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/OG0000004_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.000010 0.003963 1.021863 0.000010
+1 0.000010 0.000001 0.003934 1.021834 0.000010
+2 0.003963 0.003934 0.000001 1.017795 0.003573
+3 1.021863 1.021834 1.017795 0.000001 1.021473
+4 0.000010 0.000010 0.003573 1.021473 0.000001

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

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

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

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

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000020_tree_id.txt.dist.phylip_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 0.77881864	Before NNI:     tree length is 0.78168400
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 0.75837559

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000024_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.033089 0.537437 0.367036 0.033582
+1 0.033089 0.000001 0.542669 0.372268 0.038813
+2 0.537437 0.542669 0.000001 0.505358 0.520985
+3 0.367036 0.372268 0.505358 0.000001 0.350584
+4 0.033582 0.038813 0.520985 0.350584 0.000001

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

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.000662 0.026102 1.057051 0.000662
+1 0.000662 0.000001 0.026764 1.056389 0.000001
+2 0.026102 0.026764 0.000001 1.083153 0.026764
+3 1.057051 1.056389 1.083153 0.000001 0.000001
+4 0.000662 0.000001 0.026764 0.000001 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000026_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.20295409	Before NNI:     tree length is 0.20295412
+	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/OG0000044_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 0.57328985	Before NNI:     tree length is 0.57328987
+	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

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

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

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

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000065_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.017933 0.606730 0.662553 0.017933
+1 0.017933 0.000001 0.604023 0.659846 0.000001
+2 0.606730 0.604023 0.000001 0.838418 0.604023
+3 0.662553 0.659846 0.838418 0.000001 0.659846
+4 0.017933 0.000001 0.604023 0.659846 0.000001

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_fastme_stat.txt

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

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000072_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.23133150	Before NNI:     tree length is 0.23133150
+	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/OG0000074_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,36 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 1.05951267	Before NNI:     tree length is 1.06048562
+	NNI      1: new tree length is 1.05905362
+	Performed 1 NNI(s).
+
+	Before SPR:     tree length is 1.06048562
+	SPR      1: new tree length is 1.05905363
+	Performed 1 SPR(s).
+
+	Explained variance : 0.68396583

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000075_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.45464975	Before NNI:     tree length is 0.45464975
+	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_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 0.39222039	Before NNI:     tree length is 0.39222037
+	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/OG0000084_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 2.91754550	Before NNI:     tree length is 2.91754550
+	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/OG0000088_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.021063 0.040185 0.233660 0.027678
+1 0.021063 0.000001 0.040916 0.234390 0.028408
+2 0.040185 0.040916 0.000001 0.240428 0.039214
+3 0.233660 0.234390 0.240428 0.000001 0.232688
+4 0.027678 0.028408 0.039214 0.232688 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_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 0.35531600	Before NNI:     tree length is 0.35531600
+	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/OG0000101_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.060226 0.159605 0.344110 0.057686
+1 0.060226 0.000001 0.160096 0.344601 0.011755
+2 0.159605 0.160096 0.000001 0.347561 0.157556
+3 0.344110 0.344601 0.347561 0.000001 0.342062
+4 0.057686 0.011755 0.157556 0.342062 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000104_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.032563 0.348978 0.783932 0.008377
+1 0.032563 0.000001 0.350545 0.785498 0.029921
+2 0.348978 0.350545 0.000001 0.792489 0.346337
+3 0.783932 0.785498 0.792489 0.000001 0.781290
+4 0.008377 0.029921 0.346337 0.781290 0.000001

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_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 1.36194150	Before NNI:     tree length is 1.36194150
+	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/OG0000115_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 1.13194500	Before NNI:     tree length is 1.13194500
+	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/OG0000125_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.003123 0.085142 0.298843 0.000001
+1 0.003123 0.000001 0.084527 0.298228 0.003123
+2 0.085142 0.084527 0.000001 0.259844 0.085142
+3 0.298843 0.298228 0.259844 0.000001 0.298843
+4 0.000001 0.003123 0.085142 0.298843 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000128_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.001731 0.139431 0.249436 0.001731
+1 0.001731 0.000001 0.139581 0.249585 0.000001
+2 0.139431 0.139581 0.000001 0.249435 0.139581
+3 0.249436 0.249585 0.249435 0.000001 0.249585
+4 0.001731 0.000001 0.139581 0.249585 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000128_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.32009171	Before NNI:     tree length is 0.32009175
+	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/OG0000132_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.071469 0.138525 0.941144 0.091839
+1 0.071469 0.000001 0.209994 0.910452 0.061146
+2 0.138525 0.209994 0.000001 1.079670 0.230364
+3 0.941144 0.910452 1.079670 0.000001 0.849305
+4 0.091839 0.061146 0.230364 0.849305 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000134_tree_id.txt.dist.phylip_fastme_stat.txt

