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

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+When publishing work that uses OrthoFinder please cite:
+  Emms D.M. & Kelly S. OrthoFinder: phylogenetic orthology inference for comparative 
+  genomics (2019), Genome Biology 20:238
+
+  Emms D.M. & Kelly S. OrthoFinder: solving fundamental biases in whole genome
+  comparisons dramatically improves orthogroup inference accuracy (2015), Genome
+  Biology 16:157
+
+If you use the species tree in your work then please also cite:
+  Emms D.M. & Kelly S. STRIDE: Species Tree Root Inference from Gene Duplication
+  Events (2017), Mol Biol Evol 34(12): 3267-3278
+
+  Emms D.M. & Kelly S. STAG: Species Tree Inference from All Genes (2018), bioRxiv
+  https://doi.org/10.1101/267914
+
+OrthoFinder also depends on a number of tools which make its analysis possible.
+These tools are cited in the OrthoFinder paper, but are also being used in any
+analysis that uses OrthoFinder. In order to recognise the contributions that these 
+authors have made, please also consider citing the following as you feel is appropriate: 
+
+DIAMOND protein alignment:
+  Buchfink B., Xie C. & Huson D.H. Fast and sensitive protein alignment using
+  DIAMOND (2015) Nat Methods 12:59-60
+
+MCL clustering algorithm:
+  Van Dongen S. Graph clustering by flow simulation (2000). PhD Thesis, 
+  University of Utrecht, The Netherlands. 
+
+ETE Tree library for all tree handling:
+  Huerta-Cepas J., Serra F. and Bork P. ETE 3: Reconstruction, analysis and
+  visualization of phylogenomic data (2016) Mol Biol Evol
+
+DendroBLAST distance algorithm for orthogroup trees:
+  Kelly S., Maini, P.K. DendroBLAST: approximate phylogenetic trees in the absence
+  of multiple sequence alignments (2013) PLoS ONE 
+  https://doi.org/10.1371/journal.pone.0058537
+
+FastME tree inference:
+  Lefort V., Desper R., Gascuel O. FastME 2.0: A Comprehensive, Accurate, and Fast
+  Distance-Based Phylogeny Inference Program (2015) Mol Biol Evol 32:10 
+
+Non-default options (these tools are not ordinarily used but are among the more
+common options that can be selected by the user):
+
+MAFTT:
+  Katoh K. & Standley D.M. MAFFT Multiple Sequence Alignment Software Version 7:
+  Improvements in Performance and Usability (2013) Mol Biol Evol 30:4
+
+FastTree:
+  Price M.N., Dehal P.S., and Arkin A.P. FastTree 2 -- Approximately
+  Maximum-Likelihood Trees for Large Alignments. (2010) PLoS ONE, 5(3)
+  doi:10.1371/journal.pone.0009490
+
+BLAST protein alignment:
+  Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. Basic local
+  alignment search tool (1990) J. Mol. Biol. 215:403-410

