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/OG0000025_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

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

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.004268 0.069228 0.195174 0.004134
+1 0.004268 0.000001 0.064959 0.190905 0.000134
+2 0.069228 0.064959 0.000001 0.138625 0.065093
+3 0.195174 0.190905 0.138625 0.000001 0.191040
+4 0.004134 0.000134 0.065093 0.191040 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000040_tree_id.txt.dist.phylip

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

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000040_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 1.98994367	Before NNI:     tree length is 1.98844500
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 0.91295205

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000067_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.005709 0.093975 0.025175 0.000001
+1 0.005709 0.000001 0.092151 0.023351 0.005709
+2 0.093975 0.092151 0.000001 0.092443 0.093975
+3 0.025175 0.023351 0.092443 0.000001 0.025175
+4 0.000001 0.005709 0.093975 0.025175 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000083_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 0.08685950	Before NNI:     tree length is 0.08685950
+	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/OG0000086_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 0.13827776	Before NNI:     tree length is 0.13827775
+	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/OG0000087_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.000001 0.004185 0.110104 0.002090
+1 0.000001 0.000001 0.004185 0.110104 0.002090
+2 0.004185 0.004185 0.000001 0.109326 0.004181
+3 0.110104 0.110104 0.109326 0.000001 0.110100
+4 0.002090 0.002090 0.004181 0.110100 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

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.067287 0.074289 0.088766 0.029386
+1 0.067287 0.000001 0.090087 0.104565 0.081785
+2 0.074289 0.090087 0.000001 0.105895 0.088787
+3 0.088766 0.104565 0.105895 0.000001 0.103264
+4 0.029386 0.081785 0.088787 0.103264 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000093_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.000001 0.211222 0.271866 0.000001
+1 0.000001 0.000001 0.211222 0.271866 0.000001
+2 0.211222 0.211222 0.000001 0.227542 0.211222
+3 0.271866 0.271866 0.227542 0.000001 0.271866
+4 0.000001 0.000001 0.211222 0.271866 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000095_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 2.36056775	Before NNI:     tree length is 2.36056775
+	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/OG0000106_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.013405 0.403182 0.428875 0.027392
+1 0.013405 0.000001 0.397378 0.423070 0.021588
+2 0.403182 0.397378 0.000001 0.346952 0.391531
+3 0.428875 0.423070 0.346952 0.000001 0.417223
+4 0.027392 0.021588 0.391531 0.417223 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000122_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.016869 0.122159 0.193046 0.016869
+1 0.016869 0.000001 0.126900 0.197787 0.000001
+2 0.122159 0.126900 0.000001 0.196205 0.126900
+3 0.193046 0.197787 0.196205 0.000001 0.197787
+4 0.016869 0.000001 0.126900 0.197787 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000154_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 0.30862250	Before NNI:     tree length is 0.30862250
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 0.99110660

