diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000000.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000000.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b81277affdb19bb12f15154b7ecf48d24e19934a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000000.fa
@@ -0,0 +1,307 @@
+>PROKKA_00064
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGFTRLAYTEALEDERTVTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYT
+>PROKKA_01337
+MTHANAPLTPTGRLRMVQRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLASEGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRAHGRESEAGRASKRGAG
+RRVGYTYLHSAIDGFTRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNN
+YRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSERARREALQV
+WVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYI
+>PROKKA_01952
+MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLPSRPHRSPAQLDPVLV
+AQIHALRRERKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRLRDLTPAGEDLRQRPQ
+KITARGPGHMVHLDVKKIGKIPDGGGWRAHGRESEAGRASKRGAGRRVGYTYLHSAIDGY
+TRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVITDNGNNYRAVDFTAKVVSLGG
+RHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAVWVNHYNYHRPHTSCG
+DAPPASLAPARVNNVMPSYS
+>PROKKA_02068
+MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLPSRPHRSPAQLDPVLV
+AQIHALRRERKWSARRIHHHLVSEGHQVCLRTVGRWLHRAGISRLRDLTPAGEDLRRQPA
+RRITARGPGHMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRGPGRRVGYTYLHSAIDG
+FTRLAYTEALPDERAATTVSFFCRARAFFAAHGITVDRVITDNGNNYRAADFTAKVVSLG
+GRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSEQARREALAVWVNHYNYHRPHTSC
+GDAPPASLAPARVNNVMTSYI
+>PROKKA_02111
+MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLPSRPHRSPAQLDPEVV
+AQIQTLRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRLRDLTPAGEDLRQRPQ
+KITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPGRRVGYTYLHSAIDGF
+TRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIRIDRVITDNGNNYRAVDFTRKVVSLGG
+RHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAVWVNHYNYHRPHTSCG
+DAPPASLAPARVNNVMPSYI
+>PROKKA_02278
+MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLPSRPHRSPAQLDPEVV
+AQIQTLRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRLRDLTPAGEDLRQRPQ
+KITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPGRRVGYTYLHSAIDGF
+TRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIRIDRVITDNGNNYRAVDFTRKVVSLGG
+RHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAVWVNHYNYHRPHTSCG
+DAPPASLAPARVNNVMPSYN
+>PROKKA_00012
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPEVVAQIQTLRRREKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYN
+>PROKKA_00041
+MTHANAPLTPTGRLRMVHRHLNDGIPQSHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGRIPEGGGWRTHGRDSEAGRASKRGS
+GQRVGYTYLHSAIDGYTRLAYTEALEDERTVTTIGFYCRARAFFAAHGITVDRVVTDNGN
+NYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALQ
+VWVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYT
+>PROKKA_00137
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLLDRP
+SRPRRSPAQLDPEVVAQIQTLRRREKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRAHGRESEAGRASKRGAG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYT
+>PROKKA_00312
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRDSEAGRASKRGAG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVITDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSEQARREALQV
+WVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYT
+>PROKKA_00352
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+SRPHHCPAQLDIAILAEIEALRRDQKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIPDGGGWRAHGRDCENARAAKRGPG
+RRVGYTYLHSAVDGFTRLAYTEALPDERAATTVSFFCRARAFFAAHGITVDRVITDNGAN
+YRAAEFTMKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVIYARPYTSEQARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYN
+>PROKKA_01118
+MVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGAGRRVGYTYLHSAIDGFTRLAYTEAL
+EDEKAVTTIGFFCRARAFFAEHGITVDRVITDNGNNYRAADFTAKVVSLGGRHHRIRPYT
+PRHNGKVERYNRLMVDEVLYARPYSSEQARREALQVWVNHYNYHRPHTSCGNAPPASLAP
+ARVNNVMPSYN
+>PROKKA_01160
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGAG
+RRVGYTYLHSAIDGFTRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNN
+YRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYS
+>PROKKA_01236
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRDSEAGRASKRGPG
+RRVGYTYLHSAIDGFTRLAYTEALEDERTVTTIGFFCRARAFFAAHGITVDRVITDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRPHTSCGDAPPTSLAPARVNNVMPSYN
+>PROKKA_01818
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPEVVAQIQTLRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIRIDRVITDNGNN
+YRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYI
+>PROKKA_01821
+MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLPSRPHRSPAQLDPVLV
+AQIHALRRERKWSARRIHHHLVSEGHQLCLRTVGRWLHRAGISRLRDLTPAGEDLRRQPA
+RRITARGPGHMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRGPGRRVGYTYLHSAIDG
+FTRLAYTEALPDERAATTVSFFCRARAFFAAHGIRIDRVITDNGNNYRAVDFTAKVVSLG
+GRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARREALAVWVNHYNYHRPHTSC
+GDAPPASLAPARVNNVMTSYT
+>PROKKA_01968
+MVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGPGRRVGYTYLHSAIDGFTRLAYTEAL
+EDERAATTVSFYCRARAFFAAHGITVDRVITDNGNNYRAADFTAKVVSLGGRHHRIRPYT
+PRHNGKVERYNRLMVDEVLYARPYTSEQARREALAVWVNHYNYHRPHTSCGDAPPTSLAP
+ARVNNVMPSYI
+>PROKKA_01971
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLLDRP
+SRPHRSPAQLDPEVVAQIQTLRRREKWSARRIHHYLVSEGHQLCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGAG
+RRVGYTYLHSAIDGFTRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNN
+YRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYS
+>PROKKA_02077
+MIHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLLDRP
+SRPRRSPAQLDPVLVAQIHALRRERKWSARRIHHHLASEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVITDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYS
+>PROKKA_00044
+MVHLDVKKIGKIPDGGGWRAHGRDSQAGRASKRGAGRRVGYTYLHSAIDGFTRLAYTEAL
+EDERAVTTIGFFCRARAFFAAHGITLDRVITDNGNNYRAADFTAKVVSLGGRHHRIRPYT
+PRHNGKVERYNRLMVDEVLYARPYSSETARREAMQVWVNHYNYHRPHTSCGGAPPASLAP
+ARVNNVMPSYT
+>PROKKA_00146
+MTTIGFFCRARAFFAAHGITVDRVVTDNGNNYRAADFTRKVVSLGGRHHRIRPYTPRHNG
+KVERYNRLMVDEVLYARPYTSEAARREALQVWVNHYNYHRPHTSCGDTPPASLAPVRVNN
+VMTSYT
+>PROKKA_00227
+MTHANAPLTPTGRLRMVQRHLHEGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+CRPRRSPAQLDPALVTQILTLRRECKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAMTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARREALQV
+WVNHYNYHRPHTSCGNAPPASLAPARVNNVMPSYT
+>PROKKA_00556
+MTHANAPLTPTGRLRMVQRHLIDGIPQSHVAAEFRVSRPTVATWVARYLAEGAAGLQDRS
+SRPHHCPDQLDAEVVTELETLRRDHKWSARRIHHHLLAQGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPAKKITARAPGHMVHLDVKKIGKIPDGGGWRAHGRDSQAGRASKRGA
+GRRVGYTYLHSAIDGFTRLAYTEALEDERAVTTIGFFCRARAFFAAHGITLDRVITDNGN
+NYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARREAMQ
+VWVNHYNYHRPHTSCGGAPPASLAPARVNNVMPSYS
+>PROKKA_00692
+MTHANAPLTPTGRLRMVQRHLIDGIPQSHVAAEFRVSRPTVATWVARYLAEGAAGLQDRS
+SRPHHCPDQLDAEVVTELETLRRDHKWSARRIHHHLLAQGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPAKKITARAPGHMVHLDVKKIGKIPDGGGWRAHGRDSQAGRASKRGA
+GRRVGYTYLHSAIDGFTRLAYTEALEDERAVTTIGFFCRARAFFAAHGITLDRVITDNGN
+NYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARREAMQ
+VWVNHYNYHRPHTSCGGAPPASLAPARVNNVMPSYT
+>PROKKA_00779
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLPSASRPGGSPRGAGAHGAPGREEDRKDPRGGGWRAHGRDSEAGRASKRGP
+GARVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFYCRARAFFAAHGITVDRVVTDNGN
+NYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARREALQ
+VWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT
+>PROKKA_01499
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGKIPEGGGWRAHGRDSEAGRASKRGP
+GARVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFYCRARAFFAAHGITVDRVVTDNGN
+NYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARREALQ
+VWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT
+>PROKKA_01505
+MVHLDVKKVGRIPDGGGWRIHGRNSDQARTAGRAKSAGAKRGYTYLHSAVDGFSRLSYTE
+PLTDEKGPTAAAFLARAKAWFAAHGISHIHRVITDNGACYRSADFARIVGNRTRHQKTRP
+YTPRHNGKVERYQRILAEELLYAREFESEEARDTAIGIWNIHYNYHRPHSGAGGHPPASR
+LRAGVTNVWPSYS
+>PROKKA_01737
+MTHANAPLTPTGRLRMVQRHLHEGIPQAHVAAEFRVSRPTVATWVARYRAEGEVGLQDRS
+CRPRRSPAQLDPALVTQILTLRRECKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARREALQV
+WVNHYNYHRPHTSCGNAPPASLAPARVNNVMPSYT
+>PROKKA_01768
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+CRVGYTYLHSAIDGYTRLAYTEALEDEKAMTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARREALQV
+WVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT
+>PROKKA_02336
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+CRVGYTYLHSAIDGYTRLAYTEALEDEKAMTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARREALQV
+WVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT
+>PROKKA_02339
+MAYTESLENEKATTAVAFLNRAREWFASHGITRIERVITDNGACYRSAAFTAALDGADHR
+RTRPYTPKHNGKVERYNRILAEEFLYARTWTSEEQREKALETWNLHYNYHRPHGVHDGKP
+PASATPSRVNNVLASYS
+>PROKKA_02472
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGKIPEGGGWRAHGRDSEAGRASKRGP
+GARVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFYCRARAFFAAHGITVDRVVTDNGN
+NYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARREALQ
+VWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT
+>PROKKA_02555
+MTHANAPLTPTGRLRMVQRHLHEGIPQAHVAAEFRVSRPTVATWVARYRAEGEVGLQDRS
+CRPRRSPAQLDPALVTQILTLRRECKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARREALQV
+WVNHYNYHRPHTSCGNAPPASLAPARVNNVMPSYT
+>PROKKA_02613
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGKIPEGGGWRAHGRDSEAGRASKRGP
+GARVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFYCRARAFFAAHGITVDRVVTDNGN
+NYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARREALQ
+VWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYN
+>PROKKA_02632
+MVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGAGRRVGYTYLHSAIDGFTRLAYTEAL
+EDERAATTVSFYCRARAFFAAHGIRIDRAVTDNGNNYRAAEFTRKVVSLGGRHHRIRPYT
+PRHNGKVERYNRLMVDEVLHARPYSSETARREALQVWVNHYNYHRPHTSCGNAPPASLAP
+ARVNNVMTSYT
+>PROKKA_02637
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+CRVGYTYLHSAIDGYTRLAYTEALEDEKAMTTIGFFCRARAFFAAHGITVDRVVTDNGNN
+YRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARREALQV
+WVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYI
+>PROKKA_00274
+MTHANAPLTPTGRLRMVQRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLASEGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVITDNGNN
+YRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYS
+>PROKKA_00518
+MAQRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLPSRPHRSPAQLDPVLV
+AQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRLRDLTPAGEDLRQRPQ
+KITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGAGRRVGYTYLHSAIDGF
+TRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNNYRAADFTAKVVSLGG
+RHHRIRPYTPRHNGKVERYNRLMVDEVIYARPYSSEQARREALAVWVNHYNYHRPHTSCG
+DAPPTSLAPARVNNVMPSYN
+>PROKKA_00800
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVTQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNN
+YRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRSHTSCGDAPPASLAPARVNNVMPSYT
+>PROKKA_00879
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNN
+YRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYN
+>PROKKA_01175
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVTQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNN
+YRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALAV
+WVNHYNYHRSHTSCGDAPPASLAPARVNNVMPSYI
+>PROKKA_01546
+MTHANAPLTPTGRLRMVQRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLASEGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGITVDRVITDNGNN
+YRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYS
+>PROKKA_01570
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPQKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGPG
+RRVGYTYLHSAIDGYTRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNN
+YRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARREALQV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYT
+>PROKKA_01997
+MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLPSRPHRSPAQLDPVLV
+AQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRLRDLTPAGEDLRQRPQ
+KITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRGPGRRVGYTYLHSAIDGF
+TRLAYTEALEDERAATTVSFYCRARAFFAAHGITVDRVITDNGNNYRAADFTAKVVSLGG
+RHHRIRPYTPRHNGKVERYNRLMVDEVIYARPYTSEQARREALTVWVNHYNYHRPHTSCG
+DAPPTSLAPARVYNVMPSYS
+>PROKKA_02102
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+CRPRRSPAQLDPEVVAQIQTLRRREKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRPQKITARGPGRMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGFTRLAYTEALPDERAATTVSFFCRARAFFAAHGIRIDRVITDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYT
+>PROKKA_02106
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+CRPRRSPAQLDPEVVAQIQTLRRREKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRPQKITARGPGRMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRGPG
+RRVGYTYLHSAIDGFTRLAYTEALPDERAATTVSFFCRARAFFAAHGIRIDRVITDNGNN
+YRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARREALAV
+WVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYNYLFGLLMVTRSPECALLGHGPDQRG
+WLLDTYLRGLRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000001.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000001.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6263f772b190b8bcf352d56c87652fe0063187c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000001.fa
@@ -0,0 +1,235 @@
+>PROKKA_00174
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT
+>PROKKA_00589
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT
+>PROKKA_00602
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKLPVVAEHLDAARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAAGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVSNTGSEVNPDTAPALEFSA
+>PROKKA_00603
+MTAPHILDPAGLLGEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPSSSRTAQR
+NGYRHRDLDTRVGTLDVAIPKLRSGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGVNALSKSQVSRMATELDEQVEAFRHRPLGVAGPFTFVAADALSMKVREGGRV
+VNAVVLLATGVNADGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHTGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAASVHAQFDRLLD
+YVSGKLPTVAEHLDAARADILAFTTFPKDVWTQVWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVTNTGDEVDPDTELTLGLSA
+>PROKKA_00623
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVTDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDAVGIFPNR
+DAVIRLVGAVLAEQTDEWAEGRRYLGLELLARCSNQDPDTPSTTGASAEVMPTLA
+>PROKKA_00713
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT
+>PROKKA_01070
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKLPVVAEHLDAARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAAGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVSNTGSEVNPDTAPALEFSA
+>PROKKA_01202
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKLPAVAEHLGDARADILAFTTFPKDVWTQVWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTPVEDTGSEVGTDTDTALELSA
+>PROKKA_01394
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQTLGITGLSKSQVSEMSKDLDAQVEAFRTRPLDAGPYRFVAADALVLKVREHGRVV
+KVAAMVATGINNDGYREILGLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLVE
+AAGAVFGTAQWQRCRTHYAANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMIDS
+LATHLPAAAEHLEGARDEVLTFTKFPKEVWKKIWSNNPNERLNKEIRRRTDVVGIFPSRV
+EVIRLLGAVLAEQHDEWTESRRYMSLELLTATDTMLAEAAAKAAAEQAALQVSDTMTDDP
+GHAALAA
+>PROKKA_01399
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT
+>PROKKA_01504
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVAGAWPGSGWSPLMPTPGSR
+TPSPRTCPVRCGNAAAPTTRRT
+>PROKKA_01505
+MGITPKSMWPAVKAMLHSGYDQPDAASVNAQFDRLLDYVSEKLPVVAEHLDAARADILAF
+TTFPKDVWTQIWSNNPAERLNREIRRRTDAAGIFPNRAAIVRLVGAVLAEQTDEGPRAVA
+TRALGATRACC
+>PROKKA_02030
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKLPAVAEHLGDARADILAFTTFPKDVWTQVWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTPVEDTGSEVGTDTDTALELSA
+>PROKKA_02064
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFSATGLWARPARSCSSPPTP
+>PROKKA_02065
+MFLAADALTMKVREGGRVVNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVA
+RGLAGVALVTSDSHRGLVEAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSV
+YDQPDGPAVHAQFERLLDYVQDRLPAVAAHLDAARQDILAFTSFPRDVWCQIWSNNPAER
+LNREIRRRTDAVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQE
+TVMSTEVMPTLQT
+>PROKKA_02226
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+INAVAMVATGVNADGRREVLGLRVATTETGAAWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT
+>PROKKA_02229
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGQASQSRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFERLLD
+YVQDRLPAVAAHLDAARQDILAFTSFPRDVWCQIWSNNPAERLNREIRRRTDAVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT
+>PROKKA_02231
+MVADCYLAGVSTRRMDKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFL
+AADALTMKVREGGRVVNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGL
+AGVALVTSDSHRGLVEAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQ
+PDGPAVHAQFERLLDYVQDRLPAVAAHLDAARQDILAFTSFPRDVWCQIWSNNPAERLNR
+EIRRRTDAVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVM
+STEVMPTLQT
+>PROKKA_02232
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPNGCSSAANGPSPH
+>PROKKA_02266
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFERLLD
+YVQDRLPAVAAHLDAARQDILAFTSFPRDVWCQIWSNNPAERLNREIRRRTDAVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT
+>PROKKA_02271
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKLPVVAEHLDAARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAAGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVSNTGSEVNPDTAPALEFSA
+>PROKKA_01126
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQTRHHGPVEIAGLRDE
+>PROKKA_01127
+MSKDLDAQVEAFRTRPLDAGPYRFVAADALVLKVREHGRVVKVAAMVATGINNDGYREIL
+GLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLVEAAGAVFGTAQWQRCRTHYA
+ANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMIDSLATHLPAAAEHLEGARDEV
+LTFTKFPKEVWKKIWSNNPNERLNKEIRRRTDVVGIFPSRVAVIRLLGAVLAEQHDEWTE
+SRRYMSLELLTATDTMLAEAAAKAAAEQAALQVSDTMTDDPGHAALAA
+>PROKKA_00691
+MTAPHILDPAGLLREALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPGRATQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMATELDEHVESFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHTGLR
+EAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAQAVDAQFDRLLD
+YVSEKLPAVAEHLDAARADILAFTTFPKDVWTQVWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLHRCRLTPVSNTGDEVDTDTALELSA
+>PROKKA_00721
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKLPVVAEHLDAARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVSNTGNEVNPDTAPALEFSA
+>PROKKA_00896
+MTAPHILDPAGLLREALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPGRATQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMATELDEHVESFRHRPLGEALPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHTGLR
+EAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAQAVDAQFDRLLD
+YVSEKLLYGGRAPGRCPGGHPGLHDLPEGRVDAGLVEQSGRAAQPRDPPPHRRGGHLPQP
+GSHRQAGRCGAGRADR
+>PROKKA_02500
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKLPVVAEHLDAARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVSNTGNEVNPDTAPALEFSA
+>PROKKA_02671
+MTAPHILDPAGLLGEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPSSSRTAQR
+NGYRHRDLDTRVGTLDVAIPKLRSGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGVNALSKSQVSRMATELDEQVEAFRHRPLGVAGPFTFVAADALSMKVREGGPV
+VNAVVLLATGVNADGHREVLGLRVATSETGAAWNEFFADLVARGLAGLRLVTSDAHTGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAASVHAQFDRLLD
+YVSEKLPTVAEHLDAARADILAFTTFPKDVWTQVWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVTNTGDEVDPDTELTLGLSA
+>PROKKA_01344
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQTLGITGLSKSQVSEMSKDLDAPVEAFRTRPLDAGPYRFVAADALVLKVREHGRVV
+KVAAMVATGINNDGYREILGLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLVE
+AAGAVFGTAQWQRCRTHYAANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMIDS
+LATHLPAAAEHLEGARDEVLTFTKFPKEVWKKIWSNNPNERLNKEIRRRTDVVGIFPSRV
+AVIRLLGAVLAEQHDEWTESRRYMSLELLTATDTMLAEAAAKAAAEQAALQVSDTMTDDP
+GHAALAA
+>PROKKA_01996
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQTLGITGLSKSQVSEMSKDLDAQVEAFRTRPLDAGPYRFVAADALVLKVREHGRVV
+KVAAMVATGINNDGYREILGLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLVE
+AAGAVFGTAQWQRCRTHYAANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMIDS
+LATHLPAAAEHLEGARDEVLTFTKFPKEVWKKIWSNNPNERLNKEIRRRTDVVGIFPSRV
+AVIRLLGAVLAEQHDEWTESRRYMSLELLTATDTMLAEAAAKAAAEQAALQVSDTMTDDP
+GHAALAA
+>PROKKA_02197
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKLPAVAEHLGDARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTPVEDTGSEVGTDTDTALELSA
+>PROKKA_02214
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKLPAVAEHLGDARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTPVEDTGSEVGTDTDTALELSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000004.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000004.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b0ea19752cf357100762ab79a63583504c3454d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000004.fa
@@ -0,0 +1,190 @@
+>PROKKA_00376
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>PROKKA_01393
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>PROKKA_02069
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPLTQTS
+>PROKKA_02112
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>PROKKA_02277
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>PROKKA_00355
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>PROKKA_01012
+MGRTQWPLTDVPRDRGGSFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIG
+TDLSHETISNITDAVSEEVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGV
+DLEGIKHVLGIWVQDTEGSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSM
+VQTCVVHLIRAAMRFVAYQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAA
+ATWANSWERFIPFLQFPPMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLA
+ICNIEDKRAAERARDRGKPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>PROKKA_01015
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVCKRP
+>PROKKA_01125
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>PROKKA_01746
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>PROKKA_01819
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>PROKKA_02016
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>PROKKA_00228
+MVQTCVVHLIRAAMRFVAYQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSA
+AATWANSWERFIPFLQFPPMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWL
+AICNIEDKRAAERARDRGKPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>PROKKA_00229
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEAPKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYA
+>PROKKA_00643
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEAPKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>PROKKA_00895
+MVQTCVVHLIRAAMRFVAYQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSA
+AATWANSWERFIPFLQFPPMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWL
+AICNIEDKRAAERARDRGKPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>PROKKA_00899
+MTDTADAQNPLAGVLSADQVDALVNAAEDLGEGRHGVEELLSRMTQAVLERALETEMSEH
+LGYEAGDPAGAGTGNSRNGKTTKSVQTLQGPGQITVPRDRNGSFEPVIVPKRSRRLGRVE
+DMILSLYARGMTTRDIGSHLEEIYGSKVSAATISRVTDVVADEVAQWQSRPLETVYPIVY
+IDAIWLKIRDGGVVTNKACHVAVGVDLEGRKQVLGLWLGVSEGAKFWANVLTEIRNRGTK
+DILILCCDGLSGLPAAVNSIYPETVVQTCVVHLLRSAMKYASYADRKTMAKDMRPIYTAA
+TVEAAQLALEAFAEIWQTKAPGAVLAWRTAWEDFIPFLAFTPEIRKVIYTTNQIESINYQ
+LRKITKTRGSFPSDEAAIKLVYLGIRNIETRRGGELGTGTQGWHQALNAFAVQFPNRLPL
+>PROKKA_01506
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEAPKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>PROKKA_02100
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYGKGSEDASKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>PROKKA_01829
+MSESTTEMTGPMIDPVTGEIIDQKDLAEQLLAQAKEQGVRLVGPGGLLNQLTKNVLETAL
+EAELTEHLGHDHGQTPIAANMRNGTRSKTVLTEIGPVEIEVPRDRDGSFEPVIVPKRKRR
+LDGTDQIVLSLSARGLTTGEIAVHFEEVYGAKVSKDTISRITEKVAGELAEWSSRPLDPL
+>PROKKA_00116
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>PROKKA_01547
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>PROKKA_01549
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>PROKKA_01880
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>PROKKA_01974
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000005.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000005.fa
new file mode 100644
index 0000000000000000000000000000000000000000..731b169afe74b7c155a456c9758281827f1a0d13
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000005.fa
@@ -0,0 +1,162 @@
+>PROKKA_01778
+MDGDQDEMAGPGVLAVPEREWEQARLRAGVIGRLAEHDPVGLAAVDEAAMELGISRRRVY
+VLLERYRRGSGLVTDLVPRRSDGGKGGGRLTEPVEQIIRELVCQRYLTRQKRSIASLHRE
+ITRACAVQGLPAPARNTVAARIARMNPVEVGRRREGAESVRPLQSAGDEVPVVESILDQV
+QIDHTVMDLIVVDDRDRQPIGRPYLTVAIDVCSRCLVGMVVTLEPPSAVSVGLCLAHAAG
+DKRPWLERLGIDAAWPMSGKPKALYVDNAREFKSEALTRGCDQHGISLDYRPLGRPHYGG
+IVERVIGTAMRQIHELPGTTFSNPVERGAYDAEKMAALTIAELERWLVLAVATYHDTVHS
+TLGQTPAGRWVESVAATSTPMTTANPTAFLVDFLPVFRRKLTRTGFVLDHVHYFANALKP
+WIARREALERFLIRRDPRDISRIWVLDPEGTAYIEVPYRALSNPAVSVWEHRQALARLRE
+RGATEVDESGLFRMIEQMRTISETAQKTTKRTRRERQRRTQTGTTTTRPTPPVPEPPVVP
+TDLDVVARFGEIEQW
+>PROKKA_01282
+MSHANAALTPRHRLIVGRLVVDDGWPISEVAARFQVSWPTVKRWADRYRTGEPMQDRSSR
+PHHSPNKTNQQTARRCVRLRLRLREGPVQLASRLGIAPSTVHRILTDVHLNRLSHVDRAT
+GEPVRRYEHDHPGSMLHVDVKKLGNIPDGGGWRYVGRRQGDKNRAATPDKPKNKHYDPLM
+GMAYVHTVIDDHSRVAYTEIHDDETARTATAVLIRAVEWFNARGVTVERVLSDNGGAYRS
+HLWRDTCAELGIRHKRTRPYRPQTNGKIERFHRTLADGWAYARCYTSEAERRGELDDWLH
+YYNHHRPHTACGNLPPFSRLINVSGQYS
+>PROKKA_02274
+MSHANAALTPRTRLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPSTMPTRTSPAVVKQIVAARWRQRLGPAQIASELGIPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDAYTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYARFYSSETERRAALP
+GWLHFYNHHRVHSAIGATPATRLNNLPGHHT
+>PROKKA_00226
+MSHANAALTPRARLRLAKLIVDEHWAVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPATMPTRTSPAVVKQIVAARRRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHT
+>PROKKA_00227
+MVVQLRTVEKWGPARIAGHLSTVGDGSINISPATVWRILNRNGISRLRDLDMPTGESKRE
+PRRYEHAAPGDMIHVDVKKVGRIPEGGGWAVHGRGTEEALASRRVASRRPGYVYIHAAVD
+DHSRLAYAEVHPDERAGTAAAFWLRAVLFYREHGITTFSRCLTDNGPAYRSKVFNDALAG
+TGTAHKYTRPHTPRTNGKVERFNRTMKEEWLYVRAYASDGERTAALAAFLNTYNHDRPHS
+SLGNKPPASRVPITSYRVQPQPKVLDVPQIEGLGHEPTLFDLL
+>PROKKA_00312
+MSHANAALTPRARLRLAKLIVEEHWAVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPATMPTRTSPAVVKQIVAARWRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHT
+>PROKKA_00315
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPSTMPTRTPPAVVKQIVAARWRRRLGPAQIASELGIPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFARLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYARFYGSESERRSALP
+GWLHFYNHHRHHSAIGAPPISRIDNNLPGHHT
+>PROKKA_00448
+MVDRSSRPATMPTRTSPAVVKQIVAARRRRRLGPVQIASELGMPASTVHAVLVRCRINRL
+ARLDRVTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGT
+RDARYQPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVL
+SDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETER
+RAALPGWVHFYNHHRVHSAIGAAPASRLNNLPGHHS
+>PROKKA_00627
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPATMPTRTPPAVVKQIVAARWRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHT
+>PROKKA_00631
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPSTMPTRTPPAVVKQIVAARWRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHI
+>PROKKA_00641
+MSHADAALTPRHRLKVARLVVDDGWPISEAAARFQVSWPTVKRWVDRYLSGEPMSDRSSR
+PKSSPNRTPRVVAKRCVSLRMRLREGPVQLAARLGIAPSTVHRILTTARMNRLSYVDRAT
+GEPIRRYEHPHPGSLVHVDVKKLGNIPDGGGWRYVGRLQGGRNRAATPDKPRNQYGGPKL
+GYAFVHTVIDDHSRVAYTEVHDDETAITAVAVLHRAVEWFADLGVTIERVLSDNGGAYRS
+HLWRDTCEALSITPKRTRPYRPQTNGKVERFHRTMADGWAYARCYTSEAERRGALSGWLH
+QYNQHRPHTACSNQPPFSRLINVPEQYT
+>PROKKA_00645
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPSTMPTRTPPAVVKQIVAARWRRRLGPAQIASELGIPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFARLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYARFYGSESERRSALP
+GWLHFYNHHRHHSAIGAPPISRIDNNLPGHHT
+>PROKKA_00652
+MSHPNAALTPRHGLLVGRLVVDDGWPISEVAARFQVSWPTVKRWADRYRTGQPMQDRSSR
+PHHSPNKTSAKTTRRCIQLRLRLREGPVQLACRLGIAPSTVHRILTDAHLNRLSHVDRAT
+GEPVRRYEHDHPGAMLHVDVKKLGNIPDGGGWRYVGRRQGEKNRAATPGKPRNKYRDPLM
+GKAYVHTVIDDHSRVAYAEIHDDETAITATAVLVRAVEWFNARGVTVERVLSDNGGAYKS
+HLWRDTCVELGIKHKRTRPYRPQTNGKIERFHRTLADGWAYARCYTSEDERPGELEGWLH
+YYNHHRPHTACGDQPPFSRLTNVPGQYT
+>PROKKA_00678
+MDASERWRILRLHVEDAIPLATLARSTGVTERTLQRWLARYRTGGYAALADDARADHGVR
+RTAPELVRLVEGLALTKPRPSIATIHRQVGVHCAERGLPSPSYSAVRSIVNGLDPGMVTL
+ALEGPASYRDKHELLLRRRADRPNAIWQADHTMLDLLIVGPNGKPARPWLTVILDDYSRA
+ICGYMVFLGAPSAANTALALRQAIWHKPEPDWPVCGIPDVLYTDHGSDFTSHRLGDTAAV
+LHLRIIHSQVARPQGRGKIERFFGTINTELLPTLPGHFAAGSSAPTPALDLGGVDSAIST
+FIRSYNARTHRELRTSPLHAWIADGWLPRLPESLEQLDGFLLTVPTTRVVQRDGIHFEGL
+RYTAATLAPFVGSTVSVRYDPRDVTEIRVFHRDVFLCTAISTEHQTETISLKQIQAARNA
+HRRALRGQIHERIAIVNPKLDDTTTPAAVETDRPRLKTYEEDRS
+>PROKKA_00751
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPSTMPTRTPPAVVKQIVAARWRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHT
+>PROKKA_01361
+MTHLNAALTPRHRLKVARLVVEDGHPISEVAARFQVSWPTVKRWVDRYLAGESMNDRSSR
+PKSSPKKTNKAVTKRCVSLRMRLREGPIQLAARLGIAPSTVHRILTAARLNRLSYVDRAT
+GEPVRRYEHPHPGSLVHVDVKKIGNIPDGGGWRYVGRRQGQKNRAATPDKPKNKWHSPKL
+GYAFVHTVIDDHSRVAYTEVHDDETAITAVAVLHRAVEWFAERGVTIERVLSDNGGAYRS
+YLWRDTCEALSIRPKFTRPYRPQTNGKVERFHRTMGDGWAYARCYTSEQERRDALPDWLH
+HYNQHRPHSACGNQPPFSRLINVPGQYN
+>PROKKA_01794
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPSTMPTRTPPAVVKQIVAARWRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHT
+>PROKKA_01820
+MSHANAALTPRHRLKVAQLVVDDGWPISEVAARFQVSWPTVKRWADRHRAGESMQDRSSR
+PHHSPNKTSPTVTRRCIQLRLRLREGPVQLACRLGIAPSTVHRILTDAHLNRLSHVDRAT
+GEPVRRYEHDHPGAMLHVDVKKLGNIPDGGGWRYVGRRQGEKNRAATPGKLRSKYSDPLM
+GKAYVHTVIDDHSRVAYAEIHDDETAVTASAVLVRAVEWFNRRGVTVERVLSDNGGAYRS
+HLWRDTCHELGIKHKRTRPYRPQTNGKIERFHRTLADGWAYARCYTSEAERRGELDGWLH
+YYNQHRPHTACGNQPPFSRLTNVPDQYI
+>PROKKA_01832
+MSHKNAALTPRHRLKVARLVVEDGWPISEIAARFQVSWPTVKRWVDRYLAGESMEDRSSR
+PRVSPNKTPKTVTKRCVSLRMRLREGPVQLAARLGIAPSTVHRILTTARLNRLSYVDRAT
+GEPIRRYEHPHPGSLVHVDVKKLGNIPDGGGWRYVGRLQGERNRAATPGKPKNKWHNPKL
+GYAFVHTVIDDHSRVAYTEVHDDETAITAVAVLHRAVEWFANRGVTIERVLSDNGGAYRS
+HLWRDTCD
+>PROKKA_01835
+MSHANAALTPRARLRLAKLIVDEHWAVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPATMPTRTSPAVVKQIVAARRRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHI
+>PROKKA_01890
+MSHANAALTPRARLRLAKLIVDEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPATMPTRTPPAVVKQIVAARRRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFARLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWLHFYNHHRVHSAIGAAPASRLNNLPGHHT
+>PROKKA_02162
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPSTMPTRTPPAVVKQIVAARWRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHI
+>PROKKA_02206
+MPASTVHAVLVRCRINRLARLDRVTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFV
+GRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVL
+RRAVAHFAQLGVEVERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHR
+TLADGWAYAKFYGSETERRAALPGWVHFYNHHRVHSAIGAAPASRLNNLPGHHS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000006.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000006.fa
new file mode 100644
index 0000000000000000000000000000000000000000..60f69bef0f1ffcb49f4a901937713145f3151168
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000006.fa
@@ -0,0 +1,100 @@
+>PROKKA_00157
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>PROKKA_01034
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>PROKKA_01292
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>PROKKA_01384
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETGDSQNVRTE
+>PROKKA_02077
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>PROKKA_01011
+MVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIK
+ICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWA
+GTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRH
+SSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>PROKKA_01104
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>PROKKA_01112
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>PROKKA_01114
+MSERIACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINRFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>PROKKA_02023
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMEIGDSQNVRTE
+>PROKKA_01214
+MACRLVGLSRSAYRRPLKGDTVADPDRALRQWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>PROKKA_00588
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVASRGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>PROKKA_00590
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVVDWAGTR
+TGLWADPVS
+>PROKKA_01250
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>PROKKA_01339
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTH
+>PROKKA_01885
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLGHV
+>PROKKA_02205
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVASRGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000010.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000010.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ffa83c86a507bf20814f9f295ba75a5d7334cb4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000010.fa
@@ -0,0 +1,79 @@
+>PROKKA_00454
+MLHPTFATPDLTTFCRLDELGLVAVGQLIEPDRATIECRVVEDDPWCRKCGVEGVPRDTV
+TRRLAHEPFGHRPTTLLVRVRRYRCGHCRRTWRQDMTRAAAPRAKISRGGLEWALRGIVI
+DHLTVTRVAAGLGVSWSAANAAVLAEGKRRLIDDPARFDGVTTIGVDEHVWRHTRLGDKY
+VTVIIDLTPARNKTGPARLLDMVEGRSKAVFKQWLAARPADWAKRIEVVAMDGFAGFKTA
+AAEELPDAVPVMDPFHVVRLAGDALDVCRRRVQQDTTGHRGLKGDPLYKARRTLHTGASL
+LTDRQRARLDAVFASEEHIEVEATWGIYQRIVAAYREPDKKKAKAMMQEVIATISSGVPA
+ALVEVRKLGRTMKQRAGDILAFFDRPGTSNGPTEAINGRLEHLRGSALGFRNLTHYIARS
+LLEAGGFRPALHPRS
+>PROKKA_00845
+MRRYRCSGCGYVWRQDTTASAEPRAKLSRRALRWALEGIVVQHLTVARVAEGLGVAWDTA
+NDAVLAEGKRVLIDEEHRFEGVKVVGVDEHVWRHTRRGDRYVTVIIDLTPVRDGTGPARL
+LNMVEGRSKQAFKTWLADRPQDWRDGVEVVAMDGFTGFKTAAVEELPDVVTVLDPFHVTR
+LAGEALDECRRRVQQAICGHRGRKGDPLYAARRTLSTGVDLLNDKQKDRLDTLFADDAHV
+EVEVTWSVYQRMIAAYRHENRRHGRELMARLIDSISTGVPKALVEITKLGRTLKKRAADV
+LAYFDRPSTSNGPTEAINGRLEHLRGSALGFRNLTNYIARSLLETGGFRPRLHPGFG
+>PROKKA_01392
+MSLLTDRQEEHLSVLFAHEKHAAVEAAWEIYQAMVAAYREFDRAKAKAKMEKVIAALSKK
+VPDTLEELGKLGRTLTKRAADVLAFFERLGTSNGPTEAINGRLEHLRGSALGFRNLTNYI
+ARSLLESGGFRPLLHPQMR
+>PROKKA_01124
+MSLLTDRQKEHLSVLFAHEKHAAVEAAWEIYQAMVAAYREFDRAKAKAKMEKVIAALSKK
+VPDTLEELGKLGRTLTKRAADVLAFFERLGTSNGPTEAINGRLEHLRGSALGFRNLTNYI
+ARSLLESGGFRPLLHPQTR
+>PROKKA_00108
+MLILWRQRVWRCAEPGCARGTFVEQLPSLVAPRGSITTRAISWAIGQLRREHGTIAGLAR
+QLGTSWKTLWRAIRPELEHLADDESRFEGVTSLGVDEHIWHHVDRRRRGPRELTGMVDLS
+RDEHGRVRARLLDLVPGRSGKAYAGWLAERGDAFRRGVQVAALDPFAGYKTAIDQRLDDA
+TAVLDAFHVVKLGTQVVDEVRRRVQQATLGHRGRKGDPLYGIQTILRAGAEHLTDKQLAR
+LAAAIESDPAHEEVFVAWQCAQDLRAAYRSGNLADGRAIAERLADSLHTSPIPEVARLGR
+TLRRWRAAFLAYFTTNRSSNGGTEAINGIIELHRRLARGFRNRDNYRLRMLLAAGGLTP
+>PROKKA_00508
+MVDLSRDEHGRVRARLLDLVPGRSGKAYAGWLAERGDAFRRGVQVAALDPFAGYKTAIDQ
+RLDDATAVLDAFHVVKLGTQVVDEVRRRVQQATLGHRGRKGDPLYGIQTILRAGAEHLTD
+KQLARLAAAIESDPAHEEVFVAWQCAQDLRAAYRSGNLADGRAIAERLADSLHTSPIPEV
+ARLGRTLRRWRAAFLAYFTTNRSSNGGTEAINGIIELHRRLARGFRNRDNYRLRMLLAAG
+GLTP
+>PROKKA_00509
+MLILWRQRVWRCAEPGCARGTFVEQLPSLVAPRGSITTRAISWAIGQLRREHGTIAGLAR
+QLGTSWKTLWRAIRPELEHLADDESRFEGVTSLGVDEHIWHHVDRRRRGPKS
+>PROKKA_01091
+MLILWRQRVWRCAEPGCARGTFVEQLPSLVAPRGSITTRAISWAIGQLRREHGTIAGLAR
+QLGTSWKTLWRAIRPELEHLADDESRFEGVTSLGVDEHIWHHVDRRRRGPKS
+>PROKKA_01092
+MTRSGVACRSRRWTRSCGYKTAIDQRLDDATAVLDAFHVVKLGTQVVDEVRRRVQQATLG
+HRGRKGDPLYGIQTILRAGAEHLTDKQLARLAAAIESDPAHEEVFVAWQCAQDLRAAYRS
+GNLADGRAIAERLADSLHTSPIPEVARLGRTLRRWRAAFLAYFTTNRSSNGGTEAINGII
+ELHRRLARGFRNRDNYRLRMLLAAGGLTP
+>PROKKA_00630
+MPEPTLYCRARGDYCTCCDLLVGLPGLHVLTAERDDHDRLVVTVESAPEPMGCRSCGVIA
+RGHGRIEVSLVDAPAFGRPVRIIWRKRRWLCPDPACEVGSFIEQDEKVAAPRAVLTTRAC
+RWAIEQIRREHASVNGIRRQLGTGWRTVWDSIQPLLQAADEDPSRFEGVAILGVDEHVWH
+HVSTKPIHHGGRGPKELTGMVDLTRDEGGRTRARLLDLVPGRSGRVYKDWLDQRGDAFRA
+RIEVATLDPFHGYKNAIDDQLEDARSVLDAFHVVKLATTVVDDVRRRVQQQIHGHRGRKS
+DPLYRVRNVLRAGAENLTDRQRDRLETAWAAHEQHIEVEIAWLCAQKVRSAYRQGTHAAG
+RAVAEKILATFTSCPIPEVARLGKTLNRWRREFLGYFDTNGASNGGTEAINGLIELHRRI
+ARGFRNRDNYRLRMLLIGGGLDMTHHTQR
+>PROKKA_00638
+MPEPTLYCRARGDYCTCCDLLVGLPGLHVLTAERDDHDRLVVTVESAPEPMGCRSCGVIA
+RGHGRIEVSLVDAPAFGRPVRIIWRKRRWLCPDPACEVGSFIEQDEKVAAPRAVLTTRAC
+RWAIEQIRREHASVNGIRRQLGTGWRTVWDSIQPLLQAADEDPSRFEGVAILGVDEHVWH
+HVSTKPIHHGGRGPKELTGMVDLTRDEGGRTRARLLDLVPGRSGRVYKDWLDQRGDAFRA
+RIEVATLDPFHGYKNAIDDQLEDARSVLDAFHVVKLATTVVDDVRRRVQQQIHGHRGRKS
+DPLYRVRNVLRAGAENLTDRQRDRLETAWAAHEQHIEVEIAWLCAQKVRSAYRQGTHAAG
+RAVAEKILATFTSCPIPEVARLGKTLNRWRREFLGYFDTNGASNGGTEAINGLIELHRRI
+ARGFRNRDNYRLRMLLIGGGLDMTHHTQR
+>PROKKA_00839
+MPEPTLYCRARGDYCTCCDLLVGLPGLHVLTAERDDHDRLVVTVESAPEPMGCRSCGVIA
+RGHGRIEVSLVDAPAFGRPVRIIWRKRRWLCPDPACEVGSFIEQDEKVAAPRAVLTTRAC
+RWAIEQIRREHASVNGIRRQLGTGWRTVWDSIQPLLQAADEDPSRFEGVAILGVDEHVWH
+HVSTKPIHHGGRGPKELTGMVDLTRDEGGRTRARLLDLVPGRSGRVYKDWLDQRGDAFRA
+RIEVATLDPFHGYKNAIDDQLEDARSVLDAFHVVKLATTVVDDVRRRVQQQIHGHRGRKS
+DPLYRVRNVLRAGAENLTDRQRDRLETAWAAHEQHIEVEIAWLCAQKVRSAYRQGTHAAG
+RAVAEKILATFTSCPIPEVARLGKTLNRWRREFLGYFDTNGASNGGTEAINGLIELHRRI
+ARGFRNRDNYRLRMLLIGGGLDMTHHTQR
+>PROKKA_01343
+MSLLTDRQKEHLSVLFAHEKHAAVEAAWEIYQAMVAAYREFDRAKAKAKMEKVIAALSKK
+VPDTLEELGKLGRTLTKRAADVLAFFERLGTSNGPTEAINGRLEHLRGSALGFRNLTNYI
+ARSLLESGGFRPLLHPQMR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000013.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000013.fa
new file mode 100644
index 0000000000000000000000000000000000000000..024a66a3bfe11a0c66512a5eac4f4aea3e9f75af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000013.fa
@@ -0,0 +1,60 @@
+>PROKKA_00341
+MKELAAVGIPVAVTCRVLKLSRQPYYRWLADPVTDAELAEAYRANALFDAHQDDPEFGYR
+FLVDEAKEAGEVMCERSAWRICRDNGWWSVFGKKRGKNGKKPGPPVHDDLVERDFTAGGS
+NQLWLTDVTEHRTAEGKLYMCAIKDVFSGRIVGYSIDSRMKARLAVQALQNAVARRGDVA
+GCIVHSDRGSQFRSRKFVHALNRHGLVGSMGKVGAAGDNAAMESFFALLQKNVLDRRSWT
+TRDELRIAIVTWTERTYHRRRRQARLGRLTPIEYETMMKPAVTLPA
+>PROKKA_01765
+MYPLVSELAADQIPVAVSLRVLKLARQPYYRWRDQPVAVSEVEQAYRANALHAAHLNDPE
+FGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCGFGAKRGKYGTRPGPPVHDDHVRRDFS
+AEAPNRLWLTDITEHPTSEGKLYLCAIKDLYAGRIVGYSMAGRMQASLAVNALEQAVARR
+GGTDAVAGCIVHSDRGSQFRSALFQDALTTHGLIGSMGQVGAAGDNAAMESFFALLQKNV
+LDRRDWDTRDELRAGIITWIERTYHRRRRQVRLGRLTPVEYELIMDHTPADAA
+>PROKKA_00706
+MMYPHVKELATDGIPVVVSVRMLKLARQPYCRWLENPLTRTDLDQAYRANALHAAHQNEK
+ALAHRSAS
+>PROKKA_02276
+MYPLVSELAADGVPVAVSLRVLKLARQPYYRWREKPVAVSEVEQAHRANALHAAHLNDPE
+FGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCAFGAKRGKNGRRPGPPVHDDRVRRDFS
+AEAPNRLWLTDITEHPTGEGKLYLCAIKDVHAGRIVGYSMAGRMQASLAVNALEQAVARR
+GGTDAVAGCIVHSDRGSQFRSALFQDALTAHGVIGSMGQVGAAGDNAAMESFFALLQKNV
+LDRRDWDTRDELRAGIITWIERSYHRRRRQVRLGRLTPVEYELIMDHTPADPA
+>PROKKA_02495
+MHDDRVRRDFSAEAPNRLWLTDITEHPTGEGKLYLCAIKDVHAGRIVGYSMAGRMQASLA
+GNALEQAVARRGGTDAVAGCIVHSDRGSQFRSALFQDALTAHGLIGSMGQVGAAGDNAAM
+ESFFALLQKNVLDRRDWDTRDELRAGIITWIERTYHRRRRQVRLGRLTPVEYELIMDHTP
+ADPA
+>PROKKA_02496
+MYPLVSELAADGVPVAVSLRVLKLARQPYYRWRDQPVAVSEVEQAHRANALHAAHLNDPE
+FGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCAFGGQARQERALYLALPCMMTASAGTS
+LPKLRTGCG
+>PROKKA_02615
+MYPLVSELAADGVPVAVSLRVLKLARQPYYRWRDQPVAVSEVEQAHRANALHAAHLNDPE
+FGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCAFGAKRGKNGRRPGPPVHDDRVRRDFS
+AEAPNRLWLTDITEHPTGEGKLYLCAIKDVHAGRIVGYSMAGRMQASLAGNALEQAVARR
+GGTDAVAGCIVHSDRGSQFRSALFQDALTAHGLIGSMGQVGAAGDNAAMESFFALLQKNV
+LDRRDWDTRDELRAGIITWIERTYHRRRRQVRLGRLTPVEYELIMDHTPADPA
+>PROKKA_02636
+MEQAHRANALHAAHLNDPEFGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCAFGAKRGK
+NGRRPGPPVHDDRVRRDFSAEAPNRLWLTDITEHPTGEGKLYLCAIKDVHAGRIVGYSMA
+GRMQASLAVNALEQAVARRGGTDAVAGCIVHSDRGSQFRSALFQDALTAHGVIGSMGQVG
+AAGDNAAMESFFALLQKNVLDRRDWDTRDDLRAGIITWIERAYHRRRRQVRLGRLTPVEY
+ELIMDHTPADPA
+>PROKKA_01887
+MHPLVRELAVDGIPVAVTCRVLKIARQPYYRWLASPVTPAELDEAYRANALFDAHKDDPE
+FGYRFLADEAREAGESMAERTAWRICSDMGWWSAFGKKRGRNGKKPGSPVHDDLCAVTDE
+KGRIRHQFNADAVNELWIGDITEHRTGEDRLYLCAFKDVYSNRIVGYSIDSRMKSSLAVT
+ALNNAVARRGEVAGCVVHTDRGSQCRSRKFVHALNRHGMVGSMGRVGATGDNAAMASFFA
+LLQKNVLERRSWATREDLRIAIVTWIERTYHRRRRQVALGRLTPIEYEAIMTTPASQAA
+>PROKKA_00898
+MYPLVRELAVDGIPVAVTCRVLKIARQPYYRWLASPVTPAELDETYRANALFDAHKDDPE
+FGYRFLADEAREAGELMAERTAWRICSDMGWWSAFGKKRGRNGKKPGSPVHDDLCAATDE
+KGRIWHQFNADAVNELWIGDITEHRTGEGRLYLCAFKDVYSNRIVGYSIDSRMKSSLAVT
+ALNNAVARRGEVAGCVVHTDRGSQFRSRKFVHALNRHGMVGSMGRVGAAGDNAAMESFFS
+LLQKNVLDRRSWATREDLRIAIVTSIERTYHRRRRQAALGRLTPIEYEAIMTTPASQAA
+>PROKKA_01544
+MTYPLVAELADAGILVTVSCRVLKLARQPYYRWRNAPVRDADMLRAYRINALHDAHHDDP
+TFGYRYLADEARRAGWRMSRRTAWKLCSQAGILSSAQRRRRGKGKKTGPPVFDDHVQRVF
+RADAPNRLWLTDITEHRTSEGKLYCCAIKDVFSNRIVGYSISDRMTAKLAVDAVRNAVAR
+RGEVAGCILHADRGSQFRSRAMARELRRHDMVGSMGRVGAAGDNAAMESFWSLLQTNVLN
+QQRWTTRQELRLVIVVWIERKYHRQRAQDILGGLTPIEFEAKLAEPHTLAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000014.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000014.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb8be2961d7574669f2c5cf2b8a1b0ebf91c9978
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000014.fa
@@ -0,0 +1,97 @@
+>PROKKA_00160
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA
+>PROKKA_01074
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA
+>PROKKA_02060
+MNEAVPHFDLAIIGSGGGAFAAAIRATNLDKRVVMIERGTVGGTCVNTGCIPSKALLAAA
+EARHTAQDAGRFPGLTATAGPVDMEALIAGKRALVENVRSDKYVDLVADYGWELRHGNAV
+FTGTAADPALEVTAQDGTRETITAAHYLVATGSTPWAAPINGLDTVDYLTSTTAMELDEV
+PESLLVIGGGYVALEQAQLFARLGSKVTMLVRSRLASGEEPEASRALMSVFANEGIRVIR
+RSTVSSITQDTDGGIAAQADIAGGRETLRASKVLVATGRRPVTDGLNLAGVSVKTGDKGE
+VVVEDTLVSSNPRVWAAGDVTGHPEYVYVAASHGTLMVDNAFSDAGRAVDYSHLPRVTFT
+SPNLAVVGMTDKQARDAGIRCECRVVPLEYIPRAVVNRDTRGFIKMVADADTGRIVGITA
+VAKEAGDLAATGVYILQAGMTVDQVANLWSPYLTMAEGIKIVAQSFKTDVSKLSCCAA
+>PROKKA_00298
+MPTKYDLAIIGSGGGAFAAAIRATTLGKSVVMIERGTLGGTCVNTGCVPSKALIAAADAR
+HSAADAADRFPGIATTAGPVDMPALIAGKQALVESLRGEKYADVADSYGWAVRRGDAAFA
+GTPDAPVLQVAGDDGSTETIEAGHFLVATGSRPWAPPIDGLDETGYLTSTTAMELTELPE
+SLLVLGGGYVALEQAQLFARLGSQVTVLVRSRLASKEEPEVSRTLEEVFADEGIRVVRRA
+LPTRVSRDAATGQAVVTADVAGGREEFRADQVLVALGRRPVTDGLGLDRVGVETGDLGEV
+VVSDRMQSSHPRIWAAGDVTGHPEFVYVAAHHGTLVAENAFADADRAVDYARLPRVTFTG
+PAIGAVGMTEKDVVAAGIRCDCRVLPLHHVPRALVNRDTRGFVKIVVDADTGKILGITAV
+AKDAGELAAAGVHVLGKTVAEVADAWAPYLTMAEGIRIAAKAFTTDPSLLSCCA
+>PROKKA_00337
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTCGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA
+>PROKKA_00346
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA
+>PROKKA_00793
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPLPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTCGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA
+>PROKKA_00723
+MTATANSRSYDLAMIGSGGAAFAAAIRATSLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPLPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA
+>PROKKA_02220
+MNEAVPHFDLAIIGSGGGAFAAAIRATNLDKRVVMIERGTVGGTCVNTGCIPSKALLAAA
+EARHTAQDAGRFPGLTATAGPVDMEALIAGERALVENVRSDKYVDLVADYGWELRHGNAV
+FTGTAADPALEVTAQDGTRETITAAHYLVATGSTPWAAPINGLDTVDYLTSTTAMDLDEV
+PESLLVIGGGYVALEHAQLFARLGSKVTMLVRSRLASGEEPEASRALMSVFANEGIRVIR
+RSTVSSITQDTDGGIAAQADIAGGRETLRASKVLIATGRRPVTDGLNLAGVSVKTGDKGE
+VVVEDTLVSSNPRVWAAGDVTGHPEYVYVAASHGTLMVDNAFSDAGRAVDYSHLPRVTFT
+SPNLAVVGMTDKQARDAGIRCECRVVPLEYIPRAVVNRDTRGFIKMVADADTGRIVGITA
+VAKEAGDLAATGVYILQAGMTVDQVANLWSPYLTMAEGIKIVAQSFKTDVSKLSCCAA
+>PROKKA_01023
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPLPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDGHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000015.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000015.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fbdbb3f6db95fff7c58f5e8d29a880e6d4a15993
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000015.fa
@@ -0,0 +1,105 @@
+>PROKKA_00355
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIE
+KAVEAVTSELLSASREIETKDQIAATASISAADKQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENATLDLLGSARKVVITKDETTIVEGGGDAEQIAGRVAQIRSEIENTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFGGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKTLDDGHGLNAAT
+GEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM
+>PROKKA_01656
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVE
+LEDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKRGIE
+VAVAAVEQRLQENARPVEGKEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVVQA
+NKPLFVIAEDIEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGAQVVSP
+DLGMKLEQADLDVLGSARRITVTKDETTIVDGGGAPEDVEARIAQIKAEAAATDSDWDRE
+KLQERLAKLSGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+TVLDTDADVQALTGDAAVGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFNA
+KTGVYGDLIADGVIDPVKVTRSALANATSIAALVLTTETLVADKPADEDEAGHQH
+>PROKKA_00071
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPCGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIE
+KAVEAVTSELLSASREIETKDQIAATASISAADKQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENATLDLLGTARKVVVTKDETTIVEGGGDAEQIAGRVAQIRSEIENTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFGGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKTLDDGHGLNAAT
+GEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM
+>PROKKA_01361
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVE
+LEDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKKGIE
+VAVAAVERRLQENARPVEGQEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVLQA
+NKPLFVIAEDIEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGAQVVSP
+DLGMKLEQADLDVLGSARRITVTKDETTIVDGGGAAEDVEARVAQIKAESAATDSDWDRE
+KLQERLAKLSGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+TALDTDADVQALTGDAAVGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFNA
+KTGVYGDLIADGVIDPVKVTRSALANATSIAALVLTTETLVADKPADEDEAGHQH
+>PROKKA_01238
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVE
+LDDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKKGIE
+VAVAAVEQRLQENARPVEGKEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDPYVLINSGKISNVQELLPVLEKVLQA
+SRPLFVIAEDIEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMLQDIAVLTGAQVVSP
+DLGMKLEQADLDVLGSARRITVTKDETTIVDGGGSAEDVEARVAQIKAESAATDSDWDRE
+KLQERLAKLAGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+SVLDTDADVQALTGDAASGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFNA
+KTGVYGDLIADGVIDPVKVTRSALANAASIAALVLTTETLVADKPEDEDEHQH
+>PROKKA_02606
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIE
+KAVDAVTAELLSASREIETKEQIAATASISAADKQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENATLDLLGTARKVVITKDETTIVEGAGDAEQIAGRVAQIRAEIENTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFGGLTLEGDEATGANIVKVAIEAPLKQIAFNAGMEPGVVADKVKTLQDGHGLNAAT
+GEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM
+>PROKKA_01149
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIARDVE
+LEDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPNEVKKGIE
+TAVAAVEKRLQENARPVEGKEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGYLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVLQA
+NKPLFVIAEDVEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGATVVSP
+DLGMKLEQADLDVLGSARRVTVTKDATTIVDGGGEAADVEARVSQIKAEVAATDSDWDRE
+KLQERLAKLAGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+SVLDEDAEVTALTGDAATGVEIVRKALKEPLRWIAQNAGEDGYVVVSKVAEMKPNEGFNA
+KTGVYGDLIADGVIDPVKVTRSALANAASIAALVLTTETLVADKVEDEDEHQH
+>PROKKA_02465
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPISLKRGIE
+KAVEAVTSELLSAAREIETKDQIAATASISAADAQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISTVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENASLDLLGTARKVVITKDETTIVEGAGDADQIAGRVAQIRSEIANTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFEGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKSLESGHGLNAAT
+GEYVDLMAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM
+>PROKKA_00362
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIE
+KAVEAVTSELLSASREIETKDQIAATASISAADKQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENATLDLLGTARKVVVTKDETTIVEGGGDAEQIAGRVAQIRSEIENTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFGGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKTLDDGHGLNAAT
+GEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM
+>PROKKA_01586
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVE
+LEDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKKGIE
+VAVAAVERRLQENARPVEGQEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVLQA
+NKPLFVIAEDVEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGAQVVSP
+DLGMKLEQADLDVLGSARRITVTKDETTIVDGGGAAEDVEARVAQIKAEAAATDSDWDRE
+KLQERLAKLSGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+TVLDTDADVQALTGDAAVGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFNA
+KTGVYGDLIADGVIDPVKVTRSALANAASIAALVLTTETLVADKPADEDEAGHQH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000016.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000016.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8421a10d7e607fec325bb3b0d32a77501ba8ebc6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000016.fa
@@ -0,0 +1,90 @@
+>PROKKA_00992
+MTPTPSRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGVAP
+DHPRIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALDVP
+GVELAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLPT
+EIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEAS
+EKAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEQFLDEDGDGRVDGLRM
+RRMELDGSGGVRPTGETVDYPVQAVYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDADG
+APVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWRAQEPSEESVIELLESRG
+VPYTTWAGWHALDEHEKSLGVQATEAGPVARERVKVVDREEMTRISREGVLLGAGG
+>PROKKA_01771
+MTVRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGVAPDHP
+RIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAVLDVPGVE
+LAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLPTEIP
+DNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEASEKA
+IEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGLRMRRM
+ELDGSGGVRPTGETVDYPVQAIYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDADGAPV
+PGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLESREVPY
+TTWAGWHALDEHEKSLGAQATEAGPVARERVKVVDREEMTRISRDGASVPTA
+>PROKKA_00706
+MTLTPSSSRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALD
+VPGVELAGSFGGADFAAWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDA
+ASEKAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTDETVDYPVQAIYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDA
+DGAPVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLES
+REVPYTTWAGWHALDEHEKSLGAQATEAGPVARERVKVVDREEMTRISRESVLLGAGG
+>PROKKA_01478
+MTVRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGVAPDHP
+RIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAVLDVPGVE
+LAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLPTEIP
+DNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEASEKA
+IEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGLRMRRM
+ELDGSGGVRPTGETVDYPVQAIYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDADGAPV
+PGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLESREVPY
+TTWAGWHALDEHEKSLGAQATEAGPVARERVKVVDREEMTRISRDGASVPTA
+>PROKKA_01106
+MTERPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGVAPDHP
+RIKGIVNALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAWLDVPGVE
+LAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLPTEIP
+DNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEASEKA
+IEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGLRMRRM
+ELDGAGGVRPTDETVDYPVQAVYRAVGYFGSPLDGVEFDAARGVVPNDEGRVLDADGVPV
+PGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDVDGLWTAQDPAEESVIDLLEAREVPY
+TTWEGWQALDAHEKSLGAQATEAGPVERERVKVVDREEMTRISREGAWAPTA
+>PROKKA_01897
+MTLTPSSPKPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVNALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAWLD
+VPGVELAGSYGGADFASWYDGHPDVPRHWPLDATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDE
+ASEKAIEENNQVRTMVGTLTNWLMEQEDREQSASRRLHLHFLQAPEQFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTGETVDYPVQAVYRAVGYFGSPLDGVEFDAARGVVPNDEGRVLDA
+DGVPVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLES
+REVRYTTWAGWLALDDHEKALGVQATEAGPVERERVKVVDREEMTRISRESVLLGAGG
+>PROKKA_01032
+MTERPDRPLRIAVVGAGPAGVYTADILTKEERDFQVSIDLFDRYPAPFGLIRYGVAPDHP
+RIKGIVTALHKVMDRGDIRFIGNVDVGTTVSLEDLRRLYDVVVFTTGAVRDAALDVPGVE
+LEGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLVTEIP
+DNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEASEKA
+IEENNQVRTMVGTLTNWLMEQEDRTEQASRRLHLHFLQAPEEFLDADGDGRVDGLRMRRM
+ELDGQGGITPTDETVDYDVQAVYRAVGYFGSPVPGVEFDDVRGVIPNAEGRVLDAAGHPV
+PGLYTSGWIKRGPVGLIGSTKGDSLETIKHLIEDEPGLYTAEDPSEQAVLDLLAERGVDY
+TTWEGWHALDAHEKALGAEATQAGPVERERVKVVDRAEMTRISRAGTGLA
+>PROKKA_01844
+MTPTPSSSRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVNALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALD
+VPGVELAGSFGGADFAAWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDE
+ASEQAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEQFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTGETVDYPVQAVYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDA
+DGAPVPGLYASGWIKRGPVGLIGHTKGDSLETITHLIEDEPGLWRAQEPSEESVIELLES
+REVPYTTWAGWHALDDHEKSLGAQATEAGPVARERVKVVDREEMTRISRKSILLGAGG
+>PROKKA_00935
+MTLTPSSSRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVNALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALD
+VPGVELAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDE
+ASEKAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTDETVDYPVQAIYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDA
+DGAPVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLES
+REVPYTTWAGWHALDEHEKSLGAQATEAGPVARERVKVVDREEMTRISRESVLLGAEG
+>PROKKA_01700
+MTARPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGVAPDHP
+RIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALDVPGVE
+LAGSFGGADFAAWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLPTEIP
+DNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEASEKA
+IEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGLRMRRM
+ELDGSGGVRPTGETVDYPVQAVYRAVGYFGSPVEGVEFDEVRGVIPNAQGRVLDADGAPV
+PGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLESREVPY
+TTWAGWHALDDHEKSLGAQATEAGPVARERVKVVDREEMTRISRDGASVPTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000019.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000019.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9aeb8d71e8777b885b94b91dc82f6c209f5496a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000019.fa
@@ -0,0 +1,27 @@
+>PROKKA_00342
+MPAPYPQEFRDDVVRVARSREEGVTLAQIAKDFGTHEMTLSKWMRQADVEDGAKPGTTKA
+ESAENRELKKRIRLLEQENEVLRRAAAYLSQANLPGKGSTRS
+>PROKKA_01766
+MPAPYPKEFRDDVVRVAQNREPGTHLKDIAKDFGISESCLTNWIRQADIEAGNIPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK
+>PROKKA_02275
+MPAPYPQEFRDEVVRVAQNREPGTQLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK
+>PROKKA_02497
+MPAPYPQEFRDDVVRVAQNREPGTHLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK
+>PROKKA_02616
+MPAPYPQEFRDDVVRVAQNREPGTHLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK
+>PROKKA_02634
+MPAPYPQEFRDDVVRVAQNREPGTQLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK
+>PROKKA_01886
+MSKPYPKEFRDDVVRIARNREPGVELSQIAKDFGIHFTTLYAWMKKADIEDGDRPGTTEA
+QYAELREAKRRIRTLEQEVEVLRRAAAYLSQAHLPGK
+>PROKKA_00899
+MSKPYPKEFRDDVVRVARNRGPGVELSQIAKDSGIHVTTLYAWMKKADIEDGDRPGTTEA
+QSAELREAKRRIRTLEQEVEVLRRAAAYLSQAHPPGK
+>PROKKA_01543
+MPGPCPREFREDVVAVARSRESGVTIKQIATDFGVSEATLQNWLRQADVEDGNRPGQTAA
+DAAEARELKKRIRLLEQENEVLRRAAAYLSQANLRLGGSPK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000022.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000022.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c45663cc618d65967cc986c7666084661f9beb76
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000022.fa
@@ -0,0 +1,109 @@
+>PROKKA_00633
+MSTPHHHDHPTDQTAEHPDPNPPAGHANHTDHAAHHPADAAAHGQAMPQGHAHSALDEDH
+QVHDHGQHAGHSTAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGT
+VIYLYGGMPFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELAL
+LVVIMLLGHWMEMRALGAASSALDALAALLPEEAEKVVDGDTITVPITELAVGDVVLVRA
+GARVPADGTILEGAAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTVRVKVAAVGTDTT
+LAGIQRMVADAQESSSRAQALADRAAALLFWFALVAAIITAIVWTAIGQPTDAVTRTVTV
+LVIACPHALGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHV
+VTAVTAMPGVSEAELLAVAAAAEADSEHPVARAIVTAAGQHPQASTLRKRGTDFSAAMGR
+GVRATVDGSEILVGGPNMLRELNLTMPAEITEHTASWTARGAGVLHVLREGSVIGAVAVE
+DKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTEL
+QSRGLSVAMVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQ
+ASYTKMIQNLVWATGYNVLAVPLAAGVLAPIGFVLSPAVGAILMSVSTIVVALNAQLLRR
+IDLDPEHLAPLERPRSQAALQPAAVS
+>PROKKA_01289
+MTDPTTHHHDHAGVATTESGHRDDSRAENEDHTMEHGDHAGHGHHGGGHAGHGDHVGQFR
+RLFWINLIIAIPVVAFSPMFAMLLGYSVPSWAGWVAAVLGSVMYAWGGTPFLTGAVSELK
+SRQPGMMLLIALGITVAFLASWAATVGLVHPELEFWWELALLIVIMLLGHWIEMRSLAQT
+TSALDSLAALLPDEAERIEGDDVVKVDPAELRVGDVVIVRPGGSVPADGTIVDGRADMDE
+SMITGESHPVARGEGENVTAGTVATDSGLRVEITATGDDTALAGINRLVAEAQGSSSRAQ
+RIADRAAALLFWFALGAALITAVVWTLFGLPDDAVVRTITVLVIACPHALGLAIPLVVSI
+ATERAARGGVLIKDRLALESMRQVDAVLFDKTGTLTKGEPTVTGVEPTGGLNAEQLLALA
+ASAEADSEHPLARSIVTAAKEKGLAVEPASGFTSSPAVGVTATVADHEIRVGGPRLLEET
+GQDEIGVADEWRAEGAIILHVLRDGKVIGGLKLADEVRPESRDAVDALHQLGVEVVMITG
+DAEAVANEVGRELGIDRVFAGVRPEDKSAKVDQLQKEGKKVAMVGDGVNDAPALAQADVG
+IAIGAGTDVAIASAGVILASSDPRSVLSVIQLSRAAYRKMRQNLWWAAGYNLLSVPLAAG
+VLAPVGFVMPMSVGAILMSISTVVVALNAQLLRRIDLAPAASTRSVLEHQK
+>PROKKA_01008
+MTDPTTHHHDHAGVATTESGHRDDSRAENEDHTMEHGDHAGHGHHGGGHAGHGDHVGQFR
+RLFWINLIIAIPVVAFSPMFAMLLGYSVPSWAGWVAAVLGSVMYAWGGTPFLTGAVSELK
+SRQPGMMLLIALGITVAFLASWAATVGLVHPELEFWWELALLIVIMLLGHWIEMRSLAQT
+TSALDSLAALLPDEAERIEGDDVVKVDPAELRVGDVVIVRPGGSVPADGTIVDGRADMDE
+SMITGESHPVARGEGENVTAGTVATDSGLRVEITATGDDTALAGINRLVAEAQGSSSRAQ
+RIADRAAALLFWFALGAALITAVVWTLFGLPDDAVVRTITVLVIACPHALGLAIPLVVSI
+ATERAARGGVLIKDRLALESMRQVDAVLFDKTGTLTKGEPTVTGVEPTGGLNAEQLLALA
+ASAEADSEHPLARSIVTAAKEKGLAVEPASGFTSSPAVGVTATVADHEIRVGGPRLLEET
+GQDEIGVADEWRAEGAIILHVLRDGKVIGGLKLADEVRPESRDAVDALHQLGVEVVMITG
+DAEAVANEVGRELGIDRVFAGVRPEDKSAKVDQLQKEGKKVAMVGDGVNDAPALAQADVG
+IAIGAGTDVAIASAGVILASSDPRSVLSVIQLSRAAYRKMRQNLWWAAGYNLLSVPLAAG
+VLAPVGFVMPMSVGAILMSISTVVVALNAQLLRRIDLAPAASTRSVLEHQK
+>PROKKA_00405
+MSTPHHHDHPTDQTAEHPDPNPHAGHANHTDHAAHHPADAATHGQAMPQGHAHSALDEDH
+QVHDHGQHAGHSTAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGT
+VIYLYGGMPFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELAL
+LVVIMLLGHWMEMRALGAASSALDALAALLPEEAEKVVDGDTITVPITELAVGDVVLVRA
+GARVPADGTILEGAAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTVRVKVAAVGTDTT
+LAGIQRMVADAQASSSRAQALADRAAALLFWFALVAAIITAIVWTVMGQPTDAVTRTVTV
+LVIACPHALGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHV
+VTAVTAMPGVSEAELLAVAAAAEADSEHPVARAIVTAAGQHPQASTLRKRGTDFSAAMGR
+GVRATVDGSEILVGGPNMLRELNLTVPAEITEHTASWTARGAGVLHVLREGSVIGAVALE
+DKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTEL
+QSRGLSVAMVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQ
+ASYTKMIQNLVWATGYNVLAVPLAAGVLAPIGFVLSPAVGAILMSASTIVVALNAQLLRR
+INLDPGHLAPLGAPRPEAALQPATS
+>PROKKA_00711
+MTDPNSQQHHGHETDTPAHGEHHHGSVSAHASADAHGTREGQHTGHQGHAMDHGQHSGHT
+GLDEHGGHDEHAQHGGYGDHSGHGGHGDHVGQFRRLFWINLVIAIPAVALSPMFAMLLGY
+EVPGWAGWVAAALGTVMYVWGGRPFLTGAVSELKSRKPGMMLLIALAITVAFFASWAATL
+GLVHHELEFWWELALLIVIMLLGHWIEMRSLAQTTSALDSLAALLPDEAERVEGENVVKV
+APADLDVGDVVLVRPGGSVPADGTIVDGRAEMDESMITGESRPVSRGEGQTVTAGTVATD
+SGLRVEITATGDDTALAGINRLVAEAQNSSSRAQRIADKAAAWLFWFALGAALVTAVVWT
+LIGMPDEAVVRTITVLVIACPHALGLAIPLVVSIATERAARGGVLVKDRLALESMRQVDA
+VLFDKTGTLTKGEPTVTGVEPTGELDADQVLALAASAEADSEHPLAKAIVTAAKDKGFAL
+QQASGFSSSPAVGVTATVSGQEVRVGGPRLLEETGQHEVGTAEAWRSEGAIILHVLRGGQ
+VVGGLRLADEVRPESRYAVDALHALGVEVVMITGDAEAVANEVGKELGIDRVFAGVRPED
+KSAKVSQLQEEGKRVAMVGDGVNDAPALAQADVGIAIGAGTDVAIASAGVILASSDPRSV
+LSIIQLSRRAYGKMKQNLWWAAGYNLLSVPLAAGILAPVGLVLPMSIGAILMSASTVVVA
+LNAQLLRRIDLTPEASTRSVLERQK
+>PROKKA_02196
+MSTPHHHDHPTDQTAEHPDPNPHAGHANHTDHAAHHPADAATHGQAMPQGHAHSALDEDH
+QVHDHGQHAGHSTAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGT
+VIYLYGGMPFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELAL
+LVVIMLLGHWMEMRALGAASSALDALAALLPEEAEKVVDGDTITVPITELAVGDVVLVRA
+GARVPADGTILEGTAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTVRVKVAAVGTDTT
+LAGIQRMVADAQESSSRAQALADRAAALLFWFALVAAIITAIVWTAIGQPTDAVTRTVTV
+LVIACPHALGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHV
+VTAVTAMPGVSEAELLAVAAAAEADSEHPVARAIVTAAGQHPQASTLRKRGTDFSAAMGR
+GVRATVDGSEILVGGPNMLRELNLTMPAEITEHTASWTARGAGVLHVLREGSVIGAVAVE
+DKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTEL
+QSRGLSVAMVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQ
+ASYTKMIQNLVWATGYNVLAVPLAAGVLAPIGFVLSPAVGAILMSASTIVVALNAQLLRR
+INLDPGHLAPLGAPRPEAALQPATS
+>PROKKA_00598
+MSTPHHHDHPTDQTAEHPDPNPHAGHANHTDHAAHHPADAATHGQAMPQGHAHSALDEDH
+QVHDHGQHAGHSTAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGT
+VIYLYGGMPFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELAL
+LVVIMLLGHWMEMRALGAASSALDALAALLPEEAEKVVDGDTITVPITELAVGDVVLVRA
+GARVPADGTILEGAAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTVRVKVAAVGTDTT
+LAGIQRMVADAQESSSRAQALADRAAALLFWFALVAAIITAIVWTAIGQPTDAVTRTVTV
+LVIACPHALGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHV
+VTAVTAMPGVSEAELLAVAAAAEADSEHPVARAIVTAAGQHPQASTLRKRGTDFSAAMGR
+GVRATVDGSEILVGGPNMLRELNLTMPAEITEHTASWTARGAGVLHVLREGSVIGAVAVE
+DKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTEL
+QSRGLSVAMVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQ
+ASYTKMIQNLVWATGYNVLAVPLAAGVLAPIGFVLSPAVGAILMSVSTIVVALNAQLLRR
+IDLDPEHLAPLERPRSQAALQPAAVS
+>PROKKA_01247
+MTDPTTHHHDHAGVATTESGHRDDSRAENEDHTMEHGDHAGHGHHGGGHAGHGDHVGQFR
+RLFWINLIIAIPVVAFSPMFAMLLGYSVPSWAGWVAAVLGSVMYAWGGTPFLTGAVSELK
+SRQPGMMLLIALGITVAFLASWAATVGLVHPELEFWWELALLIVIMLLGHWIEMRSLAQT
+TSALDSLAALLPDEAERIEGDDVVKVDPAELRVGDVVIVRPGGSVPADGTIVDGRADMDE
+SMITGESHPVARGEGENVTAGTVATDSGLRVEITATGDDTALAGINRLVAEAQGSSSRAQ
+RIADRAAALLFWFALGAALITAVVWTLFGLPDDAVVRTITVLVIACPHALGLAIPLVVSI
+ATERAARGGVLIKDRLALESMRQVDAVLFDKTGTLTKGEPTVIGVEPTGGLNAEQLLALA
+ASAEADSEHPLARSIVTAAKEKGLAVEPASGFTSSPAVGVTATVADHEIRVGGPRLLEET
+GQDEIGVADEWRAEGAIILHVLRDGKVIGGLKLADEVRPESRDAVDALHQLGVEVVMITG
+DAEAVANEVGRELGIDRVFAGVRPEDKSAKVDQLQKEGKKVAMVGDGVNDAPALAQADVG
+IAIGAGTDVAIASAGVILASSDPRSVLSVIQLSRAAYRKMRQNLWWAAGYNLLSVPLAAG
+VLAPVGFVMPMSVGAILMSISTVVVALNAQLLRRIDLAPDASTRSVLEHQK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000023.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000023.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fcec1d7fd6e38b3834264a9e2ac8281241d194e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000023.fa
@@ -0,0 +1,52 @@
+>PROKKA_02238
+MAHDDANTTTTDQLTLQDPTKRYPVISPPEQSLPGTGLDAEMTPKVDLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDAQHVLEVLQAEGRTAVGIPGD
+LRDKTFCVDLVAQAVEKLGGLDVLVNNGGKQVAQDSIEDIDDEQLEATFDINILAQFRLV
+KAALPHLKPGSTIINTTSVVAYMAPEQLVDYSATKAAINTFTKALGQQLAPKGIRVNAVA
+PGPIWTPLQPSGGQKPEALPEFGQSTPLGRAGQPTELAPAYVFLASPESSYVVGATIPVT
+GGMPTP
+>PROKKA_01940
+MAHDDANTTTTDQLTLQDPTKRYPVISPPEETLPGTGLDAEMTPKADLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDAQHVLEVLQAEGRTAVGIPGD
+LRDKTFCVDLVAQAVEKLGGLDVLVNNAGKQVAQDSIEDIDDEQLEATFDVNILAQFRLV
+KAALPHLKPGSTIINTTSVVTYMAPPQLVDYASTKAAINTFTKALGQQLAPKGIRVNAVA
+PGPIWTPLQPSGGQKSEDLPEFGQSTPLGRAGQPTELAPAYVFLASPESSYVVGATIPVT
+GGMPTP
+>PROKKA_00513
+MANDDANTTTTDQLTLQDPVKRYPVISPPEQSLPGTGLDAEMTPKADLGEHSYRGTGRLT
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDARNVLAVLEKEGRTAVGIAGD
+LRDRQFCQDVVAQAVEAMGGLDVLVNNGGKQVAQKEFEAIDDEQLEATFDVNILAQFRLV
+RAALPHLKPGASIINTTSVVSYMPPETLIDYASTKAAINNFTKGLGQQLAPKGIRVNAVA
+PGPIWTPLQPSGGQPTEELPDFGQSTPLGRAGQPTELAPAFVFLASAESSYVVGATIAVT
+GGMPTP
+>PROKKA_00440
+MTDVSTSTDTAVGDSDTRPAAARTDAPAATVLLAGRAALVTGGTLGIGSGIAASLRDAGA
+RVAVTGLTEQECAAAREAGFPAYVLDVRDRAACAEVVGAVVEEFGGLDVLASNAGIYPQA
+RIADMTDEDIDLIFDVNVKGTIHAVQAALPALVASGRGRVVITSSITGNHTGYPAWSHYG
+ATKAAQLGFVRSAAIELARQGVTVNAVLPGNIITPGLEEMGQEYLDSMARSVPAGHLGEP
+ADIGATVAFLASDGARYITGQGIVVDGGQILPETPEALEGL
+>PROKKA_00454
+MANDDTNTTTTDQLTLQDPTKRYPVISPPEQSLPGTGLDAEMTPKADLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVLTYLPEEEKDAQHVKEVIEAEGRKAVTVSGD
+LRDKQFCKDLVERAVQELGGLDILVNNGGKQVAQEEFEQIDDEQLEATFDINILAQFRLV
+RAALPHLKPGSTIINTTSVVAYMAPEQLVDYSSTKAAINTFTKALGQQLAPKGIRVNAVA
+PGPIWTPLQPSGGQKPEALPEFGQSTPLGRAGQPTELAPAYVFLASPESSYVVGATIPVT
+GGMPTP
+>PROKKA_00650
+MGIHYARDSTAAEAVVERVNEAGASGVLIRADLAEGAAGAAHLATRWRDEVRRHDARGTD
+VLVSNAGINGAQSLSELDEGTVARVVNVNLVAPLMLVHHLSDHINDHGRVIGISSGFARI
+AAPTHVAYTASKAGLEAAFRAIAAELAERDITVNTVRPGVIDTDINADWINEPGARDAVA
+AAAALRRVGQPDDVADIVAFLASHSSRWMTGQSLDATGGTQL
+>PROKKA_01865
+MSTHDLPDPLTQFPRFAPERQTQEEPGLSARMDPEPDCGEDTYVGIGRLKGRRALVTGGD
+SGIGRAVALAYAREGADVVFTHLPEEAEDAARTTELLDAEGVRHVAREVDLRDEAATRAL
+VRDAVKFLGGLDLIANVAGEQRYVDDLAELDPRQVRDTFEINVFALIWIVQEALPHLPAG
+AAIVNTASTQATTPLPGLVDYAGTKGAIVSITKALAQQLTPRGIRVNAVVPGAIWTPIQV
+SLGRAPEQVDVLGQDAPLGRPGQPAEMAPAYVFLASTEASYVSGEVLGATGGTLY
+>PROKKA_02170
+MAHDDANTTTTDQLTLQDPTKRYPVISPPEETLPGTGLDAEMTPKADLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDAQHVLEVLQAEGRTAAGIPGD
+LRDKTFCADLVAQAVEKLGGLDVLVNNGGKQVAQDSIEDIDDEQLEATFDINILAQFRLV
+KAALPHLKPGSTIINTTSVVAYMAPEQLVDYSATKAAINTFTKALGQQLAPKGIRVNAVA
+PGPIWTPLQPSGGQKPEALPEFGQSTPLGRAGQPTELAPAYVFLASPESSYVVGATIPVT
+GGMPTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000024.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000024.fa
new file mode 100644
index 0000000000000000000000000000000000000000..29e1b0630e916a0249cef9d7b1bbae13e1cc8974
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000024.fa
@@ -0,0 +1,101 @@
+>PROKKA_02297
+MSSDQRTASAPRHALPPQDGVPAVKVGTRVSRGPGRVTALDGLRGIAVLAVLVFHAWPTF
+LRGGFVGVDMFFVLSGFLITTGLVRGVDAGRGVALGTFWMKRVRRLIPAMLMALVGTTAL
+AWLAVDEFPAGLGRQWFGALTYTSNWVMILEGGDYFNRASPPLFEHLWSLAIEEQFYILW
+PLLLWGLLLLTWPPRSTVNSGRVADRRRILAVAVAAVASAAWMAWGSWHGFEQARLYFGT
+DTHAFGLLFGACVAIGLAHVPRPEHGGPEPRTSATRVAVAWGAVAVLAAGFALVDGGHAS
+TYRGVLAGLSAVVAFIVWHVVQGDRRDSLSRALGNGFLRWWGRRSYAAYLWHWPLLVIMR
+VMVPVDAPGWVEPVAAGAILLLTALIADLSTRLIEEPILHEGFRGAFGRWGAAARRAFTG
+GAGPIGQLAAAATALGLVAVPAAAVAAVVHSPAQTQLEQDIAQAEESLKAAEAAQQAARE
+SRAAEQSKRAEASASASPGSAAPGDAEGSAGATSSPGSSAEPSGLGLGDPAVTRPTYSKE
+QLTAALPPSELGTDVTLIGDSVSLSAAPTLMEELPGMLLEAEVGYQIWDAADELEKLKAD
+GQLSDVVVVALGANGTTHRGDWEKILAAVGEDRLLVLVVPHGPMDWIADVQVQMAAQAKA
+HPDRIVLADWDAAAKQHVTDFSADGVHPRADGQAMYAQLVRLTIEDRLGARR
+>PROKKA_01990
+MSSDQRTAPVPRHALSPQDGVPAVKVGTRVSRGPGRVTALDGLRGIAVLAVLVFHAWPTF
+LRGGFVGVDMFFVLSGFLITTGLVRGVDAGRGVALGTFWMKRVRRLIPAMLMALVGTTAL
+AWLAVDEFPAGLGRQWFGALTYTSNWVMILEGGDYFNRASPPLFEHLWSLAIEEQFYILW
+PLLLWGLLLLTWPPRSTVNSGRVADRRRILAVAVAAVASAAWMAWGSWHGFEQARLYFGT
+DTHAFGLLFGACVAIGLAHVPRPEHGGPEPRTSATRVAVAWGAVAVLAAGFALVDGGHAS
+TYRGVLAGLSAVVAFIVWHVVQGDRRDSLSRALGNGFLRWWGRRSYAAYLWHWPLLVIMR
+VMVPVDAPGWVEPVAAGAILLLTALIADLSTRLIEEPILHEGFTGAFGRWGAAARRAFTG
+GAGPIGRLAAAATALGLVAVPAAAVAAVVHSPAQTQLEQDIAQAEESLKAAQAAQQAARE
+SRAAEQTKRAEASASGAPGSAAPGDAEGSAGATPSPGSSAEPSGLGLGDPAVTRPTYSKE
+QLTAALPPSELGPDVTLIGDSVSLSAAPTLLEQLPGMLLEAEVGYQIWDAADEIEKLKAD
+GQLSDVVVVALGANGTTHRGDWEKILAAVGEDRLLVLVVPHGPMDWIADVQVQMEAQAKA
+HPDRIVLADWDAAAKQHVTDFSADGVHPRADGQAMYAQLVRLTIEDRLGARR
+>PROKKA_00439
+MVRRDVWPTIAGVPSLTPSSPVRSAEERTDRGGGSRTRPLVHADRPGIRVSPGPGRIPAL
+DGLRGVAVLAVLVFHAWPALLPGGFVGVDMFFVLSGFLITTGLVRGVDGGRGLRLGPFWM
+RRVRRLVPSMVVALVCCTALAWLAVAEFPAGLGRQWLGALTYTSNWVMILSGSDYFAAAT
+PPLFEHLWSLAIEEQFYVLWPLVVAGLLTLFWPREPTLRGAFRADRARVLTVLALAAASA
+VWMAVGLRGGAPHTRLYFGTDTHAFGLLLGAAVALMLAHTRRPEHGGAVMRNPPVRSAIA
+WGLFAALLAAFVLVDGREDVTYLGVLAGLSLVVTLLLFHVVQGNRQDSFSRAMSGDVLRW
+WGRRSYAAYLWHWPLLVILRTALPVDAPAWVDPVAAGGVLVLTAGIADLSTRWMEEPIVQ
+RGFRGAFAHWRAGLRTATRGIGGKAAAGAAGLALVAVPVAAVAAVVHSPAETALQRQIAE
+AEAALEQARQAQAAARAEASARAEAERAGAAEEAVAKDSQEDAPGAGAGGDAGSAAPTAS
+STPSDTAAPSAGEDPAVEVAADPTASAEPEPTAEPEPEPPLTGDPSVTRPAFTGAELTEP
+MPPSSVGPDVTLLGDSVALSAAPELLAALPGIAVEAEVGFQVRDAAARLAELDAAGMLTD
+VVVVSLGANGNAELGDWDRILAAAGPERLLVLVVPHGPMDWIGPAQQEMAEQAALHPDRV
+VLADWDAASAHVDEWSADGVHPKGNGQGIYARLVRLTVEARLGLR
+>PROKKA_01839
+MAVLSVLVFHAGVTALPGGFVGVDVFFVISGFLITGLLLKEVDRTGRVGLAEFYARRARR
+ILPAALAVIVLTVAAGLLVYPVSEWTRLGSVAVASALSVVNWLFARESTDYFAQEEAASP
+FQHYWSLAVEEQFYLVWPLLLILVTVGVAALRRRGAGDAAPDADAGARRRPSAPVAARRV
+LLASAVIGLASFVHSVSYSASDPGAAYFVTTTRVWELALGAGLAAALVVLPVIRPAVRTV
+LGWAGLGMIAVSLVLITGAMAYPGSVALLPVVGSALVILAGAHEDGSTPGHPARLLATRP
+MQWVGDLSYSLYLVHWPVLTLAAWRFPDGRLPLWLGLILAVVSVGLAWALRRWVEVPAMH
+GSLLAGRRRALTRGGLGMAAVAAAGALVLAAGAALAPARPGEESPVAGARAVMDGQDPMA
+ALAAGMRIVPDPAVAKEDRSPRSAAGASSRTPRPRAWSPRRACWRTASPTRSATSGTAPC
+PTSWTGSTRTSCWSRAPGGRPWRRTPRRRWPRRGGS
+>PROKKA_00392
+MTVSTSDHHAARPAPRHAQAALADGPAPRTGLRVSRGPGRITALDGLRGIAVLAVLVFHA
+WPEALPGGFVGVDMFFVLSGFLITTGLVRGVDAGKGLRLPSFWMRRIRRLVPAMVVALVA
+CTALAWLAVAEFPTGLGRQWLGALTYTSNWLMIFDGGDYFDRASPPLFEHLWSLAIEEQF
+YVLWPLIIGGLCLVVRPKRDTYASGRVADRRRILVVLVVALASAAGMVLGSLGGADQTRL
+YFGTDTHAFGLLLGACVSMGLAHVPRPEHGGPELRTGPARTAAAWLAVVVLFTGFALVDG
+TQDATYRGVLVGLAAVVAFIVWHVAQGDRRDSLSRALGNPFLRWWGRRSYAAYLWHWPLL
+VIMRIVVPVDAPSWAEPVAAGAVLLLTAGIADLSSRYFEEPILQKGFRGAFGGWGDAARR
+AFGGAFGPGGRLAAGATALALVAVPVAAVAAVAHSPAQTQLQEDIQAAEQSLQDAQAQQQ
+AQLEARRSAQAEKSKDAEAGGAEATGSAGASASPSGSTLGDPQVTRPEFTQEELTASLPP
+SDVGSRTTLIGDSVALSAAPALLEEMPGIVVDAKVGFQIWDAADKIRAMDREGTLGDVVV
+LSLGANGTAGRGDWDKIRQAVGPDRLLVVVVPHGPMSWIEDAQRKAVEQAEAHPDQVVLA
+DWEAASTYVPGWSADGVHPGHEGQGIYAQLIRLTVEERLGLR
+>PROKKA_02437
+MPRPVDTKASYFPGLDGLRALAVGLVVAYHLGVPGTDGGLLGVGVFFTLSGYLITSLLLR
+RHERHGDLDLKNFWIRRFRRLLPAVVLVLIAVLAATALVSPDLLGARLGQSVAALLYVAN
+WHTILSGRSYFDQAEGAGPLDHLWSLAVEEQFYLVWPLVLLGLLALTRRLGPDARRRVLA
+AATLVLGAVSFVLLAVFADPAGDSTRAYEGTDTRAGGLLWGAVLAFLWRPDRVARLTGRA
+SRVVVDLVGVLGLAGVLALSATTGQEDAALYTWGLAALTVATCAALLPLVHPGSWVARVL
+GIPPLQWIGARSYGIYLWHMPVVAFLPDRVLFGQPVLRGLLIVALTLVLAALSWRLVEDP
+IRRHGLVAALARARGVLGVGAVAVLASGALVLTAALPQTSAQEIAAQEPAAPAGDAVAHP
+ALDGRTSCTSVLHVGDSTSLASGNTDRTRIADPAQRITGRYEAVGVETVVEDIAGGRSTR
+EHIDGSADLNAPEAVAAGVSRLDAGGCVVVNVGLNDAATMTKDDAWDQAAARIDAVVDAA
+DGRPVLWVGPAIMPWSSRPYYEPAGAERFTRALVDATARHPDLRVHDWARESRSHPDWYL
+SDDANHNTEAGAVAKARSMAAALTAAFPAGRPASAEKVVLGE
+>PROKKA_00587
+MTNPPVYPRGYRPRHAADGPDSTPAAARRRADWRPEIQGLRAVAVLLVVVFHIFTDRVSG
+GVDIFLFISAFFLTGSFTRKMESGRPLAVGRYWLHVFTRLMPMAVLTILTTLVAVATVYP
+LADRASWRTEALASALYVENWALAFNAVDYYAADNTSLSPFQHFWSLSVQGQVFILWPLL
+FLVSALVARRTGARPRAVLTTAFASVFVVSLLWSVTQTSQNQAFTYFDTRARLWEFALGS
+LLALALPFLHLGRRTRVFLGWAGLASMIAVGVVVDVQGAFPGWIALWPLMSATAVIVAGT
+SGSHFGVDRILASRPLTRLGDSAYALYLVHWPLLITYSVLTGSQKPGAAAGVALVLVSLG
+TAILLSARVERPLRAWGWPQTAAWRSAVVLGACAALVVAPVTLWRGAEAAESARVLEAAD
+RNNPGAAVLRPDYEPAGDPGAPVLPVVEGRYPFPEYPEECDPALEAQLTEVGAESCHVLV
+PQADPAGVVLMAGNSHVMQWSPALRRLGEERRLEVVSYTRGSCLVAPMEEQVDDSPKCPD
+FLADLNLVVEHVRPDVVFMQGTRSTYEDEEMLTPGMTGRMEEIAGTGAHVLALRDNPRFA
+AGSPTTCGTMHGVDAVTCRWTHAVLDPNTSPLAGLADAHPRIAQVQLNDMICPDRQCQPT
+VGNVHVYWDDNHLTPTYVETLAPVFIERVLAALEHDGMRLGR
+>PROKKA_02238
+MPAVKVGTRVSRGPGRVTALDGLRGIAVLAVLVFHAWPTFLRGGFVGVDMFFVLSGFLIT
+TGLVRGVDAGRGVALGTFWMKRVRRLIPAMLMALVGTTALAWLAVDEFPAGLGRQWFGAL
+TYTSNWVMILEGGDYFNRASPPLFEHLWSLAIEEQFYILWPLLLWGLLLLTWPPRSTVNS
+GRVADRRRILAVAVAAVASAAWMAWGSWHGFEQARLYFGTDTHAFGLLFGACVAIGLAHV
+PRPEHGGPEPRTSATRVAVAWGAVAVLAAGFALVDGGHASTYRGVLAGLSAVVAFIVWHV
+VQGDRRDSLSRALGNGFLRWWGRRSYAAYLWHWPLLVIMRVMVPVDAPGWVEPVAAGAIL
+LLTALIADLSTRLIEEPILHEGFRGAFGRWGAAARRAFTGGAGPIGRLAAAATALGLVAV
+PAAAVAAVVHSPAQTQLEQDIAQAEESLKAAQAAQQAARESRAAEQSKRAEASASASPGS
+AAPGDAEGSAGATSSPGSSAEPSGLGLGDPAVTRPTYSKEQLTAALPPSELGPDVTLIGD
+SVSLSAAPTLLEQLPGMLLEAEVGYQIWDAADEIEKLKADGQLSDVVVVALGANGTTHRG
+DWEKILAAVGEDRLLVLVVPHGPMDWIADVQVQMEAQAKAHPDRIVLADWDAAAKQHVTD
+FSADGVHPRADGQAMYAQLVRLTIEDRLGTRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000025.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000025.fa
new file mode 100644
index 0000000000000000000000000000000000000000..115344e9dc0d178913cb821318e34a42e389271a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000025.fa
@@ -0,0 +1,21 @@
+>PROKKA_00099
+MNFALDGRNYEIDLSKEHAAELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNAKRK
+>PROKKA_02112
+MNFALDGRNYEIDLSKEHAAELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNAKRK
+>PROKKA_00292
+MNFALDGRNYEIDLSKEHADELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNARRK
+>PROKKA_00617
+MATITTIADDFDNSTPAETTYFSVNGKEYAIDLNEEHRRELEDVLEEVAERLSKYTAVAR
+PLGKSSAPARKSSKSPSSRSGASYDAGAVRSWAEENGYKVADRGRISADVLEAYNASKKG
+>PROKKA_00670
+MAIISTVADDFDGSTPAEAVRFSVAGRDYEIDLSKEHRAELDAIMAEFQDRLKKFTDVAR
+PAGRAASTGRTPARRSSGSGVDASTVRLWAVENGFDVKDRGRIPVEVMDAYRNRGKKG
+>PROKKA_00094
+MNFALDGRNYEIDLSKEHAAELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNAKRK
+>PROKKA_02014
+MAIISTVADDFDGSTPAEAVRFSVAGRDYEIDLSKEHRAELDAIMAEFQDRLKKFTDVAR
+PAGRAASTGRTPARRSSGSGVDASTVRLWAVENGFDVKDRGRIPVEVMDAYRNRGKKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000031.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000031.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f64c5edf0832c81e97deedf1d92ec36f14c9d56
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000031.fa
@@ -0,0 +1,48 @@
+>PROKKA_00172
+MPGRLIGWPRKPTLLELLFGLAMWEHAVMQIISFFNHKGGVGKTTMLFNAAVEMGRLGKR
+ILMVDFDAQANLTAISIDDDMLSMIYAPDEDGKTVAHAFAPLVGGSGDVFAPEAIEVREG
+KVWLAAGDLRLSEFDAILPSAWTEALAGNERGFRVTSAPYRLICEIAEEIKADYVFVDLG
+PNVGALNRAVLLGSDYMIIPMAADLFSIRALPSVGNSVDTWVRQWNTARSVAPRLNFDIQ
+KGLPKVLGYVSQQFNIYRGEATLAFSHWIDEMPAQIQSGLLEPLAVHSDGKGATLADPAQ
+SKGPGVGDLKNFHSLVPHAQTLRKAIFELRADDVVRGGQVTRARQSEEQFKELCANIIAR
+AV
+>PROKKA_01408
+MGEDPDTPTTAAAARRGPRPGVQTTVEGAGAAVTSREPIPVMTIHGEPVLGPTGRPKHDF
+PEPAPLTSHGPARIISMVNQKGGVGKTTSTINLGAALAGYGRRVLMVDFDPQGALSAGLG
+ANPHELDTTVYNVLMERSVTAKDAILSTDFENMDLLPANIDLSAAEVQLVNEVAREQVLE
+RALRQVRDDYDVVLIDCQPSLGLLTVNALTASHGVIIPLTAEFFALRAVALLVETIEKVQ
+DRLNPDLEIDGVLATMFDQRTLHSKEVVGSLVAGFGDRVFETVIKRSIKFADATVAATPI
+TLFAENHDGAKAYRQLARELISRGGAP
+>PROKKA_01138
+MGEDPDTPTTAAAARRGPRPGVQTTVEGAGAAVTSREPIPVMTIHGEPVLGPTGRPKHDF
+PEPAPLTSHGPARIISMVNQKGGVGKTTSTINLGAALAGYGRRVLMVDFDPQGALSAGLG
+ANPHELDTTVYNVLMERSVTAKDAILSTDFENMDLLPANIDLSAAEVQLVNEVAREQVLE
+RALRQVRDDYDVVLIDCQPSLGLLTVNALTASHGVIIPLTAEFFALRAVALLVETIEKVQ
+DRLNPDLEIDGVLATMFDQRTLHSKEVVGSLVAGFGDRVFETVIKRSIKFADATVAATPI
+TLFAENHDGAKAYRQLARELICRGGAP
+>PROKKA_01488
+MQTSLEGAGAAVTSREPIPVMTIHGEPVLGPTGRPKHDFPEPAPLSSHGPARIISMVNQK
+GGVGKTTSTINLGAALAGYGRKVLMVDFDPQGALSAGLGANPHDLETTVYNVLMERSVTA
+RDAILPTPFEGMDLLPANIDLSAAEVQLVNEVAREQVLERALRQVRDDYDVVLIDCQPSL
+GLLTVNALTASHGVIIPLTAEFFALRAVALLVETIEKVQDRLNPDLEIDGVLATMFDQRT
+LHSKEVVGSLVAGFGDKVFETVIKRSIKFADATVAATPITLFAENHDGAKAYRQLARELI
+CRGGAP
+>PROKKA_01399
+MTPKEPIPVMTVHGEPVLGPTGRPKHEFPEPTPLAGHGPARIISMVNQKGGVGKTTSTIN
+LGAALAGYGRKVLMVDFDPQGALSAGLGADPYELDVTVYNVLMERKVTARDAILPTAFEN
+MDVLPANIDLSAAEVQLVNEVAREQVLDRALRQVKDDYDVVLIDCQPSLGLLTVNALTAS
+DGVIIPLTAEFFALRAVALLVETIEKVQDRLNPDLEIDGVLATMFDQRTLHSKEVVGSLV
+DGFGDRVFETVIKRSIKFADATVAATPITVFAENHDGAKAYRQLARELICRGGAP
+>PROKKA_02230
+MHTLMVYSEAGGVAKTTTAVSLAMSWAEQGRQVVLIDLDPRAAATKWVDVEPTEPGLHIG
+AVIGNPDPTGWVQDLAVPSGWHENLRVVPSDRSLSHQESDRADHAHLRLRMALSDLQADL
+VVIDCPNRQGGPLTQNAFTASDGVIYAARPTSDGCDGVHGARQSVAAFKQSMALLGAPDR
+LVEVGIVVSDYRDHITPKDQTVAVEELRETGLLLTPLVPARSIVPKARLACDWLGRYEKG
+EPVAAAYADLAGLIFERITA
+>PROKKA_01358
+MGEDPDTPTTAAAARRGPRPGVQTTVEGAGAAVTSREPIPVMTIHGEPVLGPTGRPKHDF
+PEPAPLTSHGPARIISMVNQKGGVGKTTSTINLGAALAGYGRRVLMVDFDPQGALSAGLG
+ANPHELDTTVYNVLMERSVTAKDAILSTDFENMDLLPANIDLSAAEVQLVNEVAREQVLE
+RALRQVRDDYDVVLIDCQPSLGLLTVNALTASHGVIIPLTAEFFALRAVALLVETIEKVQ
+DRLNPDLEIDGVLATMFDQRTLHSKEVVGSLVAGFGDRVFETVIKRSIKFADATVAATPI
+TLFAENHDGAKAYRQLARELICRGGAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000036.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000036.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85b596dce272770e12b011e6322e0295ea736e3b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000036.fa
@@ -0,0 +1,58 @@
+>PROKKA_00631
+MTGRRRYQGLAARFFLAQLLVVGASVLAAVVVASLAGPPLFHEHLEQAGAGHDAAQMLHV
+EQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAM
+GAGTEVEELAGSFNTMAARLQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD
+EPTGELMGEQLARLTRLVEDINDVSRAEEGRIELDRSPQGVSGLLHAATEAHKEAYATKG
+VALTMDADPGLAVDVDRQRMGQVLGNLLTNALRHTPAGGRVTLEARQSPSGVTLSVTDTG
+EGISPEHLPHVFERFYRGDTARDRDHGGSGVGLAISRALIQTHGGTLSATSTTAGATFTI
+DLPTKQPPTSPPTGAPVYPP
+>PROKKA_00403
+MTGRRRYQGLAARFFLAQLLVVGASVLAAVVVASLAGPPLFREHLEPAGAGHDAAQMLHV
+EQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAM
+GAGTEVEELAGSFNTMAARLQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD
+EPTGELMGEQLARLTRLVEDINDVSRAEEGRIELDRSPQGVSGLLHAATEAHKEAYATKG
+VALTMDADPGLAVDVDRQRMGQVLGNLLTNALRHTPAGGRVTLEARQSPSGVTLSVTDTG
+EGISPEHLPHVFERFYRGDTARDRDHGGSGVGLAISRALIQAHGGTLSATSTTAGATFTI
+DLPTKQPPDQPTYRRTRSSTVNTGAPPLA
+>PROKKA_01253
+MRTRLSTLLALVLVLSLAVSGITAYAVLRITVNDRIEASLQRAVEQVALLSETGVDPETG
+EPPDSAAAFIRLAMLRVLPHDNEGILGLAPDRAELAASDAVELRLEEDPELVAWALARVG
+DQEARAETVTTASATYRAVVVPVTGWGQDDAGALLLAVDVDAEVGRLDRTFLGFAGGALL
+TTVFALAVGVPLLRRVFAPLESLQEAVGEVTEHDLDRRVEVIGHDDVAALGHSFNAMLER
+LEDSFASQRRLLDDAGHELRTPVTIVQGHLEVMDPDDPADVRETTRLTLDELDRMSRLVD
+DLLVLAKAQHPDFLRPAPVDVAELTRGVLARASGFDGHVWELDGVAEATVSLDAQRITQA
+WLQLAANAVRYSEPGSVVRLGSAVEGDTLRLWVQDHGVGVRPEDRAQIFERFGRGAHGTR
+ADGSGLGLAIVSSIAAAHGGEVSLDSVPGLGSVFRIELPLSTPSRPAGSLTPGKDPA
+>PROKKA_01330
+MTRSKPTGRLSASGRARVVAWILGVSALGMVLMLVSIVLTLRWVERDAIETSLTQESDEV
+AVFAQNGRDPETGEPFATPERFVGHYLERQRVEPTELMFGGTAATPVIAQIHGDAAAPVE
+LLAPATRQAMEQPRSRGTLVDPTHGRISYANLTVTTPADTGHVVVAVFHERYEQRVMTQT
+LLLSALALAALAATAAAAWLVSSRILGHTVEFHRAVDASLKDRGLRRLPENGSEEYAGLA
+RRANDLVRRADRRLEEERRFAEDVTFALRTPLTVIEGGLRNPGGDEQERRTSYRHIGAEA
+TRVRGLLEDLVILSRLQQDDVVLERTPVDVGVLVATAAQAWRERHPDAADEPRLDVEAPA
+EGLTAVTDRARLVQVLEELLDNARHAVRFAPGSDLPRDLTAVTPLERTLSVRVREEERDG
+EPWAVVEVADRGRGIPEEDREEVFERLANASNDPYPGNGLGLPVAALLSTALDGELTLEP
+GPGAAGTVARLAVPLTADQDGEDA
+>PROKKA_00451
+MSPTPALRGRPAPGPDAALVARAARRIGLRTALACAALVLGGAGVFFGYLWWQIAHPGVD
+PRDADATVTVQLDLVDLATAAILAGAAAVLITGFASLWFSRSAVQPLADALRRQREFVSN
+ASHELRTPLTVLSARTQVLQARVPAGDPLEPLADELRRDTDVMAGVVEDMLSTARLDSAP
+EGMCDAGEVAAAACADLSLVGAEERGVRLRADLPSLPVALPEAALRRMLAALLDNALGFA
+PPGTEVTVSGERVRGVVELRVADRGAGIQGVEPDHVFDRFARGRPAAVPGSGPGAVPRSS
+HGIGLALVRETAHRYRGEVRVESTGPEGTVMLLTLPAAQEAR
+>PROKKA_02198
+MTSRRRYQGLAARFFLAQLLVVGASVLAAVVVASLAGPPLFHEHLEQAGAGHDAAQMLHV
+EQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAM
+GAGTEVEELAGSFNTMAARLQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD
+EPTGELMGGQLARLTRLVEDINDVSRAEEGRIELDRSPQGVSGLLHAATEAHKEAYATKG
+VALTMDADPGLAVDVDRQRMGQVLDNLLTNALRHTPAGGRVTLEARQSPSGVTLSVTDTG
+EGISPEHLPHVFERFYRGDTARDRDHGGSGVGLAISRALIQTHGGTLSVTSTTAGATFTI
+DLPTKQPPDQPTYRRTRLSTVNTGAPPLE
+>PROKKA_00600
+MTGRRRYQGLAARFFLAQLLVVGASVLAAVVVASLAGPPLFHEHLEQAGAGHDAAQMLHV
+EQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAM
+GAGTEVEELAGSFNTMAARLQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD
+EPTGELMGEQLARLTRLVEDINDVSRAEEGRIELDRSPQGVSGLLHAATEAHKEAYATKG
+VALTMDADPGLAVDVDRQRMGQVLGNLLTNALRHTPAGGRVTLEARQSPSGVTLSVTDTG
+EGISPEHLPHVFERFYRGDTARDRDHGGSGVGLAISRALIQTHGGTLSATSTTAGATFTI
+DLPTKQPPTSPPTGAPVYPP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000039.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000039.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0dcc9a2d8cbde6e21cfdf9538e822046cfd7948b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000039.fa
@@ -0,0 +1,121 @@
+>PROKKA_00884
+MNTHHPDRLTDAAGVRVLLYGDVDLNVIDGSATWLPSLAETLARTGASVDVQLKAVERRD
+LLTAPLRALTGVRVLTAEPAAGQGGMTPSRAADVLARRDEESRYDVVLVRGIHACLELAD
+RGAFPGRLWSYVTEYGYVEDGFPAGRVEELGRIAAASRLMLAQTPQARAVLEAMVPAAAG
+RTELLSPMVPDGLVPAERAEAPADGPVRLVYTGKFAHDWRTDLMPDVLTALHEAGVPATL
+TMVGDKVHPERDRPGWAAAMRSRLEAERPDFEWTGALSREESMARTAAADVSLGWRAPAL
+DLSLEISTKVLESCAVGVPPLLNRTVAHEELLGADYPLFVDGVRDSARDVAARIAAARHD
+LPALSRRVVEAAAPYRMAARARALTGVMDRLGLLDRRPARGGSRTRVVLAGHDLKFAGEL
+VDLLRDDPGVELRIDHWQGLHRHDEAASRRLVEWADVVVCEWAGPNAVWYARHKRPGQRL
+VVRLHMFELRGGWLSALETEAVDRLVTVSDLYRDLVREHLPIEPTRVTVIPNAVSVADLD
+RPGLPGRRFRLGLVGVVPLRKRLDRAVDLLEILRAHDERFTLHVRGRMPWEYPHEWRKPL
+QREGYLDLFARLGAGPLREAVAFEPFGADMGSWLTKIGWVLSPSTTESFHLAPAEGMVSG
+AVPLVWDRPGARGVFGDEFVLDDTDAAARRVLEAVADDARWDALSALARERVRAYDERVV
+AGLWREALGLD
+>PROKKA_00894
+MNVAGARLRRWAGRARIVGERAAATAGDAGASALRAARGARGLATLPERTWRAADVHVPD
+ASAALPLPAAAVLRRALTGARVPSLDAFSPLGPRPAAAPAVLLLPVDEPAARGWSVEAAA
+ELAARRCADLEMPAGAPGLHTVLMSDPASRRALTAALRTAGGRLPGVLVVACPDPATAAG
+RARVLAALGLVDAVLAPEGTRLDPPLARAAARAGRAVIGPDRAAETWERLAAAGRAARLD
+ALTPAEAAGPPAAPAPRVRVTAEPRRVVVAGHDLKFAGALMDRLRADGHEVRVDAWRGHA
+RHDVERSRALAAWADVVHCEWSLGNLAWYSRHLDSPHRTTRLTSRLHLQEAGTAFPSRVR
+QDALDEWVFVAEHVRAQVLRDTRFPASRTSVVPNAVAVPPTLPDGDDDRRFVLGLVGVLP
+ERKGLHRALDLLAALRRVEPRYTLRIRGHHPEEVGWMAQRPAAAAYYRAQLRRIETDPVL
+AGAVTWDPHGPDMPAWYARVGVALSVSDFESFHFTLPDGAAHGCLPAALAWAGADLLYPA
+AWLSPDVATMAEALRRATADARAWRSAVAQARRDVAHTYAEEDVVPALVRRILGGAAA
+>PROKKA_00606
+MNTHHPDRLTDAAGVRVLLYGDVDLNVIDGSATWLPSLAETLARTGASVDVQLKAVERRD
+LLTAPLRALTGVRVLPAEPAAGQGGMTPSRAADVLARRDEESRYDVVLVRGIHACLELAD
+RGAFPGRLWSYVTEYGYVEDGFPAGRVEELGRIAAASRLMLAQTPQARAVLEAMVPAAAG
+RTELLSPMVPDGLAPAERAEAPADGPVRLVYTGKFAHDWRTDLMPDVLTALHEAGVPATL
+TMVGDKVHPERDRPGWAAAMRSRLEADRPDFEWTGALSREESMARTAAADVSLGWRAPAL
+DLSLEISTKVLESCAVGVPPLLNRTVAHEELLGADYPLFVDGVRDSARDVAARIAAVRHD
+LPALSRRVVEAAAPYRVAARARALTGVMDRLGLLDRRPARGGSRTRVVLAGHDLKFAGEL
+VDLLRDDPGVELRIDHWQGLHRHDEAASRRLVEWADVVVCEWAGPNAVWYARHKRPGQRL
+VVRLHMFELRGGWLSALETDAVDRLVTVSDLYRDLVREHLPIDPARVSVIPNAVSVADLD
+RPGLPGRRFRLGLVGVVPLRKRLDRAVDLLEVLRAHDERFTLHVRGRMPWEYPHEWRKPL
+QREGYLDLFARLGAGPLREAVAFEPFGADMGSWLTKIGWVLSPSTTESFHLAPAEGMVSG
+AVPLVWDRPGARGVFGEEFVLDDTDAAARRVLEATADDARWDALSALARDRVRSYDERVV
+AGLWREALGLD
+>PROKKA_00616
+MNVAGARLRRWAGRARVVGERAVVTAGDAGASALRAARGARGTATLPERTWRAADVHVPD
+AAAALPLPAAAALRRALTGVRDPSLDAFSPLGPRPAAAPAVLLLPVDDGPAARGWSVEAA
+AELAARRCADLQMPAGAPGLHTVLVTDPASRGALIAALRPAGARLPGVLVVACPDPATAA
+GRARALAALGLVDAVLAPEGTRLDPALPSVAARAGRAVIGPDRAAETWERLAAAGRAARL
+DSLTPAEATGPPAAPGPRVRVTAEPRRVVVAGHDLKFAGALMERLRADGHEVRVDAWLGH
+ARHDAERSRALAAWADVVHCEWSLGNLAWYSRHLDSPHRTTRLTSRLHLQEAGTAFPSRV
+RQDALDEWVFVAEHVRAQVLRDTRFPAARTSVVPNAVAVPPTLPDGDDDRRFVLGLVGVL
+PERKGLHRALDLLAVLRRTEPRFTLRIRGHHPEEVGWMAQRPAAAAYYRAQLRRIETDPM
+LAGAVAWDPHGPDMPAWYARVGVALSVSDFESFHFTLPDGAAHGCLPAALAWAGADLLYP
+AAWLSPDVATMADALRRATADARAWRSAVAQARRDVAHTYAEEDVVPALVCRILGGTAT
+>PROKKA_02045
+MGEADTPAPTPEGPLAGRSFRLVAVAERPDWEPGLIAQLRAAGAAVVSTTEVVRTSSAHV
+DVLLAVDVESAAALRAAGWDRFQVWTVVQTDPGTPLMPRGLSAAGVGRAVAESRRVVVFD
+EASRSAVESTLWNAAGKVVVMPRFTAEEVEAVSFGGNRVEGPHEPGEAILVLHAGLLGSE
+GAHVLREYSDAVRARRHVRKVLVVAPGDLRVAVRSEEGQRHLARIPGASLIDGGAELSRA
+AAGRRTVTVLPRWSTPQDSRAEDLLAWAAAVGAQVWAEPGAVPPQVSGRPVGQLPGDNLS
+AALDWADQHAGGTTFGAAPINRVAQAFAPHVPALSTVPAHPNAPLKVLFVGADYKFAGDL
+VEALILRPDAEVRVDQWKTNGDRPTPNSAELLAWADVVICEFASRNAVWASQHIREHQRL
+IVHLHGYELRNPLIHDIVMDRVHTVVFASEFYRADAVVTTGWRVEQTAVIPNSVQSAELR
+RPKTADARFHLGLAGYVPELKRMDRALDLLEELLRRDDRFVLHLRGRHPWNYPYVWRHPL
+RRDTYLANYERLRSNPRLRRAVVFDDFGPDMGNWFRNIGWMLSPSTRETFHLAPAEGMAS
+GAVPVVWRREGSDGIFPPESLVTDAASAADRIHRTAGDRDAYNSAARSAIEFATRYEAGA
+VVDHWLRLILHGERPGGPPSPEHLQRARPVATALAGRADWNRVGRLLRDGRVEQAAAVAQ
+EESRPAWEQPEDVRRLAAHVNGYSALAQRAHRLVPSAPCVPPLLPLAAGADSARSLTLTE
+GPAGTYVTRSGDIAVGRGDILDDVNAEFDRLVDQAFRIGAQNRATALTVIGDEMLALAGG
+AVAGWLGIPFVWDLTSQPAARDLLMRMRALPDAPTPQGRLALLAAASATRLIGAGPAERL
+PVPFETFIGMADLDRPRRVGVIGRSLGDLVGRSWGEPVNLSPGRWREQTVPRLDVALLDA
+QVLHPRNAWRASEGNTGPLGALITHVRRHATPLAIVDLGHEGLDSAGIAQARRVDAVVTA
+HPDDVQRLHDVRIVPSQVAVSTAPWGIRSGEEHVLRPGDRVRLAMRMLGVAETH
+>PROKKA_01944
+MRQIDEMALWTSRDVGVRVRYAGAEELIRGVRSRADATHDASDGGTDLEAADVAGPGTPE
+PSDHVAEVPWRLRVLNTGRVRQIRRWIYHARRAPAHAAAARVKRLLRTPGRWSETLRRPL
+ARTRAAAPAPERADAAVATPAPAAEPTGERTLAALRAALAERPSASALHALVAALYRDGQ
+LRAPAAALEEHPELVGQFTPAQAKLARNVREQARLLDHPPVVPARAVGTALRPEAGRILY
+CAHGVHPYQSNGYAIRTRGIVAGLRDAGHDVVVAARPGFPWDAKVTRAARKKQSYPELVD
+GIEHVYSFGPSLRNQALAAYLESAVDSYLQVIARNRPAHVHAASNHITALPALIAARLSG
+LPFTYEVRGFWEYGMEPGEEGLQERGELAGRLEDLVMVEADHVFVLTAEMRDELRGRGVD
+PDRMTVTPNGVDPEQFQPLPAVGELHRRLGLDPDRAVIGYLGSLVSYEGLEDLLEACLQL
+AEERDDFQLVVAGDGPVLPRLKEIAAERDTSLPVHLLGRIDADLIPALMSEVDVVACPRT
+ATRVTRLVSPLKPLEALAAGVPVVLSDLPVLRSLAEECGGAVVFPAGDRHGLAEAIAGLL
+DDPERRLDLGRSGRAWALRERRWDVLGAHLGSGILAAVPSTGAEGGSRPLSTVRLGVIAD
+TFTTSGLAEQVQTVPLQRAGQGWRRQLAEERLDAVFVESAWSGNDGAWTRGVGHYSDEES
+ADLRALLEDCRAAGVPTVFWNKEDPVHFNRFVENARLFDLVLTTDNRSIQGYQARVDRSR
+QTVGSMAFFAQPSLHHPVTDGPAVADRPVMYAGSYYGDRYRDRSEVLRGLLHVARPFGVT
+IYDRQADLPDSPYRFPEELQPFVEGGLPYSEMVKAYRRYPLHVNVNSVTASETMFSRRVM
+EISCAGGVVASGPSAGVNHMFRGLVPTIGRREVAERAMSTLLSDPGLRNVQGWNLRRLVR
+RSHTLSDRLLVLLRRLGLAVSPDPTPGTTVVLTGPADRADWDGLLAQTRPVDRVVADEMS
+ETVRERLSAAGIEVSAGSASLDPAHLAWEWDGARLDRVVHEDLANVLLDSGYSAAVLDTT
+PVTDLATPLAVVGGAPVPSGASLVLRWGGGDDGVVTVRRGLLESVEDLGAKQRPAAVALT
+PEALDRMERPLRVVVAGHDLKFAGELINRFRSDGHEVRLDQWASHQDHDDELSRELVDWA
+DVVLCEWGLGNAVWYSKHKREGQRLYVRVHSQELFRDNWSRMNLPAVDRFIFVAPHIRDS
+ARRYRGVAARPSEVIPNIVLPGAGLKRDPDSRFVLGLVGIVPRGKRFDRALDLLAMLRRE
+DPRYSLRVKGKQPEDYPWMAAREEEMAYYGTIRERIAQDPALQGAVHLDGFSTDRAELDR
+WYSSIGIGLSVSDFESFHFTSVDGAQNGAVPAVLAWPGADRIFPAEWLSPTLESMARRIL
+GLREPEVFRAAADTARRETSARFDGGRSLDRWSELVAGE
+>PROKKA_00845
+MIQLFLRFSRRQQLVMGLFILLAVVGSVLAFLVDHAILIVALFWMLCAAVFVMIMYHRRL
+NAKINRTARAARMGSSAVAGRGGTRPATGRRISTQESLDSLQAAFARRRTVAAGLPLARK
+LIQERGDLSGAREVLDQLRGKSGLTDSEENFVRRVDSLNRLLEADYPLPARHRTCNYLPV
+RGRVLYAVGMSPVSVTNGYTSRTKGVAAGLVAQGLDVVVAPLPGKPWDKKSVVPGRRVPV
+KQRRDVSEIDGVRHVHNPGLPAWEGDLDVFFQVAADAYVREAMIEKPEFILAASNYLSAL
+PALIAARRLGVPFVYEMRGFWEVSAASVRPGWEQSDQYRLDRRYEDLVAREADRVVVITD
+EMREDLAARGIDADKVTVAPNCVDPEVFAPLGKDHALLRGLGFTDTEAPVVGFAGSVTDY
+EGLDLVTDALATLKAEGVRFNFLIIGGGAYLDTLKARIATRGLDPETRFVMNVPNADMPA
+YLSSIDVFPLARKSLPVTELVSPLKPLEAMAVGGAVVLSDVSPHKVFCGPDGDTAVSFQK
+DDLASLVERLRETLAAPDAARAMGVRARRWVKENRRWPVTGERIAASLMALAEEFRASLD
+DAERPLTDYTVAFIGDEFTTDTFVPELTALRVRPEDWRETFEDHRVDALFIESAWRGNDS
+AWTGIIGYYDDETHAPVVELIAHCRLHEIPVMFWNKEDPVHFNRFKRTAALCDYVFTTDA
+RTIVDYNALPDNQITTVASAPFAAQPLLHNPLPSTRAQDEAIAYGGTYYGDKYATRKQGL
+DFLFYESAPHGLAIYERVHNDPNSPYRLPDRFRRYARGSLSYPEMCQAYKAHPIHLNGNS
+VVDSPSMFSRRVVEITASGSTVLSSAGRGVDETLAGTVPTVTTPDEAAAYLEGWKSSEQR
+RHAGLWEAFRHVYETHTCAHRLVYMMRVAGFRVRSPQAAPIAVECAAADVPLFEAQTMRP
+ALYLVTDTTEGVDAASPVVLAAPPERAAKLQEAGIRNVVIHREGAPALDEHLVEDFSLAL
+HFGHWKAVGTRTVEWSPGDAHVRIAALTADIDEGTVLVDADVYAGSVLGERPALADDEVF
+AWQHVVEHVGKVTYTDSTAVPIDTAVVHEEADPLPPVASGEAGPPVGETQTVPLNVLVAG
+HDLKFLPQIMAQLEAAGHRVIVDQWDGHDIHDEERSLRLLAEADVIFCEWALGNVKWYSH
+HKQDDQRLVVRLHAQELRTRYLKDADLSAVDTFVFVSPVGMRRAQLLFGVPVDRSVVIGN
+TFDFERFAAPRNAPDPHALGLVGSVPHSKRLDLALDVTELLASHDPTYRLDVMGKEYHEY
+AWLMKRTAERSYFEAQYLRIESSAVLREAVRFGGHSYDIAEWYRAKPGIILSTSDHEGTH
+QAIAEGGAAGCVPVIFPWAGAEAVYDDRWVVEGVRDAADRIRRYSSDPALFLEESERAQA
+FMRERFSPEEIGAQILAVVEGRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000040.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000040.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a47a05c7cd568f96e544f0e9df885a9d7d8e339b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000040.fa
@@ -0,0 +1,63 @@
+>PROKKA_01015
+MSASTPRRRVVDNEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVV
+APAYTLTSGLGPTISTVGTHVPAILLLGFIPMLLVALGYRALNTRVPDSGTSFTWATHAF
+GPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQITGSQAIADLAGNLWVNIPLTLV
+YLALAGWISHRGMETTKHLQYILVAFQILALGAFAVAALTQSSRGAGFDPTPVQLDWFNP
+FTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAAVTVFVIIAVYILSAL
+AVISWAGIGSEGLGAGNPDNQESIFAVLAGPILGPFAVIMSSAILVSSLASLQSTMVSPA
+RTLLAMGFYRAVPARFAELSPRFNSPAFATWVCAGFAGLFYVVTRLLSENALWDTITALG
+LMICFYYGITALACVWYFRREWFTSVGNALTTFLFPLIGGLVLLVMFCVTAMDSTDPDYG
+SGSSVFGVGTVFILGMGVLAIGVVLMMWTRLRHPAYFRGETLPQTDSTRPIPIIRPDDDG
+SAVVRDPNERTHS
+>PROKKA_00729
+MSASTPRRRVVDSEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVV
+APAYTLTSGLGPTISTVGTHVPAILLLGFIPMLLVALGYRALNTRVPDSGTSFTWATHAF
+GPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQITGSQAIADLAGNLWVNIPLTVV
+YLALAGWISHRGMETTKHLQYILVAFQILALGAFAIAALTQSSRGAGFDPTPVQLDWFNP
+FTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAAVTVFVIIAVYILSAL
+AVISWAGIGSEGLGAGNPDNQESIFAVLAGPILGPFAVIMSSAILVSSLASLQSTMVSPA
+RTLLAMGFYRAVPARFAELSPRFNSPAFATWVCAGFAGLFYVVTRLLSENALWDTITALG
+LMICFYYGITALACVWYFRREWFTSVGNALTTFLFPLIGGLVLLVMFCVTAMDSTDPDYG
+SGSSVFGVGTVFILGMGVLAIGVVLMMWTRLRHPAYFRGETLPQTDSTRPIPIIRPDDDG
+TAVVRDPNERTHS
+>PROKKA_00822
+MSSVLDAAGTPATPHPSPAAPSARVPSSSGGGRLGAGRIGVPALVCMIVAASAPLTAVAG
+GITSNFAVTGLLGVPLSFLVLGVVLLLFSVGYAAMSRHVHNAGAFFAYVARGMGKPAGVG
+AALVALVSYACMQVGIAGMFGFATSSFLEGTFGIAVPWWASALAAWVLVGVLGLYRVDFS
+AKVLMGVVALEFLVVCVYTVLGLRAAPEGVSAAGLLPGQLFTSGVGAALVFSVAAFMGFE
+SGAIYNEEVKDPKRTAGRATLISVVLIAVFYAFSAWAMVMTEGPGGVVAAAQAVGPDVVF
+AFLGAHAPLWFTDLANILFIVSLLAALLAFHNIVARYAFALGREHVLPAFLAHTSTRTGA
+PVGGSLVQSGAALVVLVVFALAGSRSDDPLFPVVTLFTWLTNMGAFGLVLLMALTSVSVI
+GYLRRHRDEFGVFTRVVAPALAAVGLLTLFVLTMVNFPVLLGADGTTPLSWLLPALVVTP
+GALGTAWALWLRARRPATYAGIARGGELS
+>PROKKA_01873
+MSASTPRRRVVDSEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVV
+APAYTLTSGLGPTISTVGTHVPAILLLGFIPMLLVALGYRALNTRVPDSGTSFTWATHAF
+GPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQITGSQAIADLAGNLWVNIPLTLV
+YLALAGWISHRGMETTKHLQYILVAFQILALGAFAVAALTQSSRGAGFDPTPVQLDWFNP
+FTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAAVTVLVIIAVYILSAL
+AVISWAGIGSEGLGAGNPDNQESIFAVLAGPILGPFAVIMSSAILVSSLASLQSTMVSPA
+RTLLAMGFYRAVPARFAELSPRFNSPAFATWVCAGFAGLFYVVTRLLSENALWDTITALG
+LMICFYYGITALACVWYFRREWFTSVGNALTTFLFPLIGGLVLLVMFCVTALDSTDPDYG
+SGSSVFGVGTVFVLGMGVLAIGVVLMMWTRLRHPAYFRGETLPQTDSTRPIPIIRPDDDG
+TAVVRDPNERTHS
+>PROKKA_02256
+MLSTHQSVSVSTSSVAPVYSAVVTVPLVVGLVGSGAPLAYLLALLPILGVWAGMSANDER
+EPDKGSVYSWAVTGHPVLGWTAGWCLALTGIVATSGLAYVALDAWLPGLGAGVKVLIGAG
+IIAAATALASANVRITAAVQTAGVLVQVAATAYLAWVLARVGLTPLPPAGTVQDWVHAVL
+LAVFAFWGFDAVYALSEESHRGVPRRSAAVSLGLLAAIFLVFSALGASEDPAAVAALTHP
+VVMAGVVVSCVGAIGSTLIPTARGLSAMAERGHLSAVLAPLRAAEVVSALLAIAWLVVSL
+AVPGVFEDSIEMLSVFVGGYFTISSATAAAHASGGARMLHAATAVVMGLITAASLAWMFE
+PDYGATVVGGVGGVGLLAVGFAVLGLILAVGAGHRGRAVHPTSGV
+>PROKKA_00958
+MSASTPRRRVVDNEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVV
+APAYTLTSGLGPTISTVGTHVPAILLLGFIPMLLVALG
+>PROKKA_00959
+MPDSGTSFTWATHAFGPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQITGSQAIA
+DLAGNLWVNIPLTLVYLALAGWISHRGMETTKHLQYILVAFQILALGAFAVAALTQSSRG
+AGFDPTPVQLDWFNPFTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAA
+VTVFVIIAVYILSALAVISWAGIGSEGLGAGNPDNQESIFAVLAGPILGPFAVIMSSAIL
+VSSLASLQSTMVSPARTLLAMGFYRAVPARFAELSPRFNSPAFATWVCAGFAGLFYVVTR
+LLSENALWDTITALGLMICFYYGITALACVWYFRREWFTSVGNALTTFLFPLIGGLVLLV
+MFCVTAMDSTDPDYGSGSSVFGVGTVFILGMGVLAIGVVLMMWTRLRHPAYFRGETLPQT
+DSTRPIPIIRPDDDGTAVVRDPNERTHS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000043.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000043.fa
new file mode 100644
index 0000000000000000000000000000000000000000..96d9e7072c32864c6ce50882217f83a73b7a0b2f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000043.fa
@@ -0,0 +1,21 @@
+>PROKKA_01397
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVNRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEAQRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>PROKKA_01130
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVNRVATQLGYGVESVRMWVK
+QADIDDGVTSDVSSAEAQRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>PROKKA_00412
+MPKEQTAGKPTTRRYSPEEAAAVRMVRTMRAELGTEHGTVQRVATQLGYGVESVRMWVKQ
+ADIDDGVTSGVSSAEAQRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>PROKKA_00325
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVQRVATQLGYGVESVRMWVK
+HADIDDGVTSGVSSAEAQRVRELEQEVRKLRRANEVLKRAASFFGAELDRHYRK
+>PROKKA_00648
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRVELGTEHGTVQRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEARRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>PROKKA_02216
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRVELGTEHGTVQRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEARRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>PROKKA_01347
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVNRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEARRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000044.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000044.fa
new file mode 100644
index 0000000000000000000000000000000000000000..66009f8d6dc510d8746707b4b42c58c88d2bb6e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000044.fa
@@ -0,0 +1,40 @@
+>PROKKA_01401
+MAVSGSFPGHLWAAFHGRLHSVRDEELIPQLVELWETNYRVYGVRKLWKTARRAGIDIGR
+DQTGRLMRAAGIKGATRSKRVKTTRPDPTAARHPDLVKREFTAPAPNRLWVTDLAFVTTW
+AGVAYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFT
+SIRYGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAELVRGPARPGPWRTVEDLELAT
+LGWVSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLSESNSASLHQTQGASGPTLWSP
+TRSILDRAARPLRKF
+>PROKKA_01131
+MAPSSYYAAKTRAPSARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGRDQA
+ARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTWAGV
+AYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDPRCHSDAGSQFTSIR
+YGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAEHVRGPARPGPWRTVEDLELATLGW
+VSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK
+>PROKKA_00413
+MAPSSYYAAKTRAPSARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGRDRA
+ARLMRAAGIEGARRSKRVKTTRPDPASARYPDLVKREFTAPAPNRLWATDLTFVPTWAGV
+AYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIAMARWSRGARHEDLRCHSDAGSQFTSIR
+YGERLAEIGATPSIGTVGDSYDNSLAETVNGYYKAELVRGPARPGPWRTVEDLELATLGW
+VSWHTTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIQ
+>PROKKA_00326
+MAPSSYYAAKTRTPSARAARDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGRDQT
+ARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTWAGV
+AYVCFIIDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFTSIR
+YGERLAEIGATPSIGTVGDSYDNALAETVNGYDKAELIRGPARPGPWRTTDDVELATLGW
+VHWHNNQRLHGYLDDLPLTEFEERFYATQQGQYALVEIK
+>PROKKA_00649
+MAPSSYYAAKTRAPSARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGRDQT
+ARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTWAGV
+AYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFTSIR
+YGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAELVRGPARPGPWRTVEDLELATLGW
+VSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK
+>PROKKA_02217
+MAPSSYYAAKTRAPSARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGRDQT
+ARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTWAGV
+AYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFTSIR
+YGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAELVRGPARPGPWRTVEDLELATLGW
+VSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK
+>PROKKA_01351
+MGSFSWPLTHSDAGSQFTSIRYGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAEHVR
+GPARPGPWRTVEDLELATLGWVSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000050.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000050.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e6e2ffca0d762d40961d6c835c555ee8fc2d7ddb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000050.fa
@@ -0,0 +1,62 @@
+>PROKKA_02089
+MSTDPRRQTPAPRGSDTGTPPLPEGRARWLVASNALDAGGRSATDVALDVLAVLLLGVGA
+DGMGVLMTLSGLGFLLLGVPLGIVVDRHLSPRLLAATGLAKAAVLGSLVAAWALDALTFG
+HLAAVMTLLGVLTVLAETTQTALVPRVVPATAVARLTARLESADAALVLIVPAAAGVLVG
+SLGAGPVLGIATAFLFAAAIVALRVRLRPSAAADVPDDDGDPGVADVLSRWARFGKDAAE
+GWTVLRRTPVLWLLTMGSVAANVGMALFAPVEAVWILTDLRLGPEFLGIQITAGAVGALT
+ASSLAGRAIDRLGERRCILLGSVGCAVAVGLHLLAYADRAHAGPWLLAGAALWGFMVLLG
+NITQAAVTARACPEGTLGRVTAMRRTLTRGSVPLATLAGGALGATLGVGWALAGWQVLAV
+VSLAAVVPAARWVDAGRDDVD
+>PROKKA_01794
+MSTDPRRQTPAPRGSDTGTPPLPEGRARWLVASNALDAGGRSATDVALDVLAVLLLGVGA
+DGMGVLMTLSGLGFLLLGVPLGIVVDRHLSPRLLAATGLAKAAVLGSLVAAWALDALTFG
+HLAAVMTLLGVLTVLAETTQTALVPRVVPATAVARLTARLESADAALVLIVPAAAGVLVG
+SLGAGPVLGIATAFLFAAAIVALRVRLRPSAAADVPDDDGDPGVADVLSRWARFGKDAAE
+GWTVLRRTPVLWLLTMGSVAANVGMALFAPVEAVWILTDLRLGPEFLGIQITAGAVGALT
+ASSLAGRAIDRLGERRCILLGSVGCAVAVGLHLLAYADRAHAGPWLLAGAALWGFMVLLG
+NITQAAVTARACPEGTLGRVTAMRRTLTRGSVPLATLAGGALGATLGVGWALAGWQVLAV
+VSLAAVVPAARHLGPRTAER
+>PROKKA_00694
+MSTDPRRQTPAPRVPDTGTRPPPEGRARWLVASNALDAGGRSATDVALDVLAVLLLGVGA
+DGMGVLMTLSGLGFLLLGVPIGIVVDRHLSPRLLAATGLAKAAVLGSLVVAWALDALTFG
+HLAAVMALLGVLTVLAETTQTALVPRVVPATAVARLTARLESADAALVLIVPAAAGVLVG
+SLGAGPVLGIATSFLFAAAIVALRVRLRPSAAVDIPDDDGDPGVADVLSRWARFGKDAAE
+GWTVLRRAPVLWLLTMGSVAANVGMALFAPVEAVWILTDLRLGPEFLGVQITAGAVGALA
+ASSLAGRAIDRLGERRCILLGSVGCAVAVGLHLLAYADRAHAGPWLLAGAALWGFMVLLG
+NITQAAVTARACPEGTLGRVTAMRRTLTRGSVPLATLAGGALGATLGVGWALAGWQVLAV
+VSLAAVVPATRHLGPRTAER
+>PROKKA_01308
+MVSSPLTDDTTAPENAAPAKRLGRARWLVASNALDAGGRSATDVAIDVLAVLALGVGAAQ
+MGVLMTLSGLGFLLLGVPIGILVDRHLSPRLLVATDLAKAALLGTLVLAWALDALTFAHL
+AAVMALLGVLTVLAETTQATLVPRVVAPDTVSRLAARLESADAALGLIVPAAAGLLVAAL
+GAGPVLGIAAAFLAAAALVALKVRMNPAPVTEDTRDEETPAAAVVLTRWSRFWSEAAHGW
+TTLRRTPVLWLLTLNSMAGNIGMALFAPIEAVWVLTDLQLGPEFVGFQLTAGALGALTVS
+ALAPRAIDTLGEKGCILAGSAGCAAAVALHLAAFFDRAHAGPLLLAGAALWGFMVVLGNI
+TSGAIFARSCPEGTLGRVTAMRRTLTRGSVPLATLAGGALGAAFGPGWVLAGWQAMALLS
+LAFAFAATRLARRPQ
+>PROKKA_00662
+MTRVSAWRSRDFRRLWGASTASALGGEIGELAMPVLALVWLGASAEELSWVRVATFLPYL
+VLPLWLGVLVDRWRRRPLMITAETVSGITLLGIAGAALAGWLTVPALVAAAAVLGAMSVL
+HMLADFSFTPQVVSRAALPDANAKMTATYSAIGIGGSGVGGALVQWLTAPFAVAINGAGR
+LLSVVLLRRIQTHEPPAEAPDTSARQQAREGFLALLRHRVVRALAAEATIWNLGNEVFML
+ALTVLIVDARDDGPLVLGLIFMAGGLGAFLGAGISARLTERFGYGRSLITAMLVGNTAPL
+IGVLFSSDTSVTSLVVLAAAFFASGFGTGIANSQAVTVRQVTVPEELRGRVNASYRMLSW
+GALAIGALLGGWLISAVGGWLAAALGTAAMAASTLPVALSPVRQMRDLDDGAPPAAE
+>PROKKA_02237
+MSSPLTDDTTAPENAARAKRLGHARWLVASNALDAGGRSATDVAIDVLAVLALGVGAAQM
+GVLMTLSGLGFLLLGVPIGILVDRHLSPRLLVATDLAKAALLGTLVLAWALDALTFAHLA
+AVMALLGVLTVLAETTQATLVPRVVAPDTVSRLAARLESADAALGLIVPAAAGLLVAALG
+AGPVLGIAAAFLATAALVALKVRINPAPVTEDTQDEETPAAAVVLTRWSRFWSEAAHGWT
+TLRRTPVLWLLTLNSMAGNIGMALFAPIEAVWVLTDLQLGPEFVGFQLTAGALGALTVST
+LAPRAIDTLGEKGCILAGAAGCAAAVALHLAAFFDRAHAGPLLLAGAALWGFMVVLGNIT
+SGAIFARSCPEGTLGRVTAMRRTLTRGSVPLATLAGGALGAAFGPGWVLAGWQAMALLSL
+AFAIAATRLARRPH
+>PROKKA_02028
+MSTDPRRQTPAPRTPDTGTPPPPEGRARWLVASNALDAGGRSASDVALDVLAVLLLGVGA
+DGMGVLMALSGLGFLLLGVPIGIVVDRHLSPRLLAATGLAKAAVLGSLVVAWALDALTFG
+HLAAVMALLGVLTVLAETTQTALVPRVVPATAVARLTARLESADAALVLIVPAAAGVLVG
+SLGAGPVLGTATAFLFAAAIVALRVRLRPSAAADVPDDDGDPGVADVLSRWARFGKDAAE
+GWTVLRRTPVLWLLTMGSVAANVGMALFAPVEAVWILTDLRLGPEFLGIQITAGAVGALT
+ASSLAGRAIDRLGERRCILLGSVGCAVAVGLHLLAYADRAHAGPWLLAGAALWGFMVLLG
+NITQAAVTARACPEGTLGRVTAMRRTLTRGSVPLATLAGGALGATLGVGWALAGWQVLAV
+VSLAAVVPAARWVDAGRDDVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000052.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000052.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d09c76dfdc22c2b4debc03917f4fd85372893e91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000052.fa
@@ -0,0 +1,35 @@
+>PROKKA_02160
+MSSEETVPVRVALVDDQALIRSGLAMLVDSQPDLTVVAEAGSGREAVASVSVAGADVVLM
+DVRMPEMDGIEATRALLRRPDAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAPPEELLA
+AIRTVHRGDAVIAPSTTRRLLTHMAPRLRSDQVRSAECEEQQAAVASLTPREHEVLVLMA
+QGAANLEIAAELVLSEATVKTHVGRVLAKLGARDRVQAVLIAHRAGLVQF
+>PROKKA_01873
+MSSEETVPVRVALVDDQALIRSGLAMLVDSQPDLTVVAEAGSGREAVASVSVAGADVVLM
+DVRMPEMDGIEATRALLRRPDAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAPPEELLA
+AIRTVHRGDAVIAPSTTRRLLTHMAPRLRSDQVRSAECEEQQAAVASLTPREHEVLVLMA
+QGAANLEIAAELVLSEATVKTHVGRVLAKLGARDRVQAVLIAHRAGLVQF
+>PROKKA_00589
+MTTRVLLVDDQPLIRLGFAAILQSQDDIEVVGEAGDGAECLERAAALDPDVICMDVQMPR
+MDGIEATRALAEAGTRAAVLILTTFDRDDFLFETLEAGASGFLLKSAEAEHLIDAVRVLG
+RGDALLDPQVTRRVLRRMASAAPEGVDGPAGVGQPRDDDGAAPGQAEASDAVGKAGLTGR
+EAEILTLMARGLSNGEIAGQLFVGESTVKTHVSNVLMKLGARDRVHAVIWAFEHGVAG
+>PROKKA_00598
+MSTDAENAPVRVALVDDQALIRSGLAMLVDSQPDLTVVAEAGSGREAVASVSVAGADVVL
+MDVRMPEMDGIEATRTLLQRPDAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAPPEELL
+AAIRTVHRGDAVIAPSTTRRLMAHMAPRLRSDHARTAECEHEQAAVESLTPREREVLVLM
+AQGSANLEIAGELVLSEATVKTHVGRVLAKLGARDRVQAVLIAHRAGLVQF
+>PROKKA_02580
+MVLPDAGVRGGVRVRTSRTGVVGDIRLVEGAVSGDLDSADLLLGGVNSLGETRQVARQGR
+DVPPFLLVAEATIVEELSGIDASGAAAVLAYPLDTVELASVAHGIAGSGPFLSPRLPQLS
+VEPLGEGLSAREAEVVVALGEGLSDAEIAQALCVSVKTVHTHVLNLRRKLGARNRAHAVS
+LARSVGPLGDACSEPGLVAAL
+>PROKKA_00520
+MSPDDAQPTPIRVALVDDQALIRSGLAMLIDSQPDLTVVAQASDGREAAASVAVAGADVV
+LMDVRMPEMDGIEATRALLRRPDAPRVVVLTTFDLDEHVMDAIEAGASGFLLKDAPPEEL
+LAAIRTVHGGDAVIAPSTTRRLLAHMAPRLRQDAARSAECADEQAAVGSLTPREREVLVL
+MGQGAANPEIAAQLVLSEATVKTHVGRVLAKLSARDRVQAVLIAHRTGLVGF
+>PROKKA_02104
+MSSEETAPVRVALVDDQALIRSGLAMLVDSQPDLTVVAEAGSGREAVASVSVAGADVVLM
+DVRMPEMDGIEATRALLRRPDAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAPPEELLA
+AIRTVHRGDAVIAPSTTRRLLTHMAPRLRSDQVRSAECEEQQAAVASLTPREREVLVLMA
+QGAANLEIAAELVLSEATVKTHVGRVLAKLGARDRVQAVLIAHRAGLVQF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000060.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000060.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7cf89819d612488e6cc77b1fabc5ee5a6b4bf299
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000060.fa
@@ -0,0 +1,47 @@
+>PROKKA_00063
+MTPEWWMALAALVLLALLVVVVVVLAVRQVRLGVQHERTRLLVDALDARVGGVQRRLEEV
+PGIGTGRHEVALVLNPIKTHADRVRRELERLAEAEGLGEVLVLETQEDDPGTAMARQALD
+AGARLVIAAGGDGTVRTVAEQLAGTDVALGVVPLGTGNLLARNLDLPINDVEQCLRIAVG
+GRQRRIDTVDVRFTHEDGRVTRQTFTVIGGAGYDADIMGDTKDELKSLAGWLAYSEAGMR
+HLRGKRHEVTVALDGGQPRRFKVRTVMVANCGMLTGGVELLPQAKLDDGLLDVMVLSPRH
+ALDWARIAVKTVTRHRSSVPAMHTEQAQRVKVEFAEPMPSQLDGDATGVITALDARVQPD
+SLVVMLVAEDDASVRDDGVSAAAPVPEPAPHI
+>PROKKA_02076
+MTPEWWMALAALVLLALLVVVVVVLAARQVRLGVQHKRMRLRVDALDARVGGVQRRLEKV
+PGIGTGRHEVALVLNPIKTNAGQVRRELERLAEAEGLGEVLVLETQEDDPGTAMARQALG
+AGARLVIAAGGDGTVRTVAEQLAGTDVALGVVPLGTGNLLARNLDLPINDVEQCLRIAVG
+GRQRRIDTVDVRFTHEDGRVTRQTFTVIGGAGYDADIMGDTKDELKDLAGWLAYSEAGIR
+HLRGKRHEVTVALDGGQPRRFKVRTVMVANCGMLTGGVELLPQAKLDDGLLDVMVLSPRH
+ALDWARIAVKTVTRHRSSVPAMHTEQAQRVKVEFAEPMPSQLDGDATGVITALDARVRPD
+SLVVMLVAEDDASVRDDGVSAAAPVPEPAPHI
+>PROKKA_00201
+MTPGSPDDDGAPAVRRRVLVLLNPHAGRRRSLARAQARLRTHPGLALDLVVPDPADHAAQ
+LAAGRTALADGVDAVVVRGGDGMVAAGVGLVGDHAEATGRRVPLGIVPAGTGNDLARAAG
+LHRRDPGAALEAVLRALEDPAAPVRRIDALRLTVTRAGAVVERRWAANSVNIGFDARVNA
+RANALGAVPGPLRYLAALGLEARAFAAVEMGLGLDDGPVRRERVALVSVQNGPTIGGGIP
+LAPGARLDDGRAEATVVGPLPTAGLALLFPLVYVRAHRLLRPLCTERARRVRVAVPDGVP
+VYADGDEVLPASHGGAAVEVEAVPGAVALLG
+>PROKKA_00332
+MALVALVLGAVLAVAVIVLAVRHRGLAERHERTRGQLDAVEHRLDAAQRRLGELPGVDRP
+RQEIALVLNPVKARADEVRRTLEAMADREGLGSVLVLETEEDDPGTQMAKDALEAGVRLV
+IAAGGDGTVRTVAEQLTGTDVALGVVPLGTGNLLARNLDLPINDIEECLRIALTGRQRRI
+DTVDVRFTHEEGEVTRQTFTVIGGAGYDADIMADTKDELKDVAGWLAYSEAGMRHLRGKR
+HDVSISLDGGASRRFKVRTVMVANCGMLTGGVELLPEAKLDDGLLDVLVLSPRHALDWAR
+IAAKTVTRHGANIPVMHTEQAQRVKVEFADPMPSQLDGDATGHIVALDARVQPDSLVVML
+LDEKEASVHDDGRSEAAPVPEPAPHI
+>PROKKA_00273
+MALAALVLAALFAVAVVVLGLRLRRLDGAHERTRGQLDAVEARLGDLRRRAGRAPGVDLP
+GPQVALVLNPVKARADEVRRAMEALAEKEGLGEVLVLETTEEDPGTAMTREALTAGVRLV
+VAAGGDGTVRTVAEQLAGTDVALGVMPLGTGNLLARNLDLPINDIEECLRIALTGRQRRI
+DTVDVRLTHEDGARTRQTFTVIGGAGYDADIMGDTKDELKDMAGWLAYSEAGMRHLRGRR
+HEVSITLDGGAVQRFKVRSVMVANCGMLTGGMELLPEAKLDDGLLDVLVLSPRHALDWVR
+IAAKTLTRHRASIPVMHTEQAQRVQVRFAEPMSSQLDGDATGDITALDARIQPDSLVVML
+GDEDDASVEDGGRSAEAPVPEPAPHI
+>PROKKA_00058
+MALAALVLLAVLAVVVVVLAVRQVRLGVQHQRTRLLVDALDARVGGVQRRLEEVPGIGTG
+RHEVALVLNPIKTHADRVRRELERLAAAEGLGEVLVLETQEDDPGTAMARQALDAGARLV
+IAAGGDGTVRTVAEQLAGTDVALGVVPLGTGNLLARNLDLPINDVEQCLRIAVGGRQRRI
+DTVDVRFTHEDGRVTRQTFTVIGGAGYDADIMGDTKDELKDLAGWLAYSEAGIRHLRGKR
+HEVTVALDGGQPRRFKVRTVMVANCGMLTGGVELLPQAKLDDGLLDVMVLSPRHALDWAR
+IAVKTVTRSRSSIPVMHTEQAQRVKVEFAEPMPSQLDGDATGVITALDARVQPDSLVVML
+VAEDDASVRDDGVSAAAPVPQPAPRI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000063.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000063.fa
new file mode 100644
index 0000000000000000000000000000000000000000..44484551023a4b694d6a0777185c546dbdecbd41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000063.fa
@@ -0,0 +1,52 @@
+>PROKKA_00105
+MATKTAPKRAPGYRCTECGWTTVKWVGRCGECQSWGTVEEIGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVSEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGSPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLSAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFTVAEVGSIGEALATIPTWTGGGPAAHPEAGPGR
+>PROKKA_02118
+MATKTAPKRAPGYRCTECGWTTVKWVGRCGECQSWGTVEEIGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVSEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGSPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLSAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFTVAEVGSIGEALATIPTWTGGGPAARPEAGPGR
+>PROKKA_00038
+MSPFDLEELDMTATAPDPLDGAFTAAWLTSQTFAPVEYVVPGLIPEGLTLLVAAPKVGKS
+WMVLDLAHAAATGGKALGSISVDRRPVLYLALEDGPRRLQSRLSMLGVDGGGPDLMFLTA
+LSASPVATVAAYLERHAQDRPLVILDTLGKVRGRDGGNDQYGRDYSQMSALKTLVDAVPG
+SSLIVVHHTNKGGREDFLEAVSGTQGLAGAADSILVIRRDRNQADGTINVTSRDAREGEY
+AVTFDGSRWHTVGADLAEAAAAAESKRATAGVGDDMARVIDAVSRHPGGVGVAQIVAMTE
+LPRATVDKYLSRAVAAERIVRVERGTYAPTPLSEVSDCQIGSDPDPLDF
+>PROKKA_00285
+MATKTAAKRAPGYRCTECGWTTVKWVGRCGECQAWGTVEEVGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVAEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGGPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLAAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFTVAQVGSIGEALATIPTWTGAGAGA
+>PROKKA_00231
+MATKSSTKRAPSYRCTECGWTTVKWVGRCGECQAWGTVEEAGGAATAGRTHASTVAQAAP
+RIRDVDATLASFRTTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAA
+GGGPRDVLYLTGEESAAQVRSRADRIGALADTLRLAAETDLGRALGQIEKTDPALVIVDS
+VQTLQSTEVEGVAGGVTQVREVAASLIRTAKEKGITTILVGHVTKDGSIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGTQEPVEGT
+CVTVTLEGRRPLVAEVQALLTPSGGGSARRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAIASAKLGAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFSVAQVGTLSEALGTIPSWTGQRSPGARS
+>PROKKA_00100
+MATKTAPKRAPGYRCTECGWTTVKWVGRCGECQSWGTVEEIGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVSEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGSPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLSAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGEVPAGFTVAEVGSIGEALATIPTWTGGGPAARPEVGPGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000067.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000067.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2671b1e8e6321c614c7babe86c4cf21484a8bde6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000067.fa
@@ -0,0 +1,53 @@
+>PROKKA_00207
+MSTAENAGAGAPTRPDEHRAILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTHLAQ
+TLEKGLFDGLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVT
+AGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQMEHDERYEHADEY
+LDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAHEGRYFTVPGHAVTEPSVQRTPVI
+YQAGASTRGRAFAGKHAEAVFINSPTKELAAATVKKIRQALVDAGRDPYDVKIFAMQTIV
+TGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDVKSNAIQSAVETF
+QKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPG
+AFEDVVEFVVPALQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFALRRR
+>PROKKA_02200
+MSTAENAGAGAPTRPDEHRAILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTHLAQ
+TLEKGLFDGLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVT
+AGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQMEHDERYEHADEY
+LDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAHEGRYFTVPGHAVTEPSVQRTPVI
+YQAGASTRGRAFAGKHAEAVFINSPTKELAAATVKKIRQALVDAGRDPYDVKIFAMQTIV
+TGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDVKSNAIQSTVETF
+QKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPG
+TFEDIVEFVVPELQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFALRRR
+>PROKKA_00184
+MAEHPAARPEQDATTSTSAATSTSPASRAGRELLFNAFDMNCVAHQSPGLWRHPEDRARD
+YNTLGYWTHLAQTLEKGLFDGLFIADVLGPYSVYGGTAEAAIRSGAQTPVNDPFLLVSAM
+AAVTGHLGFGVTAGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQM
+EHDERYEHADEYLDVVYKLLEGSWEDDAVRYDKETGVFADPAKVHDIGHEGRYFKVPGAA
+VTEPSPQRTPVIYQAGASTRGRAFAGKHAEAVFINSPTKELTAATVKKIRQALVDAGRDP
+YDVKIFAMQTIVTGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDV
+KSNAIQSAVEAFQKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDV
+DGYNLAYHITPGTFEDVVEFVVPELQKLGRYKTAYTDGTLRHKLFGRGDHLPEGHHGASF
+ALRRRG
+>PROKKA_00130
+MSTAENAGAGAPTRPDEHREILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTRLAQ
+TLEKGLFDGLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVT
+AGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQMEHDERYEHADEY
+LDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAHEGTWFKVPGHAVTEPSVQRTPVI
+YQAGASTRGRAFAGKHAEAVFINSPTKELAAATVKKIRQALVDAGRDPYDVKIFAMQTIV
+TGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDVKSNAIQSAVETF
+QKASGTDEGWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPG
+TFEDIVEFVVPELQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFAFRNRRG
+>PROKKA_00132
+MSTPTPTLGIALTTQTPADARGHWTRLSQALEETSLDWAVLTDPLGTAPQAGTHRIDAVL
+AACWTATRTHRIGLVPEVTTTHTEPFHVSIGLATLDHVSHGRAGWLATVSAAPEVSALFG
+RRRHPAERTPGLQASRVDLELWEELQDAVAAVRDLWESWEPDAEIRDIATGRFIDRERVH
+HVDVEAERFSVRGPSITPRPPQGRLPVLVEAAGPAGLEAARRTADVVLLPAAEVGRTDAA
+RLPDRRRRGATPAVPVEPTRIVADVTLEGDGARVADAVRHALQAGADGARLVPNPTADPF
+DALALAADVHDRLDDIRPPDTGTVPLRECLGLAPALSPWRHPEDPTARPTDEEATA
+>PROKKA_00207
+MSTAENAGAGAPTRPDEHRAILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTHLAQ
+TLEKGLFDGLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVT
+AGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQMEHDERYEHADEY
+LDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAHEGRYFTVPGHAVTEPSVQRTPVI
+YQAGASTRGRAFAGKHAEAVFINSPTKELAAATVKKIRQALVDAGRDPYDVKIFAMQTIV
+TGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDVKSNAIQSAVETF
+QKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPG
+AFEDVVEFVVPALQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFALRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000076.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000076.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4f5b53853861d98fc2c2c6331378fe7d9b4f4f33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000076.fa
@@ -0,0 +1,165 @@
+>PROKKA_00287
+MSGPAESAAGTATPAADVVLGRFTEPTRAWFTGAFETPTPAQLGAWDAISSGRHALVIAP
+TGSGKTLSSFLWALDSFVREPAAEGTAATRVLYVSPLKALGVDVERNLRAPLVGITQTAA
+HQGRPVPRVRVGVRSGDTPAAERRRLQQDPPDILITTPESLYLMLTSQARAALTGVRTVI
+VDEVHAVAGTKRGAHLAVSLERLDALLDAPVQRIGLSATVEPAAEVARFLGGTQPVTVVR
+PASAKRWDLTVTVPVPDLTDLSSPAAAHDLGPGSSTGGLGDEGAVTGGSIWPHVEERIVD
+LVAERRSTLVFANSRRLAERLTGRLNEIWEARAEAAAAAEHPDAVPGFRTPDPTGFHGPA
+QVAGQTGTGSGTVSDFARAHHGSVSKEQRAIVEEALKTGQIRCVVATSSLELGIDMGAVD
+QVIQVESPPSVASGLQRVGRAGHQVGEVSRGVFFPKHRGDLVDTAVVAERMTAGRIESLR
+IPANPLDILAQQTVAAVAVADLDAQEWFDLVRRSAPFATLPFSAYESVLDLLAGRYPSDE
+FAELRPRILWDRENGTLAARPGAQRLAVTSGGTIPDRGLFGVFLASDGGADGTPGGAAAG
+DTAESAGTASAGSARSGGRRVGELDEEMVYESRVGDVILLGATSWRIVDITADRVLVLPA
+YGQPGKLPFWRGDAAGRPAELGDAVGRFRRELDADPEAGRTRLGAAGLDPWAQDNLLAYL
+KDQREATGVLPTEQTLVVERFTDELGDWRVVLHSPYGMAVHAPWALAVGARLAQRYGLET
+GSGAAMAADDGIVLRIPLMDAEPPGAELFEFTAEELDEIVTAEVGGSALFAARFRENAAR
+SLLLPRRDPGRRTPLWQQRQRSAQLLDVARKHPRFPVILETVREVLQDVYDLPALKELAG
+RVSSRAVRLVEVTTTAPSPFSQSILFGYIAQFIYEGDSPLAERRAAALSLDPALLSELLG
+TEELRELLDAEVIAEVEAQLQRLAPDRRARGVEGVADLLRLLGPLSVAEAARRTRAEGEA
+EEAADEAAVAGMLAELERAGRAFRLRQDGVERFAAVEDAARLRDALGTPIPHGVPTAFLD
+PVDDPLGDLVGRYARTHGPFTAAEAGAALGLGGAVVLSVLQRLATERRVSTGAFRPEGTP
+GAASLDAEWCDAEVLRRIRMRSLAALRAEVEPVDQAAYARFLADWQHLRPRTGRDGAWRP
+PATLEGVDGVATVLDQLAGTPLPASAWESLVLPARVRDYAPALLDELLATGEYVWSGVGE
+ATGNDGWVALHPADAVDLTLRLPEPAEETPADAALRAAVLEVLAGGGAWFFPQLVERVRA
+VQAAAGDGGTGTAGGTGGPDPHRDPADLARGPAVLAALWGLVWDGRVGNDTFAPVRGLLS
+LGKTAHRTGRQTPRARTARTGGAAGAAAGRGLGGRLAGVRGRGRYAGLTSSEGGARGTAG
+LTAGTVGLSAAEQARSAGRWSLLPAAEQDPTIRAHATAELLLDRYGVITRGSVVAEEVPG
+GFAGQYRLLTRMEDAGQVRRGHFVDGLGGAQFSTGAVVDRLRGFQRDEEDAAVDTAPLAL
+ALAATDPANPYGAALDWPSVPAGPDGVVPTGHRPGRKAGAVVVLIAGRLALYMERGGRTL
+LAFTEESGELRAAAEALVWALRTGHTERLSLEKVNGGPVLGTPLAEALLAAGFYSSPSGI
+RFRN
+>PROKKA_01958
+MTTSVEGFSALDPVIQHHIVNTLRWPDLRPLQKASVASLLAGHDALLLAPTAGGKTEAAF
+FPVLTRAEREQWTGTSVLYVAPLKALLNNVESRAMEYTSWLGRSASVRHGDTTQAERRRQ
+GTERPDVLMTTPESLESMLISPTVNVTDFFSELRTIIVDEVHAFAGDDRGWHLLSVLERL
+SAVVRRPIQRIGLSATVGNPEELLTWLQGGNAAAGLPASVIAPPVDRTGAAAPELRLDFV
+GSEDNAATVISRLHGGEKRLVFAESRRTVELLGNALHERDVTTFLSHSSLSLSERRRSEQ
+AFAEAQDCVIISTSTLELGIDVGDLDRVLQLGAPSTVASFLQRLGRTGRRPGAQRNMLFL
+ELKPADLLRAAGLLLLHGEGYVEPIQPPPAPHHIVAQQILALTLQKGQLQRGAALAGLQA
+LGMSDSTTYRTIEDGLLEHGHLDSDGGLLFVGPETQRRYGGLYFRDLMAVFTVEAEFPVF
+HGRTEIGSVAPNWIATDPDDQPLLILAGRSWKVSFIDWKRHLVHVERSDRGLAPRWASPP
+RALSWALSDAMRRVLLGADPAGVVLTGRAQDALADHREAEGYTAAADHTVLASTADDLRW
+WTWGGAGANALLVAALEQVAPELLGEKLRFDNFSLRLRGDVDAASLGRALRQATSNFGGD
+LAGVDPLVDDAAVRGLKFHEMLPLDLARATLAARLADHTGVARVLERPVQMLRTAEDGRM
+WG
+>PROKKA_02309
+MSGPAETAAGAPTPAADVVLGRFTEPTRAWFTGAFEAPTPAQLGAWDAISSGRHALVIAP
+TGSGKTLSSFLWALDSFVREPAAEGTAATRVLYVSPLKALGVDVERNLRAPLVGITQTAA
+HQGRPVPRVRVGVRSGDTPAAERRRLQQDPPDILITTPESLYLMLTSQARAALAGVRTVI
+VDEVHAVAGTKRGAHLAVSLERLDALLDTPVQRIGLSATVEPAAEVARFLGGTQPVTVVR
+PASAKRWDLTVTVPVPDLTDLSSPAAAHDLGPGSSTGGLGDEGAVTGGSIWPHVEERIVD
+LVAERRSTLVFANSRRLAERLTGRLNEIWEARAEAAAAAEHPDAVPGFRTPDPTGFHGPA
+QVAGQTGTGSGTVSDFARAHHGSVSKEQRAIVEEALKTGQIRCVVATSSLELGIDMGAVD
+QVIQVESPPSVASGLQRVGRAGHQVGEVSRGVFFPKHRGDLVDTAVVAERMTAGRIESLR
+IPANPLDILAQHTVAAVAVADLDAQEWFDLVRRSAPFATLPFSAYESVLDLLAGRYPSDE
+FAELRPRILWDRENGTLAARPGAQRLAVTSGGTIPDRGLFGVFLASDGGADGAPGGAAAG
+DTAESASTASAGSARSGGRRVGELDEEMVYESRVGDVILLGATSWRIVDITADRVLVLPA
+YGQPGKLPFWRGDAAGRPAELGDAVGRFRRELDADPEAGRTRLAAAGLDPWAQDNLLAYL
+KDQREATGVLPTEQTLVVERFTDELGDWRVVLHSPYGMAVHAPWALAVGARLAQRYGLET
+GSGAAMAADDGIVLRIPLMDAEPPGAELFEFTAEELDEIVTAEVGGSALFAARFRENAAR
+SLLLPRRDPGRRTPLWQQRQRSAQLLDVARKHPRFPVILETVREVLQDVYDLSALKELAG
+RVSSRAVRLVEVTTTAPSPFSQSILFGYIAQFIYEGDSPLAERRAAALSLDPALLSELLG
+TEELRELLDAEVIAEVEAQLQRLAPDRRARGVEGVADLLRLLGPLSVAEAARRTRAEGEA
+EEAADEDAVAGMLAELERAGRAFRLRQDGVERFAAVEDAARLRDALGTPIPHGVPTAFLD
+PVDDPLGDLVGRYARTHGPFTAAEAGAALGLGGAVVLSVLQRLATERRVSTGAFRPEGTP
+GATGLDAEWCDAEVLRRIRMRSLAALRAEVEPVDQAAYARFLADWQHLRPRTGRDGAWRP
+PATLEGVDGVATVLDQLAGTPLPASAWESLVLPARVRDYAPALLDELLATGEYVWSGVGE
+ATGNDGWVALHPADAVDLTLRLPEPAEETPADAALRAAVLEVLAGGGAWFFPQLVERVRA
+VQAAGGDAGGAGRAVGPDPHRDPADLARGPAVLAALWGLVWDGRVGNDTFAPVRGLLSLG
+KTAHRTGRQTPRARTARTGGAAGAAAGRGLGGRLAGVRGRGRYAGLTSPEGGARGSAGLT
+AGTVGLSAAEQARSAGRWSLLPAAEQDPTIRAHATAELLLDRYGVITRGSVVAEEVPGGF
+AGQYRLLTRMEDAGQVRRGHFVDGLGGAQFSTGAVVDRLRGFQRDEEDAAVDTAPLALAL
+AATDPANPYGAALDWPSVPAGPDGVVPTGHRPGRKAGAVVVLIAGRLALYMERGGRTLLA
+FTEDPGELRAAAEALVWALRTGRTERLSLEKVNGGPVLGTPLAEALLAAGFYSSPSGIRF
+RN
+>PROKKA_00067
+MSGPAETAAGAPTPAADVVLGRFTEPTRAWFTGAFEAPTPAQLGAWDAISSGRHALVIAP
+TGSGKTLSSFLWALDSFVREPAAEGTAATRVLYVSPLKALGVDVERNLRAPLVGITQTAA
+GLGRPVPRVRVGVRSGDTPAAERRRLQQDPPDILITTPESLYLMLTSQARSALAGVRTVI
+VDEVHAVAGTKRGAHLAVSLERLDSLLETPVQRIGLSATVEPASEVARFLGGTQPVTVVR
+PASAKRWDLTVTVPVPDLTDLSSPSAAHDLGPGSSPGGPGAEGGPGGAVTGGSIWPHVEE
+RIVDLVAERRSTLVFANSRRLAERLTGRLNEIWEARLEAAAAVEDPDAVPGFRTPGAGAG
+AASSTPATPSSSYPAQVAGQTGTGSGTVSDFARAHHGSVSKEQRAIVEEALKTGRIRCVV
+ATSSLELGIDMGAVDQVIQVESPPSVASGLQRVGRAGHQVGEVSRGVFFPKHRGDLVDTA
+VVAERMTAGRIEALRIPANPLDILAQQTVAAVAVADLDAQEWFDLVRRSAPFATLPLSAY
+ESVLDLLAGRYPSDEFAELRPRILWDRENGTLAARPGAQRLAVTSGGTIPDRGLFGVFLA
+SDGGPDGAPGGAAAGDTAESAGSARSGGRRVGELDEEMVYESRVGDVILLGATSWRIVDI
+TADRVLVLPAYGQPGKLPFWRGDAAGRPAELGDAVGRFRRELDADPAAGRERLAAAGLDA
+WAQDNLLAYLKDQREATGVLPTEQTLVVERFTDELGDWRVVLHSPYGMAVHAPWALAVGA
+RLAQRYGLETGSGAAMAADDGIVLRIPLMDAEPPGAELFEFTAEELEEIVTAEVGGSALF
+AARFRENAARSLLLPRRDPGRRTPLWQQRQRSAQLLDVARKHPRFPVILETVREVLQDVY
+DLPALKDLAGRVASRAVRLVEVTTPAPSPFSQSILFGYVAQFIYEGDSPLAERRAAALSL
+DPTLLAELLGTEELRELLDAGIIAEVEAQLQRLAPDRRARGVEGVADLLRLLGPLSAAEA
+ARRVRPEAGADDDGGAAAADVAAVGEMLAGLERAGRAFRLRQDGVERFAAVEDAARLRDT
+LGTPIPHGVPAAFLEPVDDPLGDLVSRYARTHGPFTAAEVGAALGLGGAVVLPVLQRLAT
+ERRVSTGAFRPDGAPGATGLDAEWCDAEVLRRIRLRSLAALRAEVEPVDQSAYARFLADW
+QHLRPRVGRDGAWRPPATLEGVDGVATVLDQLAGTPLPASAWESLVLPTRVRDYAPALLD
+ELLATGEYVWSGVAEAAGNDGWVALHPADAVDLTLRLPERPDGTGPDAAAPRDAALRADV
+REVLAGGGAWFFPQLVERVRAAQSARLGTGGPDGHGADLARGPAVLEALWGLVWAGEVGN
+DTFAPVRGLLSLGKTAHRTGRQTPRARTARTGGAGAGTAGRGLGGRLAGVRGRGRYAGLA
+SPDGGARGTAGPAAGMAGLSAAEQARAAGRWSLLPAAERDPTIRAHATAELLLDRYGVIT
+RGSVVAEEVPGGFAGQYRLLTRMEDAGQVRRGHFVAGLGGAQFSTGAVVDRLRGFQDDDG
+ADAPAAPRLDAFGLPLPAAPAEQRTPAALALAATDPANPYGAALDWPSVPAGPDGVVPTG
+HRPGRKAGAVVVLIRGELALYMERGGKTLLCFTQGAAELKAAAEALVWALRTGRTERLSL
+EKVNGGPVLGTPLAEAMLAAGFYSSPSGLRYRS
+>PROKKA_00046
+MREDGGEGPAPEEAAPSPAAVPDADAVLARFSEPTRRWFTGAFAAPTAAQLGAWDAISSG
+RHALVVAPTGSGKTLSSFLWALDSFVREPAEPDVSATRVLYVSPLKALGVDVERNLRAPL
+IGITQTARSLGAPVPEVRVGVRSGDTPAAERRRLQQDPPDILITTPESLYLMLTSKARSA
+LSGVRTVIVDEVHAVAGTKRGAHLAVSLERLDALLDSPVQRIGLSATVEPAAEVARFLGG
+VQPVTVVRPVSAKRWDLTVTVPLPDMTDLSTPPPSALDAGRDGAAAGVPGEATGGSIWPH
+IEERIVDLVAPRRSTIVFANSRRLAERLTGRLNEIWEARQEAAAAVHDPDLVPGFRTPST
+AGEVLTDWLGTATGQTPAGAPRPPGGSAATSFPAQVAGQTGTGSGTVSDFARAHHGSVSK
+EQRALVEEALKTGRIRCVVATSSLELGIDMGAVDQVIQVESPPSVASALQRVGRAGHQVG
+EVSRGVFFPKHRGDLVDTAVVAERMAAGRIEALRIPQNPLDILAQQTVAAVALEDVDAEE
+WFDLVRRSAPFSALPHSAYESVLDLLAGRYPSDEFAELRPRILWDRELGELSARPGAQRL
+AVTSGGTIPDRGLFGVFLATEASDGAPGGAALGDTAESASGASSGSKRSGGRRVGELDEE
+MVYESRVGDVILLGATSWRIVDITADRVLVLPAYGQPGKLPFWRGDAAGRPAELGDAVGR
+FRRELDADPDAARDRLAAAGLDEWARENLLTYLADQRESTGRLPTEQALVVERFTDELGD
+WRVVLHSPYGMAVHAPWALAVGARLAQRYGLETGSGAAMAADDGIVLRVPLMDAEPPGAE
+LFEFSAEELEEIVTAEVGGSALFAARFRENAARALLLPRRDPGRRTPLWQQRQRSAQLLD
+VARKYPSFPVILETVREVLQDVYDLPALKDLAGRIASRAVQMVEVTTPAPSPFAQSILFG
+YVAQFIYEGDSPLAERRAAALSLDPALLAELLGTEELRELLDPEVIARVEAELQRTAPDR
+RVRGAEALADLLRIVGPLSVAEAAARTLPVEDAAPAPADEAAAGAPSAAHLAAVTAHLEG
+LERTGRAYRVRLNGEERFAAVEDAARLRDALGAPIPLGVPVAFHEPVEDPVGDLVSRYAR
+THGPFTAAEAGAALGLGGAVVLPVLQALASQRRVSQGAYRPDGTPGATGLEAEWIAAEVL
+QKVRRRSLAALRAEVEPVDQAAYARFLADWQHLRPRPGRPSPATLEGVDGVATVLDQLAG
+VPLPASAWESLVLPSRVRDYTPGLLDELLATGEYVWSGTADAPGNDGWVALHPADAVDLT
+LRRPEPPAQDVAAERLTARDHLLTVLAGGGAWFFGPLVERVRADAARAAEAEAGGEDGPR
+DPHAAAATLPRGPVILEALWDLVWAGRVGNDTFAPIRGLLSLGKTAHRTGRQTPRARTAR
+TGGAALSAAGTGGRGLGGRLAGVRGRGRYAGLAAPGSGAGAGTLPGAGLVGLSAAEEARA
+AGRWSLLPDPEPDPTIRAHAAAEVLLDRYGVITRGSVVAEEVPGGFAGQYQLLTRMEDAG
+QVRRGHFVDRLGGAQFSTGAVVDRLRSFQRDEDGPSPAEEEPAPRLDAFGMPVDESPRTD
+WSGWVADGVGGWTPAPQGHGAGMGTVGGAAGAREEPLPPALALAATDPANPYGAALDWPD
+LPAGPDGVAPTGHRPGRKAGAVVVLVHGALALYMERGGRTLLAFTQDGPVLRAAAQALVW
+ALRAARTDKLSLEKVNGGPLLGTPLAEALLAAGFYSSPSGIRYRS
+>PROKKA_00293
+MSGPAETAAGAPTPAADVVLGRFTEPTRAWFTGAFEAPTPAQLGAWDAISSGRHALVIAP
+TGSGKTLSSFLWALDSFVREPAAEGTAATRVLYVSPLKALGVDVERNLRAPLVGITQTAA
+HQGRPVPRVRVGVRSGDTPAAERRRLQQDPPDILITTPESLYLMLTSQARAALAGVRTVI
+VDEVHAVAGTKRGAHLAVSLERLDALLDTPVQRIGLSATVEPAAEVARFLGGTQPVTVVR
+PASAKRWDLTVTVPVPDLTDLSSPAAAHDLGPGSSTGGLGDEGAVTGGSIWPHVEERIVD
+LVAERRSTLVFANSRRLAERLTGRLNEIWEARAEAAAAAEHPDAVPGFRTPDPTGFHGPA
+QVAGQTGTGSGTVSDFARAHHGSVSKEQRAIVEEALKTGQIRCVVATSSLELGIDMGAVD
+QVIQVESPPSVASGLQRVGRAGHQVGEVSRGVFFPKHRGDLVDTAVVAERMTAGRIESLR
+IPANPLDILAQHTVAAVAVADLDAQEWFDLVRRSAPFATLPFSAYESVLDLLAGRYPSDE
+FAELRPRILWDRENGTLAARPGAQRLAVTSGGTIPDRGLFGVFLASDGGADGAPGGAAAG
+DTAESASTASAGSARSGGRRVGELDEEMVYESRVGDVILLGATSWRIVDITADRVLVLPA
+YGQPGKLPFWRGDAAGRPAELGDAVGRFRRELDADPEAGRTRLAAAGLDPWAQDNLLAYL
+KDQREATGVLPTEQTLVVERFTDELGDWRVVLHSPYGMAVHAPWALAVGARLAQRYGLET
+GSGAAMAADDGIVLRIPLMDAEPPGAELFEFTAEELDEIVTAEVGGSALFAARFRENAAR
+SLLLPRRDPGRRTPLWQQRQRSAQLLDVARKHPRFPVILETVREVLQDVYDLPALKELAG
+RVSSRAVRLVEVTTTAPSPFSQSILFGYIAQFIYEGDSPLAERRAAALSLDPALLSELLG
+TEELRELLDAGVIAEVEAQLQRLAPDRRARGVEGVADLLRLLGPLSVAEAARRTRAEGEA
+EEAADEDAVAGMLAELERAGRAFRLRQDGVERFAAVEDAARLRDALGTPIPHGVPTAFLD
+PVDDPLGDLVGRYARTHGPFTAAEAGAALGLGGAVVLSVLQRLATERRVSTGAFRPEGTP
+GATGLDAEWCDAEVLRRIRMRSLAALRAEVEPVDQAAYARFLADWQHLRPRTGRDGAWRP
+PATLEGVDGVATVLDQLAGTPLPASAWESLVLPARVRDYAPALLDELLATGEYVWSGVGE
+ATGNDGWVALHPADAVDLTLRLPEPAEETPADAALRAAVLEVLAGGGAWFFPQLVERVRA
+VQAAAGDGGTGAAGGAVGPDPHRDPADLARGPAVLAALWGLVWDGRVGNDTFAPVRGLLS
+LGKTAHRTGRQTPRARTARTGGAAGAAAGRGLGGRLAGVRGRGRYAGLTAPEVGARGSAG
+LTAGTVGLSAAEQARSAGRWSLLPAAEQDPTIRAHATAELLLDRYGVITRGSVVAEEVPG
+GFAGQYRLLTRMEDAGQVRRGHFVDGLGGAQFSTGAVVDRLRGFQRDEEDAAVDAAPLAL
+ALAATDPANPYGAALDWPSVPAGPDGVVPTGHRPGRKAGAVVVLIAGRLALYMERGGRTL
+LAFTEEPGELRAAAEALVWALRTGRTERLSLEKVNGGPVLGTPLAEALLAAGFYSSPSGI
+RFRN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000077.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000077.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e6d0a4b07bbcc351c5fea6c5bc795f829194b09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000077.fa
@@ -0,0 +1,50 @@
+>PROKKA_00297
+MLSEKSRPVIEATAAAVAEHMPEITPLFYAHMFEAHPELLDGVFSRANQRNGEQAQALAG
+SIVKFAVHLLENPGTLPEAVLSRIAHKHTALGIVEEQYPIVYENLFWAIGEVLGDAVTPE
+VADAWTEVYWLMADALIKIEKGLYAQQANDRMWTDWKVVAKEPTGNAAVTFRFEPADDTP
+QSRGKAGGYVSVRLKVEDGLRQCRQYSLSEKAESATERVITVKLDEGGEVSPMLIQNVEV
+GDVIELSNPYGDITLEDEDSTAPLVLATAGIGITPAAAILDALAQQGSDRQVLLLHGDAS
+WEAVALREQVTESLAALAHGDARLFLGVRPEQDPEGVTTVEGVMHFDDVELPRDGHYILC
+GPLAFMQSTRSKLIDAGVPATSIRYEIFGPDLWLAA
+>PROKKA_00005
+MLSEKSRPVIEATAAAVAEHMPEITPKFYAHMFEAHPELLDGLFSRANQRNGEQAQALAG
+SIVRFAVHLLENPGTLPEAVLARIAHKHTALGITEDQYQIVYENLFWAIADVLGDAVTPE
+VAEAWTEVYWLMADALIKLEKGLYAKQANDKMWLDWKVVSKEPTGNAAVTFRFEPADDTP
+QTPGEAGGFVSVRVKVADGLRQARQYSLSDHAASTTERVITVKLDEGGEVSPMLIQNVEV
+GDVIELSNPYGDITLEDEDSTAPLVLATAGIGITPAAAILDALAQQGSDRQVLFFHGDAS
+WEAVALREQVTESLAALPHGDARLFLGVRPEQDPEGVTTVEGVMHFDDVELPRDGHYILC
+GPLAFMQSTRSKLIDAGVPATSIRYEIFGPDLWLAA
+>PROKKA_00057
+MLSEKSRPVIEATAAVVAEHMPEITPKFYAHMFEAHPELLDGVFSRANQRSGEQAQALAG
+SIVTFAVHLLEHPDTLPEAVLARIAHKHTALGIVPEQYQIVYENLFWAIADVLGEAVTPE
+VAEAWTEVYWLMADALIKIEEGLYAQQANTKMWTDWKVVAKEPTGNAAVTFRFAPADETP
+QTPGRPGGYLSVRLKVEDGLRQCRQYSLSDHAESTDERVITVKLDEGGEVSPVLIQNVEV
+GDVIELSNPYGDITLRDDAETPLVLATAGIGITPAAAILDTLASRGSQREVHFFHGDASW
+DSVALREQVAESLQALENGTGRLWLGVPPQEAPAAFTTTEGLMEFDDVELPADASYLLCG
+PLAFMQATRSKLIDAGVPATSIRYEIFGPDLWLAA
+>PROKKA_00035
+MLSEKSRPVIEATAAVVSANMPQITPAFYGHMFEAHPELLDGTFSRANQLNGEQAQALAG
+SIVHFAAHLLEHPDSLPEAVLARIAHKHTALGITEDQYQVVYENLFWAIAQVLGDAVTPE
+VAEAWTEVYWLMADALITLEKDLYAVQANDRMWTDWKVVAKEPTGNAAVTFRLEPADDTP
+QTPGRPGGYVSVRVTVADGLRQARQYSLSESASSTGQRVITVKLDEAGEVSPVLIQEVEV
+GDVVELSNPYGDITLQDSDAPLVLMTAGIGITPAAAILDSLAASGSQREVRVLHGDASWD
+SVALRDQVLEDVASLPHAQADLWFGVAPETAPEGVSVHEGKVDTAAAALPEGADYILCGP
+LAFMKSERSALIEAGVPAPRIRYEIFGPDLWIAAT
+>PROKKA_01222
+MPAHGWGARAGRTSFREHPVDVQECLWRGAHASSHDRSALHSRPSRGGSADPAPADRPPP
+PLTPAPGPAGIRDRPAGRIPAWWRDASGSLLWLVLLAVTALWVHGGGVQDLAAVGSGLTS
+LGRLTGLIASALLLAQVFLMARVPLVEQAWGQDRLTRVHRRVGFTSFTLMFAHLALITAG
+YAWDTPAGLWGTLVDFAVDYPGMLLAIAGTAALVMVVVTSFKAARARLRYESWHLIHLYG
+YLGAGLALPHQLWTGQEFLASPVATAFWWTLWAVTAGAVVVFRALLPLWCSARAGLRVQS
+VTAAGPHAVTVTVAGRGAHRLHARGGQFFQWRFLDGPGWTRAHPYSLSAAPDGRTLQFTA
+AVVGDGTGRLWDMRPGTRVLVEGPYGRMHDGVRTGRKALLMGAGIGITPMKALLESLPAD
+AGEITVVHRVSDPDDPTLHADLLAAARTRGARYIRLEGRRRPGADSWLPASAGDVDDVTA
+LRRICPDLAEHDVFVCGAPAWTDLVRQAARRGGVPAERIHDERFSF
+>PROKKA_00304
+MLSEKSRPVIEATAAVVAEHMPEITPLFYAHMFEAHPELLDGVFSRANQRNGEQAQALAG
+SIVKFAVHLLENPGTLPEAVLSRIAHKHTALGIVEEQYPIVYENLFWAIGEVLGDAVTPA
+VADAWTEVYWLMADALIKIEKGLYSQQANDRMWTDWRVVAKEPTGNAAVTFRFEPADDTP
+QSRGRAGGYVSVRLKVEDGLRQCRQYSLSEKAESTTERVITVKLDEGGEVSPMLIQNVEV
+GDVIELSNPYGDITLEDEDSTAPLVLATAGIGITPAAAILDALAQQGSDRQVLFFHGDAS
+WEAVALREQVTESLAALPHGDARLFLGVRPEQDPEGVTTVEGVMHFDDVELPRDGHYILC
+GPLAFMQSTRSKLIDAGVPATSIRYEIFGPDLWLAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000081.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000081.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07ad521af40a4ca4f1f5a793a8f976d46e825674
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000081.fa
@@ -0,0 +1,72 @@
+>PROKKA_00366
+MSMESAARMSMMRMTRGQSDAQQSLARGTVRRTIAFAGRYRTRLIVFVAASIVGAVLGVA
+SPVLAGDVVNAITGGADRGLVVRLALLIALVAVLDAALSVFTKWLSSGLGERVIYDLRTA
+VFDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANVVSVALTLGVMVAT
+SWQVTVLSLVMLPLFLVPARAVGSKLADLSRERAGHNAAMGDQMTERFSAPGATLIKLFG
+RPAAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDA
+GDVVTLALLLTRLYAPLTALANARVEIMSALVSFERVFEVLDLEPLITEPARPAALPEGP
+LSVRLRDVRFAYPTAEQVSLASLEEVAVLDTRGGEEVLHGIDVAVPAGATVALVGSSGAG
+KSTIASLVTRLHDVTSGAVEIGGVDVRDLAFADLQRAVGMVTQDGHLFHETVRANLTLAR
+PDATDEELWDAVERARLRPVVEALPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVV
+VLDEATAALDSTNERAIQEALGEALAGRTAIVIAHRLSTVRSADEILVVEAGRIVERGTH
+AALLAADGRYAELYTTQFADAE
+>PROKKA_00082
+MSMESAARMSMMRMTRGQSDAQQSLARGTVRRTIAFAGRYRTRLIVFVAASIVGAVLGVA
+SPVLAGDVVNAITGGADRGLVVRLALLIALVAVLDAALSVFTKWLSAGLGEQVIYDLRTA
+VFDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANVVSVALTLGVMVAT
+SWQVTVLSLVMLPLFLLPARAVGSKLAGLSRERAGHNAAMGDQMTERFSAPGATLIKLFG
+RPAAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDA
+GDVVTLALLLTRLYAPLTALANARVEIMSALVSFERVFEVLDLEPLITEPARPAALPEGP
+LSVRLRDVRFAYPTAEQVSLASLEEVAVLDTRGGEEVLHGIDVAVPAGATVALVGSSGAG
+KSTIASLVTRLHDVTSGAVEIGGVDVRDLAFADLQRAVGMVTQDGHLFHETVRANLTLAR
+PDATDEQLWDAVERARLRPVVEALPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVV
+VLDEATAALDSTNERAIQEALGEALAGRTAIVIAHRLSTVRSADEILVVEAGRIVERGTH
+AALLAAGGRYAELYTTQFADAE
+>PROKKA_00193
+MAPARLDPADRTQLRRHPVSLRRIARLFAPHRSTIALVVVLISAASVINLAQPFLVRAVI
+DDALPNQDVPLLIRLTAAMVGVAALTAVIGVVQTWRATAMGQHVMHSLRVRLFTHLQAQP
+LAFFTRTRGGEVQSRLTHDIAGMQSVVTSTATGVASNLTAVVATAAAMVALSPRLSLISL
+VVLPPAVWLSRRVAQLRRAVTDKRQAALAQMHTQVEEGLSVSGARLSKTLGTTGHDAERF
+TGRSHELIGLELRSQLAGRWRMATMSIVFAAIPAVIYLAAGLPPTSGGMTIGTLVAFTAL
+QGQVFRPVMGLLNIGVQWVTALAFFSRIFEYLDLDPAIKPPADPVPVDPARVRGTVRFEG
+VDFAYDDGAPALSGIELTVPAGTTTAVVGSTGSGKSTLASLVPRLHDPTAGRVSIDGIDV
+ARLDPADLAAIVGVVSQETYLIHASVRDNLRLADPEATDERLWAALETASLARTVAALPE
+GLDTLVGARGHRFSGGEQQRLAIARTVLRNPPVLVLDEATSALDNTTEARVQAALDELAE
+HRTTLLVAHRLSTVMGADQVAVLEGGRIVELGAPTELLRAGGPFAALAARGDAVVPGAAP
+AEPALAR
+>PROKKA_02595
+MESAARVSMMRMTHGQNGATQPLAKGTVRRTIAFADRYRARLIVFVLASIVGAVLGVASP
+VLAGDVVNAITGGDDGGLVVRLALLIALVAVLDAALSVFTKWLSSGLGERVIFDLRTQVF
+DHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANVVSVALTLGVMVATSW
+QVTVLSLLLLPLFLIPARAVGSKLAGLSRERAGHNAAMGDQMTERFSAPGATLIKLFGRP
+AAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDAGD
+VVTLALLLTRLYAPLTALANARVEIMSALVSFERVFEVLDLQPLIIEPARPAALPAGPLS
+VRLRDVRFSYPTAQEVSLASLEEVAVLDTRGGEEVLHGIDVAVPAGSTVALVGSSGAGKS
+TIASLVTRLHDVSSGAVELGGVDVRDLSFADLQEAVGMVTQDGHLFHDTVRGNLLLARPD
+ATEEQLWDAVERARLRPVIEALPDRLDTVVGERGYRLSGGERQRMTIARLLLAAPRVVVL
+DEATAALDSTNERAIQEALGEALTGRTAIVIAHRLSTVRSADEILVVEAGRIVERGGHAE
+LLAAGGRYAELYTTQFADAE
+>PROKKA_02454
+MSMESVARVSMMRLQRGGTAPQPLAPGTVRRTVAFAAQYRARLIVFVAASVVSAVLGVAS
+PVLAGDVVNAITGGTDRALVVRLALLIAAVALADAALSVFTKWLSSGLGERVIYDLRTRV
+FDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANAVSLALTLAVMLATS
+WQITLLSLVLLPLFLVPARMVGGRLAALSRERAGHNAAMGDQMTERFSAPGATLIKLFGE
+PGAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDAG
+DVVTMALLLTRLYAPLTSLANARIEIMSALVSFERVFEVLDLEPLITEPAHPVPVPDGPL
+AVTLDDVHFAYPSAQEVSLASLEEVAVLDTRGGEEVLHGVDVDVPAGRTVALVGSSGAGK
+STIASLVTRLYDVTSGAVRLGGVDVRDMAFADLHRAVGMVTQDGHLFHDTVRGNLLLARP
+AATDAEVWDAVDRARLRGVVESLPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVVV
+LDEATAALDSTNERAIQEALREALAGRTAVVIAHRLSTVRDADEILVVEGGRIVERGPHA
+ALLAAGGRYAELYTTQFAEGA
+>PROKKA_00373
+MSMESAARMSMMRMTRGQSDAQQSLARGTVRRTIAFAGRYRTRLIVFVAASIVGAVLGVA
+SPVLAGDVVNAITGGADRGLVVRLALLIALVAVLDAALSVFTKWLSAGLGERVIYDLRTA
+VFDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANVVSVALTLGVMVAT
+SWQVTVLSLVMLPLFLLPARAVGSKLAGLSRERAGHNAAMGDQMTERFSAPGATLIKLFG
+RPAAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDA
+GDVVTLALLLTRLYAPLTALANARVEIMSALVSFERVFEVLDLEPLITEPARPAALPEGP
+LSVRLRDVRFAYPTAEQVSLASLEEVAVLDTRGGEEVLHGIDVAVPAGATVALVGSSGAG
+KSTIASLVTRLHDVTSGAVEIGDVDVRDLAFADLQRAVGMVTQDGHLFHETVRANLTLAR
+PDATDEQLWDAVERARLRPVVEALPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVV
+VLDEATAALDSTNERAIQEALGEALAGRTAIVIAHRLSTVRSADEILVVEAGRIVERGTH
+AALLAAGGRYAELYTTQFADAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000089.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000089.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f832a4e0e3aeb29e9b38b540fa1a7e6fff3596de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000089.fa
@@ -0,0 +1,48 @@
+>PROKKA_00509
+MIPEAARTTPAPLTLWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFAALGPGRARQRAGAP
+ALLSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPI
+TVVRNGVDVPAVRAAAAGQRRTPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRL
+TLAGAGPLEGELRAQAEALGVAEAVDLPGFVEPWETMAEHDVLVQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVHETTPAAIADAVVRAAADGPGEVRVGDVETMARATA
+EATLEVLGRRVGKVGTR
+>PROKKA_00229
+MIPEDATTTPAPLTLWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLCPAAVHTHLAYADLAAFTALGAGRALRRAGAP
+ALLSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPL
+TVVRNGVDVPAVRAAAAGRRRAPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRV
+TLAGSGPLEGQLRAQAEDLGVADAVHLPGFVEPWGTMAEHDVLVQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVRETTPEAIADAVVRAAAEGPGEVRVGDVETMARATA
+EATLEVLGRRVGKGGHR
+>PROKKA_01218
+MTRRLLLFANSFPYGKQEPYLMRECHYLDAFDEVYIFSLSIRKHQRDHRRDLPLERVTVV
+PIPFKSPLFYAAVSPRALVSRAFVTELRQLLRDRRFTVARAVQALSQFSRAEHEASVIGR
+FLRDNITPSPSDETVFYAYRFLYQPYLMSRLAAKFSSSRLIGRAHGIDLFEERQSTDYLP
+GRAINLGALDELHSVSRAGAEYLRARHPEFVEKIKVSYLGTEDHGVRPPRSSSQVLRLVS
+CSEVAPVKRLELLVEALREVSDSIQVEWSHYGEGPDMDRVRAMASTLPGHVSATFHGWTR
+NDEILEAYRSGRHDVFINVSSSEGLPVSIMESSSCGLPTIATDVGGTGEIVSDGVNGRLI
+SANPMPREIAAAVEEFARMAPEAFARRSAAARETWSTHFDSDRNYRQFVAKMLS
+>PROKKA_02441
+MTPEAATTTPAPLTLWVVPVADLGGVARHVLDVAAHGLPGLRLVVLCPEGALAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFTAFGPGRARRRAGAP
+ALVSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGTGAPI
+TVVRNGVDVSAVRAAAAGQRRAPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRL
+TLAGVGPLEGQLRAQAEALGVADAVDLPGFVEPWGAMAEHDVLVQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVHETTPAAIADAVMRATVEGPGEVRVGDVETMARATA
+EATLEVLGRRAGKTSG
+>PROKKA_02325
+MIPEAATTTPAPLTLWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFTALGPGRARRRAGAP
+ALLSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPL
+TVVRNGVDVSAVRAAAAGQRRAPGEGLRILSLSRLAPEKGLDRLIAALPALRERDPGTRL
+TLAGSGPLEGQLRAQAEDLGVADAVDLPGFVEPWETMAEHDVLVQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVHETTPAAIADAVTRAAAEGPGEVRVDDVEGMAEATA
+RAERDVVETQDARRRKTR
+>PROKKA_00508
+MIPEAARTALAPLTLWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFAALGPGRARRRTSAP
+ALLSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPI
+TVVRNGVDVPAVRAAAAGQRRTPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRL
+TLAGSGPLEGQLRAQAEALGVAEAVDLPGFVEPWETMAEHDVLAQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVRETTPAAIADAVVRAAADGPGEVLVGDVETMARATA
+EATLEVLGRRVGKAGTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000091.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000091.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b2fafe96bce704ea4fa9b697aa601b6caab2d883
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000091.fa
@@ -0,0 +1,32 @@
+>PROKKA_00547
+MHPDDAPTPDLTWLDSAGSTQDELLARLDREGHRHGAAVATADQRAGRGRHSRVWSAAPG
+AALALSVYLRPESGGVPVSPAHLSWLSLVASATVAERLAARGVPTHVKWPNDVLATDGRK
+LCGVLATVALSSDGKGPGVVVGMGVNLDHRGAAPVDTATDLAEWIGADAVPAPRDLAVEL
+RDAVVAAVDRFAAGVAGQAAAVDGRHPAVAAVADRLSTLGRAVRAELPGGGVLEGTAVGL
+GPGGTLRVKRVTPDRGTIETEVSAGDVAHLRGDVHRGA
+>PROKKA_00272
+MHPDDAPTPDLTWLDSAGSTQDELLARLDREGHRHGAAVATADQRAGRGRHSRVWSAAPG
+AALALSVYLRPESGGVPVSPAHLSWLSLVASATVAERLAARGVPTHVKWPNDVLATDGRK
+LCGVLATVALSSDGKGPGVVVGMGVNLDHRGAAPVDTATDLAEWIGADAVPAPRDLAVEL
+RDAVVAAVDRFAAGVAGQTAAVDGHHPAVAAVADRLSTLGRAVRAELPGGGVLEGTAVGL
+GPGGTLRMRHVTPDRGTIETEVSAGDVAHLRGDVHRGA
+>PROKKA_02399
+MGVNLDHRGAAPVATATDLAEQIGAEAVPAPRGLAAALRDAVVGAADRFAAAVAGEAEAV
+DGRHPAVAAVTQRLSTLGREVRAELPGGDVLEGTAVALGPGGALRVSHVTADRGRIETEV
+SAGDVAHLRGDVHRGA
+>PROKKA_02400
+MHAPHDPAAPGLVWLDSAGSTQDEVLARVGREGPRHGLAVATADQRAGRGRHSRVWSAAP
+GAALALSVHLRPAAGGTPLAPVHLSWLSLVASAAVVEHLAGLGAAAHLKWPNDVLAPDGR
+KLCGVLATVAPAADGGGPGWSWAWG
+>PROKKA_02283
+MGYTWGMGTLLWLDAADSTQDELLRRLAAADGAARPGHGDGVGTADQRAGRGRHGRAWQA
+PPGAALALSVHLRPTGPSGPLAPAHLSWLSLVASAAVARRLVGLGVPAHLKWPNDVLDAE
+GRKLCGVLATLAPAPVFPGADAGETPGVVVGMGVNVDLSSGRPVPTAAALTDHLPGAEVP
+APRDLAQALLRDVAAAADRLARDLDGVVEPVDGTHPALAEVAAVLSTPGRRIRAELPGGE
+VLEGVATGLGAGGVLAVRVVTGERETITREISAGDVVHLRGDVRRGG
+>PROKKA_00550
+MHPDDAPTPDLTWLDSAGSTQDELLARLDREGHRHGAAVATADQRAGRGRHSRVWSAAPG
+AALALSVYLRPESGGVPVSPAHLSWLSLVASATVAERLAARGVLTHVKWPNDVLATDGRK
+LCGVLATVALSSDGKGPGVVVGMGVNLDHRGAAPVDTASDLAEWIGADAVPAPRDLAVEL
+RDAVVAAVDRFAAGVAGQTAAVDGRHPAVAAVADRLSTLGRAVRAELPGGGVLEGTAVGL
+GPGGTLRVKHVTPDRGTIETEVSAGDVAHLRGDVHRGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000093.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000093.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca977cd138120aa161b66289e6120b56d465ed23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000093.fa
@@ -0,0 +1,33 @@
+>PROKKA_00604
+MPKMSGIETAFCRSALWGRFARDIIVPWSLGGQDLGGDVLELGAGSGQMAAALLQRSPGM
+RLTLTDIDERMVATARRRFPTSPRLTVQQADSTALPFAESSFDVVLSFLMLHHVVNWKAA
+VAEAARVLKPGGMLIGYDLTAWSSPS
+>PROKKA_02174
+MSQNPLPAPRGDAQRGAADHHDRVSAMFDAIAGRYDLMNAVMTWGQEPRLVRRTVARANI
+PAQARVLDLATGTGDLAFEVLKQHPDAQVVGADIAAEMMEVGRARAGGDRIEWVVADATD
+LPFEAGSFDAVTHGYLLRNVADIPATLAEQFRVLRPGGWVAALETSPAPDNVLKPFSSFY
+IHRVMPQLAKLIADRPEAYAYLSSSTKAFHTPDEVADLFAEAGFVNIGHETHMFGTLATH
+WAMKPVD
+>PROKKA_01888
+MSQNPLPAPRGDAQRGAADHHDRVSAMFDAIAGRYDLMNAVMTWGQEPRLVRRTVARANI
+PAQARVLDLATGTGDLAFEVLKQHPDAQVVGADIAAEMMEVGRARAGGDRIEWVVADATD
+LPFEAGSFDAVTHGYLLRNVADIPATLAEQFRVLRPGGWVAALETSPAPDNVLKPFSSFY
+IHRVMPQLAKLIADRPEAYAYLSSSTKAFHTPDEVADLFAEAGFVNIGHETHMFGTLATH
+WAMKPVD
+>PROKKA_00578
+MFDAVAERYDLMNTVMTWGQEPRLVRHTVARANVPAHGRVLDLATGTGDLAFEVLRQHPD
+ATVVGADISAEMMEVGRRREGGDRVEWVVADAQDLPFEDASFDSVTHGYLLRNVADIPAA
+LAEQFRVLRPGGWMAALETSPPPANIIRPFSTFYMHQVMPRLARVITDKPEAYEYLSSST
+KAFHAPEEIADMLAHAGFVNIGHETHMFGTLATHWAMKPVA
+>PROKKA_00505
+MSETSPSPLPRPASLAHDADHGARVSGMFDAIAGRYDLMNTVMTWGQEPRLVRRTVERAN
+VPAAARVLDLATGTGDLALEILKQHPDAHVVAADFAPEMMEVGRTRPNGDRIEWVEADAL
+ALPFADGEFDSLTHGYLLRNVANIPAALAEQFRVLRPGGWVAALETSPAPDNLIKPFSSF
+YMHRIMPRLARLITDRAEAYEYLSSSTRAFHTPEEIAGMLADAGFVNIGHELHMFGTLAT
+HWAMKPLD
+>PROKKA_02119
+MSQNPLPAPRGDAQRGAADHHDRVSAMFDAIAGRYDLMNAVMTWGQEPRLVRRTVARANI
+PAQARVLDLATGTGDLAFEVLKQHPDAQVVGADIAAEMMEVGRARAGGDRIEWVVADATD
+LPFEAGSFDAVTHGYLLRNVADIPATLAEQFRVLRPGGWVAALETSPAPDNVLKPFSSFY
+IHRVMPQLAKLIADRPEAYAYLSSSTKAFHTPDEVADLFAEAGFVNIGHETHMFGTLATH
+WAMKPVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000095.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000095.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2fec1fb842a639ff458bd79e5a251ac7050cac94
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000095.fa
@@ -0,0 +1,42 @@
+>PROKKA_00611
+MTSTDPTPAKAASAPNRQRRAKIIVWVVLAALVLAGVVAFFAARAPSTPEAAPAQAGQAA
+SSGTGQTAASEAAPVVRPDSRVLSQAPNEKAVLVEFLDFECEGCKAAHPVVEELRAEYAD
+TVTFVHRYFPLPGHPNSMTAAVAVEAAAQQGAYEAMYQKMFDTQEQWSHTGQDRSPVFRG
+YAEDLGLDMTAYDKAVADPATRARIEADVADGVALGVQGTPTFFLDGQVLTLNTLEQFRA
+EVDAAASN
+>PROKKA_00327
+MSTPTRNPTPSDPSTPGTTSRKAKTIVWVVLAAVVLAGLIVGVVAASGPRDAAPQGSGQT
+ASSGTGQSAPSEATPVMRPDSRVLSKAPNEQAVLVEFLDFECEGCKAAYPVVEELRAEYA
+DTVTFVHRYFPLPGHPNSMTAAVAVEAAGQQGQYEAMYQQMFDTQEQWSHTTEDRSPVFR
+GYAEDLGLDMAAYDAAVADPATRDRIEADVADGTALGVQGTPTFFLDGQMLTLNTLEQFR
+AEVDAAATTD
+>PROKKA_01771
+MTSPDPTASTPSSPTPSRQRRAKIVVWVLLGLVVAAALIGYLVARGTATAQQQDPNQSTA
+QSTGQSTGSAGQLVRENSRVLSQAPNEKAVLVEFLDFECEACAAAYPFVEDLRAEYADTV
+TFVHRYFPLPGHPNSVTAAIAVEAAAQQGAYESMYQKMFETQTEWSHTTEDRSPVFRAYA
+EELGLDMAAYDAAVADPATRDRVELDVADGTALGVAGTPTFYLDGEPLTVNSLEEFTAAV
+EAATQD
+>PROKKA_02344
+MSTPTRNPTPANSSTSGTTSRKAKTIVWVVLAAVVVAGVIAGVVAVGAARNATPDAAATQ
+AGQSAAQGSGPTTAEEAGELVVRPNSRVLSKAPNEQAVLVEFLDFECEGCGAAYPVVEEL
+RAEYADTVTFVTRYFPLPGHRNAMPAAVAVEAAAQQGEYEAMYQRMFETQAQWGEATEDK
+SPVFRGYAEELGLDMAAYDKAVADPATRARVEADVADGIALGVQGTPTFFLDGEMLTLTS
+LEQFRAEVDAAASN
+>PROKKA_01190
+MSWRTIRTEAGSAVLLVVVTAVALLWANSPLSEAYFGLWDVEIGFDVGGFGLHMNLHHWI
+NDGLMMTFFLVVGLEVRQEFAHGTLRDASRARLALIAGVVGVALPAVFYILIVAAAGGEG
+LGGWGAVVGTDTAFLLGALALVGPKLSGQLRVFLLTLTVVDDFLAVSIIGIVYSDEIRLV
+PLLIAGACLVGLWLLGRSRQWSATPYVLIVIVLWFATVESGVHASLAGMVAGLLIPAYPT
+RRQQVVEARQLFRDFWQSPSAASARAVDRGLAQGISVNERMHEVLRMPTALVIVPIFALA
+NAGVDLRGGVLVDSFQSSVTWGVIVGLVLGKLLGIGLATFVAVKLGAGRLPEGVGMGSVF
+GGAALSGIGFTVSLLVIGLAFGSTSDLGRQATVGVLVAMVLATALGWLIFRVAAKRWGEE
+TADLPMVLTPPVDPEVDHIRGPEDAQLTLVEYIDFECAYCAHATGSWDDLRSRFGDDLRY
+VVRQLPHHPHGPLAARASEAASNQGMFWPWLDFVFTRQDALEREDLIRYAEELGLDVAQF
+TADLDSAAVGARVERDLESADASGAHATPTFFVDGRRLLGSYDARTLTSALEASRRGTRT
+QEVRS
+>PROKKA_02008
+MSTPTRNPTPSDPSTPGTTSRKAKTIVWVVLAAVVLAGLIVGVVAASGPRDAAPQGSGQT
+ASSGTGQSAPSEATPVMRPDSRVLSKAPNEQAVLVEFLDFECEGCKAAYPVVEELRAEYA
+DTVTFVHRYFPLPGHPNSMTAAVAVEAAGQQGQYEAMYQQMFDTQEQWSHTTEDRSPVFR
+GYAEDLGLDMAAYDAAVADPATRDRIEADVADGTALGVQGTPTFFLDGQMLTLNTLEQFR
+AEVDAAATTD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000099.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000099.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e06432eb7b50f0333a67b088d2d7e0925bd5aef2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000099.fa
@@ -0,0 +1,34 @@
+>PROKKA_00630
+MNSGTGTGTDTGTGPAAGRVLVVDDEKPLARMVATYLERAGYEVALTHTGPAAVQAARVH
+EPDVIVLDLGLPGLDGIEVCRRVRAFSECYVLMLTARGDEHHRLEGLAVGADDYITKPFS
+VRELVARVGAVMRRPRTTVSAPEPERVCGDLVIDLAAHEARVSGQVVQLTRTEFDLLAAL
+SGRPHQAFSRRQLIDIVWDPAWVGDERLVDVHIKNLRRKLDADPARYIDTVRGVGYRMAE
+Q
+>PROKKA_00402
+MNSGTGTGTDTGTGPAAGRVLVVDDEKPLARMVATYLERAGYEVALTHTGPAAVQAARVH
+EPDVMVLDLGLPGLDGIEVCRRVRAFSECYVLMLTARGDEHHRLEGLAVGADDYITKPFS
+VRELVARVGAVMRRPRTTVSAPEPERVCGDLVIDLAAHEARVSGQVVQLTRTEFDLLAAL
+SGRPHQAFSRRQLIDIVWDPAWVGDERLVDVHIKNLRRKLDTDPARYIDTVRGVGYRMAE
+Q
+>PROKKA_00452
+MTGPDLLLIEDDDRLGPLLRDLLSLDWEVTWSPTLAAARAELDRRLFAVLVVDRGLPDGD
+GVDLVRELRARGVAVPALLLTAYGELEDRVHGLDAGANDYLVKPFEVAELQARLRALTRD
+YSGRGAGVEIGSWMFYPDNRTVESPYTGRILLTEKESALLAVLASAPDTAFTRAHLLSAV
+FEHGEQEGTVDTYVHYLRRKTDRSLVETVRGVGYRLGTPT
+>PROKKA_01060
+MARLLMLTRAASAVEVLPALDLLTHDVERADPRAALAAGREDVDGVLLDATSGLAEARTL
+ARDLASLAPEVPVVAVMAEGALTAVGPEWSLADIVLTGAGPAEVDARVRLLRPADAPVAG
+GAAERLAVGGVEIDPVGYRARLDGRALNLTFREFELLKHLAQSPGRAFSREQLLREVWGD
+DYFGGTRTVDVHVRRLRAKLGPDREQMIGTVRNVGYRFTPRPDGDA
+>PROKKA_02199
+MNSGTGTGTDTGTGPAAGRVLVVDDEKPLARMVATYLERAGYEVALTHTGPAAVQAARVH
+EPDVMVLDLGLPGLDGIEVCWRVRAFSECYVLMLTARGDEHHRLEGLAVGADDYITKPFS
+VRELVARVGAVMRRPRTTVSAPEPERVCGDLVIDLAAHEARVSGQVVQLTRTEFDLLAAL
+SGRPHQAFSRRQLIDIVWDPAWVGDERLVDVHIKNLRRKLDADPARYIDTVRGVGYRMAE
+Q
+>PROKKA_00601
+MNSGTGTGTDTGTGPAAGRVLVVDDEKPLARMVATYLERAGYEVALTHTGPAAVQAARVH
+EPDVIVLDLGLPGLDGIEVCRRVRAFSECYVLMLTARGDEHHRLEGLAVGADDYITKPFS
+VRELVARVGAVMRRPRTTVSAPEPERVCGDLVIDLATHEARVSGQVVQLTRTEFDLLAAL
+SGRPHQAFSRRQLIDIVWDPAWVGDERLVDVHIKNLRRKLDADPARYIDTVRGVGYRMAE
+Q
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000104.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000104.fa
new file mode 100644
index 0000000000000000000000000000000000000000..330c23f16aff9b511975293a4e951cb0c4a07ff4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000104.fa
@@ -0,0 +1,115 @@
+>PROKKA_00731
+MAWSVRILGGAAPETWRVEHFPADADEQDRAVRERFPARSLHRCAAGPRSVTYAERVGSA
+PARGPELAVVTEHGPDAGRLVPLGEGGLSTGRGGARLLLDDPSAPSRPMRLRLAPTGLHV
+HDGPRDTGRLWDGRSPLPVGRTALGLVRGPGAALPRPVTPEPPAVDLGSPPARQSVVIPL
+VAALGPLVLGVALVLMMGNPVFLLFGVLSVTVALVMLAMQRRTRLRHARLLAARADALVR
+RRAQAALSPGAVARAVRSGATDRFGLTSGADEAVAVSWGSGVGALSLSRDDPDEAWVEAV
+TSRRTVMTTSPPESRVVVLGPPRDVAGACRWAVFQLLRHAVAADGAFVVEAGGVRRTWWS
+GGSGPRLLVSAPEDAALDPAWRAWRAAIGGDAGTTPTARADLPWTRYDFTGPSPAPGDAV
+VDLRGRTVVVPAEQQRFEDVTADGLADGTLVAWLTELADDVVDLGLLPADDGDGTLTPPG
+QVGARDAVDGLTVTLARSGDETGVVEMDLAADGPHLLIAGTTGSGKSDLLLSLLLGAAAH
+HPPAEVAFLLLDFKGGASFGPLGALPHTMSLETNHVGTASLRALSAIRAELHRREALFAE
+AGVSDYPGFRRRHPDAALPRLVVAIDELRVLVDDHPDAAAVLQRLAATGRSLGFHLILAT
+QRATGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAAARLDPRRPGSAILSTAGRPTVS
+FRASQWTVDGGTPVWRRLGEAAAAPAVAPWEAVVSVLVENYAAGDWPTPPPVVTPALPER
+WVPDRARRAEATALALLDDAAHGRHRPWRWPTGAEGRTAWIVEAAGGRAETLAAVVEVAL
+RSGRPVAVLDGTGEAAAAARSGTPVLTPDAEGAGEAALARLRELAAAGGTAVITGWNAWS
+GLRVGDTYRTVEEDVHDWLGRPTAAGLRLAVFGGRELATGRLLLHLPHRFFVPAGTNAEH
+RLIWPRLTEVEPLPGRAVHISPAVPEPGMPCQLASPAPA
+>PROKKA_00462
+MAWSVRILGGAAPETWRVEHFPADADEQDRAVRERFPARSLHRCAAGRRSVTYAEGVGSA
+PARGPELAVVTEHGPDAGRIVPLGEGGLSVGRGGARLLLDDPSAPSRPMRLRLAPTGLHV
+HDGPRATGRLWDGRSPLPVGRTALGLVRGPGSALPRPITPEPPVVDLGSPPARQSVVIPL
+VAALGPLVLGVALVLMMGNPMFLLFGVLSVTVALVMLAMQRRTRLRHARLLAARADAVVR
+RRARVALSPGAVARAVRSGATDRFGLTAGADEAVAVSWGSGVGALSLSRDDPDEAWVEAV
+TSRRTVMTTSPPESRVVVLGPPRDVAGACRWAVFQLLRHAVAADGAFVVEAGGVRRIWWS
+GGSGPQLLVMAPEDAALDPAWRAWRAAIGDDAGTTPTARTDLPWTRYDFTGPPPAPGDAV
+VDLRGRTVVVPAEQQRFEDMAADGLADGTLVAWLTELADDVVDLGLLPTDDGDGTLTPPG
+QVGARDAVDGLTVALARSRDEAGVVEMDLAADGPHLLIAGTTGSGKSDLLLSLLLGAAAH
+HPPAEVAFLLLDFKGGASFGPLGALPHTMSLETNHVGAASLRALSAIRAELHRREALFAE
+AGVSDYPGFRRRHPDAALPRLVVAIDELRVLVDDHPDAAAVLQRLAATGRSLGFHLILAT
+QRATGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAAARLDPRRPGSAILSTAGRPTVS
+FRASQWTVDGGTPVWRRLGEAAAAPAVAPWEAVVSVLVENYAAGDWPTPPPVVTPALPER
+WVPDRARRAEATALALLDDAAHGRHRPWRWPTGAEGRTAWIVEAAGGRAETLAAVVEVAM
+RSGRPVAVLDGTGEAATAARSGTPVLTPDSEGAGEAVLARLRELAAAGGTAVITGWNAWS
+GLRVGDTYRTVEEDVHDWLGRPAAAGLRLAVFGGRELATGRLLLHLPHRFFVPAGTNAEH
+RLVWPRLTEVEPLPGRAVHISPAVPEPGMPCQLASPAPA
+>PROKKA_02222
+MGWTVRILGGRTPETWRVSPLPRDPTLRDRAVRERAPGRSLRAVASGPGSVTYAPWGGAE
+PAPGPELSVVTERGPDGGRLAPLTGGGVSVGRGRARLLLDDPAAPSRPTRLRLAAAGLHV
+EGAVEGAPRLWDGRRPHRIGRTTLGLVRGPQPPLPPPSLPAPPCVDLGSPPAGQSLAIPL
+LTAAAPLVIGVALVLVMRNPIFLLFGLLSVAVALTMLGLQRRARMRHAALLAERAAAVTA
+HRASAALSPGDVARAVRARTPDRFGLTGAAEGPATLSWGLGMGALGLSRDDPDQAWVAAV
+TARREALTVPSPAARTVVLGPPREAAGVCRWVVFQLLRHAVAAGACLVVESGGSRRCWWA
+GGTGGALLVTAPADAALEAAWTAWTAGIGGAPGERTGAQPARIDFTGADCAPGETVVDLR
+GGMLTDPGQEQRITGLEADGIAPATLPGWAAELADDVVDLGLLPADAGAGALFPPADVGT
+RDAVDALRVSLEAGSDGGPGALALDLAADGPHLLLAGTTGSGKSDLLLSLLLGVAAHHPP
+AEAAFLLLDFKGGASFGPLAALPHTMSLETNHVGAASLRALNAIRAELHRREALFAEAGV
+SDYPAFRRRHPEAALPRLVVAVDELRVLVDDHPDAAAVLQRLAATGRSLGFHLVLATQRA
+TGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAATRLDPRRPGSAILSTAGREPVPFRA
+SRWAVDGGAPVWRRLGEAAETPAAAPWKAVVAQLVERYAAGRWPTPPPVVTPALPERWVP
+DRTRRAGATALALLDDAAHGRHRPWRWAPGGGGRAAWIVEPAGGRAEALAAVLEVGVRGG
+APVVVLDGTGEAAAIAAPEGVRLLRPDEEGAGERAAACLRELAAAGGTAVLTGWTTWAGL
+RLGESYRTLEEDAQGWLGGREAAGLRVAAFGGRELATSRLLLHLPHRFFVPAGTSAEHRL
+VWPRLVEVEPLPGRAVHVSPDVPEPGLPCQLASPGAHRSGAADAASTL
+>PROKKA_00342
+MTRRLVHRPGRTVPPARLLPEDVITGPQPVDPAMDQGSGPNLLMIVPMVAAAASMLTMMA
+FRQSPFAAVGALAMVVTLTAMLILYGSQAGKARRRRTTLRETYTRYLDRQRRRLIAEDEQ
+ARAIAASAAPPPGALLDVVRRPDRLWERRRTDEDFLQTRVGLGARPVRALRVAVQDNATQ
+VQDEFMLKQAESLATRFRTTDDMPVSLPLDSLGNLAVVGPREFGLTAARSLVLGACVQQA
+PEDLVVALLVPPERRADWPWFDRLPHARVADAASPTGNRLLVAADADDLMRMLRADLARR
+AGIAAETLRASTRDGRAATELSRLVIVVDSHGEPAAGLPLEGSHLPLVSRGITLITLVSD
+RLDEPSDVRLRLSATGGTDVTGAAEFQVDDARQDEGRPTVSHGRLDTFDAATALGVATDL
+QPLRLSADSLEHAEDDLSSTQTFLQMLGLSPELTLEELRRRWRPRGQDEFLRVPIGEDDR
+GDAVHLDLKEAAQLGMGPHGLCVGATGSGKSELLRALVFALLASHAPERMSLLLVDFKGG
+ATFAPFHGAPHVAGIITNLSDDLSLVERVYASLSGEILRRQEVLKAAGNLANITDYQVHR
+ERELAQGRSVEALPHLIVIIDEFGELLTARPDFIDLFLSIGRIGRSIGVHLLLSSQRIES
+GRLRGLETYLSYRLGLRTLSESESRTVLDTADAFHLPPLPGFGYLKVDTSVYTRFRSGYV
+SSPLEEEAAARAEQERVLTADDDVPPALPVPDYGLQLVLPTEGAEPQLSSGAGAAQVMEE
+PEDHRPTIMETLMDRLREVPSPVEPLWLPPLPEALTLDQAAGDVAVTDHGLRLPAGGDLE
+VPIGLIDDPEHQWQGLWMLDFASGSGHLIVQGGPRSGKSTLLQTIVTSLALTHSPQQVGV
+YCVDLLGSSLLPLQGLPHVGGVAIRTNREMVTRTLREVSAMLTLREKLFEAEGIDSMTTL
+RRRHADGSLPDLGSADVFLVLDGYGQVNEEFADLTPVLNGLISRGAAYGIHIITTVARQG
+EIRSTQQTFFTHRVELRLSTPSDSAIDRKAAEEVREDTPGRGLASTRLHGQVALPRVDGA
+ADPGTAAEGLAETVQRIAESARGEAMAVRVLPPTTERPPLEQLEDPGRLPVGLLEDDLSV
+RSLDIDGRERHVVALGDAQTGRSSMLRQFARHFMDTHADTEMMFVVFDPRGELKGVIPDA
+YMAGYAGNATVAVPLARALVSELEKRQSTDPKDAGPMRQARIVVLVDDYDVLTVAGDSPL
+APLLPYLPMARELKLHVFLTRRMKGASRGLYEKFLASLVSQDAVTLMFSGDRSEGVLFDG
+LRPKRLPPGRAVLIGASRRHETVQTFTGPPAPGRG
+>PROKKA_02098
+MTWRVRVLGLPVEQDWAVSELPLDVDGQDRVVAEHFAPLRVERARGGGTTLTYVAHPSGT
+PPVPAAGSGPELAVGTSAGPDAGRLVPLTAAGLTVGRGRSRMLLDDPQCPSRPVRLALGP
+SGVSVDDGRTRRTWDGLDGLPIGDSILRLVRGRQRPLPPALTPPPAQIDLGAAPAEQSLL
+VSLAMAVGPVLIGLVLAVTTRSPLFLLFGIVSLLGVGVLLGVQRRTRRRHADLLRERALD
+VVRRRVAAVSGPADVSAACRAKAEDRFGLVSARPGDGPALLWGRARGSVAFTRGDVADHW
+RSAACVDQPVLGVAAADRGTVLCGTGRPAQAAARWTLFQLLRHAVATGSSLVVRSPDGAR
+VWWPAVPGAPTIALELEDTAPLAGAWEVWTASLGAEMSETRRHGCADEVLVRCTGTPPAD
+LDADVVDLDARQATLPGQGLELTDLTPLGISADTLQWWLAELADDVAHLGLGGPPASAPP
+LRRPHDVGAHRAVRNLAVPLTSSSAGDAAPMVLDLAADGPHALIAGTTGSGKSDLLLSVL
+VGLAARHAPAEVSFVLLDFKGGASFGPLRRLPHTMSVETNHVGAASLRALQAIGAELRRR
+EALFAEARVADYPAFRAAHPDTALPRLVVAVDELRVLVDEHPDANAVLQRLAATGRSLGF
+HLLLATQRPGGAVSADVRSNLGTTIALRTATEQESWDLVGSAAASRIDPAAPGTALLARG
+TGAPVPFRASPWSAGPVRPRWTPWGVPVASAASGTDWPSVVEDLVQACRDRDLPIPEPVV
+SPPLPGSFAPDRSRRRSADVLALVDDAARARHVPWRWPLGAQGNGAWIVEPAGGRALVLA
+AVLEAAGRTSPAVLILDGSGECAAALPTVADALPDLADVTLLTPEAQPADVGEQVCGAVA
+DLAAVGGTLVITGWQSWAGVRVGETYRTLDEELHRLLGTQAARGLRVAAVGGRELVTARI
+APHLPHRFYVPAGTTPDHRLVWPPKLVEVEQLPGRAVHVHPGGPTVGVPAQLAFPAHSAA
+GAGTDSDDQQ
+>PROKKA_00695
+MAWSVRILGGAAPETWRVEHFPADADEQDRAVRERFPARSLHRCAAGPRSVTYAERVGSA
+PARGPELAVVTEHGPDAGRLVPLGEGGLSTGRGGARLLLDDPSAPSRPMRLRLAPTGLHV
+HDGPRDTGRLWDGRSPLPVGRTALGLVRGPGAALPRPVTPEPPAVDLGSPPARQSVVIPL
+VAALGPLVLGVALVLMMGNPVFLLFGVLSVTVALVMLAMQRRTRLRHARLLAARADAVVR
+RRAQAALSPGAVARAVRSGATDRFGLTSGADEAVAVSWGSGVGALSLSRDDPDEAWVEAV
+TSRRTVMTTSPPESRVVVLGPPRDVAGACRWAVFQLLRHAVAADGAFVVEAGGVRRTWWS
+GGSGPRLLVSAPEDAALDPAWRAWRAAIGGDAGTTPTARADLPWTRHDFTGPSPAPGDAV
+VDLRGRTVVVPAEQQRFEDVTADGLADGTLVAWLTELADDVVDLGLLPTDDGDGTLTPPG
+QVGARDAVDGLTVTLARSGDETGVVEMDLAADGPHLLIAGTTGSGKSDLLLSLLLGAAAH
+HPPAEVAFLLLDFKGGASFGPLGALPHTMSLETNHVGTASLRALSAIRAELHRREALFAE
+AGVSDYPGFRRRHPDAALPRLVVAIDELRVLVDDHPDAAAVLQRLAATGRSLGFHLILAT
+QRATGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAAARLDPRRPGSAILSTAGRPTVS
+FRASQWTVDGGTPVWRRLGEAAAAPAVAPWEAVVSVLVEKYAAGDWPTPPPVVTPALPER
+WVPDRARRAEATALALLDDAAHGRHRPWRWPTGAEGRTAWIVEAAGGRAETLAAVVEVAL
+RSGRPVAVLDGTGEAAAAARSGTPVLTPDVEGAGEAALARLRELAAAGGTAVITGWNAWS
+GLRVGDTYRTVEEDVHDWLGRPTAAGLRLAVFGGRELATGRLLLHLPHRFFVPAGTNAEH
+RLIWPRLTEVEPLPGRAVHISPAVPEPGMPCQLASPAPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000107.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000107.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8bbbd7e7b01441a2205f3e02bbac3697776616b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000107.fa
@@ -0,0 +1,51 @@
+>PROKKA_00769
+MTTTSASQGYRTINPATGELLKSFDNATDQQIADALDASQAAYEQWSRKSVAERAAVVKR
+ISELLAERSKDIAAVITTEMGKSLGAAVGEVRYGAQIFGYYADEAEELLADQPIKQFSGQ
+EAFVQRLPLGPLLGIMPWNFPVYQVARFVAPNLVLGNTILLKHAEINPQVAQLLEELFTE
+AGLPEGVYQNVFATHDQISTIIADPRVQGVSLTGSERAGAAVAEQAGRHLKKVVLELGGS
+DPYIVLSAPDARAAARDALATRMGNWGQACNSNKRMIVMEDLYDDFVDELVQRSSEMKPG
+DPTSRDADVYGPLSSESAADGLAEQIAEAKQAGATVHVGGERTSGPEGEGFYVSPAVITD
+VDQENPAYTQELFGMASVVYKVSSAEEAVALANDSQYGLGGAVFSTDLDEAKRVADQLEV
+GMANVNLASAAGANLPFGGVKRSGFGRELGPLALDEFANKRLYAVQGPLEG
+>PROKKA_00499
+MQGVSLTGSERAGAAVAEQAGRHLKKVVLELGGSDPYIVLSAPDARAAARDALATRMGNW
+GQACNSNKRMIVMEDLYDDFVDELVQRSSAMKPGDPTSRDADVYGPLSSESAADGLTEQI
+AAAKEAGATVHVGGERVSGPEGEGFYVSPAVITDVDQENPAYTQELFGMAAVVYKVSSAE
+EAVALANDSQYGLGGAVFSTDLDEAKRVADQLEVGMANVNLASAAGANLPFGGVKRSGFG
+RELGPMAVDEFANKRLYAVQGPLEG
+>PROKKA_00806
+MARYITRNPATGETLEEFAELPASEVESVIERADTAYRAWRERPVAERAAVLARAADLYE
+ERAEQLAQDVTTEMGKPISAARGEMKTVAGIFRYYAEQGPAMLEHERIEVAGGGTAYVRR
+DPVGVLLGVMPWNFPHYQIARFAAPNLLLGNTMILKHAGICARSALNVEQLLLDAGLPEG
+AFVNAFIGHEAVAQIVADERVQGVSLTGSDKAGQIIGEQAGRNVKKAVLELGGSDPFIVA
+GDADVARAAKDAVSGRCVNSGQTCTSSKRFIVVEEHYEQFLSAFVEGMRAVPHGDPTDES
+TVVGPLSSPEAVQEVHELVQDAVAHGATLHVGGEPGEGPGAYYPPTVLTDVDESARAFRE
+EIFGPVAVVHRVKDLDAAIELANDSPYGLSSSVYTTSAEVAEEVSARLETGMVWVNSTSK
+SSAELPFGGVKRSGIGRELGTLGIEEFANHKLVRSPEGLIGA
+>PROKKA_02161
+MTTTSASQGYRTINPATGELLKSFDTATDQQIADALDASQAAYEQWSQKSVAERAAVVKR
+ISELLAERSKDIATLITTEMGKSLGAAVGEVRFGAQIFAYYADNAEELLADQPIKDFSGQ
+EAFVERLPLGPLLGIMPWNFPVYQVARFVAPNLILGNTILLKHSEINPQTAALLEDLFRE
+AGLPEGVYQNLYATHEQVSTIIADPRVQGVSLTGSERAGAAVAEQAGRHLKKVVLELGGS
+DPYIVLSAPDARQAARDALATRMGNWGQACNSNKRMIVMEDLYDDFVDELVQRASAMKAA
+DPTSRDEDVYGPLSSESAADGLAEQIKAAKDAGATVHVGGERVSGPAGEGFYVSPAVITD
+VDQDNPAYTQELFGMAAVVYKVSSPEEAVALANDSQYGLGGAVFSTDLDEARRVADQLEV
+GMANVNLPSAAGANLPFGGVKRSGFGRELGPFAVDEFANKRLYAVKGPLQG
+>PROKKA_02057
+MTTTTSASQGYRTINPATGELIKQYDNATDQQVQDALAASQAAYEQWAATTVAERAGVVK
+RISELLAERSKDIAALITTEMGKSLGGAIGEVRFSAQIFAYYADNAEELLADQPIKDFSG
+QEAFLEKLPLGPLLGVMPWNFPVYQVARFAAPNLVLGNTILLKHSEINPQTAQLLQDLFE
+EAGLPAGVYQNLYATHDQISTIIADPRVQGVSLTGSERAGASIAEQAGRHLKKCVLELGG
+SDPYIVLSAPDARQAAREALQTRMGNWGQACNSNKRMIVMEDLYDEFVDELVKQSTALKP
+GDPTSRDEDVYGPLSSESAADGLAAQIRDAKEAGATVVGGERLSGPSGEGFYVSPAVITD
+VDQENPAYSQELFGMASVVYRVSSAEEAVALANDSQYGLGGAVFSTDLDEAKRVAEQLEV
+GMANVNLPSAQGANLPFGGVKRSGFGRELGPFAVDEFANKRLYAVKGDLQG
+>PROKKA_00733
+MTTTSASQGYRTINPATGELLKSFDNATDQQIADALDASQAAYEQWSRKSVAERAAVVKR
+ISELLAERSKDIAAVITTEMGKSLGAAVGEVRYGAQIFGYYADEAEELLADQPIKQFSGQ
+EAFVQRLPLGPLLGIMPWNFPVYQVARFVAPNLVLGNTILLKHAEINPQVAQLLEELFTE
+AGLPEGVYQNVFATHDQISTIIADPRVQGVSLTGSERAGAAVAEQAGRHLKKVVLELGGS
+DPYIVLSAPDARAAARDALATRMGNWGQACNSNKRMIVMEDLYDDFVDELVQRSSAMKPG
+DPTSRDADVYGPLSSESAADGLTEQIAAAKEAGATVHVGGERVSGPQGEGFYVSPAVITD
+VDQENPAYTQELFGMAAVVYKVSSAEEAVALANDSQYGLGGAVFSTDLDEAKRVADQLEV
+GMANVNLASAAGANLPFGGVKRSGFGRELGPMAVDEFANKRLYAVQGPLEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000110.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000110.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac38487875474d9df9f2b8e7465985131f0c5bdc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000110.fa
@@ -0,0 +1,31 @@
+>PROKKA_00965
+MTEHSAAPVLRFVDDRAVRDLEQLATRARRVADTGMRLHVVPEAGRSRTPMLAQWVSVLQ
+PAGLGDGVPVVLGLRTVPLATADGVADLDAVVALGSVTERTARMRGQDPVDLAFAVPPGR
+EHVTWTALTPPRGGWTPVAEVADEELTEVATRGADAVWDALPENPGEALVRKIRAQMWGP
+LLGGDALQFPAGMAFGAHALGFLRPGGRARLSTAGPWTRLDTPGGFVLGRPAMAV
+>PROKKA_00678
+MTEHSAAAPVLRFVDDRAVRDLEQLATRARRVADTGMRLHVVPEAGRSRTPMLAQWVSVL
+QPAGLGDGVPVVLGLRTVPLATADGVADLDAVVALGSVTERTARMRGQDPVDLAFAVPPG
+REHVTWTALTPPRGGWTPVAEVADEELAEVATRGADAVRDALPENPGEALVRKVRAQMWG
+PLLGGEALQFPAGMAFGAHALGFLRPGGRARLSTAGPWTRLDTPGGFVLGRPAMAV
+>PROKKA_01922
+MTEPSAAPVLRFADERAVRDLEQFATRARRVSDTGMRLHVVPAAGPSRTPMLAQWVSVLQ
+PAGLGDEVPVVLGLRTVPLATAEMAADLDAVVALGAVTERTARMRSRQPVDLDFSVPPGR
+EQVTWTALTPPRSGWTPAAEVADEELADVAERGVAAVRETLPENPGEAMVRKVRAQMWGP
+LLGGDALGFPAGMAFGAHALGFLQPGGRARLSTAGPWTRLDTPGGFVLGRPAMAV
+>PROKKA_00709
+MPARLILADAPPARDALTFAQRAAQAGAHGVRLQAAAALTPRGPLDRTPTILVLRTLRSD
+PELQCDVTVDTLTATADPLTLALPETALAPAWTSVEPPQHGWRLIADVTSLTLMRSARAG
+IEAVAQALPDKPGDDVVRKIRGTVWGTPDTALASLPQGVAFAAYVFGFLSRGNGATISTA
+GRWTRLTLPTGHVLLRGPVASGLTPIRRTRPRVSKSVTSIE
+>PROKKA_01871
+MPDQPSSRRDARDAARAAVPVLRLTDERAVRDLDQFATRARRVADTGMRLHVVPEAGPRR
+TPMLAQWVSVLQPHGLGDGVPVVLGLRTVGLTSADAVEDLDAVVPLGAVTERTARMLGGT
+PVALDLPVPPGRERVTWTALTPPRAGWTVRAEVPDDELAEVAVKGAEAIRDALPQDPGEA
+MVRQVRAQMWGPRLGGEIGFPAGMAFGAHALGFLRPGGRARLSTAGPWVRLDTPGGFVLG
+RSAVGV
+>PROKKA_00911
+MTEHSAAAPVLRFVDDRAVRDLEQLATRARRVADTGMRLHVVPEAGRSRTPMLAQWVSVL
+QPAGLGDGVPVVLGLRTVPLATADGVADLDAVVALGSVTERTARMRGQDPVDLAFAVPPG
+REHVTWTALTPPRGGWTPVAEVADEELAEVATRGADAVRDALPENPGEALVRKIRAQMWG
+PLLGGDALQFPAGMAFGAHALGFLRPGGRARLSTAGPWTRLDAPGGFVLGRPAMAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000113.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000113.fa
new file mode 100644
index 0000000000000000000000000000000000000000..73f29547f2fc518b491ff907c386c7f984678021
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000113.fa
@@ -0,0 +1,41 @@
+>PROKKA_01028
+MTTPSNISRRSFAGLSLAAVGAFALTACNSQAEEKSDDGAQTVRIGVVSENESHRALVKL
+AKEKHGIDVEIRNFTEYTQPNPALDNGDIDMNWFQHIAYLADYNQASGKDLTMIGTTEII
+PLPLYSKKYTDVSEFKKGDTVAIPNDTVNQARAINVLVAAGLLKLSNETIRPEVRDIDEA
+ASTVTVQPVAAQQTVNALESVQGAVINNTFSADAGIDTNTALFKDDPEDDSAKPYVNGFA
+VRREDRDNETYKKIAALYHEQPVLDESAKLSSGTSVPVQLDTAQIDETLKQYQDAIAKQG
+A
+>PROKKA_00743
+MTTPSNISRRSFAGLSLAAVGAFALTACNSQAEEKSDDGAQTVRIGVVSENESHRALVKL
+AKEKHGIDVEIRNFTEYTQPNPALDNGDIDMNWFQHIAYLADYNQASGKDLTMIGTTEII
+PLPLYSKKYTDVSEFKKGDTVAIPNDTVNQARAINVLVAAGLLKLSNETIRPEVRDIDEA
+ASTVTVQPVAAQQTVNALESVQGAVINNTFSADAGIDTNTALFKDDPEDDSAKPYVNGFA
+VRREDRDNETYKKIAALYHEQPVLDESAKLSSGTSVPVQLDTAQIDETLKQYQDAIAKQG
+A
+>PROKKA_00185
+MTSRSPLSSRSPLSPRPSRRALLAGLAGVGSAALLTGCGLRTGTAAGGGGASRTITLCAT
+EDAPYQEPVRIAERLLAERGWELKTTFVTDIIQPNIAVDRGEFDANFFQHIAYLKQFNAD
+NGTSVVPAFNVYTSPAGLFSTRYSSLEELPDGARISVPVDPSNNGRALRLLAQAGRITVR
+EGVSVIRLSQHDITANPHGYEFVEVDQQSLALTIEDADAGFLFARQSAKIGLPISESLLF
+ETAEDAVPFRVVVATREGFRDTEAGRALREAFQSEEVRRWYADYLDGALGTEAWGDDPQE
+AIAALEI
+>PROKKA_01852
+MALSPLSRRTALGAGTAALALVLSACGAGGSDTAASSAPTPDPANPVVVKVGANPVPHAQ
+ILEYVDENLAKEAGIDLEIQEFDDYQMPNTALDEGKIDANYYMHEPFFNKQVEERGLKME
+HGKGVHIEPYAAFSKKFDSVDQVPEGATVAITNDPGNQPRALKMLEQAGLLKDVKDDSAA
+LTLTPEQNPKGLTFEENQPEILVQILDDPAVDLAIINGNYFIQAGMTLEDAVVVEEISGE
+NPYANFVAWREGEKTPGVEKLDELLHSPKVKQYIEQTWPGGDVTPAF
+>PROKKA_01744
+MPTRAGDVAPSSKENPMTTPSNISRRSFAGLSLAAVGALALTACNSQAEKKGDDGAQTVR
+IGVVSENETHRALVKLAKEKHGIDVEIRNFTEYTQPNPALDNGDIDMNWFQHIAYLADYN
+QASGKDLTLIGTTEIIPLPLYSKKYKDVSEFQKGDTVAIPNDTVNQARAINVLVAAGLLK
+LSNETIRPEPKDIDEAASTVKVQTVAAQQTVNALESVQGSVINNTFSADAGIDTNTALFK
+DDPKADSAKPFVNGFAVRRADRENETYKKIAALYHEQAVLDESAKLSSGTSVPVQLDAAQ
+IDETLKQYQDAIAKQGA
+>PROKKA_00972
+MTTPSNISRRSFAGLSLAAVGAFALTACNSQAEEKSDDGAQTVRIGVVSENESHRALVKL
+AKEKHGIDVEIRNFTEYTQPNPALDNGDIDMNWFQHIAYLADYNQASGKDLTMIGTTEII
+PLPLYSKKYTDVSEFKKGDTVAIPNDTVNQARAINVLVAAGLLKLSNETIRPEVRDIDEA
+ASTVTVQPVAAQQTVNALESVQGAVINNTFSADAGIDTNTALFKDDPEDDSAKPYVNGFA
+VRREDRDNETYKKIAALYHEQPVLDESAKLSSGTSVPVQLDTAQIDETLKQYQDAIAKQG
+A
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000122.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000122.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d32f32533fa5622a869c91ea6fa55781de6ea808
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000122.fa
@@ -0,0 +1,36 @@
+>PROKKA_01152
+MGEVGTREVRLERIEDLADPRLAPYTTMTDAALRRRVDAEHGVFLAESSQVVRRALDAGH
+TPRSFLLGDRYRGSFADVLAAHPDVPVFTGPDDVLEALTGFHLHRGALAAMDRPAPRPLA
+DVLAGARRVLIAEDLVDHTNLGAVVRSAVALGWDALLLTPQAADPLYRRAIRVSMGTVFR
+LPWARLPGPVAQSLPALRAAGFAVAALEVTERAVGLDSARIEPLRTAERLALVLGQEGPG
+VRPETLAQTDADVVIPMPAGVDSLNVAAAAAVALWELRAR
+>PROKKA_00871
+MGEGGAREVRLERIEDLADPRLAPYTTMTDAALRRRVDAEHGVFLAESSQVVRRALDAGH
+TPRSFLLGDRYRGSFADVLAAHPDVPVFTGPDDVLEALTGFHLHRGALAAMDRPAPRPLA
+DVLAGARRVLIAEDLVDHTNLGAVVRSAVALGWDALLLTPQAADPLYRRAIRVSMGTVFR
+LPWARLPGPVAQSLPALRAAGFAVAALEVTERAVGLDSAWIEPLRTAERLALVLGQEGPG
+VRPETLAQTDADVVIPMPAGVDSLNVAAAAAVALWELRAR
+>PROKKA_01740
+MAEPAATAEPDGREVRLARAEDLADPRLVPYTTLTDAALRRRVDAEHGVFLAESSQVVRR
+ALAAGHTPRSFLLGDRYRGSFADVLAAHPDVPVFTGPDDVLEALTGFHLHRGALAAMDRP
+APRPLADVLAGARRVLIAEDLVDHTNLGAVVRSAVALGWDALLLTPQAADPLYRRAIRVS
+MGTVFRLPWARLEGPVAEAVPALREAGFAVAALEVTERAVGLDSPELEPLRSADRLALVL
+GQEGPGVRTETLEHTDADVVIPMPDGVDSLNVAAAAAVALWELRAR
+>PROKKA_00545
+MSSESPAQPASADQPAEAPAGVIVDPKDARLRKVRELLKGKNKASRAIIVDDEENLLAAL
+AAGVELFTVFHGEDAELPAALAAVLPADQDVQVVSTHAAKELFGVERRSRVFALARRPKP
+LTVAEVLEHPGDVLVLDGVKLMGNIGAITRSARALGAAGLVLVDADLASVTDRRLIRASR
+GMVFSLPVALASADDVAAQLAEAGVPLVSLDLGSEKALDSVAEIPGRVALLLGSEKHGPS
+ARLAETAEHTVSITIHPEVESLNVSVSAALALYERRASNPLPQA
+>PROKKA_01634
+MPDDGAPAPFPGEVRLQSAADLADPRLAPYTTLTDAALRRDVDAAHGVFLAESSPVVRRA
+LDAGHAPRSFLLGDRYRETFADVIAAHPGVPVFTGPDEVLTALTGFHLHRGALAAMDRPA
+PRSVAEALDGAHRVLIAEDLVDHTNLGAVVRSAVALGWDALLLTPRAADPLYRRAIRVSM
+GTVFRLPWARADGPLEEALPALRAAGFATAALEVTDRAVGLDSPELEPVRTAERLALVLG
+QEGPGVRPETLAAVDAHVVIPMPAGVDSLNVAAAAAVALWELRPRDTPAA
+>PROKKA_01102
+MGEGGAREVRLERIEDLADPRLAPYTTMTDAALRRRVDAEHGVFLAESSQVVRRALDAGH
+TPRSFLLGDRYRGSFADVLAAHPDVPVFTGPDDVLEALTGFHLHRGALAAMDRPAPRPLA
+DVLAGARRVLIAEDLVDHTNLGAVVRSAVALGWDALLLTPQAADPLYRRAIRVSMGTVFR
+LPWARLPGPVAQSLPALRAAGFAVAALEVTERAVGLDSAWIEPLRTAERLALVLGQEGPG
+VRPETLAQTDADVVIPMPAGVDSLNVAAAAAVALWELRAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000125.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000125.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ff1186acf954b584bbe92b96c11212d14f15eed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000125.fa
@@ -0,0 +1,43 @@
+>PROKKA_01334
+MTEHTAPTPLPLSLLDLALVRDGAPMGEAFAESVEQARVAEAAGFRRVWYAEHHNMPSIA
+SSATAVLIAHVAAHTDSIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDLGLGRAPGT
+DQRTLQALRRDPSAAERFPQDVLELQGYLTGQSLIPGIDAYPGKGTNVPLYILGSSAFGA
+QLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHFIAAANVIAADTEEVAER
+EWQAAQRARIRMMLGRGRTLTDDEVEMLLHSPAGQQVLGMLECTAVGTGPTTAAWLHDFA
+ARVQADELIITTAAQDAGVRRRTLELLGEHVVRA
+>PROKKA_01055
+MTEHTAPTPLPLSLLDLALVRDGAPMGEAFAESVEQARVAEAAGFRRVWYAEHHNMPSIA
+SSATAVLIAHVAAHTDSIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDLGLGRAPGT
+DQRTLQALRRDPSAAERFPQDVLELQGYLTGQSLIPGIDAYPGKGTNVPLYILGSSAFGA
+QLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHFTAAANVIAADTEEVAER
+EWQAAQRARIRMMLGRGRTLTDDEVEMLLHSPAGQQVLGMLECTAVGTGPTTAAWLHDFA
+ARVQADELIITTAAQDAGVRRRTLELLGEHVVRA
+>PROKKA_01557
+MTEHTAPTPLPLSLLDLATVRDGASVAEAVAESVEQAQAAERAGFRRVWYAEHHNMPAIA
+SSATSVLIAHVAAHTESIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDLGLGRAPGT
+DQRTLQALRRDPSAAERFPQDVLELQGYLTGRTRIPGIEAYPGKGTDVPLYILGSSAFGA
+QLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHFIAAANVIAADTREEADR
+EWEAARRARIRMMLGRGRTLSDDEVEMLLHSPAGQQVLTMLECTAVGTGEETATWLRDFA
+AKVQADELIITTAAQDAGVRRRTLELLGEHVVRA
+>PROKKA_00131
+MSIPLSVFDPVLLPAETDPREAIDDARTLAAAADALGYRRLWHGEHHLNPGVLGSNPALT
+LALVGPVTQHIRLGSAASLVGPRTPLVLAEDFGLLAAAFPGRIDLGLGRAAAPGGPPPGT
+RAETPTGDGGPAQDPQREPAGAGASSGQDPAAGPSEVDGVVIPAAPDLSAALGSPLRAAS
+RALLPTPSTPALDYGAQVDLLLGLLDGTAQHDGAALGQVVARPAVDVEPWVLGSGPGVSA
+EVAARRGLRFGANYHVSPAGTVAAVRRYRELFRPSPEVPCPVVSVSAEVLIADTAAEARR
+RASGYAAWVLSIRSGAGAVPYPSPAHPEPSRTPQEEALVADRLQTRFVGTAEQVAERLDA
+LARLTGADELLISASAHRVEHRVETLTRLAEIWRTA
+>PROKKA_01453
+MTADVRPVVPPETAPAGVPLSLLDLATVRGDQRIGEALGQSVELAQTAEAQGFTRVWYAE
+HHNMPGIASSATAVLLAHVAAHTERIRVGSGGVMLPNHSPLVVAEQFGTLAELHPGRVDL
+GLGRAPGTDQRTLQALRRSPEAADRFPQDVLELQGYLRGESRMPGIDAYPGRGTDVPLWI
+LGSSAFGANLAAQLGLGYAFASHFAPQMLEHAARLYREHFTPTDALDAPHFIAAANVVVA
+DTDEEAQRLWEATRRSRVRMFLGRGRHLTEDELDMLMDSPAGEQVLGMLRHTAVGTPDVV
+RAWLDDFAARVEADELIVTAAAVDHPARVRTLELLGEHVIRR
+>PROKKA_01290
+MTEHTAPTPLPLSLLDLALVRDGAPMGEAFAESVEQARVAEAAGFRRVWYAEHHNMPSIA
+SSATAVLIAHVAAHTDSIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDLGLGRAPGT
+DQRTLQALRRDPSAAERFPQDVLELQGYLTGQSLIPGIDAYPGKGTNVPLYILGSSAFGA
+QLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHFIAAANVIAADTEEVAER
+EWQAAQRARIRMMLGRGRTLTDDEVEMLLHSPAGQQVLGMLECTAVGTGPTTAAWLHDFA
+ARVQADELIITTAAQDAGVRRRTLELLGEHVVRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000126.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000126.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a354a5d572e52b427518c7dd4377f803c92766ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000126.fa
@@ -0,0 +1,37 @@
+>PROKKA_01341
+MTTHTSTAQRSSKYPTTIGIDVGGTGMKGGLVRLGSGPKAGTLRGDRFRIPTPQTAMPEP
+VAATLAAITAELDGREKAPKPSAPLGVCFPSIVKDGVCLSANNIDHSWIGTDLRGTFEEH
+LRRPVTVVNDADAAGLAEARYGAGRGVRGLVHVITLGTGIGGAMIHDGMLVPNFEVGSLE
+LDGVMAESRASAKARERDQLSWAEYAERLQRFFSHVERIFSPDLFIVGGGISKRPDDYLP
+LLRLRTPIVPAQLQNNAGIVGAALAAHGSLADGN
+>PROKKA_01061
+MTTHTSTAQRSSKYPTTIGIDVGGTGMKGGLVRLGSGPKAGTLRGDRFRIPTPQPAMPEP
+VAATLAAITAELDGREKAPKPSAPLGVCFPSIVKDGVCLSANNIDHSWIGTDLRGRFEEH
+LRRPVTVVNDADAAGLAEARYGAGRGVRGLVHVITLGTGIGGAMIHDGVLVPNFEVGSLE
+LDGVMAESRASAKARERDQLSWAEYAERLQRFFSHVERIFSPDLFIVGGGISKRPDDYLP
+LLRLRTPIVPAQLQNNAGIVGAALAAHGSLADGN
+>PROKKA_01551
+MTTHTTTAQRSSKHPTTIGIDVGGTGMKGGLVRLGSGPKSGTLRGDRFRIPTPQPAMAEP
+VAATLAAITAELDARDKAPAPTAPLGVCFPSIVKDGVCLSANNIDPSWIGTDLKAAFEEH
+LRRPVRVVNDADAAGLAEARYGAGRGVSGLVLVITLGTGIGGAMVHDGVLVPNFEVGSLE
+LDGVMAETRASAKAREREDLSWAEYAQRLQRFFSHVEHVFSPDLFIVGGGISKRPDDYLP
+LLSLRTPIVPAQLRNNAGIVGAALAAHDSLADAR
+>PROKKA_01415
+MHRSRPAPPSPPAPSAYPRRLLGVDLGGTAAKAGVLELARDGRARILARSRAAHAGADPA
+SAVTRAAADALSRAGVRVPDGAGFACAAWLDPATGRARASPHLPSLVGIRPAALLTPVLE
+AAGAAGHGLVPVALNDADAAALAESRLGAARPAPGDLPGAPTLFVALGTGVGGAVIVDGA
+VLPGARGMHGEAGHICVDPDGPACPCGARGCWELYASASALARTLPGRPIADVLEAAVAG
+PGPERDAVLDAGEWLGRGLAPAVCLLDPVRVVVGGGLMAAGELLLPTARAALRRALPTAA
+ADRPPELVAAALGNDAGWIGAALADGARV
+>PROKKA_01447
+MSFPNTGVIPRLPPAPSKHPSVLGVDIGGTGMKGGIVRLGHGPKSGTLRGDRFRLDTPQP
+ASPATMARTLAQIVSELDHREKAPDADSRVGVCFPSIVQHGVCRSANNIDPSWIGVSLQD
+TFEEALQRPVTVVNDADAAGLAEARYGAGAGVPGLVMVITLGTGIGGAMINDGVLVPNFE
+VGSLELDGVMAESRASAKAREREGLDWPEYALRLQRFFSHLERIFSPDLFIVGGGISKRP
+HDYLPLLQLETPIVPAMLQNNAGIVGAALAAHADPADGLLR
+>PROKKA_01296
+MTTHTSTAQRSSKYPTTIGIDVGGTGMKGGLVRLGSGPKAGTLRGDRFRIPTPQPAMPEP
+VAATLAAITAELDGREKAPKPSAPLGVCFPSIVKDGVCLSANNIDHSWIGTDLRGRFEEH
+LRRPVTVVNDADAAGLAEARYGAGRGVRGLVHVITLGTGIGGAMIHDGVLVPNFEVGSLE
+LDGVMAESRASAKARERDQLSWAEYAERLQRFFSHVERIFSPDLFIVGGGISKRPDDYLP
+LLRLRTPIVPAQLQNNAGIVGAALAAHGSLADGN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000131.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000131.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b7528fa3fff9cf604e91f0f77aad9a6cdb793f67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000131.fa
@@ -0,0 +1,30 @@
+>PROKKA_01549
+MSALQPQPTDKHASWAWSESRATEDDVVLRARERAAELEVPPVSEGTAALLTVLAATRAP
+AAVVEVGTGAGVSGLALMRGLPERTVLTTVDPDAEAQRAAREAFSEARLPTSRTRMITGR
+SRLVLPRLTSGAYEMVLVDGDPAARQFDVEQAARMLAPGGVLVVVDALDGDRVPRPAVRD
+ESTVSARAVDRLIREDEHWLSAVVPSGTGVLIAVRR
+>PROKKA_01259
+MSALQPQPTVKHASWAWSESRATEDDVVLRARERAAELEVPPVSEGTAALLTVLAATRAP
+AAVVEVGTGAGVSGLALMRGLPERTVLTTVDPDAEAQRAAREAFSEARLPTSRTRMITGR
+SRLVLPRLTSGAYEMVLVDGDPAARQFDVEQAARMLAPGGVLVVVDALDGDRVPRPAVRD
+ESTVSARAVDRLIREDEHWLSAVVPSGTGVLIAVRR
+>PROKKA_01376
+MSALQPQPTVKHASWAWTESRGVEDEVVLRARERSAELDVRPVSEGTAALLTVLAATRAP
+SAVVEVGTGAGVSGLAMMRGLPERTVLTTVDPDAEAQRAAREAFSEARLPTGRTRMITGR
+SRLVLPRLTSGAYEMVVVDGDPASRQFDVEQAARMLAPGGVLVLVDALDADRVPRPAVRG
+ESTVSARAVDRLIREDEGWVSAVVPSGTGVLIAVRR
+>PROKKA_01267
+MSALHPQPTDKHASWAWAEARTAESEVLLRARERSAELGVRAVGEGTSALLTVLAATRAP
+SAVVEIGTGAGVSGLALMRGLPERTVLTTVDPDAEAQRAAREAFSEAHLPTSRTRMISGR
+SRLVLPRLTTGAYEMVVVDGEPASRAFDVEQAARMLAPGGLLVVVDALDSDRVPRAAVRE
+DSTVSARDVDRLVREDEAWVSAVVPTGTGVLLAVRR
+>PROKKA_01296
+MDPRRRALLDRLWQEGRDFDAAQPDRLDRRRNLEPESAELLNILVRTLAPAEVLELGTST
+GFSALWIADALEPHGGRLTTVDPDAPRLAEARTNLEAAGVADVVTVRQADAADVLADAED
+GCLPLVFLDAERPAYPDYWPDLARILAPGGLLVVDNCLSHADDVRPFRALVDASPGFRST
+LVPVGAGLLLVSKDRPGHGSGVG
+>PROKKA_01476
+MSALQPQPTDKHASWAWSESRATEDDVVLRARERAAELDVPPVSEGTAALLTVLAATRAP
+AAVVEVGTGAGVSGLALMRGLPERTVLTTVDPDAEAQRAAREAFSEARLPTSRTRMITGR
+SRLVLPRLTSGAYEMVLVDGDPAARQFDVEQAARMLAPGGVLVVVDALDGDRVPRPAVRD
+ESTVSARAVDRLIREDEHWLSAVVPSGTGVLIAVRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000136.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000136.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dbc9f5d7e6f905ed532821e484423cd2d04563f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000136.fa
@@ -0,0 +1,34 @@
+>PROKKA_01584
+MIARLRAASAEDRLLLIGLPLLVAALLIGWTVWVRGAALDDVEARLLTWPTVLRLTAEHL
+ALVGVSTVLVVATAVPLGVLLSRPAARRFTPVAMGLANAGQAAPVIGVIVLLAMAWGFGF
+RVAVLALSLYAFLPVLANTLAGLRGVDPTVVEAARGMGMSPLQTLLRVELPLALPVIMAG
+LRTALVLLVGTGAFATFIDAGGLGLLIQTGIVLFRFPLLVSGAILVAALALMIEWIGRLV
+ETLATPRGLA
+>PROKKA_02249
+MISSLFSWFADPAHWAGPNGVPARVLEHLGYSVLALVIAAAIAFPVGVWIGHTGRGRRVV
+VALSSALRALPTLGLLTFLAIVLDIRLRQALIPTVMVLVILAIPPLLAGTYAGLQAVPRE
+VVHAARANGHSTGQLIGQVELPIALPMAVGGLRSATLQVIATTSVASYLGLGGLGRYLFD
+ALAVQDYVTMLAGAVLIAVLALLCDGLLLLVQRILTPAGLRARG
+>PROKKA_01295
+MIARLRAASAEDRLLLIGLPLLVATLLIGWTVWVRGAALDDVEARLLTWPTVLRLTAEHL
+ALVGVSTVLVVATAVPLGVLLSRPAARRFTPVAMGLANAGQAAPVIGVIVLLAMAWGFGF
+RVAVLALSLYAFLPVLANTLAGLRGVDPTVVEAARGMGMSPLQTLLRVELPLALPVIMAG
+LRTALVLLVGTGAFATFIDAGGLGLLIQTGIVLFRFPLLVSGAILVAALALMIEWIGRLV
+ETLATPRGLA
+>PROKKA_01338
+MIARLRAASAEDRLLLIGLPLLVAALLIGWTVWVRGAALDDVEARLLTWPTVLRLTAEHL
+ALVGVSTVLVVATAVPLGVLLSRPAARRFTPVAMGLANAGQAAPVIGVIVLLAMAWGFGF
+RVAVLALSLYAFLPVLANTLAGLRGVDPTVVEAARGMGMSPLQTLLRVELPLALPVIMAG
+LRTALVLLVGTGAFATFIDAGGLGLLIQTGIVLFRFPLLVSGAILVAALALMIEWIGRLV
+ETLATPRGLA
+>PROKKA_00458
+MIADLFAWFADPAHWTGPGGVPARVAEHLGYSLLALAIAAVIALPAGVAIGHTGKGRRVV
+VAVSSALRALPTLGLLTFLAIVLQVGLRQALIPAVIVLVVLAVPPLLAGAYAGVHAVPRD
+VVVAARANGHSTRQLVSQVEVPLALPMIVGGLRSASLQVLATTSVAAYLGLGGLGRYLFD
+ALAVQDYTTMLAGAVLIALLALVSDAVLLLFQRLVTPA
+>PROKKA_01511
+MIARLRAASAEDRLLLIGLPLLVAALLIGWTVWVRGAALDDVEARLLTWPTVLRLTAEHL
+ALVGVSTVLVVATAVPLGVLLSRPAARRFTPVAMGLANAGQAAPVIGVIVLLAMAWGFGF
+RVAVLALSLYAFLPVLANTLAGLRGVDPTVVEAARGMGMSPLQTLLRVELPLALPVIMAG
+LRTALVLLVGTGAFATFIDAGGLGLLIQTGIVLFRFPLLVSGAILVAALALMIEWIGRLV
+ETLATPRGLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000137.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000137.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a6d56fbdc984ce9637f4229fc5e1bbacda45d96
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000137.fa
@@ -0,0 +1,40 @@
+>PROKKA_01585
+MSTDRDAGAEIRLESLTKLYPGQDRPAVDALDLIIPAGETVVFVGPSGCGKTTSLKMINR
+LIEPTSGRILIGGEDITRRDPTRLRRQIGYVVQGGGMMPHLSVAENVGLVPRLLKWDRRR
+IADRVDELLDLVGLDPAIYRDRFPRELSGGQQQRVGVARGLAADPPVLLMDEPFGAVDPL
+TRQRLQKEMLDIQARVGKTIVMVTHDVDEAVLLGDRILVLEPGAHVAQYATPEEVLARPA
+TEFVADFVGSGAGLKRLGLRSVDSLPLRPIAQHPTGTLPGEPVLDAATPISEALAALVMA
+PTEEIAVVRDGTVIGLLDYPTLRAHARASDEQARP
+>PROKKA_02251
+MIRFEHVEKTFPDGTRAVEDFSLEVPSHTTTVLLGSSGCGKTTLLQMVNRMVDPTGGRVL
+IEGRDVASLDPVKLRRGIGYVMQNAGLLPHRTVLDNVLTVPRLTGRISRQDRDHAHELLE
+LVGLPAAVASRYPSQLSGGQRQRVGAARALAPDPDVLLMDEPFSAVDPVVRADLQAEMLR
+IQRELSKTVLFVTHDVDEAVLLGDEVLVLREGARVAQHGTGEDILLRPADDFVRSFVGGA
+RRELHVEDRTGTPIVVDASGRVAGTLVQP
+>PROKKA_01296
+MSTDRDAGAEIRLESLTKLYPGQDRPAVDALDLIIPAGETVVFVGPSGCGKTTSLKMINR
+LIEPTSGRILIGGEDITRRDPTRLRRQIGYVVQGGGMMPHLSVAENVGLVPRLLKWDRRR
+IADRVDELLDLVGLDPAIYRDRFPRELSGGQQQRVGVARGLAADPPVLLMDEPFGAVDTL
+TRQRLQKEMLDIQARVGKTIVMVIHDVDEAVLLGDRILVLEPGAHVAQYATPEEVLARPA
+TEFVADFVGSGAGLKRLGLRSVDSLPLRPIAQHPTGTLPGGPVLDAATPISEALAALVMA
+PAEEIAVVRDGTVIGLLDYPTLRAHARAGDEQARP
+>PROKKA_01337
+MSTDRDAGAEIRLESLTKRYPGQDRPAVDALDLLIPAGETVVFVGPSGCGKTTSLKMINR
+LIEPTSGRILIGGEDITRRDPTRLRRQIGYVVQGGGMMPHLSVAENVGLVPRLLKWDRRR
+IADRVDELLDLVGLDPAVYRDRFPRELSGGQQQRVGVARGLAADPPVLLMDEPFGAVDPL
+TRQRLQQEMLDIQARVGKTIVMVTHDVDEAVLLGDRILVLEPGAHVAQYATPEEVLARPA
+TEFVADFVGSGAGLKRLGLRSVDSLPLRPIAHHPTGTLPDGPVLDAATPISEALAALVTA
+PTEEIAVVRDGTVIGLLDYPTLRAHARAGDEQARP
+>PROKKA_00456
+MIRFEHVGKVFDDGTAAVEDFSLEVPSHTTTVLLGSSGCGKTTLLQMVNRMVDPTSGRVW
+IDDADVASVDPVRLRRRIGYVMQQAGLLPHRTVLDNVLTVPRLTGRVSAADRSRAHELLE
+LVGLPADAARRRPDQLSGGQRQRVGVARALASDPDILLMDEPFSAVDPVVRAELQAELLR
+IQRELAKTVLFVTHDVDEAVLLGDEVLVLRTGAQVAQRGRGEEILLHPADGFVDRFVGGD
+RRRLHVEERAGTATVVDAAGRVAGLLETP
+>PROKKA_01512
+MSTDRDAGAEIRLESLTKLYPGQDRPAVDALDLIIPAGETVVFVGPSGCGKTTSLKMINR
+LIEPTSGRILIGGEDITRRDPTRLRRQIGYVVQGGGMMPHLSVAENVGLVPRLLKWDRRR
+IADRVDELLDLVGLDPAIYRDRFPRELFGGQQQRVGVARGLAADPPVLLMDEPFGAVDPL
+TRQRLQKEMLDIQARVGKTIVMVTHDVDEAVLLGDRILVLEPGAHVAQYATPEEVLARPA
+TEFVADFVGSGAGLKRLGLRSVDSLPLRPIAQHPTGTLPGGPVLDAATPISEALAVLVTA
+PAEEIAVVRDGTVIGLLDYPTLRAHARAGDEQARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000138.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000138.fa
new file mode 100644
index 0000000000000000000000000000000000000000..345b2bc2a35f4f4a23a292cbe18283e703ac2b5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000138.fa
@@ -0,0 +1,36 @@
+>PROKKA_01601
+MDTFRHQGLTFDVRDGGPAEGEVVLLLHGFPQDATSWRHVEPLLHAAGLRTLAPDQRGYS
+PGAAPRATAAYRLPALVGDAVALADAAGARRVHVVGHDWGGAVAWALATAHPERVASLTV
+LSTPHPAALARALRGPDQLRRSWYIAAFQAPALPERILARRLGSLLQRGQVPGAEHYARR
+FSTPQSLRGPVNWYRANPDLVTTTRSAPVTVPTTYVWGTRDAALGPRAAELTAGQVAGEY
+RFVKLDADHWLPEREADAVARAILDRVR
+>PROKKA_01313
+MDTFRHQGLTFDVRDGGPAEGEVVLLLHGFPQDATSWRHVEPLLHAAGLRTLAPDQRGYS
+PGAAPRATAAYRLPALVGDAVALADAAGARRVHVVGHDWGGAVAWALATAHPERVASLTV
+LSTPHPAALARALRGPDQLRRSWYIAAFQAPALPERILARRLGSLLQRGQVPGAEHYARR
+FSTPQSLRGPVNWYRANPDLVTTTSSAPVSVPTTYVWGTRDAALGPRAAELTAGQAAGEY
+RFVALDADHWLPEREADAVARAILDRVR
+>PROKKA_00271
+MLHRREYGDPDGVPVLHFHGTPGSGREAAALDAAARAAGVRLIAPDRPGMGRTPHLPGRR
+LAHWPAEVTRLLDELGIDRAAILAWSGGGPYAVACLARIPERLTAVALLAPAGLLRGIPW
+ANRLFPRLYLPAAGAIARARDWAPAAALGVFRWRRMRSRLADGPPAASPEREPLAPSSAA
+VLAASWREAFRQGHAGPVQDEQVINEDWSPLLTSARRAPVPVRIWHGRRDRVVPHRHSRR
+LAAALGAFLVDAHDGDHPGALLTAGPEALGWLAASAE
+>PROKKA_01201
+MTGGDALWGRVDAFRHQGLTFDVRDGGPAEGEVVLLLHGFPQDSTSWRHVEPLLHAAGLR
+TLAPDQRGYSPGAAPRATAAYRLPALVGDAVALADAAGARRVHVVGHDWGGAVAWALATA
+HPERVASLTVLSTPHPAALARALRGSDQLRRSWYIAAFQAPALPERILSRRLGSLLQRGQ
+VPGAEHYARRFSTPQSLRGPVNWYRANPDLVTTTRSAPVSVPTTYVWGTRDAALGPRAAE
+LTAGQVAGEYRFVALDADHWLPEREADAVARAILDRVR
+>PROKKA_01824
+MTIPGFALEHIPLPSGVTLRVATGGEGPAVVLLHGHPRTHATWHRVAPALADAGLRVVCP
+DLRGYGQSSAPEPSDDLHTHSDRTMAGDIALLMTHLGHDHFSVVGHDRGSYVAYRTALDF
+PERVDRMAVLDCVPILEALERADARFAEKWWHWFFFASPHAERVICADPLAWYQPDAQKM
+GQENYQDMVAAISDPQTVRSMIADYRASLHVDRDADARDRARGHQIQCPTLVAWSKHDDM
+EDLYGNPAEVWESWCAHRPESAVIDSGHHMAEDNPEQLTAVLTEFFLPS
+>PROKKA_01528
+MDTFRHQGLTFDVRDGGPAEGEVVLLLHGFPQDATSWRHVEPLLHAAGLRTLAPDQRGYS
+PGAAPRATAAYRLPALVGDAVALADAAGARRVHVVGHDWGGAVAWALATAHPERVASLTV
+LSTPHPAALARALRGPDQLRRSWYIAAFQAPALPERILARRLGSLLQRGQVPGAEHYARR
+FSTPQSLRGPVNWYRANPDLVTTTSSAPVSVPTTYVWGTRDAALGPRAAELTAGQAAGEY
+RFVALDADHWLPEREADAVARAILDRVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000139.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000139.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8cf88959c6df83a79400458587e8602943c41d05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000139.fa
@@ -0,0 +1,59 @@
+>PROKKA_01604
+MTATLVASGLAGGHGHRTLFEDLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQERERVPGETVAGYIARRTGCAEATREMDASASGLADPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARIQREWSSQGVRNAMKKSPDN
+DKLRRRANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSLQVNAGERIGITGPNGAGKSTLLRALLGRQAPDEGTAALGSSVQIG
+EIDQARSLLAGTVPLAAAVEALVPEMASGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER
+>PROKKA_01316
+MTATLVASGLAGGHGHRTLFEDLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQERERVPGETVAGYIARRTGCAEATREMDASASGLADPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARIQREWSSQGVRNAMKKSPDN
+DKLRRRANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSLQVNAGERIGITGPNGAGKSTLLRGLLGRQAPDEGTAALGSSVQIG
+EIDQARSLLAGTVPLAAAVEALVPEMASGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER
+>PROKKA_01275
+MPWEPVVRYIGLRAGSAETTAEMDLAATSLAGPDFTNVAANRVSAALARWLATGTTDLEK
+CIRIVLANLGLEMDDIPTGWVALEADVVVDTAGAMIVRFLYVHVVNRCFYASAYDDIRKV
+IARGVAVAGPAHWTGGTAPGLTWAGTSAQN
+>PROKKA_01290
+MTATLVASHLAGGHGHRTLFESLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQEHERVPGESVAAYIGRRTGCAAATAEMDEAAEALGAPDAGDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLERLERFVQELRGGVVLVSHDREFLARCVTRVLELDLAQHSN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKADLVSRARVQREWSSQGVRNAMKKSPDN
+DKLRRKANAESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGTAPRSSSVVATLNE
+AVFRQGSFTLGPVSLQVNAGERVGITGPNGAGKSTLLRGLLGRQDPDDGAASLGSSVQVG
+EIDQARSLLAGPTPLADAFEALVPEMASGEVRTLLAKFGLRADHVTRPVDELSPGERTRA
+GLALLQARGVNLLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER
+>PROKKA_01198
+MTATLVASGLAGGHGHRTLFDALDLTVAPGDVVGVVGANGAGKSTLLRILGGNLAPQTGT
+VSLAPSDAFVGWLPQEHERVSGETVAGYIARRTGCAEATREMDASAEALAGPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARTQREWSSQGVRNAMRKSPDN
+DKLRRKANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSLQVNAGERIGITGPNGAGKSTLLRGLLGRQAPDEGTAALGSSVQIG
+EIDQARSLLAGAVPLAAAFETLAPEMTSGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRLDRRW
+HVADGRVTER
+>PROKKA_01531
+MTATLVASGLAGGHGHRTLFEDLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQEHERVPGETVAGYIARRTGCAEATREMDASASGLADPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARIQREWSSQGVRNAMKKSPDN
+DKLRRRANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSRQVNAGERIGITGPNGAGKSTLLRGLLGRQAPDEGMAALGSSVQIG
+EIDQARSLLVGTVPLAAAVEALVPEMASGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000140.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000140.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea3cabc7fd1efd78634a6bcd64474c10f99f35ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000140.fa
@@ -0,0 +1,52 @@
+>PROKKA_01624
+MRDASAAAGPPVDCRTVALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVV
+NLPDERLPQLAEIFGSERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVV
+RAFDDGDVVHVDGKVDPASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEAL
+KAALAVLERGETIFAAKDKDKLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRD
+LVAPADAVFLDAKLESDLVELSEEEAAEMLEMAGQDESGLDQLARVGFSTLGLQTYLTAG
+PKETRAWTIPVGATAPEAAGVIHTDFQRGFIKAEIVSFDDLIAAGSMADAKAAGKVRMEG
+KDYVMKDGDVVEFRFNV
+>PROKKA_01330
+MRDASAAAGPPVDCRTVALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVV
+NLPDERLPQLAEIFGSERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVV
+RAFDDGDVVHVDGKVDPASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEAL
+QAALAVLERGETIFAAKDKDKLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRD
+LVAPADAVFLDAKLESDLVELSEEEAAEMLEMAGQDESGLDQLARVGFSTLGLQTYLTAG
+PKETRAWTIPVGATAPEAAGVIHTDFQRGFIKAEIVSFEDLIAAGSMADAKAAGKVRMEG
+KDYVMKDGDVVEFRFNV
+>PROKKA_01273
+MALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVVNLPDERLPQLAEIFGS
+ERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVVRAFDDGDVVHVDGKVD
+PASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEALKAALAVLERGETIFAA
+KDKDKLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRDLVAPADAVFLDAKLES
+DLVELSEEEAAEMLEMAGQNESGLDQLARVGFSTLGLQTYLTAGPKETRAWTIPVGATAP
+EAAGVIHTDFQRGFIKAEIVSFEDLIAAGSMADAKAAGKVRMEGKDYVMKDGDVVEFRFN
+V
+>PROKKA_00781
+MSHAHHHGGGSSAAVLDSSLTRLGLVGSPNSGKSTLFNALTGLRVKTGNYPGVTVSRAEG
+VMVAEDGTRVVLEDLPGTYSLDPISPDEQVVADLLALDPADADHPQALLLVADATTLRRG
+LTMVAHALAVELPATLVLTFGDELALRGGSVDVTRLSRALGIPVLAATAGDARQREAVRA
+HLATDPAGWAVPPVAPPTDPAGIAAWIDSVLEAARYAVPRPDGRTRRIDDVLLHPVWGTL
+VFLVTMFAFFQVIFTVAAPLQALVEELFGWLGERAAALIPIEWLGRFVAEALIGGVGGVV
+VFLPQILLLFLMISLLESTGYMTRAAFLMDRVMSRFGLEGRSFVALLSSLACAVPGIMAT
+RSLPSARDRLATMMAAPSMTCSARLPVYVLLISLLVPSEVRWGPVGLQGLVMFALYLGGA
+TASMLTAAFWSRVVGRRQAAMPFYMEMPPYRLPKARTVVTSMWASAEGFLRKVTSIILVT
+TALLWVLLNVPVRSEEEMAGAGVAMDDPAAVAQYTIDHSAAAAVGKAVEPAFEPLGFDWR
+IDVGVLASLAAREVFVATLGQMAAAEDPEDPGDALASWTVTDDAGVERPLFTPDVVAALL
+VFFMLALQCMSTLAVMRRETGTWRWPLLAFGYYFTLAWLAAFAVRHVVLALT
+>PROKKA_01182
+MALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVVNLPDERLPQLAEIFGS
+ERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVVRAFDDGDVVHVDGKVD
+PASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEALKAALAVLERGETIFAA
+KDKDKLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRDLVAPADAVFLDAKLES
+DLVELSEEEAAEMLEMAGQDESGLDQLARVGFSTLGLQTYLTAGPKETRAWTIPVGATAP
+EAAGVIHTDFQRGFIKAEIVSFDDLIAAGSMNDAKAAGKVRMEGKDYVMKDGDVVEFRFN
+V
+>PROKKA_01551
+MGPPVDCRTVALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVVNLPDERL
+PRLAEIFGSERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVVRVFDDGD
+VVHVDGKVDPASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEALQAALAVL
+ERGETIFAAKDKDTLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRDLVAPADA
+VFLDAKLESDLVELSEEEAAEMLEMAGQDESGMDQLARVGFSTLGLQTYLTAGPKETRAW
+TIPVGATAPEAAGVIHTDFQRGFIKAEIVSFDDLIAAGSMNDAKAAGKVRMEGKDYVMKD
+GDVVEFRFNV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000141.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000141.fa
new file mode 100644
index 0000000000000000000000000000000000000000..84d4679d96956be07eaffa71b66829ec0d0dd9bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000141.fa
@@ -0,0 +1,30 @@
+>PROKKA_01636
+MTENANQNAPLTGKTVAFLATNGVEQVELTSPWEAVIAAGATPVLVSSKSGTITAMKSDW
+EHGESFEVNTTVKDAKAEDFHGLVMPGGTLNADTLRIDKDVQAFVRAFFEQHKPVAAICH
+APWTLIEAGVVDGRRLTSYASLESDLKNAGAQWVDEEVVVDNGLTTSRTPDDLDAFNAKL
+VEELGEGKHEDQTA
+>PROKKA_01341
+MTENANQNAPLTGKTVAFLATNGVEQVELTSPWEAVIAAGATPVLVSPESGTITAMQSDW
+DHGESFDVNTTVKDAKAEDFDGLVMPGGTLNADAMRVNKDAQAFVRAFFEQHKPVAAICH
+APWTLIEAGVVEGRRLTSYPSLKTDLKNAGAQWVDEEVVVDNGLTTSRSPEDLDAFNAKL
+VEELGEGKHEDQTA
+>PROKKA_01259
+MTENAAQNAPLTGKTVAFLATNGVEQVELTSPWEAVIAAGATPVLVSPESGTITAMQSDW
+DHGESFEVNTTVKDAKAEDFDGIVLPGGTLNADAMRVNKDAQAFVRAFFEQHKPVAAICH
+APWTLIEAGVVEGRKMTSYSSLKTDLKNAGAQWVDEEVVVDAGLTTSRSPEDLDAFNAKL
+VEELAEGKHEDQTA
+>PROKKA_01168
+MTENAVQNAPLTGKTVAFLATNGVEQVELTSPWEAVIAAGATPVLVSPESGTITAMQSDW
+DHGESFEVNTTVKDAKAEDFHGLVMPGGTLNADAMRVNKDAQAFVRAFFDQHKPVAAICH
+APWTLIEAGVVDGRRLTSYASLESDLKNAGAQWVDEEVVVDNGLTTSRSPEDLDAFNAKL
+VEELGEGKHEDQTA
+>PROKKA_01210
+MAVDLQGKRVTILAADGVERVELDQPREALDRAGARTEVLSVDEGEIKARENDLDPAGTF
+GVDGLVAEASGADYDALVLPGGTVNPDKLRIDEDAVAFVRDFAENGKPVVAICHGPWTLI
+EADVATGRTLTSFPSIRTDLRNDGANVVDQEVVVDKNLITSRSPEDLPAFSEAIVAQLAG
+TTTKEEETS
+>PROKKA_01565
+MTENAVQNAPLSGKTVAFLATDGVEQVELTSPWEAVIAAGATPVLVSPKSGTITAMKSDW
+EHGESFEVNTTVKDAKAEDFHGLVMPGGTLNADALRIDTDAQAFVRAFFEQHKPVAAICH
+APWTLIEAGVVDGRRLTSYASLESDLKNAGAQWVDEEVVVDSGLTTSRTPDDLDAFNAKL
+VEELGEGKHEDQTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000146.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000146.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ce35d78f83e6171927ff36ff3384c6c3301dda2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000146.fa
@@ -0,0 +1,66 @@
+>PROKKA_01795
+MSTAPRRRVTGYPSTSGDDVQLNTTTLIRHAARTHGDQEIVYRTPDGGWDRYTYAEAYER
+IRRAANAMTGLGVSPGDRVGVIDWNSRRHYELYWAIPGIGATMVQVNLRLAPEDLVHVLT
+DSGCTTVFVDESLLRHAEVIAPRLPEVTTWVVMTDRPLSEIETTLPGVRHYEDLLASASP
+DVDWPEVEETSAYGACYTTGTTGRPKGVFYSHRAIVLHSYALAASIGMTLRDATMIITPM
+FHGQAWGLPQAATLMANKIVLPGRYMAEDTAPLTDALIAEEVTITSGAPAIFQPMLAYIE
+TLDEKPDLSRLRMISGATEPSLSLMRGFRDLTGAEVVHAYGATETTPLVTVNRYKPGVLA
+RLDEPALMDLKRKQGLPLTNVDLRIVGPGDENLPFDGVSQGEICVRGPWVTTGYHGMSEA
+DAEGRFLDGYWRSGDVGTVDSDGYLKVTDRLKDVIKSGGEWISSIDMENLLTSHPAITEA
+AVVGLPHPKWQERPYVQVMLRPGATITLAEVHEHLSGAFASWQLPERVDVVTELPRTSVG
+KIDKKTIRGRHTDLYADASEAARPGGGAGDVEEGGRA
+>PROKKA_02050
+MQTTDTVLGTPSTMGDDEQLTTTRLLRDAARTFGDQQIIHTRGGGSRWQTTTYAAVWERV
+RRIAAALRAEGVGPGDRVGLLLWNDVRHLESYFSVPLLGATMVQLNLRLAPTDLAYVITH
+AQVGTIVVDETLLELAAALEPHLPDGVRWIVAGDGELPADWAGRDDVLSYEALLDGHEPL
+ETGGLPNVSERSASGACYTTGTTGRPKGVFYSHRATWLHAHAVVSTLGMTMADTALLLTP
+MFHAQCWGLPFAAVAVGARLVLPGRFNLTDTPWLTSTLVDHGVTVAPAAPAILMPMLHHL
+RTLETPPRMDGVRLLCGATEPPVAMMRGFDELTGAEVIHAYGATETSPIVSLNRMKPSLM
+DTLSEDERWNLKRFQGLVVVGVDVKITDPLGELLPPGEENVGEIRLRGPWVTTSYADNAE
+ATEAGFDDEGYWRSGDLGYLSPEGYLKVTDRLKDVVKSGGEWISSIDLENHIMTVPGVRD
+AAVIGVPHPQWEERPLALVVRDEDSDVDQDAVLAALAERFATWQLPDEVRFVTEIDRTGV
+GKVNKRKLRADYADALTSGR
+>PROKKA_01756
+MQTTDTVLGTPSTMGDDEQLTTTRLLRDAARTFGDQQIIHTRGGGSPWQTTTYAAVWERV
+RRMAAALRAEGVGPGDRVGLLLWNDVRHLESYFSVPLLGATMVQLNLRLAPTDLAYVITH
+AQVGTIVVDETLLELAAALEPHLPGGIRWIVAGDGELPADWAGRDDVLSYEALLDGHEPL
+ETADLPNVSERSASGACYTTGTTGRPKGVFYSHRATWLHAHAVVSTLGMTMADTALLLTP
+MFHAQCWGLPFAAVAVGARLVLPGRFNLTDTPWLTSTLVDHGVTVAPAAPAILMPMLHHL
+RTLETPPRMDGVRLLCGATEPPVAMMRGFDELTGAEVIHAYGATETSPIVSLNRMKPSLM
+DTLSEDERWNLKRFQGLVVVGVDVKITDPLGELLPPGEENVGEIRLRGPWVTTSYADNAE
+ATEAGFDDEGYWRSGDLGYLSPEGYLKVTDRLKDVVKSGGEWISSIDLENHIMTVPGVRD
+AAVIGVPHPQWEERPLALVVRDEDSGVDQDAVLAALAERFATWQLPDEVRFVTEIDRTGV
+GKVNKRKLRADYADALTSGR
+>PROKKA_01081
+MSTAPRRRVTGYPSTSGDDVQLNTTTLIRHAARTHGDQEIVYRTPDGGWDRYTYAEAYER
+IRRAANAMTGLGVSPGDRVGVIDWNSRRHYELYWAIPGIGATMVQVNLRLAPEDLVHVLT
+DSGCTTVFVDESLLRHAEVIAPRLPEVTTWVVMTDRPLSEIETTLPGVRHYEDLLASASP
+DVDWPEVEETSAYGACYTTGTTGRPKGVFYSHRAIVLHSYALAASIGMTLRDATMIITPM
+FHGQAWGLPQAATLMANKIVLPGRYMAEDTAPLTDALIAEEVTITSGAPAIFQPMLAYIE
+TLDEKPDLSRLRMISGATEPSLSLMRGFRDLTGAEVVHAYGATETTPLVTVNRYKPGVLA
+RLDEPALMDLKRKQGLPLTNVDLRIVGPGDENLPFDGVSQGEICVRGPWVTTGYHGMSEA
+DAEGRFLDGYWRSGDVGTVDSDGYLKVTDRLKDVIKSGGEWISSIDMENLLTSHPAITEA
+AVVGLPHPKWQERPYVQVMLRPGATITLAEVHEHLSGAFASWQLPERVDVVTELPRTSVG
+KIDKKTIRGRHTDLYADASEAARPGGGAGDVEEGGRA
+>PROKKA_00730
+MNSATAPVLGTPSTMGDDEQLTTSRLFRDAARTYPDQSITHRTIDGEWKVTDYAATWERM
+QRVAAGLASLGVGPRDRVGLLLWNDLRHFECYFAVPLTGATMVQLNLRLAPQDLAYVIGH
+SGARTIVVDATLLPLAEALGPHLPEDTRWIVATDGALPDSWAGRADTMSYEDLIERSAPI
+EDAPDMDERSASGACYTTGTTGRPKGVFYSHRATWLHAFAIAANTGMTMDDTVMLLTPMF
+HAQCWGLPYASVAVGARVVLPGRFTMQDTALLTESLVEHGVTVAPAAPAILLPMLHYLEG
+MEETPHLPGLRFLCGATEPPVALMQGFDRLMGAEIIHAYGATETSPVVSVNRLRPALAER
+LSEDEQWDLKRYQGLVVTGVDVKVVDPMGQPLPPGERNVGEVMIRGPWITRSYFENPEAT
+EKGFDDEGYWRSGDVGHLSEEGYLKIADRMKDVVKSGGEWISSIDLENHLLTVPGVSEAA
+VVGVPHPTWQERPIALVVRTAGADLSEEQVKAALGARFASWQVPDRVLFVDELDRTSVGK
+LDKKRLRQVYADALAQGDGPGAPSA
+>PROKKA_01984
+MQTTDTVLGTPSTMGDDEQLTTTRLLRDAARTFGDQQIIHTRGGGSPWQTTTYAAVWERV
+RRMAAALHAEGVGPGDRVGLLLWNDVRHLESYFSVPLLGATMVQLNLRLAPTDLAYVITH
+AQVGTIVVDETLLELAAALEPHLPGGIRWIVAGDGELPADWAGRGDVLSYEALLDGQEPL
+ETADLPNVSERSASGACYTTGTTGRPKGVFYSHRATWLHAHAVVSTLGMTMADTALLLTP
+MFHAQCWGLPFAAVAVGARLVLPGRFNLTDTPWLTSTLVDHGVTVAPAAPAILMPMLHHL
+RTLETPPRMDGVRLLCGATEPPVAMMRGFDELTGAEVIHAYGATETSPIVSLNRMKPSLM
+DTLSEDERWNLKRFQGLVVVGVDVKITDPLGELLPPGEENVGEIRLRGPWVTTSYADNAE
+ATEAGFDDEGYWRSGDLGYLSPEGYLKVTDRLKDVVKSGGEWISSIDLENHIMTVPGVRD
+AAVIGVPHPQWEERPLALVVRDEDSDVDQDAVLAALAERFATWQLPDEVRFVTEIDRTGV
+GKVNKRKLRADYADALTSGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000152.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000152.fa
new file mode 100644
index 0000000000000000000000000000000000000000..56a9c763333273bcd622cb8d7287e0b78b5cd78b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000152.fa
@@ -0,0 +1,59 @@
+>PROKKA_01939
+MEATVEQITAAITALNDKYWYVVMALLFVAGVWFTIRTVGVQVRMLPEMLRSVTAKSQTG
+FENDGVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWLLAIIGGATAFVESTL
+AQLYKQKGSDGYFGGPAYYIRDGLGAKWLAAVFAVAITVTYGFVFNAVQSNSISESVQAN
+WGASSTTAWIVGLGLAALTGLVIFGGVRRLSAVTNVLVPVMATFYIFLALIVMVVNITEV
+PGMIALIVGHAFGLREVAGAAVGMTMVMQGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQ
+GFVQSLGVYFDTLIVCSATAFVILLSNPAYGRGEAIGMQVTQGALQQAVGAWAGPALTVI
+IFFLAWSSVLGNTYYGEANIRYLAGRHAGPAITVFRVLVLVCVVGGALGSVALVWNLADT
+FAALMATINLVAIIPLGGLAVKLLRDYERKLKAGMNPGFHISDLPEARNVALWRDEPKTS
+PLQD
+>PROKKA_01635
+MEATVEQITAAVTAFNDKYWYVVMALLFVAGVWFTIRTVGVQVRMLPEMLRSVTAKSQTG
+FENDGVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWLLAIIGGATAFVESTL
+AQLYKQKGADGYFGGPAYYIRDGLGAKWLAAVFAVAITVTYGFVFNAVQSNSISESVQAN
+WGASSTTAWIVGLGLAALTGLVIFGGVRRLSAVTNVLVPVMATFYIFLALIVMVVNITEV
+PGMIALIVGHAFGLREVAGAAVGMTMVMQGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQ
+GFVQSLGVYFDTLIVCSATAFVILLSNPAYGRGEALGMQVTQGALQQAVGAWAGPALTVI
+IFFLAWSSVLGNTYYGEANIRYLAGRHAGRAITVFRVLVLVCVVGGALGSVALVWNLADT
+FAALMATINLVAIIPLGGLAVKLLRDYERKLKAGMDPGFHISDLPEARNVALWRDEPKTS
+PLQD
+>PROKKA_00920
+MEAITAAVSAFNDKYWYVVMALLFTAGVWFTIRTVGVQVRMLPEMLRSVTAGSQKGFEND
+GVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWVLAIIGGATAFVESTLAQLY
+KQKGPDGFYGGPAYYIRDGLRSKWLAAVFAVAITVTYGFVFNAVQSNSISESVQANWGVS
+TTTAWIVGVALAVITGLVIFGGVRRLSAVTNVIVPVMAVFYLVLALIVMAVNITEIPGLI
+ALIVGHAFGLQEVTGAAVGMAMVMMGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQGFVQ
+SLGVYFDTLIVCSATAFIILLSNPSYGDGEALGMAVTQGALQQAVGAWAGPALTVIIFFL
+AWSSVLGNTYYGEANIRYLAGKRADAAITVFRVLVLLCVVGGALGSVALVWNLADTFAAL
+MATINLVAIIPLGGLAVKLLRDYERKLKAGEDPGFHVSDLPEARNVALWQDTPETAPLQK
+>PROKKA_00854
+MGALADAISAFNSKYWYLVMALLAFAGVWFTVRTVGVQVRMLPEMIRSVAAKSPEGGADD
+GVSPFRAFTISAASRVGTGNVAGVAIAIVLGGPGAVFWMWVMAILGGATAFVESTLAQLY
+KRKDRDGFFGGPAYYIRDGLGLKWLAALFAVAITVTYGFVFNAVQSNSISESVQANWGAS
+TTTAWIVGVALAVITALVIFGGVQRLSSVTNVIVPVMAVAYVLLAVVVMVINITEIPAMF
+ALIVRHALGFEQVAGAAVGMAMVMQGVRRGMFSNEAGMGSAPNAAAAAAVSHPAKQGFVQ
+SLGVYFDTLLVCSATAFIILLSNPEYGNTDALGMVVTQNALQQAVGAWAGPFLTVVIFFL
+AWSSVLGNTYYGEANIRYLAGERAPQWITAFRVLVLLCVVGGALGTVSLVWNLADTFAAL
+MATINLVAIIPLGGLAVKLLQDYERKLKAGEDPHFRLADLPEAKNVPLWGDEDAELMRTE
+QGHGAGAREELHHADRPGRGHGGGSHSA
+>PROKKA_02134
+MDAFVTAATDGLGELSGIIWGPFVLIPLLFLTGLYLTIRLGFVQFLRLGAGLHLGLLRRK
+DDGDAEGEISQFQALTTALAATVGTGNIVGVATAIAVGGPGALFWMWVTGVLGMASKYSE
+AFLAVRFRTTDDAGEKSGGPQYYLQRGIKGGLGKGLALFFSVAALLACFGIGNMTQGNSI
+AVNVDSAFGVPTWITGAVLAVMTMVVLVGGIKSIGKVTAGFVPVMIVFYVLGALWILIVN
+ASAIPSAFATIFTEAFTGSAAVGGFTGSAMIVAVQYGMARGIFSNESGMGSAAIAAAAAQ
+TTHPVRQGLVSMTQTFIDTIIVVTCTGLVLITTGTWTEGKATAATMTSDAFATGLPGNWG
+HWIVTIGLVMFAYSTILGWSYYGERQVERLFGTRLIMPFRVLFSLVVFFGCTTELDLAWT
+FSDVMNGLMAIPNLLGLLILSGLIARETRLYLKHDPKLVATEAQIRDFMAEDPGYREWLA
+QEKQLDRAHAEHLHPHATGGSSVR
+>PROKKA_01858
+MEATVEQITAAITALNDKYWYVVMALLFVAGVWFTIRTVGVQVRMLPEMLRSVTAKSQTG
+FENDGVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWLLAIIGGATAFVESTL
+AQLYKQKGSDGYFGGPAYYIRDGLGAKWLAAVFAVAITVTYGFVFNAVQSNSISESVQAN
+WGASSTTAWIVGLGLAALTGLVIFGGVRRLSAVTNVLVPVMATFYIFLALIVMVVNITEV
+PGMIALIVGHAFGLREVAGAAVGMTMVMQGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQ
+GFVQSLGVYFDTLIVCSATAFVILLSNPAYGRGEAIGMQVTQGALQQAVGAWAGPALTVI
+IFFLAWSSVLGNTYYGEANIRYLAGRHAGPAITVFRVLVLVCVVGGALGSVALVWNLADT
+FAALMATINLVAIIPLGGLAVKLLRDYERKLKAGMNPGFHISDLPEARNVALWRDEPKTS
+PLQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000154.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000154.fa
new file mode 100644
index 0000000000000000000000000000000000000000..478969ace7cfe62a7cd3df0836c6b3f3216ec83a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000154.fa
@@ -0,0 +1,24 @@
+>PROKKA_01983
+MTPALISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGVIAAGLAV
+AGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVVGLFLGFAVGLFASQWARTR
+DARAALSSSIGALTAMGVGMLVEFCCALGSLTAVGVGALVHGLTA
+>PROKKA_01677
+MTPALISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGVIAAGLAV
+AGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVVGLFLGFAVGLFASQWARTR
+DARAALSSSIGALTAMGMGMLVEFCCALGSLTAVGVGALVHGLTA
+>PROKKA_00875
+MTLAIVVSVLAVLLLIVGVVGTVYPILPGSMLILVTAVAWAWILGSGASWTFGLLAAGLA
+VAGMSASAVLTGRRLLRERVTRGPIAAGVVGAIVGFFVIPVVGLFIGFAVGLFGSQWART
+KDARAALASSWGALKAMGLGMLVELGCAMLALVSVGVGILVHFVF
+>PROKKA_00810
+MTPALISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGLIAAGLAV
+AGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVAGLFLGFAVGLFASQWARTR
+DARTALSSSIGALTAMGVGMLVEFCCALGSLTAVGVGALVHGVTA
+>PROKKA_00823
+MTFAILVSLLAVLLLIVGLVGTVYPVLPGSVLNAVVSLAWAWVLGSVASWTFGLIACAFS
+IAGMSASAALTGRRLVKERIPRGPILTGVAAAVVGFFVIPVVGVFVGFAAGLFGAEWARR
+RDARAALTSSWGALKAMGLGMLVEFGCAMVALASVGAGALVHVLSL
+>PROKKA_01909
+MTPALISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGVIAAGLAV
+AGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVVGLFLGFAVGLFASQWARTR
+DARAALSSSIGALTAMGVGMLVEFCCALGSLTAVGVGALVHGLTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000155.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000155.fa
new file mode 100644
index 0000000000000000000000000000000000000000..382fc58db688ed06c02ea9b04b2737d14a82dfad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000155.fa
@@ -0,0 +1,30 @@
+>PROKKA_01985
+MSPQKTVGVLALQGDVREHVHVLESLGARTRPVRRPADLEGLDGIVLPGGESSVMDRLAR
+IMGMRDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVDS
+FEEDLDIPAVAAEPVHAVFIRAPAVLQAGEGVEVLASVPASRLSVPAADPGLDGDARLPV
+AVRQGHLLATAFHPEVTGDWSFHRAFLAGL
+>PROKKA_01679
+MSPQKTVGVFALQGDVREHVHVLEALGARTRPVRRPADLEGLDGIVLPGGESSVMDRLAR
+IMGLKDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVDS
+FEEDLDIPAVAAEPVHAVFIRAPAVLQAGEGVEVLASVPTSRLSVPAADPGLDGDARLPV
+AVRQGHLLATAFHPEVTGDWSFHRAFLAGLRPPRAPRR
+>PROKKA_00872
+MSALLVGVFALQGDVREHVRVLEGLGARTRPVRRAADLTGLDGIVLPGGESSVMDRLAGL
+MGLKEPLADAIGAGLPAYGTCAGIILLAREIQNPAPGQGSLGVLDVTVRRNAFGAQVDSF
+EADLEVPAVSAEPVHAVFIRAPAVLRAGGEVEVLASVPASRLSAAPPELGLDDAAQVPVA
+VRQGRVLATSFHPEVTGDHSFHREFLRGL
+>PROKKA_00808
+MSPQKTVGVFALQGDVREHVHVLESLGARTRPVRRPADLEGLDGIVLPGGESSVMDRLAR
+IMGLKDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVDS
+FEEDLDVPAVAAEPVHAVFIRAPAVVQAGEGVEVLASVPASRLSLPAADPGLDGDARLPV
+AVRQGHLLATAFHPEVTGDWSFHRAFLAGL
+>PROKKA_00818
+MRAVQKTVGVFALQGDVREHVHVLEALGARTRPVRRPADLAGLDGIVLPGEESSVMDRLA
+RIMGLRDPLAEAVRAGLPVYGTCAGMILLAAGIENPAPGQGSLGVLDVTVRRNAFGSQAD
+SLEADLQVPAVSADPMHAVLIRAPAVVRVGEGVEVLASVPAARAVAASSSTAETDDGAPA
+ADLPVAVRAGNVSATSFHPEVTGDWSFHRAFLAGL
+>PROKKA_01911
+MSPQKTVGVFALQGDVREHVHVLEALGARTRPVRRPADLEGLDGIVLPGGESSVMDRLAR
+IMGLKDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVDS
+FEEDLDVPAVAAEPVHAVFIRAPAVLQAGEGVEVLASVPASRLSVPAADPGLDGDARLPV
+AVRQGHLLATAFHPEVTGDWSFHRAFLAGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000156.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000156.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f78ff6072775672495d9bbc7cacf52cd4ee4d40b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000156.fa
@@ -0,0 +1,54 @@
+>PROKKA_02014
+MSHTVASPAAPVPARDRREERKVIAGTVVGTTIEWYDFFIFAQATALVFAALFFQPMGEN
+GSQIAAWVTLGISFLVRPLGAIVAGHLGDRFGRKLVLSLTLIGMGLATTLIGLLPTYAQI
+GVWAPILLVALRLLQGLSAGGEWGGAALLSVEHAPHGKRGLFGSAPQIGVPLGMILATGV
+LFIVRSTMSEEQFLTWGWRIPFLISVILIVVGYLIRKAVEESPVFKEMQQLKVDESAPLG
+ELFRHHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLVGGVGWFI
+FTLLGGWVSDKIGRKLTFVFGYGFLIVWAFPLFGLLNTASLPLFSLGLFVLTLGLGPSYG
+PQSAMYAEMFPARVRFSGVSIGYALGTIIGGAFAPLLADQLVKTGWENVAWYIIVISAIS
+LIAVLFVPKGIQDRELHDEQVVATRSNPVVPT
+>PROKKA_01724
+MSHTVASPAAPAPARDRREERKVIAGTVVGTTIEWYDFFIFAQATALVFAALFFQPMGES
+GSQIAAWATLGISFLIRPLGAIVAGHLGDRFGRKFVLSLTLIGMGLATTLIGLLPTYAQI
+GVWAPILLVALRLLQGLSAGGEWGGAALLSVEHAPHGKRGLFGSAPQIGVPLGMILATGV
+LFIVRSTMSEEQFLTWGWRIPFLISVVLIVVGYLIRKAVEESPVFKEMQQLKVDESAPLG
+ELFRHHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLVGGVGWFI
+FTLLGGWVSDKIGRKLTFILGYGFLIIWAFPLFGLLNTASLPLFSLGLFVLTLGLGPSYG
+PQSAMYAEMFPARVRFSGVSIGYALGTIIGGAFAPLLADQLVKTGWENVAWYIIVISAVS
+LIAVLFVPKGIQDRELHDEQVVATRSNPVVPA
+>PROKKA_00129
+MAEFSAAPTAHPAESDTHVSPAQRRKAFVGAIAGHLIEWYDYGVYGFLAVYVAANFFKSE
+NPMVGILAAFAVFALSFFVRPLGGLFFGPLADKIGRRKTLMIVLGLMCGATAVIGMLPTY
+ATIGVFAPILLVLMRLVQGFSAGGEVSTISAFVAEYAVKGRRGFATSFLMVTAASGLLLG
+GVVANGLGAIIGTEAMAEWGWRLPFLLAGVLGVVAVFIRMKLEDSPEFRRLHSEGKTSKT
+PLRETLRYQRQLFLMGALITLLGSTFYLVLTYLTTYMRTILELTPGAIFWLVLLTGAAAA
+AFMPVGGAISDRMGDRRPMLAIGAVLVAGAVVWFFLTAPGTDGGLPLVPSLLALGITTGL
+YCGVPYATMTELMPAHVRSTGIALGYNVPVAVFGGSAPFIASWLINETGDVASPMYFFLL
+TAAIALVGVAMLRPTDLLGHEDVPVTGSIDAVGGKVTRTVAPRPKADAL
+>PROKKA_00826
+MSHTTVAHGAEHPARTRDRAEERKVLAGTLVGTTIEWYDFFIYAQAAALVFAPLFFAPMG
+EQGAQIASWASLGISFLVRPLGAIVAGHMGDRFGRKLVLSLTLIGMGAATVLIGLLPTYA
+SIGIWAPILLVVFRLLQGFSAGGEWGGAALLSVEHAPRGKRGLFGSAPQIGVPLGMLLAT
+GVLFAVRASMTNEQFLAWGWRIPFLISVILIFIGYIIRKAVEESPVFKEMQQLKKDESAP
+LGELFRNHTKEVVLAALIFAANNAVGYLVIAWFSKYGQKNLGMAPNDTLIAALVGGFGWF
+IFTLFGGWISDKIGRKTAFVAGYALIIAWAFPMFQMMNTASLPMFAAALFILSIGLGPSY
+GPQSAMYAEMFPARVRFSGVSIGYAIGAIIGGAFAPLIADLLLNDGGWVPVAWYMIIISA
+VSLIAVLFVPKGIQDRNLHDEGVVVAETGTREPVA
+>PROKKA_00765
+MSHTVASPAVAAARDPREERKVLAGTLVGTTIEWYDFFIFAQATALVFATLFFQPMGESG
+AQIAAWVTLGISFLVRPLGAIIAGHLGDKFGRKLVLSLTLIGMGAATTLIGLLPTYAQIG
+VWAPILLVLLRLLQGFSAGGEWGGAALLAVEHAPHGKRGLFGSAPQIGVPLGMILATGVL
+FLVRSTMSEEQFLTWGWRIPFLVSVLLIVVGYFIRKAVEESPVFKEMQQLKVDESAPLGE
+LFRHHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLVGGVGWFIF
+TLLGGWISDKIGRKTTFVIGYAILIAWAFPMFQLLNTASLLLFSLALFVLTMGLGPSYGP
+QSAMYAEMFPARVRFSGVSIGYAIGTIIGGAFAPLIADELVKSGWPSVAWYIIGISAISL
+IAVLFVPKGIQDRELHDEEVVATRSNPVVPA
+>PROKKA_01952
+MSHTVASPAAPVPARDRREERKVIAGTVVGTTIEWYDFFIFAQATALVFAALFFQPMGES
+GSQIAAWVTLGISFLVRPLGAIIAGHLGDRFGRKLVLSLTLIGMGLATTLIGLLPTYAQI
+GVWAPILLVALRLLQGLSAGGEWGGAALLSVEHAPHGKRGLFGSAPQIGVPLGMILATGV
+LFIVRSTMSEEQFLTWGWRIPFLISVALIVVGYLIRKAVEESPVFKEMQQLKVDESAPLG
+ELFRNHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLIGGVGWFI
+FTLLGGWISDKIGRKLTFVLGYGFLIVWAFPLFGLLNTASLPLFSLGLFVLTLGLGPSYG
+PQSAMYAEMFPARVRFSGVSIGYALGTIIGGAFAPLLADQLVKTGWENVAWYIIVISAIS
+LIAVLFVPKGIQDRELHDEQVVATRSNPVVPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000160.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000160.fa
new file mode 100644
index 0000000000000000000000000000000000000000..55ae04ae58282c2649b5f701447335c20f4e3d02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000160.fa
@@ -0,0 +1,25 @@
+>PROKKA_02072
+MTTKRPSVLFVCVKNGGKSQMAAALMRHHAGDAIEVHSAGTRPGTALNAQSTEAIAEVGA
+DMSSAVPQPVTPELLRSVDHVIVIGDEAVIKPVEGMTAPVTTWYTDEPSQRGIEGMERMR
+LVRDDIDIHVRKLLTDLTQPST
+>PROKKA_00736
+MSEPTTLDTHVLQRSAEHLAECYAGVFSPETVERYVFESYATLSRTAKVRTYLASTASHF
+ADNRLRALAQSEGKIASPVPQVLFVCVHNIGRSQIAAALLTHHAGDKVEVRSAGSLPGSE
+VHPLVVQALAERGIDLSGAYPKPLTDDVVRAADYVITMGCGDACPVYPGKRYLDWEIADP
+AAETPDGVRAIVDAIDTRVKALWDELRSAT
+>PROKKA_00740
+MTAETTPETTKPSVLFVCVHNAGRSQMAAAYLQRLAGGRIEVRSAGSAPADTVNPAAVEA
+MAEEGIDISANQPKVLSEQAVKDSDVVITMGCGDACPFFPGKRYEDWKLDDPAGRGVEGV
+RPIRDEIKTRIQQLITELLPAESTAN
+>PROKKA_00741
+MTTPESASRPSVLFVCAKNGGKSQMAAALMEHHAAGAVQVHSAGTKPGKSINALSAEVIA
+EAGADMSAGHPKPIDPDLLARVDRVVVLGDEARVEPVDGMAGTIVTWHTDEPSTRGIEGI
+ERMRLVRDDIDARVRTLLTELTGSPAS
+>PROKKA_00488
+MTSDRPSVMFVCVHNAGRSQMAAAYAQHLSGGAVEVRSAGSAPADQVNPAVVEAMAEEGI
+DLSAERPKVLTPEAVQASDAVITMGCGDACPLYPGKRYEDWVLEDPAGRGVDAVRPIRDE
+IRGRVAGLLRELGVEPVA
+>PROKKA_02000
+MTTKRPSVLFVCVKNGGKSQMAAALMRHHAGDAIEVHSAGTRPGTALNAQSTEAIAEVGA
+DMSSAVPQPVTPELLRRVDQVIVIGDEAVIKPVEGMTAPVTTWHTDEPSQRGIEGMERMR
+LVRDDIDTHVRKLLTDLTGTAN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000161.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000161.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c2d417fde42d6abcd8a5b59a5b638f780ee4d194
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000161.fa
@@ -0,0 +1,42 @@
+>PROKKA_02079
+MPDIIEFPLPASSDDPHWRAYCRLGDEYNHELIGTTEWDETPTDALIQAAAETDHTQRRY
+LAYVDGEAVGYARVLINHVDDPDAAALNVYVLPRHRGRGHGRALAERLVQDTAGLTRFET
+WPLTPRPVAGQRTLTPPNGAGAVPAEHPGVRLAQSYGFALVQIERVSRYDFADPGIDPAV
+ALAEAERVSSDYELHAWEGAADASLQDDLAVLKARMATDVPSGERTVVEQVWDAARVRRM
+DEQILTTGRLFRAVARHRATGRIVALSELVAPRSRPDGLIDQWDTIVLPEHRGHRLGMRV
+KAANLIAVRDALPEARAIITWNAEENRHMLDVNEALGFRPVLVEASMEAPAPLRRR
+>PROKKA_01783
+MPDIIEFPLPASSDDPHWRAYCHLGDEYNHELIGTTEWDETPRDALIQAAAETDHTQRRY
+LAYVDGEAVGYARVLINHVDDPDAAALNVYIHPRHRGRGHGRALAERLVLDTAGLTRFET
+WPLTPRPVAGQRTLTPPNGAGAVPAEHPGVRLAQSYGFALVQTERVSRYDFADPGIDPAV
+ALAEAEGVSSDYELHAWEGAADASLQDDVAVLKARMATDVPSGERTVVEQVWDAARVRRM
+DEQILTTGRLFRAVARHRATGRIVALSELVAPRSRPDGLIDQWDTIVLPEHRGRRLGMRV
+KAANLIAVRDALPGARAIITWNAEENRHMLDVNEALGFRPVLVEASMEAPAPLRRR
+>PROKKA_00705
+MPDIIEFPLPASSDDPHWRAYCQLGDEYNHELIGTTEWDETPTDALIQAAAETDHTLRRY
+LAYVDGEAVGYARVLINHVDDPDAASLTVYVHPRHRGRGHGRALAERLVLDTAGLTRFET
+WPLTPRPAVGQRALTPPNGAGMVPAGHPGVRLAQSYGFALVQIERVSRYDFADPGIDPAV
+AVAEAERVSSGYELHAWEGAADASLQDDLAVLKARMATDVPSGERTVVEQVWDAARVRRM
+DEQILTTGRLFRAVARHRATGRIVALSELVAPRSRPDGLIDQWDTIVLPEHRGHRLGMRV
+KAANLIAVRDALPEARAIITWNAEENRHMLDVNEALGFRPVLVEASMEAPAPLRRR
+>PROKKA_00615
+MPDIIEFPLPASSDDPHWRAYCQLGDEYNHELIGTTEWDETPTDALIQAAAETDYTQRRY
+LAYVDGEAVGYARVLINHVDDPDAASLNVYVHPRHRGRGHGRALAERLVQDTAGLTRFET
+WPLTPRPVAGQRALTPPNGAGVVPAEHPGVRLAQSYGFALVQIERVSRYDFADPGIDPAV
+ALAEAERVSSDYELHAWEGAADAALQDDLAVLKARMATDVPSGERTVVEQVWDAARVRRM
+DEQILTTGRLFRAVARHRATGRIVALSELVAPRSRPDGLIDQWDTIVLPEHRGHRLGMRV
+KAANLIAVRDALPEARAIITWNAEENRHMLDVNEALGFRPVLVEASMEAPAPLRRR
+>PROKKA_00619
+MPDILEFPLPATADEAHWQAYCRLNRDHNHELLGTTEWDESPDDALLDAAAESDYTLRRF
+LALDDGTPVGNGRILVNHVDEPDAASLSVFIHPDHRRRGHGRALAERIAREADGFTRFET
+WPMTPLPAEGERALRPSSGAGAVPADHPGVRLALSYGFALGQVERVSRYDVLTPAVDPAD
+ALAEAERPGADYEVLTWEGPADEAVRADLAVLKERMATDVPSGDLTVAEQTWDAGRVRRQ
+EEQILLTGRLFRAAVRHRDTGRIVGVNELVAPRSRTSGLVDQWDTIVSPEHRGHRLGMRV
+KAANLVALRRALTEARAIITWNAEENRPMLDVNEALGFQPILVEAEMQAHGPLRRVVP
+>PROKKA_02017
+MPDIIEFPLPVSSDDPHWRAYCQLGDEYNHELIGTTEWDETPTDALIQAAAETDHTLRRY
+LAYVDGEAVGYARVLINHVDDPDAAALNVYVHPRHRGRGHGRALAERLVLDTAGLTRFET
+WPLTPPPVAGQRALTPPNGAGAVPAEHPGVRLAQSYGFALAQIERVSRYDFADPGIDPAV
+ALAEAERVSSDYELHAWEGAADASLQDDLAVLKACMATDVPSGERTVVEQVWDAARVRRM
+DEQILTTGRLFRAVARHRATGRIVALSELVAPRSRPDGLIDQWDTIVLPEHRGHRLGMRV
+KAANLIAVRDALPEARAIITWNAEENRHMLDVNEALGFRPVLAEASMEAPAPLRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000162.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000162.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16212ea6156b06480e5f276362d92db98a606804
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000162.fa
@@ -0,0 +1,22 @@
+>PROKKA_02093
+MTDTTTARPKRPAHRDDGPPVRGIGHLRHPAVSGGLIGVIGGGAFLFGGIAGLPAEHRAT
+LRGIAISLISFTLVVVLLRRRMLPTVPTPARGALRVYGIAVVAMLAFLPVTRLVALALDA
+PTAQIALVAAVVGGHFLPFARAFQAPVFWWIGGAMAALGLAGAALAALGDPVAGPAGAAA
+AGVAMLVIVAAQGLLASPRQD
+>PROKKA_01800
+MSHVMRGGTMTDTTTARPMRPAHFDDDPPVRGIGHLRHPVVWGGLIGVVGGGAFLFGGIA
+GLPAEHQGTLRGSAIALIGFTLVVVLLRRRVLPAVQAPARGASTGSPSSRCWRSSP
+>PROKKA_01801
+MLALLPVTRLVALALDAPTAQIALVAAVVGGHFLPFARAFQAPVFWWIGGAMAVLGLAGA
+VVAVLGDPVAGPAGAAEAGAAMLVIVAAQGLLASPRQD
+>PROKKA_00685
+MSHVTRGGTMTDTTTARPMRPTHHDDDPPVRGIGHLRHPVVSGGLIDGAMAAQGLLASPR
+PD
+>PROKKA_00555
+MERDSTHARGIAHPMHPAVLGAVVGMVGGSLFMLLSRPELPFPWPTVTLVAWIALLAAAA
+WAVFLAPRRLRDVGAPSRHAGPIYGLSVLGMVALIIASPHLVRALGIEAAQPAVVVMAVG
+LHFIPFASAFGARVFAWLGGSLTAIGLAGVIAAAVVGAPAGAVAAVLAGAAMLAFLAVDA
+RRGA
+>PROKKA_00601
+MSHVMRGGTMTATTTARPMRPTHHDDDPPVRGVGHLRHPVVSGGLIDGAMAAQGLLASPR
+QD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000165.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000165.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4af88eaf5579662dcf16f532c7208fdd3cf1bdf5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000165.fa
@@ -0,0 +1,24 @@
+>PROKKA_02162
+MRADARANRQDLLAAAGRLIATQGAAMSLRGVAQEAGVGVRTLYRHFPTRRDLLDAVLED
+VVARTGGILQAFLDGVGGDGHGGGTEARWRRLAEDLGAVNLASLAAARDDFDPADRPPEA
+LIAEAERVILELADQVVAEARRAGLVGPDVTGADYLFGLLMVTRSPECALLGHGPDQRGW
+LLDTYLRGLRP
+>PROKKA_01875
+MILELADQVVAEARRAGLVGPDVTGADYLFGLLMVTRSPECALLGHGPDQRGWLLDTYLR
+GLRP
+>PROKKA_01876
+MRADARANRQDLLAAAGRLIATQGAAMSLRGVAQEAGVGVGTLYRHFPTRRDLLDAVLED
+VVARTGGILQAFLDGVGGDGHGGGTEARWRRLAEDLGAVNLASLAAARDDFDPADRPPRP
+SSPRPSV
+>PROKKA_00595
+MRADARANRQDLLAAAGRLLEEQGAAMSLRGVAQEAGVGVGTLYRHFPTRRDLLDAVLED
+VVARVSGILHAFLDGGGSADRRWRRLAEELAAVNLTSLVTAGDDLEAADRPQEALIVEAE
+QVIISLTDRAVTEARRAGLVALGVTGTRYLTGLLAVTRPPAGELLARHADQRDWLLGVYL
+RGLRP
+>PROKKA_00518
+MQEEDTPPAEAMGRAEDAVMGLADRAVDLAREAGLVGDDVTGRAYMNGLIAVTRPPLPAL
+ESCRDDLEDWLLTVFLRGLRPAA
+>PROKKA_02107
+MRADARANRQDLLAAAGRLIATQGAAMSLRGVAQEAGVGVGTLYRHFPTRRDLLDAVLED
+VVARTGGILQAFLDGVGGDGHGGGTEARWRRLAEDLGAVNLASLAAARDDFDPADRPPEA
+LIAEAERVILELADQVVAEARRAGLMGPDVTGADYLLWVMRFLARGPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000168.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000168.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6295d1f23c58ba374109583be9011ee398277bb0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000168.fa
@@ -0,0 +1,42 @@
+>PROKKA_02252
+MTAQTPATPAIPETMKAVVMRAPGDVVVEEVDTPRVAQPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSQAQYMRVELADGSLVKVPGGEPSDPDRLADYLAASDVLGTGWYAAVAAQAGPGKT
+IAVVGDGAVGLCAVLGAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQVRE
+LTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFGRQIHLEGGP
+APVRRFLPELIERIQSGEIQPGRVFTARRPIDDAAEAYQAMDERREIKVLLEV
+>PROKKA_02276
+MTTETPTLAAPEIPATMKAVVMRAPGDVVVEEVDTPRVAQPTDVVLKLAAACVCGSDLWP
+YRGHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVN
+AGEYTGSQAQYMRVELADGSLVKVPGGEPSDPDRLTDYLAASDVLGTGWYAAVAAQAGPG
+KTIAVVGDGAVGLCAVLAAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQV
+RELTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFGREIHLEG
+GPAPVRRFLPELIERIQSGEIQPGRVFTARRPIDDAAEAYQAMDERREIKVLLEV
+>PROKKA_01951
+MTAQTLATPAIPETMKAVVMRAPGDVVVEEVDTPRVAQPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSRAQYMRVELADGSLVKVPGGEPSDPDRLADYLAASDVLGTGWYAAVAAQAGPGKT
+IAVVGDGAVGLCAVLAAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQVRE
+LTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFAREIHLEGGP
+APVRRFLPELIERIQSGEIQPGRVFTARMPLDDAAEAYRAMDERREIKVLLEV
+>PROKKA_00489
+MTAQTPATPAVPETMKAVIMRAPGDVVVEEVDTPRVAKPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSQAQYMRVELADGSLVKVPGGEPADPDRLADYLAASDVLGTGWYAAVAANAGPGKT
+IAVVGDGAVGLCAVLAAKTLGAEQVIAFSRHEDRAALAREFGADVIIAERGEEGAAKVKE
+LTNGYGAHGVCEAVGTQESMDQALASVRPGGHVGFVGVSHDQTIDGSRLFGLEIHLEGGP
+APVRRFLPELIERIQAGEIQPGRVFTARMPIDDAAEAYKAMDERREIKVLLEV
+>PROKKA_00435
+MTAQTPTTPAIPETMKAVVMRAPGDVVVEEVDTPRVVQPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSQAQYMRVELADGSLVKVPGGEPSDPDRLADYLAASDVLGTGWYAAVAAQAGPGKT
+IAVVGDGAVGLCAVLAAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQVRE
+LTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFGREIHLEGGP
+APVRRFLPELIERIQSGEIQPGRVFTARMPLDDAAEAYRAMDERREIKVLLEV
+>PROKKA_02183
+MTAQTLATPAIPETMKAVVMRAPGDVVVEEVDTPRVAQPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSQAQYMRVELADGSLVKVPGGEPSDPDRLADYLAASDVLGTGWYAAVAAQAGPGKT
+IAVVGDGAVGLCAVLAAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQVRE
+LTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFAREIHLEGGP
+APVRRFLPELIERIQSGEIQPGRVFTARMPLDDAAEAYQAMDERREIKVLLEV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000169.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000169.fa
new file mode 100644
index 0000000000000000000000000000000000000000..905cb4482f26ca493fe768b83014f7affcf0780a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000169.fa
@@ -0,0 +1,50 @@
+>PROKKA_02265
+MDVTFTPLDPAGADRDALVALLTENAWPFHTRPRVTRPEAEKAVDGGAWEDEDHRTFWIE
+HPEHGRVGVVRLEDLTDPTPLFDLRVAERFRGRGLGAQILTALTRHVFETMPAVDRFEGQ
+TREDNVPMLRTFRRAGWVKEAHYRRGWPVDGGEPLASVAYAMLRQDWASGTTTPVPADVD
+APPPAGRKEGAAAGGRAPDWPLPTARLTLRPHREDDLGWLQEMYMQPVVVRHLLDEPWDE
+ATARAKLAKRITWDDLGGPSGAVSLVVEHAGVPVGDVILWLTDRERGVAEIGWALDPRHA
+GQGFAREAAAALLDLGFETSGLHRVVAQMDARNTASARLAETLGMRREAHHRQDLWSKGE
+WTDTLVYAMLASDRGVRGHL
+>PROKKA_01960
+MDVTFTPLDPAGADRDALVALLTENAWPFHTRPRVTRPEAEKAVDGGAWEDEDHRTFWIE
+HPEHGRVGVVRLEDLTDPTPLFDLRVAERFRGRGLGAQILTALTRRVFETMPAVDRFEGQ
+TREDNVPMLRTFRRAGWVKEAHYRRGWPVDGGEPLASVAYAMLRQDWASGTTTPVPADVD
+APPPAGRKEGAAAGGRAPDWPLPTARLTLRPHREDDLGWLQEMYMQPEVVRHLLDEPWDE
+ATARAKLAKRITWDDLGGPSGAVSLVVEHAGVPVGDVILWLTDRERGVAEIGWALDPRHA
+GQGFAREAAAALLDLGFETSGLHRVVAQMDARNTASARLAETLGMRREAHHRQDLWSKGE
+WTDTLVYAMLASDRGGGGPSMTANGLLRSPHAARDREGVDSRGSPGVRTEVLEDLQVEKP
+LVRAGGLGEHRLVGADVDDLPHTEAGGLLRLKDRQVSVAGDAVDLGEPPRGPHLVCRPHH
+GPHTTQRDRPGGAAVVVMGDDPACRGQGPSLTHSPGGQQDQLVDFPHGDRVTAAFLLPVR
+ERGAADGADGDVHGRSVGAGPHPGARGASSPVMLGIGLEARRVKARTTHPHRVHRIDAMT
+RTGAFTIAGLAAFAISTGILVLLLITGSETPRETMAFFALIIGCYALSALCFAAAKRVLL
+ALLSGALAVVSFPLALFIGYVVEMLQSQQ
+>PROKKA_00469
+MDVTFTPLDPAGADRDALVALLTENAWPFHTRPLVTRPEAEEAVDGGAWEDEDHRTFWIE
+HPEHGRVGVVRLEDLTDPTPLFDLRVAERFRGRGLGAQILTALTRHVFETMPAVDRFEGQ
+TREDNVPMLRTFRRAGWVKEAHYRRGWPVDGGEPLASVAYAMLRQDWASGTTTPVPADVD
+APPPAGRKEGAAAGGRAPDWPLPTARLTLRPHREDDLGWLQEMYTQPEVVRHLLDEPWDE
+ATAREKLAKRITWDDLGGPSGAVSLVVEHAGVPVGDVILWLTDRERGVAEIGWALDPRHA
+GQGFAREAAAALLDLGFETSGLHRVVARMDARNTASARLAETLGMRREAHHRQDWWSKGE
+WTDTLVYAMLASDRG
+>PROKKA_00641
+MAERFRGRGLGAQILAALTRHVFETMPAVDRFEGQTREDNIPMLRAFRRAGWVKEAHYRR
+GWPVEGGEPLASVAYAVLRQDWETGTTTPVPADVDVPSRRKRDVGAESNGHIPDWPMRTE
+RLTLRPHREDDLGWLQEMYAQPEVVRHLLDEPWDEPTARQKLVRRIEWNDLAGPSGVASL
+VIEHAGVPVGDVILWLTNRERGVAEIGWALDPRHAGQGFAREAAAAMLALGFEVHGLHRV
+VAQMDARNTASARLAEAIGLRREAHHRQDWWSKGKWTDTLVYATLSSDRD
+>PROKKA_00419
+MDVTFTPLDPAGADRDALVALLTENVWPFHMRPRITRSEAEEAVDGGAWEDEDHRTLWIE
+HPEHGRVGVVRLDELTDPTPLFDLRVTERFRGRGLGAPILTALTRLVFETMPAVDRFEGQ
+TREDNVPMLRTFRRAGWVKEAHYRRGWPVEGGEPLASVAYAVLRQDWETGTTTPVPAEVD
+VPPQVEHGEGAAAVGPAPDWPLRTERLTLRPHREDDLGWLRDMYARPEVVRHLLDEPWDE
+ATARQKLAKRIAWDGLAGPSGAVSLVVEHRGVPVGDVILWLTDRERGVAQIGWALHPEHA
+GQGFAREAAAALLTLAFETYDLHRVVAQMDARNTASAQLAEAVGLRREAHHRQDWWSKGE
+WTDTLVYATLASDRG
+>PROKKA_02198
+MVRLEDLTDPTPLFDLRVAERFRGRGLGAQILTAITRHVFETMPAVDRFEGQTREDNVPM
+LRTFRRAGWVKEAHYRRGWPVDGGEPLASVAYAMLRQDWASGTTTPVPADVDAPPPAGRK
+EGAAEGGRAPDWPLPTARLTLRPHREDDLGWLQEMYTQPEVVRHLLDEPWDEATARAKLA
+KRITWDDLGGPSGAVSLVVEHAGVPVGDVILWLTDRERGVAEIGWALDPRHAGQGFAREA
+AAALLDLGFETSGLHRVVAQMDARNTASARLAETLGMRREAHHRQDLWSKGEWTDTLVYA
+MLASDRGVRGHL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000176.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000176.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6aa617886152c2e5239786650c3a237eaeba0c9f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000176.fa
@@ -0,0 +1,41 @@
+>PROKKA_00003
+MYLSHLTVADFRSYRWADLELTPGSTVLLGANGVGKTNLVEAIGYLGAQQSHRVSSDAQL
+VRFGRDRARIAGRVHRGSRAVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLSLVTGEPGGRRRLLDQLMVQLRPALGEAAADYERVLRQRNALLKSSRGSRRWGPEEDA
+TLAVWDEHLCAAGARLLHGRLHVLRLLARPLQEMYAALTNGSKAAAYAYESTVPLARGTH
+AEVPAVADLAVDMRRTLETQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRMAAYDVLVADDPDPDARPVLILDDVFAELDAARRRRLAALVHRAEQVIVTAAALE
+DVPEELTAHRVLIRQDAEGSEAVAAAAPVEGDIREPRREGGADG
+>PROKKA_02008
+MYLSHLTVADFRSYRWADLELTPGSTVLLGANGVGKTNLVEAIGYLGAQQSHRVSSDAQL
+VRFGRDRARIAGRVHRGSRAVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLGLVTGEPGGRRRLLDQLMVQLRPALGEAAADYERVLRQRNALLKAGRGSRRWGPEEDA
+TLAVWDEHLCAAGARLLHGRLHVLRLLARPLQEMYAALTNGSKAAAYAYESTVPLARGTH
+AEVPAVADLAVDMRRTLETQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRMAAYDVLVADDPDPDARPVLILDDVFAELDAARRRRLAALVHRAEQVIVTAAALE
+DVPEELTAHRVLIRQDAEGSEAVAAAAPVEGDIREPRREGGADG
+>PROKKA_00421
+MHLSHLTVADFRSYRWADLELGPGSTVLLGANGVGKTNLVEAVGYLGSHQSHRVSSDAQL
+VRFGQDRARIAGRVHRGSRTVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLNLVTGEPGGRRRLLDQLMVQLRPALGEAAADFERVLRQRNALLKSARKARRWGPEEEA
+TLEVWDEHLCAAGARLLHGRLHVLRLLAHPLREMYGALTNGSKAATYAYESTVPLARGTH
+AEVPPVAELAADMRRALVAQRDEEQARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRLAAYDVLVADDPDPDGRPVLILDDVFAELDAARRRRLAALVGRAEQVIVTAAALE
+DVPAELAGPRVLIRQDAEGSEAVPAAAPVEGDIRAPRGAGGTEGEAPGARRGRRRRRRHA
+PADPAEDDPDG
+>PROKKA_00374
+MHLSHLTVQDFRSYRWADLELSPGSTVLLGANGVGKTNLVEAIGYLGSHQSHRVSQDAQL
+VRFGQDRARIAGRVHRGARSVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLGLVTQDPGGRRRFLDQLMVQLRPALGQAAADYERVLRQRNALLKSARKARRWGAEEDA
+TLAVWDEHLCAAGARLLHGRLHVLRLLAHPLQEDYAALTNGSKTATYSYESTVPAARGTH
+VQAPPVAELAASMHAALVEQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRLAAYDVLVADDSDPEGRPVLILDDVFAELDAARRERLAGLVGRAEQVIVTAAALA
+DIPASLAGHRVLIRQDAEGSEAVAAAEPVEGDIRAPRPGAAPGAAASEAEEPEDGDARA
+>PROKKA_00003
+MYLSHLTVADFRSYRWADLELTPGSTVLLGANGVGKTNLVEAIGYLGAQQSHRVSSDAQL
+VRFGRDRARIAGRVHRGSRTVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLSLVTGEPGGRRRLLDQLMVQLRPALGEAAADYERVLRQRNALLKSSRGSRRWGPEEDA
+TLAVWDEHLCAAGARLLHGRLHVLRLLARPLQEMYAALTNGSKAAAYAYESTVPLARGTH
+AEVPAVADLAADMHRTLEAQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRMAAYDVLVADDPDPDARPVLILDDVFAELDAARRRRLAALVHRAEQVIVTAAALE
+DVPEELTAHRVLIRQDAEGSEAVAAAAPVEGDIREPRREGGADG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000178.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000178.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb63f5422c43a2c42cac1cfa54122c164c771626
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000178.fa
@@ -0,0 +1,65 @@
+>PROKKA_00005
+MPENPAEEPTAASAAPNPEAVPDAVGQPETPVKDRKVPGEYGASAITVLEGLEAVRKRPG
+MYIGSTGPRGLHHLVYEVVDNSVDEALAGYATGIDVTLQADGGVRVADDGRGIPVDLHPT
+EGRPTVEVVMTILHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSF
+ADGGVPQGELVKGEATDATGTVQTFYPDPEIFDSIEFDYETLRARFQQMAFLNRGLRITL
+TDERVQESNEVVDDEIAGEGAAGEDVAENGLAEDAEQEPQRRSVTYLYENGLLDYVQHLN
+SAKKVEYVHDNVIAFEAEDVSDGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEG
+FRAALTSLVNRYAREKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSE
+ARGFVSKAVTDHLGDWFERNPGPAKEIIRKAIMASHARLAARKARDNARRKSPLESFGMP
+GKLADCSSKDPERCEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGN
+AEIQSMITAFGTNIGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAG
+HVFLAQPPLYRIKWSNAPHDYVFSDEERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQ
+ELWDTTMDPEHRTLLQVTMEDAAAADAVFSMLMGEDVESRRTFIQQNAKDIRFLDV
+>PROKKA_02010
+MPENPAEEPTAASAAPNPEAVPDAVGQPETPVKDRKVPGEYGASAITVLEGLEAVRKRPG
+MYIGSTGPRGLHHLVYEVVDNSVDEALAGYATGIDVTLQADGGVRVADDGRGIPVDLHPT
+EGRPTVEVVMTILHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSF
+ADGGVPQGELVKGEATDATGTVQTFYPDPEIFDSIEFDYETLRARFQQMAFLNRGLRITL
+TDERVQESNEVVDDEIAGEGAAGEDVAENGLAEEAEQEPQRRSVTYLYENGLLDYVQHLN
+SAKKVEYVHDDVIAFEAEDVSDGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEG
+FRAALTSLVNRYAREKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSE
+ARGFVSKAVTDHLGDWFERNPGPAKEIIRKAIMASHARLAARKARDNARRKSPLESFGMP
+GKLADCSSKDPERCEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGN
+AEIQSMITAFGTNIGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAG
+HVFLAQPPLYRIKWSNAPHDYVFSDEERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQ
+ELWDTTMDPEHRTLLQVTMEDAAAADAVFSMLMGEDVESRRTFIQQNAKDIRFLDV
+>PROKKA_00419
+MLAAPSPDAAPETPEAPALAKDRRVPGEYGASAITVLEGLEAVRKRPGMYIGSTGPRGLH
+HLVYEVVDNSVDEALAGYASGIDVTLQADGGVRVADDGRGIPVDLHPTEGKPTVEVVMTI
+LHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSFADGGVPQGELVQ
+GEATDATGTVQTFYPDPEIFDSIEFDWETLRARFQQMAFLNKGLRITLTDERVQEDNEVV
+DDEIAGEAAAEENAEQGLDEAAAQAPQRRQVTYLYENGLLDYVQHLNSAKKVDFVHEDVI
+AFEAEDAEAGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEGFRAALTSLVNRYA
+REKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSEARAFVSKAVTDHL
+GDWLERNPGPAKEVIRKAIMASHARMAARKARDNARRKSPLESFGMPGKLADCSSKDPSR
+CEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGNAEIQSMITAFGTN
+IGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAGHVFLAQPPLYRIK
+WSNAPHDYVFSDAERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQELWDTTMDPEHRT
+LLQVSMEDAAAADAVFSMLMGEDVESRRNFIQQNAKDIRFLDV
+>PROKKA_00371
+MVDAAPEQPEQPSAPAPDTNPAHQVQEYGASAITVLEGLEAVRKRPGMYIGSTGPRGLHH
+LVYEVVDNSVDEALAGFADGIDVTLQADGGVRVQDNGRGIPVDIHPTEGKPTVEVVMTIL
+HAGGKFGGGGYAVSGGLHGVGISVVNALSTRVETEIRRQGHAWRMSFANGGIPQGELVKG
+EATEETGTVQTFWPDPEIFESVEFDYETLRARFQQMAFLNKGLRITLTDERVQEDNEVQE
+DEIVGEGTAGEDAAAENGLDDEQTPQRRCVTYLYEDGLLDYVKHLNSSKRAELVHEDVIA
+FDAEDAERGMALEVAMQWTTAYSESVHTYANTINTHEGGTHEEGFRSALTALVNRYAREK
+EILKAKDDNLSGEDIREGLTAVVSVKLSEPQFEGQTKTKLGNSEARGFVSKVVTDHLGDW
+LERNPGPAKDIIRKAVQASHARMAARKARDNARRKSPLESFGMPGKLADCSSKDPARCEV
+YIVEGDSAGGSAKQGRNPDTQAILPLRGKILNVERARLDKALGNAEIQSMITAFGTNIGE
+EFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAGHVFLAQPPLYRIKWSN
+APHDYVFSDEERDAAIEAGLARGWRYPKDNGVQRYKGLGEMNYQELWDTTMDPEHRTLLQ
+VTMEDAAAADQVFSMLMGEDVESRRNFIQQNAKDIRFLDI
+>PROKKA_00005
+MPENPAEEPTAASAAPNPEAVPDAVGQPETPVKDRKVPGEYGASAITVLEGLEAVRKRPG
+MYIGSTGPRGLHHLVYEVVDNSVDEALAGYATGIDVTLQADGGVRVADDGRGIPVDLHPT
+EGRPTVEVVMTILHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSF
+ADGGVPQGELVKGEATDATGTVQTFYPDPEIFDSIEFDYETLRARFQQMAFLNRGLRITL
+TDERVQESNEVVDDEIAGEGAAGEDVAENGLAEEAEQEPQRRSVTYLYENGLLDYVQHLN
+SAKKVEYVHDDVIAFEAEDVSDGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEG
+FRAALTSLVNRYAREKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSE
+ARGFVSKAVTDHLGDWFERNPGPAKEIIRKAIMASHARLAARKARDNARRKSPLESFGMP
+GKLADCSSKDPERCEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGN
+AEIQSMITAFGTNIGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAG
+HVFLAQPPLYRIKWSNAPHDYVFSDEERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQ
+ELWDTTMDPEHRTLLQVTMEDAAAADAVFSMLMGEDVESRRTFIQQNAKDIRFLDV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000181.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000181.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26defa0d436bbe710ab5bdf248c6f58a55dff3f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000181.fa
@@ -0,0 +1,10 @@
+>PROKKA_00009
+MGRLARVALVVSAAAAAYGARLWRENSARKDVWATATDDLPEDADGVEPAPED
+>PROKKA_02014
+MGRLARVALVVSAAAAAYGARLWRENSAGKDVWATATDDLPEDADGVEPAPED
+>PROKKA_00415
+MGRLARVALVAGAAAAAYGARLWQQNREGKDIWATATDDLPEDAEGVEPAPED
+>PROKKA_00367
+MRLARIATLVAGAAAAYGVRSWRQQREDKAVWASATDSLEPRKAPAEDGRGEDEETPQG
+>PROKKA_00009
+MGRLARVALVVSAAAAAYGARLWRENSAGKDVWATATDDLPEDADGVEPAPED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000183.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000183.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2c43167db2af75470e6d4178fb0b35436be955b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000183.fa
@@ -0,0 +1,40 @@
+>PROKKA_00014
+MARKTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG
+RRKAQDAKKEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH
+EVQQQFAAARKDAEKAAKKGRRRGGRKAKQLRRDGRQAAKGLRKDAKKAAKGARKDAQRS
+AALFSDRAGQAKDAAAAGGLTLAGLLATGLSALQEQGGKVAPQVQARLADAGDYAQRRKE
+EVLPVAAARLADGAAHARKTAHDVEVPDALEQALIKLTGDKAIVQRLRQGAEQYAGAAEK
+DLNRAAGRRASRSGGRAWIVAGMAAAAAGAGFALWRLTKPVQDPWTAPVPGPITANIPVV
+EANNPYAQQQKVVAEAGSAAAGQGVRVDTATPDPVAAANAKVLGVQPGQQR
+>PROKKA_02032
+MARTTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG
+RRKAQDAKQEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH
+EVQQQFAAARKDAEKAAKKGRHRGGRKAKQLRRDGRQAAKGARKDAQRSAALFSDRAGQA
+KDAAAAGGLTLAGLLATGLSALQEQGGKVGPQVQARLADAGDYAQRRKEEVLPVAAARLA
+DGAAHARKTAHDVEVPDALEQALIRLTGDKAIVQRLRKGAEQYAGAAEKDLNRAAGRRTS
+RSGGRAWIVAGMAAAAAGAGYALWRLTKPVQDPWTAPVPGPIAANIPVVEANNPYAQQQK
+VVAEAGSAAAGEGVRVDTAAPDPVAAANAKVLGVQPGQQR
+>PROKKA_00383
+MARTTLNDEIQHDGGADTFVTRQTENLRHWAAPKLEAARTWGEYGAAFTGVGASVAAEEG
+RRAAHDAKQEYGPRVEKQAKRAGDAVADRYAKLAPAVATGAGVLQDVLHRLQEQAQEAGH
+EAQKQFADARKDAEKAAEKGRKRGAKKAKQVRRAGRGARKDVTKAARGARKDARQAGSFL
+ADRAGQAGSAAAAGGLTLAGALAAAVNALQEQGEKLAPQVQARLSDAGDYAQRRKEEVVP
