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Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000000_tree.txt

@@ -0,0 +1 @@
+(((GCF_023573625_PROKKA_02102:5e-09,GCF_023573625_PROKKA_02106:0.00288249):0.0206525,(GCF_003691675_PROKKA_00352:0.042443,(GCF_005280335_PROKKA_01505:0.25879,GCF_005280335_PROKKA_02339:0.304882):0.287255):0.0287259):0.0103334,((GCF_005280335_PROKKA_00227:0.0028477,(GCF_005280335_PROKKA_01737:0,GCF_005280335_PROKKA_02555:0):0.00300792):0.043213,((GCF_003691675_PROKKA_00137:5e-09,GCF_003691675_PROKKA_01971:0.0353709):0.00702144,(((GCF_003691675_PROKKA_00041:0.0194533,((((GCF_005280335_PROKKA_01499:0,GCF_005280335_PROKKA_02472:0):5e-09,GCF_005280335_PROKKA_02613:0.00287677):5e-09,GCF_005280335_PROKKA_00779:0.0758185):0.00356263,(((GCF_005280335_PROKKA_01768:0,GCF_005280335_PROKKA_02336:0):5e-09,GCF_005280335_PROKKA_02637:0.00289763):5e-09,GCF_005280335_PROKKA_00146:5e-09):0.0419983):0.0311409):0.0442562,(GCF_003691675_PROKKA_01118:0.00999489,(GCF_005280335_PROKKA_02632:0.0613057,(GCF_005280335_PROKKA_00044:5e-09,(GCF_005280335_PROKKA_00556:0.00288709,GCF_005280335_PROKKA_00692:5e-09):6e-09):0.0411965):0.016226):0.0374734):0.0251797,(GCF_003691675_PROKKA_00012:0.00638885,(((GCF_003691675_PROKKA_00312:0.011895,(GCF_002008305_PROKKA_01952:5e-09,GCF_002008305_PROKKA_01337:0.0432482):0.0130261):0.00430081,((GCF_002008305_PROKKA_02278:5e-09,(GCF_002008305_PROKKA_02111:5e-09,GCF_003691675_PROKKA_01818:5e-09):0.00292862):0.0270247,((GCF_003691675_PROKKA_02077:0.0168131,(GCF_002008305_PROKKA_00064:0.00555023,(GCF_002008305_PROKKA_02068:0.00889823,GCF_003691675_PROKKA_01821:0.0119179):0.0277276):0.0154651):0.00348074,(GCF_023573625_PROKKA_00274:0,GCF_023573625_PROKKA_01546:0):0.0164863):0.00929313):0.0190404):5e-09,(GCF_003691675_PROKKA_01236:0.00942898,(GCF_023573625_PROKKA_00879:5e-09,((GCF_023573625_PROKKA_01570:0.00291278,(GCF_023573625_PROKKA_00800:6e-09,GCF_023573625_PROKKA_01175:0.00288019):0.0057635):0.00250032,(GCF_003691675_PROKKA_01160:0.00385663,(GCF_003691675_PROKKA_01968:0.00515122,(GCF_023573625_PROKKA_01997:0.00693576,GCF_023573625_PROKKA_00518:0.0138941):0.00300346):0.00298165):0.00434738):0.000801834):0.0169932):0.00287359):0.0232115):0.0122406):0.0171617):0.022268):0.0103334);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000001_tree.txt

