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Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000000.fa +369 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000001.fa +289 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000002.fa +113 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000003.fa +131 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000004.fa +226 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000005.fa +184 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000006.fa +103 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000009.fa +112 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000010.fa +118 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000013.fa +78 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000014.fa +101 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000015.fa +80 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000016.fa +91 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000022.fa +88 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000023.fa +57 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000024.fa +104 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000025.fa +29 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000034.fa +36 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000039.fa +189 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000040.fa +63 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000042.fa +36 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000043.fa +22 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000044.fa +50 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000045.fa +56 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000050.fa +64 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000051.fa +50 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000057.fa +60 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000060.fa +49 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000063.fa +48 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000067.fa +48 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000069.fa +90 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000070.fa +43 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000074.fa +49 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000076.fa +144 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000077.fa +48 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000080.fa +31 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000081.fa +54 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000082.fa +54 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000089.fa +55 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000091.fa +37 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000093.fa +37 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000094.fa +37 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000095.fa +54 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000097.fa +31 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000099.fa +37 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000101.fa +55 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000103.fa +61 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000107.fa +55 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000110.fa +37 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000111.fa +37 -0

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000000.fa ADDED Viewed

	@@ -0,0 +1,369 @@

+>GCF_002008305_PROKKA_00064
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGFTRLAYTEALEDERTVTTIGFFCRARAFFAAHGIT-VDRVVTD
+NGNNYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYT---------------------
+----------------
+>GCF_002008305_PROKKA_01337
+MTHANAPLTPTGRLRMVQRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLASEGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRAHGRESEAGRASKRG-
+-AGRRVGYTYLHSAIDGFTRLAYTEALEDERAATTVSFYCRARAFFAAHGIT-VDRVITD
+NGNNYRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSERARRE
+ALQVWVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYI---------------------
+----------------
+>GCF_002008305_PROKKA_01952
+---------------MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRAHGRESEAGRASKRG-
+-AGRRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIT-VDRVITD
+NGNNYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYS---------------------
+----------------
+>GCF_002008305_PROKKA_02068
+---------------MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGFTRLAYTEALPDERAATTVSFFCRARAFFAAHGIT-VDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYI---------------------
+----------------
+>GCF_002008305_PROKKA_02111
+---------------MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPEVVAQIQTLRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIR-IDRVITD
+NGNNYRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYI---------------------
+----------------
+>GCF_002008305_PROKKA_02278
+---------------MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPEVVAQIQTLRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIR-IDRVITD
+NGNNYRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYN---------------------
+----------------
+>GCF_003691675_PROKKA_00012
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPEVVAQIQTLRRREKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-PGRRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIT-VDRVVTD
+NGNNYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYN---------------------
+----------------
+>GCF_003691675_PROKKA_00041
+MTHANAPLTPTGRLRMVHRHLNDGIPQSHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGRIPEGGGWRTHGRDSEAGRASKRG-
+-SGQRVGYTYLHSAIDGYTRLAYTEALEDERTVTTIGFYCRARAFFAAHGIT-VDRVVTD
+NGNNYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALQVWVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYT---------------------
+----------------
+>GCF_003691675_PROKKA_00137
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLLDRP
+SRPRRSPAQLDPEVVAQIQTLRRREKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRAHGRESEAGRASKRG-
+-AGRRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIT-VDRVVTD
+NGNNYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYT---------------------
+----------------
+>GCF_003691675_PROKKA_00312
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRDSEAGRASKRG-
+-AGRRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIT-VDRVITD
+NGNNYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSEQARRE
+ALQVWVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYT---------------------
+----------------
+>GCF_003691675_PROKKA_00352
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+SRPHHCPAQLDIAILAEIEALRRDQKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPDGGGWRAHGRDCENARAAKRG-
+-PGRRVGYTYLHSAVDGFTRLAYTEALPDERAATTVSFFCRARAFFAAHGIT-VDRVITD
+NGANYRAAEFTMKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVIYARPYTSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYN---------------------
+----------------
+>GCF_003691675_PROKKA_01118
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------MVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-AGRRVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFFCRARAFFAEHGIT-VDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSEQARRE
+ALQVWVNHYNYHRPHTSCGNAPPASLAPARVNNVMPSYN---------------------
+----------------
+>GCF_003691675_PROKKA_01160
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-AGRRVGYTYLHSAIDGFTRLAYTEALEDERAATTVSFYCRARAFFAAHGIT-VDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYS---------------------
+----------------
+>GCF_003691675_PROKKA_01236
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRDSEAGRASKRG-
+-PGRRVGYTYLHSAIDGFTRLAYTEALEDERTVTTIGFFCRARAFFAAHGIT-VDRVITD
+NGNNYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPTSLAPARVNNVMPSYN---------------------
+----------------
+>GCF_003691675_PROKKA_01818
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPEVVAQIQTLRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIR-IDRVITD
+NGNNYRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYI---------------------
+----------------
+>GCF_003691675_PROKKA_01821
+---------------MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHQLCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGFTRLAYTEALPDERAATTVSFFCRARAFFAAHGIR-IDRVITD
+NGNNYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYT---------------------
+----------------
+>GCF_003691675_PROKKA_01968
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------MVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-PGRRVGYTYLHSAIDGFTRLAYTEALEDERAATTVSFYCRARAFFAAHGIT-VDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPTSLAPARVNNVMPSYI---------------------
+----------------
+>GCF_003691675_PROKKA_01971
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLLDRP
+SRPHRSPAQLDPEVVAQIQTLRRREKWSARRIHHYLVSEGHQLCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-AGRRVGYTYLHSAIDGFTRLAYTEALEDERAATTVSFYCRARAFFAAHGIT-VDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYS---------------------
+----------------
+>GCF_003691675_PROKKA_02077
+MIHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLLDRP
+SRPRRSPAQLDPVLVAQIHALRRERKWSARRIHHHLASEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIT-VDRVITD
+NGNNYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYS---------------------
+----------------
+>GCF_005280335_PROKKA_00044
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------MVHLDVKKIGKIPDGGGWRAHGRDSQAGRASKRG-
+-AGRRVGYTYLHSAIDGFTRLAYTEALEDERAVTTIGFFCRARAFFAAHGIT-LDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARRE
+AMQVWVNHYNYHRPHTSCGGAPPASLAPARVNNVMPSYT---------------------
+----------------
+>GCF_005280335_PROKKA_00146
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------------MTTIGFFCRARAFFAAHGIT-VDRVVTD
+NGNNYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARRE
+ALQVWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT---------------------
+----------------
+>GCF_005280335_PROKKA_00227
+MTHANAPLTPTGRLRMVQRHLHEGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+CRPRRSPAQLDPALVTQILTLRRECKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGYTRLAYTEALEDEKAMTTIGFFCRARAFFAAHGIT-VDRVVTD
+NGNNYRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARRE
+ALQVWVNHYNYHRPHTSCGNAPPASLAPARVNNVMPSYT---------------------
+----------------
+>GCF_005280335_PROKKA_00556
+MTHANAPLTPTGRLRMVQRHLIDGIPQSHVAAEFRVSRPTVATWVARYLAEGAAGLQDRS
+SRPHHCPDQLDAEVVTELETLRRDHKWSARRIHHHLLAQGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPAKKITARAPGHMVHLDVKKIGKIPDGGGWRAHGRDSQAGRASKRG-
+-AGRRVGYTYLHSAIDGFTRLAYTEALEDERAVTTIGFFCRARAFFAAHGIT-LDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARRE
+AMQVWVNHYNYHRPHTSCGGAPPASLAPARVNNVMPSYS---------------------
+----------------
+>GCF_005280335_PROKKA_00692
+MTHANAPLTPTGRLRMVQRHLIDGIPQSHVAAEFRVSRPTVATWVARYLAEGAAGLQDRS
+SRPHHCPDQLDAEVVTELETLRRDHKWSARRIHHHLLAQGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRPAKKITARAPGHMVHLDVKKIGKIPDGGGWRAHGRDSQAGRASKRG-
+-AGRRVGYTYLHSAIDGFTRLAYTEALEDERAVTTIGFFCRARAFFAAHGIT-LDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARRE
+AMQVWVNHYNYHRPHTSCGGAPPASLAPARVNNVMPSYT---------------------
+----------------
+>GCF_005280335_PROKKA_00779
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLPSASRPGGSPRGAGAHGAPGREEDRKDPRGGGWRAHGRDSEAGRASKRG-
+-PGARVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFYCRARAFFAAHGIT-VDRVVTD
+NGNNYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARRE
+ALQVWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT---------------------
+----------------
+>GCF_005280335_PROKKA_01499
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGKIPEGGGWRAHGRDSEAGRASKRG-
+-PGARVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFYCRARAFFAAHGIT-VDRVVTD
+NGNNYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARRE
+ALQVWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT---------------------
+----------------
+>GCF_005280335_PROKKA_01505
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------MVHLDVKKVGRIPDGGGWRIHGRNSDQARTAGRAK
+SAGAKRGYTYLHSAVDGFSRLSYTEPLTDEKGPTAAAFLARAKAWFAAHGISHIHRVITD
+NGACYRSADF-ARIVGNRTRHQKTRPYTPRHNGKVERYQRILAEELLYAREFESEEARDT
+AIGIWNIHYNYHRPHSGAGGHPPASRLRAGVTNVWPSYS---------------------
+----------------
+>GCF_005280335_PROKKA_01737
+MTHANAPLTPTGRLRMVQRHLHEGIPQAHVAAEFRVSRPTVATWVARYRAEGEVGLQDRS
+CRPRRSPAQLDPALVTQILTLRRECKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIT-VDRVVTD
+NGNNYRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARRE
+ALQVWVNHYNYHRPHTSCGNAPPASLAPARVNNVMPSYT---------------------
+----------------
+>GCF_005280335_PROKKA_01768
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGCRVGYTYLHSAIDGYTRLAYTEALEDEKAMTTIGFFCRARAFFAAHGIT-VDRVVTD
+NGNNYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARRE
+ALQVWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT---------------------
+----------------
+>GCF_005280335_PROKKA_02336
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGCRVGYTYLHSAIDGYTRLAYTEALEDEKAMTTIGFFCRARAFFAAHGIT-VDRVVTD
+NGNNYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARRE
+ALQVWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT---------------------
+----------------
+>GCF_005280335_PROKKA_02339
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------MAYTESLENEKATTAVAFLNRAREWFASHGITRIERVITD
+NGACYRSAAFTAALD--GADHRRTRPYTPKHNGKVERYNRILAEEFLYARTWTSEEQREK
+ALETWNLHYNYHRPHGVHDGKPPASATPSRVNNVLASYS---------------------
+----------------
+>GCF_005280335_PROKKA_02472
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGKIPEGGGWRAHGRDSEAGRASKRG-
+-PGARVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFYCRARAFFAAHGIT-VDRVVTD
+NGNNYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARRE
+ALQVWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYT---------------------
+----------------
+>GCF_005280335_PROKKA_02555
+MTHANAPLTPTGRLRMVQRHLHEGIPQAHVAAEFRVSRPTVATWVARYRAEGEVGLQDRS
+CRPRRSPAQLDPALVTQILTLRRECKWSARRIHHHLVSEGHQLCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIT-VDRVVTD
+NGNNYRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARRE
+ALQVWVNHYNYHRPHTSCGNAPPASLAPARVNNVMPSYT---------------------
+----------------
+>GCF_005280335_PROKKA_02613
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRAGISRL
+RDLTPAGEDLRRQPARRITARGPGHMVHLDVKKIGKIPEGGGWRAHGRDSEAGRASKRG-
+-PGARVGYTYLHSAIDGFTRLAYTEALEDEKAVTTIGFYCRARAFFAAHGIT-VDRVVTD
+NGNNYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARRE
+ALQVWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYN---------------------
+----------------
+>GCF_005280335_PROKKA_02632
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------MVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-AGRRVGYTYLHSAIDGFTRLAYTEALEDERAATTVSFYCRARAFFAAHGIR-IDRAVTD
+NGNNYRAAEFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLHARPYSSETARRE
+ALQVWVNHYNYHRPHTSCGNAPPASLAPARVNNVMTSYT---------------------
+----------------
+>GCF_005280335_PROKKA_02637
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGCRVGYTYLHSAIDGYTRLAYTEALEDEKAMTTIGFFCRARAFFAAHGIT-VDRVVTD
+NGNNYRAADFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEAARRE
+ALQVWVNHYNYHRPHTSCGDTPPASLAPVRVNNVMTSYI---------------------
+----------------
+>GCF_023573625_PROKKA_00274
+MTHANAPLTPTGRLRMVQRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLASEGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIT-VDRVITD
+NGNNYRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYS---------------------
+----------------
+>GCF_023573625_PROKKA_00518
+---------------MAQRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-AGRRVGYTYLHSAIDGFTRLAYTEALEDERAATTVSFYCRARAFFAAHGIT-VDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVIYARPYSSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPTSLAPARVNNVMPSYN---------------------
+----------------
+>GCF_023573625_PROKKA_00800
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVTQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-PGRRVGYTYLHSAIDGYTRLAYTEALEDERAATTVSFYCRARAFFAAHGIT-VDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRSHTSCGDAPPASLAPARVNNVMPSYT---------------------
+----------------
+>GCF_023573625_PROKKA_00879
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-PGRRVGYTYLHSAIDGYTRLAYTEALEDERAATTVSFYCRARAFFAAHGIT-VDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYN---------------------
+----------------
+>GCF_023573625_PROKKA_01175
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVTQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-PGRRVGYTYLHSAIDGYTRLAYTEALEDERAATTVSFYCRARAFFAAHGIT-VDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALAVWVNHYNYHRSHTSCGDAPPASLAPARVNNVMPSYI---------------------
+----------------
+>GCF_023573625_PROKKA_01546
+MTHANAPLTPTGRLRMVQRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLASEGHQLCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGRIPEGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGYTRLAYTEALEDEKAVTTIGFFCRARAFFAAHGIT-VDRVITD
+NGNNYRAVDFTRKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYSSETARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPTRVNNVMPSYS---------------------
+----------------
+>GCF_023573625_PROKKA_01570
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-PGRRVGYTYLHSAIDGYTRLAYTEALEDERAATTVSFYCRARAFFAAHGIT-VDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSEQARRE
+ALQVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMPSYT---------------------
+----------------
+>GCF_023573625_PROKKA_01997
+---------------MVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+RDLTPAGEDLRQRP-QKITARGPGHMVHLDVKKIGKIPDGGGWRTHGRESEAGRASKRG-
+-PGRRVGYTYLHSAIDGFTRLAYTEALEDERAATTVSFYCRARAFFAAHGIT-VDRVITD
+NGNNYRAADFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVIYARPYTSEQARRE
+ALTVWVNHYNYHRPHTSCGDAPPTSLAPARVYNVMPSYS---------------------
+----------------
+>GCF_023573625_PROKKA_02102
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+CRPRRSPAQLDPEVVAQIQTLRRREKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRP-QKITARGPGRMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGFTRLAYTEALPDERAATTVSFFCRARAFFAAHGIR-IDRVITD
+NGNNYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYT---------------------
+----------------
+>GCF_023573625_PROKKA_02106
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAEGEAGLQDRS
+CRPRRSPAQLDPEVVAQIQTLRRREKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISRL
+PDLAPTGEDLRQRP-QKITARGPGRMVHLDVKKIGRIPDGGGWRAHGRDSENARAAKRG-
+-PGRRVGYTYLHSAIDGFTRLAYTEALPDERAATTVSFFCRARAFFAAHGIR-IDRVITD
+NGNNYRAVDFTAKVVSLGGRHHRIRPYTPRHNGKVERYNRLMVDEVLYARPYTSETARRE
+ALAVWVNHYNYHRPHTSCGDAPPASLAPARVNNVMTSYNYLFGLLMVTRSPECALLGHGP
+DQRGWLLDTYLRGLRP

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000001.fa ADDED Viewed

	@@ -0,0 +1,289 @@

+>GCF_002008305_PROKKA_00174
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRL--------------PAV----AGHLDAAREDILAFTSFPRDVWSQIWSNNPAER
+LNREIRRRTDSVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARC-REPLTTEQ
+ETVMSTEVMPTLQ---------------T
+>GCF_002008305_PROKKA_00589
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRL--------------PAV----AGHLDAAREDILAFTSFPRDVWSQIWSNNPAER
+LNREIRRRTDSVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARC-REPLTTEQ
+ETVMSTEVMPTLQ---------------T
+>GCF_002008305_PROKKA_00602
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKL--------------PVV----AEHLDAARADILAFTTFPKDVWTQIWSNNPAER
+LNREIRRRTDAAGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARC-RLTTVSNT
+GSEVNPDTAPALEFS-------------A
+>GCF_002008305_PROKKA_00603
+MTAPHILDPAGLLGEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPSSSRTAQR
+NGYRHRDLDTRVGTLDVAIPKLRSGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGVNALSKSQVSRMATELDEQVEAFRHRPLGVAGPFTFVAADALSMKVREGGRV
+VNAVVLLATGVNADGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHTGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAASVHAQFDRLLD
+YVSGKL--------------PTV----AEHLDAARADILAFTTFPKDVWTQVWSNNPAER
+LNREIRRRTDAVGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARC-RLTTVTNT
+GDEVDPDTELTLGLS-------------A
+>GCF_002008305_PROKKA_00623
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVTDRL--------------PAV----AGHLDAAREDILAFTSFPRDVWSQIWSNNPAER
+LNREIRRRTDAVGIFPNRDAVIRLVGAVLAEQTDEWAEGRRYLGLELLARCSNQDPDTPS
+TTGASAEVMPTL----------------A
+>GCF_002008305_PROKKA_00713
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRL--------------PAV----AGHLDAAREDILAFTSFPRDVWSQIWSNNPAER
+LNREIRRRTDSVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARC-REPLTTEQ
+ETVMSTEVMPTLQ---------------T
+>GCF_002008305_PROKKA_01070
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKL--------------PVV----AEHLDAARADILAFTTFPKDVWTQIWSNNPAER
+LNREIRRRTDAAGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARC-RLTTVSNT
+GSEVNPDTAPALEFS-------------A
+>GCF_002008305_PROKKA_01202
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKL--------------PAV----AEHLGDARADILAFTTFPKDVWTQVWSNNPAER
+LNREIRRRTDAVGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARC-RLTPVEDT
+GSEVGTDTDTALELS-------------A
+>GCF_002008305_PROKKA_01394
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQTLGITGLSKSQVSEMSKDLDAQVEAFRTRPL-DAGPYRFVAADALVLKVREHGRV
+VKVAAMVATGINNDGYREILGLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLV
+EAAGAVFGTAQWQRCRTHYAANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMID
+SLATHL--------------PAA----AEHLEGARDEVLTFTKFPKEVWKKIWSNNPNER
+LNKEIRRRTDVVGIFPSRVEVIRLLGAVLAEQHDEWTESRRYMSLELLTAT-DTMLAEAA
+AKAAAEQA--ALQVSDTMTDDPGHAALAA
+>GCF_002008305_PROKKA_01399
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRL--------------PAV----AGHLDAAREDILAFTSFPRDVWSQIWSNNPAER
+LNREIRRRTDSVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARC-REPLTTEQ
+ETVMSTEVMPTLQ---------------T
+>GCF_002008305_PROKKA_01504
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVAGAWPGSGWSPLMPTPGSR
+TPSPRTCP----VRCGNAAAPT--------------------------------------
+------------------------------------------------------------
+-----TRRT---------------------------------------------------
+-----------------------------
+>GCF_002008305_PROKKA_01505
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------------MGITPKSMWPAVKAMLHSGYDQPDAASVNAQFDRLLD
+YVSEKL--------------PVV----AEHLDAARADILAFTTFPKDVWTQIWSNNPAER
+LNREIRRRTDAAGIFPNRAAIVRLVGAVLAEQTD---EGPRAVATRALGAT-RACC----
+-----------------------------
+>GCF_002008305_PROKKA_02030
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKL--------------PAV----AEHLGDARADILAFTTFPKDVWTQVWSNNPAER
+LNREIRRRTDAVGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARC-RLTPVEDT
+GSEVGTDTDTALELS-------------A
+>GCF_002008305_PROKKA_02064
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFSATGL------------------------
+------------------------------------------------------------
+-----------WAR----------------------------------------------
+------------------------------------------------------------
+---------------PARS-------------------------------C-SSPPTP--
+-----------------------------
+>GCF_002008305_PROKKA_02065
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------MFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFERLLD
+YVQDRL--------------PAV----AAHLDAARQDILAFTSFPRDVWCQIWSNNPAER
+LNREIRRRTDAVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARC-REPLTTEQ
+ETVMSTEVMPTLQ---------------T
+>GCF_002008305_PROKKA_02226
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+INAVAMVATGVNADGRREVLGLRVATTETGAAWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRL--------------PAV----AGHLDAAREDILAFTSFPRDVWSQIWSNNPAER
+LNREIRRRTDSVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARC-REPLTTEQ
+ETVMSTEVMPTLQ---------------T
+>GCF_002008305_PROKKA_02229
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGQASQSRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFERLLD
+YVQDRL--------------PAV----AAHLDAARQDILAFTSFPRDVWCQIWSNNPAER
+LNREIRRRTDAVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARC-REPLTTEQ
+ETVMSTEVMPTLQ---------------T
+>GCF_002008305_PROKKA_02231
+------------------------------------------------------------
+---------------------------------------------MVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFERLLD
+YVQDRL--------------PAV----AAHLDAARQDILAFTSFPRDVWCQIWSNNPAER
+LNREIRRRTDAVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARC-REPLTTEQ
+ETVMSTEVMPTLQ---------------T
+>GCF_002008305_PROKKA_02232
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPN-----------------------GCSS---
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------AAN-------------------------GPS----------
+------------------------------------------------------------
+---------------PH-------------------------------------------
+-----------------------------
+>GCF_002008305_PROKKA_02266
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFERLLD
+YVQDRL--------------PAV----AAHLDAARQDILAFTSFPRDVWCQIWSNNPAER
+LNREIRRRTDAVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARC-REPLTTEQ
+ETVMSTEVMPTLQ---------------T
+>GCF_002008305_PROKKA_02271
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKL--------------PVV----AEHLDAARADILAFTTFPKDVWTQIWSNNPAER
+LNREIRRRTDAAGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARC-RLTTVSNT
+GSEVNPDTAPALEFS-------------A
+>GCF_003691675_PROKKA_01126
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQT------------------------------------------------RHHGPV
+-----------------EIAGLR-------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------DE-------------------------
+-----------------------------
+>GCF_003691675_PROKKA_01127
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------MSKDLDAQVEAFRTRPL-DAGPYRFVAADALVLKVREHGRV
+VKVAAMVATGINNDGYREILGLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLV
+EAAGAVFGTAQWQRCRTHYAANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMID
+SLATHL--------------PAA----AEHLEGARDEVLTFTKFPKEVWKKIWSNNPNER
+LNKEIRRRTDVVGIFPSRVAVIRLLGAVLAEQHDEWTESRRYMSLELLTAT-DTMLAEAA
+AKAAAEQA--ALQVSDTMTDDPGHAALAA
+>GCF_005280335_PROKKA_00691
+MTAPHILDPAGLLREALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPGRATQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMATELDEHVESFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHTGLR
+EAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAQAVDAQFDRLLD
+YVSEKL--------------PAV----AEHLDAARADILAFTTFPKDVWTQVWSNNPAER
+LNREIRRRTDAVGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLHRC-RLTPVSNT
+GDEVDTDT--ALELS-------------A
+>GCF_005280335_PROKKA_00721
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKL--------------PVV----AEHLDAARADILAFTTFPKDVWTQIWSNNPAER
+LNREIRRRTDAVGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARC-RLTTVSNT
+GNEVNPDTAPALEFS-------------A
+>GCF_005280335_PROKKA_00896
+MTAPHILDPAGLLREALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPGRATQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMATELDEHVESFRHRPLGEALPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHTGLR
+EAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAQAVDAQFDRLLD
+YVSEKLLYGGRAPGRCPGGHPGLHDLPEGRVDAGLVEQSGRAAQPRD---------PPP-
+-----HRRG---GHLPQPGS-HRQAGRCGAGRADR-------------------------
+-----------------------------
+>GCF_005280335_PROKKA_02500
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKL--------------PVV----AEHLDAARADILAFTTFPKDVWTQIWSNNPAER
+LNREIRRRTDAVGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARC-RLTTVSNT
+GNEVNPDTAPALEFS-------------A
+>GCF_005280335_PROKKA_02671
+MTAPHILDPAGLLGEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPSSSRTAQR
+NGYRHRDLDTRVGTLDVAIPKLRSGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGVNALSKSQVSRMATELDEQVEAFRHRPLGVAGPFTFVAADALSMKVREGGPV
+VNAVVLLATGVNADGHREVLGLRVATSETGAAWNEFFADLVARGLAGLRLVTSDAHTGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAASVHAQFDRLLD
+YVSEKL--------------PTV----AEHLDAARADILAFTTFPKDVWTQVWSNNPAER
+LNREIRRRTDAVGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARC-RLTTVTNT
+GDEVDPDTELTLGLS-------------A
+>GCF_023573625_PROKKA_01344
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQTLGITGLSKSQVSEMSKDLDAPVEAFRTRPL-DAGPYRFVAADALVLKVREHGRV
+VKVAAMVATGINNDGYREILGLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLV
+EAAGAVFGTAQWQRCRTHYAANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMID
+SLATHL--------------PAA----AEHLEGARDEVLTFTKFPKEVWKKIWSNNPNER
+LNKEIRRRTDVVGIFPSRVAVIRLLGAVLAEQHDEWTESRRYMSLELLTAT-DTMLAEAA
+AKAAAEQA--ALQVSDTMTDDPGHAALAA
+>GCF_023573625_PROKKA_01996
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQTLGITGLSKSQVSEMSKDLDAQVEAFRTRPL-DAGPYRFVAADALVLKVREHGRV
+VKVAAMVATGINNDGYREILGLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLV
+EAAGAVFGTAQWQRCRTHYAANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMID
+SLATHL--------------PAA----AEHLEGARDEVLTFTKFPKEVWKKIWSNNPNER
+LNKEIRRRTDVVGIFPSRVAVIRLLGAVLAEQHDEWTESRRYMSLELLTAT-DTMLAEAA
+AKAAAEQA--ALQVSDTMTDDPGHAALAA
+>GCF_023573625_PROKKA_02197
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKL--------------PAV----AEHLGDARADILAFTTFPKDVWTQIWSNNPAER
+LNREIRRRTDAVGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARC-RLTPVEDT
+GSEVGTDTDTALELS-------------A
+>GCF_023573625_PROKKA_02214
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKL--------------PAV----AEHLGDARADILAFTTFPKDVWTQIWSNNPAER
+LNREIRRRTDAVGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARC-RLTPVEDT
+GSEVGTDTDTALELS-------------A

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000002.fa ADDED Viewed

	@@ -0,0 +1,113 @@

+>GCF_002008305_PROKKA_01069
+MFRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRGLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_002008305_PROKKA_01387
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_003691675_PROKKA_00320
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_003691675_PROKKA_00332
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFSDARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEEGTWDAVLARLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+VELQESA
+>GCF_003691675_PROKKA_00787
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEEGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_003691675_PROKKA_01117
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATSITRHTGGW
+IELQESA
+>GCF_003691675_PROKKA_01328
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_003691675_PROKKA_01659
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEEGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+VELQESA
+>GCF_003691675_PROKKA_02266
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_005280335_PROKKA_00757
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_005280335_PROKKA_01280
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRIAAEGTWDTVLATLTAAADAQGLVDWSVSVDSTIARAHQHATNTTRHTGGW
+IELQESA
+>GCF_005280335_PROKKA_01303
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_005280335_PROKKA_01313
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRIAAEGTWDTVLATLTAAADAQGLVDWSVSVDSTIARAHQHATNTTRHTGGW
+IELQESA
+>GCF_005280335_PROKKA_01318
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRIAAEGTWDTVLATLTAAADAQGLVDWSVSVDSTIARAHQHATNTTRHTGGW
+IELQESA
+>GCF_005280335_PROKKA_02332
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_005280335_PROKKA_02348
+MSRFQMLSDAQWELIAPMLPTRTGRPGRPFTGARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_005280335_PROKKA_02630
+MSRFQMLSDAQWELIAPMLPTRTGRPGRPFTGARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_020097155_PROKKA_00316
+MSRFQTLSDAQWELIAPMLPARTGRQGRPFADARTMVEAIIYRYRCGIPWRDLPEVYGPW
+QTVWTWHRRMAEEGTWDTVLATLTAAADAEGLIDWSVAVDSTIARAHQHATNTTRLTGGW
+IELQESA
+>GCF_020097155_PROKKA_00621
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRMAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+IELQESA
+>GCF_020097155_PROKKA_00626
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRMAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+IELQESA
+>GCF_020097155_PROKKA_01795
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_020097155_PROKKA_01837
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_020097155_PROKKA_02208
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_020097155_PROKKA_02231
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFSDARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEEGTWDAVLARLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+VELQESA
+>GCF_023573625_PROKKA_00113
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+VELQESA
+>GCF_023573625_PROKKA_01019
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFSDARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEEGTWDAVLARLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_023573625_PROKKA_01540
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+VELQESA
+>GCF_023573625_PROKKA_01883
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+VELQESA

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000003.fa ADDED Viewed

	@@ -0,0 +1,131 @@

+>GCF_002008305_PROKKA_01068
+------------------------------------------------------------
+-----------------------------------------MLLPLLEQLRVTRPVGRPR
+TRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPIGLDADAYKG
+RNVIERQYAHLKPWRGLATRYDKYAIIYRAAVVLNAVIAWSKRLSDMP
+>GCF_002008305_PROKKA_01386
+------------------------------------------------------------
+--------------------MDGTGLPLVSLITPGQAGDSPMLLPLLEQLRVTRPVGRPR
+TRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPVSLDADAYKG
+RNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWSKRLSDMP
+>GCF_002008305_PROKKA_02280
+MAAEGTWDTVLTKLTAATDAQGLVDWSVSVDSTIARAHQHATNTTGTQGDRSSDTNLREE
+PANHGVGRSRGGLSTKIHQLVDGAGMPLVNLITPGQAGDSPMLLPLLEQLRVARPVGRTR
+TRPEAVLGDKAYSSQPVRAHLRARRIKAVIPEPADPRGHRKRSGPRGGRPVGPDAAAYKG
+RNVIERQYAHLKQWRRLATRYDKYATVYRAAVLLNAVTAWSKLLSDTP
+>GCF_003691675_PROKKA_00319
+------------------------------------------------------------
+-----------------------------------------MLLPLLEQLRVTRPVGRPR
+TRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPVSLDAAAYKG
+RNVIERQYAHLKQWRGLATRYDKYAIVYRSAVVLNAVIAWSKRLSDMP
+>GCF_003691675_PROKKA_00788
+------------------------------------------------------------
+-----------------------------------------MLLPLLEQLRVTRPVGRPR
+TRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPVSLDADAYKG
+RNVIERQYAHLKQWRGLATRYDKYAIVYRSAVVLNAVIAWSKRLSDMP
+>GCF_003691675_PROKKA_01116
+------------------------------------------------------------
+-----------------------------------------MLLPLLAQLRVTRPVGRPR
+TRPAAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPVSLDADAYKG
+RNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWSKRLSDMP
+>GCF_003691675_PROKKA_01327
+------------------------------------------------------------
+-----------------------------------------MLLPLLEQLRVTRPVGRPR
+TRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPVSLDADAYKG
+RNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWSKRLSDMP
+>GCF_003691675_PROKKA_01658
+------------------------------------------------------------
+--------------------MDGTGLPLVSLITPGQAGDSPMLLPLLEQLRVTRPVGRPR
+TRPAAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPVGLDADAYKG
+RNVIERQYAHLKQWRGLATRYDKYAIVYRSAVVLNAVIAWSKRLSDMP
+>GCF_003691675_PROKKA_02267
+------------------------------------------------------------
+-----------------------------------------MLLPLLEQLRVTRPVGRPR
+TRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPVSLDAAAYKG
+RNVIERQYAHLKQWRGLATRYDKYAIVYRSAVVLNAVIAWSKRLSDMP
+>GCF_005280335_PROKKA_00758
+------------------------------------------------------------
+-----------------------------------------MLLPLLEQLRVTRPVGRPR
+TRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPVSLDADAYKG
+RNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWSKRLSDMP
+>GCF_005280335_PROKKA_01281
+------------------------------------------------------------
+-----------------------------------------MLLPLLGQLRVTRPVGRPR
+TRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPVGLDADAYKG
+RNVIERQYAHLKQWRGLATRYDKYATIYRAAVVLNAVLAWSKRLSDMP
+>GCF_005280335_PROKKA_01304
+------------------------------------------------------------
+-----------------------------------------MLLPLLEQLRVTRPAGRPR
+TRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPVGLDADAYKG
+RNVIERQYAHLKQWRGLATRYDKYATIYRAAVVLNAVLAWSKRLSDMP
+>GCF_005280335_PROKKA_01312
+------------------------------------------------------------
+-----------------------------------------MLLPLLGQLRVTRPVGRPR
+TRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPVGLDADAYKG
+RNVIERQYAHLKQWRGLATRYDKYATIYRAAVVLNAVLAWSKRLSDMP
+>GCF_005280335_PROKKA_01317
+------------------------------------------------------------
+-----------------------------------------MLLPLLGQLRVTRPVGRPR
+TRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPVGLDADAYKG
+RNVIERQYAHLKQWRGLATRYDKYAIVYRSAVVLNAVIAWSKRLSDMP
+>GCF_005280335_PROKKA_02331
+------------------------------------------------------------
+-----------------------------------------MLLPLLEQLRVTRPVGRPR
+TRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPVSLDADAYKG
+RNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWSKRLSDMP
+>GCF_005280335_PROKKA_02347
+------------------------------------------------------------
+-----------------------------------------MLLPLLEQLRVTRPVGRPR
+TRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRRRRGSAGGRPVGLDADAYKG
+RNVIERQYAHLKQWRGLATRYDKYATIYRAAVVLNAVLAWSKRLSDMP
+>GCF_005280335_PROKKA_02614
+------------------------------------------------------------
+---------------------------------------------------MTRPVGRPR
+TRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPVSLDADAYKG
+RNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWSKRLSDMP
+>GCF_005280335_PROKKA_02631
+------------------------------------------------------------
+-----------------------------------------MLLPLLEQLRVTRPVGRPR
+TRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRRRRGSAGGRPVGLDADAYKG
+RNVIERQYAHLKQWRGLATRYDKYATIYRAAVVLNAVLAWSKALSDTP
+>GCF_020097155_PROKKA_00317
+------------------------------------------------------------
+-----------------------------------------MLLPLLEQLRVTRPAGRPR
+TRPDAVLGDKAYSSRAIRAHLRSRRIRAVIPEPADQRGHRRRRGPRGGRPVGLDATAYKG
+RNVIERRYAHLKQWRGLATRYDKYSIVYRAAVVLNAVLAWSKRLSDMP
+>GCF_020097155_PROKKA_00625
+------------------------------------------------------------
+-----------------------------------------MLLPLLEQLRVTRPVGRPR
+TRPEAVLGDKAYSSRAIRTHLRARGIKAVISEPADQQGHRRRRGARGGRPVGLDADAYKG
+RNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWSKRLSDMP
+>GCF_020097155_PROKKA_01796
+------------------------------------------------------------
+-----------------------------------------MLLPLLEQLRVTRPVGRPR
+TRPEAVLGDKAYSSRAIRTHLRARRIKAVIPEPADQQGHRRRRGARGGRPVSLDADAYKG
+RNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWSKRLSDMP
+>GCF_020097155_PROKKA_01836
+------------------------------------------------------------
+-----------------------------------------MLLPLLEQLRVTRPVGRPR
+TRPEAVLGDKAYSSRAIRTHLRARRIKAVIPEPADQQGHRRRRGARGGRPVSLDADAYKG
+RNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWSKRLSDMP
+>GCF_020097155_PROKKA_02207
+------------------------------------------------------------
+-----------------------------------------MLLPLLEQLRVTRPVGRPR
+TRPEAVLGDKAYSSRAIRTHLRARRIKAVIPEPADQQGHRRRRGARGGRPVSLDADAYKG
+RNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWSKRLSDMP
+>GCF_023573625_PROKKA_00114
+------------------------------------------------------------
+--------------------MDGTGLPLVSLITPGQAGDSPMLLPLLEQLRVTRPVGRPR
+TRPAAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPVSLDADAYKG
+RNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWSKRLSDMP
+>GCF_023573625_PROKKA_01539
+------------------------------------------------------------
+-----------------------------------------MLLPLLEQLRVTRPVGRPR
+TRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPVSLDADAYKG
+RNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWSKRLSDMP
+>GCF_023573625_PROKKA_01884
+------------------------------------------------------------
+--------------------MDGTGLPLVSLITPGQAGDSPMLLPLLAQLRVTRPVGRPR
+TRPAAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPVSLDAAAYKG
+RNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWSKRLSDMP

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000004.fa ADDED Viewed

	@@ -0,0 +1,226 @@

+>GCF_002008305_PROKKA_00376
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_002008305_PROKKA_01393
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_002008305_PROKKA_02069
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTP--------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------LTQTS-------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------
+>GCF_002008305_PROKKA_02112
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_002008305_PROKKA_02277
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_003691675_PROKKA_00355
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_003691675_PROKKA_01012
+M-----------------------------------------------------------
+----------------------------------GRTQWPLT----------DVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_003691675_PROKKA_01015
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVCK----
+--RP--------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------
+>GCF_003691675_PROKKA_01125
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_003691675_PROKKA_01746
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_003691675_PROKKA_01819
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_003691675_PROKKA_02016
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_005280335_PROKKA_00228
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------MVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_005280335_PROKKA_00229
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEAPKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYA----------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------
+>GCF_005280335_PROKKA_00643
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEAPKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_005280335_PROKKA_00895
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------MVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_005280335_PROKKA_00899
+MTD-----TA-----------DAQNPLAGVLSADQVDALVNAAEDLGEGRHGVEELLSRM
+TQAVLERALETEMSEHLGYEAGDPAGAGTGNSRNGKT--TKSVQTLQGPGQITVPRDRNG
+SFEPVIVPKRSRRLGRVEDMILSLYARGMTTRDIGSHLEEIYGSKVSAATISRVTDVVAD
+EVAQWQSRPLETVYPIVYIDAIWLKIRDGGVVTNKACHVAVGVDLEGRKQVLGLWLGVSE
+GAKFWANVLTEIRNRGTKDILILCCDGLSGLPAAVNSIYPETVVQTCVVHLLRSAMKYAS
+YADRKTMAKDMRPIYTAATVEAAQLALEAF-AEIWQTKAPGAVLAWRTAWEDFIPFLAFT
+PEIRKVIYTTNQIESINYQLRKITKTRGSFPSDEAAIKLVYLGIRNIETRRGGEL-----
+--------------GTGTQGWHQALNAFAVQFPNRL-P-L
+>GCF_005280335_PROKKA_01506
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEAPKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_005280335_PROKKA_02100
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYGKGSEDASKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_020097155_PROKKA_01829
+MSESTTEMTGPMIDPVTGEIIDQKDLAEQ---------LLAQAKEQGVRLVGPGGLLNQL
+TKNVLETALEAELTEHLGHDHGQTPIA--ANMRNGTR--SKTVLTEIGPVEIEVPRDRDG
+SFEPVIVPKRKRRLDGTDQIVLSLSARGLTTGEIAVHFEEVYGAKVSKDTISRITEKVAG
+ELAEWSSRPLDPL-----------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------
+>GCF_023573625_PROKKA_00116
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_023573625_PROKKA_01547
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_023573625_PROKKA_01549
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_023573625_PROKKA_01880
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_023573625_PROKKA_01974
+MT---------MIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPAL
+VKAALERGLQAELTSHLGYEKGSSEALKHANSRNGTT--PKTVESEVGPIELDVPRDRGG
+SFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSE
+EVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTE
+GSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVA
+YQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFP
+PMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRG
+KPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000005.fa ADDED Viewed

