEKQVTI
+IDAFEAVGACARGLMSEEDLLRIEKAIVPTEGACGGMYTANTMASVGEALGMSLPGSATP
+PSPDRRRDDFARRSGAAVVNLLRQGITARDIMTKEAFENAIAVTMAFGGSTNAVLHLLAI
+AREAGVDLSLEDFNRVGDRTPHIADLKPFGRYVMTDVDRVGGVPVVMKALLDEGLLHGDA
+LTVTGRTVAENLAELAPDPVDGDVIRTMDRPMHPNGGIAILHGSLAPEGAVVKSAGFDAD
+VFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPRGGPGMREMLAITGAIKGAGLGK
+DVLLLTDGRFSGGTTGLCIGHIAPEAADGGPIGLVRDGDRIRVDIAGRTLDVQVAEEELE
+ARRREWTPVPPKFTTGVLGKYAKLVHSAAEGAYLG*
+>NZ_CP083691.1_1949
+MDTSAADRTPQDVVTAPDMKPRSRDVTDGMERTAARGMLRAVGLGDEDFAKPQIGIASSW
+NEITPCNLSLDRLAQASKDGVHAAGGFPLEFGTVSVSDGISMGHEGMHFSLVSREVIADS
+VETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDGTEKQV
+TIIDAFEAVGACARGLMSEEDLLRIEKAIAPGEGACGGMYTANTMASIGEALGMSLPGSA
+AAPSADRRRDAFARRSGEAVVNMLRLGITARDVMTKPAFENAIAVTMAFGGSTNAVLHLL
+AIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRVGGVPVVMKALLDEGLLHG
+DTLTVTGKTLAENLAALDPDPVDGTVIRTMENALHPNGGIAILHGSLAPEGAVVKSAGFD
+ADVFEGTARVFDRERAAMDALEEGVIQAGDVVVIRYEGPKGGPGMREMLAITGAIKGAGL
+GKDVLLITDGRFSGGTTGLCIGHIAPEAADGGPIGLVRDGDRIRVDIASRTLDLLVEEAE
+LEARRTSWQPVPPKFTTGVLGKYAKLVHSAAEGAYLG*
+>NZ_CP097650.1_769
+MLTRLRGMDSAASTPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIG
+IASSWNEITPCNLSLDRLAQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSRE
+VIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDG
+TERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALGMS
+LPGSAAAPSADRRRDAFARRSGEAVVKMIRQGITARDIMTKPAFENAIAVTMAFGGSTNA
+VLHLLAIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDE
+GLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDAMHPNGGIAILHGSLAPEGAVVK
+SAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITGAI
+KGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLL
+VDEAELAARRESWKPVEPKFTTGVLGKYAKLVHSAAEGAYLG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000744.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000744.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d1d38737330de71d31d7358980c93271cca0493c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000744.fa
@@ -0,0 +1,54 @@
+>NZ_CP042169.1_820
+MTDARAPYYLTTAISYPNGEPHIGHAYEYIASDAMARFQRLDGRDVRFLTGTDEHGQKME
+QTAQQQGVSALELATRNAAVFKEMDDDVLDISYDRFIRTTDTDHAEAVREIWRRMEANGD
+IYLGSYAGWYSVRDERYFGEDETEVGQDGVRRAVETGTEVTWTEEESYFFRLSKYQQPLL
+DHYREHPDFAAPRYRFNEVIRFVEAGLEDLSISRTSFQWGIDLPAPADPDAADADRRADH
+VTYVWVDALTNYLTGAGWPAEDPEAFARYWPADLHVIGKDISRFHCIFWPAFLMSAGLEL
+PRRVMIHGFLNNNGAKMSKSLGNVVHPREWVARYGLDAIRFFLLREFPFGADGSYSHEAV
+VSRKNADLANNLGNLAQRSLSMVAKNCGAAVPEPGEFTEADRAVLAQVDALLERSRSAYA
+VQDFHDALEETWRVLGEINAYFADQAPWVLRKTDEPRMRTVLYVTLQAVRRVALLAQPVM
+PGSASRLLDLLGVPAEGDAGRTGASGTGPRSFAAFHEDLVPGTPLPAPQPVFPRHEEPAE
+D*
+>NZ_CP033200.1_551
+MTDARAPYYLTTAISYPNGEPHIGHAYEYIASDAMARFQRLDGRDVRFLTGTDEHGQKME
+QTAQQQGVSALELATRNAAVFKEMDDDVLDISYDRFIRTTDTDHAEAVREIWRRMEANGD
+IYLGSYAGWYSVRDERYFGEDETEVGQDGVRRAVETGTEVTWTEEESYFFRLSKYQQPLL
+DHYREHPDFAAPRYRFNEVIRFVEAGLEDLSISRTSFQWGIDLPAPADPDAADADRRADH
+VTYVWVDALTNYLTGAGWPADDPEAFARYWPADLHVIGKDISRFHCIFWPAFLMSAGLEL
+PRRVMIHGFLNNNGAKMSKSLGNVVHPREWVARYGLDAIRFFLLREFPFGADGSYSHEAV
+VSRKNADLANNLGNLAQRSLSMVAKNCGAAVPEPGEFTEADRAVLAQVDALLERSRSAYA
+VQDFHDALEETWRVLGEINAYFADQAPWVLRKTDEPRMRTVLYVTLQAVRRVALLAQPVM
+PGSASRLLDLLGVPAEGDAGRTGASGTGPRSFAAFHEDLVPGTPLPAPQPVFPRHEEPAE
+D*
+>NZ_CP040019.1_2048
+MTDARAPYYLTTAISYPNGEPHIGHAYEYIATDAMARFQRLDGRDVRFLTGTDEHGQKME
+QTAQREGVTALELATRNAAVFKEMDDEVLDISYDRFIRTTDADHAEAVQEIWRRMEANGD
+VYLGSYAGWYSVRDERYFGEDETAVGEDGVRRAVETGTEVTWTEEESYFFRLSKYQEPLL
+EHYRRNPEFAAPRYRFNEVIRFVEDGLEDLSISRTSFDWGVPLPAPVDPDAEVADRRADH
+VTYVWVDALTNYLTGAGWPGRDPEAFGRYWPADLHVIGKDISRFHCIFWPAFLMSAGIEL
+PKRVMIHGFLNNNGAKMSKSLGNVVHPRDWVARYGLDAIRFFLLREFPFGADGSYSHEAV
+VGRKNADLANNLGNLAQRSLSMVAKNCEAAVPQPGPLTAEDEAVLAQVDALLERSRTAYA
+VQDFHDALEETWRVLGEVNAYFADQAPWVLRKTDEARMRTVLYVTLQAVRRVALLVQPVM
+PASASRLLDLLGVPAEGDAGRTGASGQGPRSFAAFHEDLVPGTALPKPEGVFPRHEEPAE
+A*
+>NZ_CP083691.1_1944
+MTDTRAPYYVTTAIHYPNGEPHIGHAYEVVGADALARFMRLDGRDVFFLTGTDEHGQKMA
+QTAERLGVTPMELATRNSAAFKAMDDEVLGVSYDRFIRTTDEDHHRASQEIWRRMEANGD
+VYLDRYAGWYSVRDERFFDEDETEVREDGQRYAAETGTEVTWTEEESWFFRLSKYQEPLL
+ALYRDDPEFAAPRSRFNEVIRFVEGGLEDLSISRTSFDWGIDVPAPADGAASDAHHVMYV
+WVDALTNYLTGVGFPDESSESFRRFWPADVHVIGKDISRFHCVFWPAFLMSAGIELPKRV
+MIHGFLNNNGEKMSKSLGNVVAPRDWVARYGLDAVRFFLLREFPFGADGSYSHEAVVGRK
+NADLANNLGNLAQRSLSMVAKNCGGGVPEPGSLTEADTAVLAQVDALLEHSRAAYTVQDF
+HGALEETWRVLGEVNAYFADQAPWVLKKTDEPRMRTVLYVTLQAVRRVALLVQPVMPASS
+SRLLDLLGVPAEGDAGATAASNAGPRSFAAFGEDLMPGTALPRPEGVFPRHEDPAEG*
+>NZ_CP097650.1_778
+MTDARAPYYLTTAISYPNGEPHIGHAYEYIASDAMARFQRLDGRDVRFLTGTDEHGQKME
+QTAQQQGVSALELATRNAAVFKEMDDDVLDISYDRFIRTTDTDHAEAVREIWRRMEANGD
+IYLGSYAGWYSVRDERYFGEDETEVGQDGVRRAVETGTEVTWTEEESYFFRLSKYQQPLL
+DHYREHPDFAAPRYRFNEVIRFVEAGLEDLSISRTSFQWGIDLPAPADPDAADADRRADH
+VTYVWVDALTNYLTGAGWPAEDPEAFARYWPADLHVIGKDISRFHCIFWPAFLMSAGLEL
+PRRVMIHGFLNNNGAKMSKSLGNVVHPREWVARYGLDAIRFFLLREFPFGADGSYSHEAV
+VSRKNADLANNLGNLAQRSLSMVAKNCGAAVPEPGEFTEADRAVLAQVDALLERSRSAYA
+VQDFHDALEETWRVLGEINAYFADQAPWVLRKTDEPRMRTVLYVTLQAVRRVALLAQPVM
+PGSASRLLDLLGVPAEGDAGRTGASGTGPRSFAAFHEDLVPGTPLPAPQPVFPRHEEPAE
+D*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000745.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000745.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30ad17a26412e250326ac8311431471a1fc0e81c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000745.fa
@@ -0,0 +1,36 @@
+>NZ_CP042169.1_821
+MTETTRSSADPLDIAVIGGDGIGPEVTDQAAAVLQAALRAEGRPEARLTPYPLGAEHWLE
+TGEALTDEVLESLRRHDAILFGAVGAAPGDERIPSGLIERGMLLKLRFALDHGVNLRPAT
+LLPGAVSPLAAPGEIDFTVVREGTEGPYVGNGGAIRVDTPHEIATEVSVNTAFGVRRVVE
+DAFRRADAGERKRLTLVHKHNVLVHAGHLWRRTVESVGADFPAVTWDYMHVDAAMIFLAT
+DPARFDVIVTDNLFGDIITDLAAAVTGGIGLAASGNINVEGTAPSMFEPVHGSAPDIAGQ
+GIADPVAAILSAALLLEHVGETGAAARVRTAVWAHLKDRVDGARGTTAEVGADVAARV*
+>NZ_CP033200.1_552
+MTETTRSSADPLDIAVIGGDGIGPEVTDQAAAVLQAALRAEGRPEARLTPYPLGAEHWLE
+TGEALTDEVLESLRRHDAILFGAVGAAPGDERIPSGLIERGMLLKLRFALDHGVNLRPAT
+LLPGAVSPLAAPGEIDFTVVREGTEGPYVGNGGAIRVDTPHEIATEVSVNTAFGVRRVVE
+DAFRRADAGERKRLTLVHKHNVLVHAGHLWRRTVESVAADFPAVTWDYMHVDAAMIFLAT
+DPARFDVIVTDNLFGDIITDLAAAVTGGIGLAASGNINVEGTAPSMFEPVHGSAPDIAGQ
+GIADPVAAILSAALLLEHVGETGAAARVRTAVWAHLKDRVDGARGTTAEVGADVVARV*
+>NZ_CP040019.1_2047
+MTESTRPSADPLDIAVIGGDGIGPEVTEQAAAVLQAALGAEGRPEARLTPYPLGAEHWLR
+TGEALPDETLEALRGHDAILFGAVGAAPGDERIPSGLIERGMLLRLRFELDHGVNLRPAA
+LLPGAVSPLAEPGTIDFTVVREGTEGPYVGNGGAIRTGTPHEIATEVSVNTAHGVRRVVE
+DAFARAAAGERKRLTLVHKHNVLVHAGHLWRRTVEAVAADFPEVSWDYMHVDAATIFLTT
+DPARFDVIVTDNLFGDILTDLAAAVTGGIGLAASGNINVEGTAPSMFEPVHGSAPDIAGQ
+GVADPVAAILSAALLLEHVGETGAAQRVRTAVWAHLKDRVDGARGSTAEVGADVAARV*
+>NZ_CP083691.1_1943
+MTESTRTSAAPLDIAVIGGDGIGPEVTDQAVAVLEAALAAEGRPAPRLTPYALGAEHWLA
+TGEALTDETLEALRGHEAILFGAVGAAPGDQRIPSGLIERGILLRLRFELDHGVNLRPSR
+LYPGTTSPLAEPGEIAFTVVREGTEGPYVGNGGAIRTGTEHEIATEVSVNTAHGVRRVVR
+DAFRRASATERRRLTLVHKHNVLVHAGHLWRRTVEEVAAEFPEVAHDYMHVDAATIVMTT
+DPARFDVIVTDNLFGDILTDLAGAVTGGIGLAASANINVERTAPSMFEPVHGSAPDIAGQ
+GIADPVAAILSAGLLLEHVGERAAADRIDRAVWAHLAERGPQRGSTAEVGVDVVRRVRES
+SAA*
+>NZ_CP097650.1_779
+MTETTRSSADPLDIAVIGGDGIGPEVTDQAAAVLQAALRAEGRPEARLTPYPLGAEHWLE
+TGEALTDEVLESLRRHDAILFGAVGAAPGDERIPSGLIERGMLLKLRFALDHGVNLRPAT
+LLPGAVSPLAAPGEIDFTVVREGTEGPYVGNGGAIRVDTPHEIATEVSVNTAFGVRRVVE
+DAFRRADAGERKRLTLVHKHNVLVHAGHLWRRTVESVAADFPAVTWDYMHVDAAMIFLAT
+DPARFDVIVTDNLFGDIITDLAAAVTGGIGLAASGNINVEGTAPSMFEPVHGSAPDIAGQ
+GIADPVAAILSAALLLEHVGETGAAARVRTAVWAHLKDRVDGARGTTAEVGADVVARV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000746.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000746.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3eedf3b5c8a9202d97387f3caf147e510b76c463
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000746.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_822
+MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG
+PLSLDPAAAVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEELF
+LGSLRAQLEADRAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE
+LKPVTIWVSRDYARAGKGGTGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE
+LGGMNVFFVHADGRLVTPALTGTILEGVTRSSILQLGRDMGLTVEERRVTLAEWAEGVRS
+GEITEVFACGTAAVVTPIGRLLDGDDVIESAGGADVALKIRTELEGIQTGRVEDRHGWLH
+RLV*
+>NZ_CP033200.1_553
+MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG
+PLSLDPAAAVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEELF
+LGSLRAQLEADRAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE
+LKPVTIWVSRDYARAGKGGTGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE
+LGGMNVFFVHADGRLVTPALTGTILEGVTRSSILQLGRDMGLTVEERRVTLAEWAEGVRS
+GEITEVFACGTAAVVTPIGRLLDGDDVIESAGGTDVTLRIRAELEGIQTGRVEDRHGWLH
+RLV*
+>NZ_CP040019.1_2046
+MSETVFTRQPHLSPLSEEERVEILQDPGFGKVFTDHMVSIDWTWSEDGGAWHDARVEPYG
+PLSLDPSASVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEEMF
+LGSLKAQLEADRDWVPTGEGQSLYLRPFMFATEAFLGVRPAKEVRYMVIASPAGNYFGGE
+LKPVTIWVSREYARAGRGGMGAAKTGGNYAASLLPQLEAASKGADQVVFLDQYHDDSIEE
+LGGMNVFFVFDDGRLVTPELTGTILEGVTRSSILQLGRDMGLTVEERRITLAEWAEGVRS
+GAIREVFACGTAAVVTPIGRLLDGDDVIESAGGTEVTLKIRAELEGIQTGRVEDRHGWLH
+RLV*
+>NZ_CP083691.1_1942
+MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG
+PLSLDPSAAVLHYGQEIFEGLKAYGHEDGSVWTFRPEANAARLNRSARRLALPELPEELF
+LGSLRAQLEADQAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE
+LTPVTIWVSRDYARAGKGGMGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE
+LGGMNVFFVHADGRLVTPELTGTILEGVTRSSILQLGRDMGMSVEERRVTLAEWAEGVRT
+GAITEVFACGTAAVVTPIGRLLDGDDVIESTGGTEVAMKIRAELEGIQTGTVEDRYGWMH
+RLV*
+>NZ_CP097650.1_780
+MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG
+PLSLDPAAAVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEELF
+LGSLRAQLEADRAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE
+LKPVTIWVSRDYARAGKGGTGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE
+LGGMNVFFVHADGRLVTPALTGTILEGVTRSSILQLGRDMGLTVEERRVTLAEWAEGVRS
+GEITEVFACGTAAVVTPIGRLLDGDDVIESAGGTDVTLRIRAELEGIQTGRVEDRHGWLH
+RLV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000756.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000756.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d18a16219a7ffca10a8e61b2a60c24d2021d184
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000756.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_834
+MEKFTTHTGVGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS
+GGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV
+ERIWKELENRPGTPVTVDLVTRTVECGDVTAPFQIDDDTRHRLLEGLDDIAVTLGHQAEI
+DAYEADRPAYKPTTLPARTAG*
+>NZ_CP033200.1_565
+MEKFTTHTGVGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS
+GGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV
+ERIWKELENRPGTTVTVDLVTRTVECGDVTAPFQIDDDTRRRLLEGLDDIAVTLGHQAEI
+DAYEADRPAYKPTTLPARTAG*
+>NZ_CP040019.1_2033
+MEKFTTHTGIGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS
+AGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV
+ERIWKELENRPGTTVTVDLVSRTVECGDVTAPFQIDDDTRHRLLEGLDDIAVTLDHQDEI
+DAYERARPSYKPTTLPARTAG*
+>NZ_CP083691.1_1924
+MDKFTTHTGIGVPLRASNVDTDQIIPAVYLKRVSRTGFEDALFAGWRQDPDFILNTEPYS
+AGSVLVAGPDFGTGSSREHAVWALKDYGFKVVVSSRFADIFRGNSAKQGLVAAQVEPEDV
+ERIMKQLENQPGAAVTVDLEHLTVECGGVTAAFEIDEDARHRLLHGLDDIAITLSHADAI
+AAYEAGRPSYKPTTLPARTAD*
+>NZ_CP097650.1_792
+MEKFTTHTGVGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS
+GGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV
+ERIWKELENRPGTPVTVDLVTRTVECGDVTAPFQIDDDTRHRLLEGLDDIAVTLGHQAEI
+DAYEADRPAYKPTTLPARTAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000764.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000764.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee4efe53484b66a9223c1390de71216a52a3a72f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000764.fa
@@ -0,0 +1,70 @@
+>NZ_CP042169.1_842
+MAAEAPVTDLPLSEVLGGKLPARLERELGLTTVGDLLDHVPRRWIERGELTPIAALPYDA
+EVTVVAVVESVTTRRMHSRPGFIVDVTVADPSVAGVPGASLSMAFFNGHDARRRLAPGMT
+AMFQGRTTEYRGRITLNNPDFALLDDDVAPGEVDVRPVPLYRATGKLPSWTVRSAVARVL
+ETVDLGRIPELLTERIRAEAAAALDLDVPLPGTAQAYRDLHAPNDVAATGPARTALALRE
+ALLVQAALAWRRNRERAVPAVPRPPRAGGLLEALDARLPFALTPGQVAVGEQLSAELARD
+APMSRLLQGDVGAGKTLVALRAMLQVVDAGGQAALVAPTEVLAAQHHRALLRLMGPLAEA
+GTLGAGDGPATRIALVTGSLKTAARREALLALASGEAGIAVGTHALLSEKVGFAELALAV
+VDEQHRFGVDQREALRRANPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRQPVT
+THVARMAHGPRVIGRVWELIAEHVAAGHQAFVVCPRIDPDDADPGHANVEEMTPRLRGLP
+ALAGLRIDAVHGRMDQAEQDAAMQAFARGETDVLVATTVVEVGVDVPNATVMAILDADDF
+GLSTLHQLRGRVGRGPGAAVCLLATRLPDGHPSLRRLEVLAQEQDGMRIAQEDLAQRGVG
+DVLGAAQSGLASGLHHVDVIADAPLIAVAADAVAQVMAAGPGLSAHPALAAEVARWEAEH
+LTAADYLEKG*
+>NZ_CP033200.1_573
+MAAEAPVTDLPLSEVLGGKLPARLEKELGLTTVGDLLDHVPRRWIERGELTPIAALPHDA
+EVTVVAVVESVTTRRMHSRPGFIVDVTVADPSVAGVPGASLSMAFFNGHDARRRLAPGMT
+AMFQGRTTEYRGRITLNNPDFALLDDDVAPGEVDVRPVPLYRATGKLPSWTVRSAVARVL
+ETVDLGRIPELLTERIRAEAAAALDLDAPLPGTAQAYRDLHAPHDVAATGPARTALALRE
+ALLVQAALAWRRDRERAVPAVPRPPRPGGLLEALDARLPFALTPGQVAVGEQLSAELARD
+APMSRLLQGDVGAGKTLVALRAMLQVVDAGGQAALVAPTEVLAAQHHRALLRLMGPLAEA
+GTLGAGDGPATRVALVTGSLKTTARREALLALASGEAGIAVGTHALLSEKVGFAELALAV
+VDEQHRFGVDQREALRRANPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRQPVT
+THVARMAHGPRVIGRVWELIAEHVAAGHQAFVVCPRIDPDDADPGHANVEEMTPRLRSLP
+ALAGLRIDAVHGRMDQAEQDAAMQAFARGETDVLVATTVVEVGVDVPNATVMAILDADDF
+GLSTLHQLRGRVGRGPGAAVCLLATRLPDGHPSLRRLEVLAQEQDGMRIAQEDLAQRGVG
+DVLGAAQSGLASGLRHVDVIADAPLIAVAADAVTRVMAAGPGLSAHPALAAEVARWEAEH
+LTAADYLEKG*
+>NZ_CP040019.1_2025
+MGAEVRVTDLPLSEVLDGRLPARLDKELGLATVGDLLDHVPRRWIERGELTPIAALPWDA
+EVTVVAVVESVTTRRMHSRPGFIVDVTVADPAADGAPGASLSMAFFNGHDARRRLAPGMT
+AMFQGRTTAYRGRITLNNPDFALLDDDVAPGDVDVRPVPLYRATGKLPSWTVRSAVARVL
+ADVDLTRIPELLTPRLRAEAAAALDLDAPLPDTARAYRDLHAPEEVEATGPARTALALRE
+ALVVQAALAWRRDRERAVPAVPRPPRAGGLLDALDARLPFALTPGQAEVGEQLAAELTRD
+APMSRLLQGDVGAGKTLVALRAMLQVVDAGGQAALVAPTEVLAAQHHRALLALMGPLAEA
+GTLGAGDGPATKVVLVTGSLKTQARREALLALASGEAGIAVGTHALLSDKVGFAELALAV
+VDEQHRFGVDQREALRRSNPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRQPVA
+THVARMDHGPRVIGRVWELIAEHAAAGRQAFVVCPRIDPDDADPGHANVEEMAPRLRSLP
+ALAGLRIEAVHGRMDQAEQDAAMQAFARGETDVLVATTVIEVGVDVPNATVMAVLDADDF
+GLSTLHQLRGRVGRGPDAAVCLLATRLPDEHPSLRRLEVLAQEQDGMRIAQEDLATRGVG
+DVLGAAQSGLASGLRHVDVLRDAPLIAVAADAVGRIMAEGPGLSAHPALAAEVARWESEH
+LTAADYLEKG*
+>NZ_CP083691.1_1916
+MAADGVLDLPLGEVLSGRLPGRLEKELGLATVGGLLDHVPRRWVERGELTPIAALPVDAE
+VTVVARVEHVATRRMRSRAGFIVDVTVADPSVAGTAGASLSMAFFNGHDAQRRLAPGVTA
+MFQGKTSLYRGAVTLNNPDFALLDDDVAPGEVDTRPVPIYRATGRMPSWTVRSAVRRVLE
+TVDLDAIPELLTEPIRARATLALGLPETLPGTAEAYRRLHAPDAVEQTGPARTALSLREA
+LVVQGALAWRRSREKAVPAVPRPRRAGGLLEALDARLPFELTPGQRAVGEELAAELSGPH
+PMSRLLQGDVGAGKTLVALRAMAQAVDAGGQAAFVAPTEVLAAQHHRALLALLGPLAREA
+GTLGAAAQEGPGTDVVLVTGSQRSAQRRAALLKLASGEAGIAVGTHALLAERVQFAELAL
+AVVDEQHRFGVDQREALRRANPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRTP
+VATHVARMAHGPRVIARVWEVVAEHCAAGRQAFVVCPRIDPDDADPAHANVTEMAERLRA
+LPVLGGLRIGEVHGRMDQAEQDAAMQAFARGETDVLVATTVVEVGVDVPNATVMAVLDAD
+DFGLSTLHQLRGRVGRGQDAAICLLATRLADGHPSLRRLEVLEATRDGMRIAQADLAQRG
+VGDVLGAAQSGLASGLTHVDVIGDADVIGVAADVVADLMAAAPGLSAHPALAAEVSRWEA
+AHLTAADYLEKG*
+>NZ_CP097650.1_800
+MAAEAPVTDLPLSEVLGGKLPARLEKELGLTTVGDLLDHVPRRWIERGELTPIAALPYDA
+EVTVVAVVESVTTRRMHSRPGFIVDVTVADPSVAGVPGASLSMAFFNGHDARRRLAPGMT
+AMFQGRTTEYRGRITLNNPDFALLDDDVAPGEVDVRPVPLYRATGKLPSWTVRSAVARVL
+ETVDLGRIPELLTERIRAEAAAALDLDAPLPGTAQAYRDLHAPHDVAATGPARTALALRE
+ALLVQAALAWRRDRERAVPAVPRPPRAGGLLEALDARLPFALTPGQVAVGEQLSAELARE
+APMSRLLQGDVGAGKTLVALRAMLQVVDAGGQAALVAPTEVLAAQHHRALLRLMGPLAEA
+CTLGAGDGPATRVVLVTGSLKTAARREALLALASGEAGIAVGTHALLSEKVGFAELALAV
+VDEQHRFGVDQREALRRANPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRQPVT
+THVAQMAHGPRVIGRVWELIAEHVAAGHQAFVVCPRIDPDDADPGHANVEEMTPRLRGLP
+ALAGLRIDAVHGRMDQVEQDAAMQAFARGETDVLVATTVVEVGVDVPNATVMAILDADDF
+GLSTLHQLRGRVGRGPGAAVCLLATRLPDGHPSLRRLEVLAQEQDGMRIAQEDLAQRGVG
+DVLGAAQSGLASGLHHVDVIADAPLIAVAADAVAQVMAAGPGLSAHPALAAEVARWEAEH
+LTAADYLEKG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000768.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000768.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0570953363ca7010d087d1a4b4e5cb740892a37f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000768.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_846
+MTVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAGLADV
+LMITGRNKRALEDHFDRHPALEAALEHKGDTKRLAQIHESDLVGDIHYVRQGEALGLGHA
+VNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSAYGVA
+AVQAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGGEIQL
+TDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGTRHEDLGADLRAWLREF
+TAGL*
+>NZ_CP033200.1_577
+MTVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAGLADV
+LMITGRNKRALEDHFDRHPALEAALEHKGDAKRLAQIHESDLVGDIHYVRQGEALGLGHA
+VNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSAYGVA
+AVEAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGGEIQL
+TDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGARHEDLGADLRAWLREF
+TAGL*
+>NZ_CP040019.1_2021
+MTVPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVAEARRAGLQDVLM
+ITGRNKRALEDHFDRHPALEATLERKGDATRLAQIRESDLVGDIHYVRQGEALGLGHAVN
+CARRHVGDEPFAVLLGDDIIGDGEALLARMIDVQQRLGGSVVALMEVPEEAVSAYGVAAV
+EAVPGEGEDVVRVTGLVEKPAREDAPSTLAVIGRYVLASQVFDVLDRTPPGRGGEIQLTD
+ALQTLADDDGEGGGVHAVVFDGRRYDTGDKLGYLQAVVEFGTRHEELGGDLRAWLKAFAA
+GL*
+>NZ_CP083691.1_1912
+MTEQSTAASPTRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVAEAVSAG
+LGDVLMITGRNKRALEDHFDRHPALEQVLEAKGDTKRIDLIRASDLVGDIHYVRQGEALG
+LGHAVGCARRHVGDEPFAVLLGDDLIGEDEGLLARMIDVQHRLGGSVIALMEVPEDAVSA
+YGVAAVAPVDGEDDDVVAVTSLVEKPARGDAPSNLAIIGRYVLAPQVFEVLERTAPGRGG
+EIQLTDALQTLAAGEGEGFGVHAVVFRGRRYDTGDKLGYLQAVVELGVRHPELGGDLREW
+LKGFAAGL*
+>NZ_CP097650.1_804
+MTVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAGLADV
+LMITGRNKRALEDHFDRHPALEAALEHKGDATRLAQIHESDLVGDIHYVRQGEALGLGHA
+VNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSAYGVA
+AVQAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGGEIQL
+TDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGTRHEDLGADLRAWLREF
+TAGL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000769.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000769.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f5954e6f40509d0a92408d5d6160b5f51848ea7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000769.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_847
+MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWPAPAGVSTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER*
+>NZ_CP033200.1_578
+MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWPAPAGVSTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER*
+>NZ_CP040019.1_2020
+MDTTQRQDADSSWVIPVRDLTRGAGVQRELTAQWPAPAGVTTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECSRCLLPLHEGITVDLQELYLTGASEDEAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER*
+>NZ_CP083691.1_1911
+MATTVPSGAPSPWVLSVRDLARGAGVQRELTTRLPAPAAVSMPMLGIPEGDPVDLELRLE
+AVHEGVLVTGTAHADLTGECSRCLLPLHEGITVDLQELFLADPPAEGDDEQPLVEHETVD
+LEPVFRDAVVTALPFQPLCRPDCEGLCADCGIRLEDAPAGHAHERVDPRWAALAALADTT
+EETSITETEKR*
+>NZ_CP097650.1_805
+MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWRAPAGVSTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000770.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000770.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2db8adb05e28914839af75ee42f1e53057788957
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000770.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_848
+MAVPKRKMSRANTRARRSQWKATAPALVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK
+GRKVADA*
+>NZ_CP033200.1_579
+MAVPKRKMSRANTRARRSQWKATAPALVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK
+GRKVADA*
+>NZ_CP040019.1_2019
+MAVPKRKMSRANTRARRSQWKATAPTLVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK
+GRKVADA*
+>NZ_CP083691.1_1910
+MAVPKRKMSRANTRARRSQWKAEAPSLVKTVENGRVSYRLPHQAELKTDAAGTPLFYEYK
+GRKVADA*
+>NZ_CP097650.1_806
+MAVPKRKMSRANTRARRSQWKATAPALVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK
+GRKVADA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000782.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000782.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6620921552ada054737ad215551a27d5ef5425ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000782.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_874
+MFNSLSDRLTATFRSLKGKGRLSEADIDATAREIRRALLDADVAVPVVRQFIAQIKERAL
+SAEVAQALNPGQQVVKIVNEELVGILGGETRRIQHAKTGTTVIMLVGLQGAGKTTLAGKL
+AHLLKSQGHTPLLVACDLQRPNAVKQLQVGGERAGVPVYAPHPGVSSEFEAATGDPVQVA
+RDGVAEANTKYHDVVIIDTAGRLGVDAELMQQAADIRAAVDPDEVLFVIDAMIGQDAVAT
+AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMAS
+RILDMGDVLSLIEQAEQNWDRTEAEKMARKFADQEDFTLDDFLAQMQQLKKMGSLKKMLM
+MMPGAQGMRQQLEQFDESSIGRVEAIIHSMTPHERVAPKIINGSRRARIARGSGVSVSEV
+NGLLERFAEAQKMMKRMAAGGGIPGMPGTPGGASRKGKGKGKNAKRDRVKSGNPAKAAAE
+RKAIEERRARAAQAQAGAVFGRDGAGMDGFDPSTLNLPAGFEKYLKDR*
+>NZ_CP033200.1_602
+MFNSLSDRLTATFRSLKGKGRLSEADIDATAREIRRALLDADVAVPVVRQFIAQIKERAL
+GAEVAQALNPGQQVVKIVNEELVGILGGETRRIQHAKTGTTVIMLVGLQGAGKTTLAGKL
+AHLLKSQGHTPLLVACDLQRPNAVKQLQVGGERAGVPVYAPHPGVSSEFEAATGDPVQVA
+RDGVAEANTKYHDVVIIDTAGRLGVDAELMQQAADIRAAVDPDEVLFVIDAMIGQDAVAT
+AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMAS
+RILDMGDVLSLIEQAEQNWDRTEAEKMARKFADQEDFTLDDFLAQMQQLKKMGSLKKMLM
+MMPGAQGMRQQLEQFDESSIGRVEAIIHSMTPHERVAPKIINGSRRARIARGSGVSVSEV
+NGLLERFAEAQKMMKRMAAGGGIPGVPGMPGGASRKAKGKGKNAKRDRVKSGNPAKAAAE
+RKAIEERRARAAQAQAGAVFGRDGAGMDGFDPSTLNLPAGFEKYLKDR*
+>NZ_CP040019.1_2000
+MFNSLSDRLTATFRSLKGKGRLTEADIDATAREIRRALLDADVAVPVVRQFIAQIKERAL
+GEEVAQALNPGQQVVKIVNEELVGILGGETRRIRHAKTGTTVIMLVGLQGAGKTTLAGKL
+AHLLKAQGHTPLLVACDLQRPNAVKQLQVGGERAGVPVFAPHPGVSSEFEAATGDPVQVA
+RDGVAEANAKYHDVVIIDTAGRLGVDAELMQQAADVRAAVEPDEVLFVIDAMIGQDAVAT
+AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMAS
+RILDMGDVLSLIEQAEQNWDRSEAEKMAKKFADQEDFTLDDFLNQMQQLKKMGSLKKMLM
+MMPGAQGMRQQLEQFDESSIGRVEAVIHSMTPHERVAPKIINGSRRARIAKGSGVSVSEV
+NGLLERFAEAQKMMKRMAAGGGMPGMPGAPGGVSRKAKGKNAKRNKVKSGNPAKAAAERK
+ALEERQARAAQAQAGAVFGRDGGAGMDGFDPSSLNLPAGFEKYLKDR*
+>NZ_CP083691.1_1895
+MFTSLSDRLTATFRNLKGKGRLTEADIDATAREIRRALLDADVAVPVVRQFIAQIKERAL
+GEEVSQALNPGQQVVKIVNEELVAILGGETRRIQHAKTGTTVIMLVGLQGAGKTTLAGKL
+AHLLKSQGHTPLLVACDLQRPNAVKQLQVNGERAGVPVFAPHPGVSSEFEAATGDPVQVA
+RAGIDEANTKYHDVVIIDTAGRLGVDAELMQQAADIRAAVQPDEVLFVIDAMIGQDAVAT
+AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMAS
+RILDMGDVLSLIEQAEQNWDRAEAEKMAKKFADQEDFTFDDFLTQMQQLKKMGSMKKLLG
+MMPGAQGMRQQLEQFDESSIGRVEAIIHSMTPHERVAPKIINGSRRARIAKGSGVQVTEV
+NALLERFAEAQKMMKKLAGGGVPGMPGMGPGPGRKSKGRNAKKTKVKSGNPAKAAAERRA
+LEERRSRPAAGGVFGQGGTMPDMTDFDPSQLNLPAGFEKYLKDR*
+>NZ_CP097650.1_821
+MFNSLSDRLTATFRSLKGKGRLSEADIDATAREIRRALLDADVAVPVVRQFIAQIKERAL
+GAEVAQALNPGQQVVKIVNEELVGILGGETRRIQHAKTGTTVIMLVGLQGAGKTTLAGKL
+AHLLKSQGHTPLLVACDLQRPNAVKQLQVGGERAGVPVYAPHPGVSSEFEAATGDPVQVA
+RDGVAEANTKYHDVVIIDTAGRLGVDAELMQQAADIRAAVDPDEVLFVIDAMIGQDAVAT
+AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMAS
+RILDMGDVLSLIEQAEQNWDRSEAEKMARKFADQEDFTLDDFLAQMQQLKKMGSLKKMLM
+MMPGAQGMRQQLEQFDESSIGRVEAIIHSMTPHERVAPKIINGSRRARIARGSGVSVSEV
+NGLLERFAEAQKMMKRMAAGGGIPGMPGMPGGASRKAKGKGKNAKRDRVKSGNPAKAAAE
+RKAIEERRARAAQAQAGAVFGRDGAGMDGFDPSTLNLPAGFEKYLKDR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000788.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000788.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c783fcd1ba9e86d77bada9e1329d94949abcb2a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000788.fa
@@ -0,0 +1,29 @@
+>NZ_CP042169.1_880
+MRTSEPRDPRRSRGSVASGAGSSPGTTAAPASGASRWWAWLGLTVVAAVVVAAVLRALTG
+PVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLHHGDVVVFDGAGSLAPYRSAGSLERGLE
+DVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLREGEPLDEPYLGRPVTADEPAAA
+GTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRGTVD
+APSGDTP*
+>NZ_CP033200.1_608
+MRTSEPRDPRRSRGSVASGAGSSSGPTAAPASGTSRWWAWLGLTVVAAVVVAAVLRALTG
+PVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLHHGDVVVFDGAGSLAPYRSAGSLERGLE
+DVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLRNGEPLDEPYLGRPVTADEPAAA
+GTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRGTMD
+APSGDTP*
+>NZ_CP040019.1_1994
+MSHPEPRDPRRSRGSAVSRSVAPGSGRGTTPARGSGGTAWWAWIGLTVAAAVGAAAVLRA
+LTGPVYLIPSGSMEPTLHPGDRVRVDASAAGGEGVRRGDVVVFDGAGSLAPYRSVGSLER
+GLEDVARSWGLGASGDAFVKRVLALPGDRLECCAPDGRLLRDGAPVDEPYLGRPVTAQDP
+AADGSWTFEVPEGRMVVLGDNRSASRDSRALLGGAGGGLIPLKRVEGRAAEVVWPLDRRG
+PVDASAPEAAPGAAP*
+>NZ_CP083691.1_1889
+MRAQEPRDRNRSRGSRASGEAGRPWWALVLLTLAGAVVAAALLRAFTGPVYLVPSGSMEP
+TLLPGDRVHVDTAAADGAGLEHGDVVVFDGAGSLAPYRSRTALDRGLEDVAAFWGVGAAQ
+DVYVKRVLALPGDTLSCCTADGRLERNGAPLDESYLGRTVDAAAPASRSTWAFEVPEGRM
+VVLGDNRDVSRDSRALLGAPGGGLIPVEKVIGRVDSVAWPLDRRGDVPAGAQDGSRG*
+>NZ_CP097650.1_827
+MRTSEPRDPRRSRGSVASGAGSSSGPTAAPASGTSRWWAWLGLTVVAAVVVAAVLRALTG
+PVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLQRGDVVVFDGAGSLAPYRSAGSLERGLE
+DVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLREGEPLDEPYLGRPVTADEPAAA
+GTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRGTVD
+APSGDTP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000789.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000789.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b0e500a2d01d83a1f627599cc15fec63d578e9f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000789.fa
@@ -0,0 +1,26 @@
+>NZ_CP042169.1_881
+MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR
+GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ
+EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG
+TDPDAFATVPDAPAPEART*
+>NZ_CP033200.1_609
+MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR
+GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ
+EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG
+TDPDAFATVPDAPAPEART*
+>NZ_CP040019.1_1993
+MSRPDHRLVPPAAGHAHDSGAAPADDAARPAGPTGALLGHAVPSGAGSQALPAEPGRGPL
+RAVLAVVVLTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPEPYPVRRGDVV
+VFDDTKGWLADGGHVIKRVVGLPGDTVSFTPGEAALRVNGVPVAEPYLAPGDAPAQDAFE
+ATVPAGRLWVLGDHRSASADSRAHRDGPGGGFVSLDDVVGRARFVVWPLDRIGGAGAAPE
+AFEAVPDARGAGS*
+>NZ_CP083691.1_1888
+MAEAPVTPAAAGTADPAAAPAAEHPGHPLRAAAVTVAVTLALLLAVQLLLVRMFAIPSAS
+MEPTLRPGDRVAVDLLVPGPLELRRGDVVVFRDARGWLAGAEAVHADPLHAAVAALGLGT
+QEGHLVKRVVGLPGDRVRWSPEDARLEVNGVPVDEPYVAGPAAQEAFDVVVPDGGLWVLG
+DHRSASQDSRQHQHGPGGGMVSVDDVVGRVEGVVWPLDRAGAVGPGPLAKLP*
+>NZ_CP097650.1_828
+MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR
+GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ
+EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG
+TDPDAFATVPDAPAPEART*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000791.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000791.fa
new file mode 100644
index 0000000000000000000000000000000000000000..887b122f2db4ca7c3d64d758fca08a664cdbaa37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000791.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_883
+MSADDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQADGDVFFEIL
+LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPTEDLTVPPDGQLPS*
+>NZ_CP033200.1_611
+MSADDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQADGDVFFEIL
+LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPTEDLTVPPDGQLPS*
+>NZ_CP040019.1_1991
+MSTDDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQSDGDVFFEIL
+LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPRDELQVPPDGQLPD*
+>NZ_CP083691.1_1886
+MSTDDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANAVTLTPHQTDGEVFFELT
+LEDAWVWDVYRTARFIRRVRVLTFKDVNIEELPRDELQVPEDGGLRGDLGR*
+>NZ_CP097650.1_830
+MSADDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQADGDVFFEIL
+LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPTEDLTVPPDGQLPS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000792.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000792.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c33db652aebf6cd0de966429110eb12688e85a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000792.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_884
+MTGTAEQVGAQPPGERRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGELDIVA
+HHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVRAHAADRRGTPWRVDAVA
+VLVPRTGGIRFDLLQDVRP*
+>NZ_CP033200.1_612
+MTGTAERIGAQPPGDRRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGELDIVA
+HHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVRAHAADRRGTPWRVDAVA
+VLVPRTGGIRFDLLQDVRP*
+>NZ_CP040019.1_1990
+MTGTAEKVGADSPGGGRGSRAHTALGRFGEDAAARWLADRGYVIADRNWRGEAGELDLVA
+HHAGWWVGVEVKTRSGLAFGDPLESIDRRKLLRLHRLTAAWVRAHGEGRRAERWRVDAVA
+VLVPRTGGIRFDLLQDVRP*
+>NZ_CP083691.1_1885
+MVPLDTTTTTPAARRGSTAHTALGRYGEDAAARWLAERGYQIVARNWRGEDGELDLVARH
+GPWWVGVEVKTRSGLAYGDPLEAIGRRKLLRLHRLTAAWVREAAAREGRPLRSQQWRVDA
+VAVLVPRTGGVHFDLVQDVRP*
+>NZ_CP097650.1_831
+MTGTAEQVGAQPPGERRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGELDIVA
+HHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVRAHAADRRGTPWRVDAVA
+VLVPRTGGIRFDLLQDVRP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000793.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000793.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b2f5afd263dacb59b260d727c75608c5ae6a2f43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000793.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_885
+MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE
+TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA
+RRQVTAPEPEPTRAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG
+ILPPLDRRTALECAALRSLRGGDARVRRRGGTSQGFDGEIDRTPPFEAPHHSASRSALVG
+GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ
+LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP
+ASETTSQVAVRVAAAADRQARRWATAAERGVVPPGLRRNAHVPAGVLRHGPYAVPRAARR
+PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA*
+>NZ_CP033200.1_613
+MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE
+TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA
+RRQVTAPEPEPARAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG
+ILPPLDRRTALECAALRSLRGGDARVRRRGGTAQGFDGDIDRTPPFEAPHHSASRSALVG
+GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ
+LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP
+ASETTSQVAARVAAAADRQARRWATAAERGLAPSGLRRNAHVPAGVLRHGPYAVPRAARR
+PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA*
+>NZ_CP040019.1_1989
+MSGIGRTRSISLSGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGAGHDLAIVLAAYAADGRVRGVEGPVFLAELGLDGALHRSPE
+TVAMVMASVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVILAFGGEPEGEAPQRRP
+VRPADDDGAPGLGPGAPDLSEVAGQAEARFALEVAAAGAHHLLLRGAPGAGKTMLAERLP
+GILPPLDRRTALECAALRSLRGADALARRGVGQGSAGTRAAGDLDRTPPFEAPHHSASMA
+ALVGGGANLARPGAVSLAHGGVLFLDEAPEFERRALESLRQPLESGEVLLHRARGTVAYP
+ARFQLVLAANPCPCGKGGGNGVECRCSVTERRRYGQRLSGPLLDRVDLQVTVRPVQARQL
+AGAPAAETSAQVAARVAEAARRQAERWARAAEEGLVAPGLRRNAHAPAGVLRHGPYAVPR
+AARRAADEAVDHGLLSARGHARVLRLAWTLADLRGAETPAPEDTDVALTLRHQEEDET*
+>NZ_CP083691.1_1884
+MSGIGRTRSISLTGLRGTVVDVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGAAHDLAIVLAAYAADGRVQGVDGPVFLAELGLDGTLHRAPE
+TVAMVMAAVDAGHDRVVVAADAVAEAELVPGARVRGFAHLHEAILAFGGRPDASVARPSG
+PSGTAGRGPAAGQEGPSGPVPDLAEVAGQAEARFALEVAAAGGHHLLLSGPPGAGKTMLA
+ERLPGILPPLDDRTALETAALRSLRGLEPSARGLRRTPPFEAPHHSASMAALVGGGTGLG
+RPGAVSLAHGGVLFLDEAPEFERRALDALRQPLESGEMIVHRAHGSVAYPARFQLVLAAN
+PCPCGFGSGTGAHCRCTSLQRRKYAARLSGPLLDRVDVQVSVRPVRADQLAAAPEAEPSR
+AVAARVAAAVAAQDARWAAAAREGSLPPGVCRNAHVPAALLRSGRFAVPPEARATADRAV
+DRGELSARGHGRVLRLAWTLADLRGASCPEAQDVEIALQLRIRSEEDR*
+>NZ_CP097650.1_832
+MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE
+TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA
+RRQVTAPEPEPTRAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG
+ILPPLDRRTALECAALRSLRGGDARVRRRGGTSQGFDGEIDRTPPFEAPHHSASRSALVG
+GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ
+LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP
+ASETTSQVAVRVAAAADRQARRWATAAERGVVPPGLRRNAHVPAGVLRHGPYAVPRAARR
+PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000794.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000794.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fda9bb7de00be81584473d2cd18fe32b40bbf653
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000794.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_886
+MTTHVTPAADHVAGPRRPDAARLARAALTRLVEPGDALAVQTVTALGPERALALLTGRET
+IQPAERDLLADLAGAPDTLPRRWAAGLARWAPRAARLEPERDLVTLHRLGGGLLIPEDDA
+WPAALADLGEEAPLGLWFRGSGTLPPADRMLAVVGSREATAYGRTVTARCAAHAVQQGAC
+VISGGAYGIDGAAHRAALQAPAAPEDAADRDGVPPTVAVLAGGLDRFYPAGHEDLLRAVM
+AAGLLVSEMPPGASPTRYRFLQRNRVIAALAGAVLVVEARWRSGAQNTAGHAFGLGREVG
+VVPGPVTSPSSAGCHRLLQESPARLVTTEQEALALLGQGPARSGDTGGRTSARAAPEPAA
+RPTDGLTMEEALVHEALPLRQAVPADRITVSAGLALPTVLACLSRLQRAGLAERVEDRWR
+RG*
+>NZ_CP033200.1_614
+MTTYVTPAADHVAGPRRPDAARLARAALTRLLEPGDALAVQTVTALGPERALALLTGRET
+IQPAERDLLADRAGAPDTLPRRWAAGLARWAPRAARLEPERDLVTLHRLGGGLLIPEDDA
+WPAALADLGEEAPLGLWFRGSGTLPPADRMLAVVGSREATAYGRTVTARCAAHAVQQGAC
+VISGGAYGIDGAAHRAALQALAAPGDAADRDGVPPTVAVLAGGLDRFYPAGHEDLLRAVM
+AAGLLVSEMPPGASPTRYRFLQRNRVIAALAGAVLVVEARWRSGAQNTAGHAFGLGREVG
+VVPGPVTSPSSAGCHRLLQESPARLVTTEQEALALLGQAPARSGGAGGRASTRAAPEPAT
+RPTDGLTMEEALVHEALPLRQAVPADRITVSAGLALPTVLACLSRLQRAGLAERVEDRWR
+RG*
+>NZ_CP040019.1_1988
+MTADTAHDHPVAAAQGPDTQRPDAHRPDTQRPDAQRPDTQRPDAARIARAALTRLVEPGD
+ALAVHAVAALGPERALVLLTGREAIQPAERDLLAEHAGAPDTLARRWSAGLDRWAPRAAR
+LDPVRDLVALHRLGGGLLVPEDEAWPAALDDLGEAAPLGLWFRGPGTLPPASRALAVVGS
+REATAYGRAVTTRLAAHAVQQGVCVVSGGAYGIDGAAHRAALAAPVGPEDPDAHDGPGGA
+SDRVPPTVAVLAGGLDRFYPAGHEDLLREVMAAGLLVSEMPPGASPTRYRFLQRNRVIAA
+LAGAVLVVEARWRSGAQNTAGHAFGLGREVGAVPGPVTSPSSAGCHRLLQETPARLVTSE
+TEALALLDGGAPAPRPGGTGGGNTAPPGDAPAPPPGGTGEGTRRPPRPPPPPRPCGSRTG
+*
+>NZ_CP083691.1_1883
+MTTAGETAQNARPDGPRVARAALTRLVEPGDDLALATVAALGPERALTLLTGAARIEAAE
+RDLLADRLGQDAFARRWSAGLARWAPRSARLDPVRDLVALHRLGGGLLIPEDPAWPAGLD
+DLGDAAPVGLWFRGRGTLPPLPRALAVVGSREATAYGRQVTRDVVACASAAGVCIVSGGA
+YGIDGAAHEAALETAAAAGRRSGPGSHDDAAPGVPPTVAVLAGGLDRFYPAGHERLLRAV
+MEEGLLLSEMPPGATPTRYRFLHRNRLIAALSGAVVVVEARWRSGAQNTAGHAHGLGREV
+GAVPGPVTSPSSAGCHRLLQEGPTRLIADPAQALTLLEPPRPGEPPAASPATTTRGEASR
+SPGRPTDGLTVEELLVHEALPLRRAVPVDNLTSSAGLALPTVLAVLTRLEGRRLAERRGD
+LWRRAPE*
+>NZ_CP097650.1_833
+MTTHVTPAADHVAGPRRPDAARLARAALTRLVEPGDALAVQTVTALGPERALALLTGRET
+IQPAERDLLADLAGAPDTLPRRWAAGLARWAPRAARLEPERDLVTLHRLGGGLLIPEDDA
+WPAALADLGEEAPLGLWFRGSGTLPPADRMLAVVGSREATAYGRTVTARCAAHAVQQGAC
+VISGGAYGIDGAAHRAALQALAAPGDAADRDGVPPTVAVLAGGLDRFYPAGHEDLLRAVM
+AAGLLVSEMPPGASPTRYRFLQRNRVIAALAGAVLVVEARWRSGAQNTAGHAFGLGREVG
+VVPGPVTSPSSAGCHRLLQESPARLVTTEQEALALLGQGPARSGGAGGPSSTRAAPEPAA
+RPTDGLTMEEALVHEALPLRQAVPVDRITVSAGLALPTVLACLSRLQRAGLAERVEDRWR
+RG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000796.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000796.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b3302a90bf7afd44ee15a5a527797b46626f22a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000796.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_888
+MTSTHTRGVVHILSAPTALCPHVEWALSSVLGPATSVEWEGQPVAPGQHRAEVHWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNIMVSEDRIRY
+AYEAGAGDPSVLMHELSLALGEAWDDELEPFRLAAAHANVRWLHRAV*
+>NZ_CP033200.1_616
+MTSTHTRGVVHILSAPTALCPHVEWALSSVLGPATSVEWEGQPVAPGQHRAEVHWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNIMVSEDRIRY
+AYEAGAGDPSVLMHELSLALGEAWDDELEPFRLAAAHANVRWLHRAV*
+>NZ_CP040019.1_1985
+MTSTTTRGVVHILSAPTALCPHVEWALSSVLGPETPVEWQGQPVAPGQHRTELRWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNTMVSEDRIRY
+AYEAGAGEPAVLLHELSLALGEAWDEELEPFRLAAADANVRWLHRVG*
+>NZ_CP083691.1_1881
+MPDITTNGVVHLLSAPTAVCPHVEWTLTSVLGPGDPVDWRDQPAEAGTVCAELHWSAAQG
+SGARLASALRRWPGLRFEITETPSAGVDGSRWSHTPELGVFHATTDVSGNIMVSEERIRY
+AYEAGGGDPTVLVHELSLALGEAWDDELEPFRRAAAGAPVRWLHRAG*
+>NZ_CP097650.1_835
+MTSTQTRGVVHILSAPTALCPHVEWALSSVLGPATSVEWEGQPVAPGQHRAEVHWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNIMVSEDRIRY
+AYEAGAGDPSVLMHELSLALGEAWDDELEPFRLAAAHANVRWLHRAV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000798.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000798.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2b76881820e269ae9213a61c8b5ba18db11a24c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000798.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_890
+MASKEEILAGLAEIVNEETGLDTAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDGAQA*
+>NZ_CP033200.1_618
+MASKEEILAGLAEIVNEETGLDAAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDGAQA*
+>NZ_CP040019.1_1983
+MASKEEILAGLAEIVNEETGLDTADVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDNAQA*
+>NZ_CP083691.1_1879
+MASKEEILAGLAEIVNEETGLETADVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDQAQA*
+>NZ_CP097650.1_837
+MASKEEILAGLAEIVNEETGLDTAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDGAQA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000799.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000799.fa
new file mode 100644
index 0000000000000000000000000000000000000000..62c26f57f4d208ba109c033da2d73e70dda838ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000799.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_891
+MTVTLKQHERPAASRIVAVGAYRPANLVPNEDLIGPIDSSDEWIRQRTGIVTRQRATAEE
+TVPVMAVGAAREALERAGLQGSDLDAVIVSTVTFPHATPSAAALVAHEIGATPAPAYDVS
+AACAGYCYGVAQADALVRSGTARHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA
+DEPGISPSVWGSDGERWSTISMTHSQLELRDAVEHARTTGDASAITGAEGMLWPTLRQDG
+PSVFRWAVWSMAKVAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD
+IADAGNTSAASIPLAMHRLLEENPELSGGLALQIGFGAGLVYGAQVVRLP*
+>NZ_CP033200.1_619
+MTVTLKQHERPAASRIVAVGAYRPANLVPNEDLVGPIDSSDEWIRQRTGIVTRQRATAEE
+TVPVMAVGAAREALERAGLQGSDLDAVIVSTVTFPHATPSAAALVAHEIGATPAPAYDVS
+AACAGYCYGVAQADALVRSGTARHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA
+DEPGISPSVWGSDGERWSTISMTHSQLELRDAVEHARTTGDASAITGAEGMLWPTLRQDG
+PSVFRWAVWSMAKVAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD
+IADAGNTSAASIPLAMHRLLEENPELSGGLALQIGFGAGLVYGAQVVRLP*
+>NZ_CP040019.1_1982
+MTVTLKQHERPAASRIVSVGAYRPKNLVPNEDLVGPIDSSDEWIRQRTGIVTRQRATAGE
+TVPAMAVAAGREALERAGLTGADLDAVIVSTVTFPHATPPRPPSWPTSSAPPPAPAFDVS
+AACAGYCYGVAQADALVRAGTAKHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA
+DEPGISPSVWGSDGERWETISFTHSQLELRDVVEQARTSGDASAITGSEEMVWPTLRQDG
+PSVFRWAVWSMAKVAREALDAAGVEPEDLVAFIPHQANMRIIDEFAKQLKLPESVTVARD
+IADAGNTSAASIPLAMHRLLEEDPSLSGGLALQIGFGAGLVYGAQVVRLP*
+>NZ_CP083691.1_1878
+MTVTLKQHERPAGSRIVSVGAYRPATLVPNEDLVGPIDSSDEWIRQRTGIVTRQRATPEE
+TVVTMAVGAGREALQRAGLEASDLGAVVVATVTFPYPTPSAAAAVADALGATPAPAYDIS
+AACAGYCYGVAQADALVRAGSAQHVLVVGVERLSDFIDPTDRSISFLLGDGAGAVVVSAS
+DEAGIAPSVWGSDGSRWSTISPTRSLLDLRAEVEHARETGDASAIIGAEEMLWPTLRQDG
+PSVFRWAVWSMAEKAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD
+IAEAGNTSAASIPLAMHRLLQEHPELSGGLALQIGFGAGLVYGAQVVRLP*
+>NZ_CP097650.1_838
+MTVTLKQHERPAASRIVAVGAYRPANLVPNEDLIGPIDSSDEWIRQRTGIVTRQRATAEE
+TVPVMAVGAAREALERAGLQGSDLDAVIVSTVTFPHATPSAAALVAHEIGATPAPAYDVS
+AACAGYCYGVAQADALVRSGTARHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA
+DEPGISPSVWGSDGERWSTISMTHSRLELRDAVEHARTTGDASAITGAEGMLWPTLRQDG
+PSVFRWAVWSMAKVAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD
+IADAGNTSAASIPLAMHRLLEENPELSGGLALQIGFGAGLVYGAQVVRLP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000804.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000804.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45aa7d5829a425d1e13c2a8c26342002083f7d43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000804.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_896
+MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL
+GWIGALAEDVAVDDVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF
+DVETGRPRRVSVLLDADGVEAARVVAAPGQARTRSEHEAATRDLLADR*
+>NZ_CP033200.1_624
+MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL
+GWIGALAEDVAVDEVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF
+DAETGRPRRVSVLLDADGVEAARVVAAPGQARTRGEHEAATRDLLVDR*
+>NZ_CP040019.1_1977
+MAEEPGAVPALRDDRGQDWPWPPTRGPEDAAAPRATWLVLLPGAFTPVCTGELGWLGELA
+TDLAADDVAVRVIACDAAPVLRRVREELGLPEDLVLLSDFWPHGAACAALDAFDAASGRA
+RRVSVLLDADGVEVSRVTAAPGRPRSRTEHEAATRALLGDR*
+>NZ_CP083691.1_1873
+MAEPALRDIHGTPWPWPPVVSGERAAWLVFLPGAFTPVCAGELAWLGPLAVELAAEDVGL
+RVVSCDAAPVLREVADRTGLPAECVLLSDFWPHGAAAARFGLLDETTGRPRRVSVLVDES
+GTELVRVRPGEPGGPRTAQAHRRAAEGALGRRR*
+>NZ_CP097650.1_843
+MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL
+GWIGALAEDVAVDDVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF
+DVETGRPRRVSVLLDADGVEAARVVAAPGQARTRSEHEAATRDLLADR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000813.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000813.fa
new file mode 100644
index 0000000000000000000000000000000000000000..480a6aef4d12e1ed3f00ec53d1f0b91ddf1b24f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000813.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_905
+MTDFPRTEPLGASGAPADVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGDDPAPSYE
+SVCTGTTGHAEAVRVRFDAAVVPPEVIMDLFFTGHDPTSLNRQGADVGTQYRSAVFAHDE
+AEARFFADEIARAQENYDSPIVTRVEPASAWHPAEDIHQDFYARRRSNGYCRVVIDPKLA
+KVRRNYSAWLVDA*
+>NZ_CP033200.1_633
+MTDSPRTEPLGASDAPADVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGDDPAPSYE
+SVCTGTTGHAEAVRVRFDAAVVPPEVIMDLFFTSHDPTSLNRQGADVGTQYRSAVFAHDE
+AETRFFADEIARAQANYDSPIVTRVEPASAWHPAEDIHQDFYARRRSNGYCRVVIDPKLA
+KVRRNYSAWLVDA*
+>NZ_CP040019.1_1966
+MTDSPRTEPLGASSAPADVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGDDPAPSYE
+SVCTGTTGHAEAVRVRFDAAVVPPEVIMDLFFTGHDPTSLNRQGADVGTQYRSAVFAHDE
+AEARFFADEIARAQANYDSPIVTRVEPASAWHPAEDIHQDFYARRRSDGYCRVVIDPKLA
+KVRRNYSAWLVDA*
+>NZ_CP083691.1_1860
+MSETPETPSTPAAHAPRVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGHTPDPDYEA
+VCTGQTGHAEAVRVRFDEAQVPAEVIMDLFFTGHDPTSLNRQGADVGTQYRSAVFAHDEA
+EADFFRSQLARAQELYEAPIVTTIEPAAAWHPAEWYHQDFYASRPGNGYCRVVIDPKLAA
+VRRRHAAWLTDGA*
+>NZ_CP097650.1_853
+MTDSPRTEPLGASGAPADVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGDDPAPSYE
+SVCTGTTGHAEAVRVRFDAAVVPPEVIMDLFFTGHDPTSLNRQGADVGTQYRSAVFAHDE
+AEARFFADEIARAQANYDSPIVTRVEPASAWHPAEDIHQDFYARRRSNGYCRVVIDPKLA
+KVRRNYSAWLVDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000815.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000815.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ef29fdbc1a6012fc5e97fa57ef02f66f3b13cf9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000815.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_907
+MSEVTAPPAVQARLLELQELDTALDQARAAVHRLQADPEHARLRARAQEFEEALPGLQDA
+ARTADRAGAEATEKAAATRARRDRTRERLETGQGGPKELQAMQHEDDTLTALLDDHEAAA
+LEAMEATDAAESRLSKGHAALERARAEVEARAAEVRREGQAVTQRGRDLIQRRAALAAEF
+PASLLALYEQARERNGGIGAARLVGNRSAAAGTELSPAEVARIRALPPAAVARCPESGAI
+LIRD*
+>NZ_CP033200.1_635
+MSEVTAPPAVQARLLELQELDTALDQARAAVRRLKADPEHARLRARALELEEALPGLEDA
+ARTADRAGAEATEKAAATRARRDRTRERLEAGQGGSKELQAMQHEDDTLTALLDDHEAAA
+LEAMETADAAESRLAKGHAALEQARAEVEARAAEVRREGQAVTQRGRDLIQRRAALAAEF
+PASLLALYEQARERNGGIGAARLVGNRSAAAGTELSPAEVARIRALPPAAVARCPESGAI
+LIRD*
+>NZ_CP040019.1_1964
+MSEVTAPPAVQARLLELQELDTALDQARTQIRRLKADPELARLRARAQELEDALPEVEDA
+ARTADRAGAEASEKAAATRARRDRTRERLEAGQGGSKELQAMQHEDGTLTALLDEHEGAA
+LEAMEAADEAESRLAAARQALEQARAEVDARAAEVRREGQVVTQRGRDLTQRRTALAAVF
+PAPLLALYEKARERNGGIGAARLVGRRSQASGTELSPADVARIEALPPAAVARCPESGAI
+LVRG*
+>NZ_CP083691.1_1858
+MNRVTAPAAEQARLLELQQLDLGIGRAKTRLAQLRADAALADLQKAVAAAEEAAAEQEAH
+ERETDAAAAQASERATTTRARRDRTRAHLDAGDGGSKELTALQHELEGLESLLAEHEGAA
+LAAMEAADEAEEALARARAAVDEARAAVAARADEVRAEGRRVTEEGRELAALRAGLAGRL
+PADLLARYEEARAANAGIGATRLEGRRTGAGTELSPADLDAVLATPADEVAVDPETGILI
+IRA*
+>NZ_CP097650.1_855
+MSEVTAPPAVQARLLELQELDTALDQARAAVRRLKADPEHARLRARAQEFEEALPGLQDA
+ARTADRAGAEATEKAAATRARRDRTRERLETGQGGSKELQAMQHEDDTLTALLDDHEAAA
+LEAMEAADAAESRLAQGHAALERARAEVEARAAEVRREGQAVTQRGRDLIQRRAALAAEF
+PASLLALYEQARERNGGIGAARLVGNRSAAAGTELSPAEVARIRALPPAAVARCPESGAI
+LIRD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000820.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000820.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7739a3a5ab343ddec072f8e10d0d6138de8796dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000820.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_912
+MASIRPVTVYGEPVLHRRAAEVEVIDDEIRELIEDMYVTQEAAHGVGLAAPQVGVGLRIF
+TWTFPDSGDAPNVGHVINPVLTHLDKAPREEPHPDEHTEGCLSVPGLGFPLQRPTRVRLS
+GQRVDGEMFEFEAEGWFARIMQHEYDHLNGTLYVNRLEGKWQRRWKRAQRAERLNVPGVT
+WLPGTDEDPFGHDADDHEDHEHGPDGDHGDDEA*
+>NZ_CP033200.1_640
+MASIRPITVYGEPVLHRRAAEVEVIDDEIRELIEDMYVTQDAAHGVGLAAPQVGVGLRIF
+TWTFPDSGDAPNVGHVINPVLTHLDKAPREDPHPDEHTEGCLSVPGLGFPLQRPTRVRLS
+GQRVDGEMFEFEAEGWFARIMQHEYDHLNGTLYVNRLEGKWQRRWKRAQRAERLNVPGVT
+WLPGTDEDPFGHDADDHEDHEHGPDGDHGDDEA*
+>NZ_CP040019.1_1958
+MASIRPITVYGEPVLHTRAAEVEVIDDEIRRLVEDMYVTQDAARGVGLAAPQVGVGLRVF
+TWTYPHSGDAPSVGHVINPVLTVLDKASQEATDPDEHTEGCLSVPGHGYPLQRAPRVRLA
+GQRVDGEMFEFVAEGWFARVMQHEYDHLNGTLYVNRLEGRWQRRWKRAQRAERMNVPGVT
+WLPGTDEDPFGHDELDEAEAIEQHGPDADHGRADGA*
+>NZ_CP083691.1_1852
+MPSIRPITVYGEPVLHTRAAEVEVIDDSIRELVEDMYVTQDVANGVGLAAPQVGVGLRVF
+TWTFQDTGDAPNLGHVINPVLTMLSKPSTEEPDRHEDTEGCLSVPGHGFPLKRSAHVRMT
+GQRMDGSTVDIEATGWFARILQHEYDHLNGTLYVNRLEGKWARRWKRAQRAERLNVPGVT
+WLPGTDPDPFGHDVDVDEDAPAHEHHDHDHEGHDHAQEAR*
+>NZ_CP097650.1_861
+MASIRPITVYGEPVLHRRAAEVEVIDDEIRELIEDMYVTQEAAHGVGLAAPQVGVGLRIF
+TWTFPDSGDAPNVGHVINPVLTHLDKAPREDPHPDEHTEGCLSVPGLGFPLQRPTRVRLS
+GQRVDGEMFEFEAEGWFARIMQHEYDHLNGTLYVNRLEGKWQRRWKRAQRAERLNVPGVT
+WLPGTDEDPFGHEEIEDHEH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000821.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000821.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa0b739568f8fc9647ac92ac3ed6cf8881de17bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000821.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_916
+MSVVKINAISVPEGAGPELEKRFAARKHAVDQEPGFEGFQLLRPTAGEDRYFVVTTWASE
+EDFRRWRDGRMPAAHAAEQGGRPAPVATGADLLEFEVVDLG*
+>NZ_CP033200.1_644
+MSVVKINAISVPEGAGPELEKRFAARKHAVDQEPGFEGFQLLRPTAGEDRYFVVTTWASE
+EDFQRWRDGRMPAAHAAEQGGRPAPVATGADLLEFEVVDLG*
+>NZ_CP040019.1_1953
+MSVVKINAITVPEGAGPELEKRFAVRKHAVDAEPGFEGFQLLRPTAGEDRYFVVTTWATE
+EDFQNWKGGRMPAAHAAESEGRPAPVATGAELLEFEVVDLD*
+>NZ_CP083691.1_1851
+MSVVKINAISVPEGAGPELEKRFAVRKHAVDQEPGFEGFQLLRPTAGEDRYFVVTTWASE
+EDFQRWRDGRMPAAHADEQGGRPTPVATGADLLELEVVDLG*
+>NZ_CP097650.1_863
+MSVVKINAISVPEGAGPELEKRFAARKHAVDQEPGFKGFQLLRPTAGEDRYFVVTTWASE
+EDFQRWRDGRMPAAHAAEQGGRPAPVATGADLLEFEVVDLG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000822.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000822.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a5d2c0dbd8ff597b48eab453104a3e3420fe2e49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000822.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_924
+MSETSTPTPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNILDEGIDLVIRPSAAA
+LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF
+LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY
+RAAVMAPAPGPTTEEARAIAEVVSGAQA*
+>NZ_CP033200.1_647
+MSETSTPAPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNTLDEGIDLVIRPSAAA
+LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF
+LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY
+RAAVMAPAPGPTTEEARAIAEVVSGAQA*
+>NZ_CP040019.1_1895
+MSETSTPAPENAPLVWIDCEMTGLHPHVDELVEVAVLITDAELNILDEGIDLVIRPSEAA
+LAQMDPFVRDMHTTSGLLPELEHGLTLENATARVMEYLTARVPAGKALLAGNTVGQDKLF
+LSAYMPAVVEHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIRDSITELRYY
+RAAVMAPSPGPTSEEAQAIARVVAEAQA*
+>NZ_CP083691.1_1844
+MSETSTPAPESAPLVWIDCEMTGLDPDVDVLVEVAVLITDSELNVLDEGLDLVIRPTPEA
+LAQMDPFVRDMHTSSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNSVGQDKLF
+LARYMPAVIDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIRDSITELRYY
+REAVMVPAPGPTSEEARAIAEVVSGAQA*
+>NZ_CP097650.1_869
+MSETSTPTPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNILDEGIDLVIRPSEAA
+LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF
+LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY
+RAAVMAPAPGPTTEEARAIAQVVSGAQA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000825.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000825.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb673a86931eeb7a6e7c4625731bcea55e5a4e81
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000825.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_928
+MTRREGVQLAALLVAAAALYVTHSFLRYATYEAKGYDLGIFDQVVRQYALFNAPLSSVKG
+VDFHILGDHFHPILALLAPFYWVWPDPRMLGVVMALALAASAVPVYLFARRRAGHGVALA
+AVAALLLSWPFQAMVNWDFHEVTLGVPILAWLVWALDGQRAWLATGLAALLLTVREDMGV
+TLLAVALVMAIRRFWPQAAVTAVLGVLGYWFATSVVIPHYSPTGAFGYWQFTALGPDMRS
+SVLFLLTQPWNAVAVLFDHPLKVALWLLHFVPLLFLPVLSPLTLMALPILLSRLFNDRLN
+VWAPVYQYDAILAPLLLMAALEAAHRLAGRRDTLRRLPAVLVSAALAAGLIGTAFFPQVY
+PLHRTIAGDMTMTQHARDLDHAVGLIPDGVCVEAADNAVPHLTARTHVGLHGDIGDELAT
+WMIVDTSVPELGGWDPLTPEQALARAERLGFERVWSAGDVVVLHHPDRAVSPTCTTYLEH
+R*
+>NZ_CP033200.1_651
+MTRREGVQLAALLVAAAALYVTHSFLRYATYEAKGYDLGIFDQVVRQYALFNAPLSSVKG
+VDFHILGDHFHPILALLAPFYWVWPDPRMLGVVMALALAASAVPVYLFARRRTGHGVALA
+AVAALLLSWPFQAMVNWDFHEVTLGVPILAWLVWALDGQRAWLATGLAALLLTVREDMGV
+TLLAVALVMAIRRFWPQAAVTAVLGVLGYWFATSVVIPHYSPTGAFGYWQFTALGPDMRS
+SVLFLLTQPWNAVAVLFDHPLKVALWLLHFVPLLFLPVLSPLTLMALPILLSRLFNDRLN
+VWAPVYQYDAILAPLLLMAALEAAHRLAGRRDALRRLPAVLVSTALAAGLIGTAFFPQVY
+PLHRTIVGDMTMTQHARDLDHAVALIPDGVCVEAADNAVPHLTARTYVGLHGDIGDELAT
+WMIVDTSVPELGGWDPLTPEQALARAERLGFERVWSAGDVVVLHHPDRAVSPTCTTYLEH
+R*
+>NZ_CP040019.1_1892
+MTRREGLHLGILLALASALAIVHSFLRYGIYEAKGYDLGIFDQVVRQYALFNAPLSSVKG
+VDFNILGDHFHPILALLAPFYWIWPDPRMLGIVMALALAAAAVPVYLFTRRRTGHAVSLV
+AVAALMLSWPFQAMVNWDFHEVTLGVPLMAWLVWALDGQRPWLATVLAAVLLTVREDMGV
+TLIAVALVMALRRFWPQAALVAVLGVLGYWFATSVVIPHYSPTGDFGYWQFQALGPDMGS
+SILTILTRPWEAAAALVDHPLKAALWLLHLVPLLFLPLLSPLTLMALPILLSRLWNDRLN
+VWAPVYQYDAILAPLLLMAALEGAVRLSDLLARRRRPRPAGTGAGSHASPPTRRLPAVVA
+STALATGLVGTAFFPQVFPYHRTLTGDMTMTQHARDLDHAVSLIPDGVCVEAADNAVPHL
+TARTYVGLHGDIGDELATWMIVDTSVAELGGWDPLTPDQALDRAERLGFETVWERGDVVV
+LRHPDRAVSPTCTQYLQHR*
+>NZ_CP083691.1_1840
+MPARRFPGQDRVRTWLHAPRPAVPAVAVTRRQGLHLGLVLLAFAALSITHSFLRFATYEA
+KGYDLGIFDQVVRQYALFNAPLSSVKGVDFNILGDHFHPILALLAPTYWIWPDPRMLGII
+MALALCAAAVAVYLTARRRVSHGWSLAAAGVVLFSWPFQAMVNWDFHEVTLGVPIMAWLV
+WALDGERPWLALGLGTALLTVREDMGVTVCALAVVFALRRRWVQAGLALVLGLAGYWFAT
+SVAIPHFSPTGGFGYWQFQALGPDMGSSLLTILTRPWEAVAALFDHPLKLALWLLHLVPL
+LFLPVLSPLTLLALPILLSRLWNDRLNVWAPVYQYDAILAPILLLAALEAATGLAARFPR
+VRRLPQVLLAWAGAVTLAGTAFLPQVFPFHRTLTGQMTTTQHARDLDQAVGMIPDGVCVE
+AADNAVPHLTDRTHVGLHGDIGDDLATWMIVDTSVTELGGWDPLTPDQALERARRLGFER
+VWSQGDVVVLHHPTRPVSATCTDYLRHR*
+>NZ_CP097650.1_873
+MTRREGVQLAALLVAAAALYVTHSFLRYATYEAKGYDLGIFDQVVRQYALFNAPLSSVKG
+VDFHILGDHFHPILALLAPFYWVWPDPRMLGVVMALALAASAVPVYLFARRRTGHGVALA
+AVAALLLSWPFQAMVNWDFHEVTLGVPILAWLVWALDGQRAWLATGLAALLLTVREDMGV
+TLLAVALVMAIRRFWPQAAVTAVLGVLGYWFATSVVIPHYSPTGAFGYWQFTALGPDMRS
+SVLFLLTQPWNAVAVLFDHPLKVALWLLHFVPLLFLPVLSPLTLMALPILLSRLFNDRLN
+VWAPVYQYDAILAPLLLMAALEAAHRLAGRRDTLRRLPAVLVSTALAAGLIGTAFFPQVY
+PLHRTIVGDMTMTQHARDLDHAVALIPDGVCVEAADNAVPHLTARTHVGLHGDIGDELAT
+WMIVDTSVPELGGWDPLTPEQALARAERLGFERVWSARDVVVLHHPDRAVSPTCTTYLEH
+R*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000827.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000827.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ab65fbb0f2436d81e74a5ddf2617f871f905787
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000827.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_930
+MAEFIYTMVKARKKVGDKLILDDVTMSFYPGAKIGMVGPNGAGKSTILKIMAGLDEPSNG
+EARLSPGYSVGILMQEPKLDESKTVLENVQEGVGEIYGKIQRYNQISEEMANPDADFDAL
+MGEMGELQSAIDAADAWDIDSQLEQAMDALRTPPGDEPVTNLSGGEKRRVALCKLLLEKP
+DLLLLDEPTNHLDAESVLWLEQHLASYPGAVIAVTHDRYFLDHVAEWIAEVDRGRLYPYE
+GNYSTYLETKRARLEVQGKKDAKLAKRLAEELDWVRSNTKGRQAKSKARLARYEEMAAEA
+EKTRKLDFEEIQIPPGPRLGTVVIEAKDLKKGFGDRVLIDGLSFSLPRNGIVGVIGPNGV
+GKTTLFKTIVGLEPLDGGELKIGETVKISYVDQSRSNIDPEKSLWEVVSDGLDYIKVGNV
+EMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLLLDEPTNDLDVETL
+TSLENALLEFPGCAVVVSHDRWFLDRVATHMLAYEGTAEDPANWYWYEGNFESYEANKVD
+RLGPEAARPHRMTHRKLTRD*
+>NZ_CP033200.1_653
+MAEFIYTMVKARKKVGDKLILDDVTMSFYPGAKIGMVGPNGAGKSTILKIMAGLDEPSNG
+EARLSPGYSVGILMQEPKLDESKTVLENVQEGVGEIYGKIQRYNQISEEMANPDADFDAL
+MEEMGELQSAIDAADAWDIDSQLEQAMDALRTPPGDEPVTNLSGGEKRRVALCKLLLEKP
+DLLLLDEPTNHLDAESVLWLEQHLASYPGAVIAVTHDRYFLDHVAEWIAEVDRGRLYPYE
+GNYSTYLETKRARLEVQGKKDAKLAKRLAEELDWVRSNTKGRQAKSKARLARYEEMAAEA
+EKTRKLDFEEIQIPPGPRLGTVVIEAKDLKKGFGDRVLIDGLSFSLPRNGIVGVIGPNGV
+GKTTLFKTIVGLEPLDGGELKIGETVKISYVDQSRSNIDPEKSLWEVVSDGLDYIKVGNV
+EMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLLLDEPTNDLDVETL
+TSLENALLEFPGCAVVVSHDRWFLDRVATHMLAYEGTAEDPANWYWYEGNFESYEANKVD
+RLGPEAARPHRMTHRKLTRD*
+>NZ_CP040019.1_1890
+MAEFIYTMVKARKKVGDKLILDDVTMSFYPGAKIGMVGPNGAGKSTILKIMAGLDEPSNG
+EARLSPEYTVGILMQEPKLDESKTVLENVQEGVGEIYGKIQRYNQISEEMASPDADFDAL
+MEEMGELQTAIDAADAWDIDSQLEQAMDALRTPPGDEPVTNLSGGEKRRVALCKLLLEKP
+DLLLLDEPTNHLDAESVLWLEQHLAAYPGAVIAVTHDRYFLDHVAEWIAEVDRGRLHAYE
+GNYSTYLETKRARLEVQGKKDAKLAKRLAEELDWVRSNTKGRQAKSKARLARYEEMAAEA
+EKTRKLDFEEIQIPPGPRLGTVVIEAKDLKKGFGDRVLIEGLSFSLPRNGIVGVIGPNGV
+GKSTLFKTIVGLEPLDGGELKIGETVKISYVDQSRANIDPEKSLWEVVSDGLDYIKVGQV
+EMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLLLDEPTNDLDVETL
+TSLENALLEFPGCAVVVSHDRWFLDRVATHMLAYEGTAEDPANWYWYEGNFESYEANKVE
+RLGPEAARPHRVTHRKLTRD*
+>NZ_CP083691.1_1838
+MSRFPPPPTSLERMAEFIYTMVKARKKVGDKLILDDVTMSFFPGAKIGMVGPNGAGKSTI
+LKIMAGLDEPSNGEARLSPGYSVGILLQEPKLDEDKTVLENVQQGVGEIYGKIQRYNAIS
+EEMADPDADFDALMEEMGQLQTEIDAADAWDLDSQLDQAMDALRCPPPEAQVSHLSGGEK
+RRVALCALLLSKPDLLLLDEPTNHLDAESVLWLEQHLSSYPGAVVAVTHDRYFLDHVAGW
+ICEVDRGRLYPYEGNYSTYLETKRQRLEIQGKKDAKLAKRLAEELDWVRSNAKGRQAKSK
+ARLARYEEMAAEAEKTRKLDFEEIQIPPGPRLGNVVIEATNLQKGFDGRTLIDGLSFSLP
+RNGIVGVIGPNGVGKTTLFKTIVGLEPLDGGDLKIGETVKISYVDQNRTNIDPEKSLWEV
+VSDGLDYIKVGNVEMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLL
+LDEPTNDLDVETLTSLENALLEFPGCAVVVSHDRWFLDRTATHMLAYEGTEENPANWYWY
+EGNFESYEANKVERLGPEAARPHRVTHRKLTRD*
+>NZ_CP097650.1_875
+MAEFIYTMVKARKKVGDKLILDDVTMSFYPGAKIGMVGPNGAGKSTILKIMAGLDEPSNG
+EARLSPGYSVGILMQEPKLDESKTVLENVQEGVGEIYGKIQRYNQISEEMANPDADFDAL
+MEEMGELQSAIDAADAWDIDSQLEQAMDALRTPPGDEPVTNLSGGEKRRVALCKLLLEKP
+DLLLLDEPTNHLDAESVLWLEQHLASYPGAVIAVTHDRYFLDHVAEWIAEVDRGRLYPYE
+GNYSTYLETKRARLEVQGKKDAKLAKRLADELDWVRSNTKGRQAKSKARLARYEEMAAEA
+EKTRKLDFEEIQIPPGPRLGTVVIEAKDLKKGFGDRVLIDGLSFSLPRNGIVGVIGPNGV
+GKTTLFKTIVGLEPLDGGELKIGETVKISYVDQSRSNIDPEKSLWEVVSDGLDYIKVGNV
+EMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLLLDEPTNDLDVETL
+TSLENALLEFPGCAVVVSHDRWFLDRVATHMLAYEGTAEDPANWYWYEGNFESYEANKVD
+RLGPEAARPHRMTHRKLTRD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000830.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000830.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fdeea3ff3dd0ee72bf0df810a74a25d21699a5ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000830.fa
@@ -0,0 +1,80 @@
+>NZ_CP042169.1_934
+MTTAAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI
+DFVAEQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVAN
+EENPQGVDAAVWEFKPTPRIPSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH
+LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTGAWT
+TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MVGVRAYIAKHAWQNTELPDLMTELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLIRTERFELDVAGEVTEVV
+EAAARRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG
+EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA
+EAEDGSDNQLQFVKAFALHARTTAQLDRLSALVDGTRTVPGLDLTTDLRWELLTALVAAG
+RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAVWDRVMAGELSNTEQRQALIGF
+ARVHDAALIAPFADAYFEGVEAMWDSRSHEMAETAATLGYPTAQVTPEIADRATALSERL
+ADTRAGLSRVLAEGRDETIRALAAREHATAHVHQVHAGA*
+>NZ_CP033200.1_657
+MTTAAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI
+DFVAGQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEDSRRTLGVVAN
+EENLQGVDAAVWEFTPTPRISSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH
+LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTSAWT
+TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIAQHAWGNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA
+EAVGRRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG
+EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA
+EAEDGSDNQLQFVKAFALHARTTAQLDRLAALVDGTRTVPGLDLTTDLRWELLTALVAAG
+RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAAWDRVMAGELSNTEQRQALIGF
+ARVHDAALIAPFADSYFEGVEAMWDSRSHEMAETAATLGYPTSQVSRETADRATALSERL
+ADTRAGLSRVLAEGRDETVRALAAREHATAHVHQVHAGA*
+>NZ_CP040019.1_1885
+MSSSARLNITREEAAQRAAALTVDAYEVSLDLTRGPERFRTASTVTFAASEDAVGTHTWI
+DFVASQAPEVTLNGERVAVEDYDGARLPIGPLAAQNTLVVEGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVEN
+EDQLSGVDAAVWEFVPTPRISSYITALVAGPYAAVHSELTSADGRTIPLGVYCRASLVEH
+LDADNVFELTRQGFEFFEAQYGHPYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEAMVERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTRYTGSWT
+TFSSMEKNWAYRQDQLSSTHPIKAQIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIAKHAWSNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGV
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA
+EAAGRRRPALILPNDDDLAYAKLRLDHASWEAASTRLKDVDSSLARTLLWGAAWDAVRDG
+EASAAWFADLILANIGHEQDSSVVQTLLRQLATSLGQYLPEEQSTAARAAVADRLWGLVA
+GAEDGSDSQLQFVKAFALHARTAAQLDRLAGVVDGTHTVPGLDLTTDLRWELLTALVAAG
+RAGEAEIAAAEREDATATGALAAIQARAAVPTAEAKQAAWDRVMAGELSNTEQRQALIGF
+ARAHEAALLAPFADAYFEGVEAMWDSRSHEMAETAAVLGYPAAQVSDETAQRATALSEKT
+AGTRAGLSRVLAEGRDETVRALAAREHAAAHVHEVSASA*
+>NZ_CP083691.1_1830
+MTTAAAMNITREEAAARAAALTVESYQVALDLTRGAERFGSTTTVTFSAADEAVGTQTWI
+DFMATQAPEVTLNGQAVDVADFDGARLPIGPLAAENTLVVDGLADYTTTGEGLHRFVDPV
+DDEVYLYSQFEVPDSRRMFAVFEQPDLKATFAFTVTAPAHWAVVSNQPEAAHRTLGVVET
+PEAPEGVDAAVWEFTPTPRISSYITALVAGPYKSVHSELTSADGRTVPLGVYCRGSLFEH
+LDADEVFDLTRRGFEFFEAQYGHPYPFDKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VTDAVRERRAITILHELAHMWFGDLVTMKWWNDLWLNESFAEFMSTLAAAENTRYEGAWT
+TFSSMEKNWAYRQDQLSSTHPITAEIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIEKNAWSNTELPDLMTELEAASGRDLSEWTRLWLETSGVNTLAVQVDADYAGT
+ITSLRLHQSAPDGSPAAPGDDVLRPHRIAVGFYDLDEATGRLTRTERFELDAAGEVTEVA
+EAAGRRRPALILPNDDDLAYAKIRLDDASWETAGARLADVDSSLARTLLWGAAWDTVRDG
+EASAAWFVDLILTNIGREQDSTVIQTLLRQLATAISQYLPEERSAQVRADAANRLWMLVE
+QAEPGSDAQLQFVKAFALHAREEGQLTALADVWDRSSELPGLDLTTDLRWELLTALVAAG
+RAGETEIAAAETEDPTATGALAAALARAAVPTAEAKQTAWDQVVAGTLSNTTQRQVLLGF
+QRAHDPALLAPFTDAFFGSIQDVWGSRSHEMAETVAVLGFPSSQVCQEVVDRATALSDEV
+RGTNAGLARTLAESRDEMARALKARAAA*
+>NZ_CP097650.1_879
+MTTVAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI
+DFVAEQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVAN
+EENPQGVDAAVWEFKPTPRIPSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH
+LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTSAWT
+TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIAQHAWGNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA
+EAVGRRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG
+EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA
+EAEDGSDNQLQFVKAFALHARTTAQLDRLAALVDGTRTVPGLDLTTDLRWELLTALVAAS
+RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAAWDRVMAGELSNTEQRQALIGF
+ARVHDAALIAPFADSYFEGVEAMWDSRSHEMAETAATLGYPTAQVTREIADRATALSERL
+AGTRAGLSRVLAEGRDETVRALAAREHATAHVHQVHAGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000831.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000831.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed8a5196258a8fb712d85511fa64d18735a2c438
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000831.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_938
+MRVHIATDHAGMELSAHLVEHLTTAGYEMVDHGPTEYDAQDDYPGFCINAARAVVADREQ
+GLDSLGIVLGGSGNGEQIAANKVAGVRAALAWNLDTARLARAHNDANVVAVGGRQHSLEE
+ATELIEAFLAEPFSQDERHVRRIGKIAHYETTGEVLM*
+>NZ_CP033200.1_661
+MRVHIATDHAGMELSAHLVEHLTAAGYEMVDHGPTEYDPQDDYPGFCINAARAVVADREQ
+GLDSLGIVLGGSGNGEQIAANKVVGVRAALAWNLDTARLARQHNDANVVAVGGRQHSLEE
+ATELIEAFLTEPFSQDERHVRRIAKIAHYETTGEVLM*
+>NZ_CP040019.1_1884
+MRVHIATDHAGMELSAHLVEHLRGKGYEMVDHGPEEYDALDDYPGFCINAARAVVADREK
+GLDSLGIVLGGSGNGEQIAANKVAGVRAALAWNLDTAKLAREHNDANVVAVGGRQHSLEE
+ATAIIEAFLAEPFSEDERHVRRIGKIAQYEQTGEVVM*
+>NZ_CP083691.1_1829
+MRVHIATDHAGMELSAHLVEHLTAAGYEMVDHGPTEYDAQDDYPGFCINAARAVVADREQ
+GLDSLGIVLGGSGNGEQIAANKVAGVRAALAWNLDTAKLAREHNDANVVAVGGRQHSLEE
+ATAIIEAFLAEPFSEDERHVRRIGKIAHYEQTGEVVM*
+>NZ_CP097650.1_880
+MRVHIATDHAGMELSAHLVEHLTAAGYEMVDHGPTEYDAQDDYPGFCINAARAVVADREQ
+GLDSLGIVLGGSGNGEQIAANKVAGVRAALAWNLDTARLARAHNDANVVAVGGRQHSLEE
+ATELIEAFLAEPFSQDERHVRRIGKIAHYETTGEVLM*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000832.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000832.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0bb8bac9cf36d16ced17e66e0d3f0ee7fe882ba3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000832.fa
@@ -0,0 +1,34 @@
+>NZ_CP042169.1_939
+MPEGHSVHRLARQFTDVFGGRRIRATSPQGRFAEGAALLDGQVLKRARAHGKHFFADVSG
+GHVLHVHLGMYGAWTFGGDQDFAAASSIGAPRRIGEREVHDDGAPAAEPARDADGWVQPP
+PPAATVRLRLRAEHGWADLIGASRCRALTPAEAADVVAGLGPDPLSDDDPAPFYDLARRT
+RRPIGVVLMDQAAVSGIGNIFRAEALFRVGIDPWRPARDVSASELESLWADNAALMREGV
+RLGRIVTTRPEHRPGIPAEAAWPEHASYVYQRQGLACLVCGRETIVVEEMAARKLYRCLT
+CQS*
+>NZ_CP033200.1_662
+MPEGHSVHRLARQFTDVFGGRRIRATSPQGRFAEGAALLDGQVLKRARAHGKHFFADVSG
+GHVLHVHLGMYGAWTFGGDQDFAAASSIGAPRRIGEREVHDDGAPAAEPARDADGWVQPP
+PPASTVRLRLRAEHGWADLIGANRCRALTRAEAADVVAGLGPDPLNDDDPAPFYDLARRT
+RRPIGVVLMDQGAVSGIGNIFRAEALFRAGIDPWRPAREVSAPDLAFLWADNAALMREGV
+RLGRIVTTRPEHRPGIPAEAAWPEHANYVYQRQGLACLVCGRETIVVEEMAARKLYRCLT
+CQS*
+>NZ_CP040019.1_1883
+MPEGHSIHRLARQFTDVFGGWPIRASSPQGRFAEGAARMDGQVLEAARAHGKHFFADLAD
+GHVLNVHLGMYGAWSFGGDERFDAASSIGAPRRIGEREVHADGAAAAEPDRDDDGWVLPP
+PPVPTVRLRVRAEHGWADLIGASTCRLLTPAEAGDVVAKLGPDPLNDDDPAPFLDLAGRT
+RRPIGAVLMDQAAVGGIGNIFRAEALFRAGLDPWRPSNAVPREVLRRLWSDNAELMREGV
+RLGRIVTTRPEHRPGVPAEQAWPEHANYVYQRQGSPCLVCGQDAIVVEGMAARKLYRCTV
+CQR*
+>NZ_CP083691.1_1828
+MPEGHSIHRLARQVQDVFGGQALAASSPQGRFADGAALLDGRVLERAWAHGKHFFADIEG
+GLTLNVHLGMYGAMTFGGDEAFAAASSIGAPRRIGETEDHGALAAAEPPPARPTVRLRLR
+SAHGWADLIGAGTCRVLTPQELAEVTSKLGPDPLNDDDPAAFVARAARTGRPVGVVLMDQ
+SMVGGIGNIYRAEVLFRAGLDPWTPARDVGADVLAALYADAQALMRDGVRLGRIVTTAPE
+HRPGVAAEDAWPEHANYVYRRQGMPCRVCGQDAIVREEMAARNLFRCTDCQR*
+>NZ_CP097650.1_881
+MPEGHSVHRLARQFTDVFGGRRIRATSPQGRFAEGAALLDGQVLKRARAHGKHFFADVSG
+GHVLHVHLGMYGAWTFGGDQDFAAASSIGAPRRIGEREVHDDGAPAAEPARDADGWVQPP
+PPAATVRLRLRAEHGWADLIGASRCRALTPAEAADVVAGLGPDPLSDDDPAPFYDLARRT
+RRPIGVVLMDQAAVSGIGNIFRAEALFRAGIDPWRPAREVSASDLAFLWADNAALMREGV
+RLGRIVTTRPEHRPGIPAESAWPEHANYVYQRQGLACLVCGRETIVVEEMAARKLYRCLT
+CQS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000833.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000833.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9df1a2535cbdcf69cf9b40b63be8add16c7ad2e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000833.fa
@@ -0,0 +1,31 @@
+>NZ_CP042169.1_940
+MMHGSRPALRRAASALAGRRPLSLRGATVLVTGGASGIGRLIALGAARRGAGRVVVWDLD
+LQGAEAVAAEIRSQGADAQAERVDVTDAAAVEAAAARAGEVDVAVNNAGVVTGVRLEDAT
+EEGIRRTFEVNALAPYWLTRAVLPGMRARDRGAVVTVASAAGLVGVARQTDYSATKHAAV
+GFAESLAAELRKDGSRVTSLAVCPFYIDTGMFAGVRSRVPWLLPVLDPRHVAQEVLDAVE
+AGRTRLLLPRAVGLIAPLRALPAPVFDRAMDVLGVNATMDGFTGRRSRLFAGRETAR*
+>NZ_CP033200.1_664
+MHGSRPALRRAASALAGRRPLPLHGATVLVTGGASGIGRLIALGAAHRGAGRVVVWDLDL
+QGVEAVAAEIRSQGADARAERVDVTDAAAVEAAAAGAGEVDVAVNNAGVVTGAPLEDATE
+EGIRRTFEVNALAPYWLTRAVLPGMRARDRGAVVTVASAAGLVGVARQTDYSATKHAAVG
+FAESLAAELRKDGSRVTSLAVCPFYIDTGMFAGVRSRVPWLLPVLDPHHVAQEVLDAVEA
+GRTRLLLPRAVGLIAPLRALPAPVFDRAMDVLGVNATMDGFTGRRSRLFAGRETAR*
+>NZ_CP040019.1_1882
+MPRSRTPRPALRALAGALPRRRRLPLRGTAVLITGGASGIGRLMALGAARRGAARVVVWD
+LDLSAAEAVAAEARALGAEAVAERVDVTDAAAVEAAAARAGAVDVAVNNAGVVTGARLED
+ATEEGIRRTFEVNALAPYWLTRAVLPGMKARDRGAVVVIASAAGLVGVARQTDYSATKHA
+AVGFAESLSAELRKDGSAVTALAVCPFYIDTGMFDGVRSRIPWLLPVLRQEEVAEQVLDA
+VEAGRTRLPLPRAVGLLAPLRALPTPVFDRAMDVMGVNDTMDGFTGRRPAVDVPAPDPRV
+FAPDGAAR*
+>NZ_CP083691.1_1826
+MTPILNRLRGRRPLPLAGRAVLITGAGSGIGRLMALEAARRGAAVVHVWDRDDAAARTVA
+AEVAALGARGEAACVDVTDTAAVEAAAARAEAVDVLVNNAGVVTGTPLLETTEEGIRRTF
+EVNALAGYWTTRALLPGMLERGRGAVVTVASAAGLVGVARQTDYSASKHAAVGFAESLRA
+ELRRADAPVTSLVVCPFYISTGMFAGVRTKVPALLPILEPEAVAAQVVDAVEAGRERLVL
+PPAVQLIAPLRALPVPAFDRVMDVLGVNRAMDGFTGRR*
+>NZ_CP097650.1_882
+MMHGSRPALRRAASALAGRRPLSLRGATVLVTGGASGIGRLIALGAARRGAGRVVVWDLD
+LQGAEAVAAEIRSQGADAQAERVDVTDAAAVEAAAARAGEVDVAVNNAGVVTGVRLEDAT
+EEGIRRTFEVNALAPYWLTRAVLPGMRARDRGAVVTVASAAGLVGVARQTDYSATKHAAV
+GFAESLAAELRKDGSRVTSLAVCPFYIDTGMFAGVRSRVPWLLPVLDPRHVAQEVLDAVE
+AGRTRLLLPRAVGLIAPLRALPAPVFDLAMDVLGVNATMDGFTGRRSRLFAGRETAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000834.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000834.fa
new file mode 100644
index 0000000000000000000000000000000000000000..569914d11d0a4ff8ec196d507e9d99a47538eeb0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000834.fa
@@ -0,0 +1,47 @@
+>NZ_CP042169.1_941
+MVKSTAENLSPTRVKLTVEVPFEEVKPALDKAFKDIANQVQIPGFRQGKIPARLIEQRFG
+REIVVDQAVNEGLNTWFSAAIAEAEVTPISRPEVDVTATPDAENAEGPVAFTAEFDVRPT
+IELPDYKGLKVTVEPAQATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTATVDG
+EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFETTLNGGEHDGETAVVKLELTAV
+KERELPEADDEFAQLASEFDTIAELKEDLKKQAAEEAVNRQGVEARDKVLEELAKLVEVP
+VPDGVIAEQVEQHFSAGGHTAGDDHDTAEHRAELEQNTREAFANEVILDEVAEAEEVTVD
+QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEYAEVTDTDGK
+AVDLTAFVTPGGQEALDAEAEGAEAEGADEAEEKPAEKAPAKKKSTAKKAPAEQADDAEA
+AEQA*
+>NZ_CP033200.1_665
+MVKSTAENLSPTRVKLTVEVPFEEVKPALDKAFKDIANQVQIPGFRQGKIPARLIEQRFG
+REVVVDQAVNEGLNTWFSAAIAEAELTPISRPEVDVTATPDAENAEGPVVFTAEFDVRPT
+IELPDYKGLKVTVEPAQATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTATVDG
+EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFETTLNGGEHDGETAVVKLELTAV
+KERELPEADDEFAQLASEFDTIAELKEDLKKQAAEEAVNRQGVEARDKVLEELAKLVEVP
+VPDGVIAEQVEQHFSAGGHTAGDDHDTAEHRAELEQNTREAFANEVILDEVAEAEEVTVD
+QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEYAEVTDTDGK
+AVDLTAFVTPGGQEALDAEAEGADEAAEQA*
+>NZ_CP040019.1_1881
+MVKSTAENLSPTRVKLNVEVPFEEVKPSLDKAYKDIANQVQIPGFRKGKIPARLIEQRFG
+REAVVDQAVNEGLNTWFSAAISEAELTPISRPEVDVTATPDSENAEGPVVFTAEFDVRPT
+IELPDYKGLKVTVEPAKATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTASVDG
+EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFESTLNGGEHDGKTAVVKLELTAV
+KERELPEADDEFAQLASEFDTIDELKEDLKKQAAEDAVNRQGVEARDKVLAELAKLVEVP
+VPDGVITEQVEQHFSAGGHAAGDDHDTPEHRAELEANTREAFANEVILDEVAEAEEVTVD
+QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEFAEVTDTDGK
+AVDLKAFVTPGGQEALDAEAEGADPAEAEEKPAKKAAAKKPAAKKAPAKKKAEEKADDAE
+ASEQA*
+>NZ_CP083691.1_1825
+MVKSTAENLSPTRVKLTVEVPFEEVKPVLDKAYKDIAMQVQVPGFRQGKVPARLIEQRFG
+REAVVDQAVNDGLNTWFGQALAEAEVTPISTPEVDVTATPAAAEGPVEFTAEFDVRPTIE
+LPDYKGIEVTVEPAQATDEDEQAQLDALRSRFGTLKDVDRPAAKDDFVTMDLTATVGEEQ
+VDQAQGLSYQVGAGTMLDGIDEALEGLSAGEDATFETTLNGGEHDGETATVKLVLQAVKE
+RELPEADDDFAQLASEFDTIAELKEDLKKKAAEAAETRQGVEARDKVLAELGKLVEVPVP
+ENVIAEQLEQHFSQGGHSAGDEHDTPEHREELEKNTREAFANEVILDEVAEAESVTVDQG
+ELIEYIFATSAEYGMDPNQFAMMLDQAGQIPMIMGEVRRRKALAKVLEHAVVTDTDGNAV
+DLTAFVTPAAAEEEKAEEKPAKKAPAKKAAAKKAAAKKPAAKKAEAEESEEA*
+>NZ_CP097650.1_883
+MVKSTAENLSPTRVKLTVEVPFEEVKPALDKAFKDIANQVQIPGFRKGKIPARLIEQRFG
+REIVVDQAVNEGLNTWFSAAIAEAELTPISRPEVDVTATPDAENAEGPVAFTAEFDVRPT
+IELPDYKGLKVTVEPAQATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTATVDG
+EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFETTLNGGEHDGETAVVKLELTAV
+KERELPEADDEFAQLASEFDTIAELKEDLKKQAAEEAVNRQGVEARDKVLEELAKLVEVP
+VPDGVIAEQVEQHFSAGGHTAGDDHDTAEHRAELEQNTREAFANEVILDEVAEAEEVTVD
+QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEYAEVTDTDGK
+AVDLTAFVTPGGQEALDAEAEGAEAEGADEAAEQA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000835.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000835.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf9c73e025449136d60d41508231295f52eca1a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000835.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_942
+MTDITPSMRSVDPAQREDFLYTQLLKSRIVWLGEDVRDDNANAICSQLLLLSAEDPEKDI
+YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGTKGKRYATPHARV
+LMHQPSGGIGGTESDIRIQAQLILHMKQVMAELTAEQTGQSVETILEDNARDKWFTAQEA
+LEYGFIDHIADRAASVTGGGGVRG*
+>NZ_CP033200.1_666
+MTDITPSMRSVDPAQREDFLYTQLLKSRIVWLGEDVRDDNANAICSQLLLLSAEDTEKDI
+YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGTKGKRYATPHARV
+LMHQPSGGIGGTESDIRIQAQLILHMKQVMAELTAEQTGQSVETILEDNARDKWFTAQEA
+LEYGFIDHIADRAASVTGGGGVRG*
+>NZ_CP040019.1_1880
+MTDITPSMRSVDPAQREDFLYTQLLKSRIVWLGEDVRDDNANAICSQLLLLSAEDPEKDI
+YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGTKGKRYATPHARV
+LMHQPSGGIGGTESDIRIQAQLILHMKQVMAELTAEQTGQSVETILEDNARDKWFTAKEA
+LEYGFIDHIADRAASVTGGGGVQG*
+>NZ_CP083691.1_1824
+MTDLTPRMTSVEPTQREDYLYNQLLKNRIIWLGSDVRDDNANAICSQLLLLSAEDPEKDI
+YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGAPGKRYATPHARI
+LMHQPSGGIGGTESDIRIQAQLILHMKQIMAELTAAQTGQSVETILEDNARDKWFTAQEA
+LEYGFIDRIAQSAASVTGGGGVEG*
+>NZ_CP097650.1_884
+MTDITPSMRSVDPAQREDFLYTQLLKSRIVWLGEDVRDDNANAICSQLLLLSAEDTEKDI
+YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGTKGKRYATPHARV
+LMHQPSGGIGGTESDIRIQAQLILHMKQVMAELTAEQTGQSVETILEDNARDKWFTAQEA
+LEYGFIDHIADRAASVTGGGGVRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000837.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000837.fa
new file mode 100644
index 0000000000000000000000000000000000000000..faae594a611147e74f160fa31254d7628d0fcdab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000837.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_944
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAEADETV
+LPTPQEIFDHLESFVIGQEAAKRSLAVAVYNHYKRVRGPQARGGDLADRLTERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGDVTYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPRNALLKQYQKMFLMDGVELEFEQD
+ALDAVVAQAEARGTGARGLRSIMENVLKPVMFELPSRSDVGTVVISGDVVRGEAEPTLIP
+AEVERRRRGRSA*
+>NZ_CP033200.1_668
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAEADETV
+LPTPQEIFDHLESFVIGQEAAKRSLAVAVYNHYKRVRGPQARGGDLADRLTERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGDVTYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPRNALLKQYQKMFLMDGVELEFEQD
+ALDAVVAQAEARGTGARGLRSIMENVLKPVMFELPSRSDVGTVVISGDVVRGEAEPTLIP
+AEVERRRRGRSA*
+>NZ_CP040019.1_1878
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAADSDEMV
+LPTPQEIFDHLEGYVIGQEVAKRSLAVAVYNHYKRVRGPQGRGGDLADRLTERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGEVSYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPNNALLKQYQKLFLMDGAELEFEPE
+ALDAVVELAEARGTGARGLRSIMEDVLKPVMFELPSRTDVGTVVISGEAVRGEAEPVLIP
+AEVERRRRGRSA*
+>NZ_CP083691.1_1822
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAETDELE
+LPTPREIFEHLERYVIGQEAAKRSLAVAVYNHYKRVRGPQGRGGDLAERLEERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARMLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DHDVKRAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGSGEVSYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHDQLVRVLTEPKNALLKQYQKMFLMDGVELEFEPE
+ALDAVVELAQARGTGARGLRSIMEDVLKPVMFELPSRTDVGTVVISGDVVTGQAEPLLIP
+AEVERKRRRRTA*
+>NZ_CP097650.1_886
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAEADETV
+LPTPQEIFDHLESFVIGQEAAKRSLAVAVYNHYKRVRGPQARGGDLADRLTERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGDVTYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPRNALLKQYQKMFLMDGVELEFEQD
+ALDAVVAQAEARGTGARGLRSIMENVLKPVMFELPSRSDVGTVVISGDVVRGEAEPTLIP
+AEVERRRRGRSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000839.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000839.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3e99bbc4ca7cd59af8fe74f7c0f78b636841b9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000839.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_946
+MRPTPDPAPAGRRACDSSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG
+VAELAVAGLLAVPRTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV
+PLIRAAGRVARS*
+>NZ_CP033200.1_670
+MRPTPDPAPAGRRACDSSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG
+VAELAVAGLLAVPRTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV
+PLIRAAGRVARS*
+>NZ_CP040019.1_1875
+MRRASAPRTDTAGATGTGARRMAAALAGMGVLHFARPKPFDGLIPPALPGPARAWTVGSG
+VAELAVAGMLAAPRTRRAGGRAAQALFLGVWPGNAWMAWRWRGRSWPWRALALGRLPLQV
+PMIRAAGRIARG*
+>NZ_CP083691.1_1820
+MKPTPDPAPAGRRASDGSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG
+VAELAVAGLLAVPHTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV
+PLIRAAGRVARR*
+>NZ_CP097650.1_888
+MRPTPDPAPAGRRACDSSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG
+VAELAVAGLLAVPRTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV
+PLIRAAGRVARS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000842.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000842.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc1ed82d35828c787ff606dde9ed88a34374c25a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000842.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_949
+MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER
+VARAVPAGEAATSDVILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD
+AVARVHAAGRRAVVAAHLLAPGYFHDRLGEAGADAVTDPLLPHPLVARIALDRLRSALVE
+APRGAAGGR*
+>NZ_CP033200.1_673
+MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER
+VAQAVPAGEAATSDIILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD
+AVSRVRAAGRRAVVAAHLLAPGHFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE
+APRGAAGGR*
+>NZ_CP040019.1_1872
+MSAPVLHVIACAHGTHDAAGRVVIDGLRADLAALLDAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPDTIAAAPLAGAGDDVEPRLVAVLAER
+VAQAVPAGEAATSEVILAAAGTRAADGQAQVHALAAALARATGLPVTAAFGAAATPPVPD
+AVSRVRATGRRAVAAAHLLAPGYFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE
+APRGAAGGR*
+>NZ_CP083691.1_1816
+MSAPVLHVIACAHGTHDAAGRVVIDGLRADLAALLDAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPDTIAAAPLAGAEDDVEPRLVTVLAER
+VAQAVPAGEAATSDIILAAAGTRAADGQAQVHALAAALARATGLPVTAAFGAAATPRVPD
+AVARVRATGRRAVVAAHLLAPGYFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE
+APRGAAGGR*
+>NZ_CP097650.1_891
+MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER
+VARAVPAGEAATSDVILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD
+AVARVHAAGRRAVVAAHLLAPGYFHDRLGEAGADAVTDPLLPHPLVARIALDRLRSALVE
+APRGAAGGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000846.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000846.fa
new file mode 100644
index 0000000000000000000000000000000000000000..29fcf7943bfc8a34681932c11285cf41b6140b95
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000846.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_953
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPHDGATLAAGMVRGGDEA*
+>NZ_CP033200.1_677
+MSTALLDRRAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPVRTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPHDGATLAAGMVRGGDEA*
+>NZ_CP040019.1_1868
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARSGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYSEEVFTAIADDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVLRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPQDGATLAAGMVRGGDEA*
+>NZ_CP083691.1_1812
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPQVIVAVNKIDLVDYSEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPQDGATLAAGMVRGGDEA*
+>NZ_CP097650.1_895
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPHDGATLAAGMVRGGDEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000849.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000849.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85a9a7a83df2b685bead1486f1755069f22644c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000849.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_956
+MTASDLYPTSLRLLGRPVLIVGGGRVAGRRVGALLDAGALVSVVAPEPGEEVERLAAAGL
+LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV
+RAGDVTVAVNAGGDPRRARALKDAIALALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL
+ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA
+RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA
+TGFTLVTGHEELAEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD
+QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGIPAPISTLNPTSEGA
+RA*
+>NZ_CP033200.1_680
+MTASDLYPTSLRLLGRPVLMVGGGRVAGRRMGALLDAGALVTVVAPEPGEEVERLAAAGL
+LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV
+RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL
+ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA
+RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA
+TGFTLVTGHEELSEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD
+QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGVPAPISTLNSTSEGA
+RA*
+>NZ_CP040019.1_1865
+MTASDLYPTSLRLLGRPVLMVGGGRVAGRRVGALLDAGALVTVVAPEPGEEVERLAAAGL
+LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV
+RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL
+ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA
+RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA
+TGFTLVTGHEELSEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD
+QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGARAAGVPAPILTLNPTSEGA
+RA*
+>NZ_CP083691.1_1809
+MTASDLYPTSLCLLGRPVLIVGGGRVAGRRVGALLDAGALVTVVAPEPGEEVERLAAAGL
+LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVA
+RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL
+ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA
+RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA
+TGFTLVTGHEELAEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD
+QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGVPAPISTLNPTSEGA
+RA*
+>NZ_CP097650.1_898
+MTTSDLYPTSLRLLGRPVLVVGGGRVAGRRMGALLDAGALVTVVAPKPGEEVERLAAAGL
+LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV
+RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL
+ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA
+RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSVVSVPAAAGIPVTHRGVA
+TGFTLVTGHEELSEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD
+QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGIPAPILTLNPTSEGA
+RA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000850.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000850.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20b3ef053e33531c2a741d58a0ea73366c567ab0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000850.fa
@@ -0,0 +1,100 @@
+>NZ_CP042169.1_959
+MYPLASSAPDGRTPASPRFPEIERRILAYWDEDGTFQASIDQRPTRNEDGSQNEFVFYDG
+PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS
+EIEAMGIDTFNDACRSSVLKYTDQWQDYVTRQARWVDFENDYKTLTPDFMESVIWAFSEL
+HRKGLTYRGFRVLPYCWNDETPLSNHELRMDDDVYKMRQDPSVTVTFPITGLPADPALVP
+DGGADAALAAHLAGVHVLAWTTTPWTLPTNAALAVGPQIQYAVVPAGPEGATADGDRFLL
+AVDLVGAHARELGYADADAARAAVTETIPGARLGGLAYAPLFTDVFDAHRGETFTVNGRD
+LGVEGAHRILVDDYVSTEDGTGVVHQAPAYGEDDQRVCEANGIPVMLSVDSGARFLPLFA
+REDVGRGDLREIAGVQVFEANRTIIRALRALGRVAREASYEHSYPHCWRCRTPLIYRAVT
+SWYVKVTQIKERMLELNEEITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWESD
+HPDFPRQEVYGSLAEIEEAFGRLPRNAEGEVDLHRPWVDDLTRPHPDPEAAAAGAVMRRV
+EDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALFD
+RPAFSHVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGADAMRWFLMASPILRGGNLIV
+TEEGIREGVRQVLLPAWNAYHFFTLYANTAHDGGARPEGYRAQERHTAEDPLDQYILAAA
+GRMLREVKAGLDAYEVSDATDALRGFMDTLTNWYIRRSRERFFDEDTVAFDVLYTVLEAF
+TRAAAPLMPLIAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADSLVARMDAVRRISSAGS
+ALRKGAGRRVRLPLPRLSVVVPDAAGLEGTYARIVADELNLKDVELTELSEEAIARYGIG
+TELKLNFRELGKAFGRQVPLVKQAVDAGAYEETAEGLAVTLADGETVTLAPALYELRTVS
+TGAPEGTAVGVLPGTAGFLVLDTEVSAELAAEGTARDVVRAVQAARKDAGLDVSDRVRTR
+IEGPTAVVAALEAHRGLVAEETLTVDLELVDSGAADPRKDPADDAMKTVAVSVAKADA*
+>NZ_CP033200.1_683
+MYPLASSAPDGRTPASPRFPEIERRILAYWDEDGTFQASIDQRPAFNEDGSQNEFVFYDG
+PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS
+EIEAMGIDKFNDACRSSVLKYTDQWQDYVTRQARWVDFENDYKTLTPDFMESVIWAFSEL
+HRKGLTYRGFRVLPYCWNDETPLSNHELRMDDDVYKMRQDPSVTVTFPITGLPADPALVP
+DGGADAALAAHLAGVHVLAWTTTPWTLPTNAALAVGPQIQYAVVPAGPEGATADGDRFLL
+AVDLVGAHARELGYADADAARAAVTETIPGARLGGLAYAPLFTDVFDAHRGETFTVNGRD
+LGVEGAHRILVDDYVSTEDGTGVVHQAPAYGEDDQRVCEANGIPVLLSVDSGARFLPLFA
+REDVGRGDLREIAGVQVFEANRTIIRALRALGRVAREASYEHSYPHCWRCRTPLIYRAVT
+SWYVKVTQIKERMLELNEEITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWESD
+HPDFPRQEVYGSLAEIEEAFGRLPRNAQGEVDLHRPWVDDLTRPHPDPEAAAAGAVMRRV
+EDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALFD
+RPAFSHVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGADAMRWFLMASPILRGGNLIV
+TEEGIREGVRQVLLPAWNAYHFFTLYANTAHDGGARPEGYRAQERHTAEDPLDQYILAAT
+GRMLREVKTGLDAYEVSDATDALRGFMDTLTNWYIRRSRERFFDEDTVAFDVLYTVLEAF
+TRAAAPLMPLIAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADSLVARMDAVRRISSAGS
+ALRKGAGRRVRLPLPRLSVVVPDAAGLEGTYARIVADELNLKDVELTELSEEAIARYGIG
+TELKLNFRELGKAFGRQVPLVKQAVDAGAYEETAEGLAVTLADGETVTLAPALYELRTVS
+TGAPEGTTVGVLPGTAGFLVLDTEVSAELAAEGTARDVVRAVQAARKDAGLDVSDRVRTR
+IEGPTAVVAALEAHRGLVAEETLTVDLELVDSGAADPRKDPADDAMKTVAVTVAKADA*
+>NZ_CP040019.1_1862
+MYPLASSAPDGRTPASPRFPEIERRILAYWDEDGTFQASIDQRPALNEDGSQNEFVFYDG
+PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS
+EIEAMGIDTFNDACRSSVLKYTDQWQDYVTRQARWVDFENDYKTLTPDFMESVIWAFSEL
+HRKGLTYRGFRVLPYCWNDETPLSNHELRMDDDVYKMRQDPSVTVTFPITGLPADPALVP
+DGGADAALAAHLAGVHVLAWTTTPWTLPTNAALAVGPQIQYAVVPAGPEGATADGDRFLL
+AVDLVGAHATELGYADADAARAAVTETIPGARLGGLAYEPLFTDVFDAHADETFTVNGRD
+LGVEGAHRILVDDYVSTEDGTGVVHQAPAYGEDDQRVCEANGIPVLLSVDSGARFLPLFA
+REDVGRGDLREIAGVQVFEANRTIVRALRGLGRVAREASYEHSYPHCWRCRTPLIYRAVT
+SWYVKVTQVKERMLELNEEITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWESD
+HPDYPLQEVYGSLAEIEEAFGRLPRNAEGEVDLHRPWVDDLTRPHPDPEAAAAGAVMRRV
+EDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALFD
+RPAFSNVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGADAMRWFLMASPILRGGNLVV
+TEEGIREGVRQVLLPAWNAYHFFTLYANTAHDGGARPDGYRAQERHTAEDPLDQYILAAT
+GRMLREVKTGLDAYEVSDATDALRGFMDTLTNWYIRRSRQRFFDEDTAAMDVLYTALEAF
+ARAAAPLMPLVAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADSLVARMDAVRRISSAGS
+ALRKGAGRRVRLPLPRLSVVVPDAEGLEGTYARIVADELNLKDVSLTELSDEAIARYGIG
+TELKLNFRELGKVYGKQVPLVKKAVDAGSYEETADGLAVTLADGATVTLDPALYELRTVS
+TGAPEGTAVGVLPGAAGFLVLDTEVSAELAAEGTARDVVRAVQAARKDAGLDVSDRVRTR
+IDGPAAVVAALEAHRDLVAEETLTVELELVDSGEADPRKDPADDAMKTVAVTVAKADA*
+>NZ_CP083691.1_1806
+MYPLASTDPAGATPASPLLPEIEQRILRYWDEDGTFQASIDARPAVNEDGSQNEFVFYDG
+PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS
+EIEAMGIDRFNDACRSSVLKYTEEWRRYVTRQARWVDFDNDYKTLTPDFMESVIWAFSEL
+HRKGLTYRGFRVLPYCWHDETPLSNHELRMDDDVYKMRQDPSVTVSFPILGLPDDAALVP
+AGGADAALADELAGVHVLAWTTTPWTLPTNAALAVGPEIEYAVVPAGPEGATVAAAERFL
+LAVDLVGAHAKELGYADADAARAAVERTVLGARLGGLRYEPLFTDVFEAHAGETFPVGAR
+TLTLDGVHRILVDDYVSTDDGTGVVHQAPAYGEDDQRVCEANGIPVLLSVDEGARFLPLF
+AREGQGRGDLKDIAGVQVFEANRTIIRALRALGRIAREASYEHSYPHCWRCRTPLIYRAI
+TSWYVSVTKVKDRMLELNEDITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWES
+DHPDYPLQEVYGSLAELEEAFGRLPRNADGEVDLHRPWIDDLTRPHPDPEAAAAGATMRR
+VEDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALF
+DRPAFSHVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGSDAMRWFLMASPILRGGNLI
+VTEEGIREATRQVILPLWNAWHFFTLYANTAHDGGARPEGYRASERHTAEDPLDQYVLAA
+CGTMLRQVKAALDAYEVSDAADALRAFMDTLTNWYIRRSRERFFAEDTAAMDVLSTVLEA
+FTRAAAPLLPLVAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADALVARMDLVRSITSAG
+SALRKGAKRRVRLPLAAMSVVVPDAAALEGTFTRIVADELNLKEVRLTELSEEAISRYGI
+GTELKLNFRELGKHFGRQVPLIKKAVDAGAYAEGEQGLDVTLADGAVVTLAPELYELRTV
+STGAPEGTAVGVLPGGGFLVLETAVSAELAAEGVARDVIRAVQAARKDAGLDVADRVRTR
+IEGPAPVVAALESHRDLVAQETLTVELDLVDSGAADPRRDPADDAMKTVAVAVAKAQA*
+>NZ_CP097650.1_901
+MYPLASSAPDGRTPASPRFPEIERRILAYWDEDGTFQASIDQRPTRNEDGSQNEFVFYDG
+PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS
+EIEAMGIDTFNDACRSSVLKYTDQWQDYVTRQARWVDFENDYKTLTPDFMESVIWAFSEL
+HRKGLTYRGFRVLPYCWNDETPLSNHELRMDDDVYKMRQDPSVTVTFPITGLPADPALVP
+DGGADAALAAHLAGVHVLAWTTTPWTLPTNAALAVGPQIQYAVVPAGPEGATADGDRFLL
+AVDLVGAHARELGYADADAARAAVTETIPGARLGGLAYAPLFTDVFDAHRGETFTVNGRD
+LGVEGAHRILVDDYVSTEDGTGVVHQAPAYGEDDQRVCEANGIPVLLSVDSGARFLPLFA
+REDVGRGDLREIAGVQVFEANRTIIRALRALGRVAREASYEHSYPHCWRCRTPLIYRAVT
+SWYVKVTQIKERMLELNEEITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWESD
+HPDFPRQEVYGSLAEIEEAFGRLPRNAQGEVDLHRPWVDDLTRPHPDPEAAAAGAVMRRV
+EDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALFD
+RPAFSHVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGADAMRWFLMASPILRGGNLIV
+TEEGIREGVRQVLLPAWNAYHFFTLYANTAHDGGARPDGYRAQERHTAEDPLDQYILAAT
+GRMLREVKTGLDAYEVSDATDALRGFMDTLTNWYIRRSRERFFDEDTVAFDVLYTVLEAF
+TRAAAPLMPLIAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADSLVARMDAVRRISSAGS
+ALRKGAGRRVRLPLPGLSVVVPDAAGLEGTYARIVADELNLKDVELTELSEEAIARYGIG
+TELKLNFRELGKAFGRQVPLVKQAVDAGAYEETAEGLAVTLADGETVTLAPALYELRTVS
+TGAPEGTTVGVLPGTAGFLVLDTQVTAELAAEGTARDVVRAVQAARKDAGLDVSDRVRTR
+IEGPTAVVAALEAHRGLVAEETLTVDLELVDSGAADPRKDPADDAMKTVAVTVAKADA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000852.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000852.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f784f6980de820ae7db06a456c6d1baa59d12183
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000852.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_962
+MTHHTEETLVLIKPDGVARNLVGEILARIERKGYVIADLKMLTPTRAMLERHYEEHQGKP
+FFEPLVAFMASGPVVAARVTGDSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGEAVQKN
+LVHGSDSTLSAERELAIWFG*
+>NZ_CP033200.1_686
+MTHHTEETLVLIKPDGVARNLVGEILARIERKGYVIADLKMLTPTRAMLERHYEEHQGKP
+FFEPLVAFMASGPVVAARVTGDSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGEAVQKN
+LVHGSDSTLSAERELAIWFG*
+>NZ_CP040019.1_1860
+MAQHIEETLVLVKPDGVERNLVGEILARIERKGYVIADLKMLTPTRSMLERHYEEHQGKP
+FFDPLVDFMASGPVVAVRVTGNSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGESVQKN
+LVHGSDSSLSAERELGIWFG*
+>NZ_CP083691.1_1803
+MTHHPEETLVLVKPDGVERRLTGEIIARIERKGYEVVDLKMLVPTREMLAAHYEEHEGKP
+FYEPLLEFMGSGPVVALRLAGDRVIEGFRSLAGATDPTVAAPGTIRGDYARDWGAGVQKN
+LVHGSDSTLSAERELAIWFA*
+>NZ_CP097650.1_904
+MTHHTEETLVLIKPDGVARNLVGEILARIERKGYVIADLKMLTPTRAMLERHYEEHQGKP
+FFEPLVAFMASGPVVAARVTGDSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGEAVQKN
+LVHGSDSTLSAERELAIWFG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000853.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000853.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca572eead95d8b369fb22adb47f507129be102a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000853.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_963
+MPATPLTDDIRLSPADDIPAEEARLTWYARPAGTAALLLITSLVALTATIIIIVERTLLT
+ADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLLAGARFARW
+YWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNLQTGTLPA
+PAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID*
+>NZ_CP033200.1_687
+MPATPLTDDIRLSPADDIPAEEARLTWYARPAGTAALLLITSLVALTATIIIIVERTLLT
+ADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLLAGARFARW
+YWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNLQTGTLPA
+PAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID*
+>NZ_CP040019.1_1859
+MPSTPTADRVRPAQPAETPASDGTLSWYARPAGMAWTLLVTSLVALTATIVIIVERSILA
+ADPGHRTSCDLNPWVSCGRVMQSWQAMTFGFPNTYIGIVAFSVLITVAVSLFAGARFARW
+YWLLMNVGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNIQTGTLPA
+SPGAARLARELAWPVILILYVLVFATILLELGFGVIGLD*
+>NZ_CP083691.1_1802
+MDVTETAENPPAPRAHHAAHALPEDRSLSWYARPLGTAWMLLITSIVAVTATIIIIVERS
+ILAENPNYRTSCDINPWLSCGTVMQSWQAHTFGFPNTFVGIVAFPVLITVAVSLFAGARF
+ARWYWVLMNVGILAGFAFAAWLWYSAVYSIGTLCLYCMIVWAMVILQLVLVTSRNLQTGA
+LPSSPGLARLAQDFAWPVIVLLYALVFASILLQLGLGVIGIR*
+>NZ_CP097650.1_905
+MSMPTTPPTDDVRLSPADDVPAEEARLTWYARPAGTAALLLITSLVALTATIVIIVERAL
+LTADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLLAGARFA
+RWYWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNLQTGTL
+PAPAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000854.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000854.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e27f068a004431529412107a817973cd0a2a4e50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000854.fa
@@ -0,0 +1,96 @@
+>NZ_CP042169.1_964
+MAANNEDTTRADERVEETAEQAVTQTAADTADGAEPERTAASDDAADPAEEPSAPTLQVD
+PTDPFAVPANLIEVLRTETTSRQRSEDEDAGESEDRAEGAVVSRRRRRRRRGEVDMELDG
+GEAGDPEHTVTRVRAPRQAVGTASDTVQSVKGSTRLEAKRQRRRDSRSGGRRRTVITEAE
+FLARREAVDRKMLVRQRDQRIQIAVLEDGVLAEHFVSHTTQDSMIGNVYLGKVQNVLPSM
+EAAFVDIGRGRNAVLYAGEVNWDAAQLDGKPRKIENALKSGDTVLVQVTKDPVGHKGARL
+TSQVSLPGRYLVYVPGGSMTGISRKLPDVERSRLKKILKDHLPQDAGVIVRTAAEGTSEQ
+ELQNDINRLRAQWEGIQEKASGTKVLAPELLYAEPDLTIKTVRDVFNEDFSAMLVQGEAT
+WDNIEAYVTYVAPHLLGRLHHWVPEDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVI
+DRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEIVRQLRLRDIGGIIVIDFIDMVL
+EANRDLVLRRLVECLGRDRTKHQVAEVTSLGLVQMTRKRMGTGLVEVFSETCEHCAGRGI
+LIQDTPVERGRSGGEQRGEAEGRRRRRRRGDGEGEHAHAAAATTTGAEHADSEDERQRRE
+RAEAARVALHSIAKASGKVAEDEAPAQESAPAEQAADAAEDSAAEAVEAASAGPAEAGQP
+AGTDEEETPRRRRRRGRRRSRGRAEESGDTGAEDAGSEDAARSHDDGPAESAGQTRQTEE
+EAAEPAAAAAPEHQDPVVQAEEAVAAVAEAEADAEAESPEDAAEQDDRPRRSRRRRGGRG
+RSRRGGEAASTEADADAEDHGAERATPSRHEAADADSSVAVSSEVASEPVPAEDAPAPVP
+AEDAPAPRRRRSRRASSDGVVRPAAGADASAERTADRTDAAPVEATEPSPEESTDATEVH
+EQPAAPAAVEEAVMVEPAATEPTAEPTADADQASAADAPTEAQAAPTAPVPGSPRRRSRR
+AVSSDGVHVQVQAAPGGAQGGRFTAAVAEASTPAEPQGAAPVMLGVGVKAADLARRGR*
+>NZ_CP033200.1_688
+MAANNEDTTRADERVEETAEQAVTQTAADTADGAEPERTAASDDAADPAEEPSAPTLQVD
+PTDPFAVPANLIEVLRTETTSRQRSEDEDAGESEDRAEGAVVSRRRRRRRRGEVDMELDG
+GEAGDPEHTVTRVRAPRQAVGTASDTVQSVKGSTRLEAKRQRRRDSRSGGRRRTVITEAE
+FLARREAVDRKMLVRQRDQRIQIAVLEDGVLAEHFVSHTTQDSMIGNVYLGKVQNVLPSM
+EAAFVDIGRGRNAVLYAGEVNWDAAQLDGKPRKIENALKSGDTVLVQVTKDPVGHKGARL
+TSQVSLPGRYLVYVPGGSMTGISRKLPDVERSRLKKILKDHLPQDAGVIVRTAAEGTSEQ
+ELQNDINRLRAQWEGIQEKASGTKVLAPELLYAEPDLTIKTVRDVFNEDFSAMLVQGEAT
+WDNIEAYVTYVAPHLLGRLHHWVPEDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVI
+DRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEIVRQLRLRDIGGIIVIDFIDMVL
+EANRDLVLRRLVECLGRDRTKHQVAEVTSLGLVQMTRKRMGTGLVEVFSETCEHCAGRGI
+LIQDTPVERGRSGGEQRGEAEGRRRRRRRGDGEGEHAHAAAATTTGAEHADSEDERQRRE
+RAEAARVALHSIAKASGKVAEDEAPAQESAPAEQAADAAEDSAAEAVEAASAGPAEAGQP
+AGTDEEETPRRRRRRGRRRSRGRAEESGDTGAEDAGSEDAARSHDDGPAESAGQTRQTEE
+EAAEPAAAAAPEHQDPVVQAEEAVAAVAEAEADAEAESPEDAAEQDDRPRRSRRRRGGRG
+RSRRGGEAASTEADADAEDHGAERATPSRHEAADADSSVAVSSEVASEPVPAEDAPAPVP
+AEDAPAPRRRRSRRASSDGVVRPAAGADASAERTADRTDAAPVEATEPSPEESTDATEVH
+EQPAAPAAVEEAVMVEPAATEPTAEPTADADQASAADAPTEAQAAPTAPVPGSPRRRSRR
+AVSSDGVHVQVQAAPGGAQGGRFTAAVAEASTPAEPQGAAPVMLGVGVKAADLARRGR*
+>NZ_CP040019.1_1858
+MAANEDTTGAEERAEQTEQTTAETSAAVAGQAAAESPVEDGGTVTQAQADAAEGADAPER
+TAEAADIEDEAETDTAAEPEPDEAPGAPALQFDPTDPFAVPANVMEILRTEKSERRPARD
+ERPARGAEDEEEAPGRSRRRRRPSRDRDQAETEAGAEDEAVETAEGEQDAETAERGEGAV
+VSRRRRRRRRGDVDMELDGGEDGDPENTVTRVRAPRQALSTGSDAVQGVKGSTRLEAKRQ
+RRRDSRSGGRRRTVITEAEFLARREAVDRKMLVRQREHRIQIAVLEDGVLAEHFVSNTTQ
+DSLIGNVYVGKVQNVLPSMEAAFVDIGRGRNAVLYAGEVNWDAAQLDGKPKKIENALKSG
+DTVLVQVTKDPVGHKGARLTSQVSLPGRYLVYVPGGSMTGISRKLPDVERSRLKKILKDH
+LPQDAGVIVRTAAEGTSEQELQNDINRLRAQWEGIQEKASSTKVLAPELLYAEPDLTIKT
+VRDVFNEDFSAVLVQGEATWDNIEAYVTYVAPHLLDRLHHWVPQDHDGEDLYATHRVDEQ
+LHKALERKVYLPSGGSLVIDRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEVVRQ
+LRLRDIGGIIVIDFIDMVLEANQDLVLRRLVECLGRDRTKHQVAEVTSLGLVQMTRKRMG
+TGLVEVFSETCEHCAGRGILIHDTPVERGRSGGEPRGEGEGRRRRRRKGAGEGEQAQPAE
+STTTAGGEEVDAEDERQRRERAEAARAALHSIAKASGKVSEDEDPAEQAAPAEQAADAAE
+DQAAEAVEAARQDAAEETGEAGAQDGEGAEDEDEAPRRRRRRGRRRGRGRSEEAAEAAEA
+ASEDGSRDADAAPAGQAPAADEEEAPAADPVAQAEAAVTAVAEAEADAESGGEEREAEPA
+GDEEGARPRRARRRRGGRGRSRRGADREASTADADDEAAQPAQEPAQADAGAAGDRARAS
+RAGRVGAARAARVRPGRGRGGRRAASRPAPPPFAPRFERRCRAPGRGPGRRPGVVRPGDP
+VPRGGGRRRGDRAHRGAVHGRHRGARAPGRPRPGGGGRDGRAGGGRPRPGRAGRARPAAR
+PELRARRPPSPGAVGPVARCPRTACACRSRTPPGRHGADASRRPPPSPRPPPSRAPRRP*
+>NZ_CP083691.1_1783
+MAADESTTQDTHETAEGSTTPVEATEEETAAEVAESPAGEAAEATAAPDVRFDPTNPFAV
+PEGLLPLIEAETVERRRRRPAADPVPEGAADDAHADDEDDEDRPAVSRRRRRRRRGTVDM
+ELAGGEDGDPEDTVTRVRAPRRALSTGPEAVQGVKGSTRLEAKRQRRRESRSGGRRRTVI
+TEAEFLARRESVDRKMLVRQREHRIQIAVLEDGVLAEHFVSNTTQDSMIGNVYLGKVQNV
+LPSMEAAFVDIGRGRNAVLYAGEVDWDAAQLDGKAKKIENALKSGDTVLVQVTKDPVGHK
+GARLTSQISLPGRYLVYVPGGTMTGISRKLPDVERARLKKILKDHLPQDAGVIVRTAAEG
+TSEQELQNDINRLRVQWEGIQEKASSTKTLAPELLYAEPDLTIKTVRDVFNEDFSAMLVQ
+GEATWDSIEAYVTYVAPHLLDRLHHWVPEDHDGEDLYATHRVDEQLHKALERKVYLPSGG
+SLVIDRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEVVRQLRLRDIGGIIVIDFI
+DMVLESNQDLVLRRLVECLGRDRTKHQVAEVTSLGLVQMTRKRMGTGLVEVFSEVCEHCG
+GRGILIQDTPVERNRWGHEHRAEPEARRRNKRRRGTESGEGGPAEPTAAELTEEERLRAE
+RAAAARTALMSIAKASGKAADEEPSEEAAPRAEDAPEEAADEVRPSPAGDAEEQGESESG
+GRRRKRRGRRRGRGRGGDDAARSAEEQDAPAEHPAEAAGEPAPAEAGAPDPAETATEDAD
+ADSASDAPAAQAEADEDGRSGGRRRSRRRGGRRAESPQGSGAPASAPEASVEAEQDPEEP
+AGAAEAEEALAAEEAPASPEPAAVVTFDGEPVAVPRRRRSRRATSDGVSAPRPSGMDALE
+AAVDRRAEDAAAAAQRSPATPAATPTAAPEPAPAPVAGEGPAAAAPRRRSRRAVSADGAT
+VQVQEGAAAGGGRFTAQAAQAAPAGETAAPVMLGVGVKAADIVRGE*
+>NZ_CP097650.1_906
+MAANNEDTTRADERVEETAEQAVTQTAADTAAGAVQPERTPASDDAADAPEEPSAPTLQV
+DPTDPFAVPANLIEVLRTETTSRQRSEDEDDPDTSGRSRRRRRPSREDDRAEEGAADASA
+DAEDREDASESEDRAEGAVVSRRRRRRRRGEVDMELDGGEAGDPEHTVTRVRAPRQAVST
+ASDTVQSVKGSTRLEAKRQRRRDSRSGGRRRTVITEAEFLARREAVDRKMLVRQRDQRIQ
+IAVLEDGVLAEHFVSHTTQDSMIGNVYLGKVQNVLPSMEAAFVDIGRGRNAVLYAGEVNW
+DAAQLDGKPRKIENALKSGDTVLVQVTKDPVGHKGARLTSQVSLPGRYLVYVPGGSMTGI
+SRKLPDVERSRLKKILKDHLPQDAGVIVRTAAEGTSEQELQNDINRLRAQWEGIQEKASG
+TKVLAPELLYAEPDLTIKTVRDVFNEDFSAMLVQGEATWDNIEAYVTYVAPHLLDRLHHW
+VPEDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVIDRTEAMTVVDVNTGKFTGSGGN
+LEETVTKNNLEAAEEIVRQLRLRDIGGIIVIDFIDMVLEANRDLVLRRLVECLGRDRTKH
+QVAEVTSLGLVQMTRKRMGTGLVEVFSETCEHCAGRGIIIKDTPVERGRSGGEQRGEAEG
+RRRRRRRGNGEGEHAHAAAATTTGAEHADSEDERQRRERAEAARVALHSIAKASGKVAED
+ETPAQEPAPAEQAADAAEDSVAEAVEAASTGPAEAGQPAAADEEETPRRRRRRGRRRSRG
+RAEESGDTGAEDAGSEDAARSHDDGPAESAGQTRQTEEEAAEPAAAAAPEHQDPVVQAEE
+AVAAVAEAEADAEAESPEDAAEQGDRPRRSRRRRGGRGRSRRGGEAASTEADADAEDHGA
+ERATPSRHEAADADSSVAVSSEVASEPVPAEDAPAPVPAEDAPAPRRRRSRRASSDGVVR
+PAAGADASAERTADRTDAAPVEATEPSPEESTDATEVHEQPAAPAAVEEAVMVEPAATEP
+TAEPTADADQASAADAPTEAQAAPTAPVPGSPRRRSRRAVSSDGVHVQVQAAPGGAQGGR
+FTAAVAEASTPAEPQGAAPVMLGVGVKAADLARRGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000855.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000855.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d68acfbbe4029443cf17e5a4b3f8b8dd88959a0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000855.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_965
+MVYAIVRAGGRQEKVSVGDLVTLDRVPAETGGSVELPALMLVDGDEVKAGADAAGVKVTA
+EVVSHSRGKKVVIMKYKNKTGYKKRQGHRSELSTVKITGIA*
+>NZ_CP033200.1_689
+MVYAIVRAGGRQEKVSVGDLVTLDRVPAETGGSVELPALMLVDGDEVKAGADAAGVKVTA
+EVVSHSRGKKVVIMKYKNKTGYKKRQGHRSELSTVKITGIA*
+>NZ_CP040019.1_1857
+MVYAIVRAGGRQEKVSVGDLVTLDRVPAETGGSVELPALMLVDGDKVTAGADAAGVKVTA
+EVVSHSRGKKVVIMKYKNKTGYKKRQGHRSELSTVKITGIA*
+>NZ_CP083691.1_1782
+MVYAIVRAGGRQEKVSVGDLVTLDRVPAEEGGSVELPALMLVDGDKVKAGADAADVKVTA
+EVVSHSRGKKIVIVKYKNKTGYKKRQGHRSELSTVKITGIA*
+>NZ_CP097650.1_907
+MVYAIVRAGGRQEKVSVGDLVTLDRVPAETGGSVELPALMLVDGDEVKAGADAAGVKVTA
+EVVSHSRGKKVVIMKYKNKTGYKKRQGHRSELSTVKITGIA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000861.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000861.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea6ad0e301837a7b3ead75ee6ced3447f3356963
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000861.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_971
+MTVASRTPVPAPTAGGARRRRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVVFVPTGQP
+WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGVTYTVDTLRDLRRLHPDAELF
+FITGADAMGQILTWKDVDELWDLAHFVGVTRPGHDLSDMGLGADVSLMEIPAMAISSTDC
+RERVRRGRPVWYLVPDGVVQYIAKHHLYVSEEETS*
+>NZ_CP033200.1_695
+MTVASRTPVPAPTAGGARRRRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVVFVPTGQP
+WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGVTYTVDTLRDLRRLHPDAELF
+FITGADAMGQILTWKDVDELWDLAHFVGVTRPGHDLSDMGLGADVSLMEIPAMAISSTDC
+RERVRRGRPVWYLVPDGVVQYIAKHHLYVSEEETS*
+>NZ_CP040019.1_1851
+MAVSSRTTASEPTAGGARRRRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVIFVPTGQP
+WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGMTYTVDTLRDLRRLHPDAELF
+FITGADAMGQILTWKDVDELWDLAHFVGVTRPGHDLTDMGLKDDVSLMEIPAMAISSTDC
+RERVARGRPVWYLVPDGVVQYIAKHHLYVSDEETP*
+>NZ_CP083691.1_1776
+MTSATRDPAPPPTSRRHRLGVMGGTFDPIHHGHLVAASEVAAEFGLDEVVFVPTGQPWQK
+SDTRVSPAEHRYLMTVIATASNPRFTVSRVDIERPGNTYTVDTLRDIRAKRPDSELFFIT
+GADALNQILTWKDVEELWDLAHFVGVTRPGYQLEDYGLSEDISLMEIPAMAISSTDCRRR
+VERGRPVWYLVPDGVVQYINKHHLYTPEGDRP*
+>NZ_CP097650.1_913
+MTVASRTPVTAPTAGRARRPRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVVFVPTGQP
+WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGVTYTVDTLRDLRRLHPDAELF
+FITGADAMGQILTWKDVDELWGLAHFVGVTRPGHDLSDMGLGADVSLMEIPAMAISSTDC
+RERVRRGRPVWYLVPDGVVQYIAKHHLYVSEEETS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000862.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000862.fa
new file mode 100644
index 0000000000000000000000000000000000000000..84696ca83a470398b45540ce9f13ff204f10da93
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000862.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_972
+MTVPQTTLDALTTAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE
+EALLKDEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLP
+EESTRPDAATQDDGASASHAS*
+>NZ_CP033200.1_696
+MTVPQTTLDALTTAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE
+EALLKDEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLP
+EESTRPDAATQDDGASASHAS*
+>NZ_CP040019.1_1850
+MTVPQTTLDALTVAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE
+EALLKEEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLA
+EEHTRPDAAGEGAADDAAPHAS*
+>NZ_CP083691.1_1774
+MTVPQTTLDALQVAAAAAAEKVATHIVAVDVAERLGLTDAFLIASGASERQVNAIVDGIE
+EDLLVKEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDSPAIDLGLP
+EEATRPDDALDAAAQD*
+>NZ_CP097650.1_914
+MTVPQTTLDALTTAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE
+EALLKDEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLP
+EESTRPDAAAQDDDASASHAS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000863.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000863.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f08627ab291fa96b8f3e5699497886a1ec11458
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000863.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_973
+MRLILLRHGETDWNVLDRYQGHTDIELNAEGERQARRAAGGPVGDLVEDAEELVAVCSPL
+ARARRTAEIVLEARVGAASVAVDPELMELAGGEWEGLELSAIAERWPDEHRLWRAEPALD
+AGPVGGETLRGGGERALRALRGHVPPHWADTPRDGGAHTLLVVAHGALIRAATGLLLRHE
+GEAFAAMERIGNARAAVLQGAFTADTGAEGWGDWTLEGYGI*
+>NZ_CP033200.1_697
+MRLILLRHGETDWNVLDRYQGHTDIELNAEGERQARRAAGGPVGDLVEDAEELVAVCSPL
+ARARRTAEIVLEARVGAASVAVDPELMELAGGEWEGLELSAIAERWPDEHRLWRAEPALD
+AGPVGGETLRGGGERALRALRGHVPPHWADTPRDGGAHTLLVVAHGALIRAATGLLLRHE
+GEAFAAMERIGNARAAVLQGAFTADTGAEGWGDWTLEGYGI*
+>NZ_CP040019.1_1849
+MRLILLRHGETDWNAGDRYQGRTDVELNAVGERQARRAAVGPVGDLLEEAAELVAVASPL
+ARARRTAEILLEARVGAADLALDEQLMELHGGDWEGLGLTAIAQRWPEEHRSWRAVPALD
+AGPVGGETLRAAGERALGALRGRVPQHWAVYAAAL*
+>NZ_CP083691.1_1773
+MRLVLLRHGETDWNALDRYQGRTDVPLNALGERQAAAAAAGPVGELLRSAEDLVAVSSPL
+IRARRTAEIVLEDAVGAVELAVDSRLVELGGGEWEGLDFTEIGARWPHEHHAWRTVPDLD
+GGPVGGEVLRAGGERVLAAAAAHVPEDWSTPRPARVPDARTLLIVAHGAVIRAAAGLALA
+LEGADFAHLARVSNARAVILDGTFAGEGPGAWSLLGYDV*
+>NZ_CP097650.1_915
+MRLILLRHGETDWNALDRYQGHTDIELNAEGERQARRAAGGPVGDLLEDAEELVAVCSPL
+ARARRTAEIVLQARVGAASVAVDPELMELAGGEWEGLELSAIAERWPDEHRLWRAVPALD
+AGPVGGETLRGGGERALRALRGHVPPHWADTPRDGGAHTLLAVAHGALIRAATGLLLRHE
+GEAFAAMERIGNARAAVLQGAFAPATEGWGDWTLEGYGI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000866.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000866.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3e2cc29d3b4d4313ef2b0253502a5a2bcece85ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000866.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_981
+MTATPDLEQTRHLATELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGNR
+LIDLASGIAVTSVGASHPRVVAAVQDQVAQFTHTSFMITPYEGYVAVAEQLDRTSPIPGE
+TRTALFNSGAEAVENAVKVARAYTGKQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGPF
+APEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEGF
+LPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVTG
+RAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIREHFEQNADD
+RIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRATGVILLTCGTYGNVVRFLPPLT
+IGEDLLKEGLSEVTKALQSA*
+>NZ_CP033200.1_705
+MTATPDLEQTRHLATELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGNR
+LIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTSPIPGE
+TRTALFNSGAEAVENAVKVARAYTGKQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGPF
+APEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEGF
+LPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVTG
+RAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIREHFAQNADD
+RIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRAAGVILLTCGTYGNVVRFLPPLT
+IGEDLLKEGLSEVTNALQSA*
+>NZ_CP040019.1_1838
+MSSTPDLEQSRHLATALPGPRSQALAERQKAAVPAGVATTMPVYAARAAGGILEDVDGNR
+LIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTAPISGQ
+TRTALFNSGAEAVENAVKVARSYTGKQAVAAFDHAYHGRTTLTMALTAKNMPYKHHFGPF
+APEVYRVPGSYPLRDGLSGAEAARRAIGALETQIGAENLAAVIMEPIQGEGGFIVPAEGF
+LPAVVEWCRANDVLFIADEVQSGVARTGSWFACEAEGVEPDLMTTAKGIAGGMPLSGVTG
+RAEVMDSVHPGGLGGTYGGNPVAAAAALAVFEAIEDEDLLAKATRIEEVIREHFAAHADD
+RIAEVRGRGAMMAIELVEPGTGEPDAALTAAVAAAVRATGVILLTCGTYGNVIRFLPPLT
+IGEDLLKEGLSEVTKALQSA*
+>NZ_CP083691.1_1727
+MTSPVTAPEQSRHIATELPGPKSRELAARQAGAVPAGVATTMPVFASRAGGGIIEDVDGN
+RLIDLGSGIAVTSVGASHPKVVEAVQEQVADFTHTCFMITPYEGYVAVAEKLGEKAPISG
+ETRTALFNSGSEAVENAVKVARAYTRKQAVVAFDHAYHGRTTLTMSLTAKSMPYKHSFGP
+FAPEVYRVAGSYPLRDGLNGAAAAKKAISAMEKQIGADNLAAVIMEPLQGEGGFIVPAEG
+FLQAIVEWCTANDVLFIADEVQSGFARTGAWSASELEGIEPDLMCTAKGIAGGMPLSAVT
+GRAEVMDAVHPGGLGGTYGGNPVATAASLAVFEAIEEDGLLQEAQMIERVIREHFEQNAD
+ERIAEVRGRGGMMAIEFVDPASGEPDAALTGKLAAAVRAAGVVLLTCGTYGNVVRFLPPL
+TIGEELLREGLAEVTTALQSA*
+>NZ_CP097650.1_924
+MTATPDLEQTRHLVTELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGNR
+LIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTCPIPGE
+TRTALFNSGAEAVENAVKVARAYTGRQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGPF
+APEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEGF
+LPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVTG
+RAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIRDHFEQNADD
+RIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRATGVILLTCGTYGNVVRFLPPLT
+IGEDLLKEGLSEVTKALQSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000868.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000868.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e5082fa01326be2fc1e087c94b1a8be347f20b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000868.fa
@@ -0,0 +1,31 @@
+>NZ_CP042169.1_983
+MNTTVRRALWVVLVLLCLGLVFLALRGVLAVGAVPISAAPTLSATASATPSPSPSPSSAR
+FTPSPATTATPTPTPSPSSASPTREAAVPVETQELAGTPTPSEEPTPTEEPAPSEEPAPS
+EEPTPAAAAHLSGPAAPWDEVTATPVHVDVHQDGEQIVGAGIDLTQLDEGGDLDPEPQTV
+GWYGPPQWGTTPGERSRYAGVLAGHVVYHGVRDVFWNLGDVRAGAVVVVTYDDGTQAAFE
+ADSDAVSVEKEALTQDPANRWAWEPGGDDAKVTLITCDLVPGTGMAGNAFNNWVVQATRV
+A*
+>NZ_CP033200.1_707
+MNTTVRRALWVVLVLLCLGLVFLALRGVLAVGAVPISAAPTLSATASATPSPSPSPSSAR
+FTPSPAPTATPIPTPSPSSASPTREAAVPVETQELAGTPTPSEEPTPTEEPAPSEEPAPS
+EEPTPAAAAHLSGPAAPWDEVTATPVHVDVHQDGEQIVGAGIDLTQLDEGGDLDPEPQTV
+GWYGPPQWGTTPGERSRYAGVLAGHVVYYGVRDVFWNLGDVRAGAVVVVTYDDGTQAAFE
+ADADAVSVEKEALTQDPAHRWAWEPGGDDAKVTLITCDLVPGTGMAGNAFNNWVVQATRV
+A*
+>NZ_CP040019.1_1836
+MTGPAAPWESIDAAPVHVEVHQDGERIVGASVEHTQMNEAGELDPDPQTVGWYGAPQWGT
+DPGERSPYAGILAGHVVYYGVKDVFWNLDAVRAGDVVVLTYDDGSQAVFEADADAVSVEK
+EALTQDPANRWAWEPGGDDARLTLITCDLVPGTGMAGNAFNNWVVQATRVA*
+>NZ_CP083691.1_1729
+MSTTVKRAVWALLLLICLGVGAFALRGMFAFGDVPISAAPTVSARASTASSTPSAATGSP
+SSTSASASAGPSVPAATSASSAAASTTTPASPTSSTTTPASPTSSTTPASTEAAAPAVGA
+ASSTATASSSATPTGTDSRMTKPAASWERITAAPVHIDVYADGEQVVGAPVELVQTRDDG
+ELNPDPQMAGWYGPPQWTTTPGERSAHPGVIAGHVIHSGLKDVFWNLQTLKAGSIVVITY
+DDGTQAEFRTDFDVRSMDKDDLTQSPDYAWAWELPEAGNKVTLITCDLVDGSGMTGWSTN
+NWVTQATRIG*
+>NZ_CP097650.1_926
+MNTTVRRALWVVLLLLCLSLVFLALRGVLAVGAVPISAAPTLSATASVSPSSAATTREAA
+VPVETQELAGTPTPSEEPTPTEEPAPSEEPTPAAAAHLSGPAAPWDEVTATPVHVDVHQD
+GEQIVGAGIDLTQLDEGGDLDPEPQTVGWYGPPQWGTTPGERSRYAGVLAGHVVYHGVRD
+VFWNLGDVRAGAVVVVTYDDGTQAAFEADADAVSVEKEALTQDPSHRWAWEPGGDDAKVT
+LITCDLVPGTGMAGNAFNNWVVQATRVA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000870.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000870.fa
new file mode 100644
index 0000000000000000000000000000000000000000..47394f150228d4f9807af652be0ae0725fe60bbb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000870.fa
@@ -0,0 +1,31 @@
+>NZ_CP042169.1_985
+MRTARPTRLAVALGAGVLLTGVGATPALASPAHPAGWTAEHGLPGGSFLVAGAEGETGAS
+FGTEFEVDESDVRLTVAPAMEGEARGAETEVPFTYDDELERGDFDVAAARRSLGESGTGP
+VVYTLYVLGGEVAALTYGPDADLTDADPGEPLRADQRHELGFHMLPTAWDTTLLAAPGER
+HVFISSYTGDEAAPLTLVAGPAEGRVVEVTEEETGGPRGYVYQAPEGFTGSDTVTLRATR
+DGVTTTRTVTVRFGDPRVDLYDWENGRIPGFVTFPVAGLFDDAPGQPADPDTPTSPAEPE
+TPADPADGEHTVPDTVETGRGPAAWPVAVAVLAAGVLAVVRRHRVAA*
+>NZ_CP033200.1_709
+MRTARPTRLAAALGAGVLLTGLGATPVLASPAHPAGWTAEHDLPGGSFLVASAEGETGAS
+FGTEFEVDESDVRLTVAPVLEGEARGAETEVPFTYDDELERGDFDVAAARRSLGESGTGP
+VVYTLYR*
+>NZ_CP033200.1_710
+MLPTAWDTTLLAAPGERHVFISSYTGDEAAPLTLVAGPAEGRVVEVAEEETGGPRGYVYQ
+APEGFTGSDTVTLRATRDGVTTTRTVTVRFGDPRVDLYDWENGRIPGFVTFPVAGLFDDA
+PAPGQPADPDTPTSPAEPETPADPADGEHTVPDTVETGRGPAAWPVAVAVLAAGVLAVVR
+RHRVAA*
+>NZ_CP040019.1_766
+MSARRTTRPLSTALAAAVLAGGLAASTAAPALAAPAETTDGWQNGHFVGGTFGSTELSPR
+TGSFYTQHAVKDVRVTVAPFYPAFTDLEEISYKVPGEMGPETDVEFTYDAELEAGYVDVL
+EQRRVLDEEGTAGAVFTLYVDGKATATLVFGEDRNLGDDVPGMFLDATGPQAYDFSARPT
+VDHQTRLAAPGSRLVHLQGNSTGDAPVEDSTRTVVEQPEHGTLVELPRIGDPTNWTSDGA
+NGSFASTVYVADEGFTGTDQAVFTLTDGSTGEQKTLVVTFSIGDPRAADPHLGVQGTGLP
+FDEARVWEALEAQGEDDASEAPAPESPATPAPDSTDAPEASEPSEPADEHTVPETVETGS
+GQAWWLAAVAAAGTGALVAGRRRFGLAR*
+>NZ_CP097650.1_928
+MRTARPTRLAAALGAGVLLTGLGATPALASPAHPAGWTAEHGLPGGSFLVAGAEGETGAS
+FGTEFEVDESDVRLTVAPVLEGEARGAETEVPFTYDDELERGDFDVAAARRSLGESGTGP
+VVYTLYVLGGEVAALTYGPDADLTDADPGEPLRADQRHELGFHMLPTAWDTTLLAAPGER
+HVFISSYTGDEAAPLTLVAGPAEGRVVEVTEEETGGPGGYVYQAPEGFTGSDTVTLRATR
+DGVTTTRTVTVRFGDPRVDLYDWENGRIPGFVTFPVAGPFDDAPGQPADPDTPTSPAEPE
+TPADPADGEHTVPDTVETGRGPAAWPVAVAVLAAGVLAVVRRHRVAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000871.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000871.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2883dba5f6b9f93e886379608a3b03b7a985cd47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000871.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_986
+MSTSPTVTRNDAESRYELHDGGTLLAVLDFRDNGAAVSLNRAFTIPVHRGRGHAAALTAG
+AVEDIATNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPR*
+>NZ_CP033200.1_711
+MSTSPTVTRNDAESRYELHDGGTLLAVLDFRDNGAAVSLNRAFTIPVHRGRGHAAALTAG
+AVEDIETNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPR*
+>NZ_CP040019.1_1834
+MTARDAAGGPAVTRNDAESRYELHDGGTLLAVLDYRDNGTAVALTRAFTIPVHRGHGHAA
+TLTAGAVEDIEARGGAAGGRQIVPLCWYVAQWLEEHPEKAHLVAPR*
+>NZ_CP083691.1_1724
+MDASDSPTTFTRNDAASRYELHDASGELLAALDYRDNGTAVSLTRAFTVPVHRRQGHAAT
+LTAGAVADIEARGGAAGGTTVVPMCWYVARWFEEHPEKAGLLDAR*
+>NZ_CP097650.1_929
+MTTGGCPGMSTSPTVTRNDAESRYELHDGGTLLAVLDFRDNGAAVSLNRAFTIPVHRGRG
+HAAALTAGAVEDIATNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000873.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000873.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c55965c799b8fb46347f935f8dfe115828615fa5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000873.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_988
+MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREPT
+LGATAPYVLMTPTYGGGSGPGAVPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLAGY
+IISRKCQVPLMYKFELMGTPDDVERVRGGLEGMWT*
+>NZ_CP033200.1_713
+MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREPT
+LGATAPYVLMTPTYGGGSGPGAVPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLAGY
+IISRKCQVPLMYKFELMGTPDDVERVRGGLEGLWT*
+>NZ_CP040019.1_1829
+MTVAADPGHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVQKLELPEDRVARLPLITREPT
+LGATAPYVLLTPTYGGGDGPGAVPKQVIKFLNVPGNRTWIRGVIASGNTNFHEAYCLAGY
+IIARKCQVPLMYKFELMGTPEDVDSVRGGLEGLWT*
+>NZ_CP083691.1_1716
+MTTATAGPNHMRDAEAQGLVPTDARLIYFSSASGYTHRFVEKLGLPLGQAARLPLLTREP
+TLGATAPYVLLTPTYGGGGDTGGEVPKQVIKFLNVPGNRALIRGVIASGNTNFSGAYAAA
+GYIISRKCQVPLMYKFELMGTPEDVVAVREGLERLEEGQHA*
+>NZ_CP097650.1_931
+MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREPT
+LGATAPYVLMTPTYGGGSGPGAVPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLAGY
+IISRKCQVPLMYKFELMGTPDDVERVRGGLEGLWT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000878.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000878.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2f519fe2fbd4670da7f39cea3a34df41e021d33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000878.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_998
+MTILPASPPPSVILLGGASGSGKSYLARQHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRT
+PYGEIDWDHPGTWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPDGVIVAE
+GIFAERMPAALDRAEVHYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTD
+AARRAAAMAAGFTPRRKREIIADLT*
+>NZ_CP033200.1_721
+MILLGGASGSGKSYLARQHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRTPYGEIDWDHPG
+TWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPGGVIVAEGIFAERMPAAL
+DRAGVRYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTDAARRAAAVAAG
+FTPRRKREIIADLTA*
+>NZ_CP040019.1_1818
+MILLGGASGSGKSYLARRHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRTPYGEIDWDHPG
+TWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPGGVIVAEGIFAERMPAAL
+DRAGVGYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTDAARRAAAVAAG
+FTPRRKREIIADLTA*
+>NZ_CP083691.1_1705
+MTILPASPPPSVILLGGASGSGKSYLARRHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRT
+PYGEIDWDHPGTWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPGGVIVAE
+GIFAERMPAALDRAGVGYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTD
+AARRAAAVAAGFTPRRKREIIADLTA*
+>NZ_CP097650.1_939
+MTILPASPPPSVILLGGASGSGKSYLARRHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRT
+PYGEIDWDHPGTWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPGGVIVAE
+GIFAERMPAALDRAGVRYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTD
+AARRAAAVAAGFTPRRKREIIADLTA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000881.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000881.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a8dd4d537802f1d2435dbed9fe754d396ccd4cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000881.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1002
+MCGRYVMARATSDLVALGDAEANEDLVLRQSWNVAPTAEVPILVAHADDVGAGGTRGGDG
+GAGVTRRIHVARWGLVPPWAKELSVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGYY
+EWKTPEPGAKGPDGRIAKKQPYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAKAAGEDAWV
+LSTTILTMAAPDADDDDPVLAALGQLHDRLPVPMDAETMDRWLAPDTLGSAEEADALVGQ
+VCAGAYDVAAGWSLRPVGSAVGNVRNNGPELIQEMREQQGTLL*
+>NZ_CP033200.1_725
+MCGRYVMARATSDLVALGDAEANEDLVLRQSWNVAPTAEVPILVAHADDVGAGGARGGDG
+GAGVTRRIHVARWGLVPPWAKELSVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGYY
+EWKAPEPGAKGPDGRAAKKQSYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAKAAGEDAWV
+LSTTILTMAAPDADDDDPVLAALGQLHDRLPVPMDAETMDRWLAPDTLGSAEEADALVGQ
+VCAGAYDVAAGWSLRPVGSAVGNVRNNGPELIQEMREQQGTLL*
+>NZ_CP040019.1_1815
+MCGRYVMARAAGDLVALGGGELPDERLELRRSWNVAPTSDVPILLEREADGAVRRELHVA
+RWGLVPSWAKELAVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGYYEWKAPAPGAKG
+PDGKAAKKQPYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAEAAGRDPWVLSTTILTMAAP
+DADDEDEVLGSLGDLHDRLPVPLDAETMDAWLTPGRLGSAEEADALVGQVCAGAYDVAAG
+WVLRPVGTAVGNVRNDGPELIQAEEPAQGTLL*
+>NZ_CP083691.1_1702
+MARAAGDLVALGGGLLPEEGLELRPNWNVAPTADVPILLEREDAGVVRRELHVARWGLVP
+TWAKELSVGSRAFNARSETVTSKPTFRSAVRARRCAVPVEGYYEWKAPEPGSTGPDGKAA
+VKQPFYVHPAGGGDGEGPVIWFAGLYEWWKDAGAEARGDDPWVLSTTILTMPSPADDEPG
+VLGELADLHDRLPMPMGPAAMDSWLSPDKLGSADEAAALVDEMTAQAYDVARGWELRPVG
+RAVGNVRNNGPELIAPPAEVQDALL*
+>NZ_CP097650.1_943
+MCGRYVMARATSDLVALGDAETNEELVLRQSWNVAPTAEVPILVAHADDVGAGVTRRIHV
+ARWGLVPPWAKELSVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGYYEWKTPEPGAK
+GPDGRAAKKQPYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAKAAGEDAWVLSTTILTMAA
+PDADDDDPVLAALGQLHDRLPVPMDAETMDRWLAPDTLGSAEEADALVGQVCAGAYDVAA
+GWSLRPVGSAVGNVRNNGPELIQEMREQQGTLL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000890.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000890.fa
new file mode 100644
index 0000000000000000000000000000000000000000..454b0c62633658c03461d79beb20dcd064d97514
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000890.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1014
+MTDTAAKFSEYAHPEKLVSTQWVADHVGDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE
+LNDPVTRDFVGPEAFAEFAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD
+GGRDKWIAEGRETTREVPTVARAEYPVIERDDHTERAAREDVLQAIGTTPLIDVRSRPEY
+TGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRAGAGLQEGDD
+VIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR*
+>NZ_CP033200.1_737
+MTDTAAKFSEYAHPEKLVSTQWVADHVDDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE
+LNDPVTRDFVGPEAFAEVAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD
+GGRDKWIAEGRETTREVPTVARAEYPVIERDDHTERAAREDVLQAIGTTPLIDVRSRPEY
+TGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRTDAGLREGDD
+VIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR*
+>NZ_CP040019.1_1804
+MTETATEFSQYAHPEKLVSTQWVADHVGEEGVVVLESNEDALLYATGHIPGAQRIDWHTE
+LNDPVTRDFIGPEAFAEMAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDVRLMN
+GGRDKWIAEGRETTREVPTVARGEYPVVPRDDTTERAAREDVLQAVGTTPLIDVRSRPEY
+TGETTHMDGYPQEGTLRGGHIPTAASVPWAQAANEDGTFKSREELEAVYRDGAGLKDGDD
+VIAYCRIGERSSHTWFVLKHLLGHENVRNYDGSWTEWGNSVRLPIVVGEEPGAAPAR*
+>NZ_CP083691.1_1691
+MTETPAEFAEYAHPEKLVSTQWVADHIDDEGVVVLESNEDTLLYSTGHIPGAVKIDWHTE
+LNDPVSRDFVGPEAFAELVASKGIGPDTTVVFYGDKSNWWAAYALWVFTLYGHRDVRLMN
+GGRDKWIAEGRPTTREVPEVTPAPSYPVSQRDDATDRAAREDVLAAIGSTPLVDVRSPKE
+YTGETTHMDGYPQEGTLRGGHIPTAASVPWAKAANEDGTFKSRAELEEIYKEGAGLGESD
+SVIAYCRIGERSSHTWFVLKQLLGYENVRNYDGSWTEWGNGVRLPIALGDEPGEAPAR*
+>NZ_CP097650.1_954
+MTDTAAKFSEYAHPEKLVSTQWVADHVGDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE
+LNDPVTRDFVGPEAFAEFAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD
+GGRDKWIAEGRETTREVPTVARAEYPVIERDDHTDRAAREDVLQAIGTTPLIDVRSRPEY
+TGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRAGAGLQEGDD
+VIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000900.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000900.fa
new file mode 100644
index 0000000000000000000000000000000000000000..48f8ef9dbf46c2c999b26654cf6af5d5bbbb1a09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000900.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1037
+MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE
+EISQLLYHVQTMMIARGISLEDVYRHL*
+>NZ_CP033200.1_766
+MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE
+EISQLLYHVQTMMIARGISLEDVYRHL*
+>NZ_CP040019.1_1792
+MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE
+EISQLLYHVQTMMIARGIALEDVYRHL*
+>NZ_CP083691.1_1677
+MKTFEELFAELTRKVAERPEGSGTVAQIDAGVHAIGKKIVEEAAEVWMAAEYESHDAAAE
+EISQLLYHVQTMMIAKGIGLKDVYRHL*
+>NZ_CP097650.1_985
+MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE
+EISQLLYHVQTMMIARGISLEDVYRHL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000902.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000902.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d533f23c4674239b63a4dc9ffa610d07fecf068
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000902.fa
@@ -0,0 +1,29 @@
+>NZ_CP042169.1_1039
+MSLAVRVIPCLDVDAGRVVKGVNFENLRDAGDPVELARRYNAAGADELTFLDVTASTSDR
+ATTYEVVTRTAEEVFIPLTVGGGVRTVEDVDRLLRTGADKVSVNTAAVARPEVITEITRR
+FGSQVLVLSLDARRTEDPGCASGYEVTTHGGRRGTGIDAVAWCREASERGVGEILLNSID
+ADGTREGFDLEMIRDVRAVTRVPLIASGGAGEPEHFPPAVAAGADAVLAASLFHFGPDDM
+LARVKDALRQAGHTVR*
+>NZ_CP033200.1_768
+MSLAVRVIPCLDVDAGRVVKGVNFENLRDAGDPVELARRYNAAGADEITFLDVTASTSDR
+ATTYDVVTRTAEEVFIPLTVGGGVRTVEDVDRLLRTGADKVSVNTAAVARPEVITEITRR
+FGSQVLVLSLDARRTEDPGCASGYEVTTHGGRRGTGIDTVAWCREASERGVGEILLNSID
+ADGTREGFDLEMIRDVRAVTRVPLIASGGAGEPEHFPPAVAAGADAVLAASLFHFGPDDM
+LARVKDALRQAGHTVR*
+>NZ_CP040019.1_1790
+MVKGVNFENLRDAGDPVELARRYNAAGADEITFLDVTASTADRATTYDVVTRTAEEVFIP
+LTVGGGVRTEEDVDRLLRVGADKASVNTAAVARPELITEITRRFGSQVLVLSLDARRTQD
+PGCASGYEVTTHGGRRGTGIDAVAWCREASERGAGEILLNSIDADGTRNGFDLEMIRDVR
+AVTRVPLIASGGAGVPEHFPPAVEAGADAVLAASMFHFGPDDMLARVKDALRQAGHTVR*
+>NZ_CP083691.1_1675
+MTVAVRVIPCLDVDAGRVVKGVNFENLRDAGDPVELAARYGAQGADELTFLDVTATTGDR
+ATMFDVVTRAAEQIFIPLTVGGGVRSVEDVDRLLRTGADKASVNSAAVARPELIGEIARR
+FGNQVLVLSLDARRTRDPGCASGYEVTTHGGRKGTGIDAVAWCREATERGVGEILLNSID
+ADGTRDGFDLEMIRDVRAVTTVPLIASGGAGLPEHFPPAVDAGADAVLAASMFHFGPDDM
+IGQVKDALRAAGHVVR*
+>NZ_CP097650.1_987
+MSLAVRVIPCLDVDAGRVVKGVNFENLRDAGDPVELARRYNAAGADEITFLDVTASTSDR
+ATTYDVVTRTAEEVFIPLTVGGGVRTVEDVDRLLRTGADKVSVNTAAVARPEVITEITRR
+FGSQVLVLSLDARRTEDPGCASGYEVTTHGGRRGTGIDTVAWCREASERGVGEILLNSID
+ADGTREGFDLEMIRDVRAVTRVPLIASGGAGEPEHFPPAVAAGADAVLAASLFHFGPDDM
+LARVKDALRQAGHTVR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000903.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000903.fa
new file mode 100644
index 0000000000000000000000000000000000000000..980a184595773f6ce763ecfdd0ec584fd65da5df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000903.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1040
+MSISPPDDLVASVTFDDRGLVPAIAQQEGTGEVLMMAWMNEESLRATLETGWATYWSRSR
+GELWRKGETSGHLQRVRAVHADCDGDTLLLTVDQTGPACHTGTRTCFTGRELVMPPAAVD
+PEEAAR*
+>NZ_CP033200.1_769
+MSISPPDDLVASVTFDDRGLVPAIAQQEGTGEVLMMAWMNAESLRATLETGWATYWSRSR
+GELWRKGETSGHLQRVRAVHADCDGDTLLLTVDQTGPACHTGTRTCFTGRELVMPPAAVD
+PEEAAR*
+>NZ_CP040019.1_1788
+MSISSHHDLVASLAFDDRGLVPAIAQQEGTGEVLMMAWMNAESLRLTLETGWATYWSRSR
+GELWRKGETSGHLQRVLAVHADCDADTLLLTVDQTGPACHTGTRSCFTDRLLAEPAAPAG
+DQAEGAGR*
+>NZ_CP083691.1_1674
+MSPSDVVADLPPLIFDERGLIPAIAQQHDSGEVLMMAWMNEESLRRTLEDGWATYWSRSR
+QEYWRKGETSGHLQRVLAVAADCDGDTLLLTVDQTGPACHTGTTSCFTDRRFAAPTAADE
+DPQTEDAEAVR*
+>NZ_CP097650.1_988
+MSISPPDDLVASVTFDDRGLVPAIAQQEGTGEVLMMAWMNAESLRATLETGWATYWSRSR
+GELWRKGETSGHLQRVRAVHADCDGDTLLLTVDQTGPACHTGTRTCFTGRELVMPPAAVD
+PEEAAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000905.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000905.fa
new file mode 100644
index 0000000000000000000000000000000000000000..858d9d05c6ed09d54c9a092bc41bbfcccd0b4b95
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000905.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1042
+MRRRTVVLAALAAGALVLLTAGRTWVTATGLSGGIASEATTSGGAAAPVATAMALVVMAG
+ALALTTARRLGAVIVGVLMALAGVVIASTSVTAALDPATTAAAAVADATGTTALAQDYAV
+TAWPWVAAAGGVLAALCGVVAALAGRGWRSSRRYEKAPAASEPGPAAAGEQPAQSAREAA
+QRRRVDQMDAWDELSRGNDPT*
+>NZ_CP033200.1_771
+MRRRTVVLAALAAGGLVLLTAGRTWVTATGLSGGIASEATTSGGAAAPVATAMALVVMAG
+ALALTTARRLGAVIVGVLMALAGVVIASTSVTAALDPATTAAAAVADATGTTALAQDYAV
+TAWPWVAAAGGVLAALCGVVAALAGRGWRSSRRYEKAPAASEPGPAAAGEQPAQSAREAA
+QRRRVDQMDAWDELSRGNDPT*
+>NZ_CP040019.1_1786
+MRRRTVVLAALAAGSLVLLAAGQTWVVGSGLTGGLSEEATTSGGAAAPGATAMALVVLAG
+ALALTTARRVGVVVVGALLVLAGIVIVTGAAGAALDPAGTAASAVAEATGTTAAAGSYAV
+TAWPWVAVTGGVLAALCGAVAALAGRGWVSVRRYEKAEATDAAEPAAPGRAAAPGRTEAE
+RRRTEQMDAWDELSRGNDPT*
+>NZ_CP083691.1_1672
+MRRRWIVLAALLAGVLVLAATGQTWVTASGLEGSPVPQATAGGGRVAPVATALALVVMAG
+ALALTTARRVGVVLVGVLMTLAGVVIASTAVTAALDPVAAAAGAVSELTGTTAPAAAYAV
+SAWPWVSAAGGVMAAVLGVATLVVGPRWAASRRFESPATADEPAAAAPPSRHVDRMDAWD
+ELSRGEDPT*
+>NZ_CP097650.1_990
+MRRRTVVLAALAAGGLVLLTAGRTWVTATGLSGGIASEATTSGGAAAPVATAMALVVMAG
+ALALTTARRLGAVIVGVLMALAGVVIASTSVTAALDPATTAAAAVADATGTTALAQDYAV
+TAWPWVAAAGGVLAALCGVVAALAGRGWRSSRRYEKAPAASEPGPAAAGEQPAQSAREAA
+QRRRVDQMDAWDELSRGNDPT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000915.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000915.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bbff437b217ba44448ecc54887015abc7f44b2dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000915.fa
@@ -0,0 +1,77 @@
+>NZ_CP042169.1_1052
+MLLTSLLLTLLSVVAAVPASRALGRDAGWVLAAPLLAAAGVLIAAWTGDVRTEHHPWIPA
+VGVDLDLRLNGLALVFAMIVLVIGAAILAYSSRYLSRDRTESRPGSFYLLMTAFAASMLL
+LVLADNIVVLFVAWEFTSFTSFFLIGRSGDHARDPAIRTLLVTVGGGLALLAAVALMAVR
+TGTASLSGVLASDVWSEAGFTTTVAVLLAVAAFTKSAQFPFQAWLPDSMVAISPVSAYLH
+AAAMVKAGIFLLLVFSPVLAGNPVWSALLIGSGLITALLGAVSAIRRHDLKGLLAYSTMS
+QLGLLVTAIGIGTPVALTAAIVHTVAHALFKSALFMLIGVVDHEAGTRDLRELAARHVRM
+PVTGTAIAVAALSMAGIPPLFGFISKEGLVEAALGTPGPAWLPVLVTAGIALTSVFTVAY
+SGRLVLGALGLWGPSPDGAAHSWPTGREDEVHEASATFWGVPVLAAAAGVALGLLPGVLD
+TPVSYAAEAASGAEVHAHLALWHGVNTALLVSAAIIVLGLLLVALRRPVERVASHAALPF
+SALDAVDEVRHRLIGVGAVVSRASGTLAPRPHLLIPALVLGLLAVAGVATIEDLPAVVGQ
+PSRWHDWVLVVLVGAGVIATIRAKTRIAAMVVVGVVGFGMTLWFLTLGAVDVALTQLMVE
+VLTVCVMVLLLRRLPARFSDEPTPRRMQAVLAASVAGVAATLGVLAFTGRSSMSEIAHFY
+LTQSYAQAGGTNVVNVILVDFRAVDTWGEMTVLGATALTIAALLLNRRPTPPQPSAVDMR
+SPLAHVRENLVHIRVFGRVFGVLIILLSAFLLLRGHYEPGGGFIAALVAGAGYALLYLAA
+DSDTAPELRWPYLAFIGSGIAVGTATGIVGYLTGKGFLGAAGVKVLDYGLSTTLAFDMGV
+YLAVIGLIVAAFSLLGPERPGEDPLRASSRDPGVAPAAPSSDPSAPTTTTAREEVTR*
+>NZ_CP033200.1_781
+MLLTSLLLTLLSVVAAVPASRVLGRDAGWVLAAPLLAAAGVLIAAWTGDVRTEHHPWIPA
+VGVDLDLRLNGLALVFAMIVLVIGAAILAYSSRYLSRDRTESRPGSFYLLMTAFAASMLL
+LVLADNIVVLFVAWEFTSFTSFFLIGRSGDHARDPAIRTLLVTVGGGLALLAAVALMAVR
+TGTASLSGVLASDVWSEAGFTTTVAVLLAVAAFTKSAQFPFQAWLPDSMVAISPVSAYLH
+AAAMVKAGIFLLLVFSPVLAGNPVWSALLIGSGLITALLGAVSAIRRHDLKGLLAYSTMS
+QLGLLVTAIGIGTPVALTAAIVHTVAHALFKSALFMLIGVVDHEAGTRDLRELAARHVRM
+PVTGTAIAVAALSMAGIPPLFGFISKEGLVEAALGTPGPAWLPVLVTAGIALTSVFTVAY
+SGRLVLGALGLWGPSPDGAAHSWPTGREDEVHEAPATFWGVPVLAAAAGVALGLLPGVLD
+TPVSYAAEAASGAEVHAHLALWHGVNTALLVSAAIIVLGLLLVALRRPVERVASHAALPF
+SALDAVDEVRHRLIGVGAVVSRASGTLAPRPHLLIPALVLGLLAVAGVATIEDLPAVVGQ
+PSRWHDWVLVVLVGAGVIATIRAKTRIAAMVVVGVVGFGMTLWFLTLGAVDVALTQLMVE
+VLTVCVMVLLLRRLPARFSDEPTPRRMQAVLAASVAGVAATLGVLAFTGRSSMSEIAHFY
+LTQSYAQAGGTNVVNVILVDFRAVDTWGEMTVLGATALTIAALLLNRRPTPPQPSAVDMR
+SPLAHVRENLVHIRVFGRVFGVLIILLSAFLLLRGHYEPGGGFIAALVAGAGYALLYLAA
+DSDTAPELRWPYLAFIGSGIAVGTATGIVGYLTGKGFLGAAGVKVLDYGLSTTLAFDMGV
+YLAVIGLIVAAFSLLGPERPGEDPLRASSRDPGVAPAAPSSDPSAPTTTTAREEVTR*
+>NZ_CP040019.1_1774
+MDEARHGLVRLGALVDRASGSVAPRVHLLIPACVLGAFALAGVFTVDDLPAVVGTPSRWH
+DWALVVLVGAGVVATIRAKTRISAMVVVGVVGFGVTLWFFTLGAVDVALTQLLVEVLTVC
+VMVLLLRRLPGRFRDEEAPRRVQAVVAATIAGVAATVGVLAFTGRSEMSEIAHFYLTQTY
+AQAGGVNVVNVILVDFRALDTLGEMTVLGATGLTVAALLLNRRPAPPQRSAVDLRSPLAH
+VRENLVHIRVFGRVFGVLIIALSVLLLLRGHYEPGGGFIAALVAGAGYALLYLAADHDTD
+RRLQWPYLTLIGGGIALGALTGVAGYLTGKGFLGAAGVKILGYGLSTTLAFDLGVYLAVL
+GLIVAAFSLLGPERSETEAGAEPDPTSPIADPAAEQTTGQTTEPTTAPGTAPTPAAAREE
+TSR*
+>NZ_CP083691.1_1662
+MLLTSLLLTLLAVVLAAPLGRTLGRDAGWVLALPLLTSAGALVSARAGGGGETVVERRPW
+IPSLGAHLDLRLDGLAFVFALLVLVVGAGILAYSSRYLPRDRDEARAGSFYTLMTAFAAS
+MLLLVLADNLVVLFVAWEFTSFASFLLIARSGDHARRPAIRTLLVTVGGGLCLLAAVALT
+AARTGTASLSGALASDAWADPGFAAPVAALLAVAAFTKSAQFPFQSWLPDSMVAISPVSA
+YLHAAAMVKAGIYLLLVFSPVLAGTPVWSALLIGSGLTTALLGAVSAIRRHDLKGLLAYS
+TMSQLGLLVTAIGVGTPTALAAAVVHTVAHALFKSTLFMLIGVVDHEAGTRDLRDLAARH
+VRMPVTGAAIAVAAASMAGLPPLLGFVSKEGLLDAALGAQGPAWLPGLVTAGIALTSVFT
+VAYSGRLVLGALGVWGTAPAGAADMWSAGRGEDVHEAPAAFWAVPVLGVVVTLVLGLVPG
+VLDEAVAAAATAAAGAPVHAHLALWHGVTPALLVSAGVIAAGLALVAARRPVERVASHAG
+LPFSGLGVVDGILRGAVSLGAAVSRVSGGIAPRAHLLMPALVLGAFAVAGVVASPDLPAV
+VGQPSRWHDWALVALVGVGVAATLRARTRIAAMVVVGTVGFGVTLWFFTLGAVDVALTQL
+MVEVLTVCVMVLLLRRLPARFSAESTPHRAGAVAAAVIAGVASTLSVLAFTGRREISDIA
+QYYLDRTYPDAGGHNVVNVILVDFRALDTLGEMTVLGVTGLTVAALLMNRRPAPPQPSAV
+DVRSPLAAVHENLVYARTFGRALGPIILVLSVLLLLRGHYEPGGGFIAALVGGAGYALLH
+LSADTDDEPRLRWPYLALIGGGVTLGTVAGLAGYLTGKGFLGSASVKVLGYSLGTTLAFD
+MGVYLAVLGLIVAAFRLLGPDNATADDAAPAPTTGGESAREEAAR*
+>NZ_CP097650.1_1000
+MLLTSLLLTLLSVVAAVPASRVLGRDAGWVLAAPLLAAAGVLIAAWTGDVRTEHHPWIPA
+VGVDLDLRLNGLALVFAMIVLVIGAAILAYSSRYLSRDRTESRPGSFYLLMTAFAASMLL
+LVLADNIVVLFVAWEFTSFTSFFLIGRSGDHARDPAIRTLLVTVGGGLALLAAVALMAVR
+TGTASLSGVLASDVWSEAGFTTTVAVLLAVAAFTKSAQFPFQAWLPDSMVAISPVSAYLH
+AAAMVKAGIFLLLVFSPVLAGNPVWSALLIGSGLITALLGAVSAIRRHDLKGLLAYSTMS
+QLGLLVTAIGIGTPVALTAAIVHTVAHALFKSALFMLIGVVDHEAGTRDLRELAARHVRM
+PVTGTAIAVAALSMAGIPPLFGFISKEGLVEAALGTPGPAWLPVLVTAGIALTSVFTVAY
+SGRLVLGALGLWGPSPDGAAHSWPTGREDEVHEAPATFWGVPVLAAAAGVALGLLPGVLD
+TPVSYAAEAASGAEVHAHLALLHGVNTALLVSAAIIVLGLLLVALRRPVERVASHAALPF
+SALDAVDEVRHRLIGVGAVVSRASGTLAPRPHLLIPALVLGLLAVAGVATIEDLPAVVGQ
+PSRWHDWVLVVLVGAGVIATIRAKTRIAAMVVVGVVGFGMTLWFLTLGAVDVALTQLMVE
+VLTVCVMVLLLRRLPARFSDEPTPRRMQAVLAASVAGVAATLGVLAFTGRSSMSEIAHFY
+LTQSYAQAGGTNVVNVILVDFRAVDTWGEMTVLGATALTIAALLLNRRPTPPQPSAVDMR
+SPLAHVRENLVHIRVFGRVFGVLIILLSAFLLLRGHYEPGGGFIAALVAGAGYALLYLAA
+DSDTAPELRWPYLAFIGSGIAVGTATGIVGYLTGKGFLGAAGVKVLDYGLSTTLAFDMGV
+YLAVIGLIVAAFSLLGPERPGEDPLRASSRDPGVAPAAPSSDPSAPTTTTAREEVTR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000917.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000917.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8d4a40946edca7c02f8dc40451840e1ae5c576e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000917.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_1054
+MSAVPLGQLLPLFAAVPLLSAGLLVLAGERPRLHRAVLFAVLGLVTTGGLALGVHALDGS
+VLATSLGGWPGGIGIGFAADMLSALMLVLTSALTIVGAAFAYGSRVANSQFFAPLLLILI
+GGVNGALLTADLFNLFVFIEVMLVPSYGLYVLSANRREPLRRVDGARLYVTLNLLTSTIL
+LVGVGFVYGLTGSVNLAMLAGSAAADPRIAIAAGMVLFALSIKASVAPLHGWLAWAYSST
+SPAVTALFAALHTKVAVYGLYRIYSVMYDGDARLLPLILVLSLATLVVGALASVGEHGVR
+AVLSWQMVSGIGGILVGLGLSTRLGLAAGLFYLVHHMVAMGCLLMAAGAIEVRYGTGRLA
+DLQGLARREPLIAVAFFVGLLSLVGIPPFSGFVGKLMLVSAGLDAGRGVTAALVLGASLV
+SLWVLLRVWDAWFWGAPTAPHGHRERLATAAMPIVGRAGSVPSPSGRGSSTDHERTESWA
+SQETLDPPTGVLPVTVDPDEDVTRSRIPGRLAAPAVVLAMATLALGLGGQALWTVTDLAA
+QGLMDPSRYIEAVLNP*
+>NZ_CP033200.1_783
+MSAVPLGQLLPLFAAVPLLSAGLLVLAGERPRLHRAVLFAVLGLVTTGGLALGVHALDGS
+VLATSLGGWPGGIGIGFAADMLSALMLVLTSALTIVGAAFAYGSRVANSQFFAPLLLILI
+GGVNGALLTADLFNLFVFIEVMLVPSYGLYVLSANRREPLRRVDGARLYVTLNLLTSTIL
+LVGVGFVYGLTGSVNLAMLAGSAAADPRIAIAAGMVLFALSIKASVAPLHGWLAWAYSST
+SPAVTALFAALHTKVAVYGLYRIYSVMYDGDARLLPLILVLSLATLVVGALASVGEHGVR
+AVLSWQMVSGIGGILVGLGLSTRLGLAAGLFYLVHHMVAMGCLLMAAGAIEVRYGTGRLA
+DLQGLARREPLIAVAFFVGLLSLVGIPPFSGFVGKLMLVSAGLDAGRGVTAALVLGASLV
+SLWALLRVWDAWFWGAPTAPHGHRERLATAAMPIVGRAGSVPSPSGRGSSTDHERTESWA
+SQETLDPPTGVLPVTVDPDEDVTRSRIPGRLAAPAVVLAMATLALGLGGQALWTVTDLAA
+QGLMDPSRYIEAVLNP*
+>NZ_CP040019.1_1772
+MSPEALGQLLPLFVAVPLITAGLLTLAGDRPRVHRLVVALVLCLTAGAGALIVARSLDGD
+VLATSVGGWPGGIGIGFAADMLTGLMLLLTSLLTLVGVNLAHGTRVVNSLYFGPLMLVLM
+AGVNGALLTADLFNLFVFIEVMLLPSYGLYVLSANRREPLRRVDGARLYVTLNLLTSTIL
+VVAVGFLYALTGTVNLAVMAGAAARDERVAIAGGLVLFALSIKASVVPLHGWLARAYPST
+SPAVTAIFAALHTKVAVYALYRVFSVLFDNDARFLPLLLALAGLTLAVGALASVGVHGVR
+LVLSWQMVSGIGGILVGLGLSTQLGLSAGLFYLVHHMVAMGCLLAATAAVEVRYGTGRLA
+DLRGLARREPLIAVVFFVGLLSIVGIPPFSGFVGKLMLVTAGVEAGRLVTVAVVLVGSLV
+SLWALLRVWDAWFWGEPGTPHGLRERLATAALPVVGRGAERTGPSGRGSSTDHERTESWT
+STQTIDPPTGVLPVTFAADEDVTRSRIPVRLAMPGVVLAAATLVLGLAGQALWTLTDVAA
+QGLLDPARYIEAVLAP*
+>NZ_CP083691.1_1660
+MSDHAVGLLLPLFVAVPLLSAGLLVVAGSRPRLHRAVLAAVLAGGTVGGGLLMARAADGS
+VAAAGVGGWPDGIAIAFAADMLTGLMVALTAGLTLVGAWFAYGSRVANSAHFAPFMLVLM
+AGVHGALLTADLFNLFVFIEVMLLPSYGLYVLSANRREPLRRVDGARMYVTLNLLTSTIL
+VTGVGFVYALTGSVNMAVLAGAARGDVRVALAAGLVLFALSIKASMLPMHGWLARAYPST
+SPAVTAIFAALHTKVAVYAMYRIYMVVYDGDPRLLGLILTLCLATLMVGAVASVGEHGAR
+AVLSWQMVSGIGGIMVGLGLATQAGLSAGLFYLVHHMVVMACLLTATGAIEVRYGSGRLA
+DLQGLAVREPLIAAAFFVGMLSLVGIPPFSGFAGKLALVLAGVAAGRTVTVVLVLVASLI
+SLWALLRIWDAWFWGRPRAPHGHRERLDTAALPLVHGDGVMPAAGAPVHPAGRGSSTDSE
+RAEAWASTETLDTPTGVLPVVVDPDEDHTASRIPLRLAGPAALMAAATLALGLGAEGLWS
+VTDQAARGLADPTAYIEAVLGR*
+>NZ_CP097650.1_1002
+MSAVPLGQLLPLFAAVPLLSAGLLVLAGERPRLHRAVLFAVLGLVTTGGLALGVHALDGS
+VLATSLGGWPGGIGIGFAADMLSALMLVLTSALTIVGAAFAYGSRVANSQFFAPLLLILI
+GGVNGALLTADLFNLFVFIEVMLVPSYGLYVLSANRREPLRRVDGARLYVTLNLLTSTIL
+LVGVGFVYGLTGSVNLAMLAGSAAADPRIAIAAGMVLFALSIKASVAPLHGWLAWAYSST
+SPAVTALFAALHTKVAVYGLYRIYSVMYDGDARLLPLILVLSLATLVVGALASVGEHGVR
+AVLSWQMVSGIGGILVGLGLSTRLGLAAGLFYLVHHMVAMGCLLMAAGAIEVRYGTGRLA
+DLQGLARREPLIAVAFFVGLLSLVGIPPFSGFVGKLMLVSAGLDAGRGVTAALVLGASLV
+SLWALLRVWDAWFWGAPTAPHGHRERLATAAMPIVGRAGSVPSPSGRGSSTDHERTESWA
+SQETLDPPTGVLPVTVDPDEDVTRSRIPGRLAAPAVVLAMATLALGLGGQALWTVTDLAA
+QGLMDPSRYIEAVLNP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000923.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000923.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d64f78230396cc86bba94246da45824c0103bb19
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000923.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1061
+MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY
+ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE
+KLTGN*
+>NZ_CP033200.1_790
+MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY
+ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE
+KLTGN*
+>NZ_CP040019.1_1764
+MTTTSNAPQVAINDIGTAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVESNEWMEGFESERAAWEQQY
+ADAQSRWEQHKEQVRRSFEEEANAGADTGAGMGGSSYSSEAPASDGGTLASDEALAALRE
+KLTGN*
+>NZ_CP083691.1_1653
+MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKVKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRQGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQDVTVEVLDVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDQLFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDDEGNYKYPEGFDVETNEWMEGFESERASWEQQY
+ADAQTRWEAHKEQVRRSLEEEAQAPAGNASTASSYSSEAPASDGGTLASDEALAALREKL
+TGN*
+>NZ_CP097650.1_1009
+MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY
+ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE
+KLTGN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000927.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000927.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a4dc05eb3c8645a88af9179bbda4b9cdf5731141
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000927.fa
@@ -0,0 +1,65 @@
+>NZ_CP042169.1_1066
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW
+LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGAEMDRDV
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDRLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII
+RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRI
+ADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSLDRAPATGEGAEAPAVDPASL
+PAKDLADLIEQMSQQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ*
+>NZ_CP033200.1_795
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW
+LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGAEMDRDV
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDKLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII
+RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRI
+ADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSLDRDATTGEGTEAPAVDPASL
+PAKDLADLIEQMSKQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ*
+>NZ_CP040019.1_1758
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW
+LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSVNEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGEEMDRDV
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREETEMYIFPASHYVAGDERMGRAVTAIEDELRERLQELESQDRLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPDGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII
+RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLDAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIEETERRRAVQIAYNEEHGIDPQPLRKRI
+ADITDQLAREDADTADFLKGMGGVKSGFDYGMGHRGLSSLDREEGQERAGGGPAVDAASL
+PAKDLADLIEQMSLQMHQAAADLQFELAARLRDEVGELKKELRQMRREQ*
+>NZ_CP083691.1_1648
+MSLAKQINRVVAPFEVVSPYQPSGDQPTAIAEIAERVQAGEKDVVLMGATGTGKSATTAW
+VIEQLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSINEEVERLRHSATNALLTRRDVVVVATVSCIYGLGTPEEYIAQMVTLRRGQEMDRDA
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEVESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAIATIEDELRERLQELESQDKLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGQYELSQADGVVEQII
+RPTGLVDPTVVVKPTQGQIDDLLEQIRTRTEKDERVLVTTLTKRMAEDLTEYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVSILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADRVTDSMRRAIEETERRREVQIRYNAEHGIDPQPLRKKI
+ADITDALAREDADSADFLKGMGGVKAGFDYGMGHRGLGSLDHEPPAGEVPSGSPAVDPAA
+LPAKDLAQLIEQMSAQMHQAAADLQFELAARLRDEIGDLKKELRQMKREQ*
+>NZ_CP097650.1_1014
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW
+LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGAEMDRDV
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDKLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII
+RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRI
+ADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSLDRDATTGEGTEAPAVDPASL
+PAKDLADLIEQMSKQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000929.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000929.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3c0cc560b0ba54cd361ed8d07eadf863de0dbf9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000929.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1068
+MTALALLALGLHDLLDAVLPGAWPTPRRRWLARAGAAVAAVLAAVLVAVLAPTGISVAVG
+GGLVALGLLMGWTWLHPDRPLGVVAVAAAVGLVAVLESTLAPAGLRSAPPALTLLAVTVA
+LTETGNRVTRAVLALAGRSADGGDEEAEDPAAEPTTVPSAAPTDPAADGLRGGRYIGPME
+RLLMVVLGLAQAYPVIAALMAAKGIVRFPEISADRGAGSRAEEFLIGSLASWGLAAAGAV
+VVWLALGLTAPGAA*
+>NZ_CP033200.1_797
+MTALALLALGLHDLLDAVLPGAWPAPRRRWLARAGAAVAAVLAAVLVAVLAPTGVAVAVG
+GGLVSLGLLMGWTWLHPDRPLGVVAVVAVVGLVAVLESTLAPAGLRSAPPALTLLAVALA
+LTETGNRVTRAVLALAGRPADGGDEEAEDPAAEPTTVPSAAPTDPAADGLRGGRYIGPME
+RLLMVVLGLAQAYPVIAALMAAKGIVRFPEISADRGAGSRAEEFLIGSLASWGLAAAGAV
+VVWLALGLTAPGAA*
+>NZ_CP040019.1_1755
+MTALTLIALGVHDLAAALLPRAWAARRREVLALAAGTAAAVLAAVLLVVLVPGAPALAIG
+GVLVALALLAAWWRLGAGAPLGTLGVAAVVALVAVAEIGLARTAGPAVPIAFTVVAVGLA
+LGETANRITRAVLLLAGRRADAAPAPESDAPAEAVLAPETSADDAEAPPLRGGRYIGPME
+RVLMVVLGLAHAWPVVAALMAAKGLVRFPEISADRGEGSRAEEFLVGSLASWGIAAAGGA
+LVWVGLGAPALS*
+>NZ_CP083691.1_1646
+MTALTLLALGLRDLLAVTPGRTSRHPWLALLAAVGAVLIGGVVLAGGAASAAETLSAVAL
+ALGAVLAWHALARAGSPHLRVGALGGVVGLAVAEHTGALTVAHGPVGMALLGAGLVLVET
+ANVVTRDVLRLAGRPSTDDVHDADDVHDADDDGEGLRGGRFIGPMERLLMAVLGLMAAWQ
+AVAAIMAAKGIVRFPEISKDARAGDAKGGPMGASAEEFLVGSLASWTLAAGAGLVVHLAL
+AGG*
+>NZ_CP097650.1_1016
+MTALALLALGLHDLLDAVLPGAWPAPRRRWLARAGAAVAAVLAAVLVAVLAPTGVAVAVG
+GGLVSLGLLMGWTWLHPDRPLGVVAVVAVVGLVAVLESTLAPAGLRSAPPALTLLAVALA
+LTETGNRVTRAVLALAGRPADGGDEEAEDPAAEPTTVPSAAPTDPAADGLRGGRYIGPME
+RLLMVVLGLAQAYPVIAALMAAKGIVRFPEISADRGAGSRAEEFLIGSLASWGLAAAGAV
+VVWLALGLTAPGAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000932.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000932.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8fbac5ec75349f1df09cf8b9ebc3747a4c837802
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000932.fa
@@ -0,0 +1,34 @@
+>NZ_CP042169.1_1073
+MSQIAPESPHPDTDAVVGDVTGRQGGGFTWDPAQYEGFAEHRARPFHDLVGRVRAEAPRV
+VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLERAREQAARTGAPANLRFEAVDASQW
+RPSGATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED
+PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR
+PSLQALARWDAEEGAAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF
+MAGQKPA*
+>NZ_CP033200.1_802
+MSQIAPESPHPDTDAVVGDVTGRQGGGFTWDPAQYEGFAEHRARPFHDLVGRVRAEAPRV
+VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLERAREQAARTGTPANLRFEAVDASQW
+RPSRATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED
+PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR
+PSLQALARWDAEEGSAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF
+MVGQKPA*
+>NZ_CP040019.1_1751
+MSQIAPESPHPDTDAVAGDVTGRQGGGFTWDPAQYESFAEHRARPFHDLVGRVRAEAPRV
+VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLKRAREQAARTGAPANLRFEAVDASQW
+RPSRATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED
+PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR
+PSLQALARWDAEECSAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF
+MVGQKPA*
+>NZ_CP083691.1_1642
+MSTVPAVTGRETAGFTWDPAQYEGFAEHRARPFHDLVARVEAEAPRVVVDLGCGPGTLTR
+TLAERWPAAEVIGLDDSPAMLERAREGAADADLPNLRFDRVDASQWRPGPEVDVIVSNAM
+LQWIPTHRRLIRRWLGDLHPGAWFGAQLPRPYQQASHATIVALADEPVFSEALHGVETTR
+TVAPPEEYTRLFLEAGWTPSVWETEYQQVLTGPDPVLRWTSGAALRPSLQALAAWDAEEG
+AAEGAGLLELFVARYRQAMREAYPPVPGVSDADGGPLTVFPVRRMFLVGRKPGE*
+>NZ_CP097650.1_1022
+MSQIAPESPHPDTDAVVGDVTGRQGGGFTWDPAQYEGFAEHRARPFHDLVGRVRAEAPRV
+VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLERAREQAARTGTPANLRFEAVDASQW
+RPSRATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED
+PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR
+PSLQALARWDAEEGSAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF
+MVGQKPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000939.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000939.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb4812b6de0461389f3006f97c402e85b9b69e8e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000939.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1082
+MTKIAINGYGRIGRNIVRVLRDRGHENLELVAVNDLADPEDLFWLTQYDTILGRYPGELE
+RTEKGFRIDGRDVAFFQEADPTKLPWGELGVDLVIECTGIFTTGPKAQAHLDAGAKKVLI
+SAPAKEVDGTFVMGVNEHTYDAESMHIVSNASCTTNCLAPMAKVLNDEFGIVDGIMTTIH
+AYTGDQNLHDNVHKKDRRRARAAAQNMVPTSTGAAKAIGEVIPELKGKLDGFAMRVPTIT
+GSATDLTVELTRHVEVEEINAAFKKAAESGPLQGRLVYSEDPIVSSDIITSPAACTFDAP
+LTKSIGQTVKIIGWYDNEYGYTSQLMDFADLIGSKL*
+>NZ_CP033200.1_811
+MTKIAINGYGRIGRNIVRVLRDRGHEGLELVAVNDLADPEDLFWLTKYDTILGRYPGELE
+RTEKGFRIDGRDVAFFQEADPTKLPWGELGVDLVIECTGIFTTGPKAQAHLDAGAKKVLI
+SAPAKEVDGTFVMGVNEHTYDAETMHIVSNASCTTNCLAPMAKVLNDEFGIVDGIMTTIH
+AYTGDQNLHDNVHKKDRRRARAAAQNMVPTSTGAAKAIGEVIPELKGKLDGFAMRVPTIT
+GSATDLTVELTRHVEVEEINAAFKKAAESGPLQGRLVYSEDPIVSSDIITSPAACTFDAP
+LTKSIGQTVKIIGWYDNEYGYTSQLMDFADLIGSKL*
+>NZ_CP040019.1_1742
+MTKIAINGYGRIGRNIVRVLRDRGYENLELVAVNDLADNEDLFWLTQYDTILGRYPGELE
+LTETGFRIDGRDVAFFSEPDPAKLPWGELGVDIVIECTGFFTTGPKAKAHLDAGAKKVLL
+SAPGKEVDGTFVMGVNEKNYDSATMDIVSNASCTTNCLAPMAKILNDEFGIVDGIMTTIH
+AYTGDQNLHDSVHKKDRRRARAAAQNMVPTDTGAAKAIGEVIPELKGKLDGFAMRVPTIT
+GSATDLTVELTRHVEVEEINAAFKKAAESGPLQGRLVYSEDPIVSSDIITSPAACTFDAP
+LTKSIGQTVKIIGWYDNEYGYTSQLVDFADLIGSKL*
+>NZ_CP083691.1_1633
+MTKIAINGYGRIGRNAVRVLLEQGHDDLELVAVNDLAATEDLFWLTKYDTILGRFPGELE
+LTDKGFSINGKDVAFFAETDPANLPWGELGVDIVVECTGRFTTGPAAKAHLDAGAKKVLL
+SAPGKEVDGTFVMGVNEGDYDSSTMHIVSNASCTTNCLAPMVKVLNDEFGIVDGIMTTIH
+AYTGDQNLHDNVHKKDRRRARAAAQNMVPTSTGAAKAIGEVIPELKGKLDGFAMRVPTIT
+GSATDLTVELTRHVEAEEVNEAFRRAAESGPLVGRLVYSTDPIVSSDIVTAPAACTFDAP
+LTKSIGQTVKVIGWYDNEYGYTCQLMDMASHMASKL*
+>NZ_CP097650.1_1031
+MTKIAINGYGRIGRNIVRVLRDRGHENLELVAVNDLADPEDLFWLTQYDTILGRYPGELE
+RTEKGFRIDGRDVAFFQEADPTKLPWGELGVDLVIECTGIFTTGPKAQAHLDAGAKKVLI
+SAPAKEVDGTFVMGVNEHTYDAETMHIVSNASCTTNCLAPMAKVLNDEFGIVDGIMTTIH
+AYTGDQNLHDNVHKKDRRRARAAAQNMVPTSTGAAKAIGEVIPELKGKLDGFAMRVPTIT
+GSATDLTVELTRHVEVEEINAAFKKAAESGPLQGRLVYSEDPIVSSDIITSPAACTFDAP
+LTKSIGQTVKIIGWYDNEYGYTSQLMDFADLIGSKL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000943.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000943.fa
new file mode 100644
index 0000000000000000000000000000000000000000..06575f0b43614f832bc4a659d598e54eea8137de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000943.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1086
+MKIRMHDTTTSQVAKRITQLREKSGVVALGRVLTLVISTDDAGIESAVQAANAASLEHPC
+RIVVLALGDPAAPTRLDAEIRVGGDAGASDVVVLWCAGENAHADESLVSGLLLPDAPIVV
+WWPGVPPGVPSATALGRLAHRRITDTASASAAEPALWALRAGHHEGDTDLAWTRLTLWRI
+QVAGIFDTLDVATLRSVTVDGAPDSPSTMLLAAWLTLTLKVPVTIAHSKVGHGIRAVRLR
+CTDGDVVLSRSQSQVARLYQQGRPVQRISLPRRTIQDCLAEELRRLDPDEVFGAVLHQGL
+PRTDLSPVQASER*
+>NZ_CP033200.1_815
+MKIRMHDTTTSQVAKRITQLREKSGVVALGRVLTLVISTDDAGIESAVQAANAASLEHPC
+RIVVLALGDPAAPTRLDAEIRVGGDAGASDVVVLWCAGENAHADESLVSGLLLPDAPIVV
