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experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Citation.txt

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

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000030_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02189:0.0231696,(((TT9_LFPAFLNI_00604:0,SA211_MHAAABBN_00372:0):0.00116114,((AS2_ACLBLIBL_00393:0.0420804,AS2_ACLBLIBL_00389:0.0009096):0.0170603,AS2_ACLBLIBL_00410:0.00046546):0.00100654):0.00165752,KBS0714_MOLHKGIG_00627:0.00758284):0.0231696);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000073_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00321:0.362825,(AS2_ACLBLIBL_02206:0.526506,(AS2_ACLBLIBL_00167:0.0474076,(KBS0714_MOLHKGIG_00216:-0,(SA211_MHAAABBN_02209:0,TT9_LFPAFLNI_00216:0):0):0.156687):0.601676):0.362825);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000125_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02311:0.00247425,((((AS2_ACLBLIBL_01219:2.47312,TT9_LFPAFLNI_00521:2.56614e-06):0.0674521,SA211_MHAAABBN_00243:2.56614e-06):0.0200599,AS2_ACLBLIBL_02428:0.00382862):0.00434688,KBS0714_MOLHKGIG_00521:0.0480745):0.00247425);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000154_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01764:0.404326,(AS2_ACLBLIBL_01876:0.614572,(TT9_LFPAFLNI_00955:1.95697e-06,(AS2_ACLBLIBL_01877:0.372237,(KBS0714_MOLHKGIG_01012:0,SA211_MHAAABBN_00726:0):0.0234255):0.0488932):0.108733):0.404326);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000172_tree.txt

@@ -0,0 +1 @@
+((KD337_16_NAFOICDF_00544:0.233251,KD337_16_NAFOICDF_00702:0.216236):0.0398274,((SA211_MHAAABBN_00326:0.0188012,TT9_LFPAFLNI_02007:0.0229808):0.287847,(KBS0714_MOLHKGIG_00614:0.0369522,SA211_MHAAABBN_01774:0.0629467):0.183449):0.0398274);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000270_tree.txt