@@ -0,0 +1 @@
+((((GCF_002008305_PROKKA_01202:0,GCF_002008305_PROKKA_02030:0):5e-09,(GCF_023573625_PROKKA_02197:0,GCF_023573625_PROKKA_02214:0):0.00229901):0.037448,(GCF_005280335_PROKKA_00896:0.129812,GCF_005280335_PROKKA_00691:5e-09):0.0222397):0.00854238,((GCF_002008305_PROKKA_00603:0.002284,GCF_005280335_PROKKA_02671:0.00463582):0.037088,(((GCF_003691675_PROKKA_01126:0.0284997,(GCF_023573625_PROKKA_01344:0.00226378,(GCF_003691675_PROKKA_01127:6e-09,(GCF_002008305_PROKKA_01394:0.00226318,GCF_023573625_PROKKA_01996:5e-09):5e-09):5e-09):0.00715389):0.421963,(((GCF_002008305_PROKKA_02266:5e-09,(GCF_002008305_PROKKA_02231:0.00295219,(GCF_002008305_PROKKA_02065:0.00346372,GCF_002008305_PROKKA_02229:0.00575251):0.0037022):5e-09):0.00942841,((GCF_002008305_PROKKA_00174:0,GCF_002008305_PROKKA_00589:0,GCF_002008305_PROKKA_00713:0,GCF_002008305_PROKKA_01399:0):5e-09,GCF_002008305_PROKKA_02226:0.00702547):0.00231512):0.0223796,(GCF_002008305_PROKKA_00623:0.0113847,(GCF_002008305_PROKKA_02064:0.0669297,GCF_002008305_PROKKA_02232:0.0564102):0.00503313):0.0024637):0.0834388):0.127961,(GCF_005280335_PROKKA_00721:0.00210909,(GCF_002008305_PROKKA_01504:0.144714,((GCF_002008305_PROKKA_01505:0.111612,(GCF_002008305_PROKKA_00602:0,GCF_002008305_PROKKA_01070:0,GCF_002008305_PROKKA_02271:0):5e-09):0.00460946,GCF_005280335_PROKKA_02500:5e-09):5e-09):0.00249882):0.0103711):0.0265433):0.00854238);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000003_tree.txt

@@ -0,0 +1 @@
+(((GCF_023573625_PROKKA_00114:6e-09,(GCF_003691675_PROKKA_01116:5e-09,GCF_023573625_PROKKA_01884:0.00642897):0.00642558):0.0064542,((((GCF_005280335_PROKKA_01281:0,GCF_005280335_PROKKA_01312:0):0.00752593,((GCF_005280335_PROKKA_02347:6e-09,GCF_005280335_PROKKA_02631:0.0150545):0.0150917,((GCF_002008305_PROKKA_02280:0.135022,GCF_020097155_PROKKA_00317:0.0497284):0.0472623,GCF_005280335_PROKKA_01304:5e-09):0.00757128):5e-09):0.00758893,GCF_020097155_PROKKA_00625:0.00745579):5e-09,(GCF_002008305_PROKKA_01068:0.0149832,(GCF_003691675_PROKKA_01658:0.00646513,(((GCF_003691675_PROKKA_00319:0,GCF_003691675_PROKKA_02267:0):0.00740272,GCF_003691675_PROKKA_00788:5e-09):0.00738558,GCF_005280335_PROKKA_01317:0.0074632):6e-09):0.0129635):0.00655117):0.00648215):2.5e-09,(GCF_005280335_PROKKA_02614:0.00795341,(GCF_002008305_PROKKA_01386:5e-09,((GCF_003691675_PROKKA_01327:0,GCF_005280335_PROKKA_00758:0,GCF_005280335_PROKKA_02331:0,GCF_023573625_PROKKA_01539:0):5e-09,(GCF_020097155_PROKKA_01796:0,GCF_020097155_PROKKA_01836:0,GCF_020097155_PROKKA_02207:0):0.00738984):5e-09):5e-09):2.5e-09);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000007_tree.txt

@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_01213:0,(GCF_002008305_PROKKA_00158:0,GCF_002008305_PROKKA_01293:0,GCF_002008305_PROKKA_02076:0,GCF_003691675_PROKKA_01016:0,GCF_003691675_PROKKA_01103:0,GCF_003691675_PROKKA_01115:0,GCF_003691675_PROKKA_02022:0,GCF_023573625_PROKKA_00589:0,GCF_023573625_PROKKA_00591:0,GCF_023573625_PROKKA_01251:0,GCF_023573625_PROKKA_01338:0,GCF_023573625_PROKKA_01886:0,GCF_023573625_PROKKA_02204:0,(GCF_003691675_PROKKA_01111:0.00916342,(GCF_002008305_PROKKA_01033:0.00914985,GCF_002008305_PROKKA_01383:5e-09):5e-09):5e-09):0);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000008_tree.txt