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000002_tree.txt

@@ -0,0 +1 @@
+(((GCF_005280335_PROKKA_02348:0,GCF_005280335_PROKKA_02630:0):0.0233998,((((GCF_003691675_PROKKA_00332:0,GCF_020097155_PROKKA_02231:0):0.015563,GCF_023573625_PROKKA_01019:5e-09):0.0233965,(GCF_003691675_PROKKA_00787:5e-09,(GCF_003691675_PROKKA_01659:0.0151904,GCF_020097155_PROKKA_00316:0.0567134):0.00815592):5e-09):0.00767648,(GCF_002008305_PROKKA_01387:0,GCF_003691675_PROKKA_00320:0,GCF_003691675_PROKKA_01328:0,GCF_003691675_PROKKA_02266:0):5e-09):5e-09):0.0038409,((GCF_023573625_PROKKA_01540:5e-09,((GCF_020097155_PROKKA_00621:0,GCF_020097155_PROKKA_00626:0):0.015475,(GCF_023573625_PROKKA_00113:0,GCF_023573625_PROKKA_01883:0):6e-09):0.00776783):0.00767609,((GCF_005280335_PROKKA_00757:0,GCF_005280335_PROKKA_01303:0,GCF_005280335_PROKKA_02332:0):5e-09,(GCF_002008305_PROKKA_01069:0.0155085,((GCF_003691675_PROKKA_01117:0.0153727,(GCF_020097155_PROKKA_01795:0,GCF_020097155_PROKKA_01837:0,GCF_020097155_PROKKA_02208:0):5e-09):0.00768729,(GCF_005280335_PROKKA_01280:5e-09,(GCF_005280335_PROKKA_01313:0,GCF_005280335_PROKKA_01318:0):0.0075694):0.0469002):5e-09):5e-09):6e-09):0.0038409);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000004_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01829:0.202887,(GCF_005280335_PROKKA_00899:0.362442,(((GCF_005280335_PROKKA_00228:0,GCF_005280335_PROKKA_00895:0):5e-09,(GCF_003691675_PROKKA_01012:0.00879715,GCF_005280335_PROKKA_02100:0.00889592):1.7795e-05):3.9136e-05,(((GCF_023573625_PROKKA_01547:0,GCF_023573625_PROKKA_01549:0,GCF_023573625_PROKKA_01880:0):5e-09,(GCF_002008305_PROKKA_02069:0.0235031,((GCF_002008305_PROKKA_00376:0,GCF_002008305_PROKKA_01393:0,GCF_002008305_PROKKA_02112:0,GCF_002008305_PROKKA_02277:0,GCF_003691675_PROKKA_00355:0,GCF_003691675_PROKKA_01125:0,GCF_003691675_PROKKA_01746:0,GCF_003691675_PROKKA_01819:0,GCF_003691675_PROKKA_02016:0,GCF_023573625_PROKKA_00116:0,GCF_023573625_PROKKA_01974:0):8.51e-07,GCF_003691675_PROKKA_01015:0.0260674):1.7e-08):0.00221512):0.00221677,((GCF_005280335_PROKKA_00643:0,GCF_005280335_PROKKA_01506:0):5e-09,GCF_005280335_PROKKA_00229:5e-09):5e-09):5e-09):0.491081):0.202887);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000005_tree.txt

@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_01282:0.0471932,(GCF_020097155_PROKKA_00652:0.0408064,GCF_020097155_PROKKA_01820:0.0487728):0.0350243):0.0504201,((GCF_020097155_PROKKA_01361:0.0664936,(GCF_020097155_PROKKA_00641:0.0713213,GCF_020097155_PROKKA_01832:0.0347426):0.0143019):0.0587383,(GCF_020097155_PROKKA_00227:0.736291,((GCF_003691675_PROKKA_01778:1.08339,GCF_020097155_PROKKA_00678:0.747437):1.026,(GCF_005280335_PROKKA_02274:0.0102952,((GCF_020097155_PROKKA_00315:0,GCF_020097155_PROKKA_00645:0):0.020801,((GCF_020097155_PROKKA_00631:0,GCF_020097155_PROKKA_02162:0):0.00290493,((GCF_020097155_PROKKA_00751:0,GCF_020097155_PROKKA_01794:0):5e-09,(GCF_020097155_PROKKA_01890:0.011673,(GCF_020097155_PROKKA_00627:5e-09,(((GCF_020097155_PROKKA_00226:5e-09,GCF_020097155_PROKKA_01835:0.0028778):5e-09,(GCF_020097155_PROKKA_00448:5e-09,GCF_020097155_PROKKA_02206:5e-09):0.00342437):0.00576261,GCF_020097155_PROKKA_00312:6e-09):0.00580175):5e-09):0.00290432):5e-09):0.0129056):0.00948523):0.161534):0.154764):0.178416):0.0504201);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000006_tree.txt