	@@ -0,0 +1,184 @@

+>GCF_003691675_PROKKA_01778
+MDGPGVLAVPQARLRIGRLAEHDPVGLAEAAMELGISRRRVYVLLERYRRG--SGLVTRSDGGKGGGRLTEPQIIRELVC
+QRLTRQKRSIASLHREITRACAVQGLPAPARNTV--AARIARMNPVEVGRRREGAESVRPLQSAGDEVPVVVQIDHTVMD
+LIVVD-----------------------DRDRQ---PIGRPYLTVAIDVCSRCLVGMVVTLEPPSAVSVGLCLAHAAGDK
+RRLGIDAAWPMSGKPKALYVDNAREFKSEALTRGCDQHGISLDYRPLGRPHYGGIVERVIGTAMRQILPSNPVERGAYDA
+EKMAALTIAELERWLVLAVATY-HDTVHSTLGQTPAGRWVESVAATSTPMTTANPTAFLVDFLPVRKLTRTGFVLDHVHY
+FANALKPWIARREAIRRDPRDISRIWVLDPEALSNPAVSVWEHRQALARLRERGATEVDESGLFRMIEQMRTISETAQKT
+TKPPVVPTDLDVVARFGEIEQ
+>GCF_005280335_PROKKA_01282
+MSHANAALTPRHRLIVGRLVVDDGWPISEVAARFQVSWPTVKRWADRYRTG--EPMQDRSSRPHHSPNKTNQQTARRCVR
+LR-LRLREGPVQLASRLG-------IAPSTVHRILTDVHLNRLSHV----DRATGEPV--RRYEHDHPGSMLHVDVKKLG
+NIPDGGGWRYVGRRQGDKNRAATPDK--PKNKHYDPLMGMAYVHTVIDDHSR--VAYTEIHDDETARTATAVLIRAVEWF
+NARGVTV--------ERVLSDNGGAYRSHLWRDTCAELGIRHKRTRPYRPQTNGKIERFHRTLADGW---AYARCYTSEA
+ERRGELD---------DWLHYYNHHRPHTACGNLPPFSRL-------------------INVS-----------------
+----------------------------------------GQYS------------------------------------
+---------------------
+>GCF_005280335_PROKKA_02274
+MSHANAALTPRTRLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPSTMPTRTSPAVVKQIVA
+AR-WRQRLGPAQIASELG-------IPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+AQLGVEV--------ERVLSDNGSAYRSHAWRDAYTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYARFYSSET
+ERRAALP---------GWLHFYNHHRVHSAIGATPA-TRL-------------------NNLP-----------------
+----------------------------------------GHHT------------------------------------
+---------------------
+>GCF_020097155_PROKKA_00226
+MSHANAALTPRARLRLAKLIVDEHWAVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPATMPTRTSPAVVKQIVA
+AR-RRRRLGPVQIASELG-------MPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+AQLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYAKFYGSET
+ERRAALP---------GWVHFYNHHRVHSAIGAAPA-SRL-------------------NNLP-----------------
+----------------------------------------GHHT------------------------------------
+---------------------
+>GCF_020097155_PROKKA_00227
+M----------------------------------------------------------------------------VVQ
+LR-TVEKWGPARIAGHLSTVGGSINISPATVWRILNRNGISRLRDL----DMPTGESKRPRRYEHAAPGDMIHVDVKKVG
+RIPEGGGWAVHGRG---TEEALASRRVASR------RPGYVYIHAAVDDHSR--LAYAEVHPDERAGTAAAFWLRAVLFY
+REHGITT-------FSRCLTDNGPAYRSKVFNDALAGTGTAHKYTRPHTPRTNGKVERFNRTMKEEW---LYVRAYASDG
+ERTAALA---------AFLNTYNHDRPHSSLGNKPPASRVPITSYRVQPQPKV------LDVPQI----------EGL--
+----------------------------------------GHEP-----------------TLFDLL-------------
+---------------------
+>GCF_020097155_PROKKA_00312
+MSHANAALTPRARLRLAKLIVEEHWAVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPATMPTRTSPAVVKQIVA
+AR-WRRRLGPVQIASELG-------MPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+AQLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYAKFYGSET
+ERRAALP---------GWVHFYNHHRVHSAIGAAPA-SRL-------------------NNLP-----------------
+----------------------------------------GHHT------------------------------------
+---------------------
+>GCF_020097155_PROKKA_00315
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPSTMPTRTPPAVVKQIVA
+AR-WRRRLGPAQIASELG-------IPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+ARLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYARFYGSES
+ERRSALP---------GWLHFYNHHRHHSAIGAPPI-SRID------------------NNLP-----------------
+----------------------------------------GHHT------------------------------------
+---------------------
+>GCF_020097155_PROKKA_00448
+-------------------------------------------------------MVDRSSRPATMPTRTSPAVVKQIVA
+AR-RRRRLGPVQIASELG-------MPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+AQLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYAKFYGSET
+ERRAALP---------GWVHFYNHHRVHSAIGAAPA-SRL-------------------NNLP-----------------
+----------------------------------------GHHS------------------------------------
+---------------------
+>GCF_020097155_PROKKA_00627
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPATMPTRTPPAVVKQIVA
+AR-WRRRLGPVQIASELG-------MPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+AQLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYAKFYGSET
+ERRAALP---------GWVHFYNHHRVHSAIGAAPA-SRL-------------------NNLP-----------------
+----------------------------------------GHHT------------------------------------
+---------------------
+>GCF_020097155_PROKKA_00631
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPSTMPTRTPPAVVKQIVA
+AR-WRRRLGPVQIASELG-------MPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+AQLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYAKFYGSET
+ERRAALP---------GWVHFYNHHRVHSAIGAAPA-SRL-------------------NNLP-----------------
+----------------------------------------GHHI------------------------------------
+---------------------
+>GCF_020097155_PROKKA_00641
+MSHADAALTPRHRLKVARLVVDDGWPISEAAARFQVSWPTVKRWVDRYLSG--EPMSDRSSRPKSSPNRTPRVVAKRCVS
+LR-MRLREGPVQLAARLG-------IAPSTVHRILTTARMNRLSYV----DRATGEPI--RRYEHPHPGSLVHVDVKKLG
+NIPDGGGWRYVGRLQGGRNRAATPDK--PRNQYGGPKLGYAFVHTVIDDHSR--VAYTEVHDDETAITAVAVLHRAVEWF
+ADLGVTI--------ERVLSDNGGAYRSHLWRDTCEALSITPKRTRPYRPQTNGKVERFHRTMADGW---AYARCYTSEA
+ERRGALS---------GWLHQYNQHRPHTACSNQPPFSRL-------------------INVP-----------------
+----------------------------------------EQYT------------------------------------
+---------------------
+>GCF_020097155_PROKKA_00645
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPSTMPTRTPPAVVKQIVA
+AR-WRRRLGPAQIASELG-------IPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+ARLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYARFYGSES
+ERRSALP---------GWLHFYNHHRHHSAIGAPPI-SRID------------------NNLP-----------------
+----------------------------------------GHHT------------------------------------
+---------------------
+>GCF_020097155_PROKKA_00652
+MSHPNAALTPRHGLLVGRLVVDDGWPISEVAARFQVSWPTVKRWADRYRTG--QPMQDRSSRPHHSPNKTSAKTTRRCIQ
+LR-LRLREGPVQLACRLG-------IAPSTVHRILTDAHLNRLSHV----DRATGEPV--RRYEHDHPGAMLHVDVKKLG
+NIPDGGGWRYVGRRQGEKNRAATPGK--PRNKYRDPLMGKAYVHTVIDDHSR--VAYAEIHDDETAITATAVLVRAVEWF
+NARGVTV--------ERVLSDNGGAYKSHLWRDTCVELGIKHKRTRPYRPQTNGKIERFHRTLADGW---AYARCYTSED
+ERPGELE---------GWLHYYNHHRPHTACGDQPPFSRL-------------------TNVP-----------------
+----------------------------------------GQYT------------------------------------
+---------------------
+>GCF_020097155_PROKKA_00678
+MDA-------SERWRILRLHVEDAIPLATLARSTGVTERTLQRWLARYRTGGYAALAD-DARADHGVRRTAPELVRLVEG
+LALTKPRPSIATIHRQVGVHCAERGLPSPSYSAV--RSIVNGLDPGMVTLYRDKHELL--LRRRADRPNAIWQADHTMLD
+LLIVG-----------------------PNGK-----PARPWLTVILDDYSRAICGYMVFLGAPSAANTALALRQAIWHK
+P----EPDWPVCGIPDVLYTDHGSDFTSHRLGDTAAVLHLRIIHSQVARPQGRGKIERFFGTINTELLPTLPGHFAAGSS
+APTPALDLGGVDSAISTFIRSY-NARTHRELRTSPLHAWIADGWLPRLPESLEQLDGFLLTVPTTRVVQRDGIHFEGLRY
+TAATLAPFVGSTVSVRYDPRDVTEIRVFHRDVFLCTAISTEHQTETISLKQIQAARNAHRRALRGQIERIAIVNPKLDDT
+TTPAAVETDRPRLKTYEEDRS
+>GCF_020097155_PROKKA_00751
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPSTMPTRTPPAVVKQIVA
+AR-WRRRLGPVQIASELG-------MPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+AQLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYAKFYGSET
+ERRAALP---------GWVHFYNHHRVHSAIGAAPA-SRL-------------------NNLP-----------------
+----------------------------------------GHHT------------------------------------
+---------------------
+>GCF_020097155_PROKKA_01361
+MTHLNAALTPRHRLKVARLVVEDGHPISEVAARFQVSWPTVKRWVDRYLAG--ESMNDRSSRPKSSPKKTNKAVTKRCVS
+LR-MRLREGPIQLAARLG-------IAPSTVHRILTAARLNRLSYV----DRATGEPV--RRYEHPHPGSLVHVDVKKIG
+NIPDGGGWRYVGRRQGQKNRAATPDK--PKNKWHSPKLGYAFVHTVIDDHSR--VAYTEVHDDETAITAVAVLHRAVEWF
+AERGVTI--------ERVLSDNGGAYRSYLWRDTCEALSIRPKFTRPYRPQTNGKVERFHRTMGDGW---AYARCYTSEQ
+ERRDALP---------DWLHHYNQHRPHSACGNQPPFSRL-------------------INVP-----------------
+----------------------------------------GQYN------------------------------------
+---------------------
+>GCF_020097155_PROKKA_01794
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPSTMPTRTPPAVVKQIVA
+AR-WRRRLGPVQIASELG-------MPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+AQLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYAKFYGSET
+ERRAALP---------GWVHFYNHHRVHSAIGAAPA-SRL-------------------NNLP-----------------
+----------------------------------------GHHT------------------------------------
+---------------------
+>GCF_020097155_PROKKA_01820
+MSHANAALTPRHRLKVAQLVVDDGWPISEVAARFQVSWPTVKRWADRHRAG--ESMQDRSSRPHHSPNKTSPTVTRRCIQ
+LR-LRLREGPVQLACRLG-------IAPSTVHRILTDAHLNRLSHV----DRATGEPV--RRYEHDHPGAMLHVDVKKLG
+NIPDGGGWRYVGRRQGEKNRAATPGK--LRSKYSDPLMGKAYVHTVIDDHSR--VAYAEIHDDETAVTASAVLVRAVEWF
+NRRGVTV--------ERVLSDNGGAYRSHLWRDTCHELGIKHKRTRPYRPQTNGKIERFHRTLADGW---AYARCYTSEA
+ERRGELD---------GWLHYYNQHRPHTACGNQPPFSRL-------------------TNVP-----------------
+----------------------------------------DQYI------------------------------------
+---------------------
+>GCF_020097155_PROKKA_01832
+MSHKNAALTPRHRLKVARLVVEDGWPISEIAARFQVSWPTVKRWVDRYLAG--ESMEDRSSRPRVSPNKTPKTVTKRCVS
+LR-MRLREGPVQLAARLG-------IAPSTVHRILTTARLNRLSYV----DRATGEPI--RRYEHPHPGSLVHVDVKKLG
+NIPDGGGWRYVGRLQGERNRAATPGK--PKNKWHNPKLGYAFVHTVIDDHSR--VAYTEVHDDETAITAVAVLHRAVEWF
+ANRGVTI--------ERVLSDNGGAYRSHLWRDTCD--------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------------------
+>GCF_020097155_PROKKA_01835
+MSHANAALTPRARLRLAKLIVDEHWAVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPATMPTRTSPAVVKQIVA
+AR-RRRRLGPVQIASELG-------MPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+AQLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYAKFYGSET
+ERRAALP---------GWVHFYNHHRVHSAIGAAPA-SRL-------------------NNLP-----------------
+----------------------------------------GHHI------------------------------------
+---------------------
+>GCF_020097155_PROKKA_01890
+MSHANAALTPRARLRLAKLIVDEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPATMPTRTPPAVVKQIVA
+AR-RRRRLGPVQIASELG-------MPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+ARLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYAKFYGSET
+ERRAALP---------GWLHFYNHHRVHSAIGAAPA-SRL-------------------NNLP-----------------
+----------------------------------------GHHT------------------------------------
+---------------------
+>GCF_020097155_PROKKA_02162
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRSSRPSTMPTRTPPAVVKQIVA
+AR-WRRRLGPVQIASELG-------MPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+AQLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYAKFYGSET
+ERRAALP---------GWVHFYNHHRVHSAIGAAPA-SRL-------------------NNLP-----------------
+----------------------------------------GHHI------------------------------------
+---------------------
+>GCF_020097155_PROKKA_02206
+--------------------------------------------------------------------------------
+-------------------------MPASTVHAVLVRCRINRLARL----DRVTAEPI--RRYEHPHPGSLIHVDVTKFG
+RIPDGGGHRFVGRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSR--FAYVEMHSDERSQTAIAVLRRAVAHF
+AQLGVEV--------ERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGW---AYAKFYGSET
+ERRAALP---------GWVHFYNHHRVHSAIGAAPA-SRL-------------------NNLP-----------------
+----------------------------------------GHHS------------------------------------
+---------------------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000006.fa ADDED Viewed

	@@ -0,0 +1,103 @@

+>GCF_002008305_PROKKA_00157
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>GCF_002008305_PROKKA_01034
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>GCF_002008305_PROKKA_01292
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>GCF_002008305_PROKKA_01384
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETGDSQNVRTE
+>GCF_002008305_PROKKA_02077
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>GCF_003691675_PROKKA_01011
+------------------------------------------------------------
+-MVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>GCF_003691675_PROKKA_01104
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>GCF_003691675_PROKKA_01112
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>GCF_003691675_PROKKA_01114
+MSERIACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINRFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>GCF_003691675_PROKKA_02023
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMEIGDSQNVRTE
+>GCF_005280335_PROKKA_01214
+----MACRLVGLSRSAYRRPLKGDTVADPDRALRQWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>GCF_023573625_PROKKA_00588
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVASRGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>GCF_023573625_PROKKA_00590
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVVDW
+AGTRTGLWADPVS-----------------------------------------------
+-------------------------------
+>GCF_023573625_PROKKA_01250
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>GCF_023573625_PROKKA_01339
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTH-------------
+>GCF_023573625_PROKKA_01885
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLGHV---------------------
+>GCF_023573625_PROKKA_02205
+----MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVASRGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000009.fa ADDED Viewed

	@@ -0,0 +1,112 @@

+>GCF_002008305_PROKKA_00712
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVWLPKIEEWVEASTGRIRADVV
+HAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWITEPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALR
+DRTAPSVFAALDRCFRLIGGAPTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPATAHTVAYGVGRKVPENTPMV
+SFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQGPVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRS
+AAEAEFLAIGAGARTWLVEAAAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>GCF_002008305_PROKKA_01400
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVWLPKIEEWVEASTGRIRADVV
+HAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWITEPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALR
+DRTAPSVFAALDRCFRLIGGAPTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPATAHTVAYGVGRKVPENTPMV
+SFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQGPVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRS
+AAEAEFLAIGAGARTWLVEAAAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>GCF_002008305_PROKKA_01503
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVWLPKIEEWVEASTGRIRADVV
+HAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWITEPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALR
+DRTAPSVFAALDRCFRLIGGAPTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPATAHTVAYGVGRKVPENTPMV
+SFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQGPVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRS
+AAEAEFLAIGAGARTWLVEAAAAGTSRIGQKMAEAVTLAKLAGTDQVGRRPGLPAHRRRPPHRD------AHRHRPGHRR
+LGRPRYLQHRGGSPVSIHTPNTAAPAR
+>GCF_002008305_PROKKA_02228
+--------------------------------------------------------------------------------
+---------------------------------MHRPWITEPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALR
+DRTAPSVFAALDRCFRLIGGAPTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPATAHTVAYGVGRKVPENTPMV
+SFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQGPVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRS
+AAEAEFLAIGAGARTWLVEAAAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>GCF_003691675_PROKKA_00091
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVWLPKIEEWVEASTGRIRADVV
+HAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWITEPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALR
+DRTAPSVFAALDRCFRLIGGAPTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPATAHTVAYGVGRKVPENTPMV
+SFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQGPVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRS
+AAEAEFLAIGAGARTWLVEAAAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>GCF_003691675_PROKKA_00344
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVWLPKIEEWVEASTGRIRADVV
+HAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWITEPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALR
+DRTAPSVFAALDRCFRLIGGAPTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPATAHTVAYGVGRKVPENTPMV
+SFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQGPVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRS
+AAEAEFLAIGAGARTWLVEAAAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>GCF_003691675_PROKKA_01014
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVWLPKIEEWVEASTGRIRADVV
+HAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWITEPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALR
+DRTAPSVFAALDRCFRLIGGAPTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPATAHTVAYGVGRKVPENTPMV
+SFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQGPVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRS
+AAEAEFLAIGAGARTWLVEAAAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>GCF_003691675_PROKKA_01393
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVWLPKIEEWVEASTGRIRADVV
+HAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWITEPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALR
+DRTAPSVFAALDRCFRLIGGAPTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPATAHTVAYGVGRKVPENTPMV
+SFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQGPVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRS
+AAEAEFLAIGAGARTWLVEAAAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>GCF_003691675_PROKKA_02283
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVWLPKIEEWVEASTGRIRADVV
+HAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWITEPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALR
+DRTAPSVFAALDRCFRLIGGAPTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPATAHTVAYGVGRKVPENTPMV
+SFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQGPVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRS
+AAEAEFLAIGAGARTWLVEAAAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>GCF_023573625_PROKKA_00607
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVWLPKIEEWVEASTGRIRADVV
+HAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWITEPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALR
+DRTAPSVFAALDRCFRLIGGAPTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPATAHTVAYGVGRKVPENTPMV
+SFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQGPVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRS
+AAEAEFLAIGAGARTWLVEAAAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>GCF_023573625_PROKKA_01017
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVWLPKIEEWVEASTGRIRADVV
+HAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWITEPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALR
+DRTAPSVFAALDRCFRLIGGAPTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPATAHTVAYGVGRKVPENTPMV
+SFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQGPVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRS
+AAEAEFLAIGAGARTWLVEAAAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>GCF_023573625_PROKKA_01157
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVWLPKIEEWVEASTGRIRADVV
+HAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWITEPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALR
+DRTAPSVFAALDRCFRLIGGAPTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPATAHTVAYGVGRKVPENTPMV
+SFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQGPVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRS
+AAEAEFLAIGAGARTWLVEAAAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>GCF_023573625_PROKKA_01350
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVWLPKIEEWVEASTGRIRADVV
+HAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWITEPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALR
+DRTAPSVFAALDRCFRLIGGAPTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPATAHTVAYGVGRKVPENTPMV
+SFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQGPVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRS
+AAEAEFLAIGAGARTWLVEAAAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>GCF_023573625_PROKKA_02163
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVWLPKIEEWVEASTGRIRADVV
+HAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWITEPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALR
+DRTAPSVFAALDRCFRLIGGAPTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPATAHTVAYGVGRKVPENTPMV
+SFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQGPVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRS
+AAEAEFLAIGAGARTWLVEAAAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000010.fa ADDED Viewed

	@@ -0,0 +1,118 @@

+>GCF_002008305_PROKKA_00454
+MLHPTF---ATPDLTTFCRLDELGL----VAVGQLIEPDRATIECRVVEDDPWCRKCGVE
+GVPRDTVTRRLAHEPFGHRPTTLLVRVRRYRCG--HCRR-TWRQDMTRAAAPRAKISRGG
+LEWALRGIVIDHLTVTRVAAGLGVSWSAANAAVLAEGKRRLIDDPARFDGVTTIGVDEHV
+WRHTR--------LGDKYVTVIIDLTPARNKTGPARLLDMVEGRSKAVFKQWLAARPADW
+AKRIEVVAMDGFAGFKTAAAEELPDAVPVMDPFHVVRLAGDALDVCRRRVQQDTTGHRGL
+KGDPLYKARRTLHTGASLLTDRQRARLDAVF-ASEEHIEVEATWGIYQRIVAAYREPDKK
+KAKAMMQEVIATISSGVPAALVEVRKLGRTMKQRAGDILAFFDRPGTSNGPTEAINGRLE
+HLRGSALGFRNLTHYIARSLLEAGGFRPALHPRS-
+>GCF_002008305_PROKKA_00845
+M-----------------------------------------------------------
+---------------------------RRYRCS--GCGY-VWRQDTTASAEPRAKLSRRA
+LRWALEGIVVQHLTVARVAEGLGVAWDTANDAVLAEGKRVLIDEEHRFEGVKVVGVDEHV
+WRHTR--------RGDRYVTVIIDLTPVRDGTGPARLLNMVEGRSKQAFKTWLADRPQDW
+RDGVEVVAMDGFTGFKTAAVEELPDVVTVLDPFHVTRLAGEALDECRRRVQQAICGHRGR
+KGDPLYAARRTLSTGVDLLNDKQKDRLDTLF-ADDAHVEVEVTWSVYQRMIAAYRHENRR
+HGRELMARLIDSISTGVPKALVEITKLGRTLKKRAADVLAYFDRPSTSNGPTEAINGRLE
+HLRGSALGFRNLTNYIARSLLETGGFRPRLHPGFG
+>GCF_002008305_PROKKA_01392
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------MSLLTDRQEEHLSVLF-AHEKHAAVEAAWEIYQAMVAAYREFDRA
+KAKAKMEKVIAALSKKVPDTLEELGKLGRTLTKRAADVLAFFERLGTSNGPTEAINGRLE
+HLRGSALGFRNLTNYIARSLLESGGFRPLLHPQMR
+>GCF_003691675_PROKKA_01124
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------MSLLTDRQKEHLSVLF-AHEKHAAVEAAWEIYQAMVAAYREFDRA
+KAKAKMEKVIAALSKKVPDTLEELGKLGRTLTKRAADVLAFFERLGTSNGPTEAINGRLE
+HLRGSALGFRNLTNYIARSLLESGGFRPLLHPQTR
+>GCF_005280335_PROKKA_00108
+ML----------------------------------------------------------
+----------------------ILWRQRVWRCAEPGCARGTFVEQLPSLVAPRGSITTRA
+ISWAIGQLRREHGTIAGLARQLGTSWKTLWRAIRPE-LEHLADDESRFEGVTSLGVDEHI
+WHHVDRRR-----RGPRELTGMVDLSRDEHGRVRARLLDLVPGRSGKAYAGWLAERGDAF
+RRGVQVAALDPFAGYKTAIDQRLDDATAVLDAFHVVKLGTQVVDEVRRRVQQATLGHRGR
+KGDPLYGIQTILRAGAEHLTDKQLARLAAAIESDPAHEEVFVAWQCAQDLRAAYRSGNLA
+DGRAIAERLADSLHTS---PIPEVARLGRTLRRWRAAFLAYFTTNRSSNGGTEAINGIIE
+LHRRLARGFRNRDNYRLRMLLAAGGLTP-------
+>GCF_005280335_PROKKA_00508
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------MVDLSRDEHGRVRARLLDLVPGRSGKAYAGWLAERGDAF
+RRGVQVAALDPFAGYKTAIDQRLDDATAVLDAFHVVKLGTQVVDEVRRRVQQATLGHRGR
+KGDPLYGIQTILRAGAEHLTDKQLARLAAAIESDPAHEEVFVAWQCAQDLRAAYRSGNLA
+DGRAIAERLADSLHTS---PIPEVARLGRTLRRWRAAFLAYFTTNRSSNGGTEAINGIIE
+LHRRLARGFRNRDNYRLRMLLAAGGLTP-------
+>GCF_005280335_PROKKA_00509
+ML----------------------------------------------------------
+----------------------ILWRQRVWRCAEPGCARGTFVEQLPSLVAPRGSITTRA
+ISWAIGQLRREHGTIAGLARQLGTSWKTLWRAIRPE-LEHLADDESRFEGVTSLGVDEHI
+WHHVDRRR-----RGPKS------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------------------------
+>GCF_005280335_PROKKA_01091
+ML----------------------------------------------------------
+----------------------ILWRQRVWRCAEPGCARGTFVEQLPSLVAPRGSITTRA
+ISWAIGQLRREHGTIAGLARQLGTSWKTLWRAIRPE-LEHLADDESRFEGVTSLGVDEHI
+WHHVDRRR-----RGPKS------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------------------------
+>GCF_005280335_PROKKA_01092
+MT-------------------RSG------------------------------------
+----------------------VACRSRRW---------------------------TRS
+C-----------------------------------------------------------
+------------------------------------------------------------
+-------------GYKTAIDQRLDDATAVLDAFHVVKLGTQVVDEVRRRVQQATLGHRGR
+KGDPLYGIQTILRAGAEHLTDKQLARLAAAIESDPAHEEVFVAWQCAQDLRAAYRSGNLA
+DGRAIAERLADSLHTS---PIPEVARLGRTLRRWRAAFLAYFTTNRSSNGGTEAINGIIE
+LHRRLARGFRNRDNYRLRMLLAAGGLTP-------
+>GCF_020097155_PROKKA_00630
+MPEPTLYCRARGDYCTCCDL-LVGLPGLHVLTAERDDHDRLVVTVESAPEPMGCRSCGVI
+ARGHGRIEVSLVDAPAFGRPVRIIWRKRRWLCPDPACEVGSFIEQDEKVAAPRAVLTTRA
+CRWAIEQIRREHASVNGIRRQLGTGWRTVWDSIQPL-LQAADEDPSRFEGVAILGVDEHV
+WHHVSTKPIHHGGRGPKELTGMVDLTRDEGGRTRARLLDLVPGRSGRVYKDWLDQRGDAF
+RARIEVATLDPFHGYKNAIDDQLEDARSVLDAFHVVKLATTVVDDVRRRVQQQIHGHRGR
+KSDPLYRVRNVLRAGAENLTDRQRDRLETAWAAHEQHIEVEIAWLCAQKVRSAYRQGTHA
+AGRAVAEKILATFTSC---PIPEVARLGKTLNRWRREFLGYFDTNGASNGGTEAINGLIE
+LHRRIARGFRNRDNYRLRMLLIGGGLDMTHHTQR-
+>GCF_020097155_PROKKA_00638
+MPEPTLYCRARGDYCTCCDL-LVGLPGLHVLTAERDDHDRLVVTVESAPEPMGCRSCGVI
+ARGHGRIEVSLVDAPAFGRPVRIIWRKRRWLCPDPACEVGSFIEQDEKVAAPRAVLTTRA
+CRWAIEQIRREHASVNGIRRQLGTGWRTVWDSIQPL-LQAADEDPSRFEGVAILGVDEHV
+WHHVSTKPIHHGGRGPKELTGMVDLTRDEGGRTRARLLDLVPGRSGRVYKDWLDQRGDAF
+RARIEVATLDPFHGYKNAIDDQLEDARSVLDAFHVVKLATTVVDDVRRRVQQQIHGHRGR
+KSDPLYRVRNVLRAGAENLTDRQRDRLETAWAAHEQHIEVEIAWLCAQKVRSAYRQGTHA
+AGRAVAEKILATFTSC---PIPEVARLGKTLNRWRREFLGYFDTNGASNGGTEAINGLIE
+LHRRIARGFRNRDNYRLRMLLIGGGLDMTHHTQR-
+>GCF_020097155_PROKKA_00839
+MPEPTLYCRARGDYCTCCDL-LVGLPGLHVLTAERDDHDRLVVTVESAPEPMGCRSCGVI
+ARGHGRIEVSLVDAPAFGRPVRIIWRKRRWLCPDPACEVGSFIEQDEKVAAPRAVLTTRA
+CRWAIEQIRREHASVNGIRRQLGTGWRTVWDSIQPL-LQAADEDPSRFEGVAILGVDEHV
+WHHVSTKPIHHGGRGPKELTGMVDLTRDEGGRTRARLLDLVPGRSGRVYKDWLDQRGDAF
+RARIEVATLDPFHGYKNAIDDQLEDARSVLDAFHVVKLATTVVDDVRRRVQQQIHGHRGR
+KSDPLYRVRNVLRAGAENLTDRQRDRLETAWAAHEQHIEVEIAWLCAQKVRSAYRQGTHA
+AGRAVAEKILATFTSC---PIPEVARLGKTLNRWRREFLGYFDTNGASNGGTEAINGLIE
+LHRRIARGFRNRDNYRLRMLLIGGGLDMTHHTQR-
+>GCF_023573625_PROKKA_01343
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------MSLLTDRQKEHLSVLF-AHEKHAAVEAAWEIYQAMVAAYREFDRA
+KAKAKMEKVIAALSKKVPDTLEELGKLGRTLTKRAADVLAFFERLGTSNGPTEAINGRLE
+HLRGSALGFRNLTNYIARSLLESGGFRPLLHPQMR

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000013.fa ADDED Viewed

	@@ -0,0 +1,78 @@

+>GCF_003691675_PROKKA_00341
+-----MKELAAVGIPVAVTCRVLKLSRQPYYRWLADPVTDAELAEAYRANALFDAHQDDP
+EFGYRFLVDEAKEAGEVMCERSAWRICRDNGWWSVFGKKRGKNGKKPGPPVHDDL-----
+----VERDFTAGGSNQLWLTDVTEHRTAEGKLYMCAIKDVFSGRIVGYSIDSRMKARLAV
+QALQNAVARRG---DVAGCIVHSDRGSQFRSRKFVHALNRHGLVGSMGKVGAAGDNAAME
+SFFALLQKNVLDRRSWTTRDELRIAIVTWTERTYHRRRRQARLGRLTPIEYETMMKPAVT
+LPA
+>GCF_003691675_PROKKA_01765
+-MYPLVSELAADQIPVAVSLRVLKLARQPYYRWRDQPVAVSEVEQAYRANALHAAHLNDP
+EFGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCGFGAKRGKYGTRPGPPVHDDH-----
+----VRRDFSAEAPNRLWLTDITEHPTSEGKLYLCAIKDLYAGRIVGYSMAGRMQASLAV
+NALEQAVARRGGTDAVAGCIVHSDRGSQFRSALFQDALTTHGLIGSMGQVGAAGDNAAME
+SFFALLQKNVLDRRDWDTRDELRAGIITWIERTYHRRRRQVRLGRLTPVEYELIMDHTPA
+DAA
+>GCF_005280335_PROKKA_00706
+MMYPHVKELATDGIPVVVSVRMLKLARQPYCRWLENPLTRTDLDQAYRANALHAAHQNEK
+ALAHR-------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+SAS
+>GCF_005280335_PROKKA_02276
+-MYPLVSELAADGVPVAVSLRVLKLARQPYYRWREKPVAVSEVEQAHRANALHAAHLNDP
+EFGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCAFGAKRGKNGRRPGPPVHDDR-----
+----VRRDFSAEAPNRLWLTDITEHPTGEGKLYLCAIKDVHAGRIVGYSMAGRMQASLAV
+NALEQAVARRGGTDAVAGCIVHSDRGSQFRSALFQDALTAHGVIGSMGQVGAAGDNAAME
+SFFALLQKNVLDRRDWDTRDELRAGIITWIERSYHRRRRQVRLGRLTPVEYELIMDHTPA
+DPA
+>GCF_005280335_PROKKA_02495
+------------------------------------------------------------
+--------------------------------------------------MHDDR-----
+----VRRDFSAEAPNRLWLTDITEHPTGEGKLYLCAIKDVHAGRIVGYSMAGRMQASLAG
+NALEQAVARRGGTDAVAGCIVHSDRGSQFRSALFQDALTAHGLIGSMGQVGAAGDNAAME
+SFFALLQKNVLDRRDWDTRDELRAGIITWIERTYHRRRRQVRLGRLTPVEYELIMDHTPA
+DPA
+>GCF_005280335_PROKKA_02496
+-MYPLVSELAADGVPVAVSLRVLKLARQPYYRWRDQPVAVSEVEQAHRANALHAAHLNDP
+EFGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCAFGGQARQ------------------
+----------------------------ERALYL--------------------------
+-ALP--------------CMMTASAGTSL-------------------------------
+-------------------PKLRTGCG---------------------------------
+---
+>GCF_005280335_PROKKA_02615
+-MYPLVSELAADGVPVAVSLRVLKLARQPYYRWRDQPVAVSEVEQAHRANALHAAHLNDP
+EFGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCAFGAKRGKNGRRPGPPVHDDR-----
+----VRRDFSAEAPNRLWLTDITEHPTGEGKLYLCAIKDVHAGRIVGYSMAGRMQASLAG
+NALEQAVARRGGTDAVAGCIVHSDRGSQFRSALFQDALTAHGLIGSMGQVGAAGDNAAME
+SFFALLQKNVLDRRDWDTRDELRAGIITWIERTYHRRRRQVRLGRLTPVEYELIMDHTPA
+DPA
+>GCF_005280335_PROKKA_02636
+------------------------------------------MEQAHRANALHAAHLNDP
+EFGYRLLRDEAEAAGERMAARTAWRLCRQNGWHCAFGAKRGKNGRRPGPPVHDDR-----
+----VRRDFSAEAPNRLWLTDITEHPTGEGKLYLCAIKDVHAGRIVGYSMAGRMQASLAV
+NALEQAVARRGGTDAVAGCIVHSDRGSQFRSALFQDALTAHGVIGSMGQVGAAGDNAAME
+SFFALLQKNVLDRRDWDTRDDLRAGIITWIERAYHRRRRQVRLGRLTPVEYELIMDHTPA
+DPA
+>GCF_020097155_PROKKA_01887
+-MHPLVRELAVDGIPVAVTCRVLKIARQPYYRWLASPVTPAELDEAYRANALFDAHKDDP
+EFGYRFLADEAREAGESMAERTAWRICSDMGWWSAFGKKRGRNGKKPGSPVHDDLCAVTD
+EKGRIRHQFNADAVNELWIGDITEHRTGEDRLYLCAFKDVYSNRIVGYSIDSRMKSSLAV
+TALNNAVARRG---EVAGCVVHTDRGSQCRSRKFVHALNRHGMVGSMGRVGATGDNAAMA
+SFFALLQKNVLERRSWATREDLRIAIVTWIERTYHRRRRQVALGRLTPIEYEAIMTTPAS
+QAA
+>GCF_023573625_PROKKA_00898
+-MYPLVRELAVDGIPVAVTCRVLKIARQPYYRWLASPVTPAELDETYRANALFDAHKDDP
+EFGYRFLADEAREAGELMAERTAWRICSDMGWWSAFGKKRGRNGKKPGSPVHDDLCAATD
+EKGRIWHQFNADAVNELWIGDITEHRTGEGRLYLCAFKDVYSNRIVGYSIDSRMKSSLAV
+TALNNAVARRG---EVAGCVVHTDRGSQFRSRKFVHALNRHGMVGSMGRVGAAGDNAAME
+SFFSLLQKNVLDRRSWATREDLRIAIVTSIERTYHRRRRQAALGRLTPIEYEAIMTTPAS
+QAA
+>GCF_023573625_PROKKA_01544
+MTYPLVAELADAGILVTVSCRVLKLARQPYYRWRNAPVRDADMLRAYRINALHDAHHDDP
+TFGYRYLADEARRAGWRMSRRTAWKLCSQAGILSSAQRRRRGKGKKTGPPVFDDH-----
+----VQRVFRADAPNRLWLTDITEHRTSEGKLYCCAIKDVFSNRIVGYSISDRMTAKLAV
+DAVRNAVARRG---EVAGCILHADRGSQFRSRAMARELRRHDMVGSMGRVGAAGDNAAME
+SFWSLLQTNVLNQQRWTTRQELRLVIVVWIERKYHRQRAQDILGGLTPIEFEAKLAEPHT
+LAA

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000014.fa ADDED Viewed

	@@ -0,0 +1,101 @@

+>GCF_002008305_PROKKA_00160
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDAS-RFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHP
+GDATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAME
+LDHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGI
+QIIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRT
+GDHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLP
+RVVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRI
+IGITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSC
+CAA
+>GCF_002008305_PROKKA_01074
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDAS-RFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHP
+GDATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAME
+LDHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGI
+QIIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRT
+GDHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLP
+RVVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRI
+IGITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSC
+CAA
+>GCF_002008305_PROKKA_02060
+MNEAVP--HFDLAIIGSGGGAFAAAIRATNLDKRVVMIERGTVGGTCVNTGCIPSKALLA
+AAEARHTAQDAG-RFPGLT-ATAGPVDMEALIAGKRALVENVRSDKYVDLVADYGWELRH
+GNAVFTGTAADPALEVTAQDGTRETITAAHYLVATGSTPWAAPINGLDTVDYLTSTTAME
+LDEVPESLLVIGGGYVALEQAQLFARLGSKVTMLVRSRLASGEEPEASRALMSVFANEGI
+RVIRRSTVSSITQD-TDGGIAAQADIAGGRETLRASKVLVATGRRPVTDGLNLAGVSVKT
+GDKGEVVVEDTLVSSNPRVWAAGDVTGHPEYVYVAASHGTLMVDNAFSDAGRAVDYSHLP
+RVTFTSPNLAVVGMTDKQARDAGIRCECRVVPLEYIPRAVVNRDTRGFIKMVADADTGRI
+VGITAVAKEAGDLAATGVYILQAGMTVDQVANLWSPYLTMAEGIKIVAQSFKTDVSKLSC
+CAA
+>GCF_003691675_PROKKA_00298
+MPT-----KYDLAIIGSGGGAFAAAIRATTLGKSVVMIERGTLGGTCVNTGCVPSKALIA
+AADARHSAADAADRFPGIA-TTAGPVDMPALIAGKQALVESLRGEKYADVADSYGWAVRR
+GDAAFAGTPDAPVLQVAGDDGSTETIEAGHFLVATGSRPWAPPIDGLDETGYLTSTTAME
+LTELPESLLVLGGGYVALEQAQLFARLGSQVTVLVRSRLASKEEPEVSRTLEEVFADEGI
+RVVRRALPTRVSRDAATGQAVVTADVAGGREEFRADQVLVALGRRPVTDGLGLDRVGVET
+GDLGEVVVSDRMQSSHPRIWAAGDVTGHPEFVYVAAHHGTLVAENAFADADRAVDYARLP
+RVTFTGPAIGAVGMTEKDVVAAGIRCDCRVLPLHHVPRALVNRDTRGFVKIVVDADTGKI
+LGITAVAKDAGELAAAGVHVL--GKTVAEVADAWAPYLTMAEGIRIAAKAFTTDPSLLSC
+CA-
+>GCF_003691675_PROKKA_00337
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDAS-RFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHP
+GDATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAME
+LDHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGI
+QIIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRT
+GDHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLP
+RVVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTCGFIKMVTDADTGRI
+IGITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSC
+CAA
+>GCF_003691675_PROKKA_00346
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDAS-RFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHP
+GDATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAME
+LDHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGI
+QIIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRT
+GDHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLP
+RVVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRI
+IGITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSC
+CAA
+>GCF_003691675_PROKKA_00793
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDAS-RFPGLPLPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHP
+GDATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAME
+LDHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGI
+QIIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRT
+GDHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLP
+RVVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTCGFIKMVTDADTGRI
+IGITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSC
+CAA
+>GCF_005280335_PROKKA_00723
+MTATANSRSYDLAMIGSGGAAFAAAIRATSLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDAS-RFPGLPLPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHP
+GDATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAME
+LDHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGI
+QIIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRT
+GDHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLP
+RVVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRI
+IGITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSC
+CAA
+>GCF_020097155_PROKKA_02220
+MNEAVP--HFDLAIIGSGGGAFAAAIRATNLDKRVVMIERGTVGGTCVNTGCIPSKALLA
+AAEARHTAQDAG-RFPGLT-ATAGPVDMEALIAGERALVENVRSDKYVDLVADYGWELRH
+GNAVFTGTAADPALEVTAQDGTRETITAAHYLVATGSTPWAAPINGLDTVDYLTSTTAMD
+LDEVPESLLVIGGGYVALEHAQLFARLGSKVTMLVRSRLASGEEPEASRALMSVFANEGI
+RVIRRSTVSSITQD-TDGGIAAQADIAGGRETLRASKVLIATGRRPVTDGLNLAGVSVKT
+GDKGEVVVEDTLVSSNPRVWAAGDVTGHPEYVYVAASHGTLMVDNAFSDAGRAVDYSHLP
+RVTFTSPNLAVVGMTDKQARDAGIRCECRVVPLEYIPRAVVNRDTRGFIKMVADADTGRI
+VGITAVAKEAGDLAATGVYILQAGMTVDQVANLWSPYLTMAEGIKIVAQSFKTDVSKLSC
+CAA
+>GCF_023573625_PROKKA_01023
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDAS-RFPGLPLPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHP
+GDATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAME
+LDHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGI
+QIIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRT
+GDHGEVVVDGHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLP
+RVVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRI
+IGITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSC
+CAA

