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Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000002_tree.txt

@@ -0,0 +1 @@
+(((GCF_003691675_1_GCF_003691675.1_00787:0.00123687,(((((GCF_020097155_1_GCF_020097155.1_00621:0,GCF_020097155_1_GCF_020097155.1_00626:0):0.00250577,(GCF_023573625_1_GCF_023573625.1_00113:0,GCF_023573625_1_GCF_023573625.1_01883:0):0.00507023):0.00882327,GCF_020097155_1_GCF_020097155.1_00316:0.0496737):0.0013961,GCF_003691675_1_GCF_003691675.1_01659:0.00804765):0.00487737,((GCF_003691675_1_GCF_003691675.1_00332:0,GCF_020097155_1_GCF_020097155.1_02231:0):0.00696494,GCF_023573625_1_GCF_023573625.1_01019:0.00622306):0.0154368):0.00526825):0.00217197,((((((GCF_005280335_1_GCF_005280335.1_02630:0,GCF_005280335_1_GCF_005280335.1_02348:0):0.0265228,GCF_003691675_1_GCF_003691675.1_00320:2.23522e-07):1.277e-05,GCF_003691675_1_GCF_003691675.1_01328:2.23522e-07):1.277e-05,GCF_002008305_4_GCF_002008305.4_01387:2.23522e-07):1.277e-05,GCF_003691675_1_GCF_003691675.1_02266:2.23522e-07):0.00136415,GCF_003691675_1_GCF_003691675.1_01117:0.00997735):0.00200872):0.00186499,(((GCF_005280335_1_GCF_005280335.1_01313:0,GCF_005280335_1_GCF_005280335.1_01318:0):0.00353253,GCF_005280335_1_GCF_005280335.1_01280:0.00212247):0.026897,((GCF_023573625_1_GCF_023573625.1_01540:0.00040598,(((GCF_002008305_4_GCF_002008305.4_01069:0.020798,GCF_005280335_1_GCF_005280335.1_01303:2.23522e-07):2.603e-05,GCF_005280335_1_GCF_005280335.1_00757:2.23522e-07):2.603e-05,GCF_005280335_1_GCF_005280335.1_02332:2.23522e-07):0.00147652):0.00161499,((GCF_020097155_1_GCF_020097155.1_01795:0,GCF_020097155_1_GCF_020097155.1_01837:0):0,GCF_020097155_1_GCF_020097155.1_02208:0):0.0040327):0.00138189):0.00186499);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000004_tree.txt

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+((GCF_023573625_1_GCF_023573625.1_00116:2.55001e-06,(GCF_002008305_4_GCF_002008305.4_01393:2.55001e-06,((GCF_003691675_1_GCF_003691675.1_00355:2.55001e-06,(((GCF_005280335_1_GCF_005280335.1_00895:0,GCF_005280335_1_GCF_005280335.1_00228:0):0.261294,GCF_003691675_1_GCF_003691675.1_01012:0.0329093):0.0941234,GCF_005280335_1_GCF_005280335.1_02100:0.00437312):0.00521224):9.74e-06,GCF_002008305_4_GCF_002008305.4_00376:2.55001e-06):9.74e-06):9.74e-06):4.87e-06,(GCF_002008305_4_GCF_002008305.4_02112:2.55001e-06,(GCF_023573625_1_GCF_023573625.1_01974:2.55001e-06,(GCF_003691675_1_GCF_003691675.1_01819:2.55001e-06,(GCF_002008305_4_GCF_002008305.4_02277:2.55001e-06,(GCF_003691675_1_GCF_003691675.1_01746:2.55001e-06,(GCF_003691675_1_GCF_003691675.1_01125:2.55001e-06,(GCF_003691675_1_GCF_003691675.1_02016:2.55001e-06,((GCF_023573625_1_GCF_023573625.1_01880:0,(GCF_023573625_1_GCF_023573625.1_01547:0,GCF_023573625_1_GCF_023573625.1_01549:0):0):0.00038011,(GCF_005280335_1_GCF_005280335.1_01506:2.55001e-06,(GCF_005280335_1_GCF_005280335.1_00643:2.55001e-06,((GCF_005280335_1_GCF_005280335.1_00899:0.586123,GCF_020097155_1_GCF_020097155.1_01829:0.607318):0.356428,(GCF_005280335_1_GCF_005280335.1_00229:2.55001e-06,(GCF_003691675_1_GCF_003691675.1_01015:0.0885647,GCF_002008305_4_GCF_002008305.4_02069:0.00598831):0.118524):0.351008):0.0540488):0.00010439):0.00319271):0.00074121):9.74e-06):9.74e-06):9.74e-06):9.74e-06):9.74e-06):9.74e-06):4.87e-06);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000005_tree.txt

