Add files using upload-large-folder tool

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000002_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.000013 0.011589 0.012530 0.010518
+1 0.000013 0.000001 0.011576 0.000001 0.010506
+2 0.011589 0.011576 0.000001 0.007124 0.001883
+3 0.012530 0.000001 0.007124 0.000001 0.006054
+4 0.010518 0.010506 0.001883 0.006054 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000003_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 0.02938548	Before NNI:     tree length is 0.02936100
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 0.95399652

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000012_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.022822 0.148312 0.000001 0.148312
+1 0.022822 0.000001 0.317611 0.513123 0.317611
+2 0.148312 0.317611 0.000001 0.838499 0.000001
+3 0.000001 0.513123 0.838499 0.000001 0.838499
+4 0.148312 0.317611 0.000001 0.838499 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000014_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.000001 0.003834 0.007536 0.004318
+1 0.000001 0.000001 0.003834 0.378639 0.004318
+2 0.003834 0.003834 0.000001 0.408367 0.003811
+3 0.007536 0.378639 0.408367 0.000001 0.408852
+4 0.004318 0.004318 0.003811 0.408852 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000015_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.005140 0.013480 0.025864 0.001520
+1 0.005140 0.000001 0.016888 0.029272 0.003619
+2 0.013480 0.016888 0.000001 0.028732 0.013269
+3 0.025864 0.029272 0.028732 0.000001 0.025653
+4 0.001520 0.003619 0.013269 0.025653 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000015_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 0.03831175	Before NNI:     tree length is 0.03831175
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000018_tree_id.txt.dist.phylip

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

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000018_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 1.56753375	Before NNI:     tree length is 1.56753375
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 0.99996581

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000020_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.027040 0.785285 1.033124 0.011176
+1 0.027040 0.000001 0.173219 0.535770 0.017275
+2 0.785285 0.173219 0.000001 0.540984 0.178632
+3 1.033124 0.535770 0.540984 0.000001 0.541183
+4 0.011176 0.017275 0.178632 0.541183 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000021_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 1.42524874	Before NNI:     tree length is 1.42524875
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 0.99979530

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000022_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.000001 0.036435 0.033706 0.003459
+1 0.000001 0.000001 0.597354 0.159363 0.003459
+2 0.036435 0.597354 0.000001 0.007122 0.018907
+3 0.033706 0.159363 0.007122 0.000001 0.016178
+4 0.003459 0.003459 0.018907 0.016178 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000022_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

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000023_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 0.22198615	Before NNI:     tree length is 0.22198612
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000024_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 0.73264075	Before NNI:     tree length is 0.73264075
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000031_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

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000032_tree_id.txt.dist.phylip

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

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000032_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

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000033_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 1.12662600	Before NNI:     tree length is 1.12662600
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000038_tree_id.txt.dist.phylip

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

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000038_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 0.22693587	Before NNI:     tree length is 0.22693588
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000046_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.028543 0.006428 0.435282 0.002804
+1 0.028543 0.000001 0.951871 0.420019 0.025738
+2 0.006428 0.951871 0.000001 1.008051 0.964329
+3 0.435282 0.420019 1.008051 0.000001 0.432477
+4 0.002804 0.025738 0.964329 0.432477 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000046_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,36 @@
+
+ - 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 0.85473917	Before NNI:     tree length is 0.87252888
+	NNI      1: new tree length is 0.83348363
+	Performed 1 NNI(s).
+
+	Before SPR:     tree length is 0.87252888
+	SPR      1: new tree length is 0.83348363
+	Performed 1 SPR(s).
+
+	Explained variance : 0.66328129

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000048_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.000001 0.068895 0.291112 0.067462
+1 0.000001 0.000001 0.068895 0.291112 0.067462
+2 0.068895 0.068895 0.000001 0.270294 0.010178
+3 0.291112 0.291112 0.270294 0.000001 0.268860
+4 0.067462 0.067462 0.010178 0.268860 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000048_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 0.31952325	Before NNI:     tree length is 0.31952325
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000049_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 0.18665575	Before NNI:     tree length is 0.18665575
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000058_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.004416 0.205676 0.790221 0.009196
+1 0.004416 0.000001 0.203306 0.787851 0.011831
+2 0.205676 0.203306 0.000001 0.471434 0.213092
+3 0.790221 0.787851 0.471434 0.000001 0.797637
+4 0.009196 0.011831 0.213092 0.797637 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000058_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 0.74299425	Before NNI:     tree length is 0.74299425
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 0.99028521