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000015.fa ADDED Viewed

	@@ -0,0 +1,80 @@

+>GCF_002008305_PROKKA_00355
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIELEDPYEKIGAELVKEVAKKT
+DDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIEKAVEAVTSELLSASREIETKDQIAATASISAADKQIGSLI
+AEALDKVGKEGVITVEESNTFGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVISSEVGLSLENATLDLLGSARK
+VVITKDETTIVEGGGDAEQIAGRVAQIRSEIENTDSDYDREKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRN
+AKAAVEEGIVAGGGVALIQAGA---KAFGGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKTLDDGHGLN
+AATGEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMGGMM
+>GCF_002008305_PROKKA_01656
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVELEDPYENMGAQLAKEVATKT
+NDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKRGIEVAVAAVEQRLQENARPVEGK-EVAHVAAISAQNDEVGELL
+ARAFDTVGTDGVITIEESSTTSTELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVVQ
+ANKPLFVIAEDIEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGAQVVSPDLGMKLEQADLDVLGSARR
+ITVTKDETTIVDGGGAPEDVEARIAQIKAEAAATDSDWDREKLQERLAKLSGGIGVIRVGAATEVELKERKHRIEDAVSS
+TRAALEEGIVAGGGTALINALTVLDTDADVQALTGDAAVGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFN
+AKTGVYGDLIADGVIDPVKVTRSALANATSIAALVLTTETLVADKPADEDEA----------GHQH
+>GCF_003691675_PROKKA_00071
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPCGRNVVLEKKWGAPTITNDGVSIAKEIELEDPYEKIGAELVKEVAKKT
+DDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIEKAVEAVTSELLSASREIETKDQIAATASISAADKQIGSLI
+AEALDKVGKEGVITVEESNTFGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVISSEVGLSLENATLDLLGTARK
+VVVTKDETTIVEGGGDAEQIAGRVAQIRSEIENTDSDYDREKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRN
+AKAAVEEGIVAGGGVALIQAGA---KAFGGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKTLDDGHGLN
+AATGEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMGGMM
+>GCF_003691675_PROKKA_01361
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVELEDPYENMGAQLAKEVATKT
+NDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKKGIEVAVAAVERRLQENARPVEGQ-EVAHVAAISAQNDEVGELL
+ARAFDTVGTDGVITIEESSTTSTELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVLQ
+ANKPLFVIAEDIEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGAQVVSPDLGMKLEQADLDVLGSARR
+ITVTKDETTIVDGGGAAEDVEARVAQIKAESAATDSDWDREKLQERLAKLSGGIGVIRVGAATEVELKERKHRIEDAVSS
+TRAALEEGIVAGGGTALINALTALDTDADVQALTGDAAVGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFN
+AKTGVYGDLIADGVIDPVKVTRSALANATSIAALVLTTETLVADKPADEDEA----------GHQH
+>GCF_005280335_PROKKA_01238
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVELDDPYENMGAQLAKEVATKT
+NDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKKGIEVAVAAVEQRLQENARPVEGK-EVAHVAAISAQNDEVGELL
+ARAFDTVGTDGVITIEESSTTSTELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDPYVLINSGKISNVQELLPVLEKVLQ
+ASRPLFVIAEDIEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMLQDIAVLTGAQVVSPDLGMKLEQADLDVLGSARR
+ITVTKDETTIVDGGGSAEDVEARVAQIKAESAATDSDWDREKLQERLAKLAGGIGVIRVGAATEVELKERKHRIEDAVSS
+TRAALEEGIVAGGGTALINALSVLDTDADVQALTGDAASGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFN
+AKTGVYGDLIADGVIDPVKVTRSALANAASIAALVLTTETLVADKPEDEDE------------HQH
+>GCF_005280335_PROKKA_02606
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIELEDPYEKIGAELVKEVAKKT
+DDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIEKAVDAVTAELLSASREIETKEQIAATASISAADKQIGSLI
+AEALDKVGKEGVITVEESNTFGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVISSEVGLSLENATLDLLGTARK
+VVITKDETTIVEGAGDAEQIAGRVAQIRAEIENTDSDYDREKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRN
+AKAAVEEGIVAGGGVALIQAGA---KAFGGLTLEGDEATGANIVKVAIEAPLKQIAFNAGMEPGVVADKVKTLQDGHGLN
+AATGEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMGGMM
+>GCF_020097155_PROKKA_01149
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIARDVELEDPYENMGAQLAKEVATKT
+NDIAGDGTTTATVLAQALVNEGMRQVAAGAAPNEVKKGIETAVAAVEKRLQENARPVEGK-EVAHVAAISAQNDEVGELL
+ARAFDTVGTDGVITIEESSTTSTELDVTEGMQFDKGYLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVLQ
+ANKPLFVIAEDVEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGATVVSPDLGMKLEQADLDVLGSARR
+VTVTKDATTIVDGGGEAADVEARVSQIKAEVAATDSDWDREKLQERLAKLAGGIGVIRVGAATEVELKERKHRIEDAVSS
+TRAALEEGIVAGGGTALINALSVLDEDAEVTALTGDAATGVEIVRKALKEPLRWIAQNAGEDGYVVVSKVAEMKPNEGFN
+AKTGVYGDLIADGVIDPVKVTRSALANAASIAALVLTTETLVADKVEDEDE------------HQH
+>GCF_020097155_PROKKA_02465
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIELEDPYEKIGAELVKEVAKKT
+DDVAGDGTTTATVLAQALVREGLRNVAAGADPISLKRGIEKAVEAVTSELLSAAREIETKDQIAATASISAADAQIGSLI
+AEALDKVGKEGVITVEESNTFGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISTVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVISSEVGLSLENASLDLLGTARK
+VVITKDETTIVEGAGDADQIAGRVAQIRSEIANTDSDYDREKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRN
+AKAAVEEGIVAGGGVALIQAGA---KAFEGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKSLESGHGLN
+AATGEYVDLMAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMGGMM
+>GCF_023573625_PROKKA_00362
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIELEDPYEKIGAELVKEVAKKT
+DDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIEKAVEAVTSELLSASREIETKDQIAATASISAADKQIGSLI
+AEALDKVGKEGVITVEESNTFGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVISSEVGLSLENATLDLLGTARK
+VVVTKDETTIVEGGGDAEQIAGRVAQIRSEIENTDSDYDREKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRN
+AKAAVEEGIVAGGGVALIQAGA---KAFGGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKTLDDGHGLN
+AATGEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMGGMM
+>GCF_023573625_PROKKA_01586
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVELEDPYENMGAQLAKEVATKT
+NDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKKGIEVAVAAVERRLQENARPVEGQ-EVAHVAAISAQNDEVGELL
+ARAFDTVGTDGVITIEESSTTSTELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVLQ
+ANKPLFVIAEDVEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGAQVVSPDLGMKLEQADLDVLGSARR
+ITVTKDETTIVDGGGAAEDVEARVAQIKAEAAATDSDWDREKLQERLAKLSGGIGVIRVGAATEVELKERKHRIEDAVSS
+TRAALEEGIVAGGGTALINALTVLDTDADVQALTGDAAVGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFN
+AKTGVYGDLIADGVIDPVKVTRSALANAASIAALVLTTETLVADKPADEDEA----------GHQH

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000016.fa ADDED Viewed

	@@ -0,0 +1,91 @@

+>GCF_002008305_PROKKA_00992
+--MTPTPSRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALD
+VPGVELAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDE
+ASEKAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEQFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTGETVDYPVQAVYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDA
+DGAPVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWRAQEPSEESVIELLES
+RGVPYTTWAGWHALDEHEKSLGVQATEAGPVARERVKVVDREEMTRISREGVLLGAGG
+>GCF_002008305_PROKKA_01771
+-----MTVRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAVLD
+VPGVELAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDE
+ASEKAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTGETVDYPVQAIYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDA
+DGAPVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLES
+REVPYTTWAGWHALDEHEKSLGAQATEAGPVARERVKVVDREEMTRISRDGASVPTA-
+>GCF_003691675_PROKKA_00706
+MTLTPSSSRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALD
+VPGVELAGSFGGADFAAWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDA
+ASEKAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTDETVDYPVQAIYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDA
+DGAPVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLES
+REVPYTTWAGWHALDEHEKSLGAQATEAGPVARERVKVVDREEMTRISRESVLLGAGG
+>GCF_003691675_PROKKA_01478
+-----MTVRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAVLD
+VPGVELAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDE
+ASEKAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTGETVDYPVQAIYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDA
+DGAPVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLES
+REVPYTTWAGWHALDEHEKSLGAQATEAGPVARERVKVVDREEMTRISRDGASVPTA-
+>GCF_005280335_PROKKA_01106
+-----MTERPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVNALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAWLD
+VPGVELAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDE
+ASEKAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGL
+RMRRMELDGAGGVRPTDETVDYPVQAVYRAVGYFGSPLDGVEFDAARGVVPNDEGRVLDA
+DGVPVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDVDGLWTAQDPAEESVIDLLEA
+REVPYTTWEGWQALDAHEKSLGAQATEAGPVERERVKVVDREEMTRISREGAWAPTA-
+>GCF_005280335_PROKKA_01897
+MTLTPSSPKPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVNALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAWLD
+VPGVELAGSYGGADFASWYDGHPDVPRHWPLDATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDE
+ASEKAIEENNQVRTMVGTLTNWLMEQEDREQSASRRLHLHFLQAPEQFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTGETVDYPVQAVYRAVGYFGSPLDGVEFDAARGVVPNDEGRVLDA
+DGVPVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLES
+REVRYTTWAGWLALDDHEKALGVQATEAGPVERERVKVVDREEMTRISRESVLLGAGG
+>GCF_020097155_PROKKA_01032
+-----MTERPDRPLRIAVVGAGPAGVYTADILTKEERDFQVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVTALHKVMDRGDIRFIGNVDVGTTVSLEDLRRLYDVVVFTTGAVRDAALD
+VPGVELEGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLL
+VTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDE
+ASEKAIEENNQVRTMVGTLTNWLMEQEDRTEQASRRLHLHFLQAPEEFLDADGDGRVDGL
+RMRRMELDGQGGITPTDETVDYDVQAVYRAVGYFGSPVPGVEFDDVRGVIPNAEGRVLDA
+AGHPVPGLYTSGWIKRGPVGLIGSTKGDSLETIKHLIEDEPGLYTAEDPSEQAVLDLLAE
+RGVDYTTWEGWHALDAHEKALGAEATQAGPVERERVKVVDRAEMTRISRAGTGLA---
+>GCF_020097155_PROKKA_01844
+MTPTPSSSRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVNALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALD
+VPGVELAGSFGGADFAAWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDE
+ASEQAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEQFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTGETVDYPVQAVYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDA
+DGAPVPGLYASGWIKRGPVGLIGHTKGDSLETITHLIEDEPGLWRAQEPSEESVIELLES
+REVPYTTWAGWHALDDHEKSLGAQATEAGPVARERVKVVDREEMTRISRKSILLGAGG
+>GCF_023573625_PROKKA_00935
+MTLTPSSSRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVNALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALD
+VPGVELAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDE
+ASEKAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTDETVDYPVQAIYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDA
+DGAPVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLES
+REVPYTTWAGWHALDEHEKSLGAQATEAGPVARERVKVVDREEMTRISRESVLLGAEG
+>GCF_023573625_PROKKA_01700
+-----MTARPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALD
+VPGVELAGSFGGADFAAWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDE
+ASEKAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTGETVDYPVQAVYRAVGYFGSPVEGVEFDEVRGVIPNAQGRVLDA
+DGAPVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLES
+REVPYTTWAGWHALDDHEKSLGAQATEAGPVARERVKVVDREEMTRISRDGASVPTA-

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000022.fa ADDED Viewed

	@@ -0,0 +1,88 @@

+>GCF_002008305_PROKKA_00633
+MSTP----HH-----------HDHPTDQTAE------HPDPNPPAGHANHTDHAAHHPADAAAHGQAMPQGHAHSALDE-
+----DHQVH----DHGQHAGHS--TAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGTVIYLYGGM
+PFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELALLVVIMLLGHWMEMRALGAASSALDALAA
+LLPEEAEKVVDGDTITVPITELAVGDVVLVRAGARVPADGTILEGAAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTV
+RVKVAAVGTDTTLAGIQRMVADAQESSSRAQALADRAAALLFWFALVAAIITAIVWTAIGQPTDAVTRTVTVLVIACPHA
+LGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHVVTAVTAMPGVSEAELLAVAAAAEADSEH
+PVARAIVTAAGQHPQASTLRKRGTDFSAAMGRGVRATVDGSEILVGGPNMLRELNLTMPAEITEHTASWTARGAGVLHVL
+REGSVIGAVAVEDKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTELQSRGLSVA
+MVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQASYTKMIQNLVWATGYNVLAVPLAAGVL
+APIGFVLSPAVGAILMSVSTIVVALNAQLLRRIDLDPEH--LAPLERPRSQAALQPAAVS
+>GCF_002008305_PROKKA_01289
+MTDPTT--HH-----------HDHAGVATTES----GHRDDS----RAENEDHTMEH-GDHAGH----------------
+-GH-----HGG-----GHAGHGDHVGQFRRLFWINLIIAIPVVAFSPMFAMLLGYSVPSWAG--WVAAVLGSVMYAWGGT
+PFLTGAVSELKSRQPGMMLLIALGITVAFLASWAATVGLVHPELEFWWELALLIVIMLLGHWIEMRSLAQTTSALDSLAA
+LLPDEAERIEGDDVVKVDPAELRVGDVVIVRPGGSVPADGTIVDGRADMDESMITGESHPVARGEGENVTAGTVATDSGL
+RVEITATGDDTALAGINRLVAEAQGSSSRAQRIADRAAALLFWFALGAALITAVVWTLFGLPDDAVVRTITVLVIACPHA
+LGLAIPLVVSIATERAARGGVLIKDRLALESMRQVDAVLFDKTGTLTKGEPTVTGVEPTGGLNAEQLLALAASAEADSEH
+PLARSIVTAAKEKGLAV---EPASGFTSSPAVGVTATVADHEIRVGGPRLLEETGQDEIGVADE----WRAEGAIILHVL
+RDGKVIGGLKLADEVRPESRDAVDALHQLGVEVVMITGDAEAVANEVGRELGIDRVFAGVRPEDKSAKVDQLQKEGKKVA
+MVGDGVNDAPALAQADVGIAIGAGTDVAIASAGVILASSDPRSVLSVIQLSRAAYRKMRQNLWWAAGYNLLSVPLAAGVL
+APVGFVMPMSVGAILMSISTVVVALNAQLLRRIDLAPAASTRSVLEHQ-----------K
+>GCF_003691675_PROKKA_01008
+MTDPTT--HH-----------HDHAGVATTES----GHRDDS----RAENEDHTMEH-GDHAGH----------------
+-GH-----HGG-----GHAGHGDHVGQFRRLFWINLIIAIPVVAFSPMFAMLLGYSVPSWAG--WVAAVLGSVMYAWGGT
+PFLTGAVSELKSRQPGMMLLIALGITVAFLASWAATVGLVHPELEFWWELALLIVIMLLGHWIEMRSLAQTTSALDSLAA
+LLPDEAERIEGDDVVKVDPAELRVGDVVIVRPGGSVPADGTIVDGRADMDESMITGESHPVARGEGENVTAGTVATDSGL
+RVEITATGDDTALAGINRLVAEAQGSSSRAQRIADRAAALLFWFALGAALITAVVWTLFGLPDDAVVRTITVLVIACPHA
+LGLAIPLVVSIATERAARGGVLIKDRLALESMRQVDAVLFDKTGTLTKGEPTVTGVEPTGGLNAEQLLALAASAEADSEH
+PLARSIVTAAKEKGLAV---EPASGFTSSPAVGVTATVADHEIRVGGPRLLEETGQDEIGVADE----WRAEGAIILHVL
+RDGKVIGGLKLADEVRPESRDAVDALHQLGVEVVMITGDAEAVANEVGRELGIDRVFAGVRPEDKSAKVDQLQKEGKKVA
+MVGDGVNDAPALAQADVGIAIGAGTDVAIASAGVILASSDPRSVLSVIQLSRAAYRKMRQNLWWAAGYNLLSVPLAAGVL
+APVGFVMPMSVGAILMSISTVVVALNAQLLRRIDLAPAASTRSVLEHQ-----------K
+>GCF_005280335_PROKKA_00405
+MSTP----HH-----------HDHPTDQTAE------HPDPNPHAGHANHTDHAAHHPADAATHGQAMPQGHAHSALDE-
+----DHQVH----DHGQHAGHS--TAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGTVIYLYGGM
+PFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELALLVVIMLLGHWMEMRALGAASSALDALAA
+LLPEEAEKVVDGDTITVPITELAVGDVVLVRAGARVPADGTILEGAAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTV
+RVKVAAVGTDTTLAGIQRMVADAQASSSRAQALADRAAALLFWFALVAAIITAIVWTVMGQPTDAVTRTVTVLVIACPHA
+LGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHVVTAVTAMPGVSEAELLAVAAAAEADSEH
+PVARAIVTAAGQHPQASTLRKRGTDFSAAMGRGVRATVDGSEILVGGPNMLRELNLTVPAEITEHTASWTARGAGVLHVL
+REGSVIGAVALEDKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTELQSRGLSVA
+MVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQASYTKMIQNLVWATGYNVLAVPLAAGVL
+APIGFVLSPAVGAILMSASTIVVALNAQLLRRINLDPGH--LAPLGAPRPEAALQPAT-S
+>GCF_020097155_PROKKA_00711
+MTDPNSQQHHGHETDTPAHGEHHHGSVSAHASADAHGTREGQ----HTGHQGHAMDH-GQHSGH----------TGLDEH
+GGHDEHAQHGGYGDHSGHGGHGDHVGQFRRLFWINLVIAIPAVALSPMFAMLLGYEVPGWAG--WVAAALGTVMYVWGGR
+PFLTGAVSELKSRKPGMMLLIALAITVAFFASWAATLGLVHHELEFWWELALLIVIMLLGHWIEMRSLAQTTSALDSLAA
+LLPDEAERVEGENVVKVAPADLDVGDVVLVRPGGSVPADGTIVDGRAEMDESMITGESRPVSRGEGQTVTAGTVATDSGL
+RVEITATGDDTALAGINRLVAEAQNSSSRAQRIADKAAAWLFWFALGAALVTAVVWTLIGMPDEAVVRTITVLVIACPHA
+LGLAIPLVVSIATERAARGGVLVKDRLALESMRQVDAVLFDKTGTLTKGEPTVTGVEPTGELDADQVLALAASAEADSEH
+PLAKAIVTAAKDKGFAL---QQASGFSSSPAVGVTATVSGQEVRVGGPRLLEETGQHEVGTAEA----WRSEGAIILHVL
+RGGQVVGGLRLADEVRPESRYAVDALHALGVEVVMITGDAEAVANEVGKELGIDRVFAGVRPEDKSAKVSQLQEEGKRVA
+MVGDGVNDAPALAQADVGIAIGAGTDVAIASAGVILASSDPRSVLSIIQLSRRAYGKMKQNLWWAAGYNLLSVPLAAGIL
+APVGLVLPMSIGAILMSASTVVVALNAQLLRRIDLTPEASTRSVLERQ-----------K
+>GCF_020097155_PROKKA_02196
+MSTP----HH-----------HDHPTDQTAE------HPDPNPHAGHANHTDHAAHHPADAATHGQAMPQGHAHSALDE-
+----DHQVH----DHGQHAGHS--TAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGTVIYLYGGM
+PFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELALLVVIMLLGHWMEMRALGAASSALDALAA
+LLPEEAEKVVDGDTITVPITELAVGDVVLVRAGARVPADGTILEGTAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTV
+RVKVAAVGTDTTLAGIQRMVADAQESSSRAQALADRAAALLFWFALVAAIITAIVWTAIGQPTDAVTRTVTVLVIACPHA
+LGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHVVTAVTAMPGVSEAELLAVAAAAEADSEH
+PVARAIVTAAGQHPQASTLRKRGTDFSAAMGRGVRATVDGSEILVGGPNMLRELNLTMPAEITEHTASWTARGAGVLHVL
+REGSVIGAVAVEDKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTELQSRGLSVA
+MVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQASYTKMIQNLVWATGYNVLAVPLAAGVL
+APIGFVLSPAVGAILMSASTIVVALNAQLLRRINLDPGH--LAPLGAPRPEAALQPAT-S
+>GCF_023573625_PROKKA_00598
+MSTP----HH-----------HDHPTDQTAE------HPDPNPHAGHANHTDHAAHHPADAATHGQAMPQGHAHSALDE-
+----DHQVH----DHGQHAGHS--TAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGTVIYLYGGM
+PFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELALLVVIMLLGHWMEMRALGAASSALDALAA
+LLPEEAEKVVDGDTITVPITELAVGDVVLVRAGARVPADGTILEGAAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTV
+RVKVAAVGTDTTLAGIQRMVADAQESSSRAQALADRAAALLFWFALVAAIITAIVWTAIGQPTDAVTRTVTVLVIACPHA
+LGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHVVTAVTAMPGVSEAELLAVAAAAEADSEH
+PVARAIVTAAGQHPQASTLRKRGTDFSAAMGRGVRATVDGSEILVGGPNMLRELNLTMPAEITEHTASWTARGAGVLHVL
+REGSVIGAVAVEDKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTELQSRGLSVA
+MVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQASYTKMIQNLVWATGYNVLAVPLAAGVL
+APIGFVLSPAVGAILMSVSTIVVALNAQLLRRIDLDPEH--LAPLERPRSQAALQPAAVS
+>GCF_023573625_PROKKA_01247
+MTDPTT--HH-----------HDHAGVATTES----GHRDDS----RAENEDHTMEH-GDHAGH----------------
+-GH-----HGG-----GHAGHGDHVGQFRRLFWINLIIAIPVVAFSPMFAMLLGYSVPSWAG--WVAAVLGSVMYAWGGT
+PFLTGAVSELKSRQPGMMLLIALGITVAFLASWAATVGLVHPELEFWWELALLIVIMLLGHWIEMRSLAQTTSALDSLAA
+LLPDEAERIEGDDVVKVDPAELRVGDVVIVRPGGSVPADGTIVDGRADMDESMITGESHPVARGEGENVTAGTVATDSGL
+RVEITATGDDTALAGINRLVAEAQGSSSRAQRIADRAAALLFWFALGAALITAVVWTLFGLPDDAVVRTITVLVIACPHA
+LGLAIPLVVSIATERAARGGVLIKDRLALESMRQVDAVLFDKTGTLTKGEPTVIGVEPTGGLNAEQLLALAASAEADSEH
+PLARSIVTAAKEKGLAV---EPASGFTSSPAVGVTATVADHEIRVGGPRLLEETGQDEIGVADE----WRAEGAIILHVL
+RDGKVIGGLKLADEVRPESRDAVDALHQLGVEVVMITGDAEAVANEVGRELGIDRVFAGVRPEDKSAKVDQLQKEGKKVA
+MVGDGVNDAPALAQADVGIAIGAGTDVAIASAGVILASSDPRSVLSVIQLSRAAYRKMRQNLWWAAGYNLLSVPLAAGVL
+APVGFVMPMSVGAILMSISTVVVALNAQLLRRIDLAPDASTRSVLEHQ-----------K

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000023.fa ADDED Viewed

	@@ -0,0 +1,57 @@

+>GCF_002008305_PROKKA_02238
+MAHDDANTTTTDQLTLQDPTKRYPVISPPEQSLPGTGLDAEMTPKVDLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDAQHVLEVLQAEGRTAVGIPGD
+LRDKTFCVDLVA----QAVE--KLGGLDVLVNNGGKQVAQDSIEDIDDEQLEATFDINIL
+AQFRLVKAALPHLKP---GSTIINTTSVVAYMAPEQLVDYSATKAAINTFTKALGQQLAP
+KGIRVNAVAPGPIWTPLQPSGGQKPEALPEFGQSTPLGRAGQPTELAPAYVFLASPESSY
+VVGATIPVTGGMPTP---------
+>GCF_003691675_PROKKA_01940
+MAHDDANTTTTDQLTLQDPTKRYPVISPPEETLPGTGLDAEMTPKADLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDAQHVLEVLQAEGRTAVGIPGD
+LRDKTFCVDLVA----QAVE--KLGGLDVLVNNAGKQVAQDSIEDIDDEQLEATFDVNIL
+AQFRLVKAALPHLKP---GSTIINTTSVVTYMAPPQLVDYASTKAAINTFTKALGQQLAP
+KGIRVNAVAPGPIWTPLQPSGGQKSEDLPEFGQSTPLGRAGQPTELAPAYVFLASPESSY
+VVGATIPVTGGMPTP---------
+>GCF_005280335_PROKKA_00513
+MANDDANTTTTDQLTLQDPVKRYPVISPPEQSLPGTGLDAEMTPKADLGEHSYRGTGRLT
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDARNVLAVLEKEGRTAVGIAGD
+LRDRQFCQDVVA----QAVE--AMGGLDVLVNNGGKQVAQKEFEAIDDEQLEATFDVNIL
+AQFRLVRAALPHLKP---GASIINTTSVVSYMPPETLIDYASTKAAINNFTKGLGQQLAP
+KGIRVNAVAPGPIWTPLQPSGGQPTEELPDFGQSTPLGRAGQPTELAPAFVFLASAESSY
+VVGATIAVTGGMPTP---------
+>GCF_020097155_PROKKA_00440
+MTDVSTSTDTAVG-------------------------DSDTRPAAART-DAPAATVLLA
+GRAALVTGGTLGIGSGIAASLRDAGARVAVTGLTEQECAAAR------EAGFPAYVL--D
+VRDRAACAEVVG----AVVE--EFGGLDVLASNAGI-YPQARIADMTDEDIDLIFDVNVK
+GTIHAVQAALPALVASGRGRVVITSSITGNHTGYPAWSHYGATKAAQLGFVRSAAIELAR
+QGVTVNAVLPGNIITPGLEEMGQ--EYLDSMARSVPAGHLGEPADIGATVAFLASDGARY
+ITGQGIVVDGGQILPETPEALEGL
+>GCF_020097155_PROKKA_00454
+MANDDTNTTTTDQLTLQDPTKRYPVISPPEQSLPGTGLDAEMTPKADLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVLTYLPEEEKDAQHVKEVIEAEGRKAVTVSGD
+LRDKQFCKDLVE----RAVQ--ELGGLDILVNNGGKQVAQEEFEQIDDEQLEATFDINIL
+AQFRLVRAALPHLKP---GSTIINTTSVVAYMAPEQLVDYSSTKAAINTFTKALGQQLAP
+KGIRVNAVAPGPIWTPLQPSGGQKPEALPEFGQSTPLGRAGQPTELAPAYVFLASPESSY
+VVGATIPVTGGMPTP---------
+>GCF_020097155_PROKKA_00650
+M-----------------------------------------------------------
+-----------GI------------------HYARDSTAAEAVVERVNEAGASGVLIRAD
+LAEGAAGAAHLATRWRDEVRRHDARGTDVLVSNAGINGAQ-SLSELDEGTVARVVNVNLV
+APLMLVHHLSDHIND---HGRVIGISSGFARIAAPTHVAYTASKAGLEAAFRAIAAELAE
+RDITVNTVRPGVIDTDINADWINEPGARDAVAAAAALRRVGQPDDVADIVAFLASHSSRW
+MTGQSLDATGGTQL----------
+>GCF_020097155_PROKKA_01865
+MSTHD----------LPDPLTQFPRFAPERQTQEEPGLSARMDPEPDCGEDTYVGIGRLK
+GRRALVTGGDSGIGRAVALAYAREGADVVFTHLPEEAEDAARTTELLDAEGVRHVAREVD
+LRDEAATRALVR----DAVK--FLGGLDLIANVAGEQRYVDDLAELDPRQVRDTFEINVF
+ALIWIVQEALPHLPA---GAAIVNTASTQATTPLPGLVDYAGTKGAIVSITKALAQQLTP
+RGIRVNAVVPGAIWTPIQVSLGRAPEQVDVLGQDAPLGRPGQPAEMAPAYVFLASTEASY
+VSGEVLGATGGTLY----------
+>GCF_023573625_PROKKA_02170
+MAHDDANTTTTDQLTLQDPTKRYPVISPPEETLPGTGLDAEMTPKADLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDAQHVLEVLQAEGRTAAGIPGD
+LRDKTFCADLVA----QAVE--KLGGLDVLVNNGGKQVAQDSIEDIDDEQLEATFDINIL
+AQFRLVKAALPHLKP---GSTIINTTSVVAYMAPEQLVDYSATKAAINTFTKALGQQLAP
+KGIRVNAVAPGPIWTPLQPSGGQKPEALPEFGQSTPLGRAGQPTELAPAYVFLASPESSY
+VVGATIPVTGGMPTP---------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000024.fa ADDED Viewed

	@@ -0,0 +1,104 @@

+>GCF_002008305_PROKKA_02297
+M----------------------SSDQRTA-SAPRHALPPQDGVPAVKVGTRVSRGPGRVTALDGLRGIAVLAVLVFHAW
+PTFLRGGFVGVDMFFVLSGFLITTGLVRGVDAGRGVALGTFWMKRVRRLIPAMLMALVGTTALAWLAVDEFP----AGLG
+RQWFGALTYTSNWVMILEGGDYFNRA----SPPLFEHLWSLAIEEQFYILWPLLLW----GLLLLTWPPRSTVN------
+-----SGRVADRRRILAVAVAAVASAAWMAWGSWH--GFEQARLYFGTDTHAFGLLFGACVAIGLAHVPRPEHGGPEPRT
+SATRVAVAWGAVAVLAAGFAL--VDGGHAS-TYRGVLAGLSAVVAFIVWHVVQGDRRDS---------LSRALGNGFLRW
+WGRRSYAAYLWHWPLLVIMRVMVPVDAPGWVEPVAAGAILL-LTALIADLSTRLIEEPILHEGFRGAFGRWGAAARRAFT
+GGAGPIGQLAAAATALGLVAVPAAAV--AAVVHSPAQ--------TQLEQDIAQA-------------------EESLKA
+AEAAQQA----ARESRAAEQSKRAEA-----SASASPGSAAPGDAEG--SAGATSS----------------------PG
+SSAEPSGLG--------LGDPAVTRPTYSKEQLTAALPPSELGTDVTLIGDS-------VSLS-----AAPTLMEELPGM
+LLEAEVGYQIWDAADELEKLKADGQLSDVVVVALGANGTT-----------HRGDWEKILAAVGEDRLLVLVVPHGPMDW
+IADVQV----------------------------QMAAQAKAHPD--RIVLADWDAAAKQ--------HVTDF--SADGV
+HPRAD-----GQAMYAQLVRLTIEDRLGARR-----------
+>GCF_003691675_PROKKA_01990
+M----------------------SSDQRTA-PVPRHALSPQDGVPAVKVGTRVSRGPGRVTALDGLRGIAVLAVLVFHAW
+PTFLRGGFVGVDMFFVLSGFLITTGLVRGVDAGRGVALGTFWMKRVRRLIPAMLMALVGTTALAWLAVDEFP----AGLG
+RQWFGALTYTSNWVMILEGGDYFNRA----SPPLFEHLWSLAIEEQFYILWPLLLW----GLLLLTWPPRSTVN------
+-----SGRVADRRRILAVAVAAVASAAWMAWGSWH--GFEQARLYFGTDTHAFGLLFGACVAIGLAHVPRPEHGGPEPRT
+SATRVAVAWGAVAVLAAGFAL--VDGGHAS-TYRGVLAGLSAVVAFIVWHVVQGDRRDS---------LSRALGNGFLRW
+WGRRSYAAYLWHWPLLVIMRVMVPVDAPGWVEPVAAGAILL-LTALIADLSTRLIEEPILHEGFTGAFGRWGAAARRAFT
+GGAGPIGRLAAAATALGLVAVPAAAV--AAVVHSPAQ--------TQLEQDIAQA-------------------EESLKA
+AQAAQQA----ARESRAAEQTKRAEA-----SASGAPGSAAPGDAEG--SAGATPS----------------------PG
+SSAEPSGLG--------LGDPAVTRPTYSKEQLTAALPPSELGPDVTLIGDS-------VSLS-----AAPTLLEQLPGM
+LLEAEVGYQIWDAADEIEKLKADGQLSDVVVVALGANGTT-----------HRGDWEKILAAVGEDRLLVLVVPHGPMDW
+IADVQV----------------------------QMEAQAKAHPD--RIVLADWDAAAKQ--------HVTDF--SADGV
+HPRAD-----GQAMYAQLVRLTIEDRLGARR-----------
+>GCF_005280335_PROKKA_00439
+MVRRDVWPTIAGVPSLTPSSPVRSAEERTD-RGGGSRTRPL--VHADRPGIRVSPGPGRIPALDGLRGVAVLAVLVFHAW
+PALLPGGFVGVDMFFVLSGFLITTGLVRGVDGGRGLRLGPFWMRRVRRLVPSMVVALVCCTALAWLAVAEFP----AGLG
+RQWLGALTYTSNWVMILSGSDYFAAA----TPPLFEHLWSLAIEEQFYVLWPLVVA----GLLTLFWPREPTLR------
+-----GAFRADRARVLTVLALAAASAVWMAVGLRG--GAPHTRLYFGTDTHAFGLLLGAAVALMLAHTRRPEHGGAVMRN
+PPVRSAIAWGLFAALLAAFVL--VDGREDV-TYLGVLAGLSLVVTLLLFHVVQGNRQDS---------FSRAMSGDVLRW
+WGRRSYAAYLWHWPLLVILRTALPVDAPAWVDPVAAGGVLV-LTAGIADLSTRWMEEPIVQRGFRGAFAHWRAGLRTA--
+-TRGIGGKAAAGAAGLALVAVPVAAV--AAVVHSPAE--------TALQRQIAEA-------------------EAALEQ
+ARQAQAAARAEASARAEAERAGAAEEAVAKDSQEDAPGAGAGGDA-G--SAAPTASSTPSDTAAPSAGEDPAVEVAADPT
+ASAEPEPTAEPEPEPPLTGDPSVTRPAFTGAELTEPMPPSSVGPDVTLLGDS-------VALS-----AAPELLAALPGI
+AVEAEVGFQVRDAAARLAELDAAGMLTDVVVVSLGANGNA-----------ELGDWDRILAAAGPERLLVLVVPHGPMDW
+IGPAQQ----------------------------EMAEQAALHPD--RVVLADWDAASA---------HVDEW--SADGV
+HPKGN-----GQGIYARLVRLTVEARLGLR------------
+>GCF_005280335_PROKKA_01839
+--------------------------------------------------------------------MAVLSVLVFHAG
+VTALPGGFVGVDVFFVISGFLITGLLLKEVDRTGRVGLAEFYARRARRILPAALAVIVLTVAAGLLV---YPVSEWTRLG
+SVAVASALSVVNWLFARESTDYFAQEEAA-SP--FQHYWSLAVEEQFYLVWPLLLILVTVGVAALRRRGAGDAAPDADAG
+ARRRPSAPVAARRVLLASA--VIGLASFVHSVSYS--ASDPGAAYFVTTTRVWELALGAGLAAALVVLPVIR--------
+PAVRTVLGWAGLGMIAVSLVL--ITGAM---AYPGSVALLPVVGSALV--ILAGAHEDGSTPGHP----ARLLATRPMQW
+VGDLSYSLYLVHWPVLTLAAWRFPDGRL----PLWLGLILAVVSVGLAWALRRWVEVPAMHGSLLAGRR------RALTR
+GGLGMAAVAAAGALVLAAG---------AA--LAPAR--------PGEESPVAGA-------------------RAVMD-
+-----------GQ-------------------------------------------------------------------
+---DPMAAL-------------AAGMR-IVPDPAVAKEDR-----------------------------SPRS-------
+------------AAGASSRTP---------------RPRA-----------WSPRRACWRTASPTRSATSGTAPC-PTSW
+TGSTRTSCWSRAPGGRPWRRTP-------RRR---------------------WPRRGGS--------------------
+------------------------------------------
+>GCF_020097155_PROKKA_00392
+MT-------------------VSTSDHHAARPAPRHAQAALADGPAPRTGLRVSRGPGRITALDGLRGIAVLAVLVFHAW
+PEALPGGFVGVDMFFVLSGFLITTGLVRGVDAGKGLRLPSFWMRRIRRLVPAMVVALVACTALAWLAVAEFP----TGLG
+RQWLGALTYTSNWLMIFDGGDYFDRA----SPPLFEHLWSLAIEEQFYVLWPLIIG----GLCLVVRPKRDTYA------
+-----SGRVADRRRILVVLVVALASAAGMVLGSLG--GADQTRLYFGTDTHAFGLLLGACVSMGLAHVPRPEHGGPELRT
+GPARTAAAWLAVVVLFTGFAL--VDGTQDA-TYRGVLVGLAAVVAFIVWHVAQGDRRDS---------LSRALGNPFLRW
+WGRRSYAAYLWHWPLLVIMRIVVPVDAPSWAEPVAAGAVLL-LTAGIADLSSRYFEEPILQKGFRGAFGGWGDAARRAFG
+GAFGPGGRLAAGATALALVAVPVAAV--AAVAHSPAQ--------TQLQEDIQAA-------------------EQSLQD
+AQAQQQA-QLEARRSAQAEKSKDAEA--------------------G--GAEATGS----------------------AG
+ASASPSGST--------LGDPQVTRPEFTQEELTASLPPSDVGSRTTLIGDS-------VALS-----AAPALLEEMPGI
+VVDAKVGFQIWDAADKIRAMDREGTLGDVVVLSLGANGTA-----------GRGDWDKIRQAVGPDRLLVVVVPHGPMSW
+IEDAQR----------------------------KAVEQAEAHPD--QVVLADWEAAST---------YVPGW--SADGV
+HPGHE-----GQGIYAQLIRLTVEERLGLR------------
+>GCF_020097155_PROKKA_02437
+M-------------------------------------------PR-----PVDTKASYFPGLDGLRALAVGLVVAYHLG
+VPGTDGGLLGVGVFFTLSGYLITSLLLRRHERHGDLDLKNFWIRRFRRLLPAVVLVLIAVLAATALV---SPDLLGARLG
+-QSVAALLYVANWHTILSGRSYFDQAEGA-GP--LDHLWSLAVEEQFYLVWPLVLL----GLLALTRRLGPDA-------
+-----------RRRVLAAATLVLGAVSFVLLAVFADPAGDSTRAYEGTDTRAGGLLWGAVLAFLWRPDRVAR-----LTG
+RASRVVVDLVGVLGLAGVLALSATTGQEDAALYTWGLAALTVATCAALLPLV-----------HPGSWVARVLGIPPLQW
+IGARSYGIYLWHMPVVAFLP-----DRVLFGQPVLRGLLIVALTLVLAALSWRLVEDPIRRHGLVAALA------RARGV
+LGVGAVAVLASGALVLTAALPQTSAQEIAA--QEPAA--------PAGD---AVA-------------------HPALD-
+-----------GRTSCTS--------------------VLHVGDSTS--LASGNTD----------------------RT
+RIADPAQRI--------TGRYEAVGVETVVEDIAGGRSTREH------IDGS-------ADLN------APEA-------
+------------VAAGVSRLDAGGC----VVVNVGLNDAA-----------TMTKDDAWDQAAARIDAVVDAADGRPVLW
+VGPAIM----------PWSSRPYYEPAGAERFTRALVDATARHPD---LRVHDWARESRS--------HP-DWYLSDDAN
+HNTEA-----GAVAKARSMAAALTAAFPAGRPASAEKVVLGE
+>GCF_023573625_PROKKA_00587
+MTNPPVYPRG---------------------YRPRHAADGPDSTPA-----AARRRADWRPEIQGLRAVAVLLVVVFHIF
+TDRVSG---GVDIFLFISAFFLTGSFTRKMESGRPLAVGRYWLHVFTRLMPMAVLTILTTLVAVATV---YPLADRASWR
+TEALASALYVENWALAFNAVDYYAADNTSLSP--FQHFWSLSVQGQVFILWPLLFL----VSALVARRTGARP-------
+------------RAVLTTAFASVFVVSLLWSVTQT--SQNQAFTYFDTRARLWEFALGSLLALALPFLHLGR--------
+-RTRVFLGWAGLASMIAVGVV--VDVQG---AFPGWIALWPLMSATAV--IVAGT--SGS---HFG--VDRILASRPLTR
+LGDSAYALYLVHWPLLITYSVLTGSQKP----GAAAGVALVLVSLGTAILLSARVERPLRAWGWPQTAA-W----RSAVV
+LGACAALVVAPVTLWRGAEAAESARVLEAADRNNPGAAVLRPDYEPAGD---PGAPVLPVVEGRYPFPEYPEECDPALE-
+AQLTEV-----GAESCHV--------------------LVPQADPAGVVLMAGNSHVMQW--------------------
+---SPALRR--------LGEERRLEVVSYTRGSCLVAPMEEQ------VDDSPKCPDFLADLNLVVEHVRPDV-------
+------------VFMQGTRSTYEDE----EMLTPGMTGRMEEIAGTGAHVLALRDNPRFAAGSPTTCGTMHGVDAVTCRW
+THAVLD----------PNTS--------------PLAGLADAHPRIAQVQLNDMICPDRQCQPTVGNVHV-YW----DDN
+HLTPTYVETLAPVFIERVLAALEHDGMRLGR-----------
+>GCF_023573625_PROKKA_02238
+-------------------------------------------MPAVKVGTRVSRGPGRVTALDGLRGIAVLAVLVFHAW
+PTFLRGGFVGVDMFFVLSGFLITTGLVRGVDAGRGVALGTFWMKRVRRLIPAMLMALVGTTALAWLAVDEFP----AGLG
+RQWFGALTYTSNWVMILEGGDYFNRA----SPPLFEHLWSLAIEEQFYILWPLLLW----GLLLLTWPPRSTVN------
+-----SGRVADRRRILAVAVAAVASAAWMAWGSWH--GFEQARLYFGTDTHAFGLLFGACVAIGLAHVPRPEHGGPEPRT
+SATRVAVAWGAVAVLAAGFAL--VDGGHAS-TYRGVLAGLSAVVAFIVWHVVQGDRRDS---------LSRALGNGFLRW
+WGRRSYAAYLWHWPLLVIMRVMVPVDAPGWVEPVAAGAILL-LTALIADLSTRLIEEPILHEGFRGAFGRWGAAARRAFT
+GGAGPIGRLAAAATALGLVAVPAAAV--AAVVHSPAQ--------TQLEQDIAQA-------------------EESLKA
+AQAAQQA----ARESRAAEQSKRAEA-----SASASPGSAAPGDAEG--SAGATSS----------------------PG
+SSAEPSGLG--------LGDPAVTRPTYSKEQLTAALPPSELGPDVTLIGDS-------VSLS-----AAPTLLEQLPGM
+LLEAEVGYQIWDAADEIEKLKADGQLSDVVVVALGANGTT-----------HRGDWEKILAAVGEDRLLVLVVPHGPMDW
+IADVQV----------------------------QMEAQAKAHPD--RIVLADWDAAAKQ--------HVTDF--SADGV
+HPRAD-----GQAMYAQLVRLTIEDRLGTRR-----------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000025.fa ADDED Viewed

