Add files using upload-large-folder tool

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000002_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.01185158	Before NNI:     tree length is 0.01289563
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 0.67535562

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000004_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.003934 1.017795 0.003944 0.003573
+1 0.003934 0.000001 1.021834 0.000010 0.000010
+2 1.017795 1.021834 0.000001 1.021843 1.021473
+3 0.003944 0.000010 1.021843 0.000001 0.000010
+4 0.003573 0.000010 1.021473 0.000010 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000010_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 1.171446 0.652536 1.472841 1.472714
+1 1.171446 0.000001 1.192253 0.016522 0.006381
+2 0.652536 1.192253 0.000001 1.493648 1.493521
+3 1.472841 0.016522 1.493648 0.000001 0.010141
+4 1.472714 0.006381 1.493521 0.010141 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000012_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.53949550	Before NNI:     tree length is 0.53949550
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 0.67772178

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000014_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.20770083	Before NNI:     tree length is 0.20554287
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 0.58131314

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000017_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 1.018828 0.759249 1.027331 1.021223
+1 1.018828 0.000001 1.332099 0.010081 0.016322
+2 0.759249 1.332099 0.000001 1.340602 1.334494
+3 1.027331 0.010081 1.340602 0.000001 0.006241
+4 1.021223 0.016322 1.334494 0.006241 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000019_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.21929113	Before NNI:     tree length is 0.21980737
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 0.93696507

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000020_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.13555542	Before NNI:     tree length is 0.11741950
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 0.27042417

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000023_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.785654 0.541722 0.173219 0.178632
+1 0.785654 0.000001 1.033124 0.027040 0.011176
+2 0.541722 1.033124 0.000001 0.535400 0.540813
+3 0.173219 0.027040 0.535400 0.000001 0.017275
+4 0.178632 0.011176 0.540813 0.017275 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000024_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.772929 0.764995 0.769622 0.894707
+1 0.772929 0.000001 0.874068 0.017091 0.308374
+2 0.764995 0.874068 0.000001 0.870760 0.995845
+3 0.769622 0.017091 0.870760 0.000001 0.280338
+4 0.894707 0.308374 0.995845 0.280338 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000025_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.418135 0.885723 0.417412 0.420999
+1 0.418135 0.000001 0.925916 0.017508 0.003829
+2 0.885723 0.925916 0.000001 0.925193 0.928780
+3 0.417412 0.017508 0.925193 0.000001 0.020372
+4 0.420999 0.003829 0.928780 0.020372 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000026_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.025657 0.382509 0.024680 0.026153
+1 0.025657 0.000001 0.359083 0.004083 0.028635
+2 0.382509 0.359083 0.000001 0.360934 0.385486
+3 0.024680 0.004083 0.360934 0.000001 0.027658
+4 0.026153 0.028635 0.385486 0.027658 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000026_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.39974262	Before NNI:     tree length is 0.39974262
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000029_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.55495933	Before NNI:     tree length is 0.55495925
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 0.57127693