@@ -0,0 +1,34 @@
+
+ - FastME 2.1.6.3 - 
+
+
+Papers to be cited:
+
+FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program.
+	Vincent Lefort, Richard Desper and Olivier Gascuel,
+	Molecular Biology and Evolution 32(10), 2798-800, 2015.
+BIONJ algorithm:
+	Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
+	Molecular Biology and Evolution, 14(7):685-695
+
+-------------------------------------------------------------------------------
+Settings for this run:
+
+  I                                      Input data type  Matrix          
+  D                                   Number of datasets  1               
+  M                         Initial tree building method  BIONJ           
+  N                                   NNI postprocessing  NNI_BalME       
+  S                                   SPR postprocessing  yes             
+
+-------------------------------------------------------------------------------
+Dataset 1
+	Two tree searches are performed, with NNIs and SPRs respectively.
+	The resulting tree is the best (shortest) of both.
+
+	Tree length is 0.05514575	Before NNI:     tree length is 0.05514575
+	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/OG0000141_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 0.13539750	Before NNI:     tree length is 0.13539750
+	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/OG0000152_tree_id.txt.dist.phylip_fastme_stat.txt

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

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000155_tree_id.txt.dist.phylip_fastme_stat.txt

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

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000176_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.006545 0.125731 0.163976 0.010445
+1 0.006545 0.000001 0.130464 0.168708 0.015177
+2 0.125731 0.130464 0.000001 0.154852 0.121997
+3 0.163976 0.168708 0.154852 0.000001 0.160242
+4 0.010445 0.015177 0.121997 0.160242 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000176_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 0.23127362	Before NNI:     tree length is 0.23127362
+	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/OG0000180_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 0.44758350	Before NNI:     tree length is 0.44758350
+	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/OG0000181_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 0.87951118	Before NNI:     tree length is 0.87951125
+	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/OG0000192_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.076227 0.073803 0.387025 0.080811
+1 0.076227 0.000001 0.093204 0.411330 0.100212
+2 0.073803 0.093204 0.000001 0.408906 0.062233
+3 0.387025 0.411330 0.408906 0.000001 0.415913
+4 0.080811 0.100212 0.062233 0.415913 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000196_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 0.19792650	Before NNI:     tree length is 0.19792650
+	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/OG0000215_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.017804 0.095659 0.154637 0.013792
+1 0.017804 0.000001 0.095722 0.154700 0.011104
+2 0.095659 0.095722 0.000001 0.179296 0.091710
+3 0.154637 0.154700 0.179296 0.000001 0.150688
+4 0.013792 0.011104 0.091710 0.150688 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000231_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.031412 0.045355 0.532443 0.030912
+1 0.031412 0.000001 0.047068 0.534156 0.001994
+2 0.045355 0.047068 0.000001 0.538866 0.046569
+3 0.532443 0.534156 0.538866 0.000001 0.533656
+4 0.030912 0.001994 0.046569 0.533656 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000232_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 0.89739475	Before NNI:     tree length is 0.89739475
+	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/OG0000235_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 0.36611850	Before NNI:     tree length is 0.36611850
+	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/OG0000238_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 0.30396050	Before NNI:     tree length is 0.30396050
+	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/OG0000239_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 0.97567200	Before NNI:     tree length is 0.97567200
+	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/OG0000245_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 0.76808023	Before NNI:     tree length is 0.76808025
+	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/OG0000246_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.005886 0.122937 0.218277 0.013163
+1 0.005886 0.000001 0.117051 0.212391 0.007277
+2 0.122937 0.117051 0.000001 0.196657 0.123404
+3 0.218277 0.212391 0.196657 0.000001 0.218744
+4 0.013163 0.007277 0.123404 0.218744 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000250_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.002321 0.239091 0.489223 0.053117
+1 0.002321 0.000001 0.241212 0.491344 0.055238
+2 0.239091 0.241212 0.000001 0.433572 0.258379
+3 0.489223 0.491344 0.433572 0.000001 0.508511
+4 0.053117 0.055238 0.258379 0.508511 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000251_tree_id.txt.dist.phylip

@@ -0,0 +1,6 @@
+5
+0 0.000001 0.000001 0.238064 0.207738 0.001042
+1 0.000001 0.000001 0.238064 0.207738 0.001042
+2 0.238064 0.238064 0.000001 0.147920 0.237021
+3 0.207738 0.207738 0.147920 0.000001 0.206696
+4 0.001042 0.001042 0.237021 0.206696 0.000001

Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000251_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 0.29686127	Before NNI:     tree length is 0.29686125
+	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/OG0000265_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 0.23563685	Before NNI:     tree length is 0.23563687
+	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/OG0000270_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 0.07834268	Before NNI:     tree length is 0.07834275
+	Performed 0 NNI(s).
+
+
+	Performed 0 SPR(s).
+
+	Explained variance : 1.00000000