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/OG0000003_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.020577 0.022701 0.024082 0.012167
+1 0.020577 0.000001 0.000001 0.017735 0.000001
+2 0.022701 0.000001 0.000001 0.017735 0.000001
+3 0.024082 0.017735 0.017735 0.000001 0.017735
+4 0.012167 0.000001 0.000001 0.017735 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000004_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 1.02161825	Before NNI:     tree length is 1.02161825
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 0.99999995

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000010_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 1.66957950	Before NNI:     tree length is 1.66957950
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 0.98590534

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000017_tree_id.txt.dist.phylip_fastme_stat.txt

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

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

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.017091 0.766834 0.878288 0.308374
+1 0.017091 0.000001 0.763526 0.874980 0.280338
+2 0.766834 0.763526 0.000001 0.764995 0.897421
+3 0.878288 0.874980 0.764995 0.000001 1.008876
+4 0.308374 0.280338 0.897421 1.008876 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000034_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 0.20564167	Before NNI:     tree length is 0.20680813
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 0.99803585

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000035_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.010401 0.010712 0.053922 0.010401
+1 0.010401 0.000001 0.002633 0.049158 0.000001
+2 0.010712 0.002633 0.000001 0.049469 0.002633
+3 0.053922 0.049158 0.049469 0.000001 0.049158
+4 0.010401 0.000001 0.002633 0.049158 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000035_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 0.05821300	Before NNI:     tree length is 0.05821300
+	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/OG0000037_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 2.02874111	Before NNI:     tree length is 2.02874112
+	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/OG0000041_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.061389 0.730255 0.845565 0.025427
+1 0.061389 0.000001 0.668866 0.906954 0.035962
+2 0.730255 0.668866 0.000001 0.812414 0.704828
+3 0.845565 0.906954 0.812414 0.000001 0.870992
+4 0.025427 0.035962 0.704828 0.870992 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000042_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.000001 0.529084 0.337498 0.019621
+1 0.000001 0.000001 0.529084 0.337498 0.019625
+2 0.529084 0.529084 0.000001 0.577818 0.530426
+3 0.337498 0.337498 0.577818 0.000001 0.338840
+4 0.019621 0.019625 0.530426 0.338840 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000043_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 0.07500425	Before NNI:     tree length is 0.07500425
+	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/OG0000047_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.063546 0.360024 0.290536 0.009057
+1 0.063546 0.000001 0.361437 0.291950 0.057358
+2 0.360024 0.361437 0.000001 0.472199 0.353837
+3 0.290536 0.291950 0.472199 0.000001 0.284349
+4 0.009057 0.057358 0.353837 0.284349 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000047_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 0.59529401	Before NNI:     tree length is 0.59529400
+	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/OG0000052_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.000001 0.083332 0.163271 0.010758
+1 0.000001 0.000001 0.083332 0.163271 0.010758
+2 0.083332 0.083332 0.000001 0.155523 0.075753
+3 0.163271 0.163271 0.155523 0.000001 0.155692
+4 0.010758 0.010758 0.075753 0.155692 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000054_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 0.05117575	Before NNI:     tree length is 0.05117575
+	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/OG0000056_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 0.82095675	Before NNI:     tree length is 0.82095675
+	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/OG0000060_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 0.40450025	Before NNI:     tree length is 0.40450025
+	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/OG0000062_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 0.43172233	Before NNI:     tree length is 0.43172225
+	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/OG0000063_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.003041 0.027582 1.109513 0.006043
+1 0.003041 0.000001 0.026249 1.108180 0.003001
+2 0.027582 0.026249 0.000001 1.097785 0.029250
+3 1.109513 1.108180 1.097785 0.000001 1.111181
+4 0.006043 0.003001 0.029250 1.111181 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000066_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 0.74104100	Before NNI:     tree length is 0.74104100
+	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

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.000001 0.257365 0.384085 0.007097
+1 0.000001 0.000001 0.257365 0.384085 0.007097
+2 0.257365 0.257365 0.000001 0.362880 0.255857
+3 0.384085 0.384085 0.362880 0.000001 0.382578
+4 0.007097 0.007097 0.255857 0.382578 0.000001

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

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.013206 0.082443 0.284391 0.012703
+1 0.013206 0.000001 0.084004 0.285953 0.003207
+2 0.082443 0.084004 0.000001 0.258806 0.083501
+3 0.284391 0.285953 0.258806 0.000001 0.285449
+4 0.012703 0.003207 0.083501 0.285449 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000073_tree_id.txt.dist.phylip