	@@ -0,0 +1,29 @@

+>GCF_002008305_PROKKA_00099
+M-------------------NFALDGRNYEIDLSKEHAAELREFLKPYMKK---------
+--GRAVAP-------PSPK-----VEAAQIRKWAAENGYEVSSRGRLHRDVVEAYRNAKR
+K-
+>GCF_003691675_PROKKA_02112
+M-------------------NFALDGRNYEIDLSKEHAAELREFLKPYMKK---------
+--GRAVAP-------PSPK-----VEAAQIRKWAAENGYEVSSRGRLHRDVVEAYRNAKR
+K-
+>GCF_005280335_PROKKA_00292
+M-------------------NFALDGRNYEIDLSKEHADELREFLKPYMKK---------
+--GRAVAP-------PSPK-----VEAAQIRKWAAENGYEVSSRGRLHRDVVEAYRNARR
+K-
+>GCF_020097155_PROKKA_00617
+MATITTIADDFDNSTPAETTYFSVNGKEYAIDLNEEHRRELEDVLEEVAERLSKYTAVAR
+PLGKSSAPARKSSKSPSSR-SGASYDAGAVRSWAEENGYKVADRGRISADVLEAY-NASK
+KG
+>GCF_020097155_PROKKA_00670
+MAIISTVADDFDGSTPAEAVRFSVAGRDYEIDLSKEHRAELDAIMAEFQDRLKKFTDVAR
+PAGRAASTGR----TPARRSSGSGVDASTVRLWAVENGFDVKDRGRIPVEVMDAYRNRGK
+KG
+>GCF_023573625_PROKKA_00094
+M-------------------NFALDGRNYEIDLSKEHAAELREFLKPYMKK---------
+--GRAVAP-------PSPK-----VEAAQIRKWAAENGYEVSSRGRLHRDVVEAYRNAKR
+K-
+>GCF_023573625_PROKKA_02014
+MAIISTVADDFDGSTPAEAVRFSVAGRDYEIDLSKEHRAELDAIMAEFQDRLKKFTDVAR
+PAGRAASTGR----TPARRSSGSGVDASTVRLWAVENGFDVKDRGRIPVEVMDAYRNRGK
+KG

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000034.fa ADDED Viewed

	@@ -0,0 +1,36 @@

+>GCF_002008305_PROKKA_00617
+MSLTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPPAAIPYFGLIPLGLGLWAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVEPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWENILF
+PIVLIGLGIVILVSGGAFGL
+>GCF_002008305_PROKKA_02075
+MSLTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPPAAIPYFGLIPLGLGLWAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVEPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWENILF
+PIVLIGLGIVILVSGGAFGL
+>GCF_003691675_PROKKA_00340
+MILTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPSAAIPYFGLIPLGLGLWAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVKPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWEHVLF
+PIVLIGLGIVILVSGGAFGL
+>GCF_003691675_PROKKA_01780
+MSLTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPSAAIPYFGLIPLGLGLWAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVEPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWENILF
+PIVLIGLGIVILVSGGAFGL
+>GCF_005280335_PROKKA_00718
+MNLTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPSAAIPYFGLIPLGLGLRAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVEPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWEHILF
+PIVLIGLGIVILVSGGAFGL
+>GCF_020097155_PROKKA_02214
+MILTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPSAAIPYFGLIPLGLGLWAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVKPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWEHVLF
+PIVLIGLGIVILVSGGAFGL
+>GCF_023573625_PROKKA_02003
+MTLSSALQAIGLFLVTNIDDLIVLSLFFGRGAGQRGTTVRILVGQYLGFAGILGAAVLVS
+LGAGVFLPPEVIPYFGLIPLGLGLWAAWQTWRGDDDDDDDEAKIEGKNVAAWTVAGVTFA
+NGGDNIGVYVPVFLSVGPGAVVAYCVVFLVLVAGLVGLAKFVATRRPIAEVLERWEHILF
+PIVLIGLGVFILISGGAFGL

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000039.fa ADDED Viewed

	@@ -0,0 +1,189 @@

+>GCF_002008305_PROKKA_00884
+MN------------------------------------------------------------------------------
+------THH-----------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------------------------------PDR--------------------------------------------
+--------------------------------------------------------------------------------
+------------------LTDAAGVRVLLYGDVDLNVI---DGSATWLPSLAETLAR-----------------------
+TGASVDVQLKAV-ERRDL---LTAPLRALTGVRVLTAEPAAGQGGMTPSRAADVLAR-------RDEESRYDVVLVRGIH
+ACLELADRGA--------------------------FPGRLWS--------------YVTEYGYVED--------GFPAG
+RVEELGRIA-AASRLMLAQTPQARA-VLEAMVPAAA-----------GRTELLSPMVPDGLVPAERAEAPADGPVRLVYT
+GKFAHDWRTDL-MPDVLTA----------------------------------LHEAGVPATLTMVG-------------
+--------------------------------------------------------------------------------
+--------DKVHP---------------------ERDRPGWAAAMRSRLEAERPDFEWTGA--------LSREESMAR-T
+AAADVSLGWRA----------PA-------LDLSLEISTKVLESCAVG------VPPLLN-RTVAHEELLGADYPLFVDG
+VRDSARDVAA--RIAAARHDLPALSRRVVE-AAAPYRMAARARALTGVMDRLGLLDRRPARGGS---RTRVVLAGHDLKF
+AGELVDLLRDDPGVELRIDHWQGLHRHDEAASRRLVEWADVVVCEWAGPNAVWYARH---KRPGQRLVVRLHMFELRGGW
+LSALETEAVDRLVTVSDLYRDLVREHLPIEPTRVTVIPNAVSVADLDRPGLPGRRFRLGLVGVVPLRKRLDRAVDLLEIL
+RAHDERFTLHVRGRMPWEYPHEWRKPLQREGYLDLFARLGAGP-LREAVAFEPFGAD---MGSWL-TKIGWVLSPSTTES
+FHLAPAEGMVSGAVPLVWDRPGARGVFGDEFVLDDTDAAARRVLEAVADDARWDALSALARERVR-AYDERVVAGLW-RE
+ALGLD---------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------
+>GCF_002008305_PROKKA_00894
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------------------------------------------MNVAGARLRRWAGRA---RIVGERAAATAGDAGAS
+ALRAARGARG----------------------------LATLPERTWRAAD-VHV----PDASAALPLPAAAVLRRALTG
+ARV--PSLDAFSPLGPRPAAAPAVLLLPVDE-PAARGWSVEAAAELAARRCADLEMP-AGAPGLHTV--LMSDPASRRAL
+TAALRTAGGRLPGVLVVACPDPATAAGR-----ARVLAALGLVDAVLAPEGTRLDPPLARAAARAGRAVIGP--------
+--DRAA---------ETWERLAAAGRAARLDALTPAEAAG-PPAAPA------------PRVRVTAEPRRVVVAGHDLKF
+AGALMDRLRAD-GHEVRVDAWRGHARHDVERSRALAAWADVVHCEWSLGNLAWYSRHLDSPHRTTRLTSRLHLQEAGTAF
+PSRVRQDALDEWVFVAEHVRAQVLRDTRFPASRTSVVPNAVAVPPTLPDGDDDRRFVLGLVGVLPERKGLHRALDLLAAL
+RRVEPRYTLRIRGHHPEEVGWMAQRPAAAAYYRAQLRRIETDPVLAGAVTWDPHGPD---MPAWY-ARVGVALSVSDFES
+FHFTLPDGAAHGCLPAALAWAGADLLYPAAWLSPDVATMAEALRRATADARAWRSAVAQARRDVAHTYAEEDVVPALVRR
+ILGGA---------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---AA-
+>GCF_003691675_PROKKA_00606
+MN------------------------------------------------------------------------------
+------THH-----------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------------------------------PDR--------------------------------------------
+--------------------------------------------------------------------------------
+------------------LTDAAGVRVLLYGDVDLNVI---DGSATWLPSLAETLAR-----------------------
+TGASVDVQLKAV-ERRDL---LTAPLRALTGVRVLPAEPAAGQGGMTPSRAADVLAR-------RDEESRYDVVLVRGIH
+ACLELADRGA--------------------------FPGRLWS--------------YVTEYGYVED--------GFPAG
+RVEELGRIA-AASRLMLAQTPQARA-VLEAMVPAAA-----------GRTELLSPMVPDGLAPAERAEAPADGPVRLVYT
+GKFAHDWRTDL-MPDVLTA----------------------------------LHEAGVPATLTMVG-------------
+--------------------------------------------------------------------------------
+--------DKVHP---------------------ERDRPGWAAAMRSRLEADRPDFEWTGA--------LSREESMAR-T
+AAADVSLGWRA----------PA-------LDLSLEISTKVLESCAVG------VPPLLN-RTVAHEELLGADYPLFVDG
+VRDSARDVAA--RIAAVRHDLPALSRRVVE-AAAPYRVAARARALTGVMDRLGLLDRRPARGGS---RTRVVLAGHDLKF
+AGELVDLLRDDPGVELRIDHWQGLHRHDEAASRRLVEWADVVVCEWAGPNAVWYARH---KRPGQRLVVRLHMFELRGGW
+LSALETDAVDRLVTVSDLYRDLVREHLPIDPARVSVIPNAVSVADLDRPGLPGRRFRLGLVGVVPLRKRLDRAVDLLEVL
+RAHDERFTLHVRGRMPWEYPHEWRKPLQREGYLDLFARLGAGP-LREAVAFEPFGAD---MGSWL-TKIGWVLSPSTTES
+FHLAPAEGMVSGAVPLVWDRPGARGVFGEEFVLDDTDAAARRVLEATADDARWDALSALARDRVR-SYDERVVAGLW-RE
+ALGLD---------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------
+>GCF_003691675_PROKKA_00616
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------------------------------------------MNVAGARLRRWAGRA---RVVGERAVVTAGDAGAS
+ALRAARGARG----------------------------TATLPERTWRAAD-VHV----PDAAAALPLPAAAALRRALTG
+VRD--PSLDAFSPLGPRPAAAPAVLLLPVDDGPAARGWSVEAAAELAARRCADLQMP-AGAPGLHTV--LVTDPASRGAL
+IAALRPAGARLPGVLVVACPDPATAAGR-----ARALAALGLVDAVLAPEGTRLDPALPSVAARAGRAVIGP--------
+--DRAA---------ETWERLAAAGRAARLDSLTPAEATG-PPAAPG------------PRVRVTAEPRRVVVAGHDLKF
+AGALMERLRAD-GHEVRVDAWLGHARHDAERSRALAAWADVVHCEWSLGNLAWYSRHLDSPHRTTRLTSRLHLQEAGTAF
+PSRVRQDALDEWVFVAEHVRAQVLRDTRFPAARTSVVPNAVAVPPTLPDGDDDRRFVLGLVGVLPERKGLHRALDLLAVL
+RRTEPRFTLRIRGHHPEEVGWMAQRPAAAAYYRAQLRRIETDPMLAGAVAWDPHGPD---MPAWY-ARVGVALSVSDFES
+FHFTLPDGAAHGCLPAALAWAGADLLYPAAWLSPDVATMADALRRATADARAWRSAVAQARRDVAHTYAEEDVVPALVCR
+ILGGT---------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---AT-
+>GCF_005280335_PROKKA_02045
+MGEAD---------------------------------------------------------------------------
+---------------------------------------------------------------TPAP-------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--TPEGPL------------------------------------------------------------------------
+--AGRSFRLVAVAERPDWEPGLIAQLRAAGAAVVSTTEVV------------------------RTSSAHVDVLLAVDVE
+SAAALRAAGW--------------------------DRFQVWT-------------------VVQTDPGTPLMPRGLSAA
+G---VGRAV-AESRRVVVFDEASRS-AVESTLWNAA-----------GKVVVMP---------------------RF---
+------------TAEEVEA-------------------------------------------------------------
+------------------------------------VSFGGNRVEGPH-EPGEAI----LVLHAGLLGSEGA---HVLRE
+YSDAVRARRHVRK---VLVVAP----------------GDLRVAVRSEEGQRHLA-RIPGASLIDGGAELSRAAAGRR-T
+VTVL--PRWST----------PQDSRAEDLLAWAAAVGAQVWAEPGA-------VPPQVSGRPVG--QLPGDN-------
+-LSAALDWAD--QHAGGTTFGAAPINRVAQ-AFAPH-----VPALST----------VPAHPNA---PLKVLFVGADYKF
+AGDLVEALILRPDAEVRVDQWKTNGDRPTPNSAELLAWADVVICEFASRNAVWASQH---IREHQRLIVHLHGYELRNPL
+IHDIVMDRVHTVVFASEFYRADAVVTTGWRVEQTAVIPNSVQSAELRRPKTADARFHLGLAGYVPELKRMDRALDLLEEL
+LRRDDRFVLHLRGRHPWNYPYVWRHPLRRDTYLANYERLRSNPRLRRAVVFDDFGPD---MGNWF-RNIGWMLSPSTRET
+FHLAPAEGMASGAVPVVWRREGSDGIFPPESLVTDAASAADRIHRTAGDRDAYNSAARSAIEFAT-RYEAGAVVDHWLRL
+ILHGERPGGPPSPEHLQRARPVATALAGRADWNRVGRLLRDGRVEQAAAVAQEESRPAWEQPEDVRRLAAHVNGYSALAQ
+RAHRLVPSAPCVPPLLPLAAGADSARSLTLTEGPAGTYVTRSGDIAVGRGDILDDVNAEFDRLVDQAFRIGAQNRATALT
+VIGDEMLALAGGAVAGWLGIPFVWDLTSQPAARDLLMRMRALPDAPTPQGRLALLAAASATRLIGAGPAERLPVPFETFI
+GMADLDRPRRVGVIGRSLGDLVGRSWGEPVNLSPGRWREQTVPRLDVALLDAQVLHPRNAWRASEGNTGPLGALITHVRR
+HATPLAIVDLGHEGLDSAGIAQARRVDAVVTAHPDDVQRLHDVRIVPSQVAVSTAPWGIRSGEEHVLRPGDRVRLAMRML
+GVAETH
+>GCF_020097155_PROKKA_01944
+MRQIDEMALWTSRDVGVRVRYAGAEELIRGVRSRADATHDASDGGTDLEAADVAGPGTPEPSDHVAEVPWRLRVLNTGRV
+RQIRRWIYHARRAPAHAAAARVKRLLRTPGRWSETLRRPLARTRAAAPAPERADAAVA-----TPAPAAEPTGERTLAAL
+RAALAERPSASALHALVAALYRD-GQLRAPAAALEEHPELVGQFTPAQAKLARNVREQARLLDHPPVVPARAVGTALRPE
+AGRILYCAHGVHPYQ-SNGYAIRTRGIVAGLRDAGHDVVVAARPGFPWDAKVTRAAR----KKQSYPELVDGIEHVYSFG
+PSLRNQALAAYLESAVDSYLQVIARNRPAHVHAASNHITALPALIAARLSGLPFTYEVRGFWEYGMEPGEEGLQERGE--
+LAGRLEDLVMVEADHVFVLTAEMRDELRGRGVDPDRMTVTPNGVDPEQFQPLPAVGELHRRLGL-DPDRAVIGYLGSLVS
+YEGLEDLLEACLQLAEERDDFQLVVAGDGPVLPRLKEIAAERDTSLPVHLLGRIDADLIPALMSEVDVVACPRTATRVTR
+LVSPLKPLEALAAGVPVVLSDLPVLRSL-AEECGGAVVFPAGDRHGLAEAIAGLLDDPERRLDLGRSGRAWALRERRWDV
+LGAHLGSGILAAVPSTGAE----GGSRPLSTVRLGVIADTFTTSGLAEQVQTVPLQRAGQGWRRQLAEERLDAVF---VE
+SAWSGNDGAWTRGVGHYSDEESADLRALLEDCRAAGVPTVFWNKEDPVHFNRFVENARLFDLVLTTDNRSIQGYQARVDR
+SRQTVGSMAFFAQPSLHHPVTDGPAVADRPVMYAGSYYGDRYRDRSEVLRGLLHVARPFGVTIYDRQADLPDSPYRF--P
+EELQPFVEGGLPYSEMVKAYRRYPLHVNVNSVTASETMFSRRVMEISCAGGVVASGPSAGVNHMFRGLVPTIGRREVAER
+AMSTLLSDPGLRNVQGWNLRRLVRRSHTLSDRLLVLLRRLGLAV-SPDPTPGTTVVLTGPADRADWDGLLAQT-RPVDRV
+VAD--EMSETVRE---RLSAAG-----------------IEVSAGSASLDPAHLAWEWDGA-RLDRV--VHED------L
+ANVLLDSGYSA-------------AVLD-----TTPVTDLATPLAVVG------GAPVPSGASLVLRWGGGD--------
+--DGVVTVRR--GLLESVEDLGAKQRPAAV-ALTPEALDRMER------------------------PLRVVVAGHDLKF
+AGELINRFRSD-GHEVRLDQWASHQDHDDELSRELVDWADVVLCEWGLGNAVWYSKH---KREGQRLYVRVHSQELFRDN
+WSRMNLPAVDRFIFVAPHIRDSARRYRGVAARPSEVIPNIV-LPGAGLKRDPDSRFVLGLVGIVPRGKRFDRALDLLAML
+RREDPRYSLRVKGKQPEDYPWMAAREEEMAYYGTIRERIAQDPALQGAVHLDGFSTDRAELDRWY-SSIGIGLSVSDFES
+FHFTSVDGAQNGAVPAVLAWPGADRIFPAEWLSPTLESMARRIL-GLREPEVFRAAADTARRETSARFDGGRSLDRWSEL
+VAG-----------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-----E
+>GCF_023573625_PROKKA_00845
+MIQLF-------------LRFSRRQQLVMGL----------------FILLAVVGSVLAFLVDHAILIVALFWMLCAAVF
+VMI---MYH---------------------------RRLNAKINRTARAARMGSSAVAGRGGTRPATGRRISTQESLDSL
+QAAFARRRTVAAGLPLARKLIQERGDLSGAREVLDQLRGKSG-LTDSEENFVRRVDSLNRLLEADYPLPARHRTCNYLPV
+RGRVLY-AVGMSPVSVTNGYTSRTKGVAAGLVAQGLDVVVAPLPGKPWDKKSVVPGRRVPVKQRRDVSEIDGVRHVHNPG
+LPAWEGDLDVFFQVAADAYVREAMIEKPEFILAASNYLSALPALIAARRLGVPFVYEMRGFWEVSAASVRPGWEQSDQYR
+LDRRYEDLVAREADRVVVITDEMREDLAARGIDADKVTVAPNCVDPEVFAPLGKDHALLRGLGFTDTEAPVVGFAGSVTD
+YEGLDLVTDALATLKAEGVRFNFLIIGGGAYLDTLKARIATRGLDPETRFVMNVPNADMPAYLSSIDVFPLARKSLPVTE
+LVSPLKPLEAMAVGGAVVLSDVSPHKVFCGPDGDTAVSFQKDDLASLVERLRETLAAPDAARAMGVRARRWVKENRRWPV
+TGERIAASLMALAEEFRAS--LDDAERPLTDYTVAFIGDEFTTDTFVPELTALRVRP--EDWRETFEDHRVDALF---IE
+SAWRGNDSAWTGIIGYYDDETHAPVVELIAHCRLHEIPVMFWNKEDPVHFNRFKRTAALCDYVFTTDARTIVDYNALPDN
+QITTVASAPFAAQPLLHNPLPSTRA-QDEAIAYGGTYYGDKYATRKQGLDFLFYESAPHGLAIYERVHNDPNSPYRL--P
+DRFRRYARGSLSYPEMCQAYKAHPIHLNGNSVVDSPSMFSRRVVEITASGSTVLSSAGRGVDETLAGTVPTVTTPDEAAA
+YLEGWKSSEQRRHAGLWEAFRHVYETHTCAHRLVYMMRVAGFRVRSPQAAP-IAV----ECAAADVPLFEAQTMRPALYL
+VTDTTEGVDAASP---VVLAAP-----------------PERAAKLQEAGIRNVVIHREGAPALDEH--LVED------F
+SLALHFGHWKAVGTRTVEW-SPGDAHVR-----IAALTADIDEGTVLV------DADVYAGSVLGERPALAD--------
+--DEVFAWQHVVEHVGKVTYTDSTAVPIDT-AVVHEEADPLPPVASG--------EAGPPVGETQTVPLNVLVAGHDLKF
+LPQIMAQLEAA-GHRVIVDQWDGHDIHDEERSLRLLAEADVIFCEWALGNVKWYSHH---KQDDQRLVVRLHAQELRTRY
+LKDADLSAVDTFVFVSPVGMRRAQLLFGVPVDRSVVIGNTFDFERFAAPRNAPDPHALGLVGSVPHSKRLDLALDVTELL
+ASHDPTYRLDVMGKEYHEYAWLMKRTAERSYFEAQYLRIESSAVLREAVRFGGHSYD---IAEWYRAKPGIILSTSDHEG
+THQAIAEGGAAGCVPVIFPWAGAEAVYDDRWVVEGVRDAADRIRRYSSDPALFLEESERAQAFMRERFSPEEIGAQILAV
+VEGRR---------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000040.fa ADDED Viewed

	@@ -0,0 +1,63 @@

+>GCF_002008305_PROKKA_01015
+MSASTPRRRVVDNEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVVAPAYTLTSGLGPTISTVG-T
+HVPAILLLGFIPMLLVALGYRALNTRVPDSGTSFTWATHAFGPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQIT
+GSQAIADLAGNLWVNIPLTLVYLA---LAGWISHRGMETTKHLQYILVAFQILALGAFAVAALTQSSRG---AGFDPTPV
+QLDWFNPFTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAAVTVFVIIAVYILSALAVISWAGIGSEGL
+G----AGNPDNQESIFAVLAGPILGPFAVIMSSAILVSSLASLQSTMVSPARTLLAMGFYRAVPARFAELSPRFNSPAFA
+TWVCAGFAGLFYVVTRLL---SENALWDTIT---------ALGLMICFYYGITALACVWYFRREWFTSVGNALTTFLFPL
+IGGLVLLVMFCVTAMDSTDPDYGSGSSVFG-VGTVFILGMGVLAIGVVLMMWT----RLRHPAYFRGETLPQTDSTRPIP
+IIRPDDDGSAVVRDPNERTHS
+>GCF_003691675_PROKKA_00729
+MSASTPRRRVVDSEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVVAPAYTLTSGLGPTISTVG-T
+HVPAILLLGFIPMLLVALGYRALNTRVPDSGTSFTWATHAFGPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQIT
+GSQAIADLAGNLWVNIPLTVVYLA---LAGWISHRGMETTKHLQYILVAFQILALGAFAIAALTQSSRG---AGFDPTPV
+QLDWFNPFTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAAVTVFVIIAVYILSALAVISWAGIGSEGL
+G----AGNPDNQESIFAVLAGPILGPFAVIMSSAILVSSLASLQSTMVSPARTLLAMGFYRAVPARFAELSPRFNSPAFA
+TWVCAGFAGLFYVVTRLL---SENALWDTIT---------ALGLMICFYYGITALACVWYFRREWFTSVGNALTTFLFPL
+IGGLVLLVMFCVTAMDSTDPDYGSGSSVFG-VGTVFILGMGVLAIGVVLMMWT----RLRHPAYFRGETLPQTDSTRPIP
+IIRPDDDGTAVVRDPNERTHS
+>GCF_005280335_PROKKA_00822
+MSS------VLDAAGTPATPHPSPAAPSARV--PSSSGGGRLGAGRIGVPALVCMIVAASAPLTAVAGGITSNFAVTGLL
+GVPLSFLVLGVVLLLFSVGYAAMSRHVHNAGAFFAYVARGMGKPAG-------VGAALVALVSYACMQVG-----IAGMF
+GFATSSFLEGTFGIAVPWWASALAAWVLVGVLGLYRVDFSAKVLMGVVALEFLVVCVYTVLGLRAAPEGVSAAGLLPGQL
+-------FTSG----VGAALVFSVAAFMGFESGAIYNEEVKDPKRTAGRATLISVVLIAVFYAFSA-----WAMVMTEGP
+GGVVAAAQAVGPDVVFAFLGAHAPLWFTDLANILFIVSLLAALLAFHNIVARYAFALGREHVLPAFLAHTSTRTGAPVGG
+SLVQSGAALVVLVVFALAGSRSDDPLFPVVTLFTWLTNMGAFGLVLLM--ALTSVSVIGYLRRH--RDEFGVFTRVVAPA
+LAAVGLLTLFVLTMVNFPVLLGADGTTPLSWLLPALVVTPG--ALGTAWALWL----RARRPATYAG-------------
+IAR---GGEL----------S
+>GCF_005280335_PROKKA_01873
+MSASTPRRRVVDSEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVVAPAYTLTSGLGPTISTVG-T
+HVPAILLLGFIPMLLVALGYRALNTRVPDSGTSFTWATHAFGPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQIT
+GSQAIADLAGNLWVNIPLTLVYLA---LAGWISHRGMETTKHLQYILVAFQILALGAFAVAALTQSSRG---AGFDPTPV
+QLDWFNPFTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAAVTVLVIIAVYILSALAVISWAGIGSEGL
+G----AGNPDNQESIFAVLAGPILGPFAVIMSSAILVSSLASLQSTMVSPARTLLAMGFYRAVPARFAELSPRFNSPAFA
+TWVCAGFAGLFYVVTRLL---SENALWDTIT---------ALGLMICFYYGITALACVWYFRREWFTSVGNALTTFLFPL
+IGGLVLLVMFCVTALDSTDPDYGSGSSVFG-VGTVFVLGMGVLAIGVVLMMWT----RLRHPAYFRGETLPQTDSTRPIP
+IIRPDDDGTAVVRDPNERTHS
+>GCF_020097155_PROKKA_02256
+MLSTHQ---------------------------------------------SVSVSTSSVAPVYSAVVTVPLVVGLVG-S
+GAPLAYLLALLPILGVWAGMSANDEREPDKGSVYSWAVTGH-PVLGWTAGWCLALTGIVATSGLAYVALD------AWLP
+GLGA--------GVKVLIGAGIIA---AATALASANVRITAAVQTAGVLVQVA-----ATAYLAWVLAR---VGLTPLPP
+---------AGTVQDWVHAVLLAVFAFWGFDAVYALSEESH--RGVPRRSAAVSLGLLAAIFLVFS------------AL
+G-------ASEDPAAVAALTHPVV-------MAGVVVSCVGAIGSTLIPTARGLSAMAERGHLSAVLA--------PLRA
+AEVVSALLAIAWLVVSLA---VPGVFEDSIE---------MLSVFVGGYFTISSATAAAH--ASGGARMLHAATAVVMGL
+ITAASLAWMF--------EPDYGA-TVVGG-VGGVGLLAVGFAVLGLILAVGAGHRGRAVHPT--SG-------------
+--------------------V
+>GCF_023573625_PROKKA_00958
+MSASTPRRRVVDNEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVVAPAYTLTSGLGPTISTVG-T
+HVPAILLLGFIPMLLVALG-------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------------------
+>GCF_023573625_PROKKA_00959
+--------------------------------------------------------------------------------
+--------------------------MPDSGTSFTWATHAFGPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQIT
+GSQAIADLAGNLWVNIPLTLVYLA---LAGWISHRGMETTKHLQYILVAFQILALGAFAVAALTQSSRG---AGFDPTPV
+QLDWFNPFTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAAVTVFVIIAVYILSALAVISWAGIGSEGL
+G----AGNPDNQESIFAVLAGPILGPFAVIMSSAILVSSLASLQSTMVSPARTLLAMGFYRAVPARFAELSPRFNSPAFA
+TWVCAGFAGLFYVVTRLL---SENALWDTIT---------ALGLMICFYYGITALACVWYFRREWFTSVGNALTTFLFPL
+IGGLVLLVMFCVTAMDSTDPDYGSGSSVFG-VGTVFILGMGVLAIGVVLMMWT----RLRHPAYFRGETLPQTDSTRPIP
+IIRPDDDGTAVVRDPNERTHS

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000042.fa ADDED Viewed

	@@ -0,0 +1,36 @@

+>GCF_002008305_PROKKA_01288
+MRKHLKTTVAAGVLGGALVFTGCSTGGDQDQGT-------PSTTSQH----EGHGSSSDS
+GG---MEHPMDGGPAPEGIETAASPTYPVGTEVTLTADHMEGMDGANAMIAGAYDTYTYA
+VDFTPSAGGEPVKDHKWVVQQEIKDAGDERLADGTEVTLEAEHMEGMKGAKATIASSTEE
+TVYMVDYESDGMTMTNHKWVVESELKPAS
+>GCF_002008305_PROKKA_01627
+MTMRFWTRTVAVTAASLLALTGCATGGEE-----------AATSSSH----GGHAG----
+-------HAMDGGPAPEGIEPAADPAHPVGTEVTLMADHMPGMEGAAATVVGAYETTAYS
+VDYRPTTGGPEVTDHKWVVQEELEDAGAERLPDGAAVTLAADHMPGMQGAEGTVHSSTDE
+TVYMVDYESDGMRMRNHKWVVESEIASAG
+>GCF_003691675_PROKKA_01007
+MRKHLKTTVAAGVLGGALVFTGCSTGGDQDQGT-------PSTTSQH----EGHGSSSDS
+GG---MEHPMDGGPAPEGIETAASPTYPVGTEVTLTADHMEGMDGANAMIAGAYDTYTYA
+VDFTPSAGGEPVKDHKWVVQQEIKDAGDERLADGTEVTLEAEHMEGMKGAKATIASSTEE
+TVYMVDYESDGMTMTNHKWVVESELKPAS
+>GCF_005280335_PROKKA_00620
+MKTRRLTLAAVGILASAGLITGCSTADDAGPSASPSSGQSAATSSSQPASESGSASESAS
+GG-GHMDHKMDGGPAPEGIAEAASPAHPVGSEITLTADHMPGMDGATARITGAFDTTAYS
+VDYTPTTGGEPVEDHKWVVHEELQDAGDAPLQVGDTAVMEAEHMAGMKGAEATVASVTDE
+TVYMVDYTADGMTMTNHKWVVESEIQPKG
+>GCF_020097155_PROKKA_00712
+MQRRLRTGLAAGALGVALVLAGCASGADDNQQTD------PSATEEH----QGHGGNNAE
+SGDEEMEHPMDGGPAPEGIAEASEPTYPVGTEVQLTADHMEGMEGATATISGAFDTYTYS
+VNYTPAGGGDPVTDHKWVVQEEIEDAGDARLADGTEVTLLAEHMEGMEGVKAIIASSTDE
+TVYMVDYETDGMKMTNHKWVVESEIQPAS
+>GCF_023573625_PROKKA_01246
+MRKHLMTTVAAGVLGGALVFTGCSTGGGQDQGT-------PSTTSQH----EGHGSSSDS
+GG---MEHPMDGGPAPEGIETAASPTYPVGTEVTLTADHMEGMDGANATIAGAYDTYTYA
+VDFTPSAGGEPVKDHKWVVQQEIKDAGDERLADGTEVTLEAEHMEGMKGAKATIASSTEE
+TVYMVDYESDGMTMTNHKWVVESELKPAS
+>GCF_023573625_PROKKA_01556
+MTMRFWTRTVAVTAAGLLALTGCATGGEE-----------VATSSSH----GGHAG----
+-------HAMDGGPAPEGIEPAADPAHPVGTEVTLVADHMPGMEGAAATVVGAYETTAYS
+VDYRPTTGGPEVTDHKWVVQEELEDAGAERLPDGAAVTLAADHMPGMQGAEGTVHSSTDE
+TVYMVDYESDGMRMRNHKWVVESEIAPAG

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000043.fa ADDED Viewed

	@@ -0,0 +1,22 @@

+>GCF_002008305_PROKKA_01397
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVNRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEAQRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>GCF_003691675_PROKKA_01130
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVNRVATQLGYGVESVRMWVK
+QADIDDGVTSDVSSAEAQRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>GCF_005280335_PROKKA_00412
+MPKEQTAGKPTTRRYSPEE-AAAVRMVRTMRAELGTEHGTVQRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEAQRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>GCF_020097155_PROKKA_00325
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVQRVATQLGYGVESVRMWVK
+HADIDDGVTSGVSSAEAQRVRELEQEVRKLRRANEVLKRAASFFGAELDRHYRK
+>GCF_020097155_PROKKA_00648
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRVELGTEHGTVQRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEARRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>GCF_020097155_PROKKA_02216
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRVELGTEHGTVQRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEARRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>GCF_023573625_PROKKA_01347
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVNRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEARRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000044.fa ADDED Viewed

	@@ -0,0 +1,50 @@

+>GCF_002008305_PROKKA_01401
+MAVSGSFPGHLWAAFHGRLHSVRDEELIPQLVELWETNYRVYGVRKLWKTARRAGIDIGR
+DQTGRLMRAAGIKGATRSKRVKTTRPDPTAARHPDLVKREFTAPAPNRLWVTDLAFVTTW
+AGVAYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFT
+SIRYGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAELVRGPARPGPWRTVEDLELAT
+LGWVSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLSESNSASLHQTQGASGPTLWSP
+TRSILDRAARPLRKF
+>GCF_003691675_PROKKA_01131
+MAPSSYYAAKTRAP---SARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGR
+DQAARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTW
+AGVAYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDPRCHSDAGSQFT
+SIRYGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAEHVRGPARPGPWRTVEDLELAT
+LGWVSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK------------------
+---------------
+>GCF_005280335_PROKKA_00413
+MAPSSYYAAKTRAP---SARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGR
+DRAARLMRAAGIEGARRSKRVKTTRPDPASARYPDLVKREFTAPAPNRLWATDLTFVPTW
+AGVAYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIAMARWSRGARHEDLRCHSDAGSQFT
+SIRYGERLAEIGATPSIGTVGDSYDNSLAETVNGYYKAELVRGPARPGPWRTVEDLELAT
+LGWVSWHTTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIQ------------------
+---------------
+>GCF_020097155_PROKKA_00326
+MAPSSYYAAKTRTP---SARAARDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGR
+DQTARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTW
+AGVAYVCFIIDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFT
+SIRYGERLAEIGATPSIGTVGDSYDNALAETVNGYDKAELIRGPARPGPWRTTDDVELAT
+LGWVHWHNNQRLHGYLDDLPLTEFEERFYATQQGQYALVEIK------------------
+---------------
+>GCF_020097155_PROKKA_00649
+MAPSSYYAAKTRAP---SARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGR
+DQTARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTW
+AGVAYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFT
+SIRYGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAELVRGPARPGPWRTVEDLELAT
+LGWVSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK------------------
+---------------
+>GCF_020097155_PROKKA_02217
+MAPSSYYAAKTRAP---SARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGR
+DQTARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTW
+AGVAYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFT
+SIRYGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAELVRGPARPGPWRTVEDLELAT
+LGWVSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK------------------
+---------------
+>GCF_023573625_PROKKA_01351
+MG----------------------------------------------------------
+---------------------------------------SFSWP----------------
+-------------------------------------------------LTHSDAGSQFT
+SIRYGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAEHVRGPARPGPWRTVEDLELAT
+LGWVSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK------------------
+---------------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000045.fa ADDED Viewed

	@@ -0,0 +1,56 @@

+>GCF_002008305_PROKKA_01590
+MPVAPRPSDGAASSVFTPHQQRILAVLLIPIFMSLLAVSSINVALPALQRGLDASDAELQWAISGYTLVFGMVLVPAGRA
+GDLFGRRRLFMVGLGVFALGALLSGLAPTGVLLVLARLVMGVGAGLLNPQVTGFIQSEFSGTSRARAFGALGAVVGVSVA
+VGPLLSGGLIAWLGGDLGWRATFLVNVPIALGALVVARHWLPRTAPERARRPDLDPVGVVLLAGALVAVMLPFL---DRE
+LGPWRFVLVPVGIGLAALWTRWEARYARRGRAPMVDLRLFQTRSFACGALLIAIYFTGSTSMFVVIAMFMQNGLG-----
+---YPALHAALIGLPSAVMSSVMSTVAGRVVLRTGRK-IVVLGIALALLAVVGSIGVAWANR-----EFGLSP--WWLLL
+TLAILGAGQGLVVSPNQTLSLAEVPPRHSGTAGGVLQTGQRVGTAVGTAVIVGVFLGVASGADW----------------
+--DGAFMAAFT-----LVAGCMALALLVALADLRGPRTAAPRG------------------------
+>GCF_003691675_PROKKA_01302
+MPVAPRPSDGAASSVFTPHQQRILAVLLIPIFMSLLAVSSINVALPALQRGLDASDAELQWAISGYTLVFGMVLVPAGRA
+GDLFGRRRLFMVGLGVFALGALLSGLAPTGVLLVLARLVMGVGAGLLNPQVTGFIQGEFSGASRARAFGALGAVVGVSVA
+VGPLLSGGLIAWLGGDLGWRATFLVNVPIALGALIVARQWLPRTAPERARRPDLDPVGVVLLAGALVAVMLPFL---DRG
+LGPWRFVLVPVGIGLAALWTRWEARYARRGRAPMVDLRLFQTRSFACGALLIAIYFTGSTSMFVVIAMFMQNGLG-----
+---YPALHAALIGLPSAVMSSVMSTVAGRVVLRTGRK-IVVLGIALALLAVVGSIGVAWANR-----EFGLSP--WWLLL
+TLAILGAGQGLVVSPNQTLSLAEVPPRHSGTAGGVLQTGQRVGTAVGTAVIVGVFLGVASGADW----------------
+--DGAFMAAFT-----LVAGCMALALLVALADLRGPRTAAPRG------------------------
+>GCF_020097155_PROKKA_00643
+M--------------------------LFASFMDLLDVTIVTVAAPHIAADLNASPAQLQWMLAAYTLALGSGLITGGRI
+GDDYGRRRVFLAALAAFAIASAACALAPTAGALIAVRAVQGLAGGFMVPQVFGIIRSSFEPAAMAKAFGAYGAVQGLASV
+AGPLIGGALADADLWGLGWRTIFWINIPIALVALVLGWRVLPDS--RAAARSRLDGVGALLAAVGVLLVLLPLVQGRDWG
+WPTWGWALLAAGVLVLAGFLRYENALARRGGEPVLDPDLLRVRPFVAGLAASVLFFGGLASFFLVVSIYLQAGTG-----
+---RSAWDTGLVILPYAIGSMLTSGAGVALAARAGRA-LLLTG-SLTLAA--SQALLWWLVR-----DGSTTPDYWPLAG
+AMFLGGLGLGLGAPILVNVVLAGVPGRRAGAAGGVLSTVNQIGGAVGVAVLGTVFFNAASSAGP----------------
+--ATAPAELFGDALAQVMPWQVATYLLAAVAMLALPKTAAPHQD-----------------------
+>GCF_020097155_PROKKA_00714
+M----------AGDCIRQIPRWGFVLSLAATILMMAAASAPSLFYPQIAERLGLIPVATTLVFAVYTFTLLAALLYLGPL
+SDHVGRRPVVAAGSLALALSVAMFWFAGSLAALLVARALQGLAAGLLIPALSAMM-IDFESPSH-RNIAALWNTIGPMIG
+LG---AGALGAALLLDLTSEPTTAVFGSLVLAFLIVA----------------------------TVVWSTPEL------
+---------------------VPKTQIRRGD---LRPRFTVPPHL---RRMFTVGVPVIIAGWATNGLFLALGADLVGSE
+LGGSTHTQAGIVLFALAISGVTASS---VLQRRSART-ISLYA-TSALAF--GTAVSIGAL------ALGSYP---AYVA
+SVAIVGSGFGTAFLGVLRTLMPHTASSERAAVMAVIYTVAYLAFGVPTIVAGLLV-----------------------PV
+LTLSGTMTILG-------AIIIALSLVATVLRLRIPHPAAGPAEADDFPEPPTGSHRRSAPDREEQP
+>GCF_020097155_PROKKA_01240
+M----NPSAGTSGGVFTARQRRVLAVLLVPVFMSLLAVSSINVALPSLQRGLGASDAELQWSISGYTLAFGMVLVPAGRA
+GDLLGRARLFRIGVLGFGLGALLSGLAPSGLLLVLARVLMGVGAGLLNPQVSGFIQAEFEGQARARAFGALGSTVGVSVA
+AGPLLAGGLIAVLGGDLGWRATFLVNVPIALAAVLIARGWLPEESPAPAGRRDFDPVGVALLASALVAVMLPFL---DRG
+LGPWRFALLPLGAALAAGWAVWERGYRARGRAPMVDLSLFGLPGFRNGALMIGVYFTGSTSLFIVVAMFMQNGLG-----
+---YGALQAALVGLPSAVCSSVMATVAGRLVLRAGRR-LVVVGVSLVLAAVVGSIGVVAAHQ-----AFGLSP--WWLLA
+TLGLFGMGQGLTVSPNQTLSLAEVPRPQSGTAGGILQTGQRVGTSVGSAVIVGVYLGVAGTGGP----------------
+--DRGFMAALG-----LIAVSIAAALAVAVADQR--RRARQGGR-----------------------
+>GCF_020097155_PROKKA_01828
+M----------------PRPRLLLAVILLAQFVIPLSISGTAVALPAIASDLGSDPTPLQWVVNGFNVAFAVCTIVWGAC
+SDRIGYTRSFRIGIAIAIAGGIVSMFAPNIAVLDAGRIIAGIGSAAVLTSAAPILSHLFEGKARAQAFALFGTINGLGLA
+AGPALSGLLLSA----WGWQGIFAAHT-------------------------------IVLIVAFIGAARLPQL---GRG
+GTSLR---------------------------EILDFSALKAPKF---LAMTLVPIAGAI-GFVTFLTYLPSALGAIHGL
+TAGVTGALMLVMTIPVLIAPVAVH----RLMERSHLTPTAIVAVSFACLI-VGGIGVLLLLRPDLPVALGVTP-------
+-MILLGLGFGLPLGFVDAEALAAVPAERAGAASGVINLFRIGSEAVFVAAYGALLAAVITTTLPGTTGELIASGSPGEPW
+IYHSGLMAAAG-----TMIGLVAIAGVTFLALTRAANRSAVTARQ-----------------VEVAR
+>GCF_023573625_PROKKA_01517
+MPVAPRPSDGAASSVFTPHQQRILAVLLIPIFMSLLAVSSINVALPALQRGLDASDAELQWAISGYTLVFGMVLVPAGRA
+GDLFGRRRLFLVGLGVFALGALLSGLAPTGVLLVLARLVMGVGAGLLNPQVTGFIQGEFSGASRARAFGALGAVVGVSVA
+VGPLLSGGLIAWLGGDLGWRATFLVNVPIALGALIVARQWLPRTVPERARRPDLDPVGVVLLAGALVAVMLPFL---DRG
+LGPWRFVLVPVGIGLAALWTRWEARYARRGRAPMVDLRLFQTRSFACGALLIAIYFTGSTSMFVVIAMFMQNGLG-----
+---YPALHAALIGLPSAVMSSVMSTVAGRVVLRTGRK-IVVLGIALALLAVVGSIGVAWANR-----EFGLSP--WWLLL
+TLAILGAGQGLVVSPNQTLSLAEVPPRHSGTAGGVLQTGQRVGTAVGTAVIVGVFLGVASSADW----------------
+--DGAFMAAFA-----LVAGCMALALLVALADLRGPRTAAPRG------------------------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000050.fa ADDED Viewed