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000060_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.035774 0.235500 0.259082 0.040374
+1 0.035774 0.000001 0.250692 0.274274 0.055567
+2 0.235500 0.250692 0.000001 0.224586 0.233992
+3 0.259082 0.274274 0.224586 0.000001 0.257574
+4 0.040374 0.055567 0.233992 0.257574 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000061_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 0.18519500	Before NNI:     tree length is 0.18519500
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000064_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.401021 0.438140 1.176019 0.401021
+1 0.401021 0.000001 0.084318 0.862964 0.000001
+2 0.438140 0.084318 0.000001 0.900083 0.084318
+3 1.176019 0.862964 0.900083 0.000001 0.862964
+4 0.401021 0.000001 0.084318 0.862964 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000065_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 1.06146400	Before NNI:     tree length is 1.06146400
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000068_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 1.47013200	Before NNI:     tree length is 1.47013200
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 0.99985478

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000069_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 0.50239825	Before NNI:     tree length is 0.50239825
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000070_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 0.50496022	Before NNI:     tree length is 0.50496025
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000071_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 0.32155566	Before NNI:     tree length is 0.32155563
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000078_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.019107 0.403153 0.357627 0.014092
+1 0.019107 0.000001 0.409944 0.364418 0.005167
+2 0.403153 0.409944 0.000001 0.421098 0.404929
+3 0.357627 0.364418 0.421098 0.000001 0.359403
+4 0.014092 0.005167 0.404929 0.359403 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000079_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.005019 0.076384 0.122841 0.008106
+1 0.005019 0.000001 0.074230 0.120686 0.005952
+2 0.076384 0.074230 0.000001 0.149981 0.074489
+3 0.122841 0.120686 0.149981 0.000001 0.120945
+4 0.008106 0.005952 0.074489 0.120945 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000084_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.206442 1.441622 2.769540 0.003058
+1 0.206442 0.000001 1.396978 2.724896 0.209499
+2 1.441622 1.396978 0.000001 1.456016 1.444679
+3 2.769540 2.724896 1.456016 0.000001 2.772597
+4 0.003058 0.209499 1.444679 2.772597 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000089_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 0.19795975	Before NNI:     tree length is 0.19795975
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000090_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 0.14871017	Before NNI:     tree length is 0.14871025
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000094_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 0.33318263	Before NNI:     tree length is 0.33318263
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000098_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.274700 0.248109 0.311144 0.278398
+1 0.274700 0.000001 0.019992 0.048181 0.011210
+2 0.248109 0.019992 0.000001 0.056435 0.023689
+3 0.311144 0.048181 0.056435 0.000001 0.051878
+4 0.278398 0.011210 0.023689 0.051878 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000100_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 0.23977575	Before NNI:     tree length is 0.23977575
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000102_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.000878 0.135849 0.235692 0.002160
+1 0.000878 0.000001 0.134971 0.234814 0.003038
+2 0.135849 0.134971 0.000001 0.258580 0.138009
+3 0.235692 0.234814 0.258580 0.000001 0.237852
+4 0.002160 0.003038 0.138009 0.237852 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000102_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 0.31722050	Before NNI:     tree length is 0.31722050
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000103_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.002597 0.535937 1.790285 0.031104
+1 0.002597 0.000001 0.538517 1.792864 0.033684
+2 0.535937 0.538517 0.000001 0.997111 0.534015
+3 1.790285 1.792864 0.997111 0.000001 1.788362
+4 0.031104 0.033684 0.534015 1.788362 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000103_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 1.67884567	Before NNI:     tree length is 1.67884563
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 0.99000889

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000105_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.376939 0.664289 1.161939 0.391366
+1 0.376939 0.000001 0.660513 1.174519 0.093802
+2 0.664289 0.660513 0.000001 1.755656 0.674940
+3 1.161939 1.174519 1.755656 0.000001 1.090075
+4 0.391366 0.093802 0.674940 1.090075 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000107_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.269861 0.075681 0.122738 0.019185
+1 0.269861 0.000001 0.318390 0.365447 0.252025
+2 0.075681 0.318390 0.000001 0.109497 0.067714
+3 0.122738 0.365447 0.109497 0.000001 0.114772
+4 0.019185 0.252025 0.067714 0.114772 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000109_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 1.08948650	Before NNI:     tree length is 1.08948650
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000