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

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000073_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 0.42410550	Before NNI:     tree length is 0.42410550
+	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/OG0000076_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.022705 0.122177 0.256226 0.021533
+1 0.022705 0.000001 0.120358 0.254407 0.009536
+2 0.122177 0.120358 0.000001 0.250200 0.119187
+3 0.256226 0.254407 0.250200 0.000001 0.253236
+4 0.021533 0.009536 0.119187 0.253236 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000076_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 0.32892675	Before NNI:     tree length is 0.32892675
+	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/OG0000077_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.064693 0.172379 0.267474 0.019912
+1 0.064693 0.000001 0.155393 0.250488 0.065492
+2 0.172379 0.155393 0.000001 0.276170 0.173177
+3 0.267474 0.250488 0.276170 0.000001 0.268273
+4 0.019912 0.065492 0.173177 0.268273 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_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 0.17914064	Before NNI:     tree length is 0.17914063
+	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/OG0000080_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 0.08218450	Before NNI:     tree length is 0.08218450
+	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/OG0000081_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 0.17683979	Before NNI:     tree length is 0.17683975
+	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/OG0000082_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.003822 0.042462 0.135912 0.007308
+1 0.003822 0.000001 0.046284 0.139734 0.011130
+2 0.042462 0.046284 0.000001 0.153146 0.043650
+3 0.135912 0.139734 0.153146 0.000001 0.137100
+4 0.007308 0.011130 0.043650 0.137100 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

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.003247 0.041120 0.064609 0.000001
+1 0.003247 0.000001 0.043052 0.066541 0.003247
+2 0.041120 0.043052 0.000001 0.062810 0.041120
+3 0.064609 0.066541 0.062810 0.000001 0.064609
+4 0.000001 0.003247 0.041120 0.064609 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000085_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.086231 0.539292 0.166867 0.050006
+1 0.086231 0.000001 0.454220 0.253098 0.036225
+2 0.539292 0.454220 0.000001 0.481546 0.490445
+3 0.166867 0.253098 0.481546 0.000001 0.216874
+4 0.050006 0.036225 0.490445 0.216874 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000085_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 0.63971343	Before NNI:     tree length is 0.64631413
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 0.98025360

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000088_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 0.28138637	Before NNI:     tree length is 0.28138637
+	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/OG0000091_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 1.05333025	Before NNI:     tree length is 1.05333025
+	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

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.017497 0.194118 0.195555 0.221382
+1 0.017497 0.000001 0.185131 0.186569 0.212395
+2 0.194118 0.185131 0.000001 0.007310 0.233608
+3 0.195555 0.186569 0.007310 0.000001 0.235045
+4 0.221382 0.212395 0.233608 0.235045 0.000001

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_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 1.92250738	Before NNI:     tree length is 1.93756250
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 0.98767579

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_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 0.41091764	Before NNI:     tree length is 0.41091763
+	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/OG0000108_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.008368 0.176330 0.299952 0.008368
+1 0.008368 0.000001 0.170912 0.294533 0.000001
+2 0.176330 0.170912 0.000001 0.293128 0.170912
+3 0.299952 0.294533 0.293128 0.000001 0.294533
+4 0.008368 0.000001 0.170912 0.294533 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000108_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 0.38618021	Before NNI:     tree length is 0.38618025
+	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/OG0000109_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.000001 0.794426 0.813600 0.795927
+1 0.000001 0.000001 0.794426 0.813600 0.795927
+2 0.794426 0.794426 0.000001 0.556217 0.013228
+3 0.813600 0.813600 0.556217 0.000001 0.557718
+4 0.795927 0.795927 0.013228 0.557718 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000111_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 0.27231450	Before NNI:     tree length is 0.27231450
+	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/OG0000112_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.000001 0.395663 0.989703 0.072319
+1 0.000001 0.000001 0.395663 0.989703 0.072319
+2 0.395663 0.395663 0.000001 1.338515 0.421131
+3 0.989703 0.989703 1.338515 0.000001 0.917385
+4 0.072319 0.072319 0.421131 0.917385 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000114_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.000001 1.072107 0.028420 0.000001
+1 0.000001 0.000001 1.072107 0.028420 0.000001
+2 1.072107 1.072107 0.000001 1.085138 1.072107
+3 0.028420 0.028420 1.085138 0.000001 0.028420
+4 0.000001 0.000001 1.072107 0.028420 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000115_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.000162 1.119963 0.011982 0.000324
+1 0.000162 0.000001 1.119801 0.012144 0.000162
+2 1.119963 1.119801 0.000001 1.131945 1.119639
+3 0.011982 0.012144 1.131945 0.000001 0.012306
+4 0.000324 0.000162 1.119639 0.012306 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000117_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
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+1 0.019570 0.000001 0.848510 0.702701 0.011853
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+3 0.691081 0.702701 0.789885 0.000001 0.696253
+4 0.013122 0.011853 0.842062 0.696253 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000118_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
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+1 0.000001 0.000001 0.082384 0.228627 0.000001
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+3 0.228627 0.228627 0.219301 0.000001 0.228627
+4 0.000001 0.000001 0.082384 0.228627 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000119_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
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+1 0.004751 0.000001 0.047150 0.131662 0.004445
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+3 0.131776 0.131662 0.132556 0.000001 0.131470
+4 0.002296 0.004445 0.046957 0.131470 0.000001