	@@ -0,0 +1,64 @@

+>GCF_002008305_PROKKA_02089
+-MSTDPRRQTPAPRGSDTGTPPLPEGRARWLVASNALDAGGRSATDVALDVLAVLLLGVG
+ADGMGVLMTLSGLGFLLLGVPLGIVVDR-HLSPRLLAA---TGLAKAAVLGSLVAAWALD
+ALTFGHLAAVMTLLGVLTVLAETTQTALVPRVVPATAVARLTARLESADAALVLIVPAAA
+GVLVGSLGAGPVLGIATAFLFAAAIVALRVRLRPSAAADVPDDDGDPGVADVLSRWARFG
+KDAAEGWTVLRRTPVLWLLTMGSVAANVGMALFAPVEAVWILTDLRLGPEFLGIQITAGA
+VGALTASSLAGRAIDRLGERRCILLGSVGCAVAVGLHLLAYADRAHAGPWLLAGAALW-G
+FMVLLGNITQAAVTARACPEGTLGRVTAMRRTLTRGSVPLATLAGGALGATLGVGWALA-
+-GWQVLAVVSLAAVVPAARWV---------DAGRDDVD
+>GCF_003691675_PROKKA_01794
+-MSTDPRRQTPAPRGSDTGTPPLPEGRARWLVASNALDAGGRSATDVALDVLAVLLLGVG
+ADGMGVLMTLSGLGFLLLGVPLGIVVDR-HLSPRLLAA---TGLAKAAVLGSLVAAWALD
+ALTFGHLAAVMTLLGVLTVLAETTQTALVPRVVPATAVARLTARLESADAALVLIVPAAA
+GVLVGSLGAGPVLGIATAFLFAAAIVALRVRLRPSAAADVPDDDGDPGVADVLSRWARFG
+KDAAEGWTVLRRTPVLWLLTMGSVAANVGMALFAPVEAVWILTDLRLGPEFLGIQITAGA
+VGALTASSLAGRAIDRLGERRCILLGSVGCAVAVGLHLLAYADRAHAGPWLLAGAALW-G
+FMVLLGNITQAAVTARACPEGTLGRVTAMRRTLTRGSVPLATLAGGALGATLGVGWALA-
+-GWQVLAVVSLAAVVPAARHL------GPRTAER----
+>GCF_005280335_PROKKA_00694
+-MSTDPRRQTPAPRVPDTGTRPPPEGRARWLVASNALDAGGRSATDVALDVLAVLLLGVG
+ADGMGVLMTLSGLGFLLLGVPIGIVVDR-HLSPRLLAA---TGLAKAAVLGSLVVAWALD
+ALTFGHLAAVMALLGVLTVLAETTQTALVPRVVPATAVARLTARLESADAALVLIVPAAA
+GVLVGSLGAGPVLGIATSFLFAAAIVALRVRLRPSAAVDIPDDDGDPGVADVLSRWARFG
+KDAAEGWTVLRRAPVLWLLTMGSVAANVGMALFAPVEAVWILTDLRLGPEFLGVQITAGA
+VGALAASSLAGRAIDRLGERRCILLGSVGCAVAVGLHLLAYADRAHAGPWLLAGAALW-G
+FMVLLGNITQAAVTARACPEGTLGRVTAMRRTLTRGSVPLATLAGGALGATLGVGWALA-
+-GWQVLAVVSLAAVVPATRHL------GPRTAER----
+>GCF_005280335_PROKKA_01308
+MVSSPLTDDTTAP---ENAAPAKRLGRARWLVASNALDAGGRSATDVAIDVLAVLALGVG
+AAQMGVLMTLSGLGFLLLGVPIGILVDR-HLSPRLLVA---TDLAKAALLGTLVLAWALD
+ALTFAHLAAVMALLGVLTVLAETTQATLVPRVVAPDTVSRLAARLESADAALGLIVPAAA
+GLLVAALGAGPVLGIAAAFLAAAALVALKVRMNPAPVTEDTRDEETPAAAVVLTRWSRFW
+SEAAHGWTTLRRTPVLWLLTLNSMAGNIGMALFAPIEAVWVLTDLQLGPEFVGFQLTAGA
+LGALTVSALAPRAIDTLGEKGCILAGSAGCAAAVALHLAAFFDRAHAGPLLLAGAALW-G
+FMVVLGNITSGAIFARSCPEGTLGRVTAMRRTLTRGSVPLATLAGGALGAAFGPGWVLA-
+-GWQAMALLSLAFAFAATR-----------LARRPQ--
+>GCF_020097155_PROKKA_00662
+----------------MTRVSAWRSRDFRRLWGASTASALGGEIGELAMPVLALVWLGAS
+AEELSWVRVATFLPYLVLPLWLGVLVDRWRRRPLMITAETVSGITLLGIAGAALAGW---
+-LTVPALVAAAAVLGAMSVLHMLADFSFTPQVVSRAALPDANAKMTATYSAIGIGGSGVG
+GALVQWLTAPFAVAINGAGRLLSVVLLRRIQTHEPPA-EAPDTSAR--------------
+QQAREGFLALLRHRVVRALAAEATIWNLGNEVFMLALTVLIVDARDDGPLVLGLIFMAGG
+LGAFLGAGISARLTERFGYGRSLITAMLVGNTAPLIGVLFSSDTSVTSLVVLAAAFFASG
+FGTGIANSQAVTVRQVTVPEELRGRVNASYRMLSWGALAIGALLGGWLISAVG-GWLAAA
+LGTAAMAASTLPVALSPVRQMRDLDDGAPPAAE-----
+>GCF_020097155_PROKKA_02237
+-MSSPLTDDTTAP---ENAARAKRLGHARWLVASNALDAGGRSATDVAIDVLAVLALGVG
+AAQMGVLMTLSGLGFLLLGVPIGILVDR-HLSPRLLVA---TDLAKAALLGTLVLAWALD
+ALTFAHLAAVMALLGVLTVLAETTQATLVPRVVAPDTVSRLAARLESADAALGLIVPAAA
+GLLVAALGAGPVLGIAAAFLATAALVALKVRINPAPVTEDTQDEETPAAAVVLTRWSRFW
+SEAAHGWTTLRRTPVLWLLTLNSMAGNIGMALFAPIEAVWVLTDLQLGPEFVGFQLTAGA
+LGALTVSTLAPRAIDTLGEKGCILAGAAGCAAAVALHLAAFFDRAHAGPLLLAGAALW-G
+FMVVLGNITSGAIFARSCPEGTLGRVTAMRRTLTRGSVPLATLAGGALGAAFGPGWVLA-
+-GWQAMALLSLAFAIAATR-----------LARRPH--
+>GCF_023573625_PROKKA_02028
+-MSTDPRRQTPAPRTPDTGTPPPPEGRARWLVASNALDAGGRSASDVALDVLAVLLLGVG
+ADGMGVLMALSGLGFLLLGVPIGIVVDR-HLSPRLLAA---TGLAKAAVLGSLVVAWALD
+ALTFGHLAAVMALLGVLTVLAETTQTALVPRVVPATAVARLTARLESADAALVLIVPAAA
+GVLVGSLGAGPVLGTATAFLFAAAIVALRVRLRPSAAADVPDDDGDPGVADVLSRWARFG
+KDAAEGWTVLRRTPVLWLLTMGSVAANVGMALFAPVEAVWILTDLRLGPEFLGIQITAGA
+VGALTASSLAGRAIDRLGERRCILLGSVGCAVAVGLHLLAYADRAHAGPWLLAGAALW-G
+FMVLLGNITQAAVTARACPEGTLGRVTAMRRTLTRGSVPLATLAGGALGATLGVGWALA-
+-GWQVLAVVSLAAVVPAARWV---------DAGRDDVD

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000051.fa ADDED Viewed

	@@ -0,0 +1,50 @@

+>GCF_002008305_PROKKA_02094
+MNM---------------------------------------------------------
+-------------------LQAIRRYYAGYVQFSGRASRADFWLAALYVWLLQAAV----
+--------------------RFVSTALDVFVLGAPDPSLRDAAILLVGITHALPSLALLA
+RRLHDAGFSRAWLFLGLVPFVGPLTLLVFALQPSAPRLG---------------------
+--HPAD---------ASDPVPAG----ATAARR---------------------------
+-------------
+>GCF_003691675_PROKKA_01802
+MTM---------------------------------------------------------
+-------------------LQAIRRYYAGYAQFSGRASRADFWLAALYVWLLQAVV----
+--------------------HFVSTVLDVFLLGSPDLSLRDAAVLLVGITHALPSLALLA
+RRLHDAGFSRAWLFLGLVPFVGPLTLLVFALQPSAPRLG---------------------
+--HPAD---------ASDPVPAG----ATAARR---------------------------
+-------------
+>GCF_005280335_PROKKA_00684
+MNM---------------------------------------------------------
+-------------------LQAIRRYYAGYAQFSGLASRADFWLAALYVWLLQTAV----
+--------------------HFVSTALDVFILGSPDLSLRDAAVLLVGVTHALPSLALLA
+RRLHDAGFSRAWLLLGLVPFVGPLTLLVFALQPSAPRLG---------------------
+--HPAD---------ASDPVPAGVTASATAARR---------------------------
+-------------
+>GCF_020097155_PROKKA_00599
+M-----------------------------------------------------------
+------------------------------------------------------------
+-----------------------STALDVFILGSPDLSLRDVAVLLVGITHALPSLALLA
+RRLHDAGFSHAWLFVGLVPLVGPLTLLVFALQPTAPRFG---------------------
+--HPTD---------ASDPVPAGPRPRGADPRRHVRP-----------------------
+-----------DQ
+>GCF_020097155_PROKKA_00600
+MTM---------------------------------------------------------
+-------------------RQAIRRYYAGYAQFSGRASRADFWLAALCV-----------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------
+>GCF_020097155_PROKKA_02101
+MTQPHDPSQNPYGQQPAAGQPPYGQAPSGQSQYGQADYGQTQYGQTQYGAPSPGYGYGYQ
+PGVPFPEDPRVAPAPGVGPVEAVKRFYTRYALFYGRASRSEFWWVQLYLVLVSLVLTALM
+------------FAVLVPAGAFSNTTTELSEAGAVGVLAITGLFLVFVLAHLVPSIALQV
+RRLHDAGFSGFWFFIGLVPYVGELVLLVLSVLPSKPEGA---------------------
+---------------RFDR-----------------------------------------
+-------------
+>GCF_023573625_PROKKA_02031
+MTF---------------------------------------------------------
+-------------------LRAVGRFYGRYAQFGGRGGRAEFWWVVLYLSLASLGITLLF
+GALGADTTTAAPSAVVFPGFAVSGLSVPAVDSMTEAYQAFSG---VWGLLHLVPAWALTA
+RRLHDAGLSRAWLLLALLPVLGAIALLVMVLQPSDPRVAAEHVVEVSVGHAPERESIGGL
+RDHPTILPTALNRLLVFDMCVKPPPPRSPRCRRRGLPRSPHEDAEGVAGRVREHVQGLVL
+VVGAVQDEAPAQA

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000057.fa ADDED Viewed

	@@ -0,0 +1,60 @@

+>GCF_002008305_PROKKA_00037
+M------LDEV-LAQLRSTGSETALIEVKSAAGGCPRSVRETLSAFANARG-GVVVLGLDDS--TFEPTGA-DAPALRDA
+LAGMAADDMTP-PVRGVISIENAEGGHQVVVMEVPEFAPDQKPCYITAAGRYQGSYTRSDEGDRRLTAYE----IDRL--
+--IEGQG-QPQHDREPVHGATADDLRPDLVEALTGRL-RTVQPRA--FGSLTDQECLRRANVLVDADGVLVPTLAGLLAC
+GEYPQGFFPQLSISVVVLPGTTFGDTGPHGERFVDNRTCEGPLVDMIADARDVLVRHMSRASVIDGTGR-ADRL-EYPLE
+V---IRELLVNAVMHRDYSAGA--RGTQVQVELYPDRLVVRSPGGFFGPVDPSSFGEP-DVSSSRNSVLARLLSDLPGSD
+GRMIAENRGSGIPTVLKVLEAAGMVPPEFHSTLTR-VEVDVAHDSLLTAETHEWI---QGLGQDGLTQ--WQIQALALAR
+SGRTVRNQTLQGWGAHQADATRELSDLVRRGLTVKLGDRRGA----RYTLNPDYVPPAAETGAGGLSERQQAILRAL---
+----------------------------ADGPMKATEVGDAVGTSYRTAMNALNDLIEAGLVEPT-APPRSRRRRYRLTP
+QEETA----
+>GCF_002008305_PROKKA_00568
+MDVI--QLDQTQLMAL-LSRAEGHFLDYKRTDVA-PGKLTRSLAAFCNSDG-GDIYVGIAETDGTQSWQGAADPEEFNGH
+L--QAFEEVSPFGADWNAEFITAQNESGYVLRINALKSRQVRS---DSSGKV---YKRVGAQNVPVDSEEGLQTLRRLKG
+LESFEEE-TLNVDMEEVTNST--HIIKFLVN----------------DPSPTDPELYLKRQQLIRGGK---PTVASALLF
+AELPQAMLPKRCGIKIY---RYTSSVAHRDQLYSDPVTVEGYL---YGQIYEAVDQTIDIINQAQFLDVDGLRQVRYPRE
+T---LHEVITNAVLHRDYS-----IQDDIHVRIFENRVEVQSPGRLPGHITLKNILEE---RLSRNGHLVRNINRFVDPP
+NKDV----GEGLNTAFESMRKFNLKEPIIEELENS-VMVTIRHQSLASPEQ----------------------QIMEYLA
+EHSQIRNQEARNLVGIE---------------------------------------------------------------
+--------------------------------------------SESKMKKILQGLVGTGEIEHV-PGTAKRGYAYRARA
+EAAAQEGNR
+>GCF_002008305_PROKKA_02274
+MNWSSDDLTAT-LDALRARRGDTTSVEVKRATGGVP-SMPETLCAFANMPDGGTVVCGVDEAHGEFRVVGVPDVAVLEAG
+LVAQAREAVTP-SPTLLPQVFRLEGKDVLVAHVVPLRLTDRPA---TVRGQA---YLRQSDGDYVMHAHE----LRMVEV
+AKLHADE-RVDYDVKPVTGMSEEDLVPELVTDYVAAV--RERDRR--LRDRTHQEILRQTNVLTAAGE---PTLAGLYAL
+GDYPQGRYPGLTVTAAV---QVRGGEGQARSRNLTDFT--GPVPVLLDEVMAWVRQNLGTEHVYRPDGQ-LERRPELPLA
+A---VRELLGNALVHRDLGPDTLGAGKAIQVRLTDRALFIQSPGGLRG-VSLTQLESDEHAQAAVNQRLYQIAKKLTTPD
+GASVIEGEGGGIHEVFRSARQWGLGRPQLIDT---------------------------------------GVQFKALLW
+RPRPEGARPSRREPAVEVARTPPV---------EEVPDVKAD-------APSSAVPPSSAPT-----RHEGRVLGALA--
+----------------------------AGEAVGIRDLEEATMLTARQIRYALRQPLLDGLVEMT-GGQGHKDTRYRLVS
+ARGAGD---
+>GCF_005280335_PROKKA_00464
+M---------------------------------------------ANTPGSGALIVGVSKTAELI------GTALDREW
+LRFRLYELTGR-ALTVDVQEVQVQGARLLVLYPPAAVEPI------RVEGRI---RWRVDDHCAEVDAST----WFTRQM
+YRRQYDW------SAETSNVPAGEARPAAVDIARAFLYDSGDERGEELAEAETPQLLRRLNVVAEGGM---LTNAGVLAF
+VGRPE---PALDYTHHEVAGADSSIRVHRGGRS---------LLEELADVLQAFEARNTVRHVQSGLTI-GQLR-DIPRL
+A---AREALVNGLAHREWG-----DPGATRVEHIGRTLRVTSPGGFFGGVDPSNIITH--PSVSRNPALTQLLADL----
+--RVAERQGIGVDRMVREMVRVGHPQPGIEEVAGPYVRTTLVGETLDEPWM-AWLSQVQ---PRPLTRDVSAVLILRHLV
+DRVWIDEMTAAALTQVSRAESRSM--LER----LHTATVGGGTILEAVSGVPDAVPQAWRLG-----EAAAQLLAALDQE
+TGIQRTVPDR---------RALAADYARARGRISTTELASLVGGHASNMGAPLRALETEGFLEPSNASRRGRGFFYRWVG
+DEPA-----
+>GCF_020097155_PROKKA_00427
+MD----------LGPL-LAAGETLDVEFKRRLG--KDDLYQAVVCMANGIG-GRILVGVDDDGTVVGTTADHGGAVDADL
+LAGRIQNGIEP-PLSVDVEVVPWEGKDVAVITVPQAKSSFVG----TRKGLF---VKRVVGPDGRPACMP----MTPMDV
+LRAGFDGVGLDYARAEARGAEWGHLDPTEFDRFRRLAGQSAGDSG--LAELTDAELLRTLDLLTPDGG---ISLGAVLVF
+GTSEALRRWAPTAEVLF---QDSRPHGVEANED---------LLLPLLNAFEEIETRLALRNSITPVEV-GLVRVDVPLL
+AESVRRESIANALVHRDYA-----EAGPIQVTLTGSTFSVASPGGFPRDVSPANILNR---SAPRSPALANVFKRA----
+--GLVERRGKGVQDMFASQLRAGRGAPDYSRSTHRSVIVDIPLGDEDRELL-IFLARRQNEGQRALT-----------LT
+ELRVVHEIKHGGPAGAAEAAERLR---------LPVADVRAA----ATALVEAGVLESRGNG-----RAQRYMLTARFYE
+LAEDRAAYLRLRPVDRIQQRRLIADYIREYGSITRGKAAELCQIAPTAARAVLKGMTEEGLLELR----GERRAAHYVLP
+DS-------
+>GCF_023573625_PROKKA_02208
+M-----------------RRGDTTNVEVKRAAGGVP-QLAETLCAFANMPEGGTIILGVDEARGAFNVTGVADVALLEAG
+VAAQAREGVTP-SPQIIPQTLQLDERQVLLIHVVPLRTADKPA---TVQGVA---YLRQSDGDYRMHEHE----LRMLEV
+AKLHADE-RVDYELKVATGLGEQDLVSSLVDEYVAAV--RRKNRR--LRDRTSEEILRQTSVLTSSGE---PTLAGLYAL
+GDFPQGRFPGLTVTAAV---QLPGGEGQPRNRNLEDFV--GPLPDLLRDLMAWVSDNIDTVRRYRRDGH-MEEVAELPLT
+A---VRELLANALVHRDLGPSTLGMGKGVQVRLTPRNLFIQNPGGLQG-LSLTQLQSDDHAQAAVNQRLYQFAKKLTTSD
+GASLIEGEGGGIREVFRAAERQGLPRPQLIDT---------------------------------------GVQFKAILW
+RAADRNAR-----AGVEDAKGASA---------VET-------------AVPRAVPASASPT-----RHEHAVLAALV--
+---------------------------RMPDGATLRALTSVTGLTDRQVRYALRLPLDEGIVVMD-GGQGNRQTAYRLMS
+DSRRP----

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000060.fa ADDED Viewed

	@@ -0,0 +1,49 @@

+>GCF_002008305_PROKKA_00063
+MTPEWWMALAALVLLALLVVVVVVLAVRQVRLGVQHERTRLLVDALDARVGGVQRRLEEV
+PGIGTGRHEVALVLNPIKTHADRVRRELERLAEAEGLGEVLVLETQEDDPGT-AMARQAL
+DAGARLVIAAGGDGTVRTVA------EQLAGTDVALGVVPLGTGNLLARNLDLPINDVEQ
+CLRIAVGGRQ------RRIDTVDVRFTHEDGRVTRQTFTVIGGAGYDADIMGDTKDELKS
+LAGWLAYSEA-GMRHLRGKRHEVTVALDGGQPRRFKVRTVMVANCGMLTGGVELLPQAKL
+DDGLLDVMVLSPRHALDWARIAVKTVTRHRSSVPAMHTEQAQRVKVEFAEPMPSQLDGD-
+---ATGVITALDARVQPDSLVVMLVAEDDASVRDDGVSAAAPVPEPAPHI
+>GCF_003691675_PROKKA_02076
+MTPEWWMALAALVLLALLVVVVVVLAARQVRLGVQHKRMRLRVDALDARVGGVQRRLEKV
+PGIGTGRHEVALVLNPIKTNAGQVRRELERLAEAEGLGEVLVLETQEDDPGT-AMARQAL
+GAGARLVIAAGGDGTVRTVA------EQLAGTDVALGVVPLGTGNLLARNLDLPINDVEQ
+CLRIAVGGRQ------RRIDTVDVRFTHEDGRVTRQTFTVIGGAGYDADIMGDTKDELKD
+LAGWLAYSEA-GIRHLRGKRHEVTVALDGGQPRRFKVRTVMVANCGMLTGGVELLPQAKL
+DDGLLDVMVLSPRHALDWARIAVKTVTRHRSSVPAMHTEQAQRVKVEFAEPMPSQLDGD-
+---ATGVITALDARVRPDSLVVMLVAEDDASVRDDGVSAAAPVPEPAPHI
+>GCF_005280335_PROKKA_00201
+------M-------------------------------TPGSPDD---------------
+DGAPAVRRRVLVLLNPHAGRRRSLARAQARLRTHPGLALDLVVPDPADHAAQLAAGRTAL
+ADGVDAVVVRGGDGMVAAGVGLVGDHAEATGRRVPLGIVPAGTGNDLARAAGLHRRDPGA
+ALEAVLRALEDPAAPVRRIDALRLTVTRAGAVVERRWAANSVNIGFDARVNARA-NALGA
+VPGPLRYLAALGLEARAFAAVEMGLGLDDGPVRRERVALVSVQNGPTIGGGIPLAPGARL
+DDGRAEATVVGPLPTAGLALLFPLVYVRAHRLLRPLCTERARRVRVAVPDGVPVYADGDE
+VLPASHGGAAVEVEAVPGAVALLG--------------------------
+>GCF_005280335_PROKKA_00332
+------MALVALVLGAVLAVAVIVLAVRHRGLAERHERTRGQLDAVEHRLDAAQRRLGEL
+PGVDRPRQEIALVLNPVKARADEVRRTLEAMADREGLGSVLVLETEEDDPGT-QMAKDAL
+EAGVRLVIAAGGDGTVRTVA------EQLTGTDVALGVVPLGTGNLLARNLDLPINDIEE
+CLRIALTGRQ------RRIDTVDVRFTHEEGEVTRQTFTVIGGAGYDADIMADTKDELKD
+VAGWLAYSEA-GMRHLRGKRHDVSISLDGGASRRFKVRTVMVANCGMLTGGVELLPEAKL
+DDGLLDVLVLSPRHALDWARIAAKTVTRHGANIPVMHTEQAQRVKVEFADPMPSQLDGD-
+---ATGHIVALDARVQPDSLVVMLLDEKEASVHDDGRSEAAPVPEPAPHI
+>GCF_020097155_PROKKA_00273
+------MALAALVLAALFAVAVVVLGLRLRRLDGAHERTRGQLDAVEARLGDLRRRAGRA
+PGVDLPGPQVALVLNPVKARADEVRRAMEALAEKEGLGEVLVLETTEEDPGT-AMTREAL
+TAGVRLVVAAGGDGTVRTVA------EQLAGTDVALGVMPLGTGNLLARNLDLPINDIEE
+CLRIALTGRQ------RRIDTVDVRLTHEDGARTRQTFTVIGGAGYDADIMGDTKDELKD
+MAGWLAYSEA-GMRHLRGRRHEVSITLDGGAVQRFKVRSVMVANCGMLTGGMELLPEAKL
+DDGLLDVLVLSPRHALDWVRIAAKTLTRHRASIPVMHTEQAQRVQVRFAEPMSSQLDGD-
+---ATGDITALDARIQPDSLVVMLGDEDDASVEDGGRSAEAPVPEPAPHI
+>GCF_023573625_PROKKA_00058
+------MALAALVLLAVLAVVVVVLAVRQVRLGVQHQRTRLLVDALDARVGGVQRRLEEV
+PGIGTGRHEVALVLNPIKTHADRVRRELERLAAAEGLGEVLVLETQEDDPGT-AMARQAL
+DAGARLVIAAGGDGTVRTVA------EQLAGTDVALGVVPLGTGNLLARNLDLPINDVEQ
+CLRIAVGGRQ------RRIDTVDVRFTHEDGRVTRQTFTVIGGAGYDADIMGDTKDELKD
+LAGWLAYSEA-GIRHLRGKRHEVTVALDGGQPRRFKVRTVMVANCGMLTGGVELLPQAKL
+DDGLLDVMVLSPRHALDWARIAVKTVTRSRSSIPVMHTEQAQRVKVEFAEPMPSQLDGD-
+---ATGVITALDARVQPDSLVVMLVAEDDASVRDDGVSAAAPVPQPAPRI

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000063.fa ADDED Viewed

	@@ -0,0 +1,48 @@

+>GCF_002008305_PROKKA_00105
+MATKTAPKRAPGYRCTECGWTTVKWVGRCGECQSWGTVEEIGLTSTTGRTRAATVAEVAPRIADVDATLASFRSTGVREL
+DRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAGGGGP-----RSVLYLTGEESAAQVRSRADRIGAIA---DT
+LRLTA--ETDLGRALGQIER--TDPELVIVDSVQTLQSTEVDGIAGGVSQ----VREVAASLIRTAKEKGITTVLVGHVT
+KDGTIAGPRLLEHLVDVVCQFEG--DRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVSEPVEGTCV
+TVTLEGRRPLVAEVQSLLTPSAGGSPRRTVSGVDAARVNMLLAVLQRRARFALAQDDCYVATVGGVRLSEPASDLAVAVA
+VASAKLS-------APVPQGMIAVGELGLAGEVRPVPGIGRRVREAARLGFTRALVPRSPEPLGDVPAGFTVAEVGSIGE
+ALATIPTWTGG-GPAAHPEAGPGR
+>GCF_003691675_PROKKA_02118
+MATKTAPKRAPGYRCTECGWTTVKWVGRCGECQSWGTVEEIGLTSTTGRTRAATVAEVAPRIADVDATLASFRSTGVREL
+DRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAGGGGP-----RSVLYLTGEESAAQVRSRADRIGAIA---DT
+LRLTA--ETDLGRALGQIER--TDPELVIVDSVQTLQSTEVDGIAGGVSQ----VREVAASLIRTAKEKGITTVLVGHVT
+KDGTIAGPRLLEHLVDVVCQFEG--DRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVSEPVEGTCV
+TVTLEGRRPLVAEVQSLLTPSAGGSPRRTVSGVDAARVNMLLAVLQRRARFALAQDDCYVATVGGVRLSEPASDLAVAVA
+VASAKLS-------APVPQGMIAVGELGLAGEVRPVPGIGRRVREAARLGFTRALVPRSPEPLGDVPAGFTVAEVGSIGE
+ALATIPTWTGG-GPAARPEAGPGR
+>GCF_005280335_PROKKA_00038
+MSPFD--------------------------------LEELDMTAT------------APDPLDGAFTAAWLTSQTFAPV
+EYVV-PGLIPEGLTLLVAAPKVGKSWMVLDLAHAAATGGKALGSISVDRRPVLYLALEDGPRRLQSRLSMLGVDGGGPDL
+MFLTALSASPVATVAAYLERHAQDRPLVILDTL-----GKVRGRDGGNDQYGRDYSQMSALKTLVDAVPGSSLIVVHHTN
+KGGR-------EDFLEAVSGTQGLAGAADSILVIRRDRNQADGTINVTSRDAREGE-----------------------Y
+AVTFDGSRWHTVGA-DLAEAAAAAESKRATAGVGDDMARVIDAVSRHPGGVGVAQ------IVAMTELPRATVDKYLSRA
+VAAERIVRVERGTYAPTPLSEVSDCQIG-----------------------------SDPDPL-----------------
+----------------------DF
+>GCF_005280335_PROKKA_00285
+MATKTAAKRAPGYRCTECGWTTVKWVGRCGECQAWGTVEEVGLTSTTGRTRAATVAEVAPRIADVDATLASFRSTGVREL
+DRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAGGGGP-----RSVLYLTGEESAAQVRSRADRIGAIA---DT
+LRLTA--ETDLGRALGQIER--TDPELVIVDSVQTLQSTEVDGIAGGVSQ----VREVAASLIRTAKEKGITTVLVGHVT
+KDGTIAGPRLLEHLVDVVCQFEG--DRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVAEPVEGTCV
+TVTLEGRRPLVAEVQSLLTPSAGGGPRRTVSGVDAARVNMLLAVLQRRARFALAQDDCYVATVGGVRLSEPASDLAVAVA
+VASAKLA-------APVPQGMIAVGELGLAGEVRPVPGIGRRVREAARLGFTRALVPRSPEPLGDVPAGFTVAQVGSIGE
+ALATIPTWTGA-GAGA--------
+>GCF_020097155_PROKKA_00231
+MATKSSTKRAPSYRCTECGWTTVKWVGRCGECQAWGTVEEAGGAATAGRTHASTVAQAAPRIRDVDATLASFRTTGVREL
+DRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAAGGGP-----RDVLYLTGEESAAQVRSRADRIGALA---DT
+LRLAA--ETDLGRALGQIEK--TDPALVIVDSVQTLQSTEVEGVAGGVTQ----VREVAASLIRTAKEKGITTILVGHVT
+KDGSIAGPRLLEHLVDVVCQFEG--DRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGTQEPVEGTCV
+TVTLEGRRPLVAEVQALLTPSGGGSARRTVSGVDAARVNMLLAVLQRRARFALAQDDCYVATVGGVRLSEPASDLAVAVA
+IASAKLG-------APVPQGMIAVGELGLAGEVRPVPGIGRRVREAARLGFTRALVPRSPEPLGDVPAGFSVAQVGTLSE
+ALGTIPSWTGQRSPGARS------
+>GCF_023573625_PROKKA_00100
+MATKTAPKRAPGYRCTECGWTTVKWVGRCGECQSWGTVEEIGLTSTTGRTRAATVAEVAPRIADVDATLASFRSTGVREL
+DRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAGGGGP-----RSVLYLTGEESAAQVRSRADRIGAIA---DT
+LRLTA--ETDLGRALGQIER--TDPELVIVDSVQTLQSTEVDGIAGGVSQ----VREVAASLIRTAKEKGITTVLVGHVT
+KDGTIAGPRLLEHLVDVVCQFEG--DRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVSEPVEGTCV
+TVTLEGRRPLVAEVQSLLTPSAGGSPRRTVSGVDAARVNMLLAVLQRRARFALAQDDCYVATVGGVRLSEPASDLAVAVA
+VASAKLS-------APVPQGMIAVGELGLAGEVRPVPGIGRRVREAARLGFTRALVPRSPEPLGEVPAGFTVAEVGSIGE
+ALATIPTWTGG-GPAARPEVGPGR

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000067.fa ADDED Viewed

	@@ -0,0 +1,48 @@

+>GCF_002008305_PROKKA_00207
+M------------STAENAGAGAPTRPDEHRAILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTHLAQTLEKGLFD
+GLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVTAGTAYEHPYPFARRLATLDHLTGGRVGW
+NVVTGYLPSAAQNMGQDDQMEHD-----------ERYEHADEYLDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAH
+EGRYFTVPGHAVT-EPSVQRTPVIYQAGASTRGRAFAGKHAEAVFINS--------------------------PTKELA
+AATVKKIRQALVDAGRDPYDVKIFAMQTIVTGATDE-DARAKYDDLAQYVD----PLGGLVLMSGWMGIDLSQYDLDEPI
+GDVKSNAIQSAVETFQKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPGAFEDV
+VEFVVPALQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFALRRR--
+>GCF_003691675_PROKKA_02200
+M------------STAENAGAGAPTRPDEHRAILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTHLAQTLEKGLFD
+GLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVTAGTAYEHPYPFARRLATLDHLTGGRVGW
+NVVTGYLPSAAQNMGQDDQMEHD-----------ERYEHADEYLDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAH
+EGRYFTVPGHAVT-EPSVQRTPVIYQAGASTRGRAFAGKHAEAVFINS--------------------------PTKELA
+AATVKKIRQALVDAGRDPYDVKIFAMQTIVTGATDE-DARAKYDDLAQYVD----PLGGLVLMSGWMGIDLSQYDLDEPI
+GDVKSNAIQSTVETFQKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPGTFEDI
+VEFVVPELQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFALRRR--
+>GCF_005280335_PROKKA_00184
+MAEHPAARPEQDATTSTSAATSTSPASRAGRELLFNAFDMNCVAHQSPGLWRHPEDRARDYNTLGYWTHLAQTLEKGLFD
+GLFIADVLGPYSVYGGTAEAAIRSGAQTPVNDPFLLVSAMAAVTGHLGFGVTAGTAYEHPYPFARRLATLDHLTGGRVGW
+NVVTGYLPSAAQNMGQDDQMEHD-----------ERYEHADEYLDVVYKLLEGSWEDDAVRYDKETGVFADPAKVHDIGH
+EGRYFKVPGAAVT-EPSPQRTPVIYQAGASTRGRAFAGKHAEAVFINS--------------------------PTKELT
+AATVKKIRQALVDAGRDPYDVKIFAMQTIVTGATDE-DARAKYDDLAQYVD----PLGGLVLMSGWMGIDLSQYDLDEPI
+GDVKSNAIQSAVEAFQKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGYNLAYHITPGTFEDV
+VEFVVPELQKLGRYKTAYTDGTLRHKLFGRGDHLPEGHHGASFALRRR-G
+>GCF_020097155_PROKKA_00130
+M------------STAENAGAGAPTRPDEHREILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTRLAQTLEKGLFD
+GLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVTAGTAYEHPYPFARRLATLDHLTGGRVGW
+NVVTGYLPSAAQNMGQDDQMEHD-----------ERYEHADEYLDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAH
+EGTWFKVPGHAVT-EPSVQRTPVIYQAGASTRGRAFAGKHAEAVFINS--------------------------PTKELA
+AATVKKIRQALVDAGRDPYDVKIFAMQTIVTGATDE-DARAKYDDLAQYVD----PLGGLVLMSGWMGIDLSQYDLDEPI
+GDVKSNAIQSAVETFQKASGTDEGWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPGTFEDI
+VEFVVPELQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFAFRNRRG
+>GCF_020097155_PROKKA_00132
+M------------STPTPTLGIA-------------------LTTQTPA------------DARGHWTRLSQALEETSLD
+WAVLTDPLGTAPQAG------------THRIDAVLAACWTATRTHRIGLVPEVTTTHTEPFHVSIGLATLDHVSHGRAGW
+LATVSAAPEVSALFGRRRHPAERTPGLQASRVDLELWEELQDAVAAVRDLWE-SWEPDAEIRDIATGRFIDRERVHHVDV
+EAERFSVRGPSITPRPPQGRLPVLVEA-AGPAGLEAARRTADVVLLPAAEVGRTDAARLPDRRRRGATPAVPVEPTRIVA
+DVTLEGDGARVADAVRHALQAGADGARLVPNPTADPFDALALAADVHDRLDDIRPPDTGTVPLRECLGLAPALSPWRHPE
+DPT--------------ARPTDEEATA-----------------------------------------------------
+--------------------------------------------------
+>GCF_023573625_PROKKA_00207
+M------------STAENAGAGAPTRPDEHRAILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTHLAQTLEKGLFD
+GLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVTAGTAYEHPYPFARRLATLDHLTGGRVGW
+NVVTGYLPSAAQNMGQDDQMEHD-----------ERYEHADEYLDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAH
+EGRYFTVPGHAVT-EPSVQRTPVIYQAGASTRGRAFAGKHAEAVFINS--------------------------PTKELA
+AATVKKIRQALVDAGRDPYDVKIFAMQTIVTGATDE-DARAKYDDLAQYVD----PLGGLVLMSGWMGIDLSQYDLDEPI
+GDVKSNAIQSAVETFQKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPGAFEDV
+VEFVVPALQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFALRRR--