+WWPGVPPGVPSATALGRLAHRRITDTASASAAEPALWALRAGHHEGDTDLAWTRLTLWRI
+QVAGIFDTLDVATLRSVTVDGAPDSPSTMLLAAWLTLTLKVPVTIAHSKVGHGIRAVRLR
+CTDGDVVLSRSQSQVARLYQQGRPVQRISLPRRTIQDCLAEELRRLDPDEVFGAVLHQGL
+PRTDLSPVQASER*
+>NZ_CP040019.1_1737
+MKIRMHDTTTSQVAKRITQLREKGGVVALGRVLTLVISTDDAGIEAAVEAANAASLEHPC
+RIVVLALGDPAAPTRLDAEIRVGGDAGASDVVVLWCAGENAHADESLVSGLLLPDAPIVA
+WWPGVPPAVPSETALGRLAHRRITDTASAARAEPALWTLRQGHRDGDTDLAWTRLTLWRI
+QVAGIFDTLDVAALRSVTVDGAPDSPSTMLLAAWLTLALKVPVTIAHSKAGHGIRAVRLR
+CQDGDVVLSRSQSQVARLYQQGRPVQRISLPRRTDQDCLAEELRRLDPDEVFGAVLHRGL
+PRTDLSPVQASER*
+>NZ_CP083691.1_1629
+MKIRMHDTTTSQVAKRLTALRESAGVSALGRVLTLVIVTDDAGIEAALGAANAASLEHPC
+RIVVLALGDPLAPTRLDAEIRVGGDAGASDVVVLWCQGEDAVADEPLVSGLLLPDAPIVV
+WWPGEPPAEPATTALGRLAHRRITDSATCRDAKETLQRLAAGLHDGDTDLAWTRLTLWRS
+QVAAILDNLDLADVRSVTVDGAPDSPSTLLLAAWLTWGLDRPVTIAHSKAGHGIRAVRLR
+GPEGDVVLSRSQSEVARLYQQGRPVQRISLPRRSDQDCLAEELRRLDPDEVYGDVLRVGL
+PRTDLAPVDASDR*
+>NZ_CP097650.1_1035
+MKIRMHDTTTSQVAKRITQLREKSGVVALGRVLTLVISTDDAGIESAVQAANAASLEHPC
+RIVVLALGDPAAPTRLDAEIRVGGDAGASDVVVLWCAGENAHADESLVSGLLLPDAPIVV
+WWPGVPPGVPSATALGRLAHRRITDTASASAAEPALWALRAGHHEGDTDLAWTRLTLWRI
+QVAGIFDTLDVATLRSVTVDGAPDSPSTMLLAAWLTLTLKVPVTIAHSKVGHGIRAVRLR
+CTDGDVVLSRSQSQVARLYQQGRPVQRISLPRRTIQDCLAEELRRLDPDEVFGAVLHQGL
+PRTDLSPVQASER*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000944.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000944.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9904c5f298f2b3f8fb8d5d8a37182c5e2956fe50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000944.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1087
+MAGESRTAPRNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPA
+FSLVGFGRRSWSDEEFADYVRAAVEASSRTTFDETVWDQFQGGLRFVSGAFDDEAAYVRL
+DEVLAELETSRGTRGNTAFYLSIPPDWFEAVSRHLADQGLADRSQPAEGPWRRVVIEKPF
+GHDLASAQELNAVIERVFPSDAVFRIDHYLGKETVQNILAFRFANRMFEPLWNAEHVDHV
+QITMAEDIGIGGRASYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRAEKEKVLE
+AVTVPDTPEGLAAASARGQYTSGWQGGERVTGFLDEEGFNPASVTETYAALKVGIRTRRW
+QGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHDGDEFGQNIIVIRVQPDEGVTIRFA
+SKVPGTQTEIRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIVD
+PFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRSWRRP*
+>NZ_CP033200.1_816
+MAGESRTAPRNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPA
+FSLVGFGRRSWSDEEFADYVRAAVEASSRTTFDETVWDQFQGGLRFVSGAFDDEAAYVRL
+DEVLAELETSRGTRGNTAFYLSIPPDWFEAVSRHLADQGLADRSQPAEGPWRRVVIEKPF
+GHDLASAQELNAVIERVFPSDAVFRIDHYLGKETVQNILAFRFANRMFEPLWNAEHVDHV
+QITMAEDIGIGGRASYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRAEKEKVLE
+AVTVPDTPEGLAAASARGQYTSGWQGGERVTGFLDEEGFNPASVTETYAALKVGIRTRRW
+QGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHDGDEFGQNIIVIRVQPDEGVTIRFA
+SKVPGTQTEIRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIVD
+PFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRSWRRP*
+>NZ_CP040019.1_1736
+MPGESKAAARNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPS
+FSLVGFGRRDWSDEEFAEYVRAAVEASARTTFDETVWDQFRGGLRFVSGAFDDEAAYVRL
+GEVLGELESSRGTRGNTAFYLSIPPDWFEDVSRHLADQGLADRSQPADGPWRRVVIEKPF
+GHDLASAQELNAVIERVFPPDAVFRIDHYLGKETVQNILAFRFANRMFEPIWNAEHVDHV
+QITMAEDIGIGGRAGYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRTEKEKILE
+AVQVPDTPAGLEAASARGQYTSGWQGGERITGFLDEEGFNPESVTETYAALKVGIRTRRW
+QGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHEGDEFGQNVIVIRVQPDEGVTIRFA
+SKVPGTQSEVRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIVD
+PFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRAWRRP*
+>NZ_CP083691.1_1628
+MRPEPGGPARRNPLRDPRDRRLTRIAGPSALVLFGVTGDLARKKLLPAMYDLAHRGLLPP
+SFSLVGFGRRDWSEAEFADYVRAAVEAGSRTAFNETVWDQFRGGLRFVSGAFGDADAYAR
+LDEVLTELESSRGTGGNTAFYLSIPPDWFEDVSRHLADQGLADRSQPADGPWRRVVIEKP
+FGHDLASAHELNAVIERVFPPDAVFRIDHYLGKETVQNILAFRFANRIFEPLWSAEHVDH
+VQITMAEDIGIGGRAGYYDGVGAARDVIQNHLLQLLALTAMEEPISFDAAHLRAEKEKVL
+AAVRVPCTPEGLEAASARGQYTSGWQGGEQVTGFLDEEGFNPASVTETFAALKVDIGTRR
+WQGVPFYLRAGKRLGRRVTEIAVVFKSPPHLLFPVHPGDEFGQNVIVIRVQPDEGVTIRF
+ASKVPGTQHEVRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQEEVELSWAIV
+DPFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRTWRRP*
+>NZ_CP097650.1_1036
+MAGESRTAPRNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPA
+FSLVGFGRRSWSDEEFADYVRAAVEASSRTTFDETVWDQFQGGLRFVSGAFDDEAAYVRL
+DEVLAELETSRGTRGNTAFYLSIPPDWFEAVSRHLADQGLADRSQPAEGPWRRVVIEKPF
+GHDLASAQELNAVIERVFPSDAVFRIDHYLGKETVQNILAFRFANRMFEPLWNAEHVDHV
+QITMAEDIGIGGRASYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRAEKEKVLE
+AVTVPDTPEGLAAASARGQYTSGWQGGERVTGFLDEEGFNPASVTETYAALKVGIRTRRW
+QGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHDGDEFGQNIIVIRVQPDEGVTIRFA
+SKVPGTQTEIRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIVD
+PFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRSWRRP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000948.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000948.fa
new file mode 100644
index 0000000000000000000000000000000000000000..19c81a5d1697f070a7d502b0f60ea7284df16e95
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000948.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1091
+MSSSLESPSAARVAAAEPGVVDRSPLPLRRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMIATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILILGFGANWLAAGLGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIGW
+AAVRGTVEWPAIVLFLVVFLWTPPHYWPLSMKYKRDYQQADVPMLGAIASARHVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVALVVGGWFIWESHVLQVQAQREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGAPLMHFGA*
+>NZ_CP033200.1_820
+MSSSLESPSAARVAAAEPGVVDRSPLPLRRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMIATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILILGFGANWLAAGLGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIGW
+AAVRGTVEWPAIVLFLVVFLWTPPHYWPLSMKYKRDYQQADVPMLGAIASARHVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVALVVGGWFIWESHVLQVQAQREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGAPLMHFGA*
+>NZ_CP040019.1_1732
+MSSSLESSSAARVETAPPGVVDRSKPSLSRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMAATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILVLGFGANWLAAALGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIAW
+AAVRGTVEWPAIVLFTVIFLWTPPHYWPLSMKYKRDYQEADVPMLGAIASARHVSNQVVL
+YAWATVVCSLLLVPMGWAGIVYTCVALVVGGWFVWESHVLHRQARREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGEPLMRFGA*
+>NZ_CP083691.1_1624
+MSSSVESTSPATAAPGAAAPSARPPMTVGRKARAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDLLTMIATLVGGALAAGASGAFNCYIDRDIDRVMKRTARRPLVTGEVTPREALVFSW
+TLAVVSVLVLGFGANWLAAALGVAAIFFYVVVYSLILKRRTEQNIVWGGIAGCFPVVIGW
+AAVRGTVEWPAIVLFTVIFLWTPPHYWPLSMKYKRDYQEAEVPMLGAVASARLVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVAVGVGGWFVWESHVLQREAQRPDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGGPLMPAVTGS*
+>NZ_CP097650.1_1040
+MSSSLESPSAARVAAAEPGVVDRSPLPLRRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMIATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILILGFGANWLAAGLGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIGW
+AAVRETVEWPAIVLFLVVFLWTPPHYWPLSMKYKRDYQQADVPMLGAIASARHVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVALVVGGWFIWESHVLQVQAQREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGAPLMHFGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000951.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000951.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cbb2cdf7e0a4e49ebe5e5fee12e8af8b5a60f784
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000951.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1094
+MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAGKSTTLGLCHGM
+DRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVASLYRDPLPVEP
+LLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLDPETRPVVHDVV
+REQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGSLAELTRVAEGDVVDVDFGDA
+SPDAVRAWADTLPAPLRAAGLDESARLRVAGVRGPDDLAVLAASWREHALMPTRFERAGL
+RLEQILRETAA*
+>NZ_CP033200.1_823
+MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAGKSTTLGLCHGM
+DRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVASLYRDPLPVEP
+LLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLDPETRPVVHDVV
+REQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGSLAELTRVAEGDVVDVDFGDA
+SPDAVRAWADTLPAPLRAAGLDESARLRVAGVRGPDDLAVLAASWREHALMPTRFERAGL
+RLEQILRETAA*
+>NZ_CP040019.1_1729
+MVPRPVLTPDPAPRDEPVLRLRDVHRSLGRGRARTPVLRGVDLTARAGAVTVLLGPNGAG
+KSTTLGLCHGMDRPDAGAVRVFGADPWRAPADLRARIGVMWQEGGLPPSVPARRFVGHVA
+SLYRDPMPVEPLLERLLIADVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLD
+PETRPVVHEVVREQTARGAAVLLTTHLLDDAERLADDVAILRAGRVVRAGSLADLTRVAE
+GDVVDVDFGDAAPEAVRAWADALPEPLRAAGLAEPARLRVAGVHGPAELAALAASWHRHA
+LMPTRFERAGLRLEQILRETAA*
+>NZ_CP083691.1_1621
+MPETSPHPDAPALRLHEVRRTLGRGAARTEVLRGVDLEARRGAVTVLLGPNGAGKSTTLA
+LCHGSDRPDSGTVRVFGRDPWRADADLRARLGVMWQEGGLPPSVTARRFVRHVASLHGDP
+LDPDALLGRLRIDRVADRPIRRLSGGQRQRVALAAAVVGRPDLLFLDEPTAGLDPETRPV
+VHDVVREHTARGAAVLLTTHLLDDAERLADDVAILRAGRVVRAGTLAELTRVQDGDVVDV
+RFDEARAADVRAWVAAAPASFRAVASAGAPAARVAGVRSPADLEALAASWTRAGLFPTRL
+ERAVLRLEELLQSPDADTPSPERSR*
+>NZ_CP097650.1_1043
+MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAGKSTTLGLCHGM
+DRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVASLYRDPLPVEP
+LLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLDPETRPVVHDVV
+REQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGPLSELTRVAEGDVVDVDFGDA
+SPDAVRAWADTLPAPLRAAGLGESARLRVAGVRGPDDLAVLAASWREHALMPTRFERAGL
+RLEQILRETAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000952.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000952.fa
new file mode 100644
index 0000000000000000000000000000000000000000..436637ba5c743ae224f04ceec99f3bf233960250
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000952.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1095
+MVYSDQSASPPAPAPAEGTRERVLQLVLTRGPVSAAEIGRELELTAAAVRRHLDALEEDS
+LVEVKRVTAARGAGRPSRRYVVTSHAQEHLPKDHLAVALDTLARLEELGGEEEVRRTARH
+AFREIEERFTAAVDGRETALQDRTRILARVLDEAGYAGTLRHFGAGLAPTLRADQVCQGH
+CPFQGIPARHPEFCEEETALFARLLEVDVRRLSTLAAGAHVCTTHVPLGRD*
+>NZ_CP033200.1_824
+MVYSDQSASPPAPAPAEGTRERVLQLVLTRGPVSAAEIGRELELTAAAVRRHLDALEEDS
+LVEVKRVTAARGAGRPSRRYVVTSHAQEHLPKDHLAVALDTLARLEELGGEEEVRRTARH
+AFREIEERFTAAVDGRETALQDRTRILARVLDEAGYAGTLRHFGAGLAPTLRADQVCQGH
+CPFQGIPARHPEFCEEETALFARLLEVDVRRLSTLAAGAHVCTTHVPLGRD*
+>NZ_CP040019.1_1728
+MVYSDLPSHRAAPAPAEGTRERVLQLVLTRGPVSAAEIGRELELTAAAVRRHLDALEEDA
+LVEVKRVTSARGAGRPSRRYVVTSHAQEHLPKDHLAVALHSLARLEELGGDEEVRRTARR
+AFRDVEERFAAAVDGRDTELQERTRILASVLDDAGFAGTLRHFGAGLAPTLRADQVCQGH
+CPFQGIPARHPQFCEEETELFARLLQVDVRRLSTLAAGAHVCTTHVPLGRD*
+>NZ_CP083691.1_1620
+MYSDSADPAAPAPGTRERVLERVLSHGPVSAAEIGGALGLTAAAVRRHLDALEEEGFVEV
+KVVSAARGAGRPSRRYVVAPQAQRRLGGDHLGIALQAVDRLVEVGGEGEVRRLAADALQP
+VEEAFQAAVAGREMGLEERTRVLADLLDDAGYAASIRHVGAGLAPTLRAEQLCQGHCPLQ
+GLPARHPEFCEEETALFARLLGVDVRRLSTLAAGGHVCTTHIPLGRA*
+>NZ_CP097650.1_1044
+MVYSDQSASPPAPAPAEGTRERVLQLVLTRGPVSAAEIGRELELTAAAVRRHLDALEEDS
+LVEVKRVTAARGAGRPSRRYVVTSHAQEHLPKDHLAVALDTLARLEELGGEEEVRRTARH
+AFREIEERFTAAVDGRETALQDRTRILARVLDEAGYAGTLRHFGAGLAPTLRADQVCQGH
+CPFQGIPARHPEFCEEETALFARLLEVDVRRLSTLAAGAHVCTTHVPLGRD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000953.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000953.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bcaf5bd0abf264c053a29bf629cb138bbb182b3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000953.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1096
+MTDQIVQRDSTETADPGVIQEILDKNPELNAIGAYQYGWADSDAAGEKAVRGLNEDVVRD
+ISGKKDEPEWMRDLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWEDLP
+EDIRNTYERLGIPEAERERLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPE
+IFEEYFGTVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERT
+LIIADEDSYVHYIEGCTAPIYQSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKR
+AVVEAGGTMEWIDGNIGSKVTMKYPAVYLTGEHATGETLSVAFAGKDQHQDTGSKMVHMA
+PHTNSSIVSKSVARSGGRAAYRGLVQIAEGANGSANSVVCDALLVDTVSRSDTYPYIDIR
+EDDVTLGHEATVSKVSEEQLFYLMSRGMSEDEAMAMIVRGFIEPIARELPMEYALELNKL
+IELQMEGSVG*
+>NZ_CP033200.1_825
+MTDQIVQRDSAETADPGVIQEILDKNPELNAIGAYQYGWADSDAAGEKAVRGLNEDVVRD
+ISGKKDEPEWMRDLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWEDLP
+EDIRNTYERLGIPEAERERLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPE
+IFEEYFGSVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERT
+LIIADEDSYVHYIEGCTAPIYQSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKR
+AVVEAGGTMEWIDGNIGSKVTMKYPAVYLTGEHATGETLSVAFAGKDQHQDTGSKMVHMA
+PHTNSSIVSKSVARSGGRAAYRGLVQIAEGANGSANSVVCDALLVDTVSRSDTYPYIDIR
+EDDVTLGHEATVSKVSEEQLFYLMSRGMSEDEAMAMIVRGFIEPIARELPMEYALELNKL
+IELQMEGSVG*
+>NZ_CP040019.1_1727
+MTDQIVQRDPVENADPGVIQEILDKNPELNAIGAYQYGWADSDAAGEKAVRGLNEDVVRD
+ISGKKDEPEWMRNLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWEDLP
+EDIRNTYERLGIPEAERERLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPE
+IFEEYFGTVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERT
+LIIADEDSYVHYIEGCTAPIYNSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKR
+AVVESGGTMEWVDGNIGSKVTMKYPAVYLTGEHATGETLSVAFAGKDQHQDTGSKMVHMA
+PNTSSSIVSKSVARNGGRAAYRGLVQVTEGAKNSANSVVCDALLVDTVSRSDTYPYIDIR
+EDDVTLGHEATVSKVSEEQLFYLMSRGLSEDEAMAMIVRGFIEPIARELPMEYALELNKL
+IELQMEGSVG*
+>NZ_CP083691.1_1619
+MTDQIVQQDSRGADPGVISEILEKNPELNAIGAYQYGWADSDAAGSSARRGLNEDVVKDI
+SAKKSEPEWMTKLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWDDLPE
+DIRNTYERLGIPEAERDRLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPEI
+FEEYFGTVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERTL
+IIADEDSYVHYIEGCTAPIYQSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKRA
+VVEAGGTMEWIDGNIGSKVTMKYPAVYLTGEGATGETLSVAFAGKDQHQDTGSKMVHMAP
+NTNSSIVSKSVARNGGRAAYRGLVQVNEGARGAANSVVCDALLVDTVSRSDTYPYIDIRE
+DDVTLGHEATVSRVSEEQLFYLMSRGLAEDEAMAMIVRGFIEPIARELPMEYALELNKLI
+ELQMEGSVG*
+>NZ_CP097650.1_1045
+MTDQIVQRDSAETADPGVIQEILDKNPELNAIGAYQYGWADSDAAGEKAVRGLNEDVVRD
+ISGKKDEPEWMRDLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWEDLP
+EDIRNTYERLGIPEAERERLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPE
+IFEEYFGTVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERT
+LIIADEDSYVHYIEGCTAPIYQSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKR
+AVVEAGGTMEWIDGNIGSKVTMKYPAVYLTGEHATGETLSVAFAGKDQHQDTGSKMVHMA
+PHTNSSIVSKSVARSGGRAAYRGLVQIAEGANGSANSVVCDALLVDTVSRSDTYPYIDIR
+EDDVTLGHEATVSKVSEEQLFYLMSRGMSEDEAMAMIVRGFIEPIARELPMEYALELNKL
+IELQMEGSVG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000954.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000954.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83c665fe205a5908aa0f8ff1b83b847b1ab5b377
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000954.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1097
+MTDTVENTQRTMIPGMGEEGEKLTAAQNPAARAGGRERNAAGSRADRLSSFELSDFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPAVTVAEQAGVTVETVARDDARVGSVLTP
+DDRVSAAAWNSVSEATVVTISGEVAEPVRIDVVGSSADPAAMHLTVLVEENAQADVVIAH
+RGTAVLAQNVEFDVRRDARLNVVALQAWEGDAVHVSAQQASVATNAHFKHVAVSYGGGVV
+RLTPTARFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPDCVSNVLYKGALQGTDARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGISETEARRLIVRGFLNEIIQKIGIGDVEDELTAVMEDELRIAQL*
+>NZ_CP033200.1_826
+MTDTVENTQRTMIPGMGEEGEKLTAAQNPAARAGGRERNAAGSRADRLSSFELSDFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPAVTVAEQAGVTVETVARDDARVGSVLTP
+DDRVSAAAWNSVSEATVVTISGEVAEPVRIDVVGSSADPAAMHLTVLVEENAQADVVIAH
+RGTAVLAQNVEFDVRRDARLNVVALQAWEADAVHVSAQQASVATNAHFKHVAVSYGGGVV
+RLTPTARFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPDCVSNVLYKGALQGTDARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGISETEARRLIVRGFLNEIIQKIGIGDVEDELTAVMEDELRIAQL*
+>NZ_CP040019.1_1726
+MTDTVENTQGSMIPGMGEEGEKLTVAQTSAPRAGAPERNAAGSRADRVSSYELADFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPSVTVAEQVGVRVETVARDDARVGSVLTP
+DDRVSAAAWNSVAQATVVTVSGEVAEPVRIDVVGSSAEPAAMHLTVIVEENAQADVVLAH
+RGTAVLAQNVEFDVRRDARLNVVSLQAWEDDAVHVSAQQASVATNARFKHVAVSHGGSVV
+RLTPTSRFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPRCVSNVLYKGALQGADARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGISETEARRLIVRGFLNEIIQKIGVRDVEDELTAVMEDELRIAAL*
+>NZ_CP083691.1_1618
+MENTERNMIPGMGEEGETLAGGQDAGAPVATRGQGQSRADRVSSKDLADFPVLTGREEDW
+RFTPLERLGGLHLPGGDDARLTGAAPAVTVSETAGVSVETVGRDDARVGSVLTPDDRVSA
+AAWTSFAEATVVTVSGEPGEPVRIEVTGSGVEPAAQQLTLIAEENAHADVVLTHRGSAVL
+AQNVEFEVRRGASLNVVSVQAWDDDAVHVGAHQASVARDAHLKHVTVTHGGSLVRLTPTA
+RFSDERGEAEMYGLYYADAGQHLENRLFVDHNRPNCVSNVLYKGALQGQDAHTVWVGDVL
+IRTEAEGTDSYEKNENLLLTDGARADSVPNLEIETGVIEGAGHASATGRFDETQLFYLMA
+RGIPESEARQLIVRGFLNEILQKIGIADVQDELTAVMEEELRVTAL*
+>NZ_CP097650.1_1046
+MTDTVENTQRTMIPGMGEEGEKLTVAQNPAARAGGRERNAAGSRADRLSSFELSDFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPAVAVAEQAGVTVETVARDDARVGSVLTP
+DDRVSAAAWNSVSEATVVTISGEVAEPVRIDVVGSSADPAAMHLTVLVEENAQADVVIAH
+RGTAVLAQNVEFDVRRDARLNVVALQAWEGDAVHVSAQQASVATNAHFKHVAVSYGGGVV
+RLTPTARFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPDCVSNVLYKGALQGTDARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGIPETEARRLIVRGFLNEIIQKIGVGDVEDELTAVMEDELRIAQL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000955.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000955.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08841fb31c13cbe4eb48e08aaf8c930b61202ede
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000955.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1098
+MATLQITDLHVQIATENGPKEILKGLSLTIETGETHAIMGPNGSGKSTLASTIAGHPRYE
+VTSGSITLDGEDVLEMGVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGEAPSLR
+TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV
+DALRIVSEGVNRAQAQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAEQLE
+AEGYARFEKAAAGA*
+>NZ_CP033200.1_827
+MATLQITDLHVQIETENGPKEILKGLSLTIETGETHAIMGPNGSGKSTLASTIAGHPRYE
+VTSGSITLDGEDVLEMSVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGQAPSLR
+TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV
+DALRIVSEGVNRAQAQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAEQLE
+AEGYARFEKAAAGA*
+>NZ_CP040019.1_1725
+MATLQITDLHVQIETENGPKEILKGLSLTIETGQTHAIMGPNGSGKSTLASTIAGHPRYE
+VTSGSITLDGEDVLEMGVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGEAPSLR
+TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV
+DALRIVSEGVNRAAEQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAAQLE
+AEGYARFEKAAAGV*
+>NZ_CP083691.1_1617
+MATLQITDLHVQIETENGPKEILKGLSLTINTGETHAIMGPNGSGKSTLASTIAGHPRYE
+VTSGSITLDGEDVLEMSVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTAIDGEAPSLR
+TWSKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV
+DALRIVSEGVNRAAEANEMGTLLITHYTRILNYIKPQHVHVLVDGRVAESGGPELAARLE
+SEGYARFEKAAAEA*
+>NZ_CP097650.1_1047
+MATLQITDLHVQIATENGPKEILKGLSLTIETGETHAIMGPNGSGKSTLASTIAGHPRYE
+VTSGSITLDGEDVLEMGVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGQAPSLR
+TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV
+DALRIVSEGVNRAQAQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAEQLE
+AEGYARFEKAAAGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000956.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000956.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1fdf73eafb0e00a4d7d935de744fb26f5f4aba8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000956.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1099
+MTETANQVPTEDIREALKDVIDPELGVNVVDLGLLYGLHYADDGALLVDMTLTTAACPLT
+DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI*
+>NZ_CP033200.1_828
+MTETTNQAPTEDIREALKDVIDPELGVNVVDLGLLYGLHYADDGALLVDMTLTTAACPLT
+DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI*
+>NZ_CP040019.1_1724
+MTETANQVPTEDVREALKDVIDPELGVNVVDLGLLYGLHYAEDGALLVDMTLTTAACPLT
+DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI*
+>NZ_CP083691.1_1616
+MTDTAAQTPVEDIREALKDVIDPELGVNVVDLGLLYGLHYAEDGALLVDMTLTTAACPLT
+DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGKDQMRALGFNI*
+>NZ_CP097650.1_1048
+MTETTNQAPTEDIREALKDVIDPELGVNVVDLGLLYGLHYADDGALLVDMTLTTAACPLT
+DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000957.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000957.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dd8a441aaaa9bd73ddc16c1f5cbb0378fd3a4bc4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000957.fa
@@ -0,0 +1,34 @@
+>NZ_CP042169.1_1100
+MSFNENVQIDAGRARSGGGGGLGGRGIAIGGGGGLLALLLAIFAPGLAEQLGIDTGGGSV
+GQSQYQQQTGSGGQSQPLSDEECASGADANQNTDCRVVATTEAADEFWGEYLAQFSDIQW
+RQPQLTLFQGGVSTGCGSASSATGPFYCPADESMYFDTAFFETLQTDFGAEGGPLAEEYI
+VAHEYGHHVQQVTGYLQHSKDGTTGPTSGAVRAELQADCFAGMWAGHATSTVDPESGEPF
+LKPISQDQLRQAIDAASAVGDDRIQSTHTGRVDPEAFTHGTSEQRMAWFMRGYQSAQQEP
+DIRQCDTFRAPSLDI*
+>NZ_CP033200.1_829
+MSFNENVQIDAGRARSGGGGGLGGRGIAIGGGGGLLALLLAIFAPGLAEQLGIDTGGGSV
+GQSQYQQQTGSGGQSQPLSDEECASGADANQNTDCRVIATTEAADEFWGEYLAQFSDIQW
+RQPQLTLFQGGVSTGCGSASSATGPFYCPADESMYFDTAFFETLQTDFGAEGGPLAEEYI
+VAHEYGHHVQQVTGYLQHSKDGTTGPTSGAVRAELQADCFAGMWAGHAASTVDPESGAPF
+LKPISQDQLRQAIDAASAVGDDRIQSTHTGRVDPEAFTHGTSEQRMAWFMRGYQSSQQEP
+DIRQCDTFRASSLDI*
+>NZ_CP040019.1_1722
+MGGRGLAIGGGGGLLALLLAIFAPGLAGQLGIDTGGSTGQSQYQQQGAGGTQPVSDEECS
+TGADANRNTDCRVIAATEAADQFWGEYMSQFSDVDWRQPQLTLFAGSVSTGCGSASSAMG
+PFYCPADESMYFDTSFFETLQSDFGAEGGPLAEQYIVAHEYGHHVQHVTGYLQYSRDGST
+GPESGAVRAELQADCLAGMWAGAATTTVDPESGEPYLQPISREQLRQAIDAAAAVGDDRI
+QEMSTGRVNPEAFTHGSSEQRMAWFLRGYETSQQEPDFRQCDTFRASSLDI*
+>NZ_CP083691.1_1615
+MSFNENVQINAGRARGGGGGGMGGRGLAIGGGGGILALLLAIFAPGLAEDLGIGGAGTGT
+GSSYQQQLPQSGSGTSTQPVSQADCSTGADANQNTDCRVIATTESADAFWGDYMGQYSNI
+QWRQPDLTLFTTSVSTGGCGSATSATGPFYCPADESMYFDTAFFSTLESDFGATGGPLAE
+EYIVAHEYGHHVQNVVGWLQYAQDGRTGAASNAVRSELQADCLAGMWAGHAATTKDPETG
+EAFLQPITQEQLAQAIDAAGAVGDDRIQEQYQGRVNPEAFTHGSASQRQAWFMRGYETTS
+QQSPDINQCNTFQAATLDI*
+>NZ_CP097650.1_1049
+MSFNENVQIDAGRARSGGGGGLGGRGIAIGGGGGLLALLLAIFAPGLAEQLGIDTGGGSV
+GQSQYQQQTGSGGQSQPLSDEECASGADANQNTDCRVIATTEAADEFWGEYLAQFSDIQW
+RQPQLTLFQGGVSTGCGSASSATGPFYCPADESMYFDTAFFETLQTDFGAEGGPLAEEYI
+VAHEYGHHVQQVTGYLQHSKDGTTGPTSGAVRAELQADCFAGMWAGHAASTVDPESGAPF
+LKPISQDQLRQAIDAASAVGDDRIQSTHTGRVDPEAFTHGTSEQRMAWFMRGYQSSQQEP
+DIRQCDTFRASSLDI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000958.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000958.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6bc441d500bee4ce38573542557828531bfcd028
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000958.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1101
+MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKVLAGGGQPTAGTVTR
+TGRIGYLPQDPKVEDMDQSGRDRILSARDLDQTIRRMREAEAGMAAVDDAERERAMNRYS
+RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIL
+LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM
+TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG
+VEGERAVDRVAAIRFPTPQASGKTPLRAENLSKSYGSLGIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGEETPDTGEVQAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILHALRQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNDDYRDLITLA*
+>NZ_CP033200.1_830
+MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKVLAGGGQPTAGTVTR
+TGRIGYLPQDPKVEDMDQSGRDRILSARDLDQTIRRMREAEAGMAAVDDAERERAMNRYS
+RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIM
+LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM
+TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG
+VEGERAVDRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGEETPDTGEVQAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILHALRQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNDDYRDLITLA*
+>NZ_CP040019.1_1721
+MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKILAGGGQPTAGSVTR
+TGRIGYLPQDPKVEDMDQSGRDRILSARDLDHTIRRMREAEAGMAAVDDVERQRAMDRYS
+RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIM
+LLDEPTNHLDHDSIVWLRDYLKTYPGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM
+TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG
+VEGERAADRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGEEAPDTGEVQEGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILGALRQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNEDYKDLITLA*
+>NZ_CP083691.1_1614
+MLTVTDLELRVGARLLMDEVSFRVAKGDKVGLVGRNGAGKTTLTRVLAGITQPTAGSVTV
+SGRLGYLPQDPKVEDMDQSGRDRILAARDLDQTIRRMRAAEADMASEDDAARQKAMDRYS
+RLQAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADTM
+LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDAMRQTIDVYNM
+NWKNYQAQRQQDEARRRREFANAEKKASALLAQAEKMRAKATKATAAQNMIKRAERMMRG
+VEGERAQDRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGTESPDTGEVIAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QCRTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILNALRQYEGAVVLVTHDEGAVEALAPERVVLLPDGDEDLWSDDYLDLISLA*
+>NZ_CP097650.1_1050
+MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKVLAGGGQPTAGTVTR
+TGRIGYLPQDPKVEDMDQSGRDRILSARDLDQTIRRMREAEAGMAAVDDAERERAMNRYS
+RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIM
+LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM
+TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG
+VEGERAVDRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGEETPDTGEVQAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILNALQQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNDDYRDLITLA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000963.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000963.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc6642a92b258a43422f31577b6059420e5e0366
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000963.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1108
+MTTPAPPDDWFLPDEDAVLQMRRVRVRRGTTDILGPLDWTVRAGQRWIVMGPNGAGKSTL
+LQLAAARLHPTAGDVGVLDEVLGAVDVFELRPRIGLSSAQLAAQVPANETVQDAVVTAAY
+GITGTWRERYETEDRARALGLVATWGLSRLAHRAFGTLSDGERKRVLIARALMTDPELLL
+LDEPAAGLDLAGREDLVRQLTALATDEDAPALVLVTHHLEEVPPGFTHALLLRDGGVVAA
+GPIESTLTEEHLSAAFGTDLKVTRTGGRYTAVAR*
+>NZ_CP033200.1_837
+MTTPAPPDDWFLPDEDAVLQMRRVRVRRGTTDILGPLDWTVRAGQRWIVMGPNGAGKSTL
+LQLAAARLHPTAGDVGVLDEVLGAVDVFELRPRIGLSSAQLAAQVPANETVQDAVVTAAY
+GITGTWRERYETEDRARALGLVATWGLSRLAHRAFGTLSDGERKRVLIARALMTDPELLL
+LDEPAAGLDLAGREDLVRQLTALATDEDAPALVLVTHHLEDVPPGFTHALLLRAGGVVAA
+GPIESTLTEEHLSSAFGTDLKVTRTGGRYTAVAR*
+>NZ_CP040019.1_1715
+MTLPAPSDDWFLPDEDAVLQMRRVRVRRGQTDILGPLDWTVRAGERWIVMGPNGAGKSTL
+LQIAATRLHPTGGEVAILEEVLGAVDVFELRPRIGLSSAQLAAQVPHEEKVQDAVVTAAY
+GVTGTWRESYEDEDRMRALGLVSSWGLSRLAHRRFGTLSEGERKRVLIARSLMTDPELLL
+LDEPAAGLDLAGREALVAQLSELARDEDAPALVLVTHHLEEVPPGFTHALLLRDGHAVAA
+GPIEQTLTEGHLSAAFDTPLRVTRTGGRYTAVAQ*
+>NZ_CP083691.1_1607
+MNTAPQDPSPRPVVEHDVFTPDEDAVLQLRDVAVRRGAKQILAGIDWTVRAGERWVVMGP
+NGAGKSTLLQIAASRMFPTSGDVAILDEVLGAVDVFELRPRIGLSSALLANQVRDDETVQ
+DAVITASYGMTGRWREEYEVEDRARALGLVSEWGLSRLAHRRFGTLSEGERKRVLIARAL
+MTDPELLLLDEPAAGLDVAGREALVGQLSELAADEDAPATVLVTHHLEEVPPGFTHALLL
+ADGAVVQAGPLEETLTAEHLSTAFGTPLRVTRADGRYTAVAA*
+>NZ_CP097650.1_1057
+MTTPAPPDDWFLPDEDAVLQMRRVRVRRGTTDILGPLDWTVRAGQRWIVMGPNGAGKSTL
+LQLAAARLHPTAGDVGVLDEVLGAVDVFELRPRIGLSSAQLAAQVPANETVQDAVVTAAY
+GITGTWRERYETEDRARALGLVATWGLSRLAHRAFGTLSDGERKRVLIARALMTDPELLL
+LDEPAAGLDLAGREDLVRQLTALATDEDAPALVLVTHHLEDVPPGFTHALLLRAGGVVAA
+GPIESTLTEEHLSSAFGTDLKVTRTGGRYTAVAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000964.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000964.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46faf6e9ab476bf8bf8bb280d81787a9b67eac46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000964.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1109
+MTGLLTAQLLGMDLWQVLLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQVSNA
+MGLVASGFSGTYGYRRELAQSRALLPKLTVASLLGGVIGAALLTTLPPAVFGYVAPVLLV
+VALTVVVLQPRIQGWVRRRAEDQGPTPGADSPVPVGPVTPTLWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVLLVGGTLVHANAVKTWLSLVVNLTAAAFYLVFAFDRIDWRAVLLIALSSL
+VGGLVGARIGRRISPTALRVTIVIVGLAGLVVMVMRQVSGG*
+>NZ_CP033200.1_838
+MTGLLTAQLLGMDLWQVLLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQVSNA
+MGLVASGFSGTYGYRRELAQSRALLPKLTVASLLGGVIGAALLTTLPPAVFGYVAPVLLV
+VALTVVVLQPRIQRWVRRRAEDQGPTPGADSPVPVGPVTPTLWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVLLVGGTLVHANAVKTWLSLVVNLTAAAFYLVFAFDRIDWRAVLLIALSSL
+VGGLVGARIGRRISPTALRVTIVIVGLAGLVVMVMRQVSGG*
+>NZ_CP040019.1_1714
+MIDVLGADVLGLELWQVVLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQISNA
+IGLVAAGFSGVFGYRRELKESGAVLPVLTVASLLGGVLGAFLLILLPAEVFGVAAPVLIV
+VALAFVVLQPRLQAWVRRRSAAREDGVVDVPARPSRPVSPVLWVLVFLAGVYGGYFVAAQ
+GVLLMGILGVFLVGGTLVHANAIKTWLSLAVNLVAATSYLLFAFDRIDWTAVLLIAASSM
+VGGLVGARIGRRISPTVLRIVIVVVGLAGLVSMVLRLVDGG*
+>NZ_CP083691.1_1606
+MDLLTAPVLGMDLWQVALVLLAGFWAGTINSIIGSGTLVTFPVLVAVGFPPVTAQVSNAM
+GLVASGFSGTYGYRRELRESRALLPRLTLASFLGAVIGATLLTVLPPTVFASVAPCLLVL
+ALTIVVLQPRIQAWVRRRSAGEHGHVPGADSPVPVGPASPALWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVMLVGGTLVHANAVKTWLSLTVNLTAAVFYLVFAFDRIDWRAVLLIAVSSL
+VGGSVGARIGRRMSPTALRVTIVVIGVAGLVSMLSRLAGA*
+>NZ_CP097650.1_1058
+MTGLLTAQLLGMDLWQVLLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQVSNA
+MGLVASGFSGTYGYRRELAQSRALLPKLTVASLLGGVIGAALLTTLPPAVFGYVAPVLLV
+VALTVVVLQPRIQRWVRRRAEDQGPTPGADSPVPVGPVTPTLWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVLLVGGTLVHANAVKTWLSLVVNLTAAAFYLVFAFDRIDWRAVLLIALSSL
+VGGLVGARIGRRISPTALRVTIVIVGLAGLVVMVMRQVSGG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000968.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000968.fa
new file mode 100644
index 0000000000000000000000000000000000000000..05d8fcd12dbdd4dc4fc83ee70856cf5fa208f10e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000968.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1115
+MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ
+YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV
+VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE
+KPETTPGLPDDPTQFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA
+GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNREWPLYTRQSVSP
+PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVHNEAWVEQSVLLDSVVIG
+EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTESGLTVLSKGQPVPTPH*
+>NZ_CP033200.1_844
+MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ
+YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV
+VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE
+KPETTPGLPDDPTQFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA
+GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNREWPLYTRQSVSP
+PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVHNEAWVEQSVLLDSVVIG
+EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTESGLTVLSKGQPVPTPH*
+>NZ_CP040019.1_1705
+MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ
+YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV
+VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE
+KPQTTPGLPDDPTLFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA
+GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNRDWPLYTRQSVSP
+PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVANEAWVEQSVLLDSVVIG
+EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTDSGLTVLAKDQSVPKPH*
+>NZ_CP083691.1_1601
+MVEKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGEYRLIDFALSNLVNSRFREIVVLTQ
+YKSHSLDRHISETWRMSTMLNNYVATVPAQQRRGKDWFTGSANAIYQSMNLISDARPDIV
+VVIGADHVYHMDFQQMVDHHVASGAKATVAAVRQPLELADQFGVIETDATDPGRITAFVE
+KPATTPGLADDPAQFLASMGNYVFDTDALVEALNADDANPESNNDMGGDIVPYFVGRGEA
+GVYDFTTNEVPGGTPGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNRAWPLYTRQSVSP
+PAKLVRSASRRPGTAGDSILAQGVVISGGTVAQSVLSTDVRVGNEAWVEQSVLLDSVTVG
+EGAHVRNAIIDKNVVIPAGARIGFDRAEDEANGYTVTDSGLTVLSKNQRVPDPR*
+>NZ_CP097650.1_1064
+MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ
+YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV
+VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE
+KPETTPGLPDDPTQFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA
+GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNREWPLYTRQSVSP
+PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVHNEAWVEQSVLLDSVVIG
+EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTESGLTVLSKGQPVPTPH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000974.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000974.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a08eeea6f4cdc2246fd7e91b854e7928c10bf67c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000974.fa
@@ -0,0 +1,101 @@
+>NZ_CP042169.1_1122
+MALEAPALLHRLARAHGVQPEYVGQDGSAQTVPDEALVKVLAALGVSVRPDGVAALAEAV
+EEAETAPWRDVLPPTVAARSGHRLSVPCHVAAGEPVVARVRTEDGRTLEVSVSEPVSEVR
+LVDGVERERVHVQIPADLAPGWHRLEVTSGSGSTASAVLVCAPTRLSTARPFLERRGWGA
+AAQGYSVTSADSWGIGDAADMASLAEIVARHGADFLLLHPLHAIEPGPHPADSPYSPVSR
+RFLSALVVHVPSIPEFADLPAAEQAELRSAGARVQAELERTGRIDRAAVAAVLWPALRRV
+HEVPRSPEREAAYARFRAEAGPGLDDFALWSVLRLDGDGTGPDLADPAWAPGGVEAERVR
+VERATDVDLHRWVQWIAAEQLAGVQERARAAGMRMGVMVDLAVGATRETADAWMLGDVLV
+PTMSVGAPPELFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRGAGGIRMDHVLGLF
+RLWWIPEGAGATQGAYVEYDHEAMLAVLTLEAERAGVVVVGEDLGTFEPWVQRRLAEAGV
+LGTSILWFEQEDGEPTPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTVDVA
+QERRRSAEEVRAFLAAAARRGLLAEADVDVPDAGPEVRERQIVALHRLLAQAPSALHSVA
+LVDAVGERRIQNQPGTLQDQYPNWTVPLGDGAGRMVSVEDLADSASAARLFDAVDAELRA
+SVPVGIGVSLHTSPLAQPGRGDAGGMNVYVRQAAVALARRGVRMILLTRAEEPVGADGAR
+VRMLDAGGQAPPVTVVDLAAGPSAPVPKEELAGLGAEFTRAALDWLASDAVPGGPVLGGA
+DAPPVAFVHGHYWLSGSTAAALARAAHAPYLQTMHTTAAAKMLEDPELREPAARIEAERE
+VAERADLLVVNSAAEVADLRELLDVPRARTRVLPPGADLETFTPEGAAQWPGAPEDDGAL
+RVLFAGRVQRHKGPHLLVAALGVLRERAGGAGADPGVRLHVNGAASGDDELDLAGLAARE
+GVADLVTFSGPVPAPALAAQFRAADVVAMPSASETYGLVALEAQACGTPVLAHRVGGLVY
+AVLDGVSGRHVTAGTPEAWADALAEILADRDAWAALGTGAVRHAAGHSWEAYADGLLEAV
+TAVPRRSPGLDA*
+>NZ_CP033200.1_851
+MALEAPALLHRLARAHGVQPEYVGQDGSAQTVPDEALVKVLAALGVSVRPDGVAALAEAV
+EEAETAPWRDVLPPTVAARSGHRLSVPCHVAAGEPVVARVRTEDGRTLEVSVSEPVSEVR
+LVDGVERERVHVQIPADLAPGWHRLEVTSGSGSTASAVLVCAPTRLSTARPFLERRGWGA
+AAQGYSVTSADSWGIGDAADMASLAEIVARHGADFLLLHPLHAIEPGPHPADSPYSPVSR
+RFLSALVVHVPSIPEFADLPAAEQAELRSAGARVQAELERTGRIDRAAVAAVLWPALRRV
+HEVPRSPEREAAYARFRAEAGPGLDDFALWSVLRLDGDGTGPDLADPAWAPGGVEAERVR
+VERATDVDLHRWVQWIAAEQLAGVQERARAAGMRMGVMVDLAVGATRETADAWMLGDVLV
+PTMSVGAPPELFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRGAGGIRMDHVLGLF
+RLWWIPEGAGATQGAYVEYDHEAMLAVLTLEAERAGVVVVGEDLGTFEPWVQRRLAEAGV
+LGTSILWFEQEDGEPTPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTVDVA
+QERRRSAEEVRAFLAAAARRGLLAEADVDVPDAGPEVRERQIVALHRLLAQAPSALHSVA
+LVDAVGERRIQNQPGTLQDQYPNWTVPLGDGAGRMVSVEDLADSASAARLFDAVDAELRA
+SVPVGIGVSLHTSPLAQPGRGDAGGMNVYVRQAAVALARRGVRMILLTRAEEPVGADGAR
+VRMLDAGGQAPPVTVVDLAAGPSAPVPKEELAGLGAEFTRAALDWLASDAVPGGPVLGGA
+DAPPVAFVHGHYWLSGSTAAALARAAHAPYLQTMHTTAAAKMLEDPELREPAARIEAERE
+VAERADLLVVNSAAEVADLRELLDVPRARTRVLPPGADLETFTPEGAAQWPGAPEDDGAL
+RVLFAGRVQRHKGPHLLVAALGVLRERAGGAGADPGVRLHVNGAASGDDELDLAGLAARE
+GVADLVTFSGPVPAPALAAQFRAADVVAMPSASETYGLVALEAQACGTPVLAHRVGGLVY
+AVLDGVSGRHVTAGTPEAWADALAEILADRDAWAALGTGAVRHAAGHSWEAYADGLLEAV
+TAVPRRSPGLDA*
+>NZ_CP040019.1_1699
+MSRRFLSALLVHVPDIPEFASLPAAEQDELRAAGAAVQARLERSGTIDRPAVAAALWPAL
+RRVHAVPRSPEREAAYAAFRAEAGPGLDDFALWSALRTADDVPGPDLADPAWAPGGEHAE
+RVRTERADEVDLHRWVQWVAAEQLAAVQQRARAAGMRMGVMVDLAVGATRETADAWMLGD
+VLVPGMSVGAPPEVFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRDAGGIRMDHVL
+GLFRLWWIPVGAGATQGAYVEYDHEAMLAVLTLEAERAGAVVVGEDLGTFEPWVQRRLAE
+AGVLGTSILWFEQRDGEPLPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTV
+DVAQERRRSADEVEAFLGAAVRRGLLDARDARVRPDDAAQREAQTVALHRLLAQAPSALH
+SVSLVDAVGERRIQNQPGTTQDQYPNWTLPLGDREGRMLRVEDLASSASAARLFDAVEEE
+LRASVPVGIGVSLHTSPLAQPGRGDAGGLNVYVRHAALALARRGVRMILLTRAEEPVGPE
+SARVTRLEAGGEAPAVTVVELAVGPAAPLPKAELAALTDEFTAAARAWLASDAVPGGPVL
+APQGLDGRGPGAPAAPPVAFVHGHYWLSAPTAAALAAATGAPHLHTMHTTAAVKMLEDPE
+LREPGARIEAEGAVVREADLLVVNSPAEVVDLREALGVPRARTRVLPPGADLATFTPEGP
+ALWPGDPDDDGALRVLFAGRIQRHKGPHLLVEALAVLRERAGGPGADPGVRLHVNGAPSG
+EEGLDLPGLALERGVADLVTFSEPVRAEELAAQLRAADVVAMPSASETYGLVALEAQACG
+TPVLAHRVGGLVHAVIDGASGRLVTEGSPEAWADALAAVLADRPAWDALAAGAVRHAAGH
+SWEAYADGLLEAAAGLARRQDGA*
+>NZ_CP083691.1_1594
+MPENARALLRRLARAHGVQTEYVGQDGSDQSVADETLVRVLSALGVEVDADGVAGLTEAL
+DAVDAAPWRDVLPPTVVARQGHRSTVPVHVARGAAVQVRLVQEDGRVVDLPTREAVGATL
+VVDGQERVRHDLDLPEDLPLGWHRLEAVSETGSVARATLVSAPAALTTAAPFLARRGWGV
+AAQGYSVTSSGSWGVGDAHDAGSLAELAAPHGADFLLLHPLHAVEPAGAPADSPYSPVSR
+RFLSAFLIRVTDIPEFAALPAEEQKRLAAAGRAVQEAVLTGGTIDRAAVAEVLWPALEAV
+WRAPRTSERDADYAAFRDRQGTGLDDFAAWSVLRRDALRAGVAGPDPTDPAAGPGSDGVR
+RVRAERADELDFHRWVQWIADEQLAAAQERAREAGMRMGVMLDLAVGATRGSADAWMLGD
+VLVPSMSVGAPPEVFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTLMAHAGGLRMDHVL
+GLFRLWWIPEGLGAPQGAYVHYDHEAMLAVLTLEAERAGVVVIGEDLGTFEPWVQRRLAE
+AGVLGTSILWFEQEDGVPTPPEQYRRLCMAAVNTHDLPPTAGYLEGVHIDLRERLGLYTA
+DVAAERRRSAAEVEAFLGAARKRGLLEATGPDGVETVEDRVVALHRLLAQAPSALHCVGL
+VDAVGERRIQNQPGTLQEQYPNWTVPLGDADGRVLTVEDLAGTASVSRLFDAVAAELDAS
+VPVGIAVAFHTSPLAQPGQGDAGGLNVYVRHSARALARLGVRMLLLTRAESPVGPSGVRV
+TTLPQGEGAPDVTVVELAAGPQEPVAKEELPAHREAFTAAAREWLASADVPGGPLLGAAG
+AAAARVRFVHAHYWLSGDTAAAVADDLGAPRVQTMHTTGAVKSAGDPGHPEPAERLAAEA
+DLVRRADLLVVNSPAESRDLQELLDVDRDRVRVLPPGVDLESFTPEGPSRWPGGDAVGAD
+ALRVLFAGRVQEHKGPHVLVAALAELRARAADGDPRVVLHVNGEQSGPADLDLPALAARL
+GVADLVTFSPPVPPVELAAQMRAADVVALPSASETYGLVAVEAQAAGTPVLAHRVGGLVH
+AVQDGVSGRLVIPNTASAWADALAAVREDRQAWDAMAPAAVRHARAHAWSGWAEGLLDAV
+AGLPRP*
+>NZ_CP097650.1_1071
+MALEAPALLHRLARAHGVQPEYVGQDGSAQTVPDEALVKVLAALGVSVRPDGVAALAEAL
+EEAETAPWRDVLPPTVAARSGHRLSVPCHVAAGEPVVARVRTEDGRTLEVSVSEPVSEVR
+LVDGVERERVHVQIPADLAPGWHRLEVTSGSGSTASAVLVCAPTRLSTARPFLERRGWGA
+AAQGYSVTSADSWGIGDAADMASLAEIVARHGADFLLLHPLHAIEPGPHPADSPYSPVSR
+RFLSALVVHVPSIPEFADLPAAEQAELRSAGARVQAELERTGRIDRAAVAAVLWPALRRV
+HEVPRSPEREAAYARFRAEAGPGLDDFALWSVLRLDGDGTGPDLADPAWAPGGVEAERVR
+VERATDVDLHRWVQWIAAEQLAGVQERARAAGMRMGVMVDLAVGATRETADAWMLGDVLV
+PTMSVGAPPELFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRGAGGIRMDHVLGLF
+RLWWIPEGAGATQGAYVEYDHEAMLAVLTLEAERAGVVVVGEDLGTFEPWVQRRLAEAGV
+LGTSILWFEQEDGEPTPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTVDVA
+QERRRSAEEVRAFLAAAARRGLLAEADVDVPDAGPEVRERQIVALHRLLAQAPSALHSVA
+LVDAVGERRIQNQPGTLQDQYPNWTVPLGDGAGRMVSVEDLADSASAARLFDAVDAELRA
+SVPVGIGVSLHTSPLAQPGRGDAGGMNVYVRQAAVALARRGVRMILLTRAEEPVGADGAR
+VRMLDAGGQAPPVTVVDLAAGPSAPVPKEELAGLGAEFTRAALDWLASDAVPGGPVLGGA
+DAPPVAFVHGHYWLSGSTAAALARAAHAPYLQTMHTTAAAKMLEDPELREPAARIEAERE
+VAERADLLVVNSAAEVADLRELLDVPRARTRVLPPGADLETFTPEGAAQWPGAPEDDGAL
+RVLFAGRVQRHKGPHLLVAALGVLRERAGGAGADPGVRLHVNGAASGDDELDLAGLAARE
+GVADLVTFSGPVPAPALAAQFRAADVVAMPSASETYGLVALEAQACGTPVLAHRVGGLVY
+AVLDGVSGRHVTAGTPEAWADALAEILADRDAWAALGTGAVRHAAGHSWEAYADGLLEAV
+AAVPRRSPGLDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000985.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000985.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7acf4953fa8ccb3ff7380d73d78bc6cddfb84f63
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000985.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_1133
+MSAFGRGAADGFARAAAVDVGPTPAFEGQRRLFHGAAVPPNGRDAAGWGVHRVMGTETEF
+GIHAPANPGAHHSVLSVELVNAYADLVTRSGSAVAGTEWDYTGESPLVDARGWRLPRSAA
+HPSQLTDEALVGPDGEPVHLLLSTVLANGARWYVDHAHPEYSSPETTTPRDAMVWDAAGD
+LVAQAAAEHIGQAEGAPEVLVYKNNVDGKGQSYGAHENYLVARSLDFEELTAVLLPFFAA
+RQVLVGAGRVGLGPAGERPGFQLSQRADYFEEPVGLETTIHRPIVNTRDEPHARPEAYRR
+LHVIIGDATLSQHATWLRMGMTALVLAMAEAGTAPRLTLDDPVAALQTISHDPGLRATVP
+LLERTADGPVRRHWTGLQILRSYLDAARAHCAAFGVTDPQTREVLEAWAIDLDDATADPL
+SLSDRADWAAKLRVLEGLRARTGADWTDPRLAMVDLQYADLRPARSLHRRLVAAGALRTL
+ADEAEIRAAVATPPRATRAWTRGNLVGRHGDRVAGAAWETLLLRGAGERVHRLHLAEPLV
+GAAVDLPGWWEDAAAPRPDDEALVATLAPLFGARA*
+>NZ_CP033200.1_862
+MSAFGRGAADGFARVAAVDVGPTPAFEGQRRLFHGAAVPPNGRDAAGWGVHRVMGTETEF
+GIHAPANPGAHHSVLSVELVNAYADLVTRSGSAVAGTEWDYTGESPLVDARGWRLPRSAA
+HPSQLTDEALVGPDGEPVHLLLSTVLANGARWYVDHAHPEYSSPETTTPRDAMVWDAAGD
+LVAQAAAEHIGQAEGAPEVLVYKNNVDGKGQSYGAHENYLVARSLDFEELTAVLLPFFAA
+RQVLVGAGRVGLGPAGERPGFQLSQRADYFEEPVGLETTIHRPIVNTRDEPHARPEAYRR
+LHVIIGDATLSQHATWLRMGMTALVLAMAEAGTAPRLTLDDPVAALQTISHDPGLRATVP
+LLERTADGPVRRHWTGLQILRSYLDAARAHCAAFGVTDPQTREVLEAWAIDLDDATADPL
+SLSDRADWAAKLRVLEGLRARTGADWTDPRLAMVDLQYADLRPARSLHRRLVAAGALRTL
+ADEAEIRAAVATPPRATRAWTRGNLVGRHGDRVAGAAWETLLLRGAGERVHRLHLAEPLV
+GAAVDLPGWWEDAAAPRPDDEALVATLPPLFGARA*
+>NZ_CP040019.1_1687
+MSAFGRGTADGFARAVAVDVGPTPAFEGQRRLFHGAAVPPNGRDAAGWGVHRVMGTETEF
+GIHAPANPGAHHSVLSVELVNAYADLVTRSGSAVAGTEWDYTGESPLVDARGWRLPRSAA
+HPSQLTDEALVGPDGEPVHLLLSTVLANGARWYVDHAHPEYSSPETTTPRDAMVWDAAGD
+LVAQAAAEHIGQAEGAPEVLVYKNNVDGKGQSYGAHENYLVARSLDFDELTAVLLPFFAA
+RQVLVGAGRVGLGPAGERPGFQLSQRADYFEEPVGLETTIHRPIVNTRDEPHARPEAYRR
+LHVIIGDATLSQHATWLRMGMTALVLALAEAGTAPRLVLDDPVAALQTISHDPGLRATVP
+LLEHTADGPVRRHWTGLQILRSYLDAAHAHCAAFGVTDPQTREVLEAWAIDLDDATADPL
+SLSDRADWAAKLRVLEGLRARAGADWTDPRLAMVDLQYADLRPARSLHRRLVAAGALRTL
+ADEAEIRAAVATPPRATRAWTRGNLVGRHGDRVAGAAWETLLLRGAGERVHRLHLAEPLV
+GAAVDLPGWWEDAAAPRPDDEALVATLPPLFGARA*
+>NZ_CP083691.1_1583
+MPGGIGGAPEAVAGTPAFAGQRRLFPADLTAPPGGRDAAGWGVHRVMGTESEFGIHAPAN
+PGAHHSVLSVELVNSYADLITHSGGAVAGTEWDYAGESPLVDARGWRMPRSAAHPSQLTD
+QALVGPDGEPVHLLLSTVLPNGARWYVDHAHPEYSSPEVASPREAVVWDAAGDRVAQAAA
+EHIAAAEGAPEVLVYKNNTDGKGQSYGSHENYLVARALPFDELAEVLLPFFAARQVLVGA
+GRVGVGLRGERPGFQLSQRADFFEEQVGLETTIRRPIVNTRDEPHARGDAYRRLHVIIGD
+ANLSQHATWLRMGMTALVLALAEAGTAPRIVLDDPVAALQTISHDPTLRAAVPGRERGAD
+GVWTRREWTGLQILGAYLDAAREHCARCGVDDAETAAVLDAWGTDLADAAADPLALADRA
+DWAAKLRVLEGLRARGGLDWSDPRLAMVDLQYADLRPAKSLHRRLVAAGAMRVLVEDAEV
+EAAVVAPPRSTRAWTRGNLVRHHARQVSGAAWDSVLVRAAEEAPLHRLRLEEPLVGAAED
+LPGWWDDTPGSAAPAPEPNELVTRLGELLRR*
+>NZ_CP097650.1_1082
+MSAFGRGAADGFARAVDVGPTPAFEGQRRLFHGAAVPPNGRDAAGWGVHRVMGTETEFGI
+HAPANPGAHHSVLSVELVNAYADLATRSGSAVAGTEWDYTGESPLVDARGWRLPRSAAHP
+SQLTDEALVGPDGEPVHLLLSTVLANGARWYVDHAHPEYSSPETTTPRDAMVWDAAGDLV
+AQAAAEHIGQAEGAPEVLVYKNNVDGKGQSYGAHENYLVARSLDFEELTAVLLPFFAARQ
+VLVGAGRVGLGPAGERPGFQLSQRADYFEEPVGLETTIHRPIVNTRDEPHARPEAYRRLH
+VIIGDATLSQHATWLRMGMTALVLAMAEAGTAPRLTLDDPVAALQTISHDPGLRATVPLL
+ERTADGPVRRHWTGLQILRSYLDAARAHCAAFGAADPQTREVLDAWAVDLDDATADPLSL
+SDRADWAAKLRVLEGLRARTGADWTDPRLAMVDLQYADLRPARSLHRRLVAAGALRTLAD
+EAEIRAAVATPPRATRAWTRGNLVGRHGDRVAGAAWETLLLRGAGERVHRLHLAEPLVGA
+AVDLPGWWEDAAAPRPDDEALVATLAPLFGARA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000986.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000986.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e20432d22b3765429b3a8dff97166d2d169dffc2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000986.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1134
+MIRDESIESYLGRLASGEPTPGGGATGALAVAEGAGLLAMAARFSAAEEDARASEGLIAA
+CLGLADGDERGFGAVAEAFGLPRDTLEDRARRSAAIQAALAEAVQPPRGIVDVAERALDL
+AERVLDAANPNVLSDVGAALGCVRGGLTAAAVTLETNLGPLRDEGLEGIVRTDVDRADRL
+VARADALLGRVRAAVTG*
+>NZ_CP033200.1_863
+MIRDESIESYLGRLASGEPTPGGGATGALAVAEGAGLLAMAARFSAAEEDARASEGLIAA
+CLGLADGDERGFGAVAEAFGLPRDTPEDRARRSAAIQAALAEAVQPPRGIVDVAERALDL
+AERVLDAANPNVLSDVGAALGCVRGGLTAAAVTLETNLGPLRDEGLEGVLRTDVDRADRL
+VARADALLGRVRAAVAG*
+>NZ_CP040019.1_1686
+MIRDESIEAYLGRLASGEPTPGGGATGALAVAEGAGLLAMAARFSAAEEDARASEVLIAA
+CLGLADGDERGFGAVAEAFGLPRDTPVARSRRSAAIQAALAEAVRPPRGIVDAAARALDL
+AERVLDAANPNVLSDVGAALGCIRGGLTAATVTLETNLGPLRDEGVEGILRTDVDRADRL
+VARADALLGRVRAAITG*
+>NZ_CP083691.1_1582
+MIRHETVEDHLTRLASGEPTPGGGATGALVVAQGAGLVAMAARFSGREEVAVECERVIRD
+SLAISDEDEEGFAAVADAYTLPKDGDAARARRSAAVQAALDQAVRPPRAIVDAVDRTVGL
+AERVLDDANPHVLSDVGAALGCARAGAGAAVVTLLTNLSPLHDEQLGAELRAEIARADEL
+TSRIDALAARVRERIAR*
+>NZ_CP097650.1_1083
+MIRDESIESYLGRLASGEPTPGGGATGALAVAEGAGLLAMAARFSAAEEDARASEGLIAA
+CLGLADGDERGFGAVAEAFGLPRDTPEDRARRSAAIQAALAEAVRPPRGIVDAAARALDL
+AERVLDAANPNVLSDVGAALGCVRGGLTAAAVTLETNLGPLRDEGLEGVLRTDVDRADRL
+VARADALLGRVRAAVTG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000987.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000987.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c8360a6623f6b6cde2b405f896c2240ef42eb7c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000987.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1135
+MRLWTLHPRHLDRQGLTGAWREALLAQAVLAGRTRGYRDHPQLLRFREHPDPSGAIGAFL
+SGLEAEATARGYRFDHSRIDRPCPAPDGAVRIPPAGLAPIPATTGQRDLEWRHLCAKLAA
+RSPAWLERWSDTPVPDVHPLFTIVPGPVASWERA*
+>NZ_CP033200.1_864
+MRLWTLHPRHLDRQGLTGAWREALLAQAVLAGRTRGYRDHPQLLRFREHPDPSGAIGAFL
+SGLEAEATARGYRFDHSRIDRPCPAPDGAVRIPPAGLAPIPATTGQRDLEWRHLCAKLAA
+RSPAWLERWSDTPVPDVHPLFTIVPGPVASWERA*
+>NZ_CP040019.1_1685
+MRLWTLHPRHLDRQGLTGAWREALLAQAVLAGRTRGYRDHPQLLRFREHPDPSGAVGAFL
+SGLEAEATARGYRFDHSRIDRPCPAPDGAVRIPTVGLAPIPATTGQRDLEWRHLCAKLAA
+RSPAWLERWADTPVPDVHPLFTIVPGPVASWERA*
+>NZ_CP083691.1_1581
+MRLWTLHPRHLDRQGLTGGWREALLAQAVLARRTKGYRDHPQLERFRGHGDPAAAIGAFL
+SGIALEASARGYRFDVSKIDRPLLPADGAGELVLPFRIAPIEVTTGQVAHEWGHLRAKLA
+ARSPGWLERWADVQTPDVHPLFEVVDGPIASWERP*
+>NZ_CP097650.1_1084
+MRLWTLHPRHLDRQGLTGAWREALLAQAVLAGRTRGYRDHPQLLRFREHPDPSGAVGAFL
+SGLEAEATARGYRFDHSRIDRPCPAPDGAVRIPPAGLAPIPATTGQRDLEWRHLCAKLAA
+RSPAWLEQWSDTPVPDVHPLFTIVPGPVASWERA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000989.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000989.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9676ffe50551d70f211f545de5a64ab137e6ba99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000989.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1137
+MTDADRARRIFGLETEYGVQHWNPEGRALSPEEVVRYLFRPVVEWGRSSNVFVANGSRLY
+LDVGSHPEYATAECSTLDELIASDGAGDLLLHDLVVQAEERMATDGVGGRIHLYRNNADS
+SGSSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVVPAGTWPEGEGPAHFAFS
+QRADFVQDGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTNLSEHTHLLRFGATDL
+LLRMIEAGFPLGDRVVAHPTRAVRQISHDLTGTARIALREGEASALELQEHYLERARTFV
+AAEGAHHDRVGEVLTLWGEVLDAVRTGDRSRIEDRIDWAIKLRLLEDYRARHDLGWDAPR
+LAQLDLAFHDIDPDRGLFRLLLRRGAVARLLPEDAARSAVETAPPTTRARVRADFVARAR
+ERGLDYAVDWTTLKLTDHPLHAIVTKDPFDTSSAAVDRLFGRIA*
+>NZ_CP033200.1_866
+MTDADRARRIFGLETEYGVQHWNPQGRPLSPEEVVRYLFRPVVEWGRSSNVFVANGSRLY
+LDVGSHPEYATAECSTLDELIASDGAGDLLLHDLVVQAEERMAADGVGGRIHLYRNNADS
+SGSSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVVPAGTWPEGEGPAHFAFS
+QRADFVQDGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTNLSEHTHLLRFGATDL
+LLRMIEAGFPLGDRVVAHPTRAVRQISHDLTGTARIALREGEASALELQEHYLERARAFV
+AAEGAHHDRVGEVLTLWGEVLDAVRTGDRSRIEDRIDWAIKLRLLEDYRARHDLGWDAPR
+LAQLDLAFHDIDPDRGLFRLLLRRGAVARLLPEDAARSAVEAAPPTTRARVRADFVSRAR
+ERGLDYAVDWTTLKLTDHPLHAIVTKDPFDTSSAAVDRLFERIA*
+>NZ_CP040019.1_1683
+MTDADRARRIFGLETEYGVQHWNPEGRPLSPEEVVRYLFRPVVEWGHSSNVFVSNGSRLY
+LDVGSHPEYATAECSTLDELIASDAAGDLILHDLVTRAQERMAADGISGRIHLYRNNADS
+SGSSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVVPAGTWPEGDGAAHFAFS
+QRADFVQDGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTSLSEHTHLLRFGATDL
+MLRMIEAGFPLGDRVLAHPTLAVRQISHDLTGTARVALRDGDASALELQEHYLERARAFV
+AAEGAHHERVEEILTLWEDVLEAVRTGDRSRIEDRIDWAIKLRMLEDYRARQNLDWGSAR
+LAQLDLAFHDIDPDRGLFRLLLRRGAAARLLPEDAGRLAVDAAPPTTRARVRADFIARAR
+QRGLGYAVDWTTLKLTDHPLHAIAAKDPFDASSDAVDRLFERIG*
+>NZ_CP083691.1_1579
+MTTDARRIFGLETEYGVQHWNPQARPLSPEEVVRYLFRPVLEWGRSSNVFVRNGSRLYLD
+VGSHPEYATAECSTLDELIASDAAGDLMLLDLIARAEEAMAADGIGGRIYLYRNNADSSG
+SSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVIPAGVWPEGEGRAHFAFSQR
+ADFVQEGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTNLSEATTLLRFGATDLML
+RMIEAGYPLGDHRVAHPTLAIRQISHDLTGTVRVNLREGTASALDLQDHYLSRARAFVAS
+EGAHHDRVEDVLDLWGTVVDAVRSQDFGPIEETIDWAIKLKLLRGYRDRYGLDWDAPRLA
+QLDLAFHDIAPGRGLFPLLRERGGVRRVLPEGAARAAVDAAPPSTRATVRAEFIARARAA
+GMDYAVDWTTLKLNDHPIHAISTKDPFSTDATPVDRLFERVG*
+>NZ_CP097650.1_1086
+MTDADRARRILGLETEYGVQHWNPQGRPLSPEEVVRYLFRPVVEWGRSSNVFVANGSRLY
+LDVGSHPEYATAECSTLDELIASDGAGDLLLHDLVVQAEERMAADGVGGRIHLYRNNADS
+SGSSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVVPAGTWPEGEGPAHFAFS
+QRADFVQDGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTNLSEHTHLLRFGATDL
+LLRMIEAGFPLGDRVVAHPTRAVRQISHDLTGTARIALREGEASALELQEHYLERARAFV
+AAEGAHHDRVGEVLTLWGEVLDAVRTGDRSRIEDRIDWAIKLRLLEDYRARHDLGWDAPR
+LAQLDLAFHDIDPDRGLFRLLLRRGAVARLLPEDAARSAVETAPPTTRARVRADFVARAR
+ERGLDYAVDWTTLKLTDHPLHAIVTKDPFDTSSAAVDRLFERIA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000991.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000991.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d1d81d6ceab464406f2ba31ef687ccb18c64f6ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000991.fa
@@ -0,0 +1,65 @@
+>NZ_CP042169.1_1140
+MTPPAPRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLTDTAFEKLFQRDRR
+VLRAVGVPLETLEPAGLDEGEAGVRHRVVRDALLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFQPATDLTGDDELAGYHTLMPRADPRLEALTQAVADEAVLRFPYRDARG
+RATRRTVRAWYLTLVRGRWYLTGWDLDRGAERSFRLTRMEGEPRRVERATDAPGRPEDHD
+HAGLVARLAGQADAERVRVWLAPGRGQGVRAVGEPAEPRVEDGAAPGPDWELWEAPAGPR
+EDGLAAEIGGLLGRAVPSAAHPDLTDRVRAGLAAAAEAHAGPADPALLEVPLAAPVRRRA
+RDSSEDLVGRLLDIVGLANRAGGVDRAELRARLGITDERLDADLETLRYCGMPERDFPGF
+QFEVAEVGGRVHVERAADLAGPVRLTRPEAHSLVAALQTVADLPVLDEADREAARSAQRR
+IRAAVLDAGAPDADDADDAALREAEAHTAGEPPVAVAAHWDVAVDPATVRTLLAAVAERA
+VVHLTYRSVHADALTERDVEPLALVQDGARLYLQAWCRRAEDHRVFRVDRISAPAPTGET
+FAPRARPARWRVHPDDTAGVPVLLRWAHPVRDAAAGYRPDAQADLPDGDRLTRVHLTDAA
+VAAALVGRHGGAVEVLAPADLRTSVADALGDALAALPAR*
+>NZ_CP033200.1_869
+MTPPAPRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLTDAAFEKLFQRDRR
+VLRAVGVPLETLEPAGFDEGEAGVRHRVVRDALLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFQPATDLTGDDELAGYHTLMPRADPRLEALTQAVADEAVLRFPYRDARG
+RATRRTVRAWFLTLVRGRWYLTGWDLDRAAERSFRLTRMEGEPRRLERATDAPGRPEDHD
+HADLVARLAGQADAERVRVWLAPGRGQGVRAVGEPAEPRVEDGAAPGPDWELWEAPAGPR
+EDGLAAEIGGLLGCAVPSAAHPDLTDRVRAGLAAAAESHAGPADPALLEVALAAPVRRRA
+RDSSEDLVGRLLDIVGLANRAGGVDRAELRARLGITDERLDADLETLRYCGMPERDFPGF
+QFEVAEVGGRVHVERAADLAGPVRLTRPEAHSLVAALQTVADLPVLDEADREAARSAQRR
+IRAAVLDAGAPDADDADDAALREAEAHTAGEPPVAVAAHWDVAVDPATVRTLLAAVAERA
+VVHLTYRSVHADALTERDVEPLALVQDGARLYLQAWCRRAEDHRVFRVDRISAPAPTGET
+FAARARPARWRVHPDDAAGVPVLLRWAHPVRDAAAGYRPDAQADLPDGDRLTRVHLTDAG
+VAAALVGRHGGAVQVLAPADLRASVADALGDALVALPAR*
+>NZ_CP040019.1_1679
+MAPPASRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLSDAAFEKLFQRDRR
+VLRAVGVPLETLEADSFEEEAQGVRHRVVRDAMLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFAPTPDLAADDELAGYHALTPRADPRLEALTQAVAEEAVLRFPYRDARG
+RESRRTVRAWFLTLVRGRWYLTGWDADREAERSFRLTRMEGEPRRVERAASLPGRPADHD
+HADLVARLAGQADAERVRVWLAPGRGQGVRAVGARVDPRAEDGAAPGDGWELWEAPAGTH
+EDGLAAEVGGLLGRAVPSAAEPDLARRVADALAAAARAHAGPAAPALLEAPLAPPVRRRA
+RDSSEDLVGRLLDIVGLANRADGVDRAELRARLGVTEERLDADLETLRYCGMPERDFPGF
+QFEVDEEGGRVHVRRAADLAGPVRLTRPEGHSLVAALQTVADLPVLDDADRAAARSAQRR
+IAEAVLDAGGAAASAADDEALAEAEAGTAPTPAPGGAVAAHWDVAVDPETVRTLLAAIAE
+RRVLRLDYRSVHADALSERDVEPLAVVQDGARLYLRAWCRSAGEDRVFRVDRIGAATATG
+EAFAPRARPARWRVHPDEAAGTPAVLRWAHRVRDAASGYRPEAQADLPDGDRLTRVRLTD
+ADVAAALVGRHGGAVEVLYPAAMRAHVKDALDRAVDALAAR*
+>NZ_CP083691.1_1576
+MSAHGSTAEPAERIISLLWLLLHEPLGYTREQIRRLVVGYEGLTDGAFEKLFQRDRRALR
+AVGVPLETVGDPDDEAGPRLRVDRDALLLQDVDFTVDERRALVRARRLWGDSPLRDDVVR
+AVGVLFHPGEVGGDDALEGFRTVMPRTDPRVAALSEAAAEQSVVRFSYRDAAGALTERTV
+RAWLLTLVRGRWYLTGWDADRAAERSFRLTRMESDPVVLDAGAASPAGEAPTLPAGHDHA
+ALRARLAGRAEAETVRVWLAPGRGQGFRVAGRPVPATAADGPAPGPDWELWECPSGPSED
+GAVAEAAVAVGQVLFSTVEAAAGRALAADLAAAAAVHAGDPDPAWRDVPLTAPTRRRSRA
+SSEDLVGRLLDIVGLANRAEGIGRDELQERLGVTARELDADLEVLRYCGMPEREFPGFQF
+DVEDEGGRVRVHQSSELAGPVRLTLPEAHALVAALQTVAEMTVLTPEDREAARSAQRRIR
+ASLADAGQSHAGSADAEAPRDGTGKEPGAVVAHWDVVADPDTVRTLLDAVAERAVVHLRY
+HGVRSDAVTERDVEPLAVVQDRTRLYLQAWCRRAGGPRVFRVDRIGALHRTGETFRARRV
+PAWDPRPAGDGVEAVVRWAHEVRDAADAYAPAAAATLDSGDRLTRVLLADDDAAVGLAAR
+HGGRVEILAPAALRGAVRGRLEAAARRAAGAVA*
+>NZ_CP097650.1_1089
+MTPPAPRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLTDAAFEKLFQRDRR
+VLRAVGVPLETLEPAGFDEGEAGVRHRVVRDALLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFQPATDLTGDDELAGYHTLMPRADPRLEALTQAVADEAVLRFPYRDARG
+RATRRTVRAWFLTLVRGRWYLTGWDLDRGAERSFRLTRMEGEPRRVERATDAPGRPEDHD
+HAGLVARLAGQADAERVRVWLAPGRGQGVRAVGEPAEPRVEDGAAPGPDWELWEAPAGPR
+EDGLAAEIGGLLGRAVPSAAHPDLTDRVRAGLAAAAETHAGPADPALLEVALAAPVRRRA
+RDSSEDLVGRLLDIVGLANRAGGVDRAELRARLGVTDERLDADLETLRYCGMPERDFPGF
+QFEVAEVAGRVHVERAADLAGPVRLTRPEAHSLVAALQTVADLPVLDEADREAARSAQRR
+IRAAVLDAGAPDADDADDAALREAEAHTAGEPPVAVAAHWDVAVDPATVRTLLAAVAERA
+VVHLTYRSVHADALTERDVEPLALVQDGARLYLQAWCRRAEDHRVFRVDRISAPAPTGET
+FAPRARPARWRVHPDDAAGVPVLLRWAHPVRDAAAGYRPDAQADLPDGDRLTRVHLTDAA
+VAAALVGRHGGAVEVLAPADLRTSVADALGDALAALPAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000992.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000992.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6013efee9a18381e9a141be0942bf1e474fd8e79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000992.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1141
+MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEGKGTTDERSGA
+GSTAADEPVEGRVVERDETDPRDPR*
+>NZ_CP033200.1_870
+MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEGKGTTDERSGA
+GSTAADEPVEGRVVERDETDPRDPR*
+>NZ_CP040019.1_1678
+MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEDKGAKDGKDAR
+SGSGSTAADEPVEGRVVERDETDVRPRDER*
+>NZ_CP083691.1_1575
+MRFTPTHLIVLIIVVLLLFAAPKLPALARNLGQSMRIFSSEVKQMKEENTTKKAEGAATA
+DAPSQGAGSTAAEPVEGRVVDRDVRDDR*
+>NZ_CP097650.1_1090
+MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEGKGTTDERSGA
+GSTAADEPVEGRVVERDETDPRDPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000996.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000996.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24fd4deb7b8c0986b7026ed3151394eec3fba8e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000996.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1145
+MRVLTIIPTYNEIESLPLTLGRLRDAVPESDVLVVDDASPDGTGDWADARAAEDPSVHVL
+HRTTKDGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLEAVRTADLVIGSRRV
+PGGKMVNWPTSRKMISWAGSLYPRIMLGLNLTDITAGYRAYRADTLRAIDLDAIESKGYG
+FQVDMTFRTARLGKRIVEVPITFVERELGESKMSGGIIGEAVVNVTRWGLAARWEGLRAR
+LGL*
+>NZ_CP033200.1_874
+MRVLTIIPTYNEIESLPLTLGRLRDAVPESDVLVVDDASPDGTGDWADARAAEDPSVHVL
+HRTTKDGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLEAVRTADLVIGSRRV
+PGGKMVNWPTSRKMISWAGSLYPRIMLGLNLTDITAGYRAYRADTLRAIDLDAIESKGYG
+FQVDMTFRTARLGKRIVEVPITFVERELGESKMSGGIIGEAVVNVTRWGLAARWEGLRAR
+LGL*
+>NZ_CP040019.1_1674
+MRVLTIIPTYNEIESLPLTLGRLRDAVPTSDVLVVDDASPDGTGQWADARAAQDPSVHVL
+HRTTKDGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLDAVRTADLVIGSRRV
+PGGKMVNWPASRKMISWAGSLYPRIMLGLRLTDVTAGYRAYRAETLRAIDLDAIESKGYG
+FQVDMTFRTARLGKRIVEVPITFVERELGESKMSGGIIGEAVVNVTRWGLAARWEGLRSR
+LGL*
+>NZ_CP083691.1_1571
+MRVLTIIPTYNEIESLPLTLGRLRDAVPDSDVLVVDDASPDGTGAWADARAAEDDHVHVL
+HRAEKNGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLEAVRTADLVIGSRRV
+PGGKMVNWPASRKLISAAGSLYPRIMLGLKLTDITAGYRAYRADTLRRIDLGAVQSKGYG
+FQVDMTFRVARLGLRIVEVPITFVERELGESKMSGGIVGEAVVNVTKWGLQARWETLTGR
+GPQRG*
+>NZ_CP097650.1_1094
+MRVLTIIPTYNEIESLPLTLGRLRDAVPESDVLVVDDASPDGTGDWADARAAEDPSVHVL
+HRTTKDGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLEAVRTADLVIGSRRV
+PGGKMVNWPTSRKMISWAGSLYPRIMLGLNLTDITAGYRAYRADTLRAIDLDAIESKGYG
+FQVDMTFRTARLGKRIVEVPITFVERELGESKMSGGIIGEAVVNVTRWGLAARWEGLRAR
+LGL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000997.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000997.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a125d6365d70433f0ae965850966591ffbfd4da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000997.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1146
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEEVDA*
+>NZ_CP033200.1_875
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEDVDA*
+>NZ_CP040019.1_1673
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAEAEGKPVRTHWDMLRERRSLEELQETYALQLNKLRASRGEDVDA*
+>NZ_CP083691.1_1570
+MSDRSLRGMRLGAQSLESEAGVEPAPRQRVEYRTEDGEQVFVTFAQEAEVPTTWTSKTGK
+EALRVDGEKPEENPGKPVRTHWDMLLERRSMEELEETFQIQLKKLHASRGEAV*
+>NZ_CP097650.1_1095
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEEVDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000998.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000998.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25d364b00ab0dba87c0c605830686ec8192b25d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000998.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1147
+METLIVLVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTLIIPFVDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDSINSQLRGVLDDATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQSLPKIADGQANTMFVVPAELTRALQGLGEAFAPGDGDRPTPEHAPR
+RRDSGDRAGEPGAEHSGVTPERARRPRGSRPTTADALRASGVMDAMTAGAVTAEDMPQTS
+LDEALATPQEIEPDPSAGRTPGTRPAGEADGNAVGH*
+>NZ_CP033200.1_876
+METLIVLVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTLIIPFVDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDSINSQLRGVLDDATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQSLPKIADGQATTMFVVPAELTRALQGLGEAFAPGDGDRPTPERAPR
+RRDSGDRAGEPGAEHVGVTPERARRPRGSRPTTADALRASGVMDAMTAGAVTAEDMPQTS
+LDEALATPQEIEPDPSAGRTPGTRPAGEADGNAVGH*
+>NZ_CP040019.1_1672
+METIIILVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTMIIPFVDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDSINSQLRGVLDEATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQALPKIADGESNTMFVVPAELTRALQGLGEAFSPAGDGESRRPSPSG
+ARGEAAERAGEHGGASPERPRRPRGSRPTTADALRSSGVMDAMTAGAVTAQEMPQTSLDE
+ALATPKELDPDPSAGRAPGRRPAGETDGNGVGH*
+>NZ_CP083691.1_1569
+MEFLIVLAVLAVLVGVLLASSVKIIPQARTANVERLGKYQRTAGAGLTLIIPFIDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDAINSQLRGVLDDATSRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSAILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQSLPKIAEGTSNTMFVVPAELTRALQGLGEAFSPGSPSAAGTGSSDT
+SDDAAPAAGRAATGPGGRRRGRASEGARPTTAEELRSSGLLDAMTAGALTADRMPQTSLD
+EALQTPPEAEPAPVRREPGMP*
+>NZ_CP097650.1_1096
+METLIVLVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTLIIPFVDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDSINSQLRGVLDDATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQSLPKIADGQANTMFVVPAELTRALQGLGEAFAPGDGDRPTPEHAPR
+RRDSGDRAGEPGAEHSGVTPERARRPRGSRPTTADALRASGVMDAMTAGAVTAEDMPQTS
+LDEALATPQEIEPDPSAGRTPGTRPAGEADGNAVGH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000999.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000999.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a4bf3691cc5d277088df973f4844024012cf4375
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0000999.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1148
+MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV
+EPGAPEVAPGDEVTVLRIDGATLVVRPLPRIDWEADGA*
+>NZ_CP033200.1_877
+MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV
+EPGAPDVAPGDEVTVLRIDGATLVVRPLPRIDWQADGA*
+>NZ_CP040019.1_1671
+MDWIEANAGWLWLVAAAGLIGVELLTLDLVFLMIAAGAGAAGVVALAGGPLPLQLAAFAV
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITAEAGTLTVDGDTWSARV
+EDGAPDAAPGAEVTVLRVEGATLVVRPLPQIDWEDGRS*
+>NZ_CP083691.1_1568
+MEWIEANADWLWLVLALGLVGAELLSLDLVLAMLAAGALSAGVAALAGAPLGLQLGVFVV
+VSLLTLVAVRPAAMRRLHPDPAVGASWLDGLSGRRLTATGPVTDEGGRIDVDGETWSARV
+EPGAAPAAHGQGVTVLRVEGAHLILRPDPVIDWDAPAHD*
+>NZ_CP097650.1_1097
+MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV
+EPGAPEVAPGDEVTVLRIDGATLVVRPLPRIDWEADGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001001.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001001.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4169bd1954ff3f94beff286d458105217d05c939
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001001.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1150
+MALIYTARLDPDKPEWIRRRLVAHGLPEDVTAEKVGSYRFDDPTGEIGVESMLVRVGDRL
+YQTAFAYRGDAPAEGDVVAEVEHSVLGHRWVVDAATDPDARRILAAAVRGEIPQARLEMH
+DESGTYLETRAPDLTLRVIGADATGELEVPVELSETGEADVDGPRCLIAEGDGVRAVVAR
+LT*
+>NZ_CP033200.1_879
+MALIYTARLDPDKPEWIRRRLVAHGLPEDVTAEKVGSYRLDDPAGEIGVESMVVRVGDRL
+YQTPFAYRGDAPAEGDVVAEVEHSVLGHRWVVDAATDPDARRILAAAVRGEIPQARLEMH
+DESGTYLETRAPDLTLRVIGADATGELEVPVELSETDEADVDGPRCLVAEGDGVRAVVAR
+LS*
+>NZ_CP040019.1_1669
+MALIYTAQLDPDKPEWIRRRLVAHGLPEDVDAEKVGSYRFDDPAGEVGVESMIVRVGDRL
+YQTAFAYRGEAPTEGDIVAEADHSVLGRRWVMDAATDPDARRILTAGLRGEIPQAVMDFH
+DESGAYLETRQPDVTLRLVGEGDGGELELPVELADAAEESGDGPRRLVAEGEGFTAVVAR
+LA*
+>NZ_CP083691.1_1566
+MSFIYSAQLDPDKNEWIRRALVAHGEDPDVPFTRAGSYRFDDPAGELGLEVMLVRVGGAD
+DGRLVQTPLSYRSAARDGATVLLTAEHSVLGTRWIHDALTDPEAREVLRRGVAGELAQEV
+LEVHDEHGVRTGTRQPDMTVTAVGTGPAAGELDMPYELDPADTADGGRALVAEGDGFSGL
+VVARLV*
+>NZ_CP097650.1_1099
+MALIYTARLDPDKPEWIRRRLVAHGLPEDVTAEKVGSYRFDDPTGEIGVESMLVRVGDRL
+YQTAFAYRGDAPAEGDVVAEVEHSVLGHRWVVDAATDPDARRILAAAVRGEIPQARLEMH
+DESGTYLETRAPDLTLRVIGADATGELEVPVELSETDEADVDGPRCLVAEGDGVRAVVAR
+LS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001002.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001002.fa
new file mode 100644
index 0000000000000000000000000000000000000000..273b85277010555b6107a01e185634238614fbae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001002.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_1151
+MVSVHLVPIRPTAATADDAQRLSAALLDDPRPGAAVISAAWHIDETDAAPGDGELAVTLD
+GMAAGVGLALWAVRSGSWAVLLDTEGNYDKQSALSHITAGERRRARRAPGRLVLPHGRRP
+GRASETGREADLRCAEATLQLVATVERRRSDDQHAAGRLVEAGASQREAAAELGISQQAV
+HSRLRHGLWHESRTAVAAVLPLLERLSADPGE*
+>NZ_CP033200.1_881
+MVFVHLVPIRPTAATADDARRLAAVLLDDPHPDASVAAAVWRGDEGNPDADAAPGDGELA
+VVVESMAAAVGLALWAVRTGSWAVLLDPEDALDKDSLLSYLTPAERRRARRAPGRLVLPH
+GRRPGRASETGREADLRCAEATLQLVATVERRRSDDQHAAGRLVEAGASQREAAAELGIS
+QQAVHSRLRHGLWHESRTAVAAVLPLLERLSADPGE*
+>NZ_CP040019.1_1667
+MIVLHLLPLTAPDAADAAWTRVGDELNRPGAVSSLVMPFDRQGEGSEARLVGGMDSGVEA
+VGILLSLVRSGAWAVVVEVAEGRAAGESLLQREAERARRANGHCAVLGPSGPSAAWIEPA
+LQLLGALERRRSEPQQDAGRRVEAGASQREVAAELQVSQQAVHARLRGGLWNETRALAGA
+TADALDVLARRGDRVSDGGASPSTSERG*
+>NZ_CP083691.1_1563
+MVPVAVRCGSAGAAGRWAASIPGARRLGREGGRDLIVHADDAAAAVALMLAVRRAGAGAV
+GAGVAIEQVEGALRRARRRPGGIAVSRVPGSTGTEEERGLLEAGLGVLLTLESRRSAPQQ
+AAGVLIEAGRSQREAAADLGVSQQAVQQRLRAGLWEETRTLLDALLPMARRVLEA*
+>NZ_CP097650.1_1104
+MVSVHLVLIRPTTATAEDARRLATALRDDPRPDAAVTAAMWLGDESDPVDDDAAPHDGEL
+AVVLDDAAAAVGLALWAVRTGSWAVMLDPEGGSDKDSALSYLTPAELRRARRAPGRLVLP
+AGGRPGRASESGREADLRCAEATLQLVAAVERRRSADQHAAGRLVEAGASQREAAAELGI
+SQQAVHSRLRHGLWHVSRTAVAAVLPLLERLSTDPGE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001004.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001004.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5fdf88cddc470b1eb0659156bfccf6e2ce3a16f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001004.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1153
+MVTAIVLIKTDKSSIPETAETLAALEGVGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL
+SKVDGIQDTETMLAFRAYSSEDLGEGWALGFDS*
+>NZ_CP033200.1_883
+MVTAIVLIKTDKSSIPETAETLAALEGVGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL
+SKVDGIQDTETMLAFRTYSSEDLGEGWALGFDS*
+>NZ_CP040019.1_1665
+MVTAIVMIKTDKSSIPETAETLAALEGIGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL
+SKVEGIQDTETMLAFRTYSSEDLGEGWALGFED*
+>NZ_CP083691.1_1561
+MVTAIVMITTDKSTIPETAQAIASLEGVSSVYSVTGAWDLVAMVKLKRYEDLADVIADQL
+SKVDGIEDTETMLAFRTYSTEDLEEGWALGFDG*
+>NZ_CP097650.1_1106
+MVTAIVLIKTDKSSIPETAEALAALEGVGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL
+SKVDGIQDTETMLAFRTYSSEDLGEGWALGFDS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001006.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001006.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c6e717dd4e587da087e880c013b14c40ef5b10a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001006.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1155
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTTILVLSSVT
+AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTVA
+ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK*
+>NZ_CP033200.1_885
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTTILVLSSVT
+AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTVA
+ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK*
+>NZ_CP040019.1_1663
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAENTAILNVPLAAANTLILVLSSVT
+AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTIA
+ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK*
+>NZ_CP083691.1_1558
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTVILVLSSFT
+AQFGVLAAERLQPRRTGGLFSVKSWGMVEWFILTFIMGSIFVAVQAFEYATLVSEGVTIA
+ANAYGSAFYITTGFHALHVTGGLIAFLFIIGRAFLARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK*
+>NZ_CP097650.1_1108
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTTILVLSSVT
+AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTVA
+ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001012.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001012.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da25bb83724b3fd40d8b3fc7ed51542d46de7c5c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001012.fa
@@ -0,0 +1,31 @@
+>NZ_CP042169.1_1162
+MGTTALLVLTGCSAEVQRGWYPGTRDTTNHNAQLTDLWVNSWIAAMVVGLLVWGAMIWCM
+VAYRRRKNDQGFPKQTAYNVPLETMFTAIPILTVFTLWGFTDRVQTEVDRPVDDSPLTVT
+VYGKQWSWDFNYSYEQEDGEVIEAHYSGIQAQLDGTEGVRDTLPVLYLPNDVPVHFELKS
+RDVVHSFWIPQFLQKRDMVPGKTNHLYLTPQELGSYDGKCAELCGEFHSEMLFNVEVVDE
+AEFVQRLEEMESGQVGEEYSRNPNNNPDGAGTMERDLQTPRGGGSH*
+>NZ_CP033200.1_891
+MGTTSLLVLTGCSAEVQRGWYPGTRDTTNHNAQLTDLWVNSWIAAMVVGLLAWGAMIWCM
+VAYRRRKNDQGFPKQTAYNVPLETMFTAIPILMVFTLWGFTNRVQTEVDRPVDDSPLTVT
+VYGKQWSWDFNYSYEQENGEVIEAHYSGIQAQLDGTEGVRDTLPVLYLPNDVPVHFELKS
+RDVAHSFWIPQFLQKRDMVPGKTNHLYLTPQELGSYDGKCAELCGESHSEMLFNVEVVDE
+AEFVQRLEEMEPGQVGDEYSRNPNNNPDGAGTMERDLQTPRGGGSH*
+>NZ_CP040019.1_1656
+MGTTALLVLTGCSAEVQRGWYPGTRDTTNHNAQLTDLWVNSWIAAMVVGLLAWGAMIWCM
+VAYRRRKNDQGFPKQTAYNVPLETMFTIIPILMVFTLWGFTNRVQTEVDRPVDDSPLTVT
+VYGKQWSWDFNYSYEQENGEVVEANYSGIQAQLDGTEGVRDTLPVLYLPKDVPVHFELKS
+RDVAHSFWIPQFLQKRDLIPGKTNHLYLTPQELGSYDGKCAELCGEFHSEMLFNVEVVDE
+AEFVDRLAEMEPGLVGDEYSRNPNNNPDGAREMERDLQTPRGGGSH*
+>NZ_CP083691.1_1552
+MRAQNDAGRRTRRRLTAGALGATALVALTGCSAEAQRGWLPGTDNTTNHNAQLTDLWVNS
+WIAALAVGLIAWGAMIWCMIAYRRRKNDQGFPRQTAYHMPIETMFTVIPILMVFTLWGFT
+DRVQAEVDTPIDDSPLTVTVYGKQWSWDFNYSYEKDGQTREAHFQGVQAQLDGSDGKRET
+LPTLYLPKDVPVHFELKSRDVAHSFWIPQFLQKRDMLPGKTNNLYLTPQEIGRFDGKCAE
+LCGEFHSEMLFNVEVVDEATFVQKMNEMEPGLVGDELNRNPNQNPDGARNMEVDLQTPRG
+GGNH*
+>NZ_CP097650.1_1118
+MGTTALLVLTGCSAEVQRGWYPGTRETTNHNAQLTDLWVNSWIAAMAVGLLAWGAMIWCM
+VAYRRRKNDQGFPKQTAYNVPLETMFTAIPILMVFTLWGFTDRVQTEVDRPVDDSPLTVT
+VYGKQWSWDFNYSYEQENGEVIEAHYSGIQAQLDGTEGVRDTLPVLYLPNDVPVHFELKS
+RDVAHSFWIPQFLQKRDMVPGKTNHLYLTPQELGSYDGKCAELCGEFHSEMLFNVEVVDE
+AEFVQRLEEMEPGQVGDEYSRNPNNNPDGAGTMERDLQTPRGGGSH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001013.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001013.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dd0d8417999d074ae6c8b78081c5ae963191d2da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001013.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1163
+MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAG
+GSCACGDSFH*
+>NZ_CP033200.1_892
+MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAG
+GSCACGDSFH*
+>NZ_CP040019.1_1655
+MALSADETGVEIGATQDSEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVQVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAV
+GSCACGDSFH*
+>NZ_CP083691.1_1551
+MALSAEETGVEIGATEDATGLPPHEVELTDVAAAKVRALLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAV
+GSCACGDSFH*
+>NZ_CP097650.1_1119
+MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYIMGATIDFEDTISKQGFTIDNPNAG
+GSCACGDSFH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001017.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001017.fa
new file mode 100644
index 0000000000000000000000000000000000000000..10636abfb5c3ff20f8346f0f3497e1b7b454d7f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001017.fa
@@ -0,0 +1,39 @@
+>NZ_CP042169.1_1167
+MARDPIQPPPPDPSAPHGAPAGGPTEEDTRPFLDDPPGLGWVPDGLPGFERCTLGLDTDE
+QGQNLVTVVRPRTDAPRDPARRPILSVHGWSDYFYNAPLAHAFEAAGYAFHAVDLRHYGR
+SLRAGQTPGWTDDLTRYDADLEAAFETIAQDHPLPPILMGHSTGGLIAALWADRNPGRLA
+ALVLNSPWLEMQGSAGVRLLAKSIVGPVSAMKPYATLTLPRIDHYWRTLSDQAEGEWDLH
+PLWRPPHAFEVPAAWLSAVLSGHRAVAGRLHVSVPILVLVSARGHRGTSYGEAMLTSDIV
+LDPDAMARRSLRLGDRVTVHRLPDALHDVFASPASVREAAGAATLTWLGAYAPPSATEAE
+SGAPDDGAG*
+>NZ_CP033200.1_896
+MARDPLQPPPPDPSAPHGAPAGGPTEEDTRPFLDDPPGLGWVPDGLPGFERCTLGLDTDE
+QGQNLVTVVRPRTDAARDPARRPILSVHGWSDYFYNAPLAHAFEAAGYAFHAVDLRHYGR
+SLRTGQTPGWTDDLARYDADLEAAFETIAQDHPLPPILMGHSTGGLIAALWADRNPGRLA
+ALVLNSPWLEMQGSAGVRLLAKSIVGPVSAMKPYAMLTLPRIDHYWRTLSDQAEGEWDLH
+PLWRPPHAFEVPAAWLSAVLSGHRAVAGRLDVTVPILVLVSARGHRGTSYAEAMLTSDIV
+LDPDAMARRSLRLGDRVTVHRLPDALHDVFASPASVREAAGAATLTWLGAYAPPSASEAG
+APDDGAG*
+>NZ_CP040019.1_1651
+MSIKPAEQPIPADESEPSRPPEGGPTDEDTRPLLDDPPGLGWVEDGMAGFERLTLGLDTD
+EQGQNLVTVVRPQATGPRDRTRRAILSVHGWSDYFYNAPLARAFEEAGYAFHAVDLRHYG
+RSLREGQTPGWTDDLARYDADLEAALATIAEDHPLPPVLMGHSTGGLIASLWAHRNPGRI
+SALVLNSPWLEMQGSAGVRLLAKTIVDPVSALKPYAMLTLPRIDYYWRTLSDQAEGEWDL
+HPLWRPTHAFEVPAAWLSAVLKGHRTVARRLQVSAPILVLVSARGHRGTSYDEAMLASDI
+VLDPDAMARRSLRLGDRVTVHRLPDALHDVFASPASVREAAGAATLTWLGAYAPPSASEA
+ESGAPDDGAG*
+>NZ_CP083691.1_1547
+MTLFPHVRGPWPRHGLGLPADDAAAPPTPVDPEAGWTPDVLDGFERRSLALNADRQGRNV
+VTVVRRRAASRHRDPCRRPFVAVHGWSDYFYNTPLAEAVESAGYAFHAVDLRHHGRSLRP
+GQTPGFVDRLDRHHEDLDAALALIAEDHPATPVVEAHSTGGLTTALWAADRPEAASALVL
+NSPWLQTHGGPLARAVAAPAVRRIARRDPYEILPLPRVDHYWRSLSAEADGEWDLEPAWR
+DRWAFAVPAGWLAAVLDGHTTVARGLDLPVPVLVLVSDRGGLPLATRRRAASSDVILSPR
+AQARAARRLGPGVVVHRCPGALHDVFASAPPVRRAALDATLSWLAETAPPRIAG*
+>NZ_CP097650.1_1123
+MARDPIQPPPPDPSAPHGAPAGGPTEEDTRPFLDDPPGLGWVPDGLPGFERCTLGLDTDE
+QGQNLVTVVRPRTDAPRDPARRPILSVHGWSDYFYNAPLAHAFEAAGYAFHAVDLRHYGR
+SLRTGQTPGWTDDLTRYDADLEAAFETIAQDHPLPPILMGHSTGGLIAALWADRNPGRLA
+ALVLNSPWLEMQGSAGVRLLAKSIVGPVSAMKPYAVLTLPRIDHYWRTLSDQAEGEWDLH
+PLWRPPHAFEVPAAWLSAVLSGHRAVAGRLDVSVPILVLVSARGHRGTSYAEAMLTSDIV
+LDPDAMARRSLRLGDRVTVHRLPDALHDVFASPASVREAAGAATLTWLGAYAPPSATEAE
+SGAPDDGAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001018.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001018.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a0b0726b7c2f36c0d2a8bdf47b08af2f7e9e00ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001018.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1168
+MSADRAPQPPPPHPSGAVAPRIDPRFVPRHVAIVMDGNGRWANQRGLPRTEGHRAGEAAL
+LDVVAGAVELGIGHVSAYAFSTENWRRSAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWN
+GRAPRLWTPVIRELQEAEELTRHNTGTTLHMCVNYGSRAEILDGVQAIAEEVRAGRMRPG
+EISEDVITRYLDRGFRTGQDVDVVPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWP
+DVDRRTLWAAVETYARRDRRYGGAVDTPQPAPSSGAPDSASVADGGA*
+>NZ_CP033200.1_897
+MSADRAPQSPPPHPSGAVAPRIDPRFVPRHVAIVMDGNGRWANQRGLPRTEGHRAGEAAL
+LDVVAGAVELGIGHVSAYAFSTENWRRSAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWN
+GRAPRLWTPVIRELQEAEELTRHNTGTTLHMCVNYGSRAEILDGVQAIAEEVRAGRMRPG
+EISEDVITRYLDRGFRTGQDIDVVPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWP
+DVDRRTLWAAVETYARRDRRYGGAVDTPQPAPSSGAPASDADGGA*
+>NZ_CP040019.1_1650
+MSGSGPSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIVEALTPEHGLVRAVAKGVRKT
+SSRLGSTVEPFMHTTLQLARGRGELLTVTQAQLLHPYATMLAADYDAYAVAGALAEAVER
+IPAVDEAGRRAQYRLLHGALAALARRRHDPRLILHSFLLRTLAQAGWAPTFDRCARCGAP
+GPHSAVHVALGGAVCPECRPPGAAHPAPQTLALLAALAAGDWATADSSDAAARREAAGIV
+AAYLQFHAERRLVSPVRPGPGPRPPRPARREETMRADRAPQSPPPHPSGAVAPRIDPRFV
+PRHVAIVMDGNGRWANQRGLPRTEGHRAGEAALLDVVAGAVELGVGHVSAYAFSTENWRR
+SAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWNGRAPRLWTPVIRELQEAEELTRHNTGT
+TLHMCVNYGSRAEIQDGVQALAEEVRAGRMRPADITEDVITRYLDRGFRAGQDVDVVPDV
+DLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWPDVDRRTLWEAVETYARRDRRYGGAVDT
+AQPAPSSGAPDSASDADGGA*
+>NZ_CP083691.1_1546
+MSDVPKVSPPPHPSGAVPPKLDPRFVPRHVAVVMDGNGRWANQRGLPRTEGHRAGEAALL
+DVVAGAVELGVGHVSAYAFSTENWSRSAEEVRFLMGFSKDVLRRQRDTLDSWNVRIRWNG
+RAPRLWTPVIRELREAEDLTRDNTGTTLHMCVNYGSRAEIVDGVQALAEEVAAGRMRPRD
+LTEDVITRWLDRGFRAGDRDVDVTPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDELWP
+DVDRRTLYAAVLEYAHRDRRFGGAVDAPAAD*
+>NZ_CP097650.1_1124
+MSADRAPQPPPPHPSGAVAPRIDPRFVPRHVAIVMDGNGRWANQRGLPRTEGHRAGEAAL
+LDVVAGAVELGIGHVSAYAFSTENWRRSAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWN
+GRAPRLWTPVIRELQEAEELTRHNTGTTLHMCVNYGSRAEILDGVQAIAEEVRAGRMRPG
+EISEDVITRYLDRGFRTGQDVDVVPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWP
+DVDRRTLWAAVETYARRDRRYGGAVDTPQPAPSSGAPDSASVADGGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001020.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001020.fa
new file mode 100644
index 0000000000000000000000000000000000000000..420201ce99cd2955bf7702f3fac811817744637a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001020.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1171
+MTDLVDPARAADGFRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH
+REDFQLVLVDTPGLHRPRTLLGERLNDLVAETLNEVDAVGMCLPADEAIGPGDRFIAQQL
+SYLHRTPVVAVVTKTDKVGPEQLMAQLVAVTALGDEVLGPENGGEGFAAVVPVSAVAGRQ
+VDDVLGVFAGLLPAGPPLYPDGELTDEPEAVMVAELIREAALEGVRDELPHSVAVMVEEM
+SLREDRPADRPLMDVWANVFVERDSQKGIIIGKGGSRLREIGAQARAGIERMLGTKVHLD
+LRVKVAKEWQRDPKQLGRLGF*
+>NZ_CP033200.1_900
+MTDLVDPARAADGFRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH
+REDFQLVLVDTPGLHRPRTLLGERLNDLVAETLNEVDAVGMCLPADEAIGPGDRFIAQQL
+SYLHRTPVVAVVTKTDKVGPEQLMAQLVAVTALGDEVLGPENGGEGFAAVVPVSAVAGRQ
+VDDVLGVFAGLLPAGPPLYPDGELTDEPEAVMVAELIREAALEGVRDELPHSVAVVVEEM
+SLREDRPADRPLMDVWANVFVERDSQKGIIIGKGGSRLREIGAQARAGIERMLGTKVHLD
+LRVKVAKEWQRDPKQLGRLGF*
+>NZ_CP040019.1_1648
+MTDLVDPARAADGHRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH
+REDFQLVLVDTPGLHRPRTLLGQRLNDLVAETLGEVDAVGFCLPADEAIGPGDRFIAQQL
+AHLHRTPVVAVVTKTDKVGPEQLMAQLLAVTALGEEVLGPENGGEGFAAVVPVSAVAGRQ
+VDDVLEVLRGLLPEGPPLYPDGELTDEPEAVMIAELIREAALEGVRDELPHSVAVVVEEM
+ALREGRPDDRPLMDVWANLFVERDSQKGIIIGKGGSRLREIGARARAGIERMLGTKVHLD
+LRVKVAKEWQRDPKQLGRLGF*
+>NZ_CP083691.1_1543
+MTSLLDPAVPEGHRSGFACLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVHR
+PDFQLVLVDTPGLHRPRTLLGERLNALVQETLSEVDVVGFCLPADEKIGPGDRFIAQQLA
+ALRRTPVVAIVTKTDKTDPQRVAEQLLAVTALGDEVLGPENGGRGFAAVVPVSAVAGRQV
+EDVESVLAQLLPDGPPLYPDGELTDEPEAIMVAELIREAALEDVRDELPHSVAVVVEEMN
+PREGRPEERPLLDVYANVFVERDSQKGIIIGKGGSRLRAIGTQARTGIERMLGTPVHLDL
+RVKVAKDWQRDPKHLNRLGM*
+>NZ_CP097650.1_1127
+MTDLVDPARAADGFRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH
+REDFQLVLVDTPGLHRPRTLLGERLNDLVAETLNEVDAVGMCLPADEAIGPGDRFIAQQL
+SYLHRTPVVAVVTKTDKVGPEQLMAQLVAVTALGDEVLGPENGGEGFAAVVPVSAVAGRQ
+VDDVLGVFAGLLPAGPPLYLDGELTDEPEAVMVAELIREAALEGVRDELPHSVAVVVEEM
+SLREDRPADRPLMDVWANVFVERDSQKGIIIGKGGSRLREIGAQARAGIERMLGTKVHLD
+LRVKVAKEWQRDPKQLGRLGF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001021.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001021.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6931211d7b35def1b0de6a6bc72ba034bbf38a20
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001021.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1172
+MLTPAVLFALFLVFLGLTWTLSLAESAFSYLSRRDAEDIVRERPGSKVLEIARERESHLG
+ALRVWRFVAEALSAVCLTAAADAVVDDTWLAVAIAAVVLVGVAALLGVWSPRPIGSRNEA
+AVARRLGGLVWVLRRALGPLAARLDRDRRRREVEPEDEDDFQERHLREFVARAHDADVLA
+DSEAELIQSVFSMNDTIVRSVMVPRTDVVTIDADHTLGQAMALFLRSGNSRIPVIGEDAD
+DIRGMLHLKDVTRALHHDGAATDTPVTEVMRDVRFVPESKSVATLLQELQRESTHVAVVV
+DEYGGTAGLVTLEDLIEEIVGEIYDEDDQPDRPEVEFVAPGVYSVDARMGIHDFREEFEL
+PEEDEDDDVDTVGGLLAKELGRVPIQGSRVVVQGIELVADTLEPRRNRVARLRVSETPDR
+PVRLRRREEQAHGAAPADPVA*
+>NZ_CP033200.1_901
+MLTPAVLFALFLVFLGLTWTLSLAESAFSYLSRRDAEDIVREQPGSKVLEIARERESHLG
+ALRVWRFVAEALSAVCLTAAADAVVDDTWLAVAIAAVVLVGVAALLGVWSPRPIGSRNEA
+AVARRLGGLVWVLRRALGPLAARLDRDRRRREVEPEDEDDFQERHLREFVARAHDADVLA
+DSEAELIQSVFSMNDTIVRSVMVPRTDVVTIDADHTLGQAMALFLRSGNSRIPVIGDDAD
+DIRGMLHLKDVTRALHHDGAATDTPVTEVMRDVRFVPESKSVATLLQELQRESTHVAVVV
+DEYGGTAGLVTLEDLIEEIVGEIYDEDDRPDRPEVEFVAPGVYSVDARMGIHDFREEFEL
+PEEDEDDDVDTVGGLLAKELGRVPIQGSRVVVQGIELVADTLEPRRNRVARLRVSETPDR
+PVRLRRREEQAHGAEPADPVA*
+>NZ_CP040019.1_1647
+MLTPAVLFALFLVFLALVWTLSLAESAFTYLSRRDAEDIVRRRPGSRVLDVTAERDSHLG
+ALRVWRFVAEALSAVCLTAAADAVVDNTWFAVLIAAAVLVGVAALLGVWSPRPFGSRNEA
+AVARRLGGLVWGLRRALGPLADRLGRDRRRREDELEEEDDFQERHLREVVARAHDADVLA
+DSEAELIQSVFSMNDTIVRSVMVPRTDVVTIDADHTLGQAMALFLRSGNSRIPVIGEDAD
+DIRGMLHLKDVTRALHQDGAAQSGPVTAAMRDVRFVPESKSVAALLQELQRESTHVAVVV
+DEYGGTAGLVTLEDLIEEIVGEIYDEDDLPDRAEVEMIEPGVYSVDARMGLHHFREEFEL
+PEEEDEDDDVDTVGGLLAKELGRVPIQGSRVVVQGLELLADTLEPRRNRVARLRVSETPD
+RPARLRRRDEEPHGSSAAETAA*
+>NZ_CP083691.1_1542
+MATAVSLVLLFLACLACTWVLALAESAFTYLPRKDAEDVARTRPGSRILDVTADLDGHLG
+ALRVWRFLSEAFAAMFLTAGLHALTDSVWAALAVTAVLLVGTAAVLGVWSPRPIGSRNEA
+AVAARTAGLVHGLKQALGPVGDRLGRDRRRTEAEAADEDDFHERHLREVVARAHDAEVLE
+DSEAELIASVFSMGDTLVRSVMVPRTDVVTIDADHTLGQALDLFLRSGCSRVPVIGEDSD
+DVRGMLYLKDAVRALHHEGHASQDAVTAVMREVRFVPESKPVSVLLEELQRESTHVAIVV
+DEYGGTAGLVTLEDLIEEIVGEIWDEDDRPDRPEIEELAPGVYSVDARMGIGDFREEFEL
+PEDEDEDDDVDTVGGLLAKELGRVPIRGSRVVVHGLELTADTLEPRRNRVARLKVVETED
+RPARLRRQHDPTDPD*
+>NZ_CP097650.1_1128
+MLTPAVLFALFLVFLGLTWTLSLAESAFSYLSRRDAEDIVRERPGSKVLEIARERESHLG
+ALRVWRFVAEALSAVCLTAAADAVVDDTWLAVAIAAVVLVGVAALLGVWSPRPIGSRNEA
+AVARRLGGLVWVLRRALGPLAARLDRDRRRREVEPEDEDDFQERHLREFVARAHDADVLA
+DSEAELIQSVFSMNDTIVRSVMVPRTDVVTIDADHTLGQAMALFLRSGNSRIPVIGEDAD
+DIRGMLHLKDVTRALHHDGAATDTPVTEVMRDVRFVPESKSVATLLQELQRESTHVAVVV
+DEYGGTAGLVTLEDLIEEIVGEIYDEDDQPDRPEVEFVAPGVYSVDARMGIHDFREEFEL
+PEEDEDDDVDTVGGLLAKELGRVPIQGSRVVVQGIELVADTLEPRRNRVARLRVSETPDR
+PVRLRRREEQAHGAAPADPVA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001023.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001023.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd655640282ca7d5dd05983c9377539cd7490feb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001023.fa
@@ -0,0 +1,36 @@
+>NZ_CP042169.1_1174
+MSRPRDPEVIRPIVTVPPTTPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVFPTV
+DVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGRGAG
+QLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQALQAK
+EVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGTIEV
+APLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGTQSG
+LAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARGPAERSQKRGGARRGR*
+>NZ_CP033200.1_903
+MSRPRDPEVIRPIVTVPPTTPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVFPTV
+DVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGRGAG
+QLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQALQAK
+EVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGTIEV
+APLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGTQSG
+LAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARGPAERSQKRGGARRGR*
+>NZ_CP040019.1_1645
+MVRTLGPQDALLRILGGVFPAVDLTVRDQRLEMAGPVPDVASVRRVVEDLRSIARRDQAV
+TPEVMEQVVTHVRGAAAGRGAGQLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGI
+GPAGTGKTYLAMAKAVQALQAKEVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYD
+ALHDMIEPESIPRLMEAGTIEVAPLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGF
+GARMVVTGDTSQVDLPRGTRSGLSQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYD
+AARGAEPAPRGGRGHRGR*
+>NZ_CP083691.1_1540
+MIRPIVSDPSSHVVLPPVSVPGAESVSFESAELMVRTLGAHDALLRILAGVYPDVEVTVR
+DQSLGMSGPPRHVAQARRIVEDLRSLARRDAPVTPDVVEQVVSLVRDGETGRASGTLHLD
+SILSGRGRKIRAKTLHQQDYVEAIDRATIVFGLGPAGTGKTYLAMAKAVQALQAKEVTRI
+ILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMESGTIEVAPLAY
+MRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGVRSGLAEAV
+EVLEGVDGLEMVRFDSSDVVRHSLVSAIVDAYDGARGSGSAADPRPAGRGAQRGRSGRGR
+*
+>NZ_CP097650.1_1130
+MSRPRDPEVIRPIVTVPPTTPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVFPTV
+DVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGRGAG
+QLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQALQAK
+EVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGTIEV
+APLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGTQSG
+LAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARGPAERSQKRGGARRGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001026.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001026.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5df53199bb42687040c46c148591e964b0b83bb9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001026.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1177
+MSEQPRRLQVLQAIVEDYVALREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPETDTEHMMESTVRLLAQLTQQ
+VAVAQFPYEDGSTIRHLELVSLTPTRVLVVLILSTGRVDQRHAVLDRPVDEAELSVLRGL
+LLDALLGLGPVQAATVVDDVVTRVRPEHRQSAALVAAAVQDLLEAGREDRIVLAGTANLA
+RSPGDFGASIGPILEALEEQVVLLRLLTEMEQDAHGVSVRIGSENAGSLADTSVVAAAYG
+PGAVAKLGVIGPTRMDYPGTMAAVRAIARYLSRILTT*
+>NZ_CP033200.1_906
+MSEQPRRLQVLQAIVEDYVALREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPETDTEHMMESTVRLLAQLTQQ
+VAVAQFPHEDGSTIRHLELVSLAPTRVLVVLILSTGRVDQRHAVLDRPVDEAELSVLRGL
+LLDALLGLGPVQAATVVDDVVTRVRPEHRQSAALVAAAVHDLLEAGRQDRIVLAGTANLA
+RSPGDFGASIGPILEALEEQVVLLRLLTEMEQDAHGVSVRIGSENAGSLADTSVVAAAYG
+PGAVAKVGVIGPTRMDYPGTMAAVRAIARYLSRILTT*
+>NZ_CP040019.1_1642
+MTEQPRRLQVLQAIVEEYVARREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPSTDTEHMMETTVRLLAQLTQQ
+VAVAQFPHEDGSTVRHLELVPLTPARVLVVLILSTGRVDQRHVVLETPLAEADLAVLRGL
+LLEAVLGLGPAQAAAVVDAAVARMRPEDREAAALVAGAVHALLEAGRQDRIVMAGTANLA
+RSTGDFGASIGPILEALEEQVVLLRLLTEMEHDAHGVSVRIGSENAGSLADTSVVAAAYG
+PGAVAKVGVVGPTRMDYPGTMAAVRAIARYLSRILTT*
+>NZ_CP083691.1_1537
+MTEQPRRLQVLQAIVEDYVSLREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRISEVKPLSAAERRAVRTLLDSEADTESMMEATVRLLAQLTRQ
+VAVVQFPHEDGSTVRHLDLVALTPERVLVVLILSTGRIEQRTVALARPVQDEDLAALRAV
+LLPVIEGLGPAQAAAVLDTPLEGLPPARRAAAVDVVGAVRGLLEAERQDRIVLAGTANLA
+RSTDDFHSSIGPILEALEEQVVLLRLLTEMGQDAHGVSVRIGAENGASLADTSVVAAAYG
+PGAVAKVGVIGPTRMDYPGTMAAVRAIARYLSRILTT*
+>NZ_CP097650.1_1134
+MSEQPRRLQVLQAIVEDYVALREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPETDTEHMMESTVRLLAQLTQQ
+VAVAQFPHEDGSTIRHLELVSLAPTRVLVVLILSTGRVDQRHAVLDRPVDEAELSVLRGL
+LLDALLGLGPVQAATVVDDVVTRVRPEHRQSAALVAAAVQDLLEAGREDRIVLAGTANLA
+RSPGDFGASIGPILEALEEQVVLLRLLTEMEQDAHGVSVRIGSENAGSLADTSVVAAAYG
+PGAVAKLGVIGPTRMDYPGTMAAVRAIARYLSRILTT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001028.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001028.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0baacf99217a62e23e589d87afc4f0f01e4bd82e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001028.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1179
+MNTRAQPDAGRTGHGPPAWLVSAGGRGAPLTAKQDRDRAALAHLSLAFGVLGPLVVWLLY
+RDRGPFTSQESREALNFSGPPTLITLLFFFLSLLPVVGPIFAILGALTWAAMAVYGVMGA
+SHVSKGRPFRYPFNLRILR*
+>NZ_CP033200.1_908
+MNTRAQPDAGRTGHGPPAWLVSAGGRGAPLTAKQDRDRAALAHLSLAFGVLGPLVVWLLY
+RDRGPFTSQESREALNFSGPPTLITLLFFFLSLLPVVGPIFAILGALTWAAMAVYGVMGA
+SHVSKGRPFRYPFNLRILR*
+>NZ_CP040019.1_1640
+MNPSAQPDAGRPGHEPPAWLASAGGRATPLTAKQDRDRAALAHLSLAFGVLGPLVVWLLY
+RDRGPFTSQESKEALNFSGPPTLITTLFFFLALLPVIGAIFAILGALSWAVMAVYGVMGA
+SNVSKGRPFRYPFNLRILR*
+>NZ_CP083691.1_1535
+MATTPSTTPAGETATPRRAAGGSAAHEAPAWLRDAAGGRAPLTAKQDRDRAALSHLSLAC
+GLPGPLVMWLLYRDRGPFTAQESREALNFSLAPTLLIVLLFLLGGVPLLGGLLAILGALL
+WIALALYGVMGASQVAKGRPFRYPFSPRLLR*
+>NZ_CP097650.1_1136
+MNTRAQPDAGRTGHGPPAWLVSAGGRGAPLTAKQDRDRAALAHLSLAFGVLGPLVVWLLY
+RDRGPFTSQESREALNFSGPPTLITLLFFFLSLLPVVGPIFAILGALTWAAMAAYGVMGA
+SHVSKGRPFRYPFNLRILR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001030.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001030.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09e9dd3994e90e718f034c3254081dba487ef3f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001030.fa
@@ -0,0 +1,60 @@
+>NZ_CP042169.1_1181
+MSPLASNPPVPAATDPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD
+IERERGITIKSQAVRMPWSVDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ
+GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELASLIGCDPEDVLRVSGKTG
+VGVEELLDRVVRAVPSPEGDADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKVRMM
+STGTTYELLEIGVSSPEPVPTKGLAVGEVGYLITGVKDVRQSKVGDTVTNHAHPAEQSLG
+GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL
+HLEIVRERLEREFGLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKILEVREPMASAT
+IIVPAEFIGAVMELCQAKRGNLKGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA
+SLDWKADGDQAADLVKVDILLQGEQVDAFSSITHKDNAYTYGVMMTGKLKELIPRQQYEV
+PIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE
+AFIAALSSDGAGADQAAKK*
+>NZ_CP033200.1_910
+MSPLASNPPVPAATDPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD
+IERERGITIKSQAVRMPWSVDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ
+GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELASLIGCEPEDVLRVSGKTG
+VGVEDLLDRVVRAIPGPEGDADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKVRMM
+STGTTYELLEIGVSSPEPVPTNGLAAGEVGYLITGVKDVRQSKVGDTVTNHAHPAEQSLG
+GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL
+HLEIVRERLEREFDLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKILEVREPMASAT
+IIVPAEFIGAVMELCQAKRGNLKGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA
+SLDWKADGDQVADLVKVDILLQGEQVDAFSSITHRDNAYAYGVMMTGKLKELIPRQQYEV
+PIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE
+AFIAALSSDGAGADQAAKK*
+>NZ_CP040019.1_1638
+MSPLASNPPVPAATEPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD
+IERERGITIKSQAVRMPWELDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ
+GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELATLIGCEPEDVLRVSGKTG
+VGVEDLLDRVVRSIPAPEGEADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKIRMM
+STGATHELLEIGVSSPEPTPTKGLAVGEVGYLITGVKDVRQSKVGDTVTNHAKPAAEELG
+GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL
+HLEIVRERLEREFNLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKIHEVREPMASAT
+IIVPAEFIGAVMELCQAKRGNLRGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA
+SLDWKADGDQVADLVKVDILLQGEQVDAFSSITHKDNAYSYGVMMTGKLKELIPRQQFEV
+PIQAAIGSRVIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE
+AFIAALSSDGAGADSAAKK*
+>NZ_CP083691.1_1533
+MSEAPEPIKDVPVSPLASKPPVPAATDPAVIRNFCIIAHIDHGKSTLADRMLQATGVVQP
+REMKAQYLDRMDIERERGITIKSQAVRMPWEVDGVNYALNMIDTPGHVDFTYEVSRSLAA
+CEGAILLVDAAQGIEAQTLANLYLAMENELEIIPVLNKIDLPAADPDRYAAELATLIGCE
+PDDVLRVSGKTGQGVEALLDRVVERLPAPQGVADAPARAMIFDSVYDTYRGVVTYVRVVD
+GMLSPREKIRMMSTGATHELLEIGVSSPEPMPTKGLSVGEVGYLITGVKDVRQSKVGDTV
+TNSSRPATEQIGGYEDPKPMVFSGLYPIDGSDYPNLRDALDKLKLNDAALVYEPETSVAL
+GFGFRVGFLGLLHLEIVRERLEREFDLDLISTAPNVVYEVKREDKTVVTVTNPSEFPEGK
+VLEVKEPMASATVIVPAEYIGAVMELCQTKRGHLKGMDYLSEERVEIRYWIPLAEIVFDF
+FDQLKSRTKGYASLDWKADGDQVADLVKVDILLQGEQVDAFSAITHRDNAYSYGVMMTGK
+LKELIPRQQFEVPIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKR
+MKMVGRVEVPQEAFIAALSSDGAEPAKK*
+>NZ_CP097650.1_1138
+MSPLASNPPVPAATDPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD
+IERERGITIKSQAVRMPWSVDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ
+GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELASLIGCEPEDVLRVSGKTG
+VGVEELLDRVVRAIPGPEGDADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKVRMM
+STGTTYELLEIGVSSPEPVPTKGLAAGEVGYLITGVKDVRQSKVGDTVTNHAHPAEQSLG
+GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL
+HLEIVRERLEREFDLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKILEVREPMASAT
+IIVPAEFIGAVMELCQAKRGNLKGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA
+SLDWKADGDQVADLVKVDILLQGEQVDAFSSITHRDNAYAYGVMMTGKLKELIPRQQYEV
+PIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE
+AFIAALSSDGAGADQAAKK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001031.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001031.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc2651cfc8eca86a570d9f24c86e828cfa479daa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001031.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1182
+MAFDLHRALSLGRRTARLIGALRDDARPRRAASEAGRRAGDRSGPSPFPGPPGPPGPAWD
+PTEPTDSWPMPGPGQERRPRRQDAGRHVSLPDFTGTVRVEYAPVPGPTAGPGEVVWTWVP
+YEEMDGRGKDRPVLLIGRDGAHLLGLMLTSRDRNNALARDEDYVDVGAGAWDRSGRASEV
+KLDRVVRVDPAAVRREGGVLDRAAFDRVTAALARARRRGR*
+>NZ_CP033200.1_911
+MAFDLHRALSLGRRTARLIGALRDDARPRRAASEAGRRAGERSGPSPFPGPPGPPGPAWD
+PTEPTDSWPMPGPGQERRPRRQDTDRHVSLPDFTGTVRVEYAPAPGPTAGPGEVVWTWVP
+YEEMDGRGKDRPVLLIGRDGALLLGLMLTSRDRNNALTRDEDYVDVGAGAWDRSGRASEV
+KLDRVVRVDPAAVRREGGVLDRAAFDRVTAALARARRRVR*
+>NZ_CP040019.1_1637
+MAFDLNRALALGRRAIRLIGSLRDDDARRSWTGDAAGRGSGAAPFPGPPGPAGRAWDPKE
+PTDSWPFPDRGHDGRPRGGQDRTRPASGATDPQGRALLADFTGMGRVEYAPVPGPAAGPG
+EVVWTWVPYEEMDGRGKDRPVLLVGRDGDLLLGLMLTSRDRNNARVRDEDYVDVGSGPWD
+RAGRPSEAKLDRVLRVDPAAVRREGGVLDPAAFERVGDALARAQGWRR*
+>NZ_CP083691.1_1532
+MAFDFQRALTLGRTALRLVEQVRSMSGAGTTRGAAPSSPASRAGRRRRADAEETRGARSG
+GAGSDHALLPDFTGRARVEYAPVPGATPDPGEVVWTWVPFEEMDGRGKDRPVLLVGRDGD
+LLLALMLTSKDHTNAARRDADYVDVGTGPWDRGGRASEAKLDRILRVDPAAVRREGGVLE
+RSRFDAVAEALARAQGWDR*
+>NZ_CP097650.1_1139
+MAFDLHRALSLGRRTARLIGALRDDARPRRAASEAGRRAGDRSGPSPFPGPPGPPGPAWD
+PTEPTDSWPMPGPGQERRPRRQDTGRHASLPDFTGTVRVEYAPVPGPTAGPGEVVWTWVP
+YEEMDGRGKDRPVLLIGRDGAHLLGLMLTSRDRNNARARDEDYVDVGAGAWDRSGRASEA
+KLDRVVRVDPAAVRREGGVLDRAAFDRVTAALARARRRGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001032.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001032.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2d7a74d05ebbf5d91685c0f8bb344db8375a8aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001032.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1183
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEPEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG*
+>NZ_CP033200.1_912
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG*
+>NZ_CP040019.1_1636
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG*
+>NZ_CP083691.1_1531
+MANIKSQKKRILTNEKARQRNIAVKSELKTAIRAVDKAVAAGEQDAAVEALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG*
+>NZ_CP097650.1_1140
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001034.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001034.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85a740289567e8b151d36615b3d9eb45ad78db5d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001034.fa
@@ -0,0 +1,79 @@
+>NZ_CP042169.1_1185
+MNPAPGPPNDPVDRRARHREVPGPLEARWVPALLGCLTLGILGVGWDAPARSAAALTGLA
+VAAAAILGAARSTGRIRGVATATALAGVAAALMLQHSAGPAAAASGSGWTGAVHAGSPLR
+LELTLDGPATRSEATFGPRWSVPVRVETFGHPPRAPEAAVTARLTGGGAPPATIVAPEGG
+TWAPDGGPGSRVCVVARPSRSGSTVFLAAASAPQPGPCPGGTQTAGGATGGDPGPPRREA
+LRAAFRQSAEGTVGAAPELIPGLVLGDRSAQGAALDDAMKASGLSHLSAVSGANVAMILG
+AVAITLRSARVHRAVVLSAGLAVLGVFVVVVGPEPSVLRAAVMGALGALAVFFGRARQAF
+GLLTVGGTALLVAVPALAVEPAFHLSLAATAGIVLAGAPLDRALHAGLGRMLPDVVARWL
+SASLAVTVAAHLACQPIILAMTGEVSAYAVPANLLAAPAVPPVTVLGTLAAALALPAPGI
+AAALVAVIQWPAAWIGWVAHTSASLPGALRPWPAGALGAGLGVLLVAATLLGFAAVLLLE
+RRRTAPVRRVGRSAPRTRERLPALVVLAAALAAATTGAVGAVLVPRSSGSAPPDWAVAFC
+DVGQGDMAVFRSGPRAGVVVDVGPEPGLARRCLDDLDVDRVDAVLLTHLHADHAGGLAGV
+VDRASRGAVHYATRDAPAQGREGRGGEADGVDPLADAARLRTGATGTAGPVRWHVLLADA
+RAPEENDASAQVLVTVESGAGPVTTLVTGDMEEDASAAWVAGRRSDAAAPPRVDVLKVAH
+HGARNGGTAVPRAAGARLHVVSVGADNPYGHPHRATVDALGRLGPVARTDLHGTLALTAA
+DGPDPDGAPEIAVHTVRPPSSVRTGP*
+>NZ_CP033200.1_914
+MVSPAPGPPSDPVDRRARHREVPGPLEARWVPALLVCLTLGILGVAWDAPARSAAALTGL
+AVAATTVLGAARSTGRIRGVATATTLAGVAAALMLQHSAGPAAAASASGWTGAVHAGSPL
+RLELTLDGPATRSEATFGPRWSVPVRVETFGHPPRAPEAAVTARLTGGGAPPATIAAPLD
+GTAAPGGGPGSRVCVVARPSRSGSTVFLAAAAAPQPGPCPGGAEPAGGATDGGPGPPRRE
+ALRAAFRQSAEGTVGTAPELIPGLVLGDRSAQGAALDDAMKASGLSHLSAVSGANVAMIL
+GAVAITLRSARVHRAVVLSAGLAVLGVFVVVVGPEPSVLRAAVMGALGALAVFFGRARQA
+FGLLTVGGTALLVAVPALAVEPAFHLSLAATAGIVLGGAPLDRALHAGLGRVLPDVVARW
+LSASLAVTVAAHLACQPIILAMTGEVSAYAVPANLLAAPAVPPVTVLGTLAAALALPAPG
+IAAALVAVIQWPAAWIGWVAHTSASLPGALRPWPAGALGAGLGVLLVAATLLGFAAVLLL
+ERRRAAPVRRVGRSAPRTRERLPALVVLAAALAAATTGAVGAVLVPRASGAAPPDWAVAF
+CDVGQGDMAVFRSGPRAGVVVDVGPEPGLARRCLDDLDVDRVDAVLLTHLHADHTGGLPG
+VVDRASRGAVHYATRDAPAQGRGGRGGEADGVDRPADAARLRTGATGTAGPVRWHVLLAD
+ARAPEENDASAQVLVTVESEAGPVTTLITGDMEEDASAAWVAGHRSDAAAPPRVDVLKVA
+HHGARNGGTAVPRAVGARLHMVSVGADNPYGHPHRATVDALGRLGPVARTDLHGTLALTA
+ADGPDPDGAPEITAHTVRPPSSVRTGP*
+>NZ_CP040019.1_1634
+MVSAPAGSRPPEAPGARTDPAARRGDVPGPLDARWVPALLACLTLGIVSDGWEAATRTTV
+ALACLGAAAAAVLLAARAPTPAWIRGTGTAVALAGVAVALMLQHSAVPAAALERTGWADV
+VREQAAVRVELAVTGAAVETAGTFGPRWSAPVRVRAFGHPARAPEAAVAARLSGPGTVPS
+ALGAAPDSEPAPGGRVVGPPAATVLCVVVTPDAGDGTVFLTAAAAPTPGPCPAADAAHGA
+ASVEDEPPPRREALRAAFRAAAAGTAGTAPELIPGLVLGDRSAQGRPLDAAMKASGLSHL
+SAVSGANVALLLGFTAVALRSLRVHRAVVIAAGLGLLAVFVVVVGPEPSVLRAAVMGALG
+AVAVFLGRGRQAFALLAVGGTALLVAVPSLSVEPAFHLSLAATAGIVLAGSWGDRTLHGP
+LRRVLPDAAARWLSASLAVTLAALLACQPVLLAMTGELSAYAVLANLVAAPAVAPVTVLG
+TLAAALVLPAPAVAAALVWLVQWPSAWIGVVAHAAAGLPGALRPWPSGALGVGLGALLTA
+ATLAGFAAVLVLERRRHARVRRVGEGAPLPPERTPALVLLAAVLVAAAVGGVGAVLVPRP
+AGAAPPDWAVAFCDVGQGDMAVFRSGPRAGVVVDVGREPEAARRCLEDLGVDRVEAVLLT
+HLHADHAGGLAGVADRAVPGAVRYATRDAAGVGRSGATAGEAPGVAPPAGGARLVTGERG
+AAGQARWEVLLADARAAEENDASAQLLVTVDAPAGPVTTLVTGDMEEEASGVWAAGRRSD
+AAGPPSVDVLKVAHHGARNGGTAVPRAVRARLHVVSVGAENTYGHPHPATLDALHRLGPV
+ARTDLHGTVALVAEGPDGAAGAGEIGVYTVRPPSAVRTAP*
+>NZ_CP083691.1_1529
+MSLGCAALAAVTLTLRLRIRRTGSSRVRTGAATAVVLAGLCGAVLVQHIAVERSGREQVG
+WIETVDTGGPVRLEVTAQGPATAGDSRFGPSWTRPVTVQRFGHPLRPLTPPAEATLTGTG
+SLDAAANGAEVLCVVAEPRPADGALFLAARAAPESDGCGEGSTAASSGPTGRDVLRARFR
+EAAADGVGLAPELVPGLVLGDRTAQSEQTDQAMKDAGLSHLSAVSGANCALLLGTVALVL
+RSLRCPRGVVLGAGLAVLGVFVLVVGPEPSVLRAAVMGALGALAVFLGRGRQAFGLLCAG
+GTLLLVSVPDLAGEIAFHLSLAATAGIVLVAAPVDRWLHGRLGRVLPDLAARGLSSSLAV
+TLAAHLACQPILLVMTGTVSLWAVPANLMAAPAVAPVTVLGTLAAALVVPAPWAAAPLLW
+TVQWPAAWIGVTATAASAAPGAVRPWPEGALGVALGALLTAATLAGFHAVLVLERRPTAP
+VRRVGRSARDARVRVPAGVVLAAVLAASATGAAAAVLVPRPPGTVPEGWAVAVCDVGQGD
+MTVFRSGPGSAVVADAGPDPAAASRCLDDLRIERVDALLLTHLHADHAAGAPGLSGPRAA
+AAVRHGAWSGSGGGGGEEPGLDAPAGSAPLTTGDEGRAGDVAWRVLLADPRAAEQNDSSA
+QLLVTVTTPAGPVTTLVTGDMEQEASAAWAAGTRSDAAPPPRVDLLKVAHHGARNGGLDV
+PRRVRARLQAISVGADNTYGHPAAATVAGLEELGPVLRTDRHGTVALVPGPDARLTPYTV
+RPPT*
+>NZ_CP097650.1_1142
+MVSPAPGPPSDPVDRRARHREVPGPLEARWVPALLVCLTLGILGVAWDAPARSAAALTGL
+AVAATTVLGAARSTGRIRGVATATTLAGVAAALMLQHSAGPAAAASASGWTGAVHAGSPL
+RLELTLDGPATRSEATFGPRWSVPVRVETFGHPPRAPEAAVTARLTGGGAPPATIAAPLD
+GTAAPGGGPGSRVCVVARPSRSGSTVFLAAAAAPQPGPCPGGAEPAGGATDGGPGPPRRE
+ALRAAFRQSAEGTVGTAPELIPGLVLGDRSAQGAALDDAMKASGLSHLSAVSGANVAMIL
+GAVAITLRSARVHRAVVLSAGLAVLGVFVVVVGPEPSVLRAAVMGALGALAVFFGRARQA
+FGLLTVGGTALLVAVPALAVEPAFHLSLAATAGIVLGGAPLDRALHAGLGRVLPDVVARW
+LSASLAVTVAAHLACQPIILAMTGEVSAYAVPANLLAAPAVPPVTVLGTLAAALALPAPG
+IAAALVAVIQWPAAWIGWVAHTSASLPGALRPWPAGALGVGLGVLLVAATLLGFAAVLLL
+ERRRAAPVRRVGRSAPRTRERLPALVVLAAALAAATTGAVGAVLVPRASGAAPPDWAVAF
+CDVGQGDMAVFRSGPRAGVVVDVGPEPGLARRCLDDLDVDRVDAVLLTHLHADHTGGLPG
+VVDRASRGAVHYATRDAPAQGRGGRGGEADGVDRPADAARLRTGATGTAGPVRWHVLLAD
+ARAPEENDASAQVLVTVESEAGPVTTLITGDMEEDASAAWVAGHRSDAAAPPRVDVLKVA
+HHGARNGGTAVPRAVGARLHMVSVGADNPYGHPHRATVDALGRLGPVARTDLHGTLALTA
+ADGPDPDGAPEITAHTVRPPSSVRTGP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001036.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001036.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c164d043ad1381790f7b4b9ebb1b0e7a6a11caca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001036.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1187
+MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG
+IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTVYAELARAGYAR
+ILSVHLSGELSGTVEAARLAAADAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI
+RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR
+SAARAVDRLVELAVERAGEDPVRIAVHEYGDPETAMQLAERLQPISTTPVPVVELPAVLA
+AHLGLGALGVVICPLESPTGGSGD*
+>NZ_CP033200.1_916
+MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG
+IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTAYAELARAGYAR
+ILSVHLSGELSGTVEAARLAAAEAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI
+RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR
+SAARAVDRLVELATERAGEDPVRIAVHEYGDPETAVQLAERLQPVSTTPVPVVELPAVLA
+AHLGLGALGVVICPLESPTGGSGD*
+>NZ_CP040019.1_1632
+MATIEQWRDDALVRLRSRRSQLVGRARYGLKPPRRDRTAVVTDSAAALPAAALGHSLAAG
+IRQVPLPVMVGDQIHAEGTDDLALELPLALAAGTAVRTSRPSPGAFRSVYAQLAREGYAR
+ILSVHLSGELSGTAEAARLAAVDAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMTVARI
+RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLIGTLLHVRPVLAVDDGAISLVDRPR
+SAARAVDRLVELATERAGDVPVRIAVHEYGDPETAAALAERLTPVSTTPVPVVELPAVLA
+AHLGLGALGVVVCPLESPTGGSGD*
+>NZ_CP083691.1_1527
+MASTSQWLEDAVERLRARRGQLVGRARYGLKPARRDRTGIVTDSAAALPVEVFAHPFAAG
+IRQVALPVMVGEQIHVEGDADLDLELQLALAAGTPVRTSRPAPGAFRAAYADLAQAGCAR
+ILSVHLSGELSGTVEAARLAAADAPVPVVVLDSRTAGLALGHAVLDAAVEAGFGRPLDQV
+AAIAQACADQSSVLFTVPHLEQLRRGGRIGAVPSLLGALLQVRPVLGLQDGSVHLVDRAR
+TSPRALERMVDLARERAAGGPARIAVHEYGDPAGATALAERLQSASATPVPVVPLPAVLA
+AHLGLGTLAVVLSPLEPVPSTSSSPAQAN*
+>NZ_CP097650.1_1144
+MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG
+IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTAYAELARAGYAR
+ILSVHLSGELSGTVEAARLAAAEAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI
+RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR
+SAARAVDRLVELATERAGEDPVRIAVHEYGDPETAVQLAERLQPVSTTPVPVVELPAVLA
+AHLGLGALGVVICPLESPTGGSGD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001043.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001043.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e66f0a85a18bbf6ff5d19bff29e4bc693dc65a71
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001043.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_1194
+MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIEAGLLESHEAVEATPEAELAAEDFGDFSLPGEDDPFATLESSDAHQPT
+GDPAAIEEAAETVRAEEGISEDAPEA*
+>NZ_CP033200.1_923
+MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIEADLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLESSDAHQPM
+GDPAAIEEAAETVRAEEGTSEDATEA*
+>NZ_CP040019.1_1625
+MTEQYDGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIETDLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLEPSDAGQPV
+GDPEAIEEAAEAVRAEEGTSEDAPEA*
+>NZ_CP083691.1_1520
+MTPPPPPDGPPPAAPCVPTHGQKTTREQTLETYVTDQYEGIVNPPIDSLLERVDSKYALV
+LFAAKRARQINAYYSQLHEGLFEYVGPLVDTQLNEKPLSIAMREIESDMLVMAETAAVEP
+AIELAEEEFGDFALPGDDDPFVAEPTAEGVSPEEYGAPVTTGDDDAVEDILSGADVADED
+A*
+>NZ_CP097650.1_1151
+MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIEADLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLESSDAHQPM
+GDPAAIEEAAETVRAEEGTSEDATEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001045.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001045.fa
new file mode 100644
index 0000000000000000000000000000000000000000..57e87c37f9855c2d1500313a6941eaa912ad7c3e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001045.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1196
+MALRQLSVQERAEARRKALQARQARAELKAAFAAGEVGLADIFARADADDAVARLRTVDL
+LLALPGVGEVRAREAMAGCGISPRRRLGGLGRRQREALIAYIGR*
+>NZ_CP033200.1_925
+MALRQLSVQERAEARRKALQARQARAELKAAFAAGAVGLADVFARADTEDAVARLRTVDL
+LLALPGVGEVRARETMAGCGISPRRRLGGLGRRQREALIAYIGR*
+>NZ_CP040019.1_1623
+MALRQLSVEERAEARSKALAARQERAALKADFAAGQVSLAEVFSRADAEDAIGRLRTVDL
+LQALPGVGEVRAREAMAGCGISPRRRLRGLGRRQREALIAYIGR*
+>NZ_CP083691.1_1518
+MALRQLSVEERAEARAKALRARQERATLKTSFANRDLSLQEVFARADVDPAIGRLRTVDL
+LQAMPGVGEVRASAVMEACEISPARRLKGLGRRQREALIAYIGR*
+>NZ_CP097650.1_1153
+MALRQLSVQERAEARRKALQARQARAELKAAFAAGEVGLADIFARADADDAVARLRTVDL
+LLALPGVGEVRAREAMAGCGISPRRRLGGLGRRQREALIAYIGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001046.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001046.fa
new file mode 100644
index 0000000000000000000000000000000000000000..734b88ac4f80f98e4c1310cef0f739dbb837b6e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001046.fa
@@ -0,0 +1,31 @@
+>NZ_CP042169.1_1197
+MTTTATGGAGPRAPFGRRLAHAMETAGPLCLGVDPHPGLLRQWGLSDTPAGLEAFSLTAL
+EAAVGPEGPRVAAIKPQVALYERHGSAGLAALERLLAAARDAGVLTIADAKRGDIGSTMD
+GYAAAWIADASPLAADAVTLSPYLGFGTLVPTIRAAHEVGRGVFVLALTSNPEGREVQHV
+GEGSAEGSVARRIAAAAAAENAALRGDDAWGPVGLVLGATVAAEADRLGLDLPALGGPLL
+APGFGAQGATARGMRADFGTAWPQVLATSSRGILSAGPSVASLVDTIEENRAALR*
+>NZ_CP033200.1_926
+MTTTATGGAGPRAPFGRRLAQAMETAGPLCLGVDPHPGLLRQWGLSDTPAGLEAFSLTAL
+EAAVGPEGPRVAAIKPQVALYERHGSAGLAALERLLAAARDAGVLTIADAKRGDIGSTMD
+GYAAAWIADASPLAADAVTLSPYLGFGTLVPTIRAAHEAGRGVFVLALTSNPEGREVQHV
+GEGSAEGSVARRIAAAAAAENAALRGDDAWGPVGLVLGATVAAEADRLGLDLPALGGPLL
+APGFGAQGATARGMRADFGTAWPQVLATSSRGILSAGPSVASLVDTIEENRAALR*
+>NZ_CP040019.1_1622
+MAQAGPLCLGVDPHPSLLRQWGLPDTPAGLEAFSLTGLEAAVGPDGPRVAAIKPQVALYE
+RHGSAGLAALERLLAEARDAGVLTIADAKRGDIGSTMDGYAAAWTSDASPLAADAVTLSP
+YLGFGTLVPTIEAAHAAGRGVFVLALTSNPEGREVQHVGRDAGEGAVARRIAAAAADLNA
+ALRAEDEWGPVGLVLGATVAEDAERLGLDLPGLAGPLLAPGFGAQGATAAGMREGFGRAW
+PQVLATSSRGILAGGPTVAALVERIERDRADLG*
+>NZ_CP083691.1_1517
+MSVPAASMTREPFGRRLAAAMAAAGPLCLGIDPHPSLLQAWGLPDTAAGLESFGLTALEA
+AAGDGAARVAAVKPQVALFERHGSAGLAVLERLLAEARDAGVLTIADAKRGDIGSTMDGY
+AAAWLDDASPLAADAVTLSPYLGYGTLTASIERAAAAGRGVFVLALTSNPEGASVQHVGA
+SEGQGAVAARIVTSAAADDARLAGLDGWGPVGLVVGATVAGHARELGIDLAALRGPLLAP
+GFGAQGATGAGMREAFGAAWPQVLATSSRGILAAGPTVTSLTRAIDAARADLGVEGPDPR
+HAAGRDA*
+>NZ_CP097650.1_1154
+MTTTATGGAGPRAPFGRRLAHAMETAGPLCLGVDPHPGLLRQWGLSDTPAGLEAFSLTAL
+EAAVGPEGPRVAAIKPQVALYERHGSAGLAALERLLAAARDAGVLTIADAKRGDIGSTMD
+GYAAAWIADASPLAADAVTLSPYLGFGTLVPTIRAAHEAGRGVFVLALTSNPEGREVQHV
+GEGSAEGSVARRIAAAAAAENAALRGDDAWGPVGLVLGATVAAEADRLGLDLPALGGPLL
+APGFGAQGATARGMRADFGTAWPQVLATSSRGILSAGPSVASLVDTIEENRAALR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001049.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001049.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83917142b438cd30cee8583bfbdc9dd9f947b980
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001049.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1200
+MSITSLAAALAARPVPPRTPTKDYADVWLPVTLGTLAVVLVLLGLLALGWRARRRAQAGI
+PAPAPVPTALYDAEPTLSAEGMHVGTVRGEDRLDRVAVHGLGLRSRAVLEVHDAGTHRGL
+LVLRPGAANLFIPADDLVEAGLSGGIAGKFVEPGGLVAWGWRLGDVELTSAFRPDRPEDR
+DRLLAALQTIIDPAPADPAGRAGEGDPR*
+>NZ_CP033200.1_929
+MSITSLAAALAARPVPPRTPTKDYADVWLPVTLGTLAVVLVLLGLLALGWRARRRAQAGI
+PAPAPVPTALYDAEPTLSAEGMHVGTVRGEDRLDRVAVHGLGLRSRAVLEVHDAGTHRGL
+LVLRPGAANLFIPADDLVEAGLSGGIAGKFVEPGGLVAWGWRLGDVELTSAFRPDRPEDR
+DRLLAALQTIIDPAPADPAGRAGEGDPR*
+>NZ_CP040019.1_1619
+MNALALAAATLASRPVAPQTPGKDYSDVWLPITLGTLAVILVLVGLFALGWRARRRSQAD
+LPAPAAVPAALYEQEPAASASGMHVGTVRGEHRLDRVAVHQLGLRSHAVLEVHDAGEHRG
+LLVLRPDVANLYIPAADLLEAGLSAGIAGKFVEPGGLVAWGWRLGDAELTSAFRPDRAED
+RDRLLAALQTLIDPAPARSAGRAGEGDLR*
+>NZ_CP083691.1_1514
+MSAVLPAALPLAATPVPPASPMKDYSDVWLPIVLTTVGVIALLLALIAWGWRGRRRRQAG
+IPAPATVPPEVLEREPAVSAEGMWVGTVSGTDRLDRVAVHDLGLRSSGVLEVHTAGDRPG
+VLVLRPNIAPLFVPAAHLMEAGRSAGIAGKFVEPGGLVAWGWRLGDVDVTSAFRPRRPED
+RDRVLEALQTVIDRAGRPDAGQENAR*
+>NZ_CP097650.1_1157
+MSITSLAAALAARPVPPRTPTKDYADVWLPVTLGTLAVVLVLLGLLALGWRARRRAQAGI
+PAPAPVPTALYDAEPTLSAEGMHVGTVRGEDRLDRVAVHGLGLRSRAVLEVHDAGTHRGL
+LVLRPGAANLFIPADDLVEAGLSGGIAGKFVEPGGLVAWGWRLGDVELTSAFRPDRPEDR
+DRLLAALQTIIDPAPADPAGRAGEGDPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001050.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001050.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5117f68ec0d5f663b16d4823fe1a857ddcfaa058
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001050.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1201
+MSAPSPAPLLLRSARLTTGETADVLVAEGRIAALGPDAATHAAGLDPAPEEVDCAGLVLL
+PGLVDLHTHLRQPGKEDAETVETGTRAAAMGGFTSVHAMANSTPTADTAGVVEQVWRLGR
+DAGWCDVHPVGAVTVGLAGEALADLGAMADSQARVRMFSDDGMCVHDAVLMRRALEYVKS
+FGGFVAQHAQEPNLTAGAQMNESELSGVLGLAGWPAVAEEAIIARDVLLAQHVDSRLHVC
+HVSTAGSVELIRWAKAQGVAVTAEVTPHHLLLTEELVRSYDPVFKVNPPLRRESDVMALR
+AGLADGTIDTVGTDHAPHTAETKQCEWTVAAMGMTGLETALSVVQQAMVDTGLMDWAGVA
+RVMSTAPARIAGLTDQGQADERGVPRVGAVANLVLVDPQARRTVDPEQHLTKSRNSPYRG
+MELPGAVRHTVYRGARVVADGAPARPYRHPALTETGERA*
+>NZ_CP033200.1_930
+MSAPSPAPLLLRSARLTTGETADVLVAEGRIAALGPDAATHAAGLDPAPEEVDCAGLVLL
+PGLVDLHTHLRQPGKEDAETVETGTRAAAMGGFTSVHAMANSTPTADTAGVVEQVWRLGR
+DAGWCDVHPVGAVTVGLAGEALADLGAMADSQARVRMFSDDGMCVHDAVLMRRALEYVKS
+FGGFVAQHAQEPNLTAGAQMNESELSGVLGLAGWPAVAEEAIIARDVLLAQHVDSRLHVC
+HVSTAGSVELIRWAKAQGVAVTAEVTPHHLLLTEELVRSYDPVFKVNPPLRRESDVMALR
+AGLADGTIDTVGTDHAPHTAETKQCEWTVAAMGMTGLETALSVVQQAMVDTGLMDWAGVA
+RVMSTAPARIAGLTDQGQADERGVPRVGAVANLVLVDPQARRTVDPEQHLTKSRNSPYRG
+MELPGAVRHTVYRGARVVADGAPARPYRHPALTETGERA*
+>NZ_CP040019.1_1618
+MSAPHPRPLLLRGARLTTVETADVLVAEGRIAALGAEAAAQAAGLDPAPEEVDCAGLVLL
+PGLVDLHTHLRQPGKEDAETVETGTRAAAMGGFTSVHAMANSTPTADTAGVVEQVWRLGR
+DAGWCDVHPVGAVTVGLAGEALADLGAMADSQARVRMFSDDGMCVHDAVLMRRALEYVKS
+FGGFVAQHAQEPKLTAGAQMNESELSGVLGLAGWPAVAEEAIIARDVLLAQHVDSQLHVC
+HVSTAGSVRLIRWAKEQGVRVTAEVTPHHLLLTEELVRSYDPVFKVNPPLRRESDVMALR
+EALADGTIDTVGTDHAPHTAETKQCEWTVAAMGMTGLETALSVVQHAMVDTGLMDWAGVA
+RVMSVTPASIAGLEDQGQADERGVPRVGAVANLVLVDPEARRTVDPEQHLTKSRNSPYRG
+MELPGAVRHTVYRGARVVADGAPAQPYRHPAVAEAGGRA*
+>NZ_CP083691.1_1513
+MSTTVPPALLFRGAALASGRVADVLVSDGRVAAVGEVPAVDAEGASVVEAAGTVLLPGLV
+DLHTHLRQPGKEDAETVETGTRAAARGGFTAVHAMANSTPTADTAGVVEQVWRLGREAGW
+CDVHPVGAVTVGLAGEALADIGAMADSQARVRMFSDDGMCVHDAVLMRRALEYVKSFGGF
+VAQHAQEPRLTAGAQMNESELSGVLGLAGWPAVAEEAIIARDVLLAQHVDSRLHVCHVST
+AGSVELIRWAKAQGVQVTAEVTPHHLLLTEELVRSYDPVFKVNPPLRRESDVHALRAALA
+DGTIDTVGTDHAPHTAESKQCEWTVAAMGMTGLETALSVVQQAMVDTGLMDWSGVARAMS
+TEPARIAGLQDQGQADESGEPLVGAVANLVLWDPAVRRAVDPETHATRSRNSPYRGMELP
+GAVVHTVYRGRRVVADGELTQPVVHADAPEGRA*
+>NZ_CP097650.1_1158
+MSAPSPAPLLLRSARLTTGETADVLVAEGRIAALGPDAATHAAGLDPAPEEVDCAGLVLL
+PGLVDLHTHLRQPGKEDAETVETGTRAAAMGGFTSVHAMANSTPTADTAGVVEQVWRLGR
+DAGWCDVHPVGAVTVGLAGEALADLGAMADSQARVRMFSDDGMCVHDAVLMRRALEYVKS
+FGGFVAQHAQEPNLTAGAQMNESELSGVLGLAGWPAVAEEAIIARDVLLAQHVDSRLHVC
+HVSTAGSVELIRWAKAQGVAVTAEVTPHHLLLTEELVRSYDPVFKVNPPLRRESDVMALR
+AGLADGTIDTVGTDHAPHTAETKQCEWTVAAMGMTGLETALSVVQQAMVDTGLMDWAGVA
+RVMSTAPARIAGLTDQGQADERGVPRVGAVANLVLVDPQARRTVDPEQHLTKSRNSPYRG
+MELPGAVRHTVYRGARVVADGAPARPYRHPALTETGERA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001053.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001053.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d088737ecf386661b8406e89fe370bf8609d816
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001053.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1204
+MTERASAGSAAKRGTTARSRSRQRAVEILFEAEQRGSSALEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAISEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA*
+>NZ_CP033200.1_933
+MTERASAGSAAKRGTTARSRSRQRAVEILFEAEQRGSSALEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAISEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA*
+>NZ_CP040019.1_1615
+MTEPASAASGAKRGTTARSRSRQRAVEILFEAEQRGATVAEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAVSEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA*
+>NZ_CP083691.1_1510
+MTDTPSASDAKRGTTARSRSRQRAVEILFEAEQRGTDVLQGIRTRRESTDLQVNAYTQRL
+VEGVVADQERVDEALTSYSRGWSLDRMPAVDRAILRVGAWELLFEDEVPDAVAVSEAVAL
+AAALSTDESPEFVNGLLGRLQQVKPTLLA*
+>NZ_CP097650.1_1161
+MTERASAGSAAKRGTTARSRSRQRAVEILFEAEQRGSSALEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAISEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001054.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001054.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab74ec4553f30b17dc26837ed287ec855089e4ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001054.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1205
+MTVRETDREHTHVATSNDIKNGAVLKLEGQLWNVTEFQHVKPGKGGAFVRTKMKNITTGK
+VVDKTFNAGAKVEFATVDRSDYQYLYQDGADYVFMDVKDYDQITVPGAVVGDAAKYMLEN
+TQVVIALHEGTPLYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQ
+GTRVKVDTRTGDYLGRVND*
+>NZ_CP033200.1_934
+MTVRETDREHTHVATSNDIKNGAVLKLEGQLWNVTEFQHVKPGKGGAFVRTKMKNITTGK
+VVDKTFNAGAKVEFATVDRSDYQYLYQDGADYVFMDVKDYDQITVPGAVVGDAAKYMLEN
+TQVVIALHEGTPLYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQ
+GTRVKVDTRTGDYLGRVND*
+>NZ_CP040019.1_1614
+MATSNDIKNGAVLKLEGQLWNVIEFQHVKPGKGGAFVRTKMKNITTGKVVDKTFNAGAKV
+EFATVDRSDYQYLYQDGSDYVFMDVKDYDQITVSESVVGDAAKYMLENTQVVIALNEGTP
+LYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQGTRVKVDTRTGD
+YLGRVND*
+>NZ_CP083691.1_1509
+MATTNDIKNGSVLNLEGQLWNVIEFQHVKPGKGGAFVRTKMRNITSGKVVDKTFNAGTKV
+EFATVDRSDYQYLYQDGEDYVFMDVKDYDQITVPAAVVGDAAKYMLENTQVVIAMNEGTP
+LYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQGTRVKVNTTNGE
+YLGRVND*
+>NZ_CP097650.1_1162
+MTVRETDREHTHVATSNDIKNGAVLKLEGQLWNVTEFQHVKPGKGGAFVRTKMKNITTGK
+VVDKTFNAGAKVEFATVDRSDYQYLYQDGADYVFMDVKDYDQITVPGAVVGDAAKYMLEN
+TQVVIALHEGTPLYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQ
+GTRVKVDTRTGDYLGRVND*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001056.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001056.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46ec7dd3cc3e6a7c6463bc8b9d0cfd6506fccfad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001056.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1207
+MTDTPGTAPAPGPDPSTRPVPGPVTVCPWEGMTGALEARLTAAATVAAAADEDPAARPAR
+RVVLVGPMGAGKTTVGRALAAVTGLPFVDSDELFTQVHGPIPEFFAEHGEAAFRAEEARV
+IGHVLGRPTPCVLSCGGGAVLHPGTRRALAGPDSDVVYLAVGEEEALRRVGGGAGRPVLA
+GDPAGTWRRILAEREGLYREVADLVLDTTGLTAAEAAWRIVGDAHRPRRSESHP*
+>NZ_CP033200.1_936
+MTDTPGTAPAPGPDPSTRPVPGPVTVCPWEGMIGALEARLTAAATVAAAADEDPAARPAR
+RIVLVGPMGAGKTTVGRALAAVTGLPFVDSDELFTQVHGPIPEFFAEHGEAAFRAEEARV
+IGHVLGRPAPCVLSCGGGAVLHPGTRRALAGPDSDVVYLAVGEEEALRRVGGGAGRPVLA
+GDPAGTWRRILAEREGLYREVADLVLDTTGLTAAEAAWRIVGDAHRPRRSESHP*
+>NZ_CP040019.1_1612
+MPGPVSLCAWEAMTGALEARLATAAAAADGAPAPRIVLVGPMGAGKTTVGRALAATTGLP
+FVDADELFVQVHGPIPEFFAARGEAAFREEEARVIAHVLGRPSPCVLSCGGGAVLHPATR
+RALRGPGSDVVHLAVDEAVALRRVGGGAGRPVLAGDPAGTWRRILAEREPFYREVADLVV
+DTTGLTAAEAAWRIVEGVHRPRRSESHP*
+>NZ_CP083691.1_1507
+MSAQPAPTDGVPSWEAMVRGLDGRLAETSRDPGPVVVLVGPMGAGKTTVGRALAEATGRV
+FVDSDALFEDAFGSIPAYFTSRGEPEFRRQEERVIAHVLAHPAPCVLACGGGAVLSAATR
+ARLADPRAVVVSLQVAEPEALRRLGGGAGRPVLAGDPAGRWKAVLAERAPLYAEVADLTL
+DGTGHRPGDIASRIVEAIPTLPRRHTRP*
+>NZ_CP097650.1_1164
+MTDTPGTAPAPGPDPSTRPVPGPVTVCPWEGMIGALEARLTAAATVAAAADEDPAARPAR
+RIVLVGPMGAGKTTVGRALAAVTGLPFVDSDELFTQVHGPIPEFFAEHGEAAFRAEEARV
+IGHVLGRPAPCVLSCGGGAVLHPGTRRALAGPDSDVVYLAVGEEEALRRVGGGAGRPVLA
+GDPAGTWRRILAEREGLYREVADLVLDTTGLTAAEAAWRIVGDAHRPRRSESHP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001057.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001057.fa
new file mode 100644
index 0000000000000000000000000000000000000000..304370c25b488551e0abef3110e3bdb3d95aad91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001057.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1208
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGRTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELDGLARNAALTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLGELGVRIVSHTVAFGEAALPEGHPF
+PVPEDEARLDADPVRCLDPQTSAAMVAEVDDAHRAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGLATAARRGSAAHDGIARGADGRPRRTSDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAMLEKFGGDSVAETRRNLEAFQAAVPALPEPAADVVADGPMGDPLP*
+>NZ_CP033200.1_937
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGRTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELDGLARNAALTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLGELGVRIVSHTVAFGEAALPEGHPF
+PVPEDEARLDADPVRCLDPQTSAAMVAEVDDAHRAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATAARRGTAAHDGIARGADGRPRRTTDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAMLEKFGGDSVAETRRNLEAFQAAVPALPEPGADVVADGPMGDPLP*
+>NZ_CP040019.1_1611
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGLTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELEGLARNAALTRPRPGHADLTG
+MQKYGFDDARPLLERASARETAARVALGTVARAFLAQLGVRIVSHTTAFGEAALPEGHPF
+PLPEDQDRLDADPVRCLDPETSAAMVAEVDDAHKAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATAARRGSAAHDGIVRGEDGRPRRTSDRAGGIE
+AGMSTGEVLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAVLEKFGGDSVGETRRNMAAFQAAVPALPEPSADADASGHMGDPLQ*
+>NZ_CP083691.1_1506
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQEIQDALARRRLGYGRGARMKFEQDAVTVL
+GGIRHGLTLGSPVAIQVGNTEWPKWEQVMAADPVPEEELAGLARNARLTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLAELGVRIVSHTVAFGEAALPEPHAF
+PVPEDQDRLDADPVRCIDPETSAAMVAEVDAAHKEGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATASRRGSAAHDGIARGADGRPRRTSDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAVLEKFGGDSVAETRRNMEAFTAALPALPDAPAEQPAADHMGDPLQ*
+>NZ_CP097650.1_1165
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGRTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELDGLARNAALTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLGELGVRIVSHTVAFGEAALPEGHPF
+PVPEDEARLDAEPVRCLDPQTSAAMVAEVDDAHRAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATAARRGTAAHDGIARGADGRPRRTTDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAMLEKFGGDSVAETRRNLEAFQAAVPALPEPGADVVADGPMGDPLP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001059.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001059.fa
new file mode 100644
index 0000000000000000000000000000000000000000..957a20fc09e01f8e1d03314f81d5f73769f8c781
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001059.fa
@@ -0,0 +1,43 @@
+>NZ_CP042169.1_1210
+MTGDHQHARREDHWDDLLDDEADVHDDLDVFGFAHEEADEADVGAPSQPVGAAGPRRPRT
+FLRRRGTGSHPASRVDRGAGRRRTALVLGTVLVAFAVVVGLIVRGFLSGPDHTAVEGDEV
+TFSVEPGEDLGSVAARLDRAGIVGSARAFERAARDTGSGLVRSGDFVLRERMPAAEALAV
+LQGATDGAVHYVLVERGRRLTEVLDAVAEATGLPREELEAAAQDPTRYGVPGEAGTLEGW
+LDAGEYRLPVDATAGQVLDALVRPTLAELEALDVRDPAEQQRVLTIASILEAEALPQDYQ
+QVAGAIENRLAPDNTETHGLLQIDATVTYGLGVRSLSFTSGQRQDASNPYNTYVHPGLPP
+GPIGMPSDAAVEAALDPAETDAYYWVTTDIGTGHTEFSRTYEEHQQHVRTLQRYCASNPG
+VC*
+>NZ_CP033200.1_939
+MTGDHQHARREDHWDDLLGDEADVHDDLDVFGFAHGEADEADLGVPSQPVDAAGPCRPRT
+FLRRRGSGSHPAPRVDRGAGRRRTALVLGTVLVAFAVVVGLIVRGFLGGPDHTAVEGDEV
+TFSVEPGEDLGSVAARLDRAGIVASARAFERAARDTGSGLVRSGDFVLRERMPAAEALAV
+LQGAADGAVHYVLVERGRRLTEVLDAVAEATGLPREELEAAAHDPTRYGVPGEAGTLEGW
+LDAGEYRLPVDATAEQVLDSLIRPTLAELDALDVRDPAEQQRLLTIASILEAEALPQDYR
+QVAGAIENRLAPDNTETRGLLQIDATVTYGLGVRSLSFTSGQRQDASNPYNTYVHPGLPP
+GPIGMPSDAAVEAALDPAETDAYYWVTTDIGTGHTEFSRTYEEHQQHVRTLQRYCASNPG
+VC*
+>NZ_CP040019.1_1609
+MNRPPEHDWDDLPGDEADPDDDLDVFGFVHEDADDDPDEARRLGAPAAAAGGRRRGLLRR
+RGTGSHPAAPGRSRRGSRLRGGIALGAAALAFLAVVVLVVQGFLGGADHDGIEGEELTFS
+VEPGEDLASVARRLDSAGVVASARAFERAAEDSASGVVRAGDFVMRERMPAADALAVLQG
+TADGAVHYVLVERGRRLTEVLDALAESTGLPREELAAATQDPARYGVPAEAQTLEGWLDP
+GEYRLPVEASAEEVVDALVRPVLADLAELGVDDPDEQRRVLTVASLLEAEALPRDYRTVA
+GVIENRLAPDNTETRGLLQIDAAVTYGLGVRSLSFSAGQRQDASNPYNTYVHPGLPPGPI
+GMPSDAAVAAALDPADTDAYYWVTTDIATGHTEFSRTYEEHQEHVRTLQRYCASNPGVC*
+>NZ_CP083691.1_1504
+MSAPPPPPWREDETDDDLDVFGLVDHGEDEPEPEPERVERQPAPPRPVGRARRPRVRTGG
+SHRLRAIGRNLAVERPRGAVVLAVAALAVVLVAALLVVLFSRPADRQAVSGDRVTFTVEP
+GEDLASVAARLDERGIVASDRAVLDAAEDSGQTSIGAGEYVLREQMPAADALAVLQGRAE
+GASHYVVVGRGRWLSEVLDGLAQSTGLPRADFEAAAEDPTRYGVPEQAPSLEGWLDPGEY
+YPPVGADAEQVLAELVKPRLAHLRAQGVTDPAEQQRIVTIASILEAEALPKDYPRVAGVI
+DNRLNDPDAETRGLLQVDSTVNYGLGRRNLQFSAAQRADESNTYNTYQHTGLPPGPIGMP
+SDAAIEGAVHPEPSEDLYWVTTDIATGHTEFSRTYEEHSVHQEEFRRYCAQNPGVC*
+>NZ_CP097650.1_1167
+MTGDHQHARREDHWDDLLGDEADVHDDLDVFGFAHGEADEADLGAPSQPVDAAGPCRPRT
+FLRRRGSGSHPAPRVDRGAGRRRTALVLGTVLVAFAVVVGLIVRGFLGGPDHTAVEGDEV
+TFSVEPGEDLGSVAARLDRAGIVASARAFERAARDTGSGLVRSGDFVLRERMPAAEALAV
+LQGAADGAVHYVLVERGRRLTEVLDAVAEATGLPREELEAAAHDPTRYGVPGEAGTLEGW
+LDAGEYRLPVDATAEQVLDSLIRPTLAELDALDVRDPAEQQRLLTIASILEAEALPQDYR
+QVAGAIENRLAPDNTETRGLLQIDATVTYGLGVRSLSFTSGQRQDASNPYNTYVHPGLPP
+GPIGMPSDAAVEAALDPAETDAYYWVTTDIGTGHTEFSRTYEEHQQHVRTLQRYCASNPG
+VC*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001066.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001066.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aab5873625e3f69012d12efcf0f587d8e7ffae91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001066.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1217
+MSPAAPRADHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD
+AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD
+PAPESAAALAALDHGDGRPAGPDRTALEGRLLWTRCATGVADSPLTPARLDRALGVRGTA
+RNLTTVRVLAGLPAGDRPRRTARGASGDVDIRGTPRAGRDVTVRSHPCDGVTPSSASLP*
+>NZ_CP033200.1_946
+MSPAAPRTDHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD
+AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD
+PAPEAAAALAALDHGDDRPAGPDRTALEGRLLWMRCAAGVADSPLTPARLDRALGVRGTA
+RNLTTVRVLAGLPSED*
+>NZ_CP040019.1_429
+MSEHPASPTHVLLLRAVNVGGRNRVPKADLAELAAEAGLADVAVHLNSGNVLGTPDTGDH
+VDDVAARLRALLAERLGVDTSVHAAARTELSALVDGLLASDLLAPGETLDSVDPKTVHLV
+LLDTVPHPEAGEALAAVDAGDDRAVVVGRGVWVRYAGPSHSSHLGLPRIERAASGDAPPA
+QRRVGTARNLATVRVLAGR*
+>NZ_CP083691.1_1497
+MSRAAPRTDHTHVLLLRGINVGRSNRVSNARLAAWAEAARARDVTTHLASGNVLFRLPDA
+DDDAGPAFLRAFRDAALADDGPDVPLILTTPAELRGALAMHDRLPWSGGEAKLTQLTVLA
+ESPRDGAAEALAGLDHGSGRAAGPDRSALEGRFLWIRSPGRISDSPLTPARLEKALGVTG
+TARNLATVRVLAGMA*
+>NZ_CP097650.1_1174
+MSPAAPRTDHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD
+AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD
+PAPEAAAALAALDHGDDRPAGPDRTALEGRLLWMRCAAGVADSPLTPARLDRALGVRGTA
+RNLTTVRVLAGLPSED*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001067.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001067.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b65ced5b0f334cf064269b6ea67f7fa24b3ff937
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001067.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_1218
+MPRLARLATAVTAAALSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHET
+GVFGESAAEIPAFDAVSGRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVT
+DKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTTTLRYLGGVRVGALPDSLAFSPNG
+AYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTALPAG
+VRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLED
+LWALTPTDWSTEGVLDASDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGR
+EWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLKVLTDLGYDSERECHSSLTTLGGR
+SFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPEPES
+VVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGA
+EGLTFVPADESPSGTALLIVANEVSGSTTVYEVNPTRRQ*
+>NZ_CP033200.1_947
+MPRLARLATAVTAATLSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHET
+GVFGESAAEIPAFDAVSGRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVT
+DKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTTTLRYLGGVRVGALPDSLAFSPNG
+AYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTALPAG
+VRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLED
+LWALTPTDWSTEGVLDASDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGR
+EWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLKVLTDLGYDSERECHSSLTTLGGR
+SFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPEPES
+VVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGA
+EGLTFVPADESPSGTALLIVANEVSGSTTVYEVNPTRRQ*
+>NZ_CP040019.1_1601
+MRTLSRLAAATSMVALSAAVVAPLTVAAPAANPSGRSIELTAAGTHATGVFDASAAEIPA
+FDKTTGRLFVVNAQKGAIDVLTVGEDAEPAAESVLSVAGLPAADGSVTGAGAVVNSVAVA
+GAVMAATVEAEDKTGHGWLVFFDTRTLGFLGGVRVGALPDSVALAPNGAYAVVANEGEPA
+DDFSSDPEGTISVVSVPKNARQFARLGQDAVRTVDFRAYDEGAALPEGVRVFGPDVAVPS
+GHEEAGRIARNLEPEYASIDPTGRTAYVSVQEANAVVAVDLASASLADFWALHLTDWSTE
+GVLDVSDKDGAISPAYQPVLGVPMPDGLATYKHRGQTLVVTANQGDSREWGDFVDAERVK
+DLELCGDVFPHAKALQKNEALGRLNVLTDLGYDAERGCHTELHALGGRGFSIYTADGQRL
+FDSSGMLEEQIARLIAAGELPAHAFNANNDETPSFDSRSDDKGVEPESVVVGEVQGRQYA
+FVGLERIGGVMVFDITDPTDARYVDYINERAWDAVGEDGDAGLGDMGAEGLAFVPASDSP
+SGTALLIVATEVSGSTTVYEVDPVKGGKRT*
+>NZ_CP083691.1_1496
+MSRIVRLTRLGAAAGALALSAAVVAPSAVSAPVTATAAAANPSGKTVELSLAGTHETGVF
+GESAAEIPAFDAATGRLFVVNAEKGAVDVLRVGADGAPAAETVLSAEGLRTADGSVTDGG
+ATVNSVAVSGGVLAVAVEAADKTGLGWVAFFDTTTLSYLGGVRVGALPDSIAFSPDGAYA
+VVANEGEPADDFSADPEGTISVISVPKNVRQFARLTQAAVRTVDFRAYDAGTALPEGVRV
+FGPDVQVPEGQEPAGRIARNLEPEYVTIDDTGRTAYVSVQEANAVVAVDLKSATLKDFWA
+LQLTDWSKEGVLDASNEDKAITLRNQPVLGVPMPDGVDTYRYRGQDLVVTANEGDSREWG
+DFVDAARVKDLELCTAEYPDAKALQKKPALGRLNVVTDLGYDADRDCFSQLHAFGGRSFS
+IYTADGTRLFDSAGMIEEQIAQLIADGELPESAFNANNDETPSFDSRSDDKGPEPEAVVV
+GRVQGRTYAFVGLERIGGVMVFDITDPTKATYVDYVNERNWDAEGDDAAAGLGDMGAEGL
+TFVPANESPSGTALLVVANEVSGSTTVYEVNPVRR*
+>NZ_CP097650.1_1175
+MPRLARLATAVTAATLSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHET
+GVFGESAAEIPAFDAVSGRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVT
+DKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTTTLRYLGGVRVGALPDSLAFSPNG
+AYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTALPAG
+VRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLED
+LWALTPTDWSTEGVLDASDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGR
+EWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLKVLTDLGYDSERECHSSLTTLGGR
+SFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPEPES
+VVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGA
+EGLTFVPADESPSGTALLIVANEVSGSTTVYEVNPTRRQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001069.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001069.fa
new file mode 100644
index 0000000000000000000000000000000000000000..60d7b7ddeadf0ca6df23fc4ac68c0d24839247ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001069.fa
@@ -0,0 +1,60 @@
+>NZ_CP042169.1_1220
+MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVRDEADFDPLR
+NEWVLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARL
+RHRYLDLRRPQPSRIMRLRSEVNRTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARL
+APGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD
+DVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDT
+PFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNI
+SEEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDA
+DWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPKPEFADTFDTDPGAALAY
+AYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIA
+FGWDRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEA
+EPEA*
+>NZ_CP033200.1_949
+MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVREEADFDPLR
+NEWVLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARL
+RHRYLDLRRPQPSRIMRLRSEVNRTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARL
+APGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD
+DVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKHT
+PFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNI
+SEEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDA
+DWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPKPEFADTFDTDPGAALAY
+AYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIA
+FGWDRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEA
+EPEA*
+>NZ_CP040019.1_1598
+MNPTISSGRSPDGEDAFVLRTHQLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDAS
+GFAQVVVRDEADFDPLRNEWVLQVSGVVERRPEGNENPNLPSGEIELIAETVTVLNTAAA
+LPFQVDEHVEVGEEARLRHRYLDLRRPEPSRIMRLRSEVNRTAREMLHGEGFTEVETPTL
+TRSTPEGARDFLVPARLAPGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADR
+QPEFTQLDIEASFVEQDDVIALGEKIVKAVWALVGVDVPTPIRRMTYAEAMEKYGSDKPD
+LRFGLELTDLTAYFKDTPFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAY
+VLIQEDGSLTGPVSKNISDEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGR
+RCELFTDAGNGVEAKDADWAFVWVVDAPMFEPAADAVASGDVAVGSGAWTAVHHAFTSPK
+PEFADTFDTDPGSALAYAYDIVCNGNEIGGGSIRIHRQDMQERVFSVMGLSQEDAQEKFG
+FLLEGFKYGAPPHGGIAFGWDRVVALLAGTESIREVIAFPKTGGGFDPLTAAPAPITAQQ
+RKEAGVDAKPEPKKAEGEKAEAAGQPQA*
+>NZ_CP083691.1_1493
+MLRTHHLGELNASLIGQTVTVTGWVAKRRDHGGVAFVDLRDASGRAQVVVRDEADFDPLR
+NEWVLQVTGTVERRPEGNENPNLPTGEVELIADDVVVLNTAAALPFQIDEHVEVGEEARL
+RHRYLDLRRPQPARIMRLRSEANRVARELLNEQGFVEVETPTLTRSTPEGARDFLVPARL
+APGSWYALPQSPQLFKQLLQVGGLEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD
+DVIALGEQIVKALWGLVGVEVQTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDT
+PFRVFQNEYVGAVVMPGGASQPRRTLDAWQEWAKQRGAKGLAHVLIQEDGTLTGPVSKNI
+TDEEKAGLAAAVGANPGDCVFFAAGKAKESRALLGAARVEIGRRCELFTDAGDGVEAKDA
+DWAFVWVVDAPLFEPAADAVASGDVAVGAGQWTAVHHAFTSPKPEFMDTFDTDPGSALAY
+AYDIVCNGNEIGGGSIRIHRQDVQKRVFSVMGLSEEDANEKFGFLLEGFKYGAPPHGGIA
+FGWDRVVALLAGTESIREVIAFPKTGGGYDPLTAAPAPITPQQRKEAGVDAKPEAKKAEG
+AASEGAEAQAKANDEKTAADEAQLR*
+>NZ_CP097650.1_1177
+MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVRDEADFDPLR
+NEWVLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARL
+RHRYLDLRRPQPSRIMRLRSEVNRTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARL
+APGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD
+DVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDT
+PFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNI
+SEEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDA
+DWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPKPEFADTFDTDPGSALAY
+AYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIA
+FGWDRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEA
+EPGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001072.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001072.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d17f0d8ca988f4613849fb8dafb828704923578
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001072.fa
@@ -0,0 +1,49 @@
+>NZ_CP042169.1_1223
+MQPDDQQSPATEATPASAEAAETTVPAEARPVPEIVPDAPAHGDSAQPAEAPAVPSPAAM
+KKASPAAVRPATPAAASAVPAPVVAPTVPPTPVEEAARFARVSEDGHVTLLDGQEEHAVG
+QVPDASTEDALAYFVRKYDDVRAQMALFEQRIAAGAPSSELGRALGQMTTAVNERHMVGD
+MDALRTRLAALETLLADYRAAEQEARQAAQAEQLATREAIVAEAETFAQTPAERMPWKTA
+SKRMTELFEEWKAAQKAGPRLAKSVEDDLWKRFRGARTTFDKTRRAHFSRLDAASAEAKQ
+VKERLIARAEELSTSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAA
+RKAANQEIDREYGANLKVKEQILADGQKLLPFTDVKAGRRALNELRGRWEDAGRVPRGDV
+RRMEEGFRRLEDALKQAENEHWRRTDPETKARTNSALTQLEETIAGLEADLARAQAQGDQ
+RAVKKAQEALDARLKWKQALEASASELR*
+>NZ_CP033200.1_952
+MQPDDQQSPATESTPASAEAADTTVPAEARPVPEIVPDAPAHGDSSQPAETPAVPSPAAM
+KKASPAAVRPATPAAASVAPAPVVAPTVPPTPVEEAARFARVSEDGHVTLLDGQEEHAVG
+QVPDASTEDALAYFVRKYDDVRAQMALFEQRIAAGAPSGELGRALGQMTTAVNERHMVGD
+MDALRTRLAALETLLGDYRAAEQEARQAAQAEQLATREAIVAEAETFAQTPAERMPWKTA
+SKRMTELFEEWKAAQKAGPRLAKSVEDDLWKRFRGARTAFDKTRRAHFSRLDAASAEAKQ
+VKERLIARAEELSTSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAA
+RKAANQEIDREYGANLKVKEQILADGQKLLPFTDVKAGRRALNELRGRWEDAGRVPRGDV
+RRMEEGFRKLEDALKQAENEHWRRTDPETKARTNSALTQLEETIAGLEADLARAQARGDQ
+RAVKKAQEALDARLQWKQALEASASELR*
+>NZ_CP040019.1_1595
+MPDASSEDALAYFVRKYDDVRAQMALFEQRIAAGAPSSELGKALGQMTSAVNERHMVGDM
+DALRTRLAALETLLGDYRGAEQEARQAAQAQQLATREAIVAEAEEFAATPAERMPWKTAS
+TRMTALFEEWKAAQKAGPRLSKSVEDGLWKRFRGARTAFDKTRRAHFSQLDAKSAEAKQV
+KERLIARAEELSSSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFDAR
+KAVNQEIDREYGANLKVKEQILADGKKLLPFKDVKAGRRALNELRGRWEDAGRVPRGDVR
+RMEEGFRSLEDALKQAENEHWRRTDPETKARTSSALTQLEETIAGLEADLAKAQASGDER
+AVKKAQEALDARLQWKQALEASASELS*
+>NZ_CP083691.1_1488
+MTHQPQSDDQQTPDAEQATPAAAPQQTSPAQDAPEQVVQDQTPAAQADLADALGSIESVE
+APAPAQGEEPADAAETDAEKTPEAAPSPAVPAAPSPAALKRSAAPRSAAPRPATAAVPVA
+PAPSVEPTPLGEAAAFARVSEDGHVTLLDGADEVAVGQVPDATEQDALAYFVRKYDDVRA
+QMALFEQRIAAGAPSSELGKALGQMTAAVTERHMVGDMPALRTRLAALETLLGDYRAAEA
+ERRQAAQAEQLATREAIVTEAEKFAATPAERMPWKQASARMTELFDEWKTAQKAGPRLSK
+SVEDGLWKRFRGARTQFDKTRRAHFSQLDARSAEAKQVKERLIARAEELSSSTDWGVTAG
+KYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAARKAENAAVDREFGENLKVKEQIL
+ADGQKLLPFTDLKAGRKALNELRGRWEDAGKVPRGDIRRMEDGFRKLEDALKQAENEHWR
+RTDPETKARTNSALTQLEETIAGLEADLAEAQAAGDQKRIATAQEALDARLQWKQALEAS
+ASELR*
+>NZ_CP097650.1_1180
+MQPDDQQSPATESTPASAEAADTTVPAEARPVPEIVPDAPAHGDSSQPAETPAVPSPAAM
+KKASPAAVRPATPAAASVAPAPVVAPTVPPTPVEEAARFARVSEDGHVTLLDGQEEHAVG
+QVPDASTEDALAYFVRKYDDVRAQMALFEQRIAAGAPSGELGRALGQMTTAVNERHMVGD
+MDALRTRLAALETLLGDYRAAEQEARQAAQAEQLATREAIVAEAETFAQTPAERMPWKTA
+SKRMTELFEEWKAAQKAGPRLAKSVEDDLWKRFRGARTAFDKTRRAHFSRLDAASAEAKQ
+VKERLIARAEELSTSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAA
+RKAANQEIDREYGANLKVKEQILADGQKLLPFTDVKAGRRALNELRGRWEDAGRVPRGDV
+RRMEEGFRKLEDALKQAENEHWRRTDPETKARTNSALTQLEETIAGLEADLARAQARGDQ
+RAVKKAQEALDARLQWKQALEASASELR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001073.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001073.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f40e18f0d4f6446afe20500aaa53286ce5b88a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001073.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1224
+MTTVTIEETAPAGALMLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL
+WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGQLPWTLTQSDVAA
+DATGVAPAEQDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR
+RTRRAGVVAARRRLGALLTALDVPD*
+>NZ_CP033200.1_953
+MTTVTIEETAPTGALVLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL
+WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGLLPWTLTQSDVAA
+DATGVAPAEHDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR
+RTRRAGVVAARRRLGALLAALDVPD*
+>NZ_CP040019.1_1594
+MEGLILAGEPFTPAELQALGSRGVVVPLVPGVWARPEAARRPGVRAEALWMLGGPVLAGG
+WTAIGSSAAWVLTGGAVPERLHAAVPHFHRLPAGGSPLPWTLTQSDVAAGPDGRAPAEED
+VLRIGPLRVTTPERTVEDLLLSPDPDAARTAAAVIAAHGAAGLRERLARHSRRSGVVAAR
+RRLDVLLGALEAAG*
+>NZ_CP083691.1_1487
+MHQGHGSRGGAAWELAGMTFTEPELRLLAARGTLEAVLPGVYRPVDVPSEPAGRAAALGL
+LGGPVLASGWTAVGPSAAWVHVGGPAPHRLHAAVPHFHRLPAGGAAPAWRLVQSDVAAGP
+TGAAPAEEDVQVLEGVRVTVPARTVEDLLLTGDPDDARRAARVIAAHGAEGLRDRLDRPS
+RRPGSVGARRRLRMLLDALGADG*
+>NZ_CP097650.1_1181
+MTTVTIEETAPTGALVLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL
+WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGLLPWTLTQSDVAA
+DATGVAPAEHDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR
+RTRRAGVVAARRRLGALLAALDVPD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001074.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001074.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d4fe904910d9703cf32b464e3067bcf0ec1d5ac6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001074.fa
@@ -0,0 +1,70 @@
+>NZ_CP042169.1_1225
+MSEQDPTPVPVRPRGRIARLTGRHATEYSPLLEPLMRTVRQRATKTELADIVRAFEVARA
+AHEGQMRRSGDPYITHPVAVATILAEIGVTGPTLLAALLHDTVEDTDYSLERLRADFGSD
+VALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNARTWRYVSPES
+SARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGERNPEREKHIA
+ALRTVIEDHLREHRIRATVTGRPKHYYSIYQKMVTRGKDFDDIHDLTGIRVLVDSVRDCY
+AVLGAIHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMVPGGKPVEIQIRTQEMHRQAEYG
+VAAHWRYKAQAAGQAPVQATPAWLRSVMDWQADTRDPDEFLASLRTQIGADEVYVFTPKG
+EIRTLPAGSTPVDFAYAIHTDVGHRTIGARVNGKLVPLSTPLSHGDTVEVFTSRAEDAGP
+SRDWLGFVVSPRARSKIRHHFATQRRGEQADRGRESLTRQLRKAGMTVQHVLGGEELVQL
+ATDLGYADLDGLFVALGDGHVSAQSVQERVAERLAPPTPTQAEPEGELTVGEVDLQELVP
+AQARRAPARATNDAGVLVDGDGGVMAKLARCCNPVPPDAIDGFVTRGSGVSVHRVDCPNL
+ATLLAQEPERHTPVSWAPSRDTVYLVEIQIEALDRKSLLSDVTRVLSENHVNILSASVNT
+TRDRVAMSRFVFEMGDPRFLGHVIDAVRRIDGVFDVHRT*
+>NZ_CP033200.1_954
+MSEQDPTPAPARPAPARPAPVRPRSRIARLTGRHATEYSPLLEPLMRTVRQRATKTELAE
+IVRAFEVARAAHEGQMRRSGDPYITHPVAVATILAEIGVTGPTLLAALLHDTVEDTDYSL
+ERLRADFGSEVALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNA
+RTWRYVSPESSARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGE
+RNPEREKHIAALRTVIEEHLREHRIRATVTGRPKHYYSIYQKMVTRGKDFDDIHDLTGIR
+VLVDSVRDCYAVLGVIHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMVPGGKPVEIQIRT
+QEMHRQAEYGVAAHWRYKAQVAGQAPVQATPAWLRSVMDWQADTRDPDEFLASLRTQIGA
+DEVYVFTPKGEIRTLPAGSTPVDFAYAIHTDVGHRTIGARVNDKLVPLSTPLSHGDTVEV
+FTSRAEDAGPSRDWLGFVVSPRARSKIRHHFATQRRDEQADRGRESLTRQLRKAGMAVQQ
+VLGGEELVQVATDLGYADLDGLFVALGDGHVSAQSVQERVAERLAPPTSTQAEPEGELTV
+GEVDLQELVPAQSRRAPARATNDAGVLVDGDGGVMAKLARCCNPVPPDAIDGFVTRGSGV
+SVHRVDCPNLATLLAQEPERRTPVSWAPSRDTVYLVEIQIEALDRKSLLSDVTRVLSENH
+VNILSASVNTTRDRVAMSRFVFEMGDPRFLGHVIDAVRRIDGVFDVHRT*
+>NZ_CP040019.1_1593
+MSEHDPTHAPARVAAVRPRGRIARLTGRHATEYSPLLEPLMRTVRQRATKAELADLIRAF
+EVARAAHEGQMRRSGDPYITHPVAVATILAEIGVSGPTLLAALLHDTVEDTDYSLERLRA
+DFGPEVALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNARTWRY
+VSPESSARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGERNPER
+EKHIAALRTVIEDHLREHRIRAEVTGRPKHYYSIYQKMVMRGKDFDEIHDLTGIRVLVDS
+VRDCYAVLGVIHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMGPGGRPVEIQIRTHEMHR
+QAEYGVAAHWRYKAQAAAESSSSSSGTPAWLRSVMDWQKDTRDPDEFLDSLRTQIGADEV
+YVFTPSGEIRSLPAGSTPVDFAYAIHTDVGHRTIGAKVNGKLVPLSTPLNHGDTVEAFTS
+RAEDAGPSRDWLGFVVSPRARSKIRHHFATQRRDEQAERGRESLTRQLRRAGLAVQSVLG
+GEELAQVASDMGYADLDGLLVALGDGHVSAQAVQERVSERLAPPPPARTEPQGELTVGEV
+DLAELVPAQARRTPARATNDAGVLVDGDGGVMAKLARCCNPLPPDAIDGFVTRGSGVSVH
+RLDCPNLATLLEQEPERRTPVGWAPSRHTVYLVEIQVEALDRKSLLSDVTRVLSENHVNI
+LSASVNTTRDRVAMSRFVFEMGDPRFLGHVIAAVRRIDGVFDVHRT*
+>NZ_CP083691.1_1486
+MTEQDRRPAAPPRRGRIARLTGRRATEYSPLLEPLMRTVRQSATHAEQEDIVRAFEVAER
+AHRGQMRRSGDPYITHPVAVATILAELGVTGPTLLAALLHDTVEDTDYSLEQLTADFGPQ
+VALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNARTWRYVSPES
+SAKKARETLDIYAPLAHRLGMNTVKWELEDLSFAALQPKVYAEIVRLVGERNPEREKQLA
+ALRGVLEEQLREQRVRATVTGRPKHYYSVYQKMVTQKKDFAQIYDLTGIRVLVDSVQDCY
+AVLGVVHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMGPEGKPVEIQIRTWEMHRQAEYG
+VAAHWRYKAGARGELEAGRSQQTPGWLRSVMDWQEDTRDPDEFLAALRTQIGADEVYVFT
+PKGEIRSLPADSTPVDFAYAIHTDVGHRTVGARVNGRLVPLSTVLRHGDTVEVFTSKAED
+AGPSRDWLNFVVSPRAKSKIRHHFATRRRDEQIERGREAFTRQLRKAGLSVQRVLGGEDL
+GVVAGELGYHDPDTLFAAMADGHVSPQAVTERLEARLAPPPAPTAPDAELRVGEVDLAGL
+VPEKARRAPTRSTNEAGVLVNGDGGVLAKLARCCNPVPPDEVVGFVTRGSGVSVHRGDCR
+NLATMLENEPERRVDVAWAPSRDAVYLVEIQVQALDRTSLLSDVTRVLSENHVNILSASV
+NTTRDRVAMSRFVFEMGDPKFLEHVVNAVRRIDGVFDVRRT*
+>NZ_CP097650.1_1182
+MSEQDPTPAPARPAPARPAPVRPRSRIARLTGRHATEYSPLLEPLMRTVRQRATKTELAE
+IVRAFEVARAAHEGQMRRSGDPYITHPVAVATILAEIGVTGPTLLAALLHDTVEDTDYSL
+ERLRADFGSEVALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNA
+RTWRYVSPESSARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGE
+RNPEREKHIAALRTVIEEHLREHRIRATVTGRPKHYYSIYQKMVTRGKDFDDIHDLTGIR
+VLVDSVRDCYAVLGVIHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMVPGGKPVEIQIRT
+QEMHRQAEYGVAAHWRYKAQVAGQAPVQATPAWLRSVMDWQADTRDPDEFLASLRTQIGA
+DEVYVFTPKGEIRTLPAGSTPVDFAYAIHTDVGHRTIGARVNDKLVPLSTPLSHGDTVEV
+FTSRAEDAGPSRDWLGFVVSPRARSKIRHHFATQRRDEQADRGRESLTRQLRKAGMAVQQ
+VLGGEELVQVATDLGYADLDGLFVALGDGHVSAQSVQERVAERLAPPTSTQAEPEGELTV
+GEVDLQELVPAQSRRAPARATNDAGVLVDGDGGVMAKLARCCNPVPPDAIDGFVTRGSGV
+SVHRVDCPNLATLLAQEPERRTPVSWAPSRDTVYLVEIQIEALDRKSLLSDVTRVLSENH
+VNILSASVNTTRDRVAMSRFVFEMGDPRFLGHVIDAVRRIDGVFDVHRT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001076.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001076.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dfe855b2727f89f754844dd7a1fb14dfecb74576
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001076.fa
@@ -0,0 +1,60 @@
+>NZ_CP042169.1_1227
+MAKRTPTGSAGRTLAWLAALLVVLAAILGGGVASGAASWAPKLALDLEGGTQMVLAPQTS
+TGESVTPEQLDQAVEIIRQRVDGSGVAEAEVATQGSQNVVVSLPGVPDEETRRLIQASAD
+MQFRPVLQSGPGEATPEDQRLPEDQLPKPDGEPADAYDPNWVTPALLAEFQATDCTAPRD
+PAAPPPPSDRAIVACQPSEELADGAVTPAQKYILGPVVIPGTQIKGASNGMAQAQGGVST
+NQWVVNIEFDEEGTKAFTEVTQKLTPYPEGDPRKQFAILLDGDVISAPQSNVVITNGSAQ
+ISGPTLNEQTTAQLAEQLNYGSLPISFSIESEQQISATLGRDQLFWGLIAGLIGLGLVAV
+YQFFQYRALGLLTFASIIVAGVLTWLTIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV
+YFERIKDELRAGHTVPVAVHEGWKRARRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG
+LTAIADLIVVFMFTHPLMVLLAQTRFVGEGHPMSGLDPSLLGGPSLYQGAGRFREPAHAP
+RTGLPAEASDEPADADDAAAADAPRPLAATGAPRAGSSARGGRRSRTAPPMTIAERRRAE
+RRRQEEDQ*
+>NZ_CP033200.1_956
+MAKRTPTGSAGRTLAWLAALLVVLAAILGGGVASGAASWAPKLALDLEGGTQMVLAPQTS
+TGESVTPEQLDQAVEIIRQRVDGSGVAEAEVATQGSQNVVVSLPGVPDEETRRLIQASAD
+MQFRPVLQSGPGEATPEDQRLPEDQLPKPDGEPADAYDPNWVTPALLAEFQATDCTAPRD
+PAAPPPPSDRAIVACQPSEELADGAVTPAQKYILGPVVIPGTQIKGASNGMAQAQGGVST
+NQWVVNIEFDEEGTKAFTEVTQKLTPYPEGDPRKQFAILLDGDVISAPQSNVVITNGSAQ
+ISGPTLNEQTTAQLAEQLNYGSLPISFSIESEQQISATLGRDQLFWGLIAGLIGLGLVAV
+YQFFQYRALGLLTFASIIVAGVLTWLTIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV
+YFERIKDELRAGHTVPVAVHEGWKRARRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG
+LTAIADLIVVFMFTHPLMVLLAQTRFVGEGHPMSGLDPSLLGGPSLYQGAGRFREPAHAP
+RTGLPAEDSDEPADAAAADAPRPLVATGAPRAGSSARGGGRRSRTAPPMTIAERRRAERR
+RQEEDQ*
+>NZ_CP040019.1_1591
+MAKRTPTGSARRTLAWLAALTVALTAILGWGVASGAASWAPKLALDLEGGTQMVLAPETA
+TGESVTSEQLDQAVEIIRQRVDGSGVAEAEVATQGAENVVVSLPGVPDEETRRLIQASAD
+MQFRPVLQSGSGEATPEDQRLPEDQLPQPEGEPADAYDPNWVTPALLTQYQALDCAAPRD
+PAAPPPPSDQAIVACERPADLGEGVQTPARKYILGPVVIPGTQIEGATNGLAQAQSGVST
+NQWVVNIDFDEEGAKTFSEVTQKLTPYPDGDPRKQFAILLDGDVISAPQSNAVITAGSAQ
+ISGPTLNEETTAQLAEQLNYGSLPISFSIESEQQISATLGQDQLFWGLIAGLIGLALVAV
+YQFFQYRALGLLTFASIVVAGILTYLAIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV
+YFERIKDELRAGHSVPMAVHEGWKRAKRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG
+LTAIADLIVVFMFTHPIMVLLAQTRFVGGGHRMSGLDPSLLDRQALYQGAGRLREPGGAR
+RTGSTAAPAADVAADDGARVPVPVGAAPADEASGEEGTATRGLRRPRPAQPMTIAERRRA
+ERRRQEEDQ*
+>NZ_CP083691.1_1484
+MAKTSPTRAAGRTLAWLAALIVALTAILGLGVASGQASWAPKLALDLEGGTQMVLAPTTA
+SGEQATPEQLQQAVEIIRQRVDGSGVAEAVVATQGDQNVVVSMPGVPDEETRRLIQASAD
+MQFRPVLQAVPGGQPTPQDQLVPKDQFPTPSAEPTDAYDPNWITPELADEFQRTDCTLPR
+DPNAAPPATDRAVVVCEPQQETPAGTMPATKYIVGPVVIPGTMIEKASNATAQSQTGVTT
+NEWVVNIDFDGEGTKRFTEVTQKLTPFAEGDPRKQFAIMLDGQVIAAPQSNVVITGGQAQ
+ISGPGFTEESTAQLAEQLNYGSLPISFTIESEQQISATLGRDQLFWGLIAGLIGLALVAV
+YQFFQYRALGLLTFASIVVAGALTYLAIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV
+YFERIKDELRSGHTLDAALHEGWKRAKRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG
+LTAIADLLVVFMFTHPLMVLLSRTDFVGGGHPMSGLDPRVLGVEPALYQGAGRFREPAAA
+RAARGGSHAADDDDAGSSAARRGRRSEQPMTIAERRRAERAGAAQTPAAQTPAGSAPAAD
+TEEDAL*
+>NZ_CP097650.1_1184
+MAKRTPTGSAGRTLAWLAALLVVLAAILGGGVASGAASWAPKLALDLEGGTQMVLAPQTS
+TGESVTPEQLDQAVEIIRQRVDGSGVAEAEVATQGSQNVVVSLPGVPDEETRRLIQASAD
+MQFRPVLQSGPGEATPEDQRLPEDQLPKPDGEPADAYDPNWVTPALLAEFQATDCTAPRD
+PAAPPPPSDRAIVACQPSEELADGAVTPAQKYILGPVVIPGTQIKGASNGMAQAQGGVST
+NQWVVNIEFDEEGTKAFTEVTQKLTPYPEGDPRKQFAILLDGDVISAPQSNVVITNGSAQ
+ISGPTLNEQTTAQLAEQLNYGSLPISFSIESEQQISATLGRDQLFWGLIAGLIGLGLVAV
+YQFFQYRALGLLTFASIIVAGVLTWLTIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV
+YFERIKDELRAGHTVPVAVHEGWKRARRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG
+LTAIADLIVVFMFTHPLMVLLAQTRFVGEGHPMSGLDPSLLGGPSLYQGAGRFREPAHAP
+RTGLPAEDSDEPADAAAADAPRPLVATGAPRAGSSARGGGRRSRTAPPMTIAERRRAERR
+RQEEDQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001080.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001080.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6dd49e5127dca5b581316d3e7e15e3ac6976f6f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001080.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1232
+MAGHSKWATTKHKKAVIDARRAKAFAKYIKNIEVAARAGGPDVAGNPALDLAVSKAKKAS
+VPNDNIDRAVKRGAGLTGEVIDYAEIMYEVRGPQGSALLVECLTDNKNRAAADVRAAVTR
+NGGTMADSGSVSFLFERKGLVRLPAEGNTEDGLLEAVLEGGADAEEVVVSGDSFEILSDP
+SDLQSVAKALDEAGVEYESDELEFVPTMKVDLDASGARTFLKLADALEDLDDVQNVFSNV
+DIAPEVLAELDED*
+>NZ_CP033200.1_961
+MAGHSKWATTKHKKAVIDARRAKAFAKYIKNIEVAARAGGPDVAGNPALDLAVSKAKKAS
+VPNDNIDRAVKRGAGLTGEVIDYAEIMYEVRGPQGSALLVECLTDNKNRAAADVRAAVTR
+NGGTMADSGSVSFLFERKGLVRLPAEGNTEDGLLEAVLEGGADAEEVVVSGDSFEILSDP
+SDLQSVAKALDEAGVEYESDELEFVPTMKVDLDASGARTFLKLADALEDLDDVQNVFSNV
+DIAPEVLAELDED*
+>NZ_CP040019.1_1586
+MAGHSKWATTKHKKAVIDARRAKAFAKYIKNIEVAARAGGADLAGNPALDLAVSKAKKAS
+VPNDNIDRAVKRGAGLTGEVVDYAEIMYEVRGPQGSAVLVECLTDNKNRAAAEVRTAVTR
+NGGTMADSGSVSFLFTRQGVVRLPAEGRTEDELLEAVIEAGAEEVVLSGDEFEILSDPSD
+LRAVAEALDAAGIDYESDETEFVPTMKVELEDAKGAGTFLKLADALEELDDVQNVYSNVD
+ISPEVLAELDQD*
+>NZ_CP083691.1_1479
+MSGHSKWATTKHKKAVIDQRRAKAFAKYIKGIEVAARAGGADLSGNPALDLAVSKAKKNS
+VPNDNIDRAIKRGAGLTGEVIDYTEIMYEVRGPQGSALLVECLTDNKNRAAADVRAAVTR
+NGGTMADSGSVSFLFHRKGVVRLPAAGNTEDSLLEAVLEGGADAEEVVLSGDDFEIVSEP
+GDLRAVAEALDAAGIDYETDEMEHLPTMKVELDAKGARTFLKLADALEDLDDVQNVFSNV
+DIAPEVMDELEQD*
+>NZ_CP097650.1_1189
+MAGHSKWATTKHKKAVIDARRAKAFAKYIKNIEVAARAGGPDVAGNPALDLAVSKAKKAS
+VPNDNIDRAVKRGAGLTGEVIDYAEIMYEVRGPQGSALLVECLTDNKNRAAADVRAAVTR
+NGGTMADSGSVSFLFERKGLVRLPAEGNTEDGLLEAVLEGGADAEEVVVSGDSFEILSDP
+SDLQSVAKALDEAGVEYESDELEFVPTMKVDLDASGARTFLKLADALEDLDDVQNVFSNV
+DIAPEVLAELDED*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001088.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001088.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3e55acd25464a11a1f868838fa0598d6e64e032e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001088.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_1240
+MTTQDSPLTPNSSRSACCGGHARPDTSRRTVLGRGAAVAAAGAGALALTGCTDQLREKDT
+AQDHYTGSDAVDALPAAELPVGASREVQVQGRTLMMHRVDETTVTAFTNVCTHQGCLLQV
+VDRQEGPAYACPCHGSHFDVTSGKPFGGPARQALMDYDAAVVDDRIVVKL*
+>NZ_CP033200.1_969
+MTTQDSPLTPNSSRSGCCDDHARPDTSRRTVLGRGAAVAAAGAGTLALAGCTDRLREKDT
+AQDHYTGSDAVDALPAAELPVGASREVQVQGRTLMMHRVDETTVTAFTNVCTHQGCLLQV
+VDRQEGPAYACPCHGSHFDVTSGKPFGGPARKALMDYDAAVVDDRIVVKL*
+>NZ_CP040019.1_1576