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000045_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.013044 2.552770 0.004653 0.101135
+1 0.013044 0.000001 2.539727 0.010642 0.106076
+2 2.552770 2.539727 0.000001 2.550368 1.311741
+3 0.004653 0.010642 2.550368 0.000001 0.098733
+4 0.101135 0.106076 1.311741 0.098733 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000049_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.146767 0.147573 0.146558 0.145467
+1 0.146767 0.000001 0.136225 0.014730 0.010087
+2 0.147573 0.136225 0.000001 0.136015 0.134924
+3 0.146558 0.014730 0.136015 0.000001 0.013429
+4 0.145467 0.010087 0.134924 0.013429 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000050_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.20151291	Before NNI:     tree length is 0.20151288
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000062_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.015414 1.809867 0.004325 0.009925
+1 0.015414 0.000001 1.805175 0.015054 0.020654
+2 1.809867 1.805175 0.000001 0.271309 1.815107
+3 0.004325 0.015054 0.271309 0.000001 0.005600
+4 0.009925 0.020654 1.815107 0.005600 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000064_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 1.28072100	Before NNI:     tree length is 1.28072100
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000066_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.218916 0.339775 0.213188 0.216158
+1 0.218916 0.000001 0.270454 0.024794 0.002758
+2 0.339775 0.270454 0.000001 0.264726 0.267696
+3 0.213188 0.024794 0.264726 0.000001 0.022036
+4 0.216158 0.002758 0.267696 0.022036 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000067_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.23133150	Before NNI:     tree length is 0.23133150
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000072_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.073818 0.233031 0.066151 0.066572
+1 0.073818 0.000001 0.221118 0.007667 0.007246
+2 0.233031 0.221118 0.000001 0.213452 0.213872
+3 0.066151 0.007667 0.213452 0.000001 0.000420
+4 0.066572 0.007246 0.213872 0.000420 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000072_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.26398345	Before NNI:     tree length is 0.26398350
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000074_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.10773950	Before NNI:     tree length is 0.10773950
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000075_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 1.93500350	Before NNI:     tree length is 1.93500350
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000077_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 1.09283350	Before NNI:     tree length is 1.09283350
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000080_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.230853 0.224586 0.252054 0.233992
+1 0.230853 0.000001 0.254435 0.035774 0.039012
+2 0.224586 0.254435 0.000001 0.275636 0.257574
+3 0.252054 0.035774 0.275636 0.000001 0.060214
+4 0.233992 0.039012 0.257574 0.060214 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000081_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.024347 0.418268 0.029887 0.024347
+1 0.024347 0.000001 0.404926 0.010363 0.000001
+2 0.418268 0.404926 0.000001 0.410465 0.404926
+3 0.029887 0.010363 0.410465 0.000001 0.010363
+4 0.024347 0.000001 0.404926 0.010363 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000084_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.35758064	Before NNI:     tree length is 0.35758062
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000086_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.354261 0.677430 0.345101 0.344587
+1 0.354261 0.000001 0.550555 0.046843 0.031659
+2 0.677430 0.550555 0.000001 0.541395 0.540881
+3 0.345101 0.046843 0.541395 0.000001 0.037168
+4 0.344587 0.031659 0.540881 0.037168 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000088_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.194118 0.007310 0.185132 0.233608
+1 0.194118 0.000001 0.195555 0.017497 0.221382
+2 0.007310 0.195555 0.000001 0.186569 0.235045
+3 0.185132 0.017497 0.186569 0.000001 0.212395
+4 0.233608 0.221382 0.235045 0.212395 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000093_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.52807225	Before NNI:     tree length is 0.52807225
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000095_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.417561 0.711238 1.154604 0.419442
+1 0.417561 0.000001 0.677750 1.121116 0.016950
+2 0.711238 0.677750 0.000001 1.273487 0.679631
+3 1.154604 1.121116 1.273487 0.000001 1.122996
+4 0.419442 0.016950 0.679631 1.122996 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000100_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.307708 0.819085 0.307708 0.307708
+1 0.307708 0.000001 0.837435 0.000001 0.000001
+2 0.819085 0.837435 0.000001 0.837435 0.837435
+3 0.307708 0.000001 0.837435 0.000001 0.000001
+4 0.307708 0.000001 0.837435 0.000001 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000101_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.343525 0.346665 0.340455 0.340620
+1 0.343525 0.000001 0.058480 0.024947 0.020893
+2 0.346665 0.058480 0.000001 0.055410 0.055575
+3 0.340455 0.024947 0.055410 0.000001 0.022042
+4 0.340620 0.020893 0.055575 0.022042 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000101_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.39426750	Before NNI:     tree length is 0.39426750
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000104_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.036785 0.029765 0.053416 0.038522
+1 0.036785 0.000001 0.018469 0.031906 0.037868
+2 0.029765 0.018469 0.000001 0.035099 0.030848
+3 0.053416 0.031906 0.035099 0.000001 0.054499
+4 0.038522 0.037868 0.030848 0.054499 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000112_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.30231217	Before NNI:     tree length is 0.30231225
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000115_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.27058081	Before NNI:     tree length is 0.27058075
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000118_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.28581579	Before NNI:     tree length is 0.28581575
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000121_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.226401 0.289038 0.234220 0.228147
+1 0.226401 0.000001 0.338002 0.027716 0.038711
+2 0.289038 0.338002 0.000001 0.345821 0.339748
+3 0.234220 0.027716 0.345821 0.000001 0.046530
+4 0.228147 0.038711 0.339748 0.046530 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000122_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.54066920	Before NNI:     tree length is 0.54066925
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000123_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.221096 0.344100 0.212467 0.215142
+1 0.221096 0.000001 0.342274 0.013635 0.012476
+2 0.344100 0.342274 0.000001 0.333644 0.336319
+3 0.212467 0.013635 0.333644 0.000001 0.007680
+4 0.215142 0.012476 0.336319 0.007680 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000125_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.056250 0.013124 0.023889 0.091341
+1 0.056250 0.000001 0.053023 0.072481 0.139933
+2 0.013124 0.053023 0.000001 0.029355 0.096807
+3 0.023889 0.072481 0.029355 0.000001 0.067452
+4 0.091341 0.139933 0.096807 0.067452 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000127_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.020840 0.056607 0.023030 0.027687
+1 0.020840 0.000001 0.056540 0.006557 0.014788
+2 0.056607 0.056540 0.000001 0.058730 0.063387
+3 0.023030 0.006557 0.058730 0.000001 0.016978
+4 0.027687 0.014788 0.063387 0.016978 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000128_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.089136 0.057076 0.039918 0.082460
+1 0.089136 0.000001 0.057024 0.076756 0.042734
+2 0.057076 0.057024 0.000001 0.044696 0.050348
+3 0.039918 0.076756 0.044696 0.000001 0.070080
+4 0.082460 0.042734 0.050348 0.070080 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000128_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.13341600	Before NNI:     tree length is 0.13341600
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000129_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.05093258	Before NNI:     tree length is 0.05093263
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000132_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.023543 0.899687 0.033722 0.030037
+1 0.023543 0.000001 0.206304 0.021171 0.017486
+2 0.899687 0.206304 0.000001 0.909296 0.905610
+3 0.033722 0.021171 0.909296 0.000001 0.017795
+4 0.030037 0.017486 0.905610 0.017795 0.000001

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000134_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.39040308	Before NNI:     tree length is 0.39040312
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 0.99752435