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000069.fa ADDED Viewed

	@@ -0,0 +1,90 @@

+>GCF_002008305_PROKKA_00221
+MRKAEAMPQNPTPARRRRAL------------AAAVAGASLVAAPALAVSATAVELPDGSTVSSPQGE----VQVQQQFE
+DGRYFVVLKDQPSVTAPEAGA-VPGAAPKAK---------FDPSHPRVKNYEAKLQRQQAKVAKAHGAK--AEISFQRAV
+NAFVAELTAEEAQSIAKDPAVLGVAPDEQVAPD-YSSTEFLGLPGKKGTWKSVYGK---AENAGKGVVVGVIDSGIHPDN
+PFIDGQPVQPL--KGKAKVGVPYRTADGQIAVLKADGTTATAECETG--PDFPASSCDSKLIGAYAFSDDFERFVPVDER
+APEERISPLGVFSHGTHVATTILGNTGVEQTIDDDSFGEGAGVAPAAHLISYKICWEDTDPDTGGCYTSASVAAIEQAIE
+NNVDVLNYSISGSNTSIVDPVAMAFKSAAEAGIFVAASGGNSGPGPNTVNHGSPWLTTVAAETFSNELTATVQFSDGTQL
+RGASSARTGVGPAEVIHASEVAAG--DAEAARLCLPGGLT-EEAADKIVLCERGGNARTEKSQVVEEAGGVGMILVNTPS
+GSLDADIHAVPTVHMND---NGVIEKVKSSDLTATVVPGDTTGLPEDPLPQIAGFSSRGPANAVNQELLKPDLAAPGVNV
+IAGVSPLDPDYHGNTFGLMSGTSMASPNLAGMATLLIGKYPAWSPMAVKSALMTTAGDVYNADGTVNTDNFATGAGSADP
+AAAARPGLVYDSGKEQWDALLRGD---------------IAGREVNVPSLAIPDVVGSATVTRTVTAL--ENGRWQFS-A
+SVPGFEVTASPAVLDLKAGQSADVELTVTRTDAAVNTWTHGSMSWTTAKGKAVPEVTSPVTVKAKSAAVTSAVEGSGATG
+SADVEITPGVTGELTPQVLGLGKVDSTVAAATASNSLVSS--ALAVSTVTVEEGTKSLVASINAGAAGADWDLYVI----
+------------------------TPEGKQLSRATADESETLTIANPTPGAYTVVGHLYAANGGKDTGTLETLKLREDAG
+NLTVSPNPVPVTSGKA--------TEATLSWSGLTSGTWKGLVTWDAGITTDVTVQVP
+>GCF_003691675_PROKKA_02234
+MRKAEAMPQNPTPARRRRAL------------AAAVAGASLVAAPALAVSATAVELPDGSTVSSPQGE----VQVQQQFE
+DGRYFVVLKDQPSVTAPEAGA-VPGAAPKAK---------FDPSHPRVKNYEAKLQRQQAKVAKTHGAK--AEISFQRAV
+NAFVAELTAEEAQAIAKDPAVLGVAPDEQVAPD-YSSTEFLGLPGKKGTWKSVYGK---AENAGKGVVVGVIDSGIHPDN
+PFIDGQPVQPL--KGKAKVGVPYRTADGQIAVLKADGTTATAECETG--PDFPASSCDSKLIGAYAFSDDFERFVPVDER
+APEERISPLGVFSHGTHVATTILGNTGVEQTIDDDSFGEGAGVAPAAHLISYKICWEDTDPNTGGCYTSASVAAIEQAIE
+NNVDVLNYSISGSNTSIVDPVAMAFKSAAEAGIFVAASGGNSGPGPNTVNHGSPWLTTVAAETFSNELTATVQFSDGTQL
+RGASSARTGVGPAEVIHASEVAAG--DAEAARLCLPGGLT-EEAAGKIVLCERGGNARTEKSQVVEEAGGVGMILVNTPS
+GSLDADIHAVPTVHMND---NGVIEKVKSSDLTATIVPGDTTGLPEDPLPQIAGFSSRGPANAVNQELLKPDLAAPGVNV
+IAGVSPLDPDYHGNTFGLMSGTSMASPNLAGMATLLIGKYPAWSPMAVKSALMTTAGDVYNADGTVNTDNFATGAGSADP
+AAAARPGLVYDSGKEQWDALLRGD---------------IAGRDVNVPSLAIPDVVGSATVTRTVTAL--ENGRWRFS-A
+NVPGFEVTASPAVLDLKAGQSADVELTVTRTDAAVNTWTHGSMSWTTAKGKAVPEVTSPVTVKAKSATVTSAVEGSGATG
+SADVEITPGVTGELTPQVLGLGKVDSTVAAATASNSLESS--ALAVSTVTVEEGTQSLVASINAGAAGADWDLYVI----
+------------------------TPEGKQLSRATADESETLTIADPAPGAYTVVGHLYAANGGKDTGTLETLKLREDAG
+NLTVSPNPVPVTSGKA--------TEATLSWSGLTSGTWKGLVTWDAGITTDVTVQVP
+>GCF_005280335_PROKKA_00086
+M--------TPPLSRRHRALGMTSALALVLTGASAAGATSGTGAP-AAAEADAVTAVTGAAGTADQGP----RTAPEVFE
+DGGYIVLMAEAP--VASYDGG-TPGYAPTKPGKGLGRDKGFNPKSANAKKYAAHLERGQDRALERAGAEAAPHTRYTTSL
+NGFAGELTAQEAAALASDPAVLAVVPDEIRQPDTVSSPDFLGLTGKKGLWAQVVGKKAPATDAGRGVVVGVVDSGIRPE-
+-------AASF--QDRGHPAAPADWAGG---------------CETGDEEAFPADSCNDKLIGAKYFVQGF----GAGRL
+APVETLSPLDAGGHGTHTASTAAGNAGVPAVVDGTPRGEISGMAPGAHVAAYKACWEGV--PSGGCATSDTVAAINAAVE
+DGVDVLNYSISGTTSNVVDPVEVAFMHAAAAGVFVAASSGNSGPTVSTTAHPSPWITTVAAST-QAVYEQTLVTGDGQRF
+IGSSITAPLEAETPMVHAADLAADGVDAARAALCLPGTLDATAAADMLVVCDRGENARAEKSQVVADAGGAGMVLVNVAD
+SGLNADLHALPAVHLPHTERDRLLAYVDTEEPTGRILP--TTEGTTTRVPEVAGFSSRGPSLAAASDLLKPDVSAPGVDV
+LAAYS---PDEAGEDFAYASGTSMSSPHVAGLAALVKQGRPDLGPMEIKSSLMTTAGDHASATSP-----FAEGAGFVDP
+MKILDPGLVFDTDQGDWYDYLAGQGIVFSGSGEPVSETPIDASDLNVPSIAVGELYGSQTVTRTLKNVGGNNGVWTARVE
+GMEGMDVSVSPQVIKPRRGQEQDVEITLTAAGAPAGQWATGHVVWSGPAGK---EVRIPVVARPGVADAPASVTVDRDAD
+GLELPVLSGVDGTFTTRVNGLTAGTEHIGTTVRRMFFDSTDPALTGHDFAYPRGYPTVRIEAETSAEDVDLDVYVTGSWT
+SYPVARSVTRGTGMEVFQGPIYSSAPQHRIFVVAKTGAD---GVEHDEPIDYT-LRVFFPQAGGG------------DNG
+VLSFDPASAAVKPGQTHVFHGTLNTDGTSVYTGTVDILHEGKVV----DTTQIRVQ--
+>GCF_005280335_PROKKA_00159
+MRKAEAMPHIPTPARRRRAL------------AAAVVGASLVAAPALAASAIAVELPDGSVVTSPQGE----AKVEQQFE
+DGRYFVVLKDAPSVTAQEAGAPAPGAAPKAK---------FDPDHPRVKNYEAKLQRQQEKVARDNGVE--PKTTFQRAV
+NAFVAELTAEEAMRLSKDSAVLGVAPDEQVAPD-YSSTEFLGLPGKKGTWNTTYGK---PENAGKGVVVGVIDTGIHPDN
+PFIDAEPVKPL--KGKAKVGEPYRTADGDIAVLKADGTTATAECETG--PGFPADSCDTKLIGAYAFSDDFERFVPVENR
+HPAEQLSPLGVFSHGTHVATTILGNTGVEQTIDGTSFGEGAGVAPAASLISYKICWEDNDPNTGGCYTSASVAAIEQAIE
+NNVDVLNYSISGSNTTIVDPVAMAFKSAAEAGIFVAASGGNSGPTPNTVNHSSPWLTTVAAETFSNELTGTVEFSDGTKY
+RGASSAGSDAGPAEVIHASEVAAG--DAEAARLCLPGSLT-AEAADKIVLCERGQNARVEKSAVVAEAGGVGMILANTPT
+GSLDADIHSVPTVHINDT--DGVIEKVKSSDLTATIVRGDTTGLPQDPLPQIAGFSSRGPSNAVNQEFLKPDVAAPGVNV
+IAGVSPLDPDYNGNEFGLMSGTSMASPNLAGMAALLIGKEAAWSPMAVKSALMTTAGDVFNADGSVNEDNFATGAGSADP
+KAAARPGLVYEADSTQWDALLLGE---------------IAGREVNVPSVAIPDVVGSASVTRTLTAT--ENGRWQFS-G
+SVPGFEVTASPSMLDLKKGQSAEVELTFTRTDAEVNTWAHGSMSWSTAKGKAVPTVTSPVTLKALSATATSAVEGSGAEG
+SATVEIEPGMTGELTPQILGLGKVEAAEVSAVANTSASGA--ALAGRVVNVEEGTKALVASINAGAEGVDWDLYVI----
+------------------------TPQGRQLNMATAAGDETLTIQNPVPGEYTVIGHLYSAPAGTDTASLETLKLREDVG
+NLTVDPNPVPVTTGEA--------TTAELAWSGLTEGTWKGLVTWDAGVTTDVTVTVP
+>GCF_020097155_PROKKA_00117
+------MNRHP---QRLRLL------------GAAVTAVGLMAAP-LAAPAFA----------APQAEHAVGVQAATPLK
+AGRYFVILKDAPSAVAESQAT-APGAAPSAK---------FDANHPRVKNYEAKLKRQQEKVAAQQGVT--PKVTFQRAL
+NGFVAELSAEQAQAYAEDPAVLAVTADEQVAPD-YTSTDFLGLNGKKGAWNTTFGK---AENAGRGVVVGVIDSGIYPDS
+PFLDGTPVGPRTNNGKLKAGDTFRTADGRIAVQKADGTLATAECQSG--PDFPASTCDSKLIGAYAFSDDFVRGTPVEKR
+DPAERISPLGVKSHGTHVATTIVGAKDVEQTIDGASFGLGSGVAPAAKLISYKVCWEDTDPDTGGCYSSASVAAVEKAIE
+NNVDVLNYSISGNNTSVVDPVALAFRSAAEAGIFVAASGGNSGPTPSTVNHSSPWVTTVAAETFSNELTGTLELSDGTKV
+RGASSARTGVGPAPVIHAADAAAAGVSADDARLCKPGALDPAKAAGKIVLCERGVNARVEKSAVVKDAGGVGMILVNVTP
+GSLDADIHAVPTVHTND---ASLIAKAKAGGLQATIVPGDTTGQAPDPLPQIAGFSSRGPSNAVNQEFLKPDVAAPGVNV
+IAGVSEYDSDYHGNVFGLMSGTSMASPNLAGMATLLIGKHPEWSPMAVKSALMTTAGDVYNADGTVNQDNFATGAGSADV
+AAANRPGLVYESDATQWNALILGD---------------LAGREVNVPSVALPDVLGTASVKRTVTAL--ENGRWTFS-G
+SVPGYTVTASPSVLDLKAGQKAEVTLTFTRTDAALSQWTHGSFSWTTAKGKAVPSVTSPVTLKSVPATADASVTGTGASG
+SAAVAVQPGFTGQLTPSVLGLNKVESQAVTLQPGGS--------KVTPVTVAPGTKSVTFAVDSGVDTADWDMLVQ----
+------------------------TPSKKQFTSATESSDESVTIQDPEPGTYLVLTQLYANPAGADTAALETVQLRSDAG
+NMTVTPNPIPVTTGQE--------TSATVNWTGLTSGTWRGQVTWAEGTATQVEVTVP
+>GCF_023573625_PROKKA_00222
+MRKAEAMPQNPTPARRRRAL------------AAAVAGASLVAAPALAVSATAVELPDGSTVSSPQGE----VQVQQQFE
+DGRYFVVLKDQPSVTAPEAGA-VPGAAPKAK---------FDPSHPRVKNYEAKLQRQQAKVAKAHGAK--AEISFQRAV
+NAFVAELTAEEAQAIAKDPAVLGVAPDEQVAPD-YSSTEFLGLPGKKGTWKSVYGK---AENAGKGVVVGVIDSGIHPDN
+PFIDGQPVQPL--KGKAKVGVPYRTADGQIAVLKADGTTATAECETG--PDFPASSCDSKLIGAYAFSDDFERFVPVDER
+APEERISPLGVFSHGTHVATTILGNTGVEQTIDGDSFGEGAGVAPAANLISYKICWEDTDPDTGGCYTSASVAAVEQAIE
+NNVDVLNYSISGSNTSIVDPVAMAFKSAAEAGIFVAASGGNSGPGPNTVNHGSPWLTTVAAETFSNELTATVQFSDGTQL
+RGASSARTGVGPAEVIHASEAAAG--DAEAARLCLPGGLT-EEAADKIVLCERGVNARTEKSQVVEEAGGVGMILVNTPS
+GSLDADIHAVPTVHMND---NGVIEKVKSSDLTATIVPGDTTGLPEDPLPQIAGFSSRGPANAVNQELLKPDLAAPGVNV
+IAGVSPLDPDYHGNTFGLMSGTSMASPNLAGMATLLIGKYPAWSPMAVKSALMTTAGDVYNADGTVNTDNFATGAGSADP
+AAAARPGLVYDSGKEQWDALLRGD---------------IAGRDVNVPSLAIPDVVGSATVTRTVTAL--ENGRWRFS-A
+NVPGFEVTASPAVLDLKAGQSADVELTVTRTDAAVNTWTHGSMSWTTAKGKAVPEVTSPVTVKAKSATVTSAVEGSGATG
+SADVEITPGVTGELTPQVLGLGKVDSTVAAATASNSLESS--ALAVSTVTVEEGTKSLVASINAGAAGADWDLYVI----
+------------------------TPEGKQLSRATAAESETLTIANPTPGAYTVVGHLYAANGGKDTGTLETLKLREDAG
+NLTVSPNPVPVTSGEA--------TEATLSWSGLTSGTWKGLVTWDAGITTDVTVQVP

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000070.fa ADDED Viewed

	@@ -0,0 +1,43 @@

+>GCF_002008305_PROKKA_00223
+MTA---PAPPPASPVLGVAAHDGIVAHGLARSFGAVHAVRDVSLTVPAGSVTALVGPNGS
+GKTTLLLILATLLRPDAGAVSVAGVDAVREPVEARRRLGWMPDTLGVWEELTCHDILASL
+GRLYGMGKAEASARADEQLAWVELTEFAHRPARVLSRGQQQRLSLARATVHRPSVLLLDE
+PANGLDPAARIRLRDDLRAMAAAGTAVLVSSHVLAELEEMSDRAVFLREGATVATQEFRA
+AD--DLARPYRIAGPDPT-ARDTLIRALETRGLTVTAATGAGAGQRRDGVVVQLRGEA--
+AAAALLADLVREGVLVSHFAPEGSRLENAYLGLHLEGPRTEGDRP---------------
+>GCF_003691675_PROKKA_02236
+MTA---PAPPPASPVLGVAAHDGIVAHGLARSFGAVHAVRDVSLTVPAGSVTALVGPNGS
+GKTTLLLILATLLRPDAGAVSVAGVDAVREPVEARRRLGWMPDTLGVWEELTCHDILASL
+GRLYGMGKAEASARADEQLAWVELTEFAHRPARVLSRGQQQRLSLARATVHRPSVLLLDE
+PANGLDPAARIRLRDDLRAMAAAGTAVLVSSHVLAELEEMSDRAVFLREGATVATQEFRA
+AD--DLARPYRIAGPDPT-ARDTLIRALETRGLTVTAATGAGAGQRRDGVVVQLRGEA--
+AAAALLADLVREGVLVSHFAPEGSRLENAYLGLHLEGPRTEGDRP---------------
+>GCF_005280335_PROKKA_00157
+------------------------MAHGLARSFGDVHAVRDVSLTVPSGSVTALVGPNGS
+GKTTLMLLLATLLRPDAGAVTIGGVDAVREPQEARRRLGWMPDTLGVWESLTCRDILTSL
+GRLYGMGAAEAAARAGEQLERVALTEFADRPARVLSRGQQQRLSLARATVHRPGVLLLDE
+PANGLDPAARIRLRDDVRAMAAEGTAILVSSHVLAELEEMSDRAVFVREGATLSTQEFRE
+DA--AQTRPYRIAGPASA-RPDVLVRALEARGLAVEPA--AAHGQPRAGVVVGLRGET--
+AAAELLADLVREGVPVSHFAPEGSRLENAYLGLHLDRDTAEGDRP---------------
+>GCF_005280335_PROKKA_00588
+M----------------------ITVNEVSKSFGSTPVLQDLTFSIRPGLMTGFVGGNGA
+GKTTTMRILLGVLDADSGRIEVDGAPITRD---YRAGIGYMPEERGLYPKMSVLDQLVYL
+GRLHHMRGADAKARALELLERLNLGDRAGSRLEELSLGNQQRAQIAAALVHDPVALVLDE
+PFSGLDPNAVETTLQVLRETADTGVPVLFSSHQLDLVERLCDELVILAGGRVRAS-----
+----GTRDELLAAHADPEWELHADADTGWVRGLPGIEVL------HFDGGRARFRADTPQ
+AAQRVLADAAARG-PVHRFGPVTRSLHEIFTEVT------------------------R-
+>GCF_020097155_PROKKA_00115
+MTSSVLPQPP-----------SGIVAHGLARSFGSVHAVRDVSLTAPAGSVTALVGPNGS
+GKTTLMLLLATLLRPDRGSVSVAGVDAMADPGQARRLLGWMPDTLGVWDSLTCADILTSL
+GRLYGMGQAEAATRAREQLAWVQLEPFADRPARVLSRGQQQRLSLARATVHRPAVLMLDE
+PANGLDPTSRIRLRDDVRAMAAAGVAVLVSSHVLAELEEMADRAVFVSEGATVAVRDLSG
+ADDAGRERPYRIAGPDPS-RRDELVRALQARGVPLAAPLEG----HRPGVVVRLRGED--
+AAAALLADLVAAGVPVSRLAPEGSRLENAYLDLALGGPAPHAAGPVTAAGPAPTVEGGRA
+>GCF_023573625_PROKKA_00224
+MTA---PAPPPASPVLGAAAHDGIVAHGLARSFGAVHAVRDVSLTVPAGSVTALVGPNGS
+GKTTLLLILATLLRPDAGAVSVAGVDAVREPVEARRRLGWMPDTLGVWEELTCHDILASL
+GRLYGMGKAEASARADEQLAWVELTEFAHRPARVLSRGQQQRLSLARATVHRPSVLLLDE
+PANGLDPAARIRLRDDLRAMAAAGTAVLVSSHVLAELEEMSDRAVFLREGATVATQEFRA
+AD--GLARPYRIAGPDPT-ARDTLVRALETRGLTVTAATGAGAGQRRDGVVVQLRGEA--
+AAAALLADLVREGVLVSHFAPEGSRLENAYLGLHLEGPRTEGDRP---------------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000074.fa ADDED Viewed

	@@ -0,0 +1,49 @@

+>GCF_002008305_PROKKA_00279
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWHFQHLGAR
+AAGGFGIVVAEATAVTPEGRISAWDTGLWNDEQRDAWAPIAEFIASQGALPAIQLGHAGA
+KASTVPMHPGALAG-QPILEGPDSWETLSPSGVATNSMEIRT-HAMRVDEIRETVQAFAD
+AAERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVW
+PADKVLGIRISGSDWVEGGWSIEETVRLAQELQGQVHWFDLSSAGIGDTYEGPQGPGYQV
+PLATAVKEGTEGIVV--SAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPN----W---
+-------PT-----AAALALDVPSEQVPMARQYFRAKW
+>GCF_003691675_PROKKA_00203
+-------------MPSLFDPLDVGALRLDNRIVMAPLTRQRA-GEDGVPTELPAEHYAQR
+ATA--GLLVTEGAFPSFRSRAFPGQTGLADDAQTDGWRAVAQAVHEAGGHVFVQVMHGGR
+MC-----HPDLLRGAEP--EAPSAIAPGVPVRGFSGKMEGPVPSALDTEELPRVVAEFAD
+AARRAVEAGLDGVEVHGANGYLLHEFLAPSSNTREDAYGGSPENRARLTVEVVRAVAQAI
+GAERT-ALRISPEHNVQGTIEEDRADVLATYDALLAGLADLDLAYLSVIHQDVAG-----
+DLAAHLRESFSGPLVLNSGFGAVTGLEEARRIVEDGLADAVAVGRELIANPDLARRWREG
+LPLNEPDPTTFYTGGAHGYTDYPFVDGSPSS-------
+>GCF_003691675_PROKKA_02294
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWQFQHLGAR
+AAGGFGIVVAEATAVTPEGRISPWDTGLWNDEQRDAWAPIAEFIASEGALPAIQLGHAGA
+KASTVPMHPGAPAG-QPILEGPDSWETLSPSGVATNSMEIRT-HAMRVDEIRETVQAFAD
+AAERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVW
+PADKVLGIRISGSDWVEGGWSIEETVRLAQELQGQVHWFDLSSAGIGDTYEGPQGPGYQV
+PLATAVKEGTEGIVV--SAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPN----W---
+-------PT-----AAALALDVPSEQVPMARQYFRAKW
+>GCF_005280335_PROKKA_00074
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWQFQHLGAR
+AAGGFGIVVTEATAVTPEGRISPWDTGLWNDEQRDAWAPIAEFIASEGALPAIQLGHAGA
+KASTVPMHPGAPAG-QPILEGPDSWETLSPSGVATNSMEIRT-HAMRVDEIRETVQAFAD
+AAERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVW
+PADKVLGIRISGTDWVEGGWSIEETVRLAQELQGQVHWFDLSSAGIGDTYEGPQGPGYQV
+PLATAVKEGTEGIVV--SAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPN----W---
+-------PT-----AAALALDVPSEQVPMARQYFRAKW
+>GCF_020097155_PROKKA_02346
+-------------MPDLFDPLPLGGLTLPNRVTMAPLTRQRA-GEDGVPGDLHVEYYRQR
+ASA--GLIVSEGVFPTVDSRAFPGQPGLEDEAQQAGWARVADAVHEAGGRIFVQVMHGGR
+MC-----HPDLLRGAEP--VAPSAIAPGVPVRGFSGKTDGPVPRALETEELPGIAAAFAS
+AARRAVDAGADGVEVHGANGYLLHEFTAASSNHRTDAYGGSPENRARLTVEVVRAVAAEI
+GAERT-ALRLSPEHDVQGVLEQDRADVLATYGAILDGVADLDLAYLSLLHRDVAG-----
+DLVAALRARFGGPVLLNSGFSEVTGAAEARRIVEGGLADAAVVGRALIANPDLVRRWRED
+RETNAPDPSTFYVGGAHGYTDYPSLEG-----------
+>GCF_023573625_PROKKA_00278
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWQFQHLGAR
+AAGGFGIVVAEATAVTPEGRISPWDTGLWNDEQRDAWAPIAEYIASEGALPAIQLGHAGA
+KASTVPMHPGAPAG-QPILEGPDSWETLSPSGVATNSMEIRT-HAMRVDEIRETVQAFAD
+AAERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVW
+PADKVLGIRISGSDWIEGGWSIEETVRLAQELQGHVHWFDLSSAGIGDTYEGPQGPGYQV
+PLATAVKEGTEGIVV--SAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPN----W---
+-------PT-----AAALALDVPSEQVPMARQYFRAKW

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000076.fa ADDED Viewed

	@@ -0,0 +1,144 @@

+>GCF_002008305_PROKKA_00287
+M-----SGPA-ESAAGTAT--PAADVVLGRFTEPTRAWFTGAFETPTPAQLGAWDAISSGRHALVIAPTGSGKTLSSFLW
+ALDSFVREPAAEGTAATRVLYVSPLKALGVDVERNLRAPLVGITQTAAHQGRPVPRVRVGVRSGDTPAAERRRLQQDPPD
+ILITTPESLYLMLTSQARAA---LTGVRTVIVDEVHAVAGTKRGAHLAVSLERLDALLDAPVQRIGLSATVEPAAEVARF
+LGGTQPVTVVRPASAKRWDLTVTVPVPDLTDLSSPAAAHDLGPGSSTGGLGDE----GAVTGGSIWPHVEERIVDLVAER
+RSTLVFANSRRLAERLTGRLNEIWEARAEAAAAAEHPDAVPGFRTP----------------------------DPTGFH
+GPAQVAGQTGTGSGTVSDFARAHHGSVSKEQRAIVEEALKTGQIRCVVATSSLELGIDMGAVDQVIQVESPPSVASGLQR
+VGRAGHQVGEVSRGVFFPKHRGDLVDTAVVAERMTAGRIESLRIPANPLDILAQQTVAAVAVADLDAQEWFDLVRRSAPF
+ATLPF------SAYESVLDLLAGRYPSDEFAELRPRILWDRENGTLAARPGAQRLAVTSGGTIPDRGLFGVFLASDGGAD
+GTPGGAAAGDTAESAGTASAGSARSGGRRVGELDEEMV-YESRVGDVILLGATSWRIVDITADRVLVLPAYGQPGKLPFW
+RGDAAGRPAELGDAVGRFRRELDADPEAGRTRLGAAGLDPWAQDNLLAYLKDQREATGVLPTEQTLVVERFTDELGDWRV
+VLHSPYGMAVHAPWALAVGARLAQRYGLETGSGAAMAADDGIVLRIPLMDAEPPGAELFEFTAEELDEIVTAE--VGGSA
+LFAARFRE----NAARSLLLPRRDPGRRTPLWQQRQRSAQLLDVARKHPRFPVILETVREVLQDVYDLPALKELAGRVSS
+RAVRLVEVTTTAPSPFSQSILFGYIAQFIYEGDSPLAERRAAALSLDPALLSELLGTEELRELLDAEVIAEVEAQLQRLA
+PDRRARGVEGVADLLRLLGPLSVAEAARRTRAEGEAEE------------AADEAAVAGMLAELERAGRAFRLRQDGVER
+FAAVEDAARLRDALGTPIPHGVPTAFLDPVDDPLGDLVGRYARTHGPFTAAEAGAALGLGGAVVLSVLQRLATERRVSTG
+AFRPEGTPGAASLDAEWCDAEVLRRIRMRSLAALRAEVEPVDQAAYARFLADWQHLRPRTGRDGAWRPPATLEGVDGVAT
+VLDQLAGTPLPASAWESLVLPARVRDYAPALLDELLATGEYVWSGVGEATGNDGWVALHPADAVDLTLRLPE------PA
+EETPADAAL--RAAVLEVLAGGGAWFFPQLVERVRAVQAAAGDGGTGTAGGTGGP-DPHRDPADLARGPAVLAALWGLVW
+DGRVGNDTFAPVRGLLSLGKTAHRTGRQTPRARTARTGGAAGAAA---GRGLGGRLAGVRGRGRYAGLTSSEGGARGTAG
+LTAGTVGLSAAEQARSAGRWSLLPAAEQDPTIRAHATAELLLDRYGVITRGSVVAEEVPGGFAGQYRLLTRMEDAGQVRR
+GHFVDGLGGAQFSTGAVVDRLRGFQRDE-EDA------------------------------------------------
+--------AVDTAPLALALAATDPANPYGAALDWPSVPAGPDGVVPTGHRPGRKAGAVVVLIAGRLALYMERGGRTLLAF
+TEESGELRAAAEALVWALRTGHTERLSLEKVNGGPVLGTPLAEALLAAGFYSSPSGIRFRN
+>GCF_002008305_PROKKA_01958
+M-TTSVEGFS------------ALDPVIQHHIVNTLRW-----PDLRPLQKASVASLLAGHDALLLAPTAGGKTEAAFFP
+VLTRAEREQ----WTGTSVLYVAPLKALLNNVESRAMEYTSWLGRSA------------SVRHGDTTQAERRRQGTERPD
+VLMTTPESLESMLISPTVNVTDFFSELRTIIVDEVHAFAGDDRGWHLLSVLERLSAVVRRPIQRIGLSATVGNPEELLTW
+LQGGNAAAGL-PAS-------VIAPPVDRTGAAAPELRLDF-VGSEDNAATVI----SRLHGG------EKR--------
+---LVFAESRRTVELLGNALHE---------------------------------------------------RDVTTFL
+----------------------SHSSLSLSERRRSEQAFAEAQDCVIISTSTLELGIDVGDLDRVLQLGAPSTVASFLQR
+LGRTGRRPGAQRNMLFLELKPADLLRAAGLLLLHGEGYVEPIQPPPAPHHIVAQQILA------LTLQK--GQLQRGAAL
+AGLQALGMSDSTTYRTIEDGLL------EHGHL------DSDGGLLFVGPETQR----RYGGLYFRDLMAVF--------
+----------TVE-----AEFPVFHGRTEIGSVAPNWIATDPDDQPLLILAGRSWKVSFIDWKRHLVHVERSDRGLAPRW
+ASPPRALSWALSDAMRRVL--LGADP-------AGVVLTGRAQDA----LADHREAEGYTAAADHTVLASTADDLRWW--
+----TWGGAGANALLVAALEQVAPEL-----LGEKLRFDNFSLRLRGDVDAASLGRALRQATSNFGGDLAGVDPLVDDAA
+VRGLKFHEMLPLDLARATLAARL--ADHTGVARVLERPVQMLRTAE----------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------DGR---------------MWG---
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-------------------------------------------------------------
+>GCF_003691675_PROKKA_02309
+M-----SGPA-ETAAGAPT--PAADVVLGRFTEPTRAWFTGAFEAPTPAQLGAWDAISSGRHALVIAPTGSGKTLSSFLW
+ALDSFVREPAAEGTAATRVLYVSPLKALGVDVERNLRAPLVGITQTAAHQGRPVPRVRVGVRSGDTPAAERRRLQQDPPD
+ILITTPESLYLMLTSQARAA---LAGVRTVIVDEVHAVAGTKRGAHLAVSLERLDALLDTPVQRIGLSATVEPAAEVARF
+LGGTQPVTVVRPASAKRWDLTVTVPVPDLTDLSSPAAAHDLGPGSSTGGLGDE----GAVTGGSIWPHVEERIVDLVAER
+RSTLVFANSRRLAERLTGRLNEIWEARAEAAAAAEHPDAVPGFRTP----------------------------DPTGFH
+GPAQVAGQTGTGSGTVSDFARAHHGSVSKEQRAIVEEALKTGQIRCVVATSSLELGIDMGAVDQVIQVESPPSVASGLQR
+VGRAGHQVGEVSRGVFFPKHRGDLVDTAVVAERMTAGRIESLRIPANPLDILAQHTVAAVAVADLDAQEWFDLVRRSAPF
+ATLPF------SAYESVLDLLAGRYPSDEFAELRPRILWDRENGTLAARPGAQRLAVTSGGTIPDRGLFGVFLASDGGAD
+GAPGGAAAGDTAESASTASAGSARSGGRRVGELDEEMV-YESRVGDVILLGATSWRIVDITADRVLVLPAYGQPGKLPFW
+RGDAAGRPAELGDAVGRFRRELDADPEAGRTRLAAAGLDPWAQDNLLAYLKDQREATGVLPTEQTLVVERFTDELGDWRV
+VLHSPYGMAVHAPWALAVGARLAQRYGLETGSGAAMAADDGIVLRIPLMDAEPPGAELFEFTAEELDEIVTAE--VGGSA
+LFAARFRE----NAARSLLLPRRDPGRRTPLWQQRQRSAQLLDVARKHPRFPVILETVREVLQDVYDLSALKELAGRVSS
+RAVRLVEVTTTAPSPFSQSILFGYIAQFIYEGDSPLAERRAAALSLDPALLSELLGTEELRELLDAEVIAEVEAQLQRLA
+PDRRARGVEGVADLLRLLGPLSVAEAARRTRAEGEAEE------------AADEDAVAGMLAELERAGRAFRLRQDGVER
+FAAVEDAARLRDALGTPIPHGVPTAFLDPVDDPLGDLVGRYARTHGPFTAAEAGAALGLGGAVVLSVLQRLATERRVSTG
+AFRPEGTPGATGLDAEWCDAEVLRRIRMRSLAALRAEVEPVDQAAYARFLADWQHLRPRTGRDGAWRPPATLEGVDGVAT
+VLDQLAGTPLPASAWESLVLPARVRDYAPALLDELLATGEYVWSGVGEATGNDGWVALHPADAVDLTLRLPE------PA
+EETPADAAL--RAAVLEVLAGGGAWFFPQLVERVRAVQAAGGDA--GGAGRAVGP-DPHRDPADLARGPAVLAALWGLVW
+DGRVGNDTFAPVRGLLSLGKTAHRTGRQTPRARTARTGGAAGAAA---GRGLGGRLAGVRGRGRYAGLTSPEGGARGSAG
+LTAGTVGLSAAEQARSAGRWSLLPAAEQDPTIRAHATAELLLDRYGVITRGSVVAEEVPGGFAGQYRLLTRMEDAGQVRR
+GHFVDGLGGAQFSTGAVVDRLRGFQRDE-EDA------------------------------------------------
+--------AVDTAPLALALAATDPANPYGAALDWPSVPAGPDGVVPTGHRPGRKAGAVVVLIAGRLALYMERGGRTLLAF
+TEDPGELRAAAEALVWALRTGRTERLSLEKVNGGPVLGTPLAEALLAAGFYSSPSGIRFRN
+>GCF_005280335_PROKKA_00067
+M-----SGPA-ETAAGAPT--PAADVVLGRFTEPTRAWFTGAFEAPTPAQLGAWDAISSGRHALVIAPTGSGKTLSSFLW
+ALDSFVREPAAEGTAATRVLYVSPLKALGVDVERNLRAPLVGITQTAAGLGRPVPRVRVGVRSGDTPAAERRRLQQDPPD
+ILITTPESLYLMLTSQARSA---LAGVRTVIVDEVHAVAGTKRGAHLAVSLERLDSLLETPVQRIGLSATVEPASEVARF
+LGGTQPVTVVRPASAKRWDLTVTVPVPDLTDLSSPSAAHDLGPGSSPGGPGAEGGPGGAVTGGSIWPHVEERIVDLVAER
+RSTLVFANSRRLAERLTGRLNEIWEARLEAAAAVEDPDAVPGFRTPGAG----------------AGAASSTPATPSSSY
+-PAQVAGQTGTGSGTVSDFARAHHGSVSKEQRAIVEEALKTGRIRCVVATSSLELGIDMGAVDQVIQVESPPSVASGLQR
+VGRAGHQVGEVSRGVFFPKHRGDLVDTAVVAERMTAGRIEALRIPANPLDILAQQTVAAVAVADLDAQEWFDLVRRSAPF
+ATLPL------SAYESVLDLLAGRYPSDEFAELRPRILWDRENGTLAARPGAQRLAVTSGGTIPDRGLFGVFLASDGGPD
+GAPGGAAAGDTAE-----SAGSARSGGRRVGELDEEMV-YESRVGDVILLGATSWRIVDITADRVLVLPAYGQPGKLPFW
+RGDAAGRPAELGDAVGRFRRELDADPAAGRERLAAAGLDAWAQDNLLAYLKDQREATGVLPTEQTLVVERFTDELGDWRV
+VLHSPYGMAVHAPWALAVGARLAQRYGLETGSGAAMAADDGIVLRIPLMDAEPPGAELFEFTAEELEEIVTAE--VGGSA
+LFAARFRE----NAARSLLLPRRDPGRRTPLWQQRQRSAQLLDVARKHPRFPVILETVREVLQDVYDLPALKDLAGRVAS
+RAVRLVEVTTPAPSPFSQSILFGYVAQFIYEGDSPLAERRAAALSLDPTLLAELLGTEELRELLDAGIIAEVEAQLQRLA
+PDRRARGVEGVADLLRLLGPLSAAEAARRVRPEAGADD-------DGGAAAADVAAVGEMLAGLERAGRAFRLRQDGVER
+FAAVEDAARLRDTLGTPIPHGVPAAFLEPVDDPLGDLVSRYARTHGPFTAAEVGAALGLGGAVVLPVLQRLATERRVSTG
+AFRPDGAPGATGLDAEWCDAEVLRRIRLRSLAALRAEVEPVDQSAYARFLADWQHLRPRVGRDGAWRPPATLEGVDGVAT
+VLDQLAGTPLPASAWESLVLPTRVRDYAPALLDELLATGEYVWSGVAEAAGNDGWVALHPADAVDLTLRLPERPDGTGPD
+AAAPRDAAL--RADVREVLAGGGAWFFPQLVERVRAAQSARL--------GTGGP-DGH--GADLARGPAVLEALWGLVW
+AGEVGNDTFAPVRGLLSLGKTAHRTGRQTPRARTARTGGAGAGTA---GRGLGGRLAGVRGRGRYAGLASPDGGARGTAG
+PAAGMAGLSAAEQARAAGRWSLLPAAERDPTIRAHATAELLLDRYGVITRGSVVAEEVPGGFAGQYRLLTRMEDAGQVRR
+GHFVAGLGGAQFSTGAVVDRLRGFQDDDGADAPA----APRLDAFGLPLPAAP---------------------------
+--------AEQRTPAALALAATDPANPYGAALDWPSVPAGPDGVVPTGHRPGRKAGAVVVLIRGELALYMERGGKTLLCF
+TQGAAELKAAAEALVWALRTGRTERLSLEKVNGGPVLGTPLAEAMLAAGFYSSPSGLRYRS
+>GCF_020097155_PROKKA_00046
+MREDGGEGPAPEEAAPSPAAVPDADAVLARFSEPTRRWFTGAFAAPTAAQLGAWDAISSGRHALVVAPTGSGKTLSSFLW
+ALDSFVREPAEPDVSATRVLYVSPLKALGVDVERNLRAPLIGITQTARSLGAPVPEVRVGVRSGDTPAAERRRLQQDPPD
+ILITTPESLYLMLTSKARSA---LSGVRTVIVDEVHAVAGTKRGAHLAVSLERLDALLDSPVQRIGLSATVEPAAEVARF
+LGGVQPVTVVRPVSAKRWDLTVTVPLPDMTDLSTPPPSA-LDAGRDGAAAGVP----GEATGGSIWPHIEERIVDLVAPR
+RSTIVFANSRRLAERLTGRLNEIWEARQEAAAAVHDPDLVPGFRTPSTAGEVLTDWLGTATGQTPAGAPRPPGGSAATSF
+-PAQVAGQTGTGSGTVSDFARAHHGSVSKEQRALVEEALKTGRIRCVVATSSLELGIDMGAVDQVIQVESPPSVASALQR
+VGRAGHQVGEVSRGVFFPKHRGDLVDTAVVAERMAAGRIEALRIPQNPLDILAQQTVAAVALEDVDAEEWFDLVRRSAPF
+SALPH------SAYESVLDLLAGRYPSDEFAELRPRILWDRELGELSARPGAQRLAVTSGGTIPDRGLFGVFLATE-ASD
+GAPGGAALGDTAESASGASSGSKRSGGRRVGELDEEMV-YESRVGDVILLGATSWRIVDITADRVLVLPAYGQPGKLPFW
+RGDAAGRPAELGDAVGRFRRELDADPDAARDRLAAAGLDEWARENLLTYLADQRESTGRLPTEQALVVERFTDELGDWRV
+VLHSPYGMAVHAPWALAVGARLAQRYGLETGSGAAMAADDGIVLRVPLMDAEPPGAELFEFSAEELEEIVTAE--VGGSA
+LFAARFRE----NAARALLLPRRDPGRRTPLWQQRQRSAQLLDVARKYPSFPVILETVREVLQDVYDLPALKDLAGRIAS
+RAVQMVEVTTPAPSPFAQSILFGYVAQFIYEGDSPLAERRAAALSLDPALLAELLGTEELRELLDPEVIARVEAELQRTA
+PDRRVRGAEALADLLRIVGPLSVAEAAARTLPVEDAAPAPADEAAAGAPSAAHLAAVTAHLEGLERTGRAYRVRLNGEER
+FAAVEDAARLRDALGAPIPLGVPVAFHEPVEDPVGDLVSRYARTHGPFTAAEAGAALGLGGAVVLPVLQALASQRRVSQG
+AYRPDGTPGATGLEAEWIAAEVLQKVRRRSLAALRAEVEPVDQAAYARFLADWQHLRPRPGRPS----PATLEGVDGVAT
+VLDQLAGVPLPASAWESLVLPSRVRDYTPGLLDELLATGEYVWSGTADAPGNDGWVALHPADAVDLTLRRPE------PP
+AQDVAAERLTARDHLLTVLAGGGAWFFGPLVERVRADAARAAE---AEAGGEDGPRDPHAAAATLPRGPVILEALWDLVW
+AGRVGNDTFAPIRGLLSLGKTAHRTGRQTPRARTARTGGAALSAAGTGGRGLGGRLAGVRGRGRYAGLAAPGSGAGAGTL
+PGAGLVGLSAAEEARAAGRWSLLPDPEPDPTIRAHAAAEVLLDRYGVITRGSVVAEEVPGGFAGQYQLLTRMEDAGQVRR
+GHFVDRLGGAQFSTGAVVDRLRSFQRDEDGPSPAEEEPAPRLDAFGMPVDESPRTDWSGWVADGVGGWTPAPQGHGAGMG
+TVGGAAGAREEPLPPALALAATDPANPYGAALDWPDLPAGPDGVAPTGHRPGRKAGAVVVLVHGALALYMERGGRTLLAF
+TQDGPVLRAAAQALVWALRAARTDKLSLEKVNGGPLLGTPLAEALLAAGFYSSPSGIRYRS
+>GCF_023573625_PROKKA_00293
+M-----SGPA-ETAAGAPT--PAADVVLGRFTEPTRAWFTGAFEAPTPAQLGAWDAISSGRHALVIAPTGSGKTLSSFLW
+ALDSFVREPAAEGTAATRVLYVSPLKALGVDVERNLRAPLVGITQTAAHQGRPVPRVRVGVRSGDTPAAERRRLQQDPPD
+ILITTPESLYLMLTSQARAA---LAGVRTVIVDEVHAVAGTKRGAHLAVSLERLDALLDTPVQRIGLSATVEPAAEVARF
+LGGTQPVTVVRPASAKRWDLTVTVPVPDLTDLSSPAAAHDLGPGSSTGGLGDE----GAVTGGSIWPHVEERIVDLVAER
+RSTLVFANSRRLAERLTGRLNEIWEARAEAAAAAEHPDAVPGFRTP----------------------------DPTGFH
+GPAQVAGQTGTGSGTVSDFARAHHGSVSKEQRAIVEEALKTGQIRCVVATSSLELGIDMGAVDQVIQVESPPSVASGLQR
+VGRAGHQVGEVSRGVFFPKHRGDLVDTAVVAERMTAGRIESLRIPANPLDILAQHTVAAVAVADLDAQEWFDLVRRSAPF
+ATLPF------SAYESVLDLLAGRYPSDEFAELRPRILWDRENGTLAARPGAQRLAVTSGGTIPDRGLFGVFLASDGGAD
+GAPGGAAAGDTAESASTASAGSARSGGRRVGELDEEMV-YESRVGDVILLGATSWRIVDITADRVLVLPAYGQPGKLPFW
+RGDAAGRPAELGDAVGRFRRELDADPEAGRTRLAAAGLDPWAQDNLLAYLKDQREATGVLPTEQTLVVERFTDELGDWRV
+VLHSPYGMAVHAPWALAVGARLAQRYGLETGSGAAMAADDGIVLRIPLMDAEPPGAELFEFTAEELDEIVTAE--VGGSA
+LFAARFRE----NAARSLLLPRRDPGRRTPLWQQRQRSAQLLDVARKHPRFPVILETVREVLQDVYDLPALKELAGRVSS
+RAVRLVEVTTTAPSPFSQSILFGYIAQFIYEGDSPLAERRAAALSLDPALLSELLGTEELRELLDAGVIAEVEAQLQRLA
+PDRRARGVEGVADLLRLLGPLSVAEAARRTRAEGEAEE------------AADEDAVAGMLAELERAGRAFRLRQDGVER
+FAAVEDAARLRDALGTPIPHGVPTAFLDPVDDPLGDLVGRYARTHGPFTAAEAGAALGLGGAVVLSVLQRLATERRVSTG
+AFRPEGTPGATGLDAEWCDAEVLRRIRMRSLAALRAEVEPVDQAAYARFLADWQHLRPRTGRDGAWRPPATLEGVDGVAT
+VLDQLAGTPLPASAWESLVLPARVRDYAPALLDELLATGEYVWSGVGEATGNDGWVALHPADAVDLTLRLPE------PA
+EETPADAAL--RAAVLEVLAGGGAWFFPQLVERVRAVQAAAGDGGTGAAGGAVGP-DPHRDPADLARGPAVLAALWGLVW
+DGRVGNDTFAPVRGLLSLGKTAHRTGRQTPRARTARTGGAAGAAA---GRGLGGRLAGVRGRGRYAGLTAPEVGARGSAG
+LTAGTVGLSAAEQARSAGRWSLLPAAEQDPTIRAHATAELLLDRYGVITRGSVVAEEVPGGFAGQYRLLTRMEDAGQVRR
+GHFVDGLGGAQFSTGAVVDRLRGFQRDE-EDA------------------------------------------------
+--------AVDAAPLALALAATDPANPYGAALDWPSVPAGPDGVVPTGHRPGRKAGAVVVLIAGRLALYMERGGRTLLAF
+TEEPGELRAAAEALVWALRTGRTERLSLEKVNGGPVLGTPLAEALLAAGFYSSPSGIRFRN