@@ -0,0 +1 @@
+(((GCF_002008305_PROKKA_00711:0,GCF_003691675_PROKKA_00092:0,GCF_003691675_PROKKA_00343:0,GCF_003691675_PROKKA_01013:0,GCF_003691675_PROKKA_01394:0,GCF_003691675_PROKKA_02284:0,GCF_023573625_PROKKA_00606:0,GCF_023573625_PROKKA_01349:0,GCF_023573625_PROKKA_02164:0):5e-09,(GCF_002008305_PROKKA_01398:0.0719037,(GCF_002008305_PROKKA_01502:0.00443704,GCF_002008305_PROKKA_02225:0.46793):0.00244087):0.0621436):2.5e-09,(GCF_002008305_PROKKA_02227:0.026191,(GCF_023573625_PROKKA_01016:0,GCF_023573625_PROKKA_01158:0):0.00373267):2.5e-09);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000010_tree.txt

@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00630:0,GCF_020097155_PROKKA_00638:0,GCF_020097155_PROKKA_00839:0):0.163425,((GCF_005280335_PROKKA_01092:0.0286223,(GCF_005280335_PROKKA_00508:5e-09,(GCF_005280335_PROKKA_00108:5e-09,(GCF_005280335_PROKKA_00509:0,GCF_005280335_PROKKA_01091:0):0.0174212):5e-09):0.0139274):0.231105,(GCF_002008305_PROKKA_00845:0.12347,(GCF_002008305_PROKKA_00454:0.133764,(GCF_003691675_PROKKA_01124:5e-09,(GCF_002008305_PROKKA_01392:0.0071479,GCF_023573625_PROKKA_01343:5e-09):0.00715271):0.288002):0.169868):0.855007):0.163425);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000012_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02223:0,(GCF_002008305_PROKKA_02063:0,(GCF_003691675_PROKKA_00297:0.255798,((GCF_005280335_PROKKA_00722:0.139128,(GCF_003691675_PROKKA_00338:0,GCF_003691675_PROKKA_00345:0,GCF_003691675_PROKKA_00794:0):5e-09):0.00624757,(GCF_002008305_PROKKA_01075:5e-09,(GCF_002008305_PROKKA_00159:0.0218981,(GCF_002008305_PROKKA_00156:0.0266784,(GCF_005280335_PROKKA_00720:0,GCF_023573625_PROKKA_01024:0):0.0148181):0.00599024):5e-09):0.00932758):0.240536):0.445773):0);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000013_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01887:0.0140417,(GCF_023573625_PROKKA_00898:0.0157493,(GCF_003691675_PROKKA_00341:0.124098,(GCF_023573625_PROKKA_01544:0.406222,(GCF_005280335_PROKKA_00706:0.38075,(GCF_003691675_PROKKA_01765:0.0218988,((GCF_005280335_PROKKA_02276:0.00125225,GCF_005280335_PROKKA_02636:0.0115439)0.83:0.012746,(GCF_005280335_PROKKA_02496:0.211792,(GCF_005280335_PROKKA_02495:0.00541976,GCF_005280335_PROKKA_02615:5e-09)0.423:5e-09)0.325:0.00349261)0.914:0.0204545)0.943:0.16121)0.791:0.0906104)0.887:0.0616112)0.999:0.13763)1:0.0140417);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000014_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02220:0.00402046,(GCF_002008305_PROKKA_02060:5e-09,(GCF_003691675_PROKKA_00298:0.230585,(GCF_023573625_PROKKA_01023:5e-09,(GCF_005280335_PROKKA_00723:0.00200906,((GCF_002008305_PROKKA_00160:0,GCF_002008305_PROKKA_01074:0,GCF_003691675_PROKKA_00346:0):5e-09,(GCF_003691675_PROKKA_00337:5e-09,GCF_003691675_PROKKA_00793:0.00201048):0.0020099):0.00200908):0.00201403):0.241378):0.201634):0.00402046);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000015_tree.txt