@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_01214:0.00128355,(GCF_003691675_PROKKA_01011:0.00464154,(GCF_003691675_PROKKA_01114:0.00747385,((GCF_002008305_PROKKA_00157:0,GCF_002008305_PROKKA_01034:0,GCF_002008305_PROKKA_01292:0,GCF_002008305_PROKKA_02077:0,GCF_003691675_PROKKA_01104:0,GCF_023573625_PROKKA_01250:0):5e-09,(GCF_023573625_PROKKA_01339:5e-09,((GCF_023573625_PROKKA_00588:0,GCF_023573625_PROKKA_02205:0):0.00371775,(GCF_003691675_PROKKA_01112:5e-09,(GCF_023573625_PROKKA_00590:0.0335204,(GCF_002008305_PROKKA_01384:5e-09,(GCF_003691675_PROKKA_02023:0.00278449,GCF_023573625_PROKKA_01885:0.0166207):0.000941071):5e-09):0.00372345):0.00372693):5e-09):5e-09):5e-09):0.00114838):0.00128355);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000009_tree.txt

@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_00712:0,GCF_002008305_PROKKA_01400:0,GCF_003691675_PROKKA_00091:0,GCF_003691675_PROKKA_00344:0,GCF_003691675_PROKKA_01014:0,GCF_003691675_PROKKA_01393:0,GCF_003691675_PROKKA_02283:0,GCF_023573625_PROKKA_00607:0,GCF_023573625_PROKKA_01017:0,GCF_023573625_PROKKA_01157:0,GCF_023573625_PROKKA_01350:0,GCF_023573625_PROKKA_02163:0):2.5e-09,(GCF_002008305_PROKKA_01503:0.0796831,GCF_002008305_PROKKA_02228:0.00244825):2.5e-09);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000011_tree.txt

@@ -0,0 +1 @@
+((GCF_023573625_PROKKA_02002:0.0199231,(GCF_002008305_PROKKA_02074:5e-09,((GCF_002008305_PROKKA_00616:0,GCF_003691675_PROKKA_00339:0,GCF_003691675_PROKKA_01779:0):0.0173983,GCF_005280335_PROKKA_00719:0.0143496):0.141217):0.0395808):0.0226881,((GCF_023573625_PROKKA_02005:0.893599,(GCF_002008305_PROKKA_00609:0.00206281,GCF_003691675_PROKKA_01769:0.0551862):0.105956):0.0755419,(GCF_005280335_PROKKA_02366:0.0896787,(GCF_005280335_PROKKA_00727:0.0183933,(GCF_003691675_PROKKA_00350:0.0149387,GCF_003691675_PROKKA_00789:5e-09):0.0432446):0.0328139):0.0956685):0.0226881);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000018_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01147:0.131714,(GCF_005280335_PROKKA_01236:0.163345,(GCF_002008305_PROKKA_01845:0.679573,((GCF_002008305_PROKKA_01658:5e-09,(GCF_003691675_PROKKA_01363:5e-09,GCF_023573625_PROKKA_01588:0.00305814)0.976:0.00924601)1:0.392252,(GCF_002008305_PROKKA_01559:0.00979198,(GCF_003691675_PROKKA_01269:0.0122266,GCF_023573625_PROKKA_01486:0.00911241)0.721:0.0116984)0.999:0.35765)0.911:0.20453)0.984:0.252316)1:0.131714);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000019_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01886:0.013508,(GCF_023573625_PROKKA_00899:0.0372964,((GCF_003691675_PROKKA_00342:0.0961499,GCF_023573625_PROKKA_01543:0.288029):0.0685307,(GCF_003691675_PROKKA_01766:0.0425511,((GCF_005280335_PROKKA_02497:0,GCF_005280335_PROKKA_02616:0):5e-09,(GCF_005280335_PROKKA_02275:0.0102694,GCF_005280335_PROKKA_02634:5e-09):0.0102682):0.0226592):0.162111):0.230392):0.013508);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000021_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02254:0.139388,(GCF_005280335_PROKKA_02375:0.250904,(GCF_005280335_PROKKA_02374:0.295538,(GCF_002008305_PROKKA_00570:0.00589569,((GCF_003691675_PROKKA_00295:0.00642524,(GCF_023573625_PROKKA_00572:0.00675958,GCF_002008305_PROKKA_00571:0.00644994)0.255:5e-09)0.52:0.0151776,GCF_003691675_PROKKA_00294:0.00377234)0.657:0.0051573)1:0.277528)0.515:0.0376122)1:0.139388);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000022_tree.txt