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Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000009_tree.txt

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Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000011_tree.txt

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Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000019_tree.txt

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+(((((GCF_005280335_1_GCF_005280335.1_02275:0.00604717,GCF_005280335_1_GCF_005280335.1_02634:8.83441e-07):0.0115305,(GCF_005280335_1_GCF_005280335.1_02616:0,GCF_005280335_1_GCF_005280335.1_02497:0):0.0024707):0.017677,GCF_003691675_1_GCF_003691675.1_01766:0.049677):0.140935,(GCF_023573625_1_GCF_023573625.1_00899:0.0680276,GCF_020097155_1_GCF_020097155.1_01886:0.0102924):0.187902):0.0237485,(GCF_003691675_1_GCF_003691675.1_00342:0.126053,GCF_023573625_1_GCF_023573625.1_01543:0.216031):0.0237485);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000021_tree.txt

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+(((GCF_002008305_4_GCF_002008305.4_00570:0.0291583,GCF_003691675_1_GCF_003691675.1_00294:0.00112167):0.279216,GCF_023573625_1_GCF_023573625.1_00572:2.32148e-06):0.135402,((GCF_002008305_4_GCF_002008305.4_00571:0.0101993,GCF_003691675_1_GCF_003691675.1_00295:0.00689172):0.130018,(GCF_005280335_1_GCF_005280335.1_02374:0.538221,(GCF_005280335_1_GCF_005280335.1_02375:0.331928,GCF_020097155_1_GCF_020097155.1_02254:0.433067):0.216609):0.0883956):0.135402);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000022_tree.txt

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+((GCF_023573625_1_GCF_023573625.1_01247:0.00251147,(GCF_003691675_1_GCF_003691675.1_01008:0,GCF_002008305_4_GCF_002008305.4_01289:0):0.00094753):0.0416592,(GCF_020097155_1_GCF_020097155.1_00711:0.075097,(((GCF_020097155_1_GCF_020097155.1_02196:0.00219647,GCF_005280335_1_GCF_005280335.1_00405:0.00492553):0.0102903,GCF_023573625_1_GCF_023573625.1_00598:0.00369116):0.00751134,GCF_002008305_4_GCF_002008305.4_00633:0.0137077):0.490361):0.0416592);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000030_tree.txt

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+((GCF_003691675_1_GCF_003691675.1_00360:3.70358e-06,((GCF_005280335_1_GCF_005280335.1_02217:0.857785,GCF_005280335_1_GCF_005280335.1_00191:1.29451):0.312949,GCF_005280335_1_GCF_005280335.1_00171:0.525499):0.696576):0.00056303,(GCF_023573625_1_GCF_023573625.1_02010:0.00188381,(GCF_005280335_1_GCF_005280335.1_02334:0.00266569,GCF_002008305_4_GCF_002008305.4_00169:0.00704631):0.00381069):0.00056303);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000032_tree.txt

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Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000038_tree.txt

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Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000039_tree.txt

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+(((GCF_002008305_4_GCF_002008305.4_00884:0.0113939,GCF_003691675_1_GCF_003691675.1_00606:0.00290412):0.753458,GCF_005280335_1_GCF_005280335.1_02045:1.0626):0.17617,((GCF_023573625_1_GCF_023573625.1_00845:0.860434,GCF_020097155_1_GCF_020097155.1_01944:0.589537):0.477201,(GCF_002008305_4_GCF_002008305.4_00894:0.0261265,GCF_003691675_1_GCF_003691675.1_00616:0.0431745):0.694971):0.17617);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000053_tree.txt