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000156_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.014623 0.245706 0.080910 0.012035
+1 0.014623 0.000001 0.243388 0.078591 0.013484
+2 0.245706 0.243388 0.000001 0.206604 0.244567
+3 0.080910 0.078591 0.206604 0.000001 0.079770
+4 0.012035 0.013484 0.244567 0.079770 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000179_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 0.18136075	Before NNI:     tree length is 0.18136075
+	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/OG0000188_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 1.21614150	Before NNI:     tree length is 1.21614150
+	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/OG0000204_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.000001 0.239434 0.457555 0.009568
+1 0.000001 0.000001 0.239434 0.457555 0.009568
+2 0.239434 0.239434 0.000001 0.540534 0.240357
+3 0.457555 0.457555 0.540534 0.000001 0.458477
+4 0.009568 0.009568 0.240357 0.458477 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000207_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.009375 0.136175 0.017418 0.011771
+1 0.009375 0.000001 0.139352 0.020595 0.014948
+2 0.136175 0.139352 0.000001 0.142776 0.134735
+3 0.017418 0.020595 0.142776 0.000001 0.018371
+4 0.011771 0.014948 0.134735 0.018371 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000207_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 0.15962575	Before NNI:     tree length is 0.15962575
+	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/OG0000210_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 0.59769700	Before NNI:     tree length is 0.59769700
+	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/OG0000213_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 0.09971900	Before NNI:     tree length is 0.09971900
+	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/OG0000225_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 0.65198750	Before NNI:     tree length is 0.65198750
+	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/OG0000252_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.000001 0.402419 0.327601 0.000001
+1 0.000001 0.000001 0.402419 0.327601 0.000001
+2 0.402419 0.402419 0.000001 0.257667 0.402419
+3 0.327601 0.327601 0.257667 0.000001 0.327601
+4 0.000001 0.000001 0.402419 0.327601 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000261_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 0.51402950	Before NNI:     tree length is 0.51402950
+	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/OG0000266_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.006876 0.282187 2.067150 0.029178
+1 0.006876 0.000001 0.289063 2.074026 0.036053
+2 0.282187 0.289063 0.000001 2.238115 0.304426
+3 2.067150 2.074026 2.238115 0.000001 2.089389
+4 0.029178 0.036053 0.304426 2.089389 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000316_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 0.13962568	Before NNI:     tree length is 0.13962575
+	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/OG0000320_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 0.25842335	Before NNI:     tree length is 0.25842338
+	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/OG0000322_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.000001 0.071855 0.142096 0.006804
+1 0.000001 0.000001 0.071855 0.142096 0.006804
+2 0.071855 0.071855 0.000001 0.148036 0.072537
+3 0.142096 0.142096 0.148036 0.000001 0.142778
+4 0.006804 0.006804 0.072537 0.142778 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000357_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 0.23007767	Before NNI:     tree length is 0.23007775
+	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/OG0000358_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.027084 0.269187 0.534981 0.027084
+1 0.027084 0.000001 0.267273 0.533068 0.000001
+2 0.269187 0.267273 0.000001 0.570233 0.267273
+3 0.534981 0.533068 0.570233 0.000001 0.533068
+4 0.027084 0.000001 0.267273 0.533068 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000372_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.007537 0.333001 0.362870 0.011839
+1 0.007537 0.000001 0.330415 0.360284 0.004303
+2 0.333001 0.330415 0.000001 0.349400 0.334718
+3 0.362870 0.360284 0.349400 0.000001 0.364586
+4 0.011839 0.004303 0.334718 0.364586 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000393_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.028955 0.322487 0.824793 0.057707
+1 0.028955 0.000001 0.329503 0.831809 0.064723
+2 0.322487 0.329503 0.000001 0.849917 0.319178
+3 0.824793 0.831809 0.849917 0.000001 0.821483
+4 0.057707 0.064723 0.319178 0.821483 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000395_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.022543 0.267340 0.520745 0.035252
+1 0.022543 0.000001 0.254125 0.507530 0.022037
+2 0.267340 0.254125 0.000001 0.453665 0.248408
+3 0.520745 0.507530 0.453665 0.000001 0.501812
+4 0.035252 0.022037 0.248408 0.501812 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000412_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.017333 0.612600 0.305529 0.013237
+1 0.017333 0.000001 0.595267 0.322863 0.030570
+2 0.612600 0.595267 0.000001 0.918130 0.625837
+3 0.305529 0.322863 0.918130 0.000001 0.292293
+4 0.013237 0.030570 0.625837 0.292293 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000423_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 0.12337682	Before NNI:     tree length is 0.12337675
+	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/OG0000433_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 0.08547200	Before NNI:     tree length is 0.08547200
+	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/OG0000435_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.021163 0.290076 0.507062 0.020758
+1 0.021163 0.000001 0.292064 0.509050 0.022745
+2 0.290076 0.292064 0.000001 0.560130 0.284077
+3 0.507062 0.509050 0.560130 0.000001 0.501063
+4 0.020758 0.022745 0.284077 0.501063 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000436_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.000001 0.308846 0.735846 0.007463
+1 0.000001 0.000001 0.308846 0.735846 0.007463
+2 0.308846 0.308846 0.000001 0.808325 0.304803
+3 0.735846 0.735846 0.808325 0.000001 0.731804
+4 0.007463 0.007463 0.304803 0.731804 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000453_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 0.26858500	Before NNI:     tree length is 0.26858500
+	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/OG0000457_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.013648 0.087406 0.031959 0.005819
+1 0.013648 0.000001 0.098479 0.043032 0.012268
+2 0.087406 0.098479 0.000001 0.098612 0.090651
+3 0.031959 0.043032 0.098612 0.000001 0.035204
+4 0.005819 0.012268 0.090651 0.035204 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000462_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.003711 0.044836 0.090492 0.003711
+1 0.003711 0.000001 0.042395 0.088050 0.000001
+2 0.044836 0.042395 0.000001 0.076779 0.042395
+3 0.090492 0.088050 0.076779 0.000001 0.088050
+4 0.003711 0.000001 0.042395 0.088050 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000468_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.037232 0.353168 0.300381 0.005409
+1 0.037232 0.000001 0.328592 0.275805 0.037214
+2 0.353168 0.328592 0.000001 0.396226 0.353151
+3 0.300381 0.275805 0.396226 0.000001 0.300364
+4 0.005409 0.037214 0.353151 0.300364 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000486_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 0.95771300	Before NNI:     tree length is 0.95771300
+	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/OG0000499_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 0.44135400	Before NNI:     tree length is 0.44135400
+	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/OG0000502_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.023223 0.193715 0.500968 0.048316
+1 0.023223 0.000001 0.184607 0.491860 0.039209
+2 0.193715 0.184607 0.000001 0.432785 0.183549
+3 0.500968 0.491860 0.432785 0.000001 0.490802
+4 0.048316 0.039209 0.183549 0.490802 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000502_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 0.58986675	Before NNI:     tree length is 0.58986675
+	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/OG0000513_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.015378 0.155302 0.284130 0.015378
+1 0.015378 0.000001 0.148989 0.277818 0.000001
+2 0.155302 0.148989 0.000001 0.295509 0.148989
+3 0.284130 0.277818 0.295509 0.000001 0.277818
+4 0.015378 0.000001 0.148989 0.277818 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000535_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.039667 0.382933 0.573781 0.046601
+1 0.039667 0.000001 0.400678 0.591526 0.028141
+2 0.382933 0.400678 0.000001 0.615306 0.407612
+3 0.573781 0.591526 0.615306 0.000001 0.598460
+4 0.046601 0.028141 0.407612 0.598460 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000538_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.029853 0.105905 0.302121 0.000001
+1 0.029853 0.000001 0.099651 0.295867 0.029853
+2 0.105905 0.099651 0.000001 0.287236 0.105905
+3 0.302121 0.295867 0.287236 0.000001 0.302121
+4 0.000001 0.029853 0.105905 0.302121 0.000001