@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00711:0.105881,((GCF_002008305_PROKKA_01289:0,GCF_003691675_PROKKA_01008:0):0.00125694,GCF_023573625_PROKKA_01247:0.00151652):0.0511899):0.256589,(GCF_002008305_PROKKA_00633:5e-09,((GCF_005280335_PROKKA_00405:0.00648903,GCF_020097155_PROKKA_02196:0.00124746):0.0103637,GCF_023573625_PROKKA_00598:5e-09):0.00256113):0.256589);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000023_tree.txt

@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_00513:0.113678,GCF_020097155_PROKKA_00454:0.0445661)0.292:0.00463707,((GCF_020097155_PROKKA_01865:0.494812,(GCF_020097155_PROKKA_00440:0.75221,GCF_020097155_PROKKA_00650:1.0005)0.96:0.363807)0.99:0.342567,(GCF_002008305_PROKKA_02238:0.00333617,(GCF_003691675_PROKKA_01940:0.0263141,GCF_023573625_PROKKA_02170:0.00645885)0.832:0.00646765)0.874:0.0276298)0.292:0.00463707);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000029_tree.txt

@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00726:0.00402188,((GCF_003691675_PROKKA_00790:0,GCF_023573625_PROKKA_01020:0):5e-09,((GCF_002008305_PROKKA_00163:0,GCF_002008305_PROKKA_01071:0,GCF_003691675_PROKKA_00334:0):5e-09,GCF_003691675_PROKKA_00349:0.00806332):0.00805909):0.00402188);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000032_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00093:0.106919,((GCF_003691675_PROKKA_00096:0.753052,GCF_003691675_PROKKA_00100:0.999711)0.987:0.423025,(GCF_002008305_PROKKA_00245:5e-09,(GCF_003691675_PROKKA_02257:5e-09,(GCF_005280335_PROKKA_00124:0.0119858,GCF_023573625_PROKKA_00245:0.0104521)0.955:0.0146913)0.482:0.00366845)0.978:0.172288)1:0.106919);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000034_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02214:0,(GCF_003691675_PROKKA_00340:0,(GCF_023573625_PROKKA_02003:0.198198,(GCF_005280335_PROKKA_00718:0.00848374,((GCF_002008305_PROKKA_00617:0,GCF_002008305_PROKKA_02075:0):0.00507506,GCF_003691675_PROKKA_01780:5e-09):0.0070661):5e-09):0.0154271):0);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000037_tree.txt

@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_02076:0.375524,(GCF_020097155_PROKKA_00685:0.591129,GCF_020097155_PROKKA_00686:0.887975)0.968:0.508038)0.777:0.132238,(GCF_005280335_PROKKA_02181:0.346323,(GCF_023573625_PROKKA_00713:0.00776034,(GCF_003691675_PROKKA_00479:0.0261668,GCF_002008305_PROKKA_00749:0.010459)0.766:0.00784635)0.94:0.168814)0.777:0.132238);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000038_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01023:0.0453106,((GCF_005280335_PROKKA_01099:0.0624218,(GCF_002008305_PROKKA_00836:0.127971,GCF_002008305_PROKKA_00837:0.0590392)0.477:0.526808)0.869:0.0456872,(GCF_002008305_PROKKA_01778:0.00213185,(GCF_003691675_PROKKA_01485:0.00975291,GCF_023573625_PROKKA_01707:0.00414833)0.44:0.00347634)1:0.0624721)1:0.0453106);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000039_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01944:0.302987,((GCF_002008305_PROKKA_00894:0.0271898,GCF_003691675_PROKKA_00616:0.0302301)1:0.644884,((GCF_005280335_PROKKA_02045:0.691889,(GCF_002008305_PROKKA_00884:0.00825059,GCF_003691675_PROKKA_00606:0.00961045)1:0.582421)1:0.561111,GCF_023573625_PROKKA_00845:0.742872)0.821:0.0951319)1:0.302987);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000047_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01003:0.0529808,((GCF_005280335_PROKKA_00397:0.217563,GCF_005280335_PROKKA_02641:0.804782)0.976:0.171489,(GCF_005280335_PROKKA_01068:0.0562515,(GCF_003691675_PROKKA_01503:0.0383186,(GCF_002008305_PROKKA_01806:0.00665126,GCF_023573625_PROKKA_01727:5e-09)0.909:0.0173372)0.973:0.0457164)0.998:0.101922)1:0.0529808);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000053_tree.txt