@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_01149:0.0283035,(GCF_005280335_PROKKA_01238:0.0173285,(GCF_002008305_PROKKA_01656:0.00831215,(GCF_003691675_PROKKA_01361:0.00453286,GCF_023573625_PROKKA_01586:0.0026178)0.46:0.0035327)0.911:0.00840392)0.278:0.0137265)1:0.239249,(GCF_020097155_PROKKA_02465:5e-09,(GCF_005280335_PROKKA_02606:0.0125999,(GCF_002008305_PROKKA_00355:0.00179295,(GCF_003691675_PROKKA_00071:0.00179101,GCF_023573625_PROKKA_00362:5e-09)0.769:0.00178836)0.759:0.00257201)0.815:0.0229549)1:0.239249);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000016_tree.txt

@@ -0,0 +1 @@
+((((GCF_002008305_PROKKA_01771:0,GCF_003691675_PROKKA_01478:0):0.00640386,GCF_023573625_PROKKA_01700:0.00630266):0.00346542,(GCF_005280335_PROKKA_01106:0.0334911,GCF_020097155_PROKKA_01032:0.109175):0.0194111):0.0112761,((GCF_003691675_PROKKA_00706:0.00583165,GCF_023573625_PROKKA_00935:0.00254211):0.00401193,(GCF_005280335_PROKKA_01897:0.0411368,(GCF_002008305_PROKKA_00992:0.0145508,GCF_020097155_PROKKA_01844:0.0149575):0.00218125):0.00277314):0.0112761);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000017_tree.txt

@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00880:0.0423769,(GCF_002008305_PROKKA_01915:0.00450215,(GCF_003691675_PROKKA_01611:0.00167757,GCF_023573625_PROKKA_01835:5e-09)0.915:0.0090813)0.995:0.0981629)1:0.286273,(GCF_020097155_PROKKA_02288:0.0842702,(GCF_005280335_PROKKA_02407:0.0434259,(GCF_023573625_PROKKA_00545:0.00395954,(GCF_002008305_PROKKA_00542:0.00312239,GCF_003691675_PROKKA_00267:0.0125146)0.763:0.00233325)0.983:0.0296226)0.782:0.0459401)1:0.286273);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000020_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02299:0.133083,((GCF_005280335_PROKKA_01211:0.992211,(GCF_003691675_PROKKA_00245:0.0141942,(GCF_002008305_PROKKA_00524:5e-09,GCF_023573625_PROKKA_00524:0.00253447)0.706:0.0104374)1:0.463805)0.98:0.19563,(GCF_005280335_PROKKA_02417:0.0971786,(GCF_003691675_PROKKA_00256:0.00353325,GCF_023573625_PROKKA_00535:0.0173079)0.998:0.0794717)0.96:0.109912)1:0.133083);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000024_tree.txt

@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_02437:0.576216,(GCF_005280335_PROKKA_01839:0.551945,GCF_023573625_PROKKA_00587:1.08451)0.959:0.228638)1:0.448381,(GCF_005280335_PROKKA_00439:0.233083,(GCF_020097155_PROKKA_00392:0.179118,(GCF_002008305_PROKKA_02297:0.00900788,(GCF_003691675_PROKKA_01990:0.00833318,GCF_023573625_PROKKA_02238:0.00278536)0.808:0.00318286)1:0.185176)0.922:0.12125)1:0.448381);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000025_tree.txt