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000077.fa ADDED Viewed

	@@ -0,0 +1,48 @@

+>GCF_002008305_PROKKA_00297
+MLSE------------------------------------KSRPVIEATA--AAVAEHMPEITPL---------------
+--------------------------------------------------------------------------------
+-----FYAHMFEAHPELLDGVFSRANQRNGEQAQALAGSIVKFAVH----LLENPGTLPEAVLSRIAHKHTALGIVEEQY
+PIVYENLFWAIGEVL-------GDAVTPEVADAWTEVYWLMADALIKIEKGLYAQQANDRMWTDWKVVAKEPTGNAAVTF
+RFEPADDTPQSRGKAGGYVSVRLKVEDGLRQCRQYSLSEKAESATERVITVKLDEGGEVSPMLIQNVEVGDVIELSNPYG
+DITLED-EDSTAPLVLATAGIGITPAAAILDALAQQGSDRQVLLLHGDASWEAVALREQVTESLAALAHGDARLFLGVRP
+EQD---PEGVTTVEGVMHFDDVELP--RDGHYILCGPLAFMQSTRSKLIDAGVPATSIRYEIFGPDLWLAA-
+>GCF_003691675_PROKKA_00005
+MLSE------------------------------------KSRPVIEATA--AAVAEHMPEITPK---------------
+--------------------------------------------------------------------------------
+-----FYAHMFEAHPELLDGLFSRANQRNGEQAQALAGSIVRFAVH----LLENPGTLPEAVLARIAHKHTALGITEDQY
+QIVYENLFWAIADVL-------GDAVTPEVAEAWTEVYWLMADALIKLEKGLYAKQANDKMWLDWKVVSKEPTGNAAVTF
+RFEPADDTPQTPGEAGGFVSVRVKVADGLRQARQYSLSDHAASTTERVITVKLDEGGEVSPMLIQNVEVGDVIELSNPYG
+DITLED-EDSTAPLVLATAGIGITPAAAILDALAQQGSDRQVLFFHGDASWEAVALREQVTESLAALPHGDARLFLGVRP
+EQD---PEGVTTVEGVMHFDDVELP--RDGHYILCGPLAFMQSTRSKLIDAGVPATSIRYEIFGPDLWLAA-
+>GCF_005280335_PROKKA_00057
+MLSE------------------------------------KSRPVIEATA--AVVAEHMPEITPK---------------
+--------------------------------------------------------------------------------
+-----FYAHMFEAHPELLDGVFSRANQRSGEQAQALAGSIVTFAVH----LLEHPDTLPEAVLARIAHKHTALGIVPEQY
+QIVYENLFWAIADVL-------GEAVTPEVAEAWTEVYWLMADALIKIEEGLYAQQANTKMWTDWKVVAKEPTGNAAVTF
+RFAPADETPQTPGRPGGYLSVRLKVEDGLRQCRQYSLSDHAESTDERVITVKLDEGGEVSPVLIQNVEVGDVIELSNPYG
+DITLRD--DAETPLVLATAGIGITPAAAILDTLASRGSQREVHFFHGDASWDSVALREQVAESLQALENGTGRLWLGVPP
+QEA---PAAFTTTEGLMEFDDVELP--ADASYLLCGPLAFMQATRSKLIDAGVPATSIRYEIFGPDLWLAA-
+>GCF_020097155_PROKKA_00035
+MLSE------------------------------------KSRPVIEATA--AVVSANMPQITPA---------------
+--------------------------------------------------------------------------------
+-----FYGHMFEAHPELLDGTFSRANQLNGEQAQALAGSIVHFAAH----LLEHPDSLPEAVLARIAHKHTALGITEDQY
+QVVYENLFWAIAQVL-------GDAVTPEVAEAWTEVYWLMADALITLEKDLYAVQANDRMWTDWKVVAKEPTGNAAVTF
+RLEPADDTPQTPGRPGGYVSVRVTVADGLRQARQYSLSESASSTGQRVITVKLDEAGEVSPVLIQEVEVGDVVELSNPYG
+DITLQD---SDAPLVLMTAGIGITPAAAILDSLAASGSQREVRVLHGDASWDSVALRDQVLEDVASLPHAQADLWFGVAP
+ETA---PEGVSVHEGKVDTAAAALP--EGADYILCGPLAFMKSERSALIEAGVPAPRIRYEIFGPDLWIAAT
+>GCF_020097155_PROKKA_01222
+MPAHGWGARAGRTSFREHPVDVQECLWRGAHASSHDRSALHSRPSRGGSADPAPADRPPPPLTPAPGPAGIRDRPAGRIP
+AWWRDASGSLLWLVLLAVTALWVHGGGVQDLAAVGSGLTSLGRLTGLIASALLLAQVFLMARVPLVEQAWGQDRLTRVHR
+RVGFTSFTLMF-AHLALITAGYA------WDTPAGLWGTLVDFAVDYPGMLLAIAGTAALVMVVVTSFKAARARLRYESW
+HLIHLYGYLGAGLALPHQLWTGQEFLASPVATAFWWTLWAVTAGAVVVFRALLPLWCSAR--AGLRVQSVTAAGPHAVTV
+TVA-GRGAHRLHARGGQFFQWRFLDGPGWTRAHPYSLSAAPDGRTLQFTAAVVGDGTG----RLWDMRPGTRVLVEGPYG
+R--MHDGVRTGRKALLMGAGIGITPMKALLESLPADAG--EITVVHRVSDPDDPTLHADLLAAARTRGARYIRLEGRRRP
+GADSWLPASAGDVDDVTALRRI-CPDLAEHDVFVCGAPAWTDLVRQAARRGGVPAERIHDERFSF-------
+>GCF_023573625_PROKKA_00304
+MLSE------------------------------------KSRPVIEATA--AVVAEHMPEITPL---------------
+--------------------------------------------------------------------------------
+-----FYAHMFEAHPELLDGVFSRANQRNGEQAQALAGSIVKFAVH----LLENPGTLPEAVLSRIAHKHTALGIVEEQY
+PIVYENLFWAIGEVL-------GDAVTPAVADAWTEVYWLMADALIKIEKGLYSQQANDRMWTDWRVVAKEPTGNAAVTF
+RFEPADDTPQSRGRAGGYVSVRLKVEDGLRQCRQYSLSEKAESTTERVITVKLDEGGEVSPMLIQNVEVGDVIELSNPYG
+DITLED-EDSTAPLVLATAGIGITPAAAILDALAQQGSDRQVLFFHGDASWEAVALREQVTESLAALPHGDARLFLGVRP
+EQD---PEGVTTVEGVMHFDDVELP--RDGHYILCGPLAFMQSTRSKLIDAGVPATSIRYEIFGPDLWLAA-

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000080.fa ADDED Viewed

	@@ -0,0 +1,31 @@

+>GCF_002008305_PROKKA_00359
+MQPQNPEARLLVVDDEPNIRELLSTSLRYAGFEVTAAANGREALDAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRAAGRHFPVVFLTARDGTEDKITGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTASL-DDDA-AVLRVDDLELDDDAHEVRRGGEVVELSPTEFKLLRYLMMNPNRVL
+SKAQILDHVWEYDFNGDASIVESYISYLRRKIDVGGREKMIHTKRGVGYMLRTADKR--
+>GCF_003691675_PROKKA_00075
+MQPQNPEARLLVVDDEPNIRELLSTSLRYAGFEVTAAANGREALDAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRSAGRHFPVVFLTARDGTEDKITGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTASL-DDDA-AVLRVDDLELDDDAHEVRRGGEVVDLSPTEFKLLRYLMMNPNRVL
+SKAQILDHVWEYDFNGDASIVESYISYLRRKIDVGGREKMIHTKRGVGYMLRTADKR--
+>GCF_005280335_PROKKA_01252
+MIP------VLLIEDEERIAAFVTKGMAAEGIAVTTAGTGAEGVGLAMTGAFELVILDLG
+LPDADGFDVLARIRRQDAHLPVIILTARSSAQDTVEGLTSGADDYMPKPFRFAELLARVR
+LRLRPGAPA-PEPTDTVMRHGDLELDPASHTARVDGRTVALSAREFALAEEFLRSPGQVL
+SREQLLDGAWGEDFESGSNVVDVYVRYLRAKI---GAERIL-TVRGLGYRLAGEDELSG
+>GCF_005280335_PROKKA_02602
+MQSQNPEARLLVVDDEPNIRELLSTSLRYAGFEVTAAANGREALDAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRAAGRHFPVVFLTARDGTEDKITGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTASL-DDDA-AVLRVGDLELDDDAHEVRRGGEVVELSPTEFKLLRYLMMNPNRVL
+SKAQILDHVWEYDFNGDASIVESYISYLRRKIDVGGREKMIHTKRGVGYMLRAADKR--
+>GCF_020097155_PROKKA_02461
+MQSQTPEARLLVVDDEPNIRELLSTSLRFAGFEVRAAGNGREALEAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRAAGRLFPVVFLTARDGTEDKVTGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTAPL-DDDS-AVLRVDDLELDDDAHEVRRGGEVVDLSPTEFKLLRYLMMNPNRVL
+SKAQILDHVWEYDFNGDASIVESYISYLRRKIDVGGRDKMIHTKRGVGYMFRTADKR--
+>GCF_023573625_PROKKA_00366
+MQPQNPEARLLVVDDEPNIRELLSTSLRYAGFEVTAAANGREALDAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRSAGRHFPVVFLTARDGTEDKITGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTASLDDDDA-AVLRVDDLELDDDAHEVRRGGEVVELSPTEFKLLRYLMMNPNRVL
+SKAQILDHVWEYDFNGDASIVESYISYLRRKIDVGGREKMIHTKRGVGYMLRTADKR--

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000081.fa ADDED Viewed

	@@ -0,0 +1,54 @@

+>GCF_002008305_PROKKA_00366
+MSMESAARMSMMRMTRGQSDAQQSLARGTVRRTIAFAGRYRTRLIVFVAASIVGAVLGVASPVLAGDVVNAITGGADRGL
+VVRLALLIALVAVLDAALSVFTKWLSSGLGERVIYDLRTAVFDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTL
+SGVVANVVSVALTLGVMVATSWQVTVLSLVMLPLFLVPARAVGSKLADLSRERAGHNAAMGDQMTERFSAPGATLIKLFG
+RPAAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDAGDVVTLALLLTRLYAPLTAL
+ANARVEIMSALVSFERVFEVLDLEPLITEPARPAALPEGPL--SVRLRDVRFAYPTAEQVSLASLEEVAVLDTRGGEEVL
+HGIDVAVPAGATVALVGSSGAGKSTIASLVTRLHDVTSGAVEIGGVDVRDLAFADLQRAVGMVTQDGHLFHETVRANLTL
+ARPDATDEELWDAVERARLRPVVEALPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVVVLDEATAALDSTNERAIQ
+EALGEALAGRTAIVIAHRLSTVRSADEILVVEAGRIVERGTHAALLAADGRYAELYT-----------TQFADAE
+>GCF_003691675_PROKKA_00082
+MSMESAARMSMMRMTRGQSDAQQSLARGTVRRTIAFAGRYRTRLIVFVAASIVGAVLGVASPVLAGDVVNAITGGADRGL
+VVRLALLIALVAVLDAALSVFTKWLSAGLGEQVIYDLRTAVFDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTL
+SGVVANVVSVALTLGVMVATSWQVTVLSLVMLPLFLLPARAVGSKLAGLSRERAGHNAAMGDQMTERFSAPGATLIKLFG
+RPAAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDAGDVVTLALLLTRLYAPLTAL
+ANARVEIMSALVSFERVFEVLDLEPLITEPARPAALPEGPL--SVRLRDVRFAYPTAEQVSLASLEEVAVLDTRGGEEVL
+HGIDVAVPAGATVALVGSSGAGKSTIASLVTRLHDVTSGAVEIGGVDVRDLAFADLQRAVGMVTQDGHLFHETVRANLTL
+ARPDATDEQLWDAVERARLRPVVEALPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVVVLDEATAALDSTNERAIQ
+EALGEALAGRTAIVIAHRLSTVRSADEILVVEAGRIVERGTHAALLAAGGRYAELYT-----------TQFADAE
+>GCF_005280335_PROKKA_00193
+--------MAPARLDPADR-TQLRRHPVSLRRIARLFAPHRSTIALVVVLISAASVINLAQPFLVRAVIDDALPNQDVPL
+LIRLTAAMVGVAALTAVIGVVQTWRATAMGQHVMHSLRVRLFTHLQAQPLAFFTRTRGGEVQSRLTHDIAGMQSVVTSTA
+TGVASNLTAVVATAAAMVALSPRLSLISLVVLPPAVWLSRRVAQLRRAVTDKRQAALAQMHTQVEEGLSVSGARLSKTLG
+TTGHDAERFTGRSHELIGLELRSQLAGRWRMATMSIVFAAIPAVIYLAAGLPPTSGGMTIGTLVAFTALQGQVFRPVMGL
+LNIGVQWVTALAFFSRIFEYLDLDPAIKPPADPVPVDPARVRGTVRFEGVDFAYDD-------------------GAPAL
+SGIELTVPAGTTTAVVGSTGSGKSTLASLVPRLHDPTAGRVSIDGIDVARLDPADLAAIVGVVSQETYLIHASVRDNLRL
+ADPEATDERLWAALETASLARTVAALPEGLDTLVGARGHRFSGGEQQRLAIARTVLRNPPVLVLDEATSALDNTTEARVQ
+AALDELAEHRTTLLVAHRLSTVMGADQVAVLEGGRIVELGAPTELLRAGGPFAALAARGDAVVPGAAPAEPALAR
+>GCF_005280335_PROKKA_02595
+--MESAARVSMMRMTHGQNGATQPLAKGTVRRTIAFADRYRARLIVFVLASIVGAVLGVASPVLAGDVVNAITGGDDGGL
+VVRLALLIALVAVLDAALSVFTKWLSSGLGERVIFDLRTQVFDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTL
+SGVVANVVSVALTLGVMVATSWQVTVLSLLLLPLFLIPARAVGSKLAGLSRERAGHNAAMGDQMTERFSAPGATLIKLFG
+RPAAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDAGDVVTLALLLTRLYAPLTAL
+ANARVEIMSALVSFERVFEVLDLQPLIIEPARPAALPAGPL--SVRLRDVRFSYPTAQEVSLASLEEVAVLDTRGGEEVL
+HGIDVAVPAGSTVALVGSSGAGKSTIASLVTRLHDVSSGAVELGGVDVRDLSFADLQEAVGMVTQDGHLFHDTVRGNLLL
+ARPDATEEQLWDAVERARLRPVIEALPDRLDTVVGERGYRLSGGERQRMTIARLLLAAPRVVVLDEATAALDSTNERAIQ
+EALGEALTGRTAIVIAHRLSTVRSADEILVVEAGRIVERGGHAELLAAGGRYAELYT-----------TQFADAE
+>GCF_020097155_PROKKA_02454
+MSMESVARVSMMRLQRGGT-APQPLAPGTVRRTVAFAAQYRARLIVFVAASVVSAVLGVASPVLAGDVVNAITGGTDRAL
+VVRLALLIAAVALADAALSVFTKWLSSGLGERVIYDLRTRVFDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTL
+SGVVANAVSLALTLAVMLATSWQITLLSLVLLPLFLVPARMVGGRLAALSRERAGHNAAMGDQMTERFSAPGATLIKLFG
+EPGAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDAGDVVTMALLLTRLYAPLTSL
+ANARIEIMSALVSFERVFEVLDLEPLITEPAHPVPVPDGPL--AVTLDDVHFAYPSAQEVSLASLEEVAVLDTRGGEEVL
+HGVDVDVPAGRTVALVGSSGAGKSTIASLVTRLYDVTSGAVRLGGVDVRDMAFADLHRAVGMVTQDGHLFHDTVRGNLLL
+ARPAATDAEVWDAVDRARLRGVVESLPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVVVLDEATAALDSTNERAIQ
+EALREALAGRTAVVIAHRLSTVRDADEILVVEGGRIVERGPHAALLAAGGRYAELYT-----------TQFAEGA
+>GCF_023573625_PROKKA_00373
+MSMESAARMSMMRMTRGQSDAQQSLARGTVRRTIAFAGRYRTRLIVFVAASIVGAVLGVASPVLAGDVVNAITGGADRGL
+VVRLALLIALVAVLDAALSVFTKWLSAGLGERVIYDLRTAVFDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTL
+SGVVANVVSVALTLGVMVATSWQVTVLSLVMLPLFLLPARAVGSKLAGLSRERAGHNAAMGDQMTERFSAPGATLIKLFG
+RPAAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDAGDVVTLALLLTRLYAPLTAL
+ANARVEIMSALVSFERVFEVLDLEPLITEPARPAALPEGPL--SVRLRDVRFAYPTAEQVSLASLEEVAVLDTRGGEEVL
+HGIDVAVPAGATVALVGSSGAGKSTIASLVTRLHDVTSGAVEIGDVDVRDLAFADLQRAVGMVTQDGHLFHETVRANLTL
+ARPDATDEQLWDAVERARLRPVVEALPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVVVLDEATAALDSTNERAIQ
+EALGEALAGRTAIVIAHRLSTVRSADEILVVEAGRIVERGTHAALLAAGGRYAELYT-----------TQFADAE

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000082.fa ADDED Viewed

	@@ -0,0 +1,54 @@

+>GCF_002008305_PROKKA_00386
+MTDEQ-TTT----------------AAPRRNGGDLAVETLHALGARTVFGIPGQHALGLFDALSRSPLEFVSNRVENNAA
+FAADGYARATGEVGVLFLSTGPGALTSLAGLQEAYATGVPMLVVASQIPLSGLGARRKGMLHQLDDQKA--------SAR
+NVTKAQFTVHHASGIPSAIQDAWAEAITVPQGPVWVEIPQDVLLGEVMVPPVEDALAVPYDHPPRAELVAESARWLRGAG
+RVAIVAGGGVRRSGRAAMESLREVAELLQAPVVCSPGGNTAFPWEHPLSLGGWVEDRLVTDLLEDAEVLLVVGSSLGEVT
+SNYFTLEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALEALAAALRESGSVAQDAAVWHGRTPAEVVADVNARITARLD
+AQDLGVERRLLADIRAAVPSTMQTYWDMTIAAYWAWNCWDAQDGEFHSAQGAGGLGYGFPAAFGGAVGLAHQGRTGIDGR
+VLAVAGDGSAMYSLAELAAARQHGAAVTWLIIDDGGYGILREYMEGAFGKATATELDRPDFQALAASFGVPAETVGVEDV
+RGALERAFQADGPNVVVVQTRLAMWAPSHLGEAP-------------------EV
+>GCF_003691675_PROKKA_00110
+MSDEQ-TTT----------------AAPRRNGGDLAVETLHALGARTVFGIPGQHALGLFDALSRSPLEFVSNRVENNAA
+FAADGYARATGEVGVLFLSTGPGALTSLAGLQEAYATGVPMLVVASQIPLSGLGARRKGMLHQLDDQKA--------SAR
+NVTKAQFTVHHASGIPSAIQDAWAEAITVPQGPVWVEIPQDVLLGEVMVPPVEDALAVPYDHPPRAELVAESARWLRGAG
+RVAIVAGGGVRRSGRAAMESLREVAELLQAPVVCSPGGNTAFPWEHLLSLGGWVEDRLVTDLLEDAEVLLVVGSSLGEVT
+SNYFTLEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALEALAAALRESGSVAQDAAVWHGRTPAEVVADVNARITARLD
+AQDLGVERRLLADIRAAVPSTMQTYWDMTIAAYWAWNCWDAQDGEFHSAQGAGGLGYGFPAAFGGAVGLAHQGRTGIDGR
+VLAVAGDGSAMYSLAELAAARQHGAAVTWLIIDDGGYGILREYMEGAFGKATATELDRPDFQALAASFGVPAETVGVEDV
+RGALERAFQADGPNVVVVQTRLAMWAPSHLGEAP-------------------EV
+>GCF_005280335_PROKKA_02569
+MTDEQTTTT----------------AAPRRNGGDLAVETLHALGARTVFGIPGQHALGLFDALSRSPLEFVSNRVENNAA
+FAADGYARATGEVGVLFLSTGPGALTSLAGLQEAYATGVPLVVVASQIPLSGLGARRKGMLHQLDDQKA--------SAR
+NVTKAQFTVHHASGIPSAIQDAWAEAVTVPQGPVWVEIPQDVLLGEVLVPPVQDALAVPYDHPPRAELVDESVRWLRDAQ
+RVAIVAGGGVRRSGRAAMESLREVAELLQAPVVCSPGGNTAFPWQHPLSLGGWVEDRLVTDLLEDAEVLLVVGSSLGEVT
+SNYFTLEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALEALAAALRESGSVAEDAPVWHGRTPAEVVAETMGRVAARLD
+AQDLGVERRLLADIRAAVPSAMQTYWDMTIAAYWAWNCWDAREGEFHSAQGAGGLGYGFPAAFGGAVGLAHQGRTGIDGR
+VLAVAGDGSAMYSIAELAAARQHDAAVTWLIIDDGGYGILREYMEGAFGKATATELDRPDFQALAASFGVPAETVGVEDV
+RGALERAFQADGPNVVVVQTRLAMWAPSHLGEAP-------------------EV
+>GCF_020097155_PROKKA_01756
+MSARHDAAVPQEAADMAAAAGGAGGGTARRNGGDLAVETLHALGARTVFGIPGQHALGLFDALSRSSLRFVSSRVENNAA
+FAADGYARATGEVGVLFLSTGPGALTSLAGLQEAYATGVPMLVIASQIPLSGLGARRKGMLHQLDDQKA--------SAK
+NVTKAQFTVHHASGIPSAIQDAWAEAVTVPQGPVWVEIPQDVLLGEVMVPPVQDALAVPYDHPPRAELVAESVRWLRGAE
+RVAIVAGGGVRRSGRAAMASLREVAELLQAPVVCSPGGNTAFPWGHPLSLGGWVEDRHVTELLEDAEVLLVVGSSLGEVT
+SNYFTLEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALAALADALRADETARPAERPWHGRTPADVVAEVNAKVTARLD
+AQDLGRERRLLADIRAAVPSTMQTFWDMTIAAYWGWNCWDAQDGEFHSAQGAGGLGYGFPAAFGASVGLASAGR---DAR
+VLAVAGDGSAMYSIAELAAARQHDADVTWLIIDDGGYGILREYMEGAFGKATATELARPDFAALATSFGVPAETVGVEDV
+RGALERAFQEDGPNVVVVQTRLAMWAPSHL-EAPVPADEAGPGLAETTRPEGRAA
+>GCF_020097155_PROKKA_02444
+--------------------------------------------------------------------------------
+------------------------------------------------------------MRALEDRRPRNSRSETLSGR
+GVTKAQFTVHHASGIPSAIQDAWAEAVTVPQGPVWVEIPQDVLLGEVMVPPVQDARAVPYDHPPRAELVAEVVRWLRGAG
+RVAIVAGGGVRRSGRAAMESLREVAELLQAPVVCSPGGNTAFPWEHPLSLGGWVEDRLVTDLLEDAEVLLVVGSSLGEVT
+SNYFTLEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALQALAAALRESGSVARDAAVWHGRTPAEVVADVNARITARLD
+AQDLGVERRLLADIRAAVPSTMQTYWDMTIAAYWAWNCWDAQDGEFHSAQGAGGLGYGFPAAFGGAVGLAHQGRTGIDGR
+VLAVAGDGSAMYSLAELAAARQHDVDVTWLIIDDGGYGILREYMEGAFGKATATELDRPDFQALAASFGVPAETVGVEDV
+RGALERAFQADGPNVVVVQTRLAMWAPSHLGEAP-------------------EV
+>GCF_023573625_PROKKA_00392
+MTDEQ-TTT----------------AAPRRNGGDLAVETLHALGARTVFGIPGQHALGLFDALSRSPLEFVSNRVENNAA
+FAADGYARATGEVGVLFLSTGPGALTALAGLQEAYATGVPMLVIASQIPLSGLGARRKGMLHQLDDQKA--------SAR
+NVTKAQFTVHHASGIPSAIQDAWAEAVTVPQGPVWVEIPQDVLLGEVMVPPVEDALAVPYDHPPRAELVAESVRWLRGAG
+RVAIVAGGGVRRSGRAAMESLREVAELLQAPVVCSPGGNTAFPWGHPLSLGGWVEDRLVTDLLEDAEVLLVVGSSLGEVT
+SNYFTLEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALEALAAALRESGSVAQDAAVWHGRTPAEVVADVNARITARLD
+AQDLGVERRLLADIRAAVPSTMQTYWDMTIAAYWAWNCWDAQDGEFHSAQGAGGLGYGFPAAFGGAVGLAHQGRTGIEGR
+VLAVAGDGSAMYSLAELAAARQHGAAVTWLIIDDGGYGILREYMEGAFGKATATELDRPDFQALAASFGVPAETVGVEDV
+RGALERAFQADGPNVVVVQTRLAMWAPSHLGEAP-------------------EV

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000089.fa ADDED Viewed

	@@ -0,0 +1,55 @@

+>GCF_002008305_PROKKA_00509
+M--------------------------------------------------IP-EAARTT
+PAPLT--LWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQGAAVFTGD
+VGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFAALGPGRARQRAGAPALLSTEH
+GIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPITVVRNGV
+DVPAVRAAAAGQRRTPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRLTLAGAGP
+LEGELRAQAEALGVAEAVDLPGFVEPWETM-----AEHDVLVQLSAWENLSYTLLDAAAA
+GLPAVATDVGGNGEILPP---ERLVHET-TPAAIADAVVRAAADGPGEVRVGDVETMARA
+TAEATLEVLGRRVGKVGT-R--------
+>GCF_003691675_PROKKA_00229
+M--------------------------------------------------IP-EDATTT
+PAPLT--LWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQGAAVFTGD
+VGPDAGLAASVRTLRTAVRTLCPAAVHTHLAYADLAAFTALGAGRALRRAGAPALLSTEH
+GIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPLTVVRNGV
+DVPAVRAAAAGRRRAPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRVTLAGSGP
+LEGQLRAQAEDLGVADAVHLPGFVEPWGTM-----AEHDVLVQLSAWENLSYTLLDAAAA
+GLPAVATDVGGNGEILPP---ERLVRET-TPEAIADAVVRAAAEGPGEVRVGDVETMARA
+TAEATLEVLGRRVGKGGH-R--------
+>GCF_005280335_PROKKA_01218
+MTRRLLLFANSFPYGKQEPYLMRECHYLDAFDEVYIFSLSIRKHQRDHRRDLPLERVTVV
+PIPFKSPLFYAAVSPRALVSRAFVTELRQLLRDRRFTVARAVQALSQFSRAEHEASVIG-
+-----------RFLRD---NITPSPSDETVFYAYRFLYQPYLMSRLAAKFSSSRLIGRAH
+GI---DLFEERQSTDYLPGRA--INLGALDELHSVSRAGAEYLR----ARHPEFVEKIKV
+SYLGTEDHGVRPPRSSSQVLRLVSCSEVAPVKRLELLVEALREVSD-SIQVEWSHYGEGP
+DMDRVRAMASTLPGHVSATFHGWTRNDEILEAYRSGRHDVFINVSSSEGLPVSIMESSSC
+GLPTIATDVGGTGEIVSDGVNGRLISANPMPREIAAAVEEFARMAP--------EAFARR
+SAAA-RETWSTHFDSDRNYRQFVAKMLS
+>GCF_005280335_PROKKA_02441
+M--------------------------------------------------TP-EAATTT
+PAPLT--LWVVPVADLGGVARHVLDVAAHGLPGLRLVVLCPEGALAERLREQGAAVFTGD
+VGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFTAFGPGRARRRAGAPALVSTEH
+GIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGTGAPITVVRNGV
+DVSAVRAAAAGQRRAPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRLTLAGVGP
+LEGQLRAQAEALGVADAVDLPGFVEPWGAM-----AEHDVLVQLSAWENLSYTLLDAAAA
+GLPAVATDVGGNGEILPP---ERLVHET-TPAAIADAVMRATVEGPGEVRVGDVETMARA
+TAEATLEVLGRRAGKTSG----------
+>GCF_020097155_PROKKA_02325
+M--------------------------------------------------IP-EAATTT
+PAPLT--LWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQGAAVFTGD
+VGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFTALGPGRARRRAGAPALLSTEH
+GIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPLTVVRNGV
+DVSAVRAAAAGQRRAPGEGLRILSLSRLAPEKGLDRLIAALPALRERDPGTRLTLAGSGP
+LEGQLRAQAEDLGVADAVDLPGFVEPWETM-----AEHDVLVQLSAWENLSYTLLDAAAA
+GLPAVATDVGGNGEILPP---ERLVHET-TPAAIADAVTRAAAEGPGEVRVDDVEGMAEA
+TARAERDVVETQDARRRKTR--------
+>GCF_023573625_PROKKA_00508
+M--------------------------------------------------IP-EAARTA
+LAPLT--LWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQGAAVFTGD
+VGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFAALGPGRARRRTSAPALLSTEH
+GIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPITVVRNGV
+DVPAVRAAAAGQRRTPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRLTLAGSGP
+LEGQLRAQAEALGVAEAVDLPGFVEPWETM-----AEHDVLAQLSAWENLSYTLLDAAAA
+GLPAVATDVGGNGEILPP---ERLVRET-TPAAIADAVVRAAADGPGEVLVGDVETMARA
+TAEATLEVLGRRVGKAGT-R--------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000091.fa ADDED Viewed

	@@ -0,0 +1,37 @@

+>GCF_002008305_PROKKA_00547
+MH-PDDAPTPDLTWLDSAGSTQDELLARL----DREGHRHGAAVATADQRAGRGRHSRVW
+SAAPGAALALSVYLRPESGGVPVSPAHLSWLSLVASATVAERLAARGVPTHVKWPNDVLA
+TDGRKLCGVLATVALS-----SDGK-GPGVVVGMGVNLDHRGAAPVDTATDLAEWIGADA
+VPAPRDLAVELRDAVVAAVDRFAAGVAGQAAAVDGRHPAVAAVADRLSTLGRAVRAELPG
+GGVLEGTAVGLGPGGTLRVKRVTPDRGTIETEVSAGDVAHLRGDVHRGA
+>GCF_003691675_PROKKA_00272
+MH-PDDAPTPDLTWLDSAGSTQDELLARL----DREGHRHGAAVATADQRAGRGRHSRVW
+SAAPGAALALSVYLRPESGGVPVSPAHLSWLSLVASATVAERLAARGVPTHVKWPNDVLA
+TDGRKLCGVLATVALS-----SDGK-GPGVVVGMGVNLDHRGAAPVDTATDLAEWIGADA
+VPAPRDLAVELRDAVVAAVDRFAAGVAGQTAAVDGHHPAVAAVADRLSTLGRAVRAELPG
+GGVLEGTAVGLGPGGTLRMRHVTPDRGTIETEVSAGDVAHLRGDVHRGA
+>GCF_005280335_PROKKA_02399
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------MGVNLDHRGAAPVATATDLAEQIGAEA
+VPAPRGLAAALRDAVVGAADRFAAAVAGEAEAVDGRHPAVAAVTQRLSTLGREVRAELPG
+GDVLEGTAVALGPGGALRVSHVTADRGRIETEVSAGDVAHLRGDVHRGA
+>GCF_005280335_PROKKA_02400
+MHAPHDPAAPGLVWLDSAGSTQDEVLARV----GREGPRHGLAVATADQRAGRGRHSRVW
+SAAPGAALALSVHLRPAAGGTPLAPVHLSWLSLVASAAVVEHLAGLGAAAHLKWPNDVLA
+PDGRKLCGVLATVAPA-----ADGG-GPGWSWAWG-------------------------
+------------------------------------------------------------
+-------------------------------------------------
+>GCF_020097155_PROKKA_02283
+MG--YTWGMGTLLWLDAADSTQDELLRRLAAADGAARPGHGDGVGTADQRAGRGRHGRAW
+QAPPGAALALSVHLRPTGPSGPLAPAHLSWLSLVASAAVARRLVGLGVPAHLKWPNDVLD
+AEGRKLCGVLATLAPAPVFPGADAGETPGVVVGMGVNVDLSSGRPVPTAAALTDHLPGAE
+VPAPRDLAQALLRDVAAAADRLARDLDGVVEPVDGTHPALAEVAAVLSTPGRRIRAELPG
+GEVLEGVATGLGAGGVLAVRVVTGERETITREISAGDVVHLRGDVRRGG
+>GCF_023573625_PROKKA_00550
+MH-PDDAPTPDLTWLDSAGSTQDELLARL----DREGHRHGAAVATADQRAGRGRHSRVW
+SAAPGAALALSVYLRPESGGVPVSPAHLSWLSLVASATVAERLAARGVLTHVKWPNDVLA
+TDGRKLCGVLATVALS-----SDGK-GPGVVVGMGVNLDHRGAAPVDTASDLAEWIGADA
+VPAPRDLAVELRDAVVAAVDRFAAGVAGQTAAVDGRHPAVAAVADRLSTLGRAVRAELPG
+GGVLEGTAVGLGPGGTLRVKHVTPDRGTIETEVSAGDVAHLRGDVHRGA

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000093.fa ADDED Viewed

	@@ -0,0 +1,37 @@

+>GCF_002008305_PROKKA_00604
+MPK-----------------------------------MSGIETAFCRSALWGRFARDII
+VPWSLGGQDLGGDVLELGAGSGQMAAALLQRSPGMRLTLTDIDERMVATARRRFPTSPRL
+TVQQADSTALPFAESSFDVVLSFLMLHHVVNWKAAVAEAARVLKPGGMLIGYDLT-----
+------------------------------------AWSSP-------------------
+---------------S
+>GCF_002008305_PROKKA_02174
+MSQ-NPLPAPRGDAQRGAADHHDRVSAMFDAIAGRYDLMNAVMT-------WGQEPRLVR
+RTVARANIPAQARVLDLATGTGDLAFEVLKQHPDAQVVGADIAAEMMEVGRAR-AGGDRI
+EWVVADATDLPFEAGSFDAVTHGYLLRNVADIPATLAEQFRVLRPGGWVAALETSPAPDN
+VLKPFSSFYIHRVMPQLAKLIADRPEAYAYLSSSTKAFHTPDEVADLFAEAGFVNIGHET
+HMFGTLATHWAMKPVD
+>GCF_003691675_PROKKA_01888
+MSQ-NPLPAPRGDAQRGAADHHDRVSAMFDAIAGRYDLMNAVMT-------WGQEPRLVR
+RTVARANIPAQARVLDLATGTGDLAFEVLKQHPDAQVVGADIAAEMMEVGRAR-AGGDRI
+EWVVADATDLPFEAGSFDAVTHGYLLRNVADIPATLAEQFRVLRPGGWVAALETSPAPDN
+VLKPFSSFYIHRVMPQLAKLIADRPEAYAYLSSSTKAFHTPDEVADLFAEAGFVNIGHET
+HMFGTLATHWAMKPVD
+>GCF_005280335_PROKKA_00578
+---------------------------MFDAVAERYDLMNTVMT-------WGQEPRLVR
+HTVARANVPAHGRVLDLATGTGDLAFEVLRQHPDATVVGADISAEMMEVGRRR-EGGDRV
+EWVVADAQDLPFEDASFDSVTHGYLLRNVADIPAALAEQFRVLRPGGWMAALETSPPPAN
+IIRPFSTFYMHQVMPRLARVITDKPEAYEYLSSSTKAFHAPEEIADMLAHAGFVNIGHET
+HMFGTLATHWAMKPVA
+>GCF_020097155_PROKKA_00505
+MSETSPSPLPRPASLAHDADHGARVSGMFDAIAGRYDLMNTVMT-------WGQEPRLVR
+RTVERANVPAAARVLDLATGTGDLALEILKQHPDAHVVAADFAPEMMEVGRTR-PNGDRI
+EWVEADALALPFADGEFDSLTHGYLLRNVANIPAALAEQFRVLRPGGWVAALETSPAPDN
+LIKPFSSFYMHRIMPRLARLITDRAEAYEYLSSSTRAFHTPEEIAGMLADAGFVNIGHEL
+HMFGTLATHWAMKPLD
+>GCF_023573625_PROKKA_02119
+MSQ-NPLPAPRGDAQRGAADHHDRVSAMFDAIAGRYDLMNAVMT-------WGQEPRLVR
+RTVARANIPAQARVLDLATGTGDLAFEVLKQHPDAQVVGADIAAEMMEVGRAR-AGGDRI
+EWVVADATDLPFEAGSFDAVTHGYLLRNVADIPATLAEQFRVLRPGGWVAALETSPAPDN
+VLKPFSSFYIHRVMPQLAKLIADRPEAYAYLSSSTKAFHTPDEVADLFAEAGFVNIGHET
+HMFGTLATHWAMKPVD