@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_01948:0.0118519,(GCF_023573625_1_GCF_023573625.1_02178:0.00688531,GCF_002008305_4_GCF_002008305.4_02246:2.05933e-06):0.00196763):0.0991336,(GCF_020097155_1_GCF_020097155.1_00422:1.64473,(GCF_023573625_1_GCF_023573625.1_02192:0.0110168,(GCF_002008305_4_GCF_002008305.4_02261:0.0358708,GCF_020097155_1_GCF_020097155.1_00418:0.0461942):0.00460275):0.0985952):0.0991336);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000055_tree.txt

@@ -0,0 +1 @@
+(GCF_003691675_1_GCF_003691675.1_01696:0.100453,(GCF_005280335_1_GCF_005280335.1_00855:0.0674537,(GCF_020097155_1_GCF_020097155.1_00792:0.125211,(GCF_023573625_1_GCF_023573625.1_00735:0.264599,(GCF_020097155_1_GCF_020097155.1_00870:0.790182,(GCF_005280335_1_GCF_005280335.1_01010:0.884884,GCF_020097155_1_GCF_020097155.1_00943:0.569454):0.0265043):0.296079):0.169595):0.0645251):0.100453);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000059_tree.txt

@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00048:0.0131357,GCF_002008305_4_GCF_002008305.4_00053:0.0130953):0.0243654,(GCF_003691675_1_GCF_003691675.1_02066:0.0100957,(GCF_020097155_1_GCF_020097155.1_00293:0.183162,(GCF_005280335_1_GCF_005280335.1_00346:0.0188688,GCF_020097155_1_GCF_020097155.1_00284:0.0464292):0.1045):0.102725):0.0243654);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000068_tree.txt

@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00216:0,GCF_003691675_1_GCF_003691675.1_02209:0):0,(GCF_002008305_4_GCF_002008305.4_00216:0,(GCF_005280335_1_GCF_005280335.1_00167:0.0474076,(GCF_020097155_1_GCF_020097155.1_00321:0.725649,GCF_005280335_1_GCF_005280335.1_02206:0.526506):0.601676):0.156687):0);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000070_tree.txt

@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02236:0,GCF_002008305_4_GCF_002008305.4_00223:0):0.00215106,(GCF_023573625_1_GCF_023573625.1_00224:0.00279487,(GCF_005280335_1_GCF_005280335.1_00157:0.11808,(GCF_005280335_1_GCF_005280335.1_00588:1.38933,GCF_020097155_1_GCF_020097155.1_00115:0.196804):0.0479959):0.134983):0.00215106);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000071_tree.txt

@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00236:0.00582243,(GCF_003691675_1_GCF_003691675.1_02249:0.00185525,GCF_023573625_1_GCF_023573625.1_00237:0.00135175):0.0055286):0.0240957,(GCF_005280335_1_GCF_005280335.1_00135:0.028429,(GCF_020097155_1_GCF_020097155.1_00100:0.150016,GCF_003691675_1_GCF_003691675.1_00102:0.41198):0.0803618):0.0240957);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000073_tree.txt

@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00258:0.00275811,GCF_023573625_1_GCF_023573625.1_00257:1.20469e-06):0.00625153,(((GCF_020097155_1_GCF_020097155.1_00526:0.780972,GCF_020097155_1_GCF_020097155.1_00079:0.143595):0.052061,GCF_005280335_1_GCF_005280335.1_00111:0.144119):0.0595365,GCF_003691675_1_GCF_003691675.1_02272:0.00953305):0.00625153);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000075_tree.txt

@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00281:0.00455281,GCF_002008305_4_GCF_002008305.4_00282:0.00810519):0.00100184,(((GCF_020097155_1_GCF_020097155.1_00057:0.167643,GCF_020097155_1_GCF_020097155.1_00450:2.04508):0.101533,GCF_005280335_1_GCF_005280335.1_00071:0.0693888):0.0977394,GCF_003691675_1_GCF_003691675.1_02297:0.00368381):0.00100184);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000078_tree.txt

@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00025:0.00509109,GCF_023573625_1_GCF_023573625.1_00317:7.591e-05):0.00392913,(GCF_002008305_4_GCF_002008305.4_00310:0.0061578,(GCF_020097155_1_GCF_020097155.1_00654:1.70175,(GCF_020097155_1_GCF_020097155.1_00023:0.187786,GCF_005280335_1_GCF_005280335.1_00027:0.233312):0.0146682):0.149015):0.00392913);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000079_tree.txt