+LAAARLADGAAHARKTAHDVQVPDAVEQALIALTGDKAIVRKLRKGAEQYAGSAEKDLNR
+AAGRKARSGGRGWILGGMALAAAGAGYALWRLTKPVQDPWTAPVPGPITANIPVVEANNP
+YAQQQKVVAESGSAAAGEGVRVDTAAPVTTAVPAQDPVAEANAKVLGTDR
+>PROKKA_00364
+MARTTLSNEIEHNGSADTFFARQAENLRHWAAPQLENARAWAEVTTGFGQVGGKVAAAEG
+RRLAEEEVAPRVKDSAERVNAAAKGRYEKAAPVVATGLGAAGTVLQQLLEAAQDKAQQAG
+QQVQDLAEQAQKDAKKSAKRTRKDAKKAGKRVSKKADKAQSLFASKAGDAKGAAAAGGLN
+VAGLLAAAVAAAQDRGQELAPQVKGRVEQAAQYAQDRRAEYAPKAAASLAGVAGRAEKAA
+GDVTVPASVEQLLVKLTGDKNAVKHLRQDVQSRARETQKGLKKQARQESRRGGATGWIIA
+GMAAAAAGAGLAVWKLTKPVQDPWAAPVPGPITANIPVVQADGTVNPYAKQEQAVAEARA
+AQGGMVNVRPQVG
+>PROKKA_00014
+MARTTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG
+RRKAQDAKKEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH
+EVQQQFAAARKDAEKAAKKGRRRGGRKAKQLRRDGRQAAKGLRKDAKKAAKGARKDAQRS
+AALFSDRAGQAKDAAAAGGLTLAGLLATGLSALQEQGGKVAPQVQARLADAGDYAQRRKE
+EVLPVAAARLADGAAHARKTAHDVEVPDALEQALIKLTGDKAIVKRLRQGAEQYAGAAEK
+DLNRAAGRRASRSGGRAWIVAGMAAAAAGAGFALWRLTKPVQDPWTAPVPGPITANIPVV
+EANNPYAQQQKVVAEAGSAAAGQGVRVDTATPDPVAAANAKVLGVQPGQQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000184.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000184.fa
new file mode 100644
index 0000000000000000000000000000000000000000..15b071a53204c75e3d262a4762663e6732e4e91d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000184.fa
@@ -0,0 +1,20 @@
+>PROKKA_00015
+MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA
+>PROKKA_02033
+MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA
+>PROKKA_00382
+MARMANATHIATIKTNQGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGVGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEESQQVVDRLNAVATDPRDRPLEDVVIESVEIAEA
+>PROKKA_00363
+MTRMTNATQIATIHTNQGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDQLNSVATDPRDRPLEDVVIESVEISEA
+>PROKKA_00015
+MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000185.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000185.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff917f4c0d62e1f5a900609a1ac765c56b6a6e51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000185.fa
@@ -0,0 +1,34 @@
+>PROKKA_00016
+MSTTPSDPHGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS
+GVVAGPAPTVAPAGAAASVPARRRTGFTASPVTWILLAVTTVVYAAQWMTRDQASGVTEA
+LWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLALY
+VLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVFS
+FLLPGVAWQVHMGGLLTGAVVAVVFSLAGGLRPGRARVPSVGAQVAGLVVVAAALAALTV
+LGAARVTVAGLLG
+>PROKKA_02034
+MSTTPSDPYGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS
+GVVAGPAPTSPPAAGAAATVPARRRTGFAASPVTWILLAVTTVVYAAQWMTRDQASGVTE
+ALWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLAL
+YVLSAVGGAVFALWASDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVF
+SFLLPGVAWQVHVGGLLTGAVVAVVFSLAGGLRPGRARLPSVGAQVAGLVVVAAALAALT
+VLGAARVTVAGLLG
+>PROKKA_00381
+MDCAAQGGAPAGTTTSPAAVGSPGPGGVGMAGAAGRGAPARRRTGLAAAPVTWTLIAVTV
+AAYVAQWATRDTVPGVTEALWYAGLYTSPFGLEPWRMATYALVHDLSGPTHLILNMLALW
+VIGRVLEPALGWWRFAALYVLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLVTRV
+RGGQVRSIAVLIGLNLVISFLLPGISWQVHVGGLITGAVVALVYSLAGGLRPGRASAPSA
+GAQAAGLVLVAAVLAVLTVLGADRIGLDAVLR
+>PROKKA_00362
+MSTTPSDPHGPDVAEGTPPVCPRHPGRAAYVRCASCADPVCLDCQRPAAGGLTLCPDCAA
+RLAAGVPGPASGTTTSPAPASAGAGRGGVGAALRAAPVTWTLLAVTLLVYAGQWLTRGSR
+TGVTESLWYAGAYTSAIGMEPWRMLTYALVHDVSGPTHVALNMVALWVIGRVLELALGWW
+RFLALYLVSALGGAVFALWTADPLQPVVGASGAVYGLFAALFAVTRFRGGQVTSIAVLIG
+LNLVFSFLMPGISWQVHVGGLLTGAVAGALLVSAGGPPGRSAAADGTARRSSAGVHVAGL
+VLLAAVLAVLTLVGAARLSPAALLG
+>PROKKA_00016
+MSTTPSDPHGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS
+GVVAGPAPTVAPAGAAASVPVRRRTGFAASPVTWILLAVTAVVYAAQWMTRDQASGVTEA
+LWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLALY
+VLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVFS
+FLLPGVAWQVHVGGLLTGAVVAVVFSLAGGLRPGRARVPSVGAQAAGLVVVAAALAALTV
+LGAARVTVAGLLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000187.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000187.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d7c28f13959cd5e640f8d556c341c3408a003fa3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000187.fa
@@ -0,0 +1,25 @@
+>PROKKA_00018
+MQSPEVSVLVVDNYDSFVYTLVGYLEQLGARTTVIRNDEVTPARALELAAEHTAVLISPG
+PGAPADAGVSLDLIRSAADGGRPLFGVCLGHQAIAEAFGATVTHAESLMHGKTSLVRHGE
+HPMFEGVPSPFTATRYHSLATVRPTVDEAVLEITAETEDGVVMGLAHRTAPLWGVQFHPE
+SVLTEGGYRMLGNWLESVGLSGAAERGGRLSPLVRQD
+>PROKKA_02036
+MQSPQVSVLVVDNYDSFVYTLVGYLEQLGARTTVIRNDEVTPARALELAAEHTAVLISPG
+PGAPADAGVSLDLIRSAADGGRPLFGVCLGHQAIAEAFGATVTHAESLMHGKTSLVRHGE
+HPMFEGVPSPFTATRYHSLAAVRPTVDEAVLEITAETEDGVVMGLAHRTAPLWGVQFHPE
+SVLTEGGYRMLGNWLESVGLSGAAERGGRLSPLVRQD
+>PROKKA_00379
+MSGTVPSPEVSVLVVDNYDSFVYTLVGYLEELGARTTVIRNDEVDAARALELAAEHTAVL
+ISPGPGAPADAGVSLDLIRAAADGGRPLYGVCLGHQAIAEAFGATVTHAESLMHGKTSLV
+RHGDHPMFAGLPERFTATRYHSLAAVRSTVDEAVLQITAETEDGVVMGLAHRSAPLWGVQ
+FHPESVLTEGGYRMLGNWLESVGLTGAADRGGRLSPLVRGD
+>PROKKA_00360
+MSTPPESAPTAVSVLVVDNYDSFVYTLVGYLQELGARTTVIRNDEVSPARALELAAQHDA
+VLISPGPGTPSEAGVSLDLIRSAADGGRPLYGVCLGQQAIAEAFGATVTHAESLMHGKTS
+VLTHTDHPMFAGVPARFTATRYHSLAAVRHTVDESVLEITAQTDDGVVMGLAHRTAPLWG
+VQFHPESVLTEGGYRMLGNWLESVGLVGAAERGGRLSPLVRAAD
+>PROKKA_00018
+MQSPEVSVLVVDNYDSFVYTLVGYLEQLGARTTVIRNDEVTPARALELAAEHTAVLISPG
+PGAPADAGVSLDLIRSAADGGRPLFGVCLGHQAIAEAFGATVTHAESLMHGKTSLVRHGE
+HPMFEGVPSPFTATRYHSLAAVRPTVDEAVLEITAETEDGVVMGLAHRTAPLWGVQFHPE
+SVLTEGGYRMLGNWLGSVGLSGAAERGGRLSPLVRQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000193.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000193.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a810c84a5f1db7856dc3baa63304c4c27a51942
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000193.fa
@@ -0,0 +1,25 @@
+>PROKKA_00024
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGA
+AGAGSSAVDRPAPASTPSPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRAVPVGPGTAIRIGKT
+VMELEA
+>PROKKA_02042
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGA
+AGAGSSAVDRPAPASTPSPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRALPVGPGTAIRIGKT
+VMELEA
+>PROKKA_00372
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGV
+AGAGSSAVDRPAPASTPAPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRALPVGPGTAIRIGKT
+VMELEA
+>PROKKA_00354
+MNELAVAVLRLGLLLALWILIISIVLSQGRDLVVGRRNKLRLEQARRDAGLVTAVPAAGA
+HAASADRPAPAATPAAERPAPVPPAPAPRLARTLRITEGPLAGQTVDLGGRPLLIGRAQD
+ADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTFVDGDPVTRTLPVGTSSTIRIGKTV
+MGLED
+>PROKKA_00024
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGV
+AGAGSSAADRPAPASTPSPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRALPVGPGTAIRIGKT
+VMELEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000194.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000194.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6bfda34763f5ca7e4319d742534dfc66ecf4dca9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000194.fa
@@ -0,0 +1,35 @@
+>PROKKA_00032
+MTVTLPAAITPSPAFQPVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA
+VAPKDKDQARADAVAWLTSGHTGWVRLNGYGSRWWEQDVEALAAALPAHLGGPVSEGGLA
+GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD
+TGLGESPMALAYTRSQFTIAAKATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL
+APEQCAAVNEGLSPSQEELAWAHEFLADFEADGGEIRNGSDLPRKARAEKILGLAAAFGV
+HSTRYPDQDNAITAPSDTYHY
+>PROKKA_02049
+MTVTLPAAITPSPAFQPVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA
+VAPKDKDQARADAVAWLTSGHTGWVRLNGYGSRWWEQDVEALAAALPAHLGGPVSEGGLA
+GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD
+TGLGESPQALAYTRSQFTIAAKATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL
+APEQCAAVNEGLSPSQEELAWAHEFLADFEADGGEIRNGSDLPRKARAEKILGLATAFGV
+HSTRYPDQDNAITAPSDTYHY
+>PROKKA_00366
+MTMTLPAAITPSPAFQAVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA
+VAPKDKDRARADALAWLTSGHTGWVRLNGYGSKWWEDDVAALAEALPAHLGGPVAEGGLA
+GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD
+TGLGESPMALAYTRSQFTIAAKATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL
+APEQCAAVNEGLSPSQEELAWAHEFLADFEADGSEIRNGSDLPRKARAEKILGLAAAFGV
+HSTRYPDQDNAITAPSDTYHY
+>PROKKA_00304
+MTVTLSPSPTQPFQPTPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDVEDSVA
+PADKAKALADTVEWLTSGHTAWVRLNGYGSKWWEDDVDALASALPAHLGGPVAEGGLAGV
+MLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRDTG
+LGESPMALAYTRSQFTIAAKATGLPGAIDGPTVGSTGAKLAEATAVTTEFGMTGKLCLAP
+EQCAAVNEGLSPSPEELAWAQEFLEEFAAAGGQIRNGSDLPRKARAEKIQALAAAFGVQL
+AHIPDQENRAAAPSDTYHY
+>PROKKA_00031
+MTVTLPAAITPSPAFQPVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA
+VAPKDKDQARADAVAWLTSGHTGWVRLNGYGSRWWEQDVEALAAALPAHLGGPVAEGGLA
+GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD
+TGLGESPMALAYTRSQFTIAARATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL
+APEQCAAVNEGLSPSQEELAWAHEFLADFEADGGEIRNGSDLPRKARAEKILGLATAFGV
+HSTRYPDQDNAITAPSDTYHY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000201.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000201.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0c91e90a39bc98af8e5be617ce54effda4d69d94
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000201.fa
@@ -0,0 +1,34 @@
+>PROKKA_00043
+MGRVAQYCGVIGEALVDVVVSDTATPRVHVGGSPLNVAVGLSRLERPVLFAGRLGRDAHG
+DMVASHLRENGVRCLLEPDAAATSVATARLDPTGAASYEFELDWTLPPAAALARDFDDAA
+GGPLHHMHAGSIATMLAPGDAEVMALLERISAVTTISYDPNVRPTIVPDRAFARARAEES
+VRLADVVHASDEDIAWLYPDRPLRESLQAWQQMGPAFVVMTRGAEDIVAVTAHGVVERPI
+VPVDVADTVGAGDSFTAALLAALDDRSLLGAANRGRLHAMDPADVESVLIYASRASAITA
+SRPGADPPTRAELAD
+>PROKKA_02056
+MGRVAQYCGVIGEALVDVVVSDTATPRVHVGGSPLNVAVGLSRLERPVLFAGRLGRDAHG
+DMIASHLRENGVRCLLEPDAAATSVATARLDPTGAASYEFELDWTLPPAAALARDFDDAA
+GGPLHHMHAGSIATMLAPGDAEVMALLERISAVTTISYDPNVRPTIVPDRAFARARAEES
+VRLADVVHASDEDIAWLYPDRPLRESLQAWQQMGPAFVVMTRGAEDIVAVTAHGVVERPI
+VPVDVADTVGAGDSFTAALLAALDDRSLLGAANRGRLHAMDPADVESVLIYASRASAITA
+SRPGADPPTRAELAD
+>PROKKA_00357
+MDVVVSDTATPRAHVGGSPLNVAVGLSRLGRPVLFAGRFGRDEHGDMIASHLRDNGVHCL
+LEQDAAPTSQATARLDPTGAASYEFELDWTLPPAEELAEEFAAAAGGRLRHMHAGSIATM
+LAPGDAEVMSLLERISADTTISYDPNVRPSIVPDRAFARARAEESVRLADVVHASDEDVA
+WLYPARPLVETLQAWQRMGPALVVMTRGAEDIVAVTRDGVVERPIVPVDVADTVGAGDSF
+TAALLAALDDRSLLGAENRERLNAMDPADVESVLIYASRASAITASRPGADPPTRDELAD
+>PROKKA_00299
+MGLVAEYFGVVGEALVDVVLSDTATPRAHPGGSPLNVAVGLSRLGRPVRFAGRYGTDEYG
+DMVAAHLADNGVHCVLGADDAPTSVATARLDPTGAASYEFELDWTLPEAAELERLLTGAA
+GGRLLHVHAGSIATMLAPGDASVMGLLEAVQPTATISYDPNVRPSIVPDREFARARAEES
+VRLSDVVHASDEDVAWLYPDRPLMDSLRAWQQAGPALVVMTRGAEDIVAVTAEHVLEQPI
+VPVDVADTVGAGDSFTAALLGALDDRSLLGAENRGRLHAMDLADIRSVLIYAARASAITS
+SRPGADPPMRDELAD
+>PROKKA_00038
+MGRVAQYCGVIGEALVDVVVSDTATPRVHVGGSPLNVAVGLSRLERPVLFAGRLGRDAHG
+DMIASHLRENGVRCLLEPDAAATSVATARLDPTGAASYEFELDWTLPPAAALARDFDDAA
+GGPLHHMHAGSIATMLAPGDAEVMALLERISAVTTISYDPNVRPTIVPDRAFARARAEES
+VRLADVVHASDEDIAWLYPDRPLRESLQAWQQMGPAFVVMTRGAEDIVAVTAHGVVERPI
+VPVDVADTVGAGDSFTAALLAALDDRSLLGAANRGRLHAMDPADVESVLIYASRASAITA
+SRPGADPPTRAELAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000213.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000213.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2eca68ed1a95229b22eccb76b170a3343232115a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000213.fa
@@ -0,0 +1,15 @@
+>PROKKA_00061
+MSAFETVDVNEIPADAAILDVREDDEWALGRAAGAQHIPLGQLPDRLEELDPDTDYYLIC
+RTGGRSARAAEFMTGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK
+>PROKKA_02074
+MSAFETVDVNEIPADATILDVREDDEWALGRAAGAQHIPLGQLPDRLEELDPDTDYYLIC
+RTGGRSARAAEFMTGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK
+>PROKKA_00334
+MSAFETVDVNEIPADAAILDVREDDEWALGRAAGAQHLPLGQLPDRLEELDPDTDYYVIC
+RTGGRSARAAEFMVGRGYTAINVAGGSGAWLEAGKPMEADGGAEPTVK
+>PROKKA_00275
+MSHFETVTVDQIPADAAILDVREDDEWALGRAAGAQHLPLGQLPERIEELDPDTDYYVIC
+RTGGRSARAAEYMVGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK
+>PROKKA_00056
+MSAFETVDVNEIPADAAILDVREDDEWALGRAAGAQHIPLGQLPDRLEELDPDTDYYLIC
+RTGGRSARAAEFMTGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000215.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000215.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a7026cca6b43c2188f2948d151ca2e28561ce16
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000215.fa
@@ -0,0 +1,45 @@
+>PROKKA_00065
+MIDVKDLIEQPEKYRASQEARGEDASLVDRLVEADASRRSSIAGFEQLRAEQKAFGKRVA
+QAKGEEKQALLAEVKDLAARVKEAESAAGAAEARLAELQRAFPNLIVDGVPAGGEDDFVV
+LKEVGTPRDFAAEGFEPRDHLELGELLGAIDMERGAKVSGARFSFLKGVGARLELALMQL
+GLDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYRLERDDLYLVGTSEVALAGFHA
+GEIMDVSAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFIYAAQEEAEAEHERL
+LAWEERMLAAIEVPYRVIDIAAGDLGLSAARKFDCEAWVPTQGTYRELTSTSNCTTFQAR
+RLNIRERVRTEDGSKGGTRMVATLNGTLATTRWIVAILENHQNADGSVTVPAALRPYLGG
+MERFELV
+>PROKKA_02078
+MIDVKDLIEQPEKYRASQEARGEDASLVDRVVEADASRRSSIAGFEQLRAEQKAFGKRVA
+QAKGEEKQALLAEVKDLAARVKEAESAAGAAEARLAELQRAFPNLIVDGVPAGGEDDFVV
+LKEVGTPRDFAAEGFEPRDHLELGELLGAIDMERGAKVSGARFSFLTGVGARLELALMQL
+GLDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYRLERDDLYLVGTSEVALAGYHA
+DEIMDVSAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFIYAAQEDAEAEHARL
+LAWEERMLGAIEVPYRVIDIAAGDLGLSAARKFDCEAWVPTQGTYRELTSTSNCTTFQAR
+RLNIRERVRTEDGSKGGTRMVATLNGTLATTRWIVAILENHQNVDGSVTVPAALRPYLGG
+MERFELV
+>PROKKA_00330
+MVPISGAQLTYRLRPAARLKPVIDVKDLIEQPEKYRASQEARGEDASLVDRMVEADASRR
+ASITAFEELRAEQKAFGKKVAKAQGEEKQALLAEVKDLAARVKEAEAAAGAAEGRVAELQ
+RAFPNLVLDGVPTGGEDDFVVLREVGAPRDFAAEGFEPRDHLELGELLGAIDMERGAKVS
+GARFSFLKGVGARLELAIMQMGMDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYR
+LERDDLYLVGTSEVALAGYHADEIIDVDAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQF
+NKLEMFVYATQEDAEAEHARLLEWEERMLAAIEVPYRVIDIAAGDLGLSAARKFDCEAWV
+PTQGTYRELTSTSNCTTFQARRLNIRERVRQEDGDGGARRGGTRMVATLNGTLATTRWIV
+AILENHQNADGSVTVPVALRPYLGGMERFELV
+>PROKKA_00272
+MIDVKDLIDQPEKYRVSQEARGADVSLVDQVVAADAARRAAISRFEELRAEQKAFGKRVA
+QAKGEEKQALLAEVKDLAASVKEAEAASNEAEAELLRLQRLFPNLVIEGVPQGGEDDFVV
+VKEVGTPRDFAAEGFEPRDHLELGELIGGIDMERGAKVSGARFSFLKGAAARLELALMQM
+GLDLAVENGFVPVIPPTLVRPETMQGTGFDVAHDDEIYRLERDDLYLVGTSEVALAGYHA
+DEIIDVADAPIRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFVYTTVERAEEEHAR
+LLAWEEQMLARIEVPYRVIDTAAGDLGMSAARKFDCEAWVPTQGTYRELTSTSNCTTFQA
+RRLNIRERQVKEDGTGSNAKKGGTRTVATLNGTLATTRWIVAILENHQNADGSVTVPEAL
+RPYLGGLERFELV
+>PROKKA_00059
+MIDVKDLIEQPEKYRVSQEARGEDASLVDRVVEADAARRSSIAGFEQLRAEQKAFGKRVA
+QAKGEEKQALLAEVKDLAARVKEAESAAGAAEARLAELQRAFPNLIVDGVPAGGEDDFVV
+LKEVGTPRDFAAEGFEPRDHLELGELLGAIDMERGAKVSGARFSFLKGVGARLELALMQL
+GLDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYRLERDDLYLVGTSEVALAGYHA
+DEIMDVSAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFIYAAQEDAEAEHERL
+LAWEERMLGAIEVPYRVIDIAAGDLGLSAARKFDCEAWVPTQGTYRELTSTSNCTTFQAR
+RLNIRERVRTEDGSKGGTRMVATLNGTLATTRWIVAILENHQNADGSVTVPAALRPYLGG
+MERFELV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000216.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000216.fa
new file mode 100644
index 0000000000000000000000000000000000000000..049ae04432b8323946ce8f478891fd044074dc16
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000216.fa
@@ -0,0 +1,30 @@
+>PROKKA_00066
+MTKKLVCLDVDGTIVDHDGHLHEPVRAAVRAVLDAGHHVVIATGRSRGATLPVARSLGIG
+AGFMVCSNGGVTLRLDPELEEGYEVTDLRTFDPRSVLTQLRHRLPSAKYALELPDGTFRS
+TERFQDMSFGVAAEGVTFEELMDTTAVRLVVFSTDSSAEEFGRAVEGIGLSGVTYSVGWT
+AWLDVAAAGVTKASGLEALRTVLKVAPEDTVAVGDGRNDIEMLRWAGRGVAMGQAVEEVV
+AAADEVTGHVDEHGLATVLRSLLEEPAAA
+>PROKKA_02079
+MTKKLVCLDVDGTIVDHDGHLHEPVRAAVRAVLDAGHHVVIATGRSRGATLPVARSLGID
+AGFMVCSNGGVTLRLDPELEEGYEVTDLRTFDPRSVLTQLRHRLPSAKYALELPDGTFRS
+TERFQDMSFGVAAEGVTFEELMDTTAVRLVVFSTDSSAEEFGRAVEGLGLSGVTYSVGWT
+AWLDVAAAGVTKASGLEALRTVLKVAPEDTVAVGDGRNDIEMLRWAGRGVAMGQAVEEVV
+AAADEVTGHVDEHGLATVLRSLLEEPTAA
+>PROKKA_00329
+MEKKLVCLDVDGTIVDHDGHLHEPVREAVKAVVAAGHHVVIATGRSRGATLPVAQSLGIE
+AGYMVCSNGGVTLRLDPALEDGYEVTDCRTFDPRSVLSQLRSRLPGAKYAVEVPDGSFLS
+TERFQDMSFGVAAEGTTFEELKNTTAVRLVVFSTDSSAEEFGRAVEGIGLSGVTYSVGWT
+AWLDVAAAGVTKASGLEALRTVLHVAPEHTVAVGDGRNDLEMLAWAGRGVAMGQAVREVK
+EAADEVTASVDDHGLADVLWSLVPEADRPEGVRVQEPAAA
+>PROKKA_00268
+MTKKLVCLDVDGTIVDHDGRLHEPVREAVRAVIEAGHHVVIATGRSRGATLPVAESLGID
+SGYVICSNGGATLRLDRALEDGYEVTDLRTFDPQSVLAQLRDRLPSAKYALELPDGSFLS
+TERFQDMSFGVAAEGVGFEELMATTAVRLVVFSTDSSAEEFGRAVEGIGLSGVTYSVGWT
+AWLDVAAAGVTKASALEALRTVLHVDVADTVAVGDGRNDVEMLRWAGRGVAMGQAPDEVK
+EAADEVTGGVDEHGLATVLRTLL
+>PROKKA_00060
+MTKKLVCLDVDGTIVDHDGHLHEPVRAAVRAVLDAGHHVVIATGRSRAATLPVARSLGIG
+AGFMVCSNGGVTLRLDPELEEGYEITDLRTFDPRSVLTQLRHRLPSAKYALELPDGTFRS
+TERFQDMSFGVAAEGVTFEELMDTTAVRLVVFSTDSSAEEFGRAVEGIGLSGVTYSVGWT
+AWLDVAAAGVTKASGLEALRTVLKMAPEDTVAVGDGRNDIEMLRWAGRGVAMGQAVEEVV
+AAADEVTGHVDEHGLATVLRSLLEEPAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000224.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000224.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf20fa33419637acca2092981d894bdf505648a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000224.fa
@@ -0,0 +1,20 @@
+>PROKKA_00077
+MSARDRIRLAGLSAVGHHGVFDHERRDGQPFVTDVVLHLDAGPAAAGDDLARTANYAEVA
+DTVVRLVTGEPVDLIETLADRIARAVLAEQPVVTAVEVTVHKPQAPIPHDFADAAVTVHR
+TREDLA
+>PROKKA_02090
+MSARDRIRLAGLSAVGHHGVFDHERRDGQPFVTDVVLHLDAGPAAADDDLARTANYAEVA
+DTVVRLVTGEPVDLIETLADRIARAVLAEQPVVAAVEVTVHKPQAPIPHDFADAAVTVHR
+TREDLA
+>PROKKA_00316
+MSARDRIRLTGLSAVGHHGVFDHERRDGQPFVTDVVLHLNAGPAAAGDDLARTANYAEVA
+DTVVRLVTGEPVDLIETLAERIARAVLAEQPVVEAVEVTVHKPQAPIPHDFADAAVTVHR
+TRRDAS
+>PROKKA_00257
+MSDVIRLTGLTATGRHGVFEHERRDGQPFTTDVALTLDAGPAAARDDLARTANYAEVAET
+VVRLVTGEPFDLIETLAVRIAEAVLAEQPVVTAVEVTVHKPQAPIPHDFTDVSVTVARRR
+GA
+>PROKKA_00071
+MSARDRIRLAGLSAVGHHGVFDHERRDGQPFVTDVVLHLDAGPAAAGDDLARTANYAEVA
+DTVVRLVTGEPVDLIETLADRIARTVLAEQPVVAAVEVTVHKPQAPIPHDFADAAVTVHR
+TREDLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000232.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000232.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f5afac13d5fc272c081c10e439ae7f2d2d15ed6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000232.fa
@@ -0,0 +1,30 @@
+>PROKKA_00087
+MTTNTPKNAHGSSAEGRDAKDQAKDKAQQAAGEAQGQAKAVAQDAKDKAQDLAATAKHEA
+GQVKDEAADQVQSLVGSAQEQVGAQVQTQQERFAGQVRSYTDDLHRVVSGEQPQTDLVRQ
+GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA
+VQPDSAASTSPRRHTTRPDAVHADVTPHHLDSQAPAYSSDSLSQADGRVADGAGPRRAAG
+VGDTPYGTQAPVQQGLTAERPFDQTRPGGDA
+>PROKKA_02100
+MTTNTPKNAHGSSAEGRDAKDQAKGKAQQAAGEAQGQAKAVAHDAKDKAQDLAATAKHEA
+GQVKDEAADQVQSLVGSAQEQVGAQVQTQQERLAGQVRSYTDDLHRVVSGEQPQTDLVRQ
+GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA
+AQPDSTASTSPRRHETRPDAVHADVTPHHLDSQAPAYSSDSLSQADGRVADGAGPRRAAG
+VGDVPYGTQAPVQQGLTAERPFDQTRPGGDA
+>PROKKA_00304
+MTTNTPKNAHGSSAEGRDAKDQAKDKAQQAAGEAQGQAKAVANDAKDKVQDLAATAKHEA
+GQVKDEAADQVQSLVGSAQEEVGAQVQTQQERLAGQVRSYTDDLHRVVSGEQPQTDLVRQ
+GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA
+AQPDAAAPTAPRRRDTRPEAVHADVTPHHLDSQAPAYSSDSLSQADGRVASGAGPRRAAG
+VGDTPYGVEAPEQHGLTAERPFDRSQPGGRA
+>PROKKA_00249
+MAKNHSARAADPQQSETRQKAEAAAGAAQDQAAGVAQDAKAHAQDLAQSAQQEAVAVKDE
+AVQHAKSLAGSLQDQAAQQASTQQGRLAEQSRGITDDLHRLLSGEQPQGDAVRQAVAAVA
+DRAETLTQRLETAQPMDLVDDVRRFAARRPGTFLAIALGAGVLAGRMTRGVRDASQDGPA
+SLSSAPRTPQHRRELEPQGVQADVTPHHLDSQIPAHTGDDAPRPVSDTAAGLPYGTEPLP
+TIDPLTGEPVAEDPYDQTRDGGRA
+>PROKKA_00082
+MTTNTPKNAHGSSAEGRDAKDQAKGKAQQAAGEAQGQAKAVAHDAKDKAQDLAATAKHEA
+GQVKDEAADQVQSLVGSAQEQVGAQVQTQQERLAGQVRSYTDDLHRVVSGEQPQTDLVRQ
+GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA
+AQPDSTASTAPRRHETRPDAVHADVTPHHLDSQAPAYSSDSLSQADGRVADGAGPRRAAG
+VGDVPYGTQAPVQQGLTAERPFDQTRPGGDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000235.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000235.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d825fc3c95e6b5d904ff109c8d4105280aa23b3a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000235.fa
@@ -0,0 +1,35 @@
+>PROKKA_00090
+MTPLDRVPDQRPVPAGTGLTLEDALPAPVTAEADGVSARPRLARTVAEMRSALRELVAHA
+TDDGDAEPVTVGLIPTMGALHGGHAALVRRARAENDVVAVSIFVNPLQFGDPADLEHYPR
+TLDADLDLLAAAGADVVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGASRPGHFDGVAT
+VVAKLWNIVRPAVPALRSYFGQKDAQQLTVLRRLATDLDIDVDVRAVPIVRSPEGLALSS
+RNTRLDAAGLEHALVLSRALRSLADAAAAGEPVDVQAARRMVEDEPGVELDHLVVVDRDT
+FAELGPELLCQPLRREALALVAAHVPPVRLIDTMVLPVAGPLP
+>PROKKA_02103
+MTPLDRVPDQRPVPAGTGLTLEDALPAPVTAEADGVSARPRLARTVAEMRSALRELVAHA
+TDDGDAEPVTVGLIPTMGALHGGHAALVRRARAENDVVAVSIFVNPLQFGDPADLEHYPR
+TLDADLDLLAAAGADVVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGASRPGHFDGVAT
+VVAKLWNIVRPAVPALRSYFGQKDAQQLTVLRRLATDLDIDVDVRAVPIVRSPEGLALSS
+RNTRLDAAGLEHALVLSRALRSLADAAAAGEPVDVQAARRMVEDEPGVELDHLVVVDRDT
+FAELGPELLCQPLRREALALVAAHVPPVRLIDTMVLPVAGPLP
+>PROKKA_00301
+MTPLDRVPDRTPVPPRTGLTLEDQVPEAGGTRPRLTTTKADFRAAVAELVGRAAAEDPGE
+EVSVGLVPTMGALHGGHAALARQARSENDVVAASIFVNPLQFGDRADLEHYPRTLEADLD
+LLGAVGVDVVFAPSVDEMYPGHPDAPIVSVSAGRMGEVLEGASRPGHFDGVCTVVAKLWN
+LSMPPAPAVLRSYFGQKDAQQLAVLRRLAHDLDVAVDVRAVPIVRSPEGLALSSRNTRLD
+EAGLHAALVLNRALTRLEEAAVAGRVLDVQAAREEVAAEPGVTLDHLVVVDRETLEELGA
+ELLCQPLRRDALALVAAHVPPVRLIDNRVLPAAGPLP
+>PROKKA_00246
+MTPLDRTPDRRPVPAGTGLTLEDALPVADGARRPRLARTVAEARAALRELTAAAGQERGG
+APVVVGMVPTMGALHGGHAALIRQARAENDVVVASIFVNPLQFGDPADLENYPRTLEADL
+DLLGAAGADLVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGVSRPGHFDGVVTVVAKLW
+NIVRPAVPALRSYFGQKDAQQLAILRRLAHDLDVDVEVRAVPIVRSPEGLALSSRNTRLD
+ADGLEHALVLSRALRALVDAAEAGEPIDVRAARQMVSDEPGVTLDHLVVVDRETLEELGP
+ELLCQPLRREALALVAAHVPPVRLIDNMVLPAAGPLP
+>PROKKA_00085
+MTPLDRVPDQRPVPAGTGLTLEDALPAPVTAEADGVSARPRLARTVAEMRSALRELVAHA
+TDDGDAEPVTVGLIPTMGALHGGHAALVRRARAENDVVAVSIFVNPLQFGDPADLEHYPR
+TLDADLDLLAAAGADVVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGASRPGHFDGVAT
+VVAKLWNIVRPAVPALRSYFGQKDAQQLTVLRRLATDLDIDVDVRAVPIVRSPEGLALSS
+RNTRLDAAGLEHALVLSRALRSLADAAAAGEPVDVQAARRMVEDEPGVELDHLVVVDRDT
+FAELGPELLCQPLRREALALVAAHVPPVRLIDTMVLPVAGPLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000241.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000241.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28b922556ec396bb1da82b7cef4293d6edd5a1ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000241.fa
@@ -0,0 +1,35 @@
+>PROKKA_00096
+MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD
+VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE
+GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMEVVFAPRPPAH
+REVAAAELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDADVIAKMKDDAVLVN
+TARGPVVDEAALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA
+AMAELAARNAIAMATGAEAPALVNPEVRG
+>PROKKA_02109
+MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD
+VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE
+GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH
+REVAAEELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDAEVIAKMKDDAVLVN
+TARGPVVDEVALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA
+AMAELAARNAIAMATGAEVPALVNPEVRG
+>PROKKA_00295
+MSPRFLLMTEIPEPGLGMLREAGEVTLGSEVGGNDALPALAASGDYDVVVCALAQKFDAD
+VLAQARLKGIANYAVGYNNVDVAAATEAGIAVGNTPDVLTDATADIALLLILGVSRRAHE
+GEAMMRAGEFTGWRADLLVGKDVKGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH
+REVAPEELGELAGRVEQVRWEELVERSDFLSLHVPLTADTEHLVDADVLARMKDDAVLIN
+TARGPVVDEAALVEALRAGRLFGAGLDVYEDEPAMAPGLAELDNVMLLPHLGSATRDTRA
+AMAELTARNAIAMATGGEVPALVNPDVRR
+>PROKKA_00240
+MSPRFLLMADLPEPGLGMLREAGEVVRGGDVGGNAALADLCASGEYDVVVGALDQRYDAD
+LLARARVKGIANYAVGFDNVDVPAATEHGILVGNTPDVLTAATADIALLLILGVTRRAVE
+GERMMREGRFEGWRADMLVGKDVVGATLGLAGFGRIGRAVAERALAFGMEVVFAPRPPAH
+REVPAEELGDLAGRVRQVRWEELVETADVLSLHVPLTEDTRHLVDEDVIARMKDDAVLVN
+TARGPVVDEAALVTALREGRLFGAGFDVYEDEPAMAEGLAELPNVMLLPHLGSATRDARA
+AMAELTARNAIGMATDGEAPALVNPEARG
+>PROKKA_00091
+MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD
+VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE
+GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH
+REVAAEELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDAEVIAKMKDDAVLVN
+TARGPVVDEVALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA
+AMAELAARNAIAMATGAEVPALVNPGVRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000243.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000243.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49fcfa215b98d80cb5bf72b95ca9b94df4a99d9e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000243.fa
@@ -0,0 +1,15 @@
+>PROKKA_00098
+MAAFWDYFSVLAPSIGLGLIFWLVMRSLLRSDTGERESQARRLSGADARAAREEAEAREW
+AARRRAEGGPGADPEDRAR
+>PROKKA_02111
+MADFWDYFSVLAPSIGLGLIFWLVMRSLLRSDTGERESQARRLSGADARAAREEAEAREW
+AARRRAEGGPGADPEDRAR
+>PROKKA_00293
+MATFWEYFSVLAPSIGLGLIFWLVMRSLLRSDTAERESMGRRSTGEDARAAREEADAREW
+ARRRGGDDVPRRGDDSR
+>PROKKA_00238
+MAAFWEYFSVLAPSVGIGLVFWLVMRSLLRSDTAEREARQRRGEDARAAREEAEAREWAA
+RRRGDAPAGPGGAERP
+>PROKKA_00093
+MAAFWDYFSVLAPSIGLGLIFWLVMRSLLRSDTGERESQARRLSGADARAAREEAEAREW
+AARRRAEGGPGADPEDRAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000244.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000244.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86be830b3523691952516df6e83026c1ca715b51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000244.fa
@@ -0,0 +1,80 @@
+>PROKKA_00100
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG
+DVPETLRDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVAEPSVEDAT
+EILRGLRDRYEAHHKVSITDGALKAAAGLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLGDERREKEQAWRTGADADV
+ATVDEDLIAEVLSKSTGIPVFKLTEEETDRLRNMEDELHRRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVEIVDLFVSRLGKRLAEQDLSIELTQSAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFAFSGGREALEGADLAELESG
+AGDPVDADRSV
+>PROKKA_02113
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG
+DVPETLRDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVAEPSVEDAT
+EILRGLRDRYEAHHKVSITDGALKAAAGLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLGDERREKEQAWRTGADADV
+ATVDEDLIAEVLSKSTGIPVFKLTEEETDRLRNMEDELHRRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVQIVDLFVSRLGKRLAEQDLSIELTQSAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDTTGEGEGAELTFAFSGGREALEGADLAELEPG
+AGDPVDADRSA
+>PROKKA_00291
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVKLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG
+DVPETLKDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVPEPSVEDAT
+EILRGLRDRYEAHHRVSITDGALKAAATLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLEDERRQKEEAWRTGADSDV
+ATVDEELIAEVLSKSTGIPVFKLTAEETDRLRTMEDELHKRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVEIVDLFVSRLGKRLAEQDLSIELTQAAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFGFSGGREALEGAELPELEPG
+SGETVEAGRSA
+>PROKKA_00237
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLAAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGSEGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAQEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIERG
+DVPETLKGKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVPEPSVEDAT
+QILRGLRDRYEAHHKVSITDGALSAAASLADRYISDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEVKAYEERIAEVKAQKEAAIDGQDFEGAARLRDQEKQLEEEREQKEQAWRAGQDAAV
+ATVDEDLIAEVLSLSTGIPVFKLTEEETDRLRNMEAELHQRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHADLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSSTDTSTGYERMKGKVREELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVEIVDLFVSRLAKRLAEQDLSIELTPAAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFAFAGGRAALEGDDAAEPAAL
+PAAADAPVEGREAPGADVPRGDDAGQDGPEAGGALGARLD
+>PROKKA_00095
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG
+DVPETLRDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVAEPSVEDAT
+EILRGLRDRYEAHHKVSITDGALKAAAGLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLGDERREKEQAWRTGADADV
+ATVDEDLIAEVLSKSTGIPVFKLTEEETDRLRNMEDELHRRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVEIVDLFVSRLGKRLAEQDLSIELTQSAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFAFSGGREALEGADLAELEPG
+AGDPVDADRSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000247.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000247.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bcf2455641710356685993cd2936f5b00bf688fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000247.fa
@@ -0,0 +1,35 @@
+>PROKKA_00103
+MPAPAPLVPPTVDVPHLHDAMLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL
+PRWREWLERWPTPADLAAAPTADVLTAWDRLGYPRRALRLQEAARAVVGRHDGRVPADPA
+ALRALPGIGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA
+LMPEDPARANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA
+GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGRLGSHRPDDAQWARCVAGLVSDGLLAR
+DDDGGLTFPA
+>PROKKA_02116
+MPAPAPLVPPTVDVPRLHDAVLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL
+PRWREWLERWPTPADLASAPTADVLTAWDRLGYPRRALRLQEAARAVVERHDGRVPADPA
+ALRALPGVGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA
+LMPEDPARANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA
+GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGRLGSHRPDDAQWARCVAGLVSDGLLAR
+DDDGGLTFPD
+>PROKKA_00287
+MPAHETAVPPSVDVPRLHDAVLDWFAVHARDLPWRSPDCPPWGVLVSEIMLQQTPVARVL
+PRWHAWLERWPTAADLAAAPTADVLTAWDRLGYPRRALRLQEAARAIVERHSGEVPADPA
+ALRALPGIGEYTAAAVSSFAFGLPETVVDTNVRRVIARAVGGQALPGRSLTRAEMRRAHA
+LMPEDPDRAQAWNAGVMELGALVCTARSPACERCPLADACAWVAAGSPPPEQAPRGQAWA
+GTDRQVRGAVMAAVREHGRVAGDGLRAVVVAGGRLGAHRPGDAQWERCVAGLLADGLLAR
+DDDGALAFPS
+>PROKKA_00233
+MPAHDDAAPRPDLTALQDEVLDWFAAHGRDLPWRDPDCPPWGVLVSEIMLQQTPVVRVLP
+RWRAWMERWPTPADLAAAPTADVLTAWDRLGYPRRALRLQEAARAIVERHGGEVPADPAA
+LRALPGIGEYTAAAVSSFAFGIPETVVDTNVRRVLARALRGEGLPGRTLTRAEMAAAHAA
+LPADEHRANRWNAAVMELGALVCTARSPACDRCPIRARCAWVAAGSPAPEVARRGQAWVG
+TDRQVRGAVMAAVREHGRVPRGGLREAVDGTGRLGAHTPDDAQWERAVAGLLGDGLLVAH
+DDGALAFPA
+>PROKKA_00098
+MPAPAPLVPPTVDVPRLHDAVLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL
+PRWREWLERWPTPADLASAPTADVLTAWDRLGYPRRALRLQEAARAVVERHDGRVPADPA
+ALRALPGVGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA
+LMPEDPTRANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA
+GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGWLGSHRPEDAQWARCVAGLVSDGLLAR
+DADGGLTFPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000248.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000248.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc09d4247ba155331ca6c205d2779ed268412484
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000248.fa
@@ -0,0 +1,31 @@
+>PROKKA_00104
+MPSRPTSPGSKPSPAVYRRRRLVAALLALVLLLLVGWAVVALVRAGIGAFSSEDADPSAA
+PTPVHSPSPAPATDAESSSASPTVALEDAAECQPSDLRIAASADRSEYQRGEEAELRLGI
+TNLSSTPCRTDVGTARQEFTIRTAEGDDVFSTRICQADPAEAQRVLYPHEELTAVYRWSG
+RASSQDCGRLGALAEPGPHLLTVSLGDVTSRPVALKILEELAPGAQDSSSSAAPSSATPS
+SATPSSSGSASPSGSASDPASASTTDPSPSSSR
+>PROKKA_02117
+MPSRPTSPGSKPSPAVYRRRRLVAALLALVLLLLVGWAVVSLVRAGIDAFSSEDADPSAA
+PTPVHSPSPAPATDAESGSASPTVALEDAAECQPSDLRIAASADRSEYQRGEEAELRLGI
+TNLSSTPCRKDVGTARQEFTIRTAEGDDVFSTRICQADPAEAPRVLYPHEELTAVYRWSG
+RASSQDCGRPGALAEPGPHLLTVSLGDVTSRPVALKILEELAPGAQDSSSSAAPSSATPS
+SATPSSSGSASPSGSASDPASASTTDPSPSSSR
+>PROKKA_00286
+MPSRPSSPGPKPSAAVYRRRRLVAALLALILLLLVGWGLWSLIRLGMGALSGDDAEPSVS
+APPTPVHSPSPAPPSGATPGSAAPTVALEDAAECQPSDLRLVASADKAQYLRGEEAVLRL
+GVTNLSSSPCRADVGTARQEFTVRTAEGDDVFSTRVCQADPTSSERVLTPHEELTAVYRW
+SGHASNEDCGTPGALAAAGPHLLTVTLGEQTSRPVALRIQEEAAPGAWDGASSGAPASGS
+PAPSTPASPSASPSATGSAPAASSPAPASGSPAASTPATPSASPSR
+>PROKKA_00232
+MPSASPAPRPRPSAAVLRRRRVVAGCLAAAFLLLVGWGIGALVNALLPSGRPDAEPSAAP
+TPVSSPTPAAARSLDAQAGQTQDPASVESCAPMDLRLVAAADRERYAPGEEAVLRLEVTN
+LSGRPCRTDVGTAQQEFRVTDASEQQVMSTRVCQADPTHEDVVLEPRDQKAAVYRWNGRA
+SSADCARLGPAVEPGEYRLTVTLGEVTSRPVALTVTDGTKSAAPASSPAASSAAPGPSAT
+TAPASAETSSASPSASSSSAQPSSPAPRASEPTSSAPTSSPAGSGRASSSPAAPSSSAAS
+PTR
+>PROKKA_00099
+MPSRPTSPGSKPSPAVYRRRRLVAALLALVLLLLVGWAVVSLVRAGIDAFSSEDADPSAA
+PTPVHSPSPAPATDAESGSASPTVALEDAAECQPSDLRIAASADRSEYQRGEEAELRLGI
+TNLSSTPCRTDVGTARQEFTIRTAEGDDVFSTRICQADPAEAPRVLYPHEELTAVYRWSG
+RASSQDCGRLGALAEPGPHLLTVSLGDVTSRPVALKILEELAPGAQDGGSSATPSSATPS
+SSGSASPSASASAPASASASASASASASASPSAAPATTTDPSPSPSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000249.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000249.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc05eb19eafa0e7b7982f6944a8aeec69dd4a9fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000249.fa
@@ -0,0 +1,40 @@
+>PROKKA_00106
+MTDRFATATGTVPMVDPQTRGERLGRFLRRRARAGWSRVRSSVGQAALVAVCAVGAYWFA
+EAVLGHQQPLFASTALLIALGFQREPKLRKVAEVAVGCTVGILIGDLLMVGLGRGLWQAS
+VVLFVSVMVARFLDSGATFTMQMSLQSVLVVLLPTGTGGPFVRSQDAIVGGVLALLVTFL
+SPQDVRRPAVRQLGGLYDSIATVLRDLSRALRENDSRTAWMALVASRGTHTTLEALRKEL
+RVTHEQTVFNPLHRSSRSFVEDAVNAADRSDLAVRSLRIVARRVVSVLDEGVFDDDDRER
+LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASALDPHQLGGGSVHGEAL
+VMLLRPMMVDLIEATGAEHDEARGYLPRV
+>PROKKA_02119
+MTDRFATATGTVPMVDPQTRGERLGRFLRRRARAGWSRVRSSVGQAALVAVCAVGAYWFA
+ETVLGHQQPLFASTALLIALGFQREPKLRKVAEVAVGCTVGILIGDLLMVGLGRGLWQAS
+VVLFVSVMVARFLDSGATFTMQMSLQSVLVVLLPIGTGGPFVRSQDAIVGGVLALLVTFL
+SPQDVRRPAVRQLGGLYDSIATVLRDLSRALREDDSRTAWMALVASRGTHTTLEALRKEL
+RVTHEQTVFNPLHRSSRSFVEDAVNAADRSDLAVRSLRIVARRVVSALDEGVLDDDVRER
+LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASALDPHQLGGGSVHGEAL
+VMLLRPMMVDLIEATGAEHDEARAYLPRV
+>PROKKA_00284
+MSDRFATATGTVPMVAPESRGARLRRFLRRRSRAGWSRVRSSVAHAALMAVCAVGAYWFA
+ETVLGHHQPLFSSTALLIALGFQREPTLRKVAEVAVGCTVGILIGDLLLAALGRGLWQAT
+VVVFVSVMVARFLDSGATFTMQMSLQSVLVVLLPAAQGGPFARSADALVGGLLALVVTFL
+SPQDVRRGTARHLEGLYDSMATVLRDLSRALRQEDSRTAWMALVACRGTQGTLESIRAEL
+KMAQEQATFNPLQRGSRSFVSDAANAADRSDLAVRSLRIVARRVVSVLDEGAFDDDHRER
+LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASRLDPRELGGGSLHGEAL
+VMLLRPMMVDLLEATGAPHDEARAYLPRV
+>PROKKA_00225
+MTDRHATATGTLPAVPAAAGPSGVGRFLRRRARAGWSRLRSSVGHAALMAVCAVGAYWFA
+ETVLGHAQPLFAATALLIALGFQREPRVRKVAEVAFGCTLGILIGDLMMAALGRGLWQAV
+LVVFVSVLAARFLDSGATFTMQMSLQSVLVVLLPLNADGPFARSADALVGGLLALLVTLL
+SPRDPTRLPARQLRGLYESMASVLRELSAALRAEESRTAWMALVECRRTQSTLEDVRKEL
+KVTREQTVLNPLQRPARDAADVMAVAADRSDLAVRSLRIVARRVVSILDHGAVDGDHRER
+LAAWFDDAADAVEILHRSLAEPQAEGRHRSLDVARDALGASASWLDPHELAGGTVHGEAL
+VMLLRPMMVDLIEATGASHAEALTYLPRV
+>PROKKA_00101
+MTDRFATATGTVPMVDPQTRGERLGRFLRRRARAGWSRVRSSVGQAALVAVCAVGAYWFA
+EAVLGHQQPLFASTALLIALGFQREPKLRKVAEVAVGCTVGILIGDLLMVGLGRGLWQAS
+VVLFVSVMVARFLDSGATFTMQMSLQSVLVVLLPTGTGGPFVRSQDAIVGGVLALLVTFL
+SPQDVRRPAVRQLGGLYDSIATVLRDLSRALRENDSRTAWMALVASRGTHTTLEALRKEL
+RVTHEQTVFNPLHRSSRSFVEDAVNAADRSDLAVRSLRIVARRVVSALDEGVLDDDVRER
+LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASALDPHQLGGGSVHGEAL
+VMLLRPMMVDLIEATGAEHDEARGYLPRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000250.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000250.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa08027fdef67469246e1d6f29c50fc2d8c97d18
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000250.fa
@@ -0,0 +1,40 @@
+>PROKKA_00107
+MKALRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEQGTTSEVQGNLVGAGASS
+QEAAMTAWTQGVTETAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKEEEAESAKEN
+CGDEGAFHVPAYISPIAVAYNLPGVDDVKMDAETIAKVFSGEIKNWNDEAIAAQNEGVEL
+PDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQGTKGVVGLAS
+QTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSIELDRATDES
+GVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPISEDTRKKAM
+ERIEAISVKG
+>PROKKA_02120
+MKALRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEQGTTSEVQGNLVGAGASS
+QEAAMTAWTQGVTETAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKEEEAESAKKN
+CGDEGAFHVPAYISPIAVAYNLPGVDDVKMDAETIAKVFSGEIKNWNDEAIAAQNEGVEL
+PDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQGTKGVVGLAS
+QTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSIELDRATDES
+GVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPISEDTRKKAM
+ERIEAISVKG
+>PROKKA_00283
+MKALRFGRSAALLSVAALALTACGGNGGGDASSSAPAGGSSSAAAEGSGAAAASGTLIGG
+GASSQEAAMTAWSEGVKATSPELTVQYSPDGSGAGREGFLGGAFSFAGSDAALKEDEAEQ
+AKQICGDNGAFHVPAYISPIAIAYNLEGVDEVKMDAETIAKVFSKEITTWNDPAIAEQNE
+GVELPDTPITVVHRSDDSGTTENFTAYLTEAAGDAWKYDEVETWPSEITAESAQGTRGVV
+GQAAQTDGAITYADASAVGELGTVAVKVGEEYVPYSSDAAAKTVSASVQNEDGSIELDRA
+TTEAGVYPIVLVSYHIYCNQYQNQETADQVKAFASYVVSEDGQKAAEEAAGNAPIGAETR
+DAAVERIEAITAG
+>PROKKA_00224
+MKALRFGRSAALLSVAALALTACGGGNDSASSSSSAASSSAAGSSSASSSAAGSSSASSS
+AAESSSASGSSSAAQGGYAIDVPTASGTLMGSGASSQEAAMTAWTEGVKATSPELQVQYS
+PDGSGAGRKAFLSGAATFAGSDAALKDEEKTQAQEVCGPDGAFHVPAYVSPIAVAYNLEG
+VDSLNLDADTIAKIFSKKITKWNAPEIAALNEGVELPDTAITVVHRADESGTTENFTAYL
+DQVAPEAWTYGKVKEWPGDITAESAQGTKGVVSQAAATNGAITYADESGVGSLKTAKVGK
+DGKFAEISPEAAAKIVADGKKQDDGSIELDRANAGEGVYPIVLVSYHIFCNQYGDQETVD
+QVKAFASYVISEDGQKAAQEASKSAPLDAELAKEAKTRIDAIKVG
+>PROKKA_00102
+MKAHRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEHASGSAGGEQGTTSEVQG
+NLVGAGASSQEAAMTAWTQGVTEIAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKE
+EEAESAKENCGDEGAFHVPAYISPIAVAYNLPGVDEVKMDAETIAKVFSGEIKNWNDEAI
+AAQNEGVELPDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQG
+TKGVVGLASQTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSI
+ELDRATDESGVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPI
+SEDTRKKAMERIEAISVKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000251.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000251.fa
new file mode 100644
index 0000000000000000000000000000000000000000..132eab656920d7106d091c4a55e9a2e23a0e9a6c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000251.fa
@@ -0,0 +1,35 @@
+>PROKKA_00108
+MSSTTNEAAPKPSSLRGPRRGAAGDKLLSGGALAAAVLILLVLAFVAVFLLTEAWPALQP
+GAELVSADSFFQYVWPLMAGTVMVSIIALLIATPVAIGVALFISHYAPPRIAQSVGFVID
+LLAAIPSVVYGVWGWLTLAPLMVPIYGWLNENLGFIPFFGGSATTTGRTLLTSGVVLAVM
+VLPIITALCREIFTQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIISSIMLGLGRALG
+ETMAVTMVLSGGVFSWSLVESGRNQTIPSEIALNFPEAFNMRLHELIAAGLMLFIITLAV
+NMIARAIVNKHKEFSGAN
+>PROKKA_02121
+MSSTTNEAAPKPSSLRGPRRGAAGDKLLSGGALAAAVLILLVLAFVAVFLLTEAWPALQP
+GAELVSADSFFQYVWPLMAGTVMVSIIALLIATPVAIGVALFISHYAPPRIAQSVGFVID
+LLAAIPSVVYGVWGWLTLAPLMVPIYGWLNENLGFIPFFGGSATTTGRTLLTSGVVLAVM
+VLPIITALCREIFTQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIISSIMLGLGRALG
+ETMAVTMVLSGGVFSWSLVESGRNQTIPSEIALNFPEAFNMRLHELIAAGLMLFIITLAV
+NMIARAIVNKHKEFSGAN
+>PROKKA_00282
+MTSPATEAPPRATTLKSSRGGAAGDKVFSGLSLAAGVLILLTLAFVAIFLVVRSLPALFP
+DAYGTQLKSADTFFQYVWPLMAGTIMAAVIALLLATPVAVGVALFISHYAPPKIAQPVGY
+VIDLLAAIPSVIYGIWGWLTLAPVMVPIYQWLNEYLGFIPFFGGPVTGTGRVIMTSGVVL
+AVMILPIITALCREIFRQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIVSSVMLGLGR
+ALGETMAVTLVLSAGGFSLSLIEEGRNATIPSEIALNFPEAYGIRLNELIAAGLMLFVIT
+LVVNMTARWIVNKHKEFSGAN
+>PROKKA_00223
+MSHTATEAAPSSSALKSSRAGAAGDKVFSGLALAAGVLILLILAFVAIFLVSEAWPALFP
+AEGANLESGDSFWGYVWPLMAGTVMAAIIALLLATPVAVGVALFISHYAPPKIAQPVGYV
+IDLLAAIPSVVYGIWGWLTLAPLMVPIYEWLNEYLGWLPFFGGSVTSTGRVLMTSGIVLA
+VMVVPIITALCREIFSQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIVSSIMLGLGRA
+LGETMAVTMVLSPGKFSPSVIEEGRNATIPSEIALNFPEAYGIRLNELIAAGLMLFVITL
+VVNMVARWIVNKHKEFSGAN
+>PROKKA_00103
+MSSTTNEAAPKPSSLRGPRRGAAGDKLLSGGALAAAVLILLVLAFVAVFLLTEAWPALQP
+GAELVSADSFFQYVWPLMAGTVMVSIIALLIATPVAIGVALFISHYAPPRIAQSVGFVID
+LLAAIPSVVYGVWGWLTLAPLMVPIYGWLNENLGFIPFFGGSATTTGRTLLTSGVVLAVM
+VLPIITALCREIFTQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIVSSIMLGLGRALG
+ETMAVTMVLSGGVFSWSLVESGRNQTIPSEIALNFPEAFNMRLHELIAAGLMLFIITLAV
+NMIARAIVNKHKEFSGAN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000255.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000255.fa
new file mode 100644
index 0000000000000000000000000000000000000000..525d7335646159938b2c86bf70515f7eb8b0ae08
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000255.fa
@@ -0,0 +1,25 @@
+>PROKKA_00112
+MSPRMPWLVTRDTPALRHMADLAEALHRSVHLVAQVAGTRGPEADRAARELEELDSSSSA
+TLMAFLTALRSAYVTPLPRQDLYRLASGVHATTRRVVSAGVLIQRADLEELPTHALDVLE
+TVGRQAELLARGAAEMRDLDALEATWMQLLRASRRTERIMVEWLADLGMDLLQRDYNRQR
+EVAWALHAALEALSRVNMDLGMVLVRES
+>PROKKA_02125
+MSPRMPWLVTRDTPALRHMADLAEALHRSVHLVAQVAGTRGPEADRAARELEELDSSSSA
+TLMAFLTALRSAYVTPLPRQDLYRLASGVHATTRRVVSAGVLIQRADLEELPTHALDVLE
+TVGRQAELLARGAAEMRDLDALEATWMQLLRASRRTERIMVEWLADLGMDLLQRDYNRQR
+EVAWALHAALEALSRVNMDLGMVLVRES
+>PROKKA_00278
+MSPRMPWPVTRDTPALRHIVDLAEALRRSVHLVAQVAGARGPEADRTARELEDLDAASTA
+SLMSFLTALRSAYVTPLPRQDLYRLAGGVHAATQRVVSAGVLIQRADLEHLPAHALDVLE
+TVGRQAELLGRSTTELRDLDALEATWMQLLRASRRTERIMVQWLADLGMDLLQRDFNRQR
+EVAWALQSALEALGRVNTDLGMVLVRES
+>PROKKA_00219
+MTPRPAWLVTRDSPALGHLTDLCDTLGRAVRAVAQAVAADGSERDRVERDLSALDAAATA
+ALMAFLTALRSAYVTPVPRPDLYRLADGVKTAAHRVVGAGVLVHRADLDALPRNAVELLE
+TLGRQAELLAHGTRQLRDLDALEDTWMQLERGIRRMERLMVDWLAALGTDLLQRDYNRQR
+EIASALRDAVLALDRVNTDLGVVLVRES
+>PROKKA_00107
+MSPRMPWLVTRDTPALRHMADLAEALHRSVHLVAQVAGTRGPEADRAARELEELDSSSSA
+TLMAFLTALRSAYVTPLPRQDLYRLASGVHATTRRVVSAGVLIQRADLEELPTHALDVLE
+TVGRQAELLARGAAEMRDLDALEATWMQLLRASRRTERIMVEWLADLGMDLLQRDYNRQR
+EVAWALHAALEALSRVNMDLGMVLVRES
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000256.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000256.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0b0ec6111d9c1fad61309c47d25c27ec4da3c9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000256.fa
@@ -0,0 +1,25 @@
+>PROKKA_00113
+MARHRLPAGRGASSSASGVLRPHRPRLSEPQELTHFAGGEDPQEVAAAASRLAHALVAGG
+RAEEDPAIVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATTRDGERWAAW
+YRAGHAAYASRVVAGAVEPPGPAELRRLTDTILTGAYRSEIDVAFERAAAYARVVALGQV
+EHAEGSEAAAPDRAAALTRRAARLVSTADALEAAGRAFRDGSLD
+>PROKKA_02126
+MARHRLPAGRGASSSASGVLRPHRPRLSEPQELTHFAGGEDPQEVAAAASRLAHALVAGG
+RAEEDPAIVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATTRDGERWAAW
+YRAGHAAYASRVVAGAVEPPGPAELRRLTDTILTGAYRSEIDVAFERAAAYARVVALGQV
+EHAEGSEAAAPDRAAALTRRAARLVSTADALEAAGRAFRDGSLD
+>PROKKA_00277
+MARHRQTTGRGASSSASGLVRPHRPRLSEPDELAHFAGGEDPQEVAAAASRLAHALVAGG
+RAEEDPEVVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATARDGERWAAW
+YRAGHAAHAARAVAGAVEPPGPDELRRLTDTILTGAYRSEIDVAFERAGAYGRVVALGQV
+EHAEAAEAADPALAAGLTRRAARLVSTSEALEEAARAFRNGSLD
+>PROKKA_00218
+MAHHRAPAGRGASSTASGLVRPHRPRLTDPGLIADLADGEDPQEIAAAASRLAHALVAGG
+RAEEDPDVVARLVGLVREVGVETLAGLWADAPAVSLAGALWRLYALQEATARDGERWAAW
+YRAGHAAHAARAVAGAVEPPGPEELRRLTDTILTGAYRSELDVALERAGAYARVVALGQA
+EHAAAAEHADPAHAARLTLRAARMISTAEALEAAARSWRDGSLD
+>PROKKA_00108
+MARHRLPAGRGASSSASGVLRPHRPRLSEPQELTHFAGGEDPQEVAAAASRLAHALVAGG
+RAEEDPAIVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATTRDGERWAAW
+YRAGHAAYASRVVAGAVEPPGPAELRRLTDTILTGAYRSEIDVAFERAAAYARVVALGQV
+EHAEGSEAAAPDRAAALTRRAARLVSTADALEAAGRAFRDGSLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000260.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000260.fa
new file mode 100644
index 0000000000000000000000000000000000000000..524b4570ac20c22d919eace26ecaccf4e18044c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000260.fa
@@ -0,0 +1,45 @@
+>PROKKA_00122
+MATRADRGRPVHNPDIIGFTDAELNETPIRPKWNSLGPGIVAAATGVGAADLVATLTAGS
+RYGYMLLWAVILGVIFKIVLVEGVGRWYLSTGKTIFQGWRSLGSWTSWYFGPYILIWGFV
+YGATAMSSAALPLAALFPGVDMKVYAIGLGLVGLGLVWLNRYGLIEKLMAVLIGVMFLTV
+LLSAALTAPNVGDILAGLVPRIPSGDPDVMFYVLGLAGGVGGTITLGAYAYWLREKGWNV
+PKYMRVMKFDNATSYILTGIFVIATMIMGVELLHSAGLAISSGDRGLLDVGNVLAERYGQ
+AYSVVFLVGFFAASFSSLLGVWHGVSLMFADFWTNFRRPADELDQDDAPSLASKPGRFFL
+LWLTFPPMTLLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNKKEVPAQFRNGWIRNTL
+LGLTAAVFVAIGVNELWKALQPLIGG
+>PROKKA_02136
+MAHAVDPGRPVHNPDIVGFTDAELNETPIRPRWNSLGPGIVAAATGVGAADLVATLTAGS
+RYGYMLLWAVVLGVIFKIVLVEGVGRYYLSTGKTIFQGWRTLGAWTSWYFGPYILIWGIV
+YGATAMSSTALPLAALFPGVDSKVFAIASGLIGLGLVWLDRYRLIEWLMTVLIGVMFVTV
+LLSAALTVPNLGAILAGLVPRLPSGDPQAMFYVLGLAGGVGGTITLAAYGYWLREKGWNV
+PKYLKVMRFDNATSYILTGIFVIATMVMGVELLHSAGLAISSGDKGLLDVGDVLAERYGS
+AWSTVFLIGFFAASFSSLLGVWHGVSLMFADFWTNFRRPAEELDQDDAPSLSSKPGRFFL
+LWLTLPPMALLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNTKDVPRQFRNGWVRNTL
+LGLTAAVFVAIGVNELIKALQPVLGG
+>PROKKA_00263
+MPHTADRGHPVHNPDIVGFTEAELNETPIKPRWNSLGPGIVAAATGVGAADLVATLTAGS
+RYGYMLLWAVVLGVIFKIVLVEGVGRWYLSTGKTIFQGWRQLGSWTSWYFGPYILIWGFV
+YGATAMSSTAIPLAALFPAVDAKVFAIAAGLIGLALVWLNKYGLIEKLMTALIGVMFVTV
+LISAALTAPNVGEILSGLVPRIPSGDPQVMFYVLGLAGGVGGTITLGAYAYWLREKGWNV
+PKYMKVMKFDNATSYVLTGIFVIATMIMGVELLHSAGLAISSGDKGLLDVGNVLAERYGQ
+VWSYVFLIGFFAASFSSLLGVWHGVSLMFADFWTNFRRPADELDQDDAPSLASKPARFYL
+LWLTILPMSLLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNRKDVPVQHRNGWIRNIL
+LGLTAAVFVAIGVNELIKALQSVLGG
+>PROKKA_00197
+MSHTTPPGHGLVDRHHPVHDPDIVGFTEAELNETPIKPKWNSLGPGIVAAATGVGAADLV
+ATLTAGSRYGYMLLWAVVLGVVFKIVLVEGVGRYYLSTGKTIFQGWRGLGSWTSWYFGPY
+ILIWGFVYGATAMSSTALPLAALFPGVDSKVFAIASGLVGLGLVWLNRYGLVEKVMTVLI
+GVMFVTVLISAALTVPNLGDILGGLVPRIPSGDPDVMFYVLGLAGGVGGTITLGAYGYWL
+REKGWNTPKYMRVMRFDNTVSYVLTGVFVIATMIMGVELLHSAGIAISSGDKGLLDVGDV
+LAQRYGDVWATVFLIGFFAASFSSVIGVWHGVSLMFADFWTNFRRPADELDQDDAPSLAS
+KPGRFYLLWLTFPPMVLLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNSRRVPGKFRN
+GWVRNVLLALTTAVFLVIGGNELLKALKPLIGG
+>PROKKA_00130
+MATRADRGRPVHNPDIIGFTDAELNETPIRPKWNSLGPGIVAAATGVGAADLVATLTAGS
+RYGYMLLWAVVLGVIFKIVLVEGVGRYYLSTGKTIFQGWRTLGAWTSWYFGPYILIWGIV
+YGATAMSSTALPLAALFPGVDSKVFAIAAGLIGLGLVWLDKYRLIEWLMTVLIGVMFVTV
+LLSAALTAPNLGEILAGLVPRLPSGDPQAMFYVLGLAGGVGGTITLAAYGYWLREKGWNV
+PKYLKVMRFDNATSYILTGIFVIATMVMGVELLHSAGLAISSGDKGLLDVGDVLAERYGS
+AWSTVFLIGFFAASFSSLLGVWHGVSLMFADFWTNFRRPAEELDQDDAPSLSSKPGRFFL
+LWLTLPPMALLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNTKDVPRQFRNGWVRNTL
+LGLTAAVFVAIGVNELIKALQPVLGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000266.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000266.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d44df32f86753c9ca5df323410c44693d064cfc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000266.fa
@@ -0,0 +1,25 @@
+>PROKKA_00131
+MPDSPSARATGGETALVVIDVQHSYFEHPALAAQQAELTAAVVELLRTAREAGRPVFLVR
+TEHARDRSTWTLNMLADGEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSAFHGTGLAA
+ELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIASEEPALAAAMLDFLRDE
+MRQPLLGQDEALTLLRTGLVPDRG
+>PROKKA_02145
+MPDSPSARATGGETALVVIDVQHSYFEHPALAAQQAELTAAVVELLRTAREAGRPVFLVR
+TEHARDRSTWTLNMLADGEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSAFHGTGLAA
+ELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIASEEPALAAAMLDFLRAE
+MRQPLLGQDEALTLLRTGLVPDRG
+>PROKKA_00254
+MPDSAPAPEPIAGERPSGGETALVVVDMQYSYFEHPDLAARQAELTEAVVELVRTAVEAG
+RPVVLVRTEHERDRSTWTLNMLEDGEGFAFPGTRQAAVLDEVARAARGAVEVVKTRDSAF
+HRTDLDAQLRRRGVGRLLLCGVSTHSCVFQTATDAFARDFHAATAVDAIASEDPRLSAAM
+LEFLRDEMRQPLLGREDALALLRTGLVPDQG
+>PROKKA_00651
+MNTLQNPALIVVDVQRGFDDVEYWGSRDNPDCETNISSLLTHWRDRSWPIVFVRHDSTNP
+ESTLAVGTPGNEFKEVITGDPDLLVSKTVNSSFHGTPDLDDWLRAEGIEQVVICGITTNH
+CCETTARIAGNLGYDTYFAIDATHTFDRPALDGTVLPAATVSAMTAANLHGEFATVVSTR
+TLIDGNSYAPRYEQEK
+>PROKKA_00139
+MPDSPSARATGGETALVVIDVQHSYFEHPALAAHQSELTAAVVELLRAAHEAGRPVFLVR
+TEHARDRSTWTLNMLADDEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSAFHGTGLAA
+ELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIASEEPALAAAMLDFLRDE
+MRQPLLGQDEALTLLRTGLVPDRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000269.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000269.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b1a0eb4247498ae0b9f58cce6128bc7c11b3406c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000269.fa
@@ -0,0 +1,31 @@
+>PROKKA_00136
+MTHDDGGPPPGVARGTAHLRVFQPLAAFPDAVQARLIAGGHRTRAEVEAEAAERARRRLA
+RPVADPFPEPGEDDLVRVLQDEHRSAFYCPDERGLRAEMAAAMLEETMLPRLHSAAIPPA
+ARAMNRGRALVALEDEWGLSPDPDAAVEDPQDEDGAPEHHRVQTRTATWGVPHGWLTVFD
+PEEPVQRLVDGERTAYRRAPIVAARERAGHAAAVLARHAPDAELIGELTVMVEWLGAFHP
+DSWVELDYGGLTRHVWPDDSVFDLWTLIDALEEGDEATAGVAQERLNRRWATVGMLARLT
+>PROKKA_02150
+MTHDDGGPPPGVARGTAHLRVFQPLATFPDAVQARLIAGGHRTRAEVEAEAAERARRRLA
+RPVADPFPEPGEDDLVRVLQDEHRSAFYCPDERGLRAEMAAAMLEETMLPRLHEAAIPPA
+ARAMNRGRALVALEDEWGLSPDPDAAGQDPQDEGGAPEHHRVQTRTATWGVPHGWLTVFD
+PEEPVKRLVDGERTAYRRAPIVAARERAGHAAAVLARHALDAELIGELTVMVEWLGAFHP
+DSWIELDYGGLTRHVWPDDSVFDLWTLIDALEEGDEATAGVAQERLNRRWAAVGMLARLT
+>PROKKA_00248
+MVHDDGADGPAPGGGRVPGGAPPPGIAHGTAHLRVFQPLAAYPDAVQARLIAGAHRTRAE
+VEAEAAERARRRLARPVTDPFPEPGEDDLVRVLQDEQGSAFYCPDEFGLRAEMAAAQLEE
+TMLPLAYEAAVPTAARAMNRGRVLVALEEEWGLSPDPDADRAHPDEEDGPGRDEDGPSGR
+HRVQTRTATWGVPHGWLAVFDPEEPVRRLVDGERTAYRRAPALAALERAGHAAAVLSRHA
+PDAELIAELTVMVEWLGAFHPDSHVELDYGGLTRHVWPDDSVFDLWTLIDALGEGDEATA
+GVAQGRLNRRWAAVGMLARLT
+>PROKKA_00182
+MRTAAANLRVFQPLSAYPDAVAARMVAAAHRTRAEVEAEAAERARRRLLRLPADPFPAPG
+EDDLVRVLERGGSAFYCPDELALRMEMAAEMLEASAPEALYAAAVPAAARAMNRGRALVA
+LEDEWGLSPDPDAPAPDDPQDAAHQDQDADAGTHRLQTRTSLWGVPHAWLAAFDPEEPAR
+RLVDGEDVAYRRTPVAEAVERVGHAAAVLAGAAPDAELLGELAVMIPWLQAFHPDAVLEL
+DYGRALTSLVWPDDSVFDLWTLLDALEEGDEVGAGMAQERLNRRWARVGMHAHDG
+>PROKKA_00144
+MTHDDGGPPPGVARGTAHLRVFQPLAAFPDAVQARLIAGGHRTRAEVEAEAAERARRRLA
+RPVADPFPEPGEDDLVRVLQDEHRSAFYCPDERGLRAEMAAAMLEETMLPRLHEAAIPPA
+ARAMNRGRALVALEDEWGLSPDPDAAGQDPQDEGGAPEHHRVQTRTATWGVPHGWLTVFD
+PEEPVKRLVDGERTAYRRAPIVAARERAGHAAAVLARHAPDAELIGELTVMVEWLGAFHP
+DSWIELDYGGLTRHVWPDDSVFDLWTLIDALEEGDEATAGVAQERLNRRWAAVGMLARLT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000272.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000272.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9e1827b4b867b6058d73e9040115b481f564d0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000272.fa
@@ -0,0 +1,20 @@
+>PROKKA_00139
+MSEIQHDDAVQHPSGLPLAHWLTLTEGLIAARVAESLEEHGLTRAQWQLLNTLTVAPQSR
+AELEAGFEEEQRGAVSGQIEELVESRWVTVEGDLYTLTATGRTAGARVGEAVEALRAEAT
+ADVPRDQIDDAVRVLRRIARNLGHPDA
+>PROKKA_02153
+MSEIPHDDAPVQHPSGLPLAHWLTLTEGLIAARVAESLEEHGLTRVQWQLLNTLTVAPQS
+RAELEAGFEEEQRGAVSGQIEELVESHWVTVEGDLYTLTATGRTAGARVGEAVEALRAEA
+TADVPRDQIDDAVRVLRRIARNLGHPDA
+>PROKKA_00245
+MSEIPHDDAAVQHPSGLPLAHWLTLTEGLIAVRVAESLEEHGLTRAQWQLLNTLTVAPQS
+RAELEAGFEEEHRGAVSGQIEELVESRWVTVEGDLYTLTATGRTAGARVGEAVEALRAEA
+TADVPRDQIDDAVRVLRRIARNLGHPDA
+>PROKKA_00179
+MTDNTQTPENRQTQAPRRDSHPSGLPLSHWLTVAEGLLAARVAASLEEHGLTRAQWQSLN
+ALTAAPLSAAEIGAGFEPEVRGAVVEQLDELVDAGWVTVEGDLFTLTSTGRTAGERVGEA
+VERLRGEATADLPAEHYEVTVATLRTIARNLGHPDA
+>PROKKA_00147
+MSEIQHDDAVQHPSGLPLAHWLTLTEGLIAARVAESLEEHGLTRAQWQLLNTLTVAPQSR
+AELEAGFEEEQRGAVSGQIEELVESRWVTVEGDLYTLTATGRTAGARVGEAVEALRAEAT
+ADVPRDQIDDAVRVLRRIARNLGHPDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000273.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000273.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21a54d221606c554c10672a5c606e3aabd4156de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000273.fa
@@ -0,0 +1,25 @@
+>PROKKA_00140
+MGGMTDAQTPTVPTPEQDRERLKQLIQDLAVVHGRVTLSSGKEADYYVDLRRVTLHHEAA
+PLIGRVMLRLLEENGIGCDAVGGLTMGADPVATAMMHQAGAAGRALDAFVVRKAQKSYGM
+GRQVEGPGVDGRRVVVLEDTSTTGGSALTAVEGVRNAGGDVQAVAVIVDRATGAAERVAE
+EAGVPYLYAFGKDELGLD
+>PROKKA_02154
+MGGMTDAQTPTVPTPEQDRERLKQLIQELAVVHGRVTLSSGKEADYYVDLRRVTLHHEAA
+PLIGRVMLRLLEENGIEFDAVGGLTMGADPVATAMMHQAGTVGRALDAFVVRKAQKSYGM
+GRQVEGPGVDGRRVVVLEDTSTTGGSALTAVEGVRNAGGDVQAVAVIVDRATGAAERVAE
+EAGVPYLYAFGKDELGLD
+>PROKKA_00244
+MGGMTDAQTPTVPTPEQDRERLKELIQELAVVHGRVTLSSGKEADYYVDLRRVTLHHEAA
+PLIGRVMLRLLEENGVQFETMGGLTMGADPVATAMMHQAGAQGRALDAFVVRKAQKSYGM
+GRQVEGPGVDGRDVVVLEDTSTTGGSALTAVEGVRRAGGRVQAVAVIVDRATGAAERVAE
+EADVPYLYAFGKDELGLD
+>PROKKA_00178
+MTAEHTSVAPTPEQDRERLRELIKELAVVHGRVTLSSGAEADYYVDLRRVTLHHEAAPLI
+GRVMLRLLEENGIEFETMGGLTMGADPVATAMMHQAGAQGRALDAFVVRKAQKSYGMGRQ
+VEGPGVEGRRVVVLEDTSTTGGSALTAVEGVRKAGGDVQAVAVIVDRATGAAERVAEEAG
+VPYLYAFGKDELDLD
+>PROKKA_00148
+MGGMTDAQTPTVPTPEQDRERLKQLIQDLAVVHGRVTLSSGKEADYYVDLRRVTLHHEAA
+PLIGRVMLRLLEENGIGCDAVGGLTMGADPVATAMMHQAGAAGRALDAFVVRKAQKSYGM
+GRQVEGPGVDGRRVVVLEDTSTTGGSALTAVEGVRNAGGDVQAVAVIVDRATGAAERVAE
+EAGVPYLYAFGKDELGLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000277.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000277.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6dbed9684840a8d20284dbc6fad4c1118a99c196
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000277.fa
@@ -0,0 +1,30 @@
+>PROKKA_00144
+MRAEQVTDPIAYHGEGPVWAASWGAAAEGVTAGGGLRWVDMLAGDVLSLRADGTVDRTHV
+GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC
+GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTLAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG
+>PROKKA_02158
+MRAEQVTDPITYHGEGPVWAASWGSAAEGVTAGGGLRWVDMLAGDVLSLRADGTVDRTHV
+GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC
+GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTRAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG
+>PROKKA_00240
+MRAEQVTDPITYHGEGPVWAEHWGTAASGLAAGGGLRWVDMLAGDVLSLRADGAVERTHV
+GDVAAVVRPRAGGGAVLAVERGFALMSPEGELTTLPELWGPEAGLRMNEGGCDPDGRFHA
+GTMAYAKTPGAASLHRLSPGPDGGAGEVDVVLTGATTSNGLEWSPGGSLAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGEDLGTLYITTSWENMERGEDPLAGALFAVRPGVTGLPARPFAS
+>PROKKA_00174
+MRADQVTDPLCYHGEGPVWAESWGGLRWVDMLAGDVLSLGADGGVTRRNVDPKVCAVVRP
+RVGGGAVFAVERGFALEDPDGTLHRLPPLWDDAAGLRMNEGGCDPDGRFYAGSMAYAKTP
+GAASLHRLSPAPEGGAGEVDVVLEGVTTSNGLAWSPDGSLAYYDDTPTRQVAVFDYSREE
+GLTNRRVLVDVLDGEGKPDGLCVDAEGGIWVAVISHGRIHRYTPEGVLDEVVEVPVQKTT
+ACTFGGDDLGTLYITTSWEGMERGEDPLAGALFSVRPGVAGLPTLPFAG
+>PROKKA_00152
+MRAEQVTDPIAYHGEGPVWAASWGSAAEGVTAGGGLRWVDMLAGDVLSLRTDGTVDRTHV
+GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC
+GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTRAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000281.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000281.fa
new file mode 100644
index 0000000000000000000000000000000000000000..933d5a108b80b9c647524ed6f14fd83ea3ec476c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000281.fa
@@ -0,0 +1,55 @@
+>PROKKA_00149
+MSPQTTTPTLHEIHADDVREHTPLPHDVSTQAIPVVIPEGAAPVVTVHGPVDGRQAEILT
+DEALAFLGRLHRLAEDRRRRLLEEREYTRRRITDGWNPHYLRSTRRVREDDSWRVAPLAP
+GLQDRRVEITGPVDRKMTINALNSGASGWLADFEDSSTPSWDRMLDGQVNLFDAIRDQID
+FTSPEGKEYRLRERELTDRPTIIVRPRGWHLLEDHIRVDGEPMAGALVDFGLYFFHNADE
+LIRRGHGPYFYLPKLESHLEARLWNCVFVAAQDELGIPQGTIRATVLIETITAAFQMEEI
+LYQLRNHAAGLNAGRWDYIFSIIKNFRDRGAEFVLPDRSEVTMTQPMMRAYTEQLVRACH
+RRGASAIGGMSAVIPDRRNEEANAAALEKVRADKAREAGDGFDGSWVAHPDLVPVAREEF
+DAVLGEAPNQIRTRRREDVEPDEAALLDVAATTGSVTEAGVRMNIEVGIRYIESWLRGNG
+AAAIHGLMEDAATAEISRSQIWQWAHNGTGVQLTEGGVRTANRGWMEQLIREEHARILAG
+PLPEGHRFEDAVRVFCESALPPEYPAFLTLGAYRRHFASQDDAAAKA
+>PROKKA_02163
+MSPQTTTPTLHEIHADDVREHTPLPHDVSTQAIPVVIPEGAAPVVTVHGPVDGRQAEILT
+DEALAFLGRLHRLAEDRRRRLLEEREYTRRRITDGWNPHYLRSTRRVREDDSWRVAPLAP
+GLQDRRVEITGPVDRKMTINALNSGASGWLADFEDSSTPSWDRMLDGQVNLFDAIRDRID
+FTSPEGKEYRLRERELTDRPTIIVRPRGWHLLEDHIRVDGEPMAGALVDFGLYFFHNADE
+LIRRGHGPYFYLPKLESHLEARLWNCVFVAAQDELGIPQGTIRATVLIETITAAFQMEEI
+LYQLRNHAAGLNAGRWDYIFSIIKNFRDRGAEFVLPDRSEVTMTQPMMRAYTEQLVRACH
+RRGASAIGGMSAVIPDRRNEEANAAALEKVRADKAREAGDGFDGSWVAHPDLVPVAREEF
+DAVLGEAPNQIRTRRREDVVPDEAALLDVAATTGSVTEAGVRMNIEVGIRYIESWLRGNG
+AAAIHGLMEDAATAEISRSQIWQWAHNGTGVQLTEGGVRTANRGWMEQLIREEHARILAG
+PLPEGHRFEDAVRVFCESALPPEYPAFLTLGAYRRHFAGQDDAAAKA
+>PROKKA_00234
+MTTTTVTSGRHHAAPALHHTDEPVDTAAHTPLPHDVSTQALPVVAPAGAAPVVTVHGPVT
+DRQAEILTEDALAFLGRLHRVAEDRRRRLLEEREFTRQRITEGWDPHFLRATKRVREDDS
+WRVAPLAPGLKDRRVEITGPVDRKMTVNALNSGATGWLADFEDSSTPSWERMLDGQVNLY
+DAIRGRIDFTSPEGKEYRLRGAELTDRPTIIVRPRGWHLTDDHLRVDGEPMAGGLVDFGL
+YFFHNAAELVRRGHGPYFYLPKLESHLEARLWNCVFVAAQDALGIPQGTIRATVLIETIT
+AAFQMEEILYQLRNHAAGLNAGRWDYIFSLIKNYRDRGPAYVLPDRAEVTMTQPMMRSYT
+EQLVRACHRRGASAIGGMSAVIPDRRDQAANEVAFAKVREDKTREARDGFDGSWVAHPDL
+VPVAREVFDEVLGEAPNQIRTRRREDVEPDEAGLLDVAATTGSVTEAGVRRNIEVAMRYV
+ESWLRGQGAAAIHGLMEDAATAEISRSQIWQWAHNRTAVALEDGGTRTASREWMEQLVRE
+EHARILAGPLPEGHRFEDARRVFCESALPPEYPAFLTLGAYRRHFSAERA
+>PROKKA_00819
+MMTLQTTHSDTTVNGVRVLGEPVPGQDRVLTSAALEFLAALHRGVEGRRRELMDERAARR
+RRIAEGETLDFLPATRKVREDDSWHVAPLAPGLRDRRVEITGPVDRKMTINAMNSGAKCW
+LADFEDSSTPSWENVIAGQVNLQDAIRRTISLTTPEGKEYTLGGVQLVDRPTIIVRPRGL
+HLMEDRILVDGQPVSGALADFALYFFHNAKELLRRGRGPYFYLPKTESHLEARWWNCVFV
+RAQDLLEIPQGTIRATVLIETITAAFEMEEILYQLRNHAAGLNAGRWDYIFSVIKTFRER
+GEDFVLPDRSEVTMTQPMMRAYTELLVRTCHRRGASAIGGMAAQIPNRKDPEANAAALEK
+VRSDKTREAGDGFDGSWVAHPDLVPVAMEVFDAVLKDLPNQIRTRRREDVVPDAAALVDI
+KSTTGSITEQGLRMNIEVGIRYVESWLRGNGAAAIHNLMEDAATAEISRSQIWQWIRTGS
+TARLTDGGERTVTREWVEQVTEEEFGRIERTEGDRFDDAREIFTSVALAEDFPDFLTLPA
+YERFLSAEARRRAGHGA
+>PROKKA_00157
+MSPQTTTPTLHEIHADDVREHTPLPHDVSTQAIPVVIPEGAAPVVTVHGPVDGRQAEILT
+DEALAFLGRLHRLAEDRRRRLLEEREYTRRRITDGWNPHYLRSTRRVREDDSWRVAPLAP
+GLQDRRVEITGPVDRKMTINALNSGASGWLADFEDSSTPSWDRMLDGQVNLFDAIRDQID
+FTSPEGKEYRLRERELTDRPTIIVRPRGWHLLEDHIRVDGEPMAGALVDFGLYFFHNADE
+LIRRGHGPYFYLPKLESHLEARLWNCVFVAAQDELGIPQGTIRATVLIETITAAFQMEEI
+LYQLRNHAAGLNAGRWDYIFSIIKNFRDRGAEFVLPDRSEVTMTQPMMRAYTEQLVRACH
+RRGASAIGGMSAVIPDRRNEEANAAALEKVRADKAREAGDGFDGSWVAHPDLVPVAREEF
+DAVLGEAPNQIRTRRREDVVPDEAALLDVAATTGSVTEAGVRMNIEVGIRYIESWLRGNG
+AAAIHGLMEDAATAEISRSQIWQWAHNGTGVQLTEGGVRTANRGWMEQLIREEHARILAG
+PLPEGHRFEDAVRVFCESALPPEYPAFLTLGAYRRHFAGQDDAAAKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000282.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000282.fa
new file mode 100644
index 0000000000000000000000000000000000000000..69edb53d41aa1171c8c01d3a10ab294e99ee6b0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000282.fa
@@ -0,0 +1,39 @@
+>PROKKA_00150
+MTHPAPARRRAPLAVGVAALALALAGCGSAGQSGEPASSTAAAPSGSAASAAAGSATESP
+TDPASAAASRVREALASESAEGTPRAEPRQAFETVGPGIKDGAATEAWKNTAAVRNDTVS
+VMDCTRDVLDQRTLDAVATHIPDSSNIEIVQLFASQDETHEFLTCVYNGYFEYSPGMPLA
+QVHYQHNLDGSRLEWCQEEPAAVADEYTFDPKTGKGLLALLRPGMVGGQDGAPLLPQRTA
+WACSEDGSEMVSVTMGSMEGFGDANGGLTQVKNSPVAQSTTLVTETRDHLADTVLKDAGD
+FQEVIKLSSPFFLNAQMDEETLAQAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPP
+RPFQGAAREAAESQRAAEASASASASPSPTKSASASASPSPSTSGD
+>PROKKA_02164
+MTHPAPARRRAPLAVGVAALALALAGCGSAGQSGEPASSTAAAPSGSAASAAAGSATESP
+TDPASAAASRVREALASESAEGTPRAEPRQAFETVGPGIKDGAATEAWKNTAAVRNDTVS
+VMDCTRDVLDQRTLDAVATHIPDSSNIEIVQLFASQDETHEFLTCVYNGYFEYSPGMPLA
+QVHYQHNLDGSRLEWCQEEPAAVADEYTFDPKTGKGLLALLRPGMVGGQDGAPLLPQRTA
+WACSEDGSEMVSVTMGSMEGFGDANGGLTQVKNSPVAQSTTLVTETRDHLADTVLKDAGD
+FQEVIKLSSPFFLNAQMDEETLAQAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPP
+RPFQGAAREAAESQRAAEASASASASPSPTKSASASPSPSTSGD
+>PROKKA_00233
+MREARESASAEGTPRAQPRQALETLGPGIRDGAATTAWENTAAVRNDTVSVMDCTRDVLD
+QRTLDAVATHIPDGSNIEIVQLFAAQDETHEFLTCAYNGYFEYSPGMPLAQVQYQHNLDS
+TRLDWCEDEPATVADEYTFDPETGKGLLALLRPGMIGGQDGAPLMPQRTAWACSEDGTEL
+VSVTMGSMEGYGDANGGLTQVENSPVAGSTTLVTEARDHLADTVLKDASRFHEVIKLSSP
+FFLNASMDEESLAKAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPPRPFQGAAREA
+AESQRAAEASASAAEASASRAASGSGTPSPSSTPASRTPSPSGTGG
+>PROKKA_00172
+MTHPTSAPHRAAAALGAAALALTLAGCSDSGQPSPASSTSTATAAAGSSASATGDPQSPA
+SAAASEIRAARASEKADGSERPQPREALETQGPGITSGAASAGWKSVAARYNDTVSVMDC
+TQDVLDQTTLDAVATHIPVANDIGIVQLFASRDQTHEFLTCQYQGSSSRSEGAPLVMVHY
+QHNLDGRRLEWCRPEAPVMADEYSYDESTRKGLLALLRPGMVGGADGAPLLPQRTAWACN
+EDGTQLVSVTFGAMKGYGSVNEGLTQVTNSPIANSTTLATQARDHLADTVLKDPSDFQAD
+IETSSPFFLNAQTDQETLDKAKGLPTGIIPQDQLSDQSTIDRPEGAPEPVAPGQPPRPFV
+GAARDAAESAAAESAASSSGSDSASPSDDGDGNPVVSESGTPSPSNTTD
+>PROKKA_00158
+MTHPAPARRRAPLAVGVAALALALAGCGSAGQSGEPASSTAAAPSGSAASAAAGSATESP
+TDPASAAASRVREALASESAEGTPRAEPRQAFETVGPGIKDGAATEAWKNTAAVRNDTVS
+VMDCTRDVLDQRTLDAVATHIPDSSNIEIVQLFASQDETHEFLTCVYNGYFEYSPGMPLA
+QVHYQHNLDGSRLEWCQEEPAAVADEYTFDPKTGKGLLALLRPGMVGGQDGAPLLPQRTA
+WACSEDGSEMVSVTMGSMEGFGDANGGLTQVKNSPVAQSTTLVTETRDHLADTVLKDAGD
+FQEVIKLSSPFFLNAQMDEETLAQAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPP
+RPFQGAAREAAESQRAAEASASASASPSPTKSTSASPSPSTSGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000290.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000290.fa
new file mode 100644
index 0000000000000000000000000000000000000000..62928a7b76a5b7166780ca6a72b5114e2344dd84
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000290.fa
@@ -0,0 +1,30 @@
+>PROKKA_00181
+MRISVGQFGPVGDVEENLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA
+WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH
+RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK
+VEHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADEREAVATAEVTR
+ERIDEVREFLPSLANRRTDVL
+>PROKKA_02177
+MRISVGQFGPVGDVEANLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA
+WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH
+RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK
+VDHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADEREAVVTAEVTR
+ERIDEVREFLPSLANRRTDVL
+>PROKKA_00220
+MRISVGQFGPVGDVEANLAVMARLAARAAGEGAELLVLPEEAMLGAREVGEEFPDAIAAA
+WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH
+RESDRISPGDGGVAAIELDGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK
+VEHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVVELADEREAVVTAEVTR
+ERIDEVRKFLPSLANRRTDVL
+>PROKKA_00165
+MRIAVGQFGPTGRVEDNLEAMGRLAARAAAEGAGLLVLPEEAMLTFREVEDEFAHAVAGS
+WEPFTEGLARLARQHGLAIVAGGYEPSATDRPYNTLVAVDADGAVAGAYRKLHLYDAFEH
+RESELITPGDRGLVTVEVGGLTVGLQTCYDLRFPEVSRALALAGAQVLAIPAAWFAGEHK
+VDHWRTLLRARAVENTVWVAAADTASAATVGHSAIIDPLALTLAEADDDAAPETLLCADV
+TAERVEEVRRTVPVLANRRTDVLTPPVDVEPGG
+>PROKKA_00178
+MRISVGQFGPVGDVEANLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA
+WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH
+RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK
+VDHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADEREAVVTAEVTR
+ERIDEVREFLPSLANRRTDVL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000291.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000291.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f8bff27179252ea64e3de5dcc5cc1a8e98eead6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000291.fa
@@ -0,0 +1,20 @@
+>PROKKA_00182
+MTINADGSHAVQPHTANAHTTPARPVRHAVVEEEVLEPLRPVDGWGFTNRVILVSVLVVI
+IGNVVRVLTGGLGDPNGSVALGETGHGWVVLVQSFMFGLVGGALAGAAGYLVVLLMGGAA
+RSVVRYVVGGVVGGFLGAVGLFAVFSNTVVYGSGVHLFWMLPVAGLLGGLWAGLVSSRR
+>PROKKA_02178
+MTINADGSHAVQPHAANAHTAPARPVRHAVVEEEVLEPLGPVEGWGFTNRVILVSVLVVI
+IGNVVRVLTGDLGDPNGSVALGETGHGWVVLVQSFMFGLVGGALAGAAGYLVVLLMGGAA
+RSVVRYVVGGVVGGFLGAVGLFAVFSNTVLYGAGLHLFWMLPVAGLLGGLWAGVVSSRR
+>PROKKA_00219
+MTINADGSHAVQPHSANAHTAPASPARHAVVEEEVLEPLRPVDGWGFTNRVILVSVLVVI
+IGDVVRVLTGGLGDPNGSVALGETGRGWVVLVQSFMFGLVGGALAGAAGYLIVLLMGGAA
+RSVVPYVVGGVVGGFLGAVGVFAVFSNTALYGSGLHLYWMLPVAGLLGGLWAGVVSSRR
+>PROKKA_00164
+MNTQAHGAHAVQTVGGTAAPQAPARRAVVAPEAVEPARPVDGWGFVNRILVVATVLIVAF
+ELWRAATGLLSDGPRVLGEDGVGWVAVLEAFMFALVGGAIAGAAGYGIVLLMGGAARSAA
+RYAIGGLIGGFLAAVGVIFVFSNTAALSVGGHLFWMLPLAGLIGGVWAGITSAKS
+>PROKKA_00179
+MTINADGSHAVQPHAANAHTAPARPVRHAVVEEEVLEPLGPVEGWGFTNRVILVSVLVVI
+IGNVVRVLTGDLGDPNGSVALGETGHGWVVLVQSFMFGLVGGALAGAAGYLVVLLMGGAA
+RSVVRYVVGGVVGGFLGAVGLFAVFSNTVLYGAGLHLFWMLPVAGLLGGLWAGVVSSRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000294.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000294.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea44890e9b6da4f9467182d480a985ced77978c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000294.fa
@@ -0,0 +1,45 @@
+>PROKKA_00185
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPITINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRAVFAFLAVLGLVASAMVVF
+GVGPSWILDESIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+GLMDIWLWYFFGTLAVTFAVTAITVRIPPLSRIPDECYPGVTHSPEQAVTRDRFRVARRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLGARFVIGVVCVSAIIFFSAVVPAI
+LATDIPVKMWHLLVIWVERVALTIVLATPLAHLVAALT
+>PROKKA_02181
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPVTINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRTVFALLAVLGLVASAMVVF
+GVGPSWILDKSIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAAGFSTVSATFMVIVAKTL
+GLMDIWLWYFFGTLVVTFAVTAITVRIPPLSRIPDEVYPGAVHSPELAVTRDRFRVARRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI
+LATDIPIPLWKLVVIWAERVALTILLAMPVAHLVAALT
+>PROKKA_00216
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPVTINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIATGAVYPFASGRWRTSTTRTVFALLAVLGLVASAMVVF
+GVGPSWILDESIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+GLMDIWLWYFFSALVVTFVVTAITVCIPPLSRIPDEVYPGAVHSPEQAVTRDRFRVALRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGMIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI
+LATDIPVKMWHLLVIWVERVALTIVLATPLAHLVAALT
+>PROKKA_00161
+MTHAHPADGELHTDTTAMAAIEADSPRPPARWRMVVYSLIGIVMFFVPVTINGASSIPLD
+HLVTWVRGLLGPADRYVALALIAAGAVFPFATGRWRQSVTTTVFAFLGVVGLLTACMVVF
+GFGPSWVLDKGIGPFLLDKLVIPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+DLMDHWLWYFFGTLVVTFVVTAITVRIPPLSRIPDEPFPGAVHVPEEAVTQDRFRVARRA
+AEQTLAEAPSLGRNVWLNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWVGLIFQPV
+FWALGFSDPALMASASATSIAEMFIPATMLAGHEDFVARFVIGVVCVSAIIFFSALVPAI
+LATDIPVKLWHLVVIWVERVVLTVLLATPLGHLVAALTS
+>PROKKA_00182
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPITINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRAVFAFLAVLGLVASAMVVF
+GVGPSWILDKSIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+GLMDIWLWYFFGTLAVTFAVTAITVRIPPLSRIPDECYPGVTHSPELAVTRDRFRVARRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI
+LATDIPIPLWKLVVIWAERVALTILLATPVAHLVAALT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000298.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000298.fa
new file mode 100644
index 0000000000000000000000000000000000000000..79287d44e418796e294ec57dd78ef1adfc6a125a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000298.fa
@@ -0,0 +1,20 @@
+>PROKKA_00193
+MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGKEILGHRVYASLDGLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEVVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR
+>PROKKA_02189
+MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGKEILGHRVYASLDDLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEVVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR
+>PROKKA_00207
+MSATHPERTWTGPSAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGQEILGHRVYASLDDLPVTPDLVEVFRKASDAPEMVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEIVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR
+>PROKKA_00154
+MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGKEILGHRVYASLDDLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEIVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR
+>PROKKA_00193
+MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGKEILGHRVYASLDDLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEVVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000299.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000299.fa
new file mode 100644
index 0000000000000000000000000000000000000000..87ea18adf59d4253360a4640752ef43f5fdd6e51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000299.fa
@@ -0,0 +1,49 @@
+>PROKKA_00194
+MITQPALHATGRRRVTLCDVPTLPPARLARDNGADCPEASIERTPVADHEFGFRTQALHA
+GAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL
+EGGIGAVATASGMAAEFVTFAALAAAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS
+AEAADFEAALQPNTKTVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP
+IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG
+EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANAQAVAQWLDEDPRVS
+WVRYAGLPDHPHHARAQQLLPRGVGSVFSIGVAPAATDTDDGASGPEAGRATASRFISAL
+QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPEDLIRISVGIEDTEDILWDLDQ
+ALTEATGRTRDDDGAPAAPKEA
+>PROKKA_02190
+MITQPALHGTGRRRVTLCDVPTLPPAHLARDNGRDCPEASIERTPVADHEFGFRTQALHA
+GAVPDTVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL
+EGGIGAVATASGMAAEFVTFAALAAAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS
+AEAADFEAALQPNTKTVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP
+IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG
+EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANAQAVAQWLDEDPRVS
+WVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASGPEAGRATASRFISAL
+QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPEDLIRISVGIEDTEDILWDLDQ
+ALTEATGRTRDDDGAPAAPKEA
+>PROKKA_00206
+MADHEFGFRTQALHAGAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRI
+GNPTVAAFEERVATLEGGIGAVATASGMAAEFVTFAALAGAGDHIVASSKLYGGTITQLD
+VSLRRFGVETTFVDSVEAADFEAALQPNTKAVYTEIVANPSGDVVDLPGLADVAHRHGVP
+LVVDATLTPPYLIRPIEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTE
+PVPSYGGVSWWGNFGEYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLAN
+ARAVATWLDEDPRVSWVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASG
+PEAGRATASRFISALQLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPADLIRIS
+VGIEDLEDILWDLDQALTEATGRTRDGAVVPAEQEA
+>PROKKA_00153
+MITQPALHGTGLRRVTLCDVPTLPPAHLARDNGTDCPEASIERTPVADHEFGFRTQALHA
+GAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL
+EGGIGAVATASGMAAEFVTFAALAGAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS
+AEAADFEAALQPNTKAVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP
+IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG
+EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANARAVATWLDEDPRVS
+WVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASGPEAGRATASRFISAL
+QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPADLIRISVGIEDLEDILWDLDQ
+ALTEATGRTRDGAVVPAEQEA
+>PROKKA_00194
+MITQPALHGTGRPRVTLCDAPTLPPAHLARDNGTDCPEASIERTPVADHEFGFRTQALHA
+GAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL
+EGGIGAVATASGMAAEFVTFAALAGAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS
+AEAADFEAALQPNTKAVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP
+IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG
+EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANAQAVAQWLDEDPRVS
+WVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASGPEAGRATASRFISAL
+QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPADLIRISVGIEDLEDILWDLDQ
+ALTEATGRARDGAVVPAEQEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000300.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000300.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16274fa2fed16245c11f95156c707c9a0e5c54e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000300.fa
@@ -0,0 +1,35 @@
+>PROKKA_00195
+MTARTPLPSTLAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGIPDPCAPDGAAAL
+VRLTGGVVSHVSAALWHGLPLPPRLARPAGLHLTFDRSARTHRTDLDGVVSHRVRLPSDH
+VLELPDGQRVTTAARTWFDLAGMLRPHEVDWLIADGDHLVRPPWTPTGRADPVATVSELS
+EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP
+VVDLGYRGARLALQYDGAGHRTAQQQARDARRDAYCLEREWTTLRCTWEDQRAGFGRIVG
+LVRRRLARTR
+>PROKKA_02191
+MTARTPLPSTLAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGIPDPCAPDGAAAL
+VRLTGGVVSHVSAALWHGLPLPPRLARPAGLHLTFDRSARTHRTDLDGVVSHRVRLPSDH
+VLELPDGQRVTTAARTWFDLAGMLRPHEVDWLIADGDHLVRPPWTPTGRADPVATVSELS
+EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP
+VVDLGYRGARLALQYDGAGHRTAQQQARDARRDAYCLEREWTTLRCTWEDQRAGFGRIVG
+LVRRRLARTR
+>PROKKA_00204
+MTARAPLPPALARAAFGVDELLDAGLPWDRTRAADLHRIWRGVYTAADPAALTWDRAAAL
+CRVTGGVISHTTAAAWHGIPLPRRLEASEELHLTVDRGRRQHRSARPGVVTHRLRLPPQE
+IRQVGGGLRVTSPERTWLDLAVLLRPWELDWLVVAGDHLVHHPWHPDGRRPSATTPALLD
+AALGRHVGRHGIRRAREALADVRVGADSAPETRLRLALIRAGLPEPALQIAVDPSDPRSP
+EADLGYRDARIALQYDGAAHRTPEQQARDARREAYCLELDWLPLRCTQEDLREGFIRVIG
+LVRRRLGPRGAFGATSRR
+>PROKKA_00152
+MTARTPLPPALAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGVPDPCAPDGAAAL
+ARLTGGVVSHVSAALWHGLPLPPRLARPAGLHLTFDRSARTHRSDLGGVVSHRVRLPSDH
+VLELPDGQRVTTAARTWFDLAGMFRPHEVDWLIAAGDHLVRPPWTPTGRADPVATVPGLS
+EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP
+VVDLGYRAARLALQYDGAGHRTAQQQARDARRDAYCLEREWTTLRCTWEDQRAGFGRIVG
+LVRRRLARTR
+>PROKKA_00195
+MTARTPLPSTLAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGVPDPCAPDGAAAL
+VRLTGGVVSHVSAALWHGLPLPPRLTRPAGLHLTFDRSARTHRTDLGGVVSHRVRLPSDH
+VLELPDGQRVTTAARTWFDLAGMLRPHEVDWLIAAGDHLVRPPWTPTGRAHPVATVPGLS
+EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP
+VVDLGYRGRAWPSSTTAPATARLSSRRGTPVGTRTASSGNGRPCAAPGRTSALGSGGSWG
+WSGVGSPARADPPPRPTRVELSRVPSNAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000302.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000302.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a85297ac2333e31227a82b2c0c6c3fa53419977f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000302.fa
@@ -0,0 +1,30 @@
+>PROKKA_00197
+MPHPPRPTPDDVPAAERAALRRGRLRPWLPFLLAAALCLALLGWALVALPGLPERVPTHW
+GVDGRPDAWEDASFGTVATGPLIGLGVTGFLALVSAMVTVLVPTDPGLSPWRRVRQAGVH
+RGVQECLGWSCVLIVLVLAPTTAEVLAAGAWTMPWWILPLTLTVLMVGVFPAMRASTRRW
+TRWSDRVAAELGYRPTAAERAEDEVWTPLGLKRDPDDPAVFPTKRPGYGVGVTVNLATPA
+GRWLVRGFVVVVIVGLPLALWLGAFAAR
+>PROKKA_02193
+MPHPSRPTPDDVPAAERAALRRGRLRPWLPFLLAAALCLALLGWALVALPGLPERVPTHW
+GVDGRPDAWEDTSFGTVATGPLIGLGMTGFLALVSAMVTALVPTDPGLSPWRRVRQAGVH
+RGVQECLGWPCVLIVLVLAPMTAEVLAAGAWTMPWWLLPLTLTVLMVGVFPAMRVSTRRW
+TRWSDRVAAELGYRPTAAELAEDEVWTPLGLKRDPDDPAVFPAKRPGYGVGVTVNLATPA
+GRWLVRGFVAVFIVGLPLALWLGAFAAR
+>PROKKA_00202
+MARYVPAPAPEPVPAAEEAALRQGRARPWWPYLLTAAVSVALLVWTVVAYPGLPEQVPVR
+WGIDGRPDRWEDTTFGTVAFGPIFGLGMTAFLALIAAMIPAMTGVHGATSAWRRVRQEGV
+NRGVREGMGWIALLSLLMTAPTTAEVLSAGAWRMPWWLMPLLLTALMVGVFGALRATLGR
+WTRWADGVAADLGHRPTPEELAEDKTWTPLGMKDDPEDPTVFPAKRPGYGVGTTINIGTR
+AGRLLVYGFVAVFMVALPLATWIGAYLAR
+>PROKKA_00150
+MPHPPRPTPDDVPAAERAALRRGRWIPWLPYLLTAAVSAGLLVWAIVALPGLPDRVPVHW
+GIDGRPDAWEEKSFGTVAFGPLLGLGMTALLAFCAALTPAMTATPQDASPWRRVRQEGVN
+RGVREALGWLTLLIALATAPSTVEVLSNGAWRPAWWLMPLVLTLVMLGTVGVFGPALRRW
+TGWADRTAQDLGYRADFAELAEDAKWTPLGLKNDPEDPSAFPAKREGYGVGATVNLATTT
+GRLLVYGFVALFVIGLPAALWIGAFLNR
+>PROKKA_00197
+MTHPPHPVPADVPAAERAALRRGRLRPWLPFLLAAALCLALLGWALVALPGLPERVPTHW
+GVDGRPDAWEDASFGTVATGPLIGLGMTGFLALVSAMVTALVPMDPGLSPWRRVRQPGVH
+RGVQACLGWSCVLIVLVLAPTTAEVLAAGAWTMAWWLLPLTLTVLMVGIFPAMRAGTRRW
+TRWADRVAADLGHRPTAAELAEDEVWTPLGLKRDPEDPAVFPAKRPGYGVGVTVNLATPA
+GRWLVRGFVAVFIVGLPLALWLGAFAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000303.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000303.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c84ad8c23b66685d48e73f624c5af844107cddc1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000303.fa
@@ -0,0 +1,70 @@
+>PROKKA_00202
+MTAGDDGGRGAVVGVPTLVGPADQEEPPPMTPTEDPARPDPAEEGASGAVRGPNDGVPAA
+ALATLPGPLPQALVDAADPDVHPGRPADRLHGGRGDGRPVAEADRLAFWEAAGRRLSWER
+PFTRTRSLTAPDPAAERGPEIRWYEDGTLNVAVNCVDRHVAAGRGEKVALYFEGEPGDRR
+AVTYAQLQREVAQAANALEELGIEAGDRVVVYLPVLVETIVITLACARIGAVHSLVFGGF
+SAEALRFRVEDTGAKLLVTTDGQFRRGAAVPVKANADEAVSGDNAIEHILVLDRTGHRDI
+PWTEGRDLWWHDVVDRQPDTHTPRAFDAEHPLFIMYTSGTTGQPKGLVHTSGGYLAAASW
+THDFLFSHPNPARRDDDVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRH
+FEVIERYRVTSYYTAPTLIRSLKGWHPDGIPAHADGGPDLSSIRLIGTVGESVNPEAWTW
+ARTQIGRDTPDLPMVDTWWQSETGATVLSPRPTDTAFKPGCGSRPLPGVDVAVVDDDGAP
+TPEGLQGRIVVTRTSPAMARTVWRNPARYFHSYWEDYADQGEAGWFLAGDGAKRDEDGDV
+WILGRVDDVINISGHRLSTIEIESALVAHPEVIEAGVCPVPHETTGHAAVAFVVAHESWL
+AGDDGPGASAADRAEELRRHVGRVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHQGT
+ALGDTTSLQNEPCVGQIAEVLRAGRRAQDAGTGAVRSASSAST
+>PROKKA_02197
+MTPTEDPARPDPAEEGASGAVRGPNDGVPAAALATLPGPLPQALVDAADPDVHPGRPADR
+LHGGRGDGRPVAEADRLAFWEAAGRRLSWERPFTRTRSLTAPDPAAERGPEIRWYEDGTL
+NVAVNCVDRHVAAGRGEKVALYFEGEPGDRRAVTYAQLQREVAQAANALEELGIEAGDRV
+VVYLPVLVETIVITLACARIGAVHSLVFGGFSAEALRFRVEDTGAKLLVTTDGQFRRGTA
+VPVKANADEAVSGDNAIEHVLVLDRTGHRDIPWTEGRDLWWHDVVDRQPDTHTPRAFDAE
+HPLFIMYTSGTTGQPKGLVHTSGGYLAAASWTHDFLFSHPDPARRDDDVHWCTADLAWVT
+AHTYEIYGPLSNGVTQVIYEGVPNAPHPGRHFEVIERYRVTSYYTAPTLIRSLKGWHPDG
+IPAHADGGPDLSSIRLIGTVGESVNPEAWTWARTQIGRDTPDLPMVDTWWQSETGATVLS
+PRPTDTAFKPGCGSRPLPGVDVAVVDDDGTPTPEGLQGRIVVTRTSPSMARTVWQNPARY
+FHSYWEDYADQSEAGWFLAGDGAKRDEDGDVWILGRVDDVINISGHRLSTIEIESALVAH
+PEVIEAGVCPVPHETTGHAAVAFVVAHESWLAGDDGPGASAADRAEELRRHVGRVIGPVA
+KPAEVVFVPDVPKTRSGKIMRRLLTQLHQGTALGDTTSLQNEPCVGQIAEVLRAGRRAQD
+AGPGAVRSASSAST
+>PROKKA_00190
+MTPSPLDAATRARSSAPASPGDAPTAPDAPVRRPNDGVPAEALATLPGPLPQAVVDAADP
+DVHPGRAEDLAHGGRGDGRPVAEEDRLAFWAAAGRRLTWDREFTRVSTGTPADPAAERGP
+ALRWYEDGRLNVAVNCVDRHVAAGRGEKVALYFEGEPGDREAVTYADLQRRVAQAAHALE
+DLGIGPGDRVVVYLPVLVETIVIALACARIGAVHSLVFGGFSADALRFRVEDTGAKLLVT
+TDGQHRRGQVVPVKENADAAVAGDNAIEHVLVIARCGLTGAGEIPWTEGRDLWWHDVVET
+KPTEHAPASFDAEHPLFVMYTSGTTGRPKGLVHTSAGYLAAASWTHDFLFSHPDPARRHE
+DVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRHFEVIDRYRVTSYYTAP
+TLIRSLMGWHPDGIPAEHSLESIRLIGTVGEAVNPEAWTWARTQIGRAALARTGEPVPMV
+DTWWQSETGSTVLSPRPTDHTFKPGCGSRPLPGVEVAVVDDDGAPVPAQTQGKIVVTRTS
+PSMARTVWGDPARYFHSYWEDCAEQGWFLAGDGAKTDEDGDVWILGRIDDVINISGHRLS
+TIEIESALVAHPHVVEAGVCPVPDARTGHAAVAFVVPGREWAPGPEGDEAAAALAAERAE
+ELRRHVGTVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHTGTALGDTTNLQNEVCVG
+QIAQVLADRPGR
+>PROKKA_00144
+MTAGDDGGRGAVIVVPTLVGPADQEEPPPMTPTEDPARPDPAEEGASGAVRGPNDGVPAA
+ALATLPGPLPQALVDAADPDVHPGRPADRLHGGRGDGRPVAEADRLAFWEAAGRRLSWER
+PFTRTRSLTAPDPAAERGPEIRWYEDGTLNVAVNCVDRHVAAGRGEKVALYFEGEPGDRR
+AVTYAQLQREVAQAANALEELGIEAGDRVVVYLPVLVETIVITLACARIGAVHSLVFGGF
+SAEALRFRVEDTGAKLLVTTDGQFRRGAAVPVKANADEAVSGDNAIEHVLVLDRTGHRDI
+PWTEGRDLWWHDVVDRQPDTHTPRAFDAEHPLFIMYTSGTTGQPKGLVHTSGGYLAAASW
+THDFLFSHPDPARRDGDVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRH
+FEVIERYRVTSYYTAPTLIRSLKGWHPDGIPAHADGGPDLSSIRLIGTVGESVNPEAWTW
+ARTQIGRDTPDLPMVDTWWQSETGATVLSPRPTDTAFKPGCGSRPLPGVDVAVVDDDGAP
+TPEGLQGRIVVTRTSPSMARTVWRNPARYFHSYWEDYADQGEAGWFLAGDGAKRDEDGDV
+WILGRVDDVINISGHRLSTIEIESALVAHPHVVEAGVCPVPDPKTGHAAVAFVVAHESWL
+AGDDGPGASAADRAEELRRHVGRVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHQGT
+TIGDTTSLQNEWCIPQIAEVVAARR
+>PROKKA_00204
+MTAGDDGGRGAVVGVPTLVGPADQEEPPPMTPTEDPARPDPAEEGASGAVRGPNDGVPAA
+ALATLPGPLPQALVDAADPDVHPGRPADRLHGGRGDGRPVAESDRLAFWEAAGRRLSWER
+PFTRTRSLTAPDPAAERGPEIRWYEDGTLNVAVNCVDRHVAAGRGEKVALYFEGEPGDRR
+AVTYAQLQREVAQAANALEELGIEAGDRVVVYLPVLVETIVITLACARIGAVHSLVFGGF
+SAEALRFRVEDTGAKLLVTTDGQFRRGVAVPVKANADEAVSGDNAIEHVLVLDRTGHRDI
+PWTEGRDLWWHDVVDRQPDTHTPRAFDAEHPLFIMYTSGTTGQPKGLVHTSGGYLAAASW
+THDFLFSHPDPARRDDDVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRH
+FEVIERYRVTSYYTAPTLIRSLKGWHPDKIPAHADGGPDLSSIRLIGTVGESVNPEAWTW
+ARTQIGRDTPDLPMVDTWWQSETGATVLSPRPTDTAFKPGCGSRPLPGVDVAVVDDDGAP
+TPEGLQGRIVVTRTSPSMARTVWRNPARYFHSYWEDYADQGEAGWFLAGDGAKRDEDGDV
+WILGRVDDVINISGHRLSTIEIESALVAHPEVIEAGVCPVPHETTGHAAVAFVVAHESWL
+AGDDGPGASAADRAEELRRHVGRVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHQGT
+ALGDTTSLQNEPCVGQIAEVLRAGRRAQDADTGAVRNASSAST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000308.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000308.fa
new file mode 100644
index 0000000000000000000000000000000000000000..096e33b2f996dd9157dc0f52ed77de295462ca30
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000308.fa
@@ -0,0 +1,19 @@
+>PROKKA_00210
+MRLITLGLGAALGYLLGSAEGRKNLEKMTQNAQKLWNDPKTQEKVGQVQETAQQKFAEVK
+KSDPVQKATTKVEDAMQGNDKKNDVREDRVTESNNDNITSAARHGAEPDTISDPSTPLGD
+EGPLTR
+>PROKKA_02203
+MRLITLGLGAALGYLLGSAEGRKNLEKMTQNAQKLWNDPKTQEKVGQVQETAQQKFAEVK
+KSDPVQKATTKVEDAMQGNDKKNDVREDRVTESNNDNITSAARHGAEPDTISDPSTPLGD
+EGPLTR
+>PROKKA_00181
+MRLITLGLGAALGYLLGSAEGRRNLEKMSQNAQKFWNDPKTQQKVGNLQETAQQKFADVK
+NSEQVQKATAKVEDTMNKNGSKDQVRDDRVTESNNENTTTASAHGADPDIVSDPSTPLGD
+EGPQTR
+>PROKKA_00127
+MRWFTLAVGAAAGYLLGSAEGRQNLQKMTANAQKVWNDPKTQDKVGVVKDKAQVVASDAK
+DKAASAASDAKQAVQEKTSSNQPSPASNNETVTTGNAHGADPDVVSDPSTPLADEGPAA
+>PROKKA_00210
+MRLITLGLGAALGYLLGSAEGRKNLEKMTQNAQKLWNDPKTQEKVGQVQETAQQKFAEVK
+KSDPVQKATTKVEDAMQGNDKKNDVREDRVTESNNDNVTSAARHGAEPDTVSDPSTPLGD
+EGPLTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000314.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000314.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2319f2db2dec758862e985925bbce6e9bf8e110e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000314.fa
@@ -0,0 +1,34 @@
+>PROKKA_00218
+MILHITLPEDWAAARRTGRYTASTRGASIDDVGFLHASDDAAQVGVVGAAIYPDRPDAFV
+CGLDEDELAGAGLRVRREPGDPSDPHSAEFPHVYPDEAVSGHIPCSMLTPVTDPRADARV
+HREDSAEAAALLDAGWSVRSRSWGARLHLDDDADLAPYRGHVAAAEARGIEVRRLTAVDL
+PALRALDEEAAPRFPRTDGSRHEPLPDDLEARLSTPAGLAVGAFEGGVLIGFTLTFRSPD
+RWEVDRTAVASEHENRGVAKAVKAATLLATHARGGRQWGTGGAEANAASLRMNTALGFRL
+EPAWLGLTPPMTWEEFARAPASSSLDDKVT
+>PROKKA_02212
+MILHITLPEDWAAARRTGRYTASTRGASIDDVGFLHASDDAAQVGMVGAAIYPDRPDAFV
+VGLDEDELAGAGLRVRREPGDPSDPHSAEFPHIYPDEAVSGHIPCSMLTPVTDPRADARV
+HREDSAEAAALLDAGWSVRSRSWGARLHLDDDADLAPYRGHVAVAEARGIEVRRLTAVDL
+PALRALDEEAAPRFPHTDGSRHEPLPDDLEARLSTPEGLAVGAFQGGVLIGFTLTFRSPD
+RWEVDRTAVASEHENRGVAKAVKAATVLATHARGGREWGTGGAESNAASLRMNAALGFRL
+EPAWLGLTPPTTWEEFARAPASSSLDDKVT
+>PROKKA_01604
+MILHIALPEDWAAARAAGHYTVSTRGATVDRVGFLHASEDAAQVGIVGPAVYADRPDAVV
+LAMDEAALEAAGLTVRREPGVPGDPHSPLFPHVYGGPVPVGLMTPLPRADVDPRVVREDD
+AEAIRLQDAGWTPASTSWGARLHLADDADLAPYERRVAAVRAAGFQVRRLTPDDVGQVRR
+LDGETAADYPATAASSHSPLPEDLAVRLTLPGHRGYGAFRDGVLAGFTLLDRLDDRWDVD
+RTAVHPTGRRRGLAAAVKALSVLETHREDGARTWGTGGAGANAGSLAMNRKLGFELEPLW
+LALVPALTWPEAAATSGTP
+>PROKKA_00616
+MILHLTLPEDWAAARAAGVYTASTRGAGIAEVGFLHASEDERQAGAVAAAFYADRPDAFL
+VALDEDALAAAGLEVRREPGNPADPQSELFPHVYGGPIPVALMRPLRPSLTLRPYAPDDA
+AATLDVFRAAVTGTAAAHYTPEQIRAWCPADVDADAWAARRAAAWTVVAVDGAGRVLGFA
+DLTADGVLDMLFVHPEAGGRGASHLLVGAVLAEARRRGLLRVDVRASRSARPVLEALGFT
+VDGEDPGNTVRGVVVPNTRMHADLAGSAGSPAPPGLWS
+>PROKKA_00219
+MILHITLPEDWAAARRTGRYTASTRGASIDDVGFLHASDDAAQVGMVGAAIYPDRPDAFV
+VGLDEDELAGAGLRVRREPGDPSDPHSAEFPHIYPDEAVSGHIPCSMLTPVTDPRADARV
+HREDSAEAAALLDAGWSVRSRSWGARLHLDDDADLAPYRGHVAVAEARGIEVRRLTAVDL
+PALRALDEEAAPRFPHTDGSRHEPLPDDLEARLSTPEGLAVGAFQGGVLIGFTLTFRSPD
+RWEVDRTAVASEHENRGVAKAVKAATVLATHARGGREWGTGGAESNAASLRMNAALGFRL
+EPAWLGLTPPTTWEEFARAPASSSLDDKVT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000318.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000318.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ca77995c279b234e118360064771ccc2ca54ea2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000318.fa
@@ -0,0 +1,25 @@
+>PROKKA_00225
+MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDRVRLCSVCF
+NVSEDEVCSLCRDERRDRSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ
+LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE
+YADEVTLGRAFEGRRLISG
+>PROKKA_02238
+MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDRVRLCSVCF
+NVSEDEVCSLCRDERRDRSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ
+LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE
+YADEVTLGRAFEGRRLISG
+>PROKKA_00155
+MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDKVRLCSVCF
+NVSEDEVCSLCRDERRDASQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ
+LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE
+YADEVTLGRAFEGRRLISG
+>PROKKA_00113
+MYEGAVQDLIDELGRLPGIGPKSAQRIAFHVLEADAADMLRLADAIRTVKDKVRLCSVCF
+NVSEQEVCHLCRDARRDDSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ
+LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE
+YADEVTLGRAFEGRRLISG
+>PROKKA_00226
+MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDRVRLCSVCF
+NVSEDEVCSLCRDERRDRSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ
+LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE
+YADEVTLGRAFEGRRLISG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000319.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000319.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ccdc41bae790d5731d8881e99f4119e9d08f74d0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000319.fa
@@ -0,0 +1,107 @@
+>PROKKA_00226
+MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC
+LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR
+YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP
+PEPLIAYLEQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQEGQVSYELAV
+RLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL
+PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADITNLALTDMVGATSPRLHLELLMA
+RLLLPASDETHRGLAARLEALERRLELGGAAPVEDGAPEGTTTPARSGTPAKDGGGSAGD
+ADGSGPLTGAALARAAMRRPEEPAPTAPTAPPERWTPPAPQSVAEAPEGDAAAGATGSER
+PQQPPQPKRPEPAEVGARSGDTRRPEAGSRAEPEGRPEGRPQAQDRTGAAPSSPAPAPAA
+SQVEMIRRAWPDILTALEDASRLVWMLVKDNASVAGYDGSLLTIGFQQDGPRQSLLGRGG
+DRVLGEAVHQVLGIRPRLDLILGGDAPTGDARAQSGARPAGPARTDRPERPAPQQGRPDR
+PTAQPNRPAPAPGQAPREPESSRPTPPRSAAPSTAEDDPAPPAAPPRATQQRQTPEPSPA
+WTPAAPATSWGPTPTSSTTPAPAPPADGWGGPDEEPPAWDDAPPPEEDPWDSLPAFDPDA
+EQDDSDGPEGWTPPARDAEERPVGAAGWDGPVPSVEDWGAPPQAAPAPGGAAPDAGQDSP
+VQPDAPTPGESEPSAEEVRRAYDPGPLVREEEHSIPVFARPEAELRAEFAKRFGATRPAG
+FDDGAGAAADGDSARPATPSPAPDDDAAATERRDPHPAASGAGPSSDEQRRPTGAPTADA
+TPDPGVPADDADATPRTAAGPTGSDFPGSGHPASMYPRLMERLRAGGPLEPPVNAGSSGG
+GGTGGGPGAPGGPDPDASPGSPAGGRPSAASLGARPADVEPAGGASAPPSLDARAAAIHA
+AREAAQGRGPTRPADTGPAAPATSGVGWEDEVASDDDVPLEDSGLVGRAVVERVLGGRLL
+EERPNDA
+>PROKKA_02239
+MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC
+LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR
+YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP
+PEPLIAYLEQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQEGQVSYELAV
+SLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL
+PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADVTNLALTDMVGATSPRLHLELLMA
+RLLLPTSDETHRGLAARLEALERRLELGGAAPVEEGAPEGTTTPARSGTPAADGGGSAEN
+AEGSGTLTGAALARAAMRRPEEPAPTASTAPPERWTPPAPQSVAEAPEGDAAAGATGSER
+PQQAPQPKRPEPAEVGARSGDARRPEAGSRPEPEGRPEPEGRPQAQERTGAAPAPAHGPE
+ETAAPSSPTPAPAASQVEMIRRAWPDILAALEDASRLVWMLVKDNASVAGYDGSLLTIGF
+QQDGPRQSLLGRGGDRVLGEAVHQVLGIRPRLDLILGGDAPTGDARAQSGARPAGPARTD
+RPERPAPQQGRSDRPTAQPNRPAPAPGQAPREPESSRPTPPRSAAPSTAEDDPAPPAVPP
+RATQQRQTPQPSPAWTPAAPATSWGPAPTSSTTPAPAPPADGWGGPDEEPPAWDDAPPPE
+EDPWDSLPAFDPDAEQDDSDGPEGWTPPARDAEERPVGAAGWDGPVPSVEDWGAPPQAAP
+APGGAAPDAGQDSSVRPDAPTPGESEPSAEEVRRAYDPGPLVREEEHSIPVFARPEAELR
+AEFAKRFGATRPAGFDDGAGAAADGDSARPATPSPAPDDDAAATERRDPHPAASGAGPSS
+DEQRRPTGAPTADATPDPGVPADDADAAPRAASGPTGSDFPGSGHPASMYPRLMERLRAG
+GPLEPPVNAGSSGGSGTGGGPGAPGGPDLDATPGSPAGGRPSAASLGARPADAEPAGGAS
+ALPSLDARAAAIRAAREAAQGRGPARPADTGPAAPATSGVGWEDEVASDDDVPLEDSGLV
+GRAVVERVLGGRLLEERPNDA
+>PROKKA_00154
+MSTALYRRYRPDRFEEVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC
+LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR
+YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP
+PEPLIAHLEQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQDGGVSYELAV
+SLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL
+PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADVTNLALTDMVGATSPRLHLELLMA
+RLLLPASDDTHRGLAARLEALERRLELGGVPVASADESAGGTTTSARPGAPAAAGGGSAG
+SGGAGGGEPLTGAALARAAMRRPEVQEAPTPPAQETARSEKAPAQPEPTPMPSPVGQAAP
+PAQPAQSEHPRPERWAPPAAASSPEADAPAQRPDAARPEQPAQQDRPQRQTPPPAPAGQP
+EQRQQQTAQAERPTTTERPAERPAAGAPEASPASTRPQAAERAAERPQAEADAAGSAVPS
+SAAPAPTPSQVEKVRRAWPDILAALEDASRLMWMIVKDNASVAGYDGSLLTIGFQQDGPR
+QMLLGRGGDRVLAEAVHQVLGIRPQLDLILGGDAPQGGSRHAQGQAQTPSAPRAESRADA
+PTSRPDAGEAAPTRQDRPQQQGGEPDRGQQQDRGQQQGRGQASDLGPAQGGSPSGRPTGQ
+AAAPTPGRGPSSPAPAQRPTAPQAASTTPPGAPPSDGWGRADEEPPAWDDAPPPEEDPWD
+SLPEFDPDADMDDSDGPEGWTPPAAGQDDAPVGAAGWDGPVPAAEDWGAPPQGGAPAPDG
+RRDERPAAAQGSDAPSEQPTPQGSADAGPAAETDAEPSAEEVRRAYDPGPLVREEEHTIP
+VFARPEAELRAEFAQRFGATRPAGFDDGAGAGADAESTRAAAPSPGPDDLPPGQGDDPDA
+TARRDTHPAASASGPSSAADHGSSGEPTADGTPDPGVPAEDHEHTSASDADDDGSPERAA
+GSGHPASMFPRLMERVRAGGPLEPPVNAAPPGGATPPGGGPGGGAGPSGPGSAPGSDQGP
+RPGGAPSDAQGPGAPGPDAPRGGRPSAAALGARPGGETGSPAGASAPPSLDARAAAIRAA
+REAAQGRGPARPAGNGPAAPSAPAVGWEDEVASDDDVALEDSGLVGRAVVERVLGARLLE
+ERANSA
+>PROKKA_00112
+MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC
+LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR
+YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP
+PEPLIAYLERLCQEEGVRVEPGVLPLVVRAGTGSVRDTLSVLDQLIGGAQQGQVSYDLAV
+SLLGFTPEALLDDVVDAIAADDTPTVFRVADRVVQSGQDPRRFVEDLLERFRDLVIARAL
+PDEASSILHGMPEDQVRRLAAQASQLSRAELSRLADVTNLALTDMVGATSPRLHLELLMA
+RLMLPATDDTHRGLAARLEALERRVAGGAAFSPDDDASSGAEGPAAGGAGQGGAALSGAA
+LARAAARRAEPEQAREQEPGAGSDKRAAEPATPKPATPEPVAAAPAPERPVERPAEAPAP
+SSSAPAAPAAPTAHTPSQVEKVRRAWPDILAALESDSRLMWMLVKDNATVAGYDGELLTV
+AFPQEGPRRTLQSRNGEQVLGEAVHRVLGIRPRLDLILGGDTPRGEERPKAEGRPAAAVS
+EAPAAPSTSAPPPAPQGQPTQAQPPRAQPSPEDGRRPAASAPRPQDVAVATSWDQAPAPS
+AAPWQPAPSRPAAASPAPQTGPAAPSTPDPRQDAHPGTRPGPADTTPPAAPPSDGWGHVD
+EEPPAWDDAPPPPEDPWDSLPEFDPDADMEDSPGPEGWTPGAGDDAVHGSAGSAPTSAPE
+AWGGAVPTPQDWGAPRPQDPVESPAPQGPEAGTQGTAPDAAAQGAPSPAAPAEAVPEDPE
+TARRAYDPGPLVREEELTIPVFAKPEAQLRAEFAARFGGTRPAGFDSTAASDAAAPDAQG
+PGAAARAAAHGEPVRGGQDAAEPAADREAEPEEDPQAAASAPEHPVRPSPARPTADDTPD
+PGVPQEDHAEDAAPPSATAPDDRGSGHPDSHYPALMERLRASGPLEPPVNARPAGQGGAR
+EEQVPAPVDAAPSPGRPSAASLGRPTGDPQAAIAPPAEDPRASGARAAAIQAAREAARGA
+GPRPADGAPGGPATASGPSVDWQDEVASDDDVALEDSGLVGRPVVERLLGARLLEERPLE
+PGL
+>PROKKA_00227
+MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC
+LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR
+YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP
+PEPLIAYLVQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQEGQVSYELAV
+SLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL
+PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADITNLALTDMVGATSPRLHLELLMA
+RLLLPASDETHRGLAARLEALERRLELGGAAPVEDGAPEGTTTPARSGTPAPDGGGSAEN
+AEGSGPLTGAALARAAMRRPEEPAPTAPTAPPERWTPPAPQPVAEAPEGDAAAGATGSER
+PQQPPQPGRPEPAEVGARSEDARRPEAGSRPEPEGRPEPEGRPQAQDRTGAAPAPAHGPE
+ETAAPSSPTPAPAASQVEMIRRAWPDILAALEDASRLVWMLVKDNASVAGYDGSLLTIGF
+QQDGPRQSLLGRGGDRVLGEAVHQVLGIRPRLDLILGGDAPTGDTRGQSGARPAGPARTD
+RPERPAPPQGRPDRPAAQPNRPAPAPGPAPREPESSRPAPPRSAAPSTAEDDPAPPAAPP
+RATQQRQTPQPSPAWTPAAPATSWGPTPTSSTTPAPAPPADGWGGPDEEPPAWDDAPPPE
+EDPWDSLPAFDPDAEQDDSDGPEGWTPPARDAEERPVGAAGWDGPVPSVEDWGAPPQAAP
+APGGAAPDAGQDPPVRPDAPTPGESEPSAEEVRRAYDPGPLVREEEHSIPVFARPEAELR
+AEFAKRFGATRPAGFDDGAGAAADGDSARPATPSPAPDDDAAATERRDPHPAASGAGPSS
+DEQRRPTGAPTADATPDPGVPADDSDATPRAAAGPTGSDFPGSGHPASMYPRLMERLRAG
+GPLEPPVNAGSSGGPGAPGGPDPDASPGSPAGGRPSAASLGARPADVEPAGGASAPPSLD
+ARAAAIHAAREAAQGRGPTRPADTGPAAPATSGVGWEDEVASDDDVPLEDSGLVGRAVVE
+RVLGGRLLEERPNDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000328.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000328.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f8bec473d98c99252d54ef79ebad668e4210759
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000328.fa
@@ -0,0 +1,30 @@
+>PROKKA_00238
+MKILVLAKQVPDTWQERELSLETGWVVRDGAAEPVPDEISERVMEVALGWRDAGADIEVV
+ALTVGPEDSSKTLRKMLAMGADSAVQITDDALVGSDAVQTARVIAAAVEKEGADLVLAGT
+VSTDGGTGVVPAMVAELLERPYLPHAEAPELADGELIGTVATSDADVRAAVALPAVASLT
+EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGEKI
+TDDGTAAERLVEFLAGRGLV
+>PROKKA_02251
+MKILVLAKQVPDTWQERELSLETGWVVRDGAAEPVPDEISERVMEVALGWRDAGADIEVV
+ALTVGPEDSSKTLRKMLAMGADSAVQITDDALVGSDAVQTARVIAAAVEKEGADLVLAGT
+LSTDGGTGVVPAMVAELLERPYLPHAEAPELADGELTGTVATSDADVRAAVALPAVAGLT
+EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGEKV
+TDDGTAAERLVEFLAGRGLV
+>PROKKA_00133
+MKILVLAKQVPDTWQERELSLDTGWVVRDGAAEPVPDEISERVMEVALGWRDAGTDAEIV
+ALTVGPEDSSKTLRKMLAMGADAAVQVTDDALVGSDAVETARVIAAAVEREGADLVLAGT
+VSTDGGTGVVPAMVAELLDRPYLPHAEAPQLADGELTGTVATSDADVRAAVALPAVAGLT
+EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGAKV
+SDDGTAAQQLVDFLAGRGLV
+>PROKKA_00098
+MKIAVLAKQVPDTWQERTLDMETGMAVRDGAAEPVPDEIGERVMEVALAAREAGLEAEIV
+AVTMGPADATKTLRKMLAMGADSAVHVVDDALDWSDAVQTARVLAAAVEHLGVDLVLAGS
+ESTDGATGVVPAMVAELLDRPLLPSVEAVEITPEEVRGVLVTEDARLRASVPVPAVVALT
+EKTAEPRFPNFKSIMAAKKKPLETLTLADLGLTAGPLDADRRSVMVSAAARRERAAGEKI
+VDDGTAGEQVAAFLAARGLV
+>PROKKA_00239
+MKILVLAKQVPDTWQERELSLETGWVVRDGAAEPVPDEISERVMEVALGWRDAGADIEVV
+ALTVGPEDSSKTLRKMLAMGADSAVQITDDALVGSDAVQTARVIAAAVEKEGADLVLAGT
+LSTDGGTGVVPAMVAELLERPYLPHAEAPELADGELTGTVATSDADVRAAVALPAVAGLT
+EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGEKV
+TDDGTAAERLVEFLAGRGLV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000330.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000330.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6bcc730a5993a0594676c06f80149d59d8f77585
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000330.fa
@@ -0,0 +1,52 @@
+>PROKKA_00240
+MPKQRMAGYVPLKGAPAETEPAPAPAQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRR
+MAGYVPFAREAEWLGGAPAPAAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPD
+VAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMAGYVPFAREGEWFTELAAVGGPTAPE
+MVAQEVDAPEQATAEPTAEPAAAAPARPVVAELADVEPADAEPAVAAPVAAASAPEPAPT
+APDTRSAPPASAVQPPRAATGTPARTAETDAAESAVPSRLRKALPAVAGVVVLALLAVLA
+ARWLRSLDPVADFIATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHET
+RPPANFTPTKDGLFSARGNTPKKFSLTIWMHQALDALWLLNGLIFVVLLIATGHWARIVP
+TDPHVFQHALSAGIQYLSLDWPTENGWVHYNALQMLSYALVVFVAAPLAALTGWRMSSWF
+PTEAKGLNKAFPMEVARKVHFPVMVFFVAFIVVHVFLVAFTGLLTNLNHMYTSRGGATDA
+WGLVVFLVSVAVTAAAWFFLKPAFTAPVASRFGTVGR
+>PROKKA_02253
+MPKQRMAGYVPLKGAPAETEPAPAPGQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRR
+MAGYVPFAREAEWLGGAPAPAAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPD
+VAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMVGYVPFAREGEWFTELAAVGGPTAPE
+TAAQEVVAEPATAEPAAAEPADAEPAVAAPVAAAPAAEPAPTAPDTRSAPPASTAQPPRA
+APGAATGTPARAAETDAAESAAPSRLRKALPAVAGVVVLALLAVLAGRGLRSLDPVADFI
+ATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHETRPPANFTPTKDGLF
+SARGNTPKKFSLTIWMHQALDALWLLNGVIFVVLLIVTGHWARIVPTDPHVFQHAVSAGI
+QYLSLDWPTENGWVHYNALQMLSYSLVVFVAAPLAALTGWRMSSWFPTKATGLNKAFPME
+VARKVHFPVMVFFVAFILVHVFLVAFTGLLTNLNHMYTSRGGATDAWGLVVFLVSVAVTA
+AAWFFLKPAFTAPVASRFGTVGR
+>PROKKA_00131
+MARRRRRPGGRSGLGHPAGAPAAAPAPIAASASPTQSPRPAEPAAAQPRLAEQDVAAAVA
+RPAAAAPVAVESDLVPLGQRRRMGGYVPLAREGEWFAELAAADAAPAGETAEPTVLEAAH
+DDAAPAAEAAVTEPAAPTTTAAAAAATTAAAQAPAAPAQPAAAAAAPTAPDTRSAPPASA
+AQPPRAEPAAASGRPARATKKTDAAEEAPAPSRLRKALPLVAGVVVLALVAVLAARWLRT
+LDPVADFIAAYDGHPALAEGTPVGMPPWLGWQHFLNMFLMVLIIRTGLQIRNETRPPANF
+TPKKDGAFSARGNTPKKFSLTIWTHQALDALWLLNGVVFVVLLFVTGQWARIVPTDPYVF
+HHAFSAGIQYLSLDWPTENGWVHYNALQMLSYTLVVFVAAPLAALTGWRMSSWFPTEAKG
+LNRAFPMEAARKVHFPVMLFFVLFILTHVFLVFFTGALKNLNHMYTSRGDATDAWGLVVF
+LVSVAVTAAAWFLLRPSFTAPAASKFGTVGR
+>PROKKA_00096
+MPQRMQGYTEFRGEPWPPRDRVPQAPAPTTTPAVAADERRPGRRMVGYTAFRGEPWPPVR
+EAAQPAPAPAAAASPAEVTEAAAAAVPLEATAPAGIAVPGRRMAGYTAFRGEPWPPARVG
+AAPQAPEPAPMATVEPAVATGPTPTVEPVAAGAPETTPKPAPSTGRRVAAAVGGVVVLGL
+LAVLGARWLLTLPEVAAFVARYPGVPRHPEVTPVGIPAWLAWQHFLNLFLLVLVVRTGLQ
+VRHETRPPATFTPHQPGPFAPRSATGGTYSLTVWIHQALDALWLLNGLVFVVLLFATGHW
+MRLIPTDPQTPQHMVSTALQYLSLQWPEHDGWLHYNALQMVTYAGVVFVLAPLAALTGFR
+MSSWWPSRNTALSRGFPMELARRLHYPTMLAFVLFVVVHVVLVLFSGVLHELNAMFLARN
+AADAWGLAAFLVGCAVIAAGWVLLKPAIVAPVAERFGRVSR
+>PROKKA_00241
+MPKQRMAGYVPLKGAPAETEPAPAPAQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRR
+MAGYVPFAREAEWLGGAPAPAAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPD
+VAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMAGYVPFAREGEWFTELAAVGGPTAPE
+MVAQEVVAEPATAEPAAAEPADAEPAVAAPVAAAPAAEPAPTAPDTRSAPPASTAQPPRA
+VPGAATGTPARAAETDAAESAAPSRLRKALPAVAGVVVLALLAVLAGRWLRSLDPVADFI
+ATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHETRPPANFTPTKDGLF
+SARGNTPKKFSLTIWTHQALDALWLLNGVIFVVLLIVTGHWARIVPTDPHVFQHALSAGI
+QYLSLDWPTENGWVHYNALQMLSYALVVFVAAPLAALTGWRMSSWFPTEAKGLNKAFPME
+VARKVHFPVMVFFVAFIVVHVFLVAFTGLLTNLNHMYTSRGGATDAWGLVVFLVSVAVTA
+AAWFFLKPAFTAPVASRFGTVGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000331.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000331.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bd5c1e3f3f2896d1536cdeec51bd04111886ef64
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000331.fa
@@ -0,0 +1,35 @@
+>PROKKA_00241
+MICRVATGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA
+AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA
+AAVTAGDEDGPLLECWTRPLAWDAAGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMA
+EFVAAGRLPRGAETRVPMPGLLAARPESLPTADPDVRPAVDAAATAGARFAPKPELANPS
+GAVHGGAMTLRAVTAAQAAMPDRERYDVQAVRVVFVRPGHGEMVALTRVRHAGRSLRLVD
+VDLVPVGADGVPVADKPMVQVQVTFRAARS
+>PROKKA_02254
+MISRVAAGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA
+AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA
+AVAAGDEDGPLLECWTRPLSWDAAGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMAE
+FVAAGRLPRGAETRVPMPELLAARPESLPTADPDTRPAVAAAPTAGARFAPKPELANPSG
+AVHGGAMTLRAVTAAQAAMPDRERYDVQAVRVVFVRPGHGEMVALTRVRHAGRSLRLVDV
+DLVPVGADGVPVADKPMVQVQVTFRATRS
+>PROKKA_00128
+MRWHGDRAAASGVTALTNILGHPIICDAAGRGRSASVLTVQNSLRPAADSPTGPRAHASG
+RTEQLFGIRRHAAMPERDGALNPAAFEAGPWCLDLDGRPTGAAATVIMDNATAVAVHHAA
+PGVETVVTTELQINVLAPLPAFDAAAITEGRAEGPLLECWTRPLSWDAGGGVGRAWLEDA
+EGRRIVEATGWFQAVPTGAPEHRAAFTAAADLPRGPETRVPMPGLLAARPETLPPAARAG
+RPAVTAAVAPGARFAPKPELANPSGAVHGGAMTLRAVVAAQAAMPDRELYDVQAVRVVFT
+RPGHGEMVALTRVRHAGRSLRLVDVDLVPVGEDGAPVAEKPMVQVQVTFRAAR
+>PROKKA_00095
+MDEITLNPDADARWRGPRRLLLGRPEQLAGLRRRETAEIQGDTLHPGDWEVGPWVRDLDG
+RPTGAAACVAADNLTAVALHWAAAEAYDAMVTTQLQVNVLRPLPVFDPADPADRPRLRML
+GTPLSTDALGGCARGVIVDDDGTAYVEATGWFQATPGPMSLALEAFREHAALPVAEADRA
+DLPAVTAVVADSVPAPRPGERPAVSQEMTAGLRFRAEPLLDNPGGMTHGGIQCLRAVLAA
+QAALPDRLEYDVQAVQVVFARPGLGEQVALTRVRHAGRSLRIVEVELVGVDPETGAPQAG
+RPSILAQVSFRAAQG
+>PROKKA_00242
+MISRVAAGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA
+AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA
+AAVTAGDEDGPLLECWTRPLAWDAGGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMA
+EFVAAGRLPRGAETRVPMPELLAARPESLPTADPDTRPAVAAAPTAGARFAPKPELANPS
+GAVHGGAMTLRAVTAAQAAMPDRERYDVQAVHVVFVRPGHGEMVALTRVRHAGRSLRLVD
+VDLVPAGADGVPVADKPMVQVQVTFRAARS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000332.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000332.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e067083df79337117d387b0cf0c6626de1c83072
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000332.fa
@@ -0,0 +1,40 @@
+>PROKKA_00244
+MSDAQSTATTAPAAARDGAAGEVLLEVRDGLGRITLNRPRALNALTQDMVRAIDAALTDW
+AADPAVRGVLIRGAGEKGLCAGGDVVSLRASLLAGRFAEAEEFFRDEYAMNERIAAYPKP
+YVAFMDGVVLGGGMGVSAHGSHRVATERTRAGMPETAIGFTPDVGGSFHLARAPFQAGRH
+LAATSAHASGSDAVALGLADVFVESARLDELEQALAAAFGALGPAADAGARDEAAFAAAD
+EVLARFAVAEDAQPASALVAGREWIEDVYDRETAAEVLAALDERAAAGGEHAEAAGQAAE
+AIRTKSPTAVAVAHEAQRRLAARGADLTVADALRQEFTIATHLMREPDMAEGIRALLVDK
+DKDPTWSPARLEDVSTEDVAGHFEPVSGVDPLQLG
+>PROKKA_02256
+MSDAQSTATTAPAAARDGAAGEVLLEVRDGLGRITLNRPRALNALTQDMVRAIDAALTDW
+AADPAVRGVLIRGAGEKGLCAGGDVVSLRASLLAGRFAEAEEFFRDEYAMNERIAAYPKP
+YVAFMDGVVLGGGMGVSAHGSHRVATERTRAGMPETAIGFTPDVGGSFHLARAPFQAGRH
+LAATSAHASGSDAVALGLADVFVESARLDELEQALAAAFGALGPAADAGARDEAAFAAAD
+EALARFAVAEDARPASALVAGREWIEDVYDRETAAEVLAALDERAAAGGEHAEAAGQAAE
+AIRTKSPTAVAVAHEAQRRLAARGADLTVADALRQEFTIATHLMREPDMAEGIRALLVDK
+DKDPTWSPARLEDVSAEDVAGHFEPVPGVDPLQLG
+>PROKKA_00125
+MSDAQTTTTAGSAPQAGEGGDVLLEVRDGLARITLNRPRALNALTHVMVQEIDAALVAWA
+ADPAVRGVLIRGAGEKGLCAGGDVVSLHASLTGGRFEEAAQFFRDEYRMNHRISAYPKPY
+VAFMDGIVLGGGMGVSVHGSHRVATERTRAGMPETAIGFTPDVGGSYHLARAPFHAGRHL
+AATSAHASGADAVALGLADAFVESARLDELEQAMADALGSLEAPSGDAGRDGVRDEAAFA
+AADEVLARFAMAEGERPDSALAAGREWIEDAYGRQTAAEVLAALDERAAGGGEHADAARS
+AAEAIRAKSPTAVAVAHEAQNRLAAHGQDLTVAEALRQEFTVGAHLMRAPDMPEGIRALL
+VDKDKDPKWSPARLEDVTADAVATHFEPVEGVARLELS
+>PROKKA_00094
+MSEQTSTPQAAAEDEVLFEAADGVGVITLNRPKALNALSHGMVVAVREQLAAWEEDPAVR
+AVVVRGAGERGLCAGGDVVSLHGMITTGRAAEAMGYFEDEYAMNHAISVYPKPYVAFMDG
+FVLGGGVGVSAHGSHRVVTERTRIGMPETGIGFTPDVGGSWLLARAPRNLGRHLGLTSAF
+ATGADALELGFGDVLVDSGDLDAIVAELRAEVGSAGDDADAAHAAVDAVLARHARPASEA
+PLLADAEWLEPAYAHDRVEDVFAALEATAADHADEGVRTRAAEAAETVRAKSPTAVKVTL
+EALRRLGDRAGGTGRREGVAAALEQEHTLASHLTRGHDMAEGIRAQLVDKDRNPQWSPAT
+VEEVSDEAVAAHFGPGEDAPLRLR
+>PROKKA_00244
+MSDAQTTATTAPAAAQEGAAGEVLLEVRDGLGRITLNRPRALNALTQDMVRAIDAALTDW
+AADPAVRGVLIRGAGEKGLCAGGDVVSLRSSLLAGRFAEAEEFFRDEYAMNERIAAYPKP
+YVAFMDGVVLGGGMGVSAHGSHRVATERTRAGMPETAIGFTPDVGGSFHLARAPFQAGRH
+LAATSAHASGSDAVALGLADVFVESARLDELEQALAAAFGALGPAADAGARDEAAFAAAD
+EVLARFAVAEDARPASALVAGREWIEDVYDRETAAEVLAALDERAAAGGEHAEAAGQAAE
+AIRTKSPTAVAVAHEAQRRLAARGADLAVADALRQEFTIGTHLMREPDMAEGIRALLVDK
+DKDPTWSPARLEDVSAEDVAGHFEPVPGVDPLELG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000336.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000336.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12e603f027f55414b547c960b652398a5b6ffadb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000336.fa
@@ -0,0 +1,41 @@
+>PROKKA_00251
+MTAIADRPVPAPGAPAVTPGLPHVDLLRLRDRLEPVERARLDAIEDHLQTRVRPHLTRYW
+DAEEFAFDLLPGLAELGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMI
+AGLGSERQKATWQGRLESFDALGAFCLTEPDHGSDIAGGLATTATRDGDEWVIRGAKRWI
+GAGTIADVALVWARDTADGEIKGFVVPTDTPGYEATKISGKMGLRIMQNADITLDVRLPA
+DAILPGATTFAATRALLRDSRMWVGWQGVGAQMGVLDVLRSYALRREQFGRPLAAFQLIQ
+AQIAEVAGNLAASAGMMLQVDALRQEGRMEMMHAAMAKATSTRLARSSAALARDALGGNG
+LLTEHEIAKIMGDVEAIYSYEGSYGMNTLIVGRALTGVSAFV
+>PROKKA_02263
+MTALADRPLPATGAPAVPPGLPHVDLLRLRDRLEPVERARLDAIEDHLQTRVRPHLTRYW
+DAEEFAFDLLPGLAELGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMI
+AGLGSERQKATWQGRLESFDALGAFCLTEPDHGSDIAGGLATTATRDGDEWVIRGAKRWI
+GAGTIADVALVWARDTADGEIKGFVVPTETPGYEATKISGKMGLRIMQNADITLDVRLPT
+DAILPGATTFAATRALLRDSRMWVGWQGVGAQMGVLDVLRSYALRREQFGRPLAAFQLIQ
+AQIAEVAGNLAASAGMMLQVDALRQEGRMEMMHAAMAKATSTRLARSSAALARDALGGNG
+LLTEHEIAKIMGDVEAIYSYEGSYGMNTLIVGRALTGVSAFV
+>PROKKA_00119
+MTPHADLPHVDLLRLRDGLDPAERTRLEEVEEHLQTAVRPRLAPYWDAEEFAFDLLPGLA
+GLGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMIAHLGSDAHRDRWQA
+RLESFDALGAFCLTEPEHGSDVAGGLATTATLDGDEWVIRGAKRWIGAGMIADVALVWAR
+DTADGEIKGFVVPTDTPGYEATKITGKMGLRIMQNADITLDVRLPADAQLPGAATFDAAR
+DLLRDSRMWVGWQGFGAQMGLLDSLRSYALEREQFGRPLAKFQLIQSAIAEVAGNLAATS
+GMMLQVDALRQEGRMEMMHAAMAKATSTRLARASAALARDALGGNGLLTEYEVSKMMGDV
+EAIYSYEGSYGMNTLIVGRALTGVSAFV
+>PROKKA_00087
+MTPSPTPSPASAEPAASPATGVLTVAAAVHPGHAAAPAAAVTDGLPDVDLFDLRSLLSAE
+ERAHLERIEAHLEEHVRPHLAEPWNTETLPMEMLPGLASVGLGELDFLGASRLFQNLVHV
+AIARVDLSFSALVGIHNELNIGSIERFGTEEQKQRWVPALRRFEALGAFCLTEPDHGSDI
+AGGVETTATPDGDGWILRGTKRWIGAGTVAAVALVWAKDVSDGEVKCFLVPTDAPGFSAS
+KITGKTGLRIMQNADMVFDDVRLGPEALLPGAGSFDATREMLRDSRAWVGWQGVGVQQGI
+LRTLREYALTRTQFGRPLAKFQLIQAAIAQVAGNLAAATGLMMQVQRLQDDGTLKMVHAA
+AAKATSTRLARESAALARDAMGGNGIVASYEMARFMGDVEAIYTYEGTQSINALLVGRAL
+TGVSAFV
+>PROKKA_00251
+MTALADRPLPATGAPAVPPGLPHVDLLRLRDRLEPVERARLDAIEDHLQTRVRPHLTRYW
+DAEEFAFDLLPGLAELGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMI
+AGLGSERQKATWQGRLESFDALGAFCLTEPDHGSDIAGGLATTATRDGDEWVIRGAKRWI
+GAGTIADVALVWARDTADGEIKGFVVPTDTPGYEATKISGKMGLRIMQNADITLDVRLPA
+DAILPGATTFAATRALLRDSRMWVGWQGVGAQMGVLDVLRSYALRREQFGRPLAAFQLIQ
+AQIAEVAGNLAASAGMMLQVDALRQEGRMEMMHAAMAKATSTRLARSSAALARDALGGNG
+LLTEHEIAKIMGDVEAIYSYEGSYGMNTLIVGRALTGVSAFV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000339.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000339.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12bc4a09671ef0973d84c474d6203e2baae14f67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000339.fa
@@ -0,0 +1,30 @@
+>PROKKA_00257
+MTHVAARARVPLKGLLVFLAVAAVLLLLGIVTVLRGVAADAARVDIVTVLDGNTVVVNQG
+GTERTVVLAGVTSAGRNPEGLKVGPNLCMGEESYAWLRDRLPQGATASMTTSDEGAPEGM
+ESAVISIGGGTVNVAMAEAGMAAPTDVAVGKRLAEEIAQANQEAVGRGVGLYDIEEPCTY
+QNRLYEAQFALEQIPEDAEASLTKIDERAVEYAAGLDQVRLVQQEVRALDPENGTFADLA
+YGPAKESLLAEADPVVEHGMQVLKDLNTRRNEIAARG
+>PROKKA_02271
+MTHVAARARVPLKGLLVFLAVAAVLLLLGIVTVLRGVAADAARVDIVTVLDGNTVVVNQG
+GTERTVVLAGVTSAGRNPEGLKVGPNLCMGEESYAWLRDRLPQGATASMTTSDEGAPEGM
+ESAVISIGGGTVNVAMAEAGMGAPTEVAVSERLAEEIAQANQEAVGRGVGLYDIEEPCTY
+QNRLYEAQFALEQIPEDAEASLTKIDERAVEYAAGLDQVRLVQQEIRALDPENGTFADLA
+YGPAKESLLAEADPVVEHGMQVLKDLNTRRNEIAARG
+>PROKKA_00112
+MTHVAARARVPKKGLLVFLVVAAVLLLLGALTVVRGIAADAARVNIVSVVDGNTVVVNQG
+GTQRTLVLAGVTSAGRNPEGLKVGPELCMGEQSYAWLRDRLPQGAVASVDTSREGAPEGM
+ESALVHIGGKTVNVDMAEAGMTAPTGIGVDDDMAEEIAAANRVAVGRGVGLYDVEEPCTY
+QNRLYEAQFALDQIPKDAEDSIRRIDERSVEYAAGLDQVRLVQQEIQALDPENGTFEDLA
+YGPARESLLAEADPVVEEGLQVLRDLNARRNEIAARG
+>PROKKA_00080
+MTHVAAQARVPKKGLIVFLVVAGVLLALGAASAVRGLVVARDTVEVVRVVDGNHVVVNAD
+GEERTLTLAGVRSAIRNPEGLRVGPEYCMGEEAYAWLRDRLPQGATVRVDRSDEGAPEGE
+QSAVFTVAGKEVNVDMAKAGMAAPTGLGVSGDLEEQIAQANQQAQTAGGRNNGVGLYNRD
+ETCTLGYQLYAAQTELEKVPTAPAANTVVEIDKKSVEYANALDAVRLVQQRIEGLDASSG
+DFTGLAYAPAKDRLLARANPVVDEGMQVLRDLNAQRNALAGG
+>PROKKA_00256
+MTHVAARARVPLKGLLVFLAVAAVLLLLGIVTVLRGVAADAARVDIVTVLDGNTVVVNQG
+GTERTVVLAGVTSAGRNPEGLKVGPNLCMGEESYSWLRDRLPQGATASMTTSDEGAPEGM
+ESAVISIGGGTVNVAMAEAGMAAPTEVAVGKRLAEEIAQANQEAVGRGVGLYDIEEPCTY
+QNRLYEAQFALEQIPEDAEASLTKIDERAVEYAAGLDQVRLVQQEIRALDPENGTFADLA
+YGPAKESLLAEADPVVEHGMQVLKDLNTRRNEIAARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000347.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000347.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0581c3f44b0721354dc3b165b856a637cac45440
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000347.fa
@@ -0,0 +1,40 @@
+>PROKKA_00268
+MTETLPTVEPEYDVATPLDTDFYLALADVSDAEKDVWRRARAFALEPDVLPRIREAWDRH
+EYPLDLVARLGQADLLRDGVPVDGLPEISRVAAGLAMMELSRLDGSIATMTGVQGGLAMR
+SIQLCGSEEQRAEHLPAMARGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLHGHKKW
+IGNGAAGGVTVVWARSAEDEKVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV
+PDADVLPEARSFKDTSRVLFATRVGVAWSALGKAVGCYEAAVHYAGQRVQFGRPLAAAQS
+VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASMAKYSATRAARSIAANARDLLGG
+NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV
+>PROKKA_02281
+MTETLPTVEPEYDVATPLDTDFYLALADVSDAEKDVWRRARAFALEPDVLPRIREAWDRH
+EYPLDLVARLGQADLLRDGVPVDGLPDVSRVAAGLAMMELSRLDGSIATMTGVQGGLAMR
+SIQLCGSEEQRAEHLPAMARGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLHGHKKW
+IGNGAAGGVTVVWARSAEDEKVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV
+PDADVLPEARSFKDTSRVLFATRVGVAWSALGKAVGCYEAAVHYAGQRVQFGRPLAAAQS
+VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASMAKYSATRAARSIAANARDLLGG
+NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV
+>PROKKA_00095
+MTENLPTAEPEYDVAAPLDTDFYLALGDVSDDEKEVWRRARAFALEPDVLPRIREAWDRH
+EYPLDLVARLGAADLLRDGVPVDGLPEVSRVAAGLAMMELSRLDGSIATVAGVQGGLAMR
+SIQLCGSDEQRAELLPAMSRGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLRGHKKW
+IGNGAAGGVSVVWARSAEDEQVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV
+PDADVLPEARSFKDTSRVLFATRVGVAWSALGQAVGCYEAAVQYAGQRIQFGRPLAAAQT
+VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASLAKYSATRAARSIAANARDLLGG
+NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV
+>PROKKA_00066
+MTETLPTAEPDYSTITGPLDTDAYAVFAELPDEDLALARAARAFLTPEVQKRLQEAWDTG
+EYPTELIAGLAEADLLRDGVAVEGKPAQSRLACGLAAMETSRIDGSLATVVGVQGGLAMR
+SIEMCGSDEQKAKYLPAMDRGELFGAFALTEPTHGSDSVSLQTTATKVEGGWRISGHKKW
+IGNGAAGGITVTWARSAEDGQVKGFIVQQDAEGYSAEVIRGKMSLRAIHQAHITYDDVFV
+PDEDVMPGAQSFKNTAAVLFATRLGVAWAAVGHALGCYEAAVQYAKQRVQFGRPLAESQI
+VQERLARMLSELTQVQLLVLRAARLEDAGKLTGPQASLAKYSATRTARSIAANARDLLGG
+NGILLENEVGKHFADIEAIHTYEGTETVQALIVGRDITGVGAFA
+>PROKKA_00266
+MTETLPTVEPEYDVATPLDTDFYLALADVSDAEKDVWRRARAFALEPDVLPRIREAWDRH
+EYPLDLVARLGQADLLRDGVPVDGLPDVSRVAAGLAMMELSRLDGSIATMTGVQGGLAMR
+SIQLCGSEEQRAEHLPAMARGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLHGHKKW
+IGNGAAGGVTVVWARSAEDEKVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV
+PDADVLPEARSFKDTSRVLFATRVGVAWSALGKAVGCYEAAVHYAGQRVQFGRPLAAAQS
+VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASMAKYSATRAARSIAANARDLLGG
+NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000350.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000350.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb341c1739fe3ef27c8dff5963654f7312c0351d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000350.fa
@@ -0,0 +1,30 @@
+>PROKKA_00275
+MTTPTGAIPSPHPRPFLLVQTRPEDDAAAAEVEAVQRLGGYPEGRLRVLRLDRVVQRPDV
+ATHGLDWEAELADVAAVILPGSPFTGSDPEETKSPVQRAVEAELGRMLDVVRRRDLPFLG
+CCYGVGTLGRHAGGVVDNAYGESAAPVEVTLTDEGAADPLLAGVPRTFAAYVGHKEAMSA
+LPPGAVLLAAGTDCPVQMFRLGTRQYATQFHPELDQAGILERLEIYRDHGYFAPGEYEPT
+VAGLAAVDPEHPRRILANFRTLFG
+>PROKKA_02290
+MTTPTGAIPSPHPRPFLLVQTRPEDDAAAAEVEAVQRLGGYPEGRLRVLRLDRVVQRPDV
+ATHGLDWEAELADVAAVILPGSPFTGTDPEETKSPVQRAVEAELGRMLDVVRRRDLPFLG
+CCYGVGTLGRHAGGVVDNAYGESAAPVEVTLTDEGAADPLLAGVPRTFAAYVGHKEAMSA
+LPPGAVLLAAGADCPVQMFRLGTRQYATQFHPELDQAGILERLEIYRDHGYFAPGEYEPT
+VAGLAAVDPEHPRRILANFRTLFG
+>PROKKA_00080
+MSTPSAPQPAPSADAPPSGRPFLLIQTRPEDEAARAEEEAVRRLGGFAEHQLAALRLDRT
+LDADPDARQDWAALVAGHAGVILSGSPYTSSVPQETKDELQVAVELELGRMLDAVLDADA
+PFLGCCYGVGTLGAHAGGTVDGTHAEPAGPTDVTLTEAGAADPLLEGLPPRFTAYVGHKE
+GLTVPPPGAVVLATGEACPTQMFRLGRRQYATQFHPELDQVGLVERLRIYLHHGYVDPED
+AEDTFARIESTPAPVPPRILENFRRVFG
+>PROKKA_00063
+MTETTAPAADAAAPRPFLLVQTRPEEDAAAAEAESVRRLGGYDDATLRVLRLDRRVLDAE
+GEAHAGAVDWEAELADVAGVILPGSPFTGSDPEESKSDLQVAVEAELGRLMALVLARQTP
+FLGCCYGVGTLGRAAGGVVDTTYRELPGPIDVALTSEGLRDPLLEGMPAEFAAYVGHKEA
+VRELPPGAVLLATGQACPVQMFRVGEHLYATQFHPELDQAGLLERLEIYADHGYFAAHEA
+DDMFAAIRAREAPIPPRILERFRAIYG
+>PROKKA_00273
+MTTPTGAVPSPHPRPFLLVQTRPEDDAAAAEVEAVQRLGGYPEGRLRVLRLDRVVQRPDV
+ATHGLDWEAELADVAAVVLPGSPFTGSDPEETKSPVQRAVEAELGRMLDVVRRRDLPFLG
+CCYGVGTLGRHAGGVVDNAYGESAAPVEVTLTDEGAADPLLAGVPRTFAAYVGHKEAMSA
+LPPGAVLLAAGADCPVQMFRLGTRQYATQFHPELDQAGILERLEIYRDHGYFAPGEYEPT
+VAGLAAVDPEHPRRILANFRTLFG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000351.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000351.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0294213882be272572e34d5373d11e4d5af297a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000351.fa
@@ -0,0 +1,31 @@
+>PROKKA_00277
+MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLDDTELTATAARLSH
+GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS
+LILREEGEHIAAANLGRRLLEADEVPSEPGRASRVLEVRQRQLNEPPLYDREISRALQAR
+DAEAEYQWRRARFGQLLYLRARGGSETLTDADLDSRIARELGALRTLADELEAKAATRR
+>PROKKA_02292
+MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLDDTELTATAARLSH
+GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS
+LILREEGEHIAAANLGRRLLEADEVPSEPGRASRVLEVRQRQLNEPPLYDREISRALQAR
+DAEAEYQWRRARFDQLLYLRARGGSETLTDADLDSRIARELGTLRTLADELEAKAATRR
+>PROKKA_00076
+MAPMTGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRQEERRAVPDTTFSPVDAGSPEERIVAVGKRHLEDTELTATAARLSH
+GLNLRSGSQLEDLFGMAERLYLLHEDVEGTLAALGLLTNLPWDGAVGRWKSIQAGLALAS
+QILRDEGEHIVAANLGKRLHEADEVPSEPGRAARVLEVRQRQLNEPQLYDREISRALQAR
+DAEAEYRWRRARFAQLLYLRGRGGSETLTDADLDSRIARELGTLRGLARDLDAKAAARS
+>PROKKA_00061
+MSDGGAEVAPIAGGYLRHLKAQDVRPGDSFLTRRGEPAPAVASTRVVRDDFGTPALVIAT
+LVGGREVKIAHGSVIRVRTDRPEEVKAAADTAFSPVDAGSPESRIVAVGQRHLDDAELTA
+TAARLSHGLNLRSGAQLEDVFGMAERMYLLHEDVEGTLTTLGLLTNLPWDGAVGRWKSIQ
+AALGLAALILREDGDHITAANLGSRLKEADEVPSEPGRAARVLEVRQRQLDEPQLYDREI
+SRALQARDAEAEFRWRRARFAQLLYLRGRGGSQTLTDQDLDSRIHRELGTLRQLAKRLAA
+QAARA
+>PROKKA_00276
+MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLEDTELTATAARLSH
+GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS
+LILREEGEHIAAANLGRRLLEADEVPSEPGRAARVLEVRQRQLNEPPLYDREISRALQAR
+DAEAEYQWRRARFDQLLYLRARGGSETLTDADLDSRIARELGTLRTLADELEAKAATRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000360.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000360.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5cb0d67ee82e0987259ffde3ac3cc444ce73196d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000360.fa
@@ -0,0 +1,26 @@
+>PROKKA_00292
+MDGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR
+IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY
+AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL
+GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE
+>PROKKA_02315
+MGGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR
+IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY
+AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL
+GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE
+
+>PROKKA_00062
+MRVHLVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVEIQTPVAT
+TTGLRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTYAERLPAD
+LSGRHVFVLDPMLATGGTLIESIRFLYERGAARVTCICLLGAPEGIARLEESLGDVEVDL
+YLAAQDERLDENAYIVPGLGDAGDRLYGLAE
+>PROKKA_00041
+MRLHVVDHPLVAHKLTVLRDERTPSMIFRQLTEELVMLLAYEATRGVAVTEVEVKTPVAT
+TVGTTLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTYAERLPAD
+LTGRHVFVLDPMLATGGTLIEAIRFLYERGAERVTCLCLLGAPEGVARLEEALGDVDVEL
+YLAAVDERLNEKSYIVPGLGDAGDRLYGLAE
+>PROKKA_00299
+MGGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR
+IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY
+AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL
+GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000364.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000364.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e6f7058d1c1256de5c99fea7e61a95759c3a2a53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000364.fa
@@ -0,0 +1,20 @@
+>PROKKA_00298
+MKLSAYTDVCLRVLMTLAAAEGERLTSQQIADRIQVPYNHVIKAVAELRRRGTIQVARGR
+LGGARITEAGLDQRVGELVRDLSPRAEVLDCAGHETGVPCPFAADCRLREALARAREAFM
+AELDLLTVRDLVRPGRAGATGPVSLGLPAMGSHAATV
+>PROKKA_00006
+MKLSAYTDVCLRVLMTLAAAEGERLTSQQIADEIHVPYNHVIKAVAELRRRGTIEVLRGR
+HGGAMIAAAGLDQRVGELVRTLSSRDEVIDCAGRDSGVACPYAGDCRLRGALHRAREAFL
+AELDTLRIRDLVSAGPVGGPVLLGLPEIPVTH
+>PROKKA_00056
+MKLNAYTDVCLRVLMTLAGDEGERLTSQQIADRIQVPYNHVIKAVAELRRRGAIDVARGR
+LGGATIAEAGLELRVGALVRDLAGWDEVIDCTGRESGVACPLAGDCRLRGALHRAREAFL
+AELDAVRVRDLVAAGPAAGPVLLGLPEIPLPADPRPRRRTCPAGA
+>PROKKA_00034
+MKLTAFTDVCLRVLMTLGRDAGAKMTSQEIADRIGVPYNHVVKAVGELRRRGLVDVARGR
+AGGAVITEAGLDQRVGELVRALSGRPEVVDCEGLESGTPCPLLEACSLRGALARAREAFF
+AELDRQRVRDLVSLPAEFLGLRRLPGA
+>PROKKA_00305
+MKLSAYTDVCLRVLMTLAAAEGERLTSQQIADRIQVPYNHVIKAVAELRRRGTIEVLRGR
+HGGAMIAAAGLDQRVGELVRSLSSRDEVIDCTGRDSGVACPYAGDCRLRGALHRAREAFL
+AELDTVQIRDLVSAGPVGGPVLLGLPEIPVAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000369.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000369.fa
new file mode 100644
index 0000000000000000000000000000000000000000..41a4195ec58384535f4cd4298a4920e3862c98e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000369.fa
@@ -0,0 +1,31 @@
+>PROKKA_00305
+MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+ITADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSYSVEHPAADHDGDVRR
+DDVRTDAGTAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRRDVTDADSVVVKDEHLNV
+GTERRASGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDVEVTTY
+EETPVVNKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDLDGRNDRKDRI
+>PROKKA_00020
+MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+TTADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSAADHDGDVRRDDVRTD
+AGAAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRREVTDADSVVVKDEHLNVGTERRA
+SGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDVEVTTYEETPVV
+NKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDLDGRNDRKDRI
+>PROKKA_00032
+MDRNMLDQLQNANVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+TTADGITVPFDKAFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSNVDHDRDVRHDDGLRA
+DAGTAGVAGTAGVAGVADRREDTVVDGDRRDVVDGDRRDLVDADRRDVVDGDRDSMVVKD
+EHLQVGTERQATGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDI
+EVTTYEETPVVNKTVEAEKVSLGKRQVQDTETVSEELRHEDVKIDGDATDRDLDGRTDRK
+DRI
+>PROKKA_00028
+MDRNALDQLQNGHVFSTDGEKIGSVGQVYLDDVTNEPTFVTVKTGLFGAKETFVPLQQAQ
+TTTDGITVPFTKDFVKDAPNVDADGSLTPEEEQRIYEYYSMDYSAVDTHDRRDVRDAAAA
+GTAGGVVTDRERRDVVDADRRDVVDNDRRDLVDGDADSVVVKDEKLNVGTERRATGRVRL
+RKQSYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDIEVTTYEETPVVNKTVEA
+EKVSLGKRTVQDTETVSEELTHEDVKIDGDDVDGRRR
+>PROKKA_00312
+MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+TTADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSAADHDGDVRRDDVRTD
+AGAAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRREVTDADSVVVKDEHLNVGTERRA
+SGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDVEVTTYEETPVV
+NKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDLDGRNDRKDRI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000370.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000370.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7beba10bf7a58d23f40d2dbe30ee681bcfc55fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000370.fa
@@ -0,0 +1,61 @@
+>PROKKA_00306
+MSEPLVADRRLAVVGAGPRGVMLLERILARLEGAAPDAHPRRLRIDVVDPYPPGPGRVWR
+TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVRRHQYPARAVY
+GRYLRHLYKDVVAGLRARPEVAEVVEHRAEATALHPRPDGGARLELRDPDGSVSVLDADA
+VVLCLGHQPAELSPGQMRMAAAARGRDELHYQGPQIPSDVDWETVEAGADVLVRGMGLNA
+FDLLAQLTQGRGGVYRRTGDGPGRALRYEPTGDEPRLHLMSRRGIPYLPKAEVDAFVPRG
+VTLSYLSDAAVDALTARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF
+LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYGSPFEDAVFASHEDYQRAV
+ADLMEQACVEAALGEESPFMMAVGALHAGRLRIKAWIAEGRIAEASRIRDVQGWFEPLVE
+GLASGPPLWRVEQMLAVHRAGLLTWAGPAPVVEAEEHAFTAHSPQVGAQDSLEPAVVEGA
+WLVEAMMPPNRVQAAASPLVRQMLADGVAAAGTWEDEEGVRVPATGFDVTARPYRLRAAD
+GTVHADVFVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAAAAAVLAG
+>PROKKA_00021
+MSEPLVAERRLAVVGAGPRGVMLLERILARLEGAAPDAHPRRLRIDVVDPYPPGPGRVWR
+TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVRRHQYPARAVY
+GRYLRHLYKDVVAGLRARPEVVEVVEHRAEATALHPRPDGGARLELRDADGAVSALDADA
+VVLCLGHQPAELSPGQNRMAAAARGRDELHYQGPQIPSDVDWETVEAGADVLVRGMGLNA
+FDLLAQLTQGRGGVYRRTGDGPGRALRYEPSGDEPRLHLMSRRGIPYLPKAEVDAFVPRG
+VTLSYLSDAAVDALAARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF
+LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYGSPFEDAVFASHEDYQRAV
+AELMEQTCVEAALGEESPFMMAVGALHAGRLRIKAWVAEGRITEASRIRDVQGWFEPLVE
+GLASGPPLWRVEQMLAVHRAGLLTWAGPAPVVEAEEHAFTAHSPQVGAQDSLGPAVVEGA
+WLVEAMMPPNRVQAAASPLVRQMLADGVAAAGTWEDEEGVRVPATGFDVTARPYRLRAAD
+GTVHADVFVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAAATAVLAG
+>PROKKA_00031
+MPDAQEAVRRLAVVGAGPRGVMLLERLLARLEGSAPGAHPARLRIDVVDPYPPGPGRVWR
+TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVQRHQYPARAVY
+GRYLRHLYQDVVAGLRARPEVADVVEHRAEVTALHPTPAGGARLELRDADGAASELAADA
+VVLCLGHQPAELSPGQARMAAAARGRDDLHYQGPQIPSDVDWDTVEPGARVLVRGMGLNA
+FDLLAQLTQGRGGVYRRTGDGPGRALAYEPSGREPRLHLMSRRGVPYLPKAEVDAFVPRG
+VTLSYLSDAAVDALSARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF
+LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYTAPFEDAVFASHEDYQRAV
+ADLMEQACVEAALGEESPFMMAVGALHAGRLRIKAWVAEGRIAEDSRIRDVQGWFEPLVE
+GLASGPPLWRVEQMLAVHRAGLLTWAGPVPVVDAEERAFSVRSPQVGAADSLGPAVVEGE
+WLVEAMMPPNRVQAASSPLIRGMLDDGVAAAGTWEDEEGVRVPAPGFDVTGRPHRLRAAD
+GAVHEDVYVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAVAQAVLAG
+>PROKKA_00027
+MSPPSISEPTRAIAVVGAGPRGVMVLDRLLARLEAASEPRPTGSLAVHVVDPFPPGPGRV
+WRPDQDPLLLMNTPAFFPTACAADNPGLAPSSVSLSFDQWRLARPDRAAGLERTDYPPRA
+VYGRYLEDVVAAVLDALRARPEVVAVTVHAAQAVALRAAYEGGPVAAPESPSAWRLTLRP
+VDGTPPRELQADVVVLCLGHQDAEPSAAQRRLGEAADASPALHYRGPHLPAELDVDGIAP
+GATVLVRGMGLNAFDLQARLSEGRGGRFEPTGGEPGRALRYVPSGREPVLHLLSRRGLPY
+LPKAAVDAFVPRGVRMSYLTDTEAEALVARHGQLDLAEHLWPLLHRDVVRAYYATLARVH
+PERLGGPADAGRFVRELVGMFESAGRGAPVTARHGQELLHAFAPGMRFLDIRSWAAPFQG
+AVFDDAAAYQEAVAGVLEQACGEAAAGEDSPFMQAVGTLHAGRLRIKAWIAQGLLTDASR
+IRDVQGWFEPLVEGLASGPPLVRVEQMLALHRAGLLSWAGPGPQVEADAEAGVFRARSPQ
+VGADDAVAPAVTEAAWLVEAMMPPSRVEAAATPLVRQMLADGVAAVGRWEDEDGALRSSS
+GFDVTARPHRLRGADGTVREGVLVLGLQLSGVQWGTAIAAEAGADVRDRALFLADADAAA
+RVALGG
+>PROKKA_00313
+MSEPLVAERRLAVVGAGPRGVMLLERILARLEGAAPDAHPRRLRIDVVDPYPPGPGRVWR
+TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVRRHQYPARAVY
+GRYLRHLYKDVVAGLRARPEVVEVVEHRAEATALHPRPDGGARLELRDADGAVSALDADA
+VVLCLGHQPAELSPGQNRMAAAARGRDELHYQGPQIPSDVDWETVEAGADVLVRGMGLNA
+FDLLAQLTQGRGGVYRRTGDGPGRALRYEPSGDEPRLHLMSRRGIPYLPKAEVDAFVPRG
+VTLSYLSDAAVDALAARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF
+LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYGSPFEDAVFASHEDYQRAV
+ADLMEQACVEAALGEESPFMMAVGALHAGRLRIKAWIAEGRIAEASRIRDVQGWFEPLVE
+GLASGPPLWRVEQMLAVHRAGLLTWAGPAPVVEAEEHAFTAHSPQVGAQDSLGPAVVEGA
+WLVEAMMPPNRVQAAASPLVRQMLADGVAAAGTWEDEEGVRVPATGFDVTARPYRLRAAD
+GTVHADVFVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAAATAVLAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000372.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000372.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca60ea0191868c5ccde17412053b998e21e50ff3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000372.fa
@@ -0,0 +1,72 @@
+>PROKKA_00308
+MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSADYIGT
+QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA
+GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN
+ELYATTTGAGLKGNEVLDEVAAVNAVADELEAQDAADVIVASYHDGAAGAGELAAERAAR
+AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG
+EVTGLTPRLLARSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY
+QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF
+TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG
+WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG
+YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV
+GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG
+ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKDADHPGKGRVK
+GEDHPGKGRGVQRGAATHPVFSAQAWLTAAGLPR
+>PROKKA_00023
+MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSADYIGT
+QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA
+GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN
+ELYATTTGAGLKGNEVLDEVAAVNAVADELEAQDAADVIVASYHDGAAGAGELAAERAAR
+AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG
+EVTGLTPRLLARSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY
+QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF
+TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG
+WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG
+YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV
+GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG
+ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKGADHPGKGRVK
+GEDHPGKGRGVQRGAATHPVFSAHAWLTAAGLPR
+>PROKKA_00029
+MSSLFRRHAVATAACTVLVLAPASAAPALAVETVAADETTISLLSFNDFHGALSSDFSGT
+QFADTVEDYRTAFEAQHGERSVLLTSAGDLIGGSASVSNVQQDDPTIDVMNALGLSALAA
+GNHEFDRGLDDLQDRVIPRAEFPVLAANFVDPDTLEPILASHAIFDVNGVSVAVIGAVPN
+ELYATTTGAGLQGNTVLDMVEAVNGVAAELEASGAADVIVASYHEGAAGAGDLAAELGKR
+EVFRSMVEDTHPAVDVIFNGHTHQLYQYETAGDGVARPVLQAGASGSNLAAVELTVDAAG
+EVTAVASRLLDRSTQDPAEAAAESAVTAEVYAIEQEAVAVFEDMQSQVVADLDGSLTTDY
+QKRLDEGGTWRAGGTRSAETTLGNWVADATKQTALNADPEVDLGVVNPGGLRSEILVDAF
+TGGGTFSPKPADLIGKLTLGELLDVAPFGNSISYFDIPGSSIELALEQNWRDDVRTFTLG
+WSENLTWTYDESRPQGEKVTGVWIDGEPLEQDAIYTVATQSFLADDTWVALGDPTAAPDG
+YTAFATGREDFVDLGVLDTQAISDYARLQASAEGAVGPDFAKKGVPVSGAPETVAAGEEI
+VLTLGDLVIDSDDAPAAAEVAVAFEAADGTVTELGSVTVPAGSEEVTLSGIAAPAEAGAG
+ELRMTVRYADGTETIVRHALEVTASEAPVEPTEPTDPTVPADPSEPADPADPTVPADPSE
+PADPADPSDPTDPAAPVEGDDDGDDRDEEHTVPSTVETGDASAWWLAGFGALLGAALLRG
+RRALGLTASSTPAGR
+>PROKKA_00025
+MSSIFSRRTAATLACTTLVLAPAAAPALAADASGERTISVLSFNDFHGALSEDFKGTQFA
+DTVEDYRTAFEAQHGEGSTLLTSAGDLIGGSASVSNVQQDNPTIDVMNALGLASLTAGNH
+EFDRGLDDLQGRVADRADFPVLSANFVDPNTKAPVLTSHKVFDVDGVRVAVIGASPNELY
+ATTTGAGLQGNLVVDMVDAVNAVATGIEAADEADVIIASYHDGAAGAAADLSAELGNRAT
+FDAMVERTVPAVDVIFNGHTHQLYQYQTDNGGVPRPIMQAAASGADLAAVELTVDAAGEV
+TAVTPRMLPRSTQDPAEAAAESPVTARVYEIEQQAVDVFTDMQSQVIADLSGSITTDYAT
+RIAAGMGWKAGGTRTAETTLGNWVADSLKHSVSAAEPGVDLGVVNPGGIRSELLVDQTNA
+GGVFSPKPEQLVGKLTMGEVMDVAPFGNTLTYFDLPGSSIKEALEQNWRDGERTFTLGWS
+SNLTWTYDDARAQGDKVTGVWIDGEPLQADRMYTVAAQSFLADDTWVKLGDPSKAPDGYT
+AFATGRQGFVDLGVLDTTAVLSWARAQDAADGAAHPDYAKKGVPVTGAPASVEGGQDVVL
+TLGDLVIDSDGAPAATAVDVAFQGADGAVTELGTVEVPAGQESVTLSGITAPQTAGAGEL
+VMTVRYADGTTAVVRHALEVTASAAPVDPSTPAEPTQPGEPSDPAEPTTPGEPTPSAQPT
+APVEPTAPVEPSAPAEPTAPVEPTAPAESPEPTPTAQPSTPAEPTAPTPSAPAEDGGEHA
+VPGKVQTGDQAIWLVAALGALGAGALVAVRRRAAAR
+>PROKKA_00315
+MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSGDYIGT
+QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA
+GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN
+ELYATTTGAGLKGNEVLDEVAAVNAVADELAAQDAADVIVASYHDGAAGAGELAAERAAR
+AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG
+EVTGLTPRLLTRSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY
+QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF
+TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG
+WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG
+YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV
+GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG
+ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKGADHPGKGRVK
+GEDHPGKGRGVQRGAATHPVFSAHAWLTAAGLPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000373.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000373.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d754b6d5595b58c083493d8061e84f8d08928b26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000373.fa
@@ -0,0 +1,20 @@
+>PROKKA_00311
+MRGPFARFRQERADDRELGTGLWRRAHDRLGRAMDRYWQVLAGQRGTDVLSPEERNGVVH
+AGNVLTERLPAVRALCVRLHRDHEGDGEHIPAEAADVHRELSRAAHELAATAQALALYRL
+GQGSAESVGRHAERTLGHLDRAEELGAGL
+>PROKKA_00026
+MRGPFARFRQERADDRELGTGLWRRAHDRLSRALDRYWQVLEGQRGTDVLSPEERNGVVH
+AGNVLTERLPAVRALCVRLHRDHEGDGEHIPAEAADVHRELSRAAHELAATAQALALYRL
+GQGSAESVGRHAERTLGHLDRAEELGAGL
+>PROKKA_00026
+MRGPFARFRQSCSDDRELGTGLWRRAHDRFVRAMDRYWQVLEGDRGPDLLRTEQRNGVVH
+AGNVLAERLPAVRALCVRLHRDHAGDGEHIPPEAADVHRELSRAAHELAATAQALAMHRL
+GQGSSDSVGRHAERTLAHLDRAEELAARL
+>PROKKA_00022
+MIRGPFARFRQGRSDDRELGTGLWRRSHDRYVRALDRYWQVLEDGRSAGGFTPEERNGLV
+HAGNVLAERVPAVRALAARLHAAHPGDGEQHIPPVTAPVHRELSRASHELAAAAQAVAMF
+RRGVSGSEAVSRHAQRTLDHLDRAEGLAADL
+>PROKKA_00318
+MRGPFARFRQERADDRELGTGLWRRAHDRLGRALDRYWQVLEGQRGTDVLSPEERNGVVH
+AGNVLTERLPAVRALCVRLHRDHEGDGEHIPAEAADVHRELSRAAHELAATAQALALYRL
+GQGSAESVGRHAERTLGHLDRAEELGARL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000382.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000382.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e7cbcf34bd48c27bdb2b426c16bc70a9a2fad013
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000382.fa
@@ -0,0 +1,25 @@
+>PROKKA_00322
+MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIQYSPSDGINGQEQDFLSYRNLA
+LVGDGESGPARLIGTVENTSGQDQTYTFQAEGGGSATLKVPAGESRKLEDEANTTVLERE
+GVWVGENLPVTVSGNGGTADLAVPLLSATQEQYRDLLPEGVEPSEEDLVGHLHEETHHYG
+EEH
+>PROKKA_00037
+MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIQYSPSDGINGQEQDFLSYRNLA
+LVGDGESGPARLIGTVENTSGQDQTYTFQAEGGGSATLKVPAGESRKLEDEANTTVLERE
+GVWVGENLPVTVSGNGGTADLAVPLLSATQEQYRDLLPEGVEPSEEDLVGHLHEETHHYG
+EEH
+>PROKKA_00015
+MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIEYDASDGINGEEKDFLSYRNLA
+LVGDGDSGPARLIGTLENLSDQAQTYTFQAEGGGSATVQVPAGETFKLEDDANQTVLERQ
+DAWVGELLPVTVSGNGGQTELEVPLLGATQDHYRDLLPEGVSPSDEELGSHLDEETHDYG
+GEH
+>PROKKA_00011
+MKSVASRPARRRLAAGALALTAVLGATGCSAVSPVATGIQYSASDGVNATQTGFVEVRNL
+GMVGEGASGPARLIGSLKNDSGADKTYTIAVQDGGQITVPVKAGETVKLEEQQLEVERSV
+WPGQNAQATVSADGTQLQLGVPVLSATQEQYKEYLPAGQSADTEHLDEQTATYGEGEGEQ
+H
+>PROKKA_00329
+MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIQYSPSDGINGQEQDFLSYRNLA
+LVGDGESGPARLIGTVENTSGQDQTYTFQAEGGGSATLKVPAGESRKLEDEANTTVLERE
+GVWVGENLPVTVSGNGGTADLAVPLLSATQEQYRDLLPEGVEPSEEDLVGHLHEETHHYG
+EEH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000391.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000391.fa
new file mode 100644
index 0000000000000000000000000000000000000000..74920839b02788a42649c6ae46b7eed580c1ba4c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000391.fa
@@ -0,0 +1,20 @@
+>PROKKA_00338
+MTAADTPAPRQDPLAFFLDKAVPEAWHAVGPLASAARGAAEQAGLDRQLVELVNLRVSQL
+NGCVFCLDRHTRQGADAGLSVQRLGLLPAWREAGAVYSEQERAALELAEAVTDLPEQEQL
+NYVQASTAAVLTDAQYAAVQWVAIVMNLTNRISILSHHPVRRRDG
+>PROKKA_00054
+MTAADTPAPRQDPLAFFLDKAVPEAWHAVGPLASAARAAAEQAGLDRQLVELVNLRVSQL
+NGCGFCLDRHTRQGADAGLSVQRLGLLPAWREAGAVYSEQERAALELAEAVTDLPEQEQL
+NYVQASTAAVLTDAQYAAVQWVAMVMNLTNRISILSHHPVRRRDD
+>PROKKA_02674
+MSAAENPATRKDPLAFYLDKAVPDAWKAVGGLAAAVRTAAEEAGLDRQLVELVNLRVSQI
+NGCGFCLDLHAREGAKAGLNAQRMALLPAWREAEAVYSEQERAALELAEAVTELPEQEQL
+HYVQASTAAALTDAQYAAVQWAAMVMNLTNRISILSHHPVRRRED
+>PROKKA_02486
+MSSPHDDAAPARKDPLAFYLDKAVPEAWVAVGGLAAAARRAAVEAGLDEQLMELVNLRVS
+AINGCAYCLDVHTRKGVGAGLSDQRRGLLSAWREAPEVYTELERAALELAEAVTELPEQE
+QQQYVQLSTHGVLTDAQYAAVQWLAIVMNVTNRISILSHHPVRRHDS
+>PROKKA_00345
+MTAADTPAPRQDPLAFYLDKAVPEAWHAVGPLASAARDAAEQAGLDRQLVELVNLRVSQL
+NGCVFCLDRHTRQGADAGLSVQRLGLLPAWREAGAVYSEQERAALELAEAVTDLPEQEQL
+NYVQASTAAVLTDAQYAAVQWVAIVMNLTNRISILSHHPVRRRDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000392.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000392.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8041a44e38150ca1080a53582e679fc701f90794
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000392.fa
@@ -0,0 +1,48 @@
+>PROKKA_00339
+MAAAPQAHAVAWDRVELVDDAGVIDPAQLRRDLAGIEFREPTRVAVVTERGPDLSALDDD
+RASQAFNGRVLERARAEHPDWLSADGQKWADGLVIVALDPDNRLIGVYVGEDRMLSTDQL
+RDVREAGHEAARAARWTDTVVEVTDAAAELIGRPWWQAPELWFGAGIVGVAGGGAAAAVL
+ASRRRRRRRTADLLTEARTHLTSVTLEMDATEVNASTVPEDSPHAAALMERFRGFRRQAL
+DASAELDRLEALPERSLHRTEHARAAEDVRDRARELDRLDDAVAAANTFLNRHPGWPSAW
+DQQTAPLRADLDAVGTLASSVGSAGPVRSAVAALESFRAEAQGRLEALGADLQDERLTPA
+AALDELDALRRRLTGLVSALADAEVAAFGKDEAERELLRDELRTHRGPARSARGSILDSA
+LPTDAYWTVVAFTTGHQAGERSVQDHRQAQSSSSGTGYGSSAGSFSGAGSSGRF
+>PROKKA_00055
+MTRPTHRTARRTLAAVALSAAALTGPAAAATVVALPVTAGVTGAVVATAPQAHAVAWDQV
+ELVDDAGVIDPAQLRRDLAGIEFREPTRVAVVTERGPDLSALDDDRASQAFNGRVLERAR
+AEHPDWISADGQKWADGLVIVALDPDNRLIGVYVGEDRTLSTDRLREVREAGHEAARAAR
+WTDTVVDVTDAAAELIGRPWWQAPELWFGAGIVGVAGGGAAAAALASRRRRRRRTADLLA
+EARTHLTSVTLEMDATEVNASTVPEDSPHAAALMERFRTFRRQALDASAELDRLEALPER
+SLHRTEHARAAEDVRDRARELDRLDDAVAAANTFFNRHPGWPAAWDQQTAPLRADLDAVG
+TLASSVGSAGAVRSAVAALESFRTEAQDRLEALGADLQDERLTPAAALDELDALRRRLTG
+LVSALADAEVAAFGKDEAERELLRDELRTHRGPVRSARGSILDSALPADAYWTVVAFTTG
+RQAGERSVQDHRQAQSSSSGTGYGSSGGSFSGAGSSGRF
+>PROKKA_02673
+MDEAGVVDPERLRRGLAEVEFREPTRVAVVTERGPDLSGLDDDRAAQAFNGRVLERARAE
+HPDWLSADGQTWADGLVIVALDPDNRMLGLYVGEDRSLSTDQLQDVREDGYEAARAAKWT
+DALVDVTDSAAELIGRPWWQHPGLWVGAGAVGLVGAGTGAAVMADRRKKQARTQADLESA
+RGHLTAVTLELDATEVNASTVPTDSPHAATLLERFRGFRERTLDATAEQQRLEAVPEKDL
+HRRKHREAAAALRAQTAELDGLDDAIGAANALLNRHPGWPAAWDLQTAPLREDLDAVAEL
+RDAVTDTPSVQAAVAALESFRAEASGRLDALGGDLEAERVTPAAALDELDGLRGRLTSLV
+GSVAEAEITAFSDDDEERRILREKLRSRRGTHRAARGSILDCTLPSDAYWTVVAFNAGHR
+AGERSVQERREAASSPSSSGTGYGSSGGSFSGTGSSGRF
+>PROKKA_02485
+MPEPTAPRPSRLARAPRARLLARAARPLAAAAVAGAALAGAAAPAGVAATAAAVPVAAGA
+VVAAPAAHALEWSRVDLADQAGIIDPAQLERDLAGIEFRAPTRVAVFTERGPDIRGLDEE
+RKAQAFNGRVLEFARAQRPGWISADGQKWADGLVIVAVDPDNRMLGVYQGEDRKLESGGQ
+SAVREAGTDAARDARWTDAVVDMVDEAATRIGRPWNEDPVVWLGLGGGALGVLGAGAGIT
+AAVVGPRRSRARRSAEHLEEARHHLTSVTLDWETTELNASTVPLGSRHGARLMERYRGFH
+RSALDATARLEELEAAPVKDRSAQSFVDRAGGVRDDVAALDALDDAIADANALLNRLPGW
+EDAWDRQVAPLREDLHRVPALHDRLGDVDGTAVPLAALDSFRDEARTELERLGTGLTAQT
+VAPDDAIDALERLRRRLTVRIEELARAVAQAQDGRKKQRLMQESLDGQRAVPRDRRGSIL
+DAGDGWRTYWTVTAFDAGVDAGDSAVASYESSSSGTGYGSSGGSFSGSGSSGSF
+>PROKKA_00346
+MTRPTHRIARRTLTAVALSAAALTGPAASATVVALPVTAGVTGAVVAAAPQAHAVAWDQV
+ELVDDAGVIDPAQLRRDLAGIEFREPTRVAVVTERGPDLSALDDDRASQAFNGRVLERAR
+AEHPDWLSADGQKWADGLVIVALDPDNRLIGVYVGEDRMLSTDRLREVREAGHEAARAAR
+WTDTVVDVTDAAAELIGRPWWQAPELWFGAGIVGVAGGGAAAAALASRRRRRRRTADLLA
+EARTHLTSVTLEMDATEVNASTVPEDSPHAAALMERFRNFRRQTLDASAELDRLEALPER
+SLHRTEHARAAEDVRDRARELDRLDDAVAAANTFLNRHPGWPAAWDQQTAPLRADLDAVG
+TLASSVGSAGPVRSAVAALESFRTEAQDRLEALGADLQDERLTPAAALDELDALRRRLTG
+LVSALADAEVAAFGEDEAERELLRDELRSHRGPARSARGSILDSALPADAYWTVVAFTTG
+HQAGERSVQDHRQAQSSSSGTGYGSSGGSFSGAGSSGRF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000393.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000393.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e6686df1ea8082f56d0a3cc659b9bf7d9deadfc5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000393.fa
@@ -0,0 +1,30 @@
+>PROKKA_00340
+MSSSEAAAPAHALPRVVGILGAGRAGTALARAIARIPRLSPGTAAPRVMVAGTRRPAAVQ
+RHLTIYAPEAVAVSAEDLAAEAELVVVAVPREALDDVDPLALAGPATRAVVDLTNTWGDE
+PVPAWLDDDAAPGTTRIAERWAAAGLRVPVVRAFSEISHHDLGDAGRATAPRRALAVGTE
+PADATADPAAVAAARDTVIALVTAMGFDAVPYTGLDRAGVLEPGAAGFGTAHDAGRLAAL
+LADAPTG
+>PROKKA_00056
+MSSSEAAAPADALPRVVGVLGAGRAGTALARAIARIPRLSPGTAAPRVMVAGTRRPAAVQ
+RHLTIYAPEAVAVSAEDLAAEAELVVVAVPREALDDVDPLTLAGPATRAVVDMTNTWGDE
+PVPAWLDDDGAPGTTRIAERWAAAGLRVPVVRAFSEISHHDLGDAGRATAPRRALAVGTE
+PADATADSAAVAAARDTVIALVTAMGFDAVPYTGLDRAGVLEPGAAGFGTAHDAGRLAAL
+LADAPIG
+>PROKKA_02629
+MSSSEPAAPAALPRAVGILGAGRAGTGVARAIARIPRLSPGLPEVRALVAGTRRPSAVQR
+HLTVYAPAAQAVAAEELAARAEVIVVAVPREDLDDVDPLALAGPGVRAVVDMTNTWGEEL
+LPAWLEAGPDDAPGTARIAARWAAAGLEVPVVRALSEVSHHDLDVHGRAAAPRRALAVGT
+VPAADASDPGAVVAARDAVAALVTAMGFDAVPYEGLERAAVLEPGGAGFGVAHDARELAA
+LLGAGPRG
+>PROKKA_02484
+MPHDAAPRPDQPAAFESLPASVGILGAGRAGTALARAIARIRVLHPGTAAPRVVLAATRS
+PAAVRRHLAIHAPGAEAAHPGDLATDTELTVVAVPREELDEVDPAWLAGPRTLAVVDMTN
+TWGDELVPDWLAAAAAPGLPTMPGSAAIAAHWAEAGLTAPVVRAFSEVSHHELDRDGRAQ
+PPLRALGVGADSPGPARAAVAALVTAMGFEPVEYAPLARAAALEPGTRAFTRPLPADELA
+RELA
+>PROKKA_00347
+MSSSEAAPADALPRVVGILGAGRAGTALARAIARIPRLSPGTAAPRVMVAGTRRPAAVQR
+HLTIYAPEAVAVSAEDLAAEAELVVVAVPREALDDVDPLALAGPATRAVVDLTNTWGDEP
+VPDWLDGDGSPGTARIAARWAAAGVRVPVVRAFSEISHHDLGDAGRATAPRRALAVGTEP
+ADTAADPAAVAAARDTVVALVTAMGFDAVPYTGLDRAGVLEPGAAGFGTAHDAGRLAALL
+ADAPTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000394.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000394.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2cbc9b8d6f8e5b43ef75f9b5e1e6331042ac8e85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000394.fa
@@ -0,0 +1,30 @@
+>PROKKA_00341
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEEQRE
+MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA
+KFPQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVEDAPEHIAGYAVANDISMR
+GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFPADARVLTHVNGELRQEDRVADVVFSPAE
+LVSYASQLITLNPGDLILTGTPAGVALARRDAEGRRPWLRPDDVVEVEITGLGRQRNELV
+>PROKKA_00057
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEERRE
+MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA
+KFAQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVEDAPEHIAGYAVANDISMR
+GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFSADARVLTHVNGELRQEDRVADVVFSPAE
+LVSYASQLVTLNPGDLILTGTPAGVALARRDAEGRRPWLRPDDVVEVEITGLGRQRNELV
+>PROKKA_02628
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPECRDVGEYLTAEPQEQRE
+MVESALRAAQEDRSLLLDTSTLVYDTLIPFPTKVFCVGLNYTNHIEETGQNQPEHPTLFA
+KFTQSLTGALDPVEVPEEDHLVDYEGELCIVIGEPGRRIAVEDAKEHIAGYAVANDVSMR
+GWQGRTSEWLQGKVWEASTPVGPWLVTPDELTADARIITRVNGVERQDDRIADVVFSPEE
+LVAYVSQMITLNPGDLIMTGTPAGVAVARKGADGRRPWLQAGDVVEVEITGLGRQRNELV
+>PROKKA_02480
+MKLATFRQPDSDASYPGATFAAVLTSFHPQDPQVAVRAVALPECRDVGEFLTAEPQEQKD
+MVREALEAAKEDHGLLLDVSTLVYDTLVPFPTKVFCVGLNYADHIRETGQEKPEHPTLFA
+KFAQSLTGALDPIEVPEEDHRVDYEGELCVVIGEPGRRIAVEDAKDHIAGYAVANDVSMR
+GFQGRTPEWLQGKVWEASTPVGPWLVTADEFPKDARIVTRVNGEVRQDGKVKDVVFSPAE
+LVSYVSQLVTLNPGDLIMTGTPAGVAVARRDGDGRRPWLRADDVVEVEITGLGRQRNELV
+>PROKKA_00348
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEEQRE
+MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA
+KFPQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVADAPEHIAGYAVANDISMR
+GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFPADARVLTHVNGELRQEDRVADVVFSPAE
+LVSYASQLITLNPGDLILTGTPAGVALACRDAEGRRPWLRPDDVVEVEITGLGRQRNELV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000395.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000395.fa
new file mode 100644
index 0000000000000000000000000000000000000000..61774c7d0383303647bf016291087afe08aca822
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000395.fa
@@ -0,0 +1,35 @@
+>PROKKA_00342
+MSTAPTHPPLDLDPTPATPIVLGTMAWGSVLPPPPDADPGVGPEGPAGEAQAEAAVERAR
+RALRAGIEAGVDLLDTADIYGAGRSEETVGRLLHELPYEERSALKVQTKCGIVLHETDPA
+GRRLTRYDSSPEHVRASLEGSLARLGEQRVDTLIIHRPDVLTPVADTVRAFLDAREAGLV
+GKLGVSNLGVGRVLEFQRELESQAADGTGLACVQVELGLHHRTLMEAVVLANHPDAPADA
+DAGRLGPVCAAEGIELQAWGPLGQGRFSSGDDGAAGAVGEVAAELGGSREAVVLAWLLRL
+PWDVRPVIGTQDPERVAACAEAAAAAEAMDSAQWHRLWTAARGAGLP
+>PROKKA_00058
+MSTAPTHPPLDLDPTPATPIVLGTMAWGSVLPPPPDADPGVGPEGPAGEAQAEAAVERAR
+RALRAGIEAGVDLLDTADIYGAGRSEETVGRLLHELPYEERSALKVQTKCGIVLHEADPA
+GRRLTRYDSSPEHVRASLEGSLARLGEQRVDTLIIHRPDVLTPVADTVRAFLDAREAGLV
+GKLGVSNLGVGRVLEFQRELESQAADGTGLACVQVELGLHHRTLVEAVVLANHPDAPADA
+DAGRLGPVCAAEGIELQAWGPLGQGRFSSGDDGAAGVVGEVAAELGVSREAVVLAWLLRL
+PWGVRPVIGTQDPERVAACAEAASVAEAMDSAQWHRLWTAVRGAGLP
+>PROKKA_02627
+MAWGAAPAPAPAPGEGPALLASAGPEHAEAARERARGALRAGIDAGVDLLDTADIYGAGV
+SEETVGALLHELPYEERSALKVQTKCGIVLDEVDADGRPMVRYDSSPEYVRARLEGSLAR
+LGELRVDTLVIHRPDVLTPVADTVRAFLDAREEGLVGKLGVSNLGVGRTLEFQRELAAQS
+ADGTGLACVQVELGLHHRTLVESVILANHPGAAADADVADLGRVCAAEGIELQAWGSLGQ
+GRFSSGDDGAAGVVGEIARELDTSREAVVLAWLLRLPWGVRPVIGSQDPGRIAACADAAA
+AAEAMDSAQWHRLWTAARGAPLP
+>PROKKA_02479
+MTAQDTAPQTPAASPLILGTMGWGDVERARGALRAGLEAGIGLLDTADIYGAGASEETVG
+ALLAELDPAERTRLRVQTKSGIVLHEPGPDGTPAVRYDNSPAYLHERLALSLERLGLDRV
+DTLVVHRPDVLTPVSDTVRAFLDAREAGRVDALGVSNMGTRRVLEYQHALREVSADGTGL
+ACVQVELGLHHRMLVESVVLANHPAAAPDGGAGDLGEVCAGEGIEIQAWGPLGQGRFTRG
+SDGTVPADPAEQAALAAAGGAPAVVARVARELEVSREAVVLAWLLRLPWGVRPVVGTQDP
+ARIASCAQAADAAARMDGAQWHRLWTAARGETLP
+>PROKKA_00349
+MSTAPTHPPLDLDPTPATPIVLGTMAWGSVPPPPPDADPGAGPEGPAGEAQAEAAVERAR
+RALRAGIEAGVDLLDTADIYGAGRSEETVGRLLHELPYEERSALKVQTKCGIVLHETDPA
+GRRLTRYDSSPEHVRASLEGSLARLGEQRVDTLIIHRPDVLTPVADTVRAFLDAREAGLV
+GKLGLSNLGVGRVLEFQRELESQAADGTGLACVQVELGLHHRTLVEAVVLANHPDAPADA
+DAGRLGPVCAAEGIELQAWGPLGQGRFSSGDDGAAGVVGEVAAELGVSREAVVLAWLLRL
+PWGVRPVIGTQDPERVAACAEAASVAEAMDSAQWHRLWTAARGRPLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000396.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000396.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b12f19aa40ad40dad2a05963a971ff0a65a326fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000396.fa
@@ -0,0 +1,20 @@
+>PROKKA_00343
+MTFEPVNLFTPWLAYWAAALALVVGGILLAAGIWRERRHRRHADAHGRNTEVDVLDNTRL
+QRRVGAVMLAVAAVLAGVGVWTHLAGLDTLRQNLTAKYGYTSIERIRQSGTGFIIDLTQP
+DGTVLRDEMVLVDPSGEPFVGEDIFHNPPEKYEDLPLRPAP
+>PROKKA_00059
+MTFAPVNLFTPWLAYWAAALALVVGGILLAAGIWRERRHRRHADEHGRNTEVDVLDNTRL
+QRRVGAVMLAVAAVLAGVGVGTHLAGLDTLRQNLTAKYGYTSIERIRQSGTGFIIDLTQP
+DGTVLRDEMVLVDPSGEPFVGEDIFHNPPEKYEDLPLRPAP
+>PROKKA_02626
+MAFERVDLTTPWLAYWAALLALVIGAALLAAGIWRERRHRRHAAAHGRNTEVDVLDNTRL
+QRRVGVVGLVAAVVLAGVGVWTHLAGLDALRQNLTAKYGYTDVERIRQSGTGFIIDLTQP
+DGTVLKDEMVLVDPSGEPFIGDDIFIDVIGGA
+>PROKKA_02478
+MTFAPVDLQTPWLLYWAAAVAAVVGVSLALAGRWRERDHRRRQAAAGSHVVMRVLENTRL
+QRRVGYGALVLALALAVWGAVAHVQGIDALRGNVRQKYGAEVEDVRQSGSGVTVDLVHPD
+GTREEDQYMAVEQDGEPVYGAELVESPPIGG
+>PROKKA_00350
+MTFEPVNLFTPWLAYWAAALALVVGGILLAAGIWRERRHRRHADEHGRNTEVDVLDNTRL
+QRRVGAVVLAVAAVLAGVGVWTHLAGLDTLRQNLTAKYGYTSIERIRQSGTGFIIDLTQP
+DGTVLRDEMVVVDPSGEPFVGEDIFHNPPEKYEDLPLRPAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000398.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000398.fa
new file mode 100644
index 0000000000000000000000000000000000000000..72cdee7eee829f4b8561ce12c2c84fcb0004c671
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000398.fa
@@ -0,0 +1,45 @@
+>PROKKA_00346
+MDTVETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV
+RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV
+TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG
+FAAHLVDAETGELRERLSNGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV
+ASYRRLWDELTGPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH
+AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV
+PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT
+TTMLRAVPPADAD
+>PROKKA_00062
+MDTAETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV
+RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV
+TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG
+FAAHLVDAETGELRERLSNGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV
+ASYRRLWDELTEPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH
+AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV
+PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT
+TTMLRAVPPADAD
+>PROKKA_02623
+MSERIVTVDTVETPSPDDRLTVTGAPSGDASEDPATALLALPWSTALEDWPEDVLAALPR
+GISRHVVRFARVGGGVVAVKETTEDLAFREYRLLRRLEGSPAPSVVPVAVVTGRTDGRGE
+PLPAALVTRYLHFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVL
+FRRDAGGFAAHLVDAETGELRERLSTGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPA
+ATPELFVDAYRRLWDELTGPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMML
+AAPVEVHAGYHRRRLTRLTGLQVQENQARRLLVDIEAARRAWDPFLDLEGAAHRWVVEVF
+DPVVRSVPLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRVRRDED
+AVALHPTTTMLRTVPPADED
+>PROKKA_02475
+MDEHEQPRTDPADRLTVTAAPSGDASEDPATSLLALPWERPLEDWPAEVLAALPRGISRH
+VVRFARMGAGVVAVKETTEELAFREYRLLRELEDRPSPSVVPVAVVTGRTREDGTALPAA
+LVTRHLRFSLPYRAVFSERMERRTLVRLMDALALLLVELHLEGFFWGDVSLSNVLFRRDA
+GGFAAHLVDAETGELRERLSTGQREHDLDVARVNIGGELLDLHASGLADPDVDAIATPDL
+FVESYRQLWQQLTEPTVFPRGEPWRMDRRFRRLTELGFEVEEYSLRAADAPGMMVAQPTD
+VNSGYHRRRLERLTGLHVQENQARRLLVDIEAARRSWDPFMDMDHAAHRWVIEVFDPVVR
+SVPLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLDEAVDSYVETVLRARRDEDALALH
+PTTTMLRAVPAPEADPEG
+>PROKKA_00353
+MDTAETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV
+RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV
+TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG
+FAAHLVDAETGELRERLSTGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV
+ASYRRLWDELTEPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH
+AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV
+PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT
+TTMLRAVPPADAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000399.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000399.fa
new file mode 100644
index 0000000000000000000000000000000000000000..983debf6a3ba2272fa94b29ffc7ab52ccc6f0cf1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000399.fa
@@ -0,0 +1,30 @@
+>PROKKA_00347
+MARNTSGSHTSATDARARARQIQEEQRRKDRRRRTGVIWGSVLAAVLVIGLVVAFALTRN
+GDDAAAAGPIPAAANEQGGIELTSATGLAEGAGEREVDPSEIEVPKQAASSQPETLPNTE
+ARGDGEPTRIVLYADFNCVHCADFESSNAEQIEQWLEQGEVTVEYRMVDFLSAPNNQNYS
+ARAANAAYCVADQKPEAYNGFVAALFAAYDEHQGKGLDNAALTQLAQEQGVDISSCVEDG
+TFRSAVEHTTRQARVAGVAGTPTVFVDGKNWALDGEDKTFTDWAGAKIAD
+>PROKKA_00063
+MARNTSGSHTSATDARARARQIQEEQRRKDSRRRTGVIWGSVLAVVLVIGLVVAFVLNRN
+GDDAAAAGPIPAVANEQGGIELTSATDLAEGAGEREVDPSKIEVPKQAASSQPETLPNTE
+ARGDGEPTRIVLYEDFNCVHCADFESTNGDQIEQWLEQGEVTVEYRMVDYLSAPNNQNYS
+ARAANAAYCVADQKPEAYNGFVSALFAAYDEHQGKGLDNAALTQLAQEHGADIASCVEDG
+TFRSAVEYTTRQARAAGVAGTPTVFVDGKNWALDGEDKTFIEWAGAKIAG
+>PROKKA_02622
+MARNTSGSHTSATDARARARQIQEQQRKKDGRRRTAVIWGSVLAAILVIGLIVAFALNRG
+GDEPAAAGPIPAAANEQGGIELTSATTLAEGAGAREVDASTVEVPEQGAAQQPETIPAAE
+APAEGEPSEIVLYADFNCVYCADFETSNAAQIEQWLEAGEVTVEYRMVDFRSAPNNQNYS
+ARAANAAYCVADQKPEAYNGFVTALFGTYQEHGGKGIDNAALTQLAQDNGADIASCVEDG
+TFRSAVEHTTRQAQAAGVGGTPTVFMDGENWAIGGPDQSFQEWAQSKISG
+>PROKKA_02474
+MASRNPAPSEVDARARARQMQVDQQKKARRRRTATIWGAVLAAVLVIGLIVGFVVKGNQG
+TEISATGPVPGVVNEEGGVEMTSATALADSGKSERQVDSSSVAVPETATAPEELTTIPAA
+GEPADGEPAQIVVYADFNCVHCAEFESQNSEQLQSWLRDGKATVEYRMVNFLSAPNNKNY
+SARSANAAYCVAAAKPEAYNEFTTGLFMAWEGHGGKGLSDDELIQRADALGVDIEGCLKD
+NTYRPAVEWATNKAKAASVAGTPTVFVNGKNWSTDGGDKSFVDWAKPMVEG
+>PROKKA_00354
+MARNTSGSHTSATDARARARQIQEEQRRKDSRRRTGVIWGSVLAVVLVIGLVVAFVLNRN
+GDDAATAGPIPAVANEQGGIELTSATDLAEGAGEREVDPSKIEVPKQAASSQPETLPNTE
+ARGDGEPTRIVLYEDFNCVHCADFESTNGDQIEQWLEQGEVTVEYRMVDYLSAPNNQNYS
+ARAANAAYCVADQKPEAYNGFVSALFAAYDEHQGKGLDNAALTQLAQEHGADIASCVEDG
+TFRSAVEYTTRQARAAGVAGTPTVFVDGKNWALDGEDKTFIEWAGAKIAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000400.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000400.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c738d888e7bcb4b30135ffd280ee938765fb6c1d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000400.fa
@@ -0,0 +1,56 @@
+>PROKKA_00349
+MQSSTPRSTRRIGALVAGAVLAGGTLTSSPALAAPSGAAPAAPAASPTVASPLAAAQVED
+PNADGYDSFIVTYKETAANAHAKGRANAWGKAAKEAGVSVKELRETALGSRVVTVDRKLD
+QAESAKFMADLKASGAVEAVEPDAILTATGLSPVDALYSQQWGFTGTHGMRVPGAWDRTT
+GSGATVAVIDTGITSHPDLDRNVVPGYDFISDSAAARDGGGRDSNPRDEGDWYAAGECGT
+AGASDSSWHGTHVAGTVAAVADSQGVVGVAPNAKIQPIRVLGKCGGSLSDIADAVVWAAG
+GTVAGVPANPNPADVINMSLGGSGMCGTTYQNAINAAVSRGVPVVVAAGNENQPAANVRP
+ANCQNTIVVAASTSQGARASFSNYGSAVDVTAPGANIISTVNNGATTPTTAGHAAYNGTS
+MATPHVAGLAALLLAAQPSLTPAQVESTLRSTARSMPVTCSAGCGAGLADASAAVSSLGG
+AQTEPGPAPVASLIVNGGFESGSTGWTGTPTGFVRTDAAKAASGQAFAQLNGVGRRNTTT
+VEQKVTVPASGATLTYALQVDTAETTASRSYDLLDVQVVTGATGTYTVASHSNLDKGGYA
+TRTVDLSRFAGTTVTLRFRGTEDSSAATTFRIDEVAVTAR
+>PROKKA_00065
+MQSSTPRSTRRRIGALVAGAVLAGGTLTSSPALAAPSGGAPAAPAASPTAASPLAAAQAE
+DPNADGYDSFIVTYKETAANAHAKGRANAWGKAAKEAGVSVKELRETALGSRVITADRKL
+DQAESAKFMADLKASGAVEAVEPDALLTATGLSPVDALYSQQWGFTGSHGMRVPGAWDRT
+TGSGATVAVIDTGITSHPDLDRNVVPGYDFISDSAAARDGGGRDSNPRDEGDWYAAGECG
+TAGASDSSWHGSHVAGTVAAVADSQGVVGVAPNAKIQPIRVLGRCGGSLSDIADAVVWAA
+GGTVAGVPANPNPADVINMSLGGSGVCGTTYQNAINAAVSRGVPVVVAAGNENQPAANVR
+PANCRNTIVVAASTPQGARASFSNYGSAVDVTAPGANIISTVNNGATTPTTAGHAAYNGT
+SMATPHVAGLAGLLLATKPSLTPANVESTLTSTARSMPVTCSAGCGAGLADAARAVSSLG
+GSS
+>PROKKA_02612
+MKSSVQHSTRRRVGALLAGAVLAGGALTSSPAFAAPAEGARAEQAPRPVAAAPLATVDAA
+DPNADGYDSFIVTYKETAQNNNGKGRALAWGKAAKAAGVSVKELRETALGSHVVQADRKL
+DQSESARFMADLKASGAVEDVEPNAIMTATGLSPADALYSQQWGFTGTNGMRVPGAWDYN
+TGSGVTVAVLDTGITSHPDLDRNVVAGYDFISSSAAARDGNGRDSNPRDEGDWYAAGECG
+ASQPGNSSWHGTHVAGTVAAVTDTQGVVGVAPNAKIQPVRVLGKCGGSLADIADAIVWAS
+GGSVTGVPANANPADVINMSLGGSGTCGTTYQNAINAAVNRGVPVVVAAGNENQPAANAR
+PANCSNVITVAASTSQGARSSFSNYGSAVDVTAPGSSIISTINRGLTTPTTAGHASYNGT
+SMATPHVAGLTALMLAQQPGITPAQVESTLKSTARSMPVACSAGCGAGLVDATRAVAALG
+GGSTTPTPTGVIVNGGFESGATGWTGTPSDFVGNTAGYARSGSNYGVLNGYGRSNTGTVE
+QRVTVPASGASLSYWLQVGSDETTTRSQYDTLAVQVVDGSQTTTVKSHSNLEKGTSYAQH
+TVDLSAYKGKTVTLRFRGVEDYSNSTVFRIDDVAVTAK
+>PROKKA_02471
+MTALTSPSARRRVGSLLAAAVLAGTALTAAPTLAAAERPAEPARTSPAAAAPLADPNADG
+YDSFIVTYRETAANSTAQGRAKAWGRAAREAGVSVKELRETALGSRVIATDEKLTQEESA
+AFMADLRASGAVEAVEPNVIMTRAALSPADPYYADQWGFTGVNGMRVPGAWDVSTGTGAI
+VGVIDTGQTDHADLNANTVPGYDFISDATTARDGGGRDADPRDEGDWYLAGECGQSRASN
+SSWHGSHVAGTVAAVANTQGVVGVAPGAKVQHARVLGKCGGTLADIADAIVWSSGGSVPG
+VPANPTPVDVINMSLGGQGTCGTTYQNAINAAVGRGVPVVVAAGNENQSAANARPANCQN
+TITVAATDVNGNRASYSNYGSAVDVAAPGSGIISTVNAGTTTPTAGAYAQYNGTSMATPH
+VAGTVALMLAEDATLTPAEVESSLKTNSRPIPGVCAEGCGAGLVDAAKTLASLRGGTTDP
+HPVTPVPGAEKLVNGGFESGLTGWTATGRVAASSTAGLSATGSLHAALNGKGGTSTATLT
+QKAVLPAGAAATLSYAVRVDSAETTTARQWDKLTVSVSDGATTTTLRTHSNLDKGRGYLA
+QAADLSAYAGKTVTISFSGTEDGSGATTFRIDDVSVKAG
+>PROKKA_00356
+MQSSPPRSTRRRIGALVAGAVLAGGTLTSSPALAAPSGDAPAAPAATPTAASPLAAAQVE
+DPNADGYDSFIVTYKETAATAHAKGRANAWGKAAKEAGVSVKELRETALGSRVIKADRKL
+DQAESAKFMADLKASGAVEAVEPDAILTATGLSPVDALYSQQWGFTGTHGMRVPGAWDRT
+TGSGVTVAVIDTGITSHPDLDRNVVPGYDFISDGRAARDGGGRDSNPRDEGDWYAAGECG
+TAGASDSSWHGTHVAGTVAAVADSQGVVGVAPNAKIQPIRVLGKCGGSLSDIADAVVWAA
+GGTVAGVPANPNPADVINMSLGGSGMCGTTYQNAINAAVSRGVPVVVAAGNENQPAANVR
+PANCRNTIVVAASTSQGARASFSNYGSVVDVTAPGANIISTVNNGATTPTTAGHAAYNGT
+SMATPHVAGLAALLLAEQPSLTPAQVESTLTSTARSMPVTCYAGCGAGLADATRAVSSLG
+GSS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000401.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000401.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bfce0934278c1a81f1f9e9f11038f0bf55a06cc5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000401.fa
@@ -0,0 +1,59 @@
+>PROKKA_00351
+MEQEGTQEPARFDPLIAEPPAVPTLIPVLRPAGAEDAAAVGDLALDPEDPGLLDLDPAES
+AHPAAVAVEPTEPLPPVVRPAAADPAPAPAPEPEPEESAEPDAETLPEPAADAPLTEPPL
+SEQVPTSVLAPAEADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENL
+PTQALVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDV
+ETSIIVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVH
+RLVEEIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALG
+MVSTWLVFWLKIQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLL
+PTARFVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLVGFEQLDLAEAGT
+LSYPPLLLLGLVVAAGMADAVVEQSRWPQILACGLVSGAGFGAYLAAQQVGVSDRLVPAV
+AAAAVGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFN
+AAVIVVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG
+>PROKKA_00067
+MEQEGTQEPARFDPLIAEPPAVPTLIPVLRPAGAEDAAAVGDLALDPEDPGLLDLDPAES
+AHPAAVAVEPTEPLPPVVRPAAADPAPAPAPEPEPEESAEPDAETLPEPAADAPLTEPPL
+SEQVPTSVLAPAEADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENL
+PTQALVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDV
+ETSIIVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVH
+RLVEEIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALG
+MVSTWLVFWLKIQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLL
+PTARFVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLVGFEQLDLAEAGT
+LSYPPLLLLGLVVAAGMADAVVEQSRWPQILACGLVSGVGFGAYLAAQQVGVSDRLVPAV
+AAAAVGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFN
+AAVIVVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRR
+>PROKKA_02610
+MLAPADADGALPAPDVLPEPDVTVPDPVVPVGPPEKRGRRRGRKAREVFVENLPTQALVL
+ADRLHSSPYGRRMRSTLQQRREAETHALEARTTLDFALKLGETMFSFGAASLDVETSIIV
+VTQAYGILETEVDLTNQSISLNYAPDSSRGESPYTLQRVVRSSSVNFEGLVAVHRLVEEI
+ADGRLDRAEAQRRLVEIRHQPKPFPPVFEILFAGVFVACFIPFIGGNWTGSLLGMISTWL
+VFWLKIQADRARFPEIFSTMFGAIVATVIALAAFALELPVNPAVVIAGGIMMLLPTARFV
+TAVQDAINGFPVTAAGRFLSALLVFTGVMAGIMVAVALGDLAGLEHLDLAEAGTLQHPPL
+LLLALVTAAGMSDAVVEQSRWPQILACGLVSGAGYGVFLAAQQLGIGDRLVPAAAATAVG
+FLGRLVAQRIAAPALVIVLPSMLFLLPGLMMFRSVYGFTVETGSTLLGLAGLFNAAVIVV
+AIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG
+>PROKKA_02469
+MGAEPRRGPAQGTGPLGPDRNPRKDPVRSVDPLAPQDGSPEDGGVPQGARRAGTRPDAAG
+SAPAEPAVHVALLPVLRPADARTPAGASDGDAPAGDGVDLAAAPAREPGPEDVLPPVLAP
+VAAPTVPVETLPTPEPAPAPEEEPTPAADAPLTAPPLSEPVPTSVLAPAEGDAPTAQEAA
+AAVPDVVVPDPLKQHGPEEPRGRRRRRRTREDHRAVFEEVLPTQAIVLVDRLQASPYGKR
+MRSTLRQRRDTEAAALEARTTLDFALKLGETMFGFGATSLDVETSIIVVTQAYGIHETEV
+DLTNQAISLNYAPDSSRGEVPYTLQRVVRTYSTNFEGLVAVHRLVEEISDGTLERAEAQR
+RLVEIRRRPKPYPPAVEILLAGVFVACFIPFIGGTWQGSLLGMVSTWFVFWLHTRTSVFL
+PEIYSVMIGAFLATLIALGAYALHVPVNPAIVVAGGIMMLLPTSRFVTAVQDAINGFPVT
+AAGRFISAMLVFIGIMAGIMVAVGLTDMLGIARLDLAATQSTAYPTTLLLALVVAATACD
+AVVERSGWRTLLASCAVTAAAFAAHTVVAGLGVSAQLLPAAAAAMVGFAGRIVALRVGAP
+PIVVVVPAILFLLPGFAVFRGLYEFTVESASTMAGLAGIVNALVIIVGIGAGAVFGDTLA
+RPVTERLSPARSTPGPEGHTR
+>PROKKA_00358
+MEQEGTQEPARFDPRIAEPPAVPTLIPVLRPAGAEDAAAVGDLAIDPEDPGLLDLDPAES
+AHPAAAAVAVEPTEPLPPVVRPAAADPEPEPEEPAEPEAETLPEPAADAPLTEPPLSEQV
+PTSVLAPADADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENLPTQA
+LVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDVETSI
+IVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVHRLVE
+EIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALGMVST
+WLVFWLKVQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLLPTAR
+FVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLLGFEQLDLAEAGTLSYP
+PLLLLGLVMAAGMADAVVEQSRWPQILACGLVSGAGFGAYLAAQQVGVSDRLVPAVAAAA
+VGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFNAAVI
+VVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000403.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000403.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aecb7d5cc683135e517d6df2702c9dedb930c7a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000403.fa
@@ -0,0 +1,15 @@
+>PROKKA_00353
+MSHPTPVSPDPAPDEGARARARRDELTDLERAVLDLEAATWRYGGAKDHAVRERLGLSPT
+AYYQVLNGLLDREAALAYRPLLVTRLLRKRGTRSRARRGPADPAPSTPASRQEN
+>PROKKA_00069
+MSHPTPVSPDPAPDEGARARARRDELTDLERAVLDLEAATWRYGGAKDHAVRERLGLPPT
+AYYQVLNGLLDREAALAYRPLLVTRLLRKRGTRSRARRGPADPAPSTPASRQEN
+>PROKKA_02608
+MPTSAPEPRRDALTPQERAVLDLEAATWRHGGAKDHAVRERLGLSPTAYYQVLNGLLDRE
+AALAYRPLLVARLLRKRGTRSRARRAPADPAPSTPASRQEN
+>PROKKA_02467
+MPDADPRPAAPADGPEPTPQDELTELEEAVLALEAQTWRHGGAKDHAIRERLQITPTAYY
+QVLNGLLERRAALARQPLLVSRLARSRGTRSRARRRPAPENSAPPASPQER
+>PROKKA_00360
+MSHPTPVSPDPAPDEGARARARRDELTDLERAVLDLEAATWRYGGAKDHAVRERLGLPPT
+AYYQVLNGLLDREAALAYRPLLVTRLLRKRGTRSRARRGPADPAPSTPASRQEN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000406.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000406.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7e5abe416ca4ed58fd7880ab73b6f894beaf244
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000406.fa
@@ -0,0 +1,15 @@
+>PROKKA_00357
+MSIVQIDVEDLRAKSGAVEGSIGRLQAEVSTMEANLRQLQDTWRGQAAANFQGVLTEWRA
+TQQRVEESLAGIRRAMDAAATQYQDAETANAAMFRF
+>PROKKA_00073
+MSIVQIDVEDLRAKSGAVEGSIGRLQAEVSTMEANLRQLQDTWRGQAAANFQGVLTEWRA
+TQQRVEESLAGIRRAMDAAATQYQDAETANAAMFRF
+>PROKKA_02604
+MSIVQIDVEDLRAKSGAVEGSIGRLQAEVGAMEAHLRQLQDTWRGQAAANFQGVLTEWRA
+TQQRVEESLAGIRRAMDAAAQQYQDAEAANAAMFRH
+>PROKKA_02463
+MTIVQIDVEDLRAKSGAVEGSIARLQTEVNTMEANLRQLEGTWRGQAAANFQGVLTEWRA
+TQARVEESLGGIRRAMDLAATQYSDTEAANAAMFRL
+>PROKKA_00364
+MSIVQIDVEDLRAKSGAVEGSIGRLQAEVSTMEANLRQLQDTWRGQAAANFQGVLTEWRA
+TQQRVEESLAGIRRAMDAAATQYQDAETANAAMFRF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000410.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000410.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be43902a91eedb9dff1294badbd34066ab390202
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000410.fa
@@ -0,0 +1,20 @@
+>PROKKA_00362
+MTTHDDAPRVDHRSPDAEPAEERTAVPPARGRAPRRDELLAADVDTARAGLAGLAAPDEV
+GEHVDVLVDDDRLLTHRFACRLPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGSLVAP
+PWVPYAERVNEEERERLKAVAEGRVPGAPAPDAEGDGTPEAAARG
+>PROKKA_00078
+MTTHDDAPRVDHRSPDAEPAPAEERAAVPPARRRAPRRDELLAAAVDAARAGLAGLAAPD
+EVGEHVDVLVDDDRLLTHRFACRMPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGSLV
+APPWVPYAERVNEEERERLKAVAEGRVPGAPAPEAEGDGTLGAAALG
+>PROKKA_02599
+MTDREDATPVEQEQAAPAAEEAVVKAPPARRRAPRRDDLLAAAVDEARAGLAGLAAPEEV
+GEHVDVLVDDDRLVTHRFESRLPGYAGWLWYATIARAPRSRLVTVCETGLVAGEGALVAP
+PWVPYAERVSEEERERLRAVAEGRVPGAAAPAGQPAPEGDGKG
+>PROKKA_02458
+MTEHSDTPGQTDTSGQTHTPEQAPAVAPAGPAADAAPAASARAPRRRAPKRDELLAAAVD
+EARAALTELAEEGQVGPHLGVTVDDDRLMTHRFAAEVPGYTGWVWYSTIARAPRAKKVTV
+CETGLEAGEGAVVAPAWVPYADRVSAEERERLAAVAEGRVPDAG
+>PROKKA_00369
+MTTHDDAPRVDHRSPDAEPAPAEERAAVPPARRRAPRRDELLAAAVDAARAGLAGLAAPD
+EVGEHVDVLVDDDRLLTHRFACRMPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGALV
+APPWVPYAERVNEEERERLKAVAEGRVPGAPAPETAPDDRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000411.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000411.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f1dc5e7377db0166ee1bc0cec27afef62d864f5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000411.fa
@@ -0,0 +1,40 @@
+>PROKKA_00363
+MTSPAEITIPQDLLPADGRFGAGPSKVRPEQLSALQDAAGLLGTSHRQKPVKDLVARVRS
+GVAELFSAPEGYEVILGVGGSTAFWDAAAFSLVRERAQHLSFGEFGSKFAKATDQAPFLA
+PSDIRTSEPGTRPEPEAVAGVDVYAWPHNETSTGVVAPVVRPAGIDEDALVVVDATSAAG
+GLPVDVSEADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPAFLDLATAVE
+NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLDAMTARTADSSSRVYAWAEASSFATPYV
+ARPEDRSAVICTVDFSDDVDAAAVAQVLRANGVVDVEPYRKLGRNQLRIATFAATEPEDV
+AALLRCIDHVVERLG
+>PROKKA_00079
+MTSPAEITIPQDLLPADGRFGAGPSKVRPEQLSALQDAAGLLGTSHRQKPVKDLVARVRS
+GVAELFSAPEGYEVILGVGGSTAFWDAAAFSLVRERAQHLSFGEFGSKFAKATDQAPFLA
+PSDIRTSEPGTRPEPEAVAGVDVYAWPHNETSTGVMAPVVRPAGIDEDALVVVDATSAAG
+GLPVDVSEADVYYFAPQKNFASDGGLWLALFSPRALARVTEIKESGRWIPAFLDLATAVD
+NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLDAMTARTADSSSRVYAWAEASSFATPFV
+ARPEDRSAVICTVDFSDDVDAAAVAQVLRANGVVDVEPYRKLGRNQLRIATFAAIEPEDV
+AALLRCIDHVVERLA
+>PROKKA_02598
+MAAPAEITLPQDLLPADGRFGAGPSKVRSEQLQALQDAAGLLGTSHRQKPVKDLVASVRA
+GVAELFSAPEDYEVILGVGGSTAFWDAAAFGLVRERAQHLSFGEFGSKFAKATDKAPFLG
+ASDIRTAEPGSRPEPEAVAGVDVYAWPHNETSTGVMAPVARPEGIDEDALVVIDATSAAG
+GLDVDVSQADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPDFLDLSTAVD
+NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLAAMAARTADSSSRVYAWAEASSYATPYV
+ARPEDRSGVICTVDFSDDVDAAAVAKALRANGVVDVEPYRKLGRNQLRIATFAAIDPEDV
+SALLRCIDHVVEQLG
+>PROKKA_02457
+MTDPTAITIPPEMLPQDGRFGAGPSKVRPEQLQALQEAAGLLGTSHRQKPVKDLVASVRA
+GVAELFSVPEGYEVVLGVGGSTAFWDAAAFSLVRSKAQHLSFGEFGSKFARATDNAPFLE
+ASDIRSSEPGTRPQPEAVPGVDVYAWPHNETSTGVSAPVVRPEGIDDDALVVIDATSAAG
+GLDVDVSQADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPEFLDLSIAVD
+NCLKDQTYNTPALATLVMLDAQLRWMNANGGLGFTTGRTADSASRVYAWAEASEHATPYV
+ADPAERSNVICTVDFDDAVDAAAVAQALRANGVVDVEPYRKLGRNQLRIATFAAIDPEDV
+TALLACIDHVVARLG
+>PROKKA_00370
+MTSPAEITIPQDLLPADGRFGAGPSKVRPEQLSALQDAAGLLGTSHRQKPVKDLVASVRS
+GVAELFSAPEGYEVILGVGGSTAFWDAAAFSLVRERAQHLSFGEFGSKFAKATDQAPFLA
+PSDIRTSEPGTRPEPEAVAGVDVYAWPHNETSTGVMAPVVRPAGIDEDALVVVDATSAAG
+GLPVDVSEADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPAFLDLATAVE
+NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLDAMTARTADSSSRVYAWAEASSFATPFV
+ARSEDRSAVVCTVDFSDDVDAAAVAQALRANGVVDVEPYRKLGRNQLRIATFAAIEPEDV
+AALLRCIDHVVERLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000412.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000412.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f28d1253770bc668b1965ab6f0e78eaa5c023ad4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000412.fa
@@ -0,0 +1,23 @@
+>PROKKA_00364
+MTDLIDTTEMYLRTILELEEEGIPPLRARIVERLEHSGPTVSQTVARMERDGLVHVGMDR
+RLELTVAGRERAVSVLRKHRLAERLLADVIGLEWELVHEEACRWEHVMSDQVERRLLTLL
+ENPTETPYGTPIPPRPEQASAEDWSRDMGLAGTRLSEEAATAGRFRVRGLAEGVQTDPDL
+LAQLAGAGVTPGRVVRAEAARDAGYIRVEGEAEDGAAADGGALELAAATAAHVWVERLDG
+>PROKKA_00080
+MTDLIDTTEMYLRTILELEEEGIPPLRARIVERLEHSGPTVSQTVARMERDGLVHVGTDR
+RLELTVAGRERAVSVLRKHRLAERLLADVIGLEWELVHEEACRWEHVMSDQVERRLLTLL
+ENPTETPYGTPIPPRPEQASAEDWSREMGLAGTRLSEEAATAGRFRVRGLAEGVQTDPEL
+LAQLAGAGVTPGRVVRAQAARDAGYIRVEGEAEDGAAADGGALELAEATAAHVWVERLDG
+>PROKKA_02597
+MGLAGTRLSEEAATPGRFRVRGLAEGVQTDPELLAQLAAAGVTPGRTVTAQAAIDPGYVR
+VEGEAADGAPESGALELAVETAAHVWVERLDA
+>PROKKA_02456
+MTDLIDTTEMYLRTILELEEEGTVPLRARIVERLEHSGPTVSQTVARMERDGLVHVGSDR
+RLLLTDEGRERAVAVLRKHRLAERLLSDVIGLDWAYVHDEACRWEHVMSDRVEQRLLEVL
+ENPTATPYGTPIPPRPEAQSAGEWSRDLGLAGEPLATAAATPGRFRVGSLSEGVQADPEL
+LAELQDAGVLPGGVLEAQPALEAGYVRVQGEGSAEALELSAGTAAHVWVQRL
+>PROKKA_00371
+MTDLIDTTEMYLRTILELEEEGIPPLRARIVERLEHSGPTVSQTVARMERDGLVHVGADR
+RLELTVAGRERAVSVLRKHRLAERLLADVIGLEWELVHEEACRWEHVMSDQVERRLLTLL
+ENPTETPYGTPIPPRPEQASAEDWSRDMGLAGARLSEEAATAGRFRVRGLAEGVQTDPEL
+LAQLAGAGVTPGRVVRAEAARDAGYIRVEGEAEDGAAADGGALELAEATAAHVWVERLDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000414.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000414.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a3c9fe31504564ab55b79d5651e0394c8a8a9c81
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000414.fa
@@ -0,0 +1,26 @@
+>PROKKA_00368
+MSQKSRKSRPRPSRPAARPVAESPRSRPTLRDVHVREDLAAAAEREGSPAIPVSALIVTT
+LLVGAYLHLLVLQQMTQLSGGLAMPDSLLFYGQDHIRALSAVMDEDARGQLNWVHKTAGV
+IFPIAVALTVTAVGAWRLRPVGAKWAVFGLGVLFAVVDICENIAIEQAIAAGGPGTGLAA
+ALTLTRWVLLALLALAVAVMLWAGRRRRRGPAARED
+>PROKKA_00084
+MSQKSRKSRPRPSRPAARPVAESPRSRPTLRDVNVREDLAAAAEREGSPAIPVSALIVTT
+LLVGAYLHLLVLQQMTQLSGGLAMPDSLLFYGQDHIRALSAVMDEDARGQLNWVHKTAGV
+IFPIAVALTVTAVGAWRLRPVGAKWAVFGLGVLFAVVDICENIAIEQAIAAGGPGTGLAA
+ALTLTRWVLLALLALAVAVMLWAGRRRRGRATRAA
+>PROKKA_02593
+MRGRGPALLDPAPGRQTGTGLGGWSAEVPPLSQKPRKPRKSRPSRASQSGARSGSSAARA
+AGGAERARPTLRDLNIREDLAAAGRQEGSPAIPVSALIVTTLLVGAYLHLLVLQQMTQLT
+GGLAMPDSMLFYGQDHVRALSAVMDDAARGQLNWVHKTAGVIFPIAVALTLAAVGAWRLR
+PAAAKWGALGVGVLFAVVDIAENIAIEQAIAAGGPGTGLAAALTLARWVLLALIALAIVV
+MLWAGRRRREPAARRR
+>PROKKA_02452
+MSKKQKKSRPARTGSSAAPTAEPRRAGLHDVSPRADLADAAQQEGSPAMLITALIGTTLF
+IGAYFHLLVLQQMTQLTGGLAMPDSMLFYGQDHVAALSAVMDDAARGQLNWVHKTAGVIF
+AVAVALTVAAVGAWRLKPVAAKWGALALGVLFAVVDIWEGLAIEAAIAAGGPGTGLAATL
+TAIRWVLLAVITVAVVVMLWAGRRRRPRT
+>PROKKA_00375
+MSQKSRKSRPRPSRPAARPVAESPRSRPTLRDVNVREDLAAAAEREGSPAIPVSALIVTT
+LLVGAYLHLLVLQQMTQLSGGLAMPDSLLFYGQDHIRALSAVMDEDARGQLNWVHKTAGV
+IFPIAVALTVTAVGAWRLRPVGAKWAVFGLGVLFAVVDICENIAIEQAIAAGGPGTGLAA
+ALTLTRWVLLALLALAVAVMLWAGRRRRGRATRAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000415.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000415.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df439d43e10051118fbf2cca4e7b4bd0d441c633
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000415.fa
@@ -0,0 +1,79 @@
+>PROKKA_00370
+MADLFSALGRTHLNLDRTRRPADPETALPGLVPPAVTRAAADPEAWGVDARPAAPSHTPE
+SLVAGLNPQQAAAVTHTGAPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEILAITFTN
+KAAAEMRERVAGLIGPTAQRMWISTFHSSAVRLLRNEAANIGLKSTFTIYDSADSLRLVT
+TVAKQHELDPKRFAPKALLNRISSLKNELVEADDYAATVAEGDPWGRAVAAVYRDYTARL
+RQANALDFDDLIGVTVHMFEAFPRVLDNYRRRFRHVLVDEYQDTNHAQYRLIRLLAGPAG
+DPEGVETPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAVTIKLEQNYRSTQTILD
+AANAVIERNPDRRPKRLWTAEGEGPAIVGYAAENESAEAEWIATTIDRLQDEDGIRPADV
+AVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRI
+LNEPKRGIGDRAEGAVAAWAERNRSTFSAALRDAENAPGMAARSLKAVRGFVQMMDDLGQ
+VAESAGPATVLEAVLEQSGMLAALRESEDVQDESRADNLGELVAVVRSFETTHPDGTLSD
+FLEQVALVADADQLPTAPDVEGEALAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPH
+ARSMTDEKELAEERRLAYVGLTRARRRLFLTRAEARSLWGQHQFNPPSQFLGEIPETLID
+WEREGTTRSAGSLSLTGAGTSRYAGRFGGGRPAWRSRDDDGARPQRLTRGDEPADLTVPS
+AVVRGKAPSRVQPQKEIVALSPGDRVSHATFGEGRVDAVAGAGDKTVATVTFDATGAQKR
+LLLRYAPLTKVEG
+>PROKKA_00086
+MADLFSALGRTPLNLDRTRRPADPETALPGLVPPAVTRAAADPEAWGEDARPAAPAHTPE
+SLVAGLNPQQAAAVTHTGAPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEILAITFTN
+KAAAEMRERVAGLIGPTAQRMWISTFHSSAVRLLRNEAANIGLKSTFTIYDSADSLRLVT
+TVAKQHELDPKRFAPKALLNRISSLKNELVEADDYAATVAEGDPWGRAVAAVYRDYTARL
+RQANALDFDDLIGMTVHMFEAFPRVLDNYRRRFRHVLVDEYQDTNHAQYRLIRLLSGPAD
+DPEGVETPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAATIKLEQNYRSTQTILD
+AANAVIERNPDRRPKRLWTAEGEGPAIVGYAAENESAEAEWIATTIDRLQDEDGIRPADV
+AVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRI
+LNEPKRGIGDRAEGAVAAWAERNRSTFSAALRDAENAPGMAARSLKAVRGFVQMMDDLGQ
+VAESAGPATVLEAVLEQSGMLAALRESEDLQDESRADNLGELVAVVRSFETTHPDGTLSD
+FLEQVALVADADQLPTAPDVEGEALAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPH
+ARSMTDEKELAEERRLAYVGLTRARRRLFLTRAEARSLWGQHQFNPPSQFLGEIPEALID
+WEREGTTRSAGSLSLTGAGTSRYAGRFGGGRPAWRSRDDDGARPQRLTRGDEPADLTVPS
+AVVRGKAPSRVQPQKEIVALSPGDRVSHATFGEGRVDAVAGAGDKTVATVTFDATGAQKR
+LLLRYAPLTKVEG
+>PROKKA_02592
+MPTAVTRAAADPEAWGGDPESWGRDAAPAHTPDSLVAGLNPQQSAAVTHTGAPLLIVAGA
+GSGKTRVLTHRIAWLLATGRARPHEILAITFTNKAAAEMRERVSGLIGPTAQRMWISTFH
+SSAVRLLRNEAANIGLKSTFTIYDSADSLRLVTTIAKLHELDPKRFAPKALLNRISSLKN
+ELVEADDYASTVAEGDPWGRAVAAVYRDYTARLRQANALDFDDLIGMTVHMFEAFPRVLD
+NYRRRFRHVLVDEYQDTNHAQYRLIRLLAGPAGEPEGVDTPGGELTVVGDSDQSIYAFRG
+ADIRNIVEFEQDFTDAVTIKLEQNYRSTQTILDAANAVISNNPDRRKKDLWTAEGAGAAI
+VGYAAENESAEAEWIASTIDRLQDEDGIRPADVAVFYRTNAQSRALEERLVTRGIPYRVI
+GGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRILNEPKRGIGDRAEGAVAAWAERNRTTF
+SAALRDAEHAPGMATRSLKAVNGFVQMMDDLAQVAESAGPATVLEAVLEQSGMLAALRES
+EDLQDESRADNLGELVAVVRSFEKTTPDGTLSDFLEQVALVADADQLPTAPDVEGESLAE
+AQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPHARSMTDEKELAEERRLAYVGLTRARRR
+LFLTRAEARSLWGQHQFNPPSQFLGEIPEALIDWEREGAVRSAGSLSLTGAGTSRYAGRF
+GSGGGRPAWRSRDDDGGARPQRLTRGDEPTDLTVPSAVVRGRAPSRVQPQKEIVALSPGD
+RVSHATFGQGRVDAVAGAGDKTVATVTFEDSGAQKRLLLRYAPLTKVED
+>PROKKA_02451
+MADLFSSLGRDPLFAPRTRPADPETALPGLVPTAVTRAADPEAGAWGAGRDAGAPSAGPL
+TPEGLVEGLNPQQAAAVQHTGSPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEVLAIT
+FTNKAAAEMRERIAGLIGDTARRMWISTFHSSCVRILRNEAANIGLKSTFTIYDSADSLR
+LVTQIAKVQDLDPKRFAPKALLSRISALKNELVDPEDHASRVAEGDPWGRAVAAVYTEYT
+ARLRQANALDFDDLIGMTVHMFEAFPRVLDGYRRRFRHVLVDEYQDTNHAQYRLIRLLSG
+PAGEPEGVDTPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAATIKLEQNYRSTQT
+ILDAANAVIAHNPDRRKKDLWTAEGEGPRIIGYAAENESAEAEWIASTIDRLQDEEGIRP
+ADVAVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNV
+RRILNEPKRGIGDRAEGAVAAWAERNRVPFFTALRDAENAPGMATRSLKAVQGFVQLMDD
+LAQVAESAGPATVLEAVLEQSGMLAALRESEDLQDESRADNLGELVAVVRAFEKGTPGGT
+LTDFLEQVALVADADQLPAAPDVEGEELAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGV
+FPHSRSLTDEKEMAEERRLAYVGITRARRRLHLSRAEARSLWGQHQFNPPSQFLGEIPDE
+LIEWERAGTDRSFGGLTSLAGAGTSRYANRFSGGGSGSARRGSMTGAWGDRAAGGVGGGL
+ASNRPQRLTRGEEAADLTVPSSVVRGRAPSRVQPQKEVVALSAGDRVEHATFGAGRVDAV
+AGTGDKTVATVTFDATGAQKRLLLRYAPLTRVEG
+>PROKKA_00377
+MADLFSALGRTPLNLDRTRRPADPETALPGLVPPAVTRAAADPEAWGEDARPAAPAHTPE
+SLVAGLNPQQAAAVTHTGAPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEILAITFTN
+KAAAEMRERVAGLIGPTAQRMWISTFHSSAVRLLRNEAANIGLKSTFTIYDSADSLRLVT
+TVAKQHELDPKRFAPKALLNRISSLKNELVEADDYAATVAEGDPWGRAVAAVYRDYTARL
+RQANALDFDDLIGMTVHMFEAFPRVLDNYRRRFRHVLVDEYQDTNHAQYRLIRLLAGPAG
+DPEGVETPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAVTIKLEQNYRSTQTILD
+AANAVIERNPDRRPKRLWTAEGEGPAIVGYAAENESAEAEWIATTIDRLQDEDGIRPADV
+AVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRI
+LNEPKRGIGDRAEGAIAAWAERNRSTFSAALRDAENAPGMAARSLKAVRGFVQMMDDLGQ
+VAESAGPATVLEAVLEQSGMLAALRESEDLQDESRADNLGELVAVVRSFETSHPDGTLSD
+FLEQVALVADADQLPTAPDVEGEALAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPH
+ARSMTDEKELAEERRLAYVGLTRARRRLFLTRAEARSLWGQHQFNPPSQFLGEIPEALID
+WEREGTTRSAGSLSLTGAGTSRYAGRFGGGRPAWRSRDDDGARPQRLTRGDEPADLTVPS
+GVVRGKAPSRVQPQKEIVALSPGDRVSHATFGEGRVDAVAGAGDKTVATVTFDATGAQKR
+LLLRYAPLTKVEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000416.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000416.fa
new file mode 100644
index 0000000000000000000000000000000000000000..65b17b238ed69b0159f36545a60d715d84716ad1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000416.fa
@@ -0,0 +1,40 @@
+>PROKKA_00371
+MDLYEYQARDLFEAHGVPVLAGIVAQTPDEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVHQVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSALTGIDAETAQKIVTEAGFPEELRADVAEVIQKLWEVF
+EKEDATLVEVNPLVKTGDGTILALDGKVSLDDNAQFRHEDHAALVDERTEDPLEAKAKAN
+GLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEQHGGVKPANFLDIGGGANAEVMANGLD
+VILGDEQVKSVFVNVFGGITACDQVANGIVKALEILGDTATKPLVVRLDGNAVEEGRRIL
+QEANHPLVTLAATMDEGADKAAELAHSAN
+>PROKKA_00087
+MDLYEYQARDLFEAHGVPVLAGIVAQTPDEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVHQVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSPLTGIDAETAQKIVTEAGFPEELRADVAEVIQKLWEVF
+EKEDATLVEVNPLVKTGDGTILALDGKVSLDDNAAFRHEGHAALVDERTEDPLEAKAKAN
+GLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEKHGGVKPANFLDIGGGANAEVMANGLD
+VILGDEQVKSVFVNVFGGITACDQVANGIVKALEILGDTATKPLVVRLDGNAVEEGRRIL
+QEANHPLVTLAATMDEGADKAAELAHSAN
+>PROKKA_02591
+MDLYEYQARDLFEAHGVPVLAGIVAQTPEEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVHQVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSPLTGIDAETAQKIVAEAGFPEELRADVADVIQKLWVVF
+EKEDATLVEVNPLVKTGDGKILALDGKVSLDDNAEFRHEGHAALVDERTEDPLEAKAKAN
+DLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEQHGGVKPANFLDIGGGANAEVMANGLD
+VILGDEQVKSVFVNVFGGITACDAVANGIVKALEILGDAATKPLVVRLDGNAVEEGRRIL
+QEANHPLVTLAATMDEGADKAAELAHSAN
+>PROKKA_02450
+MDLYEYQARDLFEKHGVPVLQGIVAETPEEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVNKVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSALTGLDQATADTIVAEAGFPEELRADVAAVIVKLGEVF
+KNEDATLVEVNPLVKTGDGTILALDGKVSLDDNAEFRQADHAGLVDKTTEDPLEAKAKAN
+DLNYVKLDGQVGIIGNGAGLVMSTLDVVAYAGENHGGVKPANFLDIGGGANAEVMAAGLD
+VILGDEQVKSVFVNVFGGITACDAVANGIVKALEILGDSATKPLVVRLDGNAVEEGRRIL
+QEADHPLVTLAATMDEGADKATELAHSAN
+>PROKKA_00378
+MDLYEYQARDLFEAHGVPVLAGIVAQTPDEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVHRVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSALTGIDAETAQKIVAEAGFPEELRADVAEVIQKLWEVF
+EKEDATLVEVNPLVKTGDGTILALDGKVSLDDNAAFRHEGHAALVDERTEDPLEAKAKAN
+GLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEKHGGVKPANFLDIGGGANAEVMANGLD
+VILGDEQVKSVFVNVFGGITACDAVANGIVKALEILGDTATKPLVVRLDGNAVEEGRRIL
+QEANHPLVTLAATMDEGADKAAELAHSAN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000417.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000417.fa
new file mode 100644
index 0000000000000000000000000000000000000000..42a80e8a59d97339e48863df444ade4cd18ed117
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000417.fa
@@ -0,0 +1,35 @@
+>PROKKA_00372
+MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL
+PVFGTVKEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDTAEFFAL
+SQSKTGEDGKPKTRIIGPNCPGVITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE
+LRDFGFSTAIGIGGDPVIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV
+TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE
+ILQAQA
+>PROKKA_00088
+MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL
+PVFGTVKEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDTAKFFAL
+SQSKTGEDGKPKTRIIGPNCPGIITPGEALAGITPATITGTGPIGLVSKSGTLTYQMMYE
+LRDFGFSTAIGIGGDPIIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV
+TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE
+ILEG
+>PROKKA_02590
+MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL
+PVFGSVTEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDSAKFFAL
+SQSKTGEDGKPKTRIIGPNCPGVITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE
+LRDFGFSTAIGIGGDPVIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV
+TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE
+ILQAQA
+>PROKKA_02449
+MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDEDGNAVEL
+PVFGSVAEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDSAEFFAL
+SQSKTGEDGKPKTRIIGPNCPGIITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE
+LKDFGFSTAIGIGGDPVIGTTHIDALEAFEADPETKAIVMIGEIGGDAEERAAEFIKANV
+TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETADLMRE
+IMKGL
+>PROKKA_00379
+MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL
+PVFGTVKEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDSAEFFAL
+SQSKTGEDGKPKTRIIGPNCPGIITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE
+LRDFGFSTAIGIGGDPVIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV
+TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE
+ILQAQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000418.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000418.fa
new file mode 100644
index 0000000000000000000000000000000000000000..43964461de83cc13206b48a3572c7acdc4e2f95a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000418.fa
@@ -0,0 +1,25 @@
+>PROKKA_00373
+MNDIRIVLADDEKLLRTALATLLEIEGGIRVEEVAADGHEAVEAVRRIDPDMLVTDMEMP
+GLDGVAAVATLRETHPDLPVVMLTRHARPGVLRRALKAGVTGFVTKSAEPGEIADVIRRV
+NSGQRWIDPDTTARAISDDCPLTDRELDALRATGEGYSVARIAQQLHLAEGTVRNYLSSA
+MQKTQTSTRHDAARFARRHEWL
+>PROKKA_01002
+MIRVLVADDEALIRGAVEALLALEEDLDVLPGVGTGDDAVAAARALVPDVCLLDLEMPGL
+DGVEAAREILRSVPTRVVIFTRHARPGVLRRALAERVSGFVPKSTPAEALADVLRQVAAG
+RRYVDPEIAASALSGERSPLTDRELDVLRAGRTAARVEDIAERLHLAPGTVRNHLSHAMG
+KLGVRTRHEAAERAWEEGWI
+>PROKKA_02589
+MNDIRIVLADDEKLLRTALATLLEMEGGIRVEEVAADGNEAVEAVRRIDPDLLVTDMEMP
+GLDGVAAVETLRETHPDLPVVMLTRHARPGVLRRALKAGVAGFVTKSAEPEEIADVIRRV
+NSGQRWIDPDTTARAISDDCPLTDRELDALRATGEGYSVARIAQQLHLAEGTVRNYLSSA
+MQKTQTSTRHDAARFARRHEWL
+>PROKKA_01177
+MRESADPAPSPASPPAAGLGPGAPLRLLLADDQALVRGALAALLDTEPDLTVVAQAASGD
+EVADAVETHDVDVALLDIEMPGVDGLEALRRIRDRGLGCAVLMVTTFGRPGYLERALAAG
+ARGFVVKDTPAEQLADAVRAVARGERVVDPSLAVDTLAAGPSPLTPREVDVLREALTGAS
+VRAIAGRLHLSAGTVRNHLSAAIGKTATSTRGEAATVARDRGWL
+>PROKKA_00380
+MNDIRIVLADDEKLLRTALATLLEIEGGIRVEEVAADGHEAVEAVRRIDPDMLVTDMEMP
+GLDGVAAVATLRETHPDLPVVMLTRHARPGVLRRALKAGVTGFVTKSAEPGEIADVIRRV
+NSGQRWIDPDTTARAISDDCPLTDRELDALRATGEGYSVARIAQQLHLAEGTVRNYLSSA
+MQKTQTSTRHDAARFARRHEWL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000425.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000425.fa
new file mode 100644
index 0000000000000000000000000000000000000000..31b92cf3072ed70446a120bb44eb4e8d4c69985e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000425.fa
@@ -0,0 +1,50 @@
+>PROKKA_00383
+MTLNLTIVAVYLVGMLAFGWWGKTRAASSEDYLVAGRRLGPVLFTGTMAAVVLGGAATVG
+GVGLGYEFGLSGAWLVAAIGVGVLILSVAFAPILARLKIYTVSQMLRLRYGRGGASHASS
+FVMLAYTLMLAATSTGAYASLFVVLFGWDRWLSVLVGGGIVLAYSVLGGMWSITLADMAQ
+FLIMTIGLFALMLPLSLANAGGWSAMQERLGAEFFSWDGIGVQSIVTYFVIYTLGLLIGQ
+DVWQRVFTARSPRVAQIGGATAGLYCIVYGVAGAVIGMAARTVTADIAATDDVFAWVAQN
+LLPVGVGGVALAAAVAAMMSTASGAIIAASTVMRTDILPILRGEATAAEDGAVAEDAATE
+TAAELASNRGWVLLLGAVVLGLAIVVPDVVAALTIAYDILVGGLFVAIVGGLVWKRGTGT
+AALWSMVVGTVGTLGTMGWLELNAAEPFEGVFANEPIYVGLAASAVVYVLLSLMTRPTDP
+AVLEAWRVRSRHGVDPAVRAQV
+>PROKKA_00098
+MTDTTVPLIILALYIVFVVGVGIYARRKATSDSSRDYLTGSGDVGVWVNGFAIFAAFATG
+GTMLGNIGLSYVGGWGYITAYNAGVALGYVITTFFLAKTLKNMNVATVPEFIRKRFHGRT
+LNILVPIILMATLVAYVVAQMKVGGLLGEQLFGFPYEWSVIVVGLVYIFYTFYGGMRAVT
+LTDFVQGLLMISVVVICGGIAFGQHGGPANLYEMAVAIRPKWEGTEQFPLISYIGAFIIW
+ATVNAVLPHTVMRIFAAKNERQGRASLAIGLGLYVLTAIATTIFVVAAVIIVQGEEELAS
+ADSTFLIFLAEQTPSWVAGLAFAGIFAAVMSSVSAMLLALGGAFAYDLVAELRPSMSDRS
+KRRLTSISVLGFGILTLVLSLNPPELLTLLYTAAMGMLASGLFFPTLLGIWWKRMNSSGA
+LAGLIVGVGSYLFLLWGTGMPSLSQVTVSIPLSLLACIVVSLMTKPPTDAEMERITIAHE
+REFLIQGQDDLIETAERH
+>PROKKA_00107
+MTLNLTIVAVYLVGMLAFGWWGKTRAASSEDYLVAGRRLGPVLFTGTMAAVVLGGAATVG
+GVGLGYEFGLSGAWLVAAIGVGVLILSVAFAPILARLKIYTVSQMLRLRYGRGGASHASS
+FVMLAYTLMLAATSTGAYASIFVVLFGWDRWLSVLVGGGIVLAYSVLGGMWSITLADMAQ
+FLIMTIGLFALMLPLSLANAGGWSALKERLGAEFFSWDGIGVQSIVTYFVIYTLGLLIGQ
+DVWQRVFTARSPRVAQIGGATAGLYCIVYGVAGAVIGMAARTVTADIATTDDVFAWVAQN
+LLPVGVGGVALAAAVAAMMSTASGAIIAASTVMRTDILPIFRGEATASEDGATAEDEIPE
+TAAELASNRGWVLLLGAVVLGLAIVVPNVVAALTIAYDILVGGLFVAIVGGLVWQRGTGT
+AALWSMVVGTVGTLGTMGWLELNAAEPFEGVFANEPIYVGLAASAVVYVLLSLMTRPTDP
+AVLEAWRVRSRHGVDPAVRAQV
+>PROKKA_02572
+MTLNLTIVAVYLVGMLAFGWWGKTRAASSEDYLVAGRRLGPVLFTGTMAAVVLGGAATVG
+GVGLGYEFGLSGAWLVAAIGVGVLILSVAFAPILARLKIYTVSQMLRLRYGRGGASHASS
+FVMLAYTLMLAATSTGAYASIFVVLFGWDRWLSVLVGGGIVLAYSVLGGMWSITLADMAQ
+FLIMTIGLFALMLPLSLANAGGWSAMQERLGAEFFSWDGIGVQSIVTYFVIYTLGLLVGQ
+DVWQRVFTARSPRVAQVGGATAGLYCIVYGVAGALIGMAARTVTADIATTDDVFAWVAQN
+LLPVGVGGVALAAAVAAMMSTASGAIIAASTVMRTDILPILRGEATAAEDGATAEDEAPE
+TAAELASNRGWVLLLGAVVLGLAIVVPDVVAALTIAYDILVGGLFVAIVGGLVWKRGTGT
+AALWSMVVGTLGTLGTMGWLELNAAEPFEGVFANEPIYVGLAASAVVYVLLSLMTRPTDP
+AVLEAWRVRSRHGVDAAARERL
+>PROKKA_00389
+MTLNLTIVAVYLVGMLAFGWWGKTRAASSEDYLVAGRRLGPVLFTGTMAAVVLGGAATVG
+GVGLGYEFGLSGAWLVAAIGVGVLILSVAFAPILARLKIYTVSQMLRLRYGRGGASHASS
+FVMLAYTLMLAATSTGAYASIFVVLFGWDRWLSVLVGGGIVLAYSVLGGMWSITLADMAQ
+FLIMTVGLFALMLPLSLANAGGWGAMQERLGAEFFSWDGIGVQSIVTYSVVYTLGLLIGQ
+DVWQRVFTARSPRVAQIGGATAGLYCIIYGVAGAVIGMAARTVTADIATQDDVFAWVAQN
+LLPVGVGGVALAAAVAAMMSTASGAIIAASTVMRTDILPILRGEATASEDGATAGDEAPE
+TAAELASNRGWVLLLGAVVLGLAIVVPDVVAALTIAYDILVGGLFVAIVGGLVWKRGTGT
+AALWSMVVGTVGTLGTMGWLELNAAEPFEGVFANEPIYVGLAASAVVYVLLSLMTPPTDP
+AVLEAWRVRSRHGVDAVAGASLTRNPGACDPPMPARWSGQTMRRRAILPQAPPGP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000428.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000428.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37839c6d19ffd83f7cdb04020f22ef38d8c75150
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000428.fa
@@ -0,0 +1,20 @@
+>PROKKA_00388
+MTQQHHDTDDAPSMQRPDPVAEPGDHLMFEHPDGEAVLVLDEDQVWRLLGRVGHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGPHPERNESQTD
+>PROKKA_00112
+MTQQHHDTDDAPSMQRPDPVAEPGDHLMFEHPDGEAVLVLDEDQVWRLLRRVRHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGPHPERNESQTD
+>PROKKA_02568
+MTPQHHDTADAPSMQRPDPVAEPGDHLMFEHPDGEPVLVLDEDQVWRLLRRVRHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGTHPERNESQTD
+>PROKKA_02439
+MTEHTTPSMQRPDPAVGPGSMFPHPEGEPVLKLTDEQIWKLMRGVRHARLGLAVGGEPDI
+VPVNVRAVDGVVWFRTAPGSKLAELTVNPRVVVQADGILSDQAWSVLLHGTARRADTAEE
+IAEAESMGIRPWVPTIKDFYVKVEVDSATGRHFLLGEQPERDGAEPTD
+>PROKKA_00394
+MTQQHHDTDDAPSMQRPDPVAEPGDHLMFEHPDGEAVLVLDEDQVWRLLGRVGHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGPHPERNESQTD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000432.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000432.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb87e6d03a52ac8e52799489a344c2db5cc961ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000432.fa
@@ -0,0 +1,37 @@
+>PROKKA_00393
+MTLLSDHSRALLPGRGPLLCAADPHDGAARRRLERAWTRGVLVRLCPRVYISVSDWAALR
+PWDRTVVSAVALSIARPETVFTGLTAARLHGLGPAVEPPALELRAPSPGHHGAGPLTRRP
+FAPSLMAHDRRPPGLPRRRPRWGLPEADPAAPQRVEAVLSDGQSLGTVLADPLPTVLLVL
+GAATPFRDAVATLDALVRARPEEAARWARQAESRLGSAAALRRFERAWHFADARAESAGE
+SYSRAIVHELGFVPPTALQHRHRDANGREVARTDFWWEQVRVYGEFDGLGKYDLSFFDGD
+DTARRASIRREKEREVALQLVTRAGAHWTWGDLLRPDRLARILTAAGVPRSV
+>PROKKA_00117
+MTPLSDHSRALLPGRGPLLSAADPHDGAARRRLERAWTRGVLVRLSPRVYISVSDWAALR
+PWDRAVVSAVALSIARPATVFTGLTAARLHGLGPAVEPPALELRAPSPGHHGCGPLTRRP
+LAPSLVAHDRRLPVPPRRRPRWGLPEAAPTGPQPVEAVLSDGQSLGTVLADPLPTVLLVL
+GAATPFRDAVAPLDALVRAWPEEAARWARQAESRLGSAAALRRFERAWHFADARAESAGE
+SYSRAIIHELGFVPPTALQHRHRDANGRGVARTDFWWEQVRVYGEFDGLGKYDLSFFDGD
+DTARRASIRREKEREVALQLVTRAGAHWTWGDLLRPDRLARILTAAGVPRSV
+>PROKKA_00172
+MDDAPDPRLAPLRHDGHLLPGHGPLLRAAPGAPTRARKALARLWAQGVLVRLGAGLYVPL
+AHWCALAPWDRYTLACAGYALLHPAARFTGTTAAHLHGLPLAQTPPEIRLRSPAPGHRAR
+RPLAASAFSDLADARGRRLPAPPAVRWTWNGVQAPADDGGELRRRRLASGGPEGEAPPPG
+PLPPVTVEAALSDGTLLGPVTVDALPTVQLALGSGPVFREAVVPLDGLRRRLPGPSAAWA
+ERHADRLPTRAARERFERAWGFSDPRAESAGESLSRALIHELGFAAPHLQRTVFGRDGRA
+IGRTDFWWEEVDVVGEFDGIGKYDVDLHASAAERRQAITREKEREVALRRVCRDVARWTW
+ADLREPAGLEAELVRAGVPRRR
+>PROKKA_02563
+MTALADVADLRPGTGPLLHVARREDLAARRRLERAWTRGDLVRLAAGVYLPAPTWTALSP
+WDRSTASAAALALARPATVFTGLTAARLRGLPVALELPALDLRATSPGHRGAAPLTSRPF
+SPALLATGGRLPRPPRRRPRWGLPQAPGMAPEPVEIRLSDGTGLGWGLADASATLLLVLG
+AATPFRNAVAPLDVLLATHPEAQSWAQAAEEALPTRAARERFERTWSFAAAGSESAGESY
+SRALMHELGFASPTALQHRHRDATGREVARTDFWWADARVAGEFDGIGKYDLGLHRGDDA
+ARRASIRREKEREVALQLVTRAVAHWTWEDLRAPERLARILTAAGVPRTVCPEPTDAQRH
+HRRAERR
+>PROKKA_00399
+MTLLSDHSRALLPGRGPLLSAADPHDGAARRRLERAWTRGVLVRLCPRVYISVSDWAALR
+PWDRAVVSAVALSIARPATVFTGLTAARLHGLGPAVEPPVLELRAPSPGHHGAGPLTRRP
+LAPSVVAHDRRLPVPPRRRPRWGLPEAAPAAPQPVEAILSDGQSLGTVLADPLPTVLLVL
+GAATPFRDAVAPLDALVRARPEEAARWARQAESRLKSAAALRRFERAWHFADARAESAGE
+SYSRASIHELGFVPPTALQHRHRDANGREVARTDFWWEQVRVYGEFDGLGKYDLSFFDGD
+DTARRASIRREKEREVALQLVTRAGAHWTWGDLLRPDRLARILTAAGVPRSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000436.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000436.fa
new file mode 100644
index 0000000000000000000000000000000000000000..664023ab3e22eff8bfbd8c0d19a9549899da0e71
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000436.fa
@@ -0,0 +1,19 @@
+>PROKKA_00398
+MSAPVPSSPPRPPQGAPDPGRVRTGRALLWQSVALLGMVLSFSLVLPWKLIALALGLVAL
+VLGVRVWVTSRGAERSGLPRAVASAGMAMALMGMTTAALPLLAWDATVQLEQCGASALTV
+RAQQACADEFTRQVEERTGVPQLRP
+>PROKKA_00122
+MSAPVPSSPPRPPQGAPDPGRVRTGRALLWQSVALLGMVLSFSLVLPWKLIALALGLVAL
+VLGVRVWVTSRGAERSGLPRAVASAGMAMALMGMTTAALPLLAWDATVQLEQCGASALTV
+RAQQACADEFTRQVEERTGVPQLRP
+>PROKKA_02559
+MVLSLSLVLPWKLAALVLGLVALVLGVRVWLTSRGERRAGLPRAVAAGGMALALFGTTTA
+ALPLLAWDATVELERCTSSALTVRAQQACADAFTRAVEERTGVPQLRP
+>PROKKA_02430
+MSALPPVPPSAPDRRPADAAARARVGRLLVAQSAALLAMLGAFTLVLPFKVLTLAAALAA
+LVLGVLVFTASRRTAQSLVPRAAAGAGMALALMGLTVGVFPLLLWNETAGFERCTASAVT
+VRAQQTCADDFTATVERRTGVAQLGG
+>PROKKA_00404
+MSAPVPSSPPRPPQGAPDPGRVRTGRALLWQSVALLGMVLSFSLVLPWKLIALALGLVAL
+VLGVRVWVTSRGAERSGLPRAVASAGMAMALMGMTTAALPLLAWDATVQLEQCSASALTV
+RAQQACADEFTRQVEERTGVPQLRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000439.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000439.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a454bf48e7f24b3a2e3e8f1115fd904e7fb04124
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000439.fa
@@ -0,0 +1,55 @@
+>PROKKA_00401
+MLEDTRTPSKERPLVTSAQPTTTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVST
+GSTAQRIAAAGVPVTEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVTQLRELEV
+EPFDLVVVNLYPFVDTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEV
+VQAAQSGGFDLRARRRLAALAFAHTAAYDNAVAAWTAAHFGEDTHADEIPVFPPYAGFSL
+ERAQILRYGENPHQPAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPVP
+AVAIVKHANPCGVAVTDEGTDIAQAHAKAHACDPVSAFGGVIAANRPVTAAMAAQAKDVF
+TEVVVAPSFEPEALEILTAKKNLRLLSLPEGFVRDAVEAKQVSGGMLLQITDAVDADGDD
+PATWTLAAGPAADEATLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLA
+VERANTLGAAQTGGQDVSTAGGAENVSGDGAPERARGAVAASDAFFPFADGLQILLDAGV
+RAVVQPGGSVRDEEVVAAAEAAGVTLYLTGARHFFHG
+>PROKKA_00125
+MTSAQPIPTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVSTGSTAQRIAAAGVPV
+TEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVTQLRELEVEPFDLVVVNLYPFV
+DTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEVVQAAQSGGFDLRAR
+RRLAALAFAHTAGYDNAVAAWTAAHFGEDTDADEIPVFPPYAGFSLERAQILRYGENPHQ
+PAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPVPAVAIVKHANPCGVA
+VTDEGTDIAQAHAKAHACDPVSAFGGVIAANRPVTAAMAAQVKDVFTEVVVAPAFEPEAL
+EILSAKKNLRLLSLPEGFLRDAVEAKQVSGGMLLQIADAVDADGDDPATWTLAAGPAADE
+AVLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVSSAGGAENVSGEGAPERARGSVAASDAFFPFADGLQILIDAGVKAVVQPGGSVRDEE
+VVAAAEAAGVTLYLTGARHFFHG
+>PROKKA_02556
+MTSAQPTTTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVSTGSTAQRIAAAGVPV
+TEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVAQLRDLEVEPFDLVVVNLYPFV
+DTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEVVQAAQSGGFDLRAR
+RRLAALAFAHTAGYDNAVAAWTAAHFAEDTEQDDVPIFPPYAGFSLERAEILRYGENPHQ
+PAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPAPAVAIVKHANPCGVA
+VTDEGADVAQAHAKAHACDPVSAFGGVIAANRPVTAVMAAQVKDVFTEVVVAPSFEPEAL
+QILTAKKNLRLLALPEGFVRDAVEAKQVSGGMLLQIADAVDADGDDPATWTLAAGAAADE
+ATLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVTTSEVTTAGGAENVSGEGAPERARGAVAASDAFFPFADGLQILIDAGVRAVVQPGGS
+VRDEEVVAAAEAAGVTLYLTGARHFFHG
+>PROKKA_02425
+MSSAPSVTTVLDEVPLKRALISVYDKTGLEELATGLHAAGVQLVSTGSTAQRIAAAGVPV
+TEVSEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVAQLADLDVEPFDLVVVNLYPFV
+ETVRSGADEDAVVEQIDIGGPSMVRAAAKNHASVAVVVDPARYVDVVAAAQAGGFDLRTR
+RRLASLAFAHTAAYDNAVAAWTAAHFGEDAEDEDAPVFPPYAGFSLERAATLRYGENPHQ
+PAALYVDHEAAPGIAQAELLHGKAMSYNNYVDADAAVRAAFDHAVPAVAIVKHANPCGVA
+VAGEGEDVAVAHAKAHACDPVSAFGGVIAANRPVTRAMAEQVAPIFTEVVVAPSFDEDAL
+EVLTAKKNLRLLALPEGFARDAVEAKQVSGGMLMQIADAVDADGDDPRTWTLAAGEAADE
+ATLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVSSAGGAENVSGEGAPERARGAVAASDAFFPFADGLQILVDAGVKAVVQPGGSVRDQE
+VVDAANAAGITMYLTGARHFFHG
+>PROKKA_00407
+MTSAQSIPTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVSTGSTAQRIAAAGVPV
+TEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVTQLRELEVEPFDLVVVNLYPFV
+DTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEVVQAAQSGGFDLRAR
+RRLAALAFAHTAGYDNAVAAWTAAHFGEDTDADEIPVFPPYAGFSLERAQILRYGENPHQ
+PAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPVPAVAIVKHANPCGLA
+VTDEGTDIAQAHAKAHACDPVSAFGGVIAANRPVTAAMAAQVKDVFTEVVVAPAFEPEAL
+EILSAKKNLRLLSLPEGFLRDAVEAKQVSGGMLLQIADAVDADGDDPATWTLAAGPAADE
+AVLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVSSAGGAENVSGEGAPERARGSVAASDAFFPFADGLQILIDAGVKAVVQPGGSVRDEE
+VVAAAEAAGVSLYLTGARHFFHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000441.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000441.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71b2748115f2871a4b855b60dac76bb7679032e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000441.fa
@@ -0,0 +1,25 @@
+>PROKKA_00404
+MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPEDSEPPAAAIGRLLETLMDR
+LVALDPETADREMNPRPVEPRPGASQPVADALAAYAAGDVAALDALDVTQPGTAFRQRAW
+RELRGIAPGSPATYGGLAERCGAPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY
+GTAAKQALLAHEAAHAG
+>PROKKA_00127
+MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPGDSEPPAAAIGRLLETLMDR
+LVALDPETADREMNPRPVEPRPGVSQPVADALAAYTAGDVAALDALDVAQPGTAFRQRAW
+RELRGIAPGSPATYGGLAERCGAPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY
+GTAAKQALLAHEAAHAG
+>PROKKA_02552
+MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPEGAEPHAAAIGRLLEALMDR
+LEALDPATADREMNPRPVEPHPGVSQPVADALAAYAAGDVAALDALEVAQPGTAFRQRAW
+RELRGIAPGSPATYGGLAERCGTPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY
+GTAAKRALLAHEAAHAG
+>PROKKA_02420
+MTHPPAFLPELRWTAATLPGTSLALVAVYSPEDDAVRASGVAVPEGAEPPAAAIGRLLLE
+LMDRLEELAPETAAREMDPRPVEPREGLDQTVADALAAYAAGDVDALDGLAVVQPGTAFR
+QASWEALRSITPGSPVAYGELATRAGAPKAVRAAGGACAANLAAVVVPCHRVVPASGGVG
+SYLYGSAAKAALLAHEAAHAPA
+>PROKKA_00410
+MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPEDSEPPAAAIGRLLETLMDR
+LVALDPETADREMNPRPVEPRPGVSQPVADALAAYAAGDVAALDALDVTQPGTAFRQRAW
+RELRGIAPGSPATYGGLAERCGAPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY
+GTDAKQALLAHEAAHAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000442.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000442.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68dd4eb1784cfd4549ac62ec4f060111e0fb5652
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000442.fa
@@ -0,0 +1,50 @@
+>PROKKA_00405
+MTEIRVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPTDGLRVGSESRLRIQ
+APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL
+ASWRHTHLLDDAAPGEADTADGRRGTVVTDHIEYALPGESLVSRVPGLGAAASRRTHEAF
+EAELGRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR
+VIRLVRSPKRAGALDAALWDPGRETVDEDALAEADVVVNLAGEPIAGRFTDAHKEAVHDS
+RVRGTRTLVDALARIAAREGDDARVRALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF
+LAEVVADWEAEARRAEAAGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGLGGPVATSGGES
+HDGSPWLSWIGADDIAGAFAHAVIDDGVTGPVNAVAPEPVTAREFATVLGRVLHRPAVIP
+VPDAGPRLLLGEEGRVETVAADQKVVADRLVASGYDMRDPELEGALRHVLGR
+>PROKKA_00128
+MTEITVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPTDGLRVGSESRLRIQ
+APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL
+ASWRHTHLLDDAAPGEADTADGRRGTVVTDHIEYALPGESLVSRVPGLGAAASRRTHEAF
+EAELGRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR
+VIRLVRSPKKAGALDAALWDPGRETVDEDALAEADVVVNLAGEPIAGRFSDAHKEAVHDS
+RVRGTRTLVDALARIAAREGDDARARALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF
+LAEVVADWEAEARRAETSGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGVGGPVATSGGES
+HDGSPWLSWIGADDIAGAFAHAVLDDGVTGPVNAVAPEPVTAREFATVLGRVLRRPAVIP
+VPEAGPRLLLGEEGRVETVAADQKVLADRLVASGYEMRDPELEGALRHVLGR
+>PROKKA_02551
+MTEIRVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPSDGLRVGSESRLRIQ
+APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL
+ASWRHTHLLDDAAPGEADTADGRRGTVVTDHIEYALPGEDLLGRVPGVGAAASRRAHEAF
+EAELSRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR
+VVRLVRSPKKAGALDAALWDPGRETVDEDALAGADVVVNLAGEPIAGRFTDEHKEAVHDS
+RVRGTRTLVDALARITAREGDDARARALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF
+LAEVVADWEAEARRAEAAGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGVGGPIASSGGES
+HDGSPWLSWIGADDIAGAFAHAVLDDGVTGPVNAVAPEPVTAKEFATVLGRVLRRPAVIP
+VPEAGPRLLLGEEGRVETVAADQKVVADRLVASGYDMRDPELEGALRHVLGR
+>PROKKA_02419
+MTETRVFEHRTLLRHPRRTVFDWLAAPGALQRMNPPFASELAAGPSDGLREGSQTRLRIG
+APGSLGLFAGAVDGALRAALPAAVSRRIPAALSPRLPWRARHTAYEEGRMFRDEMASGPL
+SAWRHTHSVEDAAPGEADTAEGEPGAVVVDRVEYALPGVGTAGRLPVVGRPAADAAHRVF
+EAELRRQFEFRGRVMAEDLDFHAGHPGPLVGGPARTVLVTGAGGLVGTQLCALLTGGGHR
+VIRLVRSPAQAEAEDAVLWDPAGGTVDTAALRAADVVVNLAGEPLAGRFTEKHRRAVHDS
+RVDGTRTLVDAIARLPEAERPTVLVNGSAVGWYGADAGAGPDGRGLTEDLPAGDDFLAGV
+VADWEAQARRAEELGLRVVRVRTGIVLSPTGGMLAQLLPLFLAGAGGPVATRGGRSHDGS
+PWISWIGVDDIAGVFAHAALAEGVVGAVNGTAPEPVTAKEFARVLGTVLHRPAAVPVPEF
+GPRLLLGEQGAAELVRADQKASAELVLDSGYAFRDAALEGALRRLLGR
+>PROKKA_00411
+MTEIRVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPTDGLRVGSESRLRIQ
+APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL
+ASWRHTHLLDDAAPGEADMADGRRGTVVTDHIEYALPGESLVSRVPGLGAAASRRTHEAF
+EAELGRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR
+VIRLVRSPKKAGALDAALWDPGRETVDEDALAEADVVVNLAGEPIAGRFSDAHKEAVHDS
+RVRGTRTLVDALARIAAREGDDARVRALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF
+LAEVVADWEAEARRAEAAGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGLGGPVATSGGES
+HDGSPWLSWIGADDIAEAFAHAVLDDGVTGPVNAVAPEPVTAKEFATVLGRVLRRPALIP
+VPEAGPRLLLGEEGRVETVAADQKVLADRLVASGYQMRDPELEGALRHVLGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000443.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000443.fa
new file mode 100644
index 0000000000000000000000000000000000000000..926909f3afcbc26421ede6b9db445a5e5f106b7c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000443.fa
@@ -0,0 +1,60 @@
+>PROKKA_00406
+MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLLVDGHRYVSGSMTPVPLATLASPLFHAQA
+LEDLGAVRVGERVGAVPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVLVVVPGHLGLALQSDTTDENGLGAAAMAALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMSAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAAVAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF
+TALSQLIRETGALQD
+>PROKKA_00129
+MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLMVDGHRYVSGSMTPVPLATLASPLFHAQA
+LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVFVVVPGHLGLALQSDTTDENGLGAAAMAALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMAAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAAVAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTTRVLTAQVMVALQEGFPQLALALWEALARDAF
+TALGQLIRETGALQD
+>PROKKA_02550
+MTTPVQKHLDRLTSAHTGEGDVPDGLGVAMLMVDGHRYVSGSMTSVPLATLASPLFHAQA
+LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVLVVVPGHLGLALQSDTTDENALGAAAMAALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVLELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEIRELMAAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSQHAPHLLPRDAQEAAVAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF
+TALSQLIRETGALQD
+>PROKKA_02418
+MKSPVQDRLDRLTAAHTPGTAADADATSDAGTGLALSVATVGGDHYSAGELVAVPLAGLA
+GPVVHALALEDLGVERVGEAVGTVPRPDLRTRLELEPGTGRPLTPLQDAGTMALAALVKG
+RGGRDRAARLLQQLAGLIGRETAPTDAAVRAADRAQHRARAAAWLLRSVGVLEADPDGLL
+ADVATLRAAPVTVADLALLAGTLAAHGVHPVSGERVLAEETVRAVLSALDACGMDTVDGA
+WALDVGQPGWSSARAGTVIAVVPGHMGIAVQGPADPDDADAPSPAALAALRTLVRDFELH
+PSQAAGSPRAAFRTHYRVDQAPSGSVRSAEVLELLSAHGDTAHVLELGGHVGFSQVDALA
+HVARNLPAALETIIVDVRSVSSTSHAAAVLAAQWFAYALHHGLDVVVVDRDTAAVDQVMA
+TAEASGVTLPDPLHDADDADPGHQDLGPAFRFFDSRSRAVQWAEQRLLARHAPHLLPASE
+EEAAMAPLLQHLSSEDARLLESMMDERVYEDGQIIRRAGQPFGGIYVITSGRVELTGQGT
+GGRRVRRTVLTPGMTFGEMALGQPGRQPSTVRARGRVTTRVLTAQVMYALQEGFPSLALT
+LWEALARDAYTALGQLIRETGALQD
+>PROKKA_00412
+MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLLVDGHRYVSGSMTPVPLATLASPLFHAQA
+LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSAMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVLVVVPGHLGLALQSNTTDENGLGAAAMTALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMSAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAALAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF
+TALGQLIRETGALQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000447.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000447.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90985e0de1ad8b17d0a8b97f26aa155cc15f1404
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000447.fa
@@ -0,0 +1,45 @@
+>PROKKA_00414
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDITDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPSEEEIDRKVRD
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGELQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKQKEGGHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDRGSTFDATLTHLEWLGHEQYGYIEFDPDPAVAEMLSSLAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPTTGENLTRDPEVGAELTRRAAEERRRQIEMAAERDA
+AEHEADAPRR
+>PROKKA_00134
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDITDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPSEEEIDRKVRD
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGELQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKQKEGGHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDRGSTFDATLTHLEWLGHEQYGYIEFEPDPAVAEMLSALAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPTTGENLTRDPEVGAELTRRAGEERRRQIEMAAERDA
+AEHEADAPRR
+>PROKKA_02545
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDISDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPAEEEIDRKVRN
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGVLQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKEKDGVHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDQGSTFDATLTHLEWLGHEQYGYIEFDPDPAVAEMLSSLAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPKTGENLTRDPEVGAELTRRAAEERRRQIEVAAERDA
+AADREAADTRR
+>PROKKA_02413
+MASITLNHIEKTYDDGYHAISDVNLDIEDGEFVILVGPSGSGKSTLLRMIVGLEDISGGD
+LLIDGRRVNEAAPKDRNLAMVFQNYALYPHLSVYENIAFPLRLAKDGKLSEEELDRKVRD
+AARVLELQDHLDRKPANLSGGQRQRVAMGRAIVRDADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGVLQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPATVKEQGGQYVLSSPIGDIPVPAEKAQRAAGRDIVFMGLRPEFFEDAELVEDA
+KRPHGSEFDATLTHLEWLGHEQYGYIEFEPDPEVAELLSSLAKDLDADELRPVVVTTLSA
+ESAARPGVPTRLWVDTTRVHLFDPKTGENLTRDAEAGAELTRRTAEARRRQIEAAQARDA
+EGR
+>PROKKA_00417
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDITDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPSEEEIDRKVRD
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGELQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKQKEGGHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDRGSTFDATLTHLEWLGHEQYGYIEFEPDPAVAEMLSALAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPTTGENLTRDPEVGAELTRRAGEERRRQIEMAAERDA
+AEHEADAPRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000453.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000453.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f65e0d090b4cc6db316abeb3532f6263bd6a5c03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000453.fa
@@ -0,0 +1,35 @@
+>PROKKA_00422
+MSHTTLHASPGDASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAGKSTTMRM
+LAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYGRYFGLPY
+SYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPTTGLDPQ
+ARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAELIREHASR
+EVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQRLVDEGA
+LPAPVTTLTRRASLEDVFLILTGRTLVD
+>PROKKA_00143
+MSHTTLHASPGPASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAGKSTTMRM
+LAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYGRYFGLPY
+SYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPTTGLDPQ
+ARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAELIREHASR
+EVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQRLVDEGA
+LPAPATTLTRRASLEDVFLILTGRTLVD
+>PROKKA_02536
+MSHATPASPSPSQSPADAPDAGPAPVIRARGLRKQYGDFHAVKGIDLDVRPGECFGLLGP
+NGAGKSTTMRMLAGTSQRTAGELSILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENI
+LIYGRYFGLPYSYLRPKADELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFL
+LDEPTTGLDPQARHILWDRLYRLKERGTTLLLTTHYMDEAEQLCDRLVVVDGGQIMAAGT
+PAALIREHAAREVLEARFGADRNEAAARTVQARAGDGVVHRVEVLPDRVLVYAAHADDLH
+AVVQGLVDDGALPAPVTTLTRRASLEDVFLILTGRTLVD
+>PROKKA_02406
+MTRTTSSPSPAAPAGGGAAPVILARGLRKQYGDFHAVQGIDLDVRPGECFGLLGPNGAGK
+STTMRMLAGTSQRTGGELRILGIDPEEDGPAVRARLGVVPQQDNLDEDLTARENILIYGR
+YFGLPYSYLRPKAEELLAFAQLTDKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPT
+TGLDPQARHTLWDRLYRLKERGTTLLLTTHYMDEAEQLCDRLVVVDAGRIMAAGTPASLI
+REHASREVLEARFGTDRNATAARLLRESLPGLHRLEVLPDRVLLYTEHADTLQQDLDRLV
+AEGHVTAPVTQLTRRASLEDVFLILTGRTLVD
+>PROKKA_00425
+MRLCCRLVSPTTLHAPPGPASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAG
+KSTTMRMLAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYG
+RYFGLPYSYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEP
+TTGLDPQARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAEL
+IREHASREVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQ
+RLVDEGALPAPATTLTRRASLEDVFLILTGRTLVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000455.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000455.fa
new file mode 100644
index 0000000000000000000000000000000000000000..183897dc20a910ae5581261f352902a0d3fd9214
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000455.fa
@@ -0,0 +1,25 @@
+>PROKKA_00425
+MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL
+VFAVVVYLQMRRGVRAAGRKVDTAMQNARADVAALRGREADAAAPAVAPPAPAADPLRDT
+KLDHSFKIAQVQVRVVREQLAAGAGMDREMVDRALETIDITASNARDMIKESRAGGAEGP
+VSGTVIG
+>PROKKA_00146
+MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL
+VFAVVVYLQMRRGVRAAGRKVDTAMQNARADVAALRGREADAAAPAVAPPAPAADPLRDT
+KLDHSFKIAQVQVRVVREQLAAGAGMDREMVDRALETIDITASNARDMIKESRAGGAEGP
+VSGTVIG
+>PROKKA_02532
+MSQPLTTGSGETRRGPRAGLRVGSVGFAAMIVILIVAIMFAANQNDVIGWLVVAVAAGWL
+VFALVVFLQMRRGVQAAGRKVDAAMENARADVAALRGQGAAAAPQAAAHAPAGDPMRDTK
+LDHSFKIAQVQVKVVREQLAAGGAMDREMVDRALETIDITAANARDMIKESRGQGGSEGP
+VSGTVIG
+>PROKKA_02402
+MPQSIPSGSAGTRPARAGLTVGSTGFAVMVAVLLVAIVFAANANDLIGWLVVAIAAGWLV
+FAVVVFLQMRKGVREAGRKVDTAMQNARADVAALRAPQQPAPAAAVPAAAGDPMRDTKLE
+HSFKICQVQARVITQQLDAEGPLDREMVDRALETITITAQNARDMIKESARDAEGPVSGT
+VVS
+>PROKKA_00428
+MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL
+VFAVVVYLQMRRGVQAAGRKVDTAMQNARADVAALRGRDADAAAPAVAPSAPAADPLRDT
+KLDHSFKIAQVQVRVVREQLAAGESMDREMVDRALETIDITASNARDMIKESRAGGAEGP
+VIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000461.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000461.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7be982f77c1a2734aaa1df26530e125e1638ec64
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000461.fa
@@ -0,0 +1,20 @@
+>PROKKA_00432
+MHPLDDDPHAATDRDPAPDRAALRPLRLFQTVTAVTGALSAAGVAGVLALQSTPGYARAV
+LEARSWGASEVTDADVAAFVTPAGAWPVAAAAVVLLAVVLLAGITRRIRAVRPVGSVLVV
+LGMLTAAFWMVDGGRMVQAGGGGPVVLGAVVGMLVSSAMWLRVAHRRETRDGFDG
+>PROKKA_00153
+MMGGMHPLHDDPHETTERDPGPDRAALRPLRLFQTVTAVTGALSAAGVGGVLALQATPGY
+ARAVLEARSWGASEVTDADVAAFLTPAGAGPVAAAAVVVLTLVLLAGITRRIRAVRPVGS
+VLVVLGMLTAAFWMVDGGRMVQAGGGGPVVLGAVVGMLVSSAVWLRVAHRRETRDAFDV
+>PROKKA_02525
+MHTPDDAAADADDAAARAALHDRVVRRPLRRLLTLTAVTGALSALGTAGVLALQGAPGYA
+RAVLEARSWGRAAVTDADVASFLTPPWGVPAAVLGVLAVAALLMLGVARRVRAVRPVGTV
+AVGLGLLSAAFWMVDGGRMVAAGGAGPLVLAAVVAMFLACAVWLLTAHLRATRDAFDG
+>PROKKA_02396
+MRSDDVAPASARPSGLDDPAVRGPIRRYQAMTAGTGLVSAAAVAGVLGLQSDPGYAREVL
+QSRTWGQYEVSAQQVQDFLTPPGGAVLGAVGVLLTAALLVWGAQRLWGATRWLGTALAGV
+GLLSAVFWAVDGGRMAARGASGMAVLVAVGAMAVFCAVWLVTAHSKAVREAFLG
+>PROKKA_00435
+MHPLDDDPHETTDPAPDLASLRPLRLFQTVTAVTGALSAAGVGGVLALQSTPGYARAVLE
+ARSWGASEVTDADVAAFLTPAGAWPVAAAAVVVLTLVLLAGITRRIRAVRPVGSVLVVLG
+MLTAAFWMVDGGRMVQAGGGGPVVLGAVVGMLVSSAVWLRVAHRRETRAAFDV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000462.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000462.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff079f596fad6929fd1b471438103df6e6e6c4c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000462.fa
@@ -0,0 +1,30 @@
+>PROKKA_00433
+MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAISEVKRAILARQF
+>PROKKA_00154
+MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAISEVKQAILARQF
+>PROKKA_02524
+MSHAATETEAPVAQDQTQAAGGGMGAIESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGICGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREVMPFLVAEGHEPSKERYQSQADRARYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDDAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAIAEVKQAILARQF
+>PROKKA_02395
+MSHAATETQAPAAPAQQTQGQDGGMGEIESFDITLRVRRFLPESSEESYWDEWRLTMFGT
+DRVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSQPITVE
+PIKGLPVEKDLIVDMEPFFQSYREVMPFLVAKGHEPSKERYQSQADRAIYDDTTKCILCA
+ACTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDDAGDMRLEILNDKEGVWRCRTTFNCTE
+ACPRGIQVTKAIAEVKQAILARSF
+>PROKKA_00436
+MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAISEVKQAILARQF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000463.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000463.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6cd8d67d2fb69ce4dab05d5d91b69927e00ed81a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000463.fa
@@ -0,0 +1,55 @@
+>PROKKA_00434
+MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFFNEFYVLDLLLVEEDAVREDGTA
+YKQKRTAGVVSYELATGEIHVFQAKSVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNADGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGIPTNIQAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IYAAEYAAQADWVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRGRYENVSVQDKGHRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPDRDDENFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
+>PROKKA_00155
+MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFFNEFYVLDLLLVEEDAVREDGTA
+YKQKRTAGVVSYELATGGIHVFQAKSVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNADGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGIPTNIQAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IYAAEYAAQADWVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRGRYENVSVQDKGRRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPDRDDENFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
+>PROKKA_02523
+MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFYNEFYVLDLLLVEEDAVREDGTP
+YKQKRAAGVVSYELATGEIHVFQAKSVVFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNSDGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGVPTNIKAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IYAAEYAQTADFVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRGRYENVSVQDKGKRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPDRDDANFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
+>PROKKA_02394
+MQVHKYDVVIVGAGGAGMRAAIESGQRARTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEIMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHDVEFYNEFYVLDLLLVDEDATREDGTP
+YTQKRVAGVVSYELATGEIHVFQAKAVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNAEGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGMPTNVKAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IHAAEYAAQADWVELPEGGELPTVQHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRHRYENVSVQDKGHRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPNRDDANFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
+>PROKKA_00437
+MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFFNEFYVLDLLLVEEDAVREDGTA
+YKQKRTAGVVSYELATGEIHVFQAKSVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNADGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGIPTNIQAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IYAAEYAAQADWVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRGRYENVSVQDKGHRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPDRDDENFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000468.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000468.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a7f5cab04f95c634c435e9f7554e96eeffeb3133
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000468.fa
@@ -0,0 +1,40 @@
+>PROKKA_00439
+MGIATPSAARRRRLLLPAAALGVSGLLLTACGAPPEQSEASDSGAAESEAIATVDGVGSD
+NKDYKACIVSDEGGFDDRSFNQSSYEGLKAAEEAYGITTSEAESNEPSEYTPNVTAMVNG
+DCDAVIGVGFLLGDAMKPIAAQHSDTHFFGVDVTDGDFTDNFQKLTYDTAQAAFLAGYLA
+AGTTETGAVATYGGAEIPTVTIFMDGFARGVEHYNEVKDKDVKVLGWDKDAKTGSFTGDF
+ENVANGKTNTANFINEGADIVMPVAGPVGLGTLDAVREANQGGKDVKVIWPDSDGYESTK
+DGNLILTSVKKNMGQSVTDVIAADLKDEFSAEPYVGTLENKGVELAPFHDFEDTVPQELK
+DELKDLEAKIISGELKVGSEYSPEA
+>PROKKA_00160
+MGIATPSAARRRRLLLPAAALGVSGLLLTACGAPPEQSEASGSGAAESEAIATVDGVGSD
+NKDYKACIVSDEGGFDDRSFNQSSYEGLKAAEKAYGITTSEAESNEPSEFTPNVTAMVNA
+DCDAVIGVGFLLGDAMKPIAAQHSDTHFFGVDVTAEGFSDNVQKLTYDTAQAAFLAGYLA
+AGTTETGTVATYGGMEIPTVTIFMDGFARGVEHYNEVKDKDVKVLGWDKDAKTGSFTGDF
+KNVANGKTNTANFINEGADIVMPVAGPVGLGTLDAVREANQGGKDVKVIWPDSDGYESTK
+DGNLILTSVKKNMGQSVADVIAADLKDEFSAEPYVGTLENKGVELAPFHDFEDTVPQELK
+DELKDLEAKIVSGELKVGSEYSPEA
+>PROKKA_02518
+MGTATPSAEGRRRLLLPAAVLGASALLLTACGQAPEASNSSEPAGSASATGAAAEVGSDN
+SDYTGCIVSDEGGFDDRSFNQSSYEGLKAAEEEFGIEIREAESNSVGEYVPNLNAMLDAD
+CNLVVAVGFQLGDTMKPIAEENAETKFVGVDVTAPGFPENVRNIIYDTAQGAFLAGYLAA
+GMTETGTVATYGGMEIPTVSIFMDGFARGVEHYNEVKGEDVRVLGWDTENRTGSFIGDFS
+NQNAGKTNTANFINEGADIIMPVAGPVGLGTIDAVKEANGGGKDVKVIWVDSDGYETTQD
+GEVILTSVMKRMGDAVKQVIAEDINDEFTSEAYVGTLENDGVALAPFHDFEDAVPQELKD
+ELEALEAGIVSGEIEVGSEDSPEA
+>PROKKA_02389
+MGIVSPLAGRRRLAVPAALLSSGLLLAGCGAPPAENSGSASGSGAAVSADAAAGSDNKDY
+KSCIVSDAGGFDDRSFNQSSYEGLKAAEEAYGIETNKAESKDASEFTPNVNAQVNAQCDS
+IIGVGYMLGDTIKPIAQKNPDIHFLGVDVTADGFSDNVKKLTYDTAQAAFLAGYVSAGMT
+KTGTVATYGGMEIPTVTVFMDGFAAGVEHYNEVKGKDVKVLGWDREAKTGSFTGDFDNQA
+NGKTNTANFINQGADIVMPVAGPVGLGTLDAVKEANAGGKSVAVVWPDSDGYESTKDGAL
+ILTSVVKNMGQSVSDVIGQDLKGEFSADPYVGTLENKGVELAPFHDFDSKVPQELKDEVQ
+TLQEDIISGKVKVDSEYSPKS
+>PROKKA_00442
+MGIATPSAARRRRLLLPAAALGVSGLLLTACGAPPEQSEASDSGAAESEAIATVDGVGSD
+NNDYKACIVSDEGGFDDRSFNQSSYEGLKAAEEAYGITTSEAESNEPSEYTPNVTAMVNG
+DCDAVIGVGFLLGDAMKPIAAQHSDTHFFGVDVTDGDFTDNFQKLTYDTAQAAFLAGYLA
+AGTTETGTVATYGGAEIPTVTIFMDGFARGVEHYNEVKDKDVKVLGWDKDAKTGSFTGDF
+ENVANGKTNTANFINEGADIVMPVAGPVGLGTLDAVREANQGGKDVKVIWPDSDGYESTK
+DGNLILTSVKKNMGQSVTDVIAADLKDEFSAEPYVGTLENKGVELAPFHDFEDTVPQELK
+DELKDLEAKIISGELKVGSEYSPEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000469.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000469.fa
new file mode 100644
index 0000000000000000000000000000000000000000..96468da6df2a05037b68a09a013198432e2d5af3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000469.fa
@@ -0,0 +1,50 @@
+>PROKKA_00440
+MRLELRGISKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGEIL
+LDGEPVRFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRALGVLDLEATRRRI
+REISAQYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLG
+IIRQLREDGTAIVFISHKLREVKAVSDDITVLRRGRVVGTADPSAEAAELAALMVGRSVV
+LERRKTAPTLGEETFRVEDLSVVSPTGQVLLDAVSFAVRQGEVLAVAGVQGNGQTELTEA
+IMGLVKATGSVTLDGRELIGRSTRQIIRAGVGFVPEDRSTDGLVGPFSVAENMVLNRYDV
+APAGNAVQMRPAAVRALAERRVAEFDVRTQGVDLPVSSLSGGNQQKVVMARELVDGLRLF
+IASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVLELADRIAVMYHGRIVGIV
+PGDTSRETLGLMMAGQTPDDAALASGADVAAGTPGTAGEAPAAHPTTEGERP
+>PROKKA_00161
+MRLELRGITKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGEIL
+LDGEPVRFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRALGVLDLEATRRRI
+REISAQYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLG
+IIRQLRADGTAIVFISHKLREVKAVSDDITVLRRGRVVGTAEPSAEAAELAALMVGRNVV
+LERRKTAPTLGEETFRVEDLSVVSPTGQVLLDAVSFAVRQGEVLAVAGVQGNGQTELTEA
+IMGLVKATGSVTLDGRELIGRSTRQIIRAGVGFVPEDRSTDGLVGPFSVAENMVLNRYDV
+APAGNAVQMRPAAVRALAERRVAEFDVRTQGVDLPVSSLSGGNQQKVVMARELVDGLRLF
+IASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVLELADRIAVMYHGRIVGIV
+PGDTSRETLGLMMAGQTPDDAALASGTDVAADTPGTAGAAPAAHPTTEGERP
+>PROKKA_02517
+MKLELRGITKRFGTFTANDSVDFVVRSGEVHTLLGENGAGKSTLMNVLFGLYDPTEGEIL
+VDDRPVRFAGPGEAMRAGIGMVHQHFMLVPVFTVAENIALGDEHTRAAGVLDLEATRRKI
+RAISDEYGFAVDPDAVVEDLPVGVQQRVEIIKALVRDAKVLILDEPTAVLTPQETDELLA
+IIDRLRQDGTAIVFISHKLREVKAISEHITVLRRGKVVGTAEPSASAAELAALMVGRQVS
+LNRAKTAPTLGEETFKVQDLTVVSPTGQVLVDHVSFAIRQGEILGVAGVQGNGQTELTEA
+IMGLHKATGSVTLDGRELVGRSTRQIIRAGVGYVPEDRSTDGLVGSFTVAENMVLNRFDR
+EPAGSALQLRPRAVRELAEARVQEFDVRTQGVVSPVSSLSGGNQQKVVMARELVDELRLF
+IASQPTRGVDVGSIEFLHERIVRERDNGTPVMIVSTELDEILELSDRIAVMYHGRIVGIV
+DGDASRETLGLMMAGQTPESLATETATTEEGPRA
+>PROKKA_02388
+MKLELRGITKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGQIL
+LDGEPVAFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRGAGVLDLEATRRKI
+REISDAYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLA
+IIRQLRADGTAIVFISHKLREVKAISDDITVLRRGRVVGTADPSASAAELASLMVGRDVV
+LNRRKTAPQLGEETFRVEHLTVVSPTGQVLVDDVSFGIRQGEVLAVAGVQGNGQTELTEA
+IMGLQAKAAGSIRLDGRELLGRSTRQIIHAGVGYVPEDRSTDGLVGSFSVAENMVLNRFD
+VAPAGSAVQLRPRAVRELAERRVEEFDVRTQGVDVPVSSLSGGNQQKVVMARELVDGLRL
+FIASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVRELADRIAVMYHGRIVDI
+VPGDASREHLGLLMAGQTAEDTHQEGARA
+>PROKKA_00443
+MRLELRGITKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGEIL
+LDGEPVRFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRALGVLDLEATRRRI
+REISAQYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLG
+IIRQLRADGTAIVFISHKLREVKAVSDDITVLRRGRVVGTAEPSAEAAELAALMVGRNVV
+LERRKTAPTLGEETFRVEDLSVVSPTGQVLLDAVSFAVRQGEVLAVAGVQGNGQTELTEA
+IMGLVKATGSVTLDGRELIGRSTRQIIRAGVGFVPEDRSTDGLVGPFSVAENMVLNRYDV
+APAGNAVQMRPAAVRALAERRVAEFDVRTQGVDLPVSSLSGGNQQKVVMARELVDGLRLF
+IASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVLELADRIAVMYHGRIVGIV
+PGDTSRETLGLMMAGQTPDDAALASGADVAADTPGTTGAAPAAHPTTEGERP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000471.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000471.fa
new file mode 100644
index 0000000000000000000000000000000000000000..22ab6c47747c245d36adf4e137632fe77d76ce7a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000471.fa
@@ -0,0 +1,45 @@
+>PROKKA_00442
+MSATAARPHADVVRPEAAEPARVVVRHWTTPIALTILTLLALAVFALGAPEATATFRLSH
+ASDAVVLPDLTADPVLGGWLLVGLMAVLTAVAWLATLRSGRTPGWAAALFAVAFVAAFLI
+WVIGSADNTTVFLTGLIAGSFALAVPLIFGSMAGILAERSGVVNIAIEGQLLAGAFTAAV
+VGTATGSPWAGLVAAIVAGVLVSWLLAVFSIKYLVNQVIVGVVLNVLVAGLTSFLYSTVL
+TDGDTELNAPPHFPNLRIPGLADIPVLGPILFDQTILGYAMYLLVIALWFALFRTRWGLR
+VRAVGEHPKAADTVGIDVNRTRYAAVLLGGAVAGMGGAFFTLVSASSFTKEMTAGQGFIA
+LAAVIFGRWNPIGAFFAALLFGFATNMQYVLAILGTPVPSQFMAMLPYLVTVFAVAGLVG
+RSRGPAASGVPYVKE
+>PROKKA_00163
+MSATAARPHADVVRPEAAEPARVVVRHWTTPIALTILTLLALAVFALGAPETTATFRLSH
+ASDAVVLPDLTADPVLGGWLLVGLMAVLTVVAWLATLRSGRTPGWAAALFAVAFVAAFLI
+WVIGSADNTTVFLTGLIAGSFALAVPLIFGSMAGILAERSGVVNIAIEGQLLAGAFTAAV
+VGTATGSPWAGLAAAIVAGVLVSWLLAVFSIKYLVNQVIVGVVLNVLVAGLTSFLYSTVL
+TGGDTELNAPPHFPNLRIPGLADIPVLGPILFDQTILGYAMYLLVIALWFALFRTRWGLR
+VRAVGEHPKAADTVGIDVNRTRYAAVLLGGAVAGMGGAFFTLVSASSFTKEMTAGQGFIA
+LAAVIFGRWNPIGAFFAALLFGFATNMQYVLAILGTPVPSQFMAMLPYLVTVFAVAGLVG
+RSRGPAASGVPYVKE
+>PROKKA_02515
+MSTAAQTNPVQPTPAGTGRAPSAEAPREGGTVVVRSWTTPIVFTVFTVLALVVFGLNAPD
+AAATFRVSTEADAFRIPDLVADGAGGGWIVTAILVVLTVLAWMRAARGRAVGAVLGISFA
+LVFVAGFLIWVVGSAANTSVFLTGLIAGSFALAVPLIFGSMAGILSERAGVVNIAIEGQL
+LAGAFTAALVGSMTGSPWAGLAAAVVAGVLVSVILAVFSIKYLVNQVIVGVVLNVLVAGL
+TGFLFSTVLSENSSGLNSPPRFETLRIPGLADIPVIGPILFEQTLLGYGMYLIVAVIYIG
+LFHTRWGLRVRAVGEHPKAADTLGINVLRTRYVNVLLGGAVAGMGGAFFTLVQSSSFSRE
+MTAGMGFIALAAVIFGRWNPIGAFFAALLFGFATNMQYVLAILGTPVPSQFMAMLPYLVT
+IFAVAGLVGRSRAPAASGVPYVKE
+>PROKKA_02386
+MSTAAPARESATPSERAGAASSGVVVRHWSTPVLLSVFTLVSLVVFALGASDSTAVFRIS
+EASDAVRLPDLLADPAVTGWALTAVMAAITAAAWVLTLRGRRLPGWAAGLFALAFTAAFL
+VWVVGAATNNEVFLTGLIAGSFTLAVPLIFGSMAGILSERSGVVNIAIEGQLLAGAFMAA
+VVGSLTGSPWAGLGAAIVAGVLVSWLLAVFSIRYLVNQVIVGVVLNVLVAGLTNFLFSTV
+LTADSDLNAPPRFPDLRIPLLADIPVIGPILFDQTILGYLMYAIVALLWFGLFRTRWGLR
+VRAVGEHPKAADTVGIDVNRTRYVNVLLGGAVAGMGGAFFTLVSASSFSKEMTAGQGFIA
+LAAVIFGRWNPIGAFFAALLFGFATNMQFVFAILGTPVPSPFMAMLPYLVTVFAVAGLVG
+RSRGPAAAGEPYVKE
+>PROKKA_00445
+MSATAARPHADVVRPEAAEPARVVVRHWTTPIALTILTLLALAVFALGAPEATATFRLSN
+ASDAVVLPDLTADPVLGGWLLVGLMAVLTAVAWLATLRSGRTPGWAAALFAVAFVAAFLI
+WVIGSADNTTVFLTGLIAGSFALAVPLIFGSMAGILAERSGVVNIAIEGQLLAGAFTAAV
+VGTATGSPWAGLAAAIVAGVLVSWLLAVFSIKYLVNQVIVGVVLNVLVAGLTSFLYSTVL
+TGGDTELNAPPHFPNLRIPGLADIPVLGPILFDQTILGYAMYLLVIALWFALFRTRWGLR
+VRAVGEHPKAADTVGIDVNRTRYAAVLLGGAVAGMGGAFFTLVSASSFTKEMTAGQGFIA
+LAAVIFGRWNPIGAFFAALLFGFATNMQYVLAILGTPVPSQFMAMLPYLVTVFAVAGLVG
+RSRGPAASGVPYVKE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000472.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000472.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b70442a5805d67ad4b714012230295be238034d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000472.fa
@@ -0,0 +1,20 @@
+>PROKKA_00443
+MADGQHTTTAPRVDWDRLRAAALAATEHAYVPYSGFRVGAAALTDDGRLVSGCNIENASY
+GLTLCAECALLAELRMGGGGRLAAFVCVDGAGVLTMPCGRCRQLLYEFRAPGLVLLTPAG
+ERGIDAVLPDAFGPADLERADRP
+>PROKKA_00164
+MADGQHTTTAPRVDWDRLRAAALAATEHAYVPYSGFRVGAAALTDDGRLVAGCNIENASY
+GLTLCAECALLADLRMGGGGRLAAFVCVDGAGVLTMPCGRCRQLLYEFRAPGLVLLTPAG
+ERGIDAVLPDAFGPADLERADRP
+>PROKKA_02514
+MAAEGTTTAPGVDWDRLRRAALAATEHAYVPYSGFRVGAAALTEDGRLVTGCNIENASYG
+LTLCAECALLADLRMGGGGRLAAFVCVDGQGVLTMPCGRCRQLLHEFRAPDMVLLTPAGE
+RTMGQVLPDAFGPEDLERAAAR
+>PROKKA_02385
+MTGTTTPPACAAPVAEADWDRLRAAAADAMERAYAPYSGFRVGAAALTEDGRLVSGCNVE
+NAAYGVALCAECALVGQLHMTGGGRLRAFLCVGGDGRLITPCGRCRQLLWEFRAPGLAVL
+TAAGVTTVEALLPEAFGPDALEA
+>PROKKA_00446
+MADGQHTTTAPRVDWDRLRAAALAATEHAYVPYSGFRVGAAALTDDGRLVSGCNIENASY
+GLTLCAECALLADLRMGGGGRLAAFVCVDGDGVLTMPCGRCRQLLYEFRAPGLVLLTPAG
+ERGIDAVLPDAFGPADLERADRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000475.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000475.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71b75f479400205bc6c8d989a04860830e337726
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000475.fa
@@ -0,0 +1,40 @@
+>PROKKA_00446
+MTTTQLPDTASPSPLEVDLAVLPKVSLHDHLDGGLRVGTVLDLAREAGVEVPADTVEGLA
+EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH
+LAGGLSLDEAVEAVQAGLDEAVEADAAAGHAIRVGQLVTAMRHADRAQEIAELAVRHRAA
+GVVGFDIAGAEAGFPPSRFADTFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH
+GVRLAEDISVEYGGVDEDGEQLDELTGLVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA
+AAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLSELLDLQLNAAE
+AAFLSVDEREDLAEILVAGWGEVISGDAVGPVLEELDDEDEDD
+>PROKKA_00167
+MTTTQLPDTASPSPLEVDLAVLPKVSLHDHLDGGLRVGTVLDLAREAGVEVPADTVEGLA
+EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH
+LAGGLSLDEAVEAVQAGLDEAVEAADAAGHVIRVGQLVTAMRHADRAQEIAELAVRHREA
+GVVGFDIAGAEAGFPPSRFADTFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH
+GVRLAEDISVEYGGVDEDGEQLDELTGIVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA
+AAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLSELLDLQLNAAE
+AAFLSVDEREDLAEILVAGWGEVISGDAVGPVLEELDDEDEDD
+>PROKKA_02511
+MTATQLPDTASPSPLEVDLAALPKVSLHDHLDGGLRVGTVLELATEAGVDVPADTVEGLA
+EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH
+LAGGLSLDEAVEAVQEGLDEAVDAAEAQGRLIRVGQLVTAMRHADRAQEIAELAVRHRER
+GVVGFDIAGAEAGFPPSRFAETFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH
+GVRLAEDISVEFGGVDEDGEQLDELTGLVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA
+EAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLAELLDLQLNAAE
+AAFLAVDEREDLAEILVAGWGEVISGDDAGPVLEELDEDDEDEDA
+>PROKKA_02382
+MTISSQTPADAAPSPLTIDLGALPKVSLHDHLDGGLRVATVLELAREAGVEVPADTVDGL
+ADWFAEHANGESLEKYLETFALTTSVMQTHEQLRRVAREFVEDLVADGVVYGEIRWAPEQ
+HLASGLTLDEAVEAVQEGLDEAVDAADEAGHVIRVGQLVTAMRHADRAQEIAELAVRHRD
+RGVVGFDIAGAEIGFPPSRFADTFTWLAQQHLPVTVHAGEAEGLSSIQDALVSGRALRLG
+HGVRIADDIQVEFGGLDEDGVPVDADTGIVDLGETAAWVRDRQIALEICPSSNLQTGAVD
+AAAGIAGHPIDLLVQLGFRVTVNTDNRLVSNVSLTDELYLLAETFGYSLSELLDLQLNAA
+EAAFLAVDEREDLAEILVSGWGEVISGAGGTVALEELEADTDDEADA
+>PROKKA_00449
+MTTTQLPDTASPSPLEVDLAVLPKVSLHDHLDGGLRVGTVLDLAREAGVEVPADTVEGLA
+EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH
+LAGGLTLDEAVEAVQAGLDEAVEAADAAGHVIRVGQLVTAMRHADRAQEIAELAVRHREA
+GVVGFDIAGAEAGFPPSRFADTFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH
+GVRLAEDISVEYGGVDEDGEQLDELTGLVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA
+AAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLSELLDLQLNAAE
+AAFLSVDEREDLAEILVAGWGEVISGDAVGPVLEELDDEDEDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000476.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000476.fa
new file mode 100644
index 0000000000000000000000000000000000000000..82964d7495fafe560fd210262dc1de13d064434e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000476.fa
@@ -0,0 +1,30 @@
+>PROKKA_00447
+MDRLVAVVEALRDHCPWTAALTHADLAEYLVEEAYEAVAEIESRDAAAWADVPARRADGA
+YPALAAELGDVLFQVVLHAAVSRAPGAPAETAGFRVDDAADALTAKMIRRNPLVLTPEGG
+LRPAEELAAVTPEAVELAWERVKAQERAAAGLSPAAPAHDDGGTGPGLDVGDIPARLPAL
+AAAANVVDRAARQEPDPLAAHVPAPAAEAGERPAAGWPDEAALGAELFALVRRARAAGLD
+PERALRTTVARVRAGDWSALRPSG
+>PROKKA_00168
+MDRLVAVVEALRDHCPWTAALTHADLAEYLVEEAYEAVAEIESRDAAAWADVPARRADGA
+YPALAAELGDVLFQVVLHAAVSRAPGAPAETAGFRVDDAADALTAKMIRRNPLVLTPEGG
+LRPAEELAAVTPEAVELAWERVKAQERAAAGLSSAAPAHGDGGTGPGLDVGDIPARLPAL
+AAAAKVVDRAARQEPDPLAAHVPAPAAEAGERPAAVWPDEAALGAELFALVRRARAAGLD
+PERALRTTVARVRAGDWSALRPSG
+>PROKKA_02510
+MDRLVAVVEALRDHCPWTAALTHGDLAEYLVEEAYEAVAEIEARDAAAWADVPARRADGA
+YPALAAELGDVLFQVVLHAAVSRPPGAPVSSAGFRVADAADALTVKMIRRNPLVLTPEGA
+PRSAEELARVTPEAVELAWEEVKAQERAAAGETASGEAEQAGGPASDPGFGGIPARLPAL
+AAAAKVVDRAARQPADPLARHAPLSGDPDSGHRAGHAAPDDGDPGWGDEAALGAELFALV
+RRARAAGLDPERALRGTVARVRSGDWDALRPPTAG
+>PROKKA_02381
+MSDAVDRLVATTEALRTHCPWTRALTHRSLTQYLVEEAYEALAEIEARTDAEWADVPARR
+ADGSYPALAGEMGDVLFQVVLHAAVSRAPDAPAPAAGFRLDDAADALTAKLVRRNPLVFT
+PDGAVRPPAELEGITPEAVELAWERVKRAERAAAEGGGAPDGPTGAPRPDDVGLGGIPAH
+LPALAAASAVVDRAARQDVDPLAGHVPLPERTGEAWEDEAALGAELFETVRRARAAGLDP
+ERALRGAIACVRAGDWDALRR
+>PROKKA_00450
+MDRLVAVVEALRDHCPWTAALTHADLAEYLVEEAYEAVAEIESRDAAAWADVPARRADGA
+YPALAAELGDVLFQVVLHAAVSRAPGAPAESAGFRLDDAADALTAKMIRRNPLVLTPEGG
+LRPAEELAAVTAEAVELAWERVKARERAAAGLSPAAPAHDDGGTGPGLDVGDIPARLPAL
+AAAAKVVDRAARQEPDPLAAHVPAPAAEAGERPAAGWPDEAALGAELFTLVRRARAAGLD
+PERALRATVARVRAGDWAALRPSG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000478.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000478.fa
new file mode 100644
index 0000000000000000000000000000000000000000..599d71082797102e06f026ac49b833fb6c815b5f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000478.fa
@@ -0,0 +1,51 @@
+>PROKKA_00450
+MTVSPRPAQDRTVTEQDLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRFSNGIPFP
+TTFYLTHPVLTAAVSRVEADGEMARMNDRLAQDPALAAAHRAAHEAYIAERDRVGAEAGT
+GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDEAIALVAPWWTPEVCACEGA
+WDEAAAVPTKDLSRHVRHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAVADP
+TAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVDEYARLVQRHHAGRVRFVATSA
+SRDVSNRAAFVDGVRERLGVEPEVVSGDEEAALSFAGAVSAVETADLGPEDLVLVVDLGG
+GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLRSDPPTSDEVAAARADARRLLDDAAARL
+PLERVARVVGVAGSVTTVTAEALGLSTYEPEAIHGARLPIAEFRAAAEGLVAATRAERSE
+RGFMHPGRVDVIGAGALLWSTVLERVAETAGVTEAWASEHDILDGIVLSLRS
+>PROKKA_00171
+MTVSPRPAQDRTVTEKDLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRLSNGIPFP
+TTFYLTHPVLTAAVSRVEADGEMARMNDRLAQDPALAAAHRAAHEAYIAERDRVGAEAGT
+GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDEAIALVAPWWTPEVCACEGA
+WDEAAAVPTKDLSRHVRHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAVADP
+TAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVDEYARLVQRHHAGRVRFVATSA
+SRDVSNRAAFVDGVRERLGVEPEVVSGAEEAGLSFAGAVSAVETADLGPEDLVLVVDLGG
+GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLRSDPPTSDEVTAARADALRLLDDAAARL
+PLERVARVVGVAGSVTTVTAEALGLSTYEPEAIHGARLPIAEFRAAAEGLVAATRAERAE
+RGFMHPGRVDVIGAGALLWSTVLERVAEVAGVTEAWASEHDILDGIVLSLRS
+>PROKKA_02506
+MTASTRPAHDRAVTEADLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRLTNGIPFP
+TTFYLTHPALTAAVSRVEADGEMARMNERLEQDAELAAAHRAAHEAYIAERDRVGADAGT
+GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDETIALVAPWWTPEVCACEGA
+WDEAAAVPTKDLSRHVKHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAGADP
+AAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVEEYARLVQRHHAGRVRFVATSA
+SRDVSNRAAFVDGVRERLGVEPEVVSGAEEAALSFTGAVSAVETADLGPEDLVLVVDLGG
+GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLHSDPPTSDEVAAARADARRLLDDAAARL
+PLERVARVVGVAGSVTTVTAEALGLSAYEPAAIHGARLPITEFRAAAQGLVAATRAERSE
+RGFMHPGRVDVIGAGALLWSTVLERVAETAGVTEAWASEHDILDGIVLSLRS
+>PROKKA_02378
+MTTPASRPASQEDALTETPAPQDPRAVTEQDLDTLSRQLGRPVRDVVEVGARCVCGNPLV
+ATTAPRLSNGIPFPTTFYLTHPVLTAAVSRLEAGGLMAEMNDRLAADPELAAAHRAAHEA
+YLAERERIRVASGTGEVPEIAHVSAGGLPDRVKCLHALVGHALAAGPGVDPLGDEAIAAV
+AEWWTPGVCACAGAWDEAAPVPTRDLSRHVKHLERVERLERVTVAGVDCGTNSIRLLIAR
+PAGAEDAAEPAGLPAGAPLEDVVREMRVVRLGEGVDATGAFSEAALERTFAAVDEYAHLV
+KRHHAGRVRFVATSASRDVSNREAFVQGVSERLGVEPEVISGEEEARLSFAGAVSAVDVS
+ALDDDALVLVVDLGGGSTEFVVGTPAGEVVDAVSMDMGCVRFTERFGLAGSAAADGVAAA
+RAAVEQVMDDVAARLPLERVGAAVGVAGTVTTVTAEALGLAEYDPAAIHGAVLPVERLRA
+AAEALLTADREERAARGFMHPGRVDVIGAGSLIWSTVLARVAAASGVTEAVTSEHDILDG
+IALSLRG
+>PROKKA_00453
+MTVSPRPAQDRTVTEKDLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRLSNGIPFP
+TTFYLTHPVLTAAVSRVEADGEMARMNDRLAQDPALAAAHRAAHEAYIAERDRVGAEAGT
+GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDEAIALVAPWWTPEVCACEGA
+WDEAAAVPTKDLSRHVKHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAGADP
+AAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVDEYARLVQRHHAGRVRFVATSA
+SRDVSNRAAFVDGVRERLGVEPEVVSGAEEAGLSFAGAVSAVETADLGPEDLVLVVDLGG
+GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLRSDPPTSDEVTAARADALRLLDDAAARL
+PLERVARVVGVAGSVTTVTAEALGLSTYEPEAIHGARLPIAEFRAAAEGLVAATRAERAE
+RGFMHPGRVDVIGAGALLWSTVLERVAEVAGVTEAWASEHDILDGIVLSLRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000484.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000484.fa
new file mode 100644
index 0000000000000000000000000000000000000000..180e999fb475d9729b07225a665c4dfe757ef159
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000484.fa
@@ -0,0 +1,25 @@
+>PROKKA_00460
+MLTVEKAHLLLTREDGRSESPSHHRVALAAAALADHRSAGIVTLEDVPVDRARVLVTAAG
+TTGDPVLDSSLGQVDALAGRPLVSTVAAGKPDLRKAVVAHLTETGRLTERKAFLATRHVP
+RGTERTELLAHLTAVVLDEAEPCDEDVLLLGVLQHLNLARRLLPGAHERYDRREMVRRIE
+TLTREDLLVQAVRRAVGGTCGTVTAAAAGSVA
+>PROKKA_00178
+MLTVEKAHLLLTREDGLSESPSHHRVALAAAALADHRSAGIVTLEDVPVDRARVLVTAAG
+TTGDPVLDSSLAQVDALAGRPLVSTVAAGKPDLRKAVVAHLTETGCLTERKAFLATRHVP
+RGTERTELLAHLTAVVLDEAEPSDEDVLLLGVLQHLNLARRLLPGAHERYDRREMVRRIE
+ALTREDLLVQAVRRAVGGTCGTVTAAAAGSAA
+>PROKKA_02487
+MLTAEKTHLLLTREDGRSESPSHHGVALAAAALADYRAAGIVTVEDAPVDRARVLVTAAG
+VTGHPVLDARLGKVDALAGTPVTAAVAAGRPNLRKAVIARLTETGDLAEHKAFMATRHLP
+RGGTRAELLDRLTAVVLDEREATDEDVLLLGVLQHLNLAWRLLPGTHERYGRRELVRRVE
+SLTRSDLLVQAVRRAVGGTAAAVTAAAAGSLA
+>PROKKA_02371
+MLTSEKLHLLLTREDGRSLSPSHHGVALAAAVLADLRDAGIVSLEDAPVSRARVLVTGAG
+STDHPVLDALLPELDGLRGKKVAAVVGKGRPKARKPVVAHLVETGELVEHKALLNTRHTP
+VGPGRPALVAGLTSALDGDSPSDEDRLLLGVLHQLNVLRRVLPEAGAEGESRREQSRRLE
+RLTHDDLLVQAVGRTVSTAAAAAAAAG
+>PROKKA_00460
+MLTVEKAHLLLTREDGLSESPSHHRVALAAAALADHRSAGIVTLEDVPVDRARVLVTAAG
+TTGDPVLDSSLGQVDALAGRPLVSTVAAGKPDLRKAVVAHLTETGRLTERKAFLATRHVP
+RGTERTELLAHLTAVVLDEAEPSDEDVLLLGVLQHLNLARRLLPGAHERYDRREMVRRIE
+ALTREDLLVQAVRRAVGGTSGTVTAAAAGSAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000487.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000487.fa
new file mode 100644
index 0000000000000000000000000000000000000000..471ab934385dda9dd90364c5bc4330b23ca3274b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000487.fa
@@ -0,0 +1,20 @@
+>PROKKA_00464
+MTPLSGLPLVLTALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVL
+RVMVRSVRRVQQRSPQAEAMLVERHQQHLPDEVRAGGEHLDADSEDRLRRLQEKYPGYLQ
+EPAPEPQAPDTGRD
+>PROKKA_00182
+MTPLSGLPLVLTALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVL
+RVMVRSVRRVQQRSPEAEAMLVERHQQHLPDEVRAGGEHLDADSEDRLRRLQEKYPGYLQ
+APAPEPQAPDTGRD
+>PROKKA_02483
+MSPLSGLPLVLTALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVL
+RVMVRSVRRVQQRSPEAEAMLVDRHQQHLPEDVRELAPEDEERDAQDRLRHLQEKYPGYL
+QEPAPRPQSPDDGRS
+>PROKKA_02367
+MSLAPLALSAVSLAASVSPSAPMPAVPEPTLKPGLDKQDISPGIEGFLFTALMVVMAIIV
+FRLMVRSVRRVQQRSPEAEAMLVDRHQQHLPEEVREGGERLDGDAHDRIERLRRRYPGYL
+QDPTPEPESPDTGREPR
+>PROKKA_00464
+MTPLSGLPLVLNALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVF
+RVMVRSVRRVQQRSPQAEAMLVERHQQHLPDEVRAGGEHLDADSEDRLRRLQEKYPGYLQ
+EPAPEPQAPDTGRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000493.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000493.fa
new file mode 100644
index 0000000000000000000000000000000000000000..93d47c3b5afaed019fcff51d6a17264639bceef3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000493.fa
@@ -0,0 +1,45 @@
+>PROKKA_00470
+MTAENTDQQFRIEHDTMGEVKVPVNALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA
+AAKANAELGIISQERADAIVAAADQVIAGDHDDQYPIDVFQTGSGTSSNMNTNEVLATLA
+TRALKEAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTAALVNDLVPALDHLAVSLEKKA
+EAFAGVVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIQSALPRVAEVPLGGTAVGTG
+INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNIAFSLMKINNDL
+RWMGSGPNTGLGEIAIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVALSSTNGA
+FELNVGIPVMAANLLESIRLLANTTRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV
+IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDKALDTMSMTHPE
+>PROKKA_00188
+MTAENTDQQFRIEHDTMGEVKVPVNALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA
+AAKANAELGIISQERADAIVAAADQVIAGDHDDQYPIDVFQTGSGTSSNMNTNEVLATLA
+TRALKEAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTAALVNDLVPALDHLAVSLEKKA
+EAFAGVVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIQSALPRVAEVPLGGTAVGTG
+INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNIAFSLMKINNDL
+RWMGSGPNTGLGEIAIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVALSSTNGA
+FELNVGIPVMAANLLESIRLLANTTRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV
+IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDKALDTMSMTHPE
+>PROKKA_02477
+MTAQNPEQQFRIEHDTMGEVKVPIDALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA
+AAKANAELGVISQERADAIVAAADQVIAGEHDDQYPIDVFQTGSGTSSNMNTNEVLATLA
+TRALKDAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTGALINELIPALDHLAVSLEKKE
+KAFANIVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERVESSLPRVAEVPLGGTAVGTG
+INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNVAYSIMKINNDL
+RWMGSGPNTGLGEIFIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVSLSSTNGA
+FELNVGIPVMAANLLESIRLLANTSRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV
+IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDTALDTMSMTHPE
+>PROKKA_02361
+MTAQNTEQQFRIEHDTMGEVKVPVDALYRAQTQRAVENFPISGKTLEPAHIHALAQIKKA
+AAKANAELGVISQERADAIVAAADEVISGKHDGEYPIDVFQTGSGTSSNMNTNEVLATLA
+TRRLKDAGSSEEVHPNDHVNASQSSNDVFPTSVHVAVTGALVNDLKPALEHLAESLERKA
+EEFQGIVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIEASLPRVAEVPLGGTAVGTG
+INTPQGFSARVIELLAEETGLPITEARNHFEAQANRDGLVEASGQLRNIAYSFIKINNDL
+RWMGSGPNTGLGEIALPDLQPGSSIMPGKVNPVICEAAIMVAAQVIGNDTTISLSSTNGA
+FELNVGIPVMAANLLESIRLLANTSRVMADKMIDGIEANEERCTFLAGASPSIVTPLNKV
+IGYEAAAAIAKHAVKNKMTVREAVVDLGYVERGEVTEEQLDKALDTMSMTHPGE
+>PROKKA_00470
+MTAENTDQQFRIEHDTMGEVKVPVNALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA
+AAKANAELGIISQERADAIVAAADQVIAGDHDDQYPIDVFQTGSGTSSNMNTNEVLATLA
+TRALKEAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTAALVNDLVPALDHLAVSLEKKA
+EAFAGVVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIQSALPRVAEVPLGGTAVGTG
+INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNIAFSLMKINNDL
+RWMGSGPNTGLGEIAIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVALSSTNGA
+FELNVGIPVMAANLLESIRLLANTTRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV
+IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDKALDTMSMTHPE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000494.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000494.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e0aa7b7cd8884c401b1398e3889ea0062ee678bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000494.fa
@@ -0,0 +1,25 @@
+>PROKKA_00471
+MTPHTRPETTPAPDVVVPTSDLTPAEAWEVLAEGNRRFVAGEPSHPNQNAERRSDLTAGQ
+APVAVIFGCADSRLAAEIIFDLGLGDVFVVRTAGHVIDDAVLGSIEYGVDVLEIPLVIVL
+GHNSCGAVTATVESYISGTMPRGFVRPLVERIIPSVLAGRRRGLEEVDEFVAEHVDQTCD
+HLLETSQSVRAAVESGRTAVVGLTYSLSEGTARPGRVHGDLAV
+>PROKKA_00189
+MTPHTRPETTPAPDVVVPTSDLTPAEAWEVLAEGNRRFVAGEPSHPNQNAERRSDLTAGQ
+APVAVIFGCADSRLAAEIIFDLGLGDVFVVRTAGHVIDDAVLGSIEYGVDVLEIPLVIVL
+GHNSCGAVTATVESYISGTMPRGFVRPLVERIIPSVLAGRRRGLEEVDEFVAEHVDQTCD
+HLLETSQSVRAAVESGRTAVVGLTYSLSEGTARPGRVHGDLAV
+>PROKKA_02476
+MSTENTATAAAAAHDDGAAGSRPTPQEAWETLAEGNRRFVAGDPGHPNQNAERRSTLTSG
+QEPIAVIFGCSDSRLAAEIIFDVGLGDVFVIRTAGQVIDDAVLGSLEYSVDVLKIPLIVV
+LGHDSCGAVTATVESYISGDMPPGFIRSLVERITPSVLAGRRRGLEEIDDFVAEHVDQTC
+DRLVETSQAVRDAVEAGRTAVVGLTYSLAGGTAQPGRVLGALQV
+>PROKKA_02360
+MTTAAETTPARPTPAEAWRTLQEGNRRFVAGTPGHPNQDSERRHGLTEGQAPIAVIFGCA
+DSRLAAEIIFDVGLGDVFVVRTAGHVVDDAVLGSLEYAVDSLDVPLIIVLGHDSCGAVTA
+TVESYISGTMPAGFVRSLVERITPSVLAGRRRGLEEVDDFVAEHVDQTCDRLLETSQSVR
+AAVEAGRTAVVGLTYSLAEGTASPGRVHGRIEA
+>PROKKA_00471
+MTPHTRPETTPAPDVVVPTSDLTPAEAWEVLVEGNRRFVAGEPSHPNQNAERRSDLTAGQ
+APVAVIFGCADSRLAAEIIFDLGLGDVFVVRTAGHVIDDAVLGSIEYGVDVLEIPLVIVL
+GHNSCGAVTATVESYISGTMPRGFVRPLVERIIPSVLAGRRRGLEEVDEFVAEHVDQTCD
+HLLETSQSVRAAVESGRTAVVGLTYSLSEGTARPGRVHGDLAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000496.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000496.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a0689f0fd24623095ab8dfc5f40844a4c5fff99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000496.fa
@@ -0,0 +1,35 @@
+>PROKKA_00473
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT
+GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA
+DGRVHTQSIVMRSSSGTVRTVDAEHDVKKWSKWLGDRDAR
+>PROKKA_00191
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPGTGVDMMMGIGGTPEGIVTACAIKAT
+GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA
+DGRVHTQSIVMRSSSGTVRTVDAEHDVKKWSKWLGDRDAR
+>PROKKA_02474
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVSMAGTVVIGEGEKDEAPMLFNGEEVGDGSGAPVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDLRLPVKQNVALVAKALDKPASQVTVCVLDR
+PRHEGLVKEIREAGARVKFILDGDVAAAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT
+GGVIQGRLAPTDETEKQKALDAGLDLDAVLSTNDLVTSDHCYFAATGITDGDLLRGVRFV
+DGRVVTQSIVMRSWSGTVRTVDAEHDVRKWSKWLEDRGTRTGR
+>PROKKA_02358
+MTSASSENTGYENHVPDRNLAMELVRVTEAAAIAASPWVGGGDKNRADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGERVGDGKGASVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRAAGARVKFILDGDVAGAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT
+GGVIQGRLAPTDDAEKQKALDAGLDLDAVLTTDELVTSDHCYFAATGITDGDLLRGVRFA
+GGRVHTQSIVMRSKSGTVRTVDAEHHVDKWSQWLKNRG
+>PROKKA_00473
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPGTGVDMMMGIGGTPEGIVTACAIKAT
+GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA
+DGRVHTQSIVMRSSSGTVRTVDADHDVKKWSKWLEDRDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000497.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000497.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef638be810efa5cd9cb07a410b3546ac9c09837a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000497.fa
@@ -0,0 +1,40 @@
+>PROKKA_00474
+MHVLKPVIRDYAWGSPTLLADLQGREPTGRPEAELWLGDHPGAPCVAVVADGARVGLDEV
+VAADPERCLGPAAPEGRLPFLMKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPQ
+RNYKDANHKPEMLLALTPFAAMCGFRSPEVSSDSFEALARALTERADGDTSAVAVAAARI
+SQALAAGDLEDAFTSILDPDSVWGAPGAVAQVVDVLRAAPDLAERDPSLATALEAAQHHP
+DDPGVVVAILLNRVDLAPGQAIHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHMDVP
+ELRRVVTFEALPVPSTEPERVADSVVAFRPPFEEFELLQATLEDDAVHGLDVHGPGIAVV
+TRGTASLALAGQEIELGPGEAVFLPAAETASGPLAVRAAAGAPATVHVAGLPRG
+>PROKKA_00192
+MHVLKPVIRDYAWGSPTLLADLQGREPTGRPEAELWLGDHPGAPCVAVVADGAHIGLDEV
+VAADPERCLGPAAPEGRLPFLMKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPE
+RNYKDANHKPEMLLALTPFSAMCGFRSPEVSSDSFEALARALTERADGDTSAVAVAAARI
+SQALAAGDLEDAFTSILDPDSVWGAPGAVAQVVDVLRAAPDLAERDPSLATALEAAQHHP
+DDPGVVVAILLNRVDLAPGQAIHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHVDVP
+ELRRVVTFEALPVPSTEPERVADSVVAFRPPFEEFELLQATLEDDAVHGLDVHGPGIAVV
+TRGTARLVLAGQEIELGPGEAVFLPAAETASGPLAVRAAAGAPATVHVAGLPRG
+>PROKKA_02473
+MHVLKPVIRDYAWGSPTLLARLQGREPTGRPEAEIWLGDHPGAPCGVVVGDGSVTGLDEL
+TAADRERCLGPNVDTDRLPYLAKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPH
+RNYKDANHKPEMLVALTHFSAMCGFRSPEVSSDSFEALAHALTEHADGDTSAVAVAAARI
+SQTLAAGDLEDAFTAILDPESVWAAPGSVAQVVEVLRAAEDLAERDPSLATALEVAEHYP
+DDPGVIVAILLNRVDLAPGQALHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTAKHVDVE
+ELRRVVTFEAVPVPSTEPERVADSVVAFRPPFDEFELLQATLEDDAVRELDVHGPGIAVV
+TRGSAHLGLAGQEVTLGPGESVFLPAAETATGPLAVRAADGAPATVHVTDLPRR
+>PROKKA_02357
+MHLLEAVVRDYAWGSPTLLAELEGREPSGAPEAEKWLGAHPGAPCTVSGPEGRCGLDELI
+AADPAPMLGEAARFGRLPYLMKLLAAGRPLSIQAHPTRERARAGFAAEEAAGVPVDAPHR
+NYKDDNHKPEMIVALTPFSALCGFRRPEDAAATFERMADALAEWADGDATDVGIAARRIA
+AHLAAEDVEAAFADILDPDAVWSAGGVDRLIEAVRAQPDLVAHDPALATALEVAEQCPGD
+PGVLVTLLLNRVDLVPGQAVHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHVDVPEL
+RRVVAFAPLPVPYTDPVEDGAGVVRYRPPFEEFELTRLAADAGGPSAEARVAGPAIAVAV
+DGPAVLACGADAVRLEAGAAVFLPAEETAAAPLTLSPATDDAPARVFVAALPTA
+>PROKKA_00474
+MHVLKPVIRDYAWGSPTLLADLQGREPTGRPEAELWLGDHPGAPCVAVVADGARVGLDEV
+VAADPERCLGPAAPEGRLPFLMKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPQ
+RNYKDANHKPEMLLALTPFAAMCGFRSPEVSSDSFEALARALTERADGDTSAVAVAAARI
+SQALAAGDLEDAFTSILDPDSVWGAPGAVAQVVDVLRAAPDLAERDPSLATALEAAQHHP
+DDPGVVVAILLNRVDLAPGQAIHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHVDVP
+ELRRVVTFEALPVPSTEPERVADSVVAFRPPFEEFELLQATLEDDAVHGLDVHGPGIAVV
+TRGTASLALAGQEIELGPGEAVFLPAAETASGPLAVRAAAGAPATVHVAGLPRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000498.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000498.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3aafb320d0d7d7693f14f89d495481a4fbf2cdf1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000498.fa
@@ -0,0 +1,52 @@
+>PROKKA_00475
+MSSATGSVPAGHAQPDPLRDPRVASPTERTRRALILTALTLLVPGGAQLVAGSRRLGRVA
+LRVTVTVWAVLILGLLWWLVSRASLISLMARDGVLLGLAVVLAALAVGWAVLWVDTFRLI
+RPHLLAPGARKITAAVTALALVLTSGALLYGGWAANTSRGALGEVFQEGPAVPEAEGRYN
+ILVLGADAGEGRQGLRPDSMHVVSVDARTGAIVMFSLPRNLQNAPFVEGSPLWDVYPNGF
+DCGDECILNALYTDVEEHHADLYPDAEHPGAEAMKDAAGGILGLDVSGYALMDMGGFAQL
+IDAMGGVDVVSGGYVVHRGVRPDGAWGNIWWEPGTHHFNGDDALAFARSRHWSTDYARIR
+RQQCMQAAMLEQFSPATVLTRFEGILAAGQQIVTTDLPQSQLGTFADLAERSRGQKMRRL
+TIGPPDFGDTGTHFTTYPDYDLVHRRVDEMLADESVTAGSEPTGVSATPLLTVLAVVAQE
+TQTPDVDEDDPATWPAPPTRTDGEPFTAEDLMTAEDLGQEDVLNHASSTNGLCVPAP
+>PROKKA_00193
+MSPATGSVPAGHAQPDPLRDPRVASPTERTRRALILTALTLLVPGGAQLVAGSRRLGRVA
+LRVTVTVWAVLILGLLWWLVSRASLISLMARDGVLLGLAVVLAALAVGWAVLWVDTFRLM
+RPHLLAPGARKITAAVTALALVLTSGALLYGGWAANTSRGALGEVFQEGPAVPEAEGRYN
+ILVLGADAGEGRQGLRPDSMHVVSVDARTGAIVMFSLPRNLQNAPFVEGSPLWDVYPNGF
+DCGDECILNALYTDVEEHHADLYPDAEHPGAEAMKDAAGGILGLDVSGYALMDMGGFAQL
+IDAMGGVDVVSGGYVVHRGVRPDGAWGNIWWEPGTHHFNGDDALAFARSRHWSTDYARIR
+RQQCMQAAMLEQFSPATVLTRFEGILAAGEQIVTTDLPQSQLGTFADLAERSRGQKMRRL
+TIGPPDFGDTGTHFTTYPDYDLVHRRVDEMLADESATAGSEPTGVSATPLLTVLAVVAQE
+TEAPDVDEDDPATWPAPPTRSDGEPFTAEDLMTAEDLGQEGVLNHASSTNGLCVPAP
+>PROKKA_02471
+MSPATGSVPAGHAQPDPLRDPRVASPTERTRRALILTLLTLFVPGGAQVVAGSRPLGRAA
+LRVTVAVWGVLLAGLLWWLVHRASLISLLARDGVLLVLAIALGLLAVGWAVLWIDTLRLI
+RLHLLAPGARKATAVATVLALVLTSGALLYGGWATNAGRGALGSVFGDGPAVARTEGRYN
+ILVMGGDAGEGREGLRPDSIHVASVDARSGAVVMFSLPRNLQNAPFTEGSPLWGVYPDGF
+SCGDECILNALYTDVETNHPDLYPDAENPGAEAMMDAAGGILGLEISGYALMDMGGFAQL
+IDAMGGVDLVTGGYVVHRGVRPDGEWGNIWWEPGEHHFDGKDALAFARSRHWSTDYARIR
+RQQCMQAAMLAQFSPGTVLTRFEQILDAGQQIVTTSLPQSQLGTFVDLAERSRGQKMRRL
+TIGPPDFGDTRDQFTTFPDYDLVHERVDEMLAEEPGQAGGATGGEAGHAAGVGSGASALP
+LLTVLAVAAQEAVPDEVDEDDPATWPAPPTRPDGGAYTAEDLMLAEDLGQEDLLNHASST
+NGLCAPGR
+>PROKKA_02356
+MPASAASSPVLTRDPVRDPRQATGPERRRRAGILLLLTLLVPGGAQAVAGSRRWGRIALR
+VTLAVWAAVLLALVLALTARAALVSVLANPVVLVLLGVVLVTLAIGWGLLWVDTFRLIRV
+HLLGPRARAATAAATVVALVVTSGGLGYTAWMTQSGRGALGSIFGSGPAIEAADGRYNIL
+VMGGDAGEDRVGLRPDSMHVASVDAETGAVTLFSLPRNLQNAPFTPDSPLWQAYPNGFDC
+GDDCILNALYMDVEEKHKDLYPDAEHPGAEAMMDAAGGVLGLEITGYAMMDMAGFAQLVD
+AMGGVDVVSGGYVTHRGARPDGTWGDIWWEPGTHHFGGDDALAFARSRKFATDYARIRRQ
+QCMQAAMLQQFTPATVLTRFEGIVSAGTQIVTTNVPQSQLGTFVDLADRSRGYRMARLTI
+GAPDFGTANDRFTTRPDYDLVHRRVAELLDEEPTKAGSASTAAPAASPGATPLLALTAAI
+PAPLLVAEASPAATGTGGTTRPGVDPDDPSTWPSAPTGPNGEPYSAMELMRIQDAGDEAQ
+LVRIASTNDLCAPGG
+>PROKKA_00475
+MSSATGSVPAGHAQPDPLRDPRVASPTERTRRALILTALTLLVPGGAQLVAGSRRLGRVA
+LRVTVTVWAVLILGLLWWLVSRASLISLMARDGVLLGLAVVLAALAVGWAVLWVDTFRLI
+RPHLLAPGARKITAAVTALALVLTSGALLYGGWAANTSRGALGEVFQEGPAVPEAEGRYN
+ILVLGADAGEGRQGLRPDSMHVVSVDARTGAIVMFSLPRNLQNAPFVEGSPLWDVYPNGF
+DCGDECILNALYTDVEEHHADLYPDAEHPGAEAMKDAAGGILGLDVSGYALMDMGGFAQL
+IDAMGGVDVVSGGYVVHRGVRPDGAWGNIWWEPGTHHFNGDDALAFARSRHWSTDYARIR
+RQQCMQAAMLEQFSPATVLTRFEGILAAGQQIVTTDLPQSQLGTFADLAERSRGQKMRRL
+TIGPPDFGDTGTHFTTYPDYDLVHRRVDEMLADESVTAGSEPTGVSATPLLTVLAVVAQE
+TQTPDVDEDDPATWPAPPTRTDGEPFTAEDLMTAEDLGQEDVLNHASSTNGLCVPAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000506.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000506.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c6c6db53943b1d079da995d714a5949fea8c909
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000506.fa
@@ -0,0 +1,40 @@
+>PROKKA_00484
+MASHQAGRGRDERAGAEDFDSGLDYGAFVEDDAADDPNRTQALPAMGRDDDGGAQHTSAL
+SPEDLAALRGGDAAAADRRDAGRPAADADRDIVASRAVPEGGRRPLPGADELGPLSAAVG
+ARAAGSSAAAPVDRYPEDGTAAPVAQAAALQGPTPEERARLPKAGPRLAQVLLAILAPLA
+LVLATVRLVASPVFLWLEYHRPGFPADRFGFTLADRMHYGSAGLDYVTNLAGPRYLSSLT
+HQGAPLFTEVEVDHMTDVKTVLWIAAAALVVLLVVCALLIASLLRTSPGGVRRALFAGAV
+WLPLAVIALAVLAVLGWETFFAGFHSLFFADGTWTFSVRDALIRLYPQQFWVDAAVVVGL
+VTLLASLVTLVLTWPTRRRRELSADRREQLLRTRLRWAREDDAVVR
+>PROKKA_00202
+MASHQAGRGRDERAGAEDFESGLDYGAFVQDDAADDPNRTQALPATGRDDDGGAQHTSAL
+SPEDLAALRGGDAAAADRRDADRPAPDADRDIVASRAVPESDRRPLPGADELGPLSAAVG
+ARAAGSSAAAPVDRYPEDGTAAPVAQAAALQGPTPEERARLPKAGPRLAQVLLAILAPLA
+LLLAAVRLVASPVFLWLEYHRPGFPADRFGFTLADRMHYGSAGLDYVTNLAGPRYLSSLT
+HQGAPLFTEVEVDHMTDVKTVLWIATAALVVLVVVCALLIASLLRTSPGGVRRALFAGAV
+WLPLAVIALAVLAVLGWETFFAGFHSLFFADGTWTFSVQDALIRLYPSQFWIDAAAAVGL
+ISLLTALLTLVFTWPTRRRRERTADQRSAFESTRLRWAREEDAQLR
+>PROKKA_02463
+MASHQAGRGREERAGAEDFESGLDYGAFAEDDAAEDPNRTQALPASGRDDAGVQHTSALS
+PEDLAALRGGDAAAADGRAERSAERGMPDARERDIVASRAVPSSDRRPLPGADELGPLSA
+AVGARSASGSSAADPADRYPQDASAAYAASSSAALQGPTPEERARLPKAGPRVAQVLLAI
+LAPLALLLAAVRFVASPAFLWLEYHRPGFPADRFGFDTGDRMHYGSAGLDYVTNLAGSRY
+LSSLTHQGEPLFTEAEVSHMTDVKVVLWIALAVLVALVVVCALLIAHLLRTSPGGVRRAL
+FAGALWLPLALIALAVLAVLGWEIFFAGFHSLFFADGTWTFSVRDALIRLYPEQFWVDAA
+LVVAAIAVIASLVTLVFTWPTRRRREMSADRRGQLLDTRLRWAREEDSPVR
+>PROKKA_02347
+MASHTPGRSDGAGSGSSDFESGLDYGAFVEDDDAQPTQALPRTTEEHGAQRTLAFDRDEL
+AAAAAGAGTGAGRSGAGSRAAGAAHGVAGEDITASRPAPAPAPSPASPWGADRYPSDATV
+PASAPAAADTRTPEERARLPKAGPRLAQVLLAVLAPLVLLLGAVRLVATPLFLWLEYHRP
+GFPADPYGFSTADRMTYGSAGLDYLHNLAGPRYLSELTFQGKPLLSEAAVSHMTDVKTVM
+WIATAVLVLLGLACLLLALYLRRTSPGGVRRALFAGALGLLVVIVVLAAMAATGWQGFFA
+GFHSLFFAEGTWTFSVSDPLIRLYPAQFWVDAAVAVAVLALIGIIAALVAGAPTRRRREM
+SQDRRAQLEATRLRWAREDAHGVR
+>PROKKA_00484
+MASHQAGRGRDERAGAEDFESGLDYGAFVQDDAADDPNRTQALPAMGRDDDGGAQHTSAL
+SPEDLAALRGGDAAAADRRDAGRPAADADRDIVASRAVPEGDRRPLPGADELGPLSAAVG
+ARTAGSSTAAPVDRYPEDGTAAPVAQAAALQGPTPEERARLPKAGPRLAQVLLAVLAPLA
+LLLAAVRLVASPVFLWLEYHRPGFPADRFGFTLADRMHYGSAGLDYVTNLAGPRYLSSLT
+HQGAPLFTEVEVDHMTDVKTVLWIATAALVVLVVVCALLIASLLRTSPGGVRRGLFAGAV
+WLPLAVIALAVLAVLGWETFFAGFHSLFFADGTWTFSVRDALIRLYPQQFWVDAAVVVGL
+VTLLASLVTLVLTWPTRRRRELSADHREQLLRTRLRWAREDDAVVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000512.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000512.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b3d0b72e705fa61280eb0c91558e83f83fc22fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000512.fa
@@ -0,0 +1,34 @@
+>PROKKA_00492
+MVQPSPHPAPAPLLSAADVRRIAAELDLRPTKQWGQNFVIDPNTIRRIVQAADVTADEHV
+LEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAARLPRTAAEFRPGAEDALAVLHADAMTLS
+EQALAEVRPAAAAGGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG
+PGSKVYGVPSAKAAWYADVRKAGTIGTQVFWPAPRIHSGLVAFTRREPPTGGASRREVFA
+VVDAAFAQRRKTLRAALASWAGSPQAAEDALVAAGVDPRARGEALDIAAFARIAEHGPRR
+AAEVSA
+>PROKKA_00213
+MVQPSPHPAPAPLLSAADVRRIAAELDLRPTKQWGQNFVIDPNTIRRIVQAADVTADEHV
+LEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAARLPRTAAEFRPGAEDALAVLHADAMTLS
+EQALAEVRPAAAAGGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG
+PGSKVYGVPSAKAAWYADVRKAGTIGTQVFWPAPRIHSGLVAFTRREPPAGSTSRREVFA
+VVDAAFAQRRKTLRAALASWAGSPQAAEDALVAAGVDPRARGEALDIAAFARIAEHGPRR
+AAEEVVA
+>PROKKA_02455
+MIDPNTIRRIVQAAGVGPDEHVLEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAERLPHTV
+QEFRPASADALAVLHADALRMTAADLDAVRPAAAPGGPTALVANLPYNVAVPVLLHALAE
+LPGLRHGLVMVQEEVADRLAAGPGSRVYGVPSAKAAWYAQVDKAGTIGTQVFWPAPRIHS
+GLVAFTRREPPTSAVSRAETFAVVDGAFAQRRKTLRAALAGWAGSPQAAEDALVAAGVDP
+RTRGEALGIEAFARIAEHGPRRAAGEGSA
+>PROKKA_02339
+MVPPPDAPATAPLLSAADVRRLAAELDLRPTKQWGQNFVIDPNTIRRIVAAADLAPDEHV
+LEIGPGLGSLSLGLLDAASAVTAVEIDPVTAARLPATAAEFRPERAADLAVLHADAMTLT
+AEGLDSVRPAGAASGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG
+PGSRVYGVPSAKAAWYADVRKAGVIGTQVFWPAPRIHSGLVAFTRREPPTQAVDRREVFA
+VVDAAFAQRRKTLRAALATWAGSPALAEEALVAAGVDPKARGEALDIAAFARIAEHRPEA
+AS
+>PROKKA_00491
+MVQPSPHPAPAPLLSAADVRRIAAELDLRPTKQWGQNFVIDPNTIRRIVQAADVTADEHV
+LEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAARLPRTAAEFRPGAEDALAVLHADAMTLS
+EQALAEVRPAAAAGGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG
+PGSKVYGVPSAKAAWYADVRKAGTIGTQVFWPAPRIHSGLVAFTRREPPAGGASRREVFA
+VVDAAFAQRRKTLRAALASWAGSPQAAEDALVAAGVDPRARGEALDIAAFARIAEHGPRR
+AAEEVVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000515.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000515.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37fc03e6ecc59f017589377005b55d23c52fd835
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000515.fa
@@ -0,0 +1,50 @@
+>PROKKA_00497
+MSQPSARPSAVIVLAAGQGTRMKSTTPKIMHAIGGRSLVGHALAAAWSLSPEHLVAVVRH
+ERARVAEHIETVAAQLGIDALAIADQDDVPGTGRAVELGLAALPADLEGTVVVTYGDVPL
+LTPETLARLVADHEADGNAVTVLTATLEDATGYGRIVRDAEGLVERIMEHKDALAHAEAT
+GDDSFVAIREVNSGIYAFDAALLRRTLPEISTDNVQGEKYLTDVLGMARAEGGRVASVGT
+DDVWEVEGANDRRQLSDLGRQLNDRVLRGWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG
+TQLHGATSVATGAVVGPDSTLTDTQVGEGAVVKRTDATEAVIGAGATVGPFTYLRPGTVL
+GEDGKIGAFYETKNVTVGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVNKHRTVIG
+AHVRTGSNTVFTAPVTVGDGAYTGAGAVVREDVPAGALALNAVSQRTLEGWVPAKRPGTS
+SAEAARAAGAEGSGAQG
+>PROKKA_00218
+MSQPSARPSAVIVLAAGQGTRMKSTTPKIMHAIGGRSLVGHALAAAWSLAPEHLVAVVRH
+ERARVADHLETVAAQLGIDALAIADQDDVPGTGRAVELGLAALPADLEGTVVVTYGDVPL
+LTPETLARLVADHEADGNAVTVLTATLEDATGYGRIVRDAEGLVERIMEHKDALAHAEST
+GDDSFVAIREVNSGIYAFDAALLRRTLPEISTDNVQGEKYLTDVLGMARAEGGRVASVGT
+DDVWEVEGANDRRQLSDLGRQLNDRVLRGWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG
+TQLHGATSVATGAVVGPDSTLTDTQVGEGAVVKRTDATEAVIGAGATVGPFTYLRPGTVL
+GEDGKIGAFYETKNVTVGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVAKHRTVIG
+AHVRTGSNTVFTAPVSVGDGAYTGAGAVVRDDVPAGALALNAVAQRTIEGWVPAKRPGST
+SAQAARAAGAEGSGAQG
+>PROKKA_02450
+MPQSSVRPSAVIVLAAGQGTRMKSTTPKIMHPIGGRSLVGHALAAAHSLAPEHLVAVVRY
+ERDRVAEHIESVAEGLGIASLAIADQDEVPGTGRAVELGLAALPKDLEGTVVVTYGDVPL
+LTPETLERLVAAHEADGNAVTVLTAALEDATGYGRIVRDGEGLVERIMEHKDALAHAEST
+GDSSFVEIREVNSGIYAFDAALLRRTLPAISTDNVQGEKYLTDVLGMARAEGGRVASVGT
+DDVWEVEGANDRRQLSDLGRRLNDRVLRHWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG
+TQLHGATQVATGAVVGPDTTLTDTRVGERAVVKRTDATEAVIGADATVGPFTYLRPGTVL
+GEEGKIGAFYETKKVTIGRGAKLSHLGYAGDAEIGDYTNIGCGNITANYDGEKKHRTVIG
+AHVRTGSNTVFTAPVTVGDGAYTGAGAVVREDVPAGALALNAVSQRTIEGWVPAKRPGTS
+SAQAAQAADAQGDAPQG
+>PROKKA_02334
+MPQTAVRPSAVIVLAAGQGTRMKSATPKIMHAIGGRSLVGHALAAAQSLAPEHLVTVVRH
+ERDRVAAHIEEAAADLGVTGLAIADQDEVPGTGRAVELGLAALPEDLEGTVVVTYGDVPL
+LTPETLQRLVAAHEADGNAVTVLTATLADATGYGRIVRDADGLVERIMEHKDALAHAEAT
+GDSSYVEIAEVNSGIYAFDAALLRRTLPQLSTENVQGEKYLTDVLGMARAEGGRVASVGT
+DDVWEVEGANDRRQLSDLGRQLNERVLRRWMKDGVTVVDPSSTWVDVTVELAADVTLKPG
+TQLHGSTTVATGAVVGPDSTLVDTRVGERGTVKRTDATEAVIGDDATVGPFTYLRPGTVL
+GEEGKIGAFYETKKVTIGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVDKHRTVIG
+SHVRTGSNTVFIAPVTVGDGAYTGAAATVRQDVPAGALALNAVDQRNVDGWVVSRRAGTA
+SAEAAQAAGAVGRDQATEAAQD
+>PROKKA_00496
+MSQPSARPSAVIVLAAGQGTRMKSTTPKIMHAIGGRSLVGHALAAAWSLAPEHLVAVVRH
+ERARVAEHLETVAAQLGIDALAIADQDDVPGTGRAVELGLAALPADLEGTVVVTYGDVPL
+LTPETLARLVADHEADGNAVTVLTATLEDATGYGRIVRDAEGLVERIMEHKDALAHAEST
+GDDSFVAIREVNSGIYAFDAALLRRTLPEVSTDNVQGEKYLTDVLGMARAEGGRVASVGT
+DDVWEVEGANDRRQLSDLGRQLNDRVLRGWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG
+TQLHGATSVATGAVVGPDSTLTDTQVGEGAVVKRTDATEAVIGAGATVGPFTYLRPGTVL
+GEDGKIGAFYETKNVTVGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVNKHRTVIG
+AHVRTGSNTVFTAPVTVGDGAYTGAGAVVREDVPAGALALNAVSQRTLEGWVPAKRPGTS
+SAEAARAAGAEGSGAQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000520.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000520.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1cbe717f96426785366bdd049c95adde1510d0d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000520.fa
@@ -0,0 +1,35 @@
+>PROKKA_00505
+MSATGYTVPAPPDARGGRSPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYATLG
+MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSEIL
+EAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA
+LPQVPRRDELVFVGSRYPNRVELLARLAAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP
+AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE
+VLVFEDADHLIELGRRVVADPAWGARIREAGRRRSHAEHTFAHRAAMAQGWWA
+>PROKKA_00225
+MSATGYTVAAPPEARGGRSPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYATLG
+MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSEIL
+DAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA
+LPEVPRRDELVFVGSRYPNRVELLTRLAAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP
+AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE
+VLVFEDADHLIELGRRIVADPAWGARIREAGRRRSHVEHTFAHRAAMAQGWWA
+>PROKKA_02445
+MSGTGYTVPARGARGTGRAERLFLVSPAFHGYHRSIARAWAAQGFDVTVHCYDAYATVPM
+KLRNKALLELPQKAGVDRTAARVAWDTERAVAALRAARPDRVLVIKGDSLGEAFWSEVVE
+AGLPRLLWLYDDLSRHDYSPEFLRAIGPVLSYARSEAEQLAGEGVDAHYLPNGFDPDMAL
+PSLPRREELVFVGSRYPNRVELLTTLAEAGVPVRAYGRQWSHHPVDRLRTWEVTRPALPA
+ERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYEPGEEV
+LVFENPEHLVELGRRVVAEPSWGERIREAGRSRSHAEHTFAHRAALAQEWWT
+>PROKKA_02329
+MSAGTYTIAARGERPVSGRPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYADLG
+MKLRNKLALELPQKAGLDRTAARVAWDTDRAVAALRAAAPDRVLVIKGDSLGDAFWDEVT
+GRALPRMLWLYDDLSRHDYSMDFLRGIGPVLSYARSEAESLAAQGVDAHYMPNGFDPEMV
+LPAVPRTEELVFVGSRYPNRVELLRALASAGVPVRAYGRQWSHHPVDRLRTWELSRPDLP
+AERDIPLAEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRPDVAEFYVPGEE
+VLVFEDTEHLVELGRRIVAEPAWGDRIRAAGRRRSHAEHTFSHRARMAQEWWA
+>PROKKA_00504
+MSATGYTVPAPPDARGGRSPERLFLVSPAFHGYHRSIASAWAAQGFDVAVHCYDAYATLG
+MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSAIL
+DAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA
+LPQVPRRDELVFVGSRYPNRVELLSRLTAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP
+AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE
+VLVFEDADHLIELGRRVVADPAWGARIREAGRRRSHAEHTFAHRAAMAQGWWA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000522.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000522.fa
new file mode 100644
index 0000000000000000000000000000000000000000..23169c41d3c6ab72185ffec019e3a03b894864b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000522.fa
@@ -0,0 +1,30 @@
+>PROKKA_00507
+MSILCVIPVRGGSRGLPGKNIRLLGGHPLVAWTIQAALEAEEDLHVVVSTDSAEIAEVAL
+RYGADVPGLRPAHLAQDSTPTEPVIEHVLAAERAAGVEPEGVMLLQATSPLRLPGTLDRA
+VRQFRDTGVDSLVGVVPVSPFLWRHPEDPDGEPIPDFDVTARKRRQDMTRTDLRFRENGS
+LYVTRPWVYDRLHNRLGGRIGLLELDDLEGVDIDTELDFALAEQQMDQYLAVHKVLRHRS
+DLGAPRTAETPTTGPNRTPGGAQ
+>PROKKA_00227
+MSILCVIPVRGGSRGLPGKNIRLLGGHPLVAWTIQAALEAGEDLHVVVSTDSAEIAEVAL
+RYGADVPGLRPAHLAQDSTPTEPVIEHVLAAERAAGVEPEGVMLLQATSPLRLPGTLDRA
+VRQFRDTGVDSLVGVVPVSPFLWRHAGDPDGEPIPDFDVTARKRRQDMTRADLRFRENGS
+LYVTRPWVYDRLHNRLGGRIGMLELDDLEGVDIDTELDFALAEQQMDQYLAVQKVLQHRP
+DLGAPRTAETPTTGPNRTLGGTQ
+>PROKKA_02443
+MSILCVIPVRGGSRGLPGKNIRLLGGHPLVAWTIQAALEAEADLHVVVSTDSEEIAEVAR
+RYGADVPGLRPAELAQDETPTEPVVEHALAAERAAGVEPEGVMLLQATSPLRLPGTLDRA
+VAQFRETGVDSLVGVVPVSPFLWRHAADPADPPVCDFDVAHRKRRQDMDRPDLRFRENGS
+LYVTRPWVYDELHNRLGGRIGMFELDDLEGVDIDTELDFALAEQQMDQYLAVHKVLQRVP
+DRTQLHGTSTATLGDAL
+>PROKKA_02327
+MSILCVIPVRGGSRGLPGKNIRMLGGHPLVAWTIQAALDAEADLHVVVSTDSEEIAEVAR
+KYGADVPALRPAELARDDTPTEPVVEHALAAERARGVEPEAVMLLQATSPLRLPGTLDRA
+VAAFREPGVDSVVGVVPVSPFLWRHAADPAAAPVADYDVDGRKRRQDMDRADLRFRENGS
+LYVTAPWVYDERHNRLGGRIALLELDDLEGVDIDTELDFALAEQQMDQYLAVQKLLQTRP
+DLTRTAGGAL
+>PROKKA_00506
+MSILCVIPVRGGSRGLPGKNIRLLGGHPLVAWTIQAALEAEEDLHVVVSTDSAEIAEVAL
+RYGADVPGLRPAHLAQDSTPTEPVIEHVLAAERAAGVEPEGVMLLQATSPLRLPGTLDRA
+VRQFRDTGVDSLVGVVPVSPFLWRHPEDPDGEPTPDFDVTARKRRQDMTRADLRFRENGS
+LYVTRPWVYDRLHNRLGGRIGMLELDDLEGVDIDTELDFALAEQQMDQYLAVQKVLQHRP
+DLGAPRTAETPTTGPNRTLGGTQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000523.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000523.fa
new file mode 100644
index 0000000000000000000000000000000000000000..439e2845a7d6d144d3811b6028c7bd9fbf5b2a48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000523.fa
@@ -0,0 +1,70 @@
+>PROKKA_00508
+MIIERRLTPYLVFPEDSLLAALQKMTDNRERTVFVVDSHGFLVGSLTDGDVRRWLLAQPE
+ASLDVAAADVAHRDPATAPLGATPAEMREALPAGALHLPLLDERGRLTALAINREAELRI
+GGHRIGEGHPAFLIAEIGNNHQGDVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA
+TAGEDLGAQRTLDELAKFSLSAEDMVRVFDHVREAGVALMCTPWDAPSMRVLREYPVDGV
+KIASADLTNHGLLRDAAASGLPMVLSTGMSREEEIREAAALVRSFGVPFAMLHAQSTYPA
+PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVALAAVARGAAIIEKHFTVDRGLEGNDHK
+VSLLPEEFAQMVRQTRDIEESIGVGTERVVSTGEAMNRINLAKSLVAARPLRVGATITAD
+DVTVKSPGRGLQPNELPRLVGRTLHREMAEGDFFFAGDLTDTVPTGRQFEFRRPWGLPVR
+YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFSEPMPMGFTTHLPDIFSGDFLVDLASD
+DDAVWERSIAEVQRTIDITRDLKRWFPHEEEPIMVITMGGFTLDRHIRPEERLPKYERIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL
+>PROKKA_00228
+MIIERRLTPYLVFPEDSLLAALQKMTDNRERTVFVVDSHGFLVGSLTDGDVRRWLLAHPE
+ASLDVAAADVAHRDPATASLGASPDEMREALPAGALHLPLLDERGRLTALAINREAELRI
+GGHRIGEGHPAFLIAEIGNNHQGDVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA
+TAGEDLGAQRTLDELAKFSLSAADMVRVFDHVREAGVALMCTPWDAPSMRVLREYPVDGV
+KIASADLTNHGLLRDAAASGLPMVLSTGMSREEEIRESVALVRSFGVPFAMLHAQSTYPA
+PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVALAAVARGAAIIEKHFTVDRGLEGNDHK
+VSLLPEEFAQMVRQTRDIEESIGVGTERVVSTGEAMNRINLAKSLVAARPLQAGVTITAD
+DVTVKSPGRGLQPNELPRLVGRTLHREMAEGDFFFAGDLTDTVPTGRQFQFRRPWGLPVR
+YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFREPLPMGFTTHLPDIFSGDFLVDLASD
+DDAVWERSIVEVQRTIDITRDLKRWFPNEEEPIMVITMGGFTLDRHIRPEERRPKYERIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL
+>PROKKA_02442
+MITERHLTPYLVFPEDSLLVALQKMTDNRERIVFVVDSHGFLAGSLTDGDFRRWLLANPG
+ASLEVAAVEAANRTPATGPVGASPAEVLAALPAGALHLPLLDERGRLAALAINRESELRI
+GEHRIGPGRPAFLIAEIGNNHQGSVDLARELVDLAVEAGADAVKFQLRDMDALYRQSGAG
+TAGEDLGAQRTLDELAKFSLPAEDMVRVFDHVRDAGVALMCTPWDAPSMRVLAQYPVDGV
+KIASADLTNHGLLRDAAAARLPMVLSTGMSREDEIKEAVELVRSSGVPFAVLHAQSTYPA
+PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVPLAAVARGASIIEKHFTVDRGLEGNDHK
+VSLLPEEFAQMVRQTREIEESIGVAAERVVSTGEAMNRINLAKSLVAARPLAAGETVTED
+AVTVKSPGRGLQPNELPRLVGRTLHRDMAEGDFFFAGDLTDTVPTGRQFEFRRPWGLPVR
+YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFTEPLPMGFTTHLPDIFSGDFLVDLASD
+DDAVWERSIAEVQRTIDITRDLKRWFPKEEAPIMVITMGGFTLDRHIAPAERQAKYDRIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL
+>PROKKA_02326
+MIIERHLTPYLVFPEDSLTVALQKMTDNRERIVFVVDTHGFLQGSLTDGDVRRWLLAHPG
+AALDSPAVAAANPSPATGLVGDAPSSVLAALPEGALHLPLLDERGHLTALAINRESELRI
+GSHRVGEGRPAFLIAEIGNNHQGSVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA
+TAGEDLGAQRTLDELAKFSLSVDDMVKVFDHTRAAGVALMCTPWDAPSMQVLADYPVDGV
+KIASADLTNHGLLRDAASRGIPMVLSTGMSREEEIQESAALVRSYGVPFAMLHAQSTYPA
+PYKDVNLAYLDRLAEIAQAPVGYSGHERGFHVALAAVVRGASIIEKHFTIDRSLEGNDHK
+VSLLPDEFAQMVRQTREIEESIGVAGERVVSTGEAMNRINLAKSLVAARSLTAGDVVAEA
+DVTVKSPGRGLQPNQLPQLVGRTLHRDLEEGDFFFAGDLTDSVPTGRQFEFRRPWGLPVR
+YHDYAALTKDCTPDFLEFHFSYKDLEIDIDTVFREPMPGGFTTHLPDIFAGDFLVDLASM
+DEQVWERSIAEVQRTIDITRDLKRWFPSEEAPIMVITMGGFTLDRHIRPEERQPKYERIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL
+>PROKKA_00507
+MIIERRLTPYLVFPEDSLLAALQKMTDNRERTVFVVDSHGFLVGSLTDGDVRRWLVAHPE
+ASLDVAAADVAHRDPVTAPLGASPAEMREALPTGALHLPLLDERGRLTALAINREAELRI
+GGHRIGEGHPAFLIAEIGNNHQGDVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA
+TAGEDLGAQRTLDELAKFSLSAEDMVRVFDHVREAGVALMCTPWDAPSMRVLREYPVDGV
+KIASADLTNHGLLRDAAASGLPMVLSTGMSREEEIRESVALVRSFGVPFAMLHAQSTYPA
+PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVALAAVARGAAIIEKHFTVDRGLEGNDHK
+VSLLPEEFAQMVRQTRDIEESIGVGTERVVSTGEAMNRINLAKSLVAARPLQAGATITAD
+DVTVKSPGRGLQPNELPRLVGRTLHREMAEGDFFFAGDLTDTVPTGRQFQFRRPWGLPVR
+YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFTEPMPMGFTTHLPDIFSGDFLVDLASD
+DDAVWERSIAEVQRTIDITRDLKRWFPNEEEPIMVITMGGFTLDRHIRPEERLPKYERIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000524.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000524.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3af78b613e0a2ef80b6bc8997e8694dc594795a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000524.fa
@@ -0,0 +1,35 @@
+>PROKKA_00511
+MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAADGFDVVRL
+GGPGRLGYLRALRAWDRGRGKDDVVWCNGLLPATALAGRPRRIVHLHQVPEKPLLRVFSA
+LARPGALAVLAPSRFAADRIRGARVLHNWVPAPTTPQAGRARDADEPLTVGFLGRLSEDK
+GIVTLLEAAALLRKTDPGAFVFRVAGESRFVADDEAERLATALKAAGEDVQVLGWQDTAE
+FLASVDVLAVPSQWAEVFGLVTAEAMAAGVPVVASDAGAVPEVVGSEHPFVFPQRDAAAL
+ADRLQAVRAVDLGAVAHSQQRRWESLFSPEAGRAAVAELLDDLSL
+>PROKKA_00231
+MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAADGFDVVRV
+GGPGRLGYMRALRVWDRGRGGDDVVWCNGLLPATALAGRPRRIVHLHQVPEKPLLRVFSA
+LARPGALAVLVPSRFAADRIHGARVLHNWVPGPTTPQAGRARGTDEPVTVGFLGRLSEGK
+GIVTLLEAAALLRRTDPGAFVFRIAGESRFVAEDEAERLATALKAAGEDVQVLGWQDTGE
+FLTSVDVLAVPSQWAESFGLVAAEAMAAGVPVVASDAGAVPEVVGSDHPFVVPQRDAAAL
+ANCLRAVRAVDLGEVAHSQRHRWASLFSPEAGRAAVAELLDDLSL
+>PROKKA_02440
+MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAANGFDVVRV
+GGPGRLGYLRALRAWDRDRGNDDVVWCNGLLPATALAGRPRRIVHLHQVPEKPLLRVFSA
+LARPGALAVLAPSRFAADRIRGARVLHNWVPGPTTPPARRARDADEPVTVGFLGRLSEDK
+GIVTLLEAAALLRKTDPGAFVFRVAGESRFVAEDEAERLATALKAAGEDVQVLGWQDTAE
+FLASVDVLAVPSQWAEVFGLVTAEAMAAGVPVVASDAGAVPEVVGNDHPFVFPQRDAAAL
+ADRLQAVRAGDLGAVAHSQRRRWASLFSPEAGRAAVAELLDDLSL
+>PROKKA_02323
+MTRRIWIAANQGEVGGGEVMLHHLATALHELGRDIAVVAPAAPSATAARLEADGFTVDRV
+GGPGRAGYMRALRRWHNGHREDVVWCNGLLPATALAGRPRRIVHLHQWLIRPRDRVLGTL
+AMRGALAVIAPSESVAREIPGCRVLHNWVPRPLPLSGAAPARRRPGEGGALRVGYLGRLS
+FDKGFHLLMDVAEELHREQPDEWRFFVAGEPRFTTGDDAREIRERLAASRAVTALGWQAP
+GDFLPTVDVLVVPSLAPESFGLVAAEAMAAGVPVAVSDSGALPEVAGDDHPLLFECDDHE
+ELAAALRRARQIDLAPLVAAQHRRWEALFSPEAGRAGVAALLEELHV
+>PROKKA_00510
+MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAADGFDVVRV
+GGPGRLGYLRALRAWDRGRDGDDVAWCNGLLPATALAGRPRRIVHLHQVPEKPVLRVFSA
+LARPGALAVLVPSRFAANRIRGARVLHNWVPAPTAPQTRPARGADDPVTVGFLGRLSEDK
+GIVTLLEAAALLRKTDPGAFVFRVAGESRFVAEDEADRLATALKAAGEDVQVLGWQDSGE
+FLATVDVLAVPSQWAEVFGLVTAEAMAAGVPVVASDAGAVPEVVGSDHPFVVPQRDAAAL
+ANCLRAVRAIDLGAVAHSQRHRWESLFSPEAGRAAVAELLDDLSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000527.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000527.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71e0b1ef41e81c20805573bf7d5cb0425644c641
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000527.fa
@@ -0,0 +1,31 @@
+>PROKKA_00516
+MKGIILAGGTGSRLHPITHGISKQLVPVYDKPMIYYPLSTLILAGIRDILVITTPQDAEQ
+FQRLLGDGSQFGVSLTYVQQPSPDGLAQAFVLGEEHIGVDHVALVLGDNIFYGPGMGQQL
+RRHTDVEGATVFGYWVKDPTAYGVVEFDTNGKAVSLEEKPAQPKSNFAVPGLYFYDNDVV
+EIAKDLKPSPRGELEITDVNRTYLERGTLNVEVLPRGTAWLDTGTFTDLNDASNFIHAVE
+SRQGLKVGSPEEAAWRQGLLTDDQLRERAERLVKSGYGRYLLDLLDSGR
+>PROKKA_00236
+MKGIILAGGTGSRLHPITHGISKQLVPVYDKPMIYYPLSTLILAGISDILVITTPHDAQQ
+FQRLLGDGSQFGISLSYVQQPSPDGLAQAFILGEDHIGDEHVALVLGDNIFYGPGMGQQL
+RRHAQVDGATVFGYWVVDPSAYGVVEFDDAGKAISLEEKPEEPKSNYAVPGLYFYDNDVV
+EIAKSLKPSARGELEITDVNRTYLERGTLNVEVLPRGTAWLDTGTFHDLNDASNFIRTIE
+SRQGLKVGAPEEVAWRQGLLTDDELRERAEPLVKSGYGRYLLELLESGR
+>PROKKA_02435
+MKGIILAGGTGSRLHPITHAISKQLVPVYDKPMIYYPLSTLILAGISDILVITTPHDAGQ
+FQRLLGDGSRFGISLTYVQQPSPDGLAQAFLLGEEHIGDDHVALVLGDNIFYGPGMGQQL
+RRHTEVHGATVFGYRVADPTAYGVVEFDGTGRAVSLEEKPTAPKSHYAVPGLYFYDNDVV
+EIARALKPSARGELEITDVNRTYLERGTLNVEVLPRGTAWLDTGTFHDLNDASNFIRTIE
+SRQGLKVGAPEEVAWRQGLLTDDELRERAEPLVKSGYGRYLLDLLENAR
+>PROKKA_02317
+MKGIILAGGTGSRLHPITHGISKQLVPVYDKPMIYYPLSTLILAGISDILVITTPHDAEQ
+FQRLLGDGSQFGVSLSYVQQPSPDGLAQAFILGEEHIGDDRVALVLGDNIFYGPGMGQQL
+RRHTEVEGATVFGYWVADPTAYGVVEFDGAGKAVSLEEKPKEPKSNYAVPGLYFYDNDVV
+QIAKDLKPSPRGELEITDANRVYLERGMLNVEVLPRGTAWLDTGTFHDLNDASNFIRTIE
+SRQGLKVGSPEEVAWRQGLLTDDELRQRAEPLVKSGYGRYLLGLLDRADPIGRSSR
+>PROKKA_00515
+MNPDRTALNLHHRIGPMKGIILAGGTGSRLHPITHGISKQLVPVYDKPMIYYPLSTLILA
+GISDILVITTPHDAEQFQRLLGDGSQFGISLSYVQQPSPDGLAQAFILGEDHIGDDHVAL
+VLGDNIFYGPGMGQQLRRHSEVDGATVFGYWVADPTAYGVVEFDGDGKAVSLEEKPAQPK
+SNYAVPGLYFYDNDVVEIAKELKPSARGELEITDVNRTYLERGALNVEVLPRGTAWLDTG
+TFKDLNDASNFIRTIESRQGLKVGSPEEVAWRQGLLTDNELRERAEPLVKSGYGRYLLDL
+LETGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000535.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000535.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c9423d8b4176537c970b199f1249357115826c04
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000535.fa
@@ -0,0 +1,30 @@
+>PROKKA_00533
+MGERATRQRPAAPPSLDLEVRVRLAHARITHLLDRAGIRGLHLKGYATEPGVYPDHRRSS
+DVDLLVHPADATAVIELLRSHGWEPVATFSEGSIFQHAATLWHDQLGYVDVHRLFPGLGA
+SPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRESLPAE
+SWAALREEAHRLDAGAAWHVATGEAADGVDSRQLTLFAALHESQSGLELFRTRWRSAATA
+RERAVLVARTIPVNRPHLQMRLGRPVTRADLWREQRARLGALAGWAWTKAVRRDR
+>PROKKA_00254
+MGEHATGQRPAAPPSLDLEVRVRLAHARITHLLERAGIRGLHLKGYATEPGVYPDHRRSS
+DVDLLVPPADAAAVIALLGSHGWEPVATFSQGSIFQHAATLWHDQLGYVDVHRLFPGLGA
+SPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRESLPAE
+SWAALREEARRLDAGAAWHVATGEAADGVDTRQLTLFAALHESQSGLELFRTRWRSAATV
+RERAALVARTIPVNRPHLQMRLGRPVTRADLWREQRARLGALAGWAWTKAVRRDR
+>PROKKA_02419
+MTETGTTDQRAAAQPALDLAVRVRLGHARIAYVMEEAELRGLHVKGYAAEPGVYRGRRSS
+SDVDLLVHPSDAAAAVELLASHGWAPVADFSEGSIFEHAATLWHDHLGYVDVHRLFPGLG
+TDAARTFDALWAERTTRVIAGRPVPVPGPVHQRLVVIVHAARDSHRGALDVRHIRDTSSP
+AEWDALRQEARRLHATAAWHVATGEDADGMDAHDLALFEALQDDESGLDLFRTRWRTAHS
+ARERARLVLHTLPVNRPHLQMRLGHAPTRADLWREQRSRATALARWAWTRGVRRGR
+>PROKKA_02301
+MTAAPAPLETRVRLAHARITHLMAAAGVRSLHIKGYAMGPGVYAGGRTSSDVDLLVHPAD
+LSHALDALTSHGWRRIADFAEGSVFEHAATLWHDQLGYVDVHRRLPGLGRSPVDAFEALW
+GERTTTVVAGHAVPVPSLRHQRLVVLVHGARDAGRGRFDVDHLRHTLDAGQWAELRVQAQ
+ILGAGAAWSIATGETDVAGVDEREALLLSAVRGDESGIRLLATRWHAARGWRERLHLLVR
+TVPVNRAHLQMRLGRPPTTADVLREQASRGAALTRWAAGKAVPRVGR
+>PROKKA_00533
+MLAAMGERATGQRPAAPPSLDLEVRVRLAHARITHLLDRAGIRGLHLKGYATEPGVYPDH
+RRSSDVDLLVPPADADAVIALLGSHGWEPVATFSQGSIFQHAATLWHDQLGYVDVHRLFP
+GLGASPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRES
+LPAESWAALREEAHRLDAGAAWHVATGEAADGVDSRQLTLFAALHESQSGLELFRTRWRS
+AATVRERAALVARTIPVNRPHLQMRLGRPVTRADLWREQGARLGALAGWAWTKAVRRDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000541.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000541.fa
new file mode 100644
index 0000000000000000000000000000000000000000..87862113a1b4c0a9207f4d4281526941d410791f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000541.fa
@@ -0,0 +1,45 @@
+>PROKKA_00540
+MEPVSEENSTFIPSLTIIGGGPGGYEAAMVAAKLGARVTLVERQGLGGAAVLTDVVPSKT
+LIAAADSMRRVGASVDLGVDLGGADVHADMGRVGHRILNLAHEQSSDIRAGLERVGVRVI
+DGVGRVVGPHEVSVRALDDADAGAEPEIITSDAILVAVGASPRELPTAVPDGERIFNWKQ
+VYNLKELPEHLIVVGSGVTGAEFASAYNRLGAKVTLVSSRDRVLPGEDADAAELLEKVFE
+GNGLRVVSRSRAESVERTETGVRVHLSGEGAEDTPSIEGSHALVAVGGVPNTAGLGLDDV
+GVKLTGSGHVLVDGVSRTSVPSIYAAGDCTGKLALASVAAMQGRIAVAHLLGDALKPLRP
+HLLASNIFTSPEIATVGVTQAQVDSGQYQADVLRLDFHTNPRAKMSGAEEGFVKIFARQG
+SGTVIGGVVVSPRASELIYALALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRI
+>PROKKA_00264
+MEPVTEENSTFIPSLTIIGGGPGGYEAAMVAAKLGARVTLVERQGVGGAAVLTDVVPSKT
+LIAAADSMRRVGASVDLGVDLGGAEAHADMGRVGHRILNLAHEQSSDIRAGLERVGVRVI
+DGVGRVVGPHEVSVRALDDADAGAEPEIITSDAILVAVGASPRELPTAVPDGERIFNWKQ
+VYNLKELPEHLIVVGSGVTGAEFASAYNRLGAKVTLVSSRDRVLPGEDADAAELLEKVFE
+GNGLRVVSRSRAESVERTETGVRVHLSGEGAEDTPSIEGSHALVAVGGVPNTAGLGLDDV
+GVKLSGSGHVLVDGVSRTSVPSIYAAGDCTGTLALASVAAMQGRIAVAHLLGDALKPLRP
+HLLASNIFTSPEIATVGVTQAQVDSGQYQADVLRLDFHTNPRAKMSGAEEGFVKIFARQG
+SGTVIGGVVVSPRASELIYALALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRI
+>PROKKA_02409
+MVAAKLGARVTLVERQGVGGAAVLTDVVPSKTLIATADSMRRVGLAEDLGVDLGDAEPRA
+DMRQVDRRILDLAGEQSRDIRAALERRGVRVIDGVARVVGPNEVSVRTLQDADAEPEVIT
+SDAILVAVGASPRELPTAVPDGERIFNWKQLYAMTELPEHLIVVGSGVTGAEFASAYNRL
+GAKVTLVSSRDRVLPGEDADAAELLEKVFQDNGLTVVARSRAEAVERTETGVRVELSGEG
+AADTPYVEGSHALVAVGGIPNTAGLGLEDVGVELTESGHVKVDGVSRTTVPSIYAAGDCT
+GNLALASVAAMQGRIAVAHLLGDALKPLRPHLLASNIFTSPEIATVGVTQAQVDSGQYQA
+DVLRLDFATNPRAKMSGVQEGFVKIFARQGSGTVIGGVVVSPRASELIYALALAVTHKLH
+VDDLADTFTVYPSMSGSIAEAARRLHVRI
+>PROKKA_02291
+MNVTEENTTFLPSLTIIGGGPGGYEAALVAAKLGARVTVVERAGMGGSAVLTDVVPSKTL
+IATADSMRRVMAASGLGVDLGEAQPHADMHAVDRRILELAGQQSSDIHRALEKRGVRVVI
+GDAVVTGPHEVTVRRRGIEEGEEPEVITSDAILVAVGASPRELPTARPDSERIFNWKQVY
+ALQDLPEHLIVVGSGVTGAEFASAYNQLGAAVTLVSSRDRVLPGEDPDAAELLEDVFAQN
+GLDVAGRCRAESVERTETGVRVHLSGEGADGRPYIDGSHCLLAVGGVPNTAGLGLEEVGV
+ELTESGHVKVDGVSRTTVPSIYAAGDCTGQLALASVAAMQGRIAVAHLLGDALKPLRPHL
+LASNIFTSPEIATVGVTQAQVDSGQYQADVIRLDFATNPRAKMQGVSTGFVKIFARQGSG
+TVIGGVVVAPRASDLIYSLALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRV
+>PROKKA_00543
+MEPVSEENSTFIPSLTIIGGGPGGYEAAMVAAKLGARVTLVERQGLGGAAVLTDVVPSKT
+LIAAADSMRRVGASVDLGVDLGGGDVHADMGRVGHRILNLAHEQSSDIRAGLERVGVRAI
+DGVGRVVGPHEVSVRALDDADAGAEPEIITSDAILVAVGASPRELPTAVPDGERIFNWKQ
+VYNLKELPEHLIVVGSGVTGAEFASAYNRLGAKVTLVSSRDRVLPGEDADAAELLEKVFE
+GNGLRVVSRSRAESVERTETGVRVHLSGEGAEDTPSIEGSHALVAVGGVPNTAGLGLDDV
+GVKLTGSGHVLVDGVSRTSVPSIYAAGDCTGKLALASVAAMQGRIAVAHLLGDALKPLRP
+HLLASNIFTSPEIATVGVTQAQVDSGQYQADVLRLDFHTNPRAKMSGAEEGFVKIFARQG
+SGTVIGGVVVSPRASELIYALALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000544.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000544.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f96356d40d90bbd56d3286b7a44a98b2310fcb4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000544.fa
@@ -0,0 +1,55 @@
+>PROKKA_00544
+MTQHTSEAAVDGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA
+DDELNARLLEDLAALELQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGA
+AGGFFPGLVERAEAADVVDDALAARIRSGADAAAQAYRDFADTLEAELRPHAPEADGVGI
+EYYRLASRDFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE
+RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLSKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK
+AFHTRALRLGGMGLDTLREALA
+>PROKKA_00269
+MTQHTSEAAVDGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA
+DDELNARLLEDLAALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQSIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGA
+AGGFFPGLAERAEAADVVDDALAARIRSGADTAAQAYRDFADMLEAELRPHAPEADGVGI
+DYYRLASRVFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE
+RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLTKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK
+AFHTRALRLGGMGLDTLREALA
+>PROKKA_02403
+MTQNTPVAADRGARTPSAIDALAERYVADVLALHPDEATTLGFPGHETEYADFSPAGTRA
+DDELNARLLADLEALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVIEQARAHGA
+AGGFFPGLVERAEATDVVDAALAERIRAGADAAAQAYRDFADTLQAELRPHAPEADGVGI
+ELYRLGSRAFLGAEIDLEETYRWGQEELARIIAAQEADAERIKPGATIEEARALLDADPE
+RTLNGTAALQAWMQRLSDEAVQAMKAHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLEKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRTEHEEREGEGFDLK
+AFHTRALRLGGMGLDTLRAALA
+>PROKKA_02286
+MTQTTSAPEGARTPSAVDALAERHVAAYLALRPDEATSLGMPGHETEYPDLSPAGAAALD
+ELNRTTLEELAGLEPADDVDRVTVAAMRERLGLEREIHATGRTELNNIASEAQGIRAIFD
+LMPTDTAEQWGHIAGRLENLPAALRGYAESLLASRDAGHVAAVRQVEIVVEQARAHGAEG
+GFFPGLVERAEAADVVDAALAERIRTGAAGAAAAYAEFADTLEAELRPHAPEADAVGIEH
+YRLASRVFLGAEIDLEETYRWGQEELDRIIAAQEADAERIKPGATIEEARAILDADPART
+LTGTKALQEWMQRLSDEAVEAMKAHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSRPG
+RMWWSVPAGEEEFTTWAETTTVYHEGVPGHHLQIATAMMNRGTLNLWRRNFAWTSGHGEG
+WALYAEKLMEEFGFLDDAGDHLGMLDMQRMRAARVVFDIGYHCGFEMPASEGGGEWTPEK
+GYAFLEKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEAREGADFDLKAF
+HTRALRVGGMGLDTLREALA
+>PROKKA_00547
+MTQHTSEAAADGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA
+DDELNARLLEDLAALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGG
+AGGFFPGLVERAEAADVVDDALAARIRSGADTAAQAYRDFAATLEAELRPHAPEADGVGI
+DYYRLASRVFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE
+RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLAKHLMISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK
+AFHTRALRLGGMGLDTLREALA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000549.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000549.fa
new file mode 100644
index 0000000000000000000000000000000000000000..03db5150b4712b4a415059612c5e17fe714fa62e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000549.fa
@@ -0,0 +1,30 @@
+>PROKKA_00550
+MDPRPETPSAPRPQAAGATHVGAVRDLNEDAWTLVGEPLVLAAVADGMGGHEAGEVASAA
+AIETLRRRAPEVLAPGTAHTPQELGHLIHEADAAVVEAGLGRSGTTLTVLACLDTERGRW
+AVANVGDSRVYLRPVGSPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGSR
+EALTVDVAEVPLASGDLVLLCSDGLTGELLDEEIRALIDDADTLEDALEKLIGAALWRGG
+RDNITAVLVRIP
+>PROKKA_00275
+MDPRPETPSAPRPQAAGATHVGAVRDLNEDAWTLVGEPLVLAAVADGMGGHEAGEVASAA
+AIETLRRRAPEVLAPGTAHTPQELGHLIHEADAAVVEAGLGRSGTTLTVLACLDTERGRW
+AVANVGDSRVYLRPVGSPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGSR
+EALTVDVAEVPLASGDLVLLCSDGLTGELLDEEIRALIDDADTLEDALEKLIGAALWRGG
+RDNITAVLVRIP
+>PROKKA_02396
+MEPSAETPAAAPRPEAAGATHVGAVRELNEDAWTLVGDPLVLAAVADGMGGHEAGEVASA
+AAIEVLRRRGPEVLAPGVAHTPEELGHLVHEADAAVVAAGGGRSGTTLTVLACIDTAANR
+WAVANVGDSRIYLRPAGAPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGS
+SEPLTVDVAEIPVASGDRLLLCSDGLTGELLDEEIRALIDDADELEDALVKLVEAALWRG
+GRDNVTAVLVRIP
+>PROKKA_02280
+MSEPHAADAAPAEPGAWASVPRPEAVAVTHVGAVRELNEDSWAVVGDPLLLAAVADGMGG
+HEAGEVASAAAVAELHRRAPSVLAPGVAHTPQELGALVHEANAAVLAAGGGRAGTTLTVL
+ACLDTEVGRWAVANVGDSRIYLRPVGAGVLQQVTVDHSAVQLMVDAGELTPAEARVHPRR
+NVITRALGSTQALTVDVMELDVAPGDRFLLCSDGLTGELLDDEILAIMDDAATLDEAAER
+LVEAALWRGGRDNITAVLVRIP
+>PROKKA_00553
+MDPRPETPSAPRPQAAGATHVGAVRDLNEDAWTLVGEPLVLAAVADGMGGHEAGEVASAA
+AIETLRRRAPEVLAPGTAHTPQELGHLIHEADAAVVEAGLGRSGTTLTVLACLDTERGRW
+AVANVGDSRVYLRPVGSPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGSR
+EALTVDVAEVPLASGDLVLLCSDGLTGELLDEEIRALIDDADTLEDALEKLIGAALWRGG
+RDNITAVLVRIP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000551.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000551.fa
new file mode 100644
index 0000000000000000000000000000000000000000..78d69453307ba4cd6609304f92e4895645734d74
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000551.fa
@@ -0,0 +1,20 @@
+>PROKKA_00553
+MRRIVGDPWFYPVLFVAGGLTFMIAGTRLQQVGMIVAGLVLAGYAVTYRWAVRVRSRPFA
+GAQAHVERGGVVVFWRPGCPFTRRLVKELTAQERDRAYWVNIWQEPAAATFLEGLHESRD
+GHPHQAVPTAWLRRRDYVVATDATRARLKDTLRQHAGGDA
+>PROKKA_00278
+MRRIVGDPWFYPVLFVAGGLTFMIAGTRLQQVGMIVAGLVLAGYAVTYRWAVRVRSRPFA
+GAQAHVERGGVVVFWRPGCPFTRRLVKELTAQERDRAYWVNIWQEPAAATFLEGLHESRD
+GHPHQAVPTAWLRRRDYVVATDATRARLKDTLRQHAGGDA
+>PROKKA_02392
+MRRLVGDPWFWPVLFGSAGLVFLVWGTLRRDVVVLVAALAMLWMLRRHLPQLRVRSRPLA
+GAQAHVQDGGVVVFWRPGCQYCQALLRDLDPAQRDAVYWVNIWTDKDAVPVLRRLHAGRD
+GHAHEAVPTVWARRKDFVAADEASRSRLKDMLRDARPAGGPRTREEGPR
+>PROKKA_02277
+MRRLVGDPWFWPVLFGAAGVVFLVWGTVRRDVIAIVAGVAMLWMVWQYLPALRVRSCPMA
+GAQAHVDAGGVVVFWRPACRYCLALIKDLDPAQRAAVYWVNIWTDPDAVPVLHRLHATRD
+GHAHEAVPTVWSRRRDFVVKDEATRRRLTDMLGAVRHIPESGR
+>PROKKA_00556
+MRRIVGDPWFYPVLFVAGGLTFMIAGTRLQQVGMIVAGLVLAGYAVTYRWAVRVRSRPFA
+GAQAHVERGGVVVFWRPGCSFTRRLVTELTAQERERAYWVNIWQEPAAATFLAGLHEARD
+GHPHQAVPTAWLRRRDYVVATDATRARLKDTLRQHAGGDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000552.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000552.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a5d969032955bedc4108b349788ef2943373003a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000552.fa
@@ -0,0 +1,15 @@
+>PROKKA_00555
+MPEITRDQVEHLARLAHIRMTDEELDTMSGDLEKILEHVSAVQAAAGDDVTPTSHPIALE
+NVFREDVPAGMLTQEEALDQAPDSEDGQFKVPAILDGE
+>PROKKA_00280
+MPEITRDQVEHLARLAHIRMTDEELDTMSGDLEKILKHVSAVQAAAGDDVTPTSHPIALE
+NVFREDVPAGMLTQEEALDQAPDSEDGQFKVPAILDGE
+>PROKKA_02390
+MPEITRDQVAHLARLAHIQMSDEELATVSGELEQILGHVSAVQAAAGADVAPTSHPIAMS
+NVFREDVPAGMLTQEQAVDQAPDAQDGQFKVPAILDGE
+>PROKKA_02273
+MAEITRDQVEHLARLAHIRMTDEELDVMSGELESILESVSQVQAVAGEDVVPTSHPIPLE
+NVFREDVPTGMLTQEQALDQAPDAEDGQFKVPAILDGE
+>PROKKA_00558
+MPEITRDQVEHLARLAHIRMTDEELDTMSGDLEKILEHVSAVQAAAGDDVTPTSHPIALE
+NVFREDVPAGMLTQEEALDQAPDSEDGQFKVPAILDGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000554.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000554.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0dd439e80c8a0ec1708babadbc198bffeaf98989
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000554.fa
@@ -0,0 +1,50 @@
+>PROKKA_00557
+MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG
+TLPVLNRKVVEYAIRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD
+VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASASLVDYNRAGVPLIEIVTKPIV
+GAGARAPELARAYVTAIRDIVQAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN
+VNSTRAVQHAVTHEIQRQAAVLAAGGTVTQETRHWHEDTRSTTSGRPKSDADDYRYFPEP
+DLVPVHVDAAWVERVRAAMPELPAVRNKRLKAEWGFSDEEFRDVVNAGVLDEIVATVEAG
+ASAAAARKWWMGEIARLANVREVAVAELGITPAHVVEVEELIAAKTINDKIAKQVLGLVA
+DGEGAPKEVVAAKGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMAAVGALIGPVMKA
+TRGQADAGRVREIVLERLGVS
+>PROKKA_00282
+MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG
+TLPVLNRKVVEYAIRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD
+VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASASLVDYNRAGVPLIEIVTKPIV
+GAGARAPELARAYVTAIRDIVQAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN
+VNSTRAVQHAVTHEIQRQAAVLAAGGTVTQETRHWHEDTRSTTSGRPKSDADDYRYFPEP
+DLVPVHVDAAWVERVRAAMPELPAVRNKRLKAEWGFSDEEFRDVVNAGVLDEIVATVEAG
+ASAAAARKWWMGEIARLANVREVAVAELGITPAHVVEIEELIAAKTINDKIAKQVLGLVA
+DGEGAPKEVVTAKGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMAAVGALIGPVMKA
+TRGQADAGRVREIVLERLGVS
+>PROKKA_02388
+MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG
+TLPVLNREVVEYAVRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD
+VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASNSLVDYNRAGVPLIEIVTKPIV
+GAGARAPELARAYVTAIRDIVKAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN
+VNSTRAVQHAVTHEIQRQAALLAAGGTVTQETRHWHEDTRTTTSGRPKSDADDYRYFPEP
+DLVPVHVDAAWVERVRAEMPELPAVRNKRLKAEWGYTDEEFRDVVNAGVLDEIVATVEAG
+ASPAAARKWWMGEIARLANVRETAVAELGVTPAHVVEVEELIAAKTINDKIAKQVLGLVA
+DGEGTPKEIVEAKGLAVVSDDGALTEAVDAAIAANPDVAEKIRGGKMAAVGALIGPVMKA
+TRGQADAGRVREIVLERLGVS
+>PROKKA_02271
+MSTAELMDFQEAMDRFDPVLGFEVHVELNTKSKIFSTGANAFGDEPNTNVTPLDLGLPGT
+LPVLNREAVESAIALGLALDAQIAPSCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLDV
+ELEDGTVFRVEIERAHLEDDAGKLTHQGGSGRIQGASASLVDYNRAGVPLIEIVTRPIVG
+AGDRAPEIARAYVTALRDIVKAIGISDARMEHGNVRCDANVSLMEKGASAFGTRTETKNV
+GSTRAVQHAVTHEIQRQAAILAAGGTITQETRHWHEDTRTTTSGRPKSDADDYRYFPEPD
+LLPVVVDEAWIERVRAGMPELPAVRNKRLKGEWGFSDEEFRDVVNAGVADQIAQTVEAGA
+SPAAARKWWMGEIARLANLREVEAAELGVTPAHVVEIEELIAAKTINDKIAKQVLGLVAD
+GEGAPKQIVAAQGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMQAVGALIGPVMKAT
+RGQADAGRVREIVLERLGVA
+>PROKKA_00560
+MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG
+TLPVLNRKVVEYAIRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD
+VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASASLVDYNRAGVPLIEIVTKPIV
+GAGARAPELARAYVTAIRDIVQAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN
+VNSTRAVQHAVTHEIQRQAAVLAAGGTVTQETRHWHEDTRSTTSGRPKSDADDYRYFPEP
+DLVPVHVDAAWVERVRAAMPELPAVRNKRLKAEWGFSDEEFRDVVNAGVLDEIVATVEAG
+ASAAAARKWWMGEIARLANVREVAVAELGITPAHVVEVEELIAAKTINDKIAKQVLGLVA
+DGEGAPKEVVAAKGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMAAVGALIGPVMKA
+TRGQADAGRVREIVLERLGVS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000561.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000561.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a515ff340963f4dd4479b5c3456bf5ae722e208
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000561.fa
@@ -0,0 +1,25 @@
+>PROKKA_00564
+MPLARLAGVNANPTPAVEPVVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPEHVT
+VAAVRAPLPLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTVSLL
+GFSQGMAMATSLLRLDPEAYACTVALSGFVVDPELDEPRLRELFTRDDDVARVRPKVFWG
+RGQEDPIISEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPRG
+>PROKKA_00289
+MNANPTPAVEPVVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPEHFTVAAVRAPL
+PLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTVSLLGFSQGMAM
+ATSLLRLDPEAYACTVALSGFVVDPELTEPRLRELFTRDDDVARVRPKVFWGRGQEDPII
+SEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPRG
+>PROKKA_02379
+MNNDTANTAPSSETAPFTVRWSRPEGERTEDLLILLHGYGANEDDLFGLVPHLPERFTVA
+AVRAPMTLQPGGYAWFPLSQDPVTGEIGSDAASVRTAIEDLHAWVGAVREGFRTVSLLGF
+SQGMALATSLLRLDPTAYAATVALSGFVVDPTREESGLAGLFDGDDEVARVRPKVFWGRG
+QDDPIISEARVEASHAWLNAHVDLMKIVYAGLPHAINQQELGHVKEYLEHMVR
+>PROKKA_02263
+MNDTTPRDPAPFAVRWSRPEGERTEHLLVLLHGYGADEDDLFGLVPQLPEAFTALAVRAP
+MDLPQGGAAWFPLTQDPATGEIGSDAGAVRAAVEDLHAWLPGVSGGFRTVSLLGFSQGMA
+MATSLLRLDPAAYAATVALSGFVVDPLHVEPELEGLFPADETVDAVTPKVFWGRGQEDPI
+ISAQRVEESHGWLTAHTDLTKVVYAGLPHAISPQELGHVREYLTHVVL
+>PROKKA_00567
+MPLARLAGVNANPTPAVEPVVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPEHVT
+VAAVRAPLPLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTVSLL
+GFSQGMAMATSLLRLDPEAYACTVALSGFVVDPELAEPQLRELFTRDDDVARVRPKVFWG
+RGQEDPIISEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000566.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000566.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c8765b72e89406215bc46e9b8f222da15a6e6dcf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000566.fa
@@ -0,0 +1,20 @@
+>PROKKA_00573
+MSEQWSEKDIELANRLFDMARDGDTAQLKAYLDAGVSTRLRNHAGDSFLTLAAYHEHPDT
+VAMLIEAGAEIEHANDRGQRALTCATFKRDVASMRHLLAAGADPDAGTPSARQTAQMFAG
+ADLLAVLDGGGAAPPSEA
+>PROKKA_00305
+MSEQWSEKDIELANRLFDMARDGDTAQLKAYLDAGVSTRLRNHTGDSFLTLAAYHEHPDT
+VAMLIEAGAEIEHANDRGQRALTCATFKRDVASMRHLLAAGADPDAGTPSARQTAQMFAG
+ADLLAVLDGGDAAPASEA
+>PROKKA_02360
+MTEQPQDPRQDQTAAEPAPEPAEALAAETTDAVAPEAAPGEAGQPSPEMLELAGRMFDAA
+RSGDAETLEAYIVAGLNPDLQNGKGDTFLTLAAYHDQPGVVEMLIRVGADVEKANDRGQR
+PLTCATFKGDVASMRLLLAAGADPDAGTPSARQTAQMFGGEEITAVLDEPR
+>PROKKA_02251
+MTEHQDTQGQHAPATPPAEPAVESAGPSPEMLELAGRMFDAARTGDVDTLEAYIVAGLNP
+DLQNGKGDTFLTLAAYHDQPAVVEMLIRVGADVEKANDRGQRPLTCATFKGDVASMCLLL
+AAGADPDAGTPSARQTAQMFGGERVAAVLDEAR
+>PROKKA_00574
+MSEQWSEKDIELANRLFDMARDGDTAQLKAYLDAGVSTRLRNHAGDSFLTLAAYHERPDT
+VAMLIEAGAEIEHANDRGQRALTCATFKRDVASMRHLLAAGADPDAGTPSARQTAQMFAG
+ADLLAVLDREDAAPSSEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000567.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000567.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3d5597ecf3b25e3ff3c82a7661923e3e79af456
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000567.fa
@@ -0,0 +1,45 @@
+>PROKKA_00574
+MTSSHTLPAAAVTDADDVAHYAKSAGAGRRITDDDQLHEARHPAPTTDRLTLPPLRLGPL
+TIDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALVERKPESMRIIQHDPDEVP
+RSVQLYSVDPVTTGAAVRMLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKAELFASIV
+KAAVTEAAKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFYSGTAV
+WDDIARLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVIGRGCQGRPWLFGDLQAAF
+EGRQDRFQPTLGMVADTLYRHAELLVDTFGGDETKALRDIRKHVAWYLKGYPVGSEIRTA
+LSTVPDLATMREILARVDRDQPYPGEAAEGPRGRAGAPKRPHLPDGWLDSRELNAEQQAM
+IQAAELDVSGG
+>PROKKA_00306
+MTSSHTLPAAAMTDADDVADPHAAHYAKSAGAGRRITDDDQLHEGRHPAPTTDRLTLPPL
+RLGPLTIDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALVERKPESMRIIQHD
+PDEVPRSVQLYSVDPVTTGAAVRMLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKSEL
+FASIVKAAVTEAAKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFY
+SGTAVWDDIARLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVIGRGCQGRPWLFGD
+LQAAFEGRQDRFQPTLGMVADTLYRHAELLVDTFGGDETKALRDIRKHVAWYFKGYPVGS
+EIRTALSTVPDLATMREILTRVDRDQPYPGEAAEGPRGRAGAPKRPHLPDGWLDSRELNA
+EQQAMIQAAELDVSGG
+>PROKKA_02359
+MTVSSSTTTPERGAATDGLSAADPAAGAPAAVDPHASHYAKSAGAGRRIADDEQLHEGRH
+AAPTTDRLSLPALTLGPITVDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALV
+ERKPESMRIIKHDPDEVPRSVQLYSVDPVTTGAAVRMLVEEDRADHIDLNFGCPVPKVTR
+RGGGSALPWKSELFASIVKAAVTEAGRKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVA
+AVALHGRTTRQFYSGTAVWEDIARLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVI
+GRGCQGRPWLFGDLQAAFEGRHDRFRPTLGMVADTLYRHAELLVDTFEGDELKALRDIRK
+HVAWYFKGYPVGSEIRTALSTVPDLATMAEILSRVDRDQPYPGLDAEGPRGRSGAPKRPH
+LPDGWLDSRELNAEQKAMIAAAELDVSGG
+>PROKKA_02250
+MTASHTLPDAAVDPHYAKSAGAGRRIADDDQLHEGGHAAPRSDRLNLPPLKLGPITVDVP
+VVLAPMAGITNTAFRRLCREYGGGLYVNEMVTSRALVERKPESMRIIQHDPDEVPRSVQL
+YSVDPVTTAAAVRMLVEEDRADHIDMNFGCPVPKVTRRGGGSALPWKSELFASIVKAAVT
+EASKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFYSGTAVWEDIA
+RLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVIGRGCQGRPWMFGDIQNAFEGRPE
+RFHPTLGMVADTLYRHAELLVDTFGGDEVKALRDIRKHVAWYFKGYPVGSEVRTGLSTVP
+NLATLRELLDRLDRDMPYPGAPAEGPRGRAGAPKRPHLPDGWLDSRELNEEQRAMIHAAE
+LDVSGG
+>PROKKA_00575
+MTSSHTLPAAAVTDADDVADPHAAHYAKSAGAGRRIADDDQLHEARHPAPTTDRLTLPPL
+RLGPLTIDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALVERKPESMRIIQHD
+PDEVPRSVQLYSVDPVTTGAAVRMLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKSEL
+FASIVKAAVTEASKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFY
+SGTAVWDDIARLREALPDIPVLGNGDIWSAEDAIAMVERTGVDGVVIGRGCQGRPWLFGD
+LQAAFEGRQDRFRPTLGMVADTLYRHAELLVDTFGGDETKALRDIRKHVAWYFKGYPVGS
+EIRTALSTVPDLATLREILARVDRDQPYPGEAAEGPRGRAGAPKRPHLPDGWLDSRELNA
+EQKAMIQAAELDVSGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000568.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000568.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0bfe0872e7d964631394e18e4ab8766dde85a23d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000568.fa
@@ -0,0 +1,45 @@
+>PROKKA_00575
+MAEPTTPEPAAGAPAAPSSPWTGAAHQPVLFGPEGRPPYAGRAVQTPGYPPWDRERWLPE
+PPKSSYRSDFERDRARVLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGR
+SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF
+ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT
+RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA
+EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH
+GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLDATGDRYLEPM
+FTFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI
+>PROKKA_00307
+MAEPTTPVPAAGTPAAPSSHWTGAAHQPVLFGPEGRPPYAGRAVQTPGYTPWDRERWLPE
+PPKSSYRSDFERDRARVLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGR
+SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF
+ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT
+RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA
+EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH
+GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLEATGDRYLEPM
+FTFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI
+>PROKKA_02358
+MAEGWAGPAHQPVLFGPQGRPPYAGRAVQTPGYTPWDRERWLPEPPKSSYRSDFERDRAR
+VLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGRSLGCDPDLVDTACLSH
+DLGHPPFGHNGEKALDALSADVGGFEGNAQTLRLLARLEQKKLFEDGSSAGLNLTRAALD
+AACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFREGVSGSRKSMEAQVMDLADDIS
+YSVHDVEDGVVNAAFQLKWLAIPEHRERVVETTRQWYLPLTDPAEVDEALARLEATDVWV
+SEMDGSRRALAAMKDMTSQLIGRFCTAAFDATRQVFGNEPLTRHGADVVVPAETETEIAV
+MKGIAAAYVMASEQRQPLYARQRELLAELVELLDASGDRYLEPMFAFDWREAADEAARRR
+VVLDQVASLTDSTALEWHHTLVQGAEFTRVWI
+>PROKKA_02249
+MAEPQPTLFGPADRPPYAGRPVPTPGYTDWDRRRWLAEPPKSSYRSDFERDRARVLHSAA
+LRRLGAKTQVVAPDLDDFSRTRLTHSLEVAQIGRELGRSLGCDPDLVDTACLSHDLGHPP
+FGHNGEKALDAVAEAAGGFEGNAQTLRLLARLEQKKSFPDGSSAGLNLTRAALDAACKYP
+WVREDAPLRPDGKRSRKFGVYADDLPVFEWFRQGVHGARKSMEAQVMDLADDISYSVHDV
+EDGVVNSAFQLRWITEPGERRARVLETTRDWYLPGGDLEEIDAALTRLESQDVWMGEMDG
+SRRALAGMKDMTSQLIGRFCTAAFDATREVFGNEPLTRHAADVVVPAHTEHEIAVMKGIA
+AAFVMTSEQRQPLYARQRDLLTELVDLLMTTGDRYLDPMFAADFQDAADDAARARVVIDQ
+VASLTDSTAIEWHRTLVRGETFQRVWL
+>PROKKA_00576
+MAERTTPAPADGAPAAPSSPWTGAAHQPVLFGPEGRPPYAGRAVQTPGYTPWDRERWLPE
+PPKSSYRSDFERDRARVLHSAGLRRLGDKTQVVAPDADDFARTRLTHSLEVAQVGRELGR
+SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF
+ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT
+RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA
+EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH
+GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLDATEDRYLEPM
+FAFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000573.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000573.fa
new file mode 100644
index 0000000000000000000000000000000000000000..764f1774af2906a89a2480460e4d7612f4b22539
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000573.fa
@@ -0,0 +1,50 @@
+>PROKKA_00608
+MSSACGCEAPTPGAPEEPEEHRPWWRDAAILLPVLSGVAFIAGLVLEWSGAGLVATVVFW
+VGLVLGAWTFVPGALRGLFTRGRLGIGLLMTISAIGAVILGYIEEAAALAFLYSIAEALE
+DKAMDRARAGLRALLKLVPETATIRQGGATVQVEAKDLHPGQVLVVRPGERIATDGIVRT
+GRSSLDTSAITGESIPVEVGPGDTVSAGSINTSGALEIDATAAGTDNSLTTIVHLVEQAQ
+TEKGARARLADRIAKPLVPGVLVLAVLVAALGSLFGDPELWITRALVVLVAASPCALAIA
+VPVTVVSAIGAASRFGVVIKSGAAFERLGGIRHLAVDKTGTLTRNQPTVTAVLTTPGLTE
+DQVLGWAAALEQHSTHPLAAAIIAAAPDAPGAKAVTETAGHGITGRIDGATITVGSPRWL
+DPGPLAAQVQQLEDQGMTVVIIHRDGTVAGAIGVRDELRPEVPAVVTTLTGQGIGLTMLT
+GDNARTARAIAAQAGIGDVRAELRPEDKAAAVGQLTGTRPTAMIGDGINDAPALAAAEVG
+IAMGATGSDAAIESADVAFTGHDLRLIPQALAHARRGRAIMNQNIVLSLLIIGVLLPLAI
+TGMLGLAAVVLVHEVAEVIVIGNGLRAATTRRTALASLTDRQAQRSTVG
+>PROKKA_01768
+MSAACGCEAPTPTPGAPEEHEEHRPWWRDAAILLPALSGLAFLTGLVLEWSGAGLVATVV
+FWVGLVLGAWTFVPGALRGLFTRGRLGIGLLMTISAIGAVILGYIEEAAALAFLYSIAEA
+LEDKAMDRARAGLRALLKLVPETATIRAGGATVEVEAKDLRPGQVLVVRPGERVATDGIV
+RTGRSSLDTSAITGESIPVEVGPGDTVSAGSINTAGALEIDATAAGTDNSLTTIVHLVEQ
+AQAEKGDRARLADRIAKPLVPGVLILAVLVAALGSLLGDPELWITRALVVLVAASPCALA
+IAVPVTVVSAIGAASRFGVVIKSGAAFERLGGIRHLAVDKTGTLTRNQPTVTAVLAAPGI
+TEDQVLGWAAALEQHSTHPLAAAITAATPDTPAAEGVTETAGHGITGRLDGATVTVGSPR
+WLAPGPLAAQVQGLEDQGMTVVIIHRDGAVAGAIGVRDELRPEVPTVVTTLTGQGIDLTM
+LTGDNARTARAIADQAGIDDVRAELRPEDKATAVHQLTGTRPTAMIGDGINDSPALAAAE
+VGIAMGATGSDAAIESADVAFTGHDLRLIPQALAHARRGRAIINQNIILSLLIIAVLLPL
+AITGVLGLAAVVLVHEVAEVIVIGNGLRAATTRRTALEPLTDRQAQPATTG
+>PROKKA_00728
+MRATTHTPVEELETDDEHETPWWADRAVLIPIASGVAFVAGLACEWSGAQSAALVLFWVG
+LLLGASTFVPGALRKLATGKLGIALLMTMSATGAVILGHVEEAAALAFLYSIAEALEDRA
+MDRARAGLRALLKLVPQSATVLTDGHSASVPARDLAAGQVMLIRPGERIATDGIVRSGHS
+SVDTSAITGESIPVEVGPGDEVSAGAINAAGALQVEATAPGTDNSLTTIVSLVERAQAEK
+GQRARLADRIARPLVPGVLVLAVLVALIGSLAGDPQTWITRALVVLVAASPCALAIAVPI
+TVVSAVGSASKFGVIIKSGAIFERFGDIGHVAFDKTGTLTRNQPTVTAVVPAADVTEQQV
+LAWAAALEQHSTHPLATAITHAAPHNPRRPGHHRGSRPRNPRHRRRRRSAGRQPPLGRPR
+RPHLPGP
+>PROKKA_00729
+MLVGSPRWVDPGDLTYRVRDLEAQGMTVVVVHRDGAVAGAIGVRDELRPEVPEVITTLAG
+QGIDVTMLTGDNERTARALAAQAGISDVRAELRPEGKSAAVGELSVRRPTAMIGDGINDA
+PALAAADVGIAMGATGSDAAIESADIAFTGQDLRLLPQAIAHARRGRRIVNQNIVLSLLI
+IAALPPLAITGVLGLAAVVLIHEVAEVLVILNGLRAARTHQPTRGH
+>PROKKA_02365
+MVPVFSGVAFLTGLVLEWAGLEVPALVLFWIGLLLGASTFTPGAIRKLFKGKLGIGLLMT
+ISAVGAVILGYVEEAAALAFLYSIAEALEDKAMDRARGGLRALLKLVPETATIRRDGASV
+EVPAKDLAVGQLMLVRPGERIATDGIVRTGRSSLDTSAITGESIPVEVEPGDTVSAGAIN
+TAGALEVETTAAGTDNSLTTIVDLVEKAQADKGDRARLADRIARPLVPGVLILAALVAII
+GSLLGDPELWITRALVVLVAASPCALAISVPLTVVAAIGSASKFGVIIKSGAVFERFGVI
+RHVAVDKTGTLTRNEPAVTAVLTAEGVTEKQALAWAAALEQHSTHPLAAAITAAAPGAPA
+ADGVTEQAGHGIEGTLDGARITVGSPRWLDAGTLGEQVAGLEEQGMTVVIVHRDGTPVAA
+IGVRDELRPEVPEVVRTLAAQGIGVTMLTGDNARTARALAAQAGIGDVRAELRPEDKAAA
+IAELGEKGAVAMIGDGINDAPALAAADIGIAMGATGSDAAIESADVAFTGHDLRLLPRAF
+DHARRGRHIINQNLILSLLIITALLPLALFGVLGLAAVVLVHEIAEVVVILNGLRAARTR
+KSAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000576.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000576.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e56b29a238ef2a5c153fe512b5563015fef51f9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000576.fa
@@ -0,0 +1,23 @@
+>PROKKA_00636
+MDSEKYQRVRNGAGFVAALDQSGGSTPAALHLYGIDKDAYSGPEEMFDLVHQLRTRIITS
+PSFDGERVMGAILFENTMNRQVEGSPTGDYLWNSKGIVPFLKIDQGLAPEQQGAQLMKPI
+PHLDDLLSRAVEKHMFGTKMRSVIKLPGDGVGSVVEQQFGLARQILVTGLVPIIEPEVDI
+RSPRKAEVEDQLKAAILAQLDKLGDDQSVILKVTLPERADFYREFVDHPRVIRVLALSGG
+YTRAQATTLLARNHGVIASFSRALTEGLSTAQSPAQFNAVLDEAINAIATASRT
+>PROKKA_00408
+MLCILPLDQSLHQTRSDSDFYREFVDHPRVIRVLALSGGYTRAQATTLLARNHGVIASFS
+RALTEGLSTAQSPAQFNAVLDEAINAIATASRT
+>PROKKA_02192
+MDSEKYQRVRNGAGFVAALDQSGGSTPAALHLYGIDKDAYSGPEEMFDLVHQVRTRIITS
+PSFDGERVMGAILFENTMNRQVEGSPTGDYLWNSKGIVPFLKIDQGLAPEQQGAQLMKPI
+PHLDDLLSRAVEKHMFGTKMRSVIQLPGDGVGSVVEQQFGLARQILVTGLVPIIEPEVDI
+RSPRKAEVEDQLKAAILAQLDKLGDD
+>PROKKA_02193
+MTLPERADFYREFVDHPRVIRLLALSGGYTRAQATTLLARNHGVIASFSRALTEGLSTAQ
+SPAQFNTVLDEAINAIATASRT
+>PROKKA_00595
+MDSEKYQRVRNGAGFVAALDQSGGSTPAALHLYGIDKDAYSGPEEMFDLVHQVRTRIITS
+PSFDGERVIGAILFENTMNRQVEGSPTGDYLWNSKGIVPFLKIDQGLAPEQQGAQLMKPI
+PHLDDLLSRAVEKHMFGTKMRSVIKLPGDGVGSVVEQQFGLARQILVTGLVPIIEPEVDI
+RSPRKAEVEDQLKAAILAQLDKLGDDQSVILKVTLPERADFYREFVDHPRVIRVLALSGG
+YTRAQATTLLARNHGVIASFSRALTEGLSTAQSPAQFNAVLDEAINAIATASRT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000580.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000580.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25fd1389e86f57a45b8eb7782f3192d02aeb7e27
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000580.fa
@@ -0,0 +1,35 @@
+>PROKKA_00643
+MTARLLADVDTGIDDACALLHLVGAHRLGAGPELAAVTTTGGNATARDCALNTAAVLDLA
+GRADVEVAVGAETPLRRPAVTTPETHGDGGLGHARIVRRPERLSPRPAVDVWLDELRAHP
+GETAILCTAPLTNLALALRTEPRLPFLARGIVIMGGSFYHPGNTTPTAEWNTWVDPDAAK
+EVFAAVEGLPEDRLPIVCALETTERIEYTPALLDGLLADAGAHPVGWSADRPRVAGPDAA
+TGSPVLDVLADALRFYFEFHHDYDQGYIAHLHDLFAAQVAAGQARIATRATVVDVEADSE
+LLRGTTVHDTRDIWGRRPNAQLVTANDPAEVFAAFARAVGAVVAGERTLDGGSPAR
+>PROKKA_00380
+MTARLLADVDTGIDDACALLHLVGAHRLGVGPELAAVTTTGGNATARDCALNTAAVLDLA
+GRADVEVAVGAETPLRRPAVTTPETHGDGGLGHARIVRRPERLSSRPAVDVWLDELRAHP
+GETTILCTAPLTNLALALRTEPRLPFLARGIVIMGGSFYHPGNTTPTAEWNTWVDPDAAK
+EVFAAVEGLPEDRLPIVCALETTERIEYTPALLDGLLADAGARPVGWSADRPRVAGPDAA
+TGSPVLDVLADALRFYFEFHHDYDQGYIAHLHDLFAAQVAAGQARIATRATVVDVEADSE
+LLRGTTVHDTRDIWGMRPNAQLVTANDPAEVFAAFARAVGAVVAGERTLDGGSPAR
+>PROKKA_00385
+MGARILADMDTGIDDACALLQLVGAGAELAAVTTTGGNATARECALNTAALLDLMGRTDV
+EVAVGAEAPLQRPPETTPETHGDGGLGYARLAHRPERLSARSAVDVWVEELRARPGRTTI
+LCTAPLTNLALALRAEPALPELAAGVVIMGGAFYYPGNTTPTAEWNTWCDPDAAKEVFAA
+FEGLPEDRLPLLCPLETTERIEYTPALLDALLTGVGHAPTGWSVDRARHAGPQADTGSPV
+LDVLADALRFYFEFHHDYDQGYVAHLHDLFAAQVALGTAQIRTQATVVDVEADSDLLRGT
+TVHDDRHIWGRRPNARRVVDADPAGVFAAFAQAASAAARAGDDAGR
+>PROKKA_02182
+MAAVTARLLADVDTGIDDACALLHLVGAHRLGAGPELAAVTTTGGNATARDCALNTAAVL
+DLAGRADVEVAVGAETPLRRPAVTTPETHGDGGLGHARIDRRPERLSPRPAVDVWLDELR
+AHPGETTILCTAPLTNLALALRAEPRLPFLARGIVIMGGSFYHPGNTTPTAEWNTWVDPD
+SAKEVFAAVEGLPEDRLPIVCALETTERIEYTPALLDGLLADAGARPARWDVARPRVSGP
+AADTGHPVTDVLADALRFYFEFHHDYDQGYIAHLHDLVAAQVAAGQADVTLQATVVDVEA
+DSELLRGTTVHDDRRIWGRRPNARRVTGCDPRRVFEDFAQAVGALTGAGVG
+>PROKKA_00613
+MAAVTARLLADVDTGIDDACALLHLVGAHRLGAGPELVAVTTTGGNASARDCALNTAAVL
+DLAGRADVEVAVGAETPLRRPAVTTPETHGDGGLGHARIVRHPERLSPRPAVDVWLDELR
+AHPGETTILCTAPLTNLALALRTEPRLPFLARGIVIMGGSFYHPGNTTPTAEWNTWVDPD
+AAKEVFAAVEGLPEDRLPIVCALETTERIEYTPALLDGLLADAGARPVGWSADRPRVAGP
+DAATGSPVLDVLADALRFYFEFHHDYDQGYIAHLHDLFAAQVAAGQARIATRATVIDVEA
+DSELLRGTTVHDTRDIWGRRPNAQLVTANDPAEVFAAFARAVGAVVAGERTPDGGAPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000581.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000581.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85d7656e9fbe2967ba37a7d5fa176954e175839c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000581.fa
@@ -0,0 +1,35 @@
+>PROKKA_00645
+MSHQAPPADASKVRAPRTAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELELAKRHVAAK
+GKKAGIGAGIAVVGLFFLALMVVALVVTLIGAFADPTFWFPALMVALAFLVLGLIFAGVG
+LMMVKGAMPLVPQEIVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAAREAERKK
+VEKEENKKARKNGEAAPHPDRADASEAEIRRRADLRRRHLGDIRSGLDEKTSVKGQLAAF
+AAQRKGRGVTPETAHATEQTAPFTGAARAGERTAEAEDYVKDNWQPLALLGASSAAFVAL
+AGRLRRR
+>PROKKA_00382
+MSHQAPPADASKVRAPRTAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELELAKRHVAAK
+GKKAGIGAGIAVVGLFFLALMVVALVVTLIGAFADPTFWFPALMVALAFLVLGLIFAGVG
+LMMVKGAMPLVPQEIVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAAREAERKK
+VEKKENKKARKNGEAAPHPDRADASEAEIRRRADLRRRHLGDIRSGLDEKTSVKGQLAAF
+AAQRKGRGVTPETAHATEQTAPFTGAARAGERTAEAEDYVKDNWQPLALLGASSAAFVAL
+AGRLRRR
+>PROKKA_02318
+MSHQAPPADALKAGAPRPAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELALAKGHVVAK
+GKKAGIGAGVTVVGLFFLALVVVALVVALIGAFADPTFWFPALMVAAAFLVLGAIFAGIG
+LFMVKGAMPLVPQETVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAKRAEERRK
+VEKEENKKARKNGEAAPHPDRDEASEAEIRRRADLRRRHLGDIRSGLEEKTSVKGQLAAF
+AAQRKGRGVTPQTAHATDQTAPFTGAARAGEKAAEAEDYVKDNWQPLALLGASSAAFLAL
+AGRLRRR
+>PROKKA_02177
+MSHAAPTAAPRAPRPTTPVTPQTRASSLTDLLAAVVRLLPLQLKDELALAKGQAAAKGKK
+AGIGAALAVVGLFFLALMTIALVVALIGAFANPPFWFPALMVALVFLVLGLVLAGVGAMQ
+IKGAMPLVPQETVRNLEYDLGYLKEGNDFDPAEYDRLKAERAEAKRLEKQREAERKKVEK
+EENKQARKDGLAAPHPAKDDASEDEVRRRAELRRRHLGDIRSGLDEKTSVKGQVAAFTAQ
+RKLRGTTPDTAHATEQTAPFTTAARAGEQTAAAEDYVKERWQPLALLGASGTAFAVLASR
+LRGRKG
+>PROKKA_00615
+MSHQAPPADASKARAPRTAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELALAKGHVAAK
+GKKAGIGAGVAVVGLFFLALMVVALVVTLIGAFADPSFWFPALMVALAFLVLGLIFAGVG
+LVMVKGAMPLVPQETVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAAREAERKK
+VEKEENKKARKNGEAAPHPDRDDATEAEIRRRADLRRRHLGDIRSGLDEKTNVKGQLAAF
+AAQRKGRGVTPETTHATEQTAPFTGAARAGERTAEAEDYVKDNWQPLALLGASSAAFVAL
+AGRLRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000582.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000582.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f2f86de8e90bce2bc0dcfc5fc49dece06b2cc67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000582.fa
@@ -0,0 +1,40 @@
+>PROKKA_00647
+MSDRPGIAADRPLKVLIAADTYPPHVNGAATFGHRLATALHARGHEVHVVMPRSDAGPDT
+VEHRPEATVHLLRSLPAPTHEYYRVVLPRHAKTSFRRIYREVQPDVVHAQCHYMIGEAAI
+NEAERRRIRIVSTNHFMPENLEPFLPFPQWFLDIVSRVSWKDMGRLMGKGAVVTTPTALA
+AQAMAEHAGLDNVLPVSNGIDASAYELQPGERVDHPGHPVVLFVGRLAVEKNVEVLIRAI
+AHLARTRPDLDVHAEIVGDGEQRDRIRATVDEEGAADRVLLRGHVSEEELRAAYLRADVF
+CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALAERIARIL
+DLSDAERAAMGEASHAKALHHSAQKTVDIFERLYRGATAAEVRALL
+>PROKKA_00384
+MSDRPGIAADRPLKVLIAADTYPPHVNGAATFGHRLATALHARGHEVHVVMPRSDAGPDT
+VEHRPEATVHLLRSLPAPTHEYYRVVLPRHAKTSFRRIYREVQPDVVHAQCHYMIGEAAI
+NEAERRRIRIVSTNHFMPENLEPFLPFPQWFLDIVSRVSWKDMGRLMGKGAVVTTPTALA
+AQAMAEHAGLDNVLPISNGIDASAYELQPGEKVDHPGHPVVLFVGRLAVEKNVEVLIRAI
+AHLARTRPDLDVHAEIVGDGEQRDRIRATVDEEGAADRVLLRGHVSEEELRAAYLRADVF
+CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALAERIARIL
+DLSDAERAAMGEASHAKALHHSAQKTVDIFERLYRGATAAEVRALL
+>PROKKA_02316
+MSDRPGTAADRPLKVLIAADTYPPHVNGAATFCHRLATALHARGHEVHVVMPRGEAGPDT
+VEERPEATVHLLRAIPAPTHEYYRLVMPWHAKAAFRRIYREVQPDVVHVQCHYMVGEAAI
+NEAERRRIRMVSTNHFMPENLEPFLPFPQWFLDIVSRVSWRDMGRLMGKGAAVTTPTALA
+ARAMAEHAGLDNVLPVSNGIDAAAYELQPGETVDHPGHPVVLFVGRLAVEKNVEVLIRAI
+AHLARVRPDLDVHAEIVGDGEQRDRIRAAVESEGVADRVLLRGHVSDEELRAAYLRADVF
+CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALAERVARIL
+DLPEAERAAMGEASHAKAMHHSAQKTVDVFERLYRGATPAEVRELL
+>PROKKA_02175
+MTSSARPAQERPLTVVIAADTYPPDVNGAAVFCFRLASALHERGHRVHVIAARNEPGPDT
+VEERPEATVHRLESHRAFTHEYYRLVFPWHASRSIDRILAEVRPDVVHAQCHYMIGEAAI
+NVADRRRIRTVSTNHFMPENLEPFLPFPQWFLNIVSKNSWRDMGRLMGKGAAVTTPTALA
+AAAMAEHAGLDRVLPISNGIDASAYELAPGEVVERAAHPTVLFVGRLAVEKHVDVLVRAV
+AHLARTRPDLDVHAEIVGDGEQRTALDAVIAEEGVADRVRRLGHVSDAELHTAYLRADVF
+CQPGTAELQSLVSLEAMSASTPVVLADALALPHLVDDGVNGWLFPPGDHVALAERIARVL
+DLPEAGRAAMGEASHAKAVRHSQAKTVDLFERLYRGATPAEIRAAL
+>PROKKA_00617
+MSDRPGIAADRPLKVLIAADTYPPHVNGAATFGHRLATALHARGHEVHVVMPRSDAGPDT
+VEHRPEATVHLLRSLPAPTHEYYRVVLPRHAKISFRRIYREVQPDVVHAQCHYMIGEAAI
+NEAERRRIRIVSTNHFMPENLEPFLPFPQWFLDIVSRVSWKDMGRLMGKGAVVTTPTALA
+AQAMAEHAGLDNVLPVSNGIDASAYELQPGERVDHPGHPVVLFVGRLAVEKNVEVLIRAI
+AHLARTRPDLDVHAEIVGDGEQRDRIRATVDEEGVADRVLLRGHVSEEELRAAYLRADVF
+CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALADRIARIL
+DLSDADRAAMGEASHAKALHHSAQKTVDIFERLYRGATAAEVRAML
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000583.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000583.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c94cc44e73dbc404699847ab2cc0f674f178f39
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000583.fa
@@ -0,0 +1,30 @@
+>PROKKA_00649
+MSVTSSHAAVRRAPRTAAASVALALGAAALTGVGTVSVAETAQAAETAYTVRSGDGWWII
+AQRTGVSMSRLQSLNGMTAATVLHPGMVLKTSGTATPTPAPAPSTSGSTYTVLAGDGWWI
+ISYRTGVSASILQSINGMSSSTMLHPGMVLKTTSVSTSSAPAVAPAPAPASKQAAVDYVR
+SAVRNPSSYYVWGGNGPSGFDCSGLTQQAMARAGISIPRRAGDQYLAAKSYVPISQAQPG
+DLVFYANQSTGRIYHTAMYMGGGQLAHALNEDAGLVFTSTTIMKSDMLAVAARY
+>PROKKA_00386
+MSVTSSHAASRRAPRTAAASVALALGAAALTGVGTVSVAETAQAAETTYTVRSGDGWWII
+AQRTGVSMSTLQSLNGMTAATVLHPGMVLETSGTATPAPAPAPSTSGSTYTVLAGDGWWI
+ISYRTGVSASILQSINGMTSSTMLHPGMVLKTTSVSTSSAPALAPASAPASKQAAVDYVR
+AAVRNPSSYYAWGGNGPSGFDCSGLTQQAMAQAGISIPRRAGDQYLAAKSYVPISQAQPG
+DLVFYANQSTGRIYHVAMYMGGGQLAHALNEDAGLVFTSTTIMKSDMLAVAARY
+>PROKKA_02314
+MSVTSSRAASRRAPRTAAASLALALGAGALAGVGSVTAAETAQAVETTYTVRAGDGWWVI
+SQRTGVSMSTLQSLNGMTSATMLHPGMVLKTSGTAAPAPAPAPSASTYTVLAGDGWWIIS
+YRTGVSASVLQSINGMTSSTVLHPGMVLKTSVVASSAPAPAPAPVTNGKQAAVDFVRSTV
+QNPSSYYLWGGNGPYGFDCSGLTQQAMAKAGISIPRRAGDQYNAAKSYVPISQAQPGDLV
+FYANQSTGRIYHVAMYMGGGQLAHALNEDAGLLFTSTTIMKSDMLAVAARY
+>PROKKA_02171
+MPEALLTPARRPRAAAASLALALGAGAGVTAGAAVIAPQAVAAETYTVQAGDGWWIISQR
+TGVSMATLMQLNGMTSADMLHPGMVLKTSGTVTAAAGTYTVKAGDGWYAISRATGVPVST
+LTSLNGMTITSMLYPGMVLKTTGTPASTAPAPAPAPAPVVRQSSKQAAIDFAVAKVNDPN
+TYYAWGGNGPYGYDCSGLTKAAFAAAGITIPRVSHDQYVNAPAYAPLSQAQPGDLVFWAN
+QSTGRVYHVAVYIGNGKVAHALNTTDDLVITSTDVMTSNRLAVVGRY
+>PROKKA_00619
+MSVTSPHAAARRAPRTAAASVALALGAAALTGVGTVSVAETAQAAETTYTVRSGDGWWII
+AQRTGVSMSTLQSLNGMTAATVLHPGMVLKTSGTATPAPAPAPSTSGSTYTVLAGDGWWI
+ISYRTGVSASVLQSINGMTSSTMLHPGMVLKTTSVSTSSAPAPAPAPASKQAAVDYVRSA
+VRNPSSYYVWGGNGPSGFDCSGLTQQAMARAGISIPRRAGDQYLAAKSYVPISQAQPGDL
+VFYANQSTGRIYHTAMYMGGGQLAHALNEDAGLVFTSTTIMKSDMLAVAARY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000586.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000586.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0db01de6d95eff87ae05675c16f0a73aa2f4a6e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000586.fa
@@ -0,0 +1,30 @@
+>PROKKA_00653
+MANYTAADIKALRERTGAGMMDVKKALDEADGDAEKAIEIIRVKGLKGATKREGRSAAEG
+LVAATVENGVGVMIELNCETDFVAKADKFIALGDVVLRAAVASGATDVDGLLASEHEGRT
+LGDYVTEEGALLGEKVAVRRLARVEGAYVDAYLHKTSKDLPAQVGVLLAVDADSAEAKTA
+AHDIAVHVAAYSPTYLTREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK
+EIVLVDQPFAKDPKQTVGKVASDAGTNVTGFARFRVGN
+>PROKKA_00390
+MANYTAADIKALRERTGAGMMDVKKALDEANGDAEKAIEIIRVKGLKGATKREGRSAAEG
+LVAATVENGVGVMIELNCETDFVAKADKFIALGDVVLRAAVASGATDVDGLLASDYEGRT
+LGDYVTEEGALLGEKVAVRRLARVEGAFVDAYLHKTSKDLPAQVGVLLAVDADSADAKTA
+AHDIAVHTAAYSPTYLTREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK
+EIVLVDQPFAKDPKQTVGKVASDAGTNVTGFARFRVGN
+>PROKKA_02310
+MANYTAADIKALRERTGAGMMDVKKALDEANGDAEKAIEIIRVKGLKGATKREGRSAAEG
+LVAATVENGVGVMIELNCETDFVAKAEKFITLGDVVLRAAVASGAADVESLLASEHEGRT
+LGDHVIEEGALLGEKVAVRRLARVEGALVDAYLHKTSKDLPAQVGVLLAVDADSAEAKTA
+AHDIAVHTAAYSPTYLSREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK
+EIVLEDQPFAKDPKQTVGKVASDAGTKVTGFARFRVGN
+>PROKKA_02167
+MANYTAADIKALRERTGAGMMDVKKALDEANGDADKAVEIIRVKGLKGATKREGRSAAEG
+LVAATVENGVGVMIELNCETDFVAKADKFISLGDVVLKAAVASGAADVDSLLASDHEGRT
+LGDYVTEEGALLGEKVAVRRVARVEGAHVDAYLHKTSKDLPAQVGVLLAVDADSDAAKTA
+AHDIAVHTAAYSPTYLTREDVPAETVENERRIAEESARAEGKPEQALAKIVEGRLTGFFK
+EGVLVDQPFAKDPKTTVGKVASEAGTAVTGYARFRVGN
+>PROKKA_00623
+MANYTAADIKALRERTGAGMMDVKKALDEANGDAEKAIEIIRVKGLKGATKREGRSAAEG
+LVAATVENGVGVMIELNCETDFVAKADKFIALGDVVLRAAVASGATDVDGLLASDYEGRT
+LGDYVTEEGALLGEKVAVRRLARVEGAFVDAYLHKTSKDLPAQVGVLLAVDADSADAKTA
+AHDIAVHTAAYSPTYLTREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK
+EIVLVDQPFAKDPKQTVGKVASDAGTNVTGFARFRVGN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000587.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000587.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b15b05387bbca1b1d3bff2ac0576bc33d3864874
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000587.fa
@@ -0,0 +1,30 @@
+>PROKKA_00654
+METNRAPEDPTTAHAPQTSDDTGRRRVLLKLSGEVFGGGKIGVDPETVRGIAEQIAAAAD
+QVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVTTRVQSA
+IHMEQVAESYIPLRAIRHMQKGRVVIFGAGTGLPYFSTDTVAAQRALEVGADEVLMAKSG
+VDGVYTADPKKDPTAERLTHLTYDEALLRNIRVMDLTAMTMCKDNDLDMRVFGMEGPGNV
+TRALLGEPIGTTVTV
+>PROKKA_00391
+METNRAPEDPTTAHAPQTSDDTGRRRVLLKLSGEVFGGGKIGVDPETVRGIAEQIAAAAD
+QVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVTTRVQSA
+IHMEQVAESYIPLRAIRHMQKGRVVIFGAGTGLPYFSTDTVAAQRALEVGADEVLMAKSG
+VDGVYTADPKKDPTAERLTHLTYDEALLRNIRVMDLTAMTMCKDNDLDMRVFGMEGPGNV
+TRALLGEPIGTTVTV
+>PROKKA_02309
+METNRAPEDPKTAHVPQTSDDTGRRRVLLKLSGEVFGGGKVGVDPETVRGIAEQIAVAAD
+RVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVSTRVQSA
+IHMEQVAESYIPLRAIRHMQKGRVVVFGAGTGLPYFSTDTVAAQRALEIGADEVLMAKSG
+VDGVYTADPKKDPSAELLTHLTYDEALLRNIRVMDLTAMTMCKDNNLDMRVFGMEGPGNV
+TRALLGEPIGTTVTV
+>PROKKA_02166
+MSPAQQPENHAVDAEDTGRRRVLLKLSGEVFGGGSVGIDPVTVRGIAEQIAEAAEQVEIS
+IVVGGGNFFRGAELSESGMDRRRADYMGMLGTVMNCLALQDFLLQAGVSTRVQSAIHMEQ
+VAESYIPLRAVRHMQKGRVVVFGAGTGLPYFSTDTVAAQRALEIGADEVLMAKSGVDGVY
+TADPKKDPTAQRLEHLTYDEALRKDIRVMDLTAMTMCKDNGLSMRVFGMEGPGNVTRALL
+GEEIGTSVTP
+>PROKKA_00624
+METNRAPEDPTTAHAPQTSDDTGRRRVLLKLSGEVFGGGKIGVDPETVRGIAEQIAAAAD
+QVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVTTRVQSA
+IHMEQVAESYIPLRAIRHMQKGRVVIFGAGTGLPYFSTDTVAAQRALEVGADEVLMAKSG
+VDGVYTADPKKDPTAERLTHLTYDEALLRNIRVMDLTAMTMCKDNDLDMRVFGMEGPGNV
+TRALLGEPIGTTVTV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000591.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000591.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a39cc84529c98f192752c3a9719642a38cc76c3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000591.fa
@@ -0,0 +1,35 @@
+>PROKKA_00659
+MSERMTFGRAINRGLQRALADDPKVLLMGEDIGALGGVFRITDGLQAEFGEDRVLDTPLA
+ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF
+GGGIGSPEHHSESPEAYFLHTAGLRVVSPSSPQEGYDLIRAAIASEDPVVYLEPKRRYHD
+KGDVDLDVAIPPMSPARILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS
+PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP
+PSKLEHLHLPDLDRILDGLDRALGRPNSLDSVDAFAAPETAEQFLAAQNAGEETR
+>PROKKA_00396
+MSERMTFSRAINRGLHRALADDPKVLLMGEDIGALGGVFRITDGLQAEFGEDRVLDTPLA
+ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF
+GGGIGSPEHHSESPEAYFLHTAGLRVVSPSSPQEGYDLIRAAIASEDPVVYLEPKRRYHD
+KGDVDLDVAIPPMSPARILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS
+PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP
+PSKLEHLHLPDLDRILDGLDRALGRPNSLDSVDAFAAPETAEQFLAAQNAGEETR
+>PROKKA_02304
+MSERMTFGRAINRGLHRALADDPKVLLMGEDIGALGGVFRITDGLQDEFGEDRVLDTPLA
+ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF
+GGGIGSPEHHSESPEAYFLHTPGLRVVSPSSPQEGHDLIRAAIASDDPVVYLEPKRRYHD
+KGEVDLDADIPPMSTAKILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS
+PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP
+PSKLEHLHLPDLDRILDGVDRALGRPNSLDSVDAFAAPETAEQFLAAQTAGEETR
+>PROKKA_02160
+MSEQMTFGRALNRGLHRALADDPKVLLMGEDIGRLGGVFRITDGLQEEFGVDRVVDTPLA
+EAGIVGTAIGLALRGYRPVVEIQFDGFLYPAFDQIVANLAKLRARTRGRVAVPVTIRIPY
+GGGIGSPEHHCESPEAYFLHTPGLRVVSPSSPQAGYEMIRAAIASDDPVVFFEPKRRYHD
+KGPVDLDAAPGPLSVGRVLRPGADVTLVAYGPLVKTALQAAEVAEQEGVSVELIDLRSLS
+PLDTGLVEASVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLESPPVRVTGLDIPYP
+PATLEHLHLPDLDRILEGVDRALGRPNPQDAVDAFAPPQTAEDFLSARADSSEVPA
+>PROKKA_00629
+MSERMTFGRAINRGLHRALADDPKVLLMGEDIGALGGVFRITDGLQAEFGEDRVLDTPLA
+ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF
+GGGIGSPEHHSESPEAYFLHTAGLRVVSPSSPQEGYDLIRAAIASEDPVVYLEPKRRYHD
+KGDVDLDVAIPPMSPARILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS
+PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP
+PSKLEHLHLPDLDRILDGLDRALGRPNSLDSVDAFAAPETAEQFLAAQNAGEETR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000595.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000595.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b803e2aad4c704e60eb1222d06be441aacbbc20c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000595.fa
@@ -0,0 +1,60 @@
+>PROKKA_00664
+MTENHAQGTPLFDTVLLANRGEIAVRVIRTLRRLGIRSVAVHSDADADARHVREADTAVR
+LGPAPARESYLDIDAVVDAARRTGAQAVHPGYGFLSENADFARALEAAGIVFVGPPVGSL
+DAMADKIRAKETVAAYDVPVVPGIQDPTLTDAQITAEAEHVGFPLLIKPSAGGGGKGMVA
+VRAAEELPGALASARRTARSAFGDDTLLLERLITAPRHVEVQVFADAHGATVHLGERECS
+LQRRHQKVIEEAPAPLLTGLAHGAELRERLGRAAVDAAVSVGYRGAGTVEFLVSDENPDE
+FFFMEMNTRLQVEHPVSEEVVRVRGQRLDFVELQLRIAAGEPLGFAQEDVSLDGAAVEAR
+VYAEDPANGFLPSTGPVLRWREPAGEGVRVDTLLLPSQGEERAFGTVLTIRDDEGALWEG
+LAAPDGAQPEITGFYDPMIAKLITRGADRTEALERLDAALADTVLFGVRSNLGWLRELAA
+RTDVRTGRLTTELIDGLEAWTAPALPEDLAALAAEALADVSEDAAAAEQRAAGTAWARAD
+GWRGAGAPQPGMRVRVGDEDRILTAPAADAEVDEDAGALAGVNLLAGDPRDPRSAWLHRD
+GAAWQVRRLTRAEVVEAARAAAAARRAPAGAASPEARTPMPGTVVAVSVATGDTVAAGQE
+LAVVEAMKMEHPVTAAVAGVVTVHVAEGDPVAAQALIAVVEPAENAAPEENA
+>PROKKA_00401
+MTENHAQGTPLFDTVLVANRGEIAVRVIRTLRRLGIRSVAVHSDADADARHVREADTAVR
+LGPAPARESYLDIDAVVDAARRTGAQAVHPGYGFLSENADFARALEAAGIVFVGPPVASL
+DAMADKIRAKETVAAYDVPVVPGIQDPTLTDEQITAEAERVGFPLLIKPSAGGGGKGMVA
+VRAAEELPGALASARRTARSAFGDDTLLLERLITAPRHVEVQVFADAHGATVHLGERECS
+LQRRHQKVIEEAPAPLLTGLAHGAELRERLGRAAVDAAVSVGYRGAGTVEFLVSDENPDE
+FFFMEMNTRLQVEHPVSEEVVRVRGQRLDFVELQLRIAAGGPLGFAQEDVTLDGAAVEAR
+VYAEDPANGFLPSTGPVLRWREPAGEGVRVDTLLLPSRPAEERAFGSGPQTGPAAGAVDP
+VDVDGAQPEITGFYDPMIAKLIARGADRAEALDRLDAALADTVLFGVRSNLGWLRELAAR
+EDVRTGRLTTELIDGLEAWTAPALPEDLAALAAEALADVSEDAAAAEHRAAGTAWARADG
+WRGAGAPQPGMRVRVGDEDRILTAPAADAEVDEDAGGLAGVNLLAGDPRDPRSAWLHRDG
+AAWQVRRLTRAEVVEAARAAAAARRAPASAASPEARTPMPGTVVAVSVATGDTVAAGQEL
+AVVEAMKMEHPVTAAVAGVVTVHVAEGDAVAAQALIAVVEPTEHAAPAENT
+>PROKKA_01220
+MDLDARPLAGRKLLLLDGSRKSIEIVDEAHRLGVHVIVTDYNTPEQSPAKLAADQHFQVS
+TSDVDAVVDLIRREGVDGVLAGFSDRWLATYAEICAAAQVPCYATVDQIRLFTDKKRYKA
+MLEQFGVPTITGYSVDDATSGAIPEEAFPLIVKPADGSGSRGISVVASQSELQNGLDVAL
+NYSWTQDLVIERFLPGQEATVYWVFQDGDCRVSLMWHRHMHDFGPQDRYRLPVAYSSPSS
+LLPTYLADVAPSVQAMLRSAGVRDGIMFMQGLIHEGVFHTYDIGYRVTPTQEYRVVEELC
+GYNPLSMLIHYALTGTMGQPDLAAVAEPRHPGYGFNVSTLIRPGTVGAVTGLDDVAALRG
+ILSTTAAIDAGETLPEEGWGQLRQVAVRTVGVADSLDLLRQTMRQVDELIDVRDVDGASM
+VIHPDMPPQDLDAYVL
+>PROKKA_02299
+MTENPTQGAPLFHTVLVANRGEIAVRVIRTLRRLGIRSVAVHSDADAQARHVLEADEAVR
+LGPAPARESYLDIEAVVEAARRTGAQAVHPGYGFLSENADFARALEAAGIVFVGPPMASL
+DAMADKIRAKETVAAYDVPVVPGVADPTLDDAALAAEAQRVGFPLLIKPSAGGGGKGMVA
+VHAADELPAALASARRTARSAFGDDTLLLERLIAAPRHIEVQVFADAHGTTVHLGERECS
+LQRRHQKVIEEAPAPLLTGLAHGAELRERLGKAAVDAAVSVGYRGAGTVEFLVSDEDPDA
+FFFMEMNTRLQVEHPVSEEVVRVRGQRQDFVELQLRIAAGEPLGFAQDDIALEGAAVEAR
+VYAEDPANGFLPSTGPVLRWREPQGEGVRVDTLLLPAADAADPAAVDGGQPEVTGFYDPM
+VAKVITRGADRAEALDRLDAALADTVLFGVRSNLGWLRELAAREDVRAGRLTTELIDGME
+AWNAPTLPEDLAALAAEALEEASDDAAAAERHAAGSAWARADGWRGAGAPQPGMRVRVGD
+EDRVLHGPAADAETEEDESALAGLNLLAGDPRDPRSAWLHRDGAAWQVRRLTRAEVVEAA
+RAAAAARRAPGRAQRPPRPARPCRAPSSPSRWPPGTPWPSARSWPWSRP
+>PROKKA_00634
+MTENHAQGTPLFDTVLVANRGEIAVRVIRTLRRLGIRSVAVHSDADADARHVREADTAVR
+LGPAPARESYLDIDAVVDAARRTGAQAVHPGYGFLSENADFARALEAAGIVFVGPPVASL
+DAMADKIRAKETVAAYDVPVVPGIQDPTLTDEQITAEAERVGFPLLIKPSAGGGGKGMVA
+VRAAEELPGALASARRTARSAFGDDTLLLERLITAPRHVEVQVFADAHGATVHLGERECS
+LQRRHQKVIEEAPAPLLTGLAHGAELRERLGRAAVDAAVSVGYRGAGTVEFLVSDENPDE
+FFFMEMNTRLQVEHPVSEEVVRVRGQRLDFVELQLRIAAGGPLGFAQEDVTLDGAAVEAR
+VYAEDPANGFLPSTGPVLRWREPAGEGVRVDTLLLPSRPAEERAFGSGPQTGPAAGAVDP
+VDVDGAQPEITGFYDPMIAKLIARGADRAEALDRLDAALADTVLFGVRSNLGWLRELAAR
+EDVRTGRLTTELIDGLEAWTAPALPEDLAALAAEALADVSEDAAAAEHRAAGTAWARADG
+WRGAGAPQPGMRVRVGDEDRILTAPAADAEVDEDAGALAGVNLLAGDPRDPRSAWLHRDG
+AAWQVRRLTRAEVVEAARAAAAARRAPAGAASPEARTPMPGTVVAVSVATGDTVAAGQEL
+AVVEAMKMEHPVTAAVAGVVTVHVAEGDAVAAQALIAVVEPTEHAAPAENT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000606.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000606.fa
new file mode 100644
index 0000000000000000000000000000000000000000..159cc70de5d08fc25583414b7c6009922919c2ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000606.fa
@@ -0,0 +1,81 @@
+>PROKKA_00679
+MAKVRVHELAKELGITSKEALSTLKDLGEFVSSASSTIEPPVVKKLRNAYPGAGKSAAKP
+GSTPAAPGRSAAPKPAAAPSPRAAAPTSNVGAPAPGPAAGRTAAPKPGAAPTPGPAAPTP
+AAPAEPKAPQPPATPGSAAPKPGAAAPKPGASAPKPGAPRPGNNPFSPKGGSAGPRPGAR
+PGGRGGAPRPGNNPFAPSQGMRSGREDRAPRPGGPRPPAGAGGPRPGGPRPAAGAGGPRP
+GGPRPNPGMMPKQITPAPQPARGRGRPGGGPGGGPGRPGGPGGRGGRGNAQGAFGRGGGP
+RKGRKSKRAKRQEFEQQHTREIGGVKVPKGDGTTVLRLRRGASLADFAEKIRADVADLVK
+VLFTLGEMASANQSLDEETFQLLGDELGYKVQIVSPEDEDKELLEAFDIDLEAEAANEDE
+ADLEPRPAVVTVMGHVDHGKTRLLDAIRSSNVIEGEAGGITQHIGAYQVPVEHEGEQRRL
+TFIDTPGHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNHAQSAGVPIVVAVNKI
+DKDTAAPDKIRGQLTEYGLVPEEYGGDTMFVDVSARNNINIDQLLEAILLTADAALELTA
+NPHKAARGVAIEANLDKGRGAVVTVLVQTGTLRVGDTMVVGSAHGRVRAMFDENGNAVEA
+ADPSRPVQVLGLSTVPRAGDSFLVTDDERTARQIAEKREAADRNAQLAKRRKRITLEDFD
+QAVAEGKLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVIHRGVGAITQNDVNLA
+TVDNAIIIGFNVRPAERVADLADREGVDMRFYSVIYDAIDDIENALKGMLKPEYEEVELG
+SAEVREVFRSSKWGNIAGSLVRSGLIRRNAQARLVRDGVVVSDHLKIESLRRFKDDATEV
+REGYECGIGLGSFNDIKEGDVIETFEMQEKPRV
+>PROKKA_00416
+MAKVRVHELAKELGITSKEALSTLKDLGEFVSSASSTIEPPVVKKLRNAYPGAGKSAAKP
+GSTPAAPGRSAAPKPAAAPSPRAAAPTSNAGAPAPGPAAGRTAAPKPGAAPTPGPAAPTP
+AAPAEPKAPQPPATPGSAVPKPGAAAPKPGASAPKPGAPRPGNNPFSPKGGSAGPRPGAR
+PGGRGGAPRPGNNPFAPSQGMRSGREDRAPRPGGPRPPAGAGGPRPGGPRPAAGAGGPRP
+GGPRPNPGMMPKQITPAPQPARGRGRPGGGPGGGPGRPGGPGGRGGRGNAQGAFGRGGGP
+RRGRKSKRAKRQEFEQQHTREIGGVKVPKGDGTTVLRLRRGASLADFAEKIRADVADLVK
+VLFTLGEMASANQSLDEETFQLLGDELGYKVQIVSPEDEDKELLEAFDIDLEAEAANEDE
+ADLEPRPAVVTVMGHVDHGKTRLLDAIRSSNVIEGEAGGITQHIGAYQVPVEHEGEQRRL
+TFIDTPGHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNHAQSAGVPIVVAVNKI
+DKDTAAPDKIRGQLTEYGLVPEEYGGDTMFVDVSARNNINIDQLLEAILLTADAALELTA
+NPHKAARGVAIEANLDKGRGAVVTVLVQTGTLRVGDTMVVGSAHGRVRAMFDENGNAVEA
+ADPSRPVQVLGLSAVPRAGDSFLVTDDERTARQIAEKREAADRNAQLAKRRKRITLEDFD
+QAVAEGKLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVIHRGVGAITQNDVNLA
+TVDNAIIIGFNVRPAERVADLADREGVDMRFYSVIYDAIDDIENALKGMLKPEYEEVELG
+SAEVREVFRSSKWGNIAGSLVRSGLIRRNAQARLVRDGVVVSEHLKIESLRRFKDDATEV
+REGYECGIGLGSFNDIKEGDVIETFEMQEKPRV
+>PROKKA_02284
+MMPKQITPAPAPARGGGRGRPGGGPGGGPGRPGGPGGRGGRGNAQGAFGRGGGARKGRKS
+KRAKRQEFEQAHTREIGGVKVPKGDGTTVLRLRRGASLADFAEKIRADVADLVKVLFTLG
+EMASANQSLDEDTFQLLGDELGYKVQIVSPEDEDKELLEAFDIDLEAEEANEDEADLEPR
+PAVVTVMGHVDHGKTRLLDAIRSSNVIEGEAGGITQHIGAYQVPVQHEGEDRRLTFIDTP
+GHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNHAQSAGVPIVVAVNKIDKDTAQ
+PDKIRGQLTEYGLVPEEYGGDTMFVDVSARNGINIDQLLEAVLLTADAALELTANPSKDA
+RGVAVEANLDKGRGAVVTVLVQTGTLRVGDNMVVGSAHGRVRAMFDENGAPVEEADPSRP
+VQVLGLSSVPRAGDSFLVTEDDRTARQIAEKREAADRNAQLAKRRKRITLEDFDQAVAEG
+KLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVIHRGVGAITQNDVNLATVDDAI
+IIGFNVRPAERVADLADKEGVDMRFYSVIYDAIDDIENALKGMLKPEYEEVALGSAEVRE
+VFRSSKWGSIAGSLVRSGLIRRNAQARLVRDGAVVADNLKIESLRRFKDDATEVREGYEC
+GIGLGSFNDIKEGDVIETFEMREKPRA
+>PROKKA_02145
+MAKVRVHELAKELGITSKEALSTLKDLGEFVSSASSTIEPPVVKKLRGAYPGAGAKGSAK
+PAAAAPAAPKPAGGSAPSPAAAKPAAASAPGASAPKPGSAAPQPGSAAPKPGGSAPKPGA
+SAPAPAAQKSAPAAPKAPAAPAPQAPAPKPGASAPKPGASAPKPGGAKPAPRPGNNPFTS
+KAGSAGPRPGGGRSGGPRPGNNPFAPSQGMRSGREDRAPRPGGPRPAAGAGGPRPGGPRP
+AAAGAGGPRPGGPRPNPGMMPKHITPAATPARGGGRGRPGAGGPGGGPGRPGGGPAGRGG
+GRGNAQGAFGRGGGARKGRKSKRAKRQEFEQQHTREIGGVKVLKGDGTTVVRLRRGASLA
+DFAEKIHADVADLVKVLFTLGEMASANQSLDEETFQLLGGELGYVVQIVSPEDEDKELLE
+AFDIDLEAEAAGEDEADLQPRPAVVTVMGHVDHGKTRLLDAIRSSNVTAGEAGGITQHIG
+AYQVPVEHEGSERRLTFIDTPGHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNH
+AQSAGVPIVVAVNKIDKDSAQPDKIRGQLTEYGLIPEEYGGDTMFVDVSARNNLHIDDLL
+EAILLTADAALELSANPDKAARGVAIEANLDKGRGAVVTVLVQTGTLRVGDTMVVGSAHG
+RVRAMFDENGTPVEEATPSRPVQVLGLSSVPRAGDSFLVTDDERTARQIAEKREAADRNA
+QLAKRRKRITLEDFDQAVAEGKLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVI
+HRGVGAITQNDVNLATVDNAIIIGFNVRPAERVADLADKEGVDMRFYSVIYDAIDDIENA
+LKGMLKPEYEEVQLGSAEVREVFRSSKWGAIAGSLVRSGLIRRNAQARLVRDGAVVSENL
+KIESLRRFKDDATEVREGYECGIGLGNFNDIKEGDVIETFEMQEKPRV
+>PROKKA_00649
+MAKVRVHELAKELGITSKEALSTLKDLGEFVSSASSTIEPPVVKKLRNAYPGAGKSAAKP
+GSTPAAPGRSAAPKPAAAPSPRAAAPTSNAGAPAPGPAAGRTAAPKPGAAPTPGPAAPTP
+AAPAEPKAPQPPATPGSAAPKPGAAAPKPGASAPKPGAPRPGNNPFSPKGGSAGPRPGAR
+PGGRGGAPRPGNNPFAPSQGMRSGREDRAPRPGGPRPPAGAGGPRPGGPRPAAGAGGPRP
+GGPRPNPGMMPKQITPAPQPARGRGRPGGGPGGGPGRPGGPGGRGGRGNAQGAFGRGGGP
+RKGRKSKRAKRQEFEQQHTREIGGVKVPKGDGTTVLRLRRGASLADFAEKIRADVADLVK
+VLFTLGEMASANQSLDEETFQLLGDELGYKVQIVSPEDEDKELLEAFDIDLEAEAANEDE
+ADLEPRPAVVTVMGHVDHGKTRLLDAIRSSNVIEGEAGGITQHIGAYQVPVEHEGEQRRL
+TFIDTPGHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNHAQSAGVPIVVAVNKI
+DKDTAAPDKIRGQLTEYGLVPEEYGGDTMFVDVSARNNINIDQLLEAILLTADAALELTA
+NPHKAARGVAIEANLDKGRGAVVTVLVQTGTLRVGDTMVVGSAHGRVRAMFDENGNAVEA
+ADPSRPVQVLGLSAVPRAGDSFLVTDDERTARQIAEKREAADRNAQLAKRRKRITLEDFD
+QAVAEGKLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVIHRGVGAITQNDVNLA
+TVDNAIIIGFNVRPAERVADLADREGVDMRFYSVIYDAIDDIENALKGMLKPEYEEVELG
+SAEVREVFRSSKWGNIAGSLVRSGLIRRNAQARLVRDGVVVSDHLKIESLRRFKDDATEV
+REGYECGIGLGSFNDIKEGDVIETFEMQEKPRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000609.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000609.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7329a12e3ab2cda94731881e8e5b99c3cef0804f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000609.fa
@@ -0,0 +1,20 @@
+>PROKKA_00682
+MILDAWFWTGLVIGAVSFVVCVVMTAIRRHPADASILSVAAVELFTLVYAAAAAVRQLGG
+DTLNGPGWEFWGYILTALIVPVIAVGWAVTDKTRWSNLVLAVVGPTIAVMLHRMQVIWFG
+QW
+>PROKKA_00419
+MILDAWFWTGLVIGAVSFVVCVVMTAIRRHPADASILSVAAVELFTLVYAAAAAVRQLGG
+DTLNGPGWEFWGYILTALIVPVIAVGWAVTDKTRWSNLVLAVVGPTIAVMLHRMQVIWFG
+QW
+>PROKKA_02281
+MILDAWFWAGLVIGAVSLAVCVAMTAIRRHPADSSILSVAAVELFLLVYAVAAAVRQLGG
+EGLNGPGWEFWGYVVTALLVPVIAVAWAVTDKTRWSNLVLAVVGPTVVVMLHRMQVIWFG
+QW
+>PROKKA_02142
+MILDAWFWTGAVVGGLSFVVCLAMTALRRHPADSSIVSVAAVELFLLVYGVVGAFRQLGG
+QPLNGPTWEFWGYVLTALLVPVIAVAWAVTDKTRWSNLVMAVAGPTVVVMLHRMQVIWFG
+QW
+>PROKKA_00652
+MILDAWFWTGLVIGAVSFVVCVVMTAIRRHPADASILSVAAVELFTLVYAAAAAVRQLGG
+DTLNGPGWEFWGYILTALIVPVIAVGWAVTDKTRWSNLVLAVVGPTIAVMLHRMQVIWFG
+QW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000614.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000614.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d162c8ef39ed1a2cd583678409c64f4e82110b35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000614.fa
@@ -0,0 +1,15 @@
+>PROKKA_00687
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK
+>PROKKA_00424
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK
+>PROKKA_02270
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK
+>PROKKA_02137
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK
+>PROKKA_00657
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000615.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000615.fa
new file mode 100644
index 0000000000000000000000000000000000000000..44f200bf82062f82d22c4722d259964e890f5a8d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000615.fa
@@ -0,0 +1,70 @@
+>PROKKA_00688
+MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH
+SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA
+SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDALAETADAIESSQIEA
+>PROKKA_00425
+MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH
+SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA
+SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGGSAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDALAETADAIESSQIEA
+>PROKKA_02269
+MEGPEITFAEAVIDNGAYGKRTIRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASVSTQLSGLPFSGPIGGVRMALVDDGAGKRQWVAFPKH
+SQLQDAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGASAPTEEVVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFKDYEDDAFEAVEKLATDRLTEIFSIGDKQTRESA
+SDAYHVEVMDELAGEDKPFAERRGEIAKAYGSVTKQVVRQRILKDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETSKRYLHHYNFPPYST
+GETGRVGSPKRREIGHGALAERAMVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGAFVSLTPGKDGLLHVSELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDADAETADAIESSQTEA
+>PROKKA_02136
+MEGPEITFAEAVIDNGRHGTRTVRFETGRLAQQAAGSAMVYIDEETSMLSATTVGKHPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFTKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALLDDGSGQRQWVAFPKH
+SQLEDAVFNMAVAGRVAGDDVAIMMVEAEAGENAWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLAARAGKAPVEVPVFKDYEQDAYDAVEKIATDRLTEIFSIADKQEREAA
+SDAYHLEVIEELAGEGKDFAERKGEVAKAYGSLTKQIVRRRILKDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETSKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAHVAGIAMGLVSAEVEGQTQYAALTDILGAEDAFGDMDFKVAGTSEFVT
+AIQLDTKLDGIPASVLAGALTQAREARLHILSVLEAAIDQPDELAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGAFVSLTPGKDGLLHISELRKLNEGKRVEDVEDVLGVGQKVQVEITK
+IDDRGKLSLAPVVADEDAAAGESREEDEEA
+>PROKKA_00658
+MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH
+SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA
+SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDALAETADAIESSQIEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000616.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000616.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16f7dd25683ab9d670895eb9e9b1535d25970eff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000616.fa
@@ -0,0 +1,45 @@
+>PROKKA_00689
+MSVHREIPLDFDGVLADEGNGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSRDES
+PEGYGATHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDLPMA
+VEVLTDMLTSSLIDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRPIGG
+TPETIRAVTRDHVVGHYTHWYRPDELVVTAAGHLDHDEVCRLVLAALRASGWELTQGALP
+APRRAVDTAGAAASRVRTGTHTVTKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLGGGM
+SSRLFQEIRERRGLAYNTYSFSAGYSDAGYWGLYAGCQPDRVDEVAALMEAELDRMAEAD
+VTGEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLARVREVDAGQVR
+AVAARLAAGDRARVVVAPA
+>PROKKA_00426
+MSVHREIPLDFDGVLADEGNGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSRDES
+PEGYGATHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDLPMA
+VEVLTDMLTSSLIDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRPIGG
+TPETIRAVTRDHVVGHYTHWYRPDELVVTAAGHLDHDEVCRLVLAALRASGWELTQGALP
+APRRAVDTAGAAASRVRTGTHTVTKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLGGGM
+SSRLFQEIRERRGLAYNTYSFSAGYSDAGYWGLYAGCQPDRVDEVAALMEAELDRMAEAD
+VTGEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLARVREVDAGQVR
+AVAARLAAGDRARVVVAPA
+>PROKKA_02266
+MAGMSIHREIPLDFTGVLADEGHGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSR
+DESPEGYGSTHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDL
+PMAVEVLTDMLTSSLLDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRP
+IGGTPETIRAVTREHVAGHYARWYRPDELVVTAAGNLDHDEVCRLVLAALQASGWELAPG
+ALPAPRRAVDTEGAAASRVLTGTHTVAKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLG
+GGMSSRLFQEVRERRGLAYSTYSFSAGYSDAGYWGLYAGCQPDRVDEVSALMEAELDRMA
+AEVVTEEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLERVRAVDAA
+QVRAVAARLAAGERARVVVAPA
+>PROKKA_02135
+MAGMTVQREIPLDFSGVLAEDRGAVVCRSVLPGGVRVLTESMPDQRSVTVGYWVAVGSRD
+ESPEGYGSTHFLEHLLFKGTPTRTAMDIASAFDRVGGESNAGTAKESTVYHAHVLDEDLP
+MAVEVLTDMVTSSLIDADELETERGVILEELAMDADDPVDVAHERLAAVLMDGHPLGRPI
+GGTPETIRAVTREHVVAHYRHWYRPQELVITAAGNLDHDDVCRLVLDALERSGWDLAEGA
+APAPRRTADAAGAGAVLAGTHTVAKQVEQANVIVGGQSLSTTDPDRFALGVMMSVLGGGM
+SSRLFQEIRERRGLAYSTYSFSAGYSDGGYFGLYAGCQPERVDEVAALMEAELERMAAAE
+VTAEELDRAHGQICGGTVLGMESTGARMSRLGRAELVTGEFVDLSASLARVRAVDAGRVR
+AVAARLAAGERARVVVAPA
+>PROKKA_00659
+MSVHREIPLDFDGVLADEGNGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSRDES
+PEGYGATHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDLPMA
+VEVLTDMLTSSLIDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRPIGG
+TPETIRAVTRDHVVGHYTHWYRPDELVVTAAGHLDHDEVCRLVLAALRASGWELTPGALP
+APRRAVDTAGAAASRVRTGTHTVTKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLGGGM
+SSRLFQEIRERRGLAYNTYSFSAGYSDAGYWGLYAGCQPDRVDEVAALMEAELDRMAEAD
+VTGEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLARVREVDAGQVR
+AVAARLAAGDRARVVVAPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000617.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000617.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0c03895bba732a0d0daa8c4e8372aec1261d0eed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000617.fa
@@ -0,0 +1,30 @@
+>PROKKA_00690
+MTETRTPSAVSAPDDVPRVAILGARGRMGRHAVPAVRAAEGLELVAELGSQDRLDAVLDA
+GATHVLDLTVPDASPENVAFAVEHGLHTVVGTSGWVPERRERLEAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAQAARYFESVELVELHHPDKVDAPSGTAVRTAELIGAARDAAGVPVSP
+DATEHDPDGARGAVVHGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGVV
+LGLRTVASRPGLTYGLDGYLDLG
+>PROKKA_00427
+MTETRTPSAVSAPDDVPRVAILGARGRMGRHAVPAVRAAEGLELVAELGSQDRLDAVLDA
+GATHVLDLTVPDASPENVAFAVEHGLHTVVGTSGWVPERRERLEAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAQAARYFESVELVELHHPDKVDAPSGTAVRTAELIGAARDAAGVPVSP
+DATEHDPDGARGAVVHGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGVV
+LGLRTVASRPGLTYGLDGYLDLG
+>PROKKA_02265
+MTDAPAPSAVPADDAVPRVAILGAGGKMGRHAVPAVREAAALELVAELGSADPLEAILDA
+GATHVLDLTVPDVSPRNAAFAVEHGLHTVIGTSGWGPERREALAAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAKAARFFESVELIEMHHPAKLDAPSGTAVRTAELIGQARREAGVPPSP
+DATERDPDGSRGAVVDGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGIV
+LGLRTVASRPGLTYGLDGYLDLG
+>PROKKA_02133
+MTETTPRTPVPGDATPRVAILGASGKMGRHAVPAVRAAQGLELVAELGSGDPLQAVLDAG
+ATHVLDLTVPDASPENVAFAVEHGLHVVVGTSGWGAERRAALEERLAARPGVGVLIAPNF
+SVGSVLASAFAARAARWFESVEVVELHHPAKLDAPSGTAVRTAEMIAASRAEAGVGPSPD
+ATERDPDGARGAVVDGVHVHAVRLRGLEAHQEVLLGGPGEQLTVRHDAFDRQAYMPGVVL
+ALREVAGRPGLTYGLDAVLGLD
+>PROKKA_00660
+MTETRTPSAVSAPDDVPRVAILGARGRMGRHAVPAVRAAEGLELVAELGSQDRLDAVLDA
+GATHVLDLTVPDASPENVAFAVEHGLHTVVGTSGWVPERRERLEAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAQAARYFESVELVELHHPDKVDAPSGTAVRTAELIGAARDAAGVPVSP
+DATEHDPDGARGAVVHGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGVV
+LGLRTVASRPGLTYGLDGYLDLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000620.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000620.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86b4ddf669d7dff563023998e46a9c0987450168
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000620.fa
@@ -0,0 +1,55 @@
+>PROKKA_00694
+MTAGTRLSTPPKLKRGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD
+LILPDFDYIRDRVDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE
+HRIKPRTRVVKEDDIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL
+DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF
+SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYRDD
+EIVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG
+ATVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN
+VILAGNGTVVDMTDGLVKVVGEVECGYVYVDGSSVGEISDSDLKDRRVLGEEGFLSIITV
+VNRQTGAIVSGPDVHARGVAEDEKVFEEIKPKIVRALEEAVQSSKDHTAHQLQQVVRRTV
+GTWVNRKLRRRPMIIPVVLEA
+>PROKKA_00431
+MTAGTRLSTPPKLKRGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD
+LILPDFDYIRDRVDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE
+HRIKPRTRVVKEDDIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL
+DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF
+SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYRDD
+EIVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG
+ATVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN
+VILAGNGTVVDMTDGLVKVVGEVECGYVYVDGSSVGEISDSDLKDRRVLGEEGFISIITV
+VNRQTGAIVSGPDVHARGVAEDEKVFEEIKPKIVRALEEAVQSSKDHTAHQLQQVVRRTV
+GTWVNRKLRRRPMIIPVVLEA
+>PROKKA_02260
+MTPGTRLSTPPKLKKGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD
+LILPDFDYIRDRMDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE
+HRIKPRTRVVKEDEIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL
+DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF
+SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYKDD
+EVVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG
+ANVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN
+VILAGNGTVVDMTDGLVKVVGEVDCGYVYVDGSSVGEISDSDLKDRRVLGEEGFISIITV
+VNRQTGSIVSGPDIHARGVAEDEKVFEDIKPKIARALEEAVQSSKDHTAHQLQQVVRRTV
+GTWVNRKLRRRPMIIPVVLEA
+>PROKKA_00464
+MTRSSRNSSSRRRGGGQSRRPRSSGAPGQLAKGGLRITPLGGLGEIGRNMTVFEHQGKLL
+IVDCGVLFPEDHQPGIDVILPDFTSIRDRLQDVVGVVLTHGHEDHIGGVPYLLKERPDIP
+LIGSELTLAFIEAKLKEHKIVPKTHMVVAEDKRHMGPFELEFVAVNHSIPDALAVAIRTE
+AGLILHTGDFKMDQFPLDRRITDLRHFARLGEEGVDVFLTDSTNAEVPGFTISERELTPA
+IDHVFRTAPKRIIVSSFASHVHRIQQVLDAAHASGRKVAFVGRSMVRNMGIAGDLGYLKI
+PKGLVVDFKKLQDMPDEKIALISTGSQGEPMAALGRMANQTHQIKLNKGDTVLLASSVVP
+GNETSITGIINKFTDMGVNVVHKGNAKVHVSGHASAGELVYCYNIVQPRNVMPVHGEAAH
+LHANAELAKKTGLPEDRVFITKDGDVLDLVDGRVSVAGKVEAGLVYVDGDTIGKVTEGTL
+EERRTMQEAGVVTVVAIVDPDTNQLAEPLEFMTKGFIQDASVFKGAAEKVKSALSRSNVQ
+DIDDIEKLERVIGDAVTRHLERAYRRAPLVTVVVVDA
+>PROKKA_00664
+MTAGTRLSTPPKLKRGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD
+LILPDFDYIRDRVDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE
+HRITPRTRVVKEDDIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL
+DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF
+SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYRDD
+EIVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG
+ATVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN
+VILAGNGTVVDMTDGLVKVVGEVECGYVYVDGSSVGEISDSDLKDRRVLGEEGFLSIITV
+VNRQTGTIVSGPDVHARGVAEDEKVFEEIKPKIVRALEEAVQSSKDHTAHQLQQVVRRTA
+GTWVNRKLRRRPMIIPVVLEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000627.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000627.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e82a409264d93962e19f94a055e718c368de260
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000627.fa
@@ -0,0 +1,33 @@
+>PROKKA_00705
+MTRSRRNVGGGAAHRSETTGRSGSASGASAFDDARDSDVGRMWLDLAGAPEPTSSDADAS
+DAARDAAPARDAGAPAEDVPDPAPGAAPDLGALLTRASDLPSPAPGAGPRSLPWSGREDT
+RADTERRGRRRAPAKRSGRTRPREDGRAPAEPAPQTDRPRRRPGPAPLPTAPREREEAAR
+EVVLRQLALGPRSRGQLERKLAERQAEPELIERVLDRFEEVRLVDDAAFAEVWVRSRHRS
+KGLARRALGHELQQKGVDREIAAEALEAIDGEDERAAALDLVRRRLRGRTVPGGASPEAR
+AERDKVTRRLVGMLGRKGYGGGLAFAVVKEVLAEHEE
+>PROKKA_00439
+MTRSRRNVGGGAAHRSETTGRSGSASGASAFDDARDSDVGRMWLDLAGAPEPTSSDADAA
+RDAVPARDAGTPAGDGSDPAPGAAPDLGALLTRASDLPSPAPGAGPRALPWSGREDTRAD
+TERRGRKRATTPPRRGRPRDEGRPAVDPRPAVETDRPRRRPGPAPLPTAPREREEAAREV
+VLRQLALGPRSRGQLERKLAERQAEPELIERVLDRFEEVRLVDDAAFAEVWVRSRHRSKG
+LARRALGHELQQKGVDREIAAEALEAIDGEDERTAALDLVRRRLRGRTVPGGASPEARAE
+RDKVTRRLVGMLGRKGYGGGLAFAVVKEVLAEHEE
+>PROKKA_02252
+MTRARRDAGGGAARRSERNGRSGAASGASAFDDARDTDAARMWLELAGVPEADAPAAARS
+VDEPPAAPTDGPDDPPLATAENGSSAAPSGPAAAPDEAGPPDLGSLLGRASDLPSPAPGA
+AARVLPWSADARPERGGRGARGTSSEARRARRRTARLAAADVASAPEAASTPEEANARED
+ARPRRRPGPAPLPAEPREREEAAREVVLRQLALGPRSRGQLEAKLADREAEPELIARVLD
+RFEEVRLVDDAAFAEVWVRSRHRSKGLARRAIGHELRQKGVDRDVAAEALEAIDGEDERA
+AALELVRRRLRGRRVPAGNGPHARAERDKVTRRLVGMLGRKGYGGGLAFAVVKEVLGELE
+E
+>PROKKA_02124
+MPEDPREREEAARQVVLRQLAMGPRSRRQLERKLADREAEPELVERVLDRFEEVSLVDDA
+AFAEVWVRSRARGKRLSRRAISRELHDKGVDRDVAEEALAAIEPEDERQAALELVRSKMR
+GRPAPAADGPEGRAERDKVTRRLVGMLGRKGYGPGLAFGVVKEVLAELDEA
+>PROKKA_00672
+MTRSRRNVGGGAAHRSETTGRSGSASGASAFDDARDSDVGRMWLDLAGAPEPTSSDADAA
+RDAVPARDAGTPAGDVPDPAPGVAPDLGALLTRASDLPSPAPGAGPRTLPWSGREDTRAD
+IERRGRKRATTPPRRGRPRDEGRPAVDPRPAVETDRPRRRPGPAPLPTAPREREEAAREV
+VLRQLALGPRSRGQLERKLAERQAEPELIERVLDRFEEVRLVDDAAFAEVWVRSRHRSKG
+LARRALGHELQQKGVDREIAAEALEAIDGEDERAAALDLVRRRLRGRTVPGGASPEARAE
+RDKVTRRLVGMLGRKGYGGGLAFAVVKEVLAEHEE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000629.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000629.fa
new file mode 100644
index 0000000000000000000000000000000000000000..13c69894ec6d04e0d3a3dd7ab5dab98937640f15
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000629.fa
@@ -0,0 +1,35 @@
+>PROKKA_00707
+MPAAASRPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTQAER
+EGVPHHLLDVLDVGQEASVAAFQSAVRDLFAQIRARGRTPILVGGSGLYVRAALDVLEFP
+PTDPALRAELEARAQREGLAGLRAELASLDPVSAERLQDARRIVRALEVCRLTGRPFSAF
+MPERTYAPEVAPVVQLGLRLDRAELHRRIAARVERMLAEGLLDEVRRLDVPGPDGLRQGP
+TASRAIGYAQMLAVLDGELTEAEAADQTVVATRRFARRQETWFRADPRVVWLDAQDEDVV
+AEALAVVAGDAT
+>PROKKA_00441
+MPAAAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTPAER
+EGVPHHLLDVLDVGQEASVAAFQSAARDLFDQIRARGRTPILVGGSGLYVRAALDVLDFP
+PTDPALRTELEARAQREGLAGLRAELAALDPVSAERLQDARRIVRALEVCRLTGRPFSAF
+MPERTYAPEVAPVVQLGLRLDRSELHQRIAARVERMLAEGLLDEVRRLDVPGPGGLRQGP
+TASRAIGYAQMLAVLDGELTEAEAAEQTVVATRRFARRQETWFRADPRVVWLDAQGEDVV
+AEALAVVAGGAA
+>PROKKA_02250
+MRAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDIGTAKVTEAEREG
+VPHHLLDVLDVGQEASVAAFQSAARGVFEDVRSRGRTPILVGGSGLYVRAALDVLEFPPT
+DPEVRAAVEAELAERGEAALRAELAAVDPESAAKVADARRLVRALEVHRITGRPFSAFMP
+RREHDPSVAPVVQIGLSLERAVLHERIEARVERMLAAGLLDEVRALDVPGPDGLRQGPTS
+ARAIGYAQMLAVLDGTLTPEQAAEQTVVATRRFARRQETWFRADPRVHWVDALAPDVVAQ
+ALAVVAGS
+>PROKKA_02122
+MSAAAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTQAER
+EGVPHHLLDVLDVGQEASVAAFQSAARDLFDQIRARGRTPILVGGSGLYVRAALDVLEFP
+PTDPALRAELEARAQREGLTGLRAELAALDPASAERLRDARRIVRALEVCRLTGRPFSAF
+MPERTYAPEVAPVVQLGLRLDRAELHQRIAARVERMLAGGLLDEVRRLDVPGPDGLRQGP
+TASRAIGYAQMLAVLDGELTAAEAAEQTVVATRRFARRQETWFRADPRVVWLDAQGEDVV
+AAALAVVAGDAT
+>PROKKA_00674
+MPAAAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTPAER
+EGVPHHLLDVLDVGQEASVAAFQSAARDLFDQIRARGRTPILVGGSGLYVRAALDVLDFP
+PTDPALRTELEARAQREGLAGLRAELAALDPVSAERLQDARRIVRALEVCRLTGRPFSAF
+MPERTYAPEVAPVVQLGLRLDRAELHRRIAARVERMLAGGLLDEVRRLDVPGSEGLRQGP
+TASRAIGYAQMLAVLDGELTEAEAAEQTVVATRRFARRQETWFRADPRVVWLDAQGEDIV
+AEALAVVAGDAT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000634.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000634.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02e29ec789dd6dae9a3777eab941ee765e6e38b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000634.fa
@@ -0,0 +1,65 @@
+>PROKKA_00715
+MSGGAEEVGAGGAQPRTEHEREALRLLDAAVQATGGQHRAGQREMVLQVARALESRRHLL
+VQAGTGTGKSLAYLIPAIQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDELPRE
+PVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGMIGSATDGAAGPSSLLGKEVM
+YLRAWADQTETGDRDDLEVPVTDRAWRQVSVSAVDCLGASRCPQAEECFSERARADAADA
+DVVVTNHAMLAISAFEGLAVLPAYSAVVVDEAHELQDRVTGAVTGQLSGSIVHGAATSLR
+RHTTVAVEDLIEAGAALDRAFTDTPSGLIAAGPDEVQEQALTGVLTAARQCLSDLGQDKD
+KEADADGGRQMARSRILEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGDETD
+PPQLYVAPLSVAGKLREGLFGKATTVLTSATLTVGSGERRFDSVAGDVGLAGPDAPKFEA
+LDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLRASRGGALGLFSSRRAAEDA
+AAEMRRRLGPKTTILCQGDATLSALVRQFSEEPDTSLFGTMSLWQGVDVPGNSLRLVVID
+RIPFPRPDDPLSQARTRDVARHGGNGFMRISATHAAVRMAQGAGRLVRSVTDRGVVAVLD
+PRLATERYGGYITSALPDFWRTTDRDVVRGVLARLASGD
+>PROKKA_00446
+MSEEEQEAGAGGAQPRTEHEREALRLLDAAVQATGGQHRAGQREMVLQVARALESRRHLL
+VQAGTGTGKSLAYLIPAIQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDELPRE
+PVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGVIGSATDGAAGPSSLLGKEVM
+YLRAWADQTETGDRDDLEVPVTDRAWRQVSVSAVDCLGASRCPQAEECFSERARADAADA
+DVVVTNHAMLAISAFEGLAVLPAYSAVIVDEAHELQDRVTGAVTGQLSGSIVHGAATSLR
+RHTTVAVEDLIEAGAALDRAFTDTPSGLIAAGPDEVQEQALTGVLTAARQCLSDLGQDKD
+KEADADGGRQMARSRILEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGDETD
+PPQLYVAPLSVAGKLREGLFGKATTVLTSATLTVGSGERRFDSVAGDVGLAGPDAPKFEA
+LDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLRASRGGALGLFSSRRAAEDA
+AAEMRRRLGPKTTILCQGDATLSALVRQFAEEPDTSLFGTMSLWQGVDVPGNSLRLVVID
+RIPFPRPDDPLSQARTRDVARHGGNGFMRISATHAAVRMAQGAGRLVRSVTDRGVVAVLD
+PRLATERYGGYITSALPDFWRTTDRDVVRGVLARLASGD
+>PROKKA_02243
+MSGAGTEGTTPAGEGAQPRTDHEREALRLLDAAVEATGGQQRAGQREMVLQVARALESRR
+HLLVQAGTGTGKSLAYLIPALQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDEL
+PREPVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGLLGSAADGTGGPSSLLGK
+EVMYLRAWADQTETGDRDDLDVPVTDRAWRQVSVSAIDCLGASRCPMAEECFSERARADA
+ADADVVVTNHAMLAISAFEGLAVLPAYSAVVVDEAHELQDRVTGAVTGQLSGSIVHGAAT
+SLRKHTTVAVEDLMEAGAGLDRAFTDAPSGLLAAGPDEVQEQALNAVLAAARQCLSDLGQ
+DKDKEADADGGRQMARSRVLEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGD
+ESDPPQLFVAPISVAGKLREGLFGKATTVLTSATLTVGAGERRFDSVAGDVGLAGPDAPR
+FEALDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLRASGGGALGLFSSRRAA
+EDAAAEMRRRLGPKATVLCQGDATLSALVRQFAEEPDTSLFGTMSLWQGVDVPGNSLRLV
+AIDRIPFPRPDDPLSQARTRDVARHGGNGFMRISATHAAVRMAQGAGRLVRSVHDRGVVA
+VLDSRLATERYGGYITSALPDFWRTTDRAVVLGVLGRLAETGS
+>PROKKA_02115
+MTDSTTGPAGAVPTTDREEEALRLLDVVVEATGGQQRAGQREMVLQVARALESRRHLLVQ
+AGTGTGKSLAYLIPALQHAMDQEDPVVVATATLALQAQIMKRDAPRLVQALAGELPREPV
+VALVKGRSNYLCRHKVDGGYPGDEGEETLFEVADDGGLIGSGEDGEPSSPLGKEVMYLRA
+WADVTETGDRDDLEVPVTDRAWRQVSVNAVDCLGATRCPLAEECFSERARADAADADVVV
+TNHAMLAISAFEGLAVLPAYSAVIVDEAHELQDRVTGAVTGQLSGSIVHGAATSLRRHTS
+VAVEDLAQAAAGLDRAFTDTPSGLIQGGPDDVQEQALTAVLSAARQCFSDLGKDKEGEAD
+AGRQMARSRLLEVVEVAERMLAAHPEADFPEVLWATRPGRFEPGSGWQPGDEADPPQLYV
+APISVAGRLREGLFGKATTVLTSATLTVGQGERRFDSVAGDVGLAGPDAPRFTALDVGSP
+FDYPRQGVLYVARHLPKPGRTASPESLDELEALLRASNGGALGLFSSRRAAEDAAEHMRR
+RLGRGHTVLCQGDATLSALVRQFADEPDTSLFGTMSLWQGVDVPGPSLRLVVIDRIPFPR
+PDDPLSQARTRDVARHGGNGFMRVSATHAAVRMAQGAGRLVRSVEDRGVVAVLDSRLATE
+RYGGYITSALPDFWRTTDRAVVRGVLERLAREAH
+>PROKKA_00679
+MSEEEQEAGAGGAQPRTEHEREALRLLDAAVQATGGQHRAGQREMVLQVARALESRRHLL
+VQAGTGTGKSLAYLIPAIQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDELPRE
+PVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGVIGSATDGAAGPSSLLGKEVM
+YLRAWADQTETGDRDDLEVPVTDRAWRQVSVSAVDCLGASRCPQAEECFSERARADAADA
+DVVVTNHAMLAISAFEGLAVLPAYSAVIVDEAHELQDRVTGAVTGQLSGSIVHGAATSLR
+RHTTVAVEDLIEAGAALDRAFTDTPSGLIAAGPDEVQEQALTGVLTAARQCLSDLGQDKD
+KEADADGGRQMARSRILEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGDETD
+PPQLYVAPLSVAGKLREGLFGKATTVLTSATLTVGSGERRFDSVAGDVGLAGPDAPKFEA
+LDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLSASRGGALGLFSSRRAAEDA
+AAEMRRRLGPKTTILCQGDATLSALVRQFAEEPDTSLFGTMSLWQGVDVPGNSLRLVVID
+RIPFPRPDDPLSQARTRDVARNGGNGFMRISATHAAVRMAQGAGRLVRSVTDRGVVAVLD
+PRLATERYGGYITSALPDFWRTTDRDVVRGVLARLASGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000636.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000636.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a5ffc88314f6a4a5be9e8269761d1172fb03b0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000636.fa
@@ -0,0 +1,20 @@
+>PROKKA_00717
+MTLTTAQFAGSPATARPRPATIRLTRRGRLVLRGIPVIAAAVAATLAAAFFLGVLLSPAA
+VSADTAGPATQSVTVMPGDSLWTIATTVAPEADVYEVIATIDELNGLEGRAPAPGEELFV
+PATR
+>PROKKA_00448
+MTLTTAQFAGSPATARPRPATIRLTRRGRLVLRGIPVIAAAVAATLAAAFFLGVLLSPAA
+VSADTAGPATQSVTVMPGDSLWTIATTVAPEADVYEVIATIDELNGLEGRAPAPGEELFV
+PATR
+>PROKKA_02241
+MTLMTAQFAGSPAAARRRPAAIRLTRRGRLLLRGIPVMAAAAAATLAVAFLLGVLLSPAA
+VSADTAAPATQTVTVMPGDSLWTIATTIAPEEDVYEVIAAIDELNGLEGRAPALGEELFI
+PATR
+>PROKKA_02113
+MTAVTAVLSRTHQLTSVRARPTRAVAASTRAAARTSGVRLTRRGRLLFRGLPVILSVAAA
+TVAAAFFAGVLFSPPAVSADTPAEELQTVTVMPGDSLWTIARDVAPEADRRDTMRRIDEL
+NGLEGRDPELGQELYVPPTR
+>PROKKA_00681
+MTLTTAQFAGSPATARPRPATIRLTRRGRLVLRGIPVIAAAVAATLAAAFFLGVLLSPAA
+VSADTAGPATQSVTVMPGDSLWTIATTVAPEADVYEVIATIDELNGLEGRAPAPGEELFV
+PATR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000637.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000637.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3235cc4afce39dd071b347de7dba5457f27b14c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000637.fa
@@ -0,0 +1,40 @@
+>PROKKA_00718
+MTDLSSLPLRENLRGLSPYGAPQLDVPYMLNTNENTHPVPEEVATAIAERVAAVAGGLNR
+YPDREFTGLRRALAGYLGHGLTADHVWAGNGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTVFVDGGRAEDHTLSAEHAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAQNEAAGGPGAMVVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+LGYLAADPAVADALRLVRLPYHLSAVTQATAEAALDHVDALLRTVEDIKAQRDRIVSTLR
+GLGLRPSVSDSNFVFFGHLEDASDVWRRLLDRGVLVRDVGIPHHLRVTAGTEAETTAFLT
+ALAEVLGETGDRS
+>PROKKA_00449
+MTDLSSLPLRENLRGLSPYGAPQLDVPYMLNTNENTHPVPEEVATAIAERVAAVAGGLNR
+YPDREFTGLRRALAGYLGHGLTADHVWAGNGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTVFVDGGRAADHTLSAEHAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAQNEAAGGPGAMVVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+LGYLAADPAVTDALRLVRLPYHLSAVTQATAEAALDHVDALLRTVEDIKAQRDRIVSTLR
+GLGLRPSVSDSNFVFFGHLEDASDVWGRLLDRGVLVRDVGIPHHLRVTAGTEPETTAFLT
+ALEEVLGETGHRS
+>PROKKA_02240
+MTDLSSLPLRENLRGLSPYGAPQLDVPHMLNTNENTHPVPQEVATAIAERVAAVAGGLNR
+YPDREFTALRRALARYLGHGLTEGHVWAANGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTAFVDGGRAADHTLSAERAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAENESAGGPGAMIVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+VGYLAADPAVADALRLVRLPYHLSAVTQATAEAALDHVDALLETVEDIKGQRDRIVATLR
+ELGLEPSVSDSNFVFFGRLEDAADVWRRLLERGVLVRDVGIPHHLRVTAGTEEETTAFLE
+ALEAVLAEIGHRR
+>PROKKA_02112
+MTDLSSLPLRDSLRGQSPYGAPQLDVPYMLNTNENTHPVPQAVAEAITARVAKVAGGLNR
+YPDREFTELREHLAAYLGHGITPEQVWAANGSNEVLQQILQAFGGPGRTLLSFLPSYSMY
+PLLANGTDTAFVDGGRAADHTLSAEHAAALVREHRPNVVFLASPNNPTGTALGLDVIEAI
+YAAQAQNEAEGGHGAMVVVDEAYAEFALAGTDSALTLLRGRERLIVTRTMSKAFALAGAR
+LGYLAADAAVADALRLVRLPYHLSAVTQATAIAALERVDELLETVEDIKGQRDRIVAELT
+GMGLVPAVSDSNFVFFGRLADAHAVWEALLERGVLVRDVGIPHHLRVTAGTEEETTAFLD
+ALREIVEQDPAVVSAVDAD
+>PROKKA_00682
+MTDLSSLPLRENLRGLSPYGAPQLDVPYMLNTNENTHPVPEEVATAIAERVAAVAGGLNR
+YPDREFTGLRRALAGYLGHGLTADHVWAGNGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTVFVDGGRAEDHTLSAEHAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAQNEAAGGPGAMVVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+LGYLAADPAVADALRLVRLPYHLSAVTQATAEAALDHVDALLRTVEDIKAQRDRIVSTLR
+GLGLRPSVSDSNFVFFGHLEDASDVWRRLLDRGVLVRDVGIPHHLRVTAGTEAETTAFLT
+ALAEVLGETGDRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000638.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000638.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b6cd43b0275b91bcc2684205ab867a69211ee71
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000638.fa
@@ -0,0 +1,25 @@
+>PROKKA_00719
+MAAELISGRRARMTRTTSESDVYVEMDLDGTGRAEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMTGVPSTKGAL
+>PROKKA_00450
+MAAELISGRRARMTRTTSESDVYVEMDLDGTGRAEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMTGVPSTKGAL
+>PROKKA_02239
+MAAELISGRRARMTRTTSESDVHVEMDLDGTGRAEISTSVPFYDHMLTALARHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMSGVPSTKGAL
+>PROKKA_02111
+MAAELMSGRRARMQRTTSESDVYVEMDLDGTGTSEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKRGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFEAITYHASICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRVHDVPSTKGAL
+>PROKKA_00683
+MAAELISGRRARMTRTTSESDVYVEMDLDGTGRAEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKAALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMTGVPSTKGAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000642.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000642.fa
new file mode 100644
index 0000000000000000000000000000000000000000..931f71898946265944cc58889301a211cb0623c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000642.fa
@@ -0,0 +1,35 @@
+>PROKKA_00723
+MTGSHDDGGLARDDGLGPIDETVAVPHPAARELPGHIRAALDRMREKTAGENTADTAGVP
+WQGRDLSGPGVDGSANPLHVFDEDDGTSPAEWTAVMSALTDGSAGEREVTEVLARIRVFA
+AVVPTLAGDEDDVHDHADHTGHEHDVAAHGDKAADVALVTMRAPDGRQALPVFTNVPALT
+AWNPVARPVAVWLPRACLSAVDEGCELVVIDAGAEHTYVVRRPAVWSLAQQREWTPAYRD
+QEIADEIAEVADLVPNLLNLGLAPGSGVATHTGSGAVMNGGGAGPELQIVAMPTRDADAA
+GVRLMTATLKTLLADLPLLAERADSVEITVRRP
+>PROKKA_00454
+MTGSHDDGGLARDEGLGPIDETVAVPHPAARELPGHIRAALDRMREKTAGENTADTAGVP
+WQGRDLSGPGVDGSANPLHVFDEDDGTSPAEWTAVMAALTDGSAGEREVTEVLARIRVFA
+AVVPTLAVDEDDVHDHTGHEHDVAAHGDKAADVALVTMRAPDGRQALPVFTNVPALTAWN
+PVARPVAVWLPRACLSAVDEGCELVVIDAGAEHTYVVRRPAVWSLAQQKEWTPAYRDQEI
+ADEIAQVADLVPNLLNLGLAPGSGVATHTGSGAVMNGGGAGPELQIVAMPTRDADATGVR
+LMTATLKTLLADLPVLAERADSVEITVRRP
+>PROKKA_02235
+MTHGHDDGAPAGVAGAGPIEETVAVPRPDSRELPGHIRAALDRMREKTAGPNTADTAGVP
+WEGRDLSGPGVDGSANPLHVFDEDDGTSPEEWTRVMAALTTGAAGEAEVTDVLSRIRVFA
+AVVPTLAVDEDDVHDHADHSGHEHDVAAHGDKAADVALVTMRAPDGRQALPVFTSVPALT
+AWNPIARPVAVWMPRACLSAVDEGCELVVVDAGAEHTYAVRRPAVWALAQQKPWTPSYRD
+QEIADEIAQVADLVPHLLNLGLAPGSGVATHTGSGAVMSGGGAGPELQIVAMPARDADAA
+GVRLMAATLKTLLADLPLLAERADSVEVTVRRP
+>PROKKA_02107
+MSSASSSEPAHDAEATVPVPAPGGRELPGHIRAAMERMRQKTARENTADTAGVPWAGRDL
+SGPGLEGSANPLHIFDEDDGTAPAEWARVMDALTEGTAGEAEVVDVLGRIRVFAAVVPTL
+AVDEADVHDHAAHSVHEHAQHEDAAHGDKAADVALVTMRAPDGRQALPVFTSVPALTAWN
+PLARPVAVWAPRACLSAVDEGCELVVVDAGAEHTYAVRRPAVWALAQQKPWTPSYLDQEI
+AEEIAGVADLVPNLLNLGLAPGPGVATETASGEVMNGGGSGTELTVLAMPARDADAAGIR
+LMTTTLAMLLGDLPLLAERADSVEITVRRP
+>PROKKA_00687
+MTGSHDDGGLARDDGLGPIDETVAVPHPAARELPGHIRAALDRMREKTAGENTADTAGVP
+WQGRDLSGPGVDGSANPLHVFDEDDGTSPAEWTAVMSALTDGSADEREVTEVLARIRVFA
+AVVPTLAVDEDDVHDHADHTGHEHDVAAHGDKAADVALVTMRAPDGRQALPVFTNVPALT
+AWNPVARPVAVWLPRACLSAVDEGCELVVIDAGAEHTYVVRRPAVWSLAQQREWTPAYRD
+QEIADEIAEVADLVPNLLNLGLAPGSGVATHTGSGAVMNGGGAGPELQIVAMPTRDADAA
+GVRLMTATLKTLLADLPLLAERADSVEITVRRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000644.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000644.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad8cb1e9e499a619d581a60b03c812b7e84c376f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000644.fa
@@ -0,0 +1,23 @@
+>PROKKA_00725
+MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVVERR
+LKQDCGMSLADYNLLLLLYESPEGRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV
+ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLGDLAPGEAESLTRIFSRLGRRLEGL
+C
+>PROKKA_00456
+MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVVERR
+LKQDCGMSLADYNLLLLLYESPEGRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV
+ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLGDLAPGEAESLTRIFSRLGRRLEGL
+C
+>PROKKA_02233
+MNSSSTPTPEPSETARHAWRAYFEATQMLSEMLERGLKKDSGMSLADYNLLLLLYEAPEG
+RLRMGELASGMVFSPSRITYQVKTLVARGLIERRAAECDRRGFEAVLTDEGRTAFRRAAA
+GHARQVDELFLSHLEPGEAETLERIFTRLGGRLEGLC
+>PROKKA_02105
+MTSSSTPAAEPTGPRAARHAWRAYFESTQMLQDQLERGLKAECGITLADYNLLLLLVESD
+GGRLRLGELASRMVFSPSRVTYQVKSLVARGLIERRRVECDRRGFEAVLTDAGRTAFRRA
+AVVHARQVDELFLDLLQPGEAEVLGRVFTRVGTALESRCAGRAAPSEPCGAQASNSADA
+>PROKKA_00689
+MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVLERR
+LKQDCGMSLADYNLLLLLYESPEDRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV
+ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLVDLAPGEAESLTRIFSRLGRRLEGL
+C
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000648.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000648.fa
new file mode 100644
index 0000000000000000000000000000000000000000..112533f4480442252d3513584b2801d166ebc98f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000648.fa
@@ -0,0 +1,46 @@
+>PROKKA_00729
+MDFGAYGRLLQDPRIRHLLAVGFIARFPHTAAGVILTLHVALTLGLGYGQAGLAGAAMTL
+GIAVGSPWRGRVVDAKGLRRALLPSVIAEAVIWPIVPWLPFWPMLLAVFLGGVFSLPIFS
+VVRQGLGVLTHGKDRQTAFALDSIVTETIFMMGPALGAVVAATWSSALGLTIVGLSSALG
+GILLMWFNPPTRSSQLAVVGPATEDPYTEEQDRQEAIAQAVTAAPMHVEMAAPSLATGAL
+PAITEAIPLVTGSLPVIAADGSGPTTAPRRARAERLRQWRRTHFSWVGPEVLGVLVVSMA
+AGIVMVGTEVSMVAELESQGAAASVGLVYAFWCGASAVGGLFYGAWGRQVHPYLLMALFA
+VATVPLALVDGVWALALASIPSGLLTAPTLASASSRLSHLVVEERRGEAMGFYGSAMTAG
+AAMGAPLAGVFIDGVAPSAGYVFAAAAGFVLVLLAALATVMRGRRPA
+>PROKKA_00460
+MDFGAYGRLLQDPRIRHLLAVGFIARFPHTAAGVILTLHVALTLGLGYGQAGLAGAAMTL
+GIAVGSPWRGRVVDAKGLRRALLPSVIAEAVIWPIVPWLPFWPMLLAVFLGGVFSLPIFS
+VVRQGLGVLTHGKDRQTAFALDSIVTETIFMMGPALGAVVAATWSSALGLTIVGLSSALG
+GILLMWFNPPTRSSQLAVVGPATEDPYTEEQDRQEAIAQAVTAAPMHVEMAAPSLATGAL
+PAITEAIPLVTGSLPVIAADGSGPTTAPRRARAERLRQWRRSHFSWVGSEVLGVLVVSMA
+AGIVMVGTEVSMVAELESQGAAASVGLVYAFWCGASAVGGLFYGAWGRQVHPYLLMALFA
+VATVPLALVDGVWALALASIPSGLLTAPTLASASSRLSHLVEEERRGEAMGFYGSAMTAG
+AAMGAPLAGVFIDGVAPSAGYVFAAAAGFVLVLLAALATVARGRRSA
+>PROKKA_02226
+MGFIARFPHTAAGVILTLHVALTLDLGYGQAGLAAAAMTLGIAVGSPWRGRVVDAKGLRR
+ALLPSVIAEALIWPLVPWLPFWLMLVAVFFGGVFALPIFSVVRQGLGVLTHGRDRQTAFA
+LDSIITETIFMVGPALGAVVAATWSSALGLTIVGLSSALGGVLLMWFNPPTRSSQLAVVG
+PETEDPYTEDEDREEAVAQTVHGAPMHVEMTAPSLATGALPVVTEAIPLVTGALPVIAAD
+GSGPATPTPGLTRAERLRLWRARHFAWVGPEALGVLVVSMAAGLVMVGTEVTMVAELEHA
+GMAGSVGVVYAFWCGASAVGGLFYGAWGRQVHPYLLMGLLALLTLPMAFVDGLWALALAA
+IPSGLFTAPTLASASSRLSTLVPEERRGEAMGFYGSAMTAGAAMGAPLSGVFIDAIHPAA
+GYVFAGLAGAVLVLAAALVTLARRRRVGGTSA
+>PROKKA_02100
+MDFRAYGRLLQDPRIRNLLAVGFIARFPHTAAGVILTLHVAVTLGLGYGQAGLAAAAMTL
+GIACGSPWRGRAIDRDGLRRALLPSVVAEAVIWPVVPWLPFGFLLVAVFFGGLFAVPIFS
+VVRQGLGVLTHGADRQTAFTLDSIITELVFMVGPALGAVIAATGSTALGLTVVGLSGALS
+GALLMWFNPPTRSTQLAADGPSAGDPFTEEEDREQALSQAVHTAPVRATVAAADLATGAL
+PVVTEAVPIVTGSLPVIAADGSGPVSPAPRAGRHDDGRAADGLTRDERWRLWRVRHFGWV
+TPEVLGVLVVAMAAGIALVGTEVTMVAELEHAGQEASVGVVYAFWCGASALGGLFYGAWG
+RQVHPYLLGALFALAVAPMAFVDGLWALAWASVPSGLLTAPTLAAASSRISLLVSEERRG
+EAMGYYGSAMTAGSALGAPVVGLVIDGVGPGAGYVGAAGAAVVMIGAAAILTAARRRRSP
+ARG
+>PROKKA_00693
+MDFGAYGRLLQDPRIRHLLAVGFIARFPHTAAGVILTLHVALTLGLGYGQAGLAGAAMTL
+GIAVGSPWRGRVVDAKGLRRALLPSVIAEAVIWPIVPWLPFWPMLLAVFLGGVFSLPIFS
+VVRQGLGVLTHGKDRQTAFALDSIVTETIFMMGPALGAVVAATWSSALGLTIVGLSSALG
+GILLMWFNPPTRSSQLAVVGPATEDPYTEEQDRQEAIAQAVTAAPMHVEMAAPSLATGAL
+PAITEAIPLVTGSLPVIAADGSGPTTAPRRARAERLRQWRRTHFSWVGPEVLGVLVVSMA
+AGIVMVGTEVSMVAELESQGAAASVGLVYAFWCGASAVGGLFYGAWGRQVHPYLLMALFA
+VATVPLALVDGVWALALASIPSGLLTAPTLASASSRLSHLVVEERRGEAMGFYGSAMTAG
+AAMGAPLAGVFIDGVAPSAGYVFAAAAGFVLVLLAALATVMRGRRPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000651.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000651.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9da354970ea8f787a75b40633ee00158405b6d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000651.fa
@@ -0,0 +1,30 @@
+>PROKKA_00733
+MAALLGLALGCGLFLLWWSLWSPPTERPGAARPDSRLRVLIAQSGIQRLSPAGVVSAMAV
+GGLVVGLLVLSLTSTWTIAACFAVFGAAVPWLLLSWQARRRSTALRELWPDAIDHARSAI
+RAGLTLPEALIQLGETGPEGLREPFQQFARDYRAGARFVDALDRLKARMADPVADRLVVS
+LRLTREVGGADIGRLLQTLSEFLRQDARIRAELEARQSWTVNAARLAVCAPWLVLLLLGT
+QPAAVAAYRSAAGGAVLLAGMVASVVCYRVMLRIGALPREKRVFA
+>PROKKA_00464
+MAALLGLALGCGLFLLWWSLWSPPTEKPGAARTDARLRVLIAQSGIQRLSPAGVVSAMAV
+GGLVVGLLVLSLTSTWTIAACFAVFGAAVPWLLLSWQARRRSTALRELWPDAIDHARSAI
+RAGLTLPEALIQLGETGPEGLREPFQQFARDYRAGARFVDALDRLKARMADPVADRLVVS
+LRLTREVGGADIGRLLQTLSEFLRQDARIRAELEARQSWTVNAARLAVCAPWLVLLLLGT
+QPAAVAAYRSAAGGAVLLAGMVASVVCYRVMLRIGALPREKRVFA
+>PROKKA_02220
+MAVLLGLLLGGGLFLLWWSLWSPPVQRPQTARPDSRLRVLIAQSGIRRLSPAGVVSAMAV
+GGVVTGLLILAVTRTWTIAACFALFGAAVPWLLLSWQARRRTTALRELWPDAVDHARSAI
+RAGLTLPEALIQLGESGPEGLREPFRQFARDYRSGARFVDALDRLKARMADPVADRLVVS
+LRLTREVGGADIGRLLQTLSEFLRQDARTRAELEARQSWTVNAARLAVCAPWIVLLLLGT
+QPSAVAAYQSAAGGAVLLGGLVASVVCYRVMLRIGALPEEKRVFA
+>PROKKA_02096
+MGAVLGLGLGAGLFLMWWSLWSEPVVSAEEPRGPGRLAELIARSGIERLTPAGVVGAMAA
+GCVVAALIVLAVTRTWTIAACFGLFGAALPWALLTWQATRRTRALRDLWPDAVDHVRSAV
+RAGLTLPEALTQLGETGPEGLRAPFREFARDYRSGARFLDALERLKTRMADPVADRLVAS
+LRLTREVGGADIGLLLQSLSEFLRQDARTRAELEARQSWTVNAARLAVCAPWIVLLLLGT
+QPLAVTAYQSVAGGALLLAGLVVSALCYRIMLRIGALPQEKRVFA
+>PROKKA_00697
+MAALLGLALGCGLFLLWWSLWSPPTEKPEAARPDSRLRVLIAQSGIQRLSPAGVLSAMAV
+GGLVVGLLVLSLTGTWTIAACFAVFGAAVPWLLLSWQARRRSTALRELWPDAIDHARSAI
+RAGLTLPEALIQLGETGPEGLREPFQHFARDYRAGARFVDALDRLKARMADPVADRLVVS
+LRLTREVGGADIGRLLQTLSEFLRQDARIRAELEARQSWTVNAARLAVCAPWLVLLLLGT
+QPAAVAAYRSAAGGAVLLAGMVASIVCYRVMLRIGALPREKRVFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000657.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000657.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1f23e8e285c36987e54a8c44e1efce74b2b6d0e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000657.fa
@@ -0,0 +1,40 @@
+>PROKKA_00740
+MADTDFSAEIDSLRHTLASIEQVSDLDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS
+HRQTDLKRITSLESRIEDLETMVELAAEEDEPSLLDDANQELTSIRKALEELEVVTLLSG
+EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF
+EVNAPYAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHLPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLLRKA
+EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGHIDDFVDAGI
+RWRAEQVKAAQED
+>PROKKA_00471
+MADTDFSAEIDSLRHTLASIEQVSDLDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS
+HRQTDLKRITSLESRIEDLETMVELAAEEDEPSLLDDANQELTSIRKALEELEVVTLLSG
+EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF
+EVNAPFAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHLPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLLRKA
+EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGHIDDFVDAGI
+RWRAEQVKAAQED
+>PROKKA_02189
+MADTDFSAEIDSLRHTLASIEQVSDIDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS
+HRQADLKRITSLESRIEDLETMVELAAEEDEPSLLDDANDELASIRKSLEELEVVTLLSG
+EYDPRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF
+EVNAPFAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHIPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLQRKA
+EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGAIDAFVDAGI
+RWRAEQAKAAQED
+>PROKKA_02087
+MADTDFSAEIDALRHTLASIEQVSDVEKMTAEVAELEKEAAAPDLWDDPEAAQKVTSKLS
+HRQADLKRIKSLADRIDDLETMVELAAEEDEPSLLDDANVELTSIRKALEELEVVTLLNG
+EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQKGWSTKVMDTSYAEEAGLKSATF
+EVNAPFAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHIPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLVRKA
+EEDAKKKEMAGDIKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGAIDDFIDAGI
+RWRAEQVKAAQED
+>PROKKA_00705
+MADTDFSAEIDSLRHTLASIEQVSDLDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS
+HRQTDLKRITSLESRIEDLETMVELAAEEDEPSLLDDANQELTSIRKALEELEVVTLLSG
+EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF
+EVNAPYAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHLPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLLRKA
+EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGHIDDFVDAGI
+RWRAEQVKAAQED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000658.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000658.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c598f301ccf7fe90f3be5081233f848dd5d5f5d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000658.fa
@@ -0,0 +1,35 @@
+>PROKKA_00741
+MTMRAARWHGKKDIRIEEIDSPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH
+PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF
+IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG
+GAGPIGALTAAVLKGKGLTVYVSELSELRRRKVLEAGVVDEAFDPREVDVPAKIRELHDG
+QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA
+NDHADTIRMVEDGAVDLAPFITGKIGLDDLVDRGFETLIHHNETAVKILVSPTGQGL
+>PROKKA_00472
+MTMRAARWHGKKDIRIEEIDSPSAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH
+PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF
+IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG
+GAGPIGALTAAVLKGKGLTVYVSELSELRRRKVLEAGVVDEAFDPREVDVPAKIRELHDG
+QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA
+NDHADTIRMVEDGAVDLAPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL
+>PROKKA_02188
+MTMRAARWHGKKDIRIEEIASPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH
+PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDQDRPDYNLAPDMNF
+IGLGGDGGGLAEQIAVRRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG
+GAGPIGALTAAVLKGKGLTVYVSELSELRRQKVLEAGVVDEAFDPREVDVPAKIRELHDG
+QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVLKEIDLRGTIAYA
+NDHADTIRMVEDGTVDLAPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL
+>PROKKA_02086
+MTMRAARWHGKKDIRIEEIDSPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH
+PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF
+IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVALIG
+GAGPIGALTAAVLKGKGLTVYVSELSELRRRKVLEAGVVDEAFDPREVDVPAKIRELHDG
+QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA
+NDHADTIRMVEDGAVDLTPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL
+>PROKKA_00706
+MTMRAARWHGKKDIRIEEIDSPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH
+PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF
+IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG
+GAGPIGALTAAVLKGKGLTVYVSELSELRRQKVLEAGVVDEAFDPREVDVPAKIRELHDG
+QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA
+NDHADTIRMVEDGAVDLAPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000660.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000660.fa
new file mode 100644
index 0000000000000000000000000000000000000000..071129ff0f8d4a3c3f7d9ee48e317e3b48438b6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000660.fa
@@ -0,0 +1,30 @@
+>PROKKA_00743
+MALDKTVATPAEAVADVPDGASLAVGGFGLSGNPVQLIEALLEQGATDLSVVSNNCGVDG
+WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY
+TRSGVGTQVAEGGLPMRYDADGTVVKSSQAKPTDTFVLGEGYLSQAPDEPETYVLERSIV
+TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGV
+FVHRIVEVGTDIEKRIEKRTVRASGEGRA
+>PROKKA_00474
+MALDKTVATPAEAVADVPDGASLAVGGFGLTGNPVQLIEALLEQGATDLSVVSNNCGVDG
+WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY
+TRSGVGTQVAEGGLPMRYDADGTVVKSSQAKPTDTFVLGEGYLSQTPDEPETYVLERSIV
+TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGI
+FVHRIVEVGTDIEKRIEKRTVRASGEEQA
+>PROKKA_02186
+MALDKTVATAAEAVADVPDGASLAVGGFGLSGNPIQLIEALLEQGAADLSVVSNNCGVDG
+WGLGILLGAGRIRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY
+TRSGVGTQVAEGGLPMRYDAEGNVVKSSAAKPTDTFVLGEGYVSQDPAEEQTYVLEQSIV
+TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDEVHLPGV
+FVHRIVEVGTDIEKRIEKRTVRAAGEES
+>PROKKA_02084
+MALDKTVATPAEAVADVPDGASLAVGGFGLSGNPVQLIEALLEQGAMDLSVVSNNCGVDG
+WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY
+TRSGVGIQVAEGGLPMHYDADGTVVKSSQAKPTDTFVLGEGYLNQAPGEPETYVLERSIV
+TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGV
+FVHRIVEVGTDIEKRIEKRTVRASGEEQA
+>PROKKA_00708
+MALDKTVATPAEAVADVPDGASLAVGGFGLSGNPVQLIEALLEQGATDLSVVSNNCGVDG
+WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY
+TRSGVGTQVAEGGLPMRYDADGTVVKSSQAKPTDTFVLGEGYLSQTPDEPETYVLERSIV
+TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGV
+FVHRIVEVGTDIEKRIEKRTVRASGEEQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000661.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000661.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f52bdfbf0aa9067be4163ac07d3974dfaaed6ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000661.fa
@@ -0,0 +1,25 @@
+>PROKKA_00744
+MSEQTTGRPRGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL
+GTGPYPTEEAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSAAG
+DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVFKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLALVETAPGVTEEQARALTGAPLD
+>PROKKA_00475
+MSEQTTERPQGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL
+GTGPYPTEDAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSAAG
+DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLALVETAPGVTEEQVRALTGAPLD
+>PROKKA_02185
+MSEQSTERPEGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNYIPAGRSVVLQSENGIL
+GTGPYPVEDEVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSSAG
+DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLRLVETAPGVSEEQVRDLTGAELD
+>PROKKA_02083
+MSEQTTGRPRGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL
+GTGPYPTEDAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEISAAG
+DLANWMVPGKMIKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLALVETAPGVTEEQVRALTGAPLD
+>PROKKA_00709
+MSEQTTGRPQGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL
+GTGPYPTEDAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSAAG
+DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLALVETAPGVTEEQVRALTGASLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000662.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000662.fa
new file mode 100644
index 0000000000000000000000000000000000000000..212ed017e40cd40ee434996ae01e23af1950d8d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000662.fa
@@ -0,0 +1,20 @@
+>PROKKA_00745
+MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDTYEAGMVLTGTEVKSLREGKASLVD
+GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL
+SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA
+>PROKKA_00476
+MGKNSKGKATKQPAPGERQVIANNKKARHDYTILDTYEAGIVLTGTEVKSLREGKASLVD
+GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL
+SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA
+>PROKKA_02184
+MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDVYEAGLVLTGTEVKSLREGKASLVD
+GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL
+SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRIRNRRAGVA
+>PROKKA_02082
+MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDTYEAGMVLTGTEVKSLREGKASLVD
+GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL
+SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA
+>PROKKA_00710
+MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDTYEAGMVLTGTEVKSLREGKASLVD
+GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL
+SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000664.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000664.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2566fb28aa2563dd6e46d947844da6904c9d6390
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000664.fa
@@ -0,0 +1,40 @@
+>PROKKA_00751
+MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAEVGMVTTVDRGRYAVVLPERLDE
+RITAMRARELRRTPIATGDRVAVVGDLSGEEGTLARIVRVEERSTVLRRSADDSDEVERV
+VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPDALVAHYEAL
+DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER
+ATGHVNAVTGRGRHTSSSALALPLTGDDGVPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF
+DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED
+AASSED
+>PROKKA_00481
+MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAQVGMVTTVDRGRYAVVLPDRLDE
+RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARIIRVEERSTVLRRSADDSDEVERV
+VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPDALVAHYEAL
+DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER
+ATGHVNAVTGRGRHTSSSALALPLTGDDGAPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF
+DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED
+AASSED
+>PROKKA_02179
+MGRRVDPGAWDESDVRVRPSKRGTRPRTKERPKHEDAVVGMVTTVDRGRYTVVLPERLDE
+RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARVVRVEERSTVLRRSADDSDEVERV
+VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAALMAHYESL
+DLEVMTSGAAVFEAETGDTALDGALVARVAERLQGHTSAFVGPSGVGKSTLLNALTGAER
+ATGHVNAVTGRGRHTSSSALALPLTDDDGVPLADTWVVDTPGIRSFGLGWVEPDRVVEAF
+DDLAGGLADCPRGCAHTADSPGCGLDGWVAAGHAGPSGAARLASLRRLLGNRLGPAGAED
+SASSED
+>PROKKA_02074
+MGRSLDPSAWDESHVRVRPSKRGTRPRTKQRPQHEDAQTGLVTTVDRGRYTVVLPGRAHA
+PVTAMRARELRRTPIATGDRVDVVGDLSGDEGSLARIVRVQERDTVLRRSADDSDAVERV
+VVANADTLMVMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAELVAHYEAL
+DLEVMTSGASRFEAESGDTDLDDGLVERVAERLAGHTAAFVGPSGVGKSTLLNALTGAGR
+ATGHVNAVTGRGRHTSSSALAMSLPGPDGEPVPDTWVVDTPGIRSFGLGWVEPDRVVEAF
+EDLAGGLEGCPRGCTHLADSPGCGLDAWVAEGHAGEAGPARLASLRRLLGNRTTAEAGGS
+ASSED
+>PROKKA_00715
+MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAEIGMVTTVDRGRYAVVLPDRLDE
+RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARIVRVEERSTVLRRSADDSDEVERV
+VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAALVAHYEAL
+DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER
+ATGHVNAVTGRGRHTSSSALALPLTGDDGAPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF
+DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED
+AASSED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000667.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000667.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4785237f1a4da4a12be36a7339089587b5b2fda6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000667.fa
@@ -0,0 +1,15 @@
+>PROKKA_00754
+MTADQHGHECRVAQDASLERLYQYLDGALTPEDIEQVRAHVAECPDCRHQKELEELIRSA
+VRRCCQEKAPAQLRATIMTRITQISTTTVTWG
+>PROKKA_00484
+MTVDQHGHECRDAQDASLERLYQYLDGALTPEDIEQVRAHVADCPDCRHQKELEELIRSA
+VRRCCQEKAPAQLRATIMTRITQTPMTTVTWG
+>PROKKA_02176
+MTADQHGRECRDAQEDTLERLYQYLDGALTPEEIDQVRAHVEDCEDCRHQQELEQFIRTA
+VRRSCQEKAPEQLRTTILTRITQLSTTRVTWR
+>PROKKA_02071
+MSQDGDCRGCNDGEDRLEQLYQYLDGALTPEDIDQVRAHVDQCPDCHHQQELELIIRSAL
+RRSCQEKAPAQLRATIMTRITQVSTTTVRRAG
+>PROKKA_00718
+MTADQHGHECRDAQDASLERLYQYLDGALTPEDIEQVRAHVADCPDCRHQKELEELIRSA
+VRRCCQEKAPAQLRATIMTRITQTPMTTVTWG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000668.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000668.fa
new file mode 100644
index 0000000000000000000000000000000000000000..94ceed1ed345cfb2677e2481f9f5fd3666b7d68a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000668.fa
@@ -0,0 +1,25 @@
+>PROKKA_00755
+MHNRRIRIAAVGDQLLAGAGDARAIGWWGRVLARTQAPDVELENYVLAVPHETTEDLNER
+WWGEASRRFSEETENRLVVALSDADLDLEATSTARSRLNLANVLDTASQRNIPVLVVGPT
+PTLDEQRNARLAELNAAYLDVADRRNHVYVDTFTPLVGHEQWRSDLASGQGRPGQAGHGL
+IAWLVLHRGWYQWLGLPEPTA
+>PROKKA_00485
+MHNRRIRIAAVGDHLLAGAGDARAIGWWGRVLARTQAPDVELENYVLAVPHETTEDLNER
+WWGEASRRFSEETENRLVVALSDADLDLEATSTARSRLNLANVLDTASQRNIPVLVVGPT
+PTLDEQRNARLAELNAAYLDVADRRNHVYVDTFTPLVGHEQWRSDLASGQGRPGQAGHGL
+IAWLVLHRGWYQWLGLPEPTA
+>PROKKA_02175
+MNDRRIRIAAVGDHLLAGAGDARAIGWWGRVLARTQAPGVELENYVLAVPHETTEDLNER
+WWGEASRRYSEDTENRLVVALSDADLDLEASSTARSRLNLANVLDTASQRGIPVLVVGPT
+PTLDEERNARLAELNAAYLDVADRRSHVYVDTFTPLQGHEQWRADLAAGEGRPGQAGHGL
+IAWLVLHRGWYQWLGLPEPTA
+>PROKKA_02070
+MQNRRIRIAAVGDHILAGAGDPRSIGWWGRVLARTAAPEVTLENYVLAVPHETTEQLNER
+WWGEASRRFSESAENRLVVALSDADLDLEASSSARSRLNLANVLDTASQRGITALVVGPV
+PTLDEARNDRLADLNTAYQDVAARRGHLYVDAFTPLRTHEQWRADLAAGDGVPGQAGHGL
+IAWLVLHRGWYQWLGVPEPTA
+>PROKKA_00719
+MHNRRIRIAAVGDHLLAGAGDARAIGWWGRVLARTQAPDVELENYVLAVPHETTEDLNER
+WWGEASRRFSEETENRLVVALSDADLDLEATSTARSRLNLANVLDTASQRNIPVLVVGPT
+PTLDEQRNARLAELNAAYLDVADRRNHVYVDTFTPLVGHEQWRSDLASGQGRPGQAGHGL
+IAWLVLHRGWYQWLGLPEPTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000671.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000671.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e132a95fde3088d7b8e54522f6f30f2d73031e30
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000671.fa
@@ -0,0 +1,45 @@
+>PROKKA_00758
+MEWLLLILGLALIVGTGFFVAVEFAMIAIDVPTVQRMVDAGDRGAEPLLRCLKSLSTQLS
+ACQLGITLTTLLTGYVMDPAISRLIDPLLLQVGLPAGVVGTVSLVVAMVVATLLSMLLGE
+LIPKNMSIAEPMAIGRALARPQLVFSTVFKPAILVLNGFSNGVLARVGIEAKEEISGARS
+PEELSSLVRRSAQLGTLDAQTATFLDRTLRFADRTAADVMTPRIRVETVREDQALPEVLD
+LARSTGYSRFPVIGDSSDDIRGVVHVKKVVAVPRERRADLEAGALMTEVIRVPETVHLDQ
+LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDRVTPGVLQTASGRWYF
+PAELRPDEVRTQIPALVVPEDGAYETVGGYILARLGRLAEVGDVVDVDGGTLTVERMDGR
+RIERVRFDPAAEDEETRA
+>PROKKA_00488
+MEWLLLILGLALIVGTGFFVAVEFAMIAIDVPTVQRMVDAGDRGAEPLLRCLKSLSTQLS
+ACQLGITLTTLLTGYVMDPAISRLIDPLLLQVGLPAGVVGTVSLVVAMVVATLLSMLLGE
+LIPKNMSIAEPMAIGRALARPQLVFSTVFKPAILVLNGFSNGVLARVGIEAKEEISGARS
+PEELSSLVRRSAQLGTLDAQTATFLDRTLRFADRTAADVMTPRIRVETVREDQALPEVLD
+LARSTGYSRFPVIGDSSDDIRGVVHVKKVVAVPRERRADLEAGALMTEVIRVPETVHLDQ
+LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDRVTPGVLQTASGRWYF
+PAELRPDEVRTQIPALVVPEDGAYETVGGYILARLGRLAEVGDVVDVDGGTLTVERMDGR
+RIERVRFDPAAEDEETRA
+>PROKKA_02172
+MEWLLLILGFALVLGTGFFVAVEFSMIAIDVPTVQRMVDEGDKGAEPLLRCLKSLSTQLS
+ACQLGITLTTLLTGYVMDPAISRLIDPVLLDVGVPESVVGTVSLVVAMVVATLLSMLIGE
+LIPKNMAIAEPMTIGRALARPQLLFSTVFKPAILVLNGFSNGVLARFGIEAKEEISGARS
+PEELSSLVRRSAQLGTLDEQTATFLDRTLRFADRTAADVMTPRIRVETVGEDQPLPEVVD
+LARRTGFSRFPVIGESSDDIRGVVHVKKVVAVPRERRADLEAGSLMTEVIRVPETVHLDQ
+LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDKVTPGVLQTAAGRWYF
+PAELRPDEAQAQITSLSVPEDGAYETIGGFIMARLGRLAAVGDVVSVDGGTLSVERMDGR
+RVERVRFDPAAAADKEARA
+>PROKKA_02067
+MEWILLILGLLLVLGTGFFVMVEFSLIAIDAPTVQRMVDDGDRSWEPLLTCLKSLSTQLS
+ACQLGITLTTLLTGYVMDPAISRLVDPLILAVGLPQSVAGPVSLVVAMAAATLLSMLLGE
+LVPKNMAIAEPLRLGRALARPQLVFAAVFKPAILVLNGFSNGVLHRMGLEAKEEISGARS
+PEELSSLVRRSAQLGTLDEQTATFLDRTLRFAERTAADVMTPRIRMETVGEDDGLLDVVE
+LARRSGYSRFPVIGESPDDVLGVVHVKKAVAVPMDRRADLTAGALMTDVIRVPETVHLDQ
+LLAELREASLQLAIVVDEYGGTAGVVTLEDVVEEIVGEVSDEHDRVTPGVLQTASGRWYL
+PAELRPDEAHAQIKALDVPEDGAYETIGGFVMARLGRIPAVGDVVPLDVGTLTVERMDGR
+RVDRVRFDPRPVTEEARA
+>PROKKA_00722
+MEWLLLILGLLLIAGTGFFVAVEFAMIAIDVPTVQRMVDAGDRGAEPLLRCLKSLSTQLS
+ACQLGITLTTLLTGYVMDPAISRLIDPLLLQVGLPAGVVGTVSLVVAMVVATLLSMLLGE
+LIPKNMSIAEPMTIGRALARPQLVFSTVFKPAILVLNGFSNGVLARVGIEAKEEISGARS
+PEELSSLVRRSAQLGTLDAQTATFLDRTLRFADRTAADVMTPRIRVETVGEDQALPEVLD
+LARSTGYSRFPVIGDSSDDIRGVVHVKKVVAVPRERRADLEAGALMTEVIRVPETVHLDQ
+LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDRVTPGVLQTASGRWYF
+PAELRPDEVRTQIPALVVPEDGAYETVGGYILARLGRLAEVGDVVDVDGGTLTVERMDGR
+RIERVRFDPAAEDEETRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000675.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000675.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8dde0d0451f09a5f9602dd4eedd9666220e6df3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000675.fa
@@ -0,0 +1,20 @@
+>PROKKA_00763
+MSTVSAPEPSPRAARPRATRQKAAVDRALDRIPDFVSAQELHARLQDQGERVSLATVYRT
+LQQQLDDGLVDVLRRDDGESVYRRCEDEGHHHHLVCRSCWTTVEVTAPHVEAWATAVAAE
+HGFTDADHTVEITGVCARCRTEGRTRGA
+>PROKKA_00493
+MSTVSAPEPSPRAARPRATRQKAAVDRALDRIPDFVSAQELHARLQDQGERVSLATVYRT
+LQQQLDDGLVDMLRRDDGETVYRRCEDEGHHHHLVCRICWTTVEVTAPHVEAWATAVAAE
+HGFTDADHTVEITGVCARCRTEGRTRGA
+>PROKKA_02167
+MSAPDPGPRVVRPRATRQKAAVDRALETIPDFVSAQELHARLQEEGERISLATVYRTLQQ
+QLEDGQVDVLRREDGESVYRRCEARGHHHHLVCRLCWSTVEVTAPPVEAWAARIAAEHGF
+TEAEHTVEITGVCADCAATRAADAG
+>PROKKA_02062
+MSETPGRPSEAPAPRGRSTRQKAAVDGALDAAEDFVSAQELHARLRDAGERVSLATVYRA
+LQQRLDEGTVDMLRREDGESVYRRCAAEGHHHHLVCRVCWTTVEVTAPGVEEWAARMAAE
+HGFSDPDHTVEITGVCAECRAAGRG
+>PROKKA_00727
+MSTVSAPEPSPRAARPRATRQKAAVDRALDRIPDFVSAQELHARLQDQGERVSLATVYRT
+LQQQLDDGLVDMLRRDDGESVYRRCEDEGHHHHLVCRICWTTVEVTAPHVEAWATAVAAE
+HGFTDADHTVEITGVCARCRAEGRTRAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000677.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000677.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5a8b742bfd6d0f70da1daa32ba042b870b3332ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000677.fa
@@ -0,0 +1,20 @@
+>PROKKA_00765
+MATVFSRIIAGELPARFVWQDQTCVAFLSAAPLQPGHALVVPRAEVDEWVEVDPALVTHL
+TTVAQQIGKAQVAAFSARRAGLMIAGYEIPHLHVHVWPSTSLADFDLARVDNAPDPADLD
+DAAARLRAALRDLGHGEVVPQD
+>PROKKA_00495
+MATVFSRIIAGELPARFVWQDQTCVAFLSAAPLQPGHALVVPRAEVDEWVEVDPALVTHL
+TTVAQQIGKAQVAAFSARRAGLMIAGYEIPHLHVHVWPSTSLADFDLARVDNAPDPADLD
+DAAARLRAALRDLGHGEVVPQD
+>PROKKA_02164
+MASVFSRIIAGELPARFVWQDETCVAFLSTGPLNPGHALVVPREEVDAWVDADPALVMHL
+MTVAQQLGKAQVRAFSAQRAGLMVAGYEILHLHVHVWPSNSLADFDLNRVDNSPDPAEMD
+DAAARLRAALRELGHGEVVPQD
+>PROKKA_02060
+MATVFSRIIAGELPARFVWQDEQCVAFLSLGPLAQGHTLVVPREEVDQWVDADPDLLAHL
+TRVAQAIGRVQVRAFGAQRAGLMVAGYEIPHLHVHVWPSNSMNDYDMARVDNAPEPESLD
+EAAAAIRAGLREDGHGDVVPQD
+>PROKKA_00729
+MATVFSRIVAGELPARFVWQDQTCVAFLSAAPLQPGHTLVVPRAEVDEWVEVDPALVTHL
+TTVAQQIGKAQVAAFSARRAGLMIAGYEIPHLHVHVWPSTSLADFDLARVDNAPDPADLD
+DAAARLRAALRDLGHGEVVPQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000687.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000687.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c8d38285ea58c893ef9f8c72ea742dc16231d3d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000687.fa
@@ -0,0 +1,30 @@
+>PROKKA_00778
+MAEHRTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTVALRRWS
+ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP
+DVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL
+ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG
+FHARRAGRIPRREHALASSPMAGRVTAEEDER
+>PROKKA_00509
+MAEHRTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTVALRRWS
+ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP
+DVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL
+ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG
+FHARRAGRIPRREHALASSPMAGRVTAEEDER
+>PROKKA_02152
+MAEHRTPPATPAIPPLRIGGYDLAARLIMGTGGITDLTALEGALVASGTTLTTVALRRWS
+ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP
+DVVETLEATELLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL
+ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG
+FHARRAGRIPRREHALASSPMAGRVTAEEDER
+>PROKKA_02047
+MAPHDTTERRRAREASTAVPPLRIGGYELSSRLIMGTGGITDLAALEGALVASETTLTTV
+ALRRWSTDARDGLIALLDRLGIDVLPNTAGCRTARDAVLTARLGREALETELVKVEVIAD
+DRTLLPDVVETLDATEQLAAAGFTVLAYTSDDPAMALRLEHAGAAAVMPLGSPIGSGLGI
+LNRTNLELIVSRAGVPVVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACR
+LALEAGYHAHRAGRIPRRLHALASSPMAGRIGGAEERA
+>PROKKA_00745
+MAEHRTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTVALRRWS
+ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP
+DVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL
+ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG
+FHARRAGRIPRREHALASSPMAGRVTAEEDER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000688.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000688.fa
new file mode 100644
index 0000000000000000000000000000000000000000..80f73aa834f47a4fb7d4531509111b8757d705e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000688.fa
@@ -0,0 +1,40 @@
+>PROKKA_00779
+MTAALDPAAREPRDLTALSDTQLERFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPV
+LTYLAAAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEH
+RERLTAANALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAP
+GGPLYRDVFPERPEPGEVPSCAQAGVLGVLPGIIGSLMAAEAIKLLSGVGEPLVGRLLSV
+DALTMRFRELRLVPDPERTPVTDLSAHADQAPRPDDAGAPGSAEACGAAGGEIAPAALAA
+LLADPARVASLTLLDVREDWERRLRRVEAPAAVADRHVPLEAVLAEPAALAPGRDRVLVV
+YCAAGARSARARDAVVGADPSAGGRVLSLAGGLAAWPA
+>PROKKA_00510
+MTAALDPAAREPRDLTALSDTQLERFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPV
+LTYLAAAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEH
+RERLTAANALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAP
+GGPLYRDVFPERPEPGEVPSCAQAGVLGVLPGIVGSLMAAEAIKLLSGVGEPLVGRLLSV
+DALTMRFRELRLVTDPERTPVTDLSAHAAQAPRPDDAGAPGSAEACGAAGEEIAPAALAA
+LLADPARAASLTLLDVREDWERRLRRVEAPAAVADRHVPLEAVLAEPAAHAPGQDRVLVV
+YCAAGARSARARDAVVGADPSSGGRVLSLAGGLAAWPA
+>PROKKA_02151
+MTAAPDPADREPRDLTALSDTQLQRFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPV
+LTYLAAAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEH
+RERLTAANALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAP
+GGPLYRDVFPERPEPGEVPSCAQAGVLGVLPGIIGSLMAAEAIKLLSGVGEPLVGRLLSV
+DALTMRFRELRLVADPERTPVTDLSAHADQAPGSDDAGAPGSAEACGAAGGEIDPATLAA
+LLADPARAASLTLLDVREDWERRLRRVEVPAAVADRHVPLDAVLAEPAAHAPGPDRVLVV
+YCAAGARSARARDAVVAADPSAGERVLSLVGGLAAWPA
+>PROKKA_02046
+MSRPAGEPLVPEDRAPHSLDELSDTQLQRFARHLGLDGFGPEAQLALLRSRVLVVGAGGL
+GAPVLTYLAAAGVGEVHVVDDDVVDRSNLHRQVIHVETDLGRPKTASAAETMRGLHPEIR
+VVEHRQRLAAANALELVGAVDLVVDGSDNYATRYLVADAGEITGVPVVWGAILRFAGQVS
+VFAPGGPLYRDVFPEEPEPGDVPTCAQAGVLGVLPGIVGSLMAAEAVKLLAGVGEPLTGR
+LLSVDALTMRFSTLRLVPDPERTSVTDLSAHTVPRGGADPVESGEITPAGLAALLADPER
+AAALTLLDVREDWERGLARISAPAAAEDRHVRLDEVLADPAAHSPESGRTVVVYCAAGAR
+SARAREAVVAAAPEAADRVLSLAGGHAAWADRN
+>PROKKA_00746
+MTAAREPRDLTALSDTQLERFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPVLTYLA
+AAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEHRERLT
+ATNALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAPGGPLY
+RDVFPERPEPGEVPSCAQAGVLGVLPGIIGSLMAAEAIKLLSGVGEPLVGRLLSVDALTM
+RFRELRLVPDPERTPVTDLSAHADQAPRPDDAGAPGSAEACGAAGGEIAPAALAALLADP
+ARAASLTLLDVREDWERRLRRVEAPATVADRHVPLEAVLAEPAALAPGQDRVLVVYCAAG
+ARSARARDAVVGADPSAGGRVLSLAGGLAAWPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000689.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000689.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6bc4b5cdb968ac446c81eef8447dab5cad9e530
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000689.fa
@@ -0,0 +1,55 @@
+>PROKKA_00780
+MKPEDLSALLSAVLTDAVDAGDLPAALREEITPARVKVERPRSREHGDWATNVALQLGKK
+AGMAPRDLAGLVAERLTDKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPEYGRND
+ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV
+FADSVLARLHGRDVPAGGYPGAYVQELADAVALEHPDVRELTDEAARPVVREAAYRLQMQ
+DIKDTLAAFDVHFDVFTSEQTLHDSGAIEQAVQRLREQGHVEDREGAVWLKTTDFGDDKD
+RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS
+TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVAA
+AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVETLNRTRLWLNDATAQV
+LANGLGLLGVSAPEKM
+>PROKKA_00511
+MKPEDLSALLSAVLTDAVDAGDLPAALREEITPARVKVERPRSREHGDWATNVALQLGKK
+AGMAPRDLAGLVAERLTGKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPEYGRND
+ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV
+FADSVLARLHGRDVPAGGYPGAYVQELADAVALEHPDVRELTDEAARPVVREAAYRLQMQ
+DIKDTLAAFDVHFDVFTSEQTLHDSGAIEQAVQRLRAQGHIEDREGAVWLKTTDFGDDKD
+RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS
+TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVAA
+AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVETLNRTRLWLNDATAQV
+LANGLGLLGVSAPEKM
+>PROKKA_02150
+MKPEDLSALLSAVLTDAVDAGDLPAELREEITPARVKVERPRSREHGDWATNVALQLGKK
+AGMAPRDLAGLVAERLTGKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPDYGRNA
+ALVGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV
+FADSVLARLHGRDVPEGGYPGAYVQELADAVALEHPDVRELTDEAARPVVRQAAYRLQMQ
+DIKDTLAAFDVHFDVFTSEQTLHESGAIEQAVERLREQGHIEDREGAVWLKTTDFGDDKD
+RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS
+TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVAA
+AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVDTLNRTRLWLNDATAQV
+LANGLGLLGVSAPEKM
+>PROKKA_02044
+MKPEELSALIHAQLLAAVDAGELPAELREQLSADRVKVERPRSREHGDWATNVALQFAKQ
+AGMNPREFASALASRVGEQPGVATVDVAGPGFLNITLDAAAAGELARQIVEAGEAYGRNE
+ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIVRLLRASGADVTAEYYINDAGNQMNV
+FADSVLARMAGRDVPEGGYPGAYVKDLADAVATDHPQVRELTDDAARPVVRQAAYELQMQ
+DIKDTLAAFDVHFDVFTSETRLHESGAIQAAVDRLREQGHVEDREGAVWLRTTDFGDDKD
+RVMIRANGEPTYFAADAAYYLDKRDRGFEEKVYLLGADHHGYVGRLKAIAAAAGDDPEEN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVQWLGKDALRYDLARYPADSPITIDPELLRS
+QTNDNPVYYVQYAHARACGAARTAAAHGVDRCAFDASLLTDPTESELLAQLAEFPAVVAS
+AARLREPHRVARHLEVIAGAYHSWYAAQRIVPVPLEDGTPAPVEDVNRTRLWLNDAAAQV
+LRNGLGLLGVSAPETM
+>PROKKA_00747
+MKPEDLSALLSAVLTDAVDAGDLPAALREEITPARVKVERPRSREHGDWATNVALQLGKK
+AGMAPRDLAGLVAERLTDKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPEYGRND
+ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV
+FADSVLARLHGRDVPAGGYPGAYVQELADAVALEHPDVRELTDEAARPVVREAAYRLQMQ
+DIKNTLAAFDVHFDVFTSEQTLHDSGAIEQAVQRLRAQGHVEDREGAVWLKTTDFGDDKD
+RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS
+TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVGA
+AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVETLNRTRLWLNDATAQV
+LANGLGLLGVTAPEKM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000690.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000690.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a270e2450eb1b8a6ef648b20558dbd8252b6800
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000690.fa
@@ -0,0 +1,50 @@
+>PROKKA_00781
+MRTPQPAPASPLAPAWLPAPGDPDALVPGLWAAGVDRAADGELTVQGLRASALAAEFGTP
+LLVVDEDDFRARARAFRKGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS
+GGELAIALAAGIDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELTHLAALAAEAGR
+RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPASTDRDGNVAGRSPAAVAVAAALAA
+ESIELLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV
+DEPRPAAEIADALADDVQKTVERLGLACPRISLEPGRAISGPAGLTLYTVGVTKTVDVDA
+PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSARRTSEAEPVLSRVVGKHCESGDILV
+RDVYLPADLGRGDLLAVPATGAYTHVMSSNYNALARPAVVAVSGGQARVIIRRETQEDLF
+ARETDPRLAR
+>PROKKA_00512
+MRTPQPAPASPLAPAWLPAPGDPDALVPGLWAAGVDRAADGELTVQGLRASALAAEFGTP
+LLVVDEDDFRARARAFRKGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS
+GGELAIALAAGIDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELTHLAALAAEAGR
+RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPASTDRDGNVAGRSPAAVAVAAALAA
+ESIELLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV
+DEPRPAAEIADALADDVQKTVERLGLACPRISLEPGRAISGPAGLTLYTVGVTKTVDVDA
+PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSARRTSEAEPVLSRVVGKHCESGDILV
+RDVYLPADLGRGDLLAVPATGAYTHVMSSNYNALARPAVVAVSDGQARVIIRRETQEDLF
+AREADPRLAR
+>PROKKA_02149
+MTTPQPAPASPLAPAWLPAPGDPDALAPGLWAAGVDRAADGELTVQGLRASALAVEFGTP
+LLVVDEDDFRARARAFREGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS
+GGELAIALAAGVDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELEHLAALAAEAGH
+RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPATTDRDGNVAGRSPAAVAVAAALAA
+ESIDLLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV
+DEPRPAAEIADALADDVQKTVERLGLACPRISLEPGRAISGPAGLTLYTVGVTKTVDADT
+PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSAARTSDAQAVLTRVVGKHCESGDVLV
+RDVYLPEDLGRGDLLAVPATGAYTHVMASNYNALTRPAVVAVAGGRARVIIRRETQEDLF
+AREADPRLGR
+>PROKKA_02043
+MNAGSVNLEETVTETAPQSAHPLAPAWLPAPADPDALAPLVWSSGVARDAAGELAVQGVP
+ASVLAERFGTPVLVLDEDDFRARARAFREGFDAAFESLCGGADVYFAGKSMLTLSTARWA
+AEEGLRVDTASGGELAIALRAGVLPEHIGLHGNNKSAAELATALDAGVGRIIVDSVDELE
+FLAALAAERGQIAPVMLRVTPGVHAHTHDFIATAHEDQKFGLSLTPSATGRDGNEAGVAP
+AAVAVRTALQADSIRLLGLHCHIGSQIFEADGFGLAAERVLGFLAEVKDEHGVELPELDL
+GGGHGIAYTAVDEPRPAAEIADALADDVQKAVERLGLTCPRISIEPGRAISGPAGLTLYS
+VGVTKTVDVDAPDDGTASRRYVAVDGGMSDNPRPVLYDADYTAALASRTSDAAPALSRVV
+GKHCESGDILVRDVWLPEDVARGDLLAVPATGAYTHSMSSNYNALLRPAVVAVRDGEARE
+IVRRETLDDLLRREVDPQNPA
+>PROKKA_00748
+MTTPQPAPASPLAPAWLPAPGDPDALVPGLWAAGVDRAADGELTVQGLRASALAAEFGTP
+LLVVDEDDFRARARAFREGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS
+GGELAIALAAGVDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELTHLAALAAEAGR
+RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPASSDRDGNVAGRSPAAVAVAAALAA
+ESIDLLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV
+DEPRPAAEIADALADDVQKTVERLGLRCPRVSLEPGRAISGPAGLTLYTVGVTKTVDADA
+PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSARRTSEAEPVLSRVVGKHCESGDILV
+RDVYLPADLGRGDLLAVPATGAYTHVMSSNYNALARPAVVAVSGGQARVIIRRETQEDLF
+AREADPRLAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000693.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000693.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2aab543da4048f7ce57e7e589346f72778ae632f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000693.fa
@@ -0,0 +1,35 @@
+>PROKKA_00784
+MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVEGEGEA
+TLPRDGAHLILRLAREQLRGRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATVRLRLHERVVPVV
+AIPDTELSTHVARGVLPADVPHAVAAAQAGRAALLVHALAEDPALLPAATRDWLHQEPRA
+VAMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAASWRVL
+VPCVAVDGVRVESLHHG
+>PROKKA_00515
+MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVEGEGEA
+TLPRDGAHLILRLAREHLRDRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATARLRLHERVVPVV
+AIPDTELSTHVARGVLPAEVPHAVAAAQAGRAALLVHALAEDPALLLAATRDWLHQEPRA
+VAMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAASWRVL
+VPCVAVDGVRVESLHHG
+>PROKKA_02146
+MPAPRTLAAGTAVVVAVPATSANLGPGFDSMGLALELRDEVSLTVVDGPDVAEVTGEGAD
+VLPRDGSHLILRLAHEHLRARGVRAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAADRRPPEALLEAATDFEGHPDNVAPALVGGATVSWTRDDDARPATAPLRLHERIVPVV
+AIPDTELSTHAARGVLPESVPHAVAAAQAGRAALLVHALAERPELLMAGTRDWLHQGPRA
+AAMPASAALVAGLRVRGHAAVVSGAGPTVLALCDGAEAAEQAAAAARALTADDVLAWRVL
+VPAVAADGVRVEPLHHG
+>PROKKA_02040
+MRELRDLTPGTGARVLAPATSANLGPGFDALGLALELRDEVTLTVVDGPDTAVVTGEGAA
+ELPTDGEHLVLRLAHAHLTRRRFRAPGLALTAVNRIPHARGLGSSAAAVVTAVLAAEALL
+PADERLSAAELLDVTARREGHPDNVAPALSGGASVSWHRDGGPGWATAAVALHPQITPVI
+GIPDVTLSTHAARAALPESVPHAVAAEQAGRAALLTLALASRPDLLLPATRDWLHQDARA
+SAMPPSAALVRGLREQGHAAVVSGAGPTVLVLAPTPADAERAAEAMRALAPETGAAWRVL
+VPGVAAEGARVEPLHHG
+>PROKKA_00751
+MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVVGEGEA
+TLPRDGAHLILRLAHEHLRDRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATARLRLHERVVPVV
+AIPDTELSTHVARGVLPAEVPHAVAAAQAGRAALLVHALAEDPALLPAATRDWLHQEPRA
+VTMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAAAWRVL
+VPCVAVDGVRVESLHHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000696.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000696.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68ec06573ac38ded70f685d271581d561c872168
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000696.fa
@@ -0,0 +1,34 @@
+>PROKKA_00788
+MTDVSDFIDVSDPAALENAVARAREVLADRGCVVLPTDTVYGIGADAFSPLAVAVLLAAK
+GRGRTMPPPVLIADRRVMAGLAYDVPEEAEALAERFWPGALTLILKSQPTLTWDLGETRG
+TVALRVPDDAVARELLYAVGPMAVSSANRTGMDAATTADAARSMLGESVALYLDAGPRES
+RDPSTIVDCTVTPFRVARQGSVPLEELRAVVPDLLAEGEEPPVAADRIAAEDAAAARPAD
+REA
+>PROKKA_00519
+MTDVSDFIDVSDPAALENAVARAREVLADRGCVVLPTDTVYGIGADAFSPLAVAVLLAAK
+GRGRTMPPPVLIADRRVMAGLAYDVPEEAEALAERFWPGALTLILKSQPTLTWDLGETRG
+TVALRVPDDAVARELLYAVGPMAVSSANRTGMDAATTADAARSMLGESVALYLDAGPRES
+RDPSTIVDCTVTPFRVARQGSVPLEELRAVVPDLLAEGEEPPVAADRIAAEDAAAARPAD
+REA
+>PROKKA_02143
+MSAADESEPWGQALRRATGLLAEAGVDSPRVDAELLLAHVLGLGRGELLARVFAGAAGTA
+GEAERFAALVARRARREPVQHLTGVAFFHGLDLAVGPGVFLPRPETELLVDAVLAELTAR
+PAAATVVDLCTGSGAIAAAVSAWAQEHGRDVAVIAVELDDEAAGWARRNLEPRGVYMRQG
+DALVALPELEGRVDVVVSNPPYVPEAETPVQAEARLDPARALYGGDAAGLRIPQAIAHRA
+TELLVPGGLFAMEHHETQGPALLGALDADPRFTGVCVHQDLTGRDRFLTARRSCEAAAAA
+EDGRMADVSDFIDVSDPAALEDAVARAREVLGDCGCVVLPTDTVYGIGADAFSPRAVAVL
+LAAKGRGRTMPPPVLISDRRVLAGLAYDVPDEAEALAERFWPGALTLILKSQPTLTWDLG
+ETRGTVALRVPDDAVARELLYAVGPMAVSSANRTGMPAATTAEEARGMLGESVDLYLDAG
+PREDRAPSTIVDCTVTPFRVARQGAVPLEALRELVPDLLAEGEEPPVPADRLAAEPVAEA
+PAPTPAPDGDDAADRAGREA
+>PROKKA_02036
+MSEFIDVSDPSDLTAAVERARAVLADRACVVLPTDTVYGIGADAFSPTAVAVLLAAKGRG
+RTMPPPVLISDRSVMAGLAYDVPEAAEELAERFWPGALTLILRSQPTLTWDLGETRGTVA
+LRVPDDAVTRELLYAVGPMAVSSANRTGMPAATTARGAEEMLGESVALYLDGGERATQEP
+STIVDCTVTPFRVARQGAVSLEALRAVVPDLVAEGEEPPVPAELTTPPAAPEA
+>PROKKA_00755
+MTDVSDFIDVSDPAALENAVARAREVLADRGCVVLPTDTVYGIGADAFSPLAVAVLLAAK
+GRGRTMPPPVLIADRRVMAGLAYDVPEEAEALAERFWPGALTLILKSQPTLTWDLGETRG
+TVALRVPDDAVARELLYAVGPMAVSSANRTGMDAATTADAARSMLGESVALYLDAGPRES
+RDPSTIVDCTVTPFRVARQGSVPLEELRAVVPDLLAEGEEPPVAAERIAAADDAAAARPA
+DPEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000700.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000700.fa
new file mode 100644
index 0000000000000000000000000000000000000000..114997c4d3cc4c2e9609245161e01a2d7e5a35e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000700.fa
@@ -0,0 +1,15 @@
+>PROKKA_00792
+MELHGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI
+LGLVFAFVIGA
+>PROKKA_00523
+MELHGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI
+LGLVFAFVIGA
+>PROKKA_02139
+MELHGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI
+LGLVFAFVIGA
+>PROKKA_02032
+MEISGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI
+LGLVFAFVIN
+>PROKKA_00759
+MELHGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI
+LGLVFAFVIGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000701.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000701.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c433698811b0672df53194a21b7592d733b7ae0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000701.fa
@@ -0,0 +1,25 @@
+>PROKKA_00793
+MISNGLILAAAEGANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGG
+LAKAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAEARRISE
+QAQAQIAAERQQAAAQLKGEVGSLATTLAGKIVGESLEDDARSQRVVDRFLADLDRHQSA
+GVAE
+>PROKKA_00524
+MISNGLILAAAEGANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGG
+LAKAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAEARRISE
+QAQAQIAAERQQAAAQLKGEVGSLATTLAGKIVGESLEDDARSQRVVDRFLADLDRHQSA
+GVAE
+>PROKKA_02138
+MISNGLILAAGANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGGLA
+KAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAESTRISEQA
+QAQIAAERQQAASQLKGEVGTLATTLASKIVGESLEDDARSQRVVDRFLADLDRHQSAGV
+AE
+>PROKKA_02031
+MISNGLILASAEGANPLVPNPWEILVTTVGFAVLMFIVVKFVVPALEKSYTDRVEAIEGG
+LEKAEKAQAEANKMMADYEGQLADARQEANRIREEARTEGAQIVAEARERAAAEAARITE
+QAQTQIAAERTQAAAQLKGEVGTLATTLASKIVGESLDDDARSQRVVDRFLADLDRHQSA
+GVSE
+>PROKKA_00760
+MISNGLILAAAEGANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGG
+LAKAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAEATRISE
+QAQAQIAAERQQAAAQLKGEVGSLATTLAGKIVGESLEDDARSQRVVDRFLADLDRHQSA
+GVAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000708.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000708.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4db9930951937f0f9664699239ba8bf072009719
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000708.fa
@@ -0,0 +1,25 @@
+>PROKKA_00800
+MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE
+PSPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA
+EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN
+RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF
+>PROKKA_00531
+MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE
+PSPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA
+EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN
+RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF
+>PROKKA_02130
+MRLVIARCSVTYEGRLNAHLPPATRLLMVKADGAVLVHSDGGSYKPLNWMSPPATLHTTA
+PTAEQAEQGVVEVWRVQAAKSDDRLMILIEEILADQSHELGADPGLVKDGVEADLQRLLA
+EQIGLLGDGHTLVRREYMTAIGPVDILARDPEGGTVAVELKRRGDIDGVEQLTRYLELMN
+RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF
+>PROKKA_02023
+MRLVIARCSVTYEGRLNAHLPSATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE
+PTEEQAAAGVTQVWRVQAKKSDDRLLVLLEEVLADETHELGVDPGLVKDGVEADLQRLLA
+EQIGLLGDGHTLVRREYMTAIGPVDILAKGPGGQTVAVELKRRGDIDGVEQLTRYLDLMN
+RDPLLAPVTGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDADARLF
+>PROKKA_00767
+MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE
+PFPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA
+EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN
+RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000710.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000710.fa
new file mode 100644
index 0000000000000000000000000000000000000000..122574f62e4a85f0a1e32d008b56b27da66968aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000710.fa
@@ -0,0 +1,43 @@
+>PROKKA_00802
+MEEKEPASGPDAPSVADVRAPAEPEGAEQQPVGGIPVEPAGAAAAPPSHGPTPAGRRRRL
+RLGSVLRRRRPFLEEDRVDPEPDPADGAEDPAVAAVALESPVLTGFLLAVGVTLAIGIVS
+VLRTNGQLIVWIAAALFIALGLDPLVRRVESWGAPRWVGVLTAALGLAAVAGAFVALLVP
+TVIEQSTQLVQDLPAIIDGVMRAEWFVQLDEEFHLQEAVRAQTERLAADGVAITDLFGGL
+LGLGQTVLNAVFSVLVVVVLTLYFLSSLPHMKYWAYRLAPRSRRPRIEALSEQITSSVGH
+YVMGQSFVAALNGAVAFTALAIAGAPFAVLLAAIAAFMAFIPLVGAAIGGTLLTLVSLLT
+SWQTAAVFAAIYFVYLQIEAYVISPRVMARAVPVPAAVAVIAVIAGGALLGVLGALMAIP
+LAAALALLVREVFIPRQDAR
+>PROKKA_00533
+MSLGPTVASRARRGQAGALTYAERVEEKETASGPDVAGVADVRGPAEPEGAEQPPVAGVP
+VEPVGVAAAPPSHGPTPAGRRRLPRLGSVLRRRRPFLEEDRVDPESVPVDGAEDPAVAAV
+ALESPVLTGFLLAVGVALAIGVVSVLRTNGQLIVWIAAALFIALGLDPLVRRVESWGAPR
+WVGVLTAALGLAAVAGAFVALLVPTVIEQSTQLVQDLPAIIDGVMTAEWFVQLDEEFHLQ
+EAVRAQTERLAADGVAVTDLFGGLLGFGQTVLNAVFSVLVVVVLTLYFLSSLPHMKYWAY
+RLAPRSRRPRIEALSEQITSSVGHYVMGQSFVAALNGAVAFTALAIAGAPFAVLLAAIAA
+FMAFIPLVGAAIGGTLLTLVSLLTSWQTAAVFAAIYFVYLQIEAYVISPRVMARAVSVPA
+AVAVIAVIAGGALLGVLGALMAIPLAVALLLLVREVFIPRQDAR
+>PROKKA_02128
+MEPVDPTAAPASAAPAPLPASGRVPRRRRRRGRLIPLRGVLRRRRPVFLAEDRVDPDPEH
+PEPEPTGEPPVTAVTVESPVATGFLLTVGVALALAVVWVLRTNGQLLVWIAAALFIALGL
+DPLVRRVESWGAPRWAGVLTAALGLAAVASAFVALLVPTVVEQSRQLVEGLPGTIEDVMT
+SAWFIELDQEFHIQEAVRAQTDRLTTDGAAVTDLFGGLLGIGQTVLNAFFSVFVVVVLTL
+YFLASLPHMKYWAYRLAPRSRRPQVERLSEKITSSVGHYVMGQSFVAALNGTVAFTALAV
+AGTPFAVLLAAFAAFMAFIPLVGAVIGGTVLTLLSLLTSWQTAAVFAAIYFVYLQIEAYV
+VSPRVMARAVAVPAAVAVIAVIAGGALLGVLGALMAIPLAAALSMLVREVFIPRQDAR
+>PROKKA_02021
+MDHIEDSPAPSGPSRGARRLRLGSLVRRREAFLPNERVDPLPPGSPDAAPAEPEVPELAL
+RAPVAAGFLLTMGVCLAAVLVWVVLENTQLLVWIAAALFIALGLDPVVRLVERWGAPRWV
+GVLLAALGLAAVAGAVVGMLVPAVVQQSTQLITGLPDTITQIMATPWFREVDRQLQIQHA
+VQSWLDGLTKDGAAVTQLFGGLVGIGQTVMNAVFSTIVVVVLALYFLASLPHLKYWGYRL
+APRSKRLRVEALGEEITLSVGHYVMGQTVVAVLNGTVAFIALSVAGGPFPVLLAFVAAVM
+AFIPLVGALIGGTILTAVCLLESWQAAALFAAIYFVYLQIEAYVVSPRVMARAVAVPAAV
+GVIAVIAGGTLLGVLGALMAIPTAAAVLLIVREVLIPRQDAR
+>PROKKA_00769
+MSLRPTVASPARRGQAGALTYAERVEEKETASGPDAAGVADVRAPAEPEGTEQPPVAGIP
+VEPVGVAAAPPSHGPTPAGRRRLPRLGSVLRRRRPFLEEDRVDPESVPVDGAEDPAVAAV
+ALESPVLTGFLLAVGVALAIGVVSVLRTNGHLIVWIAAALFIALGLDPLVRRVESWGAPR
+WVGVLTAALGLAAVAGAFVALLVPTVIEQSTQLVQDLPAIIDGVMTAEWFVQLDEEFHLQ
+EAVRAQTERLAADGVAVTDLFGGLLGFGQTVLNAVFSVLVVVVLTLYFLSSLPHMKYWAY
+RLAPRSRRPRIEALSEQITSSVGHYVMGQSFVAALNGAVAFTALAIAGAPFAVLLAAIAA
+FMAFIPLVGAAIGGTLLTLVSLLTSWQTAAVFAAIYFVYLQIEAYVISPRVMARAVSVPA
+AVAVIAVIAGGALLGVLGALMAIPLAAALLLLVREVFIPRQDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000711.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000711.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2fe06b3911cd7eb900f8899baf33ae9fe54bda17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000711.fa
@@ -0,0 +1,34 @@
+>PROKKA_00803
+MTDVTAQPPSDAPSHLRGAVDLSSLGTPASAGRTAPGADAGAGGGSWVIADADQGLLQQL
+VQLSAQVPVLLHLHVPGDAASEALYRQFADAVDAQAGRLVLARLDVAKEPAVLQALGLGA
+GPAVMAVVAGQPVPLVNQEVPEETLRQLMGEILEVARQNGVAGTVPAVAPARQDAGAAAA
+EAPPVPPLHRAAHEALAADDLPGAVSAWEAALADSPADAVAQQGLSAARLMLRTRDADAS
+AVRAAAADGPDDVAAQLAVADLDVLGGHVEDAFDRLVRFIALHPGDDRETARAHLVDLYT
+VVGTDDPRVQASRRQLAAALF
+>PROKKA_00534
+MTDVTAQPPSDAPSHLRGAVDLSSLGTPAPAGRTAPGADAGAGGGSWVIADADQGLLQQL
+VQLSAQVPVLLHLHVPGDAASEALYRQFADAADAQAGRLVLARLDVAKEPAVLQALGLGA
+GPAVMAVVAGQPVPLVNQEVPEETLRQLMGEILEVARQNGVAGTVPPVAPARQDADAAAA
+EAPPVPPLHRAAHEALAADDLPGAVSAWEAALADSPADAVAQQGLSAARLMLRTRDADAA
+AVRAAAADGPDDVAAQLAVADLDVLGGHVEDAFARLVRFIALHPGDDRETARAHLVDLYT
+VVGTDDPRVQASRRRLAAALF
+>PROKKA_02127
+MIPDADQRLLQQLVQLSAQVPVLLHLHVPGDASSDALYRQFADAVDAQAGRLVLARIDVA
+ADPSVLQALGLGAGPAVMAVVAGQPVPLVNQEVPAETLEQLMGEILEVARQNGVAGTVPA
+VAPARADAAEPAPAAPPVPPLHRAAHAALAADDLPGAVAAWEEALKDTPADPVAQQGLSA
+ARLMLRTRDADAAAVRSAAADAPDDAAAQLAVADLDVLGGHVEDAFARLVRFIALHPGED
+RETVRAHLVDLYTVVGVDDPRVTASRRRLAAALF
+>PROKKA_02020
+MTSQPSSPSLRGAVDLSSLRTPRPAPGAQGAGAQGAGAPGEPASWAVLDADSRLLEQLVQ
+LSTQVPVILVLHVPGDATSEALSTQFADAADAQAGTVVMARLDVVAEPQLLQAFGIGAGP
+AVVAVVAGQPVPLANQELPQEALDGLMGQLLEVARQNGVAGRVPALAPARDGAAAPQPAP
+VPPLHRRAHEALAADDLPGAVAAWEDALKESPADETARQGLSAARLMLRTRDMDAAAVRA
+AAAERPDELAAQTAVADLDVLGGHVEDAFARLVRFVAAHPGEDREAARAHLVDLYIVVGS
+EDPRVHASRRRLAAALY
+>PROKKA_00770
+MTDVTAQPPSDAPSHLRGAVDLSSLGTPAPAGRTAPGADAGAGGGSWVIADADQGLLQQL
+VQLSAQVPVLLHLHVPGDAASEALYRQFADAVDAQAGRLVLARLDVAKEPTVLQALGLGA
+GPAVMAVVAGQPVPLVNQEVPEETLRQLMGEILEVARQNGVAGTVPPVAPARQDAGAAAA
+EAPPVPPLHRAAHEALAADDLPGAVSAWEAALADSPADAVAQQGLSAARLMLRTRDADAA
+AVRAAAADGPDDVAAQLAVADLDVLGGHVEDAFARLVRFIALHPGDDRETARAHLVDLYT
+VVGTDDPRVQASRRRLAAALF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000714.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000714.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0263e0c40fe18a4e60f96fec9c86f3f531d795ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000714.fa
@@ -0,0 +1,15 @@
+>PROKKA_00806
+MSVTGEPDLNDPFAPAGGGTSVLEREELRQEIEPGDHERFAHYVRKEKITESAVTGAPVI
+ALCGKVWVPGRDPNKFPVCPTCKEIYEGLREPQDGGDGDGGGKRGGWFGGRGRG
+>PROKKA_00537
+MSVTGEPDLNDPFAPAGGGTSVLEREELRQEIEPGDHERFAHYVRKEKITESAVTGAPVI
+ALCGKVWVPGRDPNKFPVCPTCKEIYEGLREPQDGGDGDGGGKRGGWFGGRGRG
+>PROKKA_02124
+MSVTGEPDLTDPFSPAGGGTSVLEREQQLQDVEPGDHERFAHYVRKEKITESAVTGAPVI
+ALCGKVWVPGRDPQKFPVCPTCQEIYEGLREPQDGDDAGAGGGRRGGWFGGRGRG
+>PROKKA_02017
+MSISDPFQNDPLSPSGGGTSVLEREEQLQDVEPGDHERFAHYVRKEKIMESALSGEPVIA
+LCGKVWVPGRDPNKFPVCPLCQEIYDGLRDPQDGDDAGSGGGRRGGFFGRGRG
+>PROKKA_00773
+MSVTGEPDLNDPFAPAGGGTSVLEREELRQEIEPGDHERFAHYVRKEKITESAVTGAPVI
+ALCGKVWVPGRDPNKFPVCPTCKEIYEGLREPQDGGDGDGKRGGWFGGRGRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000717.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000717.fa
new file mode 100644
index 0000000000000000000000000000000000000000..47a7269d44fff7897409bc9fb642c755a88128dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000717.fa
@@ -0,0 +1,45 @@
+>PROKKA_00810
+MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE
+RHAASLRELPASVGRLQPGDPAIPTIFLED
+>PROKKA_00542
+MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE
+RHAASLRELPASVGRLQPGDPAIPTIFLED
+>PROKKA_02120
+MSQNPVTSAPQTPDDWRIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTSL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTQTGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDRRGRATAEVVGVNRGAAPDADDRPLLHRFVHAGELAAGWTGPEAVTRAAE
+RHAASLRELPATVGRLQPGDPAIPTIFLED
+>PROKKA_02011
+MTQNASAPAPSAAPWHVPTSLMTDHYELTMLCAARRAGTAERRSRFELFSRRLPDGRRYG
+VVAGTGRILEGLSRFRFSTAEVDFLADHSVVDDATLQWLADFRFSGDITGYAEGEVYFPH
+SPVLQVESTFAEACILETYLLSILNYDSAVASAASRMASAAQGRPCIEMGARRIHEEAAV
+AAARAAVIAGFAATSNLEAGRRYGVRTVGTAAHSFTLLHDSERAAFEAQVAALGRDTTLL
+VDTYDVEQGVRTAVEVAGRALRNVRLDSGDLVQQAHEVRELLDSLGNTETGIMVTSDLDE
+YAIASLRSAPVASYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASHGG
+RKDAVRRRDARGRAVAELVGVNRAPAADADDRPLLHTFVKDGELQEGWTGPEAVTRAAER
+HAASLAELPRAAARLQPGEALIPTIFQED
+>PROKKA_00779
+MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE
+RHAASLRELPASVGRLQPGDPAIPTIFLED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000718.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000718.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c20d45522042527ae24f79e04f11da304f184da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000718.fa
@@ -0,0 +1,15 @@
+>PROKKA_00811
+MSVLTRHDPSAPRAVRPAPGESVPAGATDTALLERPHEDTARDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSAAKAQRLMLEVHERGRSVVATGTKEKAELHVGAMHGYGLWATLEQAED
+>PROKKA_00543
+MSVLTRHDPSAPRAVRPAPGESVPAGATDTALLERPHEDTARDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSAAKAQRLMLEVHERGRSVVATGTKEKAELHVGAMHGYGLWATLEQAED
+>PROKKA_02119
+MSVLTSHDPTAPRAAGPAPGEAVPGGATDTAVLERPREDLALDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSESRAHRLMLEVHERGRSVVATGTREKAELHVGAMHGYGLWATLEQAED
+>PROKKA_02010
+MPHPAPPAPGADTALLERPREDLAAARPWHVVVWNDPVNLMSYVAYVFRSHFGYSAARAQ
+SLMLEVHERGRSVVFTGSREVAEGHVTAMHGFGLWATLEQAED
+>PROKKA_00780
+MSVLTRHDPSAPRAVRPAPGESVPAGATDTALLERPHEDTARDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSAAKAQRLMLEVHERGRSVVATGTKEKAELHVGAMHGYGLWATLEQAED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000722.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000722.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4f0d8442a740e51c3d4d60647ddaccc22267a852
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000722.fa
@@ -0,0 +1,30 @@
+>PROKKA_00815
+MSSPAPTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGNTRVLCTASFTEGVPRWLK
+GEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILAKGAAVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGAPFTRAELDTLLDLALIGTGELAR
+IQAETLAAATEDRA
+>PROKKA_00547
+MSSPAPTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGNTRVLCTASFTEGVPRWLK
+GEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILAKGAAVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGAPFTRAELDTLLDLALIGTGELAR
+VQAETLAAATEDRA
+>PROKKA_02115
+MTSPASTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGDTRVLCTASFTQGVPRWLK
+GEGTGWVTAEYAMLPRATNERNQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILRKDAEVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGVPFSRAELDTLLDLALTGTGELAR
+IQAETLAGAAGSAEAQA
+>PROKKA_02006
+MTESSPSTSPSVTRQDGRAVDELRPITITRGFSRQAEGSALIEFGGTRVLCTASFTEGVP
+RWLKGEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALG
+ENTIVLDCDVLDADGGTRTASITGAYVALAEAVAWAQGRGILKKDARVLTDSVSAVSVGI
+IDGVPMLDLPYVEDVKAETDMNVVVTGSGDFVEVQGTAEGVPFRRAELDVLLDLALAGTA
+ELSRIQAETLAGDVAGRA
+>PROKKA_00784
+MSSPAPTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGNTRVLCTASFTEGVPRWLK
+GEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILAKGAAVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGAPFTRAELDTLLDLALIGTGELAR
+IQAETLAAATEDRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000727.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000727.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7a38a973ba0877dededa39e59efdf4a315926ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000727.fa
@@ -0,0 +1,91 @@
+>PROKKA_00820
+MRIHRMRLEGLGPYAQAQDVDFDRLNAGGLFLLDGPTGAGKSTVLAALCFALYGTVPGGR
+SAESLVTTLREPGAVIPEVQVEFTVQGRRFEVVRSPKHERPRRRRSAAGGATVTTQATVS
+LRERVAGEWTAPLTRADEVGQQIAAVLHLDAEQFMQVVLLPQGQFAQFLTAKSDERRALL
+RRLFGTQRFDGVEEHLRVETARLDTAVAVDADVARTARAQLAEALHEALGPDWHAPEPSP
+DTDDRLLALAAERAGRAHEDARADLATARAAEQRARVTARELETRGRDLAAAEAWASRRR
+DHDAEAETAAARRRAVDAHERAGRVLAAAQRATAAADAAGTASETVTEALAHVEDEPTAA
+AWLAAARADGAADAPASRQALGEAERAAEAVARAVQDRARMGELEQEAAAAAERRAEIGR
+DRAALVESRPEREAAVAAHRAAVERGTERLGAREAVDRAVSEAAARRTAAEAAAARAVEA
+ETAARAHREAQERRREAAERHVGLLRARYEQAASELAERLVPGEPCAVCGSPEHPAPAAT
+ADTAVTEADVRDAEQARTAADRAATDAETALRAAEQTLRTAREAAAGLAPEAAREALERA
+EAERAALDQAAKDLAADRRRLTAAEKTLAGADETAAALAAEDGRLAEAAAHRAARLTELR
+DAVEAARGDAETLDARRDQVTAARRVLAALAAAQDEDARARAVADETDQALTAALAEQHF
+DDVDAARAARLEETEAAARTAAVQEWHAERARLAELEASEPVRRGRALAEAGVEPPTEEQ
+TRAAAEALAAAEAASSSRATAVGRLDSLVATVRRQSAALTEVLERSAGLIAEHTRVRGLL
+DLVRGGGENLLKMPLTSYVLAGRLEEVAAAATERLLAMTDQRYSIEYSDAVGGRGNKGLE
+LVIRDHYVDETRHPATLSGGETFMASLALALGLADTVQAEAGGIELDTLFVDEGFGSLDA
+DTLDDVLDVVDTLRTGGRTVGLVSHVERMRQEIGVRLEVRKDRRGSSLAVHDGA
+>PROKKA_00552
+MRIHRMRLEGLGPYAQAQDVDFDRLNAAGLFLLDGPTGAGKSTVLAALCFALYGTVPGGR
+SAESLVTTLREPGAVIPEVQVEFTVQGRRFEVVRSPKHERPRRRRSAAGGATVTTQATVS
+LRERVAGEWTAPLTRADEVGQQIAAVLHLDAEQFIQVVLLPQGQFAQFLTAKSDERRVLL
+RRLFGTQRFDGVEEHLRVETARLDTAVAVDADVARTARAQLAEALHEALGPDWHAPEPSP
+DTDDRLLALAAERAGRAHEDARADLATARAAEQRARVTARELETRGRDLAAAEAWASRRR
+DHDAEAETAAARRRAVDAHERAGRVLAAAQRASAAADAAGTASEAVTEALAHVEDEPTAA
+AWLAAARADGAADAPASRQALGEAERAAEAVARAVRDRDRMRELEQEAAAAAERRAEIDR
+DRAALVESRPEREAAVAAHRAVVERGTERLGAREAVDRAVSEAAARRTAAEAAAARAVEV
+ETAARAHREAQERRREAAERHVGLLRARYEQAASELAERLVPGEPCAVCGSPEHPAPAAT
+ADTAVTEADVRDAEQARTAADRAATDAETALRAAEQTLRSAGEAAAGLAPEAAREALERA
+ETERAALDQAAKDLAADRRRLTAAEKTLAGADETAAALAAEDGRLAEAAAHRAARLTELR
+DAVEAARGDAETLDARRDQVTAARRVLAALAAAQDEDARARAVADETGQALTATLAEQRF
+DDVDAARAARLEETEAADRTAAVQEWDAERARLAELEASEPVRRGRALAEAGVEPPTEEQ
+TRAAAEALAAAEAASSSRATAVGRLDSLVATVRRQSAALTEVLERSAGLIAEHTRVRGLL
+DLVRGGGENLLKMPLTSYVLAGRLEEVAAAATERLLAMTDQRYSIEYSDAVGGRGNKGLE
+LVIRDHYVDETRHPATLSGGETFMASLALALGLADTVQAEAGGIELDTLFVDEGFGSLDA
+DTLDDVLDVVDTLRTGGRTVGLVSHVERMRQEIGVRLEVRKDRRGSSLAVHDGA
+>PROKKA_02110
+MRIHRMRLQGIGPYAEAQDVDMDRLNDAGLFLLDGPTGAGKSTVLAALCYALYGSVPGGR
+SPESLVTTLRPPGAVVPEVLVEFTVQGRRFEVVRSPRHERLKKRRSASGKDTTPTPAAVS
+LREHVDGAWQEPLTRNDEVGVQVADVMHLDAAQFMQVVMLPQGRFAEFLTARSDERQRLL
+RRLFGTQRFDGVEEHLKAEAERLGSRAAADAKVAASAREQLREAVAAELGEDWHAPEPFP
+ATDEELVERTAERTREAVDAARAGRDAAAAEEAAARGTQAELRATGEALAAAAAWTERER
+AHREGAEAAAGDRTAVAAHERAGRVLGAADRSESARAAEDRAREADGTAQAAAAEDPLSA
+GWLEQARRDAAETPADDAAETSADAAALPRDAVALAERAVEEVVRAVRDRAAAERLEETE
+RTEAARRTQIVAEREAAEAERSGREEGLAAVREAVEAASARLGAQADVDRRVAEAEQGLA
+AAREAERHALAADAADRAREAARTGRDAAAQHRLGLLRSRYEQAAADLAADLEDGTPCAV
+CGSPEHPDPAPRVGTAVTEADVAAAEEGLAAAEAVLADAETARTAAHERVRASSAAAGGR
+TPAQAEEALAAARTEHAELAAVRKALAADRRRLRALETERDEAAAAETARTAEDARLQEA
+ARQRHERLLELRAGIERARGDAPDLDARGALVRAARGRLEALAGAVEVRERAVAVAADAD
+RALAAALREQEFEDVGAARAARLPAEDAAARTARVRAWDDEQARLAELAQSDAVRRGREL
+QDQQATAPTPEDLEAAAARLLEAERSRREQDEALGRRTAVAAAVERQAALLRGVLDRSAA
+LLAEHERVTGLLALVRGGGENRLKMPLASYVLAGRLEEVAAAATERLLAMTDGRYSIEYS
+DDSAGRGNKGLELVVRDHYVDETRHPSTLSGGETFMASLALALGLADTVQAEAGGVELDT
+LFVDEGFGSLDSDTLDDVLDVVDGLRSGGRTVGLVSHVERMKQEIPVRLAVTKEREGSSL
+AVHVDA
+>PROKKA_02001
+MRIHRMRLEGIGPYAEPQDLDLDPLNDAGLFLLDGPTGAGKSTVLAALCFALYGSVPGGR
+TPESLVTTLRPPGAVVPQVLVEFTVQGRRFEVLRSPRHARPKKRGGGTTATQASVSLRER
+VDGAWTAPLTRADEVGRQVAEVLRLDAAQFMQVVSLPQGRFAEFLTARSDDRQRLLRRLF
+GTQRFDGVEDRLKECAEALGTRVAADAAEAAGARAQLLEQARLELGEDWHAPDPAPEEGE
+DERLVELTRTRADAALAEARTAQQAADAAEAAARAAQDRLTADTEALRALAAWEGREREH
+RQAADHVAADRSAVALHERASHVLGAATRAEQTRAAHASTAERARAAAEAVAADALAAAW
+LDEAEDADAARRRADRETDALARAVRDRDALTRLEAEGTQADAERERLEDEARSAREKGK
+RRAAQIAELHDTVDAAAARLGAEDEVARRLAEATERAAAAGQAAERAVAQERARAARDER
+RDAQRGAAQARLDLLRSRFEQAAAELAAGLEDGSPCPVCGSAEHPDPAPRADGAVTEADV
+AAADRALEAADAALAEAEQALAAASEEHRAARERAGGQDVAAAEEALSAVRAEHEALAAA
+RTALATDRRALARRESEQRTADEAATARTAALARLSEAQARRTERAAELTAAVAAAQGDA
+ADLDARTAHVRTATRALSALVEAGDAAARAAAVAEDAAQALAGALAEQDFADVAAARAAA
+LPPDDAAARAARVRSWDVEEARLAEAAASEPLVRGRALREAGTSEPTAEEFAAAQETLRE
+ATAARTARAAVVGRREALVASLERQARRLRAVLERSSELLAEHERATGLLALVRGQGENR
+LKMPLASYVLAGRLEEVAAAATERLLAMTDRRYSIEYSDEATGRGNKGLELVIRDHYVDE
+TRHPSTLSGGETFMASLALALGLADTVQAEAGGVELDTLFVDEGFGSLDADTLDDVLDVV
+DGLRAGGRTVGLVSHVERMKQEIPVRLEVTKSRAGSTLAIHDGG
+>PROKKA_00789
+MRIHRMRLEGLGPYAQAQDVDFDRLNAGGLFLLDGPTGAGKSTVLAALCFALYGTVPGGR
+SAESLVTTLREPGAVIPEVQVEFTVQGRRFEVVRSPKHERPRRRRSAAGGATVTTQATVS
+LRERVDGEWTAPLTRADEVGQQIAAVLHLDAEQFMQVVLLPQGQFAQFLTAKSDERRVLL
+RRLFGTQRFDGVEEHLRVETARLDTAVAVDADVARTARAQLAEALHEALGPDWHAPEPSP
+DTDDRLLGLAAERAGRAHEDARADLATARAAEQRARVTARELETRGRDLAAAEAWASRRR
+DHDAEAETAAARRRAVDAHERAGRVLAAAQRATAAADAAGTASETVTEALAHVEDEPTAA
+AWLAAARADGAADAPASRQALGEAERAAEAVARAVQDRARMGELEQEAAAAAERRAEIGR
+DRAALVESRPEREAAVAAHRAAVERGTERLGAREAVDRAVSEAAARRTAAEAAAARAVEA
+ETAARAHREAQERRREAAERHVGLLRARYEQAASELAERLVPGEPCAVCGSPEHPAPAAT
+ADTTVTEADVRDAEQARTAADRAATDAETALRAAEQTLRTAREAAAGLAPEAAREALERA
+EAERAALDQAAKDLAADRRRLTAAEKTLAGADETAAALAAEDGRLAEAAAHRAARLTELR
+DAVEAARGDAETLDARRDQVTAARRVLAALAAAQDEDARARAVADETDQALTAALAEQHF
+DDVDAARAARLEETEAAARTAAVQEWHAERARLAELEASEPVRRGRALAEAGVEPPTEEQ
+TRAAAEALAAAEAASSSRATAVGRLDSLVATVRRQSAALTEVLERSAGLIAEHTRVRGLL
+DLVRGGGENLLKMPLTSYVLAGRLEEVAAAATERLLAMTDQRYSIEYSDAVGGRGNKGLE
+LVIRDHYVDETRHPATLSGGETFMASLALALGLADTVQAEAGGIELDTLFVDEGFGSLDA
+DTLDDVLDVVDTLRTGGRTVGLVSHVERMRQEIGVRLEVRKDRRGSSLAVHDGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000731.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000731.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e533dabbcbba33811966ed0e2d1bd7ebd064f25a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000731.fa
@@ -0,0 +1,20 @@
+>PROKKA_00825
+MTDTTQHRLQPGDTAPAFTLQDQEGRPVSLRDSAGKHTIVYFYPAASTPGCTTQACDFRD
+SLASLTAAGYVVLGISPDPIGKIIRFAEQEGLTFPLLSDEDHAVAEAYGAWGEKKNYGRT
+FEGLIRSTIVVGPDGKVTHAQYNVKATGHVARLRRTLGLDEA
+>PROKKA_00557
+MTDTTQHRLQPGDTAPAFTLQDQEGRPVSLRDSAGKHTIVYFYPAASTPGCTTQACDFRD
+SLASLTAAGYVVLGISPDPIGKIIRFAEQEGLTFPLLSDEDHAVAEAYGAWGEKKNYGRT
+FEGLIRSTIVVGPDGKVTHAQYNVKATGHVARLRRTLGLDEA
+>PROKKA_02097
+MSDTTQNRLQPGDIAPSFTLQDQDGRPVSLRDSAGKSTIVYFYPAASTPGCTTQACDFRD
+SLASLTAAGYVVLGVSPDPIGKIIRFAQKEGLTFSLLSDEDHAVAEAYGAWGEKKNYGRT
+YEGLIRSTVVVGPDGRVTHAQYNVKATGHVARLRRTLGLDEA
+>PROKKA_01996
+MTENTAAPARLSPGDVAPEFTLQDQDGRPVSLRDSAGKSTIVYFYPAASTPGCTTQACDF
+RDSLASLTAAGYRVLGISPDPIGKIIRFAQNEGLTFSLLSDEDHAVAAAYGAWGEKKNYG
+RTSEGLIRSTVVVGPDGKVTLAQYNVKATGHVARLRRELGLDD
+>PROKKA_00794
+MTDTTQHRLQPGDTAPAFTLQDQEGRPVSLRDSAGKHTIVYFYPAASTPGCTTQACDFRD
+SLASLTAAGYVVLGISPDPIGRIIRFAEQEGLTFPLLSDEDHAVAEAYGAWGEKKNYGRT
+FEGLIRSTIVVGPDGKVTHAQYNVKATGHVARLRRTLGLDEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000735.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000735.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b502c86e9892047a8fbc79a6adda6df2a4f79bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000735.fa
@@ -0,0 +1,60 @@
+>PROKKA_00831
+MSTTPRDARAAVPQVPTPASRPTESARVQERRPAPRPEIVEPRVPGEGSRVEPTRMTGSE
+GIIRSLEELGVTDVFGLPGGAILPTYDPLMDSDRIRHILVRHEQGAGHAAQGYHLATGKV
+GVAIATSGPGATNLVTAVADAHMDSQAVVFITGQVSSAAIGTDAFQEADIVGITMPITKH
+SRLVTRPEDVPQALAEAFHIAATGRPGPVLVDVTKDAQQGEFEFAWPPRIDLPGYRPVLR
+GHPRQIREAARLIREARRPVLYVGGGVARGEAHEELRALAERTGAPVVTTLTARGVFPDS
+HPQHLGMPGMHGGVPAVAALQQADLLITLGARFDDRVTGHLPSFAPGARVIHADIDPAEI
+SKNRTADVPIVGDVKEIIPDLVAELATDTEALPDLADWWAVLRRLQDTYPMGWTETEDGL
+LAPQEVISRLSALSGPEATYVAGVGQHQMWASQFVAYERPRQWLNSAGLGTMGFAVPAAM
+GAQVGEPDRVVWAIDGDGCFQMTNQELATCVINRIPIKIAVINNSSLGMVRQWQTLFYDG
+RYSNTDLNTGHDTARVPDFVKLADAYGAAGLRCDRREDLDDTIRQALAIDDRPVIVDFVV
+SRDAMVWPMVPAGVSNDAIQVARGMTPDWDQED
+>PROKKA_00563
+MSTTPRDARAAVPQVPTPASRPTETARVQERRPAPRPEIVEPRVPGEGSRVEPTRMTGSE
+GIIRSLEELGVTDVFGLPGGAILPTYDPLMDSDRIRHILVRHEQGAGHAAQGYHLATGKV
+GVAIATSGPGATNLVTAIADAHMDSQAVVFITGQVSSAAIGTDAFQEADIVGITMPITKH
+SRLVTRPEDVPQALAEAFHIAATGRPGPVLVDVTKDAQQGEFEFAWPPRIDLPGYRPVLR
+GHPRQIREAARLVREARRPVLYVGGGVARGEAHEELRALAELTGAPVVTTLTARGVFPDS
+HPQHLGMPGMHGGVPAVAALQQADLLITLGARFDDRVTGHLPSFAPGARVIHADIDPAEI
+SKNRTADVPIVGHVKEIIPDLVAELATDTEALPDLADWWAVLRRLQETYPMGWTETEDGL
+LAPQEVISRLSALSGTEATYVAGVGQHQMWASQFVAYERPRQWLNSAGLGTMGFAVPAAM
+GAQVGEPDRVVWAIDGDGCFQMTNQELATCVINRIPIKIAVINNSSLGMVRQWQTLFYDG
+RYSNTDLNTGYDTARVPDFVKLADAYGAAGLRCDRREDLDDTIRQALAIDDRPVIVDFVV
+SRDAMVWPMVPAGVSNDAIQVARGMTPDWDQED
+>PROKKA_02093
+MSTTPRDARAAVPPVPTPASRPEEQARPQERRPAVRPDTVEPRVPGEGNRVKPTLMTGSE
+GIIRALEELGVTDVFGLPGGAILPTYDPLMDSDQIRHILVRHEQGAGHAAQGYHLATGKV
+GVAIATSGPGATNLVTAIADAHMDSQAVVFITGQVSSAAIGSDAFQEADIVGITMPITKH
+SRLVTRPEDIPQALAEAFHIAATGRPGPVLVDVTKDAQQGEFEFAWPPRVDLPGYRPVLR
+GHPRQIREAARLIREARRPVLYVGGGVARGEAHEELRALAELTGAPVVTTLTARGVFPDA
+HPQHLGMPGMHGGVPAVAALQQADLLITLGARFDDRVTGHLPSFAPCARVIHADIDPAEI
+SKNRTADVPIVGHVKEIIPDLAAELATDTEALPDLADWWAVLRRLQDTYPMGWTETEDGL
+LAPQEVISRISALSGPEAAYVAGVGQHQMWASQFVAYERPRQWLNSAGLGTMGFAVPAAM
+GAQVGEPDRVVWAIDGDGCFQMTNQELATCVINRIPIKIAVINNSSLGMVRQWQTLFYDG
+RYSNTDLNTGHDTARVPDFVKLADAYGAAGLRCDRREDLDDTIRQALAIDDRPVIVDFVV
+SRDAMVWPMVPAGVSNDAIQVARGMTPDWDQED
+>PROKKA_01992
+MSTTPRATAPAASAGRDQRGPTRTETVEPRVPGPAAVVEPTVMNGAQGIIRSLEELGVED
+VFGLPGGAILPTYDPLMDSSRIRHILVRHEQGAGHAAQGYHLAGGRVGVAIATSGPGATN
+LVTAIADAHMDSQSVVFITGQVSSAAIGSDAFQEADIVGITIPITKHSRLVTRAEDIPAA
+LAEAFHIASTGRPGPVLVDVTKDAQQSEFEFSWPPRLDLPGYRPVLRGHPRQIREAARLI
+REARRPVLYVGGGVARGEAHEELRALAALTGAPVVTTLTARGVFPDSHPQHLGMPGMHGG
+VPAVAALQQADLLITLGARFDDRVTGHLPSFAPGAKVIHADVDPAEISKNRLADVPIVGS
+VKEIIPDLVAELGAGADLPDLAPWWATLERLRETYPLGFTAPDDGLMAPQQVISRISALS
+GPEAVYVAGVGQHQMWASQFVEYERPRQWLNSAGLGTMGFSVPAAMGAKVAQPQRTVWAI
+DGDGCFQMTNQELATCVINGIPIKVAVINNSSLGMVRQWQTLFYDQRYSNTDLNTGHGTA
+RIPDFVKLADAYGAAGLRCEREEDLDDVIRQALEIEDRPVVVDFVVSRDAMVWPMVPAGV
+SNDAIQIARGMTPDWDHED
+>PROKKA_00801
+MSTTPRDARAAVPQVPTPASRPTETARAQERRPAPRPEIVEPRVPGEGSRVEPTRMTGSE
+GIIRSLEELGVTDVFGLPGGAILPTYDPLMDSDRIRHILVRHEQGAGHAAQGYHLATGKV
+GVAIATSGPGATNLVTAIADAHMDSQAVVFITGQVSSAAIGTDAFQEADIVGITMPITKH
+SRLVTRPEDVPQALAEAFHIAATGRPGPVLVDVTKDAQQGEFEFAWPPRIDLPGYRPVLR
+GHPRQIREAARLIREARRPVLYVGGGVARGEAHEELRALAELTGAPVVTTLTARGVFPDS
+HPQHLGMPGMHGGVPAVAALQQADLLITLGARFDDRVTGHLPSFAPGARVIHADIDPAEI
+SKNRTADVPIVGHVKEIIPDLVAELATDTEALPDLADWWAVLRRLQETYPMGWTETEDGL
+LAPQEVISRLSALSGPEATYVAGVGQHQMWASQFVAYERPRQWLNSAGLGTMGFAVPAAM
+GAQVGEPDRVVWAIDGDGCFQMTNQELATCVINRIPIKIAVINNSSLGMVRQWQTLFYDG
+RYSNTDLNTGHDTARVPDFVKLADAYGAAGLRCDRREDLDDTIRQALAIDDRPVIVDFVV
+SRDAMVWPMVPAGVSNDAIQVARGMTPDWDQED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000736.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000736.fa
new file mode 100644
index 0000000000000000000000000000000000000000..60f9806f921e8eeeff1b8ac9ea01a64a645ea34c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000736.fa
@@ -0,0 +1,20 @@
+>PROKKA_00832
+MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ
+VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES
+LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRALAR
+>PROKKA_00564
+MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ
+VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES
+LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRALAR
+>PROKKA_02092
+MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ
+VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES
+LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRALAR
+>PROKKA_01991
+MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTQVPGISRMTVVVDADAHLLEQ
+VTKQLNKLINVIKVVELAGDSSVQRDHLLVKVRADASTRGQVVQAADLFRAHVVDVAPDS
+LTFEATGTREKLEAFLEMMEPHGIRELVRSGTLALARGPRSMTDRALAR
+>PROKKA_00802
+MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ
+VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES
+LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRAVAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000738.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000738.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5d618e8cfe78c7f43ec5e41d1a86f6d2ce6e4f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000738.fa
@@ -0,0 +1,50 @@
+>PROKKA_00834
+MSAAQPVVLIAEELSPATVEALGPDFEIRRTDGADRARLLEDLRDVDAVLIRSATQMDAE
+AIAAAPQLKVIARAGVGLDNVDVPAATEAGVMVVNAPTSNIISAAELTCGHILAAARNIA
+AAHGSLKAGEWKRSKYTGVELYGKRLGVIGLGRIGALVAERMKAFGMEILAYDPYVTTAR
+AQQLGASLVELDELLERADVVTIHMPKTPETVGMIGDEQFARMKDTAIIVNVARGGLVDE
+DALARALEAGTIGGAGIDVFSSEPATDLAFFAHDSAVVTPHLGASTAEAQEKAGVAVAGS
+VRLALSGELVPDAVNVAGGAIHEDVRPGLPLAEKLGRVLTALVGEQSITAVEVEIAGEIS
+EHDVSAMRLAALKGVFTDIVSDQVSYVNAPVLAEQRGVECRLTTTAVSESYRNTVTVRAA
+TAQGAQTAVTGTLTGPRQVQKLVGVDRHELEVPLADHLLVFAYQDRPGVIGVLGQALGVQ
+GVNIAGMDVSRDDEGAALAVLTLDGALSGDTAATLAAAIGAARAAEVDLSV
+>PROKKA_00566
+MSAAQPVVLIAEELSPATVEALGPDFEIRRTDGADRARLLEDLRDVDAVLIRSATRMDAE
+AIAAAPQLKVIARAGVGLDNVDVPAATEAGVMVVNAPTSNIISAAELTCGHILAAARNIA
+AAHGSLKAGEWKRSKYTGVELYGKRLGVIGLGRIGALVAERMKAFGMEILAYDPYVTTAR
+AQQLGASLVELDELLERADVVTIHMPKTPETVGMIGDEQFARMKDTAIIVNVARGGLVDE
+DALARALEAGTIGGAGIDVFSSEPATDLAFFAHDSAVVTPHLGASTAEAQEKAGVAVAGS
+VRLALSGELVPDAVNVAGGAIHEDVRPGLPLAEKLGRVLTALVGEQSITAVEVEIAGEIA
+EHDVSAMRLAALKGVFTDIVSDQVSYVNAPVLAEQRGVECRLTTTAVSESYRNTVTVRAA
+TAQGTQTAVTGTLTGPRQVQKLVGVDRHELEVPLADHLLVFAYQDRPGVIGVLGQALGVQ
+GVNIAGMDVSRDDEGAALAVLTLDGALSGDTAATLAAAIGAARAAEVDLSA
+>PROKKA_02090
+MSAAQPVVLIAEELSPATVEALGPDFEIRRTDGADRARLLEDLRDVDAVLIRSATRMDAE
+AIAAAPQLKVIARAGVGLDNVDVPAATAAGVMVVNAPTSNIISAAELTCGHILATARNIA
+AANRSLKAGEWKRSKYTGVELYGKKLGVIGLGRIGALVAERMRAFGMEILAYDPYVTTAR
+AQQLGATLVELDQLLERADFVTIHMPKTPETVGMIGDDQFARMKDTAVVVNVARGGLVDE
+DALARALDSGAIAGAGIDVFSTEPATDLAFFAQDSAVVTPHLGASTAEAQEKAGVAVAGS
+VRLALSGELVPDAVNVAGGVIHEDVRPGLPLAEKLGRVLTSLVGEQSLTAVEVEIAGEIA
+EHDVSAMRLAALKGVFTDIVSDQVSYVNAPMLAEQRGVECRLTTTPVSESYRNTVTLRAA
+TAQGTQVSVTGTLTGPRQIQKLVGVDRHELEVPLADHLLVFTYEDRPGVIGVLGQALGVQ
+GVNIAGMDVSRDDEGEALAVLTLDGALSGDTATALAAAIGASRVAEVDLSA
+>PROKKA_01989
+MSAAKPVVLIAEELSPATVEALGPDFEIRHTDGADRARLLADLPGVDAVLIRSATTMDAE
+AIAVAKDLKVIARAGVGLDNVEVPAATAAGVMVVNAPTSNIVSAAELTCGHILSVARNIA
+PANRALKAGEWKRSKYAGVELFEKKLGVIGLGRIGALVAERMKAFGMEILAYDPYISAAR
+AQQLGATLLDLDELLAQSDFITVHMPKTPETVGMISDAQFATMKDTAFIVNVARGGLIDE
+DALDRALESGAIAGAGVDVFSSEPATDLAFFRHDTAVVTPHLGASTAEAQEKAGVAVAKS
+VRLALAGELVPDAVNVAGGVIHEDVRPGLPLAEKLARVLRALAGERSLASVDVEVAGEIA
+VHDVKALRLAALKGVFTDVVSDQVSYVNAPVLAEQRGVGGQLTTAAEAGSYRNTVTVAAV
+TDEGERLSVTGTLTGPKQVEKLVGVGRHEMEVALAEHMLLFRYADRPGVVGVLGQSLGEQ
+GVNIAGMDVSRDEQGSALAVLTLDAALAPGTAPTLAAAIDADRAAEVNLAD
+>PROKKA_00804
+MSAAQPVVLIAEELSPATVEALGPDFEIRRTDGADRARLLEDLRDVDAVLIRSATRMDAE
+AIAAAPQLKVIARAGVGLDNVDVPAATEAGVMVVNAPTSNIISAAELTCGHILAAARNIA
+AAHGSLKAGEWKRSKYTGVELYGKRLGVIGLGRIGALVAERMKAFGMEILAYDPYVTTAR
+AQQLGASLVELDELLERADVVTIHMPKTPETVGMIGDEQFARMKDTAIIVNVARGGLVDE
+DALARALEAGTIGGAGIDVFSSEPATDLAFFAHDSAVVTPHLGASTAEAQEKAGVAVAGS
+VRLALSGELVPDAVNVAGGAIHEDVRPGLPLAEKLGRVLTALVGEQSITAVEVEIAGEIA
+EHDVSAMRLAALKGVFTDIVSDQVSYVNAPVLAEQRGVECRLTTTAVSESYRNTVTVRAA
+TAQGTQTAVTGTLTGPRQVQKLVGVDRHELEVPLADHLLVFAYQDRPGVIGVLGQALGVQ
+GVNIAGMDVSRDDEGAALAVLTLDGALSGDTAATLAAAIGAARAAEVDLSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000741.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000741.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46b525b1256eeda86b364a4da9ac7b8129d82d70
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000741.fa
@@ -0,0 +1,40 @@
+>PROKKA_00849
+MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG
+PLSLDPAAAVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEELF
+LGSLRAQLEADRAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE
+LKPVTIWVSRDYARAGKGGTGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE
+LGGMNVFFVHADGRLVTPALTGTILEGVTRSSILQLGRDMGLTVEERRVTLAEWAEGVRS
+GEITEVFACGTAAVVTPIGRLLDGDDVIESAGGADVALKIRTELEGIQTGRVEDRHGWLH
+RLV
+>PROKKA_00571
+MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG
+PLSLDPAAAVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEELF
+LGSLRAQLEADRAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE
+LKPVTIWVSRDYARAGKGGTGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE
+LGGMNVFFVHADGRLVTPALTGTILEGVTRSSILQLGRDMGLTVEERRVTLAEWAEGVRS
+GEITEVFACGTAAVVTPIGRLLDGDDVIESAGGTDVTLRIRAELEGIQTGRVEDRHGWLH
+RLV
+>PROKKA_02086
+MSETVFTRQPHLSPLSEEERVEILQDPGFGKVFTDHMVSIDWTWSEDGGAWHDARVEPYG
+PLSLDPSASVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEEMF
+LGSLKAQLEADRDWVPTGEGQSLYLRPFMFATEAFLGVRPAKEVRYMVIASPAGNYFGGE
+LKPVTIWVSREYARAGRGGMGAAKTGGNYAASLLPQLEAASKGADQVVFLDQYHDDSIEE
+LGGMNVFFVFDDGRLVTPELTGTILEGVTRSSILQLGRDMGLTVEERRITLAEWAEGVRS
+GAIREVFACGTAAVVTPIGRLLDGDDVIESAGGTEVTLKIRAELEGIQTGRVEDRHGWLH
+RLV
+>PROKKA_01986
+MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG
+PLSLDPSAAVLHYGQEIFEGLKAYGHEDGSVWTFRPEANAARLNRSARRLALPELPEELF
+LGSLRAQLEADQAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE
+LTPVTIWVSRDYARAGKGGMGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE
+LGGMNVFFVHADGRLVTPELTGTILEGVTRSSILQLGRDMGMSVEERRVTLAEWAEGVRT
+GAITEVFACGTAAVVTPIGRLLDGDDVIESTGGTEVAMKIRAELEGIQTGTVEDRYGWMH
+RLV
+>PROKKA_00808
+MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG
+PLSLDPAAAVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEELF
+LGSLRAQLEADRAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE
+LKPVTIWVSRDYARAGKGGTGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE
+LGGMNVFFVHADGRLVTPALTGTILEGVTRSSILQLGRDMGLTVEERRVTLAEWAEGVRS
+GEITEVFACGTAAVVTPIGRLLDGDDVIESAGGTDVTLRIRAELEGIQTGRVEDRHGWLH
+RLV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000744.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000744.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b4cc25d834ca8a16f774fc43deb94e1cb59cf53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000744.fa
@@ -0,0 +1,30 @@
+>PROKKA_00852
+MRIARFVDQAEPTYGIVEGPADADPAELTVTALQGDPFFHGIQPTGTTHRLEDVRLVAPI
+IPRSKIVGVGRNWADHAKELGNEVPASPQFFLKPNTAVVGPNEPVTLPSWSDEVSYEAEL
+AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE
+LDVEPAGGLRITSRLDGETRQDGTTTDMVFGVRELVAAASEMFTLLPGDVILTGTPGGVG
+TVQEGQRVEAEVEGIGVLATVFRR
+>PROKKA_00574
+MRIARFVDQAEPTYGIVEGPADADPAELSITALQGDPFFHGIQPTGTTHRLEDVRLVAPI
+IPRSKIVGVGRNWADHAKELGNEVPASPQFFLKPNTAVVGPNEPVTLPSWSDEVSYEAEL
+AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE
+LDVEPTGGLRITSRLDGETRQDGTTADMVFGVRELVAAASEMFTLLPGDVILTGTPGGVG
+TVQEGQRVEAEVEGIGILATVFRR
+>PROKKA_02082
+MRIARFVDQAEPTYGVVEGPADADLSELTITALQGDPFFHGIQPTSTVHRLEDVRLVAPI
+IPRSKIVGVGRNWADHAKELGNETPASPQFFLKPNTSVVGPGEPVTLPSWSDEVSYEAEL
+AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE
+LDVEPAGGLRITSRLDGQTRQDGTTADMVFGVRELVAAASEAFTLLPGDVILTGTPAGVG
+TVAEGQRVEAEVEGIGVLATVFRR
+>PROKKA_01977
+MRIARFVDQAEPTYGVVEGPADADLSALTVTALQGDPFFHGIQPTGTTHRLEDVRLVAPI
+IPRSKIVGVGRNWADHAKELGNEVPSSPQFFLKPNTSVVGPDEPVTLPSWSEEVSYEAEL
+AVVIGTICKDVPLSRVDDVVFGYTVANDLTARDAQRTDLQWARAKGFDGACPLGPWIETE
+LDVEQAGGLRVTSRLAGETRQDGTTADMVFGVKELVAAASEMFTLLPGDVILTGTPAGVG
+TVEAGQRVEAEVEGIGVLGTHVRR
+>PROKKA_00811
+MRIARFVDQAEPTYGIVEGPADADPAELSITALQGDPFFHGIQPTGTTHRLEDVRLVAPI
+IPRSKIVGVGRNWADHAKELGNEVPASPQFFLKPNTAVVGPNEPVTLPSWSDEVSYEAEL
+AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE
+LDVEPTGGLRITSRLDGETRQDGTTADMVFGVRELVAAASEMFTLLPGDVILTGTPGGVG
+TVQEGQRVEAEVEGIGILATVFRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000745.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000745.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d200a09b297f413e2d92e9a78397f75be0539d81
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000745.fa
@@ -0,0 +1,50 @@
+>PROKKA_00853
+MTDATAPVSENAPAPFADVPQVDAETPVRVRFAPSPTGTPHVGLIRTVLFNWGWARHTGG
+TLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGQIYADVIE
+KLKAGGYIYPSYSSPEETEARHRAAGRDPKLGYDGHDRDLTDEQIAAFEAEGRAPVWRLR
+MPDEDITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLL
+SSTPRQIALYRALHAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQANLFLHRDNGFIPEG
+LLNYLGLLGWSLSADEDIFTPQQFVEHFDVHKVLANPARFDEKKAIAINGTHVRMLDVAD
+FRDRLVPYLHAAGLVGEHLTEREMQILTAAAPLVQERVQLLGEAVEMLAFLFTADRDVRT
+AEGALKGMPADLGAAVAAAREALAALPEDEFTTERIEAALRAALIDGLGLKPRQAFGPVR
+VAVTGRKVSPPLFESLEILGRDSALARLDRFAAEQGLDQGRPTDA
+>PROKKA_00575
+MTDATAPVSENAPAPFVDVPQVDAETPVRVRFAPSPTGTPHVGLIRTVLFNWGWARHTGG
+TLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGQIYADVIE
+KLKAGGHIYPSYSSPEETEARHRAAGRDPKLGYDGHDRDLTDEQIAAFEAEGRAPVWRLR
+MPDEDITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLL
+SSTPRQIALYRALYAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQANLFLHRDNGFIPEG
+LLNYLGLLGWSLSADEDIFTPQQFVEHFDVHKVLANPARFDEKKAIAINGTHVRMLDVAD
+FRDRLVPYLHAAGLVGEHLTEREMEVLTAAAPLVQERVQLLGEAVEMLAFLFTADRDVRT
+AEGALKGMPADLGAAVAAAREALAALPEEEFTTERIEAALRAALIDGLGLKPRQAFGPVR
+VAVTGRKVSPPLFESLEILGRDSALARLDRFAAEQGLDQDQPTDA
+>PROKKA_02081
+MDAETPVRVRFCPSPTGTPHVGLIRTALFNWGWARHTGGTLVFRIEDTDAKRDSEESYQQ
+LLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGEIYAEVIEKLKAGGHIYPSYSSPEETEAR
+HRAAGRDPKLGYDGFDRDLTDEQVAAFEAEGRAPVWRLRMPDTDITFTDLVRGEITFKAG
+TVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLLSSTPRQIALYRALHAVGVAAY
+MPVFGHLPYVMGEGNKKLSKRDPQANLFLHREHGFIREGLLNYLALLGWSLSADEDIFTP
+EQFVEHFDVHKVLANPARFDEKKAIAINGSHVRMLDADDFRERLVPYLHAAGLVDAEPTE
+REREILAAAAPLVQERVQLLGEAVEMLAFLFTADADVATSEGALKGMPADLGAAVAAARD
+ALAALPEDGFTTERIEEALRAALIDGLGLKPRQAFGPVRVAVTGRKVSPPLFESLEILGR
+DSALARLDRFAAEQGLDQGLPTDA
+>PROKKA_01976
+MTEPTTASDTAAENAPAVFADVPQVDADTPVRVRFCPSPTGTPHVGLIRTALFNWGWARH
+TGGTLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGEIYAE
+VIEKLKAGGHIYPSYSTPEETEARHRAAGRDPKLGYDGADRDLSAEQVEAYEAEGRRPVW
+RLRMPDADITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGE
+DLLSSTPRQIALYRALHAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQSNLFLHRDRGFI
+PEGLLNYLALLGWSLSADEDIFTPEQFVEHFDIHKVLANPARFDEKKATAINGTHVRMLE
+PADFRARLVPYLQAAGLVGERLTEREERILDAAAPLVHERVALLGEAVDMLAFLFTPDAE
+IATAEGALKGMPADLPTAVAAAREALAGIDEAEFTTAAVEEALRAALIDGLELKPRQAFG
+PVRVAVTGKKVSPPLFESLEILGKESALARLDRFAAEQAAA
+>PROKKA_00812
+MTDATAPVSENAPAPFVDVPQVDAETPVRVRFAPSPTGTPHVGLIRTVLFNWGWARHTGG
+TLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGQIYADVIE
+KLKAGGHIYPSYSSPEETEARHRAAGRDPKLGYDGHDRDLTDEQIAAFEAEGRAPVWRLR
+MPDEDITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLL
+SSTPRQIALYRALYAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQANLFLHRDNGFIPEG
+LLNYLGLLGWSLSADEDIFTPQQFVEHFDVHKVLANPARFDEKKAIAINGTHVRMLDVAD
+FRDRLVPYLHAAGLVGEHLTEREMEVLTAAAPLVQERVQLLGEAVEMLAFLFTADRDVRT
+AEGALKGMPADLGAAVAAAREALAALPEEEFTTERIEAALRAALIDGLGLKPRQAFGPVR
+VAVTGRKVSPPLFESLEILGRDSALARLDRFAAEQGLDQDQPTDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000746.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000746.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e6fed15028a54e742e6e3e4611c82d036a5fe56
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000746.fa
@@ -0,0 +1,52 @@
+>PROKKA_00859
+MSRRDTPALAPRLDALGEAAELAAGRLPEDVVAGADAVVRAAGERQALSAEHTVVGFFGA
+TGSGKSSLFNALTGRDLARVAATRPTTSEPLAAVWGVGRGQGLDPDAEHGDGTGEGGGAA
+ALLDWLGVRRRHLLDEAPVLDDGRPGFLGFGRRDGADATGLILLDLPDIDSVERGNREIT
+SRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSVRDRDVVLAS
+LRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQVAAIVAQRGAAAERLGADVAARAADLAA
+ASGEGEPAGVGPGDEQRLGRELAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRA
+DPLRRLHLMPESAAPRRDRDEVARDPALHRTSLPERSGTQRAVVDGAVRTLAAAAGAGAS
+EPWAAAIRRAGREHAEELPGAVDQAIAATDLGAGRGSWWHPVLDVLQWLALLTAVVGAGW
+LGVLALAGYLQFPLPPAPTVEGFPLPTLLLVGGLALGVLLALLAIPLTRWTAAARGRHAR
+RRLEEATTDVGRRLVVDPVRAEVDRFRAFRDALARASGAPVRRGRR
+>PROKKA_00581
+MSRRDTPALAPRLDALGEAAELAAGRLPEDVVAGADAVVRAAGERQALSAEHTVVGFFGA
+TGSGKSSLFNALTGRDLARVAATRPTTSEPLAAVWGVGRGQGLDPDAEHGDGTGEGGGAA
+ALLDWLGVRRRHLLDEAPVLDDGRPGFLGLGRRDGADATGLILLDLPDIDSVERGNREIT
+SRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSVRDRDVVLAS
+LRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQVAAIVAQRGAAAERLGADVAARAADLAA
+ASGEGEPAGVGPGDEQRLGRELAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRA
+DPLRRLHLMPASTAPRRDRDEVARDPALHRTSLPERSGTQRAVVDGAVRTLAAAAGTGAS
+EPWAAAIRRAGREHAEDLPGAVDQAIAATDLGAGRGSWWHPVLDVLQWLALLTAVVGAGW
+LGVLALAGYLQFPLPPAPTVEGFPLPTLLLVGGLALGVLLALLAIPLTRWTAAARGRRAR
+RRLEEATTDVGRRLVVDPVRAEVERFHAFRDALARASGVPVRRGRR
+>PROKKA_02076
+MELSNREITSRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSV
+RDRDTVLASLRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQIAAIVERRGAAAERLGADV
+AARARDLDAASGEGEPAGVGPGDEQRLGRDLATAGGVPAVVRAVEGSYRLRSAKQTSWPV
+LRWMHSFRADPLRRLHLMPDRPAVRRDRDEVGRDPALHRTSLPERTGTQKAVVDGAVRTL
+VTAAAAGAPEPWAASVRRAGRAHAEQVPDAVDQAIAATDLGAGRGSWWHPVLNVLQWLAL
+LTAVVGAGWLGVLALAAYLQFPLPPAPVVEGFPIPTLLLVGGLALGVLLALLAIPLTRIT
+AASRGRRARRRLEEGTTDVGRRLVVDPVRAEVDRFHAFRDAVARAAGATARRGRR
+>PROKKA_01970
+MSRPAAPTLAQRLDALGTAAELARDRLPDAVVADAQAAVRAAEERQSLSAEHTVVGFFGA
+TGSGKSSLFNALTGRELAGVAATRPTTSEPLAAVWGVGRGENLDGEGGGAAALLDWLGVR
+RRHLLDDAPVLDGGRPVFLGLGHREGADATGLILLDLPDIDSVQRSHRDVTARLAGHVDV
+LVWVVDPEKYADAVIHRDFLATMASHAAVTLVLLNQVDRLTVTDRDAVLASLRRMLSGHG
+MGDVRVLPVSARTGEGLEEVGRQIAAIVSRRGAAAERLGADVSARARALDEASGPGEPAG
+AGDDDAVRLGRDLAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRADPLRRLHLL
+PERAVARRDRDPVDRDPALHRTSLPERTQTQRAVVEGAVRTLVTSASAGASEPWAASVRR
+AGREHLDELPAAVDHAIAGTDVEAGRGSWWWPVLDVLQWLALAVAVAGAGWLGAYALAAW
+LQFPLPPAPTTQGFPIPTLLLIGGLALGLLLALLAVPLTRLTAASRGRRARRRLEEAAVR
+VGRELVVDPVNAEAARHREFRSALAAAQGSGVRSRSRR
+>PROKKA_00818
+MSRRDTPALAPRLDALGEAAELAAGRLPEDVVAGADAAVRAAGERQALSAEHTVVGFFGA
+TGSGKSSLFNALTGRDLARVAATRPTTSEPLAAVWGVGRGQGLDPDAEHGDGTGEGGGAA
+ALLDWLGVRRRHLLDEAPVLDDGRPGFLGVGRRDGADATGLILLDLPDIDSVERGNREIT
+SRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSVRDRDVVLAS
+LRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQVAAIVAQRGAAAERLGADVAARAADLAA
+ASGEGEPAGVGPGDEQRLGRELAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRA
+DPLRRLHLMPESAAPRRDRDEVARDPALHRTSLPERSGTQRAVVDGAVRTLAAAAGAGAS
+EPWAAAIRHAGREHAEELPGAVDQAIAATDLGAGRGSWWHPVLDMLQWLALLTAVVGAGW
+LGVLALAGYLQFPLPPAPTVEGFPLPTLLLVGGLALGVLLALLAIPLTRWTAAARGRRAR
+RRLEEATTDVGRRLVVDPVRAEVDRFHAFRDALARASGVPVRRGRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000751.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000751.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9db7ccf9eaf4708f88947425a34b66f9befe98c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000751.fa
@@ -0,0 +1,25 @@
+>PROKKA_00864
+MEKFTTHTGVGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS
+GGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV
+ERIWKELENRPGTPVTVDLVTRTVECGDVTAPFQIDDDTRHRLLEGLDDIAVTLGHQAEI
+DAYEADRPAYKPTTLPARTAG
+>PROKKA_00586
+MEKFTTHTGVGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS
+GGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV
+ERIWKELENRPGTTVTVDLVTRTVECGDVTAPFQIDDDTRRRLLEGLDDIAVTLGHQAEI
+DAYEADRPAYKPTTLPARTAG
+>PROKKA_02071
+MEKFTTHTGIGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS
+AGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV
+ERIWKELENRPGTTVTVDLVSRTVECGDVTAPFQIDDDTRHRLLEGLDDIAVTLDHQDEI
+DAYERARPSYKPTTLPARTAG
+>PROKKA_01965
+MDKFTTHTGIGVPLRASNVDTDQIIPAVYLKRVSRTGFEDALFAGWRQDPDFILNTEPYS
+AGSVLVAGPDFGTGSSREHAVWALKDYGFKVVVSSRFADIFRGNSAKQGLVAAQVEPEDV
+ERIMKQLENQPGAAVTVDLEHLTVECGGVTAAFEIDEDARHRLLHGLDDIAITLSHADAI
+AAYEAGRPSYKPTTLPARTAD
+>PROKKA_00823
+MEKFTTHTGVGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS
+GGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV
+ERIWKELENRPGTPVTVDLVTRTVECGDVTAPFQIDDDTRHRLLEGLDDIAVTLGHQAEI
+DAYEADRPAYKPTTLPARTAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000754.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000754.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09ec782a368158d0afef3f5284b4bd97ae1fb733
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000754.fa
@@ -0,0 +1,36 @@
+>PROKKA_00867
+MSDPRTVAVLGAGSWGSAFARVLGLSTSPESARASEIVMWSRRAEVAEAITERHENPEYL
+PGITLPTCVRAVTDAAEAVRGAGVVVVAVPAQHVRETLRTVRADLAPDAVVVSLVKGLER
+GTDARMSQVCAEELGLSPDRFAVVSGPNLALEIARGEPTATVVASASRATAERIAALTAG
+RTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG
+GDTDTMAGLAGLGDLVATCASPLSRNRTAGRHIGTGLSAEEAVAAMSQTAEGIKSVSAIV
+HAARAHGVEMPISELMDRVVAGDVAVDRLAELLLARDLKSEGRTA
+>PROKKA_00589
+MSDPRTVAVLGAGSWGSAFARVLGLSTSPESARASEIVMWSRRAEVAEAITERHENPEYL
+PGITLPTCVRAVTDAAEAVRGAGVVVVAVPAQHVRETLHAVRADLAPDAVVVSLVKGLER
+GTDARMSQVCAEELGLSPDRFAVVSGPNLALEIARGEPTATVVASASRATAERIAALTAG
+RTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG
+GDPATMAGLAGLGDLVATCASPLSRNRTAGRHIGTGLSAEEAVAAMSQTAEGIKSVSAIV
+HAARAHGVEMPISELMDRVVAGDVAVDRLAELLLARDLKSEGRTA
+>PROKKA_02068
+MSDPQTVAVLGAGSWGSAFARVLGTSTSPEGARARDVVIWSRRPEVAEVVNRDHANPEYL
+PGIELPACVRAVTDAFEAVRGAGVVVVAVPAQHVRETLRTLREDLAPDAVVVSLVKGLER
+GTDARMSQVCTEELGLTPDRFAVVSGPNLALEIARGEPTATVVASGSSATAERIAALTAG
+PTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG
+GDPATMAGLAGLGDLVATCASPLSRNRTAGRHIGTGMSAEEAVAAMSQTAEGIKSVSAVV
+HVARAHGVEMPISELMDRVVAGDVAVHRLAELLLARDLKSEGRTA
+>PROKKA_01962
+MSPAPSAGPEPAFASASAGDRAGDPTRVAVLGAGSWGTAFACVLGSSTSPAGRRAREVVV
+WSRRAEVARAITEDHANPEYLPDVALPECVRAVTDAREAVAEAGVVVVAVPAQQARTVLE
+GLADALAPDAIAVSLMKGLERGTDARPSQVCQEALGIGPERFAVLSGPNLALEIARGEPT
+ATVVASASRATADRVAALTAGPTFRPYTNGDVVGVEIGGIVKNVIALAVGICDGQGLGDN
+SKASVITRGLAETTRLAVALGGEASTLAGLAGLGDLVATCASPLSRNRSAGRLMGTGLSA
+DEAVAAMKQTAEGIKSVSAVVHVARAHGVEMPISEAMDRVVAGTLDVDRLAGLLLARDLK
+SEGRHA
+>PROKKA_00826
+MSDPRTVAVLGAGSWGSAFARVLGLSTSPEPARASEIVMWSRRAEVAEAITERHENPEYL
+PGITLPTCVRAVTDAAEAVRGAGVVVVAVPAQHVRETLRTVRADLAPDAVVVSLVKGLER
+GTDARMSQVCAEELGLSPDRFAVVSGPNLALEIARGEPTATVVASASRATAERIAALTAG
+RTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG
+GDPATMAGLAGLGDLVATCASPLSRNRTAGRHIGTGLSAEEAVAAMSQTAEGIKSVSAIV
+HAARAHGVEMPISELMDRVVAGDVAVDRLAELLLARDLKSEGRTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000760.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000760.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08ca3c3476d29222e01d8404ce5f501debfc2ebe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000760.fa
@@ -0,0 +1,25 @@
+>PROKKA_00873
+MSRIIAGAAAGRPLTAVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLYAGSGALGC
+EAASRGAASVLLVERDRKAVTACRANAALVNRARGADVVRVRAGSVEQALAAEAAPVDLI
+LADPPYPVAGPPLEAVVEAAAERLAPGGLLVLERAARDAAPRRPRGLEEVEVRVYGETAL
+YLWQDER
+>PROKKA_00595
+MSRIIAGAAAGRPLTAVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLYAGSGALGC
+EAASRGAASVLLVERDRKAVTACRANAALVNRARGADVVRVRAGSVEQALAAEAAPVDLI
+LADPPYPVAGAPLEAVLEAAAGRLAPGGLFVLERAARDAAPRRPRGLEEVEVRVYGETAL
+YLWQDER
+>PROKKA_02062
+MSRIIAGAAAGRPLTSVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLFAGSGALGC
+EAASRGAASVLLVERERRAVAACRANAALVNRARGADVVQVRAGTVEQALAAGGEPADLI
+LADPPYPLAGPALEAVLEAAAARLTPGGLIVLERAARDAPPRRPAGLEEVEVRAYGETAL
+YLWQDER
+>PROKKA_01956
+MSRIIAGAAAGRPLRSVPGTGTRPTTDRTKEALFSWLQARDWLDGTRVLDLYAGSGALGC
+EAASRGAAHVTLVEKARRAAEVCRANAAALNAVLGAPVVQVAASSVEQALALPGDSADLI
+LADPPYPESGPAFHAVLAAAAARLAAGGLLVLERSARDPAPERPAGLEQVEVRTYGETAL
+YFWQDEG
+>PROKKA_00832
+MSRIIAGAAAGRPLTAVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLYAGSGALGC
+EAASRGAASVLLVERDRKAVTACRANAALVNRARGADVVRVRAGSVEQALAAEAASVDLI
+LADPPYPVAGPPLEAVVEAAAGRLAPGGLLVLERAARDVAPRRPRGLEEVEVRVYGETAL
+YLWQDER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000764.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000764.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be5375e793edacdb3343779989cb44de505d5503
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000764.fa
@@ -0,0 +1,25 @@
+>PROKKA_00877
+MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWPAPAGVSTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER
+>PROKKA_00599
+MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWPAPAGVSTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER
+>PROKKA_02058
+MDTTQRQDADSSWVIPVRDLTRGAGVQRELTAQWPAPAGVTTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECSRCLLPLHEGITVDLQELYLTGASEDEAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER
+>PROKKA_01952
+MATTVPSGAPSPWVLSVRDLARGAGVQRELTTRLPAPAAVSMPMLGIPEGDPVDLELRLE
+AVHEGVLVTGTAHADLTGECSRCLLPLHEGITVDLQELFLADPPAEGDDEQPLVEHETVD
+LEPVFRDAVVTALPFQPLCRPDCEGLCADCGIRLEDAPAGHAHERVDPRWAALAALADTT
+EETSITETEKR
+>PROKKA_00836
+MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWRAPAGVSTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000768.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000768.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b25fd8ad1d76595939050da7a2ae274c7857972
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000768.fa
@@ -0,0 +1,40 @@
+>PROKKA_00881
+MSHPPAASWTPEPLPRPEPPRDDAPPVARRRRRWPWVVGLLAVLLAALLGLGAWYTSSLG
+RTFDDHRQTVDVGALEQAAGNGPLNVLVLGSDSREGEGEQDMGQRSDTMMLVHIPADRRQ
+VYVMSVLRDSWVTVPGHGEAKINSAFDTGGYTLAVDTVELLLGVSIHHVLEVDFQGFRGV
+TNALGGVEVCNPRAFSSGQANPSYYPRGHILLQDTAALRYVRERHAFDDGDVTRVENQQR
+YLAGAMDRFLSPQILGNPARTTEVVATFSDHLGVDEGLTSGVIASLAWQLRDVRGEDVEM
+FTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDDVQRYVDEHEPTKEKKAQAAGGPAP
+VLTLLTGTTPAPVLGEDPCDD
+>PROKKA_00603
+MSHPPAASWTPEPLPRPEPPRDDAPPVARRRRRWPWVVGLLAVLLAALLGLGAWYAGSLG
+RTFDDHRQTVDVGALEQAAGDGPLNVLVLGSDSREGEGEQDMGQRSDTMMLVHIPADRRQ
+VYVMSVLRDSWVTVPGHGEAKINSAFDTGGYALAVDTVELLLGVPIHHVLEVDFQGFRGV
+TNALGGVEVCNPQAFSSGQANPSYYPRGHILLQDTAALRYVRERHAFDDGDVTRVKNQQR
+YLAGAMDRFLSPQILGNPARTTEVVATFSDHLGVDEGLTSGVIASLAWQLRDVRGEDVEM
+FTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDDVQRYVDEHEPEKEKKAQAAGGPAP
+VLTLLTGTTPAPALGENPCDD
+>PROKKA_02054
+MSQPPAASWTPEPLPRPARSPEPPRPARRRRWPWVLGVLAAVLVVLLALGAWYAVSLART
+FDDHRQTVDAGALEQAGGGEPVNVLVLGSDSRGGEGEEDMGERSDAMMLVHLPADRSQVF
+VMSVLRDSWVEIPGHGEAKVNAAFDLGGYPLAVDTVEQLLGVPVHHVVEMDFQGFRGVTN
+ALGGVEVCNPVAFSSGQTSPSYYPRGPVLLQDTAALRYVRERHAFDDGDVSRVQNQQRYL
+AGAVERFLSPQILGNPARTTEVVATFSDHLGVDAGLTSGVVASLAWQLRGVRAGDVEMFT
+VPRAGFGYSPDGDSIVELDEAKLADLRSALKDDDVQRYVAEHESEDGQDASAAGADPAPV
+LALLAQPAPTPAVGEDPCAD
+>PROKKA_01948
+MTQPPQQPWIPPERPGGAADPLEGLRGPAPAAPPTSTPPATRRSGGGRARRRRPLRRFLA
+VLGVLALLLVVALGAYGLLLARTFDGHRQTVSAAAFADPGNDGPVNFLVLGSDSRAAEDS
+AETSQRSDTMMLVHVPADRRHVYVISVLRDSLVEIPGRGQRKANAAYELGGPELTAAMLD
+KLLGVPVHHLAELDFQGFRGMTTALGGVEVCNPHAFSSGQKNPSFYPRGRIELKDTAALR
+YVRERHAFPEGDVMRVQNQQRFVRGAVAAFLDPAVVLNPPRAVDVVAGLSDHLTVDEGLD
+SATLASLAWQLRGVDRSALTMFTVPRAGYGTSPDGQDVVLLDADRMAALRDALQRDDVES
+YLRAHDPEALAAGEDVQPALAAAPGATPLLTELAAAPPAGEGTLLGEDPCGG
+>PROKKA_00840
+MSHPPAASWTPEPLPRPESPRDDASSVARRRRRWPWVVGVLAVLLAALLGLGAWYAGSLG
+RTFDDHRQTVDVGALEQAAGNGPLNVLVLGSDSREGEGEQDMGQRSDTMMLVHIPADRRQ
+VYVMSVLRDSWVTVPGHGEAKINSAFDTGGYALAVDTVELLLGVPIHHVLEVDFQGFRGV
+TNALGGVEVCNPQAFSSGQANPSYYPRGHILLQDTAALRYVRERHAFDDGDVTRVKNQQR
+YLAGAMDRFLSPEILGNPARTTEVVATFSDHLGVDEGLTSGVIASLAWQLRDVRGEDVEM
+FTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDDVQRYVDEHEPTKEKKAQAAGGPAP
+VLTLLTGTTPAPALGEDPCDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000769.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000769.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b5754ba6b04a97b7d09d300466bc9963e7d0d46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000769.fa
@@ -0,0 +1,40 @@
+>PROKKA_00882
+MTTESRRPRLLLVSHSYRPERTPPARRWGAVVAALRSAGWDVDVVAPGGVRPFAGPDGER
+VLPTPRLPLGEAGRNGRFAEAVVHALLAVPRGMATRRPDVVVATVPALPVVVPGVVLSRL
+WRRPLVLEMRDAWPDLAHEAGVHQGLLGAAMERVVTGGQRAARLVVTVTDGFAETLRGRG
+VRVVRTLGNGVDLARLAVAPRRERAAGELHVLYLGNMGESQGLERLIDAAATLRRTRPGV
+RVRLVGEGTRRPALEARNAELGSPAEILGPVHGAAVAEQYAWADTLVVALRPDWPSFRHT
+VPSKTYEVLAVGRHVTGLVTGEAARTLEAAGGADVIGPDVDDLVRHLTALADDPHRTDVG
+AGGRDWVRRHADLPAVARRYERVLRRVAGR
+>PROKKA_00604
+MTTEPRRPRLLLVSHSYRPERTPPARRWGAVVAALRSAGWDVDVVAPGGVRPFAGPDGER
+VLPTPRLPLGEAGRNGRFAEAVVHALLAIPRGMATRRPDVVVATVPALPVVVPGVVLSRL
+WRRPLVLEMRDAWPDLAHEAGVHQGLLGVAMERVVTGGQRAARLVVTVTDGFAETLRGRG
+VRVVRTLGNGVDLARLAVAPRRERDAGELHVLYLGNMGESQGLERLIDAAATLRRTRPGV
+RVRLVGEGTRRPALEARNAELGSPAEILGPVHGAAVAQQYAWADTLVVALRPDWPSFRHT
+VPSKTYEVLAVGRHVTGLVTGEAARTLEAAGGAEVIGPDVDDLVRHLTALADDPHRTDVG
+AGGRDWVRRHADLPAVARRYERLLRRVAGR
+>PROKKA_02053
+MPTEPRRPRVLLITHSYRPERTPPARRWAAVVAALRAGGWDVDVVAPGGLRAVAGDDGER
+ILRTPRLPAGRSGRNGRFLEAAVHAVLAVPRGLAARRPDVVVATVPALPVVVPGVVLSRL
+WRRPLVLEMRDAWPDLAHEAGVHQGLLGVAMERVVTGGQRAARLVVTVTDGFAETLRGRG
+VERVETLCNGVELAGLARAPARRREPGDLHVLYLGNMGESQGLERLVEAAAELRQSRPGV
+RVRLVGAGTRRGELEARNAELGSPAEILPACYGEEAAAQYAWADTLVVALRPDWPSFRHT
+VPSKTYEVLAVGRHVTGMVTGEAARTLEDAGGADVIGSRVADLVAHLTALADDPARTDVG
+EGGRPWVRLHADLPSVARRYVRLLGQLVPDYRRHA
+>PROKKA_01947
+MGERRTRAGGRAPRLLLVTHSYRPERTPPARRWAAVVQALRAAGWEVDVLVPGGLRTRVG
+EHGERLRPTPRLLGSGDGRNGRFAAAAVHAVLAVPRGLVLPRPDVVVATLPALPVVVAGR
+ALAVLRRRPLVVEMRDAWPDLAREAGVHPGLLGTLMERVVTGGQRAADLVVTVTEGFAAT
+LRGRGMRRVEVLANGVDLERVPVAPPRDRTAGELHVLYLGNLGESQGLERLVEAAARQRA
+THPGVHVRIVGDGTRRAALEALNAELEAGVEFVPPVSGAALTEQYAWADTLVVCLRPDWP