@@ -0,0 +1 @@
+(AS2_ACLBLIBL_00209:0.00868906,(TT9_LFPAFLNI_00190:0.0112119,((KBS0714_MOLHKGIG_00035:1.23626,SA211_MHAAABBN_02020:2.28121):1.23235,KBS0714_MOLHKGIG_00190:0.0810099):0.116663):0.00868906);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000406_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00393:0.0358346,(AS2_ACLBLIBL_00440:0.0207658,(KBS0714_MOLHKGIG_02296:0.00469395,(TT9_LFPAFLNI_02237:3.118e-05,SA211_MHAAABBN_01989:0.00631282):0.00095355):0.0117995):0.0358346);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000417_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00404:0.188704,(AS2_ACLBLIBL_00451:0.0274256,((SA211_MHAAABBN_01977:0.00040387,TT9_LFPAFLNI_02225:0.00523812):0.00064037,KBS0714_MOLHKGIG_02286:0.00147262):0.0104254):0.188704);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000448_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00483:0.19624,(AS2_ACLBLIBL_00554:0.120196,(KBS0714_MOLHKGIG_02190:0.0059452,(TT9_LFPAFLNI_02135:0.0101265,SA211_MHAAABBN_01904:0.00308055):0.0022373):0.138993):0.19624);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000459_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00502:0.148439,(AS2_ACLBLIBL_00575:0.291499,((TT9_LFPAFLNI_02122:0.0152616,SA211_MHAAABBN_01891:0.0116404):0.0174854,KBS0714_MOLHKGIG_02177:0.0218211):0.170734):0.148439);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000479_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00540:0.199498,(AS2_ACLBLIBL_02658:0.410321,(AS2_ACLBLIBL_00616:0.118973,(TT9_LFPAFLNI_02088:0.003488,SA211_MHAAABBN_01858:0.003953):0.14527):0.08975):0.199498);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000496_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00567:0.0008941,(AS2_ACLBLIBL_00651:0.0021568,((TT9_LFPAFLNI_02067:0.00090867,SA211_MHAAABBN_01837:7.933e-05):0.00253753,KBS0714_MOLHKGIG_02129:0.00684942):0.00231203):0.0008941);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000497_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00568:0.00582213,(AS2_ACLBLIBL_00652:0.00263175,(KBS0714_MOLHKGIG_02128:0.00231775,(TT9_LFPAFLNI_02066:0,SA211_MHAAABBN_01836:0):0.00051925):0.00770475):0.00582213);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000514_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00590:0.15632,(AS2_ACLBLIBL_00674:0.138438,(TT9_LFPAFLNI_02045:0.00150198,(SA211_MHAAABBN_01812:0,KBS0714_MOLHKGIG_02105:0):0.00160502):0.076063):0.15632);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000536_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00126:0.15976,((KBS0714_MOLHKGIG_02053:0.0125189,(SA211_MHAAABBN_01759:0.0125127,TT9_LFPAFLNI_01987:0.0127823):0.00304416):0.0966926,AS2_ACLBLIBL_00769:0.095852):0.15976);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000551_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00759:0.003658,(AS2_ACLBLIBL_00798:0.060933,((SA211_MHAAABBN_01730:0.00077125,TT9_LFPAFLNI_01958:0.00977375):0.00867525,KBS0714_MOLHKGIG_02021:8.99242e-08):0.00324375):0.003658);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000579_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00812:0.00231375,(AS2_ACLBLIBL_00877:0.318682,(KBS0714_MOLHKGIG_01981:0.00098033,(TT9_LFPAFLNI_01907:3.29924e-07,SA211_MHAAABBN_01675:0.00097895):0.00243667):0.00222161):0.00231375);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000588_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00832:0.205018,(AS2_ACLBLIBL_00891:0.018908,((TT9_LFPAFLNI_01894:0.0248917,SA211_MHAAABBN_01662:0.0107493):0.00661797,KBS0714_MOLHKGIG_01968:0.0245846):0.00265314):0.205018);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000596_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00851:0.00510231,(AS2_ACLBLIBL_00913:0.0795884,(KBS0714_MOLHKGIG_01943:0.00902362,(TT9_LFPAFLNI_01862:0.00205012,SA211_MHAAABBN_01639:0.00086287):0.00838238):0.00107487):0.00510231);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000638_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00912:0.12361,(AS2_ACLBLIBL_00974:0.11263,(SA211_MHAAABBN_01580:0.0192598,(KBS0714_MOLHKGIG_01884:0,TT9_LFPAFLNI_01804:0):0.0165292):0.119517):0.12361);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000643_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00921:0.0245887,((AS2_ACLBLIBL_00983:0.00299442,KBS0714_MOLHKGIG_01876:0.00617758):0.00187047,(SA211_MHAAABBN_01572:0.00337083,TT9_LFPAFLNI_01796:0.00283717):0.0129828):0.0245887);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000654_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00933:0.106414,(AS2_ACLBLIBL_00995:0.0710494,(SA211_MHAAABBN_01561:0.00321613,(KBS0714_MOLHKGIG_01865:0.00063963,TT9_LFPAFLNI_01785:0.00807637):0.00115187):0.0649584):0.106414);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000656_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_00936:0.221726,(((TT9_LFPAFLNI_01783:0.00202625,KBS0714_MOLHKGIG_01863:0.00633375):0.0117495,SA211_MHAAABBN_01559:0.016501):0.085602,AS2_ACLBLIBL_00997:0.0807188):0.221726);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000714_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01015:0.129215,(AS2_ACLBLIBL_01089:0.0204825,(KBS0714_MOLHKGIG_01787:0.00545275,(SA211_MHAAABBN_01494:0.00265025,TT9_LFPAFLNI_01716:0.00062175):0.00168075):0.0111418):0.129215);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000809_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01128:0.052457,(AS2_ACLBLIBL_01200:0.042573,(TT9_LFPAFLNI_01608