@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00670:0,GCF_023573625_PROKKA_02014:0):0.16136,(GCF_020097155_PROKKA_00617:0.327506,((GCF_002008305_PROKKA_00099:0,GCF_003691675_PROKKA_02112:0,GCF_023573625_PROKKA_00094:0):5e-09,GCF_005280335_PROKKA_00292:0.0247036):0.571753):0.16136);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000026_tree.txt

@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00186:0.106609,(GCF_020097155_PROKKA_00187:0.223121,GCF_020097155_PROKKA_02180:0.567515):0.153244):0.0404099,(GCF_005280335_PROKKA_00251:0.0130743,((GCF_002008305_PROKKA_00134:0,GCF_003691675_PROKKA_02148:0):5e-09,GCF_023573625_PROKKA_00142:0.00199743):0.025709):0.0404099);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000027_tree.txt

@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00724:0,(GCF_002008305_PROKKA_00161:0,GCF_002008305_PROKKA_01073:0,GCF_003691675_PROKKA_00336:0,GCF_003691675_PROKKA_00347:0,(GCF_003691675_PROKKA_00792:0,GCF_023573625_PROKKA_01022:0):0.0217507):0);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000028_tree.txt

@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00725:0.00160657,(GCF_003691675_PROKKA_00791:0.00321476,((GCF_002008305_PROKKA_01072:0,GCF_003691675_PROKKA_00335:0,GCF_003691675_PROKKA_00348:0,GCF_023573625_PROKKA_01021:0):5e-09,GCF_002008305_PROKKA_00162:5e-09):5e-09):0.00160657);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000031_tree.txt

@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_00172:1.1355,GCF_020097155_PROKKA_02230:1.40715):0.208375,(GCF_020097155_PROKKA_01399:5e-09,(GCF_005280335_PROKKA_01488:0.0190202,(GCF_002008305_PROKKA_01408:0.00287771,(GCF_003691675_PROKKA_01138:0,GCF_023573625_PROKKA_01358:0):5e-09):0.0203531):0.0619171):0.208375);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000033_tree.txt

@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_00590:0.963637,GCF_020097155_PROKKA_00524:1.11025)0.971:0.172153,(GCF_020097155_PROKKA_00077:0.322084,(GCF_005280335_PROKKA_00109:0.168366,(GCF_003691675_PROKKA_02273:0.00620004,(GCF_002008305_PROKKA_00260:5e-09,GCF_023573625_PROKKA_00258:0.00452916)0.831:0.00753046)1:0.22856)0.999:0.370411)0.971:0.172153);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000035_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02189:0.0259167,((GCF_005280335_PROKKA_00410:5e-09,(GCF_005280335_PROKKA_00389:5e-09,GCF_005280335_PROKKA_00393:0.0302627):0.0101513):0.0101082,(GCF_002008305_PROKKA_00627:0.0101356,(GCF_003691675_PROKKA_00372:0,GCF_023573625_PROKKA_00604:0):5e-09):5e-09):0.0259167);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000036_tree.txt

@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00451:1.08588,(GCF_005280335_PROKKA_01253:0.820278,GCF_005280335_PROKKA_01330:1.08257):0.273357):0.332923,(GCF_005280335_PROKKA_00403:5e-09,(GCF_020097155_PROKKA_02198:0.0127561,(GCF_002008305_PROKKA_00631:0,GCF_023573625_PROKKA_00600:0):0.00776946):0.00959987):0.332923);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000040_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02256:0.642535,(GCF_005280335_PROKKA_00822:1.33938,(GCF_003691675_PROKKA_00729:5e-09,(GCF_005280335_PROKKA_01873:0.0054313,(GCF_023573625_PROKKA_00959:0.00223951,(GCF_023573625_PROKKA_00958:5e-09,GCF_002008305_PROKKA_01015:5e-09)0.947:0.00361236)0.734:5e-09)0.563:0.00361637)0.934:0.386898)1:0.642535);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000041_tree.txt