@@ -0,0 +1 @@
+(((GCF_005280335_1_GCF_005280335.1_00019:0.0517623,(GCF_020097155_1_GCF_020097155.1_00687:0.973311,GCF_020097155_1_GCF_020097155.1_00015:0.0556756):0.042543):0.0196211,GCF_023573625_1_GCF_023573625.1_00325:0.00310519):0.000707155,(GCF_003691675_1_GCF_003691675.1_00033:0.00143222,GCF_002008305_4_GCF_002008305.4_00318:0.00358678):0.000707155);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000085_tree.txt

@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_00144:1.0942e-06,GCF_005280335_1_GCF_005280335.1_02534:0.45422):0.0181123,(GCF_023573625_1_GCF_023573625.1_00426:1.0942e-06,(GCF_002008305_4_GCF_002008305.4_00423:1.0942e-06,(GCF_005280335_1_GCF_005280335.1_02535:0.426985,GCF_020097155_1_GCF_020097155.1_02405:0.0545607):0.112307):0.0500062):0.0181123);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000086_tree.txt

@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00448:1.0173e-06,GCF_003691675_1_GCF_003691675.1_00169:0.00144544):0.00012172,(GCF_023573625_1_GCF_023573625.1_00451:0.00279306,(GCF_020097155_1_GCF_020097155.1_00683:0.879254,(GCF_020097155_1_GCF_020097155.1_02380:0.0490644,GCF_005280335_1_GCF_005280335.1_02509:0.0405486):0.0164049):0.0277779):0.00012172);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000093_tree.txt

@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00505:0.0795175,GCF_002008305_4_GCF_002008305.4_00604:1.63863):0.0645755,GCF_005280335_1_GCF_005280335.1_00578:0.083449):0.0638863,((GCF_023573625_1_GCF_023573625.1_02119:5e-07,GCF_002008305_4_GCF_002008305.4_02174:5e-07):0,GCF_003691675_1_GCF_003691675.1_01888:5e-07):0.0638863);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000096_tree.txt

@@ -0,0 +1 @@
+(((GCF_003691675_1_GCF_003691675.1_01774:0.0629467,GCF_002008305_4_GCF_002008305.4_00614:0.0369522):0.183449,(GCF_020097155_1_GCF_020097155.1_00544:0.233251,GCF_020097155_1_GCF_020097155.1_00702:0.216236):0.0796547):0.143923,(GCF_003691675_1_GCF_003691675.1_00326:0.0188012,GCF_023573625_1_GCF_023573625.1_02007:0.0229808):0.143923);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000101_tree.txt

@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00650:0.0298669,(GCF_003691675_1_GCF_003691675.1_00387:0.00714744,GCF_023573625_1_GCF_023573625.1_00620:0.00460756):0.0232114):0.0241048,((GCF_020097155_1_GCF_020097155.1_02170:0.0998882,GCF_002008305_4_GCF_002008305.4_00841:2.72111):0.166145,GCF_005280335_1_GCF_005280335.1_02313:0.0815279):0.0241048);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000102_tree.txt

@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00626:0.00215956,GCF_002008305_4_GCF_002008305.4_00656:1.81675e-06):0.000439155,(GCF_003691675_1_GCF_003691675.1_00393:1.81675e-06,(GCF_005280335_1_GCF_005280335.1_02307:0.0793687,(GCF_020097155_1_GCF_020097155.1_02164:0.1325,GCF_005280335_1_GCF_005280335.1_00162:1.50019):0.0467118):0.0556023):0.000439155);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000103_tree.txt

@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00662:0.0145909,((GCF_005280335_1_GCF_005280335.1_02263:0.114302,GCF_020097155_1_GCF_020097155.1_02443:0.882809):0.613258,GCF_005280335_1_GCF_005280335.1_02262:0.241719):0.277705):0.0082523,(GCF_002008305_4_GCF_002008305.4_00692:8.77e-06,GCF_003691675_1_GCF_003691675.1_00429:0.00258823):0.0082523);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000121_tree.txt