:0.003087,(KBS0714_MOLHKGIG_01678:0,SA211_MHAAABBN_01383:0):0.004705):0.02162):0.052457);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000838_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01158:0.0705466,((TT9_LFPAFLNI_01576:0.0256089,(KBS0714_MOLHKGIG_01646:0.00359277,SA211_MHAAABBN_01351:0.0325202):0.00620961):0.0438781,AS2_ACLBLIBL_01247:0.0577298):0.0705466);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000997_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01394:0.0651196,((KBS0714_MOLHKGIG_01412:0.006112,(SA211_MHAAABBN_01143:0.00539825,TT9_LFPAFLNI_01362:0.00659175):0.002023):0.0243005,AS2_ACLBLIBL_01487:0.0238147):0.0651196);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0000999_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01401:0.1256,((KBS0714_MOLHKGIG_01406:4.0554e-07,(SA211_MHAAABBN_01136:0.005125,TT9_LFPAFLNI_01356:4.0554e-07):0.000283):0.062504,AS2_ACLBLIBL_01490:0.086994):0.1256);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0001019_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01425:0.0483754,(((TT9_LFPAFLNI_01318:0,KBS0714_MOLHKGIG_01363:0):0.00136975,SA211_MHAAABBN_01083:1.02948e-07):0.00694575,AS2_ACLBLIBL_01530:1.02948e-07):0.0483754);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0001025_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01432:0.0616979,((KBS0714_MOLHKGIG_01356:0.008464,(SA211_MHAAABBN_01076:0.00379825,TT9_LFPAFLNI_01311:0.00353475):0.001867):0.0527105,AS2_ACLBLIBL_01536:0.0586252):0.0616979);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0001058_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01467:0.101097,(AS2_ACLBLIBL_01571:0.0218295,((KBS0714_MOLHKGIG_01320:2.80667e-07,TT9_LFPAFLNI_01276:0.0120873):0.00118425,SA211_MHAAABBN_01041:2.80667e-07):0.0457403):0.101097);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0001124_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01545:0.126465,(((TT9_LFPAFLNI_01198:4.863e-05,KBS0714_MOLHKGIG_01240:0.00266937):0.00284038,SA211_MHAAABBN_00959:0.00125263):0.116774,AS2_ACLBLIBL_01648:0.0840461):0.126465);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0001142_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01564:0.0555461,((KBS0714_MOLHKGIG_01221:0.00188315,(TT9_LFPAFLNI_01179:0.00656725,SA211_MHAAABBN_00940:0.00741575):0.00162943):0.0287178,AS2_ACLBLIBL_01667:0.0732408):0.0555461);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0001152_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01575:0.318722,(AS2_ACLBLIBL_01677:0.0868928,((TT9_LFPAFLNI_01167:0.0012005,KBS0714_MOLHKGIG_01210:0.0102125):0.007291,SA211_MHAAABBN_00929:0.0131135):0.061726):0.318722);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0001235_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01667:0.0593784,(AS2_ACLBLIBL_01774:0.0441731,((KBS0714_MOLHKGIG_01119:0.00114488,TT9_LFPAFLNI_01069:0.00130413):0.00625912,SA211_MHAAABBN_00838:0.00313888):0.0296961):0.0593784);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0001287_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01736:0.11329,(AS2_ACLBLIBL_01846:0.053115,(TT9_LFPAFLNI_00981:0.00582075,(SA211_MHAAABBN_00752:0.00721425,KBS0714_MOLHKGIG_01039:0.00686475):0.0299787):0.148656):0.11329);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0001376_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_01927:0.0754875,(((KBS0714_MOLHKGIG_00913:0,TT9_LFPAFLNI_00861:0):0,SA211_MHAAABBN_00632:0):0.052024,AS2_ACLBLIBL_02029:0.005113):0.0754875);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0001435_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02002:0.0541274,((SA211_MHAAABBN_00551:0.00433322,(TT9_LFPAFLNI_00788:0.00064028,KBS0714_MOLHKGIG_00819:0.00184572):0.00270149):0.225865,AS2_ACLBLIBL_02111:0.13377):0.0541274);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0001461_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02031:0.0956368,(AS2_ACLBLIBL_02138:0.0822405,(SA211_MHAAABBN_00524:0,(TT9_LFPAFLNI_00760:0,KBS0714_MOLHKGIG_00793:0):0):0.0018695):0.0956368);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0001477_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02049:0.0716449,(TT9_LFPAFLNI_00743:0.00595323,(AS2_ACLBLIBL_02154:0.0147811,(SA211_MHAAABBN_00507:0.00127333,KBS0714_MOLHKGIG_00776:0.00080067):0.00619731):0.00292748):0.0716449);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0001480_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02053:0.0947188,(((KBS0714_MOLHKGIG_00772:0.00794187,TT9_LFPAFLNI_00739:3.20056e-07):0.00567063,SA211_MHAAABBN_00503:0.00616987):0.0697391,AS2_ACLBLIBL_02158:0.0416714):0.0947188);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0001511_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02095:0.137308,(AS2_ACLBLIBL_02219:0.122225,(TT9_LFPAFLNI_00698:0.00726154,(SA211_MHAAABBN_00465:4.85362e-07,KBS0714_MOLHKGIG_00734:0.00398105):0.0103345):0.0673598):0.137308);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0001605_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02272:0.0635989,((TT9_LFPAFLNI_00559:0.00667015,(SA211_MHAAABBN_00281:0.0015893,KBS0714_MOLHKGIG_00556:0.0063037):0.00327209):0.0346502,AS2_ACLBLIBL_02389:0.0313912):0.0635989);

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Gene_Trees/OG0001626_tree.txt

@@ -0,0 +1 @@
+(KD337_16_NAFOICDF_02304:0.19647,(AS2_ACLBLIBL_02422:0.145463,(KBS0714_MOLHKGIG_00530:0.0452896,(TT9_LFPAFLNI_00530:0.0292366,SA211_MHAAABBN_00251:0.0327014):0.0130459):0.0473354):0.19647);