+SFRHTIPSKTYEALAVGRHVTGQLSGEAALMLERSGAADVVGPGVEDLVAHLDALADDPA
+RTRVGDAGRRWAAAHGDLPTTARRYEALLRRVAARPSRRTRTETTA
+>PROKKA_00841
+MTTEPRRPRLLLVSHSYRPERTPPARRWGAVVAALRSAGWDVDVVAPGGVRPFAGPDGER
+VLPTPRLPLGEAGRNGRFAEAVVHALLAIPRGMATRRPDVVVATVPALPVVVPGVVLSRL
+WRRPLVLEMRDAWPDLAHEAGVHQGLLGAAMERVVTGGQRAARLVVTVTDGFAETLRGRG
+VERAETLCNGVELAGLAWAPARRREPGDLHVLYLGNMGESQGLERLMEAAAELRQSRPGV
+RVRLVGAGTRRGELEARNAELGSPAEILPACYGEDAAAQYAWADTLVVALRPDWPSFRHT
+VPSKTYEVLAVGRHVTGMVTGEAARTLEDAGGADVIGPRVADLVAHLTALADDPARTDVG
+EGGRPWVRRHADLPSVARRYVRLLGQLVPDYRRHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000770.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000770.fa
new file mode 100644
index 0000000000000000000000000000000000000000..617f49026b341014355c53e3a691b95acdd4ccf3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000770.fa
@@ -0,0 +1,41 @@
+>PROKKA_00885
+MKKIETVAVIGLGYIGLPTAAILAENGVRVLGVDVSDRTVDAVNAGTVPFVEPDLAGFVA
+RGVEKGLLSASTTTPAADAYIVAVPTPFKDGHSPDLGYIEAAARGLAPQLTGDELVILES
+TSPPGATEYMAEVIFAERPELREAELDFAHCPERVLPGRVMVELVTNDRIVGGSTRRAAE
+RARDLYRTFCEGEILLTDTRTAEMAKLVENSFRDVNIAFANELSVICAEQGIDVWELIEL
+ANHHPRVNILQPGPGVGGHCIAVDPWFIVDAAPQTARLIRAAREINDGKPQWVIDQVKAA
+AFDVQQATGRAPVVAALGLAFKPNIDDLRESPALNIAAELAGQFSGSDVLVVEPHVTELP
+AALQGKDNVRLVAVDEALEAADIVVLLVDHSAFADLGDRVADKRVIDTRGQWRTDPSL
+>PROKKA_00607
+MKKIETVAVIGLGYIGLPTAAILAENGVKVLGVDVSDRTVDAVNAGTVPFVEPDLAGFVA
+RGVEKGLLSASTTTPAADAYIVAVPTPFKDGHSPDLGYIEAAARGLAPQLTGDELVILES
+TSPPGATEYMAEVIFAERPELREAELDFAHCPERVLPGRVMVELVTNDRIVGGSTRRAAE
+RARDLYRTFCEGEILLTDTRTAEMAKLVENSFRDVNIAFANELSVICAEQGIDVWELIEL
+ANHHPRVNILQPGPGVGGHCIAVDPWFIVDAAPQTARLIRAAREINDGKPQWVIDQVKAA
+AFDVQQATGRAPVVAALGLAFKPNIDDLRESPALNIAAELAGQFSGSDVLVVEPHVTELP
+AALQGKDNVRLVAVDEALEAADIVVLLVDHSAFADLGDRVADKRVIDTRGQWRTDPSL
+>PROKKA_02051
+MTTQIKDVAVIGLGYIGLPTAAILAENGVRVHGVDVSQRTVDAVNAGTVPFVEPDLADFV
+ERNVKAGRLSASLKTPQADAYIVAVPTPFKDGHSPDLGYIEAAARGLAPQLRGGELVILE
+STSPPGATEHMAAVIREARPDLDGATLDFAHCPERVLPGRVMIELVTNDRIVGGSTPEAA
+QRAKQLYETFCQGEILVTDCVTAEMAKLVENSFRDVNIAFANELSLICSDLGIDVWELIE
+LANHHPRVDILQPGPGVGGHCIAVDPWFIVDAAPQTARIIRAAREINDGKPKWVVDQAKA
+AAFDVQQATGRAPVVAVLGLAFKPNIDDLRESPALNIATEVAQQFTGSRILVVEPHVEEL
+PAALAGRDNVELVPAEDGIREADVVLLLVDHDAFASLGTTTEGKKVIDTRGQWR
+>PROKKA_01945
+MMGTPPALRCRDVNARMGIQNVTQIKTVAVIGLGYIGLPTAAILAENGLTVHGVDVSPRT
+VDAVNAGKVPFVEPDLADFVERNVAAGRLDASLETPKADAYIVAVPTPFQGDHAPDLSYI
+EAAARGLAPQLTGDELVILESTSPPGATDHMADVIREVRPDLKDAPLDFVHCPERVLPGR
+VMVELVTNDRIVGGSTPAAAERARDLYRSFCEGEILLTDCRTAEMAKLVENSFRDVNIAF
+ANELSLICAEQGIDVWELIGLANHHPRVNILQPGPGVGGHCIAVDPWFIVDAAPQTARII
+RAAREINDAKPQWVIERAKAAAFDVQQKEGRPAVVAALGLAFKPNIDDLRESPALNIAAQ
+LADEFSGSTVLVSEPHVDELPAKLQGKENVRFVPAEQAVAEADVVLLLVDHDAFAGLGEQ
+TAGKRVIDTRGQWR
+>PROKKA_00843
+MTTQIKDVAVIGLGYIGLPTAAILAENGVRVHGVDVSQRTVDAVNAGTVPFVEPDLADFV
+ERNVKAGRLSASLKTPQADAYIVAVPTPFKDGHSPDLGYIEAAARGLAPQLRGGELVILE
+STSPPGATEHMAAVIREARPDLDGVTLDFAHCPERVLPGRVMIELVTNDRIVGGSTPEAA
+QRAKQLYEAFCQGEILVTDCVTAEMAKLVENSFRDVNIAFANELSLICSDLGIDVWELIE
+LANHHPRVNILQPGPGVGGHCIAVDPWFIVDAAPQTARIIRAAREINDGKPKWVVDQAKA
+AAFDVQQATGRAPVVAVLGLAFKPNIDDLRESPALNIAIEVAQQFTGSRILVVEPHVEEL
+PAALAGRDNVELVPAEDGIREADVVLLLVDHDAFASLGATTEGKKVIDTRGQWR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000775.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000775.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e63b2dfa85b940699bd1274cc55b9db9d052faeb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000775.fa
@@ -0,0 +1,40 @@
+>PROKKA_00902
+MCETGHVEIVLIISVVLALLVGGLIVGLLDRRPAPPKGSYQGVRDADDPRPGPRHAAPGG
+STAVLERPDAEEATVDVAEPEVVEEVETAPAAPELERPEAAGSRLSRLRARLLKSNNVFG
+KGLLALLSQDRIDEDVWDEIEETLLMADLGTEPTMELVDRLKARVTVEGTRDPEQVRALL
+REELVAMVDPSMDRRLAATRRDGRPAVTLVVGVNGVGKTTTVGKLARVLVAEDRDVVLGA
+ADTFRAAAAEQLATWGARVGVPTVRSEKEGADPASVAFEAVAEGIRAEADVVLVDTAGRL
+QNKSNLMDELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLD
+GTAKGGIVVAIQRQLGVPVKLIGLGEGADDLAPFTAEGFVDALLAD
+>PROKKA_00621
+MLIVSVVAALLLGGVLVGLLDRRPAPPKGSYQGVRDADDPRPSPRHAAPSGSTAVLERPE
+VDEAPAVVAEPEPAVVEEVEPAPAKPEYERPEAAGSRLARLRARLLKSNNVFGKGLLALL
+SQDRIDDDVWDEIEETLLMADLGTEPTLELVDRLKARVTVEGTRDPEQVRTLLREELVAM
+VDPSMDRRLAATRKGDRPAVTMVVGVNGVGKTTTVGKLARVLVAEDRTVVLGAADTFRAA
+AAEQLATWGARVGVETVRSEKEGADPASVAFEAVELGIAEGVDVVLVDTAGRLQNKANLM
+DELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLDGTAKGGI
+VIAIQRQLGVPVKLIGLGEGPDDLAPFTAEGFVDALLTD
+>PROKKA_02040
+MCQTGHVEIVLIISVVLALLVGGLIVGLLDRRPAPPKGSYQGVRDADDPRPAPRHAAPGG
+STAVLERPEAEEAPVDLVEPEVVEEVEAEPAAPELERPEAAGSRLARLRARLLKSNNVFG
+KGLLALLSRDRIDEDTWDEIEETLLMADLGTEPTMVLVDRLKSRVTVEGTREPEQVRELL
+REELVAMVDPSMDRRLAASRRDGRPAVTLVVGVNGVGKTTTVGKLARVLVAEDRDVVLGA
+ADTFRAAAAEQLATWGARVGVPTVRSEKEGADPASVAYEAVAEGIRLEADVVLVDTAGRL
+QNKSNLMDELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLD
+GTAKGGIVVAIQRQLGVPVKLIGLGEGADDLAPFTAEGFVDALLAD
+>PROKKA_01938
+MITVIVISVVLALLLGVVLVGLLDRPVAPPKGTYTELRDSDDPAPAGLVADPSSAPAPEE
+ALEETGRAGSHAAAPVAEPVEAAEAPERQLERPEAAGTRLQRLRARLLKSNNVFGKGLLA
+LLSRDHIDEDVWDEIEETLLMADLGTEPTMELVDRLKARVTVDGTRDPESVRALLREELV
+AMVDPSMDRRLAATPHDGHPAVTMVVGVNGVGKTTTVGKLARVLVAEDRTVVLGAADTFR
+AAAAEQLATWGARVGVETVRSDVEGADPASVAFEAVKTGIEREADVVLVDTAGRLQNKAN
+LMDELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLDGTAKG
+GIVVAIQRQLGVPVKLIGLGEGADDLAPFSAEGFVDALLAA
+>PROKKA_00850
+MLIVSVVAALLLGGVLVGLLDRRPAPPKGSYQGVRDADDPRPSPRHAAPSGSTAVLKRPE
+VDEAPAVVAEPEPAVVEEVEPAPAKPEYERPEAAGSRLARLRARLLKSNNVFGKGLLALL
+SQDRIDDDVWDEIEETLLMADLGTEPTLELVDRLKARVTVEGTRDPEQVRTLLREELVAM
+VDPSMDRRLAATRKGDRPAVTMVVGVNGVGKTTTVGKLARVLVAEDRTVVLGAADTFRAA
+AAEQLATWGARVGVETVRSEKEGADPASVAFEAVEHGIAEGVDVVLVDTAGRLQNKANLM
+DELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLDGTAKGGI
+VIAIQRQLGVPVKLIGLGEGPDDLAPFTAEGFVDALLAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000784.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000784.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30ff176e3791c1d2b9d6f44a47383e3a12030991
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000784.fa
@@ -0,0 +1,26 @@
+>PROKKA_00911
+MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR
+GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ
+EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG
+TDPDAFATVPDAPAPEART
+>PROKKA_00630
+MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR
+GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ
+EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG
+TDPDAFATVPDAPAPEART
+>PROKKA_02031
+MSRPDHRLVPPAAGHAHDSGAAPADDAARPAGPTGALLGHAVPSGAGSQALPAEPGRGPL
+RAVLAVVVLTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPEPYPVRRGDVV
+VFDDTKGWLADGGHVIKRVVGLPGDTVSFTPGEAALRVNGVPVAEPYLAPGDAPAQDAFE
+ATVPAGRLWVLGDHRSASADSRAHRDGPGGGFVSLDDVVGRARFVVWPLDRIGGAGAAPE
+AFEAVPDARGAGS
+>PROKKA_01929
+MAEAPVTPAAAGTADPAAAPAAEHPGHPLRAAAVTVAVTLALLLAVQLLLVRMFAIPSAS
+MEPTLRPGDRVAVDLLVPGPLELRRGDVVVFRDARGWLAGAEAVHADPLHAAVAALGLGT
+QEGHLVKRVVGLPGDRVRWSPEDARLEVNGVPVDEPYVAGPAAQEAFDVVVPDGGLWVLG
+DHRSASQDSRQHQHGPGGGMVSVDDVVGRVEGVVWPLDRAGAVGPGPLAKLP
+>PROKKA_00859
+MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR
+GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ
+EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG
+TDPDAFATVPDAPAPEART
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000788.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000788.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba97a7e56f95f806fc84509a4bdb7752db2abb63
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000788.fa
@@ -0,0 +1,50 @@
+>PROKKA_00915
+MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE
+TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA
+RRQVTAPEPEPTRAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG
+ILPPLDRRTALECAALRSLRGGDARVRRRGGTSQGFDGEIDRTPPFEAPHHSASRSALVG
+GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ
+LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP
+ASETTSQVAVRVAAAADRQARRWATAAERGVVPPGLRRNAHVPAGVLRHGPYAVPRAARR
+PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA
+>PROKKA_00634
+MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE
+TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA
+RRQVTAPEPEPARAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG
+ILPPLDRRTALECAALRSLRGGDARVRRRGGTAQGFDGDIDRTPPFEAPHHSASRSALVG
+GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ
+LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP
+ASETTSQVAARVAAAADRQARRWATAAERGLAPSGLRRNAHVPAGVLRHGPYAVPRAARR
+PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA
+>PROKKA_02027
+MSGIGRTRSISLSGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGAGHDLAIVLAAYAADGRVRGVEGPVFLAELGLDGALHRSPE
+TVAMVMASVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVILAFGGEPEGEAPQRRP
+VRPADDDGAPGLGPGAPDLSEVAGQAEARFALEVAAAGAHHLLLRGAPGAGKTMLAERLP
+GILPPLDRRTALECAALRSLRGADALARRGVGQGSAGTRAAGDLDRTPPFEAPHHSASMA
+ALVGGGANLARPGAVSLAHGGVLFLDEAPEFERRALESLRQPLESGEVLLHRARGTVAYP
+ARFQLVLAANPCPCGKGGGNGVECRCSVTERRRYGQRLSGPLLDRVDLQVTVRPVQARQL
+AGAPAAETSAQVAARVAEAARRQAERWARAAEEGLVAPGLRRNAHAPAGVLRHGPYAVPR
+AARRAADEAVDHGLLSARGHARVLRLAWTLADLRGAETPAPEDTDVALTLRHQEEDET
+>PROKKA_01925
+MSGIGRTRSISLTGLRGTVVDVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGAAHDLAIVLAAYAADGRVQGVDGPVFLAELGLDGTLHRAPE
+TVAMVMAAVDAGHDRVVVAADAVAEAELVPGARVRGFAHLHEAILAFGGRPDASVARPSG
+PSGTAGRGPAAGQEGPSGPVPDLAEVAGQAEARFALEVAAAGGHHLLLSGPPGAGKTMLA
+ERLPGILPPLDDRTALETAALRSLRGLEPSARGLRRTPPFEAPHHSASMAALVGGGTGLG
+RPGAVSLAHGGVLFLDEAPEFERRALDALRQPLESGEMIVHRAHGSVAYPARFQLVLAAN
+PCPCGFGSGTGAHCRCTSLQRRKYAARLSGPLLDRVDVQVSVRPVRADQLAAAPEAEPSR
+AVAARVAAAVAAQDARWAAAAREGSLPPGVCRNAHVPAALLRSGRFAVPPEARATADRAV
+DRGELSARGHGRVLRLAWTLADLRGASCPEAQDVEIALQLRIRSEEDR
+>PROKKA_00863
+MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE
+TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA
+RRQVTAPEPEPTRAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG
+ILPPLDRRTALECAALRSLRGGDARVRRRGGTSQGFDGEIDRTPPFEAPHHSASRSALVG
+GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ
+LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP
+ASETTSQVAVRVAAAADRQARRWATAAERGVVPPGLRRNAHVPAGVLRHGPYAVPRAARR
+PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000789.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000789.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a5598bf4ba315763405c550ac7a42d42dede21a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000789.fa
@@ -0,0 +1,44 @@
+>PROKKA_00916
+MTTHVTPAADHVAGPRRPDAARLARAALTRLVEPGDALAVQTVTALGPERALALLTGRET
+IQPAERDLLADLAGAPDTLPRRWAAGLARWAPRAARLEPERDLVTLHRLGGGLLIPEDDA
+WPAALADLGEEAPLGLWFRGSGTLPPADRMLAVVGSREATAYGRTVTARCAAHAVQQGAC
+VISGGAYGIDGAAHRAALQAPAAPEDAADRDGVPPTVAVLAGGLDRFYPAGHEDLLRAVM
+AAGLLVSEMPPGASPTRYRFLQRNRVIAALAGAVLVVEARWRSGAQNTAGHAFGLGREVG
+VVPGPVTSPSSAGCHRLLQESPARLVTTEQEALALLGQGPARSGDTGGRTSARAAPEPAA
+RPTDGLTMEEALVHEALPLRQAVPADRITVSAGLALPTVLACLSRLQRAGLAERVEDRWR
+RG
+>PROKKA_00635
+MTTYVTPAADHVAGPRRPDAARLARAALTRLLEPGDALAVQTVTALGPERALALLTGRET
+IQPAERDLLADRAGAPDTLPRRWAAGLARWAPRAARLEPERDLVTLHRLGGGLLIPEDDA
+WPAALADLGEEAPLGLWFRGSGTLPPADRMLAVVGSREATAYGRTVTARCAAHAVQQGAC
+VISGGAYGIDGAAHRAALQALAAPGDAADRDGVPPTVAVLAGGLDRFYPAGHEDLLRAVM
+AAGLLVSEMPPGASPTRYRFLQRNRVIAALAGAVLVVEARWRSGAQNTAGHAFGLGREVG
+VVPGPVTSPSSAGCHRLLQESPARLVTTEQEALALLGQAPARSGGAGGRASTRAAPEPAT
+RPTDGLTMEEALVHEALPLRQAVPADRITVSAGLALPTVLACLSRLQRAGLAERVEDRWR
+RG
+>PROKKA_02026
+MTADTAHDHPVAAAQGPDTQRPDAHRPDTQRPDAQRPDTQRPDAARIARAALTRLVEPGD
+ALAVHAVAALGPERALVLLTGREAIQPAERDLLAEHAGAPDTLARRWSAGLDRWAPRAAR
+LDPVRDLVALHRLGGGLLVPEDEAWPAALDDLGEAAPLGLWFRGPGTLPPASRALAVVGS
+REATAYGRAVTTRLAAHAVQQGVCVVSGGAYGIDGAAHRAALAAPVGPEDPDAHDGPGGA
+SDRVPPTVAVLAGGLDRFYPAGHEDLLREVMAAGLLVSEMPPGASPTRYRFLQRNRVIAA
+LAGAVLVVEARWRSGAQNTAGHAFGLGREVGAVPGPVTSPSSAGCHRLLQETPARLVTSE
+TEALALLDGGAPAPRPGGTGGGNTAPPGDAPAPPPGGTGEGTRRPPRPPPPPRPCGSRTG
+>PROKKA_01924
+MTTAGETAQNARPDGPRVARAALTRLVEPGDDLALATVAALGPERALTLLTGAARIEAAE
+RDLLADRLGQDAFARRWSAGLARWAPRSARLDPVRDLVALHRLGGGLLIPEDPAWPAGLD
+DLGDAAPVGLWFRGRGTLPPLPRALAVVGSREATAYGRQVTRDVVACASAAGVCIVSGGA
+YGIDGAAHEAALETAAAAGRRSGPGSHDDAAPGVPPTVAVLAGGLDRFYPAGHERLLRAV
+MEEGLLLSEMPPGATPTRYRFLHRNRLIAALSGAVVVVEARWRSGAQNTAGHAHGLGREV
+GAVPGPVTSPSSAGCHRLLQEGPTRLIADPAQALTLLEPPRPGEPPAASPATTTRGEASR
+SPGRPTDGLTVEELLVHEALPLRRAVPVDNLTSSAGLALPTVLAVLTRLEGRRLAERRGD
+LWRRAPE
+>PROKKA_00864
+MTTHVTPAADHVAGPRRPDAARLARAALTRLVEPGDALAVQTVTALGPERALALLTGRET
+IQPAERDLLADLAGAPDTLPRRWAAGLARWAPRAARLEPERDLVTLHRLGGGLLIPEDDA
+WPAALADLGEEAPLGLWFRGSGTLPPADRMLAVVGSREATAYGRTVTARCAAHAVQQGAC
+VISGGAYGIDGAAHRAALQALAAPGDAADRDGVPPTVAVLAGGLDRFYPAGHEDLLRAVM
+AAGLLVSEMPPGASPTRYRFLQRNRVIAALAGAVLVVEARWRSGAQNTAGHAFGLGREVG
+VVPGPVTSPSSAGCHRLLQESPARLVTTEQEALALLGQGPARSGGAGGPSSTRAAPEPAA
+RPTDGLTMEEALVHEALPLRQAVPVDRITVSAGLALPTVLACLSRLQRAGLAERVEDRWR
+RG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000791.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000791.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6af2ce698810071e1c3775dfb82b1fdc54c49b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000791.fa
@@ -0,0 +1,20 @@
+>PROKKA_00918
+MTSTHTRGVVHILSAPTALCPHVEWALSSVLGPATSVEWEGQPVAPGQHRAEVHWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNIMVSEDRIRY
+AYEAGAGDPSVLMHELSLALGEAWDDELEPFRLAAAHANVRWLHRAV
+>PROKKA_00637
+MTSTHTRGVVHILSAPTALCPHVEWALSSVLGPATSVEWEGQPVAPGQHRAEVHWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNIMVSEDRIRY
+AYEAGAGDPSVLMHELSLALGEAWDDELEPFRLAAAHANVRWLHRAV
+>PROKKA_02023
+MTSTTTRGVVHILSAPTALCPHVEWALSSVLGPETPVEWQGQPVAPGQHRTELRWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNTMVSEDRIRY
+AYEAGAGEPAVLLHELSLALGEAWDEELEPFRLAAADANVRWLHRVG
+>PROKKA_01922
+MPDITTNGVVHLLSAPTAVCPHVEWTLTSVLGPGDPVDWRDQPAEAGTVCAELHWSAAQG
+SGARLASALRRWPGLRFEITETPSAGVDGSRWSHTPELGVFHATTDVSGNIMVSEERIRY
+AYEAGGGDPTVLVHELSLALGEAWDDELEPFRRAAAGAPVRWLHRAG
+>PROKKA_00866
+MTSTQTRGVVHILSAPTALCPHVEWALSSVLGPATSVEWEGQPVAPGQHRAEVHWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNIMVSEDRIRY
+AYEAGAGDPSVLMHELSLALGEAWDDELEPFRLAAAHANVRWLHRAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000792.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000792.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d0b6260b50a4e2a249912f212b74a9523853e966
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000792.fa
@@ -0,0 +1,40 @@
+>PROKKA_00919
+MTRTAVITGLGATTPIGGDVPTFWSHALQGVSGARTMEHDWVEKYELPVTFAAELAVPTS
+EVLSKVEQKRQDPATQMATVAAREAWKDAGLEGAEVDGDRLAVAFGTGIGGVWTLLDGWD
+TLRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLVRS
+GQADVVICGAAEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV
+IESEEHAKARGARVYAELAGAGVSSDSHHITAPEPEGLGATRAMRAALRSADITPEDVCH
+VNAHATSTPKGDAPEYLAMRAVFGDHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH
+GQAPVTINLDHQDPEIPLNVVTGSPARLPEGPRVAVKNSFGFGGHNAVAVFRSV
+>PROKKA_00638
+MTRTAVITGLGATTPIGGDVPTFWSHALQGVSGARTMEHDWVEKYELPVTFAAELAVPTS
+EVLSKVEQKRQDPATQMATVAAREAWKDAGLEGAEVDGDRLAVAFGTGIGGVWTLLDGWD
+TLRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLIRS
+GQADVVICGAAEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV
+IESEEHAKARGARVYAELAGAGVSSDSHHITAPEPEGLGATRAMRAALRSADIAPEDVCH
+VNAHATSTPKGDAPEYLAMRAVFGEHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH
+GQAPVTINLDHQDPEIPLNVVTGSPARLPEGPRVAVKNSFGFGGHNAVAVFRSV
+>PROKKA_02022
+MTRTAVITGLGATTPIGGDVPTFWSNALKGVSGARTMEHEWVEELGLPVTFAAELAVPTA
+DVLSKVEQKRQDPGTQMATVAAREAWRDAGLEGVELDGDRLAVAFGTGIGGVWTLLDGWD
+ILRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLIRS
+GQADVVICGASEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV
+VESEEHARARGARVYAELAGTGVTSDSHHITAPEPEGLGATRAMRAALKAADLTPEDVCH
+VNAHATSTPKGDAPEYLAMKAVFGDHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH
+GQAPVTINLENQDPEIPLNVVTGSPAQLPEGPRVAVKNSFGFGGHNAVAVFRSV
+>PROKKA_01921
+MTRTALITGLGATTPIGGDVPTFWANAQKGVSGAATMQHEWVEQYDLPVTFAAELAVPTS
+EVLSKVELKRQDPSTQMATVAAREAWADAGLADADVDPERLAVAMGTGIGGVWTILDAWD
+ALRERGPRRVMPMTVPMLMPNGAAGALSLEFGARAGARTVVAACAAGTEALDTALTLIRT
+GQADVVLCGATEAAVHPMPMAAFAAMQALSKRNDDPQSASRPYDVDRDGFVLGEGAGVMV
+VESEEHAAARGARVYARLAGTGVTSDSHHITAPEPEGLGATRAMRRALADAGLRPEDVGH
+VNAHATSTPKGDAPEYLAMKAVFGTGLDDVLVSATKSQTGHLLGASGAIESILSVLAVHH
+GVAPVTINLENQDPEIPLNVVTGTPAALPADRRVVVKNSFGFGGHNAVAVFTGV
+>PROKKA_00867
+MTRTAVITGLGATTPIGGDVPTFWSHALQGVSGARTMEHDWVEKYELPVTFAAELAVPTS
+EVLSKVEQKRQDPATQMATVAAREAWKDAGLEGAEVDGDRLAVAFGTGIGGVWTLLDGWD
+TLRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLVRS
+GQADVVICGAAEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV
+IESEEHAKTRGARVYAELAGAGVSSDSHHITAPEPEGLGATRAMRAALRSADITPEDVCH
+VNAHATSTPKGDAPEYLAMRAVFGDHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH
+GQAPVTINLDHQDPEIPLNVVTGSPARLPEGPRVAVKNSFGFGGHNAVAVFRSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000793.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000793.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b58a7b20c84ebc47780b2d2c32c8212e1dc1ff8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000793.fa
@@ -0,0 +1,15 @@
+>PROKKA_00920
+MASKEEILAGLAEIVNEETGLDTAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDGAQA
+>PROKKA_00639
+MASKEEILAGLAEIVNEETGLDAAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDGAQA
+>PROKKA_02021
+MASKEEILAGLAEIVNEETGLDTADVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDNAQA
+>PROKKA_01920
+MASKEEILAGLAEIVNEETGLETADVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDQAQA
+>PROKKA_00868
+MASKEEILAGLAEIVNEETGLDTAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDGAQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000794.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000794.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27635b5fecb35cbcce2b7145d61d2922c9aa846b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000794.fa
@@ -0,0 +1,35 @@
+>PROKKA_00921
+MTVTLKQHERPAASRIVAVGAYRPANLVPNEDLIGPIDSSDEWIRQRTGIVTRQRATAEE
+TVPVMAVGAAREALERAGLQGSDLDAVIVSTVTFPHATPSAAALVAHEIGATPAPAYDVS
+AACAGYCYGVAQADALVRSGTARHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA
+DEPGISPSVWGSDGERWSTISMTHSQLELRDAVEHARTTGDASAITGAEGMLWPTLRQDG
+PSVFRWAVWSMAKVAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD
+IADAGNTSAASIPLAMHRLLEENPELSGGLALQIGFGAGLVYGAQVVRLP
+>PROKKA_00640
+MTVTLKQHERPAASRIVAVGAYRPANLVPNEDLVGPIDSSDEWIRQRTGIVTRQRATAEE
+TVPVMAVGAAREALERAGLQGSDLDAVIVSTVTFPHATPSAAALVAHEIGATPAPAYDVS
+AACAGYCYGVAQADALVRSGTARHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA
+DEPGISPSVWGSDGERWSTISMTHSQLELRDAVEHARTTGDASAITGAEGMLWPTLRQDG
+PSVFRWAVWSMAKVAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD
+IADAGNTSAASIPLAMHRLLEENPELSGGLALQIGFGAGLVYGAQVVRLP
+>PROKKA_02020
+MTVTLKQHERPAASRIVSVGAYRPKNLVPNEDLVGPIDSSDEWIRQRTGIVTRQRATAGE
+TVPAMAVAAGREALERAGLTGADLDAVIVSTVTFPHATPPRPPSWPTSSAPPPAPAFDVS
+AACAGYCYGVAQADALVRAGTAKHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA
+DEPGISPSVWGSDGERWETISFTHSQLELRDVVEQARTSGDASAITGSEEMVWPTLRQDG
+PSVFRWAVWSMAKVAREALDAAGVEPEDLVAFIPHQANMRIIDEFAKQLKLPESVTVARD
+IADAGNTSAASIPLAMHRLLEEDPSLSGGLALQIGFGAGLVYGAQVVRLP
+>PROKKA_01919
+MTVTLKQHERPAGSRIVSVGAYRPATLVPNEDLVGPIDSSDEWIRQRTGIVTRQRATPEE
+TVVTMAVGAGREALQRAGLEASDLGAVVVATVTFPYPTPSAAAAVADALGATPAPAYDIS
+AACAGYCYGVAQADALVRAGSAQHVLVVGVERLSDFIDPTDRSISFLLGDGAGAVVVSAS
+DEAGIAPSVWGSDGSRWSTISPTRSLLDLRAEVEHARETGDASAIIGAEEMLWPTLRQDG
+PSVFRWAVWSMAEKAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD
+IAEAGNTSAASIPLAMHRLLQEHPELSGGLALQIGFGAGLVYGAQVVRLP
+>PROKKA_00869
+MTVTLKQHERPAASRIVAVGAYRPANLVPNEDLIGPIDSSDEWIRQRTGIVTRQRATAEE
+TVPVMAVGAAREALERAGLQGSDLDAVIVSTVTFPHATPSAAALVAHEIGATPAPAYDVS
+AACAGYCYGVAQADALVRSGTARHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA
+DEPGISPSVWGSDGERWSTISMTHSRLELRDAVEHARTTGDASAITGAEGMLWPTLRQDG
+PSVFRWAVWSMAKVAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD
+IADAGNTSAASIPLAMHRLLEENPELSGGLALQIGFGAGLVYGAQVVRLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000796.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000796.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba37abf61a4322cfb7ea3f47dc8f2e8e58a31b38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000796.fa
@@ -0,0 +1,40 @@
+>PROKKA_00923
+MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA
+LQGFLTWFERPTSTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAER
+DQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRAT
+ALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDAR
+AVGEALAPWFAPGPVIVGPVVDSLVSAHVSARHTLAGLSAAAAHPRASRPTPAEDLLPER
+ALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRLK
+RVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGTGSD
+>PROKKA_00642
+MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA
+LQGFLTWFERPTSTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAER
+DQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRAT
+ALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDAR
+AVGEALAPWFAPGPVIVGPVVDSLVSVHVSARHTLAGLSAAAAHPRASRPTPAEDLLPER
+ALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRLK
+RVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGAGSD
+>PROKKA_02018
+MPEPRSAASRPVSTEGRARLRSHLGALNTAVLQRLDATLPWYRGLTPDERSALGLVAQRA
+LQGFISWFDRPKTTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAER
+DQAPIREHVLHYSREVAFALADVYARAAEMRGAMDSRLEAVLLDAVLRGQDPDEIRHRAT
+ALGWRGDHRVMVMAGLAPGQDQPAFIPGLRRAAAKLDCDLLVGVQAERLVLVIGSVTDAQ
+VVGEALTPWFAPGPVILGPVVDSLVEAHVSARHTLAGLGAAPAHPRAIRPTPAEDLLPER
+ALLGDPTACEALVEGVYAPLADAGTALLDTVDAYGALGHSLEGTARELFVHANTVRYRLK
+RVAEVTGWDPLVPRDAYVLQTAVTLGRLAGSRPGVAEASA
+>PROKKA_01917
+MPAPRPSAPRRVSADGLARLRAHLGTFNTATLRRLDETLPWYRELTPDERSALGLIAQRA
+LQGFITSFERPQTTTVDVLRDVFGQSPTELTRAISLHRALQLIRTIVDVVETGVPDAVSE
+ADQPVVAEHVLHYSREIAFAIADVYARAAELRGAMDSRLEAVLLDAVLRGQEPDEIQHRA
+TAFGWRGGDGVMVMAGSARDGATAAFLPGLRRDAARLQCELLVGVQSRRLVLVVGSVSDP
+DAVAEALLPWFADGPVIVGPVVDSLLEAHVSAHHALAGLGAAAAHPRAGRPARSDDLLPE
+RALAGDATACAALVDGVYAALADAGPSLLETVDVYTACGHSLEGTARELYVHANTVRYRL
+RRAAEVTGWDPQRPRDAYVLQTAVALGRLSEGAPRL
+>PROKKA_00871
+MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA
+LQGFLTWFERPTSTGHVLQDVFGPAPTDLTRAISLHRALQLIRTMVDVVETRVPELLAER
+DQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRAT
+ALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDAR
+AVGEALARWFAPGPVIVGPVVDSLISAHVSARHTLAGLSAAAAHPRACRPTPAEDLLPER
+ALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRLK
+RVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGTGSD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000798.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000798.fa
new file mode 100644
index 0000000000000000000000000000000000000000..79caf4574bd665d7b896582e1f7161df2ef7259a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000798.fa
@@ -0,0 +1,20 @@
+>PROKKA_00925
+MQAGSTPTSTDSALLAELALSRGDLVQEWGYDDDVDVTFRDALEDALGEELLTEDDQEPA
+DAVLFWWRADDGDVMDLADALVDAQRSLDAGPVWIMTPRKGRPGHVSPADVAEAASTAGL
+HATTGAGASEDWAAQKLVQKRGG
+>PROKKA_00644
+MQAGSTPTSTDSALLAELALSRGDLVQEWGYDDDVDVTFRDALEGALGEELLTEDDQEPA
+DAVLFWWRADDGDVMDLADALVDAQRSLDAGPVWIMTPRKGRPGHVSPADVAEAASTAGL
+HATTGAGASEDWAAQKLVQKRGG
+>PROKKA_02016
+MEAGSTPTSTDSALLAELALAQGDLVQEWGYDDDVDFTFRDGLEDALGEELLTEEDQEPA
+DAVLYWWRAEDGDVTDLADALVDAQRSLDSGPVWLMTPRKGRAGHVNPADVQEAAGTAGL
+HATTGAGVSEDWAAQRLVQKRGG
+>PROKKA_01915
+METPSDGTSTHQELLDAYGLTAGELVQEWGYDDYIDFDFRDALEDALGEELLTEEDQEPA
+DAVLFWWRTDDGDVSDLTDALVDAQRSLDAGPVWLMTPRNGRPGHVSPTDVAEAAATAGL
+HVTTGAGGSADWAAVRLEKRGG
+>PROKKA_00873
+MQAGSTPTSTDSALLAELALSRGDLVQEWGYDDDVDVTFRDALEDALGEELLTEDDQEPA
+DAVLFWWRADDGDVMDLADALVDAQRSLDAGPVWIMTPRKGRPGHVSPADVAEAASTAGL
+HATTGAGASEDWAAQKLVQKRGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000799.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000799.fa
new file mode 100644
index 0000000000000000000000000000000000000000..95a70e6944b1be691a21f21d435d314fbbd0394f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000799.fa
@@ -0,0 +1,20 @@
+>PROKKA_00926
+MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL
+GWIGALAEDVAVDDVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF
+DVETGRPRRVSVLLDADGVEAARVVAAPGQARTRSEHEAATRDLLADR
+>PROKKA_00645
+MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL
+GWIGALAEDVAVDEVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF
+DAETGRPRRVSVLLDADGVEAARVVAAPGQARTRGEHEAATRDLLVDR
+>PROKKA_02015
+MAEEPGAVPALRDDRGQDWPWPPTRGPEDAAAPRATWLVLLPGAFTPVCTGELGWLGELA
+TDLAADDVAVRVIACDAAPVLRRVREELGLPEDLVLLSDFWPHGAACAALDAFDAASGRA
+RRVSVLLDADGVEVSRVTAAPGRPRSRTEHEAATRALLGDR
+>PROKKA_01914
+MAEPALRDIHGTPWPWPPVVSGERAAWLVFLPGAFTPVCAGELAWLGPLAVELAAEDVGL
+RVVSCDAAPVLREVADRTGLPAECVLLSDFWPHGAAAARFGLLDETTGRPRRVSVLVDES
+GTELVRVRPGEPGGPRTAQAHRRAAEGALGRRR
+>PROKKA_00874
+MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL
+GWIGALAEDVAVDDVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF
+DVETGRPRRVSVLLDADGVEAARVVAAPGQARTRSEHEAATRDLLADR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000804.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000804.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c96c523269b6b02d330e062a02d82ee16710f5e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000804.fa
@@ -0,0 +1,35 @@
+>PROKKA_00932
+MELLQPDAPRENLREFIDKLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYETRMTR
+EEYELEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHMNPRTARVVA
+LNKPSDRELGQWYFQRYIQHFPTAGEIVLFDRSWYNRAGVERVMGFATDEQYRRFMNQVP
+LFEKMLVDDGIHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK
+EAMFLHTDTDHAPWISIRSNDKKRARLNAMRYFLSQFEYEGKDHEVVGTPDPLIVRRGRD
+AVGD
+>PROKKA_00651
+MELLQPDAPRENLREFIDKLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYETRMTR
+EEYELEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHMNPRTARVVA
+LNKPSDRELGQWYFQRYIQHFPTAGEIVLFDRSWYNRAGVERVMGFATDEQYRRFMNQVP
+LFEKMLVDDGIHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK
+EAMFLHTDTDHAPWISIRSNDKKRARLNAMRYFLSQFEYEGKDHEVVGTPDPLIVRRGRD
+AVGD
+>PROKKA_02008
+MELLQPDAPRENLREFIDKLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYETRMTR
+EEYELEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHLNPRTARVVA
+LNKPSDRELGQWYFQRYIQHFPTAGEIVLFDRSWYNRSGVERVMGFSTDEQYRRFMNQVP
+LFEKMLADDGIHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK
+EAMFLHTDTDHAPWISIRSNDKKRARLNAMRYFLSQFEYEGKDHEVVGTPDPLIVRRGRD
+AVGD
+>PROKKA_01904
+MELLQPDAPRENLREFIDNLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYEERLSR
+EEYEIEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHLNPRTARTVA
+LSKPTERELGQWYFQRYIQHFPTAGEIVLFDRSWYNRSGVERVMGFSTDHQYDLFMRQVP
+VFEKMLVEDGVHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK
+EAMFLHTDTDHAPWISIKSNDKKRARLNAMRYFLSRFEYEGKDHDVVGVPDPLIVQRGRD
+AVGD
+>PROKKA_00881
+MELLQPDAPRENLREFIDKLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYETRMTR
+EEYELEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHMNPRTARVVA
+LNKPSDRELGQWYFQRYIQHFPTAGEIVLFDRSWYNRAGVERVMGFATDEQYRRFMNQVP
+LFEKMLVDDGIHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK
+EAMFLHTDTDHAPWISIRSNDKKRARLNAMRYFLSQFEYEGKDHEVVGTPDPLIVRRGRD
+AVGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000813.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000813.fa
new file mode 100644
index 0000000000000000000000000000000000000000..106099e0d4bfdd4264763dcfdf264e9b46586ed5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000813.fa
@@ -0,0 +1,14 @@
+>PROKKA_00941
+MTAMNVFGVVYPFVLLVIAAAVWLGIRSSGRERTHASAVEQRLRERTFTGQDRVTLEWPR
+DRRRPSLAKVVSIGESYGYRLLDKREREHVVELEFERILDDEGF
+>PROKKA_00660
+MTAMNVFGVVYPFVLLVIAAAVWLGVRSSGRERTHASALEHRLRERTFTGQDRVTLEWPR
+DRRHPSLAKVVSIGESYGYRLLDKREREHVVELEFERILDDEGF
+>PROKKA_01997
+MTLEWPRDRRRPTPAKVVAIAESYGYRLLEKRERDHVIELDFERIRDDEGF
+>PROKKA_01895
+MQTIPVMGWVFPVVLLVIAAAFWLGVRSSGGARGDSDLERRLRERTFTGAPRARLEWPRD
+RRRPTLAQLVRIGASHGYRLVSRTEAEHVYILDFQRVEDDDL
+>PROKKA_00890
+MTAMNVFGVVYPFVLLVIAAAVWLGIRSSGRERTHASAVEQRLRERTFTGQDRVTLEWPR
+DRRRPSLAKVVSIGESYGYRLLDKREREHVVELEFERILDDEGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000815.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000815.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab815528a055381b8a9aa45f45d8868b89cb4dfd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000815.fa
@@ -0,0 +1,25 @@
+>PROKKA_00943
+MASIRPVTVYGEPVLHRRAAEVEVIDDEIRELIEDMYVTQEAAHGVGLAAPQVGVGLRIF
+TWTFPDSGDAPNVGHVINPVLTHLDKAPREEPHPDEHTEGCLSVPGLGFPLQRPTRVRLS
+GQRVDGEMFEFEAEGWFARIMQHEYDHLNGTLYVNRLEGKWQRRWKRAQRAERLNVPGVT
+WLPGTDEDPFGHDADDHEDHEHGPDGDHGDDEA
+>PROKKA_00662
+MASIRPITVYGEPVLHRRAAEVEVIDDEIRELIEDMYVTQDAAHGVGLAAPQVGVGLRIF
+TWTFPDSGDAPNVGHVINPVLTHLDKAPREDPHPDEHTEGCLSVPGLGFPLQRPTRVRLS
+GQRVDGEMFEFEAEGWFARIMQHEYDHLNGTLYVNRLEGKWQRRWKRAQRAERLNVPGVT
+WLPGTDEDPFGHDADDHEDHEHGPDGDHGDDEA
+>PROKKA_01995
+MASIRPITVYGEPVLHTRAAEVEVIDDEIRRLVEDMYVTQDAARGVGLAAPQVGVGLRVF
+TWTYPHSGDAPSVGHVINPVLTVLDKASQEATDPDEHTEGCLSVPGHGYPLQRAPRVRLA
+GQRVDGEMFEFVAEGWFARVMQHEYDHLNGTLYVNRLEGRWQRRWKRAQRAERMNVPGVT
+WLPGTDEDPFGHDELDEAEAIEQHGPDADHGRADGA
+>PROKKA_01892
+MPSIRPITVYGEPVLHTRAAEVEVIDDSIRELVEDMYVTQDVANGVGLAAPQVGVGLRVF
+TWTFQDTGDAPNLGHVINPVLTMLSKPSTEEPDRHEDTEGCLSVPGHGFPLKRSAHVRMT
+GQRMDGSTVDIEATGWFARILQHEYDHLNGTLYVNRLEGKWARRWKRAQRAERLNVPGVT
+WLPGTDPDPFGHDVDVDEDAPAHEHHDHDHEGHDHAQEAR
+>PROKKA_00893
+MASIRPITVYGEPVLHRRAAEVEVIDDEIRELIEDMYVTQEAAHGVGLAAPQVGVGLRIF
+TWTFPDSGDAPNVGHVINPVLTHLDKAPREDPHPDEHTEGCLSVPGLGFPLQRPTRVRLS
+GQRVDGEMFEFEAEGWFARIMQHEYDHLNGTLYVNRLEGKWQRRWKRAQRAERLNVPGVT
+WLPGTDEDPFGHEEIEDHEH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000820.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000820.fa
new file mode 100644
index 0000000000000000000000000000000000000000..451c0c19c377d7731b7182a55df9a2eeb072fda3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000820.fa
@@ -0,0 +1,50 @@
+>PROKKA_00960
+MTRREGVQLAALLVAAAALYVTHSFLRYATYEAKGYDLGIFDQVVRQYALFNAPLSSVKG
+VDFHILGDHFHPILALLAPFYWVWPDPRMLGVVMALALAASAVPVYLFARRRAGHGVALA
+AVAALLLSWPFQAMVNWDFHEVTLGVPILAWLVWALDGQRAWLATGLAALLLTVREDMGV
+TLLAVALVMAIRRFWPQAAVTAVLGVLGYWFATSVVIPHYSPTGAFGYWQFTALGPDMRS
+SVLFLLTQPWNAVAVLFDHPLKVALWLLHFVPLLFLPVLSPLTLMALPILLSRLFNDRLN
+VWAPVYQYDAILAPLLLMAALEAAHRLAGRRDTLRRLPAVLVSAALAAGLIGTAFFPQVY
+PLHRTIAGDMTMTQHARDLDHAVGLIPDGVCVEAADNAVPHLTARTHVGLHGDIGDELAT
+WMIVDTSVPELGGWDPLTPEQALARAERLGFERVWSAGDVVVLHHPDRAVSPTCTTYLEH
+R
+>PROKKA_00673
+MTRREGVQLAALLVAAAALYVTHSFLRYATYEAKGYDLGIFDQVVRQYALFNAPLSSVKG
+VDFHILGDHFHPILALLAPFYWVWPDPRMLGVVMALALAASAVPVYLFARRRTGHGVALA
+AVAALLLSWPFQAMVNWDFHEVTLGVPILAWLVWALDGQRAWLATGLAALLLTVREDMGV
+TLLAVALVMAIRRFWPQAAVTAVLGVLGYWFATSVVIPHYSPTGAFGYWQFTALGPDMRS
+SVLFLLTQPWNAVAVLFDHPLKVALWLLHFVPLLFLPVLSPLTLMALPILLSRLFNDRLN
+VWAPVYQYDAILAPLLLMAALEAAHRLAGRRDALRRLPAVLVSTALAAGLIGTAFFPQVY
+PLHRTIVGDMTMTQHARDLDHAVALIPDGVCVEAADNAVPHLTARTYVGLHGDIGDELAT
+WMIVDTSVPELGGWDPLTPEQALARAERLGFERVWSAGDVVVLHHPDRAVSPTCTTYLEH
+R
+>PROKKA_01928
+MTRREGLHLGILLALASALAIVHSFLRYGIYEAKGYDLGIFDQVVRQYALFNAPLSSVKG
+VDFNILGDHFHPILALLAPFYWIWPDPRMLGIVMALALAAAAVPVYLFTRRRTGHAVSLV
+AVAALMLSWPFQAMVNWDFHEVTLGVPLMAWLVWALDGQRPWLATVLAAVLLTVREDMGV
+TLIAVALVMALRRFWPQAALVAVLGVLGYWFATSVVIPHYSPTGDFGYWQFQALGPDMGS
+SILTILTRPWEAAAALVDHPLKAALWLLHLVPLLFLPLLSPLTLMALPILLSRLWNDRLN
+VWAPVYQYDAILAPLLLMAALEGAVRLSDLLARRRRPRPAGTGAGSHASPPTRRLPAVVA
+STALATGLVGTAFFPQVFPYHRTLTGDMTMTQHARDLDHAVSLIPDGVCVEAADNAVPHL
+TARTYVGLHGDIGDELATWMIVDTSVAELGGWDPLTPDQALDRAERLGFETVWERGDVVV
+LRHPDRAVSPTCTQYLQHR
+>PROKKA_01879
+MPARRFPGQDRVRTWLHAPRPAVPAVAVTRRQGLHLGLVLLAFAALSITHSFLRFATYEA
+KGYDLGIFDQVVRQYALFNAPLSSVKGVDFNILGDHFHPILALLAPTYWIWPDPRMLGII
+MALALCAAAVAVYLTARRRVSHGWSLAAAGVVLFSWPFQAMVNWDFHEVTLGVPIMAWLV
+WALDGERPWLALGLGTALLTVREDMGVTVCALAVVFALRRRWVQAGLALVLGLAGYWFAT
+SVAIPHFSPTGGFGYWQFQALGPDMGSSLLTILTRPWEAVAALFDHPLKLALWLLHLVPL
+LFLPVLSPLTLLALPILLSRLWNDRLNVWAPVYQYDAILAPILLLAALEAATGLAARFPR
+VRRLPQVLLAWAGAVTLAGTAFLPQVFPFHRTLTGQMTTTQHARDLDQAVGMIPDGVCVE
+AADNAVPHLTDRTHVGLHGDIGDDLATWMIVDTSVTELGGWDPLTPDQALERARRLGFER
+VWSQGDVVVLHHPTRPVSATCTDYLRHR
+>PROKKA_00906
+MTRREGVQLAALLVAAAALYVTHSFLRYATYEAKGYDLGIFDQVVRQYALFNAPLSSVKG
+VDFHILGDHFHPILALLAPFYWVWPDPRMLGVVMALALAASAVPVYLFARRRTGHGVALA
+AVAALLLSWPFQAMVNWDFHEVTLGVPILAWLVWALDGQRAWLATGLAALLLTVREDMGV
+TLLAVALVMAIRRFWPQAAVTAVLGVLGYWFATSVVIPHYSPTGAFGYWQFTALGPDMRS
+SVLFLLTQPWNAVAVLFDHPLKVALWLLHFVPLLFLPVLSPLTLMALPILLSRLFNDRLN
+VWAPVYQYDAILAPLLLMAALEAAHRLAGRRDTLRRLPAVLVSTALAAGLIGTAFFPQVY
+PLHRTIVGDMTMTQHARDLDHAVALIPDGVCVEAADNAVPHLTARTHVGLHGDIGDELAT
+WMIVDTSVPELGGWDPLTPEQALARAERLGFERVWSARDVVVLHHPDRAVSPTCTTYLEH
+R
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000821.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000821.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ac03679f6065e616deae41383e8cea27a655325
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000821.fa
@@ -0,0 +1,24 @@
+>PROKKA_00962
+MQDLITVRGFVATDPATRHTASGAAVTGFRLATTERRFDRETAEWVDAHTNWYSISAFGQ
+LGSNTAQSVKKGNPVIVTGRLRVRDWSSGERSGTSVDVVADAVGLDLGFGSAAFQRSQRA
+AVPRPESAPRDDDASGGRAGAVGDGFSAGLPDGFQGGDAPASPGPDESDAGAPGREPAAA
+GVA
+>PROKKA_00675
+MQDLITVRGFVATDPATRHTASGAAVTGFRLATTERRFDREAAEWVDAHTNWYSISAFGQ
+LGSNTAQSVKKGNPVIVTGRLRVRDWSSGERSGTSVDVVADAVGLDLGFGSAAFQRSQRA
+AVPRPESAPRDDASGGRAGAVGDGFNVGLPDGFQGGDAPASPGPGEPDAEAPDREPAAAG
+VA
+>PROKKA_01926
+MQDIITVRGFVATDPVTRTTASGATVAGFRLATTERRFDREAGAWVDAHTNWYSVSAFGQ
+LGSNTAQSVRKGNPVIVTGRLRVRDWSTEERSGTTVDVVADAVGLDLAFGSAAFQRSQRA
+ASARPEGADEQDGQGQAGAVASAGPAEADGTAAGTGDGYVTELPPALRGGDAPATPPPPS
+SEEGDEADEADDDAHGVRALCGGVSAA
+>PROKKA_01877
+MQDTVTIRGFVATDPTTRHTASGAAVVGFRLASTERRFDRDAGMWVDAHTNWYSVSAFGQ
+LGSNTAQSVKKGNPVIVTGRLRVRDWSTEDRSGTSVDVVADAVGLDLAYGASAFMRNGRR
+ADAVERADAPVDADAGASLDAAPADGFGLALPPAFTGGDAPASSAEDAHEAAGALAVA
+>PROKKA_00908
+MQDLITVRGFVATDPATRHTASGAAVTGFRLATTERRFDRETAEWVDAHTNWYSISAFGQ
+LGSNTAQSVKKGNPVIVTGRLRVRDWSSGDRSGTSVDVVADAVGLDLGFGSAAFQRSQRA
+AVPRPESAPRDDASGGRAGAVGDGFSAGLPDGFQGGDAPASPGPDESDAGAPEREPAAAG
+VA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000822.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000822.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7bcf269096f87d555ebfa7d2609abf0978b376b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000822.fa
@@ -0,0 +1,55 @@
+>PROKKA_00963
+MAEFIYTMVKARKKVGDKLILDDVTMSFYPGAKIGMVGPNGAGKSTILKIMAGLDEPSNG
+EARLSPGYSVGILMQEPKLDESKTVLENVQEGVGEIYGKIQRYNQISEEMANPDADFDAL
+MGEMGELQSAIDAADAWDIDSQLEQAMDALRTPPGDEPVTNLSGGEKRRVALCKLLLEKP
+DLLLLDEPTNHLDAESVLWLEQHLASYPGAVIAVTHDRYFLDHVAEWIAEVDRGRLYPYE
+GNYSTYLETKRARLEVQGKKDAKLAKRLAEELDWVRSNTKGRQAKSKARLARYEEMAAEA
+EKTRKLDFEEIQIPPGPRLGTVVIEAKDLKKGFGDRVLIDGLSFSLPRNGIVGVIGPNGV
+GKTTLFKTIVGLEPLDGGELKIGETVKISYVDQSRSNIDPEKSLWEVVSDGLDYIKVGNV
+EMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLLLDEPTNDLDVETL
+TSLENALLEFPGCAVVVSHDRWFLDRVATHMLAYEGTAEDPANWYWYEGNFESYEANKVD
+RLGPEAARPHRMTHRKLTRD
+>PROKKA_00676
+MAEFIYTMVKARKKVGDKLILDDVTMSFYPGAKIGMVGPNGAGKSTILKIMAGLDEPSNG
+EARLSPGYSVGILMQEPKLDESKTVLENVQEGVGEIYGKIQRYNQISEEMANPDADFDAL
+MEEMGELQSAIDAADAWDIDSQLEQAMDALRTPPGDEPVTNLSGGEKRRVALCKLLLEKP
+DLLLLDEPTNHLDAESVLWLEQHLASYPGAVIAVTHDRYFLDHVAEWIAEVDRGRLYPYE
+GNYSTYLETKRARLEVQGKKDAKLAKRLAEELDWVRSNTKGRQAKSKARLARYEEMAAEA
+EKTRKLDFEEIQIPPGPRLGTVVIEAKDLKKGFGDRVLIDGLSFSLPRNGIVGVIGPNGV
+GKTTLFKTIVGLEPLDGGELKIGETVKISYVDQSRSNIDPEKSLWEVVSDGLDYIKVGNV
+EMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLLLDEPTNDLDVETL
+TSLENALLEFPGCAVVVSHDRWFLDRVATHMLAYEGTAEDPANWYWYEGNFESYEANKVD
+RLGPEAARPHRMTHRKLTRD
+>PROKKA_01925
+MAEFIYTMVKARKKVGDKLILDDVTMSFYPGAKIGMVGPNGAGKSTILKIMAGLDEPSNG
+EARLSPEYTVGILMQEPKLDESKTVLENVQEGVGEIYGKIQRYNQISEEMASPDADFDAL
+MEEMGELQTAIDAADAWDIDSQLEQAMDALRTPPGDEPVTNLSGGEKRRVALCKLLLEKP
+DLLLLDEPTNHLDAESVLWLEQHLAAYPGAVIAVTHDRYFLDHVAEWIAEVDRGRLHAYE
+GNYSTYLETKRARLEVQGKKDAKLAKRLAEELDWVRSNTKGRQAKSKARLARYEEMAAEA
+EKTRKLDFEEIQIPPGPRLGTVVIEAKDLKKGFGDRVLIEGLSFSLPRNGIVGVIGPNGV
+GKSTLFKTIVGLEPLDGGELKIGETVKISYVDQSRANIDPEKSLWEVVSDGLDYIKVGQV
+EMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLLLDEPTNDLDVETL
+TSLENALLEFPGCAVVVSHDRWFLDRVATHMLAYEGTAEDPANWYWYEGNFESYEANKVE
+RLGPEAARPHRVTHRKLTRD
+>PROKKA_01876
+MSRFPPPPTSLERMAEFIYTMVKARKKVGDKLILDDVTMSFFPGAKIGMVGPNGAGKSTI
+LKIMAGLDEPSNGEARLSPGYSVGILLQEPKLDEDKTVLENVQQGVGEIYGKIQRYNAIS
+EEMADPDADFDALMEEMGQLQTEIDAADAWDLDSQLDQAMDALRCPPPEAQVSHLSGGEK
+RRVALCALLLSKPDLLLLDEPTNHLDAESVLWLEQHLSSYPGAVVAVTHDRYFLDHVAGW
+ICEVDRGRLYPYEGNYSTYLETKRQRLEIQGKKDAKLAKRLAEELDWVRSNAKGRQAKSK
+ARLARYEEMAAEAEKTRKLDFEEIQIPPGPRLGNVVIEATNLQKGFDGRTLIDGLSFSLP
+RNGIVGVIGPNGVGKTTLFKTIVGLEPLDGGDLKIGETVKISYVDQNRTNIDPEKSLWEV
+VSDGLDYIKVGNVEMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLL
+LDEPTNDLDVETLTSLENALLEFPGCAVVVSHDRWFLDRTATHMLAYEGTEENPANWYWY
+EGNFESYEANKVERLGPEAARPHRVTHRKLTRD
+>PROKKA_00909
+MAEFIYTMVKARKKVGDKLILDDVTMSFYPGAKIGMVGPNGAGKSTILKIMAGLDEPSNG
+EARLSPGYSVGILMQEPKLDESKTVLENVQEGVGEIYGKIQRYNQISEEMANPDADFDAL
+MEEMGELQSAIDAADAWDIDSQLEQAMDALRTPPGDEPVTNLSGGEKRRVALCKLLLEKP
+DLLLLDEPTNHLDAESVLWLEQHLASYPGAVIAVTHDRYFLDHVAEWIAEVDRGRLYPYE
+GNYSTYLETKRARLEVQGKKDAKLAKRLADELDWVRSNTKGRQAKSKARLARYEEMAAEA
+EKTRKLDFEEIQIPPGPRLGTVVIEAKDLKKGFGDRVLIDGLSFSLPRNGIVGVIGPNGV
+GKTTLFKTIVGLEPLDGGELKIGETVKISYVDQSRSNIDPEKSLWEVVSDGLDYIKVGNV
+EMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLLLDEPTNDLDVETL
+TSLENALLEFPGCAVVVSHDRWFLDRVATHMLAYEGTAEDPANWYWYEGNFESYEANKVD
+RLGPEAARPHRMTHRKLTRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000825.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000825.fa
new file mode 100644
index 0000000000000000000000000000000000000000..03c12ea8e366b87cf69e9e5499acf89ad0a68cf2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000825.fa
@@ -0,0 +1,80 @@
+>PROKKA_00967
+MTTAAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI
+DFVAEQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVAN
+EENPQGVDAAVWEFKPTPRIPSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH
+LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTGAWT
+TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MVGVRAYIAKHAWQNTELPDLMTELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLIRTERFELDVAGEVTEVV
+EAAARRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG
+EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA
+EAEDGSDNQLQFVKAFALHARTTAQLDRLSALVDGTRTVPGLDLTTDLRWELLTALVAAG
+RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAVWDRVMAGELSNTEQRQALIGF
+ARVHDAALIAPFADAYFEGVEAMWDSRSHEMAETAATLGYPTAQVTPEIADRATALSERL
+ADTRAGLSRVLAEGRDETIRALAAREHATAHVHQVHAGA
+>PROKKA_00680
+MTTAAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI
+DFVAGQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEDSRRTLGVVAN
+EENLQGVDAAVWEFTPTPRISSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH
+LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTSAWT
+TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIAQHAWGNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA
+EAVGRRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG
+EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA
+EAEDGSDNQLQFVKAFALHARTTAQLDRLAALVDGTRTVPGLDLTTDLRWELLTALVAAG
+RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAAWDRVMAGELSNTEQRQALIGF
+ARVHDAALIAPFADSYFEGVEAMWDSRSHEMAETAATLGYPTSQVSRETADRATALSERL
+ADTRAGLSRVLAEGRDETVRALAAREHATAHVHQVHAGA
+>PROKKA_01920
+MSSSARLNITREEAAQRAAALTVDAYEVSLDLTRGPERFRTASTVTFAASEDAVGTHTWI
+DFVASQAPEVTLNGERVAVEDYDGARLPIGPLAAQNTLVVEGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVEN
+EDQLSGVDAAVWEFVPTPRISSYITALVAGPYAAVHSELTSADGRTIPLGVYCRASLVEH
+LDADNVFELTRQGFEFFEAQYGHPYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEAMVERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTRYTGSWT
+TFSSMEKNWAYRQDQLSSTHPIKAQIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIAKHAWSNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGV
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA
+EAAGRRRPALILPNDDDLAYAKLRLDHASWEAASTRLKDVDSSLARTLLWGAAWDAVRDG
+EASAAWFADLILANIGHEQDSSVVQTLLRQLATSLGQYLPEEQSTAARAAVADRLWGLVA
+GAEDGSDSQLQFVKAFALHARTAAQLDRLAGVVDGTHTVPGLDLTTDLRWELLTALVAAG
+RAGEAEIAAAEREDATATGALAAIQARAAVPTAEAKQAAWDRVMAGELSNTEQRQALIGF
+ARAHEAALLAPFADAYFEGVEAMWDSRSHEMAETAAVLGYPAAQVSDETAQRATALSEKT
+AGTRAGLSRVLAEGRDETVRALAAREHAAAHVHEVSASA
+>PROKKA_01868
+MTTAAAMNITREEAAARAAALTVESYQVALDLTRGAERFGSTTTVTFSAADEAVGTQTWI
+DFMATQAPEVTLNGQAVDVADFDGARLPIGPLAAENTLVVDGLADYTTTGEGLHRFVDPV
+DDEVYLYSQFEVPDSRRMFAVFEQPDLKATFAFTVTAPAHWAVVSNQPEAAHRTLGVVET
+PEAPEGVDAAVWEFTPTPRISSYITALVAGPYKSVHSELTSADGRTVPLGVYCRGSLFEH
+LDADEVFDLTRRGFEFFEAQYGHPYPFDKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VTDAVRERRAITILHELAHMWFGDLVTMKWWNDLWLNESFAEFMSTLAAAENTRYEGAWT
+TFSSMEKNWAYRQDQLSSTHPITAEIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIEKNAWSNTELPDLMTELEAASGRDLSEWTRLWLETSGVNTLAVQVDADYAGT
+ITSLRLHQSAPDGSPAAPGDDVLRPHRIAVGFYDLDEATGRLTRTERFELDAAGEVTEVA
+EAAGRRRPALILPNDDDLAYAKIRLDDASWETAGARLADVDSSLARTLLWGAAWDTVRDG
+EASAAWFVDLILTNIGREQDSTVIQTLLRQLATAISQYLPEERSAQVRADAANRLWMLVE
+QAEPGSDAQLQFVKAFALHAREEGQLTALADVWDRSSELPGLDLTTDLRWELLTALVAAG
+RAGETEIAAAETEDPTATGALAAALARAAVPTAEAKQTAWDQVVAGTLSNTTQRQVLLGF
+QRAHDPALLAPFTDAFFGSIQDVWGSRSHEMAETVAVLGFPSSQVCQEVVDRATALSDEV
+RGTNAGLARTLAESRDEMARALKARAAA
+>PROKKA_00913
+MTTVAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI
+DFVAEQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVAN
+EENPQGVDAAVWEFKPTPRIPSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH
+LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTSAWT
+TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIAQHAWGNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA
+EAVGRRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG
+EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA
+EAEDGSDNQLQFVKAFALHARTTAQLDRLAALVDGTRTVPGLDLTTDLRWELLTALVAAS
+RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAAWDRVMAGELSNTEQRQALIGF
+ARVHDAALIAPFADSYFEGVEAMWDSRSHEMAETAATLGYPTAQVTREIADRATALSERL
+AGTRAGLSRVLAEGRDETVRALAAREHATAHVHQVHAGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000827.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000827.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5aa1fc32ee4f4243017609dcff0b4bdbe82d2739
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000827.fa
@@ -0,0 +1,31 @@
+>PROKKA_00974
+MMHGSRPALRRAASALAGRRPLSLRGATVLVTGGASGIGRLIALGAARRGAGRVVVWDLD
+LQGAEAVAAEIRSQGADAQAERVDVTDAAAVEAAAARAGEVDVAVNNAGVVTGVRLEDAT
+EEGIRRTFEVNALAPYWLTRAVLPGMRARDRGAVVTVASAAGLVGVARQTDYSATKHAAV
+GFAESLAAELRKDGSRVTSLAVCPFYIDTGMFAGVRSRVPWLLPVLDPRHVAQEVLDAVE
+AGRTRLLLPRAVGLIAPLRALPAPVFDRAMDVLGVNATMDGFTGRRSRLFAGRETAR
+>PROKKA_00688
+MHGSRPALRRAASALAGRRPLPLHGATVLVTGGASGIGRLIALGAAHRGAGRVVVWDLDL
+QGVEAVAAEIRSQGADARAERVDVTDAAAVEAAAAGAGEVDVAVNNAGVVTGAPLEDATE
+EGIRRTFEVNALAPYWLTRAVLPGMRARDRGAVVTVASAAGLVGVARQTDYSATKHAAVG
+FAESLAAELRKDGSRVTSLAVCPFYIDTGMFAGVRSRVPWLLPVLDPHHVAQEVLDAVEA
+GRTRLLLPRAVGLIAPLRALPAPVFDRAMDVLGVNATMDGFTGRRSRLFAGRETAR
+>PROKKA_01916
+MPRSRTPRPALRALAGALPRRRRLPLRGTAVLITGGASGIGRLMALGAARRGAARVVVWD
+LDLSAAEAVAAEARALGAEAVAERVDVTDAAAVEAAAARAGAVDVAVNNAGVVTGARLED
+ATEEGIRRTFEVNALAPYWLTRAVLPGMKARDRGAVVVIASAAGLVGVARQTDYSATKHA
+AVGFAESLSAELRKDGSAVTALAVCPFYIDTGMFDGVRSRIPWLLPVLRQEEVAEQVLDA
+VEAGRTRLPLPRAVGLLAPLRALPTPVFDRAMDVMGVNDTMDGFTGRRPAVDVPAPDPRV
+FAPDGAAR
+>PROKKA_01863
+MTPILNRLRGRRPLPLAGRAVLITGAGSGIGRLMALEAARRGAAVVHVWDRDDAAARTVA
+AEVAALGARGEAACVDVTDTAAVEAAAARAEAVDVLVNNAGVVTGTPLLETTEEGIRRTF
+EVNALAGYWTTRALLPGMLERGRGAVVTVASAAGLVGVARQTDYSASKHAAVGFAESLRA
+ELRRADAPVTSLVVCPFYISTGMFAGVRTKVPALLPILEPEAVAAQVVDAVEAGRERLVL
+PPAVQLIAPLRALPVPAFDRVMDVLGVNRAMDGFTGRR
+>PROKKA_00917
+MMHGSRPALRRAASALAGRRPLSLRGATVLVTGGASGIGRLIALGAARRGAGRVVVWDLD
+LQGAEAVAAEIRSQGADAQAERVDVTDAAAVEAAAARAGEVDVAVNNAGVVTGVRLEDAT
+EEGIRRTFEVNALAPYWLTRAVLPGMRARDRGAVVTVASAAGLVGVARQTDYSATKHAAV
+GFAESLAAELRKDGSRVTSLAVCPFYIDTGMFAGVRSRVPWLLPVLDPRHVAQEVLDAVE
+AGRTRLLLPRAVGLIAPLRALPAPVFDLAMDVLGVNATMDGFTGRRSRLFAGRETAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000830.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000830.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1102fcc9b242eda4b37f2a4db43d879ad19b5bbe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000830.fa
@@ -0,0 +1,25 @@
+>PROKKA_00978
+MTQFPAGLPTGMPSLPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGAQVDDAS
+ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLQIHAQEINRMRVWMEETLASLTN
+RTPEEVSQDIDRDKFLSAEQALEYGLVDEVLASRKITRPSA
+>PROKKA_00692
+MTQFPAGLPTGMPSLPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGAQVDDAS
+ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIHAQEINRMRVWMEETLASLTN
+RTPEEVSQDIDRDKFLSAEQALEYGLVDEVLASRKITRPSA
+>PROKKA_01912
+MTQFPAGLPTGTPSMPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGSQVDDAS
+ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIQAQEINRMRVWMEQTLASLTN
+RTPEEVSRDIDRDKFLSAEQALEYGLVDEVLASRKITRPAG
+>PROKKA_01859
+MTQFPAGLPVGTPSQAAPSARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGSQVDDAS
+ADDIMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIHANEINRMRVWMEQTLASLSN
+RTPEDVSRDIDRDKFLSAEGAKEYGLVDEVLAPRKITRTGA
+>PROKKA_00921
+MTQFPAGLPTGMPSLPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGAQVDDAS
+ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIHAQEINRMRVWMEETLASLTN
+RTPEEVSQDIDRDKFLSAEQALEYGLVDEVLASRKITRPSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000831.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000831.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c57ef370f3d61b529b4b462b8579a5e2d6e49771
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000831.fa
@@ -0,0 +1,45 @@
+>PROKKA_00979
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAEADETV
+LPTPQEIFDHLESFVIGQEAAKRSLAVAVYNHYKRVRGPQARGGDLADRLTERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGDVTYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPRNALLKQYQKMFLMDGVELEFEQD
+ALDAVVAQAEARGTGARGLRSIMENVLKPVMFELPSRSDVGTVVISGDVVRGEAEPTLIP
+AEVERRRRGRSA
+>PROKKA_00693
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAEADETV
+LPTPQEIFDHLESFVIGQEAAKRSLAVAVYNHYKRVRGPQARGGDLADRLTERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGDVTYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPRNALLKQYQKMFLMDGVELEFEQD
+ALDAVVAQAEARGTGARGLRSIMENVLKPVMFELPSRSDVGTVVISGDVVRGEAEPTLIP
+AEVERRRRGRSA
+>PROKKA_01911
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAADSDEMV
+LPTPQEIFDHLEGYVIGQEVAKRSLAVAVYNHYKRVRGPQGRGGDLADRLTERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGEVSYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPNNALLKQYQKLFLMDGAELEFEPE
+ALDAVVELAEARGTGARGLRSIMEDVLKPVMFELPSRTDVGTVVISGEAVRGEAEPVLIP
+AEVERRRRGRSA
+>PROKKA_01858
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAETDELE
+LPTPREIFEHLERYVIGQEAAKRSLAVAVYNHYKRVRGPQGRGGDLAERLEERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARMLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DHDVKRAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGSGEVSYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHDQLVRVLTEPKNALLKQYQKMFLMDGVELEFEPE
+ALDAVVELAQARGTGARGLRSIMEDVLKPVMFELPSRTDVGTVVISGDVVTGQAEPLLIP
+AEVERKRRRRTA
+>PROKKA_00922
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAEADETV
+LPTPQEIFDHLESFVIGQEAAKRSLAVAVYNHYKRVRGPQARGGDLADRLTERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGDVTYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPRNALLKQYQKMFLMDGVELEFEQD
+ALDAVVAQAEARGTGARGLRSIMENVLKPVMFELPSRSDVGTVVISGDVVRGEAEPTLIP
+AEVERRRRGRSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000832.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000832.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8c1177382f10cc30be89428b015a4c152b92b15a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000832.fa
@@ -0,0 +1,25 @@
+>PROKKA_00980
+MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL
+ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHDAD
+ILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIFD
+GAVALADFPYFYEIKRARTTDPQFD
+>PROKKA_00694
+MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL
+ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHDAD
+ILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIFD
+GAVALADFPYFYEIKRARTTDPQFD
+>PROKKA_01910
+MSENTQPVVDFYFDPTCPFAWITSRWILEVEKVRDIQVKFHQMSLYMLNEGRDLPEDYRR
+STDRGLIPGRGTQHVGAEHPERLAEWYTALGTRIHNEGQKDYEAALTGAAVDLGLDPAPI
+LAATETDAEDERLREKQRAAEELVGNDVGTPVVSFNGTAFFGPVLTRIPRGEEAGRIFDG
+AVALAEYPYFYEIKRARTTDPQFD
+>PROKKA_01857
+MSENTAPVVDFYFDPTCPFAWITSRWILEVEKVRDLSVTFHQMSLYMLNEGRELPEDYRR
+HTDRGLMPGRATLHVGEHHPELLSDWYTAVGTRIHNEGNQDYEAVVTGAAAELGLDAAPI
+LEATRTDAADDDLRAKQRAAEELVGNDVGTPVVSFDGTAFFGPVMTRIPRGEEAGEIFDA
+AVRLAQFPYFYEIKRARTTDPQFD
+>PROKKA_00923
+MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL
+ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHDAD
+ILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIFD
+GAVALADFPYFYEIKRARTTDPQFD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000834.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000834.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5b515f07309e0e1793e56dd339aa672ffa1db9e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000834.fa
@@ -0,0 +1,80 @@
+>PROKKA_00982
+MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ
+VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY
+YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL
+SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP
+GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV
+FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR
+QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI
+RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL
+DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ
+IVGRWSRDEAFFNNVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP
+DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA
+AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLTRLAATVEQATRAFEAYDYARALNVTE
+QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW
+RAGSVHTAAWPGAADEVASLSFAASAGDAEVLPTVAQVLGGIRKAKSEAKVKQRTEVRSA
+VVTGPADWLEKLRGGLADLKAAGNIADLSLTQGEAGESAPLTVSDVQLAPVDDD
+>PROKKA_00696
+MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ
+VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY
+YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL
+SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP
+GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV
+FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR
+QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI
+RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL
+DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ
+IVGRWSRDEAFFNNVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP
+DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA
+AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLTRLAATVEQATRAFEAYDYARALNVTE
+QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW
+RAGSVHTAAWPGAADEVAALSFAASAGDAEVLPTVAQVLGGVRKAKSEAKVKQRTEVRSA
+VVTGPTEWLEKLRGGLADLKAAGNIADLSLTQGEAGESAPLTVSDVQLAPVEDD
+>PROKKA_01907
+MAENTQGTDTPIDASTASTPAAGAVAVPDKPGLEGLEEKLTARWAQEGTYAFDPRTTREQ
+VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMTGKNVFYPMGWDDNGLPTERRVQNY
+YGVRCDPTKPYIEGYTPPAQPAKNQRDWDVVSRKNFIELCEELAVEDEKVFEDLFTRLGL
+SVDWSMTYRTIDDVSRAVSQRAFLRNVAAGDAYLSEAPTMWDVTFRTAVAQAELEDREVP
+GAYHRYPFTAADGTQVFIETTRPELLASCSALVAHPEDERYQPLFGTMVRSPLFDVEVEV
+KAHELAKPDKGSGIAMVCTFGDLTDVTWWRELQLPTRTLIGRDGRFAAETPEWISSEAGR
+AFYAESIAGKTVFSAKEAVVTALTEAGLMDGEPKKVQHAVNFYEKGDKPLEIVTSRQWYI
+RNGGRDADRREQLIARGRELDWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYRL
+DAEGEPVYDEPIVPEDAALPVDPVAETAPGFTEDQRDQPGGFTGDPDVLDTWATSSLTPQ
+IVGRWSRDEEFFANVFPFDLRPQGHDIIRTWLFSTVVRADALNGSVPWTDTALSGWILDP
+DRKKMSKSKGNVVVPTDILEEFGSDAVRYWASSARLGADTAYEVAQMKIGRRLAIKLLNA
+AKFVLNLGATRDAVVRTPDDAARVTNALDASLLARLATTVEQATAAFDAYDYARALNVTE
+SFFWQFTDDYVELIKDRAYGGHGEAEQASVVAALATTLDSLLRLLAPFQPFATEEVWSWW
+RTGSVHRAPWPGLESEAAGLRAAAEGGDPQVLAVVAQVLGRVRKAKSEAKVKQRTQVRTA
+TVRAAAAQLDALRGGLADLKGAGNVADVTLTEADGELEVTDIELAPAEEA
+>PROKKA_01854
+MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ
+VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY
+YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL
+SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP
+GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV
+FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR
+QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI
+RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL
+DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ
+IVGRWSRDDAFFSSVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP
+DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA
+AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLARLAVSVEQATRAFEAYDYARALNVTE
+QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW
+RAGSVHTAAWPGAADEVASLSFAASSGDAEVLPTVAQVLGGVRKAKSEAKVKQRTEVRSA
+VVTGPAEWLEKLRGGLADLKAAGNIADLSLTQGEAGEAAPLTVSDVQLAPVEDD
+>PROKKA_00925
+MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ
+VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY
+YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL
+SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP
+GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV
+FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR
+QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI
+RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL
+DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ
+IVGRWSRDEAFFNNVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP
+DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA
+AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLARLAATVEQATRAFEAYDYARALNVTE
+QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW
+RAGSVHTAAWPGAADEVAALSFAASGGDAEVLPTVAQVLGGVRKAKSEAKVKQRTEVRSA
+VVTGPADWLEKLRGGLADLKAAGNIADLSLTQGEAGESAPLTVSDVQLAPAEDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000835.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000835.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b1670bfe8bdb1fcb12daf0d08e3c60e4d67f141
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000835.fa
@@ -0,0 +1,30 @@
+>PROKKA_00983
+MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG
+VSGDVVPAALDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGDGDRADWEWMYR
+VNVLGTLTMCQAFLPMLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE
+EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVMRPVAQAAQHKVIRR
+>PROKKA_00697
+MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG
+VSGDVVPAALDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGVGDRADWEWMYR
+VNVLGTLTMCQAFLPMLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE
+EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVMRPVAQAAQHKVIRR
+>PROKKA_01906
+MDVSHTTENQSPRAAVVTGATTGIGRATALELARRGWRVYAVGRRAERLDALAAQAREEA
+VPGEVVPAPLDVTDEAAVAGLVARVDTDGGIDTLVNIAGGARGTDFVGAGNREDWEWMYR
+ANVLGTLAMCQAFLPGLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTAALRLE
+EAEHNVRVIEVLPGMVHTEEFSLMRLGGDAAAAEKVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVIRPVAQAAQHKVIRR
+>PROKKA_01853
+MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG
+VSGDVVPAPLDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGDGDRADWEWMYR
+VNVLGTLTMCQAFLPMLRTHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE
+EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVMRPVAQAAQHKVIRR
+>PROKKA_00926
+MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG
+VSGDVVPAALDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGDGDRADWEWMYR
+VNVLGTLTMCQAFLPMLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE
+EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVMRPVAQAAQHKVIRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000837.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000837.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d75136278bcc9dfb002dda8825af9c986c014cd9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000837.fa
@@ -0,0 +1,48 @@
+>PROKKA_00985
+MTQVNETSRPARTPRRPSAKPHGQWKVDGTAPLNHNEEFKQQDDGLNVRERIEQVYAHEG
+FDSIPSDDLHGRFRWWGLYTQRRQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL
+RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG
+SPVAGIAADEIIDPTPVIREIADRWIGDLEISNLPRKFKTAITGHPSQDVVHEINDVSLI
+GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK
+ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP
+VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS
+VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA
+RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY
+VERVVRRYDEQREPGETFARWAHRVDEEALR
+>PROKKA_00699
+MTQVNETSRPARTPRRPSAKPHGQWKVDGTTPLNHNEEFKQQDDGLNVRERIEQVYAREG
+FDSIPSDDLHGRFRWWGLYTQRRQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL
+RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG
+SPVAGIAADEIIDPTPVIREIADRWIGDLEVSNLPRKFKTAITGHPSQDVVHEINDVSLI
+GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK
+ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP
+VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS
+VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA
+RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY
+VERLVRRYDEQREPGETFARWAHRVDEEALR
+>PROKKA_01904
+MVLDVEGDRVDAVVAGLKELGLDPEPSVFRRSTIACTGLEFCKLAIVDTKDTATAAIAQL
+EERLADLADRLPERLSLHVNGCPNSCARIQTADIGLKGQLLPDDDGGQTPGFQIHLGGGL
+ASVDRAEAGLGRSVRGLKVRADGLVDYVERLVRRYDEQREPGETFARWAHRVDEEALR
+>PROKKA_01851
+MTQVNETSRPARTPRRPSAKPHGQWKVDGTAPLNHNEEFKQQDDGLNVRERIEQVYAREG
+FDSIPSDDLHGRFRWWGLYTQRKQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL
+RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG
+SPVAGIAADEIIDPTPVIREIADRWIGDLEVSNLPRKFKTAITGHPSQDVVHEINDVSLI
+GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK
+ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP
+VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS
+VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA
+RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY
+VERLVRRYDEQREPGETFARWAHRVDEEALR
+>PROKKA_00928
+MTQVNETSRPARTPRRPSAKPHGQWKVDGTAPLNHNEEFKQQDDGLNVRERIEQVYAHEG
+FDSIPSDDLHGRFRWWGLYTQRRQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL
+RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG
+SPVAGIAADEIIDPTPVIREIADRWIGDLEISNLPRKFKTAITGHPSQDVVHEINDVSLI
+GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK
+ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP
+VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS
+VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA
+RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY
+VERVVRRYDEQREPGETFARWAHRVDEEALR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000839.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000839.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b4413da12b14f01e1a9fcfd7146c076161756dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000839.fa
@@ -0,0 +1,35 @@
+>PROKKA_00987
+MTLTHAPDPGTVSPAGPDVQDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK
+AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR
+NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY
+NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR
+PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA
+AMEDRKKDGYF
+>PROKKA_00701
+MTLTHAPDPGTVSPAGPDVQDALEAEAIHIVREVVAEFERPAMLFSGGKDSVVMLHLAAK
+AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR
+NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY
+NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR
+PAENEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA
+AMEDRKKDGYF
+>PROKKA_01902
+MTLTHAPDPGTVSPAGPDVLDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK
+AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR
+NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY
+NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPPIYYAHEREVFRRDGMWRAVGEHSR
+PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA
+AMEDRKKDGYF
+>PROKKA_01849
+MTLTHAPDPGTVSPAGPDVQDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK
+AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR
+NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY
+NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR
+PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA
+AMEDRKKDGYF
+>PROKKA_00930
+MTLTHAPDPGTVSPAGPDVQDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK
+AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR
+NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY
+NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR
+PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA
+AMEDRKKDGYF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000842.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000842.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c223dac7dfd86f17dd8f71e50695d6c8077c73d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000842.fa
@@ -0,0 +1,35 @@
+>PROKKA_00990
+MRTDTPTLDAPGRAPGAATDDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV
+LLVAIWQAFAWLAGARGEPITGPGDVVGAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV
+GVGLGLLLGQVSVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV
+VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA
+EIIAVGGPMGVGLGTLLHEGRAESDLAVVLCAVLAILAVGVLVELTAFGPAERRMLRRRG
+LLEGSTR
+>PROKKA_00704
+MRTDTPTLDAPGRAPGAATDDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV
+LLVAIWQAFAWLAGARGEPITGPGDVVGAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV
+GVGLGLVLGQVGVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV
+VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA
+EIIAVGGPMGVGLGTLLHEGRAASDLAVVLCAVLTILAVGVLVELAAFGPVERRMLRRRG
+LLEGSTR
+>PROKKA_01899
+MRTDTPTLDAPGRAPGAAADDELRELDSGLDALQAVDSARRTGLAGWDWSRVLLPVAAVV
+LLVAIWQVAAWLAGARGEPITGPGDVLGAFGALWAQGLVQQAVATSVGRAVVGFALAVVA
+GVGLGLLLAQVGVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVILTGAVPAV
+VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA
+EIIAVGAPMGVGLGTLLHQGRTESDLAVVLCAVLAILAVGVLVELTAFGPVERRMLRRQG
+LLEGSTR
+>PROKKA_01846
+MRTDTPTLDAPGRAPGAAADDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV
+LLVAIWQVAAWLAAARGEPITGPGDVLRAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV
+GVGLGLLLGQVSVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV
+VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA
+EIIAVGGPMGVGLGTLLHQGRAESDLAVVLCAVLAILAVGVLVELTAFGPVERRMLRRQG
+LLEGSTR
+>PROKKA_00933
+MRTDTPTLDAPGRAPGAATDDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV
+LLVAIWQAFAWLAGARGEPITGPGDVLGAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV
+GVGLGLVLGQVSVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV
+VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA
+EIIAVGGPMGVGLGTLLHEGRAASDLAVVLCAVLTILAVGVLVELAAFGPVERRMLRRRG
+LLEGSTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000846.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000846.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b2fe25dca63a581863f7613ae3f25ed8f86aecb3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000846.fa
@@ -0,0 +1,20 @@
+>PROKKA_00997
+MTHHTEETLVLIKPDGVARNLVGEILARIERKGYVIADLKMLTPTRAMLERHYEEHQGKP
+FFEPLVAFMASGPVVAARVTGDSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGEAVQKN
+LVHGSDSTLSAERELAIWFG
+>PROKKA_00711
+MTHHTEETLVLIKPDGVARNLVGEILARIERKGYVIADLKMLTPTRAMLERHYEEHQGKP
+FFEPLVAFMASGPVVAARVTGDSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGEAVQKN
+LVHGSDSTLSAERELAIWFG
+>PROKKA_01893
+MAQHIEETLVLVKPDGVERNLVGEILARIERKGYVIADLKMLTPTRSMLERHYEEHQGKP
+FFDPLVDFMASGPVVAVRVTGNSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGESVQKN
+LVHGSDSSLSAERELGIWFG
+>PROKKA_01839
+MTHHPEETLVLVKPDGVERRLTGEIIARIERKGYEVVDLKMLVPTREMLAAHYEEHEGKP
+FYEPLLEFMGSGPVVALRLAGDRVIEGFRSLAGATDPTVAAPGTIRGDYARDWGAGVQKN
+LVHGSDSTLSAERELAIWFA
+>PROKKA_00940
+MTHHTEETLVLIKPDGVARNLVGEILARIERKGYVIADLKMLTPTRAMLERHYEEHQGKP
+FFEPLVAFMASGPVVAARVTGDSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGEAVQKN
+LVHGSDSTLSAERELAIWFG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000849.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000849.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ae82519469deb6b581a5cf73c7daa6d2ad92e47c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000849.fa
@@ -0,0 +1,15 @@
+>PROKKA_01000
+MVYAIVRAGGRQEKVSVGDLVTLDRVPAETGGSVELPALMLVDGDEVKAGADAAGVKVTA
+EVVSHSRGKKVVIMKYKNKTGYKKRQGHRSELSTVKITGIA
+>PROKKA_00714
+MVYAIVRAGGRQEKVSVGDLVTLDRVPAETGGSVELPALMLVDGDEVKAGADAAGVKVTA
+EVVSHSRGKKVVIMKYKNKTGYKKRQGHRSELSTVKITGIA
+>PROKKA_01890
+MVYAIVRAGGRQEKVSVGDLVTLDRVPAETGGSVELPALMLVDGDKVTAGADAAGVKVTA
+EVVSHSRGKKVVIMKYKNKTGYKKRQGHRSELSTVKITGIA
+>PROKKA_01818
+MVYAIVRAGGRQEKVSVGDLVTLDRVPAEEGGSVELPALMLVDGDKVKAGADAADVKVTA
+EVVSHSRGKKIVIVKYKNKTGYKKRQGHRSELSTVKITGIA
+>PROKKA_00943
+MVYAIVRAGGRQEKVSVGDLVTLDRVPAETGGSVELPALMLVDGDEVKAGADAAGVKVTA
+EVVSHSRGKKVVIMKYKNKTGYKKRQGHRSELSTVKITGIA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000850.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000850.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f6295b8c6e1f6eb726ed0a477b6c4df304e46d38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000850.fa
@@ -0,0 +1,15 @@
+>PROKKA_01001
+MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF
+ALSAGSVAFGQRRGRKVVDIVPAAE
+>PROKKA_00715
+MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF
+ALSAGSVAFGQRRGRKVVDIVPAAE
+>PROKKA_01889
+MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF
+ALSAGSVAFGQRRGRKVVDIVPAAE
+>PROKKA_01817
+MAHKKAGSSSKNGRDSNPQYLGVKRFGGQDVNAGEILIRQRGTKFHPGRNVGRGKDDTLF
+ALSAGTVSFGQRRGRKVVDIVAAGE
+>PROKKA_00944
+MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF
+ALSAGSVAFGQRRGRKVVDIVPAAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000853.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000853.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d8e11ba7c667f4a66d2e213ada8161538c70f98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000853.fa
@@ -0,0 +1,45 @@
+>PROKKA_01004
+MQTTESTAPQDQSGRQDAEAPTPEVEEAVRQRAEWARQAVPELAVAGRARKDAVLRHMAE
+ALRANTAAILTANREDRSRGRETGTSAAMLDRLKLDEARVEALALALETLAGLPDPVGTV
+VRGGPLPNGVRMSQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILRGGSAAESTNA
+VLIQVLREALVDQGFDANIIQGIDDLGRPGVAALMAARGAVDVLVPRGGRELIQRVVREA
+RVPVIETGEGNVHLYVDASAPKQMAVDIALNSKTHRTSVCNAAETLLLHRDAEETGREVL
+RALTRAGVLLHVDEAARAWLPTLADRGDHARDAVDATEEDWGTEYLDMEMAVRVVDSLGQ
+AIEHIGRWSTGHTEAIVTNDLAAAERFITEVDAAAVIVNASTRFTDGGELGLGAEVGIST
+QKMHARGPMGLEELTTTKWILRGDGQIRR
+>PROKKA_00718
+MQTTESTAPQDQSGRQDAEAPTPEVEEAVRQRAEWARQAVPELAVAGRARKDAVLRHMAE
+ALRANTAAIITANREDRSRGRETGTSAAMLDRLKLDEARVEALALALETLAGLPDPVGTV
+VRGGPLPNGVRMSQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILRGGSAAESTNA
+VLIQVLREALVDQGFDANIIQGIDDLGRPGVAALMAARGAVDVLVPRGGRELIQRVVREA
+RVPVIETGEGNVHLYVDASAPKQMAVDIALNSKTHRTSVCNAAETLLLHRDAEETGREVL
+RALTRAGVLLHVDEAARAWLPTLADRGDHARDAVDATEEDWGTEYLDMEMAVRVVDSLGQ
+AIEHIGRWSTGHTEAIVTNDLAAAERFITEVDAAAVIVNASTRFTDGGELGLGAEVGIST
+QKMHARGPMGLEELTTTKWILRGDGQIRR
+>PROKKA_01886
+MENQESTAPQDQSAGQEAEAPSQEVVDAIRQRAEWARLAVPELATAGRTRKDAVLRHMAE
+SLRSNAAAIITANQEDRARGAEAGTSAALLDRLKLDEPRVEALALGLEALAALPDPVGAV
+VRGGTLPNGVRMTQTRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILRGGSAAQSTNA
+VLIQVLREALADQGFDPNVVQGIDDLGRPGVAALMATRGAVDVLVPRGGRELIQRVVREA
+RVPVIETGEGNVHLYLDASAPKDMAVEIALNAKTHRTSVCNAAETLLIHREAEETGREVL
+RALMRGGVLLHVDEAAKAWLPGPTDRGDHARDAVDATEEDWGTEYLDMDMAVRIVDSLDQ
+AIEHIGRWSTGHTEAIVTNDLAAAEQFITEVDAAAVIVNASTRFTDGGELGLGAEVGIST
+QKMHARGPMGLEELTTTKWILRGDGQVRR
+>PROKKA_01814
+MTTEHTETEPAERVQQTPTPEQGASADGRPGADVVAEVRSRSARARAAAPELARAGRERK
+DALLRSMADAVRAAAASILAANAEDLARGEENGTSAAMLDRLRLDEPRLESLAVALEDLA
+SLPDPVGAVVRGGDLPNGIHMQQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNAVLLRG
+GSAAEHTNAVLIQVLREALRDQGFESDLVQGIDDLGRPGVAALMSTRGAVDVLIPRGGRE
+LIQRVVAEARVPVIETGEGNVHLFIDASAPADMAVDIALNAKTHRTSVCNAAETLLLHKD
+AERAGREVLRALTRAGVLLHVDEASRARLPSPADRGQDAREPQAASDEDWGREYLDMEMA
+VRTVDSIDEAMEHVRRWSTGHTEAIVTNDLANADRWVSEVDAAAVIVNASTRFTDGGQLG
+LGAEVGISTQRMHARGPMGLEELTTTKWVLRGAGQVRR
+>PROKKA_00947
+MQTTESTAPQDQSGRQDAEAPTPEVEEAVRQRAEWARQAVPELAIAGRARKDAVLRHMAE
+ALRANTAAILTANREDRGRGRETGTSAAMLDRLKLDEARVEALALALETLAGLPDPVGTV
+VRGGPLPNGVRMSQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILRGGSAAESTNA
+VLIQVLREALVDQGFDPNIIQGIDDLGRPGVAALMAARGAVDVLVPRGGRELIQRVVREA
+RVPVIETGEGNVHLYVDASAPKQMAVDIALNAKTHRTSVCNAAETLLLHRDAEETGREVL
+RALTRAGVLLHVDEAARAWLPTLADRGDHARDAVDATEEDWGTEYLDMEMAVRVVDSLDQ
+AIEHIGRWSTGHTEAIVTNDLAAAERFITEVDAAAVIVNASTRFTDGGELGLGAEVGIST
+QKMHARGPMGLEELTTTKWILRGDGQIRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000854.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000854.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dae6b263cdaf0fceffbeaddf001244ac1ccb18fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000854.fa
@@ -0,0 +1,15 @@
+>PROKKA_01005
+MLNTSLILAAAEGHHVVNELPMDPIWYGLLVFALLMAALAATMSMRSRALRLPEPTTAVQ
+HHGTGRGSHTSGH
+>PROKKA_00719
+MLNTSLILAAAEGHHVVNELPMDPIWYGLLVFALLMAALAATMSMRSRALRLPEPTTAVQ
+HHGTGRGSHTSGH
+>PROKKA_01885
+MLNTSLVLAAAEGPHVVNELPIPTVWYGIIVFALLMAALLATMSMRSRALRLPEPTTAVQ
+HHGTGHGSHTPGH
+>PROKKA_01813
+MLNSALVLAAAEEGHHVVNELPIPPVWFGIIVFLLLMAGLLAILSMRSVGLRHAEPTTAV
+QHHGTHGTGSHSAGH
+>PROKKA_00948
+MLNTSLILAAAEGHHVVNELPMDPIWYGLLVFALLMAALAATMSMRSRALRLPEPTTAVQ
+HHGTGRSSHTSGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000855.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000855.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1208058dfbacdb2e78199ecfa48ce6e3f2ffff0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000855.fa
@@ -0,0 +1,25 @@
+>PROKKA_01006
+MTVASRTPVPAPTAGGARRRRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVVFVPTGQP
+WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGVTYTVDTLRDLRRLHPDAELF
+FITGADAMGQILTWKDVDELWDLAHFVGVTRPGHDLSDMGLGADVSLMEIPAMAISSTDC
+RERVRRGRPVWYLVPDGVVQYIAKHHLYVSEEETS
+>PROKKA_00720
+MTVASRTPVPAPTAGGARRRRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVVFVPTGQP
+WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGVTYTVDTLRDLRRLHPDAELF
+FITGADAMGQILTWKDVDELWDLAHFVGVTRPGHDLSDMGLGADVSLMEIPAMAISSTDC
+RERVRRGRPVWYLVPDGVVQYIAKHHLYVSEEETS
+>PROKKA_01884
+MAVSSRTTASEPTAGGARRRRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVIFVPTGQP
+WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGMTYTVDTLRDLRRLHPDAELF
+FITGADAMGQILTWKDVDELWDLAHFVGVTRPGHDLTDMGLKDDVSLMEIPAMAISSTDC
+RERVARGRPVWYLVPDGVVQYIAKHHLYVSDEETP
+>PROKKA_01812
+MTSATRDPAPPPTSRRHRLGVMGGTFDPIHHGHLVAASEVAAEFGLDEVVFVPTGQPWQK
+SDTRVSPAEHRYLMTVIATASNPRFTVSRVDIERPGNTYTVDTLRDIRAKRPDSELFFIT
+GADALNQILTWKDVEELWDLAHFVGVTRPGYQLEDYGLSEDISLMEIPAMAISSTDCRRR
+VERGRPVWYLVPDGVVQYINKHHLYTPEGDRP
+>PROKKA_00949
+MTVASRTPVTAPTAGRARRPRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVVFVPTGQP
+WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGVTYTVDTLRDLRRLHPDAELF
+FITGADAMGQILTWKDVDELWGLAHFVGVTRPGHDLSDMGLGADVSLMEIPAMAISSTDC
+RERVRRGRPVWYLVPDGVVQYIAKHHLYVSEEETS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000861.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000861.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b555162b5caa574f15e6c34c9ec4f9dd38ae99fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000861.fa
@@ -0,0 +1,33 @@
+>PROKKA_01019
+MEEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVAGRLELTTA
+GEAFLPVAREVLVAHRRAEQAARALASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP
+RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD
+DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALTEANSGRVAQALVAAGAGVAVVTEDP
+AFGLTPVRVIAQGRTLTVRLHAAWRGDHFAAETLEAIARRLQAFVRDRYAEPGDDAPGRG
+RSA
+>PROKKA_00733
+MDEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVAGRFELTTA
+GEAFLPVAREVLVAHRRAEQAARALASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP
+RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD
+DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALVEANSGRVAQALVATGAGVAVVTEDP
+AFGLTPVRVIAQGRTLAVRLHAAWREDHFAAETLQALARRLQAFVRDRYAEPGDDAPR
+>PROKKA_01868
+MEERLLRAFVTVAEAGTVSAAAQRLDLVQSALSRQLQRLQRELRLPLFARVGSRLELTTA
+GEAFLPVARRVLAAHRQAEQAARTLASGSLAEVAIAAPGTTLIDVVLPFVATLDEDDPRP
+RVAETQLDDSLQDAVARHDLVVMPMAPGPTVQALHLIDLPVWAYVAPGHPWADRADVALE
+ELVDVRVVAPSRSFMARRVLDGAVAVAGLTAPELSEANSGRVAQALVATGAGVAVVTEDP
+AFGLVPLRVLLDGRALSVGLHAAWRADHFAAATLARIAASLQDFVRTRYPQPGPADDIPV
+TTRASPLSAAPSQ
+>PROKKA_01760
+MDSIAAGGRALDLDHLLDPALLRTFVAVVDEGTVTAAARELGLGQSALTRHLQRLQRDLG
+LALFAPEGARLRITPAGQAWLPVARSLLAAHAHARQAARILAAGRLTELSLGAPGTTLID
+VVIPFLTVLGEGDPAVRVTETQLDDSLQDSVARLDLVVLPSTPPDDVAALPLQSMPVWAC
+VAPGHPWADRDELDAAELAGARLVLPSRSFKARRVFDAALEVAGAAPRQVVEANSGRVAQ
+ALAANGTAVAVVTEDPAFGLRPLPIRAGGRRLEVHLHAVWRRDHFAAEEIAGVAAQLRVF
+VRRRYDVAEAQDDADGSLSRAVSVD
+>PROKKA_00963
+MEEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVGGRLELTTA
+GEAFLPVAREVLVAHRRAEQAARTLASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP
+RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD
+DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALVEANSGRVAQALVATGAGVAVVTEDP
+AFGLTPVRVIAQGRALAVRLHAAWREDHFATATLEKIARRLQAFVRDRYAEPGDDAPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000862.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000862.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ababf092e5eeae7aea013d2bc06727b4bc72f2ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000862.fa
@@ -0,0 +1,31 @@
+>PROKKA_01020
+MNTTVRRALWVVLVLLCLGLVFLALRGVLAVGAVPISAAPTLSATASATPSPSPSPSSAR
+FTPSPATTATPTPTPSPSSASPTREAAVPVETQELAGTPTPSEEPTPTEEPAPSEEPAPS
+EEPTPAAAAHLSGPAAPWDEVTATPVHVDVHQDGEQIVGAGIDLTQLDEGGDLDPEPQTV
+GWYGPPQWGTTPGERSRYAGVLAGHVVYHGVRDVFWNLGDVRAGAVVVVTYDDGTQAAFE
+ADSDAVSVEKEALTQDPANRWAWEPGGDDAKVTLITCDLVPGTGMAGNAFNNWVVQATRV
+A
+>PROKKA_00734
+MNTTVRRALWVVLVLLCLGLVFLALRGVLAVGAVPISAAPTLSATASATPSPSPSPSSAR
+FTPSPAPTATPIPTPSPSSASPTREAAVPVETQELAGTPTPSEEPTPTEEPAPSEEPAPS
+EEPTPAAAAHLSGPAAPWDEVTATPVHVDVHQDGEQIVGAGIDLTQLDEGGDLDPEPQTV
+GWYGPPQWGTTPGERSRYAGVLAGHVVYYGVRDVFWNLGDVRAGAVVVVTYDDGTQAAFE
+ADADAVSVEKEALTQDPAHRWAWEPGGDDAKVTLITCDLVPGTGMAGNAFNNWVVQATRV
+A
+>PROKKA_01867
+MTGPAAPWESIDAAPVHVEVHQDGERIVGASVEHTQMNEAGELDPDPQTVGWYGAPQWGT
+DPGERSPYAGILAGHVVYYGVKDVFWNLDAVRAGDVVVLTYDDGSQAVFEADADAVSVEK
+EALTQDPANRWAWEPGGDDARLTLITCDLVPGTGMAGNAFNNWVVQATRVA
+>PROKKA_01763
+MSTTVKRAVWALLLLICLGVGAFALRGMFAFGDVPISAAPTVSARASTASSTPSAATGSP
+SSTSASASAGPSVPAATSASSAAASTTTPASPTSSTTTPASPTSSTTPASTEAAAPAVGA
+ASSTATASSSATPTGTDSRMTKPAASWERITAAPVHIDVYADGEQVVGAPVELVQTRDDG
+ELNPDPQMAGWYGPPQWTTTPGERSAHPGVIAGHVIHSGLKDVFWNLQTLKAGSIVVITY
+DDGTQAEFRTDFDVRSMDKDDLTQSPDYAWAWELPEAGNKVTLITCDLVDGSGMTGWSTN
+NWVTQATRIG
+>PROKKA_00964
+MNTTVRRALWVVLLLLCLSLVFLALRGVLAVGAVPISAAPTLSATASVSPSSAATTREAA
+VPVETQELAGTPTPSEEPTPTEEPAPSEEPTPAAAAHLSGPAAPWDEVTATPVHVDVHQD
+GEQIVGAGIDLTQLDEGGDLDPEPQTVGWYGPPQWGTTPGERSRYAGVLAGHVVYHGVRD
+VFWNLGDVRAGAVVVVTYDDGTQAAFEADADAVSVEKEALTQDPSHRWAWEPGGDDAKVT
+LITCDLVPGTGMAGNAFNNWVVQATRVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000863.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000863.fa
new file mode 100644
index 0000000000000000000000000000000000000000..96116a850f907b95f7d8f0192711202fcfddb8b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000863.fa
@@ -0,0 +1,33 @@
+>PROKKA_01021
+MSRADIAPARVRPRRWSVAVGGALLSITLATGGCSVAEEPGQTGGTEAGNTYLEGVLASP
+SQTSADPLAADIQFAGLLLRNHRDAIQQSDQVLGKDGVDQEIRATAERMKSEHEERAGRL
+ESMLEGWGVPSDDVRGAGAESTPSAQPESTEDAEPTQIVGDELRAGLLSDREKNVLAAAE
+PEEAGRIYLLQMRRLYQGALTISATEAEDGSDDAAKELASSVVEGHRKELESLAATLGEM
+GVIGSSGARTAEPSGFTGPIKIEGTGADGGSVPSDFVPEPLQRVRSFRATQKPVLPSSSS
+PSSSSASGSASASGRDAEDQRGRDAASASPSPSPADTAQATPRPSSGASPSPSASR
+>PROKKA_00735
+MSRADIAPARVRPRRWSVAVGGALLSITLATGGCSVAEEPGQTGGTEAGNTYLEGVLASP
+SQTSADPLAADIQFAGLLLRNHRDAIQQSDEVLGKDGVDQEIRATAERMKSEHEERARRL
+ESMLEGWGVPSDDVRGAGAESTPSAQPESTEDAEPTQIVGDELRAGLLSDREKNVLAAAE
+PEEAGRIYLLQMRRLYQGALTISATEAEDGSDDAAKELASSVVEGHRKELESLAATLGEM
+GVIGSSGARTAEPSGFTGPIKIEGTGADGGSVPSDFVPEPLQRVRNFRATQKPVLPSSSS
+PSSSSASGPASASGRDAEDQRGRDAASASPSPSPADTAQATPRPSSGASPSSSASR
+>PROKKA_01866
+MPVTGDELRAGLLSEREKNVLAAADAEDAGRIYLLQMHRVYQGALTISATEAESGTDEEA
+KALAASVVADHQEDMQRMVEVLADMGAIGADASHTALPSGYTGPIKIEGTGADGGPVPSD
+FVPEPVQRVQSFRATQRPVLPTSSSPGDAEDRRGRDSATASPSPTPADTARPSPSPSSAA
+SPSPSATTGSPSGTNR
+>PROKKA_01762
+MNRATDATAPVCPVRWSAAAGGLLGLSLVLAGCGTSAQPVPAGSGSNTYLEGVLATPSAT
+KADPLAADQRFVASLLQNQYQVVQEADHVLSRPDMDGEVRDMAQQHKDVANQRIGDLSSR
+LQAWGLEVPAAPEPLVDDTKPSGRPTGDPSEIQASKGQQAAADIRAGLLTASDQSALVTA
+DDDAAGRIYLLQVHRLLQGGVSLAGTESDEGTDEETKKIASDLIDADRPRMQRILEKLGE
+NGVVAAVPSPTAPNSGYQGPISLPSQAGGDGANVDYTPSALYEMWSTLPPPATSSSADGS
+STGPSPSAQPTPTPADTASPRPTPGASAQPGAASSTASTTGAASTRNG
+>PROKKA_00965
+MSRADIAPARVHPRRWSVAVGGALLSITLATGGCSVVEEPGQTGDTEAGNTYLEGVLASP
+SQTSADPLAADIQFAGLLLRNHRDAIQQSDQVLGKDGVDQEIRATAERMKSEHEERAGRL
+ESMLEGWGVPSDDVRGAGAEATPSAQPESTEDAEPAEIVGDELRAGLLSDREKNVLAAAE
+PEEAGRIYLLQMRRLYQGALTISATEAEDGSDDAAKELASSVVEGHRKELESLAATLAEM
+GVIGSSGARTAEPSGFTGPIKIEGTGADGGSVPSDFVPEPLQRVRNFRATQKPVLPSSSS
+PSSSSASGSASASGRDAEDQRGRDTASASPSPSPADTAQATPRPSSGASPSPSASR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000866.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000866.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1c5d17f901d3b18851514659cbb5a22a0d07e417
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000866.fa
@@ -0,0 +1,15 @@
+>PROKKA_01024
+MTVTVYTKPACVQCNATYRALDKKGIAYEVVDMSQDPAALERVRALGFMQAPVVVTETDS
+WSGFRPDKIAELAESAAASVA
+>PROKKA_00739
+MTVTVYTKPACVQCNATYRALDKKGIAYEVVDMSQDPAALERVRALGFMQAPVVVTETDS
+WSGFRPDKIAELAESAAASVA
+>PROKKA_01861
+MTVTVYTKPACVQCNATYRALDKKGIAYEIVDMSQDPAALERVRGLGFMQAPVVVTETDS
+WSGFRPDKIAELAEAAAASVA
+>PROKKA_01751
+MTVTVYTKPACVQCNATYRALDKKGIAYETVDMSQDPEALDRVRALGFMQAPVVITDTDS
+WSGFRPDKIAELAESAATQVA
+>PROKKA_00968
+MTVTVYTKPACVQCNATYRALDKKGIAYEVVDMSQDPAALERVRALGFMQAPVVVTETDS
+WSGFRPDKIAELAESAAASVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000868.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000868.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cbd5a2591e867a1e1e7e49b10b32b49d1f4e12a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000868.fa
@@ -0,0 +1,70 @@
+>PROKKA_01026
+MTTTAPTEADLIRQAKNMPAEWQNLGYHELNAMLNLYGADGRIQFEADHAAARQYFLQHV
+NTNTVFFHDLEEKLDYLQKNDYYETETFEQYPFEFIRGLFDRAYKAKFRFPTFLGAFKFY
+TSYALKTFDGKRYLERYEDRVAVVALHLARGDQELATHLVDEMIAGRFQPATPTFLNSGK
+KQRGELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNIREHGAPIKQIENQSS
+GVIPVMKLLEDSFSYANQLGARQGAGAVYLNAHHPDIHRFLDTKRENADEKIRIKTLSLG
+VVIPDITFQLAKKNEDMYLFSPYDVERVYGVPFSEISVTEKYYEMVDDARIKKTKINARE
+FFQTIAEIQFESGYPYVVFEDTVNAANPIKGRITMSNLCSEILQVSEASEYNEDLSYAHV
+GQDISCNLGSMNIAKTMDSPDFGRSVETAIRALTAVSVMSDIQSVPSIAKGNAASHAIGL
+GQMNLHGYLARERVHYGSEEGIDFTNMYFYAVLFHALRASNRIAIETGQRFGGFEDSKYA
+SGEFFDKYTDQEWAPATERVAELFAEAGIALPTQDDWRELKASVMEHGIFNRNLQAVPPT
+GSISYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDT
+YAAATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWTKGIKTIYYIRLRQLALEGTEVEGC
+VSCML
+>PROKKA_00741
+MTTTAPTEADLIRQAKNMPAEWQNLGYHELNAMLNLYGADGRIQFEADHAAARQYFLQHV
+NTNTVFFHDLEEKLDYLQKNDYYETETFEQYPFEFIRGLFDRAYKAKFRFPTFLGAFKFY
+TSYALKTFDGKRYLERYEDRVAVVALHLARGDQELATHLVDEMIAGRFQPATPTFLNSGK
+KQRGELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNIREHGAPIKQIENQSS
+GVIPVMKLLEDSFSYANQLGARQGAGAVYLNAHHPDIHRFLDTKRENADEKIRIKTLSLG
+VVIPDITFQLAKKNEDMYLFSPYDVERVYGVPFSEISVTEKYYEMVDDARIKKTKINARE
+FFQTIAEIQFESGYPYVVFEDTVNAANPIKGRITMSNLCSEILQVSEASEYNEDLSYAHV
+GQDISCNLGSMNIAKTMDSPDFGRSVETAIRALTAVSVMSDIQSVPSIAKGNAASHAIGL
+GQMNLHGYLARERVHYGSEEGIDFTNMYFYAVLFHALRASNRIAIETGQRFGGFEDSKYA
+SGEFFDKYTDQEWAPATERVAELFAEAGIALPTQDDWRELKASVMEHGIFNRNLQAVPPT
+GSISYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDT
+YAAATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWTKGIKTIYYIRLRQLALEGTEVEGC
+VSCML
+>PROKKA_01859
+MTLTAPTEADLIRQAKNMPAEWQNLGYHELNAMLNLYGADGRIQFEADHAAARQYFLQHV
+NTNTVFFHDLEEKLDYLQKNDYYETETFEQYPFEFIRGLFDRAYKAKFRFPTFLGAFKFY
+TSYALKTFDGKRYLERYEDRVAVVALHLARGDQELATHLVDEMIAGRFQPATPTFLNSGK
+KQRGELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNIREHGAPIKQIENQSS
+GVIPVMKLLEDSFSYANQLGARQGAGAVYLNAHHPDIHRFLDTKRENADEKIRIKTLSLG
+VVIPDITFQLAKKNEDMYLFSPYDVQRVYGVPFSEISVTEKYYEMVDDARIKKTKINARE
+FFQTLAEIQFESGYPYIVFEDTVNRANPIKGRITMSNLCSEILQVSEASEYNEDLTYSHI
+GQDISCNLGSMNIAKTMDSPDFGQSVETAIRALTAVSVMSDIQSVPSIAKGNSASHAIGL
+GQMNLHGYLARERVHYGSEEGVDFTNMYFYAVLFHALRASNKIAIETGERFGGFEDSKYA
+SGEFFDKYTDQEWTPATERVAGLFSDAGITLPTQEDWRELKASVMEHGIFNRNLQAVPPT
+GSISYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDT
+YAAATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWRKGIKTIYYIRLRQLALEGTEVEGC
+VSCML
+>PROKKA_01749
+MTVTEADLIQQAKHMPEAWQDLGYHELNAMLNLYGSDGKIQFEADHAAARQYFLQHVNTN
+TVFFHDLEEKLEYLQEKHYYEPETFAQYAPEFVKATFDRAYKAKFRFPTFLGAFKFYTSY
+ALKTFDGKRYLERYEDRVAVVALHLAAGDEALATHLVDEMISGRFQPATPTFLNAGKAQR
+GELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNVREQGAPIKHIQNQSSGVL
+PVMKLLEDSFSYANQLGARQGAGAVYLHAHHPDIHRFLDTKRENADEKIRIKTLSLGVVI
+PDITFELAKRNEDMYLFSPYDVERVYGKAFSEISVTEKYYEMVDDARIKKTKINAREFFQ
+TLAEIQFESGYPYIVFEDTVNRANPIKGRITMSNLCSEILQVSEASEYNEDLSYAHVGQD
+ISCNLGSMNIAKTMDSPDFGRSVETAIRALTAVSVMSDIQSVPSIAKGNSASHAIGLGQM
+NLHGYLAREHVHYGSEEGVDFTNIYFYTVLFHALRASNLIAQETGQKFGGFEDSTYASGE
+FFAKYTEQEWTPATARVAELFETAGIDIPTQDDWRELQAKVMEHGLFNRNLQAVPPTGSI
+SYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDTYAA
+ATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWTKGIKTIYYIRLRQLALEGTEVEGCVSC
+ML
+>PROKKA_00970
+MTTTAPTEADLIRQAKNMPAEWQNLGYHELNAMLNLYGADGRIQFEADHAAARQYFLQHV
+NTNTVFFHDLEEKLDYLQKNDYYETETFEQYPFEFIRGLFDRAYKAKFRFPTFLGAFKFY
+TSYALKTFDGKRYLERYEDRVAVVALHLARGDQELATHLVDEMIAGRFQPATPTFLNSGK
+KQRGELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNIREHGAPIKQIENQSS
+GVIPVMKLLEDSFSYANQLGARQGAGAVYLNAHHPDIHRFLDTKRENADEKIRIKTLSLG
+VVIPDITFQLAKKNEDMYLFSPYDVERVYGVPFSEISVTEKYYEMVDDARIKKTKISARE
+FFQTIAEIQFESGYPYVVFEDTVNAANPIKGRITMSNLCSEILQVSEASEYNEDLSYAHV
+GQDISCNLGSMNIAKTMDSPDFGRSVETAIRALTAVSVMSDIQSVPSIAKGNAASHAIGL
+GQMNLHGYLARERVHYGSEEGIDFTNMYFYAVLFHALRASNRIAIETGQRFGGFEDSKYA
+SGEFFDKYTDQEWAPATERVAELFAEAGIALPTQDDWRELKASVMEYGIFNRNLQAVPPT
+GSISYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDT
+YAAATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWRKGIKTIYYIRLRQLALEGTEVEGC
+VSCML
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000870.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000870.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d600a0cee6d26cfa5c0b2f480b43544cd67e0c1a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000870.fa
@@ -0,0 +1,30 @@
+>PROKKA_01031
+MTDITSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQSHNALHGWGGGYIASLNGVILPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL
+>PROKKA_00746
+MTDITSTPATSVAGDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQSHNALHGWGGGYIASLDGVVLPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHAEQTLTLRSWPAEGGL
+>PROKKA_01851
+MTDISSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQEHNALDGWGGGYIASLDGVILPGHGPGHG
+RVWLTTDREMVVGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL
+>PROKKA_01741
+MTDITSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQAHNALHGWGGGYIASLDGVILPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+PWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL
+>PROKKA_00975
+MTDITSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQSHNALHGWGGGYIASLDGVILPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000871.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000871.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b53984467c9f5f64afbf54b08a17d7ad78311779
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000871.fa
@@ -0,0 +1,30 @@
+>PROKKA_01032
+MSVAPRLRWAVQERTLGAVEDLDWAMGELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR
+DARLPGFAAAAAAARAHGFAPAVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF
+ADLFVRAFARMDVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV
+VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGI
+EVVAEQLAVLGARTSG
+>PROKKA_00747
+MSAAPRLRWAVQERTLGAVEDLDWAMDELAVFRAAAAEGRALDGLIRVYVPEPTVAFGQR
+DARLPGFEAAAAAARAHGFEPVVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF
+ADLFVRAFARMDVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV
+VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAGLE
+VVDEQLAVLTAGTAG
+>PROKKA_01850
+MSAAPRLRWAVQERTLGATDDLDWAMDELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR
+DARLPGFEAAAAAARTHGFEPAVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF
+ADLFVRAFARMGVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV
+VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGL
+KVVDEHLAVLAAGTSG
+>PROKKA_01740
+MSAAPRLRWAVQERTLGAADDLDWAMGELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR
+DARLPGFEAAAAAARAHGFEPAVRRAGGRAAAYHHGCLVVDHLSQQEDATLTQQARFAEF
+ADLFVRAFARMGVPASVGEIPGEYCPGEFSVQGPAPAYPVKLAGSAQRVVKGAFLFSTHV
+VVSDPAPLRAVLVDVYRELGLGMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGL
+EVVDEQLAVLGAGTSG
+>PROKKA_00976
+MSAAPRLRWAVQERTLGAVEDLDWAMGELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR
+DARLPGFAAAAAAARAHGFAPAVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF
+ADLFVRAFARMDVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV
+VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGI
+EVVAEQLAVLGARTSG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000873.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000873.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4eda628c8b506b09e2b4f401974fb0cc9b111ba5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000873.fa
@@ -0,0 +1,25 @@
+>PROKKA_01036
+MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV
+LTHGHDDHIRQVQEFRQMVDAPALLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR
+VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI
+RERLLSLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH
+>PROKKA_00749
+MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV
+LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR
+VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI
+RERLLPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH
+>PROKKA_01848
+MARIDHLVTSGTFSLDGETFDVDNNVWLVGGAEQCIVIDPAHDASAVWKKVNGRQVLAIV
+LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR
+VLHTPGHSPGSVCLYAPALGEAGDDGGATGVVFSGDTLFQGGPGATGRSYSDFDTIIESI
+RERLFPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH
+>PROKKA_01738
+MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV
+LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR
+VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI
+RERLFPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH
+>PROKKA_00978
+MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV
+LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDAVFPDEEPDGALAEGDVLRVAGVELR
+VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI
+RERLFPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000878.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000878.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba7d3795e727224ee855118f69a02086eb1fe638
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000878.fa
@@ -0,0 +1,109 @@
+>PROKKA_01045
+MSQAAAAGRTAAPFAHLHVASAFSAHHGVSWPEDLVAAAAAADMDLLACTDRDGLYGMAK
+HVGACLRHGITPIVGVDLAVRWSEDGDAGRVVVLARGGCHGSGYRSLCELVSAAHARTTG
+GAAGGSPWASVAELAAAAAGRVPTAANRDNPSTPELFVLLGPDSDVGRHLARRRYAAGLA
+ALHRWKAALPAGSPHADVVTHLSAPGRRLDTGHAVKTLRAARQARIPAVLTNAVRYAAPD
+GAATADVLDAVRALSSLDALHDLQPNGQGWLKSTAAMHRIAHEVAFAADDRPAPLLEATR
+RLAEACALDPETDLGWGVPRVPEAAVIGIDGPPEHVLRERTRTGLLARYPHLHTGGGLPG
+TSQAARDLQDRAEHELGIITRLGFSSYFLTVAAVVDLIEGMGIRVAARGSGASSLVNHAL
+RISHVDPMANGLIMERFLSTDRSTLPDIDIDVESARRHEIYHAVVERFGAERTTLMSMQN
+AYRARGAVRDAGLALGMPEPEVDAIAKQLWRFSASNFREALQRMPELGGLSRRIESGRAE
+GDRQLDLLVDLTERLDRLPRHISMHPCGVILGDATLLHRTPVQPSGMGLPMSQFDKHDMD
+PMGFLKLDILGVRMQSAIAYTIAEVERTTGERIDLEQVPLDDPATYAMIRTTHTLGCFQI
+ESPGQRELVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPAHYPHPDLRPV
+LAETHGVTVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHLVEEAFRTGALARGYSLD
+VIDEVWATLSAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPAAFMAAILEHDPGMYPARLM
+VAEARRMGIPVLPVDVNASSRHVHVEWVPAHPEIDDGAPGRWGIRLPLTSLSGLSEAETD
+RLDAGRPYRSLADVRDRARPTARNLERLAQLGALDCLLPPGGASRTDLVHHLELQHSTTR
+GTAPGRTAPRSRSARPRQVEGQLALDLPDTELTALAPLFPDPGPAARVRTELELTALDVT
+AHLMDSHAPYLDALGVTRAKDLLGLRTQSRVLVAGVRVATQTPPMRSGKRVVFLSVDDGT
+GCVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGDRAVSVQAVRAWDLHRPETLPDPDY
+LDATRQQWRDWLAADRRAAAARRSSRAGTGAQPLPDIPHHGTGGWPVKVRTDVGPAGGAR
+PGRTAPDRPAPEHTPIPVPHPETWELLPTPDR
+>PROKKA_00758
+MSRAAAAGRTVAPFAHLHVASAFSAHYGVSWPEDLVAAAAAADMDLLACTDRDGLYGMAK
+HVGACLRHGITPIVGVDLAVRWSEDEDAGRVVVLARGGCHGSGYRSLCELVSAAHARTTG
+GAAGGSPWASVAELAAAAAGRVPTAANRDNPPTPELFVLLGPDSDVGRHLARRRYAAGLA
+ALHRWKAALPAGSPHADVVTHLSAPGRRLDTGHAVKTLRAARQARIPAVLTNAVRYAAPD
+GAATADVLDAVRALSSLDALHDLQPNGQGWLKSTAAMHRIAHEVASAADDRPAPLLEATR
+RLAEACALDPETDLGWGVPRVPEAAVIGIDGPPEHVLRARTRTGLLARYPHLHTGGGLPG
+TSQAARDLQDRAEHELGIITRLGFSSYFLTVAAVVDLIEGMGIRVAARGSGASSLVNHAL
+RISHVDPMANGLIMERFLSTDRSTLPDIDIDVESARRHEIYHAVVERFGAERTTLMSMQN
+AYRARGAVRDAGLALGMPEPEVDAIAKQLWRFSASNFREALQRMPELGGLSRRIESGRAE
+GDRQLDLLVDLTERLDRLPRHISMHPCGVILGDAALLHRTPVQPSGMGLPMSQFDKHDMD
+PMGFLKLDILGVRMQSAIAYTIAEVERTTGERIDLEQVPLDDDATYAMIRTTHTLGCFQI
+ESPGQRELVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPAHYPHPDLRPV
+LAETHGVTVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHLVEEAFRTGALARGYSPE
+VIDEVWATLSAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPAAFMAAILEHDPGMYPARLM
+VAEARRMGIPVLPVDVNASSRHVHVEWVPAHPEVDDGAPGRWGIRLPLTSLSGLSEAETD
+RLDAGRPYRSLADVRDRARPTARNLERLAQLGALDCLLPPGGASRTDLVHHLELQHSTTR
+GTAPGRTAPRSRSARPRQVEGQMALDLPDTELTALAPLFPDPAPAARVRTELELTALDVT
+AHLMDSHAPYLDALGVTRAKDLLGLRTQSRVLVAGVRVATQTPPMRSGKRVVFLSVDDGT
+GCVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGGRAVSVQAVRAWDLHRPQTLPDPDY
+LDATRQQWRDWLAADRRAAAARRSGRAGTGAQPLPDIPHHGTGGWPVKVRTDVGPAGGAR
+PGRTAPDRPAPEHTPIPVPHPETWELLPTPDR
+>PROKKA_01844
+MGLRRRARRRRGSSRVPTAANRDNPPTPELFVLVGPDADVGRHLARRRSAAGLAALRRWK
+EALPAGSLHADVVTHLSTPGRRLDAGHAVKALRTARRAGVPAVLTNAVRYAGPDGAATAD
+VLDAVRALSSLDAVHDLQPNGQGWLKPTAAMHRVAHEVASAADERAAPLLEATRRLAEAC
+VLDPEADLGWGVPRVPEAAVIGIEGPPERVLRERTYAGLAARYPRLHAGGRLTSAAEARD
+LEARAEHELGIITRLGFSSYFLTVAAVVDLIEGMGVRVAARGSGASSLVNHALRISNVDP
+VANGLIMERFLSDARSTLPDIDIDVESARRHEIYRAVFERFGAERTTLMSMQNAYRARGA
+VRDAGLALGMPEPEVDGIAKQLWRFSASSFREALERMPELGGLSRRIESGRAEGSRQLDL
+LVDLTERLDRLPRHISMHPCGVILGDAALLHRTPVQPSGMGLPMSQFDKHDMDPMGFLKL
+DILGVRMQSAIAYTLAEVERTTGERVDLEQVPLDDPATYAMIRTTHTLGCFQIESPGQRE
+LVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPARYPHPDLRPVLAETHGV
+TVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHRVEEAFRAGALARGYSLDVIDEVWA
+TLAAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPEAFMAAILEHDPGMYPARLMVAEARRM
+GIPVLPVDVNASSRHVRVEWVPWHPELDGPPAEDAGAGGGEPGDVVARPHAEGGAEADLA
+EGAGRGPGRWGIRLPLTGLSGLSEAETERLDAGRPYRSLADVRDRARPTARNLERLAQLG
+ALDCLLPAGGASRTDLVHHLELQHSATRGSGPGRAAARSRSARPRQVDGQLALDLPDTEL
+AALTPLFPDPSVAARVRTELELTALDVTAHLMDSHAPYLDALGVTRAADLLGLRTQSRVL
+VAGVRVATQTPPMRSGKRVVFLSVDDGTGCVDASFFTEAQHASGEMLFSARLLLIEGTVR
+RTGPRAVSVQAVRAWDLHRPESLPDPDYLDATRRQWREWLAADRRAAAARRRGQEDAGAP
+RLPDIPHHGTGGWPVKVALGGAGAPSPSSDARAPAGRGVSAGAGPGAAGQGAAARVGAGG
+VPADRRPIPVPHPDTWELLPTPER
+>PROKKA_01731
+MSAFPHLHVASAFSAHHGVSWPADLAAAAAAADMDLLACTDRDGLYGTVKHVGACLARRI
+TPIVGVDLAVRWDEDEPAGRVVVLARGGCHGTGYRALCRLVSAAHARTAGGAAGGAPWVL
+VAEVAAAAAGPIPTGANPGNPPTPELFVLVGPDSDVGRHLARRRTAAGLAALRRWRAALP
+AGATRAEVVSHLSAPGRRLDTGHAVKMLRTARTARVAPILTNAVRYAAPDGAATADVLDA
+VRALSALDAVHDLQPNGQGWLKPTAAMEALAAEIAHAADEHPAALLESTRALAEACALDP
+ETDLGWGRPRVPEASVVGTVGDPRQVLRERTRAGLAARYPHLHTGAGLPGTTQAARDLQD
+RAEQELGIIDRLGFAGYFLTVAAVVELIEGMGVRVAARGSGASSLVNHALRISHVDPMAN
+GLIMERFLSDARSTLPDIDIDVESARRHEIYRAVVDRFGAERTTLMSMQNAYRARGAVRD
+AGLVLGMEEDEVDGIAKQLWRFSASSFRDALDRMPELSSLAARIDAGRAAGRHQLDLLVD
+LTERLDRLPRHISMHPCGVILSDAALLDRTPVQPSGMGLPMSQFDKHDMDPMGFLKLDIL
+GVRMQSAIAYTLQEVERTTGERIDLEQVPLDDPATYAMIRTTHTLGCFQIESPGQRELIG
+KLEPREFNDLTVDISLFRPGPMQSDMVRPFLEHRHGWAPAHYPHPHLEPVLAETHGVTVF
+HEQVLRTLDVMTGCGLARADELRRLVGGPEEHRVETFFRTAALENGYSLDVVDEVWHTLH
+AFGSFGFCKAHGAAFAVPTYHSAWLKTHHPEAFMAAVLEHDPGMYPARLMVAEARRMGIP
+VLPVDVNASTRHVHVEWVPSHPEVDGADPTTDPATGAPGRWGIRLPLTSLSGLSAAEVDR
+LDAGRPYATLADVRDRARPTARSLERLAQLGALDSLLPAGGASRTDLVHHLELQHSATRS
+TDPGRTARRSRTARPRQVDGQLALDVPDTELTALTPLFPEPSRDAAVRTELDLTALDVTA
+HLMDSHAPYLDALGVTRAEDLLSLRSQSRVLVAGVRVATQTPPMRSGKRVVFVSVDDGTG
+CVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGARAVSVQGVRAWDLHRPERLPDPDYL
+DATREQWRAWLAADRRAAAARRRGETPVGAVPDIPHHSTGGWPVKVRADVAVGRERAAVE
+RPAPAPSSRPIPVPHPETWELLPTPES
+>PROKKA_00986
+MSQAAAAGRTAAPFAHLHVASAFSAHYGVSWPEDLVAAAAAADMDLLACTDRDGLYGMAK
+HVGACLRHGITPIVGVDLAVRWSEDENAGRVVVLARGGCHGSGYRSLCELVSAAHARTTG
+GAAGGSPWASVAELAAAAAGRVPTAANRDNPPTPELFVLLGPDSDVGRHLARRRYAAGLA
+ALRRWEAALPAGSPHADVVTHLSAPGRRLDTGHAVKTLRAARQARIPAVLTNAVRYAAPD
+GAATADVLDAVRALSSLDALHDLQPNGQGWLKSTAAMHRIAHEVAFAADDRPAPLLEATR
+RLAEACALDPETDLGWGVPRVPEAAVIGIDGPPEHVLRERTRTGLLARYPHLHTGGGLPG
+TSQAARDLQDRAEHELGIITRLGFSSYFLTVAAVVDLIEGMGIRVAARGSGASSLVNHAL
+RISHVDPMANGLIMERFLSTDRSTLPDIDIDVESARRHEIYRAVVDRFGAERTTLMSMQN
+AYRARGAVRDAGLALGMPEPEVDAIAKQLWRFSASNFREALQRMPELGGLSRRIESGRAE
+GDRQLDLLVDLTERLDRLPRHISMHPCGVILGDATLLHRTPVQPSGMGLPMSQFDKHDMD
+PMGFLKLDILGVRMQSAIAYTIAEVERTTGERIDLEQVPLDDPATYAMIRTTHTLGCFQI
+ESPGQRELVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPAHYPHPDLRPV
+LAETHGVTVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHLVEEAFRTGALARGYSLE
+VIDEVWATLSAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPAAFMAAILEHDPGMYPARLM
+VAEARRMGIPVLPVDVNASSRHVHVEWVPAHPEIDDGAPGRWGIRLPLTSLSGLSEAETD
+RLDAGRPYRSLADVRDRARPTARNLERLAQLGALDCLLPPGGASRTDLVHHLELQHSTTR
+GTAPGRTAPRSRSARPRQVEGQLALDLPDTELTALAPLFPDPGPAARVRTELELTALDVT
+AHLMDSHAPYLDALGVTRAKDLLGLRTQSRVLVAGVRVATQTPPMRSGKRVVFLSVDDGT
+GCVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGDRAVSVQAVRAWDLHRPETLPDPDY
+LDATRQQWRDWLAADRRAAAARRSGRAGTGAQPLPDIPHHGTGGWPVKVRTDVGPAGGAR
+PGRTAPDRPAPEHTPIPVPHPETWELLPTPDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000890.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000890.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e833bd484c3e4f32a0a3b0a9662cdb50e647f52
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000890.fa
@@ -0,0 +1,25 @@
+>PROKKA_01061
+MTARPPRLHPSILSADFARLADDLARIPSADAVHVDVMDNHFVPNLTLGLPVVEAIRRAT
+DLPLDLHLMIEDADRWAPGYAEAGAESVTFHAEASAAPVRLARELRAAGAKAGMALRPAT
+AVEPYLDMLPELDMLLLMTVEPGFGGQAFLDVVLPKIRRARRALDGGPAPLALQVDGGVN
+RETIERAAEAGADVFVAGSAVFGAEDPDAALAGLRTAAARACH
+>PROKKA_00780
+MTARPPRLHPSILSADFARLADDLARIPSADAVHVDVMDNHFVPNLTLGLPVVEAIRRAT
+DLPLDLHLMIEDADRWAPGYAEAGAESVTFHAEASAAPVRLARELRAAGAKAGMALRPAT
+AVEPYLDMLPELDMLLLMTVEPGFGGQAFLDVVLPKIRRARRALDGGPAPLALQVDGGVN
+RETIERAAEAGADVFVAGSAVFGAADPDAALVGLRTAAARACH
+>PROKKA_01825
+MSPRAPRLHPSILSADFAHLAEELGRIRGADAVHVDVMDNHFVPNLTLGLPVVEAIRRAT
+DLPLDIHLMIEDADRWAPGYAEAGAESVTFHAEASAAPVRLARELRAAGARAGMALKPAT
+PVEPYLDMLPELDMLLLMTVEPGFGGQAFLDVVLPKIRRARRALDGAAAPLALQVDGGVN
+AETIERAAEAGADVFVAGSAVFGAEDPDAAVDGLRRAAARACC
+>PROKKA_01715
+MSAHPCIHPSILSADFARLADELARIPGSDAVHVDVMDGHFVPNLTLGLPVVEAIRAATD
+LPLDIHLMIEDADRWAPAYADAGAESVTFHAEAARAPIVLARSLRAAGAQAGLAVRPATP
+IEPYLDLLPELDMLLIMTVEPGFGGQSFLDVTLPKIRRARQALDGAPVPVRLQVDGGVNR
+ETILRAAEAGADVFVAGSAVFGADDPGAAIAGLRDLAAGVAPACHTR
+>PROKKA_01008
+MTARALRLHPSILSADFARLADELARIPSADAVHVDVMDNHFVPNLTLGLPVVEAIRRAT
+DLPLDLHLMIEDADRWAPGYAEAGAESVTFHAEASAAPVRLARELRAAGAKAGMALRPAT
+AVEPYLDMLPELDMLLLMTVEPGFGGQAFLDVVLPKIRRARRALDGGPAPLALQVDGGVN
+RETIERAAEAGADVFVAGSAVFGAEDPDAALAGLRTAAARACH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000900.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000900.fa
new file mode 100644
index 0000000000000000000000000000000000000000..223d703be8e3289b074ea9f7319cd97101bc6882
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000900.fa
@@ -0,0 +1,15 @@
+>PROKKA_01084
+MSHTANTAHTEPTTRRAARRGAVEDVVVTEDGLVLNDPTHLELPGHGNSPGAWAMVALVL
+VGFVAGCVGLLADWSVVVWIGVALMAVGVVVGIVAGKAGAGRGQHGH
+>PROKKA_00803
+MSHTANTAHTEPTTRRAARRGAVEDVVVTEDGLVLNDPTHLELPGHGNSPGAWAMVALVL
+VGFVAGCVGLLADWSVVVWIGLALMAVGVVVGIVAGKAGAGRGQHGH
+>PROKKA_01813
+MSHTANTEHTTRRAARNGAVEDVVVTEDGRVLNDPTHLELPDHGNTPGGWAMVALVLVGF
+VAGCIGLLADWMIVVWIGVALIVVGVLVGIVAGRGGSARSGHRAH
+>PROKKA_01701
+MSHTEATVNHTAQAGAHAAGHTTGHTASREVVVTEDGRVLNDPTHAKVPGHGNSPAAWAM
+AGLVVLGFLAGCIGLLNDALVIVWIGVAVIVVGVLVGIVGGKAAGRSDH
+>PROKKA_01033
+MSHTANTAHTEPTTRRAARRGAVEDVVVTEDGLVLNDPTHLELPGHGNSPGAWAMVALVL
+VGFVAGCVGLLADWSVVVWIGLALMAVGVVVGIVAGKAGAGRGQHGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000902.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000902.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5f1b6dca9c1c14c25483dd607ce23188329cf51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000902.fa
@@ -0,0 +1,45 @@
+>PROKKA_01086
+MSADRPSTEPAIEFEGPYQGQAGPYFGDYGGQWMPESLMAALQELTRTYEEARQDPAFEA
+ELRTLFRDYVNRPSLLSEVPRFAADTPGVRIFLKREDLNHTGSHKINNVIGQALLARRMG
+KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVVPVAIG
+ARTLKDAINEALRDWVASVDTTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQAGR
+LPDAVAACVGGGSNAMGLFHGFLDDPGVELYGFEAGGEGLETGRHAASITLGRTGVLHGA
+RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLHDTGRAVYEPVSDTECMDAFLRLTRT
+EGITPAIESAHALAGALRLARRWADEGLVGPDAPEGQERIIIVNLSGRGDKDVATAAAWF
+GLGTATEEKDPLEEMTPGEEQ
+>PROKKA_00805
+MSADRPSTEPAIEFEGPYQGQAGPYFGDYGGQWMPESLMAALQELTRTYEQARQDPAFEA
+ELRTLFRDYVNRPSLLSEVPRFAADTPGVRIFLKREDLNHTGSHKINNVIGQALLARRMG
+KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVVPVAIG
+ARTLKDAINEALRDWVASVDNTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQAGR
+LPDAVAACVGGGSNAMGLFHGFLDDPEVELYGFEAGGEGLETGRHAASITLGRTGVLHGA
+RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLHDTGRAVYEPVSDTECMDAFLRLTRT
+EGITPAIESAHALAGALRLARRWADEGLVGPDAPEGEERIIIVNLSGRGDKDVATAAAWF
+GLGTAAEEKDPLEEMTPGEEQ
+>PROKKA_01811
+MSADRPSTEPTVEFEGPYQGQSGPYFGDYGGQWMPESLMAALQEVQRTYEEARQDPAFEG
+ELRTLFRDYVNRPSLLSDVPRFAADSPGVRIMLKREDLNHTGSHKINNVIGQALLARRMG
+KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVVPVAIG
+ARTLKDAINEALRDWVASVDTTHYLLGTVTGPHPFPAMVRYFHSVIGEEARQQVLAQTGR
+LPHAVAACVGGGSNAMGLFHGFLDDPEVELYGFEAGGDGLETGRHAASITLGRTGVLHGA
+RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLNDTGRAVYEPVTDTECMDAFLRLTRT
+EGITPAIESAHALAGALRLARRWADEGLVGPDTPEGEERIIVVNLSGRGDKDVATAAAWF
+GLGQADAEKDPLEELTPGEEQ
+>PROKKA_01699
+MTSTESVDVAGPFQDQPGPYFGRYGGQWMPESLMAALKEVADTYEAARQDPEFLAELEDL
+YANYVNRPSLLTEAPRFAAEVPGVRIFLKREDLNHTGSHKINNVIGQALLARRMGKTRLI
+AETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVIPVTIGARTLK
+DAINEALRDWVASVDTTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQTGRLPDAV
+AACVGGGSNAMGLFHGFLDDPEVELYGFEAGGDGVETGRHAASITLGRTGVLHGARTYLM
+QDEDGQTIDSHSISAGLDYPAVGPEHAFLNDTGRATYEPVTDTECMDALLRLTRTEGITP
+AIESAHALAGALRLARRWRDEGLVGEGTPEGEERIIIVNLSGRGDKDVATAAAWFGLGEA
+DEQKDPLEEMTPGEEQ
+>PROKKA_01035
+MSADRPSTEPAIEFEGPYQGQAGPYFGDYGGQWMPESLMAALQELTRTYEQARQDPAFEA
+ELRTLFRDYVNRPSLLSEVPRFAADTPGVRIFLKREDLNHTGSHKINNVIGQALLARRMG
+KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVIPVAIG
+ARTLKDAINEALRDWVASVDNTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQAGR
+LPDAVAACVGGGSNAMGLFHGFLDDPEVELYGFEAGGEGLETGRHAASITLGRTGVLHGA
+RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLHDTGRAVYEPVSDTECMDAFLRLTRT
+EGITPAIESAHALAGALRLARRWADEGLVGPDAPEGQERIIIVNLSGRGDKDVATAAAWF
+GLGTAAEEKDPLEEMTPGEEQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000903.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000903.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ec0e939effac0707ee7571d63f4baf6b08d4bdf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000903.fa
@@ -0,0 +1,30 @@
+>PROKKA_01087
+MTVNSKTAAALDAAKAAGRTGLVAFLPAGYPSVDECVEAVVAAADNGADVIELGLPYTDP
+VMDGPVIQAATQAALQAGFHVADVFDIIRRVTQRTDAAVLVMTYWNLVDRMGVDEFARRL
+AEAGGAGLVTPDLVPEEAGAWMEASDRHGLDRVFLTAPSSTDERVRLTVDSSRGFVYAVS
+VMGVTGTRDAVSTVAETVVRRAQDAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR
+ALTDGGPQAVGALARELAAGAVREG
+>PROKKA_00806
+MTVHSKTAAALDAAKAAGRTGLVAFLPAGYPSVDECVEAVVAAAENGADVIELGLPYTDP
+VMDGPVIQAATQTALQAGFRVADVFDIIRRVTQRTDAAVLVMTYWNLVDRMGVDEFARRL
+AEAGGAGLVTPDLVPEEAGAWMEASDRHGLDRVFLTAPSSTDERVRLTVDSSRGFVYAVS
+VMGVTGTRDAVSTVAETVVRRAQDAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR
+ALTDGGPQAVGTLTRELAAGTVREG
+>PROKKA_01810
+MTVHSKTAAALDAARRAGRTGLVAYLPAGYPSVDECVEAVVAAAENGADVIELGLPYTDP
+VMDGPVIQAATQASLRAGFRVADVFEIIRRVTQRVDAAVLVMTYWNLVDRMGVDEFARRL
+AEAGGAGLVTPDLVPEEAGAWLEASDRHGLDRVFLTAPSSTDERVRLAVESSRGFVYAVS
+VMGVTGARDAVSTAAETVVRRAEEAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR
+ALGEGGPQAVGALARELAAGAVREG
+>PROKKA_01698
+MSTPDQQHEATAEKPSTAGDAIERARAAGRTALIGYLPAGYPSIDESVEAAVQLGENGVD
+VIEIGLPYSDPVMDGPVIQAATSHALANGFHTRDVFEVVRRITERTEAAVVVMTYWNLVD
+RMGVDEFARRLAEAGGAGLVTPDLVPEEAGEWFEASEEHGLDRIFLTAPSSSDERVRLAV
+ESSRGFVYGVSVMGVTGARGKVSDAAERVVARAKAAGARNVCVGLGISSADHVREIGSYA
+DGAIVGTALVKALRDGGPEAVGALARELAAGTAKES
+>PROKKA_01036
+MTVHSKTAAALDAAKAAGRTGLVAFLPAGYPSVDECVEAVVAAAENGADVIELGLPYTDP
+VMDGPVIQAATQTALQAGFRVADVFDIIRRVTQRTDAAVLVMTYWNLVDRMGVDEFARRL
+AEAGGAGLVTPDLVPEEAGAWMEASDRHGLDRVFLTAPSSTDERVRLTVDSSRGFVYAVS
+VMGVTGTRDAVSTVAETVVRRAQDAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR
+ALTDGGPQAVGTLTRELAAGTVREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000905.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000905.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e029805eda12f39d3d6f774927bf17991678ec37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000905.fa
@@ -0,0 +1,135 @@
+>PROKKA_01089
+MPVASSPASAPRAGGPVDPFVRYADVPAAQGLYDPSRETENCGLAVIATLRGTPGHDIVQ
+HALTALRALEHRGAVGADEGTGDGAGLLTQIPDELFRAVVDAELPPVGEYVAGTAFLPPV
+DGERAEAKEAVERLAEEEGLQVLAWREVPTDPSALGVGSRAAMPAFEQLFLSLADGQDGT
+EPGQSLDVRAWRVRRRAQSRAGVYFPSLSSQTIVYKGMLTTAQLEPFYPDLSDERFTTRL
+GVVHSRFSTNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGQLKHPMLGEVPEDLF
+PLISPIGSDSASFDEVAELLMLSGRPLTQAIMMMIPEAWENHATMDPARRAFYQYHSMLM
+EPWDGPAAVAFSDGTQVGAVLDRNGLRPARWWVTDDGLVVLASEVGVVPIEPSAVVRKGR
+VAPGRMFLVDTEQGRIIGDDEIKAEVASAQPWEDWVRQNLLDLESLPEREHVRHTSESIL
+QRQRIFGYTSEELRILVGPMAQTGAEPLGAMGTDTPIAVLAKRPRLLFDYFVQSFAQVTN
+PPLDAIREEQVTSMRTAIGPQGNVLSLEQVRTRQVDVPFPVIDNDQLARIQHLRDADGTR
+LTLKVNGVYRVAGGVEELRAQLKAICEQVSAAVNRGVEYVVLSDRGATAQWAPIPSLLLT
+SAVHHHLLASANRTKSSLIVEAGDVREVHHVAVLLGYGASAVNPYLAMESAEELVRTGEV
+SGVTAEQAVANLIKALGKGVQKIMSKMGISTVASYTGAQTFEALGLSRRFVDRYFVGTTS
+PLDGVGIDVVAAEIQARHEFAYPPDGNDINPYRELEVGGEYQWRREGAPHLFNPETVFRL
+QHSTRERRYDVFKDYTRRVDDQAEELMTLRGLMRLRTGERPPVPVSEVEPVESIVRRFST
+GAMSYGSISQEAHETLAIAMNRLGARSNSGEGGEDPERLLDPERRSKIKQIASGRFGVTS
+LYLATATDLQIKMAQGAKPGEGGQLMGTKVYPWVARTRHSTPGVSLVSPPPHHDIYSIED
+LAQLIHDLKRANPTARVHVKLVSESGVGTVAAGVAKARADVVLISGHDGGTGASPLNSLK
+HAGTPWEIGLAEAQQTLMLNGLRERVTVQVDGQLKTGRDVVIAALLGAEEFGFATAPLVV
+SGCIMMRVCHLDTCPVGVATQNPELRARFTGKPEFVVNFFEFIAQEVRELLSQLGFRTLD
+EAIGHRELLDVDAALHHWKSEGLDLSGILADPSVGRRPGHEDAPMRRTTEQDHDLASHID
+HRFIARLGDTLTTGTPVVMDEAVVNTDRSVGTLLGYHVTSTRLADELDDDTITVRLTGEA
+GQSLGAFLPAGVTLRLSGDANDYVGKGLSGGRVIVRPDAEAPFVAEENTVAGNVIGYGAT
+SGQLFLRGRVGERFLVRNSGATAVAEGIGDHGLEYMTGGEALILGETGRNLAAGMSGGRA
+WVLDLDREDLNPLAVREDALILEAPSAQDRLRIAELLELHRAETGSAVAAALLADLRAGG
+DAADAAWDRFTTVLPRQYDLVLRTRQAATAEGLDPDGEAVWDRLLEVTRG
+>PROKKA_00808
+MPVASSPASAPRAGGPVDPFVRYADVPAAQGLYDPSRETENCGLAVIATLRGTPGHDIVQ
+HALTALRALEHRGAVGADEGTGDGAGLLTQIPDELFRAVVDAELPPVGEYVAGTAFLPPV
+DGERAEAKEAVERLAEEEGLQVLAWREVPTDPSALGVGSRAAMPAFEQLFLSLADGQDGT
+EPGQSLDVRAWRVRRRAQSRAGVYFPSLSSQTIVYKGMLTTAQLEPFYPDLSDERFTTRL
+GVVHSRFSTNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGQLKHPMLGEVPEDLF
+PLISPIGSDSASFDEVAELLMLSGRPLTQAIMMMIPEAWENHATMDPARRAFYQYHSMLM
+EPWDGPAAVAFSDGTQVGAVLDRNGLRPARWWVTDDGLVVLASEVGVVPIEPSAVVRKGR
+VAPGRMFLVDTEQGRIIGDDEIKAEVASAQPWEDWVRQNLLDLESLPEREHVRHTSESIL
+QRQRIFGYTSEELRILVGPMAQTGAEPLGAMGTDTPIAVLAKRPRLLFDYFVQSFAQVTN
+PPLDAIREEQVTSMRTAIGPQGNVLSLEQVRTRQVDVPFPVIDNDQLARIQHLRDADGTR
+LTLKVNGVYRVAGGVEELRAQLKAICEQVSAAVNRGVEYVVLSDRGATAQWAPIPSLLLT
+SAVHHHLLASANRTKSSLIVEAGDVREVHHVAVLLGYGASAVNPYLAMESAEELVRTGEV
+SGVTAEQAVANLIKALGKGVQKIMSKMGISTVASYTGAQTFEALGLSRRFVDRYFVGTTS
+PLDGVGIDVVAAEIQARHEFAYPPDGNDINPYRELEVGGEYQWRREGAPHLFNPETVFRL
+QHSTRERRYDVFKDYTRRVDDQAEELMTLRGLMRLRTGERPPVPVSEVEPVESIVRRFST
+GAMSYGSISQEAHETLAIAMNRLGARSNSGEGGEDPERLLDPERRSKIKQIASGRFGVTS
+LYLATATDLQIKMAQGAKPGEGGQLMGTKVYPWVARTRHSTPGVSLVSPPPHHDIYSIED
+LAQLIHDLKRANPTARVHVKLVSESGVGTVAAGVAKARADVVLISGHDGGTGASPLNSLK
+HAGTPWEIGLAEAQQTLMLNGLRERVTVQVDGQLKTGRDVVIAALLGAEEFGFATAPLVV
+SGCIMMRVCHLDTCPVGVATQNPELRARFTGKPEFVVNFFEFIAQEVRELLSQLGFRTLD
+EAIGHRELLDVDAALHHWKSEGLDLSGILADPSVGRRPGHEDAPMRRTTEQDHDLASHID
+HRFIARLGDTLTTGTPVVMDEAVVNTDRSVGTLLGYHVTSTRLADELDDDTITVRLTGEA
+GQSLGAFLPAGVTLRLSGDANDYVGKGLSGGRVIVRPDAEAPFVAEENTVAGNVIGYGAT
+SGQLFLRGRVGERFLVRNSGATAVAEGIGDHGLEYMTGGEALILGETGRNLAAGMSGGRA
+WVLDLDREDLNPLAVREDALILEAPSAQDRLRIAELLELHRAETGSAVAAALLADLRAGG
+DAADAAWDRFTTVLPRQYDLVLRTRQAATAEGLDPDGEAVWDRLLEVTRG
+>PROKKA_01807
+MQHPSKTPHADPFRAFAAQPEAAGLYDPEQEKDACGLAAVATLRGPATHKIVQDALTALR
+ALEHRGAVGADEGTGDGAGIITQVPDALLRATVSFELPAAGEYAVGTAFLPQDEAARTAA
+QEAIAEAAVVEGLDLLGWRPVPTDESVLGPGSRAVVPVFEQLFLAVSAGEDVEAPGQSLD
+ARAWRLRRRAQRSGVYFPSLSSRTLVYKGMLSTAQVEPFYPDLSDERYVTRLAVVHSRFS
+TNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGELRHPLLGEVPEEMFPIVSASGS
+DSASFDEVAELIHLAGRPLSHAIMMMVPEAWENHTTMDEDRRAFYQYHSMLMEPWDGPAA
+IAFTDGVQLGSVLDRNGLRPARYWETRDGLVVLASEVGVLDIDPATVVRKGRVKPGRMFL
+LDTEQGRIIEDEEVKAEIAASAPWKDWVADSLRRIEDLPEREPVRYHGDSVRLRQRLFGY
+TDEEVRTIIEPMARHGAEPLGAMGTDTPIAALSPRPRLLFDYFTQNFAQVTNPPLDSIRE
+EQVTSMRTCIGPQASLLAAGKVTTDAVEIPFPVLDNEQLARIAAVRAEDGTRRALKVKGL
+YLVAGGAEEMRSRLKEICEQVSAAVQRGVQYVVLSDRDANAQWAPIPSLLLTSAVHHHLL
+ASASRTRTSLLVEAGDVREVHHVAVLIGYGASAVNPYLSMETAEELVRTGTLTGVTEQEA
+TRNLIHGLGKGVQKIMSKMGISTVASYCGAQTFEALGLSRSFVDRYFTGTRSPMDGVGLD
+VIAAESAARHATAFPVDGSSASTVGPRGTSGLPVGGEYKWRREGPPHLFNPETVFRLQHA
+TRERRYDIFKDYTRRVDEQSADLMTLRGLLGLATKGRERVPVSEVESVESIVKRFSTGAM
+SYGSISQEAHETLAVAMNRLGARSNSGEGGEDPERLLDPERNSRVKQIASGRFGVTSLYL
+STATDLQIKMAQGAKPGEGGQLMGAKVYPWVARTRHSTPGVSLVSPPPHHDIYSIEDLAQ
+LIHDLKRANPQARVHVKLVSETGVGTVAAGVTKAKADVVLISGHDGGTGASPLNSLKHAG
+TPWELGLSEAQQTLRLNGLRDRVTVQVDGQLKTGRDVVIAALLGAEEFGFATAPLVVSGC
+IMMRVCHLDTCPVGVATQNPELRARFTGRPEFVVTFFEYIAQEVRELLAELGLRSLDEAI
+GRQDLLHKDAAIGHFKTEGLDLSGVLSDAGVPEEAPRRRLTEQDHRLQDQADQRWLDQVA
+DAVVTETPVTVTDRLVNTDRSVGTLLGHRVTAARLDDELPRDTIRIELTGEAGQSLGAFL
+PAGVSITLSGDANDYVGKGLSGGTVALRPAPEAPFAAEENMIAGNVVGYGATSGRLFLNG
+RVGERFLVRNSGAVAVVEGIGDHGLEYMTGGTALVLGNTGRNLAAGMSGGVGFFLDLDPA
+QLNPLAVKDDELLLGRPEGADRALIRELLEEHRAATGSDLAARLLAELDGPAESAEALWE
+RFTTVLPRRYAAVQEIRTDSRDAGTDPDGDAAWARILEVTRG
+>PROKKA_01696
+MTVAPLSAPTPRSGRSDDPFVRYAAFPEPQGLYDPARETENCGLAVIATLRGTPGHDIVE
+HALTALRALEHRGAVGADEGTGDGAGLLTQLPDELFRAVLDVELPPVGEYAAGIAFLPPL
+EGERAEAKAAVEELAQAEGLDVLAWRVVPTDPSALGTGSRAAMPSFEQVFLALAEGEDGT
+EPGQSLDVRAWRLRRRTQSRAGVYFPSLSSQTIVYKGMLTTAQLEPFYPDLSDPRFTTRL
+GIVHSRFSTNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGQLKHPMLGEVPEELF
+PLISPIGSDSASFDEVAELLMLSGRPLTQAVMMMIPEAWENHATMDPARRAFYQYHSMLM
+EPWDGPAAVAFSDGTQVGAVLDRNGLRPARYWETRDGLVVLASEVGVVSIDPADVVRKGR
+VAPGRMFLVDTEQGRIVEDEEIKAEVAAAAPWEEWVSQNLLDLDALPEREHLRPSSESIQ
+QRQRIFGYTAEELRVLVGPMARDGAEPLGAMGTDTPIAVLSKRPRLLFDYFVQSFAQVTN
+PPLDAIREEQVTSMRTGIGPQGNVLSAERVHTRQVDVPFPVIDNDQLARIQHLRDGDGGR
+LALKVTGTYRVAGGAEELRTRLKEICEQVSAAVNRGVEYVVLSDRGATAQWAPIPSLLLT
+SAVHHHLLASANRTRTSLVVEAGDVREVHHVAVLLGYGASAVNPYLAMESAEELVRTGEI
+EGVTAEQAVANLIKALGKGVQKIMSKMGISTVASYTGAQTFEALGLSRRFVDRYFAGTTS
+PLDGVGLEVVAAEIQARHEFAYPPDGNDINPYRELEVGGEYQWRREGAPHLFNPETVFRL
+QHSTRERRYDVFKDYTRRVDGQAEELMTLRGLMRLRSEDRTPVPISEVEPVESIVRRFST
+GAMSYGSISQEAHETLAIAMNRLGARSNSGEGGEDPERLLDPERRSKIKQIASGRFGVTS
+LYLTTATDLQIKMAQGAKPGEGGQLMGAKVYPWVARTRHSTPGVSLVSPPPHHDIYSIED
+LAQLIHDLKRSNPAARVHVKLVSESGVGTVAAGVAKAKADVVLISGHDGGTGASPLNSLK
+HAGTPWELGLAEAQQTLMLNGLRERVTVQVDGQLKTGRDVVVAALLGAEEFGFATAPLVV
+SGCIMMRVCHLDTCPVGVATQNPELRSRFTGKPEFVVNFFEFVAQEVRELLAELGFRTLD
+EAIGHRELLDVDAALHHWKTEGLDLSGILADPSVGRRAGAADAPMRRMVDQDHDLAAHID
+NRLIARLGDTLATGAPVVMDESVVNTDRSIGTMLGHHVTSTRLADELPADTITVRLTGEA
+GQSLGAFLPAGVTLRLDGDANDYVGKGLSGGRVVVRPDATAPFAAEDNTVAGNVIGYGAT
+SGELFLRGRVGERFLVRNSGATAVAEGIGDHGLEYMTGGEALVLGETGRNLAAGMSGGRA
+WILDLDRADLNPLAVREGDLLLSTPSAADRERIAALLRTHRAETGSAVAERLLADLDAGG
+DAAQGVWDRFTTILPRRYDLVLRTRAEAVAEGLDPDGEAVWDRLLEVTRG
+>PROKKA_01038
+MPVASSPASAPRAGGPVDPFVRYADVPAAQGLYDPSRETENCGLAVIATLRGTPGHDIVQ
+HALTALRALEHRGAVGADEGTGDGAGLLTQIPDELFRAVVDAELPPVGEYVAGTAFLPPV
+DGERAEAKEAVERLAEEEGLQVLAWREVPTDPSALGVGSRAAMPAFEQLFLSLADGQDGT
+EPGQSLDVRAWRVRRRAQSRAGVYFPSLSSQTIVYKGMLTTAQLEPFYPDLSDERFTTRL
+GVVHSRFSTNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGQLKHPMLGEVPEDLF
+PLISPIGSDSASFDEVAELLMLSGRPLTQAIMMMIPEAWENHATMDPARRAFYQYHSMLM
+EPWDGPAAVAFSDGTQVGAVLDRNGLRPARWWVTDDGLVVLASEVGVVPIEPSAVVRKGR
+VAPGRMFLVDTEQGRIIGDDEIKAEVASAQPWEDWVRQNLLDLESLPEREHVRHTSESIL
+QRQRIFGYTSEELRILVGPMAQTGAEPLGAMGTDTPIAVLAKRPRLLFDYFVQSFAQVTN
+PPLDAIREEQVTSMRTAIGPQGNVLSLEQVRTRQVDVPFPVIDNDQLARIQHLRDADGTR
+LTLKVNGVYRVAGGVEELRAQLKAICEQVSAAVNRGVEYVVLSDRGATAQWAPIPSLLLT
+SAVHHHLLASANRTKSSLIVEAGDVREVHHVAVLLGYGASAVNPYLAMESAEELVRTGEV
+SGVTAEQAVANLIKALGKGVQKIMSKMGISTVASYTGAQTFEALGLSRRFVDRYFVGTTS
+PLDGVGIDVVAAEIQARHEFAYPPDGNDINPYRELEVGGEYQWRREGAPHLFNPETVFRL
+QHSTRERRYDVFKDYTRRVDDQAEELMTLRGLMRLRTGERPPVPVSEVEPVESIVRRFST
+GAMSYGSISQEAHETLAIAMNRLGARSNSGEGGEDPERLLDPERRSKIKQIASGRFGVTS
+LYLATATDLQIKMAQGAKPGEGGQLMGTKVYPWVARTRHSTPGVSLVSPPPHHDIYSIED
+LAQLIHDLKRANPTARVHVKLVSESGVGTVAAGVAKARADVVLISGHDGGTGASPLNSLK
+HAGTPWEIGLAEAQQTLMLNGLRERVTVQVDGQLKTGRDVVIAALLGAEEFGFATAPLVV
+SGCIMMRVCHLDTCPVGVATQNPELRARFTGKPEFVVNFFEFIAQEVRELLSQLGFRTLD
+EAIGHRELLDVDAALHHWKSEGLDLSGILADPSVGRRPGHEDAPMRRTTEQDHDLASHID
+HRFIARLGDTLTTGTPVVMDEAVVNTDRSVGTLLGYHVTSTRLADELDDDTITVRLTGEA
+GQSLGAFLPAGVTLRLSGDANDYVGKGLSGGRVIVRPDAEAPFVAEENTVAGNVIGYGAT
+SGQLFLRGRVGERFLVRNSGATAVAEGIGDHGLEYMTGGEALILGETGRNLAAGMSGGRA
+WVLDLDREDLNPLAVREDALILEAPSAQDRLRIAELLELHRAETGSAVAAALLADLRAGG
+DAADAAWDRFTTVLPRQYDLVLRTRQAATAEGLDPDGEAVWDRLLEVTRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000915.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000915.fa
new file mode 100644
index 0000000000000000000000000000000000000000..05eac6010601c2ee166497cdd5debded8e38958d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000915.fa
@@ -0,0 +1,20 @@
+>PROKKA_01100
+MSEHTETTPAASERVYRPGVTPELSPAELEAACAEAGLTPELVTALGGAVISPLAQKMGL
+RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDRNVVGVEISA
+THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLAPRP
+>PROKKA_00819
+MSEHTATTPAASDRVYRPGVTPELSPAELAAACAEAGLTPELVAALGGAAISPLAQKMGL
+RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDRNVVGVEISA
+THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLAPRP
+>PROKKA_01795
+MTDHAERADAAPAPTSDLVYRPGVTPELTDAQREAACAAAGLTPELVAALGGATVSPLAQ
+KMGIRFLELTPERAVATMPVAGNEQPAGLLHGGAHLVLAESLGSMAAKLHAGPERGVVGI
+EIGATHHRAARSGLVTGTATAIHLGGTLTTHEVVMTDEQGRRLSTARITNMVLRGRG
+>PROKKA_01685
+MTDTTTAPERAQALLAGLTFHAGIRPELTDEERAALATAAGMTPAVQEALGGPAVSHLAL
+KMGIRFLELSAERSVATMPVAGNEQPVGLLHGGAHLVLAESLGSLSAKVHAGPHRGAVGT
+EIGATHHRSVRSGLVTGTATAIHLGRTLTTHEIVMTDEEGRRLSTVRMTNMLLDPR
+>PROKKA_01049
+MSEHTETTPAASERVYRPGVTPELSPAELEAACAEAGLTPELVTALGGAAISPLAQKMGL
+RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDHNVVGVEISA
+THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000917.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000917.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ddb65a5f6e4e27dcbd1f43441e7b64fa01a13434
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000917.fa
@@ -0,0 +1,50 @@
+>PROKKA_01103
+MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY
+ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE
+KLTGN
+>PROKKA_00822
+MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY
+ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE
+KLTGN
+>PROKKA_01791
+MTTTSNAPQVAINDIGTAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVESNEWMEGFESERAAWEQQY
+ADAQSRWEQHKEQVRRSFEEEANAGADTGAGMGGSSYSSEAPASDGGTLASDEALAALRE
+KLTGN
+>PROKKA_01682
+MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKVKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRQGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQDVTVEVLDVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDQLFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDDEGNYKYPEGFDVETNEWMEGFESERASWEQQY
+ADAQTRWEAHKEQVRRSLEEEAQAPAGNASTASSYSSEAPASDGGTLASDEALAALREKL
+TGN
+>PROKKA_01052
+MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY
+ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE
+KLTGN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000920.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000920.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c43cef8bd2ba46b5a2fec61ffb1428273089fb57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000920.fa
@@ -0,0 +1,25 @@
+>PROKKA_01107
+MTETDPVAERPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV
+QDEFGDRVITADGELDRVEMARIVFGDEGARQRLNRIVHPRIRAAARRIVAEAGPDAVVV
+QDVPLLVETGQADAFDLVIVVEAPLEERLRRMVEDRGMSRADAEARIAAQATDEQRRAVA
+DVVIVNDADLERLASVANQVWDRFLAPGAAEPSAD
+>PROKKA_00826
+MTETDPVAERPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV
+QDEFGDRVITADGELDRVEMARIVFGDEGARQRLNRIVHPRIRAAARRIVAEAGPDAVVV
+QDVPLLVETGQADAFDLVIVVEAPLEERLRRMVEDRGMSRADAEARIAAQATDEQRRAVA
+DVVIVNDADLERLASVANQVWDRFLAPGAAEPSAD
+>PROKKA_01786
+MTESVPVADRPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV
+QDEFGDRVLTSDGELDRVALAHIVFSDPQARQRLNRIVHPRIRAAARRIVAAAGPDAVVV
+QDVPLLVETGQQDAFDLVIVVEAPLEERLRRMVEDRGMTPEDAQARIDAQATDDQRRAAA
+DVVIVNDADLERLASVANQVWDRFLAPDAAEPSAD
+>PROKKA_01678
+MTDAVTDVTLRPRLHVGLTGGIAAGKSAVAAELERCGALLVDSDALARLVLEPGTEGLAA
+VQDAFGDRVIAADGSLDRAALAQIVFADPAARQRLNGIVHPRVRRMAREIVAQAGPDAVV
+VQDVPLLVETGQADAFDLVIVVEAPAEERIRRMVEDRGMSREDALARMAAQATDEERAAV
+ADVVIVNDGDLDRLREITRRVWEGMAA
+>PROKKA_01056
+MTETDPVAERPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV
+QDEFGDRVITADGELDRVEMARIVFGDEGARQRLNRIVHPRIRAAARRIVAEAGPDAVVV
+QDVPLLVETGQADAFDLVIVVEAPLEERLRRMVEDRGMSRADAEARIAAQATDEQRRAVA
+DVVIVNDADLERLASVANQVWDRFLAPGAAEPSAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000923.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000923.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75f819ca27dfbcd3f5c2e97d96fff7d94987f668
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000923.fa
@@ -0,0 +1,30 @@
+>PROKKA_01110
+MTALALLALGLHDLLDAVLPGAWPTPRRRWLARAGAAVAAVLAAVLVAVLAPTGISVAVG
+GGLVALGLLMGWTWLHPDRPLGVVAVAAAVGLVAVLESTLAPAGLRSAPPALTLLAVTVA
+LTETGNRVTRAVLALAGRSADGGDEEAEDPAAEPTTVPSAAPTDPAADGLRGGRYIGPME
+RLLMVVLGLAQAYPVIAALMAAKGIVRFPEISADRGAGSRAEEFLIGSLASWGLAAAGAV
+VVWLALGLTAPGAA
+>PROKKA_00829
+MTALALLALGLHDLLDAVLPGAWPAPRRRWLARAGAAVAAVLAAVLVAVLAPTGVAVAVG
+GGLVSLGLLMGWTWLHPDRPLGVVAVVAVVGLVAVLESTLAPAGLRSAPPALTLLAVALA
+LTETGNRVTRAVLALAGRPADGGDEEAEDPAAEPTTVPSAAPTDPAADGLRGGRYIGPME
+RLLMVVLGLAQAYPVIAALMAAKGIVRFPEISADRGAGSRAEEFLIGSLASWGLAAAGAV
+VVWLALGLTAPGAA
+>PROKKA_01782
+MTALTLIALGVHDLAAALLPRAWAARRREVLALAAGTAAAVLAAVLLVVLVPGAPALAIG
+GVLVALALLAAWWRLGAGAPLGTLGVAAVVALVAVAEIGLARTAGPAVPIAFTVVAVGLA
+LGETANRITRAVLLLAGRRADAAPAPESDAPAEAVLAPETSADDAEAPPLRGGRYIGPME
+RVLMVVLGLAHAWPVVAALMAAKGLVRFPEISADRGEGSRAEEFLVGSLASWGIAAAGGA
+LVWVGLGAPALS
+>PROKKA_01675
+MTALTLLALGLRDLLAVTPGRTSRHPWLALLAAVGAVLIGGVVLAGGAASAAETLSAVAL
+ALGAVLAWHALARAGSPHLRVGALGGVVGLAVAEHTGALTVAHGPVGMALLGAGLVLVET
+ANVVTRDVLRLAGRPSTDDVHDADDVHDADDDGEGLRGGRFIGPMERLLMAVLGLMAAWQ
+AVAAIMAAKGIVRFPEISKDARAGDAKGGPMGASAEEFLVGSLASWTLAAGAGLVVHLAL
+AGG
+>PROKKA_01059
+MTALALLALGLHDLLDAVLPGAWPAPRRRWLARAGAAVAAVLAAVLVAVLAPTGVAVAVG
+GGLVSLGLLMGWTWLHPDRPLGVVAVVAVVGLVAVLESTLAPAGLRSAPPALTLLAVALA
+LTETGNRVTRAVLALAGRPADGGDEEAEDPAAEPTTVPSAAPTDPAADGLRGGRYIGPME
+RLLMVVLGLAQAYPVIAALMAAKGIVRFPEISADRGAGSRAEEFLIGSLASWGLAAAGAV
+VVWLALGLTAPGAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000927.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000927.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d4b96112bc6d85dc2450d75b8c8b3f3ff982dd89
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000927.fa
@@ -0,0 +1,25 @@
+>PROKKA_01116
+MPETARNRLLHDLPAVTVRTCSVSEMDNNVYLLTSKTTGAQVLIDAAAEAEAIRDLIASA
+ADDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLR
+HGDTVGADGLRLEVVALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF
+RQLFTDVSDRIFDAFDDDVVVHPGHGASTTLGAERPHLPEWAERSW
+>PROKKA_00835
+MPETARNRLLHDLPAVTVRACSVSEMDNNVYLLTSKTTGAQVLIDAAAEAEAIRDLIASA
+ADDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLR
+HGDIVGVDGLRLEVLALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF
+RQLFTDVTERIFDAFDDDVVVHPGHGASTTLGAERPHLPEWAERGW
+>PROKKA_01777
+MPETARNRLLHDLPAVTVRTSSVSEMDNNVYLLTSKTTGAQVLIDAADDAEAIRDLIASA
+AGDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLH
+HGDIVGADGLRLEVVALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF
+RQLFTDVSERIFDAFDDDVVVHPGHGASTTLGAERPHLPKWAERGW
+>PROKKA_01670
+MPATAEPRLLHDLPAVTVRAVSVSEMDNNAYVLTSKTTGAQVLIDAAAEPETLRDLLASA
+AADTPCELRLELIVTTHRHWDHVRALPALATVTGARTAAGEDDADAIAAETGVTPDVRLA
+HGSRTGAEGIELEVIALRGHTPGSVALAYRPEADEPAVLFTGDSLFPGGVGNTQGDAERF
+ASLIRDVEDRVFAAFDDDVVVHPGHGASTTLGAERPHLQEWRERGW
+>PROKKA_01066
+MPETARNRLLHDLPAVTVRACSVSEMDNNVYLLTSKTTGAQVLIDAAAEAEAIRDLIASA
+ADDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLR
+HGDIVGVDGLRLEVLALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF
+RQLFTDVTERIFDAFDDDVVVHPGHGASTTLGAERPHLPEWAERGW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000929.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000929.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b8727cb4256b5f4a57192fc86e5c8f5f112f568
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000929.fa
@@ -0,0 +1,30 @@
+>PROKKA_01120
+MTEETLQPEKPPTSEVLVIAGMSGAGRTTAAHALEDHGWDVVENMPPALFGTLAELIARS
+PEAFPRLAIVVDVRSRSYFEELYAALQHLANSGVEYRTVFLDAEDHVLLQRFEAGRRPHP
+MQGNARLLDGIRAERDVVEPLKARADVVVDTTELNVHGLATEITELFSESGPVTLRLTIM
+SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAAVADYVLSRPGVEDFLRTYVAM
+LGPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVHVQHRDMGRE
+>PROKKA_00839
+MTEETLQPEKPPTSEVLVIAGMSGAGRTTAAHALEDHGWDVVENMPPALFGTLAELIARS
+PEAFPRLAIVVDVRSRSYFEELYAALQHLANSGVEYRTVFLDAEDHVLLQRFEAGRRPHP
+MQGNARLLDGIRAERDVVEPLKARADVVVDTTELNVHGLATEITELFSESGPVTLRLTIM
+SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAAVADYVLSRPGVEDFLRTYVAM
+LGPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVHVQHRDMGRE
+>PROKKA_01773
+MSEESLRPEKPPTSEVLVITGMSGAGRTTAAHALEDHGWYVVENMPPPLFITLADLVARS
+PEAFPRLAIVVDVRSRAYFPELHAALQQLENNGVEYRMVFLEADEHVLVRRFEAGRRPHP
+LQGNASLLDGIRAERDMLAELKARADVVVDTTELNVHGLATEITELFSVSGPVTLRLTLM
+SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAEVSDYVLTRPGVEDFLRSYTAM
+LAPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVQVQHRDMGRE
+>PROKKA_01666
+MSADEHLQPDKPPSSEVLVITGMSGAGRTTAAHALQDHGWYVVENMPPQLLGTLSDLVAR
+SPEAFPRLAIVVDVRSRSYFNELRTALQQLESTGVEFRTVFLEASDEVLVRRFEAGRRPH
+PLQGNARLLDGIQAEREILSELKERADIVVDTSALNVHGLATEVTQLFSEDGPVTVRLNV
+MSFGFKYGLPSDANFVADMRFVANPHWVPELRSKTGLDPEVSGFVLGQPGVQEFLSNYLA
+ALGPVVEGYRRENKHYATLAVGCTGGKHRSVAVAEELARRVAQWPRVSVHVDHRDVGRE
+>PROKKA_01070
+MTEETLQPEKPPTSEVLVIAGMSGAGRTTAAHALEDHGWDVVENMPPALFGTLAELIARS
+PEAFPRLAIVVDVRSRSYFEELYAALQHLANSGVEYRTVFLDAEDHVLLQRFEAGRRPHP
+MQGNARLLDGIRAERDVVEPLKARADVVVDTTELNVHGLATEITELFSESGPVTLRLTIM
+SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAAVADYVLSRPGVEDFLRTYVAM
+LGPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVHVQHRDMGRE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000932.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000932.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a4ad3ab5e6fe25b863a0978e89c5431909b7e8cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000932.fa
@@ -0,0 +1,25 @@
+>PROKKA_01123
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARAGASGLILPA
+>PROKKA_00842
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARAGASGLILPA
+>PROKKA_01770
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAARDADDFAAVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEHFGSFDKFRAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARQGASGLILPA
+>PROKKA_01663
+MTEFVLPELDYDYAALEPHISAKIMELHHSKHHATYVKGANTALEKLAAAREAEDFASVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEFFGSFDKFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQQRFEAARNGASGLILPA
+>PROKKA_01073
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARAGASGLILPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000939.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000939.fa
new file mode 100644
index 0000000000000000000000000000000000000000..299215644ed82c88d5b17430cbd4638a15c4e6eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000939.fa
@@ -0,0 +1,50 @@
+>PROKKA_01130
+MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED
+SRALVPDIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ
+LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW
+DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY
+LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL
+EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR
+>PROKKA_00849
+MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED
+SRALVPDIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ
+LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW
+DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY
+LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL
+EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR
+>PROKKA_01762
+MSTLGLSATGSALEAIDRHLPTLLEDRVASRLGAQDAGLWGEAAREESARRLGWIDLFED
+SRALVRHIDALSRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVMEAAFREAGIDPRSRLVAVTDPGSPLHAECES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLTADDADNPGLQ
+LGAALGGTAPLRDKLVFTDHGSGIDGLPAWAEQLIAESTGKDGTGLLPVVVADGDPETGW
+DAPDMLQVQLVGEDAPAAPAHGVQVSGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KTAARSLLDAPARERTADRTVDGVELSGPEAVVSAADLAGVLRATADLVPENGYLAVHAY
+LSRHDDAELEEVRADLARLAGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQVTGDADLDV
+EVPGRPFSLGRLIAAQAAGDARVLVEHGRPVVTLHLPHRAAGIDAIRTAARAR
+>PROKKA_01656
+MSTFGLTATGAALDAVDRHVPALVAERFASRLAAEDADLWGPDARDEAAKRLGWISLFEE
+SRTVAAEAAALAEELRGQGLTRVVLAGMGGSSLAPEVIAATAGAELEVLDSTDPQQVAAV
+LDHDLERTVLVVSSKSGSTVETDSQRRIVEAALAAEDIDPASRIVVVTDPGSPLEEASVE
+AGYRAVFTADPTVGGRYSALTAFGLVPAALAGVDVESLLDEAEDVLDLVTADDADNPALQ
+LGAAIGGTEPLRDKLVIQDLGSGIDGFGDWVEQLIAESTGKDGTGLLPVVVRPGDPETAW
+EAPDLLKVTLVSESEESPAGGDGVRLHGSLGALLLTWEAATAVAGRLLGINPFDQPDVEA
+AKAAARELLDSPAEEAEPGTVIHGVEVSGPESVTSADDLRGVLAAVRELVPEDGYLAVHA
+YLDRHADVDLAGIRADLASALGRPVTFGWGPRFLHSTGQYHKGGPRNGVYLQVTGDAALD
+VEVPGRPFTLGRLIAAQAAGDADVLRRLGRPVVTLRLRDRSAGIAALRTAAREA
+>PROKKA_01080
+MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED
+SRALVPHIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ
+LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW
+DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY
+LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL
+EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000942.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000942.fa
new file mode 100644
index 0000000000000000000000000000000000000000..94bd6d7b2991dcec98025c5cf0f438048b6b28f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000942.fa
@@ -0,0 +1,35 @@
+>PROKKA_01133
+MSSSLESPSAARVAAAEPGVVDRSPLPLRRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMIATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILILGFGANWLAAGLGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIGW
+AAVRGTVEWPAIVLFLVVFLWTPPHYWPLSMKYKRDYQQADVPMLGAIASARHVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVALVVGGWFIWESHVLQVQAQREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGAPLMHFGA
+>PROKKA_00852
+MSSSLESPSAARVAAAEPGVVDRSPLPLRRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMIATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILILGFGANWLAAGLGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIGW
+AAVRGTVEWPAIVLFLVVFLWTPPHYWPLSMKYKRDYQQADVPMLGAIASARHVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVALVVGGWFIWESHVLQVQAQREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGAPLMHFGA
+>PROKKA_01759
+MSSSLESSSAARVETAPPGVVDRSKPSLSRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMAATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILVLGFGANWLAAALGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIAW
+AAVRGTVEWPAIVLFTVIFLWTPPHYWPLSMKYKRDYQEADVPMLGAIASARHVSNQVVL
+YAWATVVCSLLLVPMGWAGIVYTCVALVVGGWFVWESHVLHRQARREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGEPLMRFGA
+>PROKKA_01653
+MSSSVESTSPATAAPGAAAPSARPPMTVGRKARAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDLLTMIATLVGGALAAGASGAFNCYIDRDIDRVMKRTARRPLVTGEVTPREALVFSW
+TLAVVSVLVLGFGANWLAAALGVAAIFFYVVVYSLILKRRTEQNIVWGGIAGCFPVVIGW
+AAVRGTVEWPAIVLFTVIFLWTPPHYWPLSMKYKRDYQEAEVPMLGAVASARLVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVAVGVGGWFVWESHVLQREAQRPDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGGPLMPAVTGS
+>PROKKA_01083
+MSSSLESPSAARVAAAEPGVVDRSPLPLRRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMIATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILILGFGANWLAAGLGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIGW
+AAVRETVEWPAIVLFLVVFLWTPPHYWPLSMKYKRDYQQADVPMLGAIASARHVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVALVVGGWFIWESHVLQVQAQREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGAPLMHFGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000943.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000943.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2bb5331cc7956b68e1f0a2ff35c3f7a3e418bd2d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000943.fa
@@ -0,0 +1,35 @@
+>PROKKA_01134
+MSTTTPAAGTAPAGLAARLPQRLTKATMALAVASLASEIGIIVTGGAVRLTGSGLGCPTW
+PKCSPESLTNTPEMGIHGYIEFGNRTLTFVLVVIAAAMFLSLWNLRGTHRSPFWLSVGLL
+AGIPAQALVGGVVVLTNLNPWWVAGHFIVSSIMVAVATLLVVRIAAERRAGRAGVPLVDG
+ATTVRSRAAAWAAFALTWAAVYLGTVVTGTGPHSGDPGSPRHEFDPLLVTRIHVIPVYLL
+LAAALVLFFTVRRAAGASRLQRAAVLRLLLALVFQAAVGYTQHFTGLPIGVVLLHMLGSA
+LLVASATEAWDRQVARYVTAGPGAAVETATPARTVAAG
+>PROKKA_00853
+MSTTTPAAGTAPAGLAARLPQRLTKATMALAVASLASEIGIIVTGGAVRLTGSGLGCPTW
+PKCSPESLTNTPEMGIHGYIEFGNRTLTFVLVVIAAAMFLSLWNLRGTHRSPFWLSVGLL
+AGIPAQALVGGVVVLTNLNPWWVAGHFIVSSIMVAVATLLVVRIAAERRAGRAGVPLVDG
+ATTVRSRAAAWAAFALTWAAVYLGTVVTGTGPHSGDPGSPRHEFDPLLVTRIHVIPVYLL
+LAAALVLFFTVRRAAGASRLQRAAVLRLLLALVFQAAVGYTQHFTGLPIGVVLLHMLGSA
+LLVASATEAWDRQVARYVTAGPGAAVETATPARTVAAG
+>PROKKA_01758
+MASLASEIGIIVTGGAVRLTGSGLGCPTWPKCTPESLTNTPEMGIHGYIEFGNRTLTFVL
+VVIAAAMFLSLWRLRRTHRSPFWLSVGLLAGIPAQAVVGGIVVLTELDPWWVAGHFIVSS
+VMVAVATLLVIRIGAERRAGRAGVRIVDGVTTGASRAAAWAAFAFTWAAVYLGTVVTGTG
+PHGGDPDAPRHAFDPLLVTRVHVIPVYLLIAAALVLLFTVRRAEGASRLQRAAVLRLLLA
+IAVQAAIGYTQHFTGLPVVLVILHMLGSALLVAAATEVWDRQRSRYVTAGPAALLDADPT
+PVTANAR
+>PROKKA_01652
+MTASPTTARPAAGGSSARRPPDRVTGVTVGLALASLISQMVIVVTGGAVRLTGSGLGCPT
+WPKCTPESLTTTAEMGIHGIIEFGNRTLTGVLGVIALLMIATLWRLRRSHRQAFTLSLLL
+LAGIVLQAVVGGVTVWMHLDPRIVGVHFVISGALIALATMLWVRLRAEHRHGAGAPVADG
+TTTPASRTASRVAYAALWLALVVGTLVTGTGPHSGDPAAARHGFDALMITRLHVVPVYIT
+VAATLVLLWQVLRTPGSGAGQRVAAWSLLGAVLLQGLLGYWQHFTGLPVGVVAAHLAGAT
+VAVVAGTLAWQRQTSRYRAPAVA
+>PROKKA_01084
+MSTTTPAARTAPAGLAARLPQRLSKATMALAVASLASEIGIIVTGGAVRLTGSGLGCPTW
+PKCSPESLTNTPEMGIHGYIEFGNRTLTFVLVVIAAAMFLSLWNLRGTHRSPFWLSVGLL
+AGIPAQALVGGVVVLTNLNPWWVAGHFIVSSIMVAVATLLVVRIAAERRAGRAGVPLVDG
+ATTGRSRAAAWAAFALTWAAVYLGTVVTGTGPHSGDPGSPRHEFDPLLVTRAHVVPVYLL
+LAAALVLFFTVRRAAGASRLQRAAVLRLLLALVFQAAVGYTQHFTGLPIGVVLLHMLGSA
+LLVASATEAWDRQVARYVTAGPGAAVETATPARTVAAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000948.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000948.fa
new file mode 100644
index 0000000000000000000000000000000000000000..499b209e508dc377cbfecbc2d6a9140c600d36af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000948.fa
@@ -0,0 +1,40 @@
+>PROKKA_01139
+MTDTVENTQRTMIPGMGEEGEKLTAAQNPAARAGGRERNAAGSRADRLSSFELSDFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPAVTVAEQAGVTVETVARDDARVGSVLTP
+DDRVSAAAWNSVSEATVVTISGEVAEPVRIDVVGSSADPAAMHLTVLVEENAQADVVIAH
+RGTAVLAQNVEFDVRRDARLNVVALQAWEGDAVHVSAQQASVATNAHFKHVAVSYGGGVV
+RLTPTARFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPDCVSNVLYKGALQGTDARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGISETEARRLIVRGFLNEIIQKIGIGDVEDELTAVMEDELRIAQL
+>PROKKA_00858
+MTDTVENTQRTMIPGMGEEGEKLTAAQNPAARAGGRERNAAGSRADRLSSFELSDFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPAVTVAEQAGVTVETVARDDARVGSVLTP
+DDRVSAAAWNSVSEATVVTISGEVAEPVRIDVVGSSADPAAMHLTVLVEENAQADVVIAH
+RGTAVLAQNVEFDVRRDARLNVVALQAWEADAVHVSAQQASVATNAHFKHVAVSYGGGVV
+RLTPTARFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPDCVSNVLYKGALQGTDARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGISETEARRLIVRGFLNEIIQKIGIGDVEDELTAVMEDELRIAQL
+>PROKKA_01753
+MTDTVENTQGSMIPGMGEEGEKLTVAQTSAPRAGAPERNAAGSRADRVSSYELADFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPSVTVAEQVGVRVETVARDDARVGSVLTP
+DDRVSAAAWNSVAQATVVTVSGEVAEPVRIDVVGSSAEPAAMHLTVIVEENAQADVVLAH
+RGTAVLAQNVEFDVRRDARLNVVSLQAWEDDAVHVSAQQASVATNARFKHVAVSHGGSVV
+RLTPTSRFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPRCVSNVLYKGALQGADARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGISETEARRLIVRGFLNEIIQKIGVRDVEDELTAVMEDELRIAAL
+>PROKKA_01647
+MENTERNMIPGMGEEGETLAGGQDAGAPVATRGQGQSRADRVSSKDLADFPVLTGREEDW
+RFTPLERLGGLHLPGGDDARLTGAAPAVTVSETAGVSVETVGRDDARVGSVLTPDDRVSA
+AAWTSFAEATVVTVSGEPGEPVRIEVTGSGVEPAAQQLTLIAEENAHADVVLTHRGSAVL
+AQNVEFEVRRGASLNVVSVQAWDDDAVHVGAHQASVARDAHLKHVTVTHGGSLVRLTPTA
+RFSDERGEAEMYGLYYADAGQHLENRLFVDHNRPNCVSNVLYKGALQGQDAHTVWVGDVL
+IRTEAEGTDSYEKNENLLLTDGARADSVPNLEIETGVIEGAGHASATGRFDETQLFYLMA
+RGIPESEARQLIVRGFLNEILQKIGIADVQDELTAVMEEELRVTAL
+>PROKKA_01089
+MTDTVENTQRTMIPGMGEEGEKLTVAQNPAARAGGRERNAAGSRADRLSSFELSDFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPAVAVAEQAGVTVETVARDDARVGSVLTP
+DDRVSAAAWNSVSEATVVTISGEVAEPVRIDVVGSSADPAAMHLTVLVEENAQADVVIAH
+RGTAVLAQNVEFDVRRDARLNVVALQAWEGDAVHVSAQQASVATNAHFKHVAVSYGGGVV
+RLTPTARFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPDCVSNVLYKGALQGTDARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGIPETEARRLIVRGFLNEIIQKIGVGDVEDELTAVMEDELRIAQL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000951.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000951.fa
new file mode 100644
index 0000000000000000000000000000000000000000..415423cf6c981b76ce352eda8554747d84ac5c4a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000951.fa
@@ -0,0 +1,34 @@
+>PROKKA_01142
+MSFNENVQIDAGRARSGGGGGLGGRGIAIGGGGGLLALLLAIFAPGLAEQLGIDTGGGSV
+GQSQYQQQTGSGGQSQPLSDEECASGADANQNTDCRVVATTEAADEFWGEYLAQFSDIQW
+RQPQLTLFQGGVSTGCGSASSATGPFYCPADESMYFDTAFFETLQTDFGAEGGPLAEEYI
+VAHEYGHHVQQVTGYLQHSKDGTTGPTSGAVRAELQADCFAGMWAGHATSTVDPESGEPF
+LKPISQDQLRQAIDAASAVGDDRIQSTHTGRVDPEAFTHGTSEQRMAWFMRGYQSAQQEP
+DIRQCDTFRAPSLDI
+>PROKKA_00861
+MSFNENVQIDAGRARSGGGGGLGGRGIAIGGGGGLLALLLAIFAPGLAEQLGIDTGGGSV
+GQSQYQQQTGSGGQSQPLSDEECASGADANQNTDCRVIATTEAADEFWGEYLAQFSDIQW
+RQPQLTLFQGGVSTGCGSASSATGPFYCPADESMYFDTAFFETLQTDFGAEGGPLAEEYI
+VAHEYGHHVQQVTGYLQHSKDGTTGPTSGAVRAELQADCFAGMWAGHAASTVDPESGAPF
+LKPISQDQLRQAIDAASAVGDDRIQSTHTGRVDPEAFTHGTSEQRMAWFMRGYQSSQQEP
+DIRQCDTFRASSLDI
+>PROKKA_01749
+MGGRGLAIGGGGGLLALLLAIFAPGLAGQLGIDTGGSTGQSQYQQQGAGGTQPVSDEECS
+TGADANRNTDCRVIAATEAADQFWGEYMSQFSDVDWRQPQLTLFAGSVSTGCGSASSAMG
+PFYCPADESMYFDTSFFETLQSDFGAEGGPLAEQYIVAHEYGHHVQHVTGYLQYSRDGST
+GPESGAVRAELQADCLAGMWAGAATTTVDPESGEPYLQPISREQLRQAIDAAAAVGDDRI
+QEMSTGRVNPEAFTHGSSEQRMAWFLRGYETSQQEPDFRQCDTFRASSLDI
+>PROKKA_01644
+MSFNENVQINAGRARGGGGGGMGGRGLAIGGGGGILALLLAIFAPGLAEDLGIGGAGTGT
+GSSYQQQLPQSGSGTSTQPVSQADCSTGADANQNTDCRVIATTESADAFWGDYMGQYSNI
+QWRQPDLTLFTTSVSTGGCGSATSATGPFYCPADESMYFDTAFFSTLESDFGATGGPLAE
+EYIVAHEYGHHVQNVVGWLQYAQDGRTGAASNAVRSELQADCLAGMWAGHAATTKDPETG
+EAFLQPITQEQLAQAIDAAGAVGDDRIQEQYQGRVNPEAFTHGSASQRQAWFMRGYETTS
+QQSPDINQCNTFQAATLDI
+>PROKKA_01092
+MSFNENVQIDAGRARSGGGGGLGGRGIAIGGGGGLLALLLAIFAPGLAEQLGIDTGGGSV
+GQSQYQQQTGSGGQSQPLSDEECASGADANQNTDCRVIATTEAADEFWGEYLAQFSDIQW
+RQPQLTLFQGGVSTGCGSASSATGPFYCPADESMYFDTAFFETLQTDFGAEGGPLAEEYI
+VAHEYGHHVQQVTGYLQHSKDGTTGPTSGAVRAELQADCFAGMWAGHAASTVDPESGAPF
+LKPISQDQLRQAIDAASAVGDDRIQSTHTGRVDPEAFTHGTSEQRMAWFMRGYQSSQQEP
+DIRQCDTFRASSLDI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000952.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000952.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5d35f8870befa2dae9678fb38ddf0366819b54d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000952.fa
@@ -0,0 +1,50 @@
+>PROKKA_01143
+MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKVLAGGGQPTAGTVTR
+TGRIGYLPQDPKVEDMDQSGRDRILSARDLDQTIRRMREAEAGMAAVDDAERERAMNRYS
+RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIL
+LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM
+TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG
+VEGERAVDRVAAIRFPTPQASGKTPLRAENLSKSYGSLGIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGEETPDTGEVQAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILHALRQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNDDYRDLITLA
+>PROKKA_00862
+MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKVLAGGGQPTAGTVTR
+TGRIGYLPQDPKVEDMDQSGRDRILSARDLDQTIRRMREAEAGMAAVDDAERERAMNRYS
+RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIM
+LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM
+TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG
+VEGERAVDRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGEETPDTGEVQAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILHALRQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNDDYRDLITLA
+>PROKKA_01748
+MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKILAGGGQPTAGSVTR
+TGRIGYLPQDPKVEDMDQSGRDRILSARDLDHTIRRMREAEAGMAAVDDVERQRAMDRYS
+RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIM
+LLDEPTNHLDHDSIVWLRDYLKTYPGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM
+TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG
+VEGERAADRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGEEAPDTGEVQEGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILGALRQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNEDYKDLITLA
+>PROKKA_01643
+MLTVTDLELRVGARLLMDEVSFRVAKGDKVGLVGRNGAGKTTLTRVLAGITQPTAGSVTV
+SGRLGYLPQDPKVEDMDQSGRDRILAARDLDQTIRRMRAAEADMASEDDAARQKAMDRYS
+RLQAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADTM
+LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDAMRQTIDVYNM
+NWKNYQAQRQQDEARRRREFANAEKKASALLAQAEKMRAKATKATAAQNMIKRAERMMRG
+VEGERAQDRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGTESPDTGEVIAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QCRTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILNALRQYEGAVVLVTHDEGAVEALAPERVVLLPDGDEDLWSDDYLDLISLA
+>PROKKA_01093
+MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKVLAGGGQPTAGTVTR
+TGRIGYLPQDPKVEDMDQSGRDRILSARDLDQTIRRMREAEAGMAAVDDAERERAMNRYS
+RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIM
+LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM
+TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG
+VEGERAVDRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGEETPDTGEVQAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILNALQQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNDDYRDLITLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000954.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000954.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0e736836c984898962d052cc10347074560702d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000954.fa
@@ -0,0 +1,20 @@
+>PROKKA_01146
+MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMRVYLVQMLVRTACFVAAL
+FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLRAVPAQGPALAPRPDDTAAPEPVV
+LTGDLVDDPRDRAPRALGRGSSSAGSPGLPGRGGA
+>PROKKA_00865
+MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMKVYLVQMLLRTACFVAAL
+FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLRAVPAQGPALAPRPDDTAAPKPVV
+LTGDLVDDPRDRAPRALGRGSSSAGGPGLPGRGAA
+>PROKKA_01746
+MTSSAAGSRAGRPARAGRSTGPQVQGVTTASAARSEDREARMKVYLVQMLIRTVCFGAAL
+FTTGWWQLLFILGAVALPYVAVVQVNNAGPRQAGSLRAVPAEGPELTARPADAPGPASPV
+VLTGDVVDDPREVGPRALPPGSPSEGARRLPGRGAA
+>PROKKA_01640
+MAAIVREPDAVQGVTTAAAPRSADRDARTRVYVVQMAVRTACFIAALFTHGWWQILFILG
+AVVLPYVAVVRVNNTGPREAGRRRDVARTAPAVPALPAEPSPVPTGPVVLVGEVVEDDDP
+AARRALPAGSPGETGRGRP
+>PROKKA_01096
+MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMKVYLVQMLLRTACFVAAL
+FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLHAVPAQGPALAPRPDDTAAPKPVV
+LTGDLVDDPRDRAPRALGRGSSSAGGPGLPGRGAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000955.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000955.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f40c6aaf42011a9d4341fd8431daba07c4730fdd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000955.fa
@@ -0,0 +1,30 @@
+>PROKKA_01148
+MTEQDLAGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQRIEDAGGRA
+VAVGGDVTVAEDRAALLDAAVEHFGSLDVLVLNASGGMESQFGEDYALKLNRDAQAALAD
+AALERMGAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFTEKGVGF
+VVVSGDMIEGTITATLLDRAEPGAIEARREAAGKLYSVEEFAAEIASLVGREGLEVGHTE
+LVGGAEDFLGQD
+>PROKKA_00867
+MTEQDLAGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQRIEDAGGRA
+VAVGGDVTVAEDRAALLDAAVEHFGSLDVLVLNASGGMESQFGEDYALKLNRDAQAALAD
+AALERMGAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFAEKGVGF
+VVVSGDMIEGTITATLLDRAEPGAIEARREAAGKLYSVEEFAAEIASLVGREDLEVGHTE
+LVGGAEDFLQQN
+>PROKKA_01744
+MTEKDLTGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQKIEEAGGRA
+VAVGGDVTSAEDRAALLDAAVESFGSLDVLVLNASGGMESQFGEDYAMKLNRDAQAALAD
+AALERMSAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFEAKGVGF
+AVVSGDMIEGTITATLLDRAEPGAIDARREAAGRLYSVEEFAAEVAALVGRDDLEVGHTE
+LVGGARDFLARGEG
+>PROKKA_01638
+MTTQDLAGKGVVVTGSSRGIGAETAQLLAARGAGVVVNYRQKAPRANKVVQAIEAARGRA
+VAVGGDVTVAEDRAALLDAAIDNFGSLDVLVLNASGGMESQFGEDYAMTLNRDAQAALAD
+AALERMSAGGQIVFVTSHQAHFIDEVATMDAYEPVARSKRAGEDALRERIPAFEAKGVGF
+VVVSGDMIEGTITATLLNRAEPGAIEARREAAGKLYSVEEFAAEVAALVGRTDLEVGHTE
+LVGGAQDFLGQD
+>PROKKA_01098
+MTEQDLAGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQRIEDAGGRA
+VAVGGDVTVAEDRAALLDAAVEHFGSLDVLVLNASGGMESQFGEDYALKLNRDAQAALAD
+AALERMGAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFAEKGVGF
+VVVSGDMIEGTITATLLDRAEPGAIEARREAAGKLYSVEEFAAEIASLVGREDLEVGHTE
+LVGGAEDFLQQN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000956.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000956.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb7b062b20343e8d57fbb89bfde1da188beaacca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000956.fa
@@ -0,0 +1,30 @@
+>PROKKA_01149
+MSTLRRLVVTADPALLVTDAPPAGVPDDAERLTDDGLLGWRFAADEWAAAPEPGSGWDVL
+TVPATVAAAPAPLVVTDVDSTLIRQEVIELLAAHAGREAEVAEVTERAMRGELDFAASLH
+ARVEALAGLPVGVVADVVRAIRPTDGALALIEAVTAAGGRVCAVSGGFTQVLAPLAEAWG
+VHAYCANELEVQDGHLTGKVLGDVVDRAAKAAMLRAWAEDAGLTPEQAVGVGDGANDIDL
+LEAAGCGVALCAKPILREHADVVVDVPSFTPLRWLLGL
+>PROKKA_00868
+MSTLRRLVVTADPALLVTDAPPAGVPDDAERLTDDGLLGWRFAADEWAAAPEPGSGWDVL
+TVPATVAAAPAPLVVTDVDSTLIRQEVVELLAAHAGREAEVAEVTERAMRGELDFAASLH
+ARVEALAGLPVGVVADVVRAIRPTDGALALIEAVTAAGGRVCAVSGGFTQVLAPLAEAWG
+VHAYCANELEVRDGHLTGKVLGDVVDRAAKAAMLRAWAEDAGLTPEQAVGVGDGANDIDL
+LEAAGCGVALCAKPILREHADVVVDVPSFTPLRWLLGL
+>PROKKA_01743
+MSTLRRLVVTADPALLADRTPPAGVPDDAERLLEDGLLGWRFAADEWAAAPEPGPGWAVH
+TLPAAVAEAPVPLVVTDVDSTLIRQEVIELLAAHAGREAEVAAVTERAMRGELDFAASLH
+ARVEALAGLPVGVVDDVVRAIRPTAGALALIEAVTAAGGRVCAVSGGFSQVLAPLAQAWG
+VHAYCANELEVHDGHLTGRVAGDVVDRAAKAAMLRAWAEDAGLSPEQAVGVGDGANDIDL
+LDAAGAGVALCAKPVLREHADVVVDVPSFTPLRWLLGL
+>PROKKA_01637
+MTQARHLLYRAVPAGTDSPVAPAWAPLPADAEHLAADGLAGLRWEGSVPSAEEATALPED
+WALASLPQSVAAAPTPLVVTDVDSTLIQQEVIELLAAHTGREAEVAAVTERAMRGELDFA
+QSLHARVEALAGLPASVVDDVVARVRPTDGAVELIAAVNAAGGRVCAVSGGFTQVLAPLA
+EAWGVHAYCANELEVRDGHLSGKVLGDVVDRAAKAAMLRAWAEDAGLSPEQAVGVGDGAN
+DIDLLEVAGCGVALCAKPILREHADVVIDVPSFTPLRWLLGL
+>PROKKA_01099
+MSTLRRLVVTADPALLVTDAPPAGVPDDAERLTDDGLLGWRFAADEWAAAPEPGSGWDVL
+TVPATVAAAPAPLVVTDVDSTLIRQEVVELLAAHAGREAEVAEVTERAMRGELDFAASLH
+ARVEALAGLPVGVVADVVRAIRPTDGALALIEAVTAAGGRVCAVSGGFTQVLAPLAEAWG
+VHAYCANELEVRDGHLTGKVLGDVVDRAAKAAMLRAWAEDAGLTPEQAVGVGDGANDIDL
+LEAAGCGVALCAKPILREHADVVVDVPSFTPLRWLLGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000957.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000957.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bce18168a39ba1f5f1ba5ab3f42f029fcd715a59
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000957.fa
@@ -0,0 +1,30 @@
+>PROKKA_01150
+MTTPAPPDDWFLPDEDAVLQMRRVRVRRGTTDILGPLDWTVRAGQRWIVMGPNGAGKSTL
+LQLAAARLHPTAGDVGVLDEVLGAVDVFELRPRIGLSSAQLAAQVPANETVQDAVVTAAY
+GITGTWRERYETEDRARALGLVATWGLSRLAHRAFGTLSDGERKRVLIARALMTDPELLL
+LDEPAAGLDLAGREDLVRQLTALATDEDAPALVLVTHHLEEVPPGFTHALLLRDGGVVAA
+GPIESTLTEEHLSAAFGTDLKVTRTGGRYTAVAR
+>PROKKA_00869
+MTTPAPPDDWFLPDEDAVLQMRRVRVRRGTTDILGPLDWTVRAGQRWIVMGPNGAGKSTL
+LQLAAARLHPTAGDVGVLDEVLGAVDVFELRPRIGLSSAQLAAQVPANETVQDAVVTAAY
+GITGTWRERYETEDRARALGLVATWGLSRLAHRAFGTLSDGERKRVLIARALMTDPELLL
+LDEPAAGLDLAGREDLVRQLTALATDEDAPALVLVTHHLEDVPPGFTHALLLRAGGVVAA
+GPIESTLTEEHLSSAFGTDLKVTRTGGRYTAVAR
+>PROKKA_01742
+MTLPAPSDDWFLPDEDAVLQMRRVRVRRGQTDILGPLDWTVRAGERWIVMGPNGAGKSTL
+LQIAATRLHPTGGEVAILEEVLGAVDVFELRPRIGLSSAQLAAQVPHEEKVQDAVVTAAY
+GVTGTWRESYEDEDRMRALGLVSSWGLSRLAHRRFGTLSEGERKRVLIARSLMTDPELLL
+LDEPAAGLDLAGREALVAQLSELARDEDAPALVLVTHHLEEVPPGFTHALLLRDGHAVAA
+GPIEQTLTEGHLSAAFDTPLRVTRTGGRYTAVAQ
+>PROKKA_01636
+MNTAPQDPSPRPVVEHDVFTPDEDAVLQLRDVAVRRGAKQILAGIDWTVRAGERWVVMGP
+NGAGKSTLLQIAASRMFPTSGDVAILDEVLGAVDVFELRPRIGLSSALLANQVRDDETVQ
+DAVITASYGMTGRWREEYEVEDRARALGLVSEWGLSRLAHRRFGTLSEGERKRVLIARAL
+MTDPELLLLDEPAAGLDVAGREALVGQLSELAADEDAPATVLVTHHLEEVPPGFTHALLL
+ADGAVVQAGPLEETLTAEHLSTAFGTPLRVTRADGRYTAVAA
+>PROKKA_01100
+MTTPAPPDDWFLPDEDAVLQMRRVRVRRGTTDILGPLDWTVRAGQRWIVMGPNGAGKSTL
+LQLAAARLHPTAGDVGVLDEVLGAVDVFELRPRIGLSSAQLAAQVPANETVQDAVVTAAY
+GITGTWRERYETEDRARALGLVATWGLSRLAHRAFGTLSDGERKRVLIARALMTDPELLL
+LDEPAAGLDLAGREDLVRQLTALATDEDAPALVLVTHHLEDVPPGFTHALLLRAGGVVAA
+GPIESTLTEEHLSSAFGTDLKVTRTGGRYTAVAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000958.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000958.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a4db33d75b90df174a9054f36c7cb274c3fcb854
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000958.fa
@@ -0,0 +1,30 @@
+>PROKKA_01151
+MTGLLTAQLLGMDLWQVLLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQVSNA
+MGLVASGFSGTYGYRRELAQSRALLPKLTVASLLGGVIGAALLTTLPPAVFGYVAPVLLV
+VALTVVVLQPRIQGWVRRRAEDQGPTPGADSPVPVGPVTPTLWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVLLVGGTLVHANAVKTWLSLVVNLTAAAFYLVFAFDRIDWRAVLLIALSSL
+VGGLVGARIGRRISPTALRVTIVIVGLAGLVVMVMRQVSGG
+>PROKKA_00870
+MTGLLTAQLLGMDLWQVLLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQVSNA
+MGLVASGFSGTYGYRRELAQSRALLPKLTVASLLGGVIGAALLTTLPPAVFGYVAPVLLV
+VALTVVVLQPRIQRWVRRRAEDQGPTPGADSPVPVGPVTPTLWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVLLVGGTLVHANAVKTWLSLVVNLTAAAFYLVFAFDRIDWRAVLLIALSSL
+VGGLVGARIGRRISPTALRVTIVIVGLAGLVVMVMRQVSGG
+>PROKKA_01741
+MIDVLGADVLGLELWQVVLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQISNA
+IGLVAAGFSGVFGYRRELKESGAVLPVLTVASLLGGVLGAFLLILLPAEVFGVAAPVLIV
+VALAFVVLQPRLQAWVRRRSAAREDGVVDVPARPSRPVSPVLWVLVFLAGVYGGYFVAAQ
+GVLLMGILGVFLVGGTLVHANAIKTWLSLAVNLVAATSYLLFAFDRIDWTAVLLIAASSM
+VGGLVGARIGRRISPTVLRIVIVVVGLAGLVSMVLRLVDGG
+>PROKKA_01635
+MDLLTAPVLGMDLWQVALVLLAGFWAGTINSIIGSGTLVTFPVLVAVGFPPVTAQVSNAM
+GLVASGFSGTYGYRRELRESRALLPRLTLASFLGAVIGATLLTVLPPTVFASVAPCLLVL
+ALTIVVLQPRIQAWVRRRSAGEHGHVPGADSPVPVGPASPALWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVMLVGGTLVHANAVKTWLSLTVNLTAAVFYLVFAFDRIDWRAVLLIAVSSL
+VGGSVGARIGRRMSPTALRVTIVVIGVAGLVSMLSRLAGA
+>PROKKA_01101
+MTGLLTAQLLGMDLWQVLLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQVSNA
+MGLVASGFSGTYGYRRELAQSRALLPKLTVASLLGGVIGAALLTTLPPAVFGYVAPVLLV
+VALTVVVLQPRIQRWVRRRAEDQGPTPGADSPVPVGPVTPTLWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVLLVGGTLVHANAVKTWLSLVVNLTAAAFYLVFAFDRIDWRAVLLIALSSL
+VGGLVGARIGRRISPTALRVTIVIVGLAGLVVMVMRQVSGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000963.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000963.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89fb00a1b7e4b00839a9d14081d043738a00c65e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000963.fa
@@ -0,0 +1,40 @@
+>PROKKA_01158
+MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP
+GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID
+TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP
+DTAELAHEVNELISELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE
+DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR
+>PROKKA_00877
+MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP
+GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID
+TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP
+DTAELAHEVNELIAELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE
+DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR
+>PROKKA_01731
+MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGEPRDPDYHGARVLTYPNPP
+GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANMAGHLGKLMHGVPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAEKTAYLGADAVIAVSDGMRRDILACYPEVDPEKVHTVHNGID
+TEAWTPQTETDALEKYGIDPTRPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP
+DTPELAHEVNGLIAELRRTREGVVVIEGMIPRREVTQILSAATVFACPSVYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVQDGETGLLVPIEQVADGTGAPADEDAFAADFAAALTRVLE
+DPERATAMGEAGRARAIEHFSWEAIAERTIEVYEAVLR
+>PROKKA_01629
+MRIDIVTKEFPPTIYGGAGVHVAELTRVLSSRADVHVHAFGGAREPDYHGATVTSYAQPA
+GFESANGAVQTLVTDLDIVGDLDGADVIHSHTWYANMAGHLGGLMHGVPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAESTAYHGAAAVIAVSEGMRRDILRCYPDVDPAKVHTVHNGID
+TQLWTPQTGTDALTKYGIDPDRPSVAFVGRITRQKGVPHLLRAALQLPEDVQLVLCVGAA
+DTPELAREVEGLIGRLRAEREGVVVVEGMIPRGEVTQILSAATVFACPSIYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVDDGVTGLLVPVEQADDGTGTPVDEEKFAADLAKALSTVLA
+DPERATAMGEAGRARAIEHFSWETIADRTMEVYAAVAR
+>PROKKA_01108
+MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP
+GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID
+TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP
+DTAELAHEVNELISELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE
+DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000964.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000964.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5fe52c8d8d90b7bfd1fa9899793052c98bb92c5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000964.fa
@@ -0,0 +1,65 @@
+>PROKKA_01159
+MTVHEKLAPQSSTPSTEVPSDVAEIAPERPTPGSLDAAALEEALLGRWAAERRESRELVK
+DPALWRDPLLGMDEHRARVLRQLGVLVERNAVHRAFPREFGGEDNHGGNLAAFGDLVLAD
+PSLQIKAGVQWGLFSSAILHLGTAEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIATT
+ATYDEATQEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITRGVNHGVHCFYVPIRDEE
+GAFLPGVGGEDDGLKGGLNGIDNGRLHFTQVRIPRTNLLNRYGDVAEDGTYSSPIASPGR
+RFFTMLGTLVQGRVSLSLAATTASFLGLHGALAYAEQRRQFKASDPQREEVLLDYQNHQR
+RLIDRLARAYADAFASNELVEKFDDVFSGRSDTDVDRQELETLAAAVKPLTTWHALDTLQ
+EAREACGGAGFLAENRVAQMRADLDVYVTFEGDNTVLLQFVGKRLLTDYSKEFGRLNVGA
+VSRYVVHQASDALHRAGLHKAVQSVADGGSERRSANWFKDPAVQHELLTERVRAKTADIA
+GTLSGARGKGQAAQAEAFNTRQHELIEAARNHGELLQWEAFTRALEGITDETTKTVLTWL
+RDLFALRLIEDDLGWFVAHGRVSSQRARALRGYVNRLAERLRPFALELVESFGLEPEHLR
+MAVATDAETQRQEEAHAWFTARRAAGEEPEDEKAVRAREKAARGRRG
+>PROKKA_00878
+MTVHEKLAPQSSTPSTEVPSDVAEIAPERPTPGSLDAAALEEALLGRWAAERRESRELVK
+DPALWRDPLLGMDEHRARVLRQLGVLVERNAVHRAFPREFGGEDNHGGNLAAFGDLVLAD
+PSLQIKAGVQWGLFSSAILHLGTAEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIATT
+ATYDEATQEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITRGVNHGVHCFYVPIRDEE
+GAFLPGVGGEDDGLKGGLNGIDNGRLHFTQVRIPRTNLLNRYGDVAEDGTYSSPIASPGR
+RFFTMLGTLVQGRVSLSLAATTASFLGLHGALAYAEQRRQFKASDPQREEVLLDYQNHQR
+RLIDRLARAYADAFASNELVEKFDDVFSGRSDTDVDRQELETLAAAVKPLTTWHALDTLQ
+EAREACGGAGFLAENRVAQMRADLDVYVTFEGDNTVLLQLVGKRLLTDYSKEFGRLNVGA
+VSRYVVHQASDALHRAGLHKAVQSVADGGSERRSANWFKDPAVQHELLTERVRAKTADIA
+GTLSGARGKGQAAQAEAFNTRQHELIEAARNHGELLQWEAFTRALEGITDETTKTVLTWL
+RDLFALRLIEDDLGWFVAHGRVSSQRARALRGYVNRLAERLRPFALELVESFGLEPEHLR
+MAVATDAETQRQEEAHAWFTARRAAGEEPEDEKAVRAREKAARGRRG
+>PROKKA_01730
+MTVHEKLAPQSPTHTTEVPSDVAEIAPEHPEPGSLDSAALQDALLGAWAEDRRTARALVR
+DPRLHRDPLLGMDEHRERVLGQLGVLVENGAVHRMFPKEFGGDDNHGGNIAAFADLVLGD
+PSLQIKAGVQWGLFAAAILHLGTEEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIGTT
+ATYDEAAGEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITKGVNHGVHCFYVPIRDED
+GAFLPGVGGEDDGLKGGLNGIDNGRLHFDQVRVPRTNLLNRYGDVAEDGTYSSPIESPGR
+RFFTMLGTLVQGRVSLSLAATTASFLGLHGAIAYGEQRRQFNASDPEREEVLLDYQNHQR
+RLVDRLARAYADAFASNELLERFDGVFSGRADSDADRQELETLAAAIKPLATWNALDTLQ
+ETREACGGAGFMARNRIPQMRADLDVYVTFEGDNNVLLQLVGKRLLTDYSHEFGRLNVGA
+VSRYVVAQASDAIHRAGLHKAVQSVSDGGSERRSANWFKDPEVQRDLLTDRVRAKTADIA
+GTLAGVRGKTQAEQAAAFNTRQHELIEVARNQGELLQWEAFTRAVQATRDESTRTVLTWL
+RDLFALRVLEEDLGWLVAHGRLSSQRARSLRGYVNRLAERLRPFALELVEAFGLEPEHLR
+MDIATQAEAERQAEAHAWFEARRAAGEEPEDEKAVRAREKAARGRRG
+>PROKKA_01628
+MTDIRTDAASAAEALPATDAVPHDVAEIAPEDPTPGALDAAALQDLLLGSWAEAHRTARG
+LVKDERLHRDPALGMDEHRARVLDQLGILVEEKAVHRAFPADLGGQDDHGGSIAAFANLV
+LADPSLQIKAGVQWGLFSSAILHLGTREHHEKWLPGAMDLSMPGAFAMTEIGHGSDVASI
+ATTATYDEATQEFVIHTPFKAAWKDYLGNAALHGRAATVFAQLITKGVNHGVHCFYVPIR
+DESGAFLPGVGGEDDGLKGGLNGIDNGRLHFDHVRVPRTHLLNRYGDVAEDGTYSSDIAS
+PGRRFFTMIGTLVQGRVSLSLAASIASFMGLHGALAYAEQRRQFGGPEGSETLLLDYQNH
+QRRLIDRLARTYADLFAANELLEKFDHVFSGAGDTDKDREELETLAAAIKPLTTWNALDT
+LQEAREATGGMGFMAGRNRLPHLRADLDIFVTFEGDNNILLQLVGKRLLTDYSAEFGKLN
+VGAVSRWAASEASDALHRVGLHKAAQSVHDRGDQRRAANWFKDPQVQRDLLTDRVRTRVA
+DIASTLGSARGKSKAEQAAAFNSRQHELIEVARHHGELLQWEAFTRQVESLPAGQTRTVL
+TWLRDLFALRLIEDDLGWLVAHGRVSSARARVLRGYVNRLAERLRPFALELVEAFGLEPE
+HLRMEIATDAESVRQQEAADWFAARRAAGEEPVHEKTLHAGKR
+>PROKKA_01109
+MTVHEKLAPQSSTPSTEVPSDVAEIAPERPTPGSLDAAALEEALLGRWAAERRESRELVK
+DPALWRDPLLGMDEHRARVLRQLGVLVERNAVHRAFPREFGGEDNHGGNLAAFGDLVLAD
+PSLQIKAGVQWGLFSSAILHLGTAEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIATT
+ATYDEATQEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITRGVNHGVHCFYVPIRDEE
+GAFLPGVGGEDDGLKGGLNGIDNGRLHFTQVRIPRTNLLNRYGDVAEDGTYSSPIASPGR
+RFFTMLGTLVQGRVSLSLAATTASFLGLHGALAYAEQRRQFKASDPQREEVLLDYQNHQR
+RLIDRLARAYADAFASNELVEKFDDVFSGRSDTDVDRQELETLAAAVKPLTTWHALDTLQ
+EAREACGGAGFLAENRVAQMRADLDVYVTFEGDNTVLLQLVGKRLLTDYSKEFGRLNVGA
+VSRYVVHQASDALHRAGLHKAVQSVADGGSERRSANWFKDPAVQHELLTERVRAKTADIA
+GTLSGARGKGQAAQAEAFNTRQHELIEAARNHGELLQWEAFTRALEGITDETTKTVLTWL
+RDLFALRLIEDDLGWFVAHGRVSSQRARALRGYVNRLAERLRPFALELVESFGLEPEHLR
+MAVATDAETQRQEEAHAWFTARRAAGEEPEDEKAVRAREKAARGRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000968.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000968.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4eabaa47f3ba079425b33d045e37889083e6d401
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000968.fa
@@ -0,0 +1,101 @@
+>PROKKA_01164
+MALEAPALLHRLARAHGVQPEYVGQDGSAQTVPDEALVKVLAALGVSVRPDGVAALAEAV
+EEAETAPWRDVLPPTVAARSGHRLSVPCHVAAGEPVVARVRTEDGRTLEVSVSEPVSEVR
+LVDGVERERVHVQIPADLAPGWHRLEVTSGSGSTASAVLVCAPTRLSTARPFLERRGWGA
+AAQGYSVTSADSWGIGDAADMASLAEIVARHGADFLLLHPLHAIEPGPHPADSPYSPVSR
+RFLSALVVHVPSIPEFADLPAAEQAELRSAGARVQAELERTGRIDRAAVAAVLWPALRRV
+HEVPRSPEREAAYARFRAEAGPGLDDFALWSVLRLDGDGTGPDLADPAWAPGGVEAERVR
+VERATDVDLHRWVQWIAAEQLAGVQERARAAGMRMGVMVDLAVGATRETADAWMLGDVLV
+PTMSVGAPPELFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRGAGGIRMDHVLGLF
+RLWWIPEGAGATQGAYVEYDHEAMLAVLTLEAERAGVVVVGEDLGTFEPWVQRRLAEAGV
+LGTSILWFEQEDGEPTPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTVDVA
+QERRRSAEEVRAFLAAAARRGLLAEADVDVPDAGPEVRERQIVALHRLLAQAPSALHSVA
+LVDAVGERRIQNQPGTLQDQYPNWTVPLGDGAGRMVSVEDLADSASAARLFDAVDAELRA
+SVPVGIGVSLHTSPLAQPGRGDAGGMNVYVRQAAVALARRGVRMILLTRAEEPVGADGAR
+VRMLDAGGQAPPVTVVDLAAGPSAPVPKEELAGLGAEFTRAALDWLASDAVPGGPVLGGA
+DAPPVAFVHGHYWLSGSTAAALARAAHAPYLQTMHTTAAAKMLEDPELREPAARIEAERE
+VAERADLLVVNSAAEVADLRELLDVPRARTRVLPPGADLETFTPEGAAQWPGAPEDDGAL
+RVLFAGRVQRHKGPHLLVAALGVLRERAGGAGADPGVRLHVNGAASGDDELDLAGLAARE
+GVADLVTFSGPVPAPALAAQFRAADVVAMPSASETYGLVALEAQACGTPVLAHRVGGLVY
+AVLDGVSGRHVTAGTPEAWADALAEILADRDAWAALGTGAVRHAAGHSWEAYADGLLEAV
+TAVPRRSPGLDA
+>PROKKA_00883
+MALEAPALLHRLARAHGVQPEYVGQDGSAQTVPDEALVKVLAALGVSVRPDGVAALAEAV
+EEAETAPWRDVLPPTVAARSGHRLSVPCHVAAGEPVVARVRTEDGRTLEVSVSEPVSEVR
+LVDGVERERVHVQIPADLAPGWHRLEVTSGSGSTASAVLVCAPTRLSTARPFLERRGWGA
+AAQGYSVTSADSWGIGDAADMASLAEIVARHGADFLLLHPLHAIEPGPHPADSPYSPVSR
+RFLSALVVHVPSIPEFADLPAAEQAELRSAGARVQAELERTGRIDRAAVAAVLWPALRRV
+HEVPRSPEREAAYARFRAEAGPGLDDFALWSVLRLDGDGTGPDLADPAWAPGGVEAERVR
+VERATDVDLHRWVQWIAAEQLAGVQERARAAGMRMGVMVDLAVGATRETADAWMLGDVLV
+PTMSVGAPPELFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRGAGGIRMDHVLGLF
+RLWWIPEGAGATQGAYVEYDHEAMLAVLTLEAERAGVVVVGEDLGTFEPWVQRRLAEAGV
+LGTSILWFEQEDGEPTPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTVDVA
+QERRRSAEEVRAFLAAAARRGLLAEADVDVPDAGPEVRERQIVALHRLLAQAPSALHSVA
+LVDAVGERRIQNQPGTLQDQYPNWTVPLGDGAGRMVSVEDLADSASAARLFDAVDAELRA
+SVPVGIGVSLHTSPLAQPGRGDAGGMNVYVRQAAVALARRGVRMILLTRAEEPVGADGAR
+VRMLDAGGQAPPVTVVDLAAGPSAPVPKEELAGLGAEFTRAALDWLASDAVPGGPVLGGA
+DAPPVAFVHGHYWLSGSTAAALARAAHAPYLQTMHTTAAAKMLEDPELREPAARIEAERE
+VAERADLLVVNSAAEVADLRELLDVPRARTRVLPPGADLETFTPEGAAQWPGAPEDDGAL
+RVLFAGRVQRHKGPHLLVAALGVLRERAGGAGADPGVRLHVNGAASGDDELDLAGLAARE
+GVADLVTFSGPVPAPALAAQFRAADVVAMPSASETYGLVALEAQACGTPVLAHRVGGLVY
+AVLDGVSGRHVTAGTPEAWADALAEILADRDAWAALGTGAVRHAAGHSWEAYADGLLEAV
+TAVPRRSPGLDA
+>PROKKA_01726
+MSRRFLSALLVHVPDIPEFASLPAAEQDELRAAGAAVQARLERSGTIDRPAVAAALWPAL
+RRVHAVPRSPEREAAYAAFRAEAGPGLDDFALWSALRTADDVPGPDLADPAWAPGGEHAE
+RVRTERADEVDLHRWVQWVAAEQLAAVQQRARAAGMRMGVMVDLAVGATRETADAWMLGD
+VLVPGMSVGAPPEVFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRDAGGIRMDHVL
+GLFRLWWIPVGAGATQGAYVEYDHEAMLAVLTLEAERAGAVVVGEDLGTFEPWVQRRLAE
+AGVLGTSILWFEQRDGEPLPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTV
+DVAQERRRSADEVEAFLGAAVRRGLLDARDARVRPDDAAQREAQTVALHRLLAQAPSALH
+SVSLVDAVGERRIQNQPGTTQDQYPNWTLPLGDREGRMLRVEDLASSASAARLFDAVEEE
+LRASVPVGIGVSLHTSPLAQPGRGDAGGLNVYVRHAALALARRGVRMILLTRAEEPVGPE
+SARVTRLEAGGEAPAVTVVELAVGPAAPLPKAELAALTDEFTAAARAWLASDAVPGGPVL
+APQGLDGRGPGAPAAPPVAFVHGHYWLSAPTAAALAAATGAPHLHTMHTTAAVKMLEDPE
+LREPGARIEAEGAVVREADLLVVNSPAEVVDLREALGVPRARTRVLPPGADLATFTPEGP
+ALWPGDPDDDGALRVLFAGRIQRHKGPHLLVEALAVLRERAGGPGADPGVRLHVNGAPSG
+EEGLDLPGLALERGVADLVTFSEPVRAEELAAQLRAADVVAMPSASETYGLVALEAQACG
+TPVLAHRVGGLVHAVIDGASGRLVTEGSPEAWADALAAVLADRPAWDALAAGAVRHAAGH
+SWEAYADGLLEAAAGLARRQDGA
+>PROKKA_01623
+MPENARALLRRLARAHGVQTEYVGQDGSDQSVADETLVRVLSALGVEVDADGVAGLTEAL
+DAVDAAPWRDVLPPTVVARQGHRSTVPVHVARGAAVQVRLVQEDGRVVDLPTREAVGATL
+VVDGQERVRHDLDLPEDLPLGWHRLEAVSETGSVARATLVSAPAALTTAAPFLARRGWGV
+AAQGYSVTSSGSWGVGDAHDAGSLAELAAPHGADFLLLHPLHAVEPAGAPADSPYSPVSR
+RFLSAFLIRVTDIPEFAALPAEEQKRLAAAGRAVQEAVLTGGTIDRAAVAEVLWPALEAV
+WRAPRTSERDADYAAFRDRQGTGLDDFAAWSVLRRDALRAGVAGPDPTDPAAGPGSDGVR
+RVRAERADELDFHRWVQWIADEQLAAAQERAREAGMRMGVMLDLAVGATRGSADAWMLGD
+VLVPSMSVGAPPEVFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTLMAHAGGLRMDHVL
+GLFRLWWIPEGLGAPQGAYVHYDHEAMLAVLTLEAERAGVVVIGEDLGTFEPWVQRRLAE
+AGVLGTSILWFEQEDGVPTPPEQYRRLCMAAVNTHDLPPTAGYLEGVHIDLRERLGLYTA
+DVAAERRRSAAEVEAFLGAARKRGLLEATGPDGVETVEDRVVALHRLLAQAPSALHCVGL
+VDAVGERRIQNQPGTLQEQYPNWTVPLGDADGRVLTVEDLAGTASVSRLFDAVAAELDAS
+VPVGIAVAFHTSPLAQPGQGDAGGLNVYVRHSARALARLGVRMLLLTRAESPVGPSGVRV
+TTLPQGEGAPDVTVVELAAGPQEPVAKEELPAHREAFTAAAREWLASADVPGGPLLGAAG
+AAAARVRFVHAHYWLSGDTAAAVADDLGAPRVQTMHTTGAVKSAGDPGHPEPAERLAAEA
+DLVRRADLLVVNSPAESRDLQELLDVDRDRVRVLPPGVDLESFTPEGPSRWPGGDAVGAD
+ALRVLFAGRVQEHKGPHVLVAALAELRARAADGDPRVVLHVNGEQSGPADLDLPALAARL
+GVADLVTFSPPVPPVELAAQMRAADVVALPSASETYGLVAVEAQAAGTPVLAHRVGGLVH
+AVQDGVSGRLVIPNTASAWADALAAVREDRQAWDAMAPAAVRHARAHAWSGWAEGLLDAV
+AGLPRP
+>PROKKA_01114
+MALEAPALLHRLARAHGVQPEYVGQDGSAQTVPDEALVKVLAALGVSVRPDGVAALAEAL
+EEAETAPWRDVLPPTVAARSGHRLSVPCHVAAGEPVVARVRTEDGRTLEVSVSEPVSEVR
+LVDGVERERVHVQIPADLAPGWHRLEVTSGSGSTASAVLVCAPTRLSTARPFLERRGWGA
+AAQGYSVTSADSWGIGDAADMASLAEIVARHGADFLLLHPLHAIEPGPHPADSPYSPVSR
+RFLSALVVHVPSIPEFADLPAAEQAELRSAGARVQAELERTGRIDRAAVAAVLWPALRRV
+HEVPRSPEREAAYARFRAEAGPGLDDFALWSVLRLDGDGTGPDLADPAWAPGGVEAERVR
+VERATDVDLHRWVQWIAAEQLAGVQERARAAGMRMGVMVDLAVGATRETADAWMLGDVLV
+PTMSVGAPPELFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRGAGGIRMDHVLGLF
+RLWWIPEGAGATQGAYVEYDHEAMLAVLTLEAERAGVVVVGEDLGTFEPWVQRRLAEAGV
+LGTSILWFEQEDGEPTPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTVDVA
+QERRRSAEEVRAFLAAAARRGLLAEADVDVPDAGPEVRERQIVALHRLLAQAPSALHSVA
+LVDAVGERRIQNQPGTLQDQYPNWTVPLGDGAGRMVSVEDLADSASAARLFDAVDAELRA
+SVPVGIGVSLHTSPLAQPGRGDAGGMNVYVRQAAVALARRGVRMILLTRAEEPVGADGAR
+VRMLDAGGQAPPVTVVDLAAGPSAPVPKEELAGLGAEFTRAALDWLASDAVPGGPVLGGA
+DAPPVAFVHGHYWLSGSTAAALARAAHAPYLQTMHTTAAAKMLEDPELREPAARIEAERE
+VAERADLLVVNSAAEVADLRELLDVPRARTRVLPPGADLETFTPEGAAQWPGAPEDDGAL
+RVLFAGRVQRHKGPHLLVAALGVLRERAGGAGADPGVRLHVNGAASGDDELDLAGLAARE
+GVADLVTFSGPVPAPALAAQFRAADVVAMPSASETYGLVALEAQACGTPVLAHRVGGLVY
+AVLDGVSGRHVTAGTPEAWADALAEILADRDAWAALGTGAVRHAAGHSWEAYADGLLEAV
+AAVPRRSPGLDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000973.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000973.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cae8a7fa862a7388d1fb4a3b68500b450b637d37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000973.fa
@@ -0,0 +1,45 @@
+>PROKKA_01170
+MKSWSTPAPPAVPSRPDRLRLHDTATGRTRHPGNDAQRASLYVCGITPYDATHLGHASTY
+VAFDLLHRYWRAAGLEVAYVQNVTDVDDPLLERAEATGVDWRALAEEQTDLFRADMAALE
+VLAPDHYVGATEAVGLVVDAVETMLAAGRAYRVPGGDGEPDGDVYFDVRAAQSATDWRLG
+QVSAMGLDEMAAVFPERGGDPDRPGKRDPLDPLLWRVHREGEPAWDGRSLGSGRPGWHIE
+CSVISRAHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGLPLAHTYAHTGMVALDGEKMS
+KSLGNLELVSRLRARGVEPVAVRAAILAHHYRSDWEWSEQVLADAQARVARWRAALDGPH
+AAAGVAVLDAVHAALSDDLDAPRALEALDAWAAGTLPGLAEAAADPLPVVDVVAALLGLR
+LR
+>PROKKA_00889
+MKSWSTPAPPTVPSRPDRLRLHDTATGRTRHPGNDAQRASLYVCGITPYDATHLGHASTY
+VAFDLLHRYWRAAGLEVAYVQNVTDVDDPLLERAEATGVDWRALAEEQTDLFRADMAALE
+VLAPDHYVGATEAVGLVVDAVETMLAAGRAYRVPGGDGEPDGDVYFDVRAAQSATDWRLG
+QVSAMGLDEMAAVFPERGGDPDRPGKRDPLDPLLWRVHREGEPAWDGRSLGSGRPGWHIE
+CSVISRAHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGLPLAHTYAHTGMVALDGEKMS
+KSLGNLELVSRLRARGIEPVAVRAAILAHHYRSDWEWSEQVLADAQARVARWRAALDGPH
+AAAGVAVLDAVHAALSDDLDAPLALEALDAWAAGTLPGLAEAAADPVPVVDVVAALLGLR
+LR
+>PROKKA_01719
+MKSWSTPVPPAVPTRPDRLRLHDTATGAVRHPGNDAREASLYVCGITPYDATHLGHASTY
+VAFDLLNRYWRAAGLEVAYVQNVTDVDDPLLERADATGVDWRELARDQTDLFRTDMAALE
+VLAPDHYVGATEAIDLVVDAVEAMLAAGLAYRVPGDADAPDGDVYFDVRAAEAAGDWRLG
+QVSAMPLDEMAAVFPERGGDPQRPGKRDPLDPLLWRVHRDGEPAWDGRSLGEGRPGWHIE
+CSVISRAHLPSPFTVQGGGSDLRFPHHEFSAAHATAVDGRPLARHYAHTGMVALNGQKMS
+KSLGNLELVSRLRARGVEPVAVRAAILAHHYRSDWEWSEDVLARAQERVARWRAALEGPH
+AQAGSAVLDAVHAALSDDLDAPRALEALDAWAAGTLPGLDAAADAAPVAVADVASALLGL
+RLR
+>PROKKA_01617
+MKSWSTPAPRALPVQPDRLRVFDTATQALRHPGNDARTASLYVCGITPYDATHLGHATTY
+VSFDLLQRYWRAAGLEVAYTQNVTDVDDPLLERAEATGVDWRELAREQTDLFRSDMEALN
+VFAPDHYVGATEAIDLVVRAVEAMLEGGTAYRVPGTDGEPDGDVYFDSAAAQARGGWTLG
+SVSAMDRAQMEEVFPERGGDPGRPGKRDPLDPLLWRVHREGEPAWDGGALGSGRPGWHIE
+CSAIAREHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGRPLAHTFLHSGMVALDGQKMS
+KSLGNLELVSRLRARGVEPVAIRAAILDRHYRSDWEWSEDLLTAAEERVARWRSALDGPH
+ADAGAAVLAAAHTALSEDLDAPAALRVLDAWADGTLDGLSTTAEPLPVADVVDALLGLRL
+R
+>PROKKA_01120
+MKSWSTPAPPAVPSRPDRLRLHDTATGRTRHPGNDAQRASLYVCGITPYDATHLGHASTY
+VAFDLLHRYWRAAGLEVAYVQNVTDVDDPLLERAEATGVDWRALAEEQTDLFRADMAALE
+VLAPDHYVGATEAVGLVVDAVETMLAAGRAYRVPGGDGEPDGDVYFDVRAAQSATDWRLG
+QVSAMGLDEMAAVFPERGGDPDRPGKRDPLDPLLWRVHREGEPAWDGRSLGSGRPGWHIE
+CSVISRAHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGLPLAHTYAHTGMVALDGEKMS
+KSLGNLELVSRLRARGVEPVAVRAAILAHHYRSDWEWSEQVLADAQARVARWRAALDGPH
+AAAGVAVLDAVHAALSDDLDAPRALEALDAWAAGTLPGLAEAAADPLPVVDVVAALLGLR
+LR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000974.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000974.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb3b491f1a932f9b4cadd1f80eedf093714d7ccc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000974.fa
@@ -0,0 +1,35 @@
+>PROKKA_01171
+MTDATSEDQPDDALGPLRTHLTATVDALEAGRRAPTVLLLAFEGWNDAGEAATGALGALR
+EQWDAADAGRVCDGEFYDYQVTRPLVRRDADGLGTLDWPAVTLHEAFLDREGRPVAGEAA
+PPDGVRVLLAVGVEPNVRWRAFLEELFTAADAHDVDAVVTLGALLADVPHTRPLRARPTS
+PLVDVRVAVGADRPVYEGPTGIIGVIADEAARRGLPSLSLWGTVPHYVAQAPSPKTLLGL
+VEAVEDLLHVSVSTRGLEDDARAWQRGVDELAAEDPDVAAYVRQLEEAQDTQQLPEASGE
+SIAREFERYLRGRGGR
+>PROKKA_00890
+MTDATSEDQPDDVLGPLRTHLTATVDALEAGRRAPTVLLLAFEGWNDAGEAATGALGALR
+EQWDAADAGRVCDGEFYDYQVTRPLVRRDADGLGTLDWPAVTLHEALLDREGRPVAGEAA
+PPDGVRVLLAVGVEPNVRWRAFLEELFTAADARDVDAVVTLGALLADVPHTRPLRARPTS
+PLVDVRVAVGADRPVYEGPTGIIGVIADEAARRGLPSLSLWGTVPHYVAQAPSPKTLLGL
+VEAVEDLLHVSVSTRGLEDDARAWQRGVDELAAEDPDVAAYVRQLEEAQDTQQLPEASGE
+SIAREFERYLRGRGGR
+>PROKKA_01718
+MTDASSADQPDDALGPLRTHLTATVDDLEAGLRAPTVLLLAFEGWNDAGDAASGALDALR
+EQWDAAEAGRICDGEFYDYQVTRPVVRRDADGLGTLEWPAVRLHEAQLDAQGRPVAGEAA
+PPDGVRVLLAVGVEPNVRWQAFAEELFAAAAARQVDAVVTLGALLADVPHSRPLRARPTS
+PLVDVRVAVGADRPAYEGPTGIVGVIADEAARRGLPSVSLWGAVPHYVAQAPSPKTLLGL
+VEAIEDLLHVSVSTCELEDDAQAWQRGVDELAAEDPDVAAYVRQLEEAQDTQQLPEASGE
+AIAREFERYLRGRGGR
+>PROKKA_01616
+MDEQTDPGSLDGAPSPEDRLGALRAHLTATVPEVEDGSRPPAVLLLAFEGWNDAGEAATG
+ALAELSAQWEAAPAGVVCDGEYYDYQVTRPVVHRDADGLGTLEWPALRVHEARLDAHGAP
+VPDGEAVPADGLRVLLASGVEPNVRWRAYVEELLRWAEAEGVDAVLTLGALLADVPHSRP
+LRARPTSPLVAVRVAVDAGLPAYEGPTGIVGVVTDEAARRGTASLSLWGAVPHYVAQAPS
+PKTLLGLVEAVEDLLHVELLTHALRDDAQAWQRGVDELAREDPEVASYVRRLEESQDAQE
+LPEASGEAIAREFERYLRGRGRD
+>PROKKA_01121
+MTDATSEDQPDDVLGPLRTHLTATVDALEAGRRAPTVLLLAFEGWNDAGEAATGALGALR
+EQWDAADAGRVCDGEFYDYQVTRPLVRRDADGLGTLDWPAVTLHEALLDREGRPVAGEAA
+PPDGVRVLLAVGVEPNVRWRAFLEELFTAADARDVDAVVTLGALLADVPHTRPLRARPTS
+PLVDVRVAVGADRPVYEGPTGIIGVIADEAARRGLPSLSLWGTVPHYVAQAPSPKTLLGL
+VEAVEDLLHVSVSTRGLEDDARAWQRGVDELAAEDPDVAAYVRQLEEAQDTQQLPEASGE
+SIAREFERYLRGRGGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000985.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000985.fa
new file mode 100644
index 0000000000000000000000000000000000000000..719ac4342b6791690c165edf435863672962d281
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000985.fa
@@ -0,0 +1,65 @@
+>PROKKA_01183
+MTPPAPRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLTDTAFEKLFQRDRR
+VLRAVGVPLETLEPAGLDEGEAGVRHRVVRDALLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFQPATDLTGDDELAGYHTLMPRADPRLEALTQAVADEAVLRFPYRDARG
+RATRRTVRAWYLTLVRGRWYLTGWDLDRGAERSFRLTRMEGEPRRVERATDAPGRPEDHD
+HAGLVARLAGQADAERVRVWLAPGRGQGVRAVGEPAEPRVEDGAAPGPDWELWEAPAGPR
+EDGLAAEIGGLLGRAVPSAAHPDLTDRVRAGLAAAAEAHAGPADPALLEVPLAAPVRRRA
+RDSSEDLVGRLLDIVGLANRAGGVDRAELRARLGITDERLDADLETLRYCGMPERDFPGF
+QFEVAEVGGRVHVERAADLAGPVRLTRPEAHSLVAALQTVADLPVLDEADREAARSAQRR
+IRAAVLDAGAPDADDADDAALREAEAHTAGEPPVAVAAHWDVAVDPATVRTLLAAVAERA
+VVHLTYRSVHADALTERDVEPLALVQDGARLYLQAWCRRAEDHRVFRVDRISAPAPTGET
+FAPRARPARWRVHPDDTAGVPVLLRWAHPVRDAAAGYRPDAQADLPDGDRLTRVHLTDAA
+VAAALVGRHGGAVEVLAPADLRTSVADALGDALAALPAR
+>PROKKA_00902
+MTPPAPRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLTDAAFEKLFQRDRR
+VLRAVGVPLETLEPAGFDEGEAGVRHRVVRDALLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFQPATDLTGDDELAGYHTLMPRADPRLEALTQAVADEAVLRFPYRDARG
+RATRRTVRAWFLTLVRGRWYLTGWDLDRAAERSFRLTRMEGEPRRLERATDAPGRPEDHD
+HADLVARLAGQADAERVRVWLAPGRGQGVRAVGEPAEPRVEDGAAPGPDWELWEAPAGPR
+EDGLAAEIGGLLGCAVPSAAHPDLTDRVRAGLAAAAESHAGPADPALLEVALAAPVRRRA
+RDSSEDLVGRLLDIVGLANRAGGVDRAELRARLGITDERLDADLETLRYCGMPERDFPGF
+QFEVAEVGGRVHVERAADLAGPVRLTRPEAHSLVAALQTVADLPVLDEADREAARSAQRR
+IRAAVLDAGAPDADDADDAALREAEAHTAGEPPVAVAAHWDVAVDPATVRTLLAAVAERA
+VVHLTYRSVHADALTERDVEPLALVQDGARLYLQAWCRRAEDHRVFRVDRISAPAPTGET
+FAARARPARWRVHPDDAAGVPVLLRWAHPVRDAAAGYRPDAQADLPDGDRLTRVHLTDAG
+VAAALVGRHGGAVQVLAPADLRASVADALGDALVALPAR
+>PROKKA_01705
+MAPPASRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLSDAAFEKLFQRDRR
+VLRAVGVPLETLEADSFEEEAQGVRHRVVRDAMLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFAPTPDLAADDELAGYHALTPRADPRLEALTQAVAEEAVLRFPYRDARG
+RESRRTVRAWFLTLVRGRWYLTGWDADREAERSFRLTRMEGEPRRVERAASLPGRPADHD
+HADLVARLAGQADAERVRVWLAPGRGQGVRAVGARVDPRAEDGAAPGDGWELWEAPAGTH
+EDGLAAEVGGLLGRAVPSAAEPDLARRVADALAAAARAHAGPAAPALLEAPLAPPVRRRA
+RDSSEDLVGRLLDIVGLANRADGVDRAELRARLGVTEERLDADLETLRYCGMPERDFPGF
+QFEVDEEGGRVHVRRAADLAGPVRLTRPEGHSLVAALQTVADLPVLDDADRAAARSAQRR
+IAEAVLDAGGAAASAADDEALAEAEAGTAPTPAPGGAVAAHWDVAVDPETVRTLLAAIAE
+RRVLRLDYRSVHADALSERDVEPLAVVQDGARLYLRAWCRSAGEDRVFRVDRIGAATATG
+EAFAPRARPARWRVHPDEAAGTPAVLRWAHRVRDAASGYRPEAQADLPDGDRLTRVRLTD
+ADVAAALVGRHGGAVEVLYPAAMRAHVKDALDRAVDALAAR
+>PROKKA_01604
+MSAHGSTAEPAERIISLLWLLLHEPLGYTREQIRRLVVGYEGLTDGAFEKLFQRDRRALR
+AVGVPLETVGDPDDEAGPRLRVDRDALLLQDVDFTVDERRALVRARRLWGDSPLRDDVVR
+AVGVLFHPGEVGGDDALEGFRTVMPRTDPRVAALSEAAAEQSVVRFSYRDAAGALTERTV
+RAWLLTLVRGRWYLTGWDADRAAERSFRLTRMESDPVVLDAGAASPAGEAPTLPAGHDHA
+ALRARLAGRAEAETVRVWLAPGRGQGFRVAGRPVPATAADGPAPGPDWELWECPSGPSED
+GAVAEAAVAVGQVLFSTVEAAAGRALAADLAAAAAVHAGDPDPAWRDVPLTAPTRRRSRA
+SSEDLVGRLLDIVGLANRAEGIGRDELQERLGVTARELDADLEVLRYCGMPEREFPGFQF
+DVEDEGGRVRVHQSSELAGPVRLTLPEAHALVAALQTVAEMTVLTPEDREAARSAQRRIR
+ASLADAGQSHAGSADAEAPRDGTGKEPGAVVAHWDVVADPDTVRTLLDAVAERAVVHLRY
+HGVRSDAVTERDVEPLAVVQDRTRLYLQAWCRRAGGPRVFRVDRIGALHRTGETFRARRV
+PAWDPRPAGDGVEAVVRWAHEVRDAADAYAPAAAATLDSGDRLTRVLLADDDAAVGLAAR
+HGGRVEILAPAALRGAVRGRLEAAARRAAGAVA
+>PROKKA_01133
+MTPPAPRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLTDAAFEKLFQRDRR
+VLRAVGVPLETLEPAGFDEGEAGVRHRVVRDALLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFQPATDLTGDDELAGYHTLMPRADPRLEALTQAVADEAVLRFPYRDARG
+RATRRTVRAWFLTLVRGRWYLTGWDLDRGAERSFRLTRMEGEPRRVERATDAPGRPEDHD
+HAGLVARLAGQADAERVRVWLAPGRGQGVRAVGEPAEPRVEDGAAPGPDWELWEAPAGPR
+EDGLAAEIGGLLGRAVPSAAHPDLTDRVRAGLAAAAETHAGPADPALLEVALAAPVRRRA
+RDSSEDLVGRLLDIVGLANRAGGVDRAELRARLGVTDERLDADLETLRYCGMPERDFPGF
+QFEVAEVAGRVHVERAADLAGPVRLTRPEAHSLVAALQTVADLPVLDEADREAARSAQRR
+IRAAVLDAGAPDADDADDAALREAEAHTAGEPPVAVAAHWDVAVDPATVRTLLAAVAERA
+VVHLTYRSVHADALTERDVEPLALVQDGARLYLQAWCRRAEDHRVFRVDRISAPAPTGET
+FAPRARPARWRVHPDDAAGVPVLLRWAHPVRDAAAGYRPDAQADLPDGDRLTRVHLTDAA
+VAAALVGRHGGAVEVLAPADLRTSVADALGDALAALPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000986.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000986.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4a1316ae1ea50a56c517ecbe335dd804b7a93af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000986.fa
@@ -0,0 +1,15 @@
+>PROKKA_01184
+MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEGKGTTDERSGA
+GSTAADEPVEGRVVERDETDPRDPR
+>PROKKA_00903
+MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEGKGTTDERSGA
+GSTAADEPVEGRVVERDETDPRDPR
+>PROKKA_01704
+MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEDKGAKDGKDAR
+SGSGSTAADEPVEGRVVERDETDVRPRDER
+>PROKKA_01603
+MRFTPTHLIVLIIVVLLLFAAPKLPALARNLGQSMRIFSSEVKQMKEENTTKKAEGAATA
+DAPSQGAGSTAAEPVEGRVVDRDVRDDR
+>PROKKA_01134
+MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEGKGTTDERSGA
+GSTAADEPVEGRVVERDETDPRDPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000987.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000987.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c21f9e512581fbd92827edb3ccba15b56bb5eaa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000987.fa
@@ -0,0 +1,30 @@
+>PROKKA_01185
+MTEVDEVARRTRRRRKRRDNPTGEMPLREHLTELRNRLLKSALAVAVGMVIGFLVYQPVM
+AELFRPVKEIASQGHTAAVAYDTVASPFDLMLKVSMFIGLILSSPVWLYQIWAFIVPGLK
+KAEKKYALGFIAAAVPLFIFGIALGWLVMPQAVQFFVGFTPEGGANLPTASVYISFVTRL
+YLAFGVAMVLPVLLVGLNMLGILPGRTIVHHWRITVFVIMLIAAIAAPGADAISMFYMAI
+PLVVLFGVAIVLCLWGDRRRDRRSGQREVDVEAELAEGPKPLDQI
+>PROKKA_00904
+MTEVDEVARRTRRRRKRRDNPTGEMPLREHLTELRNRLLKSGLAVAVGMVVGFLVYQPVM
+AELFRPVKEIASQGHTAAVAYDTVASPFDLMLKVSMFIGLILSSPVWLYQIWAFIVPGLK
+KAEKKYALGFIAAAVPLFIFGIALGWLVMPQAVQFFVGFTPEGGANLPTASVYISFVTRL
+YLAFGVAMVLPVLLVGLNMLGILPGRTIVHHWRITVFVIMLIAAIAAPGADAISMFYMAI
+PLVVLFGVAIVLCLWGDRRRDRRQGQREMDVEAELAAGPKPLDQI
+>PROKKA_01703
+MSEVEEVARRTRRRRRRDNPTGEMPLREHLTELRNRVIKAGVAVLLGMVVGFLIYQPVMA
+ELFRPVNELSRDGRISAIAYDTVASPFDLMLKVSLFIGLIVSSPVWLYQIWAFIVPGLKK
+AEKKYALGFIAAAVPLFLLGMGLGWLVMPQAVQFFVGFTPEGGATLPTASVYISFVTRLY
+LAFGVAMVLPVLLVGLNMLGVLPGRTIVKHWRITVFLIMLIAAIAAPGADAISMVYMAVP
+LVLLFGVAIALCLWGDRRRARRAVRREQDVEAELASGPKPLHEI
+>PROKKA_01602
+MTSVDEEAAGARGRRKGRKPKNPNGEMPLREHLKELRDRLIKSVLAVVLGAVAGFALYKP
+VMEVLTRPMVEARERGVNAALAFDTVSSPFDMMLKVALFIGIVVSSPVWLYQAWAFVVPG
+LTKSEKKYAVGFLGTAIPLFLAGLYLAWLVHPQAVQFFIGFTFDGTAALPTASNFLTFSI
+TLFLVFGVSMVLPVFLVGLNLLGVLPATTILKHWRIVVFLVALIAAMAAPGSDVISMFYL
+AGPLLLLFGISILVCWLNDRRRARRSRDTAEDLEAEIAAGPRSLDEL
+>PROKKA_01135
+MTEVDEVARRTRRRRKRRDNPTGEMPLREHLTELRNRLLKSALAVAVGMVIGFLVYQPVM
+AELFRPVKEIASQGHTAAVAYDTVASPFDLMLKVSMFIGLILSSPVWLYQIWAFIVPGLK
+KAEKKYALGFIAAAVPLFIFGIALGWLVMPQAVQFFVGFTPEGGANLPTASVYISFVTRL
+YLAFGVAMVLPVLLVGLNMLGILPGRTIVHHWRITVFVIMLIAAIAAPGADAISMFYMAI
+PLVVLFGVAIVLCLWGDRRRDRRSGQREVDVEAELAEGPKPLDQI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000989.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000989.fa
new file mode 100644
index 0000000000000000000000000000000000000000..553abdc7e4c575b831d45ee2362499e4fb686e2d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000989.fa
@@ -0,0 +1,39 @@
+>PROKKA_01187
+MSAHLLTRGIIHSTTDPYAQALLVRDGMIAWLGADDSADRVADPGDERRDLDGAVVVPVF
+VEPLARPADARDALSRGTAVVTVLAGPEDTGAAPADEDVQTVVYRHADRVDAEAAGVWLP
+VGTDTDPATLTGLLTASTQAGEQAYLVPDGGADAGPAAQDVALTALRSVAEELGTAALGR
+VRHRLVVTHPVTAEDRAFLAAAGVSATVVPDADGVLHAPVASLLADAVTVCLGAGPAGDP
+WAAVRSALSHPDPDERISARSAFAAATRTPLRALPDAPAARLSVAPRLSVSAPAVFGVWD
+ADAVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRIAAEDVARDAHDA
+ATPA
+>PROKKA_00906
+MSAHLLTRGIIHSTTDPYAQALLVRDGMIAWLGADDSADRVADPGDERRDLDGAVVVPVF
+VEPLARPADARDALSRGTAVVTVLAGPEDTGAVPADEDVQTVVYRHADRVDAEAAGVWLP
+VGTDTDPATLTGLLTASTQAGEQAYLVPDGGADAGPAAQDVALTALRSVAEELGTAALGR
+VRHRLVVTHSVTAEDRAFLAAAGVSATVVPDADGVLHAPVASLLADAVSVCLGAGPAGDP
+WAAVRSALSHPDPDERISARSAFAAATRTPLRALPDAPAAGLSVAPRLSVSAPAVFGVWD
+ADAVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRIAAEDVARDAHDA
+ATPA
+>PROKKA_01701
+MGRVTAHLLTTGIIHSVTDPYAQALLVRDGVIAWLGADDSAERVADPADARTDLDGAVVV
+PAFVEPLARPEDARDALSRGTAVVTVLAGPAGDVAPAEGVQAVVYRHAEGPAEGAVGVWL
+PVAADADAADLAAALAEATRAGEQAYLVPAADAAGHGDAEAPAAAQAAAIAALRRVAEEL
+GAPALGRVRHRLVVTSPVTAEDRAFLASVAVSATVVPAADGTLRAPVASLLADAVPVALG
+AGPGRDPWAAVRAALSHPEEAERISARSAFAAATRTPLRALPDAADADLVAAPRLAVSAP
+GVFGVWEAEAVAVQSPDGRVAAWSTDTRAGTPLLPALDDQTPLPRWRATWVGGRIAAEAA
+DGDARGTGDHA
+>PROKKA_01600
+MSSTLFLNGIVHSASDPYATAALVSDGVVAWLGDDSSADRVADPDVPRVDLAGAVLAPAF
+VEPGGPSVDPAQALRHGVAIVTVLAEPGQTAQALQAAADPALQTVVYRAADTVDAEAAGV
+WLPAEGEALAALVVASTRAGEQVHLVPPAGGDPSEGQAAALAALRSAAEELGAPALGRVR
+HRVVLTAPITAEDRALLAAISASVTVGPEADGLLRAPLGTLLAEGVPVCLSTAGEAGPWA
+AVRAALSHPDEAERISARSAFTAATRTPLRVLPDAPGATVQAAPRLTVSAPATFAVWEAD
+AVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRPAAVEVADA
+>PROKKA_01137
+MSAHLLTRGIIHSTTDPYAQALLVRDGMIAWLGADDSADRVADPGDERRDLDGAVVVPVF
+VEPLARPADARDALSRGTAVVTVLAGPEDTGAAPADEDVQTVVYRHADRVDAEAAGVWLP
+VGTDTDPATLTGLLTASTQAGEQAYLVPDGGADAGPAAQDVALTALRSVAEELGTAALGR
+VRHRLVVTHPVTAEDRAFLAAAGVSATVVPDADGVLHAPVASLLADAVTVCLGAGPAGDP
+WAAVRSALSHPDPDERISARSAFAAATRTPLRALPDAPAARLSVAPRLSVSAPAVFGVWD
+ADAVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRIAAEDVARDAHDA
+ATPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000991.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000991.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a77f24ae0fbb4ee74ace2744b0f2c9f734affb2b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000991.fa
@@ -0,0 +1,15 @@
+>PROKKA_01189
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEEVDA
+>PROKKA_00908
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEDVDA
+>PROKKA_01699
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAEAEGKPVRTHWDMLRERRSLEELQETYALQLNKLRASRGEDVDA
+>PROKKA_01598
+MSDRSLRGMRLGAQSLESEAGVEPAPRQRVEYRTEDGEQVFVTFAQEAEVPTTWTSKTGK
+EALRVDGEKPEENPGKPVRTHWDMLLERRSMEELEETFQIQLKKLHASRGEAV
+>PROKKA_01139
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEEVDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000992.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000992.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7613939ad79823ed66df4fea9ae4967fa67e78f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000992.fa
@@ -0,0 +1,40 @@
+>PROKKA_01190
+METLIVLVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTLIIPFVDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDSINSQLRGVLDDATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQSLPKIADGQANTMFVVPAELTRALQGLGEAFAPGDGDRPTPEHAPR
+RRDSGDRAGEPGAEHSGVTPERARRPRGSRPTTADALRASGVMDAMTAGAVTAEDMPQTS
+LDEALATPQEIEPDPSAGRTPGTRPAGEADGNAVGH
+>PROKKA_00909
+METLIVLVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTLIIPFVDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDSINSQLRGVLDDATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQSLPKIADGQATTMFVVPAELTRALQGLGEAFAPGDGDRPTPERAPR
+RRDSGDRAGEPGAEHVGVTPERARRPRGSRPTTADALRASGVMDAMTAGAVTAEDMPQTS
+LDEALATPQEIEPDPSAGRTPGTRPAGEADGNAVGH
+>PROKKA_01698
+METIIILVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTMIIPFVDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDSINSQLRGVLDEATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQALPKIADGESNTMFVVPAELTRALQGLGEAFSPAGDGESRRPSPSG
+ARGEAAERAGEHGGASPERPRRPRGSRPTTADALRSSGVMDAMTAGAVTAQEMPQTSLDE
+ALATPKELDPDPSAGRAPGRRPAGETDGNGVGH
+>PROKKA_01597
+MEFLIVLAVLAVLVGVLLASSVKIIPQARTANVERLGKYQRTAGAGLTLIIPFIDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDAINSQLRGVLDDATSRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSAILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQSLPKIAEGTSNTMFVVPAELTRALQGLGEAFSPGSPSAAGTGSSDT
+SDDAAPAAGRAATGPGGRRRGRASEGARPTTAEELRSSGLLDAMTAGALTADRMPQTSLD
+EALQTPPEAEPAPVRREPGMP
+>PROKKA_01140
+METLIVLVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTLIIPFVDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDSINSQLRGVLDDATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQSLPKIADGQANTMFVVPAELTRALQGLGEAFAPGDGDRPTPEHAPR
+RRDSGDRAGEPGAEHSGVTPERARRPRGSRPTTADALRASGVMDAMTAGAVTAEDMPQTS
+LDEALATPQEIEPDPSAGRTPGTRPAGEADGNAVGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000996.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000996.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0eb5403d7513163eecd8015be967836045b9871
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000996.fa
@@ -0,0 +1,24 @@
+>PROKKA_01194
+MVSVHLVPIRPTAATADDAQRLSAALLDDPRPGAAVISAAWHIDETDAAPGDGELAVTLD
+GMAAGVGLALWAVRSGSWAVLLDTEGNYDKQSALSHITAGERRRARRAPGRLVLPHGRRP
+GRASETGREADLRCAEATLQLVATVERRRSDDQHAAGRLVEAGASQREAAAELGISQQAV
+HSRLRHGLWHESRTAVAAVLPLLERLSADPGE
+>PROKKA_00914
+MVFVHLVPIRPTAATADDARRLAAVLLDDPHPDASVAAAVWRGDEGNPDADAAPGDGELA
+VVVESMAAAVGLALWAVRTGSWAVLLDPEDALDKDSLLSYLTPAERRRARRAPGRLVLPH
+GRRPGRASETGREADLRCAEATLQLVATVERRRSDDQHAAGRLVEAGASQREAAAELGIS
+QQAVHSRLRHGLWHESRTAVAAVLPLLERLSADPGE
+>PROKKA_01693
+MIVLHLLPLTAPDAADAAWTRVGDELNRPGAVSSLVMPFDRQGEGSEARLVGGMDSGVEA
+VGILLSLVRSGAWAVVVEVAEGRAAGESLLQREAERARRANGHCAVLGPSGPSAAWIEPA
+LQLLGALERRRSEPQQDAGRRVEAGASQREVAAELQVSQQAVHARLRGGLWNETRALAGA
+TADALDVLARRGDRVSDGGASPSTSERG
+>PROKKA_01591
+MVPVAVRCGSAGAAGRWAASIPGARRLGREGGRDLIVHADDAAAAVALMLAVRRAGAGAV
+GAGVAIEQVEGALRRARRRPGGIAVSRVPGSTGTEEERGLLEAGLGVLLTLESRRSAPQQ
+AAGVLIEAGRSQREAAADLGVSQQAVQQRLRAGLWEETRTLLDALLPMARRVLEA
+>PROKKA_01148
+MVSVHLVLIRPTTATAEDARRLATALRDDPRPDAAVTAAMWLGDESDPVDDDAAPHDGEL
+AVVLDDAAAAVGLALWAVRTGSWAVMLDPEGGSDKDSALSYLTPAELRRARRAPGRLVLP
+AGGRPGRASESGREADLRCAEATLQLVAAVERRRSADQHAAGRLVEAGASQREAAAELGI
+SQQAVHSRLRHGLWHVSRTAVAAVLPLLERLSTDPGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000997.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000997.fa
new file mode 100644
index 0000000000000000000000000000000000000000..78c784ffd3faeec8fc94d6425b1c95f5b2818237
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000997.fa
@@ -0,0 +1,20 @@
+>PROKKA_01195
+MTSSPTARRAAPAEHRDPRGALPALAVDLLLTLLFVALGQGQHSTERGPLGLLVTAAPFL
+AGLLLMTGVTAGHRTWARAWPHGVIVWLGTVAVGMLLRVAFGLGGAPVSFVLVALGVLGV
+LLLGRRAVTAWLVRRTRR
+>PROKKA_00915
+MTSSPTARRAVPAEHRDPRGAQPALAVDLLLTLLFVALGQGQHATERGPLGLLVTAAPFL
+AGLLVMTGLTAGHRTWARVWPHGVIVWLGTVAVGMVLRVAFGLGGAPVSFVLVALGVLGV
+LLLGRRAVTAWLVRRTRR
+>PROKKA_01692
+MADTLSENRSETMAQTGGMTDSPTRRHSPASPPSPLWAATALAVDAVLVVVFVALGQDQH
+TTDRGLGGLLATALPFLLGLVAATVLTAGHRTWHRVWPHGVAVWLGTVAVGMALRVLWDQ
+GGAPLSFVLVALGVLGVFLLGRRAVTAWVIRRRARV
+>PROKKA_01590
+MSTTPLPQDSSPAAHPSDRRRGSAPWVAFALDAALVVLFVALGQREHATDRGGLALVTAA
+APFLLAWVAGTALAGGPRTWARVWPQGVVVWAVTVAAGMGLRVLWGLGGAPVPFVLVASA
+VLAVFLLGRRWASTLLAHRATDRASRAS
+>PROKKA_01149
+MTSSPTARRVVPAEHRAPRGALPALAVDLLLTVLFVALGQGQHSTERGPVGLLVTAAPFL
+AGLLLMTGLTSGHRTWARVWPHGVIVWLGTVAVGMVLRVAFGLGGAPVSFVLVALGVLGV
+LLLGRRAVTAWLVRRTRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000999.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000999.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9abc478844fe065896676ebb5aa35321104c2026
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000999.fa
@@ -0,0 +1,35 @@
+>PROKKA_01197
+MSTPENTAAVLGTSWPEVFRALTVGEDLSDDVAAWAMGEMMAGDATEGQVGGFLLALAAK
+GVTVPELRGLTEAMVQAANPVHVPGETLDVVGTGGDRLGTVNLSTMSSLVAAGAGARIVK
+HGNRGASSTAGAADVIEALGVDLSMPTRKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ
+LGVPTVFNFLGPLSNPAQVTAQALGCSSQAMVPLLAQVLADRGVRGFVFRGADGRDKITT
+SGPSTVMEVRDGVRTHELDPRELGIDLAPVQALAGRDGAYNATLVRALLAGEKGPIRDAV
+LLNAAAGLTAWDRGADAPLMERLAANMARAAESIDSGAARDVLDRWVAFSRS
+>PROKKA_00917
+MSTPENTAAVLGTSWPEVFRALTVGEDLSDDVAAWAMGEMMAGDATEGQVGGFLLALAAK
+GVTVPELRGLTEAMVQAANPVHVPGETLDVVGTGGDRLGTVNLSTMSSLVAAGAGARIVK
+HGNRGASSTAGAADVIEALGVDLSMPTRKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ
+LGVPTVFNFLGPLSNPAQVTAQALGCSSEAMVPLLAQVLADRGVRGFVFRGADGRDKITT
+SGPSTVMEVRDGVRTHELDPRELGIDLAPVQALAGRDGAYNATLVRALLAGEKGPIRDAV
+LLNAAAGLTAWDRDADAPLMERLAANMARAAESIDSGAARDVLDRWVAFSRS
+>PROKKA_01690
+MSIPNTTAAAPETTWPDVFRALTFGEDLSDEAAAWAMGEMMAGDATEGQVGGFLLALAAK
+GVTVPELRGLTEAMVQAARPVQVTGETLDIVGTGGDRLGTVNLSTMSSLVAAGAGARIVK
+HGNRGASSTAGAADVIEALGVDLSMPREKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ
+LGVPTVFNFLGPLSNPAQVSAQALGCSSEVMVPLLARVLADRGVRGFVFRGSDGRDKITT
+SGPSTVIEVRHEVTAHELDPRDFGIELAPVEALAGRDGAYNATLVHALLAGEKGPIRDAV
+LLNAATGLTAWDTEAQGPLADRLAANMARAAESLDSGAARDVLDRWVAFSRS
+>PROKKA_01587
+MRETVTHTWPEVFRRLTLGQDLDDAAAEWAMGEMMSGDATEGQVGAFLLALAAKGETVPE
+LRGLTDAMVAKARRVHVSGETLDIVGTGGDRLGTVNLSTMSSLVAAGAGARIVKHGNRGA
+SSTAGAADVIEALGVDLSMPPAKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQLGVPTV
+FNFLGPLSNPAQASAQALGCSSEEMVPLLAQVLADRGVRGFVFRGSDGRDKITTSGPSTI
+MEVRGGVTAHEIDPRDFGIELAPVEALAGRDGAYNATLVRGLLAGEHGPIRDAVLLNAAA
+GLTAWDVEAEGPLMDRLRTNMARAAESIDSGAAADVLERWVQFSRS
+>PROKKA_01151
+MSTPENTAAVLGTSWPEVFRALTVGEDLSDDVAAWAMGEMMAGDATEGQVGGFLLALAAK
+GVTVPELRGLTEAMVQAANPVHVPGETLDVVGTGGDRLGTVNLSTMSSLVAAGAGARIVK
+HGNRGASSTAGAADVIEALGVDLSMPTRKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ
+LGVPTVFNFLGPLSNPAQVTAQALGCSSEAMVPLLAQVLADRGVRGFVFRGADGRDKITT
+SGPSTVMEVRDGVRTHELDPRELGIDLAPVQALAGRDGAYNATLVRALLAGEKGPIRDAV
+LLNAAAGLTAWDRDADAPLMERLAANMARAAESIDSGAARDVLDRWVAFSRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001000.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001000.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e52dec54995e8fc29556e13eed79330a92f6527
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001000.fa
@@ -0,0 +1,25 @@
+>PROKKA_01198
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTTILVLSSVT
+AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTVA
+ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK
+>PROKKA_00918
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTTILVLSSVT
+AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTVA
+ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK
+>PROKKA_01689
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAENTAILNVPLAAANTLILVLSSVT
+AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTIA
+ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK
+>PROKKA_01586
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTVILVLSSFT
+AQFGVLAAERLQPRRTGGLFSVKSWGMVEWFILTFIMGSIFVAVQAFEYATLVSEGVTIA
+ANAYGSAFYITTGFHALHVTGGLIAFLFIIGRAFLARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK
+>PROKKA_01152
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTTILVLSSVT
+AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTVA
+ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001002.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001002.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a491818106b0b0dde08cab9d99e6998d90296b3a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001002.fa
@@ -0,0 +1,35 @@
+>PROKKA_01200
+MGEKGLEGTERRSGSLEHAGEDAPRYAIDDPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL
+DDSDNFSDQEAHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVRITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGFLVAQSDFHEPVGPVYWERG
+>PROKKA_00920
+MGEKGFEGTEHRSGSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL
+DDSDNFSDQEAHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG
+>PROKKA_01687
+MGEKGFEGTEHGSGSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTLLFFVGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEADRVAATGMISEILDESQIKRRPLLRNTLIGAAVLAPLPFIAVFRDL
+DDSDNFSDEETHNFGPERLRHTMWSEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGFLVAQSDFHEPVGPVYWERG
+>PROKKA_01584
+MGEKGYEGAERHSDALEHAGEESPRYAIDNPGLPPHRPRLADEDPRAAKRAERQVSVFFL
+ISVIGTVLFFIGYFGVGQVGNGESTSVLYLQNLLLGLGVALAMFGIGIGVVHWAKTLMPD
+HEVVEERHEIRTEADRAAAQGMIADILDESQIKRRPLLRNTLIGAAVLAPLPFIAAFRDL
+DNTDNFSDEAAKNFGPERLRHTMWHEGVRLVRDPTGSPIKASDVTLGSALHVIPDGLNDL
+EHGKLNEKAKAVVLVMRLDPSKVKISPGRENWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLAQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG
+>PROKKA_01154
+MGEKGFEGTEHRSDSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL
+DDSDNFSDEEIHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001004.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001004.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e1c772e6bd374bd07f6cb0f25b9995dba6fbe5e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001004.fa
@@ -0,0 +1,20 @@
+>PROKKA_01203
+MKVAANIFWVIGLFFVGAGTLYGFWNEWTEWAGIPAIYALGGMSWMIAWYLNAAERKYGV
+GPADDEDGQIVEYAGTYGTFAPWSWWPLGLGLACAIIVTGLAVGWWVFVIGIIAGAYFTF
+GWVYEFSRGKFAH
+>PROKKA_00922
+MKVAANIFWIIGLFFIAAATLYGFWVEWTEWAGIPAIYAVGGMSWMIAWYLNVTERKYGV
+GPADDADGQIADYAGTYGTFAPWSWWPLGLGLACAIIVTGLAVGWWIFIIGVIAGAYFTF
+GWVYEFSRGKYAH
+>PROKKA_01684
+MKVAANIFWIIGLFFIAAATLYGFWVEWTEWAGIPAIYAVGGMSWMIAWYLQSTEKKFGL
+GPADDEDGEITDYAGTYGTFAPWSWWPLGLGVACAILITGLAVGWWVFIIGAVAAAYFTF
+GWVYEFSRGKYAH
+>PROKKA_01582
+MKIASNIFWIIGAFLVAVATLYGFWVKWTEWAGIPAIYALGAMCWMIAWYVQSTDKRHGL
+GPADDEDGEIVEYAGTYGTFAPSSWWPLGVAVACAMLVTGLAVGWWIFALGVIAGVYFTF
+GWVYEFSRGKYAH
+>PROKKA_01160
+MKVAANIFWVIGLFFVGAGTLYGFWNEWTEWAGIPALYALAGMSWMIAWYLNAAERKYGV
+GPADDEDGQIVDYAGTYGTFAPWSWWPLGLGLACAIIVTGLAVGWWVFIIGVIAGAYFTF
+GWVYEFSRGKFAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001006.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001006.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e98f1c7669ebed7b845823080dbb47b963d3b3f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001006.fa
@@ -0,0 +1,31 @@
+>PROKKA_01205
+MGTTALLVLTGCSAEVQRGWYPGTRDTTNHNAQLTDLWVNSWIAAMVVGLLVWGAMIWCM
+VAYRRRKNDQGFPKQTAYNVPLETMFTAIPILTVFTLWGFTDRVQTEVDRPVDDSPLTVT
+VYGKQWSWDFNYSYEQEDGEVIEAHYSGIQAQLDGTEGVRDTLPVLYLPNDVPVHFELKS
+RDVVHSFWIPQFLQKRDMVPGKTNHLYLTPQELGSYDGKCAELCGEFHSEMLFNVEVVDE
+AEFVQRLEEMESGQVGEEYSRNPNNNPDGAGTMERDLQTPRGGGSH
+>PROKKA_00924
+MGTTSLLVLTGCSAEVQRGWYPGTRDTTNHNAQLTDLWVNSWIAAMVVGLLAWGAMIWCM
+VAYRRRKNDQGFPKQTAYNVPLETMFTAIPILMVFTLWGFTNRVQTEVDRPVDDSPLTVT
+VYGKQWSWDFNYSYEQENGEVIEAHYSGIQAQLDGTEGVRDTLPVLYLPNDVPVHFELKS
+RDVAHSFWIPQFLQKRDMVPGKTNHLYLTPQELGSYDGKCAELCGESHSEMLFNVEVVDE
+AEFVQRLEEMEPGQVGDEYSRNPNNNPDGAGTMERDLQTPRGGGSH
+>PROKKA_01682
+MGTTALLVLTGCSAEVQRGWYPGTRDTTNHNAQLTDLWVNSWIAAMVVGLLAWGAMIWCM
+VAYRRRKNDQGFPKQTAYNVPLETMFTIIPILMVFTLWGFTNRVQTEVDRPVDDSPLTVT
+VYGKQWSWDFNYSYEQENGEVVEANYSGIQAQLDGTEGVRDTLPVLYLPKDVPVHFELKS
+RDVAHSFWIPQFLQKRDLIPGKTNHLYLTPQELGSYDGKCAELCGEFHSEMLFNVEVVDE
+AEFVDRLAEMEPGLVGDEYSRNPNNNPDGAREMERDLQTPRGGGSH
+>PROKKA_01580
+MRAQNDAGRRTRRRLTAGALGATALVALTGCSAEAQRGWLPGTDNTTNHNAQLTDLWVNS
+WIAALAVGLIAWGAMIWCMIAYRRRKNDQGFPRQTAYHMPIETMFTVIPILMVFTLWGFT
+DRVQAEVDTPIDDSPLTVTVYGKQWSWDFNYSYEKDGQTREAHFQGVQAQLDGSDGKRET
+LPTLYLPKDVPVHFELKSRDVAHSFWIPQFLQKRDMLPGKTNNLYLTPQEIGRFDGKCAE
+LCGEFHSEMLFNVEVVDEATFVQKMNEMEPGLVGDELNRNPNQNPDGARNMEVDLQTPRG
+GGNH
+>PROKKA_01162
+MGTTALLVLTGCSAEVQRGWYPGTRETTNHNAQLTDLWVNSWIAAMAVGLLAWGAMIWCM
+VAYRRRKNDQGFPKQTAYNVPLETMFTAIPILMVFTLWGFTDRVQTEVDRPVDDSPLTVT
+VYGKQWSWDFNYSYEQENGEVIEAHYSGIQAQLDGTEGVRDTLPVLYLPNDVPVHFELKS
+RDVAHSFWIPQFLQKRDMVPGKTNHLYLTPQELGSYDGKCAELCGEFHSEMLFNVEVVDE
+AEFVQRLEEMEPGQVGDEYSRNPNNNPDGAGTMERDLQTPRGGGSH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001012.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001012.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf6bab132bea1a9bcdcefe58948d4a5970f9a507
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001012.fa
@@ -0,0 +1,35 @@
+>PROKKA_01211
+MSADRAPQPPPPHPSGAVAPRIDPRFVPRHVAIVMDGNGRWANQRGLPRTEGHRAGEAAL
+LDVVAGAVELGIGHVSAYAFSTENWRRSAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWN
+GRAPRLWTPVIRELQEAEELTRHNTGTTLHMCVNYGSRAEILDGVQAIAEEVRAGRMRPG
+EISEDVITRYLDRGFRTGQDVDVVPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWP
+DVDRRTLWAAVETYARRDRRYGGAVDTPQPAPSSGAPDSASVADGGA
+>PROKKA_00930
+MSADRAPQSPPPHPSGAVAPRIDPRFVPRHVAIVMDGNGRWANQRGLPRTEGHRAGEAAL
+LDVVAGAVELGIGHVSAYAFSTENWRRSAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWN
+GRAPRLWTPVIRELQEAEELTRHNTGTTLHMCVNYGSRAEILDGVQAIAEEVRAGRMRPG
+EISEDVITRYLDRGFRTGQDIDVVPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWP
+DVDRRTLWAAVETYARRDRRYGGAVDTPQPAPSSGAPASDADGGA
+>PROKKA_01676
+MSGSGPSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIVEALTPEHGLVRAVAKGVRKT
+SSRLGSTVEPFMHTTLQLARGRGELLTVTQAQLLHPYATMLAADYDAYAVAGALAEAVER
+IPAVDEAGRRAQYRLLHGALAALARRRHDPRLILHSFLLRTLAQAGWAPTFDRCARCGAP
+GPHSAVHVALGGAVCPECRPPGAAHPAPQTLALLAALAAGDWATADSSDAAARREAAGIV
+AAYLQFHAERRLVSPVRPGPGPRPPRPARREETMRADRAPQSPPPHPSGAVAPRIDPRFV
+PRHVAIVMDGNGRWANQRGLPRTEGHRAGEAALLDVVAGAVELGVGHVSAYAFSTENWRR
+SAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWNGRAPRLWTPVIRELQEAEELTRHNTGT
+TLHMCVNYGSRAEIQDGVQALAEEVRAGRMRPADITEDVITRYLDRGFRAGQDVDVVPDV
+DLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWPDVDRRTLWEAVETYARRDRRYGGAVDT
+AQPAPSSGAPDSASDADGGA
+>PROKKA_01574
+MSDVPKVSPPPHPSGAVPPKLDPRFVPRHVAVVMDGNGRWANQRGLPRTEGHRAGEAALL
+DVVAGAVELGVGHVSAYAFSTENWSRSAEEVRFLMGFSKDVLRRQRDTLDSWNVRIRWNG
+RAPRLWTPVIRELREAEDLTRDNTGTTLHMCVNYGSRAEIVDGVQALAEEVAAGRMRPRD
+LTEDVITRWLDRGFRAGDRDVDVTPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDELWP
+DVDRRTLYAAVLEYAHRDRRFGGAVDAPAAD
+>PROKKA_01168
+MSADRAPQPPPPHPSGAVAPRIDPRFVPRHVAIVMDGNGRWANQRGLPRTEGHRAGEAAL
+LDVVAGAVELGIGHVSAYAFSTENWRRSAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWN
+GRAPRLWTPVIRELQEAEELTRHNTGTTLHMCVNYGSRAEILDGVQAIAEEVRAGRMRPG
+EISEDVITRYLDRGFRTGQDVDVVPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWP
+DVDRRTLWAAVETYARRDRRYGGAVDTPQPAPSSGAPDSASVADGGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001013.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001013.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45d6ffa19749670903835150768344e4d279a8f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001013.fa
@@ -0,0 +1,55 @@
+>PROKKA_01213
+MSAHLQKSSGMKFHKYVPFQDQIEVALPDRTWPDKVIEKAPLWCAVDLRDGNQALIDPMG
+PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI
+ERTFEALEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLRGTQI
+TYEYSPESYTGTELEFARRISDEVATVLEASTDRKMILNLPATVEMSTPNVYADSIEWMH
+RNLEHRDSLLLSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL
+YSQGIDPMIDFSDMDHIKRTVEYCNQLAVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME
+VDAKAAGTDVDGIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR
+RAQIEFSHVIQDLADAQGGEVSGADLWRVFQDEYLPADAAEAQWGRYRLRSVSSASGEDG
+AFRMEAELEVDGVTQTRTAQGNGPIDAFLRILGEEGVDVRVLDYSEHALSEGGAAMAAAY
+VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRALRA
+>PROKKA_00932
+MSAHLQKSSGMKFHKYVPFQDQIEVALPDRTWPDKVITEAPRWCAVDLRDGNQALIDPMG
+PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI
+ERTFEALEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLKGTQI
+TYEYSPESYTGTELEFARRISDEVATVLEASTDRKMILNLPATVEMSTPNVYADSIEWMH
+RNLEHRDSLILSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL
+YSQGIDPMIDFSDMDHIKRTVEYCNQLAVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME
+VDAKAAGTDVDGIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR
+RAQIEFSHVIQDLADAQGGEVSGADLWRVFQDEYLPADAAEAQWGRYRLRSVSSASGEDG
+AFRMEAELEVDGVTQTRTAQGNGPIDAFLRILGEEGVDVRVLDYSEHALSEGGAAMAAAY
+VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRALRA
+>PROKKA_01675
+MSAHLQKPSGMKFHKYVPYQDQIQVSLPDRTWPDKVIEKAPLWCAVDLRDGNQALIDPMG
+PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI
+ERTFESLEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLKGTQI
+TYEYSPESYTGTELEFARRISDEVAQVLEASTDRKMILNLPATVEMATPNVYADSIEWMH
+RNLEHRDSLILSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL
+FSQGVDPMIDFSDMDHIKRTVEYCNQLPVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME
+ADAKAAGKTVDEIDWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR
+RAQIEFSHVIQEMADAQGGEVSGADLWTAFQDEYLPAEAKDEQWGRYRLRSVTSASGEDG
+AFRMEAELEVDGVTQTRTAQGNGPIDAFLRMLGEDDMDVRVLDYTEHALSEGGAAMAAAY
+VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRAVRA
+>PROKKA_01572
+MRNLQKPSGMKHGKYVPYHEQIEVHLPDRTWPDKVITEAPRWCAVDLRDGNQALIDPMGP
+ERKLRMFQLLVQMGYKEIEVGFPSASQTDFDFVRQLIEGDHIPDDVSIQVLTQAREHLIE
+RTFESLEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLTGTEIT
+YEYSPESYTGTELEFARRISDEVATVLEASTDRQMILNLPATVEMATPNVYADSIEWMHR
+NLEHRDSIILSLHPHNDRGTGVAAAELGYLAGGDRIEGCLFGNGERTGNVDLVTLGMNLF
+SQGIDPMIDFSDMDHIRRTVEYCNQLPVPERSPWGGDLVFTAFSGSHQDAIKKGFEAMEA
+DAAAAGKHVDEIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHKLDLPRR
+AQIEFSHVIQELADAHGGEVSGADLWTAFQDEYLPAENKEEAWGRYRVRSVSSESGENGA
+FRMTAEIFVDHEPQTRTAEGNGPIDAFLKILGEDGQDVRVLDYTEHALSEGGSAMAAAYV
+EAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRSLRA
+>PROKKA_01170
+MSAHLQKSSGMKFHKYVPFQDQIEVALPDRTWPDKVIEKAPLWCAVDLRDGNQALIDPMG
+PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI
+ERTFEALEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLRGTQI
+TYEYSPESYTGTELEFARRISDEVATVLEASTDRKMILNLPATVEMSTPNVYADSIEWMH
+RNLEHRDSLILSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL
+YSQGIDPMIDFSDMDHIKRTVEYCNQLAVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME
+VDAKAAGTDVDGIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR
+RAQIEFSHVIQDLADAQGGEVSGADLWRVFQDEYLPADAAEAQWGRYRLRSVSSASGEDG
+AFRMEAELEVDGVTQTRTAQGNGPIDAFLRILGEEGVDVRVLDYSEHALSEGGAAMAAAY
+VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRALRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001017.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001017.fa
new file mode 100644
index 0000000000000000000000000000000000000000..295d49ed5f7ccfc6a66135f0c8717f12c479f0f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001017.fa
@@ -0,0 +1,35 @@
+>PROKKA_01217
+MSRPRDPEVIRPIVTVPPTTPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVFPTV
+DVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGRGAG
+QLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQALQAK
+EVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGTIEV
+APLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGTQSG
+LAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARGPAERSQKRGGARRGR
+>PROKKA_00936
+MSRPRDPEVIRPIVTVPPTTPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVFPTV
+DVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGRGAG
+QLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQALQAK
+EVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGTIEV
+APLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGTQSG
+LAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARGPAERSQKRGGARRGR
+>PROKKA_01671
+MVRTLGPQDALLRILGGVFPAVDLTVRDQRLEMAGPVPDVASVRRVVEDLRSIARRDQAV
+TPEVMEQVVTHVRGAAAGRGAGQLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGI
+GPAGTGKTYLAMAKAVQALQAKEVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYD
+ALHDMIEPESIPRLMEAGTIEVAPLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGF
+GARMVVTGDTSQVDLPRGTRSGLSQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYD
+AARGAEPAPRGGRGHRGR
+>PROKKA_01568
+MIRPIVSDPSSHVVLPPVSVPGAESVSFESAELMVRTLGAHDALLRILAGVYPDVEVTVR
+DQSLGMSGPPRHVAQARRIVEDLRSLARRDAPVTPDVVEQVVSLVRDGETGRASGTLHLD
+SILSGRGRKIRAKTLHQQDYVEAIDRATIVFGLGPAGTGKTYLAMAKAVQALQAKEVTRI
+ILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMESGTIEVAPLAY
+MRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGVRSGLAEAV
+EVLEGVDGLEMVRFDSSDVVRHSLVSAIVDAYDGARGSGSAADPRPAGRGAQRGRSGRGR
+>PROKKA_01174
+MSRPRDPEVIRPIVTVPPTTPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVFPTV
+DVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGRGAG
+QLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQALQAK
+EVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGTIEV
+APLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGTQSG
+LAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARGPAERSQKRGGARRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001018.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001018.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3adbdf36b818fc5bc8d5f02738c696998c1f303a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001018.fa
@@ -0,0 +1,30 @@
+>PROKKA_01218
+MTAPLFHLEPGALAGASAGAEVVFDGAEARHAAAAMRLAPGEAVLLADGSGTLGHGTVLA
+AAPDAVSVRLDAVAEEPAPTPALVLVQALAKGDRDLMAVQAAVELGVDAVVPWEAERSIV
+RWKGPKAAKARQKWADTARAAAKQARRARVPAVRDHVSGTAVAGLARDDDGGRLVLVLHE
+DAEHGVSAVPAERLSAAVEIAVVVGPEGGIGPAELEACVAAGAVPVRLGPHVLRASTAGP
+AALAVLQHRLGRW
+>PROKKA_00937
+MTAPLFHLEPGALAGASAGAEVVFDGAEARHAAAAMRLAPGEAVLLADGSGTLGHGTVLA
+AAPDAVSVRLDAVAEEPAPTPALVLVQALAKGDRDLMAVQAAVELGVDAVVPWEAERSIV
+RWKGPKAAKARRKWADTARAAAKQARRARVPAVRDHVSGTAVAGLAWDDDGGRLVLVLHE
+DAEHGVSAVPAERLSAAVEIAVVVGPEGGIGPAELEACVAAGAVPVRLGPHVLRASTAGP
+AALAVLQHRLGRW
+>PROKKA_01670
+MTAPLFHLEPGALTGAVPGAEVSFGGPEARHAAASMRLAPGESVLLADGSGVRGHGTVLA
+AAPDAVTVRLDAVDEEPAAVPALVLVQALAKGDRDLMAVQAAVELGVDAVVPWEAERSIV
+RWKGPKAEKARQKWADTARAAAKQARRARVPEVRGHVSGTGVAGLASAPDDGARLVLVLH
+EDAERGLSEVPVERLREAAEIAVVVGPEGGVGPAELEACTAAGAVPVRLGPHVLRASTAG
+PAALAVLAHRLGRW
+>PROKKA_01567
+MTAPLFLLDAGALAGVAPGAEVAFTGAEARHAAASMRLGAGESVLVADGSGARASCVVVD
+AAPSAVTVRVESLEHDAAPRPALVLVQALAKGDRDLMAVQASTELGVDAVVPWEAERSIV
+RWKGAKAAKAHQKWEDTVRAAAKQARRARVPEVRPVVSGTAVAALAGPDRLLLVLHEDAD
+LGLGGLPDADLEAAAEVALVVGPEGGVSPAELDACTAAGAVPVRLGPHVLRASTAGPAAL
+AVLQHRLGRW
+>PROKKA_01176
+MTAPLFHLEPGALAGASAGAEVVFDGAEARHAAAAMRLAPGEAVLLADGSGTLGHGTVLA
+AAPDAVSVRLDAVAEEPAPTPALVLVQALAKGDRDLMAVQAAVELGVDAVVPWEAERSIV
+RWKGPKAAKARQKWADTARAAAKQARRARVPAVRDHVSGTAVAGLAWDDDGGRLVLVLHE
+DAEHGVSAVPAERLSAAVEIAVVVGPEGGIGPAELEACVAAGAVPVRLGPHVLRASTAGP
+AALAVLQHRLGRW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001020.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001020.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c8ed9faa90569c7ac00f88534dc8bfa1f96fd5c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001020.fa
@@ -0,0 +1,35 @@
+>PROKKA_01220
+MSEQPRRLQVLQAIVEDYVALREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPETDTEHMMESTVRLLAQLTQQ
+VAVAQFPYEDGSTIRHLELVSLTPTRVLVVLILSTGRVDQRHAVLDRPVDEAELSVLRGL
+LLDALLGLGPVQAATVVDDVVTRVRPEHRQSAALVAAAVQDLLEAGREDRIVLAGTANLA
+RSPGDFGASIGPILEALEEQVVLLRLLTEMEQDAHGVSVRIGSENAGSLADTSVVAAAYG
+PGAVAKLGVIGPTRMDYPGTMAAVRAIARYLSRILTT
+>PROKKA_00939
+MSEQPRRLQVLQAIVEDYVALREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPETDTEHMMESTVRLLAQLTQQ
+VAVAQFPHEDGSTIRHLELVSLAPTRVLVVLILSTGRVDQRHAVLDRPVDEAELSVLRGL
+LLDALLGLGPVQAATVVDDVVTRVRPEHRQSAALVAAAVHDLLEAGRQDRIVLAGTANLA
+RSPGDFGASIGPILEALEEQVVLLRLLTEMEQDAHGVSVRIGSENAGSLADTSVVAAAYG
+PGAVAKVGVIGPTRMDYPGTMAAVRAIARYLSRILTT
+>PROKKA_01668
+MTEQPRRLQVLQAIVEEYVARREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPSTDTEHMMETTVRLLAQLTQQ
+VAVAQFPHEDGSTVRHLELVPLTPARVLVVLILSTGRVDQRHVVLETPLAEADLAVLRGL
+LLEAVLGLGPAQAAAVVDAAVARMRPEDREAAALVAGAVHALLEAGRQDRIVMAGTANLA
+RSTGDFGASIGPILEALEEQVVLLRLLTEMEHDAHGVSVRIGSENAGSLADTSVVAAAYG
+PGAVAKVGVVGPTRMDYPGTMAAVRAIARYLSRILTT
+>PROKKA_01565
+MTEQPRRLQVLQAIVEDYVSLREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRISEVKPLSAAERRAVRTLLDSEADTESMMEATVRLLAQLTRQ
+VAVVQFPHEDGSTVRHLDLVALTPERVLVVLILSTGRIEQRTVALARPVQDEDLAALRAV
+LLPVIEGLGPAQAAAVLDTPLEGLPPARRAAAVDVVGAVRGLLEAERQDRIVLAGTANLA
+RSTDDFHSSIGPILEALEEQVVLLRLLTEMGQDAHGVSVRIGAENGASLADTSVVAAAYG
+PGAVAKVGVIGPTRMDYPGTMAAVRAIARYLSRILTT
+>PROKKA_01178
+MSEQPRRLQVLQAIVEDYVALREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPETDTEHMMESTVRLLAQLTQQ
+VAVAQFPHEDGSTIRHLELVSLAPTRVLVVLILSTGRVDQRHAVLDRPVDEAELSVLRGL
+LLDALLGLGPVQAATVVDDVVTRVRPEHRQSAALVAAAVQDLLEAGREDRIVLAGTANLA
+RSPGDFGASIGPILEALEEQVVLLRLLTEMEQDAHGVSVRIGSENAGSLADTSVVAAAYG
+PGAVAKLGVIGPTRMDYPGTMAAVRAIARYLSRILTT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001021.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001021.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d99e55f504f346c685775230fa7b3ca9448a05e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001021.fa
@@ -0,0 +1,30 @@
+>PROKKA_01221
+MDWSSWGPAGHDDLTRRPARTVPDVPAAPGTVVEDVASGFTGAVIGIERSGGVHVVVLED
+RRGVRRGFPLGGGFWIDGEPVTLVPPTAAAPAAPARTASGSRRVEGARARTARASRIWVE
+GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLAGAIRAFAPGPRRRLGILVDHLVTGSKE
+ERLAAEAMRVPGAAGNVLILGHPYVDVWQVIKPSVLGIPAWPVVPKGQDWKTGILRGLGW
+PHGSKEATGLGWKRLLSHVTTYADLEPSLLGRVEELIDFLTAAPEH
+>PROKKA_00940
+MDWSSWGPAGHDDLTRRPARTVPDVPATPGTVVEDVASGFTGAVSGIERSGGVHVVVLED
+RRGVRRGFPLGGGFWIDGEPVTLVPPTAAAPAAPARTASGSRRVEGARARTARASRIWVE
+GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLAGAIRAFAPGPRRRLGILVDHLVTGSKE
+ERLAAEAMRVPGAAGNVLILGHPYVDVWQVIKPSVFGIPAWPVVPKGQDWKTGILRGLGW
+PHGSKEATGLGWKRLLSHVTTYADLEPSLLGRVEELIDFLTAAPEH
+>PROKKA_01667
+MDWSSWGPAGHEEMTRRPGRPARDVPAAPGTVVEDVASGFTGAVIRVERAGGVHTVVLED
+RRGVRRGFPLGGGFWIDGEPVTLVPHVASAPRPPARTASGSRRVEGVRARTARASRIWVE
+GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLAGAIAAFDPGPRRRLGILVDHLVPGSKE
+ERIAAEAMRVPGAAGNVLILGHPYVDVWQVIKPAVLGIPTWPVVPKGQDWKTGVLQGLGW
+PHGTKEATGLGWKRLLSHVGSYADLEPSLLGRVEELIDFLTAEPER
+>PROKKA_01564
+MDWSSWGPGAHEDLARPAGRTAGEAPATPGTVVEDVASGFVGAVVRVERSGGTHVVVLED
+RRGVRRGFPLGPGFWVDGSPVVLVPPRSAAPAAAARTASGSRRVEGARARTARASRIWVE
+GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLPGAIRDFAPGPGRRLGILVDHLVAGSKE
+ERLAAEAMAVPGAAGNVLILGHPYVDVWQVIKPAVLGIDAWPVVPRGQDWKTGVLRGLGW
+PAGTKEATGLGWKRLLSHVRTYADLEPALLGRVEELIDFLTAPGA
+>PROKKA_01179
+MDWSSWGPAGHDDLTRRPARTVPDVPATPGTVVEDVASGFTGAVIGIERSGGVHVVVLED
+RRGVRRGFPLGGGFWIDGEPVTLVPPTAAAPAAPARTASGSRRVEGARARTARASRIWVE
+GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLAGAIRAFAPGPWRRLGILVDHLVTGSKE
+ERLAAEAMRVPGAAGNVLILGHPYVDVWQVIKPSVLGIPAWPVVPKGQDWKTGILRGLGW
+PHGSKEATGLGWKRLLSHVTTYADLEPSLLGRVEELIDFLTAAPEH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001023.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001023.fa
new file mode 100644
index 0000000000000000000000000000000000000000..10deb81c38cf24efc5ff180e3a1e5e177dd501ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001023.fa
@@ -0,0 +1,60 @@
+>PROKKA_01224
+MSPLASNPPVPAATDPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD
+IERERGITIKSQAVRMPWSVDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ
+GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELASLIGCDPEDVLRVSGKTG
+VGVEELLDRVVRAVPSPEGDADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKVRMM
+STGTTYELLEIGVSSPEPVPTKGLAVGEVGYLITGVKDVRQSKVGDTVTNHAHPAEQSLG
+GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL
+HLEIVRERLEREFGLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKILEVREPMASAT
+IIVPAEFIGAVMELCQAKRGNLKGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA
+SLDWKADGDQAADLVKVDILLQGEQVDAFSSITHKDNAYTYGVMMTGKLKELIPRQQYEV
+PIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE
+AFIAALSSDGAGADQAAKK
+>PROKKA_00943
+MSPLASNPPVPAATDPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD
+IERERGITIKSQAVRMPWSVDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ
+GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELASLIGCEPEDVLRVSGKTG
+VGVEDLLDRVVRAIPGPEGDADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKVRMM
+STGTTYELLEIGVSSPEPVPTNGLAAGEVGYLITGVKDVRQSKVGDTVTNHAHPAEQSLG
+GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL
+HLEIVRERLEREFDLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKILEVREPMASAT
+IIVPAEFIGAVMELCQAKRGNLKGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA
+SLDWKADGDQVADLVKVDILLQGEQVDAFSSITHRDNAYAYGVMMTGKLKELIPRQQYEV
+PIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE
+AFIAALSSDGAGADQAAKK
+>PROKKA_01664
+MSPLASNPPVPAATEPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD
+IERERGITIKSQAVRMPWELDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ
+GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELATLIGCEPEDVLRVSGKTG
+VGVEDLLDRVVRSIPAPEGEADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKIRMM
+STGATHELLEIGVSSPEPTPTKGLAVGEVGYLITGVKDVRQSKVGDTVTNHAKPAAEELG
+GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL
+HLEIVRERLEREFNLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKIHEVREPMASAT
+IIVPAEFIGAVMELCQAKRGNLRGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA
+SLDWKADGDQVADLVKVDILLQGEQVDAFSSITHKDNAYSYGVMMTGKLKELIPRQQFEV
+PIQAAIGSRVIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE
+AFIAALSSDGAGADSAAKK
+>PROKKA_01561
+MSEAPEPIKDVPVSPLASKPPVPAATDPAVIRNFCIIAHIDHGKSTLADRMLQATGVVQP
+REMKAQYLDRMDIERERGITIKSQAVRMPWEVDGVNYALNMIDTPGHVDFTYEVSRSLAA
+CEGAILLVDAAQGIEAQTLANLYLAMENELEIIPVLNKIDLPAADPDRYAAELATLIGCE
+PDDVLRVSGKTGQGVEALLDRVVERLPAPQGVADAPARAMIFDSVYDTYRGVVTYVRVVD
+GMLSPREKIRMMSTGATHELLEIGVSSPEPMPTKGLSVGEVGYLITGVKDVRQSKVGDTV
+TNSSRPATEQIGGYEDPKPMVFSGLYPIDGSDYPNLRDALDKLKLNDAALVYEPETSVAL
+GFGFRVGFLGLLHLEIVRERLEREFDLDLISTAPNVVYEVKREDKTVVTVTNPSEFPEGK
+VLEVKEPMASATVIVPAEYIGAVMELCQTKRGHLKGMDYLSEERVEIRYWIPLAEIVFDF
+FDQLKSRTKGYASLDWKADGDQVADLVKVDILLQGEQVDAFSAITHRDNAYSYGVMMTGK
+LKELIPRQQFEVPIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKR
+MKMVGRVEVPQEAFIAALSSDGAEPAKK
+>PROKKA_01182
+MSPLASNPPVPAATDPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD
+IERERGITIKSQAVRMPWSVDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ
+GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELASLIGCEPEDVLRVSGKTG
+VGVEELLDRVVRAIPGPEGDADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKVRMM
+STGTTYELLEIGVSSPEPVPTKGLAAGEVGYLITGVKDVRQSKVGDTVTNHAHPAEQSLG
+GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL
+HLEIVRERLEREFDLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKILEVREPMASAT
+IIVPAEFIGAVMELCQAKRGNLKGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA
+SLDWKADGDQVADLVKVDILLQGEQVDAFSSITHRDNAYAYGVMMTGKLKELIPRQQYEV
+PIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE
+AFIAALSSDGAGADQAAKK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001026.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001026.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7cd07c3f73d77931dae1bed2aacad6a387fa4d67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001026.fa
@@ -0,0 +1,35 @@
+>PROKKA_01227
+MSAARSPRSGRAGRTDPLAWRRAEPAPLMLLKGPEDHAARWVTDRVTQALRERHGQLEIH
+RLRAGEYQPGQLATAASPSLFAEPTLITVEGLEAMNDAFLEDALRLVQQGPGADDVTLVL
+RHTGGTRGKRLLDAVAKAGTVVECVPLKKDEERLAFVQAEFRDRRRRIDEEAARALIRAT
+GASLTELAAACAQLVDDTEGVVSVETVDTYYSGRVEATSFAVADAALEGQAARAVSLVRH
+AMATGVHPVMITAALALKARQVARMIDARRPAAELPSLLGVAPFQVRYIQQAARHWTAAG
+IAQAVEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR
+>PROKKA_00946
+MSAARSPRSGRAGRTDPLAWRRAEPAPLMLLKGPEDHAARWVTDRVTQALRERHGQLEIH
+RLRAGEYQPGQLATAASPSLFAEPTLITVEGLEAMNDAFLEDALRLVQQGPGADDVTLVL
+RHTGGNRGKKLLDAVAQAGTVVECVPLKKDEERLAFVQAEFRDRRRRIDEEAARALIRAT
+GASLTELAAACAQLVDDTEGVVTVETVDTYYSGRVEATSFAVADAALEGQAARAVSLVRH
+AMATGVHPVMITAALALKARQVARMIDARRPAAELPSLLGVAPFQVRYIQQAARHWTAAG
+IAQAVEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR
+>PROKKA_01661
+MSAARSPRSGRAGRVDPLAWRKAEPAPLMLLKGPEDHAARWVTDKVTAALRERHGELEVH
+SLRAGEYQAGQLATAASPSLFAEPTLIKVDGLESMNDAFLEDALRLVQHGPGADDVTLVL
+RHAGGSRGKRLLDAVAKAGTVVDCVPLKKDEERLAFVLAEFRDRRRRIEEDAARSLLRAT
+GASLTELAAACAQLVDDTEGTVTAAMVDTYYGGRVEATSFAVADAALEGHAARAVSLVRH
+AMATGVHPVMVTAALALKARQVARMIDAHRPAGELAALLGVAPFQVRYIQQAARHWTPAG
+IAQAMEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR
+>PROKKA_01558
+MSAARSTRSARGARGVDPLAWRRAEPAPLMLLRGPEEYAARWVADRVVATLQARHGSLET
+HRLRASDYQAGQLALAASPSLFAEPTLIRVDGLESMNDAFLEDALRLVAQGPGADDVTVL
+LRHTGGSRGKRLIDAVAAAGVVVECPALKKDEDRLALVQAEFREARRRIDEDAARALVRA
+TGASLTDLASACRQLIEDVEGTVTPQTVETYYGGRVEATSFAVADATLEGHAARAVSLTR
+HALATGVHPVMITSALAVKARQVARIIDARAGQGELASILGVAPFQVRFIQQAARHWTPA
+GIARAVEWIAQADAEVKGAARDADFAVERAVIRVATAVSR
+>PROKKA_01185
+MSAARSPRSGRAGRTDPLAWRRAEPAPLMLLKGPEDHAARWVTDRVTQALRERHGQLEIH
+RLRAGEYQPGQLATAASPSLFAEPTLITVEGLEAMNDAFLEDALRLVQQGPGADDVTLVL
+RHTGGNRGKKLLDAVAQAGTVVECVPLKKDEERLAFVQAEFRDRRRRIDEEAARALIRAT
+GASLTELAAACAQLVDDTEGVVTVETVDTYYSGRVEATSFAVADAALEGQAARAVSLVRH
+AMATGVHPVMITAALALKARQVARMIDARRPAAELPSLLGVAPFQVRYIQQAARHWTAAG
+IAQAVEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001028.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001028.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e600aeace44d87e11cc372aa35e039b01aade21
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001028.fa
@@ -0,0 +1,31 @@
+>PROKKA_01229
+MSPSHRLCDDPPAFAPDPAAVPDVDTAGPHAASRWERTPPRGPVLRWRPALLAVTVLLVA
+AAAWWAVAWLTTPAPPAAVPAAAAGAGIPQTGAPSAASTAAGTDARTPEAGPSGEASGSA
+GSTPLRVHVVGEVARPGVVSLAPGSRVADAVRAAGGPTRHARAERINLAAPLDDGQQVLV
+PSAHTPQDALDRVAGAAQAQPTPTTGGAGATGEPGGAEPRGTVDLNTADAAGLQTLPGVG
+PATAEKIIAHRETVGPFTGLQDLDAVPGIGPATLDRLRDLVSW
+>PROKKA_00948
+MRDAPDSATGPQTARMSPSHRLCDDPPAFAPDPAPAAAPDVDTAGPHAASRWERTPPRGP
+VLRWRPALLAVTVLLVAATAWWAVAWLTTPAPPAAIPAAAAGAGIPQTDAPSTAPSAAGT
+DARTSEAGPSGEASGPAGSGPLRVHVVGEVARPGVVSLAPGSRVADAVGAAGGPTRHARA
+ERINLAAPLDDGQQVLVPSARTPQDALDRVAGAAQAQPTPTTGRAGGGGEPGGAESGDTV
+DLNTADATELQTLPGVGPATAEKIIAHRETVGPFTGLQDLDAVPGIGPATLDRLRDHVSW
+>PROKKA_01659
+MSHPHRLAPDAALSDDPRRGRPASDLVPVPPALAARGPSAWERVPPRGRVLRWRPALLAV
+TVLLVAAAAWWAVAWLTSPAPPSPAPAASAVEARVEPETEDGPDAADAAPPSDGAGPAAE
+PSGGSGPVATLLRVHVVGEVERPGVVSLAPGARVADAVRAAGGATREARTERINLAAPLA
+DGRQVLVPSARTPEEDLARVAGGQDGPGGPEGGAAGTAPDAAASAPAGPARAGGSGGAGA
+GPVDLNAADAVALQTLPGVGPATAEKIIAHRETVGPFTGLQDLDAVPGVGPAALERLRDR
+VTW
+>PROKKA_01556
+MDTKTLTPAVDEPDWEDPPPRGPLLRWRTAGAGLTLVAILGLTWWLVAWLTAPAPPDAVP
+AGAVGSASAAGSAAHEASAAPLRATAATPEGQDGGGRSAAAANPSGRVRVHVVGQVRRPG
+VVELPAGARVADAVAAAGGARELARTDRINLAAPVVDGQQVVVPDAQTAVEPAAVAGEAP
+DGGPTPRTGSGASAADGSGGGPATVDLNTADLAALQTLPGVGPATAEKIIAQRESVGPFS
+GLQDLDAVPGIGPATLDRLKDHVTW
+>PROKKA_01187
+MSPSHRLCDDPPAFAPDPAPAAAPDVDTAGPHAASRWERTPPRGPVLRWRPALLAVTVLL
+VAATAWWAVAWLTTPAPPAAIPAAAAGAGIPQTDAPSTAPSAAGTDARTSEAGPSGEASG
+PAGSGPLRVHVVGEVARPGVVSLAPGSRVADAVGAAGGPTRHARAERINLAAPLDDGQQV
+LVPSARTPQDALDRVAGAAQAQPTPTTGRAGGGGEPGGAESGDTVDLNTADATELQTLPG
+VGPATAEKIIAHRETVGPFTGLQDLDAVPGIGPATLDRLRDHVSW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001030.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001030.fa
new file mode 100644
index 0000000000000000000000000000000000000000..812205dd4a8b06eccb1379b92b8df39573712c86
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001030.fa
@@ -0,0 +1,75 @@
+>PROKKA_01231
+MSQTPDSAVPATPSIPADAEYSFRDVEARWAGYWEQAGTFAPREDGSETRTVVDMFPYPS
+GDLHMGHAEAFAMGDVVARHWMQRGFDVLHPIGWDSFGLPAENAAIKRDAHPAEWTYANI
+ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRRGLAYRKDSPVNWCPQDQTV
+LANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI
+GRSEGAHVDFQVEDGPVVTVFTTRPDTLHGATFMVVAADAPLAAELAGDDVRAELEAYRE
+DLKKVSDIDRQATDRPKSGVFLGRHAVNPLTGERLPIWASDYVLADYGTGAIMAVPAHDQ
+RDLDFARAMGLPVRTVLDTGEEDPAVSGVATTGEGILVNSGELDGLDKTAAIARAIEIVQ
+ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPDCGEVLVPEDQLPVTLPTDLKGEQLA
+PKGQSPLAAATSWVEVDCPQCGGPARRDTDTMDTFVDSSWYMLRYASPNDDARVFDPEAL
+RRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNDGKAMSK
+SLGNGVDLGDQLDQFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRLARDVRA
+TGTPAGTDPADGAVALRRVTHRTVHEAQQLLDDGKFNVVVAKTMELVNAARKEIDAGAGA
+ADPAVREAAEAVAVLLSLVAPYTAEDMWVLLGHEPSVIRAGWPAVDEALLVEDTVTAVVQ
+VKGKVRDTLEVPADITAEDLEARARASQKVRNFIGDAQIVKVIVREPKLVNLVIR
+>PROKKA_00950
+MSQTPDSAVPATPSIPADAEYSFRDVEARWAGYWEQAGTFAPREDGSETRTVVDMFPYPS
+GDLHMGHAEAFAMGDVVARHWMQRGFDVLHPIGWDSFGLPAENAAIKRDAHPAEWTYANI
+ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRRGLAYRKDSPVNWCPQDQTV
+LANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI
+GRSEGAHVDFQVEDGPVVTVFTTRPDTLHGATFMVVAADAPLAAELAGDDVRAELEAYRE
+DLKKVSDIDRQATDRPKSGVFLGRHAVNPLTGERLPIWASDYVLADYGTGAIMAVPAHDQ
+RDLDFARAMGLPVRTVLDTGEEDPAVSGVATTGEGILVNSGELDGLDKTAAIARAIEIVQ
+ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPDCGEVLVPEDQLPVTLPTDLKGEQLA
+PKGQSPLAAATSWVEVDCPQCGGPARRDTDTMDTFVDSSWYMLRYASPNDDARVFDPDAL
+RRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNGGKAMSK
+SLGNGVDLGDQLDEFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRLARDVRA
+TGAPAGTDPAGGAVTLRRVTHRTVHEAQQLLDDGKFNVVVAKTMELVNAARKEIDAGAGA
+ADPAVREAAEAVAVLLSLVAPYTAEDMWVLLGHEPSVVRAGWPAVDEALLVEDTVTAVVQ
+VKGKVRDTLEVPADITAEDLEARARASQKVRNFIGDAEIVKVIVREPKLVNLVIR
+>PROKKA_01657
+MFPYPSGDLHMGHAEAFAMGDVVARHWMQRGYDVLHPIGWDSFGLPAENAAIKRDAHPAE
+WTYANIETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRKGLAYRKDSPVNWC
+PQDQTVLANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLA
+MQRNWIGRSEGAHVDFQIEDGPQITVFTTRPDTLHGATFMVVAADAPLAAELADESVRAE
+LEAYREELKKVSDIDRQATDRPKTGVFLGRHAINPLNGERLPVWASDYVLADYGTGAIMA
+VPAHDQRDLDFARAMGLPVRAVLDTGEENPAVSGVATTGDGTLVNSGELDGLDKTAAIAR
+AIEIVEGRGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCEACGEVLVPEDQLPVTLPTDL
+NGEQLAPKGQSPLAAATSWVEVACPDCGGPARRDTDTMDTFVDSSWYTLRYASPNDDTQV
+FDPEAVRRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNG
+GRAMSKSLGNGVDLGAQLDEFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRL
+ARDVREAGTPADADPATGSVALRRVTHRSVHEAGQLLDDGKFNVVIAKTMELVNAARKEI
+DGGAGAADPAVREAAEAVAVLLSLVAPYTAEDMWVMLGHEPSVVRAGWPAVDESLLVEDT
+VTAVVQVKGKVRDTLEVPADITAEDLEARARASQKVRTFIGDAEIVKVIVREPKLVNLVI
+R
+>PROKKA_01554
+MSQTPESAAPATPQVPEDAEYAFSEVEARWAGYWEQAGTFTPRGDGSATRTVVDMFPYPS
+GDLHMGHAEAFAMGDVLARYWLQRGYDVLHPIGWDSFGLPAENAAIKRNAHPAEWTYANI
+ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRKGLAYRKDSPVNWCPQDQTV
+LANEQVVDGKCERCGAEVTKRELNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI
+GRSEGAHVDFQVEDGPAVTVFTTRPDTLHGATFMVVAADAPLALELVDDEHRAALEAYRE
+ELKKASDIERQATDRPKTGVFLGRHAVNPLTGERLPMWASDYVLADYGTGAIMAVPAHDQ
+RDLDFARAMDLPVRTVVDTGEEDPAVSGVATTGEGTLVNSGELDGLSKADGIARAIEIVQ
+ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPEHGEVLVPEDQLPVLLPTDLKGGQLA
+PKGQSPLAAAEEWVNVPCPECGAPARRDSDTMDTFVDSSWYFLRYASPWDEQQVFDPELV
+KTWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNGGKAMSK
+SLGNGVDLGQQLDEFGVDAVRTTMVFASPPEDDVDWADVAPAAAGKFLARAWRLARDVRA
+AGTPAGDPAQGSAALRRVTHRTVHEAAALVEDHKFNVVVAKTMELVNATRKEIDGGAGAA
+DPAVREAAEAVAILLSLVAPYVAEDMWAMLGHEPSVVRAGWPAVDESLLVEDTVTAVVQV
+KGKVRDQLQVPADVSAADLEAAARASAKVRAFIGDAEIVKVIVREPKLVNLVIR
+>PROKKA_01189
+MSQTPDSAVPATPSIPADAEYSFRDVEARWAGYWEQAGTFAPREDGSETRTVVDMFPYPS
+GDLHMGHAEAFAMGDVVARHWMQRGFDVLHPIGWDSFGLPAENAAIKRDAHPAEWTYANI
+ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRRGLAYRKDSPVNWCPQDQTV
+LANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI
+GRSEGAHVDFQVEDGPVVTVFTTRPDTLHGATFMVVAADAPLAAELAGDDVRAELEAYRE
+DLKKVSDIDRQATDRPKSGVFLGRHAVNPLTGERLPIWASDYVLADYGTGAIMAVPAHDQ
+RDLDFARAMGLPVRTVLDTGEEDPAVSGVATTGEGILVNSGELDGLDKTAAIARAIEIVQ
+ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPDCGEVLVPEDQLPVTLPTDLKGEQLA
+PKGQSPLAAATSWVEVDCPQCGGPARRDTDTMDTFVDSSWYMLRYASPNDDARVFDPDAL
+RRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNGGKAMSK
+SLGNGVDLGDQLDEFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRLARDVRA
+TGAPAGTDPAGGAVTLRRVTHRTVHEAQQLLDDGKFNVVVAKTMELVNAARKEIDAGAGA
+ADPAVREAAEAVAVLLSLVAPYTAEDMWVLLGHEPSVVRAGWPAVDEALLVEDTVTAVVQ
+VKGKVRDTLEVPADITAEDLEARARASQKVRNFIGDAEIVKVIVREPKLVNLVIR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001031.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001031.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc8f83d637f360ead9797c8c4a5364db2e74e37d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001031.fa
@@ -0,0 +1,43 @@
+>PROKKA_01232
+MQHPVALRSLKIALAFVGLLVGAGFATGAEVIQYFVGFGWIGIVGAGLAGLLVTAGGAVI
+LQLGSVFLAADHKVVFRSVSHPVMARILDVVVTVTLFAIGVVMLAGAGSTLAQQFGWPTW
+AGSTLMTLLVLVTGMLDVEKVSAIISLITPLVVVAVVAGFVHVLVTRDGGFTAHESLAVQ
+ATTPVDPWWLSSVNYFGLVVVMAVSMCLVIGGSITHPREAFLGGLTGGLMYTALLLMAST
+LLYLGYAEIGRADVPMLRLFASIAPWLGWAMVVVIYLMIFNTAIGMFYALGRRLTADRPG
+RYRPVFAGVTLLAFAVSFVGFGDLINVVYPALGHLGIVLALVLLVWWLTHRRQISAESGL
+RLRLLALLRLREHPEKTFTAQHAVQLQEAVGDSVAAPDAVTEALEDEVAQVLEEDDALTS
+EGARPGPDAGPERPAGGSHSA
+>PROKKA_00951
+MQHPVALRSLKIALAFVGLLVGAGFATGAEVIQYFVGFGWIGIVGAGLAGLLVTAGGAVI
+LQLGSVFLAADHKVVFRSVSHPVMARILDVVVTVTLFAIGVVMLAGAGSTLAQQFGWPTW
+AGSTLMTLLVLVTGMLDVEKVSAIISLITPLVVVAVVAGFVHVLVTRDGGFTAHESLAVQ
+ATTPVDPWWLSSVNYFGLVVVMAVSMCLVIGGSITHPREAFLGGLTGGLMYTVLLLMAST
+LLYLGYAEIGRADVPMLRLFASIAPWLGWAMVVVIYLMIYNTAIGMFYALGRRLTADHPG
+RYRPVFAGVTLLAFAVSFVGFGDLMNVVYPALGHLGIVLALVLLVWWLTHRRQISAESGL
+RLRLLALLRLREHPEKTFTAQHAVQLQEAVGDSVAAPGAVTEALEDEVAQVLEEDDAVTP
+DEVHPGPDAGPERPAGGSHSA
+>PROKKA_01656
+MVFRSVSHPVMARILDVTVTVTLFAIGFVMLAGAGSTLAQQLGWPTWAGAGLMTALVLVT
+GMLDVEKVSAIISLITPLIILAVVAGFVHVLLTHEGSFTANEALAVQAATPVAPWWLSSV
+NYFGLVVVMAVSMCLVIGGSITNPREAFAGGLTGGVLYTVLLLLASVLLYLGYAEIGRAD
+VPMLQLFASIAPWLGWTMVVVIYLMIYNTAIGMLYALGRRLTAERPGRYRPVFIGVTLLA
+FAVSFVGFGDLMNVVYPALGYLGIVLALVLIAWWVLHRRQISAESGLRLRLRALLRLREH
+PEKTFTAQHAVLLQEAADESVAATAVVTEAVEEEVVQAIEADEPYGDPRRS
+>PROKKA_01553
+MQKSAALRSVQLALAFVGLLVGAGFATGAEVIQYFVGFGEVGIGGALLAGVLVAVGGAVA
+LQLGSLFLAADHKVVFRSVSHPVMARILDAVVTVTLFAIGFVMLAGAGSTLAQQLGWPVW
+AGAALMTAMVIVTGMLDVEKVSAIIGMITPLIIIAVVAGFAYVVATHEGPFTVNDSLAVQ
+AVTPVSPWWLSSINYFGLVVVMAVSMCVVIGGSTSSPREAFVGGLVGGVVYTVLLVLASV
+LLYLGYAELGTADVPMLQLFASIHPALGWAMVVVIYLMIYNTAIGMFYALGRRLTAERPG
+LYRPAFVGVTLAAFAVSFLGFGDLMNYVYPALGYLGIVLAVVLLVWWAAHRDDIAAESGL
+RLRLLALLRLREHPEKTFTRQHAVILQETAEESVAPTETVTEMMEADAVAVIEAEDPDLL
+PAADETAGRGGADHGGADGSAAARG
+>PROKKA_01190
+MQHPVALRSLKIALAFVGLLVGAGFATGAEVIQYFVGFGWIGIVGAGLAGLLVTAGGAVI
+LQLGSVFLAADHKVVFRSVSHPVMARILDVVVTVTLFAIGVVMLAGAGSTLAQQFGWPTW
+AGSTLMTLLVVVTGMLDVEKVSAIISLITPLVVVAVVAGFVHVLVTRDGGFTAHESLAVQ
+ATTPVDPWWLSSVNYFGLVVVMAVSMCLVIGGSITHPREAFLGGLTGGLMYTALLLMAST
+LLYLGYADIGRADVPMLRLFASIAPWLGWAMVVVIYLMIFNTAIGMFYALGRRLTADRPG
+RYRPVFAGVTLLAFAVSFVGFGDLMNVVYPALGHLGIVLALVLLVWWLTHRRQISAESGL
+RLRLLALLRLREHPEKTFTAQHAVQLQEAVGDSVAAPGAVTEALEDEVAQVLEEDDALTS
+GGARPGPDAGPERPAGGSHSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001032.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001032.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aab2cdf420bcda3e2ba8da58a993afdf344252d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001032.fa
@@ -0,0 +1,34 @@
+>PROKKA_01233
+MPVPTPPAAPGPPVRLRDLLRPPAAPADPRVLTGHVARTPRRRTLAVPDPVRRTPSSVAV
+WEYAPVPEAAPGSRGAPEGDPAAAPLVFVHGFRGDHHGLALLADALPEHPIHSIELPGFG
+DSEPFPHAEHTVAHHADAVAAGVAALGLPAAPVLVAHSYGTTVAAELAVRDPSRWARLVL
+LNPIAEPALQASASVTSRVLAAVAEGYYEVAARLPERPARLLLGAPPVVWVTTLATTRTR
+DRDVLAYTHDQHRRHFSGFASARMLSEAYRASSTGSVADVAARLTLPVLLVAGREDPLGS
+VPAQKALAAAIDAGGGTAELHVLDGVGHLLHYERPAACAALIRDWLRRAGR
+>PROKKA_00952
+MPVPTPPAPPGPPVRLRDLLRPPAAPADPRVLTGHPARTPRRRTLAVPDPVRRTPSSVAV
+WEYAPVPVAAPGSPGALEGDAAAAPLVFVHGFRGDHHGLALLADALPEHPIHSIELPGFG
+ASEPFPRAEHTVAHHADAVAAAVVALGLPAAPVLVAHSYGTTVAAELVAREPSRWGRLVL
+LNPIAEPALQASASATSRVLAAVAEGYYEVAARLPERSARLLLGAPPVVWATTLAMTRTR
+DRDVLAYTHDQHRRHFSGFASARMLSEAYRASSTGSVADVAARLTLPVLLVAGREDPLGS
+VPAQEALAAAIDAAGGTAELHVLDGVGHLLHYERPAACAALIRDWFRRAGR
+>PROKKA_01655
+MHGFRGDHHGLALLADALPERAITSIELPGFGDSEPFPDAEHTVAHHADAVAAVLAAMPP
+SQRPVLVAHSYGTVVGAELVARDPGRWDRLALLNPIAEPALDASASWTSRGLAALARGYY
+ELAARLPERAGRLVLGAAPVVWVTTLAMSRTPDRRVLAYTHDQHRRYFSRFASARMLSES
+YRASSTGTVADAADRLRLPVLLVAGREDPLGSVPAQEALAAAIEAGGGRAELHVLDGVGH
+LLHYERPGECAALLRAWAARGR
+>PROKKA_01552
+MPAPHDADPASPAGPRPIRPWHRLRIPAPTTPPRALTGHDVRVPRRRDVAVPDPISGAPL
+SVAVWQHDAAPSSGASVAGAARPHLVFVHGFRGDHHGLQLLADCLPEFGVSSVELPGFGA
+SDPFPDAEHTVAHHADALAAAVAALGLDAPPVLVAHSYGTVVAAHLVQRDSGAWPALALL
+NPIAEPALDASGSRADRLLAGVAEAYYEAAARLPERVSRLLLGAPPVVWVTTQAMSRTRD
+RDVLAYTHDQHRRFFSGFASARMLSESYRASSTGTVAQAADRLDLPVLLVAGREDPLGSV
+AAQEALAARIAAAGGVPELHVLDGVGHLLHYERPAACARLLREWLAAGA
+>PROKKA_01191
+MPAPTPPAAPGPPVRLRDLLRPPAAPADPRVLTDHPARTPRRRTLAVPDPVSGTPSSVAV
+WEYAPVPEAAPGSPSGLKGDTAAAPLVFVHGFRGDHHGLALLADALPEHPIHSIELPGFG
+ASEPFPHAEHTVAHHADAVAAVVAALGLPAAPVLVAHSYGTTVAAELVARDPSRWGRLAL
+LNPIAEPALQASASVTSRVLAAVAEGYYEVAARLPERSARLLLGAPPVVWVTTLAMTRTR
+DRDVLAYTHDQHRRHFSGFASARMLSEAYRASSTGSVADVAARLTLPVLLVAGREDPLGS
+VPAQEALAAAIDAGGGTAELHVLDGVGHLLHYERPAACAALIRDWLRRAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001034.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001034.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f95241e679e39ccc7c9be2f3dc6196b25f9c574
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001034.fa
@@ -0,0 +1,40 @@
+>PROKKA_01235
+MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK
+VAVETLTTTGLVQVAGEVNTSAYVEIPKIVRETILDIGYDSSANGFDGAQCGVNISIGQQ
+SSDIFAGVSRSLETREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL
+TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEEH
+VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK
+IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL
+>PROKKA_00954
+MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK
+VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ
+SSDIFAGVSRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL
+TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEEH
+VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK
+IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL
+>PROKKA_01653
+MTDAAQPSPARHADPYTGVGGGELRLFTSESVTEGHPDKICDQISDAILDAILAADPAAK
+VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ
+SSDIFAGVTRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL
+TAVRRQENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHDWVGQEQLRKDVEEH
+VIRPVIERSGLDTSGMRVIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTAVVPEER
+IIQAVNEVFDLRPAAIVKELNLLRPIYRKTAANGHFGRDDADFTWERTDRVERLRAAAGL
+>PROKKA_01550
+MSDTPTPTPSAAAQPYRGVGGGDLRLFTSESVTSGHPDKMCDQISDAILDAILAADPSAK
+VAVETLSTTGLVQVAGEVNTSAYVEIPHIVRETILDIGYDSSANGFDGAQCGVNVSIGQQ
+SSDIFAGVSRSLEAREQGSADEVDEQGAGDQGIMFGYATNETPSYMPTPIYLAHRLSERL
+TAVRRQENTPMPYLLPDGKTQVTVGYDADHRPRTVETVVVSTQHHDVVTQEQLRADVAEH
+VIRPVIERSGLDVSNARFIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYALRWVAKNVVAAGLAGRAEFQVAYAIGSARPVGLYVDTFGTNAVPEET
+IIAAVNEVFDLRPAAIVKSLNLLRPIYRKTAAHGHFGRDDADFTWERTDKVEELRRAAGV
+>PROKKA_01193
+MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK
+VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ
+SSDIFAGVSRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL
+TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEKH
+VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK
+IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001036.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001036.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88bf041c0cc389521560330f33dc3605a8896d0c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001036.fa
@@ -0,0 +1,21 @@
+>PROKKA_01237
+MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIEAGLLESHEAVEATPEAELAAEDFGDFSLPGEDDPFATLESSDAHQPT
+GDPAAIEEAAETVRAEEGISEDAPEA
+>PROKKA_00956
+MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIEADLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLESSDAHQPM
+GDPAAIEEAAETVRAEEGTSEDATEA
+>PROKKA_01651
+MTEQYDGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIETDLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLEPSDAGQPV
+GDPEAIEEAAEAVRAEEGTSEDAPEA
+>PROKKA_01548
+MTPPPPPDGPPPAAPCVPTHGQKTTREQTLETYVTDQYEGIVNPPIDSLLERVDSKYALV
+LFAAKRARQINAYYSQLHEGLFEYVGPLVDTQLNEKPLSIAMREIESDMLVMAETAAVEP
+AIELAEEEFGDFALPGDDDPFVAEPTAEGVSPEEYGAPVTTGDDDAVEDILSGADVADED
+A
+>PROKKA_01195
+MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIEADLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLESSDAHQPM
+GDPAAIEEAAETVRAEEGTSEDATEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001037.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001037.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02fe253121dd3543eb787842fb1d47c111dbab87
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001037.fa
@@ -0,0 +1,25 @@
+>PROKKA_01238
+MTDTFDPGPAPAVPVARTVVQERPPGPGVTVLAGPTAVGKGTVSAYVREHYPEAWLSVSA
+TTRPARPGEEDGVHYYFTTPEEFDSLVEADEMLEWAVVHGVHRYGTRRDRVMEAVAQGRH
+VLLEIDLQGARQVRRALPEATFVFLAPPSWEELVSRLLGRGTESPEEQRRRLETARLELA
+AEPEFDAVVVNDRVERAAEELVRLMGLDPERRPTEA
+>PROKKA_00957
+MTDTFDPGPAPAVPVARTAVQERPPGPGVTVLAGPTAVGKGTVSAYVREHYPEAWLSVSA
+TTRPARPGEEDGVHYYFTTPEEFDSLVEADEMLEWAVVHGVHRYGTRRDRVMEAVAQGRH
+VLLEIDLQGARQVRRALPEATFVFLAPPSWEELVSRLLGRGTESPEEQRRRLETARLELA
+AEPEFDAVVVNDRVERAAEELVRLMGLDPERRPTEA
+>PROKKA_01650
+MTDAFDHGPAPAVPVARTAAQERRPGPGVTVLAGPTAVGKGTVSAYVREHYPQAWLSVSA
+TTRPARPGEEDGVHYYFTTPEEFDSLVAADEMLEWAVVHGVHRYGTRRDRVMEAVAQGRH
+VLLEIDLQGARQVRESLPEATFVFLAPPSWEELVSRLVGRGTEGPEEQRRRLDTARLELA
+AEPEFDAVVVNDRVERAAEELVRLMGLDPEHSSPEA
+>PROKKA_01547
+MSDLSDLGPAPSVPGERAPSRPPAPGAGVTVLAGPTAVGKGTVSAYIREHYPQAWLSVSA
+TTRAPRPGEEDGVHYFFTTPEEFDELVAGDQMLEWAVVHGRNRYGTRRDRVAEAVAAGRH
+VLLEIDLQGARQVRRTLPEATFVFLAPPSWDELVSRLVGRGTEGPEEQRRRLETARLELA
+AEPEFDAVVVNDAVERAAAELVKLMGIDPHDAPASA
+>PROKKA_01196
+MTDTFDPGPAPAVPVARTAVQERPPGPGVTVLAGPTAVGKGTVSAYVREHYPEAWLSVSA
+TTRPARPGEEDGVHYYFTTPEEFDSLVEADEMLEWAVVHGVHRYGTRRDRVMEAVAQGRH
+VLLEIDLQGARQVRRALPEATFVFLAPPSWEELVSRLLGRGTESPEEQRRRLETARLELA
+AEPEFDAVVVNDRVERAAEELVRLMGLDPERRPTEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001043.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001043.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bfdecbbb3ecc44e55742c4aa26e155d87431c259
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001043.fa
@@ -0,0 +1,35 @@
+>PROKKA_01245
+MRHLLSTADLSRADALAVLDTAEEMAAVNQREVKKLPALRGRTVVNLFLEDSTRTRISFE
+AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV
+RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGRDLTGMRVVIVGDILHSRVAR
+SNVWLLSTLGAQVTLAAPPTLLPVGVAAWPCQVTYSLDEALDAGPDAVMMLRVQAERMGG
+AFFPSAGEYTRTWGLTDDRFARLTAGRGALLDEPVVMHPGPMNRGLEISPAAADSPRNTA
+LEQVANGVSVRMAVLHLVLNHDQEVRP
+>PROKKA_00964
+MRHLLSTADLSRADALAVLDTAEEMAAVNQREVKKLPALRGRTVVNLFLEDSTRTRISFE
+AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV
+RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGRDLTGMRVVIVGDILHSRVAR
+SNVWLLSTLGAQVTLAAPPTLLPVGVAAWPCQVTYSLDEALDAGPDAVMMLRVQAERMGG
+AFFPSAGEYTRTWGLTDDRFARLTAGRGALLDEPVVMHPGPMNRGLEISPAAADSPRNTA
+LEQVANGVSVRMAVLHLVLNHDQEVRP
+>PROKKA_01643
+MRHLLSTAGLSRADALAVLDTAEEMDAVNRREIKKLPALRGRTVVNFFFEDSTRTRISFE
+AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV
+RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGRDLAGMHVVIVGDILHSRVAR
+SNVWLLATLGAKVTLAAPPTLLPVGVSAWPCEVTYSLDEALDARPDAVMMLRVQAERMGG
+AFFPSAGEYTRTWGLTDERFARLTAGSGALLSEPVVMHPGPMNRGLEISPAAADSPRNTA
+LEQVANGVSVRMAVLHLVLNHDQEVRP
+>PROKKA_01540
+MRHLLDTADLTRAEALAVLDTAEEMAAVNAREVKKLPSLRGRTVVNLFLEDSTRTRISFE
+AAAKRLSADVISFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAAAQLAASGWV
+DSAVVNAGDGTHAHPTQALLDAFTLRHHLAAHDGVAPTGTDLTGMHVVIVGDILHSRVAR
+SNVWLLTLLGARVTLAAPPTLLPVGVASWPARVTYSLDEALADAPDAVMMLRVQAERMGG
+AYFPSAGEYTRLWGLNPARFERLTRQSGSRLDTPLVMHPGPMNRGLEICDAAADSPQNTV
+LEQVANGVSVRMAVLHLVLNQDPALAPQEARP
+>PROKKA_01203
+MRHLLSTADLSRADALAVLDTAEEMAAVNQREVKKLPALRGRTVVNLFLEDSTRTRISFE
+AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV
+RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGQDLTGMCVVIVGDILHSRVAR
+SNVWLLSTLGAQVTLAAPPTLLPVGVAAWPCQVTYSLDEALDAGPDAVMMLRVQAERMGG
+AFFPSAGEYTRTWGLTDDRFARLTAGRGALLDEPVVMHPGPMNRGLEISPAAADSPRNTA
+LEQVANGVSVRMAVLHLVLNHDQEVRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001045.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001045.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0ca4bc219d471d015b3473ef8ebec00c4cac2b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001045.fa
@@ -0,0 +1,20 @@
+>PROKKA_01247
+MTERASAGSAAKRGTTARSRSRQRAVEILFEAEQRGSSALEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAISEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA
+>PROKKA_00966
+MTERASAGSAAKRGTTARSRSRQRAVEILFEAEQRGSSALEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAISEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA
+>PROKKA_01641
+MTEPASAASGAKRGTTARSRSRQRAVEILFEAEQRGATVAEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAVSEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA
+>PROKKA_01538
+MTDTPSASDAKRGTTARSRSRQRAVEILFEAEQRGTDVLQGIRTRRESTDLQVNAYTQRL
+VEGVVADQERVDEALTSYSRGWSLDRMPAVDRAILRVGAWELLFEDEVPDAVAVSEAVAL
+AAALSTDESPEFVNGLLGRLQQVKPTLLA
+>PROKKA_01205
+MTERASAGSAAKRGTTARSRSRQRAVEILFEAEQRGSSALEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAISEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001046.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001046.fa
new file mode 100644
index 0000000000000000000000000000000000000000..99ced38accdaff9d2ca145bee9971e2349d31aaa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001046.fa
@@ -0,0 +1,25 @@
+>PROKKA_01248
+MTVRETDREHTHVATSNDIKNGAVLKLEGQLWNVTEFQHVKPGKGGAFVRTKMKNITTGK
+VVDKTFNAGAKVEFATVDRSDYQYLYQDGADYVFMDVKDYDQITVPGAVVGDAAKYMLEN
+TQVVIALHEGTPLYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQ
+GTRVKVDTRTGDYLGRVND
+>PROKKA_00967
+MTVRETDREHTHVATSNDIKNGAVLKLEGQLWNVTEFQHVKPGKGGAFVRTKMKNITTGK
+VVDKTFNAGAKVEFATVDRSDYQYLYQDGADYVFMDVKDYDQITVPGAVVGDAAKYMLEN
+TQVVIALHEGTPLYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQ
+GTRVKVDTRTGDYLGRVND
+>PROKKA_01640
+MATSNDIKNGAVLKLEGQLWNVIEFQHVKPGKGGAFVRTKMKNITTGKVVDKTFNAGAKV
+EFATVDRSDYQYLYQDGSDYVFMDVKDYDQITVSESVVGDAAKYMLENTQVVIALNEGTP
+LYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQGTRVKVDTRTGD
+YLGRVND
+>PROKKA_01537
+MATTNDIKNGSVLNLEGQLWNVIEFQHVKPGKGGAFVRTKMRNITSGKVVDKTFNAGTKV
+EFATVDRSDYQYLYQDGEDYVFMDVKDYDQITVPAAVVGDAAKYMLENTQVVIAMNEGTP
+LYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQGTRVKVNTTNGE
+YLGRVND
+>PROKKA_01206
+MTVRETDREHTHVATSNDIKNGAVLKLEGQLWNVTEFQHVKPGKGGAFVRTKMKNITTGK
+VVDKTFNAGAKVEFATVDRSDYQYLYQDGADYVFMDVKDYDQITVPGAVVGDAAKYMLEN
+TQVVIALHEGTPLYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQ
+GTRVKVDTRTGDYLGRVND
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001049.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001049.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6bfbd4b33550d6d28fb34e0642fbc77872864219
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001049.fa
@@ -0,0 +1,40 @@
+>PROKKA_01251
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGRTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELDGLARNAALTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLGELGVRIVSHTVAFGEAALPEGHPF
+PVPEDEARLDADPVRCLDPQTSAAMVAEVDDAHRAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGLATAARRGSAAHDGIARGADGRPRRTSDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAMLEKFGGDSVAETRRNLEAFQAAVPALPEPAADVVADGPMGDPLP
+>PROKKA_00970
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGRTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELDGLARNAALTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLGELGVRIVSHTVAFGEAALPEGHPF
+PVPEDEARLDADPVRCLDPQTSAAMVAEVDDAHRAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATAARRGTAAHDGIARGADGRPRRTTDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAMLEKFGGDSVAETRRNLEAFQAAVPALPEPGADVVADGPMGDPLP
+>PROKKA_01637
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGLTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELEGLARNAALTRPRPGHADLTG
+MQKYGFDDARPLLERASARETAARVALGTVARAFLAQLGVRIVSHTTAFGEAALPEGHPF
+PLPEDQDRLDADPVRCLDPETSAAMVAEVDDAHKAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATAARRGSAAHDGIVRGEDGRPRRTSDRAGGIE
+AGMSTGEVLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAVLEKFGGDSVGETRRNMAAFQAAVPALPEPSADADASGHMGDPLQ
+>PROKKA_01534
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQEIQDALARRRLGYGRGARMKFEQDAVTVL
+GGIRHGLTLGSPVAIQVGNTEWPKWEQVMAADPVPEEELAGLARNARLTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLAELGVRIVSHTVAFGEAALPEPHAF
+PVPEDQDRLDADPVRCIDPETSAAMVAEVDAAHKEGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATASRRGSAAHDGIARGADGRPRRTSDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAVLEKFGGDSVAETRRNMEAFTAALPALPDAPAEQPAADHMGDPLQ
+>PROKKA_01209
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGRTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELDGLARNAALTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLGELGVRIVSHTVAFGEAALPEGHPF
+PVPEDEARLDAEPVRCLDPQTSAAMVAEVDDAHRAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATAARRGTAAHDGIARGADGRPRRTTDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAMLEKFGGDSVAETRRNLEAFQAAVPALPEPGADVVADGPMGDPLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001050.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001050.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c81900fea80293b66be444802d457343786d7013
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001050.fa
@@ -0,0 +1,35 @@
+>PROKKA_01252
+MRPVLRAAVLGRPIAHSLSPVLHAAAYRVLGLDVDYGRRDLGEDEVLAFAAEHLGAPGAA
+DGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANTLVRDHPAAPGVVHAEN
+TDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLGANAVLFGVRDAARAAE
+VTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAAHVPADAALPPLLDAAY
+DPWPSVLAAAWSREGGPVASGLSMLLHQGVEQVRLFTARPRAAAGMPEPDWAAVTRAAAD
+ALGPAAG
+>PROKKA_00971
+MRPTLRAAVLGRPIAHSLSPVLHAAGYRVLGLDVDYGRRDLGEDEVLAFAAEHLGAPGTA
+DGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANTLVRDHPSAPGVVHAEN
+TDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLGADAVLFGVRDPARAAE
+VTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAAHVPAGAALPPLLDAAY
+DPWPSVLASAWSREGGPVASGLSMLLHQGIEQVRLFTARPRAAAGMPEPDWAAVTRAAAD
+ALGPAAG
+>PROKKA_01636
+MGAPSDVRAEASAGAPAAPRLRAAVLGRPIAHSLSPVLHGAAYGVLGLDVDYRRRDLGED
+EVGAFVAGRLGAPRTADGGDAAARGEDWLGCSVTMPLKRAVVGCAGRVSERVRLLGTANT
+LVRDHPEHPGLVSAENTDVDGILGALASAGLAERGSGGAVGILGNGGTATAAVLAAATLG
+ADEVVFGVRDAARAAEVTALADALGLAWRTVGQPELAAAAPGLRAVVATLPPRAADPLAA
+HVPVGAALPPLLDAAYDPWPSALASAWTEAGGAVASGLSMLLHQGVEQVRLFTARPRAAA
+GMPEPDWAAVTRAAARALGPAAG
+>PROKKA_01533
+MAGATFRAAVLGRPIAHSLSPVLHAAAYRALGLDVDYGRADLGEEEVGPWLAARLGAPGS
+AARPAGPSGGDWLGVSVTMPLKPAVVPLADELSARVRELGVANTLVRDHPDHPGSLLAHN
+TDVDGIVRALAERGLDAGAGGGAVGILGNGGTATAAVAAASLLRAETVVLGVRDAGRARD
+VVALADRLGLGVRVEAQDALVRQAADLRAVVATLPPRAADPLADKVPAGVLPPLLDAAYD
+PWPSAIARAWSAAGGGVASGLSMLLHQGVEQVRLFTERPRRAAGGVEPDWAEVTAAASRA
+LGLPGR
+>PROKKA_01210
+MRPTLRAAVLGRPIAHSLSPVLHAAGYRVLGLDVDYGRRDLGEDEVLAFAAEHLGAPGTA
+DGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANTLVRDHPSAPGVVHAEN
+TDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLGADAVLFGVRDPARAAE
+VTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAAHVPAGAALPPLLDAAY
+DPWPSVLASAWSREGGPVASGLSMLLHQGIEQVRLFTARPRAAAGMPEPDWAAVTRAAAD
+ALGPAAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001053.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001053.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7883be7b6c95739d2905151b740ed9b77c31f199
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001053.fa
@@ -0,0 +1,19 @@
+>PROKKA_01256
+MLRSLLLVGAGAASGWFAHRALGDRAHPATDATDAPTSDPGSAGGRAGFSARLDPERLAR
+QAGEAAADAAAAALQDGARRLAERVRAEAPWAAPYLPHTGPIISGETVEPPSHGAARPQT
+TTTQKDTPA
+>PROKKA_00975
+MLRSLLLVGAGAASGWFAHRALGDRAHPATDATDAPTSDPGSAGGRAGFSARLDPERLAR
+QAGEAAADAAAAALQDGARRLAERVRAEAPWAAPYLPHTGPIISGETVEPPSHGAARPQT
+TTTQKDTPA
+>PROKKA_01632
+MLRSLLLVTAGAASGWLAHRALGDRAAADAAPGRSDAGPQARPGRARLDPEHLARQAGQA
+VGDAAAAALNEGARRLADRVRAEAPWAAQFLPHTGPIIEGETVEPPSPSGPGGPRPQTTI
+PTTTTQKDTHA
+>PROKKA_01529
+MSRITSLLLVGAGTAAGWIAHRAVESGRRAVDQEAGRRLQETLDPTRLGRSAGQAVGDAA
+AEALAQSAQAFTERLRADAPPWVSQLIGPPRDTIEGEALDTPDTTATPSSARKDPHA
+>PROKKA_01214
+MLRSLLLVGAGAASGWFAHRALGDRAHPATDATDAPTSDPGSAGGRAGFSARLDPERLAR
+QAGEAAADAAAAALQDGARRLAERVRAEAPWAAPYLPHTGPIISGETVEPPSHGAARPQT
+TTTQKDTPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001056.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001056.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b23c2b6d8d47fb75ebc5ed7298c4746d8f35726
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001056.fa
@@ -0,0 +1,45 @@
+>PROKKA_01259
+MDDLFSAAHTGADDDGPAGTVAAPHPGAPLAVRMRPRTLDDVLGQRHLMRPGSPLRKLAE
+PDPDSAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRE
+RDLYGRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLL
+TLRPLTDDDIVGLLDRAVTQERGLNGAVVLEDDARDYLVRMAGGDARRALTVLEAAAGVA
+LDKAREAGRAGEGAVAVTEEDAAQAMDHHVQRYDKDGDQHYDVISAFIKSIRGSDVDASM
+HYLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVATAQAVQLIGMPEGRIILAQ
+AVTHLATAPKSNASYTAVNEAIADVRAGHTGAVPAHLRDAHYPGAAALGHGQGYVYSHDE
+PHAVARQQYAPDPLVGRDYYRPKPIGHEKRLTEQVAALRRIIRGD
+>PROKKA_00978
+MDDLFSAAHNGADDDGPAGTVAAPHPGAPLAVRMRPRTLDDVLGQRHLMRPGSPLRKLAE
+PDPDSAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRE
+RDLYGRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLL
+TLRPLTDDDIVGLLDRAVTQERGLNGAVVLQDDARDYLVRMAGGDARRALTVLEAAAGVA
+LDKAREAGRAGEGAVAVTDEDAAQAMDHHVQRYDKDGDQHYDVISAFIKSIRGSDVDASM
+HYLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLIGMPEGRIILAQ
+AVTHLATAPKSNASYTAVNEAIADVRAGHTGAVPAHLRDAHYPGAAALGHGQGYVYSHDE
+PHAVARQQYAPDPLVGRDYYRPKPIGHEKRLTEQVAALRRIIRGD
+>PROKKA_01628
+MADLFSAAHESDDDGPSGTVAAPRASAPLAVRMRPRTLEEVLGQRHLMRPGSPLRKLAEP
+DPGSPAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRER
+DLYDRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLLT
+LRPLTDEDIVGLVERAVADERGLNGAVDLADDARDYVVRMAGGDARRALTVLEAAAGVAL
+DKARQAGADEDAGGDGGARAGAAAPVTVTEEDAAQAMDHHVQRYDKDGDQHYDVISAFIK
+SIRGSDVDAALHWLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLI
+GMPEGRIILGQAVTHLATAPKSNASYAAVNEALADVRAGGTGQVPPHLRDAHYPGAAALG
+HGKGYVYSHDEPHAVARQQYAPDPLVGKDYYRPKPIGAEKRLVDQVAALRRITRGE
+>PROKKA_01526
+MDDLFSAAHADPDDDAPVTASGRARASAPLAVRMRPRSLDEVLGQAHLKQPGSPLRKLAE
+PAASAQAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQARR
+EREMYDRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLL
+LTLRPLDDTDLAALVDRAVADERGLNGTVEPTPNARDYVVRMAGGDARRALTVLEAAAGV
+ALDRAEARGETTGPGSAPVEVTEEDAAQAMDAQVQRYDKDGDQHYDVISAFIKSIRGSDV
+DAAMHWLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLIGMPEGRI
+VLGQAVTHLATAPKSNASYTAVNEAIADVRAGGTGVVPAHLRDSHYPGAKALGHGQGYVY
+SHDEPHAVARQQYAPDPLVGRDYYRPKPIGHERQLGPQVDALRRIIRGD
+>PROKKA_01217
+MDDLFSAAHNGADDDGPAGTVAAPHPGAPLAVRMRPRTLDDVLGQRHLMRPGSPLRKLAE
+PDPDSAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRE
+RDLYGRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLL
+TLRPLTDDDIVGLLDRAVTQERGLNGAVVLQDDARDYLVRMAGGDARRALTVLEAAAGVA
+LDKAREAGRAGEGAVAVTDEDAAQAMDHHVQRYDKDGDQHYDVISAFIKSIRGSDVDASM
+HYLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLIGMPEGRIILAQ
+AVTHLATAPKSNASYTAVNEAIADVRAGHTGAVPAHLRDAHYPGAAALGHGQGYVYSHDE
+PHAVARQQYAPDPLVGRDYYRPKPIGHEKRLTEQVAALRRIIRGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001057.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001057.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7fdbf40cf200545a7617102f224d7fd15a0e280d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001057.fa
@@ -0,0 +1,25 @@
+>PROKKA_01260
+MSPAAPRADHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD
+AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD
+PAPESAAALAALDHGDGRPAGPDRTALEGRLLWTRCATGVADSPLTPARLDRALGVRGTA
+RNLTTVRVLAGLPAGDRPRRTARGASGDVDIRGTPRAGRDVTVRSHPCDGVTPSSASLP
+>PROKKA_00979
+MSPAAPRTDHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD
+AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD
+PAPEAAAALAALDHGDDRPAGPDRTALEGRLLWMRCAAGVADSPLTPARLDRALGVRGTA
+RNLTTVRVLAGLPSED
+>PROKKA_00445
+MSEHPASPTHVLLLRAVNVGGRNRVPKADLAELAAEAGLADVAVHLNSGNVLGTPDTGDH
+VDDVAARLRALLAERLGVDTSVHAAARTELSALVDGLLASDLLAPGETLDSVDPKTVHLV
+LLDTVPHPEAGEALAAVDAGDDRAVVVGRGVWVRYAGPSHSSHLGLPRIERAASGDAPPA
+QRRVGTARNLATVRVLAGR
+>PROKKA_01525
+MSRAAPRTDHTHVLLLRGINVGRSNRVSNARLAAWAEAARARDVTTHLASGNVLFRLPDA
+DDDAGPAFLRAFRDAALADDGPDVPLILTTPAELRGALAMHDRLPWSGGEAKLTQLTVLA
+ESPRDGAAEALAGLDHGSGRAAGPDRSALEGRFLWIRSPGRISDSPLTPARLEKALGVTG
+TARNLATVRVLAGMA
+>PROKKA_01218
+MSPAAPRTDHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD
+AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD
+PAPEAAAALAALDHGDDRPAGPDRTALEGRLLWMRCAAGVADSPLTPARLDRALGVRGTA
+RNLTTVRVLAGLPSED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001059.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001059.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff20ff0164c453a8c6dccc468ae68eaa2387c23e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001059.fa
@@ -0,0 +1,20 @@
+>PROKKA_01262
+MRAVLQRARSASVTVDGKVVGSFEGEGLVILLGVTVDDTEAEAVQVARKVAGLRMLDGER
+SLTDAGAPALVVSQFTLYGDVRKGRRPSWTRAAKGNQAEPLYERFTAELEAAGVRVERGV
+FGAKMDVSLTNSGPFTLIVDSDELAGPRRG
+>PROKKA_00981
+MRAVLQRARSASVTVDGKVVGSFEGEGLVILLGVTVDDTEAEAVQVARKVAGLRMLDGER
+SLTDAGAPALVVSQFTLYGDVRKGRRPSWTRAAKGNQAEPLYERFTAELEAAGVRVERGV
+FGAKMDVSLTNSGPFTLIVDSDELAGPRRG
+>PROKKA_01626
+MRAVLQRARSASVTVAGEVVGSFEGAGLVILLGVSTQDTGAEADALAAKVATLRMLDGEA
+SLVSAGAPALVVSQFTLYGDVRKGRRPSWTGAARPEHAEPLYERFAAGLEAEGVRVERGV
+FGAQMDVTLVNDGPFTLVVDTADLTGPRRG
+>PROKKA_01522
+MRAVLQRARSASVTVDGEVVGAFDGEGLVILLGVSTEDTEAEAVQLAAKVAGLRILDGER
+SLVEASAPALVISQFTLYGDVRKGRRPSWSAAARGDQAEPLYECFAGELGTAGVRVERGV
+FRADMDVALTNAGPFTLVVDTADLAGPRRG
+>PROKKA_01220
+MRAVLQRARSASVTVDGKVVGSFEGEGLVILLGVTVDDTEAEAVQVARKVAGLRMLDGER
+SLTDAGAPALVVSQFTLYGDVRKGRRPSWTRAAKGNQAEPLYERFTAELEAAGVRVERGV
+FGAKMDVSLTNSGPFTLIVDSDELAGPRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001066.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001066.fa
new file mode 100644
index 0000000000000000000000000000000000000000..553b60ae1e8bfb33024e909872ab07e44cceecf1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001066.fa
@@ -0,0 +1,35 @@
+>PROKKA_01269
+MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF
+TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG
+VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL
+AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP
+LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL
+>PROKKA_00988
+MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF
+TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG
+VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL
+AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP
+LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL
+>PROKKA_01618
+MNRFADWGNALYSGRVSYPFVQRWRLWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF
+TVSQTAATDIAAGERAVTDVLAGGHATVTNIAPGTVRVQTEQLDDAQTRQVAANLQDAYG
+VGQDQVTSTFVGPTWGAAVSQQALLGLVIFVVLVTLFMAFYFRTWKMSLAAVIGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGQEEDPERTFEQNVNL
+AVNQTLVRSITTSIVGILPVGSILFIGAGLLGAGTLRDIALAIFVGIIVGTLSTLFIQAP
+LYALLRRGDEDVRDHDARAAARAARENRGDTVTDPDVAPWEDGARL
+>PROKKA_01513
+MNRFADWGNALYSGRISYPFVRKWKTWFLIAAALLAVAFGLTALRGGFNLGIDFRGGSEF
+TVSDAASSELDPGRAAVTDVVAGAEPTVTQVAPGTMRVQTEQLDDAQTRQVAQNLQQAYG
+VTGDHVTSTFVGPTWGQAVSQQAVIGLVIFVVLVTLFMALYFRTWKMSLAAVVGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTRGVEEDPDRTFDGSVNL
+AVNQTLVRSITTSIVGLLPVGSILFIGAGLLGAGTLRDISLAIFVGIIVGTLSTLFIQAP
+LYALLRRGDADVVAHDARVGADHDEREQEEDLADARGAVL
+>PROKKA_01227
+MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF
+TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG
+VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL
+AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP
+LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001067.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001067.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e6827620c47dc14c56fda5880562113fb88e1c44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001067.fa
@@ -0,0 +1,60 @@
+>PROKKA_01270
+MAKRTPTGSAGRTLAWLAALLVVLAAILGGGVASGAASWAPKLALDLEGGTQMVLAPQTS
+TGESVTPEQLDQAVEIIRQRVDGSGVAEAEVATQGSQNVVVSLPGVPDEETRRLIQASAD
+MQFRPVLQSGPGEATPEDQRLPEDQLPKPDGEPADAYDPNWVTPALLAEFQATDCTAPRD
+PAAPPPPSDRAIVACQPSEELADGAVTPAQKYILGPVVIPGTQIKGASNGMAQAQGGVST
+NQWVVNIEFDEEGTKAFTEVTQKLTPYPEGDPRKQFAILLDGDVISAPQSNVVITNGSAQ
+ISGPTLNEQTTAQLAEQLNYGSLPISFSIESEQQISATLGRDQLFWGLIAGLIGLGLVAV
+YQFFQYRALGLLTFASIIVAGVLTWLTIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV
+YFERIKDELRAGHTVPVAVHEGWKRARRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG
+LTAIADLIVVFMFTHPLMVLLAQTRFVGEGHPMSGLDPSLLGGPSLYQGAGRFREPAHAP
+RTGLPAEASDEPADADDAAAADAPRPLAATGAPRAGSSARGGRRSRTAPPMTIAERRRAE
+RRRQEEDQ
+>PROKKA_00989
+MAKRTPTGSAGRTLAWLAALLVVLAAILGGGVASGAASWAPKLALDLEGGTQMVLAPQTS
+TGESVTPEQLDQAVEIIRQRVDGSGVAEAEVATQGSQNVVVSLPGVPDEETRRLIQASAD
+MQFRPVLQSGPGEATPEDQRLPEDQLPKPDGEPADAYDPNWVTPALLAEFQATDCTAPRD
+PAAPPPPSDRAIVACQPSEELADGAVTPAQKYILGPVVIPGTQIKGASNGMAQAQGGVST
+NQWVVNIEFDEEGTKAFTEVTQKLTPYPEGDPRKQFAILLDGDVISAPQSNVVITNGSAQ
+ISGPTLNEQTTAQLAEQLNYGSLPISFSIESEQQISATLGRDQLFWGLIAGLIGLGLVAV
+YQFFQYRALGLLTFASIIVAGVLTWLTIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV
+YFERIKDELRAGHTVPVAVHEGWKRARRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG
+LTAIADLIVVFMFTHPLMVLLAQTRFVGEGHPMSGLDPSLLGGPSLYQGAGRFREPAHAP
+RTGLPAEDSDEPADAAAADAPRPLVATGAPRAGSSARGGGRRSRTAPPMTIAERRRAERR
+RQEEDQ
+>PROKKA_01617
+MAKRTPTGSARRTLAWLAALTVALTAILGWGVASGAASWAPKLALDLEGGTQMVLAPETA
+TGESVTSEQLDQAVEIIRQRVDGSGVAEAEVATQGAENVVVSLPGVPDEETRRLIQASAD
+MQFRPVLQSGSGEATPEDQRLPEDQLPQPEGEPADAYDPNWVTPALLTQYQALDCAAPRD
+PAAPPPPSDQAIVACERPADLGEGVQTPARKYILGPVVIPGTQIEGATNGLAQAQSGVST
+NQWVVNIDFDEEGAKTFSEVTQKLTPYPDGDPRKQFAILLDGDVISAPQSNAVITAGSAQ
+ISGPTLNEETTAQLAEQLNYGSLPISFSIESEQQISATLGQDQLFWGLIAGLIGLALVAV
+YQFFQYRALGLLTFASIVVAGILTYLAIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV
+YFERIKDELRAGHSVPMAVHEGWKRAKRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG
+LTAIADLIVVFMFTHPIMVLLAQTRFVGGGHRMSGLDPSLLDRQALYQGAGRLREPGGAR
+RTGSTAAPAADVAADDGARVPVPVGAAPADEASGEEGTATRGLRRPRPAQPMTIAERRRA
+ERRRQEEDQ
+>PROKKA_01512
+MAKTSPTRAAGRTLAWLAALIVALTAILGLGVASGQASWAPKLALDLEGGTQMVLAPTTA
+SGEQATPEQLQQAVEIIRQRVDGSGVAEAVVATQGDQNVVVSMPGVPDEETRRLIQASAD
+MQFRPVLQAVPGGQPTPQDQLVPKDQFPTPSAEPTDAYDPNWITPELADEFQRTDCTLPR
+DPNAAPPATDRAVVVCEPQQETPAGTMPATKYIVGPVVIPGTMIEKASNATAQSQTGVTT
+NEWVVNIDFDGEGTKRFTEVTQKLTPFAEGDPRKQFAIMLDGQVIAAPQSNVVITGGQAQ
+ISGPGFTEESTAQLAEQLNYGSLPISFTIESEQQISATLGRDQLFWGLIAGLIGLALVAV
+YQFFQYRALGLLTFASIVVAGALTYLAIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV
+YFERIKDELRSGHTLDAALHEGWKRAKRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG
+LTAIADLLVVFMFTHPLMVLLSRTDFVGGGHPMSGLDPRVLGVEPALYQGAGRFREPAAA
+RAARGGSHAADDDDAGSSAARRGRRSEQPMTIAERRRAERAGAAQTPAAQTPAGSAPAAD
+TEEDAL
+>PROKKA_01228
+MAKRTPTGSAGRTLAWLAALLVVLAAILGGGVASGAASWAPKLALDLEGGTQMVLAPQTS
+TGESVTPEQLDQAVEIIRQRVDGSGVAEAEVATQGSQNVVVSLPGVPDEETRRLIQASAD
+MQFRPVLQSGPGEATPEDQRLPEDQLPKPDGEPADAYDPNWVTPALLAEFQATDCTAPRD
+PAAPPPPSDRAIVACQPSEELADGAVTPAQKYILGPVVIPGTQIKGASNGMAQAQGGVST
+NQWVVNIEFDEEGTKAFTEVTQKLTPYPEGDPRKQFAILLDGDVISAPQSNVVITNGSAQ
+ISGPTLNEQTTAQLAEQLNYGSLPISFSIESEQQISATLGRDQLFWGLIAGLIGLGLVAV
+YQFFQYRALGLLTFASIIVAGVLTWLTIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV
+YFERIKDELRAGHTVPVAVHEGWKRARRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG
+LTAIADLIVVFMFTHPLMVLLAQTRFVGEGHPMSGLDPSLLGGPSLYQGAGRFREPAHAP
+RTGLPAEDSDEPADAAAADAPRPLVATGAPRAGSSARGGGRRSRTAPPMTIAERRRAERR
+RQEEDQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001069.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001069.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef3ac7737dfbbfe92c83366853b257af4340db17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001069.fa
@@ -0,0 +1,25 @@
+>PROKKA_01273
+MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLSTLHEGRPGAVQTHLVVKEDALTLY
+GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA
+RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT
+VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR
+>PROKKA_00992
+MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLATLHEGRPGAVQTHLVVKEDALTLY
+GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA
+RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT
+VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR
+>PROKKA_01614
+MIASLSGTVEHVALDRAVIAVGGFGVQFSATPQTLATLHEGRTGSVQTHLVVKEDALTLF
+GFADRHEREVFEVLITANGVGPRLALAVLSVHHPEAVRRAVTEEDENALTRVPGVGPKLA
+RKIIVELSGRLTPTGEQVPAPEEPAAPETPEAAWHADVVQAMTGLGWSEKEALKAVEATV
+AARPELDEARDVAALLRATLRDVGTAGTVRGGR
+>PROKKA_01509
+MIASLSGTVEHVGLDHAVIAVGGVGLSFSATPQTLSHLHEGRDGAVQTHLVVKEDSLTLF
+GFADRAEREVFEVLLGANGVGPRLALAILAVHRPEAVRRAVTDEDEKALTLVPGIGPKMA
+RKIIVDLAGRLAPTGEVEPEAAVVEPEAAADAWHADVVQAMTGLGWSEKEAAKAVAATVA
+THPDVDASGDVAALLRATLRDVGAAAAVRGGRRA
+>PROKKA_01231
+MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLATLHEGRPGAVQTHLVVKEDALTLY
+GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA
+RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT
+VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001072.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001072.fa
new file mode 100644
index 0000000000000000000000000000000000000000..59690e06851355fe1d8e2dc3284e554fdbc88367
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001072.fa
@@ -0,0 +1,65 @@
+>PROKKA_01276
+MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAAT
+APTFENTVRALELSGQLLRRSAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPR
+LAARVASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAREELRGINTELASLSAAYTRR
+LVADTAARAVLVTDRERLAGLSEDDLAAAAGAAAEAGHGDGDAAAGPWLLTLSLFTSQPW
+LASLQDEGMRREVFEASTGRGGSGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRA
+APSTAAVEELLAAMAPRAMANARADAATAAAHAGRADAEVAPWDWPALSAGYAREEFAVD
+ADALRPYFELDRVLTEGVFAAATALYGLTFAERPELARHLYRPGIRVFEVTGEDGAGVGL
+FVADLFARPTKSGGAWMHTVRDRADALGERPVVFTTMNVPAPAAGRPALLTLDETTTLFH
+EFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVETGEPLPA
+GTLERLEAADLWGEGHRTVEYLGATLVDWAWHSLTEETVDAATADPAAFERRVLTEAGID
+PDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLDADAVEWFREHGGMTRENGRRFADEL
+LSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA
+>PROKKA_00995
+MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAAT
+APTFENTVRALELSGQLLRRSAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPR
+LAARAASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAREELRGINTELASLSAAYTRR
+LVADTAARAVLVTDRERLAGLSEDDLAAAAGAAAEAGHGDGDAAAGPWLLTLSLFTSQPW
+LASLQDEGMRREVFEASTGRGGSGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRA
+APSTAAVEELLAAMAPRAMANARADAATAAAHAGRTDAEVAPWDWPALSAAYAREEFAVD
+ADALRPYFELDRVLTEGVFAAATALYGLTFAERPELARHLYRPGIRVFEVTGEDGAGVGL
+FVADLFARPTKSGGAWMHTVRDMADALGERPVVFTTMNVPAPAAGRPALLTLDEATTLFH
+EFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVESGEPLPA
+GTLERLEAADLWGEGHRTVEYLGAALVDWAWHSLTEETVDAATADPAAFERRVLTEAGID
+PDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLDADAVEWFREHGGMTRENGRRFADEL
+LSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA
+>PROKKA_01611
+MTPTPASSVLPADHPLATPSELPYGLPDFSAVTDAQLAEAVRAGMAAQRAEVEQILGAAT
+APTFENTVRAFELSGQLLRRSAAMFFTLVSADGTDARQGLAEELSPELAAHEDALLLDPR
+LAERVAAIDGAGLTGEDARLLEVLRRRLDLAGAGLGEAERAELGRINTELAGLTAAYTRR
+LVADTAERAVLVTDRERLAGLSEDDLASAAAAAREAGHGGADGEGGDEAGPWLLTLSLFT
+SQPWLASLEDEALRREVFEASVGRGAAGDHETLSTAMEVVRLRLRKARLLGSASWAEHAL
+KDRAAPSTTAVEELLATMAPRAMANARTDAATAAAHAGRVGGAVAPWDWPALSAAYARER
+FAVDAGALRPHFELDRVLHAGVFAAATALYGITFEERPELAGRLYRPGIRVFEVRDEDGA
+GVGLFVADLFARSTKSGGAWMHTVRDAADALDERPVVFNTMNVPAPAPGRPALLTLDEAT
+TLFHEFGHALHGLLAKGEYVSLSGTHVPRDVVEFPSQVNEVWLREPALLAEYARHVETGE
+PLPAGTLERLEAADLWGEGYRTVEYLGATLVDWAWHSLTEDTVEAATADPAAFERRVLTE
+AGIDPELVPPRYGTGYFKHIFGNDYAAGYYSYIWAEVLDADAVEWFREHGGMTRENGRRF
+AEELLSRGETRDLLESYRAFRGRDAELEPLLRRRGLVDAAA
+>PROKKA_01506
+MTQITHRLPAGHPLLSPSPLPHGLPDFAAVSDADLATGMRQGMAEQRAEVEEILSSPEAP
+TFENTVRALELSGALLRRVAPMFSTLVGSDGTDARQALAEELSPELAAHEDAILLDPRLS
+ARVAAVDDAGLAGEDARLLERTRTRLEIAGAGLDEAGRAELARLNGELATLSAAYTRRLV
+ADTAARAVLVTDRERLAGLRADDLAAAAERAAAEAGHRRADAAEGAGPWLLTLSLFTSQP
+WLADLEDAGLRREVFEASVGRGSSGEHETLTTAMRIVRLRLEKARLLGAASWAEHALRDR
+AAPSVAAVEGLLGSLTGPAMANARRDAEAVAEGDAPVVPWDWPFLSAAHAREAFDVDAGA
+LRPWFELDRVLTRGVFAAATALYGLRFAEREDLAGHLYRPAIRVWEVTDEDGRGVGLFVG
+DFFARPTKSGGAWMHNVVDASAALGTRPVVFCTMNVPAPAEGRPALLTLDEATTLFHEFG
+HVLHGLLAEGEYPSLTGTAVPRDTVEFPSQVNEVWLREPSLLADYARHVETGAELPTGTL
+ERLEAADLWGEGYRTVEYLGATLLDWAWHTLTEDTVDAATADPAGFERRVLTEAGIDVDL
+VPPRYGTGYFKHVFGNDYAAGYYSYIWAEVLDADAVEWFREHGGLTRENGRRFAEELLSR
+GDTRDVLESYRAFRGRDAELEPLLRRRGLLPEGA
+>PROKKA_01234
+MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAAT
+APTFENTVRALELSGQLLRRSAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPR
+LAARAASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAREELRGINTELASLSAAYTRR
+LVADTAARAVLVTDRERLAGLSEDDLAAAAGAAAEAGHGDGDAAAGPWLLTLSLFTSQPW
+LASLQDEGMRREVFEASTGRGGAGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRA
+APSTAAVEELLAAMAPRAMANARADAATAAAHAGRTDAEVAPWDWPALSAAYAREEFAVD
+ADALRPYFELDRVLTEGVFAAATALYGLTFAERPELARHLYRPGIRVFEVTGEDGAGVGL
+FVADLFARPTKSGGAWMHTVRDMADALGERPVVFTTMNVPAPAAGRPALLTLDEATTLFH
+EFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVESGEPLPA
+GTLERLEAADLWGEGHRTVEYLGAALVDWAWHSLTEETVDAATADPAAFERRVLTEAGID
+PDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLDADAVEWFREHGGMTRENGRRFADEL
+LSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001074.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001074.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf80863d34896b838fe645ffc4c234c5814fbec4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001074.fa
@@ -0,0 +1,20 @@
+>PROKKA_01278
+MTETPHTPHDGPTPDPARDVPAPEQTLAAPGGARLTDEEWARRLTPEEFQVLRRAGTERP
+FTGEYWDSHVKGVYACRACGSELFRSDEKFDAHCGWPSFFAPLAEDRVEYLKDTTLGMER
+IEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADDAAAPDGAR
+>PROKKA_00997
+MTETPHTPHDGPTPDPARDVPAPEQTLAAPGGARLTDEEWARRLTPEEFQVLRRAGTERP
+FTGEYWDSHVKGVYACRACGSELFRSDEKFDAHCGWPSFFAPLAEDRVEYLKDTTLGMER
+IEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADDAAAPDGAR
+>PROKKA_01609
+MTDTPQTPQDPDRTDAAQASPVVGHGAGAPRGARLTDEEWARRLTPEEFQVLRRAGTERA
+YTGEYWDSHVQGVYACRACGAELFRSDEKFDSHCGWPSFFAPLAEDRVEYLKDTTLGVER
+VEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADASGAGSDDDAAGRA
+>PROKKA_01504
+MSQNHATVPSGADDAARPAALTDEEWARRLTPEEFHVLRRAGTERPYTGEYWDSRVQGVY
+ACRACGVELFRSEEKFDSHCGWPSFFAPLAEDRVVYVKDATLGMERIEVRCAACGSHMGH
+VFAGEGYDTPTDLRYCINSISLRLTPADVAAIGTEADPAGDRA
+>PROKKA_01236
+MTETPHTPHDGPTPDPARDVPAPEQTLAAPGGARLTDEEWARRLTPEEFQVLRRAGTERP
+FTGEYWDSHVKGVYACRACGSELFRSDEKFDAHCGWPSFFAPLAEDRVEYLKDTTLGMER
+IEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADDAAAPDGAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001076.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001076.fa
new file mode 100644
index 0000000000000000000000000000000000000000..99f344a444769874879769890b6ebee61506f18e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001076.fa
@@ -0,0 +1,42 @@
+>PROKKA_01280
+MTDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTGPVAVDAERASGIRY
+GQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQDLPCLAEQGLRPDR
+LFDTELAARVAGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPEAMLTYAALDVELLV
+PLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQTLRRPVQRAVLKRL
+WEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHGRAASREAPRWIAAI
+RAGVEDAERGDAPAAQIRTGDGPPPPRAWKDRDPVADRRLRTAKARVARRAEQLGMPTEN
+LLTPDTLRRICWTPPAPITPETVDAFLTERGARPWQVENVGAIVTVALLDPDPAGA
+>PROKKA_00999
+MTDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTGPVAIDAERASGIRY
+GQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQDLPCLAEQGLRPDR
+LFDTELAARVSGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPEAMLTYAALDVELLV
+PLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQTLRRPVQRAVLKRL
+WEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHGRAASREAPRWIAAI
+RAGVEDAERDDAPAAQIRTGDGPPPPRAWKDRDPVADRRLRTAKARVARRAEQLGMPTEN
+LLTPDTLRRICWTPPAPITPETVDAFLTERGARPWQVENVGAIVTVALLDPDPAGA
+>PROKKA_01606
+MTDVPEPAEPDATPRLIAEPADGVPRVTDTPAGLEACAAALAAGTGPVAVDAERASGIRY
+GQRAMLVQLKREGAGIWLVDPEALDGLEPLQEALSGVEWILHAASQDLPCLAEQGLRPDR
+LFDTELAARVAGLPRVGLAAVLESMLGVTLAKEHSAADWSVRPLPEAMLAYAALDVELLV
+PLRAAMLELLEAEGKREWAEQEFEHVRTAPAPGPRADPWRRTSGSQTLRRPVQRAVLKRL
+WEAREDLARHRDVAPGRLIPDRSLIAAAESQPRTVPALRQTSGFHGRAASREAPPLDHRD
+PRRRRGRRARRRPARPGARRGRPAPAPGVEGPRPARRPPPEDRQGARGPARRAAGPAHGE
+PAHPGHPAPALLGAAAAADARGRGRVPPRARGPALAGGPGGRGGHRGPAGPGPRRGLSRG
+GRRADAAVGRGPTHR
+>PROKKA_01501
+MTSPTSPAVATSPDPSDRPGGEQAAPTLVAEPAGGVPVVTDTPAGLAACAAALAAGTGPV
+AVDAERASGIRYGQRAFLVQLKRAGAGIWLVDPEAFEDLAPLDEALRGVEWVLHAASQDL
+PCLADCGMRPDLLFDTELAARLAGLPRVGLAAVLESQLGLTLAKEHSMADWSTRPLPVDW
+LNYAALDVELLVELRDALAVLLEEQGKLAWAEQEFEHVRTTPPAAPRQDPWRRTSGMAAL
+KRPVQLAVLRRLWQAREDLAQHRDLAPGRLLPDSALVAAASTLPRTVPELRATRGFHGRS
+AAREAPRWITAIRAGIEDAAAGQAPPRHGPGSDAPPPPRAWRDRDPLADRRLTTAKPRIA
+RAAEALGMPPENLLTPDTLRRVCWTPPETITPETVAAALAERGARPWQVEQTSAIITVAL
+LDPDPARDR
+>PROKKA_01238
+MTDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTGPVAVDAERASGIRY
+GQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQDLPCLAEQGLRPDR
+LFDTELAARVSGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPEAMLTYAALDVELLV
+PLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQTLRRPVQRAVLKRL
+WEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHGRAASREAPRWIAAI
+RAGVEDAERGDAPAAQIRTGDGPPPPRAWKDRDPVADRRLRTAKARVARRAEQLGMPTEN
+LLTPDTLRRICWTPPAPITPETVDAFLTERGARPWQVENVGAIVTVALLDPDPAGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001080.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001080.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6de3c96601582655368cee3bd7c94e499f1c55b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001080.fa
@@ -0,0 +1,16 @@
+>PROKKA_01284
+MAGALTGAAAATPLVPTPGEAALGWTVSVVAGALWVAGFVSLGRSPLDARARLPWVGLML
+LLPVLGALIWFWWRHRYYPARRREQPAWDPNDRSAVVVPPRRRYGAPEE
+>PROKKA_01003
+MAGALTGAAAATPLVPTPGEAALGWTVSVVAGALWVAGFVSLGRSPLDARARLPWVGLML
+LLPVLGALIWFWWRHRYYPARRREQPAWDPNDRSAVVVPPRRRYGAPEE
+>PROKKA_01601
+MGGAAAAALAAAANPLMPTPVEAVLGWGLSLAVGALWIAGFVSLSRGPLDARGRLPWAGA
+MLLLPVLGALIWFWWRHRYYPARRREQPGWDPNDRGAVVVPPRRGRPVPSGIGRPDPNAG
+VAAPKGLAPRRRYGAERD
+>PROKKA_01497
+MEPWLGWTLSAVVGTIWVAGLVSLLRGPLDERRRLPWALAMVVLPVIGAGAWFWWRHRHY
+PARKAAEPGWDPNRRDPVVLPPARSGRAAPTAIGRPDPWAGHAPHPDRLPTRRYGAPED
+>PROKKA_01242
+MAGALTGAAAATPLVPTPGEAALGWTVSVVAGALWVAGFVSLGRSPLDARARLPWVGLML
+LLPVLGALIWFWWRHRYYPARRREQPAWDPNDRSAVVVPPRRRYGAPEE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001087.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001087.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6dc8e9a16bd7c912e8e1fbf61b7c2098752b36b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001087.fa
@@ -0,0 +1,26 @@
+>PROKKA_01299
+MRAVIAGAGAVGASIARELHAHGHEVVVVEARTDAARKADVGGARLVLGDACDLTVLEQC
+GALEADVLVAATGDDRVNLVCSLLSRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP
+SIMTALVEEAVETGDLVRLLRLEAGGAALSEFRVPAKHWLEGRRIGTVSWPQEAPLVAVV
+RDGAPRQASADEVLEVGDELFFLAAGSAEPALRRLLVGEGRAQGRSEAAESAGTPSS
+>PROKKA_01022
+MRAVIAGAGAVGASIARELHAHGHEVVVVEARTDAARKADVGGARLVLGDACDLTVLEQC
+GALEADVLVAATGDDRVNLVCSLLSRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP
+SIMTALVEEAVETGDLVRLLRLEAGGAALSEFRVPAKHWLEGRRIGTVSWPQEAPLVAVV
+RDGAPRQASADEVLEVGDELFFLAAGSAEPALRRLLVGEGRAQGRSEAAESAGTPSS
+>PROKKA_01593
+MRAVIAGAGAVGASVARELHAHGHEVVVVEIRPDAAHKADVGGAKLVLGDACDLALLERC
+GAMEADVLVAATGDDRANLVCSLLGRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP
+SIMTALVEEAVETGDLVRLLRLEAGGAVLSEFRVPAEHWLAGRRVGTVSWPQDAPLVAVV
+RDGVPRHATADEMLEAGDELFFLAAAAADAALRRLLVGEDRAQARPGAGSSSAAGRRPSS
+SPGAGALTDQASQSPRA
+>PROKKA_01489
+MRVVIAGAGAVGSSIARELHAHGHEVSVVESRADAAARSDLAGARTVLGDATDLGVLGRA
+GALGADVLVAATGDDRANLVASLLARSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP
+SIMTALVEEAVESGDLVRLLRLEAGGAALTEFRIPSGHWLRGRRVGTVSWPAAAPLVAIV
+RDGAPRSSTPDEVLEESDELFFLADAEAEGALRRLLVG
+>PROKKA_01257
+MRAVIAGAGAVGASIARELHAHGHEVVVVEARTDAARKADVGGARLVLGDACDLTVLEQC
+GALEADVLVAATGDDRVNLVCSLLSRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP
+SIMTALVEEAVETGDLVRLLRLEAGGAALSEFRVPAKHWLEGRRIGTVSWPQEAPLVAVV
+RDGAPRQASADEVLEVGDELFFLAAGSAEPALRRLLVGEGRAQGRSEAAESAGTPSS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001088.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001088.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c1c780bbfb65529a61906cf0cd45ddd5d9469bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001088.fa
@@ -0,0 +1,25 @@
+>PROKKA_01300
+MTEPRGPVTAAPDGAGPLPSRARLDERGRLDALGSVGGWRGIVEASLPTLVYMVGYVATQ
+QVWPSGVAAVAVALVLGVARLVQRQSPVQVLAGLAVVVLSVVVSLTTGQARDYYLWGFVT
+NAAYGLAFAVSVLVGWPAAGLVLGLVRAEGTRWRAHRRRRRAYAAATWILVAVFALRLAV
+QVPLYLGDAVTALGVARLVMGLPLYALGLWLAWSVSSPGQDDGVPADSAASERP
+>PROKKA_01023
+MTEPRGPVTAAPDGAGPLPSRARLDERGRLDALGSVGGWRGIVEASLPTLVYMVGYVATQ
+QVWPSGVAAVAVALVLGVARLVQRQSPVQVLAGLAVVVLSVVVSLTTGQARDYYLWGFVT
+NAAYGLAFAVSVLVGWPAAGLVLGLVRAEGTRWRAHRRRRRAYAAATWILVAVFALRLAV
+QVPLYLGDAVTALGVARLVMGLPLYALGLWLAWSVSSPGQDDGVPADSAASERP
+>PROKKA_01592
+MTEPRGPESPAPDVAGALPSRARVDEQGRLDALASVGGWRGIVEASLPTLVFMAGYVVSQ
+QVWPSGVAAVAVALVLGAVRLVQRQSPVQVLAGLAVVVLSVVVALTTGQARDYYLWGFVT
+NAAYGLAFALSVVVGWPAAGLVLGLVRGEGTHWRRSPRRRRAYATATWILVAVFTLRLAV
+QVPLYLADAVTALGVARLVMGLPLYALGLWLAWSVSAPAPGEDDGLRPAAEDEPAPGRA
+>PROKKA_01488
+MSAHPRPDHGPDAAPSAAEGLQALGARTRVDEDGRIDALATVGGVRGIVEASLPTLVFLV
+VFLLAGQVWTAGAAALGVAAVMTAARLAQRQSAAQALAGLLVVGVSVVLALTRGEARDFY
+LWGFVTNIAYGLALPLSAALGWPLAGLLFGMVRGEGLHWRADPARRRAYGIATLIVAAVS
+WLRLAVQAPLYLADAATALGVARVVMGLPLYALGLWLAWSVSTPRPGAPPLRRDPAAG
+>PROKKA_01258
+MTEPRGPVTAAPDGAGPLPSRARLDERGRLDALGSVGGWRGIVEASLPTLVYMVGYVATQ
+QVWPSGVAAVAVALVLGVARLVQRQSPVQVLAGLAVVVLSVVVSLTTGQARDYYLWGFVT
+NAAYGLAFAVSVLVGWPAAGLVLGLVRAEGTRWRAHRRRRRAYAAATWILVAVFALRLAV
+QVPLYLGDAVTALGVARLVMGLPLYALGLWLAWSVSSPGQDDGVPADSAASERP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001089.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001089.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f07e7fe788e7890f555f4baa345fc885a412b737
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001089.fa
@@ -0,0 +1,15 @@
+>PROKKA_01301
+MSPAVAARPTGAAGRIERRGVIASVTLPGADEATVFRAVLADRLPAPGSMAPAETLQLVW
+HGRRRVPGVMPGEWLTVRGRVTQMDGVPTLHNPEFDLVDAPEATR
+>PROKKA_01024
+MSPAVAARPTGAAGRIERRGVIASVTLPGADEATVFRAVLADRLPAPGSMAPAETLQLVW
+HGRRRVPGVMPGEWLTVRGRVTQMDGVPTLHNPEFDLVDAPEATR
+>PROKKA_01591
+MSPAAGERADAGPGDLIERRGVVASVTLPGADDATVFRAALADRLPEPGSVTPAESLQLV
+WHGRRRVPGVMPGQWLAVRGRLTRPDGVLTLHNPAFDLIDAPEAALRARPPREESP
+>PROKKA_01487
+MSPRRTPAPAGERPAGERVGVVVAVTFPGADDATVFRAALADDLPAPGRPEPQEVLHLVW
+HGRHRVAGVMPGAWMRVLGHPVAVAGEPTLFNPEFHLIDDEGGPA
+>PROKKA_01259
+MSPAVAARPTGAAGRIERRGVIASVTLPGADEATVFRAVLADRLPAPGSMAPAETLQLVW
+HGRRRVPGVMPGEWLTVRGRVTQMDGVPTLHNPEFDLVDAPEATR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001097.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001097.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b96909b55109a892394311a1be8495925a157fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001097.fa
@@ -0,0 +1,80 @@
+>PROKKA_01310
+MMARSSRSRPAEQDAPRPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLK
+PVQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV
+VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEGTVDFVPNYDNQLQQPAVLPAAY
+PNLLVNGTTGIAVGMATNMAPHNLREVVAGARHLLADPEADLEAIMAHIPGPDLPSGGRI
+VGLDGVRDAYATGRGTFRMRAAVDVEQVTARRTGLIVTELPYGVGPEKVIERIKAGVDAK
+KLSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQ
+TLGLLPLLRVYVDHRLDVVRRRTAHRLQRRQDRLHLVEGLLLALVDIDEVIEIIRSSDDT
+AAARTRLMGVFDLTQVQADHILELRLRQLTKFSRIELEAERDELQAAIAELEAILGSEAR
+LREVVSAELQAVADEFGDDRRTVLLEAETVAAPAASNAGGPTPAGAAQAGADLMVPDTAC
+WAVLTTSGRLLRTADRTPIASQGRRRKHDAFASVVATTARGEIGALTSTGALHRIQAVDL
+PAAPEPSAAPAMTGSVPAKELVPLGKGESLVALVPLDAVIALGTAQGVVKRVRPEWPLNR
+EVAEAIALKDGDAVVGAAPAVDDEDQLVFLTRAGQLLRYAASAVRPQGPAAGGVAGLRVA
+ADDAVLAFGVAPAASLTGPGDDAAAHPRPAVVVTVTDGEGDLLGSAGGSVKVTPLGEYPA
+KGRGTGGVRAHRLLKGETSLVLGWVGAGPALAASKAGVARALPVEYGRRDGSGVPVDQRI
+EAVGAGASPELLSAPPVADDPVTVSAD
+>PROKKA_01033
+MMARSSRSRPAEQDAPRPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLK
+PVQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV
+VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEGTVDFVPNYDNQLQQPAVLPAAY
+PNLLVNGTTGIAVGMATNMAPHNLREVVAGARHLLADPEADLEAIMAHIPGPDLPSGGRI
+VGLDGVRDAYATGRGTFRMRAAVAVEQVSARRTGLVVTELPYGVGPEKVIERIKAGVDAK
+KLSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQ
+TLGLLPLLRVYVDHRLDVVRRRTGHRLGKHRDRLHLVEGLLLALVDIDEVIEIIRSSDDT
+TAARTRLMGVFDLTQVQADHILELRLRQLTRFSRIELEAERDELQAAIAELEAILASDAR
+LREVVSAELQAVADEHGDDRRTVLLEAETAAAPAAGPAPSGPTPAGAAEAGADLMVPDTA
+CWALLSTSGRLLRTADRTPIAPQGRRRKHDAFASVVPTTARGEIGALTSAGALHRLQAVD
+LPVAGEPSAAPAMTAAVPAAELVPLAKGETLVALVPLDAVLALGTAHGVVKRVRPEWPLN
+RQVVDAVALKDGDAVVGAAPAPDEADQLVFLTRTGQLLRYAASAVRPQGPAGGGVAGIRL
+AAGDTVLAFGVAPAASLTETGADAAAHPRPAVVVTVTDGEADVLGSAPGSVKVTPLGEYP
+AKGRGTGGVRAHRLLKGESGLELGWIGAAPALAASRAGVARALPIEYGRRDGSGVPVDQR
+IEAVGAGASPDLVSAPPAEDDAVAVSAD
+>PROKKA_01582
+MSRSSRSRPSEQDVARPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLKP
+VQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPVV
+DGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEDTVDFVPNYDNQFQQPAVLPAAYP
+NLLVNGTTGIAVGMATNMAPHNLREVVAAARHLLADPEADLEAIMAHIPGPDLPSGGRIV
+GLDGVRDAYATGRGTFRMRAAVAVEQVSARRTGLVVTELPYAVGPEKVIERIKAGVDAKK
+LSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQT
+LGLLPLLRVYVDHRLDVVRRRTAHRLQRRQDRLHLVEGLLLALVDIDEVIEIIRSSDDTA
+AARTRLMGVFDLTQVQADHILELRLRQLTKFSRIELEAERDELQAAIAELEAILGSEARL
+REVVSAELQAVADEFGDDRRTVLLEAETVAAPAASTVGGPTPAGAAQAGADLMVPDTACW
+AVLTTSGRLLRTADRTPIASQGRRRKHDAFASVVATTARGEIGALTSTGALHRIQAVDLP
+AAPEPSAAPAMTGSVPAKELVPLGKGESLVALVPLDAVIALGTAQGVVKRVRPEWPLNRE
+VAEAIALKDGDAVVGAAPAVDDEDQLVFLTRAGQLLRYAASAVRPQGPAAGGVAGLRVAA
+DDAVLAFGVAPAASLTGPGDDAAAHPRPAVVVTVTDGEGDLLGSAGGSVKVTPLGEYPAK
+GRGTGGVRAHRLLKGETSLVLGWVGAGPALAASKAGVARALPVEYGRRDGSGVPVDQRIE
+AVGAGASPELLSAPPVADDPVTVSAD
+>PROKKA_01478
+MTTRSSRSRTAEADAPAPLPVEQENIVDVDVSQEMEASFLEYAYSVIYSRALPDARDGLK
+PVQRRILFMMSQMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV
+VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEDTVDFVPNYDNQFQQPAVLPAAY
+PNLLVNGAAGIAVGMATNMAPHNLREVVAAARHLLAHPDADLEALMAHVPGPDLPSGGRI
+VGLDGIRDAYATGRGTFRMRATASIEQVSSRRTGIVVTELPYAVGPEKVIEKIKDGVRGG
+RLQGISDVVDLTDRKHGLRLVVELKSGFNAQAVLAALYRHTPMEESFGINNVALVDGRPR
+TLGLRELLQVYVDHRMDVVRRRTVHRLGERRDRLHLVEGLLLALVDIDEVIEIIRSSDDT
+AAARTRLMQVFDLSQVQAEHILELRLRQLTKFSRIELEAERDELAAAIAELEAILASDAR
+LREVVSAELQAVADEFGDDRRTELVTADAAASVVSAPGEPALPAGTGPSDGGELMIPDTA
+CWALLTTTGRLLRTVDRTPLAPQGRRRKHDAFVSVVPTTARGEVGALTSTGRVLRLQAVE
+LPAAEESSPAPALTAARPAKDLVPLAKGESLVALVPLDAVLALGTAHGVVKRVRPEWPLN
+RDELTAIALKDGDSVVGAAPAPDDGDHLVFVTRAGQLLHFAASQVRPQGPAGGGVAGLRV
+GAEDAVIAFGVAPAASMTAEGEDPAAHPRPAVVVTVTDGDADLLGSAGGSVKVTPLGEYP
+VKGRGTGGVRAHRLLKGETHLTLAWVGASPALAASKAGVARALPVEYGRRDGSGVPVDQR
+VEAVGAGASPELVAAAPVDDSGVEVSAD
+>PROKKA_01268
+MMARSSRSRPAEQDAPRPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLK
+PVQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV
+VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEGTVDFVPNYDNQLQQPAVLPAAY
+PNLLVNGTTGIAVGMATNMAPHNLREVVAGARHLLADPEADLEAIMAHIPGPDLPSGGRI
+VGLDGVRDAYATGRGTFRMRAAVAVEQVSARRTGLVVTELPYGVGPEKVIERIKAGVDAK
+KLSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQ
+TLGLLPLLRVYVDHRLDVVRRRTGHRLGKHRDRLHLVEGLLLALVDIDEVIEIIRSSDDT
+TAARTRLMGVFDLTQVQADHILELRLRQLTRFSRIELEAERDELQAAIAELEAILASDAR
+LREVVSAELQAVADEHGDDRRTVLLEAETAAAPAAGPAPSGPTPAGAAEAGADLMVPDTA
+CWALLSTSGRLLRTADRTPIAPQGRRRKHDAFASVVPTTARGEIGALTSAGALHRLQAVD
+LPVAGEPSAAPAMTAAVPAAELVPLAKGETLVALVPLDAVLALGTAHGVVKRVRPEWPLN
+RQVVDAVALKDGDAVVGAAPAPDEADQLVFLTRTGQLLRYAASAVRPQGPAGGGVAGIRL
+AAGDTVLAFGVAPAASLTETGADAAAHPRPAVVVTVTDGEADVLGSAPGSVKVTPLGEYP
+AKGRGTGGVRAHRLLKGESGLELGWIGAAPALAASRAGVARALPIEYGRRDGSGVPVDQR
+IEAVGAGASPDLVSAPPAEDDAVAVSAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001104.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001104.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18a670f23f810b740cf163fd198ea40fe5f84c5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001104.fa
@@ -0,0 +1,66 @@
+>PROKKA_01319
+MSGPRSRLDRPLSSTERPAPVPANTEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHC
+LWEIIDNSVDEALAGFGQSIEITLHPDGSVEVEDNGRGIPVDVEPRTGLSGVEVVFTKLH
+AGGKFGGGSYAASGGLHGVGASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRP
+SPDAPFEPSTDASPLDVVGKAKRGQTGTRVRYWADEQIFVKDATFSAEELQARARQTAYL
+IPGLRITVKDLRRRPGTPGADGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGTFK
+ERVPVLGEDGRTSMQDVQRTCEVDVALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAAL
+LKVFRAQVEANARRLKAGSDKVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRI
+VSQVVEKQLTARLTSTARAQKQQVHTLLEKVVAEMKSRISARTHKENQRRKNALETSTMP
+AKLADCRSNDVASSELFIVEGDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILAN
+AECAALIQVVGGGAGRSFDLDAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAG
+RVYAAVPPLHRIEAVTRGVKEREVIYTYSEQELHATLARLEREGRSYREPIQRYKGLGEM
+DADQLAETTMDPRHRMLRRVNIAEVEAAERVFDLLMGSAVAPRKDFIVSHADELDRARID
+A
+>PROKKA_01040
+MPANTEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGFGQSI
+EITLHPDGSVEVEDNGRGIPVDVEPRTGLSGVEVVFTKLHAGGKFGGGSYAASGGLHGVG
+ASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRPSPAAPFEPSTDASPLDVVGK
+AKRGQTGTRVRYWADEQIFVKDATFSAEELQARARQTAYLIPGLRITVKDLRRRPGTPGA
+DGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGTFKERVPVLGEDGRTSMQDVQRT
+CEVDVALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAALLKVFRAQVEANARRLKAGSD
+KVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRIVSQVVEKQLTARLTSTARAQ
+KQQVHTLLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVASSELFIVE
+GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILANAECAALIQVVGGGAGRSFDL
+DAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVYAAVPPLHRIEAVTRGVK
+EREVIYTYSEQELHATLARLEREGRSYREPIQRYKGLGEMDADQLAETTMDPRHRMLRRV
+NIAEVEAAERVFDLLMGSAVAPRKDFIVSHADELDRERIDA
+>PROKKA_01572
+MPANSEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGYGQSI
+EITLHPDGSVEVEDSGRGIPVDVEPRTGLSGVEVVFTKLHAGGKFGGGSYAASGGLHGVG
+ASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRPSPDAPFEPSTDASPLDVVGK
+AKRGQTGTRVRYWADEQIFIKDAAFSADDLHARARQTAYLIPGLRITVKDLRRRPGTPGA
+EGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGSFKERVPVLGEDGRTAMQDVQRT
+CEVDLALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAALLKAFRTQVESNARRLKAGSD
+KVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRIVAQVVEKELTARLTATARAQ
+KQQVHVLLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVASSELFIVE
+GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILANAECAALIQVVGGGAGRSFDL
+DAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVFAAVPPLHRIEAVTKGVK
+EREVIYTYSEQELYATLARLEKEGRSYKEPIQRYKGLGEMDADQLAETTMDPRHRTLRRV
+NIAEVEAAERVFDLLMGSSVAPRKDFIVSHADELDRERIDA
+>PROKKA_01468
+MPANTEYSARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGFGQSI
+DVTLHPDGSVEVADNGRGIPVDVEPRTGLTGVEVVFTKLHAGGKFGGGSYAASGGLHGVG
+ASVVNALSSRLDVQVVRGGKVHQLSFRRGEPGRFQDGSRPTPDAPFEPAADAAPLDVVGK
+AKRGQTGTRVRYWADEQIFTPDATFSMEDLQARARQTAYLIPGLRIAVTDLRRLTGTAGE
+AGPVQEVYQYDGGIAEFVDHLTPAKPVTDVWRIQGSGTFTERVPVLGEDGRTQMQDVQRT
+CEVDVALRWDVGYETVFRSFVNIIATPKGGTHQSGFESALLKVFRAQVEAGARRLKAGSD
+RPDKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTPAVRRIVARVVEKELTALLTSTARGQ
+KQQVGALLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVAASELFIVE
+GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILSNAECAALIQVVGGGAGRGFDL
+DAARYGKVILMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVYAAVPPLHRIEAVTRGKK
+EREVIYTYSEAELHEVLARLEAEGRTYREPIQRYKGLGEMDADQLAETTMDPRHRMLRRV
+TISEVEAAERVFELLMGSSVAPRKAFIVSNADELDRERIDA
+>PROKKA_01275
+MPANTEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGFGQSI
+EITLHPDGSVEVEDNGRGIPVDVEPRTGLSGVEVVFTKLHAGGKFGGGSYAASGGLHGVG
+ASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRPSPDAPFEPSTDASPLDVVGK
+AKRGQTGTRVRYWADEQIFVKDATFSAEELQARARQTAYLIPGLRITVKDLRRRPGTPGA
+DGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGTFKERVPVLGEDGRTSMQDVQRT
+CEVDVALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAALLKAFRAQVEANARRLKAGSD
+KVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRIVSQVVEKQLTARFTSTARAQ
+KQQVHTLLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVASSELFIVE
+GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILANAECAALIQVVGGGAGRSFDL
+DAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVYAAVPPLHRIEAVTRGVK
+EREVIYTYSEQELHATLARLEREGRSYREPIQRYKGLGEMDADQLAETTMDPRHRMLRRV
+NIAEVEAAERVFDLLMGSAVAPRKDFIVSHADELDRERIDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001110.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001110.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e874000929680611a3f497cf92b3a867f43496ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001110.fa
@@ -0,0 +1,45 @@
+>PROKKA_01325
+MADKATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH
+AAEVADETRNAAKFGVNATLESVDMAKVRDYKDGIVAGKHKGLAGLLKMRKVQVIEGEGK
+LVSKNEVEVDGTRYTAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGNI
+YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEEFGKDNVEVAEYNLAGNGKSSILGTGGIIKMIRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS
+>PROKKA_01046
+MADKATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH
+AAEVADETRNAAKFGINATLESVDMAKVRDYKDGIVAGKHKGLAGLLKMRKVQVIEGEGK
+LVSKNEVEVDGTRYTAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGSI
+YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEKFGKDNVEVAEYNLAGNGKSSILGTGGIIKMIRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS
+>PROKKA_01566
+MADSATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKLGGTCLHWGCIPTKAYLH
+AAEVADETRNSAKFGVNATLESVDMAKVRDYKDGIVAGKHKGLTGLLKMRKVQVIEGEGK
+LVSKNEVEVDGTRYKAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVEVTIIEGLETLVPNEDPAIIKVLAREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGITMDRGFVITDERLHTGVGSI
+YAVGDIVPGLQLAHRGYQQGIFVAEEIAGNSPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEKFGKDNVEVVEYNLAGNGKSSILGTGGIIKMVRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHG
+>PROKKA_01462
+MADSATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH
+AAEVADETRNAAKVGVNATLESVDMAKVRDYKDGIVSGKHKGLAGLLKMRKVQVIEGAGK
+LVSKNEVEVDGTRYTAENIVLASGSVSKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKVFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGNI
+YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEKFGKDNVEVAEYNLAGNGKSSILGTGGIIKMVRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS
+>PROKKA_01281
+MADKATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH
+AAEVADETRNAAKFGVNATLESVDMAKVRDYKDGIVAGKHKGLAGLLKMRKVQVIEGEGK
+LVSKNEVEVDGTRYTAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGNI
+YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEKFGKDNVEVAEYNLAGNGKSSILGTGGIIKMIRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001122.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001122.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed75294a5269d60c2e9fccc43d2811e323f8cc81
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001122.fa
@@ -0,0 +1,15 @@
+>PROKKA_01339
+MTETSEFWYNVNTHQVEVGAQSDWSQLLGPFGTREEAQAAMDRVRANNETADAWDERDDD
+WDSRPVDDAS
+>PROKKA_01059
+MTETSEFWYNVNTHQVEVGAQSDWSQLLGPFGTREEAQAAMDRVRANNEAADAEDARDDD
+WDSRPVDDAS
+>PROKKA_01553
+MSEKSEYWYNVRTQQVEEGAQSDWSQLLGPFGTREEAQGAMSRVQANNEAADAADERDDN
+WDNNPFNDAD
+>PROKKA_01449
+MTDTHEPGSGYWFNVRTHQIEEGPQSDWKELLGPYQTRQDAENALARVQARNEAADAEDA
+HDDAWDASPLNDAS
+>PROKKA_01294
+MTETSEFWYNVNTHQVEVGAQSDWSQLLGPFGTREEAQAAMDRVRANNEAADAEDARDDD
+WDSRPVDDAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001125.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001125.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a191f130519a309257737f8bd96502f75162159
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001125.fa
@@ -0,0 +1,105 @@
+>PROKKA_01343
+MTVSADARPDAVKDGGFVHLHTHTEYSMLDGAAKLDDLFAEAQRLGMDSLAITDHGYLFG
+AYDFWSKAKAAGVKPIIGLEAYVAPGQQHRTDKEKTRWGEPHQRGDDVSGGGAYTHMTLL
+SETTEGMHNLFRMGSIASLDSVYAKWPRLDRELLSQYSKGLIATTGCPSGEVQTRLRLGQ
+YREAMQAASDFRDIFGKDNYYCEIMHHGLDIERRVMTDLRRLAKDLGLPFVATNDLHYTH
+EHDAKAHEALLALQSGSKLNEPSYDQGGSRFAFSGTEYYLKSPRQMRELFAELPEACDNT
+LLIAERCEVEFDTKANYMPVFPTPEGEDETSWLIKEVASGLAYRYPDGVPDHVRKQADYE
+LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLKHGLIF
+ERFLNPDRVSMPDFDVDFDDRRRSEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV
+MDQPFSMGESLTKALPPAVMAKDIPLKDIEDPAAPRYGEAAPFRELIATDPVAKEVFETA
+KGLEGLKRQWGVHAAGVIMSSVPVIDVIPIMRRLQDGQVITQFDYPMAESLGLIKMDFLG
+LRNLTIISDALENVKANQGVDLDLETLDVDDPAAYELLARGDTLGVFQLDGGPMRSLLKM
+MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGQQEITPIHPELEEPLREILDTTYGL
+IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEAAVKA
+LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE
+CRHMGITVLPPDVNESHLTFTPVGRDIRFGMGAVRNVGANVVKGMVQGREEKGSYTGFGD
+FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVAQKRKEDHGEFTFD
+LFALGGGDEDDSDAADGVAVPDLPEWAKKEKLAFEREMLGLYVSDHPLQGLDGVLAQHAD
+VQITRVLDDDGPADGAIVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSMDVMFFGQVY
+APIAMMLAEDLVVAVKGRVQRRDDGSVSLSAMELTIPELSDGPGGPVRITLPAFKATEQV
+MGQLADVLRTHEGSSEVRLSLVGQRATQEFQLGPQFRVSPNPALFGDLKILLGPACLG
+>PROKKA_01063
+MTVSADARADAVKDGGFVHLHTHTEYSMLDGAAKLDDLFAEAQRLGMDSLAITDHGYLFG
+AYDFWSKAKAAGVKPIIGLEAYVAPGHQHRTDKEKTRWGEPHQRGDDVSGGGAYTHMTLL
+SETTEGMHNLFRMGSIASLDSVYAKWPRLDRELLSQYSKGLIATTGCPSGEVQTRLRLGQ
+YREAMQAASDFRDIFGKDNYYCEIMHHGLDIERRVVTDLRRLAKDLGLPFVATNDLHYTH
+EHDAKAHEALLALQSGSKLNEPSYDQGGSRFAFSGTEYYLKSPRQMRELFAELPEACDNT
+LLIAERCEVEFDTKANYMPVFPTPEGEDETSWLIKEVASGLAYRYPDGVPDHVRKQADYE
+LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLKHGLIF
+ERFLNPDRVSMPDFDVDFDDRRRSEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV
+MDQPFSMGESLTKALPPAVMAKDIPLKDIEDPAAPRYGEAAPFRELIATDPVAKEVFETA
+KGLEGLKRQWGVHAAGVIMSSAPVIDVIPIMRRLQDGQVITQFDYPMAESLGLIKMDFLG
+LRNLTIISDALENVKANQGVDLDLETLDVDDPAAYELLARGDTLGVFQLDGGPMRSLLKM
+MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGQQEITPIHPELEEPLREILDTTYGL
+IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEAAVKA
+LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE
+CRHMGITVLPPDVNESHLTFTPVGRDIRFGMGAVRNVGANVVKGMVQGRENEGSYTGFGD
+FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVAQKRKEDHGEFTFD
+LFALGGGDEDDSDAADGVAVPDLPEWAKKEKLAFEREMLGLYVSDHPLQGLDGVLAQHAD
+VQITRVLDDDGPADGAIVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSMDVMFFGQVY
+APIAMMLAEDLVVAVKGRVQRRDDGSVSLSAMELTIPELSDGPGGPVRITLPAFKATEQV
+MGQLADVLRTHEGSSEVRLSLVGQRATQEFQLGPQFRVSPNPALFGDLKILLGPACLG
+>PROKKA_01549
+MTVSADARADAVKDGGFVHLHTHTEYSMLDGAAKLDDLFAEAERLGMDSLAITDHGYLFG
+AYDFWSQAKSAGIRPIIGLEAYVTPGHQHRTDKEKTRWGEPHQRGDDVSGGGAYTHMTLL
+SENTAGMHNLFRMSSIASLDSVYAKWPRLDRELLSQYSSGLIATTGCPSGEVQTRLRLGQ
+YDEAVAAAAEFRDIFGKDNYYCEIMHHGLDIERRVMTDLRRLAKDLGLPFVATNDLHYTH
+EHDAKAHEALLALQSGSKLNEPSYDQGGSRFAFSGTEYYLKSPRQMRELFAELPEACDNT
+LLIAERCDVEFDTKANYMPVFPTPEGEDETSWLIKEVASGLAYRYPDGVPDHVRKQADYE
+LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLKHGLIF
+ERFLNPDRVSMPDFDVDFDDRRRPEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV
+MDQPFSLGESLTKALPPAVMAKDIPLKDIEDPAAPRYGEAAPFRELIATDPVAKEVFETA
+KGLEGLKRQWGVHAAGVIMSSEPVIDVIPIMRRLQDGQVITQFDYPMAESLGLIKMDFLG
+LRNLTIISDAIENVKANQGVELDLETLDVDDAASYDLLARGDTLGVFQLDGGPMRSLLKM
+MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGQQEITPIHPELEEPLREILDTTYGL
+IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEAAVKA
+LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE
+CRHMGITVLPPDVNESHLTFTPVGRDIRFGMGAVRNVGANVVKGMVQGREDKGAYTGFGD
+FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVSQKRKEDHGEFTFD
+LFALGGPQEDESDAADGVAVPDLPEWAKKEKLAYEREMLGLYVSDHPLQGLDGVLAQHAD
+TQITRVLDDDGPADGSQVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSMDVMFFGQVY
+APIAMMLAEDLVVAVKGRVQRRDDGSVSLSAMELTIPELSDGPGGPVRISMPSFKATEQV
+VGQLADVLRTHEGSSEVRLSLVGQRGTQEFQLGPQFRVNPNPALFGDLKILLGPACLS
+>PROKKA_01445
+MSVQQETTAEATRDGGFVHLHTHTEYSMLDGAAKLDELFAEANRLGMDSLAITDHGYLFG
+AFDFWKKATDAGIKPIIGLEAYLTPGQQHRSDKEKIRWGEPHQRGDDVSGGGAYTHMTML
+AESTQGMHNLFRMGSIASLDSVYAKWPRIDRELLSQYSSGLIATTGCPSGEVQTRLRLGQ
+YKEAVEAAAEFRDIFGRDNFYCEVMQHGLDIEKRVVEDLRRLAKDLGLPFVATNDLHYTH
+EHDAKAHEALLAIQSGSKLNEPTYDQGGSRFAFSGTDYYLKSPRQMRELFAELPEACDNT
+LLIAERCETSFDTSANYMPRFPTPEGEDETSWLIKEVAKGLAYRYPEGVPDHVRKQADYE
+LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLRHGLIF
+ERFLNPDRVSMPDFDVDFDDRRRSEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV
+MDQPFSMGESLTKALPPAVMAKDIPLKDIEDPEAKRYAEAGEFRELVAADPVAKQVFETA
+KGIEGLKRQWGVHAAGVIMSSHPVIDVIPIMRRLQDGQVITQFDYPTAEGLGLIKMDFLG
+LRNLTIISDAIENIRANRGVDLDLEHLDVDDAESYALLARGDTLGVFQLDGGPMRALLKM
+MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGLQEITPIHPELAEPLKDILDTTYGL
+IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEGAVKA
+LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE
+CRHMGITVLPPDVNESFLNFTPVGDDIRFGMGAVRNVGGNVVKGMVQAREEKGLYTGFGD
+FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVQQKRKEDHGEFTFD
+LFALGGAADAADDSDASDGVAVPDLPEWPKKERLAFEREMLGLYVSDHPLQGLDGVLSQF
+ADTQITRILDDDGPADGAHVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSLDVMFFGQ
+VYAPIAMMLAEDLVVAVKGRVQRRDDGSVVLSAMELAIPELTDATGGPVRITMPAFKATE
+RVVGQLGDVLRTHEGSTEVRLSLTGQRGVQEFQLGPQYRVTPNPALFGDLKILLGPSCLG
+>PROKKA_01298
+MTVSADARADAVKDGGFVHLHTHTEYSMLDGAAKLDDLFAEAQRLGMDSLAITDHGYLFG
+AYDFWSKATAAGVKPIIGLEAYVAPGQQHRTDKEKTRWGEPHQRGDDVSGGGAYTHMTLL
+SETTEGMHNLFRMGSIASLDSVYAKWPRLDRELLSQYSKGLIATTGCPSGEVQTRLRLGQ
+YREAMQAASDFRDIFGKDNYYCEIMHHGLDIERRVMTDLRRLAKDLGLPFVATNDLHYTH
+EHDAKAHEALLALQSGSKLNEPSYDQGGSRFAFSGTEYYLKSPRQMRELFAELPEACDNT
+LLIAERCEVEFDTKANYMPVFPTPEGEDETSWLIKEVASGLAYRYPDGVPDHVRKQADYE
+LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLKHGLIF
+ERFLNPDRVSMPDFDVDFDDRRRSEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV
+MDQPFSMGESLTKALPPAVMAKDIPLKDIEDPAAPRYGEAAPFRELIATDPVAKEVFETA
+KGLEGLKRQWGVHAAGVIMSSVPVIDVIPIMRRLQDGQVITQFDYPMAESLGLIKMDFLG
+LRNLTIISDALENVKANQGVDLDLETLDVDDPAAYELLARGDTLGVFQLDGGPMRSLLKM
+MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGQQEITPIHPELEEPLREILDTTYGL
+IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEAAVKA
+LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE
+CRHMGITVLPPDVNESHLTFTPVGRDIRFGMGAVRNVGANVVKGMVQGREEKGSYTGFGD
+FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVAQKRKEDHGEFTFD
+LFALGGGDEDDSDAADGVAVPDLPEWAKKEKLAFEREMLGLYVSDHPLQGLDGVLAQHAD
+VQITRVLDDDGPADGAIVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSMDVMFFGQVY
+APIAMMLAEDLVVAVKGRVQRRDDGSVSLSAMELTIPELSDGPGGPVRITLPAFKATEQV
+MGQLADVLRTHEGSSEVRLSLVGQRATQEFQLGPQFRVSPNPALFGDLKILLGPACLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001132.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001132.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4d6277a8cded738ff0288aa5a8864afde18b3d46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001132.fa
@@ -0,0 +1,30 @@
+>PROKKA_01350
+MTAAEGPAGTARVPAGPFVHRETVRTATGAVHVAWTSVAAGNLALHVVPPDEAEGLARVS
+AARRALERVMGVPEGATLYLDQVHSADVVWADGPGRGGASAPVADAAVSRDGSRPLAVMV
+ADCLPVVVVDETTGATAVAHAGRRGLLDGVLEATVDRLLSLRPEADRTGPGLRAWIGPGV
+CGRCYEVPAAMRDEAAARLPATAATTSWGTPALDLPAGAAEVLRARGVATATIDVCTRED
+ERLFSHRRAPGEGRFAGLVWRADPDATVPRGDA
+>PROKKA_01070
+MTAAGGPAGTARVPAGPFVHRETVRTATGAVHVAWTSVAAGNLALHVVPPDEAEGPARVS
+AARRALERMMGVPEGATLYLDQVHSADVVWADGPGRGGAPAPVADAAVSRDGSRPLAVMV
+ADCLPVVVVDETTGATAVAHAGRRGLLDGVLEATVDRLLSLRPETDRTGPGLRAWIGPGV
+CGRCYEVPAAMRAEAAARLPATAATTSWGTPALDLPAGAAQVLRARGVATATIDVCTRED
+ERLFSHRRAPGEGRFAGLVWRADPDATTPRGEA
+>PROKKA_01542
+MTAAEGPVGTVPVPAGPFVHREAVATAGGTVHVAWSGVAAGNLGLHVVADEDAAGRRAVG
+EARRGLERAMGVPVGSTLYLDQVHSADAVWADGPGWGEEAGPTADAAVSRDGGRALAVMV
+ADCLPVVLVDEATGATAVAHAGRRGLVDGVLEGTVDRLLSLRPADRRDAPGLRAWIGPGV
+CGRCYEVPEQMRAEAAERVPATAATTAWGTPGLDLPAGAVAILRGRGADVAVVQACTLED
+ERLFSHRRAPGQGRFAGLVWRADEDASTPTRAA
+>PROKKA_01438
+MSLAGGPVGTQPVPSGPFVHREDLRADARGRVAHVAWTSAEAGSLAFHILGAEQEQARAD
+VVAARHRVEDAMGVPRGSVFYLEQVHSVDVVTAGPGWEEGFAPTADASVSPDGHTPLAVM
+VADCLPVVFVDGLTGATAVAHAGRRGLLDGVLENTVDALLALRPEGSAGAFGLKAWIGPG
+ISGESYEVPQAMQDEAVARIPELEATTSWGTPALALASGAQAVLRARGVAVERIALDTFT
+DERVFSHRRAPGRGRFAGLVWTTPADVDQDHDAGDARG
+>PROKKA_01305
+MTAAEGPAGTARVPAGPFVHRETVRTATGAVHVAWTSVAAGNLALHVVPPDEAEGLARVS
+AARRALERAMGVPEDATLYLDQVHSADVVWADGPGRGGAPAPVADAAVSRDGSRPLAVMV
+ADCLPVVFVDETTGATAVAHAGRRGLLDGVLEATVDRLLSLRPETDRTGPGLRAWIGPGV
+CGRCYEVPAAMRTEAAARLPATAATTSWGTPALDLSAGAAQVLRARGVTTATIDVCTRED
+ERLFSHRRAPGEGRFAGLVWRTDLDATTPRGEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001140.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001140.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cbf96c69c042f4615b5d747f7c19532aae5e98d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001140.fa
@@ -0,0 +1,55 @@
+>PROKKA_01359
+MTTPSDPPAPLTPAQQDAAFRPSHTPAAAWPALAQALAEAGIAAHVHGAAPADGVTGVSL
+DSRVVRPGDLYVAVPGARAHGAAFAATALEAGAVGVLTDAAGRALLAEQGLADVPVLEVD
+AVRTAAGTVAARVYGGGGDTGPRLLGVTGTNGKTTTSFLAAALLEALGRRSGIVGTILIR
+AGEREVPSTLTTPEATQLHALMALMREEEVDTAVMEVSSHAVAYQRIAGLRYAVAGFTNL
+TQDHLDMHGSMQEYFAAKAGLFDPARTDHAVITLDGGEGPRWGVAMARAAGAPVTTLALG
+PAAPTPGALAEHDPGLRADWEVAELAPDGLGHRFTLRHAATGRELRASVGLPGRFNVANA
+ALAVLLVLHAVGEEHLDALAAVLDVPAGEGPLAAAVPGRMEVVGREPDAVVDFAHNPDGM
+VQALRSLADARAAAGTRGRTLIVFGSAGDRDRDKRPVMGAIAARAADVLIVTDDTPHSED
+PAPIRAHILAGARAEADRIAREEGRTVVIEEVADRATAIRRAVELAGPQDGILLAGRGHE
+TTMDYDGELVPLDDRVALREALAARVAAASASGSGPAREGKVIES
+>PROKKA_01079
+MTTPSDPPAPLTPAQQDAAFRPSHTPATPWPALAQSLAGAGIAAHVHGAAPADGVTGVSL
+DSRVVRPGDLYVAVPGAHAHGAAFAARALEAGAVGVLTDAAGRALLAEQDLADAPVLEAD
+AVRTAAGTVAARVYGGGGDAGPRLVGVTGTNGKTTTSFLAAALLEALGHRSGIVGTILIR
+AGEREVPSTLTTPEATQLHALMALMREEQVDTAVMEVSSHAVAYQRIAGLRYAVAGFTNL
+TQDHLDMHGSMQEYFAAKAGLFDPARTDHAVITLDGGEGPRWGVAMARAAGAPVTTLALG
+PAAPTPGALAEHDPGVRADWEVAELAPDGLGHRFTLRHAATGRELRASVGLPGRFNVANA
+ALAVLLVLHAVGEEHLDALAAVLDVPAGEGPLAAAVPGRMEVVGREPDAVVDFAHNPDGM
+VQALRSLADARAAAGTRGRTLIVFGSAGDRDRDKRPVMGAIAARAADVVIVTDDTPHSED
+PAPIRAHILAGARAEADRIAREEGRTVVIEEVADRAAAIRRAVELAGPQDGILLAGRGHE
+TTMDYDGELVPLDDRVALREALAAGAAVASASVSGPVREGKVIES
+>PROKKA_01534
+MSSQPAQPQPLTPAQQDDAFRPSRTPATPWDELTRALQAAGVAARTHGRGPAAGVTGACL
+DSRVVRPGDLYVALPGARSHGADFARAAVDAGAAGVLTDAEGRARLAEQGLDGSAVIEVD
+SVRTAAGVVAARVYGGGQDAGPRLIGITGTNGKTTTSFLAAALLEALDRRSGVIGTILIR
+AGGREVPSTLTTPESTQLHALMALMREEQVDTAVMEVSSHAVAYQRIAGLRYAVAGFTNL
+TRDHLDMHGSMEEYFEAKAGLFDPERTARAVITVDGGEGPRWGLSMARAVRTPVTTLALG
+PAAPHPGALAEEDPDFRADWEIAELVPDGLGHRFTLRHGATGRALRASVGLPGRFNAANA
+ALAVLLVLYAVGEEHLDALAAVLDVPAGEGPLAAAVPGRMEVVGRAPDAVVDFAHNPDGM
+VQALRSLADAREAAGRSGRTLIVFGSAGDRDREKRPIMGEIAARAADVVIVTDDTPHTED
+PAPIRAQILEGARAEAARLLQAEGRTVLVEEVADRAVAIRRAAELAAPQDGILVAGRGHE
+TTMDYDGELVPLDDRQALREALAARAAAASPRASDPGSGAPRGGKVDES
+>PROKKA_01429
+MTDDAPQTTAPLTPAEQDAAFRPAAVTPVAWAEVAAALRAAGQDVRERSAAAAPAVTGAA
+LDSRVVRPGDLYVALPGARAHGAAFAAAAREAGAAGVLTDGDGVALLAEQGLDDLPVLEV
+ESVRAAAGVAAARIYGGGPDAGPRLLGVTGTNGKTTTSFLAASIVEALGERSGIIGTILT
+RAGDRQVPSTLTTPESAQLHALMALMRQEGVDTAVMEVSSHAVEYRRIAGLHYAVAGFTN
+LTQDHLDQHGTMEGYFRAKLGLFEADRTDRAVVVLDGGEGPRWGVKTARRAGAPVTTLAL
+GAASPTPGALAEEHPDVVPDWQVTDLVADGLGHRFALVHAATGRRLPASVGLPGLFNVAN
+AALAALMVLESIGEDRLDELAAVLDVPAGTGPLAAAVPGRMEVVGREPDAVVDFAHNPDG
+MVQALRALGDARAAAGRAGRTLIVFGAAGDRDATKRPLMGRIAAEHADVVIVTDDTPHTE
+DPAPIRAQLLEGAREEAARAAAAGREVRVEEFADRAAAIRRAAELAAPEDGILVAGRGHE
+TEMDYDGTLVPLDDRVALRDALAARRPGDAQEPGVAGGKVAGK
+>PROKKA_01314
+MTTPSDPPAPLTPAQQDAAFRPSHTPATPWPALAHALAEAGIAAHVHGAAPADGVTGVSL
+DSRVVRPGDLYVAVPGARAHGAAFAATALEAGAVGVLTDAAGRALLAEQGLVDVPVLEVD
+AVRTAAGTVAARVYGGGGDAGPRLVGVTGTNGKTTTSFLAAALLEALGRRSGIVGTILIR
+AGEREVPSTLTTPEATQLHALMALMREEEVDTAVMEVSSHAVAYQRIAGLRYAVAGFTNL
+TQDHLDMHGSMQEYFAAKAGLFDPARTDHAVITLDGGEGPRWGVAMARAAGAPVTTLALG
+PAAPTPGALAEHDPGLRADWEVAELAPDGLGHRFTLRHAATGRELRASVGLPGRFNVANA
+ALAVLLVLHAVGEEHLDALAAVLDVPAGEGPLAAAVPGRMEVVGREPDAVVDFAHNPDGM
+VQALRSLADARAAAGTRGRTLIVFGSAGDRDRDKRPVMGAIAARAADVLIVTDDTPHSED
+PAPIRAHILAGARAEADRIAREEGRTVVIEEVADRATAIRRAVELAGPQDGILLAGRGHE
+TTMDYDGELVPLDDRVALREALAARVAAASASGSGPAREGKVIES
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001141.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001141.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f05f91bcd9115f59f80193837e848ea295a0efd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001141.fa
@@ -0,0 +1,57 @@
+>PROKKA_01360
+MRTRILLLLVFVLLGGLALRLVYVQGIDPTGQAAAAMDQRLTHQETLPQRGSILDRDGDV
+LAASVRRYDIVVDQRLVKDFNEWDREARETVLVDVDSRLASLAEVLGMSEEEVREATIGS
+RPYAVVRRSVTPEVRDAAMALNVPGLLSEAVDRRTYPNGSVAGSIIGFMGGDGTALEGLE
+LSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAVDGADLRLTVDKDAQWFAQETLGAL
+AAEYEAEWANAVVMDVKTGDVIVMADSTTVDPADPDATEGNFRTSTVMSTPYEPGSTGKA
+LPIAAAVDAGKVTATDGFTVPGSQDFDGQTIRDFSPHPTFDMTVAGIYARSYNTGTVQIA
+EKITDEQRYEYMRSFGVGQPIDLGLPQQAGSVLVPPEQWDGRQRLTTAFGQGYTQTTLHT
+AQMYQALANGGVLIPARLIDATVDGDGAEKRWESSAEPHRVVSEETAAQMLRMMETVVTQ
+GTSKAAAIPGYRVGGKSSTAEAASDTGTYDGYNLGFTAVAPLDDPRFVVSVSMHRPPSKQ
+GSRDVSVAAATIMEYMLRQADVPATGAEPNDYRVFVDDPQDRPW
+>PROKKA_01080
+MRTRILLLLVLVLLGGLALRLVYVQGIDPTGQAAAAMDQRLTHQETLPQRGSILDRDGDV
+LAASVRRYDIVVDQRLVKDFNEWDREARETVLVDVDSRLASLAEVLGMSEEEVREATIGS
+RPYAVVRRSVTPEVRDAAMALNVPGLLSEAVDRRTYPNGSVAGSIIGFMGGDGTALEGLE
+LSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAVDGADLRLTVDKDAQWFAQETLGAL
+AAEYDAEWANAVVMDVKTGDVIVMADSTTVDPADPDATEGNFRTSTVMSTPYEPGSTGKA
+LPIAAAVDAGKVTATDGFTVPSSQDFDGQTIKDFSPHPTFDMTVAGIYARSYNTGTVQIA
+EKITDEQRYEYMRSFGVGQPIDLGLPQQAGSVLVPPEKWDGRQRLTTAFGQGYTQTTLHT
+AQMYQALANGGVLIPARLIDATVDGEGAEKRWESSAEPHRVVSEETAAQMLRMMETVVTQ
+GTSKAAAIPGYRVGGKSSTAEAASDTGTYDGYNFGFTAVAPLDDPRFVVSVSMHRPPSKQ
+GSRDVSVAAATIMEYMLRQADVPATGAEPNDYRVFVDDPQDRPW
+>PROKKA_01533
+MTDRPAFSSPRGGSTVGPAPGLPDARIRGLLLLVLVLLGGLALRLVYVQGVDPTGQAAAA
+MDKRLTHQETLPERGSILDRDGDVLASSVRRYDMVVDQRLVKDFNEWDREARKTVLVDVD
+SRLASLAEVLELPEEQVREATIGSRPYNVVKRSVTPEMRDAAMALKVPGLLAEPVDRRVY
+PNGSVAGSIVGFMGGDGTPLEGLELSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAV
+DGADLRLTLDKDAQWFAQETMGALAAEHDAEWANAVVLDAKTGDVLVMADSTTVDPADPE
+GTEPYFRSSTVMSTPYEPGSTGKALPIAAALDAGAVTATDGYTVPSSQEFDGQTIRDFAP
+HETYDMTVAGIFARSYNTGTVQVAEEISDELRYEYMRSFGVGKPIDLGLPRTAGGVLVPP
+GEWDGRQRLTTAFGQGYTQTTLHTAQMYQAMANGGVMEPARLIDATVDGDGAEKRWEPAA
+EPHRVVSEATAADMLRMMETVVTQGTSKAAAIPGYRVGGKSSTAEAASDTGRYDGYNFGF
+TAVAPLDDPRFVVSVSMHRPPSQLGSRAVTSAAAQIMEHMLRQADVPADGAAPQDYDVFV
+DDPQDRPW
+>PROKKA_01428
+MPVSRSRVSGAGSRTAPPIGTARVRSRTVLLLLLALVTVLGLRLVWVQGIDASGAAATAM
+SERLKTQEIRPERGAITDRDGAVLASTVRRYDIVVDQRLVKDFKEWDAEKRQSVLVSIDS
+RLSSLAEALGMSEDEVRAAAIGDRPWAVLKRSVTPEVRDRVLALKVPGVLADAVDRRTYP
+SGAVAGSLVGFMSSDGTPLEGLEKSQDAVLSGTPGTRTFEVGATGIRIPNAPEDVTPAVD
+GATLRLTLDKDAQWYAQEAMARLADTYSAQWANAVVMDAKTGEVLALADSATVDPGDPQA
+ADARARTPGVVYTPYEPGSTGKTATMAAALDMGLVTPETGLEVPDRLELKGQPPIRDASP
+HETYTMTVAGVYARSYNTGTVMVAEKMSDEQRYEYMRSFGIGRPIDLGLPQPARSVLAAP
+GDWDGRQRLVTAFGQGYTVTTLHTAQMFQAIANGGVLEPARLIAATVGADGTEHRWDPGV
+ASRRVVSEQTAEEMLRMMETVVTQGTSTVAQLPGYRVGGKSSTAQVAGETGTYDGYNYGF
+TAVAPLDDPRYVVSVSMNRPSAGGSSKVVAAAAADVMQHMLRQGGVPPGGAEPDDYRVFV
+DDPQERPW
+>PROKKA_01315
+MRTRILLLLVFVLLGGLALRLVYVQGIDPTGQAAAAMDQRLTHQETLPQRGSILDRDGDV
+LAASVRRYDIVVDQRLVKDFNEWDREARETVLVDVDSRLASLAEVLGMSEEEVREATIGS
+RPYAVVRRSVTPEVRDAAMALNVPGLLSEAVDRRTYPNGSVAGSIIGFMGGDGTALEGLE
+LSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAVDGADLRLTVDKDAQWFAQETLGAL
+AAEYEAEWANAVVMDVKTGDVIVMADSTTVDPADPDATEGNFRTSTVMSTPYEPGSTGKA
+LPIAAAVDAGKVTATDGFTVPGSQDFDGQTIRDFSPHPTFDMTVAGIYARSYNTGTVQIA
+EKITDEQRYEYMRSFGVGQPIDLGLPQQAGSVLVPPEQWDGRQRLTTAFGQGYTQTTLHT
+AQMYQALANGGVLIPARLIDATVDGDGAEKRWESSAEPHRVVSEETAAQMLRMMETVVTQ
+GTSKAAAIPGYRVGGKSSTAEAASDTGTYDGYNLGFTAVAPLDDPRFVVSVSLHRPPSKQ
+GSRDVSVAAATIMEYMLRQADVPATGAEPNDYRVFVDDPQDRPW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001144.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001144.fa
new file mode 100644
index 0000000000000000000000000000000000000000..47a4afbe0fc4f1da4c29e6435fb79b36501f4dc8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001144.fa
@@ -0,0 +1,20 @@
+>PROKKA_01363
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCIYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NTYLAEQEAAFSETDEDVLPGVF
+>PROKKA_01083
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCVYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NTYLAEQEAAFSETDEDVLPGVF
+>PROKKA_01530
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCVYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NAYLAEQEAAFSETDEDVLPGVF
+>PROKKA_01425
+MFLGTYTPRLDEKWRLILPAKFREELADGLVLTRGQERCVYVFSAAEFERVHEQLRSAPL
+SSRQARDYIRVFLSGASDETPDKQGRITVPSPLRQYAGLDRDVTVIGAGTRAEIWDTAAW
+AAYLAEQEAAFSETDEDVLGGIL
+>PROKKA_01318
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCIYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NTYLAEQEAAFSETDEDVLPGVF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001147.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001147.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e35acec6d8726e448dea8e7568b543e081a4280f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001147.fa
@@ -0,0 +1,40 @@
+>PROKKA_01366
+MPADVAVPRPRPADQDRFRAAVADALDRLLAEHRDLARDVHPLTAPLVDAIADLTAGGKR
+LRAVLAWLGWRAAGGEAEDPRIAEAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRRFE
+SLHREAGWRHAAEHFGVSAAILAGDVALGMSETAFARVLAGTPREDRARAELERMRFGVM
+AGQYLDVVAEMAPAARDAREAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDGLVTAFA
+RVSLPFGMAFQYRDDLLGVFGDPATTGKPAGDDLREGKQTVLIARAVELLAPDEAAALDA
+DLGDPDLGADRVAHWQGVLEACGARRAVEERVAALSHEAAGAVAGLLAHGVPEDVSAELT
+QLIDAYTSRRH
+>PROKKA_01086
+MPADVAVPRPRPRPADQDRFRAAVADALDRLLAEHRELARDIHPLTAPLVDAIADLTAGG
+KRLRAVLAWLGWRAAGGEAEDPRIAEAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRR
+FESLHREAGWRHAAEHFGVSAAILAGDVALGMSETAFARVLAGTPREDRARAELERMRFG
+VMAGQYLDVVAEMAPAARDAREAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDGLVTA
+FARVSLPFGMAFQYRDDLLGVFGDPATTGKPAGDDLREGKQTVLIARAVELLAPDEAAAL
+DADLGDPDLGADRVAHWQAVLEACGARRAVEERVAALSHEAAGAVAGLLAHGVPEDVSTE
+LTRLIDAYTPRRH
+>PROKKA_01527
+MPVDAAVTRPRPADQDRFRAAVAEELTRTLDEHRERARAVHPLTVPLVDAVGDLAAGGKR
+LRAVLGWLGWRAAGGDPENPRIARTGAALELFQAAALIHDDILDRSDTRRGMPSVHRRFE
+AEHRASGWRHDAGHFGVSAAILAGDVALGMSETAFAAALEGAGRPARARDEFERMRFGVM
+VGQYLDVAAEMAPPATDPAEAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDALVAAFA
+EVSLPFGLAFQYQDDLLGVFGDPAATGKPAGDDLREGKRTVLIARAVALLSPADAAALDA
+DLGDPGLSAERIAHWQRALEECGARQAVTDRVAALSARAAEAVGALEAHGVPADVRAELT
+ALIEAATTRRH
+>PROKKA_01422
+MPTPETASVSDFRAAVAERLTAVLDGHARGAARIHPDADPVVEAVSVLTSGGKRLRAVLC
+WLGWRAAGGSPTDPRAAVAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRRFEARHREH
+GWRHEAEHFGVSAAILAGDVALALSDSMFSRAIEGTPRAERARREMERMRFEVMVGQYLD
+VAAEMAPPAADPAAAERAARAVVEHKSARYSAVHPLALGALLAGADDDLVAAFEAVSLPF
+GMAFQLQDDLLGVFGDPAHTGKPAGDDLREGKRTVLVARAEALLPRGEAAALDAELGDPA
+LSAERVAHWQRRLEEVGARTAVADEVDRLSAEARRGLERLAALGVGTDVRGELAELIDAY
+TVRTA
+>PROKKA_01321
+MPADVAVPRPRPADQDRFRAAVADALDRLLAEHRERARDVHPLTAPLVDAIADLTAGGKR
+LRAVLAWLGWRAAGGEAEDPRIAEAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRRFE
+SLHREAGWRHAAEHFGVSAAILAGDVALGMSETAFARVLAGTPREDRARAELERMRFGVM
+AGQYLDVVAEMAPAARDAREAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDGLVTAFA
+RVSLPFGMAFQYRDDLLGVFGDPATTGKPAGDDLREGKQTVLIARAVELLAPDEVAALDA
+DLGDPDLGADRVAHWQAVLEACGARQAVEERVAVLSHEAAGAVAGLLAHGVPEDVSAELT
+RLIDAYTSRRH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001148.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001148.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c03e49764d3ed77114b072eca4c3bec34208d9b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001148.fa
@@ -0,0 +1,20 @@
+>PROKKA_01367
+MSTTSSDTPVPADAIPAELDALVGEWLSVPDVAEHLDQRVTRVHNLVHDRRLLAVRRPEP
+AVRSVPALFLTETGVLDSLQGTLVLLADAGFSDEEALRWLFTEDESLPGRPIDALRDGRK
+TEIRRRAQALAW
+>PROKKA_01087
+MSTTSSDTPVPADAIPAELDALVGEWLSVPDVAEHLDQRVTRVHNLVHDRRLLAVRRPEP
+AVRSVPALFLTETGVLDSLQGTLVLLADAGFSDEEALRWLFTEDESLPGRPIDALRDGRK
+TEIRRRAQALAW
+>PROKKA_01526
+MGRESAAPTRRSLAHVSTSSSDTPVPADAIPAELDALVGDWLTMPDVAERLDQRVTRVHN
+LVKDHRLLAVRRPDPAVRAVPALFLTETGLLEPLQGTLVLLADAGYSDEESLRWLFTEDP
+SLPGRPIDALRDGRKTEVRRRAQALAW
+>PROKKA_01421
+MTTEHPVDRVPSDAVSPELDALVGDWLTLPDVAERLDLRVTRVHNLINDRRLLAVRRPEP
+SVRAVPAAFLTERGLLEPLHGTLVLLQDAGFDDEEALRWLFTPDESLPGRPIDALRDGHK
+TEVRRRAQALGW
+>PROKKA_01322
+MSTTSSDTPVPADAIPAELDALVGEWLSVPDVAERLDQRVTRVHNLVHDRRLLAVRRPEP
+AVRSVPALFLTETGVLDSLQGTLVLLADAGFSDEEALRWLFTEDESLPGRPIDALRDGRK
+TEIRRRAQALAW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001150.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001150.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5617450aee7f2ac0640f60ea52999d2ee14b764d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001150.fa
@@ -0,0 +1,45 @@
+>PROKKA_01370
+MTEDPREKILAFGTAISEGAADIPGLDHWRSLPIAQAPSWADEADHRAAVAELSALPPLV
+FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM
+PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEQARRHDARRMVQAYHTS
+ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA
+MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR
+NPIGVKLGPTTTVADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE
+PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRELGTHPGGMHVELTGDDVAEC
+LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERRAPRA
+>PROKKA_01090
+MTEDPREKILAFGTAISEGAADIPGLDHWRSLPIAQAPSWADEADHRAAVAELSALPPLV
+FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM
+PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEQARRHDARRMVQAYHTS
+ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA
+MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR
+NPIGVKLGPTTTTADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE
+PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRELGTHPGGMHVELTGDDVAEC
+LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERRAPRA
+>PROKKA_01522
+MTEDPREKILAFGTAISEGAADIPGLDHWRSLPVAQAPSWADEAEHRAAVAELSQVPPLV
+FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM
+PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEEARRHDARRMVQAYHTS
+ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA
+MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR
+NPIGVKLGPTTSAADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE
+PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRALGTRPGGMHVELTGDDVAEC
+LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERVAPRR
+>PROKKA_01418
+MHEDPRDQIMAFGTAISEGAAPDPALDAWRELPIKQAPTWADEDDFRAAVAELSQVPPLV
+FAGEVDVLRTRLADVARGQAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM
+PVVKMGRIAGQYAKPRSSDTETRDGVTLPSFRGEIVNGFEFTEEARRHDARRMVTAYHTA
+SSTLNLVRAFTQGGFADLRSVHQWNRGFMENPAYAQYEQIAAEIDRAVRFMDAAGADFEA
+MRRTEFYAAHEALLLDYERALTRLDSRTGLPYATSAHFLWIGERTRDVDGAHVDFLSRVR
+NPIGVKLGPTTTVDDVRALADRLDPEREPGRLTFITRMGADKVRDVLPGIVAGVRDEGLQ
+PVWVTDPMHGNTVTAANGYKTRRFEDVMDELTGFFEVHRELGTHPGGMHVELTGDDVAEC
+LGGSDPVDEADFDEHYETLCDPRLNHQQSLELAFKVTDALAHPHQD
+>PROKKA_01325
+MTEDPREKILAFGTAISEGAADIPGLDHWRSLPIAQAPSWADEADHRAAVAELSALPPLV
+FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM
+PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEQARRHDARRMVQAYHTS
+ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA
+MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR
+NPIGVKLGPTTTVADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE
+PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRELGTHPGGMHVELTGDDVAEC
+LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERRAPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001151.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001151.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b65238a5ef34847a1da65735b215ed871ce04c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001151.fa
@@ -0,0 +1,25 @@
+>PROKKA_01371
+MSTFYWSAKTFAVAPATRLLFRPWVKGLGNVPAEGPAILASNHLSVSDSVFMPAMLDRQV
+HFLAKHEYFTGPGVKGWVTRRFFEAANQLPMDRSGGEASLRSLDAGLEALREGRLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDRVQPIGHVLPRIRRLGMIFGEPL
+DFSDRAEAVGDPRVLREVTDEIMEAIRRLSGQEYVDTYAADVKAGRTAAPPRARD
+>PROKKA_01091
+MSTFYWSAKTFAVAPATRLLFRPWVKGLANVPAEGPAILASNHLSVSDSVFMPAMLDRQV
+HFLAKHEYFTGPGVKGWVTRRFFEAANQLPMDRSGGEASLRSLDAGLAALREGRLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGVPVVPIAMIGTDRVQPIGHVLPRIRRLGMIFGEPL
+DFSGRAAAADDRRVLREVTDEIMEAIRRLSGQEYVDTYAADVKAGRVAAPPRAGD
+>PROKKA_01521
+MSTFYWSAKTFAVAPATRLLFRPWVKGLGNVPAEGAAILASNHLSVSDSVFMPAMLERQV
+HFLAKKDYFTGAGPKGWITRKFFEATNQLPMDRSGGEASLRSLDAGLEALREGRLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDQAQPIGRTLPRIRRIGMIFGEPL
+DFSDRAEGVTDARVLRAVTDEIMEAIRRLSGQEYVDAYAADVKSGRVPAPPRARD
+>PROKKA_01417
+MSAFYWSAKTFVVAPATRLLFRPWVKGLSHVPAEGPAILASNHLSVSDSVFMPAMLDRQV
+HFLAKQEYFTGRGAKGWATKKFFEATNQLPMDRSGGAASLRSLEAGLECLREGKLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDRVQPIGRILPTLRRLGMIFGEPL
+DFSHLQGREGDHRALRQVTDEIVEAIRRLSGQDYVDVYAADVKSGRVAVPPRAGRD
+>PROKKA_01326
+MSTFYWSAKTFAVAPATRLLFRPWVKGLGNVPAEGPAILASNHLSVSDSVFMPAMLDRQV
+HFLAKREYFTGPGVKGWVTRRFFEAANQLPMDRSGGEASLRSLDAGLEALREGRLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDQVQPIGHVLPRIRRLGMIFGEPL
+DFSDRAEAVGDPRVLREVTDEIMEAIRRLSGQEYVDTYAADVKAGRTAAPPRARD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001154.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001154.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e30d49867725007ae94380213d49fa3c9e8ef34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001154.fa
@@ -0,0 +1,50 @@
+>PROKKA_01374
+MSPPPAGRPTGPDATASGPVPILGGMATTAEHHDLLIIGSGSGNSLVSEHWKGRSVVIAD
+SGPFGGTCLNVGCIPTKMYAYPASLAALPPEARSLGVGLEFTGADFPAIRDRIFTRIDGI
+SRDGLRHRRDDLDYTSVIQEEVRFVGPRRVRTASGREITADQVVVAAGSRPTLPEIPGLD
+LPSVHTSDTVMRLDRLPRRLLVVGGGFIACEFASVFAGLGTEVVQVNRGHRLLKQHDMSV
+STTFTKIAARRWDLRTGWTPAGIEPVEDAERAADGWVRVRLDRAEGQEQTGIVEEAIEAD
+AVLIAVGRTPNTDRLDPAAAGLDVTDDGILASDEHQRALSDGAPVEGVYVLGDVANTWQL
+KHVANHEARVVAHNLEHPDDLRANTLGPVPAAVFTHPQAASVGLTVEQALADYGADAITV
+KTQPFGDVAYGWAMEDTEGVCTVVAEKATGRILGGHILGHEAANLIQPLVTGMAFGIDAH
+RLARGQYWPHPALTEVVENALLGLDVPDSGLL
+>PROKKA_01094
+MATSAEHHDLLIIGSGSGNSLISEHWKGRSVVIADSGTFGGTCLNVGCIPTKMYAYPAGL
+AALPPEARSLGVGLEFTGADFPAIRDRIFTRIDGISRDGLRYRRDDLDYTSVIQEEVRFV
+GPRRVRTASGREITADQVVVAAGSRPTLPEIPGLDLPSVHTSDTVMRLDRLPRRLLVVGG
+GFIACEFASVFAGLGTEVVQVNRGHRLLKQHDMSVSTTFTKIAARRWDLRTGWTPAGIEP
+VEDAERAADGWVRVRLDRAGGQEQTGIVEEAIEADTVLIAVGRTPNTDRLDPAAAGLDVT
+DDGVLASDEHQRALSDGAPVEGVYVLGDVANTWQLKHVANHEARVVAHNLEHPDDLRANT
+LGPVPAAVFTHPQVASVGLTVEQALADYGADAITVKTQSFGDVAYGWAMEDTEGVCTVVA
+EKATGRILGGHILGHEAANLIQPLVTGMAFGIDAHRLARGQYWPHPALTEVVENALLGLD
+VPDSGLL
+>PROKKA_01518
+MATSTEHHDLLIIGSGSGNSLVTEHWEGRSVAIADSGVFGGTCLNVGCIPTKMYAYPAGL
+AASAGAESERLGVGLEFTGADFPAIRDRIFQRIDAISEGGLRYRRDELEHTSVIQEEVRF
+VGPRRVRTASGREVTADQVVIAAGSRPTLPRIPGVDLPSVHTSDTVMRLPRLPRRLLVIG
+GGFIACEFASIFAALGSEVIHVNRGHRLLKAHDLSVSTAFTEIAARQWDVRTGWTPAGVE
+PVADPDRAAQGWVRVRLDRAEGQEQTGTVEEVVEADAVLMAIGRTPNTDRLDVDAAGLDV
+TEDGVLATDRHQRVLSGGAPVEGVYALGDVANTWQLKHVANHEARVVAHNLEHPEDLRSA
+VLAPVAAAVFTRPQVAAVGLTVEQALAEHGADAITVKTQAFGDVAYGWAMEDSEGLCTVV
+AEKATGRILGGHILGHDAANLIQPLVTGMAFGIDAHRLARGQYWPHPALTEVVENALLGL
+DVPDSGLL
+>PROKKA_01413
+MSPDPAASSAGDEVDGPDDPHVRAVSYADAMATTERFDLIILGSGSGNSLVTDHWEGRRV
+AIVDAGVFGGTCLNVGCIPTKMYAYPAQLAASGAEAERLGVGLDFTGADFEGIRDRIFGR
+IDAISEGGLRYRRDQLEHTEVVAEEAWFSGPKELTTASGRVLAGEQVVVAAGSRPTVPDV
+PGVGLPSVHTSDTIMRLPRQPKRLVILGGGYIASEFAAIFSGLGTEVVQVNRGARLLKAH
+DSSISTRFTALAARQWDVRTGWTLAGVEPVGDQRRADEGWVRVRLDAVEGQEQMVEREET
+LEADAVLLAVGRTPNTDRLRPEAAGFDVTAAGVLAVDEHQRVLSSGVPVEGVYALGDVAN
+AWQLKHVANHEARVVAHNLEHPEDLRANTLGPVPAAVFTRPQIASVGLTQDEARELLGED
+AVTVKEQAFGDVAYGWAMEDAEGVCTIVAERATGRILGAHLMGHDAANLIQPLVTAMSFG
+IDAHRLARGQYWPHPALTEVVENALLGLDVPDSGLL
+>PROKKA_01329
+MATSAEHHDLLIIGSGSGNSLISEHWKGRSVVIADSGTFGGTCLNVGCIPTKMYAYPAGL
+AALPPEARSLGVGLEFTGADFPAIRDRIFTRIDGISRDGLRYRRDDLDYTSVIQEEVRFV
+GPRRVRTASGREITADQVVVAAGSRPTLPEIPGLDLPSVHTSDTVMRLDRLPRRLLVVGG
+GFIACEFASVFAGLGTEVVQVNRGHRLLKQHDMSVSTTFTKIAARRWDLRTGWTPAGIEP
+VEDAERAADGWVRVRLDRAGGQEQTGIVEEAIEADTVLIAVGRTPNTDRLDPAAAGLDVT
+DDGVLASDEHQRALSDAAPVEGVYVLGDVANTWQLKHVANHEARVVAHNLEHPDDLRANT
+LGPVPAAVFTHPQVASVGLTVEQALADYGADAITVKTQSFGDVAYGWAMEDTEGVCTVVA
+EKATGRILGGHILGHEAANLIQPLVTGMAFGIDAHRLARGQYWPHPALTEVVENALLGLD
+VPDSGLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001165.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001165.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1bd16672a763c7b496ec5f351732ecb1f8c0dee8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001165.fa
@@ -0,0 +1,35 @@
+>PROKKA_01407
+MNSRKPRGSGRTPAVGRRGGPFQERDFQRQIGARRGAAAPREEAPFDEDAVPRTRGRRGR
+GAGAARAKAAHLDRIHDESGERLQKVLAAAGVASRRVSEDLIAEGRVEVDGVVVTEPGVR
+VDPATAVIRVDGISVQTDVTKQYFVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG
+RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA
+QVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGT
+VRALNAQELGHLKALVGL
+>PROKKA_01137
+MNSRKPRGSGRTPAVGRRGGPFQERDFQRQIGARRGAAAPREEAPFDEDAVPRTRGRRGR
+GAGAARAKAAHLDRIHDESGERLQKVLAAAGVASRRVSEDLIAEGRVEVDGVVVTEPGVR
+VDPATAVIRVDGISVQTDVTKQYFVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG
+RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA
+QVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGT
+VRALNAQELGHLKALVGL
+>PROKKA_01489
+MNSRKPRGSGRTPSVGRRGGPFQERDFQRQLGARRGPAGPRDEAPFDEDAVPRTRGRRGR
+GAGAARAKAANLDRIHDESGERLQKVLASAGVASRRVSEDLIAEGRVEVDGVIVTEPGVR
+VDPARAVIRVDGISVQTDVTKQYYVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG
+RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA
+KVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGS
+VRALSAQELGHLKALVGL
+>PROKKA_01400
+MNSRKPRGSGRTPAAGKRGGPFSERDFQRNLGARRGPARPKDEPAFDEDAAERRVRSRRG
+KGAGAARAKAQHLEEIHVEDGERLQKVLASAGVASRRVCEDLIAEGRVEVDGVVVTEPGV
+RVDPVRSRIQVDGISVQTDVTKQYFVFNKPRGVISTMLDPEGRPSIATYLKPGQENLFHV
+GRLDNETEGLLILTNDGELANRLTHPSWEVPKTYLVQTRGPLAKGVSNRLREGVELEDGL
+AKVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQG
+SVRAMTAQEQGHLKALVDL
+>PROKKA_01357
+MNSRKPRGSGRTPAVGRRGGPFQERDFQRQIGARRGAAAPREEAPFDEDAVPRTRGRRGR
+GAGAARAKAAHLDRIHDESGERLQKVLAAAGVASRRVSEDLIAEGRVEVDGVVVTEPGVR
+VDPATAVIRVDGISVQTDVTKQYFVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG
+RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA
+QVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGT
+VRALNAQELGHLKALVGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001169.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001169.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8acee9a3e9dca1a6cee445573d7d3d9cb6c4904d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001169.fa
@@ -0,0 +1,35 @@
+>PROKKA_01415
+MLYSTKTAEQKRIDLRETLKQGGAQQFPGAFTPLSAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ
+FNPKRCGHLDGKNMVELDTAVKRIAAAVHARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELEPLGVPVLANMTEFGKSELFTRRQLADAGVAMVI
+YPVTLLRSAMGAAERVLNAIKEEGTQQSQVEQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIGANHADL
+>PROKKA_01146
+MLYSTKTAEQKRIDLRQTLKQGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ
+FNPKRCGHLDGKNMVELDTAVKRIAAAVHARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELEPLGVPVLANMTEFGKSELFTRRQLADAGVAMVI
+YPVTLLRSAMGAAERVLHAIKEEGTQQSQVEQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIGANHADL
+>PROKKA_01484
+MLYSTKTAEQKRVDLRAALAEGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVALRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ
+FNPKRCGHLDGKNMVDLDTAVKRIAAAVDARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELAPLGVPVLANMTEFGKSELFTRQQLADAGVAMVI
+YPVTLLRSAMGAAERVLDAIKDEGTQASQVDQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIDENNANL
+>PROKKA_01391
+MLYSKKTAAQKRIDLRETLKQGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFEDAGLAGCHIEDQ
+FNPKRCGHLDGKNMVDLDTAVKRIAAAVDARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELAPLGVPVLANMTEFGKSELFTRQQLADAGVAMVI
+YPVTLLRSAMGAAERVLDAIREEGTQQSQVDQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIDSNNANL
+>PROKKA_01365
+MLYSTKTAEQKRIDLRQTLKQGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ
+FNPKRCGHLDGKNMVDLDTAVKRIAAAVDARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELEPLGVPVLANMTEFGKSELFTRQQLADAGVAMVI
+YPVTLLRSAMGAAERVLDAIKEEGTQQSQVEQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIGANHADL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001174.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001174.fa
new file mode 100644
index 0000000000000000000000000000000000000000..abc68ecfcd367415a73a6bca4535dfe890afdb7c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001174.fa
@@ -0,0 +1,40 @@
+>PROKKA_01421
+MPYTPGRRILVLTHTGREDAISAALQATRMFAEEGLVTVMLEQDVAAIRAAAGDPPEFAP
+ETLGVDCELEDITLGLVLGGDGSVLRAADFVRGYNVPLLAVNLGHVGFLAESERTDLHRT
+VQAIASESYVVIERMALDVVVHVEGREVARTWALNEASVEKSHRERMLEVVVSVDNSPLT
+SFGCDGVVLATPTGSTAYAFSAGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD
+VLTRTRETGVLWCDGRRTVELPPQARVEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG
+WRGPVTAQERAGVLHEVETVEPRHAGPRPDVVEPATMPLSVPSPADIQRHRDRGARHPGE
+DA
+>PROKKA_01152
+MPYTPGRRVLVLTHTGREDAISAALQATRMFAEEGLVSVMLEQDVAAIRAAAGDPPEFAP
+EALGVDCELEDITLGLVLGGDGSVLRAADFVRGHNVPLLAVNLGHVGFLAESERTDLHRT
+VQAIASESYVVIERMALDVVVLVEGREVARTWALNEASVEKSHRERMLEVVVSVDNSPLT
+AFGCDGVVLATPTGSTAYAFSGGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD
+VLTRTRETGVLWCDGRRTVELPPQARIEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG
+WRGPVTAQERAGVLHAVETVEPRHAGPRPDVVEPATMPLSVLSPADIQRHRDRGARHPGE
+DA
+>PROKKA_01478
+MPHNPGRRVLVLAHTGREDAISAALQATRILEEEGLVSVMLEQDVAAIRENADAPAGFAP
+QTLGVDCGLEDIVLGLVLGGDGSVLRAADFVRGYDVPLLAVNLGHVGFLAESERTDLQRT
+VQAIASEAYVVIERMALDVVVRVEDREVARTWALNEASVEKSNRERMLEVVISVDNAPIS
+SFGCDGVVLATPTGSTAYAFSGGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD
+VLTRTRETGVLWCDGRRTVELPPQARIEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG
+WRGPVTAQEREAVLREVETVEPRHAGPRPDVVEPATMPLSVLSAADIQRYRDRGARYPGE
+DA
+>PROKKA_01386
+MSETPSRRVLVLAHTGRADAIAAALQATAMLAEEGLDTVMLAEDVAAILESGTDAVGFRP
+LTLGRDCTLDDVQLGLVLGGDGSVLRAADFVRGHGIPLVAVNLGHVGFLAESERTDLHRT
+VKAIADGAYVVIERMALDVTVRVEGREVARTWALNEASVEKSNRERMLEVVVSVDDSPLT
+SFGCDGVVLASPTGSTAYAFSAGGPVVWPGVEALLCVPISAHALFSRPLVVGPHSTVAVD
+VLTRTRETGVLWCDGRRTVELPPRARIEVTRSAEPVRLARLRPTPFAERLVRKFRLPTEG
+WRGPVTEADRRTGPLAEVETVEPRHAAPRPDVVPPPSEPLTVLSPEALARYRGRDGREGD
+RTS
+>PROKKA_01371
+MPYTPGRRVLVLTHTGREDAISAALQATRMFAEEGLVSVMLEQDVAAIRAAAGDPPEFAP
+EALGVDCELEDITLGLVLGGDGSVLRAADFVRGHNVPLLAVNLGHVGFLAESERTDLHRT
+VQAIASESYVVIERMALDVVVLVEGREVARTWALNEASVEKSHRERMLEVVVSVDNSPLT
+AFGCDGVVLATPTGSTAYAFSGGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD
+VLTRTRETGVLWCDGRRTVELPPQARIEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG
+WRGPVTAQERAGVLHAVETVEPRHAGPRPDVVEPATMPLSVLSPADIQRHRDRGARHPGE
+DA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001181.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001181.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6ce5c223b3f025a840372db1d84dd21cde05da81
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001181.fa
@@ -0,0 +1,40 @@
+>PROKKA_01431
+MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAQRNDLPIVTTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFERGVPTALDGRALSPLEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+HVDQRWTELVYDGQWYSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIFGLSAKTASEREQRLRGSDDLQDVARLSND
+>PROKKA_01163
+MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADAREEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAERNDLPIVTTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFERGVPTALDGRALSPLEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+QVDQRWTELVYDGQWYSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIFGLSAKTASEREQRLRGGDDLQDVARLSND
+>PROKKA_01468
+MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTRDKAIDYAERNELPIVTTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFSPAPDVVTIAFERGVPTALDGRALSSLEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+TVDQRWTELVYDGQWFSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIFGLSAKTASERDQRLRGGDDLKDVARLANS
+>PROKKA_01375
+MKDRIVLAYSGGLDTSVAIGWIGEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAERNELPIATTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFEQGVPTALDGRALSALEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+QVDQRWTELVYDGQWFSPLKKSLDTFIDDTQKHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIYGLSAKTASEREQRLGGAADLADVARLSND
+>PROKKA_01381
+MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAERNDLPIVTTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFERGVPTALDGRALSPLEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+HVDQRWTELVYDGQWYSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIFGLSAKTASEREQRLRGGDDLQDVARLSND
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001187.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001187.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0db0c4c8941e027df3edaec97ffd3d4b505d71f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001187.fa
@@ -0,0 +1,40 @@
+>PROKKA_01437
+MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNQGPRDAAAAVLTENRVAAAPVVWTRRAVR
+DGRATAVVLNSGGANAATGAEGLEDARRTAEHAAAALGTAADDVLVCSTGLIGERLPMDT
+LTAGVAEAVAALSPDGGEDAAVAIKTTDTVAKTAVARGAGFTVGGMAKGAGMLAPGMATM
+LSVITTDADVPAPALDAALREAVRATFNRVDSDGCMSTNDTVILLASGASGTAPEPAAFA
+AALHEVCADLSRQLVADAEGARHDIAVRVVHAETEEAAEAVARAVGRSNLFKTAIFGQDP
+NWGRVIAAVGTVPESVAAFDPYALDVRFNGVQVCRASGVGEDRSRVDLTAREVLVEVDLH
+AGDAEATVWTNDLTHDYVHENSAYST
+>PROKKA_01169
+MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNEGPRDAAAAVLTENRVAAAPVVWTRRAVR
+DGRATAVVLNSGGANAATGAEGLEDARRPAEHAAAALGTSADDVLVCSTGLIGERLPMDT
+LTAGVAEAVAALSPDGGEDAAVAIKTTDTVAKTAVARGAGFTVGGMAKGAGMLAPGMATM
+LSVITTDADVPAPALDAALREAVRATFNRVDSDGCMSTNDTVILLASGASGTAPEPEAFA
+AALHEVCADLSRQLVADAEGARHDIAVRVVHAETEEAAEAVARAVGRSNLFKTAIFGQDP
+NWGRVIAAVGTVPESVAAFDPYALDVRFNGVQVCRASGVGEDRSRVDLSAREVLVEVDLH
+AGDAEATVWTNDLTHDYVHENSAYST
+>PROKKA_01461
+MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNDGPRRAAAAVFTANRVAAAPVLWSRQAVS
+DGRADAVVLNSGGANAATGAPGFQDAHATAEHAAEALGVSSGDVLVCSTGLIGERLDRER
+LFAGVAAAAGALSADGGEDAAVAIKTTDTVAKTAQARGEGFIVGGMAKGAGMLAPGMATM
+LCVITTDADVPAAVLDAALKDAVRTTFNRVDSDGCMSTNDTVILLASGAAGVAPDPEAFA
+ATLHEVCADLSRQLVADAEGAAHDVAVRVHGAQTEDAAEAVARAVTRSNLFKAAIFGQDP
+NWGRVIAAVGTVPEEVAAFDPYALDVSFNGVQVCRGSGVGEDRALVDLSAREVLVEVDLH
+AGDAEATVWTNDLTHDYVHENSAYST
+>PROKKA_01369
+MSVTAAQGFRAAGVTAGLKPSGKPDVAVVVNDGPSHTAAGVFTTNRVAAAPVRWSRQVLT
+DGRADAVVLNSGGANAATGHAGFQDAHRTAEHAAEALGVSAGDVVVCSTGLIGERLPLDT
+LLAGVDAAAAGLAEDGGADAALAIMTTDTVPKEAQASGEGWTVGGMAKGAGMLAPGMATM
+LCVVTTDADLPAAALRAALEEAVRTTFNRVDSDGCMSTNDTVVLLASGASGVAPEPTQFG
+AALHAVCADLARQLVGDAEGAGHDVLIRVVNASDEDAGEAVARAVSRSNLLKTAIFGQDP
+NWGRVISAVGTVPEEVAPFDADALDVSFNGVQVCRAAGVGDSRAGVDLSGREVVIEIDLH
+AGDAVVELWTNDLTHDYVHENSAYST
+>PROKKA_01387
+MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNEGPRRAAAAVLTENRVAAAPVVWTRRAVR
+DGRATAVVLNSGGANAATGAEGLADARRTAEHAAAALATAADDVLVCSTGLIGERLPMDT
+LTAGVSEAVAALSPDGGEDAAVAIKTTDTVAKTAVARGAGFTVGGMAKGAGMLAPGMATM
+LSVITTDADVPAPALDAALREAVRATFNRVDSDGCMSTNDTVILLASGASGTAPEPEAFA
+AALHEVCADLSRQLVADAEGARHDIAVRVVHAETEEAAEAVARAVGRSNLFKTAIFGQDP
+NWGRVIAAVGTVPESVAAFDPYALDVRFNGVQVCRASGVGEDRSRVDLTAREVLVEVDLH
+AGDAEATVWTNDLTHDYVHENSAYST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001188.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001188.fa
new file mode 100644
index 0000000000000000000000000000000000000000..575e5904695939b1ca9915932c8d5b484012e33a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001188.fa
@@ -0,0 +1,35 @@
+>PROKKA_01438
+MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE
+TTAEVLAGHDVVILALPHGASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH
+AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT
+SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMPR
+GILATATARLRPGVAAADVRAAWAAAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD
+ERAGRVIVCAVLDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP
+>PROKKA_01170
+MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE
+TTADVLAGHDVVILALPHEASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH
+AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT
+SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMSR
+GILATATARLRPGVAAADVRAAWAAAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD
+ERAGRVIVCAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP
+>PROKKA_01460
+MTHTVAVSGASGYAGGEALRLLAGHPDVAVGAITAHSNAGERLGALQPHLHSLADRVLEE
+TTADVLAGHDVVILALPHGASGALAAQIAERSPETLVIDAGADHRLESAADWEAFYGSEH
+AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT
+SGAGKAAKPHLLGSEVMGGMSPYGVGGGHRHTPEIEQGLSQAAGERVQISFTPTLAPMAR
+GILATATARLRPGADPAAVRGAWERAYADERFVHLLPEGLWPATKSVLGSNHVQMQLAVD
+ERAGRVIVTAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP
+>PROKKA_01368
+MTFTVAVSGASGYAGGEVLRLLAGHPEVQIGAISAHSNAGERLGSLQPHLHALADRVLDD
+TTADVLAGHDVVVLALPHGASAAVAAELAERSPRTLVIDAGADHRLESAADWERFYGTDH
+AGTWPYGLPELPGQRERLAGATRIAVPGCYPTTSILALAPGFAAGLLETRDVVIVAASGT
+SGAGRAAKPHLLGSEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVQISFTPTLAPMPR
+GILATATARLKEGVTADRVRAAWEDAYGPERFVHLLPEGQWPTTKAVVGSNHVVMQLAVD
+PHAGRVIVTAALDNLTKGTAGGALQSMNIALGLPEQLGLEIQGVAP
+>PROKKA_01388
+MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE
+TTAEVLAGHDVVILALPHGASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH
+AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT
+SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMSR
+GILATATARLRPGVAAADVRDAWAEAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD
+ERAGRVIVCAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001194.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001194.fa
new file mode 100644
index 0000000000000000000000000000000000000000..669781dd445af5b669b6173eb763b99e50289f41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001194.fa
@@ -0,0 +1,20 @@
+>PROKKA_01446
+MTAAPSRPSPPAHVRARGLWNLLNLATPLGLVGAVVAGCALRPGPHGLIEAHGWTHRFPG
+GAAFTVGDVVFTRPGLRMTPALWRHEAGHADQYALLLGLPFLPAYALAAAWSMWRTGDPA
+SRNVFERRASLALGGYIERPVVRGLRRRR
+>PROKKA_01178
+MTAAPSRPSPPAHVRARGLWNLLNLATPLGLVGAVVAGCALRPGPHGLIEARGWTHRFPG
+GAAFTVGDVVFTRPGLRMTPALWRHEAGHADQYALLLGLPFLPAYALAAAWSTWRTGDPA
+SRNVFERRAGLALGGYVERPVVRGLRPRR
+>PROKKA_01453
+MTTPDSPAGVGAGPPPLRWRTRARGLWNLVNLSTPLGLVGAVVSGCALRPGPHGLIEARG
+WRHSFPGGAAFTVGDVVFTRPGLRMTEDLWRHEAGHAAQYAGMLGLPFLPAYAAAAAWST
+WRTGDPASRNPFERGAGLALGGYVERPVRRGPRRRR
+>PROKKA_01357
+MSAAPARPTRPRGAARLRGLWNLLNLSTPLGVVGAVLAGCPLRPGPDGLLHAEGWRHRFP
+GGAAFTVGDVVFTRPGLEMTERLWRHEGAHAAQYAACLGLPFLPLYGMSAAWSSWRTGDP
+ASRNPFERGAGLERGGYVQAAVRRGPGRGALKPAGGDLRDARRA
+>PROKKA_01396
+MTAARSRPSPPAHVRARGLWNLLNLATPLGLVGAVVAGCALRPGPHGLIEARGWTHRFPG
+GAAFTVGDVVFTRPGLRMTPALWRHEAGHADQYALLLGLPFLPAYALAAAWSMWRTGDPA
+SRNVFERRAGLALGGYVERPVVRGLRPRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001195.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001195.fa
new file mode 100644
index 0000000000000000000000000000000000000000..165db53d9f3f661bfb324eae300e90a01070caef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001195.fa
@@ -0,0 +1,26 @@
+>PROKKA_01447
+MFESTRKRVRVRAWRGRRDAPTVVAMTSRAPAPAARVLLTGFEPFGGDVHNPSIAAARDA
+VGILADRGVTAEAVELPCAFGAAGPALTAALDRVRPEVAIAVGLAGGTATVRVERVAVNL
+QDARIPDNAGEQPVDRPVRADGPAALFATLPAKRAVAAIREAGVAAEPSLSAGAFVCNHV
+MYSLLDGPGTARAAGFIHVPWDTEHRPTPDTPALPAADLARAVAEAALTALAGGPDLDVP
+GGTLH
+>PROKKA_01179
+MTSRAPAPAARVLLTGFEPFGGDVHNPSIAAARDAVGILADRGVTAEAVELPCAFGAAGS
+ALTAALDRVRPEVAIAVGLAGGTAAVRVERVAVNLQDARIPDNAGDQPVDRPVRADGPAA
+LFATLPAKRAVAAIRAAGVAAEPSLSAGAFVCNHVMYALLDAPGTARAAGFLHVPWDAEH
+RPTPDTPALPAADLARAVAEAALTALAGGPDLDVPGGTMH
+>PROKKA_01452
+MTTPASASAVRVLLTGFEPFGGDGHNPSIVAARDAVALLAERGVAAEAVELPCAFAAAGP
+ALAAALERTRPEAAVAVGLAGGTAAVRVERIAMNLQDARIPDNAGDQPVDRPVRAEGPAA
+HFATLPVKRAVEAVRAAGVPAEPSLSAGAFVCNHVLYALLDAPGTARAAGFVHVPWDLAH
+RPRPDAPALPAEDLARAVAEVALVALEGGADLDVPGGTLH
+>PROKKA_01356
+MTDPVRVLLTGFEPFGGDDHNPSIEAARAAAAALTADGTPAVAVELPCVFAAAGPALAAA
+LEAHRPEIAVAVGLAGGTAAVRVERVAVNLQDARIPDNAGDRPADRPVRSGGPAAHFATL
+PVKRAVAAVREAGVPAEPSLSAGSFVCNHVMYSLLDAPAPARAAGFVHVPWSREHAPTPQ
+TPALPAADLARAVAAVARAALVEGPDLDVPGGALH
+>PROKKA_01397
+MTSRAPAPAARVLLTGFEPFGGDVHNPSIAAARDAVGILADRGVTAEAVELPCAFGAAGP
+ALTAALDRVRPEVAIAVGLAGGTATVRVERVAVNLQDARIPDNAGEQPVDRPVRADGPAA
+LFATLPAKRAVAAIREAGVAAEPSLSAGAFVCNHVMYALLDAPGTARAAGFIHVPWDTEH
+RPTPDTPALPAADLARAVAEAALTALAGGPDLDVPGGTLH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001199.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001199.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6021d8fc6e6c4c9a2b251b0ac1ff48bfc0da1c37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001199.fa
@@ -0,0 +1,33 @@
+>PROKKA_01452
+MTPHAEPMTHPRAERVRAVAALAGRSARRRTGTFLVEGPQACREALRAHLGEGPTAAAGQ
+WRAGRVLTQVYVSGGLVDRDPALAELVARVRDRPTPGGERVLVREASDEVLTAMADAVTG
+QDIVAVARMPEPQAVEAVLEEARLAAVLCRVQDPGNAGTVIRAADAAGADAVVLTPGSVD
+PFNPKVVRSTAGSLFHLPVATAVPAEAAAAAARAAGLQVWAADGYASDRLDALAPGVVAA
+PTAWLFGNEAQGLDDGELALADRRVAVPLYGAAESLNVGTAATVCLYSSAMAGARRAG
+>PROKKA_01184
+MTPPAEPLTHPRAERVRAVAALAGRPARRRTGTFLVEGPQACREALRAHLGEGPAGAARQ
+WPAGRVLTQVYVSAGLADRDSELAALVERVAADGPDGGERVFVREASDEVLTAMADAVTG
+QGVVAVARVPDQPALEDAFDGAALAAVLCRVQDPGNAGTVLRAADAAGADAVVLTAGSVD
+PFNPKVVRSTAGSLFHLPVLAGVQAEDVAVTARAAGLQVWAADGHGSDRLDALSPASLGA
+RTAWLFGNEAQGLDEAELALAERRVAVPLYGAAESLNVGTAATVCLYASAMASPTTRD
+>PROKKA_01447
+MARVKRAVNAHKKRRTMLELASGYRGQRSRLYRKAKEQMLHSFTYNYQHRHKRKGDFRRL
+WITRINAAARANGMTYNRFMQGLKLAGVEVDRRMLAEIAVSDAATFAVLVKTAREALPAD
+VNAPRRLPLVGPGTPGSPPRVRRGHRRRRGGPSDEEARPVGVCAPAPRRTRPGEPMTPPA
+EPLTHPRAERVRAVAALAGRPARRRTGTFLVEGPQACREALRAHLGEGPAGAVRQWPAGH
+VLTQVYVSAGLAERDPDLAALVERVADGGPGGERVLVREASDEVLTAMADAVTGQGIVAV
+ARIPDQPPLADAFDGAALAAVLCRVQDPGNAGTVLRAADAAGADAVVLTAGSVDPFNPKV
+VRSTAGSLFHLPVLTGAEAAAVADASRGAGLQVWAADGYGDDRLDALAPETTAAPTAWLF
+GNEAQGLDEAELALADRRVAVPLYGAAESLNVGTAATVCLYASAMAAAVRRDG
+>PROKKA_01351
+MSRAPQPDDELMQNPRAERVRAVAALAGRAARRRSGTFVVEGPQSCREALRAHLGEGPER
+TRAQWRPGAVLTQLFVAPDLFARDPGLGDLVARLHDLTGPDRVLVREATDEVLTAMSDAV
+TAQGIVAVARIPQPLTAEDAWSDARLAAVLCRVQDPGNAGTIVRAADAAGADLVAFTAGS
+VDPFGPKAVRSTAGSLFHVPLVVGTEADAAADAARAAGMQVWAADGYGADRLDALEQDVL
+GAPTAWLLGNEAQGLSAAELELADRRVAVPLYGAAESLNVATAATVCLYASAMAAPHA
+>PROKKA_01402
+MTPHAEPMTHPRAERVRAVAALAGRSARRRTGTFLVEGPQACREALRAHLGEGPAAAAGQ
+WRAGRVLTQVYMSVGLVDRDPALAELVARVRDRPTPGGECVLVRQASDEVLTAMADAVTG
+QDIVAVARMPEPQAVEAVLGEARLAAVLCRVQDPGNAGTVIRAADAAGADAVVLTPGSVD
+PFNPKVVRSTAGSLFHLPVVTAVPAEAAAAAAWAAGLQVWAADGYGSDRLDALAPGVVAA
+PTAWLFGNEAQGLDGGELALADRRVAVPLYGAAESLNVGTAATVCLYSSAMAGARRAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001202.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001202.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec58557e77206754a24e8735043317a5b53f7644
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001202.fa
@@ -0,0 +1,19 @@
+>PROKKA_01456
+MVYGKLTTMTDERQAQDATPMDAPAEIRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSP
+DARELIDLDEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGK
+GPGEKFTGPVN
+>PROKKA_01188
+MDAPAEIRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSPDARELIDLDEARKLITALAG
+LVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGKGPGEKFTGPVN
+>PROKKA_01444
+MTDERQAHDANDQDSPAEVRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSPDARELVDL
+DEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGKGPGEKFTG
+PVN
+>PROKKA_01347
+MTDQNQHQHAAGEDVPTEVREIHEVPAVEVITTTAVHLMTAAAVKVGLADSPDAREMTDL
+DEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGKGPGEKFTG
+PVN
+>PROKKA_01406
+MVYGKLTTMTDERQAQDATPMDAPAEIRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSP
+DARELIDLDEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGK
+GPGEKFTGPVN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001204.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001204.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f79bfa148f13c048b999742063df5cc6b61b6750
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001204.fa
@@ -0,0 +1,15 @@
+>PROKKA_01458
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS
+>PROKKA_01190
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS
+>PROKKA_01442
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS
+>PROKKA_01345
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRTCEVIDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS
+>PROKKA_01408
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001206.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001206.fa
new file mode 100644
index 0000000000000000000000000000000000000000..39e320e755b9a198967d016388cab04fc682544c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001206.fa
@@ -0,0 +1,51 @@
+>PROKKA_01460
+MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDLAELLAIARSGLVDAVLVAGDTESLT
+AAFLEETARLPRPVGVAALSEVRTERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEG
+RRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPGLTDPWRGADEPDDAGPGAAPAA
+ATPDGGPATADEGADPAPSPEEGEPAGPARESLVTVVWGPTGAPGRTTVAVNLAAEHAVA
+GRNTLLIDLDTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADL
+TVLTGLTRVDRWPELRPAAVSALIAAARERWDRVVVDVGFGLEQDEELSFDVPAPQRNGA
+TLAALAAADEVIAVGGPDAVALPRLVRGVEELAEVAPAARLRVVVNRLRPAAAGVAPRGQ
+VEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPA
+RRGRHRARPSQTIAAVSSDAARDATDTGRPARRRTLIPWSVRSRRTP
+>PROKKA_01192
+MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDIAELLAIARSGLVDAVLVAGDTESLT
+AAFLEETARLPRPVGVAALSEVRAERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEG
+RRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPGLTDPWRDADEPDDAGPGAAPAA
+ATPDDGPATAGEGADPAPSPEEGEPTAPARESLVTVVWGPTGAPGRTTVAVNLAAEHAMA
+GRNTLLVDLDTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADL
+TVLTGLTRVDRWPELRPAAVSALIAAAREHWDRVVVDVGFGLEQDEELSFDVPAPQRNGA
+TLAALAAADEVIAVGGPDAVALPRLVRGVEELAEAAPAARLRVVVNRLRPAAAGVAPRGQ
+VEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPA
+RRGRHRARPSQTIAAVSSDAARDATDPGRPARRRTLIPWSVRSRRTP
+>PROKKA_01440
+MTVRIALATTVLPGLDHIGPLERHQTRITVVRRAEDLAELLAIARSGLVDAVLVAGATEA
+VTGAFLEELARLPRPVGAAAISEVRAERRRLRALGVPCVRADAGPEPLAAAVVEAALAAA
+DGRRARADAVAEDEGGEDPVDGLDGIELTYGVLDDDPRLGPPLLGGDPERSAVSAARPEA
+GAGDEAVDDGRRGGRAGDDLVPADAAQGGVTRDGVAQDRAQDGFARDDAQDFAAWDADAA
+GRSVPDVDRPDPRDPDGDAAEHAEDRPDVEASGTPGDARVIVVWGPTGAPGRTTVAVNLA
+AEHAVAGRSTLLVDLDTYGPSVGAHLGLTEESAGVARAVRRADHGPLGPADLEAAGVRVR
+VAGAELTVLTGLTRVDRWPELRPSALTSLLAAARGRWERVVVDVGFGLEQDEELSFDVPA
+PQRNGATLAALAAADEVLAVGGPDAVSLPRLVRGTEELVEAAPEARLRVVVNRLRPAAAG
+VSPRSQVEAVWSRYASAGIPLAAFLPWDPAAADRALLGGQVLAEAAPNSALRRALAELAD
+VDPRGARRTGRRRRPTGQGPAGAARRHPQDEGAARPSRRRTLMPWSARSRRTP
+>PROKKA_01343
+MRVALATTLMPGRDHVGPLEQAQAEVTVVRRAEDLAELLAAARSGLVDAVLVAGDLSALA
+RGFVDEVREAPRPVAVVAMGEVRAERERVRTLGVPCLSADADPLALAAAVQSAVRARLTG
+ARPELGSETPPADPPAPAPGTPDGGDPEAVRVAAVRDREGTPRLPEPNPVRVDALAASEV
+DALFTEETSPVAAADEAGPASPDAAGPDAVTASPADTAPEDGPEGGPERGRTGRTVAVWG
+PTGAPGRTTVAVNLAAESAVAGLRTLLVDLDTYGPSVGVHLGLTEETAGLARAVHRAERG
+SVTREDLVDAAVRVRVAGGDLDVLTGLTRPDRWPEVRPGALREVLQAARDGWDRVVLDLG
+FCVEEDEELSFDVPAPQRNGATLAGLAAADRVLVVGGADAVAMPRLLRAVEALPAGVEQD
+RVRVVVNRVRPQASGVAPQAQVAGVWERYGPPIPLVAQLPWDPGAADRALLGGQVLAEAA
+PGSALRAAVLELARLDPAVAARTQSAGRGRRPAVRGLRRRLAPWSAPSPRTP
+>PROKKA_01410
+MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDIAELLAIARSGLVDAVLVAGDTESLT
+AAFLEETARLPRPVGVAALSEVRAERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEG
+RRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPGLTDPWRDADEPDDAGPGAAPAA
+ATPDDGPATAGEGADPAPSPEEGEPTAPARESLVTVVWGPTGAPGRTTVAVNLAAEHAMA
+GRNTLLVDLDTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADL
+TVLTGLTRVDRWPELRPAAVSALIAAAREHWDRVVVDVGFGLEQDEELSFDVPAPQRNGA
+TLAALAAADEVIAVGGPDAVALPRLVRGVEELAEAAPAARLRVVVNRLRPAAAGVAPRGQ
+VEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPA
+RRGRHRARPSQTIAAVSSDAARDATDPGRPARRRTLIPWSVRSRRTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001211.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001211.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e1870acaf65359160844add8c7ebbc3fcfa7f695
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001211.fa
@@ -0,0 +1,20 @@
+>PROKKA_01465
+MTTLATRPRAASDRRTADTLLHGPAHSPAVLPRGEEIARRARTEQGREELRRVRSLAAVI
+AVACVEVETGRRALRDLSAWLSPEVLDKLTRRMELLGAVAPTGPGRRPSAAVPPRTPKSA
+PRPVGARVCEVAPGRVEASATVLWEGRARAFALRLERRLSRWKVTSVEIG
+>PROKKA_01197
+MTALATRPRTASARRTADTLLHGPAHSPAVLPRGEEIARRARTEQGREELRRVRSLAAVI
+AVACVEVETGRRALRDLSAWLSPEVLDKLTRRMELLGAVAPTGPGRRPSAAVPPRTPASA
+PRPVGARVCEVAPGRVEASATVLWEGRARAFALRLERRLSRWKVTSVEIG
+>PROKKA_01435
+MIAVACVEVETGRRALRDLSAWLSPEVLDKMTRRMDLLGLAEQDRPRARSAAAGVSRAPA
+AAPRPVGARVCEVAPGRVEASATVLCDGRARAFALRLERRISRWKVTSVEIG
+>PROKKA_01338
+MTHSVRADRTMIRTSADRPAHRPAQEDPMTTLAPALAHGPTRPRPVSRTAPSRRDTESAL
+LRGPARRMSAVPTGEDLVRRAEQEDDREELRRLRSLAAVVAVACVETEAGRRPVRDLAGW
+LAPETYEKMCRRVDLLERTGTRPPSGSAPRPVGARVCAVRPGAVEASATVLVAGRARAVA
+LRIERRLSRWKVTHLEIG
+>PROKKA_01415
+MTTLATRPRAASDRRTADTLLHGPAHSPAVLPRGEEIARRARTEQGREELRRVRSLAAVI
+AVACVEVETGRRALRDLSAWLSPEVLDKLTRRMELLGAVAPTGPGRRPSAAVPPRTPASA
+PRPVGARVCEVAPGRVEASATVLWEGRARAFALRLERRLSRWKVTSVEIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001213.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001213.fa
new file mode 100644
index 0000000000000000000000000000000000000000..785f531865cf4cbe86c62b36319ca79e97d08f1f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001213.fa
@@ -0,0 +1,25 @@
+>PROKKA_01467
+MTMDVSYIARNLRLPESFRDHVVERTERLQPLAEGADTLEVRVTKSSHHKHSDETVRVEL
+TVRGPRDVVRAEADADDKLVAFDQAATRLAERLRRLRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPSGAALAAEEAAEQDAPEVGTPVRIRQKAFPATPMSVDEAVDAMELVGHDFFLFQN
+AETGVPSVVYRRRGWSYGVIRLDESLPQDHVSASEGERAYQARED
+>PROKKA_01199
+MTMDVSYIARNLRLPESFRDHVVERTERLQPLAEGADTLEVRVTKSSHHKHSDETVRVEL
+TVRGPRDVVRAEADADDKLVAFDQAATRLAERLRRMRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPSGAALAAEEAAEQDAPEVGTPVRIRQKAFPATPMSVDEAVDAMELVGHDFFLFQN
+AETGVPSVVYRRRGWSYGVIRLDESLPQDHVSASEGERAYQARED
+>PROKKA_01433
+MTMDVSYIARNLSLPESFRDHVAERTERLHTLAEGAETLEVRVTKSSHHKHSDETVRVEL
+TARGPREVVRAEADADDKQVAFDMAVTRLAERLRRMRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPNGAQMAAEDAAREQDIPEEGTPVRIREKAFPATPMTVDEAVDAMELVGHDFFLFQ
+NSETGVPSVVYRRRGWSYGVIRLDESLPADHVSATEGERAYQAREA
+>PROKKA_01335
+MTLDVSYIARGITLSDRFREHVEERLEKIEPLAEGAETLEVKVSRSSHHRHSDEGMRVEL
+TLRGAREVVRAEGDADDKAAAFDAALSRIAERLRRMRDRRKDRRHGKGSAASRGAGEIPF
+VPPLPAVGQADAPADEAPESGTPVSIRAKRFPATPMSVDRAVDAMELVGHDFYLFQDETT
+GVPSVVYRRRGWSYGVISLDESLPAHHVAPVEGERVYQASREADAE
+>PROKKA_01417
+MTMDVSYIARNISLSESFRDHVVERTERLQPLAEGADTLEVRVTKSSHHKHSDETVRVEL
+TVRGPRDVVRAEADADDKLVAFDQAATRLAERLRRMRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPSGAALAAEEAAEQDAPEVGTPVRIRQKAFPATPMSVDEAVDAMELVGHDFFLFQN
+AETGVPSVVYRRRGWSYGVIRLDESLPQDHVSASEGERAYQARED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001216.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001216.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c9f4cda282a9d68af068279d4ed90777c5e7a4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001216.fa
@@ -0,0 +1,25 @@
+>PROKKA_01471
+MGKAKILVVDDDEALAEMIGIVLRNDGFEPAFAADGTSALPAFHRERPDLVLLDLMLPGI
+DGIEVCRLIRDESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLHIGDLEIDVAGHEVTRGGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG
+>PROKKA_01203
+MGKAKILVVDDDEALAEMIGIVLRNDGFEPTFAADGTSALPAFHRERPDLVLLDLMLPGI
+DGIEVCKLIRAESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLHIGDLEIDVAGHQVTRAGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG
+>PROKKA_01429
+MSRAKILVVDDDEALAEMIGIVLRNDGFEAAFAADGTAALPAFHRERPDLVLLDLMLPGM
+DGIEVCKLLRSESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLQIGDLEIDVAGHQVTRDGAAISLTPLEFDLLVALARRPRQVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG
+>PROKKA_01331
+MSKARILVVDDDEALAEMIGIVLRNDDFEPSFAVDGTSALPAFRSARPDLVLLDLMLPGI
+DGIEVCKQIRAESDVPIIMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEQRPAEALAIGDVRIDVAGHQVSRGGAPISLTPLEFDLLVALARKPRQVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRAKVEPDPENPTVVLTVRGVGYKAGQV
+>PROKKA_01421
+MGKAKILVVDDDEALAEMIGIVLRNDGFEPAFAADGTSALPAFHRERPDLVLLDLMLPGI
+DGIEVCRLIRDESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLHIGDLEIDVAGHEVTRGGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001218.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001218.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0417292b21e8fbe321c30e3f7d85f82f644cf1c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001218.fa
@@ -0,0 +1,20 @@
+>PROKKA_01473
+MSPDYDPHASSLPGTADPAVLDELFAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHD
+LPPSDPGREAAQIARLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALAAEGRPDAEAEP
+GESPGDADD
+>PROKKA_01205
+MSPDYDPHASSLPGTADPAVLDELFAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHD
+LPPSDPGREAAQIARLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALAAEGRPDAEAEP
+GESPGDADD
+>PROKKA_01427
+MSPDYDPHASSLTGRTDPEVLAELYAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHE
+LPPSDPGREAAQIERLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALASGAGPEAPAGD
+PAADSLPDGTRTDAGDDPRRGGADA
+>PROKKA_01329
+MSHDYDPHASSLAGTADQDILEELYEIRGSIDNIDASLVYLLAERFKFTQRVGRLKARHA
+LPPSDPGREAAQIERLQDLARDADLEPEFAEKFLNFIIAEVIRHHRAIAEDEAPVARPAE
+ASDAGSADA
+>PROKKA_01423
+MSPDYDPHASSLPGTADPAVLDELFAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHD
+LPPSDPGREAAQIARLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALAAEGRPDAEAEP
+GAGSGDADD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001229.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001229.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0e64e8888c57fac2d8ff445766d775780d11e3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001229.fa
@@ -0,0 +1,30 @@
+>PROKKA_01486
+MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI
+EDDYREDQDASRSWGQKALAASQKADDFRAKGDTASADKFDNLAKVAIERQMDFERQAKS
+AEPTIASQREIVERLKTGLDQMKVKRQQLVAKRDELTARAKSAHAQSAVADAVKSIDLLD
+PTSEVSRFEEKVRREEARVRGQQEIAASSLDAQFESLEDLGEKTEVEARLAALKAGGAGQ
+AALTSGDVDADETLTLDYAAEGTAEETGTARG
+>PROKKA_01218
+MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI
+EDDYREDQDASRSWGQKALAASQKADDFRTKGDTASADKFDNLAKVAIERQMDFERQAKS
+AEPTIASQREIVERLKTGLDQMKVKRQQLVAKRDELTARAKSAHAQSAVADAVKSIDLLD
+PTSEVSRFEEKVRREEARVRGQQEIAASSLDAQFESLEDLGEKTEVEARLAALKAGGAGQ
+AALTSGDVDADETLTLDYAAEGTAEETGTARG
+>PROKKA_01416
+MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI
+EDDYREDQDAARSWGQKALAASQKADDFRTKGDAASAEKFDNLAKVAIERQMDSERQAKS
+AEPTITSQREIVERLKTGLDQMKVKRQQLVSKRDELTARAKSAHAQSAVADAVKSIDLLD
+PTSEVSRFEEKVRREEARVRGQQELAASSLDAQFESLEDLGEKTEVEARLAALKSGGAGQ
+SALTAGGSEGSDLALDYGAETTAEQGAEQTRVERG
+>PROKKA_01316
+MVKQSILGRITTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMM
+EDDYREDQEAARSWGQKALAASQKADEFRTKGEAANADKFDNLAKVAIERQMDAERQAKT
+AEPTITSQREIVDRLKTGLDQMKVKRQQLVSKRDELTARSRTAEAQTKVNEAVKSIDIMD
+PTSEISRYEEKVRREEARVRGQQELAASSLDAQFESLEDLGEQTEVEARLAALKSGSAPS
+ALTAGSEELTLDYSGAETGTQTGTAERA
+>PROKKA_01436
+MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI
+EDDYREDQDASRSWGQKALAASQKADDFRTKGDTASADKFDNLAKVAIERQMDFERQAKS
+AEPTIASQREIVERLKTGLDQMKVKRQQLVAKRDELTARAKSAHAQSAVADAVKSIDLLD
+PTSEVSRFEEKVRREEARVRGQQEIAASSLDAQFESLEDLGEKTEVEARLAALKAGGAGQ
+AALTSGDVDADETLTLDYAAEGTAEETGTARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001239.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001239.fa
new file mode 100644
index 0000000000000000000000000000000000000000..842aa7aafa4711d60681f7aae3400a8b2c7339c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001239.fa
@@ -0,0 +1,104 @@
+>PROKKA_01521
+MTREHGVDPFDDDAAAPERAARLVRTAAAPEDRITLTDEQEAIASLAPGHNAVLVLGAPG
+TGRTTVAVEYAARRIEAGLDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVRT
+WSSYAFDLLRRARVTGPLRHLEVAPRLLTGAEQDTVIAELLEGYAAGLAAAPDWPADVAP
+AVEARGFRREVRELVDRMSELGLEPGRLQELGTAHGRPEWEAAAVLLQDYRDRIDLGMAE
+AFDAAGLLSAAVRVLTERHPEDPERDAAAQAFVAAERDRLAVLVVEDLHEATPAVHDLLT
+VLGRGRDVLLTASPDTTVEGFRGARPDLLARYPGVLDPDPVPGAAPPASPDGRVRVLTRG
+HRMRAEVQDAYLRVARRVRQRTAGVERTRTETVPADGDGAVRAHVVPTRAHEDQLVLERV
+LRVHHEDGVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTLV
+DAAGALAEDPEARVEDVLDPDEVVGLLTGRYGMASALHVRRLRQDLLAAERGRGGRRTSD
+ALLAAALLDPSLAGPEHERHRALRRVHWMLRDGLEAARAPSASPETVLWALWSASGRAER
+WRSLALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGASPESFAVYMESQDLP
+VDTLARRAESGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLVDLVT
+LPADAPWPTDHRTRLREVRQDELRMLAAAVSRARRQVVVTAVRSPDEGPSDFLDLVDPPE
+RLPAEARDAAGVRRLTAVPDPITAPALVGRLRRVLEAGDEADAADGATPRAAAAAGLAVL
+AADGVGVADPRRWWGLLPLSTEAALVDPEREVVALSPSRVETALRNPLDWVLYHVGANAG
+GTLAQSVGTLVHSVAEHHPEGVPEDVRAELERRLPELGLPEGWITEIEHDRARGLVDAYI
+GYWSIARAAGRRPVAQEVRLLADLTWGGTTVRITGVVDRLEADAQGRPFIADLKTGRSAP
+TGAEMARQPQLAAYQVAVRAGGLEQVRDDPATDPALRAALAGLERPTTPAGAALVQLGAG
+TQKTKVQDQPALEDEDTWALEQVFTAARRTTGPRFLALHEAGARRCALPSVCPLCSEGRQ
+VTEWPR
+>PROKKA_01230
+MTREHGVDPFDDDAAAPERAARLVRTAAAPEDRITLTDEQEAIASLAPGHNAVLVLGAPG
+TGRTTVAVEYAARRIEAGLDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVRT
+WSSYAFDLLRRARVTGPLRHLEVAPRLLTGAEQDTVIAELLEGYAAGLAAAPDWPDDVAP
+AVEARGFRREVRELVDRMSELGLEPGCLQELGTAHGRPEWEAAAVLLQDYRDRIDLGMAE
+AFDAAGLLSAAVRVLTERHPEDPERDAAAQAFVAEERDRLAVLVVEDLHEATPAVHDLLS
+VLGRGRDVLLTASPDTTVEGFRGARPDLLARYPEVLDPDPVPGAAPPASPDGRVRVLTRG
+HRMRAAVQDAYLRVARRVRQRTAGVERTRTETVPADGDGAVRAHVVPTRAHEDQLVLERV
+LRVHHEDGVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTLL
+DAAGALAEDPEARVEDVLDPDEVVGLLTGRYGMASALHVRRLRQDLLAAERGRGGRRTSD
+ALLAAALLDPSLAGPEHERHRALRRVHWMLRDGLEAARAPSASPETVLWALWSASGRAER
+WRSLALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGASPESFAVYMESQDLP
+VDTLARRAESGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLVDLVT
+LPADAPWPTDHRTRLREVRQDELRMLAAAVSRARRQVVATAVRSPDEGPSDFLDLVDPPE
+RLPAEARDAAGVRRLTAVPDPITAPALVGRLRRVLEAGDEADAADGATPRAAAAAGLAAL
+AEDGVTVADPRRWWGLLPLSTEAALVDPEREVVALSPSRVETALRNPLDWVLYHVGANAG
+GTLAQSVGTLVHSVAEHHPEGVPEDVRAELERRLPELGLPEGWITEIEHDRARGLVDAYI
+GYWSIARAAGRRPVAQEVRLLADLTWGGTTVRITGVVDRLEADAQGRPFIADLKTGRSAP
+TGAEMARQPQLAAYQVAVRAGGLEQVRDDPATDPALRAALAGLEHPTTPAGAALVQLGAG
+TQKTKVQDQPALEDEDTWALEQVFTAARRTTGPRFLALHEAGARRCALPSVCPLCSEGRQ
+VTEWPR
+>PROKKA_01404
+MTWQADEDLLLDDDAAAPERAARLVSPAAAPAERVALTLEQEAVAAMGPGHGAVLVLGAP
+GTGRTTVAVEYAARRLESGTDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVR
+TWTSYAFDLLRRARVTGPLSHLPVAPRLLTGAEQDTVIAELLEGYAAGHAEAPRWPQDVA
+AAVETRGFRREVRELVDRMSEFGVEPGRLQELGAAHARPVWEAAAVLLQDYRDRIDLGLA
+EAFDAAGLISAAVRVLTERHPEDPERDAAALAFAAAERERLRTLVVEDLQEATPAVHDLL
+AVLGRGRDVLLTAGPDTAVEGFRGARPDLVSRYPQALDPDPVPGAPEAPSSGERTRVLTQ
+GHRMAPEVQDAFLRVARRVRQRTAAVEHTRTQTAPADGPGTVRGHVVPTRAHEDQLVLER
+VLRVHHEDEVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTL
+LAAAGVLADDPEAGVEDVLDPDEVVALLTGRYGMAGALHVRRLRQDLLAAERGRGGRRSS
+DALLAAALLDPALAGPEHERHRALRRVHWMLRAGIEAARAPSASPEAVLWALWSASGRAE
+RWRSTALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGAAPEAFAVYMESQDL
+PVDTLARRAEAGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLADLL
+TLPEGGAWPTDHRTRLREVRQDELRMLAAAVSRARRQVVVTAVRSAEDAPSDFLDLVDPP
+ERLPAPARDEAGVRRLTAVPDPITAPALAGTLRRRLEEDPGQGPAAAGLAALARDGVGVA
+DPRRWWGLLPLSTDAGLADPAQDVVALSPSRVETALHNPLNWLLYHVGATAGGTLAQSVG
+TLVHSVAEHHPEGVPEQVRAELERRLPELGLPEGWITEIEHERARALVDAYIGYWSIARD
+AGRRPVAQEVRLLAELTWGGTTVRITGVVDRLEADAEGRPFIADLKTGRSAPTGPEMARQ
+PQLAAYQVAVLAGGLAQIRDDPDADPALRAALADLARPAAPAGAALVQLGAGTQKTKVQE
+QPALGPEDDWALEQVFTAARRTVGPRFLAIHEAGGRRCALPSVCPLCSEGRQVTEWPR
+>PROKKA_01303
+MSTTPHPSEPRTEPTPQAADADPADLAALLAEPDEEPPHAAPVPARLVRGVGQDRAGVVL
+TVEQEAVAGLGEGHGAHLVLGAPGTGRSTVAVEYAARRLEAGLDPESLLVLAPSREAAAR
+LRDALTERLAAAGHGTRAVTPVRTWASYAFDLIRRARVTGPLRGLSRPPRLLSGAEQDTV
+IAELLDTYAAGLAPAPEWPRDVAQAVDTRGFRREVRELVDRMSEFGVEPGVLQELGRRHG
+RPVWEAAAELVQDYRDRLDLGMAEAFDAAGLISTAVRLLTERFPDDPERDAAALAFAEAE
+QARLRAIVVDDLQEAGPAVHDLLVHLGRGRDVLLTASPDTTVQGFRGARPDLVSRYPAAL
+DPDAVPGASSPDPDARTHVLTAGHRMSAGVQEGWLRAARRIRQRTVGVELTRTRTVPAGE
+GGAVEGHAVPSRAHEDQLVLERVLRVHHEDGVPLDGLAVIARSGARAAALGRHLEAAGVP
+VRREAAGEVLKDEPAVAPLLTLLRAVSDQAEDPEAGVALEADEAVALLRGPYGRATALNI
+RRLRQDLLAAERARGGRRTSDELLVAAFGDPALAGEETDRHRALRRLAWMHRDGLAAARE
+PGATAETVLWAVWAASGRADRWRAAALGRAEGAEGRREARRADADLDAVVALFRIAERFV
+DQFPGAAPADFSRYMESQDLPMDTLARRAETGDAVHVLTPAGAAGREWDTVIVVGLQEGA
+WPNTALRGQLLGATDLTDLLTAAAVDGAWPTDHRTRLAEVRQDELRMLAAAVSRARRRVV
+ATAVRNEDETPSDFLDLLDPVADVAAGRPLTEVPLPLTAAALVAAARRRLEAPDLPEALV
+GLEDPAAAAVLAALAEDGVAAAAPDRWWGLAPLSTDAPLTDITAEPVRLSPSRAQTALEN
+PLNWLLYHVGAQAGGTLAQSIGVLVHSVAEHHPDGEPGAVRAELERRLPELGLPEGWTTD
+LQHARARRLVEAYIRYWSQMRAEGRRPVAQEVALHVPLAWGDERVEISGVIDRLEVDATG
+RPYVVDLKTGSSKPDTAELERLPQLAAYQVAVRARGLELLAEDPATDPALRRALSAIEAP
+AEPGGAALVQLGAATKTKATVQPQPAVTADDDWALDQVFTAARRTVGPRFLAVHRPGVRC
+ALPSVCPLCTEGRQATEWHR
+>PROKKA_01448
+MTREHGEDPFDDDAAAPERAARLVRTAAAPEDRITLTDEQEAIASLAPGHGAVLVLGAPG
+TGRTTVAVEYAARRIEEGLDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVRT
+WSSYAFDLLRRARVTGPLRHLEVAPRLLTGAEQDTVIAELLEGYAAGLAAAPDWPADVAP
+AVEARGFRREVRELVDRMSELGLEPGRLQELGTAHGRPEWEAAAVLLQDYRDRIDLGMAE
+AFDAAGLLSAAVRVLTERHPEDPERDAAAQAFVAAERDRLAVLVVEDLHEATPAVHDLLT
+VLGRGRDVLLTASPDTTVEGFRGARPDLLARYPGVLDPDPVPGAAPPASPDGRVRVLTRG
+HRMRAEVQDAYLRVARRVRQRTAGVERTRTETVPADGDGAVRAHVVPTRAHEDQLVLERV
+LRVHHEDGVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTLV
+DAAGALAEDPEARVEDVLDPDEVVGLLTGRYGMASALHVRRLRQDLLAAERGRGGRRTSD
+ALLAAALLDPSLAGPEHERHRALRRVHWMLRDGLEAARAPSASPETVLWALWSASGRAER
+WRSLALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGASPESFAVYMESQDLP
+VDTLARRAESGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLVDLVT
+LPADAPWPTDHRTRLREVRQDELRMLAAAVSRARRQVVATAVRSPDEGPSDFLDLVDPPE
+RLPAEARDAAGVRRLTAVPDPITAPALVGRLRRVLEAGDEADAADGATPRAAAAAGLAAL
+AEDGVTVADPRRWWGLLPLSTEAALVDPKHEVVALSPSRVETALRNPLDWVLYHVGANAG
+GTLAQSVGTLVHSVAEHHPEGMPEDVRAELERRLPELGLPEGWITEIEHDRARGLVDAYI
+GYWSIARAAGRRPVAQEVRLLADLTWGGTTVRITGVVDRLEADAQGRPFIADLKTGRSAP
+TGAEMARQPQLAAYQVAVRAGGLEQVRDDPATDPALRAALAGLERPTTPAGAALVQLGAG
+TQKTKVQDQPALEDEDTWALEQVFTAARRTTGPRFLALHEAGARRCALPSVCPLCSEGRQ
+VTEWPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001245.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001245.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f433575ccdad77692046748d3914458f4e3bca5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001245.fa
@@ -0,0 +1,38 @@
+>PROKKA_01527
+MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDAPAKEENAKASEGSGRS
+GSRRGGRGRGRGAKTTDATDTPEATDADAEAPIADEAPAADEAPAADEAPAGDAAAGKDG
+KAAEAKSGAGRRGRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALTKAVNAT
+STDDGWATLSLIGQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEVSLVRRR
+SRRAEG
+>PROKKA_01237
+MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDAPAKEENAKASEGSGRS
+GSRRGGRGRGRGAKTTDATDTPEATDADAEAPAVDEAPAADEAPAADAAPAGDAAPAGDA
+AAGKDGKAAEAKSGAGRRGRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALT
+KAVNATSTDDGWATLSLIGQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEV
+SLVRRRSRRAEG
+>PROKKA_01398
+MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDALAKEENAKASEGSGRS
+GSRRGGRGRGRGSKTTDATDTPDADVADAEAPAADAAPAGDAATGRDGKGTEAKSGAGRR
+GRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALTKAVNATSTDDGWATLSLI
+GQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEVSLVRRRSRRAEG
+>PROKKA_01289
+MSEPTPASLRIAVLLDCDNVSPKYAGLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+ELAIQPVQQFAYTIGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLRESGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTHTEGVDDDEPAPSLQAEPSPKDEREAKEGPA
+TGNRRGSRGRGAKAKPAADVASEQPAEAEPAPVVEPAPDVTPAPESDEAAPQRAVRGRGR
+GAGRGSVLVDVDSAEVITAEDPTPPDVRADADDDAEPASRINLQSALVKAVNATSGDDGW
+ASLSLIGQHMSRTHVDFDPRDFGHAKLSTLVADQPYLETRTEGRSMEVTLKQRRRRAQG
+>PROKKA_01454
+MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDAPAKEENAKASEGSGRS
+GSRRGGRGRGRGAKTTDATDTPEATDADAEAPIADEAPAADEAPAADEAPAGDAAAGKDG
+KAAEAKSGAGRRGRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALTKAVNAT
+STDDGWATLSLIGQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEVSLVRRR
+SRRAEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001254.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001254.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4d187c4ea1950d354cecd23f8d445f6e658a4f35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001254.fa
@@ -0,0 +1,24 @@
+>PROKKA_01536
+MTDHPAATAPDEPGRGRRLPRQERRRQLLDCARAVFAAERYAGASMEQIAERAEVSKPVL
+YQHFPSKHELFLELLDAEVASLRALLEAAMDTRRDNRERVRATVAAVFEYMASPERTHRL
+IFDSGIDGDPEVRTRSEAVHRLLSSEVARTIRADTTVAEAEAEVLSRGLVGYLLGAARHW
+ADRLDADARPAAAEMARTVDALVWRGLASLPSADDAPR
+>PROKKA_01246
+MTAHPAATAPDEPGRGRRLPRHERRRQLLDCARAVFAAERYAGASMEQIAERAEVSKPVL
+YQHFPSKHELFLELLDAEVASLRALLEAAMDTRRDNRERVRATVAAVFEYMASPERTHRL
+IFDSGIDADPEVRTRSEAVHRLLSSEVARTIRADTTVAEAEAEVLSRGLVGYLLGAARHW
+ADRLDADARPAAAEMARTVDALVWRGLASLPSADDAPR
+>PROKKA_01389
+MFAAEGYAGASMDQIAERAEVSKPVLYQHFPGKHELFLELLDAEVADLQERLGAAMDTRR
+GRDNRERVRATVAAFFEYMGAPERTHRLVFDSGADQDPEVRSRSEAVHRLLSSEITRTIS
+ADTSVGEAEAEVLSRGLVGLLLGAARHWADRLDVQARPPAAEMARTVDALVWRGLATLPT
+DDDAL
+>PROKKA_01280
+MAAPARLPRAERRGQLLEVARVVFAAQGYVGTSMDEITERADVSKPVVYQHFGGKQELFL
+ELLDAEVERLRALIVEGTASTQDNRTRARSAVHAVFRYMDSPTSAHRREGGRGRGERAVA
+GPGRDRGPRRRRVLSRAALRPGVNARRPPGARPRLP
+>PROKKA_01463
+MTAHPAATAPDEPGRGRRLPRHKRRRQLLDCARAVFAAERYAGASMEQIAERAEVSKPVL
+YQHFPSKHELFLELLDAEVASLRALLEAAMDTRRGNRARVRATVAAVFEYMASPERTHRL
+IFDSGIDGDPEVRTRSEAVHRLLSSEVARTIRADTTVAEAEAEVLSRGLVGYLLGAARHW
+ADRLDADARPAAAEMARTVDDLIWRGLTSLPSADDAPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001258.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001258.fa
new file mode 100644
index 0000000000000000000000000000000000000000..315830f242fd615fb7ddc3a9063f80e5a2269cd4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001258.fa
@@ -0,0 +1,50 @@
+>PROKKA_01541
+MTDAAQHPAQTTPDQPAATPEAGADGTGAVNPQPLAERVDNRSQRPASNAFRDFMASDWA
+PSSQALPDPDASAPYAARRRAAVSARFPGERIVVPAGRLKVRSNDTDYRFRAHSAFAHLT
+GLGVDHEPDAVLVLEPTDPGAGDDGTDHTATLYFRPLAGRDTEQFYADSRSGEFWIGPRP
+TLAGLAARTGLRTAGLEELESAVTKNVAADGTAVRLLAETDQDVDALLAAVRTEAGVDLA
+AAAEADAQTAEFLSELRLVKDAWEVDRMRASVAATIAGFEDVVRALPRAVGHDRGERVVE
+GAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGAVRPGELLLLDAGVEDDSLYTADI
+TRTLPVSGTFTDVQRRIYQAVLDAADAAFAIVRPGIRFRELHAEAMRVLVDRLDGWGLLP
+VSAEVALSDEGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEPGLYF
+KEEDLAVPEEYRGIGVRIEDDILVTEDGAENLSAALPRTPDEIEAWMARLQA
+>PROKKA_01251
+MTDAAQHPAQTTPDQPAATPEAGADGTGAVNPQPLAERVDNRSQRPASNAFRDFMASDWA
+PSSQALPDPDASAPYAARRRAAVSARFPGERIVVPAGRLKVRSNDTDYRFRAHSAFAHLT
+GLGVDHEPDAVLVLEPTDPGAGDDGTDHTATLYFRPLAGRDTEQFYADSRSGEFWIGPRP
+TLAGLAARTGLRTAGLEELESAVTKNVAADGTAVRLLAETDQDVDALLAAVRTEAGVDLA
+AAAEADAQTAEFLSELRLVKDAWEIERMRASVAATIAGFEDVVRALPRAVGHDRGERVVE
+GAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGAVRPGELLLLDAGVEDDSLYTADI
+TRTLPVSGTFTDVQRRIYQAVLDAADAAFAIVRPGIRFRELHAEAMRVLVDRLDGWGLLP
+VSAEVALSDEGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEPGLYF
+KEEDLAVPEEYRGIGVRIEDDILVTEDGAENLSAVLPRTPDEIEAWMARLQA
+>PROKKA_01384
+MTDAAQHPAQHADQDRPQDPAATPEAGVDAEGAVSPQPLAQRVENRSQRPSSDAFRAFMG
+ADWAPSSDELPAQDASAPHAARRRAAVSARYPGERIVVPAGRLKVRSNDTDYRFRAHSAF
+AHLTGLGVDHEPDAVLVLEPTDPGAGDGGSDHAATLYFRPLAGRDTEQFYADARAGEFWI
+GPRPTLAGLAARTGLRTAGLEELESAVTKNVCADGTAVRLLREADQDMDALLAGVRAEAG
+MDAEAAASADAQVAEFLSELRLVKDAWEVERMRASVAATIAGFEDVVRALPRAVGHDRGE
+RVVEGAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGTVREGDLLLLDAGVEDDSLY
+TADITRTLPVSGSFTDVQRRIYQAVLDSADAAYAIVRPGIRFREIHAEAMRVLVERLADW
+GLLPVSAEVALSEDGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEP
+GLYFKEEDLAVPEEYRGIGVRIEDDILVTEDGAENLSAALPRTPDEIEAWMARLQA
+>PROKKA_01275
+MTDASAQQNDDLAPEAAADSGAALSPQPLAERVENRSQKPTSDAFRAFMASQWAPASREL
+PGPDASAPFAARRRAAVSAMFPGERIVVPAGRPKVRSNDTDYRFRAHSAFAHLTGLGVDH
+EPDAVLVLEPTDAGAGDAGTDHAATLYFRPLAGRDTEQFYSDPRAGEFWIGPRPTLAELA
+ARTGLRTAGLEELENAVTKDVAATAVRLLREADQDMDAVVAAARADAGVDAQAAGAADAA
+LAEALSELRLVKDEWEVERMRASVASTIAGFEDVVRALPRAVGHARGERVVEGAFFARAR
+EEGNDLGYDTIAASGNNATVLHWIRNTGRVREGELILVDAGVEDDSLYTADITRTLPVSG
+TYSDVQRRVYQAVLDAADAAFALVKPGIRFREIHAEAMRVLAGRLHGWGLLPVSPEEALS
+EAGQHHRRWMPHGTSHHLGLDVHDCAQARRELYLDAVLEPGMVFTIEPGLYFKAEDLAIP
+EEYRGIGVRIEDDILVTEDGAENLSAALPRTPEDVEAWMARLQG
+>PROKKA_01468
+MMGGMTDAAQHPAQTAPDQPAATPEAGADGTGAVNPQPLAERVDNRSQRPASNAFRDFMA
+SDWAPSSDALPDADASAPYAARRRAAVSARFPGERIVVPAGRLKVRSNDTDYRFRAHSAF
+AHLTGLGVDHEPDAVLVLEPADPGTGDDGTDHTATLYFRPLAGRDTEQFYADSRSGEFWI
+GPRPTLAGLAARTGLRTAGLEELESAVTKNVAADGTAVRLLAETDQDVDALLAAVRTEAG
+VDLTAAAEADAQTAEFLSELRLVKDAWEVERMRASVAATIAGFEDVVRALPRAVGHDRGE
+RVVEGAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGAVRPGELLLLDAGVEDDSLY
+TADITRTLPVSGTFTDVQRRIYQAVLDAADAAFAIVRPGIRFRELHAEAMRVLVDRLDGW
+GLLPVSAEVALSDEGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEP
+GLYFKEEDLAVPEEYRGIGVRIEDDILVNEDGAENLSAALPRTPDEIEAWMARLQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001261.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001261.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5942c2cbd2b04cd3fc4db2b6d3e083045543ec10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001261.fa
@@ -0,0 +1,45 @@
+>PROKKA_01544
+MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM
+TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR
+NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA
+DLADMLHDMSEKRRVEVASELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD
+DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA
+MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEPV
+SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDAETRP
+AT
+>PROKKA_01254
+MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM
+TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR
+NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA
+DLADMLHDMSEKRRVEVASELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD
+DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA
+MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEPV
+SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDAETRP
+AT
+>PROKKA_01381
+MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAVPPFATGLVIEVPGKKRVFVPM
+TRVTSMDSGQIITTGLINLRRFSRRGAEQTVAADLFDRRVRLTDGSGEAFLEDIGLEQQR
+NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLDWDEARWTGQAEPQAATSFLAAHEDLKPA
+DLADMLHEMPEKRRVEVARELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD
+DAADLLHELPDSQQELLLERMEPEEAEDVRRLLEYEEGTAGSVMTPVPVILPPEATVAEA
+MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAVGNIMDKDLEPV
+SDLAPIAHVTRELATYNLTSIPVVNEHHRVVGAVSVDDVLDHILPDDWRAMDHDDHDPRP
+AA
+>PROKKA_01272
+MNSPRIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGRGARSAATGLVIEVPGKKRVFVPM
+TRVTSMDSGQIITTGLINLRRFSRRGAEQTVAGDLFDRRVHLTDGSGRAVVEDLGIEQQR
+NGDWLVTDYYVRRDDGRTAFGRPRGEHLLVSWDEVAWGAAAEPQGASSFVAAHDDLKPAD
+LADMLHEMTDKRRVEVANELQDERLADVLQELPDDDQVQILSHLDIERAADVLEEMDPDD
+AADLLNELPDSQQELLLELMEPEDAEDVRRLLEYEEDTVGSIMTPVPVVLPPEATVAEAM
+ATIRQQEISPALASLVIVARPPLETPTGRYLGVVHFQRLLRYPPPEAIGNIMDKDLEPVS
+DMDSVAHVTRELATYNLTSIPVVNAQHRVVGAVSVDDVLDHILPEDWRAMDPEDHPETEG
+QD
+>PROKKA_01471
+MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM
+TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR
+NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA
+DLADMLHDMSEKRRVEVARELQNERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD
+DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA
+MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEAV
+SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDAETRP
+AT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001263.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001263.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1514a251f134d76bb71d5ee4ed131d4fcb30b994
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001263.fa
@@ -0,0 +1,40 @@
+>PROKKA_01546
+MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI
+AACPLRGTIQTDVAAAVAVVPGCESVDVRVGVMEPERRLALQDALRATRPTNPFGEGTLT
+RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM
+ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL
+DVFGTGGGAEVAERLSGVLDTQVPLLGTVPLDPALRAGGDAGEPVVVSAPESPAGRALTQ
+IAQRVAVRPRGLAGRRLPVTPR
+>PROKKA_01256
+MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI
+AACPLRGTIQTDVAAAVAVVPGCESVDVRVGVMEPERRLALQDALRATRPTNPFGEGTLT
+RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM
+ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL
+DVFGTGGGAEVAERLSGVLDTQVPLLGTVPLDPALRAGGDAGEPVVVSAPESPAGRALTQ
+IAQRVAVRPRGLAGRRLPVTPR
+>PROKKA_01379
+MSDLGLHVPEVRTDLERRVLDRLATVQDPEIRRPVTELGMVESVVETAPGTVEVTVLLTI
+EACPMRGTIQGDVAAAVADVPGCDAVDVRTGVMSPERRLALQDALRAARPANPFGEGSLT
+RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTASPTKLDRM
+ILPPVVRDVKVISIGMFLDEDRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQAVAGVIENMGPMTLPDGTVL
+DVFGAGGGQEVAERLERVLGSAVPLLGSVPLDPALRRGGDAGDPVVLSAPDSPAGRALAG
+VAERLAVRPRGLVGRRLPLSPR
+>PROKKA_01270
+MSAPALPRPEVRTPLEAAVLAALDGVVDPEIRRPITELGMVRSVAETGGGHVAVEVLLTI
+AGCPLKGTIQADVAAAVADVPGCAGVDVRLGVMTPTERAALQEALRGARPANPFAEDSLT
+RVLAVASGKGGVGKSTVTANLAVALAGRGLSVGLIDADVHGYSIPGLLGVQASPTRVGEL
+ILPPVSRGVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELVVVTTPQHAAAQVAARAGQLAAQTGQRVAGVVENMGPMALPDGTVL
+DVFGAGGGQEVADRLSGALGTSVPLLGTVPLDPALRRGGDAGEPVVVSAPESPAAAALQE
+VAARLAVRPGSLRGRGLPVSPR
+>PROKKA_01473
+MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI
+AACPLRGTIQTDVAAAVADVPGCGSVDVRVGVMEPERRLALQDALRAARPTNPFGKDTLT
+RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM
+ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL
+DVFGTGGGAEVAERLSGVLGTQVPLLGTVPLDPALRAGGDAGDPVVVSAPESPAGRALAE
+IAQRLAVRPRGLAGRPLPFTPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001264.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001264.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7298922e9b02dd3120d9642978ac25b4ce11cb2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001264.fa
@@ -0,0 +1,23 @@
+>PROKKA_01547
+MFGINGSEFIILAVLAIVILGPEKLPEYTRAFTDWLRVMRDKAEGAKAQFKEETGTDFDE
+VDWRKYDPRQYDPRRIIRDALREPAGGSSTPASRAAQATGISAEDVHGGLTRQDLTDMDP
+RTLFRRPAGAGSTAAAESGAAAAQTRSTEPAAGAAAVGGAAAALMASGRAEALTEERPAA
+VETEPDPLELLGLAPAPFDVDAT
+>PROKKA_01257
+MFGINGSEFIILAVLAIVILGPEKLPEYTRAFTDWLRVMRDKAEGAKAQFKEETGTDFDE
+VDWRKYDPRQYDPRRIIRDALREPAGGSSTPASRAAQATGISAEDVHGGLTRQDLTDMDP
+RTLFRRPAGAGSTAAAESGAAAQTRSTEPAAGAAAVGGAAAALMASGRAEALTEERPAAV
+ETEPDPLELLGLAPAPFDVDAT
+>PROKKA_01378
+MHGGLTRQDLVDMDPRSLFRRPAGAGSSAAPAASSGSAAPAAGASLATGAAVGGAAAALM
+ASGRAEEAVAEERPAVEPDPLELLGLAPAPYDVDAT
+>PROKKA_01269
+MFGINGSELIVLIVLAFVVLGPEKLPEYTRALAQGIRKTRDMAEGAKTQFKEETGTDFDS
+VDWRRYDPRQYDPRRIIRDALREPADGSTAAARAQELTGVAAEDLQGGLSAQDLRDMDPR
+SLFRRPSGDGSTAAPAGGGASAPSDAPTPEDVPSAAVPVAAASPSPAGAAAAGVAAALLA
+SGRAEEVLTDPAPLQHLGTDPDPLDLLGKAPAPFDVDAT
+>PROKKA_01474
+MFGINGGEFIILAVLAIVILGPEKLPEYTRAFTDWLRVMRDKAEGAKAQFKEETGTDFDE
+VDWRKYDPRQYDPRRIIRDALREPAGGSSTPASRAAQATGVSAEDVHGGLTRQDLADMDP
+RTLFRRPAGAGSTAAAESGAAAQTRSTAPAAGAAAVGGAAAALMASGRAEALAEERPAAV
+ETAPDPLELLGLAPAPFDVDAT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001274.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001274.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f639468934462b9a852fd7d5e82a9c1a588701a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001274.fa
@@ -0,0 +1,35 @@
+>PROKKA_01558
+MTQTAAQQPSSRLVSGHGLATTAADGAVLDVWFPAPVAGPLSAADASLRDTLRALAADDA
+DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLTRPNELNLDGVFGLLTNVVWTNHG
+PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL
+GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAAHTVKAVDLSGVPNLLFRRNSTTG
+GVEALPRAGRTVELNAALHAN
+>PROKKA_01268
+MTQTAAQQPSPRLVSGHGLATTAADGAVLDVWFPTPVAGPLSAADASLRDTLRALAADDA
+DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLARPNELNLDGVFGLLTNVVWTNHG
+PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL
+GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAARTVKAVDLSGVPNLLFRRNSTTG
+GVEALPRAGRTVELNAALHAN
+>PROKKA_01367
+MTETAAQHPSARLVSGHGLATTAADGTVLDVWFPAPVAGPLADADATLAETLRSLAADDA
+DRGTTQSVVELEADLDAAPATAEDAWLRLHALSHRLVRPNELNLDGVFGLLANVVWTNFG
+PCAVEGFELTRARLRARGAVNVYGVDKFPRMTDYVVPTGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDLGGGVSIMGTLSGGGTQKVVIGEHVLL
+GANSGVGISIGDDCVVEAGLYVTAGALVTVVRPGEEPRTVKAVELSGVPNLLFRRNSATG
+VVEVLPRAGRTVELNAALHAN
+>PROKKA_01258
+MTDTSQTSSARLVSGHGLATRAADGAVLDVWFPAPVTGPLASADASLAGTLEGLAAADAD
+RGTTQDIVALEADLDVAPASAEDAWLRLHALSHRLVRPNELNLDGVFGLLTNVVWTNFGP
+CAVEGFEATRAKLRARGAVNVYGVDKFPRMTDYVVPTGVRIGDADRVRLGAHLAEGTTVM
+HEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDLGGGVSIMGTLSGGGTQKVVIGEHVLLG
+ANSGVGISIGDDSVVEAGLYVTAGTVVTVVEPGRKPRTVKAVELSGVTNLLFRRNSVTGG
+VEVLPRDGRTVALNAELHAN
+>PROKKA_01485
+MTQTAAQQPSSRLVSGHGLATTAADGAVLDVWFPAPVAGPLSAADASLRDTLRALAADDA
+DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLTRPNELNLDGVFGLLTNVVWTNHG
+PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL
+GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAARTVKAVDLSGVPNLLFRRNSTTG
+GVEALPRAGRTVELNAALHAN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001282.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001282.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b06011cf7437c6c74aa2d91b7501e57c4c7db39b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001282.fa
@@ -0,0 +1,60 @@
+>PROKKA_01568
+MKYTKLSAAAALAAGSALILSACAPGGGNAGDSSSNSASGASQGGDSGAGNVIEGDKGQK
+LTAEASGPGKADLGDVKTQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVADRMFSSFWY
+FGTDGSIIPDKDFGTYEKTSDDPLTVKYTISDDAKWSDGTPVTAGDFIVHWAANNDTIKA
+EGAETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEILISTALPAHIVAKEA
+GMSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGPYKFKDGGWQAGQ
+SITLEANPEYWGTPAATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLEGLGED
+VNVQTGDQLTWEHVDYNRGEGSVFADSPELREAFALCLPRQQIVDNLIKPIYADAQVMNL
+REVFPFQDKYQEVVDAAYPKEMDQPNIEKAKELVEKSGVSKPTVRLGYQAGNQRRTETVA
+LIKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALFAWAGSGQKASGANIYQSDGAQNQQ
+SYNNPEVDAAWDKLATSLDENEQLEQVKTIEKLLWEDFQAIPLYAHPGLVGHKADVANVR
+DTAAQSGALWNVEQWVRVQE
+>PROKKA_01278
+MKYTKLSAAAALAAGSALILSACAPGGGNAGDSSSNSASGASQGGDSGAGNVIEGDKGQK
+LTAEASGPGKADLGDVKTQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVADRMFSSFWY
+FGTDGSIIPDKDFGTYEKTSDDPLTVKYTISDDAKWSDGTPVTAGDFIVHWAANNDTIKA
+EGAETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEILISTALPAHIVAKEA
+GMSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGPYKFKDGGWQAGQ
+SITLEANPEYWGTPAATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLEGLGED
+VNVQTGDQLTWEHVDYNRGEGSVFADSPELREAFALCLPRQQIVDNLIKPIYADAQVMNL
+REVFPFQDKYQEVVDAAYPKEMDQPNIEKAKELVEKSGVSKPTVRLGYQAGNQRRTETVA
+LIKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALFAWAGSGQKASGANIYQSDGAQNQQ
+SYNNPEVDAAWDKLATSLDENEQLEQVKTIEKLLWEDFQAIPLYAHPGLVGHKADVANVR
+DTAAQSGALWNVEQWVRVQE
+>PROKKA_01358
+MKYTKLSAAAALAAGSALILSACAPGGGDDADNTASSGNGGASGSASQGGEAGAPEVTEG
+DKGQKLTAPVDGPGMADLGDVETQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVADRMF
+SSFWYFGTDGSIIPNKDFGTYEKTSDDPLTVKYTISDDAKWSDGTPVTAGDFIVHWAANN
+ETVKAEGSETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEILISTALPAHI
+VAKEAGMSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGPYKFKDGG
+WQAGQSITLEANPEYWGTPAATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLE
+GLGDDVNVQTGDQLTWEHVDFNRGEGSVFADSPELREAFALCLPRQQIVDNLIKPIYADA
+QVMNAREVFPFQENYQEVVDAAFPEEMDQPNIEKAKELVEKSGVSKPTVRLGYQAGNQRR
+TETVALIKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALYAWAGSGQKASGANIYQSDG
+AQNQQSYNNPEVDAAWDKLATSLDEDEQLEQVKTIERLLWEDFQAIPLYAHPGLVGHKAD
+VANVRDTAAQSGALWNVEQWVRVQE
+>PROKKA_01249
+MKHTKLSAAAALAFGSALVLSACAPAGPAASGSSSNGGGSSAASGSSAASGSDAAGGVTT
+GEKGEKLTAPADGPGMADLGDVKTEEGSVAYSVGKDDFLSYNGVQANTYSTYNSAIVDRL
+FSGFYYFGTDGTIVRNEEFGTFEKISDDPLKVKYTINEDATWSDGTPVTAADFIVQWAAD
+NPNIVDESGKADPKTGQKPQLFESITSEPGKYIPEAPEGDPKGKEFTVTYAEPYADWEIL
+ITTALPAHVIAKGADMSLDDLVAAAKAKDSTKLVPAAKFWNNGWDFNPGELPSADMIPSM
+GPYKIKDGGWVAGQSITLEANDKYWGTPAATKNLVIKFAAPETHVQALQNKELDVIEPQA
+TVDTVSQLEGLGDSVNIQKGDQLTWEHLDFNRGTGSTFADSKELREAFALCVPRQQIVDN
+LVKPINPDATVMNAREVFPFQDNYQEVVDAAYPKEMDQPNIEKAKELVAKSGVSKPTVRL
+GYQAGNQRRAETVKLIKASCDQAGFDVQDANSNVFFKEVMPTGDYDVALYAWSGSGQKAS
+GANIYQSDGEQNQQSYSNKTVDEAWDKLAGSLDEKEQLEQVKVIEKALWEDFQAIPLYAH
+PGVVAHQADLANVRDTVAQQGALWNVEQWKRVS
+>PROKKA_01495
+MKYTKLSAAAALAAGSALILSACAPGGGNADDSSSNGSGASQGGDSGAGNVVEGDKGQKL
+TAEASGPEMADLGDVETQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVVDRMFSSFWYF
+GTDGSIIPNEDFGTYEKTSDDPLTVKYTISDDAKWSDGTPVTAGDFIFHWAANNDTVKAE
+GSETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEILISTALPAHIVAEEAG
+MSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGSYKFKDGGWQAGQS
+ITLEANPEYWGTPPATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLEGLGDDV
+NVQTGDQLTWEHVDYNRGEGSVFADSPELREAFALCLPRQQIVDNLIKPIYADAQVMNLR
+EVFPFQDKYQEVVDEAYPKEMDEPNIEKAKELVEKSGVSTPTVRLGYQAGNQRRTETVAL
+IKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALYAWAGSGQKASGANIYQSDGAQNQQS
+YNNPEVDAAWDKLATSLDENEQLEQVKTIEKLLWEDFQAIPLYAHPGLVGHKADVANVRD
+TAAQSGALWNVEQWVRVQE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001286.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001286.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5045d1f5d247d1d4467f6e8a846d3844c5472f83
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001286.fa
@@ -0,0 +1,31 @@
+>PROKKA_01573
+MTEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNAVNYLSRD
+PARARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATFRANPARL
+VLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG
+IPLTAAEDAGFEKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRWRRYNATR
+ERLFEMERQGRAYLFAPETMPIANGERSVAKLAAAHELGLDQVRREMPAIRAFLGLPASR
+>PROKKA_01283
+MTEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNAVNYLSRD
+PARARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATFRANPARL
+VLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG
+IPLTAAEDAGFEKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRWRRYNATR
+ERLFEMERQGRAYLFVPATMPISNGERSVAKLAAAHELGLDQVRREMPAIRAFLGLPASR
+>PROKKA_01351
+MRTPMTSNVTDTALLFEGGGMRASLTSAVVAELLRERIHVDFVAGISAGSSNSVNYLARD
+PERARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATFQANPARL
+VLVGFDAVTGQTRWWDRSDMGTLADLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG
+IPVTAAEEAGFEKLFVVMTRERSYVKRPERFPAFYQRTFRRYPAVAEALISRWRRYNETR
+ERLFEMERQGRAYLFVPESMPVSNGERSVAKLAAAHELGLAQVRREMPAIREFLGL
+>PROKKA_01244
+MAEQQDHTAEALTSNVTDTALLFEGGGMRASHTSAVVAELLRAGVHVDFVAGISAGSSNA
+VNYLARDPLRARQAFVDFADDPRFGNWRTFLRGKGMFNAEYIYEHAGLPEADLPYDFAAY
+RANPARLALAGFDAVTGETRWWGREDMTTLQDLMVRVRASSTMPILMPPVHLEDTVYVDG
+ALGVDGGIPVTAAEEAGLAKLLVVMTRERSYVKRPERFPAFYQRAFRRYPAVAEALVTRW
+QRYNATRERLFEMEREGTAYLFVPEVMPVSNGERSVAKLAAAHELGLAQARREMPAIKEF
+LGL
+>PROKKA_01500
+MTEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNAVNYLSRD
+PARARRSFVDFADDPRFGNWLSFLRGKGLFNAEYIYEHAGLPEADLPYDFAAFRANPARL
+VLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG
+IPLTAAEDAGFKKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRWRRYNATR
+ERLFEMERQGRAYLFAPETMPIANGERSVAKLAAAHELGLDQVRREMPAIRAFLGLPASR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001289.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001289.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c160f4dec6607d2ba4c603f81a72bb617f91c0ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001289.fa
@@ -0,0 +1,35 @@
+>PROKKA_01576
+MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL
+PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG
+HADDEEPAVERGPEAEDTVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL
+ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV
+GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTETATSAVWGLLWGSVALGVV
+LLVGRLRGNKAAPAH
+>PROKKA_01286
+MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL
+PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG
+HADDEEPAVERGPEAEETVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL
+ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV
+GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTDTATSAVWGLLWGSVALGVV
+LLVGRLRGKKAAPAH
+>PROKKA_01348
+MSGLVALLDDVAALARLAAASVDDVAAGAAKASAKAAGVVVDDAAVTPQYMAGAAANREL
+PMIWRITKGSLRNKLLIILPALLLLDWLAPWVLPWLLLAGGTYLAYEGAHKVWGKLTGHS
+PERDEPAVEKGPEAEDKVVRGAITTDFILSAEIMVISMNEVADVDFWLKAVILVVVAILI
+TAVVYGAVALIVKMDDVGLHMTQNGRTAGGRRFGAGLVKAMPHVLTAITVIGTVAMLWVG
+GHIVLVELAALGVPWPYDVQHGIVHAVEAAGGFVAWLVETLTSALWGLIWGSLALGVVLV
+VNRLRGKKDTLAH
+>PROKKA_01241
+MSGLVALLDDVAALARLAAASVDDVAAGAAKASAKAAGVVVDDAAVTPQYMEGAAAQREL
+PMILRIVRGSLRNKLVFILPGLLLLDWLAPWALPWLLLAGGTYLSFEGAEKVWHKLTGHH
+EPQEDTPAVEQGPEAEDKVVRGAITTDFILSLEIMVISMNEVSDQGFWMKAAILAIVAVV
+ITVAVYGAVALIVKMDDVGLHMHENAHTSGARRFGLGLVKAMPVVMGVISVIGTVAMLWV
+GGHIVLMELATLGLPWLYELQHTIVHAVEGAGSVIAWLVETLTSAIWGLVWGSLVVAVVG
+LVRRLRT
+>PROKKA_01503
+MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL
+PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG
+HADDEEPAVERGPEAEDTVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL
+ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV
+GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTDTATSAVWGLLWGSVALGVV
+LLVGRLRGKKAAPAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001293.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001293.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fac86c5c96a7dd98dbe1c8e7e952d35b1296cd97
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001293.fa
@@ -0,0 +1,35 @@
+>PROKKA_01580
+MTPADRAPATPAPQPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREPGVLSG
+TNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI
+ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRFSLSDAVMLKDNH
+LAALGFGSAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVDTIMLDNFS
+PAELRAGVERVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVQSLDLGLDAVVE
+EVSPRR
+>PROKKA_01290
+MTPADRAPTTPAPRPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREAGVLSG
+TNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI
+ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRFSLSDAVMLKDNH
+LAALGFGGAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVDTIMLDNFS
+PAELRAGVELVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVQSLDLGLDAVVE
+EGSPRR
+>PROKKA_01343
+MSAGTRGAWGPTPAPIADVERIVAAALAEDAPWGDVSSEAFVPADARITARVVAREAGVL
+SGTAALEAAFRLVDPATEVTLHLPDGTALAPGAVVAAVAGPARSVLRAERVALNLAQRMS
+GIATATAAHVAAVRAGGGHTRVADTRKTTPGLRVLERQAVRDGGGHNHRHGLSDAVMLKD
+NHLAALGFGGEDAPGEELTRALRAGKARLPHTVHVEVEVDRLDQLPAVLAAGVGTVMLDN
+FSLADLRAGVELVAGRAVVEASGGVSLETIGEIAATGVDVVSVGALTHSVRALDLGLDAV
+VDAADAPAPGRR
+>PROKKA_01236
+MTPADRAPATPAPQPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREAGVLSG
+TNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI
+ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRSSLSDAVMLKDNH
+LAALGFGGAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVGTIMLDNFS
+PAELRAGVELVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVRSLDLGLDAVVE
+EVSPRR
+>PROKKA_01507
+MTPADRAPTTPAPRPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREAGVLSG
+PNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI
+ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRFSLSDAVMLKDNH
+LAALGFGGAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVDTIMLDNFS
+PAELRAGVELVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVQSLDLGLDAVVE
+EGSPRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001298.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001298.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e1ff4c0b3657ebc34f9943692d01b57c522b3506
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001298.fa
@@ -0,0 +1,45 @@
+>PROKKA_01595
+MHPSVSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAF
+CEHRMLETPPEKSRIVSTRADDGAPAWQILRHPAAERLEETIPAFRRVPNLFEILSYDYW
+RLNHGYELPPDACRRRDEYLATEAGRAHVRAVVTAKLRASGRSAEEAAAMSEAELIGASA
+AFFGGTHDVVIARRHFVDGAVDDHQLASSGTLTPDEHHAFMALTADAMRDLYATTPAVRY
+VSVFQNWLKPAGASFDHLHKQLVAIDEVGAQNVAALDRLREDPQVFNQAALDVAVAHDLM
+IAANEHAVMFAGFGHRYPTVEVYSTSPVGQPWRQTAAELRAVSDLLHAAHAATGPDVPSN
+EEWHTRPPGVADPMPWRVMLKWRVSTLAGFEGATKINVNTLSPWDVRDRVLARLRELWAA
+GALADGMRIGADARVRPGMLRYAD
+>PROKKA_01307
+MHPSVSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAF
+CEHRMLETPPEKSRIVSMRADDGAPAWQILRHPAAERLEETTPAFRRVPNLFEILSYDYW
+RLNHGYELPPDARRRRDEYLATEAGRAHVRAVVAAKLRASGRSAEEAAAMSEAELIGASA
+AFFGGTHDVVIARRHFVDGAVDDHQLASSGTLTPDEHHAFLALTADAMRDLYATTPAVRY
+VSVFQNWLKPAGASFDHLHKQLVAIDEVGAQNVAALDRLREDPQVFNHAALDVAVAHDLM
+IAANEHAVMFAGFGHRYPTVEVYSTSPVGQPWRQTAAELRAVSDLLHAAHAATGPDVPSN
+EEWHTRPPGVASPMPWRVMLKWRVSTLAGFEGATKINVNTISPWDVRDRVLARLRELRAA
+GALADGMRIGADARVRPGALRYADGAARLTPPRGR
+>PROKKA_01301
+MPRTRPPAQDFLAELPDGTVKQRNPFSGTEVWTVPGRGHRPLGIARPAAQPLDPDDDGRH
+CAFCSARLLETPPEKSRVVRTEDGEHAILRDVPAEALFDTVPEFRRVPNLFEILSYEYWR
+LNHGFVPAPGVADRRAAYLATETGRAHVLAVVGNKLRAAGRSAEEVEAMPEEERIEAASG
+FFGGGHDVIIARRHFADGAQDDHALAGSGTLSPEEHRRFIALTVDSMRDLYAANPHARYV
+SVFQNWLKPAGASFDHLHKQLVAIDEVGVQNEAAIARVRRNPDAFAQDALGYAAKQGLMI
+ARNEHAAMFAGFGHRYPTVEIHSLSPTCEPWEQTDAERDAMADLIHAAHAATGADVPSNE
+EWHTRPTGVAEPLPWRVCLKWRVSTLAGFEGATKIYLNTVSPGSVRERVATRLQELQAAG
+AIADGIRIDDDGHGAV
+>PROKKA_01214
+MSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAFCEHR
+MLETPPEKARIVPTRADDDAPAWQILRHPAAERLGETTPAFRRVPNLFEILSYDYWRLNH
+GYELPPDARRRRDEYLATEAGRAHVRAVVAAKLRASGRSAEEAAAMSEAELIAASAAFFG
+GTHDVVIARRHFVDGAVDDHQLASSGTLTLDEHHAFLALTADAMRDLYATTPAVRYVSVF
+QNWLKPAGASFDHLHKQLVAIDEVGAQNAAALDRLREDPQVFNHAALDVAVAHDLVIAAN
+EHAVMFAGFGHRYPTVEVYSTSPVGQPWRQSAAELRAVSDLLHAAHAATGPDVPSNEEWH
+TRPPGFASPMPWRVMLKWRVSTLAGFEGATKINVNTLSPWDVRDRVLARLRELRAAGALA
+DGMRIGADARVRPGALRYAD
+>PROKKA_01522
+MHPSVSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAF
+CEHRMLETPPEKSRIVSMRADDGAPAWQILRHPAAERLEETTPAFRRVPNLFEILSYDYW
+RLNHGYELPPDARRRRDEYLATEAGRAHVRAVVAAKLRASGRSTEEAAAMSEAELIAASA
+AFFGGTHDVVIARRHFVDDAVDDHQLASSGTLTPDEHHAFLALTADAMRDLYATTPAVRY
+VSVFQNWLKPAGASFDHLHKQLVAIDEIGAQNAAALDRLREDPQVFNHAALDVAVAHDLV
+IAENEHAVMFAGFGHRYPTVEVYSTSPVGEPWRQDPAELRGMSDLLHAAHAATGPDVPSN
+EEWHTRPPGVADPMPWRVMLKWRVSTLAGFEGATKINVNTLSPWDVRDRVLARLRELRAA
+GALADGMRIGADARVRPGMLRYAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001299.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001299.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e56176b62811ab2f812d9e8b8b5f6e1869172216
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001299.fa
@@ -0,0 +1,50 @@
+>PROKKA_01597
+MSSRIHHPGLRSKVMSAAEAAAFIQHGTTVGMSGFTGSGYPKAVPTALAERAKELHARGE
+EFRINLHTGASTSAEMDGALAEADAVALRTPFQSDPTMRAKINAGAIEYIDTHLSHLAQT
+VWNGFYGPMTTAVIEVSGIREDGRLVPSSSVGNNKSWIDLADQVILEVNSWQSEDLEGLH
+DVYYGTALPPHRTPIMLTHPADRIGETYLRCDPAKVVAVVETHAPDRNSPFKPADADSIA
+IAQHLVEFFEHEVAQGRYDERLLPLQSGVGNIANAVMSELVKSRFTGLSAFTEVVQDGML
+DALDSGTLATASATAFSLSTEAAERFNDNAAKYRDKLILRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYREQLRDYFDRAMRGSDGLH
+TPHLLGESLSWHQRFLETGTMRQG
+>PROKKA_01309
+MSSRIHHPGLRSKVMSAAEAAAFIQHGTTVGMSGFTGSGYPKAVPTALAERAKELHARGE
+EFRINLHTGASTSAEMDGALAEADAVALRTPFQSDPTMRAKINAGAIEYIDTHLSHLAQT
+VWNGFYGPMTTAVIEVSGIREDGRLVPSSSVGNNKSWIDLADQVILEVNSWQSEDLEGLH
+DVYYGTALPPHRTPIMLTHPADRIGETYLRCDPAKVVAVVETHAPDRNSPFKPADADSIA
+IAQHLVEFFEHEVAQGRYDERLLPLQSGVGNIANAVMSELVKSRFTGLSAFTEVVQDGML
+DALDSGTLATASATAFSLSTEAAERFNDNAAKYRDKLILRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYREQLRDYFDRAMRGSDGLH
+TPHLLGESLSWHQRFLETGTMRQG
+>PROKKA_01298
+MSSRIQHAGLRAKVMSAQEAAAFIRPGTTVGMSGFTGSGYPKAVPLALAERISAAHARGE
+DFRIDLHTGASTSSEMDGALAESGGVALRTPFQSDPTMRAKINAGEVEYIDTHLSHLAQT
+VWNGFYGPMHTAVVEVSAIREDGTLVPSSSVGNNKSWLDLADEVILEVNSWQSEELEGLH
+DVYYGTALPPHRQPVMITDPADRIGQPYFECDPAKVVAVVETHGPDRNSAFKPADADSIA
+IAQHLVEFFEHEVAAGRYDERLLPLQSGVGNIANAVMAELVKSRFRGLTAFTEVVQDGML
+DALDSGTLSMASATAFSLSTEAAERFNSTVAQYKDKLILRTQEISNHPELVRRLGVLAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSVAKGGDISCIVPMVSH
+VDHTEHDVHVLVTEQGLADLRGLSPKQRARTIIAKCAHPDYRDQLQDYFDRAMRGSDGLH
+TPHLLGEALSWHQRFLETGTMRHG
+>PROKKA_01207
+MSSRIHHPGLRAKVMSAEEAAAFITPGMTVGMSGFTGSGYPKAVPMALAERIKSAHARGE
+DFRIDLHTGASTSVEMDGALAEADGVRLRTPFNTDPTMRAKINDGSVDYIDTHLSHLAQT
+VWEGFYGPMDAAVIEVSAIREDGTLVPSSSVGNNKSWLQLADKVILEVNSWQSEDLDGIH
+DVYYDTALPPHRKPVPVNHPSDRIGRTEFVVDLDKVVAVVETHGPDRNSPFKPADADSIA
+IAQHLVEFFEHEVKAGRYDEHLLPLQSGVGNVANAVMAELVKSRFHGLTAFTEVVQDGML
+DALDSGTLAMASCTAFSLSTEVAERFNDNVLQYKDKLIIRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYREQLRDYFDRAMRGSDGLH
+TPHLLGEALSWHQRFLETGTMRQG
+>PROKKA_01524
+MSSRIHHPGLRSKVMSAAEAAAFIQHGTTVGMSGFTGSGYPKAVPTALAERAKELHARGE
+EFRINLHTGASTSAEMDGALAEADAVALRTPFQSDPTMRAKINAGAIEYIDTHLSHLAQA
+VWNGFYGPMTTAVIEVSGIREDGRLVPSSSVGNNKSWIDLADQVILEVNSWQSEDLEGLH
+DVYYGTALPPHRTPIMLTHPADRIGETYLRCDPAKVVAVVETHAPDRNSAFKPADADSIA
+IAQHLVEFFEHEVAQGRYDERLLPLQSGVGNIANAVMSELVKSRFTGLSAFTEVVQDGML
+DALDSGTLATASATAFSLSTEAAERFNDNAAKYRDKLILRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYRDPLRDYFDRAMRGSDGLH
+TPHLLGEALSWHQRFLETGTMRHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001302.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001302.fa
new file mode 100644
index 0000000000000000000000000000000000000000..553b4e38e4547b4fe9d291717395587433e8e52e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001302.fa
@@ -0,0 +1,20 @@
+>PROKKA_01600
+MDAAPTPSLALEDQLCFALHRAARAVTRGYGPLLSRLGLTYPQYLVMLTLWQAEGDASAE
+TEASTPDAGALGVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDEG
+RALRASARTVPVDALTRIPLDTTERQVLMDLLNRITEAAGPR
+>PROKKA_01312
+MDAAPTPSLALEDQLCFALHRAARAVTRGYGPLLSRLGLTYPQYLVMLTLWQAESDASAE
+TEASTSDAAGALGVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDE
+GRALRASARTVPVDALTRIPLDTTERQVLMDLLNRITEAAGPR
+>PROKKA_01293
+MDAAPTPSLALEDQLCFALHRATRAVTRGYGPLLSRIGLTYPQYLVMLTLWQVEGDASAE
+TEAPTPGAGALAVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDEG
+RALRASARTVPADALTRIPLDATERQVLMCLLNRITEAVGPR
+>PROKKA_01202
+MDAAPTPSLALEDQLCFALHRATRAVTRGYGPLLSRLGLTYPQYLVMLTLWQVEGDASAE
+TDAPTPGAGALAVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDEG
+RALRESARTVPADALTRIPLDATERQVLMGLLNRITEAAGPR
+>PROKKA_01527
+MDAAPTPSLALEDQLCFALHRAARAVTRGYGPLLSRLGLTYPQYLVMLTLWQVESDASAE
+TEASTSDAAGALGVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDE
+GRALRASARTVPVDALTRIPLDTTERQVLMDLLNRITEAAGPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001303.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001303.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2bb5d0fa3d881a2dfa31026ac4059221454ce11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001303.fa
@@ -0,0 +1,34 @@
+>PROKKA_01602
+MSTPTRTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV
+ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGRGWREHAVLDGDTVQVVDTSQF
+SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAGQIARLLGASRVVGS
+AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD
+GRVAMCGAIAQYNSTEPPAAPRNLALAIGKCLTLRGFVLQKYAAQVRPEFLERVGPWVAA
+GKIQWDETVREGLENAPQAFIDLLEGANTGKMLVRL
+>PROKKA_01314
+MSTPTHTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV
+ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGRGWREHAVLDGDTVQVVDTSQF
+SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAGQIARLLGASRVVGS
+AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD
+GRVAMCGAIAQYNSTEPPAAPRNLALAIGKCLTLRGFVLQKYAAQVRPEFLERVGPWVAA
+GKIQWDETVREGLENAPQAFIDLLEGANTGKMLVRL
+>PROKKA_01292
+MSVDPYMRGRMNDVKSYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGLGWREHAV
+LDGDTVQAVDTSQFPDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAG
+QIARLLGASRVVGSAGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVG
+GDHLEAAIAALRVDGRVAMCGAIAQYNSTEPPAAPRNLALAIGKRLTLRGFVLQKYAAQV
+RPEFLERVGPWVAAGKIQWDETVREGLENAPQAFIDLLDGANTGKMLVRL
+>PROKKA_01200
+MSTPTHTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV
+ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGLGWREHAVLDGDTVQAVDTSQF
+SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSTAGQIARLLGASRVIGS
+AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD
+GRVAMCGAIAQYNSTEPPAAPRNLALAIGKRLTLRGFVLQKYAAQVRPEFLERVGPWVAD
+GKIQWDETVREGLENAPQAFIDLLEGANTGKMVVRL
+>PROKKA_01529
+MSTPTRTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV
+ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGRGWREHAVLDGDTVQVVDTSQF
+SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAGQIARLLGASRVVGS
+AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD
+GRVAMCGAIAQYNSTEPPAAPRNLALAIGKCLTLRGFVLQKYAAQVRPEFLERVGPWVAA
+GKIQWDETVREGLENAPQAFIDLLEGANTGKMLVRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001306.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001306.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85f2e9c69e56ddcf65b58fac7361824ccd776da6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001306.fa
@@ -0,0 +1,20 @@
+>PROKKA_01611
+MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI
+LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLVDAHPLTD
+DDADPALEADAEAVRVRMPVGAARAFARRTREVVDAGRPVCSDCGQPIDPDGHDCTFPDS
+>PROKKA_01322
+MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI
+LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGGIGLGWDPTTAQVLIDAHPLSD
+DDADPALEADAEAVRVRMPVGAARAFARRTREVVDAGRPFCSDCGQPIDPDGHDCTLPDS
+>PROKKA_01287
+MTESPAHVHEFDWPDRVVIGTIGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMLDEI
+LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLIDAHPLSD
+DDADPALEVDAEAVRVRMPVGAARAFARRTREVVDAGRPICSDCGQPIDPDGHDCTLPDS
+>PROKKA_01192
+MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI
+LDDLMALDGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLIDAHPLTD
+DDADPVLETDAEAVRVRMPVGAARAFARRTREVVDAGRPICSDCGQPIDPDGHDCTLPDS
+>PROKKA_01537
+MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI
+LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLIDAHPLSD
+DDADPALEADAEAVRVRMPVGAARAFARRTREVVDAGRPICSDCGQPIDPDGHDCTLPDS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001307.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001307.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1668a271c05ae01e3e9f39df7df646bae562d0ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001307.fa
@@ -0,0 +1,30 @@
+>PROKKA_01612
+MSAADVPAGELMSGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAATLAR
+REVAASLVSEALGWDIVPRTWLRDGPFGKGMVQLWQEQDPEQDAVDLFPADEVPASGWLT
+VLEGEDEGGNRLVLAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRHGVDHGLTFH
+VQDKLRTVLWGWLGEALSEEERDGVARVLDGLDGELGQGLAELLGAEEVEALAARCAQLL
+DDGIFPAPSGLTPAVPWPLF
+>PROKKA_01323
+MSAADVPAGELVAGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAGTLAR
+REVAASLVSEALGWDIVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPAGQVPASGWLT
+ILEGEDADGNRLVLAHEDSAALRRMAVFDVIVNNADRKGAHILAMPGGHRHGVDHGLTFH
+VADKLRTVLWGWLGEELSEEERDGVGRVLDGLDGELGRGLAELLSAEEVQALAERSAGLL
+DDGRFPAPSGLTPAVPWPLF
+>PROKKA_01286
+MSAADVPAGELVAGELTLTGRITTASNATFLGAIGDTSVVYKPVAGEAPLWDFPAGTLAR
+REVAAYLVSEALGWDIVPRTWLREGPFGEGMVQLWQEQDPEQDAVDLFPADEVPASGWLT
+ILEGEDEGGNRLALAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRYGVDHGLTFH
+VADKLRTVLWGWLGEALSEEERDGVARVLDGLDGELGRGLVQLLSAEEVEALAERCAQLL
+DDGVFPAPSGLTPAVPWPLF
+>PROKKA_01191
+MSAADVPAGELVDGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAGTLAR
+REVAAHLVSEALGWEIVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPADEVPAAGWLT
+ILEGEDEEGRRLALAHENSAALRRMAVFDVIVNNADRKGAHILAMPGGHRYGVDHGLTFH
+VAGKLRTVLWGWLGEALSEEERDGVGRVLDGLDGELGRGLAELLSAEEVEALAERGARLL
+DDGIFPAPSGRTPAVPWPLF
+>PROKKA_01538
+MSAADVPAGELVSGELTLTGRITTASNATFLGAVGDTPVVYKPVAGEAPLWDFPAGTLAR
+REVAAHLVSEALGWDVVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPADEVPASGWLT
+ILEGEDEDGNRLALAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRHGVDHGLTFH
+VEDKLRTVLWGWLGEALSDEERDGVARVLDGLDGELGRGLAELLSAVEIGALAERSAGLL
+DDGTFPAPSGLTPAVPWPLF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001311.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001311.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c658403711fda1340f22d53359e6f13925a6cb95
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001311.fa
@@ -0,0 +1,19 @@
+>PROKKA_01629
+MSTPTPTGPTPTPPGGELLPLISLAVEHVFNTLGRQPVFAPTILAVTADGQRGMWEHPDL
+QPEQAAATVAKISPRPTRAVAVFDGEIETADGPRPAVAVEAFDAAALASTRMVFPYLPGV
+AAAGIAARVDGDPQVVANGPNPLFG
+>PROKKA_01334
+MSTPTPTGPTPTPPGGELLPLISLAVEHVFDTLGRQPVFAPTILAVAADGQRGMWEHPDL
+EPEQAAATVAKISPRPTRAVAVFDGEIETADGPRPAVAVEAFDAAALASTRMVFPYLPGV
+AAAGIAARVDGDPQVVANGPNPLFG
+>PROKKA_01267
+MEHVFDTLGRRPVFHPTILAVTADGQRGMWEHPDLEPEQAAAEVAKISPRPARAVAVFEG
+EAATEDGPRPAVAVEAFDAAALASVRLVFTYLPGVPGAGIAAQVDGDPQVVANGPNPLFG
+>PROKKA_01175
+MTPPTHEILPLVSLAVDHVFDTLTRQAVFDPTILAVTADGARGMWTLPDLAPEQAAAEVG
+RIQPLPQRAVAVFDGEVQTPQGPRPAVAVEAFDAGAVQSVRLVFEYVPGIPGTEITGRIE
+GEPHIVANGHNPLFGQIS
+>PROKKA_01558
+MSTPTPTGPTPTPPGGELLPLISLAVEHVFDTLGRQSVFAPTILAVTADGQRGMWEHPDL
+EPEQAAATVAKISPRPTRAVAVFDGEIETADGPRPAVAVEAFDAAALASTRMVFPYLPGV
+AAAGIAARVDGDPQVVANGPNPLFG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001322.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001322.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9f5da08412f9a639ea5b2369ca7ede6bee4e661
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001322.fa
@@ -0,0 +1,60 @@
+>PROKKA_01641
+MDTPQDPPHRDDPSGGPVEPAVDAALDRVRALLRQARGTAAPDAPTALDARGWWELSLEA
+ALRDEPRESARLADSGLAALGPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR
+HLGRPRQAELESQLGAALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH
+RVHTGDLDAALELARRVIAVLGGLRAAGALLPTGSWSSAHLLLARLHLWRGEHAEADAAA
+AVVTALPAARAVLASATTVRAIAAHELDRPTAALDLALEAAERMASVGLRRGAASAAALA
+GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL
+VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA
+GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL
+LEEALALVRDAGADWQVADYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA
+ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE
+LDALREGLGAD
+>PROKKA_01346
+MDTPQDPPRRDDPSGGPVEPAVDAALDRVHALLRQARVIAAPDAPTALDARGWWELSLEA
+ALRDEPRESARLADSGLAALVPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR
+HLGRPRQAGLESQLGAALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH
+RVHTGDLDTALELTRRVIAVLGGLRAAGALLPIGSWSSAHLLLARLHLWRGEHAEADAAA
+AVVTVLPAARAVLASATTVRAIAAHELDRPTAALDLAFEAAERMASVGLRRGAASAAALA
+GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL
+VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA
+GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL
+LEEALALVRDAGADWQVADYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA
+ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE
+LDALREGLGAD
+>PROKKA_01254
+MDAPQQTPAPADVGPTAVLARVRTLLAEARTSGAPEDAVDAAPVDHDARQWWELSLEAAL
+RDEPRESARCAESGLAALGPGEDGVRLSLLRALAVAADRLGDETGLTRWVEARAALLRTL
+GRPRQAALETQLGASLVREPDGFEAAVLAGVVEEEPGVPGEDPGDTVLPEAALALAVHRV
+HASDLDGALAAARRAVESLRGLRAAGAVLPVGSWSSAHLLLSRLHLWRGEHAEADEAAAV
+VTSLPAARAVLASATTVRAIAAHEQDRPTAALALALDAADRMARVGLRRGAASAAALAGR
+VAGDLEGHEEAAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRPDEAEPLLARLVR
+REAAQGHDVEQARALVDLGHAHHDQDRSENALPLWREAAGLFEAHGRWEDAARTLLAAGA
+LVNRERDELTRPSALDLFERAVAAARRAVDEDPAVLPAALHAHGYLLCESGRPEGLELLD
+EAVALVREAEAPWQVADYTDTRARALWSLEQGAEAVSTALHAADLFTAAQDPEGAAQAEL
+FAASVVAEDGSPEQAATLFRLVSESTQSTLVRLGALTGLHQCLSAVGDHDGAARVRDDLD
+AVREQLGAD
+>PROKKA_01163
+MAEDAPALLAGRDPLAAVEALLAAARDDAALPLPAGSDAPSLRERALEALLREDPASAAR
+AAEDGLDAPGGQDPALRLALLRLRATAAAHAGDEPALEEWTARRADLLRRLGRPRQADLE
+VQLGASLLREPDAFEATVLAGVAEDERGRITADPAALEDTVLPDALLALCAQRVQAHDLD
+AALEAAEEALAVIRAQETAGVVLGEAAEPHALLMLARLHLWREEHRASDDAARAVLARPC
+AAVVRASATLVRALAAHGQDRPEAALDFALRAAEAMSRAGLRRGAASAAALVGRVAGARA
+DRQDLAVAAWELSCVHAEKAEAPEAPSLAYWWAHQLLIAGRAEEAEPVLTALVRREAAAG
+DEAAQARALVDLGHACHELDRPSEALPLWREAAELFTRRGHHADAAHTLLAAGALCHRDP
+HDAAHAGALDLFEQAVDAARRSEGDSAVLASALHALGYLRCETGRGDGLELIDEAIALAE
+GSGAAWQKADYLDTRARSLWALHRGDDAVSAALTSADLFTDAGDPSGAAQAELFAAHVVA
+EDGRPEQAATLFRLVSESTHSDLVRLGALTGLQQCLAALGEHAEADRVRADADAVRRALG
+GRD
+>PROKKA_01571
+MDTPQDPPHRDDPSGGPVEPAVDAALDRVRALLRQARGTAAPDAPTALDARGWWELSLEA
+ALRDEPRESARLADSGLAALGPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR
+HLGRPRQAGLESQLGGALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH
+RVHTGDLDAALELARRVIAVLGGLRAAGALLPTGSWSSAHLLLARLHLWRGEHAEADAAA
+AVVTALPAARAVLASATTVRAIAAHELDRPTAALDLALEAAERMASVGLRRGAASAAALA
+GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL
+VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA
+GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL
+LEEALALVRYAGADWQVANYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA
+ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE
+LDALREGLGAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001327.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001327.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9dd3c93948c170e91eafab6eccabf87932c183d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001327.fa
@@ -0,0 +1,15 @@
+>PROKKA_01646
+MPTYAYRCKDCGHAFDVVQAFTDDALTECPACGGVLRKQYGSVGVSFKGSGFYRTDSRSG
+TGGTGSAGGSTSDSAAGSSTSSTSSSSSPAAD
+>PROKKA_01351
+MPTYAYRCKDCGHAFDVVQAFTDDALTECPACGGVLRNQYGSVGVSFKGSGFYRTDSRSG
+TGGTGSAGGSTSDSAAGSSTSSTSSSSSAAAD
+>PROKKA_01247
+MPTYAYRCRDCGHAFDAVQSFTDDALTQCPECGGVLRKQYGSVGVSFKGSGFYRTDSRSA
+GSASSGSASSAGSASSSTSAGGSGTSSTSSGGSGSSGSSSSSSGSKD
+>PROKKA_01158
+MPTYAYRCKDCGHAFDAVQSFSDDALTECPVCGGVLRKQYGSVGVSFKGSGFYRTDSRGG
+APSSTPAAPSSGAASSTGTSSGSSD
+>PROKKA_01576
+MPTYAYRCKDCGHAFDVVQAFTDDALTECPACGGVLRKQYGSVGVSFKGSGFYRTDSRSG
+TGSAGGSTSDSAAGSSTSSTSSSSSAAAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001329.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001329.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2bdfd7dd7613d36215a0f44ce159e0a69173a7a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001329.fa
@@ -0,0 +1,110 @@
+>PROKKA_01648
+MTEQEFPRLARARAAARPDEGQTRPDPAAWVSSLGSGAENDTMLRFAPSAANSIDLTEAN
+SSGVSQLLLGRRTRLSTLLPAGPELDAAHEVSLGLRAKVRELAEERGIDVGALAVGVATW
+TAEEDGRRERRSAPVLLARVALTVRRGARGRDELEVQITEPARLNPALVRNLRRHHGIAL
+DPEAYQQAAYATARLEPAPAFARLREETAAIADLHIQDCLLVSTFADLGETASLPASLED
+LPVVQALYDAGTGMVPRPAALQPTGAPAEDDVAPADERLVVDVDAAQARVLEHAAAGESL
+VVAAAPGTGQTQTAAALAARLAWEGRRVLVVAERSAALADVLDRLEEADLRSIALDVPAN
+ADPELLRRQLVQAVLRSERAVDPDTARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA
+MQALAALTGLETPPATTVRLKRSVLDSTVNRQAVGEQLVRAGELGAFSAAATESRWFGAR
+VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL
+TEFTPEVFSLDVPQLVAATATSSWRRLHLVEMSSVTRSRLRRAAKDAVRPGVQPTDLHGA
+LVDAAAVLEDWNRHAAEPGTPPQVPDQGEHVMGQVGQVRERLRRLEGVLAPEAVAEAPLE
+ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLRDHGLAELLEDLRDREVPTEALTAEL
+ELAWWQSALEAMISGDDFLAMMSGTDLAEVERGFRDLDRAHLERGGARLSAALAARWREA
+LRTYRADAAVLRTLLKQGSPTVESLATITPELLQPLVPVVTTSPMALSEFPPEWRADVVV
+LLEADATALATAMGALTRAPQVVALGDPVIGRPQSFQVSVDPTATAGPLRPLRSAHDALD
+EVLPTLPLRTVHRPLERRLVRLLSALAYDGALDALPTAGEATGRDRAVTAEYLPEGTGIP
+MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEQHARRVAAAVQATAAQAPWA
+HEFLARGRGEDAADAEPFVIVPVVRAASVVRDAVILTPGYGRTPHGRVVHHFGAFSDPDG
+ERMVTVALTRARRRLHLVSALRAADLDEDRLDGGALWFLRLLEAYLGDDAADPVGMVGDP
+LLADLRDRLEEHGARVLPRYAGVMDLAVLDPRADQDEAPRPLALAGDGGEVYRALTVRQR
+SRTLPEGLEARGWEPRTLWSIDVFADPESVARELADRLGVEPADETDETDDDAR
+>PROKKA_01353
+MTEQEFPRLARARAAARPDEGQTRPDPAAWVASLGSGAENDTMLRFAPSAANSIDLTEAN
+SSGVSQLLLGRRTRLSTLLPAGPELDAAHEVSLGLRAKVRELAEERGIDVGALAVGVATW
+TAEEDGRRERRSAPVLLARVALTVRRGARGRDELEVQITEPARLNPALVRNLRRHHGIAL
+DPEAYQQAAYATARLEPAPAFARLREETAAIADLHVEDCLLVSTFADLGETASLPASLED
+LPVVQALYDAGTGMVPRPAALQPTGAPAEDDVAPADERLVVDVDAAQARVLEHAAAGESL
+VVAAAPGTGQTQTAAALAARLAWEGRRVLVVAERSAALADVLDRLEEADLRSIALDVPAN
+ADPELLRRQLVQAVLRSERAVDPDTARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA
+MQALAALTGLETPPATTVRLKRSVLDSTVNRQAVGEQLVRAGELGAFSAAATESRWFGAR
+VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL
+TEFTPEVFSLDVPQLVAATATSSWRRLHLVEMSSVARSRLRRAAKDAVRPGVQPTDLHGA
+LVDAAAVLKDWNRHAAEPGTPPQVPDQGEHVMGHVGQVREHLRRLEGVLAPEAVAEGPLD
+ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLRDHGLAELLEDLRDREVPTEALTAEL
+ELAWWQSALEAMISGDDFLAMMSGTDLTEVERGFRDLDRAHLERGGARLSAALAARWREA
+LRTYRADAAVLRTLLKQGSPTVESLATITPELLQPLVPVVTTSPMALSEFPPEWRADVVV
+LLEADATALATAMGALTRAPQVVALGDPVIGRPQSFQVSVDPTATAGPLRPLRSAHDALD
+EVLPTLPLRTVHRPLERRLVRLLSALAYDGALDALPTAGEATGRDRAVTAEYLPEGTGIP
+MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEQHARRVAAAVQATAAQAPWA
+HEFLARGRGEDAADAEPFVIVPVVRAASVVRDAVILTPGYGRTPHGRVVHHFGAFSDPDG
+ERMVTVALTRARRRLHLVSALRAADLDEDRLDGGALWFLRLLEAYLGEDAADPVGMVGDP
+LLADLRDRLEEHGARVLPRYGGVMDLAVLDPRAEQDEAPRPLALAGDGGEVYRALTVRQR
+SRTLPEGLEARGWEPRTLWAIDVFADPESVARELADRLGVEPADETDETDDDVR
+>PROKKA_01245
+MREQEFPRLARARAAARPEEGQTRPDPAAWVASLGSGAENDTMLRFAPSAANSIDVTAAN
+SSGVSQLLLGRRTRLSTLLPAGPALQAAEEVAAGLRAKVRELSEERGIDVGALAVGVATW
+TAEEDGRRERRSAPVLLARVALTVRRGARGRGELEVQITEPARLNPALVRNLRRHHGIAL
+DPEAYRQAAYATARLEQRPALARLREEAAALTGLQVEDRMLVSTFADLGETATLPASLEH
+LPVVEALYDAGTGMVPRPPALQPTEAPGEDDVAPADERLVLDLDAAQRRVVEHSAAGESL
+VVAAAPGTGQTQTAVAVAARLAWEGRRVLVVAERSAALADVHARLDEIGLRAAALDVPAH
+ADPEQLRRQLVQAVLRAERAEAPDAARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA
+MQALAALTGLPTPPATTVRLKRSVLDSTVNRQAVAEQLVRAGELGAFSAAATESRWFGAR
+VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL
+TEFTPEVFALDVPQLVAATATSTWRRTHLVEMSSVARSRLRRAAKDAVRPGVQPTDLHGA
+LVDAAAVLEDWNRHAAEPGTPPQVPDQGERVMGVVGDVRERLRRLERILAPEAVAEQPLA
+ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLKDHGLTELLTDLRDREVPTEALAAEL
+ELAWWQSALEAMISGDDFLAMMSGADLAEVERGFRELDRAHLERGADRLSAALGARWKEA
+LRTFRADAAVLRGLLKQGRPTVEALTTLAPEVLQPLVPVVTTSPMALSEFPSDWGADVVV
+LLEADATALATAVGALTRAPQVVAFGDPVIGRPQSFQVSVDPTATAGPLRPLRSAHDALA
+EVLPTVALRTVHRPLERRLVRMLSALAYEGALEALPTAGEATGRDRTVTAEYLQEGTGIP
+MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEPHARRVAAAVQATAARASWA
+LDFLSRGRGEDAEGAEPFVIVPVTRAASVVRDAVILTPGYGRTPHGRVVHHFGAFSDPGG
+ERMVAVALTRARQRLHLVSALRAADLDEDRLDGGAQWFLRLLEAYLGDGAPDPVGRVSDP
+LLADLRERLEERGARVLPRHGGVMDLAVVDPHPEDEDEDGDAPRPLALAGDGGDVYRALT
+VRERTRTLPERLEARGWDPRTLWAIEVFADPESVAQELADRLGVRPADESERDADDDGR
+>PROKKA_01156
+MTEQEFPRLARARAAVRPAEQDQERPDPAAWVASLGSGAESDTMLRFAPSAANSIDLTGA
+GTSGLSQLLLGRRTRLSTLLPAGPELDAAQEVAAALRAKVRELGEERGIDVGALALGVAT
+WSAVEDGRRERRTAPVLLARLAFSVRSGARGRDEVELQIVEHAHLNPALVRNLRRHHGLR
+LDPEAYQHAAYATSRLEPGPALALLREEAAGVEGLEVQETLLVSTFADLGDTATLPESLE
+HLPVVQALYDVGTGMVPRPAELRPTGRPDEDELPPADERLVLDADPSQLRALDHAAAGES
+LVVRTAPGTGQTQTAVNLAARLAWEGRRVLVVAERSSALADVHARLAQAGLRDAALDVPA
+HADPEDLRRQLVAAVLRAERASAPDRAAADAELEELRRRLREHVDSLHHVRPRWGCSPFQ
+AMQALASLTALDTPPATTVRLKRSVLDSTVDRHAVAGRLTRAGELGAFDRDATASRWFGA
+RVRNVQETEAAGELVEHLAGTLYTTRRAVEAAADQAGLRRPRTVDGWAEQSDLFARVERA
+LTAMDPSVFSLDVPQLVTATASSQWRRSNAVEMSSVQRSRLRRAAKDAVKPGVQVPDLHQ
+ELMEVEGILEDWRRWTAIPGSTPMVPDMADHARPAVRDVLDALDRLSQVLAPEATAGTPL
+AEQDVDDLMAAVDGLVADRPTLATLPERTLVLDELREHGLNELLEDLHAREVPVAALPAE
+LELAWWQSALEAMISGDDFLAMMSGADLTAVEQGFRAADRTLLDSGGARLAASLGAAWKA
+ALGTYRADAAVLRSLLKQGRPSVESLATITPGLLQALVPIVTTSPMALTEFPPDWDADVV
+ILLEADATALATVAGALTRAPQVVAFGDPAIGRPQSFQVSVDPTATAGPLRPLRSALSAL
+AEVLPVLDLRHVHRPLPRSLVRLVSHVAYEGAVDALPTAAEFTGRGRTLTAEYVAEGVGI
+PMTGGDVVESTDAEVARTVERVFEHIRDRPEESLAVVTVSEQHARRVAGAVQATAARAPW
+AADFLARGRTDGDEREPFVIVPVLRASTVTRDAVILTPGYGRTPHGRVVHHFGALSDPDG
+ERMLTVALTRARARMHVVTALRAADLDADRLDGGALAFRRMLEVALDDAEAAPAGRLSDP
+LLLDLRDRLAAEDALVAAHYGGAMDLAAADAAGERGRVRPLALVSDGGDAYREQSVRERS
+RRLPERLEARGWDTDTLWAIDVFADPESVAARLVGRLGLPLEEVDEDGEDDADGES
+>PROKKA_01578
+MTEQEFPRLARARAAARPDEGQTRPDPAAWVSSLGSGAENDTMLRFAPSAANSIDLTEAN
+SSGVSQLLLGRRTRLSTLLPAGPVLDAAHEVSLGLRAKVRELAEERGIDVGALAVGVATW
+TAEEDGRRERRSAPVLLARVALTVRRGARGRDELEVQITEPARLNPALVRNLRRHHGIAL
+DPEAYQQAAYATARLEPAPAFARLREETAAIADLHIQDCLLVSTFADLGETASLPASLED
+LPVVQALYDAGTGMVPRPAALQPTGAATEDDVAPAEERLVLDVDAAQARVLEHAAAGESL
+VVAAAPGTGQTQTAAALAARLAWEGRRVLVVAERSAALADVLDRLEEADLRSIALDVPAN
+ADPELLRRQLVQAVLRSERAVDPDTARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA
+MQALAALTGLETPPATTVRLKRSVLDSTVNRQAVGEQLVRAGELGAFSAAATESRWFGAR
+VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL
+TEFTPEVFSLDVPQLVAATATSAWRRLHLVEMSSVTRSRLRRAAKDAVRPGVQPTDLHGA
+LVDAAAVLEDWNRHAAEPGTPPQVPDQGEHVMGQVGQVRERLRRLEGVLAPEAVAEGPLD
+ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLRGHGLAELLEDLRDREVPTEALTAEL
+ELAWWQSALEAMISGDDFLAMMSGTDLAEVERGFRDLDRAHLERGGARLSAALAARWREA
+LRTYRADAAVLRTLLKQGSPTVESLATITPELLQPLVPVVTTSPMALSEFPPEWRADVVV
+LLEADATALATAMGALTRAPQVVALGDPVIGRPQSFQVSVDPTATAGPLRPLRSAYDTLD
+EVLPTLPLRTVHRPLERRLVRLVSALAYDGALDALPTAGEATGRDRAVTAEYLPEGTGIP
+MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEQHARRVAAAVQATAAQAPWA
+HEFLARGRGEDAAEAEPFVIVPVVRAASVTRDAVILTPGYGRTPHGRVVHHFGAFSDPDG
+ERMVTVALTRARRRLHLVSALRAADLDEDRLDGGALWFLRLLEAYLGDDAADPVGMVGDP
+LLADLRDRLEEHGARVLPRYAGVMDLAVLDPRAEQDEAPRPLALAGDGGEVYRALTVRQR
+SRTLPEGLEARGWEPRTLWSIDVFADPESVARELADRLGVEPADETDETDDDVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001331.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001331.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef19303b41cde5aac7dfc3408188b3702cb4b90f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001331.fa
@@ -0,0 +1,24 @@
+>PROKKA_01650
+MSTQHPGPEPVDPASLPDPEDITEADLPEPPPRPGREQRRFAGTQQQIRSATRLYVVCAW
+ITGIMLLLLVAEMVLKYGMHVELYAGGTTLDGDANGLGLHPTDSVTGGVNLSLFILIAHG
+WMYVVYLLASFRLWSLMRWEPLRLLAMAGGGVVPFLSFVVEKRMTRVVRDELHRFPDAAR
+RY
+>PROKKA_01355
+MSTQHPGPQPVDPASLPDPEDITEADLPEPPPRPGREQRRFSGTQQQIRSATRLYVVCAW
+ITGIMLLLLVAEMVLKYGMHVELYAGGTTLDGDANGLGLHPTDSVTGGVNLSLFILIAHG
+WMYVVYLLASFRLWSLMRWEPLRLLAMAGGGVVPFLSFMVEKRMTRVVRDELHRFPDAAR
+RY
+>PROKKA_01243
+MSHTEPVDPAALPDPEDITEADLPEAPPRPGRERRRFAGTQQQIRSATRFYVVCSWITGV
+MLLLLVAEMVFKYAWGQELFAGGTTVDGEQNILGLHPEDSVTGGVNLSLFILIAHGWMYV
+VYLLACFRLWSLMRWQPMRLLAMAGGGVVPFLSFVVEKKVTKVVRDDVHRFPDAARRY
+>PROKKA_01154
+MSQPHHDAGREAARAGEAPVDPATLPDPEDITEADLPAPPPRPGRAVRRFAGTRQQIVSA
+DRIYKVCAYITGVMLLLLVAEMVFKYGLHQELFAGGTTVDGEPHGFGLAPEKSVTGGVNL
+SLAILIAHGWMYVVYLLACFRLWSLMRWAPGRLLAMAGGGVVPFLSFVVERKVSGQVREE
+LAQFPDAARRY
+>PROKKA_01580
+MSTQHPGPQPVDPASLPDPEDITEADLPEPPPRPGREQRRFAGTQQQIRSATRLYVVCAW
+ITGIMLLLLVAEMVLKYGMHVELYAGGTTLDGDANGLGLHPTDSVTGGVNLSLFILIAHG
+WMYVVYLLASFRLWSLMRWEPLRLLAMAGGGVVPFLSFVVEKRMTRVVRDELHRFPDAAR
+RY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001332.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001332.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a7c5811bf23b3abd5a3e71b7d4a6f9f249a3ef75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001332.fa
@@ -0,0 +1,35 @@
+>PROKKA_01651
+MLRTALKPVWLATLVLALVAAAVFVALSKWQFESAETNAPPPRTQTEHAVPFLEHVRPYE
+ALLGSQADQVVTVEGEFVPGTDVLVGPRLLNGRDGYWTVTALRVAGAPDGEVVPVVRGWS
+ADADVVDPAPAGQVTVTGRLLPPDGPLPREATAEDTADRLLYRSLAPAQLVNVWDEPSYA
+AYVAAFEMVDAAGAETGAAGPGGLEPVWVAPQPEETQIIWLNVFYAVEWMLFAGFALFLW
+WRFVRDDHVRDEHERRLDEEWAAQWRAEELERRRAAAREAKERAVAAQAAAHPRQDHDDD
+GAARPDPRDPGPRGPREEQSR
+>PROKKA_01356
+MLRTALKPVWLATLVLALVAAAVFVALSKWQFESAETNAPPPRTQTENAVPFLEHVRPYE
+ALLGSQADQVVTVEGEFVPGTDVLVGPRLLDGRDGYWTVTALRVAGAPDGEVVPVVRGWS
+ADADVVDPAPAGQVTVTGRLLPPDGPLPREAAAEDTADRLLYRSLAPAQLVNVWDEPSYA
+AFVAAFEMADAAGAETGAAGPGGLEPVWVAPQPEETQIIWLNVFYAVEWMLFAGFALFLW
+WRFVRDDHVRDEHERRLDEEWAAQWRAEELERRRAAAREAKERAFAAQAAAHPRQDHDDD
+GAARPDPRDPGPRGPREEHRR
+>PROKKA_01242
+MLRTALKPVWLATLVLALVAAGLFVALSKWQFETAETNAPPPRTQTEQPVPLTDHVRPYE
+PLLARDADQVVTVPGEFLPDTDVLVGPRLLRGDEGFWTVSAFRVAGAPDGEVIPVVRGWS
+AGADVVDPAPQGDVTVTGRLLPPDGPLPRTAAEADTADRLLYASLAPGQLVNVWDEPSYA
+AFVAAFEVADAAGAEVGAGASEGGLEPVWVAPQPEETEVIWLNVFYAVEWILFAGFALFL
+WWRFVRDDHLRDERERELDEEWAAQWRAEELARRREEARLAKERAYAAQAAARPSTDPEE
+NRP
+>PROKKA_01153
+MLRTALKPKWLATLVLALVAATAFVLLSRWQFASSETAAPPPRTQTENAVPLTEHVRPGE
+PLLASQADQVVSARGEFVPGTDALVGPRLSDGREGWWTVTAFRVAGAPDGETVPVVRGWS
+EAADVVDPAPTGEVTVTGRLLPPDGPVSPADAGEDTAGRPAFSTLSPGQLVNAWDVPAYA
+AYVAAFGVTDAAGADVSAGARDGGLQPVWVPPQPEESQVVWLNVFYGVEWLLFAGFALFL
+WWRFVRDDHLRDEQEAELDAQWAARWRAEELERRRERARREKEAAARAYAAWQAGETAPD
+AAHQEPQDGPAGPRKEGQA
+>PROKKA_01581
+MLRTALKPVWLATLVLALVAAAVFVALSKWQFESAETNAPPPRTQTENAVPFLEHVRPYE
+ALLGSQADQVVTVEGEFVPGTDVLVGPRLLNGRDGYWTVTALRVAGAPDGEVVPVVRGWS
+ADADVVDPAPAGQVTVTGRLLPPDGPLPREAAAEDTADRLLYRSLAPAQLVNVWDEPSYA
+AFVAAFEMVDAAGAETGAAGPGGLEPVWVAPQPEETQIIWLNVFYAVEWMLFAGFALFLW
+WRFVRDDHVRDEHERRLDEEWAAQWRAEELERRRAAAREAKERAFAAQAAAHPRQDHDDD
+GAARPDPRDPGPRGPREEQSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001347.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001347.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b186f7d6125443b3a6a7d277f620e31fb4671c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001347.fa
@@ -0,0 +1,40 @@
+>PROKKA_01670
+MTGPLTRLEPMPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIP
+EIAARAHLEALVPTIRRALDTADVTLADLDAIAVTSGPGLAGALMVGVAGAKALATALGT
+PLYGINHLVAHVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISAEVELLGST
+IDDAAGEAYDKVARLIGAGYPGGPVIDRLAAQGDPTAFRFPRGLTAGKFVGSAEEPGPHR
+HDWSFSGLKTAVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLM
+LGGGVAANSRLRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWF
+GADPGQPVEVVSV
+>PROKKA_01375
+MPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIPEIAARAHLEA
+LVPTIRRALDTADVTLADLDAIAVTSGPGLAGALMVGVAGAKALATALGTPLYGINHLVA
+HVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISSEVELLGSTIDDAAGEAYD
+KVARLIGAGYPGGPVIDRLAAEGDPTAFRFPRGLTAGKFVGSAEEPGPHRHDWSFSGLKT
+AVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLMLGGGVAANSR
+LRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWFGADPGQPVEV
+VSV
+>PROKKA_01208
+MTGPLTRLEPMPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIP
+EIAARAHLEALVPTVRRALEAADVGLKDLDAIAVTSGPGLAGALMVGVAGAKALATALDT
+PLYGINHLVAHVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISSEVELLGST
+IDDAAGEAYDKVARLIGAGYPGGPVIDRLAAQGDPTAFRFPRGLTAGKFVGSAEEPGPHR
+HDWSFSGLKTAVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLM
+LGGGVAANSRLRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWF
+GADPGQPVEVVSV
+>PROKKA_01136
+MAPMSATATAPLVLGIESSCDETGVGIARGTALLAHEVASSVEEHVRFGGVIPEIAARAH
+LEALVPTVRRALDAAGVTLDEVDAIAVTSGPGLAGALMVGVAGAKALAVAADKPLYGINH
+LVAHVGVGLLDGVRPADWDDLPRDLGALLVSGGHTEILQVDRISSDVTLLGSTIDDAAGE
+AYDKVARLIGAGYPGGPVIDRMAQEGDPKAFRFPRGLTAGKFVGTAEEPGPHRHDWSFSG
+LKTAVSRAVEQFEAQGLEVPRTDIAASFQEAVADVITAKAVRACREHGLTHLLLGGGVAA
+NSRLRGLLADRCRSAGIELVVPPVNLCTDNGAMVAALGARLVADGVAPSDLAFGADPGQP
+VSAVSAA
+>PROKKA_01600
+MTGLLTRLEPMPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIP
+EIAARAHLEALVPTIRRALDTADVTLADLDAIAVTSGPGLAGALMVGVAGAKALATALGT
+PLYGINHLVAHVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISSEVELLGST
+IDDAAGEAYDKVARLIGAGYPGGPVIDRLAAQGDPTAFRFPRGLTAGKFVGSAEEPGPQR
+HDWSFSGLKTAVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLM
+LGGGVAANSRLRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWF
+GADPGQPVEVVSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001348.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001348.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d93fa7155022706f33796f0e796492c280c48539
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001348.fa
@@ -0,0 +1,25 @@
+>PROKKA_01671
+MSPAEPDPAGDGRPAEDAHGLPPGYLLRPMTVWDIPEVLAHEATLFPLDAWPAHFYEEEL
+AQTGPAGGRDAHGRPPTRDYRVVVRDVAAPGSADDDGPAPGEIVGYGGIMVVGDVADVQT
+VGTVAAAQGRGIGAAQLRWMAAEAAARGASSLMLEVRASNAAARRLYARHGFEELHVRRR
+YYPGGEDAVIMRKVL
+>PROKKA_01376
+MSPAEPAPTDDGRPAEDEHGLPPGYLLRPMTVWDIPEVLAHEATLFPLDAWPAHFYEEEL
+AQTGPAGGRDAHDRPPTRDYRVVVRDVPAPGSADDDGPAPGEIVGYGGIMVVGDVADVQT
+VGTVAAAQGRGIGAAQLRWMAAEAAARGASSLMLEVRASNAAARRLYARHGFEELHVRRR
+YYPGGEDAVIMRKAL
+>PROKKA_01207
+MSPVEPAPGGDERPAEDEHGLPPGYLLRPMTVWDIPEVLAQEATLFPLDAWPARFYEEEL
+AQTGPAGGRDAHGRPPTRDYRVVVRDVPAPVAPDEDGPAPGEIVGYGGIMVVGDVADVQT
+VGTVAAAQGRGIGAAQLRWMAAEAAARGASALMLEVRASNAAARRLYARHGFEELHVRRR
+YYPGGEDAVIMRKAL
+>PROKKA_01135
+MSLPDATDPGDDAAPAHGLPAGFLLRPMTVWDVPEVLEHEETLFPLDAWPGHFYAEELAQ
+AGPAGALDAHGRPTTRDYRVVVRQDTGEIVGYGGIMAVGDTADVQTIGTAAAVQGRGIGA
+AQLRWMVAAARERGAESLLLEVRESNAAARRLYARHGFEPIAVRRGYYPGGEDAVVMRRA
+L
+>PROKKA_01601
+MSPAEPAPAGDGRPAEDGHGLPPGYLLRPMTVWDVPEVLAHEATLFPLDAWPAHFYEEEL
+AQTGPAGGRDAHGRPPTRDYRVVVRDAAAPSSADDDGPAPGEIVGYGGIMVVGDVADVQT
+VGTVAAAQGRGIGAAQLRWMAAEAAARGAGFLMLEVRASNAVARRLYARHGFEELHVRRR
+YYPGGEDAVIMRKTL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001350.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001350.fa
new file mode 100644
index 0000000000000000000000000000000000000000..619872bb594d0c375f6e7f29c65b2c6c703dcf55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001350.fa
@@ -0,0 +1,25 @@
+>PROKKA_01673
+MSDHAIPAPGATLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS
+VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDAPAASAGEGEDGIVTDFS
+DEDGGQAEELRSAVVTGRGPRWAGVVLP
+>PROKKA_01378
+MSDHAIPAPGATLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS
+VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDAPAAPAGEGEDGIVTDFS
+DEDGGQAEELRSAVVTGRGPRWVGVVLP
+>PROKKA_01205
+MSRHEPPAPDPALPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAT
+VDRSVTVVEWGRGLAESLAGFPEDPDASWLDVEIVRARGGEDPAPAGPGADDGGIVTDFS
+DEDGEQAEELRSAVVTGYGPRWAGVRLP
+>PROKKA_01133
+MIAGRRAEQPLPAPVWERRVPLDGAAGTREFGAALAGVLRAGDVLILTGELGAGKTTLTQ
+GLGAGLGVREGVISPTFVLSRIHPSLADGPDLVHVDAYRLRSAGELTDLDLEATADRSVT
+VVEWGRGMAESLAGFPEDPEASWLDVEVLRARGGADLPDGPAGGDAAPDAPVIVTDFSDE
+EGEAAEEVRTAVVRAHGPRWAAVALP
+>PROKKA_01603
+MSDHEFPAPGPTLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS
+VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDGPAASAGEEDGIVTDFSD
+EDGGQAEELRTAVVTGRGPRWAGVVLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001351.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001351.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12413a6dc845e5158946cc0fae278df181e6f314
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001351.fa
@@ -0,0 +1,40 @@
+>PROKKA_01674
+MSRADVAPADTERAVRIDLAAVRHNVGVLQERIRRPDGSRPLLTAVVKADAYGHGAVAVA
+RAAAAAGADRLGVAHVREALALRAAGVRLPVLAWLHTGATDFAAAVEAEVTLGVSGWDLD
+AVADAVRGLRARGGAGPEARADLHLKADTGLGRHGCTPERWPALVARAAELEAAGLVRVE
+GVFSHLGVADEPDRAAETTAQLLRFERMAAEAAETLGHPLLRHLANTPAALARPDTHLDM
+VRVGLGLYGLSPFADVTAAEFGLRPAMSFVTVLANVKAVPAGQGVSYGFRHVTAEPTTLG
+LVPLGYADGVPRVVEGTRVHVGGRTVPVVGRIAMDQFVVDLGPDAADAPGDAVELFGPAS
+GIPVEEWAAAAGTINYELVTRIGGRVDRQHVDPTPTQEARP
+>PROKKA_01379
+MSRADVNPADTERAARIDLAAVRHNVGVLRERIRRPDGGRPLLTAVVKADAYGHGAVAVA
+RAAAAAGADRLGVAHVREALALRAAGVPLPVLAWLHTGATDFAAAVEAEVTLGVSGWDLD
+AVADAVRGLRARGGAGPEARAVLHLKADTGLGRHGCTPERWPALVARAAELEAAGLVRVE
+GVFSHLGVADEPDRAAETTAQLLRFERMAAEAAETLGHPLLRHLANTPAALARPDTHLDM
+VRVGLGLYGLSPFADVTAAEFGLRPAMSFVTVLANVKAVPAGQGVSYGFRHVTAEPTTLG
+LVPLGYADGVPRVVEGTRVHVGGRTVPVVGRIAMDQFVVDLGPDAADAPGDAVELFGPAS
+GIPVEEWAAAAGTINYELVTRIGGRVDRQHVDPTPTQEARP
+>PROKKA_01204
+MTQQDRSAGPAERTARIDLAAVRHNVAAVRARTVRQDGTRPLLTAVVKADGYGHGAVAVA
+RAAQAAGADRLGVAHVREALELRGAGLRLPILAWLHTVGTDFAAALEADVTLGVSGWDLD
+AVAAAVRALRPAPGTADSGPVRARVHLKADTGLGRHGCTPERWPAFVARAAELEAAGLVR
+VEGVFSHLGVADDPERAEETTAQLRRFEEAAAAAAAALGRPLLRHLANTPATLSRPDTHL
+DMVRVGLGLYGLSPFEGVDAAGLGLRPAMSLGTTLANVKPVPAGQGVSYGFRHVAPAPTT
+LGLVPLGYADGVPRIAEGARVHVGGRTVPVVGRIAMDQFVVDLGPDARDRPGDAVELFGP
+ASGIPADEWAAAAGTINYELVTRIGARVDRAHEGGEAPDAQEARA
+>PROKKA_01132
+MDDAPDLTPSAAEAAPAERRALVDLAAVRSNVAALRARLGRPDGASTALMAVVKADAYGH
+GAVPVARAALEAGADRLGVAHVTEALALRAAGVTAPILAWLHTRDTPFRAAVETDVALGV
+SGMWDLEAVAQAARAAGRRATVHVKADTGLGRNGCLLADLPALAARAAALQDEGVVDVEG
+LFSHLAVADELDRAAETDAQAAAFGEATVALDAAGLRPRVRHLANTPAALTRPDLHHDMV
+RVGLGLYGLSPFPDRAPAEFGLRPAMSLQTTLAAVKAVPAGQGVSYGFRHRTAEPTVLGL
+VPLGYADGVPRIAEGAPVAVAGRRVPHVGRVAMDQLVVDLGPGAAERVGDPVELFGPASG
+IPADAWAEAAGTINYELVTRISPRVPRVHVDGAAAGEVAA
+>PROKKA_01604
+MSLADVNPADTERAVRIDLAAVRHNVGVLRERIRRPDGSRPLLTAVVKADAYGHGAVAVA
+RAAAAAGADRLGVAHVREALALRAAGVRLPVLAWLHTGATDFAAAVEAEVTLGVSGWDLD
+AVAAAVRGLRARGGAGPEARAVLHLKADTGLGRHGCTPERWPAFVARAAELEAAGLVRVE
+GVFSHLGVADEPDRAAETTAQLLRFERMAAEAAETLGHPLLRHLANTPAALARPDTHLDM
+VRVGLGLYGLSPFADVTAAELGLRPAMSLVTVLANVKAVPAGQGVSYGFRHVTAEPTTLG
+LVPLGYADGVPRVAEGTRVHVGGRTVPVVGRIAMDQFVVDLGPDAADAPGDAVELFGPAS
+GIPVEEWAAAAGTINYELVTRIGGRVDRQHVDPTPTQEARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001352.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001352.fa
new file mode 100644
index 0000000000000000000000000000000000000000..396aad1d9248262e2ecc7e6e843b1dfc1d369181
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001352.fa
@@ -0,0 +1,50 @@
+>PROKKA_01675
+MTADDLTRIAVTGSAVRTAEEPLLAAGRGPELMRAAAWALAEHAAALLRERGPVAGTTVA
+ALVGPGNNGGDALFALAFLRRRGVAAVAVPVRRDDDGAPRWHAEGWAALRAAGGRRADAV
+PPEAALVVDGVLGTGFTGEYELPAAARALPAEALVLACDVPSGVDADTGEVRGEALRAAA
+TVTFGALKSGLVLGEGAGRAGTVHVADIGLGPHLPTSPAARLGVMDEAAARAAHPAPAAA
+AHKYTRGVVAVVAGSERYPGAAVLASAGALHTGAGMVHHAGPQTTRDLVLAAHPEALVSA
+EGPEPSRADAWVAGPGLDTEHDARRRWAGVLAALEERPEAALLADASALDLVTAAELRSL
+RAAGTPVVLTPHAGEWSRLRERVPADGADAADPLAALRAWTAEHGATVLLKGPRTLVVAP
+DGEAWAVTGGGPDLAMGGTGDVLSGAIGAVLAADVARRSRARRAGEDPGPAPTARLAAAA
+AWLHAQAGAEQARAGRITTATLPAALGARVARLWWPDDAEPEAVR
+>PROKKA_01380
+MTADDLTRIAVTGSAVRTAEEPLLTAGRGPELMRAAAWALAEHAAALLRERGPVAGATVA
+ALVGPGNNGGDALFALAFLRGRGVAAVAVPVRRDDDGAPRWHAEGWAALRAAGGRRADAV
+PPEAALVVDGVLGTGFTGEYELPAAARALPAEALVLACDVPSGVDADTGEVRGEALRADT
+TVTFGALKSGLVLGEGAARAGTVHVVDIGLGPHLPTSPAARLGVMDEAAARTAHPAPAAE
+AHKYTRGVVAVVAGSERYPGAAVLASAGALHTGAGMVHHAGPQTTRDLVLAAHPEALVSA
+EGPEPSRADAWVAGPGLDTEHDARRRWAGVLAALEERPEAALVADASALDLVTAAELRSL
+RAAGTPVVLTPHAGEWSRLRERVPADGADAADPLAALRAWTSEHGATVLFKGPRTLVVAP
+DGEAWVVTGGGPDLAMGGTGDVLSGAIGAVLAADVARRSRARRAGEDPGPAPTARLAAAA
+AWLHARAGADQARAGRITTATLPTALGARVAHLWWPDDAEPEAVR
+>PROKKA_01203
+MSVEELRRVAVAGSAVRAAEAPLLAAGRGPAMMRDAAWALAEHAAALLRARGPVAGTTVA
+ALVGPGNNGGDALFALAFLRRRGVAAVAVPVRHDDDGAPRWHAEGWAALRAAGGRRADAV
+PAAAALVIDGMLGTGFAGELTLPPAARALPRDAVVLACDVPSGVDADTGEVRGEALRADA
+TVTFGALKTGLLVGEGAALAGEVHPVDIGLGPQLPTSPAARLYLADEAAVRAAHPAPAPD
+AHKYTRGLVAVAAGSPRYPGAAVLSCSGALHAGAGMVHHAGPEATRDRVLAEHPEALVSA
+EGPAPDRADAWVAGPGLDTQDDARRRWEGVLSALAERPEAALVADASALELVTAAQLRAL
+REGGTPVVLTPHAGEWARLRERLPADGADAADPLAALRSWSAAHGATVLLKGPRTLTVQP
+DGEAWLVADGGPELAMGGTGDVLAGALGAVLAADVARRSRARRAEQAPGPVPTAALAAAA
+AWLHARAGAEQARAGRLTTRTLPAALGAVTARLWRAGDENGRTRG
+>PROKKA_01131
+MRAHTGTDVRAAERPLLDEGRGEALMRTAAWGLAEHVAAELRARGPVAGATVAALVGPGN
+NGGDALWALAFLRRRGVEAVAVPVRRNEAGEPVWHAAGWAALQAAGGRRSTAVPARAAVV
+VDAMLGTGARGGFTLPEPARHLPSGAAVVACDLPSGVDADTGAVPGEALAADLTVTFGAS
+KTGLLLGAGPGRAGRVVCVDIGLGPHLPADPAAGLHVVDDDAVARLHPVPARDAHKYTRG
+VVGVVAGSERYPGAAVLAVGGVLAGGAGMAHHGGPARAGDLVLAAHPAALTSADGPAPER
+ADAWVLGPGLGDGDGARERVRATVAAVLASGADGDRGPAALVVDASALDLVTGEDLAALA
+AVDARTVITPHAGEWARLRDRLPVPAADAVDVDEDGAGELARLRAWTAARGVTVLLKGPA
+SLAVAPDGQAWLMRDGGPQLGVAGTGDVLAGALGAVLAAETARARRGGDERHGAARGGRP
+SPAALAAAAAWLHARAGVRQAADGRATADTLPAALGDVVARRWWENDAHGRRP
+>PROKKA_01605
+MTADDLTRIAVTGSAVRTAEEPLLAAGRGPELMRAAAWALAEHAAALLRERGPVAGATVA
+ALVGPGNNGGDALFALAFLRRRGVAAVAVPVRRDDDGAPRWHAEGWAALQAAGGRRADAV
+PPEAALVVDGVLGTGFTGEYELPAAARALPAEALVLACDVPSGVDADTGEVRGEALRADA
+TVTFGALKSGLVLGEGAARAGTVHVVDIGLGPHLPTSPAARLGVMDEAAARTAHPAPAAE
+AHKYTRGVVAVVAGSERYPGAAVLASAGALQTGAGMVHHAGPQTTRDLVLAAHPEALVSA
+EGPEPSRADAWVAGPGLDTEHDARRRWAGVLAALEERPEAALVADASALDLVTAAELRSL
+RAAGTPVVLTPHAGEWSRLRERVPADGADATDPLAALRAWTAAHGATVLLKGPRTLVVAP
+DGEAWVVTGGGPDLAMGGTGDVLSGAIGAVLAADVARRSRARRAGEDPGPAPTARLAAAA
+AWLHAQAGADQARAGRITTATLPTALGARVARLWWPDDAEPESVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001356.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001356.fa
new file mode 100644
index 0000000000000000000000000000000000000000..521d7c4048882569d9ffdd8f014d85dcfabd5740
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001356.fa
@@ -0,0 +1,60 @@
+>PROKKA_01680
+MRRSRARSGILVRMCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQ
+LYHRKKAGKLANLAEELAEHPVPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLAFIHN
+GIIENYAELREELLAKGVEFLSETDTEVAAHLLADVYRNAAGQDLTRAMQLASQRLEGAF
+TLLAVHVDHPDRVVASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITA
+DAVEISDFRGGPAEGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGA
+LMLDELRIDPEELKAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPI
+IDPHTLVVSISQSGETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEI
+AVASTKAFLAQITAAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAGKDQVKE
+LARSMADATSVLFLGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPV
+FVVMPSPLDRHSLHAKVVSNIQEVRARGARTFAVAERGDAAVRAQAEVVFEVPETQPMLM
+PLLTTVPLQIFALELATAKGYDVDQPRNLAKSVTVE
+>PROKKA_01384
+MCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQLYHRKKAGKLANL
+AEELAEHPIPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLALIHNGIIENYAELREEL
+LAKGVEFLSETDTEVAAHLLADVYRHAAGQDLTRAMQLASQRLEGAFTLLAVHVDHPDRV
+VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITADAVEISDFRGGPA
+DGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGALMLDELRIDPEEL
+KAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPHTLVVSISQS
+GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT
+AAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAAKDQVKELARSMADATSVLF
+LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPVFVVMPSPLDRHSL
+HAKVVSNIQEVRARGARTFAVAERGDAAVRGQAEVVFEVPETQPMLMPLLTTVPLQIFAL
+ELATAKGYDVDQPRNLAKSVTVE
+>PROKKA_01198
+MCGIVGYIGQPSSTREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGELYHRKKAGKLANL
+AQELEEHPVPTGLVGIGHTRWATHGGPTDVNAHPHVADEGRLAMIHNGIIENYAELREEL
+LAKGAEFLSETDTEVAAHLLTDVYRNAGGQDLTRSLQLASQRLEGAFTLLAVHVDHPDRV
+VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITAEGVEITDFAGSPA
+EGKRFTVDWDASAAEKGGYETFMEKEIHDQPQAVQDTLLGRMDAAGTLVLDELRIDPEEL
+KAVNKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPNTLVVSISQS
+GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT
+AAYLLGLYLAQLNKKLFSGQIKDILADLHAIPGKIQEILDDKEQVKELARSMADTSSVLF
+LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQAVFVVMPSPMDRHSL
+HAKVVSNIQEVRARGARTFVVAERGDQAVRSHAEVVIEVPETQPMLMPLLTTVPLQIFAL
+ELASAKGYDVDQPRNLAKSVTVE
+>PROKKA_01127
+MRMCGIVGYIGQPSSTREHDALEVLMEGLRRLEYRGYDSAGVAVVADGELYHRKKAGKLA
+NLAAELEAEPVPSAQVGIGHTRWATHGGPTDVNAHPHVADEGRLALIHNGIIENYAELRA
+ELLEKGVTFLSETDTEVAAHLLADVYRGAGEGDLTRTMQLASQRLEGAFTLLAVHVDHPD
+RVVASRRNSPLVVGVGEGENFLGSDVSGFIDFTKEAIELEQDQVVTITADAVEITDFQGA
+PAQGKAFTVDWDASAAEKGGFDTFMEKEIHDQPQAVQDTLLGRTDATGALVLDELRIDPE
+ELKAVRKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDDHTLVVSIS
+QSGETMDTLMAVRYAKEQGARTLSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQ
+ITAAYLLGLYLAQLNKKLFTGQIKDILADLAEIPGKIQEILDSSTPVRELARSMADTSSV
+LFLGRNVGFPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDEGQAVFVVMPSPLDRH
+SLHAKVVSNIQEVRARGARTFVVAERGDEAVRDHAEVVFEVPETQPVLMPLLTTVPLQIF
+ALELASAKGYDVDQPRNLAKSVTVE
+>PROKKA_01609
+MCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQLYHRKKAGKLANL
+AEELAEHPIPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLALIHNGIIENYAELREEL
+LAKGVEFLSETDTEVAAHLLADVYRNAAGQDLTRAMQLASQRLEGAFTLLAVHVDHPDRV
+VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITADAVEISDFRGGPA
+EGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGALMLDELRIDPEEL
+KAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPHTLVVSISQS
+GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT
+AAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAAKDQVKELARSMADATSVLF
+LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPVFVVMPSPMDRHSL
+HAKVVSNIQEVRARGARTFAVAERGDAAVRGQAEVVFEVPETQPMLMPLLTTVPLQIFAL
+ELATAKGYDVDQPRNLAKSVTVE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001358.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001358.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fcbb13c48b7e275523ed92c49c0bb1bf2da178bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001358.fa
@@ -0,0 +1,20 @@
+>PROKKA_01684
+MLQGFKDFIMKGNVLDLAVAVIIGAAFGKIVNALVEAVLMPLIAAAVGSPNFDSFAVLTV
+NGNDVKFGVLLTAIVNFLLIAAAVYFAIVMPMNKMIEARNRRLGIDPAEEEVPADVAVLT
+EIRDLLAERRGGPTSGTTTL
+>PROKKA_01388
+MLQGFKDFIMKGNVLDLAVAVIIGAAFGKIVNALVEAVLMPLIAAAVGSPNFDSFAVLTV
+NGNDVKFGVLLTAIVNFLLIAAAVYFAIVMPMNKMIEARNRRLGIDPAEEEVAADVAVLT
+EIRDLLAERRGGPTSGTTTL
+>PROKKA_01194
+MKGNVIDLAVAVVIGAAFGAVINAVVDSVLMPLIAALFAAPSFDDWLVLDINGVLVKFGV
+VLTAVVNFLLIAAAIYFAIVLPMNKMIERRNRRLGIDPAEEEVPEDVALLTEIRDLLSAQ
+RGGAAGTTHTTL
+>PROKKA_01124
+MKGNVVDLAVAVVIGAAFGKVVTALVDSVLMPLIAALFKAPSFDSWLVLNLNGVDVKFGV
+VLTAIVNFLLIAAAVYFCIVLPMNTMIERRNRRLGITPAEDEVAPDVAVLTEIRDLLARQ
+NGAPRV
+>PROKKA_01613
+MLQGFKDFIMKGNVLDLAVAVIIGAAFGKIVNALVEAVLMPLIAAAVGSPNFDSFAVLTV
+NGNDVKFGVLLTAIVNFLLIAAAVYFAIVMPMNKMVEARNRRLGIDPAEEEVPADVAVLT
+EIRDLLAERRGGPTSGTTTL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001361.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001361.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a1e8217cf12923477f596742141e471d5f8be26e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001361.fa
@@ -0,0 +1,26 @@
+>PROKKA_01688
+MAENTSPTPDPRTRGEHGTEHTAQAPFAVTRDYAAEVDEIRELGRKLGGEKKTPTPDPQA
+WREGYPYKTKLSRKSYERRKRELQIELLKMQLWVKETGQKVLIIFEGRDAAGKGGAIKRF
+NEHLNPRGARTVALEKPTEEEASQWYFQRYIQHLEFMRETPELERMLLNSGVHIIKFWFS
+VSQREQLNRFAARETDPVRRWKLSPTDLASLDKWDDYTNAKEAMFFYTHTADAPWTVVKS
+NDKKRARLEAIRHVLHTLPYPDKDERIVHRPDPQICGPANELAEYGEVSGGSFPRVR
+>PROKKA_01392
+MGSFSWPLTAIKRFNEHLNPRGARTVALEKPTEEEASQWYFQRYIQHLEFMRETPELERM
+LVNSGVHIIKFWFSVSQREQLNRFAARETDPVRRWKLSPTDLASLDKWDDYTNAKEAMFF
+YTHTADAPWTVVKSNDKKRARLEAIRHVLHTLPYPDKDERIVHRPDPQICGPANELAEYG
+EVSGGSFPRVR
+>PROKKA_01190
+MTGRSPVRCAVRSNTTSGAAAAENTSTTTETTPAGGHAMEDTADAPWTVVKSNDKKRARL
+EAIRHVLHTLPYPDKDERIVHRPVPHICAPATELFETGEDSGGSFPRVR
+>PROKKA_01120
+MAENTTTPPTDPSADGVLAGEHPLESGRREQPFAVTEDYAAEVDEIRELGRTLHGDSLPS
+PDPTAWREGYPYKTKLSRKTYERRKRELQIELLKMQLWVKETGQKVLIIFEGRDAAGKGG
+AIKRFNEHMNPRGARTVALEKPTEAEASQWYFQRYIQHLPSGGEIVMFDRSWYNRAGVER
+VMGYCTPQQYLEFMRETPELERMLSNSGIHIIKFWFSVSRREQLNRFAARETDPVRRWKL
+SPTDLASLDKWDDYTNAKEAMFFYTHTADAPWTVVKSNDKKRARLEAMRHVLYTLPYPNK
+DERIVHLPDPQICASADVLSEIDEADGGSFPRVR
+>PROKKA_01617
+MQLWVKQTGQKVLIIVEGRDAAGKGGAIKRFNEHLNPCGARTVALEKPTEEEAPQWYFQC
+YIQHLEFMRETPELERMLVNSGVHIIKFWFSVSQREQLNRFAARETDPVRRWKLSPTDLA
+SLDKWDDSTNAKEAMFFYTHTADAPWTVVKSNDEKRARLEAIRHVLHTLPYPDKDERIVH
+RPDPQICGPANELAEYGEVSGGSFPRVCGGGFSRAPPPRTPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001364.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001364.fa
new file mode 100644
index 0000000000000000000000000000000000000000..64f8a33e7eeafcf964d6eb0565d4364f8cfd8ce4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001364.fa
@@ -0,0 +1,31 @@
+>PROKKA_01691
+MSEQHRPDAPTAPGEPPSVRVRLGLAYDGGTFHGWARQPGLDSVQGALEDGLERILRRPV
+RTVVAGRTDAGVHARGQVVHLDLTETEWAGLTRGRPGLEPATSLIRRLGGVLSGWGGAVV
+VHGARRAPAGFDARFSALWREYEYRIDDAPAARDPRTRGFTHWHGAALDDRLMALEADAV
+LGLHDFLSFCRPRAGATTIREVQHLEVRRDEDGVVRVRIRADAFCHNMVRAIVGALLQVG
+EGAREPGWLAHRVARPARDSEVRLAPPGGLTLLAVGYPDEAEELHRRAEGTRAKRTL
+>PROKKA_01398
+MSEQHRPDAPSAPGEPASVRVRLDLAYDGGTFHGWARQPGLDSVQGALEDGLERILRRPV
+RTVVAGRTDAGVHARGQVVHLDLTETEWAGLTRGRPGLEPATSLTRRLGGVLSGWGGAVV
+VHGARRAPAGFDARFSALWREYEYRIDDAPAARDPRTRGFTHWHGAALDDRLMALEADAV
+LGLHDFLSFCRPRAGATTIREVTHLEVRRDEDGVVRVRIRADAFCHNMVRAIVGALLQVG
+ERAREPGWLAHRVARPARDSEVRLAPPGGLTLLAVGYPDEAEELHRRAEGTRAKRTL
+>PROKKA_01187
+MTEQPAPSAPRPSAAGEEPVRVRLDLAYDGGAFRGWARQPGLDSVQGALEDGLERILRRP
+VRTVVAGRTDAGVHARGQVVHLDLAEGEWAGLTRGRPDLEPGASLARRLGGVLSGWDGAV
+VVHGARRAPAGFDARFSALWREYEYRIDDAPDRRDPRTRAFTHWHGAALDERLMALEADA
+VLGLHDFLSFCRPREGATTIREVQDLRVARDEDGSVRVRIRADAFCHNMVRAVVGALLQV
+GEGSREPGWLGLRVATPARDSQVRLAPPRGLTLLAVGYPEDGEGLRRRAEGTRARRTL
+>PROKKA_01117
+MVGMPDDALPAAPVEPRPEPTTGLPREGEVRLRLDLAYDGSDFRGWAAQPGLATVQGALE
+GALETIVRRPVRTVVAGRTDAGVHARGQVVHCDLTEAEWSALARGRADVDPADALVRRLQ
+GVLRPWQGAVVVRGARRAPDGFDARFSALWRAYEYRISDRPETRDPLARHGVLWHGARVD
+ERLMAVEAGALLGLHDFLSFCRPREGATTVREVQDAEVVRTPDGLVRVRLRADAFCHSMV
+RTIVGALLEVGEGRRTPGWTAARVAGPVRDSAARLAPAHGLTLLEVGYPETGEELRARAE
+GTRARRAPLADLG
+>PROKKA_01620
+MSEQHRPDAPSAPGEPASVRVRLDLAYDGGTFHGWARQPGLDSVQGALEDGLERILRRPV
+RTVVAGRTDAGVHARGQVVHLDLTETEWAGLTRGRPGLEPATSLIRRLGGVLSGWGGAVV
+VHGARRAPAGFDARFSALWREYEYRIDDAPAARDPRTRGFTHWHGAALDDRLMALEADAV
+LGLHDFLSFCRPRAGATTIREVKHLEVRRDEDGVVRIRIRADAFCHNMVRAIVGALLQVG
+EGAREPGWLAHRVARPARDSEVRLAPPGGLTLLAVGYPDEAEELRRRAEGTRAKRTL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001366.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001366.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24eee7908c26c3620d42fe9923ce598f2cb9ce6c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001366.fa
@@ -0,0 +1,35 @@
+>PROKKA_01693
+MLIAQRPTLTEEVVSDRRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL
+HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEVHN
+PDLHIATLNAKGKFDMELTIERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEA
+TRVEQRTDFDRLILDVETKENMLPRDAVASAGSTLVELFGLARSLNVEAEGIDLGDEPDV
+VEGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEK
+LQELGLSLKDSPAGYDPQAHARQMDDDPFSDF
+>PROKKA_01400
+MLIAQRPTLTEEVVSDRRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL
+HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEIHN
+PDLHIATLNAKGKFDMELTIERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEA
+TRVEQRTDFDRLILDVETKENMLPRDAVASAGSTLVELFGLARSLNVEAEGIDLGDEPEV
+VEGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEK
+LQELGLSFKDSPAGYDPQAHARQMDDDPFSDF
+>PROKKA_01185
+MLIAQRPTLTEEVVSDRRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL
+HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEVHN
+PDLHIATLNAKGKFDMELTVERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEA
+TRVEQRTDFDRLILDVETKESMLPRDAVASAGSTLVELFGLARSLNVEAEGVDLGDEPQT
+AEGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEK
+LYELGLSLKDSPAGYDPQAHARQMDDDPFSDF
+>PROKKA_01115
+MLIAQRPTLTEEVVSDHRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL
+HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGSGVVTAADITAPAGVEIHN
+PDLHIATLNAKGKFDMELTVERGRGYVTAAQNKSADQEIGRIPVDSIYSPVLKVTFKVEA
+TRVEQRTDFDRLILDVETKESMLPRDAVASAGSTLVELFGLAKGLNVEAEGIDLGEAPAE
+ADGSADLAQPIEDLELTVRSYNCLKREGIHTVGELVARSEADLMDIRNFGAKSIDEVKEK
+LYELGLSLKDSPAGFDPQAHASQDDDPFSDF
+>PROKKA_01622
+MLIAQRPTLTEEVVSDRRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL
+HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEIHN
+PDLHIATLNAKGKFDMELTIERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEA
+TRVEQRTDFDRLILDVETKENMLPRDAVASAGSTLVELFGLARSLNVEAEGIDLGDEPEV
+VEGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEK
+LQELGLSLKDSPAGYDPQAHARQMDDDPFSDY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001368.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001368.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b242ac54c2994d608c61da1475877cce6dd0c49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001368.fa
@@ -0,0 +1,20 @@
+>PROKKA_01695
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK
+>PROKKA_01402
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK
+>PROKKA_01183
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK
+>PROKKA_01113
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDRDIRVKDLTDDQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK
+>PROKKA_01624
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001369.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001369.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bdab200a6525048e772d086a50e7c73076d178bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001369.fa
@@ -0,0 +1,10 @@
+>PROKKA_01696
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG
+>PROKKA_01403
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG
+>PROKKA_01182
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG
+>PROKKA_01112
+MKVQPSVKRICDKCQVVRRKGRVLVICENPRHKQRQG
+>PROKKA_01625
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001373.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001373.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0130307e03b7665c4d91c8e3da72d9af3a5618b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001373.fa
@@ -0,0 +1,45 @@
+>PROKKA_01700
+MLKAIARIVRTPDLLRKIAFTLALIAVYRMGAFVPAPGVDYPAVQQCLAAGNAQGGLYSF
+VNMFSGGALLQVSVFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL
+TLALALLQATTMASLARTGALLGCSLPLLRDGSILTVLLVVIALTTGCLIVMWFGERITE
+NGVGNGMSLLIFTSIAAGFPAGLGQVVQTQGWRVFAIVMGIGLLTMLAIVFVEESQRRIP
+VQYAKRQIGSRTVGGSSTYIPVKVNMANVIPVIFASSVLMLPSILIQFNTPQDGSAPAPW
+ITWLSRYFGPGDHPVYMALYFLLIIGFTYFYVSITFNPVEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITLVGALYLGIVAMIPLIAFAVIGTSQNFPLGGTSILIMVGVGLQTVKQ
+VSAQMEQRHYEGLLR
+>PROKKA_01407
+MLKAIARIVRTPDLLRKIAFTLALIAVYRMGAFVPAPGVDYPAVQQCLAAGNAQGGLYSF
+VNMFSGGALLQVSVFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL
+TLALALLQATTMASLARTGALLGCSLPLLRDGSILTVLLVVIALTTGCLIVMWFGERITE
+NGVGNGMSLLIFTSIAAGFPAGLGQVVQTQGWRVFAIVMGIGLLTMLAIVFVEESQRRIP
+VQYAKRQIGSRTVGGSSTYIPVKVNMANVIPVIFASSVLMLPSILIQFNTPQDGSAPAPW
+ITWLSRYFGPGDHPVYMALYFLLIIGFTYFYVSITFNPVEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITLVGALYLGIVAMIPLIAFAVIGTSQNFPLGGTSILIMVGVGLQTVKQ
+VSAQMEQRHYEGLLR
+>PROKKA_01178
+MFKAIARIVRTPDLLRKIAFTLGIIAVYRMGAFVPSPGVDYPAVQQCLAAGNAQGGLYSF
+VNMFSGGALLQVSIFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQSTLTQYTRYL
+TLALSLLQATTMASLARTGALLGCQLPLLRNDSILTVLLVVVVLTAGCIIVMWLGERVTE
+NGVGNGMSLLIFASIAAGFPAGLGQVVQTQGWRVFAIVMLIGLLTMLAIVFVEESQRRIP
+VQYAKRQIGSRTVGGSSTFIPIKVNMANVIPVIFASSVLMLPGILIQFNTPQDGTAPAPW
+IAWLSRYFGNGDHPVYMAVYFLMIIGFTYFYVSITFNPQEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITLAGALYLGIVAMIPLIAFVVIGASQNFPFGGTSILIMVGVGLQTVKQ
+VNAQMEQRHYEGLLR
+>PROKKA_01108
+MFKAIARIVRTQDLRRKILFTLALVAVYRLGAFIPAPGVDYAAVRQCLAAGSAQGGLYSF
+VNMFSGGALLQVSIFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL
+TIALAVLQGTTMASLARTGALLGCRVPLLHDQSIATVLLVVVVLTTGCVIVMWLGERITE
+NGIGNGMSLLIFASIAAGFPAGIGQVLQTQGWRTFAIVMVVGLLTMLAVVFVEESQRRIP
+VQYAKRQIGTRTVGGTSTFIPIKVNMANVIPVIFASSVLMLPGILAQFNTPQDGSAPPAW
+VSFLSTYFVGGDHPLYMALYLLMIIGFTYFYVSITFNPQEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITLPGALYLGIVAMIPLIAFVLIGANQNFPFGGTSILIMVGVGLQTVKQ
+ISAQMEQRHYEGLLR
+>PROKKA_01629
+MLKAIARIVRTPDLLRKIAFTLGLIAVYRMGAFVPAPGVDYPAVQQCLAAGNAQGGLYSF
+VNMFSGGALLQVSVFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL
+TLALALLQATTMASLARTGALLGCSLPLLRDGSILTVLLVVIALTTGCLIVMWFGERITE
+NGVGNGMSLLIFTSIAAGFPAGLGQVVQTQGWRVFAIVMGIGLLTMLAIVFVEESQRRIP
+VQYAKRQIGSRTVGGSSTYIPVKVNMANVIPVIFASSVLMLPGILIQFNTPQDGSAPAPW
+ITWLSRYFGSGDHPVYMALYFLLIIGFTYFYVSITFNPVEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITFVGALYLGIVAMIPLIAFAVIGTSQNFPLGGTSILIMVGVGLQTVKQ
+VSAQMEQRHYEGLLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001377.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001377.fa
new file mode 100644
index 0000000000000000000000000000000000000000..182e5b35c35bf45c72186c238ff11d8e888b964a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001377.fa
@@ -0,0 +1,20 @@
+>PROKKA_01704
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIDAVVFDRGGNKYHGRVAAVADGAREG
+GLQL
+>PROKKA_01411
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLQL
+>PROKKA_01174
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAWA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLKL
+>PROKKA_01104
+MSTLKVKGKGKFNARTRRHLRVRKRISGTAVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRAFDGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLQL
+>PROKKA_01633
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLQL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001382.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001382.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a850ea79cae91b26a86a3ed9afb85540b31276dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001382.fa
@@ -0,0 +1,20 @@
+>PROKKA_01709
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI
+>PROKKA_01416
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI
+>PROKKA_01169
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI
+>PROKKA_01099
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIRFDENAAVILKNDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI
+>PROKKA_01638
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001385.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001385.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f1fb1cd25ded07c5fdaafbbcbd670f13657517d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001385.fa
@@ -0,0 +1,20 @@
+>PROKKA_01712
+MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR
+GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVTEDVAREALRL
+AIHKLPLKARIIRREGGE
+>PROKKA_01419
+MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR
+GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVTEDVAREALRL
+AIHKLPLKARIIRREGGE
+>PROKKA_01166
+MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR
+GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVSEEVAREALRL
+AIHKLPLKARVIRREGGE
+>PROKKA_01096
+MLIPRRVKHRKQHHPKRSGMAKGGTTVTFGEWGIQALSPAYVTNRQIEAARIAMTRYIKR
+GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVSEEVAREALRL
+AIHKLPLKARIIRREGGE
+>PROKKA_01641
+MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR
+GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVTEDVAREALRL
+AIHKLPLKARIIRREGGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001388.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001388.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92a1b3a9d26a511e86e4cdd5119f061fcd9ff621
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001388.fa
@@ -0,0 +1,15 @@
+>PROKKA_01715
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR
+>PROKKA_01422
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR
+>PROKKA_01163
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR
+>PROKKA_01093
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTFRGHVKDDKKGKRR
+>PROKKA_01644
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001389.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001389.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5bb36303447c79eb1ac44de87c2d8e6ee1cd48a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001389.fa
@@ -0,0 +1,30 @@
+>PROKKA_01716
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
+>PROKKA_01423
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
+>PROKKA_01162
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
+>PROKKA_01092
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLIDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLQQGDVVEAG
+PNADIKPGNNLPLRNIPVGTTIHAVELRPGGGAKMARSAGASIQLVAREGKYAQLRLPSG
+EIRNVDVRCRATVGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNPNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
+>PROKKA_01645
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001392.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001392.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ddee3c699fc995b621052e753b2c8379602512e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001392.fa
@@ -0,0 +1,25 @@
+>PROKKA_01719
+MTNTQNIKGLLGTKLGMTQVWDEDNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYSLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVGASHGAHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
+>PROKKA_01426
+MTNTQNIKGLLGTKLGMTQVWDEDNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYSLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVGASHGQHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
+>PROKKA_01159
+MTNTQNIKGLLGTKLGMTQVWDENNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFDKAGVTPRRHLVELRTADAAEYSLGQDLTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVSASHGAHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGVDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
+>PROKKA_01089
+MTNTQNVKGLMGTKLGMTQVWDEDNKLIPVTVVQADANVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYTLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVSASHGAHKNHRKPGSVGGASTPARVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
+>PROKKA_01648
+MTNTQNIKGLLGTKLGMTQVWDEDNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYSLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVGASHGAHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001397.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001397.fa
new file mode 100644
index 0000000000000000000000000000000000000000..676e1073c20740942555941de07313d390fca656
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001397.fa
@@ -0,0 +1,65 @@
+>PROKKA_01724
+MAQDVLTDLHKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGGATTDWMEQEKE
+RGITITSAAVTCFWNDHQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGARPLVMQLPIGAENDFVGVVDL
+LSMKAFVWPGDAKGDVTMGASYETREIPAELQEKAEEYRNELVEAVAETSEELMEKYLEG
+EELTVEEIQAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGSVKGHAV
+NDEEEVLEREASKEAPFSALAFKIATHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPANPIILESMTFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVNALVPLS
+EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE
+>PROKKA_01431
+MAQDVLTDLHKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGGATTDWMEQEKE
+RGITITSAAVTCFWNDHQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGARPLVMQLPIGAENDFVGVVDL
+LSMKAFVWPGDAKGDVTMGASYETREIPAELQEKAEEYRNELVEAVAETSEELMEKYLEG
+EELTVEEIQAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGSVKGHAV
+NDEEEVLEREASKEAPFSALAFKIATHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPANPIILESITFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVNALVPLS
+EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE
+>PROKKA_01154
+MAQDVLTDLNKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGASTTDWMEQEKE
+RGITITSAAVTCFWNDNQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVNRLGARPLVMQLPIGAENDFVGVVDL
+LSMKAFVWPGDAKGDVTMGAEYETREIPAELQEKAEEYRAQLVEAVADTSEELMEKYLEG
+EELTTEEIQAGVRHLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGAVKGHDV
+KDEEVELEREASKDAPFSALAFKIASHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDAAHPIILESMTFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTADGEIYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVKALVPLS
+EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE
+>PROKKA_01084
+MAQDVLTDLNKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGASTTDWMEQEKE
+RGITITSAAVTCFWKNNQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGAKPLVMQLPIGSESDFIGVVDL
+LTMKAFVWPGDAKGDVTMGAEYETQEIPADLQEKAEEYRTQLLEAVADTSEELMEKYLEG
+EEISEEEIVAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGAVKGHAV
+GDEEQVLEREPSKEAPFSALAFKIASHPFFGTLTFIRVYSGRLEGGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPQNPIILESMTFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNDETGQTEIGGMGELHLDVFVDRMRREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPVLLEPLMAVEVRTPEEFMGDVVGDLNSRRGQIQSMEDATGVKVVNALVPLS
+EMFGYIGDLRSRTQGRAVYSMTFHSYSEVPKNVADEIIQKSQGE
+>PROKKA_01653
+MAQDVLTDLHKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGGATTDWMEQEKE
+RGITITSAAVTCFWNDHQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGARPLVMQLPIGAENDFVGVVDL
+LSMKAFVWPGDAKGDVTMGASYETREIPAELQEKAEEYRNELVEAVAETSEELMEKYLEG
+EELTVEEIQAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGSVKGHAV
+NDEEEVLEREASKEAPFSALAFKIATHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPANPIILESMTFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVNALVPLS
+EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001400.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001400.fa
new file mode 100644
index 0000000000000000000000000000000000000000..acd72c49fb718878efe2996e70beef4d3e7ba2a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001400.fa
@@ -0,0 +1,115 @@
+>PROKKA_01727
+MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC
+ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL
+APKDLEKVIYFAAYMITSVDEEARHRDLANLQAEYDQETRVLADQRDSDIAAVAADLEKD
+LAKLESEGAKAAEKKKARDAADKTMAQIRKRADADLDRKEQVWDRFKNLKVADLEGDEGL
+YRAMRDKYGQYFEGSMGAEAIQRRLQTFDLEAESEMLRETIKTGKGQRKTRALKRLKVVN
+AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL
+GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK
+RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR
+PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ
+MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDEVGAGN
+LYATVGEAIMAFDGGDLHLNAPARIGVEGFVPSADVPAPEGWSEGEIALIETTLGKVLFN
+ELLPDDYPWLDKQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS
+DITSDFDKAAIMEGYEEQAQRVQQQYDKGLIADDERRSELIDIWNKATDEVAAAMKDGLP
+ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH
+GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTERGLSVTIAAPNADGELVAHE
+QVENSAFARTLAQDVTGEDGTVLASAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT
+CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ
+ELFEARTPKGVAPISEVAGRVTIEDTETSVRLLLTPDDGSEEIAYPVLRRARILVADGEH
+VPVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR
+ITVIESGDTDLLPGELTDRARFVAANRAAVAEGRQPASGRDELMGITKASLATDSWLSAA
+SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA
+SPAGFADFDYPGLDQSLGENDFHAVSLDDYGRGGDFRA
+>PROKKA_01434
+MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC
+ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL
+APKDLEKVIYFAAYMITSVDEEARHRDLANLQAEYDQETRVLADQRDSDIAAVAADLEKD
+LAKLESEGAKAAEKKKARDAADKTMAQIRKRADADLDRKEQVWDRFKNLKVADLEGDEGL
+YRAMRDKYGQYFEGSMGAEAIQRRLQTFDLEAESEMLRETIKTGKGQRKTRALKRLKVVN
+AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL
+GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK
+RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR
+PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ
+MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDEVGAGN
+LYATVGEAIMAFDGGDLHLNAPARIGVEGFVPSADVPAPEGWSEGEIALIETTLGKVLFN
+ELLPDDYPWLDKQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS
+DITSDFDKAAIMEGYEEQAQRVQQQYDKGLIADDERRSELIDIWNKATDEVAAAMKDGLP
+ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH
+GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTERGLSVTIAAPNADGELVAHE
+QVENSAFARTLAQDVTGEDGTVLASAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT
+CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ
+ELFEARTPKGVAPISEVAGRVTIEDTEASVRLLLTPDDGSEEIAYPVLRRARILVADGEH
+VPVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR
+ITVIESGDTDLLPGELTDRARFVAANRAAVAEGRQPASGRDELMGITKASLATDSWLSAA
+SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA
+SPAGFADFDYPGLDQSLGENDFHAVSLDDYDRGGDFRA
+>PROKKA_01151
+MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC
+ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL
+APKDLEKVIYFAAYMITSVDEEGRHRDLANLQAEYDQETRVLADQRDADIAAVAADLEKD
+LAKLESEGAKAAEKKKARDAADKTMSQIRKRADAELDRKEQVWDRFKNLKVADLEGDEGL
+YRTMRDKYGQYFEGSMGAEAIQRRLQTFDLAAESEMLRETIKTGKGQRKTRALKRLKVVN
+AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL
+GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK
+RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR
+PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ
+MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDAVGAGN
+AYATVGEAVMAFDGGDLHLNAPVKIGVDGFVPSTAVPAPEGWSEGELAVIETTLGKVLFN
+ELLPADYPWLDTQATKGSLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS
+DITSDFDKAAIMEGYEEQALRVQQQYEKGLIADDERRSELIDIWNKATDEVAAAMKDGLP
+ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH
+GARKGLADTALKTANSGYLTRRLVDVSQDVIVREEDCGTERGLSVTIAVPNADGELVAHE
+QVENSAFARTLAQDVTGEDGSVLASGGADVGDVLIDQLVGAGVSEIKVRSVLTCESAVGT
+CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ
+ELFEARTPKGVAPISEVAGRVTIEDTDASVRLLLTPDDGSEEIAYPVLRRARILVADGEH
+VAVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR
+ITVIESGETDLLPGELTDRARFVAANRSAVAEGRQPASGRDELMGITKASLATDSWLSAA
+SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA
+SPAGFADFDYPGLDQQLGESDFHAVSLDDYGRGGDFRS
+>PROKKA_01080
+MTTENPFGLMRIGLATADDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC
+ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL
+APKDLEKVIYFAAYMITSVDEEARHRDLPNLQAEHDQETRVLEDQRDADIAAVAADLEKD
+LAKLEAEGAKAAEKKKARDAADKTMAQIRKRADAELDRKAQVWDRFKNLKVADLEGDEGL
+YRAMRDKFGAYFEGSMGAEAIQRRLQTFDLAAESELLRETIKTGKGQRKTRALKRLKVVN
+AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL
+GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK
+RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNVKSAKRMVERFR
+PQVWDVLEEVISEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ
+MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRAEGKGAGR
+QFATVGEAVMAFDNGELHLNAPATIGVEGFVPSAAVAAPEGWTEGEVALIETTLGKVIFN
+DLLPADYPWLDTQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS
+DITSDFDKASIMQGYEDQAQRVQAQYDKGLIADDERRSELIDIWNKATDEVAAAMKAGLS
+ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH
+GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTGRGLSVTIAEPNHDGELVVRE
+QVENSAFARTLAQAVTAEDGTVLAEAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT
+CAKCYGRSMATGKLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ
+ELFEARTPKGVAPISEVAGRVTIEDTDASVRLILTPDDGSEEIAYPVLRRARLLVADGEH
+VAVGTQLVAGAVDPKQVLRVLGPRAAQRFLVQEVQDVYQSQGVGIHDKHVEVIVRQMLRR
+ITVIESGETDLLPGELTDRSRFVAANRAAVAEGKQPAAGRDELMGITKASLATDSWLSAA
+SFQETTRVLTQAAMEGKEDPLLGLKENVIIGKLIPAGTGLDRYTQTTVEPTEEAKANLFA
+APVGFADFDYPGLDQPLGEAEFHAVSLDDYGRGGDFRA
+>PROKKA_01656
+MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC
+ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL
+APKDLEKVIYFAAYMITSVDEEARHRDLANLQAEYDQETRVLADQRDSDIAAVAADLEKD
+LAKLESEGAKAAEKKKARDAADKTMAQIRKRADADLDRKEQVWDRFKNLKVADLEGDEGL
+YRAMRDKYGQYFEGSMGAEAIQRRLQTFDLEAESEMLRETIKTGKGQRKTRALKRLKVVN
+AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL
+GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK
+RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR
+PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ
+MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDEVGAGN
+LYATVGEAIMAFDGGDLHLNAPARIGVEGFVPSADVPAPEGWSEGEIALIETTLGKVLFN
+ELLPDDYPWLDKQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS
+DITSDFDKAAIMEGYEEQAQRVQQQYDKGLIADDERRSELIDIWNKATDEVAAAMKDGLP
+ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH
+GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTERGLSVTIAAPNADGELVAHE
+QVENSAFARTLAQDVTGEDGTVLASAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT
+CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ
+ELFEARTPKGVAPISEVAGRVTIEDTETSVRLLLTPDDGSEEIAYPVLRRARILVADGEH
+VPVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR
+ITVIESGDTDLLPGELTDRARFVAANRAAVAEGRQPASGRDELMGITKASLATDSWLSAA
+SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA
+SPAGFADFDYPGLDQSLGENDFHAVSLDDYGRGGDFRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001402.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001402.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00b7dc83466a09790ace4b8ca4dfff53830737ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001402.fa
@@ -0,0 +1,20 @@
+>PROKKA_01729
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK
+DEFDVVLEAAGDKKIGVIKEVRAITSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE
+GAGATVTLK
+>PROKKA_01436
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK
+DEFDVVLEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE
+GAGATVTLK
+>PROKKA_01149
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAAGAAGGDAAAAEEKD
+EFDVVLESAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLEG
+AGATVTLK
+>PROKKA_01078
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAMAAAGAPAGGDAAAAEEKD
+EFDVILEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLEG
+AGATVTLK
+>PROKKA_01658
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK
+DEFDVVLEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE
+GAGATVTLK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001404.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001404.fa
new file mode 100644
index 0000000000000000000000000000000000000000..218c4527919980c00b12f3a54bf26fd458f5601c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001404.fa
@@ -0,0 +1,25 @@
+>PROKKA_01731
+MAQRSKAYKAAKAAIGEDLYSPVEAIRLAKETNPSKTDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGDRAEAARAAGADVVGDDDLIARISEGWVDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE
+AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVPMDPNVTSVDSSEL
+>PROKKA_01438
+MAQRSKAYKAAKAAIGEDLYSPVEAIRLAKETNPSKIDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGDRAEAARAAGADVVGDDDLIARISEGWVDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE
+AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVPMDPNVTSVDSSEL
+>PROKKA_01147
+MAQRSKAYKAAKAAIGEDVYSPVEAIRLAKETNPSKTDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGERAEAARAAGADVVGDDDLIAKISEGWVDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVTDIKGGKIDFRVDKHSNLHFIIGKTSFE
+AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVSMDPNVTSVDSSEL
+>PROKKA_01076
+MAQRSKAYKAAKAAIGDTVYAPAEAIALAKETNPSKTDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGERAEAARAAGADHVGDDDLIAKIADGWTDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE
+ANQLVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVQMDPNAAPPKDEAQA
+>PROKKA_01660
+MAQRSKAYKAAKAAIGEDLYSPAEAIRLAKETNPSKTDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGDRAEAARAAGADVVGDDDLIARISEGWVDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE
+AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVPMDPNVTSVDSSEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001405.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001405.fa
new file mode 100644
index 0000000000000000000000000000000000000000..60b6bc58541d8ac8a48cbecc5f8efff39e4fd565
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001405.fa
@@ -0,0 +1,20 @@
+>PROKKA_01732
+MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI
+TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA
+NDVQAAAKIIAGTARSMGITVEG
+>PROKKA_01439
+MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI
+TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA
+NDVQAAAKIIAGTARSMGITVEG
+>PROKKA_01146
+MAPKKKVSGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI
+TVYEDRSFTFITKTPPAAELIKKAAGVAKGSATPHTAKVGKLTQAQCEEIAQTKMEDLNA
+NDVKAAAKIIAGTARSMGITVEG
+>PROKKA_01075
+MAPKKKVAGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATEAQRGNVIPVEI
+TVYEDRSFTFITKTPPAVELIKKAAGVQKGSSTPHTAKVGTLTQAQCEEIAQSKMEDLNA
+NDVKAAAKIIAGTARSMGITVEG
+>PROKKA_01661
+MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI
+TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA
+NDVQAAAKIIAGTARSMGITVEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001409.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001409.fa
new file mode 100644
index 0000000000000000000000000000000000000000..978242491431eae56b74b6554851bb1a0746a416
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001409.fa
@@ -0,0 +1,25 @@
+>PROKKA_01737
+MTDPAPRTAVNVDDHAIFRSGLRADLDPDRLAIVGEAGDVDEAVRAVLDLAPDVVLLDVH
+LPGGAGGGGAEVAERVLARRPAQRFLALSVSDAAEDVVAVIRAGARGYITKTASGAEVAD
+AAVRVADGDAVFSPRLAGFVLDAFRGTAPASPPVPAAATSGAAAPDEDLDRLSAREREVM
+RLIARGYTYREAGAELFISDRTVETHVSSVLRKLQLSNRHELTRWAARRGYA
+>PROKKA_01444
+MTDPAPRTAVIVDDHAIFRSGLRADLDPDRLAIVGEAGDVDEAVRTVLDLVPDVVLLDVH
+LPGGAGGGGAEVAERVLARRPAQRFLALSVSDAAEDVVAVIRAGARGYITKTASGVEVAD
+AAVRVADGDAVFSPRLAGFVLDAFRGTAPASPPVPAAATSGAAAPDEDLDRLSAREREVM
+RLIARGYTYREAGAELFISDRTVETHVSSVLRKLQLSNRHELTRWAARRGYA
+>PROKKA_01141
+MSVPAPRTAVIVDDHAIFRSGLRADLDPARLAIVGEAGDVDEAVRAVLELAPDVVLLDVH
+LPGGAGGGGAEVAERVLARRPAQRFLALSVSDAAEDVVAVIRAGARGYITKTASGAEVVD
+AAVRVAGGDAVFSPRLAGFVLDAFRGAAAPAAAPASPAVPDEDVDRLSAREREVMRLIAR
+GYTYREAGAELFISDRTVETHVSSVLRKLQLSNRHELTRWAARRGYA
+>PROKKA_01070
+MTVHADPVVPTAVVVDDHAIFRSGLRADLDASRLRIVGEAGDVDEAVRVVLQLAPDVVLL
+DVHLPGGAGGGGAEVASRVLAERPGQRLLALSVSDAAEDVVAVIRAGARGYITKSAAGAE
+VVEAALRVAGGDAVFSPRLAGFVLDAFRGLPTESAPAGPAPSEGDLDRLSAREREVMRLI
+ARGYTYREAGAELFISDRTVESHVSSVLRKLQLSNRHELTRWAARHGWA
+>PROKKA_01666
+MTDPAPRTAVIVDDHAIFRSGLRADLDPDRLAIVGEAGDVDEAVRTVLDLAPDVVLLDVH
+LPGGAGGGGAEVAERVLARRPAQRFLALSVSDAAEDVVAVIRAGARGYITKTASGAEVAD
+AAVRVADGDAVFSPRLAGFVLDAFRGTAPAPPLVPAAAASGAAAPDEDLDRLSAREREVM
+RLIARGYTYREAGAELFISDRTVETHVSSVLRKLQLSNRHELTRWAARRGYA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001411.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001411.fa
new file mode 100644
index 0000000000000000000000000000000000000000..806bc75afdbc2789d31d65fc8bfdf73530985b1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001411.fa
@@ -0,0 +1,36 @@
+>PROKKA_01739
+MTSTHDPFTGPGPHVAPDGAAAGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG
+VAERYRIDPLLARGVFVAVCMVSAGLGLLAYAAAWAVLPDPDGRVQFGRLRRGEWQDATV
+AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLVGLGALAVLVWWLVTRWDGRAQARVAPG
+RVPDADQPAHAVPRPAWYVGGGPRERAAEVTDPHGFRPEWIDPATGTWRDHVHSRERRAA
+TRLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP
+TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG
+>PROKKA_01446
+MTSTHDPFTGPGPHVAPDGAASGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG
+VAERYRIDPLLARGVFVAVCMVSAGLGLLAYAAAWAVLPDADGRVQFGRLRRREWQDATV
+AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLLGLGALAVLVWWLVTRWDGRAQARVAPG
+RAPDADQPSHAVPRPAWYVGGGPRERAAEVTDPHGFHPEWIDPATGTWRDHVHSRERRAA
+ARLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP
+TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG
+>PROKKA_01139
+MRRSDSSWVGGVLAGVAERYRVDPLLARGVFVALCVVSAGFGLLAYAVAWALLPDGDGTV
+HYGRLRRGEWQDATVAIAVIGGIGVLNVVLGAGFTLLAPVVGGPGSLLGLAAVAVLVWWL
+VTRWDGSTQSRVGPAPASEPEASGRAAARPAWYLRRDDARAAASRQDAHGFRADWLDPET
+GTWRSPVHSRELRAAARLAEEEQAAPAGPSGRGSAVVAAPRRLSPAVQAVTYAVAALAAA
+AAVGASLLVGVGSLTLLAVPAIVAALAVIAPVMLAALLTGRRPGSLAPASGILVGAAALQ
+VAVAVAVL
+>PROKKA_01068
+MDTAHDPFPAPRSSPATRPLPPGPASDARSRSAGTDGPAPDGLEVLPVWLRRPVEGWGVR
+RSRSSWVGGVLAGVAERYRIDPLLSRGVFVALCVVSAGIGLLGYALAWAVLPDADGRVHY
+GRLRRGEWSDAPVAIAAIAAIGALNVVLGAGFTLIAPVLGGPGSLIGLTALAVLVWWLVT
+RWDGEGERRMAPAQPARDAAARPAAEPSWYLRRHRPESATVDAHGFRSDWIDPETGSWRE
+QPHSREHRAAARLAEAQVRAAGQAAGRRPAGTGRGSHSAVKPLLGRGTRIATCVVAAGVA
+LAVSLAMVLGNVSTSATLFPVWPALAALGVMAAVMTAGLLRGRRPGLLAPLSGILVGVVA
+LQVCAHLLFTPLP
+>PROKKA_01668
+MTSTHDPFTGPGPHVAPDGAAAGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG
+VAERYRIDPLLARGVFVAVCMISAGLGLLAYAAAWAVLPDADGRVQFGRLRRGEWQDATV
+AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLVGLGALAVLVWWLVTRWDGRAQARVAPG
+RVPDADQPAHAVPRPAWYVGGGPRERAAEVTDPHGFRPEWIDPATGTWRDHVHSRERRAA
+ARLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP
+TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001418.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001418.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b98bfc208b6b701e72c00baf79e0b01d404c8de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001418.fa
@@ -0,0 +1,35 @@
+>PROKKA_01746
+MAEHPTPTTSDADGMPRVVTPRPEEASAVLDLADRAGAADGHPPLSDQTRVLLARGGQLW
+WGATRGPDGAIDGAAVLVPEGTAAVLELVVDPTARRTGRGTVLADAAAAAVRDLAREETT
+SVWAHGMLPGAVRLARRHGLEPVRELRRMRLSHAALAALPEVRLADGVALRGFVPGQDEQ
+AWLDVNAAAFADHPEQGSLTRADLDDRMAEDWFDADGLLLAAREADGRLLGFHWTKVEPD
+AGADGPRVGEVYAVGVSPDAQGLGLGRALTLAGLHRMAEQGVDVVDLYVDADNTAAVTLY
+ASLGFELFAADAQYRRP
+>PROKKA_01453
+MAEHPTPTTSDADGMPRVVTPRPEEASAVLDLADRAGAADGHPPLSDQTRVLLARGGQLW
+WGATRGPDGAIDGAAVLVPEGTAAVLELVVDPTARRTGRGTVLADAAAAAVRDLAREETT
+SVWAHGMLPGAVRLARRHGLEPVRELRRMRLSHAALAALPEVRLADGVALRGFVPGQDEQ
+AWLDVNAAAFADHPEQGSLTRADLDDRMAEDWFDADGLLLAAREADGRLLGFHWTKVEPD
+AGADGPRVGEVYAVGVSPDAQGLGLGRALTLAGLHRMAEQGVDVVDLYVDADNTAAVTLY
+ASLGFELFAADAQYRRP
+>PROKKA_01131
+MAENPVPATPTDPAAPRVSEPRPDEVDAVLALADRAQAADGHPPLSDQTRVVLARGRQRW
+WGVVREADGSVSGAAVLAPEGGEDSGSVLELVVDPEARRAGRGAALADAAAAAVRERGLE
+STTSVWAHGMLPGSDALARRHGLEPVRELRRMRLPHEALADLPQPQLADGVALRGFVPGR
+DEQAWLDANAAAFADHPEQGGLTRADLEDRMAEDWFEAEGLLLAVREEDDALLGFHWTKV
+EPQAGPGPRVGEVYAVGVTPATQGLGLGRALTLAGLHRMAGQGVDVVDLYVDADNAAAVR
+LYESLGFGLFAADAQHRRP
+>PROKKA_01059
+MSEQPASPALPPTPGVVSPGTPSDVDAALALADRAHRSDGHPPLNDQTRAVLARDAQRWW
+GLTRDEAGAVTGVAVLAPEGEAAGPGVVELAVDPAHRGAGLGAALAEAAADAVRERGEAR
+RTSAWAHGALPGALALARRHGLEPVRELRRMRLDPAGLGALPPTRLPEGVTLRGFVPGRD
+EDAWLALNAAAFADHPEQGSLTRADLDAREAEDWFEAAGLLLAEDAEGTPVGYHWTKVTP
+AEAGAPSEGEVYAVGISPAAQGRGLGRALTLAGLHHMAGRGVDAVDLYVDADNVPAVRLY
+ESLGFALAAADVQLRPAR
+>PROKKA_01675
+MAEHPTPTTSDADGMPRVVTPRPEEASAVLDLADRAGAADGHPPLSDQTRVLLARGGQLW
+WGATRGTDGAIDGAAVLVPEGAAAVLELVVDPTARRTGRGTVLADAAAAAVRDLAREATT
+SVWAHGMLPGAVRLARRHGLEPVRELRRMRLSHAALAALPEVRLADGVALRGFVPGQDEQ
+AWLDVNAAAFADHPEQGSLTRADLDDRMAEDWFDADGLLLAAREADGRLLGFHWTKVEPD
+AGADGPRVGEVYAVGVSPDAQGLGLGRALTLAGLHRMAEQGVDVVDLYVDADNTAAVALY
+ASLGFELFAADAQYRRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001419.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001419.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eac076c1730f01b5b5f2ef91e0f5271b29a7339a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001419.fa
@@ -0,0 +1,35 @@
+>PROKKA_01747
+MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPGGLEVMVIHRPRYDDWSWPKGK
+LDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPGKRGARQSKEVWYWAAEVDGQRA
+LPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRAASRGRLRTVPLLVLRHAKAKPRS
+SWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSSPWRRCVETLAPLVKSSRLALKTK
+GAFTETTAREKPQKTRKVMAELMGRSRPLVVCTHRPVLPTLFEVVEDAAAGRTDRVLRAL
+PTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD
+>PROKKA_01454
+MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPGGLEVMVIHRPRYDDWSWPKGK
+LDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPGKRGARQSKEVWYWAAEVDGQRA
+LPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRAASRGRLRTVPLLVLRHAKAKPRS
+SWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSSPWRRCVETLAPLVKSSRLALKTK
+GAFTETTAREKPQKTRKVMAELMGRSRPLVVCTHRPVLPTLFEVVEDAAAGRTDRVLRAL
+PTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD
+>PROKKA_01130
+MPSTPTERVARWSTEDRAADGPRAEVLAAGVVPWRRTPGGRLEVLVIHRPRYDDWSWPKG
+KLDPGETLPQCAVRELREEVGLALRPGIPLCVTEYEVSGKRGARLTKEVWYWAADAGAQR
+AVPDGDEVDEVRWVRPEEAEALLTNETDREPLELLVRADSRGRLRTLPLLVLRHAKAKPR
+SSWSRAEQERPLAATGRRQALAVEGLVAAWAPDRLVSSPWRRCVETLAPLVKSSRLPLKT
+KGAFTETAAKEKPKKTRKAMHELLGRQRAQVVCTHRPVLPVLFEVVEDAARRQERVLRAM
+PREDPWLRPGAVLVVHRSLDGDVVAVEAYDPWDD
+>PROKKA_01058
+MTRPLSWDGIPDPIPPEDPRTMSAHPDDRAAAWSTPDGAVTAPGAEVLAAGMIPWRPGAE
+GLEVLVIHRPRYDDWSWPKGKVDDGETLPEAAARELAEEVALTLRPGLPLAVTRYDVPDR
+KGKGMLSKEVWYWAGEATGQRPTPDGDEVDEARWVSSARAREMLSNATDLEPLDRLERAD
+ARGHLRTVPLLVLRHAKAKPRSSWSRAEQERPLAATGRRQAHSVARLIAVWRPERVVSSP
+WRRCVETLAPFVKATRLPLKTKSAFTETTAREKPKKTRRAFRDLLARRRPQVLCLHRPVI
+PSILEEVDDAAARPASDVLAALPRRDPHLRPGGVLVLHQGLDAKGAVVAAEVYDPWSD
+>PROKKA_01676
+MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPGGLEVMVIHRPRYDDWSWPKGK
+LDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPGKRGARQSKEVWYWAAEVDGQRA
+LPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRAASRGRLRTVPLLVLRHAKAKPRS
+SWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSSPWRRCVETLAPLVKSSRLPLKTK
+GAFTETTAREKPKKTRKVMAELMGRSRPLVVCTHRPVLPTLFEVVEDAAAGQADRVLRAL
+PTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001424.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001424.fa
new file mode 100644
index 0000000000000000000000000000000000000000..57108196c7ef1400238974542a55fa7645969f3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001424.fa
@@ -0,0 +1,40 @@
+>PROKKA_01752
+MRSRAASLEGMTSAAPASVNAPDAAAVPTVGLVGWRGMVGSVLLQRMAEEGDFARVHPVF
+FSTSNAGGPAPVLEGMAGDPGVLQDAYDVDALKALPVILTAQGGDYTQAVYPKLRAAGWD
+GIWIDAASTLRMADTSVIALDPVNRGVIDAALANGTKDFIGGNCTVSCMLMGLGGLFKAG
+LVEWGTAMTYQAASGGGARHMRELLTQYAELGGAVRAELADPASAILEIDRKVIELQRGG
+LDSTQFGVPLGGSLIPWIDSDLGDGVSREERKAYDETNKVLGLTGADRIPFDSLCVRIGA
+MRSHSQALTLKLTQDVPLDEVEQIIAADNEWVQVVPNTKEVTVTDLTPIAATGTLQIPVG
+RLRKLNMGPEYLSAFTVGDQLLWGAAEPVRRMLMIATGNL
+>PROKKA_01459
+MRSRAASLEGMTSAAPASVNAPDAAAVPTVGLVGWRGMVGSVLLQRMAEEGDFARVHPVF
+FSTSNAGGPAPVLEGMAGDPGVLQDAYDVDALKALPVILTAQGGDYTQAVYPKLRAAGWD
+GIWIDAASTLRMADTSVIALDPVNRGVIDAALANGTKDFIGGNCTVSCMLMGLGGLFKAG
+LVEWGTAMTYQAASGGGARHMRELLTQYAELGGAVRAELADPASAILEIDRKVIELQRGG
+LDSTQFGVPLGGSLIPWIDSDLGDGVSREERKAYDETNKVLGLTGADRIPFDSLCVRIGA
+MRSHSQALTLKLTQDVPLDEVEQIIAADNEWVQVVPNTKEVTVTDLTPIAATGTLQIPVG
+RLRKLNMGPEYLSAFTVGDQLLWGAAEPVRRMLMIATGNL
+>PROKKA_01125
+MTSAAPPPSPPPDAAAVPTVGLIGWRGMVGSVLMQRMAEEGDFARIRPVFFSTSNAGGPA
+PTFEGLPGDAGPLQDAYDLNVLASLPVIVTAQGGDYTKDVYPRLRAAGWDGIWIDAASTL
+RMEDTSVIALDPVNRSVIDAALASGVKDFIGGNCTVSCMLMGLGGLFKAGLVEWGTAMTY
+QAASGGGARHMRELLTQYADLGGVVRDELADPASAILEIDRKVLELQRDGLDATQFGVPL
+GGSLIPWIDSDLGNGVSREEQKAFDETNKVLGLRGEDRIAFDSLCVRIGAMRSHSQALTL
+KLTRDVPLDEVEQIIAEDNEWVRLVANTKEASVAELTPIAATGTLQIPVGRLRKLNMGPE
+YLSAFTVGDQLLWGAAEPVRRMLMIATGNL
+>PROKKA_01050
+MTSAAPAPVSPAAPAAVPTVGIVGWRGMVGSVLMQRMAEEGDFARIHPVFFSTSNAGRPA
+PVFEGMDGDAGTLQDAHDVEALKALPIIVTAQGGDYTKAVYPALRAAGWDGIWIDAASTL
+RMEDSSVIVLDPVNRSVIDAALASGTKDFIGGNCTVSCMLMGLGGLFREGLVEWGTAMTY
+QAASGGGARHMRELLTQYAALGGVVAEELADPSSAILEIDRKVLELQRGGLDASQFGVPL
+GGSLIPWIDSDLGNGVSREEQKAYDETNKVLGLTGDDRIPFDSLCVRIGAMRSHSQALTL
+KLTRDVPLDEITEIVADGTEWAQVVPNEKEASLRDLTPIAASGTLQIPVGRLRKLNMGPE
+YLSAFTVGDQLLWGAAEPIRRMLMIATGNL
+>PROKKA_01681
+MTSAAPASVNAPDAAAVPTVGLVGWRGMVGSVLLQRMAEEGDFARIHPVFFSTSNAGGPA
+PVLEGMAGDPGVLQDAYDVDALKALPVILTAQGGDYTQAVYPKLRAAGWDGIWIDAASTL
+RMADTSVIALDPVNRGVIDAALANGTKDFIGGNCTVSCMLMGLGGLFKAGLVEWGTAMTY
+QAASGGGARHMRELLIQYAELGGAVRAELADPASAILEIDRKVIELQRDGLDSTQFGVPL
+GGSLIPWIDSDLGDGVSREERKAYDETNKVLGLTGADRIPFDSLCVRIGAMRSHSQALTL
+KLTRDVPLDEVEQIIAADNEWVQVVPNTKEATVTDLTPIAATGTLQIPVGRLRKLNMGPE
+YLSAFTVGDQLLWGAAEPVRRMLMIATGNL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001425.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001425.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9965d9a05ec711535e9523bd113d6f0d2f32afde
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001425.fa
@@ -0,0 +1,40 @@
+>PROKKA_01753
+MSERLADHTTTRVGGPARAWVTARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADAGFP
+GTVVRLAFEGIHVLDGPLPGEGETPPAGDGARSADHEGEAVVVRIAAGHPWDDAVAWTVA
+HGLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVALRAWDREAGDVVELTPADLRFGY
+RDSVIKRSMLETGAPSPRWIVLSIDLRLRRASSDAEPTAPVRYGQLAAALDVEEGAHAPL
+AVVRREVLALRAAKGMVSDPADPDTWSTGSYFTNPIVPASVRASLPDGAPAFAAGQAEDG
+TPLVKLSAAWLIDRAGFAKGFGLPEVAPREGGPDGRGADGTGLAGGRASVSTKHTLAMTN
+RGDATTEDVLTVARTVRDGVRERFGVELHPEPMIIGTSL
+>PROKKA_01460
+MSERLADHTTTRVGGPARAWVTARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADAGFP
+GTVVRLAFEGIHVLDGPLPGEGETPPAGDGARSADHEGEAVVVRIAAGHPWDDAVAWTVA
+HGLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVALRAWDREAGDVVELTPADLRFGY
+RDSVIKRSMLETGAPSPRWIVLSIDLRLRRASSDAEPTAPVRYGQLAAALDVEEGAHAPL
+AVVRREVLALRAAKGMVSDPADPDTWSTGSYFTNPIVPASVRASLPDGAPAFAAGQAEDG
+TPLVKLSAAWLIDRAGFAKGFGLPEVAPREGGPDGRGADGTGLAGGRASVSTKHTLAMTN
+RGDATTEDVLTVARTVRDGVRERFGVELHPEPMIIGTSL
+>PROKKA_01124
+MSERLAEHTTTRVGGPARAWETARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADAGFP
+GTVVRLAFEGIEVRAGDEAHGGDADDQDPAAGGDRAGEAVVVRVAAGHPWDDAVAWTVEH
+GLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVSLRAWDREAGQVVELGAEELEFDYR
+DSIIKRSMLETGAPSPRWIVLSIDLRLRRASGAAEPTAPVRYGQLASALDVAEGTHAPLA
+VVRREVLALRAAKGMVSDPQDPDTWSTGSYFTNPIVPAAVRASLPEGAPAFAAGRAADGT
+ELVKLSAAWLIDHAGFAKGFGLPDVAPREGGPDGRGADGAGLAGGRASVSTKHTLAMTNR
+GDASTEDVLTIARTVRDGVKARFGVDLHPEPMIIGTSL
+>PROKKA_01049
+MSERLSDHTTTRVGGPARAWVEARTEAEAVAAVRAADAAGEPLFVLGGGSNTLMADAGFE
+GTVVHMGFTGVEVLPAEGAADGAGDVVVRVAAGHVWDEAVAWTVEHGLAGVEALSGIPGS
+AGATPVQNVGAYGADVSQVLVSLRAFDRAAGQVVELSAEDLRFGYRDSVIKRSMFEDGSP
+SPRWIVLSIDLRLRRAEEGAEPTAPVRYAQLARALEVEEGADVSLAQVREHVLALRASKG
+MVSDAADHDTWSTGSYFTNPIVPATVRVTLPEGAPAFAAGTDEDGTPLVKLSAAWLIDHA
+GYGKGFGLPDAPRREGDADGSGPDGRGLAGGRAALSTKHTLAVTNRGGASTEDVLTVARA
+VRDGVKARFGVDLHHEPMIIGTRL
+>PROKKA_01682
+MSERLADHTTTRVGGPARAWVTARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADSGFP
+GTVVRLAFEGIGVLDGPVPGEGEAPPVGDGARLADHEGEAVVVRVAAGHPWDDAVAWTVA
+HGLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVALRAWDREAGDVVELTPADLRFGY
+RDSVIKRSMLETGAPSPRWIVLSIDLRLRRASSDAEPTAPVRYGQLAAALDVEEGAHAPL
+AVVRREVLALRAAKGMVSDPADPDTWSTGSYFTNPIVPASVRASLPDGAPAFAAGQAEDG
+TPLVKLSAAWLIDRAGFAKGFGLPEVAPREGGPDGRGADGTGLAGGRASVSTKHTLAMTN
+RGDATTEDVLTVARTVRDGVRERFGVELHPEPMIIGTSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001426.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001426.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2b8b1179c2d4ee110a381b72824094a036f45847
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001426.fa
@@ -0,0 +1,20 @@
+>PROKKA_01754
+MSTAPRLSDLARGEVVGTRTVTFTRADLVAYAGASGDRNPIHWSPSFAEHVGLPGVIAHG
+MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTGRTDDDGAPVPGATLEVVGTVG
+AVDEAAGTVRIDLNVTNPDAAKPRVLTKAQAVVRLADPAGESA
+>PROKKA_01461
+MSTAPRLSDLARGEVVGTRTVTFTRADLVAYAGASGDRNPIHWSPSFAEHVGLPGVIAHG
+MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTGRTDDDGAPVPGATLEVVGTVG
+AVDEAAGTVRIDLNVTNPDAAKPRVLTKAQAVVRLADPAGESA
+>PROKKA_01123
+MSTAPRLSELSKGETIGTRTVPLTRADLVAYAGASGDHNPIHWSPSFAERVGLPGVIAHG
+MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTGQTGDDGAPVPGATLQVVGKVG
+AVDEAAGTVRIDLDVTNPDAEKPRVLTKAQAVVRLAEPAPAAGESA
+>PROKKA_01048
+MRAQSARPVLAELAKGQSIGSRTVPLTRAGLVAYAAASGDHNPIHWNQAFAASVGLPGVI
+AHGMLTMGAAVQLVTDWAGDPGAVVDYQTRFTAMVPVADTTGQTDDAGAPVPGAVLEVSG
+AVGAIDAEAGTVRIDLTVNDPAQAKPRVLTKAQALVRLTRAVETPEETA
+>PROKKA_01683
+MSTAPRLSDLARGEVVGTRTVTFTRADLVAYAGASGDRNPIHWSPTFAEHVGLPGVIAHG
+MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTVRTDDDGAPVPGATLEVVGTVG
+AVDEAAGTVRIDLNVTNPDAAKPRVLTKAQAVVRLADPAGESA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001430.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001430.fa
new file mode 100644
index 0000000000000000000000000000000000000000..219af5364e391a2ca5a040369ffd0ff56c9f41b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001430.fa
@@ -0,0 +1,26 @@
+>PROKKA_01760
+MPQNSEDRPLARGLGRAAGRAAQSFRENQRADDARLRAERARLTAEDEERLERRRADRER
+DLVARDAAESDAGLVHPLLKVARLYWLAVTVVLIGIAGAFLWNGARAQDSGEPVIDPLTG
+MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA
+NGLLIILAVVMLLGAALVWLPPVRSRVRR
+>PROKKA_01467
+MPQNSEDRPLARGLGRAAGRAAQSFRENQRADDARLRAERARLTAEDEERLERRRADRER
+DLVARDAAESDAGLVHPLLKVARLYWLAVTVVLIGIAGAFLWNGARAQDSGEPVIDPLTG
+MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA
+NGLLIILAVVMLLGAALVWLPPVRSRVRR
+>PROKKA_01117
+MPQNSEDRPLARGLGRAAGRAARSFQESQRADDARLRAERARLAAEDEERLSRRREDRER
+GLAERDAAESDAGLVHPLLRIARMYWLALTVVLAVVAGAFVWNGMRARESGEPVVDPLTG
+IESVGVLGGATGQFTMGVTVALFAAAALWGWIGLLRRRRSAIGTLTFIALLLAAPAFLRA
+NGLLIVLAVIMLVGAALLWLPPVRSRLRR
+>PROKKA_01042
+MADNSAENSSDRIARAAGRAARAFREGQDAERIRREQARAEAPRTADADGSRATGLRERA
+VRAAAQAAERAEPLKERVGHAAGEAGRSFKENQAQDAARLRGVREQVRADDDAARAERQA
+ERERALDARDETEAGRVHPLLRLTRLWWLAVSLLLLGLATAFVYNGVRADRDGGEVIDPV
+TGLQSIGPLGGATGQYTVGGVLAALALVTLWGWVGLLRRRRASLGTLTTVAVLLAIPAVL
+RPNPLFIVLGAAMAIGAVLLWLPPVRSRVRR
+>PROKKA_01689
+MPQNSEDRPLARGLGRAAGRATQSFRENQRADDARLRAERARLTAEDEERLERRRADRER
+DLAARDAAESDAGLVHPLLKVARLYWLAVTVVLVGIAGAFIWNGARAQDSGEPVIDPLTG
+MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA
+NGLLIILAVVMLLGAALVWLPPVRSRVRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001431.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001431.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e622c9810440f86aa2fdf52cfe74dc0c1e2a32dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001431.fa
@@ -0,0 +1,40 @@
+>PROKKA_01761
+MTLTAFVNAHVVPVAAEPFDGALLVEDGRITALGPDVEAPDGAEVVDCEGRWVLPGFVDA
+HVHLGMHAEGEVGATADVNEMTDPVMAGVRAIDAVDPNEPGWKDALAGGVTTVNVNPGSG
+NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA
+FLRAQGYMARRAEAEREDKPFTRDPHLDALALVLERTIPWRQHCHRTDDVATALRLADEF
+GYDLVLDHGTEAHPLAGQLAARGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI
+ITDHPVVPIDFLVYQAALSVKEGLDRETALRAITLHPARVLGLDDRIGSLEVGKDADLVL
+WSGDPLDVMQRALRVWIGGRQVMEYDLATARPVVASARPVED
+>PROKKA_01468
+MTLTAFVNAHVVPVAAEPFDGALLVEDGRITALGPDVEAPDGAEVVDCEGRWVLPGFVDA
+HVHLGMHAEGEVGATADVNEMTDPVMAGVRAIDAVDPNEPGWKDALAGGVTTVNVNPGSG
+NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA
+FLRAQGYMARRAEAEREDKPFTRDPHLDALALVLERTIPWRQHCHRTDDVATALRLADEF
+GYDLVLDHGTEAHPLAGQLAARGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI
+ITDHPVVPIDFLVYQAALSVKEGLDRETALRAITLHPARVLGLDDRIGSLEVGKDADLVL
+WSGDPLDVMQRALRVWIGGRQVMEYDLATARPVVASARPVED
+>PROKKA_01116
+MTVTAFVNAHVVPVESAPFDGALIVEDGRITALGPDVAAPEGADVVDCEGKWLLPGFVDA
+HVHLGMHAEGEVGTTSDVNEMTDPVMAGVRAIDAVDPNEPGWRDALAGGVTTVNVNPGSG
+NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA
+FLKAQGYLARQEEAEREGKPFTKDPHMEALGQVLRREIPWRQHCHRTDDIATALRIADEF
+GYELVLDHGTEAHPVADLLAERGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI
+ITDHPVIPIDFLVYQAALSVKEGLDPETALRAITLNPAKVLGLDDRIGSLAVGKDADLVL
+WSGDPLDVMQRALRVWIGGRCVMEYDLATARPVVASARPVED
+>PROKKA_01041
+MSITAFTNVHVVPVESDPFDGVLLAEDGRISALGPDVEIPAGADVVDCGGRWLLPGFVDA
+HVHLGMHAEGEVGATADVNEMTDPVMAGVRALDAVDPNEPGWRDALAGGITTVNVNPGSG
+NPIGGQAVAMHTHGRTVDEMVLRAPSGVKSALGENPKTVYKEQGRTPSTRLGTALVIRRA
+FMEAQGYMARRTEAEADGKPFTKDPHMEALALVLERRIPWRQHCHRTDDVATALRIADEF
+GYDLVLDHGTEAHPLADVLAERGVPVLIGPLFTTKSKPELRGRSLRNPGRLARAGVEISI
+ITDHPVVPIDFLVYQAALAVKEGLDRDTALRAITLNPAKVLGLADRIGSLAPGKDADLVL
+WSGDPLDVMQRALRVWIGGRPVMEYDAAAARPVVASARPAED
+>PROKKA_01690
+MTLTAFVNAHVVPVAAEPFDGTLLVEDGRITALGPDVEAPDGAEVVDCEGRWLLPGFVDA
+HVHLGMHAEGEVGATADVNEMTDPVMAGVRAIDAVDPNEPGWKDALAGGVTTVNVNPGSG
+NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA
+FLRAQGYMARRAEAEREDKPFTRDPHLDALALVLERTIPWRQHCHRTDDVATALRLADEF
+GYDLVLDHGTEAHPLADQLAARGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI
+ITDHPVVPIDFLVYQAALSVKEGLDRETALRAITLHPARVLGLDDRIGSLEVGKDADLVL
+WSGDPLDVMQRALRVWIGGRQVMEYDLATARPVVASARPVED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001432.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001432.fa
new file mode 100644
index 0000000000000000000000000000000000000000..024dc3387ff9ac8eee594b11b8855038e0af5a55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001432.fa
@@ -0,0 +1,40 @@
+>PROKKA_01762
+MTEQNVHEDPHATTPDTGAEDAAAHPQGGGFGTRAVHAGQHLDEVFGAVVPPIHLSSTYA
+PTAVGELRRGYDYGRGTNPTRDALQEQLAALEAGVDESGAPRATGLTFASGLAAETALIM
+GAGRPGMTIVLGNDVYGGSYRLISRVLAPWGVEHVVVDMGDAEQVAAAVERAAAAGPVMV
+WLETPSNPMMKISDVAAVAEAAHAHGALLVVDNTFATPYLQSPIALGADVVVHSTTKYIG
+GHSDVIGGALVIPDAALAEQVKFQQFAAGAVNGPMDAYLTTRGLKTLGVRMDRHQANAQA
+VAEWLTGRAEVSQVLYPGLPDHPGHELAQRQMRGFGGMVSLRLSGGAAAARRVAESTRLF
+QLAESLGGIESLMNYPAEMTHASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALGSL
+>PROKKA_01469
+MTEQNVHEDPHATTPDTGAEDAAAHPRGGGFGTRAVHAGQHLDEVFGAVVPPIHLSSTYA
+PTAVGELRRGYDYGRGTNPTRDALQEQLAALEAGVDESGAPRATGLTFASGLAAETALIM
+GAGRPGMTIVLGNDVYGGSYRLISRVLAPWGVEHVVVDMGDAEQVAAAVERAAAAGPVMV
+WLETPSNPMMKISDVAAVAEAAHAHGALLVVDNTFATPYLQSPIALGADVVVHSTTKYIG
+GHSDVIGGALVIPDAALAEQVKFQQFAAGAVNGPMDAYLTTRGLKTLGVRMDRHQANAQA
+VAEWLTGRAEVSQVLYPGLPDHPGHELAQRQMRGFGGMVSLRLSGGAAAARRVAESTRLF
+QLAESLGGIESLMNYPAEMTHASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALGSL
+>PROKKA_01115
+MTTHEQRPAGFGTRAVHAGQDLDEVYGAVVPPVHLSSTYAPVRVGELRRGYDYGRGTNPT
+RDALQTQLAALEAGVGEDGTPNALALTFASGLAAETALIMGAAEPGTTIVMGNDVYGGSY
+RLISKVLAKWGIRHAVVDMGDTAKVAAAVESAAAQGPVMVWLETPSNPLMKVSDIAAIAE
+VAHGHDALLVVDNTFATPYLQTPLALGADVVVHSTTKYIGGHSDVIGGALVIKDPELGAQ
+VQFQQFAAGAVNGPWDAYLTTRGLKTLGVRMDRHQANAQAVAEWLAGRPEVTQVLYPGLP
+DHPDHELAARQMRGFGGMVSFRLTGGAAAARTVAESTRLFQLAESLGGIESLMNYPAEMT
+HASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALEALAG
+>PROKKA_01040
+MTEQNAHEQPHDTAPTGPEATEGPAEGFGTRAVHAGQHLDEVYGAVVPPLHISSTYAPTA
+IGELRRGYDYGRGTNPTRDALQEQLAALEAGVDDAGTPKATGLTFASGLAAETALIMGAG
+QPGMTIVMGNDVYGGSYRLISRVLKPWGVDHAVVDMGEPEQVAAAVEQAAASGPVMVWLE
+TPSNPMMKISDVAAVAEAAHGRGAQLVVDNTFATPYLQNPIALGADVVVHSTTKYIGGHS
+DVIGGALVIPDAELAEKVKFQQFAAGAVNGPVDAYLTTRGLKTLGVRMDRHQANAQALAE
+WLTEQSAVSQVLYPGLPDHPGHELAKRQMRGFGGMVSVRFHGGAAAAKKVAESTRLFQLA
+ESLGGIESLMNYPAEMTHASVAGTELAVPDDLVRLSVGIEDASDLIADLEQAIAGLAG
+>PROKKA_01691
+MTEQNVHEDPHATTPDTGAEDAAAHPRGGGFGTRAVHAGQHLDEVFGAVVPPIHLSSTYA
+PTAVGELRRGYDYGRGTNPTRDALQEQLAALEAGVDESGAPRATGLTFASGLAAETALIM
+GAGRPGMTIVLGNDVYGGSYRLISRVLAPWGVEHVVVDMGDAEQVAAAVERAAATGPVMV
+WLETPSNPMMKISDVAAVAEAAHAHGALLVVDNTFATPYLQSPIALGADVVVHSTTKYIG
+GHSDVIGGALVIPDAALAEQVKFQQFAAGAVNGPMDAYLTTRGLKTLGVRMDRHQANAQA
+VAEWLTGRAEVSQVLYPGLPDHPGHELAQRQMRGFGGMVSLRLSGGAAAARRVAESTRLF
+QLAESLGGIESLMNYPAEMTHASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALGSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001440.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001440.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb0ebbf93a0cc2e8968f3fdf0947264098ef27d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001440.fa
@@ -0,0 +1,20 @@
+>PROKKA_01773
+MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW
+RRSAGADAPEGEWQDEGGTFSEFLTDLLAWTFEDPEDDGEGLDR
+>PROKKA_01480
+MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW
+RRSAGADAPEGEWQDEGGTFSEFLTDLLAWTFEDPEDDDEGPDR
+>PROKKA_01104
+MPAKPPAPVHLPAFQRLVPDLLGDAWAEDDGLSPADVEARLGQSPAAGQLGAGFMVPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDAEETVVWGLPVDNLALPDPLVW
+RRSSGAEAEEGDWQDEGGTFSEFITDLLAWTFEDPEDDDGRDER
+>PROKKA_01029
+MPAKPPAPVYLPGFQRLVPDLLGDTWAKDDGLAPADVEARLAESPAAEQLGTGFMVPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDEGETVVWGLPVDNLALPDPLVW
+RRDTGADAEEGDWQDEGGTFSEFITDLLVWTFEDPEDDAAEDAR
+>PROKKA_01702
+MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW
+RRSAGADAPEGEWQDEGGTFSEFLTDLLAWAFEDPEDDDEGPDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001450.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001450.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89ad3100fdd4c22a97090ae325f69b9c2deb4e70
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001450.fa
@@ -0,0 +1,49 @@
+>PROKKA_01787
+MASRTASPPPSPAPSPAAPRGALDRYFRITERGSSVGQEFRGGLATFLAMSYIVVLNPLI
+LSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWARHPFAVAAGLGVSAFVSITIATTPG
+LTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPESLKSGIVVGIGLFIALIGLVNAGFV
+RRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLLTAVLVIRKVRGAILIGIVVATILAN
+VLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTAPDLHLLGSVDLFGAFTSVGGLMASL
+LVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPDLNRVLAADALAVAVGGAASGSAHQI
+FVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLIHLVPFEAVAPALVVVGFMMCQHVVQ
+IDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVAYAVIRTGQGRGREVHPLLWFVALAF
+VAYFGLGVVRAALGLN
+>PROKKA_01494
+MASRTASPPPSPAPSPAAARGALDRYFRITERGSSVGQEFRGGLATFLAMSYIVVLNPLI
+LSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWARHPFAVAAGLGVSAFVSITIATTPG
+LTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPEALKSGIVVGIGLFIALIGLVNAGFV
+RRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLLTAVLVIRKVRGAILIGIVAATILAN
+VLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTAPDLHLLGSVDLFGAFTSVGGLMASL
+LVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPDLNRVLAADALAVTVGGGASGSAHQI
+FVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLIHLVPFEAVAPALVVVGFMMCQHVVQ
+IDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVAYAVIRTGQGRGREVHPLLWFVALAF
+VAYFGLGVVRAALGLN
+>PROKKA_01089
+MGQEFRGGLATFLAMSYIVVLNPLILSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWA
+RHPFAVAAGLGVSAFVSITIATTPGLTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPE
+ALKSGIVVGIGLFIALIGLVNAGFVRRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLL
+TAVLVIRKVRGAILIGIVAATILANVLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTA
+PDLHLLGSVDLFGAFTSVGGLMASLLVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPD
+LNRVLAADALAVAVGGGASGSAHQIFVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLI
+HLVPFEAVAPALVVVGFMMCQHVVQIDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVA
+YAVIRTGQGRGREVHPLLWFVALAFVAYFGLGVVRASLGLN
+>PROKKA_01015
+MSSRTTGATPPGTAPSNPASPAGPRSGLDRFFGISALGSSVGQEVRGGIATFLAMSYIVV
+LNPLILSGPDSTGAVLGIPRVAAATALVAAVATLAMGLWARHPFALASGLGVNAFLAITV
+ATTPGLTWPDVMGLVVIAGLVMVVLVATGFRTAVFNAVPEALKTAIVVGIGLFIALIGLV
+NAGFVRRLPDAAGTTVPVGLGTGGELAGWPVLVFIVGLLVTAILVIRNVRGAILVGIVTA
+TVLANILEAVFHIGPSVGADGSHNPTGWALVAPSLPEWAAPDLSLLGSARPFGAFEAVGG
+LMGALLVFAILLSVFFDAMGSTVGLAREAGSMDEHGNVPRLNRVLMVDALAVTGGGAASA
+SAGQIYVESGTGIGEGARTGLASVVTGLMFVATIFLTPLIHLVPFEAVAPALVVVGFMMC
+SQVVRIDWTDWGAALPAFLTFILMPFTYSIANGIGAGMIAYAVIRTGQGRAREVHPLLWV
+VAAAFVLYFGMGVFRGILGLA
+>PROKKA_01716
+MASRTASPPPSPAPSPAAPRGALDRYFRITERGSSVGQEFRGGLATFLAMSYIVVLNPLI
+LSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWARHPFAVAAGLGVSAFVSITIATTPG
+LTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPEALKSGIVVGIGLFIALIGLVNAGFV
+RRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLLTAVLVIRKVRGAILIGIVAATILAN
+VLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTAPDLHLLGSVDLFGAFTSVGGLMASL
+LVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPDLNRVLAADALAVTVGGGASGSAHQI
+FVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLIHLVPFEAVAPALVVVGFMMCQHVVQ
+IDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVAYAVIRTGQGRGREVHPLLWFVALAF
+VAYFGLGVVRAALGLN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001452.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001452.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46d3afa8b5477a64ddfa97ba38d402bd11af6633
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001452.fa
@@ -0,0 +1,35 @@
+>PROKKA_01799
+MSTPQPDAARPDRDRLPEQVSDLFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPT
+VRIAFDRPEVRNAFRPGTVDELYRALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQ
+RIRGRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHV
+VADLTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEEMVAM
+GAVNEAVDHERLEEVALEYAADINRQSPQALRMLKFAFNLPDDGMAGQQVFAGEATRMAY
+MTDEAVEGRDAFLQKRDPDWSAFPYHF
+>PROKKA_01496
+MSTPQPDAARPDRDRLPEQVSDVFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPT
+VRIAFDRPEVRNAFRPGTVDELYRALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQ
+RIRGRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHV
+VADLTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEEMVAM
+GAVNEAVDHERLEEVALEYAADINRQSPQALRMLKFAFNLPDDGMAGQQVFAGEATRMAY
+MTDEAVEGRDAFLQKRDPDWSAFPYHF
+>PROKKA_01074
+MTETTPAAARDRLPEKVSDLFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPTVRI
+AFDRPEVRNAFRPGTVDELYRALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQRIR
+GRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHVVAD
+LTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEEMVALGAV
+NEAVDHERLEEVALEYAADINAQSPQALRMLKFAFNLADDGMAGQQVFAGEATRMAYMTD
+EAVEGRDAFLQKRDPDWSAFPYHF
+>PROKKA_01010
+MPAVRFSNDSIPGGIHVTNENAVVATTVLSMTESTPHHDRDRLPEKVSDVFDPTRWRVVE
+GFEFEDMTYHRQVERDADGRWVRDLPTVRIAFDRPEVRNAFRPGTVDELYRALDHARMTP
+DVGTVLLTGNGPSPKDGGHAFCSGGDQRIRGRDGYRYAEGETAETIDPARAGRLHILEVQ
+RLMRNSPKVVIAVVNGWAAGGGHSLHVVADLTLASRQHGKFKQTDATVGSFDAGYGSALL
+AREVGQKRAREIFFTAREYSAEEMVAMGAVNEAVDHERLEEVALEYAADINRQSPQAIRM
+LKFAFNLPDDGMAGQQVFAGEATRMAYMTDEAVEGRDAFLQKRDPDWSAFSYYF
+>PROKKA_01720
+MSTPQPDAARPDRDRLPEQVSDIFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPT
+VRIAFDRPEVRNAFRPGTVDELYHALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQ
+RIRGRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHV
+VADLTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEKMVAM
+GAVNEAVDHERLEEVALEYAADINRQSPQALRMLKFAFNLPDDGMAGQQVFAGEATRMAY
+MTDEAVEGRDAFLQKRDPDWSAFPYHF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001454.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001454.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ce211de485115cdccc64887dea06e34d8170348
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001454.fa
@@ -0,0 +1,40 @@
+>PROKKA_01801
+MPATADALARATDALAAAFDGGAPVELTADGAVLPRPEARDSRRCGDPDAVAVVRTSGST
+GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP
+GPFTPAAFATGAAALPDDAGPRLISLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL
+DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVTAAVAPDGPDAPPRVRLAGPMV
+AAGYLDDPARTAAHFVPAADGARAFLTEDTGILSPTDDGGVRLAVTGRLDDVVITGGVKV
+SAAAVTAALEAHPGVAAAHVAGVPDPEWGARLCAAVVPVRPAAAPDEAVLRAHVRAALGA
+AAVPKTWLLLEALPLLSTGKTDRQALAARFTAG
+>PROKKA_01498
+MPATADALARATDALAAAFDGGDPVELTADGAVLPRPEARDSRRCGDPDAVAVVRTSGST
+GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP
+GPFTPAAFATGAAALPDNAGPRLVSLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL
+DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVTAAVAPDGPDAPPRVRLAGPMV
+AAGYLDDPARTAAHFVTAVDGARAFLTEDTGILSPTDDGGVRLAVTGRLDDVVITGGVKV
+SAAAVTAVLEAHPGVAAAHVAGVADPEWGQRLCAAVVPADPASPVGENALRAHIRDALGA
+AAVPKTWLALDALPLLSTGKTDRQALAARFTAAG
+>PROKKA_01072
+MPATADALARATDALAAAFDGGDPVELTADGAVLPRPEARDPRRCGDPDAVAVVRTSGST
+GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGIAVLSRSIAAGTAPVALPP
+GPFTPAAFATGAAALPDHAGPRLVSLVPTQLARLLAADTDPAGRTALRSFDRVLVGGARL
+DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVAVAVAPDGPDAPPRVRLAGPMV
+AVGYLDDPARTAAHFVPAADGARAFLTEDTGVLSPTDDGGVRLAVTGRLDDVVITGGVKV
+SAAAVTAVLEAHPGVAAAHVAGVADPEWGQRLCAAVVPADPASPVGENALRAHIRDALGA
+AAVPKTWLALDALPLLSTGKTDRQALAARFAAAG
+>PROKKA_01008
+MPATADALARATDALAAAFDGGAPVELTADGAVLPRPEARDPRRCGDPDAVAVVRTSGST
+GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP
+GPFTPAAFATGAAALPDDAGPRLVSLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL
+DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVAVAVAPDGPDAPPRVRLAGPMV
+AAGYLDDPARTAAHFVPAADGARAFLTEDTGVLSPTDDGGVRLAVTGRLDDVVITGGVKV
+SAAAVTAVLEAHPGVAAAHVAGVPDPEWGARLCAAVVPAHPAAAPDEAVLRAHVRAALGA
+VAVPKTWLVLDALPLLSTGKTDRQALAARFTAG
+>PROKKA_01722
+MPATADALARATDALAAAFDGGAPVELTADGAALPRPEARDPRRCGDPDAVAVVRSSGST
+GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP
+GPFTPAAFATGAAALPDDAGPRLVSLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL
+DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVAAAVAPDDPDAPPRVRLAGPMV
+AAGYLDDPARTAAHFVTAADGTRAFLTEDTGVLSPTDDGGVRLAVTGRLDDVVITGGVKV
+SAAAVTAVLEAHPGVAAAHVAGVPDPEWGARLCAAVVPAHEAAAPDEAVLRAHVRAALGA
+AAVPKTWLVLEALPLLSTGKTDRQALAARFTAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001455.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001455.fa
new file mode 100644
index 0000000000000000000000000000000000000000..db9014b7b8ab4e49ea93ee49ae4618db1384f76f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001455.fa
@@ -0,0 +1,30 @@
+>PROKKA_01802
+MAATLSQWVAAARPRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN
+DYSDGIRGTDDERVGPFRLTVSGLVPAARVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV
+GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSGLAWAGAIGCG
+LISTALLMANNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL
+LLVPIGGLLAIRPIRTVLRADDRRALIPVLRATGVIGIVYAITFTLGALL
+>PROKKA_01499
+MAATLSQWVAAARLRTLPMAIAPVIVGSAAAAELGRFHLGAALLALVVSLALQVGVNYAN
+DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFASFGLAGLAGLGLILLSGHWWFLLV
+GVACVVAAWYYTGGKKPYGYLGLGEVFVFVFFGLVAVLGTTYTQAGQVSGLAWAGAIGCG
+LISTALLMANNIRDIPTDRAVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPWL
+LLVPLGGLLAIRPVRTVLRAQDRRALIPVLRATGVIGIVYALTFTLGVLL
+>PROKKA_01071
+MAATLSQWVAAARLRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN
+DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV
+GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSRLAWAGAIGCG
+LISTALLMANNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL
+LLVPIGGLLAIRPIRTVLRADDRRTLIPVLRATGVIGIVYALTFTLGVLL
+>PROKKA_01007
+MAATLSQWVAAARLRTLPMAVAPVIVGSAAAHALDQFRPGRALLALVVSLALQIGVNYAN
+DYSDGIRGTDDARVGPFRLTVSGLVPAKTVKHAAFACFGVAAVAGLALVALSGTWWLLIV
+GVASIVAAWYYTGGKKPYGYMGLGEVFVFVFFGLVAVLGTTYTQALAVNGLAWAGAVGCG
+LISTALLMANNIRDIPTDREVGKMTLAARIGDGPARASYVAMLAVAVVLPLLFTGAHPWL
+WLVLAAGAVAVKPCLTVLHAHERAALIPVLKATGIVGVVYAAAFALGVAL
+>PROKKA_01723
+MAATLSQWVAAARPRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN
+DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV
+GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSGLAWAGAIGCG
+LISTALLMVNNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL
+LLVPIGGLLAIRPIRTVLRADDRRALIPVLRATGVIGLVYAITFTLGVLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001457.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001457.fa
new file mode 100644
index 0000000000000000000000000000000000000000..204b2bcd7dd3cf1065c7a3777c197a0a0a49f051
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001457.fa
@@ -0,0 +1,20 @@
+>PROKKA_01804
+MGRFIIPAAIILAGLTLYALFEALLTPAREVRSLPKAAWVAVIVLVPLVGPLLWLLLGRA
+RPAGAGGRPAPRPTGAPDDDEAFLRSLRVQRRQVAREQDLDRREAELRAREEELRRRREQ
+GDDDADPDGDGPRA
+>PROKKA_01501
+MGRYIIPAAIVLVGLTLYALFEALMTPAHEVRSLPKWGWVAVVVLLPLVGPLLWLVLGRA
+RVARGTARPAPRGPGAPDDDEAFLRSLRVQRRQAEREQELDRRDAELKAREEELRRRRER
+GEEPDADDPDAPTP
+>PROKKA_01069
+MGRYIIPAAIVLVGLTLYALFEALMTPAHEVRSLPKWGWVAVVVLLPLVGPLLWLVLGRA
+RVARGTARPAPRGPGAPDDDEAFLRSLRVQRCQAEREQELDRRDAELKAREEELRRRRER
+GEEPDADDPDAPTP
+>PROKKA_01005
+MARILVPTAILLVALTLFALFDALLTPAGRHRGMPKWAWIPTVLLLPLAGPLLWLFLGRP
+VPLFSGRTAAPASRPASPDDDDEFLRTLRVQRAQTERARNLDRREAELRAREEELRRRRE
+RGEDDATGEPDADA
+>PROKKA_01725
+MGRFIIPAAIILAGLTLYALFEALLTPAREVRSLPKAAWVAVIVLVPLVGPLLWLLLGRA
+RPAGAGGRTAPRPSGAPDDDEAFLRSLRVQRRQDAREQDLDRREAELRAREEELRRRREQ
+GDDDADPDGDGPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001458.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001458.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e4df2f7a5ef04c58abae257f930cf4331ca7652c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001458.fa
@@ -0,0 +1,30 @@
+>PROKKA_01807
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRAVGFFTRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL
+>PROKKA_01504
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRALGFFLRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL
+>PROKKA_01067
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLAGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRALGFFRRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL
+>PROKKA_01002
+MQDNRFAEIALDGSLLAAAPVAFLAGLISFLSPCVLPLVPGYLGYVSGLGGAALDGARRG
+RVALGAALFVLGFTVVFMVMNILFAQVAFRILRDLSWVMQLLGVLVILMGVVFMGGLRWF
+QTERKVHVKPAAGLTGAPLLGMTFGLGWAPCIGPTLAAVFALSYTQDSSSVARAALLAFV
+YCLGLGLPFVLISFGVERGMRALGFFRRHRRGVMVFGGAVLILLGAVMVTGLWTQWMVQL
+QTWFQNEWVMPL
+>PROKKA_01728
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRALGFFRRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001460.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001460.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4837dfb5c32a86d9c66ba6d945fc5c841bd86c12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001460.fa
@@ -0,0 +1,15 @@
+>PROKKA_01811
+MTADLPAATARVQLLVKPGCHLCAEAEATVVQVCDARGEAWEAVDGAAHPDLLERFVDEV
+PVLFVDGVQRDFWRVDPARLGRLLDAPRA
+>PROKKA_01508
+MTADLPAATARVQLLVKPGCHLCAEAEATVAQVCDARGEAWEAVDGAAHPALLERFADEV
+PVLFVDGVQRDFWRVDPARLGRLLDAPRA
+>PROKKA_01063
+MSTLLPASAARVQLLVKPGCHLCEDAAATVAQVCGARGEAWEAVDGAAHPDLLERFVDEV
+PVLFVDGVQRDFWRVDPARLGRLLDAPRP
+>PROKKA_00998
+MAAMMTPPASAARVQLLVKPGCHLCAEAEAVVAEVCDARGTAWERVDGPAHPDLLETYAE
+EVPVLFVDGVQRDFWRVDAQRLGRLLDGPAA
+>PROKKA_01732
+MTADLPAATARVQLLVKPGCHLCAEAEAAVAQVCDARGEAWEAVDGAAHPALLERFADEV
+PVLFVDGVQRDFWRVDPARLGRLLDAPRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001464.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001464.fa
new file mode 100644
index 0000000000000000000000000000000000000000..73b9d73af5779c9497a3f7ba65176d7d789668ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001464.fa
@@ -0,0 +1,25 @@
+>PROKKA_01815
+MADTPQRTDPNAPVLVVGLGRFGAATAEELVAQGREVLAVERDPVLVQRYAPSLTHVVEA
+DATDSEALRQLGAQDFSTAVVGVGTSIEASVLITVNLVDLEIPHIWVKAISEAHGTILKR
+IGANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLAESHVRSKY
+GVTVVGVKTPGEDFTYAQPDTRVGPRDTLIVSGHTDLIDRFAARP
+>PROKKA_01512
+MADTPQRTDPNAPVLLVGLGRFGAATAEELVAQGREVLAVERDPVLVQRYAPSLTHVVEA
+DATDSEALRQLGAQDFSTAVVGVGTSIEASVLITVNLVDLEIPHIWVKAISEAHGTILKR
+IGANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLAESKVRSKY
+GVTVVGVKTPGEDFTYAQPDTRVGPRDTLIVSGHTDLIDRFAARP
+>PROKKA_01059
+MADPQRTDPNAPVLVVGLGRFGAATAEELVAQGREVLAIERDPVLVQRFAPSLTHVVEAD
+ATDPEALRQLGAQDFSTAVVGVGTSIEASVLITANLVDLEIQHIWVKAISEAHGTILKRI
+GANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLGESNVRSKYG
+VTVVGVKTPGEDFTYAQPDTRVGARDTLIVSGHTDLIDRFAARP
+>PROKKA_00994
+MADQPRTDPNAPVLVIGLGRFGAATAEELVTQGREVLAIERDPVLAQRFAPTLTHVVEAD
+ATDAEALRQLGAQDFDVAVVGVGTSIEASVLITANLVDLEIPHIWVKAISDAHGTILKRI
+GAQHIIFPEKDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPTETVGFTLEESNVRQKYG
+VTIVGVKTPGEDFTYAQPHTRVGPRDTLIVSGHTDLIDRFAARP
+>PROKKA_01736
+MADTPQRTDPNAPVLVVGLGRFGAATAEELVAQGREVLAVERDPVLVQRYAPSLTHVVEA
+DATDPEALRQLGAQDFSTAVVGVGTSIEASVLITVNLVDLEIPHIWVKAISEAHGTILKR
+IGANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLAESHVRSKY
+GVTVVGVKTPGEDFTYAQPDTRVGPRDTLIVSGHTDLIDRFAARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001466.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001466.fa
new file mode 100644
index 0000000000000000000000000000000000000000..605fb59e8007b08462ea64371eeb9a15abc5d202
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001466.fa
@@ -0,0 +1,31 @@
+>PROKKA_01817
+MADATAHLAPAARFGADIPVTLSSSSVFPLGTQDVFATAEDLGYDGVEVMVTHNAWSQDA
+RRLTRLSERHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAATVVAHPPFRWQ
+GTYAVRFAEGIHELMAETGVVIAVENMYPWRAYGREAKMYLPHWNPLPEPYEHICWDFSH
+AAIARADSLAAVRELGPRLRHVHLTDGNDSGKDDHLVPGEGTQRVAETLRHLAAEGLAGA
+VCVEVGTRGVEYAGQREEKLAASLAFAREHLAAGGTDHHDDDGVPRPTTKETDRP
+>PROKKA_01514
+MPDSTAHLAPAARFGADIPVTLSSSSVFPLGTQDVFATAEDLGYDGVEVMVTHNAWSQDA
+RRLTRLSERHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAATVVAHPPFRWQ
+GTYAVRFAEGIHELMAETGVVIAVENMYPWRAYGRKAKMYLPHWNPLPEPYEHICWDFSH
+AAIARADSLAAVRELGPRLRHVHLTDGDDSGKDDHLVPGEGTQPVAETLRHLATAGLAGT
+VCVEVGTRGVEYAGQREEMLAASLAFAREHLAAGGTDHHHDGGVLRPTTKEMDRP
+>PROKKA_01053
+MAGSTAHLAPAPRFGSDIPVTLSSSSVFPLGTQDVFATAQDLGYDGVEVMVTHNAWSQDA
+DRLKRLSARHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAPVVVAHPPFRWQ
+GTYASGFAEGIHEIMADTGVVIAVENMYPWRAHGREATMYLPHWDPMPEPYEHVCWDFSH
+AAIAREDSLEALRRLGSRVRHIHLTDGNDSGKDDHLVPGEGTQKVAESVRHLAADGFAGT
+VCVEVGTRGVEYAGQREEKLAASLAFAREHLAAGGTKDDDGAPGA
+>PROKKA_00991
+MTGPSGAGSRPWDPHGRHLEPPLVSTAHLAPAPRFGAEIPVTLSSSSVFPLGTQDVFATA
+ADLGYDGVEVMVTHNATSQDARALARLSERTGMRIDSIHAPTLLFTQQVWGSAWSKIVRS
+VELARAVGAVTVVAHPPFRWQGSYASQFARRTAEIMEATGVVIAVENMYPWRAHGRDLTM
+YLPHWDPVPEPYEHVTWDFSHAAIAREDSLANIRGLGGRLRHVHLTDGVDGTKDAHLVPG
+EGTQNVAESLRFLGREGLAGTVCVEVGTRGVEYAGQREEKLSASLAFAREHLGQNDQSGR
+HES
+>PROKKA_01738
+MPDSTAHLAPAARFGADIPVTLSSSSVFPLGTQDVFATAEDLGYDGVEVMVTHNAWSQDA
+RRLTRLSERHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAATVVAHPPFRWQ
+GTYAVRFAEGIHELMAETGVVIAVENMYPWRAYGREAKMYLPHWNPLPEPYEHICWDFSH
+AAIARADSLAAVRELGPRLRHVHLTDGNDSGKDDHLVPGEGTQRVAETLRHLAAEGLAGA
+VCVEVGTRGVEYAGQREEKLAASLAFAREHLAAGGTDHHDDDGVPRPTTKETDRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001474.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001474.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0430e70749ab92bbfd391c8e25452ac79a1f00b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001474.fa
@@ -0,0 +1,19 @@
+>PROKKA_01825
+MTEHPTSASPSGRRTGARTAGRPRALRGGETGAVTAEYAVLLPVIAFVLVSVLLAGAAAV
+QQVRGQDAAASAARILARGDDEAAARDAVARMAGDDASLSHTVEGGWVTVEVVQPGPGPL
+AWAEVLTLTAHAAAPDQRPGTPAAGPEDRS
+>PROKKA_01522
+MTEHPTSAPPSARRTGARTAGRPRGLRGGETGAVTAEYAVLLPVIAFVLVSVLLAGAAAV
+QQVRGQDAAASAARILARGDDEAAARDAVARMAGDDASLSHTVEGGWVTVEVVQPGPGPL
+AWAEALTLTAHAAAPEQRPGTPAAGPEDRS
+>PROKKA_01044
+MTAEYAVLLPVIAFVLAAVLLAGAAAVQQVRGQDAATAAARILARGDGEAEARRAVARMA
+GDDAALAHTADGGWVAVEVSQPGPGPLAWAEALTLTARAAAPQQHPGAAVDPDGGRT
+>PROKKA_00983
+MADLPAEAPRPGRLRGARAGASGTVAFRDAERGEGERGAVTAEYAVLLPAAVAVLVAVLL
+AGVAAVHQVRAQDAAASAARILARGDAESLARDAVGRMAGGDAALEARTAEGWVTVTVTR
+PGPGPLAAVTLSAEAVAPVQATSPTPPGRTPGITAPTGEAAP
+>PROKKA_01746
+MTEHPTSASPSGRRTGARTAGWPRALRGGETGAVTAEYAVLLPVIAFVLVSVLLAGAAAV
+QQVRGQDAAASAARILARGDDEAAARDAVARMAGDDASLSHTIKGGWVTVEVVQPGPGPL
+AWAEALTLTAHAAAPDQRPGTPAAGPEDRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001479.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001479.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff14bfc2507e635587593f0cd85f4c59de8a293a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001479.fa
@@ -0,0 +1,30 @@
+>PROKKA_01831
+METEPTDTPTGETRLALVRRARRIDRILAETYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP
+ARLEDLVALPGVGRKTEFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA
+LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGEGETDPERARALLAYELK
+PGREELLELLRAGRTRRELRALGHGLEA
+>PROKKA_01528
+MEPEPTDTPTGETRLALVRRARRIDRILAETYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP
+ARLEDLVALPGVGRKTAFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA
+LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGEGETDPERARALLAYELK
+PGREELLELLRAGRTRRELRALGHGLEA
+>PROKKA_01037
+MDAEQADTPTGESRLALVRRARRIDRELAATYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAAAMAGASEAELQGLVRSTGFYRNKASAILRLSQELVERHGGEVP
+GRLEDLVALPGVGRKTAFVVLGNAFGRPGITVDTHFGRLARRLGFTQDTDPVKVEHAVAE
+LFPRRDWTMLSHRLIFHGRRICHARRPACGACPIARWCPSYGEGETDPEKARALLSYELK
+PGREELLALMRAGLSRRELRARGHGLDA
+>PROKKA_00977
+MAPADTTTPTGETPLALTRRARRIDRALAEAYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAVTPALFARFPDAVAMAGADEVELQELVRPTGFYKNKASAVLRLSRELVERFDGEVP
+DRLEDLVTLPGVGRKTAFVVLGNAFGRPGITVDTHFGRLARRLGFTEETDPVKVEHAVAA
+LFPPRDWTMLSHHLVFHGRRVCHARKPACGACPIARWCPSYGAGETEPEAARALLSYELK
+PGREELLARMRAGATRRQLRDEGWTLEA
+>PROKKA_01752
+METESTGTPTGETRPALVRRARRINRILAETYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP
+ARLEDLVALPGVGRKTAFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA
+LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGAGETDPERARALLAYELK
+PGREELLELLRAGRTRRELRALGHGLEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001480.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001480.fa
new file mode 100644
index 0000000000000000000000000000000000000000..053e1fd2d8acdea09a36f1134ef1e446940cdc46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001480.fa
@@ -0,0 +1,60 @@
+>PROKKA_01832
+MDEQIPTFPPPAEFAAQAVAGADLYEEAAEDRLAYWARRAREVLHWEQDFTDVLDWSDAP
+FAKWFVGGTTNAAYNALDRHVEAGHGDRVAIHFEGEPGDTRTYTYADLAAEVRRAANAFE
+SLGVTKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSSDALRSRVDDAEAKLVVT
+ADGSFRRGKPSMLKPAVDQALSAPGHTAEHVLVVRRNEAEVEMTEGRDLWWHDVVDAQSD
+EHELVWHDAEHPLYILYTSGTTGKPKGILHTTGGYLVQAAATHHDTFDLHPESDVFWCTA
+DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKYGVSILYTAPTAIRTFM
+KWGRHIPDEYDLSSLRVLGSVGEAINPEAWRWYHEVIGAGRCPIVDTWWQTETGAHMLTP
+LPGVTTLKPGSAQRPVPGVVLEVVDELGEPMTDTSAGFLVVREPWPSMLRGIWGDRERFK
+ETYWSRFPGMYFAGDGARYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPSVAES
+AVVGAKDETTGEAVVAFVLLTAVAVAADRDVAEVEEELRQHVGKDIGPIAKPKRVLVVPE
+LPKTRSGKIMRRLLKDVAEGRDPGDSTTLADPTVMQRIVETLAPKA
+>PROKKA_01529
+MDEQIPTFPPPAEFAAQAVAGADLYEEAAEDRLAYWARRAREVLHWEQDFTDVLDWSDAP
+FAKWFVGGTTNAAYNALDRHVEAGHGDRVAIHFEGEPGDTRTYTYADLAAEVRRAANAFE
+SLGVTKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSSDALRSRVDDAEAKLVVT
+ADGSFRRGKPSMLKPAVDQALSAPGHTAEHVLVVRRNEAEVEMTEGRDLWWHDVVDGQSD
+EHELVWHDAEHPLYILYTSGTTGKPKGILHTTGGYLVQAAVTHHDTFDLHPESDVFWCTA
+DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKYGVSILYTAPTAIRTFM
+KWGRHIPDEYDLSSLRVLGSVGEAINPEAWRWYHEVIGAGRCPIVDTWWQTETGAHMLTP
+LPGVTTLKPGSAQRPVPGVVLEVVDELGEPMTDTSAGFLVVREPWPSMLRGIWGDRERFK
+ETYWSRFPGMYFAGDGARYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPSVAES
+AVVGAKDETTGEAVVAFVLLTAVAVAADRDVAEVEEELRQHVGKDIGPIAKPKRVLVVPE
+LPKTRSGKIMRRLLKDVAEGRDPGDSTTLADPTVMQRIVETLAPKA
+>PROKKA_01036
+MDEQIPTFPPPAEFAAQAVAGADLYEEAAEDRLAYWARRAREVLHWEQDFTEVLDWSDAP
+FAKWFVGGTTNAAYNALDRHVEAGNGDRVAVHFEGEPGDTRTYTYAELASEVRRTANAFE
+SLGVAKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSADALRSRVDDAEAKLVVT
+ADGSFRRGKPSMLKPAVDEALSAPGHSVQHVLVVRRNEAEVSLVEGRDLWWHDVVPAQSD
+EHELVWHDAEHPLYILYTSGTTGKPKGILHTTGGYLVQTAATHHDTFDLHPETDVYWCTA
+DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKYGVSILYTAPTAIRTCM
+KWGRQIPDEYDLSSLRVLGTVGEAINPEAWRWYHEVIGGGRCPIVDTWWQTETGAHMLTP
+LPGVTTLKPGSAQTPVPGVTLEVVDEIGEPMKDTSAGFLVAREPWPSMLRGIWGNPERFK
+ETYWSRFPGMYFAGDGARYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPSVAES
+AVVGAADETTGEAVVAFVLLTEEAAAAGRDVAEVEEELRQHVGRDIGPIAKPKRVLVVPE
+LPKTRSGKIMRRLLKDVAEGRDPGDATTLADPTVMQRIVETLAPGA
+>PROKKA_00976
+MDETRATYPPSEQFAAQAVAGADLYEEAAADRLAYWARRAREHLHWEQDFTQVLDWSDAP
+FARWFADGTTNAAYNALDRHVEAGRGDRTAIVFEGEPGDTRTYTYADLAAEVRRAANAFE
+SLGVAKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSADALRSRVDDAEAKLVVT
+ADGSFRRGRPSMLKPAVDQALSAEGHTVEHVVVVRRNEADVDWTEGRDLWWHDVVPTASD
+EHEVVWHEAEHPLFILYTSGTTGKPKGILHTTGGYLVQTAATHHDTFDLHADTDVYWCTA
+DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKHGVTILYTAPTAIRTFM
+KWGRQIPDGYDLSSLRVLGTVGEAINPEAWRWFHDVIGGGRCPIVDTWWQTETGAHMLTP
+LPGVTELKPGSAQRPVPGVVLEVVDELGEPMEGSTAPGFLVAREPWPSMLRGIWGDPERF
+KETYWSRFPGMYFAGDGAQYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPKVAE
+SAVVGAADETTGEAVVAFVLLTEEATAAGEDVEAVQEELRQHVGKDIGPIAKPKRVLVVP
+ELPKTRSGKIMRRLLKDVAEGRRPGDATTLADPTVMDRITEAVGS
+>PROKKA_01753
+MDEQIPTFPPPAEFAAQAVAGADLYEEAAKDRLAYWARRAREVLHWEQDFTDVLDWSDAP
+FAKWFVGGTTNAAYNALDRHVEAGHGDRVAIHFEGEPGDTRTYTYADLAAEVRRAANAFE
+SLGVTKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSSDALRSRVDDAEAKLVVT
+ADGSFRRGKPSMLKPAVDQALSAPGHTAEHVLVVRRNEAEVEMTEGRDLWWHDVVDGQSD
+EHELVWHDAEHPLYILYTSGTTGKPKGILHTTGGYLVQAAVTHHDTFDLHPESDVFWCTA
+DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKYGVSILYTAPTAIRTFM
+KWGRHIPDEYDLSSLRVLGSVGEAINPEAWLWYHEVIGAGRCPIVDTWWQTETGAHMLTP
+LPGVTTLKPGSAQRPVPGVVLEVVDELGEPMTDTSAGFLVVREPWPSMLRGIWGDRERFK
+ETYWSRFPGMYFAGDGARYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPSVAES
+AVVGAKDETTGEAVVAFVLLTAVAVAADRDVAEVEEELRQHVGKDIGPIAKPKRVLVVPE
+LPKTRSGKIMRRLLKDVAEGRDPGDSTTLADPTVMQRIVETLAPKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001486.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001486.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f20092b08c2f96c331b013705ac7bea5526252a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001486.fa
@@ -0,0 +1,20 @@
+>PROKKA_01839
+MTEQSSAPTWGDGAVAARLAELGIDRPAVAAPVGSYVPALRDGDLVLTSGQLPFVAGALP
+ATGKVGAEVTPERAQELARACAVNAVAAVHELVGDLDRVAQVVKVVGFVASDPAFTGQPG
+VVNGASDVLAEIFGEAGRHARSAVGVAVLPMDAPVEVEITVRVR
+>PROKKA_01536
+MTAQSSAPAWGDGAVAARLAELGIDRPAVAAPVGSYVPALRDGDLVLTSGQLPFVAGALP
+ATGKVGAEVTPERAQELARVCAVNAVAAVHELLGDLDRVAQVVKVVGFVASDPAFTGQPG
+VVNGASDVLAEIFGEVGRHARSAVGVAVLPMDAPVEVEITVRVR
+>PROKKA_01029
+MAEKAQAPTWGEGAVADRLAELGLERPAVAAPVGSYVPAIRDGDLVLTSGQLPFVAGSLP
+ATGKVGAEVSAERAQELARVCAVNAVAAVHELIGDLDRVAQVVKVVGFVASDPSFTGQPG
+VLNGASDVLAEIFGEAGRHARSAVGVAVLPLDAPVEVEITVRVR
+>PROKKA_00970
+MAGQNAWGGGPAAERLAALGIERPAVAAPVGSYVPAVRDGDLVLTSGQLPFVAGALPRTG
+KVGAEVTLEQAQELARTAAVNAVAAVHELVGDLEAVVQVVKVVGFVASAPDFTAQPAVVN
+GASDVLAEIFGEAGRHARSAVGVAVLPLDSPVEVEITVRVR
+>PROKKA_01760
+MTAQSSAPAWGDGAVAARLAELGIDRPAVAAPVGSYVPALRDGDLVLTSGQLPFVAGALP
+ATGKVGAEVTPERAQELARVCAVNAVAAVHELLGDLDRVAQVVKVVGFVASDPAFTGQPG
+VVNGASDVLAEIFGEVGRHARSAVGVAVLPMDAPVEVEITVRVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001487.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001487.fa
new file mode 100644
index 0000000000000000000000000000000000000000..536b2cb945a2c857fb471b74b2b190766287e361
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001487.fa
@@ -0,0 +1,10 @@
+>PROKKA_01840
+MTQQTQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGNNPVAYLKRPKAA
+>PROKKA_01537
+MTQQTQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGNNPVAYLKRPKAA
+>PROKKA_01028
+MTEQTKWEYATIPLLIHATKQILDQWGEDGWELVAVVPGPDGPNPVAYLKRPKAA
+>PROKKA_00969
+MTQRIQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGANPVAYLKRPKDA
+>PROKKA_01761
+MTQQTQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGNNPVAYLKRPKAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001491.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001491.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38b7feee2eac7966296ca6b06736a41afde9743f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001491.fa
@@ -0,0 +1,50 @@
+>PROKKA_01847
+MKTLVLGNGGREHALLTALSRDPQVSALHAAPGNAGMADLATLHAVEATDPAAVVELARE
+LGADLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGS
+RVCTTAAEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAEACFAAGGTVVIED
+FLDGPEVSLFVICDGEDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFTDEVM
+DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLETPLGG
+LLADAAAGRLGADRRLEWSDDVAVDVVMASAGYPASSSTGDVITGLADAAALEGVHVIHA
+GTAASGEDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI
+TVPGTGGAK
+>PROKKA_01543
+MKTLVLGNGGREHALLTALSRDPQVSALHAAPGNAGMADLATLHAVEATDPAAVVELARE
+LGADLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGS
+RVCTTAAEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAEACFAAGGTVVIED
+FLDGPEVSLFVICDGEDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFTDEVM
+DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLETPLGG
+LLADAAAGRLGADRRLEWSDDVAVDVVMASAGYPASSSTGDVITGLADAAALEGVHVIHA
+GTAASGEDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI
+TVPGTGGAK
+>PROKKA_01021
+MKTLVLGNGGREHALLAALSRDPQVGELHAAPGNAGMAALAALHAVEATDPDAVVALARE
+LAADLVVVGPEAPLAAGVSDALREAGFAVFGPSRAAAQLEASKAFAKEVMAAAGVPTAGS
+RTCATAEEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAQACFDAGGTVVIED
+FLDGPEVSLFVVCDGTDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFAEEVM
+DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLTTPLGG
+LLADAAAGRLGADRALEWSDDVAVDVVMASAGYPATSSQGDVITGLTDAEALEGVHVIHA
+GTATSGDDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI
+AVPAAVGQAGQAGEDAR
+>PROKKA_00963
+MKILVLGNGGREHALLRALSRDPQVGELHAAPGNAGMADAAVLHPVTATDPEAVVALARD
+LAVDLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGA
+RVCATEAEVDAALTAFGAPHVVKDDGLAAGKGVVVTSDRAAALDHARACLSAGGTVVVED
+FLDGPEVSLFVLCDGEHAVPLTPAQDFKRIHDGDAGPNTGGMGAYTPLQWLPEGFVDEVM
+ERVARPVLAEMSRRDTPFAGVLFIGLAVTENGPEVIEFNVRFGDPETQSVLARLETPLGQ
+LLADAAAGRLGADRELRWSDDVAVDVVLASAGYPASSHSGDVIAGLEDALALEGVDVLHA
+GTARTEDGDVVTAGGRVLAVVGRGATLEQARERAYAGVAKIRFDGAQHRTDIAIKAERGE
+ITVPERRRGYAGAEALELPGWRHVYSGKVRDLYEPADAEPGTSETLLVVASDRISAYDFV
+LEPPIPGKGAVLTRLSLWWFEQLAGVANHVVSTDVPAEVAGRAMVVKRLDMHPIECIARG
+YLTGSGLAEYREHATVTGIPLPDGLVDGSRLEPPIFTPSAKAEVGEHDENITFEQTVERV
+GAPTAEALRAATLEVYTRAEAIARKAGIILADTKVEFGADPVTGELVLGDEVLTPDSSRF
+WDAEAYEPGRAQASFDKQFVRDWLTSPESGWDRTSGEEPPALPADVVERTRARYVEAYER
+LTGRRFEA
+>PROKKA_01767
+MKTLVLGNGGREHALLTALSRDPQVSALHAAPGNAGMADLATLHAVEATDPAAVVELARE
+LGADLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGS
+RVCTTAAEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAEACFAAGGTVVIED
+FLDGPEVSLFVICDGEDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFTDEVM
+DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLETPLGG
+LLADAAAGRLGADRRLEWSDDVAVDVVMASAGYPASSSTGDVITGLADAAALEGVHVIHA
+GTAASGEDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI
+TVPGTGGAK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001493.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001493.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f6b87cbe6e3e866ac5546043c290fb0a2288dfd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001493.fa
@@ -0,0 +1,25 @@
+>PROKKA_01849
+MSVRVMLVDDHPVVRAGVRAVVEAHPDLTVVAEAADGAEAIGVLEAGEPAVDVVLMDLQM
+GAGMDGVTATRAVRERWPGVQVLILTTFDTEADILAAVNAGAAGYLLKDAPSEEIASAVR
+QAAAGRKALAPQVAATLMGRMSGGSEVLSEREIQLLELIARGATNKVAAKELFISEATVK
+THLVHIFQKLGVDNRTRAVDEARRRRIIR
+>PROKKA_01545
+MSARVMLVDDHPVVRAGVRAVVEAHPDLTVVAEAADGAEAIGVLEAGEPAVDVVLMDLQM
+GAGMDGVTATRAVRERWPGVQVLILTTFDTEADILAAVNAGAAGYLLKDAPSEEIASAVR
+QAAAGRKALAPQVAATLMGRMSGGSEVLSEREIELLELIARGATNKVAAKELFISEATVK
+THLVHIFQKLGVDNRTRAVDEARRRRIIR
+>PROKKA_01019
+MTVHVMLVDDHPVVRAGVRAVVEAHPDLRVVAEAADGAEALRILEAASGPVDVVLMDLQM
+GEGMDGVSATRAVRERRPDVQVLILTTFDTEADILAAVDAGAAGYLLKDAPSEEIARAVR
+QAAAGQKALAPQVAATLMGRMAGGADVLSAREIELLELIARGATNKAAAKELFISEATVK
+THLVHVFQKLGVDNRTRAVDEARRRRIIR
+>PROKKA_00961
+MSVRVMLVDDHPVVRAGVRAVLEADPELTVVAEAGDGAAALDVLQARPGEVDAVLMDLQM
+GEGMDGVSATRRLRAAHPGIPVLILTTFDTEADILAALDAGAAGYLLKDAPAEQIADAVH
+RAVAGRPALTPDVAERLLGRTTGATAASALSAREIELLELIARGDTNREAARALFLSEAT
+VKTHLVHIFQKLGVDTRTQAVHEARARRIIR
+>PROKKA_01769
+MSVRVMLVDDHPVVRAGVRAVVEAHPDLSVVAEAADGAEAIGVLEAGEPAVDVVLMDLQM
+GAGMDGVTATRAVRERWPGVQVLILTTFDTEADILAAVNAGAAGYLLKDAPSEEIASAVR
+QAAAGRKALAPQVAATLMGRMSGGSEVLSEREIQLLELIARGATNKVAAKELFISEATVK
+THLVHIFQKLGVDNRTRAVDEARRRRIIR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001496.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001496.fa
new file mode 100644
index 0000000000000000000000000000000000000000..435798b74e9e5ebc8bdda8df9727a3eee5351bc8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001496.fa
@@ -0,0 +1,35 @@
+>PROKKA_01853
+MTHATVAPAGETLALSDAVELVETVRNGFVESRTAGAAVVTGPDGRVLAGLGPADALIYP
+RSTLKPFQAVASLRHGAALEGEALSIACGSHRGTLRHQALAERMLADAGLDASALQCPPA
+WPADTSEVVAQVRRDGESAAATPLAFNCSGKHAGFLAACAASGHDVATYLDPAHPLQREV
+DAVIAEYCGEPVAHTGVDGCGAPAAVISLAGLARGIGRVAAAPGRADADPHAAAVATAML
+EHPWAVHGETSSNTVVMRELGLLAKAGADGVLVMAAPDGTAVAVKALDGGTRAGDLVALA
+LLARFAPDHVDRATLPGVLAAVVPPVLGRGEPVGEIRLAAPVRDLVGDVLPAFEARA
+>PROKKA_01549
+MTHATIAPAGETFALSDAVELVETVRNGFVESRTAGAAVVTSPDGRVLAGLGPADALIYP
+RSTLKPFQAVASLRHGAALEGEALSIACGSHRGTLRHQALAERMLADAGLDASALRCPPA
+WPADTSEVVAQVRRDGESAAATPLAFNCSGKHAGFLAACAASGHDVATYLDPAHPLQREV
+DAVIAEYCGEPVAHTGVDGCGAPAAVISLAGLARGIGRVAAAPGRADADPHAAAVATAML
+EHPWAVHGETSSNTVVMRELGLLAKAGADGVLVMAAPDGTAVAVKALDGGTRAGDLVALA
+LLARFAPDHVDRATLPGVLAAVVPPVLGRGEPVGEIRLAAPVRDLVGDVLPTFEARA
+>PROKKA_01015
+MTQTPSATFALADAVELVHVVRNGFVESRTPGAAVVTGPDGTVLAALGPVDALIYPRSTL
+KPFQAIASLRHGARLEGQEVAIACGSHRGTAAHRELAARILAEAGLSAADLQCPPDYPAD
+AAEIVRFAQDLEHGAEKTPLAYNCSGKHAGFLAACVAAGHEVGTYLEPDHPLQAEVERVI
+EEYCGEPVAHTGTDGCGAPAAVLSLTALARGIGKVASAPSRRDAEIHAATVANAMLEHPW
+AVHGQSSSNTVVMRELGLLAKLGADGVMVMAAPDGTAVAVKALDGGTRAGNLVALALLAQ
+FAPDHVDADRLPAVLETVAPKILGKGEPVGAVRLARPVLDLLD
+>PROKKA_00957
+MTQTSAAPAGQTFALADAVELVEVVRGGFVESRTAGAAVVTGPDGEVLAALGPADALVYP
+RSTLKPFQAIASLRHGARLEGEALAIACGSHTGSEAHQQLAARVLADHGLAPEALQCPSA
+LPEVAGEVARLAAQAGTAEIATPLAYNCSGKHAGFLAACAASGHDVGTYLDPEHPLQREV
+DAVIAEYCGEPVAHTGVDGCGAPAAVVSLAGLARGIGAVSKAPGREGAEPHAAAVARAML
+AHPWAVQGPGKANTVVMEELGLVAKLGADGVMVMGAPDGTAVAVKALDGGTRAGNLVALA
+LLGRFAADQVDAGRLAEVSARVAPSILGRGAPVGEVRLAAPVRQLVGA
+>PROKKA_01773
+MTHATVAPAGETFALSDAVELVETVRNGFVESRTAGAAVVTGPDGRVLAGLGPADALIYP
+RSTLKPFQAIASLRHGAALAGEALSIACGSHRGTLRHQALAERMLADAGLDASALRCPPA
+WPADTSEVVAQVRRDGEAAAATPLAFNCSGKHAGFLAACAASGHDVATYLDPAHPLQREV
+DAVIAEYCGEPVAHTGVDGCGAPAAVISLAGLARGIGRVAAAPGRADADPHAAAVATAML
+EHPWAVHGETSSNTVVMRELGLLAKAGADGVLVMAAPDGTAVAVKALDGGTRAGDLVALA
+LLARFAPDHVDRATLPGVLAAVVPPVLGRGEPVGEIRLAAPVRDLVGDVLPAFEARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001497.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001497.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2733cedaf6f293aa876c5f56dd50fe48ddb1332a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001497.fa
@@ -0,0 +1,20 @@
+>PROKKA_01854
+MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRATAVRFALEELATRVPGN
+SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTTWEDATAAGGVRASGV
+RADLGAHLPLVRP
+>PROKKA_01550
+MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRAMAVRFALEELATRVPGN
+SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTSWDEATAAGGVRASGV
+RADLGAHLPLVRP
+>PROKKA_01014
+MTTGSVPRRRIPVPEGHAALTSWARTHAQDPAAAAALPRSTRATAVRFALEELATRVPGN
+AVEVRVPPFGVAQAIPGPRHTRGTPPNVVEMDAVTWLSLATGLLGWADAVGTGAVRASGT
+RADLGAHLPLIRP
+>PROKKA_00956
+MTTGSVPKRRVPVVEGHAALTAWARAHAEDPAAAAALPRSTRATAVRFALEELATRAPGN
+SVEVRVPPFGVAQCIPGPRHTRGTPPNVVETDPVTWLSLATGLTRWNDAVASGAVRASGV
+RADLAGHLPLVRP
+>PROKKA_01774
+MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRAMAVRFALEELATRVPGN
+SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTTWEDATAAGGVRASGV
+RADLGAHLPLVRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001498.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001498.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7acd425b91cbe3124c766f52629beed3957c2201
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001498.fa
@@ -0,0 +1,20 @@
+>PROKKA_01855
+MTSAPEPTPDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYSGIPL
+SFSETFGFASLLSMLGTSVLGLLVWLLLDRRSRSTARTVVLERTDDPAVADVRLDRVDAG
+APPARTTPTERTPEQ
+>PROKKA_01551
+MTSAPEPTPDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYSGIPL
+SFSETFGFAALLSMLGTGVLGLIVWLLLDRRSRSTARTVVLERTDDPAVADVRLDRVDAG
+TPPARTTSTERTPEQ
+>PROKKA_01009
+MTTGPERSQHQHAYTVRRAPRLAAVLAVALALGLVIALVITTAVHGSPTPPADPYSGIPL
+SFSETFGFAALLSMLGTGVLGLVVWLLLDRRSRATTRTVVLERTDDPAAADIRLDRSAAD
+ALRSRTAPTERTPEQ
+>PROKKA_00953
+MTSGPERSTPSAPQQQEYVLRRAPRLSAAVIVSALVGVVLALLGTAAVHAGPQPPADPYS
+GMPLSFASTFGYMVVAAVLACLVLGLLVWLLLDRRSRRTQRTVLLERTDDPAAADVALPR
+PEAVAPAARPAADPSDGRTPEQ
+>PROKKA_01775
+MTSAPEPTPDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYSGIPL
+SFSETFGFASLLSMLGTSVLGLLVWLLLDRRSRSTARTVVLERTDDPAVADVRLDRVDAG
+APPARTTPTERTPEQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001500.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001500.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75febb07f7b8f719898f48870940b0598afa2ca2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001500.fa
@@ -0,0 +1,40 @@
+>PROKKA_01857
+MTPNQTPSSAAPITYASAGVDVEAGDRAVELMKDAVKATHTPEVMGGIGGFAGMWDASAL
+LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGAQPLFMTDYIACG
+KVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLAADEYDVAGAATGVVEADMVLGA
+ERVQSGDVVIGMASSGIHSNGYSLVRRVVNAAGWSLDREVTELGCTLGEELLVPTRIYSR
+ACLDLVQRLNGHEGGSDLPVRAFSHVTGGGLAANLARVLPQGLMATVERDTWSLPPVFRL
+VGELGRVPQSDLERTLNLGVGMVAVVDPEVAATSISVLVDAGIDAWEMGTIGALTDDAAA
+AGLNFVQGAKGVDGGAVLMRGQYAA
+>PROKKA_01553
+MTPNQTPSSAAPITYASAGVDVEAGDRAVELMKDAVKATHTPEVMGGIGGFAGMWDASAL
+LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGAQPLFMTDYIACG
+KVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLAVDEYDVAGAATGVVEADMVLGA
+ERVQSGDVVIGMASSGIHSNGYSLVRRVVNAAGWSLDREVTELGCTLGEELLVPTRIYSR
+ACLDLVQRLNGHEGGSDLPVRAFSHVTGGGLAANLARVLPQGLMATVERDTWSLPPVFRL
+VGELGRVPQSDLERTLNLGVGMVAVVDPEVAATSISVLVDAGIDAWEMGTIGALTDDAAA
+AGLDFVHGAKGVDGGAVLMRGQYAA
+>PROKKA_01007
+MTENQNTAHDAPITYASAGVDVEAGDRAVELMKDAVKATHSPEVMGGIGGFAGMWDASAL
+LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGATPLFMTDYIACG
+KVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLGVDEYDVAGAATGVVDADMVLGA
+DRVQTGDVLIGMASSGIHSNGYSLVRRVVNAAGWSLDREVSELGRTLGEELLEPTRIYAR
+SCLDLVQRLNGHDGGSGLPVRAFSHVTGGGLAANLARVLPQGLMATVERETWSLPPVFRL
+LAEAGRVPQPDLERTLNLGVGMVAVVDPEIAAKSISVLVDAGIDAWEMGTIGHVTDEAAG
+AGLDFVQGAKGVDGGAVLMRGAYAA
+>PROKKA_00951
+MTDAPRTETQTADALDAPLTYAAAGVDVEAGDRAVELMKDAVKATHTAEVLGGVGGFAGM
+WDASALTGYRKPLLATSTDGVGTKVAIAQALDRHDTIGQDLVGMVVDDIVVVGAKPLFMT
+DYIACGKVVPERVADIVRGVAEGCRLAGTALVGGETAEHPGLLAVDEYDVAGAATGVVEA
+DRVLGAERVRSGDVVIGMASSGIHSNGYSLVRRVINAAGWQLDRDVDELGRTLGEELLEP
+TRIYTRACLDLMDSLNGTEGGADLSLRGFSHVTGGGLAANLARVLPQGMMATVDRGTWAL
+PPVFRLVGELGRVPLADLERTLNLGVGMVAVVAADAADRAVAAIEAAGIPAWVMGGIDEV
+TEQAQAAGEDYVQGAKGVDGGAVLMTGTYAD
+>PROKKA_01777
+MTPNQTPSSAAPITYASAGVDVEAGDRAVELMKDAVKATHTPEVMGGIGGFAGMWDASAL
+LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGAQPLFMTDYIACG
+RVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLAAEEYDVAGAATGVVEADMVLGA
+ERVQSGDVVIGMASSGIHSNGYSLVRRVVNAAGWSLDREVTELGCTLGEELLVPTRIYSR
+ACLDLVQRLNGHDGGSDLPVRAFSHVTGGGLAANLARVLPQGLMATVERDTWSLPPVFRL
+VGELGRVPQSDLERTLNLGVGMVAVVDPEVAATSISVLVDAGIDAWEMGTIGALTDDAAA
+AGLDFVQGAKGVDGGAVLMRGQYAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001502.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001502.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b44f5dc5036ef5f11ed68d09110bd3c9f836387e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001502.fa
@@ -0,0 +1,35 @@
+>PROKKA_01859
+MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLMEESRPLVITGAGVSTDS
+GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNEAHRILARWA
+AEGRIAGVLTQNVDGLHAEAGRAAGMPEDRLIELHGDLARVACLNCGATESRRDLDLRLE
+AANPGYLERVAIDPDAVNPDGDVSLDQHWVEEFTMVGCRVCGSVKLKPDVVYFGESVPPA
+RRAAAEAMADDGGTVLAVGTSLAVMSGYRFVLRAERAGHETGLINLGPTRADAKARWRWR
+APVADALAWLDARL
+>PROKKA_01555
+MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLMEESRPLVITGAGVSTDS
+GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNEAHRILARWA
+AEGRIAGILTQNVDGLHAEAGRAAGMPEDRLIELHGDLARVACLNCGATESRRDLDLRLE
+AANPGYLERVAIDPDAVNPDGDVSLDQHWVEEFTMVGCRVCGSVKLKPDVVYFGESVPAA
+RRAAAEAMADDGGTVLAVGTSLAVMSGYRFVLRAERAGHETGLINLGPTRADAKARWRWR
+APVADALAWLDARL
+>PROKKA_01004
+MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLLEETRPLVITGAGVSTDS
+GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNAAHRILAGWA
+VRGLVSGILTQNVDGLHAQAAAEAGAPEDRLIELHGDLARVVCLHCGATESRRDLDVRLE
+AANLGYLERVSIDPEAVNPDGDVTLDRHWVDEFAMVGCLRCGSVELKPDVVYFGESVPVA
+RREAAEAMADDGGAVLAVGTSLAVMSGYRFVLRAERAGKDTGLINLGSTRADPKASWRWR
+APVADALAWLDSRL
+>PROKKA_00947
+MTPVRHPSQDGHQAALRSIARVVGETAPLQDPETASRGLLRMLEAGRPLVITGAGVSTDS
+GIPDYRGPNGTLHRHRPMTYQEFRDDPAARHRYWARSFVGWRHMDEAAPNAAHHVLADWV
+RRDVVAGIVTQNVDGLHAQAFAAAGAAPSRLIALHGDLARVVCLQCGAMEDRTSLDARLA
+AANPGYLEAVTVDPDAVNPDGDVTLDQRWVDAFTMVGCRVCGSVQLKPDVVYFGENVPPA
+RRDAARALAEEADSVLAVGTSLAVMSGFRFVLDAERAGKEVGVITLGPTRADPKAQWRWR
+TRVAEALAWLDARL
+>PROKKA_01779
+MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLMEEFRPLVITGAGVSTDS
+GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNEAHRILARWA
+AEGRIAGILTQNVDGLHAEAGRAAGMPEDRLIELHGDLARVACLNCGATESRRDLDLRLE
+AANPGYLERVAIDPDAVNPDGDVSLDQHWVEEFTMVGCRVCGSVKLKPDVVYFGESVPAA
+RRAAAEAMADDGGTVLAVGTSLAVMSGYRFVLRAERAGHETGLINLGPTRADAKARWRWR
+APVADALAWLDARL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001504.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001504.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bcfc4399b77c7fee4c7006fac959f652b30c9230
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001504.fa
@@ -0,0 +1,46 @@
+>PROKKA_01861
+MRRTPTLLAAATLAATLTAAPVSLAAPAAPAAPAKAPMGTTQTADRGLGPGQNRAGGNPN
+SPKKLVRSISSDHLRQDITAFAAIADEHGNRAAGTPGFQASLDYAVGELEEAGYDVELQE
+FEITYTETLRDRLQQTGPVQRDLEHTVFTSSPSAQVTDAPLAAPAGAATGCADADWAGAD
+LTGSVALVSRGDCTFAQKSQVAAASGAEAVIIYNNAEGALNGTLGAAPGDVVGTVGVTRE
+LGADLLAQTRAGGATVTLDLEQLVEQRPTWNVLAETRTGSDDDVVMLGAHLDGVPEGPGI
+HDNASGVAATLEVARQAAKANKAESKVRFALWGAEEIGLLGSHHYVDTLTAAEREDIILY
+TNLDMVAPLDHQNTLGVLTADWSIGAESLLGAQLDRDGHGHQPEGSNGRSDYAPFVDAGI
+ASTGLLSIRDDNYHTPQDDIDNVSITTLTHTARAVANLIGTLQQDADALGTR
+>PROKKA_01557
+MGYVAYVTSTPTMRMPMRRTPTLLAAATLAATLTAAPVSLAAPAAPAKAPVATTQTADRG
+LGPGQNRAGGSTNSPKKLVRSISSDHLRQDIEAFAAIADEHGNRAAGTPGFQASLDYAVG
+ELEEAGYDVELQEFEITYTETLRDRLQQTGPVQRDLEHTVFTSSPSAQVTDAPLTAPAGA
+ATGCADADWAGADLTGSVALVSRGDCTFGQKSQVAAASGAEAVIIYNNAEGALNGTLGTE
+PGDVVGTVGVTRELGADLLAQTRAGGATVTLDLEQLVEQRPTWNVLAETRTGSDDDVVML
+GAHLDGVPAGPGIHDNASGVAATLEVARQAAKANKAESKVRFALWGAEEIGLLGSHHYVD
+TLTAAEREDIILYTNLDMVAPLDHQNTLGVLTADWSIGAESLLGAQLDRDGHAHQPEGSN
+GRSDYAPFVDAGIASTGLLSIRDDNYHTPQDDIDNVSITTLTHTARAVANLIGTLQQDAD
+ALGTR
+>PROKKA_00999
+MSMRRRPALLAASVLAASLAVAPAAAAIPGHAAGGPAPAASAADRAGGNPNSPEKLVAAI
+SAANLERDIRAFADIAEEHGNRAAGTPGYDASVDYAVAELEKAGYDVELEEFEITYTETL
+RNEFTQEGPVQRELPHEVLTYSPSATAESAQLAVPTGALGCTTADWGGADLTGRIALVSR
+GECPFAQKSTTAAELGAEAVVIYNNADGPLNGTLGAPSDDYVGTVGITRDLGQELVAQAA
+AGPVTVSLDLEQLVEQRPTVNILAETRTGRDDNVVMVGAHLDGVPAGPGIHDNASGSAVT
+LEVARQMAKVNKTGNTVRFALWGAEEIGLLGAAHHVAELSQSERDAIAMYVNLDMVAPLD
+HQNTLGVLTGDFSLGAESFLQEQLERDGHEHGPAGNGGNSDYAPFVAAGIPATGLLSYRD
+DNYHTAQDDIENVSITSLTHSARAVANLVGTFMHDTSSVNDKCNAGKSGKPKQC
+>PROKKA_01510
+MSTSSLSRRSFLALAGAAGAAGAFAMPAWGLDDVRPGAARAPRLTGQDRQIINQIRPARA
+VDHLTLLTEEIGQRYTGTPAEHRAADYIAAQLEGYGYDVELEWFDVPDRRVGLLEAPELD
+GRWSWGVGSAAAAAQDVTVAGRVVLAPSGSVADLTGMVLMRVVTASEDITPLAVAAQARG
+AVAVIATRRDSNPPGQASAFAPALTTARLDIPVVGVSQVQKHALLGVLAAGPLRLTVSTV
+EHRGTRSANVVGTRAGRKGPGKGGRERVMLGAHYDSVIGSRGANDNASGTAACLELARVM
+RNAPTAADLSFGFWGSEEVGLVGSRIHAQAMPADERSRLRGVFNNDMIATSWDPAEKYWL
+LDLRGEANDVNRAVYAAGERLGYRTSMSDLFTMGRSDHQSFSEIGVPSGNFGWLHRDGFI
+LEPEYHSSDDTVKENISVERLMAAMEIQGCAAYALASR
+>PROKKA_01781
+MRRTPTLLAAATLAATLTAAPVSLAAPAAPAAPAKASAATAQTADRGLGPGQNRAGGNPN
+SPEKLVRSISSDHLRQDIEAFAAIADEHGNRAAGTPGFQASLDYAVGELEEAGYDVELQE
+FEITYTETLRDRLQQTGPVQRDLEHTVFTSSPSAQVTDAPLAAPAGAATGCADADWAGAD
+LTGSVALVSRGDCTFAQKSQVAAASGAEAVIIYNNAEGALNGTLGAAPGDVVGTVGVTRE
+LGADLLAQTRAGGATVTLDLEQLVEQRPTWNVLAETRTGSDDDVVMLGAHLDGVPEGPGI
+HDNASGVAATLEVARQAAKANKAESKVRFALWGAEEIGLLGSHHYVDTLTAAEREDIILY
+TNLDMVAPLDHQNTLGVLTADWSIGAESLLGAQLDRDGHTHQPEGSNGRSDYAPFVDAGI
+ASTGLLSIRDDNYHTPQDDIDNVSITTLTHTARAVANLIGTLQQDADALGTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001505.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001505.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d99803e69456bb7bbbc2d0bc11d79c16d9bd5016
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001505.fa
@@ -0,0 +1,80 @@
+>PROKKA_01862
+MDAKFTTKSQEALSAAAMNASTAGNPQVEPAHLLKALMDQRESVAVAVLKAAGADPDAVS
+TAASSAIRRLPSTQGSTVAQPQFSRAALQVVQNARTQAEQRSDEFVSTEHLLLGVAADSG
+EAGEALRSNGASLEALAAALTLVRGDSRVTTQDPETTFQSLEKYGTDLTEIARSGKLDPV
+IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL
+DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK
+PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVFVGEPSVDDTIAILRGLKERYEAH
+HKVAIADSALVAAATLSHRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD
+RLTMEELALEGETDPASIERLDALRAEKADREEELTALTARWDAEKATLNQAGDLRAKVD
+ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSATEPMVSEEVTADD
+IAEVVSAWTGIPAGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN
+RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG
+YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI
+LTSNLGSQFLVDPTLDEAAKRESVMSVVRGAFKPEFLNRLDEIVQFDALTVAELTRIVDL
+QVESLQARLTDRRLTLEVSDAAKAWLAATGFDPAYGARPLRRLVQREIGDRLARGILAGE
+IADGDTVVVDRVEGENGLTVTRKG
+>PROKKA_01558
+MDAKFTTKSQEALSAAAMNASTAGNPQIEPAHLLKALMDQRESVAVAVLKAAGADPDAVS
+TAASSAIQRLPSTQGSTVAQAQLSRAALQVVQNARTQAEQRSDQFVSTEHLLLGVAADPG
+EAGEALRSNGASLEALAAALTQVRGDSRVTTQDPETTFQSLEKYGTDLTELARSGKLDPV
+IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL
+DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK
+PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVYVGEPSVDDTIAILRGLKERYEAH
+HKVAIADSALVAAAALSDRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD
+RLTMEELALEGETDPASVERLEALRAEKADREEELTALTARWDAEKATLNEAGDLRAKVD
+ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSSTEPMVSEEVTADD
+IAEVVSAWTGIPSGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN
+RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG
+YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI
+LTSNLGSQFLVDPTLDEAAKRESVMSVVRAAFKPEFLNRLDEIVLFDALTVDELTRIVDL
+QVESLQARLTDRRLTLEVSDAAKAWLAETGFDPAYGARPLRRLVQREIGDQLARGILAGE
+IADGDTVVVDRVEGENGLTVTRKG
+>PROKKA_00998
+MDAKFTTKSQEALSAAAMNASTAGNPQIEPAHLLKALMDQRESVAVAVLKAAGADPDAVS
+TAASSAIRRLPSTQGSTVAQAQLSRAALQVVQNARTQAEQRSDQFVSTEHLLLGVAADPG
+EAGEALRSNGASLEALAAALTQVRGDSRVTTQDPENTFQSLEKYGTDLTEVARSGKLDPV
+IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL
+DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK
+PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVYVGEPSVDDTIAILRGLKERYEAH
+HKVAIADSALVAAATLSHRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD
+RLTMEELALEGETDPSSVERLEALRAEKADREEELTALTARWDAEKATLNEAGDLRAKVD
+ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSTTEPMVSEEVTADD
+IAEVVSAWTGIPAGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN
+RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG
+YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI
+LTSNLGSQFLVDPTLDEAAKRESVMSVVRAAFKPEFLNRLDEIVQFDALTVAELTRIVDL
+QVESLQARLTDRRLTLEVSDAAKAWLAETGFDPAYGARPLRRLVQREIGDRLARGILAGE
+IADGDTVVVDRAEGEEGLTVASA
+>PROKKA_00945
+MNPSPQFTTKSQEALSAAAMNASTASNPAVEPAHLLKALMDQRDSVAVAVLKAAGADPDV
+VSVAASTAIHGLPKASGATVSEARLSPAAGAVVKAAQQQASAHGDEYVSTEHLLLGLAAD
+GGEAGRALTDAGASLAALQAAFTQVRGDERVTTPDPEATFQSLEKYGTDLTAVARSGKLD
+PVIGRDQEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLI
+SLDLGAMIAGAKYRGEFEERLKSVLEEIKKSDGQIVTFIDEIHTVVGAGASEGAMDAGNM
+LKPMLARGELRLIGATTLDEYRENIEKDPALERRFQQVYVGEPSVDDTIAILRGLKERYE
+AHHKVAIADSALVAAATLSDRYISGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDALRRQ
+VDRITMEELALDGESDPGSVERLAGLRAEKADKEEELRALTARWEAEKASLNEAGDLRAR
+VDELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAQEGQQGDVEAMVSENVTA
+DDIAEVISAWTGIPAGRMLASETEKLLSMEEHLGDRLIGQKDAVRAVSDAVRRARAGIAD
+PNRPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHAVSRLVGAPPGY
+VGYDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVI
+LILTSNLGSQFLVDQTMPEQARKDAVMDVVRAAFKPEFLNRLDEIVTFDALGVEDLARIV
+DLQVASLGERLQQRRLTLDVTDAAREWLALTGYDPAYGARPLRRLVQREIGDQLARALLS
+GAVQDGDTVVVDRAGEDTADGLTVAARRA
+>PROKKA_01782
+MDAKFTTKSQEALSAAAMNASTAGNPQVEPAHLLKALMDQRESVAVAVLKAAGADPDAVS
+TAASSAIRRLPSTQGSTVAQPQFSRAALQVVQNARTQAEQRSDEFVSTEHLLLGVAADSG
+EAGEALRSNGASLEALAAALTLVRGDSRVTTQDPETTFQSLEKYGTDLTEIARSGKLDPV
+IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL
+DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK
+PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVFVGEPSVDDTIAILRGLKERYEAH
+HKVAIADSALVAAATLSHRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD
+RLTMEELALEGETDPASIERLDALRAEKADREEELTALTARWDAEKATLNQAGDLRAKVD
+ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSATEPMVSEEVTADD
+IAEVVSAWTGIPAGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN
+RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG
+YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI
+LTSNLGSQFLVDPTLDEAAKRESVMSVVRGAFKPEFLNRLDEIVQFDALTVAELTRIVDL
+QVESLQARLTDRRLTLEVSDAAKAWLAATGFDPAYGARPLRRLVQREIGDRLARGILAGE
+IADGDTVVVDRVEGENGLTVTRKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001508.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001508.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24dfd016ad5465d3014f2a80a2fb1fe41b314123
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001508.fa
@@ -0,0 +1,30 @@
+>PROKKA_01865
+MTRIHSRLLGAVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDV
+PYPPFEFEENGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI
+TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV
+QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVESLPTGEQLGMAVGPQKAQL
+GSAVNRALQELRNDGTVAELQERWFGQAQEDYR
+>PROKKA_01561
+MTRIHSRLLGAVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDI
+PYPPFEFEEKGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI
+TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV
+QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVESLPTGEQLGMAVGPQKAQL
+GSAVNRALQELRNDGTVAELQERWFGQAQEDYR
+>PROKKA_00995
+MGLTASAALLTGCAVLGGDSGVAGVVSDDDLSTTYNLVQPGVLTVCSDIPYPPFEFELDG
+ELTGYDIQLVHAIAEELELGVNVIDSSFEAIESGASLTGCDLNASSISITEQRQRAMAFT
+LPYLDDDLVLVAATDSGITDVESAKGRRVGVQAATTGDAYAKENGLNPIEFEDGGMQVQA
+LQAGTVDALLGNQSVILYSLKDDERFEVVENLPTGEQLGMAVAPQNAQLGSAVNRALQQL
+RNDGTVAELQERWFGLAQEDYR
+>PROKKA_00933
+MPRTPSRALGAVGAGLSAALLSGCAVIGGDAGTTGPLAEDDLRATYRLHEPGVLTVCADV
+PYPPFEFEQDGQLTGYDIDLTRKLAETMDLQLKVVDTSFEAIESGASLTGCDLNASAISI
+TEPRQHVMAFTLPYLDDDLVLVARKDSGITDVASAQGKRVGVQTATTGEEYAQSQGLDTV
+QFEDGGMQVQALQAGTVDALLGNQSVLLYSLKDDPRFGVVESLPTGEQLGMGVAPDNALL
+GSAVNRALQTLRNDGTVAELQQKWFGTAQKDYQ
+>PROKKA_01785
+MTRIHSRLLGTVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDV
+PYPPFEFEENGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI
+TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV
+QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVELLPTGEQLGMAVGPQKAQL
+GSAVNRALQELRNDGTVAELQERWFGQAQEDYR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001511.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001511.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e42974f1eb61475c6d44931c3fa20a3c387cd85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001511.fa
@@ -0,0 +1,25 @@
+>PROKKA_01868
+MSIVQIPLRLASGAFILNSGLNKRGISAEQAQGLRDMGARGLPALANLSPEQFKKFLVTT
+EIGVGSALLAPFVPGWLAGSALTAFSGGLFSMYLNTPEMTEADGVRPSQEGTGVAKDIFL
+VGSGLAIAADSVANRPGKRRKAAKKRAARIEGARDAKVQAIRDAQDEKVAAIHAAREEQV
+AALREARDELKKLRKKA
+>PROKKA_01564
+MSIVQIPLRLASGAFILNSGLNKRGISAEQAQGLRDMGARGLPALANLSPEQFKKFLVTT
+EVGVGAALLAPFVPGWLAGSALTAFSGGLFSMYLNTPEMTEADGVRPSQEGTGVAKDIFL
+VGSGLAITADSVANRPGKRRKAAKKRAARIEGARDAKVQAIRDAQDEKVAAIHAAREEQV
+AALREARDELKKLRKKA
+>PROKKA_00992
+MSIVQIPLRLASGAFILNSGLNKRNISEEQAAGMRDMGAQGVPYLAKLTPAQFKNFIVAT
+EVGTGAALLAPFVPGWLAGSALTAFSGGLMSMYLNTPAMTEKDGVRPSQEGTGVAKDVFL
+VGSGLAIAADSVANRSGKRRKAAKKRAARIGNARDAKVQAIRDAQDEKVAAIHAARDEQV
+AALREAREELKKLRQKA
+>PROKKA_00930
+MSIIQIPLRLTSGAFILNSGLGKRKLGEEQAAYLQNMAAKGVPSLAKLSPSQFKNFITAT
+EIGTGAALLAPFVPGWLAGSALTAFSGGLMSMYLNTPEMTEADGVRPSQDGTAVAKDVFL
+LGAGLAVTADSVVNRPGKRKKAAKKRAARISDARDAKVDAIRAAQDEKVAAIHEAREQQV
+AALREARQELAKLRKKA
+>PROKKA_01788
+MSIVQIPLRLASGAFILNSGLNKRGISAEQAQGLRDMSARGLPALANLSPEQFKKFLVTT
+EIGVGSALLAPFVPGWLAGSALTAFSGGLFSMYLNTPEMTEADGVRPSQEGTAVAKDIFL
+VGSGLAIAADSVANRPGKRRKAAKKRAARIEGARDAKVQAIRDAQDEKVAAIHAAREEQV
+AALREARDELKKLRKKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001513.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001513.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6556df3c0b210e2cb1f0b036e0ae35f9ff9fe338
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001513.fa
@@ -0,0 +1,47 @@
+>PROKKA_01870
+MHPVLPSPRRGRAALGLAAVALVALSACARTEPQPEPAPATTAASALPSMDMAPFTVEVP
+SHDLERVPEASVAVLEGEDPDHHGAWLQVSGAPAWTDAMAGAVRDQIDQYRRDTDPSADP
+RLEIQPQLAVVAEDIAAARLLATERRGTDSVSTSHVIWYSAREDRVLETADLFTPDGWDA
+FRAEVRQRMANDPDVIGSRLDSAVDAPEQVENRRVWDAVVFLPDGSLMLEADQASMAPAA
+AGVLTVRIPRDTATAWLSDLGHVAADAASAPADLRLPDRSTPTPEEQQPEPAPEPEPETS
+SWTEEATGAPVPPPSAPADTAAPTPSVTTPVPSSTAPSSSAPAPTRSATPSSPSSPPTSS
+SPSGTGSGSPTPSTPDPTPTSATPTPTSPTPTSPSPSGPSTSASGPSTSAPATDPAPDPT
+ESAPEPTATTASASASPTSGDRSSSTP
+>PROKKA_01566
+MHPVLPSPRRGRAALGLAAVALVTLSACARTEPQPEPAPATTAASALPSMDMAPFTVEVP
+SHDLERVPEASVAVLEGEDPDHHGAWLQVPGAPAWTEAMAEAVRAQIDQYRRDTDPSADP
+RLEIQPQLAVVAEDIAAARLLATERRGTDSVSTSHVIWYSAREDRVLETADLFTPDGWDA
+FRAEVRQRMANDPDVIGSRLDSAVDAPEQVENRRVWDAVVFLPDGSLMLEADQASMAPAA
+AGVLTVRIPRDTATAWLSDLGHVAADAASAPADLRLPDRSTPTPEEQQPEPAPEPEPETS
+SWTEEATGAPVPPPSAPADTAAPTPSVTTPVPSSTAPSSSAPAPTRSATPSSPSSPPTSS
+SPSGTGSGSPTPSTPDPTPTSATPTPTSPTPTSPSPSGPSTSASGPSTSAPATDPAPDPT
+ESAPEPTATTASASASPTSGDRSSSTP
+>PROKKA_00990
+MSTPASPSARRARAALGLAAVALVALSACARTEPAPEPAPSTASATALPPMDMAPFTVDV
+PSLDLDRVPGASIAVLEGTDPDHRGAWLQVPEAPAWTEAMAGSVRGQIDAYRRDTDRGAD
+PRLEVQPRLAVVGEDIAAARLLSTETRGTDSVSSSHVVWYSAREDRVLETRDLFTDEGWD
+AFRTEVRQRMKNDPDVVRERLASAVDSPELVENRRIWDAVVLLPDGSVMLEADQASMAPA
+AAGVLTVRIPRDTAAPWLSDLGDAATDAARTPADLRLPDRSTPSPSTSAPEPAESSWTPE
+ATGAPVPPRVPVPDPTTTAPSVDPGGDRDPSTSSAPPSSRPGTTAPSPVAGPQHPGPHHP
+GPHHLRADRPGARPLDDDGAPAPGADQPDAHADADPVDSHADADAHDAHPDPDRDGDHGP
+ADRPGAGARAGADDAAAERHERLRPRDPGRAGLSRPTPGCPGRPRTGACPARRRPAPPPH
+GLT
+>PROKKA_00928
+MHRLSPASTVRLRAGAGLLALGMLGLTACGSGDDAASSSPAPSSAAATQELPSMDMAPFT
+LDVPSLDLDKVPGASLAVIQGQDPEYHAAWLQVPGAPAWTQAMDESVRGLVAQYQRDTDR
+TASPVLDVQPRLAVAGRDVAAARLLSTERRGDRSVSAVHVVWYAAREDRVLSTEDLFTAD
+GWAAFRREVGARMAGDPAVVQDRLRSAVDAPAQVENVRVWDALTFLPDGSALLEVDQAAM
+SPADAGVLTARIPADTVRPWLSALGVSAQDAARSPEALVLPERPSAAPASEGGDAAVPAP
+GQPSSDGATTSAPGQGSVPPAPGLPGAPAPGTPGTASQGGGSPGTAPQDTGSQHTGSQGT
+GSQGTGASAPGASPSATRGDAGPAPTSSSAAPAPTGTGAPAPAPLPMPAPTTSSATPSGP
+APAPTGGTPAPSPTTVAPTEPSPSADPTTSEPAPSSDPAPAPTDTASPAPTASSPSTPAD
+VTGTATASGPLPATGGSTDPVTPTPAA
+>PROKKA_01790
+MHPVLPSPRRGRAALGLAAVALVTLSACARTEPQPEPAPATTAASALPSMDMAPFTVEVP
+SHDLERVPEASVAVLEGEDPDHHGAWLQVPGAPAWTEAMAEAVRAQIDQYRRDTDPSADP
+RLEIQPQLAVVAEDIAAARLLATERRGTDSVSTSHVIWYSAREDRVLETADLFTPDGWDA
+FRAEVRQRMANDPDVIGSRLDSAVDAPEQVENRRVWDAVVFLPDGSLMLEADQASMAPAA
+AGVLTVRIPRDTAAPWLSDLGHVAADAASAPADLRLPDRSTPTLEEQQPEPETSSRTQEA
+TDAPVPPPSAPADTAAPTPSATTPVPSSTVPSSTAPSSSVPTSTGSATPSSPTSPASSSS
+PSGTGSGSPTPSTPDPSPTSATPTPTSPSPSGPSTSAPATAPAPDPTESAPEPTATTASA
+PAPPTSGDRSSGTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001514.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001514.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c01c788079a1645d4db18436ed79c963ef98efb5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001514.fa
@@ -0,0 +1,35 @@
+>PROKKA_01871
+MTEHLPRPCPDAPGPDAVPPPAERVHAHDHNRDKDPALVRREPVSFVRRGARLNAGRQAV
+WDRQAERVLVDVPRGRGATSVDGQARLDWAGVFGREAPLLVDIGSGLGESTAQAAADRPD
+WNVLAVEVYVPGLAALMTRVEQQGLENVRAVEANAPELLDALLTPGSVSEVWVFFPDPWH
+KKRHHKRRLVSPAFADRVARVLTPGGVLRLATDWSGYAVQMREVLEAHPEFENLFPGRAA
+GEDSPLTRVRREGRETEVGAQPLPAGWESAAEEERPLRAGLGEARAGAAAADPVDHDGGW
+APRFEGRPITSFEAKSQRAGRLVFDLAYRRR
+>PROKKA_01567
+MTEHLPRPCPDAPGPDAVPPPAERVHAHDHNRDKDPALVRREPVSFVRRGARLNAGRQAV
+WDRQAERVLVDVPRGRGATSVDGQARLDWAGVFGREAPLLVDIGSGLGESTAQAAADRPD
+WNVLAVEVYVPGLAALMTRVEQQGLENVRAVEANAPELLDALLTPGSVSEVWVFFPDPWH
+KKRHHKRRLVSPAFADRVARVLTPGGVLRLATDWSGYAVQMREVLEAHPGFENLFPGRAA
+GEDSPLTRVRREGRETEVGAQPLPAGWESAAEEERPLRAGLGEARAGAAAADPVDHEGGW
+APRFEGRPITSFEAKSQRAGRLVFDLAYRRR
+>PROKKA_00989
+MTEQPPAPDAPSRGTPANDGRDGVLAPHERAHEHDHNRDKDPALMRREPVSFVRRGARLN
+SGRQAVWDRQAQRVLVDVPRERGATSVARDARLDWDAAFGRRAPLLVDIGSGLGESTAQA
+AADRPDWNVLAVEVYVPGLAALMTRVEQSGLENVRAVEANAPELMDHLLAPGSVSEVWVF
+FPDPWHKKRHHKRRLVSPAFADRVARVLAPGGVLRLATDWSGYAVRMREVMEAHPEFENL
+HPGRAAGEKSPLTRVRREGREAEVGAQPLPAGWESAAEDERPLRAGLGEALEAAVAEDPV
+DHEGGWAPRFEGRPVTSFEAKSRRAGRLVFDLAYARR
+>PROKKA_00926
+MTGGPENAHERDHDREKDPELIRREPVSFVRRGARMTTGRQAVWDRMAETVLVDVPRHRA
+ATSVAPDAHLDWDAAFGRHAPLLVDIGSGLGESTAQGAADHPDWNVLSVEVYLPGLAALM
+AQVESRGLENVRAVEANAPELLDHLLPAGSAQEVWVFFPDPWHKKRHHKRRLVNAAFADR
+VARVLAPGGVLRLATDWSGYAVQMREVMESHPDFVNLHPGRAAGEESPLTRVRREGRELE
+VGAQPLPAGFDPARPASELPERAGLGEAVEASLAEDPVDHDGGWAPRFEGRPLTQFEGKA
+LRAGRLVFDLAYARR
+>PROKKA_01791
+MTEHLPRPRPDAPDPDAVPPPAERVHAHDHNRDKDPALVRREPVSFVRRGARLNAGRQAV
+WDRQAERVLVDVPRGRGATSVDAQARLDWAGVFGREAPLLVDIGSGLGESTAQAAADRPD
+WNVLAVEVYVPGLAALMTRVEQQGLENVRAVEANAPELLDALLTPGSVSEVWVFFPDPWH
+KKRHHKRRLVSPAFADRVARVLAPGGVLRLATDWSGYAVQMREVLEAHPEFENLFPGRAA
+GEDSPLTRVRREGRETEVGAQPLPAGWERAAEEERPLRAGLGEARAGAAAADPVDHEGGW
+APRFEGRPITSFEAKSQRAGRLVFDLAYRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001515.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001515.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3940c39aa3ad163dddeaa00a6161af78047a05a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001515.fa
@@ -0,0 +1,35 @@
+>PROKKA_01872
+MQERLRADMARRDGLGRQARSALDGIVHALKPEGMDPHLPARHLLDYVLEGPDGPRAVVA
+AGDPATATHLTWLVSGMGIRPQTALWGTAREAAHLAAAQRAAGAPRPVVIGWLGYPAPTP
+WRVVLDGPGRRGGAMLAADVRAWWEFLRHGPGEDDDVAPALRARGTAVHGAVEAHSYGSL
+VAAHALRLLADRGLQPDDAEAPWPAERPVEALVVSGTVGLPAALAARSAHLGLRSGRTFR
+ALAPGDLLARVGRAVGRRRDWTDAAVLPVAPRPGLAGAAVRGHRTARWSPTAPEDAPRGY
+RDAGSVTLAATARVTAGLPLSPVPDGADPAGPVAPA
+>PROKKA_01568
+MQERLRADMARRDGLGRQARSALDGIVHALKPEGMDPHLPARHLLDYVLEGPDGPRAVVA
+AGDPATATHLTWLVSGMGIRPQTAMWGTAREAAHLAAAQRAAGAPRPVVIGWLGYPAPTP
+WRVVLDGPGRRGGAMLAADVWAWWEFLRHGPGEDDDATLALRARGTAVHGAVEAHSYGSL
+VAAHALRLLADRGLQPDDAEAPWPAERPVEALVVSGAVGLPAALATRAAHLGLRSGRTFR
+ALAPGDLLARVGRAVGRRRDWTDAAALPVAPRPGLAGAAVRGHHTARWSPTASEDAPRGY
+RDAGSVTLAATARVTAGLPLSPAPDGADPAGPVAPV
+>PROKKA_00988
+MARRDGLGRQARSALDGIVHALKPEGMDPHLPARHLLDYVLDGPDGPRAVVAAGDPATAT
+HLTWLVSGMGIRPHTAMWGTAREAAQLAAAQRAAGAPRPAVLAWLGYAAPTPWRILLDGP
+GRRGGERLADDVAAWWDFARTGAGETEDRAGEPDDDRPSLRARGTALHGAVEAHSYGSLV
+AAHALRLLAERGLQPDDVEVLDDTDGGADADAGAQDTARPAERPVEALVVSGAVGLPAAF
+AARAGRLGLPPGRVFRAQAPGDVLARVGRALGRRRDWTDAVLLPVTPRPGLEGGAVHGHR
+TARWSPAAGTDAPRGYRDPGTVTLAATARVTAGLPLPPEPA
+>PROKKA_00925
+MDLPEQARAAAARLDADRARARDGRLSARQLAALDGAEHALRRDSMDAAIPERVLVDWDL
+DAPDGPVAAVAVGELERPTHLTWQVSGMGIAASTAAWGSAREAGQLLLAQRAAGAPRPCV
+VAWLGYPAPPWWRTLDDGLARRGGARLAEAVRETRPGPSHGAGTAVHTAIEAHSYGTLVA
+THALEGLAAGDPPLTVDALALSGALGLPRRLAGRLEALGLAAGRVFEARAPGDRLAWLGR
+TLAGRAPWPEAVALPVAADPAAGLAGVRGHNTARWRPEDGDDGAPRGYRDPGSVTLAALA
+RVTAGLPVAGGGPRSGQRRA
+>PROKKA_01792
+MAARSRVRERLRADMARRDGLGRRARSALDGIVHALKPEGMDPHLPARHLLDYVLDGPDG
+PRAVVAAGDPATATHLTWLVSGMGIRPQTAMWGTAREAAHLAAAQRAAGAPRPVVIAWLG
+YPAPTPWRVVLDGPGRRGGAMLAADVRAWWEFMRHGPGEDDAAAPALRARGTAVHGAMEA
+HSYGSLVAAHALRLLADRGLQPDDAEAPWPAERPVEALVVSGAVGLPAALAARAAHLGLR
+SGRVFRALAPGDLLARVGRAVGRRRDWTDAAVLPVAPRPGLAGAGVRGHHTARWSPTAPG
+DAPRGYRDAGSVTLAATARVTAGLPLPPVPDGADPAGPVAPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001517.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001517.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aee4bb534638a8c0ee2caec49ab27814e1ab32aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001517.fa
@@ -0,0 +1,32 @@
+>PROKKA_01874
+MASQDWMDKDFYATLGVSKDASDADVKKAYRKLARMYHPDQNPGDEAAEKKFKEISEAYA
+VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRATQSEPDLSDL
+FSGMFSGAAGQPGGFGPGGFGDAGYARPRPTKGADRTATTTISFRGSIQGTTVSLRGPDG
+ETIEVKIPKGIRDGQKVRARGKGSPGPAGRGDLLVTVHVREHEFFRRDGDDLRITVPITF
+PEAALGATIEVPTLERPVKVKVPAGSQCGRVLRLKGRGVERGKTTGDLLVELRVTVPTTL
+NDDARAAVEALQSATAGDDPRRELARKAAW
+>PROKKA_01570
+MASQDWMDKDFYATLGVSKDASDADVKKAYRKLARTHHPDQNPGDEAAEKKFKEISEAYA
+VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRTTQSEPDLSDL
+FSGMFSGAAGQPGGFGPGGFGDAGYARPRPTKGADRTATTTISFRGSIQGTTVSLRGPDG
+ETIEVKIPKGIRDGQKVRARGKGSPGPAGRGDLLVTVHVREHEFFRRDGDDLRITVPITF
+PEAALGATIEVPTLDRSVKVKVPAGSQCGRVLRLKGRGVERGTTTGDLLVELRVTVPTTL
+NDDARAAVEALQSATAGDYPRRELARKAAW
+>PROKKA_00986
+MSLRAADGETIEVKIPKGIRDGQKVRARGKGAPGAAGRGDLLVTVHVREHEFFRRDGDDL
+RITVPVTFPEAALGATIEVPTLERPVKMKVPAGSQSGRVLRLKGRGVERGTTKGDLLVEL
+HVTVPTELNDDARAAVEALQSALAGDDPRRELARKAAW
+>PROKKA_00923
+MASQDWLEKDFYQVLGVSKDASESDIKKAYRTLARKHHPDQNPGDAAAEQRFKEISEAYD
+VLSDPKDRQEYDAIRSMGGGARFGAPGGFGGAGGGAGAGGFEDVFGGMFGGGGGSRTFRT
+GGAQGGPDLSDLLGAFTGGGAGGFGGGQGFGGGGFGQPAPTKGADRTATTTISFRGAVEG
+TTVSLRAADGETVDVRIPKGVKDGQKVRARGKGSPGTAGRGDLIVTVQVREHPFFQRDGD
+DLRITVPVTFAEAALGATVEVPTLDRPVKVKVPAGSQSGRVLRLKGRGVAGAKHTGDLLV
+ELQVAVPAELSAEARGAVEAYAAATAGDDVREGLAGKAQW
+>PROKKA_01794
+MASQDWMDKDFYATLGVSKDASESDVKKAYRKLARTHHPDQNPGDEAAEKKFKEISEAYA
+VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRTTQSGPDLSDL
+FSGMFGGAAGQTGGFGDAGYPRPRPTKGADRTATTTISFRGSIQGTTVSLRAPDGETIEV
+KIPKGIRDGQKVRARGKGSPGAAGRGDLLVTVHVREHEFFHRDGDDLRITVPVTFPEAAL
+GATIEVPTLERPVKVKVPAGSQSGRVLRLKGRGVERGTTTGDLLVELHVTVPTELDDDAR
+AAIEALQSALAGDDPRRELARKAAW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001519.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001519.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6471a17a97ec2162b2804a00593a09522a428e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001519.fa
@@ -0,0 +1,60 @@
+>PROKKA_01876
+MSRAVGIDLGTTNSVVAALEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN
+NPERTFASVKRHMGTDWTAEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVTRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE
+AAEQAKKELSSATSTNISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFEDVI
+KEAGVKVSDIDHVILVGGSTRMPAVSDLVKELTGGKEPNKGVNPDEVVAIGAAVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSKEDIDRMVKDAEAHADEDRKRREAADRRNQAEQSAYSVERLLQDNADKLPEDVKT
+EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG
+DDEDIVDAEVVDEDDEKKA
+>PROKKA_01572
+MSRAVGIDLGTTNSVVAVLEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN
+NPERTYASVKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVKRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE
+AAEQAKKELSSATSTSISLQYLSVTPEGPVHLDEHLSRAKFEDLTKDLLERTRKPFEDVI
+KEAGVKVSDIDHVILVGGSTRMPAVSDLVKELTGGKEPNKSVNPDEVVAIGAAVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSQEDIDRMVKDAEAHADEDKKRREAADRRNQAEQSAYSVERLLQDNGDKLPEDVKT
+EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG
+DDEDIVDAEVVDEDDEKKA
+>PROKKA_00983
+MSRAVGIDLGTTNSVVAALEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN
+NPERTYASVKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVTRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE
+AAEQAKKELSSATSTSISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFEDVI
+KEAGVKVSDIDHVVLVGGSTRMPAVSDLVKELTGGKEPNKSVNPDEVVAIGAAVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSKEDIDRMVKDAEAHADEDKKRREAADRRNQAEQSAYSVDKLLQDNADKLPEDVKT
+EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG
+DDEDIVDAEVVDEDDEKKA
+>PROKKA_00921
+MSRAVGIDLGTTNSVVAVLEGGDPVVIANAEGARTTPSVVAFSKGGEVLVGEVAKRQAVN
+NPDRTYASVKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVKRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATSGDNRLGGDDWDQRIVDWLLQQAKSKGADLSNDKIALQRLKE
+AAEQAKKELSSATSTNISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFNDVI
+KEAGVKVSDIDHVVLVGGSTRMPAVSELVKELTGGKEPNKGVNPDEVVAIGASVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSKEDIDRMVKDAESHAEEDKARREAAERRNQAEQSAYSVDKLLADNADKLPEDVTT
+EVQADVDALKAALEKQDNDDEVKAAFEKLQASQVKIGEALYAQQSAEGAQPDAESGSAQA
+DEDIVDAEVVEDEDEKKN
+>PROKKA_01796
+MSRAVGIDLGTTNSVVAVLEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN
+NPERTFASIKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVKRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE
+AAEQAKKELSSATSTNISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFEDVI
+KEAGVKVSDIDHVILVGGSTRMPAVSELVKELTGGKEPNKSVNPDEVVAIGAAVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSQEDIDRMVKDAEAHADEDKKRREAADRRNQAEQSAYSVEKLLQDNGDKLPEDVKT
+EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG
+DDEDIVDAEVVDEDDEKKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001524.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001524.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35af2d96f27b8b3fceb883f0aaf4a4ef190c06f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001524.fa
@@ -0,0 +1,20 @@
+>PROKKA_01884
+MTDTATLLDWLAAFLLVSGAFFSLVAGVGLFVLPDLLARMHAAAKPQVLGLLLMLAGLAI
+EWRSWVWLPVLLLAWVTQMVTAPVASHLVGRTGYRTKHARRELLHRDELAAVVRRAEPPA
+DPGPRRAGARPRGRR
+>PROKKA_01580
+MTDTATLLDWLAAFLLVSGAFFSLVAGVGLFVLPDLLARMHAAAKPQVLGLLLMLAGLGI
+VWRSWVWLPVLFLAWITQMVTAPVASHLVGRTGYRTKHARRELLHRDELAAVGRRAEPPA
+DPGPRRAGARPRGRR
+>PROKKA_00974
+MTETATFLDWLSAALLVSGAFFTLVAGVGLLLLPDLLARMHASAKPQVLGLMLMLAGLAI
+AWESWPWVPVLFLAWVTQMVTAPVASHLVGRTAYRTKHARRELLHRDELAAIARRVEPAP
+ELDPRSPESRRRRRR
+>PROKKA_00912
+MDAAWTDWLAAALLVGGAFFSLVAGVGMTLLPDLLSRMHASAKPQVLGLLLMACGVAVLW
+QAWAWVPVLVLAWVTQMITAPVASHLISRTGYRTKHVRRDLLHRDDLAAQAEPGPREDPD
+AR
+>PROKKA_01804
+MTDTATLLDWLAAFLLVSGAFFSLVAGVGLFVLPDLLARMHAAAKPQVLGLLLMLAGLAI
+EWRSWVWLPVLLLAWVTQMVTAPVASHLVGRTGYRTKHARRELLHRDELAAVVRRAEPPA
+DPGPRRAGARPRGRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001527.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001527.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7715b8c97de3ee16a78c934a8ea575d5cc68b5be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001527.fa
@@ -0,0 +1,55 @@
+>PROKKA_01887
+MSIGTLPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWD
+TGVAAVHLGGWPAPLGISLVVDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIF
+HPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTMGGTAQRIRAGVTYVVVSVLS
+SVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP
+DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA
+QTDIKRILSFILVSHIGYMIFGLGLATEAGLAATVYYVAHHITVQTALFLVTGLIENRAG
+TANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGKVGLLRGGVEQATPLAYTLVG
+VSLLVSLLTLLVVVRVWTRAFWRRVEDVEHPPAQLVAAYERAVARGERPRPLEPGLVLPT
+TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHD
+ARK
+>PROKKA_01583
+MSIGSVPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWD
+TGVAAVHLGGWPAPLGISLVVDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIF
+HPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTMGGTAQRIRAGITYVVVSVLS
+SVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP
+DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA
+QTDIKRILSFILVSHIGYMIFGLGLATEAGLAATVYYVAHHITVQTTLFLVTGLIENRAG
+TANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGKVGLLRGGVEQATPLAYTLVG
+VSLLVSLLTLLVVVRVWTRAFWRRVEDLEHPPAQLVAAYERAVARGERPRPLEPGLVLPT
+TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHD
+ARK
+>PROKKA_00971
+MSIGSVPMTDLAPLAVMMPVLGAAVTFMLVRRPRAQVVVTVAALVLTLLLNCLLLAAVWE
+GGVASVHVGGWPAPLGITLVVDRLSALMLVVSALITLAVLLYASAQGMVNRDEGGPVSIF
+HPTFLILVAGVFNAFLAGDLFNLYVGFEILLTASYVLLTMGGTAQRIRAGITYVVVSVIS
+SVVFLIAIAMVYAATGTVNMADLAVKLGELPSDVQMVLHVLLLVGFGIKAAVFPLSFWLP
+DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA
+QTDIKRILSFILVSHIGYMIFGLGLATQMGLAATVFYVGHHITVQTALFLVTGLIENRAG
+TANIDRLGSLAKVSPFISVLFLIPALNLGGIPPFSGFLGKVGLLRGGVEQGTGLSYTLVG
+VSLLASLLTLLVVVRVWTRAFWRKVEDVEHPPAQLVAAYERTIDRGLRPRRLEPGLVLPT
+AALVVMTLAFTVLAGPLFDLADAAATDMLDRTPYIASVLDEAAAERAAETLSHDPTEVHD
+ARH
+>PROKKA_00909
+MLGSTPLTDLAPLAVMLPVLGAAITFALVGRARAQVVVTVSALTLTLVLDCLLLADVWTG
+GVAVVELAAWPAPVGITMVVDRLSALLLVVSSLITLAVLLYASAQGLINKDEGGPVSIFH
+PTFLVLVAGVSNAFLAGDLFNLYVGFEILLTASYVLLTLGGTEARIRAGITYVVVSVISS
+VLFLIAIAMIYAATGTVNMADLAVKLGELPHDLQLVLHVMLLAGFGIKAAVFPLSFWLPD
+SYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPAEHVNGLLMGVAALTMLVGILGALAQ
+SGLKRILSFILVSHIGYMVFGLALATQVGLAATVYYVGHHITVQTALFLVTGLIEQRAGT
+ASIDRLGSLAKVSPLLGVLFLVPALNLGGIPPFSGFLGKVGLIRGGVEDGGVLAWVLVGV
+SLLVSLLTLLVLVRAYTRAFWRKVEDVEHPTPQLVAAYERVTRRGLRPKPLSRGLVLPTA
+GLVAMTLAFTVFAGPLYDLADRAAVDMLERSPYISAVLGPEAADRAAVTLSHDPSEVHDA
+GR
+>PROKKA_01807
+MSIGTLPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWD
+TGVAAVHLGGWPAPLGISLVVDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIF
+HPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTMGGTAQRIRAGVTYVVVSVLS
+SVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP
+DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA
+QTDIKRILSFILVSHIGYMIFGLGLATEAGLAATVYYVAHHITVQTALFLVTGLIENRAG
+TANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGKVGLLRGGVEQATPLAYTLVG
+VSLLVSLLTLLVVVRVWTRAFWRRVEDVEHPPAQLVAAYERAVARGERPRPLEPGLVLPT
+TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHD
+ARK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001528.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001528.fa
new file mode 100644
index 0000000000000000000000000000000000000000..503646a0f96c23085eb3279df922b55a376d4b81
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001528.fa
@@ -0,0 +1,24 @@
+>PROKKA_01888
+MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIVLINNGAIMLLFLSSGGTGLAPLFV
+RGRDPHEYADTLPQALILTAIVIGFAVIAFLTAMIYRSWLLVREDEVEVDAEDVKIARMP
+AWDAEDDAELVEESSEFLDDAADPNAHYEHATESRPHVRHASPTPPAHPGPASAVRAHRA
+DGGPRP
+>PROKKA_01584
+MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIMLINNGAIMLLFLASGGVGLAPLFV
+RGRDPHEYADTLPQALILTAIVIGFAVVAFLTAMIYRSWLLVREDEVEVDAEDVKIARMP
+AWDAEDDAELVEESSEFLDDAADPNAHYEHATEARPQVQHATPAPQAPTGSGAASRGRRP
+EGGERA
+>PROKKA_00970
+MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIMLINNGAIMLLFLASGGVGLAPLFV
+RGRDPHEYADTLPQALILTAIVIGFAVTAFLTAMIYRSWLISREDEVEVDAEDVKIASQG
+AWDAEDDSELVEEHSEFMDASTDPNAHYEHTTEARPQVQHVIPAPPTAAGSREAARGRRP
+EGGERA
+>PROKKA_00908
+MTPTVDLALLAVMGVLFATGIYLLLERSLTRILVGVMLINNAAVVLLFLTSGGAGLAPLY
+DADTAPEDYADMLPQALILTAIVIGFATTAFLTAMIYRSWQLRREDDVATDVEDVKIAAQ
+SGWDAEDDSVLTEEDSEFMDDASDPNAEYEFATAAAPRARAVRPGRATVQGGGGRP
+>PROKKA_01808
+MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIVLINNGAIMLLFLSSGGTGLAPLFV
+RGRDPHEYADTLPQALILTAIVIGFAVVAFLTAMIYRSWLLVREDEVEVDAEDVKIARMP
+AWDAEDDAELVEESSEFLDDAADPNAHYEHATEARPQVQHATPAPQAPTGSGAASRGRRP
+EGGERA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001534.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001534.fa
new file mode 100644
index 0000000000000000000000000000000000000000..58c5de85ae7b1118d3cd766a10a0f57d9c95c606
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001534.fa
@@ -0,0 +1,65 @@
+>PROKKA_01900
+MMVGMTAPQTPNPVPSADAPAAVPRAATRVRASELVGRGWLNTGGEQVTLEDLRGKVVLL
+DFWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYAIEHPV
+LDDPELTTWQAYSARAWPTLVVVDPEGYIAAHLSGEGHVAGLYGLVRELVAEHEAKGTLH
+RGSGPYVPPAPVARDLSFPGKAVSLGGRGSRPGSFLVSDTGHHRLLEVAEDLTTVLRAFG
+GGDPATADAGQAELAFPTPGEKGHADGGPDEALFNEPQGLALLPEDVAERVGYDVVVADS
+VNHRLRGLRLSDGHVSTLAGNGVQKLIDSERAKEAAAVDDEGDIAVDLADLPGEPTAISL
+SSPWDVVWHPALGRVVIAMAGTHQLFDFDPVTGALAVHAGTALEGLLDGDAGRAWFAQPS
+GLSVGADGALWVADSETSAVRWVRTGEDGRREVGTAVGAGLFDFGHVDGEADRARLQHPL
+GVTALPDGSVLIADTYNGAIRRYAPAGEDAAGRAVPATVTTVARGLLEPSDVLVEHDADG
+NDTAIVVVESNAHRLTRLAVPEEFLTVDEGARQTQRPRTPVVAGDLDLTIGFAAPTGQKL
+DDRWGDPTQLKISSSPEELLLEGAGTSTGLHRTLRLNPEVEEGVLHITARAAACDGEKGQ
+PIPDHAACHLYQQDWGIPVTVHTPDRAPEGAETRLDLDLRGIH
+>PROKKA_01596
+MMVDMTAPQTPNPAPTADAPAAVPRAATRVRASELVGRGWLNTGGEQVSLEDLRGKVVLL
+DFWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYAIEHPV
+LDDPELTTWQAYSARAWPTLVVVDPEGYIAAHLSGEGHVAGLYGLVRELVAEHEAKGTLH
+RGSGPYVPPAPVARDLSFPGKAVSLGGRGSRPGTFLVSDTGHHRLLEVAEDLTTVLRAFG
+GGDPATADAGQAELAFPTPGEKGHADGGPDQALFNEPQGLALLPEDVAQRVGYDVVVADS
+VNHRLRGLRLSDGHVSTLAGNGVQKLIDSERAKEAAAVDDEGDVAVDLADLPGEPTAISL
+SSPWDVVWHPALGRVVIAMAGTHQLFDFDPVTDALAVHAGTALEGLLDGEAGRAWFAQPS
+GLSVGADGTLWVADSETSAVRWVRTGEDGRREVGTAVGAGLFDFGHVDGEADRARLQHAL
+GVTALPDGSVLIADTYNGAIRRYAPAGEDAAGRAVPATVTTVARGLLEPSDVLVEHDADG
+NDTAIVVVESNAHRLTRLAVPEEFLTVDEGARQTQRPRTPVVAGDLDLTIGFAAPTGQKL
+DDRWGDPTQLKVSSSPEELLLEGAGTSTGLHRTLRLNPEVEEGVLHITARAAACDGEKGQ
+PIPDHAACHLYQQDWGIPVTVHTPDRAPEGAETRLDLDLRGIH
+>PROKKA_00958
+MMVGMTDPQTPPAVSPDAAPSDAAPAAVPRAASRVRASELVGRGWLNTGGEQVTLEDLRG
+KVVILDFWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYT
+IEHPVLDDPELTTWQAYSARAWPTLVVVDPEGYIAAHLSGEGHVAGLYSLVRELVAEHEA
+KGTLHRGSGPYVPPAPVARDLKFPGKAISLAGRGTAPGTFLVADTGHHRLLEVAEDLTTV
+LRAVGGGDPAGAGEEQAGLAFPTPGEKGHADGGPEQALFNEPNGLALLPEDVAERVGYDV
+VVADTVNHRLRGLRLADGGVSTVAGNGVQKLIDSERAKEASAGDAEDVAVDLSDLPGEPT
+AISLSSPWDVAWDPAAGRVVIAMAGTHQLFDFDPVAGALAVHAGTGLEGLLDGDAGSAWF
+AQTSGLSLGPDGTLWAADSETSAVRWLRTGEDGRREVGTAVGTGLFDFGFVDGEAAQARL
+QHPLGVTALPDGSVLIADTYNGAVRRYAPAGEDAAGRPVAAAVSTVARGLQEPSDVLVEH
+DADGAPAAIVVVETNAHRLVRLAVPEEYLTVDEGARQTQRPRTPMVAGDVDLAIGFAAPS
+GQKLDDRWGDPTQLKVSSSPEELLLEGAGTSTGLSRTLRLNPAVAEGVLHITARAAACDG
+EKGQPIPDHAACHLYQQDWGIPVTVHAPEGAPEGAETRLDLDLRGIH
+>PROKKA_00898
+MRRPLPADARRAWAMMEGMTEQQTSAPSVPRSGSRVRASSLVGRRWLNTGGTEVSLEDLR
+GKVVILDFWTFCCINCLHVADELRPLEEEFSDVLVTVGVHSPKFEHEADPDALDAAVERY
+DIAHPVLDDPTLVTWQAYSARAWPTLVVVDPEGYIVAHLSGEGHVAGLYSLVRELVAEHE
+AKGTLHRGSGPYVAPAPVARDLKFPGGAVSLEGRGSRPGSFLVADTGHHRIVELAADLTT
+VLRAIGGGDPAEAPAEAADLAFPTPATRGHRDGGPETALFSEPNGLLLLPEDVAARAGVD
+VVVADTVNHRLRGIDLATGEVTTLAGNGVQKLIDSERVREAAAGDESAAADLSDLPGDPT
+GISLSSPWDVAWDAAAGRVIVAMAGTHQLFSYDPVARVLAVHAGTGLEGLLDGPADTAWF
+AQTSGLSFAQDGTLWLADSETSAVRWLRTAEDGTRQVGTAVGTGLFDFGYVDGAPEQARL
+QHPLGVTALPDGSVLVADTYNGAIRRYAPAAEDAAGRPVEAAVSTVTRELKEPSDVLVEP
+GEDGAPAEIVVVETGAHQLVRISVPAEYLTVDEGARQTARPSTDVAAGDLDLSVGFAAPA
+GQKLDDRWGDPTQLKVSSSPEELLLDGAGTSVGLTRTLRLNPAVAEGVLHITARAAACDG
+EKDGPIPDSAACHLYQQDWGIPVRVHAADQAPDGAETRLDLDLRGIH
+>PROKKA_01820
+MMVDMTAPQTPNPAPTADAPAAVPRAATRVRASELVGRGWLNTGGEQVSLEDLRGKVVLL
+DFWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYAIEHPV
+LDDPELTTWQAYSARAWPTLVVVDPEGYIAAHLSGEGHVAGLYGLVRELVAEHEAKGTLH
+RGSGPYVPPAPVARDLSFPGKAVSLGGRGSRPGTFLVSDTGHHRLLEVAEDLTTVLRAFG
+GGDPATADAGQAELAFPTPGEKGHADGGPDQALFNEPQGLALLPEDVAQRVGYDVVVADS
+VNHRLRGLRLSDGHVSTLAGNGVQKLIDSERAKEAAAVDDEGDVAVDLADLPGEPTAISL
+SSPWDVVWHPALGRVVIAMAGTHQLFDFDPVTSALAVHAGTALEGLLDGEAGRAWFAQPS
+GLSVGADGTLWVADSETSAVRWVRTGEDGGREVGTAVGAGLFDFGHVDGEADRARLQHAL
+GVTALPDGSVLIADTYNGAIRRYAPAGEDAAGRAVPATVTTVARGLLEPSDVLVEHDADG
+NDTAIVVVESNAHRLTRLAVPEEFLTVDEGARQTQRPRTPVVAGDLDLTIGFAAPTGQKL
+DDRWGDPTQLKISSSPEELLLEGAGTSTGLHRTLRLNPEVEEGVLHITARAAACDGEKGQ
+PIPDHAACHLYQQDWGIPVTVHTPDRAPEGAETRLDLDLRGIH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001536.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001536.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f04f8c8824e704158c5734b1d4b3a0032ed25260
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001536.fa
@@ -0,0 +1,70 @@
+>PROKKA_01902
+MSAATAPARGSHPAENDDAARPGPSGPVGVPRWIWVLVAAAGAAGLAAAGWLTGVTAARQ
+LSDPGWITRWGVPVGELVSNVAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA
+APLPEHPAFTRVMRIAAVSAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI
+SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHTGAVN
+SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG
+LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG
+PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL
+PPALEGARWITMWRFDWLWVAIIAFLTLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL
+WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI
+LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFLFA
+LVMIGSDPLPRRPPYALRLVLLMATMVFHAFIGVAMTTSTGLLQASWFGNMGRDWGPTAL
+EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA
+RMHGTPATDAPSGAEPAARDSSTGPEEARDVR
+>PROKKA_01598
+MSAATAPARGSHPTENDDAARPGPSGPVGVPRWIWVLVAAAGAAGLAAAGWLTGVTAARQ
+LSDPGWITRWGVPVGELVSNLAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA
+APLPEHPAFTRVMRIAAVGAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI
+SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHNGAVN
+SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG
+LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG
+PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL
+PPALEGARWITMWRFDWLWVAIIAFLSLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL
+WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI
+LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLQTHVGHEFMNVHFLLTGFLFA
+LVMIGSDPLPRRPPYALRLVLLMATMIFHAFIGVAMTTSTGLMQASWFGNMGRDWGPTAL
+EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA
+RMHGTPVTDAPSGAEPVARDSSTGPEEARDVR
+>PROKKA_00956
+MLVAAAGAGALAVAAWLTGITAVRELSDPGWITRWGVPAGELVSNLAMTMAIAAIIFAAG
+ILPPHAAGTERWHRSAAQRRADAQEGPLPEHPAFTRTLRVAAVSAGVWTVAALAVGILSY
+SDLAGIPVTAGEGFTAGLVAYVAGISVGQAWFWVTVIAAVVTTLVIAVRSHNGLFWTGIL
+AMIGIVPLALIGHAAGGDDHYGAVNSIGLHLLGVVVWVGGLLVLVAISDTLVGPDGAQGR
+ARAPREQGPTPLLHTALSRYSVLAGLGLVTVALSGVVNASIRMDDPAQLTSPYGMLVVIK
+FLATLGLGLVGLMHRRWVIPRLDAGPDRPSPAPARRLLWQLIAVEAVVMAAVMGLSAVLS
+RTAPPVPEELAPDATPARILTGYELPPELTGARWITEWRLDWLWVAIIAFLALWYLRSVW
+RLHRRGDRWPVLRTLSWMVGLAVLLWATSGSPAVYGRVLFSSHMMGHMTLTMISPLFLVL
+GAPITLALRALPSRTDGSRGPREWILWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFF
+RFSLETHVGHEFMNVHFLLTGFLFALVMVGSDPLPSRPAYPLRLVLLLATMVFHAFIGVA
+MTGSAGLIQASWFGNMGRDWGPSALEDQHIGGAVMWGIGEFPTVVMAVMVAVLWYRNDRR
+NAERLDRRADRDGDAELHRWNEMYARMHGTPAAPAEPAPAAASPADPTPAASAPRPRRPG
+DPRWPLSTAHPPEDPAGPEDRAAPARWPRPPSSGCWR
+>PROKKA_00896
+MPTSTAVPPATAQHPLGVPRPVLLGAAVVGVLALVLAAWFAGVTAPRELSDPGALTRWGV
+PVGKAVNNAAMAVTIGALIFAAGILPPHAAGTERWHRSPRQRAQDAEEGPRPEHPAFGRV
+MAVAAAAAGVWTVAALAVGVLSYSDLAGIPVSAGGSFTDGLLAYTLDISVGRAWFWVTVI
+AAVVTTLAIGVRSHTGLFWTGVLAMLGIVPLALIGHAAGGDDHYGAVNSIGLHLLGVVVW
+VGGLLVLALISDTLVGPNGAQGRGASLRRQGPAPLLHTVVSRYSVLAGLGLVTVALSGVV
+NASIRMDDPAQLLSPYGTMVLTKAGAVLLLGGIGLLHRRWIIPRLDDDGAAESPPAARRL
+LWQLIAVEAVVMAAVVGVSAVLARTAPPVPEELAPDATPARILTGYELPPELTGDRWFTM
+WRWDWLWVAIIAFLAVWYVRAAWQLRRRGDRWPVLRTLSWLIGLAVLAWATSGAPAVYGM
+VLFSAHMVGHMVLTMIVPLFLVLGAPITLALRALPARTDGTRGPREWILWIVHSPWGAFI
+TNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFIFATVMVGADPLPSR
+PPYPLRLVLLLATMVFHAFIGVAMTTSTGLLQASWFGSIGRDWGPDALTDQHIGGGIMWG
+IGEFPTVLMAVTVAVLWARSDTKTAARLDRRADQDGDAELARWNQMYAAMNHPGADQDPA
+RGDRP
+>PROKKA_01822
+MSAATAPARGSHPAENDDAARPGPSGPVGVPRWIWMLVAAAGAAGLAAAGWLTGVTAARQ
+LSDPGWITRWGVPVGELVSNLAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA
+APLPEHPAFTRVMRIAAVSAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI
+SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHTGAVN
+SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG
+LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG
+PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL
+PPALEGARWITMWRFDWLWVAIIAFLTLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL
+WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI
+LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFLFA
+LVMIGSDPLPRRPPYALRLVLLMATMVFHAFIGVAMTTSTGLLQASWFGNMGRDWGPTAL
+EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA
+RMHGTPATDAPSGAEPAARDSSTGPEEARDVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001538.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001538.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f73bcd0829b06658a9c667d8bc051bbacb9c853
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001538.fa
@@ -0,0 +1,25 @@
+>PROKKA_01904
+MTTTSPRAPRRLGAAAVLAVAALGLTACAGDDAGSAPSASDASSVAPATDAAPASDASPA
+ASTADGQAAGLTITDPWTKATEEGMTGSFGMLENSSDQDLHIVGVRSELGETVELHEMVS
+GEDGQMVMQESPDGFTVPAGGSLELAPGGNHVMFMGLTDPIEPGEDVTYDLELEDGSTLE
+VTSVVRPFTGANESYHGGQSHESEDHADH
+>PROKKA_01600
+MTTTSPRAPRRLGAAAVLAVAALGLTACAGDDAGSAPSASDASSVAPATGASSAASTADG
+QAAGLTITDPWTKATEEGMTGSFGMLENSSDQDLHIVGVRSELGETVELHEMVSGEDGQM
+VMQQSPDGFTVPAGGSFELAPGGNHVMFMGLTDPIEPGEDVTYDLELEDGSTLEVTSVVR
+PFTGANESYHGGESHESEDHADH
+>PROKKA_00954
+MTTPRSARCLSAAAVMAAAALGLTACAGGADDAASSSSSAPTAATSSAPAEGQGAPLTVS
+DPWTKATEDGMTGSFGLLENSSDEDLHVVGVSAEVGAKAGLHVMVADEDGQMVMQQSPDG
+FTVPAGGSFELAPGGAHVMLMGLTEPIEPGEEVAYELELEDGSTVEVVSVARPYTGANES
+YDGGEAEESDEHADH
+>PROKKA_00894
+MTMKHPSQTVSRRLSLAALAAAGSLALAACGGASAPASSSSSAAASSATATTPEAAGSAA
+SSSATAADSSAAPLTMTDAWTKATDGAMTGSFGTLENTSDAPVHVVAVTSDRTDRVELHE
+MAADGKGQMTMQQSPDGFTVPAGGTFELVPGGDHVMFMGLTQPVKAGAEVSYTLKTEDGR
+TLEVTSVARPFTGADESYHGGEASSSMSGMGMNSSMPAGSGHADH
+>PROKKA_01824
+MTTTSPRAPRRLGAAAVLAVAALGLTACAGDDAGSAPSASDASSVAPATDASPAASTADG
+QAAGLTITDPWTKATEEGMTGSFGMLENSSDQDLHIVGVRSELGETVELHEMVSGEDGQM
+VMQQSPDGFTVPAGGSFELAPGGNHVMFMGLTDPIEPGEDVTYDLELEDGSTLEVTSVVR
+PFTGANESYHGGDSHESEGHADH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001540.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001540.fa
new file mode 100644
index 0000000000000000000000000000000000000000..179101718f39e6a9637cbd11f596bc7bdb08e802
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001540.fa
@@ -0,0 +1,25 @@
+>PROKKA_01906
+MRSAVAAAPWAPSGLEDPRPRVVRGPARLARGWAGALAMTALAALFHTAAEPGHGFPEVG
+VVAFAAVLAAPLCTALAGRALSLWRTAAAVAIAQGLFHVLYGLAAGGPAVAPAAGVDPAH
+LGHARPGTGALLAPGEALSSAPTGHLTDLRMLAAHVIAAVLTVLVLRRGEALVLTIAERV
+VAAVCPPPAAHGPLPTPARVRVPVPPALRPATSLALLSSPGRRGPPFALAA
+>PROKKA_01602
+MRSAVAAAPWAPSGLEDPRPRVVRGPARLARGWAGALAMTALAALFHTAAEPGHGFPEVG
+VVAFAAVLAAPLCTALAGRALSLWRTAAAVAIAQGLFHVLYGLAAGGHAVAPAAGVDPAH
+LGHARPGTGALLASGEALSGAPTGHLTDLRMLAAHVIAAVLTVLVLRRGEALVLTIAERV
+VAAVCPPPAAHGPLPTPARVRVPVPPVLRPATSLVLLSSPGRRGPPFALAA
+>PROKKA_00952
+MRSAVDAAPHAFGRPHPAPGRVVRGPARLARGVAGALAMTVLAALFHAAAVPGAGLPDVR
+VAAFAAVLAAPVCTALAGRALSLWRTAAAVAVAQGLFQVLYGIAAGGHAVAPAAGVDPAH
+LHHAAAAAGPLVSVSAGPAAGHVHAAEPLMLAAHAAAAVLTVLVLRRGEALVLAVAERVL
+QAVLPRAASAGPLPLPSPARVPALPAPRPTESLVLLGTPGRRGPPFALAA
+>PROKKA_00892
+MGTPTPVPSRAVAGPARVLRGAAGALAMTLLAALFHSAAASTPLPAPALLLFSAVLAAPV
+CTLLAGRALSLWRTAAAVAVAQGLFHALYSVAAGGRSVATAAGVAPAHLAHSHVGAARPL
+LTVDAASETSAHAAHAGTPGMLLAHLAAAALTVAVLRHGERMLVAAAERVLQAAPVWRLL
+VALAAGLLPTPRPVRVPAWRAPSAPAAVVVLASPGRRGPPAFALAA
+>PROKKA_01826
+MRSAVAAAPWAPSGLEDAPPRVVRGPARLVRGWAGALAMTALAALFHTAAEPGHGFPEVG
+VVAFAAVLAAPLCTALAGRALSLWRTAAAVAIAQGLFHVLYGLATGGHAVAPAAGVDPAH
+LGHAHPGAGALLAPGEALSGAPTGHLTDLRMLAAHVIAAVLTVLVLRRGEALVLTIAERV
+VAAVCPPPAAHGPLPTPARVRVPVPPALRPATSLALLSSPGRRGPPFALAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001547.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001547.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bd15e7235973e222f6a5ef05f1ff4bacd0df8baa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001547.fa
@@ -0,0 +1,30 @@
+>PROKKA_01919
+MTTTTATPGPTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDVAAHL
+ERVRAAAEGRRIALILVTHRHADHTGGVDAFHAATGAPVRAADPDWCRGGAAVLTPDERI
+DAAGTPMLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS
+LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLEQIRAALAALPETEAATITPED
+LAPRIYPGLTGTVARVAVQTVAAHLRHLRED
+>PROKKA_01615
+MTTTTATPGPTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDVAAHL
+ERVRAATEGRRIALILVTHRHADHTGGVDAFHAATGAPVRAADPDWCRGGAAVLTPDERI
+DVAGTPVLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS
+LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLEQIRAALAALPETEAATITPED
+LAPRIYPGLTGTVARVAVQTVAAHLRHLREG
+>PROKKA_00941
+MTTTPATPGLTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDAAAHL
+ERVRAAAEGRRIALILVTHRHADHTGGVDAFHTATGAPVRAADPDWCRGGAAVLTPDERI
+DVAGTPVLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS
+LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLAQVSAALAELGEDEAATVTPEQ
+LAPRIYPGLEGTVARVAVQTVAAHLRHLREG
+>PROKKA_00876
+MTTTPATPGLTPAPLVRCVTAQNPSPMTLAGTNTYVLFADDADAAVVLDPGPAEDAEGHL
+ERVRQAAEGRRIELVLVSHRHADHTGGIDAFHAGTGAPVRAADPSHCRGGGLPLTPDEEI
+VRAGVRILAWHTPGHTSDSYSFAVPESGPHGAVLTGDTILGAGTTMLDHPDGTLTDYLAS
+LARLQAAGPLTVLPAHGPVPAPLDVIARDYIDHREGRLFQLRRALDGMDPARAAMVTPSE
+LVGVIYPEVTGQVARVAEQVLAAHLAYLRRG
+>PROKKA_01839
+MTTTTATPGLTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDVAAHL
+ERVRAAAEGRRIALILVTHRHADHTGGVDAFHAATGAPVRAADPDWCRGGAAVLTPDERI
+DAAGTPVLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS
+LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLEQIRAALAALPETEAATITPED
+LAPRIYPGLTGTVARVAVQTVAAHLRHLREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001549.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001549.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba2385e8ee1d888a504da90225e736b3df01d756
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001549.fa
@@ -0,0 +1,45 @@
+>PROKKA_01922
+MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVIAPIIEQVRHGGEQTLLDLAERFDGV
+RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW
+IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL
+LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA
+EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA
+FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEALVGRIRNAGAVFV
+GPYAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL
+AEDERLPAHGAAIRARFA
+>PROKKA_01618
+MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVVAPIIEQVRHGGEQTLLDLAERFDGV
+RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW
+IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL
+LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA
+EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA
+FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEDLVGRIRNAGAVFV
+GPHAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL
+AEDERLPAHGAAIRARFA
+>PROKKA_00938
+MEADRPRGPGPAAAVVVPRRCTPTPAPPTSLEDPVLSVTDLRQIDTAAADLSRIIPRADV
+DVASTVPVVAPILEQVRTGGEAALLELAERFDGVRPPALRVPAEALAAALEGLDADVRAA
+LEESIRRARLVHAAQLPQDSTVELGEGASVQNHWIPVDRVGLYVPGGRAVYPSSVVMNVV
+PAQAAGVGSLAVTSPPQADHGGLPHPTVLAACALLGVDEVYAAGGAQAVAMLAHGVRDER
+GGWLCAPVDMVTGPGNVYVAAAKRALQGIIGVDAEAGPSEIAVIADGTARADWVAADLIS
+QSEHDPLAASVLITDSEDLVRDVLAAIEAQVPGSFHEEQIRVALTGPQSGVLLVRDLDQA
+VEVSDRYATEHLEIQTRDPEAVAARIRNAGAVFVGPHAPVPLGDYSAGSNHVLPTSGTAR
+HSSGLSTVTFLRLQQRIRYTETGLKELAEGISVLAEDERLPAHGVAVRARFA
+>PROKKA_00873
+MEADRTALDPQEEPVLSVTDLRELDTAAADLSAIVPRAEVDVAYTVPVVAPIIEQVRTGS
+EQTLLDLAERFDGVRPPALRVPAEALTAALEGLDPAVRAALEESIARARKVHAAQVPSGS
+TVELGEGAVVENRWVPVERVGLYVPGGRAVYPSSVVMNVVPAQAAGVESLVVTSPPQRDH
+GGLPHPTVLAACALLGVDEVYAAGGAQAVAMLALGVRADDGDGWLCAPVRMVTGPGNVYV
+AAAKRALQGVIGTDAEAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSADL
+LRDVLASVEAQVPGSFHEEQIRVALTGPQSGVLLVRDMEQALEVSDLYATEHLEIHTRDA
+DALAARVRNAGAVFVGPYSPVPLGDYSAGSNHVLPTSGTARFSSGLNTVTFLRSQQLIRY
+GEAGLKALADGISALAEDERLPAHGVAVRARFA
+>PROKKA_01842
+MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVIAPIIEQVRHGGEQTLLDLAERFDGV
+RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW
+IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL
+LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA
+EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA
+FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEALVGRIRNAGAVFV
+GPYAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL
+AEDERLPAHGAAIRARFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001550.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001550.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0cae1a9f4cb34b03e05da05f60c9b951e6c525b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001550.fa
@@ -0,0 +1,20 @@
+>PROKKA_01923
+MSGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI
+LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRD
+RR
+>PROKKA_01619
+MSGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI
+LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRD
+RR
+>PROKKA_00937
+MSGSVRVSGAVRVDAWLWAVRVYKTRSAATAAVRGGHVRVNDEPVKAAHTLAVGDRVRVR
+KDQRERILEVTGLIGTRVGAPVAVTNYIDHSPPPIPRELLAVPHRERGAGRPTKRDRRKL
+DELRGRASDERS
+>PROKKA_00872
+MGAVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI
+LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRA
+STGRG
+>PROKKA_01843
+MSGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI
+LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRD
+RR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001553.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001553.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9a53ad9431d713325e308d60439fa15c98397b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001553.fa
@@ -0,0 +1,15 @@
+>PROKKA_01927
+MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGNGFKELQENDRVEFETQDGPKGLQ
+AANVTKL
+>PROKKA_01623
+MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGGGFKELQENDRVEFETQDGPKGLQ
+AANVTKL
+>PROKKA_00934
+MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGSGFKELQENDRVEFETQDGPKGLQ
+AANVTKI
+>PROKKA_00865
+MAVGTVKWFNSEKGYGFIAPEDGSADVFVHFSAIQGNGFKELQENDRVEFETQQGPKGLQ
+AADVTKL
+>PROKKA_01846
+MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGGGFKELQENDRVEFETQDGPKGLQ
+AANVTKL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001560.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001560.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d820ee60e0e1b2828f1e7385f572d6febe16f4f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001560.fa
@@ -0,0 +1,55 @@
+>PROKKA_01935
+MSALTEVAAPGTDLPRRRARGRGDGLGPWWLVAAVLPVAFLLVFFAWPVAAMLWRGIGGD
+ADAFTGAVDLTAFGETLARERTWRILGQTLGMAAAGTVVSVALGLPTAFVLHRRRVPGRA
+VLRALVLVPFVLPTVVVGVAFRALLAPGGPLGFTGLDQTTTAVVLAMVFFNVSVVVRQVG
+ALWNALDPRQTEAARTLGASPWRAFRTVTLPQLAPAIAASAALVFLFCASAFGIVQTLGR
+PGYGTLESEIWVQTSVYLDLRTAAVFSVLQFAVVLVAVVVSGVTAARTQRALRLRETPPA
+RLTRADAVPVAVMLAVVALVVAPILTLVVRSFHTRHGWGLGNYRLLSTSAGSGFVGGSTP
+ARALEQSLRVAVDATLVTLVVAVPLALLLTRPFRSRAALAAQRALDGALLLPLGVSAVTV
+GFGFVVSLRAAFPELAASGVLVPLAQAVVALPLAVRALVPVLAAVDPRLREAARTLGAGP
+WRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLASPSAPTLPVLIARLLGRPGADN
+YGMALAAATVLAVLSAGIMLVCERLRPRGPAGAGGL
+>PROKKA_01631
+MSALTEVAAPGTDLPRRRARGRGDGLGPWWLVAAVLPVAFLLVFFAWPVAAMLWRGIGGD
+ADAFTGAVDLTAFGQTLARERTWRILGQTLGMAAAGTVVSVALGLPTAFVLHRRRVPGRA
+VLRALVLVPFVLPTVVVGVAFRALLAPGGPLGFTGLDQTTTAVVLAMVFFNVSVVVRQVG
+ALWNALDPRQTEAARTLGASPWRAFRTVTLPQLAPAIAASAALVFLFCASAFGIVQTLGR
+PGYGTLESEIWVQTSVYLDLRTAAVFSVLQFAVVLAAVVVSGVTAARTQRALRLRETPPA
+RLTRADAVPVAVMLAVVALVVAPILTLVVRSFHTRHGWGLGNYRLLSTSAGSGFVGGSTP
+AQALEQSLRVAVDATLVTLVVAVPLALLLTRPFRSRAALAAQRALDGALLLPLGVSAVTV
+GFGFVVSLRAAFPELAASGVLVPLAQAVVALPLAVRALVPVLAAVDPRLREAARTLGAGP
+WRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLASPSAPTLPVLIARLLGRPGADN
+YGMALAAATVLAVLSAGIMLVCERLRPRGPAGAGGL
+>PROKKA_00924
+MDGPARGGGLLTVGLTSVPAPVGGPGAPPGAPGPAASGGRRRRRTAGGDGIGAWWLLAAV
+VPVAFLLVFFAWPVGAMLWRGVSAEGVLDLGAFAEVLGRERTWRIVGQTLGMAAAGTVLA
+VALGLPAAFVLHRRAFPGRAALRAVITVPFVLPTVVVGVAFRALLAPGGPFGWTGLDQST
+AAVVLAMVFFNVSVVVRQVGALWASLDPRQAEAARTLGSSGWRAFRTVTLPQLAPALASS
+AALVFLFCASAFGIVQTLGRPGVGTLESEIWVQTVVYFDLGTAAVFSTLQFLVVLAAVLV
+SGATARRTRRALRLRDAPVRRLTRADAAPVAVTLATALLVLAPLATLLVRSFHSSEGWGL
+RNYRLLASSPGAGFSGGVTPAQALEHSLRIALDATLLTLLIGVPLALLLTRPVRSAAGRR
+AQRGLDGALLLPLGVSAVTVGFGFVVSLRAEAPALAASGALVPIAQAVVALPLVVRSLVP
+VLGAVDPRLREAARTLGAGPLRVLATVDGPFLLRGLGVAAGFAFAVSLGEFGATSFLSSP
+DYQTLPLLIVKLLGRPGADNYGMALAAATVLAVLSAGTMMACERLGPRAAASRGGI
+>PROKKA_00858
+MPTPAPARGRRRATLRPPRGRRAAGDGLAPLWLLSAAVPVAFLLVLFAWPVAAMLWRGVA
+SVDAAGDPTGGLDLSAFAQTLGAPRTWRILGNTLGLAAAGTAASVALGVPTAFALHRRAF
+PGRGLARAVVTVPFVLPTVVVGAAFRALLAADGPLGWTGLDQTSTAVVMAMVFFNVSVVV
+RQVGGLWAALDPRQAEAARTLGASPWRAFRTVTLPQLAPAVAGAAALVFLFCASAFGIVQ
+TLGRPGPGTLETEIWAQTTVYLDLRTAAVLSTVQLAVVLAAILASGAAAARARRALRLGE
+APARPLTRADAVPAAVTLAVLALVVAPILALLAGSLHSAEGWGLRNYRLLATSPGTGFAG
+GVTPAQALEQSLRTAVDATVVTLVVAVPLALVLTRPVRSRAGRAAQRALDGALLLPLGVS
+AVTVGFGFIVSLRATAPDLAASGALVPLAQSVIAVPLAVRALVPVLGAVDPRLREAARTL
+GAGPWRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLAAADRPTLPVLIARLIGRP
+GADNHGMALAAAVVLAVLSAGALLACERLRPRGAAPSGGL
+>PROKKA_01854
+MSALTEVAAPGTDLPRRRARGRGDGLGPWWLVAAVLPVAFLLVFFAWPVAAMLWRGIGGD
+ADAFTGAVDLTAFRETLARERTWRILGQTLGMAAAGTVVSVALGLPTAFVLHRRRVPGRA
+VLRALVLVPFVLPTVVVGVAFRALLAPGGPLGFTGLDQTTTAVVLAMVFFNVSVVVRQVG
+ALWNALDPRQTEAARTLGASPWRAFRTVTLPQLAPAIAASAALVFLFCASAFGIVQTLGR
+PGYGTLESEIWVQTSVYLDLRTAAVFSVLQFAVVLAAVVVSGVTAARTQRALRLRETPPA
+RLTRADAVPVAVMLAVVALVVAPILTLVVRSFHTRHGWGLGNYRLLSTSAGSGFVGGSTP
+AQALEQSLRVAVDATLVTLVVAVPLALLLTRPFRSRAALVAQRALDGALLLPLGVSAVTV
+GFGFVVSLRAAFPELAASGVLVPLAQAVVALPLAVRALVPVLAAVDPRLREAARTLGAGP
+WRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLASPSAPTLPVLIARLLGRPGADN
+YGMALAAATVLAVLSAGIMLVCERLRPRGPAGAGGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001561.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001561.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f99cbc2c634e3b4c31a84c20bb39d146ed4884b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001561.fa
@@ -0,0 +1,26 @@
+>PROKKA_01936
+MTPTTTGASLRLRDVAIRYPDGSTPVRGTDLDVAAGEIVALVGASGSGKSTILRGIAGLE
+DVVAGTVELDGRDVAAVPTHRRGVGMVFQDGQLFPHRTVGRNVAYGLESAGWDRARRRAR
+VAELLDLVGLTELTDRPVQRLSGGQAQRVALARSLAPAPRVLLLDEPLSALDADLRRRLA
+EDIRAVLRAAGTTGVVVTHDLAEAAVMADRTVRLGAGGRIAAEEDGPAVASQA
+>PROKKA_01632
+MTPTTTGASLRLRDVAIRYPDGSTPVRGTDLDVAAGEIVALVGASGSGKSTILRGIAGLE
+DVVAGTVELDGRDVAAVPTHRRGVGMVFQDGQLFPHRTVGRNVAYGLESAGWDRARRRAR
+VAELLDLVGLTELTDRPVQRLSGGQAQRVALARSLAPAPRVLLLDEPLSALDADLRRRLA
+EDIRAVLRAAGTTGVVVTHDLAEAAVMADRTVRLGAGGRIAAEEAGPAVASPA
+>PROKKA_00923
+MARTTRTSRGATPGSATRGHDDDGRAGLRLRALSVAYPDGATPVRGLDLELAPGEIVALV
+GASGSGKSTVLRGIAGLEDVVGGVVEIDGEDVAAVPTHRRGVGMVFQDGQLFPHRSVARN
+VAYGLEAAGWPRERRRARVAELLELVDLAELAERPVQSLSGGQAQRVALARSLAPRPRVL
+LLDEPLSALDADLRARLAVQIREVLRAAGVTAVVVTHDLAEAAVMADRTVRLGAGGRLAG
+PGEGEPDEGAGPGPEGDAR
+>PROKKA_00857
+MPARMHHHDAAPALRLRGLAVAYPDGSVPVTRADLDLAPGEIVALLGPSGSGKSTVLRGI
+AGLEDVPAGAVELAGRDVTAVPTHRRGVGMVFQDGQLFPHRTVARNVAYGVEAAGWDRSR
+RDARVAELLELVDLAALADRPVQTLSGGQAQRVALARSLAPSPAVLLLDEPLSALDADLR
+TRLAADIRTVLRAEGVSAVVVTHDAAEAAVMADRTVRMGADGVLHGAAADGARTAG
+>PROKKA_01855
+MTPTTTGASLRLRDVAIRYPDGSTPVRGTDLDVAAGEIVALVGASGSGKSTILRGIAGLE
+DVVAGTVELDGRDVAAVPTHRRGVGMVFQDGQLFPHRTVGRNVAYGLESAGWDRARRRAR
+VAELLDLVGLTELTDRPVQRLSGGQAQRVALARSLAPAPRVLLLDEPLSALDADLRRRLA
+EDIRAVLRAAGTTGVVVTHDLAEAAVMADRTVRLGAGGRIAAEEDGPAVASQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001565.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001565.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f922cf5982a9473c4658a69a2bbfa79887f0c104
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001565.fa
@@ -0,0 +1,40 @@
+>PROKKA_01942
+MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVARQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAIMSGTADLVVAGGVQSMS
+AIPLSLSNTAARELGFPDPFTGSESWAARYGDEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADSRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERSGG
+RYGLQTMCEGGGQANVTVIERL
+>PROKKA_01638
+MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVGRQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSRSNTAARDLGFPDPFTGSESWAARYGSEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDATKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG
+RYGLQTMCEGGGQANVTVIERL
+>PROKKA_00914
+MPEAYIIDAVRTPVGRRGKGLAQVHPLDLAAAPLREIVGRQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSHSNRAAAEFGFADPFTGSESWAARYGNEEISQFRGAEMMARHWNLDRDVLEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERSGG
+RYGLQTMCEGGGQANVTVIERL
+>PROKKA_00852
+MGEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPIRELVGRQDVDSAEYDEVILGCIDQLG
+PQAMDVARSAWLAAGLSEDVPGSTIERQCGSGQQAIHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSRSNTAARELGFPDPFTGSESWAARYGDEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAASASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAFALRRMGLGIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG
+RYGLQTMCEGGGQANVTVIERL
+>PROKKA_01861
+MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVGRQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSRSNTAARDLGFPDPFTGSESWAARYGSEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDATKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG
+RYGLQTMCEGGGQANVTVIERL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001568.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001568.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2171a17af784f5ce58285e18e4d3266ab28a7384
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001568.fa
@@ -0,0 +1,30 @@
+>PROKKA_01947
+MSTAPTPSSSDDAPAVLVETRPGVVRLTLNRPAKGNALGLTMAREVLAAIAAAEADESVH
+VLTLTGAGRIFCGGGDVQAMAAAPAGPERRAMIQELGEAAGEVAVALTGSRLLVLAGVNG
+TAAGAGLGLMLGGDVVLVREDAQLVTAFSALGMTPDTGVSYWLPRVLGPVRATQLLLGGR
+RLNGTEAVGWGLATEAAAGDAFAARLAELEDELVAGPAHTYGPTKALTRGADVEALRAHV
+RQEAASIAAASEHPEAVRRVEAFAGR
+>PROKKA_01641
+MTTAPTPSPHDDAPAVLVETRPGVVRLTLNRPAKGNALGLTMAREVLAAIAAAEADESVH
+VLTLTGAGRIFCGGGNVQAMAAAPAGPERRAMIQELGEAAGEVAVALTGSRLLVLAGVNG
+TAAGAGLGLMLGGDVVLVREDAQLVTAFSALGMTPDTGVSYWLPRVLGPVRATQLLLGGR
+RLNGTEAVAWGLATEAVAGGAFAARLAELEDDLVAGPAHTYGPTKALARGADVEALRAHV
+RQEAASIAAASEHPEAVRRVEAFAGR
+>PROKKA_00911
+MSGDGGAADVATVRVEARPGVVRLTLDRPAQGNALSLAMARELTAAVRASEADPDVHVLT
+LTGAGRFFCGGGDLAAMGAASPAERPAVLRELADAASEVALALVRSRLLVVAGVNGTAAG
+AGLGLVLNADVVLVGDDALLLAAYAGIGLVPDTGVSWWLPRAVGPVRAAELTLRGRRLTG
+AEAVEWGVASEAVSGDEFEARLAALEDELAAGAVHAYGPTKALLRGPEIVGYAEHLDRET
+AAISAASGHPEAVRRVDAFLRR
+>PROKKA_00847
+MTTAPTPSSSDDAPAVLVETRPGVVRLTLNRPAKGNALGLTMAREVLAAIAAAEADESVH
+VLTLTGAGRIFCGGGDVQAMAAAPAGPERRAMIQELGEAAGEAAVALTGSRLLVLTGVNG
+TAAGAGLGLMLGGDVVLVREDAQLVTAFSALGMTPDTGVSYWLPRVLGPVRATQLLLGGR
+RLNGAEAVAWGLATEAVAGDAFAARLTELEDELVAGPTHTYGPTKALARGADAEALRAHV
+RQEAASIAAASEHPEAVRRVEAFAGR
+>PROKKA_01866
+MSTAPTPSSSDDAPAVLVETRPGVVRLTLNRPAKGNALGLTMAREVLAAIAAAEADESVH
+VLTLTGAGRIFCGGGDVQAMAASPAGPERRAMIQELGEAAGEVAVALTGSRLLVLTGVNG
+TAAGAGLGLMLGGDVVLVREDAQLVTAFSALGMTPDTGVSYWLPRVLGPVRATQLLLGGR
+RLNGAEAVAWGLATEAVAGDAFTARLAELEDELVAGPAHTYGPTKALARGADVEALRAHV
+RQEAASIAAASEHPEAVRRVEAFAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001571.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001571.fa
new file mode 100644
index 0000000000000000000000000000000000000000..187ee5a3b7afae104cd461b4edadbe1cfbf1ad82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001571.fa
@@ -0,0 +1,40 @@
+>PROKKA_01963
+MTSHTDPSHPAAHPVSRRTLLGGAGLVVASAALLSTPAGTAHAATGPTPFTLGVASGDPW
+PDGVVLWTRLAVDPLALDGLGGMPDQSFRVEYQVATDEGFRKVVRSGAVTTDRAQGYAVH
+VTLTGLRPGTEYFYRFRALGHLSRVGRTVTAPARGSNPSRLTMTVASCANWEHGYFTAYG
+HMAAERPDLMVHLGDYYYEIMPYGYPVSSGVPRAHRNGESRTLAQYRARMAQYKTDPHLQ
+DAHAAAPWLVIFDDHELENNWADETPEIWDPSFLARRAAAFQAYYENMPLRASSVPRGID
+MQLYRRIHWGDLATFHLLDTRQYRSDQANLDLVKVVDADARDSRRTITGAAQEAWLREGF
+ETSVARWDLITQQVPFVQYDRTSGPLLWGDMDTWDGYVASRDRVVSAWTAAGVRNPVVLT
+GDIHEAFASDIKQDFNDLSSESVGVELITTSITSGGDGSDAAAEALAWNPHIKFNNDLRG
+YLRVDLSAQLLEARFRVVDYVSELGSSVRTRAVFGVGDGEHRLHRIA
+>PROKKA_00894
+MPLRASSVPRGIDMQLYRRIHWGDLATFHLLGTRQYRSDQANLDLVKVVDADARDPRRTI
+TGAAQEAWLREGFETSVARWDLITQQVPFVQYDRISGPLLWGDMDSWDGYVASRDRVVSA
+WTAAGVRNPVVLTGDIHEAFASDIKRDFNDLSSESVGVELITTSITSGGDGSDAAAEALA
+WNPHIKFNNDLRGYLRVDLSAHMLEARFRVVDYVSELGSSVRTRAVFGVGDGEHRLHRIA
+>PROKKA_00439
+MSSPSPTLSRRRLLGLSGASAAVLALGVNAPDAAHAEPLPQRDGLFGLGVASGYPRPDGA
+VLWTRLAPEPLAENGHGGMPLRSVPVKWEVARTADFRRIVARGTALAQPELAHSVHPRVE
+GLAPGTEHFYRFVVGPQTSPVGRFVTLPAAGAATDDYTVGLISCQAWYHGHFAAHRHLAQ
+EEDLDLTVFLGDYIYEYGITAANLWRQGAEVTPAHAVEIETLEQYRLRYALTKSDPHLQA
+LHARAAAVAIWDDHEVQNNYVGAASSTGIPEELFAHRIAVAYRAFYENLPVDIDALPEGP
+ESDIVAGLDVGALARISLLDTRQFRDAPPADAADRERENRTMLGAAQERWVTERLRTSQS
+QWNVLAGGVVLAPISDDRTDQWDGYPAARRRLLTEMKRAGNAVMLTGDIHKHVAAELRGE
+SAGLPAGPAGVELVTTSAASDGDGAKTDKYTPDWVRHDYVRHYDGRRGYLHLRFTPAQLT
+SSFWVVPWVESDDTAPKELSARFTTPAGSSRLIEA
+>PROKKA_00834
+MAAAALISTPAGTAHAAAGPNPFTLGVASGDPWPDGFVIWTRLATMPLNRDGFGGMPDAS
+FTVEWQVSRHADFRSTVRTGTTTTSRAQGYAVHVTLTGLRAGTEFFYRFRCNGHLSRTGG
+AVTAPALGSMPGHLTATEAERLIRAAGFAPVRLGGIDESIRMEVTGELHPFGGLDGTLPT
+TANVEQLRG
+>PROKKA_01889
+MSSHTDPAHPTAHPVSRRTLLGGAGLVVASAALLSTPAGTAHAATGPTPFTLGVASGDPW
+PDGVVLWTRLAVDPLALDGLGGMPDQSFRVEYQVATDEGFRKVVRSGAVTTDRTQGYAVH
+VTLTGLRPGTEYFYRFRALGHLSRVGRTVTAPARGSNPSSLTMTVASCANWEHGYFTAYG
+HMAAERPDLMVHLGDYYYEIMPYGYPVSSGVPRAHRNGESRTLAQYRARMAQYKTDPHLQ
+DAHAAAPWLVIFDDHEVENNWADETPEIWDPNFLARRAAAFQAYYENMPLRASSVPRGID
+MQLYRRIHWGNLATFHLLDTRQYRSDQANLDLVKVVDADARDSRRTITGAAQEAWLREGF
+ETSVARWDLITQQVPFVQYDRSSGPVLWGDMDSWDGYVASRDRVVSAWTTAGVRNPVVLT
+GDIHEAFASDIKQDFNDLSSESVGVELITTSITSGGDGSDAAAEALAWNPHIKFNNDLRG
+YLRVDLSAQLLEARFRVVDYVSELGSSVRTRAVFGVGDGEHRLHRIA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001576.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001576.fa
new file mode 100644
index 0000000000000000000000000000000000000000..826c9510c77383ebfa3db476639e9efd05c48e09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001576.fa
@@ -0,0 +1,39 @@
+>PROKKA_01971
+MAPARRRVLYYAHQHGAGHLRHAAGLASTGAFDVTVVTAHPRAAELLPADVPVIPLPSDL
+VPGHEQPARSPLHWSPVGPEIRARFDALHAAAQRVGPDVCVVDVSVEAALFLRLAGWPVL
+HRRMHGERTDPAHALVYAEADGLFAHYAAELEVPAWRAAHADRVTYLGVADVTGRLGTRT
+TTTSTARAAPRVAVIAGTGGGGVRAADLARAASAVPEATWEVYGPIAGVGEPEAPGGLAA
+EAMPATVTLHGWVQAPARRAADADVVVVSAGHNAVVDAARSGRPVVLAPEPRPFDEQRVF
+VREIHRAAGVPWCAWEDPDADWAGAVRGALADPTAADRLAGLLLVAPDEYRRRWEAAIEG
+ALG
+>PROKKA_01665
+MAPARRRVLYYAHQHGAGHLRHAAGLASTGAFDVTVVTAHPRAAELLPADVPVIPLPSDL
+VPGHQQPARSPLHWSPVGTEIRARFDALHAAAQRVDPDVCVVDVSVEAALFLRLAGWPVL
+HRRMHGERTDPAHALVYAEADGLFAHYAAELEVPAWRAAHADRVTYLGVADVTGRLGTRA
+TTTSSAGAAPRVAVIAGTGGGGVRAADLARAASAVPEATWEVYGPIAGVGEPEAPGGLAA
+EAMPATVTLHGWVQAPARRAADADVVVVSAGHNAVVDAARSGRPVVLAPEPRPFDEQRVF
+VREIHRAAGVPWCAWEDPDADWAGAVRGALADPAAADRLAGLLLVAPGEYRRRWEAAIEG
+ALG
+>PROKKA_00888
+MSDGAAAVSRPGASARPSRRRRVLYYAHQHGSGHVRHAANLAATGAFDVTVVSAHPDAAR
+MLLAGTPVLPLPSDVVPGHVQPERSPLHWTPVGPQIRDRFAALHDAARDVRPDVCVVDVS
+VEAALFLRLAGWPVLHRRMHGERTDPAHALVYAEADGLFAHYAEELEDPAWREAHAGRTA
+FLGVPDVTGRLGARATTTTATTTAAGGSAPRVAVIAGTGGGGVRAADLARAAAAVPEATW
+EVYGPVAGADELQAPGGAAGSRSSDADATTGTAPTAGVALPANVTLHGWVEAPASRAAEA
+DVVVVSAGHNAAVDAARSGRPVVLAPEPRPFDEQHVFAREARRAAGVPWCAWEDPDADWA
+GAVRGALADPSAADRLAALLLVEPGEYRRRWEAAVEAALEATQG
+>PROKKA_00829
+MSGRRLRVLHYAHQHGSGHVRHAATLIRADVADVTVATAHPDAARLLPTGTRIVPLPTDI
+VPGHGQPEGSPLHHTPVGPAIQARFDALHDAARAVRPDVCVVDVSAEAALFLRLAGYPVV
+HRRMHGDRTDPAHRLVYAEADALFAHYGEVLEDPAWQAEFGARTAHLGVPDADGRLGRTA
+APARAGEAPRVVAVTGTGGGGVAARDIARAARSTPGARWHVIGPVRDAGGADLPENLELQ
+GWVEDVPAALAAADVVVVSAGHNAAVDAAHSGRPVVLAPEERPFAEQRRFAEAVERAAGV
+PWRAWEDPEADWAGAVARALGDPAAADRLAAALLRPPAEHAAGWGALLERAAASAQ
+>PROKKA_01897
+MAPARRRVLYYAHQHGAGHLRHAAGLASTGAFDVTVVTAHPRAAALLPADVPVIPLPSDL
+VPGHQQPARSPLHWSPVGTEIRARFDALHAAAQRVDPDVCVADVSVEAALFLRLAGWPVL
+HRRMHGERTDPAHALVYAEADGLFAHYAAELEVPAWRAAHADRVTYLGVADVTGRLGTRA
+TTTSSAGAAPRVAVIAGTGGGGVRAADLARAASAVPEATWEVYGPIAGVGEPEAPGGLAA
+EAMPATVTLHGWVQAPARRAADADVVVVSAGHNAVVDAARSGRPVVLAPEPRPFDEQRVF
+VREIHRAAGVPWCAWEDPDADWAGAVRGALADPAAADRLAGLLLVAPDEYRRRWEAAIEG
+ALG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001577.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001577.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8738372b3b4f38c6b3f3e1acb34aa481c7715b4f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001577.fa
@@ -0,0 +1,38 @@
+>PROKKA_01972
+MRISVLTHMLHPIRSPYEGGLEMHTAMTVEHLVRRGHDVTVYAREGTRVPGDVVAVLPAE
+GAGPGRAGARVREEAARRACALILDDDSDAVLNNSLSPAPLELLRARPVVTVLHTPATLA
+EVLAVVDAPGWTAPDHHRWASVSASNALAWQHRLPRVDVVPNGIELHQWVSDAVPVRGRA
+VWSGRITAEKGLHVAIDAARIAGMELHFAGPISDEEYHAREVVPRLGPDTVYHGHLDHHA
+LPHMLATGEVFLATPLWAEPFGLAVVEAMALGVPVAALLSGAMGEIVAPQAGALAVHHTA
+QELAVSIRHARRKDRGRVRAWACRFSAETMVEGYVDLLEQAAEDARDLAAAEDAYGFDPH
+GVPRPSADAADLESL
+>PROKKA_01666
+MRISVLTHMLHPIRSPYEGGLEMHTAMTVEHLVRRGHDVTVYAREGTRLPGDVVAVLPAE
+GAGPGRAGARVREAAARRACALILDDDSDAVLNNSLSPAPLELLRARPVVTVLHTPATLA
+EVLAVVDAPGWTAPDHHRWASVSASNALAWQHRLPRVDVVPNGIELHHWVSDAVPVRGRA
+VWSGRITAEKGLHVAIDAARIAGMELHFAGPISDEEYHAREVVPRLGPDTVYHGHLDHHA
+LPHMLATGEVFLATPLWAEPFGLAVVEAMALGVPVAALLSGAMGEIVAPQAGALAVHHTA
+QELAVSIRHARRKDRGRVRAWACRFSAETMVEGYVDLLEQAAEDARDLAAAEDAYGFDPQ
+GVPRPSADAADLESL
+>PROKKA_00887
+MRISVLTHMLHPIRSPYAGGLEMHTAMTVEHLVRRGHDVTVYAREGTRLPADVVPVLPAE
+GAGPGKEGDRLREEATRRACEMVLADDSDAVLNNSLSPAPLELLRERPMITVLHTPATLA
+EVLAVVDHPDWRAPQHHRWASVSASNALAWQHRLPRVDVVPNGIELHHWVSDAVPVRGRA
+VWSGRITAEKGLHVAIDAARIAGMELHFAGPISDEEYHAREVVPRLGPDTVYHGHLDHQT
+LPHMLATGEVFLATPLWAEPFGLAVVEAMALGVPVAALLSGAMGEIVAPQAGALAVHHTA
+QELAVSIRHARRKDRGRVRAWACRFSAETMVEGYLDLLEQAAEDARDGELV
+>PROKKA_00828
+MRIDVLTHPLHPIRSPYEGGLEMHTAMTVEHLVAAGHQVRVHARAGTRIPGADVVSLLAA
+APDAPGAEGQAVREGALAGACQRILADAPDAVLNNSLSPQPLIRLRSLPMLTVLHTPATL
+EPVLEVTDAPGWTPPAHHRWASVSVSNALAWRHRLPSVDVVPNGIDLDRWVSDRAPVPGR
+AVWSGRITPEKGLHMAIDAARAVGMELHAAGPVSDPAYYAERVAPRLGEDVVHHGHLDHT
+ALPDLLATGEVFLSTPLWAEPFGLATVEAMALGVPVAALLTGAMGEIVAPQAGALAVHHS
+VEALADAIRYARRKDRARVADWARRFSADTMVAGYLDLLEQAVADHADDAELRKVPA
+>PROKKA_01898
+MRISVLTHMLHPIRSPYEGGLEMHTAMTVEHLVRRGHDVTVYAREGTRLPGDVVAVLPAE
+GAGPGRAGARVREAAARRACALILDDDSDAVLNNSLSPAPLELLRARPVVTVLHTPATLA
+EVLAVVDAPGWTAPDHHRWASVSASNALAWQHRLPRVDVVPNGIELHHWVSDAVPVRGRA
+VWSGRITAEKGLHVAIDAARIAGMELHFAGPISDEEYHAREVVPRLGPDTVYHGHLDHHA
+LPHMLATGEVFLATPLWAEPFGLAVVEAMALGVPVAALLSGAMGEIVAPQAGALAVHHTA
+QELAVSIRHARRKDRGRVRAWACRFSAETMVEGYVDLLEQAAEDARDLAAAEDAYGFDPQ
+GVPRPSADAADLESL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001584.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001584.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec04b19e6792d943efe468c03ccccdeccd50e709
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001584.fa
@@ -0,0 +1,40 @@
+>PROKKA_01984
+MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGAGSGASDQDYRDAGAELVDD
+VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV
+TRGRSLPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIGETVADADLVIGSVLI
+PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTSALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGVLTLPSVATAVAD
+ELGLDPRKDVRVTSEVLAEA
+>PROKKA_01678
+MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGVGSGASDQDYRDAGAELVDD
+VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV
+TRGRSLPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIGETVADADLVIGSVLI
+PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTSALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGALTLPSVATAVAD
+ELGLDPQKDVRVTSEVLAEA
+>PROKKA_00873
+MLIGVPTEVKNNEFRVALTQGGVLELVRRGHEVLVQAGAGVGSGISDQVYLDAGAQLVQD
+PDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPECTRAILDSGTTAIAYETV
+TRGRALPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIAETVADADLVVGSVLI
+PGAAAPKLVTAEMVEQMRPGSVLVDIAIDQGGCFENSRPTTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTAALTNATLPYIQRIADLGWREALAADEGFASGLNAHEGALTLPSVAEAMAG
+PLGLDPRKDARTTADVLASA
+>PROKKA_00809
+MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGVGSGASDQDYRDAGAELVDD
+VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV
+TRGRALPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRMRTLASSHLNIGETVADADLVIGSVLI
+PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTAALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGVLTLSSVATAVAD
+ELGLDPQKDVRVTSEVLAEA
+>PROKKA_01910
+MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGAGSGASDQDYRDAGAELVDD
+VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV
+TRGRSLPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIGETVADADLVIGSVLI
+PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTSALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGVLTLPSVATAVAD
+ELGLDPRKDVRVTSEVLAEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001586.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001586.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0209a547f35b03f87cea06d9065233eabd8678d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001586.fa
@@ -0,0 +1,30 @@
+>PROKKA_01988
+MPVRNRRAAALPAKLSRSWLLVNAATPDAFAPALASEADSVIFDLEAAVPEEQKDAARRH
+VVDALSGGMTAWVRISATSTDHWQRDLEALAGLDGVRGVVLAETKEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGGLPGAIDGPPGNTDGEDAVIESSAVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA
+>PROKKA_01682
+MPVRNRRAAALPAKLSRSWLLVNAATPDAFAPALASEADSVIFDLEAAVPEEQKDAARQH
+VVDALSGGMTAWVRISATSTDHWQRDLEALTGLDGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGGLPGAIDGPPGNTDGEDAVIESSVVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA
+>PROKKA_00869
+MPVRNRRAAALPAKLSRSWLLVNAARPEDFAPALASEADSVIFDLEAAVPEDKKDAARQH
+VVDALSGGMTAWVRIAATSTDHWQRDLEALAGVDGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGGLPGAIDGPPGNTDGEDAVVDSSAVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA
+>PROKKA_00806
+MPVRNRRAAALPAKLSRSWLLVNAARPEDFAPGLASEADSVIFDLEAAVPEEHKDAARQN
+VIEALSGGMTAWVRISATTSEHWARDLEALEGLSGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGRLPGAVDGPPGAGDDEAAVAASSEVTHSMGMTGRLCLNRGQVEWVNRALSPSEDELTW
+AHDLLDKHAAGAAVGDGSYLPRLRRAEKIADLADSYGLWNA
+>PROKKA_01914
+MPVRNRRAAALPAKLSRSWLLVNAATPDAFAPALASEADSVIFDLEAAVPEEQKDAARQH
+VVDALSGGMTAWVRISATSTDHWQRDLEALAGLDGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGRLPGAIDGPPGNTDGEDAVIESSAVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001587.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001587.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75dc48aa170e5ada5f632d7c281bc9f4db123c2b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001587.fa
@@ -0,0 +1,32 @@
+>PROKKA_01989
+MRPPSPPRALRLMGAVAAACLLAGCAVDPGLAEDSASDDGVPLPATEGYQPLTVYLAVAE
+TEAVPGTSGRPFGCGDLLVPVQTVPTDTEDEADAALDFLFADEQGWHGDPSLWNAVFDAR
+ETLTPTGHRREGDVEIFTFTGTVTPEDDCTAERIRAQLQATAAAFTSAGQVRLEVDGRDL
+DDVLGLEPLRLGESVDVPQGDPTPSGEPSDESGEQTWAPEGESPEDTWAPAEPSDETWAP
+AEESSWGPAEPTQGTWSPGPEPSAP
+>PROKKA_01683
+MRPTPPSRALRLTGAVAAACLLAGCAVAPDLAEDSASDDGVPLPATEGYQPLTVYLAVAE
+PEAVPGTSGRPFGCGDLLVPVQTVPTDTEDEADAALDFLFADERGWHGDPSLWNAVFDAR
+ETLTPTGHRRAGDVEIFTFTGTVTPEDDCTAERIRAQLQATAAAFTSAGQVRLEVDGRDL
+DDVLGLEPLRLGESVDVPQGDPTPSGEPSDGSGEQTWAPEGESSEDTWAPAEPSTWAPTE
+ESSWGPAEPTQGTWSPGQEPSAP
+>PROKKA_00868
+MRQRPASRAVLLVGAAAAVGLLGGCAAEPGAPAADGSAQGDALPRPEVDGYAPLTVWLTV
+PAAEAVPGSTGRAYGCDDLLVPVQTVPADAPDDADAALDFLFSDERGWHGDPSLWNAVFE
+TRESLTPTGHRLEGDVDVFTFTGTVTAEGECEAERIRAQLQETAAAHTSAGQVRLEVDGR
+PLDDVLGLAPLALGDEVDVPESGADPSESPTEPADEPWEEPAEDPWAEPTEDTWSEPTED
+PWAESEESAEPSPTAWEEPAEETWEPQDETAPTEEDAPTEWDGTVDDGSASEDVPAEVEE
+PPAQDEGADAADESAPAEDAGADGAGNLGIGDPDATEPSAP
+>PROKKA_00805
+MRIRPTPRVRLAAVLATSAALTSGCGALTGQGLDEPKELTVHLTVPRADAASSFEGRPYG
+CDDLLVPVTTAPSSGVDHGDAALDFLFSDLQGEHGDPALQNAVKATADTLHPTGHHRDGS
+TEVFTFDGTVTAEDECAAQRIRAQLQETARAQSPVPDVRLEVGGRPLDEVLGLPALSLGD
+PVKGGAASTPRATPTPESTPSPTATPTPTPTTVPGSSASPAPTSASPTATPAPSTSAAPS
+TTGPSSASPTAETSSAAPASPDPASADPATAAPTSASATAGGASPSVEPTDGTSLRSPGA
+GDATATTAPLDGLDGGAAGGTGTGGADATAPGGAPSAGAAAGAGAGSSATG
+>PROKKA_01915
+MRPPSPSRALRITGAVAAACLLAGCAVDPGLAEDSASDDGVPLPATEGYQPLTVYLAVAE
+AEAVPGTSGRPFGCGDLLVPVQTVPTDTEDEADTALDFLFADERGWHGDPSLWNAVFDAR
+ETLTPTGHRRAGDVEIFTFTGTVTPEDDCTAERIRAQLQATAAAFTSAGQVRLEVDGRDL
+DDVLGLEPLRLGEPVDVPRGVPAPSGEPSDGSGEQTWAPEGESSWGPAEPTQGTWSPAQE
+PSTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001595.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001595.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83bedad0bec23de6596c5490ee5093f795bd0d8b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001595.fa
@@ -0,0 +1,44 @@
+>PROKKA_01999
+MSHDVEAPAGVPGSVAVVGGGVAGFAVVRELRRRGFAGEIALVDPQGVPYDRPPLSKEFL
+TGDADARRLLLAPPTWFAEHGVELVEDAAVRVVPGGVHPDGGPAPHRVETASGRVLEADA
+VVLATGGRPRALDVAGADHPDLITLRTRSDAEALRDRLTFGAEVAVVGGGFTGAEVAAAA
+RRSLAAVTLVTGTDAPARAAVGPALAARLHRMHVEHGVAVEVGRAAWIEHRDADGGAALP
+AAHRLHLHDGRTVDADVVVLAGGTVPDTALAEDAGLEVADGVLTDAMGRTTVPGILAVGD
+AARARESAWATSRHWEPALRSGAAAAAALLGEQTDAPGAPWFWSDRYDAHVEAVGDMTVP
+AGGRIVDREVRGVVVASFALAADGTLRGAASIDDPMTVKAARRIIDRGIVVDAAALADPA
+VPVKSLARG
+>PROKKA_01693
+MSHDVEAPAGVPGSVAVVGGGVAGFAVVRELRRRGFAGGIALVDPQGVPYDRPPLSKEFL
+TGDADAHRLLLAPPAWFAEHGVELVEDEAVRVVPGGVHPDGGPAPHRVETASGRVLDADA
+VVLATGGRPRALDVAGADHPDLITLRTRADAEALRDRLTFGAEVAVVGGGFTGAEVAAAA
+RRSLAAVTLVTGTDAPARAAVGPALAARLHRMHAEHGVAVEVGRAAWIEHRDADGGAALP
+AAHRLHLHDGRTVDADVVVLAGGTVPDTALAEDAGLEVADGVLTDAMGRTTVPGILAVGD
+AARARESAWAPSRHWEPALRSGAAAAAAILGEEADAPGAPWFWSDRYDAHVEAVGDMTVP
+AGGRIVDREVRGTVVASFALAADGTLRGAASIDDPMTVKAARRIIDRGIVVDAAALADPA
+VPVKSLARG
+>PROKKA_00858
+MSGDVDARAGAPASVVVVGGGVAGFGAVRELRRRGHTGSLALVEPQGVPYDRPPLSKDYL
+TGETDAHRLLFAPPSWFAEHDVELVEEAAVRLTPGGAHPDGDPVPHRVELASGRVLEAEA
+VVLATGGRPRPLDVEGATHPDLITLRTRADADALRERLHFGAEVAVVGGGFTGAEAASSA
+RQALAGVTLVTATDAPALRAVGPALAARLHRMHAEHGVAVEVGRVARIEHRDDDGGAALP
+AAHRLHLGDGRTVDADVVVLAGGTVPDTALAEEAGLEVADGILVDEAGRTSVPGILAVGD
+TARATGSAWGPSPHWEPALRSGAAAAAALLGEEPEPPGAPWLWSDRHGCHVEAVGDMAVP
+PGGASVDREARGAAVASFVLDAEGRMRGAASIDDPMTVKAARRIIDRGIVVDPQALADPT
+VPLKSLARG
+>PROKKA_00794
+MTVPASVLVVGGGVAGFGTVRELRRRGFEGKLTLVDPQGLPYDRPPLSKDFLTGETDAHR
+LLFAPPAWFAEHAVELVTARVDRMDLTGEHPAAVLDDGTVRAADAVVLAPGGRPRPLDVP
+GGDRPGVLVLRTRADAEAIAARLHFGARVVVVGAGLTGSEVASAAREAMAEVTLVSASPA
+PAAAAVGPALAARLHALHAARGVDVVQGRVLRIEHADDAPGLDAPHRVHVALADGGEAAL
+DADLVVAAVGILPDAALAAEAGLELAVDGGILVDAAQRTSDPRVLAVGDAARRRDAAYAA
+PAMHWEPALQDAADAAAALLGEDLPERGAPWFWSDRHGVHVEGVGAMRPPEGGRIVDREV
+RGTVVASFALAADGAMVGAASVDDPMAVKAARRIVDRGIVVDPERLADPSVPVKALLRG
+>PROKKA_01925
+MSHDVEAPAGVPGSVAVVGGGVAGFAVVRELRRRGFAGGIALVDPQGVPYDRPPLSKEFL
+TGDADAHRLLLAPPAWFAEHGVELVEDEAVRVVPGGVHPDGGPAPHRVETASGRVLDADA
+VVLATGGRPRALDVAGADHPDLITLRTRADAEALRDRLTFGAEVAVVGGGFTGAEVAAAA
+RRSLAAVTLVTGTDAPARAAVGPALAARLHRMHAEHGVAVEVGRAAWIEHRDADGGAALP
+AAHRLHLHDGRTVDADVVVLAGGTVPDTALAEDAGLEVADGVLTDAMGRTTVPGILAVGD
+AARARESAWAPSRHWEPALRSGAAAAAAILGEEADAPGAPWFWSDRYDAHVEAVGDMTVP
+AGGRIVDREVRGTVVASFALAADGTLRGAASIDDPMTVKAARRIIDRGIVVDAAALADPA
+VPVKSLARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001596.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001596.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b1cd9f3b9a55101b64e52ef12580d0190b55598
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001596.fa
@@ -0,0 +1,15 @@
+>PROKKA_02000
+MAEPIHIGAAADVPEGEAIVVPAATAGTRDDVAVFHTDAGEFHAIDDTCTHEDASLAEGW
+LEDDRVECPLHAAQFCLRTGEALCLPATKGVGVHRVEEREGQLYLVPGA
+>PROKKA_01694
+MAEPIHIGAAADVPEGEAIVVPAATAGTRDDVAVFHTDAGEFHAIDDTCTHEDASLAEGW
+LEDDRVECPLHAAQFCLRTGEALCLPATKGVGVHRVEEREGQLYLVPGA
+>PROKKA_00857
+MAEPIHIGAAADIPEGEAVVVPAATAGTSDDVAVFHAEDGAFYAIDDTCTHEDASLAEGW
+LEGTQVECPLHSAQFCLKSGEALCLPATRPVGTHPVQERDGQLYLTPGA
+>PROKKA_00793
+MSREINVGPASAVPEGESLLVPNDTTGTKDHIGVFHAEDGAFYAIDNTCTHQDYALSEGF
+VEDCRVECPLHGASFDLRTGEALSLPATKPVGTHRVEERDGDLWLTVEDGE
+>PROKKA_01926
+MAEPIHIGAAADVPEGEAIVVPAATAGTRDDVAVFHTDAGEFHAIDDTCTHEDASLAEGW
+LEDDRVECPLHAAQFCLRTGEALCLPATKGVGVHRVEEREGQLYLVPGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001605.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001605.fa
new file mode 100644
index 0000000000000000000000000000000000000000..690104d1f48affdab76117394c958cc3866f68c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001605.fa
@@ -0,0 +1,40 @@
+>PROKKA_02012
+MTETTDAPTTGKRRATFNTLEVSELRRLTEDSVEVTFAVPEELADDYDYVPGQYVALRKE
+LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGTFSTWANESLEVGEKIDVMNPQGAFTSRT
+HVTSLNDAQKVAAEKVAEKKDTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS
+AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD
+EWFLCGPFELVQLTRETLAARGVPEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI
+EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA
+LEKDEVEKGYVLTCQTRPTSDSITLDFDA
+>PROKKA_01722
+MTETTDVPTTGKRRATFNTLEVSELRRLTDDSVEITFAVPEELADDYDYVPGQYVALRKE
+LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGKFSTWANESLEVGEKIDVMNPQGAFTSRT
+HVTSLNDAQKVAAEKVAEKKDTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS
+AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD
+EWFLCGPFELVQLTRETLAARGVSEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI
+EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA
+LEKDEVEKGYVLTCQTRPTSDSITLDFDA
+>PROKKA_00830
+MTETTVTPATGKRRATFNTLEVSELRRLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE
+LDGQEVRRSYSICAIPKRGEIRVAVKKDIGGKFSTWANEVLEVGEKIDVMNPQGAFTSRS
+HVTSLNDAEKVAAEKVAQNKNTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS
+AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDAEKLTTLLDRVIDVDGTD
+EWFLCGPFELVQLARETLSARGVDEDDVRFELFTTGRPENPQGHSGRVVEADPSGDNVTI
+EFNLDGLSGKVESPKSAHETILNAALRVRSDVPFACAGGVCGTCRAKVTDGEYEMDENYA
+LEKDEVEAGYVLTCQTRATSDSITVDYDA
+>PROKKA_00767
+MTETTDAPITGKRRATFNTLEVSGLRKLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE
+LDGAELRRSYSICAVPQRGEIRVAVKKDLGGTFSTWANEVLEVGEKIDVMNPQGAFTSRT
+NVTSMNDPEAVAAEAVKQDQTHLVALAAGSGITPIMAIAKSVLAASDSARFDLIYANRSA
+MDVMFAEEIGDLKDKYPARFTVNHVLSREQRVAPLLSGRIDDEKLNTLLDRVIDVENTDE
+WFLCGPFELVQLARDTLSERGVAEDDVRFELFTTGKPEAPQGQSGRGVEADPSGDNVTIE
+FNLDGLSAKVESPKSAHETILNAALRVRSDVPFACAGGVCGTCRAKVTEGEFTMEENYAL
+EKDEVEQGYVLTCQTRPTTDSIKVDFDA
+>PROKKA_01950
+MTETTAAPTTGKRRATFNTLEVSELRRLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE
+LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGKFSTWANESLEVGEKIDVMNPQGAFTSRT
+HVTSLNDAQKVAAEKVAENKDTHLVAFAAGSGITPIMAIAKAVLAASESSRFDLVYANRS
+AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD
+EWFLCGPFELVQLTRETLAARGVSEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI
+EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA
+LEKDEVEKGYVLTCQTRPTSDSITLDFDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001606.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001606.fa
new file mode 100644
index 0000000000000000000000000000000000000000..803b3e2e2b93471938ca0b2465ffcf235967bf26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001606.fa
@@ -0,0 +1,30 @@
+>PROKKA_02013
+MIEITVENGVAEIVLDAPQRMNALDEAALAELQAAYERAAAGVESGEVRAVLLRGEGRGF
+CAGRDISAVVPAEDDATAYLRDRVTPVLRAMSEIPVPTFAAVQGACLGVGLGLAIATDVV
+YVAKDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELLSGAEAVQAGLFSRA
+LPADELLEFTRAKVAQVASGATLAFRASKELVAQVRDRRVGLWESLDAENIAQGELCGTA
+DYAEGFQAFQEKRKPEFTGRG
+>PROKKA_01723
+MIEITVENGVAEIVLDAPQRMNALDEAALAELQAAYERAAAGVESGEVRAVLLRGEGRGF
+CAGRDISAVVPAEDDATAYLRDRVTPVLRAMSEIPVPTFAAVQGACLGVGLGLAIATDVV
+YVAEDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELLSGAEAVQAGLFSRA
+LPADELLEFTRAKVAQVASGATLAFRASKELVAQVRDHRVGLWESLDAENIAQGELCGTA
+DYAEGFQAFQEKRKPEFTGRG
+>PROKKA_00829
+MTVADGVAEVRLNAPKKMNSLDEAALADLHEAYRRAAAGVESGEVRAVLLHGEGRGFCAG
+RDISAVDPAEDDATAYLRDKVTPVLRAMSEIGVPTFAAVQGACLGVGLGLAIATDVVYVA
+EDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELISGEEAVRAGLFSRSVPA
+DELLEFTRAKAAKAAQGATLAFRASKELVRQIRDERVGLWESLDAENIAQGDLCNTADYA
+EGFKAFQEKRRPEFTGRG
+>PROKKA_00766
+MIELAIADRVAVITLNAPQKMNSLDEQALADLADAYAQASAGAESGEVRAILLRGEGRGF
+CAGRDISNVVPADDDATAYLRDKVTPVLKAISEAPVPTFAAVQGACLGVGLGLAIASDVV
+YVAENAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELISGAEAVQAGLFSRA
+VPAEELDGFTREKVAKVADGATLAFRASKELVRQIRDRRVGLWESLDAENVAQGELCDTA
+DYAEGFTAFQEKRKPEFTGRP
+>PROKKA_01951
+MIEITVENGVAEIVLDAPQRMNALDEAALAELQAAYERAAAGVESGEVRAVLLRGEGRGF
+CAGRDISAVVPAEDDATAYLRDRVTPVLRAMSEIPVPTFAAVQGACLGVGLGLAIATDVV
+YVAEDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELLSGAEAVQAGLFSRA
+LPADELLEFTRAKVAQVASGATLAFRASKELVAQVRDHRVGLWESLDAENIAQGELCGTA
+DYAEGFQAFQEKRKPEFTGRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001608.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001608.fa
new file mode 100644
index 0000000000000000000000000000000000000000..133546bcd5b86574332cb0b6d158c8379a5038c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001608.fa
@@ -0,0 +1,30 @@
+>PROKKA_02017
+MTDFSHFSALHVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESTREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRLSKRVFHLPRGAHPHVDEIAQA
+ILFESDAKFERMQAFLDRKKK
+>PROKKA_01726
+MDDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESKCEPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPEALLDAADALADRIAQQDPLAVRLSKRVFHLPREAHPHVDEIAQA
+ILFESEAKFERMQAFLDRKKK
+>PROKKA_00804
+MTDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESKREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPEALEVAAHALADRIAKQDPLAVRISKRVFHLPREAHPHVDEIAQA
+ILFESEAKFDRMQAFLDRKKK
+>PROKKA_00763
+MADFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESKREPGRFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETGLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRISKRVFHLPREAHPHVDEIAQA
+ILFESQAKFERMQAFLDRKKK
+>PROKKA_01954
+MTDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESTREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRLSKRVFHLPREAHPHVDEIAQA
+ILFESEAKFERMQAFLDRKKK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001611.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001611.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f4d2fb56a7689ed1256791daaff9112dab21b69
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001611.fa
@@ -0,0 +1,20 @@
+>PROKKA_02021
+MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI
+AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDDEARHFQPKVVHVDADNRIVELGVD
+PADGLLDGLSRPPLSREWNEAQAEL
+>PROKKA_01730
+MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI
+AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDDEARNFQPKVVHVDADNRIVELGID
+PADGLLDGLSRPPLSREWNEAQAEL
+>PROKKA_00798
+MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAAQILPGELVSIVDVTNGARLETYTI
+AGERGSGVIGINGAAAHLVHPGDIVILIAYAQMDEEEARHIQPRVVHVDGENKIVELGAD
+PADGLLDGVSRPPLSREWNEAQAEL
+>PROKKA_00759
+MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI
+AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDAEARHFQPKVVHVDADNRIVELGVD
+PADGLLDGLSRPPLSREWNEAQAEL
+>PROKKA_01958
+MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI
+AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDDEARNFQPKVVHVDADNRIVELGVD
+PADGLLDGLSRPPLSREWDEAQAEV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001615.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001615.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9de06e85c69fb64a5c1152584ed6287e752cc3d0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001615.fa
@@ -0,0 +1,33 @@
+>PROKKA_02025
+MTTSRLPLLGALAVGALALAGCAGGGAEPSSPAPSSASSTTTAASSASPAASSSTAPTSP
+AASASTASMGGASASGSLSLEMPPALDGQRTLAVQAAVQRAAGPGSEVGLSAASPLERQT
+ELRQRAAGLEQTVDAGASPASTRSAEQQACLDATRSDLERDAEAGAADLGLTAQPETAAT
+TGGGPTSTPVPSFTASPDAEVTPLGVRVTVYPTEEAARAALEDARAAAQACTGVDLAGLG
+VESVTRTEHEGGTAYTALPAPGGSVYSHLTAVQDGARTVAVAQADADGGVPADAEDRAAS
+IVADVLAALDGEG
+>PROKKA_01734
+MTTSRLPLLGALAVGALALAGCAGGGGAEPSSPAPSSASSTTTAASSAPTSPAASSSTES
+TGAAESTAGASASGSLSLEMPPALDGQRTLAVQAAVQRAAGPGSEVGLSAASPLERQTEL
+RQRAAGLEQAVDAGASPASTRSAEQQACLDATRSDLERDAEAGAADLGLTAQPETAATTG
+GGPTTTPAPSFTASPDAEVTPLGVRVTVYPTEEAARAALEDARAAAQACTGVDLAGLDVE
+SVTRTEHEGGTAYTALPAPGGSVYSHLTAVQDGARTVAVAQADADGGVPADAEDRAASIV
+ADVLAALDGEG
+>PROKKA_00794
+MTPSRLPLLGVLAVGALALAGCAGGGAEPSSPAPSPASSSASPTTTAASSASTSPAASAS
+ASSTPTATALSLDLPEELSGESATRLRAVVQDAAGPAAELGQTFSSPLERRAALEEDAAI
+VDALEEDAGDDAGRRACVDATRAAREADQASGAAQAAWYAQPQTASTTGGSTDGTAASGR
+PGLQVEPLGVQVAVYPDEATARSVAEAARDAAEACEGQEMSSMGVSSVEPLTGAPGETAF
+TVVPVSGSIIYAVSTVVQVGDRVYAVSQGEDGAGVPEGAEERAVALVEDLEAALEG
+>PROKKA_00756
+MTHMTAVPSRRLRAGFALGAAALVLTGCAGGGGSASSSTAAGSPTAGGAGSSVTSPAASS
+SAASSSALSLSMPDRFGNEARTGLTEAVTAAAPEGFEVTTRSVSPLERKTDLEDQATILT
+DGPLEPAAEGSSASPTYTEAQQRCADAAAERFRTEAAAGGAQLRSDAMPTVAGGGYTSVR
+ADVVAYPDVSAAVAALADGSAPIELCTDVQVPGAEQPTDIAPVTGIGDEAVGGELAGGRW
+LAVRRGTDVVSVMVAGPGETAPAGAADQARALAEQVLEAVPAG
+>PROKKA_01962
+MTTPRLPLLGALAVGALALAGCAGGGGAEPSSPAPSSASSTTTAASSASTSPAASSSTAP
+TSPAASASTESTAGASASSSLSLEMPPALDGQRTLAVQTAVQRAAGPGSEVGLSAASPLE
+RQTELRQRAAGLEQAVDAGASPAPTRSAEQQACLDATRSALERDAEAGAADLGLTAQPET
+AATTGVGPTTTPAPSFTASPDAEVTPLGVRVTVYPTEEAARAALEDARAAAQACTGVDLA
+GLGVESVTRTEHEGGAAYTALPAPGGSVYSHLTAVQDGARTVAVAQADADGGVPADAEDR
+AASIVTDVLAALDGEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001619.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001619.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5ad9859ef26acdaa659f1ee05e46b86ca7705851
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001619.fa
@@ -0,0 +1,27 @@
+>PROKKA_02033
+MTDLDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKSWDAPYFHAA
+DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGAGWWELGILLFDP
+TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW
+EGRRWDSVQLAVLRRDWWPASTDG
+>PROKKA_01740
+MTDLDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKSWDAPYFHAA
+DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGAGWWELGILLFDP
+TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW
+EGRRWDSVQLAVLRRDWWPASTDG
+>PROKKA_00787
+MTELDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKWWDAPYFHAA
+DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGSGWWELGILLFDP
+TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW
+EGRRWDSVRLALLRRDWDSARASV
+>PROKKA_01226
+MDTHRSTPVVALRPVEAGDEEFLWTWIHGTPDAEWKRWDAPYFHAAEQAAPMGRAAFARS
+FAPWPDDADRRIITADGAAIGLVTRHEEAPAGGGWWELGILLFDPSRWGGGIGTRALAAW
+TEATLTETDAHVLTLTTWSGNARMAGAAERAGFRMCARVPESRAWDGRRWDSLRFALLRG
+DHEGEQASAPEPPARRPELADLTVVTGRIPDAAALRALYDAVGWTAYTRNPDALAAGVAG
+SACVATAWAGQELVGLARVVSDGHTIAYLQDVLVHPERRRQGVAGKLLDAVFAPFAHVRQ
+QVLITDEEPGQRAFYEACGFRQFGGGGPVPGRTFVRFAG
+>PROKKA_01968
+MTDLDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKSWDAPYFHAA
+DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGAGWWELGILLFDP
+TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW
+EGRRWDSVQLAVLRRDWWPASTDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001625.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001625.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab71ca7ca94cd7327bfae20bfae63b5e15dddea8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001625.fa
@@ -0,0 +1,25 @@
+>PROKKA_02052
+MTTVFYDDQGRPEPPFAAGEAATLLGFLDFLRATIEWKTADLDTAALHRRLPGHPSAMTL
+GGLLKHLAFVEFWWFEAVALGEPTSAPWVGADFDADPDWDWHSAAQDSAADLRALWQGQV
+ERSRQIVVDLLAADGDDGAAALARAHRIREGRDPVSLRWILTHMIEEYGRHAGHADLLRE
+GIDGQTGE
+>PROKKA_01758
+MTTVFYDDQGRPEPPFAAGEAATLLGFLDFLRATIEWKTADLDTAALHRRLPGHPSAMTL
+GGLLKHLAFVEFWWFEAVALGEPTSTPWVGADFDADPDWDWHSAAQDSAADLRALWQGQV
+ERSRQIVVDLLAADGDDGAAALARAHRIREGRDPVSLRWILTHMIEEYGRHAGHADLLRE
+GIDGQAGE
+>PROKKA_00770
+MTTVFYDDQGRPEPPETAGEAETLLGFLEFLRATFAWRTGGLDEAALRRRLDGHPSEMTL
+GGMLKHLAFVEFWWFEAVALGAPTSEPWVSVDWAADEDWDWHSAAEDSAADLRALWEGQV
+ERSRQAVQELLAADGDPLGRVLESYDGRRRVTLRWILTHMIEEYARHNGHADLLREQIDG
+QTGE
+>PROKKA_00740
+MTTVFYDEQGRPEPPHAADEAATLLAFLDFQRATFAWRTSGLDDAALRRRLDGHPSEMTL
+GGMLKHLAFVEFFWFEVTAHGKPTSEPWVSVDWDADADWDWHSAAEDAAEELRDLWRESV
+ERSRAVVVRLLADGPAALDTTHPAWGGRADVSLRWILTHMIEEYARHNGHADLLREQIDG
+QTGE
+>PROKKA_01986
+MTTVFYDDQGRPEPPFAAGEAATLLGFLDFLRATIEWKTADLDTAALRRRLPGHPSAMTL
+GGLLKHLAFVEFWWFEAVALGEPTSAPWVGADFDADPDWDWHSAAQDSAADLRALWQGQV
+ERSRQIVVDLLAADGDDGAAALARAHRIREGRDPVSLRWILTHMIEEYGRHAGHADLLRE
+GIDGQTGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001626.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001626.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7bdcbdb79755e0ef53dca334da7aca5ab9a3ca4c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001626.fa
@@ -0,0 +1,79 @@
+>PROKKA_02053
+MASPSPASAHPSAPESGTGLGFTGVEGITGLTASEVAEREAAGLVNVQSRDTSRSLGQIL
+RVHVFTLFNLAIALCAVVVILMGRWLDLLFSLAAVANVVIGVVQEYSAKRKLDRIALLHQ
+DDVLVIRDGARVPLPMAQIVRDDVVVLRRGDQVPVDGEVLVSDGLDMDEALLTGENDPVP
+KTPGDAVLSGSAVVAGAGLVRATAVGSASHAARLSAEARRYSAIHSELRGALEKVARWLT
+IALVPIIAVIVHGQMTAVGGWSLALSQPREAALEPALIASVAAVTSMIPQGLALMTTIAF
+AVSALKLAQQEVLIQEQPAVEVLARVDTVCLDKTGTLTEGGVRFDRLAAPASADASPDAH
+DDGAPAEVGDGARAVLAWFGADPDVNPTAAALREPFTAVPAVDPAAQVAFSSARRWSAVA
+FGPEAGAAAGTWLLGAPEALVDERLLGPDAAEAVRAQVHADADAGRRVLLLARTDEPLIG
+DALPAGGVPVAVVTFRENVRPDAAETLGYFHAQGVRAVVISGDSPRTVAAVAREVGLEVA
+GQAYDGRTLPDDPDALADVMEEHSVFGRVSPDQKKAMVQALQSRGHVVAMTGDGVNDALA
+LKTADLGIAMGNAAPATKAVSRMVLLDGRFDRLPRVLGEGRQVIANMERLAHIYLTKTTY
+ALLFGVVFSLFAWQFPLLPRQASTVDFIMIGAPTFFLALLPNPRRYVPGFLGRALRFAIP
+SGAVILLSMVALQTYVRLTAGDVDLARQQAAFMITLTLVGLWVLSVMSRPLSARVVVLIL
+AMYAVLAAVVLVPVSRWYHQMEVPPTDVLVAALVIAAVGCGLIELIHQVHRRHVARMLAA
+AGA
+>PROKKA_01759
+MASPSPASAHPSAPESGTGLGFTGAAGITGLTAAEVAEREAAGLVNVQSRDTSRSLGQIL
+RVHVFTLFNLAIALCAVVVILMGRWLDLLFSLAAVANVVIGVVQEYSAKRKLDRIALLHQ
+DDVVVIRDGARVPLPMARIVRDDVVVLRRGDQVPVDGEVLVSDGLDMDEALLTGENDPVP
+KTPGDAVLSGSAVVAGAGLVRATAVGSASHAARLSAEARRYSAIHSELRGALEKVARWLT
+IALVPIIAVIVHGQMTAVGGWSLALSQPREAALEPALIASVAAVTSMIPQGLALMTTIAF
+AVSALKLAQQEVLIQEQPAVEVLARVDTVCLDKTGTLTEGGVRFDRLTAPASADASPDAH
+DDGAPAEVGDGARAVLAWFGADPDVNPTAAALREPFTAVPAVDPAAQVAFSSARRWSAVA
+FGPEAGAAAGTWLLGAPEALVDERLLGPDAAEAVRAQVHADADAGRRVLLLARTDAPLIG
+DALPAGGVPVAVVTFRENVRPDAAETLDYFHAQGVRTVVISGDSPRTVAAVAREVGLEVA
+GQAYDGRTLPDEPGELAAVMAEHDVFGRVSPDQKKAMVQALQSRGHVVAMTGDGVNDALA
+LKTADLGIAMGNAAPATKAVSRMVLLDGRFDRLPRVLGEGRQVIANMERLAHIYLTKTTY
+ALLFGVVFSLFAWQFPLLPRQASTVDFIMIGAPTFFLALLPNPRRYVPGFLGRALRFAIP
+SGAVILLSMVALHAYVRLTAGDVDLARQQAAFMITLTLLGLWVLSVMSRPLSARVVVLIL
+AMYAVLAAVVLVPASRWYHRMEVPPTDVLVAALVVAALGCGLIEVIHQVHRRHVARVLAA
+AGA
+>PROKKA_00769
+MTPPAPAPPPAAAPGALSGVSGLTSAEVAEREAAGLTNRQSKDTSRSLAEILRVHVLTLF
+NLAIALCAVVVISLGRWLDLLFSLAAIANVVIGVVQEYSAKRKLDRIALLHQDDAVVVRD
+GARVSLPMARIVRDDVVVLRRGDQVPVDGEVLASDGLDLDEALLTGENDPVPKAPGDAVL
+SGSSVVAGTGLMRATAVGPASHAARLSAEARRFSAIRSELRGALEKVARWLTIGLVPIIA
+VIVHGQMTAVGGWAHALAQPREAALEPALIASVAAVTSMIPQGLALMTTIAFAVSALKLA
+QHEVLIQEQPAVEVLARVDTVCLDKTGTLTEGGVRFHELLAPASASPSTSTSTDDDGAPA
+DVDAAARAVLAWFGADPDANPTAAALHEPFADAPPHEPADHVAFSSARRWSAVAFGPEVG
+AATGTWLLGAPEALLGDADARPGEAGTGRDDVAAVRAQADALSDEGLRVLLLARTDAPLA
+GNALPAGRVPAAVVTFRENVRPDAAETLGYFHAQGVRTVVISGDSPRTVAAVAREVGMDV
+PGHARDGRTLPEDPEALADVMAEHDVFGRVSPDQKKAMVAALQSRGHVVAMTGDGVNDAL
+ALKTADLGIAMGNAAPATKAVSRMVLLDGRFDRLPAVLGEGRQVIANMERLAHIYLTKTT
+YALLFGVVFSLLAWQFPLLPRQASTVDFIMIGLPTFFLALLPNPRRYVPGFLGRALRFAI
+PSGVVILLSMVALQVYVRLAADHVDLAQQQTAFMITLTLVGLWVLSVMSRPLTRRVVLLV
+LAMYAVLAAVVLVPASRWYHQMEVPPADVLVAALVIAAVGCALIELIHQVHRRHVARVLA
+AAGA
+>PROKKA_00126
+MTHTPPSPAPAADAGPAALAGLTSAQVAERVAAGRVNVQPKDTSRSFGTILRSHVLTLFN
+LVIALCATVIVVLGRWFDLLFSLAAVANVVIGVVQENSARRALDRIALLHQDGVLVVRDG
+ARREVRIEEVVLDDVVVLRRGDQVPVDGAVLTSEGLDVDESLLTGESDPVPKAPGDAVLS
+GSAVVAGTALVRATAVGADSHAAKLAVQARRFTRAHSELRAALEKVARWLTIALVPIVAV
+ILHGQVTAAGGWSRVLGSEDQPALEAALVATVAAVTAMIPQGLALMTTISFALAALKLAR
+RAVLIQEQPAVEILARVDTVCLDKTGTLTEGGIVFHGAHAPVGAPALPHDDDAAVALDPG
+ARAVLAWFGADPDANPTAAALREPFPAAPASSPTGVVPFSSVRRWSAVTFGPDADAAHPG
+MAGTWLLGAPEALADAAHLGPERTAALTEACTAPADRGLRTVLLCRASDAPAGETLPAGR
+EPVAVLTFAEDVRPDAAQTLGYFREQGVAVKVISGDSPRTVAAVARAVGMEVPGDAVDGR
+TLPADPAELADVLESHEVFGRVAPEQKQAMVAALQSRGHVVAMTGDGVNDALALKTADLG
+IAMGNAAPATKAVSRMVLLDGRFDRLPDVLREGRQVIANMERLAHIYLTKTSYALLFGLV
+FSLLAWPFPLLPRQASTADFLMIGAPTFFLALLPNPRRYVPGFLRRALLFAVPAGVTIVA
+AMLAVSWYARHLSSKPVDTAQLQTASLITLTLLGLWVLTCISRPLRPLMCGVVAGMYALL
+AAAVLVPASRWYHQMELPAPDLLAASLAIALGGCVVVEAVHRIHHARVTVPGRRAAEG
+>PROKKA_01987
+MASPSPASAHPSAPESGTGLGFTGVAGITGLTAAEVAEREAAGLVNVQSRDTSRSLGQIL
+RVHVFTLFNLAIALCAVVVILMGRWLDLLFSLAAVANVVIGVVQEYSAKRKLDRIALLHQ
+DDVVVIRDGARVPLPMAQIVRDDVVVLRRGDQVPVDGEVLVSDGLDMDEALLTGENDPVP
+KTPGDAVLSGSAVVAGAGLVRATAVGSASHAARLSAEARRYSAIHSELRGALEKVARWLT
+IALVPIIAVIVHGQMTAVGGWSLALSQPREAALEPALIASVAAVTSMIPQGLALMTTIAF
+AVAALKLAQQEVLIQEQPAVEVLARVDTVCLDKTGTLTEGGVRFDRLTAPASADASPDAH
+DDGAPAEVGDGPRAVLAWFGADPDVNPTAAALREPFTAVPAVDPVAQVAFSSARRWSAVA
+FGPEAGAAAGTWLLGAPEALVDEWHLGPDAAEAVRAQVHADADAGRRVLLLARTDEPLIG
+EALPAGGVPVAVVTFRENVRPDAAETLDYFHAQGVRTVVISGDSPRTVAAVAREVGLEVA
+GQAYDGRTLPEDPGALADVMAEHDVFGRVSPDQKKAMVQALQSRGHVVAMTGDGVNDALA
+LKTADLGIAMGNAAPATKAVSRMVLLDGRFDRLPRVLGEGRQVIANMERLAHIYLTKTTY
+ALLFGVVFSLFAWQFPLLPRQASTVDFIMIGAPTFFLALLPNPRRYVPGFLGRALRFAIP
+SGAVILLSMVTLQTYVRLTAGDVDLPRQQAAFMITLTLLGLWVLSVMSRPLSARVVVLIL
+AMYAVLAAVVLVPASRWYHQMEVPPTDVLVAALVIAALGCGLIEIIHQVHRRHVARVLAA
+AGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001632.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001632.fa
new file mode 100644
index 0000000000000000000000000000000000000000..66feb5bf453f93ad38b355304301c58f4b4d3ca3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001632.fa
@@ -0,0 +1,29 @@
+>PROKKA_02080
+MNLDQLQALRAIADEGSFEAAAYELDVSASAVSQRIRALEREVGQVLLRRGTPCEPTEAG
+IGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPADVLGTWFGPVLAEAADWEDTVLD
+LHVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAGPLGSMRYVPLASPALLARHAADDVV
+DLGAMPMMRYNAKDDLQRLALSGAGLDIAPPTHLAPSFDGFHRSVRAGLGWGMLVDAQAV
+EDVRAGRLVRVPGLDDVLVPLYWQAATLPVTRLVRLTRAVREAAQRTLERG
+>PROKKA_01784
+MPKLCFMNLDQLQALRAIADEGSFEAAAYELGVSASAVSQRIRALEREVGQVLLRRGTPC
+EPTEAGVGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPADVLGTWFGPVLAEAADW
+DDTVLDLHVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAEPLGSMRYVPLASPALRARH
+AAGDVVDLGAMPMMRYNAKDDLQRLALSGAGLDVAPPTHLAPSFDGFHRSVRAGLGWGML
+VDAQAVEDVRAGRLVRVPGLDDVLVPLYWQAATLPVTRLVRLTRAVREAAQRTLERG
+>PROKKA_00704
+MNLDQLQVLLRRGTPCEPTEAGVGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPAD
+VLGTWFGPVLAEAADWDDLVLDLHVEDQDHSAQLLRRGEVLAAVTTEPQPVQGCAAEPLG
+SMRYVPLVAPALLARHAAGDVVDLGAMPMMRYNVKDDLQRLALSDAGLDVAPPTLPVTRL
+VRLTRAVREAAQRTLEPG
+>PROKKA_00614
+MNLDQLQALRAIADEGSFEAAAYELGVSASAVSQRIRALEREVGQVLLRRGTPCEPTEAG
+VGLVRVARHMRVLEQEAWAGLGRMAAGRSVTSLAVPADVLGTWFGPVLAEAADWDDTVLD
+LRVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAEPLGSMRYVPLASPALLARHAAGDVV
+DLGAMPMMRYNAKDDLQRLALSGAGLDVAPPTHLAPSFDGFHRSVRAGLGWGMLVDAQAV
+EDVRAGRLVRVPGLDDVLVPLYWQATTLPVTRLARLTQAVREAAQRTLERG
+>PROKKA_02018
+MPKLCFMNLDQLQALRAIADEGSFEAAAYDLGVSASAVSQRIRALEREVGQVLLRRGTPC
+EPTEAGVGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPADVLGTWFGPVLAEAADW
+DDTVLDLHVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAEPLGSMRYVPLASPALLARH
+AAGDVVDLGAMPMMRYNAKDDLQRLALSGAGLDVAPPTHLAPSFDGFHRSVRAGLGWGML
+VGAQAVEDVRAGRLVRVPGLDDVLVPLYWQAATLPVTRLVRLTRAVREAAQRTLERG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001634.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001634.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce1d8f4b741055e6f4611d481bb57049abdc1c6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001634.fa
@@ -0,0 +1,20 @@
+>PROKKA_02082
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQQRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG
+>PROKKA_01787
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQQRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG
+>PROKKA_00701
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQRRKRGERRAALSDLVGEASSAGLYGQNAESYREALRQARADLRGERG
+>PROKKA_00611
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQQRKRGERRAALSDLVAEASSAELYDQKAESYREALRQARADLRGERG
+>PROKKA_02021
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQRRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001635.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001635.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5597ca2560e323f2243aa87ec7c311e7eb91940
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001635.fa
@@ -0,0 +1,20 @@
+>PROKKA_02083
+MDPDASPRVRLTADDPRPGSRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
+>PROKKA_01788
+MDPDASPRVRLTADDPRPGSRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
+>PROKKA_00700
+MDPDASPRARLTADDPRPGGRPATSTEGPHRQLDQQSSPELWGRLIAAVFALDGVEEGHS
+TVSPATSRAVHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
+>PROKKA_00610
+MDPDASPRARLTADDPRPGGRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRAVHLTGRPKERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLPPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
+>PROKKA_02022
+MDPDASPRVRLTADDPRPGSRPVTSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001636.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001636.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86998b768f7668b44e54bd82d89b6ce0985803cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001636.fa
@@ -0,0 +1,35 @@
+>PROKKA_02084
+MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGEQLREGKLDALALAVADQERAGIDIVC
+DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR
+ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP
+AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGEEWRQYETSFP
+LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF
+VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE
+>PROKKA_01789
+MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGEQLREGKLDALALAVADQERAGIDIVC
+DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR
+ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP
+AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGEEWRQYETSFP
+LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF
+VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE
+>PROKKA_00699
+MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGEQLREGQLDALALAVADQERAGIDIVC
+DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPASVFVDDAKALR
+ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP
+AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGQEWRQYETSFP
+LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDVVETPEEVAATLRETLEF
+VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE
+>PROKKA_00609
+MTTLIPTTLVGSLPKPGWLAEEETLWSPWKLEGERLREGKLDALALAVADQERAGIDIVC
+DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR
+ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP
+AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGVKANNDWKATLGEEWRQYETSFP
+LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF
+VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE
+>PROKKA_02023
+MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGERLHEGKLDALALAVADQERAGIDIVC
+DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR
+ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAAGVDVVQFDEP
+AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGEEWRQYETSFP
+LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF
+VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001637.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001637.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be71b76834baef02041ac061428b07e3d2dad5e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001637.fa
@@ -0,0 +1,35 @@
+>PROKKA_02085
+MSHATLVPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGTDRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAVTSPGTEEPDGFGDLHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQEHFVGPHRDLLERWAAAHAARDNEETR
+>PROKKA_01790
+MSHATLVPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGTDRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAVTSPGTEEPDGFGDLHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQEHFVGPHRDLLERWAAAHAARDNEETR
+>PROKKA_00698
+MSHATLAPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGADRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAATSPGTEEPDGFGDKHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEASRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLVATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQAHFVGPHRDLLERWAAAHAARDTEETR
+>PROKKA_00608
+MSHATLVPSTVPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGADRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERETG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAATSPGTEEPDGFGDLHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQEHFVGPHRDLLERWAAAHAARDTEETR
+>PROKKA_02024
+MSHATLVPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGADRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAATSPGTEEPDGFGDLHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQAHFVGPHRDLLERWAAAHAARDTEETR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001639.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001639.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1f3a063b72d10db531593c8dbc018d5176c1d64e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001639.fa
@@ -0,0 +1,45 @@
+>PROKKA_02087
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAAASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREDAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVTAAGPAVPATTPAVPETAAVTQEVR
+>PROKKA_01792
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAAASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREDAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVTAAGPAVPATTPAVPETAAVTQEVR
+>PROKKA_00696
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLTRSKFLHDLGPTLAPASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSARLAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREDAGIAETTVRLSIGLECPDDLITDLDRA
+LAVVSAAGPAVLATTPAVPETTAVTQEVR
+>PROKKA_00606
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALAGLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAPASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPETVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREAAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVSAAGPAVPAATPAVPETAAVTQEVR
+>PROKKA_02026
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAPASAAQFIQGLETLDLRVARHTATAL
+AVAQHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTREQREAAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVTAAGPAVPAATPAVPETAAVTQEVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001641.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001641.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ed33be5c3439ea6ea8acd7f414e2df544904120
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001641.fa
@@ -0,0 +1,29 @@
+>PROKKA_02092
+MHPDPAETNRRAYDDARVVALYDLDNPPGEDHAYFRRAAEESGARRIVDLGCGTGSLTVT
+LAGDDRAVVGIDPAEAMLRVARARPGGDRVEWRRGTAELIEPASADLVIMSGNVAMHLIG
+QDWHDALQRIAAGLVPGGRLLFETRNPVRRAWEDWQQEPTERTTAAGRLVESEATSTPDA
+DGVVVHRWRTEYSDEGVVREGEEHLQFRSVEQVTQDLAAAGLAVDRVWSDWHGRPFDEAE
+HPLMIIEARPQGA
+>PROKKA_00686
+MHPDPAETNRRAYDDARVVALYDLDNPPGEDHAYFRRAAEESGAQRIVDLGCGTGSLTVT
+LTGDDRAVVGIDPAEAMLRVARARPGGDRVEWRRGTAELIEPASADLVIMSGNVAMHLIG
+QDWHGALRRIAAGLVPGGRLLFETRNPVRRAWEDWQQETTERTTAAGRLVESEATSAPDA
+DGVVVHRWRTEYSDEGVVREGEEHLQFRSVEQVTEDLAAAGLAVDRVWSDWHGRPFDAAE
+HPLMIIEACPQGA
+>PROKKA_00413
+MTPSDPNGATYDDARLAALYDHDNPPGEDHAYFRQVADESRARRIVDLGCGTGSLTVTFA
+GEGRAVVGIDPAEAMLAVARARPGGNAVTWRQGTAELIEPASADLVVMSGNVAMHLIGEV
+WHATLRRVATGLVPGGRLVFETRNPVLRAWEDWSHGPTERTTPAGRLLETETVTAPDADG
+VVLMRSRTVFLADGALVEAEQRLQFRSAAQVRADLDAVGLTVERISGDWHRTPFDDATDR
+LMGVEARKA
+>PROKKA_00602
+MHLDPAETNRRAYDDDRVVALYDLDNPPGEDHAYVRRAAEESGARRIVDLGCGTGSLTVT
+LTGDDRAVVGIDPAEAMLRVARARPGGDRVEWRRGTAELIEPGSADLVIMSGNVAMHLIG
+QDWHGALRRIAAGLVPGGRLLFETRNPVRRAWEDWQQEPTERTTAAGRLVESEATSAPDA
+DGVVVHRWRTEYPDEGVVSEGEEHLQFRSVEQVTQDLAAAGLAVDRVWSDWRGRPFDAAE
+HPLMIIEACPQGA
+>PROKKA_00937
+MTDTNPSRGTDTYAHGHQPSVLASHATRTADNSCGYFLDRVRPGQRILDIGCGPGSITLD
+LAALVGDEGRVTGVDFSAEAIAAARLAAADRGDVVTEFLVGDVFELDLEPASFDVVHAHQ
+VMQHLTDPVAALEAMARFVKPGGILAAGRRLRAWAHQADLHVVLARSSAWSYATTESAAW
+WGNSQAERVTSSSFAQRAADQGVTPEQLTAMADDWRTWGQHPDAWFFLPHGEIIAVPSPH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001645.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001645.fa
new file mode 100644
index 0000000000000000000000000000000000000000..413a0610d5b7120b23f02ba7398f869defb11ca6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001645.fa
@@ -0,0 +1,15 @@
+>PROKKA_02103
+MIYLLALLGVIGCMLLVDRRFELFLWHRPLPALLVLAAGVAYFFAWDLWGIAEGVFLHRQ
+SPYMTGVMLAPQLPLEEGFFLLFLSQITMVLFTGALRLLRGRRGDARAATPADPTDGGSR
+>PROKKA_01810
+MIYLLALLGVIGCMLLVDRRFELFLWHRPLPALLVLAAGVAYFFAWDLWGIAEGVFLHRQ
+SPYMTGVMLAPQLPLEEGFFLLFLSQITMVLFTGALRLLRGRRGDARAATPADPTDGGSR
+>PROKKA_00676
+MVYLLTLLAVIGCMALLDWRHRLFLWARPGAATAVLAVGMAYFLAWDVWGIAEGVFLHRD
+SPYMTGIMLAPQLPLEEGFFLLFLSQITMVLFTGAVRILEHRAGGTTAAGGTR
+>PROKKA_00591
+MYLAALLLLCGCYLAIDARWRLALFSATPGRALAVLAAGLAFFLAWDLTGIAADVFWHGA
+DDVSVGLFLAPELPVEELVFLWFLCHQTLVYVEGLPRLTAWARARRAGRGEGATAS
+>PROKKA_02043
+MIYLLALLGVIGCMLLVDRRFELFLWHRPLPALLVLAAGVAYFFAWDLWGIAEGVFLHRQ
+SPYMTGVMLAPQLPLEEGFFLLFLSQITMVLFTGALRLLRGRGRDARAATPADPTDGGSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001646.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001646.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d18a84a127930a9ff076cbeafe5cf35890a089ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001646.fa
@@ -0,0 +1,30 @@
+>PROKKA_02104
+MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPAWLVVLGVVFFLVPYNLAMYGINDVFDF
+ASDLRNPRKGGVEGSVLGDPAVRRRVLAWSVLLPVPFVAVLAGWSAVRGEWAAVLVLAVS
+LFAVVAYSWAGLRFKERPFLDAATSATHFVSPAVYGLALAGATPTPALAALLGAFFLWGM
+ASQMFGAVQDVVPDREGGLASVATVLGARRTVLLAAGLYAAAGLLLLATDPPGPLAALLA
+VPYVVNTLRFRRITDATSGAAHRGWQLFLPLNYVTGFLVTLLLIGWALTRGAAA
+>PROKKA_01811
+MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPAWLVVLGVVFFLVPYNLAMYGINDVFDF
+ASDLRNPRKGGVEGSVLGDPAVRRRVLAWSVLLPVPFVAVLAGWSAVRGEWAAVLVLAVS
+LFAVVAYSWAGLRFKERPFLDAATSATHFVSPAVYGLALAGATPTPALAALLGAFFLWGM
+ASQMFGAVQDVVPDREGGLASVATVLGARRTVLLAAGLYAAAGLLLLATDPPGPLAALLA
+VPYVVNTLRFRRITDATSGAAHRGWQLFLPLNYVTGFLVTLLLIGWALTRGAAA
+>PROKKA_00675
+MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPTWLVVLGTVFFLVPYNLAMYGINDVFDF
+ASDLRNPRKGGVEGSVLADPAVRRRVLRWSCLVAVPFVAVLAGWSIARGQWDALAVLAVS
+LFAVVAYSWAGLRFKERPFLDAATSATHFVSPALYGLVLAGAAFTPALWALLGGFFLWGM
+ASQMFGAVQDVLPDREGGLASVATVLGARPTVWLAAALYAGAGLLMLGTEWPGPLAALLA
+VPYVLNVLRFRAVTDATSGAAHRGWRLFLPLNYVTGFLVTLLLIGWALARGGV
+>PROKKA_00593
+MIRTLFWASRPVSWVNTAYPFLAAVLLTGGLPWWLVALGGFFFLVPYNLAMYGINDVFDF
+ESDLRNPRKGGVEGSVLADPAVRRRVLAWSALTPAPFAAVLAGRSVLRGEWAAVAVLAVS
+LFAVVAYSWAGLRFKERPFLDAVTSSTHFVSPAVYGLVLAGAEFTPALWSLLGGFFLWGM
+ASQMFGAVQDVVPDREGGLASVATVLGARPTVLAAAALYAAAGLLMLPTDWPGPLAALLA
+APYLLSTLRFRHVTDATSGEAHRGWRTFLWLNYLTGFLVTLLLIWWALVR
+>PROKKA_02044
+MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPAWLVVLGVVFFLVPYNLAMYGINDVFDF
+ASDLRNPRKGGVEGSVLGDPAVRRRVLAWSVLLPVPFVAVLAGWSAVRGEWAAVLVLAVS
+LFAVVAYSWAGLRFKERPFLDAATSATHFVSPAVYGLVLAGATPTPALAALLGAFFLWGM
+ASQMFGAVQDVVPDREGGLASVATVLGARRTVLLAAGLYAAAGLLLLATDPPGPLAALLA
+VPYVVNTLRFRRITDATSGAAHRGWQLFLPLNYVTGFLVTLLLIGWALTRGAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001650.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001650.fa
new file mode 100644
index 0000000000000000000000000000000000000000..82c81143e12e5ef8ab32ec8b5a385d57b4b7528f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001650.fa
@@ -0,0 +1,25 @@
+>PROKKA_02109
+MQTPATPSPHDRPSPVARPWMAASDVPVAGPDDVERVVLLSPAGEAVGTEAKATVHRRTE
+DGGTPLHLAFSCHVYDEAGRFLLTRRALGKAAFPGVWTNGFCGHPGPGEPPAEAVLRRAP
+QELGVEVSDVVEVLPDFRYRAADASGMEEHEICPVFRARMHGDPAPERDEVAEWCWVEPA
+DLAAALAAVPRAFSPWLVEQWQQGAFDPR
+>PROKKA_01816
+MQTPATPSPPDRPSPVARPWLAASDVPVAGPDDVERVVLLSPEGEAVGTEAKATVHRRTE
+DGGTPLHLAFSCHVYDEADRFLLTRRALGKAAFPGVWTNGFCGHPGPGESPAEAVLRRAP
+QELGVEVSDVVEVLPDFRYRAADASGMEEHEICPVFRARMHGDPAPERDEVAEWCWVEPA
+DLAAALAAVPRAFSPWLVEQWQQGAFDPR
+>PROKKA_00669
+MQTPATPSPHDRPSPVVRPWMAAPDLPIAGPDGVERVVLLSPAGEAVGTEAKAAVHRRTE
+DGGTPLHLAFSCHVYDDAGRFLLTRRALGKKAFPGVWTNGFCGHPGPGESPAQAVLRRAP
+QELGAEVSDVVEVLPDFRYRAADASGMEEHEICPVFQARMHGDPAPERDEVAEWCWVEPA
+DLAAALAAVPRAFSPWLVEQWQQGAFEAR
+>PROKKA_00586
+MQQGPSDPRTVEEVEERVVLLGADGAPIGTEAKASVHRNAADGGTPLHLAFSCHVYGPDG
+RFLLTRRALGKKAFGGVWTNGFCGHPAPGEAPAEAVLRRAPQELGVGVREVTPLLPGFRY
+RAADAGGVEEHEVCPVFRAECDGDPVPERDEVAEWCWVEVADLTAALASVPRVFSPWLVM
+QWEQGAFGPR
+>PROKKA_02049
+MQTPATPSPHDRPSPVVRPWMAASDVPVTGPDDVEHVVLLSPAGEAVGTEAKATVHRRTE
+DGGTPLHLAFSCHVYDEADRFLLTRRALGKAAFPGVWTNGFCGHPSPGESPAEAVLRRAP
+QELGVEVSDVVEVLPDFRYRAADASGMEEHEICPVFRARMHGDPAPERDEVAEWCWVEPA
+DLAAALAAVPRAFSPWLVEQWQQGAFDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001652.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001652.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3edfa1ba841224fd52a5e243e11cbd20e7c56a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001652.fa
@@ -0,0 +1,20 @@
+>PROKKA_02113
+MTGAPILPLLVLNGPNLNLLGTREPEVYGTATLDDVRALTEARAAEHGLTVDFRQSNHEG
+ELIDWIQEARTSHAGVLINPAAYSHTSIAIRDALAAVDRPIAEVHISNIHRREAFRHHSH
+VSAVADVVIAGAGVQGYTLAVDWLAAAVRR
+>PROKKA_01820
+MTGAPILPLLVLNGPNLNLLGTREPEVYGTATLDDVRALTEARAAEHGLTVDFRQSNHEG
+ELVDWIQEARTSHGGVLINPAAYSHTSVAIRDALAAVDRPIAEVHISNVHRREAFRHHSH
+VSAVADVVIAGAGVQGYALAVDWLAAAVRR
+>PROKKA_00667
+MRETGASPRTFVRETGASVVVRSYTGPMTTAPSALPLLVLNGPNLNLLGTREPEIYGSDT
+LDDVRSRTEARAAGHGLAVDFRQSNHEGELVDWIQEARTSHAGILINPAAYSHTSVAIRD
+ALSAVGRPIVEVHISNIHRREPFRHHSHVSAVADAVIAGAGVLGYELGIDWLAAAVRR
+>PROKKA_00583
+MTDSMPAATAARLPLLVLNGPNLNMLGTREPEKYGFETLEDVRALTAARAAEHGLEVDFR
+QSNHEGELVDWIQEARTGFSGILINPAAYSHTSVAIRDALAAVPVPIVEVHITNIHAREE
+FRHHSVVSAVATTVIAGAGTQGYALGVEVLAARLAR
+>PROKKA_02051
+MTATPALPLLVLNGPNLNLLGTREPEVYGTATLDDVRALTEARAAEHGLTVDFRQSNHEG
+ELIDWIQEARTSHAGVLINPAAYSHTSIAIRDALAAVDRPIAEVHISNVHRREAFRHHSH
+VSAVADVVIAGAGVQGYALAVDWLATTVRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001654.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001654.fa
new file mode 100644
index 0000000000000000000000000000000000000000..58a7a702d1c14e1ede10d4ad9725cdd39faa2e18
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001654.fa
@@ -0,0 +1,45 @@
+>PROKKA_02115
+MSDYQPRRPGSKPTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGHQLS
+APKRREAATAERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKERQEKA
+KEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMETDRGD
+TIKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTAEIVE
+QIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPSPEG
+LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID
+AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW
+TASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD
+>PROKKA_01823
+MSDYQPRRPGSKSTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGHQLS
+APKRREAATAERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKERQEKA
+KEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMETDRGD
+TVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTAEIVE
+QIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPSPEG
+LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID
+AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW
+TASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD
+>PROKKA_00665
+MSDYQPRRPGSNPAPARRTDRAGKPALGRPKRGLIDESEARQLAEDRERMRRAGVGHQLS
+APKRREAATAERPQVMPQTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLAERQAKA
+KEIGLPAFRAKQLSVHYFERYTTDPEQMTDLPKDKREVIAEAFFPPLLTEVRRMETDRGD
+TVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTAEIVE
+QIVRANQVIAEGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPAPEG
+LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID
+AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW
+TASEKDVTREFVERLNAAGIPTTLRDTRGKEIDGACGQLAAGDEDA
+>PROKKA_00581
+MEGMSDYTPRRPGSKPTPARQKDRAGKPALGRPRRGMIDEPEARQLAEDRERMHRAGVGH
+QLSAPPRRAAEVDADRPQVMPKTEGWQQPMGPDGRPQLQFKQPRVSQPPQHLADMTLAER
+QAKAKEIGLPAFRAKQLSVHYFEHFTTDPEQMTDLPKGKREEIAEAFFPPLLTEVRRLTT
+DRGDTVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTA
+EIVEQIVRANQVIAEGGLGGTRRDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDP
+APEGLGMSARHVTLSTVGLVPAIKKLAQEGVPLTFALSLHAPDDELRDELIPVNARWKAD
+EAIDAAYEYFLATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTP
+GSIWTASEKDVTREFVDRLNAAGIPATLRDTRGKEIDGACGQLAADDEDVAARA
+>PROKKA_02053
+MSDYQPRRTGSKPTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGHQLS
+APKRREAATAERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKERQEKA
+KEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMETDRGD
+TVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSPAEIVE
+QIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPSPEG
+LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID
+AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW
+TASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001656.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001656.fa
new file mode 100644
index 0000000000000000000000000000000000000000..80672ee4cf46cbc9b02eb16119bb1ca10cedb7d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001656.fa
@@ -0,0 +1,40 @@
+>PROKKA_02118
+MSVRSLLPDLGTSATGTPEAAVPPFARAVLWAHGDDAWRGEGGWTVLLDGPDRLRRLSAL
+WQAAVAGRPDPTAPLRGWISSTFADDSPEPAVLRIPADLRRATPSGVRDVAQHVDADALA
+AAVAADRGARLLADGEVPLPADVADLAWDDAGYAAGVRELLTRMADSGGELAKVVISRTM
+TVPADDADLWRAIGELRREYPQTWVFAVGGLLGATPEVLATRHAGLVGSRVLAGSMPRGA
+DEEEDAALRERLASDPRLAEEHRWAARSVLDALAPVVDLADDDPAPTVLTLPNVHHLATS
+VRGRLRDGRGTVLDVVAALHPTAAVGGTPTPDAVRVIAEVEPVDRGRYAGPVGWLDQDGD
+GEIALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKFLPMRRALGVAED
+>PROKKA_01826
+MGAMSVRSLLPDLGAPATGAPEAAVPPFARAVLWAHGDDAWRGEGGWTVLLDGTDRLRRL
+SALWQTAVAGRPDPTAPLRGWISSTFADDSPEPAVLRIPADLRRATPSGVRDVAQHVDAD
+ALAAAVAADRGARLLADGAVPLPAGVADRAWDDAGYAAGVRELLTRMADSGGELAKVVIS
+RTMTVPADDADLWRAIGELRREYPQTWVFAVGGLLGATPEVLATRHAGLVGSRVLAGSMP
+RGADEEEDAALRERLASDPRLAEEHRWAARSVLDALAPVVDLADDDPAPTVLTLPNVHHL
+ATSVRGRLRDGRGTVLDVVAALHPTAAVGGTPTPDAVRVIAEVEPVDRGRYAGPVGWLDQ
+DGDGEIALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKFLPMRRALGVAED
+>PROKKA_00662
+MSVPTLLPELGTAAAEAAVPPFARAVLWAHGDAAWRGDDGWTVLVDGPDRLRRLSALWQA
+AVAGREDPAAPVRGWVSAPFSDDSVEPAVLRVPARLRRSTASGIRETPQHVDAAALADAV
+AADGGGRLLPDGEVPLPADTSESAWDDAGYAAGVRELLARMAASDGALAKVVISRTLTVP
+ADDADLWRAIRALRREYPQTWVFAVGGLLGATPEILATRHAGLVGSRVLAGSLPRGEDEA
+EDAALRARLATDPRLGEEHRWAARSVLDALAPVVDLADPDPAPTVLTLPNVHHLATSVRG
+RLRDGRGTVLDVVAALHPTAAVGGTPTPEAVRVISEVEPVDRGRYAGPVGWLDQDGDGEI
+ALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKLLPMRRALGIDLD
+>PROKKA_00579
+MPPVPSVAVAALAARALSPSGSAAGRVPAFARAVVWAREDTVRVGVGGHTVLLDGPDRLR
+RLSALWRAAVAARPEPASPALAWVSSAFDDASPVPSVLRVPARVLQAGPDGVVEVPVAMP
+REALAAAVAACPGARLTEAGEVPLPADDPALAWDDAGYAAGVEEVVARMEASAGALSKVV
+VSRTETVPAGEDRLWAAVDALRAEYPQTWTFAVGGLVGATPEMLATRRDGVVASRVLAGS
+LPRGVDEGDDARLRARLAADPRLLREHHWAARSVLDALAPVVELEDAHPAPFVLTLPNVH
+HLATDVRGRLRPGEGAVLDVVAALHPTAAVGGTPTAEALEVIRAVEPVDRGRYAGPVGWL
+DQDGDGEIALALRCGQQVPGGVRLQAGGGIVPGAAAEEEVVEVGVKLLPMRRALGVA
+>PROKKA_02056
+MGAMSVRSLLPDLGTPATGTPEAAVPPFARTVLWAHGDDAWRGEGGWTVLLDGTGRLRRL
+SALWQAAVAGRPDPTAPLRGWISSTFADDSPEPAVLRIPADLRRATPSGVRDVAQHMDAD
+ALAAAVAADRGARLLADGAVPLPADVADRAWDDAGYAAGVRELLTRMADSDGELAKVVIS
+RTMTVPADDADLWRAIGALRREYPQTWVFAVGGLLGATPEVLATRHAGLVGSRVLAGSMP
+RGADEEEDAALRDRLASDPRLAEEHRWAARSVLDALAPVVDLADDDPAPTVLTLPNVHHL
+ATSVRGRLRDGRGTVLDVVAALHPTAAVGGTPTPDAVRVIAEVEPVDRGRYAGPVGWLDQ
+DGDGEIALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKFLPMRRALGVAED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001657.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001657.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30fc514e2598b01579b72c5f320967b56488d483
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001657.fa
@@ -0,0 +1,30 @@
+>PROKKA_02119
+MAPIPPDPHADHAPAVDDMPLDTTAAPDIPAAVDPVPHGMAAHVLEREVGPLRARFPGVA
+DEATVRQLLFDSYAELAETSRHPEMLPTISVQHAASRLRARAINQGSIESRHPRVLFVCH
+GNAGRSQMAAALLENRTHGEVRARSAGTEPAGEVISTAFEAMNEIGIPLHHTYTKGLDPD
+VLRAAEIVVLFDGADPFEIPEGAQVQKWSVPSIRGMSLEQVRGVRDALDLEVRGLIADLG
+EAATPLPEEGTRVGRPLDLYPPGV
+>PROKKA_01827
+MTPIPPDPHADHAPAVDDMPLDTTAAPDIPAAVDPVPHGMAAHVLEREVGPLMARFPGVA
+DEATVRQLLFDSYAELAETSRHPEMLPTISVQHAASRLRARAINQGSIESRHPRVLFVCH
+GNAGRSQMAAALLENRTHGEVRARSAGTEPAGEVISTAFEAMNEIGIPLHHTYTKGLDPD
+VLRAAEIVVLFDGADPFEIPEGAQVQKWSVPSIRGMSLEQVRGVRDALDLEVRGLIADLG
+EAATPLPEEGTRVGRPLDPYPPGV
+>PROKKA_00661
+MAAIPPDPHADRTPAVDDLPLDAASPDGRAAAPVGLEPEGMAANVLEREIEHLMERFPCV
+GDEETVRAVVMDSYAQLAATSRHPDMLPNTTVQHASARLRAMAINQGSIESRHPRVLFVC
+HGNAGRSQMAAALLENRTGGAVKSRSAGTSPAGEVISTAFDAMSEIGIPLHHSYTKGVDE
+DVLKAAEVVVLFDGAEPLDIPEGTEVQEWSVPSIRGMSLEQVRGVRDALDLQVRGLIADL
+GEEGSDAPPPGEGAPVA
+>PROKKA_00578
+MAPHPSDPAADLPAADVPLDPTGALPVVAPAPEGMASHVLDREAEHLHARYPEVGDVAMA
+RALLEDSYARLARTTRHPEMLPVTAANYAAARLRARAIAQGSVESRHPRVLFVCHGNAGR
+SQMAAALLENRSGGTVASRSAGTSPAGSVLPMALDVMNEIGLPLHHAFPKGVDRDILQAA
+QLVVLFDGAEEDLLDVPAGVEVQHWSVPSIRGLALEQVRGVRDALDLQVRGLIAELTALE
+GEEQGGAADPAA
+>PROKKA_02057
+MTPIPPDPHADHAPAVDDMPLDTTAAPDTPAAVDPVPHGMAAHVLEREVGPLMARFPGVA
+DEATVRQLLFDSYAELAATSRHPEMLPTTAVQHAASRLRARAINQGSIESRHPRVLFVCH
+GNAGRSQMAAALLENRTHGEVRARSAGTEPAGEVISTAFEAMNEIGIPLHHTYTKGLDPD
+VLRAAEIVVLFDGADPFEIPEGAQVQNWSVPSIRGMSLEQVRGVRDALDLQVRGLIADLG
+EAAADAPLPDADTRAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001660.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001660.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5153ffc66313589f7feb43a8207348b3a92d5007
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001660.fa
@@ -0,0 +1,20 @@
+>PROKKA_02123
+MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRRNFRRDEDEGYLTASQGAALLTLGALVR
+IARNEDHADLEALLEHAEADEVDLTAFIGQFSDEDIETLRELIGVVIREPSCSELYQLWE
+ESGELEQWLEYSRECLP
+>PROKKA_01831
+MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRKNFRRDEDEGHLTASQGAALLTLGALVR
+IARNEDHADLEALLEHAETDEVDLTAFIDQFSDEDVETLRELIGVVIREPSCSELYQLWE
+ESGELEQWLEYSRECLP
+>PROKKA_00656
+MGAWGRNVFQNDTALDLVDEVLDGSFDLDEFRKDFRREEDEGYLDASQGAALLALGALVR
+IARNEDHADLDVLLEHAEAEEVDLTDFIDQFSDEDIQTLRELIGVVIREPSCSELYELWE
+ESGELEQWLEYSRQCLP
+>PROKKA_00574
+MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRRNFRRDEDEGYLTASQGAALLALGALVR
+IARNEDHADLEALLEHAETDEVDLTAFIDQFSDEDIETLRELIGVVIREPSCSELYQLWE
+ESGELEQWLEYSRECLP
+>PROKKA_02061
+MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRKNFRRDEDEGHLTASQGAALLTLGALVR
+IARNEDHADLEALLEHAETDEVDLTAFIDQFSDEDVETLRELIGVVIREPSCSELYQLWE
+ESGELEQWLEYSRECLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001664.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001664.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9859adb293bc368f06c7a4b70470d6d5c424ddbc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001664.fa
@@ -0,0 +1,35 @@
+>PROKKA_02128
+MTTMKAAVVTQFGTEADVTEVERPTPGQHEALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSVD
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFDEMRHGKIEGRVVIDYAMQD
+>PROKKA_01836
+MTTMKAAVVTQFGTEADVTEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSVD
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFDEMRHGKIEGRVVIDYAMQD
+>PROKKA_00652
+MTTMKAAVVTQFGKEADVQEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSAD
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFEEMRHGKIEGRVVIDYAMQD
+>PROKKA_00568
+MTTMKAAVVSQFGKEADVKEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWGACGHCQYCRTGWETLCEEQINGGYSMN
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFEEMRHGKIEGRVVIDYAMQD
+>PROKKA_02066
+MTTMKAAVVTQFGTEADVTEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSVD
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFDEMRHGKIEGRVVIDYAMQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001668.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001668.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aaacdcd50ddadcb5cd15c68b9dc27d1f3ae435c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001668.fa
@@ -0,0 +1,25 @@
+>PROKKA_02132
+MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAVRRAFAAEA
+RGDVEPGRAPASFYVGVDENGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAAR
+LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVEADLDGAPFPVPQLRFD
+VPTTAA
+>PROKKA_01840
+MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAIRRAFAAEA
+RGDVEPGRVPASFYVGVDEAGHLVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAAR
+LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVEADLDGAPFPVPQLRFD
+VPTTAA
+>PROKKA_00648
+MLPDPSPTVTVDGLLLRPLRTADEIAAREADAELHREGFDFLMAGTRSFPAIRRAFAADA
+RGDVEPGRVPASFYVGVDEAGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAVR
+LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVETGLDGAPFPEPKLRFD
+VPTTAA
+>PROKKA_00564
+MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAIRRAFAAEA
+RGDVEPGRVPASFYVGVDENGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAVR
+LLRGALTLLAAHGVSTALLTCDETNTASVATIRACGGVLRDRVEAGLDGAPFPVPKLRFD
+VPTTAA
+>PROKKA_02070
+MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAVRRAFAAEA
+RGDVEPGRAPASFYVGVDENGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAAR
+LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVEADLDGAPFPVPQLRFD
+VPTTAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001670.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001670.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76948d025751ffeafae7587107c8da3705f3be03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001670.fa
@@ -0,0 +1,30 @@
+>PROKKA_02134
+MLSAPTLTRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA
+VRGRELRGRLAEVWALAAVDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAVE
+RLAAMAALALAETAMDGELVRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRSY
+RARLAEAAEAAPATDPAGPEEAEAPEAVADEAAPADKPRQETEKEKKERKKAEKKAEKKA
+RKKAEKKARKKKSDKKKD
+>PROKKA_01842
+MLSAPTLSRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA
+VRGRELRGRLAEVWALAAGDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAVE
+RLAAMAALALAETAMDGELTRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRSY
+RARLAEAAESAPAADPAGPEEAEAPEAVVDSEAAADEPRRETKKEKKERRKAEKKARKKA
+EKKAGKKKSDKKKD
+>PROKKA_00638
+MLSPRTLARLSSVAAFLNTAPGPRGGQEAPERFTAATQLPALVPELQEGEVRLRLAAAAA
+VRARELRERLTRVWALAATDESAAVERVNELLAEAGPLRLTAGGDVVGLAPAQVPADAVE
+RLAAMATLALAETAMDGELARLRVCEGEDCENALVDGSRNRSKRFCDEANCANRTHVRSY
+RARLAEAAEAAPATDPAGPEEAEGTEAVVDEAAPADEPLQETEKEKKERRKAQKKARKKA
+EKKAGKKKSDKKKSDKKKD
+>PROKKA_00561
+MLSPHTLARLASISAFLNTAPGVRGGQEAEERLTAGTQLPALVPELQEGESRLRVAAAAR
+TRAHELRARLTELWAAADAEDVPAAVAAVNELLAETGPLRLEVSDGSADLAPAQVPADAV
+ERLTAMAALALTEAALEGELTRLRVCAGEDCENTLVDASRNRSKRFCDAANCANRTHVRS
+YRARLAEAEDTQADVEAADAAPLPEVAPEADPQDATDLEAIEAAEGVESAVQEPVKKDST
+KDKKSKSEKKARRAAKKKAEKESEAAAEGKKGKREKSKKSEKHKKKAAKD
+>PROKKA_02072
+MLSAPTLSRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA
+GRGRELRGRLAEVWALAAVDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAVE
+RLAAMAALALAETAMDGELTRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRSY
+RARLAEAAESAPAADPAGPEEAEAPEAVVDSEAAADEPRRETKKEKKERRKAEKKARKKA
+EKKAGKKKSDKKKD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001671.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001671.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d1e9b49f4e5803e7b6272a85b946f3fe9f68e084
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001671.fa
@@ -0,0 +1,20 @@
+>PROKKA_02136
+MSAPSPRPSADRAGSGRPARGGLRTTVKGPLVFSAVLGLIGGVIAGITASGGTQNPLRID
+IALIAFGVFFMTSLVVVAMLQLAARENPDHLSQGSGVNRSSEEMFRKAAADRRAQAARER
+REQGGTGGDAPRA
+>PROKKA_01844
+MSAPSPRPSADRAGSGRPARGGLRTTVKGPLVFSAVLGLIGGVIAGITASGGTQNPLRVD
+IALIAFGVFFMTSLVVVAMLQLAARENPDHLSQGSGVNRSSEEMFRKAAADRRAQAAAER
+REQGGTGGDAPRA
+>PROKKA_00636
+MSAPSPRPSADRAGTGRPARGGLRTTVKGPLVFSAVLGVIGGVIAGITASGGTQNPLRID
+IALIAFGVFFMTSLVVVAMLQLAARENPDHLSAGSGINRSSEETFQKAAAERRAQVARER
+REQDGTGGDAPRA
+>PROKKA_00560
+MSAQSPRPSDDRTRPGAGRPARGGLRTTVKGPLVFSAVLGLVGGVVAALTASGGTANPLR
+IDIGLIAFGVFFMTSLVVVAMLQLASRENPDHLSRGSGVNRSSEETFQRRAAERRAKAAA
+ERRAAQGDAGR
+>PROKKA_02074
+MSAPSPRPSADRAGSGRPARGGLRTTVKGPLVFSAVLGLIGGVIAGITASGGTQNPLRVD
+IALIAFGVFFMTSLVVVAMLQLAARENPDHLSQGSGVNRSSEEMFRKAAADRRAQAAAER
+REQGGTGGDAPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001677.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001677.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8af0af8c2dfe7f6a0f742686aba75ae6c525348
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001677.fa
@@ -0,0 +1,40 @@
+>PROKKA_02143
+MNLRTLLREALTAARTAPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPAARV
+LTVTDSGGTGFLTGATVATLAGLDSAEAALARDMPVDTVNAAIGAGGTRVAVTHVVGTVD
+RGVELTRGRLPGPGEVVVPEAKLAELGLAQPSGALESGDGRQWAVVGAFEALTPFEDLAD
+YAIAVPAAPASLVVQQVRVLAPDTAGTRAMQDSALAVIDPDPRSSQVQTARALAAGNATI
+TGELAGLGRSLLLLILGAGAFFVAIVVLADVLIRRRDLGRRRTLGIGRADLVLLVAVRTA
+APAVLGAVVGAGTGYAVVVGQGGALGLDFVAGVAVLAALTAVVASLLPAAFAAFRDPVRV
+MRTA
+>PROKKA_01850
+MNLRTLLREAVTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPGARV
+LTVTDTGGTGFLTGATAATLAGLDTAEAALARDSPMDAVNTGIGRGGARVAVTNVVGTLD
+RGIVLTRGRLPAPGEVVVPEAKLAELGLAQPSGAIEATDGGQWAVVGAFQAQDPFQDLDG
+YALTVPAAPDALVMQQVRVLAADTAGTRAMQEAALAVIDPDPRASSIQTARALSAGNQVI
+TGELAGLGRSLLLLILGAGAFFVSIVVLADVLIRRRDLGRRRTLGIGRGDLILLVAVRTA
+VPALLGAVLGSGAGYAVVAGQGGTLGVDFVAAVAVLAALTALLASLAPAAFAAFRDPVRV
+MRTA
+>PROKKA_00629
+MNLRTLLREALTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPAARV
+LTVTDSGGTGFLTGATVTTLAGLDAAEAALARDMPVDTVNAAIGAGGTRVAVTHVVGTLD
+RGVELTRGRLPGPGEVVVPEAKLAELGLAQPSGALESGDGRQWAVVGAFEARTPFEDLDG
+YALAVPATPASLVVQQVRVLALDTAGTRAMQDSALAVIDPDPRSSQVQPARALAAGNETI
+TGELAGLGRSLLLLILGAGAFFVAIVVLADVLIRRRDLGRRRTLGIGRADLVLLVAVRTA
+APAMRGAAVGAGAGHGLVLAQGSALGSAFVVGAAVLAVLTAVVASLLPAAFAAFRDPVRV
+MRTA
+>PROKKA_00553
+MNLRTLLREAVTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPGARV
+LTVTDTGGTGFLTGATAATLAGLDTAEAALARDSPMDAVNTWIGRGGARVAVTNVVGTLD
+RGIELTRGRLPAPGEVVVPEAKLAELGLAQPSGAIEATDGRQWAVVGAFQAQDPFQDLDG
+YALTVPAAPDALVMQQVRVLAADTAGTRAMQEAALAVIDPDPRASSIQTARALSAGNQVI
+TGELAGLGRSLLLLILGAGAFFVSIVVLADVLIRRRDLGRRRTLGIGRGDLILLVAVRTA
+VPALLGAVLGSGAGYAVVAGQGGTLGVDFVAAVAVLAALTALLASLAPAAFAAFRDPVRV
+MRTA
+>PROKKA_02080
+MNLRTLLREAVTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPGARV
+LTVTDTGGTGFLTGATAATLAGLDTAEAALARDSPMDAVNTGIGRGGARVAVTNVVGTLD
+RGIVLTRGRLPAPGEVVVPEAKLAELGLAQPSGAIEATDGRQWAVVGAFQAQDPFQDLDG
+YALTVPAAPDALVMQQVRVLAADTAGTRAMQEAALAVIDPDPRASSIQTARALSAGNQVI
+TGELAGLGRSLLLLILGAGAFFVSIVVLADVLIRRRDLGRRRTLGIGRGDLILLVAVRTA
+VPALLGAVLGSGAGYAVVAGQGGTLGVDFVAAVAVLAALTALLASLAPAAFAAFRDPVRV
+MRTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001678.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001678.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6856f9360817e54c657c46771971058364bf8261
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001678.fa
@@ -0,0 +1,25 @@
+>PROKKA_02144
+MNAELSVADLRFAYTRGAEELFDGLTHRFTPGAVTALTGPSGRGKSTLLYVLGLMLTPSA
+GVVRLGDVDASALPDRRRARLRATSVGFVFQDAELDPSRPILDSVVEPGLYAGLSRRELE
+GRARILLERFGLGHRAEHRPGQVSGGQAQRVAVCRALVNTPAVVLADEPTGNLDPDNASL
+VLDALAEAAGEGRTVVVATHDPAVVARADEVVRL
+>PROKKA_01851
+MTGPATPGTPAAPVVPAALAVEDLRFAYTRAAEELFDGLTHAFTPGAVTALTGPSGRGKS
+TLLYVLGLMLTPTSGVVRLGDVDASTRPDRERSRLRATSVGFVFQDSELDPSRPILDSVV
+EPGLYAGLERQTLEDRARALLERFGLAHRADHRPGQVSGGQAQRVAVCRALVNAPAVVLA
+DEPTGNLDPDNAGLVMDALADAAAEGRTVVVATHDPAVVARADEVVRL
+>PROKKA_00628
+MNAELSVADLRFAYTRGAEELFDGLTHRFTPGAVTALTGPSGRGKSTLLYVLGLMLTPSA
+GVVRLGDVEASALPDRRRARLRATSVGFVFQDAELDPSRPILDSVVEPGLYAGLERRVLE
+ERARALLERFGLGHRAEHRPGQVSGGQAQRVAVCRALVNTPAVVLADEPTGNLDPDNASL
+VLDALAETAAEGRTVVVATHDPAVVARADEVVRL
+>PROKKA_00552
+MTGPATPGTPAAPGTPAALAVEDLRFAYTRAAEELFDGLTHAFTPGGVTALTGPSGRGKS
+TLLYVLGLMLTPTSGVVRLGDVDASTRPDRERSRLRATSVGFVFQDSELDPSRPILDSVV
+EPGLYAGLERQTLEDRARALLERFGLAHRADHRPGQVSGGQAQRVAVCRALVNAPAVVLA
+DEPTGNLDPDNAGLVMDALADAAAEGRTVVVATHDPAVVARADEVVRL
+>PROKKA_02081
+MTGPATPGTPAAPVVPAALAVEDLRFAYTRAAEELFDGLTHAFTPGAVTALTGPSGRGKS
+TLLYVLGLMLTPTSGVVRLGDVDASTRPDRERSRLRATSVGFVFQDSELDPSRPILDSVV
+EPGLYAGLERQTLEDRARALLERFGLAHRADHRPGQVSGGQAQRVAVCRALVNAPVVVLA
+DEPTGNLDPDNAGLVMDALADAAAEGRTVVVATHDPAVVARADEVVRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001679.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001679.fa
new file mode 100644
index 0000000000000000000000000000000000000000..57fdcb321e41a5c89078c86eb6befd683867cd97
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001679.fa
@@ -0,0 +1,35 @@
+>PROKKA_02145
+MTRPLRWATLAGVLLIVAVLAFWAGRATLTPPAQAEQRPSEDALVTVAEQELGRVITLGV
+SVTREQAPAAVNALSGVVTRAGESGEVAAGDVLYAVAQQPVITVQGELPQWRALGEGATG
+SDVAAFQRMLAATGAKVEVTGTWDEATAVAWNGWLTERDYPAADTVELGQLVVLESLPAA
+LSVDAKATAVGGALAGGETIVARPGDEPTFAIEVNQDQAAIIPAGTAVTVPHGEHEWEAV
+AGESTADDQGLIRIPLTAPDGGAVCGADCDSLPAEASTSLLSKVNVVPPVTGPVVPVSAL
+RTQPDGAARVTVVRDGVQEERTVIVRGSADGLAVVDGVDAGETVRVLNGAP
+>PROKKA_01852
+MNRPARWAALVLALVAVAALAFWAGRVTLTPPAQAEQRPAASALVTVAEQELGRVITLGV
+SVSREQTPAAVNALTGVVTRAGESGEVAAGEVLYAVAQKPVLVLQGELPQWRPLGEGTSG
+DDVAAFQRMLAATGAKVEATGTWDEATADAWDDWLTERGYPAADTVELGQLVVLDALPAP
+LSVDAKTTAVGTTLAGGENVVARPGDQPDFALEVNQEQAALIPAGTQVTVPHGEHEWKAV
+AGESTSDEQGLIRITLTAPDGGVVCGEDCDTLPADATTSLLSQVSVVPPVSGPVVPVSAL
+RTQPDGAATVTVVRDGAAEDRAVTVLGSADGLAVVDGVDAGEQVRVLNGTR
+>PROKKA_00627
+MSKVTRWAALVLTLVLVAALAFWAGRATLTPPAQADQRPSEDAVVTVAEQELGRVITLGV
+SVAREQAPAAVNALSGVVTRAGESGEVAAGDVLYAVAQQPVIAVQGELPQWRALDEGATG
+SDVAAFQRMLAATGAKVEVTGTWDEATAVAWNGWLTERDYPAAGTVELGQLVVLESLPAA
+LSVDAKATAVGGALAGGETIVARPGDEPTFAIEVNQDQAAMIPAGTAVTVPHGEHEWEAV
+AGESTADDQGLIRIPLTAPDGGAVCGADCDSLPAEASTSLLSKVNVVPPVTGPVVPVSAL
+RTQPGGAVVVTVVQDGVEEERTVTVRGSADGLAVVDGVDAGETVRVLNGAP
+>PROKKA_00551
+MTRPARWAALVLAVVLVAALAFWAGRVTLTPPAQAEQRPSEDAVVTVAEQELGRVITLGV
+SVTREQAPAAVNALSGVVTRAGQSGEVAAGDVLYAVAQKPVIAVQGELPQWRALGEGATG
+SDVTAFQRMLTATGTKVKATGTWDEATATAWNAWLTTRGYPAADTVELGQLVVLESLPTA
+LSVDAKATAVGGTLAGGETIVARPGDEPTFAIEVNQDQAAMIPAGTAVTVPHGEHEWKAV
+AGESISDEQGLIRITLTAPDGGVVCGEDCDTLPADPTTSLLSQVSVVPPVSGPVVPVSAL
+RTQPDGAATVTVVRDGAAEDRTVTVLGSADGLAVVDGVDAGEQVRVLNGTR
+>PROKKA_02082
+MNRPARWAALVLALVAVAALAFWAGRVTLTPPAQAEQRPAASALVTVAEQELGRVITLGV
+SVSREQTPAAVNALTGVVTRAGESGEVAAGEVLYAVAQKPVLVLQGELPQWRPLGEGTSG
+DDVAAFQRMLAATGAKVEATGTWDEATADAWDDWLTERGYPAADTVELGQLVVLDALPAP
+LSVDAKTTAVGTTLAGGEKVVARPGDQPDFALEVNQEQAALIPAGTQVTVPHGEHEWKAV
+AGESTSDEQGLIRITLTAPDGGVVCGEDCDTLPADATTSLLSQVSVVPPVSGPVVPVSAL
+RTQPDGAATVTVVRDGAAEDRTVTVLGSADGLAVVDGVDAGEQVRVLNGTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001690.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001690.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e568eebc13ceaa9abf382aa2f59c2086ce71866
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001690.fa
@@ -0,0 +1,46 @@
+>PROKKA_02159
+MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG
+MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSLSLLMVPLTVYNLAANAPRSVSVAGL
+LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPLAMVIMAIGCGLMVLTAWAFGDVVR
+NRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYA
+AAAKPALAVTALETIGQTGRSALADMRQLLGVLRETGETVAGVPGVTDDDARRPAADVVA
+SPDGRGTRLPPGRRPQPRLADLPALVETMRLSGLEVSLLETGTPRRTLPAGGELAAYRIV
+QEALTNTLRHGGPDADAFVTLAWTAHGLDLQIDDDGCGAAADPATRGSGQGLRGAAERTA
+LFGGTLETGPRVGAGYRVSAHLPYSAV
+>PROKKA_01872
+MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG
+MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSMSLLMVPLTVYNLAANAPRSISVAGL
+LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPLAMVIMAIGCGLMVLTAWAFGDVVR
+NRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYA
+AAAKPALAVTALETIGQTGRSALADMRQLLGVLRETGETVAGVPGVTDDDARRPAADVVA
+SPDGRGTRLPPGRRPQPRLADLPALVETMRLSGLEVSLLETGTPRRTLPAGGELAAYRIV
+QEALTNTLRHGGPDADAFVTLAWTAHGLDLQIDDDGCGAAADPATRGSGQGLRGAAERTA
+LFGGTLETGPRVGAGYRVSAHLPYSAV
+>PROKKA_00599
+MNPLHRIDQWMRAHPVRTDVLVSVLLFAVLGLTPWVMLGSLAGPTPGSIVASILIALALI
+APWAFRRVRPVASAAAVAAAAVAHLVAGPEFSLALVLVPMTVYNLAANAPRWASFTGLVA
+ALLGGVANGIRVGLFPDPAMRPDGVYEPVDPSLEALLVMVFGCAAVVLTAWAFGDVVRHR
+RLAVRALEDRNRRLETMALQERRLAASDERNHIAREMHDIVAHSLQVIISQADGARYAAA
+AKPELAVATLDTIGLTGRAALADMRQLLGVLRETGETVAGVPGVAPDDGAPGPAAGASDE
+GAAGAADEGAAGAADEGAAGAGTAGAGTTPGAGRTRLPADVASRDGRGARQPPGHRPQPT
+LADVPALIETMRLSGLEVSLLETGAPRRPLPPGGELAAYRIVQEALTNTLRHGGPQASAF
+LTLAWTGRGLDVQSDDDGRGADADPGTRGSGHGLRGVAERVALFGGTVETGPRAGAGYRV
+SAHLPYSAV
+>PROKKA_00521
+MNPLRRLDVLLRRHPVRTDVTAAVLLTLVLVLAPLVMLGGGVGSPAAWQTAGTVVAGLLM
+TGAWGLRRVRPVAAAGVTVAGALLHLAVGPEFTIALAMVPATVYNLAAIGPRWASLAGLA
+TGLAGGLANGLKVWLFPPRFTTPDGVQVQSPAEPVAMVVMAVLCGMAVLTAWAFGDVVRN
+RRLAVQALEDRARRLETQALQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYAA
+AAKPELAVETLETIGQTGRSALADMRQLLGVLRGPAEPTGGPDRARRDPAAPDGHRAPPG
+LADLPALFQTLRLSGLEISLLEQGSPRRDLPAGGELTAYRTVQEALTNTLRHGGEGAHAF
+LTLRWTARGLEIQADDDGRSQADAETTGSGQGLRGIAERVALFGGTMEAGPRVGAGWRVW
+AELPYADV
+>PROKKA_02103
+MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG
+MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSLSLLMVPLTVCNLAANAPRSVSVAGL
+LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPLAMVIMAIGCGLVVLTAWAFGDVVR
+NRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYA
+AAAKPALAVTALETIGQTGRSALADMRQLPGVLRETGETVAGVPGVTDDDTRRPADPAPD
+RADPTGTRPDVVAAPDGRGARLPPGRRPQPRLADLPALVETMRLSGLEVSLLETDTPRRA
+LPAGGELAAYRIVQEALTNTLRHGGPDADAFVTLAWTARGLDLQIDDDGRGAAADPATRG
+SGQGLRGAAERTALFGGTLETGPRVGTGYRVSAHLPYSAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001691.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001691.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e7ded723227736df473ab4c550fabccdc91fdff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001691.fa
@@ -0,0 +1,14 @@
+>PROKKA_02161
+MTGSILDHPAPTTSRASDPAAERAQRDSECVAFFVALVTAAVVMLGLSLFTGVEGLLRLA
+LTAGAGLLAGAVAWATARPVLEDDAPGD
+>PROKKA_01874
+MTGSILDHPTPTTSRASDPAAEQAQRDSECVAFFVALVTAAVVMLGLSLFTGVEGLLRLA
+LTAGAGLLAGAVAWATARPVLEDDAPGD
+>PROKKA_00596
+MTAAVVILGLSLFTQVEGLPRLLVTAASGLLAGAVTWSVTQPVLEDEVLHG
+>PROKKA_00519
+MSAAPAPSPAAPAVPPVTAVPPAAREPEGTSPSDRERERGDAECLAFFLALVTAALVMAG
+LALATDLGPLLRVLLSLGASGLAGALTLAFTRPSLED
+>PROKKA_02105
+MTGSILDHPAPTTSRASDPAAERAQRDSECVAFFVALVTAAVVMLGLSLFTGVEGLLRLA
+LTAGAGLLAGAVAWATARPVLEDDAPGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001698.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001698.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a4aa1aebd0b62864876874d397c0067c4c85795
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001698.fa
@@ -0,0 +1,35 @@
+>PROKKA_02175
+MAPSPLSRRSLLASGGVGLTLLLAACSTGPAGGSASSSSAGASSSDAAGGDAAFPRSIEH
+VYGTTEIPQRPTRVATVSWVNQDVTLALGVVPVGMAAVEFGGNAEKSTDWFDAKLAETEG
+AQKPVQWSEASGIDAEAIAAVKPDVILAVYSGITQEDYDRLSKIAPTVAYPKDVPAYGTS
+WQQSTEVIGRVLGKEQEAEELIADLEQQIKDAGEKHADLQGASFVYGTIDPAAADQISIY
+TDVDNRPKFLELLGMEQAPVVTENSPEDQAFFFTWSPERADELESDVFVSWAAQDSVREA
+IESDPLLGSIPAVKAGALVLQTDEQEVLSVSAISPLSIPFALEKVVPPIAEAAKTAQG
+>PROKKA_01889
+MAPSPLSRRSLLASGGVGLTLLLAACSTGPAGGSASSSSAGASSSDAAGGDAAFPRSIEH
+VYGTTEIPQRPARVATVSWVNQDVALALGVVPVGVAAVEFGGNAEKSTDWFDAKLAETEG
+AQKPVQWSEASGIDAEAIAAVKPDVILAVYSGITQEDYDRLSKIAPTVAYPKDVPAYGTS
+WQQSTEVIGRVLGKEQEAEELIADLEQQIKDAGEKHAGLQGASFVYGTIDPAAADQISIY
+TDVDNRPKFLELLGMEQAPVVTENSPEDQAFFFTWSPERADELESDVFVSWAAQDSVREA
+IESDPLLGSIPAVKAGALVLQTDEQEVLSVSAISPLSIPFALEKVVPPIAEAAKTAQG
+>PROKKA_00577
+MATVSWVNQDVALALGVVPVGMAAVEFGGNAEKSTDWFDAALEKVEGAERPVTWSEAAGI
+DAEAVASVRPDVILAAYSGLTREDYDRLSKIAPVVAYPKDVPAFGTPWQQSTRMIGQALG
+KDAEAEALVEDVEGRIAAAAQKHPDLKDATFVYGTVDPTAADQISVYTLVDNRPRFLESL
+GMKQAPVVAENSPKDQAFFFTWSPERADELESDVLVSWALDASVADAIEADPLLSALPAV
+QKDGLVLQVDQQEVLSVSAISPLSIPFALERIVPPIAEAAARSRG
+>PROKKA_00504
+MPQSPSRRSVLAAGGSGLALLLAACSTGPAGSSVPSSSPASSAGSAAASSSASGSAAYPL