+MTAQDSTPTPDPSAVAPPSAPAGCCGGRAAADAARPEASRRTVLGRGAAVAAAGAGALAL
+SGCTEQLREKENAQDHFAGADAVEALPAADLPVGAAREVEVEGRTLMMHRVDETTVTAFT
+NVCTHQGCLLQVVDRAEGPSFACPCHGSHFDVQTGKPFGGPARQPLMDYEAVVDGDRIVV
+KL*
+>NZ_CP083691.1_1470
+MTSQDPAPHTSASPCCSGCSAEPAGSSRRSVLGAGSLVALAGAGSVVLSGCTQQLKDEAA
+AGDHHVGSETTDAMALAELPVGGTTSVQVQGRTLLLHRADESTVTAFSNVCTHQGCLVQV
+VDRPEGTAYACPCHGSNFDVATGEPFGGPAKAPLTDYQAAIEGDRIVVKL*
+>NZ_CP097650.1_1197
+MTTQDSPLTPNSSRSGCCDDHARPDTSRRTVLGRGAAVAAAGAGTLALAGCTDRLREKDT
+AQDHYTGSDAVDALPAAELPVGASREVQVQGRTLMMHRVDETTVTAFTNVCTHQGCLLQV
+VDRQEGPAYACPCHGSHFDVTSGKPFGGPARKALMDYDAAVVDDRIVVKL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001090.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001090.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d98e06dfcfc90c21017bf0cefacc62340bc450b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001090.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_1243
+MSIVRLYRESVGDDGARLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQAEGDQL
+LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATAIERRTVERLRVEMTHQLAWRGLG
+EVEDVVEEVGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQEG*
+>NZ_CP033200.1_972
+MSIVRLYRETVGDDGTRLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQVEGDQL
+LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATVIERRTVERLRVEVTHQLAWRGLG
+EVEDVVEEAGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQEG*
+>NZ_CP040019.1_1573
+MSIVRLYRETTNEDGSRLFEYREAWADVEGGEFVVHHGRVGHPGTVGEQPLADEAEGEEL
+LAAFLAQGAEEGFAEADPAGFALLPVAFRLRGREASDIERRNVEHLRVEVTHQLAWRGLG
+EVEDVTEEPGALVLAVRTPHARKAAAEIPVAARRADGVQPNKVEVRSAVQED*
+>NZ_CP083691.1_1467
+MSISRLYRDRTEEDGRRSFEYREAWIDPSGELFTVHHGRVGHPGTVGDQPLTSEAEGAEL
+MDAFLAQGEADGFAPADEDAFDVLEVAYRLRGRAITEIERRHGRTLREEVTHQLAWRGLG
+EVTDVVDGDGELVLVVRTPHAPKAAAEVPAAAKRAHGIQPNKVEVRRVDAPRTPAGAAPD
+ADGEG*
+>NZ_CP097650.1_1200
+MSIVRLYRETVGDDGTRLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQVEGDQL
+LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATVIERRTVERLRVEVTHQLAWRGLG
+EVEDVVEEAGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQEG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001104.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001104.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40064f0326019f5e6df4a1fbeaf97653be231508
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001104.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1265
+MGDMSPFRRSHEPGRPDHRSGTPEAEGRQREARTLDGSGGLDASLVRAGFYPDLVAHAIA
+VELEGRTPDAHLVHVDTHFDYEEIHRHITALVLAGDTLLAVHLDDHAADPAGQAVLAQVS
+TEMVPVRALGSVVLTTGHADPARFRPSDPVAEMTLGLMWAGGQRLDLQPAGCADPQCDLD
+HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATT*
+>NZ_CP033200.1_998
+MGDMSPFRRSHEPGRPDHRPDAPEAEGRQREARTLDGSGGLDASLVRAGFYPDLVAHAIA
+VELEGRTPDAHLVHVDTHFDYEEIHRHITALVLAGDTLLAVHLDDHAADPAGQAVLAQVS
+TEMVPVRALGSVVLTTGHADPARFRPSDPVAEMTLGLMWAGGQRLDLQPAGCADPQCDLD
+HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATT*
+>NZ_CP040019.1_1558
+MEPMSPFRRSHESGRPEHRPGAPASGEHRHEARTLEGAGGLGASLARAGFYPELVAHAIA
+VELGERTPDAHLVHVDTHFDYEEIHRHITVLVLAQDALLAVHLDDHAADAAGQAVLAQVS
+TEMVPVRALGSVVLTTGHADPARFSPADPVAEMTLALIWAGGQRLDLQPAGCADPQCDLD
+HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATA*
+>NZ_CP083691.1_1452
+MEGMTPLRWNNHDDSASDGRRPAGEVRRTRQTVDATGTLEQALARAGYYPELVSHAVALE
+LEGRTVHAHLVHVDTHFDYEEIHRHITVLVVADDVMLAVHLDDHAADPAGHSVLAQVATE
+MVPLRAIESVLITTGHATPERYRPTDPVAEVTLGVQWAGGQRLDLQPAGCADPQCDADHG
+YTGTSVREDLVIRVAADAEGQGAVDAALAFARTLRRVHLAAVA*
+>NZ_CP097650.1_1222
+MGDMSPFRRSHEPGRPDHRPDAPEAEGRQREARTLDGSGGLDASLVRAGFYPDLVAHAIA
+VELEGRTPDAHLVHVDTHFDYEEIHRHITALVLAGDTLLAVHLDDHAADPAGQAVLAQVS
+TEMVPVRALGSVVLTTGHADPARFRPSDPVAEMTLGLMWAGGQRLDLQPAGCADPQCDLD
+HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001110.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001110.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71136c2d703b41e65bd5f3641b6fd63e80a1b4ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001110.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1273
+MTNVSGNASYEYSRAALLAVTEVEAPLEVTSDDLDERLADVLRRLKLPPHLLQRVAGVRA
+RRNWDASQDFQEAAAQAGTAALAAAGIGPERVGLLINTSVTRATLEPSVAVRIHHMMGLP
+TSATNFDITNACLGFVNGLMLASTLVDAGQVDYAVVVASEDASKVQDATVENLHASTTNR
+GNFMEQFASLTLGCGAAAAVVGSIEDHPDAHRIVRGITRAGTDHHDLCVGDHRGMYTDST
+ALLNDGLELVMDAWNDTPAEWAWKDADRFITHQVSQLHTNAISESAGLPLDRIPTTFPVL
+GNVGPASLPITLVREMDELSAGDTVVCLGVGSGLNTAMLEIQW*
+>NZ_CP033200.1_1004
+MTNVSGNASYEYSRAALLAVTEVEAPVEVTSQDLDDQLAEVLTRLRLPGSLLERVAGVRS
+RRNWDETEDFQEAAARAGVAALEQAGVPRERVGLLVNTSVTRATLEPSVAVRIHHLMGLP
+TSATNFDITNACLGFVNGLMLASTLVDAGQIDYAVVVAAEDASKVQAATVANLHAETTHR
+GNFMEQFASLTLGSGAAAAVVGRIEDHPDAHRIVRGITRAGTDHHGLCVGDHHGMYTDST
+ALLKDGLELVMDAWHDVPAEWAWPQADRFITHQVSQMHTDAIAESAHLDPARIPTTFPTL
+GNVGPASLPITLVREMDALEDGDTVVCLGVGSGLNTAMLEIEW*
+>NZ_CP040019.1_1550
+MTNVSGNASYEYSRAALLAVTEVEAPLEVTSDDLDERLADVLRRLKLPPHLLQRVAGVRA
+RRNWDASQDFQEAAAQAGTAALAAAGIGPERVGLLINTSVTRATLEPSVAVRIHHMMGLP
+TSATNFDITNACLGFVNGLMMASTLVDAGQVDYAVVVASEDASKVQDATVENLHASTTNR
+GNFMEQFASLTLGCGAAAAVVGSIEDHPDAHRIVRGITRAGTDHHDLCVGDHRGMYTDST
+ALLNDGLELVMDAWNDTPAEWAWKDADRFITHQVSQLHTNAISESAGLPLDRIPTTFPVL
+GNVGPASLPITLVREMDELSAGDTVVCLGVGSGLNTAMLEIQW*
+>NZ_CP083691.1_1444
+MVQVPHVSGNASFEFSRAALLSVTEVQAPLEVTSDDLDEQLADVLTRLRLPRHLLERVAG
+VKVRRAWDAQKDFQQAAAEAGTAALAAAGVAPGQVGLLVNTSVTRATLEPSVAVRIHDLM
+GLPTSATNFDITNACLGFVNGLMLASTMVDAGQIDYAVVVAAEDASKVQASTVANLHAET
+TVRGNFMEQFASLTLGSGAAAAVVGRTDEHPDAHRILRGITRAGTDHHQLCVGDHNGMFT
+DSNALLKDGLELVMDAWHDVPAEWGWDHAARYVTHQVSQMHTDAISESAGIPLEKLPTTF
+PVLGNVGPASLPITLVREQDSLRRGDAVVCLGVGSGLNTAMLEIQW*
+>NZ_CP097650.1_1228
+MTNVSGNASYEYSRAALLAVTEVEAPVEVTSQDLDDQLAEVLTRLRLPGSLLERVAGVRS
+RRNWDETEDFQEAAARAGVAALEQAGVPRERVGLLVNTSVTRATLEPSVAVRIHHLMGLP
+TSATNFDITNACLGFVNGLMLASTLVDAGQIDYAVVVAAEDASKVQAATVANLHAETTHR
+GNFMEQFASLTLGSGAAAAVVGRIEDHPDAHRIVRGITRAGTDHHGLCVGDHHGMYTDST
+ALLKDGLELVMDAWHDVPAEWAWPEADRFITHQVSQMHTDAIAESAHLDPARIPTTFPTL
+GNVGPASLPITLVREMDALEDGDTVVCLGVGSGLNTAMLEIEW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001121.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001121.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b33303df3fcd2ff18d503d75a8460e3b8e2e2d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001121.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1284
+MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN
+HMKLGVKFLIGVIVFVAALIGRRKSNRGEVVPTGLAHAVGGLGLVNILVAVLWQ*
+>NZ_CP033200.1_1015
+MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN
+HMKLGVKFLIGVIVFVAALTGRRKSNRGEVVPTGLAHAVGGLGLVNILVAVLWQ*
+>NZ_CP040019.1_1538
+MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN
+HMKLGVKFLIGVIVFVAALIGRRKSNRGEVVPTGLAHAVGGLGLVNILVAVLWQ*
+>NZ_CP083691.1_1432
+MEILHNVVVAIHIVSAAAIVGGWFAHFKNPTVTVSQWWGALGMILSGVVLFGWAMTGEPN
+HMKLGIKFLIGVIVFIAALLGRRKANRGEVVPKGLAHAVGGMGLVNILVAVLWS*
+>NZ_CP097650.1_1239
+MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN
+HMKLGVKFLIGVIVFVAALIGRRKSNRGEVVPTGMAHAVGGLGLVNILVAVLWQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001122.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001122.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c0d866f191ded01c92f614b939f6b6b2f4af3a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001122.fa
@@ -0,0 +1,56 @@
+>NZ_CP042169.1_1285
+MRDWDEADGGAAGRVGGGPETEPERSSEPGTAAPRAPGWEPVRLLGAGAQAEVWLVEDGR
+GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM
+VQRVGPLSPGQAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV
+GGASGAGATPGFAAPEALAAVEGAGAEPGASPAVGAPSDVHAWAALGWYALTGRAPGAAG
+HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV
+AHLLPTVLPGSGPTRRRRGRRAAPRRRALARRRGAAPRRGVLVAAGLATALAVGGGTAGL
+WWPASLGDATEGAPEPAGAVPAGTSVDAARPADGTPESGTPARVPDAGAPGEDAAGEDAV
+DVGEALAAVGHARTAALIDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGLEVTV
+EQAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGEGPEGR
+DGGAAGRTWRVETVDPR*
+>NZ_CP033200.1_1016
+MRDWDEADGGAAGRVGGGPETEPERSSEPGTAAPRAPGWEPVRLLGAGAQAEVWLVEDGR
+GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM
+VQRVGPLSPGQAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV
+GGASGAGATPGFAAPEALAAVEGAGAEPGASPAVGAPSDVHAWAALGWYALTGRAPGAAG
+HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV
+AHLLPTVLPGSGPTRRRRRRAAPRRRALALRRGAAPRRGVLVAAGLATALAVGGGTAGLW
+WPASLGDATEGAPEPAGAVPAGTSVDAARPADGTPESGTPARVPDAGAPGEDAAGEDAVD
+VGEALAAVGHARTAALIDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGLEVTVE
+QAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGEGPEGRD
+GGAAGRTWRVETVDPR*
+>NZ_CP040019.1_1537
+MRDWDEADDGAVGRVGGGPETEPERTSELGTAAPRAPGWAPVRLLGAGAQAEVWLVEDGR
+GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM
+VQRVGPLSPGHAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV
+GGASGAGATPGFAAPEALAAVQGAGAEPEASPAVGAPSDVHAWAALGWYALTGRAPGAAG
+HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV
+AHLLPTVLPGSGPTRRRRRRAGPGRRALVGRRGAAPRRGVLLAAGLATALAVGGGTAGLW
+WPAAPGSAAEGAPAEGAPEPAGTEPTGTPVDAARPADGTPESGTPARATDTGAPGEDAAG
+ADAVDVGEALAAVGQARTAALTDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGL
+EVTVEQAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGED
+PEARDGGAAGRTWRVETVDPR*
+>NZ_CP083691.1_1431
+MEAEDAERSGGVPPVGRPATDDWFADGGRDVSAWADPPRGGEGPAAVEPGVGDVGSPAEL
+GPADRPPQAPGLRVVSRIGMGGQAEAWLVRREDGTECVLKVPRADGDPDAVAKEAAVYGH
+LRHPHLLRVLGTVDTDRGTGVLSERLPAGSLASMVHDAGPLRPGQAVTVLVPVAQALAHL
+HEHGVVHGDVSPGNVLFGVDGRPALADLGVARVVGGPRGRGGTPGFTAPEDEAGVGEGGA
+AADVYAWGALGWFALTGRAPGPREHRAPLPVLVPDVPVELALLLSAALDPDPAGRPGAAE
+AAVAAYDAAPPEPVPLHESAPAEVAHLLPTVVPPARPGGSGDARRSRPRAGGRRDAGRGR
+GGRKRRNRSPRSRGWHPVMLVGAAVLAGTVVSAAVGGLTDRPEDQGEGAGSRAVAAPPTS
+PTAAPANPRASVTPTGAADPKDAITPTRDGGVPSAAGTGPAAVLPAEDAAAALAAVAEGR
+TAALTDPDPARVDAYAVPDGPAWRRDRAIQDQLREGGSAFSGLVVTLEAVGRPRPAEAGG
+SGGAEAGWVVVPAVLRMSAHTVLDDAGSVVGEVPASEEDVSVTLVPGGEGRWRAAAVDPR
+*
+>NZ_CP097650.1_1240
+MRDWDEADGGAAGRVGGGPETEPERSSEPGTAAPRAPGWAPVRLLGAGAQAEVWLVEDGR
+GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM
+VQRVGPLSPGQAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV
+GGASGAGATPGFAAPEALAAVQGAGAEPGASPAVGAPSDVHAWAALGWYALTGRAPGAAG
+HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV
+AHLLPTVLPGSGPTRRRRRRAGPGRRALARRRGAAPRRGVLVAAGLATALAVGGGTAGLW
+WPASLGDATEGAPEPAGAVPAGTSVDAARPADGTRESGAPARVPDTGAPGEDAAGEDAVD
+VGETLAAVGHARTAALTDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGLEVTVE
+QAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGEGPEGRD
+GGAAGRTWRVETVDPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001125.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001125.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81e1ee02d73907ce34832c83c3537d5f47a8fa99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001125.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1288
+MTKNSQPPASSSGSTSATLKEVKAMQRERRLREKEQAKAQRRDKRATKGPGVISQLKQAY
+AMTKAHDPKVGLWMLLAFLGALVVGLVIGLLLDNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVSEQPAAVNPKTQDLVYRAVGRPGVVLVTEGPSPR
+VAALVVKEEKAMRRFLPGVPVTVVESGNGQGQVPLHELPGTLKGMKKALTAQEVQAVDKR
+LTALNTNRLPIPKGVDPNKVRPSRRAMRGR*
+>NZ_CP033200.1_1019
+MTKNSQPPASSSGSTSATLKEVKAMQRERRLREKEQAKAQRRDKRATKGPGVISQLKQAY
+AMTKAHDPKVGLWMLLAFLGALVVGLVIGLLLDNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVSEQPAAVNPKTQDLVYRAVGRPGVVLVTEGPSPR
+VAALVVKEEKAMRRFLPGVPVTVVESGNGQGQVPLHELPGTLKGMKKALTAQEVQAVDKR
+LTALNTNRLPIPKGVDPNKVRPGRRAMRGR*
+>NZ_CP040019.1_1534
+MTKNSQPPASSSGSTSADLKQVKAMQRDRRRRVKEETRAQRRDKRANRGPGIISQLKQAY
+AMTKANDPKVGLWMLLAFVGVLVLGLVIGLLLNNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVPEQPVAVNPKTQDVVYRAVGRPGVVLVTEGPSNR
+IAALVGKEEKAMRRFLPGVPVTVVEAGNGQGQVPLHELPRTLKSMKKALTAQEVQAVDKR
+VNALNVNRLPIPKGVDPMKARPSRRAMRGR*
+>NZ_CP083691.1_1428
+MAKNPSTSPSSSGSSSLKEVKAMQRDRRAQLKADAKAERAQKRANAGPGIISQLKQVFAI
+TRQQNPRLVLWMVLAFASVLVLGLVVGLLLHNWITWLLLAIPFGVLAAVIVMNRLGERAM
+FDRLEGQTGAAGATLSSLGRGWIVGEQPSAVNPKTHDLVYRAIGKPGVVLVTEGPASRVG
+KLVSKEQKAMERFLPGVPVHVVETGRGEGQIPLREVPKTLKALPKKLTAQEVSAVDKRLS
+ALGTQKPPIPKGVDPMRARPDRRGMRGR*
+>NZ_CP097650.1_1243
+MTKNSQPPASSSGSTSATLKEVKAMQRERRLREKEQAKAQRRDKRATKGPGVISQLKQAY
+AMTKAHDPKVGLWMLLAFLGALIVGLVIGLLLDNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVSEQPAAVNPKTQDLVYRAVGRPGVVLVTEGPSPR
+VAALVVKEEKAMRRFLPGVPVTVVESGNGQGQVPLHELPGTLKGMKKALTAQEVQAVDKR
+LTALNTNRLPIPKGVDPNKVRPSRRAMRGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001132.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001132.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cff7a444c3e7db161a6fb7afc046698088d3b35f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001132.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1297
+MSQRQNPVAPSSHNGPRPAGPTAPEPGSFAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT
+PDEGKASDVYDAAGVERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP
+SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT
+IVVTDDGAEILTLP*
+>NZ_CP033200.1_1027
+MSQRQNPAVPSSHNGPRPAGPTAPEPGSLAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT
+PDEGNASDVYDAAGIERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP
+SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT
+IVVTDDGAEILTLP*
+>NZ_CP040019.1_1526
+MSHRQSTASPSSHNGPRPEGPAAPQPGSLAPVGTLTPGAPSPAPPVPASIPRPEYVGRAT
+ADEGNASDVYDAAGIERIRAAGRLAARAMEHTAAYIRPGVTTDELDRIAHAYLVEHGAYP
+SCLGYRGFPRSICTSMNEVICHGIPDSTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLEPGMVFTIEPMLTLGTIDWDQWDDGWTVVTRDRRRTAQFEHT
+LVVTDDGAEILTLP*
+>NZ_CP083691.1_1420
+MSTTARPTSQPSHNGPRPEGPPAPEPGSRAPLGTLTPGAPSPAPAVPASIVRPEYVGRAT
+ADEGNASDVYDTEGIGRIREAGRIAAQAMEHTAEHIRPGITTDELDRIAHEFIVAAGAYP
+SCLGYRGFPRSICTSVNEVICHGIPDGTVLEDGDIVNLDITAYKDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIKAVKPGREINVIGRAIESYARRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHNRLMVPGMVFTIEPMITLGGIDWEQWDDGWTVVTKDRRRTAQFEHT
+LVVTEDGAEILTLP*
+>NZ_CP097650.1_1251
+MSQRQNPAVPSSHNGPRPAGPTAPEPGSLAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT
+PDEGKASDVYDAAGIERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP
+SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT
+IVVTDDGAEILTLP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001140.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001140.fa
new file mode 100644
index 0000000000000000000000000000000000000000..525df6e6a1268fd657bcb682d1a4885262654a14
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001140.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1306
+MTAPATAGPTPTDPRAREIADALAAVHARIADAARDAGREAEPALVVVTKTHPAEDVVRL
+AALGVTDVGENRDQEARPKAEAVAAALGADAPRWHFVGQLQTNKAKYVVRYASVVESVDR
+PELAEALSRALVLRREREPEAAIPDLECLVQVDVDDRADEDRPEGIGPRGGARPEDVPAL
+ADVIAGLPGLRLGGLMCVAPRGLDPEHAFRRLAALGARLRQTHPEATALSMGMSADLEAA
+VRAGATQVRIGSDVLGARDAVG*
+>NZ_CP033200.1_1036
+MTAPATAGPTPTDPRTREIADALAAVRARLADAARDAGREAEPALVVVTKTHPAEDVVRL
+AALGVTDVGENRDQEARPKAEAVAAALGADAPRWHFVGQLQTNKAKYVVRYASVVESVDR
+PELAEALSRALLLRREREPEAAIPDLECLVQVDVDDRADEDRPEGIGPRGGARPEDVPAL
+TDAIAGLPGLRLGGLMCVAPRGLDPEDAFRRLAALGAHLRQTHPEATALSMGMSADLEAA
+VRAGATQVRIGSDVLGARDAVG*
+>NZ_CP040019.1_1517
+MSTPEQHPTPHDAAAETRTREIAAGLAAVRERIARAAREAGRADEPALVVVTKTHPAEDV
+VRLAGLGVAAVGENRDQEARPKAAAVAEALGDAAPRWHFIGQLQTNKAKHAARYASVVES
+VDRTELAEALSRALVLRREREPGVEVPDLECLVQVDVDDRADEDRPEGIGPRGGAAPEDV
+PALAAAIAALPGLRLGGLMCVAPRGLDPEASFRRLAALGEELRSAHPDASTLSMGMSADL
+ESAVRAGATQVRIGSDVLGARPAVG*
+>NZ_CP083691.1_1411
+MAEPLQDDPRVAEIAAGLDGVRRRIADAAAAAGRADLPELIVVSKTHPAEDVVALAGLGV
+RQVGENRDQEARPKAAAVAEALGGAGVPAPAWHFIGQLQTNKAKHVARYASAVHSVDRLD
+LVDALSRAVVLRREREGADAVSALDCLVQVDVDDRADEDRPEGIGPRGGAAPEDVPELAR
+AIAAADGLRLRGLMCVAPRAADPAAAFARLAALSARVRAEHPDADALSMGMSGDLEAAVA
+AGATHVRVGSDILGARGAVG*
+>NZ_CP097650.1_1260
+MTAPATAGPTPTDPRAREIADALAAVRARIADAARDTGRAAEPALVVVTKTHPAEDVVRL
+AALGVTDVGENRDQEARPKAEAVAAALGADAPRWHFVGQLQTNKAKYVVRYASVVESVDR
+PELAEALSRALLLRREREPEAAIPDLECLVQVDVDDRADEDRPEGIGPRGGARPEDVPAL
+ADVIAGLPGLRLGGLMCVAPRGLDPEDAFRRLAALGAGLRQTHPEATALSMGMSADLEAA
+VRAGATQVRIGSDVLGARDAVG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001141.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001141.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dfcf2fed0c5e0e82936c8494c28393b48d2ee37a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001141.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1307
+MTAAEGPAGTARVPAGPFVHRETVRTATGAVHVAWTSVAAGNLALHVVPPDEAEGLARVS
+AARRALERVMGVPEGATLYLDQVHSADVVWADGPGRGGASAPVADAAVSRDGSRPLAVMV
+ADCLPVVVVDETTGATAVAHAGRRGLLDGVLEATVDRLLSLRPEADRTGPGLRAWIGPGV
+CGRCYEVPAAMRDEAAARLPATAATTSWGTPALDLPAGAAEVLRARGVATATIDVCTRED
+ERLFSHRRAPGEGRFAGLVWRADPDATVPRGDA*
+>NZ_CP033200.1_1037
+MTAAGGPAGTARVPAGPFVHRETVRTATGAVHVAWTSVAAGNLALHVVPPDEAEGPARVS
+AARRALERMMGVPEGATLYLDQVHSADVVWADGPGRGGAPAPVADAAVSRDGSRPLAVMV
+ADCLPVVVVDETTGATAVAHAGRRGLLDGVLEATVDRLLSLRPETDRTGPGLRAWIGPGV
+CGRCYEVPAAMRAEAAARLPATAATTSWGTPALDLPAGAAQVLRARGVATATIDVCTRED
+ERLFSHRRAPGEGRFAGLVWRADPDATTPRGEA*
+>NZ_CP040019.1_1516
+MTAAEGPVGTVPVPAGPFVHREAVATAGGTVHVAWSGVAAGNLGLHVVADEDAAGRRAVG
+EARRGLERAMGVPVGSTLYLDQVHSADAVWADGPGWGEEAGPTADAAVSRDGGRALAVMV
+ADCLPVVLVDEATGATAVAHAGRRGLVDGVLEGTVDRLLSLRPADRRDAPGLRAWIGPGV
+CGRCYEVPEQMRAEAAERVPATAATTAWGTPGLDLPAGAVAILRGRGADVAVVQACTLED
+ERLFSHRRAPGQGRFAGLVWRADEDASTPTRAA*
+>NZ_CP083691.1_1410
+MSLAGGPVGTQPVPSGPFVHREDLRADARGRVAHVAWTSAEAGSLAFHILGAEQEQARAD
+VVAARHRVEDAMGVPRGSVFYLEQVHSVDVVTAGPGWEEGFAPTADASVSPDGHTPLAVM
+VADCLPVVFVDGLTGATAVAHAGRRGLLDGVLENTVDALLALRPEGSAGAFGLKAWIGPG
+ISGESYEVPQAMQDEAVARIPELEATTSWGTPALALASGAQAVLRARGVAVERIALDTFT
+DERVFSHRRAPGRGRFAGLVWTTPADVDQDHDAGDARG*
+>NZ_CP097650.1_1261
+MTAAEGPAGTARVPAGPFVHRETVRTATGAVHVAWTSVAAGNLALHVVPPDEAEGLARVS
+AARRALERAMGVPEDATLYLDQVHSADVVWADGPGRGGAPAPVADAAVSRDGSRPLAVMV
+ADCLPVVFVDETTGATAVAHAGRRGLLDGVLEATVDRLLSLRPETDRTGPGLRAWIGPGV
+CGRCYEVPAAMRTEAAARLPATAATTSWGTPALDLSAGAAQVLRARGVTTATIDVCTRED
+ERLFSHRRAPGEGRFAGLVWRTDLDATTPRGEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001144.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001144.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f97dc726f7fabbf9fc786ebc87c0efdad2ab2b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001144.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1310
+MSRDESTRPAAEGRFADLGRVHLLGIGGVGVSGVARILQEQGVAVSGSDAKDLPVMRELA
+AGGARITVGYDAAHLGRDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALAMRGHR
+VLAVAGTHGKTTTSSMAAMAFSDAGWDPTFAVGAAVAGLGTNARAGRGEWFIAEADESDG
+TLVNYPSTIGIVTTVEADHLDHYGTEEAVHQVFRDFAGGLPAAAQGGVLVACLDDAGAAD
+LAAWAREHAAADVVTYGSAPRDGVAPDLLVTDLAVEPGETGVGQRATFRMAGGPERTLHL
+QVPGRHNALNAAAVVLAAVRAGMAFEAAVRGVEAFRGTARRFEFRGAARGVRVFDDYAHH
+PTEVAAAVSAGRAVAGDARVHVLFQPHLFSRTRDFAAEFAAALSGADAVRVLPVYAAREE
+PMPGVDSSLIASRLTTGAAEDRVVAEDRAEAVRSLAAGATAGDVVLTMGAGDVTALGADL
+LAELGRDAAPGVAHP*
+>NZ_CP033200.1_1040
+MSRDESTRPAAEGRFADLGRVHLLGIGGVGVSGVARILQEQGVAVSGSDAKDLPVMRELA
+AGGARITVGYDAAHLGRDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALAMRGHR
+VLAVAGTHGKTTTSSMAAMAFSDAGWDPTFAVGAAVAGLGTNARAGQGEWFIAEADESDG
+TLVNYPSTIGIVTTVEADHLDHYGTEEAVHQVFRDFAGGLPAAAQGGVLVACLDDAGAAD
+LAAWAREHAAADVVTYGSAPRDGVAPDLLVTDLAVEPGETGVGQRATFRMAGGPERTLHL
+QVPGRHNALNAAAVVLAAVRAGMAFEAAVRGVEAFRGTARRFEFRGAARGVRVFDDYAHH
+PTEVAAAVSAGRAVAGDARVHVLFQPHLFSRTRDFAAEFAAALSGADAVRVLPVYAAREE
+PMPGVDSSLIASRLTTGAAEDRVVAEDRAEAVRSLAAGATAGDVVLTMGAGDVTALGPDL
+LAELGRDAAPGVAHP*
+>NZ_CP040019.1_1513
+MSRDESTRPVAEGRFDELGRVHLLGIGGVGVSGVARILQDQGVAVSGSDAKDLPVMRELA
+AAGARITVGYDAAHLGEDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALAMRGHR
+VLAVAGTHGKTTTSSMAAMAFASAGWDPTFAVGAAVAGLGTNARAGQGEWFIAEADESDG
+TLVNYPTTIAVVTTVEADHLDHYGTEEAVHQVFRDFAAGLPDAASGGVLVACLDDDGAAG
+LAAWAREHAAARVLTYGTGPRDGVAPDLLVADLAVEPGESGVGQRATLRLASGPEATLHL
+QVPGRHNALNAAAVALAAVQAGMGFEDAVRGLEAFRGTARRFEFRGAGRGVKVFDDYAHH
+PTEVTAAVSAGRAVAGDGRVHVLFQPHLFSRTREFAAEFAAALSAADVVRVLPVYAAREE
+PMEGVDSSLIAGRLTTAADADRAVAEDRAVAVRELAAGAESGDVILTMGAGDVTALGADL
+VAALGPDAAPGAAGR*
+>NZ_CP083691.1_1407
+MTTQQTPEGRARRERVAALGRVHLLGIGGVGVSGVARILQDQGVAISGSDAKDLPVMHDL
+AAGGARITVGYDAAHVGDDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALAMEGH
+RVLAVAGTHGKTTTSSMAAMAFTDAGWDPTFAVGAAVAGLGTNARAGAGEWFVAEADESD
+GTLVNYPTTIAVVTTVEADHLDHYGTEEAVHEVFRVFAGQLPAAEDGGALVACLDDEGAA
+GLAAWAHEHARAAVVTYGTGPRDGVEPDLLVDGVTVEPGESGVGQRARFTLADGTSAEVR
+LQVPGRHNALNAAAVALAAVRAGMSLREAVHGLEQFRGTARRFEFRGAERGVRVFDDYAH
+HPTEVVAAVSAARAVAGEGRVHVLFQPHLFSRTRDFAAEFAAALSGADRVRVLPVYAARE
+EPMEGVDATLITRALTTPDPADRTVAVDRAAAVRELAAGAREGDVILTMGAGDVTALGPD
+LVAALAADPSVDA*
+>NZ_CP097650.1_1264
+MSRDESTRPAAEGRFADLGRVHLLGIGGVGVSGVARILQEQGVAVSGSDAKDLPVMRELA
+AGGARITVGYDAAHLGRDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALAMRGHR
+VLAVAGTHGKTTTSSMAAMAFSDAGWDPTFAVGAAVAGLGTNARAGQGEWFIAEADESDG
+TLVNYPSTVGIVTTVEADHLDHYGTEEAVHQVFRDFAGGLPAAAQGGVLVACLDDAGAAD
+LAAWAREHAAADVVTYGSAPRDGVAPDLLVTDLAVEPGETGVGQRATFRMADGPERTLHL
+QVPGRHNALNAAAVVLAAVRAGMAFEAAVRGVEAFRGTARRFEFRGAARGVRVFDDYAHH
+PTEVAAAVSAGRAVAGDARVHVLFQPHLFSRTRDFAAEFAAALSGADAVRVLPVYAAREE
+PMHGVDSSLIASRLTTGAAEDRVVAEDRAEAVRSLAAGATAGDVVLTMGAGDVTALGPDL
+LAELGRDAAPGVAHP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001147.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001147.fa
new file mode 100644
index 0000000000000000000000000000000000000000..47534c23d81901253de41cf7e6bdeeb34833c325
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001147.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1313
+MTGPASDAAPAPVRRPRADTARTADLTSWDAPGWAGLRVVVTGLGLTGFSVADTLAELGA
+AVVVVEGDDGPENRARAETLRIVGVREVLLDRAATQALPEVDGAAADLVVTSPGWRPDQP
+LLMAAHAAGLPIWSDVELAWRLRERAGRKTADWVCLTGTNGKTTTVTMVEAILRADGRRA
+VACGNVGTPVLDAIRDPQGFDVLALELSSFQLHWTHGLAPASSAVLNLAEDHVDWHGSME
+EYAAAKGKVYANTRVACVFNEQDPLTRTLVERADVQEGCRAIGFTTDTPGLSDIGVVDGI
+LVDRAFLDNRRHEAIALAERADLGPVAPRHTVANAAAAAALTRAVGVSPAAVAEGLRSYD
+RGEHRIQLVATSRDVMWVNDSKATNPHAADASLAAFSSVVWLAGGLPKGVTYHELVAAHA
+HRLRAVVLLGRDTSALRAALAAHAPEVPVHAPLAAADGTGPADGAAVMAEAVRVADGLAR
+PGDIVLMAPAAASMDQFRSYAARGDAFIEAVAGLMREHGWDVHDDAAPDAD*
+>NZ_CP033200.1_1043
+MTGPASAAAPAPVRRPRADTARTADLTSWDAPGWAGLRVVVTGLGVTGFSVADTLAELGA
+AVVVVDGDDGPENRARAETLRIVGVREVLLDRAATQVLPEVDGAAADLVVTSPGWRPDQP
+LLMAAHAAGLPIWSDVELAWRLRERAGRKTADWVCLTGTNGKTTTVTMVEAILRADGRRA
+VACGNVGTPVLDAIRDPQGFDVLALELSSFQLHWTHGLAPASSAVLNLAEDHVDWHGSME
+EYAAAKGKVYANTRVACVFNEQDPVTRTLVERADVQEGCRAIGFTTDTPGLSDIGVVDGI
+LVDRAFLDNRRHEAIALAERADLGPVAPRHTMANAAAAAALTRAVGVSPAAVAEGLRSYD
+RGEHRIQLVATSRDIMWVNDSKATNPHAADASLAAFSSVVWLAGGLPKGVTYHELVAAHA
+HRLRAVVLLGRDTSALRAALAAHAPDVPVHAPLAAADGTGPADGAAVMAEAVRVADGLAR
+PGDTVLMAPAAASMDQFRSYAARGDAFIEAVAGLMREHGWDVHDDAAPDTD*
+>NZ_CP040019.1_1510
+MSASENTALVPVRRPLADTGRTAALTSWDAEGWAGLRVVVAGLGVTGFSVADTLAELGAV
+VVVVDGNDGPENQARAETLRIVGVHEVLLDAEATQSLPEVDGAPAELVVTSPGWRPDQPL
+LMAAHAAGLPIWSDVELAWRVRERAGRPTADWVCLTGTNGKTTTVTMVEAILRADGRRAI
+ACGNVGTPVLDAIRDPEGYDVLALELSSFQLHWTHRVAPASSAVLNLAEDHVDWHGSMEE
+YAAAKGKVYENTRVACVFNEHDPVTRTLVERADVQDGCRAVGFTTDTPGLSDVGVVDGIL
+VDRAFTENRRHEAIALAERTDLGPVAPRHTMANAAAAAALTRAVGVAPAAVAEGLRSYDR
+GEHRIQLVATSRDVMWVNDSKATNPHAADASLAAFTSVVWIAGGLPKGVTYEELVGAHAH
+RLRAVVLLGTDASALRSALAAHAPDVPVHAPLADADGTGPADGAAVMAEAVRVADGLARP
+GDTVLMAPAAASMDQFRSYAQRGEAFIDAVAALMREHGWDTDAGTAAP*
+>NZ_CP083691.1_1404
+MSAPVMRPHADTDRTRGLRTWDDAGWAGLRVVVTGLGVSGFSAADTLAELGARVVVVDGR
+DSPENRAKADTLRIVGVADVLLSEDATHSLPEVDGERPDLVVTSPGWRPDQPLLMAAHEA
+GLPIWSDVELAWRLRERAGRRTADWVCLTGTNGKTTTVTMVEAILRADGRRALACGNVGT
+PVLDAVRDPEGFDTLAVELSSFQLHWTHSIVPASSAVLNLAEDHVDWHGSMEEYAAAKGK
+VYERTTVACVFNEADALTRTLVERADVAEGCRAVGFTTDTPGLSDVGVVDGIIVDRAFLE
+NRRHEAIALAERSDLGAVAPRHTVANACAAAALTRAVGVSPEAVAEGLRSYDRGEHRIQL
+VATSRDVMWVNDSKATNPHAADASLAAFSSVVWIAGGLPKGVTYDELVSAHAGRLREVIL
+LGTDTSELRRALAAHAPEVPVHAPLADADGHGSPDGRAVMAEAVRLADAHACPGDTVLMA
+PAAASMDQFRSYAERGDAFIAAVAELMREHGWDVDSEADAPA*
+>NZ_CP097650.1_1267
+MTGPASDAAPAPVRRPRADTARTADLTSWDAPGWAGLRVVVTGLGLTGFSVADTLAELGA
+AVVVVDGDDGPENRARAETLRIVGVREVLLDRAATQVLPEVDGAAADLVVTSPGWRPDQP
+LLMAAHAAGLPIWSDVELAWRLRERAGRKTADWVCLTGTNGKTTTVTMVEAILRADGRRA
+VACGNVGTPVLDAIRDPEGFDVLALELSSFQLHWTHGLAPASSAVLNLAEDHVDWHGSME
+EYAAAKGKVYANTRVACVFNEQDPLTRTLVERADVQEGCRAIGFTTDTPGLSDIGVVDGI
+LVDRAFLDNRRHEAIALAERADLGPVAPRHTMANAAAAAALTRAVGVSPAAVAEGLRSYD
+RGEHRIQLVATSRDIMWVNDSKATNPHAADASLAAFSSVVWLAGGLPKGVTYHELVAAHA
+HRLRAVVLLGRDTSALRAALAAHAPDVPVHAPLAAADGTGPADGAAVMTEAVRVADGLAR
+PGDTVLMAPAAASMDQFRSYAARGDAFIEAVAGLMREHGWDVHDDAAPDTD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001148.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001148.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cbd73d50cea9fed0e1ede9a1bd39fb96b72669b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001148.fa
@@ -0,0 +1,56 @@
+>NZ_CP042169.1_1315
+MIALTAAQIAEAVSGTLSATLDPATVLVHVTPDSREVTAEGTLYVAKPGERADGHDFIDA
+ALGAGAAAVLAERATHAPDGAAHPAIIVEDAVLAMGALAREVVRRVRGHSPTTVIGITGS
+AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELDTRFLVVEMGADHVGNIA
+YLCDIVRPDIGVVLMVGTAHAGSFGGVANIARTKGELVEALGPEGVAVLNLDDERVAGMA
+ARTAAPITWFTADERGVARAAEDVAAGRASGLVAARDVRADDQERPVFDLQVGTEEAAVR
+HPVASGLTGLHHVHNVLAAAAAAHAAGMDPAEIARGLDGLGPASRFRMERTDRADGVTII
+NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA
+QLLVVGAGARPLYIGALNEGSWGEEAHFVDDAAQAEAFLAEHLRPGDLVLVKSSNGVGLA
+ALGERLATADAVAAPSASPKESRP*
+>NZ_CP033200.1_1045
+MIALTAAQIAEAVSGTLSATLDPATVLVHVTPDSREVTAEGTLYVAKPGERADGHDFIDA
+ALGAGAAAVLAERATHAPDGAAHPAIIVEDAVLAMGALAREVVRRVREHSPTTVIGITGS
+AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELDTRFLVVEMGADHVGNIA
+YLCDIVRPDIGVVLMVGTAHAGSFGGVANIARTKGELVEALGPDGVAVLNLDDERVAGMA
+ARTAAPITWFTADERGVARAAEDVAASRASGLVAARDVRSDDQERPVFDLQVGTDEAAVR
+HPVASGLTGLHHVHNVLAAAAAAHAAGMDPAEIARGLDGLGPASRFRMERTDRADGVTII
+NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA
+QLLVVGAGARPLYIGALNEGSWGEEAHFVDDAAQAEAFLAEHLRPGDLVLVKSSNGVGLA
+ALGERLATADAVAAPSASPKESRP*
+>NZ_CP040019.1_1509
+MIALTAAQIAEAVSGTLSPALDPQTVLVHVTPDSREVAAEGTLYVAKPGERADGHDFIDA
+ALAAGAVAVLAERPTQAPDGAEHPSIVVEDAVLAMGALAREVVSRIREHSPTTVIGITGS
+AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELETRYLVVEMGADHVGNIA
+YLCDIVRPDVGVVLMVGTAHAGSFGGVANIAATKGELAEAVGPEGAVILNLDDDRVAAMA
+SRAQAPVTWFTADEAGAARAAQDVAAGRAAGLVAARALHADDHERAAFDLQIGADADAPR
+HPLTSGLTGLHHAHNVLAAAAAAHAAGMAPADVARVLDGLGPTSRFRMERTDRPDGVTII
+NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA
+QLLVVGAGARPLYIGALNEGSWGDEAHFVEDVAQAEEFLAEHLAPGDLVLVKSSNGVGLA
+ALGERLATAGASDPAPRPVRLPEGVPTVIGLLIGGVLGLVLSAAGTPLFIRFLVKRGYGQ
+FVRDDGPTTHKTKRGTPTMGGAVIIGAFVLAYLLTHGILALLGVGFGGPTASGLILLFLT
+VGMAFVGFVDDFTKITKQQSLGLTPRGKIILQGLIGTAFAVLALNFPDDRGLTPASTAIS
+FARDVPWLDLAFAGPVVGLILFVIWSNLITTATTNAVNLTDGLDGLATGATAMITGAYVL
+MSIFQSSQACSLVDEPGCYEVRDPMDLALLGAILTGSLLGFLWWNTSPAKIFMGDTGSLG
+LGGALAGFAILSRTELLVVLLAGLMVAITVSVIVQVGWFRISGGKRVFLMAPLQHHFELK
+GWAEVTVVVRFWLVSLMCVTAGLAVFYGEWIVRQGGLAGVTP*
+>NZ_CP083691.1_1402
+MIALTAAQIAEAVSGTLSSTLDPETVLVHVTPDSREVVGEGTLYVAKPGEHADGHDYIDA
+ALAAGASAVLAERPTQDADGAAHPAILVADAVLAMGALAREVVRRIREHSPTTVIGITGS
+AGKTTTKDLLAALLSTQGPTVAPVGSFNGEVGVPLTVFRAALDTRYLVVEMGADHVGNIA
+YLCDVVTPDIGVVLMVGTAHAGSFGGVENIAKTKGELVEALGPDGVAVLNRDDGRVAAMA
+SRTQAPVVWFSTEESGAAAAAEDVAAGRASGLSVARALTADAEERPVFDLQLGADLDAPR
+HAVRAGLTGLHHAHNMLAAAAAAQAAGMDPADIARGLDGLGPTSRHRMERSERADGVSII
+NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARIREHTLVGESVVRLNIS
+QLLVVGAGARPLYIGAMNEGSWGDEAHFVDDVEQAEAFLAEALQPGDIVLVKSSNGVGLA
+ALGDRLAAADVTPSTASPSDTTKETRP*
+>NZ_CP097650.1_1269
+MIALTAAQIAEAVSGTLSATLDPATVLVHVTPDSREVTAEGTLYVAKPGERADGHDFIDA
+ALGAGAAAVLAERATHAPDGAAHPAIIVEDAVLAMGALAREVVRRIRGHSPTTVIGITGS
+AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELDTRFLVVEMGADHVGNIA
+YLCDIVRPDIGVVLMVGTAHAGSFGGVANIARTKGELVEALGPDGVAVLNLDDERVAGMA
+ARTAAPITWFTADERGVARAAEDVAAGRASGLVAARDVRADDQERPVFDLQVGTDEAAVR
+HPVASGLTGLHHVHNVLAAAAAAHAAGMDPAEIARGLDGLGPASRFRMERTDRADGVTII
+NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA
+QLLVVGAGARPLYIGALNEGSWGEEAHFVDDAAQAEAFLAEHLRPGDLVLVKSSNGVGLA
+ALGERLATADAVAAPSASPKESRP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001150.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001150.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d5fd89607d7a1dd60012e22992eed499577be29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001150.fa
@@ -0,0 +1,57 @@
+>NZ_CP042169.1_1317
+MRTRILLLLVFVLLGGLALRLVYVQGIDPTGQAAAAMDQRLTHQETLPQRGSILDRDGDV
+LAASVRRYDIVVDQRLVKDFNEWDREARETVLVDVDSRLASLAEVLGMSEEEVREATIGS
+RPYAVVRRSVTPEVRDAAMALNVPGLLSEAVDRRTYPNGSVAGSIIGFMGGDGTALEGLE
+LSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAVDGADLRLTVDKDAQWFAQETLGAL
+AAEYEAEWANAVVMDVKTGDVIVMADSTTVDPADPDATEGNFRTSTVMSTPYEPGSTGKA
+LPIAAAVDAGKVTATDGFTVPGSQDFDGQTIRDFSPHPTFDMTVAGIYARSYNTGTVQIA
+EKITDEQRYEYMRSFGVGQPIDLGLPQQAGSVLVPPEQWDGRQRLTTAFGQGYTQTTLHT
+AQMYQALANGGVLIPARLIDATVDGDGAEKRWESSAEPHRVVSEETAAQMLRMMETVVTQ
+GTSKAAAIPGYRVGGKSSTAEAASDTGTYDGYNLGFTAVAPLDDPRFVVSVSMHRPPSKQ
+GSRDVSVAAATIMEYMLRQADVPATGAEPNDYRVFVDDPQDRPW*
+>NZ_CP033200.1_1047
+MRTRILLLLVLVLLGGLALRLVYVQGIDPTGQAAAAMDQRLTHQETLPQRGSILDRDGDV
+LAASVRRYDIVVDQRLVKDFNEWDREARETVLVDVDSRLASLAEVLGMSEEEVREATIGS
+RPYAVVRRSVTPEVRDAAMALNVPGLLSEAVDRRTYPNGSVAGSIIGFMGGDGTALEGLE
+LSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAVDGADLRLTVDKDAQWFAQETLGAL
+AAEYDAEWANAVVMDVKTGDVIVMADSTTVDPADPDATEGNFRTSTVMSTPYEPGSTGKA
+LPIAAAVDAGKVTATDGFTVPSSQDFDGQTIKDFSPHPTFDMTVAGIYARSYNTGTVQIA
+EKITDEQRYEYMRSFGVGQPIDLGLPQQAGSVLVPPEKWDGRQRLTTAFGQGYTQTTLHT
+AQMYQALANGGVLIPARLIDATVDGEGAEKRWESSAEPHRVVSEETAAQMLRMMETVVTQ
+GTSKAAAIPGYRVGGKSSTAEAASDTGTYDGYNFGFTAVAPLDDPRFVVSVSMHRPPSKQ
+GSRDVSVAAATIMEYMLRQADVPATGAEPNDYRVFVDDPQDRPW*
+>NZ_CP040019.1_1507
+MTDRPAFSSPRGGSTVGPAPGLPDARIRGLLLLVLVLLGGLALRLVYVQGVDPTGQAAAA
+MDKRLTHQETLPERGSILDRDGDVLASSVRRYDMVVDQRLVKDFNEWDREARKTVLVDVD
+SRLASLAEVLELPEEQVREATIGSRPYNVVKRSVTPEMRDAAMALKVPGLLAEPVDRRVY
+PNGSVAGSIVGFMGGDGTPLEGLELSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAV
+DGADLRLTLDKDAQWFAQETMGALAAEHDAEWANAVVLDAKTGDVLVMADSTTVDPADPE
+GTEPYFRSSTVMSTPYEPGSTGKALPIAAALDAGAVTATDGYTVPSSQEFDGQTIRDFAP
+HETYDMTVAGIFARSYNTGTVQVAEEISDELRYEYMRSFGVGKPIDLGLPRTAGGVLVPP
+GEWDGRQRLTTAFGQGYTQTTLHTAQMYQAMANGGVMEPARLIDATVDGDGAEKRWEPAA
+EPHRVVSEATAADMLRMMETVVTQGTSKAAAIPGYRVGGKSSTAEAASDTGRYDGYNFGF
+TAVAPLDDPRFVVSVSMHRPPSQLGSRAVTSAAAQIMEHMLRQADVPADGAAPQDYDVFV
+DDPQDRPW*
+>NZ_CP083691.1_1400
+MPVSRSRVSGAGSRTAPPIGTARVRSRTVLLLLLALVTVLGLRLVWVQGIDASGAAATAM
+SERLKTQEIRPERGAITDRDGAVLASTVRRYDIVVDQRLVKDFKEWDAEKRQSVLVSIDS
+RLSSLAEALGMSEDEVRAAAIGDRPWAVLKRSVTPEVRDRVLALKVPGVLADAVDRRTYP
+SGAVAGSLVGFMSSDGTPLEGLEKSQDAVLSGTPGTRTFEVGATGIRIPNAPEDVTPAVD
+GATLRLTLDKDAQWYAQEAMARLADTYSAQWANAVVMDAKTGEVLALADSATVDPGDPQA
+ADARARTPGVVYTPYEPGSTGKTATMAAALDMGLVTPETGLEVPDRLELKGQPPIRDASP
+HETYTMTVAGVYARSYNTGTVMVAEKMSDEQRYEYMRSFGIGRPIDLGLPQPARSVLAAP
+GDWDGRQRLVTAFGQGYTVTTLHTAQMFQAIANGGVLEPARLIAATVGADGTEHRWDPGV
+ASRRVVSEQTAEEMLRMMETVVTQGTSTVAQLPGYRVGGKSSTAQVAGETGTYDGYNYGF
+TAVAPLDDPRYVVSVSMNRPSAGGSSKVVAAAAADVMQHMLRQGGVPPGGAEPDDYRVFV
+DDPQERPW*
+>NZ_CP097650.1_1271
+MRTRILLLLVFVLLGGLALRLVYVQGIDPTGQAAAAMDQRLTHQETLPQRGSILDRDGDV
+LAASVRRYDIVVDQRLVKDFNEWDREARETVLVDVDSRLASLAEVLGMSEEEVREATIGS
+RPYAVVRRSVTPEVRDAAMALNVPGLLSEAVDRRTYPNGSVAGSIIGFMGGDGTALEGLE
+LSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAVDGADLRLTVDKDAQWFAQETLGAL
+AAEYEAEWANAVVMDVKTGDVIVMADSTTVDPADPDATEGNFRTSTVMSTPYEPGSTGKA
+LPIAAAVDAGKVTATDGFTVPGSQDFDGQTIRDFSPHPTFDMTVAGIYARSYNTGTVQIA
+EKITDEQRYEYMRSFGVGQPIDLGLPQQAGSVLVPPEQWDGRQRLTTAFGQGYTQTTLHT
+AQMYQALANGGVLIPARLIDATVDGDGAEKRWESSAEPHRVVSEETAAQMLRMMETVVTQ
+GTSKAAAIPGYRVGGKSSTAEAASDTGTYDGYNLGFTAVAPLDDPRFVVSVSLHRPPSKQ
+GSRDVSVAAATIMEYMLRQADVPATGAEPNDYRVFVDDPQDRPW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001151.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001151.fa
new file mode 100644
index 0000000000000000000000000000000000000000..009a900c9a93cee5cc0cc0bd599abbd32907a37d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001151.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1318
+MTLHEEMSMAAHARIAESLRPGSTPVAPARPTPQERTPLSVVPAPLPRSRSGVTVLCVLV
+VLAALAAVLVMNITMSNRQYALLDLRQEQQAVTETNERLAEQVGHLEAPQNLAARADALG
+MVAPAGTASVDAGTGQFSGEAQAAQDGDISATYVAPPADADAVRQGTAGDGQDEIEGPRT
+LGGEDASAAPDQDAADR*
+>NZ_CP033200.1_1048
+MTLHEEMSMAAHARIAESLRPGSTPVAPARPAPQERTPLSVVPAPLPRSRSGVTVLCVLV
+VLAALAAVLVMNITMSNRQYALLDLRQEQQAVIETNERLAEQVGNLEAPQNLAARADALG
+MVAPAGTASVDAGTGEFGGEAQAAQDGDVSATYVAPPADADVVRQGASAEGQDEIEGPRT
+LGGEDASAAADQDAADR*
+>NZ_CP040019.1_1506
+MTLHEEMSMAAHARIAEPLRHTGAPARPAPQERTPLSVVPAPLPRSRSGMTVLCVVVLLA
+ALAAVLVMNITMSNRQYALLDLRQEQQAVTEVNERLAEQVGYLEAPQNVAARADALGMVA
+PAGTASVDAATGEFRGEAQPAREGEISATFVAPPVNADAVRQGSAGSADADRGDIEGPRT
+LGAPAAAPGAAASDDRDASDR*
+>NZ_CP083691.1_1399
+MTAYEETGMSAQAWRDEARTAWPRTGATPEREHRQRTPLSVVPTPLPRSGSGVAVLCGLV
+LLVALGLVLVMNITMSNRQFTLLDLRAQQTTLTETNERLAEQAGYLDAPQNLAARAGAMG
+MVSPGATSTVDVASGAVAGPSTGAGSTTLPEGRIAPPADADLARQGEAQGQIPGPRTVDP
+AAPTAAPSGETAPTPAPTDAPAGR*
+>NZ_CP097650.1_1272
+MTLHEEMSMAAHARIAESLRPGSTPVAPARPTPQERTPLSVVPAPLPRSRSGVTVLCVLV
+VLAALAAVLVMNITMSNRQYALLDLRQEQQAVTETNERLAERVGHLEAPQNLAARADALG
+MVAPAGTASVDAGTGQFSGEAQAAQDGDISATYVAPPADADAVRQGTAGDGQDEIEGPRT
+LGGEDASAAPDQDAADR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001158.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001158.fa
new file mode 100644
index 0000000000000000000000000000000000000000..040b7b0cdfc0e184f933a034cadfda5cad8b05b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001158.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1325
+MPRSAVPHTPVRSRCLRSVLTGGAVPLLLLTGLPAQAHAQEAAVHTVRPGDSLTRISAAR
+GVSVADLLRFNGLGLETVLYPGDELRLTGAAAPAPAAGTYTVQPNDGWWVIARRTGVSAA
+QLQRLNGMSASSMLHPGMVLTTQRTAAAPKAPASPAPTTTPATAPASTTPTAAGGTVRYT
+VVSGDSLWGISQRFEVSIPRLRELNGLTRASTLHPGDVLVISDGTLEVEPVSAVQAVGDT
+FLGRTYAPHVTASANENLRLLRAVPQPTPEQMQQIVRETAERMGVDPRLALGHAYTESRF
+RMASVSPGNAVGAMQVIPITGEFASELVGRELNLLDPHDNAVAGVAFIKYVQDRTPTLDE
+GIGAYYQGLGGVLDSGLNPEARDYVAKVRAAMAMF*
+>NZ_CP033200.1_1055
+MPRSAVSHTPVRSRRLRSVLTGGAVPLLLLTGLPAQAHAQEAAVHTVRPGDTLTRISAAR
+GVSVADLLRFNGLGLETVLYPGDELRLTGAAAPAPAVGTYTVQPNDGWWIIARRTGVSAA
+QLQRLNGMSASSMLHPGMVLTTQRTAAAPKTPASTAPATTPASAPASTAPAAAGGTVRYT
+VVSGDSLWGISQRFEVSIPRLRELNGLTRASTLHPGDVLVISDGTLEVEPVSAVQAVGDT
+FLGRTYAPHVTASANENLRLLRSVPQPTPEQMQQIIRETAERMGVDPRLALGHAYTESRF
+RMASVSPGNAVGAMQVIPITGEFASELVGRELNLLDPHDNAVAGIAFIKYVQDRTPTLDQ
+GIGAYYQGLGGVLDSGLNPEARDYVAKVRAAMAMF*
+>NZ_CP040019.1_1499
+MPRSSVSHTPSRRLRHALAGGAVPLLLLTGLPAQAQAQEAPVHTVRPGDTLTAISAAHGV
+PLVDLFRLNGLDHESIIYPGDAIRLTGEAAPAAAAGTYTVQPDDGWWIIARRTGVSAAEL
+QRLNGMSASTMLHPGMVLTTAGKAAAPAPTPAPPRCSLAPATRDVVRYAVVSGDSMWGIS
+QRFEMSIPRLRELNGLTRSSMLHPGQVLVISDGTLEVEPVSDVQPIGDTFLGRTYPAHVT
+ASANENLRLLQSVPQPSPEQMREIVRETAVRMDVDPRLALGHAYTESRFRMASVSPANAI
+GAMQVIPITGEFASELVGRELNLLDPYDNAVAGVAYIKYVQDRTPTLDTGIGAYYQGLGG
+VLQGGLSAEGRTYVATVRAAMAMF*
+>NZ_CP083691.1_1392
+MPPARKVTPLMPQPAAPRASATTARRSLGLVAGGVVPLLMTGALPVAAQAAEAAHAAPRT
+HTVRAGENPYRIAEAEGVRLSDLLRLNGLRADSVIYTGQVLALTGAPAPAAAPGTVEVER
+GEGWWQVSRRAGVDAAVLQRINGLGARSMLHPGQILLTEAPARPTTPATPVAAAPAPVRQ
+AAPTTYTVRNGDSMWSISQRVEVSIPRLRELNGLTWRSVLHTGDVLVIADGTEQAPVIDG
+PVGSTFLSTTYAPHVTASANDNLRALQAVPQPSPAEVQALVRQTALELGVDPALALGHAY
+TESRFQHASVSPGNAIGAMQVIPITGEFASQLVGRELNVLDVRDNVTAGVVLIKYLQEHT
+DTVDQGISAYFTGLGGSDDPVKQQEARNYVARVKAAAAMF*
+>NZ_CP097650.1_1279
+MPRSAVPHTPVRSHRLRSVLTGGAVPLLLLTGLPAQAHAQEAAVHTVRPGDSLTRISAAR
+GVSVADLLRFNGLGLETVLYPGDELRLTGAAAPAPAAGTYTVQPNDGWWVIARRTGVSAA
+QLQRLNGMSASSMLHPGMVLTTQRTAAAPKAPASPAPTTTPATAPASTAPTAAGGTVRYT
+VVSGDSLWGISQRFEVSIPRLRELNGLTRASTLHPGDVLVISDGTLEVEPVSAVQAVGDT
+FLGRTYAPHVTASANENLRLLRSVPQPTPEQMQQIVRETAERMGVDPRLALGHAYTESRF
+RMASVSPGNAVGAMQVIPITGEFASELVGRELNLLDPHDNAVAGVAFIKYVQDRTPTLDE
+GIGAYYQGLGGVLDSGLNPEARDYVAKVRAAMAMF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001165.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001165.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85fbb68c74ff52a64cf2af9f01ed43194908c54c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001165.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1333
+MTPTAGPGRPPALGAQGTLFDEGRTQGDDVGFRGPTACKAAGITYRQLDYWARTDLVAPT
+VRSASGSGSQRLYSFRDILVLKVVKRLLDTGVSLQQIRTAVGHLRERGVEDLAQITLMSD
+GASVYECTSADEVVDLVQGGQGVFGIAVGRVWREVEGSLAELPRESVVGAPEPGDELAGR
+RRARRSA*
+>NZ_CP033200.1_1063
+MTPTAGPGRPPALGAQGTLFDEGRTQGDDVGFRGPTACKAAGITYRQLDYWARTDLVAPT
+VRSASGSGSQRLYSFRDILVLKVVKRLLDTGVSLQQIRAAVGHLRERGVEDLAQITLMSD
+GASVYECTSADEVVDLVQGGQGVFGIAVGRVWREVEGSLAELPRESVVGAPEPGDELAGR
+RRARRSA*
+>NZ_CP040019.1_1490
+MTPTAGSGRPPALGAQGTLFDEDVTPGDDVGFRGPTACKAAGITYRQLDYWARTDLVVPT
+VRGAAGSGSQRLYSFRDILVLKVVKRLLDTGVSLQQIRTAVGHLRERGVEDLAQITLMSD
+GASVYECTSADEVVDLVQGGQGVFGIAVGRVWREVEGSLAELPRESVIVAPEPGDELAGR
+RRARRSA*
+>NZ_CP083691.1_1383
+MTPHAGPGLPLGIDGRQGRLFDVDALAPGGDVGYRGPTACKAAGITYRQLDYWARTDLVV
+PTVRGASGSGTQRLYSFRDILVLKVVKRLLDTGVSLQQIRTAVAHLRERGVDDLAQITLM
+SDGASVYECTSPDEVVDLVQGGQGVFGIAVGRVWREVEGSLAELPGEVLGDDHAPEDELS
+ARRRARRPARTAS*
+>NZ_CP097650.1_1287
+MTPTAGPGRPPALGTQGTLFDEGATRGDDVGFRGPTACKAAGITYRQLDYWARTDLVVPT
+VRSASGSGSQRLYSFRDILVLKVVKRLLDTGVSLQQIRTAVGHLRERGVEDLAQITLMSD
+GASVYECTSADEVVDLVQGGQGVFGIAVGRVWREVEGSLAELPRESVVGAPEPGDELAGR
+RRARRSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001169.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001169.fa
new file mode 100644
index 0000000000000000000000000000000000000000..788aa1bfaee0a367c22ce8bdef2bac6d169eb603
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001169.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1337
+MSSIPEGLKYSAEHEWIAEAGAAGTVRVGITDFAQDALGDVVYVDLPEVGTEVTAGTAVG
+EVESTKSVSDIYAPVSGTVAAVNDELDGEPGLVNSAPYEGGWLFEITLADEAQLEGLMDA
+EGYASHTS*
+>NZ_CP033200.1_1067
+MSSIPEGLKYSAEHEWIAKAGAAGTVRVGITDFAQDALGDVVYVDLPEVGTEVTAGTAVG
+EVESTKSVSDIYAPVSGTVAAVNDELDGEPGLVNSAPYEGGWLFEITLADEAQLEGLMDA
+EGYASHTS*
+>NZ_CP040019.1_1486
+MSSIPEGLKYSAEHEWIAEAGQAGTVRIGITDFAQDALGDVVYVDLPEVGSEVTAGTAVG
+EVESTKSVSDIYAPVTGTVAAVNEDLDGEPGLVNSAPYEGGWLFEVTLADEAQLEGLLDA
+EGYASHTS*
+>NZ_CP083691.1_1379
+MSSIPEGLKYSTDHEWAQDAAEPGVVRVGITDFAQDALGDVVYVDLPSVGDEVTAGAAIG
+EVESTKSVSDIMAPVSGTVTAVNEELDGEPALVNSAPYEGGWLVEIKLSDPAEVDGLLDA
+AGYAAHVG*
+>NZ_CP097650.1_1291
+MSSIPEGLKYSAEHEWIAEAGAAGTVRVGITDFAQDALGDVVYVDLPEVGTEVTAGTAVG
+EVESTKSVSDIYAPVSGTVAAVNDELDGEPGLVNSAPYEGGWLFEITLADEAQLEGLMDA
+EGYASHTS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001174.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001174.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d68ca852af9573dcf3dff650b94f34cb47943496
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001174.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1363
+MNSRKPRGSGRTPAVGRRGGPFQERDFQRQIGARRGAAAPREEAPFDEDAVPRTRGRRGR
+GAGAARAKAAHLDRIHDESGERLQKVLAAAGVASRRVSEDLIAEGRVEVDGVVVTEPGVR
+VDPATAVIRVDGISVQTDVTKQYFVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG
+RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA
+QVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGT
+VRALNAQELGHLKALVGL*
+>NZ_CP033200.1_1103
+MNSRKPRGSGRTPAVGRRGGPFQERDFQRQIGARRGAAAPREEAPFDEDAVPRTRGRRGR
+GAGAARAKAAHLDRIHDESGERLQKVLAAAGVASRRVSEDLIAEGRVEVDGVVVTEPGVR
+VDPATAVIRVDGISVQTDVTKQYFVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG
+RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA
+QVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGT
+VRALNAQELGHLKALVGL*
+>NZ_CP040019.1_1463
+MNSRKPRGSGRTPSVGRRGGPFQERDFQRQLGARRGPAGPRDEAPFDEDAVPRTRGRRGR
+GAGAARAKAANLDRIHDESGERLQKVLASAGVASRRVSEDLIAEGRVEVDGVIVTEPGVR
+VDPARAVIRVDGISVQTDVTKQYYVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG
+RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA
+KVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGS
+VRALSAQELGHLKALVGL*
+>NZ_CP083691.1_1373
+MNSRKPRGSGRTPAAGKRGGPFSERDFQRNLGARRGPARPKDEPAFDEDAAERRVRSRRG
+KGAGAARAKAQHLEEIHVEDGERLQKVLASAGVASRRVCEDLIAEGRVEVDGVVVTEPGV
+RVDPVRSRIQVDGISVQTDVTKQYFVFNKPRGVISTMLDPEGRPSIATYLKPGQENLFHV
+GRLDNETEGLLILTNDGELANRLTHPSWEVPKTYLVQTRGPLAKGVSNRLREGVELEDGL
+AKVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQG
+SVRAMTAQEQGHLKALVDL*
+>NZ_CP097650.1_1312
+MNSRKPRGSGRTPAVGRRGGPFQERDFQRQIGARRGAAAPREEAPFDEDAVPRTRGRRGR
+GAGAARAKAAHLDRIHDESGERLQKVLAAAGVASRRVSEDLIAEGRVEVDGVVVTEPGVR
+VDPATAVIRVDGISVQTDVTKQYFVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG
+RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA
+QVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGT
+VRALNAQELGHLKALVGL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001181.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001181.fa
new file mode 100644
index 0000000000000000000000000000000000000000..62d829c3673928d661597a117415f2543b4e01df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001181.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1375
+MPEISASAGRSPLRDLHVPRPVKKSKTVYEGRVWDIARESFRLDPADKSREPLTRELMVH
+PGAVAILAVRTKLTTTGPREQVALVRQYRHPVGMELWEIPAGLRDVDGEDLHQVAVRELA
+EEADLRAREWHTLVDYYTTPGGSSEAIRVFLARQIEEIPDGERHTRQDEEAAMPLVWVGL
+DEVTDAVLDGRVHNPSTVVAVLALGAHRAQGWRRLRPVDAPFVPDRQAPGADWPA*
+>NZ_CP033200.1_1116
+MPEIPASAGRSPLRDLHVPRPVKKSKTVYEGRVWDIARESFRLDPADKSQDPLTRELMVH
+PGAVAILAVRTKLTTTGPREQVALVRQYRHPVGMELWEIPAGLRDVDGEDLHQVAVRELA
+EEADLRALEWHTLVDYYTTPGGSSEAIRVFLARQIEEIPDGERHTRQDEEAAMPLVWVGV
+DEVTDAVLDGRVHNPSTVVAILALCAHRAQGWRRLRPVDAPFVPDRHGPGADWPA*
+>NZ_CP040019.1_1454
+MPEISACAGRSPLRDLHVPRPVKKSKTVYEGRVWDIARESFRMDPEHKGQDPLTRELMVH
+PGAVAVLAVRTQLSTVGPREQVALVRQYRHPVGMELWEVPAGLRDVDGEDLHQVAVRELA
+EEADLRAREWHTLVDYYTSPGGSTEAIRVFLARQVEVIPEAERHARTDEEAAMPLAWVGL
+DEVTDAVLDGRVHNPSTVVAILALCAHRAQGWRRLRPVDAPFVPDRHGPGADWPA*
+>NZ_CP083691.1_1361
+MAEVPASAGRSPLRDLSLPRRVKKSKTVFEGRVWDIARESFRMDPDDKGQEPLTRELMVH
+PGAVAVLALRTHLTTAGPVEQVALVRQYRHPVGMELWEVPAGLRDVAGEPLVETARRELR
+EEADLEAAEWHTLADFFTTPGGSTEAIRVFLARQVSAVPEGARHEREGEEASMPLAWVNT
+DEVLDAVLDGRIHNPSTVVAVLALHAHRAQAWRRLRPPDAPFVPDRRGPGADRPA*
+>NZ_CP097650.1_1324
+MPEIPASAGRSPLRDLHVPRPVKKSKTVYEGRVWDIARESFRLDPADKSREPLTRELMVH
+PGAVAILAVRTKLTTTGPREQVALVRQYRHPVGMELWEIPAGLRDVDGEDLHQVAVRELA
+EEADLRAREWHTLVDYYTTPGGSSEAIRVFLARQIEEIPDGERHTRQDEEAAMPLVWVGV
+DEVTDAVLDGRVHNPSTVVAVLALGAHRAQGWRRLRPVDAPFVPDRQAPGADWSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001187.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001187.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7baa98d78e6749d330e9866de307d77913156fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001187.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1381
+MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP
+TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES
+LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD
+EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT
+PLITNADGTKFGKSEGNAVWLDAEMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAQKVADEPFRREAQRRLAWEVTALAHGEETTTKVIEASQAVFGGGDLTTVDPDTLTAVL
+AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT
+RDDALAGRHLLVRRGKKNMAGADLGEA*
+>NZ_CP033200.1_1122
+MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP
+TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES
+LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD
+EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT
+PLITNADGTKFGKSEGNAVWLDAKMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAQKVADEPFRREAQKRLAWEVTALAHGEETTTKVIEASHAVFGGGDLTTVDPDTLTAVL
+AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT
+RDDALAGRHLLVRRGKKSMAGADLGEG*
+>NZ_CP040019.1_1448
+MAPDNEERAARLRAQANDPSFENVWQELLWRGLVHVSTDEAALEEALAGEPISYYCGFDP
+TAASLHLGHLVQLLTLRRLQLAGHRPMALVGGATGLIGDPRQTSERVLNSQETVAGWVES
+LREQIQPYLSFEGENAATMVNNLDWTAGMSALDFLREVGKNFRVGTMMKKEIVAKRLNSE
+EGISYTEFSYQVLQGNDFLELYRRHGVSLQTGGSDQWGNLTAGTELIRKVEGVPAHALGT
+PLITNADGTKFGKSEGNAIWLDAAMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAQKVADEPFRREAQKRLAWEVTSLAHGEEATTKVIEASQAVFGGGDLGEVDAETLGAIL
+SELPQADRTQWEGEPGTVTAVELLVSTGLVGSKSEARRTVKEGGASVNNERVSDADRVYT
+REDALAGRHLLVRRGKKNMAGADFGSQDADRG*
+>NZ_CP083691.1_1354
+MAETTVTRAERLRQQANDPSFENVWQELTWRGLVHVSTDEAALEEALAGEPISYYCGFDP
+TAPSLHLGHLVQLLLMRRLQLAGHRPVALVGGATGLIGDPRQTSERVLNTREVVQEWVES
+LRAQIEPYLAFEGDNGARMVNNLDWTASMSALDFLREVGKNFRVGTMVKKEIVAKRLHSE
+EGISYTEFSYQVLQGNDFLELYRQHGVTLQSGGSDQWGNLTSGTELIRKVEGAHVHALGT
+PLITNSDGTKFGKSEGNAIWLDADMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAAKVDAEPFRREAQKRLAWEVTALAHGEEAARTVIDASAAVFGGGDLSEVDVDVLSAVL
+AELPQADAAQWGAAGKPTAVELLVSTGLVSSNSEARRTIKEGGASVNNVKVADAEQVFGA
+DEALAGRYLLVRRGKKNMAAADLRSGE*
+>NZ_CP097650.1_1330
+MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP
+TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES
+LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD
+EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT
+PLITNADGTKFGKSEGNAVWLDAEMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAQKVADEPFRREAQRRLAWEVTALAHGEETTTKVIEASQAVFGGGDLTTVDPDTLTAVL
+AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT
+RDDAFAGRHLLVRRGKKNMAGADLGEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001188.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001188.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09926aa0661cc41e6ded0fb599da1761e122596c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001188.fa
@@ -0,0 +1,70 @@
+>NZ_CP042169.1_1382
+MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFAS
+LYEDRLAQLYAVDDRLVFGRLDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAG
+AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLGEDGVRADAQGALLAAVTARR
+TGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG
+VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDA
+VAHAVAQRQRLLVEPRRLMIDGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRE
+LAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCWMPLTPEKLIGDLLTREDLLR
+AAAPWLSDAEVGALLRPADAPWTEADVPLLDEAAELLGRLDTPGRGGESAAQHERNLENA
+RASLENMHQTLADLGVDGVVDAEQLAAANEARGVRRTTAETAAHDRTWTYGHVVVDEAQE
+LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSP
+ARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGDVAALALDAVEAERDRVPEAL
+TAVIAPAERTGELLTALRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVLPERI
+VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE*
+>NZ_CP033200.1_1124
+MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFAS
+LYEDRLAQLYAVDDRLVFGRLDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAG
+AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLGEDGVRADAQGALLAAVTARR
+TGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG
+VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDA
+VAHAVAQRQRLLVEPRRLMIDGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRE
+LAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCWMPLTPEKLIGDLLTREDLLR
+AAAPWLSDVEVGALLRPADAPWTEADVPLLDEAAELLGRLETPGRGGESAAQHERNLENA
+RASLENMHQTLADLGVDGVVDAEQLAAANETRGVRRTTAETAAHDRTWTYGHVVVDEAQE
+LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSP
+ARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGDVAALALEAVEVERDRVPEAL
+TAVIAPAGRTGELLTVLRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVSPERI
+VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE*
+>NZ_CP040019.1_1447
+MTDAVSVRQSELELERARVAERYARLDALREEKERQLAAVRRTGLEGSLQNHSERDAFAS
+LYEDRLAQLLAVDDRLVFGRLDLDPERAGDPDEERYIGRIGLTTEEHERLLVDWRAAEAG
+AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDVLDPDLLGQEGVRADAQGALLAAVTARR
+TGRMGDIVATIQAEQDEVIRAPLAGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG
+VLIVGPSTAFMRYIERVLPSLGETGVVMASLGTLMPGVQAGPERDLDAAAVKGRLEMAQV
+IAHAVAQRQRLLAQPRRLMIEGTAVKLKPAAVRRARDRARATGKPHNEARVTFVKILVRE
+LAEKLSKKLEKSSGAPVQRDLLLEDVRTSRDVRVALNLCWMPLTPQKLVGDLLTREHLLR
+AAAPWLSDGEVGALLRPADAPWTEADVPLLDEAAELLGRLEAPAKGGESAAQHERNLENA
+RASLENMHQTLADMGVDGVVDAEQLAAANEARAVRRTTAETAAHDRTWTYGHVVVDEAQE
+LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLEPEFGDRWRLEELTVNYRSP
+ARVMRWASQVAQAAGLEVSRPRAVREGEHAPRLTVRPGADLVALTLDAVAGERDRVPEGL
+VAVITAAAHAPELLAALRERWGRARVDTAPLPGVEIVVATPWETKGLEFDAVVLAAPERL
+VDDARGVVGDLYVAMTRATQSLSVVSTAAVAALPAGLADPPA*
+>NZ_CP083691.1_1353
+MTDTVSSRQAELELERERVAVRYARLDALRAEKEEQLARVRRSGLQGSVQNHSERDAFAS
+LYEDRLAQLYAVDERLVFGRLDLDADDAGDVEQRYIGRIGLTDEGQERLLVDWRAQEAGA
+FYQATAARRLGVGRRRHLLLRGREVRDFEDDVLDPSLIAEGAAGAQSQGALLAAVTARRT
+GRMGDIVATIQAEQDEVIRADTSGALVVQGGPGTGKTAVALHRAAYLLYTHRDRLAKSGV
+LVVGPSNAFMRYIERVLPSLGETGVVMASLGTLMPGVQAGPDRSARAAELKGRLEMADVV
+AAAVAQRQRLIPETRRLEIEGTVVKLKPAMVRRARDRARATGKPHNEARTTFVKILVREL
+AEKLRKKLEKSSGVPVQRDLLLEDVRTARDVRVALNLCWMPLTPQKLVGDLLTKEHLLRA
+AAPGLSDGDVAALLRTDPDAWVESDVPLLDEAAELLGELEEPHRPGESEAQHRRNVENAQ
+ASLENMHQTLAELGVDGVVDAEQLAAANEVRAVRRTTAEQAAHDRTWTFGHVVVDEAQEL
+SPMQWRLLARRCPLKSFTVVGDIAQASRRGGARSWKDVLGPEFGDRMRLEELTVNYRSPA
+RITRWAAQVAQAAGLEISSPEAVREGEHEPLLTVEPGADPTRLAQRVVEAERGRVGDGLV
+AVIVPADDAAEHLTHLQDRWGSLVDRAPAPGVEVVVVTARETKGLEFDAVVLVSPERIVA
+DADGVVGDLYVAMTRCTQSISVVSGAAEEELPAGLMPVPA*
+>NZ_CP097650.1_1331
+MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFAS
+LYEDRLAQLYAVDDRLVFGRLDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAG
+AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLGEDGVRADAQGALLAAVTARR
+TGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG
+VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDA
+VAHAVAQRQRLLVEPRRLMIDGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRE
+LAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCWMPLTPEKLIGDLLTREDLLR
+AAAPWLSDAEVGTLLRPADAPWTEADVPLLDEAAELLGRLETPGRGGEFAAQHERNLENA
+RASLENMHQTLADLGVDGVVDAEQLAAANEARGVRRTTAETAAHDRTWTYGHVVVDEAQE
+LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSP
+ARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGDVAALALDAVEVERDRVPEAL
+TAVIAPAGRTGELLTVLRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVSPERI
+VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001195.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001195.fa
new file mode 100644
index 0000000000000000000000000000000000000000..60ddf8755e46ae0ba611f6cb528487e18cc8e4b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001195.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1389
+MTPHTDPATAAAPVLSTADRLDRAESKAEVLVEALPWIRRFAGTVMVVKYGGNAMVSEEL
+RRAFAEDIVFLHHVGVHPVVVHGGGPQINAMLDRLGIASEFRGGLRVTTEEAMDVVRMVL
+TGQVGRELVGLVNSHGPYAVGFSGEDAGLLRARRTGAVVDGQEVDLGLVGEVTGVDPTAI
+LDVIESGRIPVVSSVAPEINDDGEPTGQVLNVNADTAAAALAAALGAAKLVLLTDVEGLY
+ADWPDRDSLISSLTAAQLRALLPSLASGMIPKMAACLAAVDAGVQRAHVVDGRRPHSMLL
+EVFTSAGVGTQVVPDAEPTAPTTPEEDA*
+>NZ_CP033200.1_1131
+MSPHTDPATAAAPVLSTADRLDRAESKAEVLVEALPWIRRFAGTVMVVKYGGNAMVSEEL
+RRAFAEDIVFLHHVGVHPVVVHGGGPQINAMLDRLGIASEFRGGLRVTTEEAMDVVRMVL
+TGQVGRELVGLVNSHGPYAVGFSGEDAGLLRARRTGAVVDGQEVDLGLVGEVTGVDPTAI
+LDVIESGRIPVVSSVAPEINDDGEPTGQVLNVNADTAAAALAAALGAAKLVLLTDVEGLY
+ADWPDRDSLISSLTAAQLRALLPSLASGMIPKMAACLAAVDAGVQRAHVVDGRRPHSMLL
+EVFTSAGVGTQVVPDAEPTAPTTPEEDA*
+>NZ_CP040019.1_1439
+MSQSSSRQPDPVTTAAAPVLSAADRLDRAESKAEVLIEALPWIQRFAGSVMVIKYGGNAM
+VSDELRRAFAEDVVFLHHVGVHPVVVHGGGPQINAMLDRLGIESEFRGGLRVTTEEAMDV
+VRMVLTGQVGRELVGLVNSHGPYAVGFSGEDAGLLRARRTGAVVDGQEVDLGLVGEVTGV
+DPTAILDVVRSGRIPVVSSVAPEIDEHGEPTGQVLNVNADTAAAALASALGAAKLVLLTD
+VEGLYADWPDRESLISSLTAGQLRALLPSLASGMIPKMAACLAAVDAGVQRAHVVDGRRP
+HSMLLEVFTSAGVGTPVVPDADTAGRPAPTTVQEDA*
+>NZ_CP083691.1_1346
+MTGQPAPADPTTPSVPVLSTAQRLERAASKAEVLVEALPWVQRFAGATMVIKYGGNAMVS
+DELRRAFAEDVVFLHHVGVHPVVVHGGGPQINAMLERLGIESEFRGGLRVTTPEAMEVVR
+MVLTGQVGRELVGLINSHGAYAVGSSGEDAGLFRARRTGAVVDGETVDLGLVGEVTAVNP
+EAIRDVIDAGRIPVVSSVAPEIGDDGEPTGEVLNVNADTAAAALAAGLGAAKLVLLTDVE
+GLYADWPDRDSLISSLTASQLRGLLPGLQSGMIPKMAACLHAVDSGVHRAHVVDGRRPHS
+MLLEVFTSDGVGTQVVPDPTPATRPASAPTTATAQEDA*
+>NZ_CP097650.1_1338
+MSPHTDPATAAAPVLSTADRLDRAESKAEVLVEALPWIRRFAGTVMVVKYGGNAMVSEEL
+RRAFAEDIVFLHHVGVHPVVVHGGGPQINAMLDRLGIASEFRGGLRVTTEEAMDVVRMVL
+TGQVGRELVGLVNSHGPYAVGFSGEDAGLLRARRTGAVVDGQEVDLGLVGEVTGVDPTAI
+LDVIESGRIPVVSSVAPEIDDDGQPTGQVLNVNADTAAAALAAALGAAKLVLLTDVEGLY
+ADWPDRDSLISSLTAAQLRALLPSLASGMIPKMAACLAAVDAGVQRAHVVDGRRPHSMLL
+EVFTSAGVGTQVVPDAEPTAPTTPEEDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001199.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001199.fa
new file mode 100644
index 0000000000000000000000000000000000000000..451cd15d9c42e20cf4ba7ce875021858a022cf1d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001199.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1394
+MSTDPYVPGVGTDAATVEHIALDLDVRLAANRVSGTAVLRVRLTKQSRRIELDLYRLRVS
+RVDAVVDGRAVASSFTQPGRAPSRLVVDLDESRPEGTLVELTVVYAGTPTLRRSPWGTIG
+WEELTDGVLVAGQPHGASTWLPCVDSPTSRSTAEITLTCDAGYLPVANGVGAPVRTRGSR
+VTWRWRLHQRVPAYLLSVQIGRYRLVDAAPPAEGLPPLRLVVSPRTEQRALRALAPQPAM
+MATFIDAYGPYPFEDYTAVVADEELEIPLEAASMSLFGTNHLDGSWESERLIAHEMSHQW
+FGNAVTLGRWSDLWLHEGFACWSEWLWAEASGRSSITSMARRAWQKLAAHPVEQALAEPG
+PEEMFEDWVYKRGALTVEALRHLLGTDLFGSMLRAWVREHRFGTVDSLGLRTHVHAWAPH
+AGVSRAQVDELFDAWTLRPELPPFPG*
+>NZ_CP033200.1_1136
+MSTDPYVPGVGTDAATVEHIALDLDVRLAANRVSGTAVLRVRLTKQSRRIELDLYRLRVS
+RVDAVVDGRAVASSFTQPGRAPSRLVVDLDESRPEGTLVELTVVYAGTPTLRRSPWGTIG
+WEELTDGVLVAGQPHGASTWLPCVDSPTSRSTAEITLTCDAGYLPVANGVGAPVRTRGSR
+VTWRWRLDQPVPAYLLSVQIGRYRLVDAAPPAEGLPPLRLVVSPRTEQRALRALAPQPAM
+MATFIDAYGPYPFEDYTAVVADEELEIPLEAASMSLFGTNHLDGSWESERLIAHEMSHQW
+FGNAVTLGRWSDLWLHEGFACWSEWLWAEASGRSSITSMARRAWQKLAAHPVEQALAEPG
+PEEMFEDWVYKRGALTVEALRHLLGTDLFGSMLRAWVREHRFGTVDSLGLRTHVHAWAPH
+AGVSRAQVDELFDAWTLRPELPPFPG*
+>NZ_CP040019.1_1434
+MSTDPYVPGVGTDAAVIEHVVLDLDVRLAANRVSGTAVLSVRLTRQSRRIELDLHRLRVS
+KVGAAVDGRALPASFSQPRRWPSRLVVDLGESRPEGTLVELTVAYAGTPTPRRSPWGTIG
+WEELTDGVLVAGQPHGASTWLPCVDSPVSRSTADITLTCDAGYLPVANGVGAPVRTRGSR
+VTWRWRLTQPVPAYLLTVQIGRYRLVDAAAPADGLPPLRLVASTRTEQRARAALATQPAM
+MAAFIAAYGPYPFEEYTAVVADDVLEIPLEAAGMSLFGTNHLDGSWESERLIAHEMAHQW
+FGNAVTLGRWADLWLHEGFACWSEWLWAEASGRSSIASMARRAWQRLAEDPVEHVLTEPG
+AAEMFEDWVYKRGALTVEALRVLLGREVFGSMLRAWVDEHRFGTVDTAGLRAHVHAWAPR
+AQVTPEQVDELFEAWTRRPELPPFPG*
+>NZ_CP083691.1_1341
+MSTDPYIPGVGSDTATIEHLRVELDVRLASNRVAGVAELHVRLCRQSDTVELDLHRLAVD
+GAAGTHDGRPLKVRATTPRNRPHRVVVHLGASLPEGSLVVLRLSYSGHPRPRRSPWGTIG
+WEELTDGVLVAGQPHGASTWVPCIDSPAVRQTADITVTCDAGYLPVANGRGTRLRSRGSR
+ETWRWVMDRPVPAYLLTLQIGRYRQVTAPGSGTPESAAAGGVPPLRLVVSPRLQARAEAA
+MAGQGRMMEAFTAAYGPYPFDDYAAVVADDVLEIPLEAAGLSLFGVNHLDGSWESERLIA
+HEMAHQWFGNAVTLGRWSDLWLHEGFACYSEWLWAEASGRAALRHEAKQAWHGLKRQGED
+LVLAAPGAADMFDDRVYKRGALTVLAVRTLLGDAVFGEMLRDWVARHRFATVDTPGFRAH
+VLAWAPRADVAPEDVDALFDAWTLRPELPAFPG*
+>NZ_CP097650.1_1343
+MSTDPYVPGVGTDAATVEHIALDLDVRLAANRVSGTAVLRVRLTKQSRRIELDLYRLRVS
+RVDAVVDGRAVASSFTQPGRAPSRLVVDLDESRPEGTLVELTVVYAGTPTLRRSPWGTIG
+WEELTDGVLVAGQPHGASTWLPCVDSPTSRSTAEITLTCDAGYLPVANGVGAPVRTRGSR
+VTWRWRLDQPVPAYLLSVQIGRYRLVDAAPPAEGLPPLRLVVSPRTEQRALRALAPQPAM
+MATFIDAYGPYPFEDYTAVVADEELEIPLEAASMSLFGTNHLDGSWESERLIAHEMSHQW
+FGNAVTLGRWSDLWLHEGFACWSEWLWAEASGRSSITSMARRAWQKLAAHPVEQALAEPG
+PEEMFEDWVYKRGALTVEALRHLLGTDLFGSMLRAWVREHRFGTVDSLGLRTHVHAWAPH
+AGVSRAQVDELFDAWTLRPELPPFPG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001202.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001202.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9cb284d6e35185678f2edd0b4d3e55edaeb383af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001202.fa
@@ -0,0 +1,39 @@
+>NZ_CP042169.1_1397
+MTPSPETGAEPTAPVAEISPVDAEAVEAAVQAALAAYEAAADLDELKAARLAHTGDRAPL
+TLANKAIGALPKERKAEAGKLMGAARGRLGKALAARTEVLEAEQAARILREETVDVTTAV
+RRRRVGARHPLSLTMDRVSEIFVGMGWEIAEGPELESEWFNFDSLNFAPDHPAREMQDTF
+FVDPAEAHLLLRTHTSPVQMRSLLERGAPTYVLCPGRTFRTDELDATHTPVFHQFEGLAV
+DKGLTMAHLRGTLEYFARQMFGAEAAIRLRPNFFPFTEPSAELDIWHPGAKGGPRWIEWG
+GCGMVHPNVLRAAGLDPEEYSGFAFGMGVERTLMFRNEVPDMHDMIEGDVRFSQHFGMEV
+*
+>NZ_CP033200.1_1139
+MTPSPETGAEPTAPVAEISPVDAEAVEAAVQAALAAYEAAADLDELKAARLAHTGDRAPL
+TLANKAIGALPKERKAEAGKLMGAARGRLGKALAARTEVLEAEQAARILREETVDVTTAV
+RRRRVGARHPLSLTMDRVSEIFVGMGWEIAEGPELESEWFNFDSLNFAPDHPAREMQDTF
+FVAPAEAHLLLRTHTSPVQMRSLLERGAPTYVLCPGRTFRTDELDATHTPVFHQFEGLAV
+DKGLTMAHLRGTLEYFARQMFGAEAAIRLRPNFFPFTEPSAELDIWHPGAKGGPRWIEWG
+GCGMVHPNVLRAAGLDPEEYSGFAFGMGVERTLMFRNEVPDMHDMIEGDVRFSQHFGMEV
+*
+>NZ_CP040019.1_1431
+MTPSPETGAEPTAPAAEISPVDAAAVDAAVQAALAAFDAATDLDELKAARLAHTGDRAPL
+TLANKGIGALPKERKAEAGKLMGDARGRLNKALAARTEVLEAEQAERILREETVDVTAAV
+RRRRVGARHPLSLTMDRVSEIFVGMGWEIAEGPELESEWFNFDSLNFAPDHPAREMQDTF
+FVEPSEAHLLLRTHTSPVQMRSLLERGAPTYVLCPGRTFRTDELDATHTPVFHQFEGLAV
+DRGLTMAHLRGTLEYFARQMFGEEAAIRLRPNFFPFTEPSAELDIWHPGAKGGPRWIEWG
+GCGMVHPNVLRAAGLDPEEFSGFAFGMGVERTLMFRNEVPDMRDMIEGDVRFSQHFGMEV
+*
+>NZ_CP083691.1_1338
+MTSSPETGASEDAPQLSPVDGPAVDAAVAEALAAFEAAADLEELKAARLAHQGDRAPLTL
+ANKAIGTLPKEQKAEAGKTMGAARSRIGKALAARTEVLEAEHAARMLAEETVDVTAAAAR
+RLPGARHPLSLLQERVSDIFVGMGWEIAEGPELEHDWFNFNALNFPPDHPAREMQDTFFV
+EPLESNLLLRTHTSPVQVRSMLERGAPVYVLCPGRTFRTDELDATHTPVFHQFEGLAVDR
+GLTMADLRGTLEYFARQMFGPEAEIRLRPNFFPFTEPSAEMDIWHPQAKGGPRWIEWGGC
+GMVHPNVLRSAGIDPEEFSGFAFGMGIERTLMFRNEVPDMRDMIEGDVRFSQHFGMEL*
+>NZ_CP097650.1_1346
+MTPSPETGAEPTAPVAEISPVDAEAVEAAVQAALAAYEAAADLDELKAARLAHTGDRAPL
+TLANKAIGALPKERKAEAGKLMGAARGRLGKALAARTEVLEAERAARILREETVDVTTAV
+RRRRVGARHPLSLTMDRVSEIFVGMGWEIAEGPELESEWFNFDSLNFAPDHPAREMQDTF
+FVAPAEAHLLLRTHTSPVQMRSLLERGAPTYVLCPGRTFRTDELDATHTPVFHQFEGLAV
+DKGLTMAHLRGTLEYFARQMFGAEAAIRLRPNFFPFTEPSAELDIWHPGAKGGPRWIEWG
+GCGMVHPNVLRAAGLDPEEYSGFAFGMGVERTLMFRNEVPDMHDMIEGDVRFSQHFGMEV
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001204.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001204.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f108edf47b5c71a452538850c08760517f8c162f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001204.fa
@@ -0,0 +1,26 @@
+>NZ_CP042169.1_1400
+MFESTRKRVRVRAWRGRRDAPTVVAMTSRAPAPAARVLLTGFEPFGGDVHNPSIAAARDA
+VGILADRGVTAEAVELPCAFGAAGPALTAALDRVRPEVAIAVGLAGGTATVRVERVAVNL
+QDARIPDNAGEQPVDRPVRADGPAALFATLPAKRAVAAIREAGVAAEPSLSAGAFVCNHV
+MYSLLDGPGTARAAGFIHVPWDTEHRPTPDTPALPAADLARAVAEAALTALAGGPDLDVP
+GGTLH*
+>NZ_CP033200.1_1142
+MTSRAPAPAARVLLTGFEPFGGDVHNPSIAAARDAVGILADRGVTAEAVELPCAFGAAGS
+ALTAALDRVRPEVAIAVGLAGGTAAVRVERVAVNLQDARIPDNAGDQPVDRPVRADGPAA
+LFATLPAKRAVAAIRAAGVAAEPSLSAGAFVCNHVMYALLDAPGTARAAGFLHVPWDAEH
+RPTPDTPALPAADLARAVAEAALTALAGGPDLDVPGGTMH*
+>NZ_CP040019.1_1429
+MTTPASASAVRVLLTGFEPFGGDGHNPSIVAARDAVALLAERGVAAEAVELPCAFAAAGP
+ALAAALERTRPEAAVAVGLAGGTAAVRVERIAMNLQDARIPDNAGDQPVDRPVRAEGPAA
+HFATLPVKRAVEAVRAAGVPAEPSLSAGAFVCNHVLYALLDAPGTARAAGFVHVPWDLAH
+RPRPDAPALPAEDLARAVAEVALVALEGGADLDVPGGTLH*
+>NZ_CP083691.1_1332
+MTDPVRVLLTGFEPFGGDDHNPSIEAARAAAAALTADGTPAVAVELPCVFAAAGPALAAA
+LEAHRPEIAVAVGLAGGTAAVRVERVAVNLQDARIPDNAGDRPADRPVRSGGPAAHFATL
+PVKRAVAAVREAGVPAEPSLSAGSFVCNHVMYSLLDAPAPARAAGFVHVPWSREHAPTPQ
+TPALPAADLARAVAAVARAALVEGPDLDVPGGALH*
+>NZ_CP097650.1_1349
+MTSRAPAPAARVLLTGFEPFGGDVHNPSIAAARDAVGILADRGVTAEAVELPCAFGAAGP
+ALTAALDRVRPEVAIAVGLAGGTATVRVERVAVNLQDARIPDNAGEQPVDRPVRADGPAA
+LFATLPAKRAVAAIREAGVAAEPSLSAGAFVCNHVMYALLDAPGTARAAGFIHVPWDTEH
+RPTPDTPALPAADLARAVAEAALTALAGGPDLDVPGGTLH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001206.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001206.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a00fbb883264376c09d450c8a566fe288d9f2f63
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001206.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1402
+MGLALLDDVAAPTRLLAARRSAPAPLRGLWEFPGGKVEPGEGVQEALLRECREELGVAVR
+LGPEVAAPEPDGWELANGARMRVFWGVLAEEGTTPRALQDHDLLAWLPLAGPGVRHLDWI
+PADRPIVAEVLRGAATAFSAGR*
+>NZ_CP033200.1_1144
+MGLALLDDVAAPTRLLAARRSAPAPLRGLWEFPGGKVEPGEGVQEALLRECREELGVAVR
+LGPEVAAPEPDGWELANGARMRVFWGVLAEEGTTPRALQDHDLLAWLPLAGPGVRHLDWI
+PADRPIVAEVLRGAATAFSAGR*
+>NZ_CP040019.1_1427
+MVGLALLDDAAAPSRLLAARRSAPAVLRGLWEFPGGKVETGEGPREALAREVREELGVAV
+RLGAEVPSPDPEGWELANGARMRVLWGVLAEEGAEPAALEDHDLLAWVPLSGAGAHHLDW
+IPADRPIVSAVVAGAATAFAAAP*
+>NZ_CP083691.1_1330
+MSPATPQTPPVPSAPRPVVGVALVDDAARPTALLAARRSAPASLAGLWEFPGGKVEPEEG
+ADAALHRELVEELGVRVRLGTEVAAPEGPGWELANGARMRVWFGVLREDSGAPAALQDHD
+RLEWTPLTAEALHALDWIPADRPIVDALLAAVEAGRLGL*
+>NZ_CP097650.1_1351
+MTSATPARPAPAARPTTSPRDGARPRQVVGLALLDDVAAPTRLLAARRSAPAPLRGLWEF
+PGGKVEPGEGVQEALLRECREELGVAVRLGPEVAAPEPDGWELANGARMRVFWGVLAEEG
+ATPRALQDHDLLAWLPLAGPGVRHLDWIPADRPIVAEVLRGAATAFSAGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001211.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001211.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a27a5fc85bd954913fb1cbe2cefb9853832afb34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001211.fa
@@ -0,0 +1,19 @@
+>NZ_CP042169.1_1409
+MVYGKLTTMTDERQAQDATPMDAPAEIRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSP
+DARELIDLDEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGK
+GPGEKFTGPVN*
+>NZ_CP033200.1_1151
+MDAPAEIRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSPDARELIDLDEARKLITALAG
+LVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGKGPGEKFTGPVN*
+>NZ_CP040019.1_1421
+MTDERQAHDANDQDSPAEVRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSPDARELVDL
+DEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGKGPGEKFTG
+PVN*
+>NZ_CP083691.1_1323
+MTDQNQHQHAAGEDVPTEVREIHEVPAVEVITTTAVHLMTAAAVKVGLADSPDAREMTDL
+DEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGKGPGEKFTG
+PVN*
+>NZ_CP097650.1_1358
+MVYGKLTTMTDERQAQDATPMDAPAEIRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSP
+DARELIDLDEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGK
+GPGEKFTGPVN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001213.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001213.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb8a631077fbb7135d13317b946155831fd9090c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001213.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1411
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS*
+>NZ_CP033200.1_1153
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS*
+>NZ_CP040019.1_1419
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS*
+>NZ_CP083691.1_1321
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRTCEVIDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS*
+>NZ_CP097650.1_1360
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001216.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001216.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b3a218bd4c67f2740528cb3ff08f449f257e8701
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001216.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1414
+MSASAEGGRLRRPRWRDPRLLVGLVLVLASIAGVVALVASAQQTAAYWTAAEDLPPGTPI
+ASGDLRPVEVNLSEAGERYLSADAPAPEGRMVSGTVRAGELLPAAALVDADPDGRRPVGV
+ALDEPLPSGVGVGDRVDVWVAMPAEGGRGHADPARLAEALEISEVAAEQNGFGGSGTTRV
+QLLAPEETLPRIVDAKVKDARVTLVPAHGVR*
+>NZ_CP033200.1_1156
+MSASAEGGRLRRPRWRDPRLLVGLMLVLASIAGVVALVASSQRTAAYWTAAEDLPPGTPI
+AAGDLRPVEVNLSEAGERYLSADAPAPEGRMVSGTVRAGELLPAAALVDADPDGRRPVGV
+ALDEPLPSGVGVGDRVDVWVAMPAEGGRGHADPARLAEALEISEVTAEQSGFGGSGTTRV
+QLLAPEETLPRIVDAKVKDARVTLVPAHGVR*
+>NZ_CP040019.1_1416
+MSTSTSASAEGGRLRRPRWRDPRLLVGLVLVLASVAGVVALVASSQRTSAYWAAAVDLPP
+GTPLEAGQLRAVEVNLADAEGKYVAAAPDSAPSGRMVASTVRAGELLPAAALVDADPEGR
+RPVGVRLREPLAGGVGVGDRVDVWVAMPAEGGRGHADPERLAEALEIAEVATEQGSIGGS
+GETRVQLLAPEATLPRVVDAQVKDARITLVPAHGVR*
+>NZ_CP083691.1_1318
+MTTDPTAPAEGARLRRPRWRDPRLLVGLVLVLASLAGVTAIVAGAQRTQTYWAAARDLAP
+GAPVPADAFVPVDANLADAAGHYLRADAPAPAGKVVGAVVRAGELVPADALADVDPQRRR
+PVGVQLAEPLPAGTSAGDRVDVWVAARQDDGRDYEAPRRIAEGLEISELTEAEGGFGTGA
+TTRLQLMAGEDVLAQLLDAKVSEARITVVPALGEG*
+>NZ_CP097650.1_1363
+MSASAEGGRLRRPRWRDPRLLVGLVLVLASIAGVVALVASAQRTAAYWTAAEDLPPGTPI
+ASGDLRPVEVNLSEAGERYLSADAPAPEGRMVSGTVRAGELLPAAALVDADPDGRRPVGV
+ALDEPLPSGVGVGDRVDVWVAMPAEGGRGHADPARLAEALEISEVTAEQNGFGGSGTTRV
+QLLAPEETLPRIVDAKVKDARVTLVPAHGVR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001218.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001218.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4f0087109f60d1a382e9440ac170f7b84728eab7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001218.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1416
+MRWNGLFDDLEAHWADLGWQETVAEAAELTRAEWMALSLADRLRGARGRQVRLHLAWGEV
+VDGVVHTVGQGWVGVHVDGSGSAIVAVDCVAAVEADLTRAVAAPELAAAGWGTVLRGIAR
+TRQPVAVTGRLGAALAEGTVDRVGGDHLDIARHPRDEARRAAAVRGRLVIPFGALGTVRT
+ALRPA*
+>NZ_CP033200.1_1158
+MRWNGLFDDLEAHWVDLGWQETVAEAAELTRAEWMALSLVDRLRGARGRQVRLHLAWGEV
+VDGVVHTVGQGWVGVHVDGSGSAIVAVDCVAAVEADLTRAALAPELAAAGWGTVLRGIAR
+TRQPVAVTGRLGAALAEGTVDRVGGDHLDIARHPLDEARRAAAVRGRLVIPFGALGTVRT
+ALRPA*
+>NZ_CP040019.1_1414
+MRWDGLFDDLEARWADLGWRQSEAEAAELTRAEWMALTLADRLRGERGRPVRLHLAWGEA
+LDGVLHAVGEDWAGLHLSGGRSAVVPLPGVAAVEAGLHRAVPAPTGPATGLGAVLRGIAR
+ERVPVVVTGTRGVTLVEGTVDRVGRDHLDVSRHPRDEARRAAAVRGRLVVPFTALGVVRT
+ASRLA*
+>NZ_CP083691.1_1316
+MRWDGLFEDLEARWSALEWDATRAEAAELTRGEWAALTLEERLRGARGETVRLHLVWGEH
+RDVRLGTVGDGWVSVNAAAADSLLVPLTSVVAWEGPLGAASTAPEGVRSRPGLPAALRQL
+ARARAAVRVVAGNGVELGEGTIDRVGRDHVDLARHPRDEARRAGQVRGRLVVPLAALGLV
+ATPGPLG*
+>NZ_CP097650.1_1365
+MRWNGLFDDLEAHWADLGWQETVAEAAELTRAEWMALSLADRLRGARGRQVRLHLAWGEV
+VDGVVHTVGQGWVGVHVDGSGSAIVAVDCVAAVEADLTRAALAPELAAAGWGTVLRGIAR
+TRQPVAVTGRLGAALAEGTVDRVGGDHLDIARHPRDEARRAAAVRGRLVIPFGALGTVRT
+ALRPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001229.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001229.fa
new file mode 100644
index 0000000000000000000000000000000000000000..58e178dc28ea3f770d710995a615b9484f28ce15
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001229.fa
@@ -0,0 +1,41 @@
+>NZ_CP042169.1_1428
+MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLRLEEARERIAAAL
+GAHPTEVILTSGGTEADNLAIQGLYRARRAAAPERTRIVLTGIEHHAVLDVVDWLAAHEG
+AEPVLVPVDDDGRVDLAAWGAALATAPERTALATLMWANNEIGTVQPVAEAARLAADHGV
+PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALLVRRDVTLEAVVHGGGQER
+RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP
+ATGQALSPGTRRLPGNVHITVPGRTADALLFSFDMAGLDTSSGSACTAGVAEPSHVVAAL
+PGRTEADARATQRFTLGRTTTPAEAAALIDALRTLLGPGV*
+>NZ_CP033200.1_1170
+MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLHLEEARERIAAAL
+GAHPPEVILTSGGTEADNLAVQGLYRARRAVAPERTRIVLTGIEHHAVLDVVDWLAAHEG
+AEPVLVPVDDDGRVDLAAWGAALAAAPERTALATLMWANNEIGTVQPVAEAARLAADHGI
+PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALFVRRDVTLEAVVHGGGQER
+RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP
+ATGEPLPPGTRRLPGNVHITVPGRTADALLFSFDMAGLDTSSGSACTAGVAEPSHVVAAL
+PGRTEADARATQRFALGRTTTPAEAAALIDALRTLLGPGV*
+>NZ_CP040019.1_1402
+MPSAATPRPLGERVHLDHAATTAVRPSALAALAEAAALPGNPASLHASGRRAKLALEQAR
+EAVAAALGAHPSEVVLTSGGTEADNLAVQGLFRARRAADPQRLRIVLTGAEHHAVLDAVD
+WLAAHEGAEPVIVPVDADGVVDLAAWEAALAAAPERTALAALMWANNEIGTVQPVAEAAR
+IAAAHGVPLHTDAVQAVGAVPVDFAASGAATLAVSGHKAGAPVGVGALLVRRDVALTPVV
+HGGGQERRLRSGTVSVALAAALAAALTEAVAEQPAEAVRLGVLRDRVIEAVEALETVVLT
+GPRDADPATGEPLPPGTRRLPGNVHVTVPGRTADALLFTFDTAGLDTSSGSACTAGVAEP
+SHVVAALPGRTEADARATQRFTLGRTSTSADVDALIAALRALAPAPRRGAPTPKGAPTTK
+EESR*
+>NZ_CP083691.1_1303
+MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLHLEEARERIAAAL
+GAHPTEVILTSGGTEADNLAVQGLYRARRAAAPERTRIVLTGIEHHAVLDVVGWLAAHEG
+AEPVLVPVDDDGRVDLAAWGAALAAAPERTALATLMWANNEIGTVQPVAEAARLAADHGV
+PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALLVRRDVTLEAVVHGGGQER
+RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP
+ATGEPLPPGTRRLPGNVHITVPGRTADALLFFFDMAGLDTSSGSACTAGVAEPSHVVAAL
+PGRTEADARATQRFTLGRTTTPAEAAALIDGLRTLLGPASRLDRPSVVERGVRP*
+>NZ_CP097650.1_1377
+MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLHLEEARERIAAAL
+GAHPSEVILTSGGTEADNLAVQGLYRARRAVAPERTRIVLTGIEHHAVLDVVDWLAAHEG
+AEPVLVPVDDDGRVDLAAWGAALAAAPERTALATLMWANNEIGTVQPVAEAARLAADHGI
+PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALFVRRDVTLEAVVHGGGQER
+RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP
+ATGEPLPPGTRRLPGNVHITVPGRTADALLFSFDMAGLDTSSGSACTAGVAEPSHVVAAL
+PGRTEADARATQRFALGRTTTPAEAAALIDALRTLLGPGV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001239.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001239.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26785b3001c2500a9e4cbcde3306ccad1e443f96
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001239.fa
@@ -0,0 +1,41 @@
+>NZ_CP042169.1_1440
+MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLVLGPNGLGWL
+PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYASQVAIGALVTLV
+LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG
+GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV
+VAMIAAAAHGVVSWITSVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP
+GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA
+WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL
+LAGLSWAVVGIWGAIAVIAIIAAVWLRRTDPGRRTPAQQAVRASSR*
+>NZ_CP033200.1_1182
+MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLALGPNGLGWL
+PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYSSQVAIGALVTLV
+LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG
+GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV
+VAMIAAAAHGVVSWITAVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP
+GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA
+WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL
+LAGLSWAVVGIWGAIAVIAIIAAVWLRRTDPGRRTPAQQAVRASSR*
+>NZ_CP040019.1_1392
+MQEQFTAWSVLVDAGLIGALLAVGTLARAVIKPLQTLMIPASVIAGILGLVLGPNVLGWL
+PFSTQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGSFASYGVLIYASQVAIGALVALL
+VLQPLFSTPDSFAALLFAGWAGGFGSAAAVGQAYAANGDMTVTSLAYTSATVGMIVGVVG
+GIIQAKIGARRGHAKEFAGLTSIPDELRTGVLDQVQERPVIGRHTFSAASVESLAFQVGV
+VAMIAAAAHGVVTWITAVWPNIVGEDGPKLIIPAFAVAFILGLIGRVVFQATKTAKFLDP
+GSLNSVSGTATDILIVCGIASIAPTVVVDYWQPLLVLFVIGLALALFLGLVVAPRVMTDA
+WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL
+IAGLSWAVVGIWGAIAIAAILAAIWLRRTDPGVRSPAQQAVRAASR*
+>NZ_CP083691.1_1290
+MTWFQGVWPSIVGPEGPKLMIPAFAVAFVLGIIGRLLLQVTKTATFLDSASLNSVSGTAT
+DILIVCGIASIAPKVVLDYWQPLLILFVVGLALAVLLGLVVAPHVMTESWFEKQLFTWGW
+ATGAVATGVAMLRIVDPKLKSGTMEQFGVAYITVVPVEIAAVSFVPLLIIAGLSWAVVGI
+WDAIAEAAIIAAVFLVRSDPARKSAVPA*
+>NZ_CP097650.1_1389
+MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLALGPNGLGWL
+PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYSSQVAIGALVTLV
+LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG
+GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV
+VAMIAAAAHGVVSWITAVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP
+GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA
+WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL
+IAGLSWAVVGIWGAIAIIAIIAAVWLRRTDPGRRTPAQQAVRASSR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001254.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001254.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7aa20f0e6fa1fe2a4549db3389082e3d70a4c909
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001254.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1477
+MPPRLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGAAVTPATLGFLVTAVGLPVLGI
+VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGG
+LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALMAAAVVAPMSTGALPSP
+TPAYADGALVRGLLDGYNTMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA
+AMAVVYASLAYVGATSHGAFAQAANGGDVLARSASHFFGAAGVYLIAAIVVVACLKTCIG
+LIVACTEMFAEMFPGSYRLWASLFLVVSFALANLGLEAIIAWSVPVLMFLYPIAVVVILL
+GLAWAWVRDHPAVARWVVACTGLAAFFDLLGALPEALATTPPVTALTGLAGRVLPGYAVG
+FGWVVPALVGLVVGTVAAASRPRPRRGEREAIPVTAGHGRTAAD*
+>NZ_CP033200.1_1197
+MPPRLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGAAVTPATLGFLVTAVGLPVLGI
+VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGG
+LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALVAAAVVAPMSTGALPSP
+TPAYADGALVRGLLDGYATMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA
+AMTVVYASLAYVGATSHGAFAQATNGGDVLARSASHFFGTAGAYLIAAIVFVACLKTCIG
+LIVACAEMFAEMFPGSYRLWAGLFLVVSFALANLGLEAIIAWSVPVLMFLYPIAVVVILL
+GLAWAWVRDRPAVARWVVACTGLAAFFDLLGALPEALVTTPPVTALTGLAGRVLPGYAVG
+FGWVVPALVGLVVGTLAAASRPRSRRGEREAIPVTAGHGRTAAD*
+>NZ_CP040019.1_1377
+MPPHLRPGQTLLLASLVFGLFFGAGNLIFPASLGRDAGAAVTPATLGFLVTAVGLPVLGI
+VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGS
+LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALVAAAVVTPMSTGALPSP
+APAYADGALVRGLLDGYTTMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA
+AMAVVYASLAYIGATSHGAFAQAANGGDVLARTASHFFGTAGAYLIAAIVFVACLKTCIG
+LIVACAEMFAEMFPGSYRLWAGLFLVVSFALANLGLEAIIAWSVPVLMLLYPIAVVVILL
+GLAWAWVRDRPAVARWVVACTGLAAVFDLLGALPEALGTTALVTALTGLAGRVLPGYAVG
+FGWVVPALVGLVVGAVAAASRPRPRRGEREATPIAAGHGRTAAD*
+>NZ_CP083691.1_39
+MSARLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGSAVVPATLGFLLTAVGLPVLGI
+IASALTRSRSVREMTAPISPWFATAFTCLLYLAIGPLFAIPRTATVSYEIGVAPLAGDGP
+WLPVFTLVFFGVAAVAAFRPGRLLDWVGRFLTPVFLLLLGALAVAAVVAPMSSGDLPAPA
+GPYADGALTAGILDGYNTMDALASLAFAVLIVEAAGRLGVDSPRRLAVELGKAGIVGGLG
+MAVVYGALAYIGATSHGALPGAASGGAVLAGTASHYFGPAGTWLIAAIVLAACLKTSIGL
+IVACGEMFAEMFPGSYRVWASVFLLVSLVIANLGLEAIIAWSIPVLMFLYPLAIVIIALG
+LGWGWVRHHLTVARAVVAFTAVAAVFDLLAALPETLAATGPVTALTDLAGRILPWYENGF
+GWVVPALVGLVVGLVLEAARGRGRSAAVADA*
+>NZ_CP097650.1_1404
+MPPRLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGAAVTPATLGFLVTAVGLPVLGI
+VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGG
+LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALVAAAVVAPMSTGALPSP
+TPAYADGALVRGLLDGYATMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA
+AMAVVYASLAYVGATSHGAFAQAANGGDVLARTASHFFGTAGAYLIAAIVFVACLKTCIG
+LIVACAEMFAEMFPGSYRLWASLFLVVSFALANLGLEAIIAWSVPVLMFLYPIAVVVILL
+GLAWAWVRGRPAVARWVVACTGLAASFDLLGALPEALATTPPVTALTGLAGRVLPGYAVG
+FGWVVPALVGLVVGTVAAASRPRPRRGEREAIPVTAGHGRTAAD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001258.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001258.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5111f0b0194f93cc80bdec6873cd287d81f25cd5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001258.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1481
+MTPLRIGTRGSALATTQTSHVAETLTERSGLAHELVVIRTEGDVTTGSLASLGGTGVFAS
+ALRAAVLDGVVDAAVHSLKDLPAAQPETLEIAAVPARADLRDALCARDGLTLATLPEGAR
+VGTGSPRRVAQLKALRPDLELVDIRGNVQTRLARVPGLEQHDDHAPAAAGSPRGDLDAVI
+LACAGLNRLGLDHVITERIDPEVMVPAPGQGALAVEIRAEDESFLGRALLDPEAPVGRLH
+AALELVDDRDTHVAVTAERALLRRLEAGCAAPIGAVARVTDGEAGAPRIEMTAMVAALDG
+SRVLRRTSSVQLDPVPTDVAGDPAAGDEWLEDTLFVAAEALGVHVAEQFVAEGADLLPGT
+VRGVDRGDGAPRPDDPA*
+>NZ_CP033200.1_1202
+MTPLRIGTRGSALATTQTTHVAETLTERSGLAHELVVIRTEGDVTTGSLASLGGTGVFAS
+ALRAAVLDGVVDAAVHSLKDLPAVQPETLEIAAVPARADLRDALCARDGLTLATLPEGAR
+VGTGSPRRVAQLKALRPDLELVDIRGNVQTRLARVPGLEQHDDHAPAAAGSPRGDLDAVI
+LACAGLDRLGLDHVITERIDPEVMVPAPGQGALAVEIRAEDESFLGRALLDPEAPVGRLH
+AALELVDDRDTHVAVTAERALLRRLEAGCAAPIGAVARVTDGEAGAPRIEMTAMVAALDG
+SRVLRRTSSVQLDPVPTDVAGDPAAGDEWLEDTLFVAAEALGVHVAEQFVAEGADLLPGT
+VRGVDRGDGAPRPDDPA*
+>NZ_CP040019.1_1373
+MSTLRIGTRGSALATTQTTHVAQALAERAGLEHELVVIRTEGDVTTGSLASLGGTGVFAS
+ALRAAILDGAVDLAVHSLKDLPAAQPDTLEIAAVPERADLRDALCARDGLTLATLPEGAR
+VGTGSPRRVAQLKALRPDLVLVDIRGNVQTRLARVPGLEQHDDGAPAAAGSPRGDLDAVI
+LACAGLDRLGLDHVITERIDPDVMVPAPGQGALAVEVRAEDESFLGAALLEPDAPVGRLR
+AGLELVDDRATHVAVTAERALLRRLEAGCAAPIGAVARVVDGEAGAPRIEMTAMVAAVDG
+SRVLRRTSSVQLDPVPEDLAADPAAADEWLEDTLFVAAEALGVHVAEQFVAEGADLLPGT
+VRGVDRGDGAPQPDDPA*
+>NZ_CP083691.1_1263
+MSGPGAPAGDGLRVGTRGSALATTQTTHVAEALTDRSGMPHELVVIRTEGDVTTGSLASL
+GGTGVFASALRSAVLDGRVDLAVHSLKDLPAAQPAGLEIAAVPPRADLRDALCARDGLTL
+ATLPEGARVGTGSPRRVAQLRALRPDLELVDIRGNVQTRLARVAGHEVHDDDAPAAAGAP
+RGDLDAVVLACAGLDRLGLQHVITERIDPEVMLPAPGQGALAVEIREEDGPLLGPSAVDP
+DSHAGRLRAALELVDDRDTHVAVTAERALLLRLEAGCAAPIGAVARVEEGTAVDGSPAPR
+IVMSAMVAAVDGSQVLRRTSSVQLDAVPEDVAGDPAEADEWIEDTLFMAAGALGVHLAEL
+FVAEGADLLPGTVRGVAKPDPEA*
+>NZ_CP097650.1_1408
+MTPLRIGTRGSALATTQTSHVAETLTERSGLAHELVVIRTEGDVTTGSLASLGGTGVFAS
+ALRAAVLDGVVDAAVHSLKDLPAAQPETLEIAAVPARADLRDALCARDGLTLATLPEGAR
+VGTGSPRRVAQLKALRPDLELVDIRGNVQTRLARVPGLEQHDDHAPAAAGSPRGDLDAVI
+LACAGLDRLGLDHVITERIDPEVMVPAPGQGALAVEIRAEDESFLGRALLDPEAPVGRMH
+AALELVDDRDTHVAVTAERALLRRLEAGCAAPIGAVARVSDGEAGAPRIEMTAMVAALDG
+SRVLRRTSSVQLDPVPADVAGDPAAADEWLEDTLFVAAEALGVHVAEQFVAEGADLLPGT
+VRGVDRGDGAPRPDDPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001261.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001261.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9bb534a0d401f0e4c4b17e487941be8f955d79fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001261.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1484
+MSGTALVVGGGIAGLVAAHRLSAAGWDVTLAEATSVLGGAVSPRFLDVPSHGETGAPETQ
+TLELDGGAESFAVRGAAVRALVEELGLGEKIVAPEPLGSWLHGPAGPVRAPRLGIVGIPG
+DLDAEDLAAALTPAGLERARQDAEAPMDRWAAALAAGEPVTVAQVVADRLGDEVLDRLVA
+PVVAGVHSADPAVVELERVAPGLLAAAVEHGGLAAGVAALRSTGTPGSLVAGLDGGMVRL
+TGRLVEALREDGATVLRGVRVAALSRVPATGGWWAQISDRDDEVVRGLDVDRVVLAVDGV
+TAWDLLAPLSAEALDPDAGPALGEGIALATLVVEAAGLDDAPRGTGVLVGAGTDVAAKAL
+THVTAKWAWLREVVARPQEDGVARHPHRHVLRLSYGRQGGGPEALGHRSADEELLAQALV
+DTATLTGVPLAEEDVVARTVTRWRRSIPPQAGPDRAKADTLIDWARDVPGLDLVGSWVHG
+TGLAAVVAGVDRTLGADAPPAG*
+>NZ_CP033200.1_1205
+MSGTALVVGGGIAGLVAAHRLSAAGWDVTLAEATSVLGGAVSPRFLDVPSHGETGAPETQ
+TLELDGGAESFAVRGAAVRALVEELGLGEKIVAPEPLGSWLHGPAGPVRAPRLGIVGIPG
+DLDAEDLAAALTPAGLERARQDAEAPMDRWAAALAAGEPVTVAQVVADRLGDEVLDRLVA
+PVVAGVHSADPAVVELERVAPGLLAAAVEHGGLAAGVAALRSTGTPGSLVAGLDGGMVRL
+TGRLVEALREDGATVLRGVRVAALSRVPATGGWWAQISDRDDEVVRGLDVDRVVLAVDGV
+TAWDLLAPLSAEALDPDAGPALGEGIALATLVVEAAGLDDAPRGTGVLVGAGTDVAAKAL
+THATAKWAWLREVVARPQEDGVARHPHRHVLRLSYGRQGGGPEALGHRSADEELLAQALV
+DTATLTGVPLAEEDVVARTVTRWRRSIPPQAGPDRAKADTLIDWARDVPGLDLVGSWVHG
+TGLAAVVAGVDRTLGADAPPAG*
+>NZ_CP040019.1_1370
+MTGTALVVGGGIAGLVAAHRLCAAGWEVTLAEATSVLGGAVSARFLDVPSHGETGAPESQ
+TLELDAGAESFAVRGTAVRALLEELGLGGKVVAPEPLGSWLHGPAGPVPAPRLGLVSIPG
+DLEAEDLAAALSGPGLARAREDAVAPMDRWADALAAGEPVTVAAIVADRLGEEVLKRLVA
+PVVAGVHSADPAVVELERVAPGLLASAVEHGGLAAGVAALRGSSTPGSLVAGVDGGMSRV
+TGRLVDALREAGATVLRGVRVAALSRVPAMGGWWAQISDRDDEVVRGLDVDRVVLAVDGA
+TAWDLLAPLSGGDLDPDAGPALGDGVALTTLVVEAPGLDAAPRGTGMLVGAGTDVAAKAL
+THATAKWAWLREVVARPDHDGVARHPHRHVVRLSYGRSGAEPGGLGHRSTDEELLARAVV
+DAAALTGVPLSEQDVVARAVVRWRPSIPPQAGPDREAADALIAWSRGQAGLDLVGSWVHG
+TGLAAVVASVDRAFDAPPPAG*
+>NZ_CP083691.1_1260
+MSGSALVVGGGIAGLLAARRLNQQGWEVTLAEATSVLGGTLSARFLDVPSVSDSGAVERQ
+TLELDGGAESFAVRGAAVRALVDELGLGDDVVSPEPLGSWLHGPAGAVPAPRVGLVGIPG
+DLDAPDVAAALSPAGLERARRDLTEPMDRWAAARAAGEPVTVAALVADRLGDDVLERLVV
+PVVGGVHSADPAVVDVERVAPGLLAAAVEQGSLARGVAALRGGQTPGAAVAGVDGGMAKV
+TGRLVQTLREDGVTVLRGVRVAALSRLGADGRWWAQISDRDEEVVRGLEADRVVLAVDGV
+AAWELLAPVSGDAVDPDAGPALGEGVALATLVVEAPGMDAAPRGTGLLVAPGTDVRAKAL
+THSTAKWAWLRSVVDRPDESGAPRHPHRHVLRLSYGRHGGAAGDLGFRSADEDLLAAAVA
+DAEALTGVELSADDVLASTVTRWRRPIPPQHGPDREAMDRLIAWAQDVPGLDLVGSWVHG
+TGLAAVVAGVERTVAPAAA*
+>NZ_CP097650.1_1411
+MSGTALVVGGGIAGLVAAHRLSAAGWDVTLAEATSVLGGAVSPRFLDVPSHGETGAPETQ
+TLELDGGAESFAVRGAAVRALVEELGLGEKIVAPEPLGSWLHGPAGPVRAPRLGIVGIPG
+DLDAEDLAAALTPAGLERARQDAEAPMDRWAAALAAGEPVTVAQVVADRLGDEVLDRLVA
+PVVAGVHSADPAVVELERVAPGLLAAAVEHGGLAAGVAALRSTGTPGSLVAGLDGGMVRL
+TGRLVEALREDGATVLRGVRVAALSRVPATGGWWAQISDRDDEVVRGLDVDRVVLAVDGV
+TAWDLLAPLSAEALDPDAGPALGEGIALATLVVEAAGLDDAPRGTGVLVGAGTDVAAKAL
+THATAKWAWLREVVARPQEDGVARHPHRHVLRLSYGRQGGGPEALGHRSADEELLAQALV
+DTATLTGVPLAEEDVVARTVTRWRRSIPPQAGPDRAKADTLIDWARDVPGLDLVGSWVHG
+TGLAAVVAGVDRTLGADAPPAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001263.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001263.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4d7934dfe0995e83685fc440d0514238177f3ddf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001263.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1486
+MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEADAAGV
+EAARAGLLSAVAASTSLPDEDVHAAFRTLDADATARHLFEVGAGLDSAVVGEREIAGQVR
+RALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRGLTDA
+AAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWALALG
+GEAVAGAVAEADVIIGSSGGERQISPERLQELRKGGRRPLTVVDLALSRDFDPAVADLPD
+VDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTLGVLD
+RELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEAVFGI
+EAPGRPAPAVGTVEAVCPAHEDEGGAARIA*
+>NZ_CP033200.1_1207
+MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEADAAGV
+EAARAGLLSAVAASTSLPDEDVHTAFRTLDADATARHLFEVGAGLDSAVVGEREIAGQVR
+RALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRGLTDA
+AAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWALALG
+GEAVAGAVAEADVIIGSSGGERQISPERLQELRKGGRRPLTVVDLALSRDFDPAVADLPD
+VDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTLGVLD
+RELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEAVFGI
+EAPGRPAPAVGTVEAACPAHEDDGGAARIA*
+>NZ_CP040019.1_1368
+MADVVTVFSLVASHQHLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEAD
+ESGVEAAREGLVAAVAAHSSLPDEAVRSAFRVLDSEATARHLFEVGAGLDSAVVGEREIA
+GQVRRALSMARESGTASGSLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLTEELRG
+LADDDAKAAFWADASVLLIGTGAYAGTTLAQLAERGATAVAVHSASGRAEQFVEDRGGWA
+LALGGGAVAGAVAEADVIIGSSGGERQISPERLQELREDVDRPLTVVDLALSRDFDPAVG
+DLPDVDLITLESVRLAAPEQARAAVAEARVLVDGAVAEYRAAQRGRSADASIKALRRHTL
+AALDREMERVRARHGCTAAAEEVEFALRRMVNQLLHEPIVRAKRLAAEGRLDRYEDGLEA
+VFGIEPPGSTSSPAERPDAGCPAHEDEAGTARIA*
+>NZ_CP083691.1_1258
+MDVAVTVFSLVASHKDLSLDTVARLSAGSAGVGSALASSTDDGAVVLATCNRVEVYADAR
+DADAARERIVAAIAEQSGLPEDAVRSAFRVLDDDASARHLFEVGAGLDSAVVGEREIAGQ
+VRRALVDARDAGTATGSLTRLFESATRTAKDVGSHTALGATGRSVVSVALDLAEELRGLT
+DAMARRTFWQEANVLLIGTGAYAGTTLAQLADRGAQAVGVHSASGRAAQFVADRGGWALA
+LGGADVAGAVAEADVIIGSSGGDRQISPERMAGLRRGAERPVTVVDLALSRDFDPAVGEL
+EGVDLITLESVRLAAPEQAQAAVAEARGLVETALEEYTSARRGRTADAAIKALRGHTMAA
+LDREMERVRARHGCTAAADEVQFALRRMVNQLLHTPSVRARELAAQGRLDEFEHALEVLF
+DIPVPGTRPADAPGDACPATEADDARRTA*
+>NZ_CP097650.1_1413
+MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAIVLATCNRVEIYAEADGAGV
+EAARTGLLSAVAASTSLPDEDVHTAFRTLDADATARHLFEVGAGLDSAVVGEREIAGQVR
+RALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRGLTDA
+AAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWALALG
+GEAVAGAVAEADVIIGSSGGERQISPERLQELREGGRRPLTVVDLALSRDFDPAVADLPD
+VDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTLGVLD
+RELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEAVFGI
+EAPGRPAPAVGTVEAACPAHEDDGGAARIA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001266.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001266.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b585ff09b2f1361bc584888dc6eaf32985a7d7b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001266.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1489
+MTPHALGLRGPADPTLLERLAALRTELELPPAFPAPVLAEAEAAAREVHAGLTGSPDHAD
+RTALPFVTVDPAGSTDLDQALLLTPADDDGILVRYAIADVPAFVTPGGAVDGEARRRGQT
+VYLPDGRVPLHPEVLSEDAASLLPDREHPAFVWTFLLDAAGAVVETGLERARIRSRAQLT
+YGQVQAFLDAQPGAQAPTTPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAAR
+GGASLNLPDQEVRVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTM
+PAPDTDAVAAFRERTRALGAPWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTA
+FDAQAEDPALRTPPDEPAQAALAAPYAHATAPLRRLVDRFVLALCHAHAIGAPAPAWVRS
+ALPALPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDPA
+VSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWPHSSR*
+>NZ_CP033200.1_1210
+MSSHALGLRGPADPALLERLAALRTELELPSAFPTPVLAEAEAAAHGVHVGLAGSPDHAD
+RTALPFVTVDPAGATDLDQALLLTPSDDDGILVRYAIADVPAFVAPGGAVDAEARRRGQT
+VYLPDGRVPLHPEVLSEDAASLLPDRERPAFVWTFLLDAAGAVVETGLERARVRSRAQLT
+YGQVQAFLDARPGAQAPATPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAAR
+GGASLNLPDQEVLVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTM
+PAPDADAVAAFRERTRALGVPWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTA
+FDAQAEDPALRTPPAEPAQAALAAPYAHATAPLRRLVDRFVLALCHAHASGAPAPAWVRS
+ALPELPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDPA
+VSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWSHSSR*
+>NZ_CP040019.1_1365
+MPHRAVALRGRPDPALIERLAALRTELELPAGFPPEVLEEADAAARDVLAALASDPAYAD
+RTDVPFVTVDPAGSTDLDQALYLEAADGDAITVRYAIADVPAFVAPGGAVDVEARRRGQT
+VYLPDGRVPLHPEALSEDAASLLPDRERPAFVWTFVLDAAGAVVDTSLERARIRSRAQLT
+YAQVQAFLDALPDAKAPAAPRPGLDEADHAAHRGWDAPLRDSLALLPEVGRRRAAQEAAR
+GGASLNLPDQEVHVAEDGRHCLVQRAPLPAEDHNAQLSLMTGMAAARLMLEAGVGILRTM
+PAPDAEAVAAFRSRTRALGAPWEEGQDYGAYLRTLDPADPGHLAVLHEATSLFRGAGYTA
+FDAHAEDPELRTPPSEPEQAALAAPYAHATAPLRRLVDRFVLALCHAHATGAPAPEWARA
+ALPEVPALMTESSRRTSAADRAATDLVEAAALQDHVCAELEGIAVRRVKGGAEVWLLDPA
+VTLRVPGEAEPGTRVRVRIEGVDRASGEVTASGVDWPHSSR*
+>NZ_CP083691.1_1255
+MPHHALEVRGGPDAALAARLRALRAELDVPGEFPADVLTEAERAAAEVPGRVAADPDRAD
+LTAVPFVTVDPAGSTDLDQALHLQAGPGRDELTVRYAIADVPGFVAPEGAVDAEARRRGQ
+TVYLPDGRVPLHPEVLSEDAASLLPEVERPTFVWTFVLDAEGAVASTDLVRARIRSRAQL
+AYPQVQALLDDDAAPEAADWPAEVRASLALLPEVGARRTAQEAARGGASLSMPDQEISVV
+DGAYTLVQRVPLAAEDHNAQLSLMTGMAAARIMLEAGVGILRTMPAPDPDAVDAFRARTR
+ALGLPWGEELDYGAYLRTVDPTDPRGLAVMHAATTLFRGAGYTAFDRGSVDPALRALPED
+PEQAALAAPYAHTTAPLRRLVDRFVLVLCHAHVAGEPVPDWVRRALPDLPALMAESGRRA
+SAADRAATDLVEAALLAARVGSVLEGTAVRTSEKGTDVQLTDPAVSLRVPGRAEPGTVVR
+VRVDAVDVAAGKVTASGVDWPHSAR*
+>NZ_CP097650.1_1416
+MSSHALGLRGPADPALLERLAALRTELELPSAFPTPVLAEAEAAAHGVHVGLAGSPDHAD
+RTALPFVTVDPAGATDLDQALLLTPSDDDGILVRYAIADVPAFVAPGGAVDAEARRRGQT
+VYLPDGRVPLHPEVLSEDAASLLPDRERPAFVWTFLLDAAGAVVETGLERARIRSRAQLT
+YGQVQAFLDAQPGAQAPTTPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAAR
+GGASLNLPDQEVRVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTM
+PAPDTDAVAAFRERTRALGAPWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTA
+FDAQAEDPALRTPPDEPAQAALAAPYAHATAPLRRLVDRFVLALCHAHAIGAPAPAWVRS
+ALPALPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDPA
+VSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWPHSSR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001274.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001274.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec5830a8aa8e9cd394b039d7a4b40464029049c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001274.fa
@@ -0,0 +1,23 @@
+>NZ_CP042169.1_1498
+MFGINGSEFIILAVLAIVILGPEKLPEYTRAFTDWLRVMRDKAEGAKAQFKEETGTDFDE
+VDWRKYDPRQYDPRRIIRDALREPAGGSSTPASRAAQATGISAEDVHGGLTRQDLTDMDP
+RTLFRRPAGAGSTAAAESGAAAAQTRSTEPAAGAAAVGGAAAALMASGRAEALTEERPAA
+VETEPDPLELLGLAPAPFDVDAT*
+>NZ_CP033200.1_1219
+MFGINGSEFIILAVLAIVILGPEKLPEYTRAFTDWLRVMRDKAEGAKAQFKEETGTDFDE
+VDWRKYDPRQYDPRRIIRDALREPAGGSSTPASRAAQATGISAEDVHGGLTRQDLTDMDP
+RTLFRRPAGAGSTAAAESGAAAQTRSTEPAAGAAAVGGAAAALMASGRAEALTEERPAAV
+ETEPDPLELLGLAPAPFDVDAT*
+>NZ_CP040019.1_1356
+MHGGLTRQDLVDMDPRSLFRRPAGAGSSAAPAASSGSAAPAAGASLATGAAVGGAAAALM
+ASGRAEEAVAEERPAVEPDPLELLGLAPAPYDVDAT*
+>NZ_CP083691.1_1246
+MFGINGSELIVLIVLAFVVLGPEKLPEYTRALAQGIRKTRDMAEGAKTQFKEETGTDFDS
+VDWRRYDPRQYDPRRIIRDALREPADGSTAAARAQELTGVAAEDLQGGLSAQDLRDMDPR
+SLFRRPSGDGSTAAPAGGGASAPSDAPTPEDVPSAAVPVAAASPSPAGAAAAGVAAALLA
+SGRAEEVLTDPAPLQHLGTDPDPLDLLGKAPAPFDVDAT*
+>NZ_CP097650.1_1425
+MFGINGGEFIILAVLAIVILGPEKLPEYTRAFTDWLRVMRDKAEGAKAQFKEETGTDFDE
+VDWRKYDPRQYDPRRIIRDALREPAGGSSTPASRAAQATGVSAEDVHGGLTRQDLADMDP
+RTLFRRPAGAGSTAAAESGAAAQTRSTAPAAGAAAVGGAAAALMASGRAEALAEERPAAV
+ETAPDPLELLGLAPAPFDVDAT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001280.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001280.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e40115c25052801dd0d60fd00b91ee7228d1ff57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001280.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1505
+MLRTKLLTLSAVTAAAALSLTACAPSSSQGGGGDAAGSSSAGESTSSGSGESLRIGIKFD
+QPGLGYREGSAQPTGFDTDVARYVADKLGVAEQDIEWVQTPSANRENALENGEVDMIFAT
+YSITDARKERVAFAGPYFVAGQDLLVRADDTAITGPESLDGKNLCSVTGSTSAQKIKDQF
+ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAAADANKGKFKVVGNTFTTERYG
+VGLPKDSERCEDINEAIKEMKDSGEWEKALESNTEGTGYTYDETLNSGEDAEFEPCA*
+>NZ_CP033200.1_1226
+MLRTKLLTLSAVTAAAALSLTACAPSSSQGGGGDAAGSSSAGESTSSGSGERLRIGIKFD
+QPGLGYREGSAQPTGFDTDVARYVADKLGVAEKDIEWVQTPSANRENALENGEVDMIFAT
+YSITDARKERVDFAGPYFVAGQDLLVRADDTAITGPESLEGKNLCSVTGSTSAQKIKDQF
+ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAAADANKGKFKVVGNTFTTERYG
+VGLPKDSERCEDINEAIKEMKDSGEWEKALESNTEGTGYTYDETLNSGEDAEFEPCA*
+>NZ_CP040019.1_1349
+MFRKKLLTLSAVTAAAALSLTACSPSAQQGGGEGSGSASAGGSQSAGSGEGLRIGIKFDQ
+PGLGFREGSGAPTGFDTDVARYVADKLGVAEGDIEWVQTPSANRENALENGEVDMIFATY
+SITDARKERVDFAGPYFVAGQDLLVRADDTEITGPDALDGKNLCSVTGSTSAQKIKDQFA
+SGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAATDANKGKFKVVGNTFTTERYGV
+GIAKGDDRCEDINDAIKEMKDSGAWKESLDANTEGTGYEYDEALNSGADAEFESCS*
+>NZ_CP083691.1_1239
+MARSRILSVAAVAAAAALSLSACSPSSSGGSGSASSASGSTAAQSGSSDTLRIGIKYDQP
+GLGFREGQNAPTGFDTDVARYVAGKLGVAEDKIEWVQTPSANRENALENGEVDMIFATYS
+ITDARKQRVDFAGPYFVAGQDLLVRQDDTSITGPDSLNGKNLCSVTGSTSAQKIKDNYAS
+GVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAATDANKGKFKVVGQPFTTERYGVG
+LQKGSDKCKDINEAIKAMKDSGEWEKSLKANTEGTGYEYSEDKNSGADAEFEPCA*
+>NZ_CP097650.1_1432
+MLRTKLLTLSAVTAAAALSLTACAPSSSQGGGGDAAGSSSAGESTSSGSGESLRIGIKFD
+QPGLGYREGSAQPTGFDTDVARYVADKLGVAEQDIEWVQTPSANRENALENGEVDMIFAT
+YSITDARKERVAFAGPYFVAGQDLLVRADDTAITGPESLDGKNLCSVTGSTSAQKIKDQF
+ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAAADANKGKFKVVGNTFTTERYG
+VGLPKDSERCEDINEAIKEMKDSGEWKKALESNTEGTGYTYDETLNSGEDAEFEPCA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001282.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001282.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ead97e4253b9b2996c9a8f4a03e9e844fcc085f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001282.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1507
+MSAQASVLFDAPGPIARRRILLANLVSLAAVLVVAVLVLIQMNATGQLSGRRWLAAVDGN
+AWRNYYLPGLQFTLQSAGIAVVSSVVFGLVFGFLRLAPVGPVRWLAAVVVEFFRAVPVLV
+MMVFFYQLFAQVARSGAIQPQDGPYYAVIAALTLYNGSVIAELVRSGVRSLPRGQREAAA
+AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGNG
+NILQSLVVAAMIFIVINFLLTWAATRLSRRLSSRTAGDASAPTTPRVGAPTDTAG*
+>NZ_CP033200.1_1228
+MSAQASVLFDAPGPIARRRILLANLVSLAAVLVVAVLVLIQMNATGQLSGRRWLAAVDGN
+AWRNYYLPGLQFTLQSAGIAVVSSVVFGLVFGFLRLAPVGPVRWLAAVVVEFFRAVPVLV
+MMVFFYQLFAQVARSGAIQPQDGPYYAVIAALTLYNGSVIAELVRSGVRSLPRGQREAAA
+AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLHYARQLGSGNG
+NILQSLVVAAMIFIVINFLLTWAATRLSRRLSSRTAGDASAPTTPRVGAPTDTAG*
+>NZ_CP040019.1_1347
+MSSQASVLFDAPGPLARRRILIANLVALAAVLALAVAVLMRMADADQLEARRWTAALDAN
+AWTNYYLPGLQFTVQAAAIAVLTSVVFGLVLGFLRLAPFAPVRGAAGLVVEFFRAVPVLI
+MMVFFYQVFAQVARTGVIAPADGPYYAVIVALTLYNGSVIAELVRSGVRSLPKGQREAAA
+AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGQG
+NILQSLVVAALIFIVINFLLTWVATRLSRRLSSRTAGDAGAPTTPVVGAPTDKPA*
+>NZ_CP083691.1_1237
+MSAQASVLFDAPGPATRRRILIVNLVALALVLAVAVVVGMALQDRGQLEPRRWLAALDAN
+AWTNYYLPGLQFTLQSAGIAVVTSVVFGLVFGFLRLAPVAPVRWLAAVVVEFLRAVPVLV
+MMVFFYQAFALAARGGAINAADSPYYAVIVGLTLYNGSVIAELVRSGVTGLPKGQREAAA
+AIGMTPNQSLRLVEVPQALVAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGQG
+NILQTLVVAAVIFILINMLLTWLATLLSRRLSSRTSGRTKPHAGSTAVTIGKD*
+>NZ_CP097650.1_1434
+MSAQASVLFDAPGPIARRRILLANLVSLAAVLVVAVLVLIQMNATGQLSGRRWLAAVDGN
+AWRNYYLPGLQFTLQSAGIAVVSSVVFGLVFGFLRLAPVGPVRWLAAVVVEFFRAVPVLV
+MMVFFYQLFAQVARSGAIQPQDGPYYAVIAALTLYNGSVIAELVRSGVRSLPRGQREAAA
+AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGNG
+NILQSLVVAAMIFIVINFLLTWAATRLSRRLSSRTAGDASAPTTPRVGAPTDTAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001286.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001286.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d04cf7bc053d5ce500f192b8f49c4824c4f57cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001286.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1512
+MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPALIRRALTEAADAHGYPTTHG
+TDDLRRAVVDWYARRRGVSGLDPAAVVPTVGSKEFIAWLPTLLGLGAGDVVVHPEAAYPT
+YAVGALLAGAEAVAADDLDALAPEVRERVRLVWTNSPANPTGAVLDAAALRRTVDAARDV
+GAVVCGDECYAELGWDAWDGAVVPCILSDEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA
+GDPQLVATLINTRKHAGMIVPAPVQHAMAVALADDAHVAEQKDRYRRRRDALRTALEASG
+HTVDHSEAGLYLWTRRADLDPADATAQDSWDLLGELADLGIIAGPGVFYGAGGDGYVRVA
+ITATDEAVARAAARLTARGPRTG*
+>NZ_CP033200.1_1233
+MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPALIRRALTEAADAHGYPTTHG
+TDALRRAVVDWYARRRGVSGLDPAAVVPTVGSKEFIAWLPTLLGLGAGDVVVHPEAAYPT
+YAVGALLAGAEAVAADGLDALAPEVRERVRLVWTNSPANPTGAVLDAAALRRTVDAARGV
+GAVVCGDECYAELGWDAWDGAVVPCILSDEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA
+GDPELVATLVNTRKHAGMIVPAPVQHAMAVALADDAHVAEQKDRYRRRRDALRTALEASG
+HTVDHSEAGLYLWTRRADLDPADATAQDSWDLLGDLADLGIIAGPGVFYGAGGDGYVRVA
+ITATDEAVARAAARLTARGPRTG*
+>NZ_CP040019.1_1343
+MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPELIRRALTEAADAHGYPTTHG
+TADLRRAVVDWYARRRGVAGLDPEAVVPTVGSKEFIAWLPTLMGLGAGDVVVHPEAAYPT
+YAMGALIAGAEAVAADDLASLAPEVRERVRLVWTNSPANPTGAVLDAAALKRVVDDARAL
+GAVVCGDECYAELGWDEWDGELVPCILSEEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA
+GDPGLVATLVNTRKHAGMIVPAPVQHAMAVALADEGHVAQQKDRYRRRRDALRAALEASG
+HAVDHSEAGLYLWTRRADTDPAAATEQDSWDLLGELADLGIIAGPGVFYGAGGHGYVRVA
+ITASDEAVEQAARRLAARGPLRR*
+>NZ_CP083691.1_1233
+MLTLPDYPWDTLAPYRERAAAHPEGTVDLSIGTPVDPTPALIRDALTAAADAHGYPTTHG
+TAELRQAVVDWFARRRGVPGLDPEAVLPTVGSKELIAWLPTLLGLGAGDVVVFPATAYPT
+YAIGAQIAGAEAVAADTLAELDDDVRSRVRLVWTNSPANPTGAVLDAAELRAIVDDARAL
+GAVVCGDECYAELGWDEWEDRVVPCILAPEVSGGDLTGLLSVYSLSKQSNLAGYRAAFVG
+GDPELIAPLTNTRKHAGMIVPGPVQHAMAVALRDDAHVAAQRDLYRERRAALKAALESAG
+YAVDHSEAGLYLWTRRADLAPGQGTAQDSWDLLGELAELGIVAGPGVFYGAAGHGHVRVA
+ITASDEAVAAGAARLTARGPLPR*
+>NZ_CP097650.1_1439
+MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPALIRRALTEAADAHGYPTTHG
+TDALRRAVVDWYARRRGVSGLDPAAVVPTVGSKEFIAWLPTLLGLGAGDVVVHPEAAYPT
+YAVGALLAGAEAVAADDLDALAPEVRERVRLVWTNSPANPTGAVLDAAALRRTVDAARGV
+GAVVCGDECYAELGWDAWDGAVVPCILSDEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA
+GDPELVATLVNTRKHAGMIVPAPVQHAMAVALADDAHVAEQKDRYRRRRDALRTALEASG
+HTVDHSEAGLYLWTRRADLDPADATAQDSWDLLGDLADLGIIAGPGVFYGGDGYVRVAIT
+ATDEAVARAAARLTARGPRTG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001289.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001289.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c570e188fd1f7cccb6d4670f833a28b30b908e05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001289.fa
@@ -0,0 +1,60 @@
+>NZ_CP042169.1_1516
+MSANDKKGRSMFGKKKENDVTDGGQGSHAASSADLEARGAAVPGSSGAGGVPPGPATSAM
+GVVARHDDLGGEPVLAFRDVDVKFATEFGEVHAVKGVTFDVKPGEVVALVGESGSGKSVT
+SATAMGLLPGNADVTGSVKLAGREVLTMTPGQLRGIRGDEVAMVFQEPMTALNPVLTVGD
+QLTEALELHGIAYGTEADKRAVELLTMVGIPDAATRLKQYPHQFSGGQRQRIVIAMAISC
+SPKVIIADEPTTALDVTVQAEILELLRSLKNKMNTGILLITHNMGVVADMADRVCVMLHG
+ELVEQGSVHQVLQHARHPYTQKLLSAVPRLGEPLEVAEPEPVTATQTQARYAIEAENLHL
+EYDHRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKSVLGLLTIAEGSLRIQGHDL
+ATMPKAEQRALRKNIGVVFQDPAASLDPRFPIGDIITEPMVVHKVGDRRSRLARAEELLD
+AVRLPRSVVNRYPHELSGGQRQRISIARALTLDPQVLIADEPTSALDVSVQAAVLDMFAE
+LQQRYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTEEVLHRPKEEYTRRLLAAAP
+VPDPDQQAERRQERREFLASLGEGVY*
+>NZ_CP033200.1_1237
+MSANDKKGRSMFGKKNQNDVTAGGQGSHAASSADLEARGAAVPGSSGAGGVPPGPATSAM
+GVVARHDDLGGEPVLAFRDVDVKFATEFGEVHAVKGVTFDVKPGEVVALVGESGSGKSVT
+SATAMGLLPGNADITGSVQLAGREVLTMTPGQLRDIRGDEVAMVFQEPMTALNPVLTVGD
+QLTEALELHGIAYGTEADKRAVELLTMVGIPDAATRLKQYPHQFSGGQRQRIVIAMAISC
+SPKVIIADEPTTALDVTVQAEILELLRSLKNKMNTGILLITHNMGVVADMADRVCVMLHG
+ELVEQGSVHQVLQHARHPYTQKLLSAVPRLGEPLEVAEPEPVTATQTQARYAIEAENLHL
+EYDHRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKSVLGLLTIAEGSLRIQGHDL
+ATMPKAEQRALRKNIGVVFQDPAASLDPRFPIGDIITEPMVVHKVGDRRSRLARAEELLD
+AVRLPRSVVNRYPHELSGGQRQRISIARALTLDPQVLIADEPTSALDVSVQAAVLDMFAE
+LQQRYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTEEVLHRPKEEYTRRLLAAAP
+VPDPDQQAERRQERREFLASLGEGVY*
+>NZ_CP040019.1_1339
+MTAHGNDKEGRPMSGKKNQHDAAGTEATAVGTGAGEHGSHSADLDARGAAVPGSSGTGGP
+TPGPATSSMGVVARHDDLDGKPVLAFRDVDVKFGTEFGEVHAVKGVTFDVKPGEVVALVG
+ESGSGKSVTSATAMGLLPSNADITGSVQLAGREVLDMTPGQLRGIRGDEVAMVFQEPMTA
+LNPVLTVGDQLTEALELHGIAYGTEADKRAVELLTMVGIPDAAERLKQYPHQFSGGQRQR
+IVIAMAISCSPKVIIADEPTTALDVTVQAEILELLRSLKNKMNTGILLITHNMGVVADMA
+DRVCVMLHGELVEQGTVHQVLQHAQHPYTQKLLSSVPRLGATYEVAEPEPVTATQTTAKY
+AIEAEDLHLEYDYRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKSVLGLLTIAEG
+SLRIQGHDLAAMPKSEQRKLRKNIGVVFQDPAASLDPRFPIGDVITEPMVVHKVGDRRSR
+LARAEELLDAVRLPRSVVNRYPHELSGGQRQRVSIARALTLDPQVLIADEPTSALDVSVQ
+AAVLDMFAELQQRYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTKEVLHNPREEY
+TRRLLAAAPVPDPDQQAERRQERRDFLASLGEGVY*
+>NZ_CP083691.1_1229
+MSSKAFDPKDSGTTETSAEDLRARAETLPGSSGEAPQGVVTTATGSLKVPGPATTTMGVV
+EHHDDLGGEPVLAFQDVAVRFATEFGSVHAVKGVTFDVKPGEVVALVGESGSGKSVTSST
+AMGLLPPSADITGSVKLGGREVLTMTDSQLRSIRGQDVAMVFQEPMTALNPVLTVGDQLT
+EALQLHGLAFGTEATKRAVELLTMVGIPDAADRLKQYPHQFSGGQRQRIVIAMAISCSPR
+VIIADEPTTALDVTVQAEILELLRSLKDKMNTGILLITHNMGVVADMADRVCVMLHGELV
+ESGTVQQVLQRPQHPYTQRLLAAVPRLGEALETAEPEPVTSTQTAVKYAIEAEDLCIEYD
+HRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKAVLGLLPVASGALRLQGEDLATM
+KAAEQRALRRKIGVVFQDPAASLDPRFPIGDVITEPMVIHGVGDRRSRLARAEELLDAVR
+LPRDVVNRYPHELSGGQRQRVSIARALTLDPEVLIADEPTSALDVSVQAAVLEMFAELQT
+RYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTGRVLHHPQAEYTQRLLAAAPVPD
+PDQQAERRRERRRLLASFGESAY*
+>NZ_CP097650.1_1443
+MSANDKKGRSMFGKKNENDVTADGQGSHAASSADLEARGAAVPGSSGAGGVPPGPATSAM
+GVVARHDDLGGEPVLAFRDVDVKFATEFGEVHAVKGVTFDVKPGEVVALVGESGSGKSVT
+SATAMGLLPGNADVTGSVQLAGRDVLTMTPGQLRDIRGDEVAMVFQEPMTALNPVLTVGD
+QLTEALELHGIAYGTEADKRAVELLTMVGIPDAATRLKQYPHQFSGGQRQRIVIAMAISC
+SPKVIIADEPTTALDVTVQAEILELLRSLKNKMNTGILLITHNMGVVADMADRVCVMLHG
+ELVEQGSVHQVLQHARHPYTQKLLSAVPRLGEPLEVAEPEPVTATQTQARYAIEAENLHL
+EYDHRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKSVLGLLTIAEGSLRIQGHDL
+ATMPKAEQRALRKNIGVVFQDPAASLDPRFPIGDIITEPMVVHKVGDRRSRLARAEELLD
+AVRLPRSVVNRYPHELSGGQRQRISIARALTLDPQVLIADEPTSALDVSVQAAVLDMFAE
+LQQRYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTEEVLHRPKEEYTRRLLAAAP
+VPDPDQQAERRQERREFLASLGEGVY*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001293.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001293.fa
new file mode 100644
index 0000000000000000000000000000000000000000..950c79ef745a3c85f32723a3a6d5542b1f765180
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001293.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1521
+MDPFWTALALTTFAGLATVLGGVLAIVGREPSGRGLGAALGLAAGVMLAVSFLEMLPAAV
+EGLGGAVGPAATAVAVAALILGAGSYVLLERAVPDPVSEMPGDVDDPAGLDRRRMLRLGT
+VTALAIGLHNLPEGFVTFAGTLQDPSVGLALAVAMAVHNVPEGVAVAVPVRQATGSRRKA
+FAWAAFTGIAEPLGALIGWLLLAPFLTPALLAAVFAAVAGVMVTVSLDALLPAARAAGGR
+AAALGGVLLGVAAMALSLDLLS*
+>NZ_CP033200.1_1242
+MDPFWTALALTTFAGLATVLGGVLAIVGREPSGRGLGAALGLSAGVMLAVSFLEMLPAAV
+EGLGGAVGPAATAVAVAALALGAGAYVLLERAVPDPVSEMPGDVDDPAGLDRRRMLRLGT
+VTALAIGLHNLPEGFVTFAGTLQDPSVGLALAVAMAVHNVPEGVAVAVPVRQATGSRCKA
+FAWAAFTGIAEPLGALIGWLLLAPFLTPALVAAVFAAVAGVMVTVSLDALLPAARAAGGR
+GAALGGVLLGVAAMALSLDLLA*
+>NZ_CP040019.1_1332
+MDPLWIALALTAFAGLATVLGGVLAVVGKEPSGRGLGAALGLAAGVMIAVSFLEMLPVAV
+EGLAGAVGGAATALAVGALAVGTAGYVLLERAVPVPAAGVPDDVDGPDGLSRLRLMRLGM
+VTALAIGLHNVPEGFVTFAGALQDPSVGVALAVAMAVHNVPEGIAVAVPVRRATGSRRKA
+FAWTAFTGLAEPVGALVGWLLLAPFLTPALVAVVFAAVTGVMITVSLDALLPAARAAGGR
+AATLAGVLLGVAAMAISLDLLG*
+>NZ_CP083691.1_1224
+MEPFWTAVALTSLAGAATIVGGALGALGRPVSDRALAAALGLAAGVMLTVGAVEMGPAAA
+RGLATAVGDGPGVLAAGAAVGGGALAYLLIDRLLPEAATPSGSSASAAREARVGRLGVAT
+ALAIGAHNLPEGFVTFAGALEDSAVGLALAVAMAVHNVPEGIAVSVPVRRATGSARTGFL
+WAATAGILEPAGALLGYWLLRPLLTDAVLGGVYGAVTGVMAALSLAALLPGAVRCGGVPT
+ALAGAAAGAAAMLGSLSLLA*
+>NZ_CP097650.1_1448
+MDPFWTALALTTFAGLATVLGGVLAIVGREPSGRGLGAALGLAAGVMLAVSFLEMLPASV
+EGLGGAVGPAATAVAVAALTLGAGSYVLLERAVPDPVSEMPGDVDDPAGLDRRRMLRLGT
+VTALAIGLHNLPEGFVTFAGTLQDPSVGLALAVAMAVHNVPEGVAVAVPVRQATGSRRKA
+FAWAAFTGIAEPLGALIGWLLLAPFLTPALLAAVFAAVAGVMVTVSLDALLPAARAAGGR
+AAALGGVLLGVAAMALSLDLLS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001296.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001296.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2464ea5d1e3b046252bfbd8624a3651c46425803
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001296.fa
@@ -0,0 +1,34 @@
+>NZ_CP042169.1_1524
+MTEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNAVNYLSRD
+PARARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATFRANPARL
+VLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG
+IPLTAAEDAGFEKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRWRRYNATR
+ERLFEMERQGRAYLFAPETMPIANGERSVAKLAAAHELGLDQVRREMPAIRAFLGLPASR
+*
+>NZ_CP033200.1_1245
+MTEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNAVNYLSRD
+PARARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATFRANPARL
+VLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG
+IPLTAAEDAGFEKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRWRRYNATR
+ERLFEMERQGRAYLFVPATMPISNGERSVAKLAAAHELGLDQVRREMPAIRAFLGLPASR
+*
+>NZ_CP040019.1_1329
+MRTPMTSNVTDTALLFEGGGMRASLTSAVVAELLRERIHVDFVAGISAGSSNSVNYLARD
+PERARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATFQANPARL
+VLVGFDAVTGQTRWWDRSDMGTLADLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG
+IPVTAAEEAGFEKLFVVMTRERSYVKRPERFPAFYQRTFRRYPAVAEALISRWRRYNETR
+ERLFEMERQGRAYLFVPESMPVSNGERSVAKLAAAHELGLAQVRREMPAIREFLGL*
+>NZ_CP083691.1_1221
+MAEQQDHTAEALTSNVTDTALLFEGGGMRASHTSAVVAELLRAGVHVDFVAGISAGSSNA
+VNYLARDPLRARQAFVDFADDPRFGNWRTFLRGKGMFNAEYIYEHAGLPEADLPYDFAAY
+RANPARLALAGFDAVTGETRWWGREDMTTLQDLMVRVRASSTMPILMPPVHLEDTVYVDG
+ALGVDGGIPVTAAEEAGLAKLLVVMTRERSYVKRPERFPAFYQRAFRRYPAVAEALVTRW
+QRYNATRERLFEMEREGTAYLFVPEVMPVSNGERSVAKLAAAHELGLAQARREMPAIKEF
+LGL*
+>NZ_CP097650.1_1451
+MTEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNAVNYLSRD
+PARARRSFVDFADDPRFGNWLSFLRGKGLFNAEYIYEHAGLPEADLPYDFAAFRANPARL
+VLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG
+IPLTAAEDAGFKKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRWRRYNATR
+ERLFEMERQGRAYLFAPETMPIANGERSVAKLAAAHELGLDQVRREMPAIRAFLGLPASR
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001298.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001298.fa
new file mode 100644
index 0000000000000000000000000000000000000000..39e16f03812ecccc26c304121a1e9aa17cd04105
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001298.fa
@@ -0,0 +1,19 @@
+>NZ_CP042169.1_1526
+MKLTDDLLQKFNDQITLEFEASMVYRQLAIAADDLDLSGMAAWLRHQADEEIVHANKFID
+HVADRDSFPTIGAIPAPPVQAGLSALEIFRAALAHEQKVSEAIRELYRATESAGDLNSRP
+LLNWFLDEQIEEEATVSEIVGQLELVGDDGSGLLRIDGRLGSRPVETTENDA*
+>NZ_CP033200.1_1247
+MKLTDDLLQKFNDQITLEFEASMVYRQLAIAADDLDLSGMAAWLRHQADEEIVHANKFID
+HVADRDSFPTIGAIPAPPVQAGLSALEIFRAALAHEQKVSEAIRELYRATESAGDLNSRP
+LLNWFLDEQIEEEATVSEIVGQLELVGDDGSGLLRIDGRLGSRPVETTENDA*
+>NZ_CP040019.1_1327
+MTGVTAADGLDLSGMAAWLRHQADEEIVHANKFIDHVTDRGSDAAGDLSSRPLLNWFLEE
+QIEGEATPPL*
+>NZ_CP083691.1_1219
+MSIDKDLTRKFNEQITLEFEASMVYRQLAIAADMQDLSGMAAWLRHQADEEIVHANKFID
+HVVDREASAVIGAIPAPDVPEHITPVQIFEAALAHERKVSEAIRELYRAAEAAGDLSSRP
+LLNWFLEEQIEEEATVGEIVGQLKLVGEDGSGLLRIDSALGARPVETTENAG*
+>NZ_CP097650.1_1453
+MKLTDDLLQKFNDQITLEFEASMVYRQLAIAADDLDLSGMASWLRHQADEEIVHANKFID
+HVADRDSFPTIGAIPAPPVQAGLSALEIFRAALAHEQKVSEAIRELYRATESAGDLNSRP
+LLNWFLDEQIEEEATVSEIVGQLELVGDDGSGLLRIDGRLGSRPVETTENDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001299.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001299.fa
new file mode 100644
index 0000000000000000000000000000000000000000..36fadf0a38717ad6f4282d78628afefc961c557d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001299.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1527
+MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL
+PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG
+HADDEEPAVERGPEAEDTVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL
+ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV
+GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTETATSAVWGLLWGSVALGVV
+LLVGRLRGNKAAPAH*
+>NZ_CP033200.1_1248
+MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL
+PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG
+HADDEEPAVERGPEAEETVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL
+ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV
+GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTDTATSAVWGLLWGSVALGVV
+LLVGRLRGKKAAPAH*
+>NZ_CP040019.1_1326
+MSGLVALLDDVAALARLAAASVDDVAAGAAKASAKAAGVVVDDAAVTPQYMAGAAANREL
+PMIWRITKGSLRNKLLIILPALLLLDWLAPWVLPWLLLAGGTYLAYEGAHKVWGKLTGHS
+PERDEPAVEKGPEAEDKVVRGAITTDFILSAEIMVISMNEVADVDFWLKAVILVVVAILI
+TAVVYGAVALIVKMDDVGLHMTQNGRTAGGRRFGAGLVKAMPHVLTAITVIGTVAMLWVG
+GHIVLVELAALGVPWPYDVQHGIVHAVEAAGGFVAWLVETLTSALWGLIWGSLALGVVLV
+VNRLRGKKDTLAH*
+>NZ_CP083691.1_1218
+MSGLVALLDDVAALARLAAASVDDVAAGAAKASAKAAGVVVDDAAVTPQYMEGAAAQREL
+PMILRIVRGSLRNKLVFILPGLLLLDWLAPWALPWLLLAGGTYLSFEGAEKVWHKLTGHH
+EPQEDTPAVEQGPEAEDKVVRGAITTDFILSLEIMVISMNEVSDQGFWMKAAILAIVAVV
+ITVAVYGAVALIVKMDDVGLHMHENAHTSGARRFGLGLVKAMPVVMGVISVIGTVAMLWV
+GGHIVLMELATLGLPWLYELQHTIVHAVEGAGSVIAWLVETLTSAIWGLVWGSLVVAVVG
+LVRRLRT*
+>NZ_CP097650.1_1454
+MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL
+PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG
+HADDEEPAVERGPEAEDTVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL
+ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV
+GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTDTATSAVWGLLWGSVALGVV
+LLVGRLRGKKAAPAH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001302.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001302.fa
new file mode 100644
index 0000000000000000000000000000000000000000..088f85499e3c1cdaf5991dd2b0d772e6ff51ec89
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001302.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1530
+MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA
+PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR
+ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL
+EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL
+FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVAEPART
+ALERMLAVAPKQSAAQSAGAGT*
+>NZ_CP033200.1_1251
+MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA
+PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR
+ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL
+EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL
+FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVADPART
+ALERMLAVAPKQSAAQSAGAGT*
+>NZ_CP040019.1_1322
+MTATPETTASVARTLTLVARDPARGSACSSDLTTGPWAFDAGLPAYGPGASQDDAIPADA
+PVQGRIPEEYQQASDEELHARIAAAKAALGDRAVVLGHFYQRDEVVRHADFVGDSFQLAR
+ASQGRPEAEAIVFCGVHFMAETADLLSTPEQAVILPNLAAGCSMADMADLDSVQDAWEQL
+EEVYGTEPDADGRVPLLPVTYMNCSAALKGFVGERGGIVCTSSNASAVLEWAFERAQRVL
+FFPDQHLGRNTGRAMGIELERMPMWNPRLPLGGNTEETLRDARVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVRVIVHPECPLPVVEAADESGSTDHIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPDAVADPARA
+ALERMLAVAPRQSVAQGAGA*
+>NZ_CP083691.1_1214
+MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA
+PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR
+ASQGRPAAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL
+EAVYGTEPDDDGRMPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL
+FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALREAKVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPVSVADPART
+ALERMLAVAPKQSAAQSAAQSAGAGT*
+>NZ_CP097650.1_1457
+MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA
+PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR
+ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL
+EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL
+FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVADPART
+ALERMLAVAPKQSAAQSAGAGT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001303.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001303.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b87a7495ca19a4b33f8701bd40ff729a58291f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001303.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1531
+MTPADRAPATPAPQPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREPGVLSG
+TNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI
+ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRFSLSDAVMLKDNH
+LAALGFGSAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVDTIMLDNFS
+PAELRAGVERVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVQSLDLGLDAVVE
+EVSPRR*
+>NZ_CP033200.1_1252
+MTPADRAPTTPAPRPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREAGVLSG
+TNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI
+ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRFSLSDAVMLKDNH
+LAALGFGGAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVDTIMLDNFS
+PAELRAGVELVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVQSLDLGLDAVVE
+EGSPRR*
+>NZ_CP040019.1_1321
+MSAGTRGAWGPTPAPIADVERIVAAALAEDAPWGDVSSEAFVPADARITARVVAREAGVL
+SGTAALEAAFRLVDPATEVTLHLPDGTALAPGAVVAAVAGPARSVLRAERVALNLAQRMS
+GIATATAAHVAAVRAGGGHTRVADTRKTTPGLRVLERQAVRDGGGHNHRHGLSDAVMLKD
+NHLAALGFGGEDAPGEELTRALRAGKARLPHTVHVEVEVDRLDQLPAVLAAGVGTVMLDN
+FSLADLRAGVELVAGRAVVEASGGVSLETIGEIAATGVDVVSVGALTHSVRALDLGLDAV
+VDAADAPAPGRR*
+>NZ_CP083691.1_1213
+MTPADRAPATPAPQPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREAGVLSG
+TNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI
+ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRSSLSDAVMLKDNH
+LAALGFGGAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVGTIMLDNFS
+PAELRAGVELVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVRSLDLGLDAVVE
+EVSPRR*
+>NZ_CP097650.1_1458
+MTPADRAPTTPAPRPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREAGVLSG
+PNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI
+ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRFSLSDAVMLKDNH
+LAALGFGGAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVDTIMLDNFS
+PAELRAGVELVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVQSLDLGLDAVVE
+EGSPRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001306.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001306.fa
new file mode 100644
index 0000000000000000000000000000000000000000..93bc232f1ae65a5d63da033043b6b65c469256d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001306.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1542
+MAEPRPGDVRVTPGPGAPRGLVIPAGELVERFSHASGPGGQGVNTADSRVQLSLDLAATS
+ALDDVQRARVLARLAPRLAGTVLTVSVAEHRAQRRNRVAARERLAALLREALAPPTPRRA
+TKPTRGSRRRRLEAKHRRSEVKRTRRRPGLD*
+>NZ_CP033200.1_1265
+MAEPRPGDVRVTPGPGAPRGLVIPAGELVERFSHASGPGGQGVNTADSRVQLSLDLAATS
+ALDDVQRARVLARLAPRLAGTVLTVSVAEHRAQRRNRVAARERLAALLREALAPPTPRRA
+TKPTRGSRRRRLEAKHRRSEVKRTRRRPGLD*
+>NZ_CP040019.1_1278
+MADLRVEPGPGAPRGLVIPAAELMERFSHASGPGGQGVNTADSRVQLSLDLATTTALDES
+QRARALAVLGPRLAGTVLTVAAEEHRAQRRNRVAARERLAAMLREALIPETPRRATRPTR
+GSRRRRLEAKRQRSETKQLRRRPGV*
+>NZ_CP083691.1_1196
+MDDLRVPPGPGVPRGLRIPAAELSERFSHGSGPGGQGVNTADSRVQLSLDLAATTALTDA
+QRIRLLEGLAPRLAGTVLTVDAAEHRAQRRNRTAARERLAALLREALVPETPRRATKPTR
+GSQRRRLQAKARRSEVKQSRRRPRMD*
+>NZ_CP097650.1_1469
+MAEPRPGDVRVTPGPGAPRGLIIPAGELVERFSHASGPGGQGVNTADSRVQLSLDLAATS
+ALDDVQRARVLARLAPRLAGTVLTVSVAEHRAQWRNRVAARERLAALLREALAPPTPRRA
+TTPTRGSRRRRLEAKRRRSEVKRTRRRPGLD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001307.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001307.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb6d2c1c604d5b33eb2155d4e343becb37002b25
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001307.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_1545
+MALHLQRYREIAHVMARNGLMATAVQAGLSRWLPLEEGEPHLGIDAEARPELFVRTFEEL
+GVTFVKLGQLISARPDVFPEAYCAAFARLTDSTSAVPFEAVARTVEEDLGADVDTLFAWF
+DRAPLATASIGQAHRARLHDGRAVVVKVRKPGVVEQVQADLEILRTLAATWSRASRTFAD
+LDVPAMVDEFDRSLRAELDYVVEARACEEIAAGFRDTPGVRFPWIEWDLTTSRVLTMQEL
+SGLRVDDLAGLDAAGIDREELAYRAADVLLAMVFEHGVFHADPHPGNLFIEPDGTVGFID
+FGSVGRISPSLRRRFAGLAMALARQDTDGLVRALLDIAPPRGPVDRRRLRLEVARIVGRL
+EGRELEDIRVAQLISEIFALVRRHRLSLPPELVQLLRMLIIVDGIGRRLHPGFDYTRVLD
+PFALRLVGEHLDPRRVAGRIGRATIAAAELGIDLPEYARKVMERIDDGGIDVTVRASELE
+PLVTRLERTGDRVVAAMVVAAMITGGTNVLVAYKDRLGRFAGPVVAAGGAALTGGSAYLA
+WISRPRRRPR*
+>NZ_CP033200.1_1268
+MALHLQRYREIAHVMARNGLRATAVQAGLSRWLPLEEGEPHLGIDAEARPELFVRTFEEL
+GVTFVKLGQLISARPDLFPEAYCAAFARLTDSTTAVPFEAVARTVEEDLGADVDTLFAWF
+DRAPLATASIGQAHRARLHDGRAVVVKVRKPGVVEQAQADLEILRTLAATWSRASRTFAD
+LDVPAMVDEFDRSLRAELDYVVEARACEEIAAGFRDTPGVRFPWIEWDLTTSRVLTMQEL
+SGLRVDDLAGLDAAGIDREELAYRAADVLLAMVFEHGVFHADPHPGNLFIEPDGTVGFID
+FGSVGRISPSLRRRFAGLAMALARQDTDGLVRALLDIAPPRGPVDRRRLRLEVARIVGRL
+EGRELEDIRVAQLVSEIFALVRRHRLSLPPELVQLLRMLIIVDGIGRRLHPGFDYTRVLD
+PFALRLVGEHLDPRRVAGRIGRATIAAAELGIDLPEYARKVMERIDDGGIDVTVRASELE
+PLVTRLERTGDRVVAAMVVAAMITGGTNVLVAYKDRLGRFAGPVVAAGGAALTGGSAYLA
+WISRPRRRPR*
+>NZ_CP040019.1_1305
+MPSRLHRSREIALILGRNGLQATALAAGLGRWLPAADARTARDAVLRPDMLVDVFEQLGT
+TFVKLGQLISARPDMFPESICTAFARLTDDTTPVPFEAMAATVLEDFGASVDELYAWFDP
+VPLATASIGQAHRARLHDGRDVVVKIRKPGVVEQVRTDLEILRTVASRLSRASRALQDMD
+VVSLVDEFDRALRAELDYLVEARACEQIAENLRDVPGVRVPWVDWATTSSRVLTMEEITG
+FRVDDLASLDAAGIDRADLAYRAAEVLMGMVFEDGLFHADPHPGNVFIEADGGIGFIDFG
+SVGRISSGMRRRFARMAMALVRQDPDGLVRALVAIAPPRGDLDRRALRLEVSRITGRLEG
+RDLADIRVDQLVGQIFGIVRRHRLALPPELVQLFRMLIIVDGLGKRLHPGFDYTRVLNPF
+AVRVAGEELDPRRVAGRIGQAGLAAAELGLDLPEYARKVIDHLEDGGLDVTLRTGELEPL
+VARMERTGDRVVAALVVAAMITGGTNVLVAYKDRLGRFAGPVVAAGGAALTGGSAYLAWT
+GRPRRMRRRPRG*
+>NZ_CP083691.1_1192
+MALHLQRYREIAHVMARNGLDATARLAGLGRWLAPQDPTARRPLDAEARPELLVRTFEEL
+GTTFVKLGQLISTRPDLFPESYCTAFARLTDRATPVPYAAIARTVEEDFGAPVDELFAEF
+DRTPLATASVGQVHGAVLHDGRDVVVKVRKPGVVEAVTADLEILRTLTGRLVRASRTLAD
+MDVAGMVDQFDRSLRAELDFVVEARACEEIAAGFTGTPGVRFPWIAWELTSARVLTMERM
+AGMRVDDLPALEAAGIDREELAYRAADVLMRMVFQHGVFHADPHAGNVFIEPDGTIGFID
+FGSVGRIGPGVRERISGLAMALARQDVDGLVRALLEIAPPRGPVDRRRLRSEVGRIVARV
+DGRDLQDIKVPQLVSEVFAIVRRHRLSLPPELVQVFRMVLIVDGLGRRLDPGFDYTRVLD
+PFVRRMVMDQLDPRRLARRLRRATITTADIGLELPQYLRTLMERIEDGGIDVNVRTSELE
+PLVARVERTGDRVVAALVVAAMITGGTNVLVAYKDRLGPFAGPLVAAGGAALTSGSAYLA
+WISRPRRAPRR*
+>NZ_CP097650.1_1472
+MALHLQRYREIAHVMARNGLMATAVQAGLSRWLPLEEGEPHLGIDAEARPELFVRTFEEL
+GVTFVKLGQLISARPDVFPEAYCAAFARLTDSTSAVPFEAVARTVEEDLGADVDTLFAWF
+DRAPLATASIGQAHRARLHDGRAVVVKVRKPGVVEQVQADLEILRTLAATWSRASRTFAD
+LDVPAMVDEFDRSLRAELDYVVEARACEEIAAGFRDTPGVRFPWIEWDLTTSRVLTMQEL
+SGLRVDDLAGLDAAGIDREELAYRAADVLLAMVFEHGVFHADPHPGNLFIEPDGTVGFID
+FGSVGRISPSLRRRFAGLAMALARQDTDGLVRALLDIAPPRGPVDRRRLRLEVARIVGRL
+EGRELEDIRVAQLISEIFALVRRHRLSLPPELVQLLRMLIIVDGIGRRLHPGFDYTRVLD
+PFALRLVGEHLDPRRVAGRIGRATIAAAELGIDLPEYARKVMERIDDGGIDVTVRASELE
+PLVTRLERTGDRVVAAMVVAAMITGGTNVLVAYKDRLGRFAGPVVAAGGAALTGGSAYLA
+WISRPRRRPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001308.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001308.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71b4eb70675d7d3f22a843a300975803ec9a8abb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001308.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1546
+MHPSVSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAF
+CEHRMLETPPEKSRIVSTRADDGAPAWQILRHPAAERLEETIPAFRRVPNLFEILSYDYW
+RLNHGYELPPDACRRRDEYLATEAGRAHVRAVVTAKLRASGRSAEEAAAMSEAELIGASA
+AFFGGTHDVVIARRHFVDGAVDDHQLASSGTLTPDEHHAFMALTADAMRDLYATTPAVRY
+VSVFQNWLKPAGASFDHLHKQLVAIDEVGAQNVAALDRLREDPQVFNQAALDVAVAHDLM
+IAANEHAVMFAGFGHRYPTVEVYSTSPVGQPWRQTAAELRAVSDLLHAAHAATGPDVPSN
+EEWHTRPPGVADPMPWRVMLKWRVSTLAGFEGATKINVNTLSPWDVRDRVLARLRELWAA
+GALADGMRIGADARVRPGMLRYAD*
+>NZ_CP033200.1_1269
+MHPSVSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAF
+CEHRMLETPPEKSRIVSMRADDGAPAWQILRHPAAERLEETTPAFRRVPNLFEILSYDYW
+RLNHGYELPPDARRRRDEYLATEAGRAHVRAVVAAKLRASGRSAEEAAAMSEAELIGASA
+AFFGGTHDVVIARRHFVDGAVDDHQLASSGTLTPDEHHAFLALTADAMRDLYATTPAVRY
+VSVFQNWLKPAGASFDHLHKQLVAIDEVGAQNVAALDRLREDPQVFNHAALDVAVAHDLM
+IAANEHAVMFAGFGHRYPTVEVYSTSPVGQPWRQTAAELRAVSDLLHAAHAATGPDVPSN
+EEWHTRPPGVASPMPWRVMLKWRVSTLAGFEGATKINVNTISPWDVRDRVLARLRELRAA
+GALADGMRIGADARVRPGALRYADGAARLTPPRGR*
+>NZ_CP040019.1_1279
+MPRTRPPAQDFLAELPDGTVKQRNPFSGTEVWTVPGRGHRPLGIARPAAQPLDPDDDGRH
+CAFCSARLLETPPEKSRVVRTEDGEHAILRDVPAEALFDTVPEFRRVPNLFEILSYEYWR
+LNHGFVPAPGVADRRAAYLATETGRAHVLAVVGNKLRAAGRSAEEVEAMPEEERIEAASG
+FFGGGHDVIIARRHFADGAQDDHALAGSGTLSPEEHRRFIALTVDSMRDLYAANPHARYV
+SVFQNWLKPAGASFDHLHKQLVAIDEVGVQNEAAIARVRRNPDAFAQDALGYAAKQGLMI
+ARNEHAAMFAGFGHRYPTVEIHSLSPTCEPWEQTDAERDAMADLIHAAHAATGADVPSNE
+EWHTRPTGVAEPLPWRVCLKWRVSTLAGFEGATKIYLNTVSPGSVRERVATRLQELQAAG
+AIADGIRIDDDGHGAV*
+>NZ_CP083691.1_1191
+MSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAFCEHR
+MLETPPEKARIVPTRADDDAPAWQILRHPAAERLGETTPAFRRVPNLFEILSYDYWRLNH
+GYELPPDARRRRDEYLATEAGRAHVRAVVAAKLRASGRSAEEAAAMSEAELIAASAAFFG
+GTHDVVIARRHFVDGAVDDHQLASSGTLTLDEHHAFLALTADAMRDLYATTPAVRYVSVF
+QNWLKPAGASFDHLHKQLVAIDEVGAQNAAALDRLREDPQVFNHAALDVAVAHDLVIAAN
+EHAVMFAGFGHRYPTVEVYSTSPVGQPWRQSAAELRAVSDLLHAAHAATGPDVPSNEEWH
+TRPPGFASPMPWRVMLKWRVSTLAGFEGATKINVNTLSPWDVRDRVLARLRELRAAGALA
+DGMRIGADARVRPGALRYAD*
+>NZ_CP097650.1_1473
+MHPSVSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAF
+CEHRMLETPPEKSRIVSMRADDGAPAWQILRHPAAERLEETTPAFRRVPNLFEILSYDYW
+RLNHGYELPPDARRRRDEYLATEAGRAHVRAVVAAKLRASGRSTEEAAAMSEAELIAASA
+AFFGGTHDVVIARRHFVDDAVDDHQLASSGTLTPDEHHAFLALTADAMRDLYATTPAVRY
+VSVFQNWLKPAGASFDHLHKQLVAIDEIGAQNAAALDRLREDPQVFNHAALDVAVAHDLV
+IAENEHAVMFAGFGHRYPTVEVYSTSPVGEPWRQDPAELRGMSDLLHAAHAATGPDVPSN
+EEWHTRPPGVADPMPWRVMLKWRVSTLAGFEGATKINVNTLSPWDVRDRVLARLRELRAA
+GALADGMRIGADARVRPGMLRYAD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001311.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001311.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5896410a2ee101a613c4f9862bc66cf0b9ad0fa2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001311.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1550
+METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGTNPEQLFAAGYAACFHS
+ALQMVARASRADITDSSVGARVGIGRQGEGFGLEVTLEVVLPNVPADQARALMEQAHQVC
+PYSNATRGNIDVVLELGEA*
+>NZ_CP033200.1_1273
+METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGTNPEQLFAAGYAACFHS
+ALQMVARASRADITDSSVGARVGIGRQGEGFGLEVTLEVVIPNVPADQARALMEQAHQVC
+PYSNATRGNIDVVLELGEA*
+>NZ_CP040019.1_1272
+METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGANPEQLFAAGYAACFHS
+ALQMVARASRADITDSSVGARVGIGRQGEGFGLEVTLEVVLPHVPADQARALMEQAHQVC
+PYSNATRGNIDVVLELGEA*
+>NZ_CP083691.1_1180
+METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGSNPEQLFAAGYAACFHS
+ALQMVARASRADITDSSVGARVGIGRQGEGFGLEVTLEVVLPHVPADQARALMEQAHQVC
+PYSNATRGNIDVVLELGEA*
+>NZ_CP097650.1_1477
+METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGTNPEQLFAAGYAACFHS
+ALQMVARASRADITDSSVGVRVGIGRQGEGFGLEVTLEVVLPNVPADQARALMEQAHQVC
+PYSNATRGNIDVVLELGEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001312.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001312.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c16ca6669dc45308eeeba658010ad9b55ac2d027
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001312.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1551
+MDAAPTPSLALEDQLCFALHRAARAVTRGYGPLLSRLGLTYPQYLVMLTLWQAEGDASAE
+TEASTPDAGALGVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDEG
+RALRASARTVPVDALTRIPLDTTERQVLMDLLNRITEAAGPR*
+>NZ_CP033200.1_1274
+MDAAPTPSLALEDQLCFALHRAARAVTRGYGPLLSRLGLTYPQYLVMLTLWQAESDASAE
+TEASTSDAAGALGVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDE
+GRALRASARTVPVDALTRIPLDTTERQVLMDLLNRITEAAGPR*
+>NZ_CP040019.1_1271
+MDAAPTPSLALEDQLCFALHRATRAVTRGYGPLLSRIGLTYPQYLVMLTLWQVEGDASAE
+TEAPTPGAGALAVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDEG
+RALRASARTVPADALTRIPLDATERQVLMCLLNRITEAVGPR*
+>NZ_CP083691.1_1179
+MDAAPTPSLALEDQLCFALHRATRAVTRGYGPLLSRLGLTYPQYLVMLTLWQVEGDASAE
+TDAPTPGAGALAVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDEG
+RALRESARTVPADALTRIPLDATERQVLMGLLNRITEAAGPR*
+>NZ_CP097650.1_1478
+MDAAPTPSLALEDQLCFALHRAARAVTRGYGPLLSRLGLTYPQYLVMLTLWQVESDASAE
+TEASTSDAAGALGVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDE
+GRALRASARTVPVDALTRIPLDTTERQVLMDLLNRITEAAGPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001322.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001322.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5bea49f1939522c5aea7f2b3ffa5802d0bf0ea75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001322.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1580
+MSTPTPTGPTPTPPGGELLPLISLAVEHVFNTLGRQPVFAPTILAVTADGQRGMWEHPDL
+QPEQAAATVAKISPRPTRAVAVFDGEIETADGPRPAVAVEAFDAAALASTRMVFPYLPGV
+AAAGIAARVDGDPQVVANGPNPLFG*
+>NZ_CP033200.1_1296
+MSTPTPTGPTPTPPGGELLPLISLAVEHVFDTLGRQPVFAPTILAVAADGQRGMWEHPDL
+EPEQAAATVAKISPRPTRAVAVFDGEIETADGPRPAVAVEAFDAAALASTRMVFPYLPGV
+AAAGIAARVDGDPQVVANGPNPLFG*
+>NZ_CP040019.1_1245
+MEHVFDTLGRRPVFHPTILAVTADGQRGMWEHPDLEPEQAAAEVAKISPRPARAVAVFEG
+EAATEDGPRPAVAVEAFDAAALASVRLVFTYLPGVPGAGIAAQVDGDPQVVANGPNPLFG
+*
+>NZ_CP083691.1_1152
+MTPPTHEILPLVSLAVDHVFDTLTRQAVFDPTILAVTADGARGMWTLPDLAPEQAAAEVG
+RIQPLPQRAVAVFDGEVQTPQGPRPAVAVEAFDAGAVQSVRLVFEYVPGIPGTEITGRIE
+GEPHIVANGHNPLFGQIS*
+>NZ_CP097650.1_1509
+MSTPTPTGPTPTPPGGELLPLISLAVEHVFDTLGRQSVFAPTILAVTADGQRGMWEHPDL
+EPEQAAATVAKISPRPTRAVAVFDGEIETADGPRPAVAVEAFDAAALASTRMVFPYLPGV
+AAAGIAARVDGDPQVVANGPNPLFG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001327.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001327.fa
new file mode 100644
index 0000000000000000000000000000000000000000..62d0e991053f5dc29c6a824de5a5a32eb7fc6e61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001327.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1585
+MDQPVTEGASAASDVPVSAPARAGETSAERPWPLRRLSENLKAHIERAPATWIEGQLIEF
+KNNRGNVYMTMRDLEEEVSLPLTAWRNVAMTLDGTVQQGSRVVARVKPNFWLKAGRLSMN
+VQEMRPVGLGDLLARVELLRRALAEEGLTSPARKRPLPLLPRRIGLITGRDSDAKKDVLR
+NTLLRWPAAEFEIREVAVQGAEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS
+DEALVRAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQEAAGLADA
+RLRLAAAVERRVRAEAEGLAALRSRPVLARPHVMVDTRQEETDRWRERGRSALGHRLVRE
+EDALTQLRARVRALSPQRTLDRGYAVVQHAGQVVRDADQVAPDDRLDILVAAGRIAADVV
+ATHRTTPTPSHERTRQA*
+>NZ_CP033200.1_1301
+MDQPVTEGASAASDVPVSAPARAGETSAERPWPLRRLSENLKAHIERAPATWIEGQLIEF
+KNNRGNVYMTMRDLEEEVSLPLTAWRNVATTLDGTVQQGSRVVARVKPNFWLKAGRLSMN
+VQEMRPVGLGDLLARVELLRRALAEEGLTSPARKRPLPLLPHRIGLITGRDSDAKKDVLR
+NTLLRWPAAEFETREVAVQGAEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS
+DEALVRAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQEAAGLADA
+RLRLAAAVERRVRAEAEGLAALRSRPVLARPHVMVDIRQEETDRWRERGRSALGHRLVRE
+EDALTQLRARVRALSPQRTLDRGYAVVQHAGQVVRDADQVAPDDRLDILVAVGRIAADVV
+ATHRPTPTPSHERTRQA*
+>NZ_CP040019.1_1239
+MDPSSTAHVEADALLDAGVPATASQTSAERPWPLRRLSENLKLHIERAPATWIEGQLIEY
+KTNRGNVYMTMRDLEEEYSLPVTAWRNVAVTFEGTVQQGSRVVARVKPNFWTKAGRLSMV
+VQEMRPVGLGDLLARVELLRRRLGEEGLLDPARKRPLPLLPGLVGLITGRDSDAKKDVLR
+NAQLRWPAVRFEVREVAVQGPEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS
+DEALVRAVAAARTPVVSAIGHEADRPVLDDVADVRASTPTDAAKRIVPDAAQEAAGIAEA
+RRRLAAAVERRVQREGEGLAQLRSRPVLADPVVMVDGREQDLHAWRERARRATAHRLTRE
+RDAVEHLVARVRALSPQQTLDRGYAVVQQEGRLIRDAAQVAPGEDVDILVASGRISAEVT
+AVRPGRVGGVGTVQDEDEQAGTKEQA*
+>NZ_CP083691.1_1147
+MEESAAREEGTVVVPATASETSPERPWPLHRLSENLKLHIERAPATWIEGQLIEHKNNRG
+NLYMTMRDLEEEVSLPLTAWRAVAAGIDPSVQQGSRVVARVKPNFWVKGGRLSMVVQEMR
+PVGLGDLLARVELLRRRLAEEGLTSPARKRQLPVLPGVIGLITGRDSDALKDVVRNTHLR
+WPAAVFEVREVAVQGPDAPRQVAAALAELDARPEVEVIVIARGGGALEEVVLPFSDEALV
+RAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQESVGIREARLRLA
+GAVERRVRGEADALAALRSRPVLAHPHVMVDTRTEDLGRWQERGRVALGHRLAREADAVS
+ALRAQVRALSPQQTLDRGYAVVQHAGHVVRRAEDVTPGDDLDVLVAAGRIEAYVTDVTPV
+ETPSPTQEDA*
+>NZ_CP097650.1_1514
+MDQPVTEGASAAPDVPVSAPARAGETSAERPWPLRRLSENLKAHIERAPATWIEGQLIEF
+KNNRGNVYMTMRDLEEEVSLPLTAWRNVAMTLDGTVQQGSRVVARVKPNFWLKAGRLSMN
+VQEMRPVGLGDLLARVELLRRALAEEGLTSPARKRPLPLLPHRIGLITGRDSDAKKDVLR
+NTLLRWPAAEFEIREVAVQGAEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS
+DEALVRAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQEAAGLADA
+RLRLAAAVERRVRAEAEGLAALRSRPVLARPHVMVDTRQEETDRWRERGRSALGHRLVRE
+EDALTQLRARVRALSPQRTLDRGYAVVQHAGQVVREADQVATDDRLDILVAAGRIAADVV
+ATHRTTPTPSHERTRQA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001330.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001330.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d6361a6ef146fe959ced3989506a1850cffaa98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001330.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1589
+MPTPHPRQIRQSAKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPDAVL
+AAMHQHLPHAQGYSDSKGIYSARTAVSQYYESRGIRDIGVDDVFIGNGVSEMITMVLQAL
+VDDGDEILVPSPDYPLWTGATTLAGGRAVHYRCVEEEGWEPDLEHIESLVTERTKGIVLI
+NPNNPTGAVYSRAVLQGIVDVARRHNLVLMADEIYEKITYDGARHINAAGLSDDVLTLTF
+SGLSKAYRVAGYRSGWVAVSGPKHRAADFLEGLTLLANMRMCANVPAQHAIQVALGGYQS
+INDLVLPGGRLLEQRNLAQDRLNAIPGVSVQPAHGALYLFPRLDPEVYAIDDDEAFVIEL
+LRAKKILVSHGGAFNYPHSDHFRLVTLPSVKDLDVALDRLEDFLEDWRERHG*
+>NZ_CP033200.1_1305
+MPTPHPRQIRQSAKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPDAVL
+AAMHQHLPHAQGYSDSKGIYSARTAVSQYYESRGIRDIGVDDVFIGNGVSEMITMVLQAL
+VDDGDEILVPSPDYPLWTGATTLAGGRAVHYRCVEEEGWEPDLEHIESLVTERTKGIVLI
+NPNNPTGAVYSRAVLQGIVDVARRHNLVLMADEIYEKITYDGARHINAAGLSDDVLTLTF
+SGLSKAYRVAGYRSGWVAVSGPKHRAADFLEGLTLLANMRMCANVPAQHAIQVALGGYQS
+INDLVLPGGRLLEQRNLAQDRLNAIPGVSVQPAHGALYLFPRLDPEVYAIDDDEAFVIEL
+LRAKKILVSHGGAFNYPHSDHFRLVTLPSVKDLDVALDRLEDFLEDWRERHG*
+>NZ_CP040019.1_1235
+MPTPRPRQIRQSAKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPDAIL
+QAMYRHLPHAQGYSDSQGIYSARTAVSQYYESRGIRDIGVEDVFIGNGVSEMISMVLQAL
+VDDGDEILVPSPDYPLWTGATTLAGGRAVHYRCVEEEGWAPDLEHIESLVTERTKGIVLI
+NPNNPTGAVYSRQILQGIIDVARRHGLVLMADEIYEKITYDGARHINAAGLSDDVLTLTF
+SGLSKAYRVAGFRSGWVAVSGPKHRARDFLEGLTLLANMRMCANVPAQHAIQVALGGYQS
+IDDLVLPGGRLLEQRNLAQKRLNDIPGVSVQPAQGALYLFPRLDPEVYAIEDDQEFVIDL
+LRAKKILVSHGGAFNYPHTDHFRLVTLPSVEDLDVALDRLEDFLEDWRERRG*
+>NZ_CP083691.1_1143
+MAPSTPREFRQSSKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPDAIL
+QAMYQHLPHAQGYSDSKGIYSARTAVSQYYESRGIRDISVDDVFIGNGVSEMITMVLQAL
+VDDGDEILVPSPDYPLWTGATTLSGGRAVHYRCVEEEGWAPDLEHLESLITERTKGLVII
+NPNNPTGAVYSREVLNGVVDIARRHNLVLLADEIYEKITYDGARHINAAGLSDDVLTLTF
+SGLSKAYRVAGYRSGWVAVSGPKHRAKDFLEGLTLLSNMRMCANVPAQHAIQVALGGYQS
+IEDLILPGGRLLEQRNLAQKRLNDIPGVSVQPAHGALYLFPRLDPEVYAIDDDEKFVIEL
+LQAKKILVSHGGAFNYPQPDHFRLVTLPSVKDLDIALDRLEDFLEDWRERRG*
+>NZ_CP097650.1_1518
+MGGMPTPHPRQIRQSAKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPD
+AVLAAMHQHLPHAQGYSDSKGIYSARTAVSQYYESRGIRDIGVDDVFIGNGVSEMITMVL
+QALVDDGDEILVPSPDYPLWTGATTLAGGRAVHYRCVEEEGWEPDLEHIESLVTERTKGI
+VLINPNNPTGAVYSRAVLQGIVDVARRHNLVLMADEIYEKITYDGARHINAAGLSDDVLT
+LTFSGLSKAYRVAGYRSGWVAVSGPKHRAADFLEGLTLLANMRMCANVPAQHAIQVALGG
+YQSINDLVLPGGRLLEQRNLAQDRLNAIPGVSVQPAHGALYLFPRLDPEVYAIDDDEAFV
+IELLRAKKILVSHGGAFNYPHSDHFRLVTLPSVKDLDVALDRLEDFLEDWRERHG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001331.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001331.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c3642a49e33f67c7503877e2baf8d613e6155822
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001331.fa
@@ -0,0 +1,38 @@
+>NZ_CP042169.1_1590
+MSRPAHRRPTALAASALALSLALGACARQADAPPTPSASGTPITVVHGGEGLEGAVAAVL
+ARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAVAADPAVALPSPPPPTSTP
+SSTPTGTEAGPSADAVPTPSATASTAVPSPTALPVGDPAADAQAAGRVLETLLAEETAAA
+GTPQDEAPAVLSSSAGVLRLTAVVTQTTAARLELESITDLNGWCESLTAVAPPPLTAAAD
+PDAATALRARLDRLAGCRPETWLADTEDPSAALVADEAQVALLTDTDPEIDANTLVPLED
+DGRVLPEGRLTAVGSAATLDDDAERRIAEVMSALDGDGLRELERLTTGADPLPAAEAAQY
+WLVDHGLEDAPEDWFVPRGSWF*
+>NZ_CP033200.1_1306
+MSRPAHRRPTALAASALALSLALGACARQADAPPTPSASGAPITVVHGGEGLEAAVAAVL
+ARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAAAADPAAALPSPPTPTPTP
+TPTGTEAGTSTGTVPTPSATASTAAPSPTALPVGDPAADAPAAGRVLETLLAGQTAAAGT
+PQDEAPAALSSSAGVLRLTAVVTQTTAARLELESITDLNGRCESLTAVAPPALTSAADAA
+TALRARLDRLAGCRPETWLADTEDPTAAVVADEAQVALLTGTDPEIDANTLIPLEDDGRV
+LPEGRLTAVGSAATLDDDAERRIAEVMSALDGDGLRELERLTTGADPLPVAEAAQYWLVD
+QGLEDAPEDWFVPRGSWF*
+>NZ_CP040019.1_1234
+MPTASESSDAADASATPEPTPLPDGEPAADAAEAGRVVERLLQGDAEAGASPEPGDAVAV
+LGSSAGVLRLSAVVTATTAARLELDALEDLNGRCEGLTAALPAGLAGDPQANAALHARLD
+RLAGCRPGTWREEDASAAAVVVADQAQLGLLSATDPEIPASMLVPLEDPERVLPEGRLAA
+VGAPDALDDDAQRRIEEVLSALDEDGLRELERITTGADALPPAEAARYWLVDQGLEDVPE
+GWFMPRDSWF*
+>NZ_CP083691.1_1142
+MTRPAERPRTSRVRAAAGASALSLALALSGCGAPRAGAPADPTGAPVTVVHTSDPLDSAV
+AAVVARHLRHRGHPVTLEDAGDATPWSAAAGDTVAVVDTLRLALQADPAAVLPPEPEDAA
+ASRAAAAPTPSESSLEPIDPSAPARVPATGSATPSPTPLASGLPAADADAAQAVVDAALS
+RVAAGADAAAPTPAASRSAATPTGPSPRVLADSAGTLRLAAVVTATTASREGLDSIDDLD
+GRCGDLTLAVPAALAAAVSDGLLAHRLDDFAGCRPADWRTDAADVGPAVVADAAQVGLTY
+RTDPDIPPNGLVLLEDPDRVLPEGRIAVVGERETLDDDAQSALGEVMDRLDDDGIAELAR
+LTEGGDALPADEAAQYWLVSQRLEDAPEDWVVPADPWF*
+>NZ_CP097650.1_1519
+MSRPAHRRPTALAASALALSLALGACARQADAPPTPSASGTPITVVHGGEGLEGAVAAVL
+ARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAAAADPAAALPSPPSPTSTP
+SSTPTGTEAGTSADAVPTASTAAPSPTALPVGDPAADAPAAGRVLETLLAEETAAAGTPQ
+AEAPAVLSSSAGVLRLTAVVTQTTAARLELESITDLNGRCESLTAVAPPTLTAAADADAA
+TALRTRLDRLAGCRPETWLADTEDPTAAVVADEAQVALLTGTDPEIDANTLVLLEDDGRV
+LPEGRLTAVGSAATLDDDAERRIAEVMSALDGDGLRELERLTTGDDPLPVAEAAQYWLVD
+HGLEDAPEDWFVPRGSWF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001332.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001332.fa
new file mode 100644
index 0000000000000000000000000000000000000000..164d1e70d4c007af063e0743e54574128253e82d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001332.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1591
+MSTTPAAPDAAGAHPAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIELGES
+PEEACLREVWEETGHTAELTGLLGVTTGTIPVEKRLRGEPLPLLTVQVLYTARITGGVLR
+PEVGGSSTDARWFDLAELSELRTASWVTEALARAGVDT*
+>NZ_CP033200.1_1307
+MSTTPAAPDAAGAHPAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIELGES
+PEEACLREVWEETGHTAELTGLLGVTTGTIPVERRLRGEPLPLLTVQVLYTARITGGVLR
+PEVGGSSTDARWFDLAELSGLRTASWVTEALARAGVAT*
+>NZ_CP040019.1_1233
+MSPTPVPDAEPARADAPAGPFQTRAGAYALIVDGGRVLLSSWQGPEHLVWTLPGGGIELG
+ESPEEACRREVWEETGHTAELTGLLGVTTGVIPAERRLRGEALPLLTVQVLYTARITGGV
+LRPEVGGSSTDARWFDLAGLDAVRTAPWVREALARAGAAA*
+>NZ_CP083691.1_1141
+MSAASPTAASTAPGPFETRAGAYALIVEDGRVLMSAWAGPTGIVWTLPGGGIELGESPEE
+ACVREVEEETGHTAELTGLLGVTTGTIPVERRLRGEPLPLLTVQVLYTARLTGGVLRPEA
+DGSSVDAAWFALDGLADVRTSAWVDRALALAGLAADDAAGTAR*
+>NZ_CP097650.1_1520
+MSTTPAAPDAAGAHPAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIELGES
+PEEACLREVWEETGHTAELTGLLGVTTGTIPVEKRLRGEPLPLLTVQVVYTARITGGVLR
+PEVGGSSTDARWFDLAELSELRTASWVTEALARAGVDT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001340.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001340.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f60f825dad7ac0b3b291e34609eefc581e57bc9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001340.fa
@@ -0,0 +1,110 @@
+>NZ_CP042169.1_1599
+MTEQEFPRLARARAAARPDEGQTRPDPAAWVSSLGSGAENDTMLRFAPSAANSIDLTEAN
+SSGVSQLLLGRRTRLSTLLPAGPELDAAHEVSLGLRAKVRELAEERGIDVGALAVGVATW
+TAEEDGRRERRSAPVLLARVALTVRRGARGRDELEVQITEPARLNPALVRNLRRHHGIAL
+DPEAYQQAAYATARLEPAPAFARLREETAAIADLHIQDCLLVSTFADLGETASLPASLED
+LPVVQALYDAGTGMVPRPAALQPTGAPAEDDVAPADERLVVDVDAAQARVLEHAAAGESL
+VVAAAPGTGQTQTAAALAARLAWEGRRVLVVAERSAALADVLDRLEEADLRSIALDVPAN
+ADPELLRRQLVQAVLRSERAVDPDTARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA
+MQALAALTGLETPPATTVRLKRSVLDSTVNRQAVGEQLVRAGELGAFSAAATESRWFGAR
+VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL
+TEFTPEVFSLDVPQLVAATATSSWRRLHLVEMSSVTRSRLRRAAKDAVRPGVQPTDLHGA
+LVDAAAVLEDWNRHAAEPGTPPQVPDQGEHVMGQVGQVRERLRRLEGVLAPEAVAEAPLE
+ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLRDHGLAELLEDLRDREVPTEALTAEL
+ELAWWQSALEAMISGDDFLAMMSGTDLAEVERGFRDLDRAHLERGGARLSAALAARWREA
+LRTYRADAAVLRTLLKQGSPTVESLATITPELLQPLVPVVTTSPMALSEFPPEWRADVVV
+LLEADATALATAMGALTRAPQVVALGDPVIGRPQSFQVSVDPTATAGPLRPLRSAHDALD
+EVLPTLPLRTVHRPLERRLVRLLSALAYDGALDALPTAGEATGRDRAVTAEYLPEGTGIP
+MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEQHARRVAAAVQATAAQAPWA
+HEFLARGRGEDAADAEPFVIVPVVRAASVVRDAVILTPGYGRTPHGRVVHHFGAFSDPDG
+ERMVTVALTRARRRLHLVSALRAADLDEDRLDGGALWFLRLLEAYLGDDAADPVGMVGDP
+LLADLRDRLEEHGARVLPRYAGVMDLAVLDPRADQDEAPRPLALAGDGGEVYRALTVRQR
+SRTLPEGLEARGWEPRTLWSIDVFADPESVARELADRLGVEPADETDETDDDAR*
+>NZ_CP033200.1_1315
+MTEQEFPRLARARAAARPDEGQTRPDPAAWVASLGSGAENDTMLRFAPSAANSIDLTEAN
+SSGVSQLLLGRRTRLSTLLPAGPELDAAHEVSLGLRAKVRELAEERGIDVGALAVGVATW
+TAEEDGRRERRSAPVLLARVALTVRRGARGRDELEVQITEPARLNPALVRNLRRHHGIAL
+DPEAYQQAAYATARLEPAPAFARLREETAAIADLHVEDCLLVSTFADLGETASLPASLED
+LPVVQALYDAGTGMVPRPAALQPTGAPAEDDVAPADERLVVDVDAAQARVLEHAAAGESL
+VVAAAPGTGQTQTAAALAARLAWEGRRVLVVAERSAALADVLDRLEEADLRSIALDVPAN
+ADPELLRRQLVQAVLRSERAVDPDTARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA
+MQALAALTGLETPPATTVRLKRSVLDSTVNRQAVGEQLVRAGELGAFSAAATESRWFGAR
+VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL
+TEFTPEVFSLDVPQLVAATATSSWRRLHLVEMSSVARSRLRRAAKDAVRPGVQPTDLHGA
+LVDAAAVLKDWNRHAAEPGTPPQVPDQGEHVMGHVGQVREHLRRLEGVLAPEAVAEGPLD
+ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLRDHGLAELLEDLRDREVPTEALTAEL
+ELAWWQSALEAMISGDDFLAMMSGTDLTEVERGFRDLDRAHLERGGARLSAALAARWREA
+LRTYRADAAVLRTLLKQGSPTVESLATITPELLQPLVPVVTTSPMALSEFPPEWRADVVV
+LLEADATALATAMGALTRAPQVVALGDPVIGRPQSFQVSVDPTATAGPLRPLRSAHDALD
+EVLPTLPLRTVHRPLERRLVRLLSALAYDGALDALPTAGEATGRDRAVTAEYLPEGTGIP
+MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEQHARRVAAAVQATAAQAPWA
+HEFLARGRGEDAADAEPFVIVPVVRAASVVRDAVILTPGYGRTPHGRVVHHFGAFSDPDG
+ERMVTVALTRARRRLHLVSALRAADLDEDRLDGGALWFLRLLEAYLGEDAADPVGMVGDP
+LLADLRDRLEEHGARVLPRYGGVMDLAVLDPRAEQDEAPRPLALAGDGGEVYRALTVRQR
+SRTLPEGLEARGWEPRTLWAIDVFADPESVARELADRLGVEPADETDETDDDVR*
+>NZ_CP040019.1_1223
+MREQEFPRLARARAAARPEEGQTRPDPAAWVASLGSGAENDTMLRFAPSAANSIDVTAAN
+SSGVSQLLLGRRTRLSTLLPAGPALQAAEEVAAGLRAKVRELSEERGIDVGALAVGVATW
+TAEEDGRRERRSAPVLLARVALTVRRGARGRGELEVQITEPARLNPALVRNLRRHHGIAL
+DPEAYRQAAYATARLEQRPALARLREEAAALTGLQVEDRMLVSTFADLGETATLPASLEH
+LPVVEALYDAGTGMVPRPPALQPTEAPGEDDVAPADERLVLDLDAAQRRVVEHSAAGESL
+VVAAAPGTGQTQTAVAVAARLAWEGRRVLVVAERSAALADVHARLDEIGLRAAALDVPAH
+ADPEQLRRQLVQAVLRAERAEAPDAARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA
+MQALAALTGLPTPPATTVRLKRSVLDSTVNRQAVAEQLVRAGELGAFSAAATESRWFGAR
+VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL
+TEFTPEVFALDVPQLVAATATSTWRRTHLVEMSSVARSRLRRAAKDAVRPGVQPTDLHGA
+LVDAAAVLEDWNRHAAEPGTPPQVPDQGERVMGVVGDVRERLRRLERILAPEAVAEQPLA
+ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLKDHGLTELLTDLRDREVPTEALAAEL
+ELAWWQSALEAMISGDDFLAMMSGADLAEVERGFRELDRAHLERGADRLSAALGARWKEA
+LRTFRADAAVLRGLLKQGRPTVEALTTLAPEVLQPLVPVVTTSPMALSEFPSDWGADVVV
+LLEADATALATAVGALTRAPQVVAFGDPVIGRPQSFQVSVDPTATAGPLRPLRSAHDALA
+EVLPTVALRTVHRPLERRLVRMLSALAYEGALEALPTAGEATGRDRTVTAEYLQEGTGIP
+MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEPHARRVAAAVQATAARASWA
+LDFLSRGRGEDAEGAEPFVIVPVTRAASVVRDAVILTPGYGRTPHGRVVHHFGAFSDPGG
+ERMVAVALTRARQRLHLVSALRAADLDEDRLDGGAQWFLRLLEAYLGDGAPDPVGRVSDP
+LLADLRERLEERGARVLPRHGGVMDLAVVDPHPEDEDEDGDAPRPLALAGDGGDVYRALT
+VRERTRTLPERLEARGWDPRTLWAIEVFADPESVAQELADRLGVRPADESERDADDDGR*
+>NZ_CP083691.1_1133
+MTEQEFPRLARARAAVRPAEQDQERPDPAAWVASLGSGAESDTMLRFAPSAANSIDLTGA
+GTSGLSQLLLGRRTRLSTLLPAGPELDAAQEVAAALRAKVRELGEERGIDVGALALGVAT
+WSAVEDGRRERRTAPVLLARLAFSVRSGARGRDEVELQIVEHAHLNPALVRNLRRHHGLR
+LDPEAYQHAAYATSRLEPGPALALLREEAAGVEGLEVQETLLVSTFADLGDTATLPESLE
+HLPVVQALYDVGTGMVPRPAELRPTGRPDEDELPPADERLVLDADPSQLRALDHAAAGES
+LVVRTAPGTGQTQTAVNLAARLAWEGRRVLVVAERSSALADVHARLAQAGLRDAALDVPA
+HADPEDLRRQLVAAVLRAERASAPDRAAADAELEELRRRLREHVDSLHHVRPRWGCSPFQ
+AMQALASLTALDTPPATTVRLKRSVLDSTVDRHAVAGRLTRAGELGAFDRDATASRWFGA
+RVRNVQETEAAGELVEHLAGTLYTTRRAVEAAADQAGLRRPRTVDGWAEQSDLFARVERA
+LTAMDPSVFSLDVPQLVTATASSQWRRSNAVEMSSVQRSRLRRAAKDAVKPGVQVPDLHQ
+ELMEVEGILEDWRRWTAIPGSTPMVPDMADHARPAVRDVLDALDRLSQVLAPEATAGTPL
+AEQDVDDLMAAVDGLVADRPTLATLPERTLVLDELREHGLNELLEDLHAREVPVAALPAE
+LELAWWQSALEAMISGDDFLAMMSGADLTAVEQGFRAADRTLLDSGGARLAASLGAAWKA
+ALGTYRADAAVLRSLLKQGRPSVESLATITPGLLQALVPIVTTSPMALTEFPPDWDADVV
+ILLEADATALATVAGALTRAPQVVAFGDPAIGRPQSFQVSVDPTATAGPLRPLRSALSAL
+AEVLPVLDLRHVHRPLPRSLVRLVSHVAYEGAVDALPTAAEFTGRGRTLTAEYVAEGVGI
+PMTGGDVVESTDAEVARTVERVFEHIRDRPEESLAVVTVSEQHARRVAGAVQATAARAPW
+AADFLARGRTDGDEREPFVIVPVLRASTVTRDAVILTPGYGRTPHGRVVHHFGALSDPDG
+ERMLTVALTRARARMHVVTALRAADLDADRLDGGALAFRRMLEVALDDAEAAPAGRLSDP
+LLLDLRDRLAAEDALVAAHYGGAMDLAAADAAGERGRVRPLALVSDGGDAYREQSVRERS
+RRLPERLEARGWDTDTLWAIDVFADPESVAARLVGRLGLPLEEVDEDGEDDADGES*
+>NZ_CP097650.1_1529
+MTEQEFPRLARARAAARPDEGQTRPDPAAWVSSLGSGAENDTMLRFAPSAANSIDLTEAN
+SSGVSQLLLGRRTRLSTLLPAGPVLDAAHEVSLGLRAKVRELAEERGIDVGALAVGVATW
+TAEEDGRRERRSAPVLLARVALTVRRGARGRDELEVQITEPARLNPALVRNLRRHHGIAL
+DPEAYQQAAYATARLEPAPAFARLREETAAIADLHIQDCLLVSTFADLGETASLPASLED
+LPVVQALYDAGTGMVPRPAALQPTGAATEDDVAPAEERLVLDVDAAQARVLEHAAAGESL
+VVAAAPGTGQTQTAAALAARLAWEGRRVLVVAERSAALADVLDRLEEADLRSIALDVPAN
+ADPELLRRQLVQAVLRSERAVDPDTARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA
+MQALAALTGLETPPATTVRLKRSVLDSTVNRQAVGEQLVRAGELGAFSAAATESRWFGAR
+VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL
+TEFTPEVFSLDVPQLVAATATSAWRRLHLVEMSSVTRSRLRRAAKDAVRPGVQPTDLHGA
+LVDAAAVLEDWNRHAAEPGTPPQVPDQGEHVMGQVGQVRERLRRLEGVLAPEAVAEGPLD
+ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLRGHGLAELLEDLRDREVPTEALTAEL
+ELAWWQSALEAMISGDDFLAMMSGTDLAEVERGFRDLDRAHLERGGARLSAALAARWREA
+LRTYRADAAVLRTLLKQGSPTVESLATITPELLQPLVPVVTTSPMALSEFPPEWRADVVV
+LLEADATALATAMGALTRAPQVVALGDPVIGRPQSFQVSVDPTATAGPLRPLRSAYDTLD
+EVLPTLPLRTVHRPLERRLVRLVSALAYDGALDALPTAGEATGRDRAVTAEYLPEGTGIP
+MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEQHARRVAAAVQATAAQAPWA
+HEFLARGRGEDAAEAEPFVIVPVVRAASVTRDAVILTPGYGRTPHGRVVHHFGAFSDPDG
+ERMVTVALTRARRRLHLVSALRAADLDEDRLDGGALWFLRLLEAYLGDDAADPVGMVGDP
+LLADLRDRLEEHGARVLPRYAGVMDLAVLDPRAEQDEAPRPLALAGDGGEVYRALTVRQR
+SRTLPEGLEARGWEPRTLWSIDVFADPESVARELADRLGVEPADETDETDDDVR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001347.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001347.fa
new file mode 100644
index 0000000000000000000000000000000000000000..15e6fab95334cd843cc6655f7a9b0588c2dc6b65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001347.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1608
+MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD
+VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVAK*
+>NZ_CP033200.1_1324
+MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD
+VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK*
+>NZ_CP040019.1_1215
+MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD
+VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK*
+>NZ_CP083691.1_1125
+MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGTRVPVD
+VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK*
+>NZ_CP097650.1_1538
+MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD
+VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001348.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001348.fa
new file mode 100644
index 0000000000000000000000000000000000000000..82755e6f90f08b6642faad6349b9895b775b7ec6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001348.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1610
+MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV
+GGHDITTTPSRRIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERHVSDAI
+DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR
+AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILRPEVLERIFKTPCSVV
+DGPHGPLAVYY*
+>NZ_CP033200.1_1326
+MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV
+GGHDITTTPSRKIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERHVSDAI
+DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR
+AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILCPEVLERIFKTPCSVV
+DGPHGPLAVYY*
+>NZ_CP040019.1_1213
+MIELRGVVKRHSDEVCIGPVDLDIEAGGITALVGPNGAGKSTVLTMIGRLQDVDAGTIAV
+GGQDITSTPSRRIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERYVSEAI
+DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR
+AADMLGRTVVIVLHDINFAARYADHIVAMGDGQVVETGTPGEILRPEVLERIFRTPCSVV
+DGPHGPLAVYY*
+>NZ_CP083691.1_1123
+MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV
+GGHDITTTPSRKIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERHVSDAI
+DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR
+AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILRPEVLERIFKTPCSVV
+DGPHGPLAVYW*
+>NZ_CP097650.1_1540
+MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV
+GGHDITTTPSRKIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTCGRLTLEDERHVSDAI
+DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR
+AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILRPEVLERIFKTPCSVV
+DGPHGPLAVYY*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001350.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001350.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08a0bfba48ae6ee6cecdf7520563554d2193e36e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001350.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1612
+MTLDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVVVTAALIVVS
+LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE
+WAGLGLLVTMVLVPGAGLVTRMAGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA
+VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL
+GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRMNL
+PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG*
+>NZ_CP033200.1_1328
+MILDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLAGIVVTAVLVVVS
+LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE
+WAGLGLLVTMVLVPGAGLVTRMAGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA
+VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL
+GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL
+PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG*
+>NZ_CP040019.1_1211
+MTDLHPGVADARTRLPEPGPGERVCWVPPTVLRPQRSRWQRTWPLLAGVAVTVLLAVVSL
+FVGVYDVGAEGGREMFAITRVPRTVALVLAGAAMAMCGLIMQLMTQNRFVEPSTTGTTEW
+AGLGLLVTMILIPGASIVTRMTGAVLFAFVGTMVFFLFLRRVRLQSSLIVPIVGIMLGAV
+VGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLVVCVAVFVIADRFTVAGLG
+KDVATNVGLNYNAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNIVSMVRGDNLRTNLP
+WVVMVGIWVVIVCDLIGRTVIAPFEVPISLILGLVGAVVFLGLLIRQAKHG*
+>NZ_CP083691.1_1121
+MTLDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVLVTAALIVVS
+LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE
+WAGLGLLVTMVLVPGSGLVTRMVGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA
+VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL
+GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL
+PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG*
+>NZ_CP097650.1_1542
+MILDVRHHVADAPPRLEELGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVVVTAALIVVS
+LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE
+WAGLGLLVTMVLVPGAGLVTRMVGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA
+VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFLIADRFTVAGL
+GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL
+PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001351.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001351.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0932841bed6b625ba28985fdb6be6e733ed3ee25
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001351.fa
@@ -0,0 +1,36 @@
+>NZ_CP042169.1_1613
+MPRSVSAPRLARLALTSVAALALVGCSAGGAATGSSSASASGESSASASAAGGSSAASGG
+IAAGVTVTDMSGAEVTLPEEVDSVIATDNRAFRTLDDWGVELSAAPKQIMYKGEGGPSYL
+QDDSVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVVDTDFDVTQTP
+MDEGLKELTTLLGEATGHEADAEKLIADFDAATQRAKDAYDPEQTVMGLIASGGELSYVA
+PSTGRAIGPFFDMLELTPALEQSGTDNHQGDDISVEAIAKSNPDWLIVMDRDAAIGEENA
+TAAELIERSEALQDVTAVKEGNIVYLPADFYVAEDIQNHTTVMEDLAKAFEGAQ*
+>NZ_CP033200.1_1329
+MPSSARAPRLARLALTSVAALALVGCSAGGAATGSSSASASGESSASASASGESSASASA
+AGGSSAASGGIATGVTVTDMSGAEVTLPEEVDSVIATDNRTFRTLDDWGVELSAAPKQIM
+YKGEGGPSYLQDDSVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVV
+DTDFDVTQTPMDEGLKELTTLLGEATGHEADAEKLIADFDAATQRAKDAYDPEQTVMGLI
+ASGGELSYVAPSTGRAIGPFFDMLELTPALEQSGTDNHQGDDISVEAIAKSNPDWLIVMD
+RDAAVGEENATAAELIERSEALQDVTAVKEGNIVYLPTDFYVAEDIQNHTTVMEDLAKAF
+EGAQ*
+>NZ_CP040019.1_1210
+MQRSPRTPRLKALALASVAALALVGCSAGGAAEGPASGSADTGSAAGSGSASAPAGDGVA
+AGATVTDMSGAEITLPEEIDSVITTDNRTFRTLDEWGVELSAAPKQLMFKGEGGPGYLQD
+DEVADIGNHREPDMEVFVTAEPDVVFNGQRFNERKAEIDELTGDAAVIDTDFDPKQKPMD
+EGLKELTTLLGEATGHQDDAAALNKEFDDAVAKAKGAYDSEQTVMGLISTGGELSYVAPG
+TGRSIGPMFDILGLTPALEQAGSDNHQGDDISVEAIAQSNPDWLIVMDRDAATGEANATA
+AELIERSEALKDVTAVKEGNIVYLPQDFYVAEDIQNYTTVMDDLAKAFEGAR*
+>NZ_CP083691.1_1120
+MRTARLSTAAALASLAALTLAGCGAGGPAAEGSSPASSAASSSPASSAASSSATAGGVAA
+GVTVTDMSGTEVTLPEEVDSVIATDNRIFRTLDDWGVELSAAPKQIMYKGEGGPSYLQDD
+SVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVVDTNFDVTQTPMDE
+GLKKLTTLLGEATGHEADAEKLIADFDAATQLAKDAYDPEQTVMGLIASGGELSYAAPST
+GRSIGPFFDMLDLTPALDQSGTDNHQGDDISVEAIAKSNPDWLIVMDRDAAVGEENATAA
+ELIERSEALQDVTAVKEGNIVYLPADFYVSEDIQNHTTVMEDLAKAFEGAQ*
+>NZ_CP097650.1_1543
+MPRSARAPRLARLALTSVAALALVGCSAGGAATGSSSASASGESSASASASGGSSAASGG
+IATGVTVTDMSGAEVTLPEEVDSVIATDNRIFRTLDDWGVELSAAPKQIMYKGEGGPSYL
+QDDSVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVVDTNFDVTQTP
+MDEGLKELTTLLGEATGHEADAEKLIADFDAATQRAKDAYDPEQTVMGLIASGGELSYVA
+PSTGRAVGPFFDMLELTPALEQSGTDNHQGDDISVEAIAKSNPDWLIVMDRDAAIGEENA
+TAAELIERSEALQDVTAVKEGNIVYLPADFYVAEDIQNHTTVMEDLAKAFEGAQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001352.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001352.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8fe80db7e8636156be1a9db642068ae4927284b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001352.fa
@@ -0,0 +1,43 @@
+>NZ_CP042169.1_1614
+MARPRPAARPSRPSAAASEEDDTALAPVLESEGRALLDSLAGYREADALAVSSRLRAAGH
+PPERVAAALTQAALRSRAEARLGPEARRMLFTRDGLEQATRPLVAGLHADRLAAAGARRV
+ADLGCGLGLDARAFADRGLDVVAVERDAVVAAAAEVNLAGHRGARVVHGDAVAWARAHVP
+AEADAVWLDPARRQVGGGGSARVFDPEAFSPPLSVVTDIAATGVPVGVKLGPGLPHEAVP
+AGAEAEWVSVDGDVVEAALWFNAAARPGVRRAARVMTVHGGKTTTAQLVSGADFGDSPEV
+EAVGEEGMAGLVGAVLHEPDGAVIRAGLVTDLAVSWPVPTRQLDPHLAYLVAPEPVHDGL
+ARAHRIEAVHGFHLASLRRWAKETGVGRLDVKKRGIRETPEEVRRAVLGGAKPGRRGGAG
+RHATLVLARVGRSRFALEVTPLD*
+>NZ_CP033200.1_1330
+MARPRPASRSPRPTAAASEADDTALAPVLEPEGRALLDSLAGYREADALAVSSRLRAAGH
+PPERVAAALTQAALRSRAEARLGPEARRMLFTRDGLEQATRPLVAGLHADRLAAAGARRV
+ADLGCGLGLDARAFADRGLDVVAVERDAVVAAAAEVNLAGHRGARVVHGDAVAWARAHVP
+AEADAVWLDPARRQVGGGGSARVFDPEAFSPPLSVVTDIAATGVPVGVKLGPGLPHEAVP
+EGAEAEWVSVDGDVVEAALWFNAAARPGVRRAARVMTVRGGETTTAQLVSGADFGDSPEV
+EAVGEEGMAGLVGAVLHEPDGAVIRAGLVTDLAASWPVPTRQLDPHLAYLVAPEPVRDGL
+ARAHRIEAVHGFHLASLRRWAKETGVGRLDVKKRGIRETPEEVRRAVLGGAKPGRRGGAG
+RHATLVLARVGRSRFALEVTPLD*
+>NZ_CP040019.1_1209
+MLTQADLRARAVPRLGPDARGMLFTRDGLEQATRPVVAALHAQRMAAAGARTVADLGCGL
+GLDARAFADAGLGVVAVERDAVVAAAAEVNLTDRPGARVVHGDAVPWAREHVPAQADAVW
+LDPARRQVGGGGSARVFDPEAFSPPLSVVEELAATGVPVGVKLGPGLPHEAVPAGAEAEW
+VSVDGDVVEAALWFNAAARPGVRRAARVIDTRGGQATTAELVSGADFGDSPGVEAVGEEG
+MPGLVGRCSTSRTAPSSGPGSSRTWRSPGRRRPASWTRTWPIWWPPSTRPTRWPGRTGST
+RSTISTSSLCAGGRRRRGSAAWT*
+>NZ_CP083691.1_1119
+MARSQRPARPSRPRPRPADRPGRPRAAESAADATRLEPVLDPAGRVLLDGLGDVSGQDPL
+ALSSRLRAAGHDADTVAAALTQAGLRHAGRAKLGALADGMLLTRDGLEQATRAVVAEHRA
+RRLQEAGVRSLADLGCGIGADALVYARAGLDVTAVERDPTVAAAAAANLATLAPAGAASV
+VTGDAEAWAAAHADEVDALWLDPARRRLGSSGTARVFDPEAFSPPLSFVLGLADGGRPVG
+VKLGPGLPHEHVPAAAEAEWVSVDGDVVEVTLWFGPLAQAPGRRTATLLDTRGSAVHRLV
+PAAASSPAVEAVGEEGVDGLVGQVLLEPDGAVIRAGLVTDLAVELGPAVRLLDPHLAYLV
+APDAAPHPLARGYRVLAVHEFRTKALARWARETGVGRLDVKKRGVRETPEQVRAAVLGRG
+TPGGRHATLVLARVGERRVAFEVEPLPAG*
+>NZ_CP097650.1_1544
+MARPRPASRSPRPTAAASEADATALTPVLEPEGRALLDSLAWYREADALAVSSRLRAAGH
+PPERVAAALTQAALRSRAEARLGRQARRMLFTRDGLEQATRPLVAGLHADRLAAAGARCV
+ADLGCGLGLDARAFADRGLDVVAVERDAVVAAAAEVNLAGHRGARVVHGDAVAWARAHVP
+AEADAVWLDPARRQVGGGGSARVFDPEAFSPPLSVVTDIAATGVPVGVKLGPGLPHEAVP
+AGAEAEWVSVDGDVVEAALWFNAAARPGVRRAARVMTVRGGETTTAQLVSGADFGDSPEV
+EAVGEEGMAGLVGAVLHEPDGAVIRAGLVTDLAASWPVPTRQLDPHLAYLVAPEPVHDGL
+ARAHRIEAVHGFHLASLRRWAKETGVGRLDVKKRGIRETPEEVRRAVLGGAKPGRRGGAG
+RHATLVLARVGRSRFALEVTPLD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001356.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001356.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89ecb1953cd1e7d7dbeb902066ba426149b64ec8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001356.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1618
+MRTRTLTRRAALTGLLGSAALGFTACTSSGYPADPDGTLDRVTGGVLRVGVVHHPPHVDV
+SGAEPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHA
+SITRDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR*
+>NZ_CP033200.1_1334
+MTITRRAALAGLLGGAALGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDASGA
+EPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHASIT
+RDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR*
+>NZ_CP040019.1_1205
+MTITRRAALTGLLGGAVLGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDASGA
+EPVGPEPDLIRGFAAAHDAEIAWTVSGEEALLTALEKGDVDLVAGGLTSDSPWTTHASLT
+RDYAEAAGPDGEPVKLVMAVPPGENQMLAALEAHLDAQAREAGR*
+>NZ_CP083691.1_1115
+MQTPRRTLLTGALAAAGVVLTGCTSSGYPADPDGTLDRITGGTLRVGASHHPPHVDAAGA
+EPQGPEPDLVRAFAAERDARVEWTVSGEEALMTALKQGDLDLVVGGLTKKSPWTTDAGLT
+RPYAETTGPDGEKAELVMAVPLGENQFQSALERFLDAHGEEAGA*
+>NZ_CP097650.1_1548
+MTITRRAALAGLLGGAALGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDASGA
+EPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHASIT
+RDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001358.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001358.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a12639f61faada7f0846d900eb1f8ab1f18b41bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001358.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1621
+MTGPLTRLEPMPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIP
+EIAARAHLEALVPTIRRALDTADVTLADLDAIAVTSGPGLAGALMVGVAGAKALATALGT
+PLYGINHLVAHVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISAEVELLGST
+IDDAAGEAYDKVARLIGAGYPGGPVIDRLAAQGDPTAFRFPRGLTAGKFVGSAEEPGPHR
+HDWSFSGLKTAVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLM
+LGGGVAANSRLRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWF
+GADPGQPVEVVSV*
+>NZ_CP033200.1_1337
+MPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIPEIAARAHLEA
+LVPTIRRALDTADVTLADLDAIAVTSGPGLAGALMVGVAGAKALATALGTPLYGINHLVA
+HVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISSEVELLGSTIDDAAGEAYD
+KVARLIGAGYPGGPVIDRLAAEGDPTAFRFPRGLTAGKFVGSAEEPGPHRHDWSFSGLKT
+AVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLMLGGGVAANSR
+LRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWFGADPGQPVEV
+VSV*
+>NZ_CP040019.1_1186
+MTGPLTRLEPMPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIP
+EIAARAHLEALVPTVRRALEAADVGLKDLDAIAVTSGPGLAGALMVGVAGAKALATALDT
+PLYGINHLVAHVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISSEVELLGST
+IDDAAGEAYDKVARLIGAGYPGGPVIDRLAAQGDPTAFRFPRGLTAGKFVGSAEEPGPHR
+HDWSFSGLKTAVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLM
+LGGGVAANSRLRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWF
+GADPGQPVEVVSV*
+>NZ_CP083691.1_1113
+MAPMSATATAPLVLGIESSCDETGVGIARGTALLAHEVASSVEEHVRFGGVIPEIAARAH
+LEALVPTVRRALDAAGVTLDEVDAIAVTSGPGLAGALMVGVAGAKALAVAADKPLYGINH
+LVAHVGVGLLDGVRPADWDDLPRDLGALLVSGGHTEILQVDRISSDVTLLGSTIDDAAGE
+AYDKVARLIGAGYPGGPVIDRMAQEGDPKAFRFPRGLTAGKFVGTAEEPGPHRHDWSFSG
+LKTAVSRAVEQFEAQGLEVPRTDIAASFQEAVADVITAKAVRACREHGLTHLLLGGGVAA
+NSRLRGLLADRCRSAGIELVVPPVNLCTDNGAMVAALGARLVADGVAPSDLAFGADPGQP
+VSAVSAA*
+>NZ_CP097650.1_1551
+MTGLLTRLEPMPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIP
+EIAARAHLEALVPTIRRALDTADVTLADLDAIAVTSGPGLAGALMVGVAGAKALATALGT
+PLYGINHLVAHVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISSEVELLGST
+IDDAAGEAYDKVARLIGAGYPGGPVIDRLAAQGDPTAFRFPRGLTAGKFVGSAEEPGPQR
+HDWSFSGLKTAVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLM
+LGGGVAANSRLRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWF
+GADPGQPVEVVSV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001361.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001361.fa
new file mode 100644
index 0000000000000000000000000000000000000000..adba4f68d8ebd949fa29ebb09e274da6ff83dea5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001361.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1624
+MSDHAIPAPGATLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS
+VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDAPAASAGEGEDGIVTDFS
+DEDGGQAEELRSAVVTGRGPRWAGVVLP*
+>NZ_CP033200.1_1340
+MSDHAIPAPGATLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS
+VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDAPAAPAGEGEDGIVTDFS
+DEDGGQAEELRSAVVTGRGPRWVGVVLP*
+>NZ_CP040019.1_1183
+MSRHEPPAPDPALPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAT
+VDRSVTVVEWGRGLAESLAGFPEDPDASWLDVEIVRARGGEDPAPAGPGADDGGIVTDFS
+DEDGEQAEELRSAVVTGYGPRWAGVRLP*
+>NZ_CP083691.1_1110
+MIAGRRAEQPLPAPVWERRVPLDGAAGTREFGAALAGVLRAGDVLILTGELGAGKTTLTQ
+GLGAGLGVREGVISPTFVLSRIHPSLADGPDLVHVDAYRLRSAGELTDLDLEATADRSVT
+VVEWGRGMAESLAGFPEDPEASWLDVEVLRARGGADLPDGPAGGDAAPDAPVIVTDFSDE
+EGEAAEEVRTAVVRAHGPRWAAVALP*
+>NZ_CP097650.1_1554
+MSDHEFPAPGPTLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS
+VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDGPAASAGEEDGIVTDFSD
+EDGGQAEELRTAVVTGRGPRWAGVVLP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001364.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001364.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b806992ced9373cea6e21d5ca1ce4d99cbbb65fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001364.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1627
+MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP
+GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA
+AEEESA*
+>NZ_CP033200.1_1343
+MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP
+GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA
+AEEESA*
+>NZ_CP040019.1_1180
+MIVGVGMDVVDVPRFRAQLERTPALRERLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP
+GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEAQGITHWHLSLSHDGDVAAAYVVAERRA
+GEDGA*
+>NZ_CP083691.1_1107
+MIVGIGVDVVDVPRFERQLARTPALRERLFTEEERDLSLRSLAARFAAKEAIAKALGAPP
+GMMWHHCSIPRPAHGDGRPEVRLTDSVRDRADELGVTHWHLSLSHDGDVAVAYVVAERHD
+*
+>NZ_CP097650.1_1557
+MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAVAKAMGAPP
+GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA
+AEEESA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001366.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001366.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12ecf8efd4de9f3505cb2afbaed6fc2337104ae0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001366.fa
@@ -0,0 +1,65 @@
+>NZ_CP042169.1_1629
+MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHA
+HVAGIGHGQRYGYRVHGPWDPARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPD
+RIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYETHVKGMTKLHPAVPEELRGT
+YAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS
+SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEG
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGLWSEWNGMYRDAVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRGPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG
+EAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNV
+YCQDNEISWIDWSAMDDSLVAFTRDLIALRRDHAVFRRRHHFDGRPAARDVEAPLPDIVW
+LEPDATAKTEDDWGAEARSIGFYLNGHMLTRGDEEGEEPYRDFYVLMNAWWEPVPYTLPG
+PTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQVPEGA*
+>NZ_CP033200.1_1345
+MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHA
+HVAGIGHGQRYGYRVHGPWDPARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPD
+RIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYETHVKGMTKLHPAVPEELRGT
+YAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS
+SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEG
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGLWSEWNGMYRDAVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRGPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG
+EAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNV
+YCQDNEISWIDWSAMDDSLVAFTRDLIALRRDHAVFRRRHHFDGRPAARDVEAPLPDIVW
+LEPDATAKTEDDWGAEARSIGFYLNGHMLTRGDEEGEEPYRDFYVLMNAWWEPVPYTLPG
+PTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQVPEGA*
+>NZ_CP040019.1_1178
+MHTVDIGQPYPLGATVDETGTNFAVALAREAESVELCLVDEDGVETRLPVVERHGTTWHV
+HVAGVGHGQRYGYRVTGPWDPSRGLWHNPAKILVDPYARAFAGEHEWGQQHHSYDFDEPD
+RMDTSDNLGTTMLGVVTDDDFDWGEDAPPNIEMTDTVVYETHVKGMTMRHPAVPEELRGT
+YAGMAHPEVVRHLTDLGVTAVELMPVHQFVDDATLQEKGLSNYWGYNTLGFFAPHAAYAA
+SQEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSMRGLDNAGYYHLVEA
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRHWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSAFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGIWSEWNGMYRDTVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRSPGASVNFVTAHDGFTLRDLVSYNEKHNAANGEDNNDG
+ESHNRSWNCGVEGETDDPEVLTLRARQQRNFLATLLISQGVPMISHGDELGRTQGGNNNV
+YCQDNEISWIDWSAVDDSLVAFTRDLIALRHDHAVFRRRHHFDGRPAARDVEAPLPDIVW
+LEPDATAKTEDDWGAEARSIGFYLNGHTLTRGDEDEEGPYRDFYVLMNAWWEPVPYTLPG
+PLFPETWEVVVDTSSHVAPSGSRPRVRAGEVLEVPARSTVILRQVPEGA*
+>NZ_CP083691.1_1105
+MHTVDIGQPYPLGATVDEAGTNFAVAVGREVEAVELCLIAEDGSEERIPVTERHDTTWHV
+HVAGIGGGQRYGWRVHGPWDPARGLWHNPHKLLADPYARAFTGDYAWGQQHFSYAFDEPD
+RMDTADSRGTSMVGVVVDDDFDWGDDAPPQRLLTDTVVYETHVKGLTALHPDVPEELRGT
+YAGVAHPSVLEHLTSLGVTAVELMPVHQFVNDSILQEKGLSNYWGYNSLGYLAPHAAYSS
+ADTVGGQVHEFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPLLSFRGFDNAGYYHLVEG
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGIWSEWNGMYRDTVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRNPGASVNFVTAHDGFTLRDLVSYNEKHNHANGEDNNDG
+DSHNRSWNCGVEGETDDPEVLTLRARQQRNFLTTLMVSEGVPMLSHGDELGRTQKGNNNV
+YCQDNELSWIDWSTRDDALIAFTRDVIALRRDHAVFRRRQHFDGRPAERDVEAPLPDIVW
+LEPDATAKTEADWGAEARSIAFYLNGHDLQRREGEPDEAFRDFYVLMNAWWEPVPYTLPG
+PLFPGEWEIVVDTSSHVAPAGTRPHVVAGEVIEVPGRSTMILREVVRQEQG*
+>NZ_CP097650.1_1559
+MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHA
+HVAGIGHGQRYGYRVHGPWDPARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPD
+RIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYETHVKGMTKLHPAVPEELRGT
+YAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS
+SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEG
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGLWSEWNGMYRDTVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRSPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG
+DAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNV
+YCQDNEISWIDWSAMDDSLVAFTRDLIALRRDHAVFRRRHHFDGRPAARDIEAPLPDIVW
+LEPDATAKTEDDWGAEARSLGFYLNGHTLPRGDEEGEEPYRDFYVLMNAWWEPVPYTLPG
+PTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQVPEGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001368.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001368.fa
new file mode 100644
index 0000000000000000000000000000000000000000..499cbac6e5c315a9eb8db11fd5f264bb3a5d6134
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001368.fa
@@ -0,0 +1,36 @@
+>NZ_CP042169.1_1633
+MDRVTYTPPTSELPLVGPEEPADAVPDGHQRSPFVELDRQTWARLASEMAQPFDQADVER
+LRGLGEHLSLREVAEVYLPLSRLLSINVEASAALRSATNAFLGERTGRTPYVIGVAGSVA
+VGKSTTARVLQEMLRRWPTTPRVELVTTDGFLHPNAVLHERGIMSRKGFPESYDRRALLR
+FMADVKSGAQEVRAPVYSHITYDIVPGEEQVVHRPDVLIVEGLNVLAPPRTRADGTAGLS
+VSDFFDFSVYVDARASWIRSWYIDRFMGLRSGAFADPRSYFHRYSSLSDAEAQATAESIW
+DSINGPNLEQNVRPTRGRARLVLTKNAQHEVTRVLLRKV*
+>NZ_CP033200.1_1348
+MDRVTYTPPTSELPLVGPEEPADAVPDGHQRSPFVELDRQTWARLASEMAQPFDQADVER
+LRGLGEHLSLREVAEVYLPLSRLLSINVEASAALRSATNAFLGERTGRTPYVIGVAGSVA
+VGKSTTARVLQEMLRRWPTTPRVELVTTDGFLHPNAVLHERGIMSRKGFPESYDRRALLR
+FMADVKSGAQEVRAPVYSHITYDIVPGEEQVVHRPDVLIVEGLNVLAPPRTRADGTAGLS
+VSDFFDFSVYVDARASWIRSWYIDRFMGLRSGAFADPRSYFHRYSSLSDAEAQATAESIW
+DSINGPNLEQNVRPTRGRARLVLTKNAHHEVTRVLLRKV*
+>NZ_CP040019.1_1174
+MKDSTQPAPSVPEDLEDDLVSDHHRSPFVELERQTWARLATEMAQPFDQGDVERLRGLGE
+HLSLREVAEVYLPLSRLLSINVEASGALRSATNAFLGERTGRTPYVIGVAGSVAVGKSTT
+ARVLQEMLRRWPTTPRVELITTDGFLHPNAVLQERGIMARKGFPESYDRRALLRFMVDVK
+SGAQEVRAPVYSHITYDIVPGEEQVVRRPDVLIVEGLNVLAPPVTRADGTAGLSVSDFFD
+FSVYVDARADWIRSWYIERFMGLRSGAFADPRSYFHRYATLSDAEAQGTAESIWDSINGP
+NLQQNVQPTRGRARLVLTKNAQHEVTRVLLRKV*
+>NZ_CP083691.1_1102
+MRADAPPPPPPPCAVVLAGRRDAVAGRRPRACHDGPVKDTRDGGGGAPTAPADAPGPASA
+GDPHLSPFVELERQTWARLADQLDQPFDQDDVERLRGLGETLSLREVAEVYLPLSRLLGI
+HVEAAGALRRATNEFLGERTGRTPYVIGVAGSVAVGKSTTARVLQEMLRRWPSTPRVELI
+TTDGFLHPNAVLQERGIMDRKGFPESYDRRALLRFMADVKSGAAEVSAPVYSHVTYDIVP
+ERRQVVHRPDVLIVEGLNVLAPPLLRADGTPGLSVSDFFDFSVYVDARADWIRDWYVERF
+MGLRSSAFRDPDAFFHRYASLSDEEARETARSIWDRINGPNLAQNVQPTRGRARLVLTKN
+RQHEVTRVLMRKV*
+>NZ_CP097650.1_1562
+MDRVTYTPPTSELPLVGPEEPADAVPDGHQRSPFVELDRQTWARLASEMAQPFDQADVER
+LRGLGEHLSLREVAEVYLPLSRLLSINVEASAALRSATNAFLGERTGRTPYVIGVAGSVA
+VGKSTTARVLQEMLRRWPTTPRVELVTTDGFLHPNAVLHERGIMSRKGFPESYDRRALLR
+FMADVKSGAQEVRAPVYSHITYDIVPGEEQVVHRPDVLIVEGLNVLAPPRTRADGTAGLS
+VSDFFDFSVYVDARASWIRSWYIDRFMGLRSGAFADPRSYFHRYSSLSDAEAQATAESIW
+DSINGPNLEQNVRPTRGRARLVLTKNAQHEVTRVLLRKV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001369.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001369.fa
new file mode 100644
index 0000000000000000000000000000000000000000..678a1ab1925ac511bc6f46a8f52cd1c3b59a6179
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001369.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1635
+MLQGFKDFIMKGNVLDLAVAVIIGAAFGKIVNALVEAVLMPLIAAAVGSPNFDSFAVLTV
+NGNDVKFGVLLTAIVNFLLIAAAVYFAIVMPMNKMIEARNRRLGIDPAEEEVPADVAVLT
+EIRDLLAERRGGPTSGTTTL*
+>NZ_CP033200.1_1350
+MLQGFKDFIMKGNVLDLAVAVIIGAAFGKIVNALVEAVLMPLIAAAVGSPNFDSFAVLTV
+NGNDVKFGVLLTAIVNFLLIAAAVYFAIVMPMNKMIEARNRRLGIDPAEEEVAADVAVLT
+EIRDLLAERRGGPTSGTTTL*
+>NZ_CP040019.1_1172
+MKGNVIDLAVAVVIGAAFGAVINAVVDSVLMPLIAALFAAPSFDDWLVLDINGVLVKFGV
+VLTAVVNFLLIAAAIYFAIVLPMNKMIERRNRRLGIDPAEEEVPEDVALLTEIRDLLSAQ
+RGGAAGTTHTTL*
+>NZ_CP083691.1_1101
+MKGNVVDLAVAVVIGAAFGKVVTALVDSVLMPLIAALFKAPSFDSWLVLNLNGVDVKFGV
+VLTAIVNFLLIAAAVYFCIVLPMNTMIERRNRRLGITPAEDEVAPDVAVLTEIRDLLARQ
+NGAPRV*
+>NZ_CP097650.1_1564
+MLQGFKDFIMKGNVLDLAVAVIIGAAFGKIVNALVEAVLMPLIAAAVGSPNFDSFAVLTV
+NGNDVKFGVLLTAIVNFLLIAAAVYFAIVMPMNKMVEARNRRLGIDPAEEEVPADVAVLT
+EIRDLLAERRGGPTSGTTTL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001382.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001382.fa
new file mode 100644
index 0000000000000000000000000000000000000000..84722289ac3e48a4ad69cceaf086e60f4cc89367
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001382.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1649
+MIGRRSLELKTAPQLQAMQRAGVVLSEALDATLAAAAPGVTTAELDAVFAGVLAERGATS
+NFLGYYDFPASICTSVNDEVVHGIPGDRVLQTGDVLKVDGGAIVDGWHADSARTVILGSS
+EAGTAGPADERLSAITREALWVGIAAFASATHVGDIGDAIDDFVSAQPGEELGILEEYVG
+HGIGSAMHLPPDVFNYRTGHRGPKIRPGLALAIEPMLVRGSIDTKVLADDWTVVTLDGAR
+ASQWEHSVCRHDGGVWVLTAPDGGASELARFGVVPVPPGE*
+>NZ_CP033200.1_1367
+MIGRRSLELKTAPQLQAMQRAGVVLSEALDATLTAAAPGVTTAELDAVFAGVLAERGATS
+NFLGYYDFPASICTSVNDEVVHGIPGDRVLQTGDVLKVDGGAIVDGWHADSARTVILGSS
+AAGTADPADERLSAITREALWVGIAAFASATHVGDIGDAIDDFVSAQPGEELGILEEYVG
+HGIGSAMHLPPDVFNYRTGHRGPKIRPGLALAIEPMLVRGSIDTKVLADDWTVVTLDGAR
+ASQWEHSVCRHDGGVWVLTAPDGGASELARFGVVPVPPGE*
+>NZ_CP040019.1_1158
+MVGRRSLELKTTPQLQTMRRAGVVLSEALDATLAAAAPGVTTAELDAVFAGVLAEHGATS
+NFLGYYDFPATICASVNEEVVHGIPGDRVLQAGDVLKVDGGAIVDGWHADSARTLVLGSS
+EAGTADEGDERLSAITREALWVGIAAFATAKHVGDIGDAIDDFVSAQPGEPLGILEEYVG
+HGIGSSMHMPPDVFNYRTGHRGPKVRPGLALAVEPMLVRGGIETRVLEDDWTVVTVDGAR
+ASQWEHSVCRHAGGLWVLTAPDGGASELERFGVVPVPPGE*
+>NZ_CP083691.1_1087
+MFSRRSIELKTTPQLQTMQRAGVVLSEALDAAVAAAAPGVTTAEVDAVFADVLAQHGATS
+NFLGYYGYPATVCASVNEEVVHGIPGERVLQQGDVLKIDGGAIVDGWHSDSARTLILGSS
+EAGTADPEDERLSEITRQALWVGIAAFAQARHVGEIGDAVDDFVTSQPGAPLGILEDYVG
+HGIGSAMHLAPDVFNYRTGHRGPKVQHGMALAIEPMLVRGGIETRTLEDEWTVVTTDGAR
+ASQWEHTVCRHPGGVWVLTAPDGGAAELAAHGVVPVPPGE*
+>NZ_CP097650.1_1578
+MIGRRSLELKTAPQLQAMQHAGVVLSEALDATLTAAAPGVTTAELDAVFAGVLAERGATS
+NFLGYYDFPASICTSVNDEVVHGIPGDRVLQTGDVLKVDGGAIVDGWHADSARTVILGSS
+AAGTADPADERLSAITREALWVGIAAFASATHVGDIGDAIDDFVTAQPGEELGILEEYVG
+HGIGSAMHLPPDVFNYRTGHRGPKIRPGLALAIEPMLVRGSIDTKVLADDWTVVTLDGAR
+ASQWEHSVCRHDGGVWVLTAPDGGASELARFGVVPVPPGE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001385.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001385.fa
new file mode 100644
index 0000000000000000000000000000000000000000..885336ad995b6b0c490279b63e84f1970590019e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001385.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1652
+MADNDAIKVHDLRPAPGAKTAKTRVGRGEASKGKTAGRGTKGTKARYQVRAGFEGGQLPL
+QMRLPKLRGFKNPFRTEYQVVNLDKLSAHFPEGGEVTVDALVSKGLVRRGQPVKVLGTGE
+ITSAVQVKANAFSSSAVEKIQAAGGSTETL*
+>NZ_CP033200.1_1370
+MADNDAIKVHDLRPAPGAKTAKTRVGRGEASKGKTAGRGTKGTKARYQVRAGFEGGQLPL
+QMRLPKLRGFKNPFRTEYQVVNLDKLSAHFPEGGEVTVDALVSKGLVRRGQPVKVLGTGE
+ITSAVQVKANAFSSSAVEKIQAAGGSTETL*
+>NZ_CP040019.1_1155
+MADNDAIKVHDLRPAPGAKTAKTRVGRGEASKGKTAGRGTKGTKARYQVRAGFEGGQLPL
+QMRLPKLRGFKNPFRTEYQVVNLDKLSAHFPEGGEVTVDALVSKGLVRRGQPVKVLGTGE
+ITSAVQVKVDAFSASAVEKIQAAGGSTETL*
+>NZ_CP083691.1_1084
+MAENDAIKVHDLRPAPGAKTAKTRVGRGEGSKGKTAGRGTKGTKARYQVRAGFEGGQLPL
+QMRLPKLRGFKNPFRTEYQVVNLDKLSEMFPEGGEVTVETLVSKGLVRKNQPVKVLGTGE
+ITSAVQMKADAFSASAIEKIKAAGGSAETV*
+>NZ_CP097650.1_1581
+MADNDAIKVHDLRPAPGAKTAKTRVGRGEASKGKTAGRGTKGTKARYQVRAGFEGGQLPL
+QMRLPKLRGFKNPFRTEYQVVNLDKLSAHFPEGGEVTVDALVSKGLVRRGQPVKVLGTGE
+ITSAVQVKANAFSSSAVEKIQAAGGSTETL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001388.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001388.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e40e91832966a9c5c1c2e697998c0420855755b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001388.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1655
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIDAVVFDRGGNKYHGRVAAVADGAREG
+GLQL*
+>NZ_CP033200.1_1373
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLQL*
+>NZ_CP040019.1_1152
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAWA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLKL*
+>NZ_CP083691.1_1081
+MSTLKVKGKGKFNARTRRHLRVRKRISGTAVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRAFDGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLQL*
+>NZ_CP097650.1_1584
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLQL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001392.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001392.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f6974f9cd34f482e73a954eaef2b3577dba559e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001392.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1659
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKDGVSKTVKVRFAKASGKEL*
+>NZ_CP033200.1_1377
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKDGVSKTVKVRFAKASGKEL*
+>NZ_CP040019.1_1148
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGR
+QVAEAPIHISNVAVVDPETKKPTRVGYRFETVEKNGESKTVKVRFAKASGKEL*
+>NZ_CP083691.1_1077
+MAKIKKDDLVQVLSGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQNNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKNGEQVTVKVRFAKASGKEL*
+>NZ_CP097650.1_1588
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKDGVSKTVKVRFAKASGKEL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001393.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001393.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4da19b7f3a7e6874716e8ac79dbb063a2fcc1d6e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001393.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1660
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI*
+>NZ_CP033200.1_1378
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI*
+>NZ_CP040019.1_1147
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI*
+>NZ_CP083691.1_1076
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIRFDENAAVILKNDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI*
+>NZ_CP097650.1_1589
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001397.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001397.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a44f4be8dce6c1091220ab0eb0dfbbbd4d374a3e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001397.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1664
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGVRRSGGERR
+RRNDRAERAPRQENAGAGAETPAAAPAEGGNA*
+>NZ_CP033200.1_1382
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGERRGGGERR
+RRNDRAERAPRQENAGAGAETPAAAPAEGGNA*
+>NZ_CP040019.1_1143
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCAGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGDRRGGGGGE
+RRRRNDRAERAPRQENAGAGAETPAAAPAEGGNA*
+>NZ_CP083691.1_1072
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTDGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTYGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGERRGPGGGE
+RRRRNDRAERAPRQENAGAGAEQSAAAPAEGGNA*
+>NZ_CP097650.1_1593
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGERRGGGERR
+RRNDRAERAPRQENAGAGAETPAAAPAEGGNA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001400.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001400.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6d48069338e8f29e4711547887e010bbe57b798
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001400.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1667
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR*
+>NZ_CP033200.1_1385
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR*
+>NZ_CP040019.1_1140
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR*
+>NZ_CP083691.1_1069
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLIDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLQQGDVVEAG
+PNADIKPGNNLPLRNIPVGTTIHAVELRPGGGAKMARSAGASIQLVAREGKYAQLRLPSG
+EIRNVDVRCRATVGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNPNGKPEGRTRRPNKESDKLIVRRRRTGKNKR*
+>NZ_CP097650.1_1596
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001402.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001402.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81e4930a74ce599431345fccc7787868899fccc9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001402.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1669
+MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ*
+>NZ_CP033200.1_1387
+MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ*
+>NZ_CP040019.1_1138
+MAENSVKTVQVDLPAEIFDVQSNVPLMHQVVVAQLAAARQGTHKVKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGIVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ*
+>NZ_CP083691.1_1067
+MAENTVKTVQVELPAEIFDVQANVPLMHQVVVAQLAAARQGTHKVKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGIVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLESLNTGRKNVLLVIDRADDLTALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTKVAYEAYVAQASGAKKEDAQ*
+>NZ_CP097650.1_1598
+MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001404.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001404.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d8b767ce545d4a745edb7e0a7e7c4c16df0d5f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001404.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1671
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL*
+>NZ_CP033200.1_1389
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL*
+>NZ_CP040019.1_1136
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL*
+>NZ_CP083691.1_1065
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL*
+>NZ_CP097650.1_1600
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001405.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001405.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ec797448c880e8327708f273e6ba108e959d1b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001405.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1672
+MSLPSPRRLFAVTAMAEMFTWAGLLIAMGLKYGGVTERVVPIAGGVHGFVFLCYLVVTVA
+VWIDGRWPVARGLLGLGSTIVPFMTVPFERAQRRRGEPASRWQVVDRAPGERRPLERLLV
+VVLRHPVVSALLAVAVVAVVFTLLLNAGPPTEWGR*
+>NZ_CP033200.1_1390
+MSLPGPRRLFAVTAMAEMFTWAGLLIAMGLKYGGVTERVVPIAGGVHGFVFLCYLVVTVA
+VWIDGRWPVARGLLGLGSTIVPFMTVPFERAQRRRGEPASRWQVVDRAPGERGPLERLLV
+VVLRHPVVSALLAVAVVAVVFTLLLNAGPPTEWGR*
+>NZ_CP040019.1_1135
+MSLPSPRSLFRVTAAAEMVTWAGLLTAMALKYTGVTDAVMPIAGGIHGFVFLCYFVVTVA
+VWIDGRWPAARGLLGLGSAVVPFMTVPFERAQLRRGEPARHWRVLEGEPGERTGAQRVLA
+AVLGRPLVSALVALIAVVVVFTLLLNAGPPTEWGR*
+>NZ_CP083691.1_1064
+MRVPGPRSLYRATAVAEMATWTLLLLAMALKYGGVTAALMPAAGGVHGFVFLCYAAVVVA
+VWIDGRWGVGRGLLALGSAVVPYMTVPMERALLRRGEPAPRWRVLEEAGRTSATDRLLRT
+VLRRPRVSALAVLVAVVVVFSLLLRAGPPTEWFSR*
+>NZ_CP097650.1_1601
+MSLPSPRRLFAVTAMAEMFTWAGLLIAMGLKYGGVTERVVPIAGGVHGFVFLCYLVVTVA
+VWIDGRWPVARGLLGLGSTIVPFMTVPFERAQRRRGEPASRWQVVDRAPGERRPLERLLV
+VVLRHPVVSALLAVAVVAVVFTLLLNAGPPTEWGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001409.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001409.fa
new file mode 100644
index 0000000000000000000000000000000000000000..185e640554cfcc417e001161e219bd2507f93322
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001409.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1676
+MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLVDGKKSTAERIVYGALEGARAKNGADPVA
+TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL
+MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW*
+>NZ_CP033200.1_1394
+MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLVDGKKSTAERIVYGALEGARAKNGADPVA
+TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL
+MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW*
+>NZ_CP040019.1_1131
+MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLIDGKKSTAERIVYGALEGARAKNGADPVA
+TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL
+MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW*
+>NZ_CP083691.1_1060
+MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLIDGKKSTAERIVYGALEGVRAKNGADPVA
+TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL
+MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW*
+>NZ_CP097650.1_1605
+MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLVDGKKSTAERIVYGALEGARAKNGADPVA
+TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL
+MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001411.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001411.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e44533fcc34f53e30e754e3715c3cfe6f81cd40e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001411.fa
@@ -0,0 +1,115 @@
+>NZ_CP042169.1_1678
+MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC
+ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL
+APKDLEKVIYFAAYMITSVDEEARHRDLANLQAEYDQETRVLADQRDSDIAAVAADLEKD
+LAKLESEGAKAAEKKKARDAADKTMAQIRKRADADLDRKEQVWDRFKNLKVADLEGDEGL
+YRAMRDKYGQYFEGSMGAEAIQRRLQTFDLEAESEMLRETIKTGKGQRKTRALKRLKVVN
+AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL
+GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK
+RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR
+PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ
+MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDEVGAGN
+LYATVGEAIMAFDGGDLHLNAPARIGVEGFVPSADVPAPEGWSEGEIALIETTLGKVLFN
+ELLPDDYPWLDKQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS
+DITSDFDKAAIMEGYEEQAQRVQQQYDKGLIADDERRSELIDIWNKATDEVAAAMKDGLP
+ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH
+GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTERGLSVTIAAPNADGELVAHE
+QVENSAFARTLAQDVTGEDGTVLASAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT
+CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ
+ELFEARTPKGVAPISEVAGRVTIEDTETSVRLLLTPDDGSEEIAYPVLRRARILVADGEH
+VPVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR
+ITVIESGDTDLLPGELTDRARFVAANRAAVAEGRQPASGRDELMGITKASLATDSWLSAA
+SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA
+SPAGFADFDYPGLDQSLGENDFHAVSLDDYGRGGDFRA*
+>NZ_CP033200.1_1396
+MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC
+ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL
+APKDLEKVIYFAAYMITSVDEEARHRDLANLQAEYDQETRVLADQRDSDIAAVAADLEKD
+LAKLESEGAKAAEKKKARDAADKTMAQIRKRADADLDRKEQVWDRFKNLKVADLEGDEGL
+YRAMRDKYGQYFEGSMGAEAIQRRLQTFDLEAESEMLRETIKTGKGQRKTRALKRLKVVN
+AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL
+GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK
+RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR
+PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ
+MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDEVGAGN
+LYATVGEAIMAFDGGDLHLNAPARIGVEGFVPSADVPAPEGWSEGEIALIETTLGKVLFN
+ELLPDDYPWLDKQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS
+DITSDFDKAAIMEGYEEQAQRVQQQYDKGLIADDERRSELIDIWNKATDEVAAAMKDGLP
+ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH
+GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTERGLSVTIAAPNADGELVAHE
+QVENSAFARTLAQDVTGEDGTVLASAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT
+CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ
+ELFEARTPKGVAPISEVAGRVTIEDTEASVRLLLTPDDGSEEIAYPVLRRARILVADGEH
+VPVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR
+ITVIESGDTDLLPGELTDRARFVAANRAAVAEGRQPASGRDELMGITKASLATDSWLSAA
+SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA
+SPAGFADFDYPGLDQSLGENDFHAVSLDDYDRGGDFRA*
+>NZ_CP040019.1_1129
+MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC
+ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL
+APKDLEKVIYFAAYMITSVDEEGRHRDLANLQAEYDQETRVLADQRDADIAAVAADLEKD
+LAKLESEGAKAAEKKKARDAADKTMSQIRKRADAELDRKEQVWDRFKNLKVADLEGDEGL
+YRTMRDKYGQYFEGSMGAEAIQRRLQTFDLAAESEMLRETIKTGKGQRKTRALKRLKVVN
+AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL
+GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK
+RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR
+PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ
+MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDAVGAGN
+AYATVGEAVMAFDGGDLHLNAPVKIGVDGFVPSTAVPAPEGWSEGELAVIETTLGKVLFN
+ELLPADYPWLDTQATKGSLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS
+DITSDFDKAAIMEGYEEQALRVQQQYEKGLIADDERRSELIDIWNKATDEVAAAMKDGLP
+ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH
+GARKGLADTALKTANSGYLTRRLVDVSQDVIVREEDCGTERGLSVTIAVPNADGELVAHE
+QVENSAFARTLAQDVTGEDGSVLASGGADVGDVLIDQLVGAGVSEIKVRSVLTCESAVGT
+CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ
+ELFEARTPKGVAPISEVAGRVTIEDTDASVRLLLTPDDGSEEIAYPVLRRARILVADGEH
+VAVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR
+ITVIESGETDLLPGELTDRARFVAANRSAVAEGRQPASGRDELMGITKASLATDSWLSAA
+SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA
+SPAGFADFDYPGLDQQLGESDFHAVSLDDYGRGGDFRS*
+>NZ_CP083691.1_1057
+MTTENPFGLMRIGLATADDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC
+ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL
+APKDLEKVIYFAAYMITSVDEEARHRDLPNLQAEHDQETRVLEDQRDADIAAVAADLEKD
+LAKLEAEGAKAAEKKKARDAADKTMAQIRKRADAELDRKAQVWDRFKNLKVADLEGDEGL
+YRAMRDKFGAYFEGSMGAEAIQRRLQTFDLAAESELLRETIKTGKGQRKTRALKRLKVVN
+AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL
+GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK
+RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNVKSAKRMVERFR
+PQVWDVLEEVISEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ
+MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRAEGKGAGR
+QFATVGEAVMAFDNGELHLNAPATIGVEGFVPSAAVAAPEGWTEGEVALIETTLGKVIFN
+DLLPADYPWLDTQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS
+DITSDFDKASIMQGYEDQAQRVQAQYDKGLIADDERRSELIDIWNKATDEVAAAMKAGLS
+ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH
+GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTGRGLSVTIAEPNHDGELVVRE
+QVENSAFARTLAQAVTAEDGTVLAEAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT
+CAKCYGRSMATGKLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ
+ELFEARTPKGVAPISEVAGRVTIEDTDASVRLILTPDDGSEEIAYPVLRRARLLVADGEH
+VAVGTQLVAGAVDPKQVLRVLGPRAAQRFLVQEVQDVYQSQGVGIHDKHVEVIVRQMLRR
+ITVIESGETDLLPGELTDRSRFVAANRAAVAEGKQPAAGRDELMGITKASLATDSWLSAA
+SFQETTRVLTQAAMEGKEDPLLGLKENVIIGKLIPAGTGLDRYTQTTVEPTEEAKANLFA
+APVGFADFDYPGLDQPLGEAEFHAVSLDDYGRGGDFRA*
+>NZ_CP097650.1_1607
+MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC
+ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL
+APKDLEKVIYFAAYMITSVDEEARHRDLANLQAEYDQETRVLADQRDSDIAAVAADLEKD
+LAKLESEGAKAAEKKKARDAADKTMAQIRKRADADLDRKEQVWDRFKNLKVADLEGDEGL
+YRAMRDKYGQYFEGSMGAEAIQRRLQTFDLEAESEMLRETIKTGKGQRKTRALKRLKVVN
+AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL
+GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK
+RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR
+PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ
+MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDEVGAGN
+LYATVGEAIMAFDGGDLHLNAPARIGVEGFVPSADVPAPEGWSEGEIALIETTLGKVLFN
+ELLPDDYPWLDKQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS
+DITSDFDKAAIMEGYEEQAQRVQQQYDKGLIADDERRSELIDIWNKATDEVAAAMKDGLP
+ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH
+GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTERGLSVTIAAPNADGELVAHE
+QVENSAFARTLAQDVTGEDGTVLASAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT
+CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ
+ELFEARTPKGVAPISEVAGRVTIEDTETSVRLLLTPDDGSEEIAYPVLRRARILVADGEH
+VPVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR
+ITVIESGDTDLLPGELTDRARFVAANRAAVAEGRQPASGRDELMGITKASLATDSWLSAA
+SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA
+SPAGFADFDYPGLDQSLGENDFHAVSLDDYGRGGDFRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001418.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001418.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20fae50083b6914ffadace7c8888f3dbe7f9695e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001418.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1685
+MAANGGGPAPTPSRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVAFMI
+LLVMGLDWVFGTVAGLLFGAGGL*
+>NZ_CP033200.1_1403
+MAANGGGPTPTPSRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVAFMI
+LLVMGLDWVFGTVAGLLFGAGGL*
+>NZ_CP040019.1_1122
+MTDIAANGGGSTPAPDRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVA
+FMILLVMGLDWVFGTVAGLLFGGGGGL*
+>NZ_CP083691.1_1050
+MTANHGSSASGPESRRRGPFGRIALFLRQVLDELRKVVTPTGDELLKMTGVVLAFVAVMI
+LLVMGLDWVFGTLAGLLFGAGPA*
+>NZ_CP097650.1_1614
+MAANGGGPAPTPSRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVAFMI
+LLVMGLDWVFGTVAGLLFGAGGL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001419.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001419.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aab3be71192115cb5b080bbcd0ea051d345c5818
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001419.fa
@@ -0,0 +1,41 @@
+>NZ_CP042169.1_1686
+MAAPARRVSARLSAIAPSATLAVDARAKELKAAGRPVIGFGAGEPDFPTPDYIVEAAVAA
+ARDPKNHRYSPASGLPELREAIADKTLRDSGVSLEAAQVLVTNGGKQAVYNAFAALLDPQ
+DEVLVPAPYWTTYPEAIRLAGGVPVEVFAGPEQGYKVTVDQLDESVTDRTKVLLFVSPSN
+PTGAVYSPEETAAIGQWARERGLWVVTDEIYEHLTYDGMPFTSIVRAVPELAEQSVILNG
+VAKTYAMTGWRVGWMAGPLDVVKAATNLQSHATSNVANVSQRAALAAIAGPLDAVAEMKT
+AFDRRRRAMVEAMDAVPGFHCPTPQGAFYAYVDVREALAKTYRGGVTPATSAELAAFILD
+EAEVAVVPGEAFGPSGYLRLSYALGDADLAEGVERIRALLSA*
+>NZ_CP033200.1_1404
+MAAPARRVSARLSAIAPSATLAVDARAKELKAAGRPVIGFGAGEPDFPTPDYIVEAAVAA
+ARDPKNHRYSPAAGLPELREAIAAKTLRDSGVSLEAAQVLVTNGGKQAVYNAFAALLDPQ
+DEVLVPAPYWTTYPEAIRLAGGVPVEVFAGPEQGYKVTVDQLDESVTDRTKVLLFVSPSN
+PTGAVYSPEETAAIGQWARERGLWVVTDEIYEHLTYDGMPFTSIVRAVPELAEQSVILNG
+VAKTYAMTGWRVGWMAGPLDVVKAATNLQSHATSNVANVSQRAALAAIAGPLDAVAEMKT
+AFDRRRRAMVEAMDAVPGFHCPTPQGAFYAYVDVREALAKTYRGGVTPATSAELAAFILD
+EAEVAVVPGEAFGPSGYLRLSYALGDADLAEGVERIRALLSA*
+>NZ_CP040019.1_1121
+MIGFGAGEPDFPTPAYIVEAAVAAAKDPKNHRYSPAAGLPELREAIAAKTLRDSGVAIDV
+AQVLVTNGGKQAVYNTFAALLDPQDEVLVPSPYWTTYPEAIRLAGGVPVDVFAGPEAGYK
+VSVEQLEAAVTERTKALLFVSPSNPTGAVYSPEETEAVGRWALDRGLWVITDEIYEHLTY
+DGMPFTSILKAVPELAEQAVILNGVAKTYAMTGWRVGWMAGPLDVIKAATNLQSHATSNV
+SNVSQRAALAAVAGPLDAVDEMKVAFDRRRRAMVEAMNAVPGFHCPTPQGAFYAYVDVRE
+ALGRTYRGGVTPTTSAELATFILDEAEVAVVPGEAFGPSGYLRLSYALGDDDLAEGVERI
+RALLSE*
+>NZ_CP083691.1_1049
+MTRAPSNRAGTSAPDGGSVGWPHGRRVRVRRPPEQMRKVPMATPAHRVSARLSAIAPSAT
+LAVDAKAKALKAAGRPVIGFGAGEPDFPTPDYIVEAAVAAARDPKNHRYSPAAGLPELRE
+AIAAKTLRDSGVELDASQVLVTNGGKQAVYNAFAALLDPQDEVLVPSPFWTTYPEAIRLA
+GGVPVDVFAGPDQGYKVTVDQLEAAHTERTKVLLFVSPSNPTGAVYSPEETRAIGEWALA
+KGLWVVTDEIYEHLTYDGVPFTSILKAVSGLAEQGVILNGVAKTYAMTGWRVGWLAGPLD
+VVKAATNLQSHATSNVANVSQRAALAAVAGPLDAVEEMKTAFDRRRRAMVEALNRVPGFH
+CPTPEGAFYAYVDVREALGRTYTGGVTPATSAELADFILDQAEVAVVPGEAFGPSGYLRL
+SYALGDEDLAEGVERIRALLSA*
+>NZ_CP097650.1_1615
+MAAPARRVSARLSAIAPSATLAVDARAKELKAAGRPVIGFGAGEPDFPTPDYIVEAAVAA
+ARDPKNHRYSPAAGLPELREAIAAKTLRDSGVSLEAAQVLVTNGGKQAVYNAFAALLDPQ
+DEVLVPAPYWTTYPEAIRLAGGVPVEVFAGPEQGYKVTVDQLDEAVTDRTKVLLFVSPSN
+PTGAVYSPEETAAIGRWARERGLWVVTDEIYEHLTYDGMPFTSIVRAVPELAEQSVILNG
+VAKTYAMTGWRVGWMAGPLDVVKAATNLQSHATSNVANVSQRAALAAIAGPLDAVAEMKT
+AFDRRRRAMVEAMDAVPGFHCPTPQGAFYAYVDVREALGKTYRGDVTPTTSAELAAFILD
+EAEVAVVPGEAFGPSGYLRLSYALGDADLAEGVERIRALLSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001422.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001422.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d16717807802256db7bfb7f49b637a0c9b3f6677
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001422.fa
@@ -0,0 +1,36 @@
+>NZ_CP042169.1_1689
+MTSTHDPFTGPGPHVAPDGAAAGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG
+VAERYRIDPLLARGVFVAVCMVSAGLGLLAYAAAWAVLPDPDGRVQFGRLRRGEWQDATV
+AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLVGLGALAVLVWWLVTRWDGRAQARVAPG
+RVPDADQPAHAVPRPAWYVGGGPRERAAEVTDPHGFRPEWIDPATGTWRDHVHSRERRAA
+TRLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP
+TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG*
+>NZ_CP033200.1_1407
+MTSTHDPFTGPGPHVAPDGAASGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG
+VAERYRIDPLLARGVFVAVCMVSAGLGLLAYAAAWAVLPDADGRVQFGRLRRREWQDATV
+AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLLGLGALAVLVWWLVTRWDGRAQARVAPG
+RAPDADQPSHAVPRPAWYVGGGPRERAAEVTDPHGFHPEWIDPATGTWRDHVHSRERRAA
+ARLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP
+TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG*
+>NZ_CP040019.1_1118
+MRRSDSSWVGGVLAGVAERYRVDPLLARGVFVALCVVSAGFGLLAYAVAWALLPDGDGTV
+HYGRLRRGEWQDATVAIAVIGGIGVLNVVLGAGFTLLAPVVGGPGSLLGLAAVAVLVWWL
+VTRWDGSTQSRVGPAPASEPEASGRAAARPAWYLRRDDARAAASRQDAHGFRADWLDPET
+GTWRSPVHSRELRAAARLAEEEQAAPAGPSGRGSAVVAAPRRLSPAVQAVTYAVAALAAA
+AAVGASLLVGVGSLTLLAVPAIVAALAVIAPVMLAALLTGRRPGSLAPASGILVGAAALQ
+VAVAVAVL*
+>NZ_CP083691.1_1046
+MDTAHDPFPAPRSSPATRPLPPGPASDARSRSAGTDGPAPDGLEVLPVWLRRPVEGWGVR
+RSRSSWVGGVLAGVAERYRIDPLLSRGVFVALCVVSAGIGLLGYALAWAVLPDADGRVHY
+GRLRRGEWSDAPVAIAAIAAIGALNVVLGAGFTLIAPVLGGPGSLIGLTALAVLVWWLVT
+RWDGEGERRMAPAQPARDAAARPAAEPSWYLRRHRPESATVDAHGFRSDWIDPETGSWRE
+QPHSREHRAAARLAEAQVRAAGQAAGRRPAGTGRGSHSAVKPLLGRGTRIATCVVAAGVA
+LAVSLAMVLGNVSTSATLFPVWPALAALGVMAAVMTAGLLRGRRPGLLAPLSGILVGVVA
+LQVCAHLLFTPLP*
+>NZ_CP097650.1_1618
+MTSTHDPFTGPGPHVAPDGAAAGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG
+VAERYRIDPLLARGVFVAVCMISAGLGLLAYAAAWAVLPDADGRVQFGRLRRGEWQDATV
+AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLVGLGALAVLVWWLVTRWDGRAQARVAPG
+RVPDADQPAHAVPRPAWYVGGGPRERAAEVTDPHGFRPEWIDPATGTWRDHVHSRERRAA
+ARLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP
+TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001425.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001425.fa
new file mode 100644
index 0000000000000000000000000000000000000000..187cd636f44ca49d7fca85e11d6a5acc27694054
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001425.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1692
+MTTSRSPLLDLAVAEPQGPAGGAVEGRGPDAGVAAHYGRPLPEQRALARGRALVDLSHRA
+VLSVSGPDRLSWLHTLGTQHVETLPPGTSTEILFLDVQGRIEHAAHLLEDGTAAWLVTDR
+EDGPGLAAWLTSMRFSHDVTLRDHTGAVAVVGATAPVPGWEDRTVWLDPWPRVGAGGWAY
+TADPDPATHPGADWSWREYLVTRADLEATVRALGTGVLAGWSLAGTTAAEALRIEAGRPR
+RALDVDDRAIPHELDLLRTAVHLEKGCYRGQETVARVHNLGRPPRRLTRLLLDGSGHALP
+EHGAPVILRPAEDTPEARAAARPVGTVTAAAQHHEAGAVALALLKRTVPVDAELLVREDA
+PGEDGVAEGGWIAASQEPLVSPDAGQVVGRPRGVGRLR*
+>NZ_CP033200.1_1410
+MTTSRSPLLDLAVAEPQGPAGGAVEGRGPDAGVAAHYGRPLPEQRALARGRALVDLSHRA
+VLSVSGPDRLSWLHTLGTQHVETLPPGTSTEILFLDVQGRIEHAAHLLEDGTAAWLVTDR
+EDGPGLAAWLTSMRFSHDVTLRDHTGAVAVVGATAPVPGWEDRTVWLDPWPRVGAGGWAY
+TADPDPATHPGADWSWREYLVTRADLEATVRALGTGVLAGWSLAGTTAAEALRIEAGRPR
+RALDVDDRAIPHELDLLRTAVHLEKGCYRGQETVARVHNLGRPPRRLTRLLLDGSGHALP
+EHGAPVILRPAEDTPEARAAARPVGTVTAAAQHHEAGAVALALLKRTVPVDAELLVREDA
+PGEDGVAEGGWIAASQEPLVSPDAGQVVGRPRGVGRLR*
+>NZ_CP040019.1_1114
+MTGAEPAQRSPLLDLASAEPHGPAGGAVEGVGPDAGVAAHYGRPLPEQRALARGRALVDL
+SHRAVLSVSGPDRLTWLHTLGTQHVADLPAGTSTEILFLDAQGRIEHAAHLLEDGTAAWL
+VTDREDGPGLAAWLASMRFSHQVTLRDHTGAVAVVGSTAPVPGWEDRTVWVDPWPHVGVG
+GWAYTADPRPESHPGADWSWREHLVTRADLEATVRTLGTGPLEGWSLAGTTAAEALRIEA
+GRPRMATDVDERALPHELDLLRTAVHLEKGCYRGQETVARVHNLGRPPRRLTRLMLDGSV
+HALPPHGAPVILRPAEDTPQARAAARPVGAVTSSAQHHEAGAVALALLKRSVPVDAELLV
+CEDLPGDAEAGDAADAAETGWIAAAQEPLVSPAAGQVVGRPRGVGRLR*
+>NZ_CP083691.1_1042
+MTEPRPEPAPAVRAARRSPLLAPPPAAPGGPAEGAVEGVGQDAGVAAHYGRPLVEQRALA
+RGRALVDLSQKTVVSVSGPDRLSWLHTLSTQHLKDRPAGTSTEALFLDANGRIEIAVHLL
+EDGAAAWLIADPAHADVLVTWLRSMVFSHRVTLRDHTGVVAVVGAMAPVPGWEDRTVWLD
+PWPRVDVGGWPYSPDPDPAAHPGAGWSWREYLVTRGDLVATVDRLGTGELEGWSLAGALA
+AEALRIEAGRPRPAVDADARAIPHELDILRTAVHLEKGCYRGQETVARVYNLGRPPRRLT
+QLLLDGSSHALPAAGAAVILRPEPDTADARAAARPVGTVTSAVQHHEAGAVALAVLKRAV
+PVAAELLVREEAAGGGEPEWIAASQQALVSPDAGQVVGRPAGLSRRA*
+>NZ_CP097650.1_1621
+MTTSRSPLLDLAVAEPQGPAGGAVEGRGPDAGVAAHYGRPLPEQRALARGRALVDLSHRA
+VLSVSGPDRLSWLHTLGTQHVETLPPGTSTEILFLDVQGRIEHAAHLLEDGTAAWLVTDR
+EDGPGLAAWLTSMRFSHDVTLRDHTGAVAVVGATAPVPGWEDRTVWLDPWPRVGAGGWAY
+TADPDPATHPGADWSWREYLITRADLEATVRALGTGVLAGWSLAGTTAAEALRIEAGRPR
+RALDVDDRAIPHELDLLRTAVHLEKGCYRGQETVARVHNLGRPPRRLTRLLLDGSVHALP
+EHGAPVILRPAEDTPEARAAARPVGTVTAAAQHHEAGAVALALLKRTVPVDAELLVREDA
+PGEDGAAEGGWIAASQEPLVSPDAGQVVGRPRGVGRLR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001430.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001430.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b44dff7d7daf3441d605499994f66af3a65e086a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001430.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1697
+MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPGGLEVMVIHRPRYDDWSWPKGK
+LDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPGKRGARQSKEVWYWAAEVDGQRA
+LPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRAASRGRLRTVPLLVLRHAKAKPRS
+SWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSSPWRRCVETLAPLVKSSRLALKTK
+GAFTETTAREKPQKTRKVMAELMGRSRPLVVCTHRPVLPTLFEVVEDAAAGRTDRVLRAL
+PTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD*
+>NZ_CP033200.1_1415
+MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPGGLEVMVIHRPRYDDWSWPKGK
+LDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPGKRGARQSKEVWYWAAEVDGQRA
+LPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRAASRGRLRTVPLLVLRHAKAKPRS
+SWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSSPWRRCVETLAPLVKSSRLALKTK
+GAFTETTAREKPQKTRKVMAELMGRSRPLVVCTHRPVLPTLFEVVEDAAAGRTDRVLRAL
+PTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD*
+>NZ_CP040019.1_1109
+MPSTPTERVARWSTEDRAADGPRAEVLAAGVVPWRRTPGGRLEVLVIHRPRYDDWSWPKG
+KLDPGETLPQCAVRELREEVGLALRPGIPLCVTEYEVSGKRGARLTKEVWYWAADAGAQR
+AVPDGDEVDEVRWVRPEEAEALLTNETDREPLELLVRADSRGRLRTLPLLVLRHAKAKPR
+SSWSRAEQERPLAATGRRQALAVEGLVAAWAPDRLVSSPWRRCVETLAPLVKSSRLPLKT
+KGAFTETAAKEKPKKTRKAMHELLGRQRAQVVCTHRPVLPVLFEVVEDAARRQERVLRAM
+PREDPWLRPGAVLVVHRSLDGDVVAVEAYDPWDD*
+>NZ_CP083691.1_1036
+MTRPLSWDGIPDPIPPEDPRTMSAHPDDRAAAWSTPDGAVTAPGAEVLAAGMIPWRPGAE
+GLEVLVIHRPRYDDWSWPKGKVDDGETLPEAAARELAEEVALTLRPGLPLAVTRYDVPDR
+KGKGMLSKEVWYWAGEATGQRPTPDGDEVDEARWVSSARAREMLSNATDLEPLDRLERAD
+ARGHLRTVPLLVLRHAKAKPRSSWSRAEQERPLAATGRRQAHSVARLIAVWRPERVVSSP
+WRRCVETLAPFVKATRLPLKTKSAFTETTAREKPKKTRRAFRDLLARRRPQVLCLHRPVI
+PSILEEVDDAAARPASDVLAALPRRDPHLRPGGVLVLHQGLDAKGAVVAAEVYDPWSD*
+>NZ_CP097650.1_1626
+MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPGGLEVMVIHRPRYDDWSWPKGK
+LDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPGKRGARQSKEVWYWAAEVDGQRA
+LPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRAASRGRLRTVPLLVLRHAKAKPRS
+SWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSSPWRRCVETLAPLVKSSRLPLKTK
+GAFTETTAREKPKKTRKVMAELMGRSRPLVVCTHRPVLPTLFEVVEDAAAGQADRVLRAL
+PTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001431.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001431.fa
new file mode 100644
index 0000000000000000000000000000000000000000..63d7b27cc25aca3a9df665fec1505a5eace904d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001431.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1698
+MENTAAQSQPEKIVHERLTVTRDPDRQRFELRQDGTFIGFLGYDQETVRGADGEDTVVLR
+LQHTIIDEQFGRRGYARALVTMVLDRLRAEGDRIVPECSYVEDYLRRYPEYQDMVFHG*
+>NZ_CP033200.1_1416
+MENTAAQSQPEKIVHERLTVTRDPDRQRFELRQDGTFIGFLGYDQETVRGADGEDTVVLR
+LQHTIIDEQFGRRGYARALVTMVLDRLRAEGDRIVPECSYVEDYLRRYPEYQDMVFHG*
+>NZ_CP040019.1_1108
+MENTAAKSQPEKIVHERLKVTRDPDRERFELRQDGTFIGFLGYAQETVPGPDGEDRTVVR
+LQHTIIDEAHGRKGYARALVTMVLDRLRAEGDSIVAECSYVEDYLRRYPEYQDMVFNG*
+>NZ_CP083691.1_1035
+METTANQHPEKIVHERLQVTRDPDRQRFEMRQDGVFIGFLGYDVEELPAADGGEDETVVR
+LQHTIIDEAHGRKGYARALVTIVLDRLRAEGEKISPECSYVQDYLRRYPEYQDMVREV*
+>NZ_CP097650.1_1627
+MENTAAQSQPEKIVHERLTVTRDPDRQRFELRQDGTFIGFLGYDQETVRGADGEDTVVLR
+LQHTIIDEQFGRRGYARALVTMVLDRLRAEGDRIVPECSYVEDYLRRYPEYQDMVFHG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001432.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001432.fa
new file mode 100644
index 0000000000000000000000000000000000000000..94e0b73a8d669f480440c33ee4958c53f0f0bd9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001432.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1699
+MGRVSIPTPYEDLLADVMAHGAVKTDRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKS
+VALELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAK
+VVEQIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSA
+DLFLGVPFNIASYALLTVMVAQQTGLTPGEFVWTGGDVHIYANHEEQVREQLSREPYPYP
+RLRLRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV*
+>NZ_CP033200.1_1417
+MGRVSIPTPYEDLLADVMAHGAVKTDRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKS
+VALELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAK
+VVEQIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSA
+DLFLGVPFNIASYALLTVMVAQQTGLTPGEFVWTGGDVHIYANHEEQVREQLSREPYPYP
+RLRLRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV*
+>NZ_CP040019.1_1107
+MSIPTPYEDLLADVMANGAVKSDRTGTGTRSVFGRQMRFDLSRSFPLITTKRVHFKSVAL
+ELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAKVVE
+QIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSADLF
+LGVPFNIASYALLTVIVAQQTGLAPGEFVWTGGDVHIYANHEEQVREQLSREPYPYPRLW
+LRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV*
+>NZ_CP083691.1_1031
+MSIPTPYEDLLADVLAHGAVKADRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKSVAL
+ELLWFLRGDSNVRWLQERGVTIWDEWADEGGELGPVYGVQWRSWPTPDGGSIDQIAKVVE
+QIRTSPDSRRHLVTAWNPAEVDEMALPPCHAMFQFYVAPDVDGAPGVLSCQLYQRSADLF
+LGVPFNIASYALLTLMVAQQTGLTPGEFVWTGGDCHIYANHEEQVREQLSREPYPYPTLR
+IRRTPESIFDYEYDDFELVDYRHHPAIKAPVAV*
+>NZ_CP097650.1_1628
+MGRVSIPTPYEDLLADVMAHGAVKTDRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKS
+VALELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAK
+VVEQIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSA
+DLFLGVPFNIASYALLTVMVAQQTGLTPGEFVWTGGDVHIYANHEEQVREQLSREPYPYP
+RLRLRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001440.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001440.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed80c16f15eb9a963afe101692918d050b71d45f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001440.fa
@@ -0,0 +1,66 @@
+>NZ_CP042169.1_1707
+MSDILDPQTTAEVAPELAEAEQEATGTVPQVDAAPEAPAEPAAPEAPAEPAGPTFLDLGL
+DARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTD
+VTGRADTPQVLVLAPTRELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQ
+VVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDRILASTPDTKQTALFS
+ATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEEHDG
+VIAFVRTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAAR
+GLDVERISHVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQ
+VEEMAVPSVADVNAARKRRFADGITRTLERASEEELAVFGEIVAAYVDEHEAEPARVAAA
+LGMMAQGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPAREPAA
+GNVTYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEA
+AANAEINGRRLGLRKDTGRPTRAERDGEDRGERRGGFRKDRGERGERGGFRGDRDGGQRG
+GYRKDRDDRGSREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR*
+>NZ_CP033200.1_1425
+MSDILDPQTTAEVAPELAEAEQEATGTVPQVDAAPEAPAEPAAPEAPAEPAGPTFLDLGL
+DARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTD
+VTGRADTPQVLVLAPTRELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQ
+VVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDRILASTPDTKQTALFS
+ATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEEHDG
+VIAFVRTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAAR
+GLDVERISHVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQ
+VEEMAVPSVADVNAARKRRFADGITRTLERASEEELAVFGEIVAAYVDEHEAEPARVAAA
+LGMMAQGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPAREPAA
+GNVTYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEA
+AANAEINGRRLGLRKDTGRPTRAERDGEDRGERRGGFRKDRGERGERGGFRGDRDGGQRG
+GYRKDRDDRGSREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR*
+>NZ_CP040019.1_1099
+MSDALDPQTTPEAQVDAAELAEARQEAAEAAAPKAETPETAAAATETDSAPEAETAEEPE
+APAEPAGPTFLDLGLDARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTG
+AFALPALARLAETADVNGRADTPQVLVLAPTRELALQVADAFDSYAKHLEDVSVLAVYGG
+SPYGPQLAGLRRGAQVVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDR
+ILASTPDTKQTALFSATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWK
+LEAFTRILETEDHDGVIAFVRTRAGTEELAQKLNRAGFKAVAISGDIAQKQREKTVEDLK
+AGRVDILVATDVAARGLDVERISLVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPR
+ERFLLKQIERTTRQQVEEMAVPAVKDVNAARKRRFADGITRTLERASEEELAVFGEIVAA
+YVEEHDAEPSRVAAALGMMAQGGRPLLAKEQEIPTGPRGRKERDGGRDGGREHGTADGRG
+SRGPAREPAAGNATYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELP
+ADLTPAQLEAAANIEISGRRLGLRKDTGRPTRAERDGDERRGGFRKDRGERGGHGGHRGG
+FRKDRDERGFRGDREERGGFRGDRDDRGDRGGFRKDREDRGGFRKDREDRGDRGGFRKDR
+EDRGGFRKDRDERGGFRGGKAGGRKPRWGAQERSDRGPRR*
+>NZ_CP083691.1_1023
+MTPHETIPADDQAPVDLTEFDPELAETTAEAPAAEQDADDAEADAEPAGPTFLSLGLDAR
+VLAAVEDLGYQRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETQDVNG
+RSQAPQILALAPTRELALQVAEAFESYAKHLDDVSVLAVYGGAPYGPQLAGLRRGAQVVV
+GTPGRVIDHLERGNLDLSQLQTLVLDEADEMLRMGFAEEVDRILAETPDSKQTALFSATM
+PPAIRRISAQYLNDPEEVAVARQSTTGTNIRQRYLQIAHQWKFEAMTRILETEDHEGVIA
+FVRTRAGTDELAQRLNQAGFSAVAISGDVAQKQREKTVDDLKAGRVDILVATDVAARGLD
+VERISLVVNYDIPQDAESYVHRIGRTGRAGRSGDAVLFMTPRERFLLKQIERTTRQEVEE
+MQVPTVAQVNEARTRGVVAGIGRTLETASEADLDTYARMVAEYVEANDVDPARAAAALAL
+MAQGGRPLLTEADEVPAGGRVRRDRDRDDRRERGDRSERGDRDGRGSRGPRREPAAGNAT
+YWIGVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHALVELPADLTAAQLDAAANT
+EINGRRLNLRKDTGRPTRAERDGDGERGHRGPREDRGGFRRDRGDRGGFRRDRGERPERG
+GFRKDRDDRGPREDRGGFRHDRDDRGGRPGARKPRWGSDDRRDRGPRR*
+>NZ_CP097650.1_1636
+MSDILDPQTTAEAAPELAEAEQEATGTVPQVDAAEPAAPEAPAGPAGPTFLDLGLDARVL
+AAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTDVTGRA
+DTPQVLALAPTRELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQVVVGT
+PGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDRILASTPDTKQTALFSATMPP
+AIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEEHDGVIAFV
+RTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAARGLDVE
+RISHVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQVEEMA
+VPSVADVNAARKRRFADGITRTLERASEEELAVFGEIVAAYVDEHEAEPARVAAALGMMA
+QGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPAREPAAGNATY
+WIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEAAANAE
+INGRRLGLRKDTGRPTRAERDGEDRGGFRKDRGERGERGGFRGDRDGGQRGGYRKDRDDR
+GSREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001450.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001450.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d04202b039ea01b091fa45b968d6023f0df639e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001450.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1719
+MVRVSPSSPAVRPGVTPDGAAPDTGALPTVSPAPADDPRGLALGFTAYFVWGLLPLYMAV
+LAPAGALEIVVVRIGFALIFCLLLLTVMRRLRELGTALATPGRWGTTGLAAGIIAVNWLL
+YAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWVAVGIAVAAVVVMSAAMGQ
+VPWIALGLATSFGLYGFVKKRFPSPVHAVTAMTAETVVLIPVFVVGSVLLAQAGLLTTVT
+EGPGHFWLMAGLGVLTAVPLILFSAAARSLTLTTLGMLQYTAPILQFLVAVTVLGEQMPA
+ARWAGFGLIWLSLAVFTLDQLNASRLQRRAVRAGQGAHA*
+>NZ_CP033200.1_1437
+MVRVSPSSPAVRPGVTPDGAAPDTGALPTVSPAPADDPRGLALGFTAYFVWGLLPLYMAV
+LAPAGALEIVVVRIGFALIFCLLLLTVMRRLRELGTALATPGRWGTTGLAAGIIAVNWLL
+YAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWVAVGIAVAAVVVMSAAMGQ
+VPWIALGLATSFGLYGFVKKRFPSPVHAVTAMTAETVVLIPVFVVGSVLLAQAGLLTTVT
+EGPGHFWLMAGLGVLTAVPLILFSAAARSLTLTTLGMLQYTAPILQFLVAVTVLGEQMPA
+ARWAGFGLIWLSLAVFTLDQLNASRLQRRAVRAGQGAHA*
+>NZ_CP040019.1_1087
+MARVSPSPASRRPGVPPDAAAPDTGALPAVSPAPANDPRGLALGFTAYFLWGLLPLYMAR
+LAPAGAVEIVVVRVGFALVFCLVLLALMRRLRELRTSLATPARWGATALAAGFIGTNWLL
+YAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWAAVGIAVAAVVVMSVAMGQ
+VPWIALGLAFSFGLYGFVKKRFPTPVHAVTTMTAETVVLLPAFAVGMVWLGQAGLLTTFT
+EGPAHFWLMAGLGVLTAVPLILFSAAAKALTLTTLGMLQYTAPILQFIVAVTVLGEQMPV
+ARWAGFGLIWVSLLVFTLDQVRVSRLHRRAARAGHGARA*
+>NZ_CP083691.1_1012
+MAQVSHSPSPSGPDAPRDGVPVEAAAPDTGALPTITPAPANDPRGLALGFAAYVIWGLLP
+LYMAATAPAGAVEIVVVRVVFALIFCLLLLAVMRRLPELRTALATRARWGSITLAAAFIA
+VNWLLYAHSVTSGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWIAVGIAVVAVVVMS
+VAMGQVPWIALGLAFTFGMYGFVKKRFPVPVHAVTTMTAETVVLLPAFAVGMVFLVQAGL
+LTTVSEGPGHFWMMAGLGVLTAVPLILFSAATQSLTLTTLGMLQYIAPIMQFLVAVAVLG
+EHMPAARWAGFALIWLSLVVFTLDQANASRVQRRAARAAGRART*
+>NZ_CP097650.1_1648
+MVRVSPSSPAVRPGVTPDGAAPDTGALPTVSPAPADDPRGLALGFTAYFVWGLLPLYMAM
+LAPAGALEIVVVRIGFALIFCLLLLTVMRRLRELGTALATPGRWGTTGLAAGIIAVNWLL
+YAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWVAVGIAVAAVVVMSAAMGQ
+VPWIALGLATSFGLYGFVKKRFPSPVHAVTAMTAETVVLIPVFVVGSVLLAQAGLLTTVT
+EGPGHFWLMAGLGVFTAVPLILFSAAARSLTLTTLGMLQYTAPILQFLVAVTVLGEQMPA
+ARWAGFGLIWLSLAVFTVDQLNASRLQRRPVRVRRGAHA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001452.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001452.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0e599be15b412918d0f7f31a2c0bc0d01838efc9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001452.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1721
+MTAPAPVSHAPDDYVCPFCGLVASDVSDPGNRCELGDTVYQDEDLLVLIAVDGFGDHEGH
+AMVCPAEHYENLYDLPPRVLQRIALMAQQVALAMKRAWAPDGVSTRQHNEPAGNQHVWHY
+HLHVFPRFEGDMLYRQLRHPVAPEVRAGKARELAAALDPAPTRLD*
+>NZ_CP033200.1_1439
+MTAPAPVSHAPDGYVCPFCGLVAGDVSDPGNRCELGDTVYQDEDLIVLIAVDGFGDHEGH
+AMVCPAEHYENLYDLPPRVLQRIALMAQQVALAMKRAWAPDGVSTRQHNEPAGNQHVWHY
+HLHVFPRFEGDMLYRQLRHPVAPEVRAGKARELAAALDPAPTRLD*
+>NZ_CP040019.1_1085
+MSGPRLRSHAPEGYVCPFCGLVAGDVSDPGNRCELADTVYQDEDLLVLIAVDGFGDHEGH
+AMVCPAGHYENLYELPPRVLQRIALMAREVALAMKRAWSPDGVSTRQHNEPAGNQHVWHY
+HLHVFPRFEGDLLYRQLRHPVSPEVRALKARELAAELDPAPTFLD*
+>NZ_CP083691.1_1009
+MSAQPLSHAPEGYVCPFCGLVAGDVSDPGNRCELEDTVYQDEDVLVLIAVDGFGEHDGHA
+MVCPSGHYENLYDLPPRVLQRIALMAQQVALAMKRAWGPDGVSTRQHNEPAGNQHVWHYH
+LHVFPRYEDDLLYRQLRHPVAPEVRAARARELAAALDPAPTLLD*
+>NZ_CP097650.1_1650
+MTAPAPVSHAPDGYVCPFCGLVAGDVSDPGNRCELGDTVYQDEDLLVLIAVDGFGDHEGH
+AMVCPAEHYENLYDLPPRVLQRIALMAQQVALAMKRAWAPEGVSTRQHNEPAGNQHVWHY
+HLHVFPRFEGDMLYRQLRHPVAPEVRALKARELAAALDPVPTRLD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001454.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001454.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9638f99d139991b23e84239aace12d9ebe2c4714
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001454.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1723
+MTDTPTSPAPDSTSAVVRRADVLISGCGPAGATAAAHLAAAGLDVVVLEKTAHPREKVCG
+DGLTPQAVRELQLLGVPHRGEPGDDGGWRVIRGLRLRAGERSVDVPWAPTQTWPDYALTR
+TRRDFDALLADLARTRGAEVRERHAVTGVVRDEAGRVVGLDAELIAPNGRKTGETARFTA
+PIVLACDGVSARAAVSAGLHRREDRPMGVAVRAYYTAGAAVDGAIPAPPGDRGEWMESWL
+RLPDAEGNPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLKSWTGALTADWGIA
+EQTRTSRILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARLAADLAV
+QAHAAGTDGAADAILSRYPVITQHLWGRHFALGARFARLIGDPRVMKAALGAGMAAPPLL
+RAAVKVMGNTVDARGGDAVDRAVRVLEALTPALTTAGGAPLGRLAR*
+>NZ_CP033200.1_1441
+MTGTPTSPAPASTPAVVRRADVLISGCGPAGATAAAHLAAAGLDVVVLEKTAHPREKVCG
+DGLTPQAVRELQLLGVPHRGEPGDDGGWRVIRGLRLRAGERSVDVPWAPTQTWPDYALTR
+TRRDFDALLADLARTRGAEVRERHAVTGVVRDEAGRVVGLDAELIAPNGRKTGETARFTA
+PIVLACDGVSARAAVSAGLHRREDRPMGVAVRAYYTAGAAVDGAIPAPPGDRGEWMESWL
+RLPDAEGNPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLKSWTGALTADWGIA
+EQTRTSRILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARLAAELAV
+QAHAAGTDGAADAILSRYPVITQHLWGRHFALGARFARLIGDPRVMKAALGAGMAAPPLL
+RAAVKVMGNTVDARGGDAVDRAVRVLEALTPALTTAGGAPLGRLAR*
+>NZ_CP040019.1_1083
+MTAAPSSSPSESAPPPVVRRADVLISGGGPAGATAAAHLAAAGLDVVVLEKTAHPREKVC
+GDGLTPQAVRELQLLGVPHRGEPGDDGGWQVIRGLRLRAGERSVDVPWPETRSWPDYALT
+RTRRDFDALLADLARERGAEVRERHAVTSVVRDDAGRVCGLDAELIAPNGRKTGETARFE
+APVVLSCDGVSARAAVSAGIHRREDRPMGVAVRAYYTAGPAADGAVPAPPGDRGEWMESW
+LRLPDAQGRPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLKSWSGALTPDWGI
+SEQTRVSKILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARIAADLA
+VQAHAAGSDAAADTVLSRYPVITQHLWGRHFALGARFARLIGDPRVMRASLGAGMAVPPL
+LRAVVKVMGNTVDPERGDAVDRAVRVLEALTPALTTADSAPLGRLAR*
+>NZ_CP083691.1_1006
+MTEHPTPAAAPVVRRADVLISGAGPAGATAAAHLAAAGLDVVVLEKSAFPREKVCGDGLT
+PQAVQEIRNLGIEHQGGPGDDGGWHAVRGLRLRAGERSVDVPWPATQSWPDYALTRTRKD
+LDALLADTARARGAEVRERHAVTGVTRDDAGRVDGLEAELIAENGRKTGERVRFAAPLVL
+ACDGVSARAAVSMDVHRRTDRPMGVAVRAYYTAGPVGADGAVPRPPGDRVDWMESWLRLP
+DEHGNPLPGYGWLFPLADGTVNVGLGILDTSPLFGKLDYRALLKQWSGALSEDWGISEET
+RTSKILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARIAADLAVQAH
+AAPNTPAADAVLARYPVITQHLWGRHFRLGTVFARLIGEPRVMRAALATGMAVPPLLRTV
+ARVMGNVVDPSGGDAVDRAVRILESVTPSLTTADAPGVGRLAR*
+>NZ_CP097650.1_1652
+MTGTPTSPAPASTPAVVRRADVLISGCGPAGATAAAHLAAAGLDVVVLEKTAHPREKVCG
+DGLTPQAVRELQLLGVPHRGEPGDDGGWRVIRGLRLRAGERSVDVPWAPTQTWPDYALTR
+TRRDFDALLADLARTRGAEVRERHAVTGVVRDEAGRVIGLDAELIAPNGRKTGETARFTA
+PIVLACDGVSARAAVSAGLHRREDRPMGVAVRAYYTAGAAVDGAIPAPPGDRGEWMESWL
+RLPDAEGNPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLRSWTGALTADWGIA
+EQTRTSRILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARLAADLAV
+QAHAAGTDGAADAILSRYPVITQHLWGRHFALGARFARLIGDPRVMKAALGAGMAAPPLL
+RAAVKVMGNTVDARGGDAVDRAVRVLEALTPALTTAGGAPLGRLAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001455.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001455.fa
new file mode 100644
index 0000000000000000000000000000000000000000..987a0366b1b4c289760bd7f45232846851f31f92
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001455.fa
@@ -0,0 +1,60 @@
+>NZ_CP042169.1_1724
+MTSVDSLSVARAVATALIDAGMRDAVVCPGSRSAPLAYALAALEHAGQVRLHVRVDERSA
+GFLAHGLSLASGRPVGVLTTSGTAVGNLVPALMESFHAGTRVIALTADRPPELHGTGANQ
+TTDQRDVFGTHVRHAASLGCDAADGVDTEQHLRHVRATVRRALLAAEGVVAETDSDDGAP
+GPVTMAEAPAGPVHLNLHFRDPLVPSPEEAAAMGAAAAAPHTPAPAVAPTGASPAAAASA
+YRAPGAVLSGLPELDVARLDQRRTVVLACHGAGPVAAAFALSLGLPLLAEPSSNARFSAN
+AIAAYPLLLGAAGGRDADAHPLAARIQRVVLFGRPTLTRTVNALLARPDVATALHAPEPA
+PWFEPGRRRETPVETLEELAAFAGQGEPGWLAAWQHASMRAQAAVEDVLVTTDAGDRLSP
+QTVAHVSAAMVRGPLVLGSSSVIRDVDLTWRPPSAPDAEVYANRGLAGIDGTVSTAAGVA
+LARGRRTVALLGDLTALHEAGGLLVGPTETEPDLDLVVLNDNGGAIFASLEHGAVAEAPG
+MADPVERLFGTPHGVDLAALAAAYGVPHTRVTDRVDLVRALSDPVRGRRLLEVRCDRADR
+PRVAAALAAAVRATFPPACPVPDPAPDAGPAPAPPTAELAAEEAPQ*
+>NZ_CP033200.1_1442
+MTSVDSLSVARAVATALIDAGMRDAVVCPGSRSAPLAYALAALERAGEVRLHVRVDERSA
+GFLAHGLSLASGRPVGVLTTSGTAVGNLLPALMESIHAGTRVIALTADRPPELHGTGANQ
+TTDQRGVFGTHVRHAASLGCDAADGVDAEQHLRHVRATVRRALLAAEGVVAEAGSDDGAP
+GPVTMAEAPAGPVHLNLHFRDPLVPSPEEAAAMGAAAAPHTPAPAVAPTGASPAAAASAY
+RAPGAVLSGLPELDVARLDQRRTVVLACHGAGPVAAAFALSLGLPLLAEPSSNARFSANA
+IAAYPLLLGAAGGRDADAHPLAARIERVVLFGRPTLTRTVNALLARPDVATALHAPEPAP
+WFEPGRRRETPVETLEELAAFAGQGEPGWLAAWQHASMRAQAAVEDALVTTDAGDRLSPQ
+TVAHVSAAMVRGPLVLGSSSVIRDVDLTWRPPSAPDAEVYANRGLAGIDGTVSTAAGVAL
+ARGRRTVALLGDLTALHEAGGLLVGPTETEPDLDLVVVNDDGGAIFASLEHGAVAEAPGM
+ADPVERLFGTPHGVDLAALAAAYGLPHTRVTDRVDLVRALSDPVRGRRLLEVRCDRADRP
+RVAAALAAAVRATFPPACPVPDPAPDAGPAPAPPTAELAAEEAPQ*
+>NZ_CP040019.1_1082
+MTSVDSLSVARAVADALIEAGMRDAVVCPGSRSAPLAYALAERERAGAVRLHVRVDERSA
+GFLAHGLSLASGRPVGVLTTSGTAVGNLLPALMESFHAGTRVIALTADRPTELHGTGANQ
+TTSQEGVFALHVRHAASIGCDAPAGRDADAHLRAVGAVVHRALLAADGVVADGPGHDDGG
+HVPEPGPVTVGEAPAGPVHLNLQFRAPLVPAPDEAAAMGSARQSAPQSPADPASEAAVHS
+AYRAPGALLSGFPELDVARLTQRRTVVLACHGAGPVAAAFALALGLPLLAEPSSNARFSV
+DAIAAYPLLLGSAGGRGPDSHPLAGRIERVVLFGRPTLTRPVTALLAREDVETVLFAPEP
+APWFEPGRRRERPIETLEELADFAGHGEAGWLSAWQRASMRAQAAVEDVLVAEDLRHGLS
+PQSVAQVGAAVTRGPLVLGSSSVIRDVDLTWRPPTAPDAEVYANRGLAGIDGTVSTAAGV
+ALARGMRTVALLGDLTALHDVGGLLVGPTEVEPDLELVVVNDDGGAIFAGLEHGAVAAVP
+GLAAPVERLFATPHGVDVAALAAAYGIPHVAVSDRVGLIHCLADPVRGRRIVEVRCSRAD
+RPRVAAALAEAVRATFPAAADSAPADTDPAPADPAAEEAPQ*
+>NZ_CP083691.1_1005
+MSSVDSTTLARTVAAALLEGGMREAVVCPGSRSAPLVYALAEAERRGRIRLHVRVDERSA
+AFLAHGISLATGRPVGVLTTSGTAVGNLLPALMEAFHAGTRLVALTADRPAEMHGTGANQ
+TTRQDGLFALHTRGAASISADLAPGEGAEEHLGRVAATVRRLLVRAEGLVVDPAAARPDL
+AEAPAGPVHLNLPFRAPLVPDAGQLAAMAAPAAPGDDADRPAEPAPWRAPGSDLTARVDL
+DVSRRPERRTVVLACHGAGPVAAAFAMALGLPLLAEPSSNARFTVNAVAAYPLLLGPAGG
+APGSDQGHPLAECIERVVLFGRPTLTRTVTALLDRPDVEAVLYSPEPAPWFEPGRRPERV
+VTDLGELADFAGQGAAGWVPAWQRASHRAQNAVEDALVRADRRHGLSPQSVAHVVPAVTR
+GPLVLGSSSLIRDVDLTWRPPTAPDAGVFANRGLAGIDGTIATAAGVALGTGRRTVALIG
+DLTALHDAGGLLVGDGEPEPDLDVVVVNDAGGAIFAGLEHGQVAGHAGMADVVERFFGTP
+HRVDLAALAAAYGVPHVLVEDRVELVHVLGAPERGRRLVEVRVHRADRPAVAAAIARAVA
+EAVAADPVPACTGAAAPEEES*
+>NZ_CP097650.1_1653
+MTSVDSLSVARAVATALIDAGMRDAVVCPGSRSAPLAYALAALERAGEVRLHVRVDERSA
+GFLAHGLSLASGRPVGVLTTSGTAVGNLLPALMESIHAGTRVIALTADRPPELHGTGANQ
+TTDQRGVFGTHVRHAASLGCDAADGVDAEQHLRHVRATVRRALLAAEGVVAEAGSDDGAP
+GPVTMAEAPAGPVHLNLHFRDPLVPSPEEAAAMGAAAAPHTPAPAVAPTGASPAPAASTY
+RAPGAVLSGLPELDVARLDQRRTVVLACHGAGPVAAAFALSLGLPLLAEPSSNARFSANA
+IAAYPLLLGAAGGRDADAHPLAARIERVVLFGRPTLTRTVNALLARPDVATALHAPEPAP
+WFEPGRRRETPVETLEELAAFAGQGEPGWLAAWQHASMRAQAAVEDVLVSTDAGGRLSPQ
+TVAHVSAAMVRGPLVLGSSSVIRDVDLTWRPPSAPDAEVYANRGLAGIDGTVSTAAGVAL
+ARGRRTVALLGDLTALHEAGGLLVGPTETEPDLDLVVVNDDGGAIFASLEHGAVAEAPGM
+ADPVERLFGTPHGVDLAALAAAYGLPHTRVTDRVDLVRALSDPVRGRRLLEVRCDRADRP
+RVAAALAAAVRATFPPACPVPDPAPDAGPAPAPPTAELAAEEAPQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001456.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001456.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d39db5e6ff24921903409dd7ea01f6ad85d507d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001456.fa
@@ -0,0 +1,31 @@
+>NZ_CP042169.1_1728
+MPPTARAPRRLPSWTWWLALAACVAGVVLVYAALVWSSAGQVLEYQVFRAVEERYADTVP
+DVTSQVVRILPLALAVGMALASLGALAVARWRRRGLLALLVLAGSNLTTQLLKAALPRPE
+HADGVPWSGGNSLPSGHMTLATGAAVAALLLVPARWRPLTTVLGAVVSSCTGAVAYTEAW
+HRPSDMAAAALVSAAWGLLAVPFARYDGAPRPAPRGARGVEATLWSLGVAGLAAGLTLLA
+LTLDTPATSGAGPHPAAEPAGILLSASPAVLLWGALGTAFRRGRAD*
+>NZ_CP033200.1_1446
+MPPTARAPRRLPSWTWWLALAACVAGVVLVYAALVWSSAGQVLEYQVFRAVEERYADTVP
+DVTSQVVRILPLALAVGMALASLGALAVARWRRRGLLALLVLVGSNLTTQLLKAALPRPE
+HADGVPWSGGNSLPSGHMTLAMGAAVAALLLVPARWRPLTTVLGAVVSACTGAVAYTEAW
+HRPSDMAAAALVSAAWGLLAVPFARYDGAPRPAPRGARGVEATLWSLGVAGLAAGLTLLA
+LTLGTPATSGAGPHPAAEPAGILLSASPAVLLWGALGTAFRRGRAD*
+>NZ_CP040019.1_1079
+MVAMPRTARPPLRVPSWPWWAALAACVAGVVLLYAALVWSSAGQVLEYQVFRAVEERYAD
+TVPDLASRVVRLLPLTLAAGVALASLGALAVPRWRRRGLLALAALIGANLTTQLLKAVLP
+RPEHAAGVPFSGGNSLPSGHMTLAAGAAVAALLLVPARWRPVTAVLGTAVSALTGAVAYT
+EAWHRPSDMAAAALVAAGWGLLAVPLALHEDGPRPAPRGARAAEIGMWTVGAVGMAAGLV
+LLWLTLEAPAAAGASPHPAAEPAGILLSAAPVVLCWGALATAFRRSRTA*
+>NZ_CP083691.1_1001
+MVGMTVTPPPGSPADAAARPVASSRRPRGSRWAWLLGLAAAAGVVALVHAVFVGTSGGQL
+LEYQVFHAVEDRWGTRSTGPAQRILTVLPVVLAGAATLAALACLIPRRTRRRGVVALVAL
+AGANVGTQALKESLGRPSFANHVPWAGGNSLPSGHTTLAASAAVAALLLVPARWRPAVAV
+VGAGATALTGSAAYLEAWHRPSDMAAAFGVAAFWAVLVAPWRRAADHRPRHASRAALAVE
+RMLWTLGVAGVLVGLGLAVATLGSPAVSADPHPLAAPAGALLSGTPALVLCAALLTGLRR
+AEQH*
+>NZ_CP097650.1_1657
+MPPTARAPRRLPSWTWWLALAACVAGVVLVYAALVWSSAGQVLEYQVFRAVEERYADTVP
+DVSSQVVRILPLALAVGMALASLGALAVARWRRRGLLALLVLAGSNLTTQLLKAALPRPE
+HADGVPWSGGNSLPSGHMTLATGAAVAALLLVPARWRPLTTVLGAVVSSCTGAVAYTEAW
+HRPSDMAAAALVSAAWGLLAVPFARYDGAPRPAPRGARGVEATLWSLGVAGLAAGLTLLA
+LTLDTPATSGAGPHPAAEPAGILLSASPAVLLWGALGTAFRRGRAD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001457.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001457.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4aedc39cd1fcde6ce7838ad92a15e9fb42218321
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001457.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1729
+MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLH
+GAEGETMDVGSPLITIGAAGESGEGSAPAAGTEALAVPPATGAAAAEAARPGALSYREEE
+MAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHRATSRSRPSKRGRGAARPTPAP
+TAGAGAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEGSAPQAAPAQAPL
+VAAVPAAEAAAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVT
+ALLELRASLKAKDSENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDGVHL
+GLAVQTDRGLMVPSVEHAEKLSADELTAAVNDTVSRARAGRAAPAELTRGTFTLNNYGPL
+GTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHRVTDGATASAFLT
+FVADCLHDPTAALARI*
+>NZ_CP033200.1_1447
+MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLH
+GAEGETMDVGSPLITIGAAGESGEGSAPAAGTEALAVPPATGAAAAEAARPGALSYREEE
+MAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHRATSRSRPSKRGRGAARPTPAP
+TAGAGAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEGSAPQAAPAQAPL
+VAAVPAAEAAAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVT
+ALLELRAALKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGQDEIVEVDGVHL
+GLAVQTDRGLMVPSVEHAEKLSADELTAAINDTVSRARAGRAAPAELTRGTFTLNNYGPL
+GTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHRVTDGATASAFLT
+FVADCLHDPTAALARI*
+>NZ_CP040019.1_1078
+MSNTFLLPDLGEGLTEADIVRWLVAEGDEVVVDQPIVEVETAKALVEVPSPYAGTVLTLH
+GAEGQTMEVGRPLITVGAAGESGEGSAPVAGTEAQAVPPATGEDAAEADRPGALSYREEE
+MAGVQPKPDKARGGDGDVAGSDEEASGAVLIGYGTSGHSATSRTRPSKRGRRGAGTTTAG
+GSGAASGQGEQAGQARAPRVTSPIVRKLAREQGVDVAALTGTGPDGLITRADVLSAAQGG
+DAPQAAAAPAAQPAATAGAASTVGAGSADARTGLAVVARTPISGVRKVIADQLSRSRREV
+PEVTAWLDVDVTALLELRAALKAKDAENAPSLLGLIARFTLAGLRRYPVMNARIEAGADG
+KDEIVEVDGVHLGLAVQTDRGLMVPSVEHAERLSADELTAAINETVTRAREGKAAPAELT
+RGTFTLNNYGPLGTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHR
+VTDGATASAFLTFVADCLNDPQSALARI*
+>NZ_CP083691.1_1000
+MSNTFLLPDLGEGLTEADIVRWLVAEGDEVAVDQPMVEVETAKALVEVPSPFAGTVLTLH
+GAEGETMEVGAPLITVGAVGESAGDAPPPSSAADAGTAPAADGAVPGALSYREEERAGVQ
+PKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHTATSRSRPSKRARGGAGTTQAAAGAAP
+AASGRAPRVTSPIVRKLARERGVDVATLTGTGPDGLITRADVLGAAGGASAPQDAQAPAP
+VQTAPSAAAQAPAVAAGATDARTGLAVVARTPISGVRKVIADQLSRSRREVPDVTAWLDV
+DVTALLELRAQLKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDG
+VHLGLAVQTDRGLMVPSVEHAEKMSADELTRAINDTVSRAREGRAAPAELTRGTFTLNNY
+GPLGTDGATPILNIPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHRVTDGATASA
+FLTFVADCLNDPQAALARI*
+>NZ_CP097650.1_1658
+MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLH
+GAEGETMDVGSPLITIGAAGESGEGSAPVAGTEALAVPPSTGADAAEAARPGALSYREEE
+MAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHRATSRSRPSKRGRGATRPTPAP
+TAWAGAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEGSAPQAAPAQAPS
+VAAVPAAEAAAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVT
+ALLELRAALKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDGVHL
+GLAVQTDRGLMVPSVEHAEKLSADELTAAVNDTVSRARAGRAAPAELTRGTFTLNNYGPL
+GTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIMVRKVTEMTVTFDHRVTDGATASAFLT
+FVADCLHDPTAALARI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001458.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001458.fa
new file mode 100644
index 0000000000000000000000000000000000000000..10ad42655cba0b101a818e2acab5596771f01863
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001458.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1730
+MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITIRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK
+AELDLDQLRAEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA
+AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA*
+>NZ_CP033200.1_1448
+MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITLRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK
+AELDLDQLRAEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA
+AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA*
+>NZ_CP040019.1_1077
+MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTKRFGEERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPMTIRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRAAIRLDDPVVFMEPKKMYWTK
+AELDLEDLRAEFEERWGRVEEKKEHGEAWARAAVVRAGSDVTLVSYGPSVPTCLAAARAA
+EEEGLSVEVVDLRTVNPLDEDTMVASVSKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA*
+>NZ_CP083691.1_999
+MANLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTQRFGDERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQVASHVAKMRNRTKGGAPMPIVIRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYLMLRSAIRLDDPVVFMEPKKMYWTK
+ADLDLDELRAEFDEQWARAQEKTAQGEAWARAAVVRQGADVTLVSYGPSVPTCLAAAQAA
+AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNVDRILDAIDDLNWDLDAEEARA*
+>NZ_CP097650.1_1659
+MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITIRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK
+AELDLDQLREEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA
+AEEGLSVEVVDLRTVNPLDEDTMTASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLGAEEARA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001460.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001460.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ac564aff14450534622984f5774562de20beba1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001460.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1732
+MAAEPLDRVDRAIVRELTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD
+PVKVGFGASAHVTMKLRQHDWRELRATLLAIPEVSHVSLVGGNMDVILLVRARDTADLRR
+VIFDELQTLPSVVDTQTYMVFDDQASGQTIPPDETAD*
+>NZ_CP033200.1_1450
+MAAEPLDRVDRAIVRELTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD
+PVKVGFGASAHVTMKLRQHDWRELRATLLAIPEVSHVSLVGGNMDVILLVRARDTADLRR
+VIFDELQTLPSVVDTQTYMVFDDQASGQTIPPDETAD*
+>NZ_CP040019.1_1075
+MPTEALDRVDRAIVRALTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD
+PVKVGFGASAHVTLKLRQHNWRELRATLLAIPEVWHVSLVGGNVDVILLVRARDTADLRR
+VIFDELQTLPGVVDTQTYMVFDDHASGQTLPPEDPAA*
+>NZ_CP083691.1_997
+MSTSSPLDRVDRAIVRELSQDGRLSVAALAERVHVSRAHCYSRLNRLQNSGVITGFSARV
+DPVKTGFTASAHVMLKLRQHDWRELRAALLAIPEVWHVSLVGGNMDVVLLVRARDTADLR
+HVIFEKLQSLPAVVDTQTYMIFDDHASGQTMPPEEGADAPRTPTAFG*
+>NZ_CP097650.1_1661
+MAAEPLDRVDRAIVRELTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD
+PVKVGFGASAHVTMKLRQHDWRELRATLLAIPEVSHVSLVGGNMDVILLVRARDPADLRR
+VIFDELQTLPSVVDTQTYMVFDDQASGQTIPPDETAD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001464.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001464.fa
new file mode 100644
index 0000000000000000000000000000000000000000..61a31ba8d8213a6f87f98b8214c3cbfb51c7b62c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001464.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1747
+MLALLDDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGDRLALFQ
+SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLNLDLPTAIG
+VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITVLAARPWSSSPRDPAP
+VTDGKLRFTAAVATSALAVREIPGISEGLVRVVALRHGGVARIAGSADRIEPGDEVVLDG
+TEKNIDAAVQAFGRRTGADPARVMNPLQTSMVIVTARALADRRLGTLSLRERFGTDVARL
+RRDDVESLATPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSDLDWISLGTGMALGY
+LLGMVTIPLPGGASFSLGPAAGCILVGLALGAIGRTGPTVWEPSTEIALTLRQFGLMIFL
+GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLIAAARLLGQSVDRTYGALAGIT
+GQPAILDYALSRSTDARVTEGYAQLFALIMVVKIATVPFLL*
+>NZ_CP033200.1_1455
+MLALLNDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGDRLALFQ
+SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLNLDLPTAIG
+VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITLLAARPWSSSPRDPAP
+VTDGKLHFTAAAATSALAVREIPGISEGLVRVVALRHGGVARIAGSADRIEPGDEVVLDG
+TEKNIDAAVQAFGRRTDADPAQVMNPLQTAMVIVTARALADRRLGTLSLRERFGTDVARL
+RRDDVESLATPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSNLDWISLGTGMALGY
+LLGLVTIPLPGGASFSLGPAAGCILVGLTLGAIGRTGPTVWEPSTEIALTLRQLGLMLFL
+GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLITAARLLGQSVDRTFGALAGIT
+GQPAILDYALSRSTDVRVTEGYAQLFALIMVVKIATVPFML*
+>NZ_CP040019.1_1055
+MLALLNDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGDRLVLFQ
+SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLNLDLPTAIG
+VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITLLAARPWSSSPRDPAP
+VTDGKLRFTAAAATSALAVREIPGISEGLVRVVALRHGGVARIAGSADRIEPGDEVVLDG
+TEKNIDAAVQAFGRRTDADPAQVMNPLQTSMVIVTARALADRRLGTLSLRERFGTDVARL
+RRDDVESLPTPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSDLDWISLGTGMALGY
+LLGLVTIPLPGGASFSLGPAAGCILVGLALGAIGRTGPTVWEPSTEIALTLRQLGLMLFL
+GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLIAAARLLGQSVDRTFGALAGIT
+GQPAILDYALSRSTDARVTEGYAQLFALIMVVKIATVPFML*
+>NZ_CP083691.1_990
+MLALLNDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGHRLALFQ
+SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLHLDLPTAIG
+VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITLLAARPWSSSPRDPAP
+VTDGKLRFTAAAATSALAVREIPGISEGLVRVVALRHGGVARIAGSADRIEPGDEVVLDG
+TEKNIDAAVQAFGRRTDADPARVMNPLQTSMVIVTARALADRRLGTLSLRERFGTDVARL
+RRDDVESLATPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSNLDWISLGTGMALGY
+LLGMVTIPLPGGASFSLGPAAGCILVGLALGAIGRTGPTVWEPSTEIALTLRQFGLMLFL
+GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLIAAARLLGQSVDRTFGALAGIT
+GQPAILDYALSRSTDARVTEGYAQLFALIMVVKIATVPFML*
+>NZ_CP097650.1_1668
+MLALLNDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGDRLALFQ
+SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLHLDLPTAIG
+VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITLLAARPWSSSPRDPAP
+VTDGKLRFTAAAATSALAVRDIPGISEGLVRVVALRHGGMARIAGSADRIEPGDEVVLDG
+TEKNIDEAVQAFGRRTDADPARVMNPLQTSMVIVTARALADRRLGTLSLRERFGTDVARL
+RRDDVESLATPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSDLDWISLGTGMALGY
+LLGMVTIPLPGGASFSLGPAAGCILVGLALGAIGRTGPTVWEPSTEIALTLRQFGLMLFL
+GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLIAAARLLGQSVDRTYGALAGIT
+GQPAILDYALSRSTDARVTEGYAQLFALIMVVKIATVPFML*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001474.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001474.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f35ca1de0df05ba0c449dba81add08daf0eab6fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001474.fa
@@ -0,0 +1,48 @@
+>NZ_CP042169.1_1761
+MAGPRPTPHARRHGGVRRPGGLPRPGQASTLESSTDLRTVLRRSGRAVSSVVGGSPARAA
+LSAFALMALVFTGLLALPWAAADGHATPLHDAMFTAVSAFSVTGLTTVNTAAHWSPAGQV
+IILVAIQIGGLGILSIASLLTLAVSRHLGLRSKLATQQAGMTSGSLGEVGQLLRVVVVTV
+LTAEAALALVLVPRFAAISGSWLTGLWHGVFYSVSAFNNAGFTLHVDGLPEIMHDPVIIT
+VLGVGVFLGALGFPVVMVLLEKGWRFREWNLHTKLTVEVTLALLVLGAVALFFFEAGNPA
+TQAGMGFWQRVGHSLFGSVMTRSGGFAIDDTNAHRPESLLLMDALMFVGGGSASTAGGIK
+VTTLAIMFLAIVAEARGDREVTAHGRTIAPESLRVAIAVLALGATLVLVATLALVHITDE
+SLQRPLFEVISAFGTCGLSVGVSAESPPAGKYVLTAMMFAGRVGTITFAAALALRQRRVL
+YRYPVERPVIG*
+>NZ_CP033200.1_1469
+MAGPRPTPHARRHGGVRRPGGLPRPGQASTLESSTDLRTVLRRSGRAVSSVVGGSPARAA
+LSAFALMALVFTGLLALPWAAADGHATPLHDAMFTAVSAFSVTGLTTVNTAVHWSPAGQV
+IILVAIQIGGLGILSMASLLTLAVSRHLGLRSKLATQQAGMTSGSLGEVGQLLRVVVLTV
+LTAEAALALFLVPRFAAISGSWLTGLWHGVFYSVSAFNNAGFSLHVDGLPEIMHDPVIIT
+VLGVGVFFGALGFPVVMVLLEKGWRFRQWNLHTKLTVEVTLALLVLGAVALFFFEAGNPA
+TQAGMGFWQRVGHSLFGSVMTRSGGFAIDDTNAHRPESLLLMDALMFVGGGSASTAGGIK
+VTTLAIMFLAIVAEARGDREVTAHGRTIAPESLRVAIAVLALGATLVLVATLALVHITDE
+SLQRPLFEVISAFGTCGLSVGVSAESPPAGKYVLTAMMFAGRVGTITFAAALALRQRRVL
+YRYPVERPVIG*
+>NZ_CP040019.1_1042
+MSTLESSSELRTALRRSSRAVSSVVSGSPARAALSAFLLVSLVFTALLSLPWASADGRPT
+ALHDAMFTAVSAVSVTGLTTLNTAEHWSVAGQVIILVAIQIGGLGILSMASLLTLAVSRH
+LGLRSKLATQEAGMTTGNVGEVGRLLRVVVVTVLTCEAALAVFLVPRFAAESGSWLTGLW
+HGVFYSVSAFNNAGFSLHVDGLSAVAHDPVILTVIAVGVFAGALGFPVVMVLLDKGWRYR
+AWNLHTKLTVEVTLALLVLGAVLLFFFEAGNPGTNGDLGVVERIWRSLFGSVMTRSGGFA
+IDDTNAHRPESLLLMDALMFVGGGSASTAGGIKVTTLAVMFLAILAEARGDREVTAHGRT
+IAPETLRVAISVLALGATLVLVATLALVNIMDESLQRPLFEVISAFATCGLSVGVSAEAP
+PAGKYLLAAMMFAGRVGTITFAAALALRQRRVLYRYPVERPILG*
+>NZ_CP083691.1_976
+MPSGALSPARRVVTAVTGVVAGSPARAALSAFALGALLFTGLLMLPAAATDGRVTPLHDA
+MFTAVSAFSVTGLTTLDTAEHWTPLGQVILLAAMQIGGLGILSMASLLTLAVSRHLGLRT
+KLATQESGMTTGNMGEVGHLLKVVVLTVLTCEGALAVILVPRFAALSDSWATGLWQGVFY
+SVSAFNNAGFTIHEGGTAAFMHDPVILTVIAVGVFAGALGFPVVMVLVDKGWRFRSWNLH
+TKLTVEVTLVLLVVGAVALFFFEAGNPATHGDMVVGQRIGHSFFGSVMTRSGGFAIDDTN
+SHRPESLLLMDALMFVGGGSASTAGGIKVTTLAVMFLAIVAEARGDKEVTVHGRTIAPET
+LRVAISVLALGATLVLLATLALVSIVDQPLQRPLFEVVSAFGTCGLSVGVSAEAPPAGKY
+LLTAMMFAGRVGTITFAAALALRQRRVLYRYPVERPILG*
+>NZ_CP097650.1_1682
+MAGPRPTPHARRHGGVRRPGGLPRPGQASTLESSTDLRTALRRSGRAVSSVVGGSPARAA
+LSAFALMALVFTGLLALPWAAADGHATPLHDAMFTAVSAFSVTGLTTVNTAEHWSPAGQV
+VILVAIQIGGLGILSMASLLTLAVSRHLGLRSKLATQQAGMTSGSLGEVGQLLRVVVVTV
+LTAEAALALVLVPRFAAISGSWLTGLWHGVFYSVSAFNNAGFTLHVDGLPEIMHDPVVIT
+VLGVGVFLGALGFPVVMVLLEKGWRFREWNLHTKLTVEVTLALLVLGAVALFFFEAGNPA
+TQAGMGFWQRVGHSLFGSVMTRSGGFAIDDTNAHQPESLLLMDALMFVGGGSASTAGGIK
+VTTLAIMFLAIVAEARGDREVTAHGRTIAPESLRVAIAVLALGATLVLVATLALVHITDE
+SLQRPLFEVISAFGTCGLSVGVSAESPPAGKYVLTAMMFAGRVGTITFAAALALRQRRVL
+YRYPVERPVIG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001480.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001480.fa
new file mode 100644
index 0000000000000000000000000000000000000000..281abb9851570c62081050cd7a837bd11c1360b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001480.fa
@@ -0,0 +1,55 @@
+>NZ_CP042169.1_1767
+MSPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATLALDREHAEAARRV
+VAGHLAGPGRHDDAAGPGDRPGTRGLAAAVGAWLLGDPVPAADLDAALPSLGLAGAVAAG
+LVVEGPDGRVRGAVDLSPYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGA
+TQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSERALAFTRFNLLLNADVLGLDRER
+LEDRVRLAAGDLLAPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGREGDRIVAELI
+AALPDVLAEGGTAQLLANWEIPAGDTADADTAPWDARPRSWVASGMQAWFIQRDRQDPAG
+YAETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRGWVVA
+EELTQAVDEALGTAWAAAVARRDRLTAGAGAGDAVGDPALAALRGLHLRVAADVTEERHQ
+RFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGELSVGQLVGAVAALLELDDVGRA
+GLLAALRELYEDGFLVEG*
+>NZ_CP033200.1_1475
+MSPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATRALDREHAEAARRV
+VAGHLAGPGRHDDAAGPGDRHGTRGLAAAVGAWLLGDSVPAADLDAALPRLGLAGAVAAG
+LVVEGPDGRVRGAVDLSPYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGA
+TQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSERALAFTRFNLLLNADVLGLDRDR
+LEDRVRLAAGDLLAPVTGERFDLVVSNPPFVITPRTDPGAPVLIYRDGGREGDRIVAELI
+AALPDVLAEGGTAQLLANWEIPAGDTANADTAPWDARPRSWVAPGMQAWFLQRDRQDPAG
+YAETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRGWVVA
+EELTQPVDEALGAAWAAAVARRDRLAAGAGAGDAVGDPALAALRGLHLRVAADVTEERHQ
+RFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGELSVGQLVGAVAALLELDDVGRA
+GLLAALRELYEDGFLVEG*
+>NZ_CP040019.1_1031
+MKPPAPSPSSPSLPAPRLTPATAAALDADLAALPYTTAAVEELLGPVATAALDREHAEPA
+RRVVARVLTAAPGDHTQALYDDGALGSGARPLEAGIGSPAARRALAALVSVWMLGDAADA
+ADVAAALPALGLDGAREAGLVAEEGGGTVRGTVDLSPYEADEPGRMWVASDQTALQRRGP
+LPEDHVLGIGRASLTLAGATQRRPVACALDVGVGCGIQTLHLLAHAEHVTATDLSERALE
+FTRFNLLLNADVLGLDRERLEDRVRLAAGDMLAPVAGERFDLVVSNPPFVITPRTDPDAP
+VLTYRDGGREGDRIVAELVAALPAHLTEGGTAQLLANWEIPAGAAAIPAAAAASADGDLA
+DTAGPAPWDARPRSWIAPGMQGWIIQRDAQDPAGYAETWLQDSSLELDPHRYEAAYRGYL
+EDFAARGVAGVGFGHVWLRRPVDDGAQGRAWTVAEELTQPVDEALGAAWAAAVARRDRLA
+AGAPDGAGDPALAALRGLHLRVAEDVSEERHGRFGAEHPEVILARQGAGFRRTARLDTAT
+AGVLSASDGELSVGQLVGAVAALLELDDAGRAGLLAAIRELYEDGFLVERAED*
+>NZ_CP083691.1_969
+MSLPAPHLSPAAAAALAADLTALPYTTDVVETLLGPVATAALDREHAVAARRVVAGVLAA
+PAARDAAAASRPLAAVVGAFMLGEPVPAADLAAALPALGLDGAVEAGLVVLDGADTGAER
+ARATVDLSPYAADEPGPMWVASDQTALQRRGPLPEDHVLGIGRASLTLAGATQRRPVARA
+LDLGVGCGVQTLHLLAHAEHVTATDLSERALDFTRFNLLLNADVLRLDRERLEDRVRLAA
+GDLLGPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGREGDRLVAELIAALPEHLVE
+GGTAQLLANWEIPAGAAEIPAGAAEVPAGDDAPPAWDARPRSWVGPGMQAWFVQRDRQDP
+AGYAETWLQDSSLELDPAAYEAAYRGYLDDFAARGVTGVGFGHVWLRRPAADRSQGRAWT
+VAEELTQPLDEALGTAWAAAVARRDRLAAGPEAGATDAVVTGDPALAALRGLHLRVAEDV
+TEERHSRFGAEHPEVILARQGAGFRRTARLDTATAGVLSASDGELSVGQLVGAVAALLEL
+DDAGRAGLLAAVRELHEDGFLLEA*
+>NZ_CP097650.1_1688
+MSPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATLALDREHAEAARRV
+VAGHLAGPGRHDDAAGPGDRPGTRGLAAAVGAWLLGDPVPAADLDAALPSLGLAGAVAAG
+LVVEGPDGRVRGAVDLSPYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGA
+TQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSERALAFTRFNLLLNADVLGLDRER
+LEDRVRLAAGDLLAPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGGEGDRIVAELI
+AALPDVLAEGGTAQLLANWEIPAGDTADADTAPWDARPRSWVAPGMQAWLLQRDRQDPAG
+YAETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRAWVVA
+EELTQPVDEALGTAWAAAVARRDRLAAGAGAGDAVGDPALAALRGLHLRVAADVTEERHQ
+RFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGELSVGQLVGAVAALLELDDVGRA
+GLLAALRELYEDGFLVEG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001486.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001486.fa
new file mode 100644
index 0000000000000000000000000000000000000000..931a64f36786993a676d51c44a1e98718cfd0ebc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001486.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1773
+MTHRSHSAQPAVTRPSGRNRLARVVDAAGEETGAITAEYGILTLAAVGFAGVLAVVLTSP
+DVQSLLVDLVSGALQRD*
+>NZ_CP033200.1_1481
+MTHRSHSAQPAVTRPSERDRLARVVDAAGEETGAITAEYGILTLAAVGFAGVLAVVLTSP
+DVQSLLVDLVTGALQRD*
+>NZ_CP040019.1_1025
+MTQLSHTVHDALATAAERHHLARVADAAADETGAITAEYGILTLAAVGFAGVLAVVLTSP
+DVQSLLVELVSGALQRD*
+>NZ_CP083691.1_963
+MTHNSTALTETLVPLVGPQRAAALATWAEDETGAQTAEYGILTLAAVGFAGVLAVVLTSP
+EVRELLVDLVSQALQRG*
+>NZ_CP097650.1_1694
+MTHRSHSAQPAVTRPSGRNRLARVVDAAGEETGAITAEYGILTLAAVGFAGVLAVVLTSP
+DVQSLLVDLVSGALQRD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001487.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001487.fa
new file mode 100644
index 0000000000000000000000000000000000000000..19957dccec5d8c98572caa8c78f5c169d3719cc5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001487.fa
@@ -0,0 +1,37 @@
+>NZ_CP042169.1_1774
+MLVGALRRWAALVAAGLTEEQAWRETACTLPACGSGPGEAGAACCAHHRARRRAEALAWD
+VPASHAPTGEAARGGGTLPWRTPARDPGWALVDAALAAGARAGAAPAAVARRLAHSLEAD
+VDAARARRSAAAGPGATSRLLQWLPLGGLGLAWLLGTSPWDLARSPFGAVVAAVGLLFWL
+AGRSWTRLLLRAAAREPAAVGAAVVLDVLAALLSAGRSLPAALDDLGRTLPGARGLRATA
+ALLLWGRDWDEAWAGLDTDPVWIETAARLRPLHRSGMAGARTLAETAAAVRQQTRRADER
+AAEELAVRLVMPLGLCLLPAFVCWGVVPVVMALLGAGPG*
+>NZ_CP033200.1_1482
+MSPTTATGPARRSHAGRAVALLPWRAGRVPPEEETEVLIGVLRRWAALVAAGLTEEQAWR
+ETACTLPACGSEPSEAGTACCAHHHARRRAEALAWDVPAAHAPTGEAARRGGTLPWRTPA
+RDPGWALVDAALAAGARAGAAPAAVARRLAHSLEADVDAARARRSAAAGPGATSRLLQWL
+PLGGLGLAWLLGTSPGDLVRSPFGAVVAAVGLLFWLAGRSWTRLLLRAAAREPAAVGAAV
+VLDVLAALLSAGRSLPAALDDLGRTLPGARGLRATAALLLWGRDWDEAWVGLDTDPVWAE
+TAARLRPLHRSGMAGARTLAETAAAVRQQTRRADERAAEELAVRLVMPLGLCLLPAFVCW
+GVVPVVMALLGAGPG*
+>NZ_CP040019.1_1024
+MSTAAPEDATEELVVVLRRWAALVSAGLTEEAAWRETVRMLPDDDGHARHAARLRAERLA
+WDAAGDLSTGRDAPDVRGLRRDEHPPGDTHDASPDRSRRRWCPPWRTPPPDPGWALVDAA
+LAAGARAGAAPAVVVRRLAESLEADVDAARARRSAAAGPAATARLLQWLPLGGVGLAWLL
+GSSPWETVSTPFGAVVAAVGLLFWLAGRSWTRLLLRSAAREPAALTAPVVLDVLAALLGA
+GRSLPAALDDLARTLPGARGLRVTSALLLWGRGWDEAWAGIGEETVWAEAAARLRPLHRS
+GMAGARTLAESAAAARQQGRRADERAAEELAVRLVMPLGLCLLPAFVCWGVIPVVMALLG
+AGA*
+>NZ_CP083691.1_962
+MIALPGRAEERAEERAQEVVEALRRWAGLTAAGMTPAEAWTAVAQASSPCGRPTPGCCPR
+HEALRRAALARWGGPGRGAEGGQPRPGERSPWDLADAALAAAARAGASFSRTAARLADAL
+EADVDASRARRTAAAGPRATARLLSWLPVGGLGLAWLLGMGPADLLATGFGWVLLVLGGV
+LTAAGRAWTRLALRRGARPLGEASPGVVVDVAAVLLGAGRSLPAALDDVSAHLPGAADLR
+VVAVLLRWGADWDEAWAPVTEEPRWAALGERLRPLHRTGMAGEAVLHQTAAALRQETRRA
+DERGAEELAVRLVVPLGLCQLPAFVCWGVAPMALALLGAR*
+>NZ_CP097650.1_1695
+MLVGVLRRWAALVSAGLTEEQAWRETACTLPACGPGPSEAGTACCAHHRARRRAEALAWD
+VPASHAPTGEAARGGGTLPWRTPARDPGWALVDAALAAGARAGAAPAAVARRLAHSLEAD
+VDAARARRSAAAGPGATSRLLQWLPLGGLGLAWLLGTSPWDLARSPFGAVVAAVGLLFWL
+AGRSWTRLLLRAAAREPAAVGAAVVLDVLAALLSAGRSLPAALDDLGRTLPGARGLRTTA
+TLLLWGRDWDEAWAGLDTDPVWIETAARLRPLHRSGMAGARTLAETAAAVRQQTRRADER
+AAEELAVRLVMPLGLCLLPAFVCWGVVPVVMALLGAGPG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001490.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001490.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3aadb5c156aae0f3b29544fa8e38792277e96cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001490.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1778
+METEPTDTPTGETRLALVRRARRIDRILAETYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP
+ARLEDLVALPGVGRKTEFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA
+LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGEGETDPERARALLAYELK
+PGREELLELLRAGRTRRELRALGHGLEA*
+>NZ_CP033200.1_1486
+MEPEPTDTPTGETRLALVRRARRIDRILAETYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP
+ARLEDLVALPGVGRKTAFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA
+LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGEGETDPERARALLAYELK
+PGREELLELLRAGRTRRELRALGHGLEA*
+>NZ_CP040019.1_1019
+MDAEQADTPTGESRLALVRRARRIDRELAATYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAAAMAGASEAELQGLVRSTGFYRNKASAILRLSQELVERHGGEVP
+GRLEDLVALPGVGRKTAFVVLGNAFGRPGITVDTHFGRLARRLGFTQDTDPVKVEHAVAE
+LFPRRDWTMLSHRLIFHGRRICHARRPACGACPIARWCPSYGEGETDPEKARALLSYELK
+PGREELLALMRAGLSRRELRARGHGLDA*
+>NZ_CP083691.1_958
+MAPADTTTPTGETPLALTRRARRIDRALAEAYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAVTPALFARFPDAVAMAGADEVELQELVRPTGFYKNKASAVLRLSRELVERFDGEVP
+DRLEDLVTLPGVGRKTAFVVLGNAFGRPGITVDTHFGRLARRLGFTEETDPVKVEHAVAA
+LFPPRDWTMLSHHLVFHGRRVCHARKPACGACPIARWCPSYGAGETEPEAARALLSYELK
+PGREELLARMRAGATRRQLRDEGWTLEA*
+>NZ_CP097650.1_1699
+METESTGTPTGETRPALVRRARRINRILAETYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP
+ARLEDLVALPGVGRKTAFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA
+LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGAGETDPERARALLAYELK
+PGREELLELLRAGRTRRELRALGHGLEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001491.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001491.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fbef4a03575abfe0eee830a85d02b33b02543ab0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001491.fa
@@ -0,0 +1,60 @@
+>NZ_CP042169.1_1779
+MDEQIPTFPPPAEFAAQAVAGADLYEEAAEDRLAYWARRAREVLHWEQDFTDVLDWSDAP
+FAKWFVGGTTNAAYNALDRHVEAGHGDRVAIHFEGEPGDTRTYTYADLAAEVRRAANAFE
+SLGVTKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSSDALRSRVDDAEAKLVVT
+ADGSFRRGKPSMLKPAVDQALSAPGHTAEHVLVVRRNEAEVEMTEGRDLWWHDVVDAQSD
+EHELVWHDAEHPLYILYTSGTTGKPKGILHTTGGYLVQAAATHHDTFDLHPESDVFWCTA
+DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKYGVSILYTAPTAIRTFM
+KWGRHIPDEYDLSSLRVLGSVGEAINPEAWRWYHEVIGAGRCPIVDTWWQTETGAHMLTP
+LPGVTTLKPGSAQRPVPGVVLEVVDELGEPMTDTSAGFLVVREPWPSMLRGIWGDRERFK
+ETYWSRFPGMYFAGDGARYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPSVAES
+AVVGAKDETTGEAVVAFVLLTAVAVAADRDVAEVEEELRQHVGKDIGPIAKPKRVLVVPE
+LPKTRSGKIMRRLLKDVAEGRDPGDSTTLADPTVMQRIVETLAPKA*
+>NZ_CP033200.1_1487
+MDEQIPTFPPPAEFAAQAVAGADLYEEAAEDRLAYWARRAREVLHWEQDFTDVLDWSDAP
+FAKWFVGGTTNAAYNALDRHVEAGHGDRVAIHFEGEPGDTRTYTYADLAAEVRRAANAFE
+SLGVTKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSSDALRSRVDDAEAKLVVT
+ADGSFRRGKPSMLKPAVDQALSAPGHTAEHVLVVRRNEAEVEMTEGRDLWWHDVVDGQSD
+EHELVWHDAEHPLYILYTSGTTGKPKGILHTTGGYLVQAAVTHHDTFDLHPESDVFWCTA
+DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKYGVSILYTAPTAIRTFM
+KWGRHIPDEYDLSSLRVLGSVGEAINPEAWRWYHEVIGAGRCPIVDTWWQTETGAHMLTP
+LPGVTTLKPGSAQRPVPGVVLEVVDELGEPMTDTSAGFLVVREPWPSMLRGIWGDRERFK
+ETYWSRFPGMYFAGDGARYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPSVAES
+AVVGAKDETTGEAVVAFVLLTAVAVAADRDVAEVEEELRQHVGKDIGPIAKPKRVLVVPE
+LPKTRSGKIMRRLLKDVAEGRDPGDSTTLADPTVMQRIVETLAPKA*
+>NZ_CP040019.1_1018
+MDEQIPTFPPPAEFAAQAVAGADLYEEAAEDRLAYWARRAREVLHWEQDFTEVLDWSDAP
+FAKWFVGGTTNAAYNALDRHVEAGNGDRVAVHFEGEPGDTRTYTYAELASEVRRTANAFE
+SLGVAKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSADALRSRVDDAEAKLVVT
+ADGSFRRGKPSMLKPAVDEALSAPGHSVQHVLVVRRNEAEVSLVEGRDLWWHDVVPAQSD
+EHELVWHDAEHPLYILYTSGTTGKPKGILHTTGGYLVQTAATHHDTFDLHPETDVYWCTA
+DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKYGVSILYTAPTAIRTCM
+KWGRQIPDEYDLSSLRVLGTVGEAINPEAWRWYHEVIGGGRCPIVDTWWQTETGAHMLTP
+LPGVTTLKPGSAQTPVPGVTLEVVDEIGEPMKDTSAGFLVAREPWPSMLRGIWGNPERFK
+ETYWSRFPGMYFAGDGARYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPSVAES
+AVVGAADETTGEAVVAFVLLTEEAAAAGRDVAEVEEELRQHVGRDIGPIAKPKRVLVVPE
+LPKTRSGKIMRRLLKDVAEGRDPGDATTLADPTVMQRIVETLAPGA*
+>NZ_CP083691.1_957
+MDETRATYPPSEQFAAQAVAGADLYEEAAADRLAYWARRAREHLHWEQDFTQVLDWSDAP
+FARWFADGTTNAAYNALDRHVEAGRGDRTAIVFEGEPGDTRTYTYADLAAEVRRAANAFE
+SLGVAKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSADALRSRVDDAEAKLVVT
+ADGSFRRGRPSMLKPAVDQALSAEGHTVEHVVVVRRNEADVDWTEGRDLWWHDVVPTASD
+EHEVVWHEAEHPLFILYTSGTTGKPKGILHTTGGYLVQTAATHHDTFDLHADTDVYWCTA
+DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKHGVTILYTAPTAIRTFM
+KWGRQIPDGYDLSSLRVLGTVGEAINPEAWRWFHDVIGGGRCPIVDTWWQTETGAHMLTP
+LPGVTELKPGSAQRPVPGVVLEVVDELGEPMEGSTAPGFLVAREPWPSMLRGIWGDPERF
+KETYWSRFPGMYFAGDGAQYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPKVAE
+SAVVGAADETTGEAVVAFVLLTEEATAAGEDVEAVQEELRQHVGKDIGPIAKPKRVLVVP
+ELPKTRSGKIMRRLLKDVAEGRRPGDATTLADPTVMDRITEAVGS*
+>NZ_CP097650.1_1700
+MDEQIPTFPPPAEFAAQAVAGADLYEEAAKDRLAYWARRAREVLHWEQDFTDVLDWSDAP
+FAKWFVGGTTNAAYNALDRHVEAGHGDRVAIHFEGEPGDTRTYTYADLAAEVRRAANAFE
+SLGVTKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSSDALRSRVDDAEAKLVVT
+ADGSFRRGKPSMLKPAVDQALSAPGHTAEHVLVVRRNEAEVEMTEGRDLWWHDVVDGQSD
+EHELVWHDAEHPLYILYTSGTTGKPKGILHTTGGYLVQAAVTHHDTFDLHPESDVFWCTA
+DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKYGVSILYTAPTAIRTFM
+KWGRHIPDEYDLSSLRVLGSVGEAINPEAWLWYHEVIGAGRCPIVDTWWQTETGAHMLTP
+LPGVTTLKPGSAQRPVPGVVLEVVDELGEPMTDTSAGFLVVREPWPSMLRGIWGDRERFK
+ETYWSRFPGMYFAGDGARYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPSVAES
+AVVGAKDETTGEAVVAFVLLTAVAVAADRDVAEVEEELRQHVGKDIGPIAKPKRVLVVPE
+LPKTRSGKIMRRLLKDVAEGRDPGDSTTLADPTVMQRIVETLAPKA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001493.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001493.fa
new file mode 100644
index 0000000000000000000000000000000000000000..04792787087832b4c2fa17b899b09997379e31d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001493.fa
@@ -0,0 +1,14 @@
+>NZ_CP042169.1_1781
+MSTAAIVMMSLAILLVWGGLAVSAIHLLRHPDDSSGDLAIEDDLAPAVWEREDGLLDAQH
+R*
+>NZ_CP033200.1_1489
+MSTAAIVMMSLAILLVWGGLAVSAIHLLRHPDDSSGDLAIEDELAPAVWEREDGRLDAQH
+R*
+>NZ_CP040019.1_1016
+MSTAAIVMMSLAILLVWGGLALSAVHLLRHPDDSSGDLALGDRLAPAAWEREDELGREDV
+RLGARRG*
+>NZ_CP083691.1_956
+MHTPALIMMVIAMLTVWGGLVLSAVHLLKHPDETSGTLADAVDVDHTL*
+>NZ_CP097650.1_1702
+MSTAAIVMMSLAILLVWGGLAVSAIHLLRHPDDSSGDLAIEDELAPAVREREDGRLDARH
+R*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001496.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001496.fa
new file mode 100644
index 0000000000000000000000000000000000000000..601d6efeedc395798aa4a69fd469ac329904da41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001496.fa
@@ -0,0 +1,34 @@
+>NZ_CP042169.1_1785
+MSADPAGLLLPVPGQEEDLTRQWLDRRFRQVRPARPGSSVVLVRDGDDGPEVFLRHRAGR
+TPLGRVGLPGGALIESDADSCPWYGPEPSQWARTFGTTDRRRARQHVVAAVRELHDEAGV
+LLAGRSDTDVVSTARIETWGGGRSSLEEGSESLPHLLAARGLGVRADLLRPVMRWRSAPH
+VHRRFDTAVFATMTPPLQSAPASEEPGPELQAWVSARRALAGPLRLPGPAGAEGTAPFDQ
+VATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDDGTPRMRVKRATRD
+*
+>NZ_CP033200.1_1493
+MSADPAGLLLPVPEQEEDLTRQWLDRRFRQVRPARPGSAVVLVRDGDDGPEVFLRHRAGR
+TPLGRVGLPGGALIESDADLCPWYGPEPSQWAHTFGTTDRRRARQHVVAAVRQLHDEAGV
+LLAGRSDTDVVSTARVETWGGGRSSLEEGSESLPHLLASRGLGLRADLLRPVMRWHSAPH
+VHRRFDTAVFATTTPPVQSAPASEEPGPELQAWVPACRALAGPLRLPGPAGAEGTAPFDQ
+VATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDDGTPRMRVERATRD
+*
+>NZ_CP040019.1_1012
+MVLVRDGEDGPEVFLRHRPGRTPLGRVGLPGGALSEADADACAWFGPDPAHWARVLGTTD
+RRCARQQVVAAVRELHDEAGVLLAGRTDADVVLDARGETWGGGGSSLEEGAESLPRMLAA
+RGLGLRTDLLRPVARWHSAPHAHRRFDTAVFAAAVPPLQRPLERPETAPALQAWVSARRA
+VAGPVPLPGPAGEEGVAPLDQVATPLTQVLVRRVAAHRTAAAFLLSLTQGAGHGPVPEYR
+LVTEAGDDGAPRMRVERVTRD*
+>NZ_CP083691.1_952
+MSAEPDAPRVRVPGHEEELTRQWLAQRHRQVRPARPASAVVLVRDGADGVEVLLRHRSGR
+TPLGRIGLPGGSLVDSDADPCTWYGPAPDEWARALGLADRRRVRQHVVAAVRELFEESGV
+LLAGPADMDLVQDARGETWGASRSSLEEGDESLPRLLGDRGLGLRTDLLRGVGRWLSAPH
+SPRRFDTVVFAAALPPQQELVHRPEGPVLQGWFSARRLLSEPAALPGPDGWLGESGVVAL
+EEVSTPMTQLVLRRVAEHRTAAGFLLSPAGCRGPVPVVKLRTEAEHDDLATGTLYTVAER
+VDPVG*
+>NZ_CP097650.1_1706
+MSADPAGLLLPVPEQEEDLTRQWLDRRFRQVRPARPGSAVVLVRDGDDGPEVFLRHRAGR
+TPLGRVGLPGGALIESDADLCPWYGPEPSQWAHTFGTTDRRRARQHVVAAVRQLHDEAGV
+LLAGRSDTDVVSTARVETWGGGRSSLEEGSESLPHLLASRGLGLRADLLRPVMRWHSAPH
+VHRRFDTAVFATTTPPVQSAPASEEPGPELQAWVPACRALAGPLRLPGPAGAEGTAPFDQ
+VATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDDGTPRMRVERATRD
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001497.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001497.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d47b88f4bc8882132986eb9ad47a64a60f60e127
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001497.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1786
+MTEQSSAPTWGDGAVAARLAELGIDRPAVAAPVGSYVPALRDGDLVLTSGQLPFVAGALP
+ATGKVGAEVTPERAQELARACAVNAVAAVHELVGDLDRVAQVVKVVGFVASDPAFTGQPG
+VVNGASDVLAEIFGEAGRHARSAVGVAVLPMDAPVEVEITVRVR*
+>NZ_CP033200.1_1494
+MTAQSSAPAWGDGAVAARLAELGIDRPAVAAPVGSYVPALRDGDLVLTSGQLPFVAGALP
+ATGKVGAEVTPERAQELARVCAVNAVAAVHELLGDLDRVAQVVKVVGFVASDPAFTGQPG
+VVNGASDVLAEIFGEVGRHARSAVGVAVLPMDAPVEVEITVRVR*
+>NZ_CP040019.1_1011
+MAEKAQAPTWGEGAVADRLAELGLERPAVAAPVGSYVPAIRDGDLVLTSGQLPFVAGSLP
+ATGKVGAEVSAERAQELARVCAVNAVAAVHELIGDLDRVAQVVKVVGFVASDPSFTGQPG
+VLNGASDVLAEIFGEAGRHARSAVGVAVLPLDAPVEVEITVRVR*
+>NZ_CP083691.1_951
+MAGQNAWGGGPAAERLAALGIERPAVAAPVGSYVPAVRDGDLVLTSGQLPFVAGALPRTG
+KVGAEVTLEQAQELARTAAVNAVAAVHELVGDLEAVVQVVKVVGFVASAPDFTAQPAVVN
+GASDVLAEIFGEAGRHARSAVGVAVLPLDSPVEVEITVRVR*
+>NZ_CP097650.1_1707
+MTAQSSAPAWGDGAVAARLAELGIDRPAVAAPVGSYVPALRDGDLVLTSGQLPFVAGALP
+ATGKVGAEVTPERAQELARVCAVNAVAAVHELLGDLDRVAQVVKVVGFVASDPAFTGQPG
+VVNGASDVLAEIFGEVGRHARSAVGVAVLPMDAPVEVEITVRVR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001498.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001498.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1dd7186c4cc1809eef028e67cb06791c3b47d148
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001498.fa
@@ -0,0 +1,10 @@
+>NZ_CP042169.1_1787
+MTQQTQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGNNPVAYLKRPKAA*
+>NZ_CP033200.1_1495
+MTQQTQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGNNPVAYLKRPKAA*
+>NZ_CP040019.1_1010
+MTEQTKWEYATIPLLIHATKQILDQWGEDGWELVAVVPGPDGPNPVAYLKRPKAA*
+>NZ_CP083691.1_950
+MTQRIQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGANPVAYLKRPKDA*
+>NZ_CP097650.1_1708
+MTQQTQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGNNPVAYLKRPKAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001500.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001500.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8a75e54d6f4f6d195ed4aea65c1b6dd3420d31f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001500.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1789
+MPPAASPTRRMLRSAAPAAVGMAATAGLGLAWGLAEAEARTVRTHRLAVLPAGSAPLRVL
+HLSDIHLLPRHRAKRAWLRGLDALEPDLVVNTGDNVSAAASVPLVLDALGPLLARPGVFV
+PGSNDYYAPKAANPLRYFAGPSRMDEDRPRLPSDVLFGAFRAAGWADLTNRGAALAVPTR
+AGTTLEVLAAGTDDPHLGLDAWAGFPGAAPDENAGRPGDDGRFRLGVTHAPYRRVLDAMT
+ADGADLLLAGHTHGGQVCVPFLGALVTNCDLPRRQASGVSTWTAAGRTVPLEVSAGLGTA
+PSAPVRFACRPEAVVLDLVPRG*
+>NZ_CP033200.1_1497
+MPPAASPTRRMLRSAAPAAVGMAATAGLGLAWGLAEAEARTVRTHRLAVLPAGSAPLRVL
+HLSDIHLLPRHRAKRAWLRGLDALEPDLVVNTGDNVSAAASVPLVLDALGPLLARPGVFV
+PGSNDYYAPKAANPLRYFAGPSRMDEDRPRLPSDVLFGAFRAAGWADLTNRGAALAVPTR
+AGTTLEVLAAGTDDPHLGLDAWAGFPGAAPDENAGRPGDDGRFRLGVTHAPYRRVLDAMT
+ADGADLLLAGHTHGGQVCVPFLGALVTNCDLPRRQASGVSTWTAAGRTVPLEVSAGLGTA
+PSAPVRFACRPEAVVLDLVPRG*
+>NZ_CP040019.1_1008
+MRPSATAPRRLVRAGSRAAVGMGTAAALGLAWGLVEAEARVVRTHRLAVLPAGADPVRVL
+HLSDIHLLPRNRSRMAWLRGLDALEPDLVVNTGDNISAAASVPLVLDALGPLLRRPGVFV
+PGSNDYYEPKPANPFRYFAGPSRMDEDRARLPTEALFGAFRAAGWADLTNRGSVLSVPTR
+AGTVLEVLAAGTDDPHLGLDAWGGFPAPAPAPAPAPGDAAASGPASAHDDGAARPGGDGR
+FRLGVTHAPYRRVLDAMTVDGADLLLAGHTHGGQVCLPGFGALVTNCDLPRAQASGVSTW
+TAAGRTVPLEVSAGLGTAPSAPVRFACRPEAVVLELLPCA*
+>NZ_CP083691.1_948
+MTDAPGPRLRRLTHTAAWAAGGASALGAGALVWGRVEAEARVVRTHTVPVLPAGARPLRV
+LHLSDIHLLPRHRRRLEWLCSLADLEPDLVVDTGDNISSAASIPLLLDALAPLLAVPGVF
+VPGSNDYFTPKPANPLRYLRGPSELEASRSRLPTEDLFSAFRAAGWTDLTDRAADVVVGS
+GPDAVRIRAAGTDDPHLGLDRWPGFDLADEGAAGDAPLLRLGVTHAPYRRVLDAMTADGA
+DLLLAGHTHGGQVCLPFAGALVTNCDLPRSQASGLSSWTAAGRTVPLEVSAGIGTAPSAP
+VRTFCRPEAVVLDLVPRA*
+>NZ_CP097650.1_1710
+MRPAASPARRMFCAAAPAAAGLAATAGLGLAWGLAEAEARTVRTHRLAVLPAGSAPLRVL
+HLSDIHLLPRHRAKRAWLRGLDALEPDLVVNTGDNVSAAASVPLVLDALGPLLARPGVFV
+PGSNDYYAPKAANPLRYFAGPSRMDADRPRLPSDVLFGAFRAAGWADLTNRGAALAVPTR
+AGTTLEVLAAGTDDPHLGLDAWAGFPGSAPDGGAGRPGDDGRFRLGVTHAPYRRVLDAMT
+ADGADLLLAGHTHGGQVCVPFLGALVTNCDLPRRQASGVSTWMAAGRTVPLEVSAGLGTA
+PSAPVRFACRPEAVVLDLVPRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001502.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001502.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1780acc1879f3edabda4f9e99b1b6f6180010928
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001502.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1794
+MKTLVLGNGGREHALLTALSRDPQVSALHAAPGNAGMADLATLHAVEATDPAAVVELARE
+LGADLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGS
+RVCTTAAEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAEACFAAGGTVVIED
+FLDGPEVSLFVICDGEDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFTDEVM
+DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLETPLGG
+LLADAAAGRLGADRRLEWSDDVAVDVVMASAGYPASSSTGDVITGLADAAALEGVHVIHA
+GTAASGEDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI
+TVPGTGGAK*
+>NZ_CP033200.1_1501
+MKTLVLGNGGREHALLTALSRDPQVSALHAAPGNAGMADLATLHAVEATDPAAVVELARE
+LGADLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGS
+RVCTTAAEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAEACFAAGGTVVIED
+FLDGPEVSLFVICDGEDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFTDEVM
+DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLETPLGG
+LLADAAAGRLGADRRLEWSDDVAVDVVMASAGYPASSSTGDVITGLADAAALEGVHVIHA
+GTAASGEDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI
+TVPGTGGAK*
+>NZ_CP040019.1_1003
+MKTLVLGNGGREHALLAALSRDPQVGELHAAPGNAGMAALAALHAVEATDPDAVVALARE
+LAADLVVVGPEAPLAAGVSDALREAGFAVFGPSRAAAQLEASKAFAKEVMAAAGVPTAGS
+RTCATAEEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAQACFDAGGTVVIED
+FLDGPEVSLFVVCDGTDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFAEEVM
+DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLTTPLGG
+LLADAAAGRLGADRALEWSDDVAVDVVMASAGYPATSSQGDVITGLTDAEALEGVHVIHA
+GTATSGDDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI
+AVPAAVGQAGQAGEDAR*
+>NZ_CP083691.1_944
+MKILVLGNGGREHALLRALSRDPQVGELHAAPGNAGMADAAVLHPVTATDPEAVVALARD
+LAVDLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGA
+RVCATEAEVDAALTAFGAPHVVKDDGLAAGKGVVVTSDRAAALDHARACLSAGGTVVVED
+FLDGPEVSLFVLCDGEHAVPLTPAQDFKRIHDGDAGPNTGGMGAYTPLQWLPEGFVDEVM
+ERVARPVLAEMSRRDTPFAGVLFIGLAVTENGPEVIEFNVRFGDPETQSVLARLETPLGQ
+LLADAAAGRLGADRELRWSDDVAVDVVLASAGYPASSHSGDVIAGLEDALALEGVDVLHA
+GTARTEDGDVVTAGGRVLAVVGRGATLEQARERAYAGVAKIRFDGAQHRTDIAIKAERGE
+ITVPERRRGYAGAEALELPGWRHVYSGKVRDLYEPADAEPGTSETLLVVASDRISAYDFV
+LEPPIPGKGAVLTRLSLWWFEQLAGVANHVVSTDVPAEVAGRAMVVKRLDMHPIECIARG
+YLTGSGLAEYREHATVTGIPLPDGLVDGSRLEPPIFTPSAKAEVGEHDENITFEQTVERV
+GAPTAEALRAATLEVYTRAEAIARKAGIILADTKVEFGADPVTGELVLGDEVLTPDSSRF
+WDAEAYEPGRAQASFDKQFVRDWLTSPESGWDRTSGEEPPALPADVVERTRARYVEAYER
+LTGRRFEA*
+>NZ_CP097650.1_1714
+MKTLVLGNGGREHALLTALSRDPQVSALHAAPGNAGMADLATLHAVEATDPAAVVELARE
+LGADLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGS
+RVCTTAAEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAEACFAAGGTVVIED
+FLDGPEVSLFVICDGEDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFTDEVM
+DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLETPLGG
+LLADAAAGRLGADRRLEWSDDVAVDVVMASAGYPASSSTGDVITGLADAAALEGVHVIHA
+GTAASGEDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI
+TVPGTGGAK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001505.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001505.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3175c8ccd494d63b92fce481fda3bc75c50caad9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001505.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1797
+MSVAPRAAVPPAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPEASSGPFPAT
+TLVLLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVAHHGDFAWVA
+FPLFFVVLHVVDRVARQAWVRHVVGPALVVAMAVVVVAGMAAGAGGVRVPAVIGPLVGAA
+VAVVLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLTQG
+LASIVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGTGAPSLIEAL
+ERAVAGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLANVGAHAGARRAR
+VTLGYLGDELTVDVADDGAGFDPAVVAARPRAGAAGADPGAGTGVGLASVRERLAAVGGE
+ATVESAPGEGTVVALRVPLVAAGAGRSADPEQTESEETA*
+>NZ_CP033200.1_1504
+MSVAPRAAVPPAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPDASGPFPATT
+LVLLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVGHHGDFAWVAF
+PLFFVVLHVVDRVARQAWVRHVVGPALVVAMAAVVVAGMAAGAGGVRVPAVIGPLVGAAV
+AVVLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLTQGL
+ASIVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGTGAPSLVEALE
+RAVTGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLANVGAHAGARRARV
+TLGYLGDELTVDVADDGAGFDPAVVVARARAGAAGADPGAGTGVGLASVRERLAAVGGEA
+TVESAPGEGTVVALRVPLAAAGAGRSADPEQTESEETA*
+>NZ_CP040019.1_1000
+MPTTRPSADTAGAPAETGAAAVLAGLRVALHVAFAVLLAVGLGRALADLSRTGAPAPAVL
+ALTGCTALLAGVYLAGTLVERRRWGRGEDVGRGPALLWLALVLALWGLLVAQHRDFAWVA
+FPLFFVALHVVARTARTAMARRIAGPVLVAAMAAVVVAGMAAGVDEGVRPAAVIGPLVGA
+AVAVVLSGAYRALHQESERQRDVAEQLRAAQAELARTQHRAGVGEERERLAREIHDTLTQ
+GLASIVLVSRAAQDALDAQDPALARTRMETVRTTAAENLDESRRFVRDLRATGGASLVAA
+VERAVAGFAERQAAAGTPVAADVEVVGTPVPLAEAVEAALLRAVQASLANVAAHARATRA
+RVTLAWMPGELAVDVADDGVGFRPEAVVTGDAGTQGTGAGTQGARAGRASRPGAGTGVGL
+ASVRERLAGVGGHASVESAPGEGTVVALRVPLPAAAGRAEEDEGRERG*
+>NZ_CP083691.1_941
+MRTSDPADGPRGANGTAALLSGLRVAVHVGFAVLLALALVRALAGPDAGARLTGRPALAL
+VGLTVVLAGVYLTGTVAERRLHAAGRAPGRTAAGTWLAVLLGVWALAVLRHPDMMWVAFP
+LFFVALHAVHVILGRPRLALACVAAMTVVVVVASLERGTAPGAVLGPAVGAAVAVVVFHA
+CRLLVVESERQRSVAEQLRATRAELAASERHAGVLAERERLAREIHDTLTQGLASIVLVS
+RAAQDAVRAGDAALADERLETVRTTAAENLAESRAFVRGLRAPVDGVQGGADRAGSALEA
+ALGAAVRGFRARRQALGRPVEAELAVVGEPVAVGEAVETVLVRAAQSSLANVDQHARTDR
+CRVTLTWMDGEVALDVADDGVGFDPEAARARASRAAVSDPAAPRPAEEGTGVGLAGLAER
+VAGVGGRVDVESAPGQGCVVAVRIPVPRQHERRGA*
+>NZ_CP097650.1_1717
+MSVAPRAAAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPEASSGPFPVTTLV
+LLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVAHHGDFAWVAFPL
+FFVVLHVVDRVARQAWVRHVVGPALVVAMAVVVVAGMAAGAGGVRVPAVIGPLVGAAVAV
+VLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLTQGLAS
+IVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGTGAPSLIEALERA
+VTGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLANVGAHAGAHRARVTL
+GYLGDELTVDVADDGAGFDPAVVAARPRAGAAGADPGAGTGVGLASVRERLAAVGGEATV
+ESAPGEGTVVALRVPLVAAGAGRSADPEQTESEETA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001508.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001508.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8148130d993abd60df70730fc197c801c39d0cb5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001508.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1801
+MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRATAVRFALEELATRVPGN
+SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTTWEDATAAGGVRASGV
+RADLGAHLPLVRP*
+>NZ_CP033200.1_1508
+MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRAMAVRFALEELATRVPGN
+SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTSWDEATAAGGVRASGV
+RADLGAHLPLVRP*
+>NZ_CP040019.1_996
+MTTGSVPRRRIPVPEGHAALTSWARTHAQDPAAAAALPRSTRATAVRFALEELATRVPGN
+AVEVRVPPFGVAQAIPGPRHTRGTPPNVVEMDAVTWLSLATGLLGWADAVGTGAVRASGT
+RADLGAHLPLIRP*
+>NZ_CP083691.1_937
+MTTGSVPKRRVPVVEGHAALTAWARAHAEDPAAAAALPRSTRATAVRFALEELATRAPGN
+SVEVRVPPFGVAQCIPGPRHTRGTPPNVVETDPVTWLSLATGLTRWNDAVASGAVRASGV
+RADLAGHLPLVRP*
+>NZ_CP097650.1_1721
+MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRAMAVRFALEELATRVPGN
+SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTTWEDATAAGGVRASGV
+RADLGAHLPLVRP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001511.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001511.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad905e6089563f5d7130e33aff46a180412eebf6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001511.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1804
+MTPNQTPSSAAPITYASAGVDVEAGDRAVELMKDAVKATHTPEVMGGIGGFAGMWDASAL
+LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGAQPLFMTDYIACG
+KVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLAADEYDVAGAATGVVEADMVLGA
+ERVQSGDVVIGMASSGIHSNGYSLVRRVVNAAGWSLDREVTELGCTLGEELLVPTRIYSR
+ACLDLVQRLNGHEGGSDLPVRAFSHVTGGGLAANLARVLPQGLMATVERDTWSLPPVFRL
+VGELGRVPQSDLERTLNLGVGMVAVVDPEVAATSISVLVDAGIDAWEMGTIGALTDDAAA
+AGLNFVQGAKGVDGGAVLMRGQYAA*
+>NZ_CP033200.1_1511
+MTPNQTPSSAAPITYASAGVDVEAGDRAVELMKDAVKATHTPEVMGGIGGFAGMWDASAL
+LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGAQPLFMTDYIACG
+KVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLAVDEYDVAGAATGVVEADMVLGA
+ERVQSGDVVIGMASSGIHSNGYSLVRRVVNAAGWSLDREVTELGCTLGEELLVPTRIYSR
+ACLDLVQRLNGHEGGSDLPVRAFSHVTGGGLAANLARVLPQGLMATVERDTWSLPPVFRL
+VGELGRVPQSDLERTLNLGVGMVAVVDPEVAATSISVLVDAGIDAWEMGTIGALTDDAAA
+AGLDFVHGAKGVDGGAVLMRGQYAA*
+>NZ_CP040019.1_989
+MTENQNTAHDAPITYASAGVDVEAGDRAVELMKDAVKATHSPEVMGGIGGFAGMWDASAL
+LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGATPLFMTDYIACG
+KVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLGVDEYDVAGAATGVVDADMVLGA
+DRVQTGDVLIGMASSGIHSNGYSLVRRVVNAAGWSLDREVSELGRTLGEELLEPTRIYAR
+SCLDLVQRLNGHDGGSGLPVRAFSHVTGGGLAANLARVLPQGLMATVERETWSLPPVFRL
+LAEAGRVPQPDLERTLNLGVGMVAVVDPEIAAKSISVLVDAGIDAWEMGTIGHVTDEAAG
+AGLDFVQGAKGVDGGAVLMRGAYAA*
+>NZ_CP083691.1_932
+MTDAPRTETQTADALDAPLTYAAAGVDVEAGDRAVELMKDAVKATHTAEVLGGVGGFAGM
+WDASALTGYRKPLLATSTDGVGTKVAIAQALDRHDTIGQDLVGMVVDDIVVVGAKPLFMT
+DYIACGKVVPERVADIVRGVAEGCRLAGTALVGGETAEHPGLLAVDEYDVAGAATGVVEA
+DRVLGAERVRSGDVVIGMASSGIHSNGYSLVRRVINAAGWQLDRDVDELGRTLGEELLEP
+TRIYTRACLDLMDSLNGTEGGADLSLRGFSHVTGGGLAANLARVLPQGMMATVDRGTWAL
+PPVFRLVGELGRVPLADLERTLNLGVGMVAVVAADAADRAVAAIEAAGIPAWVMGGIDEV
+TEQAQAAGEDYVQGAKGVDGGAVLMTGTYAD*
+>NZ_CP097650.1_1724
+MTPNQTPSSAAPITYASAGVDVEAGDRAVELMKDAVKATHTPEVMGGIGGFAGMWDASAL
+LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGAQPLFMTDYIACG
+RVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLAAEEYDVAGAATGVVEADMVLGA
+ERVQSGDVVIGMASSGIHSNGYSLVRRVVNAAGWSLDREVTELGCTLGEELLVPTRIYSR
+ACLDLVQRLNGHDGGSDLPVRAFSHVTGGGLAANLARVLPQGLMATVERDTWSLPPVFRL
+VGELGRVPQSDLERTLNLGVGMVAVVDPEVAATSISVLVDAGIDAWEMGTIGALTDDAAA
+AGLDFVQGAKGVDGGAVLMRGQYAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001513.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001513.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b1d30b4bc88483ecb938de0c270ac3ba6b1cedde
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001513.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1807
+MGRGRQKAKATKQAREMKYFSPGTDLSALERELTGGRTRGPEQDQEPEYEDPYADLYAED
+EDDDARAR*
+>NZ_CP033200.1_1514
+MGRGRQKAKATKQAREMKYFSPGTDLSALERELTGGRTRGPEQDQEPEYEDPYADLYAED
+EDDDARAR*
+>NZ_CP040019.1_985
+MGRGRQKAKATKQAREMKYFSPGTDLSALERELTGGRTRAPEPELDQKPEYEDPYADLYT
+DDDEDDDARAR*
+>NZ_CP083691.1_927
+MGRGRQKAKATKQAREMKYMSLGTDLSALERELTGGRTDAPAVEPEVDYEDPYADLYADD
+DEDDDSRVR*
+>NZ_CP097650.1_1727
+MGRGRQKAKATKQAREMKYFSPGTDLSALERELTGGRTRSPEPDQEPEYEDPYEDLYAED
+EDDDARAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001515.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001515.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ecf41d4f1d81bd5c34422430d0a3adf93f09f136
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001515.fa
@@ -0,0 +1,80 @@
+>NZ_CP042169.1_1809
+MDAKFTTKSQEALSAAAMNASTAGNPQVEPAHLLKALMDQRESVAVAVLKAAGADPDAVS
+TAASSAIRRLPSTQGSTVAQPQFSRAALQVVQNARTQAEQRSDEFVSTEHLLLGVAADSG
+EAGEALRSNGASLEALAAALTLVRGDSRVTTQDPETTFQSLEKYGTDLTEIARSGKLDPV
+IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL
+DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK
+PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVFVGEPSVDDTIAILRGLKERYEAH
+HKVAIADSALVAAATLSHRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD
+RLTMEELALEGETDPASIERLDALRAEKADREEELTALTARWDAEKATLNQAGDLRAKVD
+ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSATEPMVSEEVTADD
+IAEVVSAWTGIPAGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN
+RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG
+YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI
+LTSNLGSQFLVDPTLDEAAKRESVMSVVRGAFKPEFLNRLDEIVQFDALTVAELTRIVDL
+QVESLQARLTDRRLTLEVSDAAKAWLAATGFDPAYGARPLRRLVQREIGDRLARGILAGE
+IADGDTVVVDRVEGENGLTVTRKG*
+>NZ_CP033200.1_1516
+MDAKFTTKSQEALSAAAMNASTAGNPQIEPAHLLKALMDQRESVAVAVLKAAGADPDAVS
+TAASSAIQRLPSTQGSTVAQAQLSRAALQVVQNARTQAEQRSDQFVSTEHLLLGVAADPG
+EAGEALRSNGASLEALAAALTQVRGDSRVTTQDPETTFQSLEKYGTDLTELARSGKLDPV
+IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL
+DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK
+PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVYVGEPSVDDTIAILRGLKERYEAH
+HKVAIADSALVAAAALSDRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD
+RLTMEELALEGETDPASVERLEALRAEKADREEELTALTARWDAEKATLNEAGDLRAKVD
+ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSSTEPMVSEEVTADD
+IAEVVSAWTGIPSGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN
+RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG
+YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI
+LTSNLGSQFLVDPTLDEAAKRESVMSVVRAAFKPEFLNRLDEIVLFDALTVDELTRIVDL
+QVESLQARLTDRRLTLEVSDAAKAWLAETGFDPAYGARPLRRLVQREIGDQLARGILAGE
+IADGDTVVVDRVEGENGLTVTRKG*
+>NZ_CP040019.1_980
+MDAKFTTKSQEALSAAAMNASTAGNPQIEPAHLLKALMDQRESVAVAVLKAAGADPDAVS
+TAASSAIRRLPSTQGSTVAQAQLSRAALQVVQNARTQAEQRSDQFVSTEHLLLGVAADPG
+EAGEALRSNGASLEALAAALTQVRGDSRVTTQDPENTFQSLEKYGTDLTEVARSGKLDPV
+IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL
+DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK
+PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVYVGEPSVDDTIAILRGLKERYEAH
+HKVAIADSALVAAATLSHRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD
+RLTMEELALEGETDPSSVERLEALRAEKADREEELTALTARWDAEKATLNEAGDLRAKVD
+ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSTTEPMVSEEVTADD
+IAEVVSAWTGIPAGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN
+RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG
+YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI
+LTSNLGSQFLVDPTLDEAAKRESVMSVVRAAFKPEFLNRLDEIVQFDALTVAELTRIVDL
+QVESLQARLTDRRLTLEVSDAAKAWLAETGFDPAYGARPLRRLVQREIGDRLARGILAGE
+IADGDTVVVDRAEGEEGLTVASA*
+>NZ_CP083691.1_926
+MNPSPQFTTKSQEALSAAAMNASTASNPAVEPAHLLKALMDQRDSVAVAVLKAAGADPDV
+VSVAASTAIHGLPKASGATVSEARLSPAAGAVVKAAQQQASAHGDEYVSTEHLLLGLAAD
+GGEAGRALTDAGASLAALQAAFTQVRGDERVTTPDPEATFQSLEKYGTDLTAVARSGKLD
+PVIGRDQEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLI
+SLDLGAMIAGAKYRGEFEERLKSVLEEIKKSDGQIVTFIDEIHTVVGAGASEGAMDAGNM
+LKPMLARGELRLIGATTLDEYRENIEKDPALERRFQQVYVGEPSVDDTIAILRGLKERYE
+AHHKVAIADSALVAAATLSDRYISGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDALRRQ
+VDRITMEELALDGESDPGSVERLAGLRAEKADKEEELRALTARWEAEKASLNEAGDLRAR
+VDELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAQEGQQGDVEAMVSENVTA
+DDIAEVISAWTGIPAGRMLASETEKLLSMEEHLGDRLIGQKDAVRAVSDAVRRARAGIAD
+PNRPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHAVSRLVGAPPGY
+VGYDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVI
+LILTSNLGSQFLVDQTMPEQARKDAVMDVVRAAFKPEFLNRLDEIVTFDALGVEDLARIV
+DLQVASLGERLQQRRLTLDVTDAAREWLALTGYDPAYGARPLRRLVQREIGDQLARALLS
+GAVQDGDTVVVDRAGEDTADGLTVAARRA*
+>NZ_CP097650.1_1729
+MDAKFTTKSQEALSAAAMNASTAGNPQVEPAHLLKALMDQRESVAVAVLKAAGADPDAVS
+TAASSAIRRLPSTQGSTVAQPQFSRAALQVVQNARTQAEQRSDEFVSTEHLLLGVAADSG
+EAGEALRSNGASLEALAAALTLVRGDSRVTTQDPETTFQSLEKYGTDLTEIARSGKLDPV
+IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL
+DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK
+PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVFVGEPSVDDTIAILRGLKERYEAH
+HKVAIADSALVAAATLSHRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD
+RLTMEELALEGETDPASIERLDALRAEKADREEELTALTARWDAEKATLNQAGDLRAKVD
+ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSATEPMVSEEVTADD
+IAEVVSAWTGIPAGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN
+RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG
+YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI
+LTSNLGSQFLVDPTLDEAAKRESVMSVVRGAFKPEFLNRLDEIVQFDALTVAELTRIVDL
+QVESLQARLTDRRLTLEVSDAAKAWLAATGFDPAYGARPLRRLVQREIGDRLARGILAGE
+IADGDTVVVDRVEGENGLTVTRKG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001517.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001517.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b61fe0dbc13c17b659656e5a83196a7ec479b824
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001517.fa
@@ -0,0 +1,27 @@
+>NZ_CP042169.1_1811
+MGALALVGCAGGGGEASSSSADASKSAPTGAGSDLTDEQEERVEALEDVLLTPETAPGGV
+FTGMETQAGGGEPISTSLSLTGVTPTGACADLIEQINTQQAPGLGGALAQYEVDPAAVTG
+LAGSQAGAFGMVAVTDDGTDLLAPFGKLADTCGTFGDPDGVEAAFTKVPGVPDAAHIALG
+NSGMDTALFTMTVGGVTDGDELVYLGMVGLDEEIAAETLRAQVEAFEARER*
+>NZ_CP033200.1_1518
+MGAHALVGCAGGGGEASSSASADASESGPTGAGSDLTDEQEERVEALEDVLLTPQTAPDG
+VFTGMETQAGGGEPISTSLSLTGVTPTGACADLIEQINTQQAPGLGGALAQYEVDPAAVT
+GLAGSQAGAFGMVAVTEDGTDLLEPFGELADTCGTFGDPDGVEAAFTTVPGVPDAVHISL
+GNSGMDTALFTMIVGGVTDGDELVYLGMVGLDEEIAAETLRAQVEAFEKRER*
+>NZ_CP040019.1_978
+MEALEDVLLTPQTAPDGVFTDMETQAGGGGEPISTSLSLTGVTPTGACADLIEQINTQQA
+PGLGGALAQYEVDPDAVTGLAGSQAGAFGMVAVTEGGTDLLAPFGELADTCGTFGDPDGV
+EAAFTKVPGVPDAAHIALGNSGMDTALFTMTVGGVTDGDELVYLGMVGLDEEIAAETLRA
+QVEAFEKRER*
+>NZ_CP083691.1_916
+MSRTATSRPRLRALLPLTATAALLASGCAAPGPAASSSATPSSSASSAAAESSSSPTVST
+GPASSSDASSSAAAASSSADASATTSSSSAADLAASSPAAGGASVENPLEPLLLLATAAP
+QEVFSSRTVQSGADQPLTMSLTLTGVTPTGRCQELVDEINATHEPMDVASLATYQVNPAS
+PAVVDQETGAFTMIGTSTAPADLMAPYGELVSACGTLEGEQGQKAEFTAVPGVPDAATVT
+MTTPGQSRKLVMTVGGASEGRDHVYMLMLGLDADVSQQVLADQVAAFQER*
+>NZ_CP097650.1_1731
+MLRPAAPARPAVALSLLAVGALALVGCGGGGGEASSSSADASESAPTGAGSDLTDEQEER
+VEALEDVLLTPETAPGGVFTGMETQAGGGEPISTSLSLTGVTPTGACADLIEQINTQQAP
+GLGGALAQYEVDPAAVTGLAGSQAGAFGMVAVTDDGTDLLAPFGKLADTCGTFGDPDGVQ
+AAFTKVPGVPDAVHIALGNSGMDTALFTMTVGGVTDGDELVYLGMVGLDEEIAAETLRAQ
+VEAFEARER*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001518.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001518.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e8dea40571e80c2c1024fc4376af5d03fb3ba60
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001518.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1812
+MTRIHSRLLGAVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDV
+PYPPFEFEENGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI
+TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV
+QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVESLPTGEQLGMAVGPQKAQL
+GSAVNRALQELRNDGTVAELQERWFGQAQEDYR*
+>NZ_CP033200.1_1519
+MTRIHSRLLGAVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDI
+PYPPFEFEEKGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI
+TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV
+QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVESLPTGEQLGMAVGPQKAQL
+GSAVNRALQELRNDGTVAELQERWFGQAQEDYR*
+>NZ_CP040019.1_977
+MGLTASAALLTGCAVLGGDSGVAGVVSDDDLSTTYNLVQPGVLTVCSDIPYPPFEFELDG
+ELTGYDIQLVHAIAEELELGVNVIDSSFEAIESGASLTGCDLNASSISITEQRQRAMAFT
+LPYLDDDLVLVAATDSGITDVESAKGRRVGVQAATTGDAYAKENGLNPIEFEDGGMQVQA
+LQAGTVDALLGNQSVILYSLKDDERFEVVENLPTGEQLGMAVAPQNAQLGSAVNRALQQL
+RNDGTVAELQERWFGLAQEDYR*
+>NZ_CP083691.1_914
+MPRTPSRALGAVGAGLSAALLSGCAVIGGDAGTTGPLAEDDLRATYRLHEPGVLTVCADV
+PYPPFEFEQDGQLTGYDIDLTRKLAETMDLQLKVVDTSFEAIESGASLTGCDLNASAISI
+TEPRQHVMAFTLPYLDDDLVLVARKDSGITDVASAQGKRVGVQTATTGEEYAQSQGLDTV
+QFEDGGMQVQALQAGTVDALLGNQSVLLYSLKDDPRFGVVESLPTGEQLGMGVAPDNALL
+GSAVNRALQTLRNDGTVAELQQKWFGTAQKDYQ*
+>NZ_CP097650.1_1732
+MTRIHSRLLGTVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDV
+PYPPFEFEENGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI
+TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV
+QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVELLPTGEQLGMAVGPQKAQL
+GSAVNRALQELRNDGTVAELQERWFGQAQEDYR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001519.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001519.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54ef3e55277cc3f0e01f37eeb1beab2a629a3dea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001519.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1813
+MSTQAPVSPAPAMKPGRARRRRRLSLIIQAAVFVLALVVLAVLIDWGALAENVLNFPAVA
+PMFPNVILVGLGNTLFYTVTSFVVGLLGGIVLALMRLSSFGPYRWLATAYVEFFRGVPAL
+LVFLAFGYGVPFAFGVSWPIPVVVMVALGMVSAAYIAETLRAGLQAVPRGQMEAARSLGM
+PTWRAMVTIVIPQAFRIVLPPLTNEVILLTKDSSLVYVLGLAAHEYELTKFGRDGISALD
+AGMTPILVAGLFYLVITVPLSLLARRFETRSTKKGH*
+>NZ_CP033200.1_1520
+MSTQAPVSPAPAMKPGRARRRRRLSLIIQAAVFVLALVVLAVLIDWGALAENVLNFPAVA
+PMFPNVILVGLGNTLFYTVTSFVVGLLGGIVLALMRLSSFGPYRWLATAYVEFFRGVPAL
+LVFLAFGYGVPFAFGVSWPIPVVVMVALGMVSAAYIAETLRAGLQAVPRGQMEAARSLGM
+PTWRAMVTIVIPQAFRIVLPPLTNEVILLTKDSSLVYVLGLAAHEYELTKFGRDGISALD
+AGMTPILVAGLFYLVITVPLSLLARRFEARSTKKGH*
+>NZ_CP040019.1_976
+MFVLAIVVLALLIDWGTIGENVLNFPAVAPLFPNIILVGLGNTLFYTATSFVVGLLGGIA
+LALMRMSAFAPYRWLATAYVEFFRGVPALLVFLAFGYGVPFAFGVSWPIPVVVMTALGMV
+AAAYIAETLRAGLQAFPPGQMEAARSLGMPAWQAMITIVIPQAFRIVLPPLTNEVILLTK
+DSSLVYVLGLAAHEYELTKFGRDGISALDAGMTPILVAGLFYLVITVPLSLLARRFEARS
+TKKGH*
+>NZ_CP083691.1_913
+MSTQASPAPRTAAAPSRAGRRRTLSVAVQAAVFVLAIVVVALLADWQAIAENVLNFSAAG
+PMFPNVILVGLGNTIFYTVTAFVVGLLGGMLLALMRMSSFAPYRWLATAYVEFFRGIPAL
+LVFLAFGYGVPFAFGVSWPIPVVVMIALGMVSAAYIAETLRAGLQAVPKGQMEAARSLGM
+PHWRAMLTIVIPQAFRVVLPPLTNEVILLTKDSSLVYVLGLAAHEYELTKFGRDGIAALD
+AGMTPILVAGLCYLVITIPLSLLARRFEARSSRKAH*
+>NZ_CP097650.1_1733
+MSTQAPVSPAPAMKPGRARRRRRLSLIIQAAVFVLALVVLAVLIDWGTLTENVLNFPAVA
+PMFPNVILVGLGNTLFYTVTSFVVGLLGGIVLALMRLSSFGPYRWLATAYVEFFRGVPAL
+LVFLAFGYGVPFAFGVSWPIPVVVMVALGMVSAAYIAETLRAGLQAVPRGQMEAARSLGM
+PTWRAMVTIVIPQAFRIVLPPLTNEVILLTKDSSLVYVLGLAAHEYELTKFGRDGISALD
+AGMTPILVAGLFYLVITVPLSLLARRFETRSTKKGH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001521.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001521.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fe178043c92bf4c2d4a139e748adc248559a236b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001521.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1815
+MSIVQIPLRLASGAFILNSGLNKRGISAEQAQGLRDMGARGLPALANLSPEQFKKFLVTT
+EIGVGSALLAPFVPGWLAGSALTAFSGGLFSMYLNTPEMTEADGVRPSQEGTGVAKDIFL
+VGSGLAIAADSVANRPGKRRKAAKKRAARIEGARDAKVQAIRDAQDEKVAAIHAAREEQV
+AALREARDELKKLRKKA*
+>NZ_CP033200.1_1522
+MSIVQIPLRLASGAFILNSGLNKRGISAEQAQGLRDMGARGLPALANLSPEQFKKFLVTT
+EVGVGAALLAPFVPGWLAGSALTAFSGGLFSMYLNTPEMTEADGVRPSQEGTGVAKDIFL
+VGSGLAITADSVANRPGKRRKAAKKRAARIEGARDAKVQAIRDAQDEKVAAIHAAREEQV
+AALREARDELKKLRKKA*
+>NZ_CP040019.1_974
+MSIVQIPLRLASGAFILNSGLNKRNISEEQAAGMRDMGAQGVPYLAKLTPAQFKNFIVAT
+EVGTGAALLAPFVPGWLAGSALTAFSGGLMSMYLNTPAMTEKDGVRPSQEGTGVAKDVFL
+VGSGLAIAADSVANRSGKRRKAAKKRAARIGNARDAKVQAIRDAQDEKVAAIHAARDEQV
+AALREAREELKKLRQKA*
+>NZ_CP083691.1_911
+MSIIQIPLRLTSGAFILNSGLGKRKLGEEQAAYLQNMAAKGVPSLAKLSPSQFKNFITAT
+EIGTGAALLAPFVPGWLAGSALTAFSGGLMSMYLNTPEMTEADGVRPSQDGTAVAKDVFL
+LGAGLAVTADSVVNRPGKRKKAAKKRAARISDARDAKVDAIRAAQDEKVAAIHEAREQQV
+AALREARQELAKLRKKA*
+>NZ_CP097650.1_1735
+MSIVQIPLRLASGAFILNSGLNKRGISAEQAQGLRDMSARGLPALANLSPEQFKKFLVTT
+EIGVGSALLAPFVPGWLAGSALTAFSGGLFSMYLNTPEMTEADGVRPSQEGTAVAKDIFL
+VGSGLAIAADSVANRPGKRRKAAKKRAARIEGARDAKVQAIRDAQDEKVAAIHAAREEQV
+AALREARDELKKLRKKA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001524.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001524.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e5f7268c3f85d5a8ab1a3bdd2ff77140657eadc5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001524.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1818
+MTEHLPRPCPDAPGPDAVPPPAERVHAHDHNRDKDPALVRREPVSFVRRGARLNAGRQAV
+WDRQAERVLVDVPRGRGATSVDGQARLDWAGVFGREAPLLVDIGSGLGESTAQAAADRPD
+WNVLAVEVYVPGLAALMTRVEQQGLENVRAVEANAPELLDALLTPGSVSEVWVFFPDPWH
+KKRHHKRRLVSPAFADRVARVLTPGGVLRLATDWSGYAVQMREVLEAHPEFENLFPGRAA
+GEDSPLTRVRREGRETEVGAQPLPAGWESAAEEERPLRAGLGEARAGAAAADPVDHDGGW
+APRFEGRPITSFEAKSQRAGRLVFDLAYRRR*
+>NZ_CP033200.1_1525
+MTEHLPRPCPDAPGPDAVPPPAERVHAHDHNRDKDPALVRREPVSFVRRGARLNAGRQAV
+WDRQAERVLVDVPRGRGATSVDGQARLDWAGVFGREAPLLVDIGSGLGESTAQAAADRPD
+WNVLAVEVYVPGLAALMTRVEQQGLENVRAVEANAPELLDALLTPGSVSEVWVFFPDPWH
+KKRHHKRRLVSPAFADRVARVLTPGGVLRLATDWSGYAVQMREVLEAHPGFENLFPGRAA
+GEDSPLTRVRREGRETEVGAQPLPAGWESAAEEERPLRAGLGEARAGAAAADPVDHEGGW
+APRFEGRPITSFEAKSQRAGRLVFDLAYRRR*
+>NZ_CP040019.1_971
+MTEQPPAPDAPSRGTPANDGRDGVLAPHERAHEHDHNRDKDPALMRREPVSFVRRGARLN
+SGRQAVWDRQAQRVLVDVPRERGATSVARDARLDWDAAFGRRAPLLVDIGSGLGESTAQA
+AADRPDWNVLAVEVYVPGLAALMTRVEQSGLENVRAVEANAPELMDHLLAPGSVSEVWVF
+FPDPWHKKRHHKRRLVSPAFADRVARVLAPGGVLRLATDWSGYAVRMREVMEAHPEFENL
+HPGRAAGEKSPLTRVRREGREAEVGAQPLPAGWESAAEDERPLRAGLGEALEAAVAEDPV
+DHEGGWAPRFEGRPVTSFEAKSRRAGRLVFDLAYARR*
+>NZ_CP083691.1_907
+MTGGPENAHERDHDREKDPELIRREPVSFVRRGARMTTGRQAVWDRMAETVLVDVPRHRA
+ATSVAPDAHLDWDAAFGRHAPLLVDIGSGLGESTAQGAADHPDWNVLSVEVYLPGLAALM
+AQVESRGLENVRAVEANAPELLDHLLPAGSAQEVWVFFPDPWHKKRHHKRRLVNAAFADR
+VARVLAPGGVLRLATDWSGYAVQMREVMESHPDFVNLHPGRAAGEESPLTRVRREGRELE
+VGAQPLPAGFDPARPASELPERAGLGEAVEASLAEDPVDHDGGWAPRFEGRPLTQFEGKA
+LRAGRLVFDLAYARR*
+>NZ_CP097650.1_1738
+MTEHLPRPRPDAPDPDAVPPPAERVHAHDHNRDKDPALVRREPVSFVRRGARLNAGRQAV
+WDRQAERVLVDVPRGRGATSVDAQARLDWAGVFGREAPLLVDIGSGLGESTAQAAADRPD
+WNVLAVEVYVPGLAALMTRVEQQGLENVRAVEANAPELLDALLTPGSVSEVWVFFPDPWH
+KKRHHKRRLVSPAFADRVARVLAPGGVLRLATDWSGYAVQMREVLEAHPEFENLFPGRAA
+GEDSPLTRVRREGRETEVGAQPLPAGWERAAEEERPLRAGLGEARAGAAAADPVDHEGGW
+APRFEGRPITSFEAKSQRAGRLVFDLAYRRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001527.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001527.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d594957c3f2f62fccdafbf5b3ded85d7491c95e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001527.fa
@@ -0,0 +1,32 @@
+>NZ_CP042169.1_1821
+MASQDWMDKDFYATLGVSKDASDADVKKAYRKLARMYHPDQNPGDEAAEKKFKEISEAYA
+VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRATQSEPDLSDL
+FSGMFSGAAGQPGGFGPGGFGDAGYARPRPTKGADRTATTTISFRGSIQGTTVSLRGPDG
+ETIEVKIPKGIRDGQKVRARGKGSPGPAGRGDLLVTVHVREHEFFRRDGDDLRITVPITF
+PEAALGATIEVPTLERPVKVKVPAGSQCGRVLRLKGRGVERGKTTGDLLVELRVTVPTTL
+NDDARAAVEALQSATAGDDPRRELARKAAW*
+>NZ_CP033200.1_1528
+MASQDWMDKDFYATLGVSKDASDADVKKAYRKLARTHHPDQNPGDEAAEKKFKEISEAYA
+VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRTTQSEPDLSDL
+FSGMFSGAAGQPGGFGPGGFGDAGYARPRPTKGADRTATTTISFRGSIQGTTVSLRGPDG
+ETIEVKIPKGIRDGQKVRARGKGSPGPAGRGDLLVTVHVREHEFFRRDGDDLRITVPITF
+PEAALGATIEVPTLDRSVKVKVPAGSQCGRVLRLKGRGVERGTTTGDLLVELRVTVPTTL
+NDDARAAVEALQSATAGDYPRRELARKAAW*
+>NZ_CP040019.1_968
+MSLRAADGETIEVKIPKGIRDGQKVRARGKGAPGAAGRGDLLVTVHVREHEFFRRDGDDL
+RITVPVTFPEAALGATIEVPTLERPVKMKVPAGSQSGRVLRLKGRGVERGTTKGDLLVEL
+HVTVPTELNDDARAAVEALQSALAGDDPRRELARKAAW*
+>NZ_CP083691.1_904
+MASQDWLEKDFYQVLGVSKDASESDIKKAYRTLARKHHPDQNPGDAAAEQRFKEISEAYD
+VLSDPKDRQEYDAIRSMGGGARFGAPGGFGGAGGGAGAGGFEDVFGGMFGGGGGSRTFRT
+GGAQGGPDLSDLLGAFTGGGAGGFGGGQGFGGGGFGQPAPTKGADRTATTTISFRGAVEG
+TTVSLRAADGETVDVRIPKGVKDGQKVRARGKGSPGTAGRGDLIVTVQVREHPFFQRDGD
+DLRITVPVTFAEAALGATVEVPTLDRPVKVKVPAGSQSGRVLRLKGRGVAGAKHTGDLLV
+ELQVAVPAELSAEARGAVEAYAAATAGDDVREGLAGKAQW*
+>NZ_CP097650.1_1741
+MASQDWMDKDFYATLGVSKDASESDVKKAYRKLARTHHPDQNPGDEAAEKKFKEISEAYA
+VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRTTQSGPDLSDL
+FSGMFGGAAGQTGGFGDAGYPRPRPTKGADRTATTTISFRGSIQGTTVSLRAPDGETIEV
+KIPKGIRDGQKVRARGKGSPGAAGRGDLLVTVHVREHEFFHRDGDDLRITVPVTFPEAAL
+GATIEVPTLERPVKVKVPAGSQSGRVLRLKGRGVERGTTTGDLLVELHVTVPTELDDDAR
+AAIEALQSALAGDDPRRELARKAAW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001528.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001528.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2a3e75f2409270081ad351f4dd29530ba4652be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001528.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1822
+MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETGEPRVSAESAAEQAEDGDALAQAER
+ILDEAGAQAGTEAPQPEASDREAELEADLRRLQAEYVNYKRRVDRDRDLARDAGVLKAVT
+ALLPVLDDIDAARAAGDLTDGPFAAIATKLDTALAGLGLERHDQEALAGVEFDPAVHEAV
+MRQPHAEVPADHVVQVFRNGYVRDGRVLRAAQVMVSAGDE*
+>NZ_CP033200.1_1529
+MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETGEPRVSAESAAEQAEDGDALAQAER
+ILDEAGAEAGTQAPQPAASDREAELETDLRRLQAEFVNYKRRVDRDRDLARDAGVLKAVT
+ALLPVLDDIDAARAAGDLTDGPFAAIATKLDTVLAGLGLERHDQAALAGVEFDPALHEAV
+MRQPHAEVPADHVVQVFRNGYVRDGRVLRAAQVMVSAGDE*
+>NZ_CP040019.1_966
+MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETGEPRVSAESAAEQAEDGDALTQAER
+ILDEAGAQAGTEAPQPAASDREAELETDLRRLQAEYVNYKRRVDRDRALAQDLGVLKAVT
+ALLPVLDDLDAARAAGDLTDGPFAAIATKLDTALAGLGLERHDQEALAGVEFDPSVHEAV
+MRQPHAEVPADHVVQVFRNGYVRDGRVLRAAQVMVSAGDE*
+>NZ_CP083691.1_903
+MSENQNETPSPEEPVIRDRRRIDPETGQARTPGAGEDTVPAQEQGQAPQDSGDALSQAEQ
+ILDEAGAAAEAEALPAAGSDREAELLEDLRRLQAEYVNYKRRVDRDRDVAKEQGVLKAVT
+ALLPVLDDLDAARAAGDLEDGPFAAIAAKLMTALEGLGLEREDQEALAGVEFDPVRHEAV
+MRQPHAEVPADHVVQVFRNGYARDGRVLRAAQVMVSAGQD*
+>NZ_CP097650.1_1742
+MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETDEPRVSAESAAEQAEDGDALAQAER
+ILDEAGAQAGTEAPQPEASDREAELEADLRRLQAEFVNYKRRVDRDRDLARDAGVVKAVT
+ALLPVLDDIDAARAAGDLTDGPFAAIATKLDTALAGLGLERHDQEALAGVEFDPAVHEAV
+MRQPHAEVPADHVVQVFRNGYLRDGRVLRAAQVMVSAGDE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001534.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001534.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77b03f96cddb5b8fbb4e198a8856d9f71e72e052
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001534.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1831
+MTDTATLLDWLAAFLLVSGAFFSLVAGVGLFVLPDLLARMHAAAKPQVLGLLLMLAGLAI
+EWRSWVWLPVLLLAWVTQMVTAPVASHLVGRTGYRTKHARRELLHRDELAAVVRRAEPPA
+DPGPRRAGARPRGRR*
+>NZ_CP033200.1_1538
+MTDTATLLDWLAAFLLVSGAFFSLVAGVGLFVLPDLLARMHAAAKPQVLGLLLMLAGLGI
+VWRSWVWLPVLFLAWITQMVTAPVASHLVGRTGYRTKHARRELLHRDELAAVGRRAEPPA
+DPGPRRAGARPRGRR*
+>NZ_CP040019.1_956
+MTETATFLDWLSAALLVSGAFFTLVAGVGLLLLPDLLARMHASAKPQVLGLMLMLAGLAI
+AWESWPWVPVLFLAWVTQMVTAPVASHLVGRTAYRTKHARRELLHRDELAAIARRVEPAP
+ELDPRSPESRRRRRR*
+>NZ_CP083691.1_893
+MDAAWTDWLAAALLVGGAFFSLVAGVGMTLLPDLLSRMHASAKPQVLGLLLMACGVAVLW
+QAWAWVPVLVLAWVTQMITAPVASHLISRTGYRTKHVRRDLLHRDDLAAQAEPGPREDPD
+AR*
+>NZ_CP097650.1_1751
+MTDTATLLDWLAAFLLVSGAFFSLVAGVGLFVLPDLLARMHAAAKPQVLGLLLMLAGLAI
+EWRSWVWLPVLLLAWVTQMVTAPVASHLVGRTGYRTKHARRELLHRDELAAVVRRAEPPA
+DPGPRRAGARPRGRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001536.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001536.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b25b747cd6b4a0741c01a7e2be86ed82b2321b45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001536.fa
@@ -0,0 +1,26 @@
+>NZ_CP042169.1_1833
+MPGSDSARRGVVRPDRIRGIVAQWPLILVMVAVWCALWQDFAPHVALTGLAFALLIIGLF
+PMPSIPFSGRLNPWWSLVFTVRFLVDVVRASVNVAGTVLLRGRRARGSIVGVPLRSHDDL
+IITLVSHALALVPGSIVLDVDRVRSVLYLHVLDATTDEDVAGFRAKALDVEAGIIRAVGT
+REDLELVRRFPSSAPPAARPPKEEA*
+>NZ_CP033200.1_1540
+MPGSDSARRDVVRPDRVRGIVAQWPLILVMVAVWCALWQDFAPHVALAGLAFALLILGLF
+PMPSIPFSGRLNPWWSLVFTVRFLVDVVRASVNVTGVVLLRGRRARGSIVGVPLRSHDDL
+IITLVSHALVLVPGSIVLDVDRVRSVLYLHVLDATTDEDVEGFRAKALDVEAGIIRAVGT
+REDLELVHRYPDTAPPEEESAERRRPAAPRPGGTAPIGSTADHAKEGT*
+>NZ_CP040019.1_954
+MPGTDPARDAAGAERPARPHRVRDMVGQWPLIAVLVLLWCAVWEDYSLHVALAGLAFSLL
+VMVLFPMPRIPFSGRLNPWWFLVFTAQFLGDVVRSSVEVSKVVLLRGRAARSSIVGVRLR
+SHDDLVITLVSHALALVPGSIVLDVDRARSILYLHVLDATTDEDIEDFRAKALRVEAGII
+KAVGTREDLELVHRYPDTAPPEEESAERRRPAAPRPGGTAPIGSTADHAKEGT*
+>NZ_CP083691.1_891
+MPAAETTSPASAPTRPAPGGVRSVLRQWPLLLALVLMWCAVWQDFSAHVALTGLLFSLLV
+VVLFPMPPIPFGGRFHPGHALVFTGRFLADVVASSLSVTRVILTRGRTVRSSVVRVPLRS
+HDDIVLTLVSHALALVPGSIVLDMDRANGVLYLHVLDATTDADVADYRAKALRVEADIIR
+AVGTRADVAVLRDHPDSAPDPEGVEERRRHPAYRAELLPDTPGPVAPAPVDARPEPDAPG
+GDR*
+>NZ_CP097650.1_1753
+MPGSDSARRGVVRPDRIRGIVAQWPLILVMVAVWCALWQDFAPHVALTGLAFALLIIGLF
+PMPSIPFSGRLNPWWSLVFTVRFLVDVVRASVNVAGTVLLRGRRARGSIVGVPLRSHDDL
+IITLVSHALALVPGSIVLDVDRVRSVLYLHVLDATTDEDVAGFRAKALDVEAGIIRAVGT
+REDLELVRRFPSSAPPAARPPKEEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001538.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001538.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8fb5bf4a5554af20a2f08034f529d3bf6ebbf9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001538.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_1835
+MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIVLINNGAIMLLFLSSGGTGLAPLFV
+RGRDPHEYADTLPQALILTAIVIGFAVIAFLTAMIYRSWLLVREDEVEVDAEDVKIARMP
+AWDAEDDAELVEESSEFLDDAADPNAHYEHATESRPHVRHASPTPPAHPGPASAVRAHRA
+DGGPRP*
+>NZ_CP033200.1_1542
+MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIMLINNGAIMLLFLASGGVGLAPLFV
+RGRDPHEYADTLPQALILTAIVIGFAVVAFLTAMIYRSWLLVREDEVEVDAEDVKIARMP
+AWDAEDDAELVEESSEFLDDAADPNAHYEHATEARPQVQHATPAPQAPTGSGAASRGRRP
+EGGERA*
+>NZ_CP040019.1_952
+MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIMLINNGAIMLLFLASGGVGLAPLFV
+RGRDPHEYADTLPQALILTAIVIGFAVTAFLTAMIYRSWLISREDEVEVDAEDVKIASQG
+AWDAEDDSELVEEHSEFMDASTDPNAHYEHTTEARPQVQHVIPAPPTAAGSREAARGRRP
+EGGERA*
+>NZ_CP083691.1_889
+MTPTVDLALLAVMGVLFATGIYLLLERSLTRILVGVMLINNAAVVLLFLTSGGAGLAPLY
+DADTAPEDYADMLPQALILTAIVIGFATTAFLTAMIYRSWQLRREDDVATDVEDVKIAAQ
+SGWDAEDDSVLTEEDSEFMDDASDPNAEYEFATAAAPRARAVRPGRATVQGGGGRP*
+>NZ_CP097650.1_1755
+MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIVLINNGAIMLLFLSSGGTGLAPLFV
+RGRDPHEYADTLPQALILTAIVIGFAVVAFLTAMIYRSWLLVREDEVEVDAEDVKIARMP
+AWDAEDDAELVEESSEFLDDAADPNAHYEHATEARPQVQHATPAPQAPTGSGAASRGRRP
+EGGERA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001540.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001540.fa
new file mode 100644
index 0000000000000000000000000000000000000000..93bcb562241148426d00c176d2514961c9d5018d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001540.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1837
+MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTYLASDAFGPDERGTAWLS
+TAMAVAGVVIAVTAPVLGRRADGAGRRRLWLALTTGAVIACTAACFWVTPEESSLLLGVT
+LIALGTVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLGGILLLLIVFVGFVSGDA
+HWFGVTEDAALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPAADGGPRRESVLGSYREL
+GATLARMWREDRNTLWFLVASAVFRDGVGAVFVYGAILGTTVYGLAASDVILFAIAANVV
+AALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLAFWVGGLALCLFVGPVQS
+ASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALALHPDNRVVIPVIAVVLVA
+GGLLFARVTEPITRSAESVR*
+>NZ_CP033200.1_1544
+MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTYLASDAFGPDERGTAWLS
+TAMAVAGVVIAVTAPVLGRRADGAGRRRRGLGLTTGAVIACTAACFWVTPEESSLLLGVT
+LIALGAVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLGGILLLLIVFVGFVSGDA
+HWFGVTEDEGLNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPSPGGGPRRESLAASYRAL
+GSTLARMWREDRNTLWFLLSSAVFRDGVGAVFVYGAILGTTVYGLAASDVILFAIAANVV
+AALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLAFWVGGLALCLFVGPVQS
+ASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALALHPDNRVVIPVIAVVLVA
+GGLLFARVTEPITRSAESVR*
+>NZ_CP040019.1_950
+MPGMDPAASAVPDAALPRLATAAPRRQVVAWALWDWGSAAFNAVMVTFVFGTYLASDAFG
+PDERGTAWLSTALAVAGVVIALTAPVMGRRADGAGRRRLWLGVMTAAVIACTTACFLVTP
+QESSLLLGVTMIALGTVFFEFAEVQVNAILVQISTPATIGRISGIGWGAGYLGGILLLLI
+VFVGFVSGDAHWFGITGDEALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPTPGGGPRR
+ESLAASYRALGSTLARMWRQDRNTLWFLVSSAVFRDGVGAVFVYGAILGTTVYGLAASDV
+ILFAIVANVVAAAGAFAGGRLDDAIGPRRVILGSLAAMVLVAAGLALASGTLAFWIGGLA
+LCLFVGPVQSASRAFLGRLTTERTAGEVFGLYATTGRAVGFITPMLVTLALAAVPDNRVV
+IPVIVLVLIVGGVLFARVTDPVTRSAEPAP*
+>NZ_CP083691.1_887
+MPRMSSPAPHAAPQPCPAPHGGAGPAPARVPRGRVVAWAAWDWGSAAFNAVMVTFVFGTY
+LASDAFGPDDRGTQWLSAANALAGVVIALTAPALGRLADGTGRRRLWIALTTGAVIACTA
+ACFLVTPEESMLGLGVTLIALGTVFFEIASVHINAILLQISTPATIGRVSGFGWGAGYLG
+GIVLLLIVFVGFVSGDDHWFGVGEERALNIRVVALVAAAWFLVFALPVLAASPEPPAARG
+ADGSPRRESLVESYRGLGRTLARMWRQDRLTLRFLAASAVFRDGVGAVFVYGAILGTTLY
+GLAAQDVVLFAIVANVVAALGAFAGGRLDDALGPRRVILGSLAAMVVVAAALVLAEGTAA
+FWAGGLALCLFVGPVQSASRAFLGRLTVPETAGEAYGLYATTGRAIGFITPALVSAALAV
+WGDSRVIIPVIALVLLAGGALLLGVREPEGPTVAGARPGTGPRAAR*
+>NZ_CP097650.1_1757
+MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTYLASDAFGPDERGTAWLS
+TAMAVAGVVIAVTAPVLGRRADGAGRRRRGLALTTGAVIACTAACFWVTPEESSLLLGVT
+LIALGTVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLGGILLLLIVFVGFVSGDA
+HWFGVTEDAALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPAADGGPRRESVLGSYREL
+GATLARMWREDRNTLWFLVASAVFRDGVGAVFVYGAILGTTVYGLATSDVILFAIAANVV
+AALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLAFWVGGLALCLFVGPVQS
+ASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALALHPDNRVVIPVIAVVLVA
+GGLLFARVTEPITRSAESVR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001547.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001547.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a1e4225f29d790fd61b113a61470b5d064b26f79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001547.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1849
+MPTTDPAVRPDDHHGSGGREGARPAPGGPSRRGLLLGAGAVGGGLLGTALGYGAGHASAS
+TAPGASAAPGAGASPSEVMGDTGIEGDVGRAGWAEPGGQAARVAVSSPVGTDTVPFHGPR
+QAGVDTPAQAHAVFLALDLREDADRVRIERMLRLLTDDAARLTQGRATIADTEPELAAAP
+ARLTVTFGFGPELVRRVAPDRAPAWLRPLPAFEQIDRLDPAFSDGDLLLQICGDDRMSVA
+HTRRMLLKAARPFATERWVQEGFRSARGAHPTGTTMRNLFGQVDGTGNPAADTPHLDRVV
+WGVGAEQVGVTPWIPDGTSVVIRRIEMLMDTWDELDRPAKEKVIGRRLGTGAPLTGEQEH
+DEPDFDAVGPTGFPVISDIAHLRRARGEEPEYGMLRRGYNYDDPRGALEAGSGLIFAAYQ
+ADVDRQFVPVQARLAESDHLNLWTVPVGSAVFAIPPGCAEGGFVGDALFA*
+>NZ_CP033200.1_1556
+MPTTDPVVRSDDHHGPDDHHGPDGREGARPTPGGPSRRGLLLGAGAVGGGLLGTALGYGA
+GHASASTAPGASAASGTGASPSEVMGDTGIEGDVGRAGWAEPGGQAARVAVSSPVGTDTV
+PFHGPRQAGVDTPAQAHAVFLAFDLHEDTDRVRIERMLRLLTDDAARLTQGRATIADTEP
+ELAAAPARLTVTFGFGPELVRRVAPDRAPAWLRPLPAFEQIDRLDPAFSDGDLLLQICGD
+DRMSVAHARRMLLKAARPFATERWVQEGFRSARGAHPTGTTMRNLFGQVDGTGNPAADTP
+HLDRVVWGVGAEQVGVTPWIADGTSVVIRRIEMLMDTWDELDRPAKEKVIGRRLGTGAPL
+TGEQEHDEPDFDAVGPAGFPVISDIAHLRRARGEEPEYGMLRRGYNYDDPRGALEAGSGL
+IFAAYQADVDRQFVPVQARLAESDHLNLWTVPVGSAVFAIPPGCAEGGFVGDALFA*
+>NZ_CP040019.1_938
+MGGGLLGTALGYGAGHASAAPAAPAASGAAGAGASPSEVMGDTGIEGEVGRAGWAEPGGQ
+SARVAVSSPVGTDTVPFHGPRQAGVDTPAQAHAVFLAFDLLPDTDRLGIERMLRLLTDDA
+ARLTQGRATIADTEPELAAAPARLTVTFGFGPELLARVAPDRAPAWLRPLPAFPQIDRLD
+PAFGDGDLLLQICGDDRMSVAHARRMLIKAARPFAAERWAQEGFRASRGAHPTGTTMRNL
+FGQVDGTANPAAQTPHLDRVVWGVGAEQVGITPWIQDGTSLVVRRIEMLLDTWDELDRPG
+KERVIGRTLGTGAPLTGEQEHDEPDFVALGPAGFPVIPDISHLRRARMDVPEYGMLRRGY
+NYDDPRGAIESGAGLIFAAYQADVDRQFVPVQERLAESDHLNLWTVPVGSAVFAIPPGCA
+EGGFVGDVLFA*
+>NZ_CP083691.1_877
+MPTTDPSRRGVLFGLGAVGGGLLGGAVGYGAGAAQATPAPGGAPSGVDASPSGVMEDTGL
+EGEVGRAGWAEPGGEASRVAVSSPVGTDTVPFHGPRQAGVDTPAQTHAMLVALDLLPETD
+RAGVRALLRLLSDDAARLTQGRATLADTEPELAAAPARLTVTFGFGPELLARVAPERAPA
+WLKPLPAFPTIDALEDRWSGGDLLLQICGDDRISVAHARRMLGKVARPFAEVRWVQEGFR
+AARGTHPTGTTMRNLFGQVDGTANPQGGSPALERIVWGAGQEAADLGIAPWIPDGTSLVV
+RRIDMLMDTWDELDRPAKEKVIGRTLGTGAPLTGELETDAPDLEAIGPTGFPVIPDTAHL
+RRARGPEPEYGMLRRGYNYDDGAGASGTGAGLIFAAFQADVDRQYIPVQERLAASDHLNL
+WTRPVGSAVFAIPPGCAEGGFVGDVLFA*
+>NZ_CP097650.1_1769
+MPTTDPAVRPDDHHGPDGREGARPAPGGPSRRGLLLGAGAVGGGLLGTALGYGAGHASAS
+TAPGASAAPGAGASPSEVMGDTGIEGDVGRAGWAEPGGQAARVAVSSPVGTDTVPFHGPR
+QAGVDTPAQAHAVFLAFDLHEDTGRVRIERMLRLLTDDAARLTQGRATIADTEPELAAAP
+ARLTVTFGFGPELVRRVAPDRAPAWLRPLPAFEQIDRLDPAFSDGDLLLQICGDDRMSVA
+HARRMLLKAARPFATERWVQEGFRSARGAHPTGTTMRNLFGQVDGTGNPAADTPHLDRVV
+WGVGAEQVGVTPWITDGTSVVIRRIEMLMDTWDELDRPAKEKVIGRRLGTGAPLTGEQEH
+DEPDFDAVGPTGFPVISDIAHLRRARGEEPEYGMLRRGYNYDDPRGALEAGSGLIFAAYQ
+ADVDRQFVPVQARLAESDHLNLWTVPVGSAVFAIPPGCTEGGFVGDALFA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001549.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001549.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ac0454d064b88de8261b98d8b9ac3d290938e56
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001549.fa
@@ -0,0 +1,23 @@
+>NZ_CP042169.1_1851
+MHHQTTPVRRAARAATGLTLLPALVVAGAAPAAAHDELIRTAPAVGETATTAPSEVSLTF
+SGELIDGEGIQNLLQVRDADGNQWQSAAGTVDGSTFSAPLCEGLPNGDYEVAYRVVYSDG
+HSEERSFDFAVDDPAAPAAGTAPQGCGTAVAGASTAASPEAAAGQGDAASAEATAQADAS
+DAAQPADTDALPAWVWVAGIAGLAVLVVAFLLMGRRARALGHLDDGR*
+>NZ_CP033200.1_1558
+MHHQTTPVRRAARAAAGLALLPALVVAGAAPAAAHDELIRTAPAVDETVTTAPSEVSLTF
+SGELIDGEGIQNLLQVRDADGNQWQSAAGTVDGPTFSAPLCEGLPNGDYEVAYRVVYSDG
+HSEERSFDFAVDDPAAPAAGTAPQGCGSAVAGASIAASPEATASQGDAASAAATAQADAS
+HAAQPADSDALPAWVWVAGIAGLAVLVVAFLLMGRRARALGHLDDGR*
+>NZ_CP040019.1_936
+MAAAPAASDASTPASAGSGAGTGEASEAPAEQGSAEAGESAEAGALPAWVWAVGVAGLLV
+LVVALILMGRRARALGHLDDGR*
+>NZ_CP083691.1_875
+MNPTPMHPSTPRRAARAAAALTLLPGLAVAAAAPALAHDELLKAVPADGAALAEAPDAVS
+LTFSGDLISGQGIQSIVRVTDAAGNQWQKGDVQVSGPTLTAPLCPDLAQGEYTAAYRVVY
+SDGHSEEQSLDFSVTDPSAPAAGTAPSGCGVAAAGTASSTAAPASSAEQTGAEQSGAAST
+PAAASSTPAESGASAGVPATVWMLGAAGVAVIAVGLAVMGRKARALGRD*
+>NZ_CP097650.1_1771
+MHHQTTPVRRAARAAAGLTLLPALVVAGAAPAAAHDELIRTAPAVGETATTAPSEVSLTF
+SGELIDGEGIQNLLQVRDADGNQWQSAAGTVDGPTFSAPLCEGLPNGDYEVAYRVVYSDG
+HSEERSFDFAVDDPAAPAAGTAPQGCGTAVAGASTAASPEATAGQGDAASAEATAQADAS
+DAAQPADSDALPAWVWVAGIAGLAVLVVAFLLMGRRARALGHLDDGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001550.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001550.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d3e3e598cba6be9c98ac655d43c95a7b77138b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001550.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1852
+MRSAVAAAPWAPSGLEDPRPRVVRGPARLARGWAGALAMTALAALFHTAAEPGHGFPEVG
+VVAFAAVLAAPLCTALAGRALSLWRTAAAVAIAQGLFHVLYGLAAGGPAVAPAAGVDPAH
+LGHARPGTGALLAPGEALSSAPTGHLTDLRMLAAHVIAAVLTVLVLRRGEALVLTIAERV
+VAAVCPPPAAHGPLPTPARVRVPVPPALRPATSLALLSSPGRRGPPFALAA*
+>NZ_CP033200.1_1559
+MRSAVAAAPWAPSGLEDPRPRVVRGPARLARGWAGALAMTALAALFHTAAEPGHGFPEVG
+VVAFAAVLAAPLCTALAGRALSLWRTAAAVAIAQGLFHVLYGLAAGGHAVAPAAGVDPAH
+LGHARPGTGALLASGEALSGAPTGHLTDLRMLAAHVIAAVLTVLVLRRGEALVLTIAERV
+VAAVCPPPAAHGPLPTPARVRVPVPPVLRPATSLVLLSSPGRRGPPFALAA*
+>NZ_CP040019.1_935
+MRSAVDAAPHAFGRPHPAPGRVVRGPARLARGVAGALAMTVLAALFHAAAVPGAGLPDVR
+VAAFAAVLAAPVCTALAGRALSLWRTAAAVAVAQGLFQVLYGIAAGGHAVAPAAGVDPAH
+LHHAAAAAGPLVSVSAGPAAGHVHAAEPLMLAAHAAAAVLTVLVLRRGEALVLAVAERVL
+QAVLPRAASAGPLPLPSPARVPALPAPRPTESLVLLGTPGRRGPPFALAA*
+>NZ_CP083691.1_874
+MGTPTPVPSRAVAGPARVLRGAAGALAMTLLAALFHSAAASTPLPAPALLLFSAVLAAPV
+CTLLAGRALSLWRTAAAVAVAQGLFHALYSVAAGGRSVATAAGVAPAHLAHSHVGAARPL
+LTVDAASETSAHAAHAGTPGMLLAHLAAAALTVAVLRHGERMLVAAAERVLQAAPVWRLL
+VALAAGLLPTPRPVRVPAWRAPSAPAAVVVLASPGRRGPPAFALAA*
+>NZ_CP097650.1_1772
+MRSAVAAAPWAPSGLEDAPPRVVRGPARLVRGWAGALAMTALAALFHTAAEPGHGFPEVG
+VVAFAAVLAAPLCTALAGRALSLWRTAAAVAIAQGLFHVLYGLATGGHAVAPAAGVDPAH
+LGHAHPGAGALLAPGEALSGAPTGHLTDLRMLAAHVIAAVLTVLVLRRGEALVLTIAERV
+VAAVCPPPAAHGPLPTPARVRVPVPPALRPATSLALLSSPGRRGPPFALAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001551.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001551.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b32b07a2469916c46f00c46cd3aad37a95dcbcce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001551.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_1853
+MAMNRKELVAAVAERSGNTQAAVSDVLDALFEVFTAQVKKGEKVSIPGWLAVERTERKER
+TGRNPRTGEEITIPAGHSVKVTAGSKLKAAASE*
+>NZ_CP033200.1_1560
+MAMNRKELVAAVAERSGNTQAAVSDVLDALFEVFTAQVKKGEKVSIPGWLAVERTERKER
+TGRNPRTGEEITIPAGHSVKVTAGSKLKAAASE*
+>NZ_CP040019.1_934
+MAMNRKELVAAVAERSGNTQAAVSDVLDALFEVFTAQVKKGEKVSIPGWMAVERTERKER
+TGRNPRTGEEITIPAGYSVKVTAGSKLKAAASE*
+>NZ_CP083691.1_873
+MAMNRKELVAAVAERSGNTQAAVSDVLDALFEAFTAQVKKGEKVSIPGWLAVERTERKER
+TGRNPRTGEEITIPAGYSVKVTAGSKLKAAASE*
+>NZ_CP097650.1_1773
+MNRKELVAAVAERSGNTQAAVSDVLDALFEVFTAQVKKGEKVSIPGWLAVERTERKERTG
+RNPRTGEEITIPAGHSVKVTAGSKLKAAASE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001553.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001553.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68573f11f6c3a8cc6ddb92a8f3d0a3db13bfdb89
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001553.fa
@@ -0,0 +1,10 @@
+>NZ_CP042169.1_1855
+MAKDKDVRPIIKLKSTAGTGFTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER*
+>NZ_CP033200.1_1562
+MAKDKDVRPIIKLKSTAGTGFTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER*
+>NZ_CP040019.1_932
+MAKDKDVRPIIKLKSTAGTGYTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER*
+>NZ_CP083691.1_871
+MAKDKDVRPIIKLKSTAGTGYTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER*
+>NZ_CP097650.1_1775
+MAKDKDVRPIIKLKSTAGTGFTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001560.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001560.fa
new file mode 100644
index 0000000000000000000000000000000000000000..625d6cf2e653f35d05243ce4d004df6f4895caf3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001560.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1869
+MSGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI
+LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRD
+RR*
+>NZ_CP033200.1_1576
+MSGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI
+LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRD
+RR*
+>NZ_CP040019.1_920
+MSGSVRVSGAVRVDAWLWAVRVYKTRSAATAAVRGGHVRVNDEPVKAAHTLAVGDRVRVR
+KDQRERILEVTGLIGTRVGAPVAVTNYIDHSPPPIPRELLAVPHRERGAGRPTKRDRRKL
+DELRGRASDERS*
+>NZ_CP083691.1_854
+MGAVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI
+LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRA
+STGRG*
+>NZ_CP097650.1_1789
+MSGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI
+LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRD
+RR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001561.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001561.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e50f1f8aa71dea4753ce75a479e23b7d3f8b752
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001561.fa
@@ -0,0 +1,17 @@
+>NZ_CP042169.1_1870
+MTLVEYTRRHPDADHLDPEKESVLEEAVGTGTQQITVDAQQGAVLRVIVLCPSDATGETE
+ILTSRGGGGTKTWMAGSEALCGGWSAATPPVDEAGPMTFTVTVDNDKPFRMVLTAPSA*
+>NZ_CP033200.1_1577
+MTLVEYTRQHPDADYLDPEKESVLEEAVGTGTQQITVDAQQGAVLRVIVMCPSDATGETE
+ILTSRGGGGTKTWMAGSEALCGGWSAATPPVDEAGPMTFTVTVDNDKPFRMVLTAPSA*
+>NZ_CP040019.1_919
+MPHRRRRPCVPVALSVAAALGLSLSACASTTTAGVGSQSPAPSSAAGAASSAAGTSSAAP
+TTSAALTTSGTAAEIAGDEAAAQAQDDAATRTALNRAVAEDGIPYAELDPSLTPVPDGAS
+ILWEGLAVGAQSLRVDARAGEEYTVVLLCAEQDGSRRSLVMATVPGEDFSDVMAESPGCG
+HWSAGLPAREADGPLTLTGVVPDGGPFRMVVYRSEG*
+>NZ_CP083691.1_850
+MTLEEYTRQNPDSDYLHPETESVLQEKVGTGTQQITVDAQEGAVLRVILLCPSDATGKTD
+IHTSRGAEGEKTWMAGSEALCGGWSAATPPVEKAGPMTFSATVDNDKPFRMVLTAPAA*
+>NZ_CP097650.1_1790
+MTLVEYTRRHPDADHLDPEKESVLEEAVGTGTQQITVDAQQGAVLRVIVLCPSDATGETE
+ILTSRSGGGTKTWMAGSEALCGGWSAATPPPVDEAGPMTFTATVDNDKPFRMVLTAPSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001565.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001565.fa
new file mode 100644
index 0000000000000000000000000000000000000000..87c3d70b930a6fadbded77e5f70338a5e1aaf970
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001565.fa
@@ -0,0 +1,62 @@
+>NZ_CP042169.1_1874
+MNNRLLIVATLSLAALVVVLVAAIGGGAWWVLAVLLVALLVLAVWDMTQKRHAILRNYPV
+LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSIVYARAKGLDSHKAFGTERDTSEIG
+YEFLLHSTAPVNPPEEPPTVRIGGPDCRRPVDISLMNISSMSFGSLSANAVIAMNKGAGL
+GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNEDGTFSPEKFAEKAVLPEVKGITI
+KISQGAKPGLGGMLPKEKISPEIAEAREIPMDKDCLSPASHSAFRTPREMVKFIEQLREL
+SDGKPIGIKFCVGSRVDVLAMTKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT
+EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVKRLIQGADFTMSARAMMMATGCIQAQ
+KCHTNECPVGVATQDPRLMRALDVEDKGNRVFNYHRLTVREAVQIMASMGLTHPSQLNTR
+MLRRRVDHLSTRSYASIYHWLRTDELLNDPPAGWAMDWEEADADHFGEHARVDYLTERDP
+QWRSELLIPGREAAGAPVQGSPISGTGSTLVDARRTESVPLTTSPMPRVSSLGEGESLCT
+PGGRRRAPQDPAPAATAGETPTDENEGLPAEAGERPERQDGEEVTRRGTTGRVEGEHRGE
+GRVG*
+>NZ_CP033200.1_1582
+MNNRLLIVATLSLAALVVVLVAAIGGGAWWVLAVLLVALLVLAVWDMTQKRHAILRNYPV
+LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSIVYARAKGLDSHKAFGTERDTSEIG
+YEFLLHSTAPVNPPEEPPTVRIGGPDCRQPVDISLMNISSMSFGSLSANAVVAMNKGAGL
+GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNEDGTFSPEKFAEKAVLPEVKGITI
+KISQGAKPGLGGMLPKEKISPEIAEAREIPMDKDCLSPASHSAFRTPREMVKFIEQLREL
+SDGKPIGIKFCVGSRVDVLAMTKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT
+EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVRRLIQGADFTMSARAMMMATGCIQAQ
+KCHTNECPVGVATQDPRLMRALDVEDKGNRVFNYHRLTVREAVQIMASMGLTHPSQLNTR
+MLRRRVDHLSTRSYASIYHWLRTDELLNDPPAGWAMDWEEADADHFGEHARVDYLTERDP
+EWRSELLIPGREAGGAPVQGSPISGTGSTLVDARQTESVPLTTSPMPRVSSLGEGESLSP
+HGGRRRAPQDPAPAATAGETPTDENEGLPAEAGERPERQDGEEVTQRGTTGRVEGEHRGE
+GRVG*
+>NZ_CP040019.1_913
+MNNRLLIVATLSLGALVVVLVAAIGNGAWWVLAAIVVGLLILAVRDMTQKRHAILRNFPV
+LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSLVYARSKGLDSHKAFGTERDTSEIG
+YEFLLHSSAPVNAPAEAPTVRIGGPDCRQPVDISLMNISSMSFGSLSANAVQAMNKGAGL
+GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNGDGTFSAEKFAAKAALPEVKGITI
+KMSQGAKPGLGGMLPKEKITAEIAEAREIPMDQDCLSPASHSAFRTPREMVRFIGHLREL
+SDGKPVGIKFCVGSRVDVLAMCKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT
+EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVKRLIQGADFTMSARAMMMATGCIQAQ
+KCHTNECPVGVATQDPRLMRALDVTDKSNRVFNYHRLTVREAVQIMASMGVTHPSQLNTR
+MLRRRVDHLATRSYASIYHWLRTDELLNDPPAGWAMDWDEADGDHFGEHARVDYLTERDP
+EWRSELLIPGRQEQGAPVQGSPASGAGSRVAVGDSRDTAPVTTSPLPRVSTLAEGETLYS
+RSTRSHDPAREQAGVTQRVDTDGNDGLSPHAGEDPERQDGEEVTQRGTTGRVDAEPRGEG
+RVG*
+>NZ_CP083691.1_1564
+MNSKTLAAAAAALGVAGVAVRDLTQKQHALRHNFPVLARARWALETIGPELRQYIVAANN
+EERPFSRDQRRWVYTSSKGKNNYYGFGTDNDVEHTSYAVVKHRTFSDVAPMSALALDPGK
+ALPSAKVLGGPRGRRHAFRPNSVVNVSAMSFGSLSPQAITALNKGAALGGFMHNTGEGGL
+SDHHRQGGDLMLQIGTGYFGCRDAHGNFDMEKLAAVVESAPVRALEIKLSQGAKPGLGGH
+LPGAKVNAEIARIRGVEEGKDVASPSRHSEFSTVDEMLDFVERVAERTGLPVGIKSAVGD
+LGFWHELADAMADGTRGVDFITIDGGEGGTGAAPLIFSDSVAFPFRVAFTEVYRIFAARG
+LTDRVTWIGSGKLGLPDNALVAFALGVDMVNVAREAMLAIGCIQAQKCHLDTCPAGVATQ
+NPWLAAGLDPQEKSQRLVGYVQTLRRDLIKVSEAAGVPHPALLSPDDVALVEQTRSQTPL
+REIYGYERGWGVPGEEIRAEITRIMVDEDSSRADEDHLVQHEPLPQDDVDTTH*
+>NZ_CP097650.1_1794
+MNNRLLIVATLSLAALVVVLVAAIGGGAWWVLAVLLVALLVLAVWDMTQKRHAILRNYPV
+LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSIVYARAKGLDSHKAFGTERDTSEIG
+YEFLLHSTAPVNPPEEPPTVRIGGPDCRRPVDISLMNISSMSFGSLSANAVIAMNKGAGL
+GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNEDGTFSPEKFAEKALLPEVKGITI
+KISQGAKPGLGGMLPKEKISPEIAEAREIPMDKDCLSPASHSAFRTPREMVKFIEQLREL
+SDGKPIGIKFCVGSRVDVLAMTKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT
+EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVKRLIQGADFTMSARAMMMATGCIQAQ
+KCHTNECPVGVATQDPRLMRALDVEDKGNRVFNYHRLTVREAVQIMASMGLTHPSQLNTR
+MLRRRVDHLSTRSYASIYHWLRTDELLNDPPAGWAMDWEEADADHFGEHARVDYLTERDP
+QWRSELLIPGRAAAGAPVQGSPISGTGSTLVDARQTESVPLTTSPMPRVSSLGEGESLSP
+HGGRRRAPQDPAPAATAGETPTDENEGLPAEAGERPERQDGEEVTQRGTTGRVEGEHRGE
+GRVG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001568.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001568.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8c86be2576e3f18d0b612f70d443c37747d0561
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001568.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_1878
+MSAAQPAGVTPPPASSSPASDWDIRRPHRMWPRMLVIVLTLAGLVLVVQFFQGIASIAAP
+VFLGLNLVIVAYPLQAWLIRRGLHPVLGAATTVLLVVAVMAVFGGMMVWSGLELVAELPK
+YADRFQQIVLDVSHWLNERGVTPDMVSQQLASIDMSAVTGTAVSAITKIATNVYAVFGLL
+VTVIMGMFFLAMDSMDVERRVRLLSTARHEFGHALVEFAQGVRRYWVVTTVFGLIVAVLD
+VIALMLIGVPLALVWGVLSFLTNYIPNIGFIIGLLPPAVLGLAAGGWSDFLWVVVSYSVL
+NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN
+ARWINALIASDLKGMERRQSSLLERLRPAAWRSDAHGKDEDRAPTDGGDDDGPATDEVTG
+GAGAAPGR*
+>NZ_CP033200.1_1586
+MSAAQPAGVTPPSASSSPASDWDIRRPHRMWPRMLVIVLTLAGLVLVVQFFQGIASIAAP
+VFLGLNLVIVAYPLQAWLIRRGLHPVLGAATTVLLVVAVMAVFGGMMVWSGLELVAELPK
+YADRFQQIVLDVSHWLNERGVTPDMVSQQLASIDMSAVTGTAVSAITKIATNVYAVFGLL
+VTVIMGMFFLAMDSMDVERRVRLLSTARHEFGHALVEFAQGVRRYWVVTTVFGLIVAVLD
+VIALMLIGVPLALVWGVLSFLTNYIPNIGFIIGLLPPAILGLAAGGWSDFLWVVVSYSVL
+NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN
+ARWINALIASDLKGMERRQSSLLERLRPAAWRSDAHGGDEDRASADGGDDDGPATDEVTG
+EAGAAPGR*
+>NZ_CP040019.1_909
+MSAAQPVGAAPTPSAAGPVSDWDIRRPHRMWPRMLVIVLTLAGLVLLVQFFQGIASIAAP
+VFLGLNLVIVAYPLQAWLIRRGVHPVLGAAASVVVVVAVLGAFVGMIVWSGLELVAELPK
+YSGQFQQIVLDVSNWLNARGVTPDMVSQQLASIDVSAVTSAAVSALTKIATNLYAVLGLL
+VTVVMGMFFLAMDSMDVERRVRLLSTARLELGEALIDFAHGVRRYWVVTTVFGLIVAALD
+VIALVLIGVPLALVWGVLSFLTNYIPNVGFIIGLIPPAILGLAAGGWTSFLWVVVSYSVL
+NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN
+SRWVNSLIASDLKGMERRQHSLLERLRVGRRGEGRAGKADAEAVAGADVAAAGVEAALDV
+DDAAAGARRPEAAPTGSTLTEPARTEPGPAAPADAADGPGLTGGAAPAPGR*
+>NZ_CP083691.1_842
+MSASAPPAVTGTSTPATEWDNRRPHRMWPRMLVIVLTLAGLVVLVQFFQGIASIAAPVFL
+GLNLVIVAYPLQAWLIRRGLHPVLGAATTVVVVCAVIAAFLGMIAWSGMELLTELPKYAG
+QFQQIMHDASQWLSDHGVTPDMVNQQLASVDMSAVTGAAVSALTTIASNLYAVLGLLITV
+IMGMFFLAMDSMAVERRVRLLSTARHELGQALIDFADGVRRYWIVTTVFGLIVAVLDMVA
+LVIIGVPLALVWGVLSFLTNYIPNVGFIIGLVPPAILGLAAGGWPAFLWVVVSYSVLNFV
+LQSIIQPKVAGDAVGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLVKAVLIDADPNSRW
+VNSLIASDLKGMERRQSSMLERLRLPRELIRHGGSTASHATAADVQGDDDVAPERTAEDA
+APAQDRRRVRAAAQEARLEGPPPSTLRAPRVDLPGEPEPATADGSAPPEAGAAPGR*
+>NZ_CP097650.1_1798
+MSAAQPAGVTPPPASSSPASDWDIRRPHRMWPRMLVIVLTLAGLVLVVQFFQGIASIAAP
+VFLGLNLVIVAYPLQAWLIRRGLHPVLGAATTVLLVVAVMAVFGGMMVWSGLELVAELPK
+YADRFQQIVLDVSHWLNERGVTPDMVSQQLASIDMSTVTGTAVSAITKIATNVYAVFGLL
+VTVIMGMFFLAMDSMDVERRVRLLSTARHEFGHALVEFAQGVRRYWVVTTVFGLIVAVLD
+VIALMLIGVPLALVWGVLSFLTNYIPNIGFIIGLLPPAVLGLAAGGWSDFLWVVVSYSVL
+NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN
+ARWINALIASDLKGMERRQSSLLERLRPAAWRSDAHGGDEDRASADGGDDEGPAADEVTG
+EAGAAPGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001571.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001571.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac8ca298f8df005dfc57188f2a7336c75d03b488
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001571.fa
@@ -0,0 +1,26 @@
+>NZ_CP042169.1_1881
+MTPTTTGASLRLRDVAIRYPDGSTPVRGTDLDVAAGEIVALVGASGSGKSTILRGIAGLE
+DVVAGTVELDGRDVAAVPTHRRGVGMVFQDGQLFPHRTVGRNVAYGLESAGWDRARRRAR
+VAELLDLVGLTELTDRPVQRLSGGQAQRVALARSLAPAPRVLLLDEPLSALDADLRRRLA
+EDIRAVLRAAGTTGVVVTHDLAEAAVMADRTVRLGAGGRIAAEEDGPAVASQA*
+>NZ_CP033200.1_1589
+MTPTTTGASLRLRDVAIRYPDGSTPVRGTDLDVAAGEIVALVGASGSGKSTILRGIAGLE
+DVVAGTVELDGRDVAAVPTHRRGVGMVFQDGQLFPHRTVGRNVAYGLESAGWDRARRRAR
+VAELLDLVGLTELTDRPVQRLSGGQAQRVALARSLAPAPRVLLLDEPLSALDADLRRRLA
+EDIRAVLRAAGTTGVVVTHDLAEAAVMADRTVRLGAGGRIAAEEAGPAVASPA*
+>NZ_CP040019.1_906
+MARTTRTSRGATPGSATRGHDDDGRAGLRLRALSVAYPDGATPVRGLDLELAPGEIVALV
+GASGSGKSTVLRGIAGLEDVVGGVVEIDGEDVAAVPTHRRGVGMVFQDGQLFPHRSVARN
+VAYGLEAAGWPRERRRARVAELLELVDLAELAERPVQSLSGGQAQRVALARSLAPRPRVL
+LLDEPLSALDADLRARLAVQIREVLRAAGVTAVVVTHDLAEAAVMADRTVRLGAGGRLAG
+PGEGEPDEGAGPGPEGDAR*
+>NZ_CP083691.1_839
+MPARMHHHDAAPALRLRGLAVAYPDGSVPVTRADLDLAPGEIVALLGPSGSGKSTVLRGI
+AGLEDVPAGAVELAGRDVTAVPTHRRGVGMVFQDGQLFPHRTVARNVAYGVEAAGWDRSR
+RDARVAELLELVDLAALADRPVQTLSGGQAQRVALARSLAPSPAVLLLDEPLSALDADLR
+TRLAADIRTVLRAEGVSAVVVTHDAAEAAVMADRTVRMGADGVLHGAAADGARTAG*
+>NZ_CP097650.1_1801
+MTPTTTGASLRLRDVAIRYPDGSTPVRGTDLDVAAGEIVALVGASGSGKSTILRGIAGLE
+DVVAGTVELDGRDVAAVPTHRRGVGMVFQDGQLFPHRTVGRNVAYGLESAGWDRARRRAR
+VAELLDLVGLTELTDRPVQRLSGGQAQRVALARSLAPAPRVLLLDEPLSALDADLRRRLA
+EDIRAVLRAAGTTGVVVTHDLAEAAVMADRTVRLGAGGRIAAEEDGPAVASQA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001576.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001576.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f55b1ba18fdbfb84cff5ccad9e0e0d4f676ea908
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001576.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1888
+MPDQITHPTDAAAHPSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYTQLRDGAHRVA
+RRLQDTGLPAGTRVAAYATNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGAE
+LLVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEPSVLETARDETLDAAAPEAEVSA
+TDLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSMIALDFTAEDRPLVAMPLYHSAAMHVF
+LLPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLRK
+AQYGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHV
+EARVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAG
+YIQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVVGLPDERWIEAVTAVVVLKEG
+AELTAETVRAHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR*
+>NZ_CP033200.1_1596
+MPDQITHPTDAGHLSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYAQLRDGAHRVAR
+RLQDTGLPAGTRVAAYATNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGAEL
+LVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEPSVLETAQDETLDAAAPEAEVSAT
+DLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSIIALDFTAEDRPLVAMPLYHSAAMHVFL
+LPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLHKA
+QYGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHVE
+ARVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAGY
+IQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLKEGA
+ELTAETVRTHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR*
+>NZ_CP040019.1_896
+MTEQTSPAAPTADSPSPEDTIGRLFTRAAARHPETVALRFEDRDWTYAQLLDGVHRVARR
+LLATGLPRGTRVAAYGANSDAYAVLFLACVTAGYVHVPVNFALKGGELAHALEDSGAEVL
+VADAGMLERVEQVRADGGGAGLRHVWTMLPAGHAEPSLLETARDEAADATAPDVPVTATD
+LAQLLYTSGTTSTPKGAMMSHRALITEYLSSIIALDFTAEDRPLVAMPLYHSAAMHVFLL
+PYLSLGATVRLLATPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLRKAQ
+YGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHVEA
+RVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAGYI
+QVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLKEGAE
+LTAETVRTHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR*
+>NZ_CP083691.1_833
+MPDQITHPTDAAAHLSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYAQLRDGAHRVA
+RRLQGTGLPAGTRVAAYATNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGTE
+LLVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEPSVLETAQDEALDAAAPEAEVSA
+TDLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSIIALDFTAEDRPLVAMPLYHSAAMHVF
+LLPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLRK
+AQYGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHV
+EARVMTADGVPAAPGMPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAG
+YIQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLKEG
+AELTAETVRTHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR*
+>NZ_CP097650.1_1808
+MPDQITHPTDAGHLSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYAQLRDGAHRVAR
+RLQDTGLPAGTRVAAYATNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGAEL
+LVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEPSVLQTAQDETLDAAAPEAEVSAT
+DLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSIIALDFTAEDRPLVAMPLYHSAAMHVFL
+LPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLHKA
+QYGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHVE
+ARVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAGY
+IQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLKEGA
+ELTAETVRAHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001577.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001577.fa
new file mode 100644
index 0000000000000000000000000000000000000000..965891b2c0f5543a4408ab5e04a88b4cf6e686df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001577.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1889
+MTRTQKPTYDVVTPLDVDYLDAFGEATDEDRAHWDRARAYGREVLERIDGHWDRAEYPFD
+LVARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC
+ASPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG
+AAGGITIVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA
+RLPDVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER
+LAQMLDEVTAMQTRCVAVARLQAAGRLRDEQASLLKYACTRGARRVAQIARDMLGGNGIL
+LEHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA*
+>NZ_CP033200.1_1597
+MTRRQKPTYDVVTPLDVDYLDAFGEATEEDRAHWDRARAYGREVLERIDGHWDRAEYPLD
+LVARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC
+ASPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG
+AAGGITIVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA
+RLPDVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER
+LAQMLDEVTAMQTRCVAVARLQAAGRLRDEQASLLKYACTRGARRVAQIARDMLGGNGIL
+LEHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA*
+>NZ_CP040019.1_895
+MTRTQKPTYDVVTPLDVDYLDAFGEATDEDRAHWDRARAYGREVLERIDGHWDRAEYPLD
+LVARAGELDLLTDGLEVPGHPVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC
+AGPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG
+AAGGITIVWARDTGDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA
+RLPNVATFKDAVRVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER
+LAQMLDEVTAMQARCVAVARLQASGRLRDEQASLLKYACTRGARRVAQTARDMLGGNGIL
+LEHRVIRHFADVEALHTYEGTESVQALILGRDLTGMSAFA*
+>NZ_CP083691.1_832
+MRRQKPTYDVVTPLDVDYLDAFGEATEEDRAHWDRARAYGREVLERIDGHWDRAEYPLDL
+VARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHCA
+SPEQQERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNGA
+AGGITFVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDAR
+LPGVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQERL
+AQMLDEVTAMQTRCVVVARLQAAGRLRDEQASLLKYACTRGARRVAQIARDMLGGNGILL
+EHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA*
+>NZ_CP097650.1_1809
+MTRTQKPTYDVVTPLDVDYLDAFGEATDEDRAHWDRARAYGREVLERIDGHWDRAEYPLD
+LVARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC
+ASPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG
+AAGGITIVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA
+RLPGVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER
+LAQMLDEVTAMQTRCVAVARLQAAGLLRDEQASLLKYACTRGARRVAQIARDMLGGNGIL
+LEHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001580.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001580.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e7261101e32d3d69049799f1e5522ad2567eec0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001580.fa
@@ -0,0 +1,68 @@
+>NZ_CP042169.1_1896
+MINSAEPRHVHELFSSQTKAHYVVPPYQREYSWHRAQWEALFADLVESEDEHFLGTIITL
+SRTKDSLSGPVLEVIDGQQRLTTLTILLAAVHSHLQDAEDLDEDARFERMTLRRELVRDE
+AKAPRLTPQVQGANRADYQAMLADAGLPVKSEKKAYYPSRKVAKAFWFFRAAITELAEER
+GESLSTTALSVLAAARRALIVNIEVASAADAFVLFESLNNRGVPLTPVDLIKNSFLARAE
+HRAGMEVEEAFELWSDTLAHLGDSYATHERFLRHFYNAFRGDLPPVKLAPVATRKNLIRI
+YETLLDQDLEGTVRSLERAAQVYGRIAGGGDVDEPTSLDQELTALRRAQAAPSYVLVMWL
+LVRQEKAGWSEEDLAAVARLLVSFFVRRNLTGFPATYALPRLFMDVIDQVAAGEPDRLLT
+IVRGSLVAASASDATFRERLEGPVYEENRDVTRFLLATLAEDAMTKETRVDLWAQSGKTF
+VWTIEHILPQGENLPQEWVDALGGPEAAAETQNRFVHTLGNLTITGFNSTLGNQTFLRKR
+DRIDHQGRAIGYRNGLALNAELAEKEAWSSADIEARTVRLVERALERFAL*
+>NZ_CP040019.1_889
+MVAAREVTLQELLGGSYQYTVPLYQRTYSWGRPQWQRLWEDVVDVADHRRDNPSATHFIG
+SLVLAGFRDNGPGGVQRWLVVDGQQRLTTLTLLLAAVRDHRAEHEGPMHADRVNEKYLVN
+KWEDGDLRYKVLPTQADRAAYRGRIEHAPDAAEGSRISEAHQFFLTKLFGLSQPSADGEE
+EQLTLAEVESAVVAGLSIVSVTTGENDNAHRIFESLNNTGLKLTQGDLLRNYLFMQLPTR
+ADEVYTTLWLPLQNLLSNEELETLFWLDLVQQDPKVRQTEIYAGQQRRMRGLQDESQVRA
+EVERFLALGRLYDVMLRPEKEKDAAVRFRLARLRAWRTTTTFPITLHLMERRSLGDIDSD
+ELARALLYLESYLVRRLVFGRYSDGLNTTLLAATADIQGQDDPADALQRFLSSGRKHFAS
+DDQIRQAVITAPFYTTGRAAHRKLILRWIEESYGSKEPVDLDSATIEHVMPQTLTEEWER
+ALAGQLEAHQDLREVHTELLHTLGNLTLTGYNSELSNGPFAVKRAELAKSGIRMNQEIST
+VPVWGPAQIRARAERLADRIVGIWPGPSAEAASGVAHTAWQTLTDAVEAIPAGSWTSYGE
+LARLIGSHPVPVGTYLARTALPHAHRVLQAGGTVSPSFRWTDVHRKDDPHDVLAAEGVRF
+SEDGRAYGGQRLVAEQLAELIDVDVDLTDPRSLAAPGNDPALRDRWVDRLHDHNDPESAR
+ALIEVQRGWVERGGRAEFADNAAGGCFLVVPRASARAIWPVILYPTYGVEVVFYHLAKWP
+PFTDEALLDDFRGRLNLIPGVEFGPEALRRRPSIRPQILQPAAAQEAFLDALEWFLHTIQ
+EDDRSA*
+>NZ_CP083691.1_279
+MSHERVYRIGSPGAEPLVPVSFAEAGLRERQDLQEWVIAHPEILGEDIRIVAFEFDRWED
+ADGGRQRDRLDVLGLDQSGCLVLAELKRDAAPDTVEMQAIKYAAMASRFTEEKLVAWHAA
+MLGRLENRPVSEEEAREALTDHAGELDVEQLRRPRIVLVAGAFTRSTTAAVVWLTEMGLD
+ITLQRVQAYRMGGDDVVITVSQLFPVPDVEEFTVSPMRMESTARRTSSTRSPSTVRRLVK
+AGTLPDGTVLTLVPTTEVNAETREAIADWISDDPRRGRATWWNDPTKPMEWELDGNRYRP
+SRIVQQALREATGITRSPRGPAWWVTESGMSLTELAGDVENGAFDWTQLHRLLCELPAGR
+WTTYGEVARLIGTAPQPLGGHFRTCTLCRNAYRVLDANGAVSSGFTWGDPQETRTQQEVL
+EAEGISFDGGRAAPSQRLQPSELESVWKVAQAALGE*
+>NZ_CP083691.1_827
+MVAAREVTLQELLGGSYQYTVPLYQRTYSWGRPQWQRLWEDVVDVADHRRDNPSATHFIG
+SLVLAGFRDNGPGGVQRWLVVDGQQRLTTLTLLLAAVRDHRAEHEGPMHADRVNEKYLVN
+KWEDGDLRYKVLPTQADRAAYRGRIEHAPDAAEGSRISEAHQFFLTKLLGLSQPSAAGEE
+EPLTLAEVESAVVAGLSIVSVTTGENDNAHRIFESLNNTGLKLTQGDLLRNYLFMQLPTR
+ADEVYTTLWLPLQNLLSNEELETLFWLDLVQQDPKVRQTEIYAGQQRRMRDLQDESQVRA
+EVGRFLALGRLYDVMLRPEKEKDAAVRFRLARLRAWRTTTTFPITLHLMERRSLGDIDSD
+ELARAFLYLESYLVRRLVFGRYSDGLNTTLLAATADVQGQDDPADALQRFLSTGRKHFAS
+DDQIRQAVMTAPFYTTGRAAHRKLILRWIEESYGSKEPVDLDSATIEHVMPQTLTEEWER
+ALAGQLEAHQDLREVHTELLHTLGNLTLTGYNSELSNGPFAVKRAELAKSGIRMNQEISA
+EPVWGPAQIRARAERLADRIVDIWPGPSAEAASGVAHTAWQTLTDAVEAIPAGSWTSYGE
+LARLIGSHPVPVGTYLARTALPHAHRVLQAGGTVSPSFRWTDVHRTDDPHDVLAAEGVRF
+SEDGRADGGQRLVAEQLAELIDVDVDLIDPRSLAAPGNDPALRDRWVDRLHDHNDPESAR
+ALIEVQRGWVERGGRAEFADNAAGGCFLVVPRTSARAIWPVILYPTYGVEVVFYHLAKWP
+PFTDEALLDDFRGRLNLIPGLEFGPEALRRRPSIRPQTLQPAAAQEAFLDALEWFLHTVQ
+EDDRSA*
+>NZ_CP097650.1_1818
+MVAAREVTLQELLGGSYQYTVPLYQRTYSWGRPQWQRLWEDVVDVADHRRDNPSATHFIG
+SLVLAGFRDNGPGGVQRWLVVDGQQRLTTLTLLLAAVRDHRAEHEGPMHADRVNEKYLVN
+KWEDGDLRYKVLPTQADRGAYRGRIEHAPDAAEGSRISEAHQFFLTKLLGLSQPSADGEE
+EPLTLAEVESAVVAGLSIVSVTTGENDNAHRIFESLNNTGLKLTQGDLLRNYLFMQLPTR
+ADEVYTTLWLPLQNLLSNEELETLFWLDLVQQDPKIRQTEIYAGQQRRMRGLQDESQVRA
+EVERFLALGRLYDVMLRPEKEKDAAVRFRLARLRAWRTTTTFPITLHLMERRSLGDIDSD
+ELARALLYLESYLVRRLVFGRYSDGLNTTLLAATADIQGQDDPADALQRFLSSGRKHFAS
+DDQIRQAVMTAPFYTTGRAAHRKLILRWIEESYGSKEPVDLDSATIEHVLPQTLTEEWER
+ALAGQLEAHQDLREVHTELLHTLGNLTLTGYNSELSNGPFAVKRAELAKSGIRMNQEISA
+EPVWGPAQIRARAERLADRIVGIWPGPSAEAASGVAHTAWQTLTDAVEAIPDGSWTSYGE
+LARLIGSHPVPVGTYLARTALPHAHRVLQAGGTVSPSFRWSDVHRTDDPHDVLAAEGVRF
+SEDGRADGGQRLLAEQLAELIDVDVDLTDPRSLAAPGNDPALRDRWVDRLHDHNDPETAR
+ALIEVQRGWVERGGRAEFADNAAGGCFLVVPRTSARAIWPVILYPTYGVEVVFYHLAKWA
+PFTDETLLDEFRGRLNLIPEVEFGPESLRRRPSIKPQTLQPAAAQEAFLDALEWFLRTVQ
+EDDRTS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001584.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001584.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b82d58c976f42013b9c1b6a777b7cc2b1c47308b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001584.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1914
+MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALQRVGAEVELLTAEDVAAFRGLV
+PLLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPAGTTLTLHDIPQPAEGDGRYRR
+RGEAYARLAQAVAGVVVSSQHERALLADLVDVAADVVPLPVQDRRAAAARAEPVVPESMA
+GLDQDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSAGHDDLVAELT
+RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGR
+YTEEMERLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPERTWLDPAVDLSPGAEGCARMLF
+DVLRRVHRWT*
+>NZ_CP033200.1_1620
+MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALRRVGAEVELLTAEDVAAFRGLV
+PVLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRR
+RGEAYARLAQAVDGVVVSSQHERALLADLVDVAADVVPLPVEDRRAAAARAEPVVPESMA
+GLDRDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSAGHDDLVAELT
+RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGR
+YTEEMERLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPERTWLGPGVDLSPGAEDCARMLF
+DVLRRVHRWT*
+>NZ_CP040019.1_873
+MESQPQGRVLYVIVGPPEHGVVRHARQTAAALRRVGAEVELLTAEDVAAFHGLVPLMAEA
+RSLGAAVHLDVTDALFGPTAAAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRRRGEAYA
+RLARHAAGVVVSSQHERALLAELVDADADVVPLPVEDRRAEAARAESVVPENMAGLDQDV
+VLFGFVYPGKGHALALEALTELHRQWGPNSGAPRRLTALGPVSAGHDDLVAELTRDAEAR
+GLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGRYTEEME
+RLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPEHTWLDPAVDLSPGAEDCARMLFDVLRRV
+HRWT*
+>NZ_CP083691.1_813
+MTSHAQGRVLYLSVGSRGHGVVHHGLLTAEELAQVGLDVESLHTEDATGFVGLAPVLARA
+REARRAVHVDVTDSLFGPSPAAAADTLSRILPDGATVTLHDVPQPAEGEARFLERAEAYV
+RIAQAAAGVVVSSEHERALLHAIVDVDAHVVPLPVEDRRAAREAVRLPEALEGLDRDVVI
+FGHLYPGKGHAEAIDALAELDRQWGPSPHRPRRVTALGAVAARHEFLVDELTARAEVSGL
+QFRVTGFVPDEVLDPALRAAAVPLAAHHNVSASGSLASWMSVGRRPIVPAGRYTQEMARL
+RPGTLRIVQVGTSGPEYALAEAVAEAVEEPSRTWQARGTSLAPGPRACARMLAAALADVH
+GWAWPR*
+>NZ_CP097650.1_1841
+MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALRRVGAEVELLTAEDVAAFRGLV
+PVLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRR
+RGEAYARLAQAVDGVVVSSQHERALLADLVDVAADVVPLPVEDRRAAAARAEPVVPESMA
+GLDRDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSIGHDDLVAELT
+RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRTIASAGR
+YTEEMERLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPERTWLDPAVDLSPGAEDCARMLF
+DVLRRVHRWT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001586.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001586.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd9bf233836b1ef300efba26944f1b15c0ef6f9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001586.fa
@@ -0,0 +1,39 @@
+>NZ_CP042169.1_1916
+MAPARRRVLYYAHQHGAGHLRHAAGLASTGAFDVTVVTAHPRAAELLPADVPVIPLPSDL
+VPGHEQPARSPLHWSPVGPEIRARFDALHAAAQRVGPDVCVVDVSVEAALFLRLAGWPVL
+HRRMHGERTDPAHALVYAEADGLFAHYAAELEVPAWRAAHADRVTYLGVADVTGRLGTRT
+TTTSTARAAPRVAVIAGTGGGGVRAADLARAASAVPEATWEVYGPIAGVGEPEAPGGLAA
+EAMPATVTLHGWVQAPARRAADADVVVVSAGHNAVVDAARSGRPVVLAPEPRPFDEQRVF
+VREIHRAAGVPWCAWEDPDADWAGAVRGALADPTAADRLAGLLLVAPDEYRRRWEAAIEG
+ALG*
+>NZ_CP033200.1_1622
+MAPARRRVLYYAHQHGAGHLRHAAGLASTGAFDVTVVTAHPRAAELLPADVPVIPLPSDL
+VPGHQQPARSPLHWSPVGTEIRARFDALHAAAQRVDPDVCVVDVSVEAALFLRLAGWPVL
+HRRMHGERTDPAHALVYAEADGLFAHYAAELEVPAWRAAHADRVTYLGVADVTGRLGTRA
+TTTSSAGAAPRVAVIAGTGGGGVRAADLARAASAVPEATWEVYGPIAGVGEPEAPGGLAA
+EAMPATVTLHGWVQAPARRAADADVVVVSAGHNAVVDAARSGRPVVLAPEPRPFDEQRVF
+VREIHRAAGVPWCAWEDPDADWAGAVRGALADPAAADRLAGLLLVAPGEYRRRWEAAIEG
+ALG*
+>NZ_CP040019.1_871
+MSDGAAAVSRPGASARPSRRRRVLYYAHQHGSGHVRHAANLAATGAFDVTVVSAHPDAAR
+MLLAGTPVLPLPSDVVPGHVQPERSPLHWTPVGPQIRDRFAALHDAARDVRPDVCVVDVS
+VEAALFLRLAGWPVLHRRMHGERTDPAHALVYAEADGLFAHYAEELEDPAWREAHAGRTA
+FLGVPDVTGRLGARATTTTATTTAAGGSAPRVAVIAGTGGGGVRAADLARAAAAVPEATW
+EVYGPVAGADELQAPGGAAGSRSSDADATTGTAPTAGVALPANVTLHGWVEAPASRAAEA
+DVVVVSAGHNAAVDAARSGRPVVLAPEPRPFDEQHVFAREARRAAGVPWCAWEDPDADWA
+GAVRGALADPSAADRLAALLLVEPGEYRRRWEAAVEAALEATQG*
+>NZ_CP083691.1_811
+MSGRRLRVLHYAHQHGSGHVRHAATLIRADVADVTVATAHPDAARLLPTGTRIVPLPTDI
+VPGHGQPEGSPLHHTPVGPAIQARFDALHDAARAVRPDVCVVDVSAEAALFLRLAGYPVV
+HRRMHGDRTDPAHRLVYAEADALFAHYGEVLEDPAWQAEFGARTAHLGVPDADGRLGRTA
+APARAGEAPRVVAVTGTGGGGVAARDIARAARSTPGARWHVIGPVRDAGGADLPENLELQ
+GWVEDVPAALAAADVVVVSAGHNAAVDAAHSGRPVVLAPEERPFAEQRRFAEAVERAAGV
+PWRAWEDPEADWAGAVARALGDPAAADRLAAALLRPPAEHAAGWGALLERAAASAQ*
+>NZ_CP097650.1_1843
+MAPARRRVLYYAHQHGAGHLRHAAGLASTGAFDVTVVTAHPRAAALLPADVPVIPLPSDL
+VPGHQQPARSPLHWSPVGTEIRARFDALHAAAQRVDPDVCVADVSVEAALFLRLAGWPVL
+HRRMHGERTDPAHALVYAEADGLFAHYAAELEVPAWRAAHADRVTYLGVADVTGRLGTRA
+TTTSSAGAAPRVAVIAGTGGGGVRAADLARAASAVPEATWEVYGPIAGVGEPEAPGGLAA
+EAMPATVTLHGWVQAPARRAADADVVVVSAGHNAVVDAARSGRPVVLAPEPRPFDEQRVF
+VREIHRAAGVPWCAWEDPDADWAGAVRGALADPAAADRLAGLLLVAPDEYRRRWEAAIEG
+ALG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001595.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001595.fa
new file mode 100644
index 0000000000000000000000000000000000000000..22f8be1c3f23798bbb75c5553f0a4a8a98241546
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001595.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1930
+MSDERARSFSASTASAADDGARGTGTTRVKRGLADMMKGGVIMDVVNAEQARIAEDAGAV
+AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF
+IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA
+VKHIRTIRKEIAQLQGLAQDELYVAAKELQAPYELVREVAETGALPVVMFTAGGVATPAD
+AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV
+GDLPAPHRLAERGW*
+>NZ_CP033200.1_1636
+MSDERARNFSASTASAADDGARGTGTTRVKRGLADMMKGGVIMDVVNAEQARIAEDAGAV
+AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF
+IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA
+VKHIRTIRKEIAQLQGLAQDELYVAAKELQAPYELVREVAETGTLPVVMFTAGGVATPAD
+AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV
+GDLPAPHRLAERGW*
+>NZ_CP040019.1_855
+MSDERARSFSASTASAADDGARGTGTTRVKRGLADMMKGGVIMDVVNAEQARIAEDAGAV
+AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF
+IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA
+VKHIRTIRKEIAQLQGLAQDELYVAAKELQAPYELVREVAETGALPVVMFTAGGVATPAD
+AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV
+GDLPAPHRLAERGW*
+>NZ_CP083691.1_790
+MSDDRAQSFSASTGAAADDGARGTGTTRVKRGLADMLKGGVIMDVVTPEQARIAEDAGAV
+AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF
+IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA
+VKHIRTIRKEIAQLQGLAQDELYVAAKELQAPYELVCEVAETGALPVVMFTAGGVATPAD
+AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV
+GDLPAPHRLAERGW*
+>NZ_CP097650.1_1857
+MSDERARSFSASTASAADDGARGTGTTRVKRGLADMMKGGVIMDVVNAEQARIAEDAGAV
+AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF
+IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA
+VKHIRTIRKEIAQLQGLAQDELYVAAKELRAPYELVREVAETGTLPVVMFTAGGVATPAD
+AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV
+GDLPAPHRLAERGW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001596.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001596.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7c649fc6f4f976f0aa352156906427287a73761
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001596.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1932
+MPVRNRRAAALPAKLSRSWLLVNAATPDAFAPALASEADSVIFDLEAAVPEEQKDAARRH
+VVDALSGGMTAWVRISATSTDHWQRDLEALAGLDGVRGVVLAETKEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGGLPGAIDGPPGNTDGEDAVIESSAVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA*
+>NZ_CP033200.1_1638
+MPVRNRRAAALPAKLSRSWLLVNAATPDAFAPALASEADSVIFDLEAAVPEEQKDAARQH
+VVDALSGGMTAWVRISATSTDHWQRDLEALTGLDGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGGLPGAIDGPPGNTDGEDAVIESSVVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA*
+>NZ_CP040019.1_853
+MPVRNRRAAALPAKLSRSWLLVNAARPEDFAPALASEADSVIFDLEAAVPEDKKDAARQH
+VVDALSGGMTAWVRIAATSTDHWQRDLEALAGVDGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGGLPGAIDGPPGNTDGEDAVVDSSAVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA*
+>NZ_CP083691.1_789
+MPVRNRRAAALPAKLSRSWLLVNAARPEDFAPGLASEADSVIFDLEAAVPEEHKDAARQN
+VIEALSGGMTAWVRISATTSEHWARDLEALEGLSGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGRLPGAVDGPPGAGDDEAAVAASSEVTHSMGMTGRLCLNRGQVEWVNRALSPSEDELTW
+AHDLLDKHAAGAAVGDGSYLPRLRRAEKIADLADSYGLWNA*
+>NZ_CP097650.1_1859
+MPVRNRRAAALPAKLSRSWLLVNAATPDAFAPALASEADSVIFDLEAAVPEEQKDAARQH
+VVDALSGGMTAWVRISATSTDHWQRDLEALAGLDGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGRLPGAIDGPPGNTDGEDAVIESSAVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001605.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001605.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f1a5100c592b8e7e36b61bc1f60858d80ac1df9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001605.fa
@@ -0,0 +1,44 @@
+>NZ_CP042169.1_1943
+MSHDVEAPAGVPGSVAVVGGGVAGFAVVRELRRRGFAGEIALVDPQGVPYDRPPLSKEFL
+TGDADARRLLLAPPTWFAEHGVELVEDAAVRVVPGGVHPDGGPAPHRVETASGRVLEADA
+VVLATGGRPRALDVAGADHPDLITLRTRSDAEALRDRLTFGAEVAVVGGGFTGAEVAAAA
+RRSLAAVTLVTGTDAPARAAVGPALAARLHRMHVEHGVAVEVGRAAWIEHRDADGGAALP
+AAHRLHLHDGRTVDADVVVLAGGTVPDTALAEDAGLEVADGVLTDAMGRTTVPGILAVGD
+AARARESAWATSRHWEPALRSGAAAAAALLGEQTDAPGAPWFWSDRYDAHVEAVGDMTVP
+AGGRIVDREVRGVVVASFALAADGTLRGAASIDDPMTVKAARRIIDRGIVVDAAALADPA
+VPVKSLARG*
+>NZ_CP033200.1_1649
+MSHDVEAPAGVPGSVAVVGGGVAGFAVVRELRRRGFAGGIALVDPQGVPYDRPPLSKEFL
+TGDADAHRLLLAPPAWFAEHGVELVEDEAVRVVPGGVHPDGGPAPHRVETASGRVLDADA
+VVLATGGRPRALDVAGADHPDLITLRTRADAEALRDRLTFGAEVAVVGGGFTGAEVAAAA
+RRSLAAVTLVTGTDAPARAAVGPALAARLHRMHAEHGVAVEVGRAAWIEHRDADGGAALP
+AAHRLHLHDGRTVDADVVVLAGGTVPDTALAEDAGLEVADGVLTDAMGRTTVPGILAVGD
+AARARESAWAPSRHWEPALRSGAAAAAAILGEEADAPGAPWFWSDRYDAHVEAVGDMTVP
+AGGRIVDREVRGTVVASFALAADGTLRGAASIDDPMTVKAARRIIDRGIVVDAAALADPA
+VPVKSLARG*
+>NZ_CP040019.1_842
+MSGDVDARAGAPASVVVVGGGVAGFGAVRELRRRGHTGSLALVEPQGVPYDRPPLSKDYL
+TGETDAHRLLFAPPSWFAEHDVELVEEAAVRLTPGGAHPDGDPVPHRVELASGRVLEAEA
+VVLATGGRPRPLDVEGATHPDLITLRTRADADALRERLHFGAEVAVVGGGFTGAEAASSA
+RQALAGVTLVTATDAPALRAVGPALAARLHRMHAEHGVAVEVGRVARIEHRDDDGGAALP
+AAHRLHLGDGRTVDADVVVLAGGTVPDTALAEEAGLEVADGILVDEAGRTSVPGILAVGD
+TARATGSAWGPSPHWEPALRSGAAAAAALLGEEPEPPGAPWLWSDRHGCHVEAVGDMAVP
+PGGASVDREARGAAVASFVLDAEGRMRGAASIDDPMTVKAARRIIDRGIVVDPQALADPT
+VPLKSLARG*
+>NZ_CP083691.1_777
+MTVPASVLVVGGGVAGFGTVRELRRRGFEGKLTLVDPQGLPYDRPPLSKDFLTGETDAHR
+LLFAPPAWFAEHAVELVTARVDRMDLTGEHPAAVLDDGTVRAADAVVLAPGGRPRPLDVP
+GGDRPGVLVLRTRADAEAIAARLHFGARVVVVGAGLTGSEVASAAREAMAEVTLVSASPA
+PAAAAVGPALAARLHALHAARGVDVVQGRVLRIEHADDAPGLDAPHRVHVALADGGEAAL
+DADLVVAAVGILPDAALAAEAGLELAVDGGILVDAAQRTSDPRVLAVGDAARRRDAAYAA
+PAMHWEPALQDAADAAAALLGEDLPERGAPWFWSDRHGVHVEGVGAMRPPEGGRIVDREV
+RGTVVASFALAADGAMVGAASVDDPMAVKAARRIVDRGIVVDPERLADPSVPVKALLRG*
+>NZ_CP097650.1_1870
+MSHDVEAPAGVPGSVAVVGGGVAGFAVVRELRRRGFAGGIALVDPQGVPYDRPPLSKEFL
+TGDADAHRLLLAPPAWFAEHGVELVEDEAVRVVPGGVHPDGGPAPHRVETASGRVLDADA
+VVLATGGRPRALDVAGADHPDLITLRTRADAEALRDRLTFGAEVAVVGGGFTGAEVAAAA
+RRSLAAVTLVTGTDAPARAAVGPALAARLHRMHAEHGVAVEVGRAAWIEHRDADGGAALP
+AAHRLHLHDGRTVDADVVVLAGGTVPDTALAEDAGLEVADGVLTDAMGRTTVPGILAVGD
+AARARESAWAPSRHWEPALRSGAAAAAAILGEEADAPGAPWFWSDRYDAHVEAVGDMTVP
+AGGRIVDREVRGTVVASFALAADGTLRGAASIDDPMTVKAARRIIDRGIVVDAAALADPA
+VPVKSLARG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001607.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001607.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b6b862de34673e32dc95287fe426ca46b670e20
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001607.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1947
+MGRITASAARITLVAMTDDAQQTPAVVAPHKKVGMLPPYAAGKPPVAVPGLHPYKLSSNE
+NPYAPVSGVIDRVRQVVTGPEGAPSTLCRYPDTLSTGLRQALAAHLDVPADDVVTGAGSL
+GALAQVITAFAGHGEAGEGDEVIFAWRSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAML
+EAITERTRVILLCTPNNPTGPVLTTAEVEDFLARVPAHILVVIDEAYVEFVRDEDAVKGL
+EMYRKHANVVVLRTFSKAHGLANLRVGYSVSQPEITKALRTVATPFAVSTVAEEAAIASL
+EHLDEVLERVQIVVDERERVAAALAEAGWDLPASQANFVWLPLGERTQAFAEAAQARALS
+VRAFAGEGVRVSIGEKEANDRFLEVARDFLA*
+>NZ_CP033200.1_1669
+MVPLTASAARITLVAMTDDAQQTPAVVAPHKKVGMLPPYAAGKPPVAVPGLHPYKLSSNE
+NPYAPVPGVIDRVRQVVTGPEGAPSTLCRYPDTLSTGLRQALAAHLDVPADDVVTGAGSL
+GALAQVITAFAGHGEAGEGDEVIFAWRSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAML
+EAITERTRVILLCTPNNPTGPVLTTAEVEDFLARVPAHILVVIDEAYVEFVRDEDAVKGL
+EMYRKHANVVVLRTFSKAHGLANLRVGYSVSQPEITKALRTVATPFAVSTVAEEAAIASL
+EHLDEVLERVQVVVDERERVAAALAEAGWDLPSSQANFVWLPLGERTQAFAEAAQARALS
+VRAFADEGVRVSIGEKEANDRFLEVARDFLT*
+>NZ_CP040019.1_823
+MTDDAQLTPAAVAPHKKVGMLPPYAAGKPPVAVPGLRPYKLSSNENPHAPVAGVIERVRG
+VVTGPEGAPSTLCRYPDTLSTGLREALAAHLDVPADDVVTGAGSLGALSQVITAFAGHGE
+AGRGDEVIFAWRSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAMLAAITDRTRVILLCTP
+NNPTGPVLTTAEVEGFLAEVPEHVLVVIDEAYVEFVRDEDAVRGLDMYRKHANVVVLRTF
+SKAHGLANLRVGYSVSRPEITKALRTVATPFAVSTVAEEAAIASLEHLDEVLEGVQLVVD
+ERERVAAALAEAGWDVPASQANFVWLPLGERTADFAAAAQAKALSVRAFAGEGVRVSIGE
+QEANDRFLEVARDFLK*
+>NZ_CP083691.1_759
+MTDVTSGSSGVAAHRKVSLLPPYAAGKPPVAVPGLRPYKLSSNENPFAPVPAVVERIHEV
+VAGAEGEPSPVCRYPDPLSTALRERLAAHLDVPADDIVTGGGSLGALTQVITAFAGDGGE
+DGAPDEVVFAWRSFEAYPIVVRTAGAKDVQVPLTADGRHDLPAMLAAITERTKVMLLCTP
+NNPTGPVLTTAEVEDFLAQVPPHVLVVIDEAYVEFVRHPDAVDGPAMYRRHPNVVVLRTF
+SKAHGLANLRVGYSVSRPEVTASLRTVAVPFAVSTVAEQAAIASLDHLDEVLERVQTVVD
+ERERVVAALAEAGWDVPETHANFVWLPLGERGADFAAAAGERALSVRAFPEGVRVSISER
+EANDRFLEVARAFQR*
+>NZ_CP097650.1_1886
+MGRITASAARITLVAMTDDAPQTPAVVAPHKKVGMLPPYAAGKPPVAVPGLHPYKLSSNE
+NPYAPVSGVIDRVRQVVTGPEGAPSTLCRYPDTLSTGLRQALAAHLDVPADDVVTGAGSL
+GALAQVITAFAGHGEAGEGDEVIFAWHSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAML
+EAITERTRVILLCTPNNPTGPVLTTAEVEDFLARVPAHILVVIDEAYVEFVRDEDAVKGL
+EMYRKHANVVVLRTFSKAHGLANLRVGYSVSQPEITKALRTVATPFAVSTVAEEAAIASL
+EHLDEVLERVQVVVDERERVAAALAGAGWDLPSSQANFVWLPLGERTQAFAEAAQAQALS
+VRAFAGEGVRVSIGEQEANDRFLEVARDFLT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001608.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001608.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bdc814466092978263af2e297941b6c0128df281
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001608.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1948
+MAEHDGGPVREGAPSQTLSRALTLLEAVVEAPEPPTIADLADGLGVHRSVAYRMLRTFET
+HGLLRRDGLGRVHAAPGLAVLARRVEQDLRAAAMPHLTAVSTDLGMTAFLVVWDGAHCLT
+LATAEPPSGNLVTQRPGTRHPLGVGAPGMAIAVALTGQEWARLPGEAAPERPELDDVRER
+GWAVSSDEVITGVSSVAVPLRVPGQLPAALAVVYATRPEDPARLGDRLGEAARAVAVAFG
+AA*
+>NZ_CP033200.1_1670
+MAEHDGGPVREGAPSQTLSRALTLLETVVEAPEPPTIADLADGLGVHRSVAYRMLRTFEA
+HGLLRRDGLGRVHAAPGLAVLARRVEQDLRAAAMPHLTAVSTDLGMTAFLVVWDGAHCLT
+LATAEPPSGNLVTQRPGTRHPLGVGAPGMAIAVALTGQEWARLPGEAPPERPELDDVRER
+GWAVSSDEVITGVSSVAVPLRVPGQLPAALAVVYATRPEDPARLGDRLGEAARAVAVAFG
+AA*
+>NZ_CP040019.1_822
+MAEDDGGPAPAREGAPSQTLSRALALLEAVVEAAEPPTIAELADGLGVHRSVAYRVLRTF
+EAHGLLRRDPLGRVHSAPGLAVLARRVEQDLRTAAMPHLSAVSADLGMTAFLVVGDGSTC
+LTLATVEPPRGNLVTQRPGTRHPLGIGAPGMAVALALPEQEWEQRRGDAAPERPELGEAR
+ERGWAVSRDEVITGVSSVAVPLSVPGQLPAALAVVYATRPEDPERLGGRLKEAAQAVAAS
+LGAA*
+>NZ_CP083691.1_758
+MDPHDDSVPAVSAPPPSAPGVRPGAPSQTLSRALTMLELVADRPTPPSIAELADDLGVHR
+SVAYRMLRTFEVHGLLRRDAAGLVHGAPGLVTLAGGVEQDLRAAAVTELSRVSDALAMTA
+FLVVWDGRDCLTLATVEPPRGNLVTQRPGTRHPLGVGAPGIAIASVLPAEGQDRPAVREA
+RARGWAASRDEVITGVGSVAAPVPAAAGMPAALAVVFTSPAVDEEAVGAELAAAARRLGA
+VLGEG*
+>NZ_CP097650.1_1887
+MAEHDGGPVREGAPSQTLSRALTLLETVVEAPEPPTIADLADGLGVHRSVAYRVLRTFET
+HGLLRRDGLGRVHAAPGLAVLARRVEQDLRAAAMPHLTAVSTDLGMTAFLVVWDGAHCLT
+LATAEPPSGNLVTQRPGTRHPLGIGAPGMAIAVALTGQEWARLPGEAPPERPELDDVRER
+GWAVSSDEVITGVSSVAVPLRVPGQLPAALAVVYATRPEDPARLGDRLGEAARAVAVAFG
+AA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001611.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001611.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6877cdc70e34426521702396a6f510ff755c94a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001611.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1952
+MTQTSSPQHLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE
+IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNEQLLSGRA
+KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG
+WEILYELSHGTPEQKQMAQDAVNRFYGPALQMFGPTDEDSPNSRQSMAWKVKRFSNDDLR
+QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGDGPMNTQRMARR
+IQAHEDGAWVREAAAAYARRQAEQNAPAETHLIGA*
+>NZ_CP033200.1_1674
+MTQTSSPQHLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE
+IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNEQLLSGRA
+KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG
+WEILYELSHGTPEQKQMAQDAVNRFYGPALQMFGPPDEDSPNSRQSMAWKVKRFSNDDLR
+QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGDGPMNTQRMARR
+IQAHEDGAWVREAAAAYARRQAEQNAPAETHLIGA*
+>NZ_CP040019.1_818
+MTQTSSTTRLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE
+IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDVLNDQLLEGKA
+KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRSSYGPYGRAMVRICKEESFHQRQG
+WEILYELSHGTPEQKQMAQDAVDRFYGPALQMFGPPDEDSPNSKQSMAWKVKRFSNDELR
+QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDELMSVIKGNGPMNTQRLARR
+IQAHEDGAWVRDAAAAYARRQAEQHAPAETHLIGA*
+>NZ_CP083691.1_754
+MTQTSSSPHLASVPSPDDAAGQENFDRLIQEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE
+IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNEQLLSGRA
+KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG
+WEILYELSHGTPEQKQMAQDAVNRFYGPALQMFGPPDEDSPNSQQSMAWKVKRFSNDELR
+QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGNGPMNTQRLARR
+VQAHEDGAWVREAAAAYARRQAEQHVPADTQLIGA*
+>NZ_CP097650.1_1891
+MTQTSSPQHLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE
+IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNAQLLSGRA
+KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG
+WEILYELSHGTPEQKQMAQDAVDRFYGPALQMFGPPDEDSPNSRQSMAWKVKRFSNDDLR
+QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGDGPMNTQRMARR
+IQAHEEGAWVREAAAAYARRQAEQNAPAETHLIGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001615.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001615.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2f10399fc183b74bbdf66e4653dde974449d7b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001615.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1956
+MTETTDAPTTGKRRATFNTLEVSELRRLTEDSVEVTFAVPEELADDYDYVPGQYVALRKE
+LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGTFSTWANESLEVGEKIDVMNPQGAFTSRT
+HVTSLNDAQKVAAEKVAEKKDTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS
+AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD
+EWFLCGPFELVQLTRETLAARGVPEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI
+EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA
+LEKDEVEKGYVLTCQTRPTSDSITLDFDA*
+>NZ_CP033200.1_1678
+MTETTDVPTTGKRRATFNTLEVSELRRLTDDSVEITFAVPEELADDYDYVPGQYVALRKE
+LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGKFSTWANESLEVGEKIDVMNPQGAFTSRT
+HVTSLNDAQKVAAEKVAEKKDTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS
+AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD
+EWFLCGPFELVQLTRETLAARGVSEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI
+EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA
+LEKDEVEKGYVLTCQTRPTSDSITLDFDA*
+>NZ_CP040019.1_814
+MTETTVTPATGKRRATFNTLEVSELRRLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE
+LDGQEVRRSYSICAIPKRGEIRVAVKKDIGGKFSTWANEVLEVGEKIDVMNPQGAFTSRS
+HVTSLNDAEKVAAEKVAQNKNTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS
+AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDAEKLTTLLDRVIDVDGTD
+EWFLCGPFELVQLARETLSARGVDEDDVRFELFTTGRPENPQGHSGRVVEADPSGDNVTI
+EFNLDGLSGKVESPKSAHETILNAALRVRSDVPFACAGGVCGTCRAKVTDGEYEMDENYA
+LEKDEVEAGYVLTCQTRATSDSITVDYDA*
+>NZ_CP083691.1_750
+MTETTDAPITGKRRATFNTLEVSGLRKLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE
+LDGAELRRSYSICAVPQRGEIRVAVKKDLGGTFSTWANEVLEVGEKIDVMNPQGAFTSRT
+NVTSMNDPEAVAAEAVKQDQTHLVALAAGSGITPIMAIAKSVLAASDSARFDLIYANRSA
+MDVMFAEEIGDLKDKYPARFTVNHVLSREQRVAPLLSGRIDDEKLNTLLDRVIDVENTDE
+WFLCGPFELVQLARDTLSERGVAEDDVRFELFTTGKPEAPQGQSGRGVEADPSGDNVTIE
+FNLDGLSAKVESPKSAHETILNAALRVRSDVPFACAGGVCGTCRAKVTEGEFTMEENYAL
+EKDEVEQGYVLTCQTRPTTDSIKVDFDA*
+>NZ_CP097650.1_1895
+MTETTAAPTTGKRRATFNTLEVSELRRLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE
+LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGKFSTWANESLEVGEKIDVMNPQGAFTSRT
+HVTSLNDAQKVAAEKVAENKDTHLVAFAAGSGITPIMAIAKAVLAASESSRFDLVYANRS
+AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD
+EWFLCGPFELVQLTRETLAARGVSEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI
+EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA
+LEKDEVEKGYVLTCQTRPTSDSITLDFDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001619.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001619.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b18f06d597cf9f17e68a31f5c9c9f815e6ee00a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001619.fa
@@ -0,0 +1,16 @@
+>NZ_CP042169.1_1963
+MDEPTLLRVALPVANTPGHHLDQRLWLSRAARPVDPETFGRA*
+>NZ_CP033200.1_1684
+MDEPTLLRVALPVANTPGHHLDQRLWLSRAARPVDPETFGRA*
+>NZ_CP040019.1_2489
+MDALDLPALAGARALELPGSELTHPFGPEADVYKVRGRVFMLVLEARGAMLVNLKAVPED
+GAALREAYPAQVTPGYHMSKRHWISLGPPPADPHDDDAPARLDAALVRDLVTESYLLVLE
+RSVPRRDWPVDPATFGRG*
+>NZ_CP083691.1_744
+MDEPTLLRIARDRALELPGSAASHPFGPDTEVVKVQGKLFVVFIDHDGRRLVNVKARPED
+GAQLRAALPAAITPGYHMDKRHWLSLAAHPDLDEQLVRDLVTESYLLVVAKLPRTRRPVD
+PDTFGRA*
+>NZ_CP097650.1_1901
+MDEPTLLRIARDRALELPGSAASHPFGPDTEVMKVQGKLFAVFIDHDGRRLVNVKARPED
+GAQLRAALPAAITPGYHMDKRHWLSLAAHPDLDEQLVRDLVTESYLLIVAKLPRTRRPVD
+PETFGRV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001625.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001625.fa
new file mode 100644
index 0000000000000000000000000000000000000000..759d44c7197d2dc4bbecbbe20fcebec78839ff2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001625.fa
@@ -0,0 +1,33 @@
+>NZ_CP042169.1_1969
+MTTSRLPLLGALAVGALALAGCAGGGAEPSSPAPSSASSTTTAASSASPAASSSTAPTSP
+AASASTASMGGASASGSLSLEMPPALDGQRTLAVQAAVQRAAGPGSEVGLSAASPLERQT
+ELRQRAAGLEQTVDAGASPASTRSAEQQACLDATRSDLERDAEAGAADLGLTAQPETAAT
+TGGGPTSTPVPSFTASPDAEVTPLGVRVTVYPTEEAARAALEDARAAAQACTGVDLAGLG
+VESVTRTEHEGGTAYTALPAPGGSVYSHLTAVQDGARTVAVAQADADGGVPADAEDRAAS
+IVADVLAALDGEG*
+>NZ_CP033200.1_1690
+MTTSRLPLLGALAVGALALAGCAGGGGAEPSSPAPSSASSTTTAASSAPTSPAASSSTES
+TGAAESTAGASASGSLSLEMPPALDGQRTLAVQAAVQRAAGPGSEVGLSAASPLERQTEL
+RQRAAGLEQAVDAGASPASTRSAEQQACLDATRSDLERDAEAGAADLGLTAQPETAATTG
+GGPTTTPAPSFTASPDAEVTPLGVRVTVYPTEEAARAALEDARAAAQACTGVDLAGLDVE
+SVTRTEHEGGTAYTALPAPGGSVYSHLTAVQDGARTVAVAQADADGGVPADAEDRAASIV
+ADVLAALDGEG*
+>NZ_CP040019.1_778
+MTPSRLPLLGVLAVGALALAGCAGGGAEPSSPAPSPASSSASPTTTAASSASTSPAASAS
+ASSTPTATALSLDLPEELSGESATRLRAVVQDAAGPAAELGQTFSSPLERRAALEEDAAI
+VDALEEDAGDDAGRRACVDATRAAREADQASGAAQAAWYAQPQTASTTGGSTDGTAASGR
+PGLQVEPLGVQVAVYPDEATARSVAEAARDAAEACEGQEMSSMGVSSVEPLTGAPGETAF
+TVVPVSGSIIYAVSTVVQVGDRVYAVSQGEDGAGVPEGAEERAVALVEDLEAALEG*
+>NZ_CP083691.1_739
+MTHMTAVPSRRLRAGFALGAAALVLTGCAGGGGSASSSTAAGSPTAGGAGSSVTSPAASS
+SAASSSALSLSMPDRFGNEARTGLTEAVTAAAPEGFEVTTRSVSPLERKTDLEDQATILT
+DGPLEPAAEGSSASPTYTEAQQRCADAAAERFRTEAAAGGAQLRSDAMPTVAGGGYTSVR
+ADVVAYPDVSAAVAALADGSAPIELCTDVQVPGAEQPTDIAPVTGIGDEAVGGELAGGRW
+LAVRRGTDVVSVMVAGPGETAPAGAADQARALAEQVLEAVPAG*
+>NZ_CP097650.1_1907
+MTTPRLPLLGALAVGALALAGCAGGGGAEPSSPAPSSASSTTTAASSASTSPAASSSTAP
+TSPAASASTESTAGASASSSLSLEMPPALDGQRTLAVQTAVQRAAGPGSEVGLSAASPLE
+RQTELRQRAAGLEQAVDAGASPAPTRSAEQQACLDATRSALERDAEAGAADLGLTAQPET
+AATTGVGPTTTPAPSFTASPDAEVTPLGVRVTVYPTEEAARAALEDARAAAQACTGVDLA
+GLGVESVTRTEHEGGAAYTALPAPGGSVYSHLTAVQDGARTVAVAQADADGGVPADAEDR
+AASIVTDVLAALDGEG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001626.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001626.fa
new file mode 100644
index 0000000000000000000000000000000000000000..029985274fea6bdf78c48f0a5bd15ca3655e1b67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001626.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1970
+MPQSSPTPRRGRPGYDRQTLLAECVELFNRHGYEATSMGMLATHLGISKSAIYHHVESKE
+AILDHAVTEALDALEACLDDVVASGVDAGAQVEAAIRGTLGVLAEKQPEVTLLLRLRGNS
+AVEVAAVERRREITRRFGDLLEAAQAAGAVRSDVTPRNLARLALGMINSIVDWYRPDRGV
+PGQEGPGQMIDAVTGVVLGGLRG*
+>NZ_CP033200.1_1691
+MPQSSPTPRRGRPGYDRQTLLAECVELFNRHGYEATSMGMLAAHLGISKSAIYHHVESKE
+AILDHAVTEALDALEACLDDVVASGADAGAQVEAAIRGTLGVLAEKQPEVTLLLRLRGNS
+AVEVAAVERRREITRRFGDLLEAAQAAGAVRSDVTPRNLARLALGMINSIVDWYRPDRGV
+PGQQGPDQMIDAVTGVVLGGLRG*
+>NZ_CP040019.1_777
+MPHSSTAPRRGRPGYDRQTLLTVCVDVFNRHGYEATSMGMLAQHLGISKSAIYHHVESKE
+AILEQALDDALDALEASLDGVMADFAGPGEQVEAAVRGTLRVLVEKMPEVTLLLRLRGNS
+AVELAAMERRRAITRRLGEMIAAAQEAGAVRGDITPRNLARLALGMINSIVDWYRPESDS
+PGHKSVTEMVDAVTRVVLGGLRG*
+>NZ_CP083691.1_737
+MPQSSPTPRRGRPGYDRQTLLAECVELFNRHGYEATSMGMLATHLGISKSAIYHHVESKE
+AILDHAVTEALDALEACLDDVVASGADAGAQVEAAIRGTLGVLAEKQPEVTLLLRLRGNS
+AVEVAAVERRREITRRLGDLLESAQAAGAVRSDVTPRNLARLALGMINSIVDWYRPDGAD
+PGHKSVEEMVAAVTGVVMGGLRG*
+>NZ_CP097650.1_1908
+MPQSSPTPRRGRPGYDRQTLLAECVELFNRHGYEATSMGMLAAHLGISKSAIYHHVESKE
+AILDHAVTEALDALEACLDDVVASGADAGAQVEAAIRGTLGVLAEKQPEVTLLLRLRGNS
+AVEVAAVERRREITRRFGDLLEAAQAAGAVRSDVTPRNLARLALGMINSIVDWYRPDRGV
+PGQQGPDQMIDAVTGVVLGGLRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001632.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001632.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4d14be6f9df9b42970999a2ab8d0852e3bbd7231
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001632.fa
@@ -0,0 +1,36 @@
+>NZ_CP042169.1_1980
+MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT
+RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL
+LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM
+NGALNAFTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLARLRRLATQAQEAAARRV
+ERTLERRLRSPGAPAFPDDDADGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL
+DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPEDEKG*
+>NZ_CP033200.1_1699
+MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT
+RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL
+LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM
+NGALNGYTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV
+ERTLERRLRSPGAPAFPDDDTHGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL
+DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPADPRD*
+>NZ_CP040019.1_764
+MDVQQFFADLSDVPWLLTTLDLIGIFFFATSGALLASRKEFDLVGSMALALLAGLGGGFT
+RDILLDRGLPASLENPIYLAPPVLVSLLVYVKALHPNRLNLTITLFDAGGLALFTVSGVL
+IAHSMDVHPVSTVVVAMVAALGGGVLRDIVANEVPSIFDPRGVYVMPTFVGATVATIAAM
+NGVLNAFTGFLIAFLIFAVRMLAYRYQWRLFGADISQDKESLDRLRRLATQAQDAAARRV
+ERARERRLRSASGPGGMDVGEAEAIADRAVHHPPAPAGYHYDAVEDAYTRDHAFDDDGEP
+GSASYGPRQEYEDQVRVDEYDPETQTITVIDPASRQQVRLDPATGVMDVTDLRTGRTRSY
+DDPEHDWIADDAEDDARG*
+>NZ_CP083691.1_730
+MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT
+RDILLDRGLPASLENPVYLAPPVLVSLLVYVKLIHPNRLNLTITLFDAAGLALFTVSGVL
+LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM
+NGALNAFTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV
+ERTLERRLRAPGAPAFPDDDTHGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL
+DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPEDSRD*
+>NZ_CP097650.1_1916
+MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT
+RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL
+LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM
+NGALNGYTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV
+ERTLERRLRSPGAPAFPDDDTHGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL
+DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPADPRD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001634.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001634.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad0b7b52de32913b77403cd642b17c4bdd999d00
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001634.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_1989
+MTTSETTSETTSETPDTSATTHGRPTERRGHVAELLSATVARQPDAVALRIGEARMTYRE
+LDQVTAATAGWLRHRGVGPGDRVAVMLPNVPAFVAVYEALMRLGAVMVPLNPLFTARELG
+YFLEDSGARMLWAMPGLPAVDEVAGNVDVEVVTLDLEAVGRECAAEGIAPVTEITPRDPD
+DDAVLLYTSGTTGRPKGARLTHTNLRSNAMATATGLGRLGPDDVVFAALPMFHVFGLSVV
+LNGAVFAGSTLSLMPRFVPEAAYDQLQDHGITFLPGVPTMHGAFLSVARARREAGAEPAD
+FSRLRMPLSGGASLPVETLRAAEKLFGVPVLEGYGLSENAGACFFNPVDAPTRPGTVGRP
+VDGFEFRIVAMDGTEVPEEDLETSGELRIRGEGIMAGYWGRPEDTEAAFDEDGWFRTGDI
+ARRDEAGYVMIVDRLKDVIIRGGMNVYPREVEEVLYEHPDVVEAAVVGVPDERLGEEIAA
+FVSLAPGSTATGEELQAFAAERLARYKQPREVTIMDGLPKNATGKILRRELRQG*
+>NZ_CP033200.1_1707
+MTTSETPDTSATTHGRPTERRGHVAELLSATVARQPDAVALRIGEARMTYRELDQVTAAT
+AGWLRHRGVGPGDRVAVLLPNVPAFVAVYEALMRLGAVMVPLNPLFTARELEYFLEDSGA
+RVLWAMPGLPAVDEVAGNVDVEVVTLDLEAVGRECAAEGIAPVTEITLRDPDDDAVLLYT
+SGTTGRPKGARLTHTNLRSNAMATATGLGRLGPDDVVFAALPMFHVFGLSVVLNGAVFAG
+STLSLMPRFVPEAAYDQLQDHGVTFLPGVPTMHGAFLSVARARREAGAEPEDFSRLRMPL
+SGGASLPVETLRAAEKLFGVPVLEGYGLSENAGACFFNPVDAPTRPGTVGRPVDGFEFRI
+VAMDGTEVPEEDLETSGELRIRGEGIMAGYWGRPEDTAAAFDQDGWFRTGDIARRDEAGY
+VMIVDRLKDVIIRGGMNVYPREVEEVLYEHPDVVEAAVVGVPDERLGEEIAAFVSLAPGS
+AVTGEQLQAFAAERLARYKQPREVTVLDGLPKNATGKILRRELRQG*
+>NZ_CP083691.1_718
+MTTSETPDTSTTTHGRPTERRGHVAELLSATVARQPDAVALRIGEARMTYRELDQVTAAT
+AGWLRHRGVGPGDRVAVLLPNVPAFVAVYEALMRLGAVMVPLNPLFTARELGYFLADSGA
+RMLWAMPGLQAVDEVAGNVDVEVVTLDLEAVGRECAAEGIAPVTEITPRDPDDDAVLLYT
+SGTTGRPKGARLTHTNLRSNAMATATGLGRLGPDDVVFAALPMFHVFGLSVVLNGAVFSG
+STLSLMPRFEPEAAYDQLQDHGVTFLPGVPTMHGAFLTVARARREAGAEPADFSRLRMPL
+SGGASLPVDTLHAAEKLYGVPVFEGYGLSENAGACFFNPVDAPTRPGTVGRPVDGFEFRI
+VAMDGTEVPEEDLETSGELRIRGEGIMAGYWGHPEDTVAAFDADGWFRTGDIARRDEAGY
+VLIVDRLKDVIIRGGMNVYPREVEEVLYEHPDVVEAAVVGVPDERLGEEIAAFVSLAPGS
+TVTGEELQAFAAERLARYKQPREVTVLDGLPKNATGKILRRELRG*
+>NZ_CP083691.1_724
+MNSALPATDPHRGDVCALLEAGHDRDPRAVAWREDGVDTTYAELLELVQATAGVLRRQGV
+GPGDRVALLMPNTLAFPAVYYGALWLGAVVVPLNPLSTDRELEYFLTDSQAVLLWSMRGT
+SAAAEAAQAVGVPHLQSSPADLRDVVAGAEPVRERTPRTSEEADAVVIYTSGTTGQSKGA
+RLSHRTVASSAVLTSEALDWLQAGHTVLGVLPFFHVFGMSAALNMPLYTGCRNSVVTRFA
+PHTALEQVVRDEVRALPAVPTMIGALLRALRSARAKGDDVDLSALRYILSGGAPLPVETL
+HEAEEEFGVPVREGYGLTESCGPVSFNPMLRPSRAGTVGQPLPGVEFRLVTTDGVEVPAG
+DTETPGELRIHGPVLMTGYLGEPQADAASFDDEGWLRTGDVATRDEEDYYRIVGRLKDII
+IHGGYNVYPREVEEAFYEHPAVSEAAVLGVPDERFGEKVVAYVALQDGPEVEVAELNAFV
+RERLASYKWPSQVTVMDALPKNTTGKIVKDLLR*
+>NZ_CP097650.1_1924
+MTNSETPDTSATTVGRPTERRGHVAELLSATVARQPDAVALRIGEASMTYRELDQVTAAT
+AGWLRHRGVGPGDRVAMMLPNIPAFVAVYEALMRLGAVMVPLNPLFTARELEYFLEDSGA
+RMLWAMPGLPAVDGVAGNVDVEVVTLDLEAVGRECDAEGITPVTEITPRDPDDDAVLLYT
+SGTTGRPKGARLTHTNLRSNAMATATGLGRLGPDDVVFAALPMFHVFGLSVVLNGAVFAG
+STLSLMPRFVPEAAYDQLQDHGITFLPGVPTMHGAFLSVARARREAGTEPADFSRLRMPL
+SGGASLPVETLRAAETLFGVPVLEGYGLSENAGACFFNPVDAPTRPGTVGRPVDGFEFRI
+VAMDGTEVPEEDLETSGELRIRGEGIMAGYWGRPEDTEAAFDEDGWFRTGDIARRDEAGY
+VMIVDRLKDVIIRGGMNVYPREVEEVLYEHPDVVEAAVVGVPDERLGEEIAAFVSLAPGS
+AVTGEELQAFAAERLARYKQPREVTILDGLPKNATGKILRRELRQG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001635.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001635.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45264179866d008ebd06b23fdc25bf67640e3f3e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001635.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_1996
+MTTVFYDDQGRPEPPFAAGEAATLLGFLDFLRATIEWKTADLDTAALHRRLPGHPSAMTL
+GGLLKHLAFVEFWWFEAVALGEPTSAPWVGADFDADPDWDWHSAAQDSAADLRALWQGQV
+ERSRQIVVDLLAADGDDGAAALARAHRIREGRDPVSLRWILTHMIEEYGRHAGHADLLRE
+GIDGQTGE*
+>NZ_CP033200.1_1714
+MTTVFYDDQGRPEPPFAAGEAATLLGFLDFLRATIEWKTADLDTAALHRRLPGHPSAMTL
+GGLLKHLAFVEFWWFEAVALGEPTSTPWVGADFDADPDWDWHSAAQDSAADLRALWQGQV
+ERSRQIVVDLLAADGDDGAAALARAHRIREGRDPVSLRWILTHMIEEYGRHAGHADLLRE
+GIDGQAGE*
+>NZ_CP040019.1_754
+MTTVFYDDQGRPEPPETAGEAETLLGFLEFLRATFAWRTGGLDEAALRRRLDGHPSEMTL
+GGMLKHLAFVEFWWFEAVALGAPTSEPWVSVDWAADEDWDWHSAAEDSAADLRALWEGQV
+ERSRQAVQELLAADGDPLGRVLESYDGRRRVTLRWILTHMIEEYARHNGHADLLREQIDG
+QTGE*
+>NZ_CP083691.1_723
+MTTVFYDEQGRPEPPHAADEAATLLAFLDFQRATFAWRTSGLDDAALRRRLDGHPSEMTL
+GGMLKHLAFVEFFWFEVTAHGKPTSEPWVSVDWDADADWDWHSAAEDAAEELRDLWRESV
+ERSRAVVVRLLADGPAALDTTHPAWGGRADVSLRWILTHMIEEYARHNGHADLLREQIDG
+QTGE*
+>NZ_CP097650.1_1931
+MTTVFYDDQGRPEPPFAAGEAATLLGFLDFLRATIEWKTADLDTAALRRRLPGHPSAMTL
+GGLLKHLAFVEFWWFEAVALGEPTSAPWVGADFDADPDWDWHSAAQDSAADLRALWQGQV
+ERSRQIVVDLLAADGDDGAAALARAHRIREGRDPVSLRWILTHMIEEYGRHAGHADLLRE
+GIDGQTGE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001637.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001637.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a320beb034deaa13204641b9c8e8507a559aae1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001637.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_1999
+MDSTLFTRSADRAAHNDVNFRTRKWVKPEDLNANNTLFGGSLLRWVDEEAAIYATLQLGN
+PRCVTKLISEINFLASAKQGDMIEMGLRATEFGRTSLTMRAKVRNIVTGEMILTIDKIVF
+VSLGEDGKPVPHGFTEITYDRDRLPLDNPL*
+>NZ_CP033200.1_1717
+MDSTLFTRSADRAAHDDVNFRTRKWVKPEDLNANNTLFGGSLLRWVDEEAAIYATLQLGN
+PRCVTKLISEINFLASAKQGDMIEMGLRATEFGRTSLTMRAKVRNIVTGEMILTIDKIVF
+VSLGEDGKPVPHGFTEITYDRDRLPLDNPL*
+>NZ_CP040019.1_695
+MDTSTAPGADHGRAADDISYRTRKWVKPEDLNANGTLFGGSLLRWIDEEAAIYAIIQLGN
+PRSVTKLISEINFRSSARQGDMIEMGLRAVEFGRTSLTMRAKVRNIISGEVILTIEKIVF
+VSLDEDGNPVPHGYTDITFDRDRLPQDTAR*
+>NZ_CP083691.1_709
+MATHHAPNLTAHEDDDVSYRTRKWVKPEDLNANGTLFGGSLLRWIDEEAAIYSIIQLGNP
+RSVTKLISEIEFSASARQGDMIEMGLRAVKFGRTSLTMRAKVRNIVTGEVILTIDKIVFV
+SLDEEGRPQPHGYTDITYDRDRLPLDTSR*
+>NZ_CP097650.1_1934
+MPAATVKPSTGTSRQVASGVAGSGWGRMVIGRVPPVWSVADPSGDPTARSSTSPHRAPSL
+VPASASLYRGAMDSTLFTRSADRAAHDDVNFRTRKWVKPEDLNANNTLFGGSLLRWVDEE
+AAIYATLQLGNPRCVTKLISEINFLASAKQGDMIEMGLRATEFGRTSLTMRAKVRNIVTG
+EMILTIDKIVFVSLGEDGKPVPHGFTEITYDRDRLPLDNPL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001639.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001639.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b7162796164630e979c9176a1a06c1681efba3ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001639.fa
@@ -0,0 +1,29 @@
+>NZ_CP042169.1_2001
+MSPDRSVTLTGVRVEADGPEGAVVLLDGVDLTLAAPRVAVIGENGSGKSTLARAIAGLAD
+VVAGEVTVHGVDAVRDVKALRRTVGFVFANPAAQMVMPTVREDVELTVKSLRDDAGRRLT
+KDDVAARVAAALQEHRLTALADRACLSLSSGQAQRLAMCSVMTAGPSLVIADEPTSLLDG
+RHRRIVADRLLAADPSAPDGFQLLLVTHDLELARACDEAVWIHSGRVERTGPAEEVVEAY
+ERFLDHAVAAELR*
+>NZ_CP033200.1_1719
+MSPDRSVTLTGVRVEADGPEGVVVLLDGVDLTLTAPRVAVIGENGSGKSTLARAIAGLAD
+VVAGEVTVHGVDAVRDVKALRRTVGFVFANPAAQMVMPTVREDVELTVKSLRDDAGRRLT
+KDDVAARVAAALQEHRLTALADRACLSLSSGQAQRLAMCSVMTTGPSLVIADEPTSLLDG
+RHRRIVADRLLAADPSAPDGFQLLLVTHDLELARACDEAVWVHGGRVERTGPAEDVVEAY
+EHFLDHAVAAELR*
+>NZ_CP040019.1_747
+MEQTTGVRLRGARVEADGPEGVVALLQDVDLDLTAPRVAVVGENGSGKSTLARAVAGLVD
+VVAGEVTVHGVDAVRDVKALRRVVGMVFANPAAQAVMPTVREDVELTVKSLRDDDGRRLS
+KDDVAARVAAALAEHRLTELAERPCLALSSGQAQRLAMCSVMAGRPRLVIADEPTSLLDG
+RHRRIIADRLLAADGFQLLLVTHDLELARACDDAVWVHEGRVRAVGPAGEVVDAYAAFLD
+EAVAAESAEAAAGDPAAVNPAGASAEARP*
+>NZ_CP083691.1_710
+MTGRTPPTRAPHDDDAAVRLAGVQVAAPGGPVLLDGVDLHLTAPRVAVVGENGSGKSTLA
+RAVAGLAEVTAGEVAVHGVDAVRDVKALRRTVGMVFANPAAQMVMPTVREDVELTVKALT
+DDAGRRLSRAEVAARVDAALAEHRLTDLAERPCLSLSSGQAQRLAMCSVLVGAPRLVIAD
+EPTSLLDGRHRRIVADRLLGGAERGEFQLLLVTHDLDLARACDAAVWVHSGRVERHGPAA
+ETVAAYEAFLDDAVARELA*
+>NZ_CP097650.1_1936
+MLLDGVDLTLTAPRVAVIGENGSGKSTLARAIAGLADVVAGEVSVHGVDAVRDVKALRRT
+VGFVFANPAAQMVMPTVREDVELTVKSLRDDAGRRLAKDDVAARVAAALEEHRLTALADR
+ACLSLSSGQAQRLAMCSVMTAGPSLVIADEPTSLLDGRHRRIVADRLLAADPSAPDGFQL
+LLVTHDLELARACDEAVWIHGGHVERTGPAEDVVEAYERFLDHAVAAELR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001641.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001641.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8608adedd296615400ec78c61ca185165a4bfcae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001641.fa
@@ -0,0 +1,42 @@
+>NZ_CP042169.1_2015
+MSTTTKDVEQPRVMKEMSFLDRWLPVWILAAMAVGLLMGRFIPGLNTALEAVKIGSVSLP
+IAIGLLVMMYPVLAKVRYDETRRIGADRRLLVTSLVLNWIVGPALMFALAWIFLADLPEY
+RTGLIIVGLARCIAMVLIWNDLACGDREAAAVLVAINSVFQVIAFGALGWFYLQALPSWL
+GLPTTSAEFSIGAIVLSVLIFLGIPLVAGFLTRILGERAKGRTWYEERFLPKIGPWALYG
+LLFTIVLLFALQGDAIISAPGDVARIALPLLVYFVVMFLGSFLLGRAIGLDYAKSTTVAF
+TASGNNFELAIAVAIGTFGVTSGQALAGVVGPLIEVPVLVALVYVALAMGRRLFPGDTTA
+PTR*
+>NZ_CP040019.1_543
+MPSRAVAPSPATGPAARPAERPVLQEMSFLDRWLPVWILAAMAAGLLLGRLVPGLAEALD
+AFTVAGVSVPIALGLLVMMYPVLAKVRYDETHRIAADRRLMGTSLVLNWIVGPALMFALA
+WLFLADLPEYRTGLIIVGLARCIAMVLIWNDLACGDREAAVVLVAVNSVFQVVAFGALGW
+FYMQVLTGWLGLPTTTAGFSVGAIVLSVLVFLGVPLLAGFLTRVLGERARGRAWYEGRFL
+PRIGPWALYGLLFTIVLLFALQGEAITTSPGDVARIALPLLVYFTVMFLLGLVASRAVGL
+DYARSTTVAFTASGNNFELAIAVAIATFGVHSGQALAGVVGPLIEVPVLVGLVYVARWLA
+PRLFPGDPTVPPPRPRPHRQEHPVTEHAPTDRRPSVLFVCVHNAGRSQMAAGWLEHLSGG
+RVEVRSAGSAPKDRINPSAVAVMAEAGIDLSANTPKVLTTEAVRESDVVITMGCGDTCPV
+FPGKRYEDWAVEDPAGQGVNAVRPIRDEIRGRVEALLADLLPEG*
+>NZ_CP040019.1_726
+MSVSTTAPAPHQPVLKEMSFLDRWLPAWILLAMAAGLLLGRFVPGLNTALEAVKIGEVSL
+PIAIGLLVMMYPVLAKVRYDEAHRVAGDKWLMITSLVLNWIVGPALMFALAWMLLPDLPE
+YRTGLIIVGLARCIAMVFIWNDLACGDREAAAVLVAINSVFQVVAFGALGWFYLQVLPSW
+LGLPTTSADFSVWAIVLSVLVFLGVPLLAGFLTRLLGERAKGRTWYEERFLPRIGPWALY
+GLLFTIVLLFALQGEAITSNPWDVARIALPLLAYFVLMFGIALLASKAVGLNYAKSTTVA
+FTAAGNNFELAIAVAIGTFGVTSGQALAGVVGPLIEVPVLVGLVYVSLWAGRKLFPGDPT
+VPARPQAAAAHRA*
+>NZ_CP083691.1_471
+MSSTPRTTAEAAPVAARLSSLDRLLPVWIGAAMLVGLLLGRLVPGLGGVLAAVEVDGVSL
+PIALGLLVMMYPVLAKVRYDRLDSVTGDRRLLVASLVLNWVFGPLLMFALAWIFLADLPE
+YRTGLIIVGLARCIAMVIIWNDLACGDREAAAVLVALNSIFQVIAFAALGWFYLSVLPGW
+LGLPQTGLDVSPWDIARSVLIFLGIPLLAGFLSRVIGERRWGRAAYEGSFLPTIGPWALY
+GLLFTIVVLFALQGEQIAARPWDVARIALPLLVYFAVMWGLGYTVGRRLGLGYERTTTLA
+FTAAGNNFELAIAVAIATFGATSGQALAGVVGPLIEVPVLVGLVYVSLWLRRRFPPAADA
+GTPASAMTVPATTAQENR*
+>NZ_CP097650.1_1944
+MSTTTKDVEQPRVMKEMSFLDRWLPVWILAAMAVGLLLGRLIPGLNTALEAVKIGSVSLP
+IAIGLLVMMYPVLAKVRYDETRRIGADRRLLVTSLVLNWIVGPALMFALAWIFLADLPEY
+RTGLIIVGLARCIAMVLIWNDLACGDREAAAVLVAINSVFQVIAFGALGWFYLQALPSWL
+GLPTTSAEFSIGAIVLSVLIFLGIPLVAGFLTRILGERAKGRTWYEERFLPKIGPWALYG
+LLFTIVLLFALQGDAIISAPVDVARIALPLLVYFVVMFLGSFLLGRAIGLDYAKSTTVAF
+TASGNNFELAIAVAIGTFGVTSGQALAGVVGPLIEVPVLVALVYVALAMGRRLFPGDTTA
+PTR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001645.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001645.fa
new file mode 100644
index 0000000000000000000000000000000000000000..531a4b77b5464a0d89c2f9caada42adfee023bda
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001645.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_2027
+MDPDASPRVRLTADDPRPGSRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG*
+>NZ_CP033200.1_1744
+MDPDASPRVRLTADDPRPGSRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG*
+>NZ_CP040019.1_684
+MDPDASPRARLTADDPRPGGRPATSTEGPHRQLDQQSSPELWGRLIAAVFALDGVEEGHS
+TVSPATSRAVHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG*
+>NZ_CP083691.1_594
+MDPDASPRARLTADDPRPGGRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRAVHLTGRPKERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLPPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG*
+>NZ_CP097650.1_1967
+MDPDASPRVRLTADDPRPGSRPVTSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001650.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001650.fa
new file mode 100644
index 0000000000000000000000000000000000000000..162b35c76d42dfa364be0534bebac802622cbb30
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001650.fa
@@ -0,0 +1,28 @@
+>NZ_CP042169.1_2032
+MCVRLPDMTQSTPGGPATDLPDFRPSGNQGVDPALYEIENAAMDREGALWAALQEAAPWT
+GRTLLDLGAGTGFWLPRYADAAETIAVEPDARLLGAARARPGGARVLYGSAEQIPLPEAS
+VDVVHARFAYFFPHPRWDVRPGLDEVTRVLRPGGALVVIDNDTERGQFAELLRASTNAAA
+QGQDTYAREWWAGIGAETREVMSSWTFDSRADLEAVLRLEFERGVADAWLAEHPAATSLS
+YGYLLHVWR*
+>NZ_CP033200.1_1749
+MCVRLPDMTQSTPGGPATDLPDFRPSGNQGVDPALYEIENAAMDREGALWAALQEAAPWT
+GRTLLDLGAGTGFWLPRYADAAETIAVEPDARLLGAARARPGGARVLYGSAEQIPLPEAS
+VDVVHARFAYFFPHPRWDVRPGLDEVTRVLRPGGALVVIDNDTERGQFAELLRASTNAAA
+QGQDTYAREWWAGIGAETREVMSSWTFDSRADLEAVLRLEFERGVADAWLAEHPAATSLS
+YGYLLHVWR*
+>NZ_CP040019.1_570
+MTATPELPDFVPASNQGGDPAVYEVENAALDREGTLWAALQEAAPWAGRTLLDLGAGTGF
+WLPRYADAAEVIAVEPDTRLLDAARARPGGARVRRGSAERIPLAEASVDVVHARFAYFFP
+HPQWDVRPGLEEVARVLRPDGALVVIDNDTERGEFAELLVRSDAAADQGQDTYARRWWAD
+VGAETREVMSSWTFDTRADLEAVLRLEFPAELAEEWLAAHPEATSLTYGYLLHVWRPRG*
+>NZ_CP040019.1_679
+MELPDFRPSGNQGVDPALYEIENAAMDREGALWAALQEAAPWAGRTLLDLGAGTGFWLPR
+YADAAETIAVEPDARLLGAARARPGGARVLYGSAEQIPLPEASVDVVHARFAYFFPHPHW
+DVRPGLDEVTRVLRPGGALVVIDNDTERGQFAELLRASTNAAAQGQDTYAREWWAGVGAE
+TREVMSSWTFDSRADLEAVLRLEFERGVADAWLAEHPAATSLSYGYLFHVWR*
+>NZ_CP097650.1_1972
+MEGGCVRLPGMTQSTPGGPATGLPDFRPSGNQGVDPALYEIENAAMDREGALWAALQEAA
+PWAGRTLLDLGAGTGFWLPRYADAAETIAVEPDVRLLGAARARPGGARVLYGSAEQIPLP
+EASVDVVHARFAYFFPHPRWDVRPGLDEVTRVLRPGGALVVIDNDTERGQFAELLRASTN
+AAAQGQDTYAREWWAGVGAETREVMSSWTFDSRADLEAVLRLEFERGVADAWLAEHPAAT
+SLSYGYLLHVWR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001652.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001652.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f6921f4b1170cc6c108a49b5c43d7ecb5922b28
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001652.fa
@@ -0,0 +1,43 @@
+>NZ_CP042169.1_2039
+MSPSAPQRRAARAATFAATLAAAAIALTACGADAAPFSPASAPASASDGAESPAGEATAA
+SSVSEEDRVDPTQTTEVSAVTPRILLSHEDGLTLLDAESGEVVKEQDVTGFTRLSNAGNG
+KDVLVTTGNGWEVFSTGIQAKAHGDHVHHYESAPGMTGVTFPGEHPGHVVTHNGRTTLFA
+DGTGAIRTFDSTHLDKATPDLMPVMTEAETEDPHHGVALELSDGALFTTQGTEDSRDALQ
+VIDPKTGEVTAETDDCPGSHGEAAAQPTEAGDVVVMGCENGPVVYRDGEFHKVDVETEYQ
+RSGNLFGLHDSPIVLGDHKVEEEPKEAVERPTEIALIDTRTDELTTVDLGSSYWFRSLGR
+AEDGSAVVLTYDGEANVIDEETGEVTAEYPVIEPWKEKDEWQEPGPILKVAGNTAYVTDA
+EAQKLVAVDLETGETVLEKDLEFAPVEMAVVTGQPESVKPDEAADAASGHDEHTDHDH*
+>NZ_CP033200.1_1759
+MSHSAPQRRSARTAALSATLAAAAIALTACGADAAPSGPTSAPAPAADGAESPSGEARAA
+SSVSEGDRVDPTRTTEVSAVTPRILLSHEGGLTLLDAESGEVVREQDVPGFTRLSNAGNG
+KDVLVTTGNGWEVFSTGIQAKAHGDHVHHYESAPGMTGVTFPGEHPGHVVTHNGRTTLFG
+DGTGAIRTFDSAHLDKATPDLMPVMTEAETEDPHHGVALELSDGTLFTTQGTEDSRNTLQ
+VIDPKTSEVTAETDDCPGSHGEAAAQPTEAGDVVVMGCENGPVVYRDGEFHKVDVETEYQ
+RSGNLFGLHDSPIVLGDHKVEEEPEEAVERPTAIALIDTRTDELTTVDLGSSYWFRSLGR
+AEDGSAVVLTYDGEVTVIDEETGEVTAEYPVIEPWKEKDEWQEPGPILKVAGNTAYVTDA
+EAQKLVAVDLETGETVLEKDLEFAPVEMAVVTGEPESVKPEEGADAESGHDEHADHDHGH
+ESDEHTDHDH*
+>NZ_CP040019.1_667
+MSHSAPQCRSTRTAASDGAESTSGETTAASSVSEEERVDPTRTTEVSAVTPRILLSHEDG
+LTLLDAESGEVVKEQDVPGFTRLSDAGNGKDVLVTTGNGWEVFSTGIQAKAHGDHVHNDE
+SAPGMTGVTFPGEDPGHVVTHNGRTTLFADGTGAIRTFDATHLDKATPDLMPVMTEAETE
+DPHHGVALELYDGTLFTTQGTEDSRDTLQVIDSTTGEVTAETDDCPGSHGEAAAQPTEAG
+DVVVTGCENGPVVYRDGEFHKVEVETEYQRSGNLFGLHDSPIVLGDHKVEEEPTEAVERP
+TAIALIDTRTDELTTVDLGSSYWFRSLGRAEDGSAVVLTYDGEVNVIDEETGEVTAEYAV
+IEPWKEKDEWQEPGPILKVAGNTAYVTDAEAQKLVVVDLETGETVLEKDLDFAPVEMAVV
+TGQPESVKPEEAADAESGHDEHTDHDH*
+>NZ_CP083691.1_582
+MTPRILLSHEDGLTLLDAESGEVVKEQDVAGFTRLSNAGNGKDVLVTTGNGWEVFSTGIQ
+AKAHGDHFHNYESAPGMTGVTFPGEHPGHVVTHNGRTTLFADGTGAIRTFDSAHLDKATP
+DLMPVMTEAETEDPHHGVALELSDGTLFTTQGTEDSRNTLQVIDPTAGEVKAETDDCPGS
+HGEAAAQPTEAGDVVVMGCENGPVVYRDGEFHKVDVETEYQRSGNLFGLHDSPIVLGDYK
+VEEEPKEAVERPTEIALIDTRTDELTTVDLGSSYWFRSLGRAEDGSAVVLTYDGEVNVID
+EETGEVTAEYPVIEPWKEKDEWQEPGPILKVAGNTAHVTDAEAQKLVAVDLETGETVLEK
+DLEFAPVEMAVVTGQRESVKPEEAADAESGHDEHTDHDH*
+>NZ_CP097650.1_1979
+MTGVTFPGEHPGHVVTHNGKTTLFADGTGAIRTFDSAHLDKATPDLMPVMTEAETEDPHH
+GVALELSDGALFTTQGTEDSRNTLQVIDPKTGEVTAETDDCPGSHGEAAAQPTEAGDVVV
+MGCENGPVVYRDGEFHKVDVETEYQRSGKLFGLHDSPIVLGDHKVEEEPKEAVERPTEIA
+LIDTRTDELTTVDLGSSYWFRSLGRAEDGSAVVLTYDGEVNVIDEETGEVTAEYPVIEPW
+KEKDEWQEPGPILKVAGNTAYVTDAEAHKLVAVDLETGETVLEKDLEFAPVEMAVVTGQP
+ESVKPEEGAHGDEDHDDDGHEGHDHGAEPSEGHEGHDH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001654.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001654.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27fab4a0eafdcc161330dd5d35363eda37b3b18c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001654.fa
@@ -0,0 +1,54 @@
+>NZ_CP042169.1_2043
+MASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRA
+GARNPSDLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRI
+ADIVGTAADTAGVAQLVYLSGLHPDTVPVAELSDHMRSRALVAERLERAATPALTFEAGV
+IIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQACALPEPVQLRAQI
+GNGHPQSFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLA
+EEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPS
+DPEWAGTTVYTDERERESDLPAQEVWPVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGL
+TRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQLSTEPREGGGSVYRQ
+RAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRL
+PLRRNPLDRRARGAGGAQSRD*
+>NZ_CP033200.1_1762
+MASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRA
+GARNPSDLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRI
+ADIVGTAADTAGVAQLVYLSGLHPDTVPVAELSDHMRSRALVAERLERAATPALTFEAGV
+IIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQACALPEPVQLRAQI
+GNGHPQSFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLA
+EEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPS
+DPEWAGTTVYTDERERESDLPAQEVWPVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGL
+TRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQLSTEPREGGGSVYRQ
+RAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRL
+PLRRNPLDRRARGAGGAQSRD*
+>NZ_CP040019.1_664
+MGGRLIPELLAAGFDVRAGARNPSDLADRPWSEGVEAVELDLTEADLVEAAMQDVHTVLY
+LVHSMGGGGDFVTQEQRIADIVGTAADTAGVAQLVYLSGLHPDTIPVAELSDHMRSRALV
+AERLEQAATPALTFEAGVIIGSGSTSFEMIRHLAERLPVMPGPSWLKNRVEPLAIRDVLY
+YLLQACALPEPVQLRAQIGNGHPQSFASVLVDYAKAAGLSRRIVIPTPFPLQTLAGFWIG
+TVTPIPVAVALPLAASLAEEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDV
+TFDADVHAAADPADPLPSDPAWSGTTVYTDERERESDLPPQDVWPVIESVGGANGWYSTP
+MLWKVRGLADKLVGGPGLIRGRRDQDRLRRGDAVDWWRVEDVEHGRRLTLRAEMKAGGRA
+WLQMSTEPRDGGGSVYRQRAIFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEAQRRTT
+GGERRRPRSLARALVDRLPLRRNPLDRGASA*
+>NZ_CP083691.1_578
+MSTPSTSRGSGLTSAAASGDTPAGTGATTASLSPLGLALPDGHDRRVLVTGATGYVGGRL
+IPELLAAGFRVRAGARTPRDLEDRPWSDRVEVVELDLEKPDLVKAAMQDVHTALYLVHSM
+GAGGDFVEQEQKIADIVATAADEAGITQLVYLSGLHPAGKPVEELSDHMRSRALVAERLE
+AAATPALTFEAGVVIGSGSASFEMIRHLSERLPIMPGPSLLKNRVEPIAVRDVLHYLVQA
+CALEEPVQLHAQIGNGRPQSFASVLVDYAEVAGLSKRIVIPTPLPLSRLAGLWVGVVTPI
+PVKVALPLAASLAEDAVVEDHAIRDVIPAPEGGLTSYKEAVRRALAAEKNGPLDVTFEAD
+VYDSSDPAAPLPSDPEWAGHTVYTDDRERESDLAPEDVWPVIESIGGRNGWYSTPLLWKV
+RGYMDKVVGGPGLMRGRRDQDHLRRGDAVDWWRVEEVDPGHRLTLRAEMKAGGRAWLQLT
+TEPREQGGSVYRQRAIFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEAERRRTGGARR
+RTRGLVRALADRLPLRRSPLDRRAG*
+>NZ_CP097650.1_1984
+MASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRA
+GARNPSDLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRI
+ADIVGTAADTAGVAQLVYLSGLHPDTVPVAELSDHMRSRALVAERLERAATPALTFEAGV
+IIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQACALPEPVQLRAQI
+GNGHPQPFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLA
+EEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPS
+DPEWAGTTVYTDERERESDLPAQEVWPVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGL
+TRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQLSTEPREGGGSVYRQ
+RAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRL
+PLRRNPLDRRARGAGGAQSRD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001656.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001656.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4aeab9456322c7b339e1a83e186a255f39c3e64d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001656.fa
@@ -0,0 +1,18 @@
+>NZ_CP042169.1_2047
+MIYLLALLGVIGCMLLVDRRFELFLWHRPLPALLVLAAGVAYFFAWDLWGIAEGVFLHRQ
+SPYMTGVMLAPQLPLEEGFFLLFLSQITMVLFTGALRLLRGRRGDARAATPADPTDGGSR
+*
+>NZ_CP033200.1_1766
+MIYLLALLGVIGCMLLVDRRFELFLWHRPLPALLVLAAGVAYFFAWDLWGIAEGVFLHRQ
+SPYMTGVMLAPQLPLEEGFFLLFLSQITMVLFTGALRLLRGRRGDARAATPADPTDGGSR
+*
+>NZ_CP040019.1_660
+MVYLLTLLAVIGCMALLDWRHRLFLWARPGAATAVLAVGMAYFLAWDVWGIAEGVFLHRD
+SPYMTGIMLAPQLPLEEGFFLLFLSQITMVLFTGAVRILEHRAGGTTAAGGTR*
+>NZ_CP083691.1_575
+MYLAALLLLCGCYLAIDARWRLALFSATPGRALAVLAAGLAFFLAWDLTGIAADVFWHGA
+DDVSVGLFLAPELPVEELVFLWFLCHQTLVYVEGLPRLTAWARARRAGRGEGATAS*
+>NZ_CP097650.1_1988
+MIYLLALLGVIGCMLLVDRRFELFLWHRPLPALLVLAAGVAYFFAWDLWGIAEGVFLHRQ
+SPYMTGVMLAPQLPLEEGFFLLFLSQITMVLFTGALRLLRGRGRDARAATPADPTDGGSR
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001657.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001657.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0cd19b9e2243e8b9b1e07a15f0d2f40c534d8f7a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001657.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_2048
+MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPAWLVVLGVVFFLVPYNLAMYGINDVFDF
+ASDLRNPRKGGVEGSVLGDPAVRRRVLAWSVLLPVPFVAVLAGWSAVRGEWAAVLVLAVS
+LFAVVAYSWAGLRFKERPFLDAATSATHFVSPAVYGLALAGATPTPALAALLGAFFLWGM
+ASQMFGAVQDVVPDREGGLASVATVLGARRTVLLAAGLYAAAGLLLLATDPPGPLAALLA
+VPYVVNTLRFRRITDATSGAAHRGWQLFLPLNYVTGFLVTLLLIGWALTRGAAA*
+>NZ_CP033200.1_1767
+MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPAWLVVLGVVFFLVPYNLAMYGINDVFDF
+ASDLRNPRKGGVEGSVLGDPAVRRRVLAWSVLLPVPFVAVLAGWSAVRGEWAAVLVLAVS
+LFAVVAYSWAGLRFKERPFLDAATSATHFVSPAVYGLALAGATPTPALAALLGAFFLWGM
+ASQMFGAVQDVVPDREGGLASVATVLGARRTVLLAAGLYAAAGLLLLATDPPGPLAALLA
+VPYVVNTLRFRRITDATSGAAHRGWQLFLPLNYVTGFLVTLLLIGWALTRGAAA*
+>NZ_CP040019.1_659
+MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPTWLVVLGTVFFLVPYNLAMYGINDVFDF
+ASDLRNPRKGGVEGSVLADPAVRRRVLRWSCLVAVPFVAVLAGWSIARGQWDALAVLAVS
+LFAVVAYSWAGLRFKERPFLDAATSATHFVSPALYGLVLAGAAFTPALWALLGGFFLWGM
+ASQMFGAVQDVLPDREGGLASVATVLGARPTVWLAAALYAGAGLLMLGTEWPGPLAALLA
+VPYVLNVLRFRAVTDATSGAAHRGWRLFLPLNYVTGFLVTLLLIGWALARGGV*
+>NZ_CP083691.1_577
+MIRTLFWASRPVSWVNTAYPFLAAVLLTGGLPWWLVALGGFFFLVPYNLAMYGINDVFDF
+ESDLRNPRKGGVEGSVLADPAVRRRVLAWSALTPAPFAAVLAGRSVLRGEWAAVAVLAVS
+LFAVVAYSWAGLRFKERPFLDAVTSSTHFVSPAVYGLVLAGAEFTPALWSLLGGFFLWGM
+ASQMFGAVQDVVPDREGGLASVATVLGARPTVLAAAALYAAAGLLMLPTDWPGPLAALLA
+APYLLSTLRFRHVTDATSGEAHRGWRTFLWLNYLTGFLVTLLLIWWALVR*
+>NZ_CP097650.1_1989
+MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPAWLVVLGVVFFLVPYNLAMYGINDVFDF
+ASDLRNPRKGGVEGSVLGDPAVRRRVLAWSVLLPVPFVAVLAGWSAVRGEWAAVLVLAVS
+LFAVVAYSWAGLRFKERPFLDAATSATHFVSPAVYGLVLAGATPTPALAALLGAFFLWGM
+ASQMFGAVQDVVPDREGGLASVATVLGARRTVLLAAGLYAAAGLLLLATDPPGPLAALLA
+VPYVVNTLRFRRITDATSGAAHRGWQLFLPLNYVTGFLVTLLLIGWALTRGAAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001660.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001660.fa
new file mode 100644
index 0000000000000000000000000000000000000000..977def887a632bced8278157ebd9cdabb4264bf5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001660.fa
@@ -0,0 +1,36 @@
+>NZ_CP042169.1_2051
+MGEARTGGEAALSGVTAELDAALRHAAAQAPGSAAFAELLDSLHVHVGAGKLIRPRLVEL
+GWRLATADPVPPSGRAAVDRLGAAFELLHTALLVHDDVIDRDVLRRGQPAVHASARHRLE
+ARGVPAADAAHAGVAVALIAGDVLLTQAFRLAATCAADTARAAEAAAVVFDAAAVTAAGE
+LEDVLLGLSRHTGEEPDPDRILAMQRLKTAHYTVGAPLRAGALLAGADPDLARAMGEAGA
+DLGAAYQVIDDVLGVFGDPGETGKSADGDLREGKATVLTAHGRRIPAVRALLDAGPATPA
+DIEAARRALEAAGAREHALDVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS*
+>NZ_CP033200.1_1770
+MGEARTGGEAALSGVTAELDAALRHAAAQAPGSAAFAELLDSLHVHVGAGKLIRPRLVEL
+GWRLATADPVPPSGRAAVDRLGAAFELLHTALLVHDDVIDRDVLRRGQPAVHASARHRLE
+ARGVPAADAAHAGVAVALIAGDVLLTQAFRLAATCAADTARAAEAAAVVFDAAAVTAAGE
+LEDVLLGLSRHTGEEPDPDRILAMQRLKTAHYTVGAPLRAGALLAGADPDLARAMGEAGA
+DLGAAYQVIDDVLGVFGDPGETGKSADGDLREGKATVLTAHGRRIPAVRALLDAGPATPA
+DIEAARRALEAAGAREHALDVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS*
+>NZ_CP040019.1_656
+MSAGREGVVAELEAALSRAAGLAPESAAFAELLAGLRTHAGAGKLIRPRLVELGWRAAAD
+GPVPAAERPAVDRLGAAFELLHTGLLVHDDVIDRDVVRRGERTVHEATRRRLAARGVPEA
+EAAHAGTAVALIGGDVLLVEALRLAMTCTPDPGRAAPVAAVVLDAATASAAGELEDVLLG
+LARHTGEEPEPERILAMQRLKTAHYTVSAPLRVGGAAGGGGSRRRRGAGEAAAPTWAWPT
+RWWTTCSGCSAPRSRPASPPTATCARARPPCSPRTAAATPPSAPCSTPAPATPEELEAAR
+RALEAAGAREHALQVAEELTRRAAEHLAVLPLGEAACAEFADACHAVLTRSS*
+>NZ_CP083691.1_572
+MNPLAAGIGGAAPWSASAATPGLDDAGRARAAVRAELDRVFAETPLCADAPDSFHLLWAR
+LREAVSGGKLVRPRLVDLGWRTVRRAPASSGVPRGGTGEEEAADLRAVARVGAAFELLHA
+ALIVHDDVIDRDDLRRGRPTVAEQYRRDAVRDGVPAGEAEHVGRSAGIIAGDLLLTAAFR
+LAAASGARVRAAEAAESVFRAASAAAAGELEDVLLALHRHTGHHPEAGRILTMERLKTAG
+YSFEEPLRAGALLAGADPAHAEALAEAGALLGVAYQVVDDVLGTAGDPAVTGKPHDADLR
+EGKATLLTAHGRRDPRARAALDRVARAERHGEDLGELAAAVAEARAALVDAGSVEHALGV
+AEELVDQARALLDALPMAPAERAEFAATCGQILQREA*
+>NZ_CP097650.1_1992
+MGEARTGGEAALSGVTAELDAALRHAAAQAPGSAAFAELLDSLHVHVGAGKLIRPRLVEL
+GWRLATADPVPPSGRAAVDRLGAAFELLHTALLVHDDVIDRDVLRRGQPAVHASARHRLE
+ARGVPAADAAHAGVAVALIAGDVLLTQAFRLAATCAADTVRAAEAAAVVFDAAAVTAAGE
+LEDVLLGLSRHTGEEPDPDRILAMQRLKTAHYTVGAPLRAGALLAGADPDLARAMGEAGA
+DLGAAYQVIDDVLGVFGDPGETGKSADGDLREGKATVLTAHGRRIPAVRALLDAGPATPA
+DIEAARRALEAAGAREHALDVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001664.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001664.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f742e4eac02164fa11b695f7234a20078aa2615
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001664.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_2058
+MGTQDPRARLLEKLAKVNVCMLTTAEPDGTLVTRPMGLQQAEDGGTLWFLTRATSDVAAD
+APQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNPATEAFFGEGSSPEDPQIVLVRV
+DVQTAQFWESPGAVATAVELVKAKVTGGEAHPGDSETVRF*
+>NZ_CP033200.1_1778
+MGTQDPRTHLLEKLAKVHVCMLTTAEADGTLVTRPMGLQQAEDGGTLWFMTRSTSDVAAD
+APQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNSATEAFFGEGSSPEDPQIVLVRV
+DVNTAQFWESPGAVATAVEMVKAKVTGGTAEPGDSETVRF*
+>NZ_CP040019.1_650
+MGHKDPRTHLLEKLEKSNVCMLTTSETDGTLTTRPMGLQKAEETGTLWFMTRAASDVASD
+ASQRPVNVSVQDKDFWASVAGHGQVVRDDARKKEFWNPATEAFFGEGAKPEDPQIVLVRV
+DVESAQYWESPGAVGTVVELIKAKVTGGEAHPGESTTVQF*
+>NZ_CP083691.1_566
+MTEQDPRTALLEKIEKAGVVMLTTAEEDGTLASRPMAVQEVEQEPGVLWFITRATGDAAQ
+DSAGRPVNVAVQEKGFWASVAGHGEIVRDEARKTEYWNSATEAFFGEGARPEDPQIVLVR
+VQADSAEYWDGGGAASVVEIVKAKVTGGEARPGDHDTVEF*
+>NZ_CP097650.1_1997
+MGTQDPRARLLEKLAKVNVCMLTTAEQDGTLVTRPMGLQQAEDGGTLWFLTRATSDVAAD
+APQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNPATEAFFGEGSSPEDPQIVLVRV
+DVDTAQFWESPGAVATAVELVKAKVTGGTAEPGDSETVRF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001668.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001668.fa
new file mode 100644
index 0000000000000000000000000000000000000000..74bda4999a94b8c6aeb49e95a1852d3fd9b0c05b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001668.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_2063
+MAPIPPDPHADHAPAVDDMPLDTTAAPDIPAAVDPVPHGMAAHVLEREVGPLRARFPGVA
+DEATVRQLLFDSYAELAETSRHPEMLPTISVQHAASRLRARAINQGSIESRHPRVLFVCH
+GNAGRSQMAAALLENRTHGEVRARSAGTEPAGEVISTAFEAMNEIGIPLHHTYTKGLDPD
+VLRAAEIVVLFDGADPFEIPEGAQVQKWSVPSIRGMSLEQVRGVRDALDLEVRGLIADLG
+EAATPLPEEGTRVGRPLDLYPPGV*
+>NZ_CP033200.1_1783
+MTPIPPDPHADHAPAVDDMPLDTTAAPDIPAAVDPVPHGMAAHVLEREVGPLMARFPGVA
+DEATVRQLLFDSYAELAETSRHPEMLPTISVQHAASRLRARAINQGSIESRHPRVLFVCH
+GNAGRSQMAAALLENRTHGEVRARSAGTEPAGEVISTAFEAMNEIGIPLHHTYTKGLDPD
+VLRAAEIVVLFDGADPFEIPEGAQVQKWSVPSIRGMSLEQVRGVRDALDLEVRGLIADLG
+EAATPLPEEGTRVGRPLDPYPPGV*
+>NZ_CP040019.1_645
+MAAIPPDPHADRTPAVDDLPLDAASPDGRAAAPVGLEPEGMAANVLEREIEHLMERFPCV
+GDEETVRAVVMDSYAQLAATSRHPDMLPNTTVQHASARLRAMAINQGSIESRHPRVLFVC
+HGNAGRSQMAAALLENRTGGAVKSRSAGTSPAGEVISTAFDAMSEIGIPLHHSYTKGVDE
+DVLKAAEVVVLFDGAEPLDIPEGTEVQEWSVPSIRGMSLEQVRGVRDALDLQVRGLIADL
+GEEGSDAPPPGEGAPVA*
+>NZ_CP083691.1_562
+MAPHPSDPAADLPAADVPLDPTGALPVVAPAPEGMASHVLDREAEHLHARYPEVGDVAMA
+RALLEDSYARLARTTRHPEMLPVTAANYAAARLRARAIAQGSVESRHPRVLFVCHGNAGR
+SQMAAALLENRSGGTVASRSAGTSPAGSVLPMALDVMNEIGLPLHHAFPKGVDRDILQAA
+QLVVLFDGAEEDLLDVPAGVEVQHWSVPSIRGLALEQVRGVRDALDLQVRGLIAELTALE
+GEEQGGAADPAA*
+>NZ_CP097650.1_2002
+MTPIPPDPHADHAPAVDDMPLDTTAAPDTPAAVDPVPHGMAAHVLEREVGPLMARFPGVA
+DEATVRQLLFDSYAELAATSRHPEMLPTTAVQHAASRLRARAINQGSIESRHPRVLFVCH
+GNAGRSQMAAALLENRTHGEVRARSAGTEPAGEVISTAFEAMNEIGIPLHHTYTKGLDPD
+VLRAAEIVVLFDGADPFEIPEGAQVQNWSVPSIRGMSLEQVRGVRDALDLQVRGLIADLG
+EAAADAPLPDADTRAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001670.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001670.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d6bcfa537a46e43d62d9ec26636bb36f7a50126
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001670.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_2065
+MTTTDLKITGMTCGHCVASVQEELGEIAGVSAVDVDLNSGGVSTATVTSEAPLDPAAARA
+AVEEAGYTLVEA*
+>NZ_CP033200.1_1785
+MTTTDLKITGMTCGHCAASVREELGEIAGVSAVDVDLNAGGVSTATVTSEGPLDPAAARA
+AVEEAGYTLVEA*
+>NZ_CP040019.1_643
+MTTTDLKITGMTCGHCVASVQEELGEIAGVTAVDVDLTAGGVSTATVTSESPLDPAAARA
+AVEEAGYRLVEG*
+>NZ_CP083691.1_560
+MTTTDLKITGMTCGHCVASVREELGEIAGVSAVDVDLNAGGVSTATVTSEGPLGPAAARA
+AVEEAGYTLVEG*
+>NZ_CP097650.1_2004
+MTTTDLKITGMTCGHCAASVREELGEIAGVSAVDVDLNAGGVSTATVTSEGPLDPAAARA
+AVEEAGYTLVEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001677.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001677.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4460bb2a5b2dc3250bb90ed42ea4b9f8b712029d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001677.fa
@@ -0,0 +1,48 @@
+>NZ_CP042169.1_2074
+MSSTLATGAYRRAVDRAHESLDSVRLSLAPSSSTAPTGADQGLRAALQGLRREVRESWLR
+SLGALTPAGSALDAGASAAAPAVPGQTDPATLADDDLAAARREQRLAVALPVVRRMLIQP
+AAEAGMLAAIGNARGHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAP
+TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLLSTVDAVH
+AAWRDLPAPSRGRPRGTVPTPGPSAPPSASPGPSPAGAPHRHDEAAGLLRVTGHLPPTLD
+GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETAGPRSAPGDAPARAISLRAEVHRL
+RRALRDVGAPVELLSRPYRLVGEVHADLLCAREALRAGDLDRALHAAVGPVLPRSASPGV
+ASIRAELGEALREAVAQDADVDQLWAYLGRPEARDDVELWGAALRLLPTDSPRRALAVAT
+LERIERDLA*
+>NZ_CP033200.1_1794
+MSSTLATGAYRRAVDRAHESLAAVRLSLAPSSPTAPAGADQGLRAALQGLRREVRESWLR
+SLGALTPAVPGQTDPATLSDDDLAAARRDQRLAVALPVVRRMLIHPAAEAGMLAAIGNAR
+GHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAPTQVSRGEHLSPRVH
+PWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQATVDAVHAAWRDLPAPSRGRP
+RGTAPTPGPSAPPSASPGPSPAAAPHRHDAAAGLLRVTGHLPPTLDGVELTGRHAEILTL
+LAWHGPGLTGAELEVALYPEETAGPRPAPGDSPARAISLRAEVHRLRRALRDVGAPVALL
+SRPYRLVGEVHADLLCAREALRAGDLDRALHAAAGPVLPRSTSPGVASIRAELGEALREA
+VAQDADVDQLWAYLGRPEARDDVELWGAALRLLPTDSPRRALAVATLERIERDLA*
+>NZ_CP040019.1_634
+MSSTLATGAYRRAVDRAHESLDSVRLSLAPSSPTAPTGADQGLRTALQGLRREVRESWLR
+SLGALTPAGSALDAEAAATAPAVPGQTDPATLADDDLAAARREQRLAVALPVVRRMLIHP
+AAEAGMLAAIGNARGHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAP
+TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQATVDAVH
+AAWRDLPAPSRGRPRGTVPTPGPSAPPSASPGPSPAAAPHRHDAAAGLLRVTGHLPPTLD
+GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETAGPRSAPSDAPARAISLRAEVHRL
+RRALQDAGAPVELLSRPYRLVGEVHADLLCAREALRAGDLDRALHAAAGPVLPRSVSPGV
+ASIRAELGEALREAVAQDADVEQLWAYLGRPEARDDVELWGVALRLLPADSPRRALAVAT
+LERIERDLA*
+>NZ_CP083691.1_550
+MSSTLATGAYRRAVDRAHESLAAVRLSLAPSSPTAPTGADQGLRAALQGLRREVRESWLR
+SLGVLTPAGSALDAGASATAPAVPGQTDPATLSDDDLAAARREQRLAVALPVVRRMLIQP
+AAEAGMLAAIGNARGHLLWVEGDRTAVRHAEALGFVAGADWSEASMGTSAPGIVLATGAP
+TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQTTVDAVH
+AAWRDLPAPSRGRSRGTVPTPGPSAPPSVSPGPSPAAAPHRHDAAAGLLRVTGHLPPTLD
+GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETVGPRSAPGDAPARAISLRAEVHRL
+RRALRDVGARVELLSRPYRLVGAVHADLLCAREALRAGDLDRALHAAAGPVLPRSASPGV
+ASIRAELGEALREAVAQDADVEQLWAYLGRPEARDDVELWGAALRLLPADSPRRALAVAT
+LERIERDLT*
+>NZ_CP097650.1_2013
+MSSTLATSAYRRAVDRAHESLAAVRLSLAPSSPTAPAGADQGLRAALQGLRREVRESWLR
+SLGALTPAVPGQTDPATLSDDDLAAARRDQRLAVALPVVRRMLIHPAAEAGMLAAIGNAR
+GHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAPTQVSRGEHLSPRVH
+PWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQATVDAVHAAWRDLPAPSRGRP
+RGTAPTPGPSAPPSASPGPSPAAAPHRHDAAAGLLRVTGHLPPTLDGVELTGRHAEILTL
+LAWHGPGLTGAELEVALYPEETAGPRPAPGDSPARAISLRAEVHRLRRALRDVGAPVALL
+SRPYRLVGEVHADLLCAREALRAGDLDRALHAAAGPVLPRSASPGVASIRAELGEALREA
+VAQDADVEQLWAYLGRPEARDDVELWGAALRLLPADSPRRALAVATLERIERDLA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001678.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001678.fa
new file mode 100644
index 0000000000000000000000000000000000000000..41af5bd4199d4e1e03824794906d91c0c2a03b77
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001678.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_2075
+MTVPSSSAEHAPALEARPEMPGETVSRVAMTPAALELIRRLLPIHGPLMFHQSGGCCDGS
+APMCYPAGDFTTGAADVLLGTFALPAEGDQAAVEIPFWMSAAQFEYWKHTHLTLDVVDGR
+GSGFSVEAPEGKRFLIRSRLMAGSG*
+>NZ_CP033200.1_1795
+MTVPSSSAEHAPALEARPEMPGETLSRVAMTSAALELIRRLLPIHGPLMFHQSGGCCDGS
+APMCYPAGDFTTGAADVLLGTFALPAEGDQAAVEIPFWMSAAQFEYWKHTHLTLDVVDGR
+GSGFSVEAPEGKRFLIRSRLMAGSG*
+>NZ_CP040019.1_633
+MTVPSSSAEHAPALEARPELPGETVSRVAMTPAALELIRRLLPIHGPLMFHQSGGCCDGS
+APMCYPAGDFTTGAADVLLGTFALPAEGDQDAVEIPFWMSAAQFEYWKHTHLTLDVVDGR
+GSGFSVEAPEGKRFLIRSRLMAGSG*
+>NZ_CP083691.1_549
+MTVSSSSAEHAPALEARPELPGETVSRVAMTPAALALIRRLLPIHGPLMFHQSGGCCDGS
+APMCYPAGDFTTGAADVRLGTFVVPAEGDQAAVEIPFWMSAAQFEYWKHTHLTLDVVDGR
+GSGFSVEAPEGKRFLIRSRLMAGSG*
+>NZ_CP097650.1_2014
+MTVPSSSAEHALDARPELPGETVSRVAMTPAALELIRRLLPIHGPLMFHQSGGCCDGSAP
+MCYPAGDFTTGAADVLLGTFALPAEGDQAAVEIPFWMSAAQFEYWKHTHLTLDVVDGRGS
+GFSVEAPEGKRFLIRSRLMAGSG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001679.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001679.fa
new file mode 100644
index 0000000000000000000000000000000000000000..115e5fa9350a9700ea83edfc931827423ebaf4ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001679.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_2076
+MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAVRRAFAAEA
+RGDVEPGRAPASFYVGVDENGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAAR
+LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVEADLDGAPFPVPQLRFD
+VPTTAA*
+>NZ_CP033200.1_1796
+MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAIRRAFAAEA
+RGDVEPGRVPASFYVGVDEAGHLVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAAR
+LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVEADLDGAPFPVPQLRFD
+VPTTAA*
+>NZ_CP040019.1_632
+MLPDPSPTVTVDGLLLRPLRTADEIAAREADAELHREGFDFLMAGTRSFPAIRRAFAADA
+RGDVEPGRVPASFYVGVDEAGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAVR
+LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVETGLDGAPFPEPKLRFD
+VPTTAA*
+>NZ_CP083691.1_548
+MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAIRRAFAAEA
+RGDVEPGRVPASFYVGVDENGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAVR
+LLRGALTLLAAHGVSTALLTCDETNTASVATIRACGGVLRDRVEAGLDGAPFPVPKLRFD
+VPTTAA*
+>NZ_CP097650.1_2015
+MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAVRRAFAAEA
+RGDVEPGRAPASFYVGVDENGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAAR
+LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVEADLDGAPFPVPQLRFD
+VPTTAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001690.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001690.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb2e7adf0ead7cb9e82b6437c7800ffcf06e580a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001690.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_2089
+MTRPLRWATLAGVLLIVAVLAFWAGRATLTPPAQAEQRPSEDALVTVAEQELGRVITLGV
+SVTREQAPAAVNALSGVVTRAGESGEVAAGDVLYAVAQQPVITVQGELPQWRALGEGATG
+SDVAAFQRMLAATGAKVEVTGTWDEATAVAWNGWLTERDYPAADTVELGQLVVLESLPAA
+LSVDAKATAVGGALAGGETIVARPGDEPTFAIEVNQDQAAIIPAGTAVTVPHGEHEWEAV
+AGESTADDQGLIRIPLTAPDGGAVCGADCDSLPAEASTSLLSKVNVVPPVTGPVVPVSAL
+RTQPDGAARVTVVRDGVQEERTVIVRGSADGLAVVDGVDAGETVRVLNGAP*
+>NZ_CP033200.1_1808
+MNRPARWAALVLALVAVAALAFWAGRVTLTPPAQAEQRPAASALVTVAEQELGRVITLGV
+SVSREQTPAAVNALTGVVTRAGESGEVAAGEVLYAVAQKPVLVLQGELPQWRPLGEGTSG
+DDVAAFQRMLAATGAKVEATGTWDEATADAWDDWLTERGYPAADTVELGQLVVLDALPAP
+LSVDAKTTAVGTTLAGGENVVARPGDQPDFALEVNQEQAALIPAGTQVTVPHGEHEWKAV
+AGESTSDEQGLIRITLTAPDGGVVCGEDCDTLPADATTSLLSQVSVVPPVSGPVVPVSAL
+RTQPDGAATVTVVRDGAAEDRAVTVLGSADGLAVVDGVDAGEQVRVLNGTR*
+>NZ_CP040019.1_611
+MSKVTRWAALVLTLVLVAALAFWAGRATLTPPAQADQRPSEDAVVTVAEQELGRVITLGV
+SVAREQAPAAVNALSGVVTRAGESGEVAAGDVLYAVAQQPVIAVQGELPQWRALDEGATG
+SDVAAFQRMLAATGAKVEVTGTWDEATAVAWNGWLTERDYPAAGTVELGQLVVLESLPAA
+LSVDAKATAVGGALAGGETIVARPGDEPTFAIEVNQDQAAMIPAGTAVTVPHGEHEWEAV
+AGESTADDQGLIRIPLTAPDGGAVCGADCDSLPAEASTSLLSKVNVVPPVTGPVVPVSAL
+RTQPGGAVVVTVVQDGVEEERTVTVRGSADGLAVVDGVDAGETVRVLNGAP*
+>NZ_CP083691.1_535
+MTRPARWAALVLAVVLVAALAFWAGRVTLTPPAQAEQRPSEDAVVTVAEQELGRVITLGV
+SVTREQAPAAVNALSGVVTRAGQSGEVAAGDVLYAVAQKPVIAVQGELPQWRALGEGATG
+SDVTAFQRMLTATGTKVKATGTWDEATATAWNAWLTTRGYPAADTVELGQLVVLESLPTA
+LSVDAKATAVGGTLAGGETIVARPGDEPTFAIEVNQDQAAMIPAGTAVTVPHGEHEWKAV
+AGESISDEQGLIRITLTAPDGGVVCGEDCDTLPADPTTSLLSQVSVVPPVSGPVVPVSAL
+RTQPDGAATVTVVRDGAAEDRTVTVLGSADGLAVVDGVDAGEQVRVLNGTR*
+>NZ_CP097650.1_2027
+MNRPARWAALVLALVAVAALAFWAGRVTLTPPAQAEQRPAASALVTVAEQELGRVITLGV
+SVSREQTPAAVNALTGVVTRAGESGEVAAGEVLYAVAQKPVLVLQGELPQWRPLGEGTSG
+DDVAAFQRMLAATGAKVEATGTWDEATADAWDDWLTERGYPAADTVELGQLVVLDALPAP
+LSVDAKTTAVGTTLAGGEKVVARPGDQPDFALEVNQEQAALIPAGTQVTVPHGEHEWKAV
+AGESTSDEQGLIRITLTAPDGGVVCGEDCDTLPADATTSLLSQVSVVPPVSGPVVPVSAL
+RTQPDGAATVTVVRDGAAEDRTVTVLGSADGLAVVDGVDAGEQVRVLNGTR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001691.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001691.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37d33e0dd737ac6939430a36c736374c58f21e4c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001691.fa
@@ -0,0 +1,29 @@
+>NZ_CP042169.1_2090
+MVGLVGALLLAGCASGADAGASAHAETGSTPSKVWDAATWKPTEVIEPVLATEPEKEAAY
+REQMDRLAESGGTPEILQVQRKDWSTTPLESDQKVASCMRADGFPVEVSPTGGLRYSTPP
+AAQARAWALAMNTCIAQHPVDPSYTQDWSEPQLRLVYDYWDQYLIPCLEAQGFTVDTSTR
+PSKESFVTAFFTPGRHDWWPLQATMRGVPEERQTQVVQTCPELPPQDVFWGTSG*
+>NZ_CP033200.1_1809
+MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI
+EPLLTTEAEKERAYREQVARHAQGAGMPAPPQVERSGWYATSLESDRMVSTCLAEAGWPN
+SVGPTGGIQIDTPPESQRSAFEAAYVTCYAQHPVDPSYTQDWTDPQLRLVYDYWDQYLIP
+CLEAYGYTVDTSARPSKEAFVSAFYTPGRHQWWPFADSMRGVSAERQAEVAQTCPELPPQ
+DVFWGSSG*
+>NZ_CP040019.1_610
+MKTKFAAVTAAAVTAVLTLSGCATTAPSTSAAATGSPTEKVWDPETWTPTEKIERRMTEA
+DERERWYESQLARNAAFLGIRNPPAVTRRGWATSRQEQARWSAQCMTERGVPATYNEVMV
+GVTYDTPPPSQEAAVKLVSWTCDALFPIDPSLDQEFSDAQLRLLYDYWDQYAIPCLEDHG
+ITVDTSQRPSKETWLAAFNTPERISWWPVQDSIMGLTDARSAEVSEACPVQPPDSMLFGY
+SE*
+>NZ_CP083691.1_534
+MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI
+EPLLTTEAEKEAAQREQVERMAREAGTPELLQVRRMDWSSTTLESSQKIGECMAAAGFPV
+EVTPTGGLRYPTPPESQKRAWNLAENTCAVKHPVDPAYAHDWTEPQLRLVYDYWDQYLIP
+CLEAQGLHVDTSSRPSKESFVTSFFTQDRHDWWPFSTTMVGVSEERKAHIAQTCPELPPP
+DVFWGTAP*
+>NZ_CP097650.1_2028
+MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI
+EPLLTTEAEKERAYREQVARHAQGAGMPAPPQVERSGWYATSLESDRMVSTCLAEAGWPN
+SVGPTGGIQIDTPPESQRSAFEAAYVTCYAQHPVDPSYTQDWTDPQLRLVYDYWDQYLIP
+CLEAYGYTVDTSARPSKEAFVSAFYTPGRHQWWPFADSMRGVSAERQAEVAQTCPELPPQ
+DVFWGSSG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001694.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001694.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7beb20ae77f079e610175e17b7ecbea62070c425
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001694.fa
@@ -0,0 +1,43 @@
+>NZ_CP042169.1_2093
+MRRPSLPSLSRLPVRRLLRGAAVAAGVGLVGLPLTVAAGLTGVDMVKRGGRVRRPAPNPG
+VFDAHVEGSELRIFTSGEDLYKEMIAAIDGAQRIIKFETFIWKGDPTGQRFMDAFNRAAA
+RGVEVYVSYDGFGNLVVPPRFYRQLDPRIHVFRLPAFARPIWRGVVRHSGFNHSKIMVVD
+DEVGFAGGFNIGDDYARLWRDTHVRERGPAVWALGQSISIKWNAHHRAGEQMSWRPPDTW
+DPRVTVAANQPPLLVYPIRLSYLDAIQRAQHRILINTPYFIPDQQVLEALLHAARRGVDV
+QVMVPEDSNHIVADWASRGFFGKMLEAGITILLYRASMIHAKTATVDGIWSTVGSANVDR
+LSLGFNYESNVVVVDRDFAARMEEIFALDAQRAVRIDTPRWEDRHGLARVVEALLVPLRP
+LL*
+>NZ_CP033200.1_1818
+MAAGVGLVGLPLTVAAGLTGVDMVKRGGRVRRPAPNPGVFDAHVEGSELRIFTSGEDLYK
+EMIAAIDGAQRIIKFETFIWKGDPTGQRFMDAFNRAAARGVEVYVSYDGFGNLVVPPRFY
+RQLDPRIHVFRLPAFARPIWRGVVRHSGFNHSKIMVVDDEVGFAGGFNIGDDYARLWRDT
+HVRERGPAVWALGQSISIKWNAHHRAGEQMSWRPPDTWDPRVTVAANQPPLLVYPIRLSY
+LDAIQRAQHRILINTPYFIPDQQVLEALLHAARRGVDVQVMVPEDSNHIVADWASRGFFG
+KMLEAGITILLYRASMIHAKTATVDGIWSTVGSANVDRLSLGFNYESNVVVVDRDFAARM
+EEIFALDAQRAVRIDTPRWEDRHGLARVVEALLVPLRPLL*
+>NZ_CP040019.1_597
+MSPLPASPLHRIPVRRIVRGAALAAGTGLVGVPMAVAAGLTGVDMVKRRGRRRRPAHNPG
+VFDAPVKDCHLRIFTSGEDLYEEMLAAIDSAERIVKFETYIWKADPTGQRFIEAFNRAAA
+RGVEVYVSYDGFGNLVVPRAFYRQLDPRIRVFRLPAFARPFWRGPVRNTGFNHSKIMVVD
+DEIGFVGGFNIGDDYATFWRDTHVCERGPAVWALDQSISIKWNAHHREGEQMSWRPPESW
+DPRVTVSANQPPLLVYPIRLTYLEAIQRAQHRILINTPYFIPDQQVLQALLHAARRGVDV
+QVMVPRDSNHIVADWASRGFYAGMLEAGITILLYEASMIHAKTATVDGIWSTVGTANIDR
+LSLGFNYESNVVVVDRDFAARMEEIFAIDAEQSERVESPRWQDRHGVARMVERLLVPLRP
+LL*
+>NZ_CP083691.1_521
+MGYALRRAAVAGTTAFVGVPLATAVAVSAYDAFKHRGRKLRPAERPGTFQAQVGPDALTI
+YTAGDDVYDAMIQAIDDARETVKFETFIWKDDATGQRFVDALNRAAARGVQVWASYDGFG
+NLLIPPSFYRQFDPRVRVFRLPAFARPLWRGVVRYSGFNHSKILTVDGRVGFVGGYNVGD
+LYAAHWRDTHLRVEGPAVWGLEHSLSVLWNEGYTDMAEMPWTRPEEWEERTVVAANLPTQ
+LVYPIRNTYLNAIARAQDHIYISTPYFVPDRQVLDALKEAARRGVDVQVLVPKDSNHVVA
+DWVSRGFYSEMLDAGITILLYAAGMIHAKTATIDGRWATVGTANIDRLSLSFNYETNVSV
+VDRDFAARMEDVFRADAARSERIQSPRWKDRHGLARVVEKLLVPLRPLM*
+>NZ_CP097650.1_2037
+MHRPPLPSLSRLPVRRLLRGAAVAAGVGLVGLPLTVAAGLTGVDMVKRRGRVRRPAPNPG
+VFDAHVKGSELRIFTSGEDLYEEMIAAIDGAQRIIKFETFIWKGDPTGQRFMDAFNRAAA
+RGVEVYVSYDGFGNLVVPPRFYRQLDPRIHVFRLPAFARPIWRGVVRHSGFNHSKIMVVD
+DEVGFAGGFNIGDDYARLWRDTHVRERGPAVWALGQSISIKWNAHHRAGEQMSWRPPDTW
+DPRVTVAANQPPLLVYPIRLSYLDAIQRAQHRILINTPYFIPDQQVLEALLHAARRGVDV
+QVMVPEDSNHIVADWASRGFFGKMLEAGITILLYRASMIHAKTATVDGIWSTVGSANVDR
+LSLGFNYESNVVVVDRDFAARMEEIFALDAQRAVRIDTPRWEDRHGLARVVEALLVPLRP
+LL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001698.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001698.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cbac59fc66b94292632f7c0713b88c7482879cb0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001698.fa
@@ -0,0 +1,100 @@
+>NZ_CP042169.1_2098
+MSQTLTPAAPQDLNARRHRLRRYRAVIFDMDGVITDTAGVHAQAWKELFDGALPAVGALP
+ANAAVVAADPDVLRPFDAAADYLHHVDGRPREDGVRTFFASRGLRVPEADAPEADAAPEL
+TVLALAERKQGYFEQVLERDGVRVFPEAQDLLERLRAKGVPVALVTSSKNSRAVLTAGGV
+LDFFPVIVDGNTAVERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAAADGRFG
+LVIGVDREPELGKGRLKAAGAHLVVQDYGTLHLEDRTTTPFDPAWVLRWDHFDPASEGTR
+EVLSTLANGYWGTRGAVPGTRISSVHYPGTYMAGVFNRLTSMVQGRVVETEHMVNIQDWT
+PLVVTPRHGRPLLPGEENLVEYGQEMDLRRGVLSRTMTFEDEQGRRTTVHTRQFTSLANR
+HLAAIELTVVAENWSGDLTVRSKIEGRVANLNVSDDRTLANQHLEPVQAREIDGETVLLE
+TATNQSGIHVAVATRTRQVAPVGHHEPIRRPVDGSDLVVGQDILLHVDEGVPLVLEKVAA
+VATSHDHASASVWESAVKDAQRAQNFRNLLTLHEQRWGTNWDRFSVRIDLAEPYRHHRRS
+TAAETGGEYAPPVVAAGHSAPVGSAVPMGKDGASLRQQLALNLHTFHVLQTAYGRRRDLD
+ASVGARGLHGEGYRGHIFWDEIYVYPMLTLRRPEITRGLLMYRYRRLNEARANAQAAGWA
+GAMYPWQSGADGSEETPTELWNPRSRMWMPDNSHNQRHVSLDIAYSVLRYIEITKDTSFI
+SDYGAEMLVEISRFFMSMTLHNAVTDRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVL
+TSWVLAETARLVRWLDTIDDGLPELMEISEEEIERWEEVSTRLTVPFFEEGEEAGILAQF
+EGYQDLLEFDWEAYRAKYGNIGRMDLILQAEGDATNRYKLSKQADTLMLGYLFSSEELDR
+ILRRMGYELPQEAFERMVTYYEARSTHGSTLSRLVHAWVAARTDPDRSWDLFTEALESDL
+SDTQGGTTKEGIHLGLMAGTVDTVIRCYAGLETRDDVVRLHPRMPAQLPGARFTIRFRQQ
+PVVIHMTQREVTVAAGEGMWHDVPMIIAGREHTLSPGEKLTVPLD*
+>NZ_CP033200.1_1823
+MSQTLTPAAPQDLNARRHRLRRYRAVIFDMDGVITDTAGVHAQAWKELFDGALPAVGALP
+ANAAVVAADPDVLRPFDAAADYLHHVDGRPREDGVRTFFASRGLRVPEADAPEADAAPEL
+TVLALAERKQGYFEQVLERDGVRVFPEAQDLLERLRAKGVPVALVTSSKNSRAVLTAGGV
+LDFFPVIVDGNTAVERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAASDGRFG
+LVIGVDREPELGKGRLKAAGAHLVVQDYGTLHLEDRTTTPFDPAWVLRWDRFDPASEGTR
+EVLCTLANGYWGTRGAVPGTHISSVHYPGTYMAGVFNRLTSMVQGRVVETEHMVNIQDWT
+PLVVTPRHGRPLLPGEENLVEYGQEMDLRRGVLSRTMTFEDEQGRRTTVHTRQFTSLANR
+HLAAIELTVVAENWSGDLTVRSKIEGRVANLNVSDDRTLANQHLEPVQAREIDGETVLLE
+TATNQSGIHVAVATRTRQVAPVGHHEPIRRPVDGSDLVVGQDILLHVDEGVPLVLEKIAA
+VATSHDHANASVWESAVKDVQRAQNFRNLLTLHEQRWGTNWDRFSVRIDLAEPYRHQRRS
+TAAEAGGEYAPPVVDAGHSAPVGSAVPMGKDGASLRQQLALNLHTFHVLQTAYGRRRDLD
+ASVGARGLHGEGYRGHIFWDEIYVYPMLTLRRPEITRGLLMYRYRRLNEARANAQAEGWA
+GAMYPWQSGADGSEETPTELWNPRSRMWMPDNSHNQRHVSLDIAYSVLRYIEITKDTSFI
+SDYGAEMLVEISRFFMSMTLHNAVTDRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVL
+TSWVLAETARLVRWLDTIDDGLPELMEISEEEIERWEEVSTRLTVPFFEEGEEAGILAQF
+EGYQDLLEFDWEAYRAKYGNIGRMDLILQAEGDATNRYKLSKQADTLMLGYLFSAEELDR
+ILRRMGYELPEEAFERMVTYYEARSTHGSTLSRLVHAWVSARTDPDRSWDLFTEALESDL
+SDTQGGTTKEGIHLGLMAGTVDTVIRCYAGLETRDDVVRLHPRMPAQLPGARFTIRFRQQ
+PVVIQMTQREVTVAAGEGMWHDVPMIIAGREHTLSPGEKLTVPLG*
+>NZ_CP040019.1_593
+MDGVVTDTAGVHAQAWKELFDEALPAVGALPANAAAVAADPEALRPFDAAADYLHHVDGR
+PREDGVRTFFHSRGLRVPEADSPEAATTPQLTVLALAERKQGYFEQVLARDGVRVFPEAQ
+DLLEKLRAKGVPVALVTSSKNSRAVLGAGGVLDFFPVIVDGHTAIERGLPGKPDPAMFWE
+AARELGVDVADAMVLEDAVSGVKAAADGRFGLVIGVDREPDLGKGRLKGAGAHLVVQDYG
+TLCLEQRTTTPFDPAWVLRWDEFDPASEGTREVLCTLANGYWGTRGAVPGTRISDVHYPG
+TYMAGVFNRLTSMVQGRAVDTEHMVNIQDWTPLVVTPRGGRPLLPGEETLVDFSQEMDLR
+RGVLSRTMAFEDEQGRRTSLHTRQFTSLANRHLAAIELTVVAENWTGELTVRSTIEGRVA
+NLNVSDDRTLANQHLEPSQAREIDGETVLLETTTSQSRIDIAVATRTRQMAPVGHHEPIR
+RPVDGSDLRVGQDIRLHVEEGVPLVIEKIAAVATSHDHAQASVWESAVKDVQRANNFRNL
+LTLHEQRWGTNWDRFSVRIDIAEPYRHQRRSAAAAEGAEYAPPVVDAGRSASVGSAVPMG
+KDGASLRQQLALNLHTFHVLQTAYGRRRDLDASVGARGLHGEGYRGHIFWDEIYVYPMLT
+LRRPEITRGILMYRYRRLNEARANAQAEGWAGAMYPWQSGADGSEETPTELWNPRSRMWM
+PDNSHNQRHVSLDIAYSVLRYIEITKDTSFISDYGAEMLVEVSRFFMSMALHNADTDRYE
+IHGVMGPDEFHDGYPETPGSGLRNNAYTNVLTSWVLSETARLVRWLDTLDDGLPEIMEIT
+EEEIERWEDVSARLTVPFFEDGEEAGILAQFEGYQDLKEFDWEAYRAKYGNIGRMDLILQ
+AEGDATNRYKLSKQADTLMLGYLFSAEELDGILRRMGYELPQEAFERMVTYYEARSTHGS
+TLSRLVHAWVAARTDPDRSWDLFTEALESDLSDTQGGTTREGIHLGLMAGTVDTVIRCYA
+GLETREDVVRVDPRMPSQLPGASFTIRFRQQPVQIHMRRSEVTVRAGSGMWHDVPMIIAG
+QEHTLSPGAEITVPLG*
+>NZ_CP083691.1_517
+MTQTLTPVDQQDRNARRHRLRRYRAVIFDMDGVITDTAGVHAAAWKELFDQALPAVGALD
+ANRAAVAADPGVLRPFDPEADYLHHVDGRPREDGVRAFFASRGLTVPEVDDADAPVDLTV
+LALAERKQGFFEKVLERDGVRVFPEATDLLEKLRDKGVPVALVTSSKNSRAVLTAGGVLD
+YFPVIVDGHTAIERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAAADGRFGLV
+IGVDREHGEGGKPRLKDAGAHIVVKDYGTLRLADRTTAPFDAAWVLRWDHFDPATEGTRE
+VLCTLANGYWGTRGSIPGTRISDVHYPGTYLAGVFNRLTSMVQGRQVETEHMVNMQDWTP
+LQVIPAGGRPLIPGEETLLDYHQEMDLRRGVLSRSMRFEDAQGRITTLHTRQFQSLADRH
+LGAIELTVEAENWSGDLVVRTLVDGRVANLNVSDDRTLANQHLEPVAAREVDGETLLLET
+VTSQSRVHVAVAARTRQMAPKGHHQPIRRPVEGSDLMVGQDIHLHVEQDVPLVLEKVAAV
+ANTHDHALASVDASAIKKVQRAQNFRNLLTLHEQRWGMNWDRFSVRIDLAEEHRNQRRST
+AVLAEGEEFEAPVFEAGRSASVGSAATMGKDGASLRQQLALNLHTYHVLQTAFGKRRDLD
+ASVGARGLHGEGYRGHIFWDEIFVYPMLTLRRPEITRGILMYRYRRLNEARANAQAEGWA
+GAMYPWQSGSDGREETPAELWNPRSHMWMPDNSHNQRHVSLDIAYSVLRYIEITKDASFI
+SDYAAEMLVEISRFFTSMTLHNAETGRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVL
+TSWVLSETARLLRWLDTLDDGLPEVMEVTEEEIARWEEIAAKLTVPFFTEGPEAGILAQF
+EGYQDLLEFDWEGYRAKYGNIGRMDLILQSEGDATNRYKLSKQADTLMLPYLFSGAELEQ
+ILGRMGYELHQEALERTVEYYEARSTHGSTLSRLVHAWVAARTDPDRSWDLFTEALESDL
+SDTQGGTTREGIHLGLMAGTVDTVIRCYSGLETRDDVVRLDPRLPRQLPGARFTIRYHQQ
+PVVIHMTQRDVTVTAGEGMWHEVPMVIAGREHTLEPGGEVTVALG*
+>NZ_CP097650.1_2042
+MSQTLTPAAPQDLNARRHRLRRYRAVIFDMDGVITDTAGVHAQAWKELFDGALPAVGALP
+ANAAVVAADPDVLRPFDAAADYLHHVDGRPREDGVRTFFASRGLRVPEADAPEADAAPEL
+TVLALAERKQGYFEQVLERDGVRVFPEAQDLLERLRAKGVPVALVTSSKNSRAVLTAGGV
+LDFFPVIVDGNTALERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAAADGRFG
+LVIGVDREPELGKGRLKAAGAHLVVQDYGTLHLEDRTTTPFDPAWVLRWDRFDPASEGTR
+EVLCTLANGYWGTRGAVPGTHISSVHYPGTYMAGVFNRLTSMVQGRVVETEHMVNIQDWT
+PLVVTPRHGRPLLPGEENLVEYGQEMDLRRGVLSRTMTFEDEQGRRTTVHTRQFTSLANR
+HLAAIELTVVAENWSGDLTVRSKIEGRVANLNVSDDRTLANQHLEPVQAREIDGETVLLE
+TATNQSGIHVAMATRTRQVAPVGHHEPIRRPVDGSDLVVGQDILLHVDEGVPLVLEKIAA
+VATSHDHANASVWESAVKDVQRAQNFRNLLTLHEQRWGTNWDRFSVRIDLAEPYRHQRRS
+TAAEAGGEYAPPVVDAGHSAPVGSAVPMGKDGASLRQQLALNLHTFHVLQTAYGRRRDLD
+ASVGARGLHGEGYRGHIFWDEIYVYPMLTLRRPEITRGLLMYRYRRLNEARANAQAAGWA
+GAMYPWQSGADGSEETPTELWNPRSRMWMPDNSHNQRHVSLDIAYSVLRYIEITKDTSFI
+SDYGAEMLVEISRFFMSMTLHNAVTDRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVL
+TSWVLAETARLVRWLDTIDDGLPELMEISEEEIERWEEVSTRLTVPFFEEGEEAGILAQF
+EGYQDLLEFDWEAYRAKYGNIGRMDLILQAEGDATNRYKLSKQADTLMLGYLFSAEELDR
+ILRRMGYELPQEAFERMVTYYEARSTHGSTLSRLVHAWVAARTDPDRSWDLFTEALESDL
+SDTQGGTTKEGIHLGLMAGTVDTVIRCYAGLETRDDVVRLHPRMPAQLPGARFTIRFRQQ
+PVVIHMTQREVTVAAGEGMWHDVPMIIAGREHTLSPGDKLTVPLD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001701.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001701.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a3bf42366363a93be54ab796a81bab600efa1576
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001701.fa
@@ -0,0 +1,46 @@
+>NZ_CP042169.1_2103
+MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG
+MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSLSLLMVPLTVYNLAANAPRSVSVAGL
+LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPLAMVIMAIGCGLMVLTAWAFGDVVR
+NRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYA
+AAAKPALAVTALETIGQTGRSALADMRQLLGVLRETGETVAGVPGVTDDDARRPAADVVA
+SPDGRGTRLPPGRRPQPRLADLPALVETMRLSGLEVSLLETGTPRRTLPAGGELAAYRIV
+QEALTNTLRHGGPDADAFVTLAWTAHGLDLQIDDDGCGAAADPATRGSGQGLRGAAERTA
+LFGGTLETGPRVGAGYRVSAHLPYSAV*
+>NZ_CP033200.1_1828
+MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG
+MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSMSLLMVPLTVYNLAANAPRSISVAGL
+LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPLAMVIMAIGCGLMVLTAWAFGDVVR
+NRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYA
+AAAKPALAVTALETIGQTGRSALADMRQLLGVLRETGETVAGVPGVTDDDARRPAADVVA
+SPDGRGTRLPPGRRPQPRLADLPALVETMRLSGLEVSLLETGTPRRTLPAGGELAAYRIV
+QEALTNTLRHGGPDADAFVTLAWTAHGLDLQIDDDGCGAAADPATRGSGQGLRGAAERTA
+LFGGTLETGPRVGAGYRVSAHLPYSAV*
+>NZ_CP040019.1_583
+MNPLHRIDQWMRAHPVRTDVLVSVLLFAVLGLTPWVMLGSLAGPTPGSIVASILIALALI
+APWAFRRVRPVASAAAVAAAAVAHLVAGPEFSLALVLVPMTVYNLAANAPRWASFTGLVA
+ALLGGVANGIRVGLFPDPAMRPDGVYEPVDPSLEALLVMVFGCAAVVLTAWAFGDVVRHR
+RLAVRALEDRNRRLETMALQERRLAASDERNHIAREMHDIVAHSLQVIISQADGARYAAA
+AKPELAVATLDTIGLTGRAALADMRQLLGVLRETGETVAGVPGVAPDDGAPGPAAGASDE
+GAAGAADEGAAGAADEGAAGAGTAGAGTTPGAGRTRLPADVASRDGRGARQPPGHRPQPT
+LADVPALIETMRLSGLEVSLLETGAPRRPLPPGGELAAYRIVQEALTNTLRHGGPQASAF
+LTLAWTGRGLDVQSDDDGRGADADPGTRGSGHGLRGVAERVALFGGTVETGPRAGAGYRV
+SAHLPYSAV*
+>NZ_CP083691.1_505
+MNPLRRLDVLLRRHPVRTDVTAAVLLTLVLVLAPLVMLGGGVGSPAAWQTAGTVVAGLLM
+TGAWGLRRVRPVAAAGVTVAGALLHLAVGPEFTIALAMVPATVYNLAAIGPRWASLAGLA
+TGLAGGLANGLKVWLFPPRFTTPDGVQVQSPAEPVAMVVMAVLCGMAVLTAWAFGDVVRN
+RRLAVQALEDRARRLETQALQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYAA
+AAKPELAVETLETIGQTGRSALADMRQLLGVLRGPAEPTGGPDRARRDPAAPDGHRAPPG
+LADLPALFQTLRLSGLEISLLEQGSPRRDLPAGGELTAYRTVQEALTNTLRHGGEGAHAF
+LTLRWTARGLEIQADDDGRSQADAETTGSGQGLRGIAERVALFGGTMEAGPRVGAGWRVW
+AELPYADV*
+>NZ_CP097650.1_2048
+MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG
+MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSLSLLMVPLTVCNLAANAPRSVSVAGL
+LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPLAMVIMAIGCGLVVLTAWAFGDVVR
+NRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYA
+AAAKPALAVTALETIGQTGRSALADMRQLPGVLRETGETVAGVPGVTDDDTRRPADPAPD
+RADPTGTRPDVVAAPDGRGARLPPGRRPQPRLADLPALVETMRLSGLEVSLLETDTPRRA
+LPAGGELAAYRIVQEALTNTLRHGGPDADAFVTLAWTARGLDLQIDDDGRGAAADPATRG
+SGQGLRGAAERTALFGGTLETGPRVGTGYRVSAHLPYSAV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001710.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001710.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a26daa469991e161a7b2136ec7cc1f350d8bdbd4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001710.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_2120
+MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTLGAILTGHPVP
+EGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAGM
+ALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRSGRTPGAPSPMALVLAGAALTAGAT
+AGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALALG
+DDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRALMV
+GCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA*
+>NZ_CP033200.1_1846
+MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTLGAVLTGHPVP
+EGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAGM
+ALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRRGRTTPGAPSPMALVLAGAAITAGA
+TAGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALAL
+GDDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRALM
+AGCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA*
+>NZ_CP040019.1_560
+MPRALLLIAPAVLAVLAALASLALGARPVPVDAAVGALTEAALHGPAAVTGMDGAAVLSR
+VPRTLAAILVGAGLAVAGAALQGATRNPLGDPGLLGLTAGAVLAFALGIALGVAGSLPAV
+MALAILGTLAAAALVTAVAAGAARVSGVPGPPSPLSLVLAGAATTAGATAVTSALVVLHP
+AVRDRLRLWTVGSVARADLGDALWLAPVVLAAVAAVVVLGPGMDALALGTDLAHGLGARP
+ERVRALLLAAAVVLTAAAVALAGTVGFLGLVIPHAVRRLRPPDARTLVLACALWGAVLVL
+VADTLGRLVIAPAEVHLGVTTAVLGVPVLLALLRRRGVAA*
+>NZ_CP083691.1_487
+MPSSPTRGALLFGLLPLALLLTAGLAALALGARPVPLTTTATTLQAMLAGEGVPAGVDAA
+AVASRVPRTLTAALVGAALAVAGAALQGATRNPLGDPGLLGLSAGASLATAIGLALGVSG
+STFWVLALAAAGTLAAALLVYAVAAAASRGAGAGGAPTPIGLVLAGAAVTAGAGAVTTAL
+LVLSPVVRDRFRFWAVGTVARADLGEAALLTPVIGLGIVLALAAARGLDALALGDDLAHG
+LGARPGRTRALLLAAVVLLTAAAVALAGPVGFVGLVVPHALRRLRPGGTRTLLIGSALWG
+AVLLVAADLLGRLVIAPAEIHLGVTTVLLGVPVLLVLLRRTGLGS*
+>NZ_CP097650.1_2066
+MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTLGAVLTGHPVP
+EGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAGM
+ALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRRGRTPGAPSPMALVLAGAAITAGAT
+AGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALALG
+DDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRALMV
+GCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001712.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001712.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e39b1be2f8d953ff6f99a3608b70571b2da833c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001712.fa
@@ -0,0 +1,32 @@
+>NZ_CP042169.1_2122
+MTAPPLTVPSPAAPRAGAADDVAIRLRGLTLGYGPASAPPIVADLDLDVPAGRVTAIIGA
+NGCGKSTLLRGLTRQLAPRAGSIEVLGRDAARVSARDYARTVALLPQHPVAPEGMTVAQL
+VARGRHPHRGLLGGRAAGDDAAIASALERTDLVELADREAGTLSGGQRQRAWLALVLAQQ
+TPVVLLDEPTSYLDLSHQVEVLDLVRALPDPRGGGRATVVAVLHELNLAARSADHIVAMA
+AGRVVAQGTPGEVIVPEVLAEVFGLDADVVADPLLGHPVVLPRGDGDRR*
+>NZ_CP033200.1_1848
+MTAPPLTVPSPAAPRAGAADDVAIRLRGLTLGYGPASAPPIVEDLDLDVPAGRVTAIIGA
+NGCGKSTLLRGLTRQLAPRAGSIEVLGRDAARVSARDYARTVALLPQHPVAPEGMTVAQL
+VARGRHPHRGLLGGRAAGDDAAIASALERTDLVELADREAGTLSGGQRQRAWLALVLAQQ
+TPVVLLDEPTSYLDLSHQVEVLDLVRALPDPRGGGRATVVAVLHELNLAARSADHIVAMA
+AGRVVAQGTPGEVIVPEVLAEVFGLDADVVADPLLGHPVVLPRGDGDRR*
+>NZ_CP040019.1_558
+MTPPHPAAAPAERPGADPATGPAQDPALRLRGVRLGYGRPDTPDTVGPVDLDVPAGRVTA
+LIGANGCGKSTLLRGLTRQLPLRGGSAEVLGRDLGAYSAREYARTVALLPQHPVAPEGMT
+VAQLVQRGRHPHRGLFGTTGADDDAAVARALRHTDLEKLADREVAELSGGQRQRAWLALV
+LAQRTPVLLLDEPTSYLDLAHQVEVLDLVRGLTRPDGDEEPVTVVAVLHELSLAARVADR
+LVALRDGRVAAAGTPAEVLTPAVLAEVFDLDADVRPDPLLGHPVVLPRGAADRGAPLPSP
+TTQETR*
+>NZ_CP083691.1_485
+MTSSPPTPAAPSTAPAPALRLRGVELSYGPASAPPTVGPVDLDVPAGQVTAVIGANGCGK
+STLLRGLTRQLPLRAGTVDVLGRDAAGMSARDYARTVALLPQQPVTPEGLTVAQLVERGR
+HPWRGLLGGRAAGDDAAVAAALARTGLVDLAARDAATLSGGQRQRAWLALVLAQQTPVVL
+LDEPTSYLDLAHQVEVLDLVRTLPDPRAVGARTVEAAGGVVGGGAGTEAGPPPRATVVAV
+LHELSLAARAADHVVAMAGGRVVATGTPAEVIVPEVLAEVFGLDADVVPDPLLGHPVVLP
+RGRGDRA*
+>NZ_CP097650.1_2068
+MTAPPLTVPSPAAPRAGAADDVAIRLRGLTLGYGPASAPPIVEDLDLDVPAGRVTAIIGA
+NGCGKSTLLRGLTRQLAPRAGSIEVLGRDAARVSARDYARTVALLPQHPVAPEGMTVAQL
+VARGRHPHRGLLGGRAAGDDAAIASALERTGLVELAEREAGTLSGGQRQRAWLALVLAQQ
+TPVVLLDEPTSYLDLSHQVEVLDLVRALPDPRGGGRATVVAVLHELNLAARSADHIVAMA
+AGRVVAQGTPGEVIAPEVLAEVFGLDADVVADPLLGHPVVLPRGDGDRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001714.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001714.fa
new file mode 100644
index 0000000000000000000000000000000000000000..58e23dec8f48499aafec7a752e0701983ab908aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001714.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_2124
+MTRTVIIGGHGKVALLAAPLLAEAGHDVVSIIRNPDHAEDVRAAGAEPLVLDIEKADQEE
+LLHALRDADNVVFSAGAGGGDAQRTRAVDHDAAVASMRAAEAAGVRRYVMVSYLGASLHH
+DVPEDDPFYTYAQAKAEADEALRDSGLAWTILGPGALTDEEPSGRITVDPDLSDSDAPQR
+GASRGNVARAIVAVLSEPGTVGRKIDFVDGDVPVAEAVRGD*
+>NZ_CP033200.1_1850
+MTRTVIIGGHGKVALLAAPLLAEAGHDVVSIIRNPDHAEDVRAAGAEPLVLDIEKADQEE
+LLHALRDADNVVFSAGAGGGDAQRTRAVDHDAAVASMRAAEAAGVRRYVMVSYLGASLHH
+DVPEDDPFYAYAQAKAEADEALRDSGLAWTILGPGTLTDEEPSGRITVDPDLSDSDAPQR
+GASRGNVARAIVAVLNEPGTVGRKIDFVDGDVPVAEAVRGD*
+>NZ_CP040019.1_556
+MTRTVIIGGHGKVALLAAPLLAEAGHDVTSIIRNPEHAAEVEAAGAAPLVLDVERAGEED
+LVQAFRDADNVVFSAGAGGGDPARTRAVDHDAALATMRAAEAAGVRRYVMVSYLGASLHH
+GVPEDDSFHAYAQAKAEADEALRDSGLAWTILGPAALTLEEPTGRITVDPDLDTPDAPKG
+EVSRGNVARALVAVLADPTTVGRKIDFVDGDTPVAEAIRGA*
+>NZ_CP083691.1_483
+MDILIIGGHGKIALLTAPLLADAGHTVTSAIRNPEHADDVRTAGAEPLVLDVEHSSPAEL
+EAAMRGRDVVVWSAGAGGGDPERTYAVDRDAAIASMDAARAAGVRRYVMVSYRGASVHHG
+VPEDSSFFAYAEAKAAADEHLRGSHLDWTILGPGALTLDEPTGRVQVDPQGPSEELPGTS
+RGNVARMIAAAVDSGASIGRQVEFVDGDTPVDDVFRR*
+>NZ_CP097650.1_2070
+MTRTVIIGGHGKVALLAAPLLAEAGHDVVSLIRNPDHAEDVRAAGAEPLVLDIEKADQEE
+LVHALRDADNVVFSAGAGGGDAQRTRAVDHDAAVASMRAAEAAGVRRYVMVSYLGASLHH
+DVPEDDPFYTYAQAKAEADEALRDSGLAWTILGPGALTEEEASGRITVDPDLSGSDASQR
+EASRGNVARAIVAVLSEPGTVGRKIDFVDGDVPVAEAVRGD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001715.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001715.fa
new file mode 100644
index 0000000000000000000000000000000000000000..39b0fdd4c3b0d71373e692c414d0dc2122ce598b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001715.fa
@@ -0,0 +1,29 @@
+>NZ_CP042169.1_2125
+MPLSTLRVSLPSVRRTRPAPQGVRGRIAHAVVSRLQPRPVPPVDRRSRLAWQVSGALPLI
+GCLTSFPIGMSKDSMVIPGVGYQGGFPAGWSHALNQPAYFTWLSNALVAGTSLTLAARRE
+APTSDAFWAVRTAGLGSVMVTGIVYNAVLRGREQDTFLYRFNDALQHIVNPVLAPAVWAL
+CDPRGQITPRRAGLASVIPLMWAAATMARGPRIDWYPYPFLDVPRLGRRSVGVVLAGILA
+GFTGLMGVLGTVDRRLGLA*
+>NZ_CP033200.1_1851
+MPLSTLRVSLPSLRRTRPAPQGVRERIAHAVVSRLQPRPVPPVDRRSRLAWHVSGALPLI
+GCLTSFPIGMSKDSMVIPGVGYQGGFPAGWSHALNQPAYFTWLSNALVAGTSLTLAARRE
+APTSDAFWAVRTAGLGSVMVTGIVYNAVLRGREQDTFLYRFNDALQHIVNPVLAPAVWAL
+FDPRGQITPRRAGLASVIPLMWAAATMARGPRIDWYPYPFLDVPRLGRRSVGVVLAGILA
+GFTGLMGVLGTVDRRLGLA*
+>NZ_CP040019.1_553
+MLRLARPRSRRAPQGLGGRLVRAVAARPVPPVRPRARLAWHVSGALPLIGCLTSFPIGMS
+KDSMVIPGVGYQGGFSAGWHHALNQPAYFTWLSNALVAGTSLTLATRRTAPTSDAFWAVR
+TAGLGSVMVTGIVYNSVLRGREQDTVLYRFNDTLQHIVNPVLAPAVWALFDPRGQITPRR
+AGLASVIPLAWAALTMARGPRIDWYPYPFLDVPRHGARTVGVVLAGILAGFTGLMGLLGG
+LDRRLGGR*
+>NZ_CP083691.1_480
+MPAWLARFTRPRPAPRPSRAARAGWWAAGALPLVGCLTSFPIGASKPTMVIPGVGYHGGF
+EAGWQHALNQPAYFTWLSNAMVAGTSLTLAARRDAPTSDAFWALRTAGLGSVMVTGIVYN
+AVLRGMEQDTLLYRFNDAVQHVVNPVLAPLVWAAFDPRGQITYRRAGLAAVVPLMWATAT
+LVRGARIDWYPYPFLDVPRLGWRGVGAAVSVVLAGFSAVLGLLGQVDRRLGTR*
+>NZ_CP097650.1_2071
+MPLSTLRVSLPSVRRTRPAPQGVRERIAHAVVSRLQPRPVPPVDRRSRLAWQVSGALPLI
+GCLTSFPIGMSKDSMVIPGVGYQGGFPAGWSHALNQPAYFTWLSNALVAGTSLTLAARRE
+APTSDTFWAVRTAGLGSVMVTGIVYNAVLRGREQDTFLYRFNDALQHIVNPVLAPAVWAL
+FDPRGQITPRRAGLASVIPLMWAAVTMARGPRIDWYPYPFLDVPRLGRRSVGVVLAGILA
+GFTGLMGVLGTVDRRLGLA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001716.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001716.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d381461b3115a5e221191d137b992a55e188654
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001716.fa
@@ -0,0 +1,45 @@
+>NZ_CP042169.1_2126
+MRHPIPDYLASLITELGAVNPGETAQYIPVLAEADPDRFGIALATPTGRLHCAGDADVEF
+TIQSASKPFTYAAALVDRGFAAVDRQVGLNPSGEAFNELSLEAESHRPDNAMINAGALAV
+HQLLVGPEASREERLDRAVEIMSLLAGRRLSVDRETYESEMAVSDRNLALAHMLRSYGVL
+QDSAEEIVAGYVAQCAVRVTVKDLAVMGACLATGGIHPMTGERVLPSIVVRRVVSVMTSS
+GMYNAAGQWLADVGIPAKSGVAGGVLGALPGRVGIGVFSPRLDEVGNSARGVLACRRLSE
+DFRLHLMDGDSLGGTAVRFVEREGDRVFLHLQGVIRFGGAEAVLDALTDLRTGAEKPGTG
+WDAAVYPRWQEAAADRAALSAATGGGAVHEAAAVAARDENDGPIRTVVLNLTRVDWIDDV
+GRRLIAEGVRRLQADGVRVEVEDPERILPLEEAGAH*
+>NZ_CP033200.1_1852
+MRHPIPDYLASLITELGAVNPGETAQYIPVLAEADPDRLGIALATPTGRLHSAGDADVEF
+TIQSASKPFTYAAALVDRGFAAVDRQVGLNPSGEAFNELSLEAESHRPDNAMINAGALAV
+HQLLVGPEASRKERLDRAVEIMSLLAGRRLAVDRETYESEMAVSDRNLSLGHMLRSYGVL
+QDSAEEIVAGYVAQCAVLVTAKDLAVMGACLATGGIHPMTGERVLPSIVARRVVSVMTSS
+GMYDAAGQWLADVGIPAKSGVAGGVLGALPGRVGIGVFSPRLDEVGNSARGVLACRRLSE
+DFRLHLMDGDSLGGTAVRFVEREGDRVFLHLQGVIRFGGAEAVLDALTDLRTGAEKPGTG
+WDAAVYPRWQEAAADSAALAAATGGGAVYEAAAVAAQDENDGPIRTVVLNLTRVDRIDDV
+GRRLIAEGVRRLQADGVRVEVEDPERILPLEEAGAH*
+>NZ_CP040019.1_552
+MRHPFVDYLEGLLGSLEHVTEGDVARYIPILAEADPSLSAVAVATTSGRVHTAGDADAEF
+SIQSVSKPFTYAGALEDRGVELVDEYVALNPSGEAFNELSLEADSHRPDNAMINAGAIAV
+HQLLVGPGATPAERTERAVSLMSTLAGRRLRVDERTFESEMATADRNLALGHMLRSHGIL
+QDRAEDVVAGYIAQCSVMVTVRDLAVMGATLASGGLHPLTGERVLSSLVCRQVLSVMSSS
+GMYDAAGQWMAHVGIPAKSGVSGAVLGALPGQVGIGTYSPRLDPFGNSVRGVEMCRIMSE
+DLDLHIMEADVIGSTVVRSVRREGDTVHLHLQGVIRFGGGESVLAAMTELGTGADPDPVE
+WAHCFYPFSEEPDTAAGRAAAQDEGRTAAEALEQEAPVRAVVVHLERVDRVAPVGRRLIE
+DGLKRLRADGVQVRVEDPDGVLTGG*
+>NZ_CP083691.1_479
+MKHPVPDYLQHLVDSLREDRRGALADYIPVLAQADPERLGIALATVTGRLHSAGDDETEF
+TIQSVSKPFAYAAALQDRGLDAVDARVGLNPSGEAFNELSLEAESKRPDNAMINAGALAV
+HQLLVGPYAGRQERLDRLVGFMSTLAGRRLEIDRETFESEMATSDRNLSLAHMLRSHGII
+QDRAEDVVAGYIAQCSVRVTVRDLALMGACLASGGVHPLTGERVLPSLVCRQVLSVMSSS
+GMYDAAGQWLVNVGIPAKSGVSGAVLGALPGQVGLAVFSPRLDEVGNSVRGVEACRRMSE
+DMDLHLMEGDSLGGTVVRFARREGDTVLLHLQGVIRFGGGEAVVTAMTDLGTGAAGGGRA
+AWSEHDYPEWEDAPHGDVAAEAGDRRPVDAADPEAARAAATGDGSVHEAAACAVAEDGLP
+IRTVVLNLERVDRVTAVGRRLIDEGVDRLRADGVAVEVVDPDGLLG*
+>NZ_CP097650.1_2072
+MRHPIPDYLASLITDLGAVNPGETAQYIPVLAEADPDRFGIALATPTGRLHCAGDADVEF
+TIQSASKPFTYAAALVDRGFAAVDRQVGLNPSGEAFNELSLEAESHRPDNAMINAGALAV
+HQLLVGPEASRKERLDRAVEIMSLLAGRRLSVDWETYESEMAVSDRNLSLAHMLRSYGVL
+QDSAEEIVAGYVAQCAVLVTAKDLAVMGACLATGGIHPMTGERMLPYIVARRVVSVMTSS
+GMYDAAGQWLADVGIPAKSGVAGGVLGALPGRVGIGVFSPRLDEVGNSARGVLACRRLSE
+DFRLHLMDGDSLGGTAVRFVEREGDRVFLHLQGVIRFGGAEAVLDALTDLRTGAEKPGTG
+WDAAVYPRWQEAAADSAALSAATSGGAVHEAAAVAARDENDGPIRTVVLNLTRVDRIDDV
+GRRLIAEGVRRLQADGVRVEVEDPERILPLEEAGAH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001718.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001718.fa
new file mode 100644
index 0000000000000000000000000000000000000000..675accdeadd35bd4889605d67bd6e0dc5c562164
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001718.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_2129
+MTQPTTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLAEEARVRALAAWATTT
+ASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRCVLCDAV
+FVQVDPAAGRPVAVSDEERAAFERVLIPAED*
+>NZ_CP033200.1_1855
+MTQPTTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLAEEARVRALAAWATTT
+ASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRCVLCDAV
+FVQVDPAAGRPVAVSDEERAAFERVLIPAED*
+>NZ_CP040019.1_549
+MNGQDGGQGRTTTDGATGREAPVPFETEIQVRWSDEDRYGHVNNARLLTLTEEARVRATR
+AWSGVTPGRDVHRVVRAMEVQYEAPVVYGPELTAKVWIARIGTSSYTLRHELWQDGRRCV
+LCDAVFVHVDPETGRSVALAEDERVTLERVLIPAEADAT*
+>NZ_CP083691.1_474
+MSDSQPRPYEGVLDLRWSDMDLYGHVNNVRILTLTEEARVRALKAWDEGDVGRDVMRVVR
+AMTTEYERPVEYGPELTAKVWVRALGRTSYTLHHELWQEGVRCVTCDAVMVHLDPETGAP
+LPHDDARRARLQAVLVPAEG*
+>NZ_CP097650.1_2075
+MTQPTTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLTEEARVRALAAWATTT
+ASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRCVLCDAV
+FVQVDPAAGRPVAVSDEERAAFERVLIPAED*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001719.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001719.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5385693d8449b915b7e149be011e56d7ce46ded9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001719.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_2130
+MEQDPSPDAPAPSADVEALRGTPVSELTQLTPAASGALERLRRDVERFDLEYRSALLQVE
+ARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLSLDLDALRTNVTDIAGARV
+IVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPIHLSTGTIPVTV
+EMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVAADLDTRMERLHDQVQETD
+RDDDAAAAWEDDGGPAFEDEPTVEPGEARPGDAPGASTA*
+>NZ_CP033200.1_1856
+MEQDPSPDAPAPSADVEALRGTPVSELTQLTPAASGALERLRRDVERFDLEYRSALLQVE
+ARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLSLDLDALRTNVTDIAGARV
+IVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPIHLSTGTIPVTV
+EMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVAADLDTRMERLHDQVQETD
+RDDDAAAAWEDDGGPVFEDEPAAGPGEARPGDDAPGASTV*
+>NZ_CP040019.1_547
+MEQDRDPEESSQSTAIETLRGTPVSELTHLPPAMAGALDRLRRDVERFDLEYRSALLQVE
+ARLEVLRDEFTHLHDYNPIEHIVTRVKTPESILRKAASRGLSMDLDALRSNVTDIAGARV
+IVSFARDVYEVFRLFTRQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPVHLSTGSIPVTV
+EMQFRTSAMDFWATLEHKINYKFDGAVPPDITTELIAAARVAADLDTRMERLSDQVRQTD
+KDDDAAASWEDDGGPAFEDEGDDDGPDGDAPGTSTG*
+>NZ_CP083691.1_473
+MPRDVDHPPPADDPAPVERPAPGGRGVTSASTALEALRATPLTDLTQLPGEVADALASLR
+TDFERFDLEYRSALLQVETRLETLQDEFTHLHEYNPIEHIATRVKSPESLLRKAASRGLS
+LDLDALRSGVTDIAGARVIVSFTEDVYRVFRQFTSQPDIRVLEVEDYIRDPKPSGYRSLH
+CLVQVPVHLTTGTVPVTVELQFRTIAMDFWASLEHKINYKFAGHVPPAITTELAAAARVA
+HDLDARMERLHQAVHDAGAGPDEHDDEDDWVGHA*
+>NZ_CP097650.1_2076
+MEQDPSPDAPAPSADVEALRGTPVSELTQLTPAASGALERLRRDVERFDLEYRSALLQVE
+ARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLSLDLDALRTNVTDIAGARV
+IVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPIHLSTGTIQVTV
+EMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVAADLDTRMERLHDQVQETD
+RDDDAAAAWEDDGGPAFEDEPAAGPDGTDPGEARPGDDAPGASTV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001733.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001733.fa
new file mode 100644
index 0000000000000000000000000000000000000000..42ec78497118ac11b7d0d2f88f6f90e8d0347b27
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001733.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_2163
+MPPEPSAPSGERGPARPHPADVAARPDAPSPRATALLFALAVAAGSVMPLQGRINSRLAH
+LTGDPVLAALCSFAAGLVVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGVIGGLL
+VLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAVA
+LVVWPSLGEAGGGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTAGVL
+FLGIVWGGIALASGHGLPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLVSGN
+LLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVALASWPARRR*
+>NZ_CP033200.1_1888
+MPPESSVPSAERGPSRPRPAAVAARPEAPSPRATALLFALAVAAGSVMPLQGRINSRLAH
+LTGDPVLAALCSFAAGLAVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGMIGGLL
+VLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAVA
+LVVWPSLGEAGGGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTAGVL
+FLGIVWGGIALASGHGLPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLVSGN
+LLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVALASWPARRR*
+>NZ_CP040019.1_511
+MSARAARAARAGEGRQGSDAPAGADARPGAAGSALLFAMAIVAGSTIPVQARLNSALAER
+SGDPTLAAVASFAAGLVLVAAVTVLTPAGRRGLRAVRPALAAGRVRWWYLLAGTIGGAMV
+FSQATTVGLIGVAVFTVAVVTGQLIGGMVVDRLGLTPAGVRRMTPRRLAGAALALACVVL
+VVAPQLGARGDGGPPLWLLVALAPLAVGLATSIQQTLNARQAAAYGSVLPVTTVNFVAGT
+GILALVHLGGRLGGGVGGTLPGDWWLYLGGPMGVVFIAFSAYLVPRVGAFLTMLGLVSGK
+LLGSLAVDALAPVGEVAASPWTVVGTLGALAAVVLASGAARPARKG*
+>NZ_CP083691.1_449
+MPASSPALTPAPRSGATTALLFLLALVAGLAMPVQGRVNSALSLAVGSPALAACASFATG
+LAVLVLATLLLPSGRRGAARIPAAVRNGDVRWWQLLAGTIGAAFVLTQAWTIPLIGVAVF
+TVAVVTGQMLGGMLWDRLGWTPAGVQRISRRRLFGALLAFCAVTAVVWPRLQESGSPGAW
+LALAVLPLAAGVATSGQQAMNGHQTAHFGTPLPPTLVNFAAGTAVLAAATAVAAGTGAGM
+GPLPAAWWMYLGGPLGTVFVGLGAFLIPRVGAFLTTLGMVAGQLVGSLLLDVVAPAPGAQ
+VTWLTVVGTLGALAAMVVASSPQVPAGLRASRRRARRG*
+>NZ_CP097650.1_2103
+MPPEPSAPSGERGPARPHPADVAARPDAPSPRATALLFALAVAAGSVMPLQGRINSRLAH
+LTGDPVLAALCSFAAGLVVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGVIGGLL
+VLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAVA
+LVVWPSLGEVGGGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTAGVL
+FLGIVWGGIALASGHGMPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLVSGN
+LLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVTLASWPARRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001736.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001736.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9936cf7eba9dd3d4e9cf1ac88c0a22b490e944c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001736.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_2184
+MSAAPPPPAFGTVLHHRAHGMAPGESISPPLVHASAFHLPGADPDGAPTAPGADVPFQYA
+RWATPTWSALEAALGALEDADVAVVPSGMAAIAAVLLPLLHPGDRALLPADGYGPTRALA
+AEHLTPRGVHVDLVATQGLAHADLSGYDLVLVETPSNPGLRVADLADVAARAHANGRRDG
+AGALVVVDNTLLTPLGQRPLELGADVVVASDTKAVNGHTDALGGHVASRDPQVMARVRGW
+RTLAGGILGTHEAWLIHRGLETLEVRFARMCASAQAVAELAAGHPAVRAVVYPGLADHPD
+AEVVARQMTAAGGLVGLRFADAAAAERFIAAAQYVVPQTSFGGTHTAAERRARWGDDVPD
+GFVRLSVGVEPTAELLADLERAMTAAGGGPTA*
+>NZ_CP033200.1_1898
+MSAAPPPPAFGTVLHHRAHGMAPGESISPPLVHASAFHLPGADPDGAPTAPGADVPFQYA
+RWATPTWSALEAALGALEDADVAVVPSGMAAIAAVLLPLLHPGDRALLPADGYGATRALA
+AEHLTPRGVHVDLVATQGLAHADLSGYDLVLVETPSNPGLRVADLADVAARAHANGRRDG
+AGALVVVDNTLLTPLGQRPLELGADVVVASDTKAVNGHTDALGGHVASRDPQVMARVRGW
+RTLAGGILGTHEAWLIHRGLETLEVRFARMCASAQAVAELAAGHPAVRAVVYPGLADHPD
+AEVVARQMTAAGGLVGLRFADAAAAERFIAAAQYVVPQTSFGGTHTAAERRARWGDDVPD
+GFVRLSVGVEPTAELLADLERAMTAAGGGPTA*
+>NZ_CP040019.1_489
+MPDSAARHSAARHDVPAPPPFGPVLHHRAHGMAPGDAISPPLVHASAFHLPGAGPDGAPA
+EPAAQGGFQYARWGTPTWAALEAALGVLEDADVAVVPSGMAAIASVLLSHLRPGDRALLP
+SDGYGATRALAAEHLSPIGVHVDLVPTPALASADLSAYDLVFVETPSNPGLRVADLADVA
+ARAHANGRRGGAGALVVVDNTSLTPLGQRPLDLGADVVVASDTKALNGHSDALGGHVASR
+DADVLARVRGWRTLTGAILGTHEAWLIHRGLETLEVRFARMCASALAVAELAAGHSAVRA
+VAYPGLPDHPDAEVVARQTTAAGSVVGLEFADAAAAERFLAAARLVVPQTSFGGTHTSAE
+RRARWGDDVPAGFVRLSVGVEPTAELLADVERALEAAG*
+>NZ_CP083691.1_425
+MASPQPPAFGPVLHHRAHGMAPGDAISPPLVHASAFHLPGAGPDGAPVAPGADVAFQYAR
+WGTPTWAALEAALGVLEDADVAVVPSGMAAIAAALLPVLRPGGRALLPSDGYGATRALAA
+EHLVPAGVHVDFVSTPGLADAGFSAYDLVFVETPSNPGLRVADLADVAARAHANGRRDGK
+GALVVVDNTSLTPLGQRPLDLGADVVVASDTKALNGHTDALGGHVASRDPELMTRVRGWR
+TLAGGILGTHEAWLIHRGLETLEVRFARMCASALAVAELAAGHPAVRAVAYPGLPDHPDA
+AIVARQMTAAGGVVGLEFADAAAAERFIGAAAYVVAQTSFGGTHTAAERRARWGDDVPAG
+FVRLSVGVEPTAELLTDLARALDAAAGPA*
+>NZ_CP097650.1_2118
+MSAAPPPPAFGTVLHHRAHGMAPGESISPPLVHASAFHLPGADPDGAPTAPGADVPFQYA
+RWATPTWSALEAALGALEDADVAVVPSGMAAIAAVLLPLLHPGDRALLPADGYGPTRALA
+AEHLTPRGVHVDLVATQGLAHADLSGYDLVLVETPSNPGLRVADLADVAARAHANGRRDG
+AGALVVVDNTLLTPLGQRPLELGADVVVASDTKAVNGHTDALGGHVASRDPQVMARVRGW
+RTLAGGILGTHEAWLIHRGLETLEVRFARMCASAQAVAELAAGHPAVRAVVYPGLADHPD
+AEVVARQMTAAGGLVGLRFADAAAAERFIAAAQYVVPQTSFGGTHTAAERRARWGDDVPD
+GFVRLSVGVEPTAELLADLERAMTAAGGGPTA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001738.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001738.fa
new file mode 100644
index 0000000000000000000000000000000000000000..775f0dc3d84342562b47880ae20d6b5a1e26144c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001738.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_2189
+MTPRSLAGLALTVAALMSAFVLMAPTAPGLFVGVLTVGTFGFGPFYGEPSRQLVDRPWRR
+DTRWRDLARRVRTDWLSRQLGAVGWNAAISRRITGRADLRRIRTAAVGSLVSHAASAGLH
+AVAGVALAAVGHPVWGVVAVALGLVVHAWPALLQVSVLGRIDGLQTQIRGDQLLW*
+>NZ_CP033200.1_1903
+MTPRSLAGLALTVAALMSAFVLMAPTAPGLFVGVLTVGTFGFGPFYGEPSRQLVDRPWRR
+DTRWRDLARRVRTDWLSRQLGAVGWNAAISRRITGRADLRRIRTAAVGSLVSHAASAGLH
+AVAGVALAAVGHPVWGVVAVALGLVVHAWPALLQVSVLGRIDGLQTQIRGDQLLW*
+>NZ_CP040019.1_484
+MTPRSLAGLALAVAALAAAFALMAPTAPGLFVGVLTAGTLGFGPFYGEPTRHLVDRPWRR
+DRRWHELARRVRTDWLSRQLGAAGWNAAIRRRITGRADLRRIRTAAVGSLVSHAASVGLH
+GIAALALAVVGHPGWGLLAVLLGLVVHAWPALLQVAVLGRIDGLQAQLRGDRLLW*
+>NZ_CP083691.1_495
+MRIPAVCAAVAVVTLLAWGFRQVVPASPGAYVAVLTAATVGFGPFYGVPTRAVVDLPWRR
+LRRLRALAARAHTWWLARQLRVAGSDARIRRRIRSRADVLAFRREAVGRLLNHGLSAVLH
+AAAGVALAAAGHPLWGVVAVVAGLLVHGWPGLLQVGVLGRVDELQATVQARRGVGGAASA
+GR*
+>NZ_CP097650.1_2123
+MTPRSLAGLALTVAALMSAFVLMAPTAPGLFVGVLTVGTFGFGPFYGEPSRQLVDRPWRR
+DTRWRDLARRVRTDWLSRQLGAVGWNAAISRRITGRADLRRIRTAAVGSLVSHAASAGLH
+AVAGVALAAVGHPVWGVVAVALGLVVHAWPALLQVSVLGRIDGLQTQIRGDQLLW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001739.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001739.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad2bba8fe2ee689fbaada969fe48ab9dec2a9fd8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001739.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_2191
+MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLTDMVGQLARGGSSSAGISSF
+QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR
+GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW
+VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQVPAMFGLIFSS
+ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD
+TLFVCTMTGLMILATNSFNVLGPDGESLLAEHVPGVEEGPAWVQIAIDEALPAFGPSFVA
+IAVFLFSFTTLLSFAFYAETNVAYLIPNKTAQRAVIAIARLLLAGSMVFGSVQTSAFVWS
+LADFGVGLYTWVNIVALILLSPVAIRLFKDYDRQRRAGQDPVLDPAAIGVRNARLWEQIH
+AAYQQTGDLDRAMEHVADTAPDTRAITVVPRREG*
+>NZ_CP033200.1_1905
+MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLRDMVGQLVRGGSSSAGISSF
+QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR
+GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW
+VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQVPAMFGLIFSS
+ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD
+TLFVCTMTGLMILATNSFNVLGTGEGPPIVEHLPGVEEGPAWVQIGIDVVLPSFGPSFVA
+VAVFLFAFTTLLSFAFYAETNLAYLIPNKKAQRICIAAARLLLAASMVIGSVQTSAFVWS
+LADFGVGLYTWVNILALVLLSPVAIRLLKDYDRQRRAGQDPVLDPAAIGVRNAHLWEQIH
+AAYQQTGDLDRAMEHVADTAPDTRAITVVPRREG*
+>NZ_CP040019.1_483
+MEQFLAGANAIMWSLPMVFGLLALGLYFTIRMGAPQLRRIPDMIGQLVRGGSSSAGISSF
+QAFAMALGGRIGVGNIAGVATAISLGGPGALFWMWVTALLGAPVALAESSLAQLYKHKVR
+GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVITGPQIQANAVTAATTQAWGWDPLW
+VGLAMAVLFCVIVFGGMHRLGRTVGLVVPFMAAAYIIVGVVVVALMWQQVPAMFGLIFTS
+AFAADSLYAGMLGAAISWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAFVD
+TLFVCTVTGLMILSTNSFNVLGPDEETVLVEHVPGIEAGPAWVQTAIDSVIPAFGPAFVA
+VAVFLFSFTTLLSFAFYAETNLAYLIPNKSVQRACIAVARLGLAASMVFGAVQTSTLVWS
+FADFGVGLYTWVNILALVLLSPVAIRLMKDYDRQRRAGQDPVLDPRAIGVRNATLWEQIH
+DEYERTGDVTAALDHVADTAPDTRAISVVRSHGERGQG*
+>NZ_CP083691.1_421
+MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLKDMVGQLVRGGSSSAGISSF
+QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR
+GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW
+VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQVPAMFGLIFSS
+ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD
+TLFVCTMTGLMILATNSFNVLGPDGESLLAENVPGVEEGPAWVQIAIDAALPAFGPSFVA
+IAVFLFSFTTLLSFAFYAETNVAYLIPNKTAQRAVIAIARLLLAGSMVFGSVQSSALVWA
+FADFGVGLYTWVNIVALILLSPVAIRLFKDYDRQRRAGQDPVLDPAAIGVRNARLWEQIH
+AAYQQTGDLDRAMEHVADTAPDTRAITVVRGGPERGEG*
+>NZ_CP097650.1_2125
+MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLTDMVGQLARGGSSSAGISSF
+QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR
+GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW
+VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQIPAMFGLIFSS
+ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD
+TLFVCTMTGLMILATNSFNVLGPDEESLLAEHVPGVEEGPAWVQIAIDEALPAFGPSFVA
+IAVFLFSFTTLLSFAFYAETNVAYLIPNKTAQRAVIAIARLLLAGSMVFGSVQTSAFVWS
+LADFGVGLYTWVNIVALILLSPVAIRLLKDYDRQRRAGQEPVLDPHAIGVRNARLWEQIH
+AAYQQTGDLDRAMEHVADTAPDTRAITVVPRREG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001742.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001742.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9acf66b994373323c63c853df67075ad7b6a2236
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001742.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_2200
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ
+HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTDKEDAQ
+*
+>NZ_CP033200.1_1912
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ
+HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTDKEDAQ
+*
+>NZ_CP040019.1_459
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTTSHHLLQ
+HLPLLFVPAGVGVVAVLGLIGEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTNKKENA
+Q*
+>NZ_CP083691.1_414
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVITASHQLLQ
+HLPLLFVPAGVGVVAVLGLIQEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTNKKEDA
+Q*
+>NZ_CP097650.1_2133
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ
+HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTDKEDAQ
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001743.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001743.fa
new file mode 100644
index 0000000000000000000000000000000000000000..138b8fcaccba080cc8f53cb2b20f3ad96825dd29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001743.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_2201
+MHPITLARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTEAGISRT
+PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH
+AATGGSVDAARRLLDGHAEICAQLAAGRAADAQRALQAHLDAAGSGVVPGLPPVGPSEAG
+EPR*
+>NZ_CP033200.1_1913
+MHPITLARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTEAGISRT
+PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH
+AATGGSVDAARRLLDGHAEICAQLAAGRAADAQRALQAHLDAAGSGVVPGLPPVGPSEAG
+EPR*
+>NZ_CP040019.1_458
+MHLIILARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVRLSTEAGISRT
+PAREALLQLESWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH
+AATGGSVDAARRLLDGHAEICAQLAAGCAADAQRALQAHLDAAGTGVVVPGLPTVSQPEA
+GEPR*
+>NZ_CP083691.1_413
+MHLIILARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTDAGISRT
+PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIAMCGNAAFDEIMGTFAPRLARLIH
+AATGGSVDAARRLLDGHVQICAQLAAGRAADAQRALQAHLDAAGAGVVVPGLLPVGSSEA
+GEPR*
+>NZ_CP097650.1_2134
+MHPITLARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTEAGISRT
+PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH
+AATGGSVDAARRLLDGHAEICAQLAAGRAADAQRALQAHLDAAGSGVVPGLPPVGPSEAG
+EPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001750.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001750.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e3a6b60d654d7198ff75c87d77d6018e790aefa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001750.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_2233
+MAKLILTQEVAGLGTSGDVVEVKNGYARNYLLPRGFATVWTKGGEKQVESLQKARAARAV
+ANLEDAQAQAAQLQSATVQLERTAGAEGRLFGAVQTADVAEAIEAAGLGSVDKRSITLPA
+HIKSVGNHEAQVRLHEDVIATVQLQVVAAKAKK*
+>NZ_CP033200.1_1937
+MAKLILTQEVAGLGTSGDVVEVKNGYARNYLLPRGFATVWTKGGEKQVESLQKARAARAV
+ANLEDAQAQAAQLQSATVKLERTAGAEGRLFGAVQTADVAEAIEAAGLGSVDKRSITLPA
+HIKSVGNHEAQVRLHEDVIATVQLQVVAAKAKK*
+>NZ_CP040019.1_433
+MAKLILTQEVTGLGTSGDVVEVKNGYARNYLLPRGFATVWTKGGEKQVESLQKARAARAV
+ANLEDAQAQAEKLQSATVKLERTAGAEGRLFGAVQAADVAEAIEAAGLGSVDKRAVTLPA
+HIKSVGNHQAQVRLHEDVVAVVDLQVVAAKAKK*
+>NZ_CP083691.1_385
+MAKLILTQEVPGLGIDGDVVEVKNGYARNYLLPRGFATVWTQGGEKQVESLKAARAARAT
+ANLEEAQALAAKLQSATVRIDRKAGAEGRLFGAVQAADVAEAIEAAGLGSVSKRSVTLPN
+HIKTVGNHEAQVRLHDEVTATVALQVVAAKGSKK*
+>NZ_CP097650.1_2175
+MAKLILTQEVAGLGTSGDVVEVKNGYARNYLLPRGFATVWTKGGEKQVESLQKARAARAV
+ANLEDAQAQAAQLQSATVKLERTAGAEGRLFGAVQTADVAEAIEAAGLGSVDKRSITLPA
+HIKSVGNHEAQVRLHEDVIATVQLQVVAAKAKK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001751.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001751.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf3813a644ec3df783cd0623840e0c165a1985f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001751.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_2234
+MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ
+AVKNAREVALLPYAGAGRG*
+>NZ_CP033200.1_1938
+MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ
+AVKNAREVALLPYAGAGRG*
+>NZ_CP040019.1_432
+MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ
+AVKNAREVALLPYAGAGRG*
+>NZ_CP083691.1_384
+MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ
+AIKNAREVALLPYAGAGRG*
+>NZ_CP097650.1_2176
+MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ
+AVKNAREVALLPYAGAGRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001752.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001752.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ac35df0fd1e861e11908c95cbb5f32ff1aa62bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001752.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_2235
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW
+REAAENVAESLTKGMRVIVQGRLRARSYDDRDGNRRTSWELDVDEVGPALRFATAKVTRA
+QRGGGGGGGFGGGQQGGGFGGAPAGGGFGGNSDGGFGGAQQGGGWGGQQQGGGQAAPQDP
+WSGGGGGGWDTPSSNEPPF*
+>NZ_CP033200.1_1939
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW
+REAAENVAESLTKGMRVIVQGRLRARSYDDRDGNRRTSWELDVDEVGPALRFATAKVTRA
+QRGGGGGGGFGGGQQGGGFGGAPAGGGFGGNNDGGFGGAQQGGGWGGQQQGGGQAAPQDP
+WSGGGGGGWDTPSSNEPPF*
+>NZ_CP040019.1_431
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW
+REAAENVAESLTKGMRVIVQGRLKARSYDDRDGNRRTSWELDVDEVGPALKFATAKVTRA
+QRSGGGGGGGFGGGQQGGGFGGAPAGGGFGGNNDGGFGGAPQGGGWGGQQQGGGQAAPQD
+PWSGGGGGGGWDTPSSNEPPF*
+>NZ_CP083691.1_383
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDEEALFVRCSVW
+REAAENVAESLTKGMRVIVQGRLKANSYQDREGNKRTSWELQVDEVGPALKFATAKVTRS
+QRGGGGGGGFGGGQQGGGFGGSPQGGGGFGGGQQQSGGWGQPSGGGQSAPAQDPWSGSGG
+GGWDTPSNGEPPF*
+>NZ_CP097650.1_2177
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW
+REAAENVAESLTKGMRVIVQGRLRARSYDDRDGNRRTSWELDVDEVGPALRFATAKVTRA
+QRGGGGGGGFGGGQQGGGVGGAPAGGGFGGNNDGGFGGAQQGGGWGGQQQGGGQAAPQDP
+WSGGGGGGWDTPSSNEPPF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001754.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001754.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4111cc39aea2d846ca65390d4f73aca19dd2e889
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001754.fa
@@ -0,0 +1,50 @@
+>NZ_CP042169.1_2237
+MTPVTRDTVAELHAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG
+YVVVRDGAAVAWIVPMGARALGRHEGAEARAAGPDEAGQSAGVVPVFRVLGAHTDSPGFK
+LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ
+LAIHLDREVNEGLTLKRQRHTNPVVGALVPRGEGAGEAEADGLAARVPGDVLTALAAAAG
+VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLVALEELAREHGGAEGA
+IAYEGTVAGGVAGVAAGAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG
+QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA
+FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD
+VEHLTAAVREFFRGV*
+>NZ_CP033200.1_1942
+MTPVTRDTAAELPAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG
+YVVVRDGAAVAWIVPMGAGALGRHEGAEARAAGPDEAGPSAGVVPVFRVLGAHTDSPGFK
+LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ
+LAIHLDREVNEGLTLKRQRHTNPVVGALAPRGEGAGEAEADGLAARVPGDVLTALAAAAG
+VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLAALEELAREHGGAEGA
+IAYEGTVAGGVAGEAADAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG
+QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA
+FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD
+VEHLAAAVREFFRGV*
+>NZ_CP040019.1_427
+MTAVTRDTAPAPEMSAHVQDLAAFVTASPSSYHAAAEVARRLVAVGFTCLDEAADFPAAP
+GGYVVVRDGAALAWVVPTGAGSDVSDGAGAAGGSGAGAAVPVFRVLGAHTDSPGFKLKPN
+PATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQLAIH
+LDREVNDGLKLQRQRHTNPVVGALAPRGEGAGEAVADVSEGVDGRSAPLEQAAGAGAGVG
+AGAGEGAGAREGDGAGLEARAPGDVLSALAAAAGVDPAAVRGHDVMVADAQAPGLFGLAG
+EFFASGRLDNLSSVHAGLVALEELARANGGASGAIAYAGTVAEGVAGEAAGAPVIPVLAA
+FDHEELGSASRSGAAGPLLEEVMGRVLEALGVAGQGRARAIAGSWLLSADAGHLVHPNYA
+ERHDPVNHPRVNHGPLLKINANQRYATDAGGEAAFARWCGVAGVPFQEFVSNNDMPCGST
+IGPISATRLGIRTVDVGLGLLSMHSAREMCGVRDVEHLTAAVREFFRGV*
+>NZ_CP083691.1_380
+MSTVTSESTVTAAVPGAPALSAHLQDLAAFVQASPSSFHAAAEVARRLEAVGFTRVDPAQ
+DLPAAPGGYVSVTDGAVLAWILPEALAERAADAVPVFRLLGAHTDSPGFKLKPQHLTVTA
+DGWVQAGVEVYGGPLLNSWLDRELRFAGRLALADGRQVLAATGPVGRIPQLAIHLDRSAN
+DDLTLGRQRHTQPIVAAVAGAPDAAGTDAADGASADPVVRLTGDILELLAAQAGVDPAEV
+RGADVVVADAQQGGAFGANGEFFACGRLDNLSSVHAGLRALESLAADADRAGRGVVVAEG
+VAGEAAGAPVIPVLAAFDHEEVGSATRTGAGGPLLEELMGRLLSACGVTGQGAARSRAGS
+WLLSADAGHLVHPNYTERHDPVNHPRVNHGPLLKINANQRYSTDAAGEAAFARWCAAAGV
+PFQRFVSNNDVPCGSTIGPISATRLGVRTVDVGIGLLSMHSAREMCGADDPARLAAVARA
+FFAGV*
+>NZ_CP097650.1_2180
+MTPVTRDTAAELPAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG
+YVVVRDGAAVAWIVPMGAGALGRHEGAEARAAGPDEAGQSAGVVPVFRVLGAHTDSPGFK
+LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ
+LAIHLDREVNEGLTLKRQRHTNPVVGALAPRGEGAGEAEADGLAARVPGDVLTALAAAAG
+VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLVALEELAREHGGAEGA
+IAYEGTVAGGVAGEAAGAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG
+QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA
+FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD
+VEHLAAAVREFFRGV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001756.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001756.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4d869fe0b4ca69851a0dd7a97a5eb553fb9b4f1f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001756.fa
@@ -0,0 +1,51 @@
+>NZ_CP042169.1_2239
+MRPAPAHAATPSEPPTHAADGAPSDAVTAPGAPAGRSADSAPSGTLPAPGERGGRFQLAG
+GLAANGPGRGTGSWAGPVALTGLLVALAAVVTVLQKSPCLLHGWGAPDVYYAGCYSDWAA
+LYGGRGFAADPWAPFRAGSTFEYPVLMSVVGSVAAWITQALPFSPEQGTVVFWLVNLGFV
+VVLWAVVAVLTVRMAGRRWTDGLMVAVAPGIVLAGTINWDLWAVALLACGMYAWSRGRSL
+TAGVLFGLGAAMKLYPLLILGPLLILAVRSRRWRPFLLAAGGTVAAWAAVNVPLMAVNFQ
+AWSVFFTFSGERGPGLSSVWHAWDVTAAQAGWAFVPEDSLTLLAYGTFAVCCLGIFVLGV
+RVRHTPRLAQLTFLVVAAFVLTNKVYSPQFVVWLIPLLALALPRWRDFWVWQTVEALHFF
+AVWMYLAKGVAETPPQHSMDDSVYVAAILAHILAVLWLCGRVVWEMLHPAEDLVKRDHGG
+HPDADPLAGAYAGPARGRSGRPAAVQA*
+>NZ_CP033200.1_1944
+MRPAPAHAATPSEPPTHAADGAPCDAVADPGAPAGRSADSAPSGALPAPGERGGRFQLAG
+GLAANGPGRGTGSWAGPVALTGLLVALAAVVTVLQKSPCLLHGWGAPDVYYAGCYSDWAA
+LYGGRGFAADPWAPFRAGSTFEYPVLMSVVGSVAAWITQALPFSPEQGTVVFWLVNLGFV
+VVLWAVVAVLTVRMAGRRWTDGLMVAVAPGIVLAGTINWDLWAVALLACGMYAWSRGRSL
+TAGVLFGLGAAMKLYPLLILGPLLILAVRSRRWRPFLLAAGGTVAAWAAVNVPLMAVNFQ
+AWSVFFTFSGERGPGLSSVWHAWDVTAAQAGWAFVPEDSLTLLAYGTFAVCCLGIFVLGV
+RVRHTPRLAQLTFLVVAAFVLTNKVYSPQFVVWLIPLLALALPRWRDFWVWQTVEALHFF
+AVWMYLAKGVAETPPQHSMDDSVYVAAILAHMLAVLWLCGRVVWEMLHPAEDLVKRDHGG
+HPDADPLAGAYAGPARGRSGRPAAVQA*
+>NZ_CP040019.1_425
+MRPAPAHAATPSEPPTHAVDGPSWAGPDGRAEAGGSAVSAPPSRGPAAVPAPVPAPGDRG
+GRFQLPGGLAANRFTLGGRGGTGSWASPAALAGVLVALAAVVTVLQKAPCLLHGWGAPNV
+YYAGCYSDWAALYGGRGFAADPWAPFQAGSTFEYPVLMSLVGSVGAQLTQWLPFGAEHGT
+LVFWLVNLLFVVGLWAAVAVLTVRMAGRRWSDGLMVAVAPGVILAGTINWDLWAVALLAL
+GMYAWARERPLAAGVLIGLGAAMKIYPLLILGPLLILAVRSRRWRPFLLAAGGAVAAWAA
+VNVPLMVANFEAWSVFFTFSGERGPGLSSVWHAWDVTAAQAGWAFVPEDSLTLLAYGAFA
+VCCLGIFVLGVRVRHTPRLAQLTFLVVAAFVLTNKVYSPQFVIWLIPLVALALPRWRDFW
+AWQTVEALHFFAVWMYLAKGASGSMPQHSMDDSVYVAAILAHMLAVLWLCGRVVWEMLHP
+EDDLVRRDHTDLPGGDPLAGAYRSAQA*
+>NZ_CP083691.1_378
+MSSSPAPGAAPDDPPAPAPQARPDVPVGAHRAPRHALTTPPPGSAEGAPSAGSGAVESDE
+ATPEGEVDPRVVPAPGDRGGRFAIPGGLAANGRGRGTGAWAGPVALTALLVALGAIATVL
+QKSPCLLHGWGAPNVYYAGCYSDWAALYGGRGFAADPWAPFQAGSTFEYPVLMSLVASVG
+AQLTQWLPFPASVGTVVFWCVNLLFVVGLWAATAVLTVRTAGRRWTDGLMVAVAPGIILA
+GTVNWDLWAVALMAWGMWVWLRGRPGWAGVLFGLGAATKLYPLLILGPLLILAVRSRRFG
+PFLKATGGAVAAWLAVNLPLMLTHFESWKVFFTFSAERGPGLSSVWHAWDVVAAQAGWAA
+VPDERLGMYAYGAFAVCCLGIFVLGVVAKRPPRLAQLTFLVVAAFVLTNKVYSPQFVIWL
+IPLMALALPRWKDFWVWQTVEALHFFAVWMYLAKGASGSMPQHSMDDSVYVAAILAHMLA
+VLWLCARVVLEILDPDDDLVRGPGGDPARDPEDPSAGPADPGMTGVRPVREAVAAGVGAA
+SAQA*
+>NZ_CP097650.1_2182
+MRPAPAHAATPSEPPTHAADGAPCDAVADPGAPAGRSADSAPSGTLPAPGERGGRFQLAG
+GLAANGPGRGTGSWAGPAALTGLLVALAAVVTVLQKSPCLLHGWGAPDVYYAGCYSDWAA
+LYGGRGFAADPWAPFRAGSTFEYPVLMSVVGSVAAWITQALPFSPEQGTVVFWLVNLGFV
+VVLWAVVAVLTVRMAGRRWTDGLMVAVAPGIVLAGTINWDLWAVALLACGMYAWSRGRSL
+TAGMLFGLGAAMKLYPLLILGPLLILAVRSRRWRPFLLAAGGTVAAWAAVNVPLMAVNFQ
+AWSVFFTFSGERGPGLSSVWHAWDVTAAQAGWAFVPEDSLTLLAYGTFAVCCLGIFVLGV
+RVRHTPRLAQLTFLVVAAFVLTNKVYSPQFVVWLIPLLALALPRWRDFWVWQTVEALHFF
+AVWMYLAKGVAETPPQHSMDDSVYVAAILAHMLAVLWLCGRVVWEMLHPAEDLVKRDHGG
+HPDTDPLAGAYAGPARGRSGRPAAVQA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001757.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001757.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a6bb17e6560066e90045315320e34c071ae75168
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001757.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_2240
+MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGDYHVSDLEFVAAFDV
+DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESDVEPVDV
+AQALRDAKVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG
+VPIVGDDIKSQIGATITHRVMAKLFQDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE
+R*
+>NZ_CP033200.1_1945
+MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGVYHVSDLEFVAAFDV
+DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESEAEPVDV
+AQALRDAEVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG
+VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE
+R*
+>NZ_CP040019.1_424
+MATTPIRVAIAGVGNCATSLIQGVEYYRDAKATDTVPGLMHVQFGDYHVSDLQFVAAFDV
+DAKKVGLDLSEAILASENNTIKLADVPHADVTVQRGPTLDGLGKYYAETIEESDAEPVDV
+AQALRDAQVDVLVCYLPVGSQLATEHYAQTAIDAGVAFVNALPVFIAGTPEWADKFTAAG
+VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAKLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGTGGPILSASSYFMKSPPVQHNDDEARELVEAFIRGDIE
+R*
+>NZ_CP083691.1_377
+MAENPIRVAIAGVGNCATSLIQGVEYYKDAQASDTVPGLMHVQFGDYHVSDLEFVAAFDV
+DAKKVGLDLSEAILASENNTIKISDVPATGVTVQRGPTLDGLGKYYRETIEESSAEPVDV
+VQALKDAKVDVLVSYLPVGSEEADKFYAQCAIDAKVAFVNALPVFIAGTQEWADKFTEAG
+VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAELAEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHADDEAHELVEAFIRGDIE
+R*
+>NZ_CP097650.1_2183
+MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGDYHVSDLEFVAAFDV
+DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESEAEPVDV
+AQALRDAKVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG
+VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE
+R*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001760.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001760.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a61d13c75c57696d4d69565a7d73b275e9c854be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001760.fa
@@ -0,0 +1,61 @@
+>NZ_CP042169.1_2246
+MPQPIAVGAVLGGRYRITQHVVTSADQDMVFLGTDQVLNRRVTVLVASRENATQVASSAR
+ELATGERTDDVQVLDLGLSEGRTYLIAGGDPDPDVLLGLAYPQELYVEPFQTDSLGSELF
+GESRTGDPHAYDDDEAYYTDLDRRLRADEDEAQRRPGFLNRLSERLAERVRPSDGTAAKA
+AAGASALAAADAATRKQQEERERAEREAAERAERERKEAAERAERERKEAAERAERERKE
+AEEKARAEREAAERAERERKEAAERAERERREAEERAEEERRAEAERARRQAEQEAEERA
+AREREAEQARLAAEREEAERRELERRAEARRRAEEERAREAAEREAEKRAAQEREAAERE
+AQAGTAALPAVAAGAAAAQAPDADADGATPPTEPVESVAAEKTDPPEPVAPDTEAIPVRR
+QRPVPRRAIVAESAPTAHEESRGTAAPVAAGAGVATAAGAAAAGSTAAAAAPDAQAAPAT
+TGGGDGATVADPGDGHGRTRGGGPLALLLVLGLLAALVVGGVLLAQNLRGGPAPQAASSE
+SESASSESASDTPSPSESTSPSPTPSSESAAAAPQPVQALRSVPDLPEHEAEHDADLSNL
+IDGDPTTVWRTFAYARPNFGGYVESMNLVVQLEERTEVNEVTLQSTGATGGAWFAYIADS
+PEGANAKEIGNGTFDQDTVSIPVPFEGTEAEAEYVIVSLTSLPQLEGTTSDLPFGLRLGE
+IAVR*
+>NZ_CP033200.1_1951
+MPQPIAVGAVLGGRYRITQHVVTSADQDMVFLGTDQVLNRRVTVLVASRENATQVASSAR
+ELATGERNDDVQVLDLGLSEGRTYLIAGGDPDPDVLLGLAYPQELYVEPFQTDSLGSELF
+GESRTGDPHAYDDDEAYYTDLDRRLRADEDEAQRRPGFLNRLSERLAERVRPSDGTAAKA
+AAGASALAAADAATRKQQEERERAEREAAERAERERKEAEEKARAEREAAERAERERKEA
+AERAERERREAEERAEEERRAEAERARRQAEQEAEERAAREREAEQARLAAEREEAERRE
+LERRAEARRRAEEERAREAERREAEKREAQEREAAEREAQEREAAEREAQAGTAALPAVA
+AGAAAAQATDADADGATPPTEPVEPVESVAAEKTDPPEPVAPDTEAIPVRRQRPVPRRAI
+VAESAPPVHEESRSTAAPVAAGTATGATAAAAGSTSAAAAPDALAAPATTGGDDGATVAD
+PGDGNGRTRGGGPLALLLVLGLLAALVVGGVLLAQNLRGGPAPQAAAASSESASSESASD
+TPSPSESTSPSPTPTSESAAAAPQPVQALRSVPDLPEHEAEHDADLSNLIDGDPTTVWRT
+FAYARPNFGGYVESMNLVVQLEERTEVNEVTLQSTGATGGAWFAYIADSPEGANAKEIGN
+GTFDQDTVSIPVPFEGTEAEAEYVIVSLTSLPQLEGTTSDLPFGLRLGEIAVR*
+>NZ_CP040019.1_419
+MAPGAAETDTVETRADEPAAAEPESTATAPAEDVDPEPTAPAPVVPASTAPDSAPDTEAI
+PVRRQRPVPRRAMVVEPTTPDADRSPDAQRSRGAGAPLAAAGAGAVAAAGATAASAAAAG
+AAPSATSAPSTASAAPEATAAGTSPADGDGGAPVDPDQGGSRRGGWPLALLLLAVLVGAL
+VLGGVLLAQNLRGAPHRAGRPARLPHRDRRGARTRRQPPPTQSDEASPTEASPTESSPAA
+STSASPTESETAAAAPQPARALRMVPDLPAHESEHDGELPNLIDGDPSTAWRTFAYARPN
+FGGYVESMNLVVELEDRAEVNEVTLQSTGATGGAWFAYIADSPEGENAREIGNGTFDQDS
+VTVPVPFDGAEAEAEYVIVSLTSLPRLDGTTPDLPFGLRLGEIGVR*
+>NZ_CP083691.1_371
+MPQPLAVGSVLGGRYRITDHVVTSADQNMVFQGADQVLNRRVTVLVASPENATQVAASAR
+ELATGERQDDVQVLDLGLSEGRTYLIAGGNPDPDVLLGLAYAQELYVEPFQTDSLGSEIF
+GESRTEQAHEYDDDDAYYADLDRRLRADQKQSQRRPGFLNRISEKLNERVRPADGTAAKA
+AAGASALAAADAATKAQLAEQERAEREAREAQERAEREEAQEAERREREAQERAERERLE
+RAAAAQAEKDRAAREAAEAEAAARREREAQRHAEAETRRREEEAAAAAALAAAAPAADAD
+PADAPTQAVPVTEPASTPEAVPAPVRRPRPAPRRALPAVASAAAVAASVSAEEGASAAEA
+APAESVAPEAVPTATATSSAAIAVAEAEPAVTEHREEAHAAPVAGGAGAGAPAAGATAAP
+ARSTSGKGWLMVLGLLALLALAGLAGLFLLGQNTRSVEPAPSASASSAAPSTAQASSAPP
+AASSSAAPTASSSAAPSTEPAPSTSAAAPAPTAAPQAVAVTRQVPEMPELEAPNDATLAN
+LIDGDPNTAWQSYTYARPNFGGYVGSMNLVVQLQERTTISEVQLENRGATGGKWIAYVAN
+TAQGGEGDARVIGQGTFDEDSITIPVDIAENQGQYVILSITGLPQLEGAGQRPYGLQLTE
+IGVR*
+>NZ_CP097650.1_2189
+MPQPIAVGAVLGGRYRITQHVVTSADQDMVFLGTDQVLNRRVTVLVASRENATQVASSAR
+ELATGERTDDVQVLDLGLSEGRTYLIAGGDPDPDVLLGLAYPQELYVEPFQTDSLGSELF
+GESRTQDPHAYDDDEAYYTDLDRRLRADEDEAQRRPGFLNRLSERLAERVRPSDGTAAKA
+AAGASALAAADAATRKQQEERERAEREAAERAERERKEAEERARAEREAAERAERERKEA
+AERAERERREAEERAEEERRAEAERARRQAEQEAEDRAAREREAEQARLAAEREEAERRE
+LERRTEARRRAEEERAREAERREAEKRAAQEREAAEREAEKREAQAGTAALPAVAAGAAA
+AQTTDADADGATPPVEPVEPVEPVAAEKTDAPEPVAPDTEAIPVRRQRPVPRRAIVAESA
+PPVHEESRSTAAPVAAGAATGATAAAAGSTSAAAAPDALAAPATTEGDDGATVADPGDGN
+GRTRGGGPLALLLVLGLLAALVVGGVLLAQNLRGGPAPQAAAASSESESASSESASDTPS
+PSESTSPSPTPTSESAAAAPQPVQALRSVPDLPEHEAEHDADLSNLIDGDPTTVWRTFAY
+ARPNFGGYVESMNLVVQLEERTEVNEVTLQSTGATGGAWFAYIADSPEGANAQEIGNGTF
+DQDTVSIPVPFEGTEAEAEYVIVSLTSLPQLEGTTSDLPFGLRLGEIAVR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001763.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001763.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b110240dfaf7ebefd3b2f0f5b2848ad46a2975e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001763.fa
@@ -0,0 +1,29 @@
+>NZ_CP042169.1_2251
+MTERGSAYERRPGLDPQDRGDRPAPVGQPAPPLTDALRPAAVELFGEALPRAEAYVAHLA
+DTGIEWGLIGPREAPRLWERHVLNCAVVEELLPQGALVADVGSGAGLPGLCLALARPDCQ
+FLLIEPLERRVEWLDMVVADLGLENVDVIRGRAEQVSGNLDVDVVAARAVSALKTLVPLT
+MPMLQGAGELLAIKGRSAADEIAAARKVLRKYGGAEPEILTVGEGLLPETTTVVRVSARP
+R*
+>NZ_CP033200.1_1956
+MTEQGSAYERRPGLDPRDRGDRPAPVGQPAPPLTDALRPAAVELFGEALPRAEAYVAHLA
+DTGIEWGLIGPREAPRLWERHVLNCAVVEELLPQGALVADVGSGAGLPGLCLALARPDCQ
+FLLIEPLERRVEWLDMVVADLGLENVDVIRGRAEQVSGNLDVDVVTARAVSALKTLVPLT
+MPMLQGAGELLAIKGRSAADEIAAARKVLRKYGGAEPEILTVGEGLLPETTTVVRVSARP
+R*
+>NZ_CP040019.1_413
+MPEQASPYERRPGLDPKERGDRPAPVGQPAPPLIDALRPAAVELFGEDLPRAERYVAHLA
+DTGIEWGLIGPREAPRLWERHVLNCAVVEELIPEGALVADVGSGAGLPGLCLALARPDCR
+FLLIEPLERRVEWLDMVVEDLGLENVDVIRGRAEQVSGNLDVDVVTARAVSALKTLVPLT
+MPMLQGDGQLLAIKGRAAADEIAAARKVLRKYGGDEPEILTVGEGLLPETTTVVRVSARA
+R*
+>NZ_CP083691.1_366
+MSAPQLTAELRPAAEDLFGEALPLAERYVDHLATTGIEWGLLGPREVPRLWGRHVLNCAV
+VARLLPEGSLVADVGSGAGLPGLCLALARPDCRFTLIEPLERRVAWLEMVIADLGLTNVE
+VVRGRSEQVADEIQVDIVTARAVSALKTLLPLTMPLLRSSGHLLAIKGRSAAEEITAAQK
+PLRKYGGGDPEIVTVGEGLLPEPTTVVRVPARRAR*
+>NZ_CP097650.1_2194
+MTERGSAYERRPGLDPRDRGDRPAPVGQPAPPLTDALRPAAVELFGEALPRAEAYVAHLA
+DTGIEWGLIGPREAPRLWERHVLNCAVVEELLPQGALVADVGSGAGLPGLCLALARPDCQ
+FLLIEPLERRVEWLDMVVADLGLENVDVIRGRAEQVSGNLDVDVVTARAVSALKTLVPLT
+MPMLQGAGELLAIKGRSAADEIAAARKVLRKYGGAEPEILTVGEGLLPETTTVVRVSARP
+R*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001768.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001768.fa
new file mode 100644
index 0000000000000000000000000000000000000000..240f5e524d683eeb5c6f23c006edb9983fe1ec79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001768.fa
@@ -0,0 +1,12 @@
+>NZ_CP042169.1_2256
+MTKRTFQPNNRRRARKHGFRARMRTRAGRAILSARRGKNRAELSA*
+
+>NZ_CP033200.1_1961
+MTKRTFQPNNRRRARKHGFRARMRTRAGRAILSARRGKNRAELSA*
+>NZ_CP040019.1_408
+MTKRTFQPNNRRRARKHGFRARMRTRAGRAILAARRGKGRAELSA*
+>NZ_CP083691.1_361
+MTKRTFQPNNRRRARKHGFRARMRTRAGRAILSTRRGKGRAELSA*
+>NZ_CP097650.1_2199
+MTKRTFQPNNRRRARKHGFRARMRTRAGRAILSARRGKNRAELSA*
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001771.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001771.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b01c5ece525287f967627551817830f7228ed4a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001771.fa
@@ -0,0 +1,39 @@
+>NZ_CP033200.1_316
+MTAPHIVDPERLLREALGEASPDLLRHLLQTIINALLSADADAVCGAEYGTASESRTTQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMATELDEHIEAFRHRPLSDTGPFVFLAADALTMKVREGGRV
+INAVAMVATGVNADGRREVLGLRVATTESGAAWNEFFADLVARGLTGVKLVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFDRLLD
+YVQDRLPAVTAHLDAAREDILAFTGFPKDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+EAVIRLVGAVLAEQTDEWAEGRRYLGLELLARCSGLDADTTSTTILGTEVMPTLET*
+>NZ_CP033200.1_355
+MTAPHIVDPERLLREALGEASPDLLRHLLQTIINALLSADADAVCGAEYGTASESRTTQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMATELDEHIEAFRHRPLSDTGPFVFLAADALTMKVREGGRV
+INAVAMVATGVNADGRREVLGLRVATTESGAAWNEFFADLVARGLTGVKLVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFDRLLD
+YVQDRLPAVTAHLDAAREDILAFTGFPKDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+EAVIRLVGAVLAEQTDEWAEGRRYLGLELLARCSGLDADTTSTTILGTEVMPTLET*
+>NZ_CP033200.1_1077
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPLTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGTAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKLPAVAEHLGDARADILAFTTFPKDVWTQIWSNNPAERLNREIRCKRP*
+>NZ_CP033200.1_1923
+MTAPHIVDPERLLREALGEASPDLLRHLLQTIINALLSADADAVCGAEYGTASESRTTQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMATELDEHIEAFRHRPLSDTGPFVFLAADALTMKVREGGRV
+INAVAMVATGVNADGRREVLGLRVATTESGAAWNEFFADLVARGLTGVKLVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFDRLLD
+YVQDRLPAVTAHLDAAREDILAFTGFPKDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+EAVIRLVGAVLAEQTDEWAEGRRYLGLELLARCSGLDADTTSTTILGTEVMPTLET*
+>NZ_CP033200.1_1971
+MTAPHIVDPERLLREALGEASPDLLRHLLQTIINALLSADADAVCGAEYGTASESRTTQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMATELDEHIEAFRHRPLSDTGPFVFLAADALTMKVREGGRV
+INAVAMVATGVNADGRREVLGLRVATTESGAAWNEFFADLVARGLTGVKLVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFDRLLD
+YVQDRLPAVTAHLDAAREDILAFTGFPKDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+EAVIRLVGAVLAEQTDEWAEGRRYLGLELLARCSGLDADTTSTTILGTEVMPTLET*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001775.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001775.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a58127802176716eab565b88633ed9aafce84291
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001775.fa
@@ -0,0 +1,34 @@
+>NZ_CP033200.1_2086
+MSVNLPPSPGGGPTEHAVEHALAPVEAGATQATTEAAADTRGTSVWGAAFQRLRRNPAAI
+AGAVIVLLFVLVAVLAPVLAPYAGTATPGMREIRPTHVPGPGEVAGYPLGLDRFGGDVLS
+KLIWGAQASLLIGVVSTAFGLAGGMLLGLLAGTFGGWVDSVVMRVVDILLSVPNLLLAVS
+IAAILGQTPFAVMIAIGVAQVPVFARLLRSSMLTQKGSDYVLAAQTLGLSRGRITMSHVL
+PNSLGPVIVQATLTLATAVIDAAALSFLGLGGGRPETAEWGRMLTYAQAELGINPWLAFL
+PGLCIAITALGFTLLGESLREALDPTSRRR*
+>NZ_CP040019.1_81
+MTAVLTSSQTPPPPSDSSAAASPVSLVPATRRPRRADLGLAFALTGAAVLLVAALWPQLL
+ATHDPRALDLAAPLQAPSLDHWFGTDQNGRDLYSRIVHGTGPSLLIGLGAAAVGVGLGML
+LGIVAAFGGRWADAAVSRTVEVLFAFPSLLLALMLITVYGPSVSTLILAVGVGTAPGYAR
+LVRGQVLAVRGSAYVQAAEVIGHPPMTILLQHIVPNAVRPLVAVFMLGVGQAIVWASGLA
+FLGFGVAPPSPEWGALLEAGRPYITAAWWLEIFPGLAVLATALTATALGRHLEARLQGET
+R*
+>NZ_CP040019.1_254
+MSVNLPPSPGSGPAEHAVDHALAPVEAGATQETTEAAADARGTSVWGAAFQRLRRNPAAI
+AGAVIVALFVLVAVLAPVLAPYAGTDTPGMREIRPTHVPGPGEVDGYPLGLDRFGGDVLS
+KLIWGAQASLIIGVVSTAFGLVGGMLLGLLAGTFGGWVDSVVMRTVDILLSVPNLLLAVS
+IAAILGQTPFAVMIAIGVAQVPIFARLLRSSMLTQKGSDYVLAAQTLGLSRGRITMSHVL
+PNSLGPVIVQATLTLATAVIDAAALSFLGLGGGRPETAEWGRMLTYAQAELGINPWLAFL
+PGLCIAIAALGFTLLGESLREALDPTSRRR*
+>NZ_CP083691.1_127
+MTSAPAVAAEPTPAASATPSDPAGARRRARPRLGLLLSAGFLVVVLLAALFPSLLAPGDP
+FAGASGATLEPPGPGHWLGTDHLGRDLYTRVVHGTGLTVATAAAAVAGALVVGGTLGLAS
+GYVGGVADTLLMRVVDVLLSIPSLLLSLAVVAGLGFGPVQVAVAVGIGSVASFARIGRAQ
+ALRISQAPFVEAAPSFGTRRILVLLHHVVPNAVGPLVSLAVLEFGSALLAVSALSFLGYG
+EPRPAAEWGGLISDGRSYLAVAPWLTALPGLVIAATVLALQQVATSPAPADAPR*
+>NZ_CP097650.1_122
+MSVNLPPSPGGGPTEHAVEHALAPVEAGATQATTEAAADTRGTSVWGAAFQRLRRNPAAI
+AGAVIVLLFVLVAVLAPVLAPYAGTATPGMREIRPTHVPGPGEVAGYPLGLDRFGGDVLS
+KLIWGAQASLLIGVVSTAFGLAGGMLLGLLAGTFGGWVDSVVMRVVDILLSVPNLLLAVS
+IAAILGQTPFAVMIAIGVAQVPVFARLLRSSMLTQKGSDYVLAAQTLGLSRGRITMSHVL
+PNSLGPVIVQATLTLATAVIDAAALSFLGLGGGRPETAEWGRMLTYAQAELGINPWLAFL
+PGLCIAITALGFTLLGESLREALDPTSRRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001779.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001779.fa
new file mode 100644
index 0000000000000000000000000000000000000000..74f2ee99f75e176866df7b2c50723e46e2c47bc5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001779.fa
@@ -0,0 +1,35 @@
+>NZ_CP040019.1_502
+MKAWQFSGTGKPLELNEVPEPTPGPGEVVVDVKAAGICHSDVSAIDDAGWMPLFPELPHT
+MGHENAGVISAVGEGMDHWKVGDRVGLAPMNSKGEAIGYHTWEGGFGPKLRATDDNLVKL
+PDEVPFDLGAMATDAGLTAYHAVVAKGGVKKGMKVGIIGLGGLGYIGAKVAALMGAEVYG
+AEVNPKTRELKDEIGLTAVAESILEFKDVGLELVVDYAGFGTTTAEGITALKKDGVFVQV
+GMGKLEAPLNTYELITKTISVLGSNSGTKEDLAGIYELMQRGELNPPINRITQADIPDAI
+ETLRAGGVIGRYIAMYDDAK*
+>NZ_CP040019.1_795
+MHQAYAVYEGDTAIHEIEVETPEATGRSVLLKVLRSGVCHTDTHLREGGYDLGSRGTMSL
+TDRGVPYPLVMGHEVVGEVTAVGDEVQDVRVGQRMLVYPWIGCGECRMCREGRDNACAAG
+KNLGVARHGGYAETLWVPDAKYLVDIGDLDPSWTATLACSGITAYSAVDQVLPLDEEESV
+VVIGAGGLGLTAIALLSARGHRTVVAVDRSEKNLELARQMGASATVVSDDDVAAALKEAL
+GGGAAAVIDFVNNGATATLGFDSLAKAGQMVQVGLFGGEVTLPNALLSLKMIRISGSFVG
+TLQQMKDLVQIARTTDLPKIPIIERQLSAEQVAASLDDLTAGTVSGRVVLTA*
+>NZ_CP040019.1_929
+MTTMKAVRFTAYKTFPELKEIERPTPGPGEVLLKVAGAGACHSDVAVYDEFEAGMNPLVD
+PEYTLGHETSGWVEELGEGVTGFEVGSAQLVYGPVGCGHCPACSRGQDTYCQNVAEMDYA
+GIGLGRDGGMAEYVTVPARNLVPLGDADPVPASALADAGLTPYHAIKLALPRLNRAGTYA
+LVVGLGGLGLMAVQILKDLTGATVIATDMKPEAMAEAEKYGAVTVPSGEDQVARIREITG
+GRGVDAAFDFVGIAATARAALDSAAVQSRVTIVGIGNGSTIDWSFLSTPYEAELVTTYWG
+TVEELHELAGLYRDGKVEPLYTTYAMDGALQAYRDLQDGKISGRAVVVPHGQA*
+>NZ_CP040019.1_2341
+MKALYESGPHAGFEFTERPEPECGAHDVKIRVFTTGICGTDLHIEAYDAAAQAMIQAPMI
+PGHEFYGEVVEVGDLVEHVEVGHRVSGEGHVVCGMCRNCRAGRRQMCINTVSVGVQRDGA
+FAEYVVIPEANVWVHKGEHVTPELGAIFDPLGNAVHTALSFPLVGEDVLITGAGPIGLMA
+IPIARHAGARYIAITDVSAERLELARSMGADAAIDVSATRIREAQRELGLAEGFDVGLEM
+SGRASALQEMVANMNHGGKIALLGLPAEEIAIDWQTVVTHMLTIKGIYGREMFETWYAMA
+AMLQTNATLRERVESVVTDVIAAADWKRGFDAARAGATGKIVLDWRNL*
+>NZ_CP083691.1_868
+MVTMRAVRFEAYQQFPALKDVEKPVPGPGEALLKVAGAGACHSDVAVYSEFQPGMNPLID
+PEYTLGHETSGWVEELGDGVVGLEKGEAMLVYGPTGCGRCRACSRGQDTYCENVAAMAAA
+AVGLGRDGGMAEYVSVPARNLVPLGDADPIPASALADAGLTPYHAVKLALPTLGRPGACA
+LVVGLGGLGLMAVQIIKALTGATVIATDMKEDAMAQAEAYGAVTVPGGEGQVERIRELTG
+GRGVDAAFDFVGVAATARLALDCAAVQSRVTIVGLGNGSTIDWSFLSTPYEAELVSTYWG
+TLEELHEVARLYRDGRIEPLHTTYSLDDALQAYRDLQDGKVAGRAVVVPHGGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001785.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001785.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d953ff85baa6ec49358e4aefc0d87f643d9ca21d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001785.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_56
+MTDPHASHDPRREAARPSWYGSEAGAGSSGTGSSAAGWPDAPAGDADRAAWDRAPSYAEQ
+EGQTRPAYGQPYGYGQDANTVPAYGYGQGTPGHGFGAPLQPGQTEGIGRSVASMILGIIS
+VVGGFTFLLPPIVGVVLGHIGLKREPHGRGMAIAGLVMNYVSLALLLLAVVFLVILVIAG
+MSLGDYTST*
+>NZ_CP033200.1_2025
+MTDPHASHDPRREAARPSWYGSEAGAGSSGTGSSAAGWPDAPAGDADRAAWDRAPSYAEQ
+EGQTRPAYGQPYGYGQDANTVPAYGYGQGTPGHGFGAPLQPGQTDGVGRSVASMILGIIS
+VVGGFTFLLPPIVGVVLGHIGLKREPHGRGMAIAGLVMNYVSLALLLLAVVFLVILVIAG
+ISLGDYTST*
+>NZ_CP040019.1_323
+MTEPHPAHDPHRRADGGQPSWYGGGASGGGSSAASWPDGPAADADRAGWEQAPSYAEQQA
+APAYGGDAGHGQDGYAPAGYAPAPGHGRPAYGFGAPLAPGQTEGTGRSVASMILGIVSIV
+GGFTLVVPPIVGVILGHLGLKREPNGRGMAIAGLVMNYLSLAFVLLGVVLLTILVAAGMA
+ASEYSTY*
+>NZ_CP097650.1_51
+MTDPHASHDPRREAARPSWYGSEAGAGSSGTGSSAAGWPAAPTGDADRAAWDRAPSYAEQ
+EGQTRPAYDQPYGYGQDANTVPAYGYGQGTPGHGFGAPLQPGQTEGIGRSVASMILGIIS
+VVGGFTFLLPPIVGVVLGHIGLKREPHGRGMAIAGLVMNYVSLALLLLAVVFLVILVIAG
+ISLGDYTST*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001787.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001787.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac8fbe8a972573d3ce522a6c6ad7db59e0d0ec75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001787.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_80
+MRIMTVCLGNICRSPAAEAVLNRKLAEAGLHDVEVTSAGTSDEHVGARPHHLTREVGGEL
+GYEFPTVGVQLSADLVDEADLILVMDEANLADARRLATTDEQRDRIHLMGEFASDADSAG
+VREVPDPYGYPRPQFEEMYRQIEDAADGVVAAIRDGRL*
+>NZ_CP033200.1_2049
+MRIMTVCLGNICRSPAAEAVLNRKLAEAGLDDVEVTSAGTSDEHVGARPHHLTREVGGEL
+GYEFPTVGVQLSADLVDDADLILVMDEANLADARRLATTDEQRDRIHLMGEFASDADRAG
+VREVPDPYGYPRPQFEEMYRQIEDAADGVVAAIRDGRL*
+>NZ_CP040019.1_296
+MTVCLGNICRSPAAEAVLHRKLAEAGLADEVTVTSAGTADYHVGDRPHELTRAVGGELGY
+AFESVGVHLAAGHLDEADLVLVMDESNLADVRALAATDEQRAKVRMMGEFASDADTAGVL
+EVPDPYGHPRAQFEDMYRQLEDAADGVVAAIRDGRL*
+>NZ_CP097650.1_74
+MGVQLSAELVDDADLILVMDEANLADTRRLATTDEQRDRIHLMGEFASDADSAGVREVPD
+PYGYPRPQFEEMYRQIEDAADGVVAAIRDGRL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001792.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001792.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02191edf39089208798706826aaf91a6bb2c206f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001792.fa
@@ -0,0 +1,34 @@
+>NZ_CP042169.1_146
+MGWGDGLSGLLAFITQMALVLMLGHILANTGPVRRLLARLASIPRTPLAAYIFVFVVAAA
+ASLITWGLGLVVGALLAKEVAAQARERGLVLHFPMLVAAGFSGFVVWHMGYSGSGPLTAA
+TPGSFLTESLDGRTVPVSETTFSWWNITAAVVTVLVVALALFLVAPRAGDRIVELEIDAR
+DQDAVPAPEIETPADRLDASRVPTLLVGAMLVVYLVMHFVGGGTLTLDIVNWSFLALILL
+LVRSPHELIGLTQSAASNVGEILLQFPLYAGILGMMTTTGLVAVLSDAFVAISNPVTFGL
+LAFLAAGLVNFFVPSGGGQFAVQGPIMLQAGDALGVDPAITIMAVSYGDQWTNMIQPFWA
+IPLLAIAGLKMRDILGYTTVVLLASGLVFGGTLLLVSL*
+>NZ_CP033200.1_2116
+MGWGDGLSGLLAFITQMALVLMLGHILANTGPVRRLLARLASIPRTPLAAYIFVFVVAAA
+ASLITWGLGLVVGALLAKEVAAQARERGLVLHFPMLVAAGFSGFVVWHMGYSGSGPLTAA
+TPGSFLTESLGGRTVPVSETTFSWWNITAAVVTVLVVALALFLVAPRAGDRIVELEIDAR
+DQDAVSAPEIETPADRLDASRVPTLLVGAMLVIYLVMHFVGGGTLTLDIVNWSFLALILL
+LVRSPHELIGLTQSAASNVGEILLQFPLYAGILGMMTSTGLVAVLSDAFVAISNPVTFGL
+LAFLAAGLVNFFVPSGGGQFAVQGPIMLQAGDALGVDPAITIMAVSYGDQWTNMIQPFWA
+IPLLAIAGLKMRDILGYTTVVLLASGLVFGGTLLLVSL*
+>NZ_CP040019.1_221
+MPAPPPPAASPPHADGRATSDGNAFSRAMRPVNTVMERFIPSSLMFSILLTAIVAVLALI
+LTPTAPVDVLMGWGNGLSGLLAFMTQMALILLLGHILANTGPVRALLTALARVPRSAVQA
+YSFVFVVAALASLVTWGLGLVVGGLLAREVAAQGRERGLRLHFPLLVAAGFSGFVVWHMG
+YSASGPLTAATPGSFLEDSLGGRTVPISDTVFTWWNLTAAAVAIVAVTLVLYLIAPRGDD
+RIHELDVDARERAVVTEPELETPADRLDASRIPTLLVGLALAAFLVVHFVQGGTLTLDIV
+NWSFLALIFLLVRSAQELIQLTAHAASNVGEILLQFPLYAGILGMMTASGLIQIFSDALV
+AVANPTTFGLLAFLAAGLVNFFVPSGGGQFAVQGPIMLSAGAELGVDPAITIMAVSYGDQ
+WTNMIQPFWALPLLAIAGLRMRDILGYTTVVLLVTGVVFAGTMLLVSL*
+>NZ_CP097650.1_154
+MSATSTRPPTPRPPGRAAREGTFFSRAMRPLNTTMERFIPSSLVFTIVLTFAVAALCLLL
+TPAGPADVVVGWGDGLSGLLAFITQMALVLMLGHILANTGPVRRLLARLASIPRTPLAAY
+IFVFVVAAAASLITWGLGLVVGALLAKEVAAQARECGLVLHFPMLVAAGFSGFVVWHMGY
+SGSGPLTVATPGSFLTESLDGRTVPVSETTFSWWNITAAVVTVLVVALALFLVAPRAGDR
+IVELEIDARDQDAVSAPEIETPADRLDASRVPTLLVGAMLVVYLVMHFVGGGTLTLDIVN
+WSFLALILLLVRSPHELIGLTQSAASNVGEILLQFPLYAGILGMMTTTGLVAVLSDAFVA
+ISNPVTFGLLAFLAAGLVNFFVPSGGGQFAVQGPIMLQAGDALGVDPAITIMAVSYGDQW
+TNMIQPFWAIPLLAIAGLKMRDILGYTTVVLLASGLVFGGTLLLVSL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001795.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001795.fa
new file mode 100644
index 0000000000000000000000000000000000000000..595de0b6add64dcad9e049a3116308b519e1904c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001795.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_192
+MARPQTVLTVVAARRLTPHLVRLTLGGEQFDAVHARWAEKGATDQYVKLLFADPALGLEP
+PYDLDALRERLAPEQLPVRRTYTVRHMDAAARTMDVDFVVHGASDGGAAPGHDGGLAGAW
+AASEPVGQQVAFLGPGGAYRPDPTADWHLLAGDEAALPAIAAALEDLAATDAAAAGVALI
+EVTDAGDEVPLTAPAGVEVRWLHRGGPFTPETTRFAAAVEGAAWRDGRVHAFVHGEREQV
+KRVRAYLTDVRGVDRRQLSVSAYWAYGRAEDVFQAEKQTPVGQIFEDGATGG*
+>NZ_CP033200.1_2144
+MARPQTVLTVVAAHRLTPHLVRLTLGGEQFDAVHARWAEKGATDQYVKLLFADPALGLEP
+PYDLDALRERLAPEQLPVRRTYTVRRMDAAARTMDVDFVVHGASDDGAAPGRDGGLAGAW
+AASEPVGQQVAFLGPGGAYRPDPTADWHLLAGDEAALPAIAAALEDLAATDAAAVGVALI
+EVTDARDEVPLTAPAGVEVRWLHRGDPFTPETTRFAAAVEDAAWREGRVHAFVHGEREQV
+KRVRAYLTDVRGVDRRQLSVSAYWAYGRAEDVFQAEKQTPAGQIFEDGTTGG*
+>NZ_CP040019.1_185
+MTRPATPGRPARPQTVLTVVRTERLTPHMVRVSLGGDEFAAFHARWAEKGATDQYIKLLF
+ADPALGLTPPYDLDALRERLAPEQMPVRRTYSVRAVDVAAGTVDVDFVVHGDDGLAGPWA
+ASVQPGEQVCFGGPGGNYRPDPAADWHLFAGDEAALPAIAAGLEDLATTAPDAVGTALIE
+VEGPEDEQPVTAPAGVEVRWLHRGAEFTPQSTRWAAALREEPWREGRVHAFVHGEREQVK
+AARAYLADERGVDRRDLSVSAYWAFGRAEETFQAEKQTPLGQIFPDGTTGG*
+>NZ_CP097650.1_195
+MARPQTVLTVVAARRLTPHLVRLTLGGEQFDAVHARWAEKGATDQYVKLLFADPALGLEP
+PYDLDALRERLAPEQLPVRRTYTVRHMDAAARTMDVDFVVHGASDGGAAPGHDGGLAGAW
+AASEPVGQQVAFLGPGGAYRPDPTADWHLLAGDEAALPAIAAALEDLAATDAAAAGVALI
+EVTDAGDEVPLTAPAGVEVRWLHRGGPFTPETTRFAAAVEGAAWRDGRVHAFVHGEREQV
+KRVRAYLTDVRGVDRRQLSVSAYWAYGRAEDVFQAEKQTPVGQIFEDGATGG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001798.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001798.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6acbe53536fd2019b0de0405eb25766e3344d1d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001798.fa
@@ -0,0 +1,18 @@
+>NZ_CP042169.1_210
+MTANHSRHTAAADGQGAAAEHAGTGTATTDPRRDTRSRWGCSSRLGGGTGRLMGVSLAVG
+VVGALGLGSAAWATTVAAGHADSLAWIAAGAMALNGLLFGLLLTWLALVDRHSIRGADTN
+PEESIEGRWYEKATSGAFHDTLVVVGLGAAILSFGGYVISPAAVGAALFVLMGCAAAIRY
+QIQKRRG*
+>NZ_CP033200.1_2159
+MATTPHTTTDLARDRRPRWGRSARLGGGSGRLILVSLVAGVVIALLIGAASYGLASSQGD
+AGPRFPAVTGAVMAASALPVGAALAWLFLVDRTTLRGAVRDTEETIEGRWLEKAQSGAFG
+DLLVVLGLGTFVVALAGWQPSLPLVGAGLLLFAGASVAVRYALQKRRG*
+>NZ_CP040019.1_159
+MNTTADPRSRSASGPERAASTSAAATPAGSAAPSAWGRSARLGGGTGRLVVVSLVFGVLL
+AAMLGVIAYGLAGTADPADPRRPWVLGLVVASGALPVLAGTVWMLLVDRATIKGAVRDPE
+ESIESRWYDAAAGGAFHDLLVVLGLGTFVVSMTGWTAELSLVGAGLVLFMMADVAIRYRV
+QKRRG*
+>NZ_CP097650.1_210
+MATTPHTTTDLARDRRPRWGRSARLGGGSGRLILVSLVAGVVIALLIGAASYGLASSQGD
+AGPRFPAVTGAVMAASALPVGAALAWLFLVDRTTLRGAVRDTEETIEGRWLEKAQSGAFG
+DLLVVLGLGTFVVALAGWQPSLPLVGAGLLLFAGASVAVRYALQKRRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001801.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001801.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f36eeeb51b731cc5d2d9ac31d39a39c3e220354
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001801.fa
@@ -0,0 +1,31 @@
+>NZ_CP042169.1_235
+MDVLAEAGELGLGGIYVGEEHGGTGLARTDAILIFEELAKADPAFAAYISIHNMVAWMID
+SFGSDEQRARWIPDLVGMEHLASYCLTEPGAGSDAAALKTRAVRDGDHYVLNGVKQFISG
+AGSSGYYVVMCRTADTGARGISAVVVHKDTPGLSFGPSEKKMGWHTQPTRQVIFEDVRVP
+VADRLGEEGDGFRIAMKGLNGGRLNIGACSIGGGLAALDKATRYLKERSAFGEPLTTKQA
+LVFELADMSVKLETAHTMLMRAADALDRNDPDTVRLCAMAKLVATESGYEAADTALQLHG
+GYGYLHEYGVEKLVRDLRVHRILEGSNEIMRMIVGRGLIG*
+>NZ_CP033200.1_2203
+MFPITDDQKALVDAVRDFAEQRVAPHALDWDAEKHFPVDVLAEAGELGLGGIYVGEEHGG
+TGLERTDAILIFEELAKADPAFAAYISIHNMVAWMIDSFGSDEQRARWIPDLAGMEYLAS
+YCLTEPGAGSDAAALKTRAVRDGDHYVLNGVKQFISGAGASDCYVVMCRTADTGARGISA
+VVVHKDTPGLSFGPNEKKMGWHTQPTRQVIFEDVRVPVADRLGEEGDGFRIAMKGLNGGR
+LNISACSIGGGLAALDKATRYLKERSAFGEPLTTKQALVFELAEMAVKLETAHTMLMRAA
+DALDRNDPDTVRLCAMAKLVATEHGYEAADTALQLHGGYGYLHEYGVEKLVRDLRVHRIL
+EGSNEIMRMIVGRGLIG*
+>NZ_CP040019.1_119
+MFPITDDQEALVDAVRDFAQQRVAPHALEWDAEKHFPVDVLAEAGELGLGGIYVGEEHGG
+TGLERKDAILIFEELSKADPAFAAYISIHNMVAWMIDSYGNDEQRAQWIPELMSMEHLAS
+YCLTEPGAGSDAAALKTRAVRDGDDYVLNGVKQFISGAGSSDYYVVMCRTADTGAKGISA
+VVVHKDTPGLSFGPNEKKMGWHTQPTRQVIFEDVRVPVANRLGEEGDGFRIAMKGLNGGR
+LNIGACSIGGGLAALDKATRYLKERSAFGEPLTTKQALVFELADMAVKLETAHTLLMRAA
+DALDRNDPDTVRLCAMAKLVATESGYEAADAALQLHGGYGYLHEYGVEKLVRDLRVHRIL
+EGSNEIMRMIVGRGLIGG*
+>NZ_CP097650.1_235
+MFPITDDQKALVDAVRDFTEQRVAPHALDWDAEKHFPVDVLAEAGELGLGGIYVGEEHGG
+TGLERTDAILIFEELAKADPAFAAYISIHNMVAWMIDSFGSDEQRARWIPDLAGMEHLAS
+YCLTEPGAGSDAAALKTRAVRDGDHYVLNGVKQFISGAGASDCYVVMCRTADTGARGISA
+VVVHKDTPGLSFGPNEKKMGWHTQPTRQVIFEDVRVPVAGRLGEEGDGFRIAMKGLNGGR
+LNIGACSIGGGLAALDKATRYLKERSAFGEPLTTKQALVFELADMSVKLETAHTMLMRAA
+DALDRNDPDTVRLCAMAKLVATEHGYEAADTALQLHGGYGYLHEYGVEKLVRDLRVHRIL
+EGSNEIMRMIVGRGLIG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001803.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001803.fa
new file mode 100644
index 0000000000000000000000000000000000000000..febc3599ca608b0b3aeb62bef5e841105da3ef92
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001803.fa
@@ -0,0 +1,23 @@
+>NZ_CP042169.1_244
+MLNLCAPERTVRRNTHLALVLTAIAGILNSVGFVAVATYTSHMTGIVASMADAAVLHAPG
+LVGTGLLALAMFILGAVVCALVFNWGRVNGLRSRYANILLLEGVGMLVFGLLAEHVRDAH
+RPLVVVAVLCFTMGLQNALITRIGAWPIRTTHVTGMVTDIGVELGKILYRNGPGAAAPVV
+GEPRRVGLLALLVALFFLGGVAGAAGYLWLGFEVVIPVAGVLLLIAHRPLVQDLQDA*
+>NZ_CP033200.1_2212
+MLNLCAPERTVRRNTHLALVLTAIAGILNSVGFVAVATYTSHMTGIVASMADAAVLHAPG
+LVGTGLLALAMFILGAVVCALVFNWGRVNGLRSRYANILLLEGVGMLVFGLLAEHVRDAH
+RPLVVVAVLCFTMGLQNALITRIGAWPIRTTHVTGMVTDIGVELGKILYRNGPGAAAPVV
+GEPRRVGLLALLVALFFLGGVAGAAGYLWLGFEVVIPVAGVLLLIAHRPLIQDLQDAWLT
+RRPRRP*
+>NZ_CP040019.1_110
+MLNLCAPERTVRRNTHLALVLTAIAGILNSVGFVAVATYTSHMTGIVASMADATVLHAPG
+LVSTGLLALAMFILGAVVCALVFNWGRVNGLRSRYANILLLEGVGMLAFGLLAEHVRDAH
+RPLVVVAVLCFTMGLQNALITRIGAWPIRTTHVTGMVTDLGVELGKILYRNAPGTAAPVV
+GEPRRVGLLALLVALFFLGGVAGAAGYLWLGFEVVIPVAGVLLLIAHRPLIQDLRDAWLT
+RRPRRR*
+>NZ_CP097650.1_244
+MLNLCAPERTVRRNTHLALVLTAIAGILNSVGFVAVATYTSHMTGIVASMADAAVLHAPG
+LVGTGLLALAMFILGAVVCALVFNWGRVNGLRSRYANILLLEGVGMLVFGLLAEHVRDAH
+RPLVVVAVLCFTMGLQNALITRIGAWPIRTTHVTGMVTDIGVELGKILYRNGPGAAAPVV
+GEPRRVGLLALLVALFFLGGVAGAAGYLWLGFEVVIPVAGVLLLIAHRPLIQDLQDAWLT
+RKPRRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001810.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001810.fa
new file mode 100644
index 0000000000000000000000000000000000000000..61a93fde3476515302eacf20fcebf5343c1137b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001810.fa
@@ -0,0 +1,36 @@
+>NZ_CP042169.1_292
+MALALVLVGCAAPQGDEGTAAGSSGATDAAVSSPASVDGSEASSSQGRSSDAASSPAAAS
+SGEGSPSAAADPAGPAVPLAARSHEGVPMRAFTAEERPPQFVLFSFDGGRQDARWKTFLD
+AAADSDAKFTVFQSAINLIETANRENYTAPGNTPGYVGTEFGGDEAEVAQRIENINTAHA
+AGHEIGTHYAGHLCALATYGGDKWSTAEWEQEYGSFRDILSDPAAYNPGSSLPALEVTPE
+DVKGGRLPCLDGQWDQLVPMWKDNGLEYDTSRAAAASGVAWPYQEDGIWEFEMPMTWSPV
+LAEKGAASPFVMAMDYNFWISGNGGRDIPEDVARLTDFQYRTYRYMYDSALAGNRAPLVF
+GNHFNDWGLNAFNPAVEKVMREVCVEEDTYCVTYQQMIAWLELQDPEVLAAWRDQARSAT
+GTDAEALGW*
+>NZ_CP033200.1_9
+MSFPRRSARTVDTPSPRRRRWWGTSVALALVLAGCAAPQGDEGTAAGSSGATDAAVSSPA
+SANGSEASSSQGRSSDAASSGEGSPSAAADPAVPLAARSHEDVPMRAFTAEERPPQFVLF
+SFDGGRQDARWKTFLDAAADSDAKFTVFQSAINLIETANRENYTAPGNEPGYVGTEFGGD
+EAEVAQRIENINTAHAAGHEIGTHYAGHLCAPTRYGADQWSTAEWKQEYGSFTDILSDPG
+AYNPGSSLPALEVTPDDVKGGRLPCLDGEWDQLVPMWKDNGLEYDTSRAAAASGVAWPYQ
+EDGIWEFEMPMTWSPVLAEKDAASPFVMAMDYNFWISGNGGKDIPEDVARLTDFQYRTYR
+YMYDSAFAGNRAPLVFGNHFNDWGLNAFNPAVEKVMREVCVEEDTYCVTYQQMIAWLELQ
+DPEVLAAWRDQARSATGTDAEALGW*
+>NZ_CP040019.1_46
+MPLHRQPAPFRARRVWGTSVALALVLAGCAAPQEGDAQGAASETSSSSAPAPSASAPSDA
+GPASPSGSTGTDASETAAAPSSSASGDSAGPTASADPATPLAARSHEGVPMRAYAADERP
+PQFVLFSFDGGRQDARWKTFMDAAEDSGAKFTVYQTGINLIESANRENYAAPGNEPGYVG
+TELGGDAAEVAQRIGNINAAHAAGHEIGTHYNGHLCSPTPHGGDKWTTAEWEQEYSTFEE
+IITDPGAFNPGSALPALDITPEDIKGGRPPCLDGQWDQLVPMWKEHGLVYDTSRSASATG
+VAWPYQEDGIWQFEMPIVWSPVLAEQGKPSPLVMAMDYNFWISGNGGKDDPADTARLTAF
+QHRTYRYMFSSAHAGNRAPLVFGNHFNDWGLNAFNPAVEQTMREVCDEPDTYCVTYQQMV
+DWLELQDPAVLEAWRAQPRSATGDDAAALG*
+>NZ_CP097650.1_299
+MSFPRPSARTVDTPSPRRRRWWGTSVALALVLAGCAAPQGDEGTAAGSSGATDAAVSSPA
+SADGSEASSSQGRSSDAASSQAASSFGEGSPSAAADPADPALPLAARSHEGVPMRAFTAE
+ERPPQFVLFSFDGGRQDARWKTFLDAAADSDAKFTVFQSAINLIETANRENYTAPGNEPG
+YVGTEFGGDEAEVAQRIENINTAHAAGHEIGTHYAGHLCAPTRYGADQWSTAEWKQEYGS
+FTDILSDPGAYNPGSSLPALEVTPDDVKGGRLPCLDGEWDQLVPMWKDNGLEYDTSRAAA
+ASGVAWPYQEDGIWEFEMPMTWSPVLAEKDAASPFVMAMDYNFWISGNGGKDIPEDVSRL
+TDFQYRTYRYMYDSAFVGNRAPLVFGNHFNDWGLNAFNPAVEKVMREVCVEEDTYCVTYQ
+QMIAWLELQDPEVLAAWRDQARSATGTDAEALSW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001812.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001812.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d442e519911ecfeaae4d0b207f93f4d530674e33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001812.fa
@@ -0,0 +1,28 @@
+>NZ_CP042169.1_315
+MLTAVELGLIYAVVALGVYLTFRILDFPDLTVDGSFTTGAATAAVLITGGTPVPLAMLAA
+FVAGALAGLVTGLLHTKGRIDGLLAGILTMIALYSINLRIMGKANIPLLGQDTLFTWLDD
+LGLARNWGSILVLFLGVFVVKLILDWFLHTDLGLALQATGDNEEMIRSYGVSTDRMKILG
+LMISNGLVALGGSLLAMYQGFADISMGIGLILVGLASVIVGQAVFGQRTVFWATLAVIVG
+AVLYRLIIQFALNAGLSPNDMKLISAALVVVALLLPRFGFAKRLSLRTRGTAATPGPAAA
+APATAGMPLTGEPGGAAPAASVPEEAPRA*
+>NZ_CP033200.1_40
+MLTAVELGLIYAVVALGVYLTFRILDFPDLTVDGSFTTGAATAAVLITGGTPVPLAMLAA
+FVAGALAGLVTGLLHTKGRIDGLLAGILTMIALYSINLRIMGKANIPLLGQDTLFTWLDD
+LGLARNWGSILVLFLGVFVVKLILDWFLHTDLGLALQATGDNEEMIRSYGVSTDRMKILG
+LMISNGLVALGGSLLAMYQGFADISMGIGLILVGLASVIVGQAVFGQRTVFWATLAVIVG
+AVLYRLIIQFALNAGLSPNDMKLISAALVVVALLLPRFGFAKRLSLRTRGTAATPGPAAA
+APATAGMPLTGEPGGAAPAASVPEEAPRA*
+>NZ_CP040019.1_4
+MLTAVELGLIYAVVALGVYLTFRILDFPDLTVDGSFTTGAATAAVLITGGTPVPLAMVAA
+FVAGTLAGLVTGLLHTKGKIDGLLAGILTMIALYSINLRIMDKANIPLLGQDTLFSWLGD
+MGLARNWGSVLVLFLGVFVLKMILDWFLHTDLGLSLQATGDNEEMIRSYGVSTDRMKILG
+LMISNGLVALGGSLLAMYQGFADISMGIGLILVGLASVIVGQAVFGQRTVFWATFAVIVG
+AVLYRLIIQAALNAGLSPNDMKLISAALVVLALLLPRFGLAKRLSLRSKSTAAPAQAETP
+ATATPAASAATAEEQTRA*
+>NZ_CP097650.1_322
+MLTAVELGLIYAVVALGVYLTFRILDFPDLTVDGSFTTGAATAAVLITGGTPVPLAMLAA
+FVAGALAGLVTGLLHTKGRIDGLLAGILTMIALYSINLRIMGKANIPLLGQDTLFTWLGD
+LGLARNWGSILVLFLGVFVVKLILDWFLHTDLGLALQATGDNEEMIRSYGVSTDRMKILG
+LMISNGLVALGGSLLAMYQGFADISMGIGLILVGLASVIVGQAVFGQRTVFWATLAVIVG
+AVLYRLIIQFALNAGLSPNDMKLISAALVVVALLLPRFGFARRLSLRTRGTAATPAPAAA
+APATAGMPLTGEPGGATPAASVSEEAPRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001813.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001813.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90955220622443a7738f32e6cb49e340cb6f16e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001813.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_316
+MLEISQVSKTFFPNTVNERRALQGIDLHLAEGDFVTVIGSNGAGKSTILNTIAGKLLPDT
+GTVAVGGKDVTRMPDHRRAASIGRVFQDPTAGTAPNLTIEENMALAWRRGHARGLSRGVS
+RARRAMFRDELTKLELGLENRLTAKVGLLSGGQRQALSLLMATFSGPKILLLDEHTAALD
+PSRAELVTRLTRQVVAEHRLTTLMVTHNMSQALEVGNRLIMMHDGRIILELDEQEKAGRT
+PADLLAEFAKIKGAVVDDKTMLS*
+>NZ_CP033200.1_41
+MLEISQVSKTFFPNTVNERRALQGIDLHLAEGDFVTVIGSNGAGKSTILNTIAGKLLPDT
+GTVAVGGKDVTRMPDHRRAASIGRVFQDPTAGTAPNLTIEENMALAWRRGHARGLSRGVS
+RARRAMFRDELTKLELGLENRLTAKVGLLSGGQRQALSLLMATFSGPKILLLDEHTAALD
+PSRAELVTRLTRQVVAEHRLTTLMVTHNMSQALEVGNRLIMMHDGRIILELDEQEKAGRT
+PADLLAEFGKIKGAVVDDKTMLS*
+>NZ_CP040019.1_3
+MLEISQVSKTFFPNTVNERRALQGIDLHLAEGDFVTVIGSNGAGKSTILNTIAGKLLPDT
+GTVKVSGKDVTRMADHRRAAWIGRVFQDPTAGTAPNLTIEENMALAWRRGHTRGLARGVS
+RSRRGLFREELTKLELGLEDRLTAKVGLLSGGQRQALSLLMATFSGPKILLLDEHTAALD
+PSRAELVTRLTQQVVAEHRLTTLMVTHNMSQALEVGNRLIMMHDGRIILELDEAQKAGRT
+PADLLAEFAKIKGAVVDDKTMLS*
+>NZ_CP097650.1_323
+MLEISQVSKTFFPNTVNERRALQGIDLHLAEGDFVTVIGSNGAGKSTILNTIAGKLLPDT
+GTVAVGGKDVTRMPDHRRAASIGRVFQDPTAGTAPNLTIEENMALAWRRGHARGLSRGVS
+RARRAMFRDELTKLELGLENRLTAKVGLLSGGQRQALSLLMATFSGPKILLLDEHTAALD
+PSRAELVTRLTRQVVAEHRLTTLMVTHNMSQALEVGNRLIMMHDGRIILELDEQEKAGRT
+PADLLAEFGKIKGAVVDDKTMLS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001819.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001819.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ada4994164362a4ccc276fc43b5db6a696561a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001819.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_455
+MTATPQTPAQPLQDDAPVVSVVMGSDSDWPVMSAAAEALRELDVPVEVGVVSAHRMPHEM
+VEFGARAHERGIRVIVAGAGGAAHLPGMLAAVTPLPVIGVPVKLKSLDGMDSLLSIVQMP
+AGVPVATVSIDGARNAGLLAARILASADTAEGDRLRAALAEHADELNAQARAKGARLRER
+MAADR*
+>NZ_CP033200.1_182
+MTATPQTPAQPLQDDAPVVSVVMGSDSDWPVMSAAAEALRELDVPVEVGVVSAHRMPHEM
+VEFGARAHERGIRVIVAGAGGAAHLPGMLAAVTPLPVIGVPVKLKSLDGMDSLLSIVQMP
+AGVPVATVSIDGARNAGLLAARILASADTAEGDRLRAALAEHADELNAQARAKGARLRER
+MAADR*
+>NZ_CP083691.1_2304
+MTAEQTTQPTSDAPCTRPLQEEAPVVSVVMGSDSDWPVMGQAVEALRELGVPVEVGVVSA
+HRMPHEMVDFGARAHERGIRVIVAGAGGAAHLPGMLAAVTPLPVIGVPVKLRSLDGLDSL
+LSIVQMPAGVPVATVSVDGARNAGLLAARILAAGTDDGAAHLRAALQDVAAGLNAQARAK
+GARLHERAADGA*
+>NZ_CP097650.1_455
+MTATPQTPAQPLQDDAPVVSVVMGSDSDWPVMSAAAEALRELDVPVEVGVVSAHRMPHEM
+VEFGARAHERGIRVIVAGAGGAAHLPGMLAAVTPLPVIGVPVKLKSLDGMDSLLSIVQMP
+AGVPVATVSIDGARNAGLLAARILASADTAEGDRLRAALAEHADELNAQARAKGARLRER
+MAADR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001821.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001821.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0448396b286d06b042726ddb0a095ed520c4e47c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001821.fa
@@ -0,0 +1,22 @@
+>NZ_CP042169.1_501
+MVSAAPSFAASLRKDPGINGWVLNTTTNHGGCRYSLEVNSAPTRGGATPDGAPWGLYLYD
+VSKDASYSGAKLVYWVRGTHTATQNPITWQAATGHSTKWSGPVRGAAQTKADGFKYTPYT
+WTYTGTINPADVKSDGRLYLETFHVKATNFSMSENGQCLPLDYWTYREIVVDPDGPTGPQ
+QPMTLSFERRNGPSGPYVPGAQGRMAVTPDAEATANLQQLSS*
+>NZ_CP040019.1_2380
+MSAHSASTTASGLGRRAVATGLAWSVPAVAMVSAAPSFAVSLRKDPGINGWVLNTTTRDR
+DGCLRSLEVNSAPSNPGTTPDGAPFGLYLYDVSPQGVYTNAKLVYWVRGNHVAQNKITWG
+TGAQHSAKWKGPETGAPQTKADGAVYTPYTWTYTGTIDPRNVKKDGRLYLENFHVYTNVF
+SQREPRGCVPLDYWTYREIVVDPDGPAGPEKSQTLHFERRNGDSGPYAPRAQGRSAATPD
+AEATAELQQLSS*
+>NZ_CP083691.1_2259
+MNARSAHTTASGPSRRAVATGLAWSVPAVAMVSAAPSFAISLRKDPGINGWVQVTPSGRA
+GCASGYSLDVTSAPAGGGRTPDGAPWGLYLYDFSSEGVYTNAKLVYWVRGDHVKQNPITW
+KAATGHSSKWEGPVTGSPQRKADGFTYTPYTWTYTGTINPANVKSDGRLYLENFHVTSST
+FSQLEGGRCVPLDYWAYREIVADPDGPNGPQSPRTLHFERRAGMSGAYVSGGQARMAASP
+DAEGTSQL*
+>NZ_CP097650.1_501
+MVSAAPSFAASLRKDPGINGWVLNTTTNHGGCRYSLEVNSAPTRGGATPDGAPWGLYLYD
+VSKDASYSGAKLVYWVRGTHTATQNPITWQAATGHSTKWSGPVRGAAQTKADGFKYTPYT
+WTYTGTINPANVRSDGRLYLETFHVQATNFSMSENGQCLPLDYWTYREIVVDPDGPTGPQ
+QPMTLSFERRNGPSGPYVPGAQGRMAVTPDAEATANLQQLSS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001823.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001823.fa
new file mode 100644
index 0000000000000000000000000000000000000000..716afbc2de634e457d7d520a3a029da5a6aa189a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001823.fa
@@ -0,0 +1,32 @@
+>NZ_CP042169.1_554
+MTAMPSPAASTRASRPAGPRPGVGHAVSVADLGASYGEGPVLEGVQFDLEPGELLAVLGP
+SGCGKTTLLRCLAGFERIESGRISLAGSVVALPRVHVPAHRRHVAVVPQDGALFPHLSVA
+ENVGFGLRRRRPGRMARIQECLELVDLAGHGERMPHELSGGQQQRVALARAMAPRPPLIL
+LDEPFGALDASLRSGLRRDVRQALKEDGATAVLVTHDQSEALSMADRAAVMRAGRLRQLG
+TPDEVYAHPADAWVAAFVGEASLLPLLDVTGPERDGGRRIGRTALGPVPLHGARAATAVP
+GDLVVVRPEHVRGTLDPTVDVDGVEAARVWTPATVVDVDYRGHDSVATVQLADGTRAQAR
+VEGALPPLDAACGVRLAGPCAVVAPGE*
+>NZ_CP033200.1_295
+MTAMPSPAASTRASRPAGPRPGVGHAVSVADLGASYGEGPVLEGVQFDLEPGELLAVLGP
+SGCGKTTLLRCLAGFERIESGRISLAGSVVALPRVHVPAHRRHVAVVPQDGALFPHLSVA
+ENVGFGLRRRRPGRMARIQECLELVDLAGHGERMPHELSGGQQQRVALARAMAPRPPLIL
+LDEPFGALDASLRSGLRRDVRQALKEDGATAVLVTHDQSEALSMADRAAVMRAGRLRQLG
+TPDEVYAHPADAWVAAFVGEASLLPLLDVTGPERDGGRRIGRTALGPVPLHGARAATAVP
+GDLVVVRPEHVRGTLDPTVDVDGVEAARVWTPATVVDVDYRGHDSVATVQLADGTRAQAR
+VEGALPPLDAACGVRLAGPCAVVAPGE*
+>NZ_CP040019.1_2311
+MTAMPSPAASTRASRPAGPRPGVGHAVSVADLGASYGEGPVLEGVQFDLEPGELLAVLGP
+SGCGKTTLLRCLAGFERIESGRISLAGSVVALPRVHVPAHRRHVAVVPQDGALFPHLSVA
+ENVGFGLRRRRPGRMARIQECLELVDLAGHGERMPHELSGGQQQRVALARAMAPRPPLIL
+LDEPFGALDASLRSGLRRDVRQALKEDGATAVLVTHDQSEALSMADRVAVMRAGRLRQLG
+TPDEVYAHPADAWVAAFVGEASLLPLLDVTGPERDGGRRIGRTALGPVPLHGARAATAVP
+GDLVVVRPEHVRGTLDPTVDVDGVEAARVWTPATVVDVDYRGHDSVATVQLADGTRAQAR
+VEGALPPLDAACGVRLAGPCAVVAPGE*
+>NZ_CP097650.1_555
+MTAMPSPAASTRASRPAGPRPGVGHAVSVADLGASYGEGPVLEGVQFDLEPGELLAVLGP
+SGCGKTTLLRCLAGFERIESGRISLAGSVVALPRVHVPAHRRHVAVVPQDGALFPHLSVA
+ENVGFGLRRRRPGRMARIQECLELVDLAGHGERMPHELSGGQQQRVALARAMAPRPPLIL
+LDEPFGALDASLRSGLRRDVRQALKEDGATAVLVTHDQSEALSMADRAAVMRAGRLRQLG
+TPDEVYAHPADAWVAAFVGEASLLPLLDVTGPERDGGRRIGRTALGAVPLHGARAATAVP
+GDLVVVRPEHVRGTLDPTVDVDGVEAARVWTPATVVDVDYRGHDSVATVQLADGTRAQAR
+VEGALPPLDAACGVRLAGPCAVVAPGE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001825.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001825.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6e78c60724c613d82f5816207f1db7513f44940
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001825.fa
@@ -0,0 +1,32 @@
+>NZ_CP042169.1_556
+MPQSRALSRGVRLSAVSATLLLALTACAGGTGGSGSDSASGAASGSASAAESDKKVTLYS
+GRSEDLVQPILDEFTDETGIEVEVRYDKTPAMAAQLIEEGEGSPADVFLSQDAGALGAVA
+KEGLFTPLAQETLDRVPETYRDDEGDWVGLTGRVRVLAYNEEKVPEADLPTSVDELTDPK
+WKGRVGVAPTNASFQTFVTALRLQKGEDEARTWLEDFAANDPQRREKNGEILADVDAGTL
+DTGLVNHYYLFELAREKGVAPEELGASLHFFPDGDLGSLVNVSGMGLVGEQEDGDAAALV
+EYLLSEDGQSYFAEETGEYPLVEGVEQPAGFPELSEVKAPDVDLNDLDDLQTTIQMIQEA
+GLL*
+>NZ_CP033200.1_297
+MPQSRALSRGVRLSAVSATLLLALTACAGGTGGSGSDSASGAASGSASAAESDKKVTLYS
+GRSEDLVQPILDEFTDETGIEVEVRYDKTPAMAAQLIEEGEGSPADVFLSQDAGALGAVA
+KEGLFTPLAQETLDRVPETYRDDEGDWVGLTGRVRVLAYNEEKVPEADLPTSVDELTDPK
+WKGRVGVAPTNASFQTFVTALRLQKGEDEARTWLEDFAANDPQRREKNGEILADVDAGTL
+DTGLVNHYYLFELAREKGVAPEELGASLHFFPDGDLGSLVNVSGMGLVGEQEDGDAAALV
+EYLLSEDGQSYFAEETGEYPLVEGVEQPAGFPELSEVKAPDVDLNDLDDLQTTIQMIQEA
+GLL*
+>NZ_CP040019.1_2309
+MPQSRALSRGVRLSAMSATLLLALTACAGGTGGSGSDSASGAASGSASAAESDKKVTLYS
+GRSEDLVQPILDEFTDETGIEVEVRYDKTPAMAAQLIEEGEGSPADVFLSQDAGALGAVA
+KEGLFTPLAQETLDRVPETYRDDEGDWVGLTGRVRVLAYNEEKVPEADLPTSVDELTDPK
+WKGRVGVAPTNASFQTFVTALRLQKGEDEARTWLEDFAANDPQRREKNGEILADVDAGTL
+DTGLVNHYYLVELAREKGVAPEELGASLHFFPDGDLGSLVNVSGMGLVGEQEDGDAAALV
+EYLLSEDGQSYFAEETGEYPLVEGVEPPAGFPELSEVKAPDVDLNDLDDLQTTIQMIQEA
+GLL*
+>NZ_CP097650.1_557
+MPQSRALSRGVRLSAVSATLLLALTACAGGTGGSGSDSASGAASGSASAAESDKKVTLYS
+GRSEDLVQPILDEFTDETGIEVEVRYDKTPAMAAQLIEEGEGSPADVFLSQDAGALGAVA
+KEGLFTPLAQETLDRVPETYRDDEGDWVGLTGRVRVLAYNEEKVPEADLPTSVDELTDPK
+WKGRVGVAPTNASFQTFVTALRLQKGEDEARTWLEDFAANDPQRREKNGEILADVDAGTL
+DTGLVNHYYLFELAREKGVAPEELGASLHFFPDGDLGSLVNVSGMGLVGEQEDGDAAALV
+EYLLSEDGQSYFAEETGEYPLVEGVEQPAGFPGLSEVKAPDVDLNDLDDLQTTIQMIQEA
+GLL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001829.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001829.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b7c250c9ff8c74074c0afb59f3ee434b65394df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001829.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_606
+MTSSLTTRRTFLGASVGALALAGLAACADPAISPQPSGRILPTDPLVAEYEKRRAASGTT
+VTHRLSAAPLETSLQGRGLTTWGYNDGLNGPLLRAQTGDLLKVSVANDLPEDTSVHWHGL
+ALRNDADGVQGVTQDPIAAGGRYTYGFRLSHPGTYWYHSHFDTQRERALYGALIVEDPNE
+PLSYDQEWVVILDDWLDGITGTPQDVVEELSAGMDMSGDMEGMAGMAGMDHGSMSQDSSS
+GMPMKHMLMGAESDYLGGDAGDVKIPVHLFNGRPPSDPDTFSSTPGNRIRLRLINAAGDT
+AYRVGIPGQELTITHTDGFPVQPRQADTVVLGMGERLDVLITLGDQAVPVLALPEGKTGH
+AYGIIAAGPKTTLSGRLPQTLGGTVLDGSRLKAHESVLLPPKDPTTTHEVRLTGSMMEYD
+WGINGRRFDPANPFEGAFELRLDERVRVTMTNDTDMWHPMHLHGHTFQLADHGARKDTVI
+IKPRQTIVFDFEADNPGQWLTHCHNAYHAEAGMMGVFSYIH*
+>NZ_CP040019.1_386
+MTSSLTTRRTFLGASVGALALAGLTACADPAISPQPSGRILPTDPLVAEYEKRRAASGTT
+VTHRLSAAPLETSLQGRGLTTWGYNDGLNGPLLRAQTGDLLKVSVANDLPEGTSVHWHGL
+ALRNDADGVQGLTQDPIAAGGRYTYGFRLSHPGTYWYHSHFDTQRERALYGALIVEDPNE
+PLSYDQEWVVILDDWLDGITGTPQDVVEELSAGMDMSGDMEGMAGMDHGSMSQDSSSGMP
+MKHMLMGAESDYLGGDAGDVKIPVHLFNGRPPSDPDTFSSTPGNRIRLRLINAAGDTAYR
+VGIPGQELTITHTDGFPVQPRQADAVVLGMGERLDVLITLGDQAVPVLALPEGKTGHAYG
+IIAAGPKTTLSGRLPQTLGGTVLDGSRLKAHESVLLPPKDPTRTHEVRLTGSMMEYDWGI
+NGRRFDPANPFEGAFELRLDERVRVTMTNDTDMWHPMHLHGHTFQLADHGARKDTVIIKP
+RQTIVFDFEADNPGQWLTHCHNAYHAEAGMMGVFSYIH*
+>NZ_CP083691.1_2152
+MTSSLTTRRTFLGASVGALALAGLAACADPAISPQPSGRILPTDPLVAEYEKRRAASGTT
+VTHRLSAAPLETSLQGRGLTTWGYNDGLNGPLLRAQTGDLLKVSVANDLPEDTSVHWHGL
+ALRNDADGVQGVTQDPIAAGGRYTYGFRLSHPGTYWYHSHFDTQRERALYGALIVEDPNE
+PLSYDQEWVVILDDWLDGITGTPQDVVEELSAGMDMSGDMEGMAGMAGMDHGSMSQDSSS
+GMPMKHMLMGAESDYLGGDAGDVKIPVHLFNGRPPSDPDTFSSTPGNRIRLRLINAAGDT
+AYRVGIPGQELTITHTDGFPVQPRQADAVVLGMGERLDVLITLGDQAVPVLALPEGKTGH
+AYGIIAAGPKTTLSGRLPQTLGGTVLDGSRLKAHESVLLPPKDPTRTHEVRLTGSMMEYD
+WGINGRRFDPANPFEGAFELRLDERVRVTMTNDTDMWHPMHLHGHTFQLADHGARKDTVI
+IKPRQTIVFDFEADNPGQWLTHCHNAYHAEAGMMGVFSYIH*
+>NZ_CP097650.1_580
+MTSSLTTRRTFLGASVGALALAGLAACADPVISPQPSGRILPTDPLVAEYEKRRAASGTT
+VTHRLSAAPLETSLQGRGLTTWGYNDGLNGPLLRAQTGDLLKVSVANDLPEDTSVHWHGL
+ALRNDADGVQGVTQDPIAAGGRYTYGFRLSHPGTYWYHSHFDTQRERALYGALIVEDPNE
+PLSYDQEWVVILDDWLDGITGTPQDVVEELSAGMDMSGDMEGMAGMAGMDHGSMSQDSSS
+GMPMKHMLMGAESDYLGGDAGDVKIPVHLFNGRPPSDPDTFSSTPGNRIRLRLINAAGDT
+AYRVGIPGQELTITHTDGFPVQPRQADAVVLGMGERLDVLITLGDQAVPVLALPEGKTGH
+AYGIIAAGPKTTLSGRLPQTLGGTVLDGSRLKAHESVLLPPKDPTRTHEVRLTGSMMEYD
+WGINGRRFDPANPFEGAFELRLDERVRVTMTNDTDMWHPMHLHGHTFQLADHGARKDTVI
+IKPRHTIVFDFEADNPGQWLTHCHNAYHAVAGMMGVFSYIH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001832.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001832.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0415811d5314dc74d11fd91f306e67f4ff199074
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001832.fa
@@ -0,0 +1,28 @@
+>NZ_CP042169.1_613
+MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA
+LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG
+HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH
+SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHYWTIELTRPAEKQEV
+LETFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVALWEDILTVDGNELYYTY
+TVDNQAIVIPENIDAIRALTGTVDDGGESIRCTDRALGVRQDFVRSSVAAR*
+>NZ_CP040019.1_393
+MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA
+LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG
+HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH
+SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHYWTIELTRPAEKQEV
+LEAFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVALWEDILTVDGNELYYTY
+TVDNQAIVVPENIDAIRALTGTVDDGGESIRRTDRALGVRQDFVRSSVAAR*
+>NZ_CP083691.1_2145
+MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA
+LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG
+HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH
+SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHNWTIELTRPAEKQEV
+LEAFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVVLWEDILTVDGNELYYTY
+TVDNQAIVVPENIDAIRALTGTVDDGGESIRRTDRALGVRQDFVRSSVAAR*
+>NZ_CP097650.1_573
+MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA
+LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG
+HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH
+SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHYWTIELIRPAEKQEV
+LEAFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVALWEDILTVDGNELYYTY
+TVDNQAIVVPENIDAIRALTGTVDDGGESIRRTDRALGVRQDFVRSSVAAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001833.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001833.fa
new file mode 100644
index 0000000000000000000000000000000000000000..601a33c40b5c38f0de3ad19ab52ede26f6213dda
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001833.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_617
+MTLMQIPTDHGTIGLNVEESGHGRPVVLIHGWPLTLDSWKDQVAALSPHYRVITYDRRGF
+GASEKPAGGYDYDTMTADLYGLLTELDLRDVTLVGFSMGGGEVARYMSRFGADRIHSVVF
+AGAVPPYLLKTDDNPDGPLTEKQAAEMRAGLEKDRESFFDDFTTTFFSTPKLAGLTSSLK
+VTEEQRQEAIRMALQSDQTAALACMDAFGATDFRRDLPAVTVPALVLHGDADQIVPFEGS
+GKRTHKAIDGSRVELVKDAPHGFNTSHSEEFNRILLEFLAE*
+>NZ_CP033200.1_363
+MTLMQIPTDHGTIGLNVEEAGHGRPVVLIHGWPLTLDSWKDQVAAVSPHYRVITYDRRGF
+GVSEKPTGGYDYDTMTADLHGLLTELDLRDVTLVGFSMGGGEVARYMSRFGADRIHSVVF
+AGAVPPYLLKTDDNPDGPLTEKQAAEMRAGLEKDRESFFDDFTTTFFSTPKLAGLTSSLK
+VTEEQRQEAIRMALQSDQTAALACMDAFGATDFRRDLPAVTVPALVLHGDADQIVPFKGS
+GKRTHKAIDGSRVELVKDAPHGFSISHSEEFNRILLEFLAE*
+>NZ_CP083691.1_2137
+MTLMQIPTDHGTIGLNVEEAGHGRPVVLIHGWPMTLDSWKDQVAALSPHYRVITYDRRGF
+GASEKPAGGYDYDTMTADLHGLLTELDLRDVTLVGFSMGGGEVARHMSRFGADRIHSVVF
+AGAVPPYLLKTEDNPDGPLTEKQAAEMRAGLEKDREAFFDDFTTTFFSTPKLAGLTSSLK
+VTEEQRKEAIRMALQSDQTAALACMDAFGATDFRRDLPAVTVPTLVLHGDADQIVPFKGS
+GKRTHKAIDGSRVELVKDAPHGFSISHSEEFNRILLEFLAE*
+>NZ_CP097650.1_585
+MTLMQIPTDHGTIGLNVEEAGHGRPVVLIHGWPLTLDSWKDQVAALSPHYRVITYDRRGF
+GVSEKPAGGYDYDTMTADLHGLLTELDLRDVTLVGFSMGGGEVARYMSRFGSDRIHSVVF
+AGAVPPYLLKTDDNPDGPLTEKQAAEMRAGLEKDRESFFDDFTTTFFSTPKLAGLTSSLK
+VTEEQRQEAIRMALQSDQTAALACMDAFGATDFRRDLPAVTVPALVLHGDADQIVPFKGS
+GKRTHKAIDGSRVELVKDAPHGFSISHSEEFNRILLEFLAE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001835.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001835.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b6a3f2e3b49b49dd99f3e562870f02e242ae1e67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001835.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_624
+MSVIDVGLREGHEYRVRDTWLTVPNLITLARFALVPVFVWLTVDGRHLDAFVILAVLSGT
+DWVDGYVARRFDMISTVGRWLDPVADRLSLLVVAVTFVATGIAPLWLALAIAIPDLVLAA
+VCLWLFGGSPDLPVTVLGKVRTALLLVGTPLLLLARVPGVDGGPWSGVALALVGAGCLLH
+ILAAGDYLVRAVGKARGLRADGQDPREHPSRRG*
+>NZ_CP033200.1_370
+MRVIDVGLREGHEYRVRDTWLTVPNLITLARFALVPVFVWLTVDGRHLDAFVILAVLSGT
+DWVDGYVARRFDMISTVGRWLDPVADRLSLLVVAVTFVATGIAPLWLALAIAIPDLVLAA
+VCLWLFGGSPDLPVTVLGKVRTALLLVGTPLLLLARVPGVDGGPWSGVALALVGAGCLLH
+ILAAGDYLVRAVGKARGLRADGQDPREHPSRRG*
+>NZ_CP040019.1_2272
+MRLIDVGLREGHEYRVRDTWLTVPNVITLVRLALVPVFVWLTVTDQFLAAFLTLAFLSST
+DWVDGYIARRFDMISTVGRWLDPVADRLSLVTVALTFVLTGIAPAWLVLSILIPDVVLTL
+VCLRLFGGSPDLKVTVLGKVRTALLLAGTPLLLLARVPGVDQDLWGGLALVLVGAGCVLH
+VLAAVDYLVRAVRKARELRAAGVDPRDRRARPAQGA*
+>NZ_CP097650.1_593
+MRVIDVGLREGHEYRVRDTWLTVPNLITLARFALVPVFVWLTVDGRHLDAFVILAVLSGT
+DWVDGYVARRFDMISTVGRWLDPVADRLSLLVVAVTFVATGIAPLWLALAIAIPDVVLAA
+VCLWLFGGSPDLPVTVLGKVRTALLLVGTPLLLLARVPGVDGGPWSGVALALVGAGCLLH
+ILAAGDYLVRAVGKARGLRADGQDPREHPSRRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001838.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001838.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d707adeb0cb912c6b225f620d4ea99aba584002d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001838.fa
@@ -0,0 +1,17 @@
+>NZ_CP042169.1_643
+MTERVEIEQRGRYADELAVGQVYLHRPGRTLTEADNVLFTTLTMNPQALHLDHAYAADQP
+FGRPLVNSMLTLSTLVGLAVGQTTQGTLVAQLGLGEIAFPKPVFHGDTLYGRSEVTAIRE
+SSSRPGQRIVTFAMTGENQHGDVVVRAQRTCLMWTAQAHAEAKAKAADAAGTGERA*
+>NZ_CP033200.1_389
+MTERVEIEQRGRYADELAVGQVYLHRPGRTLTEADNVLFTTLTMNPQALHLDHAYAADQP
+FGRPLVNSMLTLSTLVGLAVGQTTQGTLVAQLGLGEIAFPKPVFHGDTLYGRSEVTAIRE
+SSSRPGQRIVTFAMTGENQHGDVVVRAQRTCLMWTAQAHAEAKAKAADAAGTGERA*
+>NZ_CP040019.1_2252
+MGRAEPGAAPERVEIVQRGRYADELAVGQVYLHRPGRTLTEADNVLFTTLTMNPQALHLD
+HAFAQTQSFGRPLVNSMLTLSTLVGLAVAQTTQGTLVAQLGLGEIAFPAPVFHGDTLYGR
+SEVRAVRESSSRPGQRIVTFAMTGENQHGDVVVRAERTCLMWTEAAHADARAQAAADAAE
+ERA*
+>NZ_CP097650.1_612
+MTERVEIEQRGRYADELAVGQVYLHRPGRTLTEADNVLFTTLTMNPQALHLDHAYAAAQP
+FGRPLVNSMLTLSTLVGLAVGQTTQGTLVAQLGLGEIAFPKPVFHGDTLYGRSEVTAIRE
+SSSRPGQRIVTFAMTGENQHGDVVVRAQRTCLMWTAQAHAEAKAKAADAAGTGERA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001839.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001839.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1668cbff978fe31827cea08b9e14a8d9ed8639fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001839.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_644
+MSALTLGPAVMFTPADRPERYATALERADAVILDLEDAVIPEARPAARDAVAAAWAGRAT
+GGVDGGPLDEDRVVVRVNPAGTADHDADLAMLAGTGWRTLMLAKAESAAQVDGVVAALGP
+QTRVVALCETAAGILAAAELAAHPHVGALMWGAEDLVASMGGSSSRTPEGAYRSVVQHAR
+ATVLLAAAAHGAAAWDAVHLDLGDEAGLAAEAEDAAALGCTATVCLHPRQVPVVRSAYTP
+APEAVERARRVLAAAEGRHGAFELDGTMVDEVVLAQARAVLRRADAARPAGA*
+>NZ_CP033200.1_390
+MSALTLGPAVMFTPADRPERYATALERADAVILDLEDAVTPDARPTARDAVAAAWAGRAT
+GGVDGGPLDEDRVVVRVNPAGTADHDADLAMLAGTGWRTLMLAKAESAAQVDGVVAALGP
+QTRVVALCETAAGILAAADLAAHPHVGALMWGAEDLVASMGGSSSRTPEGAYRSVVQHAR
+ATVLLAAAAHGAAAWDAVHLDLGDEAGLAAEAEDAVALGCTATVCLHPRQVPVVRSAYTL
+APEAVERARRVLAAAEGRHGAFELDGAMVDEVVLAQARAVLRRADAPRPASA*
+>NZ_CP040019.1_2251
+MSALALGPAVMFTPADRPERYAKALERADAVILDLEDAVTPDARPAARDAVRAAWEGRAA
+GGADGGPLDVARVVVRVNPAGGADYTADLAMLAETGWRTLMLAKAESAAQVDGLVAAMGE
+DVRVVALCETAAGVLAAAELAAHPNVGALMWGAEDLVASMGGSSSRTADGAYRSVVTHAR
+AAVLLAAAAHGAAAWDAVHLDLADEAGLAAEAEDAVALGCAATVCLHPRQVPVVRSAYTP
+AAEAVERAHRVLSEAEGRRGAFELDGAMVDEVVLAQARAVLRRAEAAGAAAG*
+>NZ_CP097650.1_613
+MSALTLGPAVMFTPADRPERYATALERADAVILDLEDAVTPDARPTARDAVAAAWAGRVT
+GGVDGGPLDEGRVVVRVNPAGTADHDADLAMLAGTGWRTLMLAKAESAAQVDGVVAALGP
+QTRVVALCETAAGILAAADLAAHPHVGALMWGAEDLVASMGGSSSRTPEGAYRSVVQHAR
+ATVLLAAAAHGAAAWDAVHLDLGDEAGLAAEAEDAVALGCTATVCLHPRQVPVVRSAYTP
+APEAVERARRVLAAAEGRHGAFELDGAMVDEVVLAQARAVLRRADAARPASP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001840.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001840.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4207862461bfc4af3d1b81640f4e13a3bb50037c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001840.fa
@@ -0,0 +1,12 @@
+>NZ_CP042169.1_655
+MTSRTVVRTCIGCRSRADQQELVRVALDSSTEPPSVVWDPERRRPGRGAWLHPGEDCLHL
+ALRRRAFGRAFRSAVDADALGRTAEAPADRPTDEGGSEI*
+>NZ_CP033200.1_401
+MTSRTVVRTCIGCRSRADQQELVRVALDSSTEPPSVVWDPERRRPGRGAWLHPGEDCLLL
+ALRRRAFGRAFRSAVDADALGRTAEAPADRPTDEGGSEI*
+>NZ_CP083691.1_2098
+MSPRTVVRTCVGCRSQADQQELMRVALEPGTTPPTVVWDPLRRRPGRGAWVHPGPECLQL
+ALRRRAFHRAFRGQVDPDGLEAGTRASAARPTDEGGSEI*
+>NZ_CP097650.1_624
+MTSRTVVRTCIGCRSRADRQELVRVALDSSTEPPSVVWDPERRRPGRGAWLHPGEDCLHL
+ALRRRAFGRAFRSAVDADALGRTAEAPADRPTDEGGSEI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001847.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001847.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb98ca69d7399b834f85c5c94f5dd40c713197ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001847.fa
@@ -0,0 +1,44 @@
+>NZ_CP042169.1_926
+MRPAAPATTGARGPRPSRVAAQPEPEAAVRRGTWASVLITVGSWGVGWLPMTPDSVFSGT
+TLLNPLRVYLPGVLLSTVLLAAGSLLLVRSWLELGRALRGRWEEHGRLVARAAWWWSAPL
+MLALPIFSRDVFSYLQQGRLLASGLDPYSQGVSALPGWFMQGADSIWAESPSPYGPLFLL
+FAETTWRATGGNIELSVTAFRLLALAGLALCLWAVPRLAAVAGRCGPWATWVAVANPLFL
+LYMIAGAHNDALMSGLMLAGILLMVRLPRRRVHALWGIVLIALSVAIKPLTALVLPFVAL
+LLPTGWARFRAADPRLRRRDRLGPWFTTAVISLAVLTILGAGSGLWFGWVPAMLTSGDAA
+FPYAPVGLLGLLLGAVVEAVTPLGARDVAAAFYTVMTVSALGFTAWLALRRRPLDPVFSA
+AAVLVVAVATAPIVQPWYLLWVLPLLACALRPLPWGADHPRWLGWVTALAVLLLTGVGVV
+DQLSVAQWLPVLAVRVFTLVLMLAGIGWIIHRDPVTAPLFPGRRRPPLEVVEPRAAAASP
+TPPEAGVPPDAPPDGPPSTAAHPASSSTRIPQERP*
+>NZ_CP033200.1_649
+MRPAAPATTGARGPRPSRVAAQPEPEAAVRRGTWASVLITVGSWGVGWLPMTPDSVFSGT
+TLLNPLRVYLPGVLLSTVLLAAGSLLLVRSWLELGRALRGRWEEHGRLVARAAWWWSAPL
+MLALPIFSRDVFSYLQQGRLLASGLDPYSQGVSALPGWFMQGADSIWAESPSPYGPLFLL
+FAETTWRATGGNIELSVTAFRLLALAGLALCLWAVPRLAAVAGRCGVWATWVAVANPLFL
+LYMIAGAHNDALMSGLMLAGILLMVRPPRRRVHALWGIVLIALSVAIKPLTALVLPFVAL
+LLPTGWARFRAADPRLRRRDRLGPWFTTAVISLAVLTILGAGSGLWFGWVPAMLTSGDAA
+FPYAPVGLLGLLLGAVVEAVTPLGARDVAAAFYTAMTVSALGFTAWLALRRRPLDPVFSA
+AAVLVVAVATAPIVQPWYLLWVLPLLACALRPLPWGADHPRWLGWVTALAVLLLTGVGVV
+DQLSVAQWLPVLAVRVFTLVLMLAGIGWIIHRDPVTAPLFPGRRRPPLEVVEPRAAAASP
+TPPEAGVPPDAPPDGPPSTAAHPASSSTRIPQERP*
+>NZ_CP083691.1_1842
+MTLAVDGARRDDGGPSGRGSRALNGPAAAPEPAAAVREGLWAALAVMVASWGVGWQPMTP
+LSVFSGSTLLVPLRTGLAGVLLCAVLLAVGVFALVRAWLRLGRSLQGRWTADGHLAARAA
+LFWSLPLLAALPIFSRDVFSYLQQGRLVALGLDPYEDGISRLPGWFMHGADSIWAESPSP
+YGPLFLLSAEGIWRLTGGQVELSVAAFRLLALAGLALCLWAVPRLAAAAGREPAWAVWVS
+VANPLFLLYMVAGAHNDALMTGLLLAGAALLVRVGRRRVVALAGLVLVALSVAIKPLTAL
+TLPFLAMLLPGGWSRFRVGARRLGRVERIGPWITAAVIAAAVLTVLGAGTGLWFGWVRAM
+TTSGDAAFPYAPVGLLGLGLGWAVDLVSDVPARQAAGWFYSAMTCAALAFTAWMALRRSP
+REPLVASAAVLVVAIVTAPIIQPWYLLWFLPLLACAPRPLPGVVDHPRWLGWVLTALVLA
+LCGVGVVDQISVAQWLPLGLVRVVAALACLVAAWALVRRDPSTAVLFPRRRRPPDETIEP
+RGRPAPRRALAAPTTPTAPVQE*
+>NZ_CP097650.1_871
+MRPAAPATTGARRPRPTRAAAQPEPGAAVRRGTWASVLITVGSWGVGWLPMTPDSVFSGT
+TLLNPLRVYLPGVLLSTVLLAAGSLLLVRSWLELGRALRGRWEEHGRLVAHAAWWWSAPL
+MLALPIFSRDVFSYLQQGRLLASGLDPYSQGVSALPGWFMQGADSIWAESPSPYGPLFLL
+FAETTWRATGGSIELSVTAFRLLALAGLALCLWAVPRLAAVAGRCGPWATWVAVANPLFL
+LYMIAGAHNDALMSGLMLAGILLMVRPPRRRVHALWGIVLIALSVAIKPLTALVLPFVAL
+LLPTGWARFRAADPRLRRRDRLGPWFTTAVISLAVLTILGAGSGLWFGWVPAMLTSGDAA
+FPYAPVGLLGLLLGAVVEAVTPLGARDVAAAFYTVMTVSALGFTAWLALRRRPLDPVFSA
+AAVLVVAVATAPIIQPWYLLWVLPLLACALRPLPWGADHPRWLGWVTALAVLLLTGVGVV
+DQLSVAQWLPVLAVRVFTLVLMLAGIGWIIHRDPVTAPLFPGRRRPPLEVVEPRAEAASS
+TPPEAGVPPDAPPDGPPSTAAHPASSSTRIPQERP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001848.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001848.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb22cb05d75a8c062d8f78d8995524075f436556
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001848.fa
@@ -0,0 +1,16 @@
+>NZ_CP042169.1_961
+MTPDQPETGGATEQGRFGDEPWRPERETRAQRQWRPGTRRRRRSVRALFTSTILMLEAVL
+IFFLGLMLFGMHRDEPGAWWFVAGYSALAVVAVLTCALVRKPVGIAIGWAIQAVLLASGF
+WEYSMFVVGALFALTWAYAVIKGGAMDVENAQRDRLEAAWEAEHGR*
+>NZ_CP033200.1_685
+MTPDQPETGGATEQGRFGDESWRPARETRAQRQWRPGTRRRRRSVRALFTSTILMLEAVL
+IFFLGLMLFGMHRDEPGAWWFVAGYSALAVVAVLTCALVRKPVGIAIGWAIQAVLLASGF
+WEYSMFVVGALFALTWAYAVIKGGAMDVENAQRDRLEAAWEAEHGR*
+>NZ_CP083691.1_1804
+MSGPTEPRPGRPADERFGAEDWRPARETKTQRAWRPGQRKRARSVRAMFASTVLCLEAVL
+LFFLGMTLFGLNRGADHAPWVAVAFTALAAVAVLDCALVRKPLGVAIGWAIQAVLIASGF
+WEYSMFVIGPLFALTWWYAITKGDQIDRENAARARAQAAWEASHPEEAGPRT*
+>NZ_CP097650.1_903
+MTDDQPETGGATEQGRFGDEPWRPARETRAQRQWRPGTRRRRRSVRALFTSTILMLEAVL
+IFFLGLMLFGMHRDEPGAWWFVAGYSALAVVAVLTCALVRKPVGIAIGWAIQAVLLASGF
+WEYSMFVVGALFALTWAYAVIKGGAMDVENAHRDRLEAAWEAEHGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001849.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001849.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b8b3d04c7b7112f40d6d0939c4d3b7f2bd7e4a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001849.fa
@@ -0,0 +1,32 @@
+>NZ_CP042169.1_974
+MSRTDAPIRTALIGYGFAGKTFHVPLLHATEGLALTHVVSSRPDAVHADLPDVVVVPDVD
+KLLARHDVDLVVIAAPNDQHAPLARTALRAGRHVVVDKPFTLSLAEARELRDLAVETGRV
+LRVFQNRRFDSDFLGIAELVRSGRLGDVVHLESRIDRFRPTVRDRWREAAVPGGGIWFDL
+GPHLVDQALLLFGVPERVDADLAALRPGAPVEDWAHCVLQYPGRRVVLQASMLVAGGSPR
+FAVHGTRGSAVKELPDRQEVQLRAGLLPGAEGWGVDPDPILLHDGEGNTERVPAPIGAQQ
+RSYAGVRDAILGRASSDAATPDQAVAVMAVLEAAVASAREGRAVEPALTAAERAAYPGVS
+PAPTAAERHHRSAEPR*
+>NZ_CP033200.1_698
+MSRTDAPIRTALIGYGFAGKTFHVPLLHATEGLALTHVVSSRPDAVHADLPDVVVVPDVD
+KLLARHDVDLVVIAAPNDQHAPLARTALRAGRHVVVDKPFTLSLAEARELRDLAVETGRV
+LRVFQNRRFDSDFLGIAELVRSGRLGDVVHLESRIDRFRPTVRDRWREAAVPGGGIWFDL
+GPHLVDQALLLFGVPERVDADLAALRPGAPVEDWAHCVLQYPGRRVVLQASMLVAGGSPR
+FAVHGTRGSAVKELPDRQEVQLRAGLLPGAEGWGVDPDPILLHDGEGNTERVPAPIGAQQ
+RSYAGVRDAILGRASSDAATPDQAVAVMAVLEAAVASAREGRAVEPALTAAERAAYPGVS
+PAPTAAERHHRSAEPR*
+>NZ_CP040019.1_1847
+MPPTDAPIRTALIGYGFAGKTFHVPLLHATDGLALTHVVSSRPDAVHADLPDVVVVPDVD
+ALLARHDVDLVVIAAPNDQHAPLARTALGAGRHVVVDKPFALSLAEARELRDLAAATGRV
+LRVFQNRRFDSDFLGIAELVRSGRLGDVVHLESRIDRFRPTVRDRWREAAVPGGGIWFDL
+GPHLVDQALLLFGVPDRVDADLAALRPGAPVEDWAHCVLQYPGRRVVLQASMLVAGGSPR
+FAVHGTRGTAVKELPDQQEAQLRAGLLPGAEGWGVDPDPILLHDGEGNIERAPAPTGAQQ
+RSYAGVRDAILGRPNGDAATPDQAVAVMAVLEAAVASAREGRAVKPALTAVERAAYPGVS
+LAPTAAERHHRSAAAR*
+>NZ_CP097650.1_916
+MSRTDAPIRTALIGYGFAGKTFHVPLLHATEGLALTHVVSSRPDAVHADLPDVVVVPDVD
+ALLAWHDVDLVVIAAPNDQHTPLARAALRAGRHVVVDKPFTLSLAEARELRDLAAETGRV
+LRVFQNRRFDSDFLGIAELVRSGRLGDVVHLESRIDRFRPTVRSRWREASVPGGGIWFDL
+GPHLVDQALLLFGVPERVDADLAALRPGAPVEDWAHCVLQYPGRRVVLQASMLVAGGSPR
+FAVHGTRGTAVKELPDQQEAQLRAGLLPGAEGWGVDPDPILLHDGEGNTERVPAPTGAQQ
+RSYTGVRDAILGRPNGDAATPDQAVAVMAVLEAAVASAREGRAVEPALTAVERAAYPGVS
+PAPTAAERHHRSAAAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001850.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001850.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9b121c37d97044f2524627bbd4d542f53f017b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001850.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_976
+MDETTEPPRARRRRGRPLSPALSREAIADAALAVARTEGYEGLTMAAVGRRLGVAPSALY
+NHISGKHELLVLLQDAVMGEVSLVELEAAIRGEVPVVAALRAWARSYRDVFAAHPPLIPL
+IATLPIEGAPSTQRVYETVCAVLARTGLAPEQVLARVIALESFIYGSAYDVDAPADIFEV
+AGAQERLPALGAAAEAFRAGGGTRATGARNPYADAPFEEGLDLLLAGLGD*
+>NZ_CP033200.1_700
+MAAVGRRLGVAPSALYNHISGKHELLVLLQDAVMGEVSLVELEAAIRGEVPVVAALRAWA
+RSYRDVFAAHPPLIPLIATLPIEGAPSTQRVYETVCAVLARTGLAPEQVLARVIALESFI
+YGSAYDVDAPADIFEVAGAQERLPALGAAAEAFRAGGGTRATGARNPYADAPFEEGLDLL
+LAGLGD*
+>NZ_CP040019.1_1844
+MDETPEPPRTRRRRGRPLSPALSREAIADAALAVARTEGYEGLTMAAVGRRLGVAPSALY
+NHISGKHELLVLLQDAVMGEVSLVELEAAIRGEAPVVAALRAWARSYRDVFAAHPPLIPL
+IATLPIEGAPSTQRVYETVCAVLARTGLAPGQVLARVIALESFIYGSAYDVDAPADIFEV
+AGAQERLPAFGAAAEAFREGGGTRATGARNPYADAPFEEGLDLLLAGLDD*
+>NZ_CP097650.1_918
+MDETTEPPRARRRRGRPLSPALSREAIADAALAVARTEGYEGLTMAAVGRRLGVAPSALY
+NHISGKHELLVLLQDAVMGEVSLVELEAAIRGEVPVVAALRAWARSYRDVFAAHPPLIPL
+IATLPIEGAPSTQRVYETVCAVLARTGLAPEQVLARVIALESFIYGSAYDVDAPADIFEV
+AGAQERLPALGAAAEAFRAGGGTRATGARNPYADAPFEEGLDLLLAGLGD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001857.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001857.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4d5633cb4c407cbecb01fefe3267be30b0ff1b1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001857.fa
@@ -0,0 +1,32 @@
+>NZ_CP042169.1_1070
+MEINGLTWGLTIALIVGLLAFDYFAHVRKAHTPSIREAAIWSGVYVGLALVFGLVFFAFG
+DTQHAVEYYTGYLLEKALSVDNLFVFLVIMASFRVPREYQQKVLLFGITFALISRTLFIL
+LGAAVIAAWSDVFYLFGLFLLIIAGGQLKGEMSGDAEGAQDEADNVMVRLVKRFLPASEQ
+FDGDRLFTTVDGKRLMTPMLLVMIAIGATDILFAFDSIPAIFGVTQEAYIVFTATAFSLM
+GLRQLYFLIDGLLDRLVYLAYGLSALLAFIGVKLILHALHENNLPFINGGENVPVVEIPT
+TLSLVVVVVILAITVAISLASPKGQALRALQNAEKYSYRYSKLPEDADPAERERAAALMD
+RWTARAEAVDQRWRDQLLEHKDAWSAIIRTAHETRLADPRDDDARGVSEQIVRQDGPTV*
+>NZ_CP033200.1_799
+MEINGLTWGLTIALIVGLLAFDYFAHVRKAHTPSIREAAIWSGIYVGLALLFGLVFFAVG
+DTQHAVEYYTGYLLEKALSVDNLFVFLVIMASFRVPREYQQKVLLFGITFALISRTLFIL
+LGAAVIAAWSDVFYLFGLFLLIIAGGQLKGEMSGDAEGAQDEADNVMVRLVKRFLPASEQ
+FDGDRLFTTVDGKRLMTPMLLVMIAIGATDILFAFDSIPAIFGVTQEAYIVFTATAFSLM
+GLRQLYFLIDGLLDRLVYLAYGLSALLAFIGVKLILHALHENNLPFINGGENVPVVEIPT
+TLSLVVVVVILAITVAISLASPKGQALRALQNAEKYSYRYSKLAEDADPAERERAAALMD
+RWTARAEALDQRWRDQLLEHKDAWSAIIRTAHETRLADPRDDDARGVSEQIVRQDGPTV*
+>NZ_CP040019.1_1754
+MEINGLTWGLTITLIVGLLAFDYFAHVRKAHTPTIREAAIWSGIYVGLALLFGLVFFAVG
+DTQHAVEYYTGYLLEKALSVDNLFVFLVIMASFRVPREYQQKVLLFGITFALISRTIFIL
+LGAAVIAAWSDVFYLFGLFLLVIAGGQLKGEMAGDADDAKDEADNIMVRMVKRFLPASDR
+FDGDKLFTLENGKRVMTPMLLVMIAIGATDILFAFDSIPAIFGVTTEAYIVFTATAFSLM
+GLRQLYFLIDGLLDRLVYLAYGLSALLAFIGVKLILHALHENNLPFINGGENVPVVTIPT
+TLSLVVVVVILAITVVVSLYSPKGQALRALQNAEKFSYRYSKLDETADPAERSRAAALMD
+EWTAKAEGLDQKWRDELLEHKDTWSGIIRTAHETRLADPRDDDARGVSERIVRQDGPTV*
+>NZ_CP097650.1_1019
+MEINGLTWGLTIALIVGLLAFDYFAHVRKAHTPSIREAAIWSGVYVGLALVFGLVFFAFG
+DTQHAVEYYTGYLLEKALSVDNLFVFLVIMASFRVPREYQQKVLLFGITFALISRTLFIL
+LGAAVIATWSDVFYLFGLFLLIIAGGQLKGEMSGDAEGAQDEADNVMVRLVKRFLPASEQ
+FDGDRLFTTVDGKRLMTPMLLVMIAIGATDILFAFDSIPAIFGVTQEAYIVFTATAFSLM
+GLRQLYFLIDGLLDRLVYLAYGLSALLAFIGVKLILHALHENNLPFINGGENVPVVEIPT
+TLSLVVVVVILAITVAISLASPKGQALRALQNAEKYSYRYSKLPEDADPAERERAAALMD
+RWTARAEAVDQRWRDQLLEHKDAWSAIIRTAHETRLADPRDDDARGVSEQIVRQDGPTV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001858.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001858.fa
new file mode 100644
index 0000000000000000000000000000000000000000..397192f8fb4f96594318320b58b740169e9baf81
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001858.fa
@@ -0,0 +1,13 @@
+>NZ_CP042169.1_1103
+MIGAVPGEPGMDLLGALASGRLDPAAGASTARSPHAAVDGPERPVCSRRGCTAEAAWALE
+WNNPRVHAPDRVKTWLACTDHRPFLDDFLSARGFLRRSRPLDPAATQAPEVDTPETPQEP
+PRP*
+>NZ_CP033200.1_832
+MDLLGALASGRLDPAAGASAARSPHAAADGPERPVCSRRGCTAEATWALEWNNPRVHAPD
+RVKTWLACADHRPFLDDFLSARGFLRRSRPLDPPATEAPEVETPETPQEPPRP*
+>NZ_CP083691.1_1612
+MTGPDLLGALAAGLDPSLPAVRREPSAEGPAAVTADGAPVCSARGCRAAAAWVLEWNNPR
+VHAPDRVKTWAACPDHREHLSDFLASRGFLRRTRPLHAAAGPAATDPTTPGEPRR*
+>NZ_CP097650.1_1052
+MDLLGALASGRLDPAAGASAARSPHAAADGPERPVCSRRGCTAEATWALEWNNPRVHAPD
+RVKTWLACADHRPFLDDFLSARGFLRRSRPLDPPATEAPEVETPETPQEPPRP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001859.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001859.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e2872c4200a205e0e9fbf2ebcd431b12b522906b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001859.fa
@@ -0,0 +1,18 @@
+>NZ_CP042169.1_1113
+MPVGAATLRELPLVGETSPELAALVDRAHREARALNRLLGVHPLALGTVAPADVLGADAT
+AALRTGLAAGLGVAPTAWEDPGVVLAPAADADPELLHVVLLHTTAVVAGPPALVARLADA
+DVSDLLDDASLGAHLRGPVEDVSAAWLHAADRQALSLDPDGGAAHVARHAELTAVLETRP
+VVVERVGMRDRDAQRAADAVGLRRVGRERVLRVAAP*
+>NZ_CP033200.1_842
+MPVGAATLRELPLVGETSPELAALVDRAHREARALNRLLGVHPLALGTVAPADVLGADAT
+AALRTGLAAGLGVAPTAWEDPGVVLAPAADADPELLHVVLLHTTAVVAGPPALVARLADA
+DVSDLLDDASLGAHLRGPVEDVSAAWLHAADRQALSLDPDGGAAHVARHAELTAVLETRP
+VVVERVGMRDRDAQRAADAVGLRRVGRERVLRVAAP*
+>NZ_CP040019.1_1707
+MNALSLNPRGGAEHLARHAGLVAALRERPVVVETEAAGDRAALRAANELGLRRVGRELRF
+LVR*
+>NZ_CP097650.1_1062
+MPVGAATLRELPLVGETSPELAALVDRAHREARALNRLLGVHPLALGTVAPADVLGADAT
+AALRTGLAAGLGVAPTAWEDPGVVLAPAADADPELLHVVLLHTTAVVAGPPALVARLADA
+DVSDLLDDASLGAHLRGPVEDVSAAWLHAADRQALSLDPDGGAAHVARHAELTAVLETRP
+VVVERVGMRDRDAQRAADAVGLRRVGRERVLRVAAP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001860.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001860.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b9c44b188aaa85b47b5528055ca76584de19780b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001860.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1118
+MNPVTSTARDGRSVRWDRHRAERRLELVRAARSAVHALGAHASMEEIASHAGTSKTVYYR
+YFGDREGLRLAVSERVTAHMERRLLEVADEPVSEPEALRRMVEVYLTVAATSPEVYAFAV
+APSPAAAEAPVLGPFLERVYAMLESGLARGMAARGHAPAPADPLALWPRAAVGLVRAAAE
+TWLRTPAAGRIPVEAMARAIADWLLTGLIGAAPGAALEPAAADAVRARPHSRTGASS*
+>NZ_CP033200.1_847
+MNPVTSTARDGRSVRWDRHRAERRLELVRAARSAVHALGAHASMEEIASHAGTSKTVYYR
+YFGDREGLRLAVSERVTAHMERRLLEVADEPVSEPEALRRMVEVYLTVAATSPEVYAFAV
+APSPAAAEAPVLGPFLERVYAMLESGLARGMAARGHAPAPADPLALWPRAAVGLVRAAAE
+TWLRTPAAGRIPVEAMARAIADWLLTGLIGAAPGAALEPAAADADRARPHSRTGASS*
+>NZ_CP083691.1_1598
+MLVRAARAAVHELGPTASMDEIAAHAGTSKSVFYRYFGDRAGLRQAVAERVTASMERRLR
+EAAVDAPDGVSALHRMVAECLSVAASSPAVYAFAVTQGGAADGTGPDLGPFFERIAALLA
+EGLARTLPAADAGPGTTLVLWPRVAVGTVRAAVEAWLATEESVRPDPVRTAHDVAGWLLA
+GLRSADPSASPAADTHTPTQQGEPS*
+>NZ_CP097650.1_1067
+MNPVTSTARDGRSVRWDRHRAERRLELVRAARSAVHALGAHASMEEIASHAGTSKTVYYR
+YFGDREGLRLAVSERVTAHMERRLLEVADEPVSEPEALRRMVEVYLTVAATSPEVYAFAV
+APSPAAAEAPVLGPFLERVYAMLESGLARGMAARGHAPAPADPLALWPRAAVGLVRAAAE
+TWLRTPAAGRIPVEAMARAIADWLLTGLIGAAPGAALEPAAADADRARPHSRTGASS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001862.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001862.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b2a2d95d52c3cd3ea4209148bfbd32eee4cf128
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001862.fa
@@ -0,0 +1,12 @@
+>NZ_CP042169.1_1247
+MTTETAADETGTDAGAHRHGYISDKDRYRNRMKRIEGQARGITKMIDDEKYCIDILTQVS
+ALTRALQGVATGLLDDHLKHCVLDAAKKGDEDAAIAKIQEATDAINRLVRS*
+>NZ_CP033200.1_976
+MTTETAADETGTDAGAHRHGYISDKDRYRNRMKRIEGQARGITKMIDDEKYCIDILTQVS
+ALTRALQGVATGLLDDHLKHCVLDAAKKGDEDAAIAKIQEATDAINRLVRS*
+>NZ_CP083691.1_693
+MSVDNDSHQHGYISDKERYLGRMKRIEGQARGIAKMIDEEKYCIDILTQVSALTRALQGV
+ATGLLDDHLKHCVLDAAKLSDEAAVEKIQEATDAINRLVRS*
+>NZ_CP097650.1_1204
+MTTETAADETGADTGAHRHGYISDKDRYRNRMKRIEGQARGITKMIDDEKYCIDILTQVS
+ALTRALQGVATGLLDDHLKHCVLDAAKKGDEDAAIAKIQEATDAINRLVRS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001863.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001863.fa
new file mode 100644
index 0000000000000000000000000000000000000000..534832dad831cf28cb20b10c43f618d30bef3ee9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001863.fa
@@ -0,0 +1,37 @@
+>NZ_CP042169.1_1263
+MAELRLTGPTEDGDALRLSGPEGEEHTLPLSPYLRRLVIEGAAPEDGRPAEDGPAAWHDM
+TEMDVPGADDEDAEGPVDAATHADDAAAEDERAPEAPSGPARPDEDLALTPRIDPRPVAD
+DSTADGPTPAPLTDQESVKAAATQEAVPLTPREIQQRIRAGASVEQVARESGNAFSRIRT
+YGHPVLAERDWIARQARAVEVWVGGPDLYSDLVQDGGPTTLGELAAHRLAELGVDEASLE
+WDAWREDQAGWTVAARFAVAGARSLPTREEPPALWTFRPAGRHLEPENAWARALSEAEAW
+DLVPRAPAAEPVTDDVDAEDAVTPAGAHSPAADRDADLLEILRVRRGQRVGADLESDDAL
+AHLIAREHQDRSRREAAQAPERLAPVDAEGALTTADDAPVVDAPEPAAETDRAEDTAADV
+ADAGVEDEGAEPAPRERAARPAMPTVTPRPRARSAARRASVPSWDEIVFGRKGD*
+>NZ_CP033200.1_996
+MAELRLTGPTEDGDALRLSGPEGEEHTLPLSPYLRRLVIEGAAPEDGRPAEDGPAAWHDM
+TEMDVPGADDEDAEGPVDAATHADDAAAEDERAPEAPSGPARPDEDLALTPRIDPRPVAD
+DSTADGPTPAPLTDQESVKAAATQEAVPLTPREIQQRIRAGASVEQVARESGNAFSRIRT
+YGHPVLAERDWIARQARAVEVWVGGPDLYSDLVQDGGPTTLGELAAHRLAELGVDEASLE
+WDAWREDQAGWTVAARFAVAGARSLPTREEPPALWTFRPAGRHLEPENAWARALSEAEAW
+DLVPRAPAAEPVTDDVDAEDAVTPAGAHSPAADRDADLLEILRVRRGQRVGADLESDDAL
+AHLIAREHQDRSRREAAQAPERLAPVDAEGALTTADDAPVVDAPEPAAETDRAEDTAADV
+ADAGVEDEGAEPAPRERAARPAMPTVTPRPRARSAARRASVPSWDEIVFGRKGD*
+>NZ_CP083691.1_1454
+MAELRLTGTTEDGHALRLAAPDGTEHTLERTPFLRRLALDDVARPDAVPAAEPADGAAPA
+SPAQADEPSAEAPAPEVPRPAPSPAQEPAAPVTAVAEQADVRAAATAEAQPLSPRDIQAR
+IRAGASVEQVARESGNAFSRVRTYGYPVLAERGYIAQQARAVQVWVGGPDLYSGTVADGG
+PTTLGALAEHRVRELGTDPASLEWDAWRESGGVAWTVVARFPLPPRGRALTAEEPPARWS
+FRPAGGRLDPENAWARILSDAEAWDVFTAEEPLTREDDAAAPQQGGGEEASGGDAPAAVT
+PLGASPSSVGVDADLLEILRARRGRRVGQDAESDDALAHLIARGVAEREARQDGAEADHT
+EQAETEPAAPGRAARLLRGLPSLREEVAKDGADGRPPVEADSPAAEAAPAVDAAGREDAV
+TPQAPGKTDAGKTVAGPSGADRTETGQAGTMQADAEPSDAPVAAPQEEEPARTARRERPA
+MPTPRPRARSAARRASVPSWDDIVFGKKSD*
+>NZ_CP097650.1_1220
+MAELRLTGPTEDGDALRLSGPEGEEHTLPLSPYLRRLVIEGAAPEDGRPAEDGPAAWHDM
+TEMDVPRADAEEPVDATTHADDAAEEGERAPDVPSGPARPDEDLALTPRIDPRPVADDST
+ADGPTPAPLTDQESVKAAATQEAVPLTPREIQQRIRAGASVEQVARESGNAFSRIRTYGH
+PVLAERDWIARQARAVEVWVGGPDLYSDLVQDGGPTTLGELAAHRLAELGVDEASLEWDA
+WREDQAGWTVAARFAVAGARSLPTREEPPALWTFRPAGRHLEPENAWARALSEAEAWDLV
+PRAPAAEPVTDDVDAEDAVTPAGAHSPAADRDADLLEILRVRRGQRVGADLESDDALAHL
+IAREHQDRSRREAAQAPERLAPVDAEGALTTADDAPVVDAPEPAAETDRAEDTAADVADA
+GVEDEGAEPAPRERAARPAMPTVTPRPRARSAARRASVPSWDEIVFGRKGD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001864.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001864.fa
new file mode 100644
index 0000000000000000000000000000000000000000..892514ba5e612e5071fd8c26b253e6927e38356f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001864.fa
@@ -0,0 +1,28 @@
+>NZ_CP042169.1_1272
+MSVPVLLLAVVAVALAGPVPVLLGRAAWPARSPVLAALAWQAVALAGGLALLGAPLVWGL
+LPWGEGLVAAAPRLAAHLAGDAAAAPRPTGLPVGLHLMAVGAGAGIAVHLLLTTAVTAVR
+TLRARARHRDAVELVATGPADAGRWPGGARGARELPVDDPLAYCVPGSPRGGEALTVVSS
+GLLARLSPEELDAVVAHERAHLDQHHGLLRLAFAAWARACAWLPTAETARLAVVQVTEML
+ADDAALRRAPADVLVRALAQAAPGPDAGPAGQTDATGPTSAGLGDRAARLLTRPAPLPAA
+AAALVAAASLALPAATAAALLGLP*
+>NZ_CP040019.1_1551
+MSVPVLLLAVVAVALAGPVPVLLGRAAWPARSPVLAALAWQAVALAGGLALLGAPLVWGL
+LPWGEGLVAAAPRLAAHLAGDAAAAPRPTGLPVGLHLMAVGAGAGIAVHLLLTTAVTVVR
+TLRARARHRDAVELVATGPTDAGRWPGGARGARELPVDDPLAYCVPGSPRGGEALTVVSS
+GLLARLSPEELDAVVAHERAHLDQHHGLLRLAFAAWARACAWLPTAETARLAVVQVTEML
+ADDAALRRAPADVLVRALAQAAPGPDAGPAGQTDATGPTSAGLGDRAARLLTRPAPLPAA
+AAALVAAASLALPAATAAALLGLP*
+>NZ_CP040019.1_2615
+MTAGILTMALCTGLVALAVFGPWLLRHAAPALVRVPRLAIVVVAGGIGVWLVTLLAIGPV
+LAWAGAGPALLPERAAEVCQRCLTAANPFSADTTETLIPAVLLLALPVALALALGAGLAR
+QMVRRSSRSRDAARTLLHGARRQLLHGHEVALVDAEHPFALTFPDRHGGIVLSTGAVRAL
+GPGELAAVLAHEHAHLHQRHHLITALVDSIAAYLRWVPLIRAVADALPHYLEIAADDQAR
+RHAGTRALVSALVKLGERTHPAMPQHSCPVALHAAGPERIRHLVHPSAGLAGALPAVAIA
+AYLVGMAALAALVHLPYVSAALTGCTI*
+>NZ_CP083691.1_1445
+MSFSVLVLAAVALCLAGPVPVLLGRAAWPSRSPGLAVLAWQAVALAGGLALVGTPLLWGL
+HPWGDGLLDAVPALLADLTSPDSGIARPGSAPAEVHLLAVGAGLTVALHLLLTTAVTALR
+TLRARSRHRAALELIATDPERADDWPGGPRGARELPVDLPLAYCVPGVPGGGTPLTVVSR
+GLLERLSPEELRAVLLHERAHLAQHHGLLRLAFASWARACAWLPSAETARAGVVLVTEML
+ADDAARRTAPAPVLARALALTVRPAEAPGASASGPDAEPDAESGGLGRRVARLLDPPAPV
+PGAVAGAAAAACLALPLAVLAVILGPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001870.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001870.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4569246351aeb18f45b49d2989ff78fdee638eb4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001870.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1367
+MTARPYRVLVVEDEQLTAETYVAHLDRLPGFEVAAVAGSLLAARQVAAAGLHANGRFPFD
+VVLLDMNLPDGHGLDFLRQLRAAGFHGGVLALTAATDLPVVRRAVAYGVTQYLVKPFGFD
+EFADRLGGFRAASAMLAGDGALDGQEQVDAVFRVSRERRAEALPKGLTESTLREVVELLG
+ADPETALSAAEVGERLGISRVTARRYLEHLERIRRVRRSARHGGRGRPEQEYRWAGRT*
+>NZ_CP033200.1_1107
+MTARPYRVLVVEDEQLTAETYVAHLDRLPGFEVAAVAGSLLAARQVAAAGLHADGRFPFD
+VVLLDMNLPDGHGLDFLHQLRAAGFHGGVLALTAATDLPVVRRAVAYGVTQYLVKPFGFD
+*
+>NZ_CP083691.1_1368
+MSAERPYRVLIVEDEELTAQTCADHVTRLPGFTVVGAVGTVDAARRLVAAALDRDGRFPF
+DVLLLDMNLPDGHGLDLLQQLRAAGFQGGVLALTAATELSVVRRAIALGVVQYLVKPFGF
+EAFAQRMTGFRSAAALLAGPGRLSGQEHVDDVFRAGQRRGVEELPKGLSAGTLQAVLDLV
+HDADGGRSASEAAAGLGLSRVTARRYLEHLERIGRVRRRARHGGRGRPEQEYVWAPGAPS
+A*
+>NZ_CP097650.1_1316
+MTARPYRVLVVEDEQLTAETYVAHLDRLPGFEVAAVAGSLLAARQVAAAGLHANGRFPFD
+VVLLDMNLPDGHGLDFLRQLRAAGFHGGVLALTAATDLPVVRRAVAYGVTQYLVKPFGFD
+EFADRLGGFRAASAMLAGDGALDGQEQVDAVFRVSRERRAEALPKGLTEGTLREVVELLG
+ADPETALSAAEVGERLGISRVTARRYLEHLERIRRVRRSARHGGRGRPEQEYRWAGRT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001871.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001871.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb0ee7a24ea4b04434520e596bfbbc614d5a893d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001871.fa
@@ -0,0 +1,44 @@
+>NZ_CP042169.1_1373
+MFVTGGVASSLGKGLTASSLGHLLKARGLRVVMQKLDPYLNVDPGTMNPFQHGEVFVTED
+GAETDLDIGHYERFLDEDLDGLDNVTTGQVYSTVIARERRGEYLGDTVQVIPHITDEICR
+RMRLPAEPRGDRPAPDVIITEIGGTVGDIESQPFLEAARQVRQDVGRDDVFFLHVSLVPY
+IGPSQELKTKPTQHSVAALRSIGIQPDAIVLRSDRAVPDDVRGKIARMCDVPQDAVVNCA
+DAPSIYDIPRVIHDQGLDAHVVQSLDLKFKDVDWTAWDALMDAVHHPEHELTVALVGKYV
+DLPDAYLSVTEALRAGGFAHRAKVGIRWVAADECATPEGAAVALADVDAVCVPGGFGVRG
+LEGKLGALRHAREQRIPTLGLCLGLQSMVIEYARNVLGLEDADSTEFDPETASPVIATMA
+EQEQIVAGEGDLGGTMRLGAFPATLRPGSVVAEAYGTTEVTERHRHRYEVNNAYRDRLEE
+AGLAICGTSPDGALVEFVELPRDVHPYYVSTQAHPEFSSRPTRPHPLFAGLVAAGLARRA
+DAAARR*
+>NZ_CP033200.1_1114
+MFVTGGVASSLGKGLTASSLGHLLKARGLRVVMQKLDPYLNVDPGTMNPFQHGEVFVTED
+GAETDLDIGHYERFLDEDLDGLDNVTTGQVYSTVIARERRGEYLGDTVQVIPHITDEICR
+RMRLPAEPRGDRPAPDVIITEIGGTVGDIESQPFLEAARQVRQDVGRDDVFFLHVSLVPY
+IGPSQELKTKPTQHSVAALRSIGIQPDAIVLRSDRAVPDDVRGKIARMCDVPQDAVVNCA
+DAPSIYDIPRVIHDQGLDAHVVQSLDLKFKDVDWTAWDALMDAVHHPEHELTVALVGKYV
+DLPDAYLSVTEALRAGGFAHRAKVGIRWVAADECATPEGAAVALADVDAVCVPGGFGVRG
+LEGKLGALRHAREQRIPTLGLCLGLQSMVIEYARNVLGLEDADSTEFDPETASPVIATMA
+EQEQIVAGEGDLGGTMRLGAFPATLRPGSVVAEAYGTTEVTERHRHRYEVNNAYRDRLEE
+AGLAICGTSPDGALVEFVELPRDVHPYYVSTQAHPEFSSRPTRPHPLFAGLVAAGLARRA
+DAAARR*
+>NZ_CP040019.1_1456
+MFVTGGVASSLGKGLTASSLGHLLKARGLRVVMQKLDPYLNVDPGTMNPFQHGEVFVTED
+GAETDLDIGHYERFLDEDLDGLDNVTTGQVYSTVIARERRGEYLGDTVQVIPHITDEICR
+RMRLPAEPRGDRPAPDVIITEIGGTVGDIESQPFLEAARQVRQDVGRDDVFFLHVSLVPY
+IGPSQELKTKPTQHSVAALRSIGIQPDAIVLRSDRAVPDDVRGKIARMCDVPQDAVVNCA
+DAPSIYDIPRVIHDQGLDAHVVQSLDLKFKDVDWTAWDALMDAVHHPEHELTVALVGKYV
+DLPDAYLSVTEALRAGGFAHRAKVGIRWVAADECATPEGAAAALADVDAVCVPGGFGVRG
+LEGKLDALRHAREQRIPTLGLCLGLQSMVIEYARNVLGLEDADSTEFDPETASPVIATMA
+EQEQIVAGEGDLGGTMRLGAFPATLRPGSVVAEAYGTTEVTERHRHRYEVNNAYRDRLEE
+AGLAICGTSPDGALVEFVELPRDVHPYYVSTQAHPEFSSRPTRPHPLFAGLVAAGLARRA
+DAAARR*
+>NZ_CP097650.1_1322
+MFVTGGVASSLGKGLTASSLGHLLKARGLRVVMQKLDPYLNVDPGTMNPFQHGEVFVTED
+GAETDLDIGHYERFLDEDLDGLDNVTTGQVYSTVIARERRGEYLGDTVQVIPHITDEICR
+RMRLPAEPRGDRPAPDVIITEIGGTVGDIESQPFLEAARQVRQDVGRDDVFFLHVSLVPY
+IGPSQELKTKPTQHSVAALRSIGIQPDAIVLRSDRAVPDDVRGKIARMCDVPQDAVVNCA
+DAPSIYDIPRVIHDQGLDAHVVQSLDLKFKDVDWTAWDALMDAVHHPEHELTVALVGKYV
+DLPDAYLSVTEALRAGGFAHRAKVGIRWVAADECATPEGAAVALADVDAVCVPGGFGVRG
+LEGKLGALRHAREQRIPTLGLCLGLQSMVIEYARNVLGLEDADSTEFDPETASPVIATMA
+EQEQIVAGEGDLGGTMRLGAFPATLRPGSVVAEAYGTTEVTERHRHRYEVNNAYRDRLEE
+AGLAICGTSPDGALVEFVELPRDVHPYYVSTQAHPEFSSRPTRPHPLFAGLVAAGLARRA
+DAAARR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001874.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001874.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b6063b25dc2811596c8c76e47cf4477b37bcf56
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001874.fa
@@ -0,0 +1,47 @@
+>NZ_CP042169.1_1423
+MTVSGPGLSAAPAAEPGAEPVEPAAGRPRSWVPGPAWRALRRRWRRSLRLRTAVLAALLS
+ILAGLVVAAFLTQQITQALFEARYEQVQAEARRGLSQVRETFAQTTATDAQSTDVLVTQT
+LRALEGDSGTTIRRRYHLAPLPGSESAYVGTISSAGLDPAVIPQELQDAVASGPGVYDAS
+VALPDPGGGTRPGLVFGAQVVLPPGATYGLYLVYDLADVQSSLDSVLGVLLVFGVGFLVI
+NVLVSWWVSRRVTLPVQQAARAAESLSSGNLAVRMPVDGEDEMARLGMSFNRMADSIQDQ
+IGQLAQLSQMQQRFVSDVSHELRTPLTTVRMAADVLYGSREDFDPVNRRSTELLYHQVDR
+FQAMLADLLEITRFDAGAATPALEATDMLELARDVVLTSQPLADQSGVPVYVVPMDRDRA
+DGHVAWVDPRRIERILRNLVNNAIEHAEGRPVDVLVAADEEAVTFAVVDHGIGMSPEQVQ
+RVFDRFWRADPSRKRTTGGSGLGLAIATEDTRLHGGRLEAWGELGEGSTFMVTLPRAPRP
+AAQGAEAPEPIGRSVLPIPPRYSTADRRYADDLSRPVPQEADADADAVGRVADVAATAAD
+APPCARQDEQALTAPTRPVRRVPPGDPADGPAAGDRTGEDAAEEAR*
+>NZ_CP033200.1_1165
+MTVSGPDVSAAPAAESGAEPVEPAAARPRSWGPGPAWRALRRRWRRSLRLRTAVLAALLS
+ILAGLVVAAFLTQQITQALFEARYEQVQSEARRGLSQVRETFAQTTATDAQSTDVLVTQT
+LRALEGDSGTTIRRRYHLAPLPDSESAYVGTISSAGLDPAVIPQELQDAVASGPGVYDAS
+VALPNPGGGTRPGLVFGAQVVLPPGATYGLYLVYDLADVQSSLDSVLGVLLVFGVGFLVI
+NVLVSWWVSRHVTLPVQQAARAAESLSSGNLAVRMPVDGEDEMARLGMSFNRMADSIQDQ
+IGQLAQLSQMQQRFVSDVSHELRTPLTTVRMAADVLYGSREDFDPVSRRSTELLYHQVDR
+FQAMLADLLEITRFDAGAATPALEATDMLELARDVVLTSQPLADQIGVPVYMVPMDRDRA
+DGHVAHVDPRRIERILRNLVNNAIEHAEGRPVDVLVAADEEAVTFAVVDHGIGMSPEQVQ
+RVFDRFWRADPSRKRTTGGSGLGLAIATEDTRLHGGRLEAWGELGEGSTFMVTLPRAPRP
+AVQGAEAPEPIGRSVLPIPPRYSTADRRYADDLSRPVPQEADADAVGTVADVATAAPPSA
+RQAEQALTAPTRPVRVVPAEDPAHGSAPGDPTGDDPAEEAR*
+>NZ_CP083691.1_1308
+MTAPAEPPQPAETGDPDETGATSAPASAGPSTSAAPPRAGLRRRLRRRWNGSLQLRTAVL
+AGLLTLLASLMISGLITQQVAQALFDARHQQVEAEARRGLARVQSTFANAAATDQQATDA
+LVSQTMRALELDGGTTIRRRFRLEPLPGGTAASVGTVSSQGLDADVIPQDLRDAVASGPG
+VYDASIALPAADGNTRPGLAYGTQVVLPPGATYALYLVYDLSDVQESLDSVLGVLLMFGS
+GFLLVTVLVSWWAAHSVVRPVQQAATAAESISGGNLAVRMPVRGDDEMARLGTSFNRMAD
+SIQAQITQLAQLSRMQQRFVSDVSHELRTPLTTVRMAADVLYGSREDFDPVNRRSTELLY
+HQVDRFQAMLADLLEITRFDAGAAQLALEDTDLLALARDVVLTAAPLADQAKVPVYLVPL
+PLEEGLDCVAQVDPRRIERILRNLVNNAIEHAEGSPVDVLVAADEGAVSVAVVDEGIGMS
+PEQVQRVFDRFWRADPSRKRTTGGSGLGLAIATEDTRLHGGRLEAWGELGVGSVFMVTLP
+RRNGAESPVRRAVLPMPPSYDRGGRRLAADLHTPVTGPEGTGVHDAAALPERGREQEL*
+>NZ_CP097650.1_1372
+MTVSGPGLSAAPAAEPGAEPVEPAAGRPRSWVPGPAWRALRRRWRRSLRLRTAVLAALLS
+ILAGLVVAAFLTQQITQALFEARYEQVQAEARRGLSQVRETFAQTTATDAQSTDVLVTQT
+LRALEGDSGTTIRRRYHLAPLPGSESAYVGTISSAGLDPAVIPQELQDAVASGPGVYDAS
+VALPDPGGGTRPGLVFGAQVVLPPGATYGLYLVYDLADVQSSLDSVLGVLLVFGVGFLVI
+NVLVSWWVSRRVTRPVQQAARAAESLSSGNLAVRMPVDGEDEMARLGTSFNRMADSIQDQ
+IGQLAQLSQMQQRFVSDVSHELRTPLTTVRMAADVLYGSREDFDPVNRRSTELLYHQVDR
+FQAMLADLLEITRFDAGAATPALEATDMLELARDVVLTSQPLADQIGVPVYVVPMDRDRA
+DGHVAWVDPRRIERILRNLVNNAIEHAEGRPVDVLVAADEEAVTFAVVDHGIGMSPEQVQ
+RVFDRFWRADPARKRTTGGSGLGLAIATEDTRLHGGRLEAWGELGEGSTFMVTLPRAPRP
+AAQGAEAPEPIGRSVLPIPPRYSTADRRYADDLSRPVPQEADADAVGTVADVTAAAADAP
+PSARQAEQALTAPTRPVRMVPPADGTAAGGWTGDDGAEEAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001876.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001876.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed406f2aa0655ed622a146dbc56407f0e7c47838
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001876.fa
@@ -0,0 +1,36 @@
+>NZ_CP042169.1_1430
+MVGSFLVAIVTGTGALLLPASYQGRAPTPLEAAFTATSATTVTGLGVVDTQTFWTPLGQL
+VILTLIKLGGLGVMTFTSLLGLVILRRLGLTQRLDAAASTRAEGIGDLPRVLRALILYST
+AVEASVALLLSLRFWLGAGMSPGQALWQGVFHAVSAFNNAGFALFSDNLMGFVSDPFICL
+PIAAAIILGGLGLPVVLTLRRDLRRPERWNLTVRLVLVGTAVLLVGGTLMYLVLEWSNPR
+TLGGLDPASRVLAAFFQSVTTRTAGFNTLDYGQMHPVTLFATDVLMFIGGGPAGTASGVK
+ITTASVLLFIVLAEIRGEGAVHAFGRRLSRTTHREAITVIMLSATAIAVATMALMGLSSF
+TTDQILFECVSAFSTVGLSTGITAQLPPAAQGILMLLMFVGRIGPATVAGSLALTDRTRH
+FEYPKERPLIG*
+>NZ_CP033200.1_1172
+MVGSFLVAIVTGTGALLLPASYQGRAPTPLEAAFTATSATTVTGLGVVDTQTFWTPLGQL
+VILTLIKLGGLGVMTFTSLLGLVILRRLGLTQRLDAAASTRAEGIGDLPRVLRALILYST
+AVEASVALLLSLRFWLGAGMSPGQALWQGVFHAVSAFNNAGFALFSDNLMGFVSDPFICL
+PIAAAIILGGLGLPVVLTLRRDLRRPERWNLTVRLVLVGTAVLLVGGTLMYLVLEWSNPR
+TLGGLDPASRVLAAFFQSVTTRTAGFNTLDYGQMHPVTLFATDVLMFIGGGPAGTASGVK
+ITTASVLLFIVLAEIRGEGAVHAFGRRLSRTTHREAITVIMLSATAIAVATMALMGLSSF
+TTDQILFECVSAFSTVGLSTGITAQLPPAAQGILMLLMFVGRIGPATVAGSLALTDRTRH
+FEYPKERPLIG*
+>NZ_CP083691.1_1301
+MVGSFLVAIVTGTGALLLPASYQGRAPTPLEAAFTATSATTVTGLGVVDTQTFWTPLGQV
+VILALIKLGGLGVMTFTSLLGLVILRRLGLTQRLDAAASTRAEGIGDLPRVLQALILYST
+AVEASVALLLSLRFWLGAGMSPGQALWQGIFHAVSAFNNAGFALFSDNLMGFVSDPFICL
+PIAAAIILGGLGLPVVLTLRRHLRRPERWNLTVRLVLVGTAVLLVGGTLMYLVLEWSNPR
+TLGGLDPASRVLAAFFQSVTTRTAGFNTLDYGQMHPVTLFGTDVLMFIGGGPAGTASGVK
+ITTASVLLFIVLAEIRGEGAVHAFGRRLSRTTHREAITVIMLSATAIAVATMAIMGLSSF
+TTDQILFECVSAFGTVGLSTGITAQLPPTAQGILMLLMFVGRIGPATVAGSLALTDRTRH
+FEYPKERPLIG*
+>NZ_CP097650.1_1379
+MVGSFLVAIVTGTGALLLPASYQGRAPTPLEAAFTATSATTVTGLGVVDTQTFWTPLGQL
+VILTLIKLGGLGVMTFTSLLGLVILRRLGLTQRLDAAASTRAEGIGDLPRVLRALILYST
+AVEASVALLLSLRFWLGAGMSPGQALWQGVFHAVSAFNNAGFALFSDNLMGFVSDPFICL
+PIAAAIILGGLGLPVVLTLRRDLRRPERWNLTVRLVLVGTAVLLVGGTLMYLVLEWSNPR
+TLGGLDPASRVLAAFFQSVTTRTAGFNTLDYGQMHPVTLFATDVLMFIGGGPAGTASGVK
+ITTASVLLFIVLAEIRGEGAVHAFGRRLSRTTHREAITVIMLSATAIAVATMALMGLSSF
+TTDQILFECVSAFSTVGLSTGITAQLPPAAQGILMLLMFVGRIGPATVAGSLALTDRTRH
+FEYPKERPLIG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001879.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001879.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f967ea01f706c98f7592d1e8439334b90edec9b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001879.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1537
+MSEFLASRWPDILFRAWQHGWLVLQALAIATVLAIALAVIATRIKALTPIANAFTAVGLT
+LPSFALIGVLIPLVGIGTVPAVVVVVFYALLPILRNALVGLRGVDPEVLEAARGMGMGPV
+ALFTRVRLPLAWPVILTGIRVAGQLGMGVAAVAAYVLGPGLGSYIFTGLVSLGGANALNY
+ALVGTLGIVVVALVLDGLLVLLGRLTISKGLRA*
+>NZ_CP033200.1_1259
+MSEFLASRWPDILFRAWQHGWLVLQALAIATVLAIALAVIATRIKALTPIANAFTAVGLT
+LPSFALIGVLIPLVGIGTVPAVVVVVFYALLPILRNALVGLRGVDPEVLEAARGMGMGPV
+ALFTRVRLPLAWPVILTGIRVAGQLGMGVAAVAAYVLGPGLGSYIFTGLVSLGGANALNY
+ALVGTLGIVVVALVLDGLLVLLGRLTISKGLRA*
+>NZ_CP040019.1_1314
+MSEFLASRWPDILFRAWQHGWLVLQALAIATVLAIALAVIATRIKALTPIANALTAVGLT
+LPSFALIGVLIPLVGIGTVPAVVVVVFYALLPILRNALVGLRGVDPDVLEAARGMGMGPV
+ALFTRVRLPLAWPVILTGIRVAGQLGMGVAAVAAYVLGPGLGSYIFTGLVSLGGANALNY
+ALVGTLGIVVVALLLDGLLVLLGRLTISKGLRA*
+>NZ_CP097650.1_1464
+MSEFLASRWPDILFRAWQHGWLVLQALAIATVLAIALAVIATRIKALTPIANAFTAVGLT
+LPSFALIGVLIPLVGIGTVPAVVVVVFYALLPILRNALVGLRGVDPEVLEAARGMGMGPV
+ALFTRVRLPLAWPVILTGIRVAGQLGMGVAAVAAYVLGPGLGSYIFTGLVSLGGANALNY
+ALVGTLGIVVVALVLDGLLVLLGRLTISKGLRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001880.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001880.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49b2b78a6ebb5236dc016688145ab11757757a0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001880.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1539
+MTATRSGGAATSRLNAKVVGISVAAALGGFLFGFDTSVINGAVDALAGEFGLGAGLTGFA
+VSSALIGCALGAWFAGPIANRRGRVPVMVIAAILFLVSAIGSGLAFGVVDLIFWRVVGGL
+GVGAASVIAPAYIAEVSPAHVRGRLGSLQQLAIVLGIFAALLTDALFATMAGGAAQPFWL
+GVDAWRWMFLAEAVPAVLYGLFALKLPESPRYLVARGRTDEAAEVLHEFTGVDRVNLMIE
+DIRRSLDSERRESLADLRGPSAGLQPIVWIGILLSVFQQAVGINVIFYYSTTLWRSVGFG
+ESDALTVTVITSVTNIAVTLIAIALVDRVGRRPMLIAGSAGMTVSLGLMALAFSFAQTGG
+AESVSLPQPWSTVALVAANAFVVFFGATWGPLVWVLLGEMFPNRIRAGALAVAAAAQWAA
+NFTVSTTFPWLADIGLTLAYGLYAVMAALSLAFVAAFVPETKGKTLEEMSDVVVRSPGQR
+RAVRAEAERDLRG*
+>NZ_CP033200.1_1261
+MTATRSGGAATSRLNAKVVGISVAAALGGFLFGFDTSVINGAVDALAGEFGLGAGLTGFA
+VSSALIGCALGAWFAGPVANRRGRVPVMVIAAILFLVSAIGSGLAFGVVDLIFWRMVGGL
+GVGAASVIAPAYIAEVSPAHVRGRLGSLQQLAIVLGIFAALLTDALFATMAGGAAQPFWL
+GVDAWRWMFLAEAVPAVLYGLFALKLPESPRYLVARGRTDEAAEVLHEFTGVDRVNLMIE
+DIRRSLDSERRESLADLRGPSAGLQPIVWIGILLSVFQQAVGINVIFYYSTTLWRSVGFG
+ESDALTVTVITSVTNIAVTLIAIALVDRVGRRPMLIAGSAGMTVSLGLMALAFSFAQTGG
+AESVSLPQPWSTVALVAANAFVVFFGATWGPLVWVLLGEMFPNRIRAGALAVAAAAQWAA
+NFTVSTTFPWLADIGLTLAYGLYAVMAALSLAFVAAFVPETKGKTLEEMSDVVVRSPGQR
+RAVRAEAERDLRG*
+>NZ_CP040019.1_1312
+MTATRSGGAATSRLNAKVVGISVAAALGGFLFGFDTSVINGAVDALAGEFGLGPGLTGFT
+VSSALIGCALGAWFAGPIANRRGRVPVMVIAAILFLVSAIGSGLAFGVVDLIFWRMVGGL
+GVGAASVIAPAYIAEVSPAHVRGRLGSLQQLAIVLGIFAALLSDALFATMAGGAAQPFWL
+GVDAWRWMFLAEAVPAVLYGLFALKLPESPRYLVARGRTDEAAEVLHEFTGVDRVNLMIE
+DIRRSLDSEHRESLADLRGPAAGLQPIVWIGILLSVFQQAVGINVIFYYSTTLWRSVGFG
+ESDALTVTVITSVTNIAVTFIAIALVDRVGRRPMLIAGSAGMAVSLGLMALAFSFAETGG
+AESVSLPQPWSTVALVAANAFVVFFGATWGPLVWVLLGEMFPNRIRAGALAVAAAAQWAA
+NFTVSTTFPWLADIGLTLAYGLYALMAALSLAFVAAFVPETKGKTLEQMSDIVVRSPGQR
+RAGRAEAERDLRG*
+>NZ_CP097650.1_1466
+MTATRSGGAATSRLNAKVVGISVAAALGGFLFGFDTSVINGAVDALAGEFGLGAGLTGFA
+VSSALIGCALGAWFAGPIANRRGRVPVMVIAAILFLVSAIGSGLAFGVVDLIFWRVVGGL
+GVGAASVIAPAYIAEVSPAHVRGRLGSLQQLAIVLGIFAALLTDALFATMAGGAAQPFWL
+GVDAWRWMFLAEAVPAVLYGLFALKLPESPRYLVARGRTDEAAEVLHEFTGVDRVNLMIE
+DIRRSLDSERRESLADLRGPSAGLQPIVWIGILLSVFQQAVGINVIFYYSTTLWRSVGFG
+ESDALTVTVITSVTNIAVTLIAIALVDRVGRRPMLIAGSAGMTVSLGLMALAFSFAQTGG
+AESVSLPQPWSTVALVAANAFVVFFGATWGPLVWVLLGEMFPNRIRAGALAVAAAAQWAA
+NFTVSTTFPWLADIGLTLAYGLYAVMAALSLAFVAAFVPETKGKTLEEMSDVVVRSPGQR
+RAVRAEAERDLRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001885.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001885.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0dbfaa60465aed845da2f4b077e6b35ff394b6b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001885.fa
@@ -0,0 +1,16 @@
+>NZ_CP042169.1_1620
+MTGHDHPRPESISAAVDEQMLADFLNQHLLGSRSGVKAFRAAEQTWAGTPQEAALRRLGD
+AVQDDQDRLEALIGELGLRTPLVDRAAGAAAEVGGRLNPVNALRTRGSGWTQIELDLLQG
+MLQAKSAMWDVLEQLAPHLPAVDAAEMQALRQRTADQQREVQRITSATLEGRFLAG*
+>NZ_CP033200.1_1336
+MTGHEHPRPESTSAAVDEQMLEDFPNQHLLGSRSGVKAFRAAEQTWAGTPQEAALRRLGD
+AVQDDQDRLEALIGELGLRTPLVDRAAGAAAEVGGRLNPVNALRTRGSGWTQIELDLLQG
+MLQAKSAMWHVLEQLAPHLPAVDAAEMQALRQRAADQQREVQRITSATLEGRFLAG*
+>NZ_CP040019.1_1203
+MTGHEHPRPEPLSAAVDEQMLEDFLNQHLLGSRSGVKAFRAAEQTWAGTPQEDALRRLGD
+AVQDDQERLEALIGELGLRTPLVDRAAGAAAEVGGRLNPVNALRTRGSGWTQIELDLLQG
+MLQAKAAMWHVLEALAPHEPVLDAGEMAALYERAQDQQRAVQRIAEDTLLERFLR*
+>NZ_CP097650.1_1550
+MTGHEHPRPESTSAAVDEQMLADFLNQHLLGSRSGVKAFRAAEQTWAGTPQEAALRRLGD
+AVQDDQDRLEALIGELGLRTPLVDRAAGAAAEVGGRLNPVNALRTRGSGWTQIELDLLQG
+MLQAKSAMWHVLEQLAPHLPAVDAAEMHALRQRTGDQQREVQRITSATLEGRFLAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001890.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001890.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef098957ec5ef0f27b6ed6f91fb5484d045f58f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001890.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1733
+MRPRSASAARTREALRDAVQIYAPSTVYAVGLGAMTPALAVAALALGLDAARAAAVVLLV
+GLGSLVANGPASALAARAGERVTMVVSAVLGTAGAGLAWATTAGVSSGPSAAGVAEPGRL
+ALFLAAVLAVGMAGAGFNLARQAYLAVAVPATHRARAMSTLGGTVRIGTFLGPFLGAAAQ
+APLGLDGAFAAAAAAMAVGALLCLRIRDLPVPASGPAAGEDSAPAGRPRLLDVARARRGA
+LLTAGFGVVAVSAARAARNAVIPLWATHLGLDAATASLVFGLAGAADLLLFYPSGRLMDR
+FGRRAVAVPCLTLLGAGFLTVSLTREPTAFAAAAVLLGIGNGFGAGIVMTLGADHSPPNA
+RAQFLGLWRSMSDAGMLAGPLLLSGVTAAAGLAVGVGSLAVVCGLGAVVFAAVLPRGPGA
+VADPPAVVVRSR*
+>NZ_CP033200.1_1451
+MRPRSASAARTREALRDAVQIYAPSTVYAVGLGAMTPALAVAALALGLDAARAAAVVLLV
+GLGSLVANGPASALAARAGERVTMVVSAGLGTVGAGLAWATTAGVSSGPSAAGVAEPGRL
+ALFLAAVLAVGMAGAGFNLARQAYLAVAVPATHRARAMSTLGGTVRIGTFLGPFLGAAAQ
+APLGLDGAFAAAAAAMAVGALLCLRIRDLPVPASDPAAGEEPGPAGRPRLLDVARARRGA
+LLTAGFGVVAVSAARAARNAVIPLWATHLGLDAATASLVFGLAGAADLLLFYPSGRLMDR
+FGRRAVAVPCLTLLGAGFLAISLTREPTAFAAAAVLLGIGNGFGAGIVMTLGADHSPPNA
+RAPFLGLWRSMSDAGMLAGPLLLSGATAAAGLAVGVGSLAVVCGVGAVVFAAVLPRGPGA
+VADPPPVVVRPR*
+>NZ_CP040019.1_1072
+MPRRSASAARTRQALRGAVQIYAPSTVYAVGLGAMTPALAVAALALGLDAARAAAVVVLV
+GLGSLVANAPASALAARAGERVTIVVSAFLGTAGAALAWATTAGLSSSPGREGVVEPGRL
+ALYLTAVLAMGMAGSGFNLARQAYLAVAVPPSHRARAMSTLGGTIRIGVFLGPFLGAAVQ
+AAMGLDGAFAAATAAMAVGALLCLRIRDLPASGAAAPGADPGAQPVPAHRPRVADVARAR
+REVLLTAGFGVVAVSAARAARNAVIPLWATHLGMDAASASLVFGLAGAVDLLLFYPAGRL
+MDRHGRRAVAVPCLAVLGAGFLAVSLTRDPAAFAAATVLLGIGNGFGAGIVMTLGADYWL
+LGHPVGLGRAG*
+>NZ_CP097650.1_1662
+MRPRSASAARTREALRDAVQIYAPSTVYAVGLGAMTPALAVAALALGLDAARAAAVVLLV
+GLGSLVANGPASALAARAGERVTMVVSAGLGTVGAGLAWATTAGVSSGPSAAGVAEPGRL
+ALFLAAVLAVGMAGAGFNLARQAYLAVAVPATHRARAMSTLGGTVRIGTFLGPFLGAAAQ
+APLGLDGAFAAAAAAMAVGALLCLRIRDLPVPASDPAAGEEPGPAGRPRLRDVARARRGA
+LLTAGFGVVAVSAARAARNAVIPLWATHLGLDAATASLVFGLAGAADLLLFYPSGRLMDR
+FGRRAVAVPCLTLLGAGFLAISLTREPTAFAAAAVLLGIGNGFGAGIVMTLGADHSPPNA
+RAPFLGLWRSMSDAGMLAGPLLLSGATAAAGLAVGVGSLAVVCGVGAVVFAAVLPRGPGA
+VADPPPVVVRSR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001892.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001892.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f131972569fc97989dc3bd4cb30801fa25ad03fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001892.fa
@@ -0,0 +1,36 @@
+>NZ_CP042169.1_1783
+MPLGLTWLDVLLIVALAMLLVQGHRRGLWVVLGNLVGLVGGAAIAFYALPEVAEFVTAPQ
+WRWAALIATLVLLVAAGQYVGAAIGEAIRLRVNLPALRLVDRLLGALAAGLAGALVLWLV
+AFSIAASGSTAVTREVNRSQVITALDTVMPDSLLAWAARSRSAVADLDVLPELELPAPVP
+ESDDGVRAAPAPAATPGLPSAASSPSDTATSAPSASATPEEPDDAAAASSSTAAAPSATT
+TAPASSTSTAAPSTPAASSASAAVVRLTGTAAQCNQVQSGSGVAVAPDRVLTNAHVVLGV
+DAPTVTDRARGVHAARIVHLDTAHDLAVLAVDDANLPVMPVGAELTGGASASVLGYPDGG
+PFASTPATVQAVGEVPLGDVLTGAASMVDVYTLAADIRHGYSGGPVVDTAGNLAGLVFAR
+APGSDAVGYALTADTIAPVVAAAPGMTATVPSGDCVPGG*
+>NZ_CP033200.1_1491
+MPLGLTWLDVLLIVALAMLLVQGHRRGLWVVLGNLVGLVGGAAIAFYALPEVAKFVTAPQ
+WRWAALIATLVVLVAAGQYVGAAIGEAIRLRVNLPALRLVDRLLGALATGLAGALVLWLV
+AFSIAASGSTAVTREVTRSRVIAALDTVMPDSLLAWAARSRSAVADLDVLPELELPAPVP
+ETDDGVRAAPAPAATPGLPSAASSPSAPPATSAAATPEEPDDAAAASSSTSAAPSATTTA
+PASSTSTAAPSTPAASSASAAVVRLTGTAAQCNQVQSGSGVAVAPDRVLTNAHVVLGVDA
+PTVTDRARGVHAARIVHLDTAHDLAVLAVDDADLPVMPVGAELTGGASASVLGYPDGGPF
+ASTPATVQAVGEVPLGDVLTGAASMVDVYTLAADIRHGYSGGPVVDAAGNLAGLVFARAP
+GSDAVGYALTADTIAPVVAAAPGMTATVPSGDCVPGG*
+>NZ_CP040019.1_1014
+MPLSLTWLDAVLLVLLVVLLVQGHRRGLWVVLGNLVGLVGGAAIAFYAMPEVAQLVTAPQ
+WRWAALLATLVLLVAAGQYVGAAIGEAIRLRVNLPALRLVDRILGALAAGVAGALVVWLV
+SFSMSTAGSGAVTREVARSQVIAAIDRVLPDSALAWAARSRSAVADLDMLPELRLPEPVP
+VPDDDGGVRAAPPTSSSPATTPARPAEPEDAAPASGGSATPEERPPAPPTTAPPPFPTPR
+PRRPPRPPPPRPPRPPIPSPRRPTPPNPPPPRPSRTAVPAEAAVVRLTGTAAQCGQVQSG
+SGVAVAPDRVLTNAHVVLGVDAPTVTDAQRGVHDARIVHLDTARDLAVLALDGADLPVMP
+LGAELVGGESALVMGHPDGGPFASTPATVQAVGEVPLGDVVTGAASMVDVYTLAADIRHG
+YSGGPVVDAAGSLAGLVFARAPGADPVGYALSADSIAPAVAAAPGMSATVPSGDCIPGA*
+>NZ_CP097650.1_1704
+MPLGLTWLDVLLIVALAMLLVQGHRRGLWVVLGNLVGLVGGAAIAFYALPEVAKFVTAPQ
+WRWAALIATLVVLVAAGQYVGAAIGEAIRLRVNLPALRLVDRLLGALATGLAGALVLWLV
+AFSIAASGSTAVTREVTRSRVIAALDTVMPDSLLAWAARSRSAVADLDVLPELELPAPVP
+ETDDGVRAAPAPAATPGLPSAASSPSAPPATSAAATPEEPDDAAAASSSTSAAPSATTTA
+PASSTSTAAPSTPAASSASAAVVRLTGTAAQCNQVQSGSGVAVAPDRVLTNAHVVLGVDA
+PTVTDRARGVHAARIVHLDTAHDLAVLAVDDADLPVMPVGAELTGGASASVLGYPDGGPF
+ASTPATVQAVGEVPLGDVLTGAASMVDVYTLAADIRHGYSGGPVVDAAGNLAGLVFARAP
+GSDAVGYALTADTIAPVVAAAPGMTATVPSGDCVPGG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001894.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001894.fa
new file mode 100644
index 0000000000000000000000000000000000000000..caf0f51c217122dcb130112f131718905ea700f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001894.fa
@@ -0,0 +1,18 @@
+>NZ_CP042169.1_1824
+MAEKNAAEYTVPGLSLSTGRRTAEILQGRLHALNDLQLTLKHAHWNVVGPGFIGVHEMLD
+PQIELVRGMVDVVAERIATLGVSPAGTPGALVAARTWDDYTLGRASTLEHLAALDLVYDG
+VVTDHRAAIDATEDLDPVTQDILIDQVAQLELFQWFMRSFLTTDDGRLSSAGTTTEAAAA
+GRVKGAQSAPAPKAGRTKKSDAKKSKKK*
+>NZ_CP033200.1_1531
+MAEKNAAEYTVPGLSLSTGRRTAEILQGRLHALNDLQLTLKHAHWNVVGPGFIGVHEMLD
+PQIELVRGMVDVLAERIATLGVSPAGTPGALVAARAWDDYTLGRASTLEHLAALDLVYDG
+VVTDHRAAIDATEDLDPVTQDILIDQVAQLELFQWFMRSFLTTDDGRLSSAGTTTEAAAA
+GRVKGAQSAPAPKAGRTKKSDAKKSKKK*
+>NZ_CP040019.1_964
+MAAKKNDAAFTVPGLALKDGHRVAEILQGRLHALNDLQLTLKHAHWNVVGPGFIGVHEML
+DPQIETVRAMVDVVAERIATLGVSPEGTPGALVAARTWDDYALGRASTLEHLAALDLVYD
+GVVTDHRAAIETVGELDPVSEDMLIGQVAELELFQWFMRSFLTTVDGDLSHAGATREIVA
+AARVSGAQKAPAPKKGAAKKAPAKKK*
+>NZ_CP083691.1_901
+MDSRARASTDPGLSVEDGHHVAEVLPVRLHALNDLQLTLKHAHWNVVGPGVIGVHEMPGP
+QIEKVRAMVDAIAELELFPRSMRSFPATDDGELSHADALREAEAAKQK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001895.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001895.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e771c96140fdf15f634e7b6ff5d755fcf0a9226
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001895.fa
@@ -0,0 +1,57 @@
+>NZ_CP042169.1_1825
+MPTPPDLSAFRTPAATGRPPRGLRLGLAAALAVVWFAVLGLGGPVFGRIGDVSSNDQATF
+LPASAESTRAGQEAAAFQDGEAVPAVVVGPASTADPAAAFPALADLAGRLGEVPGVTDVA
+GPIPSDDGAAVQFLAFVDSSAGAERPVADVVADLREVVADPAAADPALAGTVAADTEWHV
+GGPAGLVAELGGAFAGIDGLLLLVALAVVFVILVAVYRSVLLPVLVLLTAVAALCGAIVA
+VYGMALAGWIQLNGQAQGILSILVIGAATDYCLLLVARHREELLVRADVGEALRAAVRGS
+FGAITASASTVALALLILMASDLNSTRSLGPVAATGVAFAWLAALTLLPALLRLTGRAAF
+WPTIPSPERARRRAQRRAARGRAFTPPLDGAGRPVAGLEEDHGVWTRVGAVVARRPRLVW
+VATTVVLLALCGGLLQLRADGVAQEDVLLGDSDARQAQALLSEHFDAGAGAPAQILAPAG
+DAEAVLAAVAEDPGVAEAEVTTDAPEAAAGPPPGVTDAEGGAGAASAPEPQPRVVDGRVL
+VSATLADPGESLAAQQTVARLRDRLADLPATGEILVGGPAAQALDTNVTTQRDLRVVIPL
+ILAMLLVILAVLLRSLLAPVLLVAATVVSFGAALGVSALVFRHVFGFEDADPTVPLYGFV
+FLVALGIDYTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPL
+MFMVQLAFIVAFGVLLDTLIVRSLLIPALVRDIGPKVWWPAKVD*
+>NZ_CP033200.1_1532
+MPTPPDLSAFRTPAATGRPPRGLRLGLAAALTVVWFAVLGLGGPVFGRIGDVSSNDQATF
+LPASAESTRAGQEAAAFQDGEAVPAVVVGPASTADPAAAFPALADLAGRLGEVPGVTDVA
+GPIPSDDGAAVQFLAFVDSSAGAERPVADVVADLREVVADPAAADPALAGTVAADTEWHV
+GGPAGLVAELGGAFAGIDGLLLLVALAVVFVILVAVYRSVLLPVLVLLTAVAALCGAIVA
+VYGMALAGWIQLNGQAQGILSILVIGAATDYCLLLVARHREELLVRADVGEALRAAVRGS
+FGAITASASTVALALLILMASDLNSTRSLGPVAATGVAFAWLAALTLLPALLRLTGRAAF
+WPTIPSPERARRRAERRAARGRAFTPPRDGAGRPVAGLEEDHGVWTRVGAVVARRPRLVW
+VATTVVLLALCGGLLQLRADGVAQEDVLLGDSDARQAQALLSEHFDAGAGAPAQILAPAE
+DAEAVLAAVAEDPGVAEAEVTTDAPEAAAGPPPGALDAEGGAGAASAPEPQPRVVDGRVL
+VSATLADPGESLAAQQTVARLRDRLADLPTSGEILVGGPAAQALDTNVTTQRDLRVVIPL
+ILAMLLVVLAVLLRSLLAPVLLVAATVVSFGAALGVSALVFRHVFGFEDADPTVPLYGFV
+FLVALGIDYTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPL
+MFMVQLAFIVAFGVLLDTLVVRTLLIPALVRDIGPKVWWPAKVD*
+>NZ_CP040019.1_963
+MRTPPDLSALRSPDARRAAGSADPDSAAGRPEGLGASAAGRDGERTDGRTGDRTGERTAG
+RPSAWLRFGLAAALFVVWFAVMGLGGPTFGKIGDVSSNDQSTFLPASAESTRAGEEAAAF
+RDGEAVPAVIVAEADLSDPAQAFPALGGLAETLRGVDGVTDVAGPIPAEDGEAVQFLAFV
+DSSDGAEREVADVVEDLKGILADPAAADADLADTVAADADWHLGGPAGLATELGGAFAGI
+DGLLLLVALVVVFVILVIVYRSVLLPILVLLTAVGALCAAILAVYGMAVAGWIQLNGQAQ
+GILSILVIGAATDYCLLLVARHREELLVREEVTASLLAAVRGSFGAITASASTVALALLI
+LLVSDLNSNSSLGPIAATGILFAWLAALTLLPALLQLAGRAAFWPTVPSPENARRRATRR
+AERGRAFVQPEDAAGRPLAGLEEDHGVWTKVGAAVARRPRPVWLATLAVLLVMSAGLLQL
+QASGVAQEDVLLGESDSRQAQALLTEHFDAGSGAPAQIVAPAEDADAVLAAVEADPGVAE
+ASVTTDEAPAPAGPPPGVTGGGEGTPAEGGAGRPEAAPQPDPEPKVVDGTVLISATLADP
+GESLAAQATVERLRAELADVGSGGEVLVGGPAAQALDTNTTSQRDLVVVIPLILAMLLVI
+LSMLLRSILAPVLLVAATVISFGAAMGVSALVFRHVFGFENADPTVPLYGFVFLVALGID
+YTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPLMFMLQLAF
+IVAFGVLLDTLVVRTLLIPALVRDIGPKVWWPARAE*
+>NZ_CP097650.1_1745
+MPTAPDLSAFRTPAAPGRPSRGLRLGLAAALAVVWFAVLGLGGPVFGAIGDVSSNDQATF
+LPASAESTRAGEEAAAFQDGEAVPAVVVGPASTADPAAAFPALADLAGLLGEVPGVVDVA
+GPIPSEDGAAVQFLAFVDSSAGAERPVADVVADLREVVADPAAAAPALAGTVAADTEWHV
+GGPAGLVAELGGAFAGIDGLLLLVALVVVFVILVAVYRSVLLPVLVLLTAVAALCGAIVA
+VYGMALAGWIQLNGQAQGILSILVIGAATDYCLLLVARHREELLVRAEVGEALRAAVRGS
+FGAITASASTVALALLILMASDLNSTRSLGPVAATGVAFAWLAALTLLPALLRLTGRAAF
+WPTIPSPERARRRTERRAARGRAFTPPRDGAGRPIAGLEEDHGVWTRVGTVVARRPRPVW
+VATTVGLLALCGGLLQLRADGVAQEDVLLGDSDARQAQALLSEHFDAGAGAPAQILAPAG
+DAEAVLAAVAEDPGVAEAEVTADAPEAAAGPPPGVTDAEGGAGAASAPEPQPRVVDGRVL
+VSATLADPGESLAAQQTVARLRDRLADLPTSGEILVGGPAAQALDTNVTTQRDLRVVIPL
+ILAMLLVILAVLLRSLLAPVLLVAATVVSFGAALGVSALVFRHVFGFEDADPTVPLYGFV
+FLVALGIDYTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPL
+MFMVQLAFIVAFGVLLDTLVVRTLLIPALVWDIGPKVWWPAKAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001896.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001896.fa
new file mode 100644
index 0000000000000000000000000000000000000000..47334fc0cb441311431acea18fd2088488005551
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001896.fa
@@ -0,0 +1,16 @@
+>NZ_CP042169.1_1826
+MIKQPWGLARLPAMTTQPPSAPAEHLAVVHALRVFSESAEHAVDEAGRGVGLHRTDLRAL
+AYLMARAAAGEPVTASDLGAHLHLTRASATALVDRLAAAGHVRRHRDEGDRRRVLVEHTD
+TARRDGQRAFEPMSQRLSAALEGFSAAELRAAVRVLEAATAALTDPAPEDP*
+>NZ_CP033200.1_1533
+MIKQPWGLARLPAMTTQPPSAPAEHLAVVHALRVFSESAEHAVDEAGRGVGLHRTDLRAL
+AYLMARAAAGEPVTASDLGAHLHLTRASATALVDRLAAAGHVRRHRDEGDRRRVLVEHTD
+TARRDGQRAFEPMSQRLSAALEGFSAAELRAAVRVLEAATAALTDPAPEDP*
+>NZ_CP040019.1_962
+MTPQPAAAPAEHVAVVHALRAFSEGAEHAVDEAGRGIGLHRTDLKALAHLMRCADEDRPV
+TATDLGAHLHLTRAATTAVVDRLVASGHARRRRDDVDRRRVLVEHTDSARRDGAAAFLPM
+SLRISGALTPFTAEELRAALRVIEAATAALQAPPDAPAAPVPG*
+>NZ_CP097650.1_1746
+MTTQPPSAPAEHLAVVHALRVFSESAEHAVDEAGRGVGLHRTDLRALAYLMARAAAGEPV
+TASDLGAHLHLTRASATALVDRLAAAGHVRRRRDEGDRRRVLVEHTDTARRDGQRAFQPM
+SQRLSAALEGFSVAELRAAVRVLEAATAALTDPTPEDP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001897.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001897.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9472ff3932daab520ed3de1aedbde52e1bdce880
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001897.fa
@@ -0,0 +1,33 @@
+>NZ_CP042169.1_1839
+MRDTTADAAQVPARPDDAAVYRYLAFGEADRPFLVGGPRPAPPAPAATPSPVADLESVRA
+AIRAHGGPLASTAHVCGRPAPTPSAADASRGLRGAARTLTATRRDVAARLADSRERADVP
+VEALLNSAFVDAHADERPADRGVPRGRLAGLVDAVLPPARPAGDDAAAGLLLALREPVRE
+VFASDSFAARPYADAPTVRALFEDFLAHPRRHDPERFWRLLNLELWLRDAVDADAAPAGP
+ATAVDEAPTAPAPVKPDHEPNPGKELDLVSAEDGRRYRRFPVQTGLVDRDTDLQAYLRGE
+IEDFFRDLPADAMPQDAPWHFSVSEKIVAITQGRSYYTWEVRPSVAARVLSRLVTRTPAG
+IGLGDPTTMQLAIQEAGLPRIVLSAAAGAAGKVAGKRGVFYNVVGGNVRAIDGPTTYSTF
+PANVSAKLPPAEPDRVAAEVSAMIRAADIPAWAKASFAGTVVMDANDIGRNALGKDTAAS
+AAVLEAAFADNPLGQGRERTPLAVVVRMD*
+>NZ_CP033200.1_1546
+MRDTTADAAQVPARPDDAAVYRYLAFGEADRPFLVGGPRPAPLAPAATPSPVADLESVRA
+AIRAHGGPLASTAHVCGRPAPTPSAADASRGLRGAARTLTATRRDVAARLADSRERADVP
+VEALLNSAFVDAHADERPADRGVPRWRLAGLVDAVLPPARPADDDAAAGLLLALREPVRE
+VFASDSFAARPYADAPTVRALFEDFLAHPRRHDPERFWRLLNLELWLRDAVDPDAAPASP
+AAAVDEAAGAPAPAKPDHEPNPGKELDLVSAEDGRRYRRFPVQTGLVDRDTDLQAYLRGE
+IEDFFRDLPAEAMPQDAPWHFSVSEKIVAITQGRSYYTWEVRPSVAARALSRLVTRTPAG
+IGLGDPTTMQLAIQEAGLPRIVLAAAAGAAGKVAGKRGVFYNVVGGNVRAIDGPTTYSTF
+PANVSAKLPPAEPDRVAAEVSAMIRAADIPAWAKASFAGTVVMDANDIGRNALGKDTAAS
+AAVLEAAFADNPLGQGRERTPLAVVVRMD*
+>NZ_CP040019.1_948
+MFYNVVGGNVRAIDGPTTYSAFPANVSAKLPPADPDGVAREVSAMIRAADIPEWARRSFA
+GTVVMDANDIGRNALGRDTAASAAVLEAAFADNPLGQGRERTPLAVVVRMD*
+>NZ_CP097650.1_1759
+MRDTTADAAQVPARPDDAAVYRYLAFGEADRPFLVGGPRPAPLAPAATPSPVADLESVRA
+AIRAHGGPLASTAHVCGRPAPTPSAADAPRGLRGAARTLTATRRDVAARLADSRERADVP
+VEALLNSAFVDAHADERPADRGVPRGRLAGLVDAVLPPARHADDDAAAGLLLALREPVRE
+VFASDSFAARPYADAPTVRALFEDFLAHPRRHDPERFWRLLNLELWLRDAVDADAAPAGP
+ATAVDEAPTAPAPAKPDHEPNPGKELDLVSAEDGRRYRRFPVQTGLVDRDTDLQAYLRGE
+IEDFFRDLPADAMPQDAPWHFSVSEKIVAITQGRSYYTWEVRPSVAARALSRLVTRTPAG
+IGLGDPTTMQLAIQEAGLPRIVLSAAAGAAGKVAGKRGVFYNVVGGNVRAIDGPTTYSTF
+PANVSAKLPPAEPDRVAAEVSAMIRAADIPAWAKASFAGTVVMDANDIGRNALGKDTAAS
+AAVLEAAFADNPLGQGRERTPLAVVVRMD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001899.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001899.fa
new file mode 100644
index 0000000000000000000000000000000000000000..999dae96e06bb5ef82d6c65cc2be15fea5eedf63
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001899.fa
@@ -0,0 +1,16 @@
+>NZ_CP042169.1_1841
+MTRQSDLKTLIRARMAVTGERYTAAAAALADEWQSAERYHATVLARFFDGDRLRSIPARR
+KPRVAVLLELLRRFRAGRAYAEAEVNDLLRPAHEDVATLRRELVDYGFLARADGVYRLAD
+AGPDLDPRFAADLPVDLERRLREIRAGR*
+>NZ_CP033200.1_1548
+MTRQSDLKTLIRARMAVTGERYTAAAAALADEWQSAERYHATVLARFFDGDRLRSIPARR
+KPRVAVLLELLRRFGAGRAYAEAEVNDLLRPAHEDVATLRRELVDYGFLDRADGVYRLAD
+AGPDLDPRFAADLPVDLERRLREIRAGG*
+>NZ_CP040019.1_946
+MTRQSDLKTLIRARMAVTGERYTAAAAALAHEWETAERFHATVLARFFDGERLRSIPALR
+KPRVAVLLELLRRFAPDRAYTEPEVNDLLRPAHEDVATLRRELVDYGFLDRADGVYRMAD
+AGPDVDPRFAADLPVDLERRLRQLRAGR*
+>NZ_CP097650.1_1761
+MTRQSDLKTLIRARMAVTGERYTAAAAALADEWQSAERYHATVLARFFDGDRLRSIPARR
+KPRVAVLLELLRRFRAGRAYAEAEVNDLLRPAHEDVATLRRELVDYGFLARADGVYRLAD
+AGPDLDPRFAADLPVDLERRLREIRAGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001901.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001901.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e4380254834ddb8a8ce19ac2baf3272f08aa8e8e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001901.fa
@@ -0,0 +1,35 @@
+>NZ_CP042169.1_1858
+MSHADIPHAGPDGSTPSGTAPKTDSRAASATRRTALLGAMFLMATSAIGPGFITQTATFT
+VQMGAAFAFAILVSILIDVAVQMNVWRVIGVSGMRAQELANRVLPGLGWVLAALVFLGGM
+VFNIGNIAGTGLGANAMLGVDPLIGGGVSALIALLIFLSKRAGVALDRIVVALGAVMILL
+MLYVAITSAPPVGEALRQSVMPEKVDFFVIVTLVGGTIGGYITYAGAHRMIDSGVKGVDD
+VQDITRSSVASILVTGLMRALLFLAILGVVASGAVLSKDSLAASAFQAAAGDIGLRMFGI
+VLWAAAVTSVIGASYTSISFVTRSTTSVRTRNLLTVAFIVVCTALYLALRQAPQTLLVFA
+GAFNGMILPVGFAALLYVAWRRRDLLHGYRYPAWLLVMGALAWLVSVFIAVRGFVPMVTM
+ITGA*
+>NZ_CP033200.1_1565
+MSHADIPHAGPDGSTPSGTAPKTDSRAASATRRTALLGAMFLMATSAIGPGFITQTATFT
+VRMGAAFAFAILVSILIDIAVQMNVWRVIGVSGMRAQELANRVLPGLGWVLAALVFLGGM
+VFNIGNIAGTGLGANAMLGVDPLIGGGVSALIALLIFLSKRAGVALDRIVVALGAVMILL
+MLYVAITSAPPVGEALRQSVMPEEVDFFVIVTLVGGTIGGYITYAGAHRMIDSGVKGVDD
+VQDITRSSVASILVTGLMRALLFLAILGVVASGAVLSKDNLAASAFQAAAGDIGLRMFGI
+VLWAAAVTSVIGASYTSISFVTRSTTSARTRNLLTVAFIVVCTALYLALRQAPQTLLVFA
+GAFNGMILPVGFAALLYVAWRRRDLLHGYRYPGWLLVIGALAWIVSVFIAVRGFIPMVEM
+ITGA*
+>NZ_CP083691.1_865
+MSHADPTAHARGDAAAGEAVQASSSNRRTALLGAMFLMATSAIGPGFITQTATFTVQLGA
+AFAFAILVSILIDIAVQMNVWRVIGVSGMRAQELANSVLPGLGWVLAVLVFVGGLVFNIG
+NIAGTGLGANAMLGVDPLIGGAVSAVIALLVFLSKRAGVALDRIVVVLGAVMILLMLYVA
+VTSAPPVGEALRQSVFPEKVDFFVIVTLVGGTIGGYITYAGAHRMIDSGVKGVDDVEAIT
+RSSVLSILVTGVMRVLLFLAILGVVASGVALAKDNLAASAFQAAAGDIGLRMFGIVLWAA
+ALTSVIGASYTSVSFVTKSTTTTRTRNLLTVAFIVVCTVLYLALRQTPQTLLVFAGAFNG
+MILPIGFAALLWVAWRRRDLLGGYRYPTWLLVIGALSWLLSVFIAVRGFLPMVQMITGA*
+>NZ_CP097650.1_1778
+MSHADIPYAGPDGSTPSGTAPKTDSRAASATRRTALLGAMFLMATSAIGPGFITQTATFT
+VRMGAAFAFAILVSILIDVAVQMNVWRVIGVSGMRAQELANRVLPGLGWVLAALVFLGGM
+VFNIGNIAGTGLGANAMLGVDPLIGGGVSALIALLIFLSKRAGVALDRIVVALGAVMILL
+MLYVAITSAPPVGEALRQSVMPEEVDFFVIVTLVGGTIGGYITYAGAHRMIDSGVKGVDD
+VQDITRSSVASILVTGLMRALLFLAILGVVASGAVLSKDNLAASAFQAAAGDIGLRMFGI
+VLWAAAVTSVIGASYTSISFVTRSTTSARTRNLLTVAFIVVCTALYLALRQAPQTLLVFA
+GAFNGMILPVGFAALLYVAWRRRDLLHGYRYPGWLLVIGALAWIVSVFIAVRGFIPMVEM
+ITGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001903.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001903.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d65ab50da0192c6ae0902f284f20d6c7a5a4fb3a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001903.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1860
+MRVPTRDGVTGDDLAPGAGDGESAPAPAPVAAAAQLRQRIAAAGLVPGERLGEVALAAEL
+QVSRNSLREAFTMLASEGLVERRPHRGVFVAAPGPEDVRGLYRTRRVIQLGALEHGELTP
+GAARQLRCAQDLLSGGPDTPARVLGDANHRVHVGIVDLAGAPELTRLMASVQARVRLAFH
+PMDEQTRLHVQFADRNRWIVERLLAGDLPAVHAVFGDYLDEAEQFVLAHLAAVGD*
+>NZ_CP033200.1_1567
+MRVPARGGVTGEGLAPGVGGGESAPAPAPVAAAAQLRQRIAAAGLVPGERLGEVALAAEL
+QVSRNSLREAFTMLASEGLVERRPHRGVFVAAPGPEDVRGLYRTRRVIQLGALEHGELTP
+GAARQLRCAQDLLSGGPDTPARVLGDANHRVHVGIVDLAGAPELTRLMASVQARVRLAFH
+PMDEQTRLHVQFADRNRWIVERLLAGDLPAVHAVFGDYLDEAEQFVLAHLAAVGD*
+>NZ_CP083691.1_863
+MTAPAAQGAADALRRRIGEARLQPGERLGEVALAAELGVSRNSLREAFSELAVEGLVVRR
+PHRGVFVAAPGAEDVRGLYRTRRVIQLGALQHGWLTPAAEERIGRSAELLGRPEPAVREL
+GDANHLLHLGIVDLAASPDLSRVMSSVLARVRLSFLPLDLETGLHQAFAERNRWIAGRLL
+AGDLDAVHAMLEGYLDEAEAFVLRHLDGAAHGLRG*
+>NZ_CP097650.1_1780
+MRVPARGGVTGEGLAPGVGGGESAPAPAPVAAAAQLRQRIAAAGLVPGERLGEVALAAEL
+QVSRNSLREAFTMLASEGLVERRPHRGVFVAAPGPEDVRGLYRTRRVIQLGALEHGELTP
+GAARQLRCAQDLLSGGPDTPARVLGDANHRVHVGIVDLAGAPELTRLMASVQARVRLAFH
+PMDEQTRLHVQFADRNRWIVERLLAGDLPAVHAMFGDYLDEAEQFVLAHLAAVGD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001906.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001906.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5562a2f4f8512aacad343446db20c021adde16b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001906.fa
@@ -0,0 +1,88 @@
+>NZ_CP042169.1_1876
+MTAMFSAQDHDDLDRVLSATGGIPDPADLHALADDAVAQVRRWLAESRDHEADFAARQLA
+GALKEPGGLDFIVRFVDHVVRPEDPAIAARALRELAGRAPGFLPPALRAVLGVGGRAAPL
+VPRIAVPTARRVLRHMVSHLIVDARDRQLGKAIAALRDEHTRLNINLLGEAILGQGEADR
+RLEGIAALIRRDDVDYVSVKVSAATAPHAPYAFDEAVADITERLTPLFELARDRDTFINL
+DMEEYRDLDLTLNVFTALLEQPGLRDYEAGIVLQAYLPDALAAMVRLQEWAARRVAAGGA
+PVKVRVVKGANLPMERMQASLTGWPLATVGSKQEADTNYKRVLNYALTPEHLAHVRIGVA
+GHNLFDVALAHRLIERRGLDPAAVEFEMLLGMATGQAAAVRADVGALLLYTPVVRPEEFD
+VAISYLVRRLEEGASPENFMSAVFDLDADADLFAREEERFRASLRHLDAAVPRPNRLQDR
+SRGEDGPTPAPVDGFANTPDTDPALPGNREWARRILAAVPGSDLGTDTVRAHRATTADDA
+RAAIAATAHPGARWGALTGHERADALDAVGRALHAGRARLLEVAAAETGKTLDQGDPEVS
+EAVDFAHYYARLARGLDAVEGARAVPVRLTLVIPPWNFPVAIPVGGVLAALGAGSPVVFK
+PAPQSERTGAVAWELIVAGLRDSGLFDDGGPLAGHDPADLVRLVTLADEDEAEVGAALVT
+DPAVERLILTGSWDTARLFKGMRPDLHLLAETSGKNAVIVTPSADLDLATKDVVQSAFGH
+AGQKCSASSLVVLVGSVGTSERFHRQLLDAASSLHVAHPVDPRAEMGPVIEAPGEKLRRG
+LTELGPGERWALRPRQLDETGRLWSPGIRSGVRPGADAHLTEYFGPVLAVMTAETLEEAI
+GIVNAVDYGLTSGLHSLDREEIDVWLRGVRAGNLYVNRGITGAIVRRQPFGGWKRSVVGP
+TTKAGGPHYLHGLVDWEDAPTWAGGEGRPGAEADGAGASWLETARALDTHAWTTVFGVAT
+DVSALEAERNVLRHVPTPVLVRRHSGPADHLLRIVSAGLRAGAPMTVSLRPTPTAEGPDA
+DGLSAEAVRGRVEKLVRSARTEGAGTAAPVDVVVEDDAAFHDRARRLALILPATEGGGDA
+RIRLVADWTGDREAAEAARSALHAALGDTPDVAVYAGPVVSAGEVELLPFLHEQAVSVTA
+HRFGTPDHLTEGVL*
+>NZ_CP033200.1_1584
+MTATFSAQDHDDLDRVLGVTGGIPDPADLHALADDAVAQVRRWLAESRDHEADFAARQLA
+GALKEPGGLDFIVRFVDHVVRPEDPAIAARALRELAGRAPGFLPPALRAVLGVGGRAAPL
+VPRIAVPTARRVLRRMVSHLIVDARDRQLGKAIAALRDEHTRLNINLLGEAILGQGEADR
+RLEGIAALIRRDDVDYVSVKVSAATAPHAPYAFDEAVADITERLTPLFELARDRDTFINL
+DMEEYRDLDLTLNVFTALLEQPGLRDYEAGIVLQAYLPDALAAMVRLQEWAARRVAAGGA
+PVKVRVVKGANLPMERMQASVTGWPLATVGSKQEADTNYKRVLNYALTPEHLAHVRIGVA
+GHNLFDVALAHRLIERRGLDPAAVEFEMLLGMATGQAAAVRADVGALLLYTPVVRPEEFD
+VAISYLVRRLEEGASPENFMSAVFDLDADADLFAREEERFRASLRHLDAAVPRPNRLQDR
+SRGEDGPTPAPVDGFANTPDTDPALPGNREWARRILAAVPGSDLGTDTVRAHRATTADDA
+RAAIAATADPGARWGALTGHERADALDAVGRALHAGRARLLEVAAAETGKTLDQGDPEVS
+EAVDFAHYYARLARGLDAVEGARAVPVRLTLVIPPWNFPVAIPVGGVLAALGAGSPVVFK
+PAPQSERTGAVAWELIVAGLRDSGLFDDRGPLAGHDPADLVRLVTLADEDEAEVGAALVT
+DPAVERLILTGSWDTARLFKGMRPDLHLLAETSGKNAVIVTPSADLDLATKDVVQSAFGH
+AGQKCSASSLVVLVGSVGTSERFHRQLLDAASSLHVAHPADPRAEMGPVIEAPGEKLRRG
+LTELGPGERWALRPRQLDETGRLWSPGIRSGVRPGADAHLTEYFGPVLAVMTAETLEEAI
+GIVNAVDYGLTSGLHSLDREEIDVWLRGVRAGNLYVNRGITGAIVRRQPFGGWKRSVVGP
+TTKAGGPHYLHGLVDWEDAPTWAGGEGRPGSEADGAGASWLETARALDTQAWTTVFGVAT
+DVSALEAERNVLRHVPTPVLVRRHSGPADHLLRIVSAGLRAGAPMTVSLRPTPTAEGPDA
+DGLSAEAVRGRVEELVRSARTEGAGTAAPVDVVVEDDAAFHDRARRLALVPPAAEGGGDA
+RIRLVADWTGDREAAEAARSALHAALGDTPDVAVYAGPVVSAGEVELLPFLHEQAVSVTA
+HRFGTPDHLTEGVL*
+>NZ_CP040019.1_912
+MTPTFSAQDHDDLDRVLTATGGIPDPADLQHLADDAVAQVRRWLADARGHEADFAAQQLA
+GALKEPGGLDFIVRFVDHVVRPEDPAIAARALRELAQQAPGFLPPALRAVFGVGGRAAPL
+VPRVAVPVARRVLRRMVSHLIVDARDRQLGEAIAALRDERTRLNVNLLGEAILGKGEADR
+RLEGIAGLIRRDDVDYVSVKVSAATAPHAPYAFDEAVADITERLTPLYELARDNGTFINL
+DMEEYHDLDLTLNVFTGLLEQPGLRDYEAGIVLQAYLPDALAAMVRLQEWAARRVAAGGA
+PVKVRVVKGANLPMELMQASLMGWPVATVASKQEADTNYKRVLNYALTPEHLRHVRIGVA
+GHNLFDVALAHRLMDRRGLGPEQVEFEMLLGMATGQAAAVKADVGSLLLYTPVVRPEEFD
+VAISYLVRRLEEGASPENFMSAVFDLDADEALFAREEERFRASLAHLDAEVPRPSRGQDR
+SRGEDGVRPAAVDGFANTPDTDPSLPGNRAWARGILEAIPGSALGAERARAHRVGTAEAA
+RAAIADTQAPGAAWGALTGAQRAEALDAVGRALHAGRGRLLEVAAAETGKTLDQGDPEIS
+EAVDFAHYYARLARGLDEVEGARAVPVRLTLVIPPWNFPVAIPVGGVLAALGAGSPVVFK
+AAPQSERTGAVAWELIVQGLRDSGLFDDGGPLAAHDPADLVRLVTMADEDEEEVGTALVT
+DPAVERLILTGGWDTAKLFKGMRPDLHLLAETSGKNAVIVTPSADLDLATKDVVHSAFGH
+AGQKCSASSLVVLVGSVATSERFHRQLLDAASSLHVAHPADPRAQMGPVIEEPGEKLRRG
+LTELGEGERWALRPRELDATGRLWSPGIRSGVRPGADAHLTEYFGPVLSVMTAATLNEAI
+DIVNAVDFGLTSGLHSLDPDEIAHWLERVHAGNLYVNRGITGAIVRRQPFGGWKRSVVGP
+TTKAGGPHYLHGLVDWVDAPSSTSESPAADRAGEGTAAGTPAAAERSWLDAARALDERAW
+AATFGSGTDVSALAAERNVLRHLPVPVLVRRASGPAEHLLRVVSAGLRAGAPMTVSIAPT
+PAAQAPGTDDLSAEALRGQVDELVRTAGAGRAEGAAPVSVVVEDAAAFHDRARQLAQIPP
+AAEGGGDARIRLVADWAQDREGARAAGAALHAALGDTPDVAVYAGPVVSAGEVELLPFLH
+EQALSVTAHRFGTPDHLTDAIL*
+>NZ_CP097650.1_1796
+MTATFSAQDHDDLDRVLGATGGIPDPADLHALADDAVAQVRRWLAESRDHEADFAARQLA
+GALKEPGGLDFIVRFVDHVVRPEDPAIAARALRELAGRAPGFLPPALRAVLGVGGRAAPL
+VPRIAVPTARRVLRHMVSHLIVDARDRQLGKAIAALRDEHTRLNINLLGEAILGQGEADR
+RLEGIAALIRRDDVDYVSVKVSAATAPHAPYAFDEAVADITERLTPLFELARDRDTFINL
+DMEEYRDLDLTLNVFTALLEQPGLRDYEAGIVLQAYLPDALAAMVRLQEWAARRVAAGGA
+PVKVRVVKGANLPMERMQASLTGWPLATVGSKQEADTNYKRVLNYALTLQHLAHVRIGVA
+GHNLFDVALAHRLIERRGLDPAAVEFEMLLGMATGQAAAVRADVGALLLYTPVVRPEEFD
+VAISYLVRRLEEGASPENFMSAVFDLDADAGLFAREEERFRASLRHLDAAVPRPNRLQDR
+SRGEDGPTPAPVDGFANTPDTDPALPGNREWARRILAAVPGSDLGTDTVRAHRATTADDA
+RAAIAATADPGARWGSLTGHERADALDAVGRALHAGRARLLEVAAAETGKTLDQGDPEVS
+EAVDFAHYYARLARGLDAVEGARAVPVRLTLVIPPWNFPVAIPVGGVLAALGAGSPVVFK
+PAPQSERTGAVAWELIVAGLRDSGLFDDRGPLAGHDPADLVRLVTLADEDEAEVGAALVT
+DPAVERLILTGSWDTARLFKGMRPDLHLLAETSGKNAVIVTPSADLDLATKDVVQSAFGH
+AGQKCSASSLVVLVGSVGTSERFHRQLLDAASSLHVAHPADPRAEMGPVIEAPGEKLRRG
+LTELGPGERWALRPRQLDETGRLWSPGIRSGVRPGADAHLTEYFGPVLAVMTAETLEEAI
+GIVNAVDYGLTSGLHSLDREEIDVWLRGVRAGNLYVNRGITGAIVRRQPFGGWKRSVVGP
+TTKAGGPHYLHGLVDWEDAPTWAGGEGRPGSVADGAGASWLETARALDTHAWTTVFGVAT
+DVSALEAERNVLRHVPTPVLVRRHSGPADHLLRIVSAGLRAGAPMTVSLRPTPTAEGPDA
+DGLSAEAVRGRVEELVRSARTEGAGTAAPVDVVVEDDAAFHDRARRLALIPPATEGGGDA
+RIRLVADWTGDREAAEAARSALHAALGDTPDVAVYAGPVVSAGEVELLPFLHEQAVSVTA
+HRFGTPDHLTEGVL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001907.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001907.fa
new file mode 100644
index 0000000000000000000000000000000000000000..84545fc335046123cc475c0da06ceca9afc87cb3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001907.fa
@@ -0,0 +1,16 @@
+>NZ_CP042169.1_1885
+MGILSSLTRTLGGGGRRSSRPTIGAHIGRSPGFGRQARSQGRRSSGLGGALLGTLGGLAL
+RELSRRGAGSTTRGRSSGAYRGGFGPSARSTGGLGTGLLGGLLGGALASRGRSGAAGRRT
+AGGRRTMGGGF*
+>NZ_CP033200.1_1593
+MGILSSLTRTLGGGGRRSSRPTIGAHIGRSPGFGRQARSQRRRSSGLGGALVGTLGGLAL
+RELSRRGAGGTTRGRGSGAYRGGFGPSARSTGGLGTGLLGGLLGGALASRGRSGAAGRRT
+AGGRRTVGGGF*
+>NZ_CP040019.1_902
+MGILSGITRALGGSRRRPTIGANTYGRRRSSGAGGALLGTLGGLALRELSRRSSGGTARG
+YGGQAGYGRTTGGYGRTSGGLGGLLGGLGGMGAGRSSSRGGGLLGGLLSGPMNSRSGRRT
+TGGRF*
+>NZ_CP097650.1_1805
+MGILSSLTRTLGGGGRRSSRPTIGAHIGRSPGFGRQARSQGRRSSGLGGALLGTLGGLAL
+RELSRRGAGSTTRGRSSGAYRGGFGPSARSTGGLGTGLLGGLLGGALASRGRSGAAGRRT
+AGGRRTMGGGF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001908.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001908.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0948153faf4562017fd08fee012625b583b6832
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001908.fa
@@ -0,0 +1,19 @@
+>NZ_CP042169.1_1891
+MGEEHTTLTSTDGEPTSGYWYTRGAREIEPVDVLNLLRRYREAERRMRARTRDSMGMGET
+HLSALRYLLRADRRGHKVRQRDLASALEITPASASALVDRLVRDGYARRAPHPQDRRSVV
+VEPTAKTDHEVRATLGAMHRSMLAAVEGLTPAELAGAAAFLRALIRSVEEHDEDEADQPA
+*
+>NZ_CP040019.1_899
+MTEDHRAPSASGYWYVSSPNSVGPVEVLNVLRAYREAERRMRRRTRDSMRMGETDLLALR
+HLLRESRAGRPVRQRDLAAALEISPASASALVDRLIRDGYARRSPHPADRRSVIIETTAR
+TDDEVRATLGRMHRSMLDAVESLSPDELAAVAKFLTALTRSVDEAAEDALEHGTEH*
+>NZ_CP083691.1_830
+MGEEHTTLTSTDGEPTSGYWYTRGAREIEPVDVLNLLRRYREAERRMRARTRDSMGMGET
+HLSALRYLLQADRRGHKVRQRDLASALEITPASASALVDRLVRDGYARRAPHPQDRRSVV
+VEPTAKTDHEVRATLGAMHRSMLAAVEGLTPAELAGAAAFLRALIRSVEEHDEDEADQPA
+*
+>NZ_CP097650.1_1811
+MGEEHTTLTSTDGEPTSGYWYTRGAREIEPVDVLNLLRRYREAERRMRARTRDSMGMGET
+HLSALRYLLRADRRGHKVRQRDLASALEITPASASALVDRLVRDGYARRAPHPQDRRSVV
+VEPTAKTDHEVRATLGAMHRSMLAAVEGLTPAELAGAAAFLRALIRSVEEHDEDEADQPA
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001909.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001909.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3876c1a10a27b75165f906a369c87126db4e1ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001909.fa
@@ -0,0 +1,13 @@
+>NZ_CP042169.1_1912
+MSELDELDFAALSAFLAWWFGKTGVDWIRREDG*
+>NZ_CP033200.1_1618
+MSELDELDFAALSAFLAWWFGKTGVDWIRREDG*
+>NZ_CP040019.1_875
+MSELDELDFVAVEIHTAGTDPASVCAVDMALVRGGEIVAAERWPVRPPTGPTSFSRLHTQ
+LHGVDEAAVADAPEWPEVAAQLDLLGEHLPFVASGADRDRGAYEAATRATGGTPQAHEWR
+DALALVGRLRPDVDPPRIATAAQALGVPDGARPAGAGSEAVRTAEVVLALARQSGRGTVR
+RLWSEAAPPTPDEPIIPESLRRRHATEPSVPPAGAHRWAPPAPAPAPASAAPAGRGGGVG
+WKLAGTAMVGIALGAALFFVASVAVIMEYLEDGRGSDATVGMGIAALSAFLAWWFGKTGV
+DWIRRQDG*
+>NZ_CP097650.1_1839
+MSELDELDFAALSAFLAWWFGKTGVDWIRREDG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001911.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001911.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f7385b86626912b5c0c81adb0fb04ca8065b9eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001911.fa
@@ -0,0 +1,16 @@
+>NZ_CP042169.1_1931
+MMAWIDGLPLLWSIGFFWMLAILRTLIVFSLGRGLASGVERTRWFARVMEGPVYVRAQRF
+IQRHGVWAIPFCYLTVGIQTAVIGSAGVARMPWRRFLPAAALGTFLWGVVYGTVGMAVVW
+AVIGAALGEGRGVLALVLILAAVAAFVVWRRRRTLRRHGAG*
+>NZ_CP033200.1_1637
+MMAWIDGLPLLWSIGFFWMLAILRTLIVFSLGRGLASGVERTRWFARVMEGPVYVRAQRF
+IQRHGVWAIPFCYLTVGIQTAVIGSAGVARMPWRRFLPAAALGTFLWGVVYGTVGMAVVW
+AVIGAALGEGRGVLALVLILAAVAAFVVWRRRRTLRRHGAG*
+>NZ_CP040019.1_854
+MMAWIDGLPLLWSIGFFWMLAILRTLIVFSLGRGLASGVERTRWFARVMEGPVYVRAQRF
+IQRHGVWAIPFCYLTVGIQTAVIGSAGVARMPWRRFLPAAALGTFLWGVVYGTVGMAVVW
+AVIGAALGEGRGVLALVLILAAVAAFVVWRRRRTLRQHGAG*
+>NZ_CP097650.1_1858
+MMAWIDGLPLLWSIGFFWMLAILRTLIVFSLGRGLASGVERTRWFARVMEGPVYVRAQRF
+IQRHGVWAIPFCYLTVGIQTAVIGSAGVARMPWRRFLPAAALGTFLWGVVYGTVGMAVVW
+AVIGAALGEGRGVLALVLILAAVAAFVVWRRRRTLRRHGAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001914.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001914.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8676eaa42c1d427b15838448be90777ca40f6599
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001914.fa
@@ -0,0 +1,52 @@
+>NZ_CP042169.1_1945
+MKILPPRSAASPRPLAPAVAVAALSILVGGLLPQSPSATTEGAPDARPRDDAARATTVGA
+AATPASAAPVEGAGVATVPQEGENLVPAEEAPAGVVLGEPVVDRPFTVAAAVWDAAADDA
+VKRVEIRVRQDGAWGPWQVLDRPVLPEDAAPARTGTDPFVAFGADGAQLRVTTVDGAAPA
+GLELSLIDPGTAATDETVASAHPAVAAEQAAETAGLPRGVKSSAVVGGEEPAEARTVATV
+SDARAKILPDVITRAQWGADESWAEDSPQFDQVRALTIHHTAGTNDYTRAQAVEQMRGIY
+AYYTKTLGWGDFPYHLITDRFGNIYEGRRGALDSNPLGTHAGGFNRGTMGVSTMGNYDVV
+APSEEVVDAMARATAYYLYRDGIDARGRVTLTSGGSTKYAAGTPVTVDTIFPHRATSATA
+CPGQHLMARFDDLRDRAEAIATAAGQPPAAVTPAPTPAPTTERSTAGTYTVQPNDGWWTI
+ARRTGVPAATLQELNGMTESTVLHPGMVLRTVADPTAPEPTPITTGTYTVQPNDGWWVIA
+RRTGVSAAELQRLNGMTASTVLHPGMVLITAATAPASPPAPAPAPGTYTVREGDGWWIIA
+HRTGVTMETLQRLNGMTATTVLHPGMVLRTGQTASAPAPSPATYVVQANDGWWLIAQRTG
+VSMERLQRLNGMTVSTMLHPGMVLRTA*
+>NZ_CP033200.1_1651
+MKILLPGSAASPRPLAPAVAVAALSVLVGGLLPQQPSATTEGAPDARPLDDAARATTAGT
+ATTPASAAPVEGAGVATVPQEGENLVPAEEAPAGVVLGEPVVDRPFTVAAAVWDAAADDA
+VERVEIRVRQDGAWGPWQVLERPVLPEDAAPARTGTDPFVAFGADGAQLRVTTVDGAAPA
+GLELSLIDPGTAATDETVASAHPAVAAEQAAETAGLPRGVKSSAVVGGAAPAEAHTVATA
+SDARAKILPDVITRAQWGADESWAEDSPQFDQVRALTIHHTAGTNDYTRAQAVEQMRGIY
+AYYTKTLGWGDFPYHLITDRFGNIYEGRRGALNSNPLGTHAGGFNRGTMGISTMGDYDVV
+APSEEVVDAMARATAYYLYRDGIDARGRVTLTSGGSTKYAAGTPVTVDTIFPHRATSATA
+CPGQHLMARFDDLRDRAEAIATAAGQPPTPATPAPTPAPTTEPSTAGTYTVQPNDGWWII
+ARRTGVPAATLQELNGMTESTVLHPGMVLRTVADPTAPEPTPITTGTYTVQPNDGWWVIA
+RRTGVSAAELQRLNGMTASTVLHPGMVLITAATAPTSPPAPAPAPAPAPDTYTVREGDGW
+WIIAHRTGVTMETLQRLNGMTATTVLHPGMVLRTGQTASAPAPSPATYVVQANDGWWLIA
+QRTGVSMERLQRLNGMTVSTLLHPGMVLRTA*
+>NZ_CP040019.1_840
+MKLSAPRSAAPARSPPAVVVAALSVLVGGLLPQQPVPTTAVPPPPPRLADAAALRTLAPA
+GSGRAPAAASEVRGAAVAAVPQEGEALADAPAGVVLGEPVVDRPFTVAAAVWDAAADHAV
+ERVEIRVRQDGAWGPWQVLERAVLPEGAAVTRTGTDPFVAFGADGAQLRLTTADGAAPAG
+LELSLIDPGTAATDEAVASAHPAVSADQAAQDAALPRGVKSSAVVGGAEPAPARTVSTAS
+EARARILPDVITRAQWGADESWAQASPQFEQVRALTIHHSAGTNDYTRAQAVEQMRAIYA
+YYTKTLDWGDFPYHLITDRFGNIYEGRRGALDANPLGTHAGGFNTGTMGISTMGNYDVVA
+PSEEVVDAMARATAYYLYRDGLDPYGRVTLTSGGSTKYAAGTPVTVDTIFPHRTTSNTAC
+PGRHLMARFDDVRDRAATIAAAAGQEAPAPEPEPIPTPEPEPTPRPEPEPIPMPEPTTPT
+TYTVQDGDGWWVIARRTGVPAATIQELNGMTESTVLHPGMVLRLVADVSAPAPTPVTTGT
+YTVQPNDGWWVIARRTGVPAEELQRLNGMTADSLLHPGMVLITAATAPAPAPAPAPAPAP
+APGTYTVRDGDGWWVIAHRTGVTMETLQRLNGMTADTLLHPGMVLVTGQNATAAAPAPAP
+ATYTVRPNDGWWIIADRTGISMAELQRLNRMTASTLLHPGMVLRIA*
+>NZ_CP097650.1_1872
+MKILLPGSAASPRPLAPAVAVAALSVLVGGLLPQQPSATTEGAPDARPLDDAARATTAGT
+ATTPASAAPVEGAGVATVPQEGENLVPAEEAPAGVVLGEPVVDRPFTVAAAVWDAAADDA
+VERVEIRVRQDGAWGPWQVLERPVLPEDAAPARTGTDPFVAFGADGAQLRVTTVDGAAPA
+GLELSLIDPGTAATDETVASAHPAVAAEQAAETAGLPRGVKSSAVVGGAAPAEAHTVATA
+SDARAKILPDVITRAQWGADESWAEDSPQFDQVRALTIHHTAGTNDYTRAQAVEQMRGIY
+AYYTKTLGWGDFPYHLITDRFGNIYEGRRGALDSNPLGTHAGGFNRGTMGISTMGDYDVV
+APSEEVVDAMARATAYYLYRDGIDARGRVTLTSGGSTKYAAGTPVTVDTIFPHRATSATA
+CPGQHLMARFDDLRDRAEAIATAAGQPPTPATPAPTPAPTTEPSTAGTYTVQPNDGWWII
+ARRTGVPAATLQELNGMTESTVLHPGMVLRTVADPTAPEPTPITTGTYTVQPDDGWWVIA
+RRTGVCAAELQRLNGMTASTVLHPGMVLITAATAPASTPAPAPAPAPGTYTVREGDGWWI
+IAHRTGVTMETLQRLNGMTATTVLHPGMVLRTGQTASAPAPSPATYVVQANDGWWLIAQR
+TGVSMERLQRLNGMTVSTLLHPGMVLRTA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001915.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001915.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2265b82925f892fac7c90fdd6e5eec56677f06e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001915.fa
@@ -0,0 +1,40 @@
+>NZ_CP042169.1_1976
+MTELTGQASEAGTIDRLMAGWVADVETPDACAAHLLCDRWPADAVAFRFVAEDMSAVDLT
+FGELADRSRRLATGLAARGVTRGDRVPVMMSKREELVITLLALWRLGAVHVPLFTAFAAG
+AARMRIEGAAARLVVAEPRQAEKLTDIPGIEIIRTGPEWDALADSAPLAEDVAVGGDGPI
+ALLFTSGTTGRPKGVPVPLRAAAAFAVYLTCAVDLRPEDLFWNAADHGWAYGLYYGIVGT
+LVLGATSVQYRGAFSPATMVEVIRSQDVTNLAGAPTMFRALAKAGEVTEDAPLRLRRVST
+AGEPLPPSVLEWGRAALGTEIRDHYGQTELGMVICTPAHPELAAPPRPGSMGVPLPGIAA
+EIRDGQIAIDAASPMFWFPGYLGEPEKTAERFTPDGRWYLTGDTARQDDDGWFFFSSRDD
+DVILAAGYRIGPFDVESVLIDHPRVQEVAVVGLPDPEGVRGEEVVAFVVPAGAVADPDAL
+AAELQAKVRDEYSKHAYPRRVHFVDRLPKTPSGKLQRFLLRQGATD*
+>NZ_CP033200.1_1695
+MTERTGQAHEAGTIDRLMAGWVADVETPDACAAHLLCDRWPADAVAFRFVAEDMSAVDLT
+FGELADRSRRLATGLAARGVTRGDRVPVMMSKREELVITLLALWRLGAVHVPLFTAFAAG
+AARMRIEGAAARLVVAEPRQAEKLTDIPGIEIIRTGPEWDALADSAPLAEDVAVGGDGPI
+ALLFTSGTTGRPKGVPVPLRAAAAFAVYLTCAVDLRPEDLFWNAADHGWAYGLYYGIVGT
+LVLGATSVQYRGAFSPATMVEVISSQDVTNLAGAPTMFRALAKAGEVTEDAPLRLRRVST
+AGEPLPPSVLEWGRAALGTEIRDHYGQTELGMVICTLAHPELAAPPRPGSMGVPLPGIAA
+EIRDGQIAIDAASPLFWFPGYLGEPEKTAERFTPDGRWYLTGDTARQDDDGWFFFSSRDD
+DVILAAGYRIGPFDVESVLIDHPRVQEVAVVGLPDPEGVRGEEVVAFVVPAGAVADPDAL
+AAELQAKVRDEYSKHAYPRRVHFVDRLPKTPSGKLQRFLLRQGAAG*
+>NZ_CP040019.1_772
+MTERTGQASEAGTIDRLMAGWVADVETPDACAAHLLCDRWPADAVAFRFVAEDMSAVDLT
+FGELADRSRRLATGLAARGVTRGDRVPVMMSKREELVITLLALWRLGAVHVPLFTAFAEG
+AARMRIEGAAARLVVAEPRQAEKLTDIPGIEIIRTGPEWDALADSAPLAEDVAVGGDGPI
+ALLFTSGTTGRPKGVPVPLRAAAAFAVYLTCAVDLRPDDLFWNAADHGWAYGLYYGIVGT
+LVLGATSVQYRGAFSPATMVEVIRSQGVTNLAGAPTMFRALAKAGEVTEDAPLRLRRVST
+AGEPLPPSVLEWGRSALGTEIRDHYGQTELGMVICTLAHPELAAPPRPGSMGVPLPGIAA
+QIRDGQIAIDAASPLFWFPGYLGEPEKTAERFTPDGRWYLTGDTARQDDDGWFFFSSRDD
+DVILAAGYRIGPFDVESVLIDHPRVQEVAVVGLPDPEGVRGEEVVAFVVPAGAVVDPDAL
+AAELQAKVRDEYSKHAYPRRVHFVDRLPKTPSGKLQRFLLRQGAAD*
+>NZ_CP097650.1_1912
+MTERTGQAHEAGTIDRLMAGWVADVETPDACAAHLLCDRWPADAVAFRFVAEDMSAVDLT
+FGELADRSRRLAAGLAARGVTRGDRVPVMMSKREELVITLLALWRLGAVHVPLFTAFAAG
+AARMRIEGAAARLVVAEPRQAEKLTDIPGIEIIRTGPEWDALADSAPLAEDVAVGGDGPI
+ALLFTSGTTGRPKGVPVPLRAAAAFAVYLTCAVDLRPEDLFWNAADHGWAYGLYYGIVGT
+LVLGATSVQYRGAFSPATMVEVIRSQDVTNLAGAPTMFRALAKAGEVAEDAPLRLRRVST
+AGEPLPPSVLEWGRAALGTEIRDHYGQTELGMVICTPAHPELAAPPRPGSMGVPLPGIAA
+EIRGGQIAIDAASPLFWFPGYLGEPEKTAERFTPDGRWYLTGDTARQDDDGWFFFSSRDD
+DVILAAGYRIGPFDVESVLIDHPRVQEVAVVGLPDPEGVRGEEVAAFVVPAGAVADPDAL
+AAELQAKVRDEYSKHAYPRRVHFVDRLPKTPSGKLQRFLLRQGAAD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001917.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001917.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6241de085c31033069d54bdb3b5cc3c2eddfa658
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001917.fa
@@ -0,0 +1,31 @@
+>NZ_CP042169.1_1988
+MRRLAEVTGLVPVEYPTTRQLGASPESRARDLNAAFADPQIRAVIATVGGEDQITVIGHL
+DADAVRADPKPFLGYSDNTNLHQWLWANGVASFYGGSTQVHLGPGPAVDEVHAASLRAAL
+LTGGRLEITEPGESEDHGVDWLDPRALTEFGTREPVPGPHDDGARGVGAGASPWRWAGPR
+RAVTGRTWGGCLEVLPWVMAAGRGPADMAVLEGGVLLIETSEELPSAGEVRRLLRILGES
+GVLGAVDAVLAARPPTRSFEVPRGAEERARRRAEQADVVLEEVGRYNPDAVVCVGVPFGH
+TRPQWVLPHGGVMTVDGAERRVWAEYC*
+>NZ_CP033200.1_1706
+MASRYAPGMTQPLVHPPKAQPGDRIAVVSPSFAAPGFAPAVHEQAMRRLAEVTGLVPVEY
+PTTRQLGASAEDRARDLNAAFADPQIRAVIATVGGEDQITVIGHLDADAVRADPKPFLGY
+SDNTNLHQWLWANGVASFYGGSTQVHLGPGPAVDEVHAASMRAAMLTGGRLEITEPGESE
+DHGVDWLDPRALTEFGERDPVPCPHDDGARGVGEGASPWRWAGPRRAVTGRTWGGCLEVL
+PWVMAAGRGPADMAVLEGGVLLIETSEELPSAGEVRRLLRILGERGVLGAVDAVLAARPP
+TSSFEAPRGAEERARRSAEQADVVVEEVGRYNPDAVVCVGVPFGHTRPQWVLPHGGVMTV
+DGVERRVWAEFG*
+>NZ_CP040019.1_756
+MEHTLVRPPKAAPGDRIAVVSPSFAAPGFAPEVHEQAMRRLRELTGLEPVEYPTTRELGA
+SPEDRARDLNAAFADPRIRAVFATVGGEDQITVIGHLDAAAVRADPKPFLGYSDNTNLHQ
+WLWAHGVASFHGGSTQVHLGPGPGVDAVHAASLRAALLTGERLEITEPGESEDVGVDWQD
+PRALAEFGQREPVAADDDGLGGPGASPWRWAGPQRSVTGRTWGGNLEVLQWVLAAGRGPV
+DVAALRGGVLLLETSEELPSATDVRRMLRVLGERGILGEVAAVLAARPPVSDFDVRPDAQ
+ERARLRRAQADVMVETVHRYNPDAVVCVGVPFGHTRPQWILPHGGEMTVDGVEKRVWAEF
+G*
+>NZ_CP097650.1_1923
+MTQPLVHPPKAQPGDRIAVVSPSFAAPGFAPAVHEQAMRRLAEVTGLVPVEYPTTRQLGA
+SPEDRARDLNAAFADPQIRAVIATVGGEDQITVIGHLDADAVSADPKPFLGYSDNTNLHQ
+WLWANGVASFYGGSTQVHLGPGPAVDEVHAASLRAALLTGGRLEITEPGESEDHGVDWLD
+PRALTEFGTREPVPGLHDDGARGVGGAPGAGASPWRWAGPQRAVTGRTWGGCLEVLPWVM
+AAGRGPADMAVLEGGVLLIETSEELPSAGEVRRLLRILGERGVLGAVDAVLAARPPTSSF
+EAPRGAEERARRSAEQADVVVEEVGRYNPDAVVCVGVPFGHTRPQWVLPHGGVMTVDGVE
+RRVWAEFG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001922.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001922.fa
new file mode 100644
index 0000000000000000000000000000000000000000..026d40d798c8d274b249ae3061e19b0584492388
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001922.fa
@@ -0,0 +1,39 @@
+>NZ_CP042169.1_2006
+MSEHFDVAVLGLGPGGEVAADRLLKAGKNVVVFERELIGGECAYWACIPSKTVLRPPEAR
+TEVQRAAGVSGAELDWAATAKYRDYMIRNLDDQAQVDGYIKEGAVVIKDEARITGPGRIQ
+AGDREITAEHIIIATGSDAVIPPLDGIDQITAWTNRETYTTSTLPERAVIIGGSAVGVET
+ATFLARFGVAITLIHCGERLLDREGPRVGELAHQYLQEAGIDIRLATSAVQARREGADSI
+IELQTRDGDPAGEVAADVVIFGTGRTPRTEGLGFEHAGVTLGDHGEIQIDDHCRAGENTW
+AIGDVTGIMPFTHVAKYQGRIAADAILGRPHPATYDGIPRVVFTDPEIAGAGLTQEQATK
+QGIRTIATELDLADAIARPWTYEQDSRGHLGLLADADRKILIGAWAVGPMAGEWIHHASL
+AIRTQLPIDTLLDQVAQFPTYHEAYQVALEQLDLTP*
+>NZ_CP083691.1_2173
+MSEHFDVAVLGLGPGGEVAADRLLKAGKNVVVFERELIGGECAYWACIPSKTVLRPPEAR
+TEVQRAAGVSGAELDWAATAKYRDYMIRNLDDQAQVDGYIKEGAVVIKDEARITGPGRIQ
+AGDREITAENIIIATGSDAVIPPLDGIDQITAWTNRETYTTSTLPERAVIIGGSAVGVET
+ATFLARFGVAITLIHCGERLLDREGPRVGELAHQYLQEAGIDIRLATSAVQARREGADSI
+IKLQTRDGDPAGEVAADVVIFGTGRTPRTEGLGFEHAGVTLGDHGEIQIDDHCRAGENTW
+AIGDVTGIMPFTHVAKYQGRIAADAILGRPHPATYDGIPRVVFTDPEIAGAGLTQEQATK
+QGIRTIATELDLADAIARPWTYEQDPRGHLGLLADADRKILIGAWAVGPMAGEWIHHASL
+AIRTQLPIDTLLDQVAQFPTYHEAYQVALEQLDLTP*
+>NZ_CP083691.1_2374
+MTEDLAPTTGPDDATPGAPDEEAVDVVVIGAGPVGENAAQYAHTAGGLEVALVEADLLGG
+ECSYWACMPSKALLRPLEVAGAAAHLGGLTDPDIDLPGLLARRDEWRSHLDDAGQVEWAE
+DAGLRVVRGHGRLAGPRRVEVLGDDGAPARVLRARHAVVVATGSTAVVPGELRGVSPWTS
+RDATGVREVPGRLAIVGGGVVAVEAATWMAALGSDVQLLVRGDRLLSGQEPVASRLVLEG
+LVDAGVRVRFGTSVERAERADVHAESDVGVPHGGPVRLTLAGSGETLEVDELLVAAGRRP
+ALDGLGLEALGLSAEDLQDESGTAVVPASDGAAPWLYAVGDVTGGPALTHWGKHRARLLG
+ERIAALATGRPAPSGEEAGEGVPEAVPQVVFTSPQVARVGVTEAQAREEGGEGELRVVDV
+PLTSAAGAALLRDDAAGRAVLVLRGDRVVGATFVGFEVAELLHAATVAIVGEVPLDRLRH
+AVAAYPTASEVWLRLVEEALGRG*
+>NZ_CP083691.1_2388
+MSSVIPDTARPSSGHAGVHRADVVVLGHGLAGLVAACELLEAGRSVVLVDQERAADLGGQ
+AWWSFGGLFLVDSPEQRRLRVRDSVDLAWSDWRETAGFTGGDDALPRAWAEAYVHFAAGE
+KRAWLRERGHRLFPVVGWAERKVPAPGVGGNSVPRFHITWGTGPGIVEPFAAVVEQAAFD
+GRLTYLPRHRVTELVTQNGAVCGVRGDRLADDDGARGTSSSRTVTGAFEVRAQAVLIASG
+GIGADHDAVRAAWPDRLGTPPERMLSGVPAYVDGSGVAAARAVGAHMLHPDRMWHYTEGV
+ANWDPVWPGHGIRILPGPSSLWLDAAGRRLPHPRWPGFDTLGALGEICRPGGARRAEGAD
+HTWFVLNERIIGREFALSGSEQNPDLTGRSLGHVLGRATQGVPAPVRAFLDHGEDFVQAA
+TVEELVDQMNELQDRTGGGGPRVELHAVRQAVAEHEDGAARAGVDPQLDAVRRARQYLGD
+RLIRTAAPHRLTDPAAGPLIAVRLRTLTRKTLGGLHTDLRGRVLDELGGPVPGLYAAGEA
+AGFGGGGMHGFRALEGTFLGGCLFSGRTAGRALAEDVA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001925.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001925.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7110483862d9b3343a790af4a5a9086468cdfe0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001925.fa
@@ -0,0 +1,36 @@
+>NZ_CP042169.1_2041
+MHRPSRSSTAAPAFAPSAPAPTAAPAFAPSVRSQVPPFTVMSILGRVAALRAAGHDVVSL
+CAGEPGGGAPPAVDAAAAAVHASGRALTYTPALGLPELRAAVAGHYRRWYGLDVRPEQVA
+ITTGSSGAFMLGFLAAFSPGDRVLLPRPGYPAYRNILTALGVEVVDVDVDAGTRYQPTVA
+HLEAALAEGPVAGLVLASPANPTGTMVSAAELAELARWCEERGVRLVSDEIYHGIVHTDG
+QGPGACAWRTSRTALVVSSFSKYWGMPGWRLGWMLMPDDLATAVDGLAGSVALCPPAAAQ
+EAAVHAFTEESYAFCAEQAGGFTATRGVVLAALPRLAWADAAPADGAFYLWARLASGMLA
+EFGSAVGYCAALLEEAGVALTPGDDFDAVHGPESVRLSFAAGPDAVHEALERIAAWHAAR
+GLA*
+>NZ_CP033200.1_1760
+MRRPSRSSTADPASTAAPAPTATPAFAPSARSQVPPFTVMSILGRVAELRAAGHDVVSLC
+AGEPGGGAPPAVDAAAAAVHASGRAFTYTPALGLPELRTAVAGHYRRWYGLDVRPEQVAI
+TTGSSGAFMLGFLAAFPPGDRVLLPRPGYPAYRNILTALGVEVVDVDVDAGTRYQPTVAH
+LEAALAEGPVAGLVLASPANPTGTMVSADELAELARWCEERGVRLVSDEIYHGIVHTDGE
+GLGACAWRTSRTALVVSSFSKYWGMPGWRLGWMLMPDDLAAAVDGLAGSVALCPPAAAQE
+AAVHAFSEESYAFCAEQAGGFTATRGVVLAALPRLGWADAAPADGAFYLWARLAPGMLAE
+FGSAVGYCAALLEEAGVALTPGDDFDAVHGPESVRLSFAAGPDAVHEALERIAAWHAARG
+LA*
+>NZ_CP040019.1_666
+MDPQPRLAPGTHHDVAALAPASPVADAAPEDQAAPGDPASPVAPAFAPSARSQVPPFTVM
+TILGRVAELRAAGRDVISLCAGEPGGGAPPTVSAAAAEVHASGSPLTYTPALGLPELRAA
+VAGHYRRWYGIDVRPEQVAITTGSSGAFMLGFLAAFSPGDRVVLPRPGYPAYRNILAALG
+CEVVEVGVDASTRYQPTVAHLEAALAEGPVAGLVLASPSNPTGTMVDADELAALASWCEA
+HGVRLVSDEIYHGIVHPRSGDDDGGPAGGGAAGGAPGASGAEGSRFPHESVGACAWATSR
+TAMVISSFSKYWGMPGWRLGWMLMPEDLAGAIDGLAGSVALCPPAAAQRAAVEAFGEDAY
+AFCEEQAGGFTATRGVVLAALPRLGWADAAPADGAFYLWARLGERQLAEFGDAVAYCTAL
+LEEAGVALTPGADFDGVHGGEFVRMSYAADAGAVAEALERIAAWHAARGLA*
+>NZ_CP097650.1_1982
+MRRPSRSSTADPASTAAPAPTATPAFAPSARSQVPPFTVMSILGRVAELRAAGHDVVSLC
+AGEPGGGAPPAVDAAAAAVHASGRAFTYTPALGLPELRTAVAGHYRRWYGLDVRPEQVAI
+TTGSSGAFMLGFLAAFPPGDRVLLPRPGYPAYRNILTALGVEVVDVDVDAGTRYQPTVAH
+LEAALAEGPVAGLVLASPANPTGTMVSADELAELARWCEERGVRLVSDEIYHGIVHTDGE
+GLGACAWRTSRTALVVSSFSKYWGMPGWRLGWMLMPDDLAAAVDGLAGSVALCPPAAAQE
+AAVHAFSEESYAFCAEQAGGFTATRGVVLAALPRLGWADAAPADGAFYLWARLAPGMLAE
+FGSAVGYCAALLEEAGVALTPGDDFDAVHGPESVRLSFAAGPDAVHEALERIAAWHAGRG
+LA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001930.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001930.fa
new file mode 100644
index 0000000000000000000000000000000000000000..656ee2c2de60cf261c4ba9c4dd8fae2e3325a32f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001930.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_2068
+MSTEPTPSSATPETESAAPSSSGLPQAAPQAAWPERVETGEHQVSYRATVAAPAHELWAM
+LADPHRHHEADGSGTVRPKVSGPHRLAVGDRFRVAMRKYGVPYTMTLTATAVDEDELVEW
+AHPGGHRWRWAFQDNGDGTTEVTETFDYSWARPAVRRAYELLRVPADNGRGIQSSLTRLA
+GRHL*
+>NZ_CP033200.1_1788
+MSTEPTPSSATPETESAAAPSSSGLPQAAPQAAWPERVETGEHQVSYRVTVAAPAHELWA
+MLADPHRHHEADGSGTVRPKVSGPHRLAVGDRFRVAMRKYGVPYTMTLTATAVDEDELVE
+WAHPGGHRWRWAFRDNGDGTTEVTETFDYSWARPAVRRAYELLRVPADNGRGIQSSLTRL
+AGRHL*
+>NZ_CP083691.1_557
+MSTEPTPSPATPETEPAAPSSSGLPQSAPQAAWPERVETGEHQVSYRATVAAPAQELWAM
+LADPHRHHEADGSGTVRPKVSGPHRLAVGDRFRVAMRKYGVPYTMTLTATAVDEDELVEW
+AHPGGHRWRWAFQDNGDGTTEVTETFDYSWARPAVRRAYELLRVPADNGRGIQSSLTRLA
+GRHL*
+>NZ_CP097650.1_2007
+MGDMSTEPTPSSATPETESAAAPSSSGLPQAAPQAAWPERVETGEHQVSYRVTVAAPAHE
+LWAMLADPHRHHEADGSGTVRPKVSGPHRLAVGDRFRVAMRKYGVPYTMTLTATAVDEDE
+LVEWAHPGGHRWRWAFQDNGDGTTEVTETFDYSWARPAVRRAYELLRVPADNGRGIQSSL
+TRLAGRHL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001931.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001931.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da44e4bc073567d92580ce378575b622e1355634
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001931.fa
@@ -0,0 +1,28 @@
+>NZ_CP042169.1_2079
+MSEHTPAHTPASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRAEVL
+DLAHGTPFTSASAMTGGADPDVLAGCEVVVITAGAKQKPGQTRLDLGAHNVEILRGLLPQ
+VQAHAPDALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQVHAS
+SVHAAILGEHGDTEFPAWSSARIGPTPLLEWPTPADPLFTRADLDEVADTVVNAAYEVIQ
+GKGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVTRVI
+QPELDAAEMRALHASADALRREARSLGF*
+>NZ_CP033200.1_1799
+MSEHTPAHSPAAPASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRA
+EVLDLAHGTPFTSASAMTGGADPDVLAGCEVVVITAGAKQKPGQTRLDLGAHNVEILRGL
+LPQVQAHAPEALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQV
+HPSSVHAAILGEHGDTEFPAWSSARIGPTPILEWPTPVDPLFTRADLDEVADTVVHAAYE
+VIQGKGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVT
+RVIQPELDDAEMRALHASADALRREARSLGF*
+>NZ_CP040019.1_621
+MSEHTPAAPASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRAEVLD
+LAHGTPFTSASAMTGGADPDVLADCEVVVITAGAKQRPGQTRLDLGAHNVEILRGLLPQV
+QAHAPDALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQVHASS
+VHAAILGEHGDTEFPAWSSARIGPTPILEWPTPAAPLFTRADLDEVADTVVHAAYEVIRG
+KGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVTRVIQ
+PELDAAEMRALHSSADALRREARSLGF*
+>NZ_CP097650.1_2018
+MSEHTPAHSPAAPASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRA
+EVLDLAHGTPFTSASAMTGGADPDVLAGCEVVVITAGAKQKPGQTRLDLGAHNVEILRGL
+LPQVQAHAPEALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQV
+HPSSVHAAILGEHGDTEFPAWSSARIGPTPILEWPTPVDPLFTRADLDEVADTVVHAAYE
+VIQGKGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVT
+RVIQPELDDAEMRALHASADALRREARSLGF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001934.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001934.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b85536ab790994e21078379d3369055ba7ada6c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001934.fa
@@ -0,0 +1,16 @@
+>NZ_CP042169.1_2115
+MTDIRRTATALTLGAAVVTGLGAPAAVAQTTAPATETATTAPASESPAPQEEEKDDNGNW
+GLWGLAGLLGLAGLAGRRKREVHAEPVRRDHHVAGAHRDHDVHRVDDRAGDVRTEGADAR
+RREADGTLGDATRRPGTGDAR*
+>NZ_CP033200.1_1841
+MTDIRRTATALTLAAAVVTGLGAPAAVAQTTAPATEAATTAPASESPAPQEEEKDDNGNW
+GLWGLAGLLGLAGLAGRRKREVHAEPVRRDHHVGGAHRDHDVHRVDDRAGDVRAEGADTR
+RPGTGDAR*
+>NZ_CP083691.1_491
+MADIRKTATALTLSAAVLVGAGAPAATAAESSTAPATETATTAPASSQSPEPEQTEEKDD
+NGNWGLWGLAGLLGLAGLAGRGKKREVVHAQPVREAPRVQPTHTENHHVDTTRVQDGVRD
+AGHRAGGTDGTPGNGR*
+>NZ_CP097650.1_2061
+MTDIRRTATALTLGAAVVTGLGAPAAVAQTTAPATETATTAPASESPAPQEEEKDDNGNW
+GLWGLAGLLGLAGLAGRRKREVHAEPVRRDHHVAGAHRDHDVHRVDDRAGDVRTEGADAR
+RREADGTLGDATRRPGTGDSR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001936.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001936.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5f2914c0be799a25e5a3746fc0539cc7bc90e3b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001936.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_2131
+MPSTAVPPRDSGAASTLPARTGHRGVSILRTAALVLVVAAFVWLALTVRLPGVDELRAQL
+DGFGWWSWLAFTVLYAAVALTPIPVTIMAVTAGVLFGAIEGTVLSVVGALLGSLGAYGIA
+RAVGREVVLRWLGRHAETVERRLEDTGFLALLTLRVAPGLPYWPVNYGAGALAVPLGIFA
+GSTAVGVIPGQLSLVAMGAFAVRPGVVNGVLLGVGWLTVGGLTLWAVRHWRRAARSAEEP
+ENPQSGHDTPSPRRRRGVS*
+>NZ_CP033200.1_1857
+MPSTAVPPRDSGAASTLPARTGHRGVSILRTAALVLVVAAFVWLALTVRLPGVDELRAQL
+DGFGWWSWLAFTVLYAAVALTPIPVTIMAVTAGVLFGAIEGTVLSVVGALLGSLGAYGIA
+RAVGREVVLRGLGRHAETVERRLEDTGFLALLALRVAPGLPYWPVNYGAGALAVPLGIFA
+GSTAVGVIPGQLSLVAMGAFAVRPGVVNGVLLGVGWLAVGGLTLWAVRRWRRAARAAEGP
+AGSEGPESPRSGQDTPSPRARRGVS*
+>NZ_CP040019.1_546
+MPSSAAPPSDAASSRPDRRGSSGSVGTASRTLLLVVVMALFIWLATSVRLPDIDTLRDRL
+ASFGFWSWLVFVLAYAGVALTPVPVTLMALTGGVLFGAVQGSVLSVAGALLGSIGAYWIA
+RALGRDVILRGLGRHADTVEEHLEDAGFLALLTLRVAPGLPYWPVNYGAGALGVPSGMFV
+GSTAVGVIPGQVSLVALGAFAVHPGVLNGVILGAGWLAVGVLTVWAARHWRRAANHDDGE
+GGED*
+>NZ_CP097650.1_2077
+MPSTAVPPRDSGAASTLPARTGHRGVSILRTAALVLVVAAFVWLALTVRLPGVDELRAQL
+DGFGWWSWLAFTVLYAAVALTPIPVTIMAVTAGVLFGAIEGTVLSVVGALLGSLGAYGIA
+RAVGREVVLRWLGRHAATVERRLEDTGFLALLTLRVAPGLPYWPVNYGAGALAVPLGIFA
+GSTAVGVIPGQLSLVAMGAFAVRPGVVNGVLLGVGWLAVGGLTLWAVRRWRRAARAAEGP
+AGSEGPESPRSGQDTPSPRARRGVS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001937.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001937.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b40b0a07eab310fe4abad88839ee9c1bb3a8f650
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001937.fa
@@ -0,0 +1,13 @@
+>NZ_CP042169.1_2132
+MSESTGFSAAEQAAIAERAQELRAQRGGKKKADALQDLLATIEEMPEPDRALAVAVHRIV
+TEVAPELDPRT*
+>NZ_CP033200.1_1858
+MSESTGFSAAEQAAIAERAQELRAQRGGRKKADALQDLLVKIEEMPEQDRAMAVGVHRIV
+TEAAPELEPRTWYGMPAYARGTDVLVFLQVSSKFGVRYTTLG*
+>NZ_CP040019.1_545
+MSESTGFSAAEKAAMAERAEELRAQRGGKKKADALQDLMEKIEAMPEQDRALAVAVHQIV
+TEVAPELEPRTWYGMPAYARGKDVLVFLQVSSKFDVRYTTLGFNESAALDDGPMWPTAYA
+LTALNDDVRARIADLVRRAVG*
+>NZ_CP097650.1_2078
+MTESTGFSAAEQAAIAERAQELRAQRGGKKKADALQDLLAKIEEMPEQDRAMAVAVHRIV
+TEAAPELEPRTWYGMPAYARGTDVLVFLQVSSKFGVRYTTLG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001938.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001938.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bdad1e6c7757a4055d8c1740996fb2f415dda86d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001938.fa
@@ -0,0 +1,8 @@
+>NZ_CP042169.1_2136
+MPHATLASVTRRPDAPPPADPRARAALRAVLTVLAVMAVLFAAVVLTLAYGPAR*
+>NZ_CP033200.1_1861
+MPRATLASVTRRPDAPPPADPRTRAALRAVLTVLAVMAVLFAAVVLTLAYGPAR*
+>NZ_CP040019.1_534
+MPRATLASVTHHPDAPPPADPRTRAALRAVLTVLAVLAVLFAAVVLTLAYGPAR*
+>NZ_CP097650.1_2081
+MPHATLASVTRRPDAPPPVDPRTRAALRAVLTVLAVMAVLFAAVVLMLAYGPAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001940.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001940.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d964f765dcd9c5bbd01aab07d247a4569b004c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001940.fa
@@ -0,0 +1,12 @@
+>NZ_CP042169.1_2147
+MTHHERDDRQALAAGETYLIHVLETSDPPGNPDHYRITDAVEAHHASTGSYDVEAGGLDA
+ARELLARHAK*
+>NZ_CP033200.1_1872
+MTHHERDDRQALAAGETYLIHVLETSDPPGNPDHYRITDAVEAHHASTGSYDVEAGGLDA
+ARELLARHAK*
+>NZ_CP040019.1_524
+MTHHDDDRSALAAGETYLVHILETSTPPGNPEHYRITDAVEAHHAETGSWDIEAAGPDAA
+RELLARHGR*
+>NZ_CP097650.1_2092
+MTHHERDDRQALAAGETYLIHVLETSDPPGNPDHYRITDAVEAHHASTGSYDVEAGGLDA
+ARELLARHAK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001941.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001941.fa
new file mode 100644
index 0000000000000000000000000000000000000000..552197638e5ad673fded4a49f4fb289a336c8a5f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001941.fa
@@ -0,0 +1,28 @@
+>NZ_CP042169.1_2151
+MVGPSLFSRLASTLLHPLAPQDVLSLLDPVHSSRQLRGVVTSVTRETPGTATIAFRPGPG
+WRAHDAGQWARIGVDVDGVRQWRSYSLSAPAGADPEITVSDIGLVSGTLVRHTKPGDVLF
+LDIPEGDFTLPDEPRPLLMLTAGSGLTPVMSMIRTLVPTRRDADVVLIHSSRTPEDALFR
+EELAELADQFPGLRVVHHHTAETGRLDLSSPAQLEGLCPDWRERAGYACGPAGFLDDAEA
+LWRREAAADLTIERFQADFAPGVAGAGGRVVFEHADVEVDAPGDVPLLVVAEEAGVAAPA
+GCRMGICHACLTPLRSGRVTDLRTGQVHGEPGELVQTCVSAAAGPLSLSL*
+>NZ_CP033200.1_1876
+MVGPSLFSRLASTLLHPLAPQDVLSLLDPVHSSRQLRGVVTSVTRETPGTATIAFRPGPG
+WRAHDAGQWARIGVDVDGVRQWRSYSLSAPAGADPEITVSDIGLVSGTLVRRTKPGDVLF
+LDVPEGDFTLPDEPRALLMLTAGSGLTPVMSMIRTLVPARADADVVLIHSSRTPEDALFR
+EELAELADQFPGLRVVHRHTADEGRLDLSSPAELEDLCPDWRDRAAYACGPAEFLDDAED
+LWRREAGEDLRIERFRADFAAGVAGAGGRVVFEHADAEADAPGDVPLLIVAEEAGVAAPS
+GCRMGICHACLTPLRSGQVTDLRSGEVHGEPGELIQTCVSAAAGPLSLDL*
+>NZ_CP040019.1_522
+MAGPSLLSRLASTLLHPLTPQDVLGLLDPVHSSRQLRGVVTSVRRETPGTATIAFRPGPG
+WRLHDAGQWARIGVDVDGVRQWRSYSLSAPAGADPEITVSDIGLVSGTLVRRTVPGDVLF
+LDVPEGDFTLPEEPRPLLMLTAGSGLTPVMSMIRTLVPARRDADVVLVHSSRTPETALFR
+EELAELADQFPCLRVVHRHTADEGRLDLSSPAELEALCPDWRERAAYACGPAPFLDDAED
+LWRREAGGELRIERFRADFAPGVAGAGGRVVFEHSDAEADAPGDVPLLIVAEEAGVAAPA
+GCRMGICHACLTPLRSGQVTDLRSGEVHGEPGDLVQTCVSAAAGPVSLDL*
+>NZ_CP097650.1_2096
+MVGPSLFSRLASTLLHPLAPQDVLSLLDPVHSSRQLRGVVTSVTRETPGTATIAFRPGPG
+WRAHDAGQWARIGVDVDGVRQWRSYSLSAPAGADPEITVSDIGLVSGTLVRRTKPGDVLF
+LDVPEGDFTLPDEPRALLMLTAGSGLTPVMSMIRTLVPARADADVVLIHSSRTPEDALFR
+EELAELADQFPGLRVVHHHTAETGRLDLSSPAQLEGLCPDWRERAGYACGPAGFLDDAEA
+LWRREAAADLTIERFQADFAPGVAGAGGRVVFEHADAEADAPGDVPLLIVAEEAGVAAPS
+GCRMGICHACLTPLRSGQVTDLRSGEVHGEPGELIQTCVSAAAGPLSLDL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001942.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001942.fa
new file mode 100644
index 0000000000000000000000000000000000000000..142ca78a2d74dc9b892e0b06169c6cb770255f72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001942.fa
@@ -0,0 +1,27 @@
+>NZ_CP042169.1_2153
+MSIPQDSGRPRPDAPTSPLAAALAQQETDPLRWEEDPAPPRRRRSFGRWMRELGWRHAVG
+VLASAFALFPLLYVLSASLDPTGTMASSNRLFSSFSGQNYVDLFSDPNRPFGRWFLNTMV
+IGVITSVMTVFLGALAAYAFSRMRFTGRRVGLLTLLLVQMFPQLLAVVAIFLLLTYIGNL
+VPVLGIGSQLGLILVYLGGALGVNTYLMYGFFNTIPPSLDEAAKLDGASHARIFFSIILR
+LVTPILAVVALLSFITTVSEFVIASVVLTDPSAQTLAVGLYGYVSETRSENWGVFAAGAV
+LAALPVMALFLFLQRYIVSGLTAGGVKG*
+>NZ_CP033200.1_1878
+MSIPQDSGRPRPDAPTSPLAAALAQQETDPLRWEEDPAPPRRRRSFGRWMRELGWRHAVG
+VLASAFALFPLLYVLSASLDPTGTMASSNRLFSSFSGQNYVDLFSDPNRPFGRWFLNTMV
+IGVITSVMTVFLGALAAYAFSRMRFTGRRVGLLTLLLVQMFPQLLAVVAIFLLLTYIGNL
+VPVLGIGSQLGLILVYLGGALGVNTYLMYGFFNTIPPSLDEAAKLDGASHARIFFSIILR
+LVTPILAVVALLSFITTVSEFVIASVVLTDPSAQTLAVGLYGYVSETRSENWGVFAAGAV
+LAALPVMALFLFLQRYIVSGLTAGGVKG*
+>NZ_CP040019.1_519
+MSIPQDPSARAPQGQAAPAAASPLAAALAQQEIDPLRWEDGAPPPRRRRSFGRWLRELGW
+RHVVGVLASAFALFPLLYVLSASLDPTGTMASSNSLFSSFSGQNYVDLFSDPSRPYGRWF
+VNTMVIGLVTSFSTVFLGALAAYAFSRMRFAGRRVGLLTLLLVQMFPQLLAVVAIFLLLT
+YIGDLVPVLGIGSQLGLILVYLGGALGVNTYLMYGFFNTVPASLDEAAKLDGASHVQIFF
+SIILRLVTPILAVVGLLSFISTVSEFVIASVVLTDPAAQTLAVGLYGYVSETRSENWGVF
+AAGAVLAAVPVMALFLFLQRYIVSGLTAGGVKG*
+>NZ_CP040019.1_2594
+MTFTLLAPHQSAAISEAGIEQAARDLTRARTLGRIGLVPAFAILTVLAVISIFPIYWMFV
+TAFRPAEQMLSTNPLPGPFSLENFQYVWDTIPILSMLGNTFVMALVIAIGQLFVAILASY
+GFSRWTFRGQKILFLLFVGSWLVPFQVTMIPNYVRIAEMGLLNNMVGVILPQLAAAFAVM
+MLKQHLDSFPRELLDASDMDGRSPWRTLWEVVVPNLRPALAALAIMLFISAWNEYLWPSL
+IMQGSNDLIQVGVRSFLGSEGNNWGAVMAASALACLPIFLIYIFLQRYVVDAFVRSGLK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001954.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001954.fa
new file mode 100644
index 0000000000000000000000000000000000000000..342555635fc1351875871ea5ad769eef0013fcf9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001954.fa
@@ -0,0 +1,32 @@
+>NZ_CP042169.1_2228
+MTTPFHAEADSFLGRADVVGLDSLFSAEEKAVALQVRGFVDEHIRPHIARWYDDAVFPRE
+IVPELGRLGVLGMPYEGHGMPGRSAVEYGLAAQELEAGDSGLRTFVSVQGSLAMGAIHKH
+GSEEQKAQWLPRMTTGEAVGCFGLTEPGAGSDPASMTTTARQEPGGDWVLDGVKRWIGLA
+TLADVAIIWAQTGEPGDGRGVRGFVVPTDTPGFRAETITQKLSMRASVQCEIHLDGVRLP
+ASAMLPADSAVGLKGPFQCLNEARYGIIWGAMGAARDSFDAVLDYAMERQQFGVPLASHQ
+LTQAKLADMAVAIGKGYLLAHQIGRAKDAGPLTPAMISAGKLDNCRVAIGIAREAREMLG
+GNGITLEHSPLRHANNLESVRTYEGTDEVHQLTLGRHLTGIGAFAPAR*
+>NZ_CP033200.1_1931
+MTTPFHAEADSFLGRADVVGLDSLFSAEEKAVALQVRGFVDEHIRPHIARWYDDAVFPRE
+IVPELGRLGVLGMPYEGHGMPGRSAVEYGLAAQELEAGDSGLRTFVSVQGSLAMGAIHKH
+GSEEQKAQWLPRMTTGEAVGCFGLTEPGAGSDPASMTTTARQEPGGDWVLDGVKRWIGLA
+TLADVAIIWAQTGEPGDGRGVRGFVVPTDTPGFRAEAITQKLSMRASVQCEIHLDGVRLP
+ASAMLPADSAVGLKGPFQCLNEARYGIIWGAMGAARDSFDAVLDYAMERQQFGVPLASHQ
+LTQAKLADMAVAIGKGYLLAHQIGRAKDAGPLTPAMISAGKLDNCRVAIGIAREAREMLG
+GNGITLEHSPLRHANNLESVRTYEGTDEVHQLTLGRHLTGIGAFAPAR*
+>NZ_CP040019.1_437
+MPSPTPFHAEADSFLGRADVVGLDALFSDQEKATALAVRAFVDEHLRPHIASWYEDAVFP
+REIVPELGRLGVLGMPYEGHGMPGRSAVEYGLAAQELEAGDSGLRTFVSVQGSLAMGAIH
+KHGSEEQKAQWLPRMTAGEAVGCFGLTEPGAGSDPASMTTTARQETGGDWVIDGVKRWIG
+LATLADVAIIWAQTGEPGDGRGVRGFVVPTDTPGFRAEAITQKLSMRASVQCEIHLDGVR
+LPASAMLPADSAVGLKGPFQCLNEARYGIIWGAMGAARDSFDAVLDYAMQRQQFGVPLAS
+HQLTQAKLADMAVAIGKGYLLAHQIGRAKDAGPLTPAMISAGKLDNCRVAIGIARDAREM
+LGGNGITLEHSPLRHANNLESVRTYEGTDEVHQLTLGRHLTGIGAFAPAR*
+>NZ_CP097650.1_2169
+MTTPFHAEADSFLGRADVVGLDSLFSAEEKAVALQVRGFVDEHIRPHIARWYDDAVFPRE
+IVPELGRLGVLGMPYEGHGMPGRSAVEYGLAAQELEAGDSGLRTFVSVQGSLAMGAIHKH
+GSEEQKAQWLPRMTAGEAVGCFGLTEPGAGSDPASMTTTARQEPGGDWVLDGVKRWIGLA
+TLADVAIIWAQTGEPGDGRGVRGFVVPTDTPGFRAEAITQKLSMRASVQCEIHLDGVRLP
+ASAMLPADSAVGLKGPFQCLNEARYGIIWGAMGAARDSFDAVLDYAMQRQQFGVPLASHQ
+LTQAKLADMAVAIGKGYLLAHQIGRAKDAGPLTPAMISAGKLDNCRVAIGIAREAREMLG
+GNGITLEHSPLRHANNLESVRTYEGTDEVHQLTLGRHLTGIGAFAPAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001956.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001956.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d36f4fa03c28c4ae945bca4439737250948c9e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001956.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_2244
+MTRPDPSAHRGAPLPSALGAWRRRPQPPLRPVTPAPAGPRSAAAASLPTVEEVSAGGVIV
+REHDGGLEVAVIARYNRGGRLEWCLPKGHPEGEEDHRQAAVREVEEETGIAGHILEPLGA
+IDYWFTVARHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVRLEDVARRLSFANERR
+IVDLARQVVDQHFPPGGARGPRP*
+>NZ_CP033200.1_1949
+MTRPDPSAHRGAPLPSALGAWRRRPQPPLRPVTPAPAGPRSAAAASLPTVEEVSAGGVIV
+REHDGGLEVAVIARYNRGGRLEWCLPKGHPEGEEDHRQAAVREVEEETGIAGHILEPLGA
+IDYWFTVARHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVRLEDVARRLSFANERR
+IVDLARQVVDQHFPPGGARGPRP*
+>NZ_CP083691.1_373
+MSSPDPTAHRGAPLPSALGAWRRRPPQPPRPLAPGAPAARPQSGAGLPTVEEVSAGGIVI
+REHAGDLEVAVIARYNRGGRLEWCLPKGHPEGAEDHRQAAVREVEEETGIAGCILEPLGS
+IDYWFTVSRHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVSIDDVARRLSFANERR
+IVDLARQVIPQHFPTGRPPGRP*
+>NZ_CP097650.1_2187
+MTRPDPSAHRGAPLPSALGAWRRRPQPPLRPVTPAPAGPRSAAAASLPTVEEVSAGGVIV
+REHDGGLEVAVIARYNRGGRLEWCLPKGHPEGEEDHRQAAVREVEEETGIAGHILEPLGA
+IDYWFTVARHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVRLEDVARRLSFANERR
+IVDLARQVVDQHFPPGGARGPRP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001962.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001962.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81d66a56140cf2bec0576a6058a25c99601eb2d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001962.fa
@@ -0,0 +1,52 @@
+>NZ_CP033200.1_1600
+MQTEKHVPEALTIEEVFTAARHYRVPVYQRAYAWTQVEISTLLADVRRARLRSEKPDTQG
+ASSDYYLGSLVVNRATTPEGVPIDEVVDGQQRLTTLTVLAAVAERVIRAGVLDPRALAVL
+DYEGRPEAGEDLATLRRRGAPAGTSFQVDAIGVAVETIAAACRRALERQTPADDQEVMFD
+GDDLAYLWKHVRLLRTELPKGTDLNHYFEVMNTRGEQLAKHEILKATLMRPLQDATDRKV
+FAHVWDACAVLDRHIQLQFSTERPKDGGEAARDAVFGGSWSALLTRDFASLRAALAPSQT
+AMASGARTIIGVLLAAGQTAVESGPSSDQCQDDADTGAYGTIVDFPNLLLHVLRVMQEKG
+EGAEPGLPRWGQDSTGAVRLEDGSLLEQFAQHGQGDAAWSQRFLVTLLRMRLLLDTYVIR
+TLATTGTQADEENWVLSRAQKLETESGERSPRRRLGVKNTFQDPQVQDAVRNLQAMFQVT
+DTRRTSKYFLYRILRWLDAQPEDGVDGVAFQHMLEDLARERLRAYEADKTWDAGVNVPNF
+VFNALDYILWDAGRTSPMEREHLREPLSDVEQEVLRRRADAFRFRYRTSVEHFYPVVPGE
+EQEALTAEDVNRFGNLCIMGRRENSQRNNLMPVSKVKQYSSDEQSLKFQLMAGILHAEGD
+WDVPQIKEHGNSMRRVIQEWQGKRP*
+>NZ_CP040019.1_888
+MQTEKHVPEALTIEEVFTAARHYRVPVYQRAYAWTQVEISTLLTDVRRARLRSEKPDTQG
+ALSDYYLGSLVVNRATTPEDVPIDEVVDGQQRLTTLTVLAAVAERVIRAGVLDPRALAVL
+DYEGRPEAGEDLATLRHRGAPAGTSFQVDAIGVAVETIAAACRRAMDRQTPADDQEVMFD
+GDDLAYLWKHVRLLRTELPKGTDLNHYFEVMNTRGEQLAKHEILKATLMRPLQDATDRKV
+FAHVWDACAVLDRHIQLQFSTERPKDGVEAARDAVFGASWSALLTRDFASLRAALAPSLT
+ATVSGARTIIGALRAAGQTAVESGSSSDQRQDDADTGAYGTIVDFPNLLLHVLRVMQEKG
+EGAEPGLPRWSQDSTGAVRLEDGSLLEQFAQHGQDDAAWSQRFLVALLRMRLLLDTYVIR
+TLATTGTQADEENWVLSRAQKLETESGERSPRRRLGVKNTFQDPQVQDAVRNLQAMFQVT
+DTRRTSKYFLYRILRWLDAQPVDSVDGVAFQHMLENLARERLRAYEADKTWDAGVNVPNF
+VFNALDYILWDAGRTSPMEREHLREPLSDVEQEVLRRRADAFRFRYRTSVEHFYPVVPGE
+EQEVLTAEDVNRFGNLCIMGRRENSQRNNLMPVSKVKQYSSDEQSLKFQLMAGILHAEGD
+WDVPQIKEHGNRMRRVIQEWQGKRP*
+>NZ_CP083691.1_826
+MQTEKHVPEALTIEEVFTAARHYRVPVYQRAYAWTQVEISTLLTDVRRARLGSEKPDTQG
+ALSDYYLGSLVVNRATTPEDVPIDEVVDGQQRLTTLTVLAAVAEHVIRAGVLDPRALAVL
+DYEGRPEAGEDLATLRHRGAPAGTSFQVDAIGVAVETIAAACRRAMDRQTPADDQEVMFD
+GDDLAYLWKHVRLLRTELPKGTDLNHYFEVMNTRGEQLAKHEILKATLMRPLQDATDRKV
+FAHVWDACAVLDRHIQLQFSTERPKDGGEAARDAVFGASWSALLTRDFASLRAALAPSLT
+ATVSGARTIIGALRAAGQTAVESGSSSDQRQDDADTGAYGTIVDFPNLLLHVLRVMQEKG
+EGAEPGLPRWGQDSTGAVRLEDGSLLEQFAQHGQDDAAWSQRFLVALLRMRLLLDTYVIR
+TLATTGTQADEENWVLSRAQKLETESGERSPRRRLGVKNTFQDPQVQDAVRNLQAMFQVT
+DTRRTSKYFLYRILRWLHAQPVDSVDGVAFQHMLENLARERLRAYEADKTWDAGVNVPNF
+VFNALDYILWDAGRTSPMEREHLREPLSDVEQEVLRRRADAFRFRYRTSVEHFYPVVPGE
+EQEVLTAEDVNRFGNLCIMGRRENSQRNNLMPVSKVKQYSSDEQSLKFQLMAGILHAEGD
+WDVPQIKEHGNRMRRVIQEWQGKRP*
+>NZ_CP097650.1_1819
+MSERNAPETLTIGEVFAAGRHYRVPVYQRSYAWTEVEVSTLLADVRRARLRSKALESRGN
+VSDYYLGAMVVNRTQTPAGDQIDEVVDGQQRLTTLTVLAAVAEQITQAGVLDPVALAVLD
+YEGRAEAGEDLATLRRRGGHRHGAFQVEAIGIAAQTVRGACERATDRQATADGQTVVFDA
+DDLAYLWNHVRLLRTELPEGTDLNHYFEVMNTRGEQLAKHEVLKAMLMRPLRDESERQVF
+AQVWDACAVLDRPVQLQFASEQLDPDISPARDAVFGDTWSTLVTTDFESLRAALEPSLAE
+TELGGRTSLDSLLSSRGAGEGTSASAEKRSDETGSYGTIIDFPNLLLHVLRVMEESGMAS
+GSGRPAWGQEPKNAVRLEDNSLLEQCAERRQDDARWSKRFLVMLLRIRFLLDTYVIRTLS
+TTGTRADEENWVLVGALKVESGAEEGSSRRRRLGVKNTFEDPAVQEAVRNLQAMFQVTDT
+RRASKYFLYRILRWLAERPVDRVDGEAFQRMLEDLARERLRAYDADEGLDLGVKVPNFVF
+NVLDYILWDLGRNPSAEAGALGAALGDVERSVLSQRAGSFRFRYRTSVEHFYPVVPGEGQ
+KVLTSTEVNRFGNLCIMGRRENSQRNNLMPVSKVKQYSSDEQSLKFQLMAGILHAEGDWD
+VPQIKEHGNSMRRVIQEWQGKRP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001969.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001969.fa
new file mode 100644
index 0000000000000000000000000000000000000000..414af5f80ea4544c7b5f1844b6f776f48a7e0882
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001969.fa
@@ -0,0 +1,20 @@
+>NZ_CP033200.1_1656
+MSITQTDTPLTQDELARTIAADIAPGSFVNLGIGQPTTVSNYLEAEKNVTLHTENGMLGF
+GPQAEGEQIDEDLINAGKIPVTELPGAAYFHHADSFAMMRGGHLDVCVLGAYQVSATGDL
+ANWSTGKPGAIPAVGGAMDLAIGAKDTYVMMDLFTKKGDPKLLAECTFPLTGVGCVSRIY
+ADRGVFLLDASGVVRVRELHGITWEELEAAHPGVRFEKLED*
+>NZ_CP040019.1_835
+MSFTQTDTPLTQDELAKVIAADIAPGSFVNLGIGQPTTVSNYLEAEKNVTLHTENGMLGF
+GPQAEGEQVDEDLINAGKIPVTELPGAAYFHHADSFAMMRGGHIDVSVLGAYQVSATGDL
+ANWSTGKPGAIPAVGGAMDLAIGAKDTYVMMDLFTKKGDPKLLAACTFPLTGVGCVSRIY
+ADRGVFLLDASGVVRVRELHGITWEELEEAHPGVRFEKLEA*
+>NZ_CP083691.1_771
+MGFTHTENPLSHEELAQVIAADIAPGSYVNLGIGQPTTVSDYLDADQHVTLHTENGMLGF
+GPQAHGEQVDEDLINAGKIPVTELPGASYFHHADSFAMMRGGHLDVCVLGAYQVSATGDL
+ANWSTGKPGAIPAVGGAMDLAIGAKDTYVMMDLFTKKGDRKLMPECTFPLTGVGCVSRIY
+ADKGVFLLDSSGVVKVRELHGITFEELQATHEGVTFEEVDASA*
+>NZ_CP097650.1_1873
+MSITQTDTPLTQDELARTIAADIAPGSFVNLGIGQPTTVSNYLEAEKNVTLHTENGMLGF
+GPQAEGEQIDEDLINAGKIPVTELPGAAYFHHADSFAMMRGGHLDVCVLGAYQVSATGDL
+ANWSTGKPGAIPAVGGAMDLAIGAKDTYVMMDLFTKKGDPKLLAECTFPLTGVGCVSRIY
+ADRGVFLLDASGVVRVRELHGITWEELEAAHPGVRFEKLED*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001970.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001970.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a1b4f6e7c76ded13b31275089c59ff926d866e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001970.fa
@@ -0,0 +1,24 @@
+>NZ_CP033200.1_1657
+MLEFVDTAAQAVSRITDGATVLIGGFGNAGQPMELIDALLESGATGLTVVNNNAGQADAG
+LALLIKERRVAKIICSFPRHSDSWHFDEAYRAGEIELELVPQGNLAERLRAGGAGIGGFF
+TPTGYGTQLAEGKEVREIDGTHYVLEAPIRGDVALIKAYAADRHGNLVYRKTARNFGPVM
+AAAAATTIVQVDEVREEPIDPEHVVTPGIYTDTVVRIDTESGEKERAERAALAEGRPKPC
+AATTTAAEPAAEGK*
+>NZ_CP040019.1_834
+MLEFVDTAAQAVSQVTDGATVLIGGFGNAGQPMELIDALLESGATGLTVVNNNAGQADAG
+LALLIKERRVAKIICSFPRQSDSWHFDEAYRAGEIELELVPQGNLAERLRAGGAGIGGFF
+TPTGYGTQLAEGKEVREIDGRHYVLESPIRGDVALIKAYAADRHGNLVYRKTARNFGPIM
+AAAAEHTVVQVDEVRDEPIDPEHVITPGIYTDVIVRIETESGAKEREEREALAAGKPKPC
+AATKTAAEKAAEGK*
+>NZ_CP083691.1_770
+MLEFVETAAEAVAQVRDGQTVLIGGFGNAGQPMELIDALLESGATGLTVVNNNAGQADAG
+LALLIKERRVAKIICSFPRQSDSWHFDEAYRAGEIELELVPQGNLAERLRAGGAGIGGFF
+TPTGYGTQLAEGKEVREIDGRHYVLESPIKGDVALIKAYAADRHGNLVYRKTARNFGPVM
+AAAAATTIVQVDEISEEPLNPEHVITPSIYVDTVVRIQTESGVKEREALAAGKPKPCLAT
+ETAAGQAAEGK*
+>NZ_CP097650.1_1874
+MLEFVDTAAQAVSRITDGATVLIGGFGNAGQPMELIDALLESGATGLTVVNNNAGQADAG
+LALLIKERRVAKIICSFPRQSDSWHFDEAYRAGEIELELVPQGNLAERLRAGGAGIGGFF
+TPTGYGTQLAEGKEVREIDGTHYVLEAPIRGDVALIKAYAADRHGNLVYRKTARNFGPVM
+AAAAATTIVQVDEVREEPIDPEHVVTPGIYTDTVVRIDTESGEKERAERAALAEGRPKPC
+AATTTAAEPAAEGK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001973.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001973.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fba4b641ff03e6a5656c7aca2dfef15f5c6dfb05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001973.fa
@@ -0,0 +1,16 @@
+>NZ_CP033200.1_1662
+MSAEQPIGHDMDRTSQEVLDAGMAVRREVLGDAHVDRAEARKDATTEDFQNLITRYAWGT
+IWTRPGLDRRMRSAVTISAMVAGGYWDECAMHPRAALRNGLTREEIQEILLQTAVYASVP
+AANIAFKLAQEDADLAEGRPL*
+>NZ_CP040019.1_830
+MSGGRTEHAGGADAGQTPLGHQMERTSQEILDAGMAVRREVLGDAHVDRAEATKDATTDD
+FQNLISRYAWGTIWTRPGLDRRMRSAVTITAMVSGGYWEECAMHLRAALRNGLSRDEIKE
+ILLQAAIYSSVPAANVAFKLAQEVFAQVDEDLAAGRPL*
+>NZ_CP083691.1_762
+MGEQPIGHDMDRTSREVHDAGMAVRREALEDAHVDRAEANKDAATEDFQNLITRYAWGTV
+WTRPGLDRRMRSAVTITAMVAGGYWDECAMHLRAALRNGLSREEVQEILLQTAVYCSVPA
+ANIAFTLAQRVFAEVDADLAAGRPL*
+>NZ_CP097650.1_1879
+MSAEQPIGHDMDRTSQEVLDAGRAVRREVLGDAHVDRAEARKDATTEDFQNLITRYAWGT
+IWTRPGLDRRMRSAVTISAMVAGGYWDECAMHPRAALRNGLTREEIQEILLQTAVYASVP
+AANIAFKLAQEDADLAEGRPL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001975.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001975.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb9b757c5efbd79e8837137779e0eff6264e9328
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001975.fa
@@ -0,0 +1,32 @@
+>NZ_CP033200.1_1664
+MTSAAADLAAVADVGLLDPAWAGSRAEAATADRTFLGHLLDVEAAWVRVLARHGLATEAE
+AAAAAAAGDPDAYDLAALARAAQGGGTPLIPALKALRAQLPAGSRAVHLGATSQDVVDSA
+LMVMVGRVGAILAEDLAAAQDALAELARAHRSTPMVARSLAQHSLPSTFGLRAANWLDGL
+GQAADRLAAAVADLPVQWGGAAGTLASLSGHVDRAHRAGTLGPEVTAFTLVEDLAAELGL
+AAPAGPWDTNRMAVTGVAAALADVVAACGKIANDVLTSARIENGELGEPLAAGRGGSSPM
+PHKQNPVLSVLIRSAALSAPGLAARVYTAAGAADDERPDGAWHAEWPALRRLLRVAGGTA
+ALTRELVSGLRVHEDRMRRNLELTGPLLVSEPIMAELAPELDEASGEPGSGKRLIQDVVD
+RSLACEGNFRALLRAAVPESVPDARLDDLLDPAAYTGEAEALVDRLLAARRGTTTPPRT*
+>NZ_CP040019.1_828
+MTDLDALDLSADAGLLNPAWAGRPVARATADRAFLQRMLEVEAAWVAVLAAHGLATDEQA
+RQAEEACDPAGYDLVALARAAQGGGNPLIPALKALRERLPAGSTAVHMGATSQDVIDTAL
+MAMAAEVGRGLGEDLRGLAAALAGLAREHRGTPMVARSLAQHSLPSTFGLRAANWLDAVG
+QAAQRLERATAALPVQWGGAAGTMASLAGHVDRAHRAGRLDESVTVFTLVEDLAARLGLS
+APAGPWDTNRMAVTGVAAALADVTAACGKIANDVLLSSRIENGELGEPLAAGRGGSSAMP
+HKQNPVLSVLVHSAALSAPGMLAQVYTAAGAANDERPDGAWHAEWPALRQLLRVAGGAAS
+LTRELAEGLRVNADRMAENLAQTGPVLVSERLMAELAPAIDEACGEPGAGKAAIQGAVDD
+SLAGRGEFRALLREAVPDTVSDDRLDELLDPAGYTGEAGALVDRILAAHAELIDT*
+>NZ_CP083691.1_760
+MTRPRVGIVGAAPAGPWDTNRMAVTGVAAALADVVAACGKVANDVLTSARIENGELGEPL
+AAGRGGSSAMPHKQNPVLSVLIHSAALSTPGLLAQVYTAAGAANDERPDGSWHAEWPALR
+QLLCVAGGAAALTRELVSGLRVHTGRMAANLALTGPLLVSERIMAELAPELDALFGGPGS
+GKAVIQGAVDASLAGEGDFAELLRAAVPAEVSDARLADLLDPVAYTGEAETLVDRILAAH
+APRLRASA*
+>NZ_CP097650.1_1881
+MHLGATSQDVVDSALMVMVGRVGAILAEDLAAAQDALAELARAHRSTPMVARSLAQHSLP
+STFGLRAANWLDGLGQAADRLAAAVADLPVQWGGAAGTLASLSGHVDRAHRAGTLGPEVT
+AFTLVEDLAAELGLAAPAGPWDTNRMAVTGVAAALADVVAACGKIANDVLTSARIENGEL
+GEPLAAGRGGSSAMPHKQNPVLSVLIRSAALSAPGLAARVYTAAGAADDERPDGAWHAEW
+PALRRLLRVAGGTAALTRELVSGLRVHEDRMRRNLELTGPLLVSERIMAELAPELDEASG
+EPGSGKRLIQDVVDRSLACEGNSRALLRAAVPESVPDARLDDLLDPAAYTGEAEALVDRL
+LAARRGTTTPPRT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001977.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001977.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f11683dc82f13857dbd6fe7557e241bb65976551
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001977.fa
@@ -0,0 +1,12 @@
+>NZ_CP033200.1_1813
+MRTADAETQRKILNRLKRARGQLDAVIREVEGEGRCKDVVTQLSAVSTALDRAGFAIVSA
+AMQYCLADPEKAEDEEKLTVAELEKLFMTLA*
+>NZ_CP040019.1_601
+MRSADPETQRKILNRLKRARGQLDAVIREVEGEGSCRDVVTQLSAVSTALDRAGFAIVSS
+AMKNCVADPERAREDESLTVEELEKLFLSLA*
+>NZ_CP083691.1_525
+MRTADAETQRKILNRLKRARGQLDAVIREVEGEGSCRDVVTQLSAVSTALDRAGFAIVSS
+AMKNCVADPEKAREDEGLTVEELEKLFLSLA*
+>NZ_CP097650.1_2032
+MIPLPATVTKEVAVRTADAETQRKILNRLKRARGQLDAVIREVEGEGRCKDVVTQLSAVS
+TALDRAGFAVVSSAMQYCLADPEKAEDEEKLTVAELEKLFMTLA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001980.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001980.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d45c4bbaabf7497d32aece16c7650041eedab32
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001980.fa
@@ -0,0 +1,36 @@
+>NZ_CP040019.1_187
+MTASRLIPPAVDPASLPRDLPGLRAHFRPVVEEIARGALERDRARLLPFEAVRALGCAGF
+SVLRVPREAGGPDVDVRTVTALLVDLAAADSNVAHLYRSHLGFLDALRFQPQPVRDRWHA
+LVLAGATVGNASTERGGNALGTLNTRLTAPAGGDDDGAPGAAWTLTGTKYYATGSIFSSH
+TRVSAAVVRADGSLAPGRGFAVVPVDAPGVCLEDDWDGFGQRLTGTGTAVFEDVAVDPRD
+VLERIPGSPEAVHEAAWFQLILLAVLAGIARAARDDAAARVAARVRTFNTGLGVPFREDP
+LIQEAVGRIAAKASAAEAVVLAAADALDASLAAGAATGADRWGFTGPVPPAFAEAELAVE
+HAQITVPELALGAAQELFLTGGASDTSVAKGLDRHWRNAQTVATHNPIAFRARAVGDYWI
+NGTLPEGLNAIGDAPAAPSSSAVDAAQPAPEPAEAGAR*
+>NZ_CP083691.1_139
+MPLTDPTDAPTPLGTVPPLVRPADLPRDLAGLRRHFAPVFARVAEGSRERDRRRILPFAE
+VRALNEAGFATLRVPAEAGGPGVDVRTAVALLIDLAEADANVAHLYRSHLGFLDSLRFQP
+AAVRERWHARILAGATVGNASTEKGGNALGTLNTVLTPPAAGDGPWTLTGTKFYATGSIF
+SSHTRVSAAQTDADGHPAPGRRFAVVPVEAPGVRLDDDWDGFGQRLTGTGTAVFDGVAVP
+PQDVLDRVPGSAEAVYEAAWFQLILLAVLAGIARAARRDAADAVAARVRTFNTGLGLPFR
+EDPLIQEAVGRIAAKAFTAEAAVLSAADALDAALADHDAGRTGSGAPEEVPASFTWAELA
+VEHAQVTVPELALGAAQELFLTGGASATSTAKGLDRHWRNAQTVATHNPIAFRARAIGDY
+WINGTVPEGLNAIGDAPAASAPLGDAPAPGEAAR*
+>NZ_CP083691.1_581
+MTTPVLDRPAPTSAADAPDTAELRARFAPVFARIAANEARRRDAAVPPHAAVRLLAETGF
+TALRLPRERGGSDATLTQLLDLLVDLAAADANLPQALHGHFMFTEQVARDVHPRLTDWWL
+DEVAAGKVFANALVDPPAATGLPGVTARRDPRDPEAFLLTGTKQYSTGTLLADWTLVAAH
+DDAGALQPLVVEVAGPGVEARDDWDGIGQRGTASGTTVYTDAPAPAWRRVDLERPAAAPG
+YPFLWLILAATQAGIAQRALDDFAEILRRRSRSYQHAASASPAHDPVLQHQLGAAAAQVR
+ALRSVVLGAVPALEAAYTAAAGAAPAIGAAATESPDDGAAEAFEAAHTEAWVAAASASSV
+AADLTLRLTSDLFETAGASAVVAGPGLDRHWRNARVLASHTPLPHRRRQIGECLLHGTPA
+PHSADAVETASSTDADPSRDSVSPSPSTPAATKEQ*
+>NZ_CP097650.1_192
+MPLTDPTDASAPPAATPVPLGAVPPLERPADLPRDLAGLRRHFAPVFARIAEGSRERDRR
+RILPFEEVRALNEAGFATLRVPAEAGGPGVDVRTAVALLIDLAEADANVAHLYRSHLGFL
+DSLRFQPEAVRERWHARILAGATVGNASTEKGGNALGTLNTVLTPAPAGDGPWTLTGTKF
+YATGSIFSSHTRVSAAQTDADGRPAPGRRFAVVPVEAPGVRLDDDWDGFGQRLTGTGTAV
+FDGVAVPPQDVLDRAPGSAEAVYEAAWFQLILLAVLAGIARAARRDAADAVAVRVRTFNT
+GLGLPFREDPLIQEAVGRIAAKAFTAEAAVLSAADALDAALADHEAGRTGSGAPEEVPAS
+FTWAELAVEHAQVTVPELALGAAQELFLTGGASATSTAKGLDRHWRNAQTVATHNPIAFR
+ARAIGDFWINGTVPEGLNAIGDAPAASAPLGADAPASGEAAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001981.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001981.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8aeeaf1c44ebcb963b1535b7372661766663c92a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001981.fa
@@ -0,0 +1,14 @@
+>NZ_CP040019.1_696
+MSAAFDHIRRDDGEHVGYLEMTDDGLFVPRDRLRRVCGDPMELEEAEELLDAVGLRVLAE
+DWLLDAADGGAARRVRIREITWDTVTVAPVLDDAAVALSVDLARAEVLTLPTDRLRPADG
+*
+>NZ_CP083691.1_405
+MAGQDAGSLARRRGYADRMTDFDHLRAEDREHVGYIEMTDDGAFVPYDLLRRRRGEPGGL
+EEAEAVLDEIGLRLLAEDWILDADGDEPLCVRILEVTRDAVVVAPALDSAAVAKSLDLTA
+TVRLPLPTARLRQA*
+>NZ_CP083691.1_681
+MTTIFDHLRADDREHVGYIEMTDDGLFIPYDLLRRRCGEPMELAEAEELLDTVGLQALGE
+QWLLRTEGDAWVPVDIREFSRESVTVAPRLDDRAVAKALDLTATVMLSLPTDRLRSAE*
+>NZ_CP083691.1_704
+MTTVLDHLRADDREHVGYIEMTDDGLFIPYDLLRRRCGEPMELAEAEELLDTVGLQALGE
+QWLLRTEGDAWVPVGIQEFSRESVTVAPRLDDRAVAKALDLTATVMLSLPTDRLRSAE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001982.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001982.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b466f45a23108532d8cddcf773629bf59ede59b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001982.fa
@@ -0,0 +1,23 @@
+>NZ_CP040019.1_717
+MIRFIDEHRDRFGVEAICRTLGATARGFITSRGYRAAKRRPASERALRDELLIEELERIH
+AENYSVYGVRKMHQAMARAGWQIGRDQTARLMRAAGLQGVRRGRKPITTRPACEPDARPD
+LVERRFAAERPHQLWVADITYVRILDGFCYVAFITDVFTRRIVGWAVSASLHTQGLPLLA
+LEHALLSTGASRGREGLVHHSDRGAQGGFNRSSQHPLGIIGGMGDGQQGLGEEDQ*
+>NZ_CP040019.1_734
+MIRFIDEHRDRFGVEAICRTLGATARGFITSRGYRAAKRRPASERALRDELLIEELERIH
+AENYSVYGVRKMHQAMARAGWQIGRDQTARLMRAAGLQGVRRGRKPITTRPACEPDARPD
+LVERRFAAERPHQLWVADITYVRILDGFCYVAFITDVFTRRIVGWAVSASLHTQGLPLLA
+LEHALLSTGASRGREGLVHHSDRGAQGGFNRSSQHPLGIIGGMGDGQQGLGEEDQ*
+>NZ_CP040019.1_2283
+MIRFIDEHRDRFGVEAICRTLGATARGFITSRGYRAAKRRPASERALRDELLIEELERIH
+AENYSVYGVRKMHQAMARAGWQIGRDQTARLMRAAGLQGVRRGRKPITTRPACEPDARPD
+LVERRFAAERPHQLWVADITYVRILGGFCYVAFITDVFTRRIVGWAVSASLHTQGLPLLA
+LEHALLSTGASRGREGLVHHSDRGAQYVSLAYSDALIAAGVSASVGTVGDSYDNALAETV
+NGLYKAELIHSKRVWESVEEVELATMGWVHWWNTARLHEALGYCTPAEVEATYTHDQDSA
+PVAS*
+>NZ_CP083691.1_399
+MIAFIDEHRDQFGVEAICRTLRATECGFITSRGYRAAKTRPRSSRTLRDEILVEELRRIH
+AENYSVYGVRKMHHAMVRAGWQVGRDQVARLMRAAGLQGVRRGRKPITTRPAGEPDARPD
+LVERRFAAERPHQLWVADITYVRTITGFCYVPFITDVYSRRIVGWAVSASLHTQGLPLLA
+LEHALLSTGASRGRQGLIHHSDRGAQYVSLAYSDALITAGVSASVGTVGDSYDNALAESV
+NGLYKAELIHSKRVWESVEAVELATLKSVHRPRPRRRRSALPT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001985.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001985.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf2df36ac0fe76ad0a746d567b78686c27028747
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001985.fa
@@ -0,0 +1,24 @@
+>NZ_CP040019.1_2292
+MTDFKWRHFQGDVILWAVRWYCRYPISYRDLEEMLAERGISVDHTTIYRWVQCYAPEMEK
+RLRWFWRRGFDPSWRLDETYVKVRGKWTYLYRAVDKRGDTIDFYLSPTRSAKAAKRFLGK
+ALRGLKHWEKPATLNTDKAPSYGAAITELKREGKLDRETAHRQVKYLNNVIEADHGKLKI
+LIKPVRGFKSIPTAYATIKGFEVMRALRKGQARPWCLQPGIRGEVRLVERAFGIGPSALT
+EAMGMLNHHFAAAA*
+>NZ_CP040019.1_2297
+MTDFKWRHFQGDVILWAVRWYCRYPISYRDLEEMLAERGISVDHTTIYRWVQCYAPEMEK
+RLRWFWRRGFDPSWRLDETYVKVRGKWTYLYRAVDKRGDTIDFYLSPTRSAKAAKRFLGK
+ALRGLKHWEKPATLNTDKAPSYGAAITELKREGKLDRETAHRQVKYLNNVIEADHGKLKI
+LIKPVRGFKSIPTAYATIKGFEVMRALRKGQARPWCLQPGIRGEVRLVERAFGIGPSALT
+EAMGMLNHHFAAAA*
+>NZ_CP040019.1_2589
+MTDFKWRHFQGDVILWAVRWYCRYPISYRDLEEMLAERGISVDHTTIYRWVQCYAPEMEK
+RLRWFWRRGFDPSWRLDETYVKVRGKWTYLYRAVDKRGDTIDFYLSPTRSAKAAKRFLGK
+ALRGLKHWEKPATLNTDKAPSYGAAITELKREGKLDRETAHRQVKYLNNVIEADHGKLKI
+LIKPVRGFKSIPTAYATIKGFEVMRALRKGQARPWCLQPGIRGEVRLVERAFGIGPSALT
+EAMGMLNHHFAAAA*
+>NZ_CP040019.1_2600
+MTDFKWRHFQGDVILWAVRWYCRYPISYRDLEEMLAERGISVDHTTIYRWVQCYAPEMEK
+RLRWFWRRGFDPSWRLDETYVKVRGKWTYLYRAVDKRGDTIDFYLSPTRSAKAAKRFLGK
+ALRGLKHWEKPATLNTDKAPSYGAAITELKREGKLDRETAHRQVKYLNNVIEADHGKLKI
+LIKPVRGFKSIPTAYATIKGFEVMRALRKGQARPWCLQPGIRGEVRLVERAFGIGPSALT
+EAMGMLNHHFAAAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001986.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001986.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00885c224f325ccd71f0a6a45e9d6a1d5048f5c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001986.fa
@@ -0,0 +1,25 @@
+>NZ_CP083691.1_297
+MDRCNRARAMGSRAAQSGRRRCHDDDGAMGALVRVHAAQSCSRSRVHPASGSRRRNPHHP
+PSRTSAAVPDTATPVPCPAPPRLHRPRPRAGPDPRAHHLTRVTTDRTGVADTPRHDRCRT
+PEGHARRGMGGLVQDHRFSTACTPCADAAGEVEQAPSMTIAARHQACRYTSTARSATEHR
+SGETSTELAARLLAEAPQRDWRLRDLAALVHLSASQLGRAFTQRFGMPPMRYLAHIRAHR
+LAELLVETDLPIGVAMTKVGWRSRGHAARQFTDVVGISPSEYRRTAIGRTLTETSPWPSA
+TQGSPVAPGRESLEKSPP*
+>NZ_CP083691.1_393
+MPTTFSDQRKLSVVLFEGFELLDVFGPVQLFGSLPDVAIEYVGPHTGPVISSKGARVVAD
+LAYEDLARPDILMVPGGQGTRTLVDDAGFLAWLGQAGSRADLVASVCTGSALLAAAGLLE
+GYSATSNKRAFTWASGFGDDVDWRPRARWVHDRDRWTSSGVAAGMDMATGMIADLYDADT
+ARAVTLRAEYEPHTDSTRDPFADVYRLG*
+>NZ_CP083691.1_639
+MRHVVTIACPGTALFDVGIPSRVFGAARTANDEPAYDVTIASPTGAGPLLTKDGVSVDLP
+GVDQIKETDTVVVASSDALLDPLVRRDMASALAPFLLQGQAVRPGVRVAAVCSGAFLLGE
+LGLLDHRTATTHWRLADQLAKLFPSTHLQTESLYIEDDGVLTSGGVAAGIDLCLHMIRQD
+YGVRIANDVARSCVVAPFREGGQAQYVQTPVPRSADPSMNDLVHWLLETLDQRHTLEDIA
+HRGHMSTRTFERRFRREHGTSPGQWLTAARIQRAKELLESTDLPVERIAELVGLGTASNL
+RTHFTRCVGRTPQAYRRSFTAGSNSTNVSGQYS*
+>NZ_CP083691.1_1739
+MDRCHRARAMGSCAAQSRRRRCHDDDRAMGALVHLHVAQSCSRSRVHPTSGRRRRNHHHP
+PPRTPATAPGAATPVPRPGPPRLHRSRTWARPDPRTHHHTRLSTGGTGVADTPGRERCRT
+AERLARRGMGGLVQDHGLLATAPPHAVVLRKAAAMSTEPSWRVCPDETTPSHACPTETAA
+HHAARLLAQDPGRDWRLRDLADLVHLSTSQLGRAFSQRFGMPPIQYLAHVRAHRLAELLI
+ETDLPIGVAMAQVGWRSRGHAARQFTAIVGVSPSAYRRTATQRASLRCPCCGQRNELPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001987.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001987.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b0053623c77e48197e8736b3d8905b18f7788838
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001987.fa
@@ -0,0 +1,24 @@
+>NZ_CP083691.1_407
+MGAMTDPTSRALRLLGLLEARAVWTGAELAERLGVTSRTLRRDVDRLRTLGYVVEADPGP
+GGGYALGRGQVVPPLLLDEDQAVAVTLALTRAAHAGDGVAAESALRALATLDALMPADLR
+HRLEGLRAASTVGAGDGPPVGPELLACADAVRRRVRLTFGYRDRRGARTERRVEPHRLVA
+RARAWLLVAHDLDRDDWRTFRVDRIVDPAVGTWAFTPRPDLAEALARLDEPTPPEAWRHR
+VSVRVHAPLESVRASLPATAGRLTALDARTTAFETGADDPAEAARWLALLGHEFEVLGDE
+PVRAAVAALADRLHRSTVQVLRG*
+>NZ_CP083691.1_628
+MASPCRRFRTPNVRNPRHAGVMADTSARILRLLSLLEARVEWPGGDLAERLGVSARTVRR
+DIDTLRELGYPVEAVPGPGGGYRLGAAGKLPPLVLDDDQAIAIALALQTAPATVTGIDDA
+VARALTTLRQVMPARLRAASEAFEVTALRNYWEFSAPPIDVATLQVVGSAIRTSSCLRFD
+YADPDGRVPGPGDADFRPPHDVEPHHLVVWAGRWYLVARDRNHGTWGTYRVDRIRPKTPA
+GRPFTPTPLDPDDLNRLVVQNPDRGDTPGQWQCVGTATLPLPADVVARWAPGGSAVAPID
+RQSCRLTIGGWSWAGVAGLFITFDTDLTNVEPSGLRDALATIRRRLEPAPLGGLRPTLQQ
+*
+>NZ_CP083691.1_1750
+MPSVKIPPLLLDADEVCSLVTGLLLLEAGGVNEAATVRTKLEQLLPPKLRQQAAATALAT
+QVITPVAAPVDWRLLGVLAEAVAQGQNLRFTYTDQHSKVSERHIRPYRHALRKGAWYLIA
+YDIQRTDWRLFRLDRIQHATPEPTATGIDVPVFPSPSIEEWLTTDFGRLPASAG*
+>NZ_CP083691.1_1786
+MLGYDIQSHPGPGGAYVLAPSIKIPPLLLDADEVCALVTGLLILEAGFADDSATTVRAKL
+ERLLPPSLRQRAVAAAAATQVLTATHAFDWPALGMIADTIAVGQHLGFAYTDQHGHASNR
+IVQPYRQVLRHGIWYLVAYDTQREDWRLFRSDRVHEPEPRTPAPGYEAHPFPDESIHRWL
+ITDFGRAAQHVN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001988.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001988.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33e6a5ef3fc8b1e8cf5fa7c4e288ab4a81dad446
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001988.fa
@@ -0,0 +1,25 @@
+>NZ_CP083691.1_645
+MDTPVMASLPAGVITLRDARRSQTREVTLEAFEIAVHPVHDQGSGLPWAPFTWFDAVAYC
+NELSRASGLQEAYTWQGRTVDWDTAADGYRLPTEAEWEYACRAGTTSPTYGLVEDIAWTS
+LDDVDSPQPVGSKAPNAWGLHDMLGNVWEWCWDYADPARYGDYRSLRGGGWADEPWSVRA
+SVRRGSAPNAVLEDVGLRLARGPVGSPGQAQGWSHEADRQRAAIRGPLPVGWTPLWEIAR
+*
+>NZ_CP083691.1_682
+MNQPSMATLSSGKITLRDARRRTTRDVELEPFEMAVHPLHDRSTGRPLTPLTWFETINLC
+NELSKAEELQPAYTRAGGGRSVTWNTSADGYRLPTEAEWEYACRAGTTSPTYGPLEDIAW
+ISLDHLEGPQPVGMKKANPYGLHDMLGNIWEWCWDYADPARYGDYRSLRGGGWADEPWSV
+RASVRRGNAPDAVLEDVGLRLARGPVGSPGQAQGWSHEADRQRAAIRGPLPVGWTPLREI
+FA*
+>NZ_CP083691.1_705
+MNQPSMATLSSGKITLRDARRGTTRDVELEPFEMAVHPLRDRSTGRPLTPLTWFETINLC
+NELSKAEELQPAYTHAGDGRSVTWNTSADGYRLPTEAEWEYACRAGTTSPTYGPLEDIAW
+TSLDHLEGPQPVGMKKANPHGLHDMLGNIWEWCWDYADPARYGDYRSLRGGGWADEPWSV
+RASVRRGNAPDAVLEDVGLRLARGPVGSPGQAQGWSHEADRQRAAICGPLPVGWTPLREI
+FA*
+>NZ_CP083691.1_1371
+MQGAIDDDMMLTGAVDEWRFIVQTLADRLDQAAHAAGTPVSTAADVDAGTPAGTVSSDHQ
+AGPDMVVIPAGTYTAGSTDAEHEAWGVPENRRDFELPQREVTIAEPFALGRTEVTVEQFQ
+AFVDDTGYQVCGGSRWWDPEDPSAMTFNPELSYLDPGFEQTPDSPSVALTRQDAQAYVDW
+LSETTGESDRLPTEDEWEWAARGGADTAFFWGDTLDEAARYANTYDTVSQAVNGFPWESL
+SVTDRFAHTAPVGSFEADGFGLYDVTGNARAFMADDWIEDLSGTAGDGSVHDGPVPFPVV
+RGGAWNYQPQNLRLDYRGAYLSAEVATTMFGFRVVRDLG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001993.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001993.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2b6cc699710667172a726004cc68f1771877bcda
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001993.fa
@@ -0,0 +1,13 @@
+>NZ_CP042169.1_26
+MSHASTVPPAADAPSRWGRAAGLSGLVMPAVLAAFSLYLLLGSLTMDTDGADFPGPDFFP
+LILSVAGLVIAAALAVEVVRVRQAPEG*
+>NZ_CP033200.1_2000
+MSQASTVSPAADAPSRWGRAAGLSALVMPAVLAAFSLYLLLGSLAMDTEGADFPGPDFFP
+LILAVAGLVIAAALAVEVVRVRQAPEGQADADGEVGQAAGPLTLFHSDFGALAWCFLGFL
+AFAVLLPWLGWILAGALLFWCVTRAFGAPHPVFDILVALFVSSLAYLGFAVALGLTLPSG
+ILGGGF*
+>NZ_CP097650.1_26
+MSHASTVPPAADAPSRWGRAAGLSALVMPAVLAAFSLYLLLGSLAMDTEGADFPGPDFFP
+LILAVAGLVIAAALAVEVVRVRQAPEGQADADGEVGQAAGPLTLFHSDFGALAWCFLGFL
+AFAVLLPWLGWILAGALLFWCVTRAFGAPHPVFDILVALFVSSLAYLGFAVALGLTLPSG
+ILGGGF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001994.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001994.fa
new file mode 100644
index 0000000000000000000000000000000000000000..29b434bd5d51177690a4aaef166c5d46cbdec719
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0001994.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_28
+METLGLLMEGFAGALTPMNLLWVVLGCLLGTAVGVMPGLGSSMAVALLLPMTFALDPTAA
+FIMFSGVYFGGLFGDSTMAILMNTPGQASAIASTFEGHRMAQDGRAAQALATAALGAFIG
+GMAASVCVVFLAPVLAEFSTSFGPAEYFALALFAFVATSSVVADSVLRGLASLVLGLGIA
+VVGIDAVTGTERFTMGSPQLFDGIPLVTVTVAILALGEVFHVASRVRREHEDLRIRRTGR
+PWLSGAEFREAAPAWLRGTAIGLPFGIVPVGGSEVPTFLAYSVKRRLDRRRAHPQFGRGA
+IRGLAAPEAAGNSTTGMAMGALLTLGLPVSATAAIMLAAFRQYGLQPGPLLFDRSPDLVW
+ALLASFFIAMIVLLAINLPFAQLWAKLLLIPKHYLYAGITLFCGLGIYATTGAVFDLLML
+LGIGVLGFLMRRYGYPLAPLMIGMVLGPLAETSLRDALLSSVGDPAVLVSTPITWVIYGI
+LAIVLAFSVRAAVVRRTRQDV*
+>NZ_CP033200.1_2001
+METLGLLMEGFAGALTPMNLLWVVLGCLLGTAVGVMPGLGSSMAVALLLPMTFALEPTAA
+FIMFSGVYFGGLFGDSTMAILMNTPGQASAIASTFEGHRMAQDGRAAQALATAALGAFIG
+GMVASVCVVFLAPVLAEFSTRFGPAEYFALALFAFVATSSVVADSVLRGLASLVLGLGIA
+VVGIDAVTGAERFTMGSPQLFDGIPLVTVTVAILALGEVFHVASRVRREHEDLRIRRTGR
+PWLSGAEFREAAPAWLRGTAIGLPFGIVPVGGSEVPTFLAYSAERRLDRRRAHPQFGRGA
+IRGLAAPEAAGNSTTGMAMGALLTLGLPVSATAAIMLAAFRQYGLQPGPLLFDRSPDLVW
+ALLASFFIAMVVLLAINLPFAQLWAKLLLIPKHYLYAGITLFCGLGIYATTGAVFDLLML
+LGIGVLGFLMRRYGYPLAPLMIGMVLGPLAETSLRDALLSSVGDPAVLVSTPITWVIYGI
+LAIVLAFSVRAAVVRRTRQDV*
+>NZ_CP097650.1_27
+METLGLLMEGFAGALTPMNLLWVVLGCLLGTAVGVMPGLGSSMAVALLLPMTFALEPTAA
+FIMFSGVYFGGLFGDSTMAILMNTPGQASAIASTFEGHRMAQDGRAAQALATAALGAFIG
+GMVASVCVVFLAPVLAEFSTSFGPAEYFALALFAFVATSSVVADSVLRGLASLVLGLGIA
+VVGIDAVTGTERFTMGSPQLFDGIPLVTVTVAILALGEVFHVASRVRREHEDLRIRRTGR
+PWLSGAEFREAAPAWLRGTAIGLPFGIVPVGGSEVPTFLAYSAERRLDRRRAHPQFGRGA
+IRGLAAPEAAGNSTTGMAMGALLTLGLPVSATAAIMLAAFRQYGLQPGPLLFDRSPDLVW
+ALLASFFIAMIVLLAINLPFAQLWAKLLLIPKHYLYAGITLFCGLGIYATTGAVFDLLML
+LGIGVLGFLMRRYGYPLAPLMIGMVLGPLAETSLRDALLSSVGDPAVLVSTPITWVIYGI
+LAIVLAFSVRAAVVRRTRQDV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002009.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002009.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c0251b351af1ea7993f7ac9d20d282b7e29b211
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002009.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_476
+MTYRDDLWDVAAGNHGVITTTEAEEAGVPAVEVRKLAQRGVLRRLAHGVYLHRQVPRDRF
+TDAAEAVATGGEDAFLDWDAVLSLYDLALVDPSVVRVGVTRRYRGSPRAHVRVTRRRPPP
+GDEDLTFHGGVRGLTINQALREALDRIPLERVAAAIEEARARGLLTVGEARSLKKDLEAR
+QNGGHRGGR*
+>NZ_CP033200.1_206
+MTYRDDLWDVAAGNHGVITTTEAEEAGVPAVEVRKLAQRGVLRRLAHGVYLHRQVPRDRF
+TDAAEAVATGGEDAFLDWDAVLSLYDLALVDPSVVRVGVTRRYRGSPRAHVRVTRRRPPP
+GDEDLTFHGGVRGLTINQALREALDRIPLERVAAAIEEARARGLLTVGEARSLKKDLEAR
+QNGGHRGGR*
+>NZ_CP097650.1_475
+MTYRDDLWDVAAGNHGVITTTEAEEAGVPAVEVRKLAQRGVLRRLAHGVYLHRQVPRDRF
+TDAAEAVATGGEDAFLDWDAVLSLYDLALVDPSVVRVGVTRRYRGSPRAHVRVTRRRPPP
+GDEDLTFHGGVRGLTINQALREALDRIPLERVAAAIEEARARGLLTVGEARSLKKDLEAR
+QNGGHRGGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002012.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002012.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35d44da984fc5befa9125bc1d77e35187278df08
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002012.fa
@@ -0,0 +1,27 @@
+>NZ_CP042169.1_503
+MGAVAPPEARPARRHASLGLVPDGQAAWTRSPWNPLVTPASPRLFEAVLAIGLVMEAFTA
+PGLPIPFAEFSAILLLLLASFRQPRRDLSQYGVLALVALALVAYLVAVTVHNDLDPTRRA
+TRITLLILLIYAIASERIDIKGVLYGMTAGALINVPLFYAGLAPDTYGGYLTGFLGDKNV
+SGLFYALLPVLLVATMQRMGPKLLVLGAGFALTFLTGSRTSMAGLLCAVVWILVSPYLGR
+VLRIALGVVLGWFVSWAEVNLADLGIFGDRTGTDWFREQIQEASAEKVADTSFFGQGLST
+AFVELDNVTMFFHNSYLGLLVEGGWPFLIVVVGAYLWLCLRPFARTHRSPSRVAVEAAAL
+IILVTSLQLGEVFITIFGAVVLGCGLLLSAQENEESQGAPAKDRAHRRKLDRIIERSRRA
+GV*
+>NZ_CP033200.1_233
+MRPSTPRDRTAARAMGAVAPPEARPARRHASLGLVPDGQAAWTRSPWNPLVTPASPRLFE
+AVLAIGLVMDAFTAPGLPIPFAEFSAILLLLLASFRQPRRDLSHYGVLALVALALVAYLV
+AVTVHNDLDPTRRATRITLLILLIYAIASERIDIKGVLYGMTAGALINVPLFYAGLAPDT
+YGGYLTGFLGDKNVSGLFYALLPVLLVATMQRMGPKLLVLGAGSVLTFLTGSRTSMAGLL
+CAVVWILVSPYLGRVLRIALGVVMGWFVSWAEENLADLGIFGDRTGTDWFRAQIQEASAE
+KVADTSFFGQGLSTAFVELDGVTMFFHNSYLGLLVEGGWPFLVVVVGAYLWLCLRPFART
+HRSPSRVAVEGAALIILVTSLQLGEVFITIFGAVVLGCGLLLSAQESDESHGAPAKDRAH
+RRKLDRIVERSRRAGR*
+>NZ_CP097650.1_503
+MRPSTPRDRTAARAMGAVAPPEARPARRHPSLGLFPDGQAAWTRSPWNPLVTPASPRLFE
+AVLAIGLVMDAFTAPGLPIPFAEFSAILLLLLASFRQPRRDLSHYGVLALVALALVAYLV
+AVTVHNDLDPTRRATRITLLILLIYAIASERIDIKGILYGMTVGALINVPLFYAGLAPDT
+YGGYLTGFLGDKNVSGLFYALLPVLLVATMQRMGPKLLVLGAGAALTFLTGSRTSMAALL
+CAVVWILVSPYLGRVLRIALGVVMGWFVSWAEENLADLGIFGDRTGTDWFRAQIQEASAE
+KVADTSFFGQGLSTAFVELDGVTMFFHNSYLGLLVEGGWPFLVVVVGAYLWLCLRPFART
+HRSPSRVAVEGAALIILVTSLQLGEVFITIFGAVVLGCGLLLSAQESDESHGAPAKDRAH
+RRKLDRIVERSRRANR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002014.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002014.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6517216b955337081cc7fd326ebfa1adb3e8b2fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002014.fa
@@ -0,0 +1,9 @@
+>NZ_CP042169.1_560
+MVGDMSLSFVSSARRRHGGLASAALFHPLVEAATGALPVIDPATGRPASEGAGAARTEAP
+RTAGTGPAQAAAEAEPSTEAGSARG*
+>NZ_CP033200.1_302
+MSLSFVSSARRRHGGLASAALFHPLVEAATGALPVIDPATGRPASEGVDAARTEASRAAG
+TGPAQAAAETEPSTQAGSARG*
+>NZ_CP097650.1_561
+MSLSFVSSARRRHGGLASAALFHPLVEAATGALPVIDPATGRPASEGVDAARTEASRAAG
+TGPAQAAAETEPSTQGGSARG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002017.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002017.fa
new file mode 100644
index 0000000000000000000000000000000000000000..80afad77764e205b5b62d4b1c22dbb3baeef7fa0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002017.fa
@@ -0,0 +1,17 @@
+>NZ_CP042169.1_578
+MTSPWVEDDELTDWEAPAAADDDGQTGTPLPYVDPEIAAELAGEGPPVWMGTRWREIEAE
+HQWEAWNTLRRWVDWFVAEYRLVTSVVPPCWYKHSDLTAELYAAMCMEYKVWEEQAPGLG
+PMMMWHPHVEMLTARLRRMVDEAGCAKIGQHKEPEAYGDRPAFNLDYDEDDFTAWAATTC
+EQHALERPEAGVKYVRARVFNGDGEEIALSNPVGLASRRTSTGVTAELMMTSSTPLAPGL
+RLTVPSATPGLEVGWQTSVNGHDWE*
+>NZ_CP083691.1_1768
+MSTHSPEPDDQYDDPGILDDQPDMFDTNALPEPPHPINWNLLSAQDLEAELLELNRWVDW
+LRHTYGLPASVIPPYWHRHPELLWELSALHLHWLCAYDPEQNGSAPLGWHRDFADARHRL
+RDWVTASGTRLDRDRPTRQTTWPGEEPQPTHGESVITDRDADFVQFIIDQVNERQAAEDA
+FYASLDDRIDPATGEVRDDVLGPEGG*
+>NZ_CP083691.1_2192
+MASPWVEDDEPDWSETAPLQDEGPTETSLPYVDPEVAAELAQEGPPVWMGTRWREIEAEH
+QWQAWNHLRRWVDWFVAEYRLGTSIVPACWYRHPDVTAELYAAMCMEYKVWDEQAPGLGP
+MMMWHPHVEMMTARLRRMVDEAGCAKIGRHKDPEAYGNRGAYELDYDESDWTRWAATERE
+EELIERPTEGVKYVRAKVVDSDGNVLGHSAPVGLRPVPNVVGVEAKVRVTSSTPAEPRMA
+VAVSSGRDDLGIEWEMSPDGAEWSTRPNDDR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002021.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002021.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bfff06d996f669331721f4c6780a5dcc7fac4797
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002021.fa
@@ -0,0 +1,15 @@
+>NZ_CP042169.1_744
+MRLFLAIRPPRAALDHLEPALDGVRDRAGRALCWTEPEQRHLTLAFHPEVPAGAVDDVVA
+VAGRIAAGHGPLDLHLAGAGEFSHRTLWVGVGGQVRELGALLAEPWLADDDGRDRRRAHL
+TVARASGAAPRPRGRRRGEPRPPAPATVLLAEAVHALAVYRGPEWTADEVEVVASRLGEG
+RSGGPLHEVLATVPLRG*
+>NZ_CP033200.1_483
+MRLFLAIRPPRAVLDHLEPAFDGVRDRAGRALCWTEPEQRHLTLAFHPEVPAGAVDDVVA
+VAGRIAAGHGPLDLHLAGAGEFSHRTLWVGVGGQVRELGALLAEPWLADDDGRDRRRAHL
+TVAPVSGAALRPRGRRRGEPRPPAPATVLLAEAVRALAVYRGPEWTADEVEVVASRLGEG
+RSGGPLHEVLATVPLRG*
+>NZ_CP097650.1_707
+MRLFLAIRPPRAALDHLEPALDGVRDRAGRALCWTEPEQRHLTLAFHPEVPAGAVDDVVA
+VAGRIAAGHGPLDLHLAGAGEFSHRTLWVGVGGQVRELGALLAEPWLADDDGRDRRRAHL
+TVAPVSGAALRPRGRRRGEPRPPAPATVLLAEAVRALAVYRGPEWTADEVEVVASRLGEG
+RSGGPLHEVLATVPLRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002025.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002025.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d3b3429db19898e3ee37bbd8cb7ab8bb1af8c5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002025.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_859
+MAEFIPAAKPLIGDEERAAVDRVLRSGMVAQGPEVAAFEEEFGAAMVDGRACVAVNSGTA
+GLHLGLLASGIGPGDEVIVPAFTFAATGNAVALTGATPVFADVDLDTYTLDPQDVRAKVT
+ERTAAVMPVHLYGHPARMDELEAICREHGLQLFEDAAQAHGARWKGRPVGTFGAWGMFSL
+YPTKNMTSGEGGMVSVGEADVARRLRLLRNQGMEVQYRNELVGFNNRMTDIHAAIGRVQL
+TKVGAWTRRRQEIAARFDAELRGVTVPTVLEGAEHVYHQYTVRLPEELAGTRADVLARLK
+DEFGVGTGVYYPVPTNELPSFGVEADLPNTRVAASTVFSIPVHPSLTDADVTRVVEAVNT
+VVAEAAA*
+>NZ_CP033200.1_590
+MAEFIPAAKPLIGDEERAAVDRVLRSGMVAQGPEVAAFEEEFGAAMVDGRACVAVNSGTA
+GLHLGLLASGIGPGDEVIVPAFTFAATGNAVALTGATPVFADVDLDTYTLDPQDVRAKVT
+ERTAAVMPVHLYGHPARMDELEAICREHGLQLFEDAAQAHGARWKGRPVGTFGAWGMFSL
+YPTKNMTSGEGGMVSVGEADVARRLRLLRNQGMEVQYRNELVGFNNRMTDIHAAIGRVQL
+TKVGAWTRRRQEIAARFDAELRGVTVPTVLEGAEHVYHQYTVRLPEELAGTRADVLARLK
+DEFGVGTGVYYPVPTNELPSFGVEADLPNTRVAASTVFSIPVHPSLTDADVTRVVEAVNT
+VVAEAAA*
+>NZ_CP040019.1_1201
+MTDRIFLSSPDVTQAEEDALVRAFRSNWIAPLGPEVDAFEAELAEYTGRAHAVVLSSGTA
+ALHLGLLNLGVGPGDLVPTSSLTFAATANAIAYTGAEPVFVDADESGNMNPALLEQALAT
+LRGEGHEVKAIVPVDLLGKTADHAAIGRIAAEHGAVVLSDAAESLGATRDGKQSAAYGVA
+AAVSFNGNKIMTTSGGGALLTDDEEMATRTRYLATQARQPVVHYEHTDIGYNYRLSNILA
+ALGRAQLNRLEEMIERRRALRIRYRELFAAVPGVEMFGEPSGADGGPTRDNFWLSSVLVD
+PDAAGFTAEDLRAHLAGQDIEARPLWKPMHLQPVFAGRRAFTDGTGERLFTTGLSLPSGS
+VLDESRISRVLDSITAFLESRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002027.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002027.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0aafc9abd27f33da5a12611ff025a56adbb5ce34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002027.fa
@@ -0,0 +1,9 @@
+>NZ_CP042169.1_914
+MTATTHILLRAEGFSCPSCVRKIEKALDALPGVTGAQVHFETQRIEVDHDPQTTTAQDLV
+EAVAKVGYTARPSAF*
+>NZ_CP033200.1_642
+MTPTTRTLLRAEGFSCPSCVRKIEKALDALPGVTGAQVHFETQRIEVDHDPQTTTAQDLV
+EAVAKVGYTARPSAF*
+>NZ_CP040019.1_1955
+MTATTHTLLRAEGFSCPSCVRKIEKAVDALPGVTGSKVHFETQRIEVDHDAERTSVQDLV
+DAVDRVGYRARPSVF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002028.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002028.fa
new file mode 100644
index 0000000000000000000000000000000000000000..148ab9643babfe79830b0b19e0a4a81b78a658eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002028.fa
@@ -0,0 +1,17 @@
+>NZ_CP042169.1_917
+MGPRAVPLAIIGDLHLDLTDAQWVNSLYAVLLAALLLSTGNLADRWGRKRLFLTGSALIA
+PYPRRPAAQHPLCCYRFGVHFHATAGVRGRLLPLASHRRLVAMNDMHSLGRLIAPAQERN
+GWSLSDLAARADRAGYDMSHASFARLKSTPVTSIKGENITMLALVLRAPVAHVVTAALES
+IGVELDSALHPSVLDVVQESPDLSTYDQELLAAVLRVMLDRRRTDHHDERDHADQDQDRE
+RGTAERGGARGGDAGAEQKTAAADAPADFDLAAHPDFELTRDRQAREWGDVGEENQDPGD
+EAGA*
+>NZ_CP040019.1_1901
+MLNHSHTPAEADPVNEPDSLQALAKAVLDKQQASARQIAEYARKAGKRLSYTTLNHMAAG
+TYRSTPTAETLQTLAWLAGVSETVAFHAAGLPVPGPPLADELPPGSDNLSPKSRAAVIQM
+LRVLIDLESNHDEHDHPDQHQDRERGTAERGGARGGDASAEQKTAAAGAPADFDLAAHPD
+FELTRDRQAREWGDAGEESQDHGEGESA*
+>NZ_CP040019.1_2059
+MERIPTSLQELAQLVLDVQGTSARQVALRAEAKGLKLKDTTLNQMKSGSYKFVPREETLR
+ALADLAGVSVETAFHAAGLTAPGPPLADELPPGSDNLSPKSRAAVIQMLRVLIDLESNDD
+HHTTNPTPAHERAQHDDGADAAPDRRRGAGRGDARPGQKTAAAGGTPARSLNPADYDLAA
+HPSFELTRDRQDREWGDVGEENQDPDQEDRRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002032.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002032.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc4a6aee6b83b2907f4bfbc22e4aeddd76e15c29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002032.fa
@@ -0,0 +1,14 @@
+>NZ_CP042169.1_1248
+MPLAIVAPIQSSRSRLRICAALTGLATSAVLLLSGFADAGPSADAGSDHSLVVEHNLDGL
+NAREIIKRLDSTKVTDRSSEFIASIEPDQLVLTDDQNNQTTVPMPEDEFYVSIAPYRSQT
+HECYFHSLTTCTGELANTDVHVTVVEATSGETLLDETLTTYDNGFVGVWLPRGIDATLTV
+SAEGRTAKKAISTRPDDPTCLTGLQLA*
+>NZ_CP033200.1_977
+MVEHNLDGLNAREIIKRLDSTKVTDRSSEFIASIEPDQLVLTDDQNNQTTVPMPEDEFYV
+SIAPYRSQTHECYFHSLTTCTGELANTDVHVTVVEATSGETLLDETLTTYDNGFVGVWLP
+RGIDATLTVSAEGRTAKKAISTRPDDPTCLTGLQLA*
+>NZ_CP097650.1_1205
+MPLAIVAPIQSSRSRLRICAALTGLATSAVLLLSGCADAGPSADAGSDHSLVVEHNLDGL
+NAREIIKRLDSTKVTDRSSEFIASIEPDQLVLTDDQNNQTTLPMPEDEFYVSIAPYRSQT
+HECYFHSLTTCTGELANTDVHVTVVEATSGETLLDETLTTYDNGFVGVWLPRGIDATLTV
+SAEGRTAKKAISTRPDDPTCLTGLQLV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002035.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002035.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ae81ebfedd8d7676229f8d6434258a84884545ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002035.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_1342
+MGNAVGSNIINVLLILGLSALVVPLAVKRRLIRFDLPLMVVLSVLLLLVSLDGRISAVDG
+LILFFGVVVHTIMSVVISRRDAKTAVNAREGTGDSATVDPADEEGAALGASVSRSLFFVL
+LGVALLVAGATLLVEGAVNIATTLGVSSLVVGLTVVAVGTSLPELATSIIAVRRGERDLA
+VGNVVGSNIFNIGVVLGLTALISLEGIPVSGAAVAFDIPVMLAAAVALLPIAFTGFAVAR
+WEGGLFVVLYAAYTGYLVLAATAHDALEGFTVAMAWFVLPLIALTLISFTAYEIGLRKGR
+RDLDQTTTST*
+>NZ_CP033200.1_1080
+MGNAVGSNIINVLLILGLSALVVPLAVKRRLIRFDLPLMVVLSVLLLLVSLDGRISAVDG
+LILFFGVVVHTIMSVVISRRDAKTAVNAREGTGDSATVDPADEEGAALGASVSRSLFFVL
+LGVALLVAGATLLVEGAVNIATTLGVSSLVVGLTVVAVGTSLPELATSIIAVRRGERDLA
+VGNVVGSNIFNIGVVLGLTALISLEGIPVSGAAVAFDIPVMLAAAVALLPIAFTGFAVAR
+WEGGLFVVLYAAYTGYLVLAATAHDALEGFTVAMAWFVLPLIALTLISFTAYEIGLRKGR
+RDLDQTTTST*
+>NZ_CP097650.1_1296
+MGNAVGSNIINVLLILGLSALVVPLAVKRRLIRFDLPLMVVLSVLLLLVSLDGRISAVDG
+LILFFGVVVHTIMSVVISRRDAKTAVNAREGTGDSATVDPADEEGAALGASVSRSLFFVL
+LGVALLVAGATLLVEGAVNIATTLGVSSLVVGLTVVAVGTSLPELATSIIAVRRGERDLA
+VGNVVGSNIFNIGVVLGLTALISLEGIPVSGAAVAFDIPVMLAAAVALLPIAFTGFAVAR
+WEGGLFVVLYAAYTGYLVLAATAHDALEGFTVAMAWFVLPLIALTLISFTAYEIGLRKGR
+RDLDQTTTST*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002038.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002038.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3d9419dab7efeab827382e89db7b76568664b015
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002038.fa
@@ -0,0 +1,9 @@
+>NZ_CP042169.1_1352
+MAMPETDLLRIGRWCRERVPEHLWDQVRVEAEIADRHVTIIETRPPWDGQGDWTRFPVAR
+LRYTVKTGQWSIYWRDRHMKFHEYTKRRPTKNVQSLLDYIGSHQDPIFWG*
+>NZ_CP033200.1_1095
+MAMPETDLLRIGRWCRERVPEHLWDQVRVEAEIADRHVTIIETRPPWDGQGDWTRFPVAR
+LRYTVKTGQWSIYWRDRHMKFHEYTKRRPTKNVQSLLDYIGSHQDPIFWG*
+>NZ_CP097650.1_1301
+MAMPETDLLRIGRWCRERVPEHLWDQVRVEAEIADRHVTIIETRPPWDGQGDWTRFPVAR
+LRYTVKTGQWSIYWRDRHMKFHEYTKRRPTKNVQSLLDYIGSHQDPIFWG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002044.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002044.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e5229aaa82f783c0c2072644758037497edef7c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002044.fa
@@ -0,0 +1,28 @@
+>NZ_CP042169.1_1568
+MTGIPFLLVFILAIALMIVMISRWKIHPFLSIMVVAFALGIIGGIPLVKSTGAEGEAPVK
+GIADVIGEGFSGIFTSIGIVIILGTLIGLILERTGGAFRIADALVRVVGKRYPVLAMQLM
+GWVVSIPVFCDSGFVILNPIRKALARRTGASPVAMTVALAAGLYTSHVFIPPTPGPIAAA
+QNLGIGDHLLLVIGLGVLVSIPALLVAYLYALYIGKRVTSPEETGTEDADELEAAYDALR
+RSYGRMPGTAASFAPIIAPILLMALGSLASVLKWTGPAGDFARFLGTPMIALAVGTLCAV
+GLLFSVRRGETFYDLTEETLRVVGPILFITAAGGVLGRVIAATDLVTFIESNAAQLSVIG
+LFFPFLVSAVLKTAQGSSTVALTTTSAMVFPMMPALGFETPVASALVVMAIAAGAMTVSH
+ANDSYFWVVTNFSGMTPSQGYRTQTMVTLLMGLTSIVFIWLLGLVLV*
+>NZ_CP042169.1_1983
+MSTDTRTATPHTRGSTRRGDRPMPVPRDPHPLVALLPLLALIALASASTLSWKIGMILPI
+VAGIVVAAVIGRLTGHSWKDMEAAMTDGVSRAMPAVFILLIIGMIIGTWISGGVIPTLIH
+YGLEFINPTFFLPMACLVTAFISLVLGSSFTSIATVGLAFMAIGGGMGVPLPIVAGAVIS
+GAFFGDKLSPLSDTTNVAPAMVGEGLFDHIRHMLWDTIPGLVLSAGLFWFIGLRVSPGGD
+VDTAARDTIQAGLSGQFTIHPALLLVVLATLVIIALRVPAIPALVLVAALGGLSGVLVQG
+RPVGAVLKDATTGYTSTTGQESVDSLLTNGGVASMFMTIGLVIVATALGGLLERTGVFRA
+LIDPLVRRIRRTGSLIAATVMASFLVGFSTGAQFLAVILPARGMVDAYRRMGLSPLNLSR
+VVEAAGTVGINLVPWGVPAVFAAGVFGLEPMEFIPWILFAFIVPALNVLYGYTGLSIKRI
+TPAEVDPEDQRD*
+>NZ_CP040019.1_1257
+MTGIPFLLVFILAVALMIVMISRWKIHPFLSIMVVAFALGIIGGIPLVKSTGAEGEEPVK
+GIADVIGEGFSGIFTSIGIVIILGTLIGLILERTGGAFRIADALVRVVGKRYPVLAMQLM
+GWVVSIPVFCDSGFVILNPIRKALARRTGASPVAMTVALAAGLYTSHVFIPPTPGPIAAA
+QNLGIGDHLLLVIGLGVLVSIPALLVAYLYALYIGKRVSSPEETGTEDADELEAAYDALR
+RSYGRMPGTAASFAPIIAPILLMALGSLASVLKWTGPAGDFARFLGTPMIALAVGTLCAV
+GLLFSVRRGETFYDLTEETLRVVGPILFITAAGGVLGRVIAATDLVTFIESNAAQLSVIG
+LFFPFLVSAVLKTAQGSSTVALTTTSAMVFPMMPALGFETPVASALVVMAIAAGAMTVSH
+ANDSYFWVVTNFSGMTPSQGYRTQTMVTLLMGLTSIVFIWVLGLVLV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002045.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002045.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a59c5dd153928d17f7d427232b9f33def5fbe36d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002045.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_1569
+MQRIIVIPDSFKGALSSREAGSAIAAGLASVTDAEVLVVPIAYGGEGTVEAFVAAAGGAL
+RSATVCGVFYGERVPVHYGLIDPDVAVVETASCAGLPLASGREDTGRATTFGVGEQILDA
+VSAGAGRVIVGAGGSATTDGGTGAAAALGVRFLDAAGEEFVPTGHTLTRIARIDSSPARD
+RLRDVDVEVMCDISNPLTGSQGAAHVFGPQKGADPASVASLDTGLVHLAGIVERDLGVAI
+DALPGSGAAGGLAGGLHAFIGATLKPGIDVVLETAGFHDLVKTADLVITGEGRIDGQSLA
+GKVPIGVAQAVRAAGRAIPVIVLAGSVGQDTDTLYDEGITAIVPIGRGPQDLATAIRRTA
+EDLTATARDVGRLVMACSPAGLRR*
+>NZ_CP040019.1_1256
+MQRIIVIPDSFKGALSSREAGSAIAAGLASVTDAEVLVVPIADGGEGTVEAFVAAAGGAL
+RSATVCGVFYGERVPVHYGLIDPDVAVVETASCAGLPLASGREDTGRATTFGVGEQILDA
+VSAGARRVIVGAGGSATTDGGTGAAAALGVRFLDVAGEEFVPTGDTLTRIARIDSTPARD
+RLRDVDVEVMCDISNPLTGPQGAAHVFGPQKGADPAAVASLDTGLVHLAGLVERDLGVAI
+DALPGSGAAGGLAGGLHAFIGATLKPGIDVVLETAGFHDLVKTADLVITGEGRIDGQSLA
+GKVPIGVAQAVRAADRAIPVIVLAGSVGQDADTLYDEGITAIVPIGRGPQDLATAIRRTA
+EDLTATARDVGRLVMACSPARLTR*
+>NZ_CP083691.1_1162
+MQSIIVIPDSFKGALSSREAGSAIATGLASATDAEVLVVPIADGGEGTVEAFVAAAGGAL
+RSATVCGVFYGERVPVHYGLIDPDVAVVETASCAGLPLASGREDTGRATTFGVGEQILDA
+VSAGARRVVVGAGGSATTDGGTGAAAALGVRFLDVAGEEFVPTGDTLIRIARIDSTPARD
+RLRDVDVEVMCDISNPLTGSQGAAHVFGPQKGADPASVASLDTGLVHLAGIVERDLGVAI
+DALPGAGAAGGLAGGLHAFIGATLKPGIDVVLETAGFHDLVKTADLVITGEGRIDGQSLA
+GKVPIGVAQAVRAAGRAIPVIVLAGSVGQDADILYDEGITAIVPIGRGPQDLATAIRRTA
+EDLTATARDIGRLVMACSPAGLTR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002048.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002048.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77ed87a9e769c0e0c94f338bf30de8d8cfdd978a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002048.fa
@@ -0,0 +1,34 @@
+>NZ_CP042169.1_1574
+MSTFNENVVELAALEHFAELGYRRVHAPEIAPGEPDAERDSYEDVVLWGRLRDALRRINT
+SADAALIAEAVKTVQRAGSQSAVDENARLHKLITEGVPVEHRGDDGLLRTTRLWLVDFDE
+PANNDWVAVNQFTIVENGKNRRPDVLVMVNGLPLALLELKNPAAGHATLKSAWNQVQTYR
+HDIPSVFVPNAVTVISDGTSAAMSSYSGAFEHYAPWKTIEGREVVSNRPALEVLIKGVFE
+PKRFLDLLKNFVVFSDETVTDKSTGQPTRALLKRVAKYHQYWAVNAAVESTVQASSPDGD
+RRGGVVWHTQGSGKSFEMVFYAAKIMRDPRMANPTLVFITDRNDLDDQLFGETFAPARIL
+PETPVQAATRSDLRAKLKRASGGIVFTTLQKFAPGEDGDANPVLTDRRNVIVIADEAHRS
+QYGFSETLDRHGRLKSGLAKHMRDALPGATYLGFTGTPIESNDKSTRAVFGDYVDVYDLT
+RAVEDGATVRIFYESRLAKIELSEADLAALDDLADEITESVEKDTATAAKSRWSRLEAVV
+GAEARLDLVARDIVEHWEKRRESLFGKGMIVTMSRRIAVRLYEKIIALRPDWHSDDPAQG
+KIKVVMTGSASDPAEFQPHIHSKDVRKDLKLRAKNADDPLELVIVRDMWLTGFDAPSMHT
+MYVDKTMQGAGLMQAIARVNRTFRDKPGGLIVDYIGVFANLQNALSEYSPSDRDQAGVPI
+DEMVQVMLEKHDIVRGLLHGVQFDSSPELTAAQRLNEYAKVLDFVMADPDRTSRFNDQVL
+ALAKAFALAGARDEAAAIRNDVRLFTDVRAAILKIQNPDSGRGGSGAVEVDTALSQLLNE
+AVTANQVVDVYMLAGIETPEISILSEEFLDSFAEKDRPNLQMGLLRRLLNDQIRTVQRTN
+VVQGRKYSEMLEETVNRYTNRSLTTAEIIAELVKLAKQMRDAQKRHEELGLREDEVAFYD
+AVVQNDSAVMELGDETLKAIAQELVTSVRQSATIDWNLKESVLAAMRSKVRRILAKYDYP
+PDAEAKAIELVIEQAELFARGVSA*
+>NZ_CP097650.1_2149
+MTHANAPLTPTGRLRMVHRHLRDLLTQSNSGGIYFTTLQKFGLTQAERDAGADHPVLSDR
+RNIIVMADEAHRSHYDTLDGYAAHLKNALPNASLIAFTGTPIAEGERDTRRVFGDDIDVY
+DLHRAVEDGATVPVSFEPRLITLSRVDGVDDESLDAAADELTAGLDEADRDRIQRGVATL
+EAVYGAPHRLQTLAEDFVRHWEDRRDAMQPTMGVPGKAMIVCATRSIAARLYERIVALRP
+EWHDDADDKGRIKVVYDANPSDTGEIKKHMRRPSALAAVKKRLKNPADELEIVIVKDMLL
+TGFDAPALHTLYVDRPLKGALLMQTLARVNRTFRGKEDGLLVAYAPLAENLQQALAEFTR
+DTRTAGTKTLAQNTEEAAEIIETMVGMLADTVGVDWKATYQSDPKNGWRKALLEVTSRLR
+SPGTPGNTDPEDPTVRPVADTFRSQASRLHRAWALAGRVAAVERFRLDVKFYEEVRTWLA
+KLDAQDRIARGEPIPEEIARLLGEMVVDSTEATGVMDIYAAAVG*
+>NZ_CP097650.1_2152
+MEEAAAPSKAELAIEGLRTDLLKEATRVTGGNEIRRAQFSERINAVMAKYTNQQLTAAEV
+IAELVEMAKEVVAEADRGRRFTPPLHDDELMFYDVVAQNEAALDVMGDDVLAQIARDLVA
+TMRRDIKTDWTVREDVKAKLRASIKRLLRKYGYPPDQQPEAIVEVMRQMEAVAPRMAEGQ
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002053.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002053.fa
new file mode 100644
index 0000000000000000000000000000000000000000..185393d7d0762eb247a9b0441565af82693ad98a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002053.fa
@@ -0,0 +1,18 @@
+>NZ_CP042169.1_1909
+MSTHRLSSTALGFAAGLGTAAAVTAARKIALMAAVGKGHPLKHRLLDAASGLVQPKYPMG
+AMSTYLNGLHFYADDLGRQVEASHFCIHLRHDLHQCVIFDRNAPDARLIGIEYIISEERF
+RSLPEEERRLWHSHHYEVSSGALTAPGVPELAEHSYFEDLIHTYGKTFHTWQYDRDDFPY
+GIPQLMMGLTGDGQVDEALLRARDERVGVDTAAKRRHRADIPVPDVVPGANSWERGRVVQ
+TTLEERPVRGRDD*
+>NZ_CP033200.1_1613
+MSTHRLSSTALGFAAGLGTAAAVTAARRIALMAAVGKGHPLKHRLLDAASGLVQPKYPMG
+AMSTYLNGLHFYADDLGRQVEASHFCIHLRHDLHQCVIFDRNAPDARLIGIEYIISEERF
+RSLPDEERRLWHSHHYEVSSGALTAPGVPELAEHSYFEDLIHTYGKTFHTWQYDRDDFPY
+GIPQLMMGLTGDGQVDEALLRARDERVGVDTAAQRRNRADIPVPDVVPGANSWERGRVVQ
+TTLEERPVRGRDD*
+>NZ_CP097650.1_1836
+MSTHRLSSTALGFAAGLGTAAAVTAARKIALMGAVGKGHPLKHRLLDAASGLVQPKYPMG
+AMSTYLNGLHFYADDLGRQVEASHFCIHLRHDLHQCVIFDRNAPDARLIGIEYIISEERF
+RSLPDEKRRLWHSHHYEVSSGALTAPGVPELAEHSYFEDLIHTYGKTFHTWQYDRDDFPY
+GIPQLMMGLTGDGQVDEALLRARDERVGVDTTAKRRNRADIPVPDVVPGANSWERGRVVQ
+TTLEERPVRGRDD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002055.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002055.fa
new file mode 100644
index 0000000000000000000000000000000000000000..311d3c895733738c2bf30d4abc3cd5d0b6a6681d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002055.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_1985
+MPRPLAPLATSLPTILTVPEGREAGLSRARLRAPDLVAIGHGLRMSRDVEATWTDYLRAV
+QSLNPSGVFSHATAARIWGMWIPGRLLEDPRVHLAKERGHGGRTSRSGLVMHQLQPDAPV
+IEYRGLRLTAPAWTWVDLAHHLSVEDLVVAGDSLLPSPHGAEARRLGHLPPRATTVDEMR
+RLAHARKNVRGIVRARAVLDLLRTGADSPPESRLRHRLHEAGFPEPQVNPPIRLSSGETV
+RVDLAWEELRLCLEFDGDQHRTDRAQWQRDRARRRGLEADDWAVTWVAGEVFTRGGRPRF
+VGDLSRLMRRQATRRGAVLPPGLPGE*
+>NZ_CP040019.1_761
+MRMSRGVEATWTDYLRAIQSLNPSGVFSHATAARIWEMWIPGRLFEDPRVHLAKERGRGG
+RTSRPGLVMHQLQPDAPVIEYRGLRLTAPAWTWVDLAHHLSVEDLVVAGDSLLPSPHGAE
+ARRLGHLPPRATTVDEMRRLAHARKNVRGIVRARAVLDLLRTGADSPPESRLRHRLHEAG
+FPEPQVNPPIRLSAGETVRVDLAWEELRLCLEFDGDQHRTDRAQWQRDRARRRGLEADDW
+AVTWVAGEVFTRGGWPRFVGDLSRLIRRQAARHGTVLPPRLPGE*
+>NZ_CP083691.1_728
+MADPSRATPPRLVTTATLRSRGVAPWELRRREYTGRGRSLWGAAGVEFTLLDHVRALQEL
+HPTGVFSHATAARLWGMWLPRDLLQEPSVDIAKVKGRGGWPSREGIRGHHLDPAAQVVRL
+HGVRVTSPAWTWVDLAARLSVEDLVVAGDSLLPDEHGATARSLGRLPCRASTVAELRRTA
+ATRKNVRGVVRARHVVGLLREGADSPAESRLRHRIVEAGFPEPEVNPALRLHDGRIVRPD
+LCWRALRMCLEFDGDHHRTERAQWQEDRARRRGLEADGWSVTWVAGEVFTRAGWGRFRGD
+LAATMRRQAHQEGVVLPPSLPGEEASLW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002056.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002056.fa
new file mode 100644
index 0000000000000000000000000000000000000000..842268712beeb7231dbbe0043782e916f573a2c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002056.fa
@@ -0,0 +1,30 @@
+>NZ_CP042169.1_1986
+MTPTTSTPATFHDTRVDQQFIAGQWRDGASGDRASDINPYTDDVVAEFALATAEDLDEAY
+RAAAAAQEEWAAMPPKDRAAVLRRAAEILEERRDEVIDWLVKEAGSTRIKADSEVSLAIA
+ITQEAASFPTRVHGKIFDSNTPNRETRVYRKPIGVVGVISPWNFPLHLSQRSVAPALALG
+NAVVLKPASDTAVTGGTLIARVFEEAGLPAGVLSVVVGSGSEIGDAFVTHPVPRLISFTG
+STVVGKQVAANAVTGDTIKKVALELGGNAPLVVLDDADLDAAVDQAVLGGYLHSGQICMS
+VQRVIVDESVYDEFLPKYEGAVKALKVGDPAEEGVLVGPIINDSQVESLRKKIASAEADG
+ARALVGGEIQGRVVPPFVWVDATADMDIAREEIFGPMTVVLKAHDEAHALELANDHEYGL
+SSAVFTQDLDRGLRFANGLAAGMSFINEMTVQDEAHVAFGGARNSGLGRFNGEWALEEFT
+TDHTIGVTRVG*
+>NZ_CP040019.1_760
+MSPTTHAAATFHSNDVSKQFIAGQWRDGAAGSTKQDLNPYDDAVVAEFALASEADLDEAY
+RAAADAQKEWAAVAPAKRAAVLRRAAELLEERRAEIVDWLVKESGSTVIKANIEVSLAVG
+ITQEAASFPTRVHGTIHPSNTPDREMRVYRKPIGVVGVISPWNFPLHLSQRSVAPALALG
+NAVVIKPASDTPVTGGTLIARLFEEAGLPAGVLSVVVGAGSEIGDAFVKHPVPRLISFTG
+STPVGKQVGANAVSGDHIKKVTLELGGNAPVVVLDDADLDAAVEQSVTGGYLHSGQICMS
+VQRVIVDEKVYDEFLPKYEGAVKSLKFGDPREEGVLVGPVVNDQQLETLKKKIASAEADG
+ARALVSGEIEGRVVPPFLWVGAEPDMEIARDEIFGPMTVVLKARDEAHALELANDHEFGL
+SSAVFTQDLDRGLRFADGLAAGMSFINEMTVQDEAHVAFGGARNSGLGRFNGEWAIEEFT
+TAHTIGVKRLG*
+>NZ_CP083691.1_727
+MTPTTHASGTFLGNDVGKQFIAGQWRDGAAGSTKQDVNPYDDSVVAEFALASEADLDEAY
+RSAAEAQKGWAETGPKERAAVMRRAAELLEEHRDEVVDWLVQEAGSTVIKANIEVSLAIA
+ITEEAATFPTRVHGKIFDSNTSNRESRVYRSPIGVVGVISPWNFPLHLSQRSVAPALALG
+NAVVIKPASDTPVTGGTLIARLFEQAGLPAGVLSVVVGAGSEIGDAFVKHPVPRLISFTG
+STPVGKQVAANAVLGENIKKVALELGGNAPLVVLDDADLDTAVEQAVTGGYLHSGQICMS
+TQRVIVDAKVYDEFLPKYEQAVKALKVGDPRGEGVLVGPIINDSQVEGLQKKIASAEADG
+ARALVGGEVEGRVVPPFVWVDVDPDMEIAKEEIFGPMTVVLKARDEEHALELANHHEFGL
+SSSVFTQDTGRGVRFAQRVAAGMTFVNEMTVQDEAHVAFGGARNSGLGRFNGEWAVEEFT
+TDHTIGVTTVG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002062.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002062.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c531b8d0511b3710acbdf124aa81a050921aa2c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002062.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_2110
+MRVPGPFPAHLQDAPFTRAQALAAGVSGSRLRSRDVERVAHGHYRWIGPVTGATPPARPL
+ATELSRLQDLAAMRPDVVVTGESVARLLGWPLPDDVKARVRPTVLRSRTRRVLREPGVRT
+RLVDLDRVLVRRDRLHGLRWTSHADTWFHLATVLDRDALVAVGDRLAREDERRGKVALAT
+RRELGAALERHTGEAGIVRAREALALVRTGSDSPAETELRLALMAAGLPEPDLQIELWDP
+DYSLWHPASADLGYRRWRIAIHYEGKTHDGAAQVGKDTRRDAVFLRQGWLNIRVAGTDRW
+RGFVETAGLVRAAIAERGGLDAGGAEDRLRN*
+>NZ_CP033200.1_1836
+MRVPGPFPAHLQDAPFTRAQALAAGVSGSRLRSRDVERVAHGHYRWIGPVTGATPPARPL
+ATELSRLQDLAAMRPDVVVTGESVARLLGWPLPDDVKARVRPTVLRSRTRRVLREPGVRT
+RLVDLDRVLVRRDRLHGLRWTSHADTWFHLATVLDRDALVAVGDRLAREDERRGKVALAT
+RRELGAALERHTGEAGIVRAREALALVRTGSDSPAETELRLALMAAGLPEPDLQIELWDP
+DYSLWHPASADLGYRRWRIAIHYEGKTHDGAAQVGKDTRRDAVFLRQGWLNIRVAGTDRW
+RGFVETAGLVRAAIAERGGLDAGGAEDRLRN*
+>NZ_CP097650.1_2056
+MRVPGPFPAHLQDAPFTRAQALAAGVSGSRLRSRDVERVAHGHYRWIGPVTGATPPARPL
+ATELSRLQDLAAMRPDVVVTGESVARLLGWPLPDDVKARVRPTVLRSRTRRVLREPGVRT
+RLVDLDRVLVRRDRLHGLRWTSHADTWFHLATVLDRDALVAVGDRLAREDERRGKVALAT
+RRELGAALERHTGEAGIVRAREALALVRTGSDSPAETELRLALMAAGLPEPDLQIELWDP
+DYSLWHPASADLGYRRWRIAIHYEGKTHDGAAQVGKDTRRDAVFLRQGWLNIRVAGTDRW
+RGFVETAGLVRAAIAERGGLDAGGAEDRLRN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002063.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002063.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ce3a5c26e687decbb6243f4ee9866ea082595d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002063.fa
@@ -0,0 +1,14 @@
+>NZ_CP042169.1_2135
+MGGRPAAGLDPPQTAQSGHADDPSSARTVFDRFVFGNHIRSFSVD*
+>NZ_CP040019.1_535
+MTTTIQDPWAQPTPAGAYDDLLVRALPVTRAQRRWEPADGPMPSLFVSHGAPPTLDDPQW
+LADLFDWAQSMPKPRAIVIVSAHWEDAPVAISSAAAGTPLVYDFGGFHPRYYELQYATPD
+ATDLAARVAGVLGQGRPGSVHQTGRGLDHGAYIPLMAMYPDADVPVVQVSMPSMDPSALL
+DLGVKLRSLREEGVLVIGSGFMTHSFAAMRDPRLFGHVDAFDKWAAEMTHAGDVDSLIGY
+LDKAPGARIAHPTADHYVPLLLTMGAANDPSSARTVFDRFVFSNHIRSFSVD*
+>NZ_CP083691.1_458
+MTLADPWAQPTPAGAYDDLLARALPLTRRQKLWEPSDGRMPALFISHGAPPTLDEPQWLN
+DLFEWAQTMPKPRAIVIVSAHWENAPAAISASAAGTPLVYDFGGFHPRYYTLRYDTPDAT
+DLARRLAGVLGAQGQEVHQHTDRGLDHGAYIPLMAMYPDADVPVLQVSMPSQDPADLLRL
+GERLRELRDEGVLVIGSGFMTHSFAAMRDPRLFGHVDAFDTWAAEMAHAGDVDALMGYLD
+RAPGARIAHPTADHYVPLLLTMGAAHDPSTTRTVFNRFVFSNHIRSFTVD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002064.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002064.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c77ec7f22f6185e270d983482a20b2ce74d1912
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002064.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_2143
+MAQHSSTPYPLVIVGSGPAGVSAARAYVDAGGPGPVLMLTSDVDHPYERPPLSKELLRGT
+AEPDPTVLDELPDAVELRRGVTVTHADLGARTLWAAEEPVRFERLILALGAHPKPLPVAD
+DDAEVHLLRSLDHARRLVASAGHARSAVVVGSGFIGCEAAASLALRGVATTLVTPDEVPQ
+QKRLGREAGDRIAQWLIGAGVELRTGVRVGQVRAPRTVHLDDGATLAPDLILAAVGVEPG
+GGWLEDSELTMHEGRIVADEHLAAAPGVWVAGDVARAHHAVAGRPIPVEHWGDALGMGEV
+AGHNAARTEVGVPGGAGQASVLAHAATADPESLRRWEAVPGFWSTIGEHTLKHAAWGDGH
+EQARMVERTGGFTLWYTDAQDRVVGVLTYNADEDYERGRELVAGRDAVGEGRGRPDPA*
+>NZ_CP033200.1_1868
+MAQHSSTPFPLVIVGSGPAGVSAARAYVDAGGPGPVLMLTSDVDHPYERPPLSKELLRGT
+AEPEPTVLEDLPDAVELRRGVTVTHADLGARTLRVGEEPVRFERLILALGAHPKPLPVAD
+DDAEVHLLRSLDHARRLVASAGHARSAVVIGSGFIGCEAAASLALRGVATTLVTPDEVPQ
+QKRLGREAGDRIAQWLIGAGVELRTGVRVGQVRAPRTVHLDDGATLAPDLILAAVGVEPG
+GGWLEDSELTMHEGRIVADEHLAAAPGVWVAGDVARAHHAVAGRPIPVEHWGDALGMGEV
+AGHNAARTEVGVPGGAGQASVLAHAATADPESLRRWEAVPGFWSTIGEHTLKHAAWGDGH
+EQARMVERTGGFTLWYMDAQDRVVGVLTYNADEDYERGRELVAGRDAVGEGRGRPDPA*
+>NZ_CP097650.1_2088
+MAQHSSTPYPLVIVGSGPAGVSAARAYVDAGGPGPVLMLTSDVDHPYERPPLSKELLRGT
+AEPDPTVLDELPDAVELRRGVTVTHADLGARTLWAAEEPIRFERLILALGARPVPLPDVE
+ADAEVHLLRSFADARRLVTSAGHARSAVVVGSGFIGCEAAASLALRGVETTLVTPDEVPQ
+QKRLGREAGDRIAQWLIGAGVELRTGVRVGQVRAPRTVHLDDGATLAPDLILAAVGVEPG
+GGWLEDSELTMHEGRIVADEHLAAAPGVWVAGDVARAHHAVAGRPIPVEHWGDALGMGEV
+AGHNAARTEVGVPGGAGQASVLAHAATADPESLRRWEAVPGFWSTIGEHTLKHAAWGDGH
+EQARMVERTGGFTLWYTDAQDRVVGVLTYNADEDYERGRELVAGRDAVGEGRGRPDPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002067.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002067.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba6441174a478eb7b59cde2a0c271b6c137732b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002067.fa
@@ -0,0 +1,33 @@
+>NZ_CP042169.1_2154
+MSPSSTASDRSDAATAALDDAARRTGPGRRRRADARGTEGLGGTLAKIVLLGLVDAFAAF
+LLFQLAAAGDWVVFALTLAVTIGINWIYLRRGGLPAKYLAPGLFFLMLFQVFVVVYSSYV
+AFTNYGAGHNSDKAAAIEIIQRSSSIRVPDSPVYDITVLEEGGDLYLLTLRDGEPVLGGA
+DQALEPVEAQMQDGEPVGVEGYTTLRFGDLLQRQDQVARLKVPLSDDAADGTLETRDGSR
+GYVYAPRLEYDEARDTFTDLESGVEYRDNGEGQFQADDGSTLQTGWRVFVGLDNFTRAFT
+DPELRDPLLRVTVWTFAFAFLSVATTFAVGLLLAIAFNRSDMRGKKVYRVMMILPYAFPA
+FLSGLVWAGLLNPEFGFVNTVFFGGADIPWLTDPWLARLSVLVVNLWLGFPYMFLVTTGA
+LQSLPEDVDEAARMDGAGPWRIFRSIKLPLLLVSVAPLLISSFAFNFNNFNIIYMLTGGG
+PRFPDAGSNIGATDLLITVVYKTAFSGVGRDYGLASALSIVIFLIVATISAISFRQTKAL
+EEIDK*
+>NZ_CP033200.1_1879
+MSPSSTASDRSDAATAALDDAARRTGPGRRRRADARGTDGLGGTLAKIVLLGLVDAFAAF
+LLFQLAAAGDWVVFALTLAVTIGINWIYLRRGGLPAKYLAPGLFFLMLFQVFVVVYSSYV
+AFTNYGAGHNSDKAAAIEIIQRSSSIRVPDSPVYDITVLEEGGDLYLLTLRDGEPVLGGA
+DQALEPVEAQMQDGEPVGVEGYTTLRFGDLLQRQDQVARLKVPLSDDAADGTLETRDGSR
+GYVYAPRLEYDEARDTFTDLESGVEYRDNGEGQFQADDGSTLQTGWRVFVGLDNFTRAFT
+DPELRDPLLRVTVWTFAFAFLSVATTFAVGLLLAIAFNRSDMRGKKVYRVMMILPYAFPA
+FLSGLVWAGLLNPEFGFVNTVFFGGADIPWLTDPWLARLSVLVVNLWLGFPYMFLVTTGA
+LQSLPEDVDEAARMDGAGPWRIFRSIKLPLLLVSVAPLLISSFAFNFNNFNIIYMLTGGG
+PRFPDAGSNIGATDLLITVVYKTAFSGVGRDYGLASALSIVIFLIVATISAISFRQTKAL
+EEIDK*
+>NZ_CP040019.1_518
+MSTSSTTSARPDAPHEDPADAGRRGLRGRRADRGPDGTAGTLVKIALLGLVDAFAAFVLF
+QLAAAGDWVVFAVTLAVTLLINWIYLRRGGLPAKYLAPGVFFLVLFQVFVVVYSSYIAFT
+NYGAGHNSDKPAAIEIIQRSSSIRVPDSPVYPVSVLEQGGDLHLLTVRDGQAVLGGADEP
+LAPVEAQMDGAEAVAVDGYTTLKFGDLLSRQDQVTQLKVPLSDDPADGTLETRDGSRAYV
+YSPRLEYDEAQDTFTDLESGVVYRDNGEGRFQADDGSTLQTGWRVFVGVDNFAKAFTDPS
+LRDPLLRVLVWTFAFAFLSVVTTFALGLLLAIAFNRADMRGKNVYRVLMILPYAFPAFLS
+GLVWAGLLNPEFGFVNNVFFGGADIPWLTDPWLARFSVIVVNLWLGFPYMFLVTTGALQS
+LPEDVDEAARMDGAGPWRIFRSIKLPLLLVSVAPLLISSFAFNFNNFNIIYMLTGGGPRF
+ADAATNIGATDLLITVVYKTAFSGVGRDYGLASALSIVIFLIVATISAISFRQTKALEEI
+DS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002068.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002068.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1be3e475239494801a6ff308cb730295098d849e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002068.fa
@@ -0,0 +1,27 @@
+>NZ_CP042169.1_2155
+MQSTTTGGLFRRPLSLTLTAAFSALALTACGGGSSAPASSSPAGATEQGTATASPSQDLS
+EAGASTITMWVDQNRQEPLQAVAEDFKEDTGITVELVVKDNSTMKDDFITQNPTGEGPDV
+IVGAHDWIGSLVQNGTIEPLELGERAGDFVESSVQAVTYEGQTWGVPYSVENIAILRNTE
+LAESTPASFDEMIAEGRKAVDAGEAEYPFVVGLDAVNGDPYHLYPFQTSMGAPVFKQAED
+GSYDTGSLAMGGPEGEAFAEKLAEYGESGVLNPNMTADIAKEQFNSGNAAYFITGPWNIE
+EAEAAGVDFEVEAIPSMGDQPAQPFVGVNAFFVSSESENQLAANEFVVNYLSTEAAQDAL
+FAEGKRPPALTASFDKAASDETVKAFGEIGENGVPMPAAPEMGAVFEFWGGAEMSIIKGE
+GDPVQTWQKMISDIEGRIGQ*
+>NZ_CP033200.1_1880
+MQSTTTGGLLRRPLSLTLTAAFSALALTACGGGSSAPASSSPAGATEQGTAAASPSQDLS
+EAGATTITMWVDQNRQEPLQAVAEDFKEDTGITVELVVKDNSTMKDDFITQNPTGEGPDV
+IVGAHDWIGSLVQNGTIEPLELGDRAGDFVESSVQAVTYEGQTWGVPYSVENIAVLRNTE
+LAESTPASFDEMIAEGQKAVDAGEAEYPFVVGLDPVNGDPYHLYPFQTSMGAPVFKQAED
+GSYDTGSLAMGGAEGEAFAEKLAEYGESGVLNPNMTADIAKEQFNSGNAAYFITGPWNVE
+EAEAAGVDFEVEAIPSMGDQPAQPFVGVNAFFVSSESENQLAANEFVVNYLSTEAAQDAL
+YAEGKRPPALTASFDKAASDETVKAFGEIGENGVPMPAAPEMGAVFEFWGGAEMSIIKGE
+GDPVQTWQKMISDIEGRIGQ*
+>NZ_CP040019.1_517
+MTSTTPRAALRRPLGLTLTAAFSALALTACGGGGGTAASSSPAAGGSASSSAAGGSDQGA
+ASSSSAGQDLTEAGAATITMWVDQNRQKPLQAVAEDFKEDTGITVELVVKDNSKMKDDFI
+TQTPTGEGPDVIVGAHDWIGSLVQNGTIAPLELGDTADAFSETSVQAVTYDGQTWGVPYS
+VENLAILRNTALAEETPASFDEMIAEGQKAVDAGDADYPFVVGLDPVNGDPYHLYPFQTS
+MGAPVFEQQEDGSYDVSSLAMGGAEGQAFAEKLAEYGESGVLNPNMTADIAKEQFNAGKA
+AYFITGPWNVDEAEEAGVDFAVEEIPSMGDQPAQPFVGVNAFFVSAESENQLAANEFVVN
+YLSSEEAQDALYAEGKRPPALTASFEKAAVDETVKAFGEIGEDGVPMPAAPEMGAVFEFW
+GGAEMSIIKGEGDPAQTWDKMISDIEGRIGQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002072.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002072.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f6bb448f8a60a13aefde1ed74df6d9d5816ae401
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002072.fa
@@ -0,0 +1,18 @@
+>NZ_CP042169.1_2187
+MTLPTPSGRWTTTARPAFAVAAALSLGGNLLSLWIGSWKSSDLPADAGYAGVLEGGWEHM
+LNQPTYFTFLSNFLVGLTSLLLALRLHRPGTLFRVLRVTGVVCIVITGVVFNVLLRDADP
+MTAVERFNDTLQHIVTPILTPVLWAVFGPRRQITWRVVWLSTLIPLAWLAFTLLRGPWLD
+WYPYTILDVPRLGYDGVAVYVVAILVFFVAVAALLRVADGLLARAGVGVGAGAEAEARVE
+ARPSP*
+>NZ_CP033200.1_1901
+MTLPTPSGRWTTTARPAFAVAAALSLGGNLLSLWIGSWKSSDLPADAGYAGVLEGGWEHM
+LNQPTYFTFLSNFLVGLTSLLLALRLHRPGTLFRVLRVTGVVCIVITGVVFNVLLRDADP
+MTAVERFNDTLQHIVTPILTPVLWAVFGPRRQITWRVVWLSTLIPLAWLAFTLLRGPWLD
+WYPYTILDVPRLGYDGVAVYVVAILVFFVAVAALLRVADGLLARAGVGVGAGAEAEARVE
+ARPSP*
+>NZ_CP097650.1_2121
+MTLPTPSGRWTTTARPAFAVAAALSLGGNLLSLWIGSWKSSDLPADAGYAGVLEGGWEHM
+LNQPTYFTFLSNFLVGLTSLLLALRLHRPGTLFRVLRVTGVVCIVITGVVFNVLLRDADP
+MTAVERFNDTLQHIVTPILTPVLWAVFGPRRQITWRVVWLSTLIPLAWLAFTLLRGPWLD
+WYPYTILDVPRLGYDGVAVYVVAILVFFVAVAALLRVADGLLARAGVGVGAGAEAEARVE
+ARPSP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002073.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002073.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be4c1f83d511842b27575683a9ce5e4711b39710
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002073.fa
@@ -0,0 +1,21 @@
+>NZ_CP042169.1_2202
+MTTKVGFIAAASHALQNGPQLFARVEDGGVVIGGRSGEVVPDSTGLYAVVAQDPDAARAE
+LRLDTSVSRSDVLYIGKAEGSLRARLERKHFADGGTAHSTLRRTLAALLVDRLDLEPVAV
+ASAGRFTLTPESGEQLTTWMRRHLAVRVWQAPAGFAEVTPLGDIEKPVIDTHTPPLNLTY
+GGTSPEAQLLRQRIRKARTAMAEQAKRGVDVVGADSSARATVGDLFRRRPRQYGLRGSVG
+LWEELAERLDDTPMPTSEYELGRLLRDALDRSLEGAEPYDEDKVNVERFNRGGMSQGLVH
+LPWWEDQAIPLLLDRWGAWADTRGLIGPEDYIGSW*
+>NZ_CP040019.1_456
+MTTKAGLIAAASHALQNGPQLFARVEDGGVVIGGRGGEVVPDSTGLYAVVAQDPDAVWAE
+LRLDTSVSRSDVLYIGKAEGSLRARLERKHFADGGTAHSTLRRTLAALLVERLGLEPVAV
+ASAGRFTLTQESGEQLTTWMRCHLAVRVWQAPAGFAEVTPLGGIEKPVIDTHTPPLNLTY
+GGTSPEAQQLRRRIREARTAMAEQAKRGVDVVEADSSARATVGDLFRRRPRQYGLRGSVG
+LWEELAERLDDTPMPTSEHELGRLLHDALERSLEGAEPYDEDKVNVERFNRGGMSQGLVH
+LPWWEDQAIPLLLDRWGAWADTQGLLGPEDYIGSW*
+>NZ_CP097650.1_2135
+MTTKAGLIVAASHALQNSPQLFARVEDGGVVIGGRSGEVVPDSTGLYAVVAQDPDAARAE
+LRLDTSVSRSDVLYIGKAEGSLRARLERKHFADGGTAHSTLRRTLAALLVDRLDLEPVAV
+ASAGRFTLTPESGEQLTTWMRRHLAVRVWQAPAGFAEVTPLGDIEKPVIDTHTPPLNLTY
+GGTSPEAQLLRQRIRKARTAMAEQAKRGVDVVGADSSARATVGDLFRRRPSQYGLRGSVG
+LWEELAERLDDTPMPTSEYELGRLLRDALDRSLEGAEPYDEDKVNVERFNRGGMSQGLVH
+LPWWEDQAIPLLLDRWGAWADTRGLLGPEDYIGSW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002078.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002078.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4cf65788a700ff4d6242a7c0715342a7b5e32e39
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002078.fa
@@ -0,0 +1,24 @@
+>NZ_CP042169.1_2232
+MPSAPPPSDLAGSTAAPRPPLWTRPFILVSATYLFVAMIFYTLMTAMALYAVTSFGASDA
+EAGVVVGAFVLGAVLTRMTTTPATFAWGRRRVLLVALACYVLTTAAYLWADSLAALTAVR
+LLNGMCFGAAGTVLATAVQRIVPPVRRSEGTGWFSTSMTLAGAVGPMVALQLSTTLGYDA
+LFWACIGFTGMALLIALFLRVPEPPLTGRFRLHRADVFSAEVAPAAGVALASGFMYGGIL
+AFMATFAQQQGYPAMVPSLFFLLFAAGTIVGRAVLGVLHDRHGDNAVVYPILAGMAVSYA
+VLALWREPAGMLAAGALLGLTYGPVVSVFQTIAIKVVRPTEIGVATGTFFLLLDLGTGLG
+PMVLGAVAAAVGIPVMYLLSGGVGMALLLYYRLVHGGRAIARRPPPA*
+>NZ_CP033200.1_1936
+MPSAPPPSDPAGSTAAPRPPLWTRPFILVSATYLFVAMIFYTLMTAMALYAVTSFGASDA
+EAGVVVGAFVLGAVLTRMTTTPATFAWGRRRVLLVALACYVLTTAAYLWADSLATLTAVR
+LLNGMCFGAAGTVLATAVQRIVPPVRRSEGTGWFSTSMTLAGAVGPMVALQLSTTLGYDA
+LFWACIGFTGMALLIALFLRVPEPPLTGRFRLHRADVFSAEVAPAAGVALASGFMYGGIL
+AFMATFAQQQGYPAMVPSLFFLLFAAGTIVGRAVLGVLHDRHGDNAVVYPILAGMAVSYA
+VLALWREPAGMLAAGALLGLTYGPVVSVFQTIAIKVVRPTEIGVATGTFFLLLDLGTGLG
+PMVLGAVAAAVGIPVMYLLSGGVGMALLLYYRLVHGGRAIARRPPPA*
+>NZ_CP097650.1_2174
+MPSAPPPSDPAGSTAAPRPPLWTRPFILVSATYLFVAMIFYTLMTAMALYAVTSFGASDA
+EAGVVVGAFVLGAVLTRMTTTPATFAWGRRRVLLVALACYVLTTAAYLWADSLATLTAVR
+LLNGMCFGAAGTVLATAVQRIVPPVRRSEGTGWFSTSMTLAGAVGPMVALQLSTALGYDA
+LFRACIGFTGMALLIALFLRVPEPPLTGRFRLHRADVFSAEVAPAAGVALASGFMYGGIL
+AFMATFAQQQGYPAMVPSLFFLLFAAGTIVGRAVLGVLHDRHGDNAVVYPILAGMAVSYA
+VLALWREPAGMLAAGALLGLTYGPVVSVFQTIAIKVVRPTEIGVATGTFFLLLDLGTGLG
+PMVLGAVVAAVGIPVMYLLSGGVGVALLLYYRLVHGGRAIARRLSPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002083.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002083.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4663e2cb296b13034047ab1a9c6b144d3df00a9f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002083.fa
@@ -0,0 +1,25 @@
+>NZ_CP033200.1_344
+MTAGVDRPADGKVAVERVDRPGRRGMRLLGPAFVAAVAYVDPGNVAANLTAGAQYGYLLV
+WVLVAANLMAMLVQYLSAKLGLVTGRSLPELLGHRLPRGRRLAYWVQAEIVAAATDLAEV
+IGGAIALHILFGIPLLAGGVIVGVVSMILLGVQSRRGQQPFEFVVVGLLAVITLGFVSGL
+FYGPISWGEAVAGMVPRFEGTQTVLLAAGMLGATVMPHAIYVHSALARDRHQGAHAHPGT
+LGRLLRATRWDVGLSLLVAGSVNIAMLLLAAANLSGVSGTDSIEGAHAAITTALGPAVGV
+LFGVGLLASGLASTAVGSYAGSEIMGGLLRWRIPQMLRRVLTLIPALLVIASGVDPTWAL
+VLSQVLLSIGIPFAMIPLVRLTGARAVMGRHANSTPLQTVAWVVVALIVALNAVLLWLTL
+TGQG*
+>NZ_CP083691.1_655
+MAAVAYVDPGNVAANLTAGAQYGYLLVWVLVAANLMAMLVQYLSAKLGLVTGRSLPELLG
+HRMPRGRRLAYWVQAEIVAAATDLAEVIGGAIALHILFGIPLLAGGVIVGVVSMILLGVQ
+SRRGQRPFEFVVVGLLAVITLGFVSGLFYGPISWGEAVAGMAPRFEGTQTVLLAAGMLGA
+TVMPHAIYVHSALARDRHQGAHTNPATLGGLLRATRWDVGLSLLVAGSVNIAMLLLAAAN
+LSGVSGTDSIEGAHAAITAALGPTVGVLFGVGLLASGLASTAVGSYAGSEIMGGLLHWRI
+PQMVRRVLTLIPALLVIASGVDPTWALVLSQVLLSVGIPFAMIPLVRLTGARAVMGRHVN
+SAPLQTAAWVVVALIVALNAVLLWLTLTGQE*
+>NZ_CP097650.1_1958
+MAAVAYVDPGNVAANLTAGAQYGYLLVWVLVAANLMAMLVQYLSAKLGLVTGRSLPELLG
+HRMPRGRRLAYWVQAEIVAAATDLAEVIGGAIALHILFGIPLLAGGVIVGVVSMILLGVQ
+SRRGQRPFEFVVVGLLAVITLGFVSGLFYGPISWGEAVAGMAPRFEGTQTVLLAAGMLGA
+TVMPHAIYVHSALARDRHQGAHTNPATLGGLLRATRWDVGLSLLVAGSVNIAMLLLAAAN
+LSGVSGTDSIEGAHAAITAALGPTVGVLFGVGLLASGLASTAVGSYAGSEIMGGLLHWRI
+PQMVRRVLTLIPALLVIASGVDPTWALVLSQVLLSVGIPFAMIPLVRLTGARAVMGRHVN
+SAPLQTAAWVVVALIVALNAVLLWLTLTGQE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002087.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002087.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c33336b63e75a8be0d181d1bb25d9128c85864f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002087.fa
@@ -0,0 +1,36 @@
+>NZ_CP033200.1_523
+MPVSAPSPSSSRPAVLGFAARYPWVLATLVVVALTLGLHLAGAEDPARWIASAYALVVAA
+WTSVGMVRDLMRGHWGVDILAVTAIVATVLVGEHLAAVLVCLMLTGGEALEDYAAGRARR
+DLSALLDRAPQRAHRLGPDGSVEDVPVEEVRAGDRLLVRPAEVLPVDGTVASAEDGGEVA
+VDLDESSLTGESLPVTHRTGSAVMSGALNGTRAFVLEATASAADSQYAAIVSLVQQAAES
+RAPMVRLADRYAVPFTAVAYLIAGLAWWLSQDPVRFAEVLVVATPCPLLIAAPVAFLGGM
+SRAATSGVIVKSGGTIEALGSVQTVGFDKTGTLTAGRPELVGVRPAAGFAQDELLRLAAS
+AEQYSVHVLADAIRAAAEERGLSLATAQDATEEATHGVVAVLEGRRVVVGKRAYVTQAAP
+DTVTADLAPGQSAVYVAVDGAFAGVLLLADRIRPESAATVQALHRLGARQVLMLTGDAEA
+TGRHIAREAGIDEVHADLLPADKVRLLSERPERPVMMVGDGVNDVPVLAAADVGVAMGAR
+GSTAASESADVVVLADDVSKVAVAVAAGQRTLQVATQSIWVGIALSLVLMVIAATGAIPA
+LVGALFQELVDVVAIVNALRAMKPGPHEAERLGDLAAAPARGERQAVSA*
+>NZ_CP040019.1_783
+MTRLSRFARSYPLVAVTLAVLALVLGLHAAGLDAAAAVIATVYVAGHIAWAAVGMVREVL
+RGHFGLDILAVVAMTASLLVGEHLAALIIVLMLTGGEALEDFAAARARRELTALLEKAPQ
+TAHLLGADGEAREVPAAQVRPGDELLVKPNEVVPVDAELLSAEAAFDESSLTGESLPSAK
+AAGDAVLSGSVNGTAAVRVRATAAAADSQYQRIVELVEQAHEQKAPVVRLADRFALPFTA
+VSLAIAGVAWWASGDPVRFAEVLVLATPCPLLIAAPVAFLGGMSQASRRGVIVKGGGVLE
+SLAHARAVAFDKTGTLTHGRPRLQRVEPAEGFTADAVLAAAAAAEAYSTHVMAEAVVRAA
+DDAGLARLSARGGTEEGTRGVRALVRGTDGGAGAGTGTDTHEPGAAVEVRVGKLAFVREV
+APDAPEARFAPGETAAYVSVDGRHAGTLVLADALRENAGETVAALRAEGFERAVMLTGDN
+EHTARSLAAEAGLDDVAHSLLPEDKVRLLAELQPRPVIMVGDGVNDAPVLAAADVGIAMG
+ARGSSAAGESADVVITRDDIGRTVEAVRIGRHTYRIALQAVLLGVALSVGLMLVAAFGHI
+PAVAGALTQELVDLACILYALRARTSPRGTPQGAAARARGRAPQEAARA*
+>NZ_CP097650.1_750
+MPVSAPSPSRPAVLGFAARYPWVLATLVVVALTLGLHLAGAEDPARWIASAYALVVAAWT
+SVGMVRDLMRGHWGVDILAVTAIVATVLVGEHLAAVLVCLMLTGGEALEDYAAGRARRDL
+SALLDRAPQRAHRLGPDGSVEDVPVEEVRAGDRLLVRPAEVLPVDGTVASAEDGGEVAVD
+LDESSLTGESLPVTRRTGSAVMSGALNGTRAFVLEATASAADSQYAAIVSLVQQAAESRA
+PMVRLADRYAVPFTAVAYLIAGLAWWLSQDPVRFAEVLVVATPCPLLIAAPVAFLGGMSR
+AATSGVIVKSGGTIEALGSVQTVGFDKTGTLTAGRPELVGVRPAAGFAQDELLRLAASAE
+QYSVHVLADAIRAAAEERGLSLATAQDATEEATHGVVAVLEGRRVVVGKRAYVTQAAPDT
+VTADLAPGQSAVYVAVDGAFAGVLLLADRIRPESAATVQALHRLGARQVLMLTGDAEATG
+RHIAREAGIDEVHADLLPADKVRLLSERPERPVMMVGDGVNDVPVLAAADVGVAMGARGS
+TAASESADVVVLADDVSKVAVAVAAGQRTLQVATQSIWVGIALSLVLMVIAATGAIPALV
+GALFQELVDVVAIVNALRAMKPGPHEAERLGDLAAAPARGERQAVSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002094.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002094.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00424a9ad5250c48753cee1feeef751f7a66299a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002094.fa
@@ -0,0 +1,15 @@
+>NZ_CP033200.1_1665
+MRIDETTERTADGRLVPTPGQTIGPFFGYANGYEQVHLPWRDGHQLVPAGRADAMRLFGT
+VYDGNGDPIPDAMIEIWQADAEGVISQEDGSLVQDGFTFTGWGRCAVDNAGRYTFSTVEP
+GVVNEDRARFIHVVVFARGLLNKLHTRVYLPEDAEAIVQDAFLTSLDEDRRRTLIGTRND
+DGSLEFDIWIQGPGEHAPKETVFLQFPGIEYPELD*
+>NZ_CP040019.1_827
+MRIDENSERDAQGRLIPTPGQTIGPFFGYADGYEQVHLPFRDGQNLVPPGRADALRLTGT
+VYDGNGDPIPDAMLEIWQADAQGVISQEDGSLVRDGFTFTGWGRATVDNVGTYTFSTVEP
+GATGEGTARFISMVVFARGLLNKLHTRVYLPEDTEALAADPLLQSLPEERRRTLIAERLD
+DGSLRFDVWIQGRGEHADKETVFLQFPGIEYPQHD*
+>NZ_CP097650.1_1882
+MRIDETTERTADGRLVPTPGQTIGPFFGYANGYEQVHLPWRDGHQLVPAGRADAMRLFGT
+VYDGNGDPIPDAMIEIWQADAEGVISQEDGSLVQDGFTFTGWGRCAVDNAGRYTFSTVEP
+GVVNEDRARFIHVVVFARGLLNKLHTRVYLPEDAEAIVQDAFLTSLDEDRRRTLIGTRND
+DGSLEFDIWIQGPGEHAPKETVFLQFPGIEYPELD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002096.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002096.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21e3b384100ba71f2885c8077e7896655c6676b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002096.fa
@@ -0,0 +1,24 @@
+>NZ_CP033200.1_1667
+MTQPPVTRTRVGIVGGGPAGLMLSHLLARQGIDNVVLESRDPETIAHTHRAGILEQPSVE
+MLTDMGVDGRVRTVGDEHRGIILRFDGESHALDFPELVGATVTLYAQNEVFVDLAAARRR
+DGGDVRFETEVLEVLDVDSDTPGVRFRSVAAGEEGPVEELRCDILVGADGSRSTVRKALQ
+RDTEGEDHFHAYPFAWFGILAEAPKSSPELIYARSEHGFGLISQRSETVQRMYFQCDPST
+RVEDWSDDRIWDRLQRIVAGPDGFTLKTGPIIDKTVLGFRSYVRTPLSHRNVFLAGDAGH
+TVPPTGAKGLNLAFADVRVLAEALESWAATGSRDLLDAYSETALTRVWKDQNFSYWMTTM
+LHARPDASEFEDMRVRGELRNVVQSRYGRQFLAEQYTGWPSA*
+>NZ_CP040019.1_825
+MTQQPVTRTRVGIVGGGPAGLMLSHLLSKQGIDNVVLESRDHETIANTHRAGILEQPSVD
+MLTGTGVDGRVKTVGDEHRGIFLRFDGESHALDFPELVGATVTLYAQNEVFVDLAAARER
+DGGDVRFETEVVEVLDIDSDTPGVRFRSVAGGEQGPVEELRCDILVGADGSRSTVRKALQ
+AGTEGKDYFTAYPFAWFGILAEAPKSSPELIYARSEHGFGLISQRSETVQRMYFQCDPAT
+RVEDWSDDRIWERLQKIVDGPDGLTLKTGPIIDKTVLGFRSFVRTPMDHRNVFLAGDAGH
+TVPPTGAKGLNLAFADVRVLFEALDSWASTGSRDLLDAYSDTVLARVWKAQNFSSWMTTM
+LHARPEASEFEDMRVRGELLNVVSSRFGQQYLAEQYTGWPHR*
+>NZ_CP097650.1_1884
+MTQPPVTRTRVGIVGGGPAGLMLSHLLARQGIDNVVLESRDPETIAHTHRAGILEQPSVE
+MLTDMGVDGRVRTVGDEHRGIILRFDGESHALDFPELVGATVTLYAQNEVFVDLAAARRR
+DGGDVRFETEVLEVLDVDSDTPGVRFRSVAAGEEGPVEELRCDILVGADGSRSTVRKALQ
+RDTEGEDHFHAYPFAWFGILAEAPKSSPELIYARSEHGFGLISQRSETVQRMYFQCDPST
+RVEDWSDDRIWDRLQRIVAGPDGFTLKTGPIIDKTVLGFRSYVRTPLSHRNVFLAGDAGH
+TVPPTGAKGLNLAFADVRVLAEALESWAATGSRDLLDAYSETALTRVWKDQNFSYWMTTM
+LHARPDASEFEDMRVRGELRNVVQSRYGRQFLAEQYTGWPSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002101.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002101.fa
new file mode 100644
index 0000000000000000000000000000000000000000..36457b705bc2883334218efde3707f4978eaabfe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002101.fa
@@ -0,0 +1,34 @@
+>NZ_CP033200.1_1751
+MVSNRLETESGWRRSRLHGVRADDTLTTATLDVRARAAALDHAVATTLADVARDFAGLDL
+FLFASDRSGRLIRLVGPWKSALGEQIRRRGLDVGVCLAEEAAGFNGIGAALELGRGVAVD
+GEEHYLDAFRAFSCFGVPLAHPGVGRVHGALSVVTFAGATPTLVEGLARHLGRQIEQALG
+AATYADELRLLTEFRRLTRGRGSAVVGVGEESILLNAAAERLVRCLDGSELRALAVRARR
+GELDGGDVGVAGGFSVADVSEASGMTLMRLERAATETTPRPTPGAGRGTWAPAVEAAREA
+RGSVSVIGEPGSGRTAAARRIAGPDAVILEVGRAQTPEDTTWLRGLEALVRRPGPPVVVD
+DVDALEPRLLPGLRRALRQGRCRIVMTAQVQPTTDVSAVLALTEHRVQLSPLRRRLAEFP
+ALLAAMAAQVHGASAPMFSPEAVRVLAQQHWPGNLVELEYVVGRVGRRAGGGRVTVAELP
+ASHRGEGTVPLLGLERAEREAIIDALESAGGNKVRAAAALGVSRATLYRRLRTLRITQEG
+*
+>NZ_CP040019.1_677
+MVSNRLEAESGWRRSQLHGVRADDALTTTTLDVRARAAALDHAVATTLADVARDFAGLDL
+FLFAADRSGRLIRLVGPWKSALGEQIRRRGLDVGVCLAEEAAGFNGIGAALELGRGVAVD
+GEEHYLDAFRAFSCFGVPLAHPGVGRVHGALNVVTFAGATPTLVEGLARHLGRQIEQALG
+AATYADELRLLTEFRRLTRGRGSAVVGVGEESILLNAAAERLVRHLDGSELRALAVRARR
+GELDGGDVGVAGGFSVADVSEASGMTLMRLERAATETTPRPTPGAGRGTWAPAVEAAREA
+RGSVSVIGEPGSGRTAAARRIAGPDAVILEVGRAQTPEDTTWLRGLEALVRRPGPAVVVD
+DVDALEPRLLPGLRRALRQGRCRIVMTAQVQPTTDVSAVLALTEHRVQLSPLRRRLAEFP
+ALLAALAAQVHGASAPTFSPEAVRVLAQQHWPGNLVELEYVVGRVGRRAGGGRVTAAELP
+ASHRGEGTVPLLGLERAEREAIIDALESAGGNKVRAAAALGVSRATLYRRLRTLRITQEG
+*
+>NZ_CP040019.1_794
+MAPEPPQADPERIRRARHELAARGLIAGSVPPALVGEQIEQSWRRSVAHEVSLDAVPQGG
+ADLDPALPLRRAAETVVRRWAEGLGQLRVSLVVADATGRILVRRALDTRDEDALDAARAA
+VGYGFGEQDLGTNGLGTPLQVKGDVYISGAEHFTDGLAGLTCAGTPVLDPVTGRAVGALA
+VASRADEAHPLMLGVARQAAAEVMEALRDETAGPDLEIARAFRGLRGPDRAVLVMSADTV
+MTDLPGLARIDAQTQAVLWETLRRRSPGEEPVRLSLPGLEGEALARRLPGAEAAYALEFD
+AVPAPEPALGRAAAAPRSGPPAGGGPERGAGTAPSVGVHPSEMAVAYDGIGDALTAAAEQ
+TGLVELTGPRGSGKRFQAVRWLRDRALAAGTADAPDPLHVELADVTGPQGEDLLRRVAAR
+GRAVVVAGTLPTAAETAQARAGLRTTVARVVLEHPEAPRVVLLRSVDASAEDDVAGQVRL
+PALAEVPQDIPALLARLSERLHPGAPPPRFSPEALQRILAWPWPDNMAGLSRLVSLLPGL
+RRGATVQVEDLPAALRAGPGSRLTRMEQAERDAIVAALREHGGNRSAAAAALGIGRATLY
+RRLKALRITV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002106.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002106.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5cfa63fb7ce1fc6fc6a8b37bad8342b83c3cb3a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002106.fa
@@ -0,0 +1,20 @@
+>NZ_CP033200.1_2133
+MVPTADDAPRREPGAVWRGLLTIFLVSAGGSLMFYTWLIYLPTHAQVAHQMDKSTTLSAS
+LVAQVIFLAAILGAGLLGDRVGRRPLVIAFGLLFVVLPFPLFGMLDGTFASFLLVQTIAL
+LAVALLFGVNGAVWSEALPTAVRAKGVATMLSLATAIFGGTAPYLITWLTAQGWTSAFPI
+YLMVVGGLTGLVMKETKDVDLAA*
+>NZ_CP083691.1_149
+MSTAATGAARPAPVPRTRPRSLKDMLAVNFGNALEWYDWNVYTIFAPVFAAQIFHADNPT
+SELLATLAVFAVGFVARPIGGYVFGAYADRVGRKRSLFAAMMITALGSLIIAFTPTYGMV
+GVLASVILVIARLLQGLAHGGEMGTSVTYLVERAPQGRRGLFGATSWVSVVVGTILATLV
+GLTINTLLTHEQVASWGWRVAFGIGGVLGLYALYLRRSLTESEHFTAAQQVVPTADDAPR
+RESGAVWRGLLTIFLVSAGGSLMFYTWLIYLPTHAQVAHHMDKSTTLSASLLAQVIFLAA
+ILGAGLLGDRVGRRPLVIAFGLLFVLLPFPLFGMLDGTFASFLLVQTIALLAVALLFGVN
+GAVWSEALPTAVRAKGVATMLSLATAIFGGTAPYLITWLTAQGWTSAFPIYLMVVGGLTG
+LTGLVMKETKDVDLAA*
+>NZ_CP097650.1_178
+MGTSVTYLVERAPQGRRGLFGATSWVSVVVGTILATLVGLAVNTLLSPEQVASWGWRVAF
+GIGGVLGLYALYLRRSLTESEHFTAAQQVVPTADDAPRRELGAVWRGLLTIFLVSAGGSL
+MFYTWLIYLPTHAQVAHQMDKSTTLSASLLAQVIFLAAILGAGLLGDRVGRRPLVIAFGL
+LFVVLPFPLFGMLDGTFASFLLVQTIALLAVALLFGVNGAVWSEVLPTAVRAKGVATMLS
+LATAIFGGTAPYLITWLTAQGWASAFPIYLMVVGGLTGLTGLFMKETKDVDLAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002107.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002107.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca3133831b53776e91be873b6b6d280fec213d06
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002107.fa
@@ -0,0 +1,15 @@
+>NZ_CP033200.1_2135
+MKYRPQHEANPLPFSPFKSSTVPRPIGWLSSVSTDGRENIAPYSQWQNLTFDPPMVMFSA
+NQYPDGRRKDTVLNAEQTGWFVWNMATYDLREAVNVSAMALEPGESEWDRIAEHGVTKVY
+ADNHPIPMVAESPVRFECRYHSTHRIKGDSNVGTIDVVFAHVDTIHIDDDVITADGRLDI
+PRIQPIARLGYFDYTVVRETFEMRVPGADGDAQAGLEGRS*
+>NZ_CP040019.1_808
+MSARTEFDPAALGDRETTLLVKSLLIPRPIAWVGTLSADGVPNLAPHSFFTVASSEPPIV
+LIGSAGRKDTLRNAEATGEFTVSLVTRALAEAANRTSAPFAPEVDEFAAASLTPEPSVVV
+GPPRVAASPAALECRLHEVHPVGDSFLLMGRVVHVSVDTDVLTTDARGRTLPDPAALGPV
+SRLGRMEWGGLGEVFELERPSAG*
+>NZ_CP083691.1_148
+MKYRPQHEANPLPFSPFKSSTVPRPIGWLSSVSTDGRENIAPYSQWQNLTFDPPMVMFSA
+NQYPDGRRKDTVLNAEQTGWFVWNMATYDLREAVNVSAMALEPSESEWDRIAEHGVTKVY
+ADNHPIPMVAESPVRFECRYHSTHRIKGDSNVGTIDVVFAHVDTIHIDDDVITADGRIDI
+PRIQPIARLGYFDYTVVRETFEMRVPGADGDAQAGLEGRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002109.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002109.fa
new file mode 100644
index 0000000000000000000000000000000000000000..895f01ee51d835770399a6be8508621a80ae2e76
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002109.fa
@@ -0,0 +1,24 @@
+>NZ_CP040019.1_122
+MPFALYMLALAVFVMGTSEFMLAGLLPAIATELDVSVGTAGLLTSAFAVGMVVGAPVMAA
+FARSWPPRLTLIVCLLVFAGSHVIGAMTPVFSLLLITRVLSALANAGFLAVALSTATTLV
+PANQKGRALSILLSGTTIATVVGVPAGALLGTALGWRTTFWAIAILCIPAAVGVIRGVTN
+NVGRSATSATSPRLRAELSQLAMPRLILAMALGALINGGTFAAFTFLAPVVTETAGLAEA
+WVSVALVMFGIGSFLGVTIAGRLSDQRPGLVLAVGGPLLLTGWIVLAVVASHPVALIVLV
+LVQGFLSFGVGSTLITRVLYAASGAPTMGGSYATAALNIGAAAGPVLGAFGLATGLGLLA
+PVWVASVLTAIALAIMLLTGRALTKTAAEAN*
+>NZ_CP040019.1_1481
+MPFALYLLALAVFAMGTSEFMLAGLVPDIAASVGVSVGTAGLLTSAFAVGMILGAPAMAA
+LTRRWPARTTLLGCVVIFAACHVVAATAETFSVLFATRVVAAVANAGFLAVALSTATRLV
+APSRKGRALAILLSGTTIAMVAGVPAGALLGTALGWRATFWAVAFLCVPAAIGILTGIRP
+QPRDTQDEANDGLSLAFELAQLRVPRLFTAMLLAALVNGGTFAAFTFLAPVVTGTAGLGQ
+VWVPVALVLFGIGSFMGVSIAGRLSDQHPRTLLVVAAPLLLVGWLLLAVLAGHSVPLLVL
+VFLLGMLAFAVGSTMIARVLYAASEAPTMGGSYATAALNIGAAAGPALGAVALESSRARA
+TLVPCGQRPR*
+>NZ_CP040019.1_2295
+MPFVLYLLAMVVFAMGTSEFMLSGLVPDISAYFGVSVGTAGLLTSAFAIGMVIGAPAMAA
+LTRRLPVKATLLGCVIVFALSHAVGALTPDFTVLFITRVIAAVVNAGFLAVALVAATKLV
+APDAKGRAVAILLAGTTVATVAGVPAGALLGAVLGWQSTFWAIALLCVPAAVGIAAGFTA
+QSDDSSREEPTSISLRAELSQLASPRLVLTMLLAALVNAGTFSTLTFLAPIVTHTAGLSQ
+WWVSVALVLFGVGSFIGVTVAGRLSDARPRIVIVGGGSVLVLGWLALATFATNPIALLGL
+VFAQGVLGFAVGSTLITRVLYAAAGAPSMAGSYATAALNVGAAAGPILAATALGVVPGAL
+GPVWVAVIVTAAALLLAIPVLRLVAPAESEVIK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002113.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002113.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d52b5007bf82e20367e292b1be434980f76601d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002113.fa
@@ -0,0 +1,20 @@
+>NZ_CP040019.1_746
+MVASALTGGDPALPGIGPVAAVREVLDAAGIALAEVAVVEVVEAYAAQVWAVLDELGLSA
+EAGAARADDWGVDPRVNAEGGALAFGHPWGASGAVAATHAVRRLQSCPPGSSALVTCAVG
+GGMGVALVLDVA*
+>NZ_CP083691.1_708
+MSAVGLDAAPVWITAVSRTPVTARSRAQAHLGAGELAAGPVGEVAAGTHPAAVVLGNGAG
+PGGNVARIAALAAGLGVATPGWTVDAQCGAGLVAVAQAAGHAVATGRACVGGGVESPSTA
+PERSIDGVSYAQAPMVPAGWDDPGMTAAADALAAARGIGRARQESFAARSHVLALAGGLR
+LPDDDGPRRLDAAALARFRAVTPGADPATAVTGATAARIADGAAAVLVTPHSAVVRETDG
+VSTASVRGVDVLRPCRVLSWSLTGVDPALPGLGPVSAVRDALDAAGRTLEGVAVVELVEA
+YAAQVLAALDDLGLTGASGTSAPGASGPATAHDPWGVDPRVNAAGGALALGHPWGASGAV
+AVVHAVRRLQAEPPGAVGLAACAVGGGMGAAMVLEVA*
+>NZ_CP097650.1_1937
+MTTTPGLWITAAARTAFTARSRGQAGLDAGALSAQAVAAVTGPAAADVAAVVLGNCTGPG
+GNLGRIAALAAGLGEHTPGWSVDAQCGAGLAGVLQAAQHAAFTGRPCVGGGVESPSTAPQ
+RSRDGVPYTQAPMVPSGWPDPGMTAAADALAAADAMPRARQEAFAARSHALALAAAGLRR
+IERVPGAPDDDGPRRLDARALARFTPVHPDADPAAAVTGGTAARIADGAAAVLVVPCERS
+PVGRDEPAGGLRPVRIVGAEIRGGDPALPGIAPVAAVERALAAADWRLGEVAVVEVVEAY
+AVQALATLDRLGLTDHARPGPASLGSDRQGLDDWGVDRRVNAAGGALALGHPWGASGAAA
+VVRAVHRLQGQPPGARAVVACAVAGGLGITMLLEVA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002118.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002118.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f9e21ca5fb7986c3c8d671e5cd3273c93a2c2b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002118.fa
@@ -0,0 +1,10 @@
+>NZ_CP040019.1_1287
+MLGALIAGGATFLTGKLADDRARQAERKEHVARVGAEFLREADRVEQYLLDYVHEHAAVP
+GDNEEWGETAELARIAWELRLFAPRPVNDAAAELVDVLEAWESGVDGRGRDVLEIHKRFV
+SVLRVYLHGEDD*
+>NZ_CP083691.1_2185
+MARVGAEFLREADRVEQYLLDYVHEHAAVPGDNEEWGETAELARIAWELRLFAPRPVNDA
+AAELVDVLEAWESGVDGRGRDVLEIHKRFVSVLRVYLHGEDD*
+>NZ_CP097650.1_115
+MDAWIGVVGTLLGAVVGGGVAYLNGTRDRKLEARRDQEKCVTEVAGELLQIVDARERYVH
+GYLEVVGEFPHDGAPDGEEDPARKTLALLELYAPAPVTTAAREYVDLMDKW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002119.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002119.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5412b3522d503586b755b5f6a4c4e8f4898046b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002119.fa
@@ -0,0 +1,37 @@
+>NZ_CP040019.1_2284
+MDGFRRSLDGQFVTVDGHDYSEVTRPKLAQADQQERLPDGSERPLPTRTLHLMAAEDGTA
+PVDLNDWERQVLDSEAAEPSLRGWYRNPSRASKQSLAIPFQDGAGQWQALRPDFVFFHAN
+QDGTIRADIVDPHGTHLADALPKLRGLAEYAQAHGMPSVGSRPSLRSRGSCGCWT*
+>NZ_CP083691.1_333
+MRYTLKDYQADAVAEILANIERAQRLRREGHLPTMALTATTGGGKTVIAAAVIEALFFGS
+DTFDFLADPGAVVLWFSDDPTLNAQSRHRLEAAAPDLIGRMTDLNAGYTKPALDPRTVYF
+INTQKFAKTSRMVRGFQPSGTEGQDTFAGLDPRVRPDMVPQTIYDIIAATIQNPDLTLYF
+FLDEAHKGMGTTARAQAEQKTIVKRLIAGQPGVPPMPVVFGISATLQRFTNAMDGIRGRL
+GLDPVQVDPARIQKSGLLKDNILLNIPHPDEVGSFETVLLRSAVRQLLESEAAWDAYVAE
+QRADHPGAEIERVVPLMVLQTPNSVTPSDIAGYLRTIMDVWPEMPAGAVAHVFGEKEAIQ
+AAGLFIPHIDPEKVQDTKRVRILLAKEAVTTGWDCPRAEVLMSFRTVSDLTKITQTLGRM
+VRTPLARRIPGNDELNSVLCLLPNFDEKAARQVVKDLTNDEVPNPIIDPVVDPDPRPEVT
+PPSGGAGASSGGGTEPANPEVPGHGTHATDRVAEPSADGQGTPARPGGLHQGETRGASGG
+GQGGAVGPVVLTDRVKVTPIENGPLWDLFDSLPTETTPSRGLGPVPLLTALGQYLSEDGL
+RPDAGEEAHRHLHGTLDYRAGQFREDVDKAVKDILEVRVRTILADRATGKERIGMFTERA
+DLAVVREAYQRAARAFTADVSRTYVNHIVGPDADEDDLREAYARVAGMASVPDIVADVKE
+EASRLVGRWFQEHRTDIKALADDRQAAYKALMEQSTEPQRGNLAKPVNWQESPVDVDKKP
+LPTRTDHILTAEDGTYPLTLNRVESSVVDQEMRRRGAIAWYRNPSRVKDESLAIAYRDGN
+AWRTMRPDFLFFHEDAQGRVRASIVDPHGHHLSDALPKLRGLARYAEQYGDEFMRIEGLT
+EVNGKMRALDMQDPKVREAVEVATSARALYESDAAVDY*
+>NZ_CP083691.1_677
+MRYTLKDYQAQAVEQVLNRLHRARKNYQDDGVLSQFSLAAATGAGKTVMAAAIIEALFFG
+SDQYTEDIAPDPGATVLWFSDDPDLNDQSRARIHAASSELDGRLRTVENSFAETTFAPGQ
+VYFLNAQKLREGARLVRGAQDPTNAATPVMAAPDMAQRTIYDVIANTVATPGRTLYFILD
+EAHRGMKTTKKNDQERATIVQRLINGTALAPTMPIVLGISATVERFTQAMAHATDRDALS
+PVQVDPALVQASGLLKDDVVLTIPEEAGAFDTTLLREAVARTKASTRAWAAYAAEQGEPN
+PVVPLLVVQVADKPSDEHLSRILDVIHQEWPELRPQDIAHVFGTHTDRHLPGQIVNYIAP
+QRVQETTHIRVLLAMEAISTGWDCPRAEVLMSFRTYKDATYVHQLLGRMVRTPLARRIPG
+NEVLNSIDCFLPHFDKTTSTAIAQTLMRGQSDMDDTTSDPGKQAARRVLFDPVTLTPNPA
+VGEDVWAVFDALPSMNIPQGATKPLKRLDILANALSHDELLPGAVKTAAHTMCKLLDGCR
+VQYSEQIAAARQDVLTLSAQRLTGRLGTTTLSTTSLELLADDRAIEEAAAAAARTLTGWI
+AGAYIDHIVPEDEEDLDLREGDIIIASLARTSEVVADLEAKADKLVQDWLSQYRVQINGL
+TDERQAVYDRVREMARQPERVALTRPKLTQADQQERLPDGSERPLPTRTLHLMAAEDGTM
+PVDLNTWERQVLDSEAAEPSFRGWYRNPSRASKQSLAIPFQDGAGQWQALRPDFLFFHAN
+QDGTIRADIVDPHGTHLADALPKLRGLAEYAQAHGDAFGRIEAVAEIEGQLRVLDMKNDV
+VQAGVHAAQDAESLYKAAPAY*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002121.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002121.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8bc3b7273e67cff994a886b86146d0b71e032f79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002121.fa
@@ -0,0 +1,9 @@
+>NZ_CP083691.1_316
+MPQKYTPEFKAKALKLIEERVRAEQCSAWVACTAVGEALGGISPHTLRNWWKQDRVDHGE
+APGLSTAEAEEIKKLRRENLELRRANEILRKASAFFAAELDRPTTR*
+>NZ_CP083691.1_400
+MQLIEERIRAKQCSGWAACAAVGEALGGISPHTLRNWWKQSHVDRGETPGVSTDEFEEMR
+RLRRENLELRRANEILRKASAFFAAEHDRPTTR*
+>NZ_CP083691.1_649
+MPQKYTPEFKARALELIEERIRAEQCSGWGACVAVGEALGGISPHTMRNWWRQGRIDRGG
+APGVSTDESEEMRRLRRENLELRRANEILRKASAFFAAELDRPTTR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002122.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002122.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c16ad19f7152226131aec8f71f4691867448cf9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002122.fa
@@ -0,0 +1,4 @@
+>NZ_CP042169.1_157
+MLTIASRLDVMNRLGRAMADPTRSRILMTLLEGPSYPAVLARDLGRV*
+>NZ_CP033200.1_320
+MLTIASRLDVMNRLGRAMADPTRSRILMTLLEGPSYPAVLARDLGRV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002123.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002123.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ef5f43f84b7e2fceead7ddf6b076e30f2e512c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002123.fa
@@ -0,0 +1,6 @@
+>NZ_CP042169.1_158
+MNPELEQALRLATDPPGGVSLEALEDLVRDDPTTWWDISEAATHLNVTAHTLRYYERIGM
+VSVPRDDAGHRRYDSPAIRRLVFITRMRTAGMPIADLQHYLALGRV*
+>NZ_CP033200.1_338
+MNPELEQALRLATDPPGGVSLEALEDLVRDDPTTWWDISEAATHLNVTAHTLRYYGRIGM
+VSVPRDDAGHRRYDSPAIRRLVFITRMRTAGMPIADLQHYLALGRV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002125.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002125.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e2761ad9f69223202645854cb8bce5744301a344
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002125.fa
@@ -0,0 +1,8 @@
+>NZ_CP042169.1_181
+MTAVPETYVFDTGPLRHFTLKGWLGVLKFLTAGHAVIPESVEQEIRDQQYQHPDLRQILD
+AEWIVVDRSEDLEFLAAFARYEEHLVAGGRNRGECGVLALGRTHGYRIVIDDNVPRVLAK
+REKLECTGTLGLLCEAIRKEQLTVPMVESLADDLIMGDYRLPFGPGGFKCWAEQQGLLG*
+>NZ_CP040019.1_204
+MTHVFDTGPLRHFTLNGWLGVLKFLTGGRIVIPESVEREIKDQQHQHAALRQILDADWIT
+VDRSDDLEYLAAFARYEEHLVDGGRNRGECGVLALGRTRGHRIVVDDNVPRVLAKNEELD
+CTGTLGLLCEAIRADKLTVSMVESLADDLLASEY*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002126.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002126.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3d949c0a9de67767d9a2a96319ec4581c569577
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002126.fa
@@ -0,0 +1,14 @@
+>NZ_CP042169.1_182
+MSQQDLATAVGLERTMVNRIEGGQRKVTALELASIADALGTRMQSFFTEPAPALVSHRSA
+QGLDTTESAVDHLLAELLADVEFLHGLHPIEGFGVRDPWEQPKSVHEADDMAARAREHVG
+YTATEPVKDLQAHLATAGLLLFSRNFGVDAADAGTVLLAEGGISLVNSTPKVGRRRLSAV
+HELGHYLLADEYTVDWRTAHTGPDIEGRLDRFARAFLLPAAVLLQEWPAAAHSGDVRTAA
+VKIAGTYLVDMSTLARRLHDLELVDASTANDIRAVQTTQTDIITHDLYPSDEMAGTTQPR
+VYQKHVIALFEAEKLSRERTLDLLDGTFDDDDLPDLPPRQEQEIWEYVS*
+>NZ_CP040019.1_203
+MVNRIEGGQRKVTALELAAIADALQARMQSFFTDPAPSIVSHRSAQGLDATESAVDHLLT
+ELAAAVEFLHGLRPIQGLATREPWEPPTSTEAVEDMAARARAEAGYGPDEPAKNLQDHLA
+TAGLLLFSQDFGADAADAGSVLLEEGGVAIVNSAPKVGRRRLSAVHEFGHYLLADEYTVD
+WRTAHTGPDIEGRIDRFARAFLLPATAMASVWPRAVTANGTRTAAVTIAGSYLVDMSTLA
+RRLRDLDLVDASTANDIRAVQTTQTDIVTHDLYPSHELEGLTQPRTYQKHVLALFEAEKI
+SRDRALGLLGGTFTDADLPELPPRQEQEIWEYVS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002128.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002128.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2fe43a7872272992a533d7142bb50d04593eab9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002128.fa
@@ -0,0 +1,16 @@
+>NZ_CP042169.1_246
+MATQARDGRFSNEVLPQDERPSRFGPGLIIAASFIGPGTITTSIVTGAEQGFVLAWAVVF
+SILATIVLQEMSGRLGLATRMSLGHALREVFSSVPARLVMAILVVAAIGIGGASYAGGDT
+VGTALALTSVTGLSQPVVVIGIVLTIGILLWTGSYKLIERVLTVMVGLLGLLFIVTAVLV
+QPPIGDLLMGMFIPRLPPGTALLAVALIGTTVVPYNLFLHASLVQEKWGPGLDSRESLRA
+ARTDTAVSISVGGVITLAVMATAFGGMYVKGMQAETGRDLASALEPLLGDAAGWVFAAGM
+FAAGFTSAVAGPLGAAYAIAGTLGQDTDLRSVPARIVWGAVLAIGAVIALTGTNPTEVIV
+IAQAANGLLLPIVAVFLMVVMNSRRLMGSHRNGPLANALGGLVCLVVIGLAVYQLGGLAG
+LWD*
+>NZ_CP033200.1_2216
+MAILVVAAIGIGGASYAGGDTVGTALALTSVTGLSQPVVVIGIVLTIGILLWTGSYKLIE
+RVLTVMVGLLGLLFIVTAVLVQPPIGDLLMGMFIPRLPPGTALLAVALIGTTVVPYNLFL
+HASLVQEKWGPGLDSRESLRAARTDTAVSISVGGVITLAVMATAFGGMYVKGMQAETGRD
+LASALEPLLGDAAGWVFAAGMFAAGFTSAVAGPLGAAYAIAGTLGQDTDLRSVPARIVWG
+AVLAIGALIALTGTNPTEVIVIAQAANGLLLPIVAVFLMVVMNSRRLMGSHRNGPLANAL
+GGLVCLVVIGLAVYQLGGLAGLWD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002130.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002130.fa
new file mode 100644
index 0000000000000000000000000000000000000000..339a8221156b34697ed2c1515e036c565d95d9b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002130.fa
@@ -0,0 +1,18 @@
+>NZ_CP042169.1_382
+MTRREVESVEDRIREHLRRDDLNSAVELLRALSPGDALELLDRSEPRMVPVLFRLLDKST
+AVRVFAAMETGQQSDLVRQLQDGQVQDLFAELRVSGQARLLDEMPATVARKMLAGLDAGA
+RGEVGRLLGYPADSVGRRLRMAPVRLREDWTVAVALENLRDHGGREQAAIVSVPVVSPQA
+RLTGVVDVSVLVTQPLDARVSEIMREPVSAVATEDAEEVARLCADRRLWTVPVTDSEGRL
+IGVFTVADALEVLDEESTEDAARAGGVEPLGRPYLATSVLALMRSRITWLLVLAIGATLT
+VQVLGVFEDTLEEMVVLSLFIPLIIGTGGNTGNQAATTVTRALALDDVRPRDAPRVMFRE
+LRVGMALGGCIGLLGLVIAGLVFSWPVGLVIGATLFTVCAFAATVGGLMPLAARTIGADP
+AVFSNPFISTLVDALGLVVYFFIAQAVLGI*
+>NZ_CP097650.1_388
+MTRREVESVEDRIREHLRRDDLDSAVELLRALSPGDALDLLDRSEPRMAPMLFRLLDKTT
+AVQVFAAMETGQQSDLVRKLQDGQVQDLFAELRVSGQARLLDEMPANVARKMLAGLDAEA
+SGKAGRLLGYPADSVGRRLRMAPVRLREDWTVSTALENLREHGGQEQAAIVSVPVVSPQA
+RLTGVVDVSVLVTQPLDARVSEIMREPVSAVATEDAEEVARLCADRRLWTVPVTDSEGRL
+IGVFTVADALEVLDEGSTEDSARAGGVEPLGRPYLATSVLSLMRSRITWLLVLAIGATLT
+VQVLGVFEDTLEEMVVLSLFIPLIIGTGGNTGNQAATTVTRALALDDVRPRDAPRVMFRE
+LRVGMALGGCIGLLGLVLAGLVFSWPVGLVIGATLFTVCAFAATVGGLMPLAARTIGADP
+AVFSNPFISTLVDALGLVVYFFIAQAVLGI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002133.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002133.fa
new file mode 100644
index 0000000000000000000000000000000000000000..14de06f0793d86e7fc7a034149d214a9727a944f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002133.fa
@@ -0,0 +1,7 @@
+>NZ_CP042169.1_492
+MGLGLNVALHDVVHRVAFSAAVPIQHRTAFLRRLGWTGITRSDIRDGCLFIGFDITMDRS
+YLNRQVLIDASAPVRIGAHVQFGPRSSIITSTHRIGDATMRGGDPEAQPVAVGDGCWIGA
+GAMILPGVIVAPGCIIAAGAVVTRDTEPNGIYAGTPARRVRDLD*
+>NZ_CP040019.1_263
+MRAAENSLRSRATGADVHPTVWVMRSAWIERGATVGGPGQRAGAVVTRSTEPNGLYAGVP
+GRRV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002134.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002134.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a7ba8472eedf3b43e9c0f65206b706109e031a99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002134.fa
@@ -0,0 +1,12 @@
+>NZ_CP042169.1_565
+MNVHSLQLAYTPEAAREVTDQIKTGLESVYHLIRSAYRGRAWEVLGYRSWDEYVTREFGN
+LHLRPPLEKRQDIVLSLREVGMSTRAIASATQISEATVRRELKHAGASKDAPGRAPASVV
+GVDGKTYEATRPARIGNLEPSMGVRGGQSDVDAVLDMPAEDFGIEPLDLVRHDEEQKNRA
+RRVLTAFNGSGAAAVPALIKAATPVASLVSPATGKALVEDEDLHGVVWDSVRCVRTLAHV
+IRSVGHVEGESQAEIRSTLRDAVDDLDEVLKKIEEGTR*
+>NZ_CP033200.1_308
+MNGYSLQLAYTPEAAREVTDQIKTGLESVYHLIRSAYRGRAWEVLGYRSWDEYVTREFGN
+LHLRPPLEKRQDIVLSLREVGMSTRAIASATQISEATVRRELKHAGASKDAPGRALASVV
+GVDGKTYEATRPARIGNLEPSMGVRGGQSDVDAVLDMPAEDFGIEPLDLVRHDEEQKGRA
+RRVLTAFNGSGAAAVPALIKAATPVASLVSPATGKALVEDEDLHGVVWDSVRCVRTLAHV
+IRSVGHVDGQSQAEIRSTLRDAVDDLDEVLKKIEEGTR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002135.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002135.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52aecfbdd8d2006e0c3dbe6ed044f695c2715a7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002135.fa
@@ -0,0 +1,8 @@
+>NZ_CP042169.1_571
+MLNGINPDGLSGWSQISGWVVGTALVVLILAVGAGVALAVWGRALFSPGGMRKGWTMVAL
+AAVGATVLGAGTAGTSWGAGLGTSELMPAGARPQSVAIEKNAPKQTCNRQAVRDFDKEEP
+SPDRAERERVISTLLGGQPALDGYEWGKEPTGTESSYTVVTSVKWYATGEVNGSGEPDCS
+AQNEATAECSPVEVHVARQSLTNGAQTGRTLTLTRGQNCS*
+>NZ_CP042169.1_572
+MSNLIHAATTVAAGVPDIAPRFDGPWMPTIQNVTGLALGTFLVVLIVAVGIGVLVWIFGK
+LSSSGRAQDVGISFVVWGIVAAALIAGAASLIGWGAGLPLF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002136.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002136.fa
new file mode 100644
index 0000000000000000000000000000000000000000..48a7d636eeae68a2387eefcef5c07787e474e51e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002136.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_574
+MATMIQESMDSEYDDVRFPQERTQGLILGLTLEQVIVVLAGVLIGMAFILRGGPAMFVGI
+GLMAVIGAFGATRFRGRSLPGWVWVAAQYLRRGATDQLEYRQGMAPAHVLELVDGEPQAP
+VSEAGPQAQRDAKGRIKPGEPARFRLPGVAGELMVYAMPNGAGFVWDPRAREAVVCAKVM
+TTRGFDLESFDAQEERSLSWGSSLAALSRLPGVVRIQASDQTTLISGAAVEDFYESKQEG
+AGRTGASIDPFLDQAFRELMKEAQSMPVHEQWLTLVVSPSKITSQVKALGGGTPALMEHM
+LKLMTTVESTLPRSGTQVTAWHSPRTLAGLSRSAFDPDASVMVSTMKADGKTAGTAPSSA
+GPMAVEVHAGHMVTDGNYHRTYKVSELPQNLARLGFLDELVFAGDFRHTVSVFLAPVERG
+AAVRSVQRRKTDWHTNSRLMNKLGRIGSLEHDQSLEDVEREEAELRRRHTGVEVVVLVTV
+TGASRSELESAAAEVVASGITAECELRPVWMEQDAAFVAGALPFGRMKL*
+>NZ_CP083691.1_1758
+MSSRKKNNSHEPEATGSELVPVKFSRLTRRGILLGLSAAQLVTVGIAIATIITALYAGGG
+MWLAYTAPVWATAVLLTWVPVAGRPVIEWVPVAGWWVYRTTIGQLLYRRRIVTPRPAGTL
+ALPGDQARLREYEDPTTGAGMIHDPHQNTLTVVCEITHPAFVLLDPAEQERRVTAWGRVL
+ATVCRSGRIATLQILERTLPDSGTGLAEWWTTHGQPDDTSWAATTYAELINRAGPAGERH
+ATTLSLSLDMRNAARQIRTAGGGIRGAAAVLRQEMNTLTAALRSADLTPSGWLTPGQIAV
+ILRSAYDPAIAATLERHGEIGHDLATAGPVAVNETWSRIRTDSAHHAVLWISEWPRSMVY
+PGFLSPILLSSGIQRSFSLICTPMRSDQAARDIRKKKVEHISDQAQRAKIGQIEDASQTA
+EYHDVLQQEADLTAGHGILRYTGLITVTATTIEDLDAHVAALEQAAIQANCETRLLAGQQ
+AKAFTAAALPLCRQV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002137.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002137.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1da691943a9c6251df277ab14b7cac7a8cbad5da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002137.fa
@@ -0,0 +1,18 @@
+>NZ_CP042169.1_575
+MREEPKVDLFQIIEPGKMSLREARVAQRKMKMAQAQAQRLRNREAREERFPQPQWGKAGP
+RGARQLRGLRTLAPRPVRTTTHTAATAYPFVAGPGLGARGLMIGKDMHGGGAFCFDPWAL
+YEAGIISGMSMMLFGQVGTGKSSLAKSLAVRQVLAGRKLSVASDKKGEWTRVVKGLGGSV
+IQVGPGLDTRLNPLDPGTRPSTDVQGEPMTDRAWASMVRTRRMSILVALVKILTDREMTS
+PEHHVLSAGLDAAVAVADAEGRPPIIPDVIRALDAARTDPDAMKAEAASVTMMTLGRVSS
+GDLAGMFDGETTVVLDEQACATSIDTSALLGASPEAVRVVNACAGAWTEAMVTTRDGGQR
+IVIYEEGWDNISSEADLRRMVEQWKLSRAYGIFNVLVLHKIADLDMAGDQSSKMAAMARS
+LLADADVKVIYRQDRSALKITTSEMELSDRERSLVRSLPKGTGLWRLGDSSFEVQNVLTR
+AELPLFDTDERMDKAKEAVA*
+>NZ_CP083691.1_1764
+MAEGGLGSDGVFVGQDLYSGGSFVYDPWVLYARGIITAPNLVLAGIVGSGKSSLAKSLYT
+RSLPFGRRVYVPGDPKGEHTAVAEAVGGKAIVLGHGLHTRLNPLDEGHRPGGLTDQEWAS
+TVASRRRDLIGALAETVLARGLTPLEHTAIDLALTATVAENEVPILPMVVDHILTPSHDP
+GGRLAEDGRLVGHALRRLVAGDLAGLFDGPSTVAFDPDLPMISLDLSRVTENSTLISVLM
+TCSSAWMESALLDPNGGQRWVIYDEAWRLMSHPALLKRMDAHWRLARHYGIANMLIFHKL
+SDLDNVGDEGSAMRSLANSLLANAETRIVYRQESDQLGPTATALGLTGTEQTLLPNLGVG
+QGLWRIKNRSFVIQHQLHPGELELFDTSSRLTAGVK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002138.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002138.fa
new file mode 100644
index 0000000000000000000000000000000000000000..362b446ac7d4b31c3e0fe6996ecbb113b9db4f66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002138.fa
@@ -0,0 +1,16 @@
+>NZ_CP042169.1_576
+MRRERGNNSVLEGDNPAETALIWLIGPAVLLYGAYLLAGFLAGRIHCGAATKPDSLFAPL
+GFLVGEHDPAAFGATAQGCTATTGGVIGWLIGLGVLALVLIGVAVTAWSRYQQSDKKFIK
+ELREREGLARSAEITKTVGRKSVLSRVKKVRPSIKKPAITDGAMRLGKAEGVDVFASYEE
+SVVLIGPPRSGKGVHLLIGAILDAPGPVITTSSRADNLGATAELRKKKGPVALFDPQGLT
+GQPSTLKWSPITGCEEPRVANQRAASLIGASGLGSSSSNAEWQAPAITIMECLLHAAALG
+ERTVDDLMRWGNNPAEAKEAVKILTEHPKAALNWNLVLKGIIEGDPKLLQSKWFGVEGAV
+KGLSVPEVRDVLRPNRFEETLDIDKFLTECGTLYIVGTKTGGSSAGPFLIAMMDAITERA
+RELAAKSPGNRLDPPLSLVLDEIANISGAWPGLTQLMADGGGVGISPFAVFQSMAQARNE
+WGEQQAQALFDAATVKVQLGGASNVSDLEQFAKLAGQRKIMRTSKSRGKDHTSVSEQIHD
+TEVVSVAELRRLPFGWGVLLNRNGRPILMQMTRWWDRKDGKQIKEAAGRYSKALLAELES
+KDPAPSTPTDADRAEDSVAALDPVPETAPAIPVR*
+>NZ_CP083691.1_2194
+MLEAIARTSKSCGKDHTSVSEQIHDTEVVSVAELRRLPFGWGILLNRNGRPILMRMTRWW
+DRKDGKQIKEAAGRYSKALLAELESKDPAPSSTPTDADRAEESVAASDPVPEAAPAIPVR
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002147.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002147.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb088e9ff42d9ea30ec1691a5cbebd93d1eb39cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002147.fa
@@ -0,0 +1,16 @@
+>NZ_CP042169.1_918
+MSANTNFFTSQQPAAVFKLKVLEDYLTPWAMKVASKAPREVAYVDGYAGAGQYDDAHKGS
+PLYAVDIARKLAAQNRIMHIHLVERDRAHAETLRHAVAAQGQGAGPVYLHHGAVEEQIDA
+ILNDIGTRPALFFLDPFGTALPYDVVASKLLLRPARSTEVLLNFSLSTVWRIGGIVRKGA
+SASSGETVTLLRGDRFLGGPWWREVFAEARRQADVSGDSSSAATAASYVAREYMQRMTGE
+TAHNVISVPIRRTPSEGPIFTLMLFYQHFAAPMLFADAAARAHRKWRQVNSENYYQGLLN
+DTQGSLFDLQETFDQQVVAEQTDVRNRAIAAIQTRLSSHLGQGQAVRICDDVPHWLGEHL
+GTAGASEVRQAIKNLQKAGIAQGYTKDMVDGRAVILPARRGR*
+>NZ_CP040019.1_2061
+MVAHATFFTEQKPAAAFKLKVLEDYLTAWSMKVASRPPHEVAYIDGYAGAGQYDDAHKGS
+PLYALDIARKLAPQNRSMHIHLVERDRAHAETLRRAVAAQGRSASPIHLHHGAVEAQIDA
+ILHQIAARPALFFLDPFGTALPYDVVASKLLLRPARSTEVLLNFSLSTVWRIGGIVRKGA
+TASPAEQLTLLRGDHFLGGPWWQEVFAHARAKADASGEDSPAATAASYVAREYMQRMTGD
+TNHRVISVPIRRTPSEGPIFILMLFYQHHAAPMLFADAAARAHKRWRQVNAGNYYRGLLD
+DAQGSLFDLEETFNQQVVAEQTEVRNRAIAFIEATLSAQLVQGQAVRICDDVPRWLGAHL
+GTAGAPEVRQAVKNLKKAGIAQAYTKEMVDGRALILPSRPAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002149.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002149.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cbd21768c8e6643676401eb4e9d3d1028aaad45b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002149.fa
@@ -0,0 +1,8 @@
+>NZ_CP042169.1_920
+MFHPWRALRTLTHVVVVWARPHPTAPAATDGATVIWLDPRMTQAERRCALTHELVHLEHG
+HRGCQPPAVEHAVRAAAARQLITLEQLADALPWSMSLDELADELWVTPLVLTDRLAGLTR
+TEREHLAALATEHSA*
+>NZ_CP040019.1_1898
+MFHPWRALRTLTHVVVVWARPHPAAPAATDGATVIWLDPRMTQAERRCALTHELVHLEHG
+HRGCQPPAVEHAVRAAAARQLITLEQLSAALPWSMSLDELADELWVTPLVLTDRLAGLTR
+AEREHLAARIPEHRDTV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002151.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002151.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c854173c7e3053f24f3c15c974406b5f9c60baa7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002151.fa
@@ -0,0 +1,16 @@
+>NZ_CP042169.1_923
+MATIQTRTNKAGRTTYRVGFYEAGRFQWLPALAREAGAQRVKAIVEDPRQGPTVARRILE
+AQVDSAPGMPTLAEFFPRYIEHRGLRCTPGTLAGYEAEAARTFLPRLGELPVDMIDRRTV
+AEWIRWQLQQPTARWRAVAARAAAATPPRPEPPLATVSPKTVRNAHALLSAVLGLAVQEG
+ILPANPARGADLPDDDVEEERGIFSRAEWARFYAAISESYQPLLIVLLVTGARWGEATAL
+QVRDLDVAASVIHVRRAWKKGKEGAVLGVPKTARGRRTIMLPDWAVETLEPLAAGRAADE
+FLLTVPGGGVIHRTNFVERHWKPALAAAGIAKHLTPHSLRHTFASWALMDGVPAQVVQHR
+LGHESLQTTSRVYAHLLLDAQRAAVDAIGWEPPPGA*
+>NZ_CP040019.1_1896
+MATISTRTSKKGVTTFRVGYYEGGRFRQMPAMLSETGARRIKAIIEDPAQGPDVARRLLE
+AHADGAEDVPTLAQCLDRYVEARAVRCSEGTLAGYRREAARTFLPRLGQLPVTAIDRPAV
+QDWIRWQMTQPTARSRAAAERAARAGTPAPSLEPVSPKTVRNAHSLLSSILYLAVQDGLI
+PTNPAHGQDLPADDVEEEKDIFTRPEWDRFYRAMTPHFQPLLALLITSGARWGEATALQV
+RDLDVDAGVIHVRRAWKKGAQGVVLGTPKTQRGRRAIMLPDHVVAMLTPLAAGRPPEDFL
+LTSPTGRVIHRTNFVERHWKPALAAAGITKDLSPHSARHTFASWALMEGVAPQIVQHRLG
+HESLETTSRRYAHLLLDAQRAAVDAIGWRPSPGT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002152.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002152.fa
new file mode 100644
index 0000000000000000000000000000000000000000..284225fb7cfdfe7adeabb8b7c7563529f6d7be43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002152.fa
@@ -0,0 +1,12 @@
+>NZ_CP042169.1_935
+MTPPTGVLPRAALVMRLLHEAGPAGLRLSQLVQRTGLPQPTAHRLLADLAEQGAVTRRGA
+AYALGDRWGPVGFEPVTPRCLIEREASRAVVQAAADELGDTVYLAARAAGGVAYLLRCDG
+DSPVRVFTVEVGEVKRLAAGYAGIALLASLPPERRRAEVDAVVARPPRRWNLTDDGALHD
+LLDTLLRQMDEQGWCGGVPVVPGVAGVACGVPARTGGIPQVSLTASAAEQRMPPARVPEV
+AEVLRAAATRLAEIGG*
+>NZ_CP033200.1_658
+MTPPTGVLPRAALVMRLLHEAGPAGLRLSQLVQRTGLPQPTAHRLLADLAEEGAVTRRGA
+AYALGDRWGPVGFEPVTPRCLIEREASRAVVQAAADELGDTVYLAARAAGGVAYLLRCDG
+DSPVRVFTVEVGEVKRLAAGYAGIALLAALPPERQRAEVDAVVARPPRRWNLTDDGALHD
+LLDTLLRQMDEQGWCGGVPVVPGVAGVACGVPARTGGIPQVSLTASAAEQRMPPARVPEV
+AEVLRAAATRLAEIGG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002154.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002154.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba5ee3b1d5ad52b85899208a4c78af116a709973
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002154.fa
@@ -0,0 +1,6 @@
+>NZ_CP042169.1_1004
+MTRSEDVIITQDAERSDVFALVESLADGQKPRALNVPAGEDAHTTPDTVETGREVPAGAL
+GALAALGAGLVLMARGRVRRV*
+>NZ_CP033200.1_727
+MTRSEDVIITQDAERSDVFALVESLADGQKPRALNVPAGEDAHTTPDTVETGREVPAGAL
+GALAAVGAGLVFLARGWVRRV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002159.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002159.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b762d267fa2290f982ea30b4f27c438d101a9766
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002159.fa
@@ -0,0 +1,8 @@
+>NZ_CP042169.1_1446
+MTASTTKSERARRQRTVYSKRLELRLTERQLQLASETAQRLSAIRGKRVTVSDYVRLLID
+DGGRGLVQRLERISQSPAGTLTQADADRVVAALQEVRDEVRRVGHNVNQMTVRAHQAKQV
+VDDLDEVKASLSQIDAHVLDAAKTFLGYEGTDEDEG*
+>NZ_CP040019.1_2158
+MTASTTKSGRARRQRTIFSKRLELRLTERQFRLASETAKRLSEIRDKKVTVSDYLRMLIE
+DGGKGLIQGLERVSHAPAGILSQADVDRIVAALQEVRDEVRRVGHNVNQMTKVAHQSGQV
+ADDLDGVKQALAGIDAHVLDAAKSFLGYEATDEEEG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002162.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002162.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be4e65b1b4312d58697e5a567ca94a110c4d3290
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002162.fa
@@ -0,0 +1,6 @@
+>NZ_CP042169.1_1449
+MSAPATAVTFPGVTLFLPDGVMTGDLTYDARTSQLAITYADGETEVLSIDLTLEGYVAAP
+GEALIKDWSEHSGFTAALVDAGIVMRVETLQIGPFDSRAYRVLVLTEAVTGR*
+>NZ_CP040019.1_2165
+MSASTATATFPGVTLFLPDGVMVGDLIYDARTSQLAIVYSDGETEVLSIDLTLEGYLPTP
+GEALIKDWSEHSGVTSALVDAGLVMRTETLVVGPFSSRAYRVLVLTPEVTGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002165.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002165.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76e6b9f38b62766a8697d73d6905a0029155fdad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002165.fa
@@ -0,0 +1,12 @@
+>NZ_CP042169.1_1557
+MCHGHDREGSDAGQSVSGRPAAHRAAADEGAERLHRSLTVLTTTGFLGGVEITIGLLAYL
+LTLHETGSHLLAGLAFSIGLVSLFLAHSELFTEGFYYPITAIAAGRGTWMELLRLWAVTL
+VMNLLGGTVMIALVVAGFPDLHGTLAESAHHFLDIGFSWQGAALAVLAGVAITLVTRMQA
+GTDSPTAMIVASVAGAIVLAGGSLFHSVMDSILIIGAILSGAHGVGWLEWLSWVWWVIPL
+NILGGLALTTAPRLLRSKEVREETGR*
+>NZ_CP033200.1_1280
+MGPVCHGHDREGSDAGQSVSGRPAAHREAADEGAERLHRSLTALTTTGFLGGVEITIGLL
+AYLLTLHETGSHLLAGLAFSIGLVSLFLAHSELFTEGFYYPITAIAAGRGTWMELLRLWA
+VTLVMNLLGGTVMIALVVAGFPDLHGTLAESAHHFLDIGFSWQGAALAVLAGVAITLVTR
+MQAGTDSPTAMIVASVAGAVVLAGGSLFHSVMDSILIIGAIPSGAHGVGWLEWLSWVWWV
+IPLNILGGLALTTAPRLLRSKEMREEKGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002166.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002166.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3abd3146cc8e99e33970acf7beb2aa06101e16cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002166.fa
@@ -0,0 +1,10 @@
+>NZ_CP042169.1_1558
+MFSASVIDDATGVNMGIGFLGVALAFGLTVVAMAYAVGHISGGHFNPAVTLGAALAGRLP
+WKLTVPYWIAQLVGGVAAGGVLLAIASGRPGYSLAENGLATNGYGELSPAGYSMGAVFLT
+EVLLTAVFLYVILGATDRRAPSGFAPLAIGLTLTLIHLISIPVSNTSVNPARSFGVALFA
+GGDALGQVWLFFVAPLLGAAVAGLSYRFVFPNTSRVTEELPEPAADGTRDAV*
+>NZ_CP033200.1_1281
+MAYAVGHVSGGHFNPAVTLGAALAGRLPWKLTVPYWIAQLVGGVAAGGVLLAIASGRPGY
+SLAENGLATNGYGELSPAGYSMGAVFLTEALLTAVFLYIILGATDRRAPSGFAPLAIGLT
+LTLIPLISIPVSNTSVNPARSFGVALFAGGDALGQVWLFFVAPLLGAAVAGLSYRFVFPN
+SSRMTEELPEPAADGTRDAV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002167.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002167.fa
new file mode 100644
index 0000000000000000000000000000000000000000..39207b91a293df43af76e2832509dfa806a855ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002167.fa
@@ -0,0 +1,9 @@
+>NZ_CP042169.1_1559
+MSFLIPSVPVSCGCRREVREETGLEVTAGRLVAVDTRPSKADGRIGLRFLFRAVHPLTAA
+DVAAIRLQEDEASEHSFVTCQEARKLLRPAIARRVDAAWDAAHCVYLEDGRPAAGVDQPA
+G*
+>NZ_CP033200.1_1282
+MVNLLLSVTFACGVAIAGLHVVNRRFIAPMYDVVLNLAAFLAAVASSVLLGHVLPAVFAA
+LAVLAWLILAVRTVRARRAGHKLEVTAGRLVAVDTRPSKADGRIGLRFLFRAVHPLTAAD
+VAAIRLQEDEASEHRFVTCQEARKLLRPAIARRVDAAWDAAHCVYLEDGRPAAGVDQPAG
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002169.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002169.fa
new file mode 100644
index 0000000000000000000000000000000000000000..880954f3e767f1d3efacc7e0162194bac70583bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002169.fa
@@ -0,0 +1,6 @@
+>NZ_CP042169.1_1567
+MSISASEARKTLFPLIERVNADRDAVEIVSRKGNAVLMPADEYAAWQETAYLFRSPANAR
+RLLDAYERARAGSVEEHALDRMDGDA*
+>NZ_CP033200.1_1288
+MSISASEARKTLFPLIERVNADRDAVEIVSRKGNAVLMPADEYAAWQETAYLFRSPANAR
+RLLDAYERARAGSVEEHALDRLDGDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002174.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002174.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a869cfa2c914c66adc67338e304f987819760ceb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002174.fa
@@ -0,0 +1,12 @@
+>NZ_CP042169.1_1741
+MQIKDRTFLVTGGASGLGEATTRALLDRGGHVVVADRAGTAPEGAVFVEADVTDAVQVAH
+AVAEATRQPGPLSGVVNCAGIGSAAKVISRDGPQPLADFERIVGVNLIGTFNVIRLAAAA
+MAENEPDDDGGRGVIVNTASVAAYEGQVGQAGYSASKGGVVAMTLPIARELAAYGIRVNT
+IAPGLFLTPMMHQLPEKARASLGEQVPYPSRLGDPAEYAHLVTHIVENQMLNGETIRLDG
+AIRMAPR*
+>NZ_CP040019.1_1064
+MQIKDRTFLVTGGASGLGEATTRALLDRGGHVVVADRAGTAPEGAVFVEADVTDAVQVAH
+AVAEATRQPGPLSGVVNCAGIGSAAKVISRDGPQPLADFERIVGVNLIGTFNIIRLAAAA
+MAENEPDDDGGRGVIVNTASVAAYEGQVGQAGYSASKGGVVAMTLPIARELAAYGIRVNT
+IAPGLFLTPMMHQLPEKARASLGEQVPYPSRLGDPAEYAHLVTHIVENQMLNGETIRLDG
+AIRMAPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002175.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002175.fa
new file mode 100644
index 0000000000000000000000000000000000000000..224874cb4bbbcda4650724e2e7b02afbad3ffd84
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002175.fa
@@ -0,0 +1,12 @@
+>NZ_CP042169.1_1743
+MTRDIIRTERIGPVTVIHLQDDRALNALGSALVAGLADALEHAQQDPEVRAVVITGSDRA
+FCAGAHIPEVLALREALTADPDAEVYLDRLFDLLAASPQPVIAAVRGLALGGGCELALAC
+DLVVAGESASFGLPEVRLGVIPGAGGTQRLVHAIGKAKATRMLMTGESVDAAWAESAGLV
+AEVAADEDVVARAVDIARRAADNAPGAVRLAVGCARRAQDLSLTDGLAHERRAFLEALAS
+DDAAEGMSAFAQKRRPVFGSR*
+>NZ_CP040019.1_1062
+MTRDIIRTERIGPVTVIHLQDDRALNALGSALVAGLADALEHAQQDPEVRAVVITGSDRA
+FCAGAHIPEVLALREALTADPDAEVYLDRLFDLLAASPQPVIAAVRGLALGGGCELALAC
+DLVVAGESASFGLPEVRLGVIPGAGGTQRLVHAIGKAKATRMLMTGESVDAAWAESAGLV
+AEVAADEDVVARAVDIARRAADNAPGAVRLAVGCARRAQDLSLTDGLAHERRAFLEALAS
+DDAAEGMSAFAQKRRPVFGSR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002184.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002184.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e321ef0e04ef9b9572ed52f5a82c7e820d142d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002184.fa
@@ -0,0 +1,16 @@
+>NZ_CP042169.1_2174
+MSAGRITVVKGDERLASIPLERVSAVVVHGNVDLSGALLRELMWRGLPCVWCTGAGRVVG
+WTNGVKPPNGGARFRQFAASAEGRVDIAREFVVAKVANQATILRRFGGMPAVVKRLRSAT
+RLASTATSTGQLFGIEGRAAAEYFAGFPGLLAPGVDAGVAESFPGRVGRGATDPLNIALN
+YGYGMLLSEVIRAVLACGLDPHAGVLHSSGRNKPALALDLMEEFRPPVVDSAILAAFNNG
+ELGRLSFTHVLGGARLTQS*
+>NZ_CP097650.1_2111
+MDEKAPKVAQIQQGVADHARVDVPTTREAQTMRGIDVRDPSLGLHGRVDRVERLPSGRLR
+VVEHKATPVKRAVRINDANRLQLVLQTMALESQGNTVEDAEVYFTTHHRRVPVEISAADR
+KAARDAVASARSVVNGETAPAPLLGDPRCMRCSHASVCLPEERQEEEVLSRIVPPDPAGE
+TLHLTVPGSRASMSAGRITVVKGDERLASIPLERVLAVVVHGNVDLSGALLRELMWRGLP
+CVWCTGAGRVVGWTNGVKPPNGGARFRQFAASAEGRVDIAREFVVAKVANQATILRRFGG
+MPAVVKRLRSATRQASTATSTGQLFGIEGRAAAEYFAGFPGLLAPGVDAGVAESFPGRVG
+RGATDPLNIALNYGYGMLLSEVIRAVLACGLDPHAGVLHSSGRNKPALALDLMEEFRPPV
+VDSAILAAFNNGELGRLSFTHVLGGARLTQTGRRKVIAAVERRLGTEFKHPVFGYRVTWR
+RAIEVQARMFLGVLDGSQEVYKGVRVR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002187.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002187.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2b0f6b1601fa9bbce59a1878e521387a42a9576
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002187.fa
@@ -0,0 +1,20 @@
+>NZ_CP042169.1_2180
+MGGLVISADFPLGVYTGHGPDGGAERFPDVARLFSALVQAAAAGTLSTGDPEAPFTAESL
+AALDWLEEHPPDALVLPGHTPVAPGVRRFAYRKEGVFLKEVGKTNYKVTGRPVSDGTALG
+GPVQWVWDDGPSGTDTQVCSTLEQLCADVPHLGEASSPVRLTVHEGEGLPAPTHRRDRNA
+SLRAVPGAVRQAMPSPGRRAELDRAHAATTLGRKPSASGDKHTTSAVPHATLPPRDHLRS
+GIFAPVEHHEPDVPWTQVLAVPVIGANSTVPEERYVSVCVALHRALVSRLGPDAPPEITG
+RYAPSVAPPANRVALHLAPGDLPNLPFSDGRDRFLVLVPRGMPGPALGMLASALAGVRRV
+VTSEHQLTVAPEEIEVYDGTEFWKAPTEGAVRTWDAQPAVVVERRLKSKPPIRDVDLAAA
+WSLGNVLRDVEPAFATKDPVARHAAVVESGAQLRGRAFRTLTPTAYVHRTDRRSPIEPFR
+LTLTLSTAVPDRAILALGQSRHLGCGLLVPTDIPGSTQERS*
+>NZ_CP097650.1_2114
+MGGLVISADFPLGVYTGHGSDGGAERFPDVARLFSALVQAAAAGTLSTGDPEAPFTAESL
+AALDWLEEHPPDALVLPGHTPVAPGVRRFAYRKEGVFLKEVGKTNYKVTGRPVSDGTALG
+GPVQWVWDDGPSGTDTQVCSTLEQLCADVPHLGEASSPVRLTVHEGEGLPAPTHRCDRNA
+SLRAVPGAVRQAMPNPGRRAELDRAHAATTLGRKPSASGDKHTTSAVPHAALPPRDHLRS
+GIFASVEQHEPDVPWTQVLAVPVIGANSTVPEERYVSVCVALHRALVSRLGPDAPPEITG
+RYAPSDAPPANRVALHLVPGDLPALPFSDGRDRFLVLVPRGMPGPALGMLASAVAGVRRV
+VTSEHQLTVAPEEIEVYDGAQFWKAPPEGAVRTWDAQPAVVVERRLKSKPPIRDVDLAAA
+WSLGNVLRDLEPAFTTKDPVARHAAVVESGAQLRGRAFRTLTPTAYVHRTDRRSPIEPFR
+LTLTLSTAVPDRAILALGQSRHLGCGLLVPTDIPGSTQERS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002191.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002191.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8dcd6092dedee53b8743e4c997cd445a006d3612
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002191.fa
@@ -0,0 +1,12 @@
+>NZ_CP042169.1_2204
+MPDLPACLEREPLTRAVVTGYAAKVTAEDRAVQRDAFIAAMVWGYGRVGYGPSRVERIMA
+QPGFEEQLADVTRITLEQGGPAAFEHIRQQRKSGVGCLKHLGAAFGTKYLYFLTKAHRES
+DIAPVLDSVVRAWFAEHAKDVDVRIGGGWTYPRKYATYVETMQAWGEELKIPADDVERLI
+FLQQQDATQEPWRESWSSAAADPEAGELLEALRLALADLGAGDDAEPHLQALEDVIADAE
+DRAPDEA*
+>NZ_CP097650.1_2137
+MPDLPACLECEPLTRAVVTGYAAKVTAEDLAVQRDAFIAAMVWGYGRVGYGPSRVERIMA
+QPGFEEQLADVTRITLEQGGPAAFEHIRQQRKSGVGCLKHLGAAFGTKYLYFLTKAHRES
+DIAPVLDSVVRAWFAEHVKDVDVRIGGGWTYPDRYRTYVTTMQAWGEELKIPADDVERLI
+FLQQQDATQEPWRESWSSAAADPEAGELLEALRLALADLGARDDAEPHLQALEDVIADAE
+DRAPDEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002192.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002192.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92f22db386ac470d58fa4df52adb7dad1347e8bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002192.fa
@@ -0,0 +1,25 @@
+>NZ_CP042169.1_2223
+MSTFQTPQYTIVELLQKARSGELQLPDFQRPYRWDDERIRSLLVTILRGHPMGVIMTLRT
+GGQNVRFKPRPITGVPAEGLKDPELLLLDGQQRTTSMVQALTGDGIVDTEDVRHHKLRRR
+YFVDVVKALGDVREQEDAVVSLPDTGIVTENIGRDVVLDVTTEEKQWELGLMPVTVLFDS
+ADCFAWMMKYQQALPERMEITQRFLSSVAQAVQTYKIPAIELDKDISKDAVATVFEKVNT
+GGLRLDVFELLTATFAGDRAYYEETGEDFRLAEDWALTEEVLRTYPVLTDMKSTDFLMAV
+SVLATLAKRREALAAGKTGQQVPQTSARREDILGMSLEDYRVWAPRLRKALPTVARHLRD
+LHIHDSRGAPYSSQVVSLLIITTLLGDRAEEHAVRARLNQWFWCGVLGELYGSTITTQLA
+KDAEQIPEWSLGKSAETPEAIIRASFSESRLGSLRTRLSAAYKGVYALIMAQQPPAKDWM
+LDQTLDFQSYDDLQVDIHHVFPRKWCDENGIEPWRRESIINKTPLAKKTNIRLRGDSPAV
+YTERLDDKGLTPQQVDAQISTHAIDPALLRAGDFDAFFNDRRRRLVSMIENAMCKPVVRD
+WEVDSESTDAPENFNDPAEMEADEPAGDEEAANVAD*
+>NZ_CP033200.1_1975
+MPDTFGHHPWTVQDLVSAVDSGHVRLPDIQRPFVWSNAKARDLMDSMYKGFPVGELMFWE
+NADPEHSRAIGTLEKSQSGSMQVIDGQQRLTSLYAVVKGKRVVREDYSQENIVIAFNPLT
+ERFDVPDNRIKRSSEWIQDIKTVFASPIDARSDYLDGLEKARGGERLSREDERRIEEAIN
+RLSRVLAYQFQVVQLKKEVSRETVADVFVRINSEGVKLSSADFILTWLSVFWEEGRQQLE
+DFARGSRFTPQELARMDETTVRWTPKNPYLTLDPGHVLRVVVAVGNRRAPLQDAYNALRG
+RDPRTREIVPANRERELAKLKDGQARALDPKNWDEFLKVIERAGMRTSAMVTAKNAVIYG
+YALWLIGRTEFGVPVDDLREVMARWYFMAQITGRFSGSAETRAQEDLNRLDGLERTPEAF
+TTAIDSLVSTTLTEDWWTVTLSEDLHTSNMSGPAYTGYVAALNILDADVLLSTLKVKDWI
+DPNRRPVKGVEKHHLFPKDYLKGALGLKSTRQINQVANQALVEWSDNIDISNEAPSAYWP
+AQVTEKAIQGERLAKQTWWHALPEGWTEMSYTDFLAARRKLIAGVTREGFRKLSDPNYQP
+SPPAHPVPASEPVLPTFEQLVLAGALPVGTHLLPTDGRTDSIAEVTPDGTILLDDQEYTS
+PGLAAKADGAEDEDGWLYWSADLAGQATILDEVRRRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002193.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002193.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27a7678b710e7b773a7d7be4a3d8e3452601cf02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002193.fa
@@ -0,0 +1,6 @@
+>NZ_CP033200.1_15
+MSAPLPSHLTIVQSADLLQVSRDTIRRLIASGDLKAYRIGPSTNRRRPIRVDRDSLLALR
+EPVTSLAALKAGEAA*
+>NZ_CP040019.1_29
+MAAAASKPRPSFDPRPRLTIAEVADYTGTSPSSVRRWIARGELRAYKYGPRAIRIDPADV
+DAMRQPVTSLADLRGGDAQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002199.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002199.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f2fa302f286445060a07ce6fd17c312c82c4411
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002199.fa
@@ -0,0 +1,10 @@
+>NZ_CP033200.1_287
+MSTERDALFQGVEGAGGPSQAAGEDMSASETSDTATACHSGVQVEQQTDSQVNTGRADAE
+AVRQSHGGAKRRRGGGGRLDTRFDDATLAALRTRAKRLGLAPSTWVRTVVRDALHASRSE
+ELDAAVAAQLLGVEERVQASADARELAAQVRPLAINVNDLDRRARAGEPVALSAEVPELI
+ELLHEVRALLGDRAAS*
+>NZ_CP040019.1_2322
+MSADQHPLFQGIEGGGAPSQAGLEDTSVSDVSDRPTACHSGVQVEQQADSQVKTGRADAE
+AVRQSHGGAKRRRGGGGRLDTRFDEATLGALRTRAERLGLAPSTWVRSVVRDALHASRSE
+ELDAAVAAHLLGVEARVQASADARELAAQVRPLAINVNDLDRRARAGEAVALSAEVPELI
+ELLREVRTLLGDRTAS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002205.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002205.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3ba22db8ea3b37fe6d076dcf5d5e3871d57cba0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002205.fa
@@ -0,0 +1,8 @@
+>NZ_CP033200.1_318
+MLLPLLGRLRVARPVGRPRTRPEAVLGDKAYSSRAIRTHLRARRIKAVIPEPADQQGHRR
+RRGSAGGRPVGLDSQAYKGRNVIERQYAHLKQWRGLATRYDKYAIVYRAAVVLNAVLAWS
+KRLSDMP*
+>NZ_CP083691.1_2183
+MLLPLLGRLRVARPVGRPRTRPEAVLGDKAYSSRAIRTHLRARRIKAVIPEPADQQGHRR
+RRGSAGGRPVGLDSQAYKGRNVIERQYAHLKQWRGLATRYDKYAIVYRAAVVLNAVLAWS
+KRLSDMP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002208.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002208.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1dc52afd1f69256a9c656fe4c0e62d2e90a56d88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002208.fa
@@ -0,0 +1,11 @@
+>NZ_CP033200.1_663
+MQNTEQTPRDASTEAGGRLWRHRIVENDTLRMTVLSMLAAAVAIGLSTLLIATPLGDALG
+VGAARRASWMTGLMTLCLMWSIYSALDTVVLYRWLGRRDSTDLHALLRTRSRGPKESVDP
+VGWRALMLGASSTLGNTATFSVMAMLVVVISMWMPEVRSVPAMRLLAVATVLASWASIVL
+AQALRYARLAAQHDPKRSRPEGESPAPPIRFRGSDSPVFSDYVALSLTLSTMMGAQDVVL
+SGRAARTAVREHALVGFLFNSMIIAALASLLLTVA*
+>NZ_CP083691.1_1490
+MDSDDGRLWLATLPALAAGASGVLIGREAAAEFPSADWRVMFYGTLGVTQVVMYVVYLWL
+TLRRFHGLDARTLERDLRTVSRGPRPGSWAVRMGLPYGSTLGWMTSVSVVALVIVVVVML
+DPATAGQPLLRVLCALVVVSSWAVLWVSQALAYARMAAQHGGIEFTGEEPPVFEDYLTLS
+AFVSALFGTGDVTLTGRRTRRAMRSHVMVAFGFNSMLVASLATLLLSRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002209.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002209.fa
new file mode 100644
index 0000000000000000000000000000000000000000..58771bb224c73be9fd7af880faa392dd12f42d8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002209.fa
@@ -0,0 +1,34 @@
+>NZ_CP033200.1_739
+MSADAWTGTATGDVAGRCHRDAHGVPTLVAASLPELAYLQGWHVATERAWQVDCEHRRVT
+GMGAEVFGPPAVANDVAARQMDLDGAARRAFDALDDAEDRAWFTRFADGVNAGLDAGARR
+APEFAAHGVKPLPFDPHTALALHLGYNVWLTNAPAALFRTLLAERFPALAAALISPRPDA
+DGSNAWAVRVGAEGAPLVAADPHRLLELPGVYQQVRLVVEAERPRDRVDVVGLAFPGVPG
+VPHVGQSEHVAWVTTSAMVSSLEMVLEDAPEGPEVLDARTERVHVRGGDPVDVRVAHTPR
+GRLVDVPGAGPVSMRFPAWDRADTGLPSARRLLTAASAAEACAVLDGHVEPVNRVIVADR
+RTVLTRHAGAVRRRDRRSAWGAARASALGRGSADGSLDQRWVRWPAPAAADDVVVAANEP
+HPDTACLTVDACAPWRSRRIREALEALAPQERTVDAMAALQTDTRTPGAPRAWLADAVDA
+LVADGVLAAESVPAWAGDAAAGSAAARWWLLVEHEVAAALIAHLPPASRALLGGPWAPWG
+DAAAWVGAALAERGPEPLRAALGITASTRDLVRAAVAAVDDAAEPPGPDGAARTWGEAHA
+LTPFLFTHEHPGGPDEPGLADVLDTIGSVRVGGTADAVCATSHAPGLAVGTHRGPVARVV
+FDLGDRTRSRWVVPFGASGLGGGHVTDQLDAWAAGRLLPVPSRPVPPSAGSGVAPARSVP
+GGAPPGRIVAEVGVGALGLTMTRVRPALDAPLIHALVTEPRAEFYGMRGHSVQDVEEVYD
+FLEFQPTHANHLVWHGGTLVALVQTYDPRAEEVGGAYEVRDGDLGFHFITAPGGLQGRAR
+ATAYRSIVDWLGARPGTRRLVIEPDVRNTRAVKTARALGFTVDREVELPGKRAALCFRDV
+R*
+>NZ_CP097650.1_956
+MSADAWTGTATGDVAGRCHRDAHGVPTLVAASLPELAYLQGWHVATERAWQVDCEHRRVT
+GMSAEVFGPPAVANDVAARQMDLDGAARQAFNALDDAEDRAWFTRFADGVNAGLDAGARR
+APEFAAHGVKPLPFDPHTALALHLGYNVWLTNAPAALFRTLLAERFPALAAALISPRPDA
+DGSNAWAVRVGAEGAPLVAADPHRLLELPGVYQQVRLVVEAERPRDRVDVVGLAFPGVPG
+VPHVGQSEHVAWVTTSAMVSSLEMVLEDAPEGPEVLDARTERVHVRGGDPVDLRVAHTPR
+GRLVDVPGAGPVSMRFPAWDRADTGLPSARRLLTAASAAEACAVLDGHVEPVNRVIVADR
+RTVLTRHAGAVRRRDRRSAWGAARASALGRGSADGSLDQRWVRWPAPAAADDVVVAANEP
+HPDTACLTVDACAPWRSRRIREALEALAPQERTVDAMAALQTDTRTPGAPRAWLADAVDA
+LVADGVLAAESVPAWAGDAAAGSAAARWWLLVEHEVAAALIAHLPPASRALLGGPWAPWG
+DAAAWVGAALAERGPEPLRAALGVAASTRDLVRAAVAAVGDAAEPPGPDDTARTWGAAHA
+LTPFLFTHEHPGGPDVPGLADVLDTIGSVRVGGTADAVCATSHAPGLAVGTHRGPVARVV
+FDLGDRTRSRWVVPFGASSLGGGHVTDQLDAWAAGRLLPVPSGPVPPSAGSGVAPARSVP
+GGAPPGRIVAEVGVGALGLTMTRVRPALDAPLIHALVTEPRAEFYGMRGHSVQDVEEVYD
+FLEFQPTHANHLVWHGGTLVALVQTYDPRAEEVGGAYEVRDGDLGFHFITAPGGLQGRAR
+ATAYRSIVDWLGARPGTRRLVIEPDVRNTRAVKTARALGFTVDREVELPGKRAALCFRAV
+H*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002211.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002211.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc6f759859c3e0ee594fe01f1a3a0f64930bc0ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002211.fa
@@ -0,0 +1,10 @@
+>NZ_CP033200.1_741
+MSAVTPPQTTVDGAAASAARRVELRPVGAQDHPLLHRWVTSPHAVYWEMTEAGLADVVAE
+YEAIAAHPHHHAHVGLVDGTATFLVEVYDPAHSELAGRYAGAPGDVGLHVLVAPTDTPVP
+GTTDLVMAAVVRWCLAQPGARRVVVEPDERNAAIRAKNLAAGFTELGPVALGSKTAMLSI
+ATPESFTASRIGVLAAGLDLTLPEPPLLLTPDRQVSA*
+>NZ_CP097650.1_958
+MSAVTPPQTTVDGAAASAARRVELRPVGAQDHPLLHRWVTSPHAVYWEMTEAGLADVVAE
+YEAIAAHPHHHAHVGLVDGTATFLVEVYDPAHSELAGRYAGAPGDIGLHVLVAPTDTPVP
+GTTDLVMAAVVRWCLAQPGARRVVVEPDERNAAIRAKNLAAGFTELGPVALGSKTAMLSI
+ATPESFTASRIGVLAAGLDLTLPEPPLLLTPDRQVSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002212.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002212.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef9859bc06283f6c02bb4020a29b92fc2ee39b40
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002212.fa
@@ -0,0 +1,18 @@
+>NZ_CP033200.1_742
+MSPASTSPRRVLAIGLGPFNLSLAALAHPLPDVEVEVVESRDAFVWHPGMMLPGAQIQVP
+FLADLVTFADPTSPYSFLAYLKAMGRLHRFYIRGSWYPLRREFSDYCAWVAAQLPGIAYA
+TTVTAVRWDDQADEFVVEAASAAGTSTHRADHVVVGTGTVPSLPAPLARVAEESARVGAS
+PVVHTGEYMGRREDIAGAGSVLVVGSGQSAAECALDLLNAGHPDLTWVTRSPRFFGMEVG
+QLTLELTSLDYERHFATLPRARRDEINASHRSLYKGISEYTIEDVYHALYERQVGPLDPA
+RLWPGTSVTDARLVAGPGAPRVEVTLRDEETGVTGGHVVDRVVAGTGYRHPDHPFLEPVR
+HLLRAEDGRTTANADHAIDVSGRRIFVHNTAEQPLGLTGPDLGMAAEHSGRILSTIAGRQ
+VYAQAESIAFQDFGAVAAGVR*
+>NZ_CP097650.1_959
+MSPASTSPRRVLAIGLGPFDLSLAALAHPLPDVEVEVVESRDAFVWHPGMMLPGAQIQVP
+FLADLVTFADPTSPYSFLAYLKAMGRLHRFYIRGSWYPLRREFSDYCAWVAAQLPGIAYG
+TTVTAVRWDEQADEFVVEAASAAGTSTHRADHVVVGTGTVPSLPAPLARVAEEAVRVGAS
+PVVHTGEYMGRREDIVEAGSVLVVGSGQSAAECALDLLNAGHPDLTWVTRSPRFFGMEVG
+QLTLELTSLDYERHFATLPRARRDEINASHRSLYKGISEHTIEDVYHALYERQVGPLDPA
+RLWPGTSVADARLVAGQGAPRVEVTLRDEETGVTARHVVDRVVAGTGYRHPDHPFLEPVR
+HLLRVEDGRTTANADHAIDVSGRRIFVHNTAEQPLGLTGPDLGMAAEHSGRILSTIAGRE
+VYAQAESIAFQDFGAVAAGVR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002213.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002213.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ae11906fff9f76c876fd3132bfbbef2f1bc75f4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002213.fa
@@ -0,0 +1,20 @@
+>NZ_CP033200.1_743
+MLPRLFGLGDPAAYLDATGRAARVAVDTAYDRAGVHPDTPSTHLADAVGAVDFSQPTGSL
+DDALAEVAELYAHQTTAYHHPRYAAHLNCPVLLSSTAADTVLGALNTAVESWDQARSAAL
+MEQRLLAEVGRWCGFAAGDGVFTSGGSASNLQAMTLARGRAVQRLTGHAGLADLPAEVLG
+SLRVFVSAATHYSIAKAAGLLGLGRHAVVVVPTDAAGRLDPGALAEAVEREVAAGAVPMA
+VVATLGTTDRGAIDPLPAIADVAERHGMWVHADAAVGGILAASAATRHELPGLHRADSVT
+MDFHKTFYVGLACSALVVRDAESLRHVTVHADYLNPEDSVHPNLADRSLQTSRRFDSLKL
+WLTLREHGAEAVVSLFAGARERTRQACGILRARPTFAVLEDPTLVTVLFRVRAEGLSEEE
+CTAVQAATHRELVAGGRALIATTVVDGVPHLKFTILNPAVTSGELEELVDVVEEAALRHV
+DAVRASRHRWRGVARTRPHGPSVAVSCTLPASAGPRPSAARVDEHGEQVCA*
+>NZ_CP097650.1_960
+MLPRLFGLGDPAAYLDATGRAARVAVDTAYDRAGVHPDTPSTHLADAVGAVDFSQPTGSL
+DDALAEVAELYAHQTTAYHHPRYAAHLNCPVLLSSTAADTVLGALNTAVESWDQARSAAL
+MEQRLLAEVGRWCGFAAGDGVFTSGGSASNLQAMTLARGRAVQRLTGHAGLADLPAEVLG
+SLRVFVSAATHYSIAKAAGLLGLGRHAVVVVPTDAAGRLDPGALAAAVEREVAAGAVPMA
+VVATLGTTDRGAIDRLPAIADVAERHGMWVHADAAVGGILAASAATRHELPALHRADSVT
+MDFHKTFYVGLACSALVVRDAESLRHVTVHADYLNPEDSVHPNLADRSLQTSRRFDSLKL
+WLTLREHGAEAVASLFAGARERTRQACGILRARPMFAVLEDPTLVTVLFRVRAEGLSEEE
+CTAVQAAMHRELVAGGRALIATTVVDGVPHLKFTILNPAVTSGELEALVDVVEEAALRHA
+DAVRAGRHRRRGAGRNRPHAPSASVSCTLPSSAGPRPSAARVVEHGEQVCA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002218.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002218.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dad2477a39784efa1f3c588967e49cca2134708e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002218.fa
@@ -0,0 +1,6 @@
+>NZ_CP033200.1_1701
+MNAKPEKDLRRTVDILFRPARVAVLIDGCYWHGCPQHYIAPKANGGYWSDKVATNRARDL
+ETTRILTERGWLVLRFWEHEDPAVVAERVVAVVNERRPRRTTGAS*
+>NZ_CP097650.1_1918
+MNAKPEKDLRRTVDILFRPARVAVLIDGCYWHGCPQHYIAPKANGGYWSDKVATNRARDL
+ETTRILTERGWLVLRFWEHEDPAVVAERVVAVVNERRPRRTTGAS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002219.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002219.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b490cc24740d5424e76120721863d7cf4dfb4ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002219.fa
@@ -0,0 +1,12 @@
+>NZ_CP033200.1_1703
+MNVFGPDILARTMSEPADPTKYGIRWQYHSRSDRHGKVASWGVAFDLLRSSSVMRQHARD
+GKIVLGVNLKLSDFETKKSKVLDLVIARPGGAATSARGESLVSLAQRYNMNLSGEEMGEL
+TSLPDIPVAPVGSVLVALEAKATMTAHVKSLPRLHDELTSSHISVHGESQTALAIGYAQV
+NVADVFVSSNPANVERIHLGQEPVVTSHKQPGDCQRVLDTLNTLRTRSSSIGIGFDAIGV
+TVLDLRNDDSPVKVVHSRPAPQPGDAFHYDSMIMRMATRYDTQFSGI*
+>NZ_CP097650.1_1920
+MNVFGPDILARTMSEPADPTKYGIRWQYHSRSDRHGKVASWGVAFDLLRSSSVMRQHARD
+GKIVLGVNLKLSDFETKKSKVLDLVIARPGGAATSARGESLVSLAQRYNMNLSGEEMGEL
+TSLPDIPVAPVGSVLVALEAKATMTAHVKSLPRLHDELTSSHISVHGESQTALAIGYAQV
+NVADVFVSSNPANVERIHLGQEPVVTSHKQPGDCQRVLDTLNTLRTRSSSIGIGFDAIGV
+TVLDLRNDDSPVKVVHSRPAPQPGDAFHYDSMIMRMATRYDTQFSGI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002222.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002222.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a1b44dece66c9fcbc4e53488635589798b03c9b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002222.fa
@@ -0,0 +1,6 @@
+>NZ_CP033200.1_1817
+MSIRYPLGYVENERKVYPQGYARERVSPGGDGEGRHDQETSAGGVSQMISLRIGRQNYRN
+VWLTRQGA*
+>NZ_CP097650.1_2036
+MSIRYPLGYVENERKVYPQGYARERVSPGGDGEGRHDQETSAGGVSQMISLRIGRQNYRN
+VWLTRQGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002225.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002225.fa
new file mode 100644
index 0000000000000000000000000000000000000000..87270749a3f4f0d11b2bcc35f5ff470173f007bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002225.fa
@@ -0,0 +1,12 @@
+>NZ_CP033200.1_1935
+MTARPVAPGIHLVQHANVNCYLIEDTDGLTLVDAGLPAVWRPLGHAVRALGRRPEDIKAL
+VLTHAHFDHVGAARRLVERLGVPVYAHRAEHYLAAHPYSYAHENPRALYPLRHPAALPIL
+GSMVAAGVFTVKGVRATAELTPGETVPVPGRPVVVPSPGHTHGHCALHLPDRDVLISGDA
+LVTLDPYTGRRGPRIIAGAATADSGLALRSLDALAATGAGTVLPGHGEPWHSGVASAVEE
+ARRHGPA*
+>NZ_CP097650.1_2173
+MTARPVAPGIHLVQHANVNCYLIEDTDGLTLVDAGLPAVWRPLGHAVRALGHRPEDIKAL
+VLTHAHFDHVGAARRLVERLGVPVYAHRAEHYLAAHPYSYAHENPRALYPLRHPAALPIL
+GSMVAAGVLAVKGVRATAELTPGETVPVPGRPVVVPSPGHTHGHCALHLPDRDVLISGDA
+LVTLDPYTGRRGPRIIAGAATADSGLALRSLDALAATGAGTVLPGHGEPWHSGVASAVEE
+ARRHGPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002226.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002226.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07fa385f6cb6f053fcf26cb1420ad6c92a8cdb6c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002226.fa
@@ -0,0 +1,10 @@
+>NZ_CP033200.1_1941
+MSESTSAAPQPSQSVPSRRRVASSLAWAVPTVVAAAAAPAEAASPLPRIDRVFQLTLAPG
+VPWTEPKVSPCASTLFTNPTRLSVTTDNSAFYYRITNLRADSTVTDVTASVLVQKSVVDK
+LSNGLTWTSETKDWSNPTLDVSGAKYIDNGIEYYRYYSTLRTAVPAPVSGTITLPRIQWY
+SNCSTNLLTQAQSTGVMANGRGSAVVNGTPLVNVGTYVRLTPRPAG*
+>NZ_CP097650.1_2179
+MSESTSAAPQPSQSVPSRRRVASSLAWAVPTVVAAAAAPAEAASPLPRIDRVFSIRRATT
+AAVPGASVSACGSGSTRLSVTTDDVNTYYRIANVRTGSTVTDVTASVLVQKDMVDAMETG
+KNPTTFTWTSSATPSWSTPVREVSGTGSPVLYTNNGIQYYRYVSKLSTPVPAPVSGTITL
+PIIGWYSNCSTTLAGVSVNGRGSAVVNGTPLVNVGTYRQL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002227.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002227.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b7709f32d4f67d5768f842957b901ffa615d2fa6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002227.fa
@@ -0,0 +1,4 @@
+>NZ_CP033200.1_1978
+MRVTSPQTLISAVFEAAERATNDLTHLIPDLDRDRAEYAVASVLLEEAWLSNR*
+>NZ_CP097650.1_1103
+MRATNQQALITAVFEAAERATDSITHLVPDLDRDRAEYALVSVLLEEAWVAQR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002229.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002229.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c24142461d4acfe199cbd1c7e4a47904151b3fa6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002229.fa
@@ -0,0 +1,10 @@
+>NZ_CP033200.1_2136
+MNKSEEAYARLTQKIETGELPPGAILSEAALIDAAETGRTPLREAVQRLIRDHWLLAGGG
+RGLQVPAISVDDQLERLEVRRSLEALAVGLACARADEEQLAAVAAHVRHLRTVEDLAAYV
+AAVGRSHELLRTIANNRYLADSLVPLQGLSRRFWLATTKGLPDEVERGRAFYVPALEAVT
+RRDAAGARAGVLALHDFLARSALDYAARRADHGSAEPPAPWAEGR*
+>NZ_CP083691.1_147
+MNKSEEAYARLTQKIETGELPPGAILSEAALIDAAETGRTPLREAVQRLIRDHWLLVGGG
+RGLQVPPISVDDQLERLEVRRSLEALAVGLACARADEEQLAAVAAHVRHLRTVEDLPAYV
+AAVGRSHELLRTIANNRYLADSLVPLQGLSRRFWLATTKGLPDEVERGRAFYVPALEAVT
+RRDSAGARAGVLALHDFLARSALDYAARRAAHGSAEPPAPWAAGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002232.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002232.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e98fe6fdee1aaa7fee9669a1d3368b53e456bfc3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002232.fa
@@ -0,0 +1,5 @@
+>NZ_CP033200.1_2176
+MTTENTASTDRASTEENLRAAVRFHVGRNDRIRKRAERAETEAAELRAALAQAHAETDRL
+RAQLTELPEAHT*
+>NZ_CP040019.1_34
+MSANERPTEADNLRQMLRFHMDRAERHRLRAEKAEAELAELRKKKEAHP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002237.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002237.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b3e61843946798979cc952ce598d74ab80310c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002237.fa
@@ -0,0 +1,12 @@
+>NZ_CP033200.1_2250
+MTEPRIAVVTGAARGIGAALARRMAEDGFAVAAVDLSAEACADVVGQIEEAGGTARAFAA
+DVAREESVAQVMDAVVAELGAPAVLINNAGVLRDNLLFKMSAQDWDTVMDVHLRGHFLMT
+RAAQRHMTEQGWGRIVNISSTSALGNRGQANYAAAKAGIQGFTKSVAIELGRFGITVNAI
+APGLIETDMTRATAERIGVPYETYVAKAAEQIPVARTGTPEDIAAAASFFARQEASFISG
+QVLYVAGGPKA*
+>NZ_CP097650.1_278
+MTEPRIAVVTGAARGIGAALARRMAEDGFAVAAVDLSAEACADVVGQIEEAGGTARAFAA
+DVAREESVAQVMDAVVAELGAPAVLINNAGVLRDNLLFKMSAQDWDTVMDVHLRGHFLMT
+RAAQRHMTEQGWGRIVNISSTSALGNRGQANYAAAKAGIQGFTKSVAIELGRFGITVNAI
+APGLIETDMTRATAERIGVPYETYVAKAAEQIPVARTGTPEDIAAAASFFARQEASFISG
+QVLYVAGGPKA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002242.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002242.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33722e761c95c63a49b6a96f02d1eb36394c4688
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002242.fa
@@ -0,0 +1,8 @@
+>NZ_CP040019.1_73
+MLLLDADTLIQAKNTYYAFDFAPGFWDWLDRGHAAGLLASVEAVGQELKRGHDELADWAS
+ARPSFFVQPGTAVPGSIAQLAAWVHGQAQYTAAARQEFLAGAGDLFLIAQAHGGSHTVVT
+SELSRPESKKRVMIPDACQAVGVPCVDLFGALRATGGLMLVLSPAS*
+>NZ_CP097650.1_1492
+MYLIDANAFIEASRHYYSFNLAPRYWSWLYEQSVAGTVGSIKAVYDEIADGDDDLSAWVR
+DNTPEEFWLEEDDDSVAAIIDLATWATGPTRQFTQAAIDEFMASADLRLVAQARALGATV
+ITREVPNAESKKRVKLPDAAAAVGVSCVQPFQAYERLGLRFA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002243.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002243.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d274cfd6120f58d6043fa32ec7f46e325d40243
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002243.fa
@@ -0,0 +1,16 @@
+>NZ_CP040019.1_74
+MTVRVAAAPDVLSWAAERAGWDDALAEKHFPRFHDWLTGTQQPTLKQLEEFAHKTHTPFG
+ALFLPEPPRMDLPIPDLRTVGGAGVSEPSPDLLDVVHECQLRQDWYRDEALRQGEEPVAL
+VGSATVDDDPEAVGARLRHELAIQPVQNKAGAESFRRRLVARLEGLGLLVMISGIVGGNT
+SRALDPQDFRGFALSDPVAPLIFVNGTDAPVAQHFTLLHETAHIVLGHSAVSGSRMRGGT
+GEEAWCNRVASAALVPLDEVRRARRDSAGVPLAELVEDLAARYCVSRSVIYLRLRVAGLV
+SEDVVSRHFEEQDADAPGRTPRRRRESGGDYYRTATVRLGKPLIRAVLRSTREGHTSYRE
+AMRLLGTHKIEVLHEMGRQAGVE*
+>NZ_CP097650.1_1493
+MTVRVSVSPDVLLWALDRSPDPDAVATAFPGVDRWVSGEAEPTVKQLHAFAARTGTAYGY
+FFLQAPPAIELPIEDFREGFEGERYRDPSVNLLAVLHQSLRRQDWYRDYAIENGFADVSV
+VGRGAGMSPLEAAADMRRELNYEVRSRVGNWSDQRKRLLAAFEALGGLTVVTSMVENNTH
+RPLDVDEFRGFSLIDDMAPLVFVNARQTINGQLFTLAHEFAHVWRGVGGISDEDLRYEPR
+NEVEQWCNDVASEFLVPSNDLRERYAGVSSLRLTEQIERLASIYRCGTLVVLQALRRNRL
+YDFEDFQTDYDAEVERLRRFERADSGPGGQFLYNQPYRIGTRLSRALISDAMAGRTRFTD
+AARLMSFKSMKNFDSYASYLGTVRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002246.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002246.fa
new file mode 100644
index 0000000000000000000000000000000000000000..811dbc8dbce6c407737b304e3248524c9a753622
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002246.fa
@@ -0,0 +1,11 @@
+>NZ_CP040019.1_96
+MTTALPDALRLTDEARERLHADCRHLHRHPELSMQEHATAAWIEEQLDEIGVERFRCGGT
+GVVGVMRHPGGAEGPVVAFRADTDGLPIEEDTGLEYASTARGTLPDGREVPVMHGCGHDT
+HVVSALAAARLLAAAPDTWGGTIVWVFQPAEETGAGAAAMLEDGLWDRAPRPEVVLGQHV
+MPLAAGKVQLIPGMAMALADSQAITFHGRQAHGSQPQDSIDPILMAAHAVTRLQGVVSRE
+TDPRDPAVVTVGTFHAGLKENIIPDSAEIALNVRTFSAASRDTVLGAIERIVRAEAQASG
+APEPSFRTIARFPRCHNDDEQSARVAAALRAELGEDHVLDGRPLMGSEDVGALADAIDVP
+LVYWFFGGFEGEDPAAFPGNHSPHFGPAMAPALDAGHRAALAGLLAYVGR*
+>NZ_CP083691.1_66
+MAAVAAELGEENVMEIGPLMGSEDVGALTDAIDVPLVSWFVGGFEGEDFGDNPANHTPQF
+GPVMEPTLTTGVHAALAGLLHYVGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002248.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002248.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4641c3a80019c6f62e5b048389c0654524ea2c9e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002248.fa
@@ -0,0 +1,24 @@
+>NZ_CP040019.1_109
+MNPTFSRRTGLRTLAAAVVAGTVTIQAPAVLARTAASTPAAGADGFRVLPYLMEPTATSM
+DLVWFSEREVPGTVVVSGPGLGDNHRGGRTRPAGTRVSTPEFQPLLAYTEKERAQSIKGL
+AQGSWLLGPASYKHRVSLTGLKAGKEYRYTVTQGGQRHTAAFRTADDGANWSDLRLIAFS
+DTETEPYGRIENREWELSMVTPYTEGSLPRPGEGSVWHQTFGSTTRYGQFTLKYPLTQDV
+ALRENIRHIDAAAPDLLLVAGDLGQGGGYQPGWDEFFRHFAGEHSDIASRVPLITSLGNW
+ETFAALNDGYGTAADRSPVVRSRNKYHAYFERTSAGTDRENPRFRGSYYRTDHGPLTILT
+LDSTNGVPDESVGAGLLSGAPFSGDDRNLTAATMPSDTQGSFTQAEYEAAFPTVFPGSTP
+ADADLPVLNPGHEQWAWTERQLADARAAGRIVIVEFHHAAYSVGVHGTPPNHEFPDDQSG
+VAMRVYTPLFEKYGVAVVISGHDEMFQRSWVDEDGDGVGFHSYDVGVAADGLRGEQYAKD
+ASGQWKPVRFNTHMEWTANTHEPETWADVDGVRQLVDGGMHYGHLQIDLKRRGREAEMTL
+TPMYVFPILDDEYRLVRTERRAYDDVQTVRFDRRGVPKPRR*
+>NZ_CP083691.1_77
+MNPAFSRRTGLRALAAAVVTGTVATTAPAALAKTAQHAPAVPAGADGFRVLPYLMEPTAT
+SMDLVWFSERPVAGTVVVSGPGLGNNHGNGRTRPAGTRVSAPELQPLLAYTQKELTQTLT
+GLPQGSWLLGAENWKHRVSLAGLKPGKEYTYTVTQGGRRHTASFRTADDGRDWSDLRLIA
+FSDTETEPYGRIENREWELSQVTPYTEGSLPRPGEGSLWQQTFGSTVRYGAFTLKYPLTQ
+DVGLRENIAHIDAADPDLLLVAGDLGQGSAYQPGWDEFFRHVAGEHSDIASRVPLITALG
+NWETFAALNGGYGTPADRSPVVRSRNKYHAYFERTGAGTDRQNPRFRGSYYRTDHGPLTI
+ITLDSTNGVPDESVNGPLSGAPISGDDRGLTAATMPTDTQGSFTQAEYEAAFPKVFPGST
+PADADLPVFNPGHAQWAWAEEQLADARAKGQIILVEFHHVPLSIGEHGTPPNHAVPDDQS
+GVAMRVYAPLLEKHGVAVVISGHDEMFQRSWVDADGDGVGFHSYDVGVASDGLRGEKYAK
+NAAGEYEPVRFNTHMEWTANTHEPETWADVDGVRQLVDGGMHYGHLQIDLKRRGQSAEMT
+LTPMYVFPILDSQYRLVRTERRAYGDVQLIRFDRNGVPLPRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002256.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002256.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb5d2a7c4f4aebd4e9018fb12722dc1f635f1c76
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002256.fa
@@ -0,0 +1,9 @@
+>NZ_CP040019.1_332
+MAALTAVVVLGVAGCTGPEGRTGTTTDGPGTSTSPPPVVQQSEAAAHPADNLPLGGEPWA
+VVTLTRGGEALDPGPWRQVRIVTSEPFILAAPELCPQPRFGITAVTESAWEATPDVAQPA
+IGCVSGHEDEAAVAALRELFDGTVQVTPPGGADVEMRLRRADVELVLSEEG*
+>NZ_CP083691.1_270
+MRPSAPPRRPRVTRMAAMTAVVVLGVAGCAGPEGRTGTTTTDGPGTSTSPPPVVQQSEAA
+AHPADNLPLGDEAWAVVSLTRGGEALDPGPWRQVRIDTSEPFILAMPELCPQPRFGITAV
+TESAWEATPDVAQPAIGCVSGHEDEAAVAALRELFDGTVQVTPPGGADVEVRLRRADVEL
+VLSEER*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002257.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002257.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8c824a929c84aaf7ffd2bb7a025024f524f1d025
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002257.fa
@@ -0,0 +1,17 @@
+>NZ_CP040019.1_334
+MGDDNARMIRRFRSSSTRRPLHRSLTRRGTRPRRRLHTDDRVSLPPSSVAGLFVVPFLAT
+HLFAWGLFASVYLIAHPGGDSVFTASMWRLTTDVAVNAGLAMEDSLLALTSTGVAVTVAL
+YIPVAAGQLVSPRGGGETQRRLGSLALATSGVFAGITTGAYIASMTHGAHPASMIPELLL
+QGLMIALSLQLGTHLFDDREELRSRLEDDERRLEMQLSDAALNSLSDDIQGKFGGDFTLP
+PMRQWAKAARTLTFRRILRLLIWFFGYLLAGAFLGALTFACTSLTLEREWDARTLALGAL
+IGIYAHFASGMITYHDQSTPALRWLVRAMGATIWLLLLTTGLVLLSASPSQGSASLGTAV
+LGVIHVLWRRRSPGEQGLRLSPFMLSHRINTTLAEEALTSVWSRQLHAGILPRPLLGTTC
+RTSPLRDAAR*
+>NZ_CP083691.1_272
+MVPFLATHLFAWGLFASVYLIAHPGGDSVFTASMWRFTTDVAVNAGLAMEDSLLALTSTG
+VTVTVALYIPVAAGQLVSPRGGGETQRRLGSLALATSGVFAGITTGAYIASMTHGAHPAS
+MIPELLLQGLMIALSLQLGTHLFDDREELRSRLEDDERRLEMQLSDAALNSLSDDIRGKL
+GGDFTLPPTRQWAKAARTLTLRRILRLLIWVFGYLLAGAFLGALTFACTSLTLEREWDAR
+TLALGALIGIYAHFASGMITYHDQSTPALRWLVRAMGATIWLLLLATGLVLLSASPSQGS
+ASLGTAVLGVIHVLWRRRSPGEQGLRLSPFMLSHRINTTLAEEALTSVWSRQLHAGILPR
+PLLGTTCRTSPLRDAAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002268.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002268.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6aa70cc9a170199dea5ed9e1908d2f4c3155b6c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002268.fa
@@ -0,0 +1,10 @@
+>NZ_CP040019.1_491
+MTLTAALLSFALLALLITITPGLDNALVLRYAGRQGSGAAFAASAGICAGLFVWALAASL
+GISALLAASEVAYTALRWIGAAYMVYLGVRMLISAIRGGYGAPGGSSVATVRSRDAFRTG
+FTVNLLNPKVGAFYVALIPQFMVTGVAPAAMGVLLAVVHIAVCMAWFVVLIALVGVVSGW
+LQRPSVQRGLDGVVGTALVGFGARLALAKA*
+>NZ_CP083691.1_427
+MTLTVALLSFALLALLITLTPGLDTALVLRYAGRQGSGAAFAASAGICAGLFVWAVAAAL
+GVSALLAASELAYTALRWIGAAYMVYLGVRMLIAAVRGTSGDHDGDAAPALVRRGQAFRT
+GFTVNLLNPKVGAFYVALIPQFMVPGVAPAVMGVLLAVVHIAVCLAWFVLLIALVGVVSG
+WLRRPAVQRGMDGVVGTALVGFGARLALAKA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002269.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002269.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f4c663cd6acf69350a699f75687f430ced4a35b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002269.fa
@@ -0,0 +1,12 @@
+>NZ_CP040019.1_494
+MTATPRPAARRFLEVDVFATGPLTGNPLAVVVDAEGLPAERMQALAAWTGFSETAFLLPP
+TDPEADYRVRIFTPREEFDFAGHPTLGSALAWLHAGGTPRTPGRLVQECGVGLVPVTVAD
+DGVLAFATPPLRRSGPLNEADVVRIAAGLGVEREAIVDHAWGENGPAWQLVRLTDADAVR
+ALRPRGHAELKVGVVGLEAAGAETACEVRAFAYGSEDPVTGSLNGALAQWLRGAGLVSPR
+YVAAQGSQVGRRGRIHVHDDGARIWVGGRAAVLVDGTIAL*
+>NZ_CP083691.1_428
+MTESHAPFPDSSPARPRRFLEVDVFATGPLTGNPLAVVVDAEGLTDGQMQAVAAWTGFSE
+TTFLLPPTDPAADYRVRIFTPREEFDFAGHPTLGTALAWLHTGGTPRTPGRGGGSTALVQ
+ECGAGLVPVTLAGDGLLAFATPPLRRSGPLGEEDVRAIAAGLRIDRDAILDHGWGDNGPG
+WQLVRVADAEAVRALEPRGHEELKVGVVGLEPEGAETAYEVRAFAYGGEDPVTGSLNGAL
+AQWLRGAGLVPPRYAAAQGSQVGRRGRIHVHDDGARIWVGGRAAVLVDGTLTL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002270.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002270.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46d9279ef99e532e35e8242390485f293406f304
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002270.fa
@@ -0,0 +1,7 @@
+>NZ_CP040019.1_496
+MSTLSEMHVIDFPGFPTVVVRGPGQSVDGLHHFMDTSFRALGAAMGQGVFAPAGPAFALY
+RGMTGQGLGESMDLEVGHPVDVPPAVPLDVDGVRVEPSSLPAGRLAVAKHTGPYELLPEA
+WEAFLDALRADGHEPGDLCWEAYDTEPGPDVDPETLVTGLAVPVRTVA*
+>NZ_CP083691.1_433
+MRIEPSDLPAGSLGVAKHTGTYELLSEAWPAFLDALRENGHEPGGLCWEAYDTPPTPDTD
+PETLVTGLAVPVRPAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002272.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002272.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7bbb6695bb5b3471d1ca3b00337010a5ff2374b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002272.fa
@@ -0,0 +1,7 @@
+>NZ_CP040019.1_505
+MVVIAGLAVRLAFDGAWTGPVGDALYAVLVFLGVAWAEAFPPARLVFGTTFTAADLGLYA
+VGVAAATAADALASRARHGSGLARGPAGS*
+>NZ_CP083691.1_460
+MSAPAAPGPTTTTPRRRSRLALAAAATVAAGLLVRVGLRGVPGAAAWTGPLGDALYAVLV
+FLLLAWIAPRARTLPLAAAAFGVCAAIELFQLTGIPAALGRAFPPARLVLGTGFLWSDLL
+LYLAGVLAAAAVDAALRRRAALSPRGSGPRGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002273.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002273.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7497802003cc73eea8ce77c7f905c3ac66653825
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002273.fa
@@ -0,0 +1,11 @@
+>NZ_CP040019.1_507
+MSLFETADDRVSVDVWSDVMCPFCLIGDRLLGQAADRAGHPVQVRYHSYQLQPDLPADRT
+RPVLDMLVDAKRMPREQVEEMDRQITARGAEVGVEFRQDIALAVNTRDAHRLSHVAAEQG
+LQHAMVQALFRAYFTQGRNVADHEVLADLAAEVGLDRQAALDALASDAHADTVDADVEAA
+RRLGIGGVPFFVVDGKYAISGAQPLEVFERALAAAWADKADGAPPAG*
+>NZ_CP083691.1_64
+MKVTVYSDVACPWCYIGKRRFETALAGFEHAEQVEVEWRSYQLDPTLPERSDLTEVEYLT
+RMKGLAEPQVRRMLDHVVMQAAGEGLTYDMDAIVVANSFPAHRVIQRARAVSAEAASALE
+EALFAAHFERGQDIGDAAVLAELGAAAGLSAEQVEEALTDERWAEAVRADLAEARAVGVT
+GVPFFVLDGKYAVSGAQPPELFAQALAQTWAERAPLRAFTPAAAADDDDAPLIGQACGPD
+GCA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002283.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002283.fa
new file mode 100644
index 0000000000000000000000000000000000000000..afd8eaf98d58c697838da63431be904966863bc3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002283.fa
@@ -0,0 +1,9 @@
+>NZ_CP040019.1_655
+MGEARRGTEQARLLRQVVLLHQEVRIHLCRLMGMHDTDYAALALLMRGRLGPSALASALG
+LSSAAATAVVDRLEAAGHAERLPHPQDRRRTMVRLLPASQEPVQAEVDRMADATGALLED
+FDERERAAIARYLAGTRDALEQWRDDVAARVAARDDVAAVDAEAGR*
+>NZ_CP083691.1_571
+MARLLDFLEKGVDVPEAIQSLDAASTALRESPMLSPISEPAPAIRPVSGELKGVTSAART
+LRRIIRLNAQIRVQMRLLMGLNETDYAALSVLMRAPTGPTELARNLHLTTAATTAVVDRL
+VSGGHAVREPHPQDRRRTLVRALPESRSQAMAEVQPMVDMVGDAMSGMTDQDRAAVERFL
+DSVADHMDAWRDDLTARVTQQAEQP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002286.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002286.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90ca7c3899b3da9a8bd7c4fdb5bd2a5f729079cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002286.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_719
+MLQRPLEPAQYVSLAYSDALIAAGVSASVGTVGDSYDNALAETVNGLYKAELIHSKRVWE
+SVEEVELATMGWVHWWNTARLHEALGYCTPAEVEATYTHDQDSAPVAS*
+>NZ_CP040019.1_729
+MLQRPLEPAQYVSLAYSDALIAAGVSASVGTVGDSYDNALAETVNGLYKAELIHSKRVWE
+SVEEVELATMGWVHWWNTARLHEALGYCTPAEVEATYTHDQDSAPVAS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002289.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002289.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0639379a94d1d740cd1923d8cdebf80fa03db7b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002289.fa
@@ -0,0 +1,14 @@
+>NZ_CP040019.1_757
+MAGGEAAVAWILGALRRELGAANLGEEDLEIVVERDRVWGSLWTVTAQGRRFWFKRPHAC
+LRREVPLRRVLSARAPGELLSTVAACAETGWQLTADQGPVLAQRAREDGPSHYVELARSL
+ARVQKSLTAADVAELRNIGLPVFETGDAVARLDEQLGWFSGLPAGHPAQCTAAERERAIE
+GMSVLVERWAVDARMLEGVVPELSVDHNDLHGGNAFVTAEGVRLSDWGDTVLAHPFASLR
+ALLVPVRNVFETEAMEQIRGAYLAEWGLGEDVGDVLDLAMMLAVPQRLSCWSALADADAW
+AEYAEYIAPLWREIGTPVAEVEVP*
+>NZ_CP083691.1_2352
+MTGTGVLDVAGRTAARDWIAGVLDLPAAALTVRVVRERSWGDVWRLSSPAGVHWFKAPHP
+RLRGEVPLRALLESRAAERVLPLVAADHERGWQLTADAGRTLAALARDDAGAPRPGEVAR
+LYAGLAGALAAMQEAVGEDDLRGRGLTEFDPAKAELSLLRELAPFRALPAAHPAHCTAEE
+EARAVAVRAALAMRWEDCGGPADPLGLDHNDLHGGNAFLGADGRVLVSDVGDAVLGHPGA
+SLRALLVPVRAEHGADAAETVRTAWLAARGQDHAAGRERLELAMLLAVPQRLRAWGALRS
+PETWAAYAEWITALWRDIGTPVDQLTTA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002290.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002290.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ed82ab050e95de40189a2930ec91b2ebebabbf7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002290.fa
@@ -0,0 +1,13 @@
+>NZ_CP040019.1_805
+MFRRTVGDHAEWKELISRSFVPLESEPLRPSRSFSGRLDVSEFGGIGLTTLAAGPHAVHR
+TERLAAAGGGGMFKVSLQLSGRGLLLQDGREVLLEPGRLAIYDTSQPYTLSFDRDFTSHV
+LMFPHTALGIAPGQAAQVTATALDEGHRLGPAVSAFLTQAADAMPVLDPATGGRLAHNVV
+DLVGTLVADLLGLPPRPAEGARPAPAEGTDDARGRQRAAVLRHIDEHLADPALSPASIAA
+AHFMSVRSLHLLFEGTGETVAATIRRRRLERCRDELGDPGNAGRPVAVVGARWGFADPAH
+FSRAFRARFGVTPGGYRRQAA*
+>NZ_CP083691.1_2427
+MAVTPAWRNATPEHMFGRVLRPDEFHTRARYASAAPAPELAPWVERYWSVCFDLDDGEAF
+RTATLDDPGVHLTVERGGVHRTAVPGPGVWVTGPQTARRFDVTLVGSGSTVGVAFAVGGT
+RAFSSGDPATVVDRSEPGAAWFPGASALGDVAESAVAAAAALDAFLAGLGPRSDPAYERF
+RAAYAAVDDPDVVRVEDVAARAGCDPRTVQRLFHRFAGVGPKWALRRARVIRAVGSLDRG
+FPGSLAELAAAHGWFDQAHFTRDFRRVTGETPAGYRARRRPDEPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002293.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002293.fa
new file mode 100644
index 0000000000000000000000000000000000000000..53cd4efa7780bced34387220d49688cfaba1ea78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002293.fa
@@ -0,0 +1,12 @@
+>NZ_CP040019.1_845
+MNDILTVGLVGVGRLGSAVGQLVAEAGHRLLVADRPGSRVFRSVVETLLPGADAVPLADV
+VERADVVILALPQPALADLDLARARGVLLDATNAWEYTDGPDSIHRMDPLAWTERVPGVP
+VVKSLNHAGYGELLMDARPAGAPGRRAFAVAGDDGAAVDLVASLVDSMGFDAVPTSAADA
+PLLEPDGAVFGRRFDEAGLREALPHAAARVG*
+>NZ_CP083691.1_783
+MNDTMTVGLIGLGKLGSAIGRLTAEAGHRILVADRPDDPVFGLVLESVLPEARAVPLAEL
+LQEADVVVLAVPQPALAGLDLTAARGIVVDATNAWEYTDGPDSEHRMDADVWAARAPGVR
+VVKSLNHAAYAELLADAREHGAAGRRALAVVGSDDDAVARASAYVDSLGFDPVPGPSAAA
+PLLEPDGPDSEHRMDADVWAARAPGVRVVKSLNHAAYAELLADAREHGAAGRRALAVVGS
+DDDAVARASAYVDSLGFDPVPGPSAAAPLLEPDGPVFGVRLDADGMRAALAEGLEADSAR
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002295.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002295.fa
new file mode 100644
index 0000000000000000000000000000000000000000..111e2ddda580f03b015f73111587e0637fd61307
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002295.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_880
+MTSTPTRAKRKQTARELAERFGVSPRTIRRTVAQERADYLADAAARHERIRALRAEGLSM
+RAIAAKEGVTVGTVHYAIHKDD*
+>NZ_CP040019.1_1293
+MTSTPTRAKRSQTARELAERFGVSPRTIQRTVAQSREDYLNEAAQRRARIRALRAEGLSM
+RAIAEREGVTVGTVHYALHKEDQQP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002296.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002296.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00b44a00bcee32fb91d58b6568270cc0cface81d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002296.fa
@@ -0,0 +1,8 @@
+>NZ_CP040019.1_891
+MSTRSSIPDAVDTDRTAGTIELLEPPREAVEWMASPAPATDLWWTATVCGEADPDWHRLE
+TTVAETIEVLVSWAQGHGLPLPYGAALRTYGNPPDLGLVA*
+>NZ_CP097650.1_1816
+MSAPGSITADGARGLATHRAPGAVELVEPPREAVEWMASSAPATDLWWTATVCGEEDPGW
+HRLESAAQIADLVHALTDPRDKLILEDEPPTRYAQIMLLGDGLFMVEIAKRFEGLGAYNW
+RIGRGRAADEAANDPQDLVQPLQELTAAETVEVLVSWAQGHGLPLPYGAALRTYGTPPDP
+GLGFDS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002299.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002299.fa
new file mode 100644
index 0000000000000000000000000000000000000000..91fa464ab800fef01e1705319108cedb3fbf2cec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002299.fa
@@ -0,0 +1,12 @@
+>NZ_CP040019.1_916
+MAAGGFTLGLGQPLTMSLVTQAVPADWRSSALAVRLMGNRAGQVVLPATAGLLAAPLGPA
+AAVWFACAVLAASGLERTAAARRRR*
+>NZ_CP083691.1_846
+MTESRTGAAAGERTTAGPGAGWLWALIGAAVLTQAATNLARPVTSYHLLSLGAPDAAVGL
+ATAAYALLPLVGALWLGRVTDRLSSAAPLVVAGAAVVAAGAAGLALATDVAAVLAASAVL
+GVGHLAFTIAGQAAIARRAPAHLLDGAFGWFTAAFSLGQMLGPLLSGGILTAVGGTPRDA
+TTLALWVSAGLALAGALPVLLAPGAPPGTRDPAAREASAESGAAPGDDAGRPTVRAILAR
+PGVGSAMLASLALLAVLDILTAFLPVVGERHGVSAAWVGALLALRGAGSLVSRVFLPRLR
+RRFSRELLLAVALWASAATIAAVPVGMTSGLLWLAAAAAVAGGLTLGVGQPLTMSVISEA
+VPHAWRSTALAVRLMGNRLGQVVLPAAAGLAAAPLGPSAAVWTACAVLAVSGAERAARSR
+RRRPPRSVRSGGGRGGSASADQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002301.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002301.fa
new file mode 100644
index 0000000000000000000000000000000000000000..29e16397356c535b8e950143bf02316dff7e84ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002301.fa
@@ -0,0 +1,10 @@
+>NZ_CP040019.1_930
+MTPADHRPEPDTAPEPEAFPALEDPYRRSLLTNEQRNAWAALSAASLGLVSQMESDLHRD
+AGLTPFEFHLLYVLGAEEVSREAEGTMPMSRAAQLVDSSLSRLSHVVRRIEERGWVERRP
+SAEDARVTLVGLTPEGRRRMEAAVPVYDRMVCRVFVDHVAEEDLAEVTRLSMRLLAGLRE
+GHWLLDAMDPHGSRRAGVAGADAGADAGAVTGATGESEEDSEGRPAS*
+>NZ_CP083691.1_869
+MTKDAHHEKDANAHPPLPPLPPVWLKDAGCSGADLAAWIALLQAASALQARVESDMHRGA
+GVTPFEAHFLAVLKEAGGEPLAMSRAAHLVDSSLSRLSHVVRRLEARGWVERLPSPEDAR
+VTLVRLMDEGRRRIDAAAGPHRALMEDVFVTALDAADRQEAARLSLKLLGVLRPGHWLFT
+EPTGPDEGADPDAASHVGEPLTSS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002304.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002304.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f4b7a8f0dcd0dac640e6a36d02c395448240645d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002304.fa
@@ -0,0 +1,10 @@
+>NZ_CP040019.1_987
+MDPVSTPTDPHRHPAPDARVRVQAGDAVVADGPLWARAALFAVPAVWLGLLIGISLIEAP
+LKFTAPGITIPLGLGIGRRVFFAMNLVEVVLAVVLLVALARVLGRPRGLTVPGPGRLWLG
+GLTAAGLLAVKAVAIRPFLNRRTDRVLAGVDDGGSSWHYLYIAVDGLLILTVVALIVAVA
+RHLLVRTTAA*
+>NZ_CP083691.1_930
+MSVPPHPTPAPDAPRPLPGAAPREAGNAVVVGGPRGARALLLAVPGVWLGLLVGISLIEA
+PLKFTAPGITIPLGLGIGRRVFFAMNLVEAVLAVVLLVALAKSLGRPRELTAPGPGRLWL
+GGLTAAGLLAVKAVFIRPFLNRRTDMVLAGVDDGGSLWHYAYVAVDGLLILTVIALIVLA
+ARHLLPASPGAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002309.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002309.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f01bc0217b6832ba4b91d227ac3638ff8dcb5a3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002309.fa
@@ -0,0 +1,15 @@
+>NZ_CP040019.1_1190
+MVLGFGGSTVLILVVGLVYATAIRALPRTGGGVLFAVLSAGRIPGFIAGWSLALGYIGII
+AMNASAVSLIFRVTFPGLLSHGKLLEVAGWEVYLAEVLVSILFIWVFALLNMKGVEFSGR
+FQFWAVVTMLTCIAVLGVSAVYAFLTKNIELPAAVPSGQSPLTSVVVILAIAPWALSSKV
+PLVRAWAAILRSPDLMDNPPLHGAGVGPPAGCRGRRTRMGGGLHLSDSTGSIRRCATPGR
+R*
+>NZ_CP040019.1_1840
+MSHVTSSPPATGPGLKKTLSSLDAYAMGFGAMIGFGWVVLVGGWLKDAGTLGSIIAIVSG
+GLIMTVVALVYAELVAAIPKAGGEHHYLLRGMGARWSFLGSWGITGGYISIVAFEAVALP
+RTAAYIWPEIESIPLWNAFGSDVYLVWALVGAGAAVVITWINYIGVKLAGIVQTIVVATL
+LVIGALLVFGAGTGGSVANFEPLFTDARGLFTVMIVVPFLFVGFDVIPQSAEELNMPPRR
+MGVMIIVSVAAATLWYIMVILTNASSMPREQLVNADLVTADAMAALFHSPAMANVLLVGG
+MAGILTSWIALLMGAARLLYAMGVSGMLPRWFGHIHPKYRTPSNAVLFIGVLSIAAPFFG
+AGALGWFVDSGSPSIVFTYMMVCIVFLLLRRREPEMDRPFRAGGATAGRVLGVTGVILTA
+GLLSLYIPGMPASIAPMAYAFFGLWWLLGLVFLFRIPRGITPGEDAEERLLERLARR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002311.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002311.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dfa469aebad7cfce4ffed35840cfbe5e8db825fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002311.fa
@@ -0,0 +1,10 @@
+>NZ_CP040019.1_1250
+MVKKLEQNMGADAMRAATGRDHAGWRAVLQDAGAQQWSHPRIAAYLVEEHGVDGWWAQGI
+TVDYEQAHQGRLPGQQADGTFSVGLTRTVPGERLEALARVEAAVSAVHGEPHGRNLTASQ
+PVVRWRLPDGGRLAAAAQAPNKTGTPVNLTMQRLPDAAAVEPTRRALEELLEAARSGEGP
+VATPGR*
+>NZ_CP083691.1_2008
+MSTSPARGANLNAIAEATGLTFEDWAAWLDARGARDLTVHAEIVGLVLERMRSGETAEVG
+SPEWWAQGVTVAYEQHIGRRRPGQRADGTFAVTASRILEGTREEVHARAVGAVRAALSDG
+GALRGVGLAKEPTESATATRLFWRAVLADGTRAELATEPRPQTAGKPAKAAVVATHSRAA
+SAEEAAAWKAFWRNLPAAL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002312.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002312.fa
new file mode 100644