@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00314:0.937969,GCF_020097155_PROKKA_01606:0.464668)0.922:0.0814579,(GCF_005280335_PROKKA_01707:0.254725,(GCF_005280335_PROKKA_01708:0.366497,(GCF_003691675_PROKKA_00900:0.00837367,(GCF_002008305_PROKKA_01181:0.0052912,GCF_023573625_PROKKA_01131:0.00523531)0.766:0.00492912)0.76:0.0531759)0.769:0.0789723)0.922:0.0814579);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000042_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00712:0.113821,(((GCF_002008305_PROKKA_01288:0,GCF_003691675_PROKKA_01007:0):0.00580768,GCF_023573625_PROKKA_01246:0.00924807):0.117612,(GCF_005280335_PROKKA_00620:0.29439,(GCF_002008305_PROKKA_01627:0.011325,GCF_023573625_PROKKA_01556:0.0103459):0.253559):0.176295):0.113821);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000043_tree.txt

@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_00412:0.00857074,(GCF_020097155_PROKKA_00648:0,GCF_020097155_PROKKA_02216:0):0.0171769):2.5e-09,(GCF_020097155_PROKKA_00325:0.0171188,(GCF_023573625_PROKKA_01347:0.00853601,(GCF_002008305_PROKKA_01397:5e-09,GCF_003691675_PROKKA_01130:0.00851276):5e-09):0.00859983):2.5e-09);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000044_tree.txt

@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01401:0.111216,GCF_020097155_PROKKA_00326:0.0842186):0.00136351,((GCF_005280335_PROKKA_00413:0.0251613,(GCF_003691675_PROKKA_01131:5e-09,GCF_023573625_PROKKA_01351:0.0533726):0.00716629):0.00346679,(GCF_020097155_PROKKA_00649:0,GCF_020097155_PROKKA_02217:0):5e-09):0.00136351);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000045_tree.txt

@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_01240:0.199431,(GCF_020097155_PROKKA_01828:1.16549,(GCF_020097155_PROKKA_00714:1.59757,GCF_020097155_PROKKA_00643:0.664171)0.752:0.128768)0.996:0.427507)0.991:0.078349,(GCF_023573625_PROKKA_01517:0.00179652,(GCF_002008305_PROKKA_01590:0.010479,GCF_003691675_PROKKA_01302:5e-09)0.869:0.00660547)0.991:0.078349);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000048_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01001:0.083454,((GCF_005280335_PROKKA_00398:0.156203,GCF_005280335_PROKKA_02643:0.809193):0.146632,((GCF_002008305_PROKKA_01808:0,GCF_003691675_PROKKA_01505:0):0.0207031,(GCF_005280335_PROKKA_01066:0.00926969,GCF_023573625_PROKKA_01729:5e-09):0.0178622):0.108492):0.083454);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000049_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00774:0.0178715,((GCF_023573625_PROKKA_00173:0.527292,GCF_023573625_PROKKA_00174:0.595234)0.852:0.277659,(GCF_005280335_PROKKA_00837:0.0460029,(GCF_023573625_PROKKA_01943:0.0033264,(GCF_003691675_PROKKA_01715:0.00786137,GCF_002008305_PROKKA_02005:0.0125602)0.729:0.0028999)1:0.0533522)0.939:0.0585172)1:0.0178715);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000050_tree.txt

@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_01308:0.0105914,GCF_020097155_PROKKA_02237:0.0127592)0.981:0.12808,(GCF_020097155_PROKKA_00662:1.78369,(GCF_005280335_PROKKA_00694:0.0183283,(GCF_003691675_PROKKA_01794:5e-09,(GCF_023573625_PROKKA_02028:0.0207894,GCF_002008305_PROKKA_02089:5e-09)0.599:0.0094745)0.829:0.0143074)0.785:0.0908522)0.981:0.12808);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000051_tree.txt