+TVEHVYGTTEIPARPERVATVSWVNQDVALALGVVPVGVPAVEFGGNADKSTDWFDAKLK
+ELGGPTPVQWSEADGIDAEAIAAVKPDVILAVYSGLTREDYDRLSKIAPVVAYPKDVPAF
+GTSWQQSTEVIGRVLGKEREAAALVADLERQIADAGAEEDGLAGASFIYGTLDPAAADQI
+SIYTAADNRPKFLELLGMELAPVVAENAPEDGAFFFTWSPERADELESDVFVSWAASADV
+ADAIEADPLLGAIPAVEKGGLVLQVDQQEVLSVSAISPLSIPYALEKVVPPIAEAARAAK
+G
+>PROKKA_02120
+MAPSPLSRRSLLASGGVGLTLLLAACSTGPAGGSASSSSAGASSSDAAGGDAAFPRSIEH
+VYGTTEIPQRPARVATVSWVNQDVALALGVVPVGMAAVEFGGNAEKSTDWFDAKLAETEG
+AQKPVQWSEASGIDAEAIAAVKPDVILAVYSGITQEDYDRLSKIAPTVAYPKDVPAYGTS
+WQQSTEVIGRVLGKEQEAEELIADLEQQIKDAGEKHAGLQGASFVYGTIDPAAADQISIY
+TDVDNRPKFLELLGMEQAPVVTENSPEDQAFFFTWSPERADELESDVFVSWAAQDSVREA
+IESDPLLGSIPAVKAGALVLQTDEQEVLSVSAISPLSIPFALEKVVPPIAEAAKTAQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001701.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001701.fa
new file mode 100644
index 0000000000000000000000000000000000000000..69804e174656aaf811fb00f94db632af3a9825ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001701.fa
@@ -0,0 +1,32 @@
+>PROKKA_02178
+MTAPPLTVPSPAAPRAGAADDVAIRLRGLTLGYGPASAPPIVADLDLDVPAGRVTAIIGA
+NGCGKSTLLRGLTRQLAPRAGSIEVLGRDAARVSARDYARTVALLPQHPVAPEGMTVAQL
+VARGRHPHRGLLGGRAAGDDAAIASALERTDLVELADREAGTLSGGQRQRAWLALVLAQQ
+TPVVLLDEPTSYLDLSHQVEVLDLVRALPDPRGGGRATVVAVLHELNLAARSADHIVAMA
+AGRVVAQGTPGEVIVPEVLAEVFGLDADVVADPLLGHPVVLPRGDGDRR
+>PROKKA_01892
+MTAPPLTVPSPAAPRAGAADDVAIRLRGLTLGYGPASAPPIVEDLDLDVPAGRVTAIIGA
+NGCGKSTLLRGLTRQLAPRAGSIEVLGRDAARVSARDYARTVALLPQHPVAPEGMTVAQL
+VARGRHPHRGLLGGRAAGDDAAIASALERTDLVELADREAGTLSGGQRQRAWLALVLAQQ
+TPVVLLDEPTSYLDLSHQVEVLDLVRALPDPRGGGRATVVAVLHELNLAARSADHIVAMA
+AGRVVAQGTPGEVIVPEVLAEVFGLDADVVADPLLGHPVVLPRGDGDRR
+>PROKKA_00574
+MTPPHPAAAPAERPGADPATGPAQDPALRLRGVRLGYGRPDTPDTVGPVDLDVPAGRVTA
+LIGANGCGKSTLLRGLTRQLPLRGGSAEVLGRDLGAYSAREYARTVALLPQHPVAPEGMT
+VAQLVQRGRHPHRGLFGTTGADDDAAVARALRHTDLEKLADREVAELSGGQRQRAWLALV
+LAQRTPVLLLDEPTSYLDLAHQVEVLDLVRGLTRPDGDEEPVTVVAVLHELSLAARVADR
+LVALRDGRVAAAGTPAEVLTPAVLAEVFDLDADVRPDPLLGHPVVLPRGAADRGAPLPSP
+TTQETR
+>PROKKA_00501
+MTSSPPTPAAPSTAPAPALRLRGVELSYGPASAPPTVGPVDLDVPAGQVTAVIGANGCGK
+STLLRGLTRQLPLRAGTVDVLGRDAAGMSARDYARTVALLPQQPVTPEGLTVAQLVERGR
+HPWRGLLGGRAAGDDAAVAAALARTGLVDLAARDAATLSGGQRQRAWLALVLAQQTPVVL
+LDEPTSYLDLAHQVEVLDLVRTLPDPRAVGARTVEAAGGVVGGGAGTEAGPPPRATVVAV
+LHELSLAARAADHVVAMAGGRVVATGTPAEVIVPEVLAEVFGLDADVVPDPLLGHPVVLP
+RGRGDRA
+>PROKKA_02123
+MTAPPLTVPSPAAPRAGAADDVAIRLRGLTLGYGPASAPPIVEDLDLDVPAGRVTAIIGA
+NGCGKSTLLRGLTRQLAPRAGSIEVLGRDAARVSARDYARTVALLPQHPVAPEGMTVAQL
+VARGRHPHRGLLGGRAAGDDAAIASALERTGLVELAEREAGTLSGGQRQRAWLALVLAQQ
+TPVVLLDEPTSYLDLSHQVEVLDLVRALPDPRGGGRATVVAVLHELNLAARSADHIVAMA
+AGRVVAQGTPGEVIAPEVLAEVFGLDADVVADPLLGHPVVLPRGDGDRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001710.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001710.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e1bec1c450414d24a5c4f0b216f8331d239ee4ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001710.fa
@@ -0,0 +1,41 @@
+>PROKKA_02190
+MPPPVPQPTRRQMLLAGSALLGSGLLAACGQDGEDAASSSVPTSSAPTSAAPAGPPPAGE
+PVAWPDVARVPHLFFHSLVVDPARAFDGDDKARGYLDFMVTVDEFDAVIRQVYERGYVLV
+SPHELYEVGEDDVVRPKTLMVPEGRTPLILSLDDCSYYLYMDGDGFADRLIVAEDGRVRN
+EYTDAQGTTHVGAFDVVPRLDDFLAEHPDFSLNGARGVLAMTGYDGVFGYRTSAREFGDS
+PTFDADVAAATEVADALKDSGWEFASHTWGHRTVPKLTMEELEFDMGHWHEEVEPILGPT
+DMLIYPFGADVTGPGKYTEDNERYRYLRELGYRSFFLVDGTSKAWGQLEPGYYRGSRINV
+DGISLAAAVSGERPVLEEFFDPRSVLDPARPESIRGPKKPSPAPSSPAAAPRTPRP
+>PROKKA_01904
+MPPPVPQPTRRQMLLAGSALLGSGLLAACGQDGEDAASSSVPTSSAPTSAAPAGPPPAGE
+PVAWPDVARVPHLFFHSLVVDPARAFDGDDKAGGYLDFMVTVDEFDAVIRQVYERGYVLV
+SPHELYEVGEDDVVRPKTLMVPEGRTPLILSLDDCSYYLYMDGDGFADRLIVAEDGRVRN
+EYTDAEGTTHIGAFDVVPRLDDFLAEHPDFSLNGARGVLAMTGYDGVFGYRTSAREFGDS
+PTFDADVAAATEVADALKDSGWEFASHTWGHRTVPKLTMEELEFDMRHWHEEVEPILGPT
+DMLIYPFGADVTGPGKYTEDNERYRYFRELGYRSFFLVDGTSKAWGQLEPGYYRGSRINV
+DGISLAAAVSGERPVLEEFFDPRSVLDPARPESIRGPKKPSPAPSSPAAAPRTPRP
+>PROKKA_00554
+MAPSRRQILLTGSALLGSGLLAACSSEGGSAPASSSPAGTPAPAPSSSSAAPAGPGPAGE
+PVAWPNTALVPHLFFHSLVVDPKRAFDGDHKEAGYLDFMVTMDEFAAILPQLYAKGYVLV
+SPHELYEVGEDDVVRPKTLMVPENRTPLVFSLDDCSYYLYMEGDGFADRLIVDEDGRVRN
+EYTDADGTTHVGSYDMVPMLDDFLEEHPDFSLNGARGVLAMTGYEGVFGYRTSAREFGDS
+PTFDADVAAATEVADAMKATGWEFASHTWGHRTVPKLELDELQRDLELWHGEVEPILGPT
+DMMIYPFGADVARTGKYEADNERYQYMRSLGYRSFFLVDGTAKAWGQLEPGYYRGSRINV
+DGISLEAAISGKRPVLDEFFDSRSVLDPARPASIRGTQQSPAAPPGGQSGSASPSATG
+>PROKKA_00483
+MEYSRRHVIFGGSALLGAGLLAACAPAQDGAAPSAGGGSSSEAASSSAAPSPSSTRPVIP
+SAPEPAGKPVAWKDVAKVPHLFFHSLVVDPEKAFHVHGESDGYLNYMVTQAEFERILPQL
+WALGYVLVSPHELYEVGRDDVVRARTLMVPENRTPLIISLDDCSYYEYMEGDGFATRLLV
+DDSGRVRTEYTDQEGKTTIGANDLVPILDDFVRDHPDFTLNGAKGVLALTGYNGVLGYRS
+SPTMYPEGPELDEAVATAKEVVAAMKETGWEFASHSWSHRSMAQMSLADLKEDCERWIED
+VQPIVGPTDMLIYPFGADIAGIEKYSGPEYEHLRSLGFRSFFLVDGSSKAWGQLEPGYYR
+GSRINVDGISLAGAKDGSRPVLDEFMDVDSVLDPARPESIHAPSYVPPEERAAASSGAPS
+ASPSS
+>PROKKA_02135
+MPPPVPQPTRRQLLLAGSALLGSGLLAACGQDGEDAASSSVPTSSAPTSAAPAGPPPAGE
+PVAWSDVARVPHLFFHSLVVDPARAFDGDDKAGGYLDFMVTVDEFDAVIRQVYERGYVLV
+SPHELYEVGEDDVVRPKTLMVPEGRTPLILSLDDCSYYLYMDGDGFADRLIVAEDGRVRN
+EYTDAEGTTHIGAFDVVPRLDDFLAEHPDFSLNGARGVLAMTGYDGVFGYRTSAREFGDS
+PTFDADVAAATEVADALKDSGWEFASHTWGHRTVPKLTMEELEFDMGHWHEEVEPILGPT
+DMLIYPFGADVTGPGTYTEDNERYRYFRELGYRSFFLVDGTSKAWGQLEPGYYRGSRINV
+DGISLAAAVSGERPVLEEFFDPRSVLDPARPESIRGPKKPSPAPSSPAAAPRSPRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001712.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001712.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf91be46d75e693142fdd06673ba21ada87a0e88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001712.fa
@@ -0,0 +1,75 @@
+>PROKKA_02195
+MLFRYELRRFRRGLPLLALLFIFLVPAIYGALYLSANWDPYGAMDRLPVAIVNEDEPVQR
+GDTTLRTGADMTERLKDDRAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG
+GTPQQAQITLRRDDANGFVIGSVTNASQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD
+AADGAAQLADGTASAEDGASRLEDGIVQAHDGSGKLAEGAGQLATGAGDLADGAAQADDG
+AQRLAEGAASAQDGAGRLADGLDQAREGSQALADGAGQLAENAPALRQGATDLSDGLAQL
+QTGSAELTDGATQVADGTQQLYDTVVPGLDQVIERQDAVAADVAAVDEDVQRVAEVAGTA
+EDGAGARIADAQTALAALAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA
+AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF
+ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA
+GQLESGATELDGGLAQLQDGAGELRAGLGTLDDGAHELASGLSDGADRVPALTEDERDEA
+ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGRRNPV
+AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL
+GTPGSALLLVLLVLQLASTGGTYPAEVLPGFFQALHPFMPMSYSIEAFRNAISGGPDQRF
+WVPVVVLMGIGAAALALDVLVVRRRRRFRMKDLHPALQA
+>PROKKA_01908
+MLFRYELRRFRRGLPLLALLFIFLVPAIYGALYLSANWDPYGAMDRLPVAIVNEDEPVQR
+GDTTLRTGADMTERLKDDRAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG
+GTPRQAQITLRRDDANGFVIGSVTNASQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD
+AADGAAQLADGTASAEDGASQLEDGIVQAHDGSGKLAEGAGQLATGAGDLADGAAQADDG
+AQRLAEGAASAQDGAGRLADGLDQARGGSQALADGAGQLAENAPALRQGATDLSDGLAQL
+QTGSAELTDGATQVADGTQQLYDTVIPGLDQVIERQDAVAADVAAVDEDVQRVAEVAGTA
+EDGAGARIADAQAALAELAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA
+AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF
+ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA
+GQLESGATELDGGLAQLQDGAGELRAGLGTLDDGAHELASGLSDGVDRVPALTEDERDEA
+ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGRRNPV
+AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL
+GTPGSALLLVLLVLQLASTGGTYPAEVLPGFFQALHPFMPMSYSIEAFRNAISGGPDQRF
+WVPVVVLMGIGAAALALDVLVVRRRRRFRMKDLHPALQA
+>PROKKA_00549
+MLFRYELRRFRRGLPLLALLFILLVPAIYGALYLSANWDPYGAMNRLPVAIVNEDEPVQR
+GDTTLRTGADMTARLKEDHAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG
+GTPQQAQITLRRDDANGFVIGSVTASSQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD
+AADGAAQLADGSASAVDGASQLEDGIVQAHDGSGRLAEGAGQLATGAGDLADGAAQADDG
+AQRLAEGATSAQDGAGRLADGLDQAREGSQALADGAGQLAENAPALRQGATDLSDGLAQL
+QTGSAELTDGATQVADGTQQLYDTVVPGLDRVIERQDAVAADVAAVDEDVQRVAEVAGTA
+GDGAGARIADAQAALAALAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA
+AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF
+ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA
+GQLESGATELDDGLAQLQDGAGELHTGLRTLDDGAHELASGLSDGVDRVPALTEDQRDEA
+ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGHRNPV
+AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL
+GTPGSALLLVLLILQLASTGGTYPAEVLPGFFRALHPFMPMSYSIEAFRNAISGGLDQHF
+WVPVVVLMGVGAAALALDVLVVRRRRRFRMKDLHPALQA
+>PROKKA_00478
+MLFRYELRRFRGVLPTIALLFIVLVPTIYGALYLSANWDPYGNLSSLPVAIVNEDRPVES
+DGKTLTTGADITEELVDQHTFDWHETTRDDAEAGLRDGRYYLVMEIPEGLSADLVSANTS
+DPQQAHITLRRNDANGFVIGSVTSSSQSKIENAVDKAAVEAYFKAVFENLATIRQGMADA
+RDGAGRLADGAGQADDGAAQLADGIVQAHDGSGQLAQGASDAQDGAGQLADGAGQLKDGA
+DQLAAGATSAKDGAVQLQTGIGQAREGSQKLADGAGQIAAKVPDLRDGATALSNGLTQLD
+TGSADLADGAHQVADGTQQLYDTVIPGLDAVIERQDKVASDVATVNQDVQTLNDAVATAG
+SGAGGDIDTASEQLQALAESNPDIAVAPEYAALQQSLTDAKEKAGSATSTAQDVADRSAA
+VNSRVQGFVSEDVAGNAKADITKLNDGAHAVAEGADTLHAGIGQANTGAQALADGVGRFA
+DALDQLAAGATALDDGLAQLEDGSGRLVDGLGKLETGAGDLADGAGRLDQGAGELQTGLG
+KLSDGATSLDSGLAQLETGSGDLKTGLDSLSDGATQLHDGLASGTDKIPALSEDAADEAA
+LVMSRPVQVDMDVLNPAGVYGRGVAPLFFSIALWVFGIAAFNVMRPVNGRLLAGRRNPLL
+LALSAWLPVGLLSVVGSLVMLAATVPLGIDPVHPWHLVGLVVFTALAFSLFAHLVMTALG
+TPGSAVLLVTLILQLGSAGGTYPADVLPPFFRWVSPLMPMTHSINAIRYALSGGQPAQFW
+GAVAFLAVFGAACLFLDMAVVRRRQRFRMKDLHPALEK
+>PROKKA_02139
+MLFRYELRRFRRGLPLLALLFIFLVPAIYGALYLSANWDPYGAMDRLPVAIVNEDEPVQR
+GDTTLRTGADMTERLKDDRAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG
+GTPQQAQITLRRDDANGFVIGSVTNASQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD
+AADGAAQLADGTASAKDGASQLEDGIVQAHDGSGKLAEGAGQLATGAGDLADGAAQADDG
+AQRLAEGAASAQDGAGRLADGLDQARGGSQALADGAGQLAENAPALRQGATDLSDGLAQL
+QTGSAELTDGATQVADGTQQLYDTVVPGLDQVIERQDAVAADVAAVDEDVQRVAEVAGTA
+EDGAGARIADAQAALAALAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA
+AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF
+ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA
+GQLESGATELDDGLAQLQDGAGELHTGLGTLDDGAHELASGLSDGVDRVPALTEDERDEA
+ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGRRNPV
+AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL
+GTPGSALLLVLLILQLASTGGTYPAEVLPGFFQALHPFMPMSYSIEAFRNAISGGLDQRF
+WVPVVVLMGIGAAALALDVLVVRRRRRFRMKDLHPALQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001714.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001714.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a09bc9d17a7974bacebf3bcf0fd82e0b9ee5f12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001714.fa
@@ -0,0 +1,25 @@
+>PROKKA_02197
+MATRPRREDVRAAILDHAARVFGREGYARSSLARIAAEAGYTKGAVYSGFAGKPDLFAAA
+CTVQFERATTRAMDGVADALDDPDLPREDLVARVAEALADVVLETTGSWPLLLHEFQAVG
+LREPAVGRAYRTLTVRRRDFLAGLLREHRVLADVPDEQVTHTAAMLLMLVHTLSVERHLA
+PEDLTVDDVRDTLAAAVRSLLP
+>PROKKA_01910
+MATRPRREDVRAAILDHAARVFGREGYARSSLARIAAEAGYTKGAVYSGFAGKPDLFAAA
+CTVQFERATTRAMDGVADALDDPDLPREDLVARVAEALADVVLETTGSWPLLLHEFQAVG
+LREPAVGRAYRTLTVRRRDFLAGLLREHRVLADVPDEQVTHTAAMLLMLVHTLSVERHLA
+PEDLTVDDVRDTLAAAVRSLLP
+>PROKKA_00547
+MATRPRREDVRAAILDHAAQVFGREGYARSSLTRIAAEAGYTKGAVYSGFAGKPDLFAAA
+CTVQFERATTQAMDGVADALDDPDLPREDLVARVAEALADVVLEPTGSWPLLLHEFQSVG
+LREPAVGRAYRVLTVRRRDFLAGLLREHRVLADVPDAQVTHTAAMLLMLVHTLTVERHLA
+PEDLTVDDVRDTLAAAVRSLLP
+>PROKKA_00480
+MGGLRGVRRFDTVGIQYHRYRKGKMASRPRHQDVRADLLQYATEAFERDGYGRASLAGIA
+ADAGYTKGAVYSGFGSKAALFAEVCGAQFEALTRRTLDVVGRELAVEGGGRADLVARLAA
+VLTSLTFDGDARWPLLLHEFQAVGLRDESVASEYRALTARRVRFLAEALGEHPRLAGLSA
+ERLERTSSLTLVLVHTLAVEHRLSPEAMDRRGGELSFTALLDSALPD
+>PROKKA_02141
+MATRPRREDVRAAILDHAARVFGREGYARSSLARIAAEAGYTKGAVYSGFAGKPDLFAAA
+CTVQFERATTRAMDGVADALDDPDLPREDLVARVAEALADVVLETTGSWPLLLHEFQAVG
+LREPAVGRAYRTLTVRRRDFLAGLLREHRVLADVPDEQVTHTAAMLLMLVHTLSVERHLA
+PEDLTVDDVRDTLAAAVRSLLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001715.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001715.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89e5b63e487db419e475f02260c25033d36ae605
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001715.fa
@@ -0,0 +1,30 @@
+>PROKKA_02198
+MDPSLVWLPAVVALAAITVGGTLQRVSGMGVGMIAAPTLSLLLGPVAGVTLSNVAASVSA
+VLLFAVLHRHVDWPRFVRLAPLLVAGSFAGAWAVRVLDAHALEILLGSSVLVAVAAVLGL
+QQRFTAQGNGAVFASGAVAGFMNTTAGIAGPALAVYAVASRWDQRSWAATLQPVFLLANL
+TSLVTKSLFGAAVPAGLHVPWPVWVAVVVGGPLGVLLGSVVARRVDPAKARVLAICLAGV
+GGTVALVRGVAGTLG
+>PROKKA_01911
+MDPSLVWLPAVVALAAITVGGTLQRVSGMGVGMIAAPTLSLLLGPVAGVTLSNVAASVSA
+VLLFAVLHRHVDWPRFVRLAPLLVAGSFAGAWAVRVLDAHALEILLGSSVLVAVAAVLGL
+QQRFTAQGNGAVFASGAVAGFMNTTAGIAGPALAVYAVASRWDQRSWAATLQPVFLLANL
+TSLVTKSLFGAAVPAGLHVPWPVWVAVVVGGPLGVLPGSVVARRVDPAKARVLAICLAGV
+GGTLALVRGVAGTLG
+>PROKKA_00545
+MSVVVLTGADGGARLGHTAPMDMSLVMLVPALVALAALMVGGALQRVSGMGVGMIAGPTL
+SLLLGPVAGVSLANVAAVVSAVLLFALLRRHVDWGRFLRLAPLLIVGSFAGAWAVRSLDV
+HALEVLLGGSVLVAIAASLGLQRRFTASGSAPAALAGTAAGFMNTTAAVAGPALAVYAVA
+SRWEQRSWAATLQPIFLLANLTSLATKSLFGTAVPASVDVHWTVWTAVVVGGPIGVLIGS
+RIAPRVNPSRARLLAICVAGVGASVALLRGIVGLLA
+>PROKKA_00481
+MAATAAAAVRTAERARSGGGVTVPVWHAPAVASRRRGARAHTAGVSISLAAVVFLCVAVG
+GVLQRISGMGVGMVAAPTLSLLVGPVAGVTMSNAAASVSALILFWMLRRHVDWPRFLRLA
+PLLVVGALAGAWTVRVMDHAWLEVVLGACVLVAIAAVLGLQDRLTLRGSAAVFGSGAVAG
+FMNTTAGVAGPALAVYAVASKWEQRSWAATLQPIFLTANVTSIVLKASLGATAGAAAVPW
+WAWAAAVAGAPAGIAVGSRLARRVDPGRARRVAVTLAGVGAAVTLVRGLASL
+>PROKKA_02142
+MDPSLVWLPAVVALAAITVGGTLQRVSGMGVGMIAAPTLSLLLGPVAGVTLSNVAASVSA
+VLLFAVLHRHVDWPRFVRLAPLLVAGSFAGAWAVRVLDAHALEILLGSSVLVAVAAVLGL
+QQRFTAQGNGAVFASGAVAGFMNTTAGIAGPALAVYAVASRWDQRSWAATLQPVFLLANL
+TSLVTKSLFGAAVPAGLHVPWPVWVAVVAGGPLGVLLGSVVARRVDPEKARVLAICLAGV
+GGTVALVRGVAGTLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001716.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001716.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8798f59ab455cd69eaecba889cee85cdd20baae9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001716.fa
@@ -0,0 +1,30 @@
+>PROKKA_02200
+MTTPTPGAGSPGSGVAGGVLAAVGALALIATVLALVLAFGPAGRDDAGAGAERRRWNGGF
+TPAPPTVNTQGYAEPVQGRVTSRFGPRPNPFGEGVVPSGVSEEALTRHDGVDLGGVPEGT
+PFHSVSDGRVLFVEAGGDAGGNLLAVDAGDGHVWRYLHAAPDSTVVDAGQRVSAGDHLAG
+VGQTGAATGVHLHLELRVDGEPVDPEAYLAERGVELGGSYPERRRGLSR
+>PROKKA_01913
+MTTPTPGAGSPGSGVAGGVLAAVGALALIATVLALVLAFGPAGRDDAGAGAERRRWNGGF
+TPAPPTVNTQGYAEPVQGRVTSRFGPRPNPFGEGVVPSGVSEEALTRHDGVDLGGVPEGT
+PFHSVSDGRVLFVEAGGDAGGNLLAVDAGDGHVWRYLHAAPDSTVVDAGQRVSAGDHLAG
+VGQTGAATGVHLHLELRVDGEPVDPEAYLAERGVELGGSYPERRRGLSR
+>PROKKA_00542
+MLAAVLAFALIGAVLWAALALGPDGVPGQQGSRRPAASTPAPPTVSAEGFAEPVRGRVTS
+RFGPRPNPFGEGSAPPSTDTDALTDHTGVDLGGVPEGTPFHSVSDGRVLFVEAGEDAGGN
+LLAVDSGDGHVWRYLHAAPDSTVVNAGQRVSAGDALAGVGQTGTATGVHLHLELRVDGTP
+VDPEPYLRERGVELGSSWERPRRR
+>PROKKA_01787
+MKKLAVIAAVLVLFSPALLLLGVGMIFSPGANASCTTSTTGPSVVGPVPDSLDVTTADGQ
+TFTLNTTQLTHAATIIQTGSQIEGVTRDGLQIALMAALTESNLRMLANTSVYPDSGNHPN
+DGDASDHDSLGLFQMRPQAGWGTVPDLMDPGYQARAFFGGPTGPNHPSPRGLLDIPGWQT
+LSKGEAAQAVEVSAYPDRYANYEPVAEQILTTLTTPTADSPQLPETGRVVFPLPEGTWVA
+TSPFGMRVHPITGENKLHTGADYSAPDGTPVLAAADGIVTHASMSGGYGGLIIIEHTTGG
+QKIATAYAHLWETGIHVNVGDQVTAGQHIGDVGSAGYSTGAHLHFELRQGGSDGEFTDPQ
+PWLDQHTSGNLPAPTTPVEQEGCNPVATQPAPPQGPDAGDPDRKVDDPTTDGQITARMLH
+VYTQALTAYPDSSWACYSPRPGTKSEHPLGRACDVTFGNAIGSRPTPQQLEAGWALTNWL
+QDNAETLGVEYLIWQGQIWSLARDAEGWRPYNGGGMHDPTDVTGGHYDHVHITVKEGS
+>PROKKA_02144
+MTTPTPGAGSPGSGVAGGVLAAVGALALIATVLALVLAFGPAGRDDAGAGAERRRWNGGF
+TPAPPTVNTQGYAEPVQGRVTSRFGPRPNPFGEGVVPSGVSEEALTRHDGVDLGGVPEGT
+PFHSVSDGRVLFVEAGGDAGGNLLAVDAGDGHVWRYLHAAPDSTVVDAGQRVSAGDHLAG
+VGQTGAATGVHLHLELRVDGEPVDPEAYLAERGVELGGSYPERRRGLSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001718.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001718.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b6bfce40f28fa51685e72d41b37c596f22a14b45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001718.fa
@@ -0,0 +1,27 @@
+>PROKKA_02202
+MPPAPTARLRFREMADADLDHLAGLLADPVVMRFYPAPRTRAEAAAWIAGNRRRYAQDGH
+GLWIIETHDDGGPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACRDHAR
+DVLGHHELVAIIHPENTASRRVAERIGMTVVGEDRTGAPEARAALGLEARTVLGMRLRPG
+A
+>PROKKA_01915
+MPPAPTARLRFREMADADLDHLAGLLADPVVMRFYPAPRTRAEAAAWIAGNRRRYAQDGH
+GLWIIETHDDGGPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACRDHAR
+DVLGHHELVAIIHPENTASRRVAERIGMTVVGEDRTGAPEARAALGLEARTVLGMRLRPG
+A
+>PROKKA_00541
+MLPAPTARLRFREMTEADLDAMAALLGDPAVMRFYPAPRTREQAAEWIAGNRRRYAQDGH
+GLWVIETLPEHSDDGEPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACR
+DHARDALGHHELVAIIHPENSVSRRVAEKIGLREAEQDFTGAAEARETMGLASRTVMAMR
+F
+>PROKKA_00472
+MTQPIPRHPDPGNTGTDALDDVVREHMLLLRRAVHGLGAYRRPEALDRSAVLLLARLEAQ
+GPMTMAELAAAFGLDVSTLQRQIGAAQRAGFVERFRDPAGGQARLHRATDAGRAALEGEL
+AARRAAVAEVTRSWPAPDVAALARLLRRFNEGSEELREQPWPRERPEAPGAAAVPAGTAR
+LRFREMTEADLDVLVGLLGDPEVMEFYPAPKTRAEVADWIAWNRRSYAEHGHGLWIVETH
+AGAFVGECGLTWQRVNGERRLEVGYHVAPVLQGRGYATEAAAACRDHARDVLGAPELVAI
+VHPENTASRRVAEKIGMEVLEEDRTGVDASYLEAIGAEARTVLGMRLA
+>PROKKA_02146
+MPPAPTARLRFREMADADLDHLAGLLADPVVMRFYPAPRTRAEAAAWIAGNRRRYAQDGH
+GLWIIETHDDGGPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACRDHAR
+DVLGHHELVAIIHPENTASRRVAERIGMTVVGEDRTGAPEARAALGLEARTVLGMRLRPG
+A
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001719.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001719.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef7936091e8a0893720628c8c5216971427a5dcf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001719.fa
@@ -0,0 +1,37 @@
+>PROKKA_02206
+MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN
+LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF
+RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA
+LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI
+DATPSQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAEPAQGEDD
+DGAPSPILAADHLARVVLGAEPRVVTQLAERVLAPLDEVSEAKRAVLEETLLAWLTHWGQ
+RAPIAAELGVHPQTVGYRVGRLRELFGEALEDPDARFDLEIVLRARRDGVG
+>PROKKA_01919
+MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN
+LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF
+RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA
+LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI
+DATPSQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAEPAQGEDD
+DGAPSPILAADHLARVVLGAEPRVVTQLAERVLAPLDEVSEAKRAVLEETLLAWLTHWGQ
+RAPIAAELGVHPQTVGYRVGRLRELFGEALEDPDARFDLEIVLRARRDGVG
+>PROKKA_00539
+MTSPRPESDWRPPWQDLPADLPGRLAHALPGIMERIIQTVPDQIPAYAAARDGRYGKNLT
+LGVTTALEQLMSLPGTSRPALSAQSRELMARLGAGEFREGRSMDALLGAYRTSARIVFRD
+LSAECARLGMDMSVVIELGESIWAYIDELSAVSAQAYAEAQSAQAGVRELHRTALAAALV
+RGGAEEKEVERLAALADWRVPARLAVVALPPDAGQAVRARLGRGGLVVERDSEVVAVVGA
+DAPARRRRLLRILAGTAAVVGPAVEWPLAPHSYRVARTLAGQEAARRAAEQRAAARPEGD
+GSAADGPGAEEAVGFEPVGGADPAPGTPILAEEHLARVVLGAEPRVVAELAERVLAPLAE
+LTDAKRAVLEQTLLSWLVHWGQRAPIAAELSVHPQTVGYRVARLRELFGDALEDPDARFD
+LELVLRARAGGMAA
+>PROKKA_00469
+MVLSAPPRSPVVTRRLLAALQGTGAVVGPEVDALEVARSLHVARAVLARRDALSGVAPGA
+AVLAEEHLADVVLGAEPEALRRLSERVLAPLDGLSDAKRATLEATLAAWLAHRGARGPMA
+AELNVHPQTVGYRVGRLRELFGGALDDADARFDLELALRSRRGQG
+>PROKKA_02150
+MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN
+LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF
+RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA
+LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI
+DATPSQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAEPAQGEDD
+DGAPSPILAADHLARVVLGAEPRVVTQLAERVLAPLDEVSEAKRAVLEETLLAWLTHWGQ
+RAPIAAELGVHPQTVGYRVGRLRELFGEALEDPDARFDLEIVLRARRDGVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001733.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001733.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad89074ad0fda0e2254155e7f11cdc7d31dc1067
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001733.fa
@@ -0,0 +1,30 @@
+>PROKKA_02257
+MHPITLARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTEAGISRT
+PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH
+AATGGSVDAARRLLDGHAEICAQLAAGRAADAQRALQAHLDAAGSGVVPGLPPVGPSEAG
+EPR
+>PROKKA_01957
+MHPITLARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTEAGISRT
+PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH
+AATGGSVDAARRLLDGHAEICAQLAAGRAADAQRALQAHLDAAGSGVVPGLPPVGPSEAG
+EPR
+>PROKKA_00474
+MHLIILARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVRLSTEAGISRT
+PAREALLQLESWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH
+AATGGSVDAARRLLDGHAEICAQLAAGCAADAQRALQAHLDAAGTGVVVPGLPTVSQPEA
+GEPR
+>PROKKA_00429
+MHLIILARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTDAGISRT
+PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIAMCGNAAFDEIMGTFAPRLARLIH
+AATGGSVDAARRLLDGHVQICAQLAAGRAADAQRALQAHLDAAGAGVVVPGLLPVGSSEA
+GEPR
+>PROKKA_02188
+MHPITLARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTEAGISRT
+PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH
+AATGGSVDAARRLLDGHAEICAQLAAGRAADAQRALQAHLDAAGSGVVPGLPPVGPSEAG
+EPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001736.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001736.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35eea5378c4da7ea2ee269be75ca737af2f4900c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001736.fa
@@ -0,0 +1,45 @@
+>PROKKA_02282
+MTENYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQSVPTAANASFYAEI
+VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLAQDGGGGGGF
+>PROKKA_01973
+MTENYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQSVPTAANASFYAEI
+VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLAQDGGGSGGF
+>PROKKA_00454
+MTEDYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQTVPTAANASFYAEI
+VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLSEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLAIDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLASDAGGGPGGF
+>PROKKA_00406
+MTEDYGDSGSYGGDRTPERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELTKVGGPAVLHELIQTVPTAANASFYAEI
+VAEKAVLRRLVSAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLAQDGGGSGGF
+>PROKKA_02221
+MTENYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQSVPTAANASFYAEI
+VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLASDAGGAGGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001738.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001738.fa
new file mode 100644
index 0000000000000000000000000000000000000000..353c52c89179dd237c00feb4c06d36489ee4054e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001738.fa
@@ -0,0 +1,21 @@
+>PROKKA_02286
+MSESKHTAPAPHGVPPTDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG
+IERFTRDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGEAQERVVIVMPLTLAG
+RTIEAEVTLTHRDEMGFRMLVGRTALAAGGLLVDPAASYVGGQPPRGVRRRNRGRA
+>PROKKA_01977
+MSESKHTAPAPHGVPPTDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG
+IERFTRDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGEAQERVVVVMPLTLAG
+RTIEAEVTLTHRDEMGFRMLVGRTALAAGGLLVDPAASYVGGQPPRGVRRRNRGRA
+>PROKKA_00451
+MSESKHTATAPHGVPPIDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG
+IERFTRDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGKAQERVVVVMPLTLAG
+RTFEAEVTLTHRDEMGFRMLVGRTALAAGGFHVDPAASYVGGQPPRGVRRRNRGRA
+>PROKKA_00404
+MGHVTESNHTPGRAAARPPHGDAHDAAPRPAQADADARPVREAATGVVVGWREWVGLPEA
+MTPWIKAKIDTGARTSALHAFGIERYTGADGAARVWFEVHPWQASAADARTVDLPVADLR
+AVRSSNGEVQERVVVMMPLRLAGRTVDAEVTLTHRDEMGFRMLVGRTALAKGFLVDPGAS
+YLGGQPPRGVRRRNRGHA
+>PROKKA_02225
+MSESKHTAPAPHGVPPTDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG
+IERFARDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGEAQERVVVVMPLTLAG
+RTIEAEVTLTHRDEMGFRMLVGRTALAAGGLLVDPAASYVGGQPPRGVRRRNRGRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001739.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001739.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1775024667c2da4e4df1bc874d53f783be98d75e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001739.fa
@@ -0,0 +1,41 @@
+>PROKKA_02287
+MSRRPARAPFAFGGVEVAAGRRHELSLPISQLVTGADVTLPVHVLHGREDGPTVWVSAAI
+HGDEVAGVEIVRRVLERLQPKHLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR
+GSLASRIAHLMMTEVIARCTVGIDLHTGADRRSNLPQIRCDLEDPQTRALAEAFGAPVLF
+HARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALDMVDPADVGL
+TEPGPDAVVDAPGPLPGEVPEERTTDVPEATDATGEDTAAVHPDVVDGEQDAPYLVWQST
+WVRARADGLVHLHVALGERVSAGDRIGALYNSFGRRLAHVKAELTGVVIGRTEAPLVHRG
+DALVHIGGWDA
+>PROKKA_01978
+MSRRPARAPFAFGGVEVPAGRRHELSLPISQLVTGADVTLPVHVLHGREDGPTVWVSAAI
+HGDEVAGVEIVRRVLERLQPTQLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR
+GSLASRIAHLMMTEVIGRCTVGIDLHTGADRRSNLPQIRCDLEDSQTRALAEAFGAPVLF
+HARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALDMVDPADIGL
+TEPGPDAVVDAPGPLPGEVPEERTTDVPEATDATGEDTAAVHPDVVDGEQDAPYLVWQST
+WVRARADGLVHLDVALGERVNAGDRIGALYNSFGRRLAHVKAELTGVVIGRTEAPLVHRG
+DALVHIGGWDA
+>PROKKA_00450
+MSRRPARAPFAFGGVEVPAGRRHELSLPISQLVTGADVTLPVHVLHGREDGPTVWVSAAI
+HGNEVAGIEIVRRVLERLQPKHLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR
+GSLASRIAHLMMTEVIGRCSVGVDLHTGADRRSNLPQIRCDLEDPQTRALAEAFGAPVLF
+HARLRDGSLRAAAREAGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALGMVDPAEVGL
+TEPGPAAVVDAPGPLPGEVPGDATTDVPEATDATGEDTEAVHADVVDGGQDAPHLVWHSS
+WVRARADGLVHLDVSLGERVAAGDRIGALYNSFGRRVAHVKAELTGVVIGRTEAPLVHRG
+DALVHIGGWDA
+>PROKKA_00403
+MSAPQKDPDRGGRTGDEAAAEKATGRRRASRAPFELAGVEVRPGRRHEVSLPVSRLVTGA
+EVTLPVHVLHGREDGPTVWVSAAVHGDEVAGIEIVRRVLERLKPSRMRGTLLALPIVNVL
+GVMTGDRYLPDRRDLNRSFPGAARGSLAARIAHLMMSEVVRRCEVGIDLHTGADRRSNLP
+QIRCDLEDPRTRALAESFGAPVLFHARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAI
+SPGVEGVLRVLAALGMVAAEDVGLATPVDAPAPLPGEVPEDRTTEVPEALDATGRDTGGV
+HADVVDGDLAAPHRVWHSRWVRARADGLVHLDVALGEQVTAGDRIGALYDSFGRRRSDVK
+AELTGVVLGRTEAPLVHRGDALVHIGELDGRPAGTFPAPSPGRRTAPSVAEGDPEAEAPP
+AATP
+>PROKKA_02226
+MSPRPARAPFAFGGVEVAAGRRHELSLPISQLVTGADVTLPVHVLHGRDDGPTVWVSAAI
+HGDEVAGVEIVRRVLERLQPKHLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR
+GSLASRIAHLMMTEVIARCTVGIDLHTGADRRSNLPQIRCDLEDPQTRALAEAFGAPVLF
+HARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALDMVDPADVGL
+TEPGPDAVVDAPGPLPGEVPEERTTDVPEATDATGEDTAAVHPDVVDGEQDAPYLVWQST
+WVRARADGLVHLDVSLGERVSAGDRIGALYNSFGRRLAHVKAELTGVVIGRTEAPLVHRG
+DALVHIGGWDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001743.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001743.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab7d539fcf0a5bb5343a151724cdcff970a43a9b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001743.fa
@@ -0,0 +1,15 @@
+>PROKKA_02292
+MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDNIDVWGRRKTAYEIQKKSEAIY
+VVVNFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE
+>PROKKA_01984
+MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDNIDVWGRRKTAYEIQKKSEAIY
+VVVNFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE
+>PROKKA_00446
+MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDKVDVWGRRKTAYEIQKKSEAIY
+VVVDFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE
+>PROKKA_00398
+MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVEKIDVWGRRKTAYEIQKKSEAIY
+VVVDFTAEPAATQELDRVLNLNETILRTKIIRPEEQKISAE
+>PROKKA_02232
+MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDNIDVWGRRKTAYEIQKKSEAIY
+VVVNFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001744.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001744.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ae7d5200a031472c8c43494502e0fc37705baa3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001744.fa
@@ -0,0 +1,50 @@
+>PROKKA_02293
+MTPVTRDTVAELHAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG
+YVVVRDGAAVAWIVPMGARALGRHEGAEARAAGPDEAGQSAGVVPVFRVLGAHTDSPGFK
+LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ
+LAIHLDREVNEGLTLKRQRHTNPVVGALVPRGEGAGEAEADGLAARVPGDVLTALAAAAG
+VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLVALEELAREHGGAEGA
+IAYEGTVAGGVAGVAAGAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG
+QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA
+FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD
+VEHLTAAVREFFRGV
+>PROKKA_01986
+MTPVTRDTAAELPAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG
+YVVVRDGAAVAWIVPMGAGALGRHEGAEARAAGPDEAGPSAGVVPVFRVLGAHTDSPGFK
+LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ
+LAIHLDREVNEGLTLKRQRHTNPVVGALAPRGEGAGEAEADGLAARVPGDVLTALAAAAG
+VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLAALEELAREHGGAEGA
+IAYEGTVAGGVAGEAADAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG
+QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA
+FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD
+VEHLAAAVREFFRGV
+>PROKKA_00443
+MTAVTRDTAPAPEMSAHVQDLAAFVTASPSSYHAAAEVARRLVAVGFTCLDEAADFPAAP
+GGYVVVRDGAALAWVVPTGAGSDVSDGAGAAGGSGAGAAVPVFRVLGAHTDSPGFKLKPN
+PATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQLAIH
+LDREVNDGLKLQRQRHTNPVVGALAPRGEGAGEAVADVSEGVDGRSAPLEQAAGAGAGVG
+AGAGEGAGAREGDGAGLEARAPGDVLSALAAAAGVDPAAVRGHDVMVADAQAPGLFGLAG
+EFFASGRLDNLSSVHAGLVALEELARANGGASGAIAYAGTVAEGVAGEAAGAPVIPVLAA
+FDHEELGSASRSGAAGPLLEEVMGRVLEALGVAGQGRARAIAGSWLLSADAGHLVHPNYA
+ERHDPVNHPRVNHGPLLKINANQRYATDAGGEAAFARWCGVAGVPFQEFVSNNDMPCGST
+IGPISATRLGIRTVDVGLGLLSMHSAREMCGVRDVEHLTAAVREFFRGV
+>PROKKA_00396
+MSTVTSESTVTAAVPGAPALSAHLQDLAAFVQASPSSFHAAAEVARRLEAVGFTRVDPAQ
+DLPAAPGGYVSVTDGAVLAWILPEALAERAADAVPVFRLLGAHTDSPGFKLKPQHLTVTA
+DGWVQAGVEVYGGPLLNSWLDRELRFAGRLALADGRQVLAATGPVGRIPQLAIHLDRSAN
+DDLTLGRQRHTQPIVAAVAGAPDAAGTDAADGASADPVVRLTGDILELLAAQAGVDPAEV
+RGADVVVADAQQGGAFGANGEFFACGRLDNLSSVHAGLRALESLAADADRAGRGVVVAEG
+VAGEAAGAPVIPVLAAFDHEEVGSATRTGAGGPLLEELMGRLLSACGVTGQGAARSRAGS
+WLLSADAGHLVHPNYTERHDPVNHPRVNHGPLLKINANQRYSTDAAGEAAFARWCAAAGV
+PFQRFVSNNDVPCGSTIGPISATRLGVRTVDVGIGLLSMHSAREMCGADDPARLAAVARA
+FFAGV
+>PROKKA_02234
+MTPVTRDTAAELPAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG
+YVVVRDGAAVAWIVPMGAGALGRHEGAEARAAGPDEAGQSAGVVPVFRVLGAHTDSPGFK
+LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ
+LAIHLDREVNEGLTLKRQRHTNPVVGALAPRGEGAGEAEADGLAARVPGDVLTALAAAAG
+VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLVALEELAREHGGAEGA
+IAYEGTVAGGVAGEAAGAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG
+QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA
+FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD
+VEHLAAAVREFFRGV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001752.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001752.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5442d60895a18674bec8328c3edba8f21a1df39d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001752.fa
@@ -0,0 +1,35 @@
+>PROKKA_02306
+MAQEQESRGGAWRALRQKWTGRTAEKGGADAEEPARLQRRRLTRPDRTRVFTTSNQKGGV
+GKTTTTVNLAAALARAGMRVMVVDIDPQGNASTALNIPHTGDVASVYDVLLGEMEIQDVV
+QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWRAEDGQERLDYVFID
+CPPSLGLLTVNAFVAAQEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPRLQVSTILLTM
+FDARTNLAVQVAEEVRTHFPEQLLNTAIPRNVRISEAPSYQQTVLTYDPASAGAVAYREA
+AAEIAGRGAPSVKG
+>PROKKA_01999
+MAQEQESRGGAWRALRQKWTGRTAEKGGADVEEPARLQRRRLTRPDRTRVFTTSNQKGGV
+GKTTTTVNLAAALARAGMRVMVVDIDPQGNASTALNIPHTGDVASVYDVLLGEMEIQDVV
+QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWREEDGQERLDYVFID
+CPPSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPRLQVSTILLTM
+FDARTNLAVQVAEEVRTHFPEQLLNTAIPRNVRISEAPSYQQTVLTYDPASAGAVAYREA
+AAEIAGRGAPTALKS
+>PROKKA_00430
+MAQEQESRGGAWRALRQKWSGRSAEQGAGEAEESSRLKARRLARPERTRVFTTSNQKGGV
+GKTTTTVNLAAALARAGMRVMVIDIDPQGNASTALNIPHTGDVASVYDVLLGEMEMHDVV
+QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWREENGQERLDYVFID
+CPPSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPKLQVSTILLTM
+FDARTNLAVQVAEEVRAHFPEQLLGTAIPRNVRISEAPSYQQTVLTYDPTSAGAVAYREA
+AAEIAGRGAPAAKG
+>PROKKA_00383
+MAKDQDSRGGTWKALKQRWSGRASDKASPEEAARLKARRLPVPDRTRVFTTSNQKGGVGK
+TTTTVNLAAALARAGMRVLVIDIDPQGNASTALNVPHAGDVASVYDVLLDEMEIHEAVQD
+APDVDGLQVVPATIDLAGAEIELVSMVAREQRLARALDRYMAWRADQGQERLDYVFIDCP
+PSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPKLQVSTILLTMFD
+ARMNLAVQVAEEVKAHFPEQLLETAIPRNVRISEAPSYQQTVVTYDPASAGAVAYREAAA
+EIARRGAPQAR
+>PROKKA_02247
+MAQEQESRGGAWRALRQKWTGRTAEKGGADAEEPARLQRRRLTRPDRTRVFTTSNQKGGV
+GKTTTTVNLAAALARAGMRVMVVDIDPQGNASTALNIPHTGDVASVYDVLLGEMEIQDVV
+QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWREEDGQERLDYVFID
+CPPSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPRLQVSTILLTM
+FDARTNLAVQVAEEVRTHFPEQLLNTAIPRNVRISEAPSYQQTVLTYDPASAGAVAYREA
+AAEIAGRGAPAVKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001756.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001756.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2796db03d9f5d51de22077a2e0e0f940f9dc49d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001756.fa
@@ -0,0 +1,20 @@
+>PROKKA_02310
+MTVTPSPFVVLEPSREWGPLRALPSALLAGLLTVYRAVVSPLYGPVCRFFPSCSAYGLEA
+VHVHGAVKGSWLAARRIGRCHPWNDGGVDPVPPGHRRWPPGRQPRILTLNHPPIPPDLPQ
+ED
+>PROKKA_02003
+MTVTPSPFVVLEPSREWGPLRALPSALLAGLLTVYRAVVSPLYGPVCRFFPSCSAYGLEA
+VHVHGAVKGSWLAARRIGRCHPWNDGGVDPVPPGHRRWPPGRQPRILTLNHPPIPPDLPQ
+ED
+>PROKKA_00426
+MAVTPSPFTVLEPSREWGPVRALPSALLAGLLTVYRAVVSPLYGQVCRFFPSCSAYGLEA
+VHVHGAVKGSWLAARRIGRCHPWNDGGVDPVPPGHRRWPPGRQPRILTLNHPPIPPDLPQ
+ED
+>PROKKA_00379
+MPASSPYTVLEPSHEWGPLRALPSTLLAWLLTAYRAVVSPLYGPVCRFFPSCSAYGLEAV
+HVHGAVRGSWLTARRLLRCHPWNDGGVDPVPPGRRRWPPGREPRIFALNHPPIPPDPSQE
+D
+>PROKKA_02251
+MTVTPSPFVVLEPSREWGPLRALPSALLAGLLTVYRAVVSPLYGPVCRFFPSCSAYGLEA
+VHVHGAVKGSWLAARRIGRCHPWNDGGVDPVPPGHRRWPPGRQPRILALNHPPIPPDLPQ
+ED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001757.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001757.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aedce19802f92ee55ab54ea7be25b9b26bbe91d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001757.fa
@@ -0,0 +1,20 @@
+>PROKKA_02311
+MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDQTRSTPPSAPRPRAGFVVSKAV
+GNAVTRNRVRRRLRAVVADQMRTAPLRELPVLVQVRALPAAAEADFALLRRETVGALGKA
+LKPHLPAASEHA
+>PROKKA_02004
+MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDQTRSTSPSAPRPRAGFVVSKAV
+GNAVTRNRVKRRLRAVVADQMRLPPLRDLPVLVQVRALPAAAEADYALLRRETVGALGKA
+LKPHLPAASEHA
+>PROKKA_00425
+MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDHTRSTSPSVPRPRAGFVVSKAV
+GNAVTRNRVKRRLRAVVAEQMRAAPLRELPVLVQVRALPPAAEADHALLRRETVGALAKA
+LRPHLPAVPRDEA
+>PROKKA_00378
+MLPRDRRVRTPEEFRRIRRTGSRAGRSTVVVSVAADTDPARPGATSQPRRPRAGFVVSKA
+VGNSVVRHRVTRRLRALLRAELDSPALRDRALLIQVKALPAAVDADHATLRRDVHGALGA
+AVRKLDQADRSR
+>PROKKA_02252
+MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDQTRSTSPSAPRPRAGFVVSKAV
+GNAVTRNRVKRRLRAVVADQMRLPPLRDLPVLVQVRALPAAAEADYALLRRETVGALGKA
+LKPHLPAASEHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001760.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001760.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c47bd9aa5ab44a7cea05b6d92fb021602cf58f8e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001760.fa
@@ -0,0 +1,45 @@
+>PROKKA_00303
+MVELVALRKTNEVAAYVRASMDRKGDRWTVDTQLRKIRALAEAKDWNVVEVYEDNAVSAT
+KKRRAGTRWAEMLDDARAGRFSMVVAVDMDRLLRSTKDLNTLIDLGLRVVTVDGEIDLST
+ADGEFRATMLAALARFEARRKAERQIRSNERRRAEGIPASTWKAFGWTREGELIEEEAAA
+VRRAFDAFLGEPSLSIRRIREDLNSAGHLTARGSEFSVDAVRYLLANSLYAGFIRHYKTG
+ELYPVQGEAFPPIVGEQTWRAAVAKLEDNVRRSARQGNQPKYLLSTIGLCGKCGATLVSG
+TNSRKQPTYRCGEQFHLTRQREPVDAMVTEAVLTRLSSVDVHDLVMPQEAAGPDREELLT
+ERNALVERVKELSPLLRDIHQPVLEITAAINDVKARIDEIDAELLDRSVSVAAKLLAEVD
+EPVGTAERREVVESKWKALDMDRRRMLVDELVTVTIEPIMPGHVKFDPDLVRIEPRRD
+>PROKKA_02232
+MRAAIYLRISLDRHGDGLAVERQREDCKRIIAQRGWEHVATYEDPSVSASSRTVTRPGYE
+RMVRDWQAGRFDAVVCWDLDRLTRQPRQLEDWIDAAEQRGLHLVTANGEADLGTDAGRMF
+ARIKAAVSRQEVDRKSARQVRAAQQRAELGKGWGPRRPFGFAEDKVTHDPAEAAVVRRMY
+DDFNAGVGQREICRRLAAEGVRTSTGREWTQPALRQFLRNPRNAGLRAYRGEIIGPAEWA
+PLVSESVYRAALDRMDAPTKRVGGSGAKHLLIGVARCGVCDSPVGTNYTATHKRQYACRA
+GHVARSAEAVDAYVSEVAVGVLSTRGAAAFTRHDDAGQVELSAEADRIRARQEALAVEFA
+DGTLTAAQLRAANARMAERLEQVTAAMVAAEGNAALRPLLEAESVAAGWERLDIPRRRAV
+IDTLMNVRILRTSQGSRFDPASVEITPRTG
+>PROKKA_02196
+MVSVVGGRVDYSVVGLQNPMRISEMPGKTAKITVSGRMPNTRGSITRTGYSYSMTSKRAV
+IYTRISRDDRGVEAGVTRQEEDCRAKAAGLGFEVVRVYTDNDIGASTRSRKVRPEYAQML
+EAARRGAFGAILAYSTSRLTRRPREAEDLIDLVERHGVQIKTVVSGDWNLETADGRAVVR
+TLAAWDAAEAERTAERVARACEQRAAEGRTHGAVPYGWTRDADGTEHLHPERAQVIRDAA
+AHVLEGGSLRSFTLDLNARGVGSPRGGKWTAPQLKQLLLRERNAGRLVRRDPNNPRHRPV
+VGKGIWPQILDEETHDRLVAHLTDPTRRKSRGSELKHMMSGILICGVCGARCRLMPGGKS
+PDGTPRPPSYGCRECFGVKRRVAQVDEWVSYMARVRLAEKDAPALLAGDDEGARKAQRER
+DEARAKLDRAADAYAEGLIDSHQLTRISANLHKKREDAEARLARARPLGGLSFDRGASPV
+QVWRRAPVAVRRTLVEMMMTVTLLPGGRGSRFDPEQHLRIVMNDLKTSVSDILVTSGTVP
+DRPTGSEDSDPPRRE
+>PROKKA_02198
+MQVEEDDRRVVAVVEDPVREPVVCEAARRVLAGESLNSIARALNERGAPTAATDREEASR
+LWTASKVRQMLQRPGYAGLRVYRGEGVGKAAWEPLIEREQWDELQALFESSRAAQGPQDH
+RAAYLLTGIARCGVCGSKLVRRATRSGKVVRKDGTVAPKRRYDTYACAAGIDRAGAGFHV
+SMSMVHLDDYVSRLVVERLSRPDVLECLAGTEGTQSDERVALRAEIAGYREHLERARAYA
+AEHLRMDLLIDQEARLQPKIDTAERRLRELAAVDPEVRRLAEAADVRATWDALDLEGQRH
+VVRVRMTPSVLPRTRPGRRGLDPERVDVTWLSDCLESP
+>PROKKA_02372
+MVELVSLRKTNEVAAYVRASMDRKGDRWTVETQLRKIRALAEAKDWEVVEVYDDNAVSAT
+KKRRAGTRWAEMLDDARAGRFSMVVAVDMDRLLRSTKDLNTLIDLGLRVVTVDGEIDLST
+ADGEFRATMLAALARFEARRKAERQIRSNDRRRAEGIPASSWKAFGWTREGELIEAEADA
+VRRAFDAFLGEPSLSIRRIREDLNSAGHLTARGSAFSVDAVRYLLANPLYAGYIKHYASG
+ELYPVQGDAFPPIVGEQTWRAAVAKLEDNVRRSARQGNQPKYLLSTIGLCGKCGATLVSG
+TNSRKQPTYRCGEQFHLTRQREPVDAMVTEAVLTRLSSVDVHDLVMPQEDDGPDREALLT
+ERNALVERVKELSPLLLDVRQPVLEITEAIRGGKARIDQIDAEILDRSVSVAAKLLGDVD
+ESLGTMERREVVESKWKALDMDRRRMLVDELVTVTIEPIAPGHVKFDPDLIRIEPRRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001763.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001763.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3df1b2297f6912809a42db6340a4d8c0616d56ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001763.fa
@@ -0,0 +1,47 @@
+>PROKKA_01860
+MLLERIYDEDLAQASYVIGCQAKNEAMVVDPRRDIQVYLDLAAKNGMTITHVTETHIHAD
+YLSGTRELAHATGAQIHLSGEGGEDWAYGFEGNLLKDGDTVTLGNITVEAVHTPGHTPEH
+LSFLVTDGAFADAPGYMLTGDFVFSGDLGRPDLLDEAAGGVDTRFEGAQQLFASLKAKFL
+TLPDHVQVFPAHGAGSACGKALGALPSTTVGYERKYAWWSDYLKNDDEQGFIDELLDGQP
+DAHAYFARMKRQNKQGPAILGELPELEELDAGGVQATLAEGAVFADTRGVDEILAGTVPG
+ALAFPSRGKVATHAGWAYDPESDDAALVLLAEDREDAHTMRDHMIRVGVDAAAAFTTSVD
+GLTLEPVPTVQADELRSRIEAGEVGAEQDTVLVDVRNKTEFSHGTVADARQLNAGKVLFH
+QEELPKDKTLVTFCQSGLRNIVAAQALRRAGFDVIELEGSYAAWQQS
+>PROKKA_00614
+MLLERIYDEDLAQASYFIGCQAKNEAIVVDPRRDVQEYLDLAAHHGMTITHVTETHIHAD
+FLSGTRELAARTGAQIHVSGEGGEDWTYGFEGNLLHDGDVITLGNITVTAQHTPGHTPEH
+LSYLITDGAFAQAPGYYLTGDFVFSGDLGRPDLLDEAAGFQDTRFAGAKQLFRSLKEKFV
+GLPDHVQVFPGHGSGSACGKALGALPSTTVGYERTYAWWAEYVANDDEQGFVDELLDGQP
+DAHAYFARMKKQNKLGPAVLGELTPLAELTGEQAVARVAAGDVLADTRSVDEIHAGTVPG
+ALALPAKDKAATHIGWAYDPEQDDAAIILLADDQGDAEAIRSHMIRVGVDAADAFVTSLD
+GFELQPAAVISPEELQRRIDAGDVVPATADAAPGEGGLALLDVRNRTEHAEGTVPASGGA
+EAAQLNSGKVLFHQGELPKDATLVTFCQSGLRNVVAAQSLRRAGFDVVELEGSYLGWLGR
+TRA
+>PROKKA_02660
+MLLERIYDEDLAQAGYFIGCQAKGEAVVIDARRDIADYLALAAKHGMRIVAVTETHIHAD
+YLSGTRELAAAVGAEVYVSGEGGADWQYGFDARRLYDRDTITIGNITIQARHTPGHTPEH
+LVFLVTDGAFASEPGYLISGDFVFAGDLGRPDLLDEAAGGVDTRFEGARQLFTSLREVFL
+TLPDHVQVHPGHGSGSACGKALGALPSTTVGYERANAWWSRHLAADDEQGFIEELLDGQP
+DAHAYFARMKKQNREGPAVLGERGPVPELAVAEVARRLEADETTFVDTRPPAQAHQGTVA
+GSLNIPDGSKTATYAAWAYDPEADSRPLVLLAEDQTAAQAIADRLLRVGIDQTAGYVTTI
+DGLPRFVPPLIEPAELAGFDAALLLDVRQRGEYAAGHIPGATQLSAARVLWHKDELPRSG
+TIVTYCQSGMRNTVAASALRRAGHAVVELDGSYNAWRAWQETTSETALA
+>PROKKA_00538
+MLLERIYDEDLSQASYFIGCQAKNEAIVVDPRRDVQEYLDLAAHHGMTITHVTETHIHAD
+FLSGTRELAARTGAQIHLSGEGGEDWTYGFEGHLLHDGDTIQLGNITVQAMHTPGHTPEH
+LSYLVTDGAFAAAPGYYLTGDFVFSGDLGRPDLLDEAAGLQDTRFAGATQLFQSLKEKFV
+NLPGHVQVFPGHGSGSACGKALGALPSTTVGYESTYAWWAEYVENDDEQGFVGELLDGQP
+DAHAYFARMKRQNKQGPAVLGELTPLAELTGEQAVARVSAGDVLADTRPVDQIHAGTVPG
+ALALPAKDKTATHIGWAYDPESDDAAIILLADAQDDAEQIRAHLIRVGVDAADAFVTSLD
+AFDLRPTAVISPEELERRIQDGGVVPATADAAPAEDGLALLDVRNRTEHADGTVPASDDA
+EAAQLSAGKVLFHQDQLPKEATIVTFCQSGLRNVVAAQALRRAGFDVVELDGSHLGWLGR
+SQA
+>PROKKA_02090
+MLLERIYDEDLAQASYVIGCQAKNEAMVVDPRRDIQVYLDLAAKNGMTITHVTETHIHAD
+YLSGTRELAHATGAQIHLSGEGGEDWAYGFEGNLLKDGDTVTLGNITVEAVHTPGHTPEH
+LSFLVTDGAFADAPGYMLTGDFVFSGDLGRPDLLDEAAGGVDTRFEGAQQLFASLKAKFL
+TLPDHVQVFPAHGAGSACGKALGALPSTTVGYERKYAWWSDYLKNDDEQGFIDELLDGQP
+DAHAYFARMKRQNKQGPAILGELPELEELDAGGVQATLAEGAVFADTRGVDEILAGTVPG
+ALAFPSRGKVATHAGWAYDPESDDAALVLLAEDREDAHTMRDHMIRVGVDAAAAFTTSVD
+GLTLEPVPTVQADELRSRIEAGEVGAEQDTVLVDVRNKTEFSHGTVADARQLNAGKVLFH
+QEELPKDKTLVTFCQSGLRNIVAAQALRRAGFDVIELEGSYAAWQQS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001768.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001768.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f150cf27afaf01ba8112681d0a89867ceab9c06
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001768.fa
@@ -0,0 +1,26 @@
+>PROKKA_00388
+MARCTVERLMRAAGLRGISRAKGPRTTVPGRGPDERQDLVQRDFTAAAPNQLWVADITYC
+RTFSGWVYAAFIIDVFSRRVLGWQLSKSLRTDLALDTLEMAFWTRQRAGQDVAGLRHHSD
+KGVQYVAVRYTQRLAQAGAVASVGSTGDSYDNALAEAFNSLFKAELIRNKGPFKSIEDLE
+IAVAEYIDWFNHRRVHGEIRLVPPVEFEDVYHHENPVPAPAGTALTSL
+>PROKKA_00330
+MHTCCRLLGVSRQGYYRYQKRPTSATELRRRWLTGLIREIHIASRGTYGYRRIHAELTMG
+MNIPCSSRLVWVLMTRAGIGGLPGPARIKRLKGVATADDLVNRKFHRLELNELWVTDITE
+HPTREGKVYCAAVLDACSRKIIGWAIDSKQDSTLVVNALDMAIRARQPDPGGIVHADHGV
+QFTSWVFTQKIRSAGLLPSFGTVGDGLDNAMMESFWSSMQIELLNRKKWKTRIELANAIF
+EYIEVFYNRHRRHSSLEYATPNDYDLARTPQALATTGS
+>PROKKA_00656
+MLETPTALIVDYIDEHKHEFGVEPICATLSAAGTQIAPSTYYAAKTRPPSVRSLRDVQVL
+VEIRRVHEANYGVYGARKVHAQLRREGLQVARCTVERLMRAAGLRGISRAKGPRTTVPGR
+GPDERQDLVQRDFTAAAPNQLWVADITYCRTFSGWVYAAFIIDVFSRRVLGWQLSKSLRT
+DLALDALEMAFWTRQRAGQDVAGLRHHSDKGLQYVAVRYTQRLAQAGAVASVGSTGDSYD
+NALAEAFNSLFKAELIRNKGPFKSIEDLEIAVAEYIDWFNHRRVHGEIRLVPPVEFEDV
+>PROKKA_01209
+MQIGAWAQGGEIELANAIFEYLEVLYNRRRRHSCLECATPYDYDPAGTPRALTTTGS
+>PROKKA_01831
+MLETPTALIVDYIDEHKHEFGVEPICATLSAAGTQIAPSTYYAAKTRPPSVRSLRDVQVL
+VEIRRVHEANYGLYGARKVHAQLRREGLQVARCTVERLMRAAGLGGISRAKGPRTTVPGR
+GPDERQDLVQRDFTAAAPNQLWVADITYCRTFSGWVYAAFIIDVFSRRVLGWQLSKSLRT
+DLALDALEMAFWTRQRAGQDVAGLRHHSDKGVQYVAVRTPSGWPRPAQSPRSARRGILTI
+SVLAEAFNSLFKAELIRNKGPFTSIEDLAIAVAEYVDWFNHRRVHGEIRLVPPVEFEDVY
+HHENPAPAPAGTALTSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001771.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001771.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b4344dd13c581514d57208f01e0c44d457bdf1db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001771.fa
@@ -0,0 +1,36 @@
+>PROKKA_00041
+MSEHQQHVGRRDPRISDEAIERGRRAHELDRAHVFHSWSAQRDLNPMTILDAEGSWVWDG
+EGRPMVDFSGQLVFTNVGHRHPKIVAAIREQAETLATVAPQHVNDARSEAARLITEWLPE
+SINHVFFTNAGAEANDHAVRMARLHTGRHKVLSAYLSYHGATRLTANLTGSLRRVGSDSA
+SDGVVHFQPAYTYRSAFGSENDEQEAERALAHLRDVIELEGPSTVAAVVLEAVPGTAGIF
+MPPPGYMAGVKELCREHGILLIIDEVMVGFGRVGEWFGHQLTGVTPDIVTFAKGVNSGYV
+PLGGVAMSDDVYESFATTPYPGGLTYSGHPLACAAAVAAITAMEEECMVANAKRIGEEII
+GPRLAEIAAAHPSVGDVRGAGAFWAVELVKDRQTRERLAPLGQVAPVMGRMMAEAKDRGL
+LLFMAENRFHLCPPLNISDEDLRFGLDVLDQVLALADEEVAAG
+>PROKKA_02054
+MSEHQQHVGRRDPRISDEAIERGRRAHELDRAHVFHSWSAQRNLTPMTILDAEGSWVWDG
+EGRPMVDFSGQLVFTNVGHRHPKIVAAIREQAETLATVAPQHVNDARSEAARLITERLPE
+SINHVFFTNAGAEANEHAVRMARLHTGRHKVLSAYLSYHGATRLTANLTGSLRRVGSDSA
+SDGVVHFQPAYTYRSAFGSESDEQEAERALAHLRDVIELEGPSTVAAVILEAVPGTAGIF
+LPPPGYMAGVKELCREHGILLIIDEVMVGFGRVGEWFGHQLTGVTPDIVTFAKGVNSGYV
+PLGGVAMSDDVYESFATTPYPGGLTYSGHPLACAAAVAAITAMEEEGMVAHAKRIGEEVI
+GPRLAEIAAAHPSVGDVRGAGAFWAVELVKDRQTRERLAPLGQVAPVMGRMMAEAKDRGL
+LLFMAENRFHLCPPLNISDEDLRFGLDVLDQVLALADEEVAAG
+>PROKKA_02171
+MTAPAEAGLLDRDAAHLWHPYGAAGARQLYAVRGARGVHLDLEGPGGERHRAIDAMASWW
+SVVHGHGHPALVEALTRQAAAFPHVMFGGLTHAPAVDLAERLVAHTPAALEHVFLADSGS
+VSVEVALKLALQYQATRGRPSRRRFLTVRGGYHGDTAAPMGVCDPVDGMHAAFTSLVARH
+LFLPRPPAARWVPEGFAAAPTAPDAAPAGHWEADDAALAAWEDEARAFTAAHADEIAGVI
+LEPVLQGAGGMRVYDPRCLTVLRELCDEHGLLLIADEIATGFGRTGRWLACEGAGVAPDV
+LCLGKALTGGTMTGAAMLCTAEVAETVSRRERGMPGALLHGPTFMGNPLMCAVASASLDL
+LTDPRDGWAAQVPRVEAGLRAGLAAAADLPAVTDVRVLGAVGVVELDRTVDVEPVTRAAV
+ARGAWVRPFRRLVYVMPPYVSTDDDVATICAAVTGAVEEVCA
+>PROKKA_00036
+MSEHQQHVGRRDPRISDEAIERGRRAHELDRAHVFHSWSAQRDLNPMTILDAEGSWVWDG
+EGRPMVDFSGQLVFTNVGHRHPKIVAAIREQAETLATVAPQHVNDARSEAARLITERLPE
+SINHVFFTNAGAEANEHAVRMARLHTGRHKVLSAYLSYHGATRLTANLTGSLRRVGSDSA
+SDGVVHFQPAYTYRSAFGSESDEQEAERALAHLRDVIELEGPSTVAAVILEAVPGTAGIF
+LPPPGYMAGVKELCREHGILLIIDEVMVGFGRVGEWFGHQLTGVTPDIVTFAKGVNSGYV
+PLGGVAMSDDVYESFATTPYPGGLTYSGHPLACAAAVAAITAMEEEGMVAHAKRIGDQII
+GPRLAEIAAAHPSVGDVRGAGAFWAVELVRDRQTRERLAPLGQVAPVMGRMMAEAKDRGL
+LLFMAENRFHLCPPLNISDEDLRFGLDVLDQVLTLADEEVAAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001773.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001773.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a5b74f7d12b88774598768eec41f969c0d4a8b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001773.fa
@@ -0,0 +1,36 @@
+>PROKKA_00051
+MSTTLQPARTDGVASEAPADARTVETHPAWLRLKAAATALQPLQVKDGSIPDPADHAAAR
+EHVETIVAAVEELAPLFPHDAAYLAALPRDFARWADGGFAEPDFLDSLVAFQPQEHRVDG
+VRHLVVFPMYTQNGSPDRHVEALVVETIWPEFIAELEAGDYGNRLFVSLRLIDFTPGYDT
+NSAVLFPETVAMREIPTFTWGAIFQDREAARFRRVVTAAAEVTQLELPAELAELLSSQEL
+AEGTFVMWDLIHDRTHMRGDLPFDPFMIKQRMPFFLYTLEEMRCDMTAFRECVAIERRLT
+ARAAAGEQLTGLEEQTRRHAGLVQHAVLFDRVFRFALTGSRVRNYDGLGGQLLFAWLHRK
+DVIQWRDVELSVDWDRLADAVVELGDAIDTLYWESIDRPKTVHWLQAYELVASVVTPHPA
+SVWAQGLPREVLAGPPKGYTDLVLDDEFPLSMFFEALEKKMRGVIESTAGIRGTDA
+>PROKKA_02064
+MSTTLQPAQADVVVPETPADARTVETHPAWLRLKAAATALQPLQVKDGSIPDPADHAAAR
+KHVETIVAAVEELAPLFPHDAAYLAALPRDFARWADGGFAEPDFLDSLVAFQPQEHRVDG
+VRHLVVFPMYTQNGSPDRHVEALVVETIWPEFIAALEAGDYGNRLFLSLRLIDFTPGYDT
+NSAVLFPETVAMREIPTFTWGAIFQDREAARFRRVVTAAAEITQLELPAELAELLSCQEL
+AEGTFVMWDLIHDRTHMRGDLPFDPFMIKQRMPFFLYTLEEMRCDMTAFRECVAIERRLT
+ARAAAGEQLTALEEQTRRHAGLVQHAVLFDRVFRFALTGSRVRNYDGLGGQLLFAWLHRK
+DVIQWRDVELSVDWDRLADAVVELGDAIDTLYWESIDRPKTVHWLQAYELVASVVTPHPA
+SVWAQGLPREVLAGPPKGYTDLVLDDEFPLSMFFEALEKKMCGVIESTAGIRGTDA
+>PROKKA_00352
+MSTSLHPPQAVIGEPEVLEDVRADVVSHPAWLRLKAAATALQGLQAKDGSVPDPADHPAA
+GGHVETITAAVAELAPLFPHDAAYLAALPRDFARWRDGGFGVPDFLDSLVAFQPQEHRVD
+GIRHLVVFPMYTQNGSSSRHVEALLVEAIWPEFIAQLEAGDYGNRLFLSLRLLDFTPGYE
+TNSAVLFPETVAMREIPTFTWGAIFQDREAARFRRVVAAAAEITRLDLPEDAAELVADQD
+LAEQTFVMWDLIHDRTHMRGDLPFDPFMIKQRMPFFLYTLEEMRCDLTAFRETVRIEREL
+SARAAAGEELTAVQAQTLRHAKLVQYAVLFDRVFRFALTGSRVRNYDGLGGQLLFAWLHR
+RHVVQWRDVKLTIDWDRLAEAVVELGDAIDRLYWESIDRPKTVHWLKAYELVASVVAPHP
+ASVWAQGLPREVLAGPPKEMTDLVLDDEFPLSMFFEALGKKLRGVIESTAGIRAADA
+>PROKKA_00046
+MSTTLQPARTDVVVPETPADARTVETHPAWLRLKAAATALQPLQVKDGSIPDPADHAAAR
+EHVETIVAAVEELAPLFPHDAAYLTALPRDFARWADGGFAEPDFLDSLVAFQPQEHRVDG
+VRHLVVFPMYTQNGSPDRHVEALVVETIWPEFIAELEAGDYGNRLFVSLRLIDFTPGYDT
+NSAVLFPETVAMREIPTFTWGAIFQDREAARFRRVVTAAAEITQLELPAELAELLSCQEL
+AEGTFVMWDLIHDRTHMRGDLPFDPFMIKQRMPFFLYTLEEMRCDMTAFRECVAIERRLT
+ARAAAGEQLTALEEQTRRHAGLVQHAVLFDRVFRFALTGSRVRNYDGLGGQLLFAWLHRK
+DVIQWRDVELSVDWDRLANAVVELGDAIDTLYWESIDRPKTVHWLQAYELVASVVTPHPA
+SVWAQGLPREVLAGPPKGYTDLVLDDEFPLSMFFEALEKKMCGVIESTAGIRGTDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001775.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001775.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc4a600db21356425fb9cf389a74ddaa4564a4ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001775.fa
@@ -0,0 +1,20 @@
+>PROKKA_00059
+MTDPHASHDPRREAARPSWYGSEAGAGSSGTGSSAAGWPDAPAGDADRAAWDRAPSYAEQ
+EGQTRPAYGQPYGYGQDANTVPAYGYGQGTPGHGFGAPLQPGQTEGIGRSVASMILGIIS
+VVGGFTFLLPPIVGVVLGHIGLKREPHGRGMAIAGLVMNYVSLALLLLAVVFLVILVIAG
+MSLGDYTST
+>PROKKA_02072
+MTDPHASHDPRREAARPSWYGSEAGAGSSGTGSSAAGWPDAPAGDADRAAWDRAPSYAEQ
+EGQTRPAYGQPYGYGQDANTVPAYGYGQGTPGHGFGAPLQPGQTDGVGRSVASMILGIIS
+VVGGFTFLLPPIVGVVLGHIGLKREPHGRGMAIAGLVMNYVSLALLLLAVVFLVILVIAG
+ISLGDYTST
+>PROKKA_00336
+MTEPHPAHDPHRRADGGQPSWYGGGASGGGSSAASWPDGPAADADRAGWEQAPSYAEQQA
+APAYGGDAGHGQDGYAPAGYAPAPGHGRPAYGFGAPLAPGQTEGTGRSVASMILGIVSIV
+GGFTLVVPPIVGVILGHLGLKREPNGRGMAIAGLVMNYLSLAFVLLGVVLLTILVAAGMA
+ASEYSTY
+>PROKKA_00054
+MTDPHASHDPRREAARPSWYGSEAGAGSSGTGSSAAGWPAAPTGDADRAAWDRAPSYAEQ
+EGQTRPAYDQPYGYGQDANTVPAYGYGQGTPGHGFGAPLQPGQTEGIGRSVASMILGIIS
+VVGGFTFLLPPIVGVVLGHIGLKREPHGRGMAIAGLVMNYVSLALLLLAVVFLVILVIAG
+ISLGDYTST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001779.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001779.fa
new file mode 100644
index 0000000000000000000000000000000000000000..531080ea3f567a271b17f19696cdbd4bfb0e358c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001779.fa
@@ -0,0 +1,28 @@
+>PROKKA_00118
+MIAHRGASAAFPEHTRAAMLHALAVGADGLECDVQLTRDREVVCWHDPTVDRTSDGRGAV
+ADHTLDRLRGLDVVSWHARRPGAEPATTTAPPAVYGGAGEQVLTLADLLAIAAAADRPLR
+LAVELKHPSPFGHELEERVLRELLRAGWDPETGRLGQVQVSLMSFHPDALRHVAPLAGTD
+PLCPLMDLMPTELPTRLARGPLSRAAVRAAARQSLAGSEALVWRGRAGMAGPSVAYVREH
+LADVKAWLAAGRRLRVWTVDEREDADSLLAQGVQELTTNRPEDVLRWVRERAAARRERMP
+TGA
+>PROKKA_02131
+MPALVIAHRGASAAFPEHTRAAMLHALAVGADGLECDVQLTRDREVVCWHDPTVDRTSDG
+RGAVADHTLDRLRGLDVVSWHARRPGAEPATTTAPPAAYGGAGEQVLTLADLLAIATAAD
+RPLRLAVELKHPSPFGHELEERVLRELLRAGWDPETGRVGQVQVSLMSFHPDALRHVAPL
+AGTDPLCPLMDLMPTELPTRLARGPLSRAAVRAAARQSLAGSEALVWRGRAGLAGPSVAY
+VREHLADVKAWLAAGRRLRVWTVDEREDAEFLLAQGVQELTTNRPEDVLRWVRERAAARR
+ERVPTGA
+>PROKKA_00200
+MTGVLPLVIAHRGASAAFPEHTRAAMLHALAVGADGIECDVQLTRDRQVVLWHDPTVDRT
+SDGRGPLADHTLAQLRALDVVSWHQGMGGDAPGDAAGRVPAVYGRRDEQVLTLADLLRMV
+LAADRPLRLAVELKHPSPFGHELEERVLRELVAAGWDAETGLMGQVRVSLMSLHPGALQY
+LAPLTGPDALCPLIDLVPDEIPSRLARGPLSRAAVRATVRQSLADAETMVWRGRAGLAGP
+SVAYVRSHLADVKAWLASGRRLRVWTVDEREDALFLAAQGVQELTTNRPADVLRWVTQAA
+TSASPGAISGRDMPSPAAR
+>PROKKA_00123
+MPALVIAHRGASAAFPEHTRAAMLHALAVGADGLECDVQLTRDREVVCWHDPTVDRTSDG
+RGAVADHTLDRLRGLDVVSWHARRPGAEPATTTAPPAAYGGAGEQVLTLADLLAIATAAD
+RPLRLAVELKHPSPFGHELEERVLRELLRAGWDPETGRVGQVQVSLMSFHPDALRHVAPL
+AGTDPLCPLMDLMPTELPTRLARGPLSRAAVRAAARQSLAGSEALVWRGRAGLAGPSVAY
+VREHLADVKAWLAAGRRLRVWTVDEREDAEFLLAQGVQELTTNRPEDVLRWVRERAAARR
+ERVPTGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001785.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001785.fa
new file mode 100644
index 0000000000000000000000000000000000000000..31225c76d33b7eac829f75e3c17bd5746d33554e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001785.fa
@@ -0,0 +1,32 @@
+>PROKKA_00177
+MTATQDAPAVDPRPAAALDPEALVDRIEAGHRLTADEAVAVLDAPDADTFRIVAAASRLR
+EKHFGRTVKVNYLVSLKTGLCPENCTYCSQRLGTEAEILRYTWLKPEEAVRQAGLGIAGG
+ASRVCMVASGTGPTDRDVDRVAGMVGDLKAQHPDVEVCACLGFLKDGQAEKLKDAGVDAY
+NHNLNTAESHYESICTSHTYEQRVDTVQRAGAAGLSSCSGLIAGMGETHEQLVEAVLALR
+DLDSDSIPVNFLMPFDGTPLQGHQQLTPLECLRILAMVRLACPDKELRIAGGREMHLRSL
+QPVGLQVANSIFLGDYLTSEGQDAEADLQMIADAGFTVLGAEERARRATADDGAPAGGCC
+AGTDDAGPCGSGAAVAAEDVRPDTGAEGAVKPELRRRGAGTAEPANA
+>PROKKA_02170
+MTATQDAAAVDPRPAAALDPEALVDRVEAGHRLTAEEAVAVLDAPDADTFRIVAAASRLR
+EKHFGRTVKVNYLVSLKTGLCPENCTYCSQRLGTEAEILRYTWLKPEEAVRQAGLGIAGG
+ASRVCMVASGTGPTDRDVDRVAGMVGDLKAQHPDVEVCACLGFLKDGQAEKLKDAGVDAY
+NHNLNTAESHYESICTSHTYEQRVDTVQRAGAAGLSSCSGLIAGMGETHEQLVEAVLALR
+DLDSDSIPVNFLMPFDGTPLQGHQQLTPLECLRILAMVRLACPDKELRIAGGREMHLRSL
+QPVGLQVANSIFLGDYLTSEGQDAEADLQMIADAGFTVLGAEERARRATADDGAPAGGCC
+AGTDGAGSCGSGAAVASEAGAAEDARPDTGAEGTVKPELRRRGAGTAEPANA
+>PROKKA_00225
+MTAAQDAAVVAPALDPEELVDRIEAGHRLTAAEAVAVLDAPDAETFRLVAAASRLRERHF
+GRTVKVNYLVSLKTGLCPEDCTYCSQRLGTEAQILKYTWLKPDEAVRQAGLGIAGGASRV
+CMVASGTGPTDRDVDRVTEMIGRLKDEHPQVEVCACLGKLKDGQAERLKAAGVDAYNHNL
+NTAESHYESICTSHTYADRVDTVERATAAGLSSCSGLIAGMGETHAQLAEAVLALRELDS
+DSIPVNFLMPFDGTPLAGHVQLTPLECLRILAVVRLACPDKELRIAGGREMHLRSLQAVG
+LQVANSIFLGDYLTSEGQDAEADLSMIADAGFTVLGAAAAPADDDGAPDGGCCGGGGCGE
+GGVEDASTRGGTSPSPSPAPRRRGAGTAEPANA
+>PROKKA_00169
+MTATQDAAAVDPRPADALDPEALVDRIEAGHRLTADEAVAVLDAPDADTFRIVAAASRLR
+EKHFGRTVKVNYLVSLKTGLCPENCTYCSQRLGTEAEILRYTWLKPEEAVRQAGLGIAGG
+ASRVCMVASGTGPTDRDVDRVAGMVGDLKAQHPDVEVCACLGFLKDGQAEKLKDAGVDAY
+NHNLNTAESHYESICTSHTYEQRVDTVQRAGAAGLSSCSGLIAGMGETHEQLVEAVLALR
+DLDSDSIPVNFLMPFDGTPLQGHQQLTPLECLRILAMVRLACPDKELRIAGGREMHLRSL
+QPVGLQVANSIFLGDYLTSEGQDAEADLQMIADAGFTVLGAEERAQQAAADDGAPAGCCG
+GGCVGTHDNSKNGAAATPSKPVLRRRGAGTGAAANA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001787.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001787.fa
new file mode 100644
index 0000000000000000000000000000000000000000..06ac2bdf0d64adb8744405ceee8ffeb16d9d8619
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001787.fa
@@ -0,0 +1,25 @@
+>PROKKA_00200
+MKTPARLAVGMLAASGLLLTGCASDPTLDESWPEIRQKVVDAESLRLRVEGTAADKEEEK
+DDASASAAPSASLGTDASQSLNVDLAGATDDSHLKGTMNMDMGAATMDIEVLRRDADVFF
+KLKADGDDLPQEMGMFSTLVGDRWIKTSADQAAQMDISLQEIMSDLEEDMPAADAFDGKD
+LKAEEVELEGRTYLKYALPEEHHEFGRTMLIDPESTTLYRLEDVNSEDEDVDANATFTEW
+NAVEAPEAPAKEDVFDLAELQELAG
+>PROKKA_00189
+MKSSLLTATGLPRAAAVLAAAGLLLTGCAADPTLDENWPEIRQKVVDAQSLRLQMDGEAA
+PDAEGSGQDSEITAAAADLSGATDDSHLKGTMDMDMGADSVDMEILRLGEEVFLKMAADG
+DGVPAEMAMFEQLVGDRWMLMPADEADSMAGISLKEIMDDLEADMPAAEAFDGKDLKAEK
+VELDGQEYLKYALPEEFHDFARTMYVHPDDETLHRLEGTGGEDAEADTTATFSEWNAVQA
+PERPAEDQIVDMAALQGLTG
+>PROKKA_00125
+MTPRLSRASLTALLGAGALALSACGGDPAPAASSSAEAASSSAAGPTVSTSPNGSDAAAS
+SSSESAASESSASDVPAGQAPEAEVVWKDIQQGLDEAESVHILAEIDGGSGSEVQRVDLA
+GDVAGTTVQGSVTGDSADFTGTMDFIHVGGQTYLKMDGSGGGDASRMAEALDGRWLVDTQ
+GMIPVDEMNPQVFLDEMKQEFSTVTDAELAAMEGEVVQVDGEEMYRYSDDSSWTMTVDKD
+NHVREFRDTKSSGEGTVTMDRWNQVTPAAAPPAAEQVTMDELSQEIASSGAGSSAGATAS
+ATVDG
+>PROKKA_00145
+MKSPKIAAAALLATGGLLLSACATQPTLEESWPEVRQKVVDAQSLHLKMDGTAKEDASGS
+ASASSSSDIQSGTIDLAGATDDSHLKGTVAAKMGDGEVNMDILRLGQDVYMRINKAEGGQ
+APEGMDAFQQIVGDRWMLMPADQASGMGELSLGTVMDDLEEDMPAADAFNGKDVKAEEVD
+LDGRKVLKYALPEEHKDFGRTMYVDKETKELYRLEDVNSVESEADATATFTEWNAVQAPE
+RPAEDEVFDMQKLSEGLAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001792.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001792.fa
new file mode 100644
index 0000000000000000000000000000000000000000..308e2574d11f0a2b4e2648026ef51440ea2a1138
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001792.fa
@@ -0,0 +1,31 @@
+>PROKKA_00243
+MDVLAEAGELGLGGIYVGEEHGGTGLARTDAILIFEELAKADPAFAAYISIHNMVAWMID
+SFGSDEQRARWIPDLVGMEHLASYCLTEPGAGSDAAALKTRAVRDGDHYVLNGVKQFISG
+AGSSGYYVVMCRTADTGARGISAVVVHKDTPGLSFGPSEKKMGWHTQPTRQVIFEDVRVP
+VADRLGEEGDGFRIAMKGLNGGRLNIGACSIGGGLAALDKATRYLKERSAFGEPLTTKQA
+LVFELADMSVKLETAHTMLMRAADALDRNDPDTVRLCAMAKLVATESGYEAADTALQLHG
+GYGYLHEYGVEKLVRDLRVHRILEGSNEIMRMIVGRGLIG
+>PROKKA_02255
+MFPITDDQKALVDAVRDFAEQRVAPHALDWDAEKHFPVDVLAEAGELGLGGIYVGEEHGG
+TGLERTDAILIFEELAKADPAFAAYISIHNMVAWMIDSFGSDEQRARWIPDLAGMEYLAS
+YCLTEPGAGSDAAALKTRAVRDGDHYVLNGVKQFISGAGASDCYVVMCRTADTGARGISA
+VVVHKDTPGLSFGPNEKKMGWHTQPTRQVIFEDVRVPVADRLGEEGDGFRIAMKGLNGGR
+LNISACSIGGGLAALDKATRYLKERSAFGEPLTTKQALVFELAEMAVKLETAHTMLMRAA
+DALDRNDPDTVRLCAMAKLVATEHGYEAADTALQLHGGYGYLHEYGVEKLVRDLRVHRIL
+EGSNEIMRMIVGRGLIG
+>PROKKA_00127
+MFPITDDQEALVDAVRDFAQQRVAPHALEWDAEKHFPVDVLAEAGELGLGGIYVGEEHGG
+TGLERKDAILIFEELSKADPAFAAYISIHNMVAWMIDSYGNDEQRAQWIPELMSMEHLAS
+YCLTEPGAGSDAAALKTRAVRDGDDYVLNGVKQFISGAGSSDYYVVMCRTADTGAKGISA
+VVVHKDTPGLSFGPNEKKMGWHTQPTRQVIFEDVRVPVANRLGEEGDGFRIAMKGLNGGR
+LNIGACSIGGGLAALDKATRYLKERSAFGEPLTTKQALVFELADMAVKLETAHTLLMRAA
+DALDRNDPDTVRLCAMAKLVATESGYEAADAALQLHGGYGYLHEYGVEKLVRDLRVHRIL
+EGSNEIMRMIVGRGLIGG
+>PROKKA_00243
+MFPITDDQKALVDAVRDFTEQRVAPHALDWDAEKHFPVDVLAEAGELGLGGIYVGEEHGG
+TGLERTDAILIFEELAKADPAFAAYISIHNMVAWMIDSFGSDEQRARWIPDLAGMEHLAS
+YCLTEPGAGSDAAALKTRAVRDGDHYVLNGVKQFISGAGASDCYVVMCRTADTGARGISA
+VVVHKDTPGLSFGPNEKKMGWHTQPTRQVIFEDVRVPVAGRLGEEGDGFRIAMKGLNGGR
+LNIGACSIGGGLAALDKATRYLKERSAFGEPLTTKQALVFELADMSVKLETAHTMLMRAA
+DALDRNDPDTVRLCAMAKLVATEHGYEAADTALQLHGGYGYLHEYGVEKLVRDLRVHRIL
+EGSNEIMRMIVGRGLIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001793.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001793.fa
new file mode 100644
index 0000000000000000000000000000000000000000..58e8fef2006c9af124361db047445d952faedc03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001793.fa
@@ -0,0 +1,40 @@
+>PROKKA_00247
+MSEKTAPTETAPVIPHFVHGERREGASGRHSDVYHPATGRVAGRVPLASAEEIDAALASA
+EEGFAAWSTLNPQRRGRILLRWVDLINENMDELATVLAQEHGKTFPDAKGDIQRGIEVVE
+FAAGAPHLLKGEFTADAGTGIDVHSMRQPLGVAVGITPFNFPAMIPLWKAGIALAAGNAF
+VLKPSERDPSVPVRLAELALEAGMPAGALNVVHGDKAAVDALIEDPRVKAVGFVGSTPIA
+QSIYAHAGRMGKRAQCFGGAKNHAVVMPDADLEMTADALVGAAFGSAGERCMAISVAVPV
+GEETADRLIALLRERVKDLRVGPSLEASSDFGPVVSKDAKERIEGYIAAGVEAGADLVED
+GRGVVVEGHEDGFYVGATLFDRVTPEMSIYREEIFGPVLSVVRAKDYEEALTLVNEHEFG
+NGVAIFTRDGDAARDFSTRVDTGMVGVNVPIPVPIAYYTFGGWKASGFGDLNQHGTDGLK
+FYTKTKTVTTRWPSGVREGASFVMPAGS
+>PROKKA_02259
+MSQKTAPTETAPVIPHFVHGERREGASGRHGDVYHPATGGVAGRVPLASAEEIDAALASA
+EEGFAAWSRLNPQRRGRILLRWVDLINENMDELATVLAQEHGKTFPDAKGDIQRGIEVVE
+FAAGAPHLLKGEFTADAGTGIDVHSIRQPLGVAVGITPFNFPAMIPLWKAGIALAAGNAF
+VLKPSERDPSVPVRLAELALEAGMPAGALNVVHGDKAAVDALIEDPRVKAVGFVGSTPIA
+QSIYAHAARMGKRAQCFGGAKNHAVIMPDADLEMAADALVGAAFGSAGERCMAISVAVPV
+GEETADRLIALLRERIKGLTVGPSLEASSDFGPVVSKDAKERIEGYIAAGVEAGAELVED
+GRGVVVEGHEDGFYVGATLFDRVTPEMSIYREEIFGPVLSVVRAKDYEEALTLVNEHEFG
+NGVAIFTRDGDAARDFSTRVDTGMVGVNVPIPVPIAYYTFGGWKASGFGDLNQHGTDGLK
+FYTKTKTVTTRWPSGVREGASFVMPAGS
+>PROKKA_00091
+MSQQSQTQQTIPHFVHGARTGTDAARTSDVFDPSTGQVQARVALASPEEVTAAVDSAAEA
+FRTWSAMNPQRRGRVLLTWVDLINANADELAETLSREHGKTFEDAKGDIQRGVEVVEFAA
+GAPHLLKGEFSTSAGTGIDVHSLRQPLGVVAGITPFNFPAMIPLWKAGIALAAGNTFVLK
+PSERDPSVPVRLAELALEAGLPAGALNVVHGDKAAVDALIDDPRVKAVGFVGSTPIAQSI
+YEHAARRGKRAQCFGGAKNHAVIMPDADLEMAADALIGAAFGSAGERCMAISVAVPVGEE
+TADRLVALLRERMASLTVGPSLDPSSDFGPVVSAQAKERIESLIQAGVDEGAELVVDGRG
+VVVEGHEGGFYVGATLFDRVRKGMRIHAEEVFGPVLCVVRAKDYEEALSLPSDHEYGNGV
+AIFTRDGDTARDFSTRVECGMVGVNVPIPVPIAYYTFGGWKASGFGDLNQHGTDGLKFYT
+KTKTVTTRWPSGPRQGGAAASEGASFVMPAGS
+>PROKKA_00247
+MSQKTAPTETAPVIPHFVHGEQREGASGRHSDVYHPATGSVAGRVPLASAEEIDAALASA
+EEGFAAWSTLNPQRRGRILLRWVDLINENMDELATVLAQEHGKTVPDAKGDIQRGIEVVE
+FAAGAPHLLKGEFTADAGTGIDVHSIRQPLGVAVGITPFNFPAMIPLWKAGIALAAGNAF
+VLKPSERDPSVPVRLAELALEAGMPAGALNVVHGDKTAVDALIEDPRVKAVGFVGSTPIA
+QSIYAHAARMGKRAQCFGGAKNHAVIMPDADLEMAADALVGAAFGSAGERCMAISVAVPV
+GEETADRLIALLRERVKDLRVGPSLEASSDFGPVVSKDAKERIEGYIAAGVEAGADLVED
+GRGVVVEGHEDGFYVGATLFDRVTPEMSIYREEIFGPVLSVVRAKDYEEALTLVNEHEFG
+NGVAIFTRDGDAARDFSTRVDTGMVGVNVPIPVPIAYYTFGGWKASGFGDLNQHGTDGLK
+FYTKTKTVTTRWPSGVREGASFVMPAGS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001795.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001795.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dcb8bca3d3591cd8d72e566e5ddd42453b6099f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001795.fa
@@ -0,0 +1,16 @@
+>PROKKA_00253
+MYTRSRNDVEKVEWGGGTSERLITAKDEMGFAVAHTIVRAGSSSKLQYRNHKEACYCIAG
+NGSVVEPDGTVHEITPGVIYVLPDHEPHDLRGGTEDMHLISVFNPAITGDEKHTLSEDGY
+SSY
+>PROKKA_02265
+MYTRSRNDVEKVEWGGGTSERLITAKDEMGFAVAHTIVRAGSSSKLQYRNHQEACYCIAG
+NGSVVEPDGTVHEITPGVIYVLPDHEPHDLRGGTEDMHLISVFNPAITGDEKHTLSEDGY
+SSY
+>PROKKA_00116
+MYTRSRNDVEKVEWGGGTSERLLTAKDEMGFAVAHTIVRAGSSSKLQYRHHQEACYCIAG
+NGSVVEPDGTVHEITPGVIYVLPDHEPHDLRGGTEDMHLISVFNPAITGDEKHTLSEDGY
+SSY
+>PROKKA_00253
+MYTRSRNDVEKVEWGGGTSERLITAKDEMGFAVAHTIVRAGSSSKLQYRNHQEACYCIAG
+NGSVVEPDGTVHEITPGVIYVLPDHEPHDLRGGTEDMHLISVFNPAITGDEKHTLSEDGY
+SSY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001801.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001801.fa
new file mode 100644
index 0000000000000000000000000000000000000000..44543386756432f1b058939d3eb33f24cef89dd0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001801.fa
@@ -0,0 +1,36 @@
+>PROKKA_00302
+MALALVLVGCAAPQGDEGTAAGSSGATDAAVSSPASVDGSEASSSQGRSSDAASSPAAAS
+SGEGSPSAAADPAGPAVPLAARSHEGVPMRAFTAEERPPQFVLFSFDGGRQDARWKTFLD
+AAADSDAKFTVFQSAINLIETANRENYTAPGNTPGYVGTEFGGDEAEVAQRIENINTAHA
+AGHEIGTHYAGHLCALATYGGDKWSTAEWEQEYGSFRDILSDPAAYNPGSSLPALEVTPE
+DVKGGRLPCLDGQWDQLVPMWKDNGLEYDTSRAAAASGVAWPYQEDGIWEFEMPMTWSPV
+LAEKGAASPFVMAMDYNFWISGNGGRDIPEDVARLTDFQYRTYRYMYDSALAGNRAPLVF
+GNHFNDWGLNAFNPAVEKVMREVCVEEDTYCVTYQQMIAWLELQDPEVLAAWRDQARSAT
+GTDAEALGW
+>PROKKA_00010
+MSFPRRSARTVDTPSPRRRRWWGTSVALALVLAGCAAPQGDEGTAAGSSGATDAAVSSPA
+SANGSEASSSQGRSSDAASSGEGSPSAAADPAVPLAARSHEDVPMRAFTAEERPPQFVLF
+SFDGGRQDARWKTFLDAAADSDAKFTVFQSAINLIETANRENYTAPGNEPGYVGTEFGGD
+EAEVAQRIENINTAHAAGHEIGTHYAGHLCAPTRYGADQWSTAEWKQEYGSFTDILSDPG
+AYNPGSSLPALEVTPDDVKGGRLPCLDGEWDQLVPMWKDNGLEYDTSRAAAASGVAWPYQ
+EDGIWEFEMPMTWSPVLAEKDAASPFVMAMDYNFWISGNGGKDIPEDVARLTDFQYRTYR
+YMYDSAFAGNRAPLVFGNHFNDWGLNAFNPAVEKVMREVCVEEDTYCVTYQQMIAWLELQ
+DPEVLAAWRDQARSATGTDAEALGW
+>PROKKA_00052
+MPLHRQPAPFRARRVWGTSVALALVLAGCAAPQEGDAQGAASETSSSSAPAPSASAPSDA
+GPASPSGSTGTDASETAAAPSSSASGDSAGPTASADPATPLAARSHEGVPMRAYAADERP
+PQFVLFSFDGGRQDARWKTFMDAAEDSGAKFTVYQTGINLIESANRENYAAPGNEPGYVG
+TELGGDAAEVAQRIGNINAAHAAGHEIGTHYNGHLCSPTPHGGDKWTTAEWEQEYSTFEE
+IITDPGAFNPGSALPALDITPEDIKGGRPPCLDGQWDQLVPMWKEHGLVYDTSRSASATG
+VAWPYQEDGIWQFEMPIVWSPVLAEQGKPSPLVMAMDYNFWISGNGGKDDPADTARLTAF
+QHRTYRYMFSSAHAGNRAPLVFGNHFNDWGLNAFNPAVEQTMREVCDEPDTYCVTYQQMV
+DWLELQDPAVLEAWRAQPRSATGDDAAALG
+>PROKKA_00309
+MSFPRPSARTVDTPSPRRRRWWGTSVALALVLAGCAAPQGDEGTAAGSSGATDAAVSSPA
+SADGSEASSSQGRSSDAASSQAASSFGEGSPSAAADPADPALPLAARSHEGVPMRAFTAE
+ERPPQFVLFSFDGGRQDARWKTFLDAAADSDAKFTVFQSAINLIETANRENYTAPGNEPG
+YVGTEFGGDEAEVAQRIENINTAHAAGHEIGTHYAGHLCAPTRYGADQWSTAEWKQEYGS
+FTDILSDPGAYNPGSSLPALEVTPDDVKGGRLPCLDGEWDQLVPMWKDNGLEYDTSRAAA
+ASGVAWPYQEDGIWEFEMPMTWSPVLAEKDAASPFVMAMDYNFWISGNGGKDIPEDVSRL
+TDFQYRTYRYMYDSAFVGNRAPLVFGNHFNDWGLNAFNPAVEKVMREVCVEEDTYCVTYQ
+QMIAWLELQDPEVLAAWRDQARSATGTDAEALSW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001803.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001803.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27b8ebe3eccb9f273a15f8eebed1f41636fe67b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001803.fa
@@ -0,0 +1,28 @@
+>PROKKA_00328
+MLTAVELGLIYAVVALGVYLTFRILDFPDLTVDGSFTTGAATAAVLITGGTPVPLAMLAA
+FVAGALAGLVTGLLHTKGRIDGLLAGILTMIALYSINLRIMGKANIPLLGQDTLFTWLDD
+LGLARNWGSILVLFLGVFVVKLILDWFLHTDLGLALQATGDNEEMIRSYGVSTDRMKILG
+LMISNGLVALGGSLLAMYQGFADISMGIGLILVGLASVIVGQAVFGQRTVFWATLAVIVG
+AVLYRLIIQFALNAGLSPNDMKLISAALVVVALLLPRFGFAKRLSLRTRGTAATPGPAAA
+APATAGMPLTGEPGGAAPAASVPEEAPRA
+>PROKKA_00044
+MLTAVELGLIYAVVALGVYLTFRILDFPDLTVDGSFTTGAATAAVLITGGTPVPLAMLAA
+FVAGALAGLVTGLLHTKGRIDGLLAGILTMIALYSINLRIMGKANIPLLGQDTLFTWLDD
+LGLARNWGSILVLFLGVFVVKLILDWFLHTDLGLALQATGDNEEMIRSYGVSTDRMKILG
+LMISNGLVALGGSLLAMYQGFADISMGIGLILVGLASVIVGQAVFGQRTVFWATLAVIVG
+AVLYRLIIQFALNAGLSPNDMKLISAALVVVALLLPRFGFAKRLSLRTRGTAATPGPAAA
+APATAGMPLTGEPGGAAPAASVPEEAPRA
+>PROKKA_00007
+MLTAVELGLIYAVVALGVYLTFRILDFPDLTVDGSFTTGAATAAVLITGGTPVPLAMVAA
+FVAGTLAGLVTGLLHTKGKIDGLLAGILTMIALYSINLRIMDKANIPLLGQDTLFSWLGD
+MGLARNWGSVLVLFLGVFVLKMILDWFLHTDLGLSLQATGDNEEMIRSYGVSTDRMKILG
+LMISNGLVALGGSLLAMYQGFADISMGIGLILVGLASVIVGQAVFGQRTVFWATFAVIVG
+AVLYRLIIQAALNAGLSPNDMKLISAALVVLALLLPRFGLAKRLSLRSKSTAAPAQAETP
+ATATPAASAATAEEQTRA
+>PROKKA_00335
+MLTAVELGLIYAVVALGVYLTFRILDFPDLTVDGSFTTGAATAAVLITGGTPVPLAMLAA
+FVAGALAGLVTGLLHTKGRIDGLLAGILTMIALYSINLRIMGKANIPLLGQDTLFTWLGD
+LGLARNWGSILVLFLGVFVVKLILDWFLHTDLGLALQATGDNEEMIRSYGVSTDRMKILG
+LMISNGLVALGGSLLAMYQGFADISMGIGLILVGLASVIVGQAVFGQRTVFWATLAVIVG
+AVLYRLIIQFALNAGLSPNDMKLISAALVVVALLLPRFGFARRLSLRTRGTAATPAPAAA
+APATAGMPLTGEPGGATPAASVSEEAPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001810.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001810.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34d439beffba5c1404e33766e50171194638820b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001810.fa
@@ -0,0 +1,20 @@
+>PROKKA_00431
+MASDHRPPHPVSPHPDDLDGGGRPVVGPDEARRRIAGHSGPDARPLIRPDARTPGVFRAL
+LGLTVASAVLYAASTLRNLLPGAAQDIADSLPEGSAQSPAMTAEAIEGALTGSVWFATLL
+GLAVYAIVLVGLTRRSNAARIMGALFASIAIFVTLLGTIRLFVFPAGDVVLPLVLGGLFA
+LVNAAWLVCAFNPGLATTFLRRRA
+>PROKKA_00152
+MASDHRPPHPVSPHPDDLDGGGRPVVGPDEARRRIAGHSGPDARPLIRPDARTPGVFRAL
+LGLTVASAVLYAASILRNLLPGAAQDIADSLPEGGAQSPAMTAEAIEGALTGSVWFATLL
+GLAVYAIVLVGLTRHSNTARIMGALFASIAIFVTLLGAIRLFVFPAGDVVLPLVLGGLFA
+LVNAAWLVCAFNPGLATTFLRRRA
+>PROKKA_02526
+MASDPRPPNPASPDPASPDGFRPGDGRPVVGPEDARRRIAGHSGPHARPLIRPNERTPGV
+FRALVGLTVASAAVYVVSLLLGLRPGAAEEIAATLPADASRSPAMTAESIQAALTGSVWV
+AVLLGLGVYALVLVGLLRRSNTARIVGAIVAALAVFVTLLGAIRLFVFPAESVVAPLLLG
+LLFALVNAAWLVCAFNPGLATTFVRRDAGPRRPA
+>PROKKA_00434
+MASDHRPPHPVSPDSDDLDGGGRPVVGPDEARRRIAGHSGPDARPLIRPDARTPGVFRAL
+LGLTVASAVLYAASILRNLLPGAAQDIADSLPEGGAQSPAMTAEAIEGALTGSVWFATLL
+GLAVYAIVLVGLTRHSNTARIMGALFASIAIFVTLLGAIRLFVFPAGDVVLPLVLGGLFA
+LVNAAWLVCAFNPGLATTFLRRRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001811.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001811.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec40c22c1035fff233811b5531e722ec14c2d3e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001811.fa
@@ -0,0 +1,28 @@
+>PROKKA_00463
+MTDQTPQAQPAAGTALPPSTGLRLMAVHAHPDDESSKGAGTMAAYAAAGAEVMVVTCTGG
+EAGTLLNPSFGDTTRADRDIAAVRREEMAEAARILGIRHAWLGFLDSGLPEGDPLPALPA
+NCFAEVPLQDAATPLISLVRRFRPHVLISYDEVGGYPHPDHLQAHAVTMEAYRAAGLADE
+YPEAGPAWEVSKVYYDCGFNPRKFRTMAAVAEADGEDVPFARRLMMFDAMDAMREVLRRR
+EAGEDVPDPEVIPPWVTADHDVTTQVDVTGFLDERDAALRAHRTQIDPDGMFFDAPHDLQ
+RRAWPWEDFALIDSRVPSELPEHDLFAGLR
+>PROKKA_00181
+MTDQTPQAQPAAGTALPPSTGLRLMAVHAHPDDESSKGAGTMAAYAAAGAEVMVVTCTGG
+EAGTLLNPSFGDTTRADRDIAAVRREEMAEAAGILGIRHAWLGFLDSGLPEGDPLPALPA
+NCFAEVPLRDAAAPLISLVRRFRPHVLISYDEVGGYPHPDHLQAHAVTMEAYRAAGLADE
+YPEAGPAWEVSKVYYDCGFNPRKFRTMAAVAEADGEDVPFARRLMMFDAMDAMREVLRRR
+EAGEDVPDPEVIPPWVTADHDVTTQVDVTGFLDERDAALRAHRTQIDPDGMFFDAPHDLQ
+RRAWPWEDFALIDSRVPSELPEHDLFAGLR
+>PROKKA_02368
+MSEPSIPAPTTASVPDSTGLRLLAVHAHPDDESSKGAATMAAYAAAGAEVLVVTCTGGEA
+GSVLNPSYAHPVRAERDIAGVRHAEMAAAARALGVRHRWLGFLDSGLPEGDPLPALPDHC
+FAEVPLETAAAPLVAVVRRFRPHVILSYDEAGGYPHPDHIRAHEVTRVAWERAGDADAYP
+GTGPAWEPLKLYYDRAFHPAKYQALHEGFLAAGEESPFTDRLEMHARMEAMREVLRRREE
+GEEVPDPEHLPPFVPPVHEVTTQIPVQDFLDERDAALRAHATQVDPEGMFFAAPNELQRS
+TWPWEDYALIESRVRTVPPETDLFAGVR
+>PROKKA_00463
+MTDQTPQAQPAAGTALPPSTGLRLMAVHAHPDDESSKGAGTMAAYAAAGAEVMVVTCTGG
+EAGTLLNPSFGDTTRADRDIAAVRREEMAEAARILGVRHAWLGFLDSGLPEGDPLPALPA
+NCFAEVPLRDAATPLISLVRRFRPHVLISYDEVGGYPHPDHLQAHAVTMEAYRAAGLADE
+YPEAGPAWEVSKVYYDCGFNPRKFRTMAAVAEADGEDVPFARRLMMFDAMDAMREVLRRR
+EAGEDVPDPEVIPPWVTADHDVTTQVDVTGFLDERDAALRAHRTQIDPDGMFFDAPHDLQ
+RRAWPWEDFALIDSRVPSELPEHDLFAGLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001812.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001812.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9b8c03c05fecf77b0f138409aa61a5996acdb59
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001812.fa
@@ -0,0 +1,20 @@
+>PROKKA_00476
+MTATPQTPAQPLQDDAPVVSVVMGSDSDWPVMSAAAEALRELDVPVEVGVVSAHRMPHEM
+VEFGARAHERGIRVIVAGAGGAAHLPGMLAAVTPLPVIGVPVKLKSLDGMDSLLSIVQMP
+AGVPVATVSIDGARNAGLLAARILASADTAEGDRLRAALAEHADELNAQARAKGARLRER
+MAADR
+>PROKKA_00194
+MTATPQTPAQPLQDDAPVVSVVMGSDSDWPVMSAAAEALRELDVPVEVGVVSAHRMPHEM
+VEFGARAHERGIRVIVAGAGGAAHLPGMLAAVTPLPVIGVPVKLKSLDGMDSLLSIVQMP
+AGVPVATVSIDGARNAGLLAARILASADTAEGDRLRAALAEHADELNAQARAKGARLRER
+MAADR
+>PROKKA_02355
+MTAEQTTQPTSDAPCTRPLQEEAPVVSVVMGSDSDWPVMGQAVEALRELGVPVEVGVVSA
+HRMPHEMVDFGARAHERGIRVIVAGAGGAAHLPGMLAAVTPLPVIGVPVKLRSLDGLDSL
+LSIVQMPAGVPVATVSVDGARNAGLLAARILAAGTDDGAAHLRAALQDVAAGLNAQARAK
+GARLHERAADGA
+>PROKKA_00476
+MTATPQTPAQPLQDDAPVVSVVMGSDSDWPVMSAAAEALRELDVPVEVGVVSAHRMPHEM
+VEFGARAHERGIRVIVAGAGGAAHLPGMLAAVTPLPVIGVPVKLKSLDGMDSLLSIVQMP
+AGVPVATVSIDGARNAGLLAARILASADTAEGDRLRAALAEHADELNAQARAKGARLRER
+MAADR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001813.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001813.fa
new file mode 100644
index 0000000000000000000000000000000000000000..57cf11ef349b163d642dc02ebf80d65d8080b9f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001813.fa
@@ -0,0 +1,31 @@
+>PROKKA_00510
+MAPAEKRVPGPRFRELDGLRGIAALAVVFSHYTGAHNSHYPQDPAAFHDAAWGAAGVQLF
+FIISGFVIFMSARRANRPSDFAISRAARLYPPYWISLVFAVVLLLLHPVPGFPFTWSQAF
+LNLTMVQRWVGVDNVVDVYWTLAVEMQFYVIILILLYLTRCRLSDRVVLWGSLAWSVISW
+AVVLFTAPHVGSDPQRDPLWVKLLNNATVAEYAPLFVLGMALYIARQTGQHRGWVAAAAV
+SAVGSTFVMRGMPLALEVLVVVLLAVTVMLRERTSVLLLAPVQWYGKISYSLYILHAIPG
+YILIHALWPYVGRNMAMLVALAVVSVLAWALQKYGEEHLGRAAKRGLTRVRSVVDARTGH
+PRSLEPAR
+>PROKKA_00230
+MTAASPNEPGAASVAPAEKRVPGPRFRELDGLRGVAALAVVFSHYTGAHNSHYPQDPAAF
+HDAAWGAAGVQLFFIISGFVIFMSARRANRPSDFAISRAARLYPPYWISLVFAVGLLLLH
+PVPGFPFTWGQALLNLTMVQRWVGVDNVVDVYWTLAVEMQFYVIILILLYLTRCRLSDRV
+VLWGSIAWSVISWGVVSFTAPHVGWDPQRDPMWVKLLNNATVAEYAPLFVLGMALYIARQ
+TGRHRGWVAAAAVSAVGSTFVMRGMPLALEVLVVVLLAVTVMLRERTSVLLLPPIQWYGK
+ISYSLYILHAIPGYILIHALWPYVGRNMAMLVALAVVSVLAWALQKYGEEHLGRAAKRGL
+TRVRSVVDARTGGPRSPGKALG
+>PROKKA_02324
+MTAASSNEPGAATVPPIEKRHPGPRFRELDGLRGIAALAVVLYHFTGHFAARFPAAPRAF
+HDFWWGEYGVQLFFLLSGFVILMTAWRAKRPSDFAISRVARLYPPYWISLAVAVSLLLWR
+PMPGFPIDPATVVANVTMVQRWFLFPNVVEVYWTLAVEMQFYVIVFVLLLVTRCRLRGRV
+LLWAAAAWTAVSWVVILAAFRVTSDNPQADPTWVKLLTNATVAEYGPLFVTGMLFYLVRE
+TGRHPGWAIASAASTALGATLLRGSEHGVMVAAVCALAWLVWRVGEQWLGKHARTGLVSL
+RDHVSPRAVASKREAAR
+>PROKKA_00509
+MTAASPNEPGAASVAPAEKRVPGPRFRELDGLRGIAALAVVFSHYAAQHNSHFPEDPPPF
+HGFEWGAAGVQLFFIISGFVIFMSARRASRPSDFAISRAARLYPPYWISLVFAVVLLLLH
+PVPGFPFTWGQALVNLTMVQRWVGVDNVVDVYWTLAVEMQFYVIILILLYLTRCRLSDRV
+VLWGSLAWSVISWGVVSFTAPHVGSDPQRDPLWVKLLNNATVAEYAPLFVLGMALYIARQ
+TGRHRGWVAAAAVSAVGSSFVMRGMPLAFEVLVVVLLAVTVMLRERTSVLLLAPIQWYGK
+ISYSLYILHAIPGYILIHTLWPYVGRNMAMLVALAVVSVLAWALQKYGEEHLGRAAKRGL
+TRVRSVVEARTGHPRSLEPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001819.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001819.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0a1233924b9fb9efe42690a36514338f917811a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001819.fa
@@ -0,0 +1,32 @@
+>PROKKA_00578
+MPQSRALSRGVRLSAVSATLLLALTACAGGTGGSGSDSASGAASGSASAAESDKKVTLYS
+GRSEDLVQPILDEFTDETGIEVEVRYDKTPAMAAQLIEEGEGSPADVFLSQDAGALGAVA
+KEGLFTPLAQETLDRVPETYRDDEGDWVGLTGRVRVLAYNEEKVPEADLPTSVDELTDPK
+WKGRVGVAPTNASFQTFVTALRLQKGEDEARTWLEDFAANDPQRREKNGEILADVDAGTL
+DTGLVNHYYLFELAREKGVAPEELGASLHFFPDGDLGSLVNVSGMGLVGEQEDGDAAALV
+EYLLSEDGQSYFAEETGEYPLVEGVEQPAGFPELSEVKAPDVDLNDLDDLQTTIQMIQEA
+GLL
+>PROKKA_00310
+MPQSRALSRGVRLSAVSATLLLALTACAGGTGGSGSDSASGAASGSASAAESDKKVTLYS
+GRSEDLVQPILDEFTDETGIEVEVRYDKTPAMAAQLIEEGEGSPADVFLSQDAGALGAVA
+KEGLFTPLAQETLDRVPETYRDDEGDWVGLTGRVRVLAYNEEKVPEADLPTSVDELTDPK
+WKGRVGVAPTNASFQTFVTALRLQKGEDEARTWLEDFAANDPQRREKNGEILADVDAGTL
+DTGLVNHYYLFELAREKGVAPEELGASLHFFPDGDLGSLVNVSGMGLVGEQEDGDAAALV
+EYLLSEDGQSYFAEETGEYPLVEGVEQPAGFPELSEVKAPDVDLNDLDDLQTTIQMIQEA
+GLL
+>PROKKA_02355
+MPQSRALSRGVRLSAMSATLLLALTACAGGTGGSGSDSASGAASGSASAAESDKKVTLYS
+GRSEDLVQPILDEFTDETGIEVEVRYDKTPAMAAQLIEEGEGSPADVFLSQDAGALGAVA
+KEGLFTPLAQETLDRVPETYRDDEGDWVGLTGRVRVLAYNEEKVPEADLPTSVDELTDPK
+WKGRVGVAPTNASFQTFVTALRLQKGEDEARTWLEDFAANDPQRREKNGEILADVDAGTL
+DTGLVNHYYLVELAREKGVAPEELGASLHFFPDGDLGSLVNVSGMGLVGEQEDGDAAALV
+EYLLSEDGQSYFAEETGEYPLVEGVEPPAGFPELSEVKAPDVDLNDLDDLQTTIQMIQEA
+GLL
+>PROKKA_00579
+MPQSRALSRGVRLSAVSATLLLALTACAGGTGGSGSDSASGAASGSASAAESDKKVTLYS
+GRSEDLVQPILDEFTDETGIEVEVRYDKTPAMAAQLIEEGEGSPADVFLSQDAGALGAVA
+KEGLFTPLAQETLDRVPETYRDDEGDWVGLTGRVRVLAYNEEKVPEADLPTSVDELTDPK
+WKGRVGVAPTNASFQTFVTALRLQKGEDEARTWLEDFAANDPQRREKNGEILADVDAGTL
+DTGLVNHYYLFELAREKGVAPEELGASLHFFPDGDLGSLVNVSGMGLVGEQEDGDAAALV
+EYLLSEDGQSYFAEETGEYPLVEGVEQPAGFPGLSEVKAPDVDLNDLDDLQTTIQMIQEA
+GLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001820.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001820.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da497ff016cc4a2b20156aa760b77021d996db44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001820.fa
@@ -0,0 +1,23 @@
+>PROKKA_00581
+MVPLMVVTLFTVVASQIRGAGERLPALAAVVPLFAAFAAVMVALGVVAARWTHLDVPAGR
+ALVFSGATRNSLVMLPLALALPASLDPAPLVVVTQTLVELGVMVSLVRLVPRLLPLHGQS
+AGAGARRTVT
+>PROKKA_00314
+MPSSPPRRALVAALLVGVLLVLLAPCVDYVIAFTALAGGAAERLLAAAPLLMLVQLVVLP
+VLLRVVAGEAAVAAVDVGPFVRALVLLILAPLALAALLQWGTARGRGGVRRTAAGVVRGC
+TAAMVPLMVVTLFTVVASQIRGVGERLPALAAVVPLFAAFAAVMVALGVVAARWARLDVP
+AGRALVFSGVTRNSLVVLPLALALPASLDPAPLVVVTQTLVELGAMVSLVRLVPRLLPLH
+GQSAGAGAGRTVT
+>PROKKA_02352
+MESAQSRRAAAVAWMERHQAALYAAGIAAGAVVGWVVPGAGRLAVLVEPVLGLLLLATFL
+AVPFAALGAALRDVRFLAALLVLNFAVVPAVVFGLSRFVAHDDALLVGVLLVLLAPCVDY
+VIAFTGLAGGAAERLLAAAPLLMLLQLLLLPVLLRVCAGPAAVAAVDVGPFVRALVLLIL
+LPLALGALVQGVARRGAPGPRRAARAVEAATGAAMVPLMAATLFLVVASQVRAVGERLPA
+LAGAVPVFVGFVAVMVPLGLAVAALARVDARSGRALVFSGATRNSLVVLPLALALPPSLD
+PAPLVVVTQTLVELVAMAVLVRLVPRLLPERAAPAEEAALAVRPEPDVTGS
+>PROKKA_00582
+MPGADAWAVLVEPVLALLLLATFLAVPFAALGAGLRDGRFLGALLVLNFVVVPAVVFGLS
+RFVAHDDALLVGVLLVLLAPCVDYVIAFTALAGGAAVAAVDVGPFVRALVMLILVPLALA
+ALLQWGAVRGRGGVRDTAAGVVRGFTVAMVPLMVVTLFTVVASQIRGVGERLPALAAVVP
+LFVAFAVVMVALGVVAARWARLDVPAGRALVSSGATRNSLVVLPLALALPASLDPAPLVV
+VTQTLVELGAMVSLVRLVPRLLPLHGQSAGAGAGRTVT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001821.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001821.fa
new file mode 100644
index 0000000000000000000000000000000000000000..570d05a92608488955384f392a7eb3b67e6846e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001821.fa
@@ -0,0 +1,12 @@
+>PROKKA_00624
+METLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNVLNRRRWQSFDQLRLAIVSWIERTY
+HRRRRQARLGKLTPVEFEMVQSVQAVAAA
+>PROKKA_00638
+METLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNVLNRRRWQSFDQLWLAIVSWIERTY
+HRRRRQARLGKLTPVEFEMVQSVQAAAAA
+>PROKKA_00752
+MESFFALLQKNVLDRRDWDTRDELRAGIITWIERSYHRRRRQVRLGRLTPVEYELIMDHT
+PADPA
+>PROKKA_00593
+METLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNVLNRRRWQSFDQLWLAIVSWIERTY
+HRRRRQARLGKLTPVEFEMVQSVQAAAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001823.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001823.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dff6f3558aadab481cf3362f66d6b5f746ce35d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001823.fa
@@ -0,0 +1,40 @@
+>PROKKA_00628
+MTSSLTTRRTFLGASVGALALAGLAACADPAISPQPSGRILPTDPLVAEYEKRRAASGTT
+VTHRLSAAPLETSLQGRGLTTWGYNDGLNGPLLRAQTGDLLKVSVANDLPEDTSVHWHGL
+ALRNDADGVQGVTQDPIAAGGRYTYGFRLSHPGTYWYHSHFDTQRERALYGALIVEDPNE
+PLSYDQEWVVILDDWLDGITGTPQDVVEELSAGMDMSGDMEGMAGMAGMDHGSMSQDSSS
+GMPMKHMLMGAESDYLGGDAGDVKIPVHLFNGRPPSDPDTFSSTPGNRIRLRLINAAGDT
+AYRVGIPGQELTITHTDGFPVQPRQADTVVLGMGERLDVLITLGDQAVPVLALPEGKTGH
+AYGIIAAGPKTTLSGRLPQTLGGTVLDGSRLKAHESVLLPPKDPTTTHEVRLTGSMMEYD
+WGINGRRFDPANPFEGAFELRLDERVRVTMTNDTDMWHPMHLHGHTFQLADHGARKDTVI
+IKPRQTIVFDFEADNPGQWLTHCHNAYHAEAGMMGVFSYIH
+>PROKKA_00400
+MTSSLTTRRTFLGASVGALALAGLTACADPAISPQPSGRILPTDPLVAEYEKRRAASGTT
+VTHRLSAAPLETSLQGRGLTTWGYNDGLNGPLLRAQTGDLLKVSVANDLPEGTSVHWHGL
+ALRNDADGVQGLTQDPIAAGGRYTYGFRLSHPGTYWYHSHFDTQRERALYGALIVEDPNE
+PLSYDQEWVVILDDWLDGITGTPQDVVEELSAGMDMSGDMEGMAGMDHGSMSQDSSSGMP
+MKHMLMGAESDYLGGDAGDVKIPVHLFNGRPPSDPDTFSSTPGNRIRLRLINAAGDTAYR
+VGIPGQELTITHTDGFPVQPRQADAVVLGMGERLDVLITLGDQAVPVLALPEGKTGHAYG
+IIAAGPKTTLSGRLPQTLGGTVLDGSRLKAHESVLLPPKDPTRTHEVRLTGSMMEYDWGI
+NGRRFDPANPFEGAFELRLDERVRVTMTNDTDMWHPMHLHGHTFQLADHGARKDTVIIKP
+RQTIVFDFEADNPGQWLTHCHNAYHAEAGMMGVFSYIH
+>PROKKA_02201
+MTSSLTTRRTFLGASVGALALAGLAACADPAISPQPSGRILPTDPLVAEYEKRRAASGTT
+VTHRLSAAPLETSLQGRGLTTWGYNDGLNGPLLRAQTGDLLKVSVANDLPEDTSVHWHGL
+ALRNDADGVQGVTQDPIAAGGRYTYGFRLSHPGTYWYHSHFDTQRERALYGALIVEDPNE
+PLSYDQEWVVILDDWLDGITGTPQDVVEELSAGMDMSGDMEGMAGMAGMDHGSMSQDSSS
+GMPMKHMLMGAESDYLGGDAGDVKIPVHLFNGRPPSDPDTFSSTPGNRIRLRLINAAGDT
+AYRVGIPGQELTITHTDGFPVQPRQADAVVLGMGERLDVLITLGDQAVPVLALPEGKTGH
+AYGIIAAGPKTTLSGRLPQTLGGTVLDGSRLKAHESVLLPPKDPTRTHEVRLTGSMMEYD
+WGINGRRFDPANPFEGAFELRLDERVRVTMTNDTDMWHPMHLHGHTFQLADHGARKDTVI
+IKPRQTIVFDFEADNPGQWLTHCHNAYHAEAGMMGVFSYIH
+>PROKKA_00603
+MTSSLTTRRTFLGASVGALALAGLAACADPVISPQPSGRILPTDPLVAEYEKRRAASGTT
+VTHRLSAAPLETSLQGRGLTTWGYNDGLNGPLLRAQTGDLLKVSVANDLPEDTSVHWHGL
+ALRNDADGVQGVTQDPIAAGGRYTYGFRLSHPGTYWYHSHFDTQRERALYGALIVEDPNE
+PLSYDQEWVVILDDWLDGITGTPQDVVEELSAGMDMSGDMEGMAGMAGMDHGSMSQDSSS
+GMPMKHMLMGAESDYLGGDAGDVKIPVHLFNGRPPSDPDTFSSTPGNRIRLRLINAAGDT
+AYRVGIPGQELTITHTDGFPVQPRQADAVVLGMGERLDVLITLGDQAVPVLALPEGKTGH
+AYGIIAAGPKTTLSGRLPQTLGGTVLDGSRLKAHESVLLPPKDPTRTHEVRLTGSMMEYD
+WGINGRRFDPANPFEGAFELRLDERVRVTMTNDTDMWHPMHLHGHTFQLADHGARKDTVI
+IKPRHTIVFDFEADNPGQWLTHCHNAYHAVAGMMGVFSYIH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001825.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001825.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d091a2ba935e4cd5e73577ed9bc4c05e0cfd9b7c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001825.fa
@@ -0,0 +1,12 @@
+>PROKKA_00632
+MTESARTPLPGATNGCSCCAPAADATAPAGHQSADPTGTSAGDATYQVEGMTCGHCVGSV
+AEAVSALDGVDDVRVELVAGGASPVTVTGPASADSVRTAIEAAGYRVRI
+>PROKKA_00404
+MTESARTPLPGATNGCSCCAPAADATAPAGHQSADPTGTSAGDATYQVEGMTCGHCVGSV
+AEAVSALDGVDDVRIELVAGGASPVTVTGPASADSVRTAIEAAGYRVRI
+>PROKKA_02197
+MTESARTPLPGATNGCSCCAPAADATAPAGHQSADPTGTSAGDATYQVEGMTCGHCVGSV
+AEAVSALDGVDDVRIELVAGGASPVTVTGPASADSVRTAIEAAGYRVRI
+>PROKKA_00599
+MTESARTPLPGATNGCSCCAPAADATAPAGHQSADPTGTSAGDATYQVEGMTCGHCVGSV
+AEAVSALDGVDDVRVELVAGGASPVTVTGPASADSVRTAIEAAGYRVRI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001829.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001829.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dd37f2925b8507d794d42b2d4f61ec7b6095b47b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001829.fa
@@ -0,0 +1,20 @@
+>PROKKA_00646
+MSVIDVGLREGHEYRVRDTWLTVPNLITLARFALVPVFVWLTVDGRHLDAFVILAVLSGT
+DWVDGYVARRFDMISTVGRWLDPVADRLSLLVVAVTFVATGIAPLWLALAIAIPDLVLAA
+VCLWLFGGSPDLPVTVLGKVRTALLLVGTPLLLLARVPGVDGGPWSGVALALVGAGCLLH
+ILAAGDYLVRAVGKARGLRADGQDPREHPSRRG
+>PROKKA_00383
+MRVIDVGLREGHEYRVRDTWLTVPNLITLARFALVPVFVWLTVDGRHLDAFVILAVLSGT
+DWVDGYVARRFDMISTVGRWLDPVADRLSLLVVAVTFVATGIAPLWLALAIAIPDLVLAA
+VCLWLFGGSPDLPVTVLGKVRTALLLVGTPLLLLARVPGVDGGPWSGVALALVGAGCLLH
+ILAAGDYLVRAVGKARGLRADGQDPREHPSRRG
+>PROKKA_02317
+MRLIDVGLREGHEYRVRDTWLTVPNVITLVRLALVPVFVWLTVTDQFLAAFLTLAFLSST
+DWVDGYIARRFDMISTVGRWLDPVADRLSLVTVALTFVLTGIAPAWLVLSILIPDVVLTL
+VCLRLFGGSPDLKVTVLGKVRTALLLAGTPLLLLARVPGVDQDLWGGLALVLVGAGCVLH
+VLAAVDYLVRAVRKARELRAAGVDPRDRRARPAQGA
+>PROKKA_00616
+MRVIDVGLREGHEYRVRDTWLTVPNLITLARFALVPVFVWLTVDGRHLDAFVILAVLSGT
+DWVDGYVARRFDMISTVGRWLDPVADRLSLLVVAVTFVATGIAPLWLALAIAIPDVVLAA
+VCLWLFGGSPDLPVTVLGKVRTALLLVGTPLLLLARVPGVDGGPWSGVALALVGAGCLLH
+ILAAGDYLVRAVGKARGLRADGQDPREHPSRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001832.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001832.fa
new file mode 100644
index 0000000000000000000000000000000000000000..890a317f2ec2208f9b48791f1e4e787669a6184d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001832.fa
@@ -0,0 +1,17 @@
+>PROKKA_00666
+MTERVEIEQRGRYADELAVGQVYLHRPGRTLTEADNVLFTTLTMNPQALHLDHAYAADQP
+FGRPLVNSMLTLSTLVGLAVGQTTQGTLVAQLGLGEIAFPKPVFHGDTLYGRSEVTAIRE
+SSSRPGQRIVTFAMTGENQHGDVVVRAQRTCLMWTAQAHAEAKAKAADAAGTGERA
+>PROKKA_00403
+MTERVEIEQRGRYADELAVGQVYLHRPGRTLTEADNVLFTTLTMNPQALHLDHAYAADQP
+FGRPLVNSMLTLSTLVGLAVGQTTQGTLVAQLGLGEIAFPKPVFHGDTLYGRSEVTAIRE
+SSSRPGQRIVTFAMTGENQHGDVVVRAQRTCLMWTAQAHAEAKAKAADAAGTGERA
+>PROKKA_02296
+MGRAEPGAAPERVEIVQRGRYADELAVGQVYLHRPGRTLTEADNVLFTTLTMNPQALHLD
+HAFAQTQSFGRPLVNSMLTLSTLVGLAVAQTTQGTLVAQLGLGEIAFPAPVFHGDTLYGR
+SEVRAVRESSSRPGQRIVTFAMTGENQHGDVVVRAERTCLMWTEAAHADARAQAAADAAE
+ERA
+>PROKKA_00636
+MTERVEIEQRGRYADELAVGQVYLHRPGRTLTEADNVLFTTLTMNPQALHLDHAYAAAQP
+FGRPLVNSMLTLSTLVGLAVGQTTQGTLVAQLGLGEIAFPKPVFHGDTLYGRSEVTAIRE
+SSSRPGQRIVTFAMTGENQHGDVVVRAQRTCLMWTAQAHAEAKAKAADAAGTGERA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001833.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001833.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40044c6cc41a904c0dc4521fb282cccfe50c1d09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001833.fa
@@ -0,0 +1,24 @@
+>PROKKA_00667
+MSALTLGPAVMFTPADRPERYATALERADAVILDLEDAVIPEARPAARDAVAAAWAGRAT
+GGVDGGPLDEDRVVVRVNPAGTADHDADLAMLAGTGWRTLMLAKAESAAQVDGVVAALGP
+QTRVVALCETAAGILAAAELAAHPHVGALMWGAEDLVASMGGSSSRTPEGAYRSVVQHAR
+ATVLLAAAAHGAAAWDAVHLDLGDEAGLAAEAEDAAALGCTATVCLHPRQVPVVRSAYTP
+APEAVERARRVLAAAEGRHGAFELDGTMVDEVVLAQARAVLRRADAARPAGA
+>PROKKA_00404
+MSALTLGPAVMFTPADRPERYATALERADAVILDLEDAVTPDARPTARDAVAAAWAGRAT
+GGVDGGPLDEDRVVVRVNPAGTADHDADLAMLAGTGWRTLMLAKAESAAQVDGVVAALGP
+QTRVVALCETAAGILAAADLAAHPHVGALMWGAEDLVASMGGSSSRTPEGAYRSVVQHAR
+ATVLLAAAAHGAAAWDAVHLDLGDEAGLAAEAEDAVALGCTATVCLHPRQVPVVRSAYTL
+APEAVERARRVLAAAEGRHGAFELDGAMVDEVVLAQARAVLRRADAPRPASA
+>PROKKA_02295
+MSALALGPAVMFTPADRPERYAKALERADAVILDLEDAVTPDARPAARDAVRAAWEGRAA
+GGADGGPLDVARVVVRVNPAGGADYTADLAMLAETGWRTLMLAKAESAAQVDGLVAAMGE
+DVRVVALCETAAGVLAAAELAAHPNVGALMWGAEDLVASMGGSSSRTADGAYRSVVTHAR
+AAVLLAAAAHGAAAWDAVHLDLADEAGLAAEAEDAVALGCAATVCLHPRQVPVVRSAYTP
+AAEAVERAHRVLSEAEGRRGAFELDGAMVDEVVLAQARAVLRRAEAAGAAAG
+>PROKKA_00637
+MSALTLGPAVMFTPADRPERYATALERADAVILDLEDAVTPDARPTARDAVAAAWAGRVT
+GGVDGGPLDEGRVVVRVNPAGTADHDADLAMLAGTGWRTLMLAKAESAAQVDGVVAALGP
+QTRVVALCETAAGILAAADLAAHPHVGALMWGAEDLVASMGGSSSRTPEGAYRSVVQHAR
+ATVLLAAAAHGAAAWDAVHLDLGDEAGLAAEAEDAVALGCTATVCLHPRQVPVVRSAYTP
+APEAVERARRVLAAAEGRHGAFELDGAMVDEVVLAQARAVLRRADAARPASP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001835.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001835.fa
new file mode 100644
index 0000000000000000000000000000000000000000..201292aa985c9a118c87d798d4ab31f2837fba73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001835.fa
@@ -0,0 +1,36 @@
+>PROKKA_00698
+METASPPTQPEHAPQDGDDAPGPRVIGLVADPGTPWALVRRIAGDVEDRLDERLPQPGGW
+RVETRQESLPVGATGGMVLEEPVRSLADGQGWDTVVAVVDLPRFDDRRGVVADVVPQLRV
+GVVCVPALGVITPARRLRETVLRIVEHIDTAPHVDPPDGELDVQSSDESGEVEEDDGPSP
+TDEPPEPDTAALRGIAPLVDVDADVTTTTRMGGGSRRTSTVYVKGWTGTLRLLAGMVMAN
+RPLLMPRDMTFTIASASAAGAYGVFFGSIWVLSSVMSPVRLAAVSVLSVVLLVAWLVTTN
+GLWTHGATHRHSSRLDNLSTVLTVGLACTVVYVLLFVTLLLVALMIIPVEYLEEELDQPG
+GVGDYVRLVWLAASMGTMAGAVGSSLDDSDRIRNATYSLRERHRRSERHEGDGAAEGPTA
+GETMSRE
+>PROKKA_00435
+METASPPTQPERAPQDGDDAPGPRVIGLVADPGTPWALVRRIAGDVEDRLDERLPQPGGW
+RVETRQESLPVGATGGMVLEEPVRSLADGRGWDTVVAVVDLPRFDDRRGVVADVVPQLRV
+GVVCVPALGVITPARRLRETVLRIVEHIDTAPHVDPPDGELDVQSSDESGEVEEDGGPSP
+ADEPPEPDTDALRGIAPLGDVDADVTTTTRMGGGSRRTSTVYVKGWAGTLRLLAGMVMAN
+RPLLMPRDMTFTIASASAAGAYGVFFGSIWVLSSVMSPVRLAAVSVLSVVLLVAWLVTTN
+GLWTHGATHRHSSRLDNLSTVLTVGLACTVVYVLLFVTLLLVALMIIPVEYLEEELDQPG
+GVGDYVRLVWLAASMGTMAGAVGSSLDDSDRIRNATYSLRERHRRSERHEGDGAAEGPTA
+EETMSRE
+>PROKKA_02256
+MSSASPPFRSASDPSAQDPSASDPRVAADGREEDPHAPADGRPPRVVGLVAGPGYPWVLV
+RRIARDFEQRLQERMPAPHGWRVETRQESLPVGADGGMVLEEPVRALADEHGWDTVIAVV
+DLPRFEDGRGVVADVVPQLRLGVVCVPALGLITPARRLRETVLRVVDHLDTVPEVDPPDG
+ELDVQSSDRSAEVEEDGAADTEELRALTPLGGTEAGVSTTTGMGGGRREASTVYVKGRTG
+TLRLLAGMVKANRPLRMPRDMTFTIASASAAGAYGVFFGSIWVLSSVMSPWRLAAVTVLS
+IVLLVAWLIATNGLWTRGTRHRHSSRLDNLSTVITVGLACTLVYAVLFATLFLVAVMIIP
+VDYLGGELERASDLSDYANLVWLAASMGTMAGAVGSSLDDSERIRNATYSLREWHRRRGW
+DEAREAADEPAAASRE
+>PROKKA_00668
+METASPPTPPEHAQQDGDDAPGPRVIGLVADPGTPWALVRRIAGDVEDRLDERLPQPGGW
+RVETRQESLPVGATGGMVLEEPVRSLADGQGWDTVVAVVDLPRFDDRRGVVADVVPQLRV
+GVVCVPALGVITPARRLRETVLRIVEHIDTAPHVDPPDGELDVQSSDESGEVEEDGGPSP
+ADEPPEPDTDALRGIASLVDVDADVTTTTRMGGGSRRTSTVYVKGWAGTLRLLAGMVMAN
+RPLLMPRDMTFTIASASAAGAYGVFFGSIWVLSSVMSPVRLAAVSVLSVVLLVAWLVTTN
+GLWTHGATHRHSSRLDNLSTVLTVGLACTVVYVLLFVTLLLVALMIIPVEYLEEELDQPG
+GVGDYVRLVWLAASMGTMAGAVGSSLDDSDRIRNATYSLRERHRRSERHEGDGAAEGPTA
+EETMCRE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001838.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001838.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c5bb6c0f223183fbf47678d230a9d08d822cd9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001838.fa
@@ -0,0 +1,21 @@
+>PROKKA_00846
+MNHEANLTAWWSSGLLLLGAAGFTTVGLVRRALGADRRRSLLAWLTPAALLAAMSLDEST
+QIHEQAGQLWEVLPFAGENPLPAFQWLILGAPAAIVVLGLLALCTVALPRRTRALTVAGG
+AVFFFGAIVLEAVPLVFGIGRSTLAYHVATHAEELTEMIGASVLVVAPWAHLHLRPAPGH
+LQVTADGVPDAGADDVVLGAGPGPAARLDDCD
+>PROKKA_00568
+MSLDESTQLHEQAGRLWEALPFAGENPLPAFQWLILGAPAAIVVLGLLALCTVALPRRTR
+ALTVAGGAVFFVGAIVLEAVPLVFGIGRSTLAYHVATHAEELTEMIGASVLVVAPWAHLH
+LRPAPGHLQVTADGVPDADADDVVLGAGPRPAARLDDCD
+>PROKKA_02089
+MVSMKRSTEQSDVPAPLADPGSGAGSVTASGAVRPAEADPAAGQPVQGRWARRVALTLIG
+VSVALAAWSFAIPFLFGLGVRELPWWRQFFDLNHETNLTAWWSSGLLLLGAIGFAVVGLV
+RRSLRADRPLALLAWLTPSALLAAMSLDEFTQIHERLGEVWDALPFTPENPLHAFQGLIL
+GVPIALAVIALLALTAMMLPRRTRALTVTGIVVFFVGAIGLEAVPLVFNIARASWAYHAV
+THLEELTEMIGSSLLIVAPWVHLHLRRAPGSLLVTTDGLPAAAEHDDAAPAGR
+>PROKKA_00805
+MSRPPEPRPAPAPTARAAAARPATPPGVQGRWARRAAGGLIGVSVLLAAWSFALPFVFGL
+GPRQVPWWREVFDVNHEANLTAWWSSGLLLLGAAGFTTVGLVRRALGADRRRSLLAWLTP
+AALLAAMSLDESTQLHEQAGRLWEALPFAGENPLPAFQWLILGAPAAIVVLGLLALCTVA
+LPRRTRALTVAGGAVFFVGAIVLEAVPLVFGIGRSTLAYHVATHAEELTEMIGASVLVVA
+PWAHLHLRPAPGHLQVTADGVPDADADDVVLGAGPRPAARLDDCD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001839.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001839.fa
new file mode 100644
index 0000000000000000000000000000000000000000..03546d94644ba6fcc169a997ec2baf2b2c5f2f98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001839.fa
@@ -0,0 +1,48 @@
+>PROKKA_00858
+MRARETMAHVPHTDQNAPDLGVDTAVRRVREHLAALELPFETVTAGQDRAERERTLHQID
+DYVLPRLDSLDAPLLAVVGGSTGAGKSTLVNALVGHEVSRSSALRPTTRQPLLLHNPADA
+HWFTGPRVLPDLARVSVHRDAAAGPVEPDQSAMDTVALVAEPALPSGIALVDAPDIDSVA
+DQNRALARQLLEAADLWIFTTTAHRYADAVPWQLLDEAAARDITVAVVLGRVPEGAAEDI
+TPDLRRMLTERGLADARIHVIPETRFDERGLLPQEHVAGLRAWLETLAADAQARGAVARR
+TVDGVLGQLAARVADLARAEEEQRHAADLLARIVGDSTDQAVGRVREATSDGTLLRGEVL
+SRWQDFVGTGEFFRGVETTIGRLRDRLGALVRGRPAPPEEVETALETGLHAVMVEAAAAA
+AEQIERRWASEPAGRALVAGRDLGALAPDTSARAADVVRDWQSDVLALVQEEGAGKRTRA
+RLAATGVNGAAVALMIISFASTGGLAGIEVGIAGGAAVVGQKLLESIFGEDAVRRMARRA
+DELLEHRVRAFLETVLADRFLPLLHLEREPQATEELRALVPVLRRGVAAGVDGPTGPEHV
+PSAAEAGEEPR
+>PROKKA_00580
+MAHVPHTDQNAPDLGVDTAVRRVREHLAALELPFETVTAGQDRAERERTLHQIDDYVLPR
+LDSLDAPLLAVVGGSTGAGKSTLVNALVGHEVSRSSALRPTTRQPLLLHNPADTHWFTGP
+RVLPDLARVSVHRDAAAGPVEPDQSAMDTVALVAEPALPSGIALVDAPDIDSVADQNRAL
+ARQLLEAADLWIFTTTAHRYADAVPWQLLDEAADRDITVAVVLGRVPEGAAEDITPDLRR
+MLTERGLADARIHVIPETRFDERGLLPQEHVAGLRAWLETLAADAQARGAVARRTVDGVL
+GQLAARVADLARAEEEQRHAADLLARIVGDSTDQAVGRVREATSDGTLLRGEVLSRWQDF
+VGTGEFFRGVETTIGRLRDRLGALVRGRPAPPEEVETALETGLHAVMVEAAAAAAEQIER
+RWASEPAGRALVAGRDLGALTPDASARAADVVRDWQSDVLALIQEEGAGKRTRARLAATG
+VNGAAVALMIISFASTGGLAGIEVGIAGGAAVVGQKLLESIFGEDAVRRMARRADELLEL
+RVRAFLETVLADRFLPLLHLEREPQATEELRALVPVLRRGVAAGVDGPTEPEHAPSAAEA
+GEESR
+>PROKKA_01971
+MESTDLTSPSAAAPIGVDTAVRRVRAHLDALELPFATATVGADRAEAERTRHQIDDYVLP
+RLDSLDAPLLAVVGGSTGAGKSTLVNALVGHEVSRSSALRPTTRQPLLLHHPDDAHWFTG
+SRVLPDLARVTVHRSASAGPVEPDSQAMDTVALVAEPSLPQGIAIVDAPDIDSVADQNRA
+LARQLLEAADLWIFTTTAHRYADAVPWELLDQAAARDITVAVVLGRVPQGAGEAIAPDLR
+RMLVEHGLPEAPIHVIPETRFGEDGLLPAEHVADLRAWLTSLAEDAQARSAVARRTVDGV
+LTQLAVRVEALAEAEHGQQETAARLAGIVADSTELALETVHRATSDGTLLRGEVLARWQD
+FVGTGEFFRGLESAVGRVRDRLGALVRGRPAPPEEVEDALETGLHAVLVEAVASAVEQVE
+RRWRSEPAGRALVEGRDLGSLPAGTSERAATLVREWQGDVLALIQEEGAGRRTRARLAAF
+GVNGAAVALMVISFASTAGLSGIELGIAGGAAAVGQKLLESIFGEDAVRRMARRASELLD
+ERVRVLLEDVVGGRFLPLLRLERDAEDTAALRALVPTLRRGVAAGVDGPQPDAAPDAPRR
+EAADAAIEEDAR
+>PROKKA_00817
+MRARETMAHVPHTDQNAPDLGVDTAVRRVREHLAALELPFETVTAGQDRAERERTLHQID
+DYVLPRLDSLDAPLLAVVGGSTGAGKSTLVNALVGHEVSRSSALRPTTRQPLLLHNPADA
+HWFTGPRVLPDLARVSVHRDAAAGPVEPDQSAMDTVALVAEPALPSGIALVDAPDIDSVA
+DQNRALARQLLEAADLWIFTTTAHRYADAVPWQLLDEAAARDITVAVVLGRVPEGAAEDI
+TPDLRRMLTERGLADARIHVIPETRFDERGLLPQEHVAGLRAWLETLAADAQARGAVARR
+TVDGVLGQLAARVADLARAEEEQRHAADLLARIVGDSTDQAVGRVREATSDGTLLRGEVL
+SRWQDFVGTGEFFRGVETTIGRLRDRLGALVRGRPAPPEEVESALETGLHAVMVEAAAAA
+AEQIERRWASEPAGRALVAGRDLGALTPDTSARAADVVRDWQTDVLALIQEEGAGKRTRA
+RLAATGVNGAAVALMIISFASTGGLAGIEVGIAGGAAVVGQKLLESIFGEDAVRRMARRA
+DELLERRVRAFLETVLADRFLPLLHLEREPQATEELRALVPVLRRGVAAGVDGPTGPEHA
+PSAAEAGEEPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001840.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001840.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb090cb4c2dcafa1229fd42ebc84c619f5050557
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001840.fa
@@ -0,0 +1,52 @@
+>PROKKA_00946
+MSTPAVTRPGRPRARFALSRRWRRPVVAGLLIAVSLVLAPEQLAHGTGHLVAAGLMLAAA
+VVAGLPIARDAIAALRVKTVGIDLLVATAAIGASLLGNFWEAAAVTFLFALGHALEDATL
+SQTRSALADLVSTAPETAVVVDADGTQRTVPAHEVAPGATVLVKAGARVPVDGVVLTGVG
+AVDEASITGESIPAEKTDGDAMYAGTVATAGLLQVQARGVGADTTLARIIHRVEAAQEAR
+ARTQQFMDRFSRWYTPAIMVLAFATGLITRDVPLALTLLVIGCPGALVISIPVAIVAGIG
+RGAKDGVLIKGGEFLERSAKVDAVAVDKTGTLTSGTPELTDVVAFEPGAEDEVLRWAARL
+EAASDHPLAAPIVAAGRDRGLLDGPLATDVDVVLGRGLTGEVDGRVVAVGNVAMLRERGV
+DPAATDRVETVAAELAEAGRTPAAVVVDGIPLGVLAIADTLRPEAAGMIRALHGIGVREV
+VMLTGDHPGVAQAVARQVGVDDVRAGLLPQDKLEAIEALQAEGRVVAMVGDGVNDAPALA
+TADIGVAMGAAGSGVAIETADIALMGDRLERLPQALDLARRTVRVMRQNIAISLVTVVAL
+LAGVFAGGVTMAVGMLVHEASVLLVIVNAMRLLRRPGQPRSTTSNSSRSAPVATGAGRPP
+CSAA
+>PROKKA_00665
+MSTLAVTRPGRTRARFTLSRRWRRPVVAGLLIAVSLVLAPEQLAHGTGHLVAAGLMLAAA
+VVAGLPIARDAIAALRVKTVGIDLLVATAAIGASLLGNFWEAAAVTFLFALGHALEDATL
+SQTRSALADLVSTAPETAVVVDADGTQRTVPAHEVAPGATVLVKAGARVPVDGVVLTGVG
+AVDEASITGESIPAEKTDGDAVYAGTVATAGLLQVEARGVGADTTLARIIHRVEAAQEAR
+ARTQRFMDRFSRWYTPAIMVLAFATGLITRDVPLALTLLVIGCPGALVISIPVAIVAGIG
+RGAKDGVLIKGGEFLERSAKVDAVAVDKTGTLTSGTPELTDVVAFEPGAEDEVLRWAARL
+EAASDHPLAAPVVAAGRDRGLLDGPLATDVDVVLGRGLTGEVDGRVVAVGNVAMLRERGV
+DPAATDRVETVAAELAEAGRTPAAVVVDGIPLGVLAIADTLRPEAAGMIRALHGIGVREV
+VMLTGDQPGVAQAVARQVGVDHVRAGLLPQDKLEAIEALQAEGRVVAMVGDGVNDAPALA
+TADIGVAMGAAGSGVAIETADIALMGDRLERLPQALDLARRTVRVMRQNIAISLVTVVAL
+LAGVFAGGVTMAVGMLVHEASVLLVIVNAMRLLRRPGQPRSTTSNSSRSAPVATGAGRPP
+CSAA
+>PROKKA_01109
+MVTLAVAAVLLVAGLVVEWTIHSEPVALALFWGAILIGGVYPLRSAIRAVRHKRLTITVL
+LVVAAIGAIALGVIEEAAMLVVIFSLGEAMEAYATDKARGSISALMELAPPTANRLNDDG
+ATKTVAVEELHPGDVVLVRPGERLPTDGAVIDGASWVDASPVTGESVPVEATAGTEVFGG
+SLNGNGVLRIEVTKEYYDTVLARVIEQVEEAQANRSGAERFADKFGAVYTPAMFALAIAV
+ALVLPLLGFEWREAIYRALVVLVVSCSCALIISVPVSVVTAIARGARDGILIKGGIYLER
+LADIKAVAFDKTGTLTRGRPTLAQVTPLDGISEDEALTLAAAVETGSEHPIATAIVAGAR
+DRGLTIPAVQDARALPGAGMEATLDGRTLHIGRPTDEDRTDGTAGPALAHAEAEGCTAVV
+LRDDTRPLAVVAVADQLRPDAESTLTELRDLGVERVLMLTGDNATVARSTAQALGLDDYR
+AELLPEDKSAAIRELREKHGVIAMVGDGVNDAPALANADLAIAMGAASTDVALETADVAL
+MADELDRLPAAIRLSRRARNNIKINIALSLTVVAILIVAALAGWMSLTTGLLLNEGSAAL
+IILNGLRMLRPGRGETRRAQVDFGTRQGSDLNSGRPCAPGSTTDGHSVAAGSSYDQREHG
+R
+>PROKKA_01991
+MSTAETTRTGERRGRTGPRLPHRWRRPALAGLLIVLSLILAPEQVAQGTAHPVAAALMLA
+AAVVAGAGIVRSAVAALRVKTIGIDLLVATAAIGATLLGNFWEAAAVTFLFALGHALEDA
+TLAKTRSALGDLVATAPETAVVLEADGTQRTVAAHEVPAGATVLVKAGARVPVDGVVLTG
+TGAVDEASITGESLPAEKSDGDDVYAGTVATAGLLHVQARGVGADTTLARIIHRVEEAQE
+ARARTQQFMDRFSRWYTPAIMVLALVTGLITRDVPLALTLLVIGCPGALVISIPVAIVAG
+IGRGAKDGVLIKGGEFLERSAKVDAVAVDKTGTLTSGTPELTDVVALEDGREDEVLGWAA
+RLEAASDHPLAAPIVAAGRDRGLLSGAMATDVDVVLGRGLTGTVEGRTVAVGNVALLRES
+GADADRTARVEAVAAELAAAGRTPMAVAVDDVPVGVLAVADTVRPEAAGMIRELHRIGVR
+EVVMLTGDQPGVAHAVARQVGVDRVRAGLLPEDKLDAITAMQAEGRVVAMVGDGVNDAPA
+LASADIGVAMGAAGSGVAIETADIALMGDRLELLPQALGLAQRTVGVMRQNIAVSLVTVA
+ALLAGVFAGGVTMSIGMLVHEASVLLVIANAMRLLRPAAGSGRGGSRAAQSRSTTSNSSS
+SAPVATGAGRPSDSAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001847.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001847.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3fa2bcf898829bebbf9167f6b41c0c5485ca59f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001847.fa
@@ -0,0 +1,12 @@
+>PROKKA_01067
+MNEKQLEPDLSLRAQRRKPTPAPQTQAPGAVIPAEPATTSDPAGGYAPLARRGAPTVALN
+VRVPEAIRDAVRREAATNPATPSQAAVIEALGHV
+>PROKKA_00786
+MNEKQLEPDLSLRAQRRKPTPAPQTPAPGAVIPAEPATTSDPAGGYAPLARRGAPTVALN
+VRVPEAIRDAVRREAATNPATPSQAAVIEALGRV
+>PROKKA_02229
+MNEKQLEPDLSLRAQRRKPTPAPHTPAPGAVIPVEPATASDPAGGYAPLARRGAPTVALN
+VRVPEAIRDAVRREAATNPATPSQAAVIEALVRAHLMN
+>PROKKA_01014
+MNEKQLEPDLSLRAQRRKPTPAPQTPAPGAVIPAEPATTSDPAGGYAPLARRGAPTVALN
+VRVPEAIRDAVRREAATNPATPSQAAVIEALGHV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001848.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001848.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2df4995dcc3bcfa8b8171b346449fa617512ab1a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001848.fa
@@ -0,0 +1,28 @@
+>PROKKA_01076
+MHGPLIVMLVTTALIVLSAIFVIMEFSLLGARRHRLEAEAGRSRAARAALKGVDELTLML
+AAAQLGITLCTFALGAITKPAVDAWLGPVLEDWGIPAAAAGTASFVLSLLAVTFLHLVIG
+EMAPKSWAIAHPETAAKAVAVPARAFVWTVRPLLLLANRLANRLVTLSGVTPVDQAAVGG
+YDAAAIRQLVEHSAAAGTLDRQNHEALAGALDLQTLTLGDLLPQGQHPVKVAPDADVEAV
+QNAAACSGHLRILVQPDHTPESVPGVVHVRDTLTMEPSAPIQPLIQQALTLPSTTPLHEA
+LASMRRNSRQLAAVTQDNRFTGVVTLTDVLRGVLPRAA
+>PROKKA_00795
+MHGPLIVMLVTTALIVLSAIFVIMEFSLLGARRHRLEAEAGRSRAARAALKGVDELTLML
+AAAQLGITLCTFALGAITKPAVDAWLGPVLEDWGIPAAAAGTASFVLSLLAVTFLHLVIG
+EMAPKSWAIAHPETAAKAVAVPARAFVWTVRPLLLLANRLANRLVTLSGVTPVDQAAVGG
+YDAAAIRQLVEHSAAAGTLDRQNHEALAGALDLQTLTLGDLLPQGQHPVKVAPDADVEAV
+QNAAACSGHLRILVQPDHTPESVPGVVHVRDTLTMEPSAPIQPLIQQALTLPSTTPLHEA
+LASMRRNSRQLAAVTQDNRFTGVVTLTDVLRGVLPRAA
+>PROKKA_02322
+MTQSPVFVILATIALIALSALFVIMEFSLLAARRHRLEAEAGTSRAARAALRSVDELTIM
+LAGAQLGITLATFALGAITKPAVDAWLGPVLTGWGLPAAVAGTASFFLSLLLVTFLHLVV
+GEMAPKSWAIAHPEFAAKAVAGPARAYVWAVRPLLAFANAVANRLVAASGVTPTDRAAVG
+GHDADSIRQLVEHSASSGALDEQAHGQISGALDLQDATVGDLVSPPRDLVTVPADATAED
+VQAASVASGHLRILVRPADGPDDGVPGVVHVRDTMVLGPREPVAPLVQEALTLPVDTALH
+EASSAMRAAGRQLAVVTSEGRTVGVVTLTDLFRRVLPVSG
+>PROKKA_01025
+MHGPLIVMLVTTALIVLSAIFVIMEFSLLGARRHRLEAEAGRSRAARAALKGVDELTLML
+AAAQLGITLCTFALGAITKPAVDAWLGPVLEDWGIPAAAAGTASFVLSLLAVTFLHLVIG
+EMAPKSWAIAHPETAAKAVAVPARAFVWTVRPLLLLANRLANRLVTLSGVTPVDQAAVGG
+YDAAAIRQLVEHSAAAGTLDRQNHEALAGALDLQTLTLGDLLPQGQHPVKVAPDADVEAV
+QNAAACSGHLRILVQPDHTPESVPGVVHVRDTLTMEPSAPIQPLIQQALTLPSTTPLHEA
+LASMRRNSRQLAAVTQDNRFTGVVTLTDVLRGVLPRAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001849.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001849.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1eab37eaba03f832f59dbc2c4c0651daaa96058f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001849.fa
@@ -0,0 +1,36 @@
+>PROKKA_01077
+MDPVLTLILGSLIILAIIAANGFFVAQEFAYMSVDRVRLQTAAKAGDRAAARALQVTRRT
+SFMLSGAQLGITVTGLMVGYVAEPMVGAALTELLGGTALPSEVVIAISTLGVLVVATLVQ
+MIIGELYPKNLAIANPEPLARALARPTQIYLGLFGWLIWVFDKAAEVLLKLLRIEPVHDV
+DSTASAEDLDRIALDSRASGSLPAEVSVLIDRVLDFPDQDVQHAMVPRSRVDEVQPQTSL
+AQVRDLMATGHTRYPVISNEHEPLGVVHLTDLLGETRMAPDTPVSALMRPALVLPTMMSL
+PDAARELDGSGQQMACIVDEFGGFVGVLTVEDLAEELVGELTDEHDLHPQEEITATGLHS
+WVLSAEAHLDELERLVGHPLPVTEAESAAGLTIDALGRLPREGEVITIDLPEDPRDFGAE
+EVYDRHLQVEVLSIQRRVPARLRIHLIEVPRSDTAGSHAAHEAQPDATTDEER
+>PROKKA_00796
+MDPVLTLILGSLIILAIIAANGFFVAQEFAYMSVDRVRLQTAAKAGDRAAARALQVTRRT
+SFMLSGAQLGITVTGLMVGYVAEPMVGAALTELLGGTALPSEVVIAISTLGVLVVATLVQ
+MIIGELYPKNLAIANPEPLARALARPTQIYLGLFGWLIWVFDKAAEVLLKLLRIEPVHDV
+DSTASAEDLDRIALDSRASGSLPAEVSVLIDRVLDFPDQDVQHAMVPRSRVDEVQPQTSL
+AQVRDLMATGHTRYPVISNEHEPLGVVHLTDLLGETRMAPDTPVSALMRPALVLPTMMSL
+PDAARELDGSGQQMACIVDEFGGFVGVLTVEDLAEELVGELTDEHDLHPQEEITATGLHS
+WVLSAEAHLDELERLVGHPLPVTEAESAAGLTIDALGRLPREGEVITIDLPEDPRDFGAE
+EVYDRHLQVEVLSIQRRVPARLRIHLIEVPRSDTAGSHAAHEAQPDATTDEER
+>PROKKA_02323
+MDPILLLILGTVVILVIILANGFFVAQEFAYMSVDRVRLAAAAENGDEAARRALAVTRRT
+SFMLSGAQLGITVTGLLVGYVAEPMVGEALTQLLGGTAIPASVVIAVSTVGVLLVATVVQ
+MIVGELYPKNLAIANPDPLARALARPTQVYLALFGWLIWVFDKSAEALLRLLRIEPVHDV
+DSTATAQDLDRIVEDSRDSGTLPAELSVLLDRILDFPERDAEHAMVPRSQTDEVGPETTV
+AEVRALMAAAHTRYPVISADHQPLGVVHLQDVLALGHAPAPDLLVTDVMRPATVVPTVMP
+LPDVTRALDDADDQLACVIDEHGGFVGVLTLEDLAEELVGDLRDEHDDEAHEEIVPVVVG
+ESWALRGDVHLDELERAIGHPLPEGEAETVSGLLIESLGRLPEEGERVAVDLPEDTRDYG
+GDVLYDRRLEVDVRRVERHVPADVEVHLVETPREDETEEDPR
+>PROKKA_01026
+MDPVLTLILGSLIILAIIAANGFFVAQEFAYMSVDRVRLQTAAKAGDRAAARALQVTRRT
+SFMLSGAQLGITVTGLMVGYVAEPMVGAALTELLGGTALPSEVVIAISTLGVLVVATLVQ
+MIIGELYPKNLAIANPEPLARALARPTQIYLGLFGWLIWVFDKAAEVLLKLLRIEPVHDV
+DSTASAEDLDRIALDSRASGSLPAEVSVLIDRVLDFPDQDVQHAMVPRSRVDEVQPQTSL
+AQVRDLMATGHTRYPVISNEHEPLGVVHLTDLLGETRMAPDTPVSALMRPALVLPTMMSL
+PDAARELDGSGQQMACIVDEFGGFVGVLTVEDLAEELVGELTDEHDLHPQEEITATGLHS
+WVLSAEAHLDELERLVGHPLPVTEAESAAGLTIDALGRLPREGEVITIDLPEDPRDFGAE
+EVYDRHLQVEVLSIQRRVPARLRIHLIEVPRSDTAGSHAAHEAQPDATTDEER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001850.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001850.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0695492a609a723ad9f41a1371b6fbe1c98afd3e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001850.fa
@@ -0,0 +1,26 @@
+>PROKKA_01111
+MKEAGLWIGFYVALALVFAGLLFALGDAQHGTEFLAGWVTEYSLSVDNLFVFLIIMAKFQ
+VPRRYQQEVLMVGIIIALIARAVFIAVGAVAIEHLTWEFYIFGAFLLWTAWQQLKDDGGD
+EESEPGVVARLTRRLNVAPDYDGNRLRTTVDGRRMFTPMVVVFITIGLTDVMFAVDSIPA
+IFGLTQNWFIVLTANIFALMGLRQRARRRPAPPAAGRGVVVRPGRLTGDVGEYPEHCGRQ
+HAAAAESAPPAGHRGPGRGRGGRRDLRHRPDP
+>PROKKA_00830
+MKEAGLWIGFYVALALVFAGLLFTLGDAQHGTEFLAGWVTEYSLSVDDLFVFLIIMATFQ
+VPRRYQQEVLMVGIIIALIARAVFIAVGAVAIEHLTWEFYIFGAFLLWTAWQQLKDDGGD
+EESEPGVVARLTRRLNVAPDYDGNRLRTTVDGRRMFTPMVVVFITIGLTDVMFAVDSIPA
+IFGLTQNWFIVLTANIFALMGLRQRARRRPAPPAAGRGVVVRPGRLTGDVGEYPEHCGRQ
+HAAAAESAPPAGHRGPGRGRGGRRDLRHRPDP
+>PROKKA_01674
+MDVLTPAFEITTLVVLGVILLFDLLYVLKRPHEPSMKEAGLWIGFYVTLALIFAGLLYVL
+GDAQHGTEFLAGWVTEYSLSVDNLFVFLIIMAKFQVPRRYQQEVLMVGIIIALVARAIFI
+AIGAVAIEHLTWVFYIFGVFLLWTAWHQLQDDDDGEEAEPGIVGRLTRRLNVAEDFDGNK
+LRTTVDGKRMFTPMVVVFITIGLTDVMFAVDSIPAIFGLTQNWFIVLTANIFALMGLRQL
+YFLLGGLMDRLVYLKHGLAFILAFIGVKLILHALHENELPFINGGNPVPVPEISTFLSLA
+VILGTLVVATVASLVWGKAADEGDARRAESATRMKQVSDAARRDGR
+>PROKKA_01061
+MALALVFAGLLFALGDAQHGTEFLAGWVTEYSLSVDDLFVFLIIMATFQVPRRYQQEVLM
+VGIIITLIARAVFIAVGAVAIEHLTWVFYIFGAFLLWTAWQQLKDDGEDEESEPGVVARL
+TRRLNVAPDYDGNRLRTTVDGRRMFTPMVVVFITIGLTDVMFAVDSIPAIFGLTQNWFIV
+LTANIFALMGLRQLYFLLGGLMDRLVFLKHGLAFILAFIGVKLVFHALHENELPFINGGH
+PVTAVPEISTFVSLGVIVGTLVLATVASLTRGPHQRARRRPAPPAAGRGVVVRPGRLTGD
+VGEYPEHCGRQHAAAAESAPPAGHRGPGRGRGGRRDLRHRPDP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001852.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001852.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4819fada34a9d667d8180819054b18960d605b5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001852.fa
@@ -0,0 +1,13 @@
+>PROKKA_01145
+MIGAVPGEPGMDLLGALASGRLDPAAGASTARSPHAAVDGPERPVCSRRGCTAEAAWALE
+WNNPRVHAPDRVKTWLACTDHRPFLDDFLSARGFLRRSRPLDPAATQAPEVDTPETPQEP
+PRP
+>PROKKA_00864
+MDLLGALASGRLDPAAGASAARSPHAAADGPERPVCSRRGCTAEATWALEWNNPRVHAPD
+RVKTWLACADHRPFLDDFLSARGFLRRSRPLDPPATEAPEVETPETPQEPPRP
+>PROKKA_01641
+MTGPDLLGALAAGLDPSLPAVRREPSAEGPAAVTADGAPVCSARGCRAAAAWVLEWNNPR
+VHAPDRVKTWAACPDHREHLSDFLASRGFLRRTRPLHAAAGPAATDPTTPGEPRR
+>PROKKA_01095
+MDLLGALASGRLDPAAGASAARSPHAAADGPERPVCSRRGCTAEATWALEWNNPRVHAPD
+RVKTWLACADHRPFLDDFLSARGFLRRSRPLDPPATEAPEVETPETPQEPPRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001857.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001857.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7871d9a04059a7fefe3ceab01494c153b1dfa172
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001857.fa
@@ -0,0 +1,34 @@
+>PROKKA_01253
+MTGDHQHARREDHWDDLLDDEADVHDDLDVFGFAHEEADEADVGAPSQPVGAAGPRRPRT
+FLRRRGTGSHPASRVDRGAGRRRTALVLGTVLVAFAVVVGLIVRGFLSGPDHTAVEGDEV
+TFSVEPGEDLGSVAARLDRAGIVGSARAFERAARDTGSGLVRSGDFVLRERMPAAEALAV
+LQGATDGAVHYVLVERGRRLTEVLDAVAEATGLPREELEAAAQDPTRYGVPGEAGTLEGW
+LDAGEYRLPVDATAGQVLDALVRPTLAELEALDVRDPAEQQRVLTIASILEAEALPQDYQ
+QVAGAIENRLAPDNTETHGLLQIDATVTYGLGVRSLSFTSGQRQDASNPYNTYVHPGLPP
+GPIGMPSDAAVEAALDPAETDAYYWVTTDIGTGHTEFSRTYEEHQQHVRTLQRYCASNPG
+VC
+>PROKKA_00972
+MTGDHQHARREDHWDDLLGDEADVHDDLDVFGFAHGEADEADLGVPSQPVDAAGPCRPRT
+FLRRRGSGSHPAPRVDRGAGRRRTALVLGTVLVAFAVVVGLIVRGFLGGPDHTAVEGDEV
+TFSVEPGEDLGSVAARLDRAGIVASARAFERAARDTGSGLVRSGDFVLRERMPAAEALAV
+LQGAADGAVHYVLVERGRRLTEVLDAVAEATGLPREELEAAAHDPTRYGVPGEAGTLEGW
+LDAGEYRLPVDATAEQVLDSLIRPTLAELDALDVRDPAEQQRLLTIASILEAEALPQDYR
+QVAGAIENRLAPDNTETRGLLQIDATVTYGLGVRSLSFTSGQRQDASNPYNTYVHPGLPP
+GPIGMPSDAAVEAALDPAETDAYYWVTTDIGTGHTEFSRTYEEHQQHVRTLQRYCASNPG
+VC
+>PROKKA_01635
+MNRPPEHDWDDLPGDEADPDDDLDVFGFVHEDADDDPDEARRLGAPAAAAGGRRRGLLRR
+RGTGSHPAAPGRSRRGSRLRGGIALGAAALAFLAVVVLVVQGFLGGADHDGIEGEELTFS
+VEPGEDLASVARRLDSAGVVASARAFERAAEDSASGVVRAGDFVMRERMPAADALAVLQG
+TADGAVHYVLVERGRRLTEVLDALAESTGLPREELAAATQDPARYGVPAEAQTLEGWLDP
+GEYRLPVEASAEEVVDALVRPVLADLAELGVDDPDEQRRVLTVASLLEAEALPRDYRTVA
+GVIENRLAPDNTETRGLLQIDAAVTYGLGVRSLSFSAGQRQDASNPYNTYVHPGLPPGPI
+GMPSDAAVAAALDPADTDAYYWVTTDIATGHTEFSRTYEEHQEHVRTLQRYCASNPGVC
+>PROKKA_01532
+MSAPPPPPWREDETDDDLDVFGLVDHGEDEPEPEPERVERQPAPPRPVGRARRPRVRTGG
+SHRLRAIGRNLAVERPRGAVVLAVAALAVVLVAALLVVLFSRPADRQAVSGDRVTFTVEP
+GEDLASVAARLDERGIVASDRAVLDAAEDSGQTSIGAGEYVLREQMPAADALAVLQGRAE
+GASHYVVVGRGRWLSEVLDGLAQSTGLPRADFEAAAEDPTRYGVPEQAPSLEGWLDPGEY
+YPPVGADAEQVLAELVKPRLAHLRAQGVTDPAEQQRIVTIASILEAEALPKDYPRVAGVI
+DNRLNDPDAETRGLLQVDSTVNYGLGRRNLQFSAAQRADESNTYNTYQHTGLPPGPIGMP
+SDAAIEGAVHPEPSEDLYWVTTDIATGHTEFSRTYEEHSVHQEEFRRYCAQNPGVC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001858.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001858.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff28c714f5f2aa6c10cb029d4ca322597f805858
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001858.fa
@@ -0,0 +1,12 @@
+>PROKKA_01290
+MTTETAADETGTDAGAHRHGYISDKDRYRNRMKRIEGQARGITKMIDDEKYCIDILTQVS
+ALTRALQGVATGLLDDHLKHCVLDAAKKGDEDAAIAKIQEATDAINRLVRS
+>PROKKA_01009
+MTTETAADETGTDAGAHRHGYISDKDRYRNRMKRIEGQARGITKMIDDEKYCIDILTQVS
+ALTRALQGVATGLLDDHLKHCVLDAAKKGDEDAAIAKIQEATDAINRLVRS
+>PROKKA_00710
+MSVDNDSHQHGYISDKERYLGRMKRIEGQARGIAKMIDEEKYCIDILTQVSALTRALQGV
+ATGLLDDHLKHCVLDAAKLSDEAAVEKIQEATDAINRLVRS
+>PROKKA_01248
+MTTETAADETGADTGAHRHGYISDKDRYRNRMKRIEGQARGITKMIDDEKYCIDILTQVS
+ALTRALQGVATGLLDDHLKHCVLDAAKKGDEDAAIAKIQEATDAINRLVRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001859.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001859.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5df5884df7d270b01e5faf124a4168d647797f98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001859.fa
@@ -0,0 +1,37 @@
+>PROKKA_01306
+MAELRLTGPTEDGDALRLSGPEGEEHTLPLSPYLRRLVIEGAAPEDGRPAEDGPAAWHDM
+TEMDVPGADDEDAEGPVDAATHADDAAAEDERAPEAPSGPARPDEDLALTPRIDPRPVAD
+DSTADGPTPAPLTDQESVKAAATQEAVPLTPREIQQRIRAGASVEQVARESGNAFSRIRT
+YGHPVLAERDWIARQARAVEVWVGGPDLYSDLVQDGGPTTLGELAAHRLAELGVDEASLE
+WDAWREDQAGWTVAARFAVAGARSLPTREEPPALWTFRPAGRHLEPENAWARALSEAEAW
+DLVPRAPAAEPVTDDVDAEDAVTPAGAHSPAADRDADLLEILRVRRGQRVGADLESDDAL
+AHLIAREHQDRSRREAAQAPERLAPVDAEGALTTADDAPVVDAPEPAAETDRAEDTAADV
+ADAGVEDEGAEPAPRERAARPAMPTVTPRPRARSAARRASVPSWDEIVFGRKGD
+>PROKKA_01029
+MAELRLTGPTEDGDALRLSGPEGEEHTLPLSPYLRRLVIEGAAPEDGRPAEDGPAAWHDM
+TEMDVPGADDEDAEGPVDAATHADDAAAEDERAPEAPSGPARPDEDLALTPRIDPRPVAD
+DSTADGPTPAPLTDQESVKAAATQEAVPLTPREIQQRIRAGASVEQVARESGNAFSRIRT
+YGHPVLAERDWIARQARAVEVWVGGPDLYSDLVQDGGPTTLGELAAHRLAELGVDEASLE
+WDAWREDQAGWTVAARFAVAGARSLPTREEPPALWTFRPAGRHLEPENAWARALSEAEAW
+DLVPRAPAAEPVTDDVDAEDAVTPAGAHSPAADRDADLLEILRVRRGQRVGADLESDDAL
+AHLIAREHQDRSRREAAQAPERLAPVDAEGALTTADDAPVVDAPEPAAETDRAEDTAADV
+ADAGVEDEGAEPAPRERAARPAMPTVTPRPRARSAARRASVPSWDEIVFGRKGD
+>PROKKA_01482
+MAELRLTGTTEDGHALRLAAPDGTEHTLERTPFLRRLALDDVARPDAVPAAEPADGAAPA
+SPAQADEPSAEAPAPEVPRPAPSPAQEPAAPVTAVAEQADVRAAATAEAQPLSPRDIQAR
+IRAGASVEQVARESGNAFSRVRTYGYPVLAERGYIAQQARAVQVWVGGPDLYSGTVADGG
+PTTLGALAEHRVRELGTDPASLEWDAWRESGGVAWTVVARFPLPPRGRALTAEEPPARWS
+FRPAGGRLDPENAWARILSDAEAWDVFTAEEPLTREDDAAAPQQGGGEEASGGDAPAAVT
+PLGASPSSVGVDADLLEILRARRGRRVGQDAESDDALAHLIARGVAEREARQDGAEADHT
+EQAETEPAAPGRAARLLRGLPSLREEVAKDGADGRPPVEADSPAAEAAPAVDAAGREDAV
+TPQAPGKTDAGKTVAGPSGADRTETGQAGTMQADAEPSDAPVAAPQEEEPARTARRERPA
+MPTPRPRARSAARRASVPSWDDIVFGKKSD
+>PROKKA_01264
+MAELRLTGPTEDGDALRLSGPEGEEHTLPLSPYLRRLVIEGAAPEDGRPAEDGPAAWHDM
+TEMDVPRADAEEPVDATTHADDAAEEGERAPDVPSGPARPDEDLALTPRIDPRPVADDST
+ADGPTPAPLTDQESVKAAATQEAVPLTPREIQQRIRAGASVEQVARESGNAFSRIRTYGH
+PVLAERDWIARQARAVEVWVGGPDLYSDLVQDGGPTTLGELAAHRLAELGVDEASLEWDA
+WREDQAGWTVAARFAVAGARSLPTREEPPALWTFRPAGRHLEPENAWARALSEAEAWDLV
+PRAPAAEPVTDDVDAEDAVTPAGAHSPAADRDADLLEILRVRRGQRVGADLESDDALAHL
+IAREHQDRSRREAAQAPERLAPVDAEGALTTADDAPVVDAPEPAAETDRAEDTAADVADA
+GVEDEGAEPAPRERAARPAMPTVTPRPRARSAARRASVPSWDEIVFGRKGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001860.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001860.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2bc4af6b00cd3ae5ebb7e07eb5b9243e0a977836
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001860.fa
@@ -0,0 +1,28 @@
+>PROKKA_01315
+MSVPVLLLAVVAVALAGPVPVLLGRAAWPARSPVLAALAWQAVALAGGLALLGAPLVWGL
+LPWGEGLVAAAPRLAAHLAGDAAAAPRPTGLPVGLHLMAVGAGAGIAVHLLLTTAVTAVR
+TLRARARHRDAVELVATGPADAGRWPGGARGARELPVDDPLAYCVPGSPRGGEALTVVSS
+GLLARLSPEELDAVVAHERAHLDQHHGLLRLAFAAWARACAWLPTAETARLAVVQVTEML
+ADDAALRRAPADVLVRALAQAAPGPDAGPAGQTDATGPTSAGLGDRAARLLTRPAPLPAA
+AAALVAAASLALPAATAAALLGLP
+>PROKKA_01577
+MSVPVLLLAVVAVALAGPVPVLLGRAAWPARSPVLAALAWQAVALAGGLALLGAPLVWGL
+LPWGEGLVAAAPRLAAHLAGDAAAAPRPTGLPVGLHLMAVGAGAGIAVHLLLTTAVTVVR
+TLRARARHRDAVELVATGPTDAGRWPGGARGARELPVDDPLAYCVPGSPRGGEALTVVSS
+GLLARLSPEELDAVVAHERAHLDQHHGLLRLAFAAWARACAWLPTAETARLAVVQVTEML
+ADDAALRRAPADVLVRALAQAAPGPDAGPAGQTDATGPTSAGLGDRAARLLTRPAPLPAA
+AAALVAAASLALPAATAAALLGLP
+>PROKKA_02666
+MTAGILTMALCTGLVALAVFGPWLLRHAAPALVRVPRLAIVVVAGGIGVWLVTLLAIGPV
+LAWAGAGPALLPERAAEVCQRCLTAANPFSADTTETLIPAVLLLALPVALALALGAGLAR
+QMVRRSSRSRDAARTLLHGARRQLLHGHEVALVDAEHPFALTFPDRHGGIVLSTGAVRAL
+GPGELAAVLAHEHAHLHQRHHLITALVDSIAAYLRWVPLIRAVADALPHYLEIAADDQAR
+RHAGTRALVSALVKLGERTHPAMPQHSCPVALHAAGPERIRHLVHPSAGLAGALPAVAIA
+AYLVGMAALAALVHLPYVSAALTGCTI
+>PROKKA_01473
+MSFSVLVLAAVALCLAGPVPVLLGRAAWPSRSPGLAVLAWQAVALAGGLALVGTPLLWGL
+HPWGDGLLDAVPALLADLTSPDSGIARPGSAPAEVHLLAVGAGLTVALHLLLTTAVTALR
+TLRARSRHRAALELIATDPERADDWPGGPRGARELPVDLPLAYCVPGVPGGGTPLTVVSR
+GLLERLSPEELRAVLLHERAHLAQHHGLLRLAFASWARACAWLPSAETARAGVVLVTEML
+ADDAARRTAPAPVLARALALTVRPAEAPGASASGPDAEPDAESGGLGRRVARLLDPPAPV
+PGAVAGAAAAACLALPLAVLAVILGPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001862.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001862.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fed052feecf5ac480b5a4b38c01fe0f61af9e194
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001862.fa
@@ -0,0 +1,17 @@
+>PROKKA_01382
+MSVTSEIARARSLIRVVPDHPSPGVAFQDITPLLADARALRECVEALVAPFEGRFDLVAG
+LEARGFLLAGAAAVLTGTGLVPLRKAGRLPAPAARADYTLEYGTASIEVSEDLRAGSRVL
+LLDDVLATGGTLAAGRRLIEARGAEVVGAACLLELRALGGRAVVPDTHVLFAA
+>PROKKA_01102
+MSVTSEIARARSLIRVVPDHPSPGVAFQDITPLLADARALRACVEALVAPFEGRFDLVAG
+LEARGFLLAGAAAVLTGTGLVPLRKAGRLPAPAARADYTLEYGNASIEVSEDLRAGSRVL
+LLDDVLATGGTLAAGRRLIEARGAEVVGAACLLELTALGGRAVVPDTHVLFAS
+>PROKKA_01893
+MSGVALSAAGRQAADVPGLERAATLFRSVPDFPTDGVVFQDITPVLADPAALRAVVEAMI
+APFEGAYDAVAGLDARGFLLAGFAAALTGTGVIPLRKAGKLPVSVAHVDYALEYGAASLE
+APPELAVPGVRVLILDDVLATGGTLAAARDLAERCGAEVAGSAVVLEVEGLGGRERCPDA
+LTLFSA
+>PROKKA_01337
+MSVTSEIARARSLIRVVPDHPSPGVAFQDITPLLADARALRECVEALVAPFEGRFDLVAG
+LEARGFLLAGAAAVLTGTGLVPLRKAGRLPAPAARADYTLEYGTASIEVSEDLRAGSRVL
+LLDDVLATGGTLAAGRRLIEARGAEVVGAACLLELRALGGRAVVPDTHVLFAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001863.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001863.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2b408fefab9996f5c94e80d0103c963c7c439ab3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001863.fa
@@ -0,0 +1,24 @@
+>PROKKA_01405
+MTEHTRDDVAPAPLVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHCLNEGV
+DLADAEAVAAAAVAMDLDQSTDPDVEAVRVGGTDVTEAIRGPEVTDTVSTVAVVIPVREE
+LHRRQRAAIAAAGRMVAEGRDITTVVAPDAHARVLLTASEAVRTARRSGQLAAAGETGVD
+AGTLHRQVAGRDARDATVSTFDRPADGVALVDSTELDFEQTVAAVLAAVEDQAGIPAVKG
+GRR
+>PROKKA_01135
+MTEHTRDDVAPAPLVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHCLHEGV
+DLADAEAVAAAAVAMDLDQSTDPDVEAVRVGGTDVTEAIRGPEVTDTVSTVAVVIPVREE
+LHRRQRAAIAAAGRMVAEGRDITTVVAPDAHARVLLTASEAVRTARRSGQLAAAGETGVD
+AGTLHRQVAGRDARDATVSTFDRPADGVALVDSTELDFEQTVAAVLAAVEDQAGIPAVKG
+GRR
+>PROKKA_01402
+MTEHTQHDDAARPALVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHVLDSG
+VDLADPDAIAGAARAMDLRQSTDPDVESVVVGGTDVTDAIREDRVTDVVSTVAVVIPVRE
+ELQRRQRAAIAGAGRIVAEGRDITTVVAPDAHARVLLTASAEARMARRSGQLQRAGAGER
+DAATLERQVSGRDARDSAVSTFDRPAEGVALVDSTELDFEQTVAAVLAAVQDQAGVDAVP
+GR
+>PROKKA_01355
+MTEHTRDDVAPAPLVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHCLHEGV
+DLADAEAVAAAAVAMDLDQSTDPDVEAVRVGGTDVTEAIRGPEVTDTVSTVAVVIPVREE
+LHRRQRAAIAAAGRMVAEGRDITTVVAPDAHARVLLTASEAVRTARRSGQLAAAGETGVD
+AGTLHRQVAGRDARDATVSTFDRPADGVALVDSTELDFEQTVAAVLAAVEDQAGIPAVKG
+GRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001864.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001864.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8653e4b73dac47d8b15fd6947a55957b5bd50e8c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001864.fa
@@ -0,0 +1,36 @@
+>PROKKA_01409
+MAHTPPAETSAPPAPATKKDRTHWLYIAVIASVVLGAAVGLLFPEFGKSLKPLGDGFVSL
+IKMMIGPVIFCTIVLGVGSIAKAATVGRVGGIALVYFMAMSTFALAVGLVVGNLIHPGEG
+LKLTPYDPNKPTAAADGTVQFLLDIIPGSLPMLPTLFIALLVGFALQQMGPADAPLLRGL
+TLIQGVVFRILMMVMWVAPIGAFGAIAAVVGSTGWSAIGAMALLMGAFYLTCIAFIVVVL
+GTVLKVVTGLSILSLMKYLGREYLLIFATSSSETALPRLIAKMEHAGVDKSVVGVTVPTG
+YSFNLDGTAIYLTMAALFVSNAMGAEMNLGEQIGLLVFMIIASKGAAGVTGAGMATLAAG
+LQAHRPELLGGMGVIVGIDKFMSEARALTNFTGNAVATLLVGRWVGELDGERARRVLSGE
+LQFDEATVAGHDGAAHDPQQSPTIAEQAYEGHPDSSLNFAMAADGDRNPAR
+>PROKKA_01139
+MAHTPPAETSAPPAPATKKDRTHWLYIAVIASVVLGAAVGLLFPEFGKSLKPLGDGFVSL
+IKMMIGPVIFCTIVLGVGSIAKAATVGRVGGIALVYFMAMSTFALAIGLVVGNLIHPGEG
+LKLTPYDPNKPQAAADGTVQFLLDIIPGYLPVLPTLFIALLVGFALQQMGPAGAPLLRGL
+TLIQGVVFRILMMVMWVAPIGAFGAIAAVVGSTGWSAIGAMALLMGAFYLTCIAFIVVVL
+GTVLKVVTGLSILSLMKYLGREYLLIFATSSSETALPRLIAKMEHAGVDKSVVGVTVPTG
+YSFNLDGTAIYLTMAALFVSNAMGAEMNLGEQIGLLVFMIIASKGAAGVTGAGMATLAAG
+LQAHRPELLGGMGVIVGIDKFMSEARALTNFTGNAVATLLIGRWVGELDGERARRVLSGE
+LKFDEATVAGHDGAAHDPQQSPTIAEQAYEGHPDSSLNFTMAADGDRNPTR
+>PROKKA_01397
+MTHASPAEAVPVKKKDRTHWLYISVIASVILGAAVGLLFPEFGKSLKPLGDGFVSLIKMM
+IGPVIFCTIVLGIGSIAKAATVGKVGGLALLYFITMSTFALAIGLVVGNFVHPGEGLKLT
+PYDPNKPKAPLDSTVQFLLDIIPGSMPVLPVLFVALLVGFALQQMGPAGAPLLRGLTLIQ
+GVVFRILMMIMWVAPLGAFGAIAAVVGSTGWSAIGAMLLLMGAFYLTCILFITLVLGTIL
+KVVTGLNIFSLLKYLGREYLLIFATSSSESALPRLIAKMEHAGVDKSVVGVTVPTGYSFN
+LDGTAIYLTMAALFVSNAMGMEMNLGEQVGLLLFMIIASKGAAGVTGAGLATLAAGLQAH
+RPELLGGMGVIVGIDKFMSEARALTNFTGNAVATLLIGQWVGELDGDRARRVLGGELKFD
+EAMVAGHGDAVLEDAKAHPSMVEQTGGSHAASTY
+>PROKKA_01359
+MAHTPPAETSAPPAPATKKDRTHWLYIAVIASVVLGAAVGLLFPEFGKSLKPLGDGFVSL
+IKMMIGPVIFCTIVLGVGSIAKAATVGRVGGIALAYFMTMSTFALAVGLVVGNLIHPGEG
+LKLTPYDPNKPQAAADGTVQFLLDIIPGSLPVLPTLFIALLVGFALQQMGPAGAPLLRGL
+TLIQGVVFRILMMVMWVAPIGAFGAIAAVVGSTGWSAIGAMALLMGAFYLTCIAFIVVVL
+GTVLKVVTGLSILSLMKYLGREYLLIFATSSSETALPRLIAKMEHAGVDKSVVGVTVPTG
+YSFNLDGTAIYLTMAALFVSNAMGAEMNLGEQIGLLVFMIIASKGAAGVTGAGMATLAAG
+LQAHRPELLGGMGVIVGIDKFMSEARALTNFTGNAVATLLIGRWVGELDGERARRVLSGE
+LKFDEATVAGHDGAAHDPQQSPTIAEQAYEGHPDSSLNFTMAADGDRNPTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001870.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001870.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46922a68eb2023ef1da4e228a6e070529fd8e95d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001870.fa
@@ -0,0 +1,47 @@
+>PROKKA_01470
+MTVSGPGLSAAPAAEPGAEPVEPAAGRPRSWVPGPAWRALRRRWRRSLRLRTAVLAALLS
+ILAGLVVAAFLTQQITQALFEARYEQVQAEARRGLSQVRETFAQTTATDAQSTDVLVTQT
+LRALEGDSGTTIRRRYHLAPLPGSESAYVGTISSAGLDPAVIPQELQDAVASGPGVYDAS
+VALPDPGGGTRPGLVFGAQVVLPPGATYGLYLVYDLADVQSSLDSVLGVLLVFGVGFLVI
+NVLVSWWVSRRVTLPVQQAARAAESLSSGNLAVRMPVDGEDEMARLGMSFNRMADSIQDQ
+IGQLAQLSQMQQRFVSDVSHELRTPLTTVRMAADVLYGSREDFDPVNRRSTELLYHQVDR
+FQAMLADLLEITRFDAGAATPALEATDMLELARDVVLTSQPLADQSGVPVYVVPMDRDRA
+DGHVAWVDPRRIERILRNLVNNAIEHAEGRPVDVLVAADEEAVTFAVVDHGIGMSPEQVQ
+RVFDRFWRADPSRKRTTGGSGLGLAIATEDTRLHGGRLEAWGELGEGSTFMVTLPRAPRP
+AAQGAEAPEPIGRSVLPIPPRYSTADRRYADDLSRPVPQEADADADAVGRVADVAATAAD
+APPCARQDEQALTAPTRPVRRVPPGDPADGPAAGDRTGEDAAEEAR
+>PROKKA_01202
+MTVSGPDVSAAPAAESGAEPVEPAAARPRSWGPGPAWRALRRRWRRSLRLRTAVLAALLS
+ILAGLVVAAFLTQQITQALFEARYEQVQSEARRGLSQVRETFAQTTATDAQSTDVLVTQT
+LRALEGDSGTTIRRRYHLAPLPDSESAYVGTISSAGLDPAVIPQELQDAVASGPGVYDAS
+VALPNPGGGTRPGLVFGAQVVLPPGATYGLYLVYDLADVQSSLDSVLGVLLVFGVGFLVI
+NVLVSWWVSRHVTLPVQQAARAAESLSSGNLAVRMPVDGEDEMARLGMSFNRMADSIQDQ
+IGQLAQLSQMQQRFVSDVSHELRTPLTTVRMAADVLYGSREDFDPVSRRSTELLYHQVDR
+FQAMLADLLEITRFDAGAATPALEATDMLELARDVVLTSQPLADQIGVPVYMVPMDRDRA
+DGHVAHVDPRRIERILRNLVNNAIEHAEGRPVDVLVAADEEAVTFAVVDHGIGMSPEQVQ
+RVFDRFWRADPSRKRTTGGSGLGLAIATEDTRLHGGRLEAWGELGEGSTFMVTLPRAPRP
+AVQGAEAPEPIGRSVLPIPPRYSTADRRYADDLSRPVPQEADADAVGTVADVATAAPPSA
+RQAEQALTAPTRPVRVVPAEDPAHGSAPGDPTGDDPAEEAR
+>PROKKA_01332
+MTAPAEPPQPAETGDPDETGATSAPASAGPSTSAAPPRAGLRRRLRRRWNGSLQLRTAVL
+AGLLTLLASLMISGLITQQVAQALFDARHQQVEAEARRGLARVQSTFANAAATDQQATDA
+LVSQTMRALELDGGTTIRRRFRLEPLPGGTAASVGTVSSQGLDADVIPQDLRDAVASGPG
+VYDASIALPAADGNTRPGLAYGTQVVLPPGATYALYLVYDLSDVQESLDSVLGVLLMFGS
+GFLLVTVLVSWWAAHSVVRPVQQAATAAESISGGNLAVRMPVRGDDEMARLGTSFNRMAD
+SIQAQITQLAQLSRMQQRFVSDVSHELRTPLTTVRMAADVLYGSREDFDPVNRRSTELLY
+HQVDRFQAMLADLLEITRFDAGAAQLALEDTDLLALARDVVLTAAPLADQAKVPVYLVPL
+PLEEGLDCVAQVDPRRIERILRNLVNNAIEHAEGSPVDVLVAADEGAVSVAVVDEGIGMS
+PEQVQRVFDRFWRADPSRKRTTGGSGLGLAIATEDTRLHGGRLEAWGELGVGSVFMVTLP
+RRNGAESPVRRAVLPMPPSYDRGGRRLAADLHTPVTGPEGTGVHDAAALPERGREQEL
+>PROKKA_01420
+MTVSGPGLSAAPAAEPGAEPVEPAAGRPRSWVPGPAWRALRRRWRRSLRLRTAVLAALLS
+ILAGLVVAAFLTQQITQALFEARYEQVQAEARRGLSQVRETFAQTTATDAQSTDVLVTQT
+LRALEGDSGTTIRRRYHLAPLPGSESAYVGTISSAGLDPAVIPQELQDAVASGPGVYDAS
+VALPDPGGGTRPGLVFGAQVVLPPGATYGLYLVYDLADVQSSLDSVLGVLLVFGVGFLVI
+NVLVSWWVSRRVTRPVQQAARAAESLSSGNLAVRMPVDGEDEMARLGTSFNRMADSIQDQ
+IGQLAQLSQMQQRFVSDVSHELRTPLTTVRMAADVLYGSREDFDPVNRRSTELLYHQVDR
+FQAMLADLLEITRFDAGAATPALEATDMLELARDVVLTSQPLADQIGVPVYVVPMDRDRA
+DGHVAWVDPRRIERILRNLVNNAIEHAEGRPVDVLVAADEEAVTFAVVDHGIGMSPEQVQ
+RVFDRFWRADPARKRTTGGSGLGLAIATEDTRLHGGRLEAWGELGEGSTFMVTLPRAPRP
+AAQGAEAPEPIGRSVLPIPPRYSTADRRYADDLSRPVPQEADADAVGTVADVTAAAADAP
+PSARQAEQALTAPTRPVRMVPPADGTAAGGWTGDDGAEEAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001871.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001871.fa
new file mode 100644
index 0000000000000000000000000000000000000000..702c5a731173ad6e19546d8af6f2a4d234a9f4fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001871.fa
@@ -0,0 +1,20 @@
+>PROKKA_01476
+MADLTRSLFAPRRGDRPTVAVLGLGRFGSGVARELMESDCHVLGVDADAEAVQALNGRLT
+HVVRADSTDEEAMRQLSVHEMDHVVVAIGGDLADSILTVSLMRRFGTHQLWAKANDDRHG
+EILRQLGVEHVVHPERDMGRRVAHLVSTSFQDFVEVEPGLAMVRATPPSRLLGRDLRATG
+LAGERGMRVVAVRSRGTWLYPPSHYVLEPEDTILLVGPTRDVERFLARD
+>PROKKA_01208
+MADLTRSLFAPRRGDRPTVAVLGLGRFGSGVARELMESDCHVLGVDADAEAVQALNGRLT
+HVVRADSTDEEAMRQLSVHEMDHVVVAIGGDLADSILTVSLMRRFGTHQLWAKANDDRHG
+EILRQLGVEHVVHPERDMGRRVAHLVSTSFQDFVEVEPGLAMVRATPPSRLLGRDLRATG
+LAGERGMRVVAVRSRGTWLYPPSHYVLEPEDTILLVGPTRDVERFLARD
+>PROKKA_01326
+MADLTRSLFAPRRGDRPTVAVLGLGRFGSGVALELMESDCHVLGVDADAEAVQALNGRLT
+HVVRADSTDEEAMRQLSVHEMDHVVVAIGGDLADSILTVSLMRRFGTHQLWAKANDDRHG
+EILRQLGVEHVVHPERDMGRRVAHLVSTSFQDFVEVEPGLAMVRATPPSRLLGRDLRATG
+LAGERGMRVVAVSSRGTWLYPPSHYVLEPEDTILLVGPTRDVERFLARD
+>PROKKA_01426
+MADLTRSLFAPRRGDRPTVAVLGLGRFGSGVARELMESDCHVLGVDADAEAVQALNGRLT
+HVVRADSTDEEAMRQLSVHEMDHVVVAIGGDLADSILTVSLMRRFGTHQLWAKANDDRHG
+EILRQLGVEHVVHPERDMGRRVAHLVSTSFQDFVEVEPGLAMVRATPPSRLLGRDLRATG
+LAGERGMRVVAVRSRGTWLYPPSHYVLEPEDTILLVGPTRDVERFLARD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001874.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001874.fa
new file mode 100644
index 0000000000000000000000000000000000000000..363a4c38509fe3e8d0f30f1fb078b689975d21d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001874.fa
@@ -0,0 +1,36 @@
+>PROKKA_01514
+MSNDARTPGSDDGRDPLEEMLRQLFGGQGPDPDEVRRAMEGLGGPGGVPFDPSQLNPAMM
+QQAMAQFQAMMSSGSGSDGPVNWALAKQAARQAVAGEDPAVGSFARREVDEALRLAELWL
+DGVTQTEPVGSVGVAWSRAEWVEATMDQWRRLTEPVAVSMSRAMSAAIEQQLPGQLPEGM
+DASLLGGLQPMLKNMGGTMFGLQLGGAVGALGKEVLSGTDIGLPVAGHRLALVPVNIEEF
+GDGLSVPDDQIRIYLALREAARMRLFLHSPWLERDLYAAVEQYAAGIRLDTEGIERAAQS
+VDPMDPGSLQAVFDGASFIAAPDATQQAALDQLELLVALVEGWVDVVVAEAARPLESAAA
+LRETMNRRRASGGPAEQAFAALVGLELRPRRLREAAAFWEHVTAEHGTEYREEIWRHPER
+QPTAEDLEDPAGYAGRRSAADASAESLDDELRKLLEGGFGDAPREG
+>PROKKA_01223
+MSNDARTPGSDDGRDPLEEMLRQLFGGQGPDPDEVRRAMEGLGGPGGVPFDPSQLNPAMM
+QQAMAQFQAMMSSGSGSDGPVNWALAKQAARQAVAGEDPAVGSFARREVDEALRLAELWL
+DGVTQTEPVGSVGVAWSRAEWVEATMDQWRRLTEPVAVSMSRAMSAAIEQQLPGQLPEGM
+DASLLGGLQPMLKNMGGTMFGLQLGGAVGALGKEVLSGTDIGLPVAGHRLALVPVNIEEF
+GDGLSVPDDQIRIYLALREAARMRLFLHSPWLERDLYAAVEQYAAGIRLDTEGIERAAQS
+VDPMDPGSLQAVFDGASFIAAPDATQQAALDQLELLVALVEGWVDVVVAEAARPLESAAA
+LRETMNRRRASGGPAEQAFAALVGLELRPRRLREAAAFWEHVTAEHGTEYREEIWRHPER
+QPTAEDLEDPAGYAGRRSAADASAESLDDELRKLLEGGFGDAPREG
+>PROKKA_01411
+MSNDPRTPGSDDGRDPLEEMLRQLFGGNGPDPDEIRRAMEGMGGPGGMPFDPSQLDPAMM
+QQAMAQFQAMMNPGPGSEGPVNWTLAKQAARQAVAGEDPAVGSFARREVDEALRLAELWL
+DGATQTEPVGSVGVAWSRAEWVEATMDQWRRLTEPVAVSMSRAMSAAIEQQLPGQLPEGM
+DASMLSGIQPMLKNMGGTMFGLQLGGAVGALGKEVLSGTDIGVPIAGHRLAMVPVNVEEF
+GDGLSVPDDQVRIYLALREAARMRLFLHSPWLERDLYAAIEQYAAGIRLDTEGIEQAARS
+VDPMDPESMQAVFDGSSFIAAPDATQRAALAQLELLVALVEGWVDVVVAEAATPLESAAA
+LRETMNRRRASGGPAEQAFAALVGLELRPRRLREAAAFWEHVTAEQGKEYREEIWRHPER
+QPTAEDLEDPAGYAGRRTAADASTDSLDDDLRKLLEGGFGDAPKEG
+>PROKKA_01441
+MSNDARTPGSDDGRDPLEEMLRQLFGGQGPDPDEVRRAMEGLGGPGGVPFDPSQLNPAMM
+QQAMAQFQAMMSSGSGSDGPVNWSLAKQAARQAVAGEDPAVGSFARREVDEALRLAELWL
+DGVTQTEPVGSVGVAWSRAEWVEATMDQWRRLTEPVAISMSRAMSAAIEQQLPGQLPEGM
+DASLLGGLQPMLKNMGGTMFGLQLGGAVGALGKEVLSGTDIGLPVAGHRLALVPVNIEEF
+GDGLSVPDDQIRIYLALREAARMRLFLHSPWLERDLYAAVEQYAAGIRLDTEGIERAAQS
+VDPMDPGSLQAVFDGASFIAAPDATQQAALDQLELLVALVEGWVDVVVAEAARPLESAAA
+LRETMNRRRASGGPAEQAFAALVGLELRPRRLREAAAFWEHVTAEHGTEYREEIWRHPER
+QPTAEDLEDPAGYTGRRSAADASTESLDDELRKLLEGGFGDAPREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001876.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001876.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d1e0cd4a12922b842291b5f847464b3bfd96bf37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001876.fa
@@ -0,0 +1,20 @@
+>PROKKA_01586
+MSEFLASRWPDILFRAWQHGWLVLQALAIATVLAIALAVIATRIKALTPIANAFTAVGLT
+LPSFALIGVLIPLVGIGTVPAVVVVVFYALLPILRNALVGLRGVDPEVLEAARGMGMGPV
+ALFTRVRLPLAWPVILTGIRVAGQLGMGVAAVAAYVLGPGLGSYIFTGLVSLGGANALNY
+ALVGTLGIVVVALVLDGLLVLLGRLTISKGLRA
+>PROKKA_01297
+MSEFLASRWPDILFRAWQHGWLVLQALAIATVLAIALAVIATRIKALTPIANAFTAVGLT
+LPSFALIGVLIPLVGIGTVPAVVVVVFYALLPILRNALVGLRGVDPEVLEAARGMGMGPV
+ALFTRVRLPLAWPVILTGIRVAGQLGMGVAAVAAYVLGPGLGSYIFTGLVSLGGANALNY
+ALVGTLGIVVVALVLDGLLVLLGRLTISKGLRA
+>PROKKA_01336
+MSEFLASRWPDILFRAWQHGWLVLQALAIATVLAIALAVIATRIKALTPIANALTAVGLT
+LPSFALIGVLIPLVGIGTVPAVVVVVFYALLPILRNALVGLRGVDPDVLEAARGMGMGPV
+ALFTRVRLPLAWPVILTGIRVAGQLGMGVAAVAAYVLGPGLGSYIFTGLVSLGGANALNY
+ALVGTLGIVVVALLLDGLLVLLGRLTISKGLRA
+>PROKKA_01513
+MSEFLASRWPDILFRAWQHGWLVLQALAIATVLAIALAVIATRIKALTPIANAFTAVGLT
+LPSFALIGVLIPLVGIGTVPAVVVVVFYALLPILRNALVGLRGVDPEVLEAARGMGMGPV
+ALFTRVRLPLAWPVILTGIRVAGQLGMGVAAVAAYVLGPGLGSYIFTGLVSLGGANALNY
+ALVGTLGIVVVALVLDGLLVLLGRLTISKGLRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001879.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001879.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0c1dd5824c173944ede2c708fafa130f7e194f85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001879.fa
@@ -0,0 +1,20 @@
+>PROKKA_01614
+MRFTQAELQQFRDRTVPDLLPDPLRLLFIGINPGLWSAATGAHFARRGNRFYPALHRAGL
+TRHLVDASDGYKAEDLAELHARGIGISNLVPRATARADELTAEDLAAAPARLDALVAAHA
+PAVVAVLGVTAYRQAFGRPKAALGEQQTPWPGTRLFVAPNPSGLNAHATLDSLAADYRAA
+GAAAGLVD
+>PROKKA_01324
+MRFTQAELQQFRDRTVPDLLPDPLRLLFIGINPGLWTAATGAHFARRGNRFYPALHRAGL
+TRHLIDASDGYKAEDLAELHARGIGISNLVPRATARADELTAEDLAAAPARLDALVAAHA
+PAVVAVLGVTAYRQAFGRPKAVLGEQQTPWPGTRLFVAPNPSGLNAHATLDSLAADYRAA
+GAAAGLVD
+>PROKKA_01285
+MRFTQAELQQFRDRTVPDLLPDPLRLLFIGINPGLWTAATGAHFARRGNRFYPALHRAGL
+TRHLIDASDGYKAEDLAELHARGIGISNLVPRASARADELTAEELAAAPARLDALVAAHA
+PAVVAVLGVTAYRQAFGRPKAALGEQETPWPGTRLFVAPNPSGLNAHATVDSLAADYRAA
+GAAAGLVD
+>PROKKA_01189
+MRFTQAELQQFRDRTVPDLLPDPLRLLFIGINPGLWTAATGAHFARRGNRFYPALYRAGL
+TRHLIDASGGYKAEDLAELHARGIGISNLVPRATARADELTAEELAAAPARLDALVAAHA
+PAVVAVLGVTAYRQAFGRPKAALGEQQTPWPGTRLFVAPNPSGLNAHATLDSLAADYRAA
+GAAAGLVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001880.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001880.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d0e83c0fe1f0675917181a60ca56722d1eb2ba2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001880.fa
@@ -0,0 +1,28 @@
+>PROKKA_01625
+MRLRFNDYRDKPAVDPRYFTDPEGHDMAVAVAGIRLAREIVSQPAMAAWAGRELAPGEQA
+QTDEEIADYVRRTHNTVYHPVGSVRMGADDDAMSPLDARLRVKGVTGLRVADASVMPEHV
+TVNPNITCVMIGEKAAQLILADRA
+>PROKKA_01331
+MRLRSNDYRDEPVVDPRYFTDPEGHDMAVAVASIRLAREIVSQPAMAAWAGRELAPGEQA
+QTDEEIADYVKRTHNTVYHPGGSVRMGADDDAMSPLDARLRVKGVTGLRVADASVMPEHV
+TVNPNITCFMIGEKAAQLILADRA
+>PROKKA_00817
+MTAEPLTTDAPDDGTPAHESDVLVIGAGSAGCVLARRLLDAGRTVTLVEAGDQDVNPDID
+DVSRLGFLWESEVDWNYRTTPQPGLAGRSLHLPRGKVMGGSHALNATIWVRGDAWDYDTW
+AAEHGCTGWSWQDVLPYFKAIENTALGEDAVRGRDGLLDISTDYPHHPIQQAMYDATVQE
+GVPENPDYNSGDVEGVGWMQLNVRDGKRFNTWRAYLKPVADHEGLTLVTGAQARRLLLDG
+TRVTGAEFDRDGETLTITADEVVLCAGALGSPEILLRSGVGPADHLREVGVDVAHDLPGV
+GRNLHDHLLVPVVGVTEKEAPAPEVAVAQVHYFAKSDPALPVADTQPIFFSVPMYTNTAG
+DPMVGPETGFSLLAGIVRPLSRGSLTLSGPAPEDPVQVDLGAYTAPEDLQAMLFSLRQCR
+RIAAQPALAEGWGATEIHPGPNVGDTDEELIAYIRNTTTTYHHQVGTCAMGSGEDAVVDP
+ATLRVYGLEGLRVADASIMPQVTSGNTNAPSVMIGERAAAMITGVEPF
+>PROKKA_01554
+MTTTTPDASTPQPDTPVYDYIVVGGGSSGAALAARLSEDPQISVALLEAGPTDVDLDEVL
+ELRRWPELLESGLDWDYPIEPQENGNSFMRHSRAKVLGGCSSHNSCIAFWPPREDLDQWE
+AMGATGWGAEHTLPLVKKLENNRAEGDHRGHDGPVELMDVPADDPAGVALLEAAAQAGIP
+TTTFNTGETVVKGANWFQINRKQDGTRASSSVSYLHPILDRENLDILTDHWVSEVLFDDD
+RRAYGVRHVADRHGRQAEIHARAEVILSAGAINTPKLLMLSGIGPAEHLAEHGLDVRVDA
+PGVGSNLQDHPEAVISWESKQPMYRDATQYWEIGIFSPTKEGLDRPDLMMHYGSVPFDMH
+TYRQGYPTADETFCLTPNVTHAKSRGTVRLRSNDYRDKPAVDPRYFTDPEGHDMAVAVAG
+IRLAREIVSQPAMAAWAGRELAPGEQAQTDEEIADYVRRTHNTVYHPVGSVRMGAEDDAM
+SPLDARLRVKGVTGLRVADASVMPEHVTVNPNITCFMIGEKAAQLILADRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001885.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001885.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2b7fc42ca24af44085bb0f6acbe110692d31ea70
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001885.fa
@@ -0,0 +1,44 @@
+>PROKKA_01766
+MTESTAPESFTQGPTDVELLEQTLAQNLDDTARRFADRAALLECGPDGDPATGRTWTYGQ
+LREESVTVAKALMAAGYEAGDRIGMWSPNVAEWVSLLYGAARAGVILVNLNPAYRAHELT
+YVVEQCDMRGLVVACADARMDPPATARAVARESAPHLRQLIMLPAGSGEDAYAHVQAGDV
+AGRHAADPVAEGTWADFLAEAARVSDEDLAVREAATGPADPVNLQYTSGTTGFPKGVTLT
+HRNVLNNGFHIGELLGYTEEDTVVIPVPFFHCFGMVIGVIATVSHGSLAVIPARSFEPVS
+ALRAVAATGATSLYGVPAMFIAMLARPEADALDLSTLRTGVMAGSTCPVEVMKKVIDRFH
+MSEVAICYGMTETAPVSTMTRRDDSLEVRTQTVGRTMPHVETKIVDPATGDVVPRGATGE
+LCTRGYSVMLGYWDAPEKTAEVLDADGWMHSGDLASMDEDGSVRIEGRIKDLVIRGGENI
+SPREVEEFLYTHPDIQDVQVVGVPDEKYGEQLMACVIMKDGVEPLTVDAVREFATGRIAH
+FKIPAYVRVLDAFPMTVSGKVRKVELREEGAKVVQAQAHAQGAG
+>PROKKA_01473
+MTESTAPESFTQGPTDVELLEQTLAQNLDDTARRFADRAALLECGPDGDPATGRTWTYGQ
+LREESVTVAKALMAAGYEAGDRIGMWSPNVAEWVSLLYGAARAGVILVNLNPAYRAHELT
+YVVEQCDMRGLVVACADARMDPPATARAVARESAPHLRQLIMLPAGSGEDAYAHVQDGDV
+AGRHAADPVAEGTWAAFLAGAARVSDEDLAAREAATRPADPVNLQYTSGTTGFPKGVTLT
+HRNVLNNGFHIGELLGYTEEDTVVIPVPFFHCFGMVIGVIATVSHGSLAVIPARSFEPVS
+ALRAVAATGATSLYGVPAMFIAMLARPEADALDLSTLRTGVMAGSTCPVEVMKKVIDRFH
+MSEVAICYGMTETAPVSTMTRRDDSLQVRTQTVGRTMPHVETKIVDPATGDVVPRGATGE
+LCTRGYSVMLGYWDAPEKTAEVLDADGWMHSGDLASMDEDGSVRIEGRIKDLVIRGGENI
+SPREVEEFLYTHPDIQDVQVVGVPDEKYGEQLMACVIMKDGVEPLTVDAVREFATGRIAH
+FKIPAYVRVLDAFPMTVSGKVRKVELREEGAKVVQAQAHAQGAG
+>PROKKA_01111
+MTPSPSVQESYTRGPSDVPMLEQTLAQNLDDAARRSGARPAVVECGPDGDPATDRSWTYE
+QLREESVTVAKALMAAGYEPGDRIGLWSPNVAEWTSLLYGAARAGVILVNLNPAYRAHEL
+TYVVEQCGMRGLVVAPADAHQDRPDIARDVACGGCPELRQLIILPTAGPITAESYAHAVD
+GVLDCRPEPTPVSEGTWSAFLAGADRVSDEELAARESAVSPEDPVNLQYTSGTTGFPKGV
+TLTHRNVLNNGFHIGELLGYSQEDTVVIPVPFFHCFGMVIGVIAAVSHGSLCVIPARGFE
+PVATLRAAAATRATSLYGVPAMFIAMLARPEADELDLSTLRTGVMAGSTCPVEVMRRVID
+RFHMAEVAICYGMTETAPVSTMTRRDDSLEVRTQTVGRTMPHVETKIVDPVSGEVVPRGS
+TGELCTRGYSVMRGYWNDEEKTAEVLDAEGWMHSGDLASMDEGGSVRIEGRIKDLVIRGG
+ENISPREVEEFLYTHPDVQDVQVVGVPDERYGEQLMACLIMKDGTRPLTPEDVRAFCEGK
+IAHFKIPAHVRVLDAFPMTVSGKVRKVELRAEGAKLVEGGDRD
+>PROKKA_01695
+MTESTAPESFTQGPTDVELLEQTLAQNLDDTARRFADRAALLECGPDGDPATGRTWTYGQ
+LREESVTVAKALMAAGYEAGDRIGMWSPNVAEWVSLLYGAARAGVILVNLNPAYRAHELT
+YVVEQCDMRGLVVACADARMDPPATARAVARESAPHLRQLIMLPAGSGEDAYAHVQDGDV
+AGRHAADPVAEGTWAAFLAGAARVSDEDLAAREAATRPADPVNLQYTSGTTGFPKGVTLT
+HRNVLNNGFHIGELLGYTEEDTVVIPVPFFHCFGMVIGVIATVSHGSLAVIPARSFEPVS
+ALRAVAATGATSLYGVPAMFIAMLARPEADELDLTTLRTGVMAGSTCPVEVMKKVIDRFH
+MSEVAICYGMTETAPVSTMTRRDDSLEVRTQTVGRTMPHVETKIVDPATGEVVPRGATGE
+LCTRGYSVMLGYWDAPEKTAEVLDADGWMHSGDLASMDEDGSVRIEGRIKDLVIRGGENI
+SPREVEEFLYTHPDIQDVQVVGVPDEKYGEQLMACVIMKDGVEPLTVDAVREFATGRIAH
+FKIPAYVRVLDAFPMTVSGKVRKVELREEGAKVVQAQAHAQGAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001890.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001890.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c80f8cf930c3b0864c8019116ea9f83c67a3e9c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001890.fa
@@ -0,0 +1,18 @@
+>PROKKA_01877
+MAEKNAAEYTVPGLSLSTGRRTAEILQGRLHALNDLQLTLKHAHWNVVGPGFIGVHEMLD
+PQIELVRGMVDVVAERIATLGVSPAGTPGALVAARTWDDYTLGRASTLEHLAALDLVYDG
+VVTDHRAAIDATEDLDPVTQDILIDQVAQLELFQWFMRSFLTTDDGRLSSAGTTTEAAAA
+GRVKGAQSAPAPKAGRTKKSDAKKSKKK
+>PROKKA_01573
+MAEKNAAEYTVPGLSLSTGRRTAEILQGRLHALNDLQLTLKHAHWNVVGPGFIGVHEMLD
+PQIELVRGMVDVLAERIATLGVSPAGTPGALVAARAWDDYTLGRASTLEHLAALDLVYDG
+VVTDHRAAIDATEDLDPVTQDILIDQVAQLELFQWFMRSFLTTDDGRLSSAGTTTEAAAA
+GRVKGAQSAPAPKAGRTKKSDAKKSKKK
+>PROKKA_00982
+MAAKKNDAAFTVPGLALKDGHRVAEILQGRLHALNDLQLTLKHAHWNVVGPGFIGVHEML
+DPQIETVRAMVDVVAERIATLGVSPEGTPGALVAARTWDDYALGRASTLEHLAALDLVYD
+GVVTDHRAAIETVGELDPVSEDMLIGQVAELELFQWFMRSFLTTVDGDLSHAGATREIVA
+AARVSGAQKAPAPKKGAAKKAPAKKK
+>PROKKA_00920
+MDSRARASTDPGLSVEDGHHVAEVLPVRLHALNDLQLTLKHAHWNVVGPGVIGVHEMPGP
+QIEKVRAMVDAIAELELFPRSMRSFPATDDGELSHADALREAEAAKQK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001892.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001892.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a3238666ef75b205b0067c3a8fa9df21fd28884
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001892.fa
@@ -0,0 +1,16 @@
+>PROKKA_01879
+MIKQPWGLARLPAMTTQPPSAPAEHLAVVHALRVFSESAEHAVDEAGRGVGLHRTDLRAL
+AYLMARAAAGEPVTASDLGAHLHLTRASATALVDRLAAAGHVRRHRDEGDRRRVLVEHTD
+TARRDGQRAFEPMSQRLSAALEGFSAAELRAAVRVLEAATAALTDPAPEDP
+>PROKKA_01575
+MIKQPWGLARLPAMTTQPPSAPAEHLAVVHALRVFSESAEHAVDEAGRGVGLHRTDLRAL
+AYLMARAAAGEPVTASDLGAHLHLTRASATALVDRLAAAGHVRRHRDEGDRRRVLVEHTD
+TARRDGQRAFEPMSQRLSAALEGFSAAELRAAVRVLEAATAALTDPAPEDP
+>PROKKA_00980
+MTPQPAAAPAEHVAVVHALRAFSEGAEHAVDEAGRGIGLHRTDLKALAHLMRCADEDRPV
+TATDLGAHLHLTRAATTAVVDRLVASGHARRRRDDVDRRRVLVEHTDSARRDGAAAFLPM
+SLRISGALTPFTAEELRAALRVIEAATAALQAPPDAPAAPVPG
+>PROKKA_01799
+MTTQPPSAPAEHLAVVHALRVFSESAEHAVDEAGRGVGLHRTDLRALAYLMARAAAGEPV
+TASDLGAHLHLTRASATALVDRLAAAGHVRRRRDEGDRRRVLVEHTDTARRDGQRAFQPM
+SQRLSAALEGFSVAELRAAVRVLEAATAALTDPTPEDP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001894.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001894.fa
new file mode 100644
index 0000000000000000000000000000000000000000..973140e6a109daabfa9ed0b95e22bfe2193829c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001894.fa
@@ -0,0 +1,14 @@
+>PROKKA_01893
+MAGRWRAGAALTIRGEFSIVIAGPVLTRYADAFGRSRARAATRRVRAREVAAADPVH
+>PROKKA_01589
+MAGRWRAGAALTIRGEFSIVIAGPVLTRYADAFGRSRARAATRRVRAREVAAADPVH
+>PROKKA_00903
+MHGTTLALVELGAVLFLLGVLGRLAARIGMSPVPLYLLGGLLIGVGGLLFSGADPSGTLR
+SPVAAIGDFSSLAAEIGVVLLLLTLGLEYSARELMTGLRGSWRSGLLDVALNFTPGAAAG
+WLLGWGPVGAVVLGGITYISSSGIIAKVLNDLGRVGNRETPVMLSVLVFEDLAMAVYLPL
+MTALVAGSAFAAGLRAVGIALVVVAAVLFTALRFGPQISRLVYSPEQETFLLKVLGLALL
+VAGVAGALQVSAGVGAFLLGIAISGAAAKQARSVLEPLRDMFAALFFVLFGMNVDPRTLP
+PVLLGALALAVVTAATKVATGYLAARAAGIGVAGRWRAGATLTIRGEFSIVIAGLATASG
+TLPAEVSAFATAFVLILAVAGPLLTRSADGFGRRRAAAARVREARRARQAPLV
+>PROKKA_01813
+MAGRWRAGAALTIRGKFSIVIAGPVLTRYADAFGRSRARAATRRVQAREVAVADPVH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001895.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001895.fa
new file mode 100644
index 0000000000000000000000000000000000000000..32202bd1786fd3ef9723bebda58c7f108df9b10a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001895.fa
@@ -0,0 +1,16 @@
+>PROKKA_01895
+MTRQSDLKTLIRARMAVTGERYTAAAAALADEWQSAERYHATVLARFFDGDRLRSIPARR
+KPRVAVLLELLRRFRAGRAYAEAEVNDLLRPAHEDVATLRRELVDYGFLARADGVYRLAD
+AGPDLDPRFAADLPVDLERRLREIRAGR
+>PROKKA_01591
+MTRQSDLKTLIRARMAVTGERYTAAAAALADEWQSAERYHATVLARFFDGDRLRSIPARR
+KPRVAVLLELLRRFGAGRAYAEAEVNDLLRPAHEDVATLRRELVDYGFLDRADGVYRLAD
+AGPDLDPRFAADLPVDLERRLREIRAGG
+>PROKKA_00963
+MTRQSDLKTLIRARMAVTGERYTAAAAALAHEWETAERFHATVLARFFDGERLRSIPALR
+KPRVAVLLELLRRFAPDRAYTEPEVNDLLRPAHEDVATLRRELVDYGFLDRADGVYRMAD
+AGPDVDPRFAADLPVDLERRLRQLRAGR
+>PROKKA_01815
+MTRQSDLKTLIRARMAVTGERYTAAAAALADEWQSAERYHATVLARFFDGDRLRSIPARR
+KPRVAVLLELLRRFRAGRAYAEAEVNDLLRPAHEDVATLRRELVDYGFLARADGVYRLAD
+AGPDLDPRFAADLPVDLERRLREIRAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001896.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001896.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c0a29c70cf07f7a2ef9dd5d787df362c96f7bf7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001896.fa
@@ -0,0 +1,18 @@
+>PROKKA_01898
+MSPSARRPAASSRPARPRPTTAPFALPDRPGWVRLAAGAVVPGVIAAAAALAALQVFVLN
+PLAAAPGDRGLGRIYADLSAAGQLGVPFVLSAVILAAGLGVAAVLWFLTWRREEVDPLAV
+LALGLASLVAASPAYFMASFGPGMALADTYGIGGADHSPWAWPIYVVSMLALTGLVAVVV
+LLLRGPAGGLGAPRRRA
+>PROKKA_01594
+MSPSARRPAASSRPARPRPTTAPLALPDRPGWVRLAAGAVVPGVIAAAAALAALQVFVLN
+PLAAAPGDRGLGRIYADLSAAGQLGVPFVLSAVILAAGLGVAAILWFLTWRREEVDPLAV
+LALGLASLVAASPAYFMASFGPGMALADTYGVGGGDHSPWAWPIYVVSMLALAGLVAVVV
+LLLRGPAGGLGAPRRRA
+>PROKKA_00961
+MAGEGALPFLLPALLCAAGLGVAAILWFLVWRREEVDPLAVLALGLASLVAATPAYFFAS
+FGMGMALADTYGIGGADHSPWARPIYVLSALALAALVAVVVLLLRGPAGGRATPRPTR
+>PROKKA_01818
+MSPSARRPAASSRPARPRPTTAPLALPDRPGWVRLAAGAVVPGVVAAVAALAALQVFVLN
+PLAAAPGDRGLGRIYADLSAAGQLGVPFVLSAVILAAGLGVAAILWFLTWRREEVDPLAV
+LALGLASLVAASPAYFMASFGPGMALADTYGIGGGDHSPWAWPIYVVSVLALAGLVAVVV
+LLLRGPAGGLGAPRRRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001897.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001897.fa
new file mode 100644
index 0000000000000000000000000000000000000000..203c847c446e53bb2b959b39339da4ce7b03767d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001897.fa
@@ -0,0 +1,35 @@
+>PROKKA_01912
+MSHADIPHAGPDGSTPSGTAPKTDSRAASATRRTALLGAMFLMATSAIGPGFITQTATFT
+VQMGAAFAFAILVSILIDVAVQMNVWRVIGVSGMRAQELANRVLPGLGWVLAALVFLGGM
+VFNIGNIAGTGLGANAMLGVDPLIGGGVSALIALLIFLSKRAGVALDRIVVALGAVMILL
+MLYVAITSAPPVGEALRQSVMPEKVDFFVIVTLVGGTIGGYITYAGAHRMIDSGVKGVDD
+VQDITRSSVASILVTGLMRALLFLAILGVVASGAVLSKDSLAASAFQAAAGDIGLRMFGI
+VLWAAAVTSVIGASYTSISFVTRSTTSVRTRNLLTVAFIVVCTALYLALRQAPQTLLVFA
+GAFNGMILPVGFAALLYVAWRRRDLLHGYRYPAWLLVMGALAWLVSVFIAVRGFVPMVTM
+ITGA
+>PROKKA_01608
+MSHADIPHAGPDGSTPSGTAPKTDSRAASATRRTALLGAMFLMATSAIGPGFITQTATFT
+VRMGAAFAFAILVSILIDIAVQMNVWRVIGVSGMRAQELANRVLPGLGWVLAALVFLGGM
+VFNIGNIAGTGLGANAMLGVDPLIGGGVSALIALLIFLSKRAGVALDRIVVALGAVMILL
+MLYVAITSAPPVGEALRQSVMPEEVDFFVIVTLVGGTIGGYITYAGAHRMIDSGVKGVDD
+VQDITRSSVASILVTGLMRALLFLAILGVVASGAVLSKDNLAASAFQAAAGDIGLRMFGI
+VLWAAAVTSVIGASYTSISFVTRSTTSARTRNLLTVAFIVVCTALYLALRQAPQTLLVFA
+GAFNGMILPVGFAALLYVAWRRRDLLHGYRYPGWLLVIGALAWIVSVFIAVRGFIPMVEM
+ITGA
+>PROKKA_00883
+MSHADPTAHARGDAAAGEAVQASSSNRRTALLGAMFLMATSAIGPGFITQTATFTVQLGA
+AFAFAILVSILIDIAVQMNVWRVIGVSGMRAQELANSVLPGLGWVLAVLVFVGGLVFNIG
+NIAGTGLGANAMLGVDPLIGGAVSAVIALLVFLSKRAGVALDRIVVVLGAVMILLMLYVA
+VTSAPPVGEALRQSVFPEKVDFFVIVTLVGGTIGGYITYAGAHRMIDSGVKGVDDVEAIT
+RSSVLSILVTGVMRVLLFLAILGVVASGVALAKDNLAASAFQAAAGDIGLRMFGIVLWAA
+ALTSVIGASYTSVSFVTKSTTTTRTRNLLTVAFIVVCTVLYLALRQTPQTLLVFAGAFNG
+MILPIGFAALLWVAWRRRDLLGGYRYPTWLLVIGALSWLLSVFIAVRGFLPMVQMITGA
+>PROKKA_01832
+MSHADIPYAGPDGSTPSGTAPKTDSRAASATRRTALLGAMFLMATSAIGPGFITQTATFT
+VRMGAAFAFAILVSILIDVAVQMNVWRVIGVSGMRAQELANRVLPGLGWVLAALVFLGGM
+VFNIGNIAGTGLGANAMLGVDPLIGGGVSALIALLIFLSKRAGVALDRIVVALGAVMILL
+MLYVAITSAPPVGEALRQSVMPEEVDFFVIVTLVGGTIGGYITYAGAHRMIDSGVKGVDD
+VQDITRSSVASILVTGLMRALLFLAILGVVASGAVLSKDNLAASAFQAAAGDIGLRMFGI
+VLWAAAVTSVIGASYTSISFVTRSTTSARTRNLLTVAFIVVCTALYLALRQAPQTLLVFA
+GAFNGMILPVGFAALLYVAWRRRDLLHGYRYPGWLLVIGALAWIVSVFIAVRGFIPMVEM
+ITGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001899.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001899.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef1de71a581180e180711b31ec45bd595f2c63eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001899.fa
@@ -0,0 +1,20 @@
+>PROKKA_01914
+MRVPTRDGVTGDDLAPGAGDGESAPAPAPVAAAAQLRQRIAAAGLVPGERLGEVALAAEL
+QVSRNSLREAFTMLASEGLVERRPHRGVFVAAPGPEDVRGLYRTRRVIQLGALEHGELTP
+GAARQLRCAQDLLSGGPDTPARVLGDANHRVHVGIVDLAGAPELTRLMASVQARVRLAFH
+PMDEQTRLHVQFADRNRWIVERLLAGDLPAVHAVFGDYLDEAEQFVLAHLAAVGD
+>PROKKA_01610
+MRVPARGGVTGEGLAPGVGGGESAPAPAPVAAAAQLRQRIAAAGLVPGERLGEVALAAEL
+QVSRNSLREAFTMLASEGLVERRPHRGVFVAAPGPEDVRGLYRTRRVIQLGALEHGELTP
+GAARQLRCAQDLLSGGPDTPARVLGDANHRVHVGIVDLAGAPELTRLMASVQARVRLAFH
+PMDEQTRLHVQFADRNRWIVERLLAGDLPAVHAVFGDYLDEAEQFVLAHLAAVGD
+>PROKKA_00881
+MTAPAAQGAADALRRRIGEARLQPGERLGEVALAAELGVSRNSLREAFSELAVEGLVVRR
+PHRGVFVAAPGAEDVRGLYRTRRVIQLGALQHGWLTPAAEERIGRSAELLGRPEPAVREL
+GDANHLLHLGIVDLAASPDLSRVMSSVLARVRLSFLPLDLETGLHQAFAERNRWIAGRLL
+AGDLDAVHAMLEGYLDEAEAFVLRHLDGAAHGLRG
+>PROKKA_01834
+MRVPARGGVTGEGLAPGVGGGESAPAPAPVAAAAQLRQRIAAAGLVPGERLGEVALAAEL
+QVSRNSLREAFTMLASEGLVERRPHRGVFVAAPGPEDVRGLYRTRRVIQLGALEHGELTP
+GAARQLRCAQDLLSGGPDTPARVLGDANHRVHVGIVDLAGAPELTRLMASVQARVRLAFH
+PMDEQTRLHVQFADRNRWIVERLLAGDLPAVHAMFGDYLDEAEQFVLAHLAAVGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001901.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001901.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fddd4388a87085e139d4944dd7389b74f8e56418
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001901.fa
@@ -0,0 +1,24 @@
+>PROKKA_01917
+MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAQTCRDAVAAG
+VTIGAHVGYRDLAGFGRRFLDCTPTELADDVLYQIGALDALARAAGGQVRYVKPHGALYN
+TIVRHEAHAQAVVDGVRAFGSDLPLLLLPGSVALDKAAAAGLRGVAEAFADRGYNPDGTL
+VSRREPGAVLHDEDDVAARMVRLATEGVVAAVDGTDVRVDAESICLHGDTPGAVAMAAAV
+RRALEGAGVSIKAFA
+>PROKKA_01613
+MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAQTCRDAVAAG
+VTIGAHVGYRDLAGFGRRFLDCTPTELADDVLYQIGALDALARAAGGQVRYVKPHGALYN
+TIVRHEAHAQAVVDGVKAFGSDLPLLLLPGSVALDKAAAAGLRGVAEAFADRGYNPDGTL
+VSRREPGAVLHDEDDVAARMVRLATEGVVAAVDGTDVRVDAESICLHGDTPGAVAMAAAV
+RRALEGAGVAIKAFA
+>PROKKA_00878
+MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAATCRAAVAAG
+VTIGAHVGYRDLAGFGRRFLDCSPTELADDVLYQIGALEALAGAAGATVRYVKPHGALYN
+TIVHHEEHAQAVVDGVAAFGADLPLLLLPGSVALEKAEKAGLRGVAEAFADRGYTPQGTL
+VSRREPGAVLHDEDEVAARMVRLATEGVVTAVDGSDVRVAAESICVHGDTPGAVSMAAAV
+RRALEDAGVTIASFA
+>PROKKA_01837
+MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAQTCRDAVAAG
+VTIGAHVGYRDLAGFGRRFLDCTPTELADDVLYQIGALDALARAAGGRVRYVKPHGALYN
+TIVRHEAHAQAVVDGVRAFGSDLPLLLLPGSVALDKAAAAGLRGVAEAFADRGYNPDGTL
+VSRREPGAVLHDEDDVAARMVRLATEGVVAAVDGTDVRVDAESICLHGDTPGAVAMAAAV
+RRALEGAGVSIKAFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001903.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001903.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b3eb6e313904af5397beb5efdf8e1dc31f21fec0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001903.fa
@@ -0,0 +1,16 @@
+>PROKKA_01940
+MGILSSLTRTLGGGGRRSSRPTIGAHIGRSPGFGRQARSQGRRSSGLGGALLGTLGGLAL
+RELSRRGAGSTTRGRSSGAYRGGFGPSARSTGGLGTGLLGGLLGGALASRGRSGAAGRRT
+AGGRRTMGGGF
+>PROKKA_01636
+MGILSSLTRTLGGGGRRSSRPTIGAHIGRSPGFGRQARSQRRRSSGLGGALVGTLGGLAL
+RELSRRGAGGTTRGRGSGAYRGGFGPSARSTGGLGTGLLGGLLGGALASRGRSGAAGRRT
+AGGRRTVGGGF
+>PROKKA_00919
+MGILSGITRALGGSRRRPTIGANTYGRRRSSGAGGALLGTLGGLALRELSRRSSGGTARG
+YGGQAGYGRTTGGYGRTSGGLGGLLGGLGGMGAGRSSSRGGGLLGGLLSGPMNSRSGRRT
+TGGRF
+>PROKKA_01859
+MGILSSLTRTLGGGGRRSSRPTIGAHIGRSPGFGRQARSQGRRSSGLGGALLGTLGGLAL
+RELSRRGAGSTTRGRSSGAYRGGFGPSARSTGGLGTGLLGGLLGGALASRGRSGAAGRRT
+AGGRRTMGGGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001906.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001906.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9bb94a6c0617cf015b747fe8c52c27a144aa93c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001906.fa
@@ -0,0 +1,8 @@
+>PROKKA_01977
+MTVGLTLYVLMWPVLVLAVLVSIARGFFADWAAARREGRSII
+>PROKKA_01670
+MTVGLTLYVLMWPVLVLAVLVAIARGFVADWAAARRQGRSII
+>PROKKA_00881
+MTLGLTLYVLMWPVLVLAVLASIAAAFFKDWREARREGRSII
+>PROKKA_01902
+MTVGLTLYVLMWPVLVLAVLVAIARGFVADWAAARREGRSII
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001907.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001907.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8af1279635ebab28b21d13a52f3ae1fced7cbc99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001907.fa
@@ -0,0 +1,16 @@
+>PROKKA_01987
+MMAWIDGLPLLWSIGFFWMLAILRTLIVFSLGRGLASGVERTRWFARVMEGPVYVRAQRF
+IQRHGVWAIPFCYLTVGIQTAVIGSAGVARMPWRRFLPAAALGTFLWGVVYGTVGMAVVW
+AVIGAALGEGRGVLALVLILAAVAAFVVWRRRRTLRRHGAG
+>PROKKA_01681
+MMAWIDGLPLLWSIGFFWMLAILRTLIVFSLGRGLASGVERTRWFARVMEGPVYVRAQRF
+IQRHGVWAIPFCYLTVGIQTAVIGSAGVARMPWRRFLPAAALGTFLWGVVYGTVGMAVVW
+AVIGAALGEGRGVLALVLILAAVAAFVVWRRRRTLRRHGAG
+>PROKKA_00870
+MMAWIDGLPLLWSIGFFWMLAILRTLIVFSLGRGLASGVERTRWFARVMEGPVYVRAQRF
+IQRHGVWAIPFCYLTVGIQTAVIGSAGVARMPWRRFLPAAALGTFLWGVVYGTVGMAVVW
+AVIGAALGEGRGVLALVLILAAVAAFVVWRRRRTLRQHGAG
+>PROKKA_01913
+MMAWIDGLPLLWSIGFFWMLAILRTLIVFSLGRGLASGVERTRWFARVMEGPVYVRAQRF
+IQRHGVWAIPFCYLTVGIQTAVIGSAGVARMPWRRFLPAAALGTFLWGVVYGTVGMAVVW
+AVIGAALGEGRGVLALVLILAAVAAFVVWRRRRTLRRHGAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001908.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001908.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a29d85d6371a7650028d1dfa080a685e0d0b85f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001908.fa
@@ -0,0 +1,24 @@
+>PROKKA_01996
+MPVRHNPQPLFRDLFTPEAVAARGGRPAAGMFLSSGDPTTAEICAGAGLDYLLIDAEHAP
+LTLQDVLAQLRTIAGYRVPTLVRVPALDTVAIKQFLDLGAQSLLVPMVDDAAMARRAVAA
+ARYPDGSAEGGVRGVGSALARSGRWNRIPGYLPGAADHVSVIVQIETAAGVRNADEIAAV
+DGIDGVFIGPSDLSASLGLLGQQSHPDVVAAVEEVITKVKAAGKIVGVNAFVPAQADAYA
+AAGADYVNVGADVALLARAAEALADRWCPAPSNAAADGQSAPRASY
+>PROKKA_01690
+MPVRHNPQPLFRDLFTPEAVAARGGRPAAGMFLSSGDPTTAEICAGAGLDYLLIDAEHAP
+LTLQDVLAQLRTIAGYRVPTLVRVPALDTVAIKQFLDLGAQSLLVPMVDDAAMARRAVAA
+ARYPDGSAEGGVRGVGSALARSGRWNRIPGYLPGAADHVSVIVQIETAAGVRNADEIAAV
+DGIDGVFIGPSDLSASLGLLGQQSHPDVVAAVEEVITKVKAAGKIVGVNAFVPAQADAYA
+AAGADYVNVGADVALLARAAEALADRWCPAPSNAAADGQSAPRASY
+>PROKKA_00797
+MPVRLNAQPLVRDLFTPEARAARGGRPAAGMFLSSGDVTAAEICAGAGMDYLLIDGEHAP
+LSLESVLAQLRAVAGYGVPVMTRVPSLDAVLVKQFLDLGAQTLLVPMVDTAEQAAEAVRA
+VRYPPHGVRGVGSALARSGRWNRIDGYLTHDADHVGLFVQIETAAGVENARSIAETSGVD
+GIFVGPSDLSASMGLIGQQTHPDVVAAVQSVIAAANAAGTVVGVNAFAEPQARAYAEAGA
+DFVNVGADVALLARAAEALADTWCPTPEAAADDDAGSRASY
+>PROKKA_01922
+MPVRHNPQPLFRDLFTPEAVAARGGRPAAGMFLSSGDPTTAEICAGAGLDYLLIDAEHAP
+LTLQDVLAQLRTIAGYRVPTLVRVPALDTVAIKQFLDLGAQSLLVPMVDDAAMARRAVAA
+ARYPDGSAEGGVRGVGSALARSGRWNRIPGYLPGAADHVSVIVQIETAAGVRNADEIAAV
+DGIDGVFIGPSDLSASLGLLGQQSHPEVVAAVEEVIAKVKAAGKFVGVNAFVPAQADAYA
+AAGADYVNVGADVALLARAAEALADRWCPAPSDAAGDGEGAPRASY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001909.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001909.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff1e767369191a0bffc0af62c7f5d1d9add0a257
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001909.fa
@@ -0,0 +1,28 @@
+>PROKKA_01997
+MPRRPAPLPPSIDPAAFTVDDARRAGVTWSRLQSSDLRRLRHGIYGPAGPAAASVREWTM
+DEVRAYQRRHPGVVVSHETAARLHGLTVPARLLAPGAVHVSVGTSGGRPVQAGLVPHRIE
+VPEGQRMTRGGVLVTTPARTLWDLCAARSALTERDVVAAGDALLCPPWLPGGGRGAPAYT
+PEELVRSLAERGRFRGRGLARAALARMRVGADSPRETRLRLALVDAGLPEPEVQCRLDPS
+DRRAPTVDLGYRQWRLALQYDGEHHRTAEQQARDVLRDRWCADHDWLSIKVMWADARDDY
+ADVVARVRRRAAEFGG
+>PROKKA_01691
+MPRRPAPLPPSIDPTAFTVDDARRAGVTWSRLQSSDLRRLRHGIYGPAGPAAVSVREWTM
+DEIRAYQRRHPDVVVSHETAARLHGLTVPARLLAPGAVHVSVGTSGGRPVQASLVPHRIE
+VPEGQRMTRGGVLVTTPARTLWDLCAARAALTERDVVVAGDALLCPPWLPGGGRGDPAYT
+PEELVRSLAERGRFRGRGLARAALARMRVGADSPRETRLRLALVDAGLPEPEVQCRLDPS
+DRRAPTVDLGYRPWRLALQYEGEHHRTAEQQARDVLRDRWCADHDWLSIKVMWADARNDY
+ADVVARVRRRAAAFGG
+>PROKKA_00796
+MPLRPVALPDSLISGPFTTRELLAAGAPAQRVRSPDLRRVAHGIHRPRSASGSTGDATAA
+ERGWLPEEVRAYQRMVPHAVVSHTTAARLHGLPLPAWAADERDVHLTFTAGAGRTRRRGL
+VAHQAGIPALDVALVAGVRVTTPPRTLWDLCSLHPRLSVEDLVVVADAVMAPGWDDEHGF
+LPGEHSAAALREALGRRGRFRGVRAAREVAERMREDVASPMETRTRLALVDQGLPEPEVQ
+VRLWGEDGAKGPVVDLAFPQWRVVVQYEGARHRTREQQERDVRRDRWCADHGWTVIKVVA
+ADVHAGLGPVAARILRLARQ
+>PROKKA_01923
+MPRRPAPLPPSIDPAAFTVDDARRAGVTWSRLQSSDLRRLRHGIYGPAGPAAVSVREWTM
+DEVRAYQRRHPDVVVSHETAARLHGLTVPARLLAPRAVHVSVGTSGGRPVQAGLVPHRIE
+VPQGQRMMRGGVLVTTPARTLWDLCAARSALTERDVVVAGDALLCPPWLPGGGRGAPACT
+PEELVRSLAERGRFQGRGLARAALARMRVGADSPRETRLRLALVDAGLPEPEVQCRLDPS
+DRRAPTVDLGYRPWRLALQYEGEHHRTAEQQARDVLRDRWCADRDWLSIKVMWADARDDY
+ADVVARVRRRAAAFGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001911.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001911.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eeedfc7d4b81aa314a2946b2ea7cc03972adbef5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001911.fa
@@ -0,0 +1,40 @@
+>PROKKA_02032
+MTELTGQASEAGTIDRLMAGWVADVETPDACAAHLLCDRWPADAVAFRFVAEDMSAVDLT
+FGELADRSRRLATGLAARGVTRGDRVPVMMSKREELVITLLALWRLGAVHVPLFTAFAAG
+AARMRIEGAAARLVVAEPRQAEKLTDIPGIEIIRTGPEWDALADSAPLAEDVAVGGDGPI
+ALLFTSGTTGRPKGVPVPLRAAAAFAVYLTCAVDLRPEDLFWNAADHGWAYGLYYGIVGT
+LVLGATSVQYRGAFSPATMVEVIRSQDVTNLAGAPTMFRALAKAGEVTEDAPLRLRRVST
+AGEPLPPSVLEWGRAALGTEIRDHYGQTELGMVICTPAHPELAAPPRPGSMGVPLPGIAA
+EIRDGQIAIDAASPMFWFPGYLGEPEKTAERFTPDGRWYLTGDTARQDDDGWFFFSSRDD
+DVILAAGYRIGPFDVESVLIDHPRVQEVAVVGLPDPEGVRGEEVVAFVVPAGAVADPDAL
+AAELQAKVRDEYSKHAYPRRVHFVDRLPKTPSGKLQRFLLRQGATD
+>PROKKA_01739
+MTERTGQAHEAGTIDRLMAGWVADVETPDACAAHLLCDRWPADAVAFRFVAEDMSAVDLT
+FGELADRSRRLATGLAARGVTRGDRVPVMMSKREELVITLLALWRLGAVHVPLFTAFAAG
+AARMRIEGAAARLVVAEPRQAEKLTDIPGIEIIRTGPEWDALADSAPLAEDVAVGGDGPI
+ALLFTSGTTGRPKGVPVPLRAAAAFAVYLTCAVDLRPEDLFWNAADHGWAYGLYYGIVGT
+LVLGATSVQYRGAFSPATMVEVISSQDVTNLAGAPTMFRALAKAGEVTEDAPLRLRRVST
+AGEPLPPSVLEWGRAALGTEIRDHYGQTELGMVICTLAHPELAAPPRPGSMGVPLPGIAA
+EIRDGQIAIDAASPLFWFPGYLGEPEKTAERFTPDGRWYLTGDTARQDDDGWFFFSSRDD
+DVILAAGYRIGPFDVESVLIDHPRVQEVAVVGLPDPEGVRGEEVVAFVVPAGAVADPDAL
+AAELQAKVRDEYSKHAYPRRVHFVDRLPKTPSGKLQRFLLRQGAAG
+>PROKKA_00788
+MTERTGQASEAGTIDRLMAGWVADVETPDACAAHLLCDRWPADAVAFRFVAEDMSAVDLT
+FGELADRSRRLATGLAARGVTRGDRVPVMMSKREELVITLLALWRLGAVHVPLFTAFAEG
+AARMRIEGAAARLVVAEPRQAEKLTDIPGIEIIRTGPEWDALADSAPLAEDVAVGGDGPI
+ALLFTSGTTGRPKGVPVPLRAAAAFAVYLTCAVDLRPDDLFWNAADHGWAYGLYYGIVGT
+LVLGATSVQYRGAFSPATMVEVIRSQGVTNLAGAPTMFRALAKAGEVTEDAPLRLRRVST
+AGEPLPPSVLEWGRSALGTEIRDHYGQTELGMVICTLAHPELAAPPRPGSMGVPLPGIAA
+QIRDGQIAIDAASPLFWFPGYLGEPEKTAERFTPDGRWYLTGDTARQDDDGWFFFSSRDD
+DVILAAGYRIGPFDVESVLIDHPRVQEVAVVGLPDPEGVRGEEVVAFVVPAGAVVDPDAL
+AAELQAKVRDEYSKHAYPRRVHFVDRLPKTPSGKLQRFLLRQGAAD
+>PROKKA_01967
+MTERTGQAHEAGTIDRLMAGWVADVETPDACAAHLLCDRWPADAVAFRFVAEDMSAVDLT
+FGELADRSRRLAAGLAARGVTRGDRVPVMMSKREELVITLLALWRLGAVHVPLFTAFAAG
+AARMRIEGAAARLVVAEPRQAEKLTDIPGIEIIRTGPEWDALADSAPLAEDVAVGGDGPI
+ALLFTSGTTGRPKGVPVPLRAAAAFAVYLTCAVDLRPEDLFWNAADHGWAYGLYYGIVGT
+LVLGATSVQYRGAFSPATMVEVIRSQDVTNLAGAPTMFRALAKAGEVAEDAPLRLRRVST
+AGEPLPPSVLEWGRAALGTEIRDHYGQTELGMVICTPAHPELAAPPRPGSMGVPLPGIAA
+EIRGGQIAIDAASPLFWFPGYLGEPEKTAERFTPDGRWYLTGDTARQDDDGWFFFSSRDD
+DVILAAGYRIGPFDVESVLIDHPRVQEVAVVGLPDPEGVRGEEVAAFVVPAGAVADPDAL
+AAELQAKVRDEYSKHAYPRRVHFVDRLPKTPSGKLQRFLLRQGAAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001914.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001914.fa
new file mode 100644
index 0000000000000000000000000000000000000000..099360d4ef585f8a94a2e3a165824bf8a4cee476
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001914.fa
@@ -0,0 +1,32 @@
+>PROKKA_02046
+MTTKDSRTRSLIDVDVLEYHRLLTPEQQEKLGEIRAALAEIVTPHVAEAWSRDEFPHEIA
+RRVGELGYNHISGMTEDPLFRGHLMAELARADISLSVYFALHNDLVGATLEALGSEEQKQ
+TWLPGLYAMEYTGCFALTEPEHGSDVAGGMATTARREGDEWVINGAKRWIGNGTMSRIAI
+VWARDEEDDQVKGFIVETDTPGYEATKIEHKTAVKIVQNADITFTDVRIPAENKLEKANT
+FADTNVILLGSRNGLGWQAVGAQQGILDAARRYALERTQFGRPIAGHQLVQSLLVQIAAN
+LAATLGMAHRAVQLEAAGEVSMTQASLVKLKTSQMCRESAALGRQMMGGNGILADVGLGR
+FFCDVEAIFTYEGTYEVNSLIVGRGLTGHSAFL
+>PROKKA_01752
+MTTTDSRTRSLIDVDVLEYHRLLTPEQQEELTEIRAALAEIVTPHVAEAWSRDEFPHEIA
+RRVGELGYNHISGMTEDPLFRGHLMAELARADISLSVYFALHNDLVGATLEALGSEEQKQ
+TWLPGLYAMEYTGCFALTEPEHGSDVAGGMATTARREGDEWVINGAKRWIGNGTMSRIAI
+VWARDEEDDQVKGFIVETDTLGYEATKIEHKTAVKIVQNADITFTDVRIPAENKLEKANT
+FADTNVILLGSRNGLGWQAVGAQQGILDAARRYALERTQFGRPIAGHQLVQSLLVQIAAN
+LAATLGMAHRAVQLEATGEVSMTQASLVKLKTSQMCRESAALGRQMMGGNGILADVGLGR
+FFCDVEAIFTYEGTYEVNSLIVGRGLTGHSAFL
+>PROKKA_00734
+MTTTDSRTRSLIDVDVLEYHRLLTPEQQEKLTEIRAALAEIVTPHVAEAWSRDEFPHEIA
+RRVGELGYNHVSGMTEDPLFRGHLMAELARADISLSVYFALHNDLVGATLEALGSEEQKQ
+TWLPGLYAMEYTGCFALTEPEHGSDVAGGMATTARREGDEWVINGAKRWIGNGTMSRIAI
+VWARDEEDDQVKGFIVETDTPGYEATKIEHKTAVKIVQNADITFTDVRIPAENKLEKADT
+FADTNVILLGSRNGLGWQAVGAQQGILDAARRYALERTQFGRPIAGHQLVQSLLVQIAAN
+LAATLGMAHRAVQLEAAGEVSMTQASLVKLKTSQMCRESAALGRQMMGGNGILADTGLGR
+FFCDVEAIFTYEGTYEVNSLIVGRGLTGHSAFL
+>PROKKA_01980
+MTTTDSRTRSLIDVDVLEYHRLLTPEQQEKLTEIRAALAEIVTPHVAEAWSRDEFPHEIA
+CRVGELGYDHISGMTEDPLFRGYLMAELARADISLSVYFALHNDLVGATLEALGSEEQKQ
+KWLPGLYAMEYTGCFALTEPEHGSDVAGGMATTARREGDEWVINGAKRWIGNGTMSRIAI
+VWARDEEDDQVKGFIVETDTSGYEATKIEHKTAVKIVQNADITFTDVRVPAENKLEKANT
+FADTNVILLGSRNGLGWQAVGAQQGILDAARRYALERAQFGRPIAGHQLVQSLLVQIAAN
+LAATLGMAHRAVQLEAAGEVSMTQASLVKLKTSQMCRESAALGRQMMGGNGILADVGLGR
+FFCDVEAIFTYEGTYEVNSLIVGRGLTGHSAFL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001915.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001915.fa
new file mode 100644
index 0000000000000000000000000000000000000000..395c8bcb5dad7746be721280e7e2775fdf1778ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001915.fa
@@ -0,0 +1,56 @@
+>PROKKA_02048
+MSEHMITWDQDADGVVTLTMDDPQARVNTMNERYQDAMDAVVDRLEAERDTVTGVVLTSA
+KKTFFAGGDLDSLAQAGPEDVESVFALTQRVKGQLRRLETLGRPVVAAINGTALGGGLEI
+ALACHRRIAVDDPGLKVGLPEVTLGLLPGGGGITRLVRMVGVERALMEWLLQGTARDARA
+AMEKGIIDEVVTDPADLVPAAKRWILEHRDDADAAAKPWDVKGFRIPGGTPAQASFASRL
+PAFAATLRRQLHGADLPAPKAILSAAVEGSQVDFDTASRIETRYFVSLVTGHTSSAMIQA
+FHSDMQALRSGAALGGPSRERSTITTAAVLGAGMMGVGIAHALALNGVDVMLKDVSLEAA
+ERGRERVGALLEGRVAKGRMSREDADAVLARVQPTEDYQDLAHVDAVIEAVFEDVELKDS
+VFAEVEKVVGPDTLLCSNTSTLPITLLQGPRERSQDFIGLHFFSPVDRMKLVEIIRGEQT
+SQRTVERAYDLVQQIRKLPILVNDGRGFYTSRVYGTLVLEAAALVEEGVDAQRIERAARH
+AGFPASPLAMMDEVSLTLIQHIRREEEKAVAEAGGERPVRPGERVVERMVDEFGRPGRAQ
+GAGFYEYPEEGPKHLWPGLAEHFATGADVPEQDLQDRLLYRMAIETARCFDDGVLTDAPS
+ANLGGVFGIGFPPHTGGPVTFMTHREGGPAAFVARADELADRYGERFRPGDTLRQRAERG
+EGPGR
+>PROKKA_01754
+MSEHMITWDQDTDGVVTLTMDDPQARVNTMNERYQDAMDAVVDRLEAERDTVTGVVLTSA
+KKTFFAGGDLDSLAQAGPEDVESVFALTQRVKGQLRRLETLGRPVVAAINGTALGGGLEI
+ALACHRRIAVDDPGLKVGLPEVTLGLLPGGGGITRLVRMVGVERALMDWLLQGTARDARA
+AMEKGILDEVVTDPADLVPAAKRWILEHRDDADAAAKPWDVKGFRIPGGTPAQASFASRL
+PAFAATLRRQLHGADLPAPKAILSAAVEGSQVDFDTASRIETRYFVSLVTGHTSSAMIQA
+FHSDMQALRSGAALGGPSRERSTITTAAVLGAGMMGVGIAHALALNGVDVMLKDVSLEAA
+ERGRERVGALLEGRVAKGRMSREDADAVLARVQPTEDYQDLAHVDAVIEAVFEDVELKDS
+VFAEVEKVVGPDTLLCSNTSTLPITLLQGPRERSQDFIGLHFFSPVDRMKLVEIIRGEQT
+SPRTVERAYDLVQQIRKLPILVNDGRGFYTSRVYGTLVLEAAALVEEGVDAQRIERAARH
+AGFPASPLAMMDEVSLTLIQHIRREEEKAVAEAGGERPVRPGERVVERMVDEFGRPGRAQ
+GAGFYEYPEQGPKHLWPGLAEHFATGADVPEQDLQDRLLYRMAIETARCFDDGVLTDAPS
+ANLGGVFGIGFPPHTGGPVTFMTHREGGPAAFVARADELADRYGERFRPGGTLRQLAERG
+EGPGR
+>PROKKA_00732
+MTENTITWDQDAEGVVTLTMDDPTAKVNTMNGHWQESMRAAVERLEQERESITGVILTSA
+KKTFFAGGDLDQLGPSGPEDAEDVFAMTEHVKSLLRRLEKLGRPVVAAINGAALGGGLEI
+ALACHRRVAVDDPRIKVGLPEVTLGLLPGGGGITRLVRMLGLEKALMDWLLQGTQYRPAQ
+AKEKGVIDELVSSPEELLPAARRWILEQGAAAAKAREGGPEETDEALGAPSYAVKPWDRK
+GFRLPGGTPQQPQLASRLPAFAATLVKTLHGADLPAPRAILSAAVEGAQVDFDTASRIET
+RYFTSLVTGRVSTAMVQAFHTEMGAIRAGAGLGERVSERHTIATAAVLGAGMMGAGIAHA
+LATSGIDVVLKDVSKENAERGKAHCADLVGKAVARGRMDQSAADEVLGRIRTTDDYADIA
+GVDAVIEAVFEDFDLKSEVFAEVEKVVGRQTLLCSNTSTLPITQLQGPRERAADFVGLHF
+FSPVDRMKLVEIIRGEQTSQETVERAYDLVQQIRKVPILVNDGRGFYTSRVFGTLVLEAA
+AMVEEGVDPQRVERTARQAGFPGAPLAMLDEVSLTLTQHVRREAEKAAEAAGTERAEQPG
+ERVVDRMVEEFDRPGRARGAGFYEYPAEGPKHLWPGLREHFAAEVDVSDEDLKDRFLYRM
+ALETAACFEAGVLTDTASADIGGILGIGYPPHTGGPATFATNRPGGLADFVSRADALADA
+YGERFRPSDWLRERAAAGQGLA
+>PROKKA_01982
+MSEHMITWDQDADGVVTLTMDDPQARVNTMNERYQDAMDAVVDRLEAERDTVTGVVLTSA
+KKTFFAGGDLDSLAQAGPEDVESVFALTQRVKGQLRRLETLGRPVVAAINGTALGGGLEI
+ALACHRRIAVDDPGLKVGLPEVTLGLLPGGGGITRLVRMVGVERALMEWLLQGTARDARA
+AMEKGIIDEVVTDPADLVPAAKRWILEHRADADAAVKPWDVKGFRIPGGTPAQASFASRL
+PAFAATLRRQLHGADLPAPKAILSAAVEGSQVDFDTASRIETRYFVSLVTGHTSSAMIQA
+FHSDMQALRSGAALGGPSRERSTITTAAVLGAGMMGVGIAHALALNGVDVMLKDVSLEAA
+ERGRERVGALLEGRVAKGRMSREDADAVLARVQPTEDYQDLAHVDAVIEAVFEDLELKDS
+VFAEVEKVVGPDTLLCSNTSTLPITLLQGPRERSQDFIGLHFFSPVDRMRLVEIIRGEQT
+SPRTVERAYDLVQQIRKLPILVNDGRGFYTSRVYGTLVLEAAALVEEGVDAQRIERAARH
+AGFPASPLAMMDEVSLTLIQHIRREEEKAVAEAGGERPVRPGERVVERMVDEFGRPGRAQ
+GAGFYEYPEQGPKHLWPGLAEHFATGADVPEQDLQDRLLYRMAIETARCFDDGVLTDAPS
+ANLGGVFGIGFPPHTGGPVTFMTHREGGPAAFVARADELADRYGERFRPGDTLRQRAERG
+EGPGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001917.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001917.fa
new file mode 100644
index 0000000000000000000000000000000000000000..762089aa2272c719557ff19270449d7ead0ecafb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001917.fa
@@ -0,0 +1,18 @@
+>PROKKA_02054
+MLVLLILATRLPGVVAGERLSVWDVAYLLLAVVVLVSEWRDYRAAVRRARR
+>PROKKA_01760
+MTIRPHSDPVTPDATWRDVPVLGFTVAAGIAVLFCLVWLLRDGLTTDYTWGLLLSPVLMS
+VPGAAVMVLWERLLARVPRLAATLVAVAALLALGLVLAWWLVEVNAQTHLFTGSTFWLLA
+VAPVCAGLAWLAHRLLPPARRPVGEPPAALDDDAWARRLAGVLRLRKDLPDARVAEIVRD
+ARARGAAAGRPLAEELGSPESYAAGFQKDRVAAPRRRAWAVTALVLLILATRLPGVVAGE
+RLSAWDVAYLLVAVVVLVWTWLDYRAAVRRARR
+>PROKKA_00766
+MSTHDHDHDPADPRRATTSAPASLEPEIEAMHAARGNEEDRDWALLLVGVLVVDGVSTAA
+ARRHLRRAAEAVAQSGEGPDELFGTPVEFAAQMRADAAEAGEPIVDSTPDASWRDVPVVG
+FTVAAAISVLFFVVWLVRDGLTTEYSWGLLAGPVLMSLLGVGAMTLWERLLPRVSRLVAV
+LAAGAAFVVVVGGLAGWLVTGGGTETLFTGSTFWLLALAPVHAALAWLANRVLPEARPVA
+TSSADPLDDDAWARELAGTLRLRMQLSDARIREIVREAQAHAADAGRPLAEEFGAPAGYA
+SRFAKDGVAGKRRMAWFFTALAGLVVLTNVAGAVEDGGIDAWSVAQILVLVLVVGVSWRE
+YRAAVRRRDAVAPGAGGR
+>PROKKA_01988
+MLLILATRLPGVVAGERPSAWDVAYLLLAVVVLVSEWCGYRAAVRRARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001922.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001922.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8cd84f08870c7bb700fa6ff27a83336bf69709cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001922.fa
@@ -0,0 +1,24 @@
+>PROKKA_02100
+MTPARPTVSVVVPVLDDAEHLRVCLALLAAQSRPALEVVVVDNGCVDDSAVLARAAGARV
+VHEPRRGVPAAAAAGLDAAVGELLVRCDADTRMPADWLERIVARFDADSGLDALTGPGTF
+HDQPGLRGRVRAALYTGAYRWGAGAAVAATPVWGSNCALRAEAWQAVRTRVHRERGDVHD
+DLDLSFQLALAGRRIRFDPDLRVEVAGRIFHSLRQRVRQGRMAVTTLQVNWARLSPGRRW
+LRRAARSRPRPHWGRGPDGQSRD
+>PROKKA_01807
+MTPARPTVSVVVPVLDDAEHLRVCLALLAAQSRPALEVVVVDNGCVDDSAVLARAAGARV
+VHEPRRGVPAAAAAGLDAAVGELLVRCDADTRMPADWLERIVARFDADSGLDALTGPGTF
+HDQPGLRGRVRAALYTGAYRWGAGAAVAATPVWGSNCALRAEAWQAVRTRVHRERGDVHD
+DLDLSFQLALAGRRIRFDPDLRVEVAGRIFHSLRQRVRQGRMAVTTLQVNWARLSPGRRW
+LRRAARSRPRPHWGRGPDGQSRD
+>PROKKA_00679
+MSGGRPAGALTVSVVIPVLDDAAHLRECLRHLARQTRPADEVIVVDNGSADESSAVARKA
+GARVVAEPLRGISAAAAAGYDAAVGDVILRCDADTRPPPDWVARAAGRFEAEPDLAALTG
+PGTFYDQPRLLARLRSRAYGAAYRFGAGAAVAGTALWGSNLGLRAEAWRAVRGRVHRRRP
+DVHDDLDLSFHLGLADVGSVVHDRRLHVGAAGRIFTSLPARVRQLRMAVTTLRLNWALLS
+PGMRWVRRARRSR
+>PROKKA_02040
+MTPARPTVSVVVPVLDDAEHLRVCLALLAAQSRPALEVVVVDNGCVDDSAMLARAAGARV
+VHEPRRGVPAAAAAGLDAAVGELLVRCDADTRMPADWLERIVARFDADPGLDALTGPGTF
+HDQPGLRGRVRAALYTGAYRWGAGAAVAATPVWGSNCALRAEAWQAVRTRVHRERGDVHD
+DLDLSFQLALAGRRIRFDPDLRVEVAGRIFHSLRQRVRQGRMAVTTLQVNWARLSPGRRW
+LRRAARSRPRPHWGRGPDGQSRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001925.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001925.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf3ed07b489504e5bfaa69393ae43e47a512a094
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001925.fa
@@ -0,0 +1,24 @@
+>PROKKA_02116
+MRPDRHSAPTSAAALAREAAILAGAGAAILLQVAHRPVGAGVAGHSRFTEDPMRRLRHTL
+AYIYAVTLPEAAPARDAVVDRVRAAHGSVRGVDAGGRPYDAADPDAQLWVAATLYAMGEQ
+VRRRMWGALDAEDADRLYRGYAPLATSLEVPASAWPVDRAAFADYWDDRVARLEVTDDAR
+RVAADLFSGQGVPAPLRAAMPLARFVTAGLLPGRVRAGLGWSWTGRDSVREARLWGLART
+LYRPLPATVRGVVVRWVLRGLPRTRKPRGAVDVEATRREVRPVWENGADV
+>PROKKA_01824
+MRPDRHSAPTSAAALAREAVILAGAGAAILLQVAHRPVGAGVAVHSRFTEDPMRRLRHTL
+AYIYAVTLPEAAPLRDAVVDRVRAAHRPVRGLDAGGHPYDAADPDAQLWVAATLYAMGEQ
+VRRRMWGALDAEDADRLYRGYAPLATSLEVPASAWPVDRAAFADYWDDRVARLEVTDDAR
+RVAADLFSGQGVPAPLRAAMPLARFVTAGLLPGRVRAGLGWSWTGRDSVREARLWGLART
+LYRPLPATVRGVVVRWVLRGLPRMPELGDAVAVRATRRDVRSVWENGGDV
+>PROKKA_00664
+MPREAHGPVSAAGLAREAAILAGAGAAILLQVAHRPVAAGVAAHSRFTEDPMRRLRHTLG
+YIYAVTLPEAAGARDAVVARVRAAHAPVRGADHEGRPYNAADADAQLWVAATLYWAGEQV
+RRRLWGALDPADADRLYRGFAPLATSLEVPAAAWPADRAAFAAYWDARIAGLEVTDDARA
+VAADLFSGRGVPAPLRAALPLARFVTAGLLPARARAGLGWDWSRRDSIREARLWVLTRTL
+YRPLPAAVRGVVVRGILRGLRRMSEAGGPAS
+>PROKKA_02054
+MRPDRRSAPTSAAALAREAVILAGAGAAILLQVAHRPVGAGVAVHSRFTEDPMRRLRHTL
+AYIYAVTLPEAASLRDAVVDRVRAAHRPVRGVDAGGHPYDAADPDAQLWVAATLYAMGEQ
+VRRRMWGALDAEDADRLYRGYAPLATSLEVPASAWPVDRAAFADYWDDRVARLEVTDDAR
+RVAADLFSGHGVPAPLRAAMPLARFVTAGLLPGRVRAGLGWSWTGRDSVREARLWGLART
+LYRPLPATVRGVVVRWVLRGLPRTRKPRGAVDVEATRREVRPVWENGADV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001930.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001930.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52ff72bebf435a7628f6a5f6ba12bb0ca6d4b793
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001930.fa
@@ -0,0 +1,16 @@
+>PROKKA_02171
+MTDIRRTATALTLGAAVVTGLGAPAAVAQTTAPATETATTAPASESPAPQEEEKDDNGNW
+GLWGLAGLLGLAGLAGRRKREVHAEPVRRDHHVAGAHRDHDVHRVDDRAGDVRTEGADAR
+RREADGTLGDATRRPGTGDAR
+>PROKKA_01885
+MTDIRRTATALTLAAAVVTGLGAPAAVAQTTAPATEAATTAPASESPAPQEEEKDDNGNW
+GLWGLAGLLGLAGLAGRRKREVHAEPVRRDHHVGGAHRDHDVHRVDDRAGDVRAEGADTR
+RPGTGDAR
+>PROKKA_00507
+MADIRKTATALTLSAAVLVGAGAPAATAAESSTAPATETATTAPASSQSPEPEQTEEKDD
+NGNWGLWGLAGLLGLAGLAGRGKKREVVHAQPVREAPRVQPTHTENHHVDTTRVQDGVRD
+AGHRAGGTDGTPGNGR
+>PROKKA_02116
+MTDIRRTATALTLGAAVVTGLGAPAAVAQTTAPATETATTAPASESPAPQEEEKDDNGNW
+GLWGLAGLLGLAGLAGRRKREVHAEPVRRDHHVAGAHRDHDVHRVDDRAGDVRTEGADAR
+RREADGTLGDATRRPGTGDSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001931.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001931.fa
new file mode 100644
index 0000000000000000000000000000000000000000..333c87a265e3713a34ab28755b306eee2dec734f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001931.fa
@@ -0,0 +1,44 @@
+>PROKKA_02172
+MSSGLPETAAVPSGHGSTRRRRPTSLARRIGAGVLLILMATILAYSFYAAGITKALLTES
+ASRDASEAWIRASEQLTAPSPGGGGDGGPGQGDLRVPGTLGQPEGTVVALVPLSGLEEHQ
+QDALIGHRVGDAGESVPLTAREAHDLLHALRDRPGGPMLDAVVGDVSYRVQAQTLTAPGP
+WVAADQVLVVGAPTGAMSDVTRQALLAVAVGLSVTVLTTAILVTLWLRRGLAPLREVAAV
+AERVAQVDMARAGLDPEDSRMPPRLLQGPDEVAVVAQALDRFTGSVEAALEQRRVQEQQM
+RRFMADASHELRTPLASVRGYAEMIAMTEELSATGRRSLDRVLFQADRMAALVDDMLLLE
+RLESVSRGRAMGLEPSEEVALAERVDLSEVVLEGVMDARAAWPDHTWVVDLPEGVEPGTQ
+RSVTGDRSQLARVVGNLLSNAAKHTPVGTTVTASVRQDQPRPGFMLVSVHDDGGGIPADR
+HATLFHRFVRGPGKGRTGPPGTEPSTGLGLAIVRSIARSHGGDVTVASEGGWTRFDVVVP
+CTPGRAGPGAAGSCCGSARAGRP
+>PROKKA_01886
+MSSGLPETAAVPSGHGSTRRRRPTSLARRIGAGVLLILMATILAYSFYAAGITKALLTES
+ASRDASEAWIRASEQLTAPSPGGGGDGGPGQGDLRVPGTLGQPEGTVVALVPLSGLEEHQ
+QDALIGHRVGDAGESVPLTAREAHDLLHALRDRPGGPMLDAVVGDVSYRVQAQTLTAPGP
+WVAADQVLVVGAPTGAMSDVTRQALLAVAVGLSVTVLTTAILVTLWLRRGLAPLREVAAV
+AERVAQVDMARAGLDPEDSRMPPRLLQGPDEVAVVAQALERFTGSVEAALEQRRVQEQQM
+RRFMADASHELRTPLASVRGYAEMIAMTEELSAAGRRSLDRVLFQADRMAALVDDMLLLE
+RLESVSRGRAMGLEPSEEVALAERVDLSEVVLEGVMDARAAWPDHTWVVDLPEGVEPGTQ
+RSVTGDRSQLARVVGNLLSNAAKHTPVGTTVTASVRQDQPRPGFMLVSVHDDGGGIPADR
+HATLFHRFVRGPGKGRTGPPGTEPSTGLGLAIVRSIARSHGGDVTVASEGGWTRFDVVVP
+CTPGRAGPGAAGSCCGSARAGRP
+>PROKKA_00580
+MSSAPPDPADASSGRGGPRPRRQSSLARRTGAGVVVILLITLTAFALFAGNTTRALTAES
+ASRNTTAAWTRAAEQLASLEAGTAFDAEPTAGDPQVPGTLGQPEGTVVALVSPADLEDHQ
+AGTLRGHRVGKAGESVPLDARQSHDIIHAIRGEPIGAPVDAAVSGEGYRFKALPMTSPGP
+WVGADQLLVVGVPTGALTAVSRRGLLMVVLGLSLTVVVTALAVFLWLRRGLAPLGEVAAM
+AERVAGMDLAHTGIDRRQTRMPKRLLQGPDEVVVVAEAMDRFTGAVEDALEERRRQEQQL
+RSFIADASHELRTPLASVRGYAEMIAMTEDLSETGRRSLDRVLHQAGRMSALVDDMLLLE
+RLESVSRGRAVGLAPSGEVPAADPVDLPEVLLEAVVDARAAWPDHQWVLDLPETLGEEGQ
+GCVTGDPAQLARLVGNLLSNGAKHTPAGTTVTTSLRIGRPLPHQVVVSVHDDGGGIPAEH
+RERLFERFARGASAGGPGREPSTGLGLAIVRSIARSHGGEASVASEAGWTRFDVVLPCAR
+WTARAQAEAAGRGGPEAPEGTGAPRE
+>PROKKA_02117
+MSSGLPETAAVPSGHGSTRRTQPTSLARRIGAGVLLILVATILAYSFFAAGITKALLAES
+ASRDASEAWIRASEQLTAPSPGGGGDARPGEGYLRAPGTLGQPEGTVVALVPLSGLEAHQ
+QDALTGHRVGDTGESVPLTAQEAHDLLHAVRDRPGGPMLDAVVGDVSYRVQAQTLTAPGP
+WVAADQVLVVGAPTGAMSDVARQALLAVAVGLSVTVLTTAILVTLWLRRGLAPLREVAAV
+AERVAQVDMARAGLDPEDSRMPPRLLQGPDEVAVVAQALERFTGSVEAALEQRRVQEQQM
+RRFMADASHELRTPLASVRGYAEMIAMTEELSAAGRRSLDRVLFQADRMAALVDDMLLLE
+RLESVSRGRAMGLEPSEEVALAERVDLSEVVLEGVMDARAAWPDHTWVVDLPEGVEPGTQ
+RSVTGDRSQLARVVGNLLSNAAKHTPVGTTVTASVRQDQPRPGFMLVSVHDDGGGIPADR
+HATLFHRFVRGPGKGRTGPPGTEPSTGLGLAIVRSIARSHGGDVTVASEGGWTRFDVVVP
+CTPGRAGPGAAGSCCGSARAGRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001934.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001934.fa
new file mode 100644
index 0000000000000000000000000000000000000000..673685d461029c64b40995ddea47bc9c6884feba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001934.fa
@@ -0,0 +1,8 @@
+>PROKKA_02192
+MPHATLASVTRRPDAPPPADPRARAALRAVLTVLAVMAVLFAAVVLTLAYGPAR
+>PROKKA_01905
+MPRATLASVTRRPDAPPPADPRTRAALRAVLTVLAVMAVLFAAVVLTLAYGPAR
+>PROKKA_00550
+MPRATLASVTHHPDAPPPADPRTRAALRAVLTVLAVLAVLFAAVVLTLAYGPAR
+>PROKKA_02136
+MPHATLASVTRRPDAPPPVDPRTRAALRAVLTVLAVMAVLFAAVVLMLAYGPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001936.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001936.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f972fb74752c1c13b8b0e1e6b6c5efa8ada22559
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001936.fa
@@ -0,0 +1,12 @@
+>PROKKA_02203
+MTHHERDDRQALAAGETYLIHVLETSDPPGNPDHYRITDAVEAHHASTGSYDVEAGGLDA
+ARELLARHAK
+>PROKKA_01916
+MTHHERDDRQALAAGETYLIHVLETSDPPGNPDHYRITDAVEAHHASTGSYDVEAGGLDA
+ARELLARHAK
+>PROKKA_00540
+MTHHDDDRSALAAGETYLVHILETSTPPGNPEHYRITDAVEAHHAETGSWDIEAAGPDAA
+RELLARHGR
+>PROKKA_02147
+MTHHERDDRQALAAGETYLIHVLETSDPPGNPDHYRITDAVEAHHASTGSYDVEAGGLDA
+ARELLARHAK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001937.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001937.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8dfebdea29cafb8f058ea9d8c35f85f5123874b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001937.fa
@@ -0,0 +1,28 @@
+>PROKKA_02207
+MVGPSLFSRLASTLLHPLAPQDVLSLLDPVHSSRQLRGVVTSVTRETPGTATIAFRPGPG
+WRAHDAGQWARIGVDVDGVRQWRSYSLSAPAGADPEITVSDIGLVSGTLVRHTKPGDVLF
+LDIPEGDFTLPDEPRPLLMLTAGSGLTPVMSMIRTLVPTRRDADVVLIHSSRTPEDALFR
+EELAELADQFPGLRVVHHHTAETGRLDLSSPAQLEGLCPDWRERAGYACGPAGFLDDAEA
+LWRREAAADLTIERFQADFAPGVAGAGGRVVFEHADVEVDAPGDVPLLVVAEEAGVAAPA
+GCRMGICHACLTPLRSGRVTDLRTGQVHGEPGELVQTCVSAAAGPLSLSL
+>PROKKA_01920
+MVGPSLFSRLASTLLHPLAPQDVLSLLDPVHSSRQLRGVVTSVTRETPGTATIAFRPGPG
+WRAHDAGQWARIGVDVDGVRQWRSYSLSAPAGADPEITVSDIGLVSGTLVRRTKPGDVLF
+LDVPEGDFTLPDEPRALLMLTAGSGLTPVMSMIRTLVPARADADVVLIHSSRTPEDALFR
+EELAELADQFPGLRVVHRHTADEGRLDLSSPAELEDLCPDWRDRAAYACGPAEFLDDAED
+LWRREAGEDLRIERFRADFAAGVAGAGGRVVFEHADAEADAPGDVPLLIVAEEAGVAAPS
+GCRMGICHACLTPLRSGQVTDLRSGEVHGEPGELIQTCVSAAAGPLSLDL
+>PROKKA_00538
+MAGPSLLSRLASTLLHPLTPQDVLGLLDPVHSSRQLRGVVTSVRRETPGTATIAFRPGPG
+WRLHDAGQWARIGVDVDGVRQWRSYSLSAPAGADPEITVSDIGLVSGTLVRRTVPGDVLF
+LDVPEGDFTLPEEPRPLLMLTAGSGLTPVMSMIRTLVPARRDADVVLVHSSRTPETALFR
+EELAELADQFPCLRVVHRHTADEGRLDLSSPAELEALCPDWRERAAYACGPAPFLDDAED
+LWRREAGGELRIERFRADFAPGVAGAGGRVVFEHSDAEADAPGDVPLLIVAEEAGVAAPA
+GCRMGICHACLTPLRSGQVTDLRSGEVHGEPGDLVQTCVSAAAGPVSLDL
+>PROKKA_02151
+MVGPSLFSRLASTLLHPLAPQDVLSLLDPVHSSRQLRGVVTSVTRETPGTATIAFRPGPG
+WRAHDAGQWARIGVDVDGVRQWRSYSLSAPAGADPEITVSDIGLVSGTLVRRTKPGDVLF
+LDVPEGDFTLPDEPRALLMLTAGSGLTPVMSMIRTLVPARADADVVLIHSSRTPEDALFR
+EELAELADQFPGLRVVHHHTAETGRLDLSSPAQLEGLCPDWRERAGYACGPAGFLDDAEA
+LWRREAAADLTIERFQADFAPGVAGAGGRVVFEHADAEADAPGDVPLLIVAEEAGVAAPS
+GCRMGICHACLTPLRSGQVTDLRSGEVHGEPGELIQTCVSAAAGPLSLDL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001938.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001938.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d285a9350b4a2a1082aa64f63a7440108f1eba42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001938.fa
@@ -0,0 +1,27 @@
+>PROKKA_02209
+MSIPQDSGRPRPDAPTSPLAAALAQQETDPLRWEEDPAPPRRRRSFGRWMRELGWRHAVG
+VLASAFALFPLLYVLSASLDPTGTMASSNRLFSSFSGQNYVDLFSDPNRPFGRWFLNTMV
+IGVITSVMTVFLGALAAYAFSRMRFTGRRVGLLTLLLVQMFPQLLAVVAIFLLLTYIGNL
+VPVLGIGSQLGLILVYLGGALGVNTYLMYGFFNTIPPSLDEAAKLDGASHARIFFSIILR
+LVTPILAVVALLSFITTVSEFVIASVVLTDPSAQTLAVGLYGYVSETRSENWGVFAAGAV
+LAALPVMALFLFLQRYIVSGLTAGGVKG
+>PROKKA_01922
+MSIPQDSGRPRPDAPTSPLAAALAQQETDPLRWEEDPAPPRRRRSFGRWMRELGWRHAVG
+VLASAFALFPLLYVLSASLDPTGTMASSNRLFSSFSGQNYVDLFSDPNRPFGRWFLNTMV
+IGVITSVMTVFLGALAAYAFSRMRFTGRRVGLLTLLLVQMFPQLLAVVAIFLLLTYIGNL
+VPVLGIGSQLGLILVYLGGALGVNTYLMYGFFNTIPPSLDEAAKLDGASHARIFFSIILR
+LVTPILAVVALLSFITTVSEFVIASVVLTDPSAQTLAVGLYGYVSETRSENWGVFAAGAV
+LAALPVMALFLFLQRYIVSGLTAGGVKG
+>PROKKA_00535
+MSIPQDPSARAPQGQAAPAAASPLAAALAQQEIDPLRWEDGAPPPRRRRSFGRWLRELGW
+RHVVGVLASAFALFPLLYVLSASLDPTGTMASSNSLFSSFSGQNYVDLFSDPSRPYGRWF
+VNTMVIGLVTSFSTVFLGALAAYAFSRMRFAGRRVGLLTLLLVQMFPQLLAVVAIFLLLT
+YIGDLVPVLGIGSQLGLILVYLGGALGVNTYLMYGFFNTVPASLDEAAKLDGASHVQIFF
+SIILRLVTPILAVVGLLSFISTVSEFVIASVVLTDPAAQTLAVGLYGYVSETRSENWGVF
+AAGAVLAAVPVMALFLFLQRYIVSGLTAGGVKG
+>PROKKA_02645
+MTFTLLAPHQSAAISEAGIEQAARDLTRARTLGRIGLVPAFAILTVLAVISIFPIYWMFV
+TAFRPAEQMLSTNPLPGPFSLENFQYVWDTIPILSMLGNTFVMALVIAIGQLFVAILASY
+GFSRWTFRGQKILFLLFVGSWLVPFQVTMIPNYVRIAEMGLLNNMVGVILPQLAAAFAVM
+MLKQHLDSFPRELLDASDMDGRSPWRTLWEVVVPNLRPALAALAIMLFISAWNEYLWPSL
+IMQGSNDLIQVGVRSFLGSEGNNWGAVMAASALACLPIFLIYIFLQRYVVDAFVRSGLK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001941.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001941.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a51102cbab8c5156ddda660bf0689f60f8f8082b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001941.fa
@@ -0,0 +1,32 @@
+>PROKKA_02218
+MQIAEQERIASPTFVLAWVVSFLQFLAFYALVTTMAVYAVRQFAASDAGAGLASSAFVIG
+ATLSRVVTGHVVDRFGKRRVLVVALVAVALSCTLYLVASSLPALVAVRMLHGASYAFAST
+AVMALAQAAIPDGRRAEATGHLALGTTLATAIGPALGLFLAGSIGYVWLFRATLGITVVS
+LVLGLLVREAPAAAGVDGERAAGEVPLEHPAPAVGFRLRSVLHPAVLPISGFMLLVGLSY
+AGILTYLNAYSVERGLTAGAGLFFLAYAAAMLVMRLTLGTLQDRRGDDAVVYPALLCFTA
+ALLVLAFATRDWQVVLAGALSGLGYGTLMPAAQAIAVNAVPSHQLGAGISTLMLFADVGL
+GLGPVLLGGLVASAGYGAMYAALAGVLVVAAGYYFVMHGRRHGRRETVARA
+>PROKKA_01931
+MQIAEQERIASPTFVLAWVVSFLQFLAFYALVTTMAVYAVRQFAASDAGAGLASSAFVIG
+ATLSRVVTGHVVDRFGKRRVLVAALVAVALSCTLYLVASSLPALVAVRMLHGASYAFAST
+AVMALAQAAIPDGRRAEATGHLALGTTLATAIGPALGLFLAGSIGYVWLFRATLGITVVS
+LVLGLLVREAPAAADVDGERAAGEVPLEHPAPAVGFRLRSVLHPAVLPISGFMLLVGLSY
+AGILTYLNAYSVERGLTAGAGLFFLAYAAAMLVMRLTLGTLQDRRGDDAVVYPALLCFTA
+ALLVLAFATRDWQVVLAGALSGLGYGTLMPAAQAIAVNAVPSHQLGAGISTLMLFADVGL
+GLGPVLLGGLVASAGYGAMYAALAGVLVVAAGYYFVMHGRRHGRRETVARA
+>PROKKA_00473
+MHHPVTAPAEAAPRIVTPVFAVAWLVNFAQYLTFYLLATTMALYAVKQFGAGDAAAGFAS
+SAFVVGATVARIFAGHVVDSLGRRRMLLVSLSVVTLACAAYLPASSLGLLVAVRLVHGAM
+YAVASTAVMTLAQSVIPASRRAEGTGYFALGTTLATALGPAAGLMLVSAAGYPGMFWATT
+AVAAVGLAFGLALRVPDEPASARPHLVRGFRLGGILHPAVVPIGVFMLLVGVAYAGVITY
+LNGYAEQRGLGAGAGLFFLAYALVTLVMRFVLGRVQDRRGDNAVVGLGLVCFAASLVLLA
+VARQDAVVVLAGALCGLGYGTLMPAAQAIAVRLVPPHQMGTGISTLYLGVDVGIGLAPLP
+LGALLAAGGYLWMYLVLAGFVVLAGVYYVLVHGRTPAARAVAR
+>PROKKA_02157
+MQIAEQERIASPTFVLAWVVSFLQFLAFYALVTTMAVYAVRQFAASDAGAGLASSAFVIG
+ATVSRVVTGHVVDRFGKRRVLVVALVAVALSCTLYLVASSLPALVAVRMLHGASYAFAST
+AVMALAQAAIPDGRRAEATGHLALGTTLATAIGPALGLFLAGSIGYAWLFRATLGITVVS
+LVLGLLVREAPAAADVDGERAAGEAPLEHPAPAVGFRLRSVLHPAVLPISGFMLLVGLSY
+AGILTYLNAYSVERGLTAGAGLFFLAYAAAMLVMRLTLGTLQDRRGDDAVVYPALLCFTA
+ALLVLAFATRDGHVVLAGALSGLGYGTLMPAAQAIAVNAVPSHQLGAGISTLMLFADVGL
+GLGPVLLGGLVASAGYGTMYAALAGVLVIAAGYYFVMHGRRHGRRETVARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001942.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001942.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ddcdee8e65c0b32bbdd79a50be01da1942b7191b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001942.fa
@@ -0,0 +1,20 @@
+>PROKKA_02221
+MTITAIDTSSLTTEAAAVLAATPGMRYAEFLTAAPAVPGIVAVVADESARAALGLTPAAG
+DVLAVDVADESLQCREVRAAFQSGRTGGSPLRQAFAALLAGELGLDVERTSPGAAGAGFA
+LTPESEETLTAWMREHLTLRAWVAQDASALEGVAREVAADLAPALQPGALEAPVAQRVAA
+MRASARRSATL
+>PROKKA_01937
+MTITAVDTPSLTAEAAAVLAATPGMRYAEFLTAAPAVPGIVAVVAEESARAALGLTPAAG
+DVLAVDVADESLQCREVRAAFQSGRTGVSPLRQAFAALLAGELGLDVERTSPGAAGVGFA
+LTPESEETLTAWMREHLTLRAWVAQDASALEGVAREVAADLAPALQPGALEAPVAQRVAA
+MRASARRSATL
+>PROKKA_00516
+MTITAAETQSLTAEATAVLAAMPGVSYAQFLAEAPEVPGIVAVVADQAARARLGVEAEET
+GLLAVTVAPYGLRARDVRAAFQSGRTAVSPLRQALAALLEDELGLDVERTSPGAAGAGFT
+LTPESEDALTAWMRAHLTLRAWATQDASVLADVADQVNADLAPALALDGVAAPSAHLRER
+LAAMTAAARRSATI
+>PROKKA_02160
+MTITAVDTPSLTTEAAAVLAATPGMRYAEFLTAAPAVPGIVAVVAEESARAALGLTPAAG
+DVLAVDVADESLQCREVRAAFQSGRTGVSPLRQAFAALLAGELGLDVERTSPGAAGAGFA
+LTPESEETLTAWMREHLTLRAWVSQDASALEGVAREVAADLAPALQPGALEAPVAQRVAA
+MRASARRSATL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001950.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001950.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4895a4b19c9a85962fc69a6e5a377f4f4d226698
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001950.fa
@@ -0,0 +1,32 @@
+>PROKKA_02284
+MTTPFHAEADSFLGRADVVGLDSLFSAEEKAVALQVRGFVDEHIRPHIARWYDDAVFPRE
+IVPELGRLGVLGMPYEGHGMPGRSAVEYGLAAQELEAGDSGLRTFVSVQGSLAMGAIHKH
+GSEEQKAQWLPRMTTGEAVGCFGLTEPGAGSDPASMTTTARQEPGGDWVLDGVKRWIGLA
+TLADVAIIWAQTGEPGDGRGVRGFVVPTDTPGFRAETITQKLSMRASVQCEIHLDGVRLP
+ASAMLPADSAVGLKGPFQCLNEARYGIIWGAMGAARDSFDAVLDYAMERQQFGVPLASHQ
+LTQAKLADMAVAIGKGYLLAHQIGRAKDAGPLTPAMISAGKLDNCRVAIGIAREAREMLG
+GNGITLEHSPLRHANNLESVRTYEGTDEVHQLTLGRHLTGIGAFAPAR
+>PROKKA_01975
+MTTPFHAEADSFLGRADVVGLDSLFSAEEKAVALQVRGFVDEHIRPHIARWYDDAVFPRE
+IVPELGRLGVLGMPYEGHGMPGRSAVEYGLAAQELEAGDSGLRTFVSVQGSLAMGAIHKH
+GSEEQKAQWLPRMTTGEAVGCFGLTEPGAGSDPASMTTTARQEPGGDWVLDGVKRWIGLA
+TLADVAIIWAQTGEPGDGRGVRGFVVPTDTPGFRAEAITQKLSMRASVQCEIHLDGVRLP
+ASAMLPADSAVGLKGPFQCLNEARYGIIWGAMGAARDSFDAVLDYAMERQQFGVPLASHQ
+LTQAKLADMAVAIGKGYLLAHQIGRAKDAGPLTPAMISAGKLDNCRVAIGIAREAREMLG
+GNGITLEHSPLRHANNLESVRTYEGTDEVHQLTLGRHLTGIGAFAPAR
+>PROKKA_00453
+MPSPTPFHAEADSFLGRADVVGLDALFSDQEKATALAVRAFVDEHLRPHIASWYEDAVFP
+REIVPELGRLGVLGMPYEGHGMPGRSAVEYGLAAQELEAGDSGLRTFVSVQGSLAMGAIH
+KHGSEEQKAQWLPRMTAGEAVGCFGLTEPGAGSDPASMTTTARQETGGDWVIDGVKRWIG
+LATLADVAIIWAQTGEPGDGRGVRGFVVPTDTPGFRAEAITQKLSMRASVQCEIHLDGVR
+LPASAMLPADSAVGLKGPFQCLNEARYGIIWGAMGAARDSFDAVLDYAMQRQQFGVPLAS
+HQLTQAKLADMAVAIGKGYLLAHQIGRAKDAGPLTPAMISAGKLDNCRVAIGIARDAREM
+LGGNGITLEHSPLRHANNLESVRTYEGTDEVHQLTLGRHLTGIGAFAPAR
+>PROKKA_02223
+MTTPFHAEADSFLGRADVVGLDSLFSAEEKAVALQVRGFVDEHIRPHIARWYDDAVFPRE
+IVPELGRLGVLGMPYEGHGMPGRSAVEYGLAAQELEAGDSGLRTFVSVQGSLAMGAIHKH
+GSEEQKAQWLPRMTAGEAVGCFGLTEPGAGSDPASMTTTARQEPGGDWVLDGVKRWIGLA
+TLADVAIIWAQTGEPGDGRGVRGFVVPTDTPGFRAEAITQKLSMRASVQCEIHLDGVRLP
+ASAMLPADSAVGLKGPFQCLNEARYGIIWGAMGAARDSFDAVLDYAMQRQQFGVPLASHQ
+LTQAKLADMAVAIGKGYLLAHQIGRAKDAGPLTPAMISAGKLDNCRVAIGIAREAREMLG
+GNGITLEHSPLRHANNLESVRTYEGTDEVHQLTLGRHLTGIGAFAPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001954.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001954.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a553ce3990daa82cbf03917ad340aa95eeb1df4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001954.fa
@@ -0,0 +1,33 @@
+>PROKKA_00238
+MTWVVTGGAGYIGAHVVRALQGAGMDVAVVDDLSTGFADFVPADVPLLRADVGDVGQVAT
+YLTRVGAAGVVHVAGYKFAGESVREPLHTYRVNVRGTLGVLEAMERAGVPAIVFSSSAAV
+YGTPDVERVTEATATAPESPYGESKLIGEWLLADQGRATGLRHTSLRYFNVVGSADPALS
+DTSPHNLFPLVFRALDRGERPRLFGADHPTPDGTCVRDYVHVADVARAHVAAARALAESR
+ALAPVYNLGSGAGTSVRQIMEAVGRVTGRDVDPVVEPRRPGDPARIVADGSLAARDLGWE
+NRHTVEDMVRSAWEARRPPETR
+>PROKKA_01224
+MPHDESMCMMNVSAPEPTRPQLPPLARHALLIIWDSVSWILALLAFLVVRYDFGLSPTQW
+DWVLAFTLIAVVGQVAAGLVTQFYLGRHRVGSFSDAGWTAVIVCAIALAIGLALSVAAPA
+FPRGVALTMPPLALVIMLAGRFLVRNVAAGRPRADASAAVPAIVYGAGNAGHQVSQLMRQ
+AEEPPYRIVGFVDDDKGKSRLRIHGLGVRGRGTDLAEVAAELGAEAVIYAISNADAEHVE
+WVSRVCTEEGLDLVVVPPLREMVGGKVTLGSLRHLSVTDLLGRRPISTDISAISDYVSGK
+VVLVTGAGGSIGSELAVQLHHLGPAKLLLLDRDESALHGVQLDIYGNGLLDTDDIILCDI
+RDEQALQAVFEHHRPQVVFHAAALKHLPMLERFPLEGWRTNVLGTRNVLQAAHSVGVQRF
+VNISTDKAAAPTSVLGATKRLAERLTAWHATTYDLPYLSVRFGNVLGSRGSVLISFRNQI
+EKGGPVTVTHPDVTRYFMTIPEACELVLQAGAIGNPGEVLVLDMGQPVKILDVAKRMIAE
+SGQNIDIHFTGLRPGEKMHEVLFSNAEANATSQHPMISEVQVPDLDPVVVAELPSDRESI
+LAMIDDEPPVERADDTQTPGLDQAGARP
+>PROKKA_02437
+MTWVVTGGAGYIGAHVVRAFRERGLPVAVVDDLSTGHREFVPDGVPFFHADVTDTAALTA
+VLRENEAEGVVHVAGYKYAGESVRVPLTAYRANVQGTASVLDAMAAAQVQSVVFSSSAAV
+YGTPAVERVTEDTPPAPESPYGESKLIGEWLLRDQERAVGIRHTSLRYFNVVGSGWADIT
+DLSPHNLFPLVFSALERGERPHIFGDDYPTPDGTCIRDYVHVQDVAEAHVAAARALTSGV
+GLHSVYNLGSGQGTSVHEIMAAVRDVTGVTDPPEVLDRRPGDPARIVADGTLAAQDLGWR
+MRHSVEDMVRSAWDAHRRLGISASGDE
+>PROKKA_00844
+MRLLVTGGAGYIGSHFVSVARQQGRADIVVVDDFSTGLRQRVPADVPVYTIDLASDAAVA
+TLTTLLKEESIDVVVHFAAKKVVADSVVQPEDYFRSNVGATVNVLAAMRAAGAASMIFSS
+SAAVYGEPDSSIVFEDTPTVPINPYGQSKLVSELALANASRAWGLRAVALRYFNVAGAED
+AILADTTTTNLMPAIRDVITRGQRLSVFGDDYPTVDGTCVRDYVHVVDLAEAHLAALPAV
+QGSTDPATRIYNVGTGSGSSVLEVVDAFRRRPGVDLDYDIQPRRPGDPGALTANVSLIEK
+ELGWVARYTRDDIVTSVIDFPPRLVT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001956.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001956.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bafac1b13653e12e056c337bc73f91d0b9d6f0a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001956.fa
@@ -0,0 +1,36 @@
+>PROKKA_00257
+MTVGHGAHGPRHSDPRYVALQTEREKHARAAARGTSVWSADQDAAVPREPLRIPELLLGA
+LLAMEAFSVPLGPVALPLNEAGMLLLLALALCRRSRRDVSALGLTAVLAAAVLLFLAIVS
+VSQGIPDLEWLRRWVRMAALVGLVGCIAGGRLSLRSLAVGLGAAMALNVPLFYAGLVPAP
+YGSFLTGILADKNVAGLYYAAMPVLALALVRTRRWKLILLVAAAVCVVLTGSRTSMAGFA
+CAVLWLWLTPRMGAGLRLVLLAVLAWAVAFAEENLARIAFFADRTGTDWLRSNIQAETAV
+RVAETPWYGRGLTTAYVDFGGATWHYHNSYAGLYTEGGVVLLLAVLGAYAFFGLRLFSAR
+LRTPSRVAVEAAAVVVFVSATQLGEVFITIPSMLVVAAGVTLWLDERDAPLESEVLERRR
+RRVLAAARRGQHAPSSGGHAVPDL
+>PROKKA_02416
+MAVRHQTRGPVDTDPRYRALLEARAAQERQAARGTAAWSRDDATGLPREPLRIPELILGA
+LLAMEAFGVRLGPLGVPLNEAAMLLLLFLALCRRSRRDTSALGLSAVLAGAVMVFLAVVS
+VNQGIPDMEWLRRWVRIAALVGLVGCIAGGRLDLRSVLTGLLAAMAANVPLFYAGVVPTP
+YGSFLTGFLADKNVAGLYYAAMPVLALAVVRSRRWKLAILLAAAVCLFLTGSRTSMAGFG
+VALVWLAVTPRLAAGLRVVLLVVLGWAVGFAEENLSRLEVFGDRTGTDWLRGTIQAATEA
+KAATTPWHGRGLTEAYVTIGRDTWLYHDSYAGLFTEGGVVLLVAVLGAYAFFGLRLFSTR
+LRTPSRVAVEAAAAVVFVTATQLGEVFITIPGMLIVAAGVSLWLRERDAPLESEVRERRR
+RQVLAAARRGSTPESSADLAAPGSA
+>PROKKA_02298
+MPPHLPSGPALQDPRYQAVLAERGRREAATARGVSVLTAEDAAGPRTSLRVPELLLGFLL
+AMEAYTLPAGGVPVPLNEAAMMVLLGLALCRRAKRRASALGVAALLAVLVGVYLAAVSLA
+MGVPDAVWLRRLVRMAALTALVGCFAARRVDLRSVLTGLLAAMAVNVPLFYAGLVPAPYQ
+GFLTGFLADKNVAGLYYAAVPVLALTFVRRPGVRLLLLSASGLCVFLTGSRTSLAGFACA
+LVWVVLTPRMGPVLRVALLALLAWAVGFAEENLARVGVYSDREGTDWFRSVIQTATGVKV
+EATPWTGQGLAQSFVELDAGRFLFHNSYAALYVEGGVVLTAAMLTAYAVYGLRLGATRLR
+TPSRVAVEAAAVVVLVTATQLGEVFVSIPSMLILAAGATLAITEADAPLDAQARARREER
+TLRQAAARGH
+>PROKKA_00536
+MTVGHGAHGPRHSDPRYVALQAEREKHARAAARGTSVWSAGQDAAAPREPLRIPELLLGA
+LLAMEAFSLPLGPVALPLNEAGMLLLLALALCRRSRRDVSALGLTAVLAAAVLLFLAVVS
+VSQGIPDLEWLRRWVRMAALVGLVGCIAGGRLSLRSLAVGLGAAMALNVPLFYAGLVPAP
+YGSFLTGVLADKNVAGLYYAAMPVLALALVRTRRWKLILLVAAAVCVVLTGSRTSMAGFA
+CAVLWLWLTPRMGAGLRLVLLAVLAWAVAFAEENLARIAFFADRTGTDWLRSNIQAETAV
+RVAETPWYGRGLTTAYVDFGGATWHYHNSYAGLYTEGGVVLLLAVLGAYAFFGLRLFSAR
+LRTPSRVAVEAAAVVVFVSATQLGEVFITIPSMLVVAAGVTLWLDERDAPLESEVLERRR
+RRVLAAARRGQHAPSSGGHAVPDL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001957.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001957.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f35efa0ae73df71f578ceb66215b7bfb440f69a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001957.fa
@@ -0,0 +1,26 @@
+>PROKKA_00323
+MIMGFIDQMRAKGHAVESICRVLRQEGCQIAARTYRAWRRRSASARDTSDAVLLNVLHDL
+VGTPEGLYGRRKMTAWLRREGHQVGAGRVDRLMRVAGMNGVRRGRPVRTTVPAKDGCRAG
+DLLNRDFTAAAPNTKWVADFTYVRTWAGFVYVAFVLDCYSQRILAWHAATAKTTPLVLTP
+LRIALWDRDRHGHPVQPGELIAHSDAGSQYTSLRFAEHLAAEGIAASIGTVADAYDNALM
+ECVIGLYKTECITTTIFHNGPYKTIADVEYATAGWVEWYNNRRLHSSLAMTTPAEYETAY
+YAALNRELAPT
+>PROKKA_02273
+MIMGFIDQMRAKGHAVESICRVLRQEGCQIAARTYRAWRRRSASARDTSDAVLLNVLHDL
+VGTPEGLYGRRKMTAWLRREGHQVGAGRVDRLMRVAGMNGVRRGRPVRTTVPAKDGCRAG
+DLLNRDFTAAAPNTKWVADFTYVRTWAGFVYVAFVLDCYSQRILAWHAATAKTTPLVLTP
+LRIALWDRDRHGHPVQPGELIAHSDAGSQYTSLRFAEHLAAEGIAASIGTVADAYDNALM
+ECVIGLYKTECITTTIFHNGPYKTIADVEYATAGWVEWYNNRRLHSSLAMTTPAEYETAY
+YAALNRELAPT
+>PROKKA_01825
+MIMGFIDQMRAKGHAVESICRVLRQEGCQIAARTYRAWRRRSASARDTSDAVLLNVLHDL
+VGTPEGLYGRRKMTAWLRREGHQVGAGRVDRLMRVAGMNGVRRGRPVRTTVPAKDGCRAG
+DLLNRDFTAAAPNTKWVADFTYVRTWAGFVYVAFVLDCYSQRILAWHAATAKTTPLVLTP
+LRIALWDRDRHGHPVQPGELIAHSDAGSQYTSLCFAEHLAAEGIAASIGTVADAYDNALM
+ECVIGLYRTECITTTIFHNGPYKTIADVEYATAGWVEWYNNRRLHSSLAMTTPAEYETAY
+YAALNRELAPT
+>PROKKA_00592
+MRVAGMNGVRRGRPVRTTVPAKDGCRAGDLLNRDFTAAAPNTKWVADFTYVRTWAGFVYV
+AFVLDCYSQRILAWHAATAKTTPLVLTPLRTALWDRDRHGHPVQPGELIAHSDAGSQYTS
+LRFAEHLAAEGIAASIGTVADAYDNALMECVIGLYKTECITTTIFHNGPYKTIADVEYAT
+AGWVEWYNNRRLHSSLAMTTPAEYETAYYAALNRELAPT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001960.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001960.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8a05bb0b5942fbc4fcc740337606a7fce372ab2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001960.fa
@@ -0,0 +1,28 @@
+>PROKKA_01645
+MAHPKTLQVFLMDGAPTGRLKCTLDNWTGLVYVVPRTSLNADGHPEAFEGTGVYLLLGQD
+ADSGDDVVYVGQAVGRANGNGLVGRIREHVRREAHDFWNRAILLSTLGDTFGPTEVTYLE
+HYFHQAATTAGRFTVDNAVAPSQGNVTQEKRAELEEYADKARLLISALGHRVFESADGSH
+AAAAAGRATQAPEAAPKRTLFTMTVNGVRAQGHPTPDGFVVLRGSGLMEGLRPSAPPGVR
+AGRERFADHIGADGVLTEDVSFTSSSAAAGFVAGGSMSGPSSWRAPDGRTLGEVEAASAA
+PEPMEDDA
+>PROKKA_00903
+MAHPKTLQVFLMDGVPTGRLKCTLDNWTGLVYVVPRTSLNADGHPEAFEGTGVYLLLGQD
+ADSGDDVVYVGQAVGRANGNGMVGRIREHVRKEAHDFWNRAILLSTLGDTFGPTEVTYLE
+HFFHQAASTTGRFTVDNAVAPSQGNVTEEKKAELEEYADKAKILISALGHRVFESADGSH
+AVVAAGRTTQAPEAVPERTLFTMTVNGVGAQGHPTPDGFVVLRGSGLMEGLRPSAPAGVR
+ASRERFAGHIGADGVLIEDVSFTSSSAAAGFVAGGSMSGPSSWRAPDGRTLGEVEAASAK
+TVPIEDDA
+>PROKKA_00842
+MAHPKTLQVFLMDGVPTGRLKCTLDNWTGLVYVVPRTSLNADGHPEAFEGTGVYLLLGQD
+ADSGDDVVYVGQAVGRANGNGMVGRIREHVRKEAHDFWNRAILLSTLGDTFGPTEVTYLE
+HFFHQAASTTGRFTVDNAVAPSQGNVTEEKKAELEEYADKAKILISALGHRVFESADGSH
+AVVAAGRTTQAPEAVPERTLFTMTVNGVGAQGHPTPDGFVVLRGSGLMEGLRPSAPAGVR
+ASRERFAGHIGADGVLIEDVSFTSSSAAAGFVAGGSMSGPSSWRAPDGRTLGEVEAASAK
+TVPIEDDA
+>PROKKA_01875
+MAHPKTLQVFLMDGAPTGRLKCTLDNWTGLVYVVPRTSLNADGHPEAFEGTGVYLLLGQD
+ADSGDDVVYVGQAVGRANGNGLVGRIREHVRREAHDFWNRAILLSTLGDTFGPTEVTYLE
+HYFHQAATTAGRFTVDNAVAPSQGNVTQEKRAELEEYADKAKLLISALGHRVFESADGSH
+AAAAAGRATQAPEAEPKRTLFTMTVNGVRAQGHPTPDGFVVLRGSGLMEGLRPSAPPGVR
+AGRERFADHIGADGVLTEDVSFTSSSAAAGFVAGGSMSGPSSWRAPDGRTLGEVEAASAA
+PEPMEDGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001970.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001970.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7065b23c286646680cb74f1a21ec5c2ba9ac6052
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001970.fa
@@ -0,0 +1,24 @@
+>PROKKA_01707
+MSTPRVTTTLLKPAQDPARVLVVGAGLGTGVQALWSLAAQQLPEDTVVVGYDLPGHGASE
+PHAEPFSMAELADAVVAAVQALQEDGTVPADLPVHFAGVSLNGCVALQLALDHADTVSGV
+AVICSAAKIGEAGSWRERAELVERAGTPTLVEGSAQRWFADGFIAAHPERTTGLLHTLQE
+ADRHSYARLCEALADFDVRGRLGEIAVPVLTIHGVADQVTPPSAGEEIAAAVPGTVTHVF
+DETAHQAPLEQPERTAAALAAFPAR
+>PROKKA_00845
+MAQPTVTTTLLKAAKSPARVLLVGAGLGTGVHALWSLAAQRMAEDTLVIGYDLPGHGASA
+PHADPYTIAELADAVVAAVARLKDEGAIPADVPLAYAGVSLNGCVALQLALEHADVVSGV
+AVVCSAAKIGEAKAWHERAELVEKAGTPTMVAGSAERWFAPGFIERHPERTTDLLHTLQE
+ADRHSYARLCEALAGFDVRERLGEIRVPVLTVHGAHDAVTPPAAGEEIAAAVPGTTVVAL
+DDAAHQAPLEQPVATAEALAAFLTTVQEAAK
+>PROKKA_00778
+MTTPEVAVTLLKPAEAPTRVLVAGAGLGTGVEALWSLAARELPADTLVVGWDLPGHGASA
+PHDAPLTVADLADAVAAAVGRLRAEGTIPADVPVHYAGVSLNGCVALQLALDHADTFASA
+TVICSAAKIGEKDAWLERAELVESAGTPTQVEGSSKRWFAEVFIAEHPERATGLLHTLQQ
+ADRHSYARLCEALAEFDVRGRLGEDTVPLMTIHGVEDQVTAPAAGEEIAAAVPGTVVHAF
+EHTAHQAPLEQPERTAEALAAFLAR
+>PROKKA_01935
+MSTPRVTTTLLKPAQDPARVLVVGAGLGTGVQALWSLAAQQLPEDTVVVGYDLPGHGASE
+PHAEPFSMAELADAVVAAVQALQEDGTVPADLPVHFAGVSLNGCVALQLALDHADTVSGV
+AVICSAAKIGEAGSWRERAELVERAGTPTLVEGSAQRWFADGFIAAHPERTTGLLHTLQE
+ADRHSYARLCEALADFDVRGRLGEIAVPVLTIHGVADQVTPPSAGEEIAAAVPGTVTHVF
+DETAHQAPLEQPERTAAALAAFPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001975.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001975.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8287b4e0827343d78393629feca492342492d60
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001975.fa
@@ -0,0 +1,19 @@
+>PROKKA_01950
+MSPLMTVGEFALATGLSAKALRFYDERGLLAPADVDAHSGYRCYAPGQIRTAAQIRVLRA
+AGLTVDDVRSVLADPASLPARLETHAAELRRRRDLEDRALALAVAGVYAAPDPDDDGGPA
+RPGPVAERTVGPTPWAGVVQRVALDEAGEESTTERANAAFVTLFQALAEAGSAPAGPLWT
+ALRPVPGAADVVETVLAVPLSGPAPAGLRVDGHEVVAGTLPRRVERYVDVRADTGEVDLL
+DDAPGGALPHPDLLGLMDAFDMEDAGAAPEIRQILADPEAGHIELAVTVREEAGAGQG
+>PROKKA_01324
+MAVEEQRLALPVDGELPEGFAVQGLRIASGVLPRREEAAVTVRVLD
+>PROKKA_00436
+MSPLMTVGEFALATGLSAKALRFYDERGLLAPADVDAHSGYRRYEPGQIRTAAQIRVLRA
+AGLTVDDVRSVLADPASLPARLEAHAAEVRRRRDLEDRALALAAAGVYAAPDPDDDGGPA
+RPGPVAERTVGPTPWAGVVQRVALDEAGEEATTERANAAFATLFQALAEAGSAPAGPPWT
+ALRPVPSAADVVETVLAVPLSGPAPAGLRVDGHEVVTGTLPRRVERYVDVRADAGEVDLL
+DDAPGGALPHPGLLGLMDAFDVEDAGTAPEIRQILADPEAGHVELAVTVREEAGAGQG
+>PROKKA_02180
+MSPLMTVGEFALATGLSAKAHAAELRRRRDLEDRALALAVAGVYAAPDPDDDGGPARPGP
+VAERTVGPTPWAGVVQRVALDEAGEESTTERANAAFATLFQALAEAGSAPAGPLWTALRP
+VPGAADVVETVLAVPLSGPAPAGLRVDGHEVVAGTLPRRVERYVDVRADTGEVDLLDDAP
+GGALPHPDLLGLMDAFDMEDAGAAPEIRQILADPEAGHIELAVTVREEAGAGQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001977.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001977.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3e825329bbcaf4ee7bd7d206fe983b088f27ff63
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001977.fa
@@ -0,0 +1,13 @@
+>PROKKA_00712
+MSAAFDHIRRDDGEHVGYLEMTDDGLFVPRDRLRRVCGDPMELEEAEELLDAVGLRVLAE
+DWLLDAADGGAARRVRIREITWDTVTVAPVLDDAAVALSVDLARAEVLTLPTDRLRPADG
+>PROKKA_00421
+MAGQDAGSLARRRGYADRMTDFDHLRAEDREHVGYIEMTDDGAFVPYDLLRRRRGEPGGL
+EEAEAVLDEIGLRLLAEDWILDADGDEPLCVRILEVTRDAVVVAPALDSAAVAKSLDLTA
+TVRLPLPTARLRQA
+>PROKKA_00697
+MTTIFDHLRADDREHVGYIEMTDDGLFIPYDLLRRRCGEPMELAEAEELLDTVGLQALGE
+QWLLRTEGDAWVPVDIREFSRESVTVAPRLDDRAVAKALDLTATVMLSLPTDRLRSAE
+>PROKKA_00721
+MTTVLDHLRADDREHVGYIEMTDDGLFIPYDLLRRRCGEPMELAEAEELLDTVGLQALGE
+QWLLRTEGDAWVPVGIQEFSRESVTVAPRLDDRAVAKALDLTATVMLSLPTDRLRSAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001980.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001980.fa
new file mode 100644
index 0000000000000000000000000000000000000000..816c8859a391886d28e2770ad977ea2ed5b8d581
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001980.fa
@@ -0,0 +1,31 @@
+>PROKKA_02247
+MSSLNTVKDTATAAGTAELETDILVIGWGKGGKTLARTLGSQGRKVTLVERDAGMVGGTC
+INVACVPTKALVHRADAVRPGDDPDAAVASAWDFRDALTSKLRDANRAMLEDLDAVTLVQ
+GEARSTGERTVEVRPAEAADGDDDGERLTIRARHVVVNTGTTPLRPEMPGVDLPGVHDSE
+TLQLQMDRSRAPRRRRLRPRPPRSSRHRRSARAA
+>PROKKA_00402
+MSEQKTTTPDLDPTGQAIATQAPLAERYDHVIVGGGMAAAKAVESIRELAPEASVAVVSA
+DTAAPVYRPDLSKTLWADADAHVEDSILATPDSEGTAPGERTAYRLGAEVTAIDPQAHTV
+TVDGRTVGYGSLLLATGAEPVAAGIPQSERVHTYRTVADYRRLKEASGPGTTAVVVGGGY
+IGTELAAGLTMAGTDVTLVVPHRPLLARMLPAELSAAVEATFQEKGVRIAEGRLASAAES
+GDAVTARLEDGTELRADLLVLALGVRPRATLAEAAGLALADQGVRVDDRLRTSAPDVYAA
+GDIATFPDALLGERRVEHADAAETQGATAGRNMVGADQAYTHTPFFWADLFDYGYEAIGE
+LDTRHRTVVDLATGEDGRPDPSTAVVYYADEAGHVRGVLLWNVWDSVPQARALIERTAQE
+PVADLGSLKGRIPLG
+>PROKKA_00715
+MTPQHVLILGSGAAGAAAARTLASRDDVRVTLVTRTGETPYTRMLIKGIAFGQTPPEMIK
+LPLPQIEVIADTVLKVDTSAKQAQLTSGAQVSYDALIVATGSMPRSLPADVFGGDDAGQG
+RVTALHSVGDALGIRKLLTGLGRPARVAIYGGGIIAAETASSLQADGHMVTLVSRSSVPG
+VGAFGAPVAERLAADHAAKVQARFGRTLQHVDETESGVTITLNDGNPVVADFLLLALGTT
+PAAPSPWTNGIDVDDHLRAAADHVYAAGGVATHHDEALDAWRIDHWEDAAAQGAHAARAA
+LHDLGVSDDPGAYLPRSPYMAMVYGQMISGVGYTAGADAHLEAGEEFIVRHEIDGIVVGV
+TGIDAVGTVYQWGQQLHGVRA
+>PROKKA_02120
+MSSLDTVKDTVTTAGTAELETDILVIGWGKGGKTLAKTLGSQGRKVTLVERDAGMVGGTC
+INVACVPTKALVHRADAVRPGDDPDAAVASAWDFRDALTSKLRDANRAMLEDLDAVTLVQ
+GEARFTGERTVEVRPAEAADGDDDGERLTIRARHVVVNTGTTPLRPEMPGVDLPGVHDSE
+TLQLQMDRTRAPRRAVVVGSGPVGLELASMLAGFGAEVTVLVRGEQILPDESDAVRDSLV
+EALQDRGVRLATGASATGFAEADGGLRVDLEEGEPIAADIVVLATGRASTAEALDPAAAG
+IELDEKGFIAVDEHLRTSAPDVWAVGDVNGGPQQTYISLDDHRIVTGQLAGDGAYSRADR
+VAVPTTVFTTPPLGSVGMTAEQAREAGHEVKVASKPVAKIAAMPRPKIEEDAHGVIEVVV
+DAATDLVLGARLHCVEAQELVNLVALAMRADVTASALRDGIWTHPSATEALNEVLGELS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001981.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001981.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e102ce46b8cb0644417c0dda1f308744e5e0d10d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001981.fa
@@ -0,0 +1,24 @@
+>PROKKA_02337
+MTDFKWRHFQGDVILWAVRWYCRYPISYRDLEEMLAERGISVDHTTIYRWVQCYAPEMEK
+RLRWFWRRGFDPSWRLDETYVKVRGKWTYLYRAVDKRGDTIDFYLSPTRSAKAAKRFLGK
+ALRGLKHWEKPATLNTDKAPSYGAAITELKREGKLDRETAHRQVKYLNNVIEADHGKLKI
+LIKPVRGFKSIPTAYATIKGFEVMRALRKGQARPWCLQPGIRGEVRLVERAFGIGPSALT
+EAMGMLNHHFAAAA
+>PROKKA_02342
+MTDFKWRHFQGDVILWAVRWYCRYPISYRDLEEMLAERGISVDHTTIYRWVQCYAPEMEK
+RLRWFWRRGFDPSWRLDETYVKVRGKWTYLYRAVDKRGDTIDFYLSPTRSAKAAKRFLGK
+ALRGLKHWEKPATLNTDKAPSYGAAITELKREGKLDRETAHRQVKYLNNVIEADHGKLKI
+LIKPVRGFKSIPTAYATIKGFEVMRALRKGQARPWCLQPGIRGEVRLVERAFGIGPSALT
+EAMGMLNHHFAAAA
+>PROKKA_02640
+MTDFKWRHFQGDVILWAVRWYCRYPISYRDLEEMLAERGISVDHTTIYRWVQCYAPEMEK
+RLRWFWRRGFDPSWRLDETYVKVRGKWTYLYRAVDKRGDTIDFYLSPTRSAKAAKRFLGK
+ALRGLKHWEKPATLNTDKAPSYGAAITELKREGKLDRETAHRQVKYLNNVIEADHGKLKI
+LIKPVRGFKSIPTAYATIKGFEVMRALRKGQARPWCLQPGIRGEVRLVERAFGIGPSALT
+EAMGMLNHHFAAAA
+>PROKKA_02651
+MTDFKWRHFQGDVILWAVRWYCRYPISYRDLEEMLAERGISVDHTTIYRWVQCYAPEMEK
+RLRWFWRRGFDPSWRLDETYVKVRGKWTYLYRAVDKRGDTIDFYLSPTRSAKAAKRFLGK
+ALRGLKHWEKPATLNTDKAPSYGAAITELKREGKLDRETAHRQVKYLNNVIEADHGKLKI
+LIKPVRGFKSIPTAYATIKGFEVMRALRKGQARPWCLQPGIRGEVRLVERAFGIGPSALT
+EAMGMLNHHFAAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001982.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001982.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b016e275b0e28fb45083ca22c525ed730be7b38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001982.fa
@@ -0,0 +1,25 @@
+>PROKKA_00310
+MDRCNRARAMGSRAAQSGRRRCHDDDGAMGALVRVHAAQSCSRSRVHPASGSRRRNPHHP
+PSRTSAAVPDTATPVPCPAPPRLHRPRPRAGPDPRAHHLTRVTTDRTGVADTPRHDRCRT
+PEGHARRGMGGLVQDHRFSTACTPCADAAGEVEQAPSMTIAARHQACRYTSTARSATEHR
+SGETSTELAARLLAEAPQRDWRLRDLAALVHLSASQLGRAFTQRFGMPPMRYLAHIRAHR
+LAELLVETDLPIGVAMTKVGWRSRGHAARQFTDVVGISPSEYRRTAIGRTLTETSPWPSA
+TQGSPVAPGRESLEKSPP
+>PROKKA_00409
+MPTTFSDQRKLSVVLFEGFELLDVFGPVQLFGSLPDVAIEYVGPHTGPVISSKGARVVAD
+LAYEDLARPDILMVPGGQGTRTLVDDAGFLAWLGQAGSRADLVASVCTGSALLAAAGLLE
+GYSATSNKRAFTWASGFGDDVDWRPRARWVHDRDRWTSSGVAAGMDMATGMIADLYDADT
+ARAVTLRAEYEPHTDSTRDPFADVYRLG
+>PROKKA_00655
+MRHVVTIACPGTALFDVGIPSRVFGAARTANDEPAYDVTIASPTGAGPLLTKDGVSVDLP
+GVDQIKETDTVVVASSDALLDPLVRRDMASALAPFLLQGQAVRPGVRVAAVCSGAFLLGE
+LGLLDHRTATTHWRLADQLAKLFPSTHLQTESLYIEDDGVLTSGGVAAGIDLCLHMIRQD
+YGVRIANDVARSCVVAPFREGGQAQYVQTPVPRSADPSMNDLVHWLLETLDQRHTLEDIA
+HRGHMSTRTFERRFRREHGTSPGQWLTAARIQRAKELLESTDLPVERIAELVGLGTASNL
+RTHFTRCVGRTPQAYRRSFTAGSNSTNVSGQYS
+>PROKKA_01773
+MDRCHRARAMGSCAAQSRRRRCHDDDRAMGALVHLHVAQSCSRSRVHPTSGRRRRNHHHP
+PPRTPATAPGAATPVPRPGPPRLHRSRTWARPDPRTHHHTRLSTGGTGVADTPGRERCRT
+AERLARRGMGGLVQDHGLLATAPPHAVVLRKAAAMSTEPSWRVCPDETTPSHACPTETAA
+HHAARLLAQDPGRDWRLRDLADLVHLSTSQLGRAFSQRFGMPPIQYLAHVRAHRLAELLI
+ETDLPIGVAMAQVGWRSRGHAARQFTAIVGVSPSAYRRTATQRASLRCPCCGQRNELPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001985.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001985.fa
new file mode 100644
index 0000000000000000000000000000000000000000..465d206657c27903c0ce5295f5ca4d64eb8895ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001985.fa
@@ -0,0 +1,12 @@
+>PROKKA_00674
+MAYLFLIIAIIFEVAGALSLRMATSGSKKKGLWLLAVLGGYGIAFFGITMALVEGLALGV
+AYGIWAASGVALTAVLSRILFKEPLTKVMAAGIGLIIVGVLMIELGAAH
+>PROKKA_00675
+MKWVFLAGAIALEVTGSLSLKAAVDAPGFFALVAVGYIGAFTLLAGALKQGMPLGVGYGI
+WGAAGVALTAILSAVIFGEPLTALMTLGIAVVIGGVLCVELGSQAATKKREGTV
+>PROKKA_02225
+MQWLFLAGAVLSEVAATLCLRVAAAGRRGFYAAVAVGYVLAFVFLTLALRAGIGLGVAYG
+IWAAAGVALTAIASHVLFKEPLTRTMILGILLIMAGVLVIEIGSSSH
+>PROKKA_02226
+MTKWFLLAGAVGSEVIASLSLKAALTHPALYAVVLLGYVSAFTFLTLVLKRGMALGVAYG
+IWGALGVAATAVLSAVLFDERITAMMGIGIALVIAGVLMVELGSHHTPDTDEQQAGAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001986.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001986.fa
new file mode 100644
index 0000000000000000000000000000000000000000..748d81970f426922508e0ede44688f1a1529a62a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001986.fa
@@ -0,0 +1,15 @@
+>PROKKA_00013
+MSTTLTLFGHSAVRLEKAGRRLAFDPGAFSDAAVLDGADAVLVTHGHPDHVVPEQLARAV
+AGTEAHVWAPRDLTGPLAEAGLDAGHVHTAVPGETFEAAGFRVEVLGGEHAVIHAEVPRP
+VNVSYLVDGAVLHPGDSFTVPDADVEVLLLPAAAPWLRIADVVDQMRAIAATHTRPIHDG
+ILSEDGKGVVDGVLSGLAEGVTDYRRLAPGEPWTF
+>PROKKA_02031
+MSTTLTLFGHSAVRLEKAGRRLAFDPGAFSDAAVLDGADAVLVTHGHPDHVVPEQLARAL
+AGTEAHVWAPRDLTGPLAEAGLAAGRVHTAVPGETFEAAGFRVEVLGGEHAVIHAEVPRP
+VNVSYLVDGAVLHPGDSFTVPDADVEVLLLPAAAPWLRIADVVDQMRAIAATHTRPIHDG
+ILSEDGKGVVDRVLSGLAEGVTDYRRLAPGELWTF
+>PROKKA_00013
+MSTTLTLFGHSAVRLEKAGRRLAFDPGAFSDAAVLDGADAVLVTHGHPDHVVPEQLARAV
+AGTEAHVWAPRDLTGPLAEAGLDAGHVHTAVPGETFEAAGFRVEVLGGEHAVIHAEVPRP
+VNVSYLVDGAVLHPGDSFTVPDADVEVLLLPAAAPWLRIADVVDQMRAIAATHTRPIHDG
+ILSEDGKGVVDGVLSGLAEGVTDYRRLAPGEAWTF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001987.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001987.fa
new file mode 100644
index 0000000000000000000000000000000000000000..93219b827f195e2772bc94e38b507d27294e8e64
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001987.fa
@@ -0,0 +1,9 @@
+>PROKKA_00027
+MTIISTGTSTPESAAAWRAALAEAALRGEDVVWFSLDGTEPDEAEAREAGVAVSVAHAQE
+RGRDAVGDLLEHAERVGASRIVVGVKHRSPVGKLLLGSAAQQIILEARVPVVCVKP
+>PROKKA_02045
+MTIISTGTSTPESAAAWRAALAEAALRGEDVVWFSLDGTEPDEAEAREAGVVASVAHAQE
+RGRDAVGDLLEHAERVGASRIVVGVKHRSPVGKLLLGSAAQQIILEARVPVVCVKP
+>PROKKA_00027
+MTIISTGTSTPESAAAWRAALAEAALRGEDVVWFSLDGTEPDEAEAREAGVVASVAHAQE
+RGRDAVGDLLEHAERVGASRIVVGVKHRSPVGKLLLGSAAQQIILEARVPVVCVKP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001988.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001988.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a731dea572396620e6e71cec77d0b832e403861e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001988.fa
@@ -0,0 +1,21 @@
+>PROKKA_00028
+MSSTSPDGPPRRRTGIGRIVFSVIAVLTVLAASAFSIRSASGGNDIRTNLTLIAPAAAGG
+GWDSFQRELQQTMRVNGLVNNVQVVNIPGAGGTIALGQLTTLEDANNLMVGGTGQIAAHA
+ARGTGPELSQVTAVSRVVEEYSLVVVPADSPYQSMDDLVTAWRADPAHVAWTGGGSFDQL
+VMADIARTADVPVADTTYIPSDGGGEAIQALLNGTAQASAGGFADIYPQVEAGRLRALGV
+VAAEPLAGVEEIPTLRSQGYDVTLTNWRALFAPPGISAEERTELEALIAEAVDTPEWKEA
+VQRNYWNPVPLSGTELEEFIAAEKERIGTLTEEIK
+>PROKKA_02046
+MSSTSPDGPPRRRTGIGRIVFSVIAVLTVLAASAFSIRSASGGNDIRTNLTLIAPAAAGG
+GWDSFQRELQQAMRVNGLVNNVQVVNIPGAGGNIALGQLTTLEDANNLMVGGTGQIAAHA
+ARGTGPELSQVTAVSRVVEEYSLVVVPADSPYQTMDDLVTAWRVDPAHVAWTGGGSFDQL
+VMADIARTAGVPVADTTYIPSDGGGEAIQALLNGTAQASAGGFADIYPQVEAGRLRALGV
+VAAEPLAGVEEIPTLRSQGYDVTLTNWRALFAPPGISAEERTELEALIAEAVDTPEWKEA
+VQRNYWNPVPLSGTELEEFIAAEKERIGTLTEEVK
+>PROKKA_00028
+MPSTSPDGPPRRRTGIGRIVFSVIAVLTVLAASAFSIRSASGGNDIRTNLTLIAPAAAGG
+GWDSFQRELQQTMRVNGLVNNVQVVNIPGAGGNIALGQLTTLEDANNLMVGGTGQIAAHA
+ARGTGPELSQVTAVSRVVEEYSLVVVPADSPYQSMDDLVTAWRADPAHVAWTGGGSFDQL
+VMADIARTADVPVADTTYIPSDGGGEAIQALLNGTAQASAGGFADIYPQVEAGRLRALGV
+VAAEPLAGVEEIPTLRSQGYDVTLTNWRALFVPPGVSAEERTELEALIAEAVDTPEWKEA
+VQRNYWNPVPLSGAELEEFIAAEKERIGTLTEEIK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001989.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001989.fa
new file mode 100644
index 0000000000000000000000000000000000000000..831022eb29e30ae3abb0b94fcc63fbeed779f06e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001989.fa
@@ -0,0 +1,13 @@
+>PROKKA_00029
+MSHASTVPPAADAPSRWGRAAGLSGLVMPAVLAAFSLYLLLGSLTMDTDGADFPGPDFFP
+LILSVAGLVIAAALAVEVVRVRQAPEG
+>PROKKA_02047
+MSQASTVSPAADAPSRWGRAAGLSALVMPAVLAAFSLYLLLGSLAMDTEGADFPGPDFFP
+LILAVAGLVIAAALAVEVVRVRQAPEGQADADGEVGQAAGPLTLFHSDFGALAWCFLGFL
+AFAVLLPWLGWILAGALLFWCVTRAFGAPHPVFDILVALFVSSLAYLGFAVALGLTLPSG
+ILGGGF
+>PROKKA_00029
+MSHASTVPPAADAPSRWGRAAGLSALVMPAVLAAFSLYLLLGSLAMDTEGADFPGPDFFP
+LILAVAGLVIAAALAVEVVRVRQAPEGQADADGEVGQAAGPLTLFHSDFGALAWCFLGFL
+AFAVLLPWLGWILAGALLFWCVTRAFGAPHPVFDILVALFVSSLAYLGFAVALGLTLPSG
+ILGGGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001993.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001993.fa
new file mode 100644
index 0000000000000000000000000000000000000000..618c65c1ba4d656b056784987e33f94362c28a73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001993.fa
@@ -0,0 +1,20 @@
+>PROKKA_00166
+MEYTKKWLPLEAQVERLVQRGLEVDDLTRALRLLESVGYYRVTGYLYPFLESEKQVDDQG
+HTKIRVLNRYQPGTALHHAEEIIDFDRQLRMLVMEGVERIEVAVRMRIGYVLGRTSPFAH
+ENPTCFDDSFTRANTDSRDPRPSKQVLWLERVKQRRDGSDEQFVAHFRQKYDDHMPVWAL
+TELLELGHLSNLYQGMLQKDAEEVATAFGIPQKKMMGSWLASLNYVRNVAAHHARLFNRK
+LQNAPSRPAAGMVPLLDHLREPAAPKGDFGTYNALAIIAYMLRPIEAERSWAPRLAELFR
+TFPTSHALSVQSMGVPEDWHTLDLWRG
+>PROKKA_00353
+MGYYRVTGYLYPFLESEKQVDDQGHTKIRVLNRYQPGTALHHAEEIIDFDRQLRMLVMEG
+VERIEVAVRMRIGYVLGRTSPFAHENPTCFDDSFTRANTDSRDPRPSKQVLWLERVKQRR
+DGSDEQFVAHFRQKYDDHMPVWALTELLELGHLSNLYQGMLQKDAEEVATAFGIPQKKMM
+GSWLASLNYVRNVAAHHARLFNRKLQNAPSRPAAGMVPLLDHLREPAAPKGDFGTYNALA
+IIAYMLRPIEAERSWAPRLAELFRTFPTSHALSVQSMGVPEDWHTLDLWRG
+>PROKKA_02025
+MRYSKPHLPYDQQVRLLASRGLNVGREGDAVRALKRIGYYRLSAYTYPMRAFTTDDAGTV
+HRSDDFVEGACLSDAVALHDFDHRLRRTLLPAIQSLEIALRTKVGYHLGKHGPLAHLDRS
+GLDPQRCDAVSRGPDHTGTKYDTWRSEYDSLQRKAGREDYMVHFATKYDGDVPVWAATEF
+MTMGCLIGLYRMMQPKDARRIAEEVGVKNPQVLFGWLKALNVLRNHCAHNARIWNRSTVY
+PPDKINRRMVEEELHHLVSADTNKVYFLTAVLAYLLRHVDPDSRFASDLRTTMGKFPSVL
+GWTPGHTMGFVDGWSTEALWSIH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001994.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001994.fa
new file mode 100644
index 0000000000000000000000000000000000000000..511c48c25f19362b8b2a02c6d4c1b2019fb455b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001994.fa
@@ -0,0 +1,18 @@
+>PROKKA_00167
+MYIHKQKLQHVSSPEKPDAVYARKLQEVIGGQYGEITVAMQYSFQAWNAHIPGKYRDLLF
+STAAEEFGHVEMLATMVAQLLEKAPVGITTDAIQDDPAVAAVIGGTDLQQAIVAGAGARP
+VDSMGNPWTGAYVTASGNLLADMTANLNAEMQGRTQVARLYHMTDDPGIRELLSFLLARD
+TMHQNQWAAAVKELQEDGLEEMPVPSNFPQKKEATEHSYTHYEFSDGQATAEGSWAAGPT
+PDGKGEFSYSSEPPAGVPMPPPTHPDSRFYGTTEVPNRVEKLAGTVQDKLHRE
+>PROKKA_02078
+MYIHKQKLQHVSSPEKPDAVYARKLQEVIGGQYGEITVAMQYSFQAWNAHIPGKYRDLLF
+STAAEEFGHVEMLATMVAQLLEKAPVGITTDAIQDDPAVAAVIGGTDLQQAIVAGAGARP
+VDSMGNPWTGAYVTASGNLLADMTANLNAEMQGRTQVARLYHMTDDPGIRELLSFLLARD
+TMHQNQWAAAVKELQEDGLEEMPVPSNFPQKKEATEHSYTHYEFSDGQATAEGSWAAGPT
+PDGKGEFSYSSEPPAGVPMPPPTHPDSRFYGTTEVPNRVEKLAGTVQDKLHRE
+>PROKKA_01781
+MYIHKQKLQHVSSPEKPDAVYARKLQEVIGGQYGEITVAMQYSFQAWNAHIPGKYRDLLF
+STAAEEFGHVEMLATMVAQLLEKAPVGITTDAIQDDPAVAAVIGGTDLQQAIVAGAGARP
+VDSMGNPWTGAYVTASGNLLADMTANLNAEMQGRTQVARLYHMTDDPGIRELLSFLLARD
+TMHQNQWAAAVKELQEDGLEEMPVPSNFPQKKEATEHSYTHYEFSDGQATAEGSWAAGPT
+PDGKGEFSYSSEPPAGVPLPPPTHPDSRFYGTTEVPNRLEKLAGTVQDKLHRE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001999.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001999.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6750619c64814aa1d5db1efbb554e40a153ea61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001999.fa
@@ -0,0 +1,21 @@
+>PROKKA_00274
+MDTHRATASLPWIDGPAVRAALSPRAAVDALEAALAAGLDPEADAPRTRVSTAAGQLLQM
+PSTRGTEVGTKLLTLTPDNPERGLPVIQGVYVLFGAPGTPGQAPRAVLDGVELTGLRTSA
+VSALGVRLLADASPRHLVVVGTGVQAWEHALTFQDVFGLERVSVVGRDADRAAALAARIE
+AELGVTASAAGPEAVAEADVVVTCTAATAPLFDGTLVPEHATVVAMGSHTTDARETDDAL
+ARRATVAVESRDSAAREAGDVTLAIDSGALAGIEDTVTLAELVAGTARRREGAPALFVTT
+GMPWQDLVVASAVAREVLG
+>PROKKA_02289
+MDTHRATASLPWIDGPAVRAALSPRAAVDALEAALAAGLDPEADAPRTRVSTAAGQLLQM
+PSTRGSEVGAKLLTLTPDNPERGLPAIQGVYVLFGAPGTPGQAPRAVLDGVELTGLRTSA
+VSALGVRLLADASPRHLVVFGTGVQAWEHALTFQDVFGLERVSVVGRDAGRAAALAARIT
+AELGVTASAAGPEAVAEADVVVTCTAATAPLFDGTLVPEHATVVAMGSHTTDARETDDAL
+ARRATVAVESRDSAAREAGDVTLAIDSGALAGIEDTVTLAELVAGTARRREGAPALFVTT
+GMPWQDLVVASAVARVVLG
+>PROKKA_00272
+MSTPISTAPGLPWIDGPAVRSALSPCAAVDALEAALAAGLDPEADAPRTRVATAAGQLLQ
+MPSTRGTEVGTKLLTLTPDNPERGLPVIQGVYVLFGAPGAPGQAPRAVLDGVELTGLRTS
+AVSTLGVRLLADASPRHLVVFGTGVQAWEHALTFQDVFGLERVSVVGRDADRAAALAARI
+EAELGVTASTADSEAVAEADVVVTCTAATAPLFDGTLVPEHATVVAMGSHTTDARETDDA
+LARRATVAVESRDSAAREAGDVTLAVASGALAGIEDTVTLAELVAGTARRREGEPALFVT
+TGMPWQDLVVASAVARVVLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002009.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002009.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26c19b0595123dcfee936380d920dbc61643968f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002009.fa
@@ -0,0 +1,15 @@
+>PROKKA_00528
+MLIVCTGNVCRSAYASRALQGRLAALVPGRVEVGSAGSQPNQALTVPPPLVRLGAEAGVA
+GLADHRPAALQPFMVAEADLVLAAAQEHMRFALREVPQAVARVFTVLELAALVRILDARN
+GRDWIPAGRGVRAFAAEAAHHRALARSSAQPLDVVDPFRGPVEGYAEMIRIMDPALETIA
+DALARAVTPTP
+>PROKKA_00249
+MLIVCTGNVCRSAYASRALQGRLAALVPGRVEVGSAGSQPNQALTVPPPLVRLGAEAGVT
+GLEGHRPAALQPFMVAEADLVLAAAQEHMRFALQEVPQAVARVFTVLELAALVRAMDQRD
+GRDWIPAGRGVRAFAAEAARHRALARSTAQPLDVVDPFRGPVEGYAEMIQIMDPALETIA
+DALARAVTPTP
+>PROKKA_00528
+MLIVCTGNVCRSAYASRALQGRLAVLAPGRVEVGSAGSQPNQALTVPPPLVRLGAEAGVT
+GLEGHRPAALQPFMVAEADLVLAAAQEHMRFALQEVPQAVARVFTVLELAALVRAMDQRD
+GRDWIPAGRGVRAFAAEAARHRALARSTAQPLDVVDPFRGPVEGYAEMIQIMDPALETIA
+DALARAVSLAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002012.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002012.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a319930afee4b61c8c4cdd96a62ec7b60ceed540
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002012.fa
@@ -0,0 +1,17 @@
+>PROKKA_00600
+MTSPWVEDDELTDWEAPAAADDDGQTGTPLPYVDPEIAAELAGEGPPVWMGTRWREIEAE
+HQWEAWNTLRRWVDWFVAEYRLVTSVVPPCWYKHSDLTAELYAAMCMEYKVWEEQAPGLG
+PMMMWHPHVEMLTARLRRMVDEAGCAKIGQHKEPEAYGDRPAFNLDYDEDDFTAWAATTC
+EQHALERPEAGVKYVRARVFNGDGEEIALSNPVGLASRRTSTGVTAELMMTSSTPLAPGL
+RLTVPSATPGLEVGWQTSVNGHDWE
+>PROKKA_01802
+MSTHSPEPDDQYDDPGILDDQPDMFDTNALPEPPHPINWNLLSAQDLEAELLELNRWVDW
+LRHTYGLPASVIPPYWHRHPELLWELSALHLHWLCAYDPEQNGSAPLGWHRDFADARHRL
+RDWVTASGTRLDRDRPTRQTTWPGEEPQPTHGESVITDRDADFVQFIIDQVNERQAAEDA
+FYASLDDRIDPATGEVRDDVLGPEGG
+>PROKKA_02241
+MASPWVEDDEPDWSETAPLQDEGPTETSLPYVDPEVAAELAQEGPPVWMGTRWREIEAEH
+QWQAWNHLRRWVDWFVAEYRLGTSIVPACWYRHPDVTAELYAAMCMEYKVWDEQAPGLGP
+MMMWHPHVEMMTARLRRMVDEAGCAKIGRHKDPEAYGNRGAYELDYDESDWTRWAATERE
+EELIERPTEGVKYVRAKVVDSDGNVLGHSAPVGLRPVPNVVGVEAKVRVTSSTPAEPRMA
+VAVSSGRDDLGIEWEMSPDGAEWSTRPNDDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002014.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002014.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b0bbd4c5ff64a1db6124d3a6b2b139406fcfbcae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002014.fa
@@ -0,0 +1,11 @@
+>PROKKA_00613
+MTMIKEPGVSPTAGLGPAAALFHGFSDPTRLAILRHLATGEHKVRELTEHLGLAQSTVSA
+HLACLTGCGLVSSRPVGRASLYSLAAEPELLEVLAAAERLLTVTGHAVELCPHSGPAATG
+ALPHDAGH
+>PROKKA_01773
+MSPAAGLGPAAALFHGFSDPTRLAILRHLATGEHKVRELTEHLGLAQSTVSAHLACLAGC
+GLVASRPVGRASLYALAAEPELLQVLAAAERLLTVTGHAVELCPHSGTPGPDGPAAA
+>PROKKA_00703
+MIQEKGATLDEVATVAYAHLFQAFAEPTRLAIVQHLASGEHRVRDLVEHMGLAQSTVSKH
+VGFLVECGLATMRPEGRSTWYSLAQSELLRTLIAAAERLLDATGTQALLCTHLRLPHTHH
+ASDTDKK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002017.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002017.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f11442aacf07ab7ba841435cf0b81e7722a5a0e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002017.fa
@@ -0,0 +1,11 @@
+>PROKKA_00808
+MTDSPIAADRDGIRYLSGAIPAADDVRALYDAVGWSAYTADMDTLMGGLQGSATVVTAFD
+GGRLVGLARVVSDGHTIAYLQDILVDPGHQRRGIASELLRRVFARFGQVRQHVLLTDTEE
+RQRAFYEAHGFRESHDVEGDELRAFVRFQSRDG
+>PROKKA_00540
+MTDSPIAADRDGIRYLSGVIPAADGGRLVGLARVVSDGHTIAYLQDILVDPGHQRRGIAS
+ELLRRVFARFGQVRQHVLLTDTEERQRAFYEAHGFRESRDVEGDELRAFVRFQSRDG
+>PROKKA_00777
+MTDSPIAADRDGIRYLSGAIPAADDVRALYDAVGWSAYTADMDTLMGGLQGSATVVTAFD
+GGRLVGLARVVSDGHTIAYLQDILVDPGHQRRGIASELLRRVFARFGQVRQHVLLTDTEE
+RQRAFYEAHGFRESRDVEGDELRAFVRFQSRDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002021.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002021.fa
new file mode 100644
index 0000000000000000000000000000000000000000..075725b3a1ae8d571134e7ea408585dba09f5857
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002021.fa
@@ -0,0 +1,15 @@
+>PROKKA_00944
+MRMDLPLAPMDEPEPCAARVPLFTGLDLEQLRRVSALARPLVLEAGDALHLAGDRTDRLC
+VVHSGRLALTLGSATGRERVVRMVEPGDSVGEHEFLTGEPARHGARAVAATRLCTFSHAE
+VARLLAEHPGIGGRVMRTLAVRLAEAEQRLAREHQPVTARIAGHLLGLPALRDEADLVVV
+LAAPKKDVASLLGTTPEAFSRGLRRLADDGLIAIEGPRVTLLDPDALEALAAE
+>PROKKA_00663
+MRMDLPLIPVDEPEPCAARVPLFTGLDLEQLRRVSALARPIVLEAGDALHLAGDRTDRLC
+VVHTGRLALTLGSATGRERVVRMVEPGDSVGEHEFLTGEPARHGARAVVATRLCTFSHAE
+VARLLAEHPGIGGRVMRALAVRLAEAEQRLAWERQPVTARIAGHLLGLPALRDEADLVVV
+LAAPKKDVASLLGTTPEAFSRGLRRLADDGLIAIEGPRVTLLNPDALEALAAE
+>PROKKA_01993
+MRRELTLTPVGEAEPCAARVPLFAGLEPDQLRRVSALARPFALEPGDVLHLPGARTERLW
+VVHTGGLALSLTSPTGRERVVRMAGPGDSVGEQEFLTGAAARHGVRAVAPTRLCTFSHEE
+IAGLMAEHPGIGRRVMRTLAVRLADAERRLAQERQPVAARIAGHLLELPAVHASGTPTVL
+LTAPKKDVASLLGTTPEAFSRGLRRLVDDGVVAVDGPRVRLLDADALEGLAAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002025.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002025.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0eaa107a07d812c24ba1430120b5e5dfb17c210
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002025.fa
@@ -0,0 +1,9 @@
+>PROKKA_01038
+MARHGRDEDEAHEAPAGAPAGAGTLAQWRIPLVGLLIGVGLGVVFGLGTERPWGTVIGCA
+MMGFALGIAWMYVERGRDGRDR
+>PROKKA_00751
+MARHGRDEDEAHEAPAGAPAGAGTLAQWRIPLVGLLIGVGLGVVFGLGTERPWGTVIGCA
+MMGFALGIAWMYVERGRDGRDR
+>PROKKA_00980
+MARHGRDEDEAHEAPAGAGTLAQWRIPLVGLLIGVGLGVVFGLGTERPWGTVLGCAMMGF
+ALGIAWMYVERGRDGRDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002032.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002032.fa
new file mode 100644
index 0000000000000000000000000000000000000000..55c8220a48a17909e4bcdada56893c412a9380b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002032.fa
@@ -0,0 +1,9 @@
+>PROKKA_01391
+MRITAFATNAPRGQLPVLELRHRRRARCEDRIRNAKDMGLMKFPLQGFAQNQVWCQIVQL
+AGVIVAWMQAIALAGHDARRWEPKRFRARLFEIPATIVRRCRHKILHSRLIAFEGVARV
+>PROKKA_01123
+MRITAFATNAPRGQLPVLELRHRRRARCEDRIRNAKDMGLMKFPLQGFAQNQVWCQIVQL
+AGVIVAWMQAIALAGHDARRWEPKRFRARLFEIPATIVRRCRHKILHSRLIAFEGVARV
+>PROKKA_01342
+MRITAFATNAPRGQLPVLELRHRRRARCEDRIRNAKDMGLMKFPLQGFAQNQVWCQIVQL
+AGVIVAWMQAIALAGHDARRWEPKRFRARLFEIPATIVRRCRHKILHSRLIAFEGVARV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002035.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002035.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3aa7a0af80f51e49b0475fbcc24ab49a03b21f84
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002035.fa
@@ -0,0 +1,10 @@
+>PROKKA_01507
+MRESGVMSRDVISDEVWAVIGPLFPAPKSTGRPPVDRRAVVEATAWRFRTGAPWRDLPER
+FGNWNTIYKNVNRWAAQGVWERVLEKTQSMAQQAGELDWVASIDSTIVRVHQHGATLPRP
+TGGLDELQEISGRAG
+>PROKKA_01747
+MIGPLFPAPKSTGRPPVDRRAVVEATAWRFRTGAPWRDLPERFGNWNTIYKNFNRWAAQG
+VWERVLERTQSMAQQAGELDWVASIDSTIVRVHQHGATLPRPTGGPDELQEIRGRAG
+>PROKKA_02235
+MIGPLFPAPKSTGRPPVDRRAVVEATAWRFRTGAPWRDLPERFGNWNTIYKNFNRWAAQG
+VWERVLERTQSMAQQAGELDWVASIDSTIVRVHQHGATLPRPTGGPDELQEIRGRAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002044.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002044.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d38dc7038d2dea1caa9e2818f537002554c267dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002044.fa
@@ -0,0 +1,21 @@
+>PROKKA_01897
+MTIRAGIVGYGNLGRSVEKLVKLQPDMELVGIFSRRTGLDTDTPVLPAERAAEHAGEIDV
+LFLCLGSATDIPEQAAGYARHFTTVDTYDNHQLIPRHRAEMDAAAREGGHVAMISTGWDP
+GLFSVNRVLGAALFPQPQQNTFWGKGLSQGHSDAVRRVPGVRRGVQYTIPSEEAIAEARA
+GRGAEITGASAHVRECYVVADEADHAAITEAITTMPDYFAPYETTVHFISEEEFERDHQG
+MPHGGHVVTSGDLGGSRSAVEFVLELESNPDFTAAAQVAYGRAAARLKAQGETGARTVLE
+VAPYLLSPTGLDELIRRDV
+>PROKKA_01593
+MTIRAGIVGYGNLGRSVEKLVKLQPDMELVGIFSRRTGLDTDTPVLPAERAAEHAGEIDV
+LFLCLGSATDIPEQAAGYARHFTTVDTYDNHQLIPRHRSEMDAAAREGGHVAMISTGWDP
+GLFSVNRVLGAALFPQPQQNTFWGKGLSQGHSDAVRRVPGVRRGVQYTIPSEEAIAEARA
+GRGAEITGASAHVRECYVVADEADHAAITEAITTMPDYFAPYETTVHFISEEEFERDHQG
+MPHGGHVVTSGDLGGSRSAVEFVLELESNPDFTAAAQVAYGRAAARLKAQGETGARTVLE
+VAPYLLSPTGLDELIRRDV
+>PROKKA_01817
+MTIRAGIVGYGNLGRSVEKLVKLQPDMELVGIFSRRTGLDTDTPVLPAERAAEHAGEIDV
+LFLCLGSATDIPEQAAGYARHFTTVDTYDNHQLIPRHRAEMDAAAREGGHVAMISTGWDP
+GLFSVNRVLGAALFPQPQQNTFWGKGLSQGHSDAVRRVPGVRRGVQYTIPSEEAIAEARA
+GRGAEITGASAHVRECYVVADEADHAAITEAITTMPDYFAPYETTVHFISEEEFERDHQG
+MPHGGHVVTSGDLGGSRSAVEFVLELESNPDFTAAAQVAYGRAAARLKAQGETGARTVLE
+VAPYLLSPTGLDELIRRDV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002045.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002045.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c4a77c540870f12fdc605e8081270cdf979990e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002045.fa
@@ -0,0 +1,12 @@
+>PROKKA_01945
+MTATLEAPQAMGRTLSAVPPVLESPAPQPAAFRQRCARLAMSAARAVTVFPEVAEARFAI
+TGTPSAPELEVDCILRDGEDTAAVIETITVHLVEDLEELLGARFHERRLELVVDRSLPRV
+GVGVVSAP
+>PROKKA_00849
+MTATLEAPQAMGRTLSAAPPVLESPAPQPAAFRQRCALLAMSAARAVTVFPEVAEARFAI
+TGTPSAPALEVDCILRDGEDTAAVIETITVHLVEDLEELLGARFHERRLELVVDRSLPRV
+GVGVVSAP
+>PROKKA_01864
+MTATLEAPQAMGRTLSAVPPVLESPAPQPAAFRQRCALLAMSAARAVTVFPEVAEARFAI
+TGTPSAPALEVDCILRDGEDTAAVIETITVHLVEDLEELLGARFHERRLELVVDRSLPRV
+GVGVVSAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002048.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002048.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6387f3a882873bb0464a2490319ff99d58c0b843
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002048.fa
@@ -0,0 +1,18 @@
+>PROKKA_01964
+MSTHRLSSTALGFAAGLGTAAAVTAARKIALMAAVGKGHPLKHRLLDAASGLVQPKYPMG
+AMSTYLNGLHFYADDLGRQVEASHFCIHLRHDLHQCVIFDRNAPDARLIGIEYIISEERF
+RSLPEEERRLWHSHHYEVSSGALTAPGVPELAEHSYFEDLIHTYGKTFHTWQYDRDDFPY
+GIPQLMMGLTGDGQVDEALLRARDERVGVDTAAKRRHRADIPVPDVVPGANSWERGRVVQ
+TTLEERPVRGRDD
+>PROKKA_01656
+MSTHRLSSTALGFAAGLGTAAAVTAARRIALMAAVGKGHPLKHRLLDAASGLVQPKYPMG
+AMSTYLNGLHFYADDLGRQVEASHFCIHLRHDLHQCVIFDRNAPDARLIGIEYIISEERF
+RSLPDEERRLWHSHHYEVSSGALTAPGVPELAEHSYFEDLIHTYGKTFHTWQYDRDDFPY
+GIPQLMMGLTGDGQVDEALLRARDERVGVDTAAQRRNRADIPVPDVVPGANSWERGRVVQ
+TTLEERPVRGRDD
+>PROKKA_01890
+MSTHRLSSTALGFAAGLGTAAAVTAARKIALMGAVGKGHPLKHRLLDAASGLVQPKYPMG
+AMSTYLNGLHFYADDLGRQVEASHFCIHLRHDLHQCVIFDRNAPDARLIGIEYIISEERF
+RSLPDEKRRLWHSHHYEVSSGALTAPGVPELAEHSYFEDLIHTYGKTFHTWQYDRDDFPY
+GIPQLMMGLTGDGQVDEALLRARDERVGVDTTAKRRNRADIPVPDVVPGANSWERGRVVQ
+TTLEERPVRGRDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002053.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002053.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4efe32a0088ea0dfdce9373c124167e9d523dfb8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002053.fa
@@ -0,0 +1,25 @@
+>PROKKA_02073
+MLTTSTTSHPVAIIGAGPIGLAAAAHLAERGLPFLILEAGTAAGAAIAEWGHTRLFSPWQ
+YNLDAAAQRLLEAAGWTAPDADVLPTGHELREHYLEPLAQLPQLAESIRYGARVTAVSRA
+GIDKTRTARREETPFLVRIQTTDGHSEDVLASAVIDASGTWSTPNPLGQAGLLAPGEQQA
+RAAGHITAPLPDVQGRDRDRFAGKRVMVTGAGHSAANTLLDLADLEADTTIIWAARTADL
+TRVYGGGDQDELAARGALGSRLRQLVDSGRIAVLTSFTITRFRADDTLTVHAVTPDGERE
+VSVDVLVPATGFRPDLGMLSELRLALDPAVEAPSQLEPLIDPEFHSCGSVEPHGERVLAH
+PETNFYIVGMKSYGRAPTFLMATGYEQVRSIAAALAGDRKAADAVHLELPETGVCTTDLG
+GGCDAPATAGDACCSSPQLIELPLGR
+>PROKKA_00737
+MEDVHARAVIDASGTWTTPNPLGQAGLPAPGEAEALAAGQITAPLPDVLGADQARFAGQH
+VLVVGAGHSAANTLLELGTLAQDTPGTRISWAVRSADVARVYGGEDRDELAARGALGTRL
+RHLVETGTIQVHPSFTITAFTTTGLGMMVQASTPAGEEHLVVDVVVPATGFRPALGMLSE
+LRLELDPAVEAPRQLGPLIDPEFHSCGSVTPHGEKMLAHPEPGFYIAGMKSYGRAPTFLM
+ATGYEQVRSIAAALAGDRTAADNVELQLPETGVCSTDLGGSCDAPAPATAADTADQGCCA
+PAPQTLPAPASRLPVLLPVQAATCC
+>PROKKA_02001
+MLTTATNPHPIVVIGAGPIGLAAAAHLAERGLPFLILEAGTAAGAAIAEWGHTRLFSPWQ
+YNLDAAAQRLLEADGWTAPDADALPTGHELREQYLEPLAQLPQLAESIRYDARVTAVSRA
+GIDRTRTTRREETPFLVRIETADGHSEDVLASAVIDASGTWSTPNPLGQAGLLAPGEQQA
+HAAGHITAPLPDVQGRDRDRFAGKRVMVTGAGHSAANTLLDLADLEADTTIIWAARTADL
+TRVYGGGDQDELAARGALGSRLRQLVDSGRIEVLTSFTITRFRADDTLTVHAVTPDGERE
+VSVDVLVPATGFRPDLGMLSELRLALDPAVEAPSQLGPLIDPEFHSCGSVEPHGERVLAH
+PETNFYIVGMKSYGRAPTFLMATGYEQVRSIAAALAGDRKAADAVHLELPETGVCTTDLG
+GSCDAPAPAGDACCSSPQLIELSVGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002055.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002055.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b0902f86908def3808d0bf0c0e8dea48ea41692c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002055.fa
@@ -0,0 +1,15 @@
+>PROKKA_02153
+MDAKPTRLRKKATREEILASLPVQARVRPSRWLLLWLIVVVCIAVFVWVIFRPPEDVSAG
+FGVWRVASFIGLALALAVLPAATMGLFRPRHVTFDERRVWTRDWSVDWADVKEVRAVAPE
+SEHTMKVALKVDERLWNEGGLRKANRWDSGRPLQGGGLTRAQPLVLTQPALAPSALTLLQ
+VFVELKKRNRRAGSPR
+>PROKKA_01866
+MDAKPTRLRKKATREEILASLPVQARVRPARWLLLWLIVVVCIAVFVWVIFRPPEDVSAG
+FGVWRVASFIGLALALAVLPAATMGLFRPRHVTFDERRVWTRDWSVDWADVKEVRAVAPE
+SEHTMKVALKVDERLWNEGGLRKANRWDSGRPLQGGGLTRAQPLVLTQPALAPSALTLLQ
+VFVELKKRNRRAGSPR
+>PROKKA_02096
+MDAKPTRLRKKATREEILASLPVQARVRPARWLLLWLIVVVCIAVFVWVIFRPPEDVSAG
+FGVWRVASFIGLALALAVLPAATMGLFRPRHVTFDERRVWTRDWSVDWADVKEVRAVAPE
+SEHTMKVALKVDERLWNEGGLRKANRWDSGRPLQGGGLTRAQPLVLTQPALAPSALTLLQ
+VFVELKKRNRRAGSPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002056.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002056.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b6417c217e51b451cd668b710a595b4df2304d50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002056.fa
@@ -0,0 +1,21 @@
+>PROKKA_02165
+MTAPDPAPTDARRAEDRSARIAVTVFPLLVLAAALVGFLAPTAAKTLLPQVNLFLGIIMF
+GMGLTLTLPDFGLVARRPLPVLLGVVAQYAIMPLLGLGVAVVLQLPPELAAGVILVGSTP
+GGTSSNVVSYLARADTALSVAMTSVSTLLAPLLTPLLTLWLAGQYMAVDGGAMAKSIVNI
+VLLPVLGGLVVRLLLRRVVDRVLPALPWVSVVFIALVVAAVVGNSASRVLSAGLLVFAAV
+VLHNGLGYLLGYGAAKLFRLPTPVARTVSIEVGMQNSGLAAGLAAQYISPAAALPGAVFS
+IWHNLSGAVLAMAYRRADGRRAAGAPGSAPANRLRN
+>PROKKA_01879
+MTAPDPAPTDARRAEDRSARIAVTVFPLLVLAAALVGFLAPTAAKTLLPQVNLFLGIIMF
+GMGLTLTLPDFGLVARRPLPVLLGVVAQYAIMPLLGLGVAVVLQLPPELAAGVILVGSTP
+GGTSSNVVSYLARADTALSVAMTSVSTLLAPLLTPLLTLWLAGQYMAVDGGAMAKSIVNI
+VLLPVLGGLVVRLLLRRVVDRVLPALPWVSVVFIALVVAAVVGNSASRVLSAGLLVFAAV
+VLHNGLGYLLGYGAAKLFRLPTPVARTVSIEVGMQNSGLAAGLAAQYISPAAALPGAVFS
+IWHNLSGAVLAMAYRRSDGRRAAGAPGSAPANRLRN
+>PROKKA_02110
+MTAPDPAPTDARRAEDRSARIAVTVFPLLVLAAALVGFLAPTAAKTLLPQVNLFLGIIMF
+GMGLTLTLPDFGLVARRPLPVLLGVVAQYAIMPLLGLGVAVVLQLPPELAAGVILVGSAP
+GGTSSNVVSYLARADTALSVAMTSVSTLLAPLLTPLLTLWLAGQYMAVDGGAMAKSIVNI
+VLLPVLGGLVVRLLLRRVVDRVLPALPWVSVVFIALVVAAVVGNSASRVLSAGLLVFAAV
+VLHNGLGYLLGYGAAKLFRLPTPVARTVSIEVGMQNSGLAAGLAAQYISPAAALPGAVFS
+IWHNLSGAVLAMAYRRSDGRRAAGAPGSAPANRLRN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002060.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002060.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b9f91ce1355c0444d9ef13cc81b2b189bd80045
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002060.fa
@@ -0,0 +1,24 @@
+>PROKKA_02204
+MTEFEDKLAQVARRARDYASSLDTEEATKNALVMPFISQVLGYDVFDPQEVVPEFVADLG
+LKKGEKIDYAIMREGKVNILVEAKKVGSELSLAHASQLVRYFHTSEARIGVLTNGRVWNF
+YTDLDKANILDERPFLVLDLLDIDPVTVPKLEQLAKGSFDLDSVIAAAEELKYVSAIKRE
+ISAEMAAPSDELVKVLAKRVYSGYMNAKAVETFTRLTEEAARQYINDRVNARLKTALGDQ
+VAPVLAAPAEPVATGDQTVLSDEENGQEGQLKPGVVTTEEEIEGFRIIKAILAGIVPMNR
+VYMRDAASYCSVILDDNNRKPIARLHFDGKVKYLVLFDADKNRTRADLENLEDIYESAEA
+LRSVVSSYVGA
+>PROKKA_01917
+MTEFEDKLAQVARRARDYASSLDTEEATKNALVMPFISQVLGYDVFDPQEVVPEFVADLG
+LKKGEKIDYAIMREGKVNILVEAKKVGSELSLAHASQLVRYFHTSEARIGVLTNGRVWNF
+YTDLDKANILDERPFLVLDLLDIDPVTVPKLEQLAKGSFDLDSVIAAAEELKYVSAIKRE
+ISAEMAAPSDELVKVLAKRVYSGYMNAKAVETFTRLTEEAARQYINDRVNARLKTALGDQ
+VAPVLAAPAEPVATGDQTVLSDEENGQEGQLKPGVVTTEEEIEGFRIIKAILAGIVPMNR
+VYMRDAASYCSVILDDNNRKPIARLHFDGKVKYLVLFDADKNRTRADLENLEDIYESAEA
+LRSVVSSYVGA
+>PROKKA_02148
+MTEFEDKLAQVARRARDYASSLDTEEATKNALVMPFISQVLGYDVFDPQEVVPEFVADLG
+LKKGEKIDYAIMREGKVNILVEAKKVGSELSLAHASQLVRYFHTSEARIGVLTNGRVWNF
+YTDLDKANILDERPFLVLDLLDIDPVTVPKLEQLAKGSFDLDSVIAAAEELKYVSAIKRE
+ISAEMAAPSDELVKVLAKRVYSGYMNAKAVETFTRLTEEAARQYINDRVNARLKTALGDQ
+VAPVLAAPAEPVATGDQTVLSDEENGQEGQLKPGVVTTEEEIEGFRIIKAILAGIVPMNR
+VYMRDAASYCSVILDDNNRKPIARLHFDGKVKYLVLFDADKNRTRADLENLEDIYESAEA
+LRSVVSSYVGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002061.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002061.fa
new file mode 100644
index 0000000000000000000000000000000000000000..744226583c3dad067756f10d84a6b49cec1b4b23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002061.fa
@@ -0,0 +1,9 @@
+>PROKKA_02205
+MTNAPNRDELPLPDYDHIPNGTLPTRITGLDESQVEQLLAYERAHGDRLPVVQVLETRLE
+ALRSGAQPSGDQVPDTPEVGGSRTGSPVTPETSGPPVEPLSRGIPADPQHPGNR
+>PROKKA_01918
+MTNAPNRDELPLPDYDHIPNGTLPTRITGLDESQVEQLLAYERAHGDRLPVVQVLETPLE
+ALRSGAQPSGDQVPDTPEVGGSRTGSPVTPETSGPPVEPLSRGIPADPQHPGNR
+>PROKKA_02149
+MTNAPNRDELPLPDYDHIPNGTLPTRITGLDESQVEQLLAYERAHGDRLPVVQVLETRLE
+ALRSGAQPSGDQVPDTPEVGGSRTGSPVTPETSGPPVEPLSRGIPADPQHPGNR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002062.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002062.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1c269879dbee4e41ad755825a016c4e02f9354de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002062.fa
@@ -0,0 +1,33 @@
+>PROKKA_02210
+MSPSSTASDRSDAATAALDDAARRTGPGRRRRADARGTEGLGGTLAKIVLLGLVDAFAAF
+LLFQLAAAGDWVVFALTLAVTIGINWIYLRRGGLPAKYLAPGLFFLMLFQVFVVVYSSYV
+AFTNYGAGHNSDKAAAIEIIQRSSSIRVPDSPVYDITVLEEGGDLYLLTLRDGEPVLGGA
+DQALEPVEAQMQDGEPVGVEGYTTLRFGDLLQRQDQVARLKVPLSDDAADGTLETRDGSR
+GYVYAPRLEYDEARDTFTDLESGVEYRDNGEGQFQADDGSTLQTGWRVFVGLDNFTRAFT
+DPELRDPLLRVTVWTFAFAFLSVATTFAVGLLLAIAFNRSDMRGKKVYRVMMILPYAFPA
+FLSGLVWAGLLNPEFGFVNTVFFGGADIPWLTDPWLARLSVLVVNLWLGFPYMFLVTTGA
+LQSLPEDVDEAARMDGAGPWRIFRSIKLPLLLVSVAPLLISSFAFNFNNFNIIYMLTGGG
+PRFPDAGSNIGATDLLITVVYKTAFSGVGRDYGLASALSIVIFLIVATISAISFRQTKAL
+EEIDK
+>PROKKA_01923
+MSPSSTASDRSDAATAALDDAARRTGPGRRRRADARGTDGLGGTLAKIVLLGLVDAFAAF
+LLFQLAAAGDWVVFALTLAVTIGINWIYLRRGGLPAKYLAPGLFFLMLFQVFVVVYSSYV
+AFTNYGAGHNSDKAAAIEIIQRSSSIRVPDSPVYDITVLEEGGDLYLLTLRDGEPVLGGA
+DQALEPVEAQMQDGEPVGVEGYTTLRFGDLLQRQDQVARLKVPLSDDAADGTLETRDGSR
+GYVYAPRLEYDEARDTFTDLESGVEYRDNGEGQFQADDGSTLQTGWRVFVGLDNFTRAFT
+DPELRDPLLRVTVWTFAFAFLSVATTFAVGLLLAIAFNRSDMRGKKVYRVMMILPYAFPA
+FLSGLVWAGLLNPEFGFVNTVFFGGADIPWLTDPWLARLSVLVVNLWLGFPYMFLVTTGA
+LQSLPEDVDEAARMDGAGPWRIFRSIKLPLLLVSVAPLLISSFAFNFNNFNIIYMLTGGG
+PRFPDAGSNIGATDLLITVVYKTAFSGVGRDYGLASALSIVIFLIVATISAISFRQTKAL
+EEIDK
+>PROKKA_00534
+MSTSSTTSARPDAPHEDPADAGRRGLRGRRADRGPDGTAGTLVKIALLGLVDAFAAFVLF
+QLAAAGDWVVFAVTLAVTLLINWIYLRRGGLPAKYLAPGVFFLVLFQVFVVVYSSYIAFT
+NYGAGHNSDKPAAIEIIQRSSSIRVPDSPVYPVSVLEQGGDLHLLTVRDGQAVLGGADEP
+LAPVEAQMDGAEAVAVDGYTTLKFGDLLSRQDQVTQLKVPLSDDPADGTLETRDGSRAYV
+YSPRLEYDEAQDTFTDLESGVVYRDNGEGRFQADDGSTLQTGWRVFVGVDNFAKAFTDPS
+LRDPLLRVLVWTFAFAFLSVVTTFALGLLLAIAFNRADMRGKNVYRVLMILPYAFPAFLS
+GLVWAGLLNPEFGFVNNVFFGGADIPWLTDPWLARFSVIVVNLWLGFPYMFLVTTGALQS
+LPEDVDEAARMDGAGPWRIFRSIKLPLLLVSVAPLLISSFAFNFNNFNIIYMLTGGGPRF
+ADAATNIGATDLLITVVYKTAFSGVGRDYGLASALSIVIFLIVATISAISFRQTKALEEI
+DS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002063.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002063.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9d41697b1058c689ebfb064742219c6006b5097
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002063.fa
@@ -0,0 +1,27 @@
+>PROKKA_02211
+MQSTTTGGLFRRPLSLTLTAAFSALALTACGGGSSAPASSSPAGATEQGTATASPSQDLS
+EAGASTITMWVDQNRQEPLQAVAEDFKEDTGITVELVVKDNSTMKDDFITQNPTGEGPDV
+IVGAHDWIGSLVQNGTIEPLELGERAGDFVESSVQAVTYEGQTWGVPYSVENIAILRNTE
+LAESTPASFDEMIAEGRKAVDAGEAEYPFVVGLDAVNGDPYHLYPFQTSMGAPVFKQAED
+GSYDTGSLAMGGPEGEAFAEKLAEYGESGVLNPNMTADIAKEQFNSGNAAYFITGPWNIE
+EAEAAGVDFEVEAIPSMGDQPAQPFVGVNAFFVSSESENQLAANEFVVNYLSTEAAQDAL
+FAEGKRPPALTASFDKAASDETVKAFGEIGENGVPMPAAPEMGAVFEFWGGAEMSIIKGE
+GDPVQTWQKMISDIEGRIGQ
+>PROKKA_01924
+MQSTTTGGLLRRPLSLTLTAAFSALALTACGGGSSAPASSSPAGATEQGTAAASPSQDLS
+EAGATTITMWVDQNRQEPLQAVAEDFKEDTGITVELVVKDNSTMKDDFITQNPTGEGPDV
+IVGAHDWIGSLVQNGTIEPLELGDRAGDFVESSVQAVTYEGQTWGVPYSVENIAVLRNTE
+LAESTPASFDEMIAEGQKAVDAGEAEYPFVVGLDPVNGDPYHLYPFQTSMGAPVFKQAED
+GSYDTGSLAMGGAEGEAFAEKLAEYGESGVLNPNMTADIAKEQFNSGNAAYFITGPWNVE
+EAEAAGVDFEVEAIPSMGDQPAQPFVGVNAFFVSSESENQLAANEFVVNYLSTEAAQDAL
+YAEGKRPPALTASFDKAASDETVKAFGEIGENGVPMPAAPEMGAVFEFWGGAEMSIIKGE
+GDPVQTWQKMISDIEGRIGQ
+>PROKKA_00533
+MTSTTPRAALRRPLGLTLTAAFSALALTACGGGGGTAASSSPAAGGSASSSAAGGSDQGA
+ASSSSAGQDLTEAGAATITMWVDQNRQKPLQAVAEDFKEDTGITVELVVKDNSKMKDDFI
+TQTPTGEGPDVIVGAHDWIGSLVQNGTIAPLELGDTADAFSETSVQAVTYDGQTWGVPYS
+VENLAILRNTALAEETPASFDEMIAEGQKAVDAGDADYPFVVGLDPVNGDPYHLYPFQTS
+MGAPVFEQQEDGSYDVSSLAMGGAEGQAFAEKLAEYGESGVLNPNMTADIAKEQFNAGKA
+AYFITGPWNVDEAEEAGVDFAVEEIPSMGDQPAQPFVGVNAFFVSAESENQLAANEFVVN
+YLSSEEAQDALYAEGKRPPALTASFEKAAVDETVKAFGEIGEDGVPMPAAPEMGAVFEFW
+GGAEMSIIKGEGDPAQTWDKMISDIEGRIGQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002067.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002067.fa
new file mode 100644
index 0000000000000000000000000000000000000000..445117cf12f1964fa7d1200e722f565891fd8e29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002067.fa
@@ -0,0 +1,18 @@
+>PROKKA_02243
+MTLPTPSGRWTTTARPAFAVAAALSLGGNLLSLWIGSWKSSDLPADAGYAGVLEGGWEHM
+LNQPTYFTFLSNFLVGLTSLLLALRLHRPGTLFRVLRVTGVVCIVITGVVFNVLLRDADP
+MTAVERFNDTLQHIVTPILTPVLWAVFGPRRQITWRVVWLSTLIPLAWLAFTLLRGPWLD
+WYPYTILDVPRLGYDGVAVYVVAILVFFVAVAALLRVADGLLARAGVGVGAGAEAEARVE
+ARPSP
+>PROKKA_01945
+MTLPTPSGRWTTTARPAFAVAAALSLGGNLLSLWIGSWKSSDLPADAGYAGVLEGGWEHM
+LNQPTYFTFLSNFLVGLTSLLLALRLHRPGTLFRVLRVTGVVCIVITGVVFNVLLRDADP
+MTAVERFNDTLQHIVTPILTPVLWAVFGPRRQITWRVVWLSTLIPLAWLAFTLLRGPWLD
+WYPYTILDVPRLGYDGVAVYVVAILVFFVAVAALLRVADGLLARAGVGVGAGAEAEARVE
+ARPSP
+>PROKKA_02175
+MTLPTPSGRWTTTARPAFAVAAALSLGGNLLSLWIGSWKSSDLPADAGYAGVLEGGWEHM
+LNQPTYFTFLSNFLVGLTSLLLALRLHRPGTLFRVLRVTGVVCIVITGVVFNVLLRDADP