index 0000000000000000000000000000000000000000..109d3f64834add0e8eb975349e89186b0fe1b5e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002312.fa
@@ -0,0 +1,11 @@
+>NZ_CP040019.1_1274
+MSADIDAYQDQLVAWRRHLHQHPEASFEEHETVRYIRAELEPRLPGATFENLTPTSLVVT
+LDTGRPGPTLGLRADIDGLAMTEDRPDLDFASTTPGRMHGCGHDGHTATIMSALVWAHDH
+RDELTGTVLGIFQHAEETPPGGAKEMVETGRFADVDYFFGFHYWSTLPTGTVDIKPGPAS
+ANSDRFEVHLRGEGAHASTPEDAVDVVTAASSLVQQLLLIPSRRVAGLDPCVVSTTWMDA
+GRQSALNVYPPEAHIGGVVRTHDDDVRDTVEAAMRDMVRGLETANPGLSCELDYLRGYDM
+VWNDPARTAVVHELCEDLFPGSVITDPPMLGGEDFAAFSRTAPATYVFVGAGNAAKGFDA
+GHHNPRFGLDEDAFPIALRLVVEVLRNGPRLAAG*
+>NZ_CP083691.1_1182
+MVQELCEDLFPGSVITDPPMLGGEDFAAFSRTAPATYVFVGAGNAAKGFDAGHHNPRFGL
+DEDAFPIALRLAVEVLRNGPRLTAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002316.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002316.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc126709ac2f7f4401b768bf4369fb06aa938f24
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002316.fa
@@ -0,0 +1,9 @@
+>NZ_CP040019.1_1659
+MLSFGIREAAGSQPATGPRRTGRSPPLEASSGASGRQTHAPSSGSRRHPCTGACAGRTTS
+VSHSVVSGFHPARTVATSSSSGRQRVAEARQPRAVRWTASHSWATQSRSGTTHRPALPFT
+RCQSWPLEALTSRGTLRHSRTESSGLLILYVRRTPSTGVTAADPAPESSPLRSNPAGSCE
+TLATMPTGIDHQILYRFAVGSAGVLPLRGLPPAAPPVPRPRGRLGGPGAADSGRLVPTGR
+SSTGSPPAGRPSGEPALSPAHARSPVSGLHGRADPLPARPLRRDPASTSPPPPFRPEQHG
+RVLPPPGPRGRGQRGPARADRPRLPDGTRRRAARW*
+>NZ_CP097650.1_1112
+MRSNPAGTCETLATMATGIDHQIPYRFAVGSAGFLPLRGLPPAAPPAPL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002321.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002321.fa
new file mode 100644
index 0000000000000000000000000000000000000000..05f6c8c5937b3d46f72e0a069bbc6263789b6bc8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002321.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_2279
+MTAFGIIWLIAVTLVSAVAVRGILRQSTGVHAADRNGSTSFLWFLVALAFLLTNLPSGID
+PFRAVGLHLGAAALLGFLLHVLTRGAPAARD*
+>NZ_CP083691.1_2138
+MTVIGIIWLSELTLVSGVAVRGLLLTHLPSGIDPFRAVGLHLGAAALSGFILHVLTRGSA
+SRAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002322.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002322.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4323324cebcdeab3bd0e094eef0a3d4fc07709e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002322.fa
@@ -0,0 +1,8 @@
+>NZ_CP040019.1_2300
+MRILGGFCYVAFITDVFTRRIVGWAVSASLHTQGLPLLALEHALLSTGASRGREGLVHHS
+DRGAQYVSLAYSDALIAAGVSASVGTVGDSYDNALAETVNGLYKAELIHSKRVWESVEEV
+ELATMGWVHWWNTARLHEALGYCTPAEVEATYTHDQDSAPVAS*
+>NZ_CP083691.1_295
+MYSRRIVGWAVSGSLHTAGLPLLALEHALVSTGASRGRQGLVHHSDRGSQYVSLAYSDAL
+ITAGVTASVGTVGDSYDNALAESVNGLYKAELIHSKRIWESVQAVELATMGWVHWWNTQR
+LHEALGYRPPAEVEAAYTHDQDPAPVAS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002323.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002323.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0daad286034b011c8b616c8ef22ce1b26e54577a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002323.fa
@@ -0,0 +1,8 @@
+>NZ_CP040019.1_2315
+MDENPSTAWTGTCGFRMLPTDDFAQGPSTARLTEVAGGAALALDYTWVHPEQGEQAGHLV
+LGRPDDGGRVTVAFTDSFHQSPEVRVLEGTAARTEGGGDAGRDRGAGAAPHPIDGDGVAV
+TMEYSGWGWTVAVRRQGGRLAMMMQNVVPAGVEGAEPGPYDVMRAAWTPAGA*
+>NZ_CP083691.1_2202
+MSLPSATDWTGTCGFRLYPTDEFSSGPSAARLTPVAGGAALALDYTWVHPDQGEQAGHLV
+IGRPDDAGRVTAALTDSFHQAPEIRVLEGASSSPEGDAHPVEGEGVAVSMEYSGWGWTVA
+VRLQGGTLAMVMQNVIPEGVEGAEPGAYDVMRAAWTRTDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002338.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002338.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5917ec39a870ab28c30df70d2d6401810441dad1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002338.fa
@@ -0,0 +1,14 @@
+>NZ_CP083691.1_314
+MGAPRELFAEHALRGEIVVLDYAAGRTRSGLPVRRHHVVVRAGDRLVHSFRWYVGAAREV
+FEVTLTFDEEWLPHRLWEPVAEAVRSARAPLAGEVDVPAVVPGAWDERPETVVVESGPGL
+DVAESLVEGLEVISASRKRWRSWSEADEVEQAVVRSMAPTLSARGGLRGRRTEVDVYAVL
+DEAVVVRRRWWGDQGTEIIEREVLRVPGRVAPWAMFVGMDVRAGWMREVSARRPVDAEAR
+SSDAEWEVIAGGERALGLLHGPRDVWAVSTGGGGLVAEWWQLPGEGLLGVFRDADSAQMM
+VGPVDGWTIYLLVLEAWLA*
+>NZ_CP083691.1_320
+MHPTVALRHFTEPADGNVASASFREAFLGGQEVVEGFLLLSYEAFFTGRGLPGRRHHVIG
+WEEDLVWHSVRWYVGSGAEIVELTLTAEAGADLEIWGGQCDRMIRNVVCQGAPEPASNLC
+WPEVPADVRAQDSWEVVTEQGLNPPWLESLRAGYDAVQEQAPWSAWAREPSLEQRRVLEQ
+ELPILSGVGERSGQGFRIEACLDGRGGAVVVVVPEGEGDGTNVRRGVRTVPVSLVVPVLL
+TWAGLRADWLRDEVMEAPGDVAPTEMAELWRGRRGADGVGSEASADWWRWWNQEGEVVAE
+WVQPLHRAPLAVFRDESRCVGVPVMPGVLYSVLQATVQEIAGSPHM*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002343.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002343.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e86858848737da4d394647ef939b69e4ee80d431
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002343.fa
@@ -0,0 +1,12 @@
+>NZ_CP083691.1_612
+MAINWRRAQYLLAEDLTDIPVRYIDELFGSNGIALGPENPQDVDTSVRRARMRRYLTTLD
+LDTNRADQQRFADVMAERYRKIALVHQHGNTDETQWKLERWTTLLRAAGFQVDTTALSVT
+WPPGPQMGTLAPDVLAHLNDPSAIEDHLERIHTTIDSDPRLAVATARSLMESTAKIVLTS
+RDKTYTATESLTKLVSRAQASLGMSPKDLGGEQPEVRRLLQSLQGIAAPISTLRNDTNVH
+HGAEVVPQWVRPRHARLVLGAAQLWCQTVLETLSDPTAPWRVTDAAAQR*
+>NZ_CP083691.1_680
+MAINWRRAQYLLAEDLTDFPVRYIDELFDGNGIALGPENPQDVDTSVRRARMRRYLTTLD
+LDINRADQQRFADVLAERYREIALVHQHGNTGETQWNLDRWTTTLQAAGFRVDTTALSVT
+WPPDPQMGTLAPDVLAHLNDPSAIEDHLERIHTTIDSDPRLAVATARSLMESTAKIVLTS
+RGETYTATESLTKLVSRAQTSLGMSPKGLGGEQPEVRQLLQSLQGIAVPISTLRNDTNVH
+HGAEVVPQWVRPRHARLVVGAAQLWCQTVLETLSDPTAPWRVVDAAAQR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002344.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002344.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0eed6584a15d525de9a62e4b9695431270db98bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002344.fa
@@ -0,0 +1,13 @@
+>NZ_CP083691.1_617
+MSTLLPIRPRPAPEEALDSYLERVATANGVTTSGFVRQLTTEARAPLRFTNIAPPPPILD
+VLASWTGTDRGLLQDCLLTRYPVIPFIDSQNRHGTRSVVAHGWVLLNRSQACPWCLAETG
+VWKITWRLAWVTACLDHDRLLATDCPGCQKPLRTTHHGALRPAGPGARCGNPRPQGQGKR
+CPFDLSRISPLSAPPPVLQQQRRVERALRGAEVEVAAIALEGTTYLRQLQALTSAAMGLS
+APTTAVQPEYSEGVPAEISTLSGRARPAPRPADIRAAAYVRRDRTIFAPP*
+>NZ_CP097650.1_2161
+MITPLPVRVTPGPNEAMDSYIERVAAANVLAITPFTHHLKRLSGSTLRFLNAAPSPELVA
+TLARLTDTPESALHELTLSRYEVVPEIHNHHRYAARAASAKGWFSLIRTQACPACVGEGQ
+PWASYWRLPWVTACLKHGCLLITRCPGCRVKLRSTRLQGLRAGGFTPLCGNPRATGRVPQ
+CEDDLGTTALTLAGQPVLVQQQVVLAALRGSTVFCHGEPVTGTEYLRRVRSIAVLLFHTV
+AISTATGLPAWAQKLRAEAQARTKERGPRWGVSAPDCPQSRAAVFLIAHQILTGPVGAGR
+GSLDVWLDLVPPSNEGTRAWAEDHTTTPDAISYLIG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002345.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002345.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a46b6799bcada69ec9c46d6f8cdfb002cbf918b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002345.fa
@@ -0,0 +1,20 @@
+>NZ_CP083691.1_618
+MTDQEHPPSALAPIVGESLSGYVRRFNATGLTPPLALPPRYADADLPPGLTDAVHRSTGL
+DAGQIRRMTMAGWPLILRGRGLHHRRGWALHRHDVWLCPSCTPLTGYRALRWRLALAPVC
+LRCHTLLTHERTFTPTRAATTEELARLRRLDELTTRALQGSKASRSHLSVLRRICAAGDA
+HEPDGDVLPRPPLGGTSRPAGNQRGTHPPGEPGIVMKQLATLDPALLNESRARAHLQQLQ
+HQDSLPSSFVVAPAPFQPESPTALALARARRRALLRQLTDLCAATGLRPQHIPTVVDPWR
+STRWSRLRDLEDQAFEALALHTLLLEALGEDATGSAVFVAHGIPAVVNQHDLLTRVRTRG
+TLTPGECDRLLARAQALVDDGLVDYAYRRGTLLAVPSLPRIPAVHLPRHPFWPARTLVPA
+WAWVEYARGLPDSGPAPDLSLESVDRFHADLDPEARLRLLEAFDTHVRGEDWAAIASAAG
+SSFPTFASAHQRSA*
+>NZ_CP097650.1_2162
+MSRPVHMPPLPGESLTGYLQRYRQSGMAPIRLDVTGVFDNASAPASVVVPVHTATGLAPE
+QIKAMTMDRWVPSIRGYRVQRRHGWKLHPHQWWICPQCTVKTGYQSLRWRLALQPVCLRC
+HTYLVDPENPQIPRPVPEATLKIVQSYDRILDDALSGSLSARQRLSGLRKTCKGMAQAMA
+HDQQPASAGAQPSTLTWWGAYPCGDPVTVGHLMTLTRAMVTRGPARRRTVPRRDRPLQSK
+RAVSGATVTAMSRARLRATVSKLAEWSQSTGLSPRHVPTIAQPSLYGTARRPSMVAQAGT
+TLALHMLLDEATGIPVSSARTRAAHGLSGEPLEHRLLHSVITRGGLEEDQQRLLLRTAED
+LITDGLIDFRLRRTVFRSQPHLPRLPTPAHWIPAGEEFSAETMTRAWIWMHVARGHPQHG
+PVASVRLDEIDDFDHLLDPETRMHLHESAAAQIDGPDLADILTTTTTHNRRARQQDLREH
+AG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002351.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002351.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e3959f44f2f5b4c1b60f6173d69fabd8bfc8a2fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002351.fa
@@ -0,0 +1,6 @@
+>NZ_CP083691.1_652
+MHAPFYSRAIPVHQIATITCGPDDGMNHGLLNWFVTGLATSPDGLRINNGGQAHIDMSTT
+EGLRSVVVVDDLSQTEQLICAVRTTCSR*
+>NZ_CP097650.1_1961
+MHAPFYSRAIPVHQIATITCGPDDGMNHGLLNWFVTGLATSPDGLRINNGGQAHIDMSTT
+EGLRSVVVVDDLSQTEQLICAVRTTCSR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002354.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002354.fa
new file mode 100644
index 0000000000000000000000000000000000000000..95a70fcbc57f021a003ac4197ba287cc253b66fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002354.fa
@@ -0,0 +1,13 @@
+>NZ_CP083691.1_679
+MSRRSLASLATAAAFVVTAVLGGAGPAAAGTTYSAPLRTAVASLPVAAENNAGYDRAAQF
+GDWKDANRDCQNTRAEVLIAESKTTPKFTTARKCTVATGKWVSSWDLRTHTSASTVQIDH
+MVPVHEAWGSGARYWTKAKRVAFYNDLGDARSLNAQTSALNSAKQARGPEQWLPPKNQCQ
+YIADWTAVKIRWGLKADATEKAFLVKKAASCANTTLKVTRY*
+>NZ_CP083691.1_2130
+MLGCSGCLGLVALGLLLLSLLVGGFTGSPSPSAASQAPDGRSAAPSAPDAPGDPAGSAPA
+PAPTPDRAEAPVSDRAEAPAPAPAPASAPAPAPGDAGEAAPSSPAAEAPAADGTALAALQ
+SLPVKGRAPKTGYSREQFGPAWADVDRNGCDTRNDVLRRDLADVVLKAGTNGCVVLSGTL
+HGPYTGEVIAFQRGPGTSTAVQIDHVVSLSDAWQKGAQGLSAGRRAAFGNDPLNLLAVQG
+SVNQSKSDGDAATWLPPLRSARCPMVARQIAVKARYGLWVTPAERDAMARVLRECPGQGL
+PAEGGPVDPSPETAAEPTPQAPAPTVQAPAPAPAAPAGGADPSFSSCRKAKAAGYGPYVQ
+GVDPEYAWYRDGDGDGMNCE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002360.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002360.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1aee8c86f2aff0aea486670d8842d02981213d9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002360.fa
@@ -0,0 +1,10 @@
+>NZ_CP083691.1_1173
+MTDRSDPRLQDESRLDAVKRAVEDVAQDAPTLAKIALEAMIRKHNPNLSGTAESAGRVGM
+RSGKVSELTAIARLKPGGAERLQRIFDLTRGNMDGAQRVSTLHDMRFVFFDDNTRILFAT
+AYDGDWDAYINDFATKIPELMDLLFQNVEGWPGIDSPTVKDFIADHQITASGWFVANPQV
+TVVDTRRLQRTEDAVNTFLDQMAGRTDLDEDTAAALKQLTDAISTPEAVDY*
+>NZ_CP097650.1_1484
+MTDRSDPRLQDESRLDAVKRAVEDVAQDAPTLAKIALEAMIREHNPDLSGTADSAGRVGM
+RSGKVSELTAIARLKPGGAERLQRIFDLTRGNMDGAQRVSTLHDMRFVFFDDNTRILFAT
+AYDGDWDAYINDFATKIPELMDLLFQNVEGWPGIDSPTVKDFIADHQITASGWFVANPQV
+TVVDTRRLQRTEDAVNTFLDQMAGRTDLDEDTAAALKQLTDTISTPEAVDY*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002361.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002361.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de27714f0a977c3fd40e8486ab0b4af2d8a12657
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002361.fa
@@ -0,0 +1,16 @@
+>NZ_CP083691.1_1174
+MTEPVTYTPDIEHSVDREEDLTREILAQMGAAQRRTAGEHKHAHRDAHAKSHAVLKATLE
+VHEGLAPELAQGIFARPGTYEAVARLSSAPGDIHTDRTPAPRGWALKVLGVEGKRLLPDL
+DSHNQDFLMVNFPTLAFGTVARYQEMLGLLEKNSQSPELLQRLTTGAARVVRGAVETVGG
+TPSATLEGLGRDNAHVLGETYFTQGALRYGDHVAKISLAPASANVRALTGQDMKVKDFSS
+ISEIVADFFSRESAEYVLRAQLATDAERMPVEDASVLWDEEEAPHQPVATLRIEAQESYS
+HPRRVYGDDALTFNPWNGVVEHQPLGSIMRVRKRAYEQSTRFRHEFNDRPAPEPTSLDEI
+PD*
+>NZ_CP097650.1_1483
+MTEPVKYTPDIEHSVDREEDLTREILAQMGAAQRRAAGEHKHAHRDAHAKSHAVLKATLE
+VHEGLAPELAQGIFARPGTYEAVARLSSAPGDIHTDRTPAPRGWALKVLGVEGKRLLPDL
+DSHNQDFLMVNFPTLAFGTVARYKEMLSLLEKNSQSPELLQRLTTGAARVVRGAVETVGG
+TPSATLEGLGRDNAHVLGETYFTQGALRYGDHVAKISLAPASENVRALTGQDMKVEDFSS
+ISEIVADFFSRESAEYVLRAQLATDPERMPVEDASVLWDEEEAPHQPVATLRIEAQESYS
+HPRRVYGDDALTFNPWNGVVEHQPLGSIMRVRKRAYEQSTRFRHEFNDRPAPEPSSLDDI
+PD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002366.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002366.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27dccae20eca0a489c7889fc54485d79adbed83d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002366.fa
@@ -0,0 +1,16 @@
+>NZ_CP083691.1_1848
+MWALVELGKRATSEPAAQLRLETLDDIEFDSAGSPAELLQIKHHTRGDGPLTAQAVDLWR
+TLNVWMDLPSADKLVLRLVTTRTLSEESGLIRLRDGENRDTSVALEELLKAARTSTSKAT
+DKWREKFLHLNETARVELVDRIIIDDGSLPAAHIDKELVRTFRYAYPTGRDDVFLHLLKG
+WWSGVSVQLLSRTLEAVTGQDLIVQVTEIADQLKSDALPIDPAVMQEHDESISDLYKDRP
+FVQQLLWIALENNRLWKAIRDYHRSFTQRSFWLRHQLLAETELDRFAFRLHDEWEQTFDS
+RIAAMKREGRTDHDVVGQEILEELARESRARLRDRFDEPWFNRGMFHALADGELGYRVGW
+HPDFESKLEEMLSHVSST*
+>NZ_CP097650.1_865
+MWALVELGKRATSEPAAQLRLETLDDIVFDSAGSPAELLQIKHHTRGDGPLTAQAVDLWR
+TLNVWMDLPSADKLVLRLVTTRTLSEESGLIRLRDGENRDTSVALDELLNAARTSTSKTT
+DKWREKFLHLNETARVELVDRIIIDDGSLPAAHIDKELVRTFRYAYPTGRDDVFLHLLKG
+WWSGVSVQLLSRTLEAVTGQDLIVQVTEIADQLKSDALPIDPAVMQEHDESISDLYKDRP
+FVQQLLWIALENNRLWKAIRDYHRSFTQRSFWLRHQLLAETELDRFAFRLHDEWEQTFDS
+RIAAMKREGRTDHDVVGQEILEELARESRARLRDRFDEPWFNRGMFHALADGELGYRVGW
+HPDFESKLEEMLSHVSST*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002369.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002369.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa808a5409a983704d878ca7223299138042c3d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002369.fa
@@ -0,0 +1,28 @@
+>NZ_CP083691.1_2265
+MALHVGLYSPWNTTDPRAWSGVISPMAEALRDVFDVTVIPPVGQRDARGERIRTRLRGMT
+GRRSLPTHTMATARLRSAVLAHQLRRHTGAPLDALVTIAASTDVLSLPDDLPIVQVTDAT
+FPAIRGFYPLATGLGRRNEREGMRVEEAGAQATDRYLVASEWAALSLTDVVGVAPHRVTV
+APFGPGTPPPADARRREPGSSLRVLAVIADWERKRGDDIVAAVARAREFRDLTLTIVGRA
+PEGLPSWVNAPGVVDRARLAELYRGHDVLVDLALANAAGVVMTDALASGLPVIATHVGGV
+DTIVRDGKTGWLVQPSGAVDATARVLTTLDAAAVTRASAAALADARARLSWRAWAATADE
+VVRAAVAERRGQASPEAQRRRALMVTPILPSTGGQESAGEHLVNDIAQVIAERSELTMLS
+SDGPANRRALERGVAFAHRLLTSAPLRCDRLPRLLGVAPALNARTVEQVRGLVASADLVD
+LQWEESALLLGPLRRMNADARIVVTLHDVLSQRFARQRELQSSRLRKGVWAARQAAATML
+EAHIVREADAVVVLSQKDADLLPKRGRRARIHVVPPAITGPLRPLRDGTGAPFLLFVAYM
+ARWENEDAMHWFVTEILPRVRAEAPDVRVAVAGGGLRDHVVAELEANDVEVLGFVHDLEP
+LYEEASAVVVPLRYGAGVKFKVVDALVRGVPVVTTTVGNEGIHPADAAIVADEPAAFAEA
+VTAVLANLPCAERYARSRATDVAREFGPNRFRARLQEVYR*
+>NZ_CP097650.1_495
+MTPRIGLYSPWDLTDPRAWSGAAHQMAEALAAVADVEIVPPVQVDDAPLERARTRARGAR
+GRRSLPRHTMATARRRSQALSQALEARVGPSLDALVAIAGSTDVLRIPANLPLVQVTDAT
+FPAICGFYPMATGLGRRGEREGQRVEHASAVRTDRWAVASQWAADSLVADVGVPASAVRV
+APFGPGVTPTSAPRVRRPQRPMRVLAVIADWQRKRGDAVVDAVQQARRHADIELTIVGHA
+PDDLPIWVHLEGVVQSDRLSDIYADHDVLLDLASANAAGVVMTDALASGLPVIATRVGGV
+ASIVQDGRTGWLVDADRAAEQAANQLRLLGESGGADQVAAASKAAAEDAARRLTWRSWAA
+AVMESVEEAVAAHAATERRIVMISPLLPSAAHQETAGEKLVRQTVDTLTADGARVTLVST
+PGPANRRAILRGGVPDHRLLSPARRITGRAARLLDLAPVLSPADLAPVRGLLRTADVVDL
+QWEESGILLPALRLTAPGARTVVTLHDVLSQRFARQRDLQLRPARRAVWEARRRAALAVE
+RLVLAMADDVVVLSDKDAALLSSRGRARVHVVPPPIPGSLRPERRDLQPTAEPQLLFVGF
+MARWANEEGMHWFVTEVLPRIRAELPGARVAVAGGGHRDHVVEELENSEIEVLGFVEDLE
+ALYNAADIVVVPLLSGAGVKFKVVEALVRGVPVVTTSVGNEGIHPADAALVADDPQDFAD
+AVLDVARYPQIAESHARAHASAVAEEFGVAGFRQRIKEIYR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002373.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002373.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a248c9ec71049ff19c90542c6f850486453026dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002373.fa
@@ -0,0 +1,3 @@
+>NZ_CP042169.1_163
+MVGQTVAYVRVSSAEQNLDRQLEAVGECDRIFEDKISGSSRAKRTGLAELMTYVRAGGTW
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002375.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002375.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34464a8c6f6c19c6e2e8b36090fd7770d249b475
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002375.fa
@@ -0,0 +1,3 @@
+>NZ_CP042169.1_234
+MSYYHGDDSHTLSPPAVSPPHHPVVDRPRGRPEPQEDEPMFPITDDQKALVDAVRDLAEQ
+RVAPHALDWDAE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002377.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002377.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40169d03dd4bdede423e3cbeb6ce4b39b0fab7aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002377.fa
@@ -0,0 +1,7 @@
+>NZ_CP042169.1_388
+MRKLIFYPNLSKGGVSAVIRGRAQAEPDVQFDAVFLHDRGGSDAFSDMANVHVRLIQESR
+SGPYLTHLAHQFDYESVSVLSHPATANVLSALDHVAVTYEFHSSSIPVIEKELGALELDR
+LAAVVVPSQIMAREIQPLLPRRLRFRLAVEPNLVDVETFGEQGSAQFLADSGFGDGPGTI
+PLLWVGRFDQGKAYAHFLRVIAALPQEYVGHVVVSLEDDPHRAERFFAEAAGLGVLERVR
+LYLNLTPQALGEFYRSVRDADGWLVSTSLKESFGYAVAEATNAGLRVAASDLPVWDLFAG
+TGLVHRVPSGSIADLVRVIREGAPVSAGAATAW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002378.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002378.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b3fbaaaa7e6d030b51e1ec971730f9029ae00d6c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002378.fa
@@ -0,0 +1,6 @@
+>NZ_CP042169.1_389
+MDYFDRIQNRLEGREAGVPGWLGAKNATRQFAAQIGIRTPEQLFKGPLSDLERFDFPERC
+IVKPGFASTSIGVHLLERRGAELWDLVKDEPVTVPGLIETLREIEGRYDLSPDDGEFLVE
+ELLSDRRGVTPPADVRCYMFQGECGFVLVEDHIAGPAAASYFNGDFSPMTDVHDRFGVHP
+GVTHLESIVDAAEPPAGAEELLAVARRVSTAVPSAFCRVDLYDTPAGPVLGEITFYPGTF
+FYKNRKVMAPEEAARLGKMWDAAEKRLAGSLLIDAPKRN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002379.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002379.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a19dd2e3eea88cbcb36df3b3bbd9d461f8d0ed78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002379.fa
@@ -0,0 +1,9 @@
+>NZ_CP042169.1_495
+MVIQLVSLTVLARFLEPAEFGVYGMAITFIGFTTLFRDLGLSSAAIQVKSLPIQLRTNLW
+WINTGTGAILALLTLATAPLIAAFYREPQVAFVVAFMAPTMLLAGAAVQYRASLARDLRL
+GAAAAIDVTGALLGLIVSVGVALAGGGVWALVLPQLVSGVVTLAGVIFVSRWLPGLPRRG
+HGTRQLVRFGGAMFVSQALTYTHRTYDVLLLGRLHGADWTGQFNRAAQMSRMPMGMIAAP
+FSKVALATMAPHQEDVHALGALARRGQVLLALPVLLAAGGLVAAAEPLVSLVLGDGWGQA
+VPFLQLIAMSEALALMASVGGWLMAARGQGSKLIRLGVISTVIKVSTVSLGSLWGPYGIV
+AGVVVAQVILWPLSLVLTGRMSGVSTREALVDSYVLVGVTASATAAGWYAGRTHIVPGGP
+VVDIVAVVVTMLATLALAAALVAPFRRDVQTFLQTVRSGVG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002382.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002382.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2fd1d8dced829e3d0386d3af7bc36e74fb4d394
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002382.fa
@@ -0,0 +1,3 @@
+>NZ_CP042169.1_498
+MPNLNDFHRPALDDVTTVDPRTPLLPFLRQLARAELVVGSSLHGVILAERLGVPARVIRS
+DAEPSFKYEDYYEGTGRANVRLAADIHHALDLGGVDSGSTVDATLAAAFPRDLWER*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002383.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002383.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e9a1126d989a97e963838c8eeb1e18d80702c34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002383.fa
@@ -0,0 +1,7 @@
+>NZ_CP042169.1_568
+MSIEAMKWAQKVAETGQLNTGQAFVLLLLGDHADEAWSCHPSQELLARRSAQTVRSVERH
+IARLRDLGLVDTESRYGDGRGRIGLRYYLREEALNDLVQDAETRMNTRPDNLSGKSETRT
+KTRPDNLSGKSETRTKTRPDNLSGKSETRMNTRPDNLSGESTHPTISADSPDNHDFADYK
+DRARTNPQEPSSVRPSVRQSGAVRAETTTDDGRRTDQVIDGGEGVGLVHRGVVLADLVQR
+VPAAADLGDGQLRSIVDVVLARASGPVRKPTAFVARSLASEFEELVTVTRPRPVAVTQAP
+AASGQVRELRTGEPCQDPDVHIPAYGQAVLADCPHCRLERRAMPRALMEAVD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002390.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002390.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1c6fa7c9094092899318bba9361994017751feef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002390.fa
@@ -0,0 +1,3 @@
+>NZ_CP042169.1_596
+MSARVKISGNLERELQRAVQDTMTTLAKDYQRMLDQLGQQYAGAPVEEIKAVLRTRWSRI
+SGTISDPELSIYAQHISEGTPITVRTS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002397.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002397.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ed3918b9d6f252911507ed4e4d45a8fb6d0283d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002397.fa
@@ -0,0 +1,6 @@
+>NZ_CP042169.1_813
+MKRPERPISSDWLDLRRPADERARAGSAPLLDALAEHFTETGADSPVDVIDVGAGTGANP
+AWLAPRLRFSQQWTLLDHDADLLELVPSQLQDARVRHVRRVTAGIEDLGSLDEAEQDRCL
+ITCSAVLDLLTMDQLAGFCDFLAERRMPALLSLSVTGDVVLDPGHWADAQITRAFNQHQR
+RGSLAGPDAVGYAAGRLRADGMRVEVAESPWKLGPADDVLLRRYLHDRAQAVIEGAPDMG
+DVVDSWLAEHLGQSDEGRLHVEVRHRELLCLPPG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002398.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002398.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d561075e2b76d5004be9ad9b09489e9f773ceb0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002398.fa
@@ -0,0 +1,4 @@
+>NZ_CP042169.1_815
+MYRLTVRDHVMIAHSLPDPFFGPAQALHGATLVVEVTWRRRELGPQSVVMDIGAATSMLS
+EVLEPLRYTNLDEHPAFAGRLSTTEAIAGHISDELRRHFDTTEFAGMEVLLREHPDAWAA
+HDVDFA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002399.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002399.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a43405189d93cc247b8d02b8755444f4848de35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002399.fa
@@ -0,0 +1,6 @@
+>NZ_CP042169.1_816
+MRSLYSGVSRGTEMLVYRGEVPPEVAGRMRAPFQEGEFPFPVKYGYLSVGVVEQGPDDLL
+GRRTFCLYPHQDRYVVPVDALTVIPDDVPSRRAVLAGPVETALNALWDAPPCIGDRIAVI
+GGGMIGASLAVLLSRFPLGRLQLVDTDPVKRDMARAMGIEAVEPEALQAECDIIYHASTT
+EAGLAQGLERLGDEGELVELSWFGSHVPAVPLGTSFHARRLRITASQVSTIGRARRYRRT
+HAARMDLVMHMLQDPVFDALISGESGFADLPGAIAGLAQGELPTLCRAIRYPDPGPRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002406.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002406.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34e6bdd91143bddb2b1e95945c42875fd51abca9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002406.fa
@@ -0,0 +1,3 @@
+>NZ_CP042169.1_1442
+MPAHGLPNTTEPVDLTSTVPPGALPPEEAAKYIGRPGALKTLTNYRSMGKGPKAISVLGK
+PVYRIEDLDAYLAAGGDAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002407.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002407.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5244a1affc091c1239148d15a691b9c72189672e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002407.fa
@@ -0,0 +1,19 @@
+>NZ_CP042169.1_1443
+MTAPAVHEASQKRLLGTQHAAKTPSQTPLAAAAYGGTPVAAAADGWTIEYVTDSATSQKY
+PARFAVLTKTVGRAGCTGSTTSFGAYPSVAAMGTGRDAIVVGFDTEFVSAEEVDEQRGWV
+GEDVHVVRRIVSYQFAAIDPTDPSRLRLAVVLPQEYHGPRGPRTARLSFEKALEIAVTAL
+GLHEHPLASGWSSQGVPRAEVVDKKGETRPGWWFNGRAGVSRALPIALVAHWQQADLTTF
+VDRRKAHNTWNAAYPERARKVSTRAGLDSRRGRWLDSSTSDILRAVISASAGMVSPTPVR
+MVLAGANKRWARPVEVSIRDTMAQSGAQPLRALGEAVGVAKLDVPGDWIARMDDYLLKDP
+VAFMDYAANDAIIALEYVSQVYGDHQEVPLTLPTAAARAVKGLMSGEIEARPDTFDDFNA
+VFGGLVKVAKNVEATTGVENQLDFYKKRELQPIDGAAATWIHASAMAFRGGYNMSAELGL
+FEQVTHDLDLQSCYPTSSATIWDVDYLHPDGVILRTVNNVELGLDDFAEGGPLTPFVGFV
+SFEFPESVAFPCLPVPAEGSMIYPRTSGGARGVWAVGPEVWLALTLGAKVTCQIGHFGRT
+LRTSDGEPSRLLRGAYKTLLDDRARAKREFGKSSFQQGVLKLMANSPYGKLAQGVMGQRG
+WDAWAQERDAVGGSAITSPWHASMTTGLVRAVLLAVLNQLHDRGYATPSCTTDGFITDAE
+LSVVDGLDLFGLGQLWRDSREALTGSREMWERKHFQTDLLNVTTRANFSRQPGGVLAHGG
+YKLPEGIVPDSQEDRDHMYDLMVSRDGALPVTMKVFPSMEELTRIENRLDFAPKVVHKQQ
+TIEFDRKRRPVPEGMTAHMVMVGEQVFEVAHVRTVPWESPEDALRGRSVDQGLKRWDEEL
+GEPVWTRSPVRRTRAQWQDYFKRLERLLDEDGRVAEAERLDRIAKGIVIAHRQEVVHIPW
+LGSDRPLAERLDAFEDFGLPRPRERFWSHARSKTERQIEIDLEAIAPYVAEMKAVDPFES
+ETFLQEVA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002408.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002408.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02dd6eb0f9ef99140d76460772660287a192333e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002408.fa
@@ -0,0 +1,3 @@
+>NZ_CP042169.1_1444
+MTVAYTLGDQTFATKKAVLAHASEVLNRASLGEVLRGHDEAFALDLLAQHPEVGRKHGAG
+IAGVAVVVMPEWGTRNFVVLREDGSIDNWSVKKCVANLRPDGTRRSP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002409.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002409.fa
new file mode 100644
index 0000000000000000000000000000000000000000..22b48f4279cb0c9f88fe4a9376a94656833ccf1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002409.fa
@@ -0,0 +1,6 @@
+>NZ_CP042169.1_1450
+MTAEPLRPNDAIAPLPTVEGGFKTVMADPPWRFQNRTGKVAPEHRRLDRYSTLSLDDICA
+LPVQDVVADDAHLYLWVPNALLPDGMRVMQEWGFRYVSNIVWAKRRKDGGPDGRGVGFYF
+RNVTELILFGVRGRMRTLPPARSQVNMIETRKREHSRKPDEQYGLIEACSPGPYLEMFAR
+KAQPGWTAWGDESGADSAPRGQVHKGYAGGAIEAPFVEPHVRLDEAVADALAEDLKTKYE
+AGASVQELVESTGYTTTRVRGLLKKANTQMRPRGRKTKQAEALFA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002410.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002410.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6fb9c5403dc3a612ac6b8e7def230b214b75bc37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002410.fa
@@ -0,0 +1,12 @@
+>NZ_CP042169.1_1451
+MSPFPSPGRISFTKFTSPEGITDVLAGVVPGVTTAAEVLQDLAAAKLADPLWDDLLSYDP
+PFEPGKSRAAGSQVAVDNELLRACREGREDRFLLLWAQLILADPRLDAIVREVFTDSTGK
+LVPEMVNASKLGAALTARHAADPDEPHDTKAVSNLLSLLERCRLVEPVKHGKTIVGVERV
+LPTAHAVPAVVRLIGERLAERGFGAQPGRELDLALALGANAWLNLTASEFRDAFDGKTPP
+AAQPQSVPGALPEDLKVIATLLRRKGQVLLQGPPGAGKTYVARRYVDWVSAGRRADSRLQ
+SIVEALPDDRRTVPAIADEIVSRGLSAVWDIVQFHPGYEYTDFVRALVAQPHGQGVTFVA
+QHRIFSLVCAVGAELARRGYELEMVLILDELNRGDIPSIFGELLYALEYREEPVASPYTV
+DGTPSLTVPHNVRVIGTMNTADRSIAVIDYALRRRFTPIDLEASDSPIRGYTGFDDETAR
+EAALYLYERTRDALSEASQGLQVGPSYFLAEPDGEDGSIAVLATRFVYEVLPLLDEYTLE
+GEVDASRVESLRQELGLGQRAKQWDQGAALAAHLVAGQPWKPAAADPEVGEPEEALSVDL
+GGPLADGGDAPASGEDTRDQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002424.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002424.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7534d411615f86e8ea7e58161dea6e85ab3a3077
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002424.fa
@@ -0,0 +1,6 @@
+>NZ_CP042169.1_1959
+MDHDRRVLVERYEALAKKLDSATNYEQPSRRFILDQCRRLDLNGVLLTNIRFPTPTDDGR
+YFLHQVDHLLLTERSVTLIENKHWTGLIFDGTLPRGEHRSWKLLFPDLDLGDDFAIQLQR
+KAETPGQIDVRIVAEDHNARSPRRQAINQAADLRTYLQSLSDCRAPDFIHPAVFYSHSDS
+YVVATDERLGRRKVDVPVLTTVGNSVHDLLLLRSREPGPSVDVRCIVDALAPQTTDITGF
+GTFAGSWTSTFT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002427.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002427.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3d86acbb20b5a8c21c111f70229a51427fe31bfb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002427.fa
@@ -0,0 +1,5 @@
+>NZ_CP042169.1_2086
+MTRTSTYGFREGTLDTVRRSMRTVAVHRDDGELVGRVVRGELAGCERTGTFRWESIGGAA
+TTVGIRRATWRSAVGRLLRPTYAVTHRPEVTAPAEGEPPAPVHDELKEIWGENVLYFAVD
+GTVQGRRVVARADWDGSVEVRAQGEDGGRPRRVARFHSGGMFSLTRVEVDHEAAGTTRDG
+ALFGVLMLLPFVARLHREESSLIEELLG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002428.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002428.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab55c26541af13743973a10788f8d19da0486221
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002428.fa
@@ -0,0 +1,3 @@
+>NZ_CP042169.1_2167
+MNLNASLGRVVEWDRDGGWGVIDSEATPGGCWVHFSHLPMLDSVPSSLTVGEEVEFLFEA
+LEAHNDQDGFLYRAIAVHPPHGGLAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002438.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002438.fa
new file mode 100644
index 0000000000000000000000000000000000000000..adaae285675f3faca67713176b60768f8a8c3f73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002438.fa
@@ -0,0 +1,4 @@
+>NZ_CP033200.1_88
+MYTTVITPRVSETDGVGHINNTVLPAWFEAGRAELFRLFNPTDSFEDWPMIVKTYTVTFD
+REIRYGADVTVECAVSRIGGTSIRLAERIVQDGTVCATGEVVYVLVGGDRRPMAIPADLR
+RELERHLIEENHD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002447.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002447.fa
new file mode 100644
index 0000000000000000000000000000000000000000..899d4c7df323fb21491ce9f9e89ca98086818f3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002447.fa
@@ -0,0 +1,3 @@
+>NZ_CP033200.1_351
+MVAAAVQGRADLIVTANLKDFPAEVLGRFNLQAQDPDEFFMNQLDLDPAQVMRSVQVQAA
+ATRNPPLTVAAVLASLERCGAGMFAEAARGQTWRL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002448.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002448.fa
new file mode 100644
index 0000000000000000000000000000000000000000..73da1b2634c7668e0c5fad3dfc4e9a77c0a0772d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002448.fa
@@ -0,0 +1,3 @@
+>NZ_CP033200.1_352
+MLLWGGEAKTPLTAGWLAVPVLGERPFIAHERLWWDADRDAQVTQTPMPDRGPNFDERPA
+AALSMALKQRPQEGQA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002453.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002453.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9511f5281158876f00d2eee9144c11660c3a924
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002453.fa
@@ -0,0 +1,7 @@
+>NZ_CP033200.1_1073
+MLHLLVDTSTWLDLSKRRDGQRWIVALRVLVHQGEVELIVPPLVIDEYERNRERVEASMT
+ASVAQRFKLIRQDLDDYGGTDTEQALSTIEDLARHAPLIGAMTTRNFDEVLELLRGGRTV
+EPTESERHAVVERGLVKQAPFHRSRNSIADALLIELYASAVAGVDLAREPHAFVTSNSED
+FSLPHGDKRQPHPDIAATFALGGSTYALGVDGLNEVLLAHFGPEIEALFADTDFVEEPRR
+LDEIVEAETRLFDRVWYHRSLQHEYRLQDANNHVEIEQLRAIAGPGRKRVEETCNLPGEL
+GPYTDFELGMLNGKLSALRWVLGSEWDFLDT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002460.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002460.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c23179b509e0375707607d52048e12a8546e8b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002460.fa
@@ -0,0 +1,6 @@
+>NZ_CP033200.1_1608
+MGNRRRLRIRASRGRSKRCRPPHPKNSSGPGSQASGVRLLSARMRPTATPPCSERLRHHA
+LSPEPLELRVGDRGSAPGRVQAESVRHARPSAHHPAPHGGGHGPAPARSRGIPRSDRTGL
+AGWSRRRRAPTRHRPGWGCEKSRDDPLRRAASSTPPAAGCEVRLWQVKWPFTLPTRKRDM
+SIPARLSHVLGVSLNGCVAVHNMQLRAFSPFLDRLSLAPIPAARALGSRLAHQSRRVFSC
+ALSDSSSSCPSCSWPPAVPVRRDRGRLAPNPHCPRLLRRCRRRPPPRRAPCS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002462.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002462.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3639d4ed82e0acc600e0cd196cb784e9ee07c1bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002462.fa
@@ -0,0 +1,2 @@
+>NZ_CP033200.1_1655
+MVRGIFWVSHSKEAIMALLRKTAAWGAAAVGAVARVQYGALSEPIGGN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002467.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002467.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1521470642bce401c521ef040ecbaeb842890282
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002467.fa
@@ -0,0 +1,2 @@
+>NZ_CP033200.1_1926
+MKYGLCAYKWVICRAIAIRSIFFTKLNPTAAIRGFLVIFGMGFAARPVGAFRLSILDDL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002469.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002469.fa
new file mode 100644
index 0000000000000000000000000000000000000000..161459f84131250dde901efe3867e0c333099133
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002469.fa
@@ -0,0 +1,3 @@
+>NZ_CP033200.1_1972
+MLLLARISPERFVRQMRVKADQKGWERIDWSALVSKQRFVKTLAVRQGEAEALLPQVEAW
+LEEGAE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002476.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002476.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd28227fd5a7e3c7d82192af379ea8c501948dbb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002476.fa
@@ -0,0 +1,4 @@
+>NZ_CP033200.1_2166
+MLTSRRIVASTLALSALLLTGCQGDPESTRSSTFPSDDYVTVTVRGQWLPPNGTTVRREK
+GKVLLNVDRETVDSNLNALLPSSPSGKWYEASYMLTRGSLVEAYVSLPGAVPGMTTACEL
+EVDGVTLDRSELVAGSGNTAICSARLPAK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002478.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002478.fa
new file mode 100644
index 0000000000000000000000000000000000000000..464c8f5ba9aa02c0d3e083c2ee9b39515876448a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002478.fa
@@ -0,0 +1,6 @@
+>NZ_CP033200.1_2168
+MPAPKVHLPLETRCSTYFVDEAGAKGSQGEYFVTAAVKTDDPDRVLRGFEAVRQESNYTN
+ADELKFGRVNKGSLPVLRRVIDDAVGAGARFGIFVLDKRHFDPWVDVEQWEGHLFATERL
+LRGMTTRRELGVALLDHISVPKEVSYGAELLARINGRMGNRRFLTAVSLDSKTCPGLQIA
+DIVASSAYHYRRGVEEMGQTQYLQQQSPKAQLARHVAETIGLGDFSDHKSDIASVRTSHP
+QSLTELRDGVASLVSEEP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002479.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002479.fa
new file mode 100644
index 0000000000000000000000000000000000000000..19a810af578eefd7321e66cdfefbd4a516232771
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002479.fa
@@ -0,0 +1,3 @@
+>NZ_CP033200.1_2169
+MPVSPCPECGRDVIPAGIGQAPRFCSTSCRQRRHRKVTRVRGELAAAETERMPLRAAYYR
+EWLARLMGD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002480.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002480.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e930c4a9d52798b0f90c26c8066f9ff25dd1ee44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002480.fa
@@ -0,0 +1,8 @@
+>NZ_CP033200.1_2170
+MSTTKTAPAYTTAEDIRAQVHAHAEEERRDASAHGAMLNLMQKIGDGREDPEPDLDAAYE
+QARISGDWEEYERIFRAHDDWADRSAKRARMANNLRSRAIPNPERRRTLKGDAGRLTLAY
+LAGALPSILDAAQRLTLHGVPSTAEAAMTADPRTRGRYLEAAAVVDAYRALRRAQAAAVT
+DINATASDSFGGPSKVSSQSVLTIGQFRDALHLDATWLSNRRNAIGQLRSSATRAHLRRY
+VPGIVEFLDDAPAELFGPITADGFPAECTTVPARAQWLATWSTRLDFWVPEFEDLQQLQH
+LYGAAINPGHWQDRKGLVLANTYEGESAADNAERLALVNLDYRRPDWDTPQSEPTAEDLD
+ATTANRAALPREQHPGLRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002481.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002481.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de4a6d55ef25816d299e3a6f9221d463f83be3d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002481.fa
@@ -0,0 +1,4 @@
+>NZ_CP033200.1_2171
+MTGPSTDGVRGGRQTWAQWYYSGAPTAQDMADRRHADTARAERARLDAEALNARHAEPRP
+DPAARLRIALTNLGPSMVPPGAGPTLADVNAAIRREAGPDRALHQQMLDLHFTQQARRRA
+AGNH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002487.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002487.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f07441f82be4206ba326c33cec28b8188b8a8b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002487.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_7
+MGRRLASAWALPALLVLSEPGRLPLVLALGVAVAAVLATRAVGAGAEEVGRSPELERLLP
+IGRDAAWSVHTVAPALVLVPWGAGLGLVLALGTHGVGPSLGPVVLCGALAGVGLAGAVVR
+TATPDPVDWGAVMQPAQTTRAAGPLVRDAVRGADAAVLAVAPLALTPLLSAVPLGFAGVA
+GVVALIAWGIGRHVRPAG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002489.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002489.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a2de13baf3dcc1304012de44df67378b0f33182
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002489.fa
@@ -0,0 +1,2 @@
+>NZ_CP040019.1_33
+MSTTTATPLTVPELIAAIRSISDEIRAIQAGLAADNAQERHP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002492.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002492.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af450423e46db8ae2d1bb7d220d668b2d20906c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002492.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_39
+MTRERIPEGLRERGTRLWKETTDVLDLEAHEELTLLEACRTADRLDALADALEDAPLTVT
+NARGDEVAQPLMVEARQQSIVLARLIAALRIPDAEDNRPQRRGVRGAYGVQMRSVS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002493.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002493.fa
new file mode 100644
index 0000000000000000000000000000000000000000..788fda3439356a10506af5a251ee28ced7fc2adc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002493.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_40
+MTVMTPIGDSVREVRATSAGDLPLHAYELRNRDFLVVQLPTGAVLAVPSDSVPPIERDLW
+EDAELRRSLWRGFDDAVCGRVTPLEDVLAELDFDLSSED*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002494.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002494.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77f5f6004e4504fe5bfe1d6fc872d4d2110a3ebe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002494.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_41
+MPGGFKVDLTDEARRVLLELKKSDLKRAKKVAKALQTLREFGPDYPGFKTHKNDSVPGPF
+GETWQAYLENHTPSAWRMFFCYGPGRGVITVFLFAPHA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002497.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002497.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3abc87c07755ac7165a23c8e22c71fd74a520160
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002497.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_69
+MERKDDRRAFLTWTLISAVGLALVIASFTWPAWLVVPGALLALVGVSQSHEYRGYSHWFG
+LLVAAVAIGGGPFHLLSLAGDLGSFLGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002500.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002500.fa
new file mode 100644
index 0000000000000000000000000000000000000000..15f4256c57dbc2710a3faef701001336e02ecf9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002500.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_94
+MPLLTRTVDPRSSDVLSLANSPVLWVFALGVFAVIIVQSALYVRAARRAAPGLGIERAEL
+STAFRSGAVASVGPSLAVVVVAIALLALFGTPAVLVRIGLIGSAAFETGAAKIAAESAGA
+PLGGPGYDQHVFALAFITMSLAGAGWMVATLLFTPLLKRGSARLSDVNPVVLTVIPAAAL
+LGAFAGLTLGEFPKSPVHVITTAVSAAVMLLLLLVARALKADWLKEWALGISIIVGLAAA
+YLAHQALLAPAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002503.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002503.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ee84533b442304abb44a9f4fd2ad5a012f1c95e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002503.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_118
+MTPEEFPPIHSQHAVVLDWVGPRWAGHLRYAVHLSEQSLAPGETELRDLWPDGAGLCWLG
+GPAVGPGPWPRNAEGAPLSHVLTLDLRTVAGASDHQGKAVWPAGRLREGLPVSGHLQVFH
+DLQTYGGDPEDGDRAGWAVTWTPEAEDGLRPALVEAPDDDGAPDPVCQLVLPYAGFTLPS
+SLDVAVTDPRDADRLEELDDALREAWTVQRGLDPTWAIPTSHVYGHGWTGDALAGGEILP
+EVLPLEEGDEHRLVLDVESWTTLQGWFGDAGHLEVWMRQSDLERGAFDRAWCLIRTD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002507.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002507.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b4b8cd58593371291aa938daca3c9a6183482ada
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002507.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_136
+MPMSDAPDAVVLALPYRRPFAFDHLLRFHAARAVPGVEHVDQAAYTRVLALPRGPAVAVV
+SDDDGAVRLELRHAHPDDVAAAAGLVRRMFDLDADPQAVDAALRQDPAAARSVTRFPGLR
+VPGSPDPHESLFRAIVGQQITVARATARLADMAARMPSLGFDGPVDRLFPTAERMAEGLH
+ALYRGPAARREALRGAAEALVEDPDLLERTRDPEALSETLVGLRGVGPWTAAYVSMRVLN
+APDVPLPGDAAVATGARLLGFDDVAAAYERVRPFRSSFTIHAWNAAAGG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002512.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002512.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bd5c30306a286e51c6879b785d5497af0f89b0e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002512.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_169
+MSTDLSELAHRFAAGHADAMADVYAEHARMVFSLCMVGLRHREDAEDAAQQVFTRAWRSR
+DTYDPRRPLGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002514.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002514.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab71a0bdff59317f7e3bcd9d301539854f1a7bf7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002514.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_171
+MPDMDSTRGALSDDAFDALVSALAEGGVRPEDLDEALHARGVTSLTPRERADLRDTLRVI
+EALRADPLLVEPPHGLWEKVAAAIEAEGDLAATPATVADLDAHRSRRRGGAGARWWVPAA
+AAVAGLLVGGGAVWLNLQPSEAPETGPVAEPQVIGDAEMDPVAATGTTASAKMTREPDGS
+LELTVDVPEVPDAAAGYYEVWLRDADASRLISLGTISSTSTTLRVPEGIDFSRYPVVDVS
+HEHFDGDPTHSGTTLWAGAMTERS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002517.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002517.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26a741c20a126e9cea338bcb4d8f9476d32f34c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002517.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_228
+MVAGLPWFAWIAIVAILVWGTLQVVQLVTGRALPGEEMKKEVEELRTRLDANEGRRPAGE
+LPARADAEGSDLERRIERLEARADRREARDREHDDWDRRAGELG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002520.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002520.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68290c7dca3ddda7fd2c63c8b103249adb770d65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002520.fa
@@ -0,0 +1,2 @@
+>NZ_CP040019.1_295
+MGAPDEVPDRTDPGTTTASRPWAAVVGLAAFAVQVPLARRVG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002521.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002521.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be38f65a38cc6fc74b440b32db3897a9c47acbd9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002521.fa
@@ -0,0 +1,7 @@
+>NZ_CP040019.1_297
+MGWSRRSATAASEPRGSAPDRAPTGPFVREMGGSVALTGRTGRRIRDDGTPVFTKARADA
+PAHLFEREAAGLRALAAAGARVPRVLAWSETGLEIEWIDDGGRRTRQTEAAFGRELAGFH
+AGSRPEAGAPDRFGSPDDVAAGWLGACPVDYTPADTWAESWVGRRILPLARRAERAGVVP
+ASARADAERLAELTDGFGADAPADHPGAAVLGSAEPSSLVHGDLWAGNRLVDADGRSWLV
+DPSAHRGHREADLAMMRLFGGFGEEAFAAYREAFPLADGWRERVLPYQAVPLLVHAVLFG
+GGYGEQAAASLRAAVRLAS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002527.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002527.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6cbbd1ceb9d5066bebaa3d489d8ab26a6261bffe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002527.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_350
+MPHRPPPSSPSPRWGRPLRGLRGLVAAGGVVLLLGSAVQPAAAQPADTAAQSAAVAHAPS
+TTATAASTPRLPRVAAVRELDARIAEAGAYLSRGSDGVLRFDAAAAAADGASADVLDLGA
+VMNQMAGPASSGPHAQAKLSLPIWGNWCGPGHGGGTPIDVLDSICRTHDRCYGARGYFAC
+SCDREIVKNIRANVHRMGSRESLVAAAVATYFAYCLCNPLK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002528.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002528.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed61e1ddde4ac00e44e8699444a233016e5e36a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002528.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_351
+MTSATSSSPASPAPAAACLVLTLAATAALPDWSGSGVARPLWALLLPAALGLAGAGLALR
+ARRPGGGGGGAAGGLGAGPALIVVTTIVSGP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002531.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002531.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a3d523355bb860f87fe288b4a9a7c873721d2774
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002531.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_376
+MPRTTLTFGGLLIAVGIISYAVTGFISWTALIPAFLGLLIAICGLIALKNTTIGLSIALV
+ISVLGVLGTSMNVLKVGELISGQAERPLAIVASTVTFVLLIVYIVTGVRLFLTARRGDKA
+EATTA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002534.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002534.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ebc46530d31796733bab99f21fc9bda2a121e35b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002534.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_415
+MSLRIHPHHCRRIVHRPILALSRDWLRRGGQGPGAGPGEWRTVSTSAALAAPRTPGSVGG
+ESRGRGSGRGGIGQRGCPARARPTGCRTDGWHAAYARPPRPLQARGRGVAQTARPPTGGV
+DGPTAPLMITGPCMLSAVIRQRRRGPSVVSVTTMSARSLASSGVGSQRRVAFHVKHSYGH
+ASRRIACSSAWMSTAGRVTVLGGVHNGPHTQRPHARPQPPHPRTEPAGGIAPTDGLRRRA
+RAQWPPQAACAGPQPFAAGAPRPAISAAASR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002537.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002537.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b42d1a50a774e1a89078fc9d30152363549b5d1a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002537.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_441
+MDAMLTGAEVQATASADQLASGLLRNDESTKFLDGVVPMLLNFRLPPEAIASLVIGQTFV
+GNTHYGRQTIYCDGGHEVVLRERTRRAGPMSAKASTSRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002542.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002542.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b54cc09e316a88b9c4a91a55fafdb63f17d5b3e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002542.fa
@@ -0,0 +1,9 @@
+>NZ_CP040019.1_462
+MVAPEAARELARRALARSHRGWTLGEVPTPAWSLPLKPPTEQVVLADPQAAQSWARGWRA
+ATLPAGIRVEWAERSWRSVGRQQVPVRVHAVTPDALVAWVGGCEAREQRVFAERVAAMRR
+LAEAWGGSGPSAAGGAGSAPQTQDDDDEAAADPRELTLAAALRRHAQRLTDLSEPDFLRV
+VAVLEWLRTTPVQGLRPRQLPIRGVDSKWFGAHRTLLEALHAPQEGGLGIVDAHPTVRVR
+ILDPALRPEGLRDLEVPLEQAAAWPIAPARVLVVENSETLLCLPDAPGAVAVWGRGFDTA
+ATVLPWLRGAELHYWGDLDSHGFAILHRYRTRLPQLRSVLMDVRTLEAFRDLCVPDPTPF
+RGALATLTSDEARALERLRAEGDVRLEQERVGWDHALSALDAHFVFCDAGDRAAGGEDAD
+GRRIAS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002546.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002546.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba97ee819d58661dc5eff94488eb3d23f6e823fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002546.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_466
+MTTTLTLLDPAGPDREALTDPTPLFDLRVAERFRGRGLGVEILTALTRHVFETMPDVDRF
+EGQTREDNSPMLRTFQRAGWVKEAHYRRGWPVEGGEPVASVAYAMLRQDWENGTTTPVPW
+E*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002547.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002547.fa
new file mode 100644
index 0000000000000000000000000000000000000000..47f09b239e809a9e8a13928db280056cd51e63b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002547.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_467
+MTHAHAPLTPTGEELRQPPQKITARAPGHMVHLDVKKIGKIPDGGGPRAHGRGTEAARAV
+RTAKHGPGAKVGYTSLHSAIDGHTRLAYTEALEDERPAAVNAAIPINECVPCRRPPARTR
+P*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002550.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002550.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c7f032b23fc8ffd81507e36ea8ab4bc0495c065
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002550.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_471
+MCGACGRGVASPTTALLNEHGLKRRALARLRGELAPGCRLTLEGDAWTLIRRSGRGEHHA
+DVEGLIASLEGGAAGDWVGAEPPREVVAAVTAGMVARARRRSD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002560.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002560.fa
new file mode 100644
index 0000000000000000000000000000000000000000..092b6b6dcd930c1122a987b892675919dbd4422b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002560.fa
@@ -0,0 +1,7 @@
+>NZ_CP040019.1_503
+MSASLAAGAGLVVVGLAARATVQDAGLFLVMTVVALSGMALGNVLIPAWVKLHAGSRTTA
+LMTVYSVFLTLGGSAGALVTAPIAAAARDDGEGWRWALGAWGAVALLPLVVWIVLARRTG
+HDFPAVGAASGDGGSLLRSPTALALTLLFGVQSMNAYVQFAWVPQILRDAGLSAGVAGAA
+VAVTAGLGIAGALLMPTVISRSRTLASWMVLFGAMTALGYVGMLVAPVAGVWLWAVILGV
+GGFAFPTVIALIPARSRDPHVTARLSGFAQPLGYVLAAIGPFAVGLLHEATGGWTAVLVL
+LACSGAVMTAAGLRVAGRVFVDDELLAPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002564.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002564.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54cd9ef1b04b1b04f815aa976f553a1b72adcf10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002564.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_520
+MDTADLPDLPAPEDRTATASRRVEAPAGVVFELIADPSRQPEWDGNDNLAQSEAGQRVTA
+VGDVFVTTLRKGVDRANHVVEYEEGRRIAWKPAEVGGEPFGQLWRWQVEGDDDGGCRVAH
+TYEWAQLTDPQRIRRALRTGPEQLRASIDRLAALAEAEAREA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002566.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002566.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f243905cd31d038c2727579ef1d4d1abd5e30dfb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002566.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_548
+MLAERLGEITVEPEDAAQAPTEEPGVIDVDDWTARRRAGSAHLTGRFCVVTAFETIAALR
+PRFAGIATGGLGRADFDAAALTDGRPRLLTQAVSPHLWEMRQKDGAVRCDGVEFLSRHGD
+DLPLWAVFERPGDGEISPHLTDTAEHALTRDTPDLVRAFELHGLRMRPRP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002568.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002568.fa
new file mode 100644
index 0000000000000000000000000000000000000000..93ec281b2c547a75c888fb57f36b3499a7d033dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002568.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_581
+MTGTTLDRPTPTSVSTSVEPRTGAHAVARTLADTAADAAPAVRTPVPPLPPTRPRPPSRP
+GATASASRSSSPW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002571.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002571.fa
new file mode 100644
index 0000000000000000000000000000000000000000..41295ecbf954eff381b8888906ef9caf0225ca09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002571.fa
@@ -0,0 +1,10 @@
+>NZ_CP040019.1_590
+MNAAPRTGEAAVARPDAWPAPASFSDSPRYVLARWITDLPAMAIGLVGSLTWIAQWPAPW
+GPLVQALMLLWVASLVLGPVVRWRTARFHVSADGVQVDSGLLSRRSESLPWDLVTSVDHR
+QPWAFQLLGITEVTCTQTGEDGSRVRLDGLAPADLAAFQRHADAAAALGRSAPAAPSRVE
+DVAASRVDDDGAPADRASTGQVDAPTGQAAAAPAAVVHRTTLADLLVLSLVYGQVLLLVP
+PVAFGLMELTDVLDLTERLESLLFSGLGSWPTALLIVALAVVVGLVATVVKFHGFTVLAT
+PEGRLRIRYGLVSTHERVITPGAVQGVVWHRNAAEQLLGRARLSVLTLDSAAQLGGNLVL
+PSMPVERARAIVAEHLPEFAGTDRRLSTGLATPAVNLVSLLALAAAFAGTWVLTAQTWGW
+PWPLAAGACLAAAAVVAGIIAVAPARLYADPAAGLFLTRRITVGERVTAVRATRLHGISA
+HHLHHARTPRGRRTAWLPTVFYFAGAPRRAMALVAAPEAVEALQAMVRHSSVPLRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002572.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002572.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e680c51b67e5ffd49ce1549c4c7a5ff22394ed83
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002572.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_591
+MLDHPNAAPSPEDAPAASARPAGDAGVTRLPRLALRVWQATTCATALPIAAVLAAVALWW
+DHPVGGPVLWILVALTAAVALADLAVVNRVRHRSYSYTVDEDEVYIAKGALVRHTVDVAV
+PQVLSVHVVRGPLQRALGLATVRFVSVVDAESLGPVELAEAQRVKEVVLRGLAARRQESA
+TALVAAGEVAP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002573.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002573.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c79dd4da6056fadaba8c0dd4e4cf923a1c0e6efb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002573.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_592
+MTTPAASTESRAVRRTERTITFLLIALATAVVVVLGLTTELTTLPRLGITLGALVVAYPV
+LRMLLYPRSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002574.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002574.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb39cb05a2678dff31fc1aa1ea75b0e5e47762b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002574.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_603
+MTVGEVAALTGVTVRTLHHYDAIGLVRPAARSAAGYRLYGPDDVARLQEVVAYRRLGFGL
+EDIPDASADRRAALVRQRELVAARIDELTRLGRALDAALGRPGDETEEDTMQNEDTRRRP
+GTRPDLDLTDADLRELFGDEYAEEFDGYQAEAEQRWGETDAWAESARRTKRYSKQDWERI
+KADQEAATGLAAAALRAGEPASSVAAMDAAEAARAHITRWFYEVSPGMHRGLGDMYAADP
+RFAKTYDDVEPGLAAYLRDAIHANADRLERDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002575.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002575.fa
new file mode 100644
index 0000000000000000000000000000000000000000..41f2d810de4eb969509b6b30a665a5ce31a6ccfb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002575.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_607
+MPKKFSPELRERAVRMVLERQATQGGPRSHSIRAVAPQLDVSEETLRMWCQRHGHEIAQA
+PVSETPAEEIRRLKRELAEARRANEILKAASAFFAAELDRPTTR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002579.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002579.fa
new file mode 100644
index 0000000000000000000000000000000000000000..153f36eea697c855ba902c83b9f244463b1bc99a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002579.fa
@@ -0,0 +1,2 @@
+>NZ_CP040019.1_615
+MGAAHVWDASTVAALDSVLTKYAQHGIHAEVTGLNEASTAMHARLTGRLGT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002580.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002580.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b15661840a7e531a4c05b75771b773fabf36210
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002580.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_630
+MIESTPAGRVSERSAPRVVLGLVLLVLIVPVVIAVFMAVYAVAEFVQGGHAPVGAPPLLV
+SVGQILAVACASVCGIRFARSRTTRARWGWTAAVVALLVLAAWPVLVGGIGLVGREACEV
+RPAPFWCE*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002596.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002596.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6711bd4fbc09bf9767a8f3e5958689874e82617b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002596.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_768
+MLLPPLDEFLRILIVTPLAYVAVVVLLRISGKRSLAKLNAFDMIVTVALGSVLASTVTAS
+GTVLVAGLTGFTVLLLLQVIVSWLTSRRRVQTSLVRSEPTLLVRHGRLLTDAVAEARLTE
+DEVRQAVRSQGIGGLDQVAAVCLESDGTLSVIPTSSLGDESALADVGAW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002599.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002599.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e813aca9b627b3328ddd6776f370f25c17ccfa87
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002599.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_784
+MRAVEHWRSAVANFNMTDIRTQLDFNLFTEFDADGLAPRERRAEEFTGLMEQLIIAARRI
+AAV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002600.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002600.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5be6788040d028391990a752f75aa280f3236dbc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002600.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_785
+MGLAAAPRPSRRIDDGGRQVLDLGGLSAVVEHYGRAHTRTDLTVLVPEAGVLDAVLQRLE
+APAARSSRNEPCGMAPTTGEVGAIPQGSFHGEVRVVPGHGAVVDATLVRAQREALAAAPP
+G*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002601.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002601.fa
new file mode 100644
index 0000000000000000000000000000000000000000..909b67962eceeed11f168dacd9cad9e889d83f8b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002601.fa
@@ -0,0 +1,7 @@
+>NZ_CP040019.1_796
+MTSTPQHITLEQLYSEWTELMTEYPTMNMRLFRAVFDEWHQPTVEPEGVTYREDVVGGVP
+GIWTLPEGADEKQVLVYTHGGGFAVGSASSHRKLAGHLAKALGVVSFVLDYRRAPEHPHP
+AAVEDGVAVIDALIEAGIRPEDITTVGDSAGGNLAVAVPLSRREQGKPLPGQVIAFSPWL
+DMENKGETLATNNDTDKLITPELLEGMIAGVLGGTTEPTAPLANPLYAEYQDFPRTYITA
+GSVESLVDNATRLEERMKAAGVDVTLVVSEGQQHVYPFEAGASDVADREIQSITAWYGQG
+R*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002608.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002608.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cbc886703faa410623e3825675730f5f224e6e53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002608.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_809
+MTQLRQILDAVSAALWGPWLLIPLLLGTGLFLAIRLGGIQVRLFTTAMSLAFGRRRKATG
+DRGEISSYQAMATALVATVGTGNIVGVATAIWIGGLAAGLPAVRAVAAVAGGPHRLAEVP
+QREGGAADQARPDQRGAPGHARQRLQRAGGVRALLLVPGGHAQGQQADQQVQHAVGHEAH
+VRGALQPGVVGGLLGRLGGAPGPGAQRAAVRAVPPRVVPV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002616.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002616.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c46d23545c1de45aa4c4c7096da570adbb3c609f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002616.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_947
+MGGVHVRAGREGRGGEHLAGGLAQGEQHVRGGVLVRGAGRRQHGVHEPLDAAAGGGALGR
+ALPRVRLHEGRVQQGLDRHGGALAGVGHAGGEPAAGGVEVADRPARLAQRARDAHRGGPG
+LRRRGGLRRGVGAADGGRGGQRTAVGADGRAQGLEVGGGGRRGGGGGGPADQEGALRLAE
+GEVAVDRRVVGAGGGLAGGRVGRGLAHGASFRDGGCGARPTAAGRGLDSTSGPRRDTVGA
+GVRRPRRGGLSGPAGGAGVWWCPRRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002618.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002618.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92c981fc6933c51066ac654274562f0073b709e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002618.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_982
+MDTARDFVSGLPEALQGLGVFLVSFIPWVEGEGAALIGVLVGVSPWLAIPVAVVGNVLAV
+AALVYAVGGTREAVLRRRRSAVAAGVGPVDADLHDDVAPPAADARMRERFERWGVPGVSM
+LGPWVFLPGHVAGPAMVGLGATKGYVMLWQVVSIVVYTVFTGLLAAGLIGWAARAGVEAS
+LPGAF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002622.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002622.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b8d5aa1ac850698148461129ec7c56b94ac0949
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002622.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_1038
+MVDGSYPLYAAAGRSSAGFVVLSALWAGLHAGLIALMSALTALLIRNRVLALLAPAVLLV
+GASIGLELTVGPAAAPLITWVHPGGLLPSNLIAAAIPGLTLGLACGAMAVVLLRRAPQMD
+RFS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002625.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002625.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9a9a23e099a970361aac0325fc9cc1fcd22787b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002625.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_1188
+MTRFQWQPGGGDRHALEREGPFKVLFVCTANICRSAYADVTSRARGIQGVEFGSAGTRAL
+VEHPIDPPMAAEVHAAGDPSQHVARQLTRDLLEKADLVLAMGPDHRRWILDAWPQHGRKV
+LLLGQAARIMSDLPADLELDRLVAHLWARRSTDPSDEVQDPYRRGPEAMAIAARQIDAAM
+DVIAPTLEHVAQR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002628.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002628.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e7b0f6c0297a3821435731e5441d5fdc94f544c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002628.fa
@@ -0,0 +1,7 @@
+>NZ_CP040019.1_1200
+MRILLSSVGRRPYLVRWFRDALAANGVEGTVLAADVDPDAPSRPFADGFVSAPKVVDPGY
+ESWLRQTLVDHDVDLAVSINDFELSTWATLPEDPAWAPLVRLDAGTQRLVEDKFATSQAL
+LEAGVTSPVTWLGSTPPSTEDAAGPFVTKGRYGSASRGLRFVDRAGLPGALEEASGEVTT
+RQGVPALQQDAVPPAELIVIQERIDGVEYGLDVVCDLEGRYAGVLARRKITMRSGETDRA
+VSVDAAPFESIARGIAEAIPHPGTIDVDVFVDASGDIYVIDINPRFGGGYPFSHMAGARV
+PECYVAWALGRKAGAEWLRCRPDVVAGKFVEITATSEGGTGADA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002637.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002637.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f5c9e799e08a16751e448e35d01b8f86d81ba65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002637.fa
@@ -0,0 +1,8 @@
+>NZ_CP040019.1_1280
+MSDFPATPRSPSEEKSEDSLDKAPPTTAPAAFDGPAESEDSTLGAMAAEQDEEAVRYAVE
+FLKTVLRLRGVRIDRAQFLTSELQKRGIAITDIARAVEDNPASAGVHMEVLDDIVSSSIA
+LETRKSSALSFAAGLPGGLAMFGTVPADVTQYYVHAFRVMQKIAYVYGWQEFLHDVKSVD
+DETLAKLASFLGVMMGVGGASASVTSFAAQVARPALQKNIAGKALTKTAWYGPLKQTLKL
+VGVKVTKDSFAKAATKVVPVAGGVISGGMTFVSLKTQSARLARHLREIPPPGVDAAEYVS
+RLVHEEPEAKGKTMRAKVGGSILAAADSLRRSDAESGTGPDASTAASAVKDAAASGRRAL
+SGAAQRLRRPKKDSPASTTDAEIGDAGAEAPDAV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002639.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002639.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b877b3f5c0b57ffc1cfa8681cd811b90605d705
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002639.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1284
+MGKRETSKRRFLMMAVLLCLAGAAIITFTDLPWRGLIGAGLSLTGIALLMAGVIAGTRAK
+ETHSPEGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002641.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002641.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3647c095494f83f99bd766693908a143ea4cf926
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002641.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1298
+MTRCRTSVRHTDAMHRDVAPYRPPLWWTVLSVLAGLLVVAVGAMVTWAGQVDDSPGLGGL
+GLINALVGVVIVVRTLLARRLLSPAAPPSPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002648.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002648.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9adc932cf4316895aff15899036b52138d22f326
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002648.fa
@@ -0,0 +1,8 @@
+>NZ_CP040019.1_1319
+MTFHVAVDARSPRMSHCSCSSPRIGVSWVSSPGGVLALVGAHVQGEHVERRAAGDPAVDA
+GGLEAGAAAQGRGVGDGHVLLPRAAGAGGQRVHVTDLGVARVFEDLARPPVVGRLVVVPL
+GDDGDVRVQGAEVVVHHVVAVAAAELVQRLGDLGRLLRDEVAPGGLAGHLEGLRDGVVRV
+DRVAGVQEEVGLRGVHRRVAAHAADLRVDAVALPRGVRGPHEGLGGGGLPAEPRAGRRGE
+AGHGRLAQAAGLVLERVRHLEAGAGGQRVREDLRGVVGGPVDPAGVQGQPASEAAAQHLP
+VLVDRAQRGVQARTAGRARPQHGRVRGDVAGGDAGRQRQTGRGQATGGVAGRTGGGGVGE
+GGGGEHGGGRRGEHRTAGGGVGQGCGGLLHGARVGHAGEGHVASG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002654.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002654.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46a56a63cdf61d9792852be2f4077dc406e4ba68
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002654.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_1467
+MQKGAVAEKLARTGARIQRGVDRVYASVDLLEKPRELYESLPDSARRNLLGAFFSKIQVR
+VTEDGLELTSERTQINEAFHDWQTHHRLATTAHVATKRTAPRESAGSRSDSQNRLTQSKR
+LNKTVLVGLTGFEPATP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002655.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002655.fa
new file mode 100644
index 0000000000000000000000000000000000000000..87a4e0de64c3c526cae64fe6e1e9f2099e05c34a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002655.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1468
+MSENTPTGFSAAYKVLSVRTSEDTRAQLEVLAQLNERSVTEETRIALEHWVEKSKSDPAV
+LKRAEQVRAEIERDAETKRNAINAVLGGKNSKAASARTTKQTQTPQGT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002656.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002656.fa
new file mode 100644
index 0000000000000000000000000000000000000000..64472752b0ab4c28ad8437aa68c3c4027e3c346e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002656.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_1469
+MVKGIYVPADDSKALEVRELTKLEDYQTAVDGWIEAVDVPVLGVTIYVNEEGLIRRLPLN
+PRASFLWWYHVPGAHHAMLVGNVILVGAPDENGDGTDVPEEVVDLLTVAREYAVAVRIGG
+SSTPSESDGKLSSVLLPLVHGDPSWCLSLTRHEDYLSAAAWAVVFRERWVAAVDVTVVSS
+VEVPRRMQILMDALPPVA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002657.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002657.fa
new file mode 100644
index 0000000000000000000000000000000000000000..592b2bb9a18d4d5968a6cbadc2c4eb0d3ebdb1f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002657.fa
@@ -0,0 +1,9 @@
+>NZ_CP040019.1_1470
+MADENVPVPVWTLATEAVAVPDLVGDADMTPERLADLRTALATFAQAPIATLEMHPIERR
+RDTAGGIMLHASSPLAQQLSQLVTQTARSAPAKVDIAASGEVLYRMVVPAKVASQVSKGL
+VKPMASKAVSGGVYSALRDSTGIVSKATFVPVAGTGATTGAAATAGVGIAGAGALTVAAP
+LVLMAVAVGASAYADHQRQKAIERITDLLEQLHDDKLEHERNRLDGCRDAIDKATSVLLD
+QGKIGQSLGLDSASHEISTAIAAVRTRLKKWQDALDELPEGPVELATLTEAFPGITNENG
+AFSAHLETARLALALKRRVLVLQAVEHAQLDGTGNPFNSFLSELRSDEQRLNDLEASING
+VLLRLASLELKRPGGLLKKVHYAPSDVDKLLTAAYRLRGLSSGVDAAGNHADVVIEIERG
+HDGSVVVFPAAAV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002662.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002662.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f106881b55f989ad988a8bd10cc578e07d3e535
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002662.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_1482
+MTPQKQVHSDILKRLVATSGVIHLSWKGFSIGSLSGRRVLYAWPDRKHLNGLWDVEADAL
+AVIEWNEDETAEWIEDANPVQLFHGRTLEPRPVEESTDRQEPLPNGVDGILEHIAAMAAC
+YSSGLKWNEEDKLKADMMNRPERWAPITVEQVRTKCRALGMRPDDVDTVAGFLQRRKEGR
+RFNVQSSYRTFHFN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002664.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002664.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da4c418aede533a4f4b37e6fed11a1ef2d5080d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002664.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_1497
+MTLLLTGVALLLGWTLGSGGLGVGATAVVPELDGLAREAAEERLVAAGLATAVTARHDEL
+RTEGTVVATSPQAGQQVDRGTPVEVTVSAGPAPVPVPDLAGVSVRHAHGVARDARFAVEV
+DARRTDPHVPAGAVLEQRPAAGERATPGTVVRVVLSEGRAVRAVPDVTGLSLAAARTSLQ
+DDGWDVREHRVPVPLPAGDEARVLHQSPAAGTPLLEGTRVELWSR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002666.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002666.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a0994cf3a28e45bce2ce44d03a1456b3cfdcce4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002666.fa
@@ -0,0 +1,12 @@
+>NZ_CP040019.1_1560
+MAGRSRAAGASAFRASSSSASSAASEGVPAGDVVVGGVGGVGRSGLGGVGDLGRGVRGRL
+RRLVRPVDDGLDLGGGRGIGVDTGRALVRGILSGAGLVRGGQAALRVHGGEAARGLVLAG
+LAVGVLAGDEVGEGVVGLHVRAHALAAAHPQDLQQVGVPVRPRGGGARRGDGLRGVGRDL
+ALVVLGLQRGVGGGAGLGAGEHVPGLGLGEDAGPRVPGLQVAAGRAEGPQGGRLLAGGQA
+GQSRHGETGGHGPAALLAAPGVPLQGGAVHADLGEAVAGEEAEGAGPAVLDDVRVEVRTA
+DPDLHGLGLLGHPAALSQHRVAVGADAGERVAALPGHLLHGGAGADALLDLTGERGSASW
+VAAAFTDSWSVSAAGEAAAGAASSSSASAAGCGVCVGGWLGVDARGQGQLLVRTGGAGGV
+LARAGRVIVVRRFLARGRVLLGGLVHLRQVVPGGGCGGGVVVARPLGVLEHEAAQVGGQG
+QRVLGAVGIQQAQGVAVLGGSGQSQLCHGGGPSHVVFSSPGARTPGRAFPDPSGRAARRT
+PTGARRDPRVRRRRDGRSSFGRAGAMVHNLRATAQAGPVCSGHGPVPSLPGTGPGAVPHQ
+RSVRTPWPPTTTPLGRTRKS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002668.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002668.fa
new file mode 100644
index 0000000000000000000000000000000000000000..283228ac96a7dd5f7383b259c11ecc7b702eeb2c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002668.fa
@@ -0,0 +1,9 @@
+>NZ_CP040019.1_1605
+MSTGSTPSDPSEQRDQSNRTAPSDHPSSRGGGPHAAAAALARLAESPARVGLVRDVRPWG
+GPRVDLRLQDGRVAAVVPHDPAAHAAPIAPHASETDDGLVVEGHGALCVPTLADAHAHLD
+SVRLGLPFRPHTGRPGVWGMMSNDRENWRHAEAPIGERVETALGMMIARGTTHVRTYAQV
+DVDAGLERLEAVLAARERFADAADVEVVAFPQAGLLLEAGSADVLAAAMDAGADVVGGID
+PCQLDRDPVRHLDAVFGLAERYGAPVDVHLHEQGSLGAFSLELIAERVRALGMQGRVTVA
+HAFALGTLPDARRDALLATLAELDVALTTIAPAGAGTLPLDRILQAGVRLGLGEDGQRDY
+WSPYGNADLLDRAWQLAFTQGFRADDDVARCLEVAAVGGRSVRDPAAPRVSADRPASART
+IAAGDAADLLLVPAETLASAVMDRPAERTVIHRGRLVAAGEPHAGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002670.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002670.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2def0ccd2ccb568fd1c3a8730ad83d03ddb96c5d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002670.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_1708
+MTGPAVTVTGPDEPAPGMTAAQEEDAHWEHLAALAQAAGVMIRAGALRALPLETEASASL
+EALAARGRDRAEALTVLLGLPEESLGTGPPEDALSAEAVVGLQWALAERVGVDPDAWSTP
+RPWARAWAARSSRSRSGGTSPPT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002674.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002674.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d72549c49e8a13479b03ea86153c531671012ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002674.fa
@@ -0,0 +1,2 @@
+>NZ_CP040019.1_1781
+MTALASLASPAALAPLAAFPAPPPGTASRSAR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002675.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002675.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6cc0af96d64e1196a1d7018bb92bd021fcca5cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002675.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1801
+MRAAAFGSATPAGRAPATPAPADPASPAGPAPTGPAAKDPAPAAPASSSEPAPAASDGDD
+RVTA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002677.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002677.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a341f7186d26b5d57216cea00523157c31138e60
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002677.fa
@@ -0,0 +1,11 @@
+>NZ_CP040019.1_1812
+MIAEDVDRAREAVEQALAAVAAPRWQDVPGGALLPDLLVQAETLSRTVAALQTALAGHLA
+EAYEHEADRQEVLGIPPGKGPHRDAADCLRDTVRIDRRTAQRRLRRAAATRPRRDFVTAP
+LADPALPEVAAVLSEGAADEAACDAVIETLTRARTDLALAAVPQDEADALLAAGESLLAA
+QLHHADLDGMRRLCARWRQHLDAVVLPDSGIPTEAELRAAQGLFHRGRRRGLHRWDLHLT
+DTQHEVLQTVAAAATNPRARGAGPSGQVDAPAGSPDLDPRTRGQRQADTLVSALQAALAL
+ATPGVLPATAGHRPQVLVTIDHETLLRRVRTASGTAAVLSEAEFTGPIDPREIRRIACDA
+EIIPAVLGGEGEILALGRSRRLFTRAQRRAVTARDGGCAAPGCTLPASWCEIHHIGHWED
+GGRTDVDNGVLLCSHHHHAVHAGWWTVAVVAGIPWFTPARHLDPRPDAPGGTGTTGSTAR
+RRPRAPGERHRRRRRRRRNRQGQWNRRTRRDGQDGQVGQVGQGQTEPVRPGPAAPPRPPV
+RRLPPPWTVLSPPWRPPGRRRPRHG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002683.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002683.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bdd2df98cec9397603b1cbbc3e8c55c36ff66e50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002683.fa
@@ -0,0 +1,2 @@
+>NZ_CP040019.1_1848
+MAHGGVIRAAVGLLLRHEGEAFAALERIDNARAAVLQGAFATDTGAEGWGDWTLEGYGI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002684.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002684.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86ff5f5d7442736bee7acdf6910fc6847424099d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002684.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1876
+MGAVFAAAMLAVGGTALATPPPAEAVTTVVITNGNFHNCTSRMNSEMKLFRMEGYTVRIA
+YKCKWFADARRWEGTFYASR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002685.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002685.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b2362cd95ab107e3caf56f4d37c485b1c725025a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002685.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_1899
+MFERFDLRPLARPHFQSLIDPGRRRISFGTTAIIFLLPLAVGILGGWAVPIPGAAPADAS
+GGAPAPASSAASAVFTALPGAAGTLVAGFLAAFVLLMNLRIKLDDSPQLPRTPAQLRSIS
+TAAMSSLYLTTVSGSALIVSLCLAIFGAPLAAIAPLAFRALVGLVLGLFTHILVNAITVL
+RRVAGAYYVLYKGEIRRVPVRGVPEHDKRAS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002690.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002690.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce8d06a628fcb3cc1ffaf1b98fd27b6bef394396
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002690.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1905
+MTTAAAPFYVENLRRAREARTARAAERTAARLEDLEDLAAARVAREAAARRAGFPSVGAL
+ERFCYRVGRHDLIKSLPLQRSAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002691.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002691.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cd23ab90c997d2dad7be81fe6b7c534fc8a75ce4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002691.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1906
+MTAAVAQTVEVPAVLTTSDLAARWQVSEEWVQDAAKAGRIPGFKVGRAWRFRVDAVLAHE
+EAEQAALSPANVFALAPGAVARRARRATA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002692.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002692.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d8c3875424c61e748fc804976c1e316a938179d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002692.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1907
+MSVHPIRLQIPFADTSLVFGFDADAERDVRLLLRFARARASHGAGGFWLEYGWDTGESQM
+VWIDPAHMPTARFDVTATPVADQGREDDMSRHLARTHHVYLTAKGWQSDTHELAVDN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002693.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002693.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cad69b01d8fd9631e70fb85c0fb66f3a66d43f94
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002693.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1908
+MAPPVIRFPENAAFTGRVKSEDLSSGVWSIPADDMGVSFAGTTVADEDACRRVDDVDQDG
+PDCEGPDGGESA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002696.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002696.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9067beb21c44e3d83f1edb2a3bf55ff400264c48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002696.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1912
+MRALVTDGLGATSVEESGEWPCRRADPDAWFSTNPYRQAEAAQACHQCPAQELCLRAALD
+LEGSTGKSYRFGVWGGHTPEDRARIARARRRLVRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002697.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002697.fa
new file mode 100644
index 0000000000000000000000000000000000000000..53e65fd8e90b64ba393ced1479dc375245b2d25d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002697.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1913
+MNDPKAKAAYHGVPCDGRCCRQNRHLGVCPHGRVCAYHLNEDARQAREERERDQIADLER
+AARMTRRRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002698.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002698.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26b549ae3b6ff81b52bb3303fe50625b07c4fae4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002698.fa
@@ -0,0 +1,2 @@
+>NZ_CP040019.1_1914
+MGDCECGRRGVLLDRELDLCILCRNRLDSAPAKEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002699.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002699.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8be07e3266e3f8330db572ee860805246c5467ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002699.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1915
+MSYHHINEDGTAVVCTAQESAWCRSRPNCDTEEWNEHGCAEHDREHALTPGHECWQARNV
+NAWGGPYPDDQPDLRPGAPVTLTYEGEGIVTWDYVNGARP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002700.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002700.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c2f508768e310aa3d434ff2660d10123a2f94ec8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002700.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_1916
+MSITREAAAALADLHAANPTMQDVAGTWQEDAVAYVAALWDAEVGRAAKEGTFLPAFASH
+TAGMRRLIAAVVAAAREDLAEAERAQHGALAAVLNRVEFQQARAAIGELPDDVAAWQTTE
+HHALITTITRELEDPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002701.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002701.fa
new file mode 100644
index 0000000000000000000000000000000000000000..090e675bccfdab14f832c0146a739d9d3108ffe4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002701.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1917
+MSARRPRTYPAGSPERAVADAVAAVYAEADLKLEALQLDLLEPRPDGTRWTPQQVQARRI
+TEALDALRDGFQEFGRGITAVAAAASKAVAALSAALTTTTRDDYTLAGPSKGAAS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002702.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002702.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b40afbf7e0e4f35d9664e22f7417c96483056193
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002702.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_1918
+MKLFVEIADLRRALQALTPHMDPKDELGVFGRIRGHATDGNLFLMATDRYTAAMAVVSLW
+DKDDLTGSIRDDALEFSAQDVKEVLTLFRAPRRKDEPEGDLLIETSPGSSDPARRLVDVS
+GLFPGKEFRLPGADVDEKFPNLARVMSRRPAPTRTVRSNLTFAGEHLKKFLAASKAYEEP
+ITLQPVAEGSNMMLVAVGESFRGMIAGWRWPEDKTPDFEGWDMQWRLWSEELLGMAPDLR
+RPEGHEEAPADGEERDWSAALEQWAKDLADRLAKEQDDSEDEGDAPEQEG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002705.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002705.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1eabe96728cd6616e2008b643a35e1f06600e9be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002705.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1921
+MTNWDDADQVNDELLGRMERPDGCTCDLEYTTDYKGRILHIYWSLELTCHHHYPRTAAQL
+ERLNSCPKQEGEA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002707.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002707.fa
new file mode 100644
index 0000000000000000000000000000000000000000..19d58a8e5daf98ce81dbeb2619fb5daf229fbe1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002707.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_1923
+MATSRTGTSEYKRWRSYVLREAERSGQHRCPYCGVTLDYRTGRLPHSAEPDHVTAWSAGG
+TNTVDNGRAICRRCNQSKGARAAPRPRAVQAAAPLRVSRRH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002708.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002708.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3dd5a0ada20747ba8c0580233a211c8895680d65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002708.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_1924
+MATANRWVRWALRPRGGRLTKVPLTVHGRHASSTRAATWTRRPAAAASRVGAGLGYVLGD
+GVGCYDLDGALDRGRLKDWARDALAAIPEPALFVEVSQSGTGLHVFVVAPPGPGTVTRHA
+GGAVERYTTGRYIAMTGVPFDVPDGLLRWATPLDAALVAARR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002710.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002710.fa
new file mode 100644
index 0000000000000000000000000000000000000000..acc4b147c037464aeb4532a341584ec6b9f65554
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002710.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_1926
+MADAPAGLGDRGLTIWERYAGVDAGVDALALEAARAADRLDELDNVIQGKGVLKLMQFRL
+RDLPDLDADEPTWRVEVQFQSVLAEARQQQAGFSAMIGRLAAMEAPKGAAAPTAAHAAAV
+QAGGNVTPLQAARSAATR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002713.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002713.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa0409d7117342c48d59b89fc40baa7e473e301b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002713.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_1929
+MPSREQLEAFNRDQALLHDLVMGALDGMARRLGRFATPDQVLTALLEAMPELVGQFGHAS
+ATLAAEWLEEVYGIRAVLGETYPLEAVTQTLRRHAGQLWQGAGPEAVVAAMRDDVARWVK
+AAGRGTLRDSATANGLRWARVPSGPITCAFCLMLASRDAVYLTRNRALRTKSGEDRYHND
+CDCIPTPIRGPQDYPTGYDPDELYSVYSEATSAVGSRANTTAILENIRRAHPGRVRDGVH
+TTN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002725.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002725.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e4849fa6a7c0f681828fabd07933c57f1a145a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002725.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_1941
+MFGVDLAAWVAAGRWLGVLELIHSLPRSSRLREAQLNDPDVAADLLELQEAQDEPEEWAP
+ALAETSLITDLLSALIGEVRSLRSEQTAIASGKKPRPVKPIPGPRTALETAKALRAEKYA
+AETLSRFGF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002726.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002726.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c256dd7e81d167358b3d24b4a63f731c27924a35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002726.fa
@@ -0,0 +1,19 @@
+>NZ_CP040019.1_1942
+MAVVGVAEVLVRPSFKSFQSEVGKAVDQATPESGPASPGSRMGKRIATGLKVAGGAAITG
+AGVVLGTALTKGFGRLTAIENAQAKLTGLGHDAGTVEGIMRNATAAVKGTAFGLGDAATA
+SAAAVAAGVQPGEELEGVLKLMGDAATIAGTDFTSMATIFNKVKASGKLQGDEILQLSEA
+GIPILQLLAQELGVTASEVSDMASEGEIDFETFRSAMEAGMGGAALKSGETLQGAFANSM
+AAIGRFGANLMSGVYPQVKGFFASFIEWMGPVEAMGKTIGEWLATALGGFVNFLTGTAVP
+GLRSFGETVAAYVGPAFSDFAAFLTGTVLPAASNLATFVSGLLTPVFAALADYITGTVLP
+AVGGLLNWFRESPQWVGLLTTGLAAAIAAVAGIGVALKGWAVATTILTGAKALLTGVLGK
+LWAVMAANPVTIVLGVLAGLAAAAVYAYQNFEQFRVIVDAAWAGIVSAAQAAWTGFLQPT
+FQSIGDWLTNVLAPAFTSFWQNGVVPAWNGIVAAVQGAWTGVILPVLSGMVQWVGTFLAP
+LFVQLWQGHVAPAFLGIASAVQSAWAVIGPALAELARVVGPVLAGAFNFLAPIVARVAQV
+LGTVLGGAVTLAVKFIFMLVGAFVDHLGGAIQGAIRFLQGLVQFISGVFTGNWAAAWEGL
+KSIVVGAFKFIWHTINVVLTVQVLGVVRGALSGLLGLFRGGLSSVTGVFSAAWNGIVSLM
+RGAWSNITGIARSGASGLTSIVNGLVNAVLGFFRSLGSGMGSIVRNAWSVARSTFGGATA
+ALRTMVSQMVQGILGFFRSMRAGITSLSKSTMTNAKNAFIKGIAALEQSVSTGLLRVQAF
+FRDLPGRIMNALGNLGGLLKDSGRALLAGFTDGITNGFSRAKDAVADGLGAIRRLFPFSP
+AKEGPFSGRGYTTYSGRALSRDFADAIADEAGYLRKQAAGFMDAADFSASSRITAGVDLV
+PLSTRDLLLDGAGRLPAALQVAHSVAGPPRSSLERLKLAAPEGRQPLTLVLEDGTAFPAY
+LDRRTDTRLAGHVAGLAQPLRQYAGAMQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002727.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002727.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d44f78a4eff4d8fa5c5f7797d05c401a85aecf80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002727.fa
@@ -0,0 +1,14 @@
+>NZ_CP040019.1_1943
+MAWSGAGSWASVSGRRMRLIWSATMSPTTVTAATSSVSVTVTHTLQTSAAIDDPSTAFVL
+SGGLGASTTSPYVRIGSLSGGSQVVSTRTVSVPLAYGKAQTLSWSASMSGLAYIPTTAKV
+SGSVPVPARPLAAPAAPSGVGVTRSSDTRHVITWTRNSPGSASAPYQNQVIQRSADNAAT
+WKTVATVGNVSSWTDTTTTAGRRYQWRVAAKNTGGTSAFASSPVVYTTPAAPTAVKAVRQ
+GMDVLVSWVKSVSPHSRSEIAWRQEGGAWQYPGWTSTGTSYVITSPDPSKPLQYAVRAEV
+ESQGVTLGSPYLWSSWVQLLALPAAPTNLSPALADAALPITLSWRYNSTDSSEQSAREIR
+WRPLGADAWKGIPKATAADSTHVVPAGLWEPGTVEWQVRTWGAHADPSPWSTPQLTRVAQ
+APSVTITSLQDGPLAASQAKIVYSFFDPEGDEQTAGSVQILDDEGSIVYQRTWTSASRGL
+TPPVRLQDGRSYTIRVRARAASGLWSEWDQVTVAVDYPEPPVGVLTAEWLPDSAAVMLTV
+AVPPPAEGEVEATSAEIWRSVDGGDWLRIAAGLPLDTALVDPTPHTSRTTAYRLTTVSDL
+PSTAEAAPVLVAPDPQGWIWLNSGPGWSRQVRMRDNARTGPSWSRASERHHMAGAKLPIA
+VRGEQRERSVSVSVRLAPNPDGGCTYAELEQFLDDADLPILYRDAKGRRWFADVSEVSGS
+EERILEEASFTVYEIDHVEAEAEAVEQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002728.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002728.fa
new file mode 100644
index 0000000000000000000000000000000000000000..225d6a19418e8d475efa70bfba146b4f9fd88a60
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002728.fa
@@ -0,0 +1,8 @@
+>NZ_CP040019.1_1944
+MTDQLHLIDAPEWGPAAVDLLAGSRDVEWIYELVHARTNRFIRTLRGVRNFRFENNLHAT
+IRSGGSCIWQGAEDIDWMEHRLRAHQRISHRGQSLQWTVGTFIVESPTRVLTDKTRGAQD
+LQLFDAMYRLDVQTSTVSEWVAHKGSNIIGTVRHLLDRQGIKHALEDSDAVFASQMSWEA
+GTTYLRMVNDMLAAANFTAVYADPQGVLRAGPARAATSRGVAWTFRDDSTAMRYAPEVTH
+NRDTYSIPNEVVLIARSDDPDTLPMSASARDTSSPYGTMRRGMVITKVEEVDAASQAILQ
+ARADLRLKEVQRPASTFTFQHLPLPLEMSQVVRFVRTRHDVDVLAVVEKTGFDDGTGLAE
+TTVREVVS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002731.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002731.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d596cd89182027b26288103b98d98922fbba06c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002731.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_1947
+MVFLFTLALAAVGAGVVTLARGDAAAAEAGLSRAALVLEGANTIGTSRILGTGAVILLVV
+ALAATTTRRWQRVVCLAVGSGLAATMLATGSRGPLLGVALGIAVVLLVSPSLRGRRVRGL
+LAVALAAAAAYWWSASRSAESVDRALGWITGDRDTSTQARQQLWDIAFDHAKRDPFGVGW
+GGFADLDSVPSDLPYPHNFVLEVLVEGGWLVGGAAVIFVIASLWRLTRQATTPAGAAVLA
+LGIFTVTNAMASGDINDNRLMWTILSSAWVSTRLSQPQSQFASPYPISAVRS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002733.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002733.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4bab472141aa37fd1e625b5deaee2c48022ab2ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002733.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_1949
+MSIPETIILALIAAAASVAAAAAGRGYTRRSKQLEAETARLAAEREREAARLAAEEARWT
+RLEADVERLAAEVQALRQENEQLRRENAAERAARGDAEDTIRDHEELIEDLLVHLIVRQD
+WEDSGSTPPPPVLSWRILAALRKRRAAMTGPIPLAHDQTTPTSQED*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002734.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002734.fa
new file mode 100644
index 0000000000000000000000000000000000000000..15457a5e0fd865633fe77752c620e3c15659037c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002734.fa
@@ -0,0 +1,7 @@
+>NZ_CP040019.1_1950
+MPTPFLTGLGRVLTTAGVTWEGVPGWETRTGFASGYRDVYGATVHTTETHDATFAKGGDA
+PTLEWVVDADGSRRGAHTYALLIGRSGKVYLIAAGPGWQAGHGSWPSKLGPNPGIPDDQA
+NFHTVGVSMDANESQYPPTEAQLVSLVKVLAALRAEWAPDRFDVMMHGEWSPARRTDPTR
+VPGGWDAIRKAVAAGAWPVQPKPTPPTPAATSSRPAPATGTYTVRPGDTLGGIAKAHGTT
+WQALAKLNALADPHLIEVGQRLRVPALPTHTVAKGEGLWGIARQHGLTVDQLANLNGLTR
+TSTIHPGQTLRLA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002739.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002739.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d0a04243e2190cc4702b2c97c4613019630df2df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002739.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_2008
+MTTTGRGSHRAYDSDRDRLLDVIGRAGTPPVDETTFRVDPLALTGHDQTTGPLSGAVVAE
+TVLVVACDALTAEIEQHHRVMHGAPGMTEAQDRRALVDRMVIDFDAFAGGVWSGTDSPHR
+HGVLLDLHTTAVRIRKRGGVVYVVPPADGSADQTRLPGLRVDHDLWLPDTEGAPVSRLLV
+AVRRHAGLMPREDDDQIGELHG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002741.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002741.fa
new file mode 100644
index 0000000000000000000000000000000000000000..29c1529f0c85af52c88047ccfa81ae38cf006c49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002741.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_2010
+MKPGPSLEKALYVGCLAAMSIIGVAVAVLGLLGQFRLVVILLGLGAVVASVLIPVHARRM
+RRFMGVAIRRAGGRGRAAAPTSSPGPAASVEVGRETMAALTRINRQLVSLREETMGGQLR
+PVSGAGSTDAADDRSDSSMAVAEALVGVRHELSVLRAEVAHLAEAPRGGRQA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002746.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002746.fa
new file mode 100644
index 0000000000000000000000000000000000000000..47c1b8bca8687dd0fa25ea63d10e3a3dde9d837b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002746.fa
@@ -0,0 +1,9 @@
+>NZ_CP040019.1_2060
+MADRGHYELPHSGHNGIELVGTFAYEDAILRALPRLPADGASVEAQFTVDLVPEPDNPHD
+RRAVSVRHRGEVLGYLSRDLAADYHLPVKRILASGARLQTGARVFAYLSWDDKPEVRVYV
+GLPAPDALTPLNDGYPATTAVLPYGRTYQVTKEDQHFEHLFDYVPRSGQGPVILTLHKSE
+AMLRNGTVRRTVEVRLDAEKAGELTAATSAHYLPVIEHAEALGRVVGVWGTITGSGLAAE
+LTIKGAKSSELTDEWLREMPIFPHLVPEAHSYEVPDAYQGEPKTKGRSRAMGGHSAARLR
+EQLDQRFVSTSPAELDTTPSPSTPSPEKKPGKPQPPANPTPVPLNRDVTRLGIGTGPRTP
+IYYTVKGKEVFVDDRDRSSAGKHPRRTAWLLIAGLAVLGLILSGVPGIGPFLTLLTLLLV
+LISGPDQLRKAKVLDIDPHGTGHPSRDWRDRERGDVGEENQDHDTEDGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002751.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002751.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dd509467fe556e19a4c0d3826f40bd79c0e62a6c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002751.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_2155
+MTTYSPASARDHYLTLREAVELGYGAYSTLRSWIAQGRLPAVKTGGRVKILRADLDALAR
+PIGPDPAPNDDLDAAIERLVAQAPALSPRQIRELQSILGGVAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002753.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002753.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0362a2f9791c9faa01d39f10607e719a79b85859
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002753.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_2161
+MPRVPIRVPLTIAACAALLTGCASGADSTDPGSTTGTTAGQGQSQSAQEGASQPADPQDK
+PKTGEQPEFASGNDLLASVNTDLINAGATACVWDIKSEGPKYNNPEAYFWAECDHKSAGE
+LEFEGSTDKPHGVEVIYWHPDPAVLKENVIGDSENPVWATGKNWVILTDSYISPNYPFYG
+ENAEASDEEKQSWRDRADRVRTETGQMLGVRFTDGRDAGNQLTTGIDGNGSGTSGSSTDA
+P*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002759.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002759.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1560549ad70eebb1379c67f46823bf29f48517c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002759.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_2174
+MSGQKGQVVGYARVSTADQNLDRQLEALGGADRIFEEKASAKDRERPVLAEMLAYVREGD
+TVVVKSPDRLARSTRDLLDLLSELKAKGVAVRFTDSPALDTGTAQGTFMLTVLGAVAELE
+RELIAERRAEGIALAKKAGKYDRGPKLSAEQIAVARQRVTEGVPKAVVARDLGVSRQTLY
+DALAGRGRYAATA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002764.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002764.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf169b347a412d49452ff13ee01b3ea7bd662067
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002764.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_2186
+MGGMGEGILSDRLRAAPTLHVRVIRTPGADFAAEVTDDDGARLALAATVHPVADWRGAGH
+AVELVCADTGRPMITVLDRADLGLGAGEVLDDGALPLGVVRPWDTGFHAAARVEAADGAE
+FELQDGWNSAVVRIMHHGRVVGLLAPAAAVPWRSRLPGGPTPEPVTLRWERLDRDGRAGQ
+GDGADPGAGPWGLAGDAAARELVALPGRLMP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002765.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002765.fa
new file mode 100644
index 0000000000000000000000000000000000000000..447835eab0172b04de1dd1c523cf7cff042ed021
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002765.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_2204
+MTAEQAREAGHQVKVASKPVATIAAMPRPKIEEDAHGVIEVVVDAATDLVLGARPHCVEA
+QGLVNLVALAMRADVMASALRDGIWTHPSATEALNEVLGELG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002769.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002769.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21b01ca9a8a2799e81d0bef5c655767cbc046ad5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002769.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_2281
+MSNQRHTTADVAAFESWLSVFRRPQTVNNRVHYATRLETWATAHGCTPWTLDTTQISAWL
+STVGK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002770.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002770.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dbf4bef87115ad5fe60bc7db3da2ecc45eb61934
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002770.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_2282
+MPKKYTPELRERAVRMVLERQAAEGGPRSHSIRAIAPQVGVGEETLRMWCNRHGHEVAPV
+PAGESPAEEIRRLKRELAEARRANEILKAASAFFARELDRPTTR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002774.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002774.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af37eb56d8270cd5c0c73eb747a0d0139e0cac24
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002774.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_2325
+MSVVIDAPRASALDRPGLDQDLIPVSQADGLDPVIAVALAAGRRAGERLTSTPLTPRQRA
+AVAAVMGGGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002776.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002776.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e1eee5a2fbbce76828883e2ea8a4b33d4ce2f4a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002776.fa
@@ -0,0 +1,8 @@
+>NZ_CP040019.1_2360
+MTTPSQDRLTIGATGAFERDNFGDLLYPMMLRDAWAAWAHTALLSRFPVSTEDLLGQAVL
+DYDDAVSTQHFDALVLTGGASVPISMTRAVQLQDHEPPVLHEDPHGLPYVPEVNPRGVNA
+DTPVFINSAGVWPTGSMRVRHRRRLLRTLQGAQLITVRDRESAELLDSWNLSAHLAPDAV
+HALSQYWPLSAHDRAPARVAIQLSDEFLDEHGDAAVRQGLLEAGRVAVERGLDEIVLFAA
+GVAPGHDDLGRMESLARTLGEDLGMVARISQERSPRDIVALIAGSGLVIGHSLHVRVVAA
+SYDVPRVSLRRAKTEAYSRSWDPAMPSGTAPARLATAVSEALSDDRRSTASADARSLVRH
+ATGMVEHLGSDIRWWSGRRAEVGRIRRGVNRRNDALKVADTVVSAGRRARASVGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002778.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002778.fa
new file mode 100644
index 0000000000000000000000000000000000000000..147ab5ae986d401d066cebcbed9be1e7f54a64e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002778.fa
@@ -0,0 +1,6 @@
+>NZ_CP040019.1_2445
+MAVGGEHRLGLAGTCRHHYRDRLVFFGGPVSQDRVQRAELRTAEADARFGLLDETEPPRQ
+RRCYGVAVLGFLLVSAWTLAEPPQLVAVDVLSLDESHVGTPSSQVHEVPLQLHYYLVWTP
+NVVARFAQSCVVGCRLWRRRELPVRSWPDGDRGSGLFHHTPRPQNAPSRRRPRVRQRPLR
+ASCPARTAAQLLDAQAHPDRDDAPRHLPVQRSDAQSCDVCRTAAPAHRPARRWRTSQPAQ
+PDSGRSNGFKDGANSPRPGHADPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002780.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002780.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa1f092568ae7c6dd3e89024b78fd030fe340b65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002780.fa
@@ -0,0 +1,5 @@
+>NZ_CP040019.1_2447
+MARVRSVKRAEEIIKLYEEIGSEFSPIRIDTGMAESTRRKRREKLFNRESRIVICVNMLG
+EGFDLPSLKIAAIHDPQKSLAVTLQFVGRFTRVGDESLGEASAFVPLQVAGVDEQLRKLY
+GEDADWNEVIRDLTERGVGQEKDRTDFELAFGSVPREVAMRSIHPKMSTVTYQSETSLTW
+NPENIYDVFEDRLLTTRLGINNKGD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002783.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002783.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba21f0976ed8148a422aa15ad052a3c41b5d27f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002783.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_2454
+MILAFIDEMRAEGYAVESILRVLRQQGLRIAARTYRAWKKPTRIAGRTITDALVEGKIRD
+LVWTIDEVAGRRRMRPEGLYGRRKMLSLIRRQGGARQVW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002784.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002784.fa
new file mode 100644
index 0000000000000000000000000000000000000000..360fa53da87074974f016fce23623375e9fde2e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002784.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_2460
+MSPRRPRVPRVDPATGAPRRAAQDAAVEPTTAPQEPAAEPRGADSRPAPSEDAGTPAAPS
+PSAAPGTGQGDGSAPSAEPERPATAEVIDLQRAQDRRQGGQAAPEHAAGSHAAGSHAAGT
+QPVEDRRAGVNAARPAASSPARPAARRPRPAPRRALS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002785.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002785.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33c7a3958beffb893ffe059fd900257e6c04bab7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002785.fa
@@ -0,0 +1,7 @@
+>NZ_CP040019.1_2530
+MADAPLGPVPRLGSPPEGSGRRPTRTAGMLCLGGRPRRLWDHPTYPPEVLVDWSSVTKTV
+TAAAASHLAAAGALDLDAPFRTWVPEIGNVPATVRDLAVHRSGMPTMHPTAARGLLRDPA
+RGALDEEELLGHCPGLFRSLREDHGRPRYSNLGYAFLGLVVERASGEDWWTAVRRLVLPA
+DRLPTVTVDPAPDLQRRPGLGPLRVSPWRLSSSAYRPAGGLWSTLSDLLAHAELASLPTA
+SRLGWHRDPSGLLVHTGSGRYSSCCAVLVPATGDSGVAHSTAVPAPRLQRRLVKALLSHL
+R*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002786.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002786.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eaca0177124e6b34c818c8268e69e19c2a86df47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002786.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_2531
+MSTIAQFADAAALPYGAKADMAAEPTLATIATTATTALTCITAAFGHHDSERLDVMSTVE
+ADASVDTMVAARRDALQG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002790.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002790.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b8df7c433394fd3eb0e64cbcef8670e7f0dbe25
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002790.fa
@@ -0,0 +1,2 @@
+>NZ_CP040019.1_2567
+MATEQGYQRIVDKNTKPFIRLNDLIASLEQKAQEFGIHDAAAEADAS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002800.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002800.fa
new file mode 100644
index 0000000000000000000000000000000000000000..986ee5b022a08cd59090780e87ee9fa5050e991e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002800.fa
@@ -0,0 +1,7 @@
+>NZ_CP040019.1_2604
+MGKRAGLAPGTRSGLWSYMAAAIDALQPQLVVIENVRGLLSSPAVRAPLEEDDDAQSNPD
+HATPGDAALREVEPDPWGLGDLAARPLRAVGAVLGDLADLRYDTQWIGLPASLVGAPHPR
+LRVFILARSRGTVQDAARHGLDSWRRVTGTGEGEAGDDRALASDHRPRAKRAGWLAEQEQ
+RTRDAVVPDRGHLRRWGRYARAIARWEHVTGRIAPALLDRTSGPRPSPEFVEWLMGLPSG
+WITDPIHQLTANQQIAALGNGVLPLQALSAMRVGALVQADAASLAGVQHPMVSRGCTVSQ
+EEEGEDEKAGESA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002801.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002801.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27cbfb58fbbdbe941c58b5ca3b1098f41ebb37da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002801.fa
@@ -0,0 +1,11 @@
+>NZ_CP040019.1_2605
+MPVAGVAGLAMDAAFPALGWWPLAFVSVTLSLVTLIGRRSWGALLVGTVFGAAFWFPHVS
+WSAQFLGEHPLSWVPWVALAGALTIYTAVLTVPIALAYRWLPRRRNAFAMRLLALPLLVA
+GAWTIRELIMGSWPYGGFPWGRVAMSQSESPIAPVASWVGVSGLGFLMVAVCAAAIEAVR
+WIVRAQPARGNATEHPRTPLASWAASIPVLGLAAVMVLVPQFPTSHAGTIRVGAVQGNGP
+AAYVDEHEPGAVLESQLAASAPLEDEQVDIVLWPEGGVDSDPLADEATAHALDDAAARYD
+APILLNAAAADGHLVYNTSFLWTSNGPTAAHAKRHPVPFGEYVPDRWFYGALVPSLVDLL
+EREYAAGVDTPAIEVDGVEVGLAICFDVAFDDVIHEGAHSGAQVLMFQTNNADFRDTDEH
+LQQLAFARMRAIETGRSVVNLSTTGTSQVLAPNGATLAALAADEPGLMIADLELRDGLTA
+AVMLAQSINTLIVSGTLAGFLVLAFLLLRDRASSRHHRVLDSSQRSSIGLHECADAHRRE
+RL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002804.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002804.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f52adf80af2f31826338366893372b0c663669fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002804.fa
@@ -0,0 +1,8 @@
+>NZ_CP040019.1_2610
+MTPRRGRSSLALAAVAALLVTGCGASEPEPVRDPYPVDGSLPVVDTSGLQLPTPFEELEV
+VDPGWDITPQYADGVYLAAGERDGVLEFTAVDVYGDVLWAAQRPASCTGFVVTTDAHGRA
+LAILGDLQITADALAATTATAYDLTTGEQVWGPVEVPGPYQGPGLVFAAPPDGFMGETGP
+RVALDPTTGDVAADESSPEGIRIIGEYHGIVLLTHEDALIARDTADDHELWRIPLAEHGW
+TAASISASLRPEPGDGLALIATSETTGALLNLDQGSIVSSTARDAAVDPTTGTLVTLDDT
+GLHGYDADDRPLWSLPVAAETTIAAIGGVFLYLREDGAIRVHNVLTGDVAQAYEPDGQGP
+IIVPTHITINGAALLLQERRHLVATIAESPLNESFPTSSHAGMSIVGARVADST*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002809.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002809.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f99346b843f32aec584b4d44c99c5038a22f0c41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002809.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_2616
+MNENTREVILHVADDPADVQRALDAAAGLHAAGLGVRVRVIVNGPALAGLTGTDAVQVPE
+HTEVAACSVGLGRRGIDPGELRPEVGTVPSAVTAIVHAQLADAAYIRI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002812.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002812.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7922c5eb549454bf7b005274a26cd4789012f99f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002812.fa
@@ -0,0 +1,3 @@
+>NZ_CP040019.1_2626
+MAIVVRIDVELARRKMPVGEFAERVGITPANVAVLKNGRAKAVRLSTLERMCEVLGCQPG
+DLLEWVPDAAAAPGPGAAPANDDDGRPGTR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002813.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002813.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d17022a9b74e6a52bbbb5d2860a5dd22b26eb066
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002813.fa
@@ -0,0 +1,4 @@
+>NZ_CP040019.1_2627
+MRHRLATWVLQGLLVLAVLLILFLQVIGLPWLGGEVARDLPAEAFMRWPVTALAIVGLAF
+VQVGLVGTIRLLALTRTDRIFTARALPWVDAIIAAFVGGGLTCAATIAYQATAVSGPPLW
+SLMLLVGTAAGLGLALLMGVMRSLLTRATALRDEMDAVI*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002816.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002816.fa
new file mode 100644
index 0000000000000000000000000000000000000000..59cfb16992223a11a99a8a4dadd6b5b846048a34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002816.fa
@@ -0,0 +1,8 @@
+>NZ_CP083691.1_44
+MMSRMSENSEPGSEADARDSGSGSVGNLELFFDLVFVYAMAQLTELVRDDVSWRGFGHGV
+LGLLAVWWAWVCYTWLTNTFTTHRVVFRCLVIAAMAAMLLAASALPTAFSTGALVFGLAL
+LAIRVIHLVMFVVDASHDDEHLRAGLLRLVPSLLIAPVLIAVAAAFPAPYRELLWIGAAI
+IDFGGPLVAGVEVFRVVPSYFVERHGLIIIIALGEAVVGLGTGASEHLQQPVVLAAAVLG
+VLIAASLWWTYFGLTAGAEQRLEDADGPERARLARDAYSYLHLPLVAGVTFFGFGASVAL
+EHVSDPLPLLPAIALSGGVGLFYAADVAYRWRDHHQLVPDRLLAAAACLLIIPPALSMPA
+WSVLAALTAVGALRLTWELVRRPRIGPATAGQVH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002817.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002817.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1017f5313de53594158901fa9baddafc6a1fcb80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002817.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_46
+MLIVLRGNAASGKSTVALLLQDRLDRPAAILSQDHFRRSIYAECEQDSLAHADLLEAAAL
+HCLGRGHHVILDGIFHAGRYGPMLERVAAASDDARFYAFDLTFAETVRRHAMRPRAAEFS
+ADEMASWYHGWQALPFVDEHRITATEAPEQIVTRILHGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002820.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002820.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2ea968d0345f96384729eed985824718754f5f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002820.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_70
+MKRLNVTARLAAAVLLAAGLSATPASAASPLPVSDGVVAEAGLAPVRDGGVDSGVRDGFC
+TVFPFMCDER*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002823.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002823.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81fe4024124d819f5267964a7792bbc4de745c64
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002823.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_133
+MNNLTPAEVVGAYFQNLADGNVEQAMSALDPNIEWHQPGENRFAGVHRGPEAVGALIGGM
+MEVSQGTFAVAPAGPLMTNGDVVAAPVRFTGRRDGEVLDQDGIDLLTVTDGRISQVRLFS
+SDGPAEDRFWGQS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002831.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002831.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d644b5a823811be5eb0bfb37e08d5a2eb2144107
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002831.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_198
+MVTTATRHHRRTPAGTLRTAAPFFAVLAARHGIPAPDAPTPARTPTTAPRATQDTRPAQD
+HLPNLEGHQ*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002839.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002839.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f738ea42fa5682c0d243a12edab3efd61a32857d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002839.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_217
+MGTKTSGVAPRDHPPFANSDDGYAWQSNWCDRCIHDQPAREGRYEDACGIWYIAECGQTP
+GEWLRQPGQRYGDQYHCIEFRSEDDGPEPPTDPEPTPPGQGELLPMEPYLGVKMFADVAA
+EVATVSTTS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002840.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002840.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c3e6cd71104257fac2c4f2d4de133210550e85d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002840.fa
@@ -0,0 +1,9 @@
+>NZ_CP083691.1_256
+MERLPAWLLETPLLAPWTVPVCVAVGVLLVLGLWVGRTRRRPWWVQALVVGVPAALALAS
+WWWVNVVWAPIPDGVAGPVFAWAALPVVVLAQAAVGPWRPRPLRWGLGGVVAVLAAVLCA
+TLGVNAHYSAYESLAVMTGRNVTWTDWDAVDTAPARQVVPVDRWTAPAGLPEHGTVSRVG
+IPATDARLAPRDAVVYLPPAYFAEERPALPVMILMAGVPGEPPDWFSAGHAAETMDAYAA
+AHHGLAPIVLSVDANGGGALTNRLCWDGPDARVETYLTQDVPAWIGRELQTDRDRTHWAI
+GGLSNGATCALQTVARTPDGFGTVLVFSGELHPSLGTEERTIAEGFGGVRAAYAANDPLS
+LFAAAQRGEGPGADGAYRGVAGVVSVGRSDAYVGMPVPQELVDAGRAAGMDLTLREYPGG
+HTWTVWSRAFADQLPWAAGRMGLG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002841.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002841.fa
new file mode 100644
index 0000000000000000000000000000000000000000..96d36266d6a55cde74efd5b0f3684093322b3686
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002841.fa
@@ -0,0 +1,16 @@
+>NZ_CP083691.1_257
+MATAATRESGTVGGTSPGPAGRVLAGALRWLRGVPATWTLLLFTALGPLLPLVDPARPGS
+LPHAPHEVATSLLFAPHPLAWALALVGVAVLGPPAEREAGSGPFAARVVLGHTASVLAVL
+GLLWAVRQVDPAWGAVLRSDAIAGPWAGLIVAFLASSGSWDSRWRRRLLTLALPVTAATV
+LFSGAPEDASLLTAVLLGGWLGRRRARRLGTDAAPVGSRSERRVLVATAVAAVVLGTFLA
+AGSPHLVGPLAGTRALFAASTVSPDMVAAACADDDRIRECARGTYILTATGPGAVLLAAL
+PLVLQLVLADGLRRGRRAALQGTLVLQSVLAALAAAHLGLAAWAVAAGPRDYPTDPSLIT
+RLILPVLVPLGVLALVLAHRGLFQARAPHGAYRRLRAVPILALAVVAMIVAVGLAVPEQF
+SPRPGVGALLADGLIALLPSTALTVLTPAALPSGPVARFLLEWLPLVPWLAGIWLLWRAQ
+HPLGGPVAQPGEAAEAARALAAEDATMAWMGTWEGCRLWRSPTHAGAVAYRVHQDVALTV
+GDPYSSARDRAVVTRQFAEFCVAHSLVPALYSVHPVTAQAVESRGWFGVQVAEEAVIRLG
+GVTFGGKRFQDLRTARNRAKKEGITARWTTWAEAGDDLRAQIRAISAAWVADKELPEMGF
+TLGGLAELDDPAVRLLLAEDEDGRLHGVTSWLPVHDAGRLVGLTLDFMRRAEGGFRPVVE
+FLLAQAVLDAQEEGLALVSLSGAPLARSQPDPSADVAPAQTGALDRLLDQLGHGLEPVYG
+FRSLHAFKEKFGPESVPLRLCVPDPAELPRVGAALTRAYLPTLTLGDLVRAGQDLRRREG
+*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002842.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002842.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f737d2b0a72b8a47fa6d9525f637c53d47bdd3e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002842.fa
@@ -0,0 +1,5 @@
+>NZ_CP083691.1_274
+MPDVLYAWPSAARVGRRVPKESLYGAGHVSPAVRELFVSSVDRITWDYKLAGGTIGISGT
+PEVPEIQVFRVRAKGDDVPDQVLAAIDRAVQQPVFFEVTRGLDDAEVRLGATYKIAGSAP
+AAEYARTAWLPACAPRRPIPTGVDMAQVYAQVLRPLLGVRMEPGERPQAIAARLVALREL
+ERRHAAVASRHRRERQFNRKVELRKELKGIEQEMEQWR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002843.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002843.fa
new file mode 100644
index 0000000000000000000000000000000000000000..367038bbc33a72963ca6d605b60cb0d818c91344
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002843.fa
@@ -0,0 +1,11 @@
+>NZ_CP083691.1_276
+MSSPERAGAGTANGTADALLDRLLHEWEHETAEFKTAETKYDRDKLGKYVSALSNEARLR
+DCSAGWFVLGVDNTRTVVGTAAFSREGQLLELSRRVAEGIDQNLTVRQIHEVERAGKRVL
+ILEIPPAPRGMPVSWQGHFYARNGESLGSLSLDKLDEIREASHQPDWTNTLIPSARLEDL
+DPDAVARARQGFHERHSRIPVEEVESWSDHEFLERARLMRLGQLTRAAVLLLGGPTAASL
+LEDHPGQLTWQLKGEQEAYEHFYPPLLLSVGDLATRIRNVKLRLMPPDELIYREVGKYED
+TSILEALYNAVAHQDYRRHSRILVVEHPDRLEITSVGEFFAGAPEDYLVDAQPPRAYRNP
+ALVQAMQTLNLVDQMGYGIHRMVSAQMRRFMPLPDYDLTRIGEVTLTLHGAVIDERFSQL
+LMARRDLPFESVLALDRVQKGLAITAEAASHLRRQGLVEGKRPRLRISPSVAAETQDMAA
+YVRTRPQSDAHYTRLLIDYLTANGGSDRKGIDALLSPLLNQALDENQTRNKISNLLAKLR
+RQGRIKNIGSRPQPHWTVVGEAGP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002853.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002853.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90cb83667297764c076c4b1bb0b0e6f576453967
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002853.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_323
+MTFALNEPEYVAVIDSVDGDLGTVELKARAVTTEVDELLGICLDSDVTSALTQFRDDALD
+KALRALTESARAVVDSGRAVATSYREFDAEVAKRATAAELGK*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002855.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002855.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2900d7314692174cfeaac0c5f5044b55d9b91c77
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002855.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_326
+MDHDAQLIEAVTVRRHRLLTALTHGTNPTEQRWHGRGRLYVAGAVLAAVICALCVLVSLV
+ISILTAWLDNREQVEQQRQQQQIEQQQRQEERERAQQELDDERQVTP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002856.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002856.fa
new file mode 100644
index 0000000000000000000000000000000000000000..389e9e105f38142a2188419a6c7e50f1e5c0d4d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002856.fa
@@ -0,0 +1,9 @@
+>NZ_CP083691.1_327
+MATKYSRVTLLGERRHADVLLPSDTPVGVLMPQILSLLAEQPGREPAVRALYRDTGAQLA
+PETTLGLAGVLDGETLRVAATTTAPDAPIVYDLHDTVAAQTDARGRWGKRARLTVLGLVA
+VFLGWWAAVQLTVGLPDEASALARLGIGAGLLLASLGVSVWSRRRAVALTLLGAGAVIAL
+NGHWWLMAVRAMPLAPAVLIGLCGGVALLLLAAQVSGQRRPLVLAAGVLAVLTGAWAAGP
+TAAGWLIGERTASVPVTVGALTAVVALLVLSVLAQAAVSHAGLAGLDDQESAGARLLRTD
+VAAAVATAHRSMVLGVLLCAASIAVSFWWISDDIVQPAFSVPFSAVLTIAVWLRAQAFPL
+TLQRAPLLLTAAWGLWCTVRLTSTAFPALAVPLLVALAVIAVLLVALQVVTVPPHVQARA
+RRLSTTLETLAVVALIPLLVGYVGLYAAMLETF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002857.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002857.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4f8ca2f8760d38b0303d97e9a856ce66a86cf12c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002857.fa
@@ -0,0 +1,8 @@
+>NZ_CP083691.1_328
+MTRTESFAHDADRRLRGRAARNPAQSAPHAVWHAFHRSTDLRRLEEAAVRLQAPVGTGRR
+IAVTSSRGGTGRTTLTAVLAQTLGRFRLEPIGAVDLDPGHGALRLRLGPLVDGPDAEDGG
+EGGEAAEREGAGPGERGAATADRVAQHIRDHGTGGAADFLAPLEASPHRVYHTAARTTRQ
+VLPQDHVAGLLTGFSRFFPVTLSDCAAGHLPVETAAAVASSHAVLHVVPADALAVDEALH
+FLTATGQHTRRTPEPHVVVAVVQHRSRTNADARDAAAALRRRGFPVHVVPFDRHLDTGVS
+VTPRLMLPRSRAVAAELAADLLERATARSAQSGHTAEDEAVDAAAEAHPAGPPVRSGSTA
+RPRGRA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002862.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002862.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98684b94411fe8d854946dcc10c04e00e3c9c98d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002862.fa
@@ -0,0 +1,6 @@
+>NZ_CP083691.1_351
+MEGIRNTTHTPALGRDDARTDGGGPLSWVEGRPASERPPGGWGPSRAPADGDVPAGDRTL
+WEDGRAPGQRGRWWVWLLRHLAAAVACGAALVITAGAVMAELFAVADAAAPYGSLPLLAA
+AAAAVGWALMLVVLLALLIVGVFGGWGLGGTLFRASGPGVWSVWDGEALTEAMGAMAAAS
+TGLGRSSSESAAQATRSPRWRRFLRWTGHAVRWVLVALLVLAAGAAAVLGAMGPSPTTLV
+VWGSAAGLVVAAVLVGCGVIGLEPGPDRSPHTRW*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002866.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002866.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc2a43a59021f79c767ba30a139efe1342af0e11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002866.fa
@@ -0,0 +1,5 @@
+>NZ_CP083691.1_398
+MSQRPACPYLPLPRATTLRDALVYTRASMSRLPDVVHGSLPLRRLMEAARPVLTAATSLL
+PLQDVLAAAAGAVLALSALLWAVLFLHRLLLCRGWHGHLVYTTDGRTAFLTIRSTSQGWE
+LSDHVATRSAKGDGRGLREALAPALRNAADAAGAPILVTAANRTLADLYRQEEPELREVG
+TTLLGRVRLVRPPRRAILPG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002867.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002867.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea406085be931b12715523a46ead9cb4bc1bf6fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002867.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_408
+MREFGETRGDAMRALAARDVAPGVVGYADGEPVAWCSISPRPQIPRLEASQLMPRTDDVD
+VWSVICSGHRRQGHTTRLLEAAVAFAREHGAPAVEAHPVDNRPDGGGAASGTDAPDRIDT
+TMAFAGTWSMFDRAGFEVVGETAAKGSGRPRLVMRRDC*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002871.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002871.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc471707740bf17c17a8922ad680d2f968f8be35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002871.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_430
+MSTLSETHVIDFPGFPTVVVHSPGQAMGTLPQFMDTAFRALGAAVQRGACAPAGPAFSKY
+RGLTGGSGEAPESADRGRRSIDPAVGLRTRGPGALVPDPEFVAGQLDWPVSKAKTEVDAT
+PGRSGVSRAWACLSQSRS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002880.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002880.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2510e0a835b4391efa29fc1f2054a1e05c049f11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002880.fa
@@ -0,0 +1,5 @@
+>NZ_CP083691.1_513
+MTAALERGRPLEGAPARPATPHRRARCTPPWPRPGVLALAAVLAALLALAGAAVGHSAAG
+SLPAGLLGGPHTSDADWTLTGILGRNLGAALLVFGGVVTGGALTAVTLPLVGVWVGATLR
+LALDAAGWEGAVGATVLYAPLEFAGVLLAAVAGLVPLAAALLRPRDADVVPGPLSRYLGA
+LPSACLLIGCALLLITAAGVVEHLVVSGR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002882.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002882.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4063e75d22872707eac98b6f8d413360a8877d78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002882.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_515
+MRLTTTHLRIALGAVGLLGLGVLATLLWGGVLPAALSSTQRGIVLTAAAVAAVAPLLGAV
+LPVTRIERPSSAVLPSLGLFGFGVLFTDALDVFPVRIIVILGGLLALAAVVAALFGGPER
+AEAAEVPERTAHRFH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002883.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002883.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f676276064295373d960419f583126f738315152
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002883.fa
@@ -0,0 +1,11 @@
+>NZ_CP083691.1_516
+MSPTLAAPVGTGHHAVPRPVPAPDAGWSRAAPAPTPRRRLSLLADLRCAELLTSLGLRMS
+LRSARLLLTVAAVAGPVLLVLAAFAGARFTALVLPPGGTLEALSVTVLPLLCGLSLGGVI
+LAEAVGRQRETVSGHPNIPYFRALDVPATLVHAVYALPRLLTAGTVWTCVGAGVLVACLS
+TTSDASPWWAAGTALLVLLPVALTAVASAVSLAVASRPPRAGGPGVLAVGVGAAALGAFA
+GAGLGRLAAGAASRPGRRPGEVSPVTAVPGQEHGVVLLAGGVLLLVLALVGVAAGRRRLR
+ARSFPLAAADPVRLRRRSAPGGGALSWAWMLWRQRRGSTRWAAERRVLWGLALVAGAAAG
+ARAVGVGRLDASLAGLPHSPLLEGDPVGAVHTVLVLGLTMVGVALGETAHGDLGRHRFGR
+HLRQAVELGAPLGVTVRGWMLALLGPALLGGVCAGVAAVLVWPPVGVLAPALVLGGVGAT
+VLADHLLPPPRTADGGVGEGMLTALLALVLASGPAALLLAGAGPLATAAGVALLLVGAAA
+CLARRLCVLTP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002884.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002884.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e55d2a1a066ef5215879ce62a7421860dfccd0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002884.fa
@@ -0,0 +1,5 @@
+>NZ_CP083691.1_532
+MTPVRGDAGTQALAAVVAATRDHRMTFPIQARVSLTSPHQPEPEVYEVRARGDGGFAAWS
+ARHDLFYDPRTGQERLVVHASPGREGFTREWVWPWLSPSHRVLAMFAPAELGIWGGNHDQ
+HRVCAARWLGECAVRVDLVRREEPAGSEATGYAEVDLGNAVVTRMLLDGEAYVLEAARVV
+DDGDVTGPVVGPHLPGWPRSFVP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002888.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002888.fa
new file mode 100644
index 0000000000000000000000000000000000000000..511d7b1b49fcc91169c12b7e76272792009b5afd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002888.fa
@@ -0,0 +1,7 @@
+>NZ_CP083691.1_602
+MTEARRPTSARSPVLRILARILTAALLLALAVLAVAVFTPHSELGQRLTTRLFLAQALAF
+AEPAGAGLTLLGLGVLALHRGAGTRRRTAVGGVAAMLLGLGVGLLAWPDAPPWAAGPATA
+TGNTGRHVRVTVFNSLDTLTAADARRLIDETDPDVLVLPEAAPSRVREALAGTGLAGGVH
+EGADSGFSRGRPAGVAPTTIAMHPRLGAYHQTAPTPTTFGAIRLEPADGADGPVVVGVHT
+GPPLPRLMDDWRGDLDRLSAVDHAAAQGPMVVAGDLNATLRHGPLADRVHLADTALRCPD
+DVGGTWPSDAPGRLRSPIDHVLVTGDVEVLSCTTLRVGASDHLAYAAELRLPGT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002892.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002892.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7441b59a1a5df534375aa8202883bbe5e33b0f5f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002892.fa
@@ -0,0 +1,13 @@
+>NZ_CP083691.1_613
+MAHTTTPPSPRGGKRLTIADVPHMRERYAASNPLPPEEVAAGSNKKFTWSCKAGPDHTWE
+AQANSIRMSKRGGCPFCAGKRPSVTNRLDVLFPDLAAEWDQELNEGPPAVVAGSEKKVWW
+RCRAADHAWQANIRNRTVLRAGCPRCAAEKSSKTRSVPLPGRELTAVAPDVAASWHPTRN
+GTLQPDEVAAFSNVPRWWQCPAGHEWEISPAGRLSKGGAGCPYCSGRLATAETSLEVQRP
+DLTLEWHPTKNAPRTPRDVKPGTSATVWWICSAGHEYESRIANRAYLGRGCPYCSGQKIG
+YGNDLATKAPLVAAEWDHERNGSLTPADVTTGVQRRFWWSCTQGHSWRTTVASRVALGTG
+CPECGAGWRRSRPEIALQFELAHLLPAAVVGDGHVQTADKDFRVDVLCPELKIAVEYDGN
+HWHMDTFERDLAKTQALVEAGWVTVRVRQNPLPLTGRHDVPCENGDPAVYPMTVRLMTSL
+LEEAAAAPTDHPIHAHLDELRLRLETYVDGGTARAVEEAERETRAHHVDRPKRDPFAPPP
+RPKPGRSLAELNPAIAAEWHPSKNGGLTPADVANARNASAWWLCSLCGAEWEAVVGQRTR
+RQTLGCPDCGKARAGAARSRPQPGLSLADLRPDLAAQWHPTRNAPLTPHDVRPGSHKRVW
+WRSPGGQEWESSVYNRTSKRPSSEVHGDAGPDSPDSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002897.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002897.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a7bcecab45b483c66c208bb4f033bf5f3c6c71b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002897.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_637
+MSTRTTQQTVEDFFSAFGAGDLDTVKNLFAPTINFTVHGSPAVPWAGTRHTRDELDTFFP
+AFAALGPATEYTIHQIVVDGDHAVALGHNEFPVLATGKSFSNDFALHFTVQDGQITGYQM
+YEDTYAVDQAFTPTN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002900.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002900.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a030a0bec998bd715c933cb9aba5e880096284c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002900.fa
@@ -0,0 +1,6 @@
+>NZ_CP083691.1_644
+MSLQRVPLAAGRRHSLVVVDGGRVLAAGPPGAGECAVTGWSDVVAVAAGNVHAARNTGRS
+HSVGLRADGTVLAVGWNAHGQCDVTGWSQVVGFAAGWRRTLGVRADGTVLAAGRRDDGAC
+DVGGWSGIVAVSAGDWHSVGLRSDGTVVATGMDTRGQGDVAGWSDVVGIAAGYLHTLGVR
+EDGTVLACGDTAAGLAGARRWRGVAAVVAGSYHSLGLTQDGRVLAAGDDGHGQCSTQTWR
+DVVAIAAGSTHSLGLRSDGVILAAGNNADGQCHWALSAPGQYN*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002901.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002901.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fc3c848547ff07a68594b6c7b99396e54e5cd723
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002901.fa
@@ -0,0 +1,5 @@
+>NZ_CP083691.1_664
+MSTPDELADEVADVRSLNALAEAWRTAPDGSRRFVPNFDPRSGGTSSRVLVLMQSPGPQT
+IAAAHTAICSEDNPGPTAAAFRAARIESGLARNDYLRWNLIPWEILGRVRPVDIDEGRHA
+LETLLKVLPVLDAIVTYGTAALNGVMRHLTLDEHPRLVPVIAAPHPSPANGRHRAEQQRR
+SVQALRLAALTHRL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002902.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002902.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fe3913411215882ae38116bf8e09dc177c6d4549
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002902.fa
@@ -0,0 +1,8 @@
+>NZ_CP083691.1_665
+MRDRRLFRELERPGLIVSNLTPNWFASIMGTGIVAVAAASLPLQFPGLRTAATVVWAIAA
+VLLVALTIATVLHWVRYRSTAAKHHLNPVISHFYGAPPMAFLTVGAGTILLGKDWIGLPA
+AVTVDWVLWTIGTIGGLLTAVLVPYLAFTRHENTPESAFGGWLMPIVPPMVSASTGALLL
+PYAPAGQARETLLWSCYGFFGLSLITSLVVITLIWNRLAQHKVGAAGMVPTLWIVLGPVG
+QSITAVNLLASNAPAVVDASTAHALLVVALVYGFAMLGFALLWTVIALAITIRTAREHLL
+FSLTWWSFTFPVGTCVTGLNGLALHSGLTVVAVLAVVYYVGLVAAWITVAVRTFHGSVIR
+GTLLAPPQPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002906.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002906.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3545f5c13e835ee3856c4f1091b5016e06afb63f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002906.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_675
+MAVFYSFHYDRDVHRVQLIEQMGALEGQPILNHQEWETVKSGGDTAIKEWISDKMKWKSA
+VIVLIGKETASREWVHYEIQKAWDDKKPLLGIRIHGLSSMGSVDSSGPNPFDKISSVSGV
+PIFDPTQTDWTGKIDSKATYNHLKDHLTTWATQGKTRL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002909.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002909.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b853b28fd7da3f5a769eaeccd9710c5617fc7f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002909.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_688
+MPRTISVANTGEWLTRIAVGDAIGITAEATTHNHRAPEVVYLPIEDAPPVTVALTWPGQR
+RSHPQVGVVATCAQDYFTRLIDIGSPPRLLSTGADGQLA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002910.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002910.fa
new file mode 100644
index 0000000000000000000000000000000000000000..29e8a536ee1b8ff37acc23a9044fd98307871481
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002910.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_690
+MPRFSRLTPETAVGASRDLLGDLVERHGQVGDMVSTMAHSPAVLGGYLDLSKAMRRAKLD
+RKVSELVSIAVQSKQGCGMCLASHISAARSLGVSDDEIALAQQGTAMTSPVAAMIALGLQ
+VYREPTSITDEQIDELRGYGYSDREISDVVGVVSLNILTGAFNLVAGLTPGD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002912.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002912.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef88c68d53ba1a8009a08ec7e2314bbb598c3f4c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002912.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_696
+MTYVIALPCVDVKDRACIDECPVDCIYEGERSLYIHPDECVDCGACEPVCPVEAIYYEDD
+LPDEWSDYSKANVEFFDELGSPGGAAKTGPTGFDHPLIAALPIQHEQTL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002913.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002913.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37e68c4213f112b2a01eb0a472dc10703f92fc0b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002913.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_699
+MTTTTPTTETHLDTCPAGGDGDASVHGYISDKTKYRNRLRRLEGQIRGIDRMVDEDRYCI
+DILTQISAVTRALENVALGLLDDHLKHCVLDAALAGGPVSEQRLGEASEAIARLVRS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002920.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002920.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b4d39fa8a4361d8bc23f39c791e708207beac308
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002920.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_763
+MALTLPITQSLSTRDVTGGVRADAPAARTLADLPLGTPGVVAGVCDAARPDVARRLFDLG
+FMPGAVVSGVRRAPLGGPVVVRVADYELTLRRDQARCVVLAGPGDVTSGACPAEDRGCRG
+CAA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002927.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002927.fa
new file mode 100644
index 0000000000000000000000000000000000000000..15d6f9cce49c528f459633fe06cfc12e21343655
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002927.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_853
+MHRTTITAPTSSRRHRSAGVAVGLAVVGLVMTACSAGKAQEPRPTTSAHVQAQGEGASRR
+SRKWREPGRWSTT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002930.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002930.fa
new file mode 100644
index 0000000000000000000000000000000000000000..623360e7e85b0a542bb5b82654966364dde0ee73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002930.fa
@@ -0,0 +1,5 @@
+>NZ_CP083691.1_897
+MTDQNPHQEPADVVAGGPSDAEEVTLDPEIAEHWELWSRVIGTMALPRLQQLQREFPEIR
+SAMLCTADGMNLRSLGVPQADVGRLAALNSSMYAVASSQAEIVSSGAASPQQAMVSLSTG
+HGHVVLASFVQPPLGQLPLSVSADTAQLGFLVVRAREAAVGIQEWLTQEQAKDASLPETR
+PSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002933.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002933.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25b38af2c0db5655721a913447e497089af1d624
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002933.fa
@@ -0,0 +1,9 @@
+>NZ_CP083691.1_908
+MPSHPRLRLTAGLAALALALTACGGAEQQPAAGSPAPASSSSSAAASTSPSSTASASSDE
+ADEASSSAASASESSAAASSSLGASTSAGAPSPTDGSGSWSPSAAGTPSAAGSSSASAPR
+STWSPAAPTAKPSAAPVHAAAPVEADLGGPTTGVAPADTPVAVSSTAPVVEKADPVHVAP
+AHPAAPSASQAPSTTQAPSASSSAATRTPSASASASASSAPAATAPAHTAPVPHAGVDCR
+AVKCIALTFDDGPGRSTARLLDILSAERVPATFYLVGHSAEINPSLVKRMTAEGHQVGNH
+SYDHPNLTTLSPAQIASQITRSDAAIRAAGGRPSTVRAPYGALNESVLSTFGGLPAAGNV
+TWTVDTRDWEHRNPAKTLAAVQQGATPGGIVLMHDIHATSVDAVPAVIAYLRSQGYTFVT
+VDTITGGVTPGTTVRRGMHP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002941.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002941.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6ceed556ea31c41789bdb17f7cdf2224bb579fbf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002941.fa
@@ -0,0 +1,5 @@
+>NZ_CP083691.1_974
+MLLLIFGPPAVGKMTVGRAVAAASDFRLFHNHMTIEPLLEVFGHGTEPFNVLTDEFRIRV
+IEEAARAGVDLAFTLVWDVTDPDDAEYVARCVAAAGDDAAFVELRADLATRLERNRTEER
+LLHKPSKRNLEWSDGNVREMEATWTMTTADGPGAAEVLLGAHPHLGLQTDDLTAEETAER
+ILAWLADVRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002944.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002944.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c37e812a96dfefea1b5aa00e32170d5b2a6e36a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002944.fa
@@ -0,0 +1,5 @@
+>NZ_CP083691.1_1011
+MTIERSSAPSGGPLPRGIQHIGVTVPDLDAATRFLADGLGAKVAYDGLRPEDEPRSGPEV
+ERQLGLPAGAEIRRQRMLVIGEGPGLEMFEVSGEQRPASGLSDLGLNHISLYCDDIDGSL
+ARLVAAGGEALSEVHGNSRHEDTPGNGSVYVRAPWGMLIELQTIPGGHTYPADAEAEVWM
+PRPR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002945.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002945.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f093e35b3e236731edd476f949bb5c6c5e069bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002945.fa
@@ -0,0 +1,8 @@
+>NZ_CP083691.1_1032
+MTLDIPLWPVLLLGLTVVGVLALAARRGPRRSARTTARQHLGLWALLALVLTGALLGPWA
+YVGLWAGDGGLSWVQADGAPTRGTVELVESAVPAELLTPGIAAVALLPALWLVGLAALAQ
+VTWPRETGPRRRAALRSRSWRHLLSRRVLVILGGATVLAAAGIAAMAGLPAVDGVQLSVH
+TGPESTQFRASADSQPAGADVAPWFAAAAATVLAAVAGVVLVVHRRGALGGLSPREDLAA
+RRIAVDRSARIGAALLAWNGLAGLLAAGAHAQARDAAGLLGDLAGRWAEGGIDVAGVTAA
+VRAQDTPDAGVSAAVLAATALIAAVLIFARPRAEERILQDGPDADPVATGGDSASGGDSA
+SGGLDRLPG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002946.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002946.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc5eaa9dfea5a5ec45509382e20becb535b728e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002946.fa
@@ -0,0 +1,7 @@
+>NZ_CP083691.1_1034
+MALFTVLLPVLTVLSVLAIVIGTALSVRPTTTSAALLARVRSHGAATAVTALLLGSISGF
+AGLAAEARPEGPEWTWDAGEWHGVPVFLDAVWLALALALLPAILVAAVTVGAQRSVPAPQ
+GRVRRAVLTPRTAASLVPRGPALPGVGIGLALGATLVLLWAEPSVPRLFPSDGAQEPEGY
+TPLAAGAQLAPWILGALVADLGAAAIGLRAIAHRPPIIGLTAAQDRAARTVAAHRLVRTV
+AWMLWLLTLGAWGSVLLSRTQRDLLHAVFPGHPAALDARPGLGWIGTVDAWTGLATLAVA
+LVLLLWRPPALGELRTGPGIDRARTAETVRTETA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002948.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002948.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc69db1119bdc6bf02ed20e6d1082fc1fe07027a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002948.fa
@@ -0,0 +1,6 @@
+>NZ_CP083691.1_1156
+MSTTTTAPGRLFGYARREFVRNVRMIEGSFFIVVLPVALYLMFGALSDWGDLPVGHGNAS
+AYTMTGMAVYGAVMATTSIAGSAAVERQSGWGRQLSLTALTPGAYLAGKCLVALAMAALP
+VLAVLAAGALTGAELDGPLRWLTTGALALVSSLPFALFGLAAALLFRSEAAVSAASGILV
+VFGFLGNLFVPLSGIMLDIGRFTPVYGAGALARWPQMEGERAPMGTEPAAADPLWLPIVN
+LLAWTAVFAVVCLLASRSRTARA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002959.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002959.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c32eeab5953a50ae5cb3b87e0cf49333c1bb7fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002959.fa
@@ -0,0 +1,5 @@
+>NZ_CP083691.1_1275
+MATVFEGGDRPWLCVLAGRAGTGKTTLAQALAQATGACCLRVDAVETALGRVQDHVGAAG
+YAVVHELAVSNLPLGHDVVVDAVHPVPASRAAWTQTAARAGARLVVLETVLPDGREHRRR
+VETREADIPGHRVPTWEDVQADGWVAWDVERDGPPDRDRHHHPRGRAARRAGGPATPVTR
+TRASEGPGAVPSGTAHP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002961.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002961.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e009a53dace0ed440d547f925a6f6ae5e63ae3a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002961.fa
@@ -0,0 +1,9 @@
+>NZ_CP083691.1_1312
+MSSRRAATAPPGSAPGGAVPVWSASRARRVVLGAQGLAGPRPAASARRVAGVAARLGVVQ
+VDSVDVLARAHLMPFHSRLEDVDPAHVAALTEGRGRRFTEAWAHEASIVPATSRAALTLL
+QGRRWPLATALPEDRRTAAAADIRALLAAHGPLTAREVRDRRASPCGPGTSWGWNWSEDK
+RVLEHLFAEGSLASAGRTASFERRYALPELLWPQGESGRAPVPPEPAAGGDARLAAALQL
+TRIALRAQGVGVADEIADHHRAPVTLTRRALEVLADRGEALEVRLDLGGTRPVPAWADPT
+ARTPRRAGACTLLNPFDPAVFHRPRVERLFGVRYRLGIYTPVDRRVRGYYPLLLLQGERL
+TAQADLGAVRRGPDPRLELRGAWSEDPAAHPGPAGPAPTPDEVADALAEEALRAARWRGL
+PRVVVPEGAPGDLTPRVRRALLERDGGRVPPGP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002965.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002965.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c9ea28ef5f760d900a242c63c0fbe3d828c6353f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002965.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_1495
+MSLVKGAQMKLKAVGVSVKPGGEVEELVIGGTVSTRGEGIDAVEIDGVVKQARVGGVEAH
+GADARRVRVGDDATCPAGLEAFRD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002974.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002974.fa
new file mode 100644
index 0000000000000000000000000000000000000000..682e2235b7141de1db4c60550c9c55fd60e1c59b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002974.fa
@@ -0,0 +1,10 @@
+>NZ_CP083691.1_1734
+MAVTQWPIEMAELSSLVLDPRNVRVRAGRGDGLAHADDEHAEQAIAKYMVEAEDLFDLMR
+DILRDGYLDNEIPVVVRDADKFIVAEGNRRTTALKIIANPKLLGNPMSLRVERMKARYPD
+HDSPTSIRVMIAPTWEAAQPLLARLHTGQPKKSWIREQQAIFYHAQLSDEVTVDDLRVRY
+PSEASTIPKKIRMGEMREVIRRLKYDDSSLRDFVMNSELKMTTFEYAYTPKKLHSALGLE
+FTKDGLLVSKDISDGQRRGLIYLLGRFKDKSLNTRSPELIAKNATEHEEFSKLLRGIVEG
+TPLEASTEDEGATKDHTNNQDGEPGEASGERNSAAPDDISRDEGRHRGTSETDEASTSGD
+ATASRGPNRGDTKSRLNMEGFEYQGTSPGMRRRFEELRRLDVRDFPNATHDLLRTVLECS
+IKDYFQSKGQPLPPGKTIGACIGELAREFQGNPKMTALINSINRKGRLTAEQYAGTTPSL
+NASNHELDHFAVGPDVHAAWDRIQPILKEIVGTKKQS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002978.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002978.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1f24b9438202c7c28e1e8430182ffa91e97b6c26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002978.fa
@@ -0,0 +1,8 @@
+>NZ_CP083691.1_1744
+MATSGKDARAAREAKLDALHERLTGAVEQLVSGEDWARALAFAARFRARSFANTILIFTQ
+HQEAYGLGLVPDPVPSHVAGYRQWQQLGRQVSKGQPGYQILAPVTGRFASATPQDAESWR
+RLGKGEKPRAGETVRTKMVGVRPAYVWDASQTTGEPIPEPPAPRLLEGHAPAGLWEGLAA
+QVLSAGFELRQVADASEIFGANGLTDYASRVVSVRTDMDPAAQVKTLAHELGHVLLHGPD
+ASEARQHRGIGEVEAESVALMVGAAHGMDTSGYTVPYVSTWAARVEGQDPVEVVKTTGER
+VRKTALGILEQLDTVQVGNGTPPGLERDTPTRDPATRQAPVAPAVSEPAGRVVSGPEAVA
+L*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002981.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002981.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1bcecb4cfe94fbe38ca9e1c61623dae2b7fb4fc0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002981.fa
@@ -0,0 +1,6 @@
+>NZ_CP083691.1_1748
+MTHTTTPTTGTAAETGRGSSATPSTPHPDRADFRTSEGLRALLEHLAEHGWRNNPQAKEL
+LEFAAERFAPLARKHGLDVWEAASAAFDVMRTPAARKAADPWAVVTHAVRITCIYEERAQ
+GLMCSVHQARRAHISAHHDPERFSDRETPLYEYHPAFHLTDLHHREDAEPSEDVGASVQA
+AVADATGLFALLGWPEASARAGVDHVTNALARIGSRRGTYEALRRDKHARALLDLPAPAW
+TCLLRVLLGHPEPAYATTTAGRGILLRLLLGETLADLLGDDALVASIVRATPGRGRVRS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002987.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002987.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ffbdfb0c338924600429e0b34707635d2c57858
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002987.fa
@@ -0,0 +1,6 @@
+>NZ_CP083691.1_1763
+MATFVDPVADAAEAYEGLRGLAHATRAFEDPADTYRVLGEVSGSVRLLRQVLDQLSRAHA
+EHRDIAFTDDRVPAEAVALAAADELHQAADGLDEVADRVMRAHEASGRIAWHTHTSLEPE
+RSQRWVNVVFLQGTEADEVLELIDVQGVQAGIAHLAQWDFGDETTGAAFVNGEVYHELPA
+GQWDCTFEADGYVLTYNPQMGYVGLVREHPDTAPDPSHDGDVVAARDAFSGVTSEPSRRA
+AAGTDWFAPKAGGAAASSSVGRSL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002990.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002990.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b2913a2c25de065a5871e83b61936ed4eadfdd7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002990.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_1767
+MAIRTQESLSGFIASDPQLTYTERGDARFYARYGQENFQREEDGTFTKLEPSFGNLVLYR
+ATAERAFQRFTKGDQFVAEGYAHDYTYERDGQRIAGEEFVAKKIGHDTARTRYDVDRTPR
+QALERQAAGQAFEPPQHHQATPATDSLSM*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002996.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002996.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cdc76d5c035efde992e1339db94cbcbb410e3288
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002996.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_1794
+MLFVDAIVVKVRDGQVRNTPFYVVMGVTVHGERDILGIWAGDGAEGARFWLQVFSELKMN
+RPGFVRGS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002998.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002998.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2c84f6f46340268ac064d68fbbe109f5a4b1893
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0002998.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_1798
+MTDQRVLRIDFVSAAGEHTRRDVEPILFAGTRGSWYLIGWCRLRGAVRWFSLDRIRKATL
+TRHPCSGHTVDEIGTPPDTAASVALD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003007.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003007.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26198996e1eed04fdaa8d97afdae14967f2e6ef3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003007.fa
@@ -0,0 +1,13 @@
+>NZ_CP083691.1_1935
+MALTIMSRVPDAQPYRDEDLDGRIGAAGLAGATLEHGLLRFHTHESGSEAARLLAFHFPP
+GFTEGWVPFAVDWRGRQYCRVRQDGVDSAVRADPGLFAASSVVDFEVFMDTVLTDPGAAR
+VLGAEDCAAALAARGISDLPFDQCLGYMLPPFAGGEDHSSNILDVPVNPYWAAMADMKNQ
+WQHRQPGAHAIAVAARDGGLTLVFDTDQDPEHSPGAGTRAERLVVTSPHGPAVYNHGLAR
+ELTDEQAREAAEAVREAFGTPDAAAPFLMDWRARCYAVERVDGRDVVVRSCPVTMTRTPV
+AEADGFRDRLAGNPALLDLFGEAEKSLLCARLRLTEIPAGDVLVPPAPPSVAGPEADDPA
+TFRLQSASVAWWLAGNLARLAREAGPERRLQGYVLTPEGRLGLQTAPADGPTPPPRPSED
+TAGLPPVRFAPRFAALAETGVVQTAQDDDAAPDKDAGDAQMAIAWYGLAGRVYNAGLFRF
+LGAEGVAQAAGHLRESFGGQAAEAVPVIVDWLGRYAVREVVEGQSMLVSYDAASGQREEL
+SRFEDGLEQILVTPVARELFDEAGFRRALDTLGLVRIGQGRCVGVKRPLFLGGDESPENW
+EDDSLDVHWSWHGRVFAQARAMPEGARIQRVEPLEDGRPLIHYTLPDGRTGDGLSGLHDG
+GAPGVSEAAAARQDGSGPKQEKGFFGRMFKG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003008.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003008.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da48ed65a48f25e6fe75d4a38ace04b689d5b01b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003008.fa
@@ -0,0 +1,6 @@
+>NZ_CP083691.1_1936
+MEIYKSHLPVDEGLLVAAGREWKRFPKLLSKDTPKGVKKFLGRRPGVELGENEFSDAHFQ
+FALLLALAGEREALVPLFRGDLLMEEAVKPARSTKMESRRVVNRWCAQRVGLSGWAEVFD
+APPNSEPGPEAHIPRVSFNFGSDKEYAGIAFDEKGDLEGAMKVTPSNYVVAVRMILDGLT
+WLLVARDVPWMNDYGWERERIEREVAWHVGVVRARLGLPLEQAPLTEDPRVDLPVEFTGF
+VSA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003009.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003009.fa
new file mode 100644
index 0000000000000000000000000000000000000000..829b76f6c65aa7d2fa607bb2f1db04453e9d636a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003009.fa
@@ -0,0 +1,10 @@
+>NZ_CP083691.1_1937
+MASSLESRADESDPPRRRPDGMNGLISRHQTAEMTCANAINALYGGTRYVQVSADGSAPP
+AGSEAYGMSREMLNSASGAGETPWGMPAVWDKPWYLDVADAVVDFGSGVWESLKGTVTGL
+LAMVNPFDWETFSATWKGIGTLAVDLAVTATPVGLLVSDERRAQSGQRLVQVGEAVLNVE
+MWKENPAKAAGMLTGDLATALVPGGAAVKGASVAAKSGKAASVLGKAARAADTVKELGTA
+AKFKVAFKAEDLVRGLSDKKFAVTDALHSKASAFAYRHPQVGAMASTMRTVWEFDVNKAA
+KVFSDGMLAKVPAVGVLADGGVMWVKSGESFSSVLRRAVDEGVSPVRSGGGGLPAGVVEG
+KGTMVMRPSPKWDLSTAEGRASYEAFVGKVDQYKQFVSSPERLGFTKPDARTIKRSDFMK
+DPDYALGRVTDLRGNQAPALLKGVEDDILRRLEDEMTRHNAAKGSRGEIADWHELPQYTQ
+ERAVRAAMKGFDLDHARDLQLGGRDAHENLQWLEKSANRSAGFAGAASSG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003010.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003010.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e5fa8dd71a8e189d7f6f9f2dd47918a450a35e0b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003010.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_1968
+MRGGVFAEIAPREVTDEVCPPVNCLSAWETEVGRFVGFRHEGDAEYWHVVLGDEARRNDR
+VLVDFSGGKYDRDQVRHAVDVLFHDRDWT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003014.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003014.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d72e7d75f88f371dd11d2f275b85e871a16b07f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003014.fa
@@ -0,0 +1,9 @@
+>NZ_CP083691.1_2032
+MEAALFRETLIGDAGLIGGLLLVAVVLRAKVRVLQWLLLPAPVIAGLLGFLLGPQVAGAW
+GLRVGAWEFTGLPFSPYVGSYTTLLIAVVFACLALSQSFSFRKATGPLAGFTGYGVLMSA
+GQVVAGMLLVLLVLGPVMGSSDAIGMVLFASWSGGFGTSAALGDVFADAGRPEITSIAFT
+SATVGMLSGIVGGVILAKIGSSRGHTRAFSTQAAFTPSLRTGVLEHDDRPVAARHTMSGS
+SIETLTLHMALVGAVVALGWLFMTTTGEVLDDFALPLFASAFLAGLLARWVVVRSGASRV
+MEPQTLKALSGAASDVLIVCGIVSIEPAFVADHLAELAVVFALGLAFCLFLGLVVAPRYL
+GESWFEKQIFTWGWATGSVATGIALLRIVDPDLESGTVEDFGYAYLPLIPVEGAAVAIAP
+LLIVAGAPWSVVAIWGVIAVVGAVVMVRQGGPDPRRTTTAARA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003016.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003016.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5bb404e8cfa431c972dd47560a1dbbf27721dfd4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003016.fa
@@ -0,0 +1,2 @@
+>NZ_CP083691.1_2125
+MSDQQSPEAKNSDAPGDQDEAMQRQAPAQVDCLAEKAEEEAEQDKGGYDH*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003023.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003023.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00966b6cba4353760c6748dfe6e11eec2f4c05fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003023.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_2178
+MDTLTGSRHKNLKELHPGSSGRSEIRILFAFDPRRQAILLVAGDKAGAWKKWYATNIPLA
+EERLDAHLHALRSTPPGA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003025.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003025.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c927af0c416f36356fbc009c44dfeea71bd10f92
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003025.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_2184
+MTLTLIPPTTPDEATQQLAQLQGTTVALAVLRRVQLVKAAEVGVTQQQLAGALGRAQSSI
+SEYLTRARTSLADRPATHPLWPAEVIDLYAAGLLPRDEVLAYLASYPYIDPAPTDDPAYT
+VTQPGEFGEVAAAHWNDKLSDTDYANLYDLLHADD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003026.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003026.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b22ed1d9620b2731107c6377ca45cba37f88e80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003026.fa
@@ -0,0 +1,6 @@
+>NZ_CP083691.1_2189
+MDVSGIPTHDGLDDAFASVGMTIPRDTPSGESITKPRRMRTAFETADSNGLKATRRLISA
+LVDELRHRDVFQHPAPEIVAAVQAVRQLITEGGATLTTDGFITTAVAFPTVDAGQRETVD
+RLIARLRRNDQDPASILGTAKDLLEATSKHVLHERAPQQRQKDMPNIVYEAMEALDLSTK
+PSSINGPSAGAIAQLHQLIARTAQAVTASRNDGGDGHGHLNPTGVSPELAEYVRVVTLAA
+TKFLLDNAT*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003027.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003027.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af196345512559d6d1e229cc2ca9fd514a1148a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003027.fa
@@ -0,0 +1,7 @@
+>NZ_CP083691.1_2190
+MDESGEVWTYSPSGSTAGSKDGDVQPARIEWLDVRGLPGYLVHPPSNDEGVSPWRRVYPF
+ADALALDVVAIETWTVPVSGDPPGAVNGWRWEEPATGLGEQALEVFDPLMYGRPAATLSQ
+LAGQADGVGRKLMNLREALMGCTTPVDLTVIWDQLDEALRLVVDAERSLTYAHRVIAEDL
+PLRKQLSRGEPPWVSSTGVNRWLTPKQMKRARRRHDVVPEDQLITYREAVVMADDLIPPL
+LAKTLAAMDKQILLDELLDDLLSRQCPGCGAGAGAYCTTASGRIAEVVHAGRRDASPMMR
+GHMELYMEVRQPNEFVPDPECGRVGPAPWDETLPGV*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003029.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003029.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2438ecffcd30767634f0233c3cad89a7c0d1428b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003029.fa
@@ -0,0 +1,2 @@
+>NZ_CP083691.1_2205
+MFDPEAIESARERLDAKQIAPEERAGQTPDVG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003030.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003030.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3e56ceb2d8b256c5564a9981849b236eb1c71391
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003030.fa
@@ -0,0 +1,8 @@
+>NZ_CP083691.1_2207
+MERRVMAPRPGWERTIASQGLVFDETVHPDGTVTHYWNESACYALTMAEVEHLEQASERL
+HAMSLEAARFLADEQSVPGSPWRALGIPREAAQLAVDSLNAGEPSLYGRFDLVYSGPDAP
+TKLLEYNADTPTGLVEAAVCQWFWKEDVFGDAVDQWNGIFEALTDRWRRIAPPEADGTPA
+RVHFAHTELDETGEDAMTVAVLRDAAEQAGVRGESLLMSQIGFDTERLRFVGADLRYLRR
+IFKLYPWEDMVTERFGPRLKLDDEVRWIEPPWKMLLSTKALTAALWHLYPGHELLLPTFL
+NDRGGLREWVRKPLHGREGAGIEIRSRAGDVSSAAGRWGAEGHVYQQFHGLPDFPAPDGA
+PNRPVLGTWMVGDECFGVGIRESDGPVTDALCRFVPNIIDG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003031.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003031.fa
new file mode 100644
index 0000000000000000000000000000000000000000..207a903da7c519f436a4597072f9d2f2a7824fcd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003031.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_2208
+MTDTFPTPLLRRRASRTLALGGTLALAAAMTGCGPDPDYRQTSEDYAQVCRDETTQERVP
+DEDCDDSAGTSHAHAGHRTGWYFIPLAGGRTVPAVGQRAGGGLTTRPGTGTTTKVPSSGG
+EFAKSGTVSRGGFGSKGGGAGS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003036.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003036.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46e84013d6f3a7a4e387e89bc98fc2e1485196ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003036.fa
@@ -0,0 +1,2 @@
+>NZ_CP083691.1_2270
+MWIIRQGKDFQEEVLVFITAKIFIESPHRLCICPPHHLAYLKKALVEELP*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003037.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003037.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4f28e826fb8cff9e676667ac1a4e39853e503609
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003037.fa
@@ -0,0 +1,4 @@
+>NZ_CP083691.1_2369
+MSDCEPCDLQSVPAMTDTAPALDVDALAADPVEQFHRWIRQVVGSGVPEATTVTFATVDA
+REQPDARTVLRAVRVRGGVRDAPLPEGARMRTVRPERVEFWQGSPEDHRHVRIVYTADDV
+GGFRGEVTRG*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003039.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003039.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da7c238699bfdf0e8f2aaa8b35e10290600b880b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003039.fa
@@ -0,0 +1,3 @@
+>NZ_CP083691.1_2376
+MTAPYRPQPQHQPQTVVVQQSRNTLIAYLLWFFLGNLGVHRMYTKRWVSGVVQLLLAWGG
+AATAWLLIGWIPLAIWAVWWIVDLFLVPGMVRDANAREAVDSWRTVGVRRF*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003041.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003041.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bddd1e5d6213f276740198467da9339fb7b7194e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003041.fa
@@ -0,0 +1,2 @@
+>NZ_CP083691.1_2434
+MTVNLVKLHVSQLNGCAPCLRLHPREAAAGGWESGCVSAEAGAALALAEDVTHL*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003050.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003050.fa
new file mode 100644
index 0000000000000000000000000000000000000000..958322d62aabaf0fe0151cf5f9722110ebae4486
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003050.fa
@@ -0,0 +1,3 @@
+>NZ_CP097650.1_158
+MIFIVVKFTVKPDWSDRWLDLTSSFTRDTRHEPGNLWFEWSRSVENPNEFILVEAFEDDA
+AEAHVNSEHFQNAMQQMRQALVETPRIISRQIEGNTWDRMGELAID*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003051.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003051.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b8c6aac0d4c857ebfb94dafe7416103680b3e9c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003051.fa
@@ -0,0 +1,3 @@
+>NZ_CP097650.1_163
+MLLYRWSRAEPVIRAELSLPSRMDRGDVVAWKERILLPEISLDQFDLSDFDVIAEDDVYF
+GISQTS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003054.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003054.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1bab6652fdee689078ec14aaccbd20d8963b9ef2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003054.fa
@@ -0,0 +1,7 @@
+>NZ_CP097650.1_749
+MSIVIGSLGGIFLWLIYQAIGTRWPEVYATARDSLDLMPRRSSVKYLLIYRGIPTFSVTV
+LALNLAVESGGDPYWTSAFVFWTYSTLAEIRSTFSPKGALRQLSTVNTVYLSASVVVTTI
+YCSVAVLVYPHFSVLVPSVRELVIALWTALFASVLAISFQRFNTRSGPDVQMEIDYSIKD
+IGQKTWSQIDSICMRENIDPCLIKALAAAEAQQRPRWIRQAERVAGRLFGGGTFGVGQWP
+SSRPIDDLTSIEFRAKQLAPVGLTPHECDIAEVYDFLDIDYFIYSWNSDESFADSARGFY
+SAFRRAKMVEHVAESDA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003055.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003055.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d6a7745c0254da289c436eeeb547b40696939a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003055.fa
@@ -0,0 +1,5 @@
+>NZ_CP097650.1_860
+MKSVLHTRTAIAAALLLGLTACGDTASPAEEDAPAAAGSSTASAPAGAEEETEADEPEQQ
+AGGTAGTREDPLPLGTPIEGEDWVVTVNEVTPDATDAVMAANQFNDAPAEGTQYLLADVT
+VEYTGDESEMIMLGTGFAFVTATGETIDAGDAFAVGPEELDTAQELYNGGTAQGNVVLQV
+PEGADGLLRVTTGMFGGEKTFVALD*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003057.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003057.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0873dfa3a8f824c7de0ab5a929f16a48457dcd03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003057.fa
@@ -0,0 +1,2 @@
+>NZ_CP097650.1_1017
+MDVLSPVFEITTLVVLGVILLLDLLYVARRPHEPSM*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003059.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003059.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7bee61617c4b538d2d0309548b70054a5fb00504
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003059.fa
@@ -0,0 +1,6 @@
+>NZ_CP097650.1_1115
+MATSGKKHWPPMGRTQWPLTSVSRTARMLGCAASTSSPSGSSASTSRPPPCRPGPRDRVV
+PRPGPCEVEAGEGLHELTNGDRWTRLGAGPPTGDGEEAAGRAPRPGSRSCRSQDASPVAR
+GLRIIPRSRPRRRPRGPATRACPRDVVGRSTPGGRCDRDLRPVHAPATVQTPVPSSSASW
+ELSPGLGGFGPLDTRFPSRGAWRGSRFPDESVREGSRFPHESAGAQRPGARRRRAGPPKR
+TGPPSSSAPVALRDRPEVSGRTCPERTRRPTRR*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003069.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003069.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eab29f64610106799ebef13b050833de1589a147
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003069.fa
@@ -0,0 +1,4 @@
+>NZ_CP097650.1_1980
+MSHFAPQRRSTRTAAFSATFAAAAIALTACGGDATPSGPTSAPASASGGAESPAGEATAA
+SSVSAEDRVDPTQTTEVSAVTPRILLSHEDGLTLLDAESGEVVKEQDITGFKRLSNAGNG
+KDVLVTTGKGWEVCSPPASRPRPTAITSTTTSPRPA*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003076.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003076.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b28277978adf3cab8ddf77b41f1fd956a08f70e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003076.fa
@@ -0,0 +1,5 @@
+>NZ_CP097650.1_2157
+MRDLVYYIATSLDGYIAAPDGDFSAFPQDPVTLKTLFDRYPETCPAHARAALGVDGPARR
+FDTVIMGYRTYEPALTVGLPGGAYPHLNQIVVTHRPLPKAPNLTAISGDVSEHIAHLKTL
+PGRDIWLCGGADVAAQLIEHIDELQLKVNPIALGTGIPVLPFDGKPHSFHLAECEQQPGE
+VLLLTYRAS*
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003078.fa b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003078.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb8d014980de25fcd94e2f6b7ffc5e7eaa0363a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260520_114207/orthofinder_output/Results_May20/Orthogroup_Sequences/OG0003078.fa
@@ -0,0 +1,3 @@
+>NZ_CP097650.1_2166
+MNPECVSLCAWPSKDQRGRPSNYCSRACRELTKRTRQRLSWECDVLEEALAEKELSWNQE
+RILQRALGHRKWALGRYPARDE*