@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00418:0.0325663,(GCF_002008305_PROKKA_02261:0.0261664,GCF_023573625_PROKKA_02192:0.0150979)0.663:0.00921526)0.958:0.115781,(GCF_020097155_PROKKA_00422:1.58451,(GCF_003691675_PROKKA_01948:0.0107584,(GCF_002008305_PROKKA_02246:5e-09,GCF_023573625_PROKKA_02178:0.00537302)0.598:2.422e-06)0.776:0.119768)0.958:0.115781);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000055_tree.txt

@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00792:0.0836997,(GCF_003691675_PROKKA_01696:0.0139572,GCF_005280335_PROKKA_00855:0.00623493)0.997:0.122743)0.993:0.115924,(GCF_023573625_PROKKA_00735:0.225294,(GCF_020097155_PROKKA_00943:0.492378,(GCF_005280335_PROKKA_01010:0.469059,GCF_020097155_PROKKA_00870:0.717824)0.826:0.105665)0.998:0.350522)0.993:0.115924);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000059_tree.txt

@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_00346:0.00709262,GCF_020097155_PROKKA_00284:0.0343756)1:0.0713523,(GCF_020097155_PROKKA_00293:0.178921,(GCF_023573625_PROKKA_00048:0.00716124,(GCF_003691675_PROKKA_02066:0.0110657,GCF_002008305_PROKKA_00053:0.00947044)0.847:0.013023)1:0.15895)1:0.0713523);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000060_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00273:0.0641015,(GCF_005280335_PROKKA_00332:0.101313,(GCF_005280335_PROKKA_00201:1.78196,(GCF_023573625_PROKKA_00058:0.0165505,(GCF_002008305_PROKKA_00063:0.00342973,GCF_003691675_PROKKA_02076:0.0271495)0.655:0.00805598)0.973:0.138072)0:5e-09)1:0.0641015);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000062_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00258:0.0828191,(GCF_005280335_PROKKA_02338:1.30606,((GCF_002008305_PROKKA_00076:0,GCF_023573625_PROKKA_00070:0):5e-09,(GCF_005280335_PROKKA_00317:0.0226349,GCF_003691675_PROKKA_02089:0.00645918):0.00318119):0.209305):0.0828191);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000066_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00149:3e-09,(GCF_002008305_PROKKA_00198:0.00331156,(GCF_023573625_PROKKA_00198:0.0166215,(GCF_003691675_PROKKA_02194:0.0101568,(GCF_003691675_PROKKA_02026:1.43223,GCF_005280335_PROKKA_00197:0.150655)0.965:0.217831)0.793:0.00643227)1:5e-09)1:3e-09);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000068_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00321:0.424257,(GCF_005280335_PROKKA_02206:0.722161,((GCF_002008305_PROKKA_00216:0,GCF_003691675_PROKKA_02209:0,GCF_023573625_PROKKA_00216:0):0.153734,GCF_005280335_PROKKA_00167:0.0486727):0.845508):0.424257);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000070_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00115:0.0627229,(GCF_005280335_PROKKA_00588:1.46708,(GCF_005280335_PROKKA_00157:0.132435,((GCF_002008305_PROKKA_00223:0,GCF_003691675_PROKKA_02236:0):0.00866475,GCF_023573625_PROKKA_00224:5e-09):0.0793393):0.0929253):0.0627229);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000071_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00100:0.0792224,(GCF_003691675_PROKKA_00102:0.474068,(GCF_005280335_PROKKA_00135:0.030695,(GCF_002008305_PROKKA_00236:0.0052112,(GCF_003691675_PROKKA_02249:0.00210409,GCF_023573625_PROKKA_00237:0.00210936)0.863:0.00542516)1:0.0556894)0.91:0.0878221)1:0.0792224);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000073_tree.txt