@@ -0,0 +1 @@
+(((GCF_003691675_PROKKA_01802:0.000133362,GCF_020097155_PROKKA_00600:0.0666336)0.596:0.017847,((GCF_020097155_PROKKA_02101:0.508887,GCF_023573625_PROKKA_02031:0.613187)0.994:0.624215,GCF_020097155_PROKKA_00599:0.111869)0.449:0.0263643)0.747:0.00668587,(GCF_002008305_PROKKA_02094:0.0409894,GCF_005280335_PROKKA_00684:0.0387512)0.747:0.00668587);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000052_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00520:0.027572,((GCF_005280335_PROKKA_00589:0.530802,GCF_005280335_PROKKA_02580:1.52373):0.28795,(GCF_005280335_PROKKA_00598:0.044012,((GCF_002008305_PROKKA_02160:0,GCF_003691675_PROKKA_01873:0):0.00810445,GCF_023573625_PROKKA_02104:5e-09):0.021444):0.0586633):0.027572);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000054_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00434:0.00303817,(GCF_023573625_PROKKA_02184:0.00403191,(GCF_005280335_PROKKA_00488:0.0161824,((GCF_002008305_PROKKA_02275:0.28969,GCF_005280335_PROKKA_00493:0.173257)0.933:0.157487,(GCF_002008305_PROKKA_02253:0.00712782,GCF_003691675_PROKKA_01952:0.00300307)0.756:0.0018574)0.866:0.00610443)0.735:0.00199749)1:0.00303817);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000056_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00353:0.221286,(GCF_005280335_PROKKA_00370:0.0256665,(GCF_005280335_PROKKA_00371:0.017816,(GCF_002008305_PROKKA_00025:0.0157216,(GCF_023573625_PROKKA_00025:0.00957219,GCF_003691675_PROKKA_02043:0.00638713)0.822:0.00717563)0.535:0.000664308)0.567:0.0198962)1:0.221286);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000057_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00427:0.509673,(GCF_005280335_PROKKA_00464:0.960635,(GCF_002008305_PROKKA_00568:1.40758,(GCF_002008305_PROKKA_00037:0.850779,(GCF_002008305_PROKKA_02274:0.190842,GCF_023573625_PROKKA_02208:0.250534)1:0.772146)0.872:0.220298)0.966:0.386398)1:0.509673);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000058_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01503:0.163223,(GCF_005280335_PROKKA_01608:0.131404,(GCF_005280335_PROKKA_00354:0.109288,(GCF_003691675_PROKKA_02062:6e-09,(GCF_023573625_PROKKA_00044:0.0140957,GCF_002008305_PROKKA_00049:5e-09)0.832:0.00561735)0.997:0.12813)1:0.365245)1:0.163223);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000061_tree.txt

@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00266:0.0507778,GCF_020097155_PROKKA_00684:0.781922)0.769:0.0146412,(GCF_005280335_PROKKA_00326:0.0759528,(GCF_023573625_PROKKA_00062:0.00531867,(GCF_002008305_PROKKA_00068:6e-09,GCF_003691675_PROKKA_02081:0.0106655)0.688:0.0065055)0.933:0.0343515)0.769:0.0146412);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000063_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00231:0.0464833,((GCF_005280335_PROKKA_00038:1.65423,GCF_005280335_PROKKA_00285:5e-09)0.577:0.00623731,(GCF_023573625_PROKKA_00100:0.00411274,(GCF_002008305_PROKKA_00105:0.00205499,GCF_003691675_PROKKA_02118:5e-09)0.833:5e-09)0.95:0.01531)1:0.0464833);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000064_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00137:0.231945,(GCF_005280335_PROKKA_00088:0.61229,(GCF_002008305_PROKKA_00119:5e-09,((GCF_003691675_PROKKA_02135:0,GCF_023573625_PROKKA_00127:0):5e-09,GCF_005280335_PROKKA_00265:0.0576621):0.00940129):0.450584):0.231945);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000065_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01975:0.234658,(GCF_002008305_PROKKA_00175:1.70614,(GCF_005280335_PROKKA_02080:0.112439,(GCF_002008305_PROKKA_00854:5e-09,(GCF_003691675_PROKKA_00576:0,GCF_023573625_PROKKA_00813:0):0.0191092):0.0968617):0.162919):0.234658);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000069_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00117:0.103974,(GCF_005280335_PROKKA_00086:1.0168,(GCF_005280335_PROKKA_00159:0.0990047,(GCF_023573625_PROKKA_00222:0.000901637,(GCF_002008305_PROKKA_00221:0.00658315,GCF_003691675_PROKKA_02234:0.00564873)0.879:0.00571932)1:0.0879877)0.958:0.0931407)1:0.103974);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000072_tree.txt