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000094.fa ADDED Viewed

	@@ -0,0 +1,37 @@

+>GCF_002008305_PROKKA_00610
+MSLGGFFAEMVQSGALLVAMPLAAIAGLVSFLSPCILPLVPGYLGYVSGLAD--PRRADN
+RRRVMTGVGLFILGFAAVFTFYGAAFGVIGGWLLQWQDALIRALGVFVVLMGLVLIGWLP
+FLQNTRRMSFQPKTGIVGAPLLGVVFGLGWTPCMGPTLSAVLALSTTTGDPWRGALLGFL
+YCLGLGIPFVLVAMGLDWVTRTLGFVRRHIRAFNIIGGILLVLVGVLMVTGIWTLWIYQL
+QNLAGTFTTPV
+>GCF_003691675_PROKKA_01770
+MSLGGFFAEMVQSGALLVAMPLAVVAGLVSFLSPCILPLVPGYLGYVSGLAD--PRRADN
+RRRVMTGVGLFIMGFAAVFTLYGAAFGVIGGWLLQWQDALIRALGVFVILMGLVLIGWLP
+FLQNTRRMSFQPRTGIAGAPLLGVVFGLGWTPCMGPTLSAVLALSTTTGDPWRGALLGFL
+YCLGLGIPFVLVAMGLDWVTRTLGFVRRHIRAFNIIGGVLLVLVGVLMVTGIWTLWIYQL
+QNLAGTFTTPV
+>GCF_005280335_PROKKA_00399
+--MGEYFAQTVQSGALLLAIPLAAIAGIVSFLSPCILPLVPGYLGYVSGLSD--PTRPDN
+RRRVMTGVGLFILGFAAVFTLYGAAFGLIGGWLLRWQDLLIRILGVLVILMGLALMGMFT
+FLQRTTTPSFTPRTGLAGAPLLGLGFGLGWTPCMGPTLSAVLALSTTTGGAWRGALLGFV
+YCLGLGIPFVLVARGLGWVSTALGFVRRHMRAFNIAGGTLLVLVGVLMATGIWTVWIYQL
+QNLAGTFTTPV
+>GCF_005280335_PROKKA_02642
+MDV----QQLVADGQLLVASVIALAAGLLSFLSPCVLPLVPGYLAYVSASAGAAPGEKPA
+RGRLVLGSLLFVAGFTAVLVALLAAAGTVGVWLLEWEQLITRVMGAVVILMGLVFIGAFG
+FMQRTTKLRIKPRTGLLGAPLLGVVFAIGWTPCLGPTLAAIMTLSVQQGSVARSVVLALA
+YCIGLGLPFVLAAFGFGWMTQTMTFFKRHIRTVNLIGGVLLILIGLLMVTGLWSQMMYAL
+QAVIGGYVTPL
+>GCF_020097155_PROKKA_02202
+--MGEYFAQTVQSGALLLAIPLAAIAGIVSFLSPCILPLVPGYLGYVSGLSD--PTRPDN
+RRRVMTGVGLFILGFAAVFTLYGAAFGLIGGWLLRWQDLLIRILGVLVILMGLALMGMLT
+FLQRTTTPSFTPRTGLAGAPLLGLGFGLGWTPCMGPTLSAVLALSTTTGGAWRGALLGFV
+YCLGLGIPFVLVARGLGWVSTALGFVRRHMRAFNIAGGTLLVLVGVLMATGIWTAWIYQL
+QNLAGTFTTPV
+>GCF_023573625_PROKKA_02004
+MSIGNYFAETVNSGALLIAAPLAMIAGIVSFLSPCILPLVPGYLGYVSGLSN--PTHPDN
+RRRVLTGVGLFILGFAAVFTLYGAAFGTIGHWLVRWQDPMIRVLGVLVIVMGLVMVGKFS
+LFQRTLKPTLAPRTGLAGAPLLGVVFGLGWTPCMGPTLSAVLALSTTTGDPWRGALLGFL
+YCLGLGIPFLLAAAGINWVTTALSYIRRNIRVFNIIGGCLLVLVGVLMVSGLWMLWMYQL
+QNLAGTFTTPV

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000095.fa ADDED Viewed

	@@ -0,0 +1,54 @@

+>GCF_002008305_PROKKA_00611
+MT------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-------------------------------------------------------------------------------S
+T----------------DPTPAKAAS------------------------------------------------------
+------------------------------------------------------------APNRQRRAKIIVWVVLAALV
+LAGVV-AFFAARAPS--TPEAAPAQAGQAASSGTGQTAAS---EAAP-VVRPDSRVLSQAPNEKAVLVEFLDFECEGCKA
+AHPVVEELRAEYADTVTFVHRYFPLPGHPNSMTAAVAVEAAAQQGAYEAMYQKMFDTQEQWSHTGQDRSPVFRGYAEDLG
+LDMTAYDKAVADPATRARIEADVADGVALGVQGTPTFFLDGQVLTLN-TLEQFRAEVDAAASN--------
+>GCF_003691675_PROKKA_00327
+MS--------------------------TP--------------------------------------------------
+--------------------------------------------------------------------------------
+-------------------------------------------------------------------------------T
+R----------------NPTPSDPST------------------------------------------------------
+------------------------------------------------------------PGTTSRKAKTIVWVVLAAVV
+LAGLIVGVVAASGPR----DAAPQGSGQTASSGTGQSAPS---EATP-VMRPDSRVLSKAPNEQAVLVEFLDFECEGCKA
+AYPVVEELRAEYADTVTFVHRYFPLPGHPNSMTAAVAVEAAGQQGQYEAMYQQMFDTQEQWSHTTEDRSPVFRGYAEDLG
+LDMAAYDAAVADPATRDRIEADVADGTALGVQGTPTFFLDGQMLTLN-TLEQFRAEVDAAATT-------D
+>GCF_003691675_PROKKA_01771
+MT--------------------------SP--------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-----------------DPTASTPSS------------------------------------------------------
+-----------------------------------------------------------PTPSRQRRAKIVVWVLLGLVV
+AAALI-GYLVARGTA----TAQQQDPNQSTAQSTGQSTGS----AGQ-LVRENSRVLSQAPNEKAVLVEFLDFECEACAA
+AYPFVEDLRAEYADTVTFVHRYFPLPGHPNSVTAAIAVEAAAQQGAYESMYQKMFETQTEWSHTTEDRSPVFRAYAEELG
+LDMAAYDAAVADPATRDRVELDVADGTALGVAGTPTFYLDGEPLTVN-SLEEFTAAVEAATQD--------
+>GCF_005280335_PROKKA_02344
+MS--------------------------TP--------------------------------------------------
+--------------------------------------------------------------------------------
+-------------------------------------------------------------------------------T
+R----------------NPTPANSST------------------------------------------------------
+------------------------------------------------------------SGTTSRKAKTIVWVVLAAVV
+VAGVIAGVVAVGAARNATPDAAATQAGQSAAQGSGPTTAE---EAGELVVRPNSRVLSKAPNEQAVLVEFLDFECEGCGA
+AYPVVEELRAEYADTVTFVTRYFPLPGHRNAMPAAVAVEAAAQQGEYEAMYQRMFETQAQWGEATEDKSPVFRGYAEELG
+LDMAAYDKAVADPATRARVEADVADGIALGVQGTPTFFLDGEMLTLT-SLEQFRAEVDAAASN--------
+>GCF_020097155_PROKKA_01190
+MSWRTIRTEAGSAVLLVVVTAVALLWANSPLSEAYFGLWDVEIGFDVGGFGLHMNLHHWINDGLMMTFFLVVGLEVRQEF
+AHGTLRDASRARLALIAGVVGVALPAVFYILIVAAAGGEGLGGWGAVVGTDTAFLLGALALVGPKLSGQLRVFLLTLTVV
+DDFLAVSIIGIVYSDEIRLVPLLIAGACLVGLWLLGRSRQWSATPYVLIVIVLWFATVESGVHASLAGMVAGLLIPAYPT
+RRQQVVEARQLFRDFWQSPSAASARAVDRGLAQGISVNERMHEVLRMPTALVIVPIFALANAGVDLRGGVLVDSFQSSVT
+WGVIVGLVLGKLLGIGLATFVAVKLGAGRLPEGVGMGSVFGGAALSGIGFTVSLLVIGLAFGSTSDLGRQATVGVLVAMV
+LATALGWLIF-----------------RVAAKRWGEETADLPMVLTP-PVDPEVDHIRGPEDAQLTLVEYIDFECAYCAH
+ATGSWDDLRSRFGDDLRYVVR--QLPHHPHGPLAARASEAASNQGMFWPWLDFVFTRQDAL-----EREDLIR-YAEELG
+LDVAQFTADLDSAAVGARVERDLESADASGAHATPTFFVDGRRLLGSYDARTLTSALEASRRGTRTQEVRS
+>GCF_023573625_PROKKA_02008
+MS--------------------------TP--------------------------------------------------
+--------------------------------------------------------------------------------
+-------------------------------------------------------------------------------T
+R----------------NPTPSDPST------------------------------------------------------
+------------------------------------------------------------PGTTSRKAKTIVWVVLAAVV
+LAGLIVGVVAASGPR----DAAPQGSGQTASSGTGQSAPS---EATP-VMRPDSRVLSKAPNEQAVLVEFLDFECEGCKA
+AYPVVEELRAEYADTVTFVHRYFPLPGHPNSMTAAVAVEAAGQQGQYEAMYQQMFDTQEQWSHTTEDRSPVFRGYAEDLG
+LDMAAYDAAVADPATRDRIEADVADGTALGVQGTPTFFLDGQMLTLN-TLEQFRAEVDAAATT-------D

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000097.fa ADDED Viewed

	@@ -0,0 +1,31 @@

+>GCF_002008305_PROKKA_00620
+MVGQTVGYVRVSSAEQNLDRQLEA-----VGECDRIFQDKISGSSRAKRTGLAELMQYVR
+EGDLVKVASMDRLGRDTRDLYAIVDELTGKGCAVQFVSERITVDKSGTSPVDG---LMLG
+ILAAFAEFERRRIKERQAEGIALAKARGKYV-QAPKLSGTDVEQARVMIEMGI-PKAEVA
+RTFGVSRQTLYTSLRRFESG--
+>GCF_003691675_PROKKA_00361
+MVGQTVAYVRVSSAEQNLDRQLEA-----VGECDRIFEDKISGSSRAKRAGLAELIGYVR
+EGDLVKVASMDRLGRDTRDLYAIVDELTDKGCAVQFVSERITVDKSGTSPVDG---LMLG
+ILAAFAEFERRRIKERQAEGIALAKARGKYV-QAPKLSGADVEQARVMIDMGI-PKAEVA
+RTFGVSRQTLYTSLSRGAGAEG
+>GCF_005280335_PROKKA_01310
+MVGQTVGYVRVSSAEQNLDRQLEA-----VGECDRIFRDKISGSSRAKRAGLAELLGYVR
+EGDLVKIASMDRLGRDTRDLYAIVDELTGKGCAVQFVSERITVDKSGTSPVDG---LMLG
+ILAAFAEFERRRIKERQAEGIALAKARGKYV-QAPKLSDTDVEQAKAMVDMGI-PKSEVA
+RTLGVSRQTLYTSLGRIASS--
+>GCF_020097155_PROKKA_00689
+MVGQTVGYVRVSSVEQNLDRQLEA-----VGECDRIFEDKISGSSRAKRTGLAELMRYVR
+EGDLVKVASMDRLGRDTRDLYAIVDELTGKGCAVQFVSERITVDKSGTSPVDG---LMLG
+ILAGFAEFERRRIKERQAEGIALAKARGKYV-QAPKMSDLDVEQARVMISIGI-PKAEVA
+RTFGVSRQTLYASLRRVAP---
+>GCF_020097155_PROKKA_02211
+MVGQAVGYVRVSSAEQNLDRQLEA-----VGECDRVFEGKISGSSRAKRTGLAELMRYVR
+EGDLVKVASMDRLGRDTRDLYAIVDELTDKGCAVQFVSERITVDKSGTSPVDG---LMLG
+ILAAFAEFERRRIKERQAEGIALAKARGKYV-QAPKLSGTDVEQARVMINMGI-PKAEVA
+RTFGVSRQTLYTSLARMGL---
+>GCF_020097155_PROKKA_02215
+M---HVGYARVSTLEQDLSAQREALERLGVENKDIYFDHGLTGTTRA-RPGLREALAATR
+DGDTLVVTKLDRLARSLPDARDIADELTTKGVA-------LSLGGSVYDPNDAVGRLLFN
+VLGMVAEFEADLIRLRTREGMAIARSKGKLKGKKPKLSPSQRKHLLTLHAAGEHTQAELA
+ELFNVSRTTIYRELRRTTTDT-

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000099.fa ADDED Viewed

	@@ -0,0 +1,37 @@

+>GCF_002008305_PROKKA_00630
+MNSGTGTGTDTGTGPAAGRVLVVDDEKPLARMVATYLERAGYEV-----ALTH----TGP
+AAVQAARVHEPDVIVLDLGLPGLDGIEVCRRVRAFS-ECYVLMLTARGDEHHRLEGLAVG
+ADDYITKPFSVRELVARVGAVMRRPRTTVSAPEPERV-CGDLVI--DLAAHEARVSGQVV
+QLTRTEFDLLAALSGRPHQAFSRRQLIDIVWDPAWVGDERLVDVHIKNLRRKLDADPARY
+IDTVRGVGYRMAEQ-----
+>GCF_005280335_PROKKA_00402
+MNSGTGTGTDTGTGPAAGRVLVVDDEKPLARMVATYLERAGYEV-----ALTH----TGP
+AAVQAARVHEPDVMVLDLGLPGLDGIEVCRRVRAFS-ECYVLMLTARGDEHHRLEGLAVG
+ADDYITKPFSVRELVARVGAVMRRPRTTVSAPEPERV-CGDLVI--DLAAHEARVSGQVV
+QLTRTEFDLLAALSGRPHQAFSRRQLIDIVWDPAWVGDERLVDVHIKNLRRKLDTDPARY
+IDTVRGVGYRMAEQ-----
+>GCF_020097155_PROKKA_00452
+M-----------TGP---DLLLIEDDDRLGPLLRDLLS-LDWEV-----TWSP----TLA
+AARAELDRRLFAVLVVDRGLPDGDGVDLVRELRARGVAVPALLLTAYGELEDRVHGLDAG
+ANDYLVKPFEVAELQARLRALTRDYSGRGAGVE-----IGSWMFYPDNRTVESPYTGRIL
+-LTEKESALLAVLASAPDTAFTRAHLLSAVFEHG--EQEGTVDTYVHYLRRKTDRS---L
+VETVRGVGYRLGTP----T
+>GCF_020097155_PROKKA_01060
+M----------------------------ARLLMLTRAASAVEVLPALDLLTHDVERADP
+RAALAAGREDVDGVLLDATSGLAEARTLARDLASLAPEVPVVAVMAEGALT--AVGPEWS
+LADIVLTGAGPAEVDARVR-LLRPADAPVAGGAAERLAVGGVEI--DPVGYRARLDGRAL
+NLTFREFELLKHLAQSPGRAFSREQLLREVWGDDYFGGTRTVDVHVRRLRAKLGPDREQM
+IGTVRNVGYRFTPRPDGDA
+>GCF_020097155_PROKKA_02199
+MNSGTGTGTDTGTGPAAGRVLVVDDEKPLARMVATYLERAGYEV-----ALTH----TGP
+AAVQAARVHEPDVMVLDLGLPGLDGIEVCWRVRAFS-ECYVLMLTARGDEHHRLEGLAVG
+ADDYITKPFSVRELVARVGAVMRRPRTTVSAPEPERV-CGDLVI--DLAAHEARVSGQVV
+QLTRTEFDLLAALSGRPHQAFSRRQLIDIVWDPAWVGDERLVDVHIKNLRRKLDADPARY
+IDTVRGVGYRMAEQ-----
+>GCF_023573625_PROKKA_00601
+MNSGTGTGTDTGTGPAAGRVLVVDDEKPLARMVATYLERAGYEV-----ALTH----TGP
+AAVQAARVHEPDVIVLDLGLPGLDGIEVCRRVRAFS-ECYVLMLTARGDEHHRLEGLAVG
+ADDYITKPFSVRELVARVGAVMRRPRTTVSAPEPERV-CGDLVI--DLATHEARVSGQVV
+QLTRTEFDLLAALSGRPHQAFSRRQLIDIVWDPAWVGDERLVDVHIKNLRRKLDADPARY
+IDTVRGVGYRMAEQ-----

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000101.fa ADDED Viewed

	@@ -0,0 +1,55 @@

+>GCF_002008305_PROKKA_00650
+MVRVSPSRPLRLLMDARY----------TRTDFHDGISRYGASLIEAVARRTDAPGPEGA
+DVEVEVAMLISDERQLALLPDGVPWHLVSGPTSPREPFVARQVARL------RPDVVF--
+-----SPMQTMGSWGRDYALILTLHDLIYYEHRTPPRNLPEPIRWLWRAYHLTKTPQRLL
+LDRADAVATVSRTTAELIDRHRLTRRPVHVIANAAQTVPEPRDPDETPDRTLLYMGSFMD
+YKDVESLVAAAPLLPGYALHLLSRISPERRGQLEARLAARRAAAGAAGADVVFHDGTDEA
+EYVRLLRRATAAVTLSRAEGFGLPVAEAMAHGTPVVCSDLPIFREIAGAGTPSFRGVPLE
+GDRAAALAARVRE-LEDPAEFAAASR-ASVAQAARFSWDESARRLLDLTAALGAAR----
+-RAARARTDRSSR
+>GCF_002008305_PROKKA_00841
+M---RGQR----MMSTSHEPLATTFIIPTGLPGPSGGSRYNKALIRAL---------EAA
+G--CSVSVC------------GVP-----GPWPRPE---ARDLERLRAALAGREQVVVDG
+LIASSAPDEIQAAAASGTRVHVLFHLSLLVDGAVPPDGSG-------RAAAL----ERRA
+LQSAHTVICTSNWAARDV-VNRYGPLPTRVVSPGTDQA--PLAVGSAPPQ-LLLLASVTP
+RKNQLAILRALAALTELDWQALLVGPDAADPDYAQRVRLFAEAAFPPGRVQVLGSRTGPG
+-LERIWSASDLLLLVSRAETFGMVVTEAVARGIPAIVGAGTGAEEALALGPHAPPGIAVA
+PDDTAALEEVLRGWLSDPAQRAAWRRSAEGARGMLPTWDDSADLMLRIL-----------
+-----------TP
+>GCF_003691675_PROKKA_00387
+MVRVSPSRPLRLLMDARY----------TRTDFHDGISRYGASLLEAVARRAAAPGPAGV
+D--VEVAMLISDERQLALLPDGVPWHLVSGPTSPREPFVARQVARL------RPDVVF--
+-----SPMQTMGSWGRDYALILTLHDLIYYEHRTPPRNLSEPIRWLWRAYHLTKIPQRLL
+LDRADAVATVSRTTAELIARHRLTRRPVHVVANAAQAVPEPRDPDETPERTLLYMGSFMD
+YKDVESLVAAAPLLPGYTLHLLSRISPERRGQLEDRLAERRAVAGADGADVVFHDGTDEA
+EYVRLLRRATAAVTLSRAEGFGLPVAEAMAHGTPVVCSDLPIFREIAGAGTASFRGVPLE
+GDRVAALAARVRE-LEDPAEFAAASR-ASVAQAARFSWDESARRLLDLTAALGVAR----
+-RAARARTGRSSR
+>GCF_005280335_PROKKA_02313
+M---SPSRPLRLLMDARY----------TRTDFHDGISRYGASLTEAVAHRAAAERGEGA
+D--VEVVMLISDERQLALLPKGVPWHRVSGPTSPREPFVARQMARL------RPDVVF--
+-----SPMQTMGSWGRRHALILTLHDLIYYEHRTPPQNLPEPIRWLWRAYHLTMTPQRLL
+LDRADAVATVSRTTADLIAAHRLTRRPVRVIANAAQPVPRPRDPEEAPERTLLYMGSFMD
+YKDVESLVDAAPLLPGYALHLLSRIDPARRAQLQERLEARRAAVGEDGAEVVFHDGTDEA
+EYVRLLRRATAAVTLSRAEGFGLPVAEAMAHGTPVVCSDLPIFREIAGAGTPSFRGVPLE
+GDRAAALAARVRE-LEDPAVFAAASR-AGVAQAARYSWDESARRLLELTRELGQARRAEA
+PRAARGRRDRSSR
+>GCF_020097155_PROKKA_02170
+M---TGSQ--LLLMDARY----------TRVDFHDGISRYGASLTEAVHRLA-----DPA
+G--LRVEMLISDERQLALLPDGVPWHRITGPTSAGEPFVARQVRAL------RPDVVF--
+-----SPMQTMGSLGRDYALILTLHDLIYYEYPTPPRNLPEPIRWLWRLYHLGYAPQRFL
+LDRADAVATVSQTTADLIAAHRLTRRPVHVVPNAPQPAGVPRDPEAAPTRELLYMGSFMD
+YKDVESILDAVPLLSGYTVRLLSRLTAERRRELAEHLRRARAAAGARGAEVVFHDGTDEA
+EYTALLRRATASVTLSRAEGFGLPVAEAQAQGTPVICSDLPIFREVAGHGTAAWNGVPLE
+GDRGAALAARVRG-LEDPAAFAAASR-ASAEHAAGYTWDRSARRLLDLVEGLLADR----
+-----------GR
+>GCF_023573625_PROKKA_00620
+MVRVSPSRPLRLLMDARY----------TRTDFHDGISRYGASLLEAVARRAAAPGPAGA
+D--VEVAMLISDERQLALLPDGVPWHLVSGPTSPREPFVARQVARL------RPDVVF--
+-----SPMQTMGSWGRDYALILTLHDLIYYEHRTPPRNLSEPIRWLWRAYHLTKIPQRLL
+LDRADAVATVSRTTAELIARHRLTRRPVHVVANAAQAVPEPRDPDETPERTLLYMGSFMD
+YKDVESLVAAAPLLPGYTLHLLSRISPERRGQLEDRLAERRAVAGADGADVVFHDGTDEA
+EYVRLLRRATAAVTLSRAEGFGLPVAEAMAHGTPVVCSDLPIFREIAGAGTPSFRGVPLE
+GDRAAALAARVRE-LEDPAEFAVASR-ASVAQAARFSWDESARRLLDLTAALGVAR----
+-RAARARTGRSTR

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000103.fa ADDED Viewed

	@@ -0,0 +1,61 @@

+>GCF_002008305_PROKKA_00692
+MAPP-----------------------------------RRAATREEPALRPAPPPAAVR
+-----------PDRPAR--R-RLPGVDAARAIALLGMITVHV-LDPVTADGAPHPAFLWF
+AGRASVLFVLLAGVGLALSTGGATPATGVRRAALRRRIARRAGLLFVLGLACGTLGVPVA
+VILCHYALLFLLALPLLGLRARALGLIAGAWLVLGPVLVFAVVAAAQAAVGRQEFFVGGR
+LWLSPGPADLLRPGLLLADLTVTGYYPVLSWGAFLVLGLALGRLPL-DRRRVAAGILGGG
+ATAWAAAGVVGAAVLRAPGTVGRVAAAIGTDPVETALTLRTGEPRLALLIPDPLWLALPT
+PHSGSVVAAVLAAGWACAVLGACL-----LARPLVGH-AALRPLVGAGRIPLTLYVGHLV
+VLALVDATGLDPADGALLTALVVLSLAAGLAAELSGRRGPLEAVMARLSRTGGERAVGG-
+----------------R
+>GCF_003691675_PROKKA_00429
+MAPP-----------------------------------RRAATREEPALRPAPPPAAVR
+-----------PDRPAR--R-RLPGVDAARAIALLGMITVHI-VDPVTADGAPHPAFLWF
+AGRASVLFVLLAGVGLALSTGGATPATGVRRAALRRRIARRAGLLFVLGLACGTLGVPVA
+VILCHYALLFLLALPLLGLRARALGLIAGAWLVLGPVLVFAVVAAAQAAVGRQEFFVGGR
+LWLSPGPADLLRPGLLLADLTVTGYYPVLSWGAFLVLGLALGRLPL-DRRRVAAGILGGG
+ATAWAAAGVVGAAVLRAPGTVGRVAAAIGTDPVETALTLRTGEPRLALLIPDPLWLALPT
+PHSGSVVAAVLAAGWACAVLGACL-----LARPLVGH-AALRPLVGAGRIPLTLYVGHLV
+VLALVDATGLDPADGALLTALVVLSLAAGLAAELSGRRGPLEAVMARLSRTGGERAVGG-
+----------------R
+>GCF_005280335_PROKKA_02262
+M---------------------------------------HGACERSPPCTPPRPPAATT
+-----------PTPSVR--RPRLRGVDAARGVALLGMVAVHV-VDPTTAAGDPHPVFLGF
+AGRASVLFVLLAGVGLALSTGGTRPAEGARRAALRRRITRRAGLLFVVGLACGALGTPVA
+VILGHYALLFLLAVPLLGLRAPALGAIAGAWLVLGPVAVFAASTAGQALLGRDEFLLDAR
+LWLSPMPEDLLTPGVLLADLVVTGYYPVLSWGAFLVLGLALGRLPL-DRARVAAALLAAG
+ALAWGAAAAAGAAVLRAPGVLERIAAGTGADPAQLTATLRTGEHRLAYLPPDPLWLALPT
+PHGGSPVAALLAAGWACAVLGLCL---------LVGA-ALDRAL--AGRTP---------
+----ADRGG-------------------------GGRRGRASCGRRRDPSRGRGGS----
+----------------R
+>GCF_005280335_PROKKA_02263
+M-----------------------------------------------------------
+-------------------R----------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------------------AASRPLTGAGRIPLTLYVGHLL
+VLAAASRLEIDASDAQLLTVLVALCLAAGLAADLTGRRGPLESAVARLSRAGEADA----
+-----PSHLR------R
+>GCF_020097155_PROKKA_02443
+MTPKHRQDPLAEPPEGDFTEARPAPGRRPSRTPWTDISRRRADAAPDTAAPPPPPPPPGK
+VGHRDAPPVSWRTQALRSAR-RLHGLDLARFLALAGMMAVHVWADAIDDRGLGGFIGTVV
+AGNAAAVFAFLAGITLIFLSGGSRGARGRDLQRARVAIAVRAVMLLVIGLGLNLIDFPAY
+DILPYYAMLFLLAIPLLGLGPAALALCAAAALLTGPVLRMVLVSTGTPVPGFDPTLISL-
+---------FARPGPTLIQLFVTGTYPAITWMAYVCAGMAAARLNLFDRQRQAFVAVGGL
+AATGVAAGLSWAALHVWDGR-ERIAEVTGIRPDLVELRASRGLSA-EMLSTTPWWLAARG
+PHLDTPLSTLHAVGVAAAVVGFVLMLTSGLMRPDGSLPAWTEPLRAAGSMSLTVYVSHLL
+LLTVP---GWEERRGWFFVGQLVLLVSFATLWRRVSAQGPLETVVSRVPKAVARALVPGR
+PAGAGPDYEPLEAADPR
+>GCF_023573625_PROKKA_00662
+MAPP-----------------------------------RRAATREEPALRPAPPPAAVR
+-----------PDRPAR--R-RLPGVDAARGIALLGMITVHV-LDPATADGAPHPAFLSF
+AGRASVLFVLLAGVGLALSTGGATPATGARRATLRRRIARRAGLLFVLGLACGTLGVPVA
+VILCHYALLFLLALPLLGLRARTLGVIAGAWLVLGPVLVFAVVAAAQAAVGRQEFFVGGR
+LWLSPGPADLLRPGLLLADLTVTGYYPVLSWGAFLVLGLALGRLPL-DRPRVAAGILGGG
+AAAWAAAGVVGAAVLRAPGTVGRVAAAIGTDPVETALTLRTGEPRLALLIPDPLWLALPT
+PHSGSVVAAVLAAGWACAVLGACL-----LARPLVGH-AALRPLVGAGRIPLTLYVGHLV
+VLALVDATGLDPADGALLAALVVLSLAAGLAAELSGRRGPLEAVMARLSRAGGERAVAG-
+----------------R

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000107.fa ADDED Viewed

	@@ -0,0 +1,55 @@

+>GCF_002008305_PROKKA_00769
+-MTTTSASQGYRTINPATGELLKSFDNATDQQIADALDASQAAYEQWSRKSVAERAAVVK
+RISELLAERSKDIAAVITTEMGKSLGAAVGEVRYGAQIFGYYADEAEELLADQPIKQFSG
+QEAFVQRLPLGPLLGIMPWNFPVYQVARFVAPNLVLGNTILLKHAEINPQVAQLLEELFT
+EAGLPEGVYQNVFATHDQISTIIADPRVQGVSLTGSERAGAAVAEQAGRHLKKVVLELGG
+SDPYIVLSAPDARAAARDALATRMGNWGQACNSNKRMIVMEDLYDDFVDELVQRSSEMKP
+GDPTSRDADVYGPLSSESAADGLAEQIAEAKQAGATVHVGGERTSGPEGEGFYVSPAVIT
+DVDQENPAYTQELFGMASVVYKVSSAEEAVALANDSQYGLGGAVFSTDLDEAKRVADQLE
+VGMANVNLASAAGANLPFGGVKRSGFGRELGPLALDEFANKRLYAVQGPLEG-
+>GCF_003691675_PROKKA_00499
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------MQGVSLTGSERAGAAVAEQAGRHLKKVVLELGG
+SDPYIVLSAPDARAAARDALATRMGNWGQACNSNKRMIVMEDLYDDFVDELVQRSSAMKP
+GDPTSRDADVYGPLSSESAADGLTEQIAAAKEAGATVHVGGERVSGPEGEGFYVSPAVIT
+DVDQENPAYTQELFGMAAVVYKVSSAEEAVALANDSQYGLGGAVFSTDLDEAKRVADQLE
+VGMANVNLASAAGANLPFGGVKRSGFGRELGPMAVDEFANKRLYAVQGPLEG-
+>GCF_005280335_PROKKA_00806
+-MAR------YITRNPATGETLEEFAELPASEVESVIERADTAYRAWRERPVAERAAVLA
+RAADLYEERAEQLAQDVTTEMGKPISAARGEMKTVAGIFRYYAEQGPAMLEHERIEVAGG
+GTAYVRRDPVGVLLGVMPWNFPHYQIARFAAPNLLLGNTMILKHAGICARSALNVEQLLL
+DAGLPEGAFVNAFIGHEAVAQIVADERVQGVSLTGSDKAGQIIGEQAGRNVKKAVLELGG
+SDPFIVAGDADVARAAKDAVSGRCVNSGQTCTSSKRFIVVEEHYEQFLSAFVEGMRAVPH
+GDPTD-ESTVVGPLSSPEAVQEVHELVQDAVAHGATLHVGGEPGEGP---GAYYPPTVLT
+DVDESARAFREEIFGPVAVVHRVKDLDAAIELANDSPYGLSSSVYTTSAEVAEEVSARLE
+TGMVWVNSTSKSSAELPFGGVKRSGIGRELGTLGIEEFANHKLVRSPEGLIGA
+>GCF_005280335_PROKKA_02161
+-MTTTSASQGYRTINPATGELLKSFDTATDQQIADALDASQAAYEQWSQKSVAERAAVVK
+RISELLAERSKDIATLITTEMGKSLGAAVGEVRFGAQIFAYYADNAEELLADQPIKDFSG
+QEAFVERLPLGPLLGIMPWNFPVYQVARFVAPNLILGNTILLKHSEINPQTAALLEDLFR
+EAGLPEGVYQNLYATHEQVSTIIADPRVQGVSLTGSERAGAAVAEQAGRHLKKVVLELGG
+SDPYIVLSAPDARQAARDALATRMGNWGQACNSNKRMIVMEDLYDDFVDELVQRASAMKA
+ADPTSRDEDVYGPLSSESAADGLAEQIKAAKDAGATVHVGGERVSGPAGEGFYVSPAVIT
+DVDQDNPAYTQELFGMAAVVYKVSSPEEAVALANDSQYGLGGAVFSTDLDEARRVADQLE
+VGMANVNLPSAAGANLPFGGVKRSGFGRELGPFAVDEFANKRLYAVKGPLQG-
+>GCF_020097155_PROKKA_02057
+MTTTTSASQGYRTINPATGELIKQYDNATDQQVQDALAASQAAYEQWAATTVAERAGVVK
+RISELLAERSKDIAALITTEMGKSLGGAIGEVRFSAQIFAYYADNAEELLADQPIKDFSG
+QEAFLEKLPLGPLLGVMPWNFPVYQVARFAAPNLVLGNTILLKHSEINPQTAQLLQDLFE
+EAGLPAGVYQNLYATHDQISTIIADPRVQGVSLTGSERAGASIAEQAGRHLKKCVLELGG
+SDPYIVLSAPDARQAAREALQTRMGNWGQACNSNKRMIVMEDLYDEFVDELVKQSTALKP
+GDPTSRDEDVYGPLSSESAADGLAAQIRDAKEAGATV-VGGERLSGPSGEGFYVSPAVIT
+DVDQENPAYSQELFGMASVVYRVSSAEEAVALANDSQYGLGGAVFSTDLDEAKRVAEQLE
+VGMANVNLPSAQGANLPFGGVKRSGFGRELGPFAVDEFANKRLYAVKGDLQG-
+>GCF_023573625_PROKKA_00733
+-MTTTSASQGYRTINPATGELLKSFDNATDQQIADALDASQAAYEQWSRKSVAERAAVVK
+RISELLAERSKDIAAVITTEMGKSLGAAVGEVRYGAQIFGYYADEAEELLADQPIKQFSG
+QEAFVQRLPLGPLLGIMPWNFPVYQVARFVAPNLVLGNTILLKHAEINPQVAQLLEELFT
+EAGLPEGVYQNVFATHDQISTIIADPRVQGVSLTGSERAGAAVAEQAGRHLKKVVLELGG
+SDPYIVLSAPDARAAARDALATRMGNWGQACNSNKRMIVMEDLYDDFVDELVQRSSAMKP
+GDPTSRDADVYGPLSSESAADGLTEQIAAAKEAGATVHVGGERVSGPQGEGFYVSPAVIT
+DVDQENPAYTQELFGMAAVVYKVSSAEEAVALANDSQYGLGGAVFSTDLDEAKRVADQLE
+VGMANVNLASAAGANLPFGGVKRSGFGRELGPMAVDEFANKRLYAVQGPLEG-

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000110.fa ADDED Viewed

	@@ -0,0 +1,37 @@

+>GCF_002008305_PROKKA_00965
+MTEH------------S-AAPVLRFVDDRAVRDLEQLATRARRVADTGMRLHVVPEAGRS
+RTPMLAQWVSVLQPAGLGDGVPVVLGLRTVPLATADGVADLDAVVALGSVTERTARMRGQ
+DPVDLAFAVPPGREHVTWTALTPPRGGWTPVAEVADEELTEVATRGADAVWDALPENPGE
+ALVRKIRAQMWGPLLGGDALQFPAGMAFGAHALGFLRPGGRARLSTAGPWTRLDTPGGFV
+LGRPAMAV--------------------
+>GCF_003691675_PROKKA_00678
+MTEH------------SAAAPVLRFVDDRAVRDLEQLATRARRVADTGMRLHVVPEAGRS
+RTPMLAQWVSVLQPAGLGDGVPVVLGLRTVPLATADGVADLDAVVALGSVTERTARMRGQ
+DPVDLAFAVPPGREHVTWTALTPPRGGWTPVAEVADEELAEVATRGADAVRDALPENPGE
+ALVRKVRAQMWGPLLGGEALQFPAGMAFGAHALGFLRPGGRARLSTAGPWTRLDTPGGFV
+LGRPAMAV--------------------
+>GCF_005280335_PROKKA_01922
+MTEP------------S-AAPVLRFADERAVRDLEQFATRARRVSDTGMRLHVVPAAGPS
+RTPMLAQWVSVLQPAGLGDEVPVVLGLRTVPLATAEMAADLDAVVALGAVTERTARMRSR
+QPVDLDFSVPPGREQVTWTALTPPRSGWTPAAEVADEELADVAERGVAAVRETLPENPGE
+AMVRKVRAQMWGPLLGGDALGFPAGMAFGAHALGFLQPGGRARLSTAGPWTRLDTPGGFV
+LGRPAMAV--------------------
+>GCF_020097155_PROKKA_00709
+MPAR------------------LILADAPPARDALTFAQRAAQAGAHGVRL---------
+------QAAAALTPRGPLDRTPTILVLRTL---RSDPELQCDVTVDTLTAT--------A
+DP--LTLALPETALAPAWTSVEPPQHGWRLIADVTSLTLMRSARAGIEAVAQALPDKPGD
+DVVRKIRGTVWGTPDTAL-ASLPQGVAFAAYVFGFLSRGNGATISTAGRWTRLTLPTGHV
+LLRGPVASGLTPIRRTRPRVSKSVTSIE
+>GCF_020097155_PROKKA_01871
+MPDQPSSRRDARDAARA-AVPVLRLTDERAVRDLDQFATRARRVADTGMRLHVVPEAGPR
+RTPMLAQWVSVLQPHGLGDGVPVVLGLRTVGLTSADAVEDLDAVVPLGAVTERTARMLGG
+TPVALDLPVPPGRERVTWTALTPPRAGWTVRAEVPDDELAEVAVKGAEAIRDALPQDPGE
+AMVRQVRAQMWGPRLGGE-IGFPAGMAFGAHALGFLRPGGRARLSTAGPWVRLDTPGGFV
+LGRSAVGV--------------------
+>GCF_023573625_PROKKA_00911
+MTEH------------SAAAPVLRFVDDRAVRDLEQLATRARRVADTGMRLHVVPEAGRS
+RTPMLAQWVSVLQPAGLGDGVPVVLGLRTVPLATADGVADLDAVVALGSVTERTARMRGQ
+DPVDLAFAVPPGREHVTWTALTPPRGGWTPVAEVADEELAEVATRGADAVRDALPENPGE
+ALVRKIRAQMWGPLLGGDALQFPAGMAFGAHALGFLRPGGRARLSTAGPWTRLDAPGGFV
+LGRPAMAV--------------------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000111.fa ADDED Viewed

	@@ -0,0 +1,37 @@

+>GCF_002008305_PROKKA_00993
+MTT--------------FAAAERARLADLLLEKGPDAPTLCGGWSTRDLAAHLWLRERRP
+DAFAALFIPPLSRHLDRLT-----AETTRRDYAEVVREWAAGP-----------------
+---SALNPMRAADRHVNAAEHFIHLEDVRRGESATGGSLPAPRSFSPDEEDALYRSLRRM
+APLFLRKSAAPVVLQGPGRAPVTVTRGAVALRAP------VTVTGEVGELLLWASGRDAV
+HV----ELDGDASAAVRTAL
+>GCF_003691675_PROKKA_00707
+MTT--------------FAAAERARLADLLLEKGPDAPTLCGGWSTRDLAAHLWLRERRP
+DAFAALFIPPLSRHLDRLT-----AETKRRDYAEVVREWAAGP-----------------
+---SALNPMRAADRHVNAAEHFIHLEDVRRGESSAGGSLPAPRPFSPDEEDALYRSLRRM
+APLFLRTSTAPVVLQGPGRAPVTVTRGAVALRAP------VTVTGEVGELLLWASGRDAV
+HV----ELDGDASAAVRTAL
+>GCF_005280335_PROKKA_01817
+MAAMADFPVTADRQGPDYAAASRAALVEALTAAGPGMPTLCAGWRTEHLAAHLALRDSSP
+TA-PGLFLPPLAAVLERRTRALGDAHAGDRGYAELVARIGRGPLPAPADDGVRGRLRGLA
+ARARGSRPGRAVAGRVQLLEFFVHTEDVRRAQDRW-----APRILADDYADALFTRLHAR
+AALLYRGEETGVVLVRRARAGSRTDNAPLTARRPGPDGVGVRVTGPAGELAMHAFGRRGA
+ALVTQDRFDADPAEDGPGAA
+>GCF_005280335_PROKKA_01896
+MTT--------------FAAAERARLADLLLEKGPHAPTLCGGWSTRDLAAHLWLRESRP
+DAFAALFIPPLSCHLDRLT-----AETTRRDYVEVVREWALGP-----------------
+---SALNPMRAADKHVNAAEHFIHLEDVRRGESAAGGSLPAPRSFSPDEEDALYRSLRRM
+APLVLRTSTAPVVLQGPGRAPVTVTRGAVALRAP------VTVTGEVGELLLWASGRDAV
+HV----ELDGDASAAVRTAL
+>GCF_020097155_PROKKA_01843
+MTT--------------FAAAERARLADLLLEKGPHAPTLCEGWSTRDLAAHLWLRENRP
+DAMASMFVKPLAGHLDRLT-----AHTKRREYVDVVGEWSQGP-----------------
+---ASLNPMRVADRHVNAAEHFIHLEDVRRGEAVAGGVTPAPRDFTPSEEDALYRSLRRM
+APLLLRKSAAPVVLQAPGRAPITVAREAVAVKAP------VTVSGPVGELLFWASGRDAV
+HV----DLDGDHAAVVRGGI
+>GCF_023573625_PROKKA_00936
+MTT--------------FAAAERARLADLLLEKGPHAPTLCGGWSTRDLAAHLWLRESRP
+DAFAALFIPPLSRHLDRLT-----ADTKRRDYAEVVREWAAGP-----------------
+---SALNPMRAADRHVNAAEHFIHLEDVRRGESSTGGSLPAPRPFSPDEEDALYRSLRRM
+APLFLRKSAAPVVLQGPGRAPVTVTRGAVALRAP------VTVTGEVGELLLWASGRDAV
+HV----EIDGDASAAVRTAL