@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00079:0.126939,GCF_020097155_PROKKA_00526:0.889959)0.912:0.0522248,(GCF_005280335_PROKKA_00111:0.0515937,(GCF_003691675_PROKKA_02272:0.0107424,(GCF_002008305_PROKKA_00258:0.00411397,GCF_023573625_PROKKA_00257:5e-09)0.862:0.014808)0.98:0.0609834)0.912:0.0522248);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000075_tree.txt

@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00057:0.26398,GCF_020097155_PROKKA_00450:1.72894)0.733:0.0354745,(GCF_005280335_PROKKA_00071:0.0172183,(GCF_003691675_PROKKA_02297:5e-09,(GCF_002008305_PROKKA_00282:0.0100593,GCF_023573625_PROKKA_00281:0.00499956)0.909:0.0101127)0.951:0.0723531)0.733:0.0354745);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000077_tree.txt

@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00035:0.0908422,GCF_020097155_PROKKA_01222:2.01679)0.843:0.0580221,(GCF_005280335_PROKKA_00057:0.0860688,(GCF_003691675_PROKKA_00005:0.0338802,(GCF_002008305_PROKKA_00297:0.013001,GCF_023573625_PROKKA_00304:0.00871193)0.978:0.0296028)0.965:0.0594053)0.843:0.0580221);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000078_tree.txt

@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_00027:0.24417,GCF_020097155_PROKKA_00023:0.194342)0.885:0.0365071,(GCF_020097155_PROKKA_00654:1.32246,(GCF_002008305_PROKKA_00310:0.00291069,(GCF_003691675_PROKKA_00025:0.00559649,GCF_023573625_PROKKA_00317:5e-09)0.878:0.0112438)0.931:0.103671)0.885:0.0365071);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000079_tree.txt

@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00015:0.0965629,GCF_020097155_PROKKA_00687:1.09006)0.703:0.0108903,(GCF_005280335_PROKKA_00019:0.0617126,(GCF_003691675_PROKKA_00033:5e-09,(GCF_002008305_PROKKA_00318:0.00802572,GCF_023573625_PROKKA_00325:0.00404751)0.789:0.00797851)0.94:0.0325911)0.703:0.0108903);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000083_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02415:0.0161681,(GCF_005280335_PROKKA_02646:1.81989,(GCF_005280335_PROKKA_02547:0.00811034,((GCF_002008305_PROKKA_00412:0,GCF_023573625_PROKKA_00415:0):5e-09,GCF_003691675_PROKKA_00132:0.00311154):0.0202945):0.0436164):0.0161681);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000085_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02405:0.0525143,(GCF_005280335_PROKKA_02535:0.101283,(GCF_005280335_PROKKA_02534:0.0969295,(GCF_002008305_PROKKA_00423:0.0165947,(GCF_003691675_PROKKA_00144:0.0118738,GCF_023573625_PROKKA_00426:0.0062224)0.916:0.011001)0.995:0.0782166)0.661:0.0184057)1:0.0525143);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000086_tree.txt

@@ -0,0 +1 @@
+(((GCF_005280335_PROKKA_02509:0.0347178,GCF_020097155_PROKKA_02380:0.0656997)0.998:0.0384262,(GCF_020097155_PROKKA_00683:0.97028,GCF_023573625_PROKKA_00451:0.00232437)0:1.0643e-05)1:2.5e-09,(GCF_002008305_PROKKA_00448:5e-09,GCF_003691675_PROKKA_00169:0.00233114)1:2.5e-09);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000093_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00505:0.0292453,(GCF_002008305_PROKKA_00604:1.54478,((GCF_002008305_PROKKA_02174:0,GCF_003691675_PROKKA_01888:0,GCF_023573625_PROKKA_02119:0):0.107953,GCF_005280335_PROKKA_00578:0.115182):0.0977326):0.0292453);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000095_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01190:0.697411,((GCF_003691675_PROKKA_01771:0.289778,GCF_005280335_PROKKA_02344:0.102409):0.0352008,(GCF_002008305_PROKKA_00611:0.133729,(GCF_003691675_PROKKA_00327:0,GCF_023573625_PROKKA_02008:0):0.0682043):0.0156544):0.697411);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000096_tree.txt