@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01147:0.00354933,((GCF_005280335_1_GCF_005280335.1_00771:1.43396,GCF_020097155_1_GCF_020097155.1_01639:0.0945169):0.0146736,GCF_005280335_1_GCF_005280335.1_01745:0.018807):0.0399278):0.00258283,(GCF_003691675_1_GCF_003691675.1_00866:0,GCF_023573625_1_GCF_023573625.1_01097:0):0.00258283);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000122_tree.txt

@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01152:0.006064,((GCF_005280335_1_GCF_005280335.1_01740:0.0136365,GCF_020097155_1_GCF_020097155.1_00545:1.91594):0.0490223,GCF_020097155_1_GCF_020097155.1_01634:0.133546):0.0534362):0.0054025,(GCF_023573625_1_GCF_023573625.1_01102:0,GCF_003691675_1_GCF_003691675.1_00871:0):0.0054025);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000125_tree.txt

@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_01334:0,GCF_023573625_1_GCF_023573625.1_01290:0):0.0009345,(GCF_003691675_1_GCF_003691675.1_01055:0.001254,(GCF_005280335_1_GCF_005280335.1_01557:0.0230717,(GCF_020097155_1_GCF_020097155.1_00131:1.74033,GCF_020097155_1_GCF_020097155.1_01453:0.080809):0.155963):0.0602017):0.0009345);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000126_tree.txt

@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_01296:0,GCF_003691675_1_GCF_003691675.1_01061:0):0.001687,(GCF_002008305_4_GCF_002008305.4_01341:0.009796,(GCF_005280335_1_GCF_005280335.1_01551:0.0524475,(GCF_020097155_1_GCF_020097155.1_01415:2.21555,GCF_020097155_1_GCF_020097155.1_01447:0.0115707):0.240493):0.0441125):0.001687);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000127_tree.txt

@@ -0,0 +1 @@
+(((GCF_002008305_4_GCF_002008305.4_01369:0.0206304,GCF_023573625_1_GCF_023573625.1_01324:0.0139016):0.00523794,GCF_003691675_1_GCF_003691675.1_01089:0.0279526):0.123173,(GCF_020097155_1_GCF_020097155.1_01419:0.355848,(GCF_002008305_4_GCF_002008305.4_01953:2.62665,GCF_005280335_1_GCF_005280335.1_01524:0.149712):0.147465):0.123173);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000137_tree.txt

@@ -0,0 +1 @@
+(((GCF_003691675_1_GCF_003691675.1_01296:0.0107404,GCF_023573625_1_GCF_023573625.1_01512:0.00705462):0.004935,GCF_002008305_4_GCF_002008305.4_01585:0.005496):0.002995,((GCF_002008305_4_GCF_002008305.4_02251:0.0624845,GCF_020097155_1_GCF_020097155.1_00456:0.143819):0.743811,GCF_005280335_1_GCF_005280335.1_01337:0.012057):0.002995);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000154_tree.txt

@@ -0,0 +1 @@
+((((GCF_020097155_1_GCF_020097155.1_00823:0.158543,GCF_005280335_1_GCF_005280335.1_00875:0.100395):0.224434,GCF_020097155_1_GCF_020097155.1_00810:0.017556):0.002525,GCF_003691675_1_GCF_003691675.1_01677:0.0042535):0.00059125,(GCF_002008305_4_GCF_002008305.4_01983:0,GCF_023573625_1_GCF_023573625.1_01909:0):0.00059125);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000158_tree.txt

@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02029:0.333538,(GCF_005280335_1_GCF_005280335.1_00789:0.344869,GCF_023573625_1_GCF_023573625.1_01966:1.4332e-06):0.12469):0.0362852,(GCF_020097155_1_GCF_020097155.1_00750:0.298897,(GCF_002008305_4_GCF_002008305.4_02031:0.201987,GCF_003691675_1_GCF_003691675.1_01738:1.4332e-06):0.0859973):0.0362852);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000164_tree.txt

@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_02122:0.0118992,GCF_023573625_1_GCF_023573625.1_02060:0.00899377):0.00105476,(GCF_003691675_1_GCF_003691675.1_01830:0.0109383,(GCF_020097155_1_GCF_020097155.1_00575:0.0308103,(GCF_005280335_1_GCF_005280335.1_00658:0.188184,GCF_020097155_1_GCF_020097155.1_00718:0.632372):0.127671):0.0136613):0.00105476);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000167_tree.txt