@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00088:0.0781417,GCF_020097155_PROKKA_02472:0.394103)1:0.0485506,(GCF_005280335_PROKKA_00120:0.0301196,(GCF_002008305_PROKKA_00250:0.00617101,(GCF_003691675_PROKKA_02262:0.00491775,GCF_023573625_PROKKA_00250:0.00185262)0.787:0.00782996)0.993:0.0346302)1:0.0485506);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000074_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02346:0.129278,(GCF_003691675_PROKKA_00203:0.0521876,(GCF_002008305_PROKKA_00279:0.00519361,(GCF_005280335_PROKKA_00074:0.00533227,(GCF_003691675_PROKKA_02294:6e-09,GCF_023573625_PROKKA_00278:0.00799105)0:6e-09)0.73:0.00545202)1:1.43336)1:0.129278);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000076_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00046:0.0505111,(GCF_002008305_PROKKA_01958:1.50018,(GCF_005280335_PROKKA_00067:0.0350465,(GCF_002008305_PROKKA_00287:0.00870315,(GCF_003691675_PROKKA_02309:0.00352282,GCF_023573625_PROKKA_00293:0.00242894)0.939:0.00324163)1:0.0389738)0.741:0.0651844)1:0.0505111);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000082_tree.txt

@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_02569:0.0292659,GCF_020097155_PROKKA_01756:0.0962103)0.446:0.00286866,((GCF_023573625_PROKKA_00392:0.00663066,(GCF_002008305_PROKKA_00386:5e-09,GCF_003691675_PROKKA_00110:0.00346887)0.875:0.00379943)0.848:0.00361157,GCF_020097155_PROKKA_02444:0.0341839)0.446:0.00286866);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000084_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02410:0.415657,(GCF_005280335_PROKKA_02542:0.663339,(GCF_005280335_PROKKA_02541:0.230212,(GCF_003691675_PROKKA_00139:0.0561719,(GCF_002008305_PROKKA_00418:5e-09,GCF_023573625_PROKKA_00421:0.00173399)0.951:0.0325798)0.792:0.0723654)0.999:0.356889)1:0.415657);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000087_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02342:0.0253247,(GCF_023573625_PROKKA_01553:1.31449,(GCF_005280335_PROKKA_02458:0.00388434,((GCF_002008305_PROKKA_00489:0,GCF_003691675_PROKKA_00210:0):0.00199757,GCF_023573625_PROKKA_00488:5e-09):0.00212173):0.0753449):0.0253247);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000088_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02336:0.0514642,(GCF_005280335_PROKKA_01221:1.41679,(GCF_003691675_PROKKA_00216:5e-09,(GCF_002008305_PROKKA_00495:0.00917144,(GCF_005280335_PROKKA_02452:0.0303728,GCF_023573625_PROKKA_00494:0.0202532)0.574:0.00494818)0.851:0.0112162)0.949:0.185651)1:0.0514642);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000089_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02325:0.0113135,(GCF_005280335_PROKKA_01218:1.78079,(GCF_003691675_PROKKA_00229:0.0305873,(GCF_005280335_PROKKA_02441:0.0504917,(GCF_002008305_PROKKA_00509:0.00992303,GCF_023573625_PROKKA_00508:0.0188854)0.947:0.0156897)0.509:0.00653855)0.83:0.0361289)1:0.0113135);