+MTAVERFNDTLQHIVTPILTPVLWAVFGPRRQITWRVVWLSTLIPLAWLAFTLLRGPWLD
+WYPYTILDVPRLGYDGVAVYVVAILVFFVAVAALLRVADGLLARAGVGVGAGAEAEARVE
+ARPSP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002068.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002068.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e7ad83cc20d6433257e585965683350d801c64d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002068.fa
@@ -0,0 +1,21 @@
+>PROKKA_02258
+MTTKVGFIAAASHALQNGPQLFARVEDGGVVIGGRSGEVVPDSTGLYAVVAQDPDAARAE
+LRLDTSVSRSDVLYIGKAEGSLRARLERKHFADGGTAHSTLRRTLAALLVDRLDLEPVAV
+ASAGRFTLTPESGEQLTTWMRRHLAVRVWQAPAGFAEVTPLGDIEKPVIDTHTPPLNLTY
+GGTSPEAQLLRQRIRKARTAMAEQAKRGVDVVGADSSARATVGDLFRRRPRQYGLRGSVG
+LWEELAERLDDTPMPTSEYELGRLLRDALDRSLEGAEPYDEDKVNVERFNRGGMSQGLVH
+LPWWEDQAIPLLLDRWGAWADTRGLIGPEDYIGSW
+>PROKKA_00472
+MTTKAGLIAAASHALQNGPQLFARVEDGGVVIGGRGGEVVPDSTGLYAVVAQDPDAVWAE
+LRLDTSVSRSDVLYIGKAEGSLRARLERKHFADGGTAHSTLRRTLAALLVERLGLEPVAV
+ASAGRFTLTQESGEQLTTWMRCHLAVRVWQAPAGFAEVTPLGGIEKPVIDTHTPPLNLTY
+GGTSPEAQQLRRRIREARTAMAEQAKRGVDVVEADSSARATVGDLFRRRPRQYGLRGSVG
+LWEELAERLDDTPMPTSEHELGRLLHDALERSLEGAEPYDEDKVNVERFNRGGMSQGLVH
+LPWWEDQAIPLLLDRWGAWADTQGLLGPEDYIGSW
+>PROKKA_02189
+MTTKAGLIVAASHALQNSPQLFARVEDGGVVIGGRSGEVVPDSTGLYAVVAQDPDAARAE
+LRLDTSVSRSDVLYIGKAEGSLRARLERKHFADGGTAHSTLRRTLAALLVDRLDLEPVAV
+ASAGRFTLTPESGEQLTTWMRRHLAVRVWQAPAGFAEVTPLGDIEKPVIDTHTPPLNLTY
+GGTSPEAQLLRQRIRKARTAMAEQAKRGVDVVGADSSARATVGDLFRRRPSQYGLRGSVG
+LWEELAERLDDTPMPTSEYELGRLLRDALDRSLEGAEPYDEDKVNVERFNRGGMSQGLVH
+LPWWEDQAIPLLLDRWGAWADTRGLLGPEDYIGSW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002072.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002072.fa
new file mode 100644
index 0000000000000000000000000000000000000000..811802890929a01abc77eaf148cdbb93d3c07c37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002072.fa
@@ -0,0 +1,15 @@
+>PROKKA_02269
+MGTIFLYEIAGTAILLLLGVGVVANVVLSKTKGNGGGWLLISFGWGLGVFAGVYVAAATG
+AHLNPAVTVGLLVSGAEEYAPGIAVTLGTTLAYFAAQLIGAFLGAALAWLAYRDHYQTET
+DQGAILGTFATGPEIRNPLWNMVTELIATFVLVFVVLLFGSTPSGLGPLAVALLVVAIGA
+SLGGPTGYAINPARDLGPRLFHAVAPIRHKGGSDWGYAWVPIVGPLVGAVLAGLAAPLFV
+>PROKKA_01962
+MGTIFLHEIAGTAILLLLGVGVVANVVLTKTKGNGGGWLLISFGWGLGVFAGVYVAAATG
+AHLNPAVTVGLLVSGAEEYAPGIAVTLGTTLAYFAAQLIGAFLGAALAWLAYRDHYQAET
+DQGAILGTFATGPEIRNPLWNMITEVIATFVLVFVILLFGSTPSGLGPLAVALLVVAIGA
+SLGGPTGYAINPARDLGPRLFHAVAPIRHKGGSDWGYAWVPIVGPLVGAVLAGLAAPLFV
+>PROKKA_02201
+MGTIFLYEIAGTAILLLLGVGVVANVVLTKTKGNGGGWLLISFGWGLGVFAGVYVAAATG
+AHLNPAVTVGLLVSGAEEYAPGIAVTLGTTLAYFAAQLIGAFLGAALAWLAYRDHYQAET
+DQGAILGTFATGPEIRNPLWNMVTEVIATFVLVFVILLFGSTPSGLGPLAVALLVVAIGA
+SLGGPTGYAINPARDLGPRLFHAVAPIRHKGGSDWGYAWVPIVGPLVGAVLAGLAAPLFV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002073.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002073.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a01e6ca44972b075a688d0a5cc764259ce7d9627
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002073.fa
@@ -0,0 +1,24 @@
+>PROKKA_02288
+MPSAPPPSDLAGSTAAPRPPLWTRPFILVSATYLFVAMIFYTLMTAMALYAVTSFGASDA
+EAGVVVGAFVLGAVLTRMTTTPATFAWGRRRVLLVALACYVLTTAAYLWADSLAALTAVR
+LLNGMCFGAAGTVLATAVQRIVPPVRRSEGTGWFSTSMTLAGAVGPMVALQLSTTLGYDA
+LFWACIGFTGMALLIALFLRVPEPPLTGRFRLHRADVFSAEVAPAAGVALASGFMYGGIL
+AFMATFAQQQGYPAMVPSLFFLLFAAGTIVGRAVLGVLHDRHGDNAVVYPILAGMAVSYA
+VLALWREPAGMLAAGALLGLTYGPVVSVFQTIAIKVVRPTEIGVATGTFFLLLDLGTGLG
+PMVLGAVAAAVGIPVMYLLSGGVGMALLLYYRLVHGGRAIARRPPPA
+>PROKKA_01980
+MPSAPPPSDPAGSTAAPRPPLWTRPFILVSATYLFVAMIFYTLMTAMALYAVTSFGASDA
+EAGVVVGAFVLGAVLTRMTTTPATFAWGRRRVLLVALACYVLTTAAYLWADSLATLTAVR
+LLNGMCFGAAGTVLATAVQRIVPPVRRSEGTGWFSTSMTLAGAVGPMVALQLSTTLGYDA
+LFWACIGFTGMALLIALFLRVPEPPLTGRFRLHRADVFSAEVAPAAGVALASGFMYGGIL
+AFMATFAQQQGYPAMVPSLFFLLFAAGTIVGRAVLGVLHDRHGDNAVVYPILAGMAVSYA
+VLALWREPAGMLAAGALLGLTYGPVVSVFQTIAIKVVRPTEIGVATGTFFLLLDLGTGLG
+PMVLGAVAAAVGIPVMYLLSGGVGMALLLYYRLVHGGRAIARRPPPA
+>PROKKA_02228
+MPSAPPPSDPAGSTAAPRPPLWTRPFILVSATYLFVAMIFYTLMTAMALYAVTSFGASDA
+EAGVVVGAFVLGAVLTRMTTTPATFAWGRRRVLLVALACYVLTTAAYLWADSLATLTAVR
+LLNGMCFGAAGTVLATAVQRIVPPVRRSEGTGWFSTSMTLAGAVGPMVALQLSTALGYDA
+LFRACIGFTGMALLIALFLRVPEPPLTGRFRLHRADVFSAEVAPAAGVALASGFMYGGIL
+AFMATFAQQQGYPAMVPSLFFLLFAAGTIVGRAVLGVLHDRHGDNAVVYPILAGMAVSYA
+VLALWREPAGMLAAGALLGLTYGPVVSVFQTIAIKVVRPTEIGVATGTFFLLLDLGTGLG
+PMVLGAVVAAVGIPVMYLLSGGVGVALLLYYRLVHGGRAIARRLSPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002078.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002078.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d42bb89bc4d4799b2f7db17cdbf0f009ea357fbf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002078.fa
@@ -0,0 +1,25 @@
+>PROKKA_00357
+MTAGVDRPADGKVAVERVDRPGRRGMRLLGPAFVAAVAYVDPGNVAANLTAGAQYGYLLV
+WVLVAANLMAMLVQYLSAKLGLVTGRSLPELLGHRLPRGRRLAYWVQAEIVAAATDLAEV
+IGGAIALHILFGIPLLAGGVIVGVVSMILLGVQSRRGQQPFEFVVVGLLAVITLGFVSGL
+FYGPISWGEAVAGMVPRFEGTQTVLLAAGMLGATVMPHAIYVHSALARDRHQGAHAHPGT
+LGRLLRATRWDVGLSLLVAGSVNIAMLLLAAANLSGVSGTDSIEGAHAAITTALGPAVGV
+LFGVGLLASGLASTAVGSYAGSEIMGGLLRWRIPQMLRRVLTLIPALLVIASGVDPTWAL
+VLSQVLLSIGIPFAMIPLVRLTGARAVMGRHANSTPLQTVAWVVVALIVALNAVLLWLTL
+TGQG
+>PROKKA_00671
+MAAVAYVDPGNVAANLTAGAQYGYLLVWVLVAANLMAMLVQYLSAKLGLVTGRSLPELLG
+HRMPRGRRLAYWVQAEIVAAATDLAEVIGGAIALHILFGIPLLAGGVIVGVVSMILLGVQ
+SRRGQRPFEFVVVGLLAVITLGFVSGLFYGPISWGEAVAGMAPRFEGTQTVLLAAGMLGA
+TVMPHAIYVHSALARDRHQGAHTNPATLGGLLRATRWDVGLSLLVAGSVNIAMLLLAAAN
+LSGVSGTDSIEGAHAAITAALGPTVGVLFGVGLLASGLASTAVGSYAGSEIMGGLLHWRI
+PQMVRRVLTLIPALLVIASGVDPTWALVLSQVLLSVGIPFAMIPLVRLTGARAVMGRHVN
+SAPLQTAAWVVVALIVALNAVLLWLTLTGQE
+>PROKKA_02013
+MAAVAYVDPGNVAANLTAGAQYGYLLVWVLVAANLMAMLVQYLSAKLGLVTGRSLPELLG
+HRMPRGRRLAYWVQAEIVAAATDLAEVIGGAIALHILFGIPLLAGGVIVGVVSMILLGVQ
+SRRGQRPFEFVVVGLLAVITLGFVSGLFYGPISWGEAVAGMAPRFEGTQTVLLAAGMLGA
+TVMPHAIYVHSALARDRHQGAHTNPATLGGLLRATRWDVGLSLLVAGSVNIAMLLLAAAN
+LSGVSGTDSIEGAHAAITAALGPTVGVLFGVGLLASGLASTAVGSYAGSEIMGGLLHWRI
+PQMVRRVLTLIPALLVIASGVDPTWALVLSQVLLSVGIPFAMIPLVRLTGARAVMGRHVN
+SAPLQTAAWVVVALIVALNAVLLWLTLTGQE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002083.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002083.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5f8024151e7d74332da33427cc0559cb5845e2d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002083.fa
@@ -0,0 +1,9 @@
+>PROKKA_00913
+MTDQRDRPLHATIAVVLAIATAGYLAPWAIAAVRGRSNVWAVFWVNLLTGWTVLGWCIAL
+YMSLTSHRRLRPWGPRGL
+>PROKKA_01694
+MTIVTDKRDRPLHATIAILLAILTGGYLAPWAVAATRGKSNVWTVFWVNLLAGWTVIGWA
+IALYMSLTSHRTARVWGARR
+>PROKKA_01144
+MTDQRDRPLHATIAVVLAIATAGYLAPWAIAAVRGRSNVWAVFWVNLLTGWTVLGWCIAL
+YMSLTSHRRLRPWGPRGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002087.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002087.fa
new file mode 100644
index 0000000000000000000000000000000000000000..decb92a6c4a62dc05865b48965ec2afaec2652f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002087.fa
@@ -0,0 +1,10 @@
+>PROKKA_01652
+MKISDRVRAMRKELLLTQQQLADLAGVSDATVRQIERGTGKSTLKSVLSVMEVLGLELEV
+TG
+>PROKKA_00207
+MSRQPASVPLTSALDTAPFGREMRALRRGAGLTQAQAADRMGVSLRWLKYLEAGTRRPRL
+QDVGRVAVMDPLTGRMATSVLQTLTPAGKITPSGPRLSLAHLARLAGWPLEPMDPSVSDA
+VTPEALAVVADVLDAAHALLDQADPHMEDLEALAATRNVSAVVHRLDHVYAALAAEDAR
+>PROKKA_00836
+MAQPHPSPLVPVGERVRAARREMGLTQQELADLAGVSDATVRQIEHGTGKGTLGSLMAVL
+EVLGLHLEVNG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002094.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002094.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5190ce629e8dd89fb8b1da9acf6f626a510d5b19
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002094.fa
@@ -0,0 +1,23 @@
+>PROKKA_01748
+MAHQAMQRGRRRMVHLTGLFAGIGGIEQGFHNALGSKVETDLLCESWAPAQIVLKNRFPG
+AELHPDVRELASLPEATDILSAGFPCQDLSQAGRTAGIRGEQSGLVTHLFELLRRRISAG
+RRLPTLLIENVPNMLALDKGAAMEFLVQEMETLGYSWAYRVVDTRFTGLPQRRRRVIVVA
+SVNLNPSEVLFADEAASRPDDHYSSDAFGFYWTEGKGGLGWAPDAIPTLKGGSTIGIASP
+PAIWVRGAEDATRALVVPREAEMESLQGFPRGWTDLDFGLSAARTRGTRSKLLGNAVSVR
+VAEWVARRVFAPGEVVCPSVDWGSSRQWPNAAAGMGGKRWRVEASEFPTLEPYEHLLEHV
+DVSSAPALSRRAVSGFRSRLLQGNLGRYPGFREAVAEADRALTEDQLITKLEA
+>PROKKA_02211
+MALTSVEVCAGAGGQALGLEAAGFKHLACVEYDKHACTTLRTNRPQWNTVEADLLEWSGA
+AYAGKTDLFAGGVPCPPFSKAGKQLGEADERNLFPRALDLIEEIGPRAVMLENVRGLLDP
+QFQEFRDGVDARLESMGYVPSWRLLNASDYGVSQLRPRVILVALKEPWAQHFTWPEPNKK
+PAPSVGELLAPLMAANGWEGAKAWAARADRIAPTLVGGSHKHGGPDLGPTRARAAWAALG
+VEGRTIAAEAPEPGFEGMPRITVQMGGMVQGFPADWQFTGAKTHGWRQVGNAFPPPVAAA
+VGKQIRKALKAAN
+>PROKKA_01976
+MAHQAMQRGRRRMVHLTGLFAGIGGIEQGFHNALGSKVETDLLCESWAPAQIVLKNRFPG
+AELHPDVRELASLPEATDILSAGFPCQDLSQAGRTAGIRGEQSGLVTHLFELLRRRISAG
+RRLPTLLIENVPNMLALDKGAAMEFLVQEMETLGYSWAYRVVDTRFTGLPQRRRRVIVVA
+SVNLNPSEVLFADEAASRPDDHYSSDAFGFYWTEGKGGLGWAPDAIPTLKGGSTIGIASP
+PAIWVRGAEDATRALVVPREAEMESLQGFPRGWTDLDFGLSAARTRGTRSKLLGNAVSVR
+VAEWVARRVFAPGEVVCPSVDWGSSRQWPNAAAGMGGKRWRVEASEFPTLEPYEHLLEHV
+DVSSAPALSRRAVSGFRSRLLQGNLGRYPGFREAVAEADRALTEDQLITKLEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002096.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002096.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c3249bb57d02aae340b1d72db6fd0ec0bf4f380
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002096.fa
@@ -0,0 +1,22 @@
+>PROKKA_01777
+MVNANEYEPLELSHLHPAAQPVARLPAAERVQRIRADRWIGYPKAVEAVERLETMLGWPA
+KQRMPNLLLVGPTNNGKSMIIERFRRQHPPSSEPDREQVPVVCVQMPSEPSPLRFYTAIL
+SVLGAPLRPRPRLVELERLALSLLREVGARMLVVDELHNVLAGRGDTRREFLNLLRFLGN
+ELRIPLVGVGTREAYLAVRSDDQLENRFEPFVLPLWEADDQARSLLASFAASFPLRKPSV
+IDTEDMARYLLARSEGTIGELAHLLTAAAVAAVESGLEAIDHRTLTMANYTGPTERRRVF
+ERELL
+>PROKKA_00635
+MDALLWHTQALTPAPAPPEPVLLREFSTLSTQDQDEYWTRMHRWMCASTLDCDRTAAIRR
+GMDRVLQRNEYARSGAKTIIGLSAPNGVGKSTFIKSYAQDRYQRMMHDQPVDKLPSRTDS
+GGSPSHWIPQVYITLRAASEVPDVNAAILSYLGYPIMGRTTKDTTLLVHAVARHGVKLLI
+LDDAHMLRAKQARARDVLDYVKFLNTMMGERDGTLVLVGANMEGGPVYQDPQVAARLHAF
+ALQPYTVQQDTTERVAWQQLLAGAEKKFMPYLDSATEGTLTRELAGQIWARTQGHLGDTH
+QLITTALLDAFDQGDTTLVSEHLQGVRLSARAEAAEADLAREATLTSRREQNRKAKR
+>PROKKA_02217
+MNSHDWHHQAVTSQPSGLKPITVRKFERLNQQEQNEHWTALNRWMAAQPIDCPRVRQTST
+RMQAEVLRNEYAPRGAKTIIGLSAANGVGKSTLIKRLAHQLYRETVPTTDPGILPTRTVG
+TGATVDWIPQVYITLRAASRIQEVNTALLSFLGYPTIGQTRATTTRVVEAIRTHGVQLLI
+LDDAHMLKTSQADARDVLDYLKFLNTELGELGGTMILVGANLEDSDVYADAQIATRLAPL
+QLQPHAIFPVSERARFQAMLRGVEEKFMCHLDTATTGTLTNELAGEIWQRTQGYLGDIHR
+LITTVILETFDAGEDVITRERLRAVPLSARATAAEASLREAATQRSRRTENRRKKKAGST
+PPAQTPSQDAAGSSSDSPTAAVPETKE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002101.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002101.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d285d7bf8f12145f865c563146fa093ec773fb2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002101.fa
@@ -0,0 +1,33 @@
+>PROKKA_02132
+MATRLRHRLLSAAALTAAGALLVTGCAQSQRDGGGSGGSGGGDAAQVDGSFIFAASSDPK
+TLDPAFASDGETFRVSRQIFEGLVGTKPGTADPAPLLAESWESSEDGLTHTFQLKEGVTF
+HDGEPFNGEAVCANFDRWYNFTGIQQSETLSYYYGKLFRGFADKPEDAVYKECEATGEHE
+VKITLAQPFAGFISSLSLPAFAMQSPKALEEYKADEVGGTAESPQMSEYARAHPTGTGPY
+KFESWSVGEDVKLTANEDYWGEGGEVTDITFRVIDDPVARRQALEAGDIDGYDLVAPADT
+AALSEAGFNVVARDPFTILYLGLNQEKEELQDVRVRQAIAHAIDKDALIAQTLPEGTEPA
+TQFIPKSVNGYSEDVTTYEHDPAKAKALLAEAGYPDGFTIDFNYPTGVSRPYMPTPEQAF
+SNLSSQLAEVGITVNAKPAKWSPDYLDQVQGTSDHGIHLLGWTGDYNDTDNFVGVFFGQE
+KPEFGFTDEELFSALEEARQIPTLEEQTPKYQEINEQISEIVPAVPLAHPAPSLAFDKRV
+ASYPASPVNDEVFNEIDLTE
+>PROKKA_00268
+MATRLRQRLLSAAALTAAGALLITGCAESQRDSGGSAGGSGSNGDAAQVDGSFIFAASSD
+PKTLDPAFASDGESFRVSRQIFEGLVGTEPGTADPAPLLAESWESSEDGLTHTFKLKEGV
+TFHDGEPFNGEAVCANFDRWYNFTGIQQAETVSYYYGKLFRGFADAPENAVYESCEANGD
+AEATVTLAQPFAGFIASLSLPAFAMQSPKALEEYKADEIGGSAESPQMSEYARAYPTGTG
+PYKFDSWSVGEDIKLSAYEDYWGEGGDVTDITFRVIDDPVARRQALEAGDIDGYDLVAPA
+DTQALSDAGFNVVARDPFTILYLGLNQQQEELKDVKVRQAIAHAIDKEALIGQTLPEGTE
+PATQFIPKSVNGFSEDVTKYEYDPEKAKQLLAEAGYADGFTIDFNYPTGVSRPYMPTPEQ
+VFSNLSNQLSQVGIQVEAKPAKWSPDYLNQVQGTADHGLHLLGWTGDYNDTDNFVGVFFG
+QEKPEFGFDNPELFSALEEARGVPTLEEQTPMYEEINKQISDFVPAIPLAHPAPSLAFDK
+RVASYPASPVNDEVFTEIDLTE
+>PROKKA_00124
+MATRLRHRLLSAAALTAAGALLVTGCAQSQRDGGGSGGSGGGDAAQVDGSFIFAASSDPK
+TLDPAFASDGETFRVSRQIFEGLVGTKPGTADPAPLLAESWESSEDGLTHTFQLKEGVTF
+HDGEPFNGEAVCANFDRWYNFTGIQQSETLSYYYGKLFRGFADKPEDAVYKECEATGEHE
+VKITLAQPFAGFISSLSLPAFAMQSPKALEEYKADEVGGTAESPQMSEYARAHPTGTGPY
+KFESWSVGEDVKLTANEDYWGEGGEVTDITFRVIDDPVARRQALEAGDIDGYDLVAPADT
+AALSEAGFNVVARDPFTILYLGLNQEKEELQDVRVRQAIAHAIDKDALIAQTLPEGTEPA
+TQFIPKSVNGYSEDVTTYEHDPAKAKALLAEAGYPDGFTIDFNYPTGVSRPYMPTPEQAF
+SNLSSQLAEVGITVNAKPAKWSPDYLDQVQGTSDHGIHLLGWTGDYNDTDNFVGVFFGQE
+KPEFGFTDEELFSALEEARQIPTLEEQTPKYQEINEQISEIVPAVPLAHPAPSLAFDKRV
+ASYPASPVNDEVFNEIDLTE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002106.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002106.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c62de9df244efbb5c8f40be790c9f6c5e3456b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002106.fa
@@ -0,0 +1,13 @@
+>PROKKA_00570
+MPDLQPVPTLADVPELGDGVVTLHPADARHAPALGALLRDADVQVLTGSVHSTAQAAAIA
+RGEAHAGPTPERLAEIYAGWAADEDRAVWTVEAEGAVLGEILLMDLDAGNRACGLRLWLA
+GAGRDRGVGTRALTLVLEHAFTTVGLHRVGLEVYDHNPRARHVYARLGFVHEGTLRQALL
+LDGEWIDCHVVGLLAHEWHARRAAPSSD
+>PROKKA_00497
+MTPDPSVDASPQAAPTVAVTADPGRAPADDAGPDERRPSEPTRVQALFYSPPELTDGRIT
+LRPAGADDAAALYPLLQDRETLLLTGSTHSSARADRIVSGEIQPWGSPEKLAEDYDAWSV
+ADDRAVWVIEEDATIVGEMVLMDLDPPNISCALRLWITGATDRGIGTAALTLALDWAFRT
+VELHRVSLDVFEHNPRAIHVYEKLGFVREGTMREALWQDGRWIDSLGMGILRREWLARQD
+G
+>PROKKA_00659
+MVDNLRAVQLYLQCGFVVEGLRRTSLIRDGGSVDEYAMAQLVLSSGSESAVVDK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002107.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002107.fa
new file mode 100644
index 0000000000000000000000000000000000000000..057459b6d2b90b3139f682caea0b5ade3d08bc9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002107.fa
@@ -0,0 +1,18 @@
+>PROKKA_00591
+MSEHTATPARAGSPAWIDYSATDFAAQQAFYEALFGWTFTDSGEEFGHYRMIAKDGASVG
+GAMDADQMTAMTGEAPAPAAWTVYLRTEDMAATLAAVREHGGTVLVDAMPVGDLGTMAMV
+AGPGGEAVGFWQADTFEGHDLPLTPGTSVWFELLSTRFDEAVEFYQAVAGWQPTLMGDDG
+APEDGHAAADAEDAAQDGPRYATDHPGEGATAGLCDATQWLPANAVGYWRMYIAVEDTDR
+ALEVIREHDGKVLDGPQDSPFGRVTTVQDPAGATFQINEALPGQE
+>PROKKA_01322
+MSITPGQPVWIDLGTTDLERSKAFYRDLFDWNFSDTGGEFGHYHMVDAGVPVGGLGPNVD
+AEGNIDASMPVWWTVYLKVEDVDATLAAVREHGGHVHVEPMQIGDMGRMAIVAAPSGAAF
+GVWEVGSFEGFDTEGRPGTPVWFEALTKDFDADAAFYAAVLGWKNVPMREGSSDEGAAEE
+DGAGMRYVTDAAGDDASAGLFDAAAFLPAEVPSHWRVYFAVPDTDAAVEKVLALGGAVVE
+PAQDSPYGRVAAVADDLGGTFMVIA
+>PROKKA_00514
+MSAQHTAIPSGSPIWIDYSAGDFATQQAFYSALFGWTFQDQGEDYGHYTMVRAGDAVIGG
+AMDGELSAQFSGGPVQPAAWTVYLKTEDIARTLGLVAEHGGQVIVEAMPVGELGSMALAM
+TPGGEAVGFWQPGEFSGHDLPLTPGTSVWFEVMSKDFAADAEFYRAVCGWDVVPMGPDGQ
+QDDAAPDEDGMPAYATDHTGEQATAGLCDAAAWLPEAVPSHWRVYFQTTDMDASVKVVEE
+KGGRIVDGPMDSPFGVVASVVDPAGATFQLNQPPARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002115.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002115.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20d993ec1e052868171cb0d847d17ddd37489f9c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002115.fa
@@ -0,0 +1,37 @@
+>PROKKA_02329
+MDGFRRSLDGQFVTVDGHDYSEVTRPKLAQADQQERLPDGSERPLPTRTLHLMAAEDGTA
+PVDLNDWERQVLDSEAAEPSLRGWYRNPSRASKQSLAIPFQDGAGQWQALRPDFVFFHAN
+QDGTIRADIVDPHGTHLADALPKLRGLAEYAQAHGMPSVGSRPSLRSRGSCGCWT
+>PROKKA_00346
+MRYTLKDYQADAVAEILANIERAQRLRREGHLPTMALTATTGGGKTVIAAAVIEALFFGS
+DTFDFLADPGAVVLWFSDDPTLNAQSRHRLEAAAPDLIGRMTDLNAGYTKPALDPRTVYF
+INTQKFAKTSRMVRGFQPSGTEGQDTFAGLDPRVRPDMVPQTIYDIIAATIQNPDLTLYF
+FLDEAHKGMGTTARAQAEQKTIVKRLIAGQPGVPPMPVVFGISATLQRFTNAMDGIRGRL
+GLDPVQVDPARIQKSGLLKDNILLNIPHPDEVGSFETVLLRSAVRQLLESEAAWDAYVAE
+QRADHPGAEIERVVPLMVLQTPNSVTPSDIAGYLRTIMDVWPEMPAGAVAHVFGEKEAIQ
+AAGLFIPHIDPEKVQDTKRVRILLAKEAVTTGWDCPRAEVLMSFRTVSDLTKITQTLGRM
+VRTPLARRIPGNDELNSVLCLLPNFDEKAARQVVKDLTNDEVPNPIIDPVVDPDPRPEVT
+PPSGGAGASSGGGTEPANPEVPGHGTHATDRVAEPSADGQGTPARPGGLHQGETRGASGG
+GQGGAVGPVVLTDRVKVTPIENGPLWDLFDSLPTETTPSRGLGPVPLLTALGQYLSEDGL
+RPDAGEEAHRHLHGTLDYRAGQFREDVDKAVKDILEVRVRTILADRATGKERIGMFTERA
+DLAVVREAYQRAARAFTADVSRTYVNHIVGPDADEDDLREAYARVAGMASVPDIVADVKE
+EASRLVGRWFQEHRTDIKALADDRQAAYKALMEQSTEPQRGNLAKPVNWQESPVDVDKKP
+LPTRTDHILTAEDGTYPLTLNRVESSVVDQEMRRRGAIAWYRNPSRVKDESLAIAYRDGN
+AWRTMRPDFLFFHEDAQGRVRASIVDPHGHHLSDALPKLRGLARYAEQYGDEFMRIEGLT
+EVNGKMRALDMQDPKVREAVEVATSARALYESDAAVDY
+>PROKKA_00693
+MRYTLKDYQAQAVEQVLNRLHRARKNYQDDGVLSQFSLAAATGAGKTVMAAAIIEALFFG
+SDQYTEDIAPDPGATVLWFSDDPDLNDQSRARIHAASSELDGRLRTVENSFAETTFAPGQ
+VYFLNAQKLREGARLVRGAQDPTNAATPVMAAPDMAQRTIYDVIANTVATPGRTLYFILD
+EAHRGMKTTKKNDQERATIVQRLINGTALAPTMPIVLGISATVERFTQAMAHATDRDALS
+PVQVDPALVQASGLLKDDVVLTIPEEAGAFDTTLLREAVARTKASTRAWAAYAAEQGEPN
+PVVPLLVVQVADKPSDEHLSRILDVIHQEWPELRPQDIAHVFGTHTDRHLPGQIVNYIAP
+QRVQETTHIRVLLAMEAISTGWDCPRAEVLMSFRTYKDATYVHQLLGRMVRTPLARRIPG
+NEVLNSIDCFLPHFDKTTSTAIAQTLMRGQSDMDDTTSDPGKQAARRVLFDPVTLTPNPA
+VGEDVWAVFDALPSMNIPQGATKPLKRLDILANALSHDELLPGAVKTAAHTMCKLLDGCR
+VQYSEQIAAARQDVLTLSAQRLTGRLGTTTLSTTSLELLADDRAIEEAAAAAARTLTGWI
+AGAYIDHIVPEDEEDLDLREGDIIIASLARTSEVVADLEAKADKLVQDWLSQYRVQINGL
+TDERQAVYDRVREMARQPERVALTRPKLTQADQQERLPDGSERPLPTRTLHLMAAEDGTM
+PVDLNTWERQVLDSEAAEPSFRGWYRNPSRASKQSLAIPFQDGAGQWQALRPDFLFFHAN
+QDGTIRADIVDPHGTHLADALPKLRGLAEYAQAHGDAFGRIEAVAEIEGQLRVLDMKNDV
+VQAGVHAAQDAESLYKAAPAY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002118.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002118.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5c1955328c4c6ac17d51a4951ec813ebb6e769c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002118.fa
@@ -0,0 +1,4 @@
+>PROKKA_00164
+MLTIASRLDVMNRLGRAMADPTRSRILMTLLEGPSYPAVLARDLGRV
+>PROKKA_00333
+MLTIASRLDVMNRLGRAMADPTRSRILMTLLEGPSYPAVLARDLGRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002119.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002119.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18b229999aa264809c265e8b2ed754f91abf2889
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002119.fa
@@ -0,0 +1,6 @@
+>PROKKA_00165
+MNPELEQALRLATDPPGGVSLEALEDLVRDDPTTWWDISEAATHLNVTAHTLRYYERIGM
+VSVPRDDAGHRRYDSPAIRRLVFITRMRTAGMPIADLQHYLALGRV
+>PROKKA_00351
+MNPELEQALRLATDPPGGVSLEALEDLVRDDPTTWWDISEAATHLNVTAHTLRYYGRIGM
+VSVPRDDAGHRRYDSPAIRRLVFITRMRTAGMPIADLQHYLALGRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002121.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002121.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0fd7c48a1ec403918bfdab317c5be51174021bcf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002121.fa
@@ -0,0 +1,8 @@
+>PROKKA_00188
+MTAVPETYVFDTGPLRHFTLKGWLGVLKFLTAGHAVIPESVEQEIRDQQYQHPDLRQILD
+AEWIVVDRSEDLEFLAAFARYEEHLVAGGRNRGECGVLALGRTHGYRIVIDDNVPRVLAK
+REKLECTGTLGLLCEAIRKEQLTVPMVESLADDLIMGDYRLPFGPGGFKCWAEQQGLLG
+>PROKKA_00213
+MTHVFDTGPLRHFTLNGWLGVLKFLTGGRIVIPESVEREIKDQQHQHAALRQILDADWIT
+VDRSDDLEYLAAFARYEEHLVDGGRNRGECGVLALGRTRGHRIVVDDNVPRVLAKNEELD
+CTGTLGLLCEAIRADKLTVSMVESLADDLLASEY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002123.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002123.fa
new file mode 100644
index 0000000000000000000000000000000000000000..29496166c3ee85ca3bc45f8a9dee89388832d67f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002123.fa
@@ -0,0 +1,5 @@
+>PROKKA_00191
+MAPHSSTPLFAVGYGKIEKVRTNFPDAFRDQKVTSQLKHFIDSTTSLTFHWGSLSIGTLR
+PWGR
+>PROKKA_00191
+MAPRSSTPLFVIGYGKIKKVRTDFPNAFRDQKVTSQLKHFIDSTTALTFH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002125.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002125.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ae6cb8d03ec6efffce765ad14f7fa6031c21ea3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002125.fa
@@ -0,0 +1,5 @@
+>PROKKA_00259
+MKTRALLASALLLASTLVGAPAAAASAASAEDDVVTTLGLGKGTAEWTCRHFGIWCD
+>PROKKA_00110
+MKLRSLAASTLLLASVLVGAPAATATSTPAAPTTGPAVTAPTGDQSGTDGLNKGAKEWAC
+RNFGVWCD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002126.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002126.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e99cc7b7c40446af690da74986c6b9d24f594f28
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002126.fa
@@ -0,0 +1,18 @@
+>PROKKA_00402
+MTRREVESVEDRIREHLRRDDLNSAVELLRALSPGDALELLDRSEPRMVPVLFRLLDKST
+AVRVFAAMETGQQSDLVRQLQDGQVQDLFAELRVSGQARLLDEMPATVARKMLAGLDAGA
+RGEVGRLLGYPADSVGRRLRMAPVRLREDWTVAVALENLRDHGGREQAAIVSVPVVSPQA
+RLTGVVDVSVLVTQPLDARVSEIMREPVSAVATEDAEEVARLCADRRLWTVPVTDSEGRL
+IGVFTVADALEVLDEESTEDAARAGGVEPLGRPYLATSVLALMRSRITWLLVLAIGATLT
+VQVLGVFEDTLEEMVVLSLFIPLIIGTGGNTGNQAATTVTRALALDDVRPRDAPRVMFRE
+LRVGMALGGCIGLLGLVIAGLVFSWPVGLVIGATLFTVCAFAATVGGLMPLAARTIGADP
+AVFSNPFISTLVDALGLVVYFFIAQAVLGI
+>PROKKA_00408
+MTRREVESVEDRIREHLRRDDLDSAVELLRALSPGDALDLLDRSEPRMAPMLFRLLDKTT
+AVQVFAAMETGQQSDLVRKLQDGQVQDLFAELRVSGQARLLDEMPANVARKMLAGLDAEA
+SGKAGRLLGYPADSVGRRLRMAPVRLREDWTVSTALENLREHGGQEQAAIVSVPVVSPQA
+RLTGVVDVSVLVTQPLDARVSEIMREPVSAVATEDAEEVARLCADRRLWTVPVTDSEGRL
+IGVFTVADALEVLDEGSTEDSARAGGVEPLGRPYLATSVLSLMRSRITWLLVLAIGATLT
+VQVLGVFEDTLEEMVVLSLFIPLIIGTGGNTGNQAATTVTRALALDDVRPRDAPRVMFRE
+LRVGMALGGCIGLLGLVLAGLVFSWPVGLVIGATLFTVCAFAATVGGLMPLAARTIGADP
+AVFSNPFISTLVDALGLVVYFFIAQAVLGI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002128.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002128.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6045356e2cb3199d2d0ba6d4d69fd78ec2f62533
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002128.fa
@@ -0,0 +1,6 @@
+>PROKKA_00502
+MADYHGFYRDELGIDVLAVRPNLAGWEGESSIQDDEHVGWRAANDAEIPPVGVADFLREW
+RHRALRKARSTKFDLHWRLRMSQQR
+>PROKKA_00501
+MADYHGFYRDELGIDVLAVRPNLAGWEGESSIQDDEHVGWRAANDAEIPPVGVADFLREW
+RHRALRKARSTKFDLHWRLRMSQQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002130.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002130.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb70ffa1c67c7fd272530cf118ba7d1461d01668
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002130.fa
@@ -0,0 +1,12 @@
+>PROKKA_00587
+MNVHSLQLAYTPEAAREVTDQIKTGLESVYHLIRSAYRGRAWEVLGYRSWDEYVTREFGN
+LHLRPPLEKRQDIVLSLREVGMSTRAIASATQISEATVRRELKHAGASKDAPGRAPASVV
+GVDGKTYEATRPARIGNLEPSMGVRGGQSDVDAVLDMPAEDFGIEPLDLVRHDEEQKNRA
+RRVLTAFNGSGAAAVPALIKAATPVASLVSPATGKALVEDEDLHGVVWDSVRCVRTLAHV
+IRSVGHVEGESQAEIRSTLRDAVDDLDEVLKKIEEGTR
+>PROKKA_00321
+MNGYSLQLAYTPEAAREVTDQIKTGLESVYHLIRSAYRGRAWEVLGYRSWDEYVTREFGN
+LHLRPPLEKRQDIVLSLREVGMSTRAIASATQISEATVRRELKHAGASKDAPGRALASVV
+GVDGKTYEATRPARIGNLEPSMGVRGGQSDVDAVLDMPAEDFGIEPLDLVRHDEEQKGRA
+RRVLTAFNGSGAAAVPALIKAATPVASLVSPATGKALVEDEDLHGVVWDSVRCVRTLAHV
+IRSVGHVDGQSQAEIRSTLRDAVDDLDEVLKKIEEGTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002135.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002135.fa
new file mode 100644
index 0000000000000000000000000000000000000000..783ba2b6d04e7aecd6d2f4e13685e9864140ca1e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002135.fa
@@ -0,0 +1,8 @@
+>PROKKA_00599
+MGRFGLHRTGSAEYKRYLRSQAWGYRRVRWFADCRQAGQEPACQVCGITLTRAGTLDLHH
+VSYKGVGQDEEGRWQAREAHNDLMPLCRDHHQRLHQIMDGKKEFFGWDRRRATIVIVARM
+VRQSQA
+>PROKKA_02242
+MGRFGLYRTGSAEYKRYLRSQAWGYRRVRWFADCRQAGQEPACQVCGVTLTEAGTLDLHH
+VSYKGVGQDEEGRWQAREAHNDLMPLCRDHHQRLHQIMDGKKEFFGWDRRRATIVIVVRM
+IRQSQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002137.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002137.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b6bbd2850ba39fef79cfa27d1df1f69ccca55ca3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002137.fa
@@ -0,0 +1,6 @@
+>PROKKA_00835
+MVSMSRPPEPRPAPAPTARAAAARPATPPGVQGRWARRAAGGLIGVSVLLAAWSFALPFV
+FGLGPRQVPWWREVFGLIRIQGVVGV
+>PROKKA_00567
+MSRPPEPRPAPAPTARAAAARPATPPGVQGRWARRAAGGLIGVSVLLAAWSFALPFVFGL
+GPRQVPWWREVFDVNHEANLTAWWSSGLLLLGAAGFTTVGLVRRALGRTGGGACSRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002138.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002138.fa
new file mode 100644
index 0000000000000000000000000000000000000000..750554b66750d2f6a2a5b7a44a2fff0233b87c8d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002138.fa
@@ -0,0 +1,12 @@
+>PROKKA_00883
+MPAGKSIRRVARAGARLLPPEQRRRVRRTGGALLRRLPPQVAEEVRGVFGIRWGDRPAHA
+RPADALGLAGGPARTRPGSASLTGRGAAAVGADPEAAARLERVLGLADTSRTERGGRAVG
+VVAAPDVRAALAAAGHRVVPLVPGTAAAVAERVEAVVVDVDGVDGPWAGALDAAGAALYL
+ELRGAVSAAAARGVTVWVLSRGRHQHRLGALALLHAEDVIVVEAGADRTPLHFTEDPGDA
+PQGIADVLAACPEESA
+>PROKKA_00605
+MPAGKSIRRVARAGARLLPPEQRRRVRRTGGALLRRLPPQLAEEVRGVFGIRWGAPPAHA
+RPADALGLAGGQARARPGNASLTGRGAAAVGADPEAAARLERALGLADTSRTEQGGRAVG
+VVAAPDVRAALATAGHRVVPLVPGTAGAVAERVEAVVVDVDGVDGPWAGALDAAGAALYL
+ELRGAVSAAAARGVTVWVLSRGRHRHRLGALALLHAEDVIVVEAGADRTPLHFTEDPGDA
+PQGIADVLAACPEESA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002139.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002139.fa
new file mode 100644
index 0000000000000000000000000000000000000000..47707ce4be83438c1ce3e0018cea6447b76089f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002139.fa
@@ -0,0 +1,18 @@
+>PROKKA_00887
+MKIAVVALGKIGLPLAVQFASKGHEVVGVDVNATVVDLVNAGTEPFPGEAHLQEKLSSTV
+ADGRLRATTDYGDAVPGADAVVLVVPLFVDDEARPDFGWMDGATTELAKHLTPGTLVSYE
+TTLPVGTTRTRWKPMLEEGSGLTEGEDFHLVFSPERVLTGRVFEDLRRYPKLIGGLTPAG
+AERAREFYEAVLDFDERPDLSRPNGVWDLGSAEASEMAKLAETTYRDVNIGLANEFARYA
+GANGIDIYRVIEASNSQPYSHIHRPGIAVGGHCIPVYPRLYLWNDPAADIVRTARAVNAS
+MPDFAVDLLAQAHGDLAGQRVVVLGAAYRGGVKETAFSGVFATVGALRTRGAEVTVDDPM
+YSDEELTALGFTPHSSGSEVDAAILQTDHAEYRALTPADLPGVRTFVDGRNVTDADAWSG
+VTRRVIGLPQDAEAAR
+>PROKKA_00609
+MKIAVVALGKIGLPLAVQFASKGHEVVGVDVNATVVDLVNAGTEPFPGEAHLQEKLSSTV
+ADGRLRATTDYGDAVPGADAVVLVVPLFVDDEARPDFGWMDGATTELAKHLTPGTLVSYE
+TTLPVGTTRTRWKPMLEEGSGLTEGEDFHLVFSPERVLTGRVFEDLRRYPKLIGGLTPAG
+AERAREFYEAVLDFDERPDLSRPNGVWDLGSAEASEMAKLAETTYRDVNIGLANEFARYA
+GANGIDIYRVIEASNSQPYSHIHRPGIAVGGHCIPVYPRLYLWNDPAADIVRTARAVNAS
+MPDFAVDLLAQAHGDLAGQRVVVLGAAYRGGVKETAFSGVFATVGALRTRGAEVTVDDPM
+YSDEELTALGFTPHSSGSEVDAAILQTDHAEYRALTPADLPGVRTFVDGRNVTDADAWSG
+VTRRVIGLPQDAEAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002147.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002147.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e792ac81914227a9d09a242555daa23a9f343a9f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002147.fa
@@ -0,0 +1,16 @@
+>PROKKA_00954
+MATIQTRTNKAGRTTYRVGFYEAGRFQWLPALAREAGAQRVKAIVEDPRQGPTVARRILE
+AQVDSAPGMPTLAEFFPRYIEHRGLRCTPGTLAGYEAEAARTFLPRLGELPVDMIDRRTV
+AEWIRWQLQQPTARWRAVAARAAAATPPRPEPPLATVSPKTVRNAHALLSAVLGLAVQEG
+ILPANPARGADLPDDDVEEERGIFSRAEWARFYAAISESYQPLLIVLLVTGARWGEATAL
+QVRDLDVAASVIHVRRAWKKGKEGAVLGVPKTARGRRTIMLPDWAVETLEPLAAGRAADE
+FLLTVPGGGVIHRTNFVERHWKPALAAAGIAKHLTPHSLRHTFASWALMDGVPAQVVQHR
+LGHESLQTTSRVYAHLLLDAQRAAVDAIGWEPPPGA
+>PROKKA_01933
+MATISTRTSKKGVTTFRVGYYEGGRFRQMPAMLSETGARRIKAIIEDPAQGPDVARRLLE
+AHADGAEDVPTLAQCLDRYVEARAVRCSEGTLAGYRREAARTFLPRLGQLPVTAIDRPAV
+QDWIRWQMTQPTARSRAAAERAARAGTPAPSLEPVSPKTVRNAHSLLSSILYLAVQDGLI
+PTNPAHGQDLPADDVEEEKDIFTRPEWDRFYRAMTPHFQPLLALLITSGARWGEATALQV
+RDLDVDAGVIHVRRAWKKGAQGVVLGTPKTQRGRRAIMLPDHVVAMLTPLAAGRPPEDFL
+LTSPTGRVIHRTNFVERHWKPALAAAGITKDLSPHSARHTFASWALMEGVAPQIVQHRLG
+HESLETTSRRYAHLLLDAQRAAVDAIGWRPSPGT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002149.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002149.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a266b3aa55a083acff84ee4797a5b6e3c4d6d25
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002149.fa
@@ -0,0 +1,12 @@
+>PROKKA_00969
+MPLTASTVTRTVSVDGASVTCHDSVTPGELDRPLVLVHGTGGTTASHFGHLFPMMATRTR
+VIAVDWAPTADPAADLTVDLLVGQVRAVVDELLGPDAAFDLLGYSLGAVVAGQLAADLGR
+RVENLVLVAGWATTDVHQRLRNEVWRHLYATSPDALARYTAFCGLSPLALRSLTPAMLDG
+ALASLTADEFTARQMDLNARVDVADRLSAVTARTLIVSCAEDIMVPPHHQYELLGIIDDA
+RLTTMTSGHAFFLERPAELMQIVDLYLREPDRHPAGAIIPETHA
+>PROKKA_00682
+MPLTASTVTRTVSVDGASVTCHDSVTPGELDRPLVLVHGTGGTTASHFGHLFPMMATRTR
+VFAVDWAPPADPAADLTVDLLVGQVRAAVDELLGPDAAFDLLGYSLGAVVAGQLAADLGR
+RVENLVLVAGWATTDVHQRLRNEVWRHLYATSPDALARYTAFCGLSPLALRSLTPAMLDG
+ALASLTADEFTARQMDLNARVDVADRLSAVTARTLIVSCAEDIMVPPHHQYELLGIIDDA
+RLTTMTSGHAFFLERPAELMQIVDLYLREPDRHPAGAIIPETHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002151.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002151.fa
new file mode 100644
index 0000000000000000000000000000000000000000..528a685dc68250b00daa3a29d12e3577b8075791
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002151.fa
@@ -0,0 +1,6 @@
+>PROKKA_01388
+MGRPPSIPAEKKTRIVLSVLAGEMSIAEAARKEKVSEQSIGRWKAEFLEAGKTALVAGRS
+GPSSREEQLEAEVAELTQALGEAHLEARVWKKSAEGRLGPSRTSR
+>PROKKA_01120
+MGRPPSIPAEKKTRIVLSVLAGEMSIAEAARKEKVSEQSIGRWKAEFLEAGKTALVAGRS
+GPSSREEQLEAEVAELTQALGEAHLEARVWKKSAEGRLGPSRTSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002154.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002154.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dab0212136b4e24fa9b6e9612cc8cad4a7d26827
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002154.fa
@@ -0,0 +1,9 @@
+>PROKKA_01493
+MTTTTPKTARQLRAEWQAEIARREAEIVAAERAEARRIDEALRRAGRARVAAVETLYEML
+GIDEQTKTRTRRDGSVQTVRADLDEAERAERLVAAVAALLEGAAGTRSAPAGGAEAVPDE
+AAQMVPEEPSGALAPLPPAAGGESAEPDPEEDEAHASDDAEEPVSDEGDEAAREEDAYAE
+EPAYGTVSDDLHEAGWQA
+>PROKKA_02201
+MTTTKTARQLRAEWQAEIARREAEIAAAEREEDRRTDEALRRAGRARVAAVEILYELLGV
+DEQTTTRTRRDGSIQTVRVDRDETERAERLVDAVRALLAHCDGLRSAPAESAPTSAPLPS
+PAGLDATVSGREQTAHAESESTSDEGWAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002159.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002159.fa
new file mode 100644
index 0000000000000000000000000000000000000000..84eb95550c0e12cd41f56f52704268aa36497d35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002159.fa
@@ -0,0 +1,8 @@
+>PROKKA_01509
+MTTPQFSVDRTRRPVATYRAISTKDAASTQRDGEAVLEVRELSSRSGQREAEVLFHDGQW
+QLCDPEHDLVPGFTFDAFPEHPFLAEAYGETWNGWDTPVVRREVLADILTALELSHRWEG
+DVTVLEVDDYEDRIVPRLDGLYDLQQAGWTVQQVELG
+>PROKKA_02214
+MTTTPPPVDRTRRPVATYRAISSRDASSTQRDGEAVLEVRRFAARDGHAEAEVLFGDGQW
+QLCDPERDLIPAFEFDAFPDHPFLAVEYGEDWNGWATPVVTRETLADVLAALELAHRWEG
+STAVLEIEDYEDRIEARADGLYDLAQAGWTVQQVEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002162.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002162.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3257864204ba7ab56815b93a5f455f04d2d7bb4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002162.fa
@@ -0,0 +1,10 @@
+>PROKKA_01607
+MFSASVIDDATGVNMGIGFLGVALAFGLTVVAMAYAVGHISGGHFNPAVTLGAALAGRLP
+WKLTVPYWIAQLVGGVAAGGVLLAIASGRPGYSLAENGLATNGYGELSPAGYSMGAVFLT
+EVLLTAVFLYVILGATDRRAPSGFAPLAIGLTLTLIHLISIPVSNTSVNPARSFGVALFA
+GGDALGQVWLFFVAPLLGAAVAGLSYRFVFPNTSRVTEELPEPAADGTRDAV
+>PROKKA_01319
+MAYAVGHVSGGHFNPAVTLGAALAGRLPWKLTVPYWIAQLVGGVAAGGVLLAIASGRPGY
+SLAENGLATNGYGELSPAGYSMGAVFLTEALLTAVFLYIILGATDRRAPSGFAPLAIGLT
+LTLIPLISIPVSNTSVNPARSFGVALFAGGDALGQVWLFFVAPLLGAAVAGLSYRFVFPN
+SSRMTEELPEPAADGTRDAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002165.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002165.fa
new file mode 100644
index 0000000000000000000000000000000000000000..80d5fb38706dd97eececd4ffc84c0c237aa2fb31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002165.fa
@@ -0,0 +1,6 @@
+>PROKKA_01616
+MSISASEARKTLFPLIERVNADRDAVEIVSRKGNAVLMPADEYAAWQETAYLFRSPANAR
+RLLDAYERARAGSVEEHALDRMDGDA
+>PROKKA_01326
+MSISASEARKTLFPLIERVNADRDAVEIVSRKGNAVLMPADEYAAWQETAYLFRSPANAR
+RLLDAYERARAGSVEEHALDRLDGDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002166.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002166.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dad646910b7c132f00c6de9ebcd8ab1b2f47664a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002166.fa
@@ -0,0 +1,12 @@
+>PROKKA_01788
+MTGTRVATERHDTALVLTLDGPDRLNAVTPTAMEALHTALGEAGRDPAIRAVILTGRGRA
+FCAGADLRDDLDPEATMRAANRVVETIRAVDVPVIAAVNGPAVGYGAALAAAADLAVAAD
+DAYLLLPFTGIGLVPDGGSSVTIARAVGRALAAEMALTGRRLGAEEARAAGLFSRVVPGP
+DLAGVAHALADAVAERPRRAVALAKAALNAADAEVVGRALEREARDQVELIRSAEFAQRS
+AAFRR
+>PROKKA_01088
+MTGTRVATERHDTALVLTLDGPDRLNAVTPTAMEALHTALGEAGRDPAIRAVILTGRGRA
+FCAGADLRDDLDPEATMRAANRVVETIRAVDVPVIAAVNGPAVGYGAALAAAADLAVAAD
+DAYLLLPFTGIGLVPDGGSSVTIARAVGRALAAEMALTGRRLGAEEARAAGLFSRVVPGP
+DLAGVAHALADAVAERPRRAVALAKAALNAADAEVVGRALEREARDQVELIRSAEFAQRS
+AAFRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002169.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002169.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b8ceb6365f2bc1403796b583406df44f038495f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002169.fa
@@ -0,0 +1,16 @@
+>PROKKA_01793
+MSTAPSSRDAVIVDAVRTPVGRRGGALRDWHPLDLLAHTLDHLVRHSGADADALDDLIAG
+CALQRGEQAGNVARNALLGAGLPIGLPGTTIDRQCGSGQQAVHFAAQGVRSGEYDWAIGC
+GVESMSRVDLGPLFAPGGPRGEWYGTRSLARFEGNLPAQGPSAELIVEKWGLTRERLDAY
+SVQSHRRAAEATREGRFTDSLVPIDGLDRNGDTVALTADEGIRADVDPQKVAALAPVFSP
+DGAITAGNSSQLSDGAAALLVAERGAAEAAGLRPKARILSMAVAADDPVLQFTAILAATR
+RALDQAGLDITDIDLVEVNEAFAPVPLIFMDEFGYPEDQLNVNGGSIAIGHPLGSTGARL
+LTQLTDELHRRQARYGLLTVCEGGGMANATILERF
+>PROKKA_01083
+MSTAPSSRDAVIVDAVRTPVGRRGGALRDWHPLDLLAHTLDHLVRHSGADADALDDLIAG
+CALQRGEQAGNVARNALLGAGLPIGLPGTTIDRQCGSGQQAVHFAAQGVRSGEYDWAIGC
+GVESMSRVDLGPLFAPGGPRGEWYGTRSLARFEGNLPAQGPSAELIVEKWGLTRERLDAY
+SVQSHRRAAEATREGRFTDSLVPIDGLDRNGDTVALTADEGIRADVDPQKVAALAPVFSP
+DGAITAGNSSQLSDGAAALLVAERGAAEAAGLRPKARIVSMAVAADDPVLQFTAILAATR
+RALDQAGLDITDIDLVEVNEAFAPVPLIFMDEFGYPEDQLNVNGGSIAIGHPLGSTGARL
+LTQLTDELHRRQARYGLLTVCEGGGMANATILERL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002173.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002173.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad7c0738866f7e5b93c5cbf42e79373519ce9f0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002173.fa
@@ -0,0 +1,14 @@
+>PROKKA_01949
+MVPASSIHTAATARTGTTYSGPMPVSAQGPRVTVVGDSSALGSTSLMNLEMPGITVDAKE
+DRTFAEGLTRLGQLKAAGRLRDIVVLGLGVNTGGTAAAQARQAMDLVGPDRELVLVTASG
+PVAWRAFTEQAMRDLAARYPGRVAVTDWEAASRYVTDFRADRIHPRAQGLSVDAQLVRLA
+ADRATGARTVTVQAGQTLSGIAVAYAVPGGWSAISRATGVPLAQLPSLNGPTLSTVLHPG
+QVLRIRCPLT
+>PROKKA_00704
+MNRSTLGTRLGASVLVVAALVSAAPAAPAVTSASGTTTTTATTGLAPGTYLAQSGDTWAY
+IAPRVGVELADLLRANGATTSTAIRAGQPLVLPAVSKHLPATSRTGTPYSGPMAPSSAGR
+RVTVVGDSIALGAASLMNLEMPGLTIDAREGRTFAQGLTRLAELKQAGRLGDVVVLGLGV
+NDGGATATQVRRAMDLVGTGRTLVLVTASGPVAWETSTNTAMRNLAATYPSRVVVADWKR
+ASAYVTDFREDRIHPRGQGASVYARLVRLAVDTAPVLRSTTPRTVTVQAGDTLSLIATRY
+GVTGGWQALATLNKISDPHMIRVGQTLLLPATSTTTTPATYTVLPGQGWYAVSRATGVPV
+TQLLSLNGATLSTEIHPGQRLRLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002174.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002174.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dae952ba05504b1ad88ab9cb738013959d9ad337
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002174.fa
@@ -0,0 +1,17 @@
+>PROKKA_01950
+MVVDYAQGVTLNAIGKKWGLTREAVRQIINRKSEFTVPELKEYRRIVAQEERSLLRAGLL
+AWSEGNRGVGLEVAAREFGVPQHRVAELLGKRADLHRANPRRRTTALRATEEELLDLLRQ
+FHAETGQATAAGYTAWAKTRGVPGHQTVAIRFGRWNAALAAAGIRQAEPVPRESRYTTDD
+LWAAAVEAFSAPDGPVTHLEFVAWLQEREGMPSDALIRNRLDVSFENLRHTALRMAATRE
+LIPGVTGGVFERRQWKAKTDEGDDAASAIDVVRRAIEDLGPTLSSGRYSAWAKEHRCPSA
+TTLQRRAGLQWGDLVAAAGGLPNARKNTGYSDEQLTEWMRRFLTETGSSSSTLYTSWQAA
+NGAPSYITVATRFGGWPQAVAAARW
+>PROKKA_01869
+MEFEVPSVSPGSESLNAPFTSKRRRELAALASMTILPSTPRAVRMAREYFEGSTLAEIGE
+RFGRTRERVRQLIRDEAGYSTKELKAYRELLADEEFRMKRAAAVSWSERHVGVPLSVASQ
+DLSLSQQELRRLLGKRVEFHLGDAKPRKTSSATPDEVLLSALREFYEETGETAAQSFTQW
+SRSHGVPTHQTVANRFGGWNAALERAGIAVTDRRRSRSKYSDAELVEALVDAWSSATPPR
+TYLELSDWLSARPGMPSAALIRNRLGVGFEEMRARALRVVAGQSMGFPGRKRTRVDWKGK
+LDPGDDPLTLVRRAIEDRGPRLTVAAYNSWAAEHGVPATPTVLRRAGTNWVQLVEAAGGT
+PNPPKPANPFTTEELRVWMERFMTESATHSQSAHEEWRQAHGGPSAQTITTRLGPWREVL
+ENLGGGQREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002175.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002175.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c298b0488cfb197d158d9d21aeccce046bd1cba0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002175.fa
@@ -0,0 +1,8 @@
+>PROKKA_02002
+MTRLPGLRPPRFLDPWRRPLAPRLPWHVVLAASIAGALTIATLSLGEDLASVPLLVGAFG
+SSCVLVFLVPHGPHSHPANVLVGHVVSAACGIAVISVLPLAWYSLAAGMGLAMAVMAGLR
+VIHAPAGATALAVMLSNADWHYLVTPVLAGALVLTACALLYRRLMWRVIGPAE
+>PROKKA_00847
+MSRLSRAPGLRRPRLLDPWRRPLLPRLPWHVILAASLAGAATIATLSIGQDLTSVPLLVG
+AFGSSCVLVFLVPHGPHSHPANVLVGHVAAAACGIAVSSVLPLAWYSLAAGMGLAMAVMA
+GLRVIHAPAGATALSVMLVEAGWDYLLAPILSGALVLTACALLYRRLMWRVIGPPPPPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002184.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002184.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f718fd670c0aabb62d0cc242f860bd7fac477517
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002184.fa
@@ -0,0 +1,16 @@
+>PROKKA_02237
+MSDFDTLSLEDLLAACAPGGSTSLLSETPLRPAGGPGAVIAPAKVIEGRGEPTYAYERRM
+ELDEAGQPRPVWTVVVDSKQSVSNRDEDAIISARRDQGTPEGEALRKVPTIEVRYGEAVE
+SDLSLPHRAFDGHIRAATLDGAPVTQTEAYRALRDATKLDARALLDAAPTALVLGAWDST
+RKSHQGRYQSCMTGEIIGVLADQDQEGGAPRTNRRAAGRVDPVAASVKPSAKDVEALVKA
+QAGELSAKLQDKVLAEAKKKGETGSSMSTLGLGHIPPVLGELGGVACRSIMRRRLLSFSA
+LRQLRFGGTTEQDVACRALLAAYALLGMALSDRELHLRANCHLVESDEPTVTLDLRYGKS
+RALAPITDEVAVQVFEAALAHAKSVAGVEWNGQTIQLVGDPAILGAASTDDVEV
+>PROKKA_02169
+MSDFDTLSLEDLLAACAPGGSTSLLSETPLQPAGGPGAVIAPAKVIEGRGEPTYAYERRM
+ELDEAGQPRPVWTVVVDSKQSVSNRDEDAIISARRDQGTPEGEALRKVPTIEVRYGEAVE
+SDLSLPHRAFDGHIRAATLDGAPVTQTEAYRALRDATKLDARALLDAAPTALVLGAWDST
+RKSHQGRYQSCMTGEIIGVLADQDQEGGAPRTNRRAAGRVDPVAASVKPSAKDVEALVKA
+QAGELSAKLQDKVLAEAKKKGETGSSMSTLGLGHIPPVLGELGGVACRSIMRRRLLSFSA
+LRQLRFGGTTEQDVACRALLAAYALLGMALSDRELHLRANCHLVESDEPTVTLDLRYGKS
+RALAPITDEVAVQVFEAALAHAESVAGVEWNGQTIQLVGDPAILGAASTDDAEV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002187.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002187.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3d015a34f88a81e68bf0096fdd14a2b7a7b57c7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002187.fa
@@ -0,0 +1,12 @@
+>PROKKA_02260
+MPDLPACLEREPLTRAVVTGYAAKVTAEDRAVQRDAFIAAMVWGYGRVGYGPSRVERIMA
+QPGFEEQLADVTRITLEQGGPAAFEHIRQQRKSGVGCLKHLGAAFGTKYLYFLTKAHRES
+DIAPVLDSVVRAWFAEHAKDVDVRIGGGWTYPRKYATYVETMQAWGEELKIPADDVERLI
+FLQQQDATQEPWRESWSSAAADPEAGELLEALRLALADLGAGDDAEPHLQALEDVIADAE
+DRAPDEA
+>PROKKA_02191
+MPDLPACLECEPLTRAVVTGYAAKVTAEDLAVQRDAFIAAMVWGYGRVGYGPSRVERIMA
+QPGFEEQLADVTRITLEQGGPAAFEHIRQQRKSGVGCLKHLGAAFGTKYLYFLTKAHRES
+DIAPVLDSVVRAWFAEHVKDVDVRIGGGWTYPDRYRTYVTTMQAWGEELKIPADDVERLI
+FLQQQDATQEPWRESWSSAAADPEAGELLEALRLALADLGARDDAEPHLQALEDVIADAE
+DRAPDEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002191.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002191.fa
new file mode 100644
index 0000000000000000000000000000000000000000..228e299d4cad671d2f2d97c1db08cec8218b9ecb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002191.fa
@@ -0,0 +1,16 @@
+>PROKKA_00093
+MSDRLRDLVLAFAGGTASASQVDLILEAGGLDDDLVQAVSRLRQEGRLARRQREAARILV
+DAATLITGARDMDEILELICRRTRLLLDSDMAYVSLNDVDQGQTYIRTTDGVLTSAYRNL
+RMPLGTGILGQAAGGATVSQTGDYLDDTSFPHIPAVDEAVRGEGVVSILAATLRVRGRRI
+GALLVADRRPRTYTPDEVDLITQTAGLSAVALSRNEEMRDLQTALDDLTVAREEIESKNV
+LLSRLGRLDQELFSVLREEASPADLAEVIGQAIGTEVKALFPADLPAHRTPAAPVVSEHP
+CQDSPNGMATLVRAFTGHRELGALEAHGSLDRDERFLFERGATALTALLLAQERGWATQM
+QQQHRLVKDLENASTETWRSVAGRLAPHRLQEGGTVRVLAVRTEQLQDTRMALRELLARR
+GGVSSIRYEVLRVISPNLTGRELHELLVSRDRSAAVCEQEALLMPEDIRVSLQGVQRTVR
+AMAALNITGVADPRWDLGLTGLAVAQLPPATVDRLVYRALEPLLSYDRQQGTELTHTAWS
+FLECDGRVSVAAERLHIHPNTLRQRIGRIGTLLGEDWHQGSHRTDLHLALRLHRVQSASR
+TG
+>PROKKA_00837
+MAFLGPGEHFRDLPGAFRTLENALAVSRVAGGLHAVDASTVGAVGMVLAGAGEASKDVTA
+RPLAPLRDLPPQRASALRETALAYLDAGTNVAETSRRLFLHRNTVLQRLEQLGAVLGPDW
+HTPPRSLDLHLALLSAARDDGGAPGAPPVRSQPRRRAEELRRPRSPAARC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002192.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002192.fa
new file mode 100644
index 0000000000000000000000000000000000000000..478a781b64a60c4b33c0cf17ecc6e47193c440f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002192.fa
@@ -0,0 +1,14 @@
+>PROKKA_00239
+MPSPLDLARQAKHRLFLLRRAREVVRQAAAVRGSERFAREYALASAGFDLPGLPAMSGPC
+AVAMVRDEADVIERSVRHLADQGIPHIVVVDNGSKDATPDILRRLAGEIPGLVVGADREP
+AYVQSAKMTRLADLASAAGATWVVPFDADELWFGAEGTLAEALAAADAPVLRAVMHNAFP
+AADGSGPLLDTIAHFNVKVAFRPRSGAVVEMGNHEVLRPGVRADGLRILHLPWRSFEQFA
+RKSRTGAQAIALADTPEDKAYHWRRLGALDDDALRAAWEALLAGQPLTDAAWYPRGTLRP
+LRSDTPTRWDEV
+>PROKKA_02434
+MDLLSPARALKHRAFLARKDAELRAEARRLRADPVFRAQYSAAEAGLKVPPLEDHPGPWA
+IAMVRNEADVIETAVRHLVRQGVDHLLIVDNLSEDDTPQVLARLAQEFPHLHVGTDHEPA
+YYQSAKMTRLADLVSAAGARWIIPFDADELWFAPQGRLVDALTRSGVPVRRAHLYNLFPT
+PDGQQWHLDTARHFDDKVAFRAWDGAVVVMGNHEVSRPGPRDGEGLRILHLPWRSFEQFA
+RKTRIGAAAVAQAELNEGEAYHWRWLGSASEDELRAVWRRLLSGEAVANAAWYPRGTLRP
+IGDTLPSSWADVQALLGPGPAEGNALSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002199.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002199.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c75d640091990fae3aa1b905ccb539bf092c6843
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002199.fa
@@ -0,0 +1,11 @@
+>PROKKA_00325
+MSTLTLSSKPLTDDRRAVLHRRIRWIVAGTITYNVIEAAIALAAGTVASSSALIGFGLDS
+IVEVLSAAAVAWQFATPDPHRREKVALRLIAFSFFGLAAFITVDAVRTLFGAGQPEHSTV
+GIVLAAVSLAIMPFVSWFERRTGRELGSASAVADSKQTLICTYLSAVLLVGLVLNSTLGW
+TWADPVAALVIAAVALKEGVEAWRGDACCTPASALIAGDQNEKDGDGCGADCACCAHSAC
+LQYRRTGW
+>PROKKA_02006
+MSTLTLSSKPLTDDRRAVLHRRIRWIVAGTITYNVIEAAIALAAGTVASSSALIGFGLDS
+IVEVLSAAAVAWQFATPDPHRREKVALRLIAFSFFGLAAFITVDAVRTLFGAGQPEHSTV
+GIVLAAVSLAIMPFLSWFERRTGRELGSASAVADSKQTLICTYLSAVLLVGLVLNSTLGW
+TWADPVAALVIAAVALKEGVEAWRGDACCTPASALIAGDQNEKDGDGCGADCACCAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002204.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002204.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5d09a5da2771a774636ccb6b6d12c9f93b87c87
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002204.fa
@@ -0,0 +1,11 @@
+>PROKKA_00686
+MQNTEQTPRDASTEAGGRLWRHRIVENDTLRMTVLSMLAAAVAIGLSTLLIATPLGDALG
+VGAARRASWMTGLMTLCLMWSIYSALDTVVLYRWLGRRDSTDLHALLRTRSRGPKESVDP
+VGWRALMLGASSTLGNTATFSVMAMLVVVISMWMPEVRSVPAMRLLAVATVLASWASIVL
+AQALRYARLAAQHDPKRSRPEGESPAPPIRFRGSDSPVFSDYVALSLTLSTMMGAQDVVL
+SGRAARTAVREHALVGFLFNSMIIAALASLLLTVA
+>PROKKA_01518
+MDSDDGRLWLATLPALAAGASGVLIGREAAAEFPSADWRVMFYGTLGVTQVVMYVVYLWL
+TLRRFHGLDARTLERDLRTVSRGPRPGSWAVRMGLPYGSTLGWMTSVSVVALVIVVVVML
+DPATAGQPLLRVLCALVVVSSWAVLWVSQALAYARMAAQHGGIEFTGEEPPVFEDYLTLS
+AFVSALFGTGDVTLTGRRTRRAMRSHVMVAFGFNSMLVASLATLLLSRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002208.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002208.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e0fc6672c17b7a49c00eb972a295afd49869bf04
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002208.fa
@@ -0,0 +1,18 @@
+>PROKKA_00769
+MSPASTSPRRVLAIGLGPFNLSLAALAHPLPDVEVEVVESRDAFVWHPGMMLPGAQIQVP
+FLADLVTFADPTSPYSFLAYLKAMGRLHRFYIRGSWYPLRREFSDYCAWVAAQLPGIAYA
+TTVTAVRWDDQADEFVVEAASAAGTSTHRADHVVVGTGTVPSLPAPLARVAEESARVGAS
+PVVHTGEYMGRREDIAGAGSVLVVGSGQSAAECALDLLNAGHPDLTWVTRSPRFFGMEVG
+QLTLELTSLDYERHFATLPRARRDEINASHRSLYKGISEYTIEDVYHALYERQVGPLDPA
+RLWPGTSVTDARLVAGPGAPRVEVTLRDEETGVTGGHVVDRVVAGTGYRHPDHPFLEPVR
+HLLRAEDGRTTANADHAIDVSGRRIFVHNTAEQPLGLTGPDLGMAAEHSGRILSTIAGRQ
+VYAQAESIAFQDFGAVAAGVR
+>PROKKA_00997
+MSPASTSPRRVLAIGLGPFDLSLAALAHPLPDVEVEVVESRDAFVWHPGMMLPGAQIQVP
+FLADLVTFADPTSPYSFLAYLKAMGRLHRFYIRGSWYPLRREFSDYCAWVAAQLPGIAYG
+TTVTAVRWDEQADEFVVEAASAAGTSTHRADHVVVGTGTVPSLPAPLARVAEEAVRVGAS
+PVVHTGEYMGRREDIVEAGSVLVVGSGQSAAECALDLLNAGHPDLTWVTRSPRFFGMEVG
+QLTLELTSLDYERHFATLPRARRDEINASHRSLYKGISEHTIEDVYHALYERQVGPLDPA
+RLWPGTSVADARLVAGQGAPRVEVTLRDEETGVTARHVVDRVVAGTGYRHPDHPFLEPVR
+HLLRVEDGRTTANADHAIDVSGRRIFVHNTAEQPLGLTGPDLGMAAEHSGRILSTIAGRE
+VYAQAESIAFQDFGAVAAGVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002209.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002209.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2638a468a1de3fb687ad7ef500163fbf2ce879df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002209.fa
@@ -0,0 +1,20 @@
+>PROKKA_00770
+MLPRLFGLGDPAAYLDATGRAARVAVDTAYDRAGVHPDTPSTHLADAVGAVDFSQPTGSL
+DDALAEVAELYAHQTTAYHHPRYAAHLNCPVLLSSTAADTVLGALNTAVESWDQARSAAL
+MEQRLLAEVGRWCGFAAGDGVFTSGGSASNLQAMTLARGRAVQRLTGHAGLADLPAEVLG
+SLRVFVSAATHYSIAKAAGLLGLGRHAVVVVPTDAAGRLDPGALAEAVEREVAAGAVPMA
+VVATLGTTDRGAIDPLPAIADVAERHGMWVHADAAVGGILAASAATRHELPGLHRADSVT
+MDFHKTFYVGLACSALVVRDAESLRHVTVHADYLNPEDSVHPNLADRSLQTSRRFDSLKL
+WLTLREHGAEAVVSLFAGARERTRQACGILRARPTFAVLEDPTLVTVLFRVRAEGLSEEE
+CTAVQAATHRELVAGGRALIATTVVDGVPHLKFTILNPAVTSGELEELVDVVEEAALRHV
+DAVRASRHRWRGVARTRPHGPSVAVSCTLPASAGPRPSAARVDEHGEQVCA
+>PROKKA_00998
+MLPRLFGLGDPAAYLDATGRAARVAVDTAYDRAGVHPDTPSTHLADAVGAVDFSQPTGSL
+DDALAEVAELYAHQTTAYHHPRYAAHLNCPVLLSSTAADTVLGALNTAVESWDQARSAAL
+MEQRLLAEVGRWCGFAAGDGVFTSGGSASNLQAMTLARGRAVQRLTGHAGLADLPAEVLG
+SLRVFVSAATHYSIAKAAGLLGLGRHAVVVVPTDAAGRLDPGALAAAVEREVAAGAVPMA
+VVATLGTTDRGAIDRLPAIADVAERHGMWVHADAAVGGILAASAATRHELPALHRADSVT
+MDFHKTFYVGLACSALVVRDAESLRHVTVHADYLNPEDSVHPNLADRSLQTSRRFDSLKL
+WLTLREHGAEAVASLFAGARERTRQACGILRARPMFAVLEDPTLVTVLFRVRAEGLSEEE
+CTAVQAAMHRELVAGGRALIATTVVDGVPHLKFTILNPAVTSGELEALVDVVEEAALRHA
+DAVRAGRHRRRGAGRNRPHAPSASVSCTLPSSAGPRPSAARVVEHGEQVCA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002211.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002211.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb30835c264d8de229ab18d0c66b5362a5abed6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002211.fa
@@ -0,0 +1,10 @@
+>PROKKA_01621
+MRRDIKKKRAALSAAVVVAGLLTAAPSAGAAPTPAGEDTPSLDAYCAEEYWTNTSVTSNI
+FKQSHSSYSSVSGAPGVTLTIATGRTFGVSGDITGELSGDVSAILAGVSAKVGTRVGVNY
+SSTNTVSGSWKVPSTYTNGGKLAIGAKRAQGTWSRQMLNKSCNVVTLRSGSFYTPWQQFY
+FQHYRL
+>PROKKA_00867
+MRMNIKKKLAALASGTVVAASLMVAPAAGAATTPGDGEAVSPDAYCAEEYWTNTSVTSNT
+FKQSYSSYSSVSGAPGVTLTIATGRTFGVSGDITGEVSGDVSAILAGVSAKVGTRVGVSY
+SSTNTVSGTWKVPSTYTNGGKLAIGAKRAQGTWNRQMLNRACNVVTLRSGSFYTPWQQFY
+FQHYKL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002212.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002212.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a1654b21b5187867a492a24c63535d3145e685cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002212.fa
@@ -0,0 +1,12 @@
+>PROKKA_01649
+MLLAYIDEIGEPGAYVGPDHPRSRTSPAFGYAGFVMPESAARGFGAKFTALKRQLFASEI
+DRAKHPGRWEFKGANLFRPDTPARFPQQLRVFDALVRSVVVDHGGKLFYYADEKQRGTPK
+QIGLDVEKREADAMRETLNRLARHAHHHGHNLMVIIDQINEKTRVERVASMYAHIFSRAG
+DFPEMRCIVEPPMHVDSSLSSNVQFADWVAAAVTRAVDHQLNDSSKYAWVTDPQRLASMR
+GSFTYESKLHLWNRGVQDINHSELFHRERRLAPTPHGQLLGASVDPAAAEKMAKIWRSGR
+>PROKKA_01881
+MPESAARGFGAKFTALKRQLFASEIDRAKHPGRWEFKGANLFRPDTPARFPQQLRVFDAL
+VRSVVVDHGGKLFYYADEKQRGTPKQIGLDVEKREADAMRETLNRLARHAHHHGHNLMVI
+IDQINEKTRVERVASMYAHIFSRAGDFPEMRCIVEPPMHVDSSLSSNVQFADWVAAAVTR
+AVDHQLNDSSKYAWVTDPQRLASMRGSFTYESKLHLWNRGVQDINHSELFHRERRLAPTP
+HGQLLGASVDPAAAEKMAKIWRSGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002213.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002213.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52d2f57ced2f5aba32f8492db9d7e01984022dfd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002213.fa
@@ -0,0 +1,10 @@
+>PROKKA_01705
+MARKSNPVYYDANGNVVQPPAKKKGGCLKYALIGLLALIVIAVLASMMGGGSNSTSEGGG
+EAASQGETSSSDEAAKVGLGQEFTVGDWATTVESVDTPVASVGPSGFSTEAQGEFVPVQI
+SAKNNAKEERTFFADSVKLVSADGAEYSYSTDASIYGTENGMNIEPTNPGNVASGYLWFD
+VPAGTEITQVKVSGGGLSLDQPVVVELD
+>PROKKA_01933
+MARKSNPVYYDANGNVVQPPAKKKGGCLKYALIGLLALIVIAVLASMMGGGSNSTSEGGG
+EAASQGETSSSDEAAKVGLGQEFTVGDWATTVESVDTPVASVGPSGFSTEAQGEFVPVQI
+SAKNNAKEERTFFADSVKLVSADGAEYSYSTDASIYGTENGMNIEPTNPGNVASGYLWFD
+VPAGTEITQVKVSGGGLSLDQPVVVELD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002215.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002215.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e7954ccbfc773b3e7a2d2c491a132d9f9786030
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002215.fa
@@ -0,0 +1,12 @@
+>PROKKA_01747
+MNVFGPDILARTMSEPADPTKYGIRWQYHSRSDRHGKVASWGVAFDLLRSSSVMRQHARD
+GKIVLGVNLKLSDFETKKSKVLDLVIARPGGAATSARGESLVSLAQRYNMNLSGEEMGEL
+TSLPDIPVAPVGSVLVALEAKATMTAHVKSLPRLHDELTSSHISVHGESQTALAIGYAQV
+NVADVFVSSNPANVERIHLGQEPVVTSHKQPGDCQRVLDTLNTLRTRSSSIGIGFDAIGV
+TVLDLRNDDSPVKVVHSRPAPQPGDAFHYDSMIMRMATRYDTQFSGI
+>PROKKA_01975
+MNVFGPDILARTMSEPADPTKYGIRWQYHSRSDRHGKVASWGVAFDLLRSSSVMRQHARD
+GKIVLGVNLKLSDFETKKSKVLDLVIARPGGAATSARGESLVSLAQRYNMNLSGEEMGEL
+TSLPDIPVAPVGSVLVALEAKATMTAHVKSLPRLHDELTSSHISVHGESQTALAIGYAQV
+NVADVFVSSNPANVERIHLGQEPVVTSHKQPGDCQRVLDTLNTLRTRSSSIGIGFDAIGV
+TVLDLRNDDSPVKVVHSRPAPQPGDAFHYDSMIMRMATRYDTQFSGI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002218.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002218.fa
new file mode 100644
index 0000000000000000000000000000000000000000..306f08beffd92b122b22b82fd797cff87a6f7806
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002218.fa
@@ -0,0 +1,6 @@
+>PROKKA_01861
+MSIRYPLGYVENERKVYPQGYARERVSPGGDGEGRHDQETSAGGVSQMISLRIGRQNYRN
+VWLTRQGA
+>PROKKA_02091
+MSIRYPLGYVENERKVYPQGYARERVSPGGDGEGRHDQETSAGGVSQMISLRIGRQNYRN
+VWLTRQGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002222.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002222.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d36b3e81e68159699cdc83c71bd0d44ed829a9df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002222.fa
@@ -0,0 +1,10 @@
+>PROKKA_01985
+MSESTSAAPQPSQSVPSRRRVASSLAWAVPTVVAAAAAPAEAASPLPRIDRVFQLTLAPG
+VPWTEPKVSPCASTLFTNPTRLSVTTDNSAFYYRITNLRADSTVTDVTASVLVQKSVVDK
+LSNGLTWTSETKDWSNPTLDVSGAKYIDNGIEYYRYYSTLRTAVPAPVSGTITLPRIQWY
+SNCSTNLLTQAQSTGVMANGRGSAVVNGTPLVNVGTYVRLTPRPAG
+>PROKKA_02233
+MSESTSAAPQPSQSVPSRRRVASSLAWAVPTVVAAAAAPAEAASPLPRIDRVFSIRRATT
+AAVPGASVSACGSGSTRLSVTTDDVNTYYRIANVRTGSTVTDVTASVLVQKDMVDAMETG
+KNPTTFTWTSSATPSWSTPVREVSGTGSPVLYTNNGIQYYRYVSKLSTPVPAPVSGTITL
+PIIGWYSNCSTTLAGVSVNGRGSAVVNGTPLVNVGTYRQL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002225.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002225.fa
new file mode 100644
index 0000000000000000000000000000000000000000..308ab02b7fbf57b0e661a1741b30b2b6ac85a1f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002225.fa
@@ -0,0 +1,10 @@
+>PROKKA_02187
+MNKSEEAYARLTQKIETGELPPGAILSEAALIDAAETGRTPLREAVQRLIRDHWLLAGGG
+RGLQVPAISVDDQLERLEVRRSLEALAVGLACARADEEQLAAVAAHVRHLRTVEDLAAYV
+AAVGRSHELLRTIANNRYLADSLVPLQGLSRRFWLATTKGLPDEVERGRAFYVPALEAVT
+RRDAAGARAGVLALHDFLARSALDYAARRADHGSAEPPAPWAEGR
+>PROKKA_00156
+MNKSEEAYARLTQKIETGELPPGAILSEAALIDAAETGRTPLREAVQRLIRDHWLLVGGG
+RGLQVPPISVDDQLERLEVRRSLEALAVGLACARADEEQLAAVAAHVRHLRTVEDLPAYV
+AAVGRSHELLRTIANNRYLADSLVPLQGLSRRFWLATTKGLPDEVERGRAFYVPALEAVT
+RRDSAGARAGVLALHDFLARSALDYAARRAAHGSAEPPAPWAAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002226.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002226.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7379003d5877514c16c66d2b591efc9a105f3d03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002226.fa
@@ -0,0 +1,6 @@
+>PROKKA_02215
+MGDYYQDNAARVLAHIGAHHDADPGPLADTGRAHHGDMHAGVVVGQDGTIHAHTRRDASG
+TYRVHLPGEDVPVDLWAARERRVIGPTVHVPLWRIFSGQGVP
+>PROKKA_00048
+MAGYYTTNAARVLAQVGAHHDADPGPLADAGRAHHGDMHAGVILGMDGTIHAHTIRDARG
+THRVHETGAEWAADLWAARNARRIGPTVHVPLWRVFSGPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002227.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002227.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c2139655728335949f3296910a134b3be19e1e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002227.fa
@@ -0,0 +1,6 @@
+>PROKKA_02224
+MYSVYAQHWQRDTEAAASARVYQVSRLRHDAAPAPGVSIFRHGRPVLTLTPDDARRIADG
+LHDAAERAERVPTTPTRKEHHS
+>PROKKA_00042
+MTRRTFITNRDRWTRDLTTATKSRANAILREHPDGGTVPGVMIFRDRLPVLTMTPDQART
+LADQLHDAADTCLEAANG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002229.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002229.fa
new file mode 100644
index 0000000000000000000000000000000000000000..340d1003b974c87754c32232e1c67038af6f98d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002229.fa
@@ -0,0 +1,21 @@
+>PROKKA_02228
+MTSPLDIEDVDLSETTRQRPDYFHPDLYAEQPPAERPGEKHRGQLRIAHRLAEAHSGRLM
+YVNGLGWHVWDGQRWAPDETAAAERAVHDVLRSALAESHDGDRNLREDVRRCETAAGIRG
+VLDIAATLEGVRVAVDALDADPHLLNVANGTLDLRTRTLRPHDPADRLTRVCRGAWTAGE
+SDGMWSDFLARVLPDDAERAYFQRVIGQAVFGAVREHLFPVLTGTGANGKGTAYTAIAHA
+LGDYAAIIDPDLLMTSARGPGGPEMMQLFGARLVIGSETEEGKPLDAALMKRLTGGDPIT
+ARHLYQAPVTWEPSHQFLYVTNHLPKVKGNDPAVWRRVRVLPFDVVIPPADRDPALPERL
+REAADAVVTWAVRGWWDYLDAGGMGEPEAVKAATDAYAVQSDAVRRFIADACVIAPGASA
+RTRELHTAWTAWAAADGAEPLAEKKFGAELDRLGYPTTRTRAGSVRQGIGLLADDD
+>PROKKA_02200
+MSVRESRPTQADETALKAFTGAEDEVTNFDGVVSYEEEPPAGFLAEPRSGLSPTARPDTE
+EHAEAVLAGLSSLSATDSEILQLATTHFVERMWDGTPGTTRHLLDLCAAVARRLGDRKHD
+GAPRFYAPRALPVSAVAAMLAHLHRYCVVDLGLPASDGVAPLLVRYADDGPLEGTYSRVT
+EASLYVDALALEPESSPKQMEELFARLAARSQVVHRCSDPNLVPVANGIFDYRTKTLREF
+DPELVFLFKAATRYVDAPPMPMIVQPDGTDWNPVDWMASLAPDPEVRHLLWEVTGALLRP
+LNAWDKWLALISPEGRNGKGTLLAMWRALLGPDAHKSATLASFGADFPDIEGLNEKSAIL
+TDENDVGRYLESSATLKSIVTGDVLSAPVKHSKAVPVAFQGLMVQCMNDLPRAKDKSSSF
+YRRLLAVPMEANFTEATENKAIKHDYVQRPEVLEWVLHHVLVEMEAFTSFSEPAACAALK
+DDVRDANDPVRVFVAEFIDQFAWDLVPTTFAHDLYKAWLVRRWPNTHPVNEAEFIRQVSG
+HMAEYGWEHKKNVRVSSRMHSHEPLINEYDLRAWMNPAYNGPDPVKRAAPLLKPSYRGWV
+RIEP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002232.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002232.fa
new file mode 100644
index 0000000000000000000000000000000000000000..84fb9cff915165d211a4196440d238dbae16e79e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002232.fa
@@ -0,0 +1,8 @@
+>PROKKA_02301
+MQTFDGLDEFERAVGTHLGHSRWRTVTQEQVDLFADTTDDHQWIHVDPERAARGPFGSTV
+AHGFLTLALLPSMVREIYRVEGMAMVVNYGSDRVRFPHPTPVGARIRAGAELTRLDRGPQ
+GALAMVTTTVEIEGVAKPACVSDSLFLLRPGKDAS
+>PROKKA_00285
+MQTFDGLDEFERAVGTHLGHSRWRTVTQEQVDLFADTTDDHQWIHVDPERAARGPFGSTV
+AHGFLTLALLPSMVREIYRVEGMAMVVNYGSDRVRFPHPTPVGARIRAGAELTRLDRGPQ
+GALAMVTTTVEIEGVAKPACVSDSLFLLRPGKDAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002237.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002237.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3d4ab4a1f14342cf730642b18878342a38b3aa5d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002237.fa
@@ -0,0 +1,14 @@
+>PROKKA_00078
+MRLAAVNPIPGLFTIAPADRDHEVGLRVGVTVLVPLLVLLAAGRMDLAVYAVFGAFTGIY
+GRNLRHGPRLQAQLRGGGLMLAVLAAATLAGRLGVSEQADPWGLVLWTTVVAGVAGVVAT
+LLAAPAGVHHNYWAMVAAVVPLVGHSTRYRVSRGLQRVIGTFLGLVLTAGIILLDPPVIV
+LVLIIAVLQVAAELYIARQYVIAQTVVTPLALLSTMLVGVTAGGAGSLMAAGGLQHLADR
+GVETVIGAAVGIVCVLFPWAWRRWVWGSPDPARAIPVVRGPGS
+>PROKKA_00062
+MTTQAPGIPLTMGRIRARRPRRKDPRPVRLADVNPFPAMFTIGPPDRGHEVGLRVGVTIL
+VPLLLLLALDRMDLASYATFAAFTGIYGRNEPHGVRLRTQLRAGLLMLGVLTAATVAGRF
+GISEAHDPWGLVLWTTVIAGAATVATGWWNLRPAGSLFHIFAFAAAASVPVKPPVVEGML
+MAVAVVVWAIAVGLSSRVLPSHRTPLTWPPSDRPDRGRRRLILLEAMWYVIAAGVAGSVA
+TLVAAPQGVRHNYWAMVAAVVPLAGHSTRYRVNRGLQRVLGTVLGLGLTALIVLLDPPAV
+GIVLVIAVLQVLAEVYIARQYVIAQTVVTPLALLSTMLVAVTVGGAGSLAEAGAFRNLQD
+RAVETVIGAVVGIVCVLYPWAWRKWVRRSPDPTREIPIVRPEQIQRPVGGRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002242.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002242.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4fbed02b8603b1fffd7ccc96d770e7fa3e60acb5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002242.fa
@@ -0,0 +1,11 @@
+>PROKKA_00104
+MTTALPDALRLTDEARERLHADCRHLHRHPELSMQEHATAAWIEEQLDEIGVERFRCGGT
+GVVGVMRHPGGAEGPVVAFRADTDGLPIEEDTGLEYASTARGTLPDGREVPVMHGCGHDT
+HVVSALAAARLLAAAPDTWGGTIVWVFQPAEETGAGAAAMLEDGLWDRAPRPEVVLGQHV
+MPLAAGKVQLIPGMAMALADSQAITFHGRQAHGSQPQDSIDPILMAAHAVTRLQGVVSRE
+TDPRDPAVVTVGTFHAGLKENIIPDSAEIALNVRTFSAASRDTVLGAIERIVRAEAQASG
+APEPSFRTIARFPRCHNDDEQSARVAAALRAELGEDHVLDGRPLMGSEDVGALADAIDVP
+LVYWFFGGFEGEDPAAFPGNHSPHFGPAMAPALDAGHRAALAGLLAYVGR
+>PROKKA_00074
+MAAVAAELGEENVMEIGPLMGSEDVGALTDAIDVPLVSWFVGGFEGEDFGDNPANHTPQF
+GPVMEPTLTTGVHAALAGLLHYVGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002243.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002243.fa
new file mode 100644
index 0000000000000000000000000000000000000000..17dda771b7722dee888a7b74ae7e5dbc77b05aed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002243.fa
@@ -0,0 +1,11 @@
+>PROKKA_00115
+MTPTSALSSRAPGLAACLALGLAALGTATAVRPWAPALSPLLLAILAGLAWRNLAPVSER
+LAPGVAFAATSVLRAGIVLLGLQLLLSDVLALGPGVIALVVGVVGVTFAATLALGRVLRL
+PWDLTVLVASGFSICGAAAVAAADSVVRARREMVATAIGLVVLFGTLMIPVMPLLTGALG
+FEEQAAGLWIGAATHEVAQVVAAGGLVGGTALSVAVTAKLARVVMLAPVMTGLAWWQRHR
+DALEPATLDDGAPTAVERPPLVPWFVVGFLLAVLVRATGWLPAGVLDAAALVQQLLLATA
+MAALGLGVHLRSIAAVGPRPLVLGAASTAVVVVVGGFGATLLA
+>PROKKA_00083
+MPARLEPGIAVAAKPVLRAGIVLLGLQLLLSDVLALGWGAVGLVVGVVALTFAAALALGR
+ALRLPWDLTALVASGFSICGAAAVAAADGVVRARREMAATAIGLVVLFGTLMIPLLPALT
+GALGLGERAAGLWIGASTHEVAQVVAAGGPRPLVLGAGSTAVALAAGRAGAALLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002246.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002246.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c3b585197b56047b364dcc67fc629b0d0b1564b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002246.fa
@@ -0,0 +1,6 @@
+>PROKKA_00170
+MSTKQTRISPISGGRRPVSPLGPALLAAAAGVVLAGVRRMRARSRRREEVAARVAADRRA
+GR
+>PROKKA_00121
+MILARIPRRSARRAVPVVEATQPPVRDRSREVSPLGPALAVALGGVVAAAARGLRARTRR
+AEAADRARVARDADA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002248.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002248.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c95230f08bd54124405cb3f7e17cae0d3177d2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002248.fa
@@ -0,0 +1,10 @@
+>PROKKA_00249
+MRHFDDPVLQAMASRRSVSQVGPSTPTDKELAGLLAAVTPVADHKALRPWRLILLRGEDR
+RRLGEALDAAAGTERERGEVNPKPYRAELLIAVVASHRPHPGVPGWEQDATAAGAAHLLE
+LALWQAGWGVMWRSGLYTDAPAVRAAHGLGDRERLLGWLYVGDVDPAFRARLEASKKPAL
+DPAPFLGRMPQG
+>PROKKA_00183
+MVCMKHFDDPVLQAMASRRSVSKVGPTTPSDEELARLLVAVTPVADHKALRPWRLITLRG
+EDRAVLGAALDAAAGVERAEGERNEKPYRAELLIAVVARHVPHPGVPEWEQHATAAGAAH
+LLELALWQAGWGVMWRSGLHANAPQVRAAHGLADDELLMGWLYVGDVDPEHRVKLAASRK
+PALDPAPFLGTMPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002253.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002253.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0e9329eaf6baf3868eec76aea66f4b8c0d320b2f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002253.fa
@@ -0,0 +1,17 @@
+>PROKKA_00347
+MGDDNARMIRRFRSSSTRRPLHRSLTRRGTRPRRRLHTDDRVSLPPSSVAGLFVVPFLAT
+HLFAWGLFASVYLIAHPGGDSVFTASMWRLTTDVAVNAGLAMEDSLLALTSTGVAVTVAL
+YIPVAAGQLVSPRGGGETQRRLGSLALATSGVFAGITTGAYIASMTHGAHPASMIPELLL
+QGLMIALSLQLGTHLFDDREELRSRLEDDERRLEMQLSDAALNSLSDDIQGKFGGDFTLP
+PMRQWAKAARTLTFRRILRLLIWFFGYLLAGAFLGALTFACTSLTLEREWDARTLALGAL
+IGIYAHFASGMITYHDQSTPALRWLVRAMGATIWLLLLTTGLVLLSASPSQGSASLGTAV
+LGVIHVLWRRRSPGEQGLRLSPFMLSHRINTTLAEEALTSVWSRQLHAGILPRPLLGTTC
+RTSPLRDAAR
+>PROKKA_00285
+MVPFLATHLFAWGLFASVYLIAHPGGDSVFTASMWRFTTDVAVNAGLAMEDSLLALTSTG
+VTVTVALYIPVAAGQLVSPRGGGETQRRLGSLALATSGVFAGITTGAYIASMTHGAHPAS
+MIPELLLQGLMIALSLQLGTHLFDDREELRSRLEDDERRLEMQLSDAALNSLSDDIRGKL
+GGDFTLPPTRQWAKAARTLTLRRILRLLIWVFGYLLAGAFLGALTFACTSLTLEREWDAR
+TLALGALIGIYAHFASGMITYHDQSTPALRWLVRAMGATIWLLLLATGLVLLSASPSQGS
+ASLGTAVLGVIHVLWRRRSPGEQGLRLSPFMLSHRINTTLAEEALTSVWSRQLHAGILPR
+PLLGTTCRTSPLRDAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002255.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002255.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a067dca8e96f91634b375ddbc460c862c0157155
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002255.fa
@@ -0,0 +1,8 @@
+>PROKKA_00368
+MVRVTEVDPATSIDELSDRAELIVRGAPGEVDAPGDGRTRITVDASETLAGEGRSASSST
+CSASPTRAPPTARRARSCSGS
+>PROKKA_01750
+MVLIARSARPVVALATALALALTGCAAEAAGPVDGDSAAAPAPTSTGASPSAEEAFWARY
+QATMVSEVDPALSFDDLTEKSTVIVRGPVMAAAGVREVDGRVVVAPADGDQTSSLLTVRV
+EERITGEAGDTVRVWVAGPAPTAEPPTESYLWYLMPADTPDALFTVSRSGVIGPDAGGTL
+STVMVPGDGEFILPDGAVTLADVQRRTEELLER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002256.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002256.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0ab7986ce24a68c1cefe38b9b1543e134ca37b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002256.fa
@@ -0,0 +1,6 @@
+>PROKKA_00394
+MWVHHLDVSYRAVKSRPASARALRDTILIEELKRIHAENYGVYGVRKMHHAMRRAGWEIG
+RDQVARLMKLASVEGVRRGRKPIITRPAGEPDARPDLVERCFTAERPNQLWGLP
+>PROKKA_00663
+MSYRAAKTRPASTRALRDEILIKEIRRVHAENYCVYGVRKMHHAMRRAGWEIGRDQVRRP
+GGSGRIHCPRRSLRRACLFRFPQIAIEHHWPVRERE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002257.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002257.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08bc1cc5307fefa0f006b69a0b1f53346ab2de92
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002257.fa
@@ -0,0 +1,4 @@
+>PROKKA_00395
+MIAFIDEHRDQFGVEAICRTLRATECGFITST
+>PROKKA_00664
+MIAFIDEHRERFGVEAICRVLSATECGFITST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002268.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002268.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2cc8bea7360e246760199582404f556534f4000e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002268.fa
@@ -0,0 +1,7 @@
+>PROKKA_00521
+MVVIAGLAVRLAFDGAWTGPVGDALYAVLVFLGVAWAEAFPPARLVFGTTFTAADLGLYA
+VGVAAATAADALASRARHGSGLARGPAGS
+>PROKKA_00476
+MSAPAAPGPTTTTPRRRSRLALAAAATVAAGLLVRVGLRGVPGAAAWTGPLGDALYAVLV
+FLLLAWIAPRARTLPLAAAAFGVCAAIELFQLTGIPAALGRAFPPARLVLGTGFLWSDLL
+LYLAGVLAAAAVDAALRRRAALSPRGSGPRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002269.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002269.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dd744f7e4bd8791cc23760b7cb572c4dc6a13a5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002269.fa
@@ -0,0 +1,11 @@
+>PROKKA_00523
+MSLFETADDRVSVDVWSDVMCPFCLIGDRLLGQAADRAGHPVQVRYHSYQLQPDLPADRT
+RPVLDMLVDAKRMPREQVEEMDRQITARGAEVGVEFRQDIALAVNTRDAHRLSHVAAEQG
+LQHAMVQALFRAYFTQGRNVADHEVLADLAAEVGLDRQAALDALASDAHADTVDADVEAA
+RRLGIGGVPFFVVDGKYAISGAQPLEVFERALAAAWADKADGAPPAG
+>PROKKA_00072
+MKVTVYSDVACPWCYIGKRRFETALAGFEHAEQVEVEWRSYQLDPTLPERSDLTEVEYLT
+RMKGLAEPQVRRMLDHVVMQAAGEGLTYDMDAIVVANSFPAHRVIQRARAVSAEAASALE
+EALFAAHFERGQDIGDAAVLAELGAAAGLSAEQVEEALTDERWAEAVRADLAEARAVGVT
+GVPFFVLDGKYAVSGAQPPELFAQALAQTWAERAPLRAFTPAAAADDDDAPLIGQACGPD
+GCA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002270.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002270.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f08cb353bf09c338cadd55b22faac76f659f0bd3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002270.fa
@@ -0,0 +1,8 @@
+>PROKKA_00552
+MPHDSARWLDEEERRAFLALMSVTMRLEPALDAQLRRDADLTHFEYSVMANLSESEGDTR
+RMSELAWLSAGSLPRLSQVVTRLERRGLVKRTPDPTDGRYTLAVLTPEGRAVVEESAPGH
+VEEVRRVVLDPLTRAQVKQLAAIGKRIVGVLDPEDRCLED
+>PROKKA_00475
+MSDAARPASDPVADTAPESVVPWLDDEERHAFLALMSVVLRLEPTLDAQLRREAGISHFE
+YTVLASLSEAEGGQRRMSELAYLSSGSLPRLSQVVTRLEKRGWVERRPDPEDGRYTLAVL
+LDEGREVVVAAAPGHVAEVRRAVVDPLTRAQLRQLTAIGRRIMGVIDPEDRCLED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002272.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002272.fa
new file mode 100644
index 0000000000000000000000000000000000000000..631356b0e65d83c5e7138687869baf032f3cbb40
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002272.fa
@@ -0,0 +1,8 @@
+>PROKKA_00571
+MSQYLISVWHAPGVHAAGTAYESEDQMRLAFERVAAFNARLEESDSLVGAGGLTPPEEAV
+VVDASAAQGPEEVAAQRRIAEGTASPEGAQLGGFWIVEAPDEATARTLAGEASYACGQPV
+ELRRLQG
+>PROKKA_00498
+MSQYMITVWHAPGVHAAGTAYESEEDMQAAFARVDDFNRMLMGSGAFVAAGGLTPPGEAR
+VVDAVAASDAGQAAAQAEVREGTLAQGDMALGGYWIVEAADDAAARGLAAQGSYACGQPV
+EVRRLQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002273.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002273.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a929e3b961435099cfe78ba14d5f71322520d20c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002273.fa
@@ -0,0 +1,15 @@
+>PROKKA_00581
+MNKDAQPSTELLSSIPEGHVEFGLHTFGDVTLDAEGRRLSHPEVLRDVVAEGVLADQAGV
+DVIGIGEHHRPDYAVSNPEMVLAAIGARTERIKLISAVTVLSSDDPVRVYQAFATLDGVT
+GGRAEVSLGRGSFIESFPLFGHDLKDYERLYEEKLDLFMKLRTEEPVSWTGTVRAPLERQ
+SVFPTTAHEHGLPAWVAVGGSPQSVVRAASHGAGLELAIIGGAPRRFAPYADLFRREVAE
+RGLEPRRVAVHVHGFVADTDEEAMELYYPHWEAAFTKLARERGGPLPTPEQFRQEAVHGA
+QHIGSPETVARRVADTVRAIGASRFGLKYSNATLPHGPMMRSIELYGSRVIPLVRDMLSE
+G
+>PROKKA_00799
+MDVKFHIDTFGDRTSTLDGELESHAQGVRHVVELAETAEQAGVDGITIGEHHRDDYTVSA
+PDMVLATIAGRTERLTLGTGVTVLSSDDPVRVYERFATLDALSSGRAEAIVGRGSFTESF
+PLFGYELSDYEELFEEKLALFAELRAEQPNPVSWTGKLTQNLEDVVLYPPLEGAEPLKAW
+VAVGGSPQSVIRAAGHDLPLMLAIIGGPSARFAPFAKLYRDAREKFGHAGETQVGFHMIG
+HIAETDEAALEQFAPHYLEHHKRLGAERGWGSMGMEGLMHEVRHSLMGVGSPETVAKKIA
+RGIADLDATRVNFKVQHGPIPHEYNRRSVELFGEKVIPLVKDMLAAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002274.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002274.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1886e19cb3f7e2ef73431e732c1cca329eeda593
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002274.fa
@@ -0,0 +1,15 @@
+>PROKKA_00592
+MPTPSSATPDPASARSASGARPADALPDDGAPVRVRLGVLVARPADPAVLDTAALAAQLD
+AAYPGLTWDVTVRQEELGDEDDDALDLLEITRDRMLDEDWDIAVGVTGEPLQQGRHTLTE
+QVSPVHAAGVLSLAHLEEAPVDAVARVVGEVLGIDPDDDAPSAADRRAAAGWARQLADDV
+EHRDREAPAAYALRVAVRNARMLLGTVRANKPWTLAVSLTRSMSTALATGALTLITTDLW
+MLSAEYNGVQTAVLGAVSVLAVTLSLIVGAHLWERPRRRAEREQVMLFNMATVLTVLIGV
+VVLHVMLMLAALAGALLLVDPDVFHVVTGEPGEFVQYVKFAWFVGGLATIGSALGAGLED
+DDAVRAAIFTRGASR
+>PROKKA_00515
+MSPARPHSPSAAAYPGLAWDVVVSAEEVGDADDDSLDLLEITRDRMLDEDWDVAVGLTGH
+ALVQGPHTLRSQVSPVHAAGVVSLDLADGGAREAVEDVVARVLGLDPDDGAPSAGERTAA
+VARARQRAEDVEARADESGASFTWRVLRANARLLLGTVRGNRPWLLAVSLTRSMSTALAA
+GALTLLTTDLWMLSAAYDGVQMSLLGLLAVAAVSLSLVVGAKLWERPRRAAEREQVAVFN
+LATVLTVVIGVLVLHALLMLAALAGALLLVDGDVFTEVTGEPASPWQYAKLAWFVGGLAT
+IGAGLGAGLEDDDDVREAIFTRGATR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002275.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002275.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f4a00af216d6f201ce321bc291e89507cd8301c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002275.fa
@@ -0,0 +1,15 @@
+>PROKKA_00618
+MTEQRRHEVTLRFLAAPTDQGHTGTVDAGRVLEWVDKAAFAAATAWAGSYCVTAYVGNIH
+FRQPVLVGQMVEVTGTVLHTGRSSMHINTVVSAGDPKTGELTEAARCLVIFVAVEEGKPV
+PVPEFVPRTLEQELAAEYAVSRIAVRDEIQAAMEGQRYTDAGTADRTVLRFLAAPTDVNW
+GGKVHGGIVMEWIDTAAYLCSTRWAGRETVAVFSGGVRFYRPLHIGDLVEVEARLIYTGE
+KGMHVAVHVRSGDPKTAQLELTTYCLTVMVARDDDGDAVPVPAWEPVSQEDKALWQHARD
+LLEIRGRAPGNRLPNHLLAERGED
+>PROKKA_00543
+MTDDAARTPASTDAARPSPGPVPAPASPTEPATPVVERRREVTLRFLAAPTDLGHSGTVD
+AGRVLEWVDKAAFAAATAWAGRYCVTVYVGNIHFRQAVEVGQMVEVTASVLHTGSSSMHI
+STTVRSGDPKTGELTEAARCLVVFVAVGEDGRPVPVPEFVPRSLEQELARDWAISRIAVR
+NEISAAMKTQRHTDAGTAERVVLRFLAAPTDVNWGGKVHGGTVMEWIDTAAYLCSSRWAG
+RDTVAVFSGGIRFLKPLHIGDLVEVEARLIYTGNKGMHVAVDVRSGDPKTDDLQLTTNCL
+TVMVARDEHGDAVPVPAWKPVTDEDRALWAHARTLLEIRAKAPGNRLPDHLLRERGEGPD
+RGEH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002283.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002283.fa
new file mode 100644
index 0000000000000000000000000000000000000000..307db73d57175724b300820e1cdcd0c335783bea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002283.fa
@@ -0,0 +1,10 @@
+>PROKKA_00754
+MSSAKNSDQRRQDRAAVLQAHWAAEAKAARKQKVLWGAGGVTAVALVGALVTVAVVTDPP
+PPTRQDIEIAGLETFEDLDAMHVNSPVDYEQDPPVGGDHASTWLNCGVYTEKVPKENAVH
+SLEHGAVWAAYDPSALSEEEITALQEALPDTHAVVSPYEGLESPITLSAWGAQVAVETPD
+DERIEEFVAKYWQSPEAPEPGAACTGGLDGPGRVA
+>PROKKA_02190
+MSTKLMADPEAKAERRRKVLVGAGALTAIAVVGGLVTLAVIQNPPPQAREDIEIAGLQTF
+EGLSANHVSTPVDYEQSPPVGGDHASAWLNCGVYTEPVPNENAVHALEHGAAWVAYDSEA
+LSQEQVDALRTALPAAYVVLAPYEGLDSPIVLSAWQAQVAVDSPEDERIEQFVAEYWQSP
+DAPEPGAACTGGLDAPGRIA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002286.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002286.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a640383fbb69fbdecdda520782d6598235c29a37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002286.fa
@@ -0,0 +1,15 @@
+>PROKKA_00827
+MATPAGAVGKGPNHNPRSTVNTSILATHAELVAQLQKEDARQDAMELTVIGQSVKGRDIH
+LASWISDPENPTILFLTQQHGNEQLTTEGAMAFIKSLGTGKMRSVLDDVNVLVVPMANPD
+GAMGDVDFSLEDYIASGDRNLTRYNANEVDLNRDHVAKTQPETRALHENVLGAYDIDYMI
+DLHHQGTRSAVDGELVSGSILYPTSPNVAPDVVEDSQRLGSVVYDAVEQYGWGNLGRYVG
+GTAETIARNGVAAEYGIATLLFEMRGMSDHEYESYVLGQRSNGYLIKQTVVTLEATTKAI
+ADGSIETADIGLWNTLPEQRTLPLAAE
+>PROKKA_02006
+MSPLTSPSLSRRGALGVLASAVALPLVAAPPAQAAGSMPTPSDTPPLAAIRDLADMLREL
+RKLERTSRGAIRVTTLAEVGTAEAHSEQGRDLYVALVGHGPRHVWLQGRIHGNEPYGLEA
+TLDVLASLGGNGSPAYRRMREEFTVHVIPMYNPDGSEANTRGTTLWDREADAPLLVGRGR
+PRTVDLNRDWGVGRFQARESRAWYEYWTMVKPEFALDIHHQWLKQDWVTGEDVTLSLGVS
+LAPGGPTLPGIRGGEYDRLARQLAGHVWLETLHRGHISTDRYDVGENTVIDIHGGVVSAM
+MMGLDWNGLNPTGHSNVAIFFETSGNTNSLGHKARGKLVQQNVLAVTAALDGMATGAVQR
+VDPAVWDRIPHTPVKYYSTDYAGLIPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002288.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002288.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d354f89c6b27bfe7c7cc6f9e3a6e7e2ca53ed21
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002288.fa
@@ -0,0 +1,11 @@
+>PROKKA_00861
+MNDILTVGLVGVGRLGSAVGQLVAEAGHRLLVADRPGSRVFRSVVETLLPGADAVPLADV
+VERADVVILALPQPALADLDLARARGVLLDATNAWEYTDGPDSIHRMDPLAWTERVPGVP
+VVKSLNHAGYGELLMDARPAGAPGRRAFAVAGDDGAAVDLVASLVDSMGFDAVPTSAADA
+PLLEPDGAVFGRRFDEAGLREALPHAAARVG
+>PROKKA_00800
+MNDTMTVGLIGLGKLGSAIGRLTAEAGHRILVADRPDDPVFGLVLESVLPEARAVPLAEL
+LQEADVVVLAVPQPALAGLDLTAARGIVVDATNAWEYTDGPDSEHRMDADVWAARAPGVR
+VVKSLNHAAYAELLADAREHGAAGRRALAVVGSDDDAVARASAYVDSLGFDPVPGPSAAA
+PLLEPDGPDSEHRMDADVWAARAPGVRVVKSLNHAAYAELLADAREHGAAGRRALAVVGS
+DDDAVARASAYVDSLGFDPVPGPSAAAPLLEPDGPVFGVRLDADGMRAALAEGLEADSAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002290.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002290.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f6b337c510125bafcadf0ee36710ca0fd9d97808
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002290.fa
@@ -0,0 +1,6 @@
+>PROKKA_00897
+MTSTPTRAKRKQTARELAERFGVSPRTIRRTVAQERADYLADAAARHERIRALRAEGLSM
+RAIAAKEGVTVGTVHYAIHKDD
+>PROKKA_01315
+MTSTPTRAKRSQTARELAERFGVSPRTIQRTVAQSREDYLNEAAQRRARIRALRAEGLSM
+RAIAEREGVTVGTVHYALHKEDQQP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002293.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002293.fa
new file mode 100644
index 0000000000000000000000000000000000000000..573756721d1950ed25f637bfe73d66b3daaa9aba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002293.fa
@@ -0,0 +1,10 @@
+>PROKKA_00910
+MPSRRPPERPVVGPAAPDVAPSRPVPGSCQRALVRRSPLILAAVVLLVSAAVLAARGETE
+AAGLSVQIAMVVPVPIALERAHRVRLPTALHAMYAALLLVAPWVGAALGGYDAWPWWDAL
+VHFYSGVPIALGCVFLLGVAAARRGLVLPPGLEALLVMALHSLVALAWEIAEFTADQALG
+AQTQKGNTDTMTDMIVGTLGALIVAFALYAHRTRGRFAWLSRFTGA
+>PROKKA_01867
+MTPHLDTHPDARPDPGSRQRALVRRSPLILAAVVLLAGAAVLAAQGHREAAGLSLQIVTV
+VPVPIALERAHRVRLPTALHAMYAALLLVAPWVGAALGGYDAWPWWDALVHFYSGVPIAL
+GCVFLLGVAAARRGLVLPPGLEALLVMALHSLVALAWEIAEFTADQALGAQTQKGNTDTM
+TDMIVGTLGALIVAFALYAHRTRGRFAWLSRFTGARTDLAGGPAQPPPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002295.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002295.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df73c2a3894f4576dfcf2e15fd1ff003b0d331c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002295.fa
@@ -0,0 +1,8 @@
+>PROKKA_00944
+MSEPERTRPETTPDGHHIVVDGRKWRAQDPHIPEALAGELVKGLMAARRLVRTDPTTARP
+RVQDAKVALGERGDPWWEPTPEGTRERLAAAMRTLLRQRDEGKTICPSDAARVAGGEAWR
+DLMDEARAVAAELHAAGAVEVRQRGERVDSAAARGPIRLAAGPQLG
+>PROKKA_01225
+MTGEPITPSDPEHSGPERTGPEHTPDGHFIIVDGRRWRATDPDIPEALRAELVKELMAAR
+RLVKSRGDAARVRVQDAKVALGERGDPWWEPTEQGRRDRLAAAMRTLLRQRGEDRTICPS
+DAARVVGGEDWRDLMPVAREVAGTLAEEGVVVVTRKGAAVDVATARGPVRIAAGPALET
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002296.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002296.fa
new file mode 100644
index 0000000000000000000000000000000000000000..791039e1da47051d22422efda5ef6aa281dd859d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002296.fa
@@ -0,0 +1,10 @@
+>PROKKA_00947
+MTPADHRPEPDTAPEPEAFPALEDPYRRSLLTNEQRNAWAALSAASLGLVSQMESDLHRD
+AGLTPFEFHLLYVLGAEEVSREAEGTMPMSRAAQLVDSSLSRLSHVVRRIEERGWVERRP
+SAEDARVTLVGLTPEGRRRMEAAVPVYDRMVCRVFVDHVAEEDLAEVTRLSMRLLAGLRE
+GHWLLDAMDPHGSRRAGVAGADAGADAGAVTGATGESEEDSEGRPAS
+>PROKKA_00887
+MTKDAHHEKDANAHPPLPPLPPVWLKDAGCSGADLAAWIALLQAASALQARVESDMHRGA
+GVTPFEAHFLAVLKEAGGEPLAMSRAAHLVDSSLSRLSHVVRRLEARGWVERLPSPEDAR
+VTLVRLMDEGRRRIDAAAGPHRALMEDVFVTALDAADRQEAARLSLKLLGVLRPGHWLFT
+EPTGPDEGADPDAASHVGEPLTSS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002299.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002299.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cd4859fe7faa1d943cd98379688c66f39b13c416
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002299.fa
@@ -0,0 +1,10 @@
+>PROKKA_01005
+MDPVSTPTDPHRHPAPDARVRVQAGDAVVADGPLWARAALFAVPAVWLGLLIGISLIEAP
+LKFTAPGITIPLGLGIGRRVFFAMNLVEVVLAVVLLVALARVLGRPRGLTVPGPGRLWLG
+GLTAAGLLAVKAVAIRPFLNRRTDRVLAGVDDGGSSWHYLYIAVDGLLILTVVALIVAVA
+RHLLVRTTAA
+>PROKKA_00949
+MSVPPHPTPAPDAPRPLPGAAPREAGNAVVVGGPRGARALLLAVPGVWLGLLVGISLIEA
+PLKFTAPGITIPLGLGIGRRVFFAMNLVEAVLAVVLLVALAKSLGRPRELTAPGPGRLWL
+GGLTAAGLLAVKAVFIRPFLNRRTDMVLAGVDDGGSLWHYAYVAVDGLLILTVIALIVLA
+ARHLLPASPGAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002301.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002301.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc5cf3c3119a85623aa8a590f17fcd61f84c29c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002301.fa
@@ -0,0 +1,12 @@
+>PROKKA_01012
+MKIPAAITGGVAAVLVLGLTSCGASEVRPDHGVTARLDRENGQVVLPIEDYAASQADEAV
+MTQARLAILRSCLQKSGHNGVKPPTSNAERAVEERPYGVWIVDRARAYGFDLPPAAETVE
+PAAPPGGWSDEADPAFNEAYEACSSEVMEQMLAVSSPATSPGTTSVIADVTARARGLAAQ
+DPVWDEARDEWQQCLRDNGLTPVAEEGAVLSAESENLSDTRDAQGQTHSVKAEEIRLATI
+EATCNEQTRLTQRLGDLEAGYQAALIKKHEAALVEEKLVTAEHLEAARAYLARHQ
+>PROKKA_00955
+MRPDPRPFRLAVIAGIALSASACAQSGAPDVPPDTSATAHLDREHGQVVLPVDEYSLDHD
+SEQLIGQARHVIMRTCLNSKGVNGLAPTATSSPAEERPYGLWRTASAAQNGYTMPRPAST
+EAPPLGGQWSEESDPAFNTAYDACNEIVRDDLDSVTPPETERTTAIDIRDDAFTLASATP
+EWKEARKQWHDCLTSRGLTPRTDDNAWSSEQGFGILTTADPQNPSPAAKQEEIRIAVIEA
+TCNEQTQLTQRLGDLEAGYQAALFKGKEAQLAQEKADNQKFVDAARAYLASHQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002304.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002304.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37e4bb48bfb84407fd34c081b9f37abee9ea6383
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002304.fa
@@ -0,0 +1,6 @@
+>PROKKA_01138
+MTARRGPLTPFFDSVRTTGFRRTRPRLVGGVAAGIASGTGVNVWLVRLALVLAGLLPVLG
+VGAYLAVWALTPWEDGTVPAERALGGR
+>PROKKA_01067
+MTPVSRPRPGGARRTPLTPVFDGIRALGFRRTRPRLVGGIAAGLAANTGVDVWLMRLVLV
+LVGLLPVLGLGAYLVVWALTPWEDGVIPAERALSGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002309.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002309.fa
new file mode 100644
index 0000000000000000000000000000000000000000..690c68a7045a21641a6a81d0a89cba8c75357135
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002309.fa
@@ -0,0 +1,11 @@
+>PROKKA_01296
+MSADIDAYQDQLVAWRRHLHQHPEASFEEHETVRYIRAELEPRLPGATFENLTPTSLVVT
+LDTGRPGPTLGLRADIDGLAMTEDRPDLDFASTTPGRMHGCGHDGHTATIMSALVWAHDH
+RDELTGTVLGIFQHAEETPPGGAKEMVETGRFADVDYFFGFHYWSTLPTGTVDIKPGPAS
+ANSDRFEVHLRGEGAHASTPEDAVDVVTAASSLVQQLLLIPSRRVAGLDPCVVSTTWMDA
+GRQSALNVYPPEAHIGGVVRTHDDDVRDTVEAAMRDMVRGLETANPGLSCELDYLRGYDM
+VWNDPARTAVVHELCEDLFPGSVITDPPMLGGEDFAAFSRTAPATYVFVGAGNAAKGFDA
+GHHNPRFGLDEDAFPIALRLVVEVLRNGPRLAAG
+>PROKKA_01205
+MVQELCEDLFPGSVITDPPMLGGEDFAAFSRTAPATYVFVGAGNAAKGFDAGHHNPRFGL
+DEDAFPIALRLAVEVLRNGPRLTAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002311.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002311.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45fe7a387d687091d267f59e26a0ca845b3b45bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002311.fa
@@ -0,0 +1,8 @@
+>PROKKA_01319
+MDNVGIAVRDLEEAVAFFEDLGLTVLGRDEVSGEFAETAVGLEGNHAKIALLATPDGHGK
+VELMQYLNPEPVEAEPTRPNEIGMHRIAFAVDDLDAALAAAVRHGCRPLRGVARYEDAFL
+LTYVRGPSGILVMLAQELKAGE
+>PROKKA_01227
+MGIRFENVGIAVEDLEEAVDFFQGLGLVVVGRDEVQGEWADTAVGLDGNHARIALLTAPD
+GGPGVELFEYLHPEALPTPDTLPHMIGMHRVAFRVDDLDAALAACDRRGYAPLRGVADYE
+GVFRLTYVRGPSGIVVMLAQATGEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002312.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002312.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac556ba6849cae4370c4fd6af2182f5f45875964
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002312.fa
@@ -0,0 +1,37 @@
+>PROKKA_01502
+MKNSTASGSGFQFDASQPYQLDAIASVVDLFDGQPKDAEKLVTTLRSAAVLPESDQAALD
+IDLTQEVGAVGNSLVLDRDLILANLQRVQDRNGLEVAPALAGDALDFDIEMETGTGKTYV
+YLRTIFDLAVRYNFTKFVILVPSVAIREGVSTSIRLMREHFENLYKPQGVTFDASIYSGK
+SAEEVQSFATSTNVQILIMTIDSIRGNANTRIIHQTRDKLNGLRPIDYLKATHPVVIMDE
+PQNMESQLSQSAVGELDPVFTLRYSATHKKQRNVVYRLDPVDAHDLGLVKQIVVAEVAQQ
+GADATPYIKLVEVRREPSWSARLELSCRKADGSLERRIVSVKQHQELSDARLTNNPIYEG
+WRINEMSIEPAYVDLTLHGFLYEGESIGASAGAIYREMIRETVREHLRKESMLRAKGIKV
+LSLFFVDKVASYLGDGTNNDDANGDFVQWFDEVFVEERAKNARYQELLPQAPSKLRRAYF
+AQIKGKKGAPNAFVDSDERRQGAREDDAYELIMQQKERLLDENEPVRFIFSHSALREGWD
+NPNVFQICTLREMGAETERRQTLGRGLRLPVAKTEDGYTRVADRGVATLTVVANESYTKF
+ADALQREYKEAGVEIGRVRRAEFSKIPLQDENGALTDDQFGYQRSVLVWEHLKDKGFIDK
+DGAVTSKFQPNQLGFDLGLPVDFAWAESIIIELVERANIGKYVKPVSKRQPRMLNKQLYS
+NPEFEEFWETISQKTTYRVRVGRDQLIENAVRAIREAPQIDALRIQVTRAGVKVLRGGAK
+GEELGTRSADLKGSYDLPDIITELQEVTSLTRKTIVDILIGSGRLGEFIGNPNDFIAMTK
+RALQSELAKIVVDGIQYERIAGSVYELRELQRDGAEEKERFLDQMYKVQHTQKTDFDYVV
+FDSDVERQFAELLDSREDIKLFMKLPAKFKIDTPVGPYNPDWAIIKQEDGEDRIYMIRET
+KSTLDDSKLRPTELAKIKSAKRHFEAIGIDDYARAVPGKWNL
+>PROKKA_00290
+MKLQFSTKQYQTDAVASVVDVFSGQPRDPGPQYQIDPGRRASTGEDAAVALTGYRNAEIA
+LSLSALLEGIQRVQRAQNLPVSTRLATSAAAPGRPNLDVEMETGTGKTYVYIKTMMEMHR
+RYGWTKFIVVVPSVAIREGVKKTFDITAQHFQQEYGTRPQTFVYDSSRLHEIEAFSSNGG
+VQVMIINIQAFNSSSKDNRRIYDVLDDFQSRRPIDVISANRPIVIIDEPQKIGAAKSLSS
+LANFNALMVLRYSATHEVDHDKVHRLDALDAFNQKLVKRIEVRGLTVRGLSGTTAYLHVS
+DIEVRQGKNPRARVETEMQSAAGTIRRKLAWVTKGTSLHDLSGGLEAYQGLTVVDVDARR
+NVVELSNGDLIESGQLADHDVTEDTKRRIQIREVISAHFHREREMFRRGIKVLSLFFIDE
+VAKYRDYDREDTLGDYARMFEEEYVEARDAVLGELETEDDAAYRDYLRRDEVSAVHEGYF
+SVDNKSRRMVDGKVAGRGDEKGQSTDTDAYDLILRDKERLLSLKEPVRFVFSHSALREGW
+DNPNVFTMGMLKRSDNEVSRRQEIGRGLRLAVDQHGVRMDDPATVHEINRLTVVTDESYT
+DFVTGLQTEIAKSLKGRPRKASVAYLTGKTLTTHEGEILTLNKEMAELLHRHLIRNGYVD
+DDDLLTQQYLNEREAGTLAMPSNEKLLGVVDFCWPLLDALHTGVDIVEPSRAMKRLPVNR
+HNLERQEFQRLWERINRKAVYRVQFDSEELVQKAVTALDEKLRVTGLTYTVETGVQGEDL
+EAEHFRSGQGFTSSAITTQKESATSGSRVRYDLLGEIAERTTLTRRTVSAILRGIRPDTF
+AAFPKNPEQFLTEAGKLINEQKAAMVIEHLAYSPLEDTYDISVFSENQTSQDFTLASEKL
+EKHVYDYVVTDSDVEKRFVTQLDASTEVAVYAKLPGGFTIPTPVGDYNPDWAIAFDEEDT
+HVRHVYFVAETKGTSSSFELRGMEDAKIRCARKFFDALNRKNAGDVRYDVVTDYNGLMDL
+VKGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002316.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002316.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1aef49daf215cb974f28707ce60097cb3265be9b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002316.fa
@@ -0,0 +1,11 @@
+>PROKKA_01924
+MTDLAAEHPRTDAVDSVSTRTHDEPFAVVGPWKDDPAAAGTAEKVKVTDEMLELVEAVRP
+TLLADGMFLVGLDIVGDKLMEVNVFSPGGLGSCQSLYGVDFAPAIIEDLERKVSVRKHYK
+GQIGNANLATI
+>PROKKA_01875
+MKIGFVVNDVATEKPVYTTTRLAMAALQAGHEAYLVGAGDVAYEPDGSLSVLAHGTQKKH
+RSLERLLEEVQDPANAAQMPVDELDVVMLRNDPADDATERPWAPTAAVSFGQLIAAAGVL
+VVNDPHTLANALSKAYFQHFPELVRPTTLISRDEALISEFIDERGGKAVLKPLQGSGGSG
+VFLVDRKESPNLSQIVEAIARDGYVVAQEYLPEAKNGDVRMFVMNGRPLEVDGRIAAFRR
+RSSSDDVRSNMSAGGTAEKVDVTDEMLALVEAVRPKLLADGMFLVGLDIVGDKLMEVNVF
+SPGGLGSCQSLYGVDFAPAIIQDLERKVATKDHYLGRIDNTRLAAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002321.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002321.fa
new file mode 100644
index 0000000000000000000000000000000000000000..255cd55745a01f70762bb01959a6d0f6999d23b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002321.fa
@@ -0,0 +1,8 @@
+>PROKKA_02345
+MRILGGFCYVAFITDVFTRRIVGWAVSASLHTQGLPLLALEHALLSTGASRGREGLVHHS
+DRGAQYVSLAYSDALIAAGVSASVGTVGDSYDNALAETVNGLYKAELIHSKRVWESVEEV
+ELATMGWVHWWNTARLHEALGYCTPAEVEATYTHDQDSAPVAS
+>PROKKA_00308
+MYSRRIVGWAVSGSLHTAGLPLLALEHALVSTGASRGRQGLVHHSDRGSQYVSLAYSDAL
+ITAGVTASVGTVGDSYDNALAESVNGLYKAELIHSKRIWESVQAVELATMGWVHWWNTQR
+LHEALGYRPPAEVEAAYTHDQDPAPVAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002322.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002322.fa
new file mode 100644
index 0000000000000000000000000000000000000000..476c68803d93d604b07dccd4533840fbc6d99ff7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002322.fa
@@ -0,0 +1,8 @@
+>PROKKA_02361
+MDENPSTAWTGTCGFRMLPTDDFAQGPSTARLTEVAGGAALALDYTWVHPEQGEQAGHLV
+LGRPDDGGRVTVAFTDSFHQSPEVRVLEGTAARTEGGGDAGRDRGAGAAPHPIDGDGVAV
+TMEYSGWGWTVAVRRQGGRLAMMMQNVVPAGVEGAEPGPYDVMRAAWTPAGA
+>PROKKA_02252
+MSLPSATDWTGTCGFRLYPTDEFSSGPSAARLTPVAGGAALALDYTWVHPDQGEQAGHLV
+IGRPDDAGRVTAALTDSFHQAPEIRVLEGASSSPEGDAHPVEGEGVAVSMEYSGWGWTVA
+VRLQGGTLAMVMQNVIPEGVEGAEPGAYDVMRAAWTRTDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002323.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002323.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e81bf7e4b91c51e18e59d2ae919d4f47a9501685
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002323.fa
@@ -0,0 +1,7 @@
+>PROKKA_02554
+MFGGGMMRDLMVGSGWLGLLACMVLGGIARLPLAAAGTRRAEGRPWAVQGVLGFGLLGLA
+LLAALPADPSPAWYPREDGDERRG
+>PROKKA_02424
+MFGGDSMMQDLMVGSGWLGLLGCMILGVLASVVLGTAGRRRVQGRPWAVPGVVGGLLLAA
+AVASALSSFGTFFGFMGIAFAVFMGIGAWNAFTTPARAAERLREQEAHAERLGAAYARGA
+ATGPPAPHSPDAAEPGQAPAHDPDWYPATPGGGPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002327.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002327.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c49171e19f540f82560faf5ea0728e2900f35ddf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002327.fa
@@ -0,0 +1,5 @@
+>PROKKA_02670
+MCRAVTCKTCGKTTWAGCGQHIAEVKRTVPAGQWCPGHDKEKEKAAATSGFFARLFGR
+>PROKKA_00542
+MCRPATCDVCGKTTWAGCGQHVDSVKASVPAGQWCDGRHTPAEQAAARKDAPARGGLLAT
+LFGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002338.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002338.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30284734c224402b0d096cc18c54b4777fda49b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002338.fa
@@ -0,0 +1,6 @@
+>PROKKA_00332
+MGAIDQSTDNDADYDVIEQTWLDAGQTVKELVDRARTLMEENDDIAAGAHQKAGNHMGLV
+HV
+>PROKKA_00337
+MTIQYDSAAAAAYEDEVLRIASRIETILGDREQQKRFVADNYQSTDNDADYDVIEQTWLE
+AGQTVKELVDRARTLMEENDEIAAGAHQKAGNHIAGMRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002343.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002343.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec8fb6fdbf4fbf411917c6de5dcf0bccadfa523c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002343.fa
@@ -0,0 +1,13 @@
+>PROKKA_00633
+MSTLLPIRPRPAPEEALDSYLERVATANGVTTSGFVRQLTTEARAPLRFTNIAPPPPILD
+VLASWTGTDRGLLQDCLLTRYPVIPFIDSQNRHGTRSVVAHGWVLLNRSQACPWCLAETG
+VWKITWRLAWVTACLDHDRLLATDCPGCQKPLRTTHHGALRPAGPGARCGNPRPQGQGKR
+CPFDLSRISPLSAPPPVLQQQRRVERALRGAEVEVAAIALEGTTYLRQLQALTSAAMGLS
+APTTAVQPEYSEGVPAEISTLSGRARPAPRPADIRAAAYVRRDRTIFAPP
+>PROKKA_02215
+MITPLPVRVTPGPNEAMDSYIERVAAANVLAITPFTHHLKRLSGSTLRFLNAAPSPELVA
+TLARLTDTPESALHELTLSRYEVVPEIHNHHRYAARAASAKGWFSLIRTQACPACVGEGQ
+PWASYWRLPWVTACLKHGCLLITRCPGCRVKLRSTRLQGLRAGGFTPLCGNPRATGRVPQ
+CEDDLGTTALTLAGQPVLVQQQVVLAALRGSTVFCHGEPVTGTEYLRRVRSIAVLLFHTV
+AISTATGLPAWAQKLRAEAQARTKERGPRWGVSAPDCPQSRAAVFLIAHQILTGPVGAGR
+GSLDVWLDLVPPSNEGTRAWAEDHTTTPDAISYLIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002344.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002344.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f3201e5db8f504ad0d4dac39b55cd4ad091728f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002344.fa
@@ -0,0 +1,20 @@
+>PROKKA_00634
+MTDQEHPPSALAPIVGESLSGYVRRFNATGLTPPLALPPRYADADLPPGLTDAVHRSTGL
+DAGQIRRMTMAGWPLILRGRGLHHRRGWALHRHDVWLCPSCTPLTGYRALRWRLALAPVC
+LRCHTLLTHERTFTPTRAATTEELARLRRLDELTTRALQGSKASRSHLSVLRRICAAGDA
+HEPDGDVLPRPPLGGTSRPAGNQRGTHPPGEPGIVMKQLATLDPALLNESRARAHLQQLQ
+HQDSLPSSFVVAPAPFQPESPTALALARARRRALLRQLTDLCAATGLRPQHIPTVVDPWR
+STRWSRLRDLEDQAFEALALHTLLLEALGEDATGSAVFVAHGIPAVVNQHDLLTRVRTRG
+TLTPGECDRLLARAQALVDDGLVDYAYRRGTLLAVPSLPRIPAVHLPRHPFWPARTLVPA
+WAWVEYARGLPDSGPAPDLSLESVDRFHADLDPEARLRLLEAFDTHVRGEDWAAIASAAG
+SSFPTFASAHQRSA
+>PROKKA_02216
+MSRPVHMPPLPGESLTGYLQRYRQSGMAPIRLDVTGVFDNASAPASVVVPVHTATGLAPE
+QIKAMTMDRWVPSIRGYRVQRRHGWKLHPHQWWICPQCTVKTGYQSLRWRLALQPVCLRC
+HTYLVDPENPQIPRPVPEATLKIVQSYDRILDDALSGSLSARQRLSGLRKTCKGMAQAMA
+HDQQPASAGAQPSTLTWWGAYPCGDPVTVGHLMTLTRAMVTRGPARRRTVPRRDRPLQSK
+RAVSGATVTAMSRARLRATVSKLAEWSQSTGLSPRHVPTIAQPSLYGTARRPSMVAQAGT
+TLALHMLLDEATGIPVSSARTRAAHGLSGEPLEHRLLHSVITRGGLEEDQQRLLLRTAED
+LITDGLIDFRLRRTVFRSQPHLPRLPTPAHWIPAGEEFSAETMTRAWIWMHVARGHPQHG
+PVASVRLDEIDDFDHLLDPETRMHLHESAAAQIDGPDLADILTTTTTHNRRARQQDLREH
+AG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002345.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002345.fa
new file mode 100644
index 0000000000000000000000000000000000000000..94ef26c11baa6ae380a9d8b1405b87cc5bd6d4f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002345.fa
@@ -0,0 +1,28 @@
+>PROKKA_00636
+MNFSVDLNIGDRVLTDAGPARVKSMWALGVELETINEPAKLVPWTDLIIRPTIDGQAQAV
+DAALHPWWDQLPEKVQQDAIFKMECVLEILTGFRSGLASLAQPHEPVVPFGPFSQASVSA
+QCEAMARLVSFEKSADRELMRRVQDGELDSPGVTPRAVHHWVRRWQASGLRGLVDGRALR
+SAQGFGALDPRFLKIAEQEFARFDGSASATNRQEIHRRIQVRMHAEGITDAHLPQRLVSD
+YLSHRFAQLGKTTRAHRSRRHRKISSTASAALHHLGHCATDVTRADNLVYDEFTGKPMSV
+EIATIMSVPARVIVAVRVFPKSVSATEVALLLYDAMRPQSMLIDQDGASDWRWCGVPTSL
+QLPEQASPLANDPASGLGEHAIPAMTPTHLRMDNGSIFRSEQLRRLALHWSITLSHSRGT
+RPTDNPHIERFHETLQRFYQQLPGYKGRNVSERGSWTGVVAEAPLLTAADLERRLRQFIA
+LDYHRRPHTGLTLPGAPEVNISPLEMFDWILATTGRIHVPQHPDLIYQFLPTRWLTPGHA
+GVEYKNMTYDAAVLDEFRSKIPGRFRDEDAKVPFHYDPRDATRLWFRHPDTDRIHEIPWR
+NRHLLHAPLTDVVRDEARRRIRARGGPKALTGALIDRQLIEEIGHLAHTRADETWTTTMA
+ASRMRFDQARRDHDEAALAHRLTTPEAPTDLEHGGRHLRLVPPDAMPDRTATNGLAGLFE
+PWPDYAQEI
+>PROKKA_02218
+MRAQMSAPIQAGDSILTEHGPVEVIAPQSTGLLVRAPGGQETLITHAQVIPRRFQNGTIA
+GVMASLYPLWDQLDQAVRDDALFKLECVNEVNTGYRRGVASLALEGEPFYPFGPGWGVSL
+RARYQAMARLVSLEKRVDRVLMRRVYDGEVQRPEIGLRTLQSWGESFEEHGLRGLIDGRA
+LRKVQDFGVIDVRYRQAADEVFGQFDGEISAVNQQEIQRRIYALLRQRGQSDVQVPDRLE
+SDFLRHYYRRLGKGTRAHRSRSLRKIATTSSAALHHPGYCASDVTRADNLVTDEYTGKPI
+SVEICTIISVPTRVVVALRVFPRSVTSFELGLVLYDAMRPFSMVAADGAIDDWRWCGVPT
+GLQMSAPQCPRHVKEDEGPLGVHYIPAVTPVEMHTDHGSTYISDQFRTLLQQFGITLSLT
+RGGRPTDNPHIERFHETLQRAYQQLPGYKGRNVSERGSVVGVQADEPLLTARQLEAYLRA
+FVAVDYHRRPHTGLIWPGTEEQALTPLEMFDAMLASTGRLHYPQHPDLIYQFLPIRWLTI
+RHAGVEYKNMAYDAEVLDEFRDCRAGAFRDKDAAAPFHYDPRDTTRLWFRHPETDRIHEI
+PWRGRHLLYAPMVEIVRDQALAQIRRRAGRRHSAKVSMLELIDEIGQLATAPRDETWAHK
+LSAARMRWDQGQRDHDEVAHARALQQAHVPKPRTSRAGRDHLLSLPGGRTEDTPPAGFGL
+ADLSEPWPDYPEEHDELA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002354.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002354.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a35273ceacc8a5d81ef7f25fc22d66e2549f989e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002354.fa
@@ -0,0 +1,9 @@
+>PROKKA_00736
+MTKSLISSAVVVLLILLVTVLTDASTWLVGLLSGLACLAGAWCAPLFQSGSPYGGTFFGG
+WQSRWDGPKAVQLLAAGAAVAVSVVLNLFGGGVPAVVGIIVALLVGALIPVPGDPAGGGH
+GADPEDARPA
+>PROKKA_00738
+MRMTPARVASAAVLAVLTLVCLLLMLDTWSFMGALLVSLIGAVLFVAGAWFAPLARSGDA
+LGGTPLRPWQAGFDGPKTTQVAGGGLVALLVALVTGGAPLVGPILGVVAAVIGGRFLRIP
+SHAQVVAAVGPEVAEASEHLPGEHHDAAPADSVADPDTDPVPVPATEAADSEKPRHEHAA
+DVSPETAPVPVIHPADAEHPHGSHAAMAHPDPVDDVPGDGEPTTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002360.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002360.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3688fc5261dd84927b7bcbd080aa10ad88ac41cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002360.fa
@@ -0,0 +1,16 @@
+>PROKKA_01197
+MTEPVTYTPDIEHSVDREEDLTREILAQMGAAQRRTAGEHKHAHRDAHAKSHAVLKATLE
+VHEGLAPELAQGIFARPGTYEAVARLSSAPGDIHTDRTPAPRGWALKVLGVEGKRLLPDL
+DSHNQDFLMVNFPTLAFGTVARYQEMLGLLEKNSQSPELLQRLTTGAARVVRGAVETVGG
+TPSATLEGLGRDNAHVLGETYFTQGALRYGDHVAKISLAPASANVRALTGQDMKVKDFSS
+ISEIVADFFSRESAEYVLRAQLATDAERMPVEDASVLWDEEEAPHQPVATLRIEAQESYS
+HPRRVYGDDALTFNPWNGVVEHQPLGSIMRVRKRAYEQSTRFRHEFNDRPAPEPTSLDEI
+PD
+>PROKKA_01532
+MTEPVKYTPDIEHSVDREEDLTREILAQMGAAQRRAAGEHKHAHRDAHAKSHAVLKATLE
+VHEGLAPELAQGIFARPGTYEAVARLSSAPGDIHTDRTPAPRGWALKVLGVEGKRLLPDL
+DSHNQDFLMVNFPTLAFGTVARYKEMLSLLEKNSQSPELLQRLTTGAARVVRGAVETVGG
+TPSATLEGLGRDNAHVLGETYFTQGALRYGDHVAKISLAPASENVRALTGQDMKVEDFSS
+ISEIVADFFSRESAEYVLRAQLATDPERMPVEDASVLWDEEEAPHQPVATLRIEAQESYS
+HPRRVYGDDALTFNPWNGVVEHQPLGSIMRVRKRAYEQSTRFRHEFNDRPAPEPSSLDDI
+PD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002361.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002361.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e00cc681ffb743960be91c56e4c7ab2806dbee2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002361.fa
@@ -0,0 +1,12 @@
+>PROKKA_01785
+MRIAVTTPMGHVGRHVTSMLIRSGVRPLLLARRPENVTPGLRKHADIVKANSTDPAQVTA
+ATQGVDAIYWVDPSVMSSDPLADYTLATEALVKAVTANGIGRVVFQSSIGAEKRHGVGEI
+DGLAGTEVALDTLDVDVTHLRCGYFFTNLLLDIDAVRQGQLTTVLPLDQPMSWVAPRDIA
+EVASLTLLNTQWHGHRVQAVHGPQDLSWRQVAETLTAHVGHQVHAEQITDTEMLQRYLAA
+GMAPMMADAILGMSTGLRDGFRPEQPRTLATTTPTTLTSWIHEELIPVL
+>PROKKA_01821
+MRIAVTTPTGNVGTHLTGMMIRAGVRPLLLARTPSKIPIDLLTHVDVVEADSTDPEQVVK
+ATRGVDAIYWVDPSTASADPLADYARATQAIVAAVEANTIARVVFQSSVGAEKRHGVGEI
+DGLAATEVALDRLDADVTHLRCGYFFTNLLLSMEDVRQGRLRTVLPLDHQFSWVSPRDIA
+EVAALTLLNPSWHGHRVQAVHGPQDLSWNDVAALLTDLTGRHVQAEQISDDLMRQQYLTA
+GMPPAMADAVLGMSTGLRDDFHPEQLRTATSTTPTSLAGWMQEELIPAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002366.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002366.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab0eb09e64ea755ead454a874e4bb71dc75e2b9e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002366.fa
@@ -0,0 +1,12 @@
+>PROKKA_01889
+MVTHDDLEITGKRSYYISHQCELSPDCFPVCVLIVSSIYDLFGEECLRRLIEHEEPRNRS
+IVRGEPVVESEVSDEVVADPVLSASHAAERDAASRPLNGYGQLNWVKSDVMLGTLKPKVA
+RIVRHQFRHRVDGGTKSGGGIVALAKVFQPRELSAIPAFSVSQFSEISSDVDTSFEFLAD
+PALEECDSLASLTARCDRRFLLGNGIEFNNVFSECLHERFAARLQTFNRCLAPRGDPLRR
+FEASFQSVQE
+>PROKKA_00896
+MVTHDDLEITGKRSYYISHQCELSPDCFPVCVLIVSSIYDLFGEECLRRLIEHEEPRNRS
+IVRGEPVVESEVSDEVVADPVLSASHAAERDAASRSLNGYGQLNWVKSDVMLGTLKPKVA
+RIVRHQFRHRVDGGTKSGGGIVALAKVFQPRELSAMPAFSVSQFSEISSDVDTSFEFLAD
+PALEECDSLASLTARCDRRFLLGNGIEFNNVFSECLHERFAARLQTFNRCLAPRGDPLRR
+FEASFQSVQE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002369.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002369.fa
new file mode 100644
index 0000000000000000000000000000000000000000..601f78ff55ecbee5da8317a9db64768f554801fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002369.fa
@@ -0,0 +1,8 @@
+>PROKKA_02318
+MEIAFASTRHFGQGEVLRHVSADYVLKDFMEMNKVPSAAMFRRSRWAEVGGYLESMRWGM
+EDYEFWVRVLRDGGIARPVPTAYYHYRSRENSRLSTLGTHAARDTHQAIVEANPEHHAIL
+LQAAFLRLEEMHDLHLEYRSYVHKWQDRFRPLIRARDFAKRAVRKMS
+>PROKKA_00519
+MDMNKVPSAAMFRRNRWEAVDGFQEGLDGQEDYAFWVRMLRDGGMARPVPAAQLHYRLRA
+TSRAATAGSEYWEATRKAIISGNADHHEALLRAAFERLDELRADLAEQKRYVQNWQRRAR
+PLIAVRNRIRSLLGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002373.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002373.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d71eed62db38cc576a654b433ee57ef966adc0fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002373.fa
@@ -0,0 +1,3 @@
+>PROKKA_00173
+MSSSRDAVLVVRAAGGRWKVENFFAAHPKTSETESLWDFTVPALLEAADRAGVHIEATAM
+NEKLARHYKRKIPDLRRLGVVCTGQVKLLRVPRPHPTS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002375.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002375.fa
new file mode 100644
index 0000000000000000000000000000000000000000..32cada4f61b77db15837943ab9248929561f55be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002375.fa
@@ -0,0 +1,11 @@
+>PROKKA_00407
+MEVEGWTHVSPSLGEYRYLSGGEGQRVTAFDVTVPDSAAHLVLQGHAWKPEFPVRVNGAP
+MVLRHVHPLDTPVAPFSPDTRVRVWDFVQHVPVSPGTASIEGVVHASLPTEKSTALLTVG
+FLDEAGRPLPGPSDLPQNPTFGPFVQLRGAAEGPLETQFQIAVPSQARWVRIQGRRGWGN
+SDVMMQAEVDVTEVRSSAAEIDAFLAEIPEGDTLLVIDTTAPPLGHETLSLRPNNLARAF
+ERAGVWVVFLPFSSLQEFPARVSDRILQVARKDFGRLVRGLTTRRRSMGDTYICSSFPSI
+GAVALGTQLKTLGWQVVYECRDDMEEFNRVGYSKWYSPALERQMLIVADKVVSVSTALDA
+KLVSMWPALRDHAVIPNAVNRHVIDQSEGLRTEESFDRREHLRVAGYVGHLTPSWFDWPL
+IAEAARRMPETVFEIIGHGAPQGMSLPSNVHLLGPRSHEQLADIVTGWKAGLIPFLDIPL
+TRSVDPNKIYEYFAWGLRCVTAPMGSVETYPSTWVHRGVDEFVEKLDEALSTPWAPGERE
+AMESFVQSSDWDDRAERLLSYYGITTEGRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002377.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002377.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d2596406e27c10007eb436b59c261bf73e5157d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002377.fa
@@ -0,0 +1,6 @@
+>PROKKA_00409
+MDYFDRIQNRLEGREAGVPGWLGAKNATRQFAAQIGIRTPEQLFKGPLSDLERFDFPERC
+IVKPGFASTSIGVHLLERRGAELWDLVKDEPVTVPGLIETLREIEGRYDLSPDDGEFLVE
+ELLSDRRGVTPPADVRCYMFQGECGFVLVEDHIAGPAAASYFNGDFSPMTDVHDRFGVHP
+GVTHLESIVDAAEPPAGAEELLAVARRVSTAVPSAFCRVDLYDTPAGPVLGEITFYPGTF
+FYKNRKVMAPEEAARLGKMWDAAEKRLAGSLLIDAPKRN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002378.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002378.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12e6bd959e04b76d095e6856ea6fda3e0987f133
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002378.fa
@@ -0,0 +1,9 @@
+>PROKKA_00517
+MVIQLVSLTVLARFLEPAEFGVYGMAITFIGFTTLFRDLGLSSAAIQVKSLPIQLRTNLW
+WINTGTGAILALLTLATAPLIAAFYREPQVAFVVAFMAPTMLLAGAAVQYRASLARDLRL
+GAAAAIDVTGALLGLIVSVGVALAGGGVWALVLPQLVSGVVTLAGVIFVSRWLPGLPRRG
+HGTRQLVRFGGAMFVSQALTYTHRTYDVLLLGRLHGADWTGQFNRAAQMSRMPMGMIAAP
+FSKVALATMAPHQEDVHALGALARRGQVLLALPVLLAAGGLVAAAEPLVSLVLGDGWGQA
+VPFLQLIAMSEALALMASVGGWLMAARGQGSKLIRLGVISTVIKVSTVSLGSLWGPYGIV
+AGVVVAQVILWPLSLVLTGRMSGVSTREALVDSYVLVGVTASATAAGWYAGRTHIVPGGP
+VVDIVAVVVTMLATLALAAALVAPFRRDVQTFLQTVRSGVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002379.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002379.fa
new file mode 100644
index 0000000000000000000000000000000000000000..31056bd61631f5892e9ed02344d83c89b5a29e35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002379.fa
@@ -0,0 +1,8 @@
+>PROKKA_00518
+MKILVYGAVHQQPNIGVSALAAGAEAVLSRAFPDADIRFRSTGPLGDGPMNLSHTAPLLK
+EMVVNRRGLRGWTRSFDLLCDIRGGDSFTDIYTSKMFFKLSAFPLYAQALRVPVVMLPQT
+IGPFENRASRILAKRFMRGCRLVMARDPRSSDFAAELGRPVDLTATDVVFAIERPEPSLK
+HRDVVLNTSGLLWHAGNRHVDSDAYRAGIRGVIDILLAEGRQITLLAHVVGRTDTGADND
+RAALAALREDYGDRLEYVVPSGLDEVRSLMASANVVVGARMHACLNALSIGVPAVPMAYS
+RKFAPLLDQLGWHHTVDLNASGEQIATAVLEEIHAVEGEDLTPVLRTARARIDAAVEALR
+QLSD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002383.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002383.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18833fc26af667e58be458e96eec3420f7a2b84b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002383.fa
@@ -0,0 +1,7 @@
+>PROKKA_00590
+MSIEAMKWAQKVAETGQLNTGQAFVLLLLGDHADEAWSCHPSQELLARRSAQTVRSVERH
+IARLRDLGLVDTESRYGDGRGRIGLRYYLREEALNDLVQDAETRMNTRPDNLSGKSETRT
+KTRPDNLSGKSETRTKTRPDNLSGKSETRMNTRPDNLSGESTHPTISADSPDNHDFADYK
+DRARTNPQEPSSVRPSVRQSGAVRAETTTDDGRRTDQVIDGGEGVGLVHRGVVLADLVQR
+VPAAADLGDGQLRSIVDVVLARASGPVRKPTAFVARSLASEFEELVTVTRPRPVAVTQAP
+AASGQVRELRTGEPCQDPDVHIPAYGQAVLADCPHCRLERRAMPRALMEAVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002384.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002384.fa
new file mode 100644
index 0000000000000000000000000000000000000000..62e2f012c44365db16d525fc521be14198749a21
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002384.fa
@@ -0,0 +1,6 @@
+>PROKKA_00591
+MTGQADRVAPAGMVLVTGDELAEAVASVRGTVVAVLGPSGNGDVVEDVLQSTWESAWHSR
+ERFDPDRGSLRTWVGTIARNRAVDHLRAVGRSRAGQEALEASAVAREKTAVSTVMEDPAE
+AVVEALAAHREVAEVMRVVESVMESSEMTARALAVVLAFGDDVVAASEAMGVSVTALRQA
+RRELVRCARVVRAAQEVARSGQAVTMRVLISCLPDDGDAGDWARQVALACAQAGGRMEAV
+TVEDVMQATGFSHSTSRQYLAETRHLLRVATTVIRNERAEK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002387.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002387.fa
new file mode 100644
index 0000000000000000000000000000000000000000..65ce4da2a346b3ab026b5fbb0201909af932f17f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002387.fa
@@ -0,0 +1,9 @@
+>PROKKA_00605
+MTESRLWLLCDARAAHRQGRAGLDRRRHERLVEMVSFARARSPFYRRLYQHLPEQLTDPV
+LLPVTGKAELMRHFDDWVTDRAVTLSAARAFVEDPALVGEKFLGRYTVGTTSGTTGTRGI
+FLWDERSLAVTTALLARLLGTWLTPADVLRMLARGGRIAMVNATGGHYASAAAAAALRKN
+RWGSDRIGVFGVHTPMAQLVAGLNDFRPAILAPYATMGALLAAEQRAGRLHINPALVVLS
+AEALPEGEYDRIAATFNAKVRQGYAATECPFLTYSCQHGWLHVNSDWVLLESVDADHRPV
+PPGQPSHTTLLSNLANKVQPILRYDLGDAVFVRPDPCPCGDPLPAIRVRGRTADLLTFHT
+PAGEPVVLTSLTVTAWVDRVPGVELVQLVHTAPTHLEVRMQFSAGTDPERLWQAVHTEIR
+RLLVDHGLGHVTVARGDGPPQPTPGGKFRAVIPLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002388.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002388.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa823d3236ca1479f884f3177402ee7ba7d11b5d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002388.fa
@@ -0,0 +1,9 @@
+>PROKKA_00606
+MPGATPIGDEAEVPTLGAVDHLRVLTRVLLGPVVKGPIVRRPAAVGLAERLDADAAGVAE
+MQRLRSRYGAGPVQLRIPGRRIALLLDPADVRRVLNDSPTPFSPATLEKRGALNHFEPAG
+SLVSTPQQRLSRRPFNEQILETPRPVHSHAEAMKAVITEEVSTLGGHVDFTGTLDWESFA
+VMWARMVRRIVLGASARDDDQVTDDLRRLRARGNFSYLMPQNRRLRERFLRRLQHYIELA
+EPGSLAALVAQTPAPDEAVPHQQVPQWLFAFDAEAWATFRALALLTNHPGATGTARSEVA
+HAPDLPFLRATVLESLRLWPTTPLILRDSTATTHWRNGTLPPDTALVIYAPFFHRDDQTL
+PQAHRFSPELWLQERDDNAWPLVPFSAGPGMCPGRNVVLLTSSLVLGELLRQHDFTAQEP
+LDTGQLPGTLSPFSSHFTVRHD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002390.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002390.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16b017c203e83904965bbf1494c9095e1f23cc0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002390.fa
@@ -0,0 +1,3 @@
+>PROKKA_00618
+MSARVKISGNLERELQRAVQDTMTTLAKDYQRMLDQLGQQYAGAPVEEIKAVLRTRWSRI
+SGTISDPELSIYAQHISEGTPITVRTS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002397.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002397.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f81e013d0986c3d98c4da05a0b96f6a7c9296263
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002397.fa
@@ -0,0 +1,6 @@
+>PROKKA_00840
+MKRPERPISSDWLDLRRPADERARAGSAPLLDALAEHFTETGADSPVDVIDVGAGTGANP
+AWLAPRLRFSQQWTLLDHDADLLELVPSQLQDARVRHVRRVTAGIEDLGSLDEAEQDRCL
+ITCSAVLDLLTMDQLAGFCDFLAERRMPALLSLSVTGDVVLDPGHWADAQITRAFNQHQR
+RGSLAGPDAVGYAAGRLRADGMRVEVAESPWKLGPADDVLLRRYLHDRAQAVIEGAPDMG
+DVVDSWLAEHLGQSDEGRLHVEVRHRELLCLPPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002398.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002398.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d396b6e320b371e8f71eba830b7ebb3b39407f5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002398.fa
@@ -0,0 +1,4 @@
+>PROKKA_00842
+MYRLTVRDHVMIAHSLPDPFFGPAQALHGATLVVEVTWRRRELGPQSVVMDIGAATSMLS
+EVLEPLRYTNLDEHPAFAGRLSTTEAIAGHISDELRRHFDTTEFAGMEVLLREHPDAWAA
+HDVDFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002399.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002399.fa
new file mode 100644
index 0000000000000000000000000000000000000000..781e73b3cdaf6efa421d03f169aff355e56871a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002399.fa
@@ -0,0 +1,6 @@
+>PROKKA_00843
+MRSLYSGVSRGTEMLVYRGEVPPEVAGRMRAPFQEGEFPFPVKYGYLSVGVVEQGPDDLL
+GRRTFCLYPHQDRYVVPVDALTVIPDDVPSRRAVLAGPVETALNALWDAPPCIGDRIAVI
+GGGMIGASLAVLLSRFPLGRLQLVDTDPVKRDMARAMGIEAVEPEALQAECDIIYHASTT
+EAGLAQGLERLGDEGELVELSWFGSHVPAVPLGTSFHARRLRITASQVSTIGRARRYRRT
+HAARMDLVMHMLQDPVFDALISGESGFADLPGAIAGLAQGELPTLCRAIRYPDPGPRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002406.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002406.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4269d28ace2619da2e9b52b5fbdea36e0c768628
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002406.fa
@@ -0,0 +1,19 @@
+>PROKKA_01491
+MTAPAVHEASQKRLLGTQHAAKTPSQTPLAAAAYGGTPVAAAADGWTIEYVTDSATSQKY
+PARFAVLTKTVGRAGCTGSTTSFGAYPSVAAMGTGRDAIVVGFDTEFVSAEEVDEQRGWV
+GEDVHVVRRIVSYQFAAIDPTDPSRLRLAVVLPQEYHGPRGPRTARLSFEKALEIAVTAL
+GLHEHPLASGWSSQGVPRAEVVDKKGETRPGWWFNGRAGVSRALPIALVAHWQQADLTTF
+VDRRKAHNTWNAAYPERARKVSTRAGLDSRRGRWLDSSTSDILRAVISASAGMVSPTPVR
+MVLAGANKRWARPVEVSIRDTMAQSGAQPLRALGEAVGVAKLDVPGDWIARMDDYLLKDP
+VAFMDYAANDAIIALEYVSQVYGDHQEVPLTLPTAAARAVKGLMSGEIEARPDTFDDFNA
+VFGGLVKVAKNVEATTGVENQLDFYKKRELQPIDGAAATWIHASAMAFRGGYNMSAELGL
+FEQVTHDLDLQSCYPTSSATIWDVDYLHPDGVILRTVNNVELGLDDFAEGGPLTPFVGFV
+SFEFPESVAFPCLPVPAEGSMIYPRTSGGARGVWAVGPEVWLALTLGAKVTCQIGHFGRT
+LRTSDGEPSRLLRGAYKTLLDDRARAKREFGKSSFQQGVLKLMANSPYGKLAQGVMGQRG
+WDAWAQERDAVGGSAITSPWHASMTTGLVRAVLLAVLNQLHDRGYATPSCTTDGFITDAE
+LSVVDGLDLFGLGQLWRDSREALTGSREMWERKHFQTDLLNVTTRANFSRQPGGVLAHGG
+YKLPEGIVPDSQEDRDHMYDLMVSRDGALPVTMKVFPSMEELTRIENRLDFAPKVVHKQQ
+TIEFDRKRRPVPEGMTAHMVMVGEQVFEVAHVRTVPWESPEDALRGRSVDQGLKRWDEEL
+GEPVWTRSPVRRTRAQWQDYFKRLERLLDEDGRVAEAERLDRIAKGIVIAHRQEVVHIPW
+LGSDRPLAERLDAFEDFGLPRPRERFWSHARSKTERQIEIDLEAIAPYVAEMKAVDPFES
+ETFLQEVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002407.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002407.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c47dca5dac467c6ae56f69f72e0aa73b96c3d617
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002407.fa
@@ -0,0 +1,3 @@
+>PROKKA_01492
+MTVAYTLGDQTFATKKAVLAHASEVLNRASLGEVLRGHDEAFALDLLAQHPEVGRKHGAG
+IAGVAVVVMPEWGTRNFVVLREDGSIDNWSVKKCVANLRPDGTRRSP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002408.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002408.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a547de1b81be42f369f6159f008bc7738d48665
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002408.fa
@@ -0,0 +1,6 @@
+>PROKKA_01498
+MTAEPLRPNDAIAPLPTVEGGFKTVMADPPWRFQNRTGKVAPEHRRLDRYSTLSLDDICA
+LPVQDVVADDAHLYLWVPNALLPDGMRVMQEWGFRYVSNIVWAKRRKDGGPDGRGVGFYF
+RNVTELILFGVRGRMRTLPPARSQVNMIETRKREHSRKPDEQYGLIEACSPGPYLEMFAR
+KAQPGWTAWGDESGADSAPRGQVHKGYAGGAIEAPFVEPHVRLDEAVADALAEDLKTKYE
+AGASVQELVESTGYTTTRVRGLLKKANTQMRPRGRKTKQAEALFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002409.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002409.fa
new file mode 100644
index 0000000000000000000000000000000000000000..82d9ff8bfa07604aa57af911e191d1420cf303ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002409.fa
@@ -0,0 +1,12 @@
+>PROKKA_01499
+MSPFPSPGRISFTKFTSPEGITDVLAGVVPGVTTAAEVLQDLAAAKLADPLWDDLLSYDP
+PFEPGKSRAAGSQVAVDNELLRACREGREDRFLLLWAQLILADPRLDAIVREVFTDSTGK
+LVPEMVNASKLGAALTARHAADPDEPHDTKAVSNLLSLLERCRLVEPVKHGKTIVGVERV
+LPTAHAVPAVVRLIGERLAERGFGAQPGRELDLALALGANAWLNLTASEFRDAFDGKTPP
+AAQPQSVPGALPEDLKVIATLLRRKGQVLLQGPPGAGKTYVARRYVDWVSAGRRADSRLQ
+SIVEALPDDRRTVPAIADEIVSRGLSAVWDIVQFHPGYEYTDFVRALVAQPHGQGVTFVA
+QHRIFSLVCAVGAELARRGYELEMVLILDELNRGDIPSIFGELLYALEYREEPVASPYTV
+DGTPSLTVPHNVRVIGTMNTADRSIAVIDYALRRRFTPIDLEASDSPIRGYTGFDDETAR
+EAALYLYERTRDALSEASQGLQVGPSYFLAEPDGEDGSIAVLATRFVYEVLPLLDEYTLE
+GEVDASRVESLRQELGLGQRAKQWDQGAALAAHLVAGQPWKPAAADPEVGEPEEALSVDL
+GGPLADGGDAPASGEDTRDQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002410.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002410.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7589e4089cfcac33d580df2c8aa25014db9b51e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002410.fa
@@ -0,0 +1,9 @@
+>PROKKA_01500
+MPAEFWKAAGCRLTKSAGESSWMLEAGDLVGVSRVSTALGDVTLQVLPKLATADVFFLAD
+YAYDQRHEPLRLLPFEQVELDALRRDPAACLLVWHARAIHRFATRWLRRDYRRVDQVLNG
+KIKGKPLISRYVSQHLAVGDPARIPCRVKERTQDTPNNRLLKAGLHYILSRSHELELPAA
+RRVAVREAKAALPLFSQVSDIRTEPVSQRDLTATTHRGAMSHYRSILLSTEALLRGEIMG
+PEVGAGVSTASFMWDMPTLFQEALRGVIDSAPGLALSVEGIGRARVHAHDGKQVRSSKVD
+PDLVLETAAGGQLVIDTKYKDVLPSDHGVDDEDVTLVADRRRIKVTRADIYQVVAYTAHD
+KWRGATGALLYPVVLAEGDTLPRPMQIRGFGPPVWMLFVDVGQQAKGNLPAFLDSVRELA
+DRSAAGAVVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002422.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002422.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a1846b1f5b08d625a52bf9c05b60ce6cae34acc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002422.fa
@@ -0,0 +1,12 @@
+>PROKKA_01960
+MTDHNPGYTLERLPFRGALPPEQEKNARMRDWPAVYVIDNEKQVYVGETTNVVARRGQHH
+MDPRKARLTTMRVVLHDEFNKSAALDLERYLIQMLSGDGAREVLNRNAGLTESDYYDRTR
+YQEMFADIFERLRAEKVFSRSREQILNSTLFKLSPFKVLTPEQEASLRHIVQLLVADDDV
+DRGPLVIEGGPGTGKTVVGVFLAKLLVDLANLTEEDVEVDLSSDHDFFDLFTHANRNALL
+RGTKGRGLRIGIVVPQQSLRQSLKRVFRRTPGLHPSMVLSVWNVGDAEERYDILIVDEAH
+RLGLRSAQSNGALNTKYTAINQRLFGDDDVSHTQLDWITQQARDVVLLVDPRQTVRPADL
+DAATMDALLARAHAEHRHHALVSQLRVKASDSYVDFFGKLLRGEHPPAPDLGEYDLRMFT
+DFGAMREAIRARDTEFTLARLAAGFAWKWQSKGFRKDPSKPDWDIELDGVRMPWNVADTD
+WVDSPGSLDEIGSIHTLQGYDLNYAGVVIGRDLQWDDTAQRVVFSRADYADTGGKKNNGY
+LSRTYSDEDLREYVINIYNVLLTRGIRGTYLYVVDAGLREQFARWFPGISGPDVTSAPFG
+VPPGGRPGEVLRTVDVGHTAEAEFILSTDDLEQARRRAEELRRSRKRTRE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002424.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002424.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d977d9bec622b462e5595d251b2f4b30481176b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002424.fa
@@ -0,0 +1,7 @@
+>PROKKA_02038
+MSTGLRGTQVITLGTAGGPRWWRHGGGTPRAGISTAVVVGGAVYLIDCGYGAGRQLVRAG
+YGLDDVEAVFLTHLHSDHIVDLTAIALFSTFEITQDDRDAIRLIGPGDRGALYPTSPHTT
+AAPTPLTPHDPTPGTAETLRRIVAAHATDLNERILDSLRPSPLDRIHAHDIVLPSNIAFD
+PDAEQPPAMDPFVVFEDSRVRVSAILVEHPPVAPAYGYRFDTDEGSVVVSGDTAATDNMR
+RLADRASLLLHEAIDLDWLVAKFPDPESPQAHAIRSHHERAHTSVADALRIADDAAVGSL
+ALHHLVPGTSGASLGRQLEGHHPFSSTVPSDLQVIPLASR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002427.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002427.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e174640dbd4ccff050a4fcb05c20798c190f26d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002427.fa
@@ -0,0 +1,3 @@
+>PROKKA_02223
+MNLNASLGRVVEWDRDGGWGVIDSEATPGGCWVHFSHLPMLDSVPSSLTVGEEVEFLFEA
+LEAHNDQDGFLYRAIAVHPPHGGLAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002428.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002428.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ee7e4d07ad8eb97dbfbb2d7135d4429431b94ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002428.fa
@@ -0,0 +1,4 @@
+>PROKKA_02233
+MTEHDTGEPYADSLPFSLVAHWSFCPRRAWLEAMDEKAPKVAQIQQGVADHARVDVPTTR
+EAQTMRGIDVRDPSLGVHGRVDRVERLPSGRLRVVEHKATPVKRAARISDANRLQLVLQT
+MALESQGNTVEDAEVYFTTHHRRVPVELSP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002438.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002438.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb1d522ed20766cccf6a4e7fa7734bcc9c4bfbde
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002438.fa
@@ -0,0 +1,2 @@
+>PROKKA_00209
+MLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002448.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002448.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75494fbadb072b7a288b92b810545770fa73c5a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002448.fa
@@ -0,0 +1,5 @@
+>PROKKA_00500
+MTTTSASQGYRTINPATGELLKSFDNATDQQIADALDASQAAYEQWSRKSVAERAAVVKR
+ISELLAERSKDIAALITTEMGKSLGAAVGEVRYSAQIFGYYADEAEELLADQPIKQFSGQ
+EAFVQRLPLGPLLGIMPWNFPVYQVARFVAPNLVLGNTILLKHAEINPQVAQLLEELFTE
+AGLPEGVYQNVFATHD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002453.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002453.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c9e9e6d48457fa65163de0df38bdae186c42aad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002453.fa
@@ -0,0 +1,8 @@
+>PROKKA_01301
+MTAQQHPAVFIGLDVGKAEHHAVALTAAGKKVYDKALPNDETRLRGILDELARAHGPALL
+VVDQPATIGALPVAVAQACDGVEVAYLPGLAMRRIADLHPGSAKTDAKDAAIIAEAARTM
+PHTLRSIRVDEEQIAELAMLAGFDDDLAAQITATSNRLRGLLTQIHPALERVLGPRITHP
+AVADLLGRYPTPAQLRTAGPGHVRARLRKHAPRLAASLTEQIFQALDEQSVVVAGTQAAA
+TVVPILAEQLAGLTRQRAGLASQVEAAVEAHPLHPVLISMPGVGIRTAARILTEVVGKDF
+VDAGHLASYAGIAPVTRRSGTSIRGEHVARGGNKRLKRALFLSAFASLSHPPSRAYYDRK
+RAQGKRHNQALIALARRRTDVLYAMLRDGTLYQDPTAPPAPSSVALAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002460.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002460.fa
new file mode 100644
index 0000000000000000000000000000000000000000..357c29841441cffc14d4e7ee5249631d08c03a78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002460.fa
@@ -0,0 +1,8 @@
+>PROKKA_01776
+MSTRWPVHPAPVTGEALTSWLRRIAHRYGAEVEDLVLDTGFCISRPGDLDVAAPEEFINQ
+LAGRTRTGTDTIRAMTLGGQTPWLLDQLEPAAEAYTTYTRQLAVLLPRGRRRDRTVEDWR
+AWLPTDAGWQHRACPRCTMESTPPCPYQLAWLVPLMLSCPVHHCRLERHNGPVGYHDFWH
+VSPGRPEPRPVGAAIRSMDQRTWQALTTGSVALPRHRVHAGLWFRLLRTLLDELGATIIE
+CGAPGRLTRQVWDRTGHPVRAGQGPWRPYEELSDQRQLQSLEAAATAIHLFETRAMTCPG
+REAEVFLPQPDISRDPGSTEQTTDPTAIRWQEIKKNFQAVVEEARTTPETARQLFNFCTM
+YRRDNDEVIQGVRSNFTELGIPSDYLSP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002462.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002462.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1730a43d1cc77f0e2d106faff0b507acec2d2b3e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002462.fa
@@ -0,0 +1,3 @@
+>PROKKA_01935
+MKYSFQANEANGAPQQAVLNGWHTNDLLGIQAKIAGDQRDQSHRLTALVFFLGLGLLGDL
+VLRNAEAFRESKGS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002467.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002467.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a577d52123ad4cb7fa2942d048891368ecd53d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002467.fa
@@ -0,0 +1,3 @@
+>PROKKA_02027
+MKDRGRLLGIAAISVTSLLWGTTGTAATFAPDAGPLAIGAAALGIGGLLQAAIAIPALRR
+A
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002476.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002476.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f910d53f446fbdbb51c120c5e5c79e47cae2968f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002476.fa
@@ -0,0 +1,3 @@
+>PROKKA_02220
+MPVSPCPECGRDVIPAGIGQAPRFCSTSCRQRRHRKVTRVRGELAAAETERMPLRAAYYR
+EWLARLMGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002478.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002478.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9434cece6740b1f67d22ac73091473fb5a83f23e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002478.fa
@@ -0,0 +1,4 @@
+>PROKKA_02222
+MTGPSTDGVRGGRQTWAQWYYSGAPTAQDMADRRHADTARAERARLDAEALNARHAEPRP
+DPAARLRIALTNLGPSMVPPGAGPTLADVNAAIRREAGPDRALHQQMLDLHFTQQARRRA
+AGNH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002480.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002480.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a7a465418017a30bae60a253fb6dd1d1a30290d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002480.fa
@@ -0,0 +1,3 @@
+>PROKKA_02225
+MTRLFRSHATYWTKNRRTARRAQALPAVQIDPEGREVPGVALITDAHPRVVLTVDEMRAL
+ALALIDAAEVARQQLAPAEPEQTEKAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002481.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002481.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3cda34a3a3057ed81d47d15e4a3e5708fba625d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002481.fa
@@ -0,0 +1,3 @@
+>PROKKA_02226
+MSTRRAYTEDDVARFMDLARGGRDRHRPTTGTRELTDRRPIPRDWPAMTNADGSPSAPLP
+TADPEKE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002487.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002487.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b2544972117ea049e04dee9cb033b8809b27f39c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002487.fa
@@ -0,0 +1,2 @@
+>PROKKA_00041
+MSTTSRPTPKHAATTAPERIAAELAYLRNECDSIRHALNRSRERA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002489.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002489.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5599267ed779d6a47fb8a5714a58a29229e1b6b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002489.fa
@@ -0,0 +1,3 @@
+>PROKKA_00045
+MTRERIPEGLRERGTRLWKETTDVLDLEAHEELTLLEACRTADRLDALADALEDAPLTVT
+NARGDEVAQPLMVEARQQSIVLARLIAALRIPDAEDNRPQRRGVRGAYGVQMRSVS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002492.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002492.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bebff11067e8348b5a4137b7c89da844593b7a4a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002492.fa
@@ -0,0 +1,2 @@
+>PROKKA_00049
+MNHLTDAECRAELERALDEVDALVRVTEPANAFMDALGRSETWTRFLTLPHAVPTTGAC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002493.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002493.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e1d44a4cfd67bbf09cb4f5c16a07812c2aeea19f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002493.fa
@@ -0,0 +1,2 @@
+>PROKKA_00050
+MNQPTRTLPQLLQPVARAATYTAVTVAGFFMLSWPSIFTGAM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002494.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002494.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab1f39e058a3c98a7fd9f098fdf90f35ed983515
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002494.fa
@@ -0,0 +1,3 @@
+>PROKKA_00077
+MERKDDRRAFLTWTLISAVGLALVIASFTWPAWLVVPGALLALVGVSQSHEYRGYSHWFG
+LLVAAVAIGGGPFHLLSLAGDLGSFLGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002497.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002497.fa
new file mode 100644
index 0000000000000000000000000000000000000000..01842f670892f476561f4502b7cacdfa04778d2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002497.fa
@@ -0,0 +1,6 @@
+>PROKKA_00102
+MPLLTRTVDPRSSDVLSLANSPVLWVFALGVFAVIIVQSALYVRAARRAAPGLGIERAEL
+STAFRSGAVASVGPSLAVVVVAIALLALFGTPAVLVRIGLIGSAAFETGAAKIAAESAGA
+PLGGPGYDQHVFALAFITMSLAGAGWMVATLLFTPLLKRGSARLSDVNPVVLTVIPAAAL
+LGAFAGLTLGEFPKSPVHVITTAVSAAVMLLLLLVARALKADWLKEWALGISIIVGLAAA
+YLAHQALLAPAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002500.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002500.fa
new file mode 100644
index 0000000000000000000000000000000000000000..41c97caeb698dde42a7aabab7f21509b14308316
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002500.fa
@@ -0,0 +1,6 @@
+>PROKKA_00126
+MTPEEFPPIHSQHAVVLDWVGPRWAGHLRYAVHLSEQSLAPGETELRDLWPDGAGLCWLG
+GPAVGPGPWPRNAEGAPLSHVLTLDLRTVAGASDHQGKAVWPAGRLREGLPVSGHLQVFH
+DLQTYGGDPEDGDRAGWAVTWTPEAEDGLRPALVEAPDDDGAPDPVCQLVLPYAGFTLPS
+SLDVAVTDPRDADRLEELDDALREAWTVQRGLDPTWAIPTSHVYGHGWTGDALAGGEILP
+EVLPLEEGDEHRLVLDVESWTTLQGWFGDAGHLEVWMRQSDLERGAFDRAWCLIRTD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002507.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002507.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0052674c62bf471ba28d35ef01b0e50d361447af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002507.fa
@@ -0,0 +1,6 @@
+>PROKKA_00176
+MRKALPTAVTAAIGLALVAPLAAAAQEGDTAALSVLHGVPDLTVDVYVDGELTLDDFTPG
+SLAGPLELPAGDYEVAITAGDAEDDSAPVLGPVDLTLAGGGDYTAAAHLDAQGNPTVTAF
+ETDTTPVAAGEGRLTVRHIAAAPAVDVWADGAVAVPGLANPDEAALELPAATLEAAVSVA
+GTTDPVIGPADVEVAEGVNTVVYAWGSATDETLALATQTVEGLQSAPENVNAGMAPAAQD
+DTALYAGAGVAALALLAGGAMAVRRKAAVRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002512.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002512.fa
new file mode 100644
index 0000000000000000000000000000000000000000..357122449f47fe27879d0669e8fafe7bb3f9db0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002512.fa
@@ -0,0 +1,4 @@
+>PROKKA_00192
+MDSDSAHAARPHDDGADLGDLMHVVFRRLRRRWSAQLEPLGVTPHQVRALRGVAEGAGGG
+IGSGAGTRAAAGSVADDDGGVRLRDLAERLRIAPRSATDVVDQLESRGLVERAADPADRR
+AVRIRLTDGGRGLLRRVHEARRTEAADFFAVLAPADRAELARLLARVAADPAEGAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002514.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002514.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f22b3a9110f5811e350ef96926523ddd28c23854
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002514.fa
@@ -0,0 +1,3 @@
+>PROKKA_00237
+MVAGLPWFAWIAIVAILVWGTLQVVQLVTGRALPGEEMKKEVEELRTRLDANEGRRPAGE
+LPARADAEGSDLERRIERLEARADRREARDREHDDWDRRAGELG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002517.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002517.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f4cf73b1f54501336000bc77109d71b9b6c57e9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002517.fa
@@ -0,0 +1,2 @@
+>PROKKA_00308
+MGAPDEVPDRTDPGTTTASRPWAAVVGLAAFAVQVPLARRVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002518.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002518.fa
new file mode 100644
index 0000000000000000000000000000000000000000..03e47af38caa64fe4bd49f7b4a8e1eec0bbbee7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002518.fa
@@ -0,0 +1,7 @@
+>PROKKA_00310
+MGWSRRSATAASEPRGSAPDRAPTGPFVREMGGSVALTGRTGRRIRDDGTPVFTKARADA
+PAHLFEREAAGLRALAAAGARVPRVLAWSETGLEIEWIDDGGRRTRQTEAAFGRELAGFH
+AGSRPEAGAPDRFGSPDDVAAGWLGACPVDYTPADTWAESWVGRRILPLARRAERAGVVP
+ASARADAERLAELTDGFGADAPADHPGAAVLGSAEPSSLVHGDLWAGNRLVDADGRSWLV
+DPSAHRGHREADLAMMRLFGGFGEEAFAAYREAFPLADGWRERVLPYQAVPLLVHAVLFG
+GGYGEQAAASLRAAVRLAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002520.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002520.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0082bce25a97ae74ceb8ff5b63142b371523d751
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002520.fa
@@ -0,0 +1,6 @@
+>PROKKA_00325
+MTHPRTAPAPLAAVAGSLGLCLSAAVLAGAPALAAPTSTPAAGQARQQPVVVMDHSGSML
+NADADAEGTTRVDAAKAATKDLIRAAPGETPVSAALQQAADALEEKEKGTIVLVSDGQPS
+CDTPPACEDAAQLTEHLTTRTTRALHGYEAAGTPITGGSSLAEAPLLLPGPATDTLASHA
+RPEQIGHRLGTDDFADGDVTGLPQEAGPGFLTTAAQFRERFPDEAAAAPPPGPGPWTPSA
+CSPWPAAPS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002521.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002521.fa
new file mode 100644
index 0000000000000000000000000000000000000000..309575b8f78109d90d631adbf8366a949437e450
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002521.fa
@@ -0,0 +1,4 @@
+>PROKKA_00328
+MLRRAWSGLVGPLGAARSAGVVGAATAAGLVAGTETAARCGPGVGAFVGVTAVDLVGGMV
+AFQLRPTREHYARTSLSRRMALAAAHVQCFALPIVGEGTWSAAAGRWAGVVVSTALLQCA
+VPAAHRRPAGLVLAAGLTTADVALAGPRQRWLGPVWFTKLVAGHATLPDPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002522.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002522.fa
new file mode 100644
index 0000000000000000000000000000000000000000..371214436ca26b3cd4b0fdc08c8eff1e531b2e93
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002522.fa
@@ -0,0 +1,4 @@
+>PROKKA_00341
+MGPTMDARTAPQDPAGSPPASAAPALLLLAPLAGDVLSTGPLATSLSSEATIAGRALTTV
+LALVGAVLLLRGGRDASRSLRAIGGLAVAAALARGAGVVIGAIDRSDSSLSWFATIWLFL
+FGGAVLAGLGVAALLRRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002527.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002527.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0e8440abbb26a2fdb84aae5abb46565346385b62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002527.fa
@@ -0,0 +1,7 @@
+>PROKKA_00378
+MALLAALLASTLRGTVEVPATVGLTQEQAEAALEDAGLVPLVSSTHSSEAPAGTVISSDP
+PEGTELDRGTQVGLRVSRGLEGVVLPGSLRGLSEDAVRRELQRLGLTVSSVQYQDDGRLE
+RGMLARTDPALSTSVPPGSSVVLHLSSGTVRVPDVVGMSAEDARRQLALSAPELRVRIQD
+EDGAATETGTVVSQDPGADARVDNRSSLTLTASTWVEATAEPTPPPSPSAEVPPPVRPSA
+PPSSSTPPSSSAPPSEEPEPSEEPEPSASPTPTPSETVDPTPSDSPSPSPSPDPTTPTPS
+PTRTTTPTEDPSPTPTLSDPAPTLTPDPEPSIDPPPSD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002528.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002528.fa
new file mode 100644
index 0000000000000000000000000000000000000000..825a58c7be8ff721a2adc1fe96ad806e5f5db898
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002528.fa
@@ -0,0 +1,4 @@
+>PROKKA_00390
+MPRTTLTFGGLLIAVGIISYAVTGFISWTALIPAFLGLLIAICGLIALKNTTIGLSIALV
+ISVLGVLGTSMNVLKVGELISGQAERPLAIVASTVTFVLLIVYIVTGVRLFLTARRGDKA
+EATTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002531.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002531.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46442585e539b17275a0427542771eb4bdfb6317
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002531.fa
@@ -0,0 +1,7 @@
+>PROKKA_00455
+MVARVGSENIELVDPGTEDSEIRPAKYLPGRRSIGVHLKMREESFARRFVSVQVNRDGGV
+IVIPFLEKWKKVRCVSLNYPLPGHPVVDPTSAVRVGDGSRAKLHYHRSGYTSVQPQDPPG
+EAPRLGVHLAPLDSIHQLPVFTVAARIPSKFPRLERAKRGDLIHATSMLGVRSLLVAGVL
+YDRSQVAPKSIGGYDSATPLTFTSGDPNVMILDLSGYGLNSVLALFFVASPVDLADTSCD
+ATVASYGSAESSGSNGVAIMAGGGYPHTFRIGDIPPLESFHSNTDLDPRVRSFSFEPSLN
+YDEIFYSE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002534.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002534.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f8820be52c74e7a50ad0c35b9513b18509b7235
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002534.fa
@@ -0,0 +1,3 @@
+>PROKKA_00465
+MEGFRVRAGKEERAREWIAFLRENPEAFRETLEPERMYVETIFSETVGDALYLWWYTLQG
+EDGAELSDSTHWLDERHAAYWRECIDPDEPSLLLIPEVHMSPERLEDAMRPLGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002536.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002536.fa
new file mode 100644
index 0000000000000000000000000000000000000000..05bf61c18bd078929defced70a82f3a43504a24f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002536.fa
@@ -0,0 +1,3 @@
+>PROKKA_00467
+MITGSETPRETIAFFALIIGCYALPALCFAAAKRVLLALLSGALAVVSFPLALSIGYVVE
+MLQSQQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002537.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002537.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7248527cf154ab11422846266f18ba2918538e0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002537.fa
@@ -0,0 +1,4 @@
+>PROKKA_00471
+MDNLRAMAALFGVSVDHLLDGTGDGAAPAVLRHPVDVASLEPYKPAGRPLGAKSHRAVRE
+AFPDAVIYPLARMRSNNRVQEFLEWGLMLAFDTPYGLFGLSDSLSNRDAYYLVEEKNRHV
+LARVTPKAVEGKELPEPVEGRTFTVGADRFRRTSRPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002538.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002538.fa
new file mode 100644
index 0000000000000000000000000000000000000000..72bd63130f8c6e6526534768525c2ccd8106de18
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002538.fa
@@ -0,0 +1,9 @@
+>PROKKA_00478
+MVAPEAARELARRALARSHRGWTLGEVPTPAWSLPLKPPTEQVVLADPQAAQSWARGWRA
+ATLPAGIRVEWAERSWRSVGRQQVPVRVHAVTPDALVAWVGGCEAREQRVFAERVAAMRR
+LAEAWGGSGPSAAGGAGSAPQTQDDDDEAAADPRELTLAAALRRHAQRLTDLSEPDFLRV
+VAVLEWLRTTPVQGLRPRQLPIRGVDSKWFGAHRTLLEALHAPQEGGLGIVDAHPTVRVR
+ILDPALRPEGLRDLEVPLEQAAAWPIAPARVLVVENSETLLCLPDAPGAVAVWGRGFDTA
+ATVLPWLRGAELHYWGDLDSHGFAILHRYRTRLPQLRSVLMDVRTLEAFRDLCVPDPTPF
+RGALATLTSDEARALERLRAEGDVRLEQERVGWDHALSALDAHFVFCDAGDRAAGGEDAD
+GRRIAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002542.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002542.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e5daa05ecf673781e9dcc04368b2ffcfa254b02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002542.fa
@@ -0,0 +1,4 @@
+>PROKKA_00482
+MTTTLTLLDPAGPDREALTDPTPLFDLRVAERFRGRGLGVEILTALTRHVFETMPDVDRF
+EGQTREDNSPMLRTFQRAGWVKEAHYRRGWPVEGGEPVASVAYAMLRQDWENGTTTPVPW
+E
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002547.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002547.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d8f6a7f540922a41cb3291af0d19e57abf18d162
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002547.fa
@@ -0,0 +1,4 @@
+>PROKKA_00490
+MPTPITSQASTAWDGDLFTGSGTTTLVTSGSGTFDVNWKARAEEAGSTTNPEELLAAAHA
+TCFTMQFSNMLKKNRTAPTHLDTTADVTFVAGEGITKIVLKVTGQVPEISAEDFERIAGE
+AKEQCPVSQALAGVKDVSVEASLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002548.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002548.fa
new file mode 100644
index 0000000000000000000000000000000000000000..39419f89438e0449bb9ab85e522735862c4fa2e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002548.fa
@@ -0,0 +1,7 @@
+>PROKKA_00492
+MTTLTHRYIDQVVGRVAADQRHDVAAELEGLLADMVEERTAAGVPEAEAERSALTELGDP
+ARLARRYRGAEEVLIGPELYPGFVLALRWLLPFVAVVALVTSAVDYAASTPVPHLGQAIG
+AVAGPLIQALFGSVGALVLLFWVLDRVLPVESREAVRRDVAPEWTVDALDDDPGSDRGAC
+SEAWASLVFLAVAAVLPVLPTSFLYVGHLNDGAPFVNQALWDFWIPAYYVLLAVGVVQAV
+WVLIRRRQTPGSLVLQAALTLVTAVFFTALVLTQQVIDPAIAAGPVQTGVHPLDWVDGLY
+VAVIWLVALWELWTLSRQWRTRRRSGRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002550.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002550.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e8878f3ceb9b2187c77dd5267b8de9e14fdb595
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002550.fa
@@ -0,0 +1,2 @@
+>PROKKA_00495
+MPFDQVTAEHAAAEGDRTLASWRAEHERFWRAHAASGFAPDMPVVCEAFRVVHRRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002560.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002560.fa
new file mode 100644
index 0000000000000000000000000000000000000000..997eebebd7e38d2572e8a6d0b6f316f487d12ded
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002560.fa
@@ -0,0 +1,4 @@
+>PROKKA_00536
+MDTADLPDLPAPEDRTATASRRVEAPAGVVFELIADPSRQPEWDGNDNLAQSEAGQRVTA
+VGDVFVTTLRKGVDRANHVVEYEEGRRIAWKPAEVGGEPFGQLWRWQVEGDDDGGCRVAH
+TYEWAQLTDPQRIRRALRTGPEQLRASIDRLAALAEAEAREA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002564.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002564.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d068769df074f2d8bf4841b5a7bdbec92597dae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002564.fa
@@ -0,0 +1,3 @@
+>PROKKA_00597
+MTGTTLDRPTPTSVSTSVEPRTGAHAVARTLADTAADAAPAVRTPVPPLPPTRPRPPSRP
+GATASASRSSSPW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002566.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002566.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9284c67ad588cb409a62559d348d55c7a937ca11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002566.fa
@@ -0,0 +1,2 @@
+>PROKKA_00605
+MLGAAGLRGLEESLRTRVDAYGGECAVRADADRLRLEVLLPRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002568.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002568.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d9542d4e6316dfc3f4be77ad988ffacd972e3b79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002568.fa
@@ -0,0 +1,5 @@
+>PROKKA_00607
+MLDHPNAAPSPEDAPAASARPAGDAGVTRLPRLALRVWQATTCATALPIAAVLAAVALWW
+DHPVGGPVLWILVALTAAVALADLAVVNRVRHRSYSYTVDEDEVYIAKGALVRHTVDVAV
+PQVLSVHVVRGPLQRALGLATVRFVSVVDAESLGPVELAEAQRVKEVVLRGLAARRQESA
+TALVAAGEVAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002571.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002571.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9de4be2a4d7203cab35297d003a28d88358959a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002571.fa
@@ -0,0 +1,3 @@
+>PROKKA_00623
+MPKKFSPELRERAVRMVLERQATQGGPRSHSIRAVAPQLDVSEETLRMWCQRHGHEIAQA
+PVSETPAEEIRRLKRELAEARRANEILKAASAFFAAELDRPTTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002572.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002572.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6332e0543e2c0e8131cef621a3dca9c6b8f55722
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002572.fa
@@ -0,0 +1,2 @@
+>PROKKA_00624
+MIAFIDEHLDQFGVEAICRTLRATECGFITST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002573.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002573.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f7b7f8e08cb222cc58aeb9bea33a3af697be5b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002573.fa
@@ -0,0 +1,3 @@
+>PROKKA_00625
+MGTVGDSYDNALAESVNGLYKAELIHAKRIWESVEAVELATMGWVHWWNTTRLHEALDYL
+TPAEVEAAYTHDQDSAPVAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002574.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002574.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4ddd5ab8484d85e0b85a7cd85edfeb094416cd7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002574.fa
@@ -0,0 +1,8 @@
+>PROKKA_00630
+MRPSSSRALAMLAAASLTALTAAPAQAAPAASTGAPSSSSKHAFEFGVIGDVPYGQAQVE
+RFPDMIDELSAQAGELEFLAHVGDIKAGSAECSDAYFWMIRGEFDRLALPLVLTPGDNDW
+TDCHRKNNGSYDPLERLDTFRDVFYPRADRTLGDTSMRLDAQDEIGLPENAHWREQRVEF
+GVVNVQGSQNSTLPWSGLGLTEQTPEQRAEVAARDAANHALIRDLFTDAERTNARGVVLM
+LQADMFEPRLAEGGVISPEDAAASQAFTKTVRLIADLSREFGKPVYLINGDSHRYTADAP
+LAAGSPWLDVYGVAPVANLQRVTVEGDATSNEWTRFTVAPNSAGKGKNAQQPLLTWERVP
+YTF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002575.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002575.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90047ae785f13b75fcc9dc30f8bff59c85a072bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002575.fa
@@ -0,0 +1,2 @@
+>PROKKA_00631
+MGAAHVWDASTVAALDSVLTKYAQHGIHAEVTGLNEASTAMHARLTGRLGT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002579.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002579.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68b5de253fde8a0eef6f70a6772a9f5b9a0d58d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002579.fa
@@ -0,0 +1,6 @@
+>PROKKA_00708
+MVSRSSHPDTETAPGRVRIRTDDGVVLLRCARGAQGEPPRLGLEDSGSTFGLALHAERCA
+APVPGVRVEVTRSGLFAERSPAGTVLLPDDGGEPLWLSAPERSAAGQILLGVVEALRAEV
+LPGHVSVPPVPAPRARVERIARWDEVLAPNGLAGGLAPGERPSQAQQALGGAWRLVLDAA
+PDLPVEARLWLAHREQVAGEKVVRLTATWHGPGADVPWHVELHVSHRLGEGQTEFLVIDG
+STQEEWTIADAVHVPGVPLTWRVHPAPRPDTAGRTGEGLYALIDALAHACPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002580.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002580.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6eeb72fcc4e4393ab2d57c0581be384896b707fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002580.fa
@@ -0,0 +1,3 @@
+>PROKKA_00709
+MAGFTLSRGGSTFLRMELFPGNNTYRAGTGKARGWSLHKDTAGHANKAWKLKDRSGSIRA
+SIYADGKFACDRYSQCAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002588.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002588.fa
new file mode 100644
index 0000000000000000000000000000000000000000..41255d1f406de15eb599943a123ff21025156397
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002588.fa
@@ -0,0 +1,3 @@
+>PROKKA_00751
+MPKKYTPELRERAVRMVLERQAAEGGPRSHSIRAIAPQVGVGEETLRMWCNRHGHEVAPV
+PAGESPAEEIRRLKRELAEARRANEILKAASAFFARELDRPTTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002596.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002596.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9005d3359857e8387916ea4748641fb931054cfa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002596.fa
@@ -0,0 +1,4 @@
+>PROKKA_00801
+MGLAAAPRPSRRIDDGGRQVLDLGGLSAVVEHYGRAHTRTDLTVLVPEAGVLDAVLQRLE
+APAARSSRNEPCGMAPTTGEVGAIPQGSFHGEVRVVPGHGAVVDATLVRAQREALAAAPP
+G
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002599.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002599.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e08e1ab58a5a00834d24b00970a2accf05550e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002599.fa
@@ -0,0 +1,6 @@
+>PROKKA_00815
+MNAALGFIGLGTMGLPMALNLAKGGFDVVGYDAFEGARTAAAEGGIALASSPRDLAERGV
+TAVISMVRDEAQNREVLLGADGVMAARPQGLTVVVMSTLDPDAMNRLAADVEDAGEATVI
+AAAVSGGQSGALEGTLSIMASGPQAAVDAAGPWFAAMGQETFYYGAEPGNSQVAKLANNL
+MLGVVMNGVAEALRFAAAYGLPQDELLRLAQASTGDSWVVRHWDAVRDWTRETALEVLRK
+DLKAAHLQGLEREIPMPFNALASTELIRAWDTLPAAADEETCR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002600.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002600.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6549232c31b640ad3f013f974350fd5273def40f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002600.fa
@@ -0,0 +1,4 @@
+>PROKKA_00816
+MTTHDLTASNPEQTERERFDRGMARMMELVGDGAGTFDHAKLVESYRDVDPELSDYIVSF
+AFGDIYSRTSLSKQQQTLVTISTLVGRGAEPQLKLHINVGFTVGLTREEIVGALIHCIPY
+VGFPHVLNALSLLKEVEAERAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002601.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002601.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ac56aa8a2259e4b9d4b95e08ebe2d86cc98e7fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002601.fa
@@ -0,0 +1,4 @@
+>PROKKA_00818
+MTALASTLPRRGRPRIRTEAGPPAGALAGPLAGALALAAAPVHGVVLVAHSHGLVTTVVL
+LAMTAWCALCGARLLRRRGRTAEAATLRMLLVSAAAMVLAHAAMIAGLPGVGGGHHHGGG
+AADTAGPDVGAARAMLGVIVLELGVGLTTALALRRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002608.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002608.fa
new file mode 100644
index 0000000000000000000000000000000000000000..62ba023544aa480363609d71de503a38ce72edf5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002608.fa
@@ -0,0 +1,4 @@
+>PROKKA_00886
+MTDAAAVLGAFFVAENARDWETYRSFLHPDVEWVLGDRVIRGIDRYVEAMQAAYGDDVRF
+RCEWSHVSESGSLVAALLVDDAGRRSLDVFEFKDGLVWKEHEFLLGRTASEAEPRSLPTQ
+GEPRSTEATEHQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002612.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002612.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30c6d163ee0db760c5c6b1818ce2f75093a85a27
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002612.fa
@@ -0,0 +1,6 @@
+>PROKKA_00965
+MGGVHVRAGREGRGGEHLAGGLAQGEQHVRGGVLVRGAGRRQHGVHEPLDAAAGGGALGR
+ALPRVRLHEGRVQQGLDRHGGALAGVGHAGGEPAAGGVEVADRPARLAQRARDAHRGGPG
+LRRRGGLRRGVGAADGGRGGQRTAVGADGRAQGLEVGGGGRRGGGGGGPADQEGALRLAE
+GEVAVDRRVVGAGGGLAGGRVGRGLAHGASFRDGGCGARPTAAGRGLDSTSGPRRDTVGA
+GVRRPRRGGLSGPAGGAGVWWCPRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002616.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002616.fa
new file mode 100644
index 0000000000000000000000000000000000000000..702cde25a745929369ae89b6ad14d20a10b3ccaa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002616.fa
@@ -0,0 +1,5 @@
+>PROKKA_01050
+MSAAELVRRWESAAQPAPTVVDVGSVLADHYRARPLDNAVFACGHLQSDDELRPDTDKML
+WTITDPVTLLRCARHAFGSLDAYLSHLESEQQEEDEAIQAEDGIERADVAYWSALEGRIP
+EEDHPYGLALTQHALGQRVTAILEVEDGAVTGFKVEGVLGRMVDEHLEGLVGYPAPGSGY
+DEAVPLMRRGDPGDEMFLQHLRQAARFGLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002617.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002617.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b99aecea916ca7e1267ac9a6e55af36fee81d5c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002617.fa
@@ -0,0 +1,3 @@
+>PROKKA_01055
+MNRYQQSRYFQDQEKTRANTASNIEFTGIGGAYSANVKAQNRQSGDQYAEQKGLGRNKIY
+NIPNATPTGQMTRLIVTNDTWTTVTVSINGWYRTN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002618.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002618.fa
new file mode 100644
index 0000000000000000000000000000000000000000..686d7798bdd15c11facfaa240b5de5e49cc0ce89
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002618.fa
@@ -0,0 +1,4 @@
+>PROKKA_01056
+MVDGSYPLYAAAGRSSAGFVVLSALWAGLHAGLIALMSALTALLIRNRVLALLAPAVLLV
+GASIGLELTVGPAAAPLITWVHPGGLLPSNLIAAAIPGLTLGLACGAMAVVLLRRAPQMD
+RFS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002623.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002623.fa
new file mode 100644
index 0000000000000000000000000000000000000000..99e87f724fe601684da4d8e1007ed260b09cc5c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002623.fa
@@ -0,0 +1,9 @@
+>PROKKA_01217
+MTFLQRVRRKAVGDGRLLRQVLTVLSGTTMAQLITIVGMIPLARLYSPTDFGLFAIAQSI
+VLAGTMVAALRYDIAIVLPESQSAARTVHRLASRIILLTCVVLAVILLLAHRVVSEHYGN
+PSFGIWLTVTALIVYAMAQIMNTQNWLIRMKQFGLISQNRVLAAALMLTAQLVCAPLVGG
+FEGLLIGMLVGQVLTLIVLNRRVPELRTSHPVDAPAIREMAVRYKKMPLLNAPNVLVDAV
+RDAGINILIGNIALGSLGQYSLANKATNAPVYLIRGAIAQVFLPLMARARPGELTPLVTR
+LLIRIGLVATPVFLVFYWLAPWLFPLLLGDQWGQAGLIAQALMPWLFMNTFTSPLANVYV
+TTERQGWLFGFAVVYAAAPLIFLTTSTLPLLPRVQVMAWIMAAALMCMLVMTLIITRQFD
+RRGQPAEVTPDMARPTKEPS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002625.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002625.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7befc1d20ece774cd329f23cffdf41c8b0b75624
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002625.fa
@@ -0,0 +1,8 @@
+>PROKKA_01269
+MLAVLRNPTYARLFSAQIIALLGTGLLTVALGLLAYDIAGSDAGAVMGTVMAIKMVAYVL
+VSPVTTALVSRLPARRVLIGADLVRAGVAVSLPFVTEAWQTYVLIFLLQSASATFTPTFQ
+AVIPSVLPDEREYTRALSLSRLAYDLESLVSPLLAAALLTVMAYNNLFFGTVIGFLVSAA
+LVALARFPAIQAPEPAPFLDRLTRGTRAYWARLELRGLLGVNLVVATTTSMVIVNTVVLV
+QADLGRPQQDVALLLAAYGGGSMVVALGLPRVLDAVPDRRVMLAGAAALPVLLLAAVGAM
+SGLDAGAQWAGLLVLWALMGAATAAVLTPSARLLRRNSTERTRPSVFAAQFSLSHACFLL
+TYPLAGLLGARIGLPAVGVVLVGIGAAGLALTVLAWRRAEGQPPVDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002628.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002628.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fbd77c2da1dab868b6ade73b6ead5eafb4ff1f03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002628.fa
@@ -0,0 +1,3 @@
+>PROKKA_01277
+MAVFDVIVNNADRKGDHLLTVPSSHRHGVDHGLTFHVGDKVRTVLWGWLSEELSEEECDG
+VVPVVAGLDGELGRGLAELLSAEGVEAAAERCTRLLDDGRFPTPSGWPPTVPWPVF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002637.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002637.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8bef3edad9bd7e6e349091c9f1955fefa592cb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002637.fa
@@ -0,0 +1,4 @@
+>PROKKA_01323
+MAYEQKTTVTDVPVEEYLATVEPARRQEQGFALLRMFREETGAEAVMWGPSMIGFGHVRF
+TYPTGHSGEMFQVGFSPRKSALSLYGLTTYGSHADLLARLGKHKVGKGCLYINKLEDVDE
+AVLREMIRVGWGDDESFVDSHDGTVIERLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002639.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002639.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5089d44e7d30c790438f5465b2602e7d11be733b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002639.fa
@@ -0,0 +1,5 @@
+>PROKKA_01326
+MALEDIQRHLAWKLQGIPQDGDLLGAAGAPAHLTYWGDLQCPHCRDFVNHDLMELVHQEV
+RAGVVTLRYRPLETATRDRGEFVAQQAAAWAAGRQGRLWEFMETFHLSQQEADSGYVTDR
+FLRAIADEIPELDLERWERDRRTDLTDHLVESERQARAAGVTGSPGLVLEADGRRRGPLR
+PTIHDLLDAVDELLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002641.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002641.fa
new file mode 100644
index 0000000000000000000000000000000000000000..87c43b8f178f75293fd7e73fa01db76cdc0550ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002641.fa
@@ -0,0 +1,3 @@
+>PROKKA_01329
+MDPDRSGQRGPKDFHRRIVRAEDPAHPATEVLRTITEPGSRGSRIRAVEGRAGEQAGPTL
+EH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002648.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002648.fa
new file mode 100644
index 0000000000000000000000000000000000000000..58646d3ed8371b8472d50d12c91fc7c5cd502727
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002648.fa
@@ -0,0 +1,6 @@
+>PROKKA_01466
+MSAPALAVPRSAVAGPRARRRPLAVGAALCLALAGCAAPGVPAGEDPDTLGGRWTELNES
+LDSARSVAVTARWARPAAVVTLAGSLEADGAYRGTSTGAEGAVEAVHADGVTYLRGEGAG
+DALDGVDPGRWLALPGPAQDLVSPAELIAQVRAELPDTLAPEDAAVEGREVTVDGERLEL
+FSGVRLDGAGPVDLYLDARGRLARVARSADATADATAAPSSRSGAAPTSNASPDPAGALL
+PRVESVDFDDWDAVPPVVAPPAADVWDRPGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002656.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002656.fa
new file mode 100644
index 0000000000000000000000000000000000000000..389148ac73b6eb8397e01431abe2e112b895973b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002656.fa
@@ -0,0 +1,5 @@
+>PROKKA_01508
+MTPQKQVHSDILKRLVATSGVIHLSWKGFSIGSLSGRRVLYAWPDRKHLNGLWDVEADAL
+AVIEWNEDETAEWIEDANPVQLFHGRTLEPRPVEESTDRQEPLPNGVDGILEHIAAMAAC
+YSSGLKWNEEDKLKADMMNRPERWAPITVEQVRTKCRALGMRPDDVDTVAGFLQRRKEGR
+RFNVQSSYRTFHFN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002657.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002657.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b99b6ef1416fb8a112a384aa95ff96d2ac6cac1a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002657.fa
@@ -0,0 +1,8 @@
+>PROKKA_01509
+MHLPIRAQGTTLADEQAKILDDEFFLSNPLSHFSSRVSMLLETARSSYEASPENEPEFFN
+ALGLDSADTALKFDTQHRSVQVAIDALSLRHQAAEALTRFIYARVAATPRKGDAKSTYLA
+IADCPNPMIKVIEANKAAHDADPHRFLQLLFPPGIVVEGPVVGAAETAVEWANHAVWLLT
+SDELSINAAHNKLKHGLATSARGDVRIELITTPPNEDGTIPTSAFGEGKSLPLFDRPMLT
+YLSRPPKDLRQGLEAVSLRVDLPVVLAQTWMMANVYAAMFHIAAREHYGKSLPEGVAPFP
+TRVVGRLPEHVIGGRPLGYRSAATLPPDGTTAPRPSGVAFFKQFWPMTVDFESKTQGVVV
+DA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002662.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002662.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d5f1c21754dd3fd9f217cb9417f153b9d2b2a81
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002662.fa
@@ -0,0 +1,9 @@
+>PROKKA_01631
+MSTGSTPSDPSEQRDQSNRTAPSDHPSSRGGGPHAAAAALARLAESPARVGLVRDVRPWG
+GPRVDLRLQDGRVAAVVPHDPAAHAAPIAPHASETDDGLVVEGHGALCVPTLADAHAHLD
+SVRLGLPFRPHTGRPGVWGMMSNDRENWRHAEAPIGERVETALGMMIARGTTHVRTYAQV
+DVDAGLERLEAVLAARERFADAADVEVVAFPQAGLLLEAGSADVLAAAMDAGADVVGGID
+PCQLDRDPVRHLDAVFGLAERYGAPVDVHLHEQGSLGAFSLELIAERVRALGMQGRVTVA
+HAFALGTLPDARRDALLATLAELDVALTTIAPAGAGTLPLDRILQAGVRLGLGEDGQRDY
+WSPYGNADLLDRAWQLAFTQGFRADDDVARCLEVAAVGGRSVRDPAAPRVSADRPASART
+IAAGDAADLLLVPAETLASAVMDRPAERTVIHRGRLVAAGEPHAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002664.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002664.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a1b223d3cd7173106cbf7a3983d7cb6ea1f4846d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002664.fa
@@ -0,0 +1,4 @@
+>PROKKA_01735
+MTGPAVTVTGPDEPAPGMTAAQEEDAHWEHLAALAQAAGVMIRAGALRALPLETEASASL
+EALAARGRDRAEALTVLLGLPEESLGTGPPEDALSAEAVVGLQWALAERVGVDPDAWSTP
+RPWARAWAARSSRSRSGGTSPPT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002666.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002666.fa
new file mode 100644
index 0000000000000000000000000000000000000000..42a85fe0d80faded192d54f9fe03dc3db262159d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002666.fa
@@ -0,0 +1,9 @@
+>PROKKA_01784
+MTAAPDAAQVADGGAALAARQRRVVRTLAASQVFSGLGNGSALAVGSVLAVELTGNAALG
+GTTTMMISAAGALAALPLARLALARGRRTALTVAYLVAALGAACMLAAPGIGGFGLLLAG
+SFGVGLGAAGNLQARFAATDLATPARRGRDLGLVVWSITIGAVAGPNLIGPGAVLARAVG
+LADTAGVFLFSVAGMLAAVAILQAGLRPDPLALRREAGLGGVASPQPPRLRAGVGAVVGD
+PRIRVGVAAVVVGHAVMVGVMAMTPVHLSRTHGAGAGGSDTLVIIGVVISLHIAGMYALS
+PVWGWAADRWGRLAATAAGFAGLLAATLVGAVGAASTGAVTAALVLLGLGWGAVTVAGSA
+WVSEVATGPRRVLVQGVTDSGMGAAAAVTAGLSGLVLARWGFTGLTVAAGLLSAALLVWV
+LRARWRYENADEVSPISDIVTS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002668.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002668.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5320eab96839371ec355768cdb772bdaa8ce707c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002668.fa
@@ -0,0 +1,2 @@
+>PROKKA_01809
+MTALASLASPAALAPLAAFPAPPPGTASRSAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002670.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002670.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7fa02bd5cdb2b0810306a7b8350e46835ccb7bc0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002670.fa
@@ -0,0 +1,11 @@
+>PROKKA_01843
+MIAEDVDRAREAVEQALAAVAAPRWQDVPGGALLPDLLVQAETLSRTVAALQTALAGHLA
+EAYEHEADRQEVLGIPPGKGPHRDAADCLRDTVRIDRRTAQRRLRRAAATRPRRDFVTAP
+LADPALPEVAAVLSEGAADEAACDAVIETLTRARTDLALAAVPQDEADALLAAGESLLAA
+QLHHADLDGMRRLCARWRQHLDAVVLPDSGIPTEAELRAAQGLFHRGRRRGLHRWDLHLT
+DTQHEVLQTVAAAATNPRARGAGPSGQVDAPAGSPDLDPRTRGQRQADTLVSALQAALAL
+ATPGVLPATAGHRPQVLVTIDHETLLRRVRTASGTAAVLSEAEFTGPIDPREIRRIACDA
+EIIPAVLGGEGEILALGRSRRLFTRAQRRAVTARDGGCAAPGCTLPASWCEIHHIGHWED
+GGRTDVDNGVLLCSHHHHAVHAGWWTVAVVAGIPWFTPARHLDPRPDAPGGTGTTGSTAR
+RRPRAPGERHRRRRRRRRNRQGQWNRRTRRDGQDGQVGQVGQGQTEPVRPGPAAPPRPPV
+RRLPPPWTVLSPPWRPPGRRRPRHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002674.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002674.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5dd4998e9c1781ea80e42df158b52b317b5358a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002674.fa
@@ -0,0 +1,7 @@
+>PROKKA_01862
+MLRANDSGNADGTGVLVTSPDADCIPVSDPADPSALHWLDVATTTRETNSLMETGPLLSM
+EELPATLALMDGARGYTEYIWSSGITEPWMWHAYTGPDKEGTVRTRIALLDFMGPEQYEA
+TSGARYAAPGLDGDALRPTDWALLRAHGLGGDDEDGVRQGPRPSRPASRTRARRRPVTTT
+PRTTTPTRSPRPWRPATAPRGGSPPSARPRRACWSASARDSAWSDPGCSHLVARTTRRLQ
+IARTASREHNPAGERWEAASTSPDGGHRSPVAAVVACAGRALIPSGSTSSVRGEGDTPTR
+RGGARDFRHRKRGTRVLHRLWTSGGGLGVSRMAVRIARGARMWTVWGGTGDP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002675.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002675.fa
new file mode 100644
index 0000000000000000000000000000000000000000..072dae06a95632d2fa32e8307713853dad32ca8c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002675.fa
@@ -0,0 +1,4 @@
+>PROKKA_01864
+MPSVLFVLSASGHWTLKDGTRYETGFWAEEFVVPHDVFADAGWDVAVATPGGVAPTVDQT
+SLGLTGGAPWKTARLKRDLERLAPVLDRPVDLASVDEAGHDVVFYPGGHGPLAERILADA
+EARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002676.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002676.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f56beb8c030b65e90e8f1b49cf09f4581262d1c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002676.fa
@@ -0,0 +1,2 @@
+>PROKKA_01881
+MAHGGVIRAAVGLLLRHEGEAFAALERIDNARAAVLQGAFATDTGAEGWGDWTLEGYGI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002677.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002677.fa
new file mode 100644
index 0000000000000000000000000000000000000000..931bf083946a86b2ce7dbe6bee9886aecc991aaf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002677.fa
@@ -0,0 +1,3 @@
+>PROKKA_01909
+MGAVFAAAMLAVGGTALATPPPAEAVTTVVITNGNFHNCTSRMNSEMKLFRMEGYTVRIA
+YKCKWFADARRWEGTFYASR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002683.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002683.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4a814d145e4f025446923266a090b0b337b4816
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002683.fa
@@ -0,0 +1,3 @@
+>PROKKA_01942
+MTTAAAPFYVENLRRAREARTARAAERTAARLEDLEDLAAARVAREAAARRAGFPSVGAL
+ERFCYRVGRHDLIKSLPLQRSAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002684.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002684.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d48defec824c9397a8e1096a139c9d1b7fe96242
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002684.fa
@@ -0,0 +1,3 @@
+>PROKKA_01943
+MTAAVAQTVEVPAVLTTSDLAARWQVSEEWVQDAAKAGRIPGFKVGRAWRFRVDAVLAHE
+EAEQAALSPANVFALAPGAVARRARRATA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002685.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002685.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0059ba4c249a0d58e523661ff91065aedd0d8205
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002685.fa
@@ -0,0 +1,3 @@
+>PROKKA_01944
+MSVHPIRLQIPFADTSLVFGFDADAERDVRLLLRFARARASHGAGGFWLEYGWDTGESQM
+VWIDPAHMPTARFDVTATPVADQGREDDMSRHLARTHHVYLTAKGWQSDTHELAVDN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002690.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002690.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc644c2ba5b9ce7891e101db4cd3d5b949fa1f9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002690.fa
@@ -0,0 +1,3 @@
+>PROKKA_01950
+MNDPKAKAAYHGVPCDGRCCRQNRHLGVCPHGRVCAYHLNEDARQAREERERDQIADLER
+AARMTRRRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002692.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002692.fa
new file mode 100644
index 0000000000000000000000000000000000000000..39ac17e6dca2bf4d72ffe7329203732a79f5a42d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002692.fa
@@ -0,0 +1,3 @@
+>PROKKA_01952
+MSYHHINEDGTAVVCTAQESAWCRSRPNCDTEEWNEHGCAEHDREHALTPGHECWQARNV
+NAWGGPYPDDQPDLRPGAPVTLTYEGEGIVTWDYVNGARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002693.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002693.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0613c1e9dcf1cd4f3ce5546c0448ce9a4569f42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002693.fa
@@ -0,0 +1,4 @@
+>PROKKA_01953
+MSITREAAAALADLHAANPTMQDVAGTWQEDAVAYVAALWDAEVGRAAKEGTFLPAFASH
+TAGMRRLIAAVVAAAREDLAEAERAQHGALAAVLNRVEFQQARAAIGELPDDVAAWQTTE
+HHALITTITRELEDPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002696.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002696.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f0b3a16f6a5855221cbdeaa1f101cc14faae0ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002696.fa
@@ -0,0 +1,9 @@
+>PROKKA_01956
+MPWLKVSDASAMHPIALAAMEAEDADERLVNELFGYVARCAVMSAQHEQDYVVTLATARV
+TAGGDARFKVLAAAAERAGYWTRTTVKDASGAERPAFRLVEEKDLFHMLLKKERAWETQR
+RADVANPELTVPVRLRDGDGCRWCGKSVAWRDRKSGRGATYDHVKPGQGAASPEDLVVAC
+RACNGARKDEENTSFSRTLMAPPFRPLYGPDTLAFLAEHDVVPEQQDTATAAERQSQRET
+APTPTTAAPATAAGSTARTATAAPRQGVRETADGQERRRGAQVRDVDGQAADAAAAHAQR
+EADARRAEAERERRLDAWLADHGISVAPAPATALSPLDVEEADWAPSEGDAGPPGGPDLQ
+IPADRQAEGSGFPGTGRDGSGREGPGLDVSGTGGARDGSGLDGGSAGSGRRRRRRGRRGG
+RGRGGEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002697.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002697.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc50552027fca6802f10d540082e51b8902dae5c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002697.fa
@@ -0,0 +1,3 @@
+>PROKKA_01957
+MRQDEYVRMMAAGMSEDQLQRGVERLARSLGWLAYHTHDSRRSSPGFPDLVLVRGDRVLF
+RELKTEKGRATPAQKTWLAALTAAGMDAGLWRPVQWFDRTIERELA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002698.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002698.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc345357481d2c9cf3d3b103eef4be175f4a5d3d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002698.fa
@@ -0,0 +1,3 @@
+>PROKKA_01958
+MTNWDDADQVNDELLGRMERPDGCTCDLEYTTDYKGRILHIYWSLELTCHHHYPRTAAQL
+ERLNSCPKQEGEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002699.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002699.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7fd19005b583f34e1212fae4f04777bb3cd0125b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002699.fa
@@ -0,0 +1,5 @@
+>PROKKA_01959
+MSELMELVDRLTVETRQILHTDAGPAVVRAAPLLEQLQDAVHPSGEGGGGSSGSVGSGAP
+LDVTALALLCQVKDEAIHLSWLARSTPGVLTLRPGLGGFTLAERIRWTASALDGRAAEAE
+MLATVRGWTASIERLFDPPRVVALRGAECPACGIARTPVLNRDLDEFVDVPALTIVQGQT
+PRASCAECGAQWHGPEVVDLAVQLGAPPSVAHLLAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002700.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002700.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f98330c2dd2fb5452cbf6484da5c6df4c3216086
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002700.fa
@@ -0,0 +1,3 @@
+>PROKKA_01960
+MATSRTGTSEYKRWRSYVLREAERSGQHRCPYCGVTLDYRTGRLPHSAEPDHVTAWSAGG
+TNTVDNGRAICRRCNQSKGARAAPRPRAVQAAAPLRVSRRH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002701.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002701.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc50289bbbc79968ffdb143513fe0c1b6396c205
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002701.fa
@@ -0,0 +1,4 @@
+>PROKKA_01961
+MATANRWVRWALRPRGGRLTKVPLTVHGRHASSTRAATWTRRPAAAASRVGAGLGYVLGD
+GVGCYDLDGALDRGRLKDWARDALAAIPEPALFVEVSQSGTGLHVFVVAPPGPGTVTRHA
+GGAVERYTTGRYIAMTGVPFDVPDGLLRWATPLDAALVAARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002705.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002705.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0e644295459b85fd65ba5570c0140348e082ad6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002705.fa
@@ -0,0 +1,9 @@
+>PROKKA_01965
+MAVLNTQEETLFLRMRDQVRRHQPTNRHRENLFNARKQLQKIGFSVPESMRSFAATVGWP
+EKAVMVPARRLKPTGFVSSREEELADELNAHLDSGYAAAVEQYAIEASVRHGCSFVFATP
+GDQTAGDPDVVLSARSALEASAIVDRRTLRTIAGLEATDEAGVWLMHVPGEVLLVDTRTG
+EHVVRERYRAAPGEVGVVPYVWDRSLDRPFGRSRITNPVIDLSGQAVRIMLRQEVQAEHF
+SSPQRVLSGAREEAFTDETGQRRPMWQVATGAIWGIPDFFDEEIGEWRRAELTQMAAASM
+QPHTDHLRTVAMMFAGETSIPISQLGIVHDNPSSADAIRQHESAMVDLVQAQIPSYMASR
+KALGRLVLAVAHRGLSPATNTALAHVHARFADPGTITRAALADRAQKFAAAYPELRGSSV
+ALRAWGFDDVEVRELQDHLQRAESAGLVRQLLEAGPGVGMSGHAEP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002707.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002707.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5dded2b3b78a60177fc6e6692df8613064586064
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002707.fa
@@ -0,0 +1,5 @@
+>PROKKA_01967
+MRRSFNPLLAGVLRFIEAGAQHGAAATPPPSPATVAAQTTPKSEPATGDADGDQGESPTE
+AGLSEAGKKAIKAERTARRTAEERVRELEAELAAQKNQEPATGSTQRNQEPATGAAPEAA
+TAAGADEDLRAKLRTAEQENWRHRALADHAIPRELVELLAGESEEEVRARAALLSRHVTA
+APLDPVPKSGVQTDASLPGSIAEYRRRIVKPNS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002708.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002708.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3067efe4c8531cf1bb2736a3154546c353b343d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002708.fa
@@ -0,0 +1,3 @@
+>PROKKA_01968
+MPMLHRQNIGSGRKNWLGSAHGVNHAQTATLDVSTFTAAADHPEGRIPSGTPVNAADRTA
+VVKWDPAAGGGALGFLIDDVDVVDGEAVPCAVLLHGAVVVEELPVEFTVPTAPTAFIFE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002710.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002710.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9471f04ec40b186cd79960da9dccaeb5c61a8bb1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002710.fa
@@ -0,0 +1,3 @@
+>PROKKA_01970
+MIVTHTTTVLRDGEPVVLLAGQHVPAWAEDLVGAHLLAESAAPAEPVEGAEPAEPVEGAE
+PAEPVEGAEPGPADAGEPKPPVAVAVVDAEAEKPAPRRRAPRKKPAEDLEPDFTRPPTEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002713.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002713.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6677141dd48a67e130832bb0e5c751771c35997d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002713.fa
@@ -0,0 +1,3 @@
+>PROKKA_01973
+MTTAGLRRVPGVRRYRALADGVRGLGTSSVVAEASLSAAERIAARARSTGEGEYQAYPTS
+VRAGWANEERAGARVVETRRVPSDARQRVLVTALRGSTTGGGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002725.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002725.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b52cfd11be9a7c0c51146068fc580c64a598497a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002725.fa
@@ -0,0 +1,4 @@
+>PROKKA_01985
+MPDRILRTSAGVLGGLIIILGLTYAWLGITWLISPTPTRLAGIEWAPIGAHTVGIWWIAG
+GLVALIGGAWSARPVAAGVGAFAAILTPAVVAGLFLVSVWHGNDRGLITAGSYLPYALLA
+AWVTWRSGRGSEDTARDMAATRHDSQEGRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002727.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002727.fa
new file mode 100644
index 0000000000000000000000000000000000000000..806dc6a613ae29fd4a89137c9d1a23737977038f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002727.fa
@@ -0,0 +1,7 @@
+>PROKKA_01987
+MPTPFLTGLGRVLTTAGVTWEGVPGWETRTGFASGYRDVYGATVHTTETHDATFAKGGDA
+PTLEWVVDADGSRRGAHTYALLIGRSGKVYLIAAGPGWQAGHGSWPSKLGPNPGIPDDQA
+NFHTVGVSMDANESQYPPTEAQLVSLVKVLAALRAEWAPDRFDVMMHGEWSPARRTDPTR
+VPGGWDAIRKAVAAGAWPVQPKPTPPTPAATSSRPAPATGTYTVRPGDTLGGIAKAHGTT
+WQALAKLNALADPHLIEVGQRLRVPALPTHTVAKGEGLWGIARQHGLTVDQLANLNGLTR
+TSTIHPGQTLRLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002728.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002728.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77e0d9a7ea71737673b2a6f0672c85b5ed198ccb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002728.fa
@@ -0,0 +1,3 @@
+>PROKKA_01988
+MTKNAILRYFTYDHLTRSPLRDVSKLFHDLAGTLDAQLPDGPEKSTALRKLLESKDAAVR
+SALDIEGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002731.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002731.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0364847385a642110fa04ac0029ff4814ee0148d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002731.fa
@@ -0,0 +1,3 @@
+>PROKKA_02025
+MRVTDGLSVEEALVHEALPLRQAVPVDRITVSAGLALPTVLASLSRLQRAGLARRVEDRW
+RRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002733.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002733.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3233a83915b2781743fe6b8a2a455624265f879b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002733.fa
@@ -0,0 +1,9 @@
+>PROKKA_02047
+MVRAAIAGEKDAARLLDQVVDLVASALARIAGSDETYRRELFDRLTVDPSGWAVPWDRLR
+APASTLSVLYNFQPFADTGSSVASKRLRVFGHTSDVIACSFLHHKKVDPTIGMISRPYLA
+RRRYLEMRPSWASWHAFADFAVQARDQADAWIAAGTRYERLYTRANWAPSHYAGALIHEA
+HPELIWTAEFSDPLSLDVQGKRRGDLLDRSDPMLARLTAPVEADFGRIPDEHFSIFGLAE
+ILPYALADSILFTNEHQMAEMLDHIYSPALRERVQGRAEVSHHPTLAPEYYDARPVTYEV
+DPTMVNVAYFGEFYVTRGITDITLAMAMLPQHIRDRIRLHVFTNFVPEGGLATRPPGFSK
+AQFDALVRRAQDGVGAHGMEHLVRFNASLPYLDFLAVTRQFDYLVVNDAQSGSRHTRNPF
+LPSKWSDYRGSQAEVWALVEDGSMLSTMPTALQTPLGDPAAARDVLWDRVEAKQEERR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002734.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002734.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e7a6c3409a0073368228117b3fc16bc66b39748b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002734.fa
@@ -0,0 +1,4 @@
+>PROKKA_02048
+MKPGPSLEKALYVGCLAAMSIIGVAVAVLGLLGQFRLVVILLGLGAVVASVLIPVHARRM
+RRFMGVAIRRAGGRGRAAAPTSSPGPAASVEVGRETMAALTRINRQLVSLREETMGGQLR
+PVSGAGSTDAADDRSDSSMAVAEALVGVRHELSVLRAEVAHLAEAPRGGRQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002738.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002738.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d36ad9ab63225d31459dbe89e9f9b9a2f1c88459
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002738.fa
@@ -0,0 +1,9 @@
+>PROKKA_02102
+MADRGHYELPHSGHNGIELVGTFAYEDAILRALPRLPADGASVEAQFTVDLVPEPDNPHD
+RRAVSVRHRGEVLGYLSRDLAADYHLPVKRILASGARLQTGARVFAYLSWDDKPEVRVYV
+GLPAPDALTPLNDGYPATTAVLPYGRTYQVTKEDQHFEHLFDYVPRSGQGPVILTLHKSE
+AMLRNGTVRRTVEVRLDAEKAGELTAATSAHYLPVIEHAEALGRVVGVWGTITGSGLAAE
+LTIKGAKSSELTDEWLREMPIFPHLVPEAHSYEVPDAYQGEPKTKGRSRAMGGHSAARLR
+EQLDQRFVSTSPAELDTTPSPSTPSPEKKPGKPQPPANPTPVPLNRDVTRLGIGTGPRTP
+IYYTVKGKEVFVDDRDRSSAGKHPRRTAWLLIAGLAVLGLILSGVPGIGPFLTLLTLLLV
+LISGPDQLRKAKVLDIDPHGTGHPSRDWRDRERGDVGEENQDHDTEDGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002739.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002739.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e807c1f42984976ef674537195036d0ccf7a5e51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002739.fa
@@ -0,0 +1,4 @@
+>PROKKA_02105
+MFHPWRALRALTHVVVVWVRPHPAAPAATNGIDVVWLDPRLTQVERRWVLAHELVHLEHS
+HRGCQPAAVEHAVRAEAARRLITLDALLASIPWSEHLAVLADELWVTEQVLLDRIAGLTP
+TERQAIAARAEVHHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002741.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002741.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e99a587b104c306fb89b4470c548a1df07fe7c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002741.fa
@@ -0,0 +1,4 @@
+>PROKKA_02166
+MHSESLDPSPVPDRHGSDPDRPDPLVVVDGAEGRVVPAPTAAPSSTHDAGGDPASGGEGV
+DPAAAEPPTLVSVGVLADWLGLSPTEPLPEVPEAPAYAQPGRCRPRRLVLLDVRFRATGG
+GADHEAYLRGHLPGAVYVSPAQPTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002746.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002746.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e15df0e0aa2a9f614764d74660d37d72f0fbc5f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002746.fa
@@ -0,0 +1,3 @@
+>PROKKA_02208
+MTTDTRLVHIITLTGQDYDDAVRVAETEGGSVDAVARHLAQWDHGAEADDAALLWPEDMP
+TRADLGCQPHQLHAARVGGLGYLVQIDHGLRMYALYRPTLTQEAAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002751.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002751.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb8a447d2f917cd26b96fe59d113fc273a42589f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002751.fa
@@ -0,0 +1,5 @@
+>PROKKA_02218
+MSGQKGQVVGYARVSTADQNLDRQLEALGGADRIFEEKASAKDRERPVLAEMLAYVREGD
+TVVVKSPDRLARSTRDLLDLLSELKAKGVAVRFTDSPALDTGTAQGTFMLTVLGAVAELE
+RELIAERRAEGIALAKKAGKYDRGPKLSAEQIAVARQRVTEGVPKAVVARDLGVSRQTLY
+DALAGRGRYAATA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002753.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002753.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1aff820fbf478e0eceb9acbe7f22f89e8701399a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002753.fa
@@ -0,0 +1,9 @@
+>PROKKA_02225
+MPRRGWDSVTVPGAVSGWRALSDRFGALPFERLGAAAVAHAEDGWIVPPIVAQDWGRAAT
+VLGELPEFAATFLPGGAAPREGERVRMPDHAVTLREILATGGESFYTGPLAARIVAHAEA
+GGALSAQDLAAHEVDWADPRSVSWGGHELYEIPPNSQGLAACVAAAVLEVLGGQHRNPDS
+ADGVHLQVEAMKQALAVLHAEVADPDWMRLGPSELLEPERIAALAARVDPERAGAAVSAP
+PTAGGTIYLSVGDRSGMMVSLIQSNYDGFGSGLVVPGTGIALHDRGAGFSLVPGHPNEVG
+GGKRPLNTIIPGFLTAGGEPVAAFGVMGGPMQPQGHVRVMHRLLVGQDVQSALDAPRWFV
+EGSGELKLEAGWGGDVARRLGDLGHPVTRTGPGDRTYGGGQVVRRLPGGDYAGGSDPRKD
+GHAVAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002759.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002759.fa
new file mode 100644
index 0000000000000000000000000000000000000000..57b2b87581e596105e304dc99edb838d555d7525
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002759.fa
@@ -0,0 +1,3 @@
+>PROKKA_02298
+MATGDTVAVGQELAVVEAMKMEHPVTAAVAGVVTVHVAEGDSVAAQALIAAVAPAGADES
+AEPAPHEASAQNA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002764.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002764.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4b290885a082acdf9b448ed1017cc01f13008f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002764.fa
@@ -0,0 +1,3 @@
+>PROKKA_02346
+MPKKYTPELRERAVRMVLERQAAEGGPRSHSIRAIAPQVGVGEETLRMWCNRHGHEVAPV
+PAGESPAEEIRRLKRELAEARRANEILKAASAFFARELDRPTTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002765.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002765.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9554e3a0967f762f53566648faf6410b5209a1b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002765.fa
@@ -0,0 +1,3 @@
+>PROKKA_02363
+MKVELLHIADCPNTGIAEANARAALDALGLGAVPVELVTIGTEAEAANTGFGGSPTILVD
+GIDLFPTTLVHSLACRVYVAENGFAGAPAATQIDEALRDRMQGGESDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002769.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002769.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b380457fa7b4327bb4d0339291af3f8a0183f936
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002769.fa
@@ -0,0 +1,6 @@
+>PROKKA_02460
+MPVEPRICITSGGDEIRLRSYINHAIYAREHGLDYRLETGIDPQIVTKFDYKVAILRRLL
+PRYDWLVWMDDDAFFTDFEADNLRRLISEAERDDISLVIAEGPTEPNGFWSRINTGVMLL
+RNDETAHSIVESTSTADLATVRAWWDDDRDGLFTHGDQDQMWWAIQTGGHADRVRIVGHR
+ELNSRGHYYEDSLTDAFVMHFTGYPDKELGIARFADRFDIGQEIVPEPLLDKYHVRVRSP
+LRGARRAWRERSVDTLAAVKYRLRPHKDRIRHVAGFLPPAVRRRWPLGHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002770.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002770.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c9275a238795af91050a7f92480c247c266586ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002770.fa
@@ -0,0 +1,6 @@
+>PROKKA_02492
+MAVGGEHRLGLAGTCRHHYRDRLVFFGGPVSQDRVQRAELRTAEADARFGLLDETEPPRQ
+RRCYGVAVLGFLLVSAWTLAEPPQLVAVDVLSLDESHVGTPSSQVHEVPLQLHYYLVWTP
+NVVARFAQSCVVGCRLWRRRELPVRSWPDGDRGSGLFHHTPRPQNAPSRRRPRVRQRPLR
+ASCPARTAAQLLDAQAHPDRDDAPRHLPVQRSDAQSCDVCRTAAPAHRPARRWRTSQPAQ
+PDSGRSNGFKDGANSPRPGHADPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002774.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002774.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6294a5ec414cbeced4217345d1156449415c5fce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002774.fa
@@ -0,0 +1,22 @@
+>PROKKA_02499
+MPVLRSLGPAYQEDLHGRNAAVLLDVLTDKSATAAKNIALAGHYGSGKSSVILGVQDGLD
+ERKIKWVNLSLSTLGIDDTKRARIQQDGSLAPLTNLIQKEIVKQLLYRKPPSDMPGSRYF
+RIDSFKPWPALMWGGVVAVGFFVIAVLLGLVSRIQDVAPASVINSHSWVAWATVGALGAF
+VGGVWFLGLRVLQNRIRVESVSAGGAAVKLSAKENSYFDEYLDEIVYFFQRTKTKVAIFE
+DLDRFKDPHIFETLRELNTVLNNSEQIKSRPIQFVYAVRDSIFEELQVDAESDGEGTKTS
+ALHASALESAPSANRTKFFDLVVPMVPFITHRSARDLLAAEFAKADHQPSTALVNLVGAH
+LTDMRVIRNIRNEYEIYRASVLGENGLKGLTADRLFAMMVYKNLHLEDFEAIRLGTSKID
+EAHRAFHKMVEYQTRHQAMRSKTTQNRVRTKALWDKHAQAAGERLQEVLPIVYRATGRGG
+KPVLRYQSQDYQLSDLTSGDFWKSLYENRDSVHLLRPGYGGIELSFDELISLTGNGTDGL
+DDAVDADVAHLQRDSRVALETKDFVMKATMAELIARTDLVMPTTDGDERNLDSIVSELLS
+PLGRDLLTKGHIDENFTLYCSDYHDIAISVSAMNFILHCVQSDRAAPHFHFDEASSIEAV
+EREMGSRFLDGESVFNVEVFDYYLPARPERLDKAMDKLAVRSGDDSSFLDAYLIDGKSRD
+VLISRLAPRWDGVFIHLAEKAPLELDVVATLVDAAITCAAKDTEYEASDQVAEFVSEHYA
+QMQAFVGETDAAKATDVMALLRRLGAQIGDLGVLGQTQRQAAVAAGLYPVTRMNLSVALD
+ESTGLALDVMNAADDSVYRHVLSNLDDYLDVLQDHEVTVDSPDAFVAVLGDVADAAEFAV
+RTVAARAADSCEVVDLTDLDDGAWGHVVSAGRFAPTVWNVSQFVSKFGVNEELIENLGTL
+NLTKAEEVDEEPRLGLAYALANSGALDSAATVRLLGQLNLPDGLDPERLSDVGLALLPTL
+LEKDLVPDTADTYALVSDRPFAFREEYFAASKQLASYVCELELSSDDLARVMRSRRLAPP
+VKRAIAHDVEFITDRLSRQSVIAFCEWASKGNDVSVELLVKLAEAGAPAEHVLGLLEPYL
+PNIELGLLDQILLGLGDDYEPLTRTGHHRPRLKDRAGTEELLKALQSRGRVSSFGREKLI
+GGIRVNMRH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002776.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002776.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6cc41c7ec972378fb176da90572eecc43a176b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002776.fa
@@ -0,0 +1,4 @@
+>PROKKA_02508
+MSPRRPRVPRVDPATGAPRRAAQDAAVEPTTAPQEPAAEPRGADSRPAPSEDAGTPAAPS
+PSAAPGTGQGDGSAPSAEPERPATAEVIDLQRAQDRRQGGQAAPEHAAGSHAAGSHAAGT
+QPVEDRRAGVNAARPAASSPARPAARRPRPAPRRALS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002778.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002778.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d57c6d0d232afb1eb2140e606fb88999f5ed265
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002778.fa
@@ -0,0 +1,3 @@
+>PROKKA_02579
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+ADASVDTMVAARRDALQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002783.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002783.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b668331e94973aefcbffe0c5c827cf3d549a12c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002783.fa
@@ -0,0 +1,4 @@
+>PROKKA_02618
+MTEKLLASAQARTRECTRAVLATVKELEASQSAITLKGVAARAGVSRNFIYTTPDVLAAV
+QKAAERQRPKLPSEPAPTAPSSDASLRTRLAAALAHNECLQQEIDRLTATNQALVEEVIE
+LQNPAPKNVTSIRKRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002784.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002784.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3fec05b68d862912fb1f0d1353b0e8b84ed4391b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002784.fa
@@ -0,0 +1,9 @@
+>PROKKA_02619
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+CHVDVVPTIKLSDGRQVIVNWKDNAFEDTNPQGFTDWLKQQDDITRGNLRKCVRLLKFIR
+DSKDSFDIPSVILTLLLGKQVTKEGADERYADVPTTLVTLLTDLHLYLQRLPDDGTMPPI
+HLPKCPGPSLNHRWDDPTKIRNFRLVVGRYAAWASTAHAAADSKAILDGWQTLFGKDFSP
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+LAVLGFVPKGSRIEFEFRSDAPGPYRVYWKVRNFGSEVGNQWRGHLMEGGYSPHHQEPSA
+ITGKHWIQAYAVQDGKVIAWAHCAVPIR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002785.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002785.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cd25923e6189ff929600524b7a58f61ef91403a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002785.fa
@@ -0,0 +1,8 @@
+>PROKKA_02620
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+SRHTTVLRFVGDVRGNAVDITKAAAAGAVLLSGDRYPKFPLSADDFGFEIDIRAFDETSP
+DYWQRAAAHIDRIIDHKLRDEVTAGRVDHVSVFAFALLPLLVHLGSKLDDTFATDVYDNH
+RVTRSWEWPDSEAAARFETSFPADPSSADEAVFVLNVSGSISDAEVPAALADLPQWTLAL
+AGATPGPGPLRSAADLAAFSAASRGLLAEVERRAKHTRRLHVLAALPLSAAIELGRVHDA
+HVHPRLAVYHRADGGYKQALELS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002786.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002786.fa
new file mode 100644
index 0000000000000000000000000000000000000000..daa74c9568ac4934ec3fe08cff53e6a8db33b731
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002786.fa
@@ -0,0 +1,4 @@
+>PROKKA_02633
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002790.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002790.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6ed494eb1a99e90edb0902952cb36bd6c0952b75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002790.fa
@@ -0,0 +1,9 @@
+>PROKKA_02649
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+YNATALEEAGVTDPDFSTWDSVEQIAAQVTAHTGKPSIDVSCVIKGGNWCMQGLFKSNGA
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+GGFMQAAEAGGWKLDAAPMPAFDGQEAVPTNSGSALFVLSDDPAKQRAGWELIKFMTSDR
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002798.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002798.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b056f8b414472f5ea854fa5a78b79768fea7ecd5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002798.fa
@@ -0,0 +1,6 @@
+>PROKKA_02663
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+GDLRIEWRDINVFGPASERAARASYAAALQGALWEYHDALFEDGERRSESELSEEALVAL
+AGELGLDTEQFAADLGSEETAQVIAANQQFGFDLGATSTPIFILGGQPIVGAQPTEVFQE
+AFQSALDAAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002800.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002800.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f21263444ffb9521b794699ea5b0da0e8cda2704
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002800.fa
@@ -0,0 +1,4 @@
+>PROKKA_02665
+MKAADGRSGDLLRLGALEAQVMDVLWDHGPATVREVIEHLPSDPAYTTIATVLTNLDRKR
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+ERRDRGDMP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002804.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002804.fa
new file mode 100644
index 0000000000000000000000000000000000000000..476bf05ab088bf10da3d4f6c9536ee69b6a161fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002804.fa
@@ -0,0 +1,3 @@
+>PROKKA_02677
+MAIVVRIDVELARRKMPVGEFAERVGITPANVAVLKNGRAKAVRLSTLERMCEVLGCQPG
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002809.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002809.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f48e019a2d1eed551a932f59ca7dff06cdb3aac8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002809.fa
@@ -0,0 +1,7 @@
+>PROKKA_00055
+MDFHRPSLEELRAAAALPSHTAAGLTHEVILTEIAAGRMKPEWSCIATNDDGDVIGRAMW
+WGRDSQEPIALDLWDVAPGTSEPGEVLTGLLTHGGVLVEAPDRRALLPHTLRVPVGWGDQ
+PEVAENVRLKMQVASANGLGRVNERLQFQWDWGETVPPNPARLRFTPASDEVFMRLFADA
+AAGSLDVMTARELEQTTAADLARDEIAYYLSCPGDRSWWRVAQTHDGEIIGLAIPSATPT
+NRNVGYLAVLPQHRGHGYVDEILAYITRFQIEDRARRITATTDAVNTPMVAAFTRAGYTL
+VEVRIDLEQS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002812.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002812.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c2046b86575ee7997204c85cca87e1a18422aa7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002812.fa
@@ -0,0 +1,4 @@
+>PROKKA_00084
+MVNRTAKRAGWDYDALAFLMGFLGAAAGGFAVAFLQLLGAEGLDAFLGLTVLFGIGPVHA
+LVAALVSPPLLAGLRRVHPRWLHVLIAGGVQAGIAAGVASLWLQNADARHLPGYVLTSGV
+LLAVAWAWALRRSAWRPAGGPADGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002813.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002813.fa
new file mode 100644
index 0000000000000000000000000000000000000000..843fc223d69aaa3f1781ba50366af63dc4ae6885
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002813.fa
@@ -0,0 +1,3 @@
+>PROKKA_00086
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002816.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002816.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a31fba9575db721041fe852680b3a434ba002135
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002816.fa
@@ -0,0 +1,9 @@
+>PROKKA_00184
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+FAVLGVPAGLAGLLKPVRESLSMLPQALLTPVVLRARRRTRVFAAGAAVQAAAVAVMAAV
+AAVGHGAGAGVVILAALAVFSLGRCLCSIASKDVQGRTVPKGQRGQLTGWSTTASGLVAI
+TLGLGIRLLGGDALSAGRLAGLLAGGALLWVGVALVYLRIREPREDPEESGGAHDDAGAA
+AVLRRSWALLRDDRPFRSFVTVRSMLLVTSLSPPFLVMLALQAGTDALAGLGGFVIASGV
+ASLIGGRLFGRAADRSSRRLMGSTAGAASAVLVAALALTSWPGLPASAAGAVLVAAYFLV
+TLLHTGVRTGRKTYLVDMASGDTRTLYTAVSNTAMGVILLVVGAVSSAIAAVTVPGALLF
+LAVLGVGGVVGGARLPEVSQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002817.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002817.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35fb17e427facb13fede728845bce753ccbc728f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002817.fa
@@ -0,0 +1,3 @@
+>PROKKA_00202
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002820.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002820.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d9d8df119d0a3ff8e96c9abe10e9f3e2c465254
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002820.fa
@@ -0,0 +1,2 @@
+>PROKKA_00208
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002831.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002831.fa
new file mode 100644
index 0000000000000000000000000000000000000000..db02a7760b2b6ee114cbb8e1b9860587143836c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002831.fa
@@ -0,0 +1,9 @@
+>PROKKA_00269
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+TLGVNAHYSAYESLAVMTGRNVTWTDWDAVDTAPARQVVPVDRWTAPAGLPEHGTVSRVG
+IPATDARLAPRDAVVYLPPAYFAEERPALPVMILMAGVPGEPPDWFSAGHAAETMDAYAA
+AHHGLAPIVLSVDANGGGALTNRLCWDGPDARVETYLTQDVPAWIGRELQTDRDRTHWAI
+GGLSNGATCALQTVARTPDGFGTVLVFSGELHPSLGTEERTIAEGFGGVRAAYAANDPLS
+LFAAAQRGEGPGADGAYRGVAGVVSVGRSDAYVGMPVPQELVDAGRAAGMDLTLREYPGG
+HTWTVWSRAFADQLPWAAGRMGLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002839.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002839.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5bed4757b5fa42ac55488f674b9fa67fd3b7290
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002839.fa
@@ -0,0 +1,5 @@
+>PROKKA_00318
+MPPSATRATVEGHLSRVATPIFEGVAAGVEMADRIMRTVPNRDNYPAFRSMATRIGAREH
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+SQSPLPFTLSGDPSTQEAIDEIILLLLWDMTTDGDIQVRVVHPLEPGVYGRAVPVDMEFQ
+VQPGGTLFSRLSYEGDDQNENLFAHIDRADNEGDGMNGLFGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002840.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002840.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2936247190373b5a30e5523012d90ef21d3eb7d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002840.fa
@@ -0,0 +1,2 @@
+>PROKKA_00319
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002841.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002841.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a5480492c66a65546a794aadecaec09832e554bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002841.fa
@@ -0,0 +1,8 @@
+>PROKKA_00322
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+GGPKTARAFGPATWAIKPEIDTIALAKAHVYGNRVLLHTATETVAYDPQGQEVWRLTRDS
+QTPPAIVPMSPTVIGLVTTGSSDNSGLAQSKPQTQVQVVDLADGSTVAEHTLDAVTNTAN
+PTAPGLSLASPDGGSEVITPDGAIRTLEDVDMAGAVGDTVITSKDEVIGTDTWSSEAFWD
+EPQYTNAAVAAANTTDLLLIEGQFGVEKTNVLVDAATGTEYARPKCGAGAFYKPMVSSPN
+GDWNVSYGAVISPDHKVTCIGGGEDEKAVDLIAVTDQGRAFGTTTEGPTLLVDARPGAEP
+TTEELAPGTVLPSGVVGGNLAVHWDPSTGVLSANPIQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002842.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002842.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ffeb1ef2576bb290bba9f499e920187479e03f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002842.fa
@@ -0,0 +1,3 @@
+>PROKKA_00328
+MFTHGSGFVKPPAPNGRPESHLFASRKPDSHNSSDTRNEACAECLSACPEYPTCSTCNQS
+TFHAHVDNPSSEIVKCRGNNAPITYTGKQSTINGNPTHINALKIDPTGVVPVESKNNA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002843.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002843.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ccf2d973f16bdf607456f6779fb317e06532f7b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002843.fa
@@ -0,0 +1,3 @@
+>PROKKA_00331
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002844.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002844.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6fc9aba8cbb262b0d35f9ca1a66c9695a4f15132
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002844.fa
@@ -0,0 +1,3 @@
+>PROKKA_00336
+MTFALNEPEYVAVIDSVDGDLGTVELKARAVTTEVDELLGICLDSDVTSALTQFRDDALD
+KALRALTESARAVVDSGRAVATSYREFDAEVAKRATAAELGK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002853.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002853.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a37b5dd940aed9c66c28c1823658a122b2734a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002853.fa
@@ -0,0 +1,6 @@
+>PROKKA_00365
+MEGIRNTTHTPALGRDDARTDGGGPLSWVEGRPASERPPGGWGPSRAPADGDVPAGDRTL
+WEDGRAPGQRGRWWVWLLRHLAAAVACGAALVITAGAVMAELFAVADAAAPYGSLPLLAA
+AAAAVGWALMLVVLLALLIVGVFGGWGLGGTLFRASGPGVWSVWDGEALTEAMGAMAAAS
+TGLGRSSSESAAQATRSPRWRRFLRWTGHAVRWVLVALLVLAAGAAAVLGAMGPSPTTLV
+VWGSAAGLVVAAVLVGCGVIGLEPGPDRSPHTRW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002855.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002855.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86a1930d04d15db28638074a4749c83ed4b99717
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002855.fa
@@ -0,0 +1,10 @@
+>PROKKA_00407
+MLKVSDVFVPGKLPKYTYNPRENSKIEDQLKDYLDELGAILAISGPTKTGKTVLVSRLVQ
+NRIWIDGGLVGSIEDFYRLVVDRAGEFTTIEVAGADEYTATDETSGEANLLGAGKFAAKD
+ATGLSTTNSKSASVNRPASQVATDALRVSGHVLVIDDFHYIEPAVQTAIIRFLKPLVMND
+VPVVLMSTFHRVGDAVRAESDMNGRLATIKIDFWSTEELMQIASLGFEKLKIIDDPTVSS
+ILAENSFGSPQLMQTFCRELCKFNGIKTQQEHPVPLAPPEQWRTFFEAAIDVEESAAWFE
+TFLAGTKLRGKKRNIYDLVNGQRHDKYGVILSGFNSTLPPLTFTSARLMEEIQVLVAGQA
+PRSSDVSAGLSNISKMAFGDSEVVDETDLSEGVEEGLTTSTSLSSLDHAPASSPLSADSR
+SNLRFANAKKRPVLEYLEKGNTSSVYILDPFFAFYVKWHAPQALSEHAKLRNVAAMDSLE
+S
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002856.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002856.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1263cffc8c8f9c101811e8084fcaad9e856c111f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002856.fa
@@ -0,0 +1,6 @@
+>PROKKA_00411
+MTVDAGVLVGENGRVRGIRASSWTPERQRRVERLLRVVEAAALLLFGVCAAVLLLTEPRL
+SGTIRSVSVEGVGARLSRYGLLFAAAVITYVPRRWKWALPGYAVSALFVVGMVKMLEGAP
+SEGFPGLQVFRTDLPWLIGLLLVPQVAGVARRAGLSVRRRYASALAWTAFVEGAGAGRND
+CGCVKNRVVQNGAQETRVLLQRFDGTRRSGQVWGVVEPSECIEVDAARAVVARTDWRNAL
+SWAALDRWGRRLPGREEAQRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002857.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002857.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f6de2c49cf1f9c838e15966da1aedc9b0ef5001b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002857.fa
@@ -0,0 +1,5 @@
+>PROKKA_00414
+MSQRPACPYLPLPRATTLRDALVYTRASMSRLPDVVHGSLPLRRLMEAARPVLTAATSLL
+PLQDVLAAAAGAVLALSALLWAVLFLHRLLLCRGWHGHLVYTTDGRTAFLTIRSTSQGWE
+LSDHVATRSAKGDGRGLREALAPALRNAADAAGAPILVTAANRTLADLYRQEEPELREVG
+TTLLGRVRLVRPPRRAILPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002866.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002866.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c88323b751ad72b620baa00ede17abff08bee7d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002866.fa
@@ -0,0 +1,5 @@
+>PROKKA_00470
+MKKTATGLTLAAALSLTAFAAAPAQADEPIFENCAEARAAGYGNFTSEHATFRHLNDIDN
+DGVVCEGPNSPYGPNGPAVAKPSPKPAARPQASLPSHVTQPDAIDNQYTYPDCKDVFAAG
+LANLPKSSKYYHADLDADLDGIGCEVNGDDAWVPAAIKAKYAPATAARAEESAAAEAPQV
+TVVPEGTPKTGPEGVALAPFALGAVALAGVAGAGVVARRRQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002867.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002867.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5e429363e4f40a0784b5e81c3a9796e6f1f3b3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002867.fa
@@ -0,0 +1,4 @@
+>PROKKA_00471
+MPDDVLPASRPTRVRVPSLGIDSSLIELGLQDDRTVEVPPTAPGSPAGWYENSPTPGSRG
+PAVLLGHVSDTEDGTGVFGHLRDIQPGALVEVDRADGTTAVFRVDRAVSYDRGGFPKDEV
+YGNTDDAQLRLITCDSYNAWTGHWDNNFVAFATLVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002871.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002871.fa
new file mode 100644
index 0000000000000000000000000000000000000000..031396b88f016e10a36e708adba23d828931c1b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002871.fa
@@ -0,0 +1,5 @@
+>PROKKA_00529
+MTAALERGRPLEGAPARPATPHRRARCTPPWPRPGVLALAAVLAALLALAGAAVGHSAAG
+SLPAGLLGGPHTSDADWTLTGILGRNLGAALLVFGGVVTGGALTAVTLPLVGVWVGATLR
+LALDAAGWEGAVGATVLYAPLEFAGVLLAAVAGLVPLAAALLRPRDADVVPGPLSRYLGA
+LPSACLLIGCALLLITAAGVVEHLVVSGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002882.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002882.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76db4985b126b9e6e073f92def0ea612c088f08a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002882.fa
@@ -0,0 +1,6 @@
+>PROKKA_00624
+MNTDRDACAYLEEILREVTPDEEARKKAASHRASLEDWLKKDLDIIRMRETGSWHHGTAI
+SRHSDVDYFVTMRGSRPSASWSALEELRSSLALGVSSAIVRTDRPAVNLMYFDSGPSVEI
+TPAYFRDTDDYDIPDPGGTGWIQSNPAVHLDYVNDAQKKTSSRAKSLIRLVKTWKARNSV
+PLSSFYLEMRVAKYALSNPTIIYDWDLRSFFKSLEGDGLREMNDPTNYGRRISTGASSLV
+DTIAAKYDIEQAVRSSSLALKAAQDGNPSLGVAHWRRLFGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002883.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002883.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d67e12b643a5b8936435e779c0ca42dcfc35146
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002883.fa
@@ -0,0 +1,13 @@
+>PROKKA_00629
+MAHTTTPPSPRGGKRLTIADVPHMRERYAASNPLPPEEVAAGSNKKFTWSCKAGPDHTWE
+AQANSIRMSKRGGCPFCAGKRPSVTNRLDVLFPDLAAEWDQELNEGPPAVVAGSEKKVWW
+RCRAADHAWQANIRNRTVLRAGCPRCAAEKSSKTRSVPLPGRELTAVAPDVAASWHPTRN
+GTLQPDEVAAFSNVPRWWQCPAGHEWEISPAGRLSKGGAGCPYCSGRLATAETSLEVQRP
+DLTLEWHPTKNAPRTPRDVKPGTSATVWWICSAGHEYESRIANRAYLGRGCPYCSGQKIG
+YGNDLATKAPLVAAEWDHERNGSLTPADVTTGVQRRFWWSCTQGHSWRTTVASRVALGTG
+CPECGAGWRRSRPEIALQFELAHLLPAAVVGDGHVQTADKDFRVDVLCPELKIAVEYDGN
+HWHMDTFERDLAKTQALVEAGWVTVRVRQNPLPLTGRHDVPCENGDPAVYPMTVRLMTSL
+LEEAAAAPTDHPIHAHLDELRLRLETYVDGGTARAVEEAERETRAHHVDRPKRDPFAPPP
+RPKPGRSLAELNPAIAAEWHPSKNGGLTPADVANARNASAWWLCSLCGAEWEAVVGQRTR
+RQTLGCPDCGKARAGAARSRPQPGLSLADLRPDLAAQWHPTRNAPLTPHDVRPGSHKRVW
+WRSPGGQEWESSVYNRTSKRPSSEVHGDAGPDSPDSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002884.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002884.fa
new file mode 100644
index 0000000000000000000000000000000000000000..19a9e0385d3a2abad05aeafdffc40893ddb699e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002884.fa
@@ -0,0 +1,5 @@
+>PROKKA_00632
+MTHQPPAEPAIIPSDTTHDQTADRKRARQWLKTLNVSPNPELVEGLIPLVSLYPKKSVLG
+FYAGRLLKKGKLPTEEAVLKLLWGQLEQIIYSIKALESRTGRDPFITPEQETEILQWVDN
+FWAQHGEGPLWSELAENFHWSRTQQNRLIHYLAARGLVTFSFAPRSLKTVRGATTIPSLE
+GPGSGS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002888.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002888.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b7944ad5e853b4339c95652ecdf4cbbf71441c6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002888.fa
@@ -0,0 +1,4 @@
+>PROKKA_00653
+MSTRTTQQTVEDFFSAFGAGDLDTVKNLFAPTINFTVHGSPAVPWAGTRHTRDELDTFFP
+AFAALGPATEYTIHQIVVDGDHAVALGHNEFPVLATGKSFSNDFALHFTVQDGQITGYQM
+YEDTYAVDQAFTPTN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002892.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002892.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f177231986b136ad5976b0c75a2a3da6fe88fcb0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002892.fa
@@ -0,0 +1,5 @@
+>PROKKA_00680
+MSTPDELADEVADVRSLNALAEAWRTAPDGSRRFVPNFDPRSGGTSSRVLVLMQSPGPQT
+IAAAHTAICSEDNPGPTAAAFRAARIESGLARNDYLRWNLIPWEILGRVRPVDIDEGRHA
+LETLLKVLPVLDAIVTYGTAALNGVMRHLTLDEHPRLVPVIAAPHPSPANGRHRAEQQRR
+SVQALRLAALTHRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002897.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002897.fa
new file mode 100644
index 0000000000000000000000000000000000000000..705420a5c9cf5e5b28238fe66da860446836d066
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002897.fa
@@ -0,0 +1,4 @@
+>PROKKA_00691
+MAVFYSFHYDRDVHRVQLIEQMGALEGQPILNHQEWETVKSGGDTAIKEWISDKMKWKSA
+VIVLIGKETASREWVHYEIQKAWDDKKPLLGIRIHGLSSMGSVDSSGPNPFDKISSVSGV
+PIFDPTQTDWTGKIDSKATYNHLKDHLTTWATQGKTRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002900.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002900.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dabc76354b2ceebe0a76e59d072de1e306955c03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002900.fa
@@ -0,0 +1,3 @@
+>PROKKA_00704
+MPRTISVANTGEWLTRIAVGDAIGITAEATTHNHRAPEVVYLPIEDAPPVTVALTWPGQR
+RSHPQVGVVATCAQDYFTRLIDIGSPPRLLSTGADGQLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002901.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002901.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7fc9a48a1580b0dc7da4419c5e164f7e505410d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002901.fa
@@ -0,0 +1,4 @@
+>PROKKA_00707
+MPRFSRLTPETAVGASRDLLGDLVERHGQVGDMVSTMAHSPAVLGGYLDLSKAMRRAKLD
+RKVSELVSIAVQSKQGCGMCLASHISAARSLGVSDDEIALAQQGTAMTSPVAAMIALGLQ
+VYREPTSITDEQIDELRGYGYSDREISDVVGVVSLNILTGAFNLVAGLTPGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002906.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002906.fa
new file mode 100644
index 0000000000000000000000000000000000000000..559085c6d18d318527023caf2ca37ec05e02d419
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002906.fa
@@ -0,0 +1,7 @@
+>PROKKA_00719
+MKAGGRLALYGAGLVVAFGGAFGLAGAVIPDSFAAAWAEGSGVNAHGEGHGDAAQETAEP
+ALNGVSASADGFVLSPVQAPTAAGEDGDLSFQILDESGEPVTEYTTAHEKDLHLIAVRTD
+GAGFQHVHPELDTSTGTWSVPWTWDEAGTYRVYADFTPAGEEAEGITLTRAIEVAGDFTP
+VETEAQPTDEVDGYTVSLNGDLTAGTSSELTISVERDGQPVTTLEPYLGAFGHLVALREG
+DLAYLHVHAEGDQPQAGDTAGPDIGFAAEAPTADRYLLYLDFQVDGQVHTAEFVIDAEHG
+DGTKTDDSHSDGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002909.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002909.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6bdad33d8fcd89ef35df2e90d4eee5affe258af5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002909.fa
@@ -0,0 +1,6 @@
+>PROKKA_00739
+MRRPSAPASRPSPAPEGSWLSRLWAAHAAFLVTGGVLLAVVVAFTSLAEEVYDSVTEGDG
+VPAVDHPALQAAISLRGPVLTGLAQFLAYAGDTPGAVAVGLVLLGLLTLARREATPAVVL
+LGGMAGAVLITVVGKSHVGRLRPPVDVALPPIVTSPSFPSGHTLNATVLMALTVYLVAIT
+PRLSLCGTHRRAVTAAAVVAGCYAVLMGLSRVYLAAHWLTDVAAGWTVGLAWAAAVVLAH
+RVWLTVQDVRRSRAGTPAAPAAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002910.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002910.fa
new file mode 100644
index 0000000000000000000000000000000000000000..025f0378222c4d4b65956f72e853f80daa0027f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002910.fa
@@ -0,0 +1,6 @@
+>PROKKA_00755
+MRSAPAALTAAALALSGALSLAGCGTDGAASGGSGGTDVASTAASSSEAPWAGRAQVDAV
+ARAVEEGTGAQMTVLDVYSRAEYRDAMERHLATVYGDEVALSQARDASQACVDANRAAAQ
+SEAESGARGLAGAGSARGQSSTDTAGYVNLTVTDFPDVEAARRSWDRHAQVRADCAGQTG
+WLGVVDARGADWPGGEAVVYEKRIPGPDGAEVRMRTAHVLDGRRQYVLNRRLDASEAGTM
+GGGDDVGILHRVAAALPAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002912.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002912.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ef37a0b70e96bb86fd81f359bd468fcde6c9ab6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002912.fa
@@ -0,0 +1,5 @@
+>PROKKA_00782
+MTGAERGGAVAAHPVPTHPEAVPGDRATLRWAVPAGLLGMVGPVGDGPAPLEALRADGTL
+RALVAEPAALRLTVGEGRTWRAEGARVRAALQEALALLAAGEATCAPEAPASVVGGPGGG
+GKARAVARAGASADSDAVLRAAVEQVLAGPAGEYLRSHGGTARILGVEDGEVELALGGTC
+HACPARGFTLQMRLEAEIRRLCPDVRAVRTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002915.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002915.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d41d998246382652b1ebacaeac4a80b53095e680
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002915.fa
@@ -0,0 +1,13 @@
+>PROKKA_00824
+MSTHPHPGDGAGIAASAAPQPAPGSPSSPAPTAPSSADRSGGHAAPGHRPATAERARTGM
+LMLAIGALGVVFGDIGTSPLYALQTLFSADHNAVTPSFAHVTGAISLVLWSLILIVTLTY
+VLNVLRADHHGEGGVLSLATLVRRHYDEATTPDSDTDVAQDAAAPGPERRRRGQWAFTAG
+LIGCSFFFGDSVITPAISVMSAVEGVAVAVPSLEHWIIPASLLILIVLYGLQRFGTGGVG
+MLFGPVMAAWFATLAVLGVGPLLDRPDILVALSPLPGLMFALQQPMVALVAMGAVVLAVT
+GAEALYADIGHFGRLPISRDWLFFVLPALALNYLGQGALILDDPGAVANPFFRLAPDWFA
+LPLTILAIAATVIASQAVITGAYSVTRQAMRLGYLPPLAVRHTSGKEAGQVYLPLVNWIL
+LAAVVLVVLMFRSSVALATAYGLAVTVTMIITTTLVLVHMATTWRRPLWQPVLLGTLVLP
+LELSFLAGNLVKVFEGGWLPLTIGGLVLGTMTVWHRGRVAVSHRWSRTEADLETFMAKAA
+HHVETGDLRRVPGHAVYLAPSARLAPAALRINLRANRGVHEKITLVHVVTEEQPYVAEAE
+RCTVREVGPLSGVHQAVIRVGFFDALDIPGTLRAHAAALGLTNRDLVQAVYVLSRSRYLT
+PRGHGPKTWGTRAFVSLSRLADQPVWQYGLPVDHTLEVGSRVRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002920.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002920.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4f172bc7029425be2abf75dfbaf1432c613353a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002920.fa
@@ -0,0 +1,4 @@
+>PROKKA_00904
+MDMHETPLPGIGVRRELDTTSGRRIGVVTHRDGQTDLILSDRDDPDACAASIPLAADEAA
+ALGALLAGPRLVAQLEEEHADLPGVSTRQLILPHESPYAGEELGSTRMRTRTGVSIVAVV
+RAGVTHPSPGPDFLLEGGDLVIVVGTGEGVRQAEKLLTV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002926.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002926.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0133e4384c1e0e8e510065945018d4276c0d6af8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002926.fa
@@ -0,0 +1,3 @@
+>PROKKA_00940
+MSVRQPRIYTIPCDRRGDFLDRWQSTAQPLMETLGFRFVRTWEGTPDPVHRPHCRGCWAP
+RSG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002927.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002927.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1fc78572066081020ea56a8917f147e8b7e99566
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002927.fa
@@ -0,0 +1,3 @@
+>PROKKA_00941
+MTSAQVASPTPLSPGHRFTWANGGTTIRSRVEVVRPGHDLTWTGIALWLVAVHRNVIETL
+PDGQARLTSTESMAGVAAALLMPEEKLQQQLQAFVEAIAAEAERRSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002930.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002930.fa
new file mode 100644
index 0000000000000000000000000000000000000000..53183d714a2b38b829ebba357176d6424441f624
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002930.fa
@@ -0,0 +1,5 @@
+>PROKKA_00973
+MTTAPTWIDAVLALVLLLALASGLRRGLALTLGSALGLLAGVAAAVLFAVPLGGLVPDPA
+WRPLAVVAAGVLLVVLGQGIGLRIGAAVRRALGRGALSRADGLLGGVAGLAVAAVVIALA
+APVARPLLPADAADEAGRSRVVAAAEHLTPEPVRQAAADLGTQARLFVAEAIAPVLPEPG
+LGGREAVRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002933.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002933.fa
new file mode 100644
index 0000000000000000000000000000000000000000..57203f2d2290896b0d108b825fc312abb470b08a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002933.fa
@@ -0,0 +1,7 @@
+>PROKKA_01014
+MSIDQNTADTTTPLATTGVRGRSRRRRTAVGALGAAGALAAVGMASAPAQAATVDASVLQ
+SIQACESGGDYTAVNPASGASGAYQFLDSTWATLAAAQGYASAADAPASVQDAAAQELYA
+QEGTTPWEASQSCWSDAASVAAMSTSTSSTTVSDAAVAQADVATPVETVAQVEPAAGAAD
+EAEADTAAGADAAAEEAAGEETDAGGTAPTAAPDAAASGEQAPAPSEPAPEPAPQGDQTG
+RQPAERPAEQGRGTAEQAEQGRGTADQREQRGQDVEQREGRTGGERQGAAPETGGDAGHQ
+EADAAC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002937.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002937.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49e648e20f15b9a3282761801c5ba407450fe5fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002937.fa
@@ -0,0 +1,7 @@
+>PROKKA_01056
+MALFTVLLPVLTVLSVLAIVIGTALSVRPTTTSAALLARVRSHGAATAVTALLLGSISGF
+AGLAAEARPEGPEWTWDAGEWHGVPVFLDAVWLALALALLPAILVAAVTVGAQRSVPAPQ
+GRVRRAVLTPRTAASLVPRGPALPGVGIGLALGATLVLLWAEPSVPRLFPSDGAQEPEGY
+TPLAAGAQLAPWILGALVADLGAAAIGLRAIAHRPPIIGLTAAQDRAARTVAAHRLVRTV
+AWMLWLLTLGAWGSVLLSRTQRDLLHAVFPGHPAALDARPGLGWIGTVDAWTGLATLAVA
+LVLLLWRPPALGELRTGPGIDRARTAETVRTETA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002938.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002938.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a1bfbe2b7d22172b889c47ba78e0d599fa30ced4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002938.fa
@@ -0,0 +1,8 @@
+>PROKKA_01081
+MGAVTEQTPDAPHPSPAPPSATGGPAPAAPPVGPLTVRPITEAEHVEVLRRHPGASFLQN
+PRWARVKTDWSGQSLGFEADGRLVGAALVLGRRLPVPGRTPLLGRSFLAYVAEGPVLDAG
+VDVVEALAALVAELHAQGAFLVRVAPPGVVRRWDADTVRKALPDPAHRMLTDLEPAEEHA
+DALELERRLREAGWRAPEVLPGFSAGQPMFQARIPLEGLDEEGVLARMSGSSRKRTRRSL
+RNDLDVVVGGPERLDEWEALQDETAERDGFTGRRKEYFARLMDELGGSELADVTYYLAEY
+QGDPVAAAFHFRQGHVCWRPYSASSQKERKRDAPRLLEFEQIRQGIADGCHWLDLGGVPG
+SVDSEDRITGLTEFKTTQGADIVQTHGEWDFPLHKTLAHAFGLYMSRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002941.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002941.fa
new file mode 100644
index 0000000000000000000000000000000000000000..255c5ecea8f69a00e292736ce2852cd8b2b42034
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002941.fa
@@ -0,0 +1,2 @@
+>PROKKA_01184
+MSLAPADAFIGWLPQEHERVPGETVAGYIARFTGRLKAELVKNI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002944.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002944.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4231111fbb66dbc0b1b692e9af3fc8f22bdb5931
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002944.fa
@@ -0,0 +1,3 @@
+>PROKKA_01216
+MLEIADGMVTFTPDSPSAAPGWSVPARQLTLGRAGVRFPGSFVVRGAEAEDIMLEVSTSE
+GARWREAGDARDLPDRSTHREVQQILVGWGARSVRPRPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002945.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002945.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b362d9a40bf659c2f3f2daa87ddde4b251f38850
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002945.fa
@@ -0,0 +1,4 @@
+>PROKKA_01220
+MQPQDLIADAAHRALDLAAPVLDGLSAEAAHTRPGGAGNSIAWLLWHAARQMDVQTVALR
+GGTTVWEAGGWARRLGVERDAQDFGLGDTAEDVSALRVTDVPALGEHLEACVDALVTWTS
+SLTTEDLGEVVDTYEGEPVTRGVRIVSMIDDAAVHVGQAAYARGLVDGWRFAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002946.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002946.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b62457ef7af1c3dcae1660b56768c56e02378182
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002946.fa
@@ -0,0 +1,3 @@
+>PROKKA_01223
+MRRITTWLLATLAGLVLLFSYHTSTDPNASATASQGTSVHMVSGASFTSAAYEQSLQSAL
+DRAHL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002948.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002948.fa
new file mode 100644
index 0000000000000000000000000000000000000000..525c404980a0938ed2d8cb274d838f991430fb65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002948.fa
@@ -0,0 +1,8 @@
+>PROKKA_01232
+MTENQHPDDPRRPEDTGGGAVPGESARHGVEEGAPEAGAAGWPDKPPSAGWPDHTPVTGT
+GHGSSAYTPGGDGAVPGPYEQPSYGQPAYGQDAGTQQAGAHGQPQGAYGADAYGAGAQHP
+GSYEQQGPYGQPTGAYGQQQPGAYGAYGQPLGGYGAYGQQPGVYVTGAGAPRPASNGLAI
+AALVCGVIALLLSFLPFIGLVSVLIGAAAVITGVLGLRRGQSKGMSIAGIVTGALGLLIS
+IAVTALTAAAVSAAVQEGGPALSSIGASLSSEANAPHEVELRATVDQGDATVNYSIGGSS
+SDQDITAEQISVTDSVTGSETLSISVTEDVTDTGSQNVTCEILVDGRSVAKETGTSSAYC
+NAGYGDY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002959.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002959.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89b42ce11a609ae0871f45ae7ceda7e80867c4fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002959.fa
@@ -0,0 +1,4 @@
+>PROKKA_01708
+MPRALIVVWALLIVPVLFCLVVVGGSAVAHASSSAGPATLRSALPLGAALLTAVAGTAAA
+RHARAPAARSVLTVAVALLLLAVAAPLVLSLFAAGTEEWCEGQPGGRGGAPITSEADVPL
+LCR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002961.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002961.fa
new file mode 100644
index 0000000000000000000000000000000000000000..094bea0faa36487b0a8610201d641185d20cb1fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002961.fa
@@ -0,0 +1,8 @@
+>PROKKA_01733
+MSETHSTSTAPSRRGVLAGGALAAAGVIAGTAAQAVPAEARGGRHPQGASMPLAFGATRR
+MKIVQFNDTQGGHAADRRTIEFMGKVLDQEKPDFALINGDVIDGSPTTDVQVKQGLNNFV
+SPMESRGVKWAVTFGNHDEDSVEEHGTSMTEDRLLEFVRQYKHNVNPPKMDGVPGHTNAQ
+ILVRGSRGAAPAFAIWLLDSGRYASEADTHGQSTDGLKSYDWIRPAQIRWYEDASAATEA
+RFGRRTPGLMFCHIPTFEHEMMWHASQAAEEASDHAEAVRRHRITGVKHEDVYHGLVNSG
+VYASVKERGEVKGIYCGHDHINTYTGDYYGVELGYAPGTGFDPYGLNDGTWDQHTLRGAR
+VFELDERNASVYAGATRIVWARDLGIDMNPEGQPLATPVPFPPYVKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002965.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002965.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c6b6f3d7cf41101c702829aac6e0d4fa5eab85f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002965.fa
@@ -0,0 +1,10 @@
+>PROKKA_01768
+MAVTQWPIEMAELSSLVLDPRNVRVRAGRGDGLAHADDEHAEQAIAKYMVEAEDLFDLMR
+DILRDGYLDNEIPVVVRDADKFIVAEGNRRTTALKIIANPKLLGNPMSLRVERMKARYPD
+HDSPTSIRVMIAPTWEAAQPLLARLHTGQPKKSWIREQQAIFYHAQLSDEVTVDDLRVRY
+PSEASTIPKKIRMGEMREVIRRLKYDDSSLRDFVMNSELKMTTFEYAYTPKKLHSALGLE
+FTKDGLLVSKDISDGQRRGLIYLLGRFKDKSLNTRSPELIAKNATEHEEFSKLLRGIVEG
+TPLEASTEDEGATKDHTNNQDGEPGEASGERNSAAPDDISRDEGRHRGTSETDEASTSGD
+ATASRGPNRGDTKSRLNMEGFEYQGTSPGMRRRFEELRRLDVRDFPNATHDLLRTVLECS
+IKDYFQSKGQPLPPGKTIGACIGELAREFQGNPKMTALINSINRKGRLTAEQYAGTTPSL
+NASNHELDHFAVGPDVHAAWDRIQPILKEIVGTKKQS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002974.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002974.fa
new file mode 100644
index 0000000000000000000000000000000000000000..32c59a91f1d8530163e9339eedb4c79cebfedeec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002974.fa
@@ -0,0 +1,5 @@
+>PROKKA_01786
+MFWWVHLLGMDTSDRSSRRRLVLIAAGSVTALVCGVGIYGLATGPRTPTSTPGTSPTITT
+SPSPSATSTAKPSASGAPLVPPVASSADPEQFARNVATTLFAWDTTTGLLPLDYTSAILA
+VGDPSGTEQAGLATDVAAYLPSRTAWQDLREYGTSQHLTIARAYIPDQWGEAVAQAPEGQ
+LAPGTVAYTIEGTRHRTGTWNGEPVASAHKVEFTVFVVCAPTYDTCHLLRLSQLDNPLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002978.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002978.fa
new file mode 100644
index 0000000000000000000000000000000000000000..494069f8384beaf5bd731d70bdc088a83247e637
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002978.fa
@@ -0,0 +1,6 @@
+>PROKKA_01797
+MATFVDPVADAAEAYEGLRGLAHATRAFEDPADTYRVLGEVSGSVRLLRQVLDQLSRAHA
+EHRDIAFTDDRVPAEAVALAAADELHQAADGLDEVADRVMRAHEASGRIAWHTHTSLEPE
+RSQRWVNVVFLQGTEADEVLELIDVQGVQAGIAHLAQWDFGDETTGAAFVNGEVYHELPA
+GQWDCTFEADGYVLTYNPQMGYVGLVREHPDTAPDPSHDGDVVAARDAFSGVTSEPSRRA
+AAGTDWFAPKAGGAAASSSVGRSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002981.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002981.fa
new file mode 100644
index 0000000000000000000000000000000000000000..243cd9cc022031ba7c7b6562295da22bc9d14bd8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002981.fa
@@ -0,0 +1,4 @@
+>PROKKA_01801
+MAIRTQESLSGFIASDPQLTYTERGDARFYARYGQENFQREEDGTFTKLEPSFGNLVLYR
+ATAERAFQRFTKGDQFVAEGYAHDYTYERDGQRIAGEEFVAKKIGHDTARTRYDVDRTPR
+QALERQAAGQAFEPPQHHQATPATDSLSM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002983.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002983.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f50f900cd72b99dbebc7fb3cca6ca05c17eca06f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002983.fa
@@ -0,0 +1,10 @@
+>PROKKA_01804
+MAGQFCFCGDVGRGIDAGVYEDAGGGLLGCVGGVLFVVDGDAGEQGAVEDASFGWVALVV
+ELVEVDEEFGELVQACSGVGVGVGEVVEPSGDLIEAGADAVLFAFEEVEGDRVGVVSLDE
+FEAFGFELVALGGQELAFVLARSFELIEHVVEDLPDVLRLGLGQGIALVGAFDLRFGAFG
+KDRGAGAVGGLAASSGAGEVLVAVPGLVAGAFDHELGSAGAVQRAFEVVVVLLGSFAAGV
+VGVEVGLDAQPGLGVDEGLVGAVVGDAAEGDGALVVGVGQDLVQSGGGDWFGRLRGGGPG
+GQATGCEFLGQARQGPVPGGVGGERETDEVGAFGVDLDLAGLASSGVGGADVEVAQRRFG
+GGATDRGLLGHAFEDFLGQVQRVELGHGGQDAVHQHPRGGLVDVLSDRHQTDVRIPQRGV
+DHGVIEPVAGEAVDLVDDAVPHRMRGRVVEHLLERASLGGLGGLAGLDELLDDDRTELFG
+LALRGFALGRDRQTLFQPVAGGLILGRDPQVADRRHLPLSPGRCGVWAWCGAGEASKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002987.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002987.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86332a4d7032bc509121fa0ebfbbccc3d1375f6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002987.fa
@@ -0,0 +1,3 @@
+>PROKKA_01830
+MLFVDAIVVKVRDGQVRNTPFYVVMGVTVHGERDILGIWAGDGAEGARFWLQVFSELKMN
+RPGFVRGS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002990.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002990.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8c0e22e659dd19285844852249c4337e3100eee4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002990.fa
@@ -0,0 +1,4 @@
+>PROKKA_01855
+MNSLPLHPLMVHLPVILIPLTVLMALPAVLSRRWFQWSAPLTLAFSLAAAVGSVLTAATG
+EQLAASDGEASALLWQHAQLGEKTRNLAMLLFLLLLVWTALSWHRSPAALRRIGERIPAL
+HLVLAVLVLLVGVAEVVVAVQAGHAGAQLVWQGEGSGTQSGGGLGTGGGRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002996.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002996.fa
new file mode 100644
index 0000000000000000000000000000000000000000..789861492ff03a04687bd3585785c9558ac0f4d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002996.fa
@@ -0,0 +1,6 @@
+>PROKKA_01943
+MKKITRSLASVAAALGLAGAGLVAAPAAQAADLTCSGIISGRTMTGDITVPGGATCTIRS
+STVTADYVYVAPNATLITENSSVSGFISVERGATLRATEGSLGDVLADSQKLIRIHGTSV
+GSLNVSQGGTVTTTRMRVRDDAYFHGMGGTVSHSWGRFSNYVSQYGSARNRFMIRSSVVG
+ADVSVQQSGHVLVGRNTVYGNIFVHDNRGTIYIEGNRADLYLSCDGNRYQPTGGNNTAWD
+KWGQCAAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002998.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002998.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92f11cf374d398e9c68c3eb42ab00ca6bdc75228
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002998.fa
@@ -0,0 +1,13 @@
+>PROKKA_01979
+MALTIMSRVPDAQPYRDEDLDGRIGAAGLAGATLEHGLLRFHTHESGSEAARLLAFHFPP
+GFTEGWVPFAVDWRGRQYCRVRQDGVDSAVRADPGLFAASSVVDFEVFMDTVLTDPGAAR
+VLGAEDCAAALAARGISDLPFDQCLGYMLPPFAGGEDHSSNILDVPVNPYWAAMADMKNQ
+WQHRQPGAHAIAVAARDGGLTLVFDTDQDPEHSPGAGTRAERLVVTSPHGPAVYNHGLAR
+ELTDEQAREAAEAVREAFGTPDAAAPFLMDWRARCYAVERVDGRDVVVRSCPVTMTRTPV
+AEADGFRDRLAGNPALLDLFGEAEKSLLCARLRLTEIPAGDVLVPPAPPSVAGPEADDPA
+TFRLQSASVAWWLAGNLARLAREAGPERRLQGYVLTPEGRLGLQTAPADGPTPPPRPSED
+TAGLPPVRFAPRFAALAETGVVQTAQDDDAAPDKDAGDAQMAIAWYGLAGRVYNAGLFRF
+LGAEGVAQAAGHLRESFGGQAAEAVPVIVDWLGRYAVREVVEGQSMLVSYDAASGQREEL
+SRFEDGLEQILVTPVARELFDEAGFRRALDTLGLVRIGQGRCVGVKRPLFLGGDESPENW
+EDDSLDVHWSWHGRVFAQARAMPEGARIQRVEPLEDGRPLIHYTLPDGRTGDGLSGLHDG
+GAPGVSEAAAARQDGSGPKQEKGFFGRMFKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003007.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003007.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b1004c336129589ec9bb1472d777ada267f587fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003007.fa
@@ -0,0 +1,2 @@
+>PROKKA_02173
+MSDQQSPEAKNSDAPGDQDEAMQRQAPAQVDCLAEKAEEEAEQDKGGYDH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003008.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003008.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5962a78673273d70b7b4d1b793131c9d7438c396
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003008.fa
@@ -0,0 +1,7 @@
+>PROKKA_02176
+MYLVPILCALTGALFLALGSERQASGVRALERGDGARPGRGGALRLLTSPVWLVGGVLML
+AGIVLNVIALAWAPLTVVQPLGAVAVVVTTLVHARVAGLRVDPATWRAVAACTLGSAAFV
+VVTVQATLPNPVPDADQETLTAWIAAGVVVVGLVAALALRGRRSALVPIVAAGVLYGFVA
+VCVRMSAVRLVDGRPPAWGVLAVLVAGAVLGVWFVQTAYRHGPPDLVVAGLTVVDPMVGV
+LVGVLVLGEMRPDAPWWVGPCLLAAAAVATVGIVRLSRSHPDVLARREERRVADTPGETT
+P
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003009.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003009.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0dba47e4128e3c67a9177e8cfeecdf92f43dfde
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003009.fa
@@ -0,0 +1,5 @@
+>PROKKA_02205
+MYVVPVEQLADRGVIRTALDDFGHAWGQRIDRWRADGQTHTEKSFAQQFWSDLLRAFGVI
+PERIDLFERGAARASTGGAGYIDFFWSGVALGEAKSLGANLDVAHAQALDYLAGGSIGQH
+EWPKYVLVTDFARIRVERLGDAGWVAEFGVEDAADHVDQLMFLAVMSREVVEPAGRCGSD
+RGVDSVMIVEVHPPRQRGPAFGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003014.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003014.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc777994cea41b16a172738e820a0c3196bdcb4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003014.fa
@@ -0,0 +1,3 @@
+>PROKKA_02227
+MDTLTGSRHKNLKELHPGSSGRSEIRILFAFDPRRQAILLVAGDKAGAWKKWYATNIPLA
+EERLDAHLHALRSTPPGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003016.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003016.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4769c92417dafa8dd5f0616a003475a9aa657368
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003016.fa
@@ -0,0 +1,4 @@
+>PROKKA_02233
+MTLTLIPPTTPDEATQQLAQLQGTTVALAVLRRVQLVKAAEVGVTQQQLAGALGRAQSSI
+SEYLTRARTSLADRPATHPLWPAEVIDLYAAGLLPRDEVLAYLASYPYIDPAPTDDPAYT
+VTQPGEFGEVAAAHWNDKLSDTDYANLYDLLHADD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003024.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003024.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0e0cc27e7e069042923d1c35d214912f571f9e42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003024.fa
@@ -0,0 +1,4 @@
+>PROKKA_02274
+MDHRTAAAASPLPSEPAVAAPVGGSDTPLTRFLRAGEAGDAAAARGALHPDVRLVSPMAG
+GAVMRGPDDVALLLGEVYAVLRGLEWVEHYADGRVHTVLGRARALGVALTDAMLVTVAED
+GRVLEIRPHLRPWAGLTAFSAALLPRLLRHPGLLARSTRPD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003025.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003025.fa
new file mode 100644
index 0000000000000000000000000000000000000000..137d6825647de63dac3f84344ec5a8d914f3260a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003025.fa
@@ -0,0 +1,15 @@
+>PROKKA_02279
+MSTAQTPREPEHGGLEPTPDQVPERDLREQHAELVERIRAARTAYYQDDAPEISDAEYDR
+LYRALEDLEALHPELASNDSPTQEVGGEASEAFAPVRHGSRMYSLEDLFSLEELETWFLR
+AAGSLAEVRPGRAPRWLVEVKIDGLAVALRYRRGRLVQAATRGDGVTGEDVTRNVMTIAD
+VPQTLTGEGWPEEFEVRGEVFMPSRAFAELNERRAEEGQAPFANPRNAAAGALRQKDPAV
+TAQRPLSMFVHGIGTVEAFGADGQEEVYGMLAGWGLPVSPYTRVVEGADEAALTRVVDVI
+EEYGRRRHELVHEIDGIVLKADAFADQRYLGHTSRVPRWAAAYKYPPEEVHTRLLDIAVN
+VGRTGRVTPFAVMEPAQVAGSTVSMATLHNQDVVKAKGVLIGDMVVLRKAGDVIPEVVGP
+VLPVRERLLAQGEDLREFVMPADCPSCGTPLAPAKEGDVDLRCPNARSCPAQVAGRVEHL
+AGRGAFDVEALGEEAARWLVIGHGPDPAEHEGMVLPEGAGPITAEAQLFDLASGTPEEVT
+GPRGEDGLTDLQRSLGDVRVWREGRTKVDGRMVPSGVFSLKPYFFTAGTAKKPAAPTANT
+LRLFDELEKAKTAPLWRVLVGLSIRHVGPAAARSLATAFGSMTALRAAAEAGERDRLAEI
+DGVGPIIADALIEWFAQDWHREIVDRWAAAGVVMEDEQDADTPRTLEGVTVVVTGSLEGF
+SRDSAKEAILVRGGKASGSVSKKTHFLVAGEAAGSKLEKAEQLGVPVLDEAGFVRLLAEG
+PAAFPSEDADAETVDAAAEGESA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003026.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003026.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b29171adadbcf70d955ba8cc4c35f8fb8ccea0e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003026.fa
@@ -0,0 +1,2 @@
+>PROKKA_02306
+MDRPRRPGLTPTPSPDGAAAEEHGVTGLASHVPSQMTPAILGAADLILAATG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003027.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003027.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bfa1e65d2825d86e4a4c0bd66c97b796671c0670
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003027.fa
@@ -0,0 +1,6 @@
+>PROKKA_02319
+MESTPPVPPLPDGRVGIVIPVYNTGSLALGAAHSARVALGSTENVVVVDDGSKHPDTLAV
+LDSLRVEGFHVIRQPNGGVSSARNTGIQQVTTPYVIALDSDDEIMPEAPHAMAEILDRHS
+DVTIVTGGAFEVVDGAEHLSSPPDGPVTRSAMRAATVLAMASMFRRSDWEAVGGFPEGLS
+VGEDWVFWMRLLRTGGKVEILDIPIARRHLGEHQVTRGYIDPRQSTQAAALVRSENSDLY
+AGQEVELIERLNAAELQLAAYRHAYRHVDRFKAGIRSLLGRARAKR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003029.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003029.fa
new file mode 100644
index 0000000000000000000000000000000000000000..57a70ef47af4d6fe0ce0213b8c384f86935ee35c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003029.fa
@@ -0,0 +1,4 @@
+>PROKKA_02421
+MSDCEPCDLQSVPAMTDTAPALDVDALAADPVEQFHRWIRQVVGSGVPEATTVTFATVDA
+REQPDARTVLRAVRVRGGVRDAPLPEGARMRTVRPERVEFWQGSPEDHRHVRIVYTADDV
+GGFRGEVTRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003030.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003030.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dffe45fc51448735d3d8cdab9e0d038a7fc76f9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003030.fa
@@ -0,0 +1,4 @@
+>PROKKA_02423
+MTQPAPGPPAPWPASGGPGLAPAPWPGPDWQRAHDQAIVFGILAVTTGMLGLVFGPLALN
+QANRARAIGPDVGVARVLAWIGIGLAALSLLFLLGYFLFFGVMMAEMLRQLSQLSSGGTF
+AALGAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003031.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003031.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e6273469475fd7486e2ccfa4ed0bcc0561db9eca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003031.fa
@@ -0,0 +1,3 @@
+>PROKKA_02428
+MTAPYRPQPQHQPQTVVVQQSRNTLIAYLLWFFLGNLGVHRMYTKRWVSGVVQLLLAWGG
+AATAWLLIGWIPLAIWAVWWIVDLFLVPGMVRDANAREAVDSWRTVGVRRF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003032.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003032.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d85b23d0d4aa0a0970e5f85fde83fa19eb3b20ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003032.fa
@@ -0,0 +1,8 @@
+>PROKKA_02483
+MRLRHLSAAMAAAALAASGAAVAHAAPSAHVSASPGARATAVADAHDVRVATYNASLNRG
+TEGELVRDLTTPDDQQAKNIAEVIQTARPEILLVNEFDHDAAGEGARLFQENYLSVGQNG
+HAPIEYRYRYTAPVNTGVPSGLDLDQNGTVGGPNDAWGFGLFPGQYGMVIYSQHPILEDR
+IRTFQDFRWADMPGNVMPEGYYTAKQERQLRLSSKSHWDVPVRIGGTSVHILAAHPTPPS
+FDGPEKRNQRRNHDEIRLWADYITGGKTAEYLYDDAGVHGGLPRGERFVILGDYNADPLD
+GDSWDGAIDQLLQNRRVRDPQPRSAGAAEASVLQGGANRTHRGDPSLDTADFNDVPAPGN
+LRVDMALPSRNLPLRGAGVFWPKQGEPGSELTGTYPFPTSDHRLTWVDVKVPGGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003037.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003037.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aefec2d6cd157388bbd9fbe4661a9f8ec941a4eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003037.fa
@@ -0,0 +1,2 @@
+>PROKKA_00117
+MFASFVATVLRNVCGVIFLNPMASRAICYCFR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003039.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003039.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c17ccc1f2db59eaf63119dec964b0f0d77ec81dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003039.fa
@@ -0,0 +1,5 @@
+>PROKKA_00162
+MMVFPAKFSELNALELSDEARLILTRIIRVAFPHPDFPDGPYERMAQKIIDASEESRWFR
+MALTQGLVTLDSMSDGHFLELPEDRALAVLKRVADLEFFGFIRRTTVLNLYDDPEVQATL
+GYEGESFSKGGYLHRGFNDLAWLPDPRIEESEEQVTEIGPLPYTVAPATPEGGVKPVPDL
+FKGTGTVDEGSKR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003041.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003041.fa
new file mode 100644
index 0000000000000000000000000000000000000000..896c32f11fef91df3ad5f8b6c69fec99353500ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003041.fa
@@ -0,0 +1,6 @@
+>PROKKA_00164
+MVADEDMDRQDACMGHNDALDGLASVRKAFALLDVVATDSRGMTAKEIAAALQMPLPTVY
+RMLKTLVASGHVVHLREESRYGLGYKLHALDTSLRRQVGTPPAVARLIQELHSRADAAAY
+YAVHRGEDIVVAYVVDSPAHPRITPMGFGFNKAAHATAFGKVLLSAMDAERRAIYLQRHG
+QPALTAATTTDPGQLEDQLEQVTRRGIAVEREEFVQGACCMAAPVLSSTGQTVGSVAVSM
+DPAYFSSHSAQMAVLLRDTAGRVGRALRGASLLQDIAAI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003051.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003051.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b377ce960c63b0e48459e105431a1f082e1f3128
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003051.fa
@@ -0,0 +1,6 @@
+>PROKKA_01159
+MATSGKKHWPPMGRTQWPLTSVSRTARMLGCAASTSSPSGSSASTSRPPPCRPGPRDRVV
+PRPGPCEVEAGEGLHELTNGDRWTRLGAGPPTGDGEEAAGRAPRPGSRSCRSQDASPVAR
+GLRIIPRSRPRRRPRGPATRACPRDVVGRSTPGGRCDRDLRPVHAPATVQTPVPSSSASW
+ELSPGLGGFGPLDTRFPSRGAWRGSRFPDESVREGSRFPHESAGAQRPGARRRRAGPPKR
+TGPPSSSAPVALRDRPEVSGRTCPERTRRPTRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003052.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003052.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9bf22c731ca5ac465a40eb5376336e7e48168abb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003052.fa
@@ -0,0 +1,3 @@
+>PROKKA_01348
+MCDAHRHPTIIRENASTMKQTYATPAHVGTNARSVTQSRFGAGAVNSRFTRSGCRAAVGS
+GRVVFTRFDLVAPLIPAARMSRPV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003054.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003054.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a1e0a8a9d0cc14b4d03232fbc76704e96222deaa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003054.fa
@@ -0,0 +1,6 @@
+>PROKKA_01548
+MLTLGSFALFRSGERNKFGPLTMLSAQFVSHNLTVQVMQYAHIHDEINEQLFSSRHLGEL
+LLETLGFSYEDFCAVREAIVRVHGEKFFAIRDFIGEMFEQRDEKKNDLAFEKDARSALMS
+MLELPGEGATLTVQEIVEASGVPADRTQAILDRFGLSFNDAEDALAVVTKFLSGDNPFRS
+ASLVKDADGNYILTGKPIGTDCFRQVVEDALKRVPAKFRRYEKRRMLVVVGHEVLDIRTG
+LR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003055.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003055.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cdd208bcc7fc3d1eaf0821bcbf5bd646006c1175
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003055.fa
@@ -0,0 +1,3 @@
+>PROKKA_01550
+MVTADDEGLAAAFERMGEILGRMNEGENPSEYVRRGPAIIAEHVQAIAESLKDADAFDVI
+ELMRMREMPMILEGYGRVNLSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003057.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003057.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0dafe2d62dcfd8dcc09116e200a77203cc329b6f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003057.fa
@@ -0,0 +1,4 @@
+>PROKKA_01877
+MSSRGNVIKRWGDKGGVGASDGSDARVVEFILNKPTKNFTCTGQYASAPENGVMVAIPAE
+LTLASGAEAAGFRGDFLHPVQFRFVGTDGKTASIDMQTSAALQCVDEKDAPNFNIGDGET
+TSGLITLDLPASEGTLILDNALMDSGWEWEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003058.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003058.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4be1c3a7170e0d36e4d6c2dcf1ee1234f920c326
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003058.fa
@@ -0,0 +1,2 @@
+>PROKKA_02029
+MAHHWRAVTEHPKGARSIQVLTMPLPELVRTLDAHELDHPQP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003059.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003059.fa
new file mode 100644
index 0000000000000000000000000000000000000000..219146c05cb0b83ee0e3be0d3914197c61367cfc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003059.fa
@@ -0,0 +1,2 @@
+>PROKKA_02030
+MTMGPSEAAAGALAMLGYVSWLRGEGSLTDDQLALAKARAA