@@ -0,0 +1 @@
+((((GCF_020097155_1_GCF_020097155.1_00491:0.134548,GCF_023573625_1_GCF_023573625.1_00166:2.39922):0.0920547,GCF_005280335_1_GCF_005280335.1_00566:0.0584983):0.0629994,GCF_003691675_1_GCF_003691675.1_01898:0.0137146):0.00501097,(GCF_023573625_1_GCF_023573625.1_02129:0.00420819,GCF_002008305_4_GCF_002008305.4_02184:0.00185681):0.00501097);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000172_tree.txt

@@ -0,0 +1 @@
+(GCF_003691675_1_GCF_003691675.1_02019:0.697218,((GCF_005280335_1_GCF_005280335.1_01501:0.616067,GCF_020097155_1_GCF_020097155.1_00288:0.551462):0.531048,((GCF_020097155_1_GCF_020097155.1_00694:0.309231,GCF_020097155_1_GCF_020097155.1_00347:0.207293):1.00149,GCF_023573625_1_GCF_023573625.1_00111:4.56598e-06):0.347121):0.697218);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000175_tree.txt

@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00002:0,GCF_023573625_1_GCF_023573625.1_00002:0):0,(GCF_003691675_1_GCF_003691675.1_02007:0,(GCF_020097155_1_GCF_020097155.1_00375:0.0955265,GCF_005280335_1_GCF_005280335.1_00422:0.0531075):0.0214555):0);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000179_tree.txt

@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02011:0.00117137,GCF_023573625_1_GCF_023573625.1_00006:0.00028863):0.00108431,(GCF_002008305_4_GCF_002008305.4_00006:0.00543937,(GCF_020097155_1_GCF_020097155.1_00370:0.0978781,GCF_005280335_1_GCF_005280335.1_00418:0.0437689):0.0306456):0.00108431);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000182_tree.txt

@@ -0,0 +1 @@
+((GCF_003691675_1_GCF_003691675.1_02029:0.0139413,GCF_002008305_4_GCF_002008305.4_00011:0.00520267):0.000822285,(GCF_023573625_1_GCF_023573625.1_00011:0.00024798,(GCF_020097155_1_GCF_020097155.1_02181:0.28413,GCF_005280335_1_GCF_005280335.1_00386:0.0743763):0.0717949):0.000822285);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000183_tree.txt

@@ -0,0 +1 @@
+(((GCF_020097155_1_GCF_020097155.1_00364:0.764763,GCF_005280335_1_GCF_005280335.1_00383:0.140139):0.229514,GCF_003691675_1_GCF_003691675.1_02032:0.0454325):0.00834649,(GCF_002008305_4_GCF_002008305.4_00014:0.00406444,GCF_023573625_1_GCF_023573625.1_00014:0.00237656):0.00834649);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000190_tree.txt

@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00021:0.00017867,GCF_003691675_1_GCF_003691675.1_02039:3.88946e-07):0.00391625,(GCF_023573625_1_GCF_023573625.1_00021:0.0094685,(GCF_005280335_1_GCF_005280335.1_00375:0.0190076,GCF_020097155_1_GCF_020097155.1_00357:0.350104):0.0025335):0.00391625);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000194_tree.txt

@@ -0,0 +1 @@
+((GCF_023573625_1_GCF_023573625.1_00031:0.00236134,GCF_003691675_1_GCF_003691675.1_02049:0.00397766):0.00121645,((GCF_020097155_1_GCF_020097155.1_00304:0.137803,GCF_005280335_1_GCF_005280335.1_00366:0.0167207):0.00964019,GCF_002008305_4_GCF_002008305.4_00032:0.00015293):0.00121645);

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Gene_Trees/OG0000196_tree.txt

@@ -0,0 +1 @@
+((GCF_002008305_4_GCF_002008305.4_00034:0.00537062,GCF_003691675_1_GCF_003691675.1_02051:0.00163337):0.00287806,(GCF_023573625_1_GCF_023573625.1_00033:0.00409888,(GCF_005280335_1_GCF_005280335.1_00362:0.0698459,GCF_020097155_1_GCF_020097155.1_00303:0.0697571):0.0414646):0.00287806);