@@ -0,0 +1 @@
+(((GCF_003691675_PROKKA_00326:0.00684469,GCF_023573625_PROKKA_02007:5e-09)1:0.358886,(GCF_002008305_PROKKA_00614:0.0274874,GCF_003691675_PROKKA_01774:0.0842955)0.996:0.183974)0.996:0.0739174,(GCF_020097155_PROKKA_00544:0.256101,GCF_020097155_PROKKA_00702:0.272871)0.996:0.0739174);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000097_tree.txt

@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_00620:0.0278938,(GCF_020097155_PROKKA_00689:0.0504549,GCF_020097155_PROKKA_02215:1.2686)0:5e-09)0.595:0.00239562,(GCF_020097155_PROKKA_02211:0.0443013,(GCF_003691675_PROKKA_00361:0.036354,GCF_005280335_PROKKA_01310:0.0605429)0.392:0.0161986)0.595:0.00239562);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000099_tree.txt

@@ -0,0 +1 @@
+((GCF_023573625_PROKKA_00601:5e-09,(GCF_020097155_PROKKA_00452:0.916914,GCF_020097155_PROKKA_01060:1.10629)0.961:0.495221)0.878:0.00204117,(GCF_002008305_PROKKA_00630:5e-09,(GCF_005280335_PROKKA_00402:0.00407998,GCF_020097155_PROKKA_02199:0.00409972)0.801:0.00409701)0.878:0.00204117);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000101_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02170:0.0617663,(GCF_002008305_PROKKA_00841:1.91988,(GCF_005280335_PROKKA_02313:0.0673918,(GCF_002008305_PROKKA_00650:0.0165221,(GCF_003691675_PROKKA_00387:0.007385,GCF_023573625_PROKKA_00620:0.0048582)0.982:0.0270805)0.967:0.0393187)0.891:0.150212)1:0.0617663);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000102_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02164:0.122944,((GCF_005280335_PROKKA_00162:1.39379,GCF_005280335_PROKKA_02307:0.0572831)0.804:0.0435128,(GCF_003691675_PROKKA_00393:5e-09,(GCF_002008305_PROKKA_00656:5e-09,GCF_023573625_PROKKA_00626:0.00354992)0.844:0.00354882)0.842:0.0215804)1:0.122944);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000103_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02443:0.682159,(GCF_005280335_PROKKA_02262:0.292904,(GCF_005280335_PROKKA_02263:0.281755,(GCF_023573625_PROKKA_00662:0.00795867,(GCF_002008305_PROKKA_00692:5e-09,GCF_003691675_PROKKA_00429:0.00479587)0.863:0.0212603)0.853:0.0892214)0.645:0.0480509)1:0.682159);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000120_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01668:0.106192,(GCF_005280335_PROKKA_01775:0.0388122,(GCF_005280335_PROKKA_00163:1.53437,(GCF_002008305_PROKKA_01118:0.00434856,(GCF_003691675_PROKKA_00837:0,GCF_023573625_PROKKA_01068:0):5e-09):5e-09):0.0344813):0.106192);

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000121_tree.txt

@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01639:0.0439273,((GCF_002008305_PROKKA_01147:0.00374438,(GCF_003691675_PROKKA_00866:0,GCF_023573625_PROKKA_01097:0):0.00386493):0.0425685,(GCF_005280335_PROKKA_01745:0.0110625,GCF_005280335_PROKKA_00771:1.43435):0